Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 2 of 335
Found at i:335219 original size:17 final size:17
Alignment explanation
Indices: 335197--335229 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
335187 CGGGTCTCAT
*
335197 TTTTATTTTTATTTTTA
1 TTTTATTTTCATTTTTA
335214 TTTTATTTTCATTTTT
1 TTTTATTTTCATTTTT
335230 TTGCTATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTATTTTCATTTTTA
Found at i:335444 original size:22 final size:19
Alignment explanation
Indices: 335419--335459 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 19
335409 TGAAATTTGG
335419 TTAAATGATTTTCATCTAAAAT
1 TTAAAT-ATTTT-AT-TAAAAT
335441 TTAAATATTTTATTAAAAT
1 TTAAATATTTTATTAAAAT
335460 AATATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 2 0.11
21 5 0.26
22 6 0.32
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (19 bp):
TTAAATATTTTATTAAAAT
Found at i:337283 original size:21 final size:21
Alignment explanation
Indices: 337226--337283 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
337216 TTTTTCTCCT
* * *
337226 CAGCTGCAGGAGCTTCAGCGG
1 CAGCGGCAGCAGCTCCAGCGG
337247 CAGCGGCAGC-GCCTCCAGCCGG
1 CAGCGGCAGCAG-CTCCAG-CGG
337269 -AGCGGCAGCAGCTCC
1 CAGCGGCAGCAGCTCC
337284 TCCACCCCCG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 1 0.03
21 26 0.84
22 4 0.13
ACGTcount: A:0.17, C:0.38, G:0.36, T:0.09
Consensus pattern (21 bp):
CAGCGGCAGCAGCTCCAGCGG
Found at i:338231 original size:96 final size:98
Alignment explanation
Indices: 338120--338319 Score: 291
Period size: 102 Copynumber: 2.0 Consensus size: 98
338110 TTTTTTATCA
* *
338120 TTTTATTTTACCC-TTTCTACTATTCATCATTTTCTGAAC-C-T-AATTTTCTATTTAAATCTTT
1 TTTTATTTTACCCTTTTC-ACTATTCATCATTTTCCG-ACTCTTAAAATTTCTATTTAAATCTTT
338181 TAAAAATTTTAAATTAATAAAAATAAAATTATATT
64 TAAAAATTTTAAATTAATAAAAATAAAATTATATT
338216 TTTTATTTTACCCTTTTCACTATTCATCATTTTCCGACTCTTAAAAAAAATTTCTATTTAAATCT
1 TTTTATTTTACCCTTTTCACTATTCATCATTTTCCGACTCTT----AAAATTTCTATTTAAATCT
*
338281 TTTAAAAATTTTAAATTGATAAAAATAAAATTATATT
62 TTTAAAAATTTTAAATTAATAAAAATAAAATTATATT
338318 TT
1 TT
338320 AATTTCATTA
Statistics
Matches: 93, Mismatches: 3, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
95 2 0.02
96 31 0.33
97 5 0.05
102 55 0.59
ACGTcount: A:0.37, C:0.12, G:0.01, T:0.49
Consensus pattern (98 bp):
TTTTATTTTACCCTTTTCACTATTCATCATTTTCCGACTCTTAAAATTTCTATTTAAATCTTTTA
AAAATTTTAAATTAATAAAAATAAAATTATATT
Found at i:351559 original size:13 final size:13
Alignment explanation
Indices: 351509--351556 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
351499 ATTCAAACTA
351509 AATATAT-AT-AT
1 AATATATAATAAT
351520 -ATATATAATAAT
1 AATATATAATAAT
351532 AATA-ATAATACAT
1 AATATATAATA-AT
351545 AATACTATAATA
1 AATA-TATAATA
351557 TAACCATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 6 0.19
11 2 0.06
12 8 0.26
13 9 0.29
15 6 0.19
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATATAATAAT
Found at i:351649 original size:21 final size:23
Alignment explanation
Indices: 351607--351650 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
351597 TACTAAATGA
*
351607 AAATTATAAAACTATTAAATATT
1 AAATTATAAAACTACTAAATATT
*
351630 AAATTA-AAAA-TACTATATATT
1 AAATTATAAAACTACTAAATATT
351651 TTCTAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 4 0.21
23 6 0.32
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATTATAAAACTACTAAATATT
Found at i:353602 original size:13 final size:13
Alignment explanation
Indices: 353584--353617 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
353574 GTCTATGCTT
353584 GATTTTATCTCTA
1 GATTTTATCTCTA
*
353597 GATTTTGTCTCTA
1 GATTTTATCTCTA
*
353610 AATTTTAT
1 GATTTTAT
353618 GGAAAACTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (13 bp):
GATTTTATCTCTA
Found at i:354933 original size:38 final size:38
Alignment explanation
Indices: 354859--354932 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
354849 AAAAATATTC
* *
354859 ATAAAAACATATAATTTATTTAAAGTATTTCAAAAAAT
1 ATAAAAACATATAATTTATTTAAAGAAATTCAAAAAAT
*
354897 ATAAAAACATTTAATTTATTTAAA-AAATTCAAAAAA
1 ATAAAAACATATAATTTATTTAAAGAAATTCAAAAAA
354933 AATTAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 10 0.30
38 23 0.70
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.35
Consensus pattern (38 bp):
ATAAAAACATATAATTTATTTAAAGAAATTCAAAAAAT
Found at i:356345 original size:20 final size:19
Alignment explanation
Indices: 356313--356365 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
356303 ATTTAATGGT
* *
356313 TATATTTAAATATTTAAAA
1 TATATTTATATATTCAAAA
*
356332 TATAGTTTATATATTCAAAT
1 TATA-TTTATATATTCAAAA
*
356352 TAAATTTTATATAT
1 TATA-TTTATATAT
356366 AATTAATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
TATATTTATATATTCAAAA
Found at i:356406 original size:30 final size:30
Alignment explanation
Indices: 356366--356422 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
356356 TTTTATATAT
356366 AATTAATA-TTTAT-TACTTAAAAATATTTAA
1 AATTAATATTTTATATA-TT-AAAATATTTAA
*
356396 AATTTATATTTTATATATTAAAATATT
1 AATTAATATTTTATATATTAAAATATT
356423 AACAACAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 15 0.62
31 7 0.29
32 2 0.08
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (30 bp):
AATTAATATTTTATATATTAAAATATTTAA
Found at i:356810 original size:30 final size:31
Alignment explanation
Indices: 356747--356814 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
356737 TTAATGGCGG
* * *
356747 GTGACTAAAAAAGAAAAATTCAAATAATTGA
1 GTGACTAAAAAAAAAAAATTCAAAGAATAGA
*
356778 GTGACTAAAAAAAAAAAATT-GAAGAATAGA
1 GTGACTAAAAAAAAAAAATTCAAAGAATAGA
356808 GTGACTA
1 GTGACTA
356815 TTTTATAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 14 0.42
31 19 0.58
ACGTcount: A:0.57, C:0.06, G:0.16, T:0.21
Consensus pattern (31 bp):
GTGACTAAAAAAAAAAAATTCAAAGAATAGA
Found at i:357085 original size:2 final size:2
Alignment explanation
Indices: 357072--357104 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
357062 GTTTTCTTCT
*
357072 TC TC TG TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
357105 TTCTTTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.03, T:0.52
Consensus pattern (2 bp):
TC
Found at i:360855 original size:13 final size:13
Alignment explanation
Indices: 360822--360868 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
360812 TAGCCTATTC
360822 TAAATTAAT-AAAA
1 TAAA-TAATAAAAA
360835 TAAA-AATAAAAA
1 TAAATAATAAAAA
*
360847 TAAATAATAAAAC
1 TAAATAATAAAAA
360860 TAAATAATA
1 TAAATAATA
360869 TCTTCTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 3 0.10
12 8 0.26
13 20 0.65
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAATAATAAAAA
Found at i:362852 original size:93 final size:93
Alignment explanation
Indices: 362691--362863 Score: 256
Period size: 93 Copynumber: 1.9 Consensus size: 93
362681 CGCCCATAAG
* * * * * *
362691 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTTGGACTCAACTTA
1 CGAACTCGGACTCAACTCAACGAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
362756 ACGAGCTCGAATGCCTAGTTACATCTCT
66 ACGAGCTCGAATGCCTAGTTACATCTCT
* *
362784 CGAACTCGGACTCAACTCAACGAATTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
* *
362849 ACGAGTTCGGATGCC
66 ACGAGCTCGAATGCC
362864 CAAACATCCT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.23
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGAATGCCTAGTTACATCTCT
Found at i:366639 original size:38 final size:38
Alignment explanation
Indices: 366583--366662 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
366573 GATGTGTATT
* * *
366583 CGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATC
1 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
* *
366621 CGGGATAAATCCTGCAGGCCTAGTGCTGGTATTATATT
1 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
366659 CGGG
1 CGGG
366663 CTTCGTGCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (38 bp):
CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
Found at i:366717 original size:43 final size:43
Alignment explanation
Indices: 366634--366907 Score: 383
Period size: 43 Copynumber: 6.4 Consensus size: 43
366624 GATAAATCCT
* * *
366634 GCAGGCCTAGTGCTGGT-AT-TATATTCGGG-CTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
366674 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
366717 GCAGGATTAGTGCCGATGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
366760 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCATTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * * * *
366803 ACAGGCTTCGTGCCGGTGATGTGTATTCGGGCATTCTTTCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
366846 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTTGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
366889 GCAGGCGTAATGCCGGTGA
1 GCAGGCTTAGTGCCGGTGA
366908 AATGATATGT
Statistics
Matches: 211, Mismatches: 20, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
40 15 0.07
41 2 0.01
42 9 0.04
43 185 0.88
ACGTcount: A:0.14, C:0.23, G:0.33, T:0.31
Consensus pattern (43 bp):
GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
Found at i:372127 original size:26 final size:26
Alignment explanation
Indices: 372091--372252 Score: 254
Period size: 26 Copynumber: 6.2 Consensus size: 26
372081 CATGAAATTC
372091 TTATCATGAAACATTTACCTAA-CTCA
1 TTATCATGAAACATTTACCTAACCT-A
*
372117 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
372143 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
* *
372169 TTATCATGAAGCATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
372195 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
372221 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
372247 TTATCA
1 TTATCA
372253 ATTTGTATCA
Statistics
Matches: 126, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
26 125 0.99
27 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:372224 original size:78 final size:78
Alignment explanation
Indices: 372091--372252 Score: 288
Period size: 78 Copynumber: 2.1 Consensus size: 78
372081 CATGAAATTC
*
372091 TTATCATGAAACATTTACCTAACTCATTATCATGAAACATTTACCTAACCCATTATCATGGAACA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCATTATCATGGAACA
372156 TTTACCTAACCTA
66 TTTACCTAACCTA
* * *
372169 TTATCATGAAGCATTTACCTAACCCATTATCATGGAACATTTACCTAACCTATTATCATGGAACA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCATTATCATGGAACA
372234 TTTACCTAACCTA
66 TTTACCTAACCTA
372247 TTATCA
1 TTATCA
372253 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (78 bp):
TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCATTATCATGGAACA
TTTACCTAACCTA
Found at i:376683 original size:46 final size:46
Alignment explanation
Indices: 376616--376831 Score: 315
Period size: 46 Copynumber: 4.7 Consensus size: 46
376606 GGCAACCTGA
376616 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
*
376662 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
* *
376708 GTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
*** * * *
376754 GAACAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
* * * *
376800 GAGTAAGACCATAGTTGAAAGACACTATGGCA
1 GTGTAAGACCATGGTTGAAAGATACCATGGCA
376832 TCATGTCAAA
Statistics
Matches: 156, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 156 1.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
Found at i:376811 original size:138 final size:130
Alignment explanation
Indices: 376566--376831 Score: 379
Period size: 138 Copynumber: 2.0 Consensus size: 130
376556 AGTGTGCTCT
*
376566 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGTAAGACCATGGT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGCAAGACCATGGT
* * * * * *
376631 TGAAAGATACCATGGCAACCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
66 TGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAAC
*
376696 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAACAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG--A-G---TG--CAAG
*
376761 ACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACT
58 ACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACC
376826 ATGGCA
123 ATGGCA
376832 TCATGTCAAA
Statistics
Matches: 119, Mismatches: 9, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
130 48 0.40
132 1 0.01
133 1 0.01
136 2 0.02
138 67 0.56
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (130 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGCAAGACCATGGT
TGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAAC
Found at i:380567 original size:12 final size:12
Alignment explanation
Indices: 380550--380580 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
380540 AGTAGTACCT
380550 CGGCCTCGACCA
1 CGGCCTCGACCA
380562 CGGCCTCGACCA
1 CGGCCTCGACCA
380574 CGGCCTC
1 CGGCCTC
380581 TTCCCCGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.13, C:0.52, G:0.26, T:0.10
Consensus pattern (12 bp):
CGGCCTCGACCA
Found at i:383785 original size:26 final size:26
Alignment explanation
Indices: 383749--383910 Score: 254
Period size: 26 Copynumber: 6.2 Consensus size: 26
383739 CATGAAATTC
383749 TTATCATGAAACATTTACCTAA-CTCA
1 TTATCATGAAACATTTACCTAACCT-A
*
383775 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
383801 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
* *
383827 TTATCATGAAGCATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
383853 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
383879 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
383905 TTATCA
1 TTATCA
383911 ATTTGTATCA
Statistics
Matches: 126, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
26 125 0.99
27 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:383882 original size:78 final size:78
Alignment explanation
Indices: 383749--383910 Score: 288
Period size: 78 Copynumber: 2.1 Consensus size: 78
383739 CATGAAATTC
*
383749 TTATCATGAAACATTTACCTAACTCATTATCATGAAACATTTACCTAACCCATTATCATGGAACA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCATTATCATGGAACA
383814 TTTACCTAACCTA
66 TTTACCTAACCTA
* * *
383827 TTATCATGAAGCATTTACCTAACCCATTATCATGGAACATTTACCTAACCTATTATCATGGAACA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCATTATCATGGAACA
383892 TTTACCTAACCTA
66 TTTACCTAACCTA
383905 TTATCA
1 TTATCA
383911 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (78 bp):
TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCATTATCATGGAACA
TTTACCTAACCTA
Found at i:385304 original size:44 final size:45
Alignment explanation
Indices: 385214--385342 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
385204 GACAGAACGA
*
385214 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
385260 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
385304 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
385343 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:387977 original size:46 final size:46
Alignment explanation
Indices: 387917--388190 Score: 415
Period size: 46 Copynumber: 6.0 Consensus size: 46
387907 TTTGACATGA
* * ** * * *
387917 TGCCATAGTGTCTTTCAATTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** *
387963 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
388009 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
388055 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
388101 TGTCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
388147 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
388191 AGAGCACACT
Statistics
Matches: 212, Mismatches: 15, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
45 4 0.02
46 208 0.98
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:398218 original size:13 final size:13
Alignment explanation
Indices: 398197--398229 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
398187 CTAAATTAAT
398197 AAAAT-AAAAATA
1 AAAATAAAAAATA
398209 AAAATAAAAAATA
1 AAAATAAAAAATA
*
398222 AAACTAAA
1 AAAATAAA
398230 TAAAACAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAATAAAAAATA
Found at i:399312 original size:21 final size:21
Alignment explanation
Indices: 399286--399346 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
399276 AACAGCGGTT
* *
399286 GCGGTGAAATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
399307 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
399328 GCGGTGAGATTAGAAACTG
1 GCGGTGAGATTAGATACTG
399347 CGGTGGAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.28, C:0.10, G:0.34, T:0.28
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:399580 original size:18 final size:18
Alignment explanation
Indices: 399557--399636 Score: 71
Period size: 18 Copynumber: 4.6 Consensus size: 18
399547 TATTTTAATG
399557 AATTATATAATTAATTTA
1 AATTATATAATTAATTTA
* *
399575 AATTAT-TTATTAGA-TAA
1 AATTATATAATTA-ATTTA
*
399592 AATGATAATAATT--TTT-
1 AATTAT-ATAATTAATTTA
*
399608 AATTATATAATCAATTTA
1 AATTATATAATTAATTTA
399626 AATTATATAAT
1 AATTATATAAT
399637 CAACAGGCCA
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
15 5 0.10
16 5 0.10
17 16 0.33
18 18 0.38
19 4 0.08
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (18 bp):
AATTATATAATTAATTTA
Found at i:410286 original size:25 final size:25
Alignment explanation
Indices: 410258--410309 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
410248 TTTTTAATAG
410258 AATTGATCAATTTGCTATTTGATCT
1 AATTGATCAATTTGCTATTTGATCT
*
410283 AATTGATCAATTTGCTCTTTGATCT
1 AATTGATCAATTTGCTATTTGATCT
410308 AA
1 AA
410310 CTTGTAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (25 bp):
AATTGATCAATTTGCTATTTGATCT
Found at i:412709 original size:13 final size:13
Alignment explanation
Indices: 412691--412716 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
412681 TAACATGTAC
412691 ATTTCTGCTACTA
1 ATTTCTGCTACTA
412704 ATTTCTGCTACTA
1 ATTTCTGCTACTA
412717 GTTATGCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
ATTTCTGCTACTA
Found at i:422804 original size:19 final size:20
Alignment explanation
Indices: 422765--422810 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
422755 CTACACTTAC
422765 TTTAAATTAAAATTTACA-T
1 TTTAAATTAAAATTTACATT
*
422784 TTTAAATTAATTATTTA-ATT
1 TTTAAATTAA-AATTTACATT
422804 TTTAAAT
1 TTTAAAT
422811 ACATAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTAAATTAAAATTTACATT
Found at i:424301 original size:1 final size:1
Alignment explanation
Indices: 424295--424322 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
424285 CTTTCTTTCC
424295 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
424323 GCTCTTATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:426226 original size:9 final size:9
Alignment explanation
Indices: 426188--426291 Score: 55
Period size: 9 Copynumber: 11.0 Consensus size: 9
426178 TTGTGAAATT
426188 ATTATAAAA
1 ATTATAAAA
* *
426197 ATGAATATAA
1 AT-TATAAAA
**
426207 ATTATGTAA
1 ATTATAAAA
426216 ATTATAAAA
1 ATTATAAAA
*
426225 ATTTTCAGAAA
1 ATTAT-A-AAA
*
426236 AATACTAAAA
1 ATTA-TAAAA
* * *
426246 TTTATTAAT
1 ATTATAAAA
*
426255 ATGATAAAA
1 ATTATAAAA
*
426264 ATTTTAAAA
1 ATTATAAAA
*
426273 ATTATATAA
1 ATTATAAAA
426282 ATTATTAAAA
1 ATTA-TAAAA
426292 CAATGAAAAA
Statistics
Matches: 68, Mismatches: 22, Indels: 9
0.69 0.22 0.09
Matches are distributed among these distances:
9 44 0.65
10 17 0.25
11 6 0.09
12 1 0.01
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (9 bp):
ATTATAAAA
Found at i:426633 original size:17 final size:18
Alignment explanation
Indices: 426608--426642 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
426598 AAAAAAAGCT
*
426608 ATTTTTTTAT-ATTTTTA
1 ATTTATTTATCATTTTTA
426625 ATTTATTTATCATTTTTA
1 ATTTATTTATCATTTTTA
426643 TGTTTCTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTATTTATCATTTTTA
Found at i:446800 original size:19 final size:19
Alignment explanation
Indices: 446776--446812 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
446766 AAAAAAAAAA
* *
446776 GGAAAATTGAGGAAATAAG
1 GGAAAAATGAGAAAATAAG
446795 GGAAAAATGAGAAAATAA
1 GGAAAAATGAGAAAATAA
446813 CAAAATTAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.27, T:0.14
Consensus pattern (19 bp):
GGAAAAATGAGAAAATAAG
Found at i:448162 original size:25 final size:25
Alignment explanation
Indices: 448133--448184 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
448123 AAGAATAATT
**
448133 TGAATATTTGATATTGCCTAATAAA
1 TGAATATCCGATATTGCCTAATAAA
* *
448158 TGAATATCCGATATTGCTTAGTAAA
1 TGAATATCCGATATTGCCTAATAAA
448183 TG
1 TG
448185 TCAAGCCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (25 bp):
TGAATATCCGATATTGCCTAATAAA
Found at i:449792 original size:42 final size:43
Alignment explanation
Indices: 449724--449879 Score: 149
Period size: 42 Copynumber: 3.7 Consensus size: 43
449714 CCTCGATTGA
449724 GATTTACGTATAAGACCATGTCTGGGACATCAGCATCATATCT
1 GATTTACGTATAAGACCATGTCTGGGACATCAGCATCATATCT
* * * * **
449767 GATTT-CGTGTAAGACCGTGTTTGGGACA-CAGGCCTCGAT-TGA
1 GATTTACGTATAAGACCATGTCTGGGACATCA-GCATC-ATATCT
* ** *
449809 GATTTACGTATAAGACCATGTCTAGGACATTGGCATCGTATCT
1 GATTTACGTATAAGACCATGTCTGGGACATCAGCATCATATCT
* * *
449852 GATTT-CGTGTAAGACCCTGTCTAGGACA
1 GATTTACGTATAAGACCATGTCTGGGACA
449880 GAGGTATCGA
Statistics
Matches: 90, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
41 2 0.02
42 52 0.58
43 36 0.40
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (43 bp):
GATTTACGTATAAGACCATGTCTGGGACATCAGCATCATATCT
Found at i:449851 original size:85 final size:86
Alignment explanation
Indices: 449699--449867 Score: 286
Period size: 85 Copynumber: 2.0 Consensus size: 86
449689 CGGAATAGTG
* *
449699 GTTTCGGGACATAGGCCTCGATTGAGATTTACGTATAAGACCATGTCTGGGACATCAGCATCATA
1 GTTTCGGGACACAGGCCTCGATTGAGATTTACGTATAAGACCATGTCTAGGACATCAGCATCATA
449764 TCTGATTTCGTGTAAGACCGT
66 TCTGATTTCGTGTAAGACCGT
** *
449785 GTTT-GGGACACAGGCCTCGATTGAGATTTACGTATAAGACCATGTCTAGGACATTGGCATCGTA
1 GTTTCGGGACACAGGCCTCGATTGAGATTTACGTATAAGACCATGTCTAGGACATCAGCATCATA
449849 TCTGATTTCGTGTAAGACC
66 TCTGATTTCGTGTAAGACC
449868 CTGTCTAGGA
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
85 74 0.95
86 4 0.05
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (86 bp):
GTTTCGGGACACAGGCCTCGATTGAGATTTACGTATAAGACCATGTCTAGGACATCAGCATCATA
TCTGATTTCGTGTAAGACCGT
Found at i:449890 original size:85 final size:85
Alignment explanation
Indices: 449705--449890 Score: 264
Period size: 85 Copynumber: 2.2 Consensus size: 85
449695 AGTGGTTTCG
* * *
449705 GGACATAGGCCTCGATTGAGATTTACGTATAAGACCATGTCTGGGACATCAGCATCATATCTGAT
1 GGACACAGGCATCGATTGAGATTTACGTATAAGACCATGTCTAGGACATCAGCATCATATCTGAT
* * *
449770 TTCGTGTAAGACCGTGTTTG
66 TTCGTGTAAGACCCTGTCTA
* ** *
449790 GGACACAGGCCTCGATTGAGATTTACGTATAAGACCATGTCTAGGACATTGGCATCGTATCTGAT
1 GGACACAGGCATCGATTGAGATTTACGTATAAGACCATGTCTAGGACATCAGCATCATATCTGAT
449855 TTCGTGTAAGACCCTGTCTA
66 TTCGTGTAAGACCCTGTCTA
* *
449875 GGACAGAGGTATCGAT
1 GGACACAGGCATCGAT
449891 ATTGAATTAC
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 90 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (85 bp):
GGACACAGGCATCGATTGAGATTTACGTATAAGACCATGTCTAGGACATCAGCATCATATCTGAT
TTCGTGTAAGACCCTGTCTA
Found at i:451685 original size:13 final size:13
Alignment explanation
Indices: 451669--451693 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
451659 CTTTTCTCCT
451669 TTTCTTTCTTTTC
1 TTTCTTTCTTTTC
451682 TTTCTTTCTTTT
1 TTTCTTTCTTTT
451694 TCTCCCCTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTCTTTCTTTTC
Found at i:454123 original size:20 final size:20
Alignment explanation
Indices: 454094--454146 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
454084 ATTATATATA
*
454094 TTAA-AATTATTATTATGAT
1 TTAATAATTATTATGATGAT
*
454113 TTAATAATTATTATGATTAT
1 TTAATAATTATTATGATGAT
454133 TTAATGAA-TATTAT
1 TTAAT-AATTATTAT
454147 ATTTTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 4 0.13
20 24 0.80
21 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (20 bp):
TTAATAATTATTATGATGAT
Found at i:454630 original size:23 final size:23
Alignment explanation
Indices: 454604--454648 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
454594 AAAATAAAGT
*
454604 AAATAAAAGAATA-AAAAAGAATG
1 AAATAAAA-AAAACAAAAAGAATG
454627 AAATAAAAAAAACAAAAAGAAT
1 AAATAAAAAAAACAAAAAGAAT
454649 AAGAAATAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.78, C:0.02, G:0.09, T:0.11
Consensus pattern (23 bp):
AAATAAAAAAAACAAAAAGAATG
Found at i:455673 original size:23 final size:22
Alignment explanation
Indices: 455638--455686 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
455628 GATTTATAAT
455638 ATTCTGGGTGTGTTTGGGTTGGA
1 ATTCTGGGTGTGTTTGGG-TGGA
455661 CATTCT-GGTGTGTTTGGGTGGA
1 -ATTCTGGGTGTGTTTGGGTGGA
455683 ATTC
1 ATTC
455687 GCGTATCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 4 0.16
22 4 0.16
23 12 0.48
24 5 0.20
ACGTcount: A:0.10, C:0.08, G:0.39, T:0.43
Consensus pattern (22 bp):
ATTCTGGGTGTGTTTGGGTGGA
Found at i:458012 original size:54 final size:53
Alignment explanation
Indices: 457845--458014 Score: 211
Period size: 53 Copynumber: 3.2 Consensus size: 53
457835 GTCCGTTACA
* * *
457845 GTCTTACACGGG-AGCACTTATCACTTTTCTCCGATGCCATAGCCCAGCTATG
1 GTCTTATACGGGAATCACTTATCACTTTTATCCGATGCCATAGCCCAGCTATG
* *
457897 GTCTTATAC--GAATCACTTGTATCACTTTAATCCGAAGCCATAGCCCAGCTATG
1 GTCTTATACGGGAATCAC-T-TATCACTTTTATCCGATGCCATAGCCCAGCTATG
* * * *
457950 GTCTTATACGGGAATCACTTATCACTTGTTTTCTGATGTCATAGCCCAACTATG
1 GTCTTATACGGGAATCACTTATCACTT-TTATCCGATGCCATAGCCCAGCTATG
458004 GTCTTATACGG
1 GTCTTATACGG
458015 ATATTGCTTA
Statistics
Matches: 101, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
50 1 0.01
51 4 0.04
52 9 0.09
53 48 0.48
54 32 0.32
55 7 0.07
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (53 bp):
GTCTTATACGGGAATCACTTATCACTTTTATCCGATGCCATAGCCCAGCTATG
Found at i:459259 original size:183 final size:183
Alignment explanation
Indices: 458951--459308 Score: 671
Period size: 183 Copynumber: 2.0 Consensus size: 183
458941 TGACAGATAC
458951 GGGTTAAGGGTGTTACAATTATTATTGAGCTCATTCACATGAATCTGTCATTTGAAATTGTGATA
1 GGGTTAAGGGTGTTACAATTATTATTGAGCTCATTCACATGAATCTGTCATTTGAAATTGTGATA
* *
459016 GACAAGAAGAAATAGCGAATGGCATGCTTATGTATGGTTATATGTATTTATCTAAAACACAAGAA
66 GACAAGAAGAAATAGAGAATGGCATGCTTATGTATGGTTATATATATTTATCTAAAACACAAGAA
459081 AATGATGGTTATATATTTGATAGATGGAGACATGAGACTATGATACGGGTTAG
131 AATGATGGTTATATATTTGATAGATGGAGACATGAGACTATGATACGGGTTAG
*
459134 GGGTTAAGGGTGTTACAGTTATTATTGAGCTCATTCACATGAATCTGTCATTTGAAATTGTGATA
1 GGGTTAAGGGTGTTACAATTATTATTGAGCTCATTCACATGAATCTGTCATTTGAAATTGTGATA
*
459199 GACAAGAAGAAATAGAGAATGGCATGCTTATGTATGGTTATATATATTTATCTGAAACACAAGAA
66 GACAAGAAGAAATAGAGAATGGCATGCTTATGTATGGTTATATATATTTATCTAAAACACAAGAA
*
459264 AATGATGGTTATATATTTGATATATGGAGACATGAGACTATGATA
131 AATGATGGTTATATATTTGATAGATGGAGACATGAGACTATGATA
459309 TATGAATATT
Statistics
Matches: 170, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 170 1.00
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.33
Consensus pattern (183 bp):
GGGTTAAGGGTGTTACAATTATTATTGAGCTCATTCACATGAATCTGTCATTTGAAATTGTGATA
GACAAGAAGAAATAGAGAATGGCATGCTTATGTATGGTTATATATATTTATCTAAAACACAAGAA
AATGATGGTTATATATTTGATAGATGGAGACATGAGACTATGATACGGGTTAG
Found at i:459963 original size:9 final size:9
Alignment explanation
Indices: 459949--459982 Score: 54
Period size: 8 Copynumber: 4.0 Consensus size: 9
459939 CAAAGGGGAG
459949 GAAAATAAA
1 GAAAATAAA
459958 GAAAATAAA
1 GAAAATAAA
459967 G-AAATAAA
1 GAAAATAAA
459975 -AAAATAAA
1 GAAAATAAA
459983 TTGTTCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 14 0.58
9 10 0.42
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (9 bp):
GAAAATAAA
Found at i:466135 original size:15 final size:14
Alignment explanation
Indices: 466115--466163 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 14
466105 GTTAATAGGG
*
466115 AAGAAAAAAAGGGAA
1 AAGAAAAAAA-AGAA
466130 AAGAAAAGAAAAGAA
1 AAGAAAA-AAAAGAA
466145 AAGAAAAAGAAAGAA
1 AAGAAAAA-AAAGAA
466160 AAGA
1 AAGA
466164 GACGAGACGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 1 0.03
15 27 0.87
16 3 0.10
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAAAGAA
Found at i:466137 original size:5 final size:5
Alignment explanation
Indices: 466127--466163 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
466117 GAAAAAAAGG
466127 GAAAA GAAAA GAAAA GAAAA GAAAA -AGAAA GAAAA GA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GA-AAA GAAAA GA
466164 GACGAGACGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 1 0.03
5 28 0.93
6 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:478776 original size:53 final size:53
Alignment explanation
Indices: 478695--478850 Score: 208
Period size: 53 Copynumber: 3.0 Consensus size: 53
478685 GACGAAAAAT
* *
478695 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAACTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAACTGGGCTATGGCATCGGTACA
* *
478747 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAACTGGGCTATGGCATCGGTACA
* ** * *
478800 ATGTGATAATGTGATTCCGTATAAGACCATGTCTGGGATATGGCTTCGGTA
1 ATGTGATAATGTGACTCCGTATAAGACCATAACTGGGCTATGGCATCGGTA
478851 TGATATGTGA
Statistics
Matches: 93, Mismatches: 9, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
51 4 0.04
52 10 0.11
53 79 0.85
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAACTGGGCTATGGCATCGGTACA
Found at i:481817 original size:46 final size:44
Alignment explanation
Indices: 481758--481872 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
481748 ACAGGACAGA
* *
481758 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
481804 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
481848 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
481873 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:481853 original size:44 final size:45
Alignment explanation
Indices: 481758--481891 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
481748 ACAGGACAGA
* *
481758 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
481804 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
481848 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
481892 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:488925 original size:53 final size:53
Alignment explanation
Indices: 488844--488994 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
488834 CTTACACGGT
* *
488844 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
488899 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
488952 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
488995 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:493612 original size:21 final size:21
Alignment explanation
Indices: 493588--493640 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
493578 TATTATTTCT
*
493588 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
493609 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
493630 AATCTCACCGC
1 AATCTCACCGC
493641 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:509677 original size:13 final size:13
Alignment explanation
Indices: 509661--509686 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
509651 AAATTTATAC
509661 TCAACTTTTATGG
1 TCAACTTTTATGG
509674 TCAACTTTTATGG
1 TCAACTTTTATGG
509687 GAAAATGGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
TCAACTTTTATGG
Found at i:511967 original size:2 final size:2
Alignment explanation
Indices: 511962--511991 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
511952 ACACACACAC
511962 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
511992 TAAATATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:515381 original size:9 final size:9
Alignment explanation
Indices: 515367--515396 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
515357 TTCAGGATTA
515367 TTTTGTTTG
1 TTTTGTTTG
*
515376 TTTTGTCTG
1 TTTTGTTTG
515385 TTTTGTTTG
1 TTTTGTTTG
515394 TTT
1 TTT
515397 ATGGTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.03, G:0.20, T:0.77
Consensus pattern (9 bp):
TTTTGTTTG
Found at i:519843 original size:18 final size:18
Alignment explanation
Indices: 519809--519847 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
519799 AGAATATAAT
*
519809 AAAAATATTTAAGAATTA
1 AAAAAGATTTAAGAATTA
519827 AAAAAGATTATAA-AATTA
1 AAAAAGATT-TAAGAATTA
519845 AAA
1 AAA
519848 TATTCTATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (18 bp):
AAAAAGATTTAAGAATTA
Found at i:519935 original size:14 final size:15
Alignment explanation
Indices: 519904--519936 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
519894 AATACATATT
519904 TTTATTTATAAATAA
1 TTTATTTATAAATAA
*
519919 TTTATTT-TAATTAA
1 TTTATTTATAAATAA
519933 TTTA
1 TTTA
519937 AAAAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTATTTATAAATAA
Found at i:525068 original size:30 final size:30
Alignment explanation
Indices: 525032--525091 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
525022 TTATTTCTAT
525032 TATAAAAACTGATCAATATATATAAAATGA
1 TATAAAAACTGATCAATATATATAAAATGA
525062 TATAAAAACTGATCAATATATATAAAATGA
1 TATAAAAACTGATCAATATATATAAAATGA
525092 AGTACACATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (30 bp):
TATAAAAACTGATCAATATATATAAAATGA
Found at i:526970 original size:8 final size:9
Alignment explanation
Indices: 526947--526980 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
526937 TAAAAATTAA
526947 ATATTTTTT
1 ATATTTTTT
526956 ATATTTTTT
1 ATATTTTTT
526965 AT-TTTTTT
1 ATATTTTTT
526973 ATCATTTT
1 AT-ATTTT
526981 ATTACCACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.35
9 11 0.48
10 4 0.17
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
ATATTTTTT
Found at i:527889 original size:54 final size:55
Alignment explanation
Indices: 527802--527916 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 55
527792 ATAGATAGAC
* * * * *
527802 AGAGCGTTAAGACTATGAACTATCATCAATTTTGCTCTACAGCTGAA-CCAAAGT
1 AGAGCATTAAGACTACGAACTAACATCAATTTTGCTCTAAAGCTGAAGCAAAAGT
*
527856 AGAGCATTAAGACTACGAACTAACATCAGTTTTGCTCTAAAGCTGAAGCAAAAGT
1 AGAGCATTAAGACTACGAACTAACATCAATTTTGCTCTAAAGCTGAAGCAAAAGT
527911 AGAGCA
1 AGAGCA
527917 AGACTCCAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
54 42 0.78
55 12 0.22
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.24
Consensus pattern (55 bp):
AGAGCATTAAGACTACGAACTAACATCAATTTTGCTCTAAAGCTGAAGCAAAAGT
Found at i:527935 original size:55 final size:52
Alignment explanation
Indices: 527809--527957 Score: 165
Period size: 54 Copynumber: 2.8 Consensus size: 52
527799 GACAGAGCGT
* * * *
527809 TAAGACTATGAACTATCATCAATTTTGCTCTACAGCTGAACCAAAGTAGAGC
1 TAAGACTATGAACTAACATCAGTTTTGCTCTAAAGCTGAACAAAAGTAGAGC
*
527861 ATTAAGACTACGAACTAACATCAGTTTTGCTCTAAAGCTGAAGCAAAAGTAGAGC
1 --TAAGACTATGAACTAACATCAGTTTTGCTCTAAAGCTGAA-CAAAAGTAGAGC
* *
527916 -AAGACTCCAATGAACTAACATCAGTTTAGCTCCAAAGACTGA
1 TAAGACT---ATGAACTAACATCAGTTTTGCTCTAAAG-CTGA
527958 CAGATTACTT
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
52 6 0.07
54 36 0.44
55 36 0.44
56 4 0.05
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (52 bp):
TAAGACTATGAACTAACATCAGTTTTGCTCTAAAGCTGAACAAAAGTAGAGC
Found at i:533239 original size:27 final size:27
Alignment explanation
Indices: 533209--533433 Score: 64
Period size: 27 Copynumber: 8.4 Consensus size: 27
533199 ATATTTGGTA
533209 ATAATAATATAAAATAATAATATGTAC
1 ATAATAATATAAAATAATAATATGTAC
* * *
533236 ATAA-AA-A-ACATATATATATATATATGC
1 ATAATAATATA-AAATA-ATA-ATATGTAC
* *
533263 AT-ATAATA-AAAGT-AT-GTA-GTA-
1 ATAATAATATAAAATAATAATATGTAC
*
533284 ATAATAATAATAATAATAATAATATCTAC
1 ATAATAAT-ATAA-AATAATAATATGTAC
* * * * *
533313 AATAA-AAGAAAAAATATTAGGAAACGTAC
1 -ATAATAATATAAAATAATA--ATATGTAC
* * * *
533342 ATAAAAATATATACATAA-AAAATTTAC
1 ATAATAATATA-AAATAATAATATGTAC
* * *
533369 AACAATAATATAAAATAATGATATGTGC
1 -ATAATAATATAAAATAATAATATGTAC
* *
533397 AAAAT-ATAT-ATATATATACATATGTAC
1 ATAATAATATAAAATA-ATA-ATATGTAC
533424 ATAA-AATATA
1 ATAATAATATA
533434 CACTAATATA
Statistics
Matches: 139, Mismatches: 35, Indels: 47
0.63 0.16 0.21
Matches are distributed among these distances:
21 2 0.01
22 6 0.04
23 3 0.02
24 3 0.02
25 13 0.09
26 14 0.10
27 53 0.38
28 25 0.18
29 12 0.09
30 8 0.06
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (27 bp):
ATAATAATATAAAATAATAATATGTAC
Found at i:533288 original size:3 final size:3
Alignment explanation
Indices: 533282--533307 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
533272 AAGTATGTAG
533282 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
533308 TCTACAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:533459 original size:15 final size:15
Alignment explanation
Indices: 533441--533492 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
533431 ATACACTAAT
533441 ATAATAATAGTTATA
1 ATAATAATAGTTATA
**
533456 ATAATAATAGCAATA
1 ATAATAATAGTTATA
* *
533471 GTAATAAT--TTGTA
1 ATAATAATAGTTATA
533484 ATAATAATA
1 ATAATAATA
533493 TATACACAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
13 9 0.31
15 20 0.69
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.37
Consensus pattern (15 bp):
ATAATAATAGTTATA
