Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold193
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: 3104049
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 172765 characters in sequence are not A, C, G, or T
File 4 of 18
Found at i:499319 original size:29 final size:29
Alignment explanation
Indices: 499286--499359 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 29
499276 AATATTAATA
499286 AAAAATTATTTTATATATTAATAATAAAAT
1 AAAAA-TATTTTATATATTAATAATAAAAT
**
499316 AAAAAT-TTTTAT-TAAAAAATTAATAAAAT
1 AAAAATATTTTATAT-ATTAA-TAATAAAAT
499345 AATAAATATTTTATA
1 AA-AAATATTTTATA
499360 AAATATATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
27 1 0.03
28 9 0.24
29 12 0.32
30 9 0.24
31 6 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
AAAAATATTTTATATATTAATAATAAAAT
Found at i:499349 original size:32 final size:32
Alignment explanation
Indices: 499298--499383 Score: 99
Period size: 32 Copynumber: 2.7 Consensus size: 32
499288 AAATTATTTT
499298 ATATATTAATAATAA-AATAAAAATTTTTATTAAA
1 ATATATTAATAA-AATAATAAAAA-TTTTA-TAAA
*
499332 A-A-ATTAATAAAATAATAAATATTTTATAAA
1 ATATATTAATAAAATAATAAAAATTTTATAAA
499362 ATATATTAA-AAAATAAATAAAA
1 ATATATTAATAAAAT-AATAAAA
499384 TATAAATTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
30 5 0.11
31 13 0.28
32 26 0.57
33 1 0.02
34 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (32 bp):
ATATATTAATAAAATAATAAAAATTTTATAAA
Found at i:499362 original size:29 final size:31
Alignment explanation
Indices: 499306--499380 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 31
499296 TTATATATTA
499306 ATAATAAAATAA-AAAT-TTTTATTAAAAA-
1 ATAATAAAATAATAAATATTTTATTAAAAAT
499334 ATTAATAAAATAATAAATATTTTA-T-AAAAT
1 A-TAATAAAATAATAAATATTTTATTAAAAAT
*
499364 ATATTAAAA-AATAAATA
1 ATAATAAAATAATAAATA
499381 AAATATAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
28 9 0.21
29 22 0.52
30 6 0.14
31 5 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (31 bp):
ATAATAAAATAATAAATATTTTATTAAAAAT
Found at i:499369 original size:40 final size:40
Alignment explanation
Indices: 499325--499417 Score: 125
Period size: 40 Copynumber: 2.3 Consensus size: 40
499315 TAAAAATTTT
499325 TATTAAAAAATTAATAAAATAATAAA-TATTTTATAAAATA
1 TATTAAAAAATTAATAAAAT-ATAAATTATTTTATAAAATA
* * * *
499365 TATTAAAAAATAAATAAAATATAAATTATTTTATTAATTT
1 TATTAAAAAATTAATAAAATATAAATTATTTTATAAAATA
*
499405 TATTAATAAATTA
1 TATTAAAAAATTA
499418 TGTTATTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 5 0.11
40 41 0.89
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (40 bp):
TATTAAAAAATTAATAAAATATAAATTATTTTATAAAATA
Found at i:499376 original size:28 final size:29
Alignment explanation
Indices: 499281--499380 Score: 84
Period size: 28 Copynumber: 3.5 Consensus size: 29
499271 TATTAAATAT
* *
499281 TAATAAAA-AATTATTTTAT-ATAT-TAA
1 TAATAAAATAAATATTTTATAAAATATAA
* *
499307 TAATAAAATAAAAATTTTTATTAAAAAATTAA
1 TAATAAAATAAATA-TTTTA-TAAAATA-TAA
*
499339 TAA-AATAATAAATATTTTATAAAATATAT
1 TAATAA-AATAAATATTTTATAAAATATAA
499368 TAA-AAAATAAATA
1 TAATAAAATAAATA
499381 AAATATAAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
26 8 0.13
27 3 0.05
28 13 0.22
29 8 0.13
30 8 0.13
31 7 0.12
32 13 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
TAATAAAATAAATATTTTATAAAATATAA
Found at i:500125 original size:18 final size:18
Alignment explanation
Indices: 500098--500141 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
500088 ATGTTTACAT
500098 TAAAAA-AAAA-TTTACTA
1 TAAAAATAAAACTTTA-TA
*
500115 TAAAAATAAAACTTTATT
1 TAAAAATAAAACTTTATA
500133 TAAAAATAA
1 TAAAAATAA
500142 TTAAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 6 0.25
18 14 0.58
19 4 0.17
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAATAAAACTTTATA
Found at i:504814 original size:94 final size:93
Alignment explanation
Indices: 504653--504841 Score: 351
Period size: 94 Copynumber: 2.0 Consensus size: 93
504643 TTCCATAATT
*
504653 CTAAATGAAACGTGTCTATTGTGCATATCAACGTTTGATAATGTTAAAACTTGTTTAATATTTTA
1 CTAAATGAAACGTGTCTATTGTGCATACCAACGTTTGATAATGTTAAAACTTGTTTAATATTTTA
504718 GTTTCATTATTTACATGCCTGAATCTTTG
66 GTTTCATTATTTACATG-CTGAATCTTTG
*
504747 CTAAATGAAACGTGTCTTTTGTGCATACCAACGTTTGATAATGTTAAAACTTGTTTAATATTTTA
1 CTAAATGAAACGTGTCTATTGTGCATACCAACGTTTGATAATGTTAAAACTTGTTTAATATTTTA
504812 GTTTCATTATTTACATGCTGAATCTTTG
66 GTTTCATTATTTACATGCTGAATCTTTG
504840 CT
1 CT
504842 CGTACTTCAC
Statistics
Matches: 93, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
93 13 0.14
94 80 0.86
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (93 bp):
CTAAATGAAACGTGTCTATTGTGCATACCAACGTTTGATAATGTTAAAACTTGTTTAATATTTTA
GTTTCATTATTTACATGCTGAATCTTTG
Found at i:507472 original size:19 final size:19
Alignment explanation
Indices: 507427--507475 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
507417 TATCGTTACA
* *
507427 TTGTATCAATACATGTTTT
1 TTGTATCGATACATGTTCT
