The DASGFF feature table report format is identical to the standard DASGFF feature table format (Section A.2, “Supported Feature Formats”).

<?xml version="1.0" standalone="no"?>
<!DOCTYPE DASGFF SYSTEM "http://www.biodas.org/dtd/dasgff.dtd">
<DASGFF>
  <GFF version="1.0" href="url">
    <SEGMENT id="AMIR_PSEAE" start="1" stop="197"
                version="0.0">
      <FEATURE id="AMIR_PSEAE.antigenic.1">
         <TYPE id="SO:0001018" category="other" reference="no" subparts="no">epitope</TYPE>
         <METHOD id="antigenic"></METHOD>
         <START>80</START>
         <END>123</END>
         <SCORE>1.246428</SCORE>
         <ORIENTATION>0</ORIENTATION>
         <PHASE>-</PHASE>
         <NOTE>pos:118</NOTE>
      </FEATURE>
      <FEATURE id="AMIR_PSEAE.antigenic.2">
         <TYPE id="SO:0001018" category="other" reference="no" subparts="no">epitope</TYPE>
         <METHOD id="antigenic"></METHOD>
         <START>4</START>
         <END>60</END>
         <SCORE>1.221857</SCORE>
         <ORIENTATION>0</ORIENTATION>
         <PHASE>-</PHASE>
         <NOTE>pos:54</NOTE>
      </FEATURE>
      <FEATURE id="AMIR_PSEAE.antigenic.3">
         <TYPE id="SO:0001018" category="other" reference="no" subparts="no">epitope</TYPE>
         <METHOD id="antigenic"></METHOD>
         <START>67</START>
         <END>76</END>
         <SCORE>1.129714</SCORE>
         <ORIENTATION>0</ORIENTATION>
         <PHASE>-</PHASE>
         <NOTE>pos:72</NOTE>
      </FEATURE>
      <FEATURE id="AMIR_PSEAE.antigenic.4">
         <TYPE id="SO:0001018" category="other" reference="no" subparts="no">epitope</TYPE>
         <METHOD id="antigenic"></METHOD>
         <START>182</START>
         <END>189</END>
         <SCORE>1.089571</SCORE>
         <ORIENTATION>0</ORIENTATION>
         <PHASE>-</PHASE>
         <NOTE>pos:184</NOTE>
      </FEATURE>
      <FEATURE id="AMIR_PSEAE.antigenic.5">
         <TYPE id="SO:0001018" category="other" reference="no" subparts="no">epitope</TYPE>
         <METHOD id="antigenic"></METHOD>
         <START>168</START>
         <END>173</END>
         <SCORE>1.068571</SCORE>
         <ORIENTATION>0</ORIENTATION>
         <PHASE>-</PHASE>
         <NOTE>pos:170</NOTE>
      </FEATURE>
      <FEATURE id="AMIR_PSEAE.antigenic.6">
         <TYPE id="SO:0001018" category="other" reference="no" subparts="no">epitope</TYPE>
         <METHOD id="antigenic"></METHOD>
         <START>152</START>
         <END>158</END>
         <SCORE>1.057000</SCORE>
         <ORIENTATION>0</ORIENTATION>
         <PHASE>-</PHASE>
         <NOTE>pos:154</NOTE>
      </FEATURE>
    </SEGMENT>
  </GFF>
</DASGFF>

Dbmotif format describes features, usually short sequence motifs, in a sequence.

The report begins with the standard report header (Section 5.5, “Introduction to Report Formats”) followed by a blank line. A number of entries equal to the number of features in the sequence then follows. An entry uses tags from the feature table of the sequence. An individual entry begins with the following block of lines:

Length = length
Start = position start of sequence
End = position end of sequence
tagname1 = tagvalue1
tagname2 = tagvalue2
tagname3 = tagvalue3

The number of tag:value pairs equals the number of named tags in the report feature table (3 in the above example).

There is then a blank line followed by a diagram illustrating the start and end of the match in the sequences. The first line of the diagram is the sequence of the match (sequence tag), the second line contains | (pipe) characters to indicate start and end points, and the third line contains the start and end positions underneath the appropriate pipe. The general format is therefore:

sequence
  |    |
start end

For example:

SARGDFLNYALSLMRSHNDE
     |        |
     8        17

Or if the start and end are identical:

MSARGDFLNYA
     |
     6

The report ends with the standard report footer (Section 5.5, “Introduction to Report Formats”).

