EMBASSY: SEQALIGN documentation.

SEQALIGN documentation

1.0 SUMMARY
2.0 INPUTS & OUTPUTS
3.0 INPUT FILE FORMAT
4.0 OUTPUT FILE FORMAT
5.0 DATA FILES
6.0 USAGE
7.0 KNOWN BUGS & WARNINGS
8.0 NOTES
9.0 DESCRIPTION
10.0 ALGORITHM
11.0 RELATED APPLICATIONS
12.0 DIAGNOSTIC ERROR MESSAGES
13.0 AUTHORS
14.0 REFERENCES

1.0 SUMMARY

Extend alignments (DAF file) with sequences (DHF file)

2.0 INPUTS & OUTPUTS

SEQALIGN reads a directory of "seed" alignments and a directory of sets of protein sequences and writes a directory of "extended" alignments. An extended alignment is a seed alignment that is extended with sequences from the appropriate sequence set. The sets directory must contain a sequence set for each seed alignment directory and the files must have the same base name. For example, sequences from "family.sets" are used to extend the seed alignment "family.aln".
Typically, the inputs are (i) DAF files (domain alignment files) containing structure-based sequence alignments and (ii) DHF files (domain hits files) containing sequence relatives (of unknown structure) of these alignments, and the output are DAF files containing the extended alignments.
The base names of the output alignments are the same as the input alignments. The paths for input and output files are specified by the user and the file extensions are set in the ACD file.

3.0 INPUT FILE FORMAT

The format of the domain alignment file is described in DOMAINALIGN documentation.
If other alignment files are used as input, all of the common file formats are supported.

The format of the domain hits file is described in SEQSEARCH documentation.
If other sequence sets are used as input, all of the common file formats are supported.

4.0 OUTPUT FILE FORMAT

The format of the domain alignment file is described in DOMAINALIGN documentation. Note however that the file will never contain 'Number' or 'Post_similar' records. Futhermore, the code before each sequence is of the form Acc_Start_End (where domain hits files were used as input sequences) or Acc_n (where other sequences were used as input), where 'Acc' is the accession number of the sequence, 'Start' and 'End' are the start and end point of the sequence in the full length sequence respectively, and 'n' is a sequential count of the sequence in the alignment.

Output files for usage example

File: 54894.daf

# TY   SCOP
# XX
# CL   Alpha and beta proteins (a+b)
# XX
# FO   Ferredoxin-like
# XX
# SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
# XX
# FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
# XX
# SI   54894
# XX
d4at1b1_0                 0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETD----QRITIGLNLPXSGEMGRKDLIKIE 0
d4at1d1_1                 0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETD----QRITIGLNLPSGXEMGRKDLIKIE 0
P00478_1_92               0 -VEAIKRGTVIDHIPAQIGFKLLSLFKLTETD----QRITIGLNLPSG-EMGRKDLIKIE 0
Q83IL8_1_92               0 -VEAIKRGTVIDHIPAQIGFKLLSLFKLTETD----QRITIGLNLPSG-EMGRKDLIKIE 0
P08421_1_92               0 -VEAIKCGTVIDHIPAQVGFKLLSLFKLTETD----QRITIGLNLPSG-EMGRKDLIKIE 0
Q8Z130_1_92               0 -VEAIKCGTVIDHIPAQVGFKLLSLFKLTETD----QRITIGLNLPSG-EMGRKDLIKIE 0
Q8ZB38_1_92               0 -VEAIKCGTVIDHIPAQIGFKLLSLFKLTATD----QRITIGLNLPSK-RSGRKDLIKIE 0
P19936_1_92               0 -VEAIKCGTVIDHIPAQIGFKLLTLFKLTATD----QRITIGLNLPSN-ELGRKDLIKIE 0
Q7MZ14_1_92               0 -VEAIRCGTVIDHIPAQVGFKLLSLFKLTETD----QRITIGLNLPSN-RLGKKDLIKIE 0
Q8K9H8_1_92               0 -VEAIKSGSVIDHIPAHIGFKLLSLFRFTETE----KRITIGLNLPSQ-KLDKKDIIKIE 0
P57451_1_92               0 -VEAIKSGSVIDHIPEYIGFKLLSLFRFTETE----KRITIGLNLPSK-KLGRKDIIKIE 0
Q9KP65_1_92               0 -VEAIKNGTVIDHIPAKVGIKVLKLFDMHNSA----QRVTIGLNLPSS-ALGSKDLLKIE 0
Q87LF7_1_92               0 -VEAIKNGTVIDHIPAQIGIKVLKLFDMHNSS----QRVTIGLNLPSS-ALGHKDLLKIE 0
Q8DCF7_1_92               0 -VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSS----QRVTIGLNLPSS-ALGNKDLLKIE 0
Q7MHF0_1_92               0 -VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSS----QRVTIGLNLPSS-ALGNKDLLKIE 0
Q8D1W6_1_92               0 -VEAIFGGTVIDHIPAQVGLKLLSLFKWLHTK----ERITMGLNLPSN-QQKKKDLIKLE 0
Q7P144_1_92               0 -VEALKQGTVIDHIPAGEGVKILRLFKLTETG----ERVTVGLNLVSR-HMGSKDLIKVE 0
P96175_1_92               0 -VEAICNGYVIDHIPSGQGVKILRLFSLTDTK----QRVTVGFNLPSH-DGTTKDLIKVE 0
Q9K1K9_1_92               0 -VEAIEKGTVIDHIPAGRGLTILRQFKLLHYG----NAVTVGFNLPSK-TQGSKDIIKIK 0
Q9JWY6_1_92               0 -VEAIEKGTVIDHIPAGRGLTILRQFKLLHYG----NAVTVGFNLPSK-TQGSKDIIKIK 0
Q970X3_1_91               0 -VSKIKNGTVIDHIPAGRALAVLRILKIAEG-----YRIALVMNVESK-KMGKKDIVKIE 0
Q9UX07_1_93               0 -VSKIRNGTVIDHIPAGRALAVLRILGIRGSEG---YRVALVMNVESK-KIGRKDIVKIE 0
P74766_1_93               0 -VSKIKNGTVIDHIPAGRAFAVLNVLGIKGHEG---FRIALVINVDSK-KMGKKDIVKIE 0
Q8ZTG2_1_93               0 -VSKIENGTVIDHIPAGRALTVLRILGISGKEG---LRVALVMNVESK-KLGKKDIVKIE 0
O58452_1_94               0 -VSAIKEGTVIDHIPAGKGLKVIEILGLSKLSNG--GSVLLAMNVPSK-KLGRKDIVKVE 0
Q8U374_1_94               0 -VSAIKEGTVIDHIPAGKGLKVIQILGLGELKNG--GAVLLAMNVPSK-KLGRKDIVKVE 0
P77919_1_94               0 -VSAIKEGTVIDHIPAGKGLKVIEILKLGKLTNG--GAVLLAMNVPSK-KLGRKDIVKVE 0
O30129_1_93               0 -VSKIKEGTVIDHINAGKALLVLKILKIQPGTD---LTVSMAMNVPSS-KMGKKDIVKVE 0
Q8TVB1_1_92               0 -VKRIEMGTVLDHLPPGTAPQIMRILDIDPTET----TLLVAINVESS-KMGRKDILKIE 0
Q8THL3_1_92               0 -IQAIENGTVIDHITAGQALNVLRILRISSAFR---ATVSFVMNAPGA--RGKKDVVKIE 0
Q8PXK6_1_92               0 -VQAIESGTVIDHIKSGQALNVLRILGISSAFR---ATISFVMNAPGA--GGKKDVVKIE 0
Q9HHN3_1_93               0 -VSKIQAGTVIDHIPAGQALQVLQILGTNGASD---DQITVGMNVTSE-RHHRKDIVKIE 0
Q58801_1_91               0 -VKKITNGTVIDHIDAGKALMVFKVLNVPKETS-----VMIAINVPSK-KKGKKDILKIE 0
O26938_1_91               0 -VKPIKNGTVIDHITANRSLNVLNILGLPDGRS----KVTVAMNMDSS-QLGSKDIVKIE 0
Q97B28_1_93               0 -ISKIKDGTVIDHIPSGKALRVLSILGIRDDVD---YTVSVGMHVPSS-KMEYKDVIKIE 0
Q9HKM3_1_93               0 -ISKIRDGTVIDHVPSGKGIRVIGVLGVHEDVN---YTVSLAIHVPSN-KMGFKDVIKIE 0
Q9YBD5_1_95               0 -VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGY-RWRIAVVINAESS-KLGRKDILKIE 0
Q7MX57_1_92               0 -VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDK----RITIGNNLRSR-SHGSKGVIKIE 0
Q8A9S4_1_92               0 -VAALKNGTVIDHIPSEKLFTVVQLLGVEQMKCN----ITIGFNLDSK-KLGKKGIIKIA 0
Q891I9_1_91               0 -ITSIKDGIVIDHIKSGYGIKIFNYLNLKNVEYS----VALIMNVFSS-KLGKKDIIKIA 0
Q97FS4_1_90               0 -INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFP----TALIMNAISK-KNKAKDIIKIE 0
P96111_1_98               0 GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGSFKGYISLP 0

d4at1b1_0                 0 NTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0
d4at1d1_1                 0 NTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0
P00478_1_92               0 NTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0
Q83IL8_1_92               0 NTFLSEEQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0
P08421_1_92               0 NTFLTEEQVNQLALYAPQATVNRIDNYDVVGKSRPSLP 0
Q8Z130_1_92               0 NTFLTDEQVNQLALYAPQATVNRIDNYDVVGKSRPSLP 0
Q8ZB38_1_92               0 NTFLTEQQANQLAMYAPDATVNRIDNYEVVKKLTLSLP 0
P19936_1_92               0 NTFLTEQQANQLAMYAPKATVNRIDNYEVVRKLTLSLP 0
Q7MZ14_1_92               0 NTFLTEQQANQLAMYAPNATVNCIENYEVVKKLPINLP 0
Q8K9H8_1_92               0 NTFLSDDQINQLAIYAPCATVNYIEKYNLVGKIFPSLP 0
P57451_1_92               0 NTFLSDEQINQLAIYAPHATVNYINEYNLVRKVFPTLP 0
Q9KP65_1_92               0 NVFISEAQANKLALYAPHATVNQIENYEVVKKLALQLP 0
Q87LF7_1_92               0 NVFINEEQASKLALYAPHATVNQIENYEVVKKLALELP 0
Q8DCF7_1_92               0 NVFINEEQASKLALYAPHATVNQIEDYQVVKKLALELP 0
Q7MHF0_1_92               0 NVFINEEQASKLALYAPHATVNQIEDYQVVKKLALELP 0
Q8D1W6_1_92               0 NVLLNEDQANQLSIYAPLATVNQIKNYIVIKKQKLKLP 0
Q7P144_1_92               0 NVALTEEQANELALFAPKATVNVIDNFEVVKKHKLTLP 0
P96175_1_92               0 NTEITKSQANQLALLAPNATVNIIENFKVTDKHSLALP 0
Q9K1K9_1_92               0 GVCLDDKAADRLALFAPEAVVNTIDNFKVVQKRHLNLP 0
Q9JWY6_1_92               0 GVCLDDKAADRLALFAPEAVVNTIDHFKVVQKRHLNLP 0
Q970X3_1_91               0 NKEVDEKEANLITLIAPTATINIIRDYEVVEKKKLKIP 0
Q9UX07_1_93               0 DRVIDEKEASLITLIAPSATINIIRDYVVTEKRHLEVP 0
P74766_1_93               0 DKEISDTEANLITLIAPTATINIVREYEVVKKTKLEVP 0
Q8ZTG2_1_93               0 GRELTPEEVNIISAVAPTATINIIRNFAVVKKFKVTPP 0
O58452_1_94               0 GKFLSEEEVNKIALVAPTATVNIIRNYKVVEKFKVEVP 0
Q8U374_1_94               0 GKFLSEEEVNKIALVAPTATVNIIREYKVVEKFKVEIP 0
P77919_1_94               0 GRFLSEEEVNKIALVAPNATVNIIRDYKVVEKFKVEVP 0
O30129_1_93               0 GMFIRDEELNKIALISPNATINLIRDYEIERKFKVSPP 0
Q8TVB1_1_92               0 GKILSEEEANKVALVAPNATVNIVRDYSVAEKFQVKPP 0
Q8THL3_1_92               0 GKELSVEELNRIALISPKATINIIRDFEVVQKNKVVLP 0
Q8PXK6_1_92               0 GKELSVEELNRIALISPKATINIIRDFVVVQKNNVVLP 0
Q9HHN3_1_93               0 GRELSQDEVDVLSLIAPDATINIVRDYEVDEKRRVDRP 0
Q58801_1_91               0 GIELKKEDVDKISLISPDVTINIIRNGKVVEKLKPQIP 0
O26938_1_91               0 NRELKPSEVDQIALIAPRATINIVRDYKIVEKAKVRL- 0
Q97B28_1_93               0 NRSLDKNELDMISLTAPNATISIIKNYEISEKFKVELP 0
Q9HKM3_1_93               0 NRFLDRNELDMISLIAPNATISIIKNYEISEKFQVELP 0
Q9YBD5_1_95               0 GYKPRQRDLEVLGIIAPGATFNVIEDYKVVEKVKLKLP 0
Q7MX57_1_92               0 DKTFEEEELNRIALIAPNVRLNIIRDYEVVEKRQVEVP 0
Q8A9S4_1_92               0 DKFFCDEEINRISVVAPYVKLNIIRDYEVVEKKEVRMP 0
Q891I9_1_91               0 NKEIDID-FTVLGLIDPTITINIIEDEKIKEKLNLELP 0
Q97FS4_1_90               0 N--VMDLDLAVLGFLDPNITVNIIEDEKIRQKIQLKLP 0
P96111_1_98               0 DRYLSKKEIKKLSAISPNTTVNIIKNSTVVEKYRIKLP 0

File: 55074.daf

# TY   SCOP
# XX
# CL   Alpha and beta proteins (a+b)
# XX
# FO   Ferredoxin-like
# XX
# SF   Adenylyl and guanylyl cyclase catalytic domain
# XX
# FA   Adenylyl and guanylyl cyclase catalytic domain
# XX
# SI   55074
# XX
d1cs4a__0                 0 MMFHKIYIQKXHXDNVSILFADIEGFTSLASQC----TAQELVMTLNELFARFDKLAAE- 0
d1fx2a__1                 0 XXNNNRAPXKEPTDPVTLIFTDIESSTALWAAX----HPDLMPDAVAAHHRMVRSLIGR- 0
Q04400_1_189              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFARFDKLAAE- 0
P40144_1_189              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFARFDKLAAE- 0
P30803_1_189              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFARFDKLAAE- 0
O95622_1_189              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFARFDKLAAE- 0
Q03343_1_189              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFARFDKLAAE- 0
O43306_1_189              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFARFDKLAAE- 0
Q01341_1_188              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFARFDKLAAE- 0
P30804_1_188              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFARFDKLAAE- 0
Q99279_1_218              0 --NNNRAPKE-PTDPVTLIFTDIESSTALWAA-----HPDLMPDAVAAHHRMVRSLIGR- 0
Q99280_6_216              0 ---------KEPTGPVTLIFTDIESSTALWAA-----HPDLMPDAVATHHRLIRSLITR- 0
P26338_1_216              0 ----NNLAPKELTDPVTLIFTDIESSTALWAA-----HPELMPDAVATHHRLIRSLIGR- 0
Q26721_1_206              0 --------------PVTLIFTDIESSTALWAA-----HPEVMPDAVATHHRLIRTLISK- 0
Q99396_1_212              0 ---------KELADPVTLIFTDIESSTAQWAT-----QPELMPDAVATHHSMVRSLIEN- 0
Q08828_1_186              0 --FHKIYIQR--HDNVSILFADIVGFTGLASQC----TAQELVKLLNELFGKFDELATE- 0
P19754_1_186              0 --FHKIYIQR--HDNVSILFADIVGFTGLASQC----TAQELVKLLNELFGKFDELATE- 0
P32870_1_186              0 --FHRIYIQK--HENVSILFADIVGFTVLSSQC----SAQELVRLLNELFGRFDQLAHD- 0
Q26896_6_216              0 ---------KEFTDPVTLIFTDIESSTALWAA-----HPGMMADAVATHHRLIRSLIAL- 0
P97490_1_186              0 --FHRIYIHR--YENVSILFADVKGFTNLSTTL----SAQELVRMLNELFARFDRLAHE- 0
P40146_1_186              0 --FHRIYIHR--YENVSILFADVKGFTNLSTTL----SAQELVRMLNELFARFDRLAHE- 0
P40145_1_186              0 --FHRIYIHR--YENVSILFADVKGFTNLSTTL----SAQELVRMLNELFARFDRLAHE- 0
Q8VHH7_1_186              0 --FNTMYMYR--HENVSILFADIVGFTQLSSAC----SAQELVKLLNELFARFDKLAAK- 0
P21932_1_186              0 --FNTMYMYR--HENVSILFADIVGFTQLSSAC----SAQELVKLLNELFARFDKLAAK- 0
O60266_1_186              0 --FNTMYMYR--HENVSILFADIVGFTQLSSAC----SAQELVKLLNELFARFDKLAAK- 0
Q27675_1_217              0 ---NNDAAPKDGDEPVTLLFTDIESSTALWAA-----LPQLMSDAIAAHHRVIRQLVKK- 0
Q25263_1_217              0 ---NNDAAPKDGDEPVTLLFTDIESSTALWAA-----LPQLMSDAIAAHHRVIRQLVKK- 0
Q91WF3_1_158              0 --FHSLYVKR--HQGVSVLYADIVGFTRLASEC----SPKELVLMLNELFGKFDQIAKE- 0
Q8NFM4_1_158              0 --FHSLYVKR--HQGVSVLYADIVGFTRLASEC----SPKELVLMLNELFGKFDQIAKE- 0
P26770_1_158              0 --FHSLYVKR--HQGVSVLYADIVGFTRLASEC----SPKELVLMLNELFGKFDQIAKE- 0
Q08462_1_186              0 --FHNLYVKR--HTNVSILYADIVGFTRLASDC----SPGELVHMLNELFGKFDQIAKE- 0
P26769_1_186              0 --FHNLYVKR--HTNVSILYADIVGFTRLASDC----SPGELVHMLNELFGKFDQIAKE- 0
Q29450_1_186              0 --FHNLYVKR--HQNVSILYADIVGFTRLASDC----SPKELVVVLNELFGKFDQIAKA- 0
P51829_1_186              0 --FHSLYVKR--HQNVSILYADIVGFTRLASDC----SPKELVVVLNELFGKFDQIAKA- 0
P51828_1_186              0 --FHSLYVKR--HQNVSILYADIVGFTQLASDC----SPKELVVVLNELFGKFDQIAKA- 0
P98999_1_150              0 -------------EQVSILFADIVGFTKMSANK----SAHALVGLLNDLFGRFDRLCEE- 0
Q9DGG6_1_181              0 -------------EQVSILFADIVGFTKMSANK----SAHALVGLLNDLFGRFDRLCED- 0
P51830_1_179              0 ---------------VSILFADIVGFTKMSANK----SAHALVGLLNDLFGRFDRLCEQ- 0


