diffseq.output

emboss的linux版本的源代码

<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: ap000504.diffseq</h3>
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<pre>
########################################
# Program: diffseq
# Rundate: Sat 15 Jul 2006 12:00:00
# Commandline: diffseq
#    [-asequence] tembl:ap000504
#    [-bsequence] tembl:af129756
# Report_format: diffseq
# Report_file: ap000504.diffseq
# Additional_files: 2
# 1: AP000504.diffgff (Feature file for first sequence)
# 2: AF129756.diffgff (Feature file for second sequence)
########################################

#=======================================
#
# Sequence: AP000504     from: 1   to: 100000
# HitCount: 119
#
# Compare: AF129756     from: 1   to: 184666
# 
# AP000504 overlap starts at 1
# AF129756 overlap starts at 6036
# 
# (AP000504) start end length sequence
# (AF129756) start end length sequence
# 
#
#=======================================


AP000504 847-847 Length: 1
Sequence: a
Sequence: t
AF129756 6882-6882 Length: 1

AP000504 1795-1795 Length: 1
Sequence: g
Sequence: a
AF129756 7830-7830 Length: 1

AP000504 2273-2273 Length: 1
Sequence: t
Sequence: 
Feature: repeat_region 7920-8351 rpt_family='MSTB'
AF129756 8307 Length: 0

AP000504 2466-2466 Length: 1
Sequence: g
Sequence: a
Feature: repeat_region 8391-8686 rpt_family='AluSg'


<font color=red>  [Part of this file has been deleted for brevity]</font>

Sequence: t
Sequence: g
AF129756 99726-99726 Length: 1

AP000504 93860-93860 Length: 1
Sequence: t
Sequence: g
AF129756 99890-99890 Length: 1

AP000504 95451-95451 Length: 1
Sequence: c
Sequence: t
AF129756 101481-101481 Length: 1

AP000504 96650-96650 Length: 1
Sequence: c
Sequence: t
AF129756 102680-102680 Length: 1

AP000504 97273-97274 Length: 2
Sequence: aa
Sequence: 
Feature: repeat_region 103299-103402 rpt_family='AluSq'
AF129756 103302 Length: 0

AP000504 97716-97716 Length: 1
Sequence: a
Sequence: g
AF129756 103744-103744 Length: 1

AP000504 97827-97827 Length: 1
Sequence: c
Sequence: t
Feature: repeat_region 103784-104083 rpt_family='AluSx'
AF129756 103855-103855 Length: 1

#---------------------------------------
#
# Overlap_end: 100000 in AP000504
# Overlap_end: 106028 in AF129756
# 
# SNP_count: 86
# Transitions: 58
# Transversions: 28
#
#---------------------------------------

#---------------------------------------
# Total_sequences: 1
# Total_hitcount: 119
#---------------------------------------
</pre>
</td></tr></table><p>
<p><h3>File: AF129756.diffgff</h3>
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<pre>
##gff-version 2.0
##date 2006-07-15
##Type DNA AF129756
AF129756	diffseq	conflict	6882	6882	1.000	+	.	Sequence "AF129756.1" ; note "SNP in AP000504" ; replace "a"
AF129756	diffseq	conflict	7830	7830	1.000	+	.	Sequence "AF129756.2" ; note "SNP in AP000504" ; replace "g"
AF129756	diffseq	conflict	8500	8500	1.000	+	.	Sequence "AF129756.3" ; note "SNP in AP000504" ; replace "g"
AF129756	diffseq	conflict	10945	10962	1.000	+	.	Sequence "AF129756.4" ; note "Insertion of 18 bases in AF129756" ; replace ""
AF129756	diffseq	conflict	10999	11001	1.000	+	.	Sequence "AF129756.5" ; note "AP000504" ; replace "aaa"
AF129756	diffseq	conflict	12915	12915	1.000	+	.	Sequence "AF129756.6" ; note "SNP in AP000504" ; replace "g"
AF129756	diffseq	conflict	15139	15139	1.000	+	.	Sequence "AF129756.7" ; note "SNP in AP000504" ; replace "g"
AF129756	diffseq	conflict	17192	17192	1.000	+	.	Sequence "AF129756.8" ; note "SNP in AP000504" ; replace "c"
AF129756	diffseq	conflict	19761	19761	1.000	+	.	Sequence "AF129756.9" ; note "SNP in AP000504" ; replace "a"
AF129756	diffseq	conflict	20291	20291	1.000	+	.	Sequence "AF129756.10" ; note "SNP in AP000504" ; replace "c"
AF129756	diffseq	conflict	20462	20462	1.000	+	.	Sequence "AF129756.11" ; note "SNP in AP000504" ; replace "g"
AF129756	diffseq	conflict	25686	25686	1.000	+	.	Sequence "AF129756.12" ; note "SNP in AP000504" ; replace "t"
AF129756	diffseq	conflict	26192	26192	1.000	+	.	Sequence "AF129756.13" ; note "SNP in AP000504" ; replace "c"
AF129756	diffseq	conflict	27227	27227	1.000	+	.	Sequence "AF129756.14" ; note "Insertion of 1 bases in AF129756" ; replace ""
AF129756	diffseq	conflict	27837	27837	1.000	+	.	Sequence "AF129756.15" ; note "SNP in AP000504" ; replace "c"
AF129756	diffseq	conflict	29328	29328	1.000	+	.	Sequence "AF129756.16" ; note "SNP in AP000504" ; replace "t"
AF129756	diffseq	conflict	29458	29458	1.000	+	.	Sequence "AF129756.17" ; note "SNP in AP000504" ; replace "a"
AF129756	diffseq	conflict	29629	29629	1.000	+	.	Sequence "AF129756.18" ; note "SNP in AP000504" ; replace "t"
AF129756	diffseq	conflict	29646	29646	1.000	+	.	Sequence "AF129756.19" ; note "SNP in AP000504" ; replace "g"
AF129756	diffseq	conflict	30838	30838	1.000	+	.	Sequence "AF129756.20" ; note "SNP in AP000504" ; replace "c"
AF129756	diffseq	conflict	31349	31349	1.000	+	.	Sequence "AF129756.21" ; note "SNP in AP000504" ; replace "c"
AF129756	diffseq	conflict	31901	31901	1.000	+	.	Sequence "AF129756.22" ; note "SNP in AP000504" ; replace "g"
AF129756	diffseq	conflict	36682	36682	1.000	+	.	Sequence "AF129756.23" ; note "SNP in AP000504" ; replace "c"
AF129756	diffseq	conflict	38225	38226	1.000	+	.	Sequence "AF129756.24" ; note "Insertion of 2 bases in AF129756" ; replace ""
AF129756	diffseq	conflict	38379	38379	1.000	+	.	Sequence "AF129756.25" ; note "SNP in AP000504" ; replace "c"
AF129756	diffseq	conflict	38537	38537	1.000	+	.	Sequence "AF129756.26" ; note "SNP in AP000504" ; replace "t"
AF129756	diffseq	conflict	39114	39114	1.000	+	.	Sequence "AF129756.27" ; note "SNP in AP000504" ; replace "t"
AF129756	diffseq	conflict	39816	39816	1.000	+	.	Sequence "AF129756.28" ; note "SNP in AP000504" ; replace "g"
AF129756	diffseq	conflict	40807	40807	1.000	+	.	Sequence "AF129756.29" ; note "SNP in AP000504" ; replace "a"
AF129756	diffseq	conflict	40977	40977	1.000	+	.	Sequence "AF129756.30" ; note "Insertion of 1 bases in AF129756" ; replace ""
AF129756	diffseq	conflict	41204	41204	1.000	+	.	Sequence "AF129756.31" ; note "SNP in AP000504" ; replace "a"
AF129756	diffseq	conflict	42548	42548	1.000	+	.	Sequence "AF129756.32" ; note "SNP in AP000504" ; replace "g"
AF129756	diffseq	conflict	45315	45315	1.000	+	.	Sequence "AF129756.33" ; note "Insertion of 1 bases in AF129756" ; replace ""
AF129756	diffseq	conflict	48382	48382	1.000	+	.	Sequence "AF129756.34" ; note "SNP in AP000504" ; replace "a"
AF129756	diffseq	conflict	50635	50635	1.000	+	.	Sequence "AF129756.35" ; note "SNP in AP000504" ; replace "t"
AF129756	diffseq	conflict	50809	50809	1.000	+	.	Sequence "AF129756.36" ; note "SNP in AP000504" ; replace "g"
AF129756	diffseq	conflict	51286	51286	1.000	+	.	Sequence "AF129756.37" ; note "SNP in AP000504" ; replace "g"
AF129756	diffseq	conflict	51645	51645	1.000	+	.	Sequence "AF129756.38" ; note "Insertion of 1 bases in AF129756" ; replace ""
AF129756	diffseq	conflict	52388	52388	1.000	+	.	Sequence "AF129756.39" ; note "SNP in AP000504" ; replace "c"
AF129756	diffseq	conflict	52646	52646	1.000	+	.	Sequence "AF129756.40" ; note "SNP in AP000504" ; replace "a"
AF129756	diffseq	conflict	53596	53596	1.000	+	.	Sequence "AF129756.41" ; note "SNP in AP000504" ; replace "a"
AF129756	diffseq	conflict	53621	53621	1.000	+	.	Sequence "AF129756.42" ; note "SNP in AP000504" ; replace "t"
AF129756	diffseq	conflict	54883	54883	1.000	+	.	Sequence "AF129756.43" ; note "SNP in AP000504" ; replace "g"
AF129756	diffseq	conflict	55377	55377	1.000	+	.	Sequence "AF129756.44" ; note "SNP in AP000504" ; replace "g"
AF129756	diffseq	conflict	55571	55571	1.000	+	.	Sequence "AF129756.45" ; note "SNP in AP000504" ; replace "c"
AF129756	diffseq	conflict	55611	55611	1.000	+	.	Sequence "AF129756.46" ; note "SNP in AP000504" ; replace "t"
AF129756	diffseq	conflict	55655	55661	1.000	+	.	Sequence "AF129756.47" ; note "Insertion of 7 bases in AF129756" ; replace ""