Length = 4
Start = position 158 of sequence
End = position 161 of sequence


SNLEVSTTSFLPTP
     |  |
   158  161


#---------------------------------------
#---------------------------------------

#---------------------------------------
# Total_sequences: 1
# Total_length: 281
# Reported_sequences: 1
# Reported_hitcount: 1
#---------------------------------------

The Debug report format is used to show the full internal values in the feature table for debugging purposes. It is not intended for general use.

Diffseq format is based on the output from the diffseq application. The report describes matches, usually short, between two sequences and features which overlap them.

The report begins with the standard report header (Section 5.5, “Introduction to Report Formats”) followed by a blank line. A number of entries equal to the number of features in the first sequence then follows. An entry uses tags from the feature table of the first sequence, which are replicated for the second sequence.

An entry begins with one of the two following blocks of lines to describe the feature in the first sequence, either

name start-end Length:length
Feature: tagvalue1
Feature: tagvalue2
Feature: tagvalue3
Sequence: sequence

or

name start Length:length
Feature: tagvalue1
Feature: tagvalue2
Feature: tagvalue3
Sequence: 

Then one of the two following blocks of lines to describe the feature in the second sequence. Either

Sequence: sequence
Feature: secondfeature1
Feature: secondfeature2
Feature: secondfeature3
name start-end Length:length

or

Sequence: 
Feature: feature
Feature: feature
Feature: feature
name start Length:length

Followed by a blank line.

In all cases, the number of Feature: records given equals the number of features in the report feature table.

The report ends with the standard report footer (Section 5.5, “Introduction to Report Formats”).

X65923 284-284 Length: 1
Feature: CDS 57-458 gene='fau' db_xref='GDB:135476' db_xref='GOA:P62861' db_xref='HGNC:3597' db_xref='HSSP:1GJZ' db_xref='InterPro:IPR006846' db_xref='UniProtKB/Swiss-Prot:P35544' protein_id='CAA46716.1'
Feature: misc_feature 279-458 note='S30 part'
Sequence: t
Sequence: c
Feature: gene 1-402 gene='FAU' locus_tag='HCM4175'
AY411291 228-228 Length: 1

#---------------------------------------
#
# Overlap_end: 458 in X65923
# Overlap_end: 402 in AY411291
# 
# SNP_count: 1
# Transitions: 1
# Transversions: 0
#
#---------------------------------------

#---------------------------------------
# Total_sequences: 2
# Total_length: 920
# Reported_sequences: 1
# Reported_hitcount: 1
#---------------------------------------

The EMBL feature table report format is identical to the standard EMBL feature table format (Section A.2, “Supported Feature Formats”).

FH   Key             Location/Qualifiers
FH
FT   misc_feature    1..6
FT                   /note="*pat pattern"
FT   misc_feature    1267..1272
FT                   /note="*pat pattern"

FeatTable format is based on the output from the cpgreport application. The report describes features in a sequence.

A number of entries equal to the number of features in the sequence is given. The report is an EMBL feature table using only the format-specific tags in the report definition: there is no requirement for tag names to match standards for the EMBL feature table.

An individual entry begins with one of the following lines. Either:

FT type start..end

or:

FT type complement(start..end)

Followed by a number of FT records equal to the number of available tags in the report feature table:

FT        /tagname1=tagvalue1
FT        /tagname2=tagvalue2
FT        /tagname3=tagvalue3

Followed by a blank line.

FT   epitope         80..123
FT                   /Max_score_pos="118"
FT   epitope         4..60
FT                   /Max_score_pos="54"
FT   epitope         67..76
FT                   /Max_score_pos="72"
FT   epitope         182..189
FT                   /Max_score_pos="184"
FT   epitope         168..173
FT                   /Max_score_pos="170"
FT   epitope         152..158
FT                   /Max_score_pos="154"

The GenBank feature table report format is identical to the standard GenBank feature table format (Section A.2, “Supported Feature Formats”).

FEATURES             Location/Qualifiers
     misc_feature    1..6
                     /note="*pat pattern"
     misc_feature    1267..1272
                     /note="*pat pattern"

The GFF feature table report format is identical to the standard GFF3 feature table format (Section A.2, “Supported Feature Formats”).