  [Part of this file has been deleted for brevity]

P40144_1_159              0 ---------------------- 0
P30803_1_159              0 ---------------------- 0
O95622_1_159              0 ---------------------- 0
Q03343_1_159              0 ---------------------- 0
Q01341_1_159              0 ---------------------- 0
P30804_1_159              0 ---------------------- 0
O43306_1_159              0 ---------------------- 0
P97490_1_162              0 ---------------------- 0
P40146_1_162              0 ---------------------- 0
P40145_1_162              0 ---------------------- 0
O30820_1_149              0 ---------------------- 0
Q03101_1_149              0 ---------------------- 0
P16065_1_143              0 ---------------------- 0
P46197_1_168              0 ---------------------- 0
P20594_1_168              0 ---------------------- 0
P16067_1_168              0 ---------------------- 0
P18293_1_168              0 ---------------------- 0
P18910_1_168              0 ---------------------- 0
P16066_1_168              0 ---------------------- 0
P55202_1_154              0 ---------------------- 0
Q07553_1_152              0 ---------------------- 0
Q02846_1_152              0 ---------------------- 0
P52785_1_150              0 ---------------------- 0
P51840_1_150              0 ---------------------- 0
O19179_1_150              0 ---------------------- 0
P55203_1_151              0 ---------------------- 0
P51842_1_152              0 ---------------------- 0
P51841_1_152              0 ---------------------- 0
O02740_1_162              0 ---------------------- 0
P51839_1_163              0 ---------------------- 0
P55204_1_150              0 ---------------------- 0
P25092_1_150              0 ---------------------- 0
P70106_1_150              0 ---------------------- 0
P23897_1_150              0 ---------------------- 0
P55205_1_154              0 ---------------------- 0
Q09435_1_161              0 ---------------------- 0
P22717_1_147              0 ---------------------- 0
O75343_1_147              0 ---------------------- 0
Q9WVI4_1_149              0 ---------------------- 0
P33402_1_149              0 ---------------------- 0
Q9ERL9_1_152              0 ---------------------- 0
P19686_1_160              0 ---------------------- 0
Q02108_1_160              0 ---------------------- 0
P19687_1_161              0 ---------------------- 0
Q07093_1_158              0 ---------------------- 0
Q02153_1_165              0 ---------------------- 0
P20595_1_165              0 ---------------------- 0
P16068_1_165              0 ---------------------- 0
P40137_1_139              0 ---------------------- 0
P23466_1_154              0 ---------------------- 0

File: seqalign.log

//
/homes/user/test/qa/domainalign-keep/daf/54894.daf
//
/homes/user/test/qa/domainalign-keep/daf/55074.daf

5.0 DATA FILES

SEQALIGN does not use a data file.

6.0 USAGE

6.1 COMMAND LINE ARGUMENTS

Extend alignments (DAF file) with sequences (DHF file).
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
   -mode               menu       [1] This option specifies the mode of
                                  SEQALIGN operation. SEQALIGN takes as input
                                  a directory of either i. single sequences,
                                  ii. set of sequences (unaligned or aligned,
                                  but typically aligned sequences within a
                                  domain alignment file)). The user has to
                                  specify which. (Values: 1 (Single
                                  sequences); 2 (Multiple sequences (e.g.
                                  sequence set or alignment)))
*  -dhfinpath          dirlist    [./] This option specifies the location of
                                  sequences, e.g. DHF files (domain hits
                                  files) (input). SEQALIGN takes as input a
                                  database of either i. single sequences, ii.
                                  sets of unaligned sequences or iii. sets of
                                  aligned sequences, e.g. a domain alignment
                                  file. A 'domain alignment file' contains a
                                  sequence alignment of domains belonging to
                                  the same SCOP or CATH family. The file is in
                                  clustal format annotated with domain family
                                  classification information. The files
                                  generated by using SCOPALIGN will contain a
                                  structure-based sequence alignment of
                                  domains of known structure only. Such
                                  alignments can be extended with sequence
                                  relatives (of unknown structure) by using
                                  SEQALIGN.
*  -dafinpath          dirlist    [./] This option specifies the location of
                                  sequences, e.g. DAF files (domain alignment
                                  files) (input). SEQALIGN takes as input a
                                  database of either i. single sequences, ii.
                                  sets of unaligned sequences or iii. sets of
                                  aligned sequences, e.g. a domain alignment
                                  file. A 'domain alignment file' contains a
                                  sequence alignment of domains belonging to
                                  the same SCOP or CATH family. The file is in
                                  clustal format annotated with domain family
                                  classification information. The files
                                  generated by using SCOPALIGN will contain a
                                  structure-based sequence alignment of
                                  domains of known structure only. Such
                                  alignments can be extended with sequence
                                  relatives (of unknown structure) by using
                                  SEQALIGN.
  [-dhfindir]          directory  [./] This option specifies the location of
                                  DHF files (domain hits files) (input). A
                                  'domain hits file' contains database hits
                                  (sequences) with domain classification
                                  information, in the DHF format (FASTA or
                                  EMBL-like). The hits are relatives to a SCOP
                                  or CATH family and are found from a search
                                  of a sequence database. Files containing
                                  hits retrieved by PSIBLAST are generated by
                                  using SEQSEARCH.
   -amode              menu       [1] This option specifies which alignment
                                  algorithm to use. (Values: 1 (CLUSTALW); 2
                                  (TCOFFEE (not yet implemented)))
  [-dafoutdir]         outdir     [./] This option specifies the location of
                                  DAF files (domain alignment files) (output).
                                  A 'domain alignment file' contains a
                                  sequence alignment of domains belonging to
                                  the same SCOP or CATH family. The file is in
                                  clustal format annotated with domain family
                                  classification information. The files
                                  generated by using SCOPALIGN will contain a
                                  structure-based sequence alignment of
                                  domains of known structure only. Such
                                  alignments can be extended with sequence
                                  relatives (of unknown structure) by using
                                  SEQALIGN.
   -logfile            outfile    [seqalign.log] This option specifies the
                                  name of log file for the build. The log file
                                  contains messages about any errors arising
                                  while SEQALIGN ran.

   Additional (Optional) qualifiers:
   -forcetype          boolean    [N] This option specifies whether to force
                                  minimal domain classification data to be
                                  written to the output file in cases where
                                  singlet sequences were given as input file
                                  and no classification data was available

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-dhfinpath" associated qualifiers
   -extension          string     Default file extension

   "-dafinpath" associated qualifiers
   -extension          string     Default file extension

   "-dhfindir" associated qualifiers
   -extension1         string     Default file extension

   "-dafoutdir" associated qualifiers
   -extension2         string     Default file extension

   "-logfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default

Standard (Mandatory) qualifiers

-mode list This option specifies the mode of SEQALIGN operation. SEQALIGN takes as input a directory of either i. single sequences, ii. set of sequences (unaligned or aligned, but typically aligned sequences within a domain alignment file)). The user has to specify which.
1 (Single sequences)
2 (Multiple sequences (e.g. sequence set or alignment))
1

-dhfinpath dirlist This option specifies the location of sequences, e.g. DHF files (domain hits files) (input). SEQALIGN takes as input a database of either i. single sequences, ii. sets of unaligned sequences or iii. sets of aligned sequences, e.g. a domain alignment file. A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. Directory with files ./

-dafinpath dirlist This option specifies the location of sequences, e.g. DAF files (domain alignment files) (input). SEQALIGN takes as input a database of either i. single sequences, ii. sets of unaligned sequences or iii. sets of aligned sequences, e.g. a domain alignment file. A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. Directory with files ./

[-dhfindir]
(Parameter 1) directory This option specifies the location of DHF files (domain hits files) (input). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. Directory ./

-amode list This option specifies which alignment algorithm to use.
1 (CLUSTALW)
2 (TCOFFEE (not yet implemented))
1

[-dafoutdir]
(Parameter 2) outdir This option specifies the location of DAF files (domain alignment files) (output). A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. Output directory ./

-logfile outfile This option specifies the name of log file for the build. The log file contains messages about any errors arising while SEQALIGN ran. Output file seqalign.log

Additional (Optional) qualifiers

-forcetype boolean This option specifies whether to force minimal domain classification data to be written to the output file in cases where singlet sequences were given as input file and no classification data was available Boolean value Yes/No No

Advanced (Unprompted) qualifiers

(none)

Associated qualifiers

"-dhfinpath" associated dirlist qualifiers

-extension string Default file extension Any string dhf

"-dafinpath" associated dirlist qualifiers

-extension string Default file extension Any string daf

"-dhfindir" associated directory qualifiers

-extension1
-extension_dhfindir string Default file extension Any string dhf

"-dafoutdir" associated outdir qualifiers

-extension2
-extension_dafoutdir string Default file extension Any string daf

"-logfile" associated outfile qualifiers

-odirectory string Output directory Any string

General qualifiers

-auto boolean Turn off prompts Boolean value Yes/No N

-stdout boolean Write first file to standard output Boolean value Yes/No N

-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N

-options boolean Prompt for standard and additional values Boolean value Yes/No N

-debug boolean Write debug output to program.dbg Boolean value Yes/No N

-verbose boolean Report some/full command line options Boolean value Yes/No Y

-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N

-warning boolean Report warnings Boolean value Yes/No Y

-error boolean Report errors Boolean value Yes/No Y

-fatal boolean Report fatal errors Boolean value Yes/No Y

-die boolean Report dying program messages Boolean value Yes/No Y

-version boolean Report version number and exit Boolean value Yes/No N

6.2 EXAMPLE SESSION

An example of interactive use of SEQALIGN is shown below. Here is a sample session with seqalign