507446 TTGTATCGATACATGTTCT
1 TTGTATCGATACATGTTCT
507465 TTGTATCGATA
1 TTGTATCGATA
507476 GATAAAACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.49
Consensus pattern (19 bp):
TTGTATCGATACATGTTCT
Found at i:507996 original size:35 final size:34
Alignment explanation
Indices: 507950--508015 Score: 114
Period size: 35 Copynumber: 1.9 Consensus size: 34
507940 GAAGTGATTG
*
507950 AGAGGTTCTATCTTAGCCTTTGTAAAAGATAGGGA
1 AGAGGTTCTATCTTAGCCTTCG-AAAAGATAGGGA
507985 AGAGGTTCTATCTTAGCCTTCGAAAAGATAG
1 AGAGGTTCTATCTTAGCCTTCGAAAAGATAG
508016 TGTTATAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 9 0.30
35 21 0.70
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (34 bp):
AGAGGTTCTATCTTAGCCTTCGAAAAGATAGGGA
Found at i:509679 original size:21 final size:21
Alignment explanation
Indices: 509628--509680 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
509618 AAATGAGTTG
509628 CAAGAAGTTAATAAGGAATTAAC
1 CAAGAAG--AATAAGGAATTAAC
* *
509651 CAATAAGAATAATGAATTAAC
1 CAAGAAGAATAAGGAATTAAC
* *
509672 TAGGAAGAA
1 CAAGAAGAA
509681 CAAAAACTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 19 0.76
23 6 0.24
ACGTcount: A:0.55, C:0.08, G:0.17, T:0.21
Consensus pattern (21 bp):
CAAGAAGAATAAGGAATTAAC
Found at i:514282 original size:32 final size:32
Alignment explanation
Indices: 514237--514354 Score: 202
Period size: 32 Copynumber: 3.7 Consensus size: 32
514227 ATTTCAACAA
*
514237 TTTT-TATCGATACAATGTATCGGTACATAAG
1 TTTTGTATCGATACAATGTATCGATACATAAG
*
514268 TGTTGTATCGATACAATGTATCGATACATAAG
1 TTTTGTATCGATACAATGTATCGATACATAAG
514300 TTTTGTATCGATACAATGTATCGATACATAAG
1 TTTTGTATCGATACAATGTATCGATACATAAG
*
514332 TTTTGTATCGATATAATGTATCG
1 TTTTGTATCGATACAATGTATCG
514355 CTACGAAGCT
Statistics
Matches: 82, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
31 3 0.04
32 79 0.96
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (32 bp):
TTTTGTATCGATACAATGTATCGATACATAAG
Found at i:514289 original size:13 final size:13
Alignment explanation
Indices: 514271--514327 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
514261 ACATAAGTGT
514271 TGTATCGATACAA
1 TGTATCGATACAA
514284 TGTATCGATACATAA
1 TGTATCGATAC--AA
514299 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
514316 TGTATCGATACA
1 TGTATCGATACA
514328 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:514308 original size:19 final size:18
Alignment explanation
Indices: 514252--514344 Score: 80
Period size: 19 Copynumber: 5.6 Consensus size: 18
514242 ATCGATACAA
*
514252 TGTATCGGTACATAAGTGT
1 TGTATCGATACATAAGT-T
514271 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
514284 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
514303 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
514316 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
514335 TGTATCGATA
1 TGTATCGATA
514345 TAATGTATCG
Statistics
Matches: 61, Mismatches: 1, Indels: 24
0.71 0.01 0.28
Matches are distributed among these distances:
13 22 0.36
15 4 0.07
17 4 0.07
19 31 0.51
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:519669 original size:32 final size:33
Alignment explanation
Indices: 519609--519670 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
519599 CACCCAGATA
519609 TATCGATACATATTACTTAGTATCGATGCATTG
1 TATCGATACATATTACTTAGTATCGATGCATTG
* *
519642 TATCGATACATGTT-CTTTGTATCGATGCA
1 TATCGATACATATTACTTAGTATCGATGCA
519671 CCATAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (33 bp):
TATCGATACATATTACTTAGTATCGATGCATTG
Found at i:522036 original size:50 final size:50
Alignment explanation
Indices: 521958--522059 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 50
521948 CATTATGATA
*
521958 AGGCTACCTTCATTATTTCACGTCTGAATAATAATCGCTTTCAAGCTTCT
1 AGGCTACCTTCATTATTTCACATCTGAATAATAATCGCTTTCAAGCTTCT
* * * *
522008 AGGCTACCTTCGTTATTTCACATTTGAATAATAGTTGCTTTCAAGCTTCT
1 AGGCTACCTTCATTATTTCACATCTGAATAATAATCGCTTTCAAGCTTCT
522058 AG
1 AG
522060 TCTTTTTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (50 bp):
AGGCTACCTTCATTATTTCACATCTGAATAATAATCGCTTTCAAGCTTCT
Found at i:530345 original size:22 final size:22
Alignment explanation
Indices: 530315--530356 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
530305 TTAAGTATAA
*
530315 ATGTCTTTCAAGATATAAATCAT
1 ATGTCTTTCAAG-TAAAAATCAT
530338 ATGT-TTTCAAGTAAAAATC
1 ATGTCTTTCAAGTAAAAATC
530357 CAAAGTATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (22 bp):
ATGTCTTTCAAGTAAAAATCAT
Found at i:530511 original size:32 final size:33
Alignment explanation
Indices: 530453--530514 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
530443 CAATCAGATG
*
530453 TATCGATACATATTGCTTTGTATCGATACATTA
1 TATCGATACATATTGCATTGTATCGATACATTA
*
530486 TATCGATACATGTT-CATTGTATCGATACA
1 TATCGATACATATTGCATTGTATCGATACA
530515 CACTAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (33 bp):
TATCGATACATATTGCATTGTATCGATACATTA