##gff-version 3
##sequence-region AMIR_PSEAE 1 196
#!Date 2010-03-03
#!Type Protein
#!Source-version EMBOSS 6.2.0
AMIR_PSEAE	antigenic	epitope	80	123	1.246	+	.	ID="AMIR_PSEAE.1";note="*pos 118"
AMIR_PSEAE	antigenic	epitope	4	60	1.222	+	.	ID="AMIR_PSEAE.2";note="*pos 54"
AMIR_PSEAE	antigenic	epitope	67	76	1.130	+	.	ID="AMIR_PSEAE.3";note="*pos 72"
AMIR_PSEAE	antigenic	epitope	182	189	1.090	+	.	ID="AMIR_PSEAE.4";note="*pos 184"
AMIR_PSEAE	antigenic	epitope	168	173	1.069	+	.	ID="AMIR_PSEAE.5";note="*pos 170"
AMIR_PSEAE	antigenic	epitope	152	158	1.057	+	.	ID="AMIR_PSEAE.6";note="*pos 154"

This report describes features, typically short sequence motifs, in a sequence. The output is a listfile (Section 6.6, “The Uniform Sequence Address (USA)”) with the start and end points of the motifs given after the sequence's full USA. This is useful as the output is a true listfile that can be read in by other EMBOSS programs.

The report begins with the standard report header (Section 5.5, “Introduction to Report Formats”) followed by a blank line. A number of lines equal to the number of motifs in the sequence then follows.

An individual entry (line) has the following format:

USA[start:end]

The report ends with the standard report footer (Section 5.5, “Introduction to Report Formats”).

########################################
# Program: fuzznuc
# Rundate: Wed  3 Mar 2010 13:26:41
# Commandline: fuzznuc
#    [-sequence] tembl:L46634
#    -pattern AAGCTT
#    -rformat listfile
#    [-outfile] Listfile
# Report_format: listfile
# Report_file: Listfile
########################################

#=======================================
#
# Sequence: tembl-id:L46634     from: 1   to: 1272
# HitCount: 2
#
# Pattern_name Mismatch Pattern
# pattern             0 AAGCTT
# 
# Complement: No
#
#=======================================

tembl-id:L46634[1:6]
tembl-id:L46634[1267:1272]

#---------------------------------------
#---------------------------------------

#---------------------------------------
# Total_sequences: 1
# Total_length: 1272
# Reported_sequences: 1
# Reported_hitcount: 2
#---------------------------------------

Motif format is based on the output from the antigenic, helixturnhelix and sigcleave applications. The report describes features, usually short sequence motifs, in a sequence.

The report begins with the standard report header (Section 5.5, “Introduction to Report Formats”) followed by a blank line. A number of entries equal to the number of motifs in the sequence then follows. An entry uses tags from the feature table of the sequence. An individual entry begins with one of the two following blocks of lines to describe the feature in the sequence.

The score will be printed if the application was run with the -rscoreshow command line qualifier that is specific to reports (see Section 6.4, “Datatype-specific Command Line Qualifiers”):

(FeatureNumber Score score length length at name start->end

If the score is not to be printed:

(FeatureNumber length length at name start->end

In either case, FeatureNumber is a simple count (from 1 up) of the features.

A blank line may or may not then be printed, followed by a diagram illustrating the start and end of the match in the sequences. The first line of the diagram has the Sequence: token followed by the sequence of the match (sequence tag), the second line contains | (pipe) characters to indicate start and end points, and the third line contains the start and end positions underneath the appropriate pipe. The general format is therefore:

sequence
  |    |
start end

For example:

 Sequence: MMSARG
           |    |
           1    6

Or if the start and end are identical:

 Sequence: D
           |
           1

Finally there are a number of lines with tag:value pairs equal to the number of available tags in the report feature table (3 in this example):

tagname1: tagvalue1
tagname2: tagvalue2
tagname3: tagvalue3

The report ends with the standard report footer (Section 5.5, “Introduction to Report Formats”).

########################################
# Program: antigenic
# Rundate: Wed  3 Mar 2010 13:20:10
# Commandline: antigenic
#    [-sequence] uniprot:p10932
#    -auto
#    -rformat motif
#    [-outfile] Motif
# Report_format: motif
# Report_file: Motif
########################################

#=======================================
#
# Sequence: AMIR_PSEAE     from: 1   to: 196
# HitCount: 6
#=======================================

Max_score_pos at "*"

(1) Score 1.246 length 44 at residues 80->123
                                                 *
 Sequence: TTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSAR
           |                                          |
          80                                          123
 Max_score_pos: 118

(2) Score 1.222 length 57 at residues 4->60
                                                             *
 Sequence: NSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSI
           |                                                       |
           4                                                       60
 Max_score_pos: 54