Found at i:533609 original size:38 final size:39
Alignment explanation
Indices: 533512--533609 Score: 103
Period size: 38 Copynumber: 2.6 Consensus size: 39
533502 TAAGGTATTT
* *
533512 AAATATATATAT-ATATATATGTATATAATAGTATTTAA
1 AAATATATATATAATATATATATATATAATAGCATTTAA
* * * *
533550 GAATATATATATAAGAAATATATA-ACTAATGGCA-TTAA
1 AAATATATATATAATATATATATATA-TAATAGCATTTAA
*
533588 AAATATATACATAATATATATA
1 AAATATATATATAATATATATA
533610 AAATACCTAA
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
38 34 0.71
39 14 0.29
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (39 bp):
AAATATATATATAATATATATATATATAATAGCATTTAA
Found at i:533611 original size:23 final size:23
Alignment explanation
Indices: 533554--533612 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 23
533544 ATTTAAGAAT
533554 ATATATATAAGAAATATATAACTA
1 ATATATATAA-AAATATATAACTA
**
533578 ATGGCAT-TAAAAATATAT-ACATA
1 AT-ATATATAAAAATATATAAC-TA
533601 ATATATATAAAA
1 ATATATATAAAA
533613 TACCTAAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
22 4 0.14
23 17 0.61
24 5 0.18
25 2 0.07
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (23 bp):
ATATATATAAAAATATATAACTA
Found at i:534049 original size:18 final size:18
Alignment explanation
Indices: 534025--534066 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
534015 CAAAAATGGG
534025 AGGAAAAATGGGGCAAGT
1 AGGAAAAATGGGGCAAGT
*
534043 GGGAAAAATGGGGCAAGT
1 AGGAAAAATGGGGCAAGT
534061 AGGAAA
1 AGGAAA
534067 GTGGCTAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.45, C:0.05, G:0.40, T:0.10
Consensus pattern (18 bp):
AGGAAAAATGGGGCAAGT
Found at i:535006 original size:30 final size:30
Alignment explanation
Indices: 534970--535027 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
534960 TTTTGAAAAA
534970 CAGAAATT-AAAAGACTCAACTCAACTCTTG
1 CAGAAATTAAAAAG-CTCAACTCAACTCTTG
*
535000 CAGAAATTAAAAAGCTCAACTCACCTCT
1 CAGAAATTAAAAAGCTCAACTCAACTCT
535028 CGCAACATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.43, C:0.26, G:0.09, T:0.22
Consensus pattern (30 bp):
CAGAAATTAAAAAGCTCAACTCAACTCTTG
Found at i:535191 original size:88 final size:89
Alignment explanation
Indices: 535058--535225 Score: 232
Period size: 88 Copynumber: 1.9 Consensus size: 89
535048 TTTTGAAAAA
* * * *
535058 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCACGTGACCCAAGGCTCAACTCACATCTCACAATATGAG
535123 TTGA-TTTTTGAAAACAAAATCTG
66 TTGATTTTTTGAAAACAAAATCTG
** * * *
535146 AAAAACAGATTTTGAAAATACCTC-GACATGTGACCCGAGGCTCAACTCACATCTCACAATGTGA
1 AAAAACAGAAATTGAAAATACCTCAG-CACGTGACCCAAGGCTCAACTCACATCTCACAATATGA
535210 GTTGATTTTTTGAAAA
65 GTTGATTTTTTGAAAA
535226 ATATAAATTG
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
87 1 0.01
88 58 0.84
89 10 0.14
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.26
Consensus pattern (89 bp):
AAAAACAGAAATTGAAAATACCTCAGCACGTGACCCAAGGCTCAACTCACATCTCACAATATGAG
TTGATTTTTTGAAAACAAAATCTG
Found at i:535335 original size:243 final size:244
Alignment explanation
Indices: 534802--535616 Score: 899
Period size: 256 Copynumber: 3.3 Consensus size: 244
534792 AACAGACATT
*
534802 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAC
1 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
** * *
534867 TTGATTTTTTG-AAACTTAA-CTTGAAAAGCAGATTTTGAAAATACCTCGATATGTGA-CTGAAG
66 TTGATTTTTTGAAAACAAAATC-TGAAAAACAGATTTTGAAAATACCTCGACATGTGACCTG-AG
* * * * *
534929 GTTCAACTCACCTCTCGCAATTTGAGTTGA-TTTTTGAAAAACAGAAATT-AAAAGACTCAACTC
129 GCTCAACTCACCTCTCACAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAA-AAT-ACCTC
* * * * *
534992 AACTCTTGCAGAAAT-TAAAAAGCTCAACTCACCTCTCGCAACATGAGTTGAAGTTTTTTTG
192 -AGT-GTG-TG--ATCT--GAAGCTCAACTCACCTCTCGCAATATGAGTTG-A-TTTTTTTG
*
535053 AAAAAAAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAAT
1 -----AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAAT
*
535118 ATGAGTTGA-TTTTTGAAAACAAAATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCC
61 ATGAGTTGATTTTTTGAAAACAAAATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCT
* * * *
535182 GAGGCTCAACTCACATCTCACAATGTGAGTTGATTTTTTGAAAAATATAAATTGAAAAAATACCT
126 GAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAAAATACCT
535247 CAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
191 CAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
* *
535301 AAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
* * ** * *
535366 TTGATTTTTTTTTTGAAAGGCAGAAAT-TG-AAAACGGAAATTGAAAATACCTCGGCGTGTGACC
66 TTGA----TTTTTTGAAA-ACA-AAATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACC
* * * *
535429 TGAGGCTCAACTCGCCTCTCACAATACGAGTTGATTTTTTG-ACAACAGAAATTG--AAATTACC
125 TGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAAAATACC
* * *
535491 TCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
190 TCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
* * ** ** *
535544 AAAAACAGAAATTGAAAATACCTCAGCA--TG-TCTTGAGGCTCAACTCATTTCTCACAATATGA
1 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGA
535606 GTTGATTTTTT
65 GTTGATTTTTT
535617 TTTTAAAAAC
Statistics
Matches: 495, Mismatches: 50, Indels: 47
0.84 0.08 0.08
Matches are distributed among these distances:
237 6 0.01
240 1 0.00
241 31 0.06
243 133 0.27
245 15 0.03
247 10 0.02
248 82 0.17
249 5 0.01
250 34 0.07
251 2 0.00
252 1 0.00
253 1 0.00
254 2 0.00
255 8 0.02
256 138 0.28
257 22 0.04
258 4 0.01
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (244 bp):
AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTTGAAAACAAAATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCTGAGGC
TCAACTCACCTCTCACAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAAAATACCTCAGTG
TGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
Found at i:535348 original size:77 final size:78
Alignment explanation
Indices: 535183--535720 Score: 358
Period size: 77 Copynumber: 6.9 Consensus size: 78
535173 ATGTGACCCG
* * * * * *
535183 AGGCTCAACTCACATCTCACAATGTGAGTTGA-TTTTTTGAAAAATATAAATTGAAAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTG--AAAATACCT
* * * *
535247 CAGTGTGTGATCTGA
64 CAGCGCGTGAGCTCA
*
535262 A-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATAGCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
535326 GCGCGTGAGC-CA
66 GCGCGTGAGCTCA
*
535338 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTGAAAGGCAGAAATTGAAAACGGA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTTGAAAGACAGAAATTG---A---A
** ** * *
535403 AATTGAAAATACCTCGGCGTGTGAC-CTG
57 AA-T--ACCT-CAGC-GCGTGAG-CTC-A
* * * * *
535431 AGGCTCAACTCGCCTCTCACAATACGAGTTGA-TTTTTTGACA-ACAGAAATTGAAATTACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
** *
535494 --GCGTGTCCT-G
66 GCGCGTGAGCTCA
*
535504 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
* * **
535569 --GCATG-TCTTG
66 GCGCGTGAGCTCA
** * * *
535579 AGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTTTTTTAAAAACAGAAATTGAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAAGACAGAAATTGAAAATACCT
* * **
535644 CA--GCATG-TCTTG
64 CAGCGCGTGAGCTCA
* ** *
535656 AGGCTCAACTAATTTCTCGCAATATGAGTTGCA---TTTTGAAA-ACAGAAATTGAAATTACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTTTGAAAGACAGAAATTGAAAATACCTC
535717 AGCG
65 AGCG
535721 TGTCTTGAGG
Statistics
Matches: 389, Mismatches: 43, Indels: 59
0.79 0.09 0.12
Matches are distributed among these distances:
72 20 0.05
73 37 0.10
74 13 0.03
75 60 0.15
76 2 0.01
77 118 0.30
78 29 0.07
79 21 0.05
80 21 0.05
81 1 0.00
82 2 0.01
83 1 0.00
85 1 0.00
86 3 0.01
87 1 0.00
88 9 0.02
89 11 0.03
90 2 0.01
91 6 0.02
92 2 0.01
93 29 0.07
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (78 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
GCGCGTGAGCTCA
Found at i:535462 original size:170 final size:166
Alignment explanation
Indices: 535238--535542 Score: 450
Period size: 170 Copynumber: 1.8 Consensus size: 166
535228 ATAAATTGAA
* * * *
535238 AAAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
1 AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCACAATACGAGTTGA-TTTTTTGAA
*
535303 AGACAGAAATTGAAAATAGCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGT
65 A-ACAGAAATTGAAAATACCTCA--GCGTG-GCCTAAGGCTCAACTCACCTCTCGCAATATGAGT
535367 TGATTTTTTTTTTGAAAGGCAGAAATTGAAAACGGAAATTG
126 TGATTTTTTTTTTGAAAGGCAGAAATTGAAAACGGAAATTG
* * * *
535408 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCACAATACGAGTTGATTTTTTGACA
1 AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCACAATACGAGTTGATTTTTTGAAA
* * *
535473 ACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
66 ACAGAAATTGAAAATACCTCAGCGTGGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
535538 TTTTT
131 TTTTT
535543 GAAAAACAGA
Statistics
Matches: 122, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
165 2 0.02
166 44 0.36
168 19 0.16
169 9 0.07
170 48 0.39
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (166 bp):
AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCACAATACGAGTTGATTTTTTGAAA
ACAGAAATTGAAAATACCTCAGCGTGGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
TTTTTTTTGAAAGGCAGAAATTGAAAACGGAAATTG
Found at i:535467 original size:93 final size:94
Alignment explanation
Indices: 535298--535468 Score: 247
Period size: 93 Copynumber: 1.8 Consensus size: 94
535288 GTTGATTTTT
* * *
535298 TTGAAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAGACAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCACAATAC
535363 GAGTTGATTTTTTTTTTGAAAGGCAGAAA
66 GAGTTGATTTTTTTTTTGAAAGGCAGAAA
* * * * *
535392 TTGAAA-ACGGAAATTGAAAATACCTCGGCGTGTGA-CCTGAGGCTCAACTCGCCTCTCACAATA
1 TTGAAAGACAGAAATTGAAAATACCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCACAATA
535455 CGAGTTGATTTTTT
65 CGAGTTGATTTTTT
535469 GACAACAGAA
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
92 2 0.03
93 60 0.88
94 6 0.09
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (94 bp):
TTGAAAGACAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCACAATAC
GAGTTGATTTTTTTTTTGAAAGGCAGAAA
Found at i:535542 original size:75 final size:73
Alignment explanation
Indices: 535392--535739 Score: 430
Period size: 75 Copynumber: 4.7 Consensus size: 73
535382 AAGGCAGAAA
* * * * *
535392 TTGAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCACAATACG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGT--CTTGAGGCTCAACTCACCTCTCACAATATG
535457 AGTTGATTTT
64 AGTTGATTTT
* * * *
535467 TTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCACAATATGAG
535532 TTGATTTTT
66 TTGA-TTTT
* **
535541 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGA
1 TTG-AAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCACAATATGA
535606 GTTGATTTTTTTT
65 GTTGA----TTTT
* * * ** *
535619 TTAAAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTAATTTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCACAATATGAG
535684 TTGCA--TT
66 TTG-ATTTT
*
535691 TTGAAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCA
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCA
535740 TTTTGAACAG
Statistics
Matches: 246, Mismatches: 21, Indels: 15
0.87 0.07 0.05
Matches are distributed among these distances:
72 47 0.19
73 33 0.13
74 7 0.03
75 88 0.36
77 63 0.26
78 8 0.03
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30
Consensus pattern (73 bp):
TTGAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCACAATATGAG
TTGATTTT
Found at i:535674 original size:152 final size:145
Alignment explanation
Indices: 535392--535742 Score: 452
Period size: 152 Copynumber: 2.4 Consensus size: 145
535382 AAGGCAGAAA
* * * ***
535392 TTGAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCACAATACG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGT--CTTGAGGCTCAACTCATTTCTCACAATACG
* * * * *
535457 AGTTGATTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTC
64 AGTTGATTTTTTAAAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTAACCTCTC
535522 GCAATATGAGTTG-ATTTTT
129 GCAATATGAGTTGCA---TT
* *
535541 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGA
1 TTG-AAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCACAATACGA
* **
535606 GTTGATTTTTTTTTTAAAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTAATTT
65 GTTGA----TTTTTTAAAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTAACCT
535671 CTCGCAATATGAGTTGCATT
126 CTCGCAATATGAGTTGCATT
*
535691 TTGAAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTT
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTT
535743 TGAACAGAAA
Statistics
Matches: 178, Mismatches: 18, Indels: 12
0.86 0.09 0.06
Matches are distributed among these distances:
148 31 0.17
149 50 0.28
150 32 0.18
152 64 0.36
153 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (145 bp):
TTGAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCACAATACGAG
TTGATTTTTTAAAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTAACCTCTCGC
AATATGAGTTGCATT
Found at i:535761 original size:49 final size:50
Alignment explanation
Indices: 535687--535791 Score: 185
Period size: 49 Copynumber: 2.1 Consensus size: 50
535677 ATATGAGTTG
*
535687 CATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACT
1 CATTTTG-AAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACT
535738 CATTTTG-AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACT
1 CATTTTGAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACT
535787 CATTT
1 CATTT
535792 CTCGCAATAT
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
49 46 0.87
51 7 0.13
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (50 bp):
CATTTTGAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACT
Found at i:535961 original size:54 final size:55
Alignment explanation
Indices: 535861--535966 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 55
535851 GAACCGAGGC
* *
535861 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGCAGAAATTGAAAAGGT
* * *
535915 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAA-CATAAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAAAAAGCAGAAATTGAAAA
535967 CAGAAATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
54 34 0.76
55 11 0.24
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (55 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGCAGAAATTGAAAAGGT
Found at i:535973 original size:13 final size:13
Alignment explanation
Indices: 535946--535979 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
535936 GAGTTGATTC
*
535946 TTGAACAACATAAA
1 TTGAA-AACAGAAA
535960 TTGAAAACAGAAA
1 TTGAAAACAGAAA
535973 TTGAAAA
1 TTGAAAA
535980 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (13 bp):
TTGAAAACAGAAA
Found at i:536027 original size:140 final size:140
Alignment explanation
Indices: 535817--536164 Score: 617
Period size: 140 Copynumber: 2.5 Consensus size: 140
535807 GAATTTTTTT
535817 TTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAA-ACAGAAATTGAAAATACCTCAGC--GTG-ACCTGAGGCTCAACTCACCTCTCGCAATA
535881 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTC
62 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTC
535946 TTGAACAACATAAA
127 TTGAACAACATAAA
*
535960 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTTGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
*
536025 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACTTCTCGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
*
536090 ACAACGTAAA
131 ACAACATAAA
*
536100 TTGAAAACAGAAATTGAAAATACCTCAGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
536165 TTGAAATTAA
Statistics
Matches: 199, Mismatches: 5, Indels: 5
0.95 0.02 0.02
Matches are distributed among these distances:
139 3 0.02
140 167 0.84
142 23 0.12
143 6 0.03
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.25
Consensus pattern (140 bp):
TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
ACAACATAAA
Found at i:536101 original size:54 final size:54
Alignment explanation
Indices: 536001--536106 Score: 126
Period size: 54 Copynumber: 1.9 Consensus size: 54
535991 GACCTGAGGC
* *
536001 TCAACTCACCTCTTGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* * *
536055 TCAACCCACTTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
536107 CAGAAATTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
54 31 0.70
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:536231 original size:72 final size:70
Alignment explanation
Indices: 536096--536262 Score: 228
Period size: 72 Copynumber: 2.3 Consensus size: 70
536086 TTGAACAACG
* * * * *
536096 TAAATTGAAAACAGAAATTGAAAATACCTCAGTGTGACCTGAGGCTCAACTCACCTCTCGCAATA
1 TAAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATA
536161 TGAGT
66 TGAGT
*
536166 TGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAA
1 T-AAATTAAAA-ACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAA
536231 TATGAGT
64 TATGAGT
*
536238 TAATTTTGAAAAACAAAAATT-AAAA
1 TAA-ATT-AAAAACAAAAATTGAAAA
536263 GGCTTAACTC
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
70 1 0.01
71 14 0.16
72 67 0.78
73 4 0.05
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.23
Consensus pattern (70 bp):
TAAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATA
TGAGT
Found at i:536357 original size:122 final size:124
Alignment explanation
Indices: 536137--536383 Score: 374
Period size: 122 Copynumber: 2.0 Consensus size: 124
536127 GTGTGACCTG
* * *
536137 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCCCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
536202 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTAATTTTGAAAAACAAAAATTAAA
66 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTAATTTTG-AAAACAAAAATTAAA
* * * *
536262 AGGCTTAACTCACCTCTCCCAATATGAG-T-CAATTTAAA-ACATAAACTAAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCCCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
* * *
536324 TGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
66 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTAATTTTGAAAACAAAAATTAAA
536383 A
1 A
536384 ATACCTCAAC
Statistics
Matches: 112, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
121 16 0.14
122 62 0.55
123 7 0.06
124 1 0.01
125 26 0.23
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.24
Consensus pattern (124 bp):
AGGCTCAACTCACCTCTCCCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTAATTTTGAAAACAAAAATTAAA
Found at i:536405 original size:71 final size:70
Alignment explanation
Indices: 536262--536436 Score: 210
Period size: 71 Copynumber: 2.5 Consensus size: 70
536252 AAAAATTAAA