Found at i:532666 original size:21 final size:22
Alignment explanation
Indices: 532633--532673 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
532623 AGACAATTTT
532633 AAAATTGAAGAGAAT-AAATAA
1 AAAATTGAAGAGAATGAAATAA
**
532654 AAAATTGTTGAGAATGAAAT
1 AAAATTGAAGAGAATGAAAT
532674 TCTTGAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.59, C:0.00, G:0.17, T:0.24
Consensus pattern (22 bp):
AAAATTGAAGAGAATGAAATAA
Found at i:532694 original size:15 final size:15
Alignment explanation
Indices: 532654--532695 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
532644 GAATAAATAA
532654 AAAATTGTTGAGAATG
1 AAAATTGTTGA-AATG
*
532670 -AAATTCTTGAAATG
1 AAAATTGTTGAAATG
*
532684 AAAATAGTTGAA
1 AAAATTGTTGAA
532696 CTAGAAAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.48, C:0.02, G:0.19, T:0.31
Consensus pattern (15 bp):
AAAATTGTTGAAATG
Found at i:534573 original size:44 final size:44
Alignment explanation
Indices: 534510--534596 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
534500 GCTTAGTTGA
* *
534510 CTTAGTTGTTGAGGAATCAATCCATATTATTTTTTATGAATCTT
1 CTTAGTTGTTGAAGAATCAATCCATATTATTTTTGATGAATCTT
*
534554 CTTAGTTGTTGAAGAATCAATCCATGTTATTTTTGATGAATCT
1 CTTAGTTGTTGAAGAATCAATCCATATTATTTTTGATGAATCT
534597 AACTCTTCCG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (44 bp):
CTTAGTTGTTGAAGAATCAATCCATATTATTTTTGATGAATCTT
Found at i:536835 original size:33 final size:33
Alignment explanation
Indices: 536793--536857 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
536783 AAAACCCAGA
* *
536793 TGTATCGATACTGCATTCTTAGTATCGATACAT
1 TGTATCGATACTACATTCTTAGTATCAATACAT
* *
536826 TGTATCGATATTACATTCTTTGTATCAATACA
1 TGTATCGATACTACATTCTTAGTATCAATACA
536858 AGGGTTCTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (33 bp):
TGTATCGATACTACATTCTTAGTATCAATACAT
Found at i:544230 original size:63 final size:63
Alignment explanation
Indices: 544157--544291 Score: 179
Period size: 63 Copynumber: 2.1 Consensus size: 63
544147 AGGCATTTTC
** *
544157 TTTTCTTTTAAGTCAAACTT-ATTTCGTTAAAATAGGTTC-AGCCTT-AGGATT-TTTGTCAAGG
1 TTTTCTTTTAAGTCAAACTTAATTTC-TTAAAATA-AATCGAG-CTTCAAGATTATTT-TCAAGG
544218 TT
62 TT
544220 TTTTCTTTTAAGTCAAACTTAATTTCTTAAAATAAATCGAGCTTCAAGATTATTTTCAAGGTT
1 TTTTCTTTTAAGTCAAACTTAATTTCTTAAAATAAATCGAGCTTCAAGATTATTTTCAAGGTT
544283 TTTTCTTTT
1 TTTTCTTTT
544292 TAAATTAAAG
Statistics
Matches: 65, Mismatches: 3, Indels: 8
0.86 0.04 0.11
Matches are distributed among these distances:
62 5 0.08
63 52 0.80
64 8 0.12
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (63 bp):
TTTTCTTTTAAGTCAAACTTAATTTCTTAAAATAAATCGAGCTTCAAGATTATTTTCAAGGTT
Found at i:552409 original size:12 final size:12
Alignment explanation
Indices: 552392--552431 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
552382 GAAAAGTTCA
*
552392 AAATTTTAAAAG
1 AAATTTAAAAAG
*
552404 AAATTTGAAAAG
1 AAATTTAAAAAG
*
552416 AAATTCAAAAAG
1 AAATTTAAAAAG
552428 AAAT
1 AAAT
552432 AGGGATGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.25
Consensus pattern (12 bp):
AAATTTAAAAAG
Found at i:552648 original size:79 final size:79
Alignment explanation
Indices: 552559--552731 Score: 199
Period size: 79 Copynumber: 2.2 Consensus size: 79
552549 TGAAAATTGA
* * * *
552559 GGTTGGAGTATCCTCTCCGAG-A-TGGTGGGGTTGGAGTATCACCGAGATAAAAAATTTAATATT
1 GGTTGGAGTATCC-C-CAGAGAAGTGATGGGGTTAGAGTATCACCAAGATAAAAAATTTAATATT
* *
552622 TTGGAAGTAAAAAT-G
64 TTGAAAGGAAAAATAG
* * * *
552637 TGGTTGGAGTATCCCCATAGAAGTTATGGGGTTAGAGTATCCCCAAGATGAAAAATTTAATATTT
1 -GGTTGGAGTATCCCCAGAGAAGTGATGGGGTTAGAGTATCACCAAGATAAAAAATTTAATATTT
552702 TGAAAGGAAAAATAG
65 TGAAAGGAAAAATAG
*
552717 AGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
552732 TCAAAAATTA
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
77 3 0.04
78 2 0.03
79 74 0.93
80 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.29
Consensus pattern (79 bp):
GGTTGGAGTATCCCCAGAGAAGTGATGGGGTTAGAGTATCACCAAGATAAAAAATTTAATATTTT
GAAAGGAAAAATAG
Found at i:552949 original size:80 final size:78
Alignment explanation
Indices: 552587--553030 Score: 373
Period size: 79 Copynumber: 5.6 Consensus size: 78
552577 GAGATGGTGG
* * * *
552587 GGTTGGAGTATCACCGAGATAAAAAATTTAATATTTTGGAAGTAAAAATGTGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGAGATGAAAAATTTAATATTTTGAAAATAAAAATG-GGTTGGAGTATCCC
* * *
552652 CAT-AGAAGTTATGG
65 C-TCAGAAATTACGA
* * ** *
552666 GGTTAGAGTATCCCCAAGATGAAAAATTTAATATTTTGAAAGGAAAAATAGAGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGAGATGAAAAATTTAATATTTTGAAAATAAAAAT-GGGTTGGAGTATCCC
* *
552731 CTCAAAAATTA-TA
65 CTCAGAAATTACGA
* * * ** * *
552744 GGCTTGAAGTATCCCTGATGGTGAAAAA-TCGATATTTTGGAAATAAAAATGAGGTTAGAGTATC
1 GG-TTGGAGTATCCCCGA-GATGAAAAATTTAATATTTTGAAAATAAAAATG-GGTTGGAGTATC
*
552808 CCCTC-GAAAATTATG-
63 CCCTCAG-AAATTACGA
* * * *
552823 GATTGGAGTATCCCTGATAGTGAAAAA-TCAATATTTTGAAAATAAAAATAGGGTTGGAGTA-CC