(3) Score 1.130 length 10 at residues 67->76
                *
 Sequence: DEIAALLAAG
           |        |
          67        76
 Max_score_pos: 72

(4) Score 1.090 length 8 at residues 182->189
             *
 Sequence: ILKIAQEL
           |      |
         182      189
 Max_score_pos: 184

(5) Score 1.069 length 6 at residues 168->173
             *
 Sequence: HQYLSR
           |    |
         168    173
 Max_score_pos: 170

(6) Score 1.057 length 7 at residues 152->158
             *
 Sequence: AKALLMQ
           |     |
         152     158
 Max_score_pos: 154


#---------------------------------------
#---------------------------------------

The report describes features, usually short sequence motifs in a sequence. This is a simple table format that does not include the feature sequence. See the "Table" format for a version without the name.

The report begins with the standard report header (Section 5.5, “Introduction to Report Formats”) followed by a blank line. An entry uses tags from the feature table of the sequence.

The first line after the header and a blank line is a header line for the table itself. This has the general format:

  Name  Start   End   tagname1  tagname2  tagname3  Sequence

or, if the score is to be printed:

  Start   End   Score  tagname1  tagname2  tagname3  Sequence

The score will be printed if the application was run with the -rscoreshow command line qualifier that is specific to reports (see Section 6.4, “Datatype-specific Command Line Qualifiers”).

In either case, the number of tag names given is equal to the number of available tags in the feature table (3 in this example). The column width is 6, or longer as required if the tag names are longer.

A number of lines equal to the number of features in the sequence then follow. These have the general format:

  name  start   end   tagvalue1  tagvalue2  tagvalue3  Sequence

or, if the score is to be printed:

  name  start   end  score   tagvalue1  tagvalue2  tagvalue3  Sequence

Missing tag values are reported as '.' (full-stop).

The report ends with the standard report footer (Section 5.5, “Introduction to Report Formats”).

########################################
# Program: antigenic
# Rundate: Wed  3 Mar 2010 13:20:24
# Commandline: antigenic
#    [-sequence] uniprot:p10932
#    -auto
#    -rformat nametable
#    [-outfile] Nametable
# Report_format: nametable
# Report_file: Nametable
########################################

#=======================================
#
# Sequence: AMIR_PSEAE     from: 1   to: 196
# HitCount: 6
#=======================================

USA                    Start     End   Score Max_score_pos
AMIR_PSEAE                80     123   1.246           118
AMIR_PSEAE                 4      60   1.222            54
AMIR_PSEAE                67      76   1.130            72
AMIR_PSEAE               182     189   1.090           184
AMIR_PSEAE               168     173   1.069           170
AMIR_PSEAE               152     158   1.057           154

#---------------------------------------
#---------------------------------------

The PIR feature table report format is identical to the standard PIR feature table format (Section A.2, “Supported Feature Formats”).

F;80-123/Region: *pos 118, epitope
F;4-60/Region: *pos 54, epitope
F;67-76/Region: *pos 72, epitope
F;182-189/Region: *pos 184, epitope
F;168-173/Region: *pos 170, epitope
F;152-158/Region: *pos 154, epitope

The report describes features, usually short sequence motifs, in a sequence.

The report begins with the standard report header (Section 5.5, “Introduction to Report Formats”) followed by a blank line. A number of entries equal to the number of motifs in the sequence then follows. An entry uses tags from the feature table of the sequence.

An individual entry begins with the following line:

type from start to end (length name)

This is followed by one of the two types of line. If the score is to be printed, i.e. the application was run with the -rscoreshow command line qualifier that is specific to reports (see Section 6.4, “Datatype-specific Command Line Qualifiers”), then the following line is given:

   Max score: score (tagname1: tagvalue1 tagname2: tagvalue2 tagname3: tagvalue3)

If the score is not to be printed:

tagname1: tagvalue1 tagname2: tagvalue2 tagname3: tagvalue3

In either case the number of tag:value pairs is equal to the number of available tags in the report feature table (3 in this example).

The report ends with the standard report footer (Section 5.5, “Introduction to Report Formats”).