* * * * * * *
536262 AGGCTTAACTCACCTCTCCCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCAGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGTG
536326 CCCCG
66 CCCCG
*
536331 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAACAAAAACTAAAAATACCTCAACGT
* **
536396 GTCTTG
65 GCCCCG
*
536402 AGGCTCAACTCA-TCTCTCGCAATATAAGTTGATTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTT
536437 CCCTTGAAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
69 25 0.27
70 6 0.07
71 60 0.66
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGTG
CCCCG
Found at i:544831 original size:21 final size:20
Alignment explanation
Indices: 544805--544858 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
544795 GGTTTCTTGG
544805 TTTTTTTTGGGGGGTTAGGTT
1 TTTTTTTTGGGGGGTTAGG-T
****
544826 TTTTTTTTTTTTGGTTAGGT
1 TTTTTTTTGGGGGGTTAGGT
544846 TTTTTTTTGGGGG
1 TTTTTTTTGGGGG
544859 CTTAATGGGC
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.04, C:0.00, G:0.31, T:0.65
Consensus pattern (20 bp):
TTTTTTTTGGGGGGTTAGGT
Found at i:545424 original size:18 final size:18
Alignment explanation
Indices: 545401--545440 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
545391 ATTTATTTAC
545401 CATTTTAATCATTTAACT
1 CATTTTAATCATTTAACT
545419 CATTTTAATCATTTAACT
1 CATTTTAATCATTTAACT
545437 -ATTT
1 CATTT
545441 AAAAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.53
Consensus pattern (18 bp):
CATTTTAATCATTTAACT
Found at i:546500 original size:19 final size:19
Alignment explanation
Indices: 546455--546500 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
546445 ATTTTCATAA
546455 TTTTA-AAAAATTCTATAT
1 TTTTATAAAAATTCTATAT
*
546473 TTTTAATAAAATTTCTAT-T
1 TTTT-ATAAAAATTCTATAT
546492 TCTTTATAA
1 T-TTTATAA
546501 TTTTTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 4 0.17
19 7 0.29
20 13 0.54
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTATAAAAATTCTATAT
Found at i:546991 original size:8 final size:7
Alignment explanation
Indices: 546929--546987 Score: 55
Period size: 7 Copynumber: 8.1 Consensus size: 7
546919 TAATTAGATC
546929 TAAAATT
1 TAAAATT
546936 TAAAATAT
1 TAAAAT-T
*
546944 AATAAATT
1 TA-AAATT
* *
546952 AAAAAAT
1 TAAAATT
*
546959 TAAAATA
1 TAAAATT
*
546966 TAAAAAT
1 TAAAATT
546973 TAAAATT
1 TAAAATT
546980 TAAAATT
1 TAAAATT
546987 T
1 T
546988 TAAAGAGTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
7 33 0.79
8 5 0.12
9 4 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
TAAAATT
Found at i:548414 original size:53 final size:58
Alignment explanation
Indices: 548366--548474 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 58
548356 CAATTATTAC
548366 AATTTTTT-ATAATTTAATCAT-AAAAAA-TTATAAAATAGTCACTTAATTATTAATA
1 AATTTTTTGATAATTTAATCATGAAAAAAGTTATAAAATAGTCACTTAATTATTAATA
* * * *
548421 AATTTTTTGATAATTTAATTATGAAAAAAGTTATAAAATATTTACCTAATTATT
1 AATTTTTTGATAATTTAATCATGAAAAAAGTTATAAAATAGTCACTTAATTATT
548475 TAATTTTATC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
55 8 0.17
56 12 0.26
57 6 0.13
58 21 0.45
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45
Consensus pattern (58 bp):
AATTTTTTGATAATTTAATCATGAAAAAAGTTATAAAATAGTCACTTAATTATTAATA
Found at i:553273 original size:5 final size:5
Alignment explanation
Indices: 553263--553290 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
553253 TAGGTAACCC
553263 AACAA AACAA AACAA AACAA AACAA AAC
1 AACAA AACAA AACAA AACAA AACAA AAC
553291 CTCCTGTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (5 bp):
AACAA
Found at i:557906 original size:27 final size:29
Alignment explanation
Indices: 557866--557920 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
557856 ACTATATCAA
*
557866 TTTTTAATAGTAAAAAT-GACTAATTTAC
1 TTTTTAATACTAAAAATGGACTAATTTAC
* *
557894 TTTTTAAT-CTAAATATGGATTAATTTA
1 TTTTTAATACTAAAAATGGACTAATTTA
557921 ACTATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (29 bp):
TTTTTAATACTAAAAATGGACTAATTTAC
Found at i:558002 original size:2 final size:2
Alignment explanation
Indices: 557995--558028 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
557985 TTATCCATAA
557995 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
558029 TGATATGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:562869 original size:20 final size:21
Alignment explanation
Indices: 562840--562879 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
562830 ATATTAAATT
562840 TTTTTCATTTAAAAAATATTA
1 TTTTTCATTTAAAAAATATTA
**
562861 TTTTT-ATTTTTAAAATATT
1 TTTTTCATTTAAAAAATATT
562880 TATATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTTCATTTAAAAAATATTA
Found at i:563628 original size:20 final size:20
Alignment explanation
Indices: 563591--563629 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
563581 TATAAATATA
*
563591 AATATTTTAAAAATAAAAAT
1 AATATTTTAAAAACAAAAAT
**
563611 AATATTTTTTAAACAAAAA
1 AATATTTTAAAAACAAAAA
563630 AAAAATTAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
AATATTTTAAAAACAAAAAT
Found at i:563996 original size:21 final size:22
Alignment explanation
Indices: 563955--564013 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 22
563945 GACCTATAAA
*
563955 AATTAATTTTTAATTACAAAAATT
1 AATTAATTTTT-TTTACAAAAA-T
563979 AA-TAATTTTTTTTA-AAAAAT
1 AATTAATTTTTTTTACAAAAAT
563999 AATTAATTTATTTTT
1 AATTAATTT-TTTTT
564014 TAATTTAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.09
21 11 0.34
22 8 0.25
23 8 0.25
24 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTAATTTTTTTTACAAAAAT
Found at i:565494 original size:16 final size:17
Alignment explanation
Indices: 565473--565506 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
565463 TTCTTTAGTA
*
565473 TTTTTGTTA-TTTTATT
1 TTTTTGGTATTTTTATT
565489 TTTTTGGTATTTTTATT
1 TTTTTGGTATTTTTATT
565506 T
1 T
565507 AACAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (17 bp):
TTTTTGGTATTTTTATT
Found at i:565689 original size:17 final size:17
Alignment explanation
Indices: 565667--565700 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
565657 TATCTATTGG
565667 ATTAAATTAAAAGTAAA
1 ATTAAATTAAAAGTAAA
*
565684 ATTAAATTAACAGTAAA
1 ATTAAATTAAAAGTAAA
565701 TTTATTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (17 bp):
ATTAAATTAAAAGTAAA
Found at i:565852 original size:26 final size:26
Alignment explanation
Indices: 565823--565902 Score: 85
Period size: 26 Copynumber: 3.2 Consensus size: 26
565813 TTTAAGTATC
565823 AATATAGATACTATTTGTCAATTACA
1 AATATAGATACTATTTGTCAATTACA
* * * * *
565849 AATAGAGA-ATTATAT-TAAAATATC-
1 AATATAGATACTATTTGTCAATTA-CA
565873 AATATAGATACTATTTGTCAATTACA
1 AATATAGATACTATTTGTCAATTACA
565899 AATA
1 AATA
565903 GAGAATTATA
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
24 12 0.30
25 12 0.30
26 16 0.40
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.36
Consensus pattern (26 bp):
AATATAGATACTATTTGTCAATTACA
Found at i:565894 original size:50 final size:50
Alignment explanation
Indices: 565819--565921 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
565809 TATCTTTAAG
565819 TATCAATATAGATACTATTTGTCAATTACAAATAGAGAATTATATTAAAA
1 TATCAATATAGATACTATTTGTCAATTACAAATAGAGAATTATATTAAAA
565869 TATCAATATAGATACTATTTGTCAATTACAAATAGAGAATTATATTAAAA
1 TATCAATATAGATACTATTTGTCAATTACAAATAGAGAATTATATTAAAA
565919 TAT
1 TAT
565922 AAGGTAAAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.37
Consensus pattern (50 bp):
TATCAATATAGATACTATTTGTCAATTACAAATAGAGAATTATATTAAAA
Found at i:567037 original size:45 final size:45
Alignment explanation
Indices: 566950--567072 Score: 144
Period size: 45 Copynumber: 2.8 Consensus size: 45
566940 GTTTGTACAT
* * * * *
566950 AGTTTCAGCCTC-AACATTATTTAAAATGGGTTTTTGTTTATAAGA
1 AGTTTCAGCTTCAAACATTCTTGAAAAT-AGTTTATGTTTATAAGA
*
566995 AG-TTCTAGCTTCAAATATTCTTGAAAATAGTTTATGTTTATAAGA
1 AGTTTC-AGCTTCAAACATTCTTGAAAATAGTTTATGTTTATAAGA
*
567040 AGTTTCAGCTTCAAACATTCTTGTAAATA-TTTA
1 AGTTTCAGCTTCAAACATTCTTGAAAATAGTTTA
567073 ATGAAGCTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
44 7 0.10
45 45 0.67
46 15 0.22
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.42
Consensus pattern (45 bp):
AGTTTCAGCTTCAAACATTCTTGAAAATAGTTTATGTTTATAAGA
Found at i:582694 original size:32 final size:32
Alignment explanation
Indices: 582654--582722 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
582644 ATGTGAAGGT
582654 AGGT-TATAGGGTTTTTCTTTTATATAATAGG
1 AGGTATATAGGGTTTTTCTTTTATATAATAGG
*
582685 AGGTATATAGGGTTTTTCTTTTATATAATTGG
1 AGGTATATAGGGTTTTTCTTTTATATAATAGG
582717 AGGTAT
1 AGGTAT
582723 TGTTAAGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 4 0.11
32 32 0.89
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.48
Consensus pattern (32 bp):
AGGTATATAGGGTTTTTCTTTTATATAATAGG
Found at i:602737 original size:29 final size:29
Alignment explanation
Indices: 602662--602738 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 29
602652 AATCACTTTT
* *
602662 ATGTATATAATT-ATATTAAATTAAAATTT
1 ATGTATA-AATTAATATTAAATCAAAATTC
*
602691 ATATATTAAATTACATATT-AATCAAAATTC
1 ATGTA-TAAATTA-ATATTAAATCAAAATTC
602721 ATGTATAAATTTAATATT
1 ATGTATAAA-TTAATATT
602739 TATCTTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
29 17 0.43
30 18 0.45
31 5 0.12
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (29 bp):
ATGTATAAATTAATATTAAATCAAAATTC
Found at i:603344 original size:18 final size:18
Alignment explanation
Indices: 603321--603420 Score: 71
Period size: 18 Copynumber: 5.3 Consensus size: 18
603311 GTTAATGATC
*
603321 AAATTTAGCTAAAAAAT-T
1 AAATTTAAC-AAAAAATAT
603339 AAATTTAACAAAAAATAT
1 AAATTTAACAAAAAATAT
*
603357 AAATATTAA-AAATTAAATTT
1 AAAT-TTAACAAA--AAATAT
*
603377 AACATTATACCATAAAAA-ATT
1 AA-ATT-TAACA-AAAAATA-T
*
603398 TAATTTAACAAAAAATAT
1 AAATTTAACAAAAAATAT
603416 AAATT
1 AAATT
603421 AAAAATTAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 20
0.71 0.08 0.22
Matches are distributed among these distances:
17 7 0.11
18 26 0.40
19 9 0.14
20 11 0.17
21 9 0.14
22 1 0.02
23 2 0.03
ACGTcount: A:0.60, C:0.06, G:0.01, T:0.33
Consensus pattern (18 bp):
AAATTTAACAAAAAATAT
Found at i:603372 original size:32 final size:32
Alignment explanation
Indices: 603332--603433 Score: 112
Period size: 32 Copynumber: 3.4 Consensus size: 32
603322 AATTTAGCTA
603332 AAAAATTAAATTTAACAAAAAATATAAATATT
1 AAAAATTAAATTTAACAAAAAATATAAATATT
* *
603364 AAAAATTAAATTTAAC----ATTATACCATA--
1 AAAAATTAAATTTAACAAAAAATATA-AATATT
*
603391 AAAAATTTAATTTAACAAAAAATAT-AA-ATT
1 AAAAATTAAATTTAACAAAAAATATAAATATT
603421 AAAAATTAAATTT
1 AAAAATTAAATTT
603434 TGCAATAACT
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
27 15 0.26
28 6 0.11
29 4 0.07
30 12 0.21
31 4 0.07
32 16 0.28
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (32 bp):
AAAAATTAAATTTAACAAAAAATATAAATATT
Found at i:605036 original size:51 final size:51
Alignment explanation
Indices: 604964--605175 Score: 325
Period size: 51 Copynumber: 4.2 Consensus size: 51
604954 CTGATCACAT
604964 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* * * * * *
605015 TTATCACTTTTCATTGGTCAGATAAGTGTAGCTAAAGCTACCACTTGTCAT
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
*
605066 TTATCATTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* * *
605117 TTATCACTTGTCATTGATCAGATAAGTGTAGCTAAAGCTACCATTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
*
605168 TTGTCACT
1 TTATCACT
605176 GATCAGAAGT
Statistics
Matches: 143, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 143 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
Found at i:605083 original size:102 final size:102
Alignment explanation
Indices: 604961--605159 Score: 371
Period size: 102 Copynumber: 2.0 Consensus size: 102
604951 ACACTGATCA
*
604961 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTATCACTTTT
1 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTATCACTTGT
*
605026 CATTGGTCAGATAAGTGTAGCTAAAGCTACCACTTGT
66 CATTGATCAGATAAGTGTAGCTAAAGCTACCACTTGT
*
605063 CATTTATCATTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTATCACTTGT
1 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTATCACTTGT
605128 CATTGATCAGATAAGTGTAGCTAAAGCTACCA
66 CATTGATCAGATAAGTGTAGCTAAAGCTACCA
605160 TTTATCACTT
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 94 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.34
Consensus pattern (102 bp):
CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTATCACTTGT
CATTGATCAGATAAGTGTAGCTAAAGCTACCACTTGT
Found at i:612311 original size:13 final size:14
Alignment explanation
Indices: 612279--612311 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
612269 ATTTGATAAA
612279 AATTAATATTAACT
1 AATTAATATTAACT
612293 AA-TAATATTAA-T
1 AATTAATATTAACT
612305 AATTAAT
1 AATTAAT
612312 TTTCATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.17
13 13 0.72
14 2 0.11
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
AATTAATATTAACT
Found at i:612556 original size:26 final size:27
Alignment explanation
Indices: 612504--612557 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
612494 ATTTTTTTTA
612504 AATACAAATATTATATTAGGCCAAAAAAT
1 AATACAAATATTATATTAGG-C-AAAAAT
612533 AATACAAATAATT-TATTAGG-AAAAA
1 AATACAAAT-ATTATATTAGGCAAAAA
612558 GTATTAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 5 0.21
29 16 0.67
30 3 0.12
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.28
Consensus pattern (27 bp):
AATACAAATATTATATTAGGCAAAAAT
Found at i:613077 original size:14 final size:14
Alignment explanation
Indices: 613058--613089 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
613048 TTTAAAATTT
613058 TGAAACTTTTGAAA
1 TGAAACTTTTGAAA
613072 TGAAACTTTTGAAA
1 TGAAACTTTTGAAA
613086 TGAA
1 TGAA
613090 TAAAACTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (14 bp):
TGAAACTTTTGAAA
Found at i:615395 original size:13 final size:14
Alignment explanation
Indices: 615364--615398 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
615354 AAATCCAAAG
615364 CTATTTTTTTAACT
1 CTATTTTTTTAACT
*
615378 TTATTTTTTTAA-T
1 CTATTTTTTTAACT
615391 CTATTTTT
1 CTATTTTT
615399 CATTTCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (14 bp):
CTATTTTTTTAACT
Found at i:622587 original size:16 final size:16
Alignment explanation
Indices: 622555--622589 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
622545 ATTATTTTTA
**
622555 AAAATTAAAAATCATT
1 AAAATTAAAAAAAATT
622571 AAAATTAAAAAAAATT
1 AAAATTAAAAAAAATT
622587 AAA
1 AAA
622590 TGCTAGCGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATTAAAAAAAATT
Found at i:622625 original size:28 final size:28
Alignment explanation
Indices: 622593--622647 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
622583 AATTAAATGC
*
622593 TAGCGTATTATTTACATGACAATTCATA
1 TAGCGTATTATCTACATGACAATTCATA
622621 TAGCGTATTATCTACATGACAATTCAT
1 TAGCGTATTATCTACATGACAATTCAT
622648 GTGTATAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (28 bp):
TAGCGTATTATCTACATGACAATTCATA
Found at i:622978 original size:35 final size:34
Alignment explanation
Indices: 622932--623004 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 34
622922 ATTAACTTAG
622932 TTTGCCACTTAAATAAATCTAAATCCCAATATCT
1 TTTGCCACTTAAATAAATCTAAATCCCAATATCT
*
622966 ATTTGCCACTTAAATAAATTTAAATCCCAATATCT
1 -TTTGCCACTTAAATAAATCTAAATCCCAATATCT
623001 TTTG
1 TTTG
623005 AAAAATTATG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 4 0.11
35 33 0.89
ACGTcount: A:0.37, C:0.21, G:0.04, T:0.38
Consensus pattern (34 bp):
TTTGCCACTTAAATAAATCTAAATCCCAATATCT
Found at i:631182 original size:24 final size:24
Alignment explanation
Indices: 631154--631208 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
631144 AGATCGATAA
* *
631154 ATTAAAA-TTTATATGTATCATCTT
1 ATTAAAAGTTTATATATATC-TATT
*
631178 ATTAAAAGTTTATTTATATCTATT
1 ATTAAAAGTTTATATATATCTATT
631202 ATTAAAA
1 ATTAAAA
631209 AATTGCATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 17 0.63
25 10 0.37
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (24 bp):
ATTAAAAGTTTATATATATCTATT
Found at i:633083 original size:10 final size:10
Alignment explanation
Indices: 633068--633093 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
633058 TCTTTATCAT
633068 TTTTATAAAA
1 TTTTATAAAA
633078 TTTTATAAAA
1 TTTTATAAAA
633088 TTTTAT
1 TTTTAT
633094 TTTTTACTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTTATAAAA
Found at i:637253 original size:7 final size:7
Alignment explanation
Indices: 637241--637281 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
637231 TGTATATACT
637241 CATATCA
1 CATATCA
637248 CATATCA
1 CATATCA
637255 CATATCA
1 CATATCA
637262 CATATCA
1 CATATCA
*
637269 CATATCT
1 CATATCA
637276 CATATC
1 CATATC
637282 GCTTGAGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.32
Consensus pattern (7 bp):
CATATCA
Found at i:638619 original size:20 final size:20
Alignment explanation
Indices: 638594--638637 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
638584 ATATTATTAA
*
638594 ATTATT-TTGAAATAATAAAT
1 ATTATTATTCAAAT-ATAAAT
*
638614 ATTATTATTCAAATTTAAAT
1 ATTATTATTCAAATATAAAT
638634 ATTA
1 ATTA
638638 AAAAACATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTATTATTCAAATATAAAT
Found at i:639299 original size:19 final size:18
Alignment explanation
Indices: 639255--639299 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
639245 TTTGAAGAAA
639255 GTGAATTTAAAATTCAAC
1 GTGAATTTAAAATTCAAC
*
639273 GTGAATTTAAAATTCGAC
1 GTGAATTTAAAATTCAAC
639291 GTAGAATTT
1 GT-GAATTT
639300 GTGTCTGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (18 bp):
GTGAATTTAAAATTCAAC
Found at i:644189 original size:7 final size:7
Alignment explanation
Indices: 644177--644216 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
644167 TCTTTCTTTC
644177 TTTTTAT
1 TTTTTAT
644184 TTTTTAT
1 TTTTTAT
644191 TTTATT-T
1 TTT-TTAT
*
644198 ATTTTAT
1 TTTTTAT
644205 TTTTTAT
1 TTTTTAT
644212 TTTTT
1 TTTTT
644217 TTATACACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 2 0.07
7 25 0.86
8 2 0.07
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTAT
Found at i:644204 original size:21 final size:21
Alignment explanation
Indices: 644178--644220 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
644168 CTTTCTTTCT
644178 TTTTATTTTTTATTTTATTTA
1 TTTTATTTTTTATTTTATTTA
*
644199 TTTTATTTTTTATTTTTTTTA
1 TTTTATTTTTTATTTTATTTA
644220 T
1 T
644221 ACACTAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTATTTTTTATTTTATTTA
Done.