1 GGTTGGAGTATCCCCGAGA-TGAAAAATTTAATATTTTGAAAATAAAAAT-GGGTTGGAGTATCC
*
552886 CCGTCAGAAATAACGA
64 CC-TCAGAAATTACGA
* * *
552902 GGTTGGAGTATCCCCGAGATGAAAACATTTAATATTTTAAAAATAAAAATGGGGTTAGAATATCC
1 GGTTGGAGTATCCCCGAGATGAAAA-ATTTAATATTTTGAAAATAAAAAT-GGGTTGGAGTATCC
* *
552967 CCTCAAAAATGACGA
64 CCTCAGAAATTACGA
* ** * *
552982 AGTCAGAGTATCCCTGAGATGAAAAAAATTAATATTTTCG-AAATAAAAA
1 GGTTGGAGTATCCCCGAGATG-AAAAATTTAATATTTT-GAAAATAAAAA
553031 CAAGGTTAGA
Statistics
Matches: 298, Mismatches: 50, Indels: 33
0.78 0.13 0.09
Matches are distributed among these distances:
77 4 0.01
78 68 0.23
79 132 0.44
80 86 0.29
81 8 0.03
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (78 bp):
GGTTGGAGTATCCCCGAGATGAAAAATTTAATATTTTGAAAATAAAAATGGGTTGGAGTATCCCC
TCAGAAATTACGA
Found at i:553005 original size:158 final size:156
Alignment explanation
Indices: 552587--553057 Score: 459
Period size: 158 Copynumber: 3.0 Consensus size: 156
552577 GAGATGGTGG
* * * * *
552587 GGTTGGAGTATCACCGAGATAAAAAATTTAATATTTTGGAAGTAAAAATGTGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGAGATGAAAAATTTAATATTTTGGAAATAAAAATGAGGTTAGAGTATCCC
* * * ** **
552652 CAT-AGAAGTTATGGGGTTAGAGTATCCCCAAGATGAAAAATTTAATATTTTGAAAGGAAAAATA
66 C-TCAAAAATTATGGAGTTAGAGTATCCCTGAGATGAAAAA-TTAATATTTTGAAAATAAAAATA
* *
552716 GAGTTGGAGTATCCCCTCAAAAATTATA
129 GAGTTGGAGTATCCCCTCAAAAATAAGA
* * * **
552744 GGCTTGAAGTATCCCTGATGGTGAAAAA-TCGATATTTTGGAAATAAAAATGAGGTTAGAGTATC
1 GG-TTGGAGTATCCCCGA-GATGAAAAATTTAATATTTTGGAAATAAAAATGAGGTTAGAGTATC
* * * *
552808 CCCTCGAAAATTATGGA-TTGGAGTATCCCTGATAGTGAAAAATCAATATTTTGAAAATAAAAAT
64 CCCTCAAAAATTATGGAGTTAGAGTATCCCTGAGA-TGAAAAATTAATATTTTGAAAATAAAAAT
* *
552872 AGGGTTGGAGTA-CCCCGTCAGAAATAACGA
128 AGAGTTGGAGTATCCCC-TCAAAAATAA-GA
** * *
552902 GGTTGGAGTATCCCCGAGATGAAAACATTTAATATTTTAAAAATAAAAATGGGGTTAGAATATCC
1 GGTTGGAGTATCCCCGAGATGAAAA-ATTTAATATTTTGGAAATAAAAATGAGGTTAGAGTATCC
* * * *
552967 CCTCAAAAATGACGAAGTCAGAGTATCCCTGAGATGAAAAAAATTAATATTTTCG-AAATAAAAA
65 CCTCAAAAATTATGGAGTTAGAGTATCCCTGAGATG--AAAAATTAATATTTT-GAAAATAAAAA
* * * *
553031 CA-AGGTTAGAGTATCTCTTCAAAAATA
127 TAGA-GTTGGAGTATCCCCTCAAAAATA
553058 GCAGGGTCGA
Statistics
Matches: 252, Mismatches: 48, Indels: 25
0.78 0.15 0.08
Matches are distributed among these distances:
156 11 0.04
157 68 0.27
158 109 0.43
159 21 0.08
160 40 0.16
161 3 0.01
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (156 bp):
GGTTGGAGTATCCCCGAGATGAAAAATTTAATATTTTGGAAATAAAAATGAGGTTAGAGTATCCC
CTCAAAAATTATGGAGTTAGAGTATCCCTGAGATGAAAAATTAATATTTTGAAAATAAAAATAGA
GTTGGAGTATCCCCTCAAAAATAAGA
Found at i:553072 original size:80 final size:80
Alignment explanation
Indices: 552775--553056 Score: 212
Period size: 80 Copynumber: 3.5 Consensus size: 80
552765 TGAAAAATCG
** ** * * * * * **
552775 ATATTTTGGAAATAAAAATGAGGTTAGAGTATCCCCTCGAAAATTATGGA-TTGGAGTATCCCTG
1 ATATTTTAAAAATAAAAACAAGGTTAGAATATCCCCTCAAAAATGACGAAGTCAGAGTATCCCTG
* *
552839 ATAGTG--AAAAATCA
66 AGA-TGAAAAAAATTA
* * * * * * * * ** *
552853 ATATTTTGAAAATAAAAATAGGGTTGGAGTA-CCCCGTCAGAAATAACGAGGTTGGAGTATCCCC
1 ATATTTTAAAAATAAAAACAAGGTTAGAATATCCCC-TCAAAAATGACGAAGTCAGAGTATCCCT
* *
552917 GAGATGAAAACATTTA
65 GAGATGAAAAAAATTA
***
552933 ATATTTTAAAAATAAAAATGGGGTTAGAATATCCCCTCAAAAATGACGAAGTCAGAGTATCCCTG
1 ATATTTTAAAAATAAAAACAAGGTTAGAATATCCCCTCAAAAATGACGAAGTCAGAGTATCCCTG
552998 AGATGAAAAAAATTA
66 AGATGAAAAAAATTA
** * * *
553013 ATATTTTCGAAATAAAAACAAGGTTAGAGTATCTCTTCAAAAAT
1 ATATTTTAAAAATAAAAACAAGGTTAGAATATCCCCTCAAAAAT
553057 AGCAGGGTCG
Statistics
Matches: 164, Mismatches: 35, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
77 4 0.02
78 37 0.23
79 15 0.09
80 104 0.63
81 4 0.02
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.27
Consensus pattern (80 bp):
ATATTTTAAAAATAAAAACAAGGTTAGAATATCCCCTCAAAAATGACGAAGTCAGAGTATCCCTG
AGATGAAAAAAATTA
Found at i:555546 original size:51 final size:52
Alignment explanation
Indices: 555445--555564 Score: 170
Period size: 51 Copynumber: 2.3 Consensus size: 52
555435 TACATTGAAG
* * *
555445 AATGTATCGATACATTTAGGTCAAAAACCCAGAATGTATCGATACAATAAAT
1 AATGTATCGATACATTTAGATCAAAAACCCAGAATGTATCAATACAATAAAA
* * * *
555497 AATGTATCAATACATTTAGAT-TAAAATCCAGAATGTATCAATATAATAAAA
1 AATGTATCGATACATTTAGATCAAAAACCCAGAATGTATCAATACAATAAAA
555548 AATGTATCGATACATTT
1 AATGTATCGATACATTT
555565 CTTTCCAGAA
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
51 41 0.68
52 19 0.32
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (52 bp):
AATGTATCGATACATTTAGATCAAAAACCCAGAATGTATCAATACAATAAAA
Found at i:563717 original size:54 final size:54
Alignment explanation
Indices: 563635--563800 Score: 305
Period size: 54 Copynumber: 3.1 Consensus size: 54
563625 AACTAGGTTA
*
563635 TTTATAACCTATTAAGTGAAATGTGAATTAAAAACACTACACAATAATAAGATT
1 TTTATAACTTATTAAGTGAAATGTGAATTAAAAACACTACACAATAATAAGATT
563689 TTTATAACTTATTAAGTGAAATGTGAATTAAAAACACTACACAATAATAAGATT