########################################
# Program: antigenic
# Rundate: Wed  3 Mar 2010 13:20:35
# Commandline: antigenic
#    [-sequence] uniprot:p10932
#    -auto
#    -rformat regions
#    [-outfile] Regions
# Report_format: regions
# Report_file: Regions
########################################

#=======================================
#
# Sequence: AMIR_PSEAE     from: 1   to: 196
# HitCount: 6
#=======================================

epitope from 80 to 123 (44 residues)
   Max score: 1.246 (Max_score_pos: 118)

epitope from 4 to 60 (57 residues)
   Max score: 1.222 (Max_score_pos: 54)

epitope from 67 to 76 (10 residues)
   Max score: 1.130 (Max_score_pos: 72)

epitope from 182 to 189 (8 residues)
   Max score: 1.090 (Max_score_pos: 184)

epitope from 168 to 173 (6 residues)
   Max score: 1.069 (Max_score_pos: 170)

epitope from 152 to 158 (7 residues)
   Max score: 1.057 (Max_score_pos: 154)


#---------------------------------------
#---------------------------------------

The report describes features, usually short sequence motifs in a sequence. This is a simple table format that includes the feature sequence. See the "Table" format for a version without the sequence.

The report begins with the standard report header (Section 5.5, “Introduction to Report Formats”) followed by a blank line. An entry uses tags from the feature table of the sequence.

The first line after the header and blank line is a header line for the table. This has the general format:

  Start   End   tagname1  tagname2  tagname3  Sequence

The number of tag names given is equal to the number of available tags in the report feature table (3 in this example). The column width is 6, or longer as required if the tag names are longer.

A number of lines equal to the number of features in the sequence then follow. These have the general format:

  start   End   tagvalue1  tagvalue2  tagvalue3  Sequence

Missing tag values are reported as '.' (full stop).

The report ends with the standard report footer (Section 5.5, “Introduction to Report Formats”).

########################################
# Program: antigenic
# Rundate: Wed  3 Mar 2010 13:20:53
# Commandline: antigenic
#    [-sequence] uniprot:p10932
#    -auto
#    -rformat seqtable
#    [-outfile] Seqtable
# Report_format: seqtable
# Report_file: Seqtable
########################################

#=======================================
#
# Sequence: AMIR_PSEAE     from: 1   to: 196
# HitCount: 6
#=======================================

  Start     End Max_score_pos Sequence
     80     123           118 TTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSAR
      4      60            54 NSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSI
     67      76            72 DEIAALLAAG
    182     189           184 ILKIAQEL
    168     173           170 HQYLSR
    152     158           154 AKALLMQ

#---------------------------------------
#---------------------------------------

SRS format is a simple parsable format that includes the feature sequence. The report describes features, usually short sequence motifs, in a sequence. See the "SRS Simple" format for a version without the sequence.

The report begins with the standard report header (Section 5.5, “Introduction to Report Formats”) followed by a blank line. A number of entries equal to the number of motifs in the sequence then follows. An entry uses tags from the feature table of the sequence.

An individual entry ends in a blank line and has the following format:

   Feature number
   Name: name
   Start:  start
   End: end
   Length: length
   Sequence: sequence
   Score: score
   tagname1:  tagvalue1
   tagname2:  tagvalue2
   tagname3:  tagvalue3

Feature number is a simple count (from 1 up) of the features. The number of lines with tag:value pairs equals the number of available tags in the feature table (3 in this example). Missing tag values are reported as '.' (full stop).

The report ends with the standard report footer (Section 5.5, “Introduction to Report Formats”).

########################################
# Program: antigenic
# Rundate: Wed  3 Mar 2010 13:19:08
# Commandline: antigenic
#    [-sequence] uniprot:p10932
#    -auto
#    -rformat srs
#    [-outfile] Srs
# Report_format: srs
# Report_file: Srs
########################################

#=======================================
#
# Sequence: AMIR_PSEAE     from: 1   to: 196
# HitCount: 6
#=======================================

Feature: 1
Name: AMIR_PSEAE
Start: 80
End: 123
Length: 44
Sequence: TTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSAR
Score: 1.246
Strand: +
Max_score_pos: 118

Feature: 2
Name: AMIR_PSEAE
Start: 4
End: 60
Length: 57
Sequence: NSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSI
Score: 1.222
Strand: +
Max_score_pos: 54

Feature: 3
Name: AMIR_PSEAE
Start: 67
End: 76
Length: 10
Sequence: DEIAALLAAG
Score: 1.130
Strand: +
Max_score_pos: 72

Feature: 4
Name: AMIR_PSEAE
Start: 182
End: 189
Length: 8
Sequence: ILKIAQEL
Score: 1.090
Strand: +
Max_score_pos: 184

Feature: 5
Name: AMIR_PSEAE
Start: 168
End: 173
Length: 6
Sequence: HQYLSR
Score: 1.069
Strand: +
Max_score_pos: 170

Feature: 6
Name: AMIR_PSEAE
Start: 152
End: 158
Length: 7
Sequence: AKALLMQ
Score: 1.057
Strand: +
Max_score_pos: 154

#---------------------------------------
#---------------------------------------

SRS simple format is a simple parsable format that does not include the feature sequence. The report describes features, usually short sequence motifs, in a sequence. See the "SRS" format for a version with the sequence.

The report begins with the standard report header (Section 5.5, “Introduction to Report Formats”) followed by a blank line. A number of entries equal to the number of motifs in the sequence then follows. An entry uses tags from the feature table of the sequence.

An individual entry ends in a blank line and has the following format:

   Feature number
   Name: name
   Start:  start
   End: end
   Length: length
   Score: score
   tagname1:  tagvalue1
   tagname2:  tagvalue2
   tagname3:  tagvalue3

Feature number is a simple count (from 1 up) of the features. The number of lines with tag:value pairs equals the number of available tags in the report feature table (3 in this example). Missing tag values are reported as '.' (full stop).

The report ends with the standard report footer (Section 5.5, “Introduction to Report Formats”).

########################################
# Program: antigenic
# Rundate: Wed  3 Mar 2010 13:21:30
# Commandline: antigenic
#    [-sequence] uniprot:p10932
#    -auto
#    -rformat simple
#    [-outfile] Simple
# Report_format: simple
# Report_file: Simple
########################################

#=======================================
#
# Sequence: AMIR_PSEAE     from: 1   to: 196
# HitCount: 6
#=======================================

Feature: 1
Name: AMIR_PSEAE
Start: 80
End: 123
Length: 44
Score: 1.246
Strand: +
Max_score_pos: 118

Feature: 2
Name: AMIR_PSEAE
Start: 4
End: 60
Length: 57
Score: 1.222
Strand: +
Max_score_pos: 54

Feature: 3
Name: AMIR_PSEAE
Start: 67
End: 76
Length: 10
Score: 1.130
Strand: +
Max_score_pos: 72

Feature: 4
Name: AMIR_PSEAE
Start: 182
End: 189
Length: 8
Score: 1.090
Strand: +
Max_score_pos: 184

Feature: 5
Name: AMIR_PSEAE
Start: 168
End: 173
Length: 6
Score: 1.069
Strand: +
Max_score_pos: 170

Feature: 6
Name: AMIR_PSEAE
Start: 152
End: 158
Length: 7
Score: 1.057
Strand: +
Max_score_pos: 154

#---------------------------------------
#---------------------------------------

The SwissProt feature table report format is identical to the standard SwissProt feature table format (Section A.2, “Supported Feature Formats”).

FT   REGION       80    123       *pos 118.
FT   REGION        4     60       *pos 54.
FT   REGION       67     76       *pos 72.
FT   REGION      182    189       *pos 184.
FT   REGION      168    173       *pos 170.
FT   REGION      152    158       *pos 154.

The report describes features, usually short sequence motifs, in a sequence. This is a TAB-delimited table format suitable for reading into spreadsheet programs such as MS Excel. An entry uses tags from the feature table of the sequence.

The first line is a header line for the table. This has the general format:

SeqName Start End Strand tagname1  tagname2  tagname3

or, if the score is to be printed (i.e. the application was run with the -rscoreshow command line qualifier that is specific to reports (see Section 6.4, “Datatype-specific Command Line Qualifiers”):

SeqName Start End Score Strand tagname1  tagname2  tagname3

In either case, the number of tag names given is equal to the number of available tags in the report feature table (3 in this example). The column width is 6, or longer as required if the tag names are longer.

A number of lines equal to the number of features in the sequence then follow. These have the general format:

name start end strand tagname1  tagname2  tagname3

or, if the score is to be printed:

name start end score strand tagname1  tagname2  tagname3

Missing tag values are reported as '.' (full stop).

SeqName	Start	End	Score	Strand	Max_score_pos
AMIR_PSEAE	80	123	1.246	+	118
AMIR_PSEAE	4	60	1.222	+	54
AMIR_PSEAE	67	76	1.130	+	72
AMIR_PSEAE	182	189	1.090	+	184
AMIR_PSEAE	168	173	1.069	+	170
AMIR_PSEAE	152	158	1.057	+	154

The report describes features, usually short sequence motifs in a sequence. This is a simple table format that does not include the feature sequence. See the "Tagseq" format for a version with the sequence.