% seqalign Extend alignments (DAF file) with sequences (DHF file). Input mode 1 : Single sequences 2 : Multiple sequences (e.g. sequence set or alignment) Select mode of operation. [1]: 2 Domain alignment directories [./]: ../domainalign-keep/daf Domain hits directory [./]: ../seqsearch-keep Alignment algorithm option 1 : CLUSTALW 2 : TCOFFEE (not yet implemented) Select number. [1]: 1 Domain alignment file output directory [./]: Domainatrix log output file [seqalign.log]: CLUSTAL W (1.83) Multiple Sequence Alignments Sequence type explicitly set to Protein Sequence format is Pearson No. of seqs=2 Sequences assumed to be PROTEIN Sequence 1: d4at1b1_0 94 aa Sequence 2: d4at1d1_1 94 aa Sequence format is Pearson No. of seqs in profile=40 Total no. of seqs =42 Sequences assumed to be PROTEIN Sequence 3: Q9YBD5_1_95 95 aa Sequence 4: Q9UX07_1_93 93 aa Sequence 5: Q9KP65_1_92 92 aa Sequence 6: Q9K1K9_1_92 92 aa Sequence 7: Q9JWY6_1_92 92 aa Sequence 8: Q9HKM3_1_93 93 aa Sequence 9: Q9HHN3_1_93 93 aa Sequence 10: Q97FS4_1_90 90 aa Sequence 11: Q97B28_1_93 93 aa Sequence 12: Q970X3_1_91 91 aa Sequence 13: Q8ZTG2_1_93 93 aa Sequence 14: Q8ZB38_1_92 92 aa Sequence 15: Q8Z130_1_92 92 aa Sequence 16: Q8U374_1_94 94 aa Sequence 17: Q8TVB1_1_92 92 aa Sequence 18: Q8THL3_1_92 92 aa Sequence 19: Q8PXK6_1_92 92 aa Sequence 20: Q8K9H8_1_92 92 aa Sequence 21: Q8DCF7_1_92 92 aa Sequence 22: Q8D1W6_1_92 92 aa Sequence 23: Q8A9S4_1_92 92 aa Sequence 24: Q891I9_1_91 91 aa Sequence 25: Q87LF7_1_92 92 aa Sequence 26: Q83IL8_1_92 92 aa Sequence 27: Q7P144_1_92 92 aa Sequence 28: Q7MZ14_1_92 92 aa Sequence 29: Q7MX57_1_92 92 aa Sequence 30: Q7MHF0_1_92 92 aa Sequence 31: Q58801_1_91 91 aa Sequence 32: P96175_1_92 92 aa Sequence 33: P96111_1_98 98 aa Sequence 34: P77919_1_94 94 aa Sequence 35: P74766_1_93 93 aa Sequence 36: P57451_1_92 92 aa Sequence 37: P19936_1_92 92 aa Sequence 38: P08421_1_92 92 aa Sequence 39: P00478_1_92 92 aa Sequence 40: O58452_1_94 94 aa Sequence 41: O30129_1_93 93 aa Sequence 42: O26938_1_91 91 aa Start of Pairwise alignments Aligning... Sequences (1:3) Aligned. Score: 35 Sequences (1:4) Aligned. Score: 34 Sequences (1:5) Aligned. Score: 65 Sequences (1:6) Aligned. Score: 51 Sequences (1:7) Aligned. Score: 50 Sequences (1:8) Aligned. Score: 37 Sequences (1:9) Aligned. Score: 45 Sequences (1:10) Aligned. Score: 35 Sequences (1:11) Aligned. Score: 40 Sequences (1:12) Aligned. Score: 45 Sequences (1:13) Aligned. Score: 34 Sequences (1:14) Aligned. Score: 83 Sequences (1:15) Aligned. Score: 92 Sequences (1:16) Aligned. Score: 46 Sequences (1:17) Aligned. Score: 36 Sequences (1:18) Aligned. Score: 38 Sequences (1:19) Aligned. Score: 38 Sequences (1:20) Aligned. Score: 72 Sequences (1:21) Aligned. Score: 63 Sequences (1:22) Aligned. Score: 64 Sequences (1:23) Aligned. Score: 39 Sequences (1:24) Aligned. Score: 32 Sequences (1:25) Aligned. Score: 66 Sequences (1:26) Aligned. Score: 98 Sequences (1:27) Aligned. Score: 65 Sequences (1:28) Aligned. Score: 78 Sequences (1:29) Aligned. Score: 45 Sequences (1:30) Aligned. Score: 63 Sequences (1:31) Aligned. Score: 37 Sequences (1:32) Aligned. Score: 56 Sequences (1:33) Aligned. Score: 32 Sequences (1:34) Aligned. Score: 46 Sequences (1:35) Aligned. Score: 37 Sequences (1:36) Aligned. Score: 70 Sequences (1:37) Aligned. Score: 83 Sequences (1:38) Aligned. Score: 93 Sequences (1:39) Aligned. Score: 100 Sequences (1:40) Aligned. Score: 46 Sequences (1:41) Aligned. Score: 35 Sequences (1:42) Aligned. Score: 41 Sequences (2:3) Aligned. Score: 37 Sequences (2:4) Aligned. Score: 33 Sequences (2:5) Aligned. Score: 65 Sequences (2:6) Aligned. Score: 52 Sequences (2:7) Aligned. Score: 51 Sequences (2:8) Aligned. Score: 36 Sequences (2:9) Aligned. Score: 45 Sequences (2:10) Aligned. Score: 35 Sequences (2:11) Aligned. Score: 40 Sequences (2:12) Aligned. Score: 45 Sequences (2:13) Aligned. Score: 33 Sequences (2:14) Aligned. Score: 83 Sequences (2:15) Aligned. Score: 92 Sequences (2:16) Aligned. Score: 45 Sequences (2:17) Aligned. Score: 36 Sequences (2:18) Aligned. Score: 36 Sequences (2:19) Aligned. Score: 36 Sequences (2:20) Aligned. Score: 72 Sequences (2:21) Aligned. Score: 63 Sequences (2:22) Aligned. Score: 64 Sequences (2:23) Aligned. Score: 39 Sequences (2:24) Aligned. Score: 32 Sequences (2:25) Aligned. Score: 66 Sequences (2:26) Aligned. Score: 98 Sequences (2:27) Aligned. Score: 65 Sequences (2:28) Aligned. Score: 78 Sequences (2:29) Aligned. Score: 45 Sequences (2:30) Aligned. Score: 63 Sequences (2:31) Aligned. Score: 37 Sequences (2:32) Aligned. Score: 56 Sequences (2:33) Aligned. Score: 31 Sequences (2:34) Aligned. Score: 45 Sequences (2:35) Aligned. Score: 36 Sequences (2:36) Aligned. Score: 70 Sequences (2:37) Aligned. Score: 83 Sequences (2:38) Aligned. Score: 93 Sequences (2:39) Aligned. Score: 100 Sequences (2:40) Aligned. Score: 45 Sequences (2:41) Aligned. Score: 34 Sequences (2:42) Aligned. Score: 41 Sequences (3:4) Aligned. Score: 51 Sequences (3:5) Aligned. Score: 41 Sequences (3:6) Aligned. Score: 42 Sequences (3:7) Aligned. Score: 42 Sequences (3:8) Aligned. Score: 36 Sequences (3:9) Aligned. Score: 45 Sequences (3:10) Aligned. Score: 42 Sequences (3:11) Aligned. Score: 38 Sequences (3:12) Aligned. Score: 51 Sequences (3:13) Aligned. Score: 48 Sequences (3:14) Aligned. Score: 40 Sequences (3:15) Aligned. Score: 39 Sequences (3:16) Aligned. Score: 41 Sequences (3:17) Aligned. Score: 44 Sequences (3:18) Aligned. Score: 39 Sequences (3:19) Aligned. Score: 42 Sequences (3:20) Aligned. Score: 41 Sequences (3:21) Aligned. Score: 42 Sequences (3:22) Aligned. Score: 38 Sequences (3:23) Aligned. Score: 35 Sequences (3:24) Aligned. Score: 43 Sequences (3:25) Aligned. Score: 41 Sequences (3:26) Aligned. Score: 39 Sequences (3:27) Aligned. Score: 38 Sequences (3:28) Aligned. Score: 41 Sequences (3:29) Aligned. Score: 40 Sequences (3:30) Aligned. Score: 42 Sequences (3:31) Aligned. Score: 42 Sequences (3:32) Aligned. Score: 36 Sequences (3:33) Aligned. Score: 26 Sequences (3:34) Aligned. Score: 41 Sequences (3:35) Aligned. Score: 49 Sequences (3:36) Aligned. Score: 43 Sequences (3:37) Aligned. Score: 41 Sequences (3:38) Aligned. Score: 39 Sequences (3:39) Aligned. Score: 39 Sequences (3:40) Aligned. Score: 41 Sequences (3:41) Aligned. Score: 43 Sequences (3:42) Aligned. Score: 43 Sequences (4:5) Aligned. Score: 43 Sequences (4:6) Aligned. Score: 45 Sequences (4:7) Aligned. Score: 45 Sequences (4:8) Aligned. Score: 48 Sequences (4:9) Aligned. Score: 56 Sequences (4:10) Aligned. Score: 37 Sequences (4:11) Aligned. Score: 52 Sequences (4:12) Aligned. Score: 80 Sequences (4:13) Aligned. Score: 67 Sequences (4:14) Aligned. Score: 39 Sequences (4:15) Aligned. Score: 35 Sequences (4:16) Aligned. Score: 56 Sequences (4:17) Aligned. Score: 48 Sequences (4:18) Aligned. Score: 50 Sequences (4:19) Aligned. Score: 50 Sequences (4:20) Aligned. Score: 33 Sequences (4:21) Aligned. Score: 46 Sequences (4:22) Aligned. Score: 35 Sequences (4:23) Aligned. Score: 40 Sequences (4:24) Aligned. Score: 45 Sequences (4:25) Aligned. Score: 45 Sequences (4:26) Aligned. Score: 36 Sequences (4:27) Aligned. Score: 39 Sequences (4:28) Aligned. Score: 36 Sequences (4:29) Aligned. Score: 45 Sequences (4:30) Aligned. Score: 46 Sequences (4:31) Aligned. Score: 48 Sequences (4:32) Aligned. Score: 39 Sequences (4:33) Aligned. Score: 31 Sequences (4:34) Aligned. Score: 59 Sequences (4:35) Aligned. Score: 72 Sequences (4:36) Aligned. Score: 35 Sequences (4:37) Aligned. Score: 38 Sequences (4:38) Aligned. Score: 36 Sequences (4:39) Aligned. Score: 36 Sequences (4:40) Aligned. Score: 59 Sequences (4:41) Aligned. Score: 52 Sequences (4:42) Aligned. Score: 51 Sequences (5:6) Aligned. Score: 51 Sequences (5:7) Aligned. Score: 50 Sequences (5:8) Aligned. Score: 38 Sequences (5:9) Aligned. Score: 38 Sequences (5:10) Aligned. Score: 36 Sequences (5:11) Aligned. Score: 38 Sequences (5:12) Aligned. Score: 46 Sequences (5:13) Aligned. Score: 41 Sequences (5:14) Aligned. Score: 68 Sequences (5:15) Aligned. Score: 64 Sequences (5:16) Aligned. Score: 48 Sequences (5:17) Aligned. Score: 39 Sequences (5:18) Aligned. Score: 38 Sequences (5:19) Aligned. Score: 35 Sequences (5:20) Aligned. Score: 58 Sequences (5:21) Aligned. Score: 90 Sequences (5:22) Aligned. Score: 60 Sequences (5:23) Aligned. Score: 40 Sequences (5:24) Aligned. Score: 39 Sequences (5:25) Aligned. Score: 91 Sequences (5:26) Aligned. Score: 65 Sequences (5:27) Aligned. Score: 63 Sequences (5:28) Aligned. Score: 69 Sequences (5:29) Aligned. Score: 44 Sequences (5:30) Aligned. Score: 90 Sequences (5:31) Aligned. Score: 41 Sequences (5:32) Aligned. Score: 57 Sequences (5:33) Aligned. Score: 31 Sequences (5:34) Aligned. Score: 48 Sequences (5:35) Aligned. Score: 45 Sequences (5:36) Aligned. Score: 58 Sequences (5:37) Aligned. Score: 68 Sequences (5:38) Aligned. Score: 65 Sequences (5:39) Aligned. Score: 65 Sequences (5:40) Aligned. Score: 50 Sequences (5:41) Aligned. Score: 42 Sequences (5:42) Aligned. Score: 42 Sequences (6:7) Aligned. Score: 98 Sequences (6:8) Aligned. Score: 33 Sequences (6:9) Aligned. Score: 40 Sequences (6:10) Aligned. Score: 38 Sequences (6:11) Aligned. Score: 36 Sequences (6:12) Aligned. Score: 45 Sequences (6:13) Aligned. Score: 45 Sequences (6:14) Aligned. Score: 53 Sequences (6:15) Aligned. Score: 52 Sequences (6:16) Aligned. Score: 47 Sequences (6:17) Aligned. Score: 36 Sequences (6:18) Aligned. Score: 40 Sequences (6:19) Aligned. Score: 40 Sequences (6:20) Aligned. Score: 44 Sequences (6:21) Aligned. Score: 48 Sequences (6:22) Aligned. Score: 51 Sequences (6:23) Aligned. Score: 36 Sequences (6:24) Aligned. Score: 35 Sequences (6:25) Aligned. Score: 50 Sequences (6:26) Aligned. Score: 52 Sequences (6:27) Aligned. Score: 60 Sequences (6:28) Aligned. Score: 51 Sequences (6:29) Aligned. Score: 36 Sequences (6:30) Aligned. Score: 48 Sequences (6:31) Aligned. Score: 39 Sequences (6:32) Aligned. Score: 53 Sequences (6:33) Aligned. Score: 33 Sequences (6:34) Aligned. Score: 48 Sequences (6:35) Aligned. Score: 40 Sequences (6:36) Aligned. Score: 45 Sequences (6:37) Aligned. Score: 52 Sequences (6:38) Aligned. Score: 51 Sequences (6:39) Aligned. Score: 52 Sequences (6:40) Aligned. Score: 47 Sequences (6:41) Aligned. Score: 35 Sequences (6:42) Aligned. Score: 41 Sequences (7:8) Aligned. Score: 32 Sequences (7:9) Aligned. Score: 40 Sequences (7:10) Aligned. Score: 38 Sequences (7:11) Aligned. Score: 35 Sequences (7:12) Aligned. Score: 45 Sequences (7:13) Aligned. Score: 44 Sequences (7:14) Aligned. Score: 52 Sequences (7:15) Aligned. Score: 51 Sequences (7:16) Aligned. Score: 47 Sequences (7:17) Aligned. Score: 36 Sequences (7:18) Aligned. Score: 40 Sequences (7:19) Aligned. Score: 40 Sequences (7:20) Aligned. Score: 44 Sequences (7:21) Aligned. Score: 48 Sequences (7:22) Aligned. Score: 50 Sequences (7:23) Aligned. Score: 36 Sequences (7:24) Aligned. Score: 35 Sequences (7:25) Aligned. Score: 48 Sequences (7:26) Aligned. Score: 51 Sequences (7:27) Aligned. Score: 59 Sequences (7:28) Aligned. Score: 50 Sequences (7:29) Aligned. Score: 36 Sequences (7:30) Aligned. Score: 48 Sequences (7:31) Aligned. Score: 38 Sequences (7:32) Aligned. Score: 52 Sequences (7:33) Aligned. Score: 32 Sequences (7:34) Aligned. Score: 48 Sequences (7:35) Aligned. Score: 40 Sequences (7:36) Aligned. Score: 45 Sequences (7:37) Aligned. Score: 51 Sequences (7:38) Aligned. Score: 50 Sequences (7:39) Aligned. Score: 51 Sequences (7:40) Aligned. Score: 46 Sequences (7:41) Aligned. Score: 35 Sequences (7:42) Aligned. Score: 41 Sequences (8:9) Aligned. Score: 43 Sequences (8:10) Aligned. Score: 36 Sequences (8:11) Aligned. Score: 77 Sequences (8:12) Aligned. Score: 48 Sequences (8:13) Aligned. Score: 45 Sequences (8:14) Aligned. Score: 34 Sequences (8:15) Aligned. Score: 36 Sequences (8:16) Aligned. Score: 50 Sequences (8:17) Aligned. Score: 41 Sequences (8:18) Aligned. Score: 42 Sequences (8:19) Aligned. Score: 41 Sequences (8:20) Aligned. Score: 32 Sequences (8:21) Aligned. Score: 36 Sequences (8:22) Aligned. Score: 33 Sequences (8:23) Aligned. Score: 38 Sequences (8:24) Aligned. Score: 45 Sequences (8:25) Aligned. Score: 39 Sequences (8:26) Aligned. Score: 39 Sequences (8:27) Aligned. Score: 34 Sequences (8:28) Aligned. Score: 39 Sequences (8:29) Aligned. Score: 41 Sequences (8:30) Aligned. Score: 36 Sequences (8:31) Aligned. Score: 46 Sequences (8:32) Aligned. Score: 34 Sequences (8:33) Aligned. Score: 36 Sequences (8:34) Aligned. Score: 51 Sequences (8:35) Aligned. Score: 45 Sequences (8:36) Aligned. Score: 33 Sequences (8:37) Aligned. Score: 35 Sequences (8:38) Aligned. Score: 36 Sequences (8:39) Aligned. Score: 39 Sequences (8:40) Aligned. Score: 51 Sequences (8:41) Aligned. Score: 49 Sequences (8:42) Aligned. Score: 42 Sequences (9:10) Aligned. Score: 32 Sequences (9:11) Aligned. Score: 51 Sequences (9:12) Aligned. Score: 57 Sequences (9:13) Aligned. Score: 55 Sequences (9:14) Aligned. Score: 42 Sequences (9:15) Aligned. Score: 41 Sequences (9:16) Aligned. Score: 52 Sequences (9:17) Aligned. Score: 47 Sequences (9:18) Aligned. Score: 51 Sequences (9:19) Aligned. Score: 51 Sequences (9:20) Aligned. Score: 34 Sequences (9:21) Aligned. Score: 38 Sequences (9:22) Aligned. Score: 38 Sequences (9:23) Aligned. Score: 40 Sequences (9:24) Aligned. Score: 36 Sequences (9:25) Aligned. Score: 38 Sequences (9:26) Aligned. Score: 44 Sequences (9:27) Aligned. Score: 35 Sequences (9:28) Aligned. Score: 39 Sequences (9:29) Aligned. Score: 42 Sequences (9:30) Aligned. Score: 38 Sequences (9:31) Aligned. Score: 49 Sequences (9:32) Aligned. Score: 35 Sequences (9:33) Aligned. Score: 31 Sequences (9:34) Aligned. Score: 52 Sequences (9:35) Aligned. Score: 53 Sequences (9:36) Aligned. Score: 34 Sequences (9:37) Aligned. Score: 40 Sequences (9:38) Aligned. Score: 41 Sequences (9:39) Aligned. Score: 45 Sequences (9:40) Aligned. Score: 52 Sequences (9:41) Aligned. Score: 49 Sequences (9:42) Aligned. Score: 54 Sequences (10:11) Aligned. Score: 34 Sequences (10:12) Aligned. Score: 43 Sequences (10:13) Aligned. Score: 35 Sequences (10:14) Aligned. Score: 36 Sequences (10:15) Aligned. Score: 36 Sequences (10:16) Aligned. Score: 40 Sequences (10:17) Aligned. Score: 32 Sequences (10:18) Aligned. Score: 33 Sequences (10:19) Aligned. Score: 31 Sequences (10:20) Aligned. Score: 40 Sequences (10:21) Aligned. Score: 37 Sequences (10:22) Aligned. Score: 35 Sequences (10:23) Aligned. Score: 28 Sequences (10:24) Aligned. Score: 63 Sequences (10:25) Aligned. Score: 36 Sequences (10:26) Aligned. Score: 35 Sequences (10:27) Aligned. Score: 37 Sequences (10:28) Aligned. Score: 36 Sequences (10:29) Aligned. Score: 32 Sequences (10:30) Aligned. Score: 37 Sequences (10:31) Aligned. Score: 34 Sequences (10:32) Aligned. Score: 40 Sequences (10:33) Aligned. Score: 28 Sequences (10:34) Aligned. Score: 42 Sequences (10:35) Aligned. Score: 38 Sequences (10:36) Aligned. Score: 37 Sequences (10:37) Aligned. Score: 35 Sequences (10:38) Aligned. Score: 35 Sequences (10:39) Aligned. Score: 35 Sequences (10:40) Aligned. Score: 36 Sequences (10:41) Aligned. Score: 35 Sequences (10:42) Aligned. Score: 35 Sequences (11:12) Aligned. Score: 53 Sequences (11:13) Aligned. Score: 51 Sequences (11:14) Aligned. Score: 38 Sequences (11:15) Aligned. Score: 39 Sequences (11:16) Aligned. Score: 49 Sequences (11:17) Aligned. Score: 43 Sequences (11:18) Aligned. Score: 48 Sequences (11:19) Aligned. Score: 46 Sequences (11:20) Aligned. Score: 34 Sequences (11:21) Aligned. Score: 36 Sequences (11:22) Aligned. Score: 38 Sequences (11:23) Aligned. Score: 36 Sequences (11:24) Aligned. Score: 43 Sequences (11:25) Aligned. Score: 39 Sequences (11:26) Aligned. Score: 41 Sequences (11:27) Aligned. Score: 38 Sequences (11:28) Aligned. Score: 38 Sequences (11:29) Aligned. Score: 41 Sequences (11:30) Aligned. Score: 36 Sequences (11:31) Aligned. Score: 45 Sequences (11:32) Aligned. Score: 39 Sequences (11:33) Aligned. Score: 38 Sequences (11:34) Aligned. Score: 50 Sequences (11:35) Aligned. Score: 46 Sequences (11:36) Aligned. Score: 34 Sequences (11:37) Aligned. Score: 36 Sequences (11:38) Aligned. Score: 39 Sequences (11:39) Aligned. Score: 41 Sequences (11:40) Aligned. Score: 50 Sequences (11:41) Aligned. Score: 56 Sequences (11:42) Aligned. Score: 50 Sequences (12:13) Aligned. Score: 71 Sequences (12:14) Aligned. Score: 47 Sequences (12:15) Aligned. Score: 43 Sequences (12:16) Aligned. Score: 62 Sequences (12:17) Aligned. Score: 53 Sequences (12:18) Aligned. Score: 54 Sequences (12:19) Aligned. Score: 51 Sequences (12:20) Aligned. Score: 40 Sequences (12:21) Aligned. Score: 45 Sequences (12:22) Aligned. Score: 43 Sequences (12:23) Aligned. Score: 47 Sequences (12:24) Aligned. Score: 47 Sequences (12:25) Aligned. Score: 45 Sequences (12:26) Aligned. Score: 45 Sequences (12:27) Aligned. Score: 48 Sequences (12:28) Aligned. Score: 45 Sequences (12:29) Aligned. Score: 46 Sequences (12:30) Aligned. Score: 45 Sequences (12:31) Aligned. Score: 52 Sequences (12:32) Aligned. Score: 39 Sequences (12:33) Aligned. Score: 34 Sequences (12:34) Aligned. Score: 60 Sequences (12:35) Aligned. Score: 79 Sequences (12:36) Aligned. Score: 40 Sequences (12:37) Aligned. Score: 46 Sequences (12:38) Aligned. Score: 45 Sequences (12:39) Aligned. Score: 45 Sequences (12:40) Aligned. Score: 61 Sequences (12:41) Aligned. Score: 60 Sequences (12:42) Aligned. Score: 54 Sequences (13:14) Aligned. Score: 40 Sequences (13:15) Aligned. Score: 40 Sequences (13:16) Aligned. Score: 64 Sequences (13:17) Aligned. Score: 51 Sequences (13:18) Aligned. Score: 59 Sequences (13:19) Aligned. Score: 57 Sequences (13:20) Aligned. Score: 38 Sequences (13:21) Aligned. Score: 40 Sequences (13:22) Aligned. Score: 39 Sequences (13:23) Aligned. Score: 45 Sequences (13:24) Aligned. Score: 39 Sequences (13:25) Aligned. Score: 41 Sequences (13:26) Aligned. Score: 38 Sequences (13:27) Aligned. Score: 45 Sequences (13:28) Aligned. Score: 41 Sequences (13:29) Aligned. Score: 38 Sequences (13:30) Aligned. Score: 40 Sequences (13:31) Aligned. Score: 56 Sequences (13:32) Aligned. Score: 39 Sequences (13:33) Aligned. Score: 33 Sequences (13:34) Aligned. Score: 62 Sequences (13:35) Aligned. Score: 66 Sequences (13:36) Aligned. Score: 40 Sequences (13:37) Aligned. Score: 39 Sequences (13:38) Aligned. Score: 40 Sequences (13:39) Aligned. Score: 36 Sequences (13:40) Aligned. Score: 65 Sequences (13:41) Aligned. Score: 56 Sequences (13:42) Aligned. Score: 54 Sequences (14:15) Aligned. Score: 83 Sequences (14:16) Aligned. Score: 46 Sequences (14:17) Aligned. Score: 35 Sequences (14:18) Aligned. Score: 33 Sequences (14:19) Aligned. Score: 32 Sequences (14:20) Aligned. Score: 68 Sequences (14:21) Aligned. Score: 66 Sequences (14:22) Aligned. Score: 67 Sequences (14:23) Aligned. Score: 41 Sequences (14:24) Aligned. Score: 32 Sequences (14:25) Aligned. Score: 69 Sequences (14:26) Aligned. Score: 83 Sequences (14:27) Aligned. Score: 67 Sequences (14:28) Aligned. Score: 86 Sequences (14:29) Aligned. Score: 45 Sequences (14:30) Aligned. Score: 66 Sequences (14:31) Aligned. Score: 36 Sequences (14:32) Aligned. Score: 59 Sequences (14:33) Aligned. Score: 30 Sequences (14:34) Aligned. Score: 47 Sequences (14:35) Aligned. Score: 43 Sequences (14:36) Aligned. Score: 69 Sequences (14:37) Aligned. Score: 93 Sequences (14:38) Aligned. Score: 84 Sequences (14:39) Aligned. Score: 83 Sequences (14:40) Aligned. Score: 47 Sequences (14:41) Aligned. Score: 39 Sequences (14:42) Aligned. Score: 38 Sequences (15:16) Aligned. Score: 48 Sequences (15:17) Aligned. Score: 36 Sequences (15:18) Aligned. Score: 35 Sequences (15:19) Aligned. Score: 35 Sequences (15:20) Aligned. Score: 71 Sequences (15:21) Aligned. Score: 64 Sequences (15:22) Aligned. Score: 64 Sequences (15:23) Aligned. Score: 41 Sequences (15:24) Aligned. Score: 32 Sequences (15:25) Aligned. Score: 64 Sequences (15:26) Aligned. Score: 93 Sequences (15:27) Aligned. Score: 66 Sequences (15:28) Aligned. Score: 80 Sequences (15:29) Aligned. Score: 45 Sequences (15:30) Aligned. Score: 64 Sequences (15:31) Aligned. Score: 37 Sequences (15:32) Aligned. Score: 58 Sequences (15:33) Aligned. Score: 30 Sequences (15:34) Aligned. Score: 48 Sequences (15:35) Aligned. Score: 41 Sequences (15:36) Aligned. Score: 71 Sequences (15:37) Aligned. Score: 83 Sequences (15:38) Aligned. Score: 98 Sequences (15:39) Aligned. Score: 92 Sequences (15:40) Aligned. Score: 48 Sequences (15:41) Aligned. Score: 42 Sequences (15:42) Aligned. Score: 40 Sequences (16:17) Aligned. Score: 55 Sequences (16:18) Aligned. Score: 47 Sequences (16:19) Aligned. Score: 51 Sequences (16:20) Aligned. Score: 44 Sequences (16:21) Aligned. Score: 48 Sequences (16:22) Aligned. Score: 41 Sequences (16:23) Aligned. Score: 50 Sequences (16:24) Aligned. Score: 42 Sequences (16:25) Aligned. Score: 48 Sequences (16:26) Aligned. Score: 50 Sequences (16:27) Aligned. Score: 48 Sequences (16:28) Aligned. Score: 45 Sequences (16:29) Aligned. Score: 47 Sequences (16:30) Aligned. Score: 48 Sequences (16:31) Aligned. Score: 54 Sequences (16:32) Aligned. Score: 42 Sequences (16:33) Aligned. Score: 34 Sequences (16:34) Aligned. Score: 91 Sequences (16:35) Aligned. Score: 56 Sequences (16:36) Aligned. Score: 48 Sequences (16:37) Aligned. Score: 46 Sequences (16:38) Aligned. Score: 50 Sequences (16:39) Aligned. Score: 48 Sequences (16:40) Aligned. Score: 92 Sequences (16:41) Aligned. Score: 60 Sequences (16:42) Aligned. Score: 54 Sequences (17:18) Aligned. Score: 42 Sequences (17:19) Aligned. Score: 43 Sequences (17:20) Aligned. Score: 33 Sequences (17:21) Aligned. Score: 39 Sequences (17:22) Aligned. Score: 32 Sequences (17:23) Aligned. Score: 35 Sequences (17:24) Aligned. Score: 32 Sequences (17:25) Aligned. Score: 38 Sequences (17:26) Aligned. Score: 38 Sequences (17:27) Aligned. Score: 39 Sequences (17:28) Aligned. Score: 35 Sequences (17:29) Aligned. Score: 41 Sequences (17:30) Aligned. Score: 39 Sequences (17:31) Aligned. Score: 46 Sequences (17:32) Aligned. Score: 35 Sequences (17:33) Aligned. Score: 34 Sequences (17:34) Aligned. Score: 56 Sequences (17:35) Aligned. Score: 47 Sequences (17:36) Aligned. Score: 36 Sequences (17:37) Aligned. Score: 35 Sequences (17:38) Aligned. Score: 38 Sequences (17:39) Aligned. Score: 36 Sequences (17:40) Aligned. Score: 55 Sequences (17:41) Aligned. Score: 52 Sequences (17:42) Aligned. Score: 42 Sequences (18:19) Aligned. Score: 90 Sequences (18:20) Aligned. Score: 32 Sequences (18:21) Aligned. Score: 36 Sequences (18:22) Aligned. Score: 31 Sequences (18:23) Aligned. Score: 36 Sequences (18:24) Aligned. Score: 32 Sequences (18:25) Aligned. Score: 36 Sequences (18:26) Aligned. Score: 36 Sequences (18:27) Aligned. Score: 39 Sequences (18:28) Aligned. Score: 34 Sequences (18:29) Aligned. Score: 42 Sequences (18:30) Aligned. Score: 36 Sequences (18:31) Aligned. Score: 46 Sequences (18:32) Aligned. Score: 34 Sequences (18:33) Aligned. Score: 33 Sequences (18:34) Aligned. Score: 47 Sequences (18:35) Aligned. Score: 51 Sequences (18:36) Aligned. Score: 32 Sequences (18:37) Aligned. Score: 34 Sequences (18:38) Aligned. Score: 35 Sequences (18:39) Aligned. Score: 35 Sequences (18:40) Aligned. Score: 53 Sequences (18:41) Aligned. Score: 57 Sequences (18:42) Aligned. Score: 48 Sequences (19:20) Aligned. Score: 32 Sequences (19:21) Aligned. Score: 35 Sequences (19:22) Aligned. Score: 30 Sequences (19:23) Aligned. Score: 38 Sequences (19:24) Aligned. Score: 35 Sequences (19:25) Aligned. Score: 34 Sequences (19:26) Aligned. Score: 35 Sequences (19:27) Aligned. Score: 36 Sequences (19:28) Aligned. Score: 33 Sequences (19:29) Aligned. Score: 41 Sequences (19:30) Aligned. Score: 35 Sequences (19:31) Aligned. Score: 45 Sequences (19:32) Aligned. Score: 36 Sequences (19:33) Aligned. Score: 32 Sequences (19:34) Aligned. Score: 50 Sequences (19:35) Aligned. Score: 50 Sequences (19:36) Aligned. Score: 33 Sequences (19:37) Aligned. Score: 33 Sequences (19:38) Aligned. Score: 35 Sequences (19:39) Aligned. Score: 34 Sequences (19:40) Aligned. Score: 52 Sequences (19:41) Aligned. Score: 54 Sequences (19:42) Aligned. Score: 46 Sequences (20:21) Aligned. Score: 56 Sequences (20:22) Aligned. Score: 59 Sequences (20:23) Aligned. Score: 42 Sequences (20:24) Aligned. Score: 36 Sequences (20:25) Aligned. Score: 57 Sequences (20:26) Aligned. Score: 71 Sequences (20:27) Aligned. Score: 53 Sequences (20:28) Aligned. Score: 69 Sequences (20:29) Aligned. Score: 40 Sequences (20:30) Aligned. Score: 56 Sequences (20:31) Aligned. Score: 34 Sequences (20:32) Aligned. Score: 52 Sequences (20:33) Aligned. Score: 28 Sequences (20:34) Aligned. Score: 43 Sequences (20:35) Aligned. Score: 41 Sequences (20:36) Aligned. Score: 86 Sequences (20:37) Aligned. Score: 68 Sequences (20:38) Aligned. Score: 70 Sequences (20:39) Aligned. Score: 72 Sequences (20:40) Aligned. Score: 43 Sequences (20:41) Aligned. Score: 38 Sequences (20:42) Aligned. Score: 36 Sequences (21:22) Aligned. Score: 60 Sequences (21:23) Aligned. Score: 40 Sequences (21:24) Aligned. Score: 41 Sequences (21:25) Aligned. Score: 95 Sequences (21:26) Aligned. Score: 64 Sequences (21:27) Aligned. Score: 59 Sequences (21:28) Aligned. Score: 67 Sequences (21:29) Aligned. Score: 44 Sequences (21:30) Aligned. Score: 100 Sequences (21:31) Aligned. Score: 40 Sequences (21:32) Aligned. Score: 55 Sequences (21:33) Aligned. Score: 29 Sequences (21:34) Aligned. Score: 50 Sequences (21:35) Aligned. Score: 43 Sequences (21:36) Aligned. Score: 57 Sequences (21:37) Aligned. Score: 66 Sequences (21:38) Aligned. Score: 65 Sequences (21:39) Aligned. Score: 63 Sequences (21:40) Aligned. Score: 50 Sequences (21:41) Aligned. Score: 42 Sequences (21:42) Aligned. Score: 42 Sequences (22:23) Aligned. Score: 34 Sequences (22:24) Aligned. Score: 29 Sequences (22:25) Aligned. Score: 60 Sequences (22:26) Aligned. Score: 63 Sequences (22:27) Aligned. Score: 60 Sequences (22:28) Aligned. Score: 69 Sequences (22:29) Aligned. Score: 35 Sequences (22:30) Aligned. Score: 60 Sequences (22:31) Aligned. Score: 32 Sequences (22:32) Aligned. Score: 54 Sequences (22:33) Aligned. Score: 33 Sequences (22:34) Aligned. Score: 42 Sequences (22:35) Aligned. Score: 39 Sequences (22:36) Aligned. Score: 56 Sequences (22:37) Aligned. Score: 66 Sequences (22:38) Aligned. Score: 65 Sequences (22:39) Aligned. Score: 64 Sequences (22:40) Aligned. Score: 42 Sequences (22:41) Aligned. Score: 34 Sequences (22:42) Aligned. Score: 35 Sequences (23:24) Aligned. Score: 34 Sequences (23:25) Aligned. Score: 40 Sequences (23:26) Aligned. Score: 40 Sequences (23:27) Aligned. Score: 35 Sequences (23:28) Aligned. Score: 41 Sequences (23:29) Aligned. Score: 59 Sequences (23:30) Aligned. Score: 40 Sequences (23:31) Aligned. Score: 41 Sequences (23:32) Aligned. Score: 33 Sequences (23:33) Aligned. Score: 30 Sequences (23:34) Aligned. Score: 46 Sequences (23:35) Aligned. Score: 47 Sequences (23:36) Aligned. Score: 44 Sequences (23:37) Aligned. Score: 41 Sequences (23:38) Aligned. Score: 40 Sequences (23:39) Aligned. Score: 39 Sequences (23:40) Aligned. Score: 47 Sequences (23:41) Aligned. Score: 39 Sequences (23:42) Aligned. Score: 40 Sequences (24:25) Aligned. Score: 40 Sequences (24:26) Aligned. Score: 31 Sequences (24:27) Aligned. Score: 34 Sequences (24:28) Aligned. Score: 34 Sequences (24:29) Aligned. Score: 32 Sequences (24:30) Aligned. Score: 41 Sequences (24:31) Aligned. Score: 43 Sequences (24:32) Aligned. Score: 39 Sequences (24:33) Aligned. Score: 25 Sequences (24:34) Aligned. Score: 41 Sequences (24:35) Aligned. Score: 46 Sequences (24:36) Aligned. Score: 35 Sequences (24:37) Aligned. Score: 34 Sequences (24:38) Aligned. Score: 31 Sequences (24:39) Aligned. Score: 32 Sequences (24:40) Aligned. Score: 43 Sequences (24:41) Aligned. Score: 39 Sequences (24:42) Aligned. Score: 41 Sequences (25:26) Aligned. Score: 67 Sequences (25:27) Aligned. Score: 61 Sequences (25:28) Aligned. Score: 68 Sequences (25:29) Aligned. Score: 44 Sequences (25:30) Aligned. Score: 95 Sequences (25:31) Aligned. Score: 41 Sequences (25:32) Aligned. Score: 56 Sequences (25:33) Aligned. Score: 31 Sequences (25:34) Aligned. Score: 48 Sequences (25:35) Aligned. Score: 44 Sequences (25:36) Aligned. Score: 58 Sequences (25:37) Aligned. Score: 69 Sequences (25:38) Aligned. Score: 65 Sequences (25:39) Aligned. Score: 66 Sequences (25:40) Aligned. Score: 51 Sequences (25:41) Aligned. Score: 42 Sequences (25:42) Aligned. Score: 41 Sequences (26:27) Aligned. Score: 66 Sequences (26:28) Aligned. Score: 78 Sequences (26:29) Aligned. Score: 46 Sequences (26:30) Aligned. Score: 64 Sequences (26:31) Aligned. Score: 38 Sequences (26:32) Aligned. Score: 56 Sequences (26:33) Aligned. Score: 32 Sequences (26:34) Aligned. Score: 50 Sequences (26:35) Aligned. Score: 41 Sequences (26:36) Aligned. Score: 71 Sequences (26:37) Aligned. Score: 83 Sequences (26:38) Aligned. Score: 94 Sequences (26:39) Aligned. Score: 98 Sequences (26:40) Aligned. Score: 50 Sequences (26:41) Aligned. Score: 41 Sequences (26:42) Aligned. Score: 41 Sequences (27:28) Aligned. Score: 65 Sequences (27:29) Aligned. Score: 42 Sequences (27:30) Aligned. Score: 59 Sequences (27:31) Aligned. Score: 34 Sequences (27:32) Aligned. Score: 65 Sequences (27:33) Aligned. Score: 29 Sequences (27:34) Aligned. Score: 48 Sequences (27:35) Aligned. Score: 42 Sequences (27:36) Aligned. Score: 55 Sequences (27:37) Aligned. Score: 67 Sequences (27:38) Aligned. Score: 67 Sequences (27:39) Aligned. Score: 65 Sequences (27:40) Aligned. Score: 48 Sequences (27:41) Aligned. Score: 39 Sequences (27:42) Aligned. Score: 39 Sequences (28:29) Aligned. Score: 47 Sequences (28:30) Aligned. Score: 67 Sequences (28:31) Aligned. Score: 35 Sequences (28:32) Aligned. Score: 60 Sequences (28:33) Aligned. Score: 31 Sequences (28:34) Aligned. Score: 46 Sequences (28:35) Aligned. Score: 41 Sequences (28:36) Aligned. Score: 67 Sequences (28:37) Aligned. Score: 85 Sequences (28:38) Aligned. Score: 81 Sequences (28:39) Aligned. Score: 78 Sequences (28:40) Aligned. Score: 45 Sequences (28:41) Aligned. Score: 39 Sequences (28:42) Aligned. Score: 38 Sequences (29:30) Aligned. Score: 44 Sequences (29:31) Aligned. Score: 38 Sequences (29:32) Aligned. Score: 40 Sequences (29:33) Aligned. Score: 35 Sequences (29:34) Aligned. Score: 50 Sequences (29:35) Aligned. Score: 45 Sequences (29:36) Aligned. Score: 42 Sequences (29:37) Aligned. Score: 46 Sequences (29:38) Aligned. Score: 46 Sequences (29:39) Aligned. Score: 45 Sequences (29:40) Aligned. Score: 48 Sequences (29:41) Aligned. Score: 40 Sequences (29:42) Aligned. Score: 41 Sequences (30:31) Aligned. Score: 40 Sequences (30:32) Aligned. Score: 55 Sequences (30:33) Aligned. Score: 29 Sequences (30:34) Aligned. Score: 50 Sequences (30:35) Aligned. Score: 43 Sequences (30:36) Aligned. Score: 57 Sequences (30:37) Aligned. Score: 66 Sequences (30:38) Aligned. Score: 65 Sequences (30:39) Aligned. Score: 63 Sequences (30:40) Aligned. Score: 50 Sequences (30:41) Aligned. Score: 42 Sequences (30:42) Aligned. Score: 42 Sequences (31:32) Aligned. Score: 34 Sequences (31:33) Aligned. Score: 35 Sequences (31:34) Aligned. Score: 56 Sequences (31:35) Aligned. Score: 50 Sequences (31:36) Aligned. Score: 35 Sequences (31:37) Aligned. Score: 34 Sequences (31:38) Aligned. Score: 37 Sequences (31:39) Aligned. Score: 37 Sequences (31:40) Aligned. Score: 57 Sequences (31:41) Aligned. Score: 52 Sequences (31:42) Aligned. Score: 50 Sequences (32:33) Aligned. Score: 35 Sequences (32:34) Aligned. Score: 42 Sequences (32:35) Aligned. Score: 36 Sequences (32:36) Aligned. Score: 51 Sequences (32:37) Aligned. Score: 59 Sequences (32:38) Aligned. Score: 58 Sequences (32:39) Aligned. Score: 56 Sequences (32:40) Aligned. Score: 42 Sequences (32:41) Aligned. Score: 34 Sequences (32:42) Aligned. Score: 39 Sequences (33:34) Aligned. Score: 36 Sequences (33:35) Aligned. Score: 30 Sequences (33:36) Aligned. Score: 29 Sequences (33:37) Aligned. Score: 30 Sequences (33:38) Aligned. Score: 30 Sequences (33:39) Aligned. Score: 32 Sequences (33:40) Aligned. Score: 35 Sequences (33:41) Aligned. Score: 32 Sequences (33:42) Aligned. Score: 35 Sequences (34:35) Aligned. Score: 54 Sequences (34:36) Aligned. Score: 46 Sequences (34:37) Aligned. Score: 47 Sequences (34:38) Aligned. Score: 50 Sequences (34:39) Aligned. Score: 48 Sequences (34:40) Aligned. Score: 92 Sequences (34:41) Aligned. Score: 63 Sequences (34:42) Aligned. Score: 56 Sequences (35:36) Aligned. Score: 42 Sequences (35:37) Aligned. Score: 41 Sequences (35:38) Aligned. Score: 40 Sequences (35:39) Aligned. Score: 41 Sequences (35:40) Aligned. Score: 56 Sequences (35:41) Aligned. Score: 53 Sequences (35:42) Aligned. Score: 51 Sequences (36:37) Aligned. Score: 69 Sequences (36:38) Aligned. Score: 70 Sequences (36:39) Aligned. Score: 70 Sequences (36:40) Aligned. Score: 46 Sequences (36:41) Aligned. Score: 38 Sequences (36:42) Aligned. Score: 36 Sequences (37:38) Aligned. Score: 84 Sequences (37:39) Aligned. Score: 83 Sequences (37:40) Aligned. Score: 47 Sequences (37:41) Aligned. Score: 40 Sequences (37:42) Aligned. Score: 39 Sequences (38:39) Aligned. Score: 93 Sequences (38:40) Aligned. Score: 50 Sequences (38:41) Aligned. Score: 41 Sequences (38:42) Aligned. Score: 40 Sequences (39:40) Aligned. Score: 48 Sequences (39:41) Aligned. Score: 40 Sequences (39:42) Aligned. Score: 41 Sequences (40:41) Aligned. Score: 60 Sequences (40:42) Aligned. Score: 54 Sequences (41:42) Aligned. Score: 51 Guide tree file created: [./seqalign-1234567890.1234.dnd] Start of Multiple Alignment Sequence:39 Score:1453 Sequence:26 Score:1426 Sequence:38 Score:1399 Sequence:15 Score:1411 Sequence:14 Score:1310 Sequence:37 Score:1348 Sequence:28 Score:1320 Sequence:20 Score:1368 Sequence:36 Score:1411 Sequence:5 Score:1309 Sequence:25 Score:1351 Sequence:21 Score:1366 Sequence:30 Score:1390 Sequence:22 Score:1287 Sequence:27 Score:1284 Sequence:32 Score:753 Sequence:6 Score:725 Sequence:7 Score:754 Sequence:12 Score:671 Sequence:4 Score:667 Sequence:35 Score:714 Sequence:13 Score:709 Sequence:40 Score:720 Sequence:16 Score:745 Sequence:34 Score:756 Sequence:41 Score:689 Sequence:17 Score:683 Sequence:18 Score:677 Sequence:19 Score:689 Sequence:9 Score:684 Sequence:31 Score:669 Sequence:42 Score:683 Sequence:11 Score:690 Sequence:8 Score:708 Sequence:3 Score:668 Sequence:29 Score:667 Sequence:23 Score:676 Sequence:24 Score:615 Sequence:10 Score:608 Sequence:33 Score:587 Alignment Score 209199 CLUSTAL-Alignment file created [./seqalign-1234567890.1234.out] CLUSTAL W (1.83) Multiple Sequence Alignments Sequence type explicitly set to Protein Sequence format is Pearson No. of seqs=2 Sequences assumed to be PROTEIN Sequence 1: d1cs4a__0 252 aa Sequence 2: d1fx2a__1 252 aa Sequence format is Pearson No. of seqs in profile=100 Total no. of seqs =102 Sequences assumed to be PROTEIN Sequence 3: Q9WVI4_1_149 149 aa Sequence 4: Q9ERL9_1_152 152 aa Sequence 5: Q9DGG6_1_181 181 aa Sequence 6: Q99396_1_212 212 aa Sequence 7: Q99280_6_216 211 aa Sequence 8: Q99279_1_218 218 aa Sequence 9: Q91WF3_1_165 165 aa Sequence 10: Q91WF3_1_158 158 aa Sequence 11: Q8VHH7_1_186 186 aa Sequence 12: Q8NFM4_1_161 161 aa Sequence 13: Q8NFM4_1_158 158 aa Sequence 14: Q29450_1_186 186 aa Sequence 15: Q29450_1_58 58 aa Sequence 16: Q27675_1_217 217 aa Sequence 17: Q26896_6_216 211 aa Sequence 18: Q26721_1_206 206 aa Sequence 19: Q25263_1_217 217 aa Sequence 20: Q09435_1_161 161 aa Sequence 21: Q08828_1_186 186 aa Sequence 22: Q08828_1_51 51 aa Sequence 23: Q08462_1_186 186 aa Sequence 24: Q08462_1_167 167 aa Sequence 25: Q07553_1_152 152 aa Sequence 26: Q07093_1_158 158 aa Sequence 27: Q04400_1_189 189 aa Sequence 28: Q04400_1_159 159 aa Sequence 29: Q03343_1_189 189 aa Sequence 30: Q03343_1_159 159 aa Sequence 31: Q03101_1_149 149 aa Sequence 32: Q02846_1_152 152 aa Sequence 33: Q02153_1_165 165 aa Sequence 34: Q02108_1_160 160 aa Sequence 35: Q01341_1_188 188 aa Sequence 36: Q01341_1_159 159 aa Sequence 37: P98999_1_150 150 aa Sequence 38: P97490_1_186 186 aa Sequence 39: P97490_1_162 162 aa Sequence 40: P70106_1_150 150 aa Sequence 41: P55205_1_154 154 aa Sequence 42: P55204_1_150 150 aa Sequence 43: P55203_1_151 151 aa Sequence 44: P55202_1_154 154 aa Sequence 45: P52785_1_150 150 aa Sequence 46: P51842_1_152 152 aa Sequence 47: P51841_1_152 152 aa Sequence 48: P51840_1_150 150 aa Sequence 49: P51839_1_163 163 aa Sequence 50: P51830_1_179 179 aa Sequence 51: P51829_109_166 58 aa Sequence 52: P51829_1_186 186 aa Sequence 53: P51828_1_186 186 aa Sequence 54: P51828_1_58 58 aa Sequence 55: P46197_1_168 168 aa Sequence 56: P40146_1_186 186 aa Sequence 57: P40146_1_162 162 aa Sequence 58: P40145_1_186 186 aa Sequence 59: P40145_1_162 162 aa Sequence 60: P40144_1_189 189 aa Sequence 61: P40144_1_159 159 aa Sequence 62: P40137_1_139 139 aa Sequence 63: P33402_1_149 149 aa Sequence 64: P32870_1_186 186 aa Sequence 65: P32870_1_58 58 aa Sequence 66: P30804_1_188 188 aa Sequence 67: P30804_1_159 159 aa Sequence 68: P30803_1_189 189 aa Sequence 69: P30803_1_159 159 aa Sequence 70: P26770_1_165 165 aa Sequence 71: P26770_1_158 158 aa Sequence 72: P26769_1_186 186 aa Sequence 73: P26769_1_163 163 aa Sequence 74: P26338_1_216 216 aa Sequence 75: P25092_1_150 150 aa Sequence 76: P23897_1_150 150 aa Sequence 77: P23466_1_154 154 aa Sequence 78: P22717_1_147 147 aa Sequence 79: P21932_1_186 186 aa Sequence 80: P20595_1_165 165 aa Sequence 81: P20594_1_168 168 aa Sequence 82: P19754_1_186 186 aa Sequence 83: P19754_1_51 51 aa Sequence 84: P19687_1_161 161 aa Sequence 85: P19686_1_160 160 aa Sequence 86: P18910_1_168 168 aa Sequence 87: P18293_1_168 168 aa Sequence 88: P16068_1_165 165 aa Sequence 89: P16067_1_168 168 aa Sequence 90: P16066_1_168 168 aa Sequence 91: P16065_1_143 143 aa Sequence 92: O95622_1_189 189 aa Sequence 93: O95622_1_159 159 aa Sequence 94: O75343_1_147 147 aa Sequence 95: O60503_1_179 179 aa Sequence 96: O60266_1_186 186 aa Sequence 97: O60266_1_54 54 aa Sequence 98: O43306_1_189 189 aa Sequence 99: O43306_1_159 159 aa Sequence 100: O30820_1_149 149 aa Sequence 101: O19179_1_150 150 aa Sequence 102: O02740_1_162 162 aa Start of Pairwise alignments Aligning... Sequences (1:3) Aligned. Score: 36 Sequences (1:4) Aligned. Score: 32 Sequences (1:5) Aligned. Score: 46 Sequences (1:6) Aligned. Score: 15 Sequences (1:7) Aligned. Score: 15 Sequences (1:8) Aligned. Score: 16 Sequences (1:9) Aligned. Score: 29 Sequences (1:10) Aligned. Score: 63 Sequences (1:11) Aligned. Score: 61 Sequences (1:12) Aligned. Score: 30 Sequences (1:13) Aligned. Score: 63 Sequences (1:14) Aligned. Score: 62 Sequences (1:15) Aligned. Score: 43 Sequences (1:16) Aligned. Score: 14 Sequences (1:17) Aligned. Score: 15 Sequences (1:18) Aligned. Score: 15 Sequences (1:19) Aligned. Score: 14 Sequences (1:20) Aligned. Score: 29 Sequences (1:21) Aligned. Score: 74 Sequences (1:22) Aligned. Score: 43 Sequences (1:23) Aligned. Score: 58 Sequences (1:24) Aligned. Score: 27 Sequences (1:25) Aligned. Score: 32 Sequences (1:26) Aligned. Score: 30 Sequences (1:27) Aligned. Score: 96 Sequences (1:28) Aligned. Score: 29 Sequences (1:29) Aligned. Score: 93 Sequences (1:30) Aligned. Score: 29 Sequences (1:31) Aligned. Score: 29 Sequences (1:32) Aligned. Score: 31 Sequences (1:33) Aligned. Score: 33 Sequences (1:34) Aligned. Score: 31 Sequences (1:35) Aligned. Score: 93 Sequences (1:36) Aligned. Score: 29 Sequences (1:37) Aligned. Score: 56 Sequences (1:38) Aligned. Score: 68 Sequences (1:39) Aligned. Score: 30 Sequences (1:40) Aligned. Score: 27 Sequences (1:41) Aligned. Score: 26 Sequences (1:42) Aligned. Score: 27 Sequences (1:43) Aligned. Score: 31 Sequences (1:44) Aligned. Score: 27 Sequences (1:45) Aligned. Score: 32 Sequences (1:46) Aligned. Score: 30 Sequences (1:47) Aligned. Score: 31 Sequences (1:48) Aligned. Score: 32 Sequences (1:49) Aligned. Score: 26 Sequences (1:50) Aligned. Score: 47 Sequences (1:51) Aligned. Score: 43 Sequences (1:52) Aligned. Score: 61 Sequences (1:53) Aligned. Score: 62 Sequences (1:54) Aligned. Score: 43 Sequences (1:55) Aligned. Score: 30 Sequences (1:56) Aligned. Score: 68 Sequences (1:57) Aligned. Score: 30 Sequences (1:58) Aligned. Score: 68 Sequences (1:59) Aligned. Score: 30 Sequences (1:60) Aligned. Score: 96 Sequences (1:61) Aligned. Score: 29 Sequences (1:62) Aligned. Score: 25 Sequences (1:63) Aligned. Score: 34 Sequences (1:64) Aligned. Score: 72 Sequences (1:65) Aligned. Score: 39 Sequences (1:66) Aligned. Score: 93 Sequences (1:67) Aligned. Score: 27 Sequences (1:68) Aligned. Score: 97 Sequences (1:69) Aligned. Score: 29 Sequences (1:70) Aligned. Score: 30 Sequences (1:71) Aligned. Score: 63 Sequences (1:72) Aligned. Score: 59 Sequences (1:73) Aligned. Score: 28 Sequences (1:74) Aligned. Score: 15 Sequences (1:75) Aligned. Score: 26 Sequences (1:76) Aligned. Score: 27 Sequences (1:77) Aligned. Score: 4 Sequences (1:78) Aligned. Score: 25 Sequences (1:79) Aligned. Score: 61 Sequences (1:80) Aligned. Score: 33 Sequences (1:81) Aligned. Score: 30 Sequences (1:82) Aligned. Score: 74 Sequences (1:83) Aligned. Score: 43 Sequences (1:84) Aligned. Score: 31 Sequences (1:85) Aligned. Score: 31 Sequences (1:86) Aligned. Score: 31 Sequences (1:87) Aligned. Score: 32 Sequences (1:88) Aligned. Score: 33 Sequences (1:89) Aligned. Score: 30 Sequences (1:90) Aligned. Score: 29 Sequences (1:91) Aligned. Score: 32 Sequences (1:92) Aligned. Score: 96 Sequences (1:93) Aligned. Score: 29 Sequences (1:94) Aligned. Score: 25 Sequences (1:95) Aligned. Score: 48 Sequences (1:96) Aligned. Score: 61 Sequences (1:97) Aligned. Score: 38 Sequences (1:98) Aligned. Score: 93 Sequences (1:99) Aligned. Score: 29 Sequences (1:100) Aligned. Score: 35 Sequences (1:101) Aligned. Score: 32 Sequences (1:102) Aligned. Score: 32 Sequences (2:3) Aligned. Score: 22 Sequences (2:4) Aligned. Score: 17 Sequences (2:5) Aligned. Score: 11 Sequences (2:6) Aligned. Score: 73 Sequences (2:7) Aligned. Score: 85 Sequences (2:8) Aligned. Score: 92 Sequences (2:9) Aligned. Score: 17 Sequences (2:10) Aligned. Score: 16 Sequences (2:11) Aligned. Score: 14 Sequences (2:12) Aligned. Score: 18 Sequences (2:13) Aligned. Score: 15 Sequences (2:14) Aligned. Score: 16 Sequences (2:15) Aligned. Score: 34 Sequences (2:16) Aligned. Score: 58 Sequences (2:17) Aligned. Score: 69 Sequences (2:18) Aligned. Score: 81 Sequences (2:19) Aligned. Score: 58 Sequences (2:20) Aligned. Score: 18 Sequences (2:21) Aligned. Score: 15 Sequences (2:22) Aligned. Score: 31 Sequences (2:23) Aligned. Score: 9 Sequences (2:24) Aligned. Score: 14 Sequences (2:25) Aligned. Score: 22 Sequences (2:26) Aligned. Score: 17 Sequences (2:27) Aligned. Score: 14 Sequences (2:28) Aligned. Score: 13 Sequences (2:29) Aligned. Score: 12 Sequences (2:30) Aligned. Score: 12 Sequences (2:31) Aligned. Score: 23 Sequences (2:32) Aligned. Score: 23 Sequences (2:33) Aligned. Score: 15 Sequences (2:34) Aligned. Score: 16 Sequences (2:35) Aligned. Score: 10 Sequences (2:36) Aligned. Score: 12 Sequences (2:37) Aligned. Score: 13 Sequences (2:38) Aligned. Score: 13 Sequences (2:39) Aligned. Score: 12 Sequences (2:40) Aligned. Score: 20 Sequences (2:41) Aligned. Score: 22 Sequences (2:42) Aligned. Score: 20 Sequences (2:43) Aligned. Score: 18 Sequences (2:44) Aligned. Score: 20 Sequences (2:45) Aligned. Score: 24 Sequences (2:46) Aligned. Score: 24 Sequences (2:47) Aligned. Score: 23 Sequences (2:48) Aligned. Score: 24 Sequences (2:49) Aligned. Score: 23 Sequences (2:50) Aligned. Score: 11 Sequences (2:51) Aligned. Score: 34 Sequences (2:52) Aligned. Score: 16 Sequences (2:53) Aligned. Score: 15 Sequences (2:54) Aligned. Score: 34 Sequences (2:55) Aligned. Score: 22 Sequences (2:56) Aligned. Score: 14 Sequences (2:57) Aligned. Score: 12 Sequences (2:58) Aligned. Score: 13 Sequences (2:59) Aligned. Score: 12 Sequences (2:60) Aligned. Score: 12 Sequences (2:61) Aligned. Score: 13 Sequences (2:62) Aligned. Score: 23 Sequences (2:63) Aligned. Score: 22 Sequences (2:64) Aligned. Score: 17 Sequences (2:65) Aligned. Score: 31 Sequences (2:66) Aligned. Score: 10 Sequences (2:67) Aligned. Score: 12 Sequences (2:68) Aligned. Score: 12 Sequences (2:69) Aligned. Score: 13 Sequences (2:70) Aligned. Score: 17 Sequences (2:71) Aligned. Score: 16 Sequences (2:72) Aligned. Score: 9 Sequences (2:73) Aligned. Score: 14 Sequences (2:74) Aligned. Score: 80 Sequences (2:75) Aligned. Score: 20 Sequences (2:76) Aligned. Score: 20 Sequences (2:77) Aligned. Score: 36 Sequences (2:78) Aligned. Score: 23 Sequences (2:79) Aligned. Score: 14 Sequences (2:80) Aligned. Score: 15 Sequences (2:81) Aligned. Score: 22 Sequences (2:82) Aligned. Score: 15 Sequences (2:83) Aligned. Score: 31 Sequences (2:84) Aligned. Score: 16 Sequences (2:85) Aligned. Score: 16 Sequences (2:86) Aligned. Score: 23 Sequences (2:87) Aligned. Score: 23 Sequences (2:88) Aligned. Score: 15 Sequences (2:89) Aligned. Score: 22 Sequences (2:90) Aligned. Score: 23 Sequences (2:91) Aligned. Score: 25 Sequences (2:92) Aligned. Score: 12 Sequences (2:93) Aligned. Score: 13 Sequences (2:94) Aligned. Score: 23 Sequences (2:95) Aligned. Score: 11 Sequences (2:96) Aligned. Score: 14 Sequences (2:97) Aligned. Score: 18 Sequences (2:98) Aligned. Score: 12 Sequences (2:99) Aligned. Score: 12 Sequences (2:100) Aligned. Score: 20 Sequences (2:101) Aligned. Score: 24 Sequences (2:102) Aligned. Score: 23 Sequences (3:4) Aligned. Score: 79 Sequences (3:5) Aligned. Score: 32 Sequences (3:6) Aligned. Score: 24 Sequences (3:7) Aligned. Score: 22 Sequences (3:8) Aligned. Score: 23 Sequences (3:9) Aligned. Score: 27 Sequences (3:10) Aligned. Score: 36 Sequences (3:11) Aligned. Score: 35 Sequences (3:12) Aligned. Score: 26 Sequences (3:13) Aligned. Score: 36 Sequences (3:14) Aligned. Score: 36 Sequences (3:15) Aligned. Score: 37 Sequences (3:16) Aligned. Score: 20 Sequences (3:17) Aligned. Score: 23 Sequences (3:18) Aligned. Score: 22 Sequences (3:19) Aligned. Score: 20 Sequences (3:20) Aligned. Score: 44 Sequences (3:21) Aligned. Score: 36 Sequences (3:22) Aligned. Score: 39 Sequences (3:23) Aligned. Score: 38 Sequences (3:24) Aligned. Score: 27 Sequences (3:25) Aligned. Score: 52 Sequences (3:26) Aligned. Score: 61 Sequences (3:27) Aligned. Score: 37 Sequences (3:28) Aligned. Score: 33 Sequences (3:29) Aligned. Score: 38 Sequences (3:30) Aligned. Score: 32 Sequences (3:31) Aligned. Score: 32 Sequences (3:32) Aligned. Score: 50 Sequences (3:33) Aligned. Score: 48 Sequences (3:34) Aligned. Score: 78 Sequences (3:35) Aligned. Score: 38 Sequences (3:36) Aligned. Score: 32 Sequences (3:37) Aligned. Score: 32 Sequences (3:38) Aligned. Score: 36 Sequences (3:39) Aligned. Score: 35 Sequences (3:40) Aligned. Score: 51 Sequences (3:41) Aligned. Score: 50 Sequences (3:42) Aligned. Score: 55 Sequences (3:43) Aligned. Score: 51 Sequences (3:44) Aligned. Score: 48 Sequences (3:45) Aligned. Score: 50 Sequences (3:46) Aligned. Score: 49 Sequences (3:47) Aligned. Score: 50 Sequences (3:48) Aligned. Score: 50 Sequences (3:49) Aligned. Score: 52 Sequences (3:50) Aligned. Score: 32 Sequences (3:51) Aligned. Score: 37 Sequences (3:52) Aligned. Score: 35 Sequences (3:53) Aligned. Score: 35 Sequences (3:54) Aligned. Score: 37 Sequences (3:55) Aligned. Score: 51 Sequences (3:56) Aligned. Score: 36 Sequences (3:57) Aligned. Score: 35 Sequences (3:58) Aligned. Score: 36 Sequences (3:59) Aligned. Score: 35 Sequences (3:60) Aligned. Score: 37 Sequences (3:61) Aligned. Score: 33 Sequences (3:62) Aligned. Score: 30 Sequences (3:63) Aligned. Score: 98 Sequences (3:64) Aligned. Score: 36 Sequences (3:65) Aligned. Score: 34 Sequences (3:66) Aligned. Score: 34 Sequences (3:67) Aligned. Score: 32 Sequences (3:68) Aligned. Score: 37 Sequences (3:69) Aligned. Score: 33 Sequences (3:70) Aligned. Score: 28 Sequences (3:71) Aligned. Score: 36 Sequences (3:72) Aligned. Score: 38 Sequences (3:73) Aligned. Score: 26 Sequences (3:74) Aligned. Score: 24 Sequences (3:75) Aligned. Score: 54 Sequences (3:76) Aligned. Score: 52 Sequences (3:77) Aligned. Score: 14 Sequences (3:78) Aligned. Score: 51 Sequences (3:79) Aligned. Score: 35 Sequences (3:80) Aligned. Score: 48 Sequences (3:81) Aligned. Score: 51 Sequences (3:82) Aligned. Score: 36 Sequences (3:83) Aligned. Score: 39 Sequences (3:84) Aligned. Score: 78 Sequences (3:85) Aligned. Score: 79 Sequences (3:86) Aligned. Score: 51 Sequences (3:87) Aligned. Score: 51 Sequences (3:88) Aligned. Score: 48 Sequences (3:89) Aligned. Score: 51 Sequences (3:90) Aligned. Score: 51 Sequences (3:91) Aligned. Score: 51 Sequences (3:92) Aligned. Score: 37 Sequences (3:93) Aligned. Score: 33 Sequences (3:94) Aligned. Score: 49 Sequences (3:95) Aligned. Score: 32 Sequences (3:96) Aligned. Score: 35 Sequences (3:97) Aligned. Score: 40 Sequences (3:98) Aligned. Score: 38 Sequences (3:99) Aligned. Score: 32 Sequences (3:100) Aligned. Score: 34 Sequences (3:101) Aligned. Score: 51 Sequences (3:102) Aligned. Score: 52 Sequences (4:5) Aligned. Score: 32 Sequences (4:6) Aligned. Score: 16 Sequences (4:7) Aligned. Score: 21 Sequences (4:8) Aligned. Score: 21 Sequences (4:9) Aligned. Score: 30 Sequences (4:10) Aligned. Score: 36 Sequences (4:11) Aligned. Score: 35 Sequences (4:12) Aligned. Score: 30 Sequences (4:13) Aligned. Score: 36 Sequences (4:14) Aligned. Score: 34 Sequences (4:15) Aligned. Score: 36 Sequences (4:16) Aligned. Score: 23 Sequences (4:17) Aligned. Score: 22 Sequences (4:18) Aligned. Score: 21 Sequences (4:19) Aligned. Score: 23 Sequences (4:20) Aligned. Score: 45 Sequences (4:21) Aligned. Score: 34 Sequences (4:22) Aligned. Score: 35 Sequences (4:23) Aligned. Score: 36 Sequences (4:24) Aligned. Score: 27 Sequences (4:25) Aligned. Score: 48 Sequences (4:26) Aligned. Score: 61 Sequences (4:27) Aligned. Score: 32 Sequences (4:28) Aligned. Score: 30 Sequences (4:29) Aligned. Score: 32 Sequences (4:30) Aligned. Score: 28 Sequences (4:31) Aligned. Score: 31 Sequences (4:32) Aligned. Score: 49 Sequences (4:33) Aligned. Score: 46 Sequences (4:34) Aligned. Score: 98 Sequences (4:35) Aligned. Score: 30 Sequences (4:36) Aligned. Score: 28 Sequences (4:37) Aligned. Score: 34 Sequences (4:38) Aligned. Score: 33 Sequences (4:39) Aligned. Score: 33 Sequences (4:40) Aligned. Score: 50 Sequences (4:41) Aligned. Score: 53 Sequences (4:42) Aligned. Score: 52 Sequences (4:43) Aligned. Score: 50 Sequences (4:44) Aligned. Score: 47 Sequences (4:45) Aligned. Score: 50 Sequences (4:46) Aligned. Score: 50 Sequences (4:47) Aligned. Score: 50 Sequences (4:48) Aligned. Score: 50 Sequences (4:49) Aligned. Score: 50 Sequences (4:50) Aligned. Score: 32 Sequences (4:51) Aligned. Score: 36 Sequences (4:52) Aligned. Score: 34 Sequences (4:53) Aligned. Score: 34 Sequences (4:54) Aligned. Score: 36 Sequences (4:55) Aligned. Score: 50 Sequences (4:56) Aligned. Score: 33 Sequences (4:57) Aligned. Score: 33 Sequences (4:58) Aligned. Score: 33 Sequences (4:59) Aligned. Score: 33 Sequences (4:60) Aligned. Score: 32 Sequences (4:61) Aligned. Score: 30 Sequences (4:62) Aligned. Score: 33 Sequences (4:63) Aligned. Score: 79 Sequences (4:64) Aligned. Score: 34 Sequences (4:65) Aligned. Score: 32 Sequences (4:66) Aligned. Score: 31 Sequences (4:67) Aligned. Score: 28 Sequences (4:68) Aligned. Score: 32 Sequences (4:69) Aligned. Score: 30 Sequences (4:70) Aligned. Score: 31 Sequences (4:71) Aligned. Score: 36 Sequences (4:72) Aligned. Score: 36 Sequences (4:73) Aligned. Score: 26 Sequences (4:74) Aligned. Score: 21 Sequences (4:75) Aligned. Score: 52 Sequences (4:76) Aligned. Score: 51 Sequences (4:77) Aligned. Score: 5 Sequences (4:78) Aligned. Score: 53 Sequences (4:79) Aligned. Score: 35 Sequences (4:80) Aligned. Score: 46 Sequences (4:81) Aligned. Score: 50 Sequences (4:82) Aligned. Score: 34 Sequences (4:83) Aligned. Score: 35 Sequences (4:84) Aligned. Score: 97 Sequences (4:85) Aligned. Score: 100 Sequences (4:86) Aligned. Score: 50 Sequences (4:87) Aligned. Score: 49 Sequences (4:88) Aligned. Score: 46 Sequences (4:89) Aligned. Score: 50 Sequences (4:90) Aligned. Score: 50 Sequences (4:91) Aligned. Score: 51 Sequences (4:92) Aligned. Score: 32 Sequences (4:93) Aligned. Score: 30 Sequences (4:94) Aligned. Score: 51 Sequences (4:95) Aligned. Score: 32 Sequences (4:96) Aligned. Score: 35 Sequences (4:97) Aligned. Score: 38 Sequences (4:98) Aligned. Score: 32 Sequences (4:99) Aligned. Score: 28 Sequences (4:100) Aligned. Score: 33 Sequences (4:101) Aligned. Score: 51 Sequences (4:102) Aligned. Score: 50 Sequences (5:6) Aligned. Score: 13 Sequences (5:7) Aligned. Score: 11 Sequences (5:8) Aligned. Score: 17 Sequences (5:9) Aligned. Score: 27 Sequences (5:10) Aligned. Score: 47 Sequences (5:11) Aligned. Score: 51 Sequences (5:12) Aligned. Score: 27 Sequences (5:13) Aligned. Score: 47 Sequences (5:14) Aligned. Score: 46 Sequences (5:15) Aligned. Score: 37 Sequences (5:16) Aligned. Score: 17 Sequences (5:17) Aligned. Score: 19 Sequences (5:18) Aligned. Score: 12 Sequences (5:19) Aligned. Score: 17 Sequences (5:20) Aligned. Score: 27 Sequences (5:21) Aligned. Score: 49 Sequences (5:22) Aligned. Score: 37 Sequences (5:23) Aligned. Score: 43 Sequences (5:24) Aligned. Score: 24 Sequences (5:25) Aligned. Score: 30 Sequences (5:26) Aligned. Score: 31 Sequences (5:27) Aligned. Score: 50 Sequences (5:28) Aligned. Score: 23 Sequences (5:29) Aligned. Score: 50 Sequences (5:30) Aligned. Score: 23 Sequences (5:31) Aligned. Score: 32 Sequences (5:32) Aligned. Score: 32 Sequences (5:33) Aligned. Score: 35 Sequences (5:34) Aligned. Score: 30 Sequences (5:35) Aligned. Score: 49 Sequences (5:36) Aligned. Score: 23 Sequences (5:37) Aligned. Score: 96 Sequences (5:38) Aligned. Score: 49 Sequences (5:39) Aligned. Score: 25 Sequences (5:40) Aligned. Score: 30 Sequences (5:41) Aligned. Score: 31 Sequences (5:42) Aligned. Score: 29 Sequences (5:43) Aligned. Score: 31 Sequences (5:44) Aligned. Score: 33 Sequences (5:45) Aligned. Score: 31 Sequences (5:46) Aligned. Score: 32 Sequences (5:47) Aligned. Score: 31 Sequences (5:48) Aligned. Score: 31 Sequences (5:49) Aligned. Score: 30 Sequences (5:50) Aligned. Score: 97 Sequences (5:51) Aligned. Score: 37 Sequences (5:52) Aligned. Score: 45 Sequences (5:53) Aligned. Score: 46 Sequences (5:54) Aligned. Score: 37 Sequences (5:55) Aligned. Score: 32 Sequences (5:56) Aligned. Score: 49 Sequences (5:57) Aligned. Score: 25 Sequences (5:58) Aligned. Score: 49 Sequences (5:59) Aligned. Score: 25 Sequences (5:60) Aligned. Score: 50 Sequences (5:61) Aligned. Score: 23 Sequences (5:62) Aligned. Score: 28 Sequences (5:63) Aligned. Score: 32 Sequences (5:64) Aligned. Score: 53 Sequences (5:65) Aligned. Score: 32 Sequences (5:66) Aligned. Score: 49 Sequences (5:67) Aligned. Score: 23 Sequences (5:68) Aligned. Score: 50 Sequences (5:69) Aligned. Score: 23 Sequences (5:70) Aligned. Score: 28 Sequences (5:71) Aligned. Score: 47 Sequences (5:72) Aligned. Score: 43 Sequences (5:73) Aligned. Score: 24 Sequences (5:74) Aligned. Score: 18 Sequences (5:75) Aligned. Score: 30 Sequences (5:76) Aligned. Score: 30 Sequences (5:77) Aligned. Score: 3 Sequences (5:78) Aligned. Score: 36 Sequences (5:79) Aligned. Score: 51 Sequences (5:80) Aligned. Score: 35 Sequences (5:81) Aligned. Score: 32 Sequences (5:82) Aligned. Score: 49 Sequences (5:83) Aligned. Score: 37 Sequences (5:84) Aligned. Score: 31 Sequences (5:85) Aligned. Score: 30 Sequences (5:86) Aligned. Score: 32 Sequences (5:87) Aligned. Score: 31 Sequences (5:88) Aligned. Score: 35 Sequences (5:89) Aligned. Score: 32 Sequences (5:90) Aligned. Score: 31 Sequences (5:91) Aligned. Score: 33 Sequences (5:92) Aligned. Score: 50 Sequences (5:93) Aligned. Score: 23 Sequences (5:94) Aligned. Score: 35 Sequences (5:95) Aligned. 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Score: 42 Sequences (63:98) Aligned. Score: 36 Sequences (63:99) Aligned. Score: 32 Sequences (63:100) Aligned. Score: 34 Sequences (63:101) Aligned. Score: 51 Sequences (63:102) Aligned. Score: 52 Sequences (64:65) Aligned. Score: 46 Sequences (64:66) Aligned. Score: 73 Sequences (64:67) Aligned. Score: 28 Sequences (64:68) Aligned. Score: 74 Sequences (64:69) Aligned. Score: 30 Sequences (64:70) Aligned. Score: 30 Sequences (64:71) Aligned. Score: 65 Sequences (64:72) Aligned. Score: 63 Sequences (64:73) Aligned. Score: 28 Sequences (64:74) Aligned. Score: 14 Sequences (64:75) Aligned. Score: 30 Sequences (64:76) Aligned. Score: 30 Sequences (64:77) Aligned. Score: 8 Sequences (64:78) Aligned. Score: 34 Sequences (64:79) Aligned. Score: 62 Sequences (64:80) Aligned. Score: 35 Sequences (64:81) Aligned. Score: 32 Sequences (64:82) Aligned. Score: 74 Sequences (64:83) Aligned. Score: 45 Sequences (64:84) Aligned. Score: 32 Sequences (64:85) Aligned. 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Score: 56 Sequences (65:101) Aligned. Score: 44 Sequences (65:102) Aligned. Score: 46 Sequences (66:67) Aligned. Score: 25 Sequences (66:68) Aligned. Score: 95 Sequences (66:69) Aligned. Score: 25 Sequences (66:70) Aligned. Score: 26 Sequences (66:71) Aligned. Score: 63 Sequences (66:72) Aligned. Score: 61 Sequences (66:73) Aligned. Score: 25 Sequences (66:74) Aligned. Score: 9 Sequences (66:75) Aligned. Score: 25 Sequences (66:76) Aligned. Score: 26 Sequences (66:77) Aligned. Score: 3 Sequences (66:78) Aligned. Score: 27 Sequences (66:79) Aligned. Score: 62 Sequences (66:80) Aligned. Score: 32 Sequences (66:81) Aligned. Score: 26 Sequences (66:82) Aligned. Score: 74 Sequences (66:83) Aligned. Score: 33 Sequences (66:84) Aligned. Score: 30 Sequences (66:85) Aligned. Score: 30 Sequences (66:86) Aligned. Score: 26 Sequences (66:87) Aligned. Score: 26 Sequences (66:88) Aligned. Score: 32 Sequences (66:89) Aligned. Score: 26 Sequences (66:90) Aligned. Score: 26 Sequences (66:91) Aligned. 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Score: 29 Sequences (67:83) Aligned. Score: 78 Sequences (67:84) Aligned. Score: 27 Sequences (67:85) Aligned. Score: 27 Sequences (67:86) Aligned. Score: 28 Sequences (67:87) Aligned. Score: 29 Sequences (67:88) Aligned. Score: 30 Sequences (67:89) Aligned. Score: 29 Sequences (67:90) Aligned. Score: 29 Sequences (67:91) Aligned. Score: 36 Sequences (67:92) Aligned. Score: 29 Sequences (67:93) Aligned. Score: 91 Sequences (67:94) Aligned. Score: 28 Sequences (67:95) Aligned. Score: 23 Sequences (67:96) Aligned. Score: 28 Sequences (67:97) Aligned. Score: 68 Sequences (67:98) Aligned. Score: 29 Sequences (67:99) Aligned. Score: 99 Sequences (67:100) Aligned. Score: 38 Sequences (67:101) Aligned. Score: 34 Sequences (67:102) Aligned. Score: 32 Sequences (68:69) Aligned. Score: 29 Sequences (68:70) Aligned. Score: 29 Sequences (68:71) Aligned. Score: 65 Sequences (68:72) Aligned. Score: 63 Sequences (68:73) Aligned. Score: 28 Sequences (68:74) Aligned. 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Score: 32 Sequences (68:102) Aligned. Score: 30 Sequences (69:70) Aligned. Score: 61 Sequences (69:71) Aligned. Score: 29 Sequences (69:72) Aligned. Score: 27 Sequences (69:73) Aligned. Score: 59 Sequences (69:74) Aligned. Score: 15 Sequences (69:75) Aligned. Score: 32 Sequences (69:76) Aligned. Score: 30 Sequences (69:77) Aligned. Score: 9 Sequences (69:78) Aligned. Score: 28 Sequences (69:79) Aligned. Score: 27 Sequences (69:80) Aligned. Score: 28 Sequences (69:81) Aligned. Score: 30 Sequences (69:82) Aligned. Score: 30 Sequences (69:83) Aligned. Score: 80 Sequences (69:84) Aligned. Score: 28 Sequences (69:85) Aligned. Score: 28 Sequences (69:86) Aligned. Score: 29 Sequences (69:87) Aligned. Score: 30 Sequences (69:88) Aligned. Score: 28 Sequences (69:89) Aligned. Score: 30 Sequences (69:90) Aligned. Score: 29 Sequences (69:91) Aligned. Score: 35 Sequences (69:92) Aligned. Score: 29 Sequences (69:93) Aligned. Score: 99 Sequences (69:94) Aligned. Score: 29 Sequences (69:95) Aligned. Score: 23 Sequences (69:96) Aligned. Score: 27 Sequences (69:97) Aligned. Score: 70 Sequences (69:98) Aligned. Score: 29 Sequences (69:99) Aligned. Score: 91 Sequences (69:100) Aligned. Score: 39 Sequences (69:101) Aligned. Score: 34 Sequences (69:102) Aligned. Score: 32 Sequences (70:71) Aligned. Score: 30 Sequences (70:72) Aligned. Score: 26 Sequences (70:73) Aligned. Score: 80 Sequences (70:74) Aligned. Score: 19 Sequences (70:75) Aligned. Score: 31 Sequences (70:76) Aligned. Score: 30 Sequences (70:77) Aligned. Score: 14 Sequences (70:78) Aligned. Score: 35 Sequences (70:79) Aligned. Score: 27 Sequences (70:80) Aligned. Score: 32 Sequences (70:81) Aligned. Score: 33 Sequences (70:82) Aligned. Score: 30 Sequences (70:83) Aligned. Score: 82 Sequences (70:84) Aligned. Score: 29 Sequences (70:85) Aligned. Score: 30 Sequences (70:86) Aligned. Score: 32 Sequences (70:87) Aligned. Score: 32 Sequences (70:88) Aligned. Score: 32 Sequences (70:89) Aligned. Score: 33 Sequences (70:90) Aligned. Score: 32 Sequences (70:91) Aligned. Score: 37 Sequences (70:92) Aligned. Score: 29 Sequences (70:93) Aligned. Score: 61 Sequences (70:94) Aligned. Score: 36 Sequences (70:95) Aligned. Score: 28 Sequences (70:96) Aligned. Score: 27 Sequences (70:97) Aligned. Score: 79 Sequences (70:98) Aligned. Score: 30 Sequences (70:99) Aligned. Score: 61 Sequences (70:100) Aligned. Score: 36 Sequences (70:101) Aligned. Score: 35 Sequences (70:102) Aligned. Score: 31 Sequences (71:72) Aligned. Score: 86 Sequences (71:73) Aligned. Score: 27 Sequences (71:74) Aligned. Score: 18 Sequences (71:75) Aligned. Score: 35 Sequences (71:76) Aligned. Score: 34 Sequences (71:77) Aligned. Score: 4 Sequences (71:78) Aligned. Score: 31 Sequences (71:79) Aligned. Score: 57 Sequences (71:80) Aligned. Score: 29 Sequences (71:81) Aligned. Score: 32 Sequences (71:82) Aligned. Score: 67 Sequences (71:83) Aligned. Score: 43 Sequences (71:84) Aligned. Score: 35 Sequences (71:85) Aligned. Score: 35 Sequences (71:86) Aligned. Score: 32 Sequences (71:87) Aligned. Score: 32 Sequences (71:88) Aligned. Score: 29 Sequences (71:89) Aligned. Score: 32 Sequences (71:90) Aligned. Score: 32 Sequences (71:91) Aligned. Score: 33 Sequences (71:92) Aligned. Score: 65 Sequences (71:93) Aligned. Score: 29 Sequences (71:94) Aligned. Score: 31 Sequences (71:95) Aligned. Score: 48 Sequences (71:96) Aligned. Score: 57 Sequences (71:97) Aligned. Score: 38 Sequences (71:98) Aligned. Score: 65 Sequences (71:99) Aligned. Score: 28 Sequences (71:100) Aligned. Score: 36 Sequences (71:101) Aligned. Score: 34 Sequences (71:102) Aligned. Score: 33 Sequences (72:73) Aligned. Score: 25 Sequences (72:74) Aligned. Score: 14 Sequences (72:75) Aligned. Score: 35 Sequences (72:76) Aligned. Score: 36 Sequences (72:77) Aligned. Score: 6 Sequences (72:78) Aligned. Score: 34 Sequences (72:79) Aligned. Score: 56 Sequences (72:80) Aligned. Score: 31 Sequences (72:81) Aligned. Score: 30 Sequences (72:82) Aligned. Score: 64 Sequences (72:83) Aligned. Score: 41 Sequences (72:84) Aligned. Score: 36 Sequences (72:85) Aligned. Score: 35 Sequences (72:86) Aligned. Score: 29 Sequences (72:87) Aligned. Score: 30 Sequences (72:88) Aligned. Score: 31 Sequences (72:89) Aligned. Score: 30 Sequences (72:90) Aligned. Score: 29 Sequences (72:91) Aligned. Score: 34 Sequences (72:92) Aligned. Score: 63 Sequences (72:93) Aligned. Score: 27 Sequences (72:94) Aligned. Score: 34 Sequences (72:95) Aligned. Score: 44 Sequences (72:96) Aligned. Score: 56 Sequences (72:97) Aligned. Score: 37 Sequences (72:98) Aligned. Score: 62 Sequences (72:99) Aligned. Score: 26 Sequences (72:100) Aligned. Score: 35 Sequences (72:101) Aligned. Score: 34 Sequences (72:102) Aligned. Score: 32 Sequences (73:74) Aligned. Score: 12 Sequences (73:75) Aligned. Score: 29 Sequences (73:76) Aligned. Score: 28 Sequences (73:77) Aligned. 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Score: 22 Sequences (74:76) Aligned. Score: 22 Sequences (74:77) Aligned. Score: 36 Sequences (74:78) Aligned. Score: 25 Sequences (74:79) Aligned. Score: 16 Sequences (74:80) Aligned. Score: 20 Sequences (74:81) Aligned. Score: 26 Sequences (74:82) Aligned. Score: 17 Sequences (74:83) Aligned. Score: 21 Sequences (74:84) Aligned. Score: 20 Sequences (74:85) Aligned. Score: 20 Sequences (74:86) Aligned. Score: 26 Sequences (74:87) Aligned. Score: 26 Sequences (74:88) Aligned. Score: 20 Sequences (74:89) Aligned. Score: 26 Sequences (74:90) Aligned. Score: 25 Sequences (74:91) Aligned. Score: 28 Sequences (74:92) Aligned. Score: 17 Sequences (74:93) Aligned. Score: 15 Sequences (74:94) Aligned. Score: 27 Sequences (74:95) Aligned. Score: 18 Sequences (74:96) Aligned. Score: 16 Sequences (74:97) Aligned. Score: 20 Sequences (74:98) Aligned. Score: 17 Sequences (74:99) Aligned. Score: 15 Sequences (74:100) Aligned. Score: 20 Sequences (74:101) Aligned. Score: 27 Sequences (74:102) Aligned. Score: 25 Sequences (75:76) Aligned. Score: 94 Sequences (75:77) Aligned. Score: 16 Sequences (75:78) Aligned. Score: 54 Sequences (75:79) Aligned. Score: 32 Sequences (75:80) Aligned. Score: 46 Sequences (75:81) Aligned. Score: 66 Sequences (75:82) Aligned. Score: 30 Sequences (75:83) Aligned. Score: 47 Sequences (75:84) Aligned. Score: 51 Sequences (75:85) Aligned. Score: 52 Sequences (75:86) Aligned. Score: 63 Sequences (75:87) Aligned. Score: 64 Sequences (75:88) Aligned. Score: 46 Sequences (75:89) Aligned. Score: 66 Sequences (75:90) Aligned. Score: 63 Sequences (75:91) Aligned. Score: 63 Sequences (75:92) Aligned. Score: 29 Sequences (75:93) Aligned. Score: 32 Sequences (75:94) Aligned. Score: 53 Sequences (75:95) Aligned. Score: 30 Sequences (75:96) Aligned. Score: 32 Sequences (75:97) Aligned. Score: 46 Sequences (75:98) Aligned. Score: 29 Sequences (75:99) Aligned. Score: 31 Sequences (75:100) Aligned. Score: 37 Sequences (75:101) Aligned. Score: 73 Sequences (75:102) Aligned. Score: 74 Sequences (76:77) Aligned. Score: 15 Sequences (76:78) Aligned. Score: 52 Sequences (76:79) Aligned. Score: 30 Sequences (76:80) Aligned. Score: 46 Sequences (76:81) Aligned. Score: 64 Sequences (76:82) Aligned. Score: 30 Sequences (76:83) Aligned. Score: 45 Sequences (76:84) Aligned. Score: 50 Sequences (76:85) Aligned. Score: 51 Sequences (76:86) Aligned. Score: 62 Sequences (76:87) Aligned. Score: 63 Sequences (76:88) Aligned. Score: 46 Sequences (76:89) Aligned. Score: 64 Sequences (76:90) Aligned. Score: 62 Sequences (76:91) Aligned. Score: 61 Sequences (76:92) Aligned. Score: 30 Sequences (76:93) Aligned. Score: 30 Sequences (76:94) Aligned. Score: 51 Sequences (76:95) Aligned. Score: 30 Sequences (76:96) Aligned. Score: 30 Sequences (76:97) Aligned. Score: 44 Sequences (76:98) Aligned. Score: 30 Sequences (76:99) Aligned. Score: 29 Sequences (76:100) Aligned. Score: 37 Sequences (76:101) Aligned. Score: 72 Sequences (76:102) Aligned. Score: 72 Sequences (77:78) Aligned. Score: 12 Sequences (77:79) Aligned. Score: 9 Sequences (77:80) Aligned. Score: 14 Sequences (77:81) Aligned. Score: 6 Sequences (77:82) Aligned. Score: 3 Sequences (77:83) Aligned. Score: 17 Sequences (77:84) Aligned. Score: 11 Sequences (77:85) Aligned. Score: 5 Sequences (77:86) Aligned. Score: 16 Sequences (77:87) Aligned. Score: 16 Sequences (77:88) Aligned. Score: 14 Sequences (77:89) Aligned. Score: 6 Sequences (77:90) Aligned. Score: 16 Sequences (77:91) Aligned. Score: 17 Sequences (77:92) Aligned. Score: 6 Sequences (77:93) Aligned. Score: 9 Sequences (77:94) Aligned. Score: 12 Sequences (77:95) Aligned. Score: 3 Sequences (77:96) Aligned. Score: 3 Sequences (77:97) Aligned. Score: 18 Sequences (77:98) Aligned. Score: 3 Sequences (77:99) Aligned. Score: 9 Sequences (77:100) Aligned. Score: 16 Sequences (77:101) Aligned. Score: 14 Sequences (77:102) Aligned. Score: 13 Sequences (78:79) Aligned. Score: 34 Sequences (78:80) Aligned. Score: 48 Sequences (78:81) Aligned. Score: 53 Sequences (78:82) Aligned. Score: 34 Sequences (78:83) Aligned. Score: 45 Sequences (78:84) Aligned. Score: 53 Sequences (78:85) Aligned. Score: 53 Sequences (78:86) Aligned. Score: 55 Sequences (78:87) Aligned. Score: 54 Sequences (78:88) Aligned. Score: 48 Sequences (78:89) Aligned. Score: 53 Sequences (78:90) Aligned. Score: 55 Sequences (78:91) Aligned. Score: 53 Sequences (78:92) Aligned. Score: 29 Sequences (78:93) Aligned. Score: 28 Sequences (78:94) Aligned. Score: 92 Sequences (78:95) Aligned. Score: 36 Sequences (78:96) Aligned. Score: 34 Sequences (78:97) Aligned. Score: 40 Sequences (78:98) Aligned. Score: 29 Sequences (78:99) Aligned. Score: 27 Sequences (78:100) Aligned. Score: 41 Sequences (78:101) Aligned. Score: 53 Sequences (78:102) Aligned. Score: 54 Sequences (79:80) Aligned. Score: 31 Sequences (79:81) Aligned. Score: 29 Sequences (79:82) Aligned. Score: 59 Sequences (79:83) Aligned. Score: 39 Sequences (79:84) Aligned. Score: 34 Sequences (79:85) Aligned. Score: 33 Sequences (79:86) Aligned. Score: 27 Sequences (79:87) Aligned. Score: 28 Sequences (79:88) Aligned. Score: 31 Sequences (79:89) Aligned. Score: 29 Sequences (79:90) Aligned. Score: 29 Sequences (79:91) Aligned. Score: 33 Sequences (79:92) Aligned. Score: 63 Sequences (79:93) Aligned. Score: 28 Sequences (79:94) Aligned. Score: 32 Sequences (79:95) Aligned. Score: 47 Sequences (79:96) Aligned. Score: 99 Sequences (79:97) Aligned. Score: 35 Sequences (79:98) Aligned. Score: 63 Sequences (79:99) Aligned. Score: 27 Sequences (79:100) Aligned. Score: 34 Sequences (79:101) Aligned. Score: 30 Sequences (79:102) Aligned. Score: 29 Sequences (80:81) Aligned. Score: 45 Sequences (80:82) Aligned. Score: 33 Sequences (80:83) Aligned. Score: 47 Sequences (80:84) Aligned. Score: 47 Sequences (80:85) Aligned. Score: 46 Sequences (80:86) Aligned. Score: 46 Sequences (80:87) Aligned. Score: 46 Sequences (80:88) Aligned. Score: 100 Sequences (80:89) Aligned. Score: 45 Sequences (80:90) Aligned. Score: 46 Sequences (80:91) Aligned. Score: 45 Sequences (80:92) Aligned. Score: 33 Sequences (80:93) Aligned. Score: 29 Sequences (80:94) Aligned. Score: 48 Sequences (80:95) Aligned. Score: 35 Sequences (80:96) Aligned. Score: 31 Sequences (80:97) Aligned. Score: 46 Sequences (80:98) Aligned. Score: 33 Sequences (80:99) Aligned. Score: 30 Sequences (80:100) Aligned. Score: 38 Sequences (80:101) Aligned. Score: 47 Sequences (80:102) Aligned. Score: 44 Sequences (81:82) Aligned. Score: 32 Sequences (81:83) Aligned. Score: 47 Sequences (81:84) Aligned. Score: 49 Sequences (81:85) Aligned. Score: 50 Sequences (81:86) Aligned. Score: 88 Sequences (81:87) Aligned. Score: 88 Sequences (81:88) Aligned. Score: 45 Sequences (81:89) Aligned. Score: 100 Sequences (81:90) Aligned. Score: 88 Sequences (81:91) Aligned. Score: 74 Sequences (81:92) Aligned. Score: 29 Sequences (81:93) Aligned. Score: 30 Sequences (81:94) Aligned. Score: 52 Sequences (81:95) Aligned. Score: 32 Sequences (81:96) Aligned. Score: 29 Sequences (81:97) Aligned. Score: 48 Sequences (81:98) Aligned. Score: 29 Sequences (81:99) Aligned. Score: 29 Sequences (81:100) Aligned. Score: 38 Sequences (81:101) Aligned. Score: 71 Sequences (81:102) Aligned. Score: 66 Sequences (82:83) Aligned. Score: 41 Sequences (82:84) Aligned. Score: 33 Sequences (82:85) Aligned. Score: 32 Sequences (82:86) Aligned. Score: 32 Sequences (82:87) Aligned. Score: 31 Sequences (82:88) Aligned. Score: 33 Sequences (82:89) Aligned. Score: 32 Sequences (82:90) Aligned. Score: 32 Sequences (82:91) Aligned. Score: 34 Sequences (82:92) Aligned. Score: 75 Sequences (82:93) Aligned. Score: 30 Sequences (82:94) Aligned. Score: 34 Sequences (82:95) Aligned. Score: 50 Sequences (82:96) Aligned. Score: 59 Sequences (82:97) Aligned. Score: 38 Sequences (82:98) Aligned. Score: 74 Sequences (82:99) Aligned. Score: 29 Sequences (82:100) Aligned. Score: 37 Sequences (82:101) Aligned. Score: 34 Sequences (82:102) Aligned. Score: 31 Sequences (83:84) Aligned. Score: 35 Sequences (83:85) Aligned. Score: 35 Sequences (83:86) Aligned. Score: 47 Sequences (83:87) Aligned. Score: 49 Sequences (83:88) Aligned. Score: 47 Sequences (83:89) Aligned. Score: 47 Sequences (83:90) Aligned. Score: 47 Sequences (83:91) Aligned. Score: 49 Sequences (83:92) Aligned. Score: 43 Sequences (83:93) Aligned. Score: 80 Sequences (83:94) Aligned. Score: 45 Sequences (83:95) Aligned. Score: 37 Sequences (83:96) Aligned. Score: 39 Sequences (83:97) Aligned. Score: 74 Sequences (83:98) Aligned. Score: 43 Sequences (83:99) Aligned. Score: 78 Sequences (83:100) Aligned. Score: 62 Sequences (83:101) Aligned. Score: 49 Sequences (83:102) Aligned. Score: 50 Sequences (84:85) Aligned. Score: 95 Sequences (84:86) Aligned. Score: 49 Sequences (84:87) Aligned. Score: 48 Sequences (84:88) Aligned. Score: 47 Sequences (84:89) Aligned. Score: 49 Sequences (84:90) Aligned. Score: 49 Sequences (84:91) Aligned. Score: 50 Sequences (84:92) Aligned. Score: 31 Sequences (84:93) Aligned. Score: 28 Sequences (84:94) Aligned. Score: 51 Sequences (84:95) Aligned. Score: 31 Sequences (84:96) Aligned. Score: 34 Sequences (84:97) Aligned. Score: 38 Sequences (84:98) Aligned. Score: 31 Sequences (84:99) Aligned. Score: 27 Sequences (84:100) Aligned. Score: 32 Sequences (84:101) Aligned. Score: 50 Sequences (84:102) Aligned. Score: 47 Sequences (85:86) Aligned. Score: 50 Sequences (85:87) Aligned. Score: 49 Sequences (85:88) Aligned. Score: 46 Sequences (85:89) Aligned. Score: 50 Sequences (85:90) Aligned. Score: 50 Sequences (85:91) Aligned. Score: 51 Sequences (85:92) Aligned. Score: 31 Sequences (85:93) Aligned. Score: 28 Sequences (85:94) Aligned. Score: 51 Sequences (85:95) Aligned. Score: 31 Sequences (85:96) Aligned. Score: 33 Sequences (85:97) Aligned. Score: 38 Sequences (85:98) Aligned. Score: 31 Sequences (85:99) Aligned. Score: 27 Sequences (85:100) Aligned. Score: 34 Sequences (85:101) Aligned. Score: 51 Sequences (85:102) Aligned. Score: 48 Sequences (86:87) Aligned. Score: 99 Sequences (86:88) Aligned. Score: 46 Sequences (86:89) Aligned. Score: 88 Sequences (86:90) Aligned. Score: 98 Sequences (86:91) Aligned. Score: 72 Sequences (86:92) Aligned. Score: 29 Sequences (86:93) Aligned. Score: 30 Sequences (86:94) Aligned. Score: 54 Sequences (86:95) Aligned. Score: 32 Sequences (86:96) Aligned. Score: 27 Sequences (86:97) Aligned. Score: 48 Sequences (86:98) Aligned. Score: 29 Sequences (86:99) Aligned. Score: 28 Sequences (86:100) Aligned. Score: 37 Sequences (86:101) Aligned. Score: 68 Sequences (86:102) Aligned. Score: 62 Sequences (87:88) Aligned. Score: 46 Sequences (87:89) Aligned. Score: 88 Sequences (87:90) Aligned. Score: 97 Sequences (87:91) Aligned. Score: 72 Sequences (87:92) Aligned. Score: 30 Sequences (87:93) Aligned. Score: 30 Sequences (87:94) Aligned. Score: 53 Sequences (87:95) Aligned. Score: 31 Sequences (87:96) Aligned. Score: 28 Sequences (87:97) Aligned. Score: 48 Sequences (87:98) Aligned. Score: 30 Sequences (87:99) Aligned. Score: 29 Sequences (87:100) Aligned. Score: 37 Sequences (87:101) Aligned. Score: 69 Sequences (87:102) Aligned. Score: 62 Sequences (88:89) Aligned. Score: 45 Sequences (88:90) Aligned. Score: 46 Sequences (88:91) Aligned. Score: 45 Sequences (88:92) Aligned. Score: 33 Sequences (88:93) Aligned. Score: 29 Sequences (88:94) Aligned. Score: 48 Sequences (88:95) Aligned. Score: 35 Sequences (88:96) Aligned. Score: 31 Sequences (88:97) Aligned. Score: 46 Sequences (88:98) Aligned. Score: 33 Sequences (88:99) Aligned. Score: 30 Sequences (88:100) Aligned. Score: 38 Sequences (88:101) Aligned. Score: 47 Sequences (88:102) Aligned. Score: 44 Sequences (89:90) Aligned. Score: 88 Sequences (89:91) Aligned. Score: 74 Sequences (89:92) Aligned. Score: 29 Sequences (89:93) Aligned. Score: 30 Sequences (89:94) Aligned. Score: 52 Sequences (89:95) Aligned. Score: 32 Sequences (89:96) Aligned. Score: 29 Sequences (89:97) Aligned. Score: 48 Sequences (89:98) Aligned. Score: 29 Sequences (89:99) Aligned. Score: 29 Sequences (89:100) Aligned. Score: 38 Sequences (89:101) Aligned. Score: 71 Sequences (89:102) Aligned. Score: 66 Sequences (90:91) Aligned. Score: 72 Sequences (90:92) Aligned. Score: 29 Sequences (90:93) Aligned. Score: 30 Sequences (90:94) Aligned. Score: 54 Sequences (90:95) Aligned. Score: 31 Sequences (90:96) Aligned. Score: 29 Sequences (90:97) Aligned. Score: 48 Sequences (90:98) Aligned. Score: 29 Sequences (90:99) Aligned. Score: 29 Sequences (90:100) Aligned. Score: 37 Sequences (90:101) Aligned. Score: 68 Sequences (90:102) Aligned. Score: 62 Sequences (91:92) Aligned. Score: 34 Sequences (91:93) Aligned. Score: 36 Sequences (91:94) Aligned. Score: 53 Sequences (91:95) Aligned. Score: 33 Sequences (91:96) Aligned. Score: 33 Sequences (91:97) Aligned. Score: 44 Sequences (91:98) Aligned. Score: 32 Sequences (91:99) Aligned. Score: 36 Sequences (91:100) Aligned. Score: 37 Sequences (91:101) Aligned. Score: 71 Sequences (91:102) Aligned. Score: 71 Sequences (92:93) Aligned. Score: 29 Sequences (92:94) Aligned. Score: 29 Sequences (92:95) Aligned. Score: 50 Sequences (92:96) Aligned. Score: 63 Sequences (92:97) Aligned. Score: 38 Sequences (92:98) Aligned. Score: 96 Sequences (92:99) Aligned. Score: 29 Sequences (92:100) Aligned. Score: 36 Sequences (92:101) Aligned. Score: 32 Sequences (92:102) Aligned. Score: 30 Sequences (93:94) Aligned. Score: 29 Sequences (93:95) Aligned. Score: 24 Sequences (93:96) Aligned. Score: 28 Sequences (93:97) Aligned. Score: 70 Sequences (93:98) Aligned. Score: 29 Sequences (93:99) Aligned. Score: 91 Sequences (93:100) Aligned. Score: 39 Sequences (93:101) Aligned. Score: 34 Sequences (93:102) Aligned. Score: 32 Sequences (94:95) Aligned. Score: 35 Sequences (94:96) Aligned. Score: 32 Sequences (94:97) Aligned. Score: 40 Sequences (94:98) Aligned. Score: 29 Sequences (94:99) Aligned. Score: 27 Sequences (94:100) Aligned. Score: 42 Sequences (94:101) Aligned. Score: 51 Sequences (94:102) Aligned. Score: 51 Sequences (95:96) Aligned. Score: 51 Sequences (95:97) Aligned. Score: 38 Sequences (95:98) Aligned. Score: 51 Sequences (95:99) Aligned. Score: 23 Sequences (95:100) Aligned. Score: 36 Sequences (95:101) Aligned. Score: 31 Sequences (95:102) Aligned. Score: 29 Sequences (96:97) Aligned. Score: 35 Sequences (96:98) Aligned. Score: 63 Sequences (96:99) Aligned. Score: 27 Sequences (96:100) Aligned. Score: 34 Sequences (96:101) Aligned. Score: 30 Sequences (96:102) Aligned. Score: 29 Sequences (97:98) Aligned. Score: 38 Sequences (97:99) Aligned. Score: 68 Sequences (97:100) Aligned. Score: 55 Sequences (97:101) Aligned. Score: 44 Sequences (97:102) Aligned. Score: 48 Sequences (98:99) Aligned. Score: 29 Sequences (98:100) Aligned. Score: 36 Sequences (98:101) Aligned. Score: 32 Sequences (98:102) Aligned. Score: 30 Sequences (99:100) Aligned. Score: 38 Sequences (99:101) Aligned. Score: 34 Sequences (99:102) Aligned. Score: 32 Sequences (100:101) Aligned. Score: 38 Sequences (100:102) Aligned. Score: 38 Sequences (101:102) Aligned. Score: 93 Guide tree file created: [./seqalign-1234567890.1234.dnd] Start of Multiple Alignment Sequence:27 Score:1663 Sequence:60 Score:2788 Sequence:68 Score:2903 Sequence:92 Score:2636 Sequence:29 Score:2617 Sequence:98 Score:2663 Sequence:35 Score:2635 Sequence:66 Score:2648 Sequence:8 Score:1579 Sequence:7 Score:1584 Sequence:74 Score:1690 Sequence:18 Score:1729 Sequence:6 Score:1649 Sequence:21 Score:1370 Sequence:82 Score:1493 Sequence:64 Score:1460 Sequence:17 Score:1546 Sequence:38 Score:1437 Sequence:56 Score:1497 Sequence:58 Score:1547 Sequence:11 Score:1410 Sequence:79 Score:1476 Sequence:96 Score:1530 Sequence:16 Score:1390 Sequence:19 Score:1511 Sequence:10 Score:1216 Sequence:13 Score:1245 Sequence:71 Score:1269 Sequence:23 Score:1410 Sequence:72 Score:1449 Sequence:14 Score:1444 Sequence:52 Score:1466 Sequence:53 Score:1494 Sequence:37 Score:1132 Sequence:5 Score:1275 Sequence:50 Score:1316 Sequence:95 Score:1361 Sequence:22 Score:360 Sequence:83 Score:363 Sequence:15 Score:402 Sequence:51 Score:404 Sequence:54 Score:405 Sequence:65 Score:403 Sequence:9 Score:812 Sequence:12 Score:878 Sequence:70 Score:942 Sequence:97 Score:397 Sequence:24 Score:903 Sequence:73 Score:948 Sequence:28 Score:887 Sequence:61 Score:915 Sequence:69 Score:930 Sequence:93 Score:956 Sequence:30 Score:962 Sequence:36 Score:977 Sequence:67 Score:980 Sequence:99 Score:1001 Sequence:39 Score:942 Sequence:57 Score:973 Sequence:59 Score:1011 Sequence:100 Score:888 Sequence:31 Score:861 Sequence:91 Score:823 Sequence:55 Score:930 Sequence:81 Score:958 Sequence:89 Score:970 Sequence:87 Score:976 Sequence:86 Score:995 Sequence:90 Score:1015 Sequence:44 Score:960 Sequence:25 Score:960 Sequence:32 Score:979 Sequence:45 Score:973 Sequence:48 Score:987 Sequence:101 Score:967 Sequence:43 Score:969 Sequence:46 Score:1018 Sequence:47 Score:997 Sequence:102 Score:1018 Sequence:49 Score:1036 Sequence:42 Score:1016 Sequence:75 Score:1032 Sequence:40 Score:1041 Sequence:76 Score:1064 Sequence:41 Score:1013 Sequence:20 Score:1007 Sequence:78 Score:942 Sequence:94 Score:969 Sequence:3 Score:934 Sequence:63 Score:951 Sequence:4 Score:956 Sequence:85 Score:989 Sequence:34 Score:1002 Sequence:84 Score:1014 Sequence:26 Score:946 Sequence:33 Score:983 Sequence:80 Score:1012 Sequence:88 Score:1038 Sequence:62 Score:749 Sequence:77 Score:1070 Alignment Score 1454950 CLUSTAL-Alignment file created [./seqalign-1234567890.1234.out] Processing /homes/user/test/qa/domainalign-keep/daf/54894.daf /shared/software/bin/clustalw -type=protein -profile1=./seqalign-1234567890.1234.aln -sequences -profile2=./seqalign-1234567890.1234.seqs -MATRIX=BLOSUM -GAPOPEN=10 -GAPEXT=0.5 -outfile=./seqalign-1234567890.1234.out Processing /homes/user/test/qa/domainalign-keep/daf/55074.daf /shared/software/bin/clustalw -type=protein -profile1=./seqalign-1234567890.1234.aln -sequences -profile2=./seqalign-1234567890.1234.seqs -MATRIX=BLOSUM -GAPOPEN=10 -GAPEXT=0.5 -outfile=./seqalign-1234567890.1234.out

Go to the output files for this example

7.0 KNOWN BUGS & WARNINGS

None.

8.0 NOTES

1. Use of CLUSTAL
clustalw must be installed on the system that is running SEQSEARCH.

2. Empty domain hits file (input)
If no sequences are given in the domain hits file then no extended alignment will be generated.

8.1 GLOSSARY OF FILE TYPES

FILE TYPE	FORMAT	DESCRIPTION	CREATED BY	SEE ALSO
Domain hits file	DHF format (FASTA-like).	Database hits (sequences) with domain classification information. The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a discriminating element (e.g. a protein signature, hidden Markov model, simple frequency matrix, Gribskov profile or Hennikoff profile) against a sequence database.	SEQSEARCH (hits retrieved by PSIBLAST). SIGSCAN (hits retrieved by sparse protein signature). LIBSCAN (hits retrieved by various types of HMM and profile).	N.A.
Domain alignment file	DAF format (CLUSTAL-like format with domain classification information).	Contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is annotated with domain family classification information.	DOMAINALIGN (structure-based sequence alignment of domains of known structure).	DOMAINALIGN alignments can be extended with sequence relatives (of unknown structure) to the family in question by using SEQALIGN.

None

9.0 DESCRIPTION

The generation of sequence alignments for large datasets such as SCOP or CATH potentially requires a lot of time for preparation of datasets, running jobs and so on, in addition to the compute time required for the alignments themselves. SEQALIGN will generate an extended alignment for each seed alignment in a directory for which a file of sequences is available, by using CLUSTALW. Sequences are added one by one to the appropriate seed alignment.

10.0 ALGORITHM

None.

11.0 RELATED APPLICATIONS

Program name	Description
cathparse	Generates DCF file from raw CATH files
domainalign	Generate alignments (DAF file) for nodes in a DCF file
domainnr	Removes redundant domains from a DCF file
domainrep	Reorder DCF file to identify representative structures
domainseqs	Adds sequence records to a DCF file
domainsse	Add secondary structure records to a DCF file
helixturnhelix	Identify nucleic acid-binding motifs in protein sequences
libgen	Generate discriminating elements from alignments
matcher	Waterman-Eggert local alignment of two sequences
matgen3d	Generate a 3D-1D scoring matrix from CCF files
oalistat	Statistics for multiple alignment files
pepcoil	Predicts coiled coil regions in protein sequences
rocon	Generates a hits file from comparing two DHF files
rocplot	Performs ROC analysis on hits files
scopparse	Generate DCF file from raw SCOP files
seqfraggle	Removes fragment sequences from DHF files
seqmatchall	All-against-all word comparison of a sequence set
seqsort	Remove ambiguous classified sequences from DHF files
seqwords	Generates DHF files from keyword search of UniProt
ssematch	Search a DCF file for secondary structure matches
supermatcher	Calculate approximate local pair-wise alignments of larger sequences
water	Smith-Waterman local alignment of sequences
wordfinder	Match large sequences against one or more other sequences
wordmatch	Finds regions of identity (exact matches) of two sequences

12.0 DIAGNOSTIC ERROR MESSAGES

The log file might contain the following messages:

Could not open seed sequence file my.file (file read error on input sequence alignment or sequence file)
Empty alignment in my.file (input alignment was empty.)
Empty singlet sequence for my.file (singlet sequence file was empty.)
Could not open domain hits file my.file (file read error on input sequence file.)
Not enough sequences found in domain hits file (insufficient sequences (i.e. < 2) in input sequence file.)

13.0 AUTHORS

Ranjeeva Ranasinghe

Jon Ison (jison@ebi.ac.uk)
The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK

14.0 REFERENCES

Please cite the authors and EMBOSS.

Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.