1 TTTATAACTTATTAAGTGAAATGTGAATTAAAAACACTACACAATAATAAGATT
* *
563743 TTTATAACTTATTAAGTGAAATGTGAATTAAAAATACTAAACAATAATAAGATT
1 TTTATAACTTATTAAGTGAAATGTGAATTAAAAACACTACACAATAATAAGATT
563797 TTTA
1 TTTA
563801 AAGATGAGAG
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 109 1.00
ACGTcount: A:0.48, C:0.08, G:0.09, T:0.34
Consensus pattern (54 bp):
TTTATAACTTATTAAGTGAAATGTGAATTAAAAACACTACACAATAATAAGATT
Found at i:563941 original size:14 final size:14
Alignment explanation
Indices: 563903--563943 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
563893 ATTAAAGATG
*
563903 AATATAATTTTTAA
1 AATATAATTTTAAA
*
563917 AAT-T-TTTTTAAA
1 AATATAATTTTAAA
563929 AATATAATTTTAAA
1 AATATAATTTTAAA
563943 A
1 A
563944 TATGACTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
12 9 0.41
13 2 0.09
14 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AATATAATTTTAAA
Found at i:567185 original size:2 final size:2
Alignment explanation
Indices: 567178--567202 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
567168 ACCGTCTGAA
567178 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
567203 CACTCTGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:573792 original size:78 final size:77
Alignment explanation
Indices: 573566--573798 Score: 234
Period size: 78 Copynumber: 3.0 Consensus size: 77
573556 TTAATACAAT
* * * * *
573566 ATTACTTAAATAACCCTAATGAATATGTTTTGATATTAAAGTTCTCACATAATCATAAAGACTCA
1 ATTACTTAAATAACCTTAATGAATATGTTTCGACATAAAAGTTCTCACATAATCCTAAAGACT-A
* ** **
573631 ATATTAAAAAAAT
65 ATTTTAAAGTACC
* * * *
573644 ATTACTTAAATAACCTT-ATGAATATGTTTCGACATAAAAGTTTTCATATTAAGCCTAGAGACTT
1 ATTACTTAAATAACCTTAATGAATATGTTTCGACATAAAAGTTCTCACA-TAATCCTAAAGAC-T
573708 AATTTTAAAGTACC
64 AATTTTAAAGTACC
* * * * * *
573722 ATTACTAAAATAATCTTAATGAACATGTGTCGACATGAAAGTTCTCACATAATCCTAAAAACTAA
1 ATTACTTAAATAACCTTAATGAATATGTTTCGACATAAAAGTTCTCACATAATCCTAAAGACTAA
*
573787 GTTTTAAGGTAC
66 -TTTTAAAGTAC
573799 TACAACCTAA
Statistics
Matches: 126, Mismatches: 25, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
77 29 0.23
78 70 0.56
79 27 0.21
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.34
Consensus pattern (77 bp):
ATTACTTAAATAACCTTAATGAATATGTTTCGACATAAAAGTTCTCACATAATCCTAAAGACTAA
TTTTAAAGTACC
Found at i:574117 original size:29 final size:28
Alignment explanation
Indices: 574085--574161 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 28
574075 AACATGTATA
* * *
574085 AAAATCACAAAATGATCTCTAGATTACAT
1 AAAATAACAAAATGATC-CTAAAATACAT
*
574114 AAAATAACCAAAATAATCCTAAAATACAT
1 AAAATAA-CAAAATGATCCTAAAATACAT
**
574143 AGAAATTGCAAAATGATCC
1 A-AAATAACAAAATGATCC
574162 CTAATATGCA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 26 0.67
30 13 0.33
ACGTcount: A:0.53, C:0.17, G:0.06, T:0.23
Consensus pattern (28 bp):
AAAATAACAAAATGATCCTAAAATACAT
Found at i:577321 original size:17 final size:17
Alignment explanation
Indices: 577299--577331 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
577289 CGATAGTTCA
*
577299 TTCTTTTTCTTTTTTTT
1 TTCTTTTTATTTTTTTT
577316 TTCTTTTTATTTTTTT
1 TTCTTTTTATTTTTTT
577332 GTGGGAGTTA
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:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (17 bp):
TTCTTTTTATTTTTTTT
Found at i:583866 original size:18 final size:19
Alignment explanation
Indices: 583835--583872 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
583825 TTATTAAATT
* *
583835 TTTTTACATATTAAGTAAA
1 TTTTTAAATATTAAATAAA
583854 TTTTTAAAT-TTAAATAAA
1 TTTTTAAATATTAAATAAA
583872 T
1 T
583873 AATATAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (19 bp):
TTTTTAAATATTAAATAAA
Found at i:585382 original size:2 final size:2
Alignment explanation
Indices: 585371--585405 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
585361 AAATGGGCTA
585371 AT AT -T 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 AT
585406 GTATGATTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:587127 original size:2 final size:2
Alignment explanation
Indices: 587120--587154 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
587110 TTGCAGTTAA
* *
587120 AT AT AT AT AT AT AT AT AT AT TT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
587155 ACATCTAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:589204 original size:61 final size:60
Alignment explanation
Indices: 589084--589204 Score: 190
Period size: 61 Copynumber: 2.0 Consensus size: 60
589074 ATCTTTTTAG
* * *
589084 GGGTTTTTTATTTTATTTATTTATTTATTTTGTTGACACTTTTTTAGTGACTTTAACACC
1 GGGTTTTTGATTTTATTTATTTATTTATATTGTTGACACTTTTTTAGTGACTTCAACACC
589144 GGGTTTTTGATTTTATTTATTTATTT-TGCATTGTTGACACTTTTTTAGTGACTTCAACACC
1 GGGTTTTTGATTTTATTTATTTATTTAT--ATTGTTGACACTTTTTTAGTGACTTCAACACC
589205 AACTAAAGCT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
59 1 0.02
60 25 0.45
61 30 0.54
ACGTcount: A:0.20, C:0.12, G:0.13, T:0.55
Consensus pattern (60 bp):