The report begins with the standard report header (Section 5.5, “Introduction to Report Formats”) followed by a blank line. An entry uses tags from the feature table of the sequence.

The first line after the header and a blank line is a header line for the table itself. This has the general format:

  Start   End   tagname1  tagname2  tagname3  Sequence

or, if the score is to be printed (i.e. the application was run with the -rscoreshow command line qualifier that is specific to reports (see Section 6.4, “Datatype-specific Command Line Qualifiers”):

  Start   End   Score  tagname1  tagname2  tagname3  Sequence

In either case, the number of tag names given is equal to the number of available tags in the feature table (3 in this example). The column width is 6, or longer as required if the tag names are longer.

A number of lines equal to the number of features in the sequence then follow. These have the general format:

  start   end   tagvalue1  tagvalue2  tagvalue3  Sequence

or, if the score is to be printed:

  start   end  score   tagvalue1  tagvalue2  tagvalue3  Sequence

Missing tag values are reported as '.' (full stop).

The report ends with the standard report footer (Section 5.5, “Introduction to Report Formats”).

########################################
# Program: antigenic
# Rundate: Wed  3 Mar 2010 13:20:53
# Commandline: antigenic
#    [-sequence] uniprot:p10932
#    -auto
#    -rformat seqtable
#    [-outfile] Seqtable
# Report_format: seqtable
# Report_file: Seqtable
########################################

#=======================================
#
# Sequence: AMIR_PSEAE     from: 1   to: 196
# HitCount: 6
#=======================================

  Start     End Max_score_pos Sequence
     80     123           118 TTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSAR
      4      60            54 NSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSI
     67      76            72 DEIAALLAAG
    182     189           184 ILKIAQEL
    168     173           170 HQYLSR
    152     158           154 AKALLMQ

#---------------------------------------
#---------------------------------------

The report describes features, usually short sequence motifs, in a sequence. The full sequence is given with features marked up below the sequence.

The report begins with the standard report header (Section 5.5, “Introduction to Report Formats”) followed by a blank line. An entry uses tags from the feature table of the sequence.

The output is given in blocks of lines. The first line in a block is a sequence position index, the second line is a sequence segment 50 residues long. Then a line is given for each available tag in the report feature table, beginning with the feature name. Features are marked up on this line with a + symbol, or the tag value if this is single letter code. For example:

          .   10    .   20    .   30    .   40    .   50
      MMSARGDFLNYALSLMRSHNDEHSDVLPVLDVCSLKHVAYVFQALIYWIK
helix HHHHHH HHHHHHHHHH           HHHHHHHHHH  HHHHHHHHHH
sheet                          EEE          EE          
turns       T             TTTTT                         
 coil                  CCC                              
          .   60    .   70    .   80    .   90    .  100
      AMNQQTTLDTPQLERKRTRELLELGIDNEDSEHENDDDTSQSATLNDKDD
helix             HHHHHHHHHHHHHHH HHHHHHH    HH         
sheet                                          EE       
turns    TT                              TTT        TTT 
 coil CCC  CCCCCCC               C          C    CCC   C

The number of tag names given is equal to the number of available tags in the feature table (3 in this example).

The report ends with the standard report footer (Section 5.5, “Introduction to Report Formats”).

########################################
# Program: fuzznuc
# Rundate: Wed  3 Mar 2010 13:27:54
# Commandline: fuzznuc
#    [-sequence] tembl:L46634
#    -pattern AAGCTT
#    -rformat tagseq
#    [-outfile] Tagseq
# Report_format: tagseq
# Report_file: Tagseq
########################################

#=======================================
#
# Sequence: L46634     from: 1   to: 1272
# HitCount: 2
#
# Pattern_name Mismatch Pattern
# pattern             0 AAGCTT
# 
# Complement: No
#
#=======================================

                     .   10    .   20    .   30    .   40    .   50
                 aagcttaaactgaggtcacacacgactttaattacggcaacgcaacagct
nucleotide_motif ++++++                                            
                     .   60    .   70    .   80    .   90    .  100
                 gtaagctgcaggaaagatacgatcgtaagcaaatgtagtcctacaatcaa
nucleotide_motif                                                   
                     .  110    .  120    .  130    .  140    .  150
                 gcgaggttgtagacgttacctacaatgaactacacctctaagcataacct
nucleotide_motif                                                   
                     .  160    .  170    .  180    .  190    .  200
                 gtcgggcacagtgagacacgcagccgtaaattcaaaactcaacccaaacc
nucleotide_motif                                                   
                     .  210    .  220    .  230    .  240    .  250
                 gaagtctaagtctcaccctaatcgtaacagtaaccctacaactctaatcc
nucleotide_motif                                                   
                     .  260    .  270    .  280    .  290    .  300
                 tagtccgtaaccgtaaccccaatcctagcccttagccctaaccctagccc
nucleotide_motif                                                   
                     .  310    .  320    .  330    .  340    .  350
                 taaccctagctctaaccttagctctaactctgaccctaggcctaacccta
nucleotide_motif                                                   
                     .  360    .  370    .  380    .  390    .  400
                 agcctaaccctaaccgtagctctaagtttaaccctaaccctaaccctaac
nucleotide_motif                                                   
                     .  410    .  420    .  430    .  440    .  450
                 catgaccctgaccctaaccctagggctgcggccctaaccctagccctaac
nucleotide_motif                                                   
                     .  460    .  470    .  480    .  490    .  500
                 cctaaccctaatcctaatcctagccctaaccctagggctgcggccctaac
nucleotide_motif                                                   
                     .  510    .  520    .  530    .  540    .  550
                 cctagccctaaccctaaccctaaccctagggctgcggccctaaccctaac
nucleotide_motif                                                   
                     .  560    .  570    .  580    .  590    .  600
                 cctagggctgcggcccgaaccctaaccctaaccctaaccctaaccctagg
nucleotide_motif                                                   
                     .  610    .  620    .  630    .  640    .  650
                 gctgcggccctaaccctaaccctagggctgcggccctaaccctaacccta
nucleotide_motif                                                   
                     .  660    .  670    .  680    .  690    .  700
                 gggctgcggcccgaaccctaaccctaaccctaaccctagggctgcggccc
nucleotide_motif                                                   
                     .  710    .  720    .  730    .  740    .  750
                 taaccctaaccctagggctgcggccctaaccctaaccctaactctagggc
nucleotide_motif                                                   
                     .  760    .  770    .  780    .  790    .  800
                 tgcggccctaaccctaaccctaaccctaaccctagggctgcggcccgaac
nucleotide_motif                                                   
                     .  810    .  820    .  830    .  840    .  850
                 cctagccctaaccctaaccctgaccctgaccctaaccctaaccctaaccc
nucleotide_motif                                                   
                     .  860    .  870    .  880    .  890    .  900
                 taaccctaaccctaaccctaaccctaaccctaaccctaaccctaacccta
nucleotide_motif                                                   
                     .  910    .  920    .  930    .  940    .  950
                 accctaaccctaaccctaaccctaaccccgcccccactggcagccaatgt
nucleotide_motif                                                   
                     .  960    .  970    .  980    .  990    . 1000
                 cttgtaatgccttcaaggcactttttctgcgagccgcgcgcagcactcag
nucleotide_motif                                                   
                     . 1010    . 1020    . 1030    . 1040    . 1050
                 tgaaaaacaagtttgtgcacgagaaagacgctgccaaaccgcagctgcag
nucleotide_motif                                                   
                     . 1060    . 1070    . 1080    . 1090    . 1100
                 catgaaggctgagtgcacaattttggctttagtcccataaaggcgcggct
nucleotide_motif                                                   
                     . 1110    . 1120    . 1130    . 1140    . 1150
                 tcccgtagagtagaaaaccgcagcgcggcgcacagagcgaaggcagcggc
nucleotide_motif                                                   
                     . 1160    . 1170    . 1180    . 1190    . 1200
                 tttcagactgtttgccaagcgcagtctgcatcttaccaatgatgatcgca
nucleotide_motif                                                   
                     . 1210    . 1220    . 1230    . 1240    . 1250
                 agcaagaaaaatgttctttcttagcatatgcgtggttaatcctgttgtgg
nucleotide_motif                                                   
                     . 1260    . 1270
                 tcatcactaagttttcaagctt
nucleotide_motif                 ++++++

#---------------------------------------
#---------------------------------------

#---------------------------------------
# Total_sequences: 1
# Total_length: 1272
# Reported_sequences: 1
# Reported_hitcount: 2
#---------------------------------------

The report describes features, usually short sequence motifs, in a sequence. This is of use only for debugging.

The report begins with the standard report header (Section 5.5, “Introduction to Report Formats”) followed by a blank line. An entry uses tags from the feature table of the sequence. The report ends with the standard report footer (Section 5.5, “Introduction to Report Formats”).