GGGTTTTTGATTTTATTTATTTATTTATATTGTTGACACTTTTTTAGTGACTTCAACACC
Found at i:591984 original size:21 final size:21
Alignment explanation
Indices: 591958--592003 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
591948 TAGGAAGGTT
591958 ATTCAGTATTAATATGTAAAA
1 ATTCAGTATTAATATGTAAAA
591979 ATTCAGTATTAATATGTAAAA
1 ATTCAGTATTAATATGTAAAA
592000 ATTC
1 ATTC
592004 TATTGCACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.39
Consensus pattern (21 bp):
ATTCAGTATTAATATGTAAAA
Found at i:594768 original size:15 final size:15
Alignment explanation
Indices: 594750--594778 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
594740 TCATATTATA
594750 TATTTTTAAATTCAT
1 TATTTTTAAATTCAT
594765 TATTTTTAAATTCA
1 TATTTTTAAATTCA
594779 AATTCATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTTTTAAATTCAT
Found at i:598349 original size:52 final size:52
Alignment explanation
Indices: 598264--598388 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
598254 ATATGAAAAG
* *
598264 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
598316 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
598368 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
598389 AAGATCAATA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:598403 original size:52 final size:52
Alignment explanation
Indices: 598264--598408 Score: 186
Period size: 52 Copynumber: 2.8 Consensus size: 52
598254 ATATGAAAAG
* * * *
598264 TTGCTTGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TAAGATAATATATCGATACATCTGGGCAAAT
*** *
598316 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATAAGATAATATATCGATACATCTGGGCAAAT
598368 TTGCCTGCATGTATCGATACA-AAGATCAATATATCGATACA
1 TTGCCTGCATGTATCGATACATAAGAT-AATATATCGATACA
598409 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
51 4 0.05
52 80 0.95
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATAAGATAATATATCGATACATCTGGGCAAAT
Found at i:598490 original size:20 final size:20
Alignment explanation
Indices: 598465--598529 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
598455 TAGCTTACAT
598465 TGTATCGATACAAAAAAATA
1 TGTATCGATACAAAAAAATA
598485 TGTATCGATAC------AT-
1 TGTATCGATACAAAAAAATA
598498 TGTATCGATACAAAAAAATA
1 TGTATCGATACAAAAAAATA
598518 TGTATCGATACA
1 TGTATCGATACA
598530 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 2 0.05
19 2 0.05
20 23 0.61
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.29
Consensus pattern (20 bp):
TGTATCGATACAAAAAAATA
Found at i:598502 original size:33 final size:33
Alignment explanation
Indices: 598460--598562 Score: 170
Period size: 33 Copynumber: 3.1 Consensus size: 33
598450 GGCAGTAGCT
598460 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
598493 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
598526 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
598559 TACA
1 TACA
598563 AATCGTTGAA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.33
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:598503 original size:13 final size:13
Alignment explanation
Indices: 598485--598542 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
598475 CAAAAAAATA
598485 TGTATCGATACAT
1 TGTATCGATACAT
598498 TGTATCGATACAAAAAAAT
1 TGTATCGATAC------AT
598517 ATGTATCGATACAT
1 -TGTATCGATACAT
598531 TGTATCGATACA
1 TGTATCGATACA
598543 ACATTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 23 0.61
14 2 0.05
19 2 0.05
20 11 0.29
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:610010 original size:2 final size:2
Alignment explanation
Indices: 610003--610042 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
609993 CCAAAGATAG
610003 AT AT AT 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 AT AT AT
610043 TCAACAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:613219 original size:21 final size:21
Alignment explanation
Indices: 613193--613232 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
613183 CCAAGGCATG
*
613193 CTCATCTATCATGAATTTCAT
1 CTCATCTATCATCAATTTCAT
613214 CTCATCTATCATCAATTTC
1 CTCATCTATCATCAATTTC
613233 CGTAATCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.42
Consensus pattern (21 bp):
CTCATCTATCATCAATTTCAT
Found at i:616218 original size:30 final size:29
Alignment explanation
Indices: 616146--616226 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
616136 AAATATATGA
* *
616146 CTTTGGGAAAAACCAAGAATTAACACATAG
1 CTTTGGGCAAAACCAAGAA-TAACAAATAG
*
616176 C-TTGGGCGAAACCAAGAATAACCAAAT-G
1 CTTTGGGCAAAACCAAGAATAA-CAAATAG
616204 TCTTTGGGCAAAACCAAGAATAA
1 -CTTTGGGCAAAACCAAGAATAA
616227 GTAAGCAATC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
28 4 0.09
29 20 0.45
30 20 0.45
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (29 bp):
CTTTGGGCAAAACCAAGAATAACAAATAG
Found at i:616531 original size:58 final size:59
Alignment explanation
Indices: 616332--616594 Score: 160
Period size: 59 Copynumber: 4.5 Consensus size: 59
616322 GACTTTAGGT
* *** * * *
616332 GAAACCAAGGTTCAAAGAAAT-GACATGGGTGAAACCAA-AGACCTAAAGACA-ACCTAAAT
1 GAAACCAAGGTTCAAAGAAATAG-CTTGGACAAAACCAACA-ACCTAAAGA-ATACTTAGAC
* * * * * * * * ** * *
616391 AAAACCAAGGTTCTAAGAAATTGCTTAGACGAAACTAGCAATCTAAAGGCTACTTTGAT
1 GAAACCAAGGTTCAAAGAAATAGCTTGGACAAAACCAACAACCTAAAGAATACTTAGAC
* * * * * * *
616450 GAAAACAGGGATCAAAGACATAGCTTGGACAAAACCAGCAACCTAAA-AACT-GTTGGTA-
1 GAAACCAAGGTTCAAAGAAATAGCTTGGACAAAACCAACAACCTAAAGAA-TACTTAG-AC
* * * *
616508 GAAACCAAGGTTTAAAGAAATAGCTCGAACAAAACCAACAACTTAAAGAATACTTAGAC
1 GAAACCAAGGTTCAAAGAAATAGCTTGGACAAAACCAACAACCTAAAGAATACTTAGAC
*
616567 GAAACCAAGGTTCAAAGAAATATCTTGG
1 GAAACCAAGGTTCAAAGAAATAGCTTGG
616595 GTGAAACTAA
Statistics
Matches: 152, Mismatches: 44, Indels: 16
0.72 0.21 0.08
Matches are distributed among these distances:
58 43 0.28
59 107 0.70
60 2 0.01
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.18
Consensus pattern (59 bp):
GAAACCAAGGTTCAAAGAAATAGCTTGGACAAAACCAACAACCTAAAGAATACTTAGAC
Found at i:616677 original size:59 final size:59
Alignment explanation
Indices: 616611--616931 Score: 194
Period size: 58 Copynumber: 5.5 Consensus size: 59
616601 CTAAAGTTTA
* * * *
616611 AAGAAATAGTCTAGATGAAACTAGAAACCTAAAAACAACTTGAATGAAACCAAGGTTCT
1 AAGAAATAGTCTAGATAAAACCAGAAACCTAAAGACTACTTGAATGAAACCAAGGTTCT
* * * **
616670 AAGAAATAG-CTAGGGTAAAACCA-AAACCTAAAGACTACCTGGACAAAACCAAGGTTC-
1 AAGAAATAGTCTA-GATAAAACCAGAAACCTAAAGACTACTTGAATGAAACCAAGGTTCT
* * * * * *
616727 AA-AGA-AGGCTTGGACAAAACCAGAAACCTAAAAACTA-TTGAATGAAAACAAGGTT-T
1 AAGAAATAGTC-TAGATAAAACCAGAAACCTAAAGACTACTTGAATGAAACCAAGGTTCT
* * * * * ** * *
616783 AAAGAAATGGCCTAAATGAAA-TAGAAATTTAAAGATTACCTGAATGAAACCAAGGTTCT
1 -AAGAAATAGTCTAGATAAAACCAGAAACCTAAAGACTACTTGAATGAAACCAAGGTTCT
* ** * * * * * * *
616842 AAAAAACGGTCT-GAATGAAACCAGAAACTTAAAGATTACTCGGATGAAACTAAGGTTTT
1 AAGAAATAGTCTAG-ATAAAACCAGAAACCTAAAGACTACTTGAATGAAACCAAGGTTCT
* * *
616901 AAGAAAT-GATTTAGACAAAACTAGAAACCTA
1 AAGAAATAG-TCTAGATAAAACCAGAAACCTA
616932 GAGATGACTA
Statistics
Matches: 197, Mismatches: 51, Indels: 28
0.71 0.18 0.10
Matches are distributed among these distances:
55 2 0.01
56 24 0.12
57 30 0.15
58 70 0.36
59 70 0.36
60 1 0.01
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.20
Consensus pattern (59 bp):
AAGAAATAGTCTAGATAAAACCAGAAACCTAAAGACTACTTGAATGAAACCAAGGTTCT
Found at i:618916 original size:40 final size:40
Alignment explanation
Indices: 618866--618941 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
618856 TGTTTTTTTT
* *
618866 TGGACAAAGAAATAACTAATTTACATTAAATAAAAACTTA
1 TGGAAAAAGAAATAACTAATTTACATCAAATAAAAACTTA
*
618906 TGGAAAAAGAAATAACTCATTTACATCAAATAAAAA
1 TGGAAAAAGAAATAACTAATTTACATCAAATAAAAA
618942 GTATAATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.57, C:0.11, G:0.08, T:0.25
Consensus pattern (40 bp):
TGGAAAAAGAAATAACTAATTTACATCAAATAAAAACTTA
Found at i:621182 original size:57 final size:58
Alignment explanation
Indices: 621103--621224 Score: 144
Period size: 59 Copynumber: 2.1 Consensus size: 58
621093 ATAATTTAAA
* * * *
621103 TATTTATATTATTTTTATATATT-TTATCG-TATTATAATAAATTTTAAA-ATATTTTT
1 TATTTATATAATTTTTACATATTATAATCGATATTAT-ATAAATTTTAAATATATTTAT
*
621159 TATTTATATCAATTTTTACATATTAATAATTGATATTATATAAATTTTAAATATATTTAT
1 TATTTATAT-AATTTTTACATATT-ATAATCGATATTATATAAATTTTAAATATATTTAT
621219 T-TTTAT
1 TATTTAT
621225 TTTTATTATT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
56 9 0.16
57 12 0.21
59 21 0.38
60 14 0.25
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (58 bp):
TATTTATATAATTTTTACATATTATAATCGATATTATATAAATTTTAAATATATTTAT
Found at i:621590 original size:15 final size:16
Alignment explanation
Indices: 621565--621601 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
621555 ATCTAAAAAT
621565 AATTATTTAATTATAA
1 AATTATTTAATTATAA
*
621581 AATT-TTTAATTATTA
1 AATTATTTAATTATAA
621596 AATTAT
1 AATTAT
621602 GAAAAGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AATTATTTAATTATAA
Found at i:626190 original size:50 final size:50
Alignment explanation
Indices: 626121--626408 Score: 281
Period size: 50 Copynumber: 5.9 Consensus size: 50
626111 TAAATAAAAA
*
626121 TATTTAAAAGATAAT-AAAAATTAAAAATTTTATATTAAATTTTGAATTAT
1 TATTTAAAA-ATAATAAAAAATTAAAAATTTTATATTAAATCTTGAATTAT
* *
626171 TATTTAAAAATAATAAAAAA-T---AATTTTATATTAAATTTTAAATTAT
1 TATTTAAAAATAATAAAAAATTAAAAATTTTATATTAAATCTTGAATTAT
626217 TATTT--AAA-AATAAAAAATGT-----TTTTATATTAAATCTTGAATTAT
1 TATTTAAAAATAATAAAAAAT-TAAAAATTTTATATTAAATCTTGAATTAT
**
626260 TATTT-AAAA-AATAAAAAGATTTAAAAAAATTATATTAAATCTTGAATTAT
1 TATTTAAAAATAATAAAAA-A-TTAAAAATTTTATATTAAATCTTGAATTAT
**
626310 TATTTAAAAAT--TAAAAAATTAAAAAAATATTTTATATTAAATCTCAAATTAT
1 TATTTAAAAATAATAAAAAATT---AAAA-ATTTTATATTAAATCTTGAATTAT
*
626362 T-TTTAAAAATAAT-AAAAATTAAAAATATTATATAATAAATCTTGAAT
1 TATTTAAAAATAATAAAAAATTAAAAAT-TT-TATATTAAATCTTGAAT
626409 CACTACTTCA
Statistics
Matches: 205, Mismatches: 12, Indels: 42
0.79 0.05 0.16
Matches are distributed among these distances:
43 35 0.17
44 14 0.07
45 3 0.01
46 30 0.15
48 4 0.02
49 13 0.06
50 60 0.29
51 17 0.08
52 28 0.14
53 1 0.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (50 bp):
TATTTAAAAATAATAAAAAATTAAAAATTTTATATTAAATCTTGAATTAT
Found at i:626194 original size:59 final size:66
Alignment explanation
Indices: 626058--626183 Score: 168
Period size: 66 Copynumber: 1.9 Consensus size: 66
626048 TCTTTATTAT
*
626058 AAAATAATAAAATTTTTAAATATATTTTATATTAAATTTTAAATTATTATTTATAAATAAAAATA
1 AAAATAATAAAA-TATTAAATATATTTTATATTAAATTTTAAATTATTATTTATAAATAAAAATA
626123 TTTA
65 --TA
* *
626127 AAAGATAATAAAA-ATTAAA-A-ATTTTATATTAAATTTTGAATTATTATTTAAAAATAA
1 AAA-ATAATAAAATATTAAATATATTTTATATTAAATTTTAAATTATTATTTATAAATAA
626184 TAAAAAATAA
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
66 35 0.66
67 1 0.02
68 5 0.09
69 3 0.06
70 9 0.17
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (66 bp):
AAAATAATAAAATATTAAATATATTTTATATTAAATTTTAAATTATTATTTATAAATAAAAATAT
A
Found at i:626216 original size:43 final size:43
Alignment explanation
Indices: 626146--626276 Score: 151
Period size: 43 Copynumber: 3.0 Consensus size: 43
626136 AAAAATTAAA
626146 AATTTTATATTAAATTTTGAATTATTATTTAAAAATAATAAAAAAT
1 AATTTTATATTAAATTTT-AA-TATTATTTAAAAA-AATAAAAAAT
626192 AATTTTATATTAAATTTTAAATTATTATTT--AAAAATAAAAAAT
1 AATTTTATATTAAATTTT-AA-TATTATTTAAAAAAATAAAAAAT
** *
626235 GTTTTTATATTAAATCTTGAATTATTATTT-AAAAAATAAAAA
1 AATTTTATATTAAAT-TTTAA-TATTATTTAAAAAAATAAAAA
626277 GATTTAAAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
43 34 0.43
44 16 0.20
46 29 0.37
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (43 bp):
AATTTTATATTAAATTTTAATATTATTTAAAAAAATAAAAAAT
Found at i:626305 original size:139 final size:142
Alignment explanation
Indices: 626121--626378 Score: 357
Period size: 139 Copynumber: 1.8 Consensus size: 142
626111 TAAATAAAAA
* ** *
626121 TATTTAAAAGATAATAAAAATTAAAAATTTTATATTAAATTTTGAATTATTATTTAAAAA-T-AA
1 TATTTAAAAAATAATAAAAATTAAAAAAATTATATTAAATCTTGAATTATTATTTAAAAATTAAA
* *
626184 -T-AAAAAATAATTTTATATTAAATTTTAAATTATTATTTAAAAATAA-AAAATGTTTTTATATT
66 TTAAAAAAAT-ATTTTATATTAAATCTCAAATTATT-TTTAAAAATAATAAAATGTTTTTATATT
626246 AAATCTTGAATTAT
129 AAATCTTGAATTAT
*
626260 TATTTAAAAAATAA-AAAGATTTAAAAAAATTATATTAAATCTTGAATTATTATTTAAAAATTAA
1 TATTTAAAAAATAATAAA-AATTAAAAAAATTATATTAAATCTTGAATTATTATTTAAAAATT--
626324 AAAATTAAAAAAATATTTTATATTAAATCTCAAATTATTTTTAAAAATAATAAAA
63 -AAATTAAAAAAATATTTTATATTAAATCTCAAATTATTTTTAAAAATAATAAAA
626379 ATTAAAAATA
Statistics
Matches: 103, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
138 3 0.03
139 51 0.50
140 1 0.01
144 13 0.13
145 28 0.27
146 7 0.07
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (142 bp):
TATTTAAAAAATAATAAAAATTAAAAAAATTATATTAAATCTTGAATTATTATTTAAAAATTAAA
TTAAAAAAATATTTTATATTAAATCTCAAATTATTTTTAAAAATAATAAAATGTTTTTATATTAA
ATCTTGAATTAT
Found at i:626692 original size:22 final size:22
Alignment explanation
Indices: 626664--626727 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
626654 TATATATATA
626664 TATATATATATTTAATTTTAGT
1 TATATATATATTTAATTTTAGT
* *
626686 TATATATACATTTAATTATAGT
1 TATATATATATTTAATTTTAGT
* * *
626708 CATATGTATATTCAATTTTA
1 TATATATATATTTAATTTTA
626728 TTAGAAAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (22 bp):
TATATATATATTTAATTTTAGT
Found at i:626909 original size:22 final size:22
Alignment explanation
Indices: 626878--626937 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
626868 AACTAAAATT
* * **
626878 ATATGCACATTCAGTTATAGTC
1 ATATGTACATTCAATTATAAAC
*
626900 ATATGTACATTTAATTATAAAC
1 ATATGTACATTCAATTATAAAC
*
626922 ATATGTACATTTAATT
1 ATATGTACATTCAATT
626938 TTGTTTAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (22 bp):
ATATGTACATTCAATTATAAAC
Found at i:628577 original size:163 final size:166
Alignment explanation
Indices: 628332--628705 Score: 470
Period size: 164 Copynumber: 2.3 Consensus size: 166
628322 ATCAGTTTTG
* * *
628332 AAAATTCCTTTTATTTTATAATTTTTTCATTTTTTTTTGAAA-TTCCCTTGTTTTCGAAATACAA
1 AAAATTCCTTTTATTTCATAAGTTTTTCATTTTTTTTTGAAATTTACCTTGTTTTCGAAATACAA
* * *** *
628396 AGTTTTCTATTTCGTAAATGTTTTTTTGG-GATTTTTCTTAGCTCATAATTTTTAAAATTCATAA
66 AGTTTTCTACTTCGTAAATATTTTGAGGGAGATTTTTCTTAGCTCATAATTATTAAAATTCATAA
* *
628460 AATATCATCATTTAATTCACATTAAATTATTTTTAA
131 AATATCATCATTTAATTCACAGTAAATTAGTTTTAA
* * * * *
628496 AAAATTCCTTTTATTTCATGAGTTCTTCATTTTTTTTT-AAATTTATC-TGTTTTCGAAATTCAG
1 AAAATTCCTTTTATTTCATAAGTTTTTCATTTTTTTTTGAAATTTACCTTGTTTTCGAAATACAA
* * * * *
628559 AGTTTTTTACTTCGTAAATATTTTGAGGGAGATTTTTCTTGGTTTATAATTATTAAAATTCATCA
66 AGTTTTCTACTTCGTAAATATTTTGAGGGAGATTTTTCTTAGCTCATAATTATTAAAATTCATAA
* * *
628624 AATATCATCATTTAATTCATAGTAAATTGGTTTTGA
131 AATATCATCATTTAATTCACAGTAAATTAGTTTTAA
*
628660 AAAATT-CATTTATTTTCATAAGTTTTTCATTTTTTCTTTGAAATTT
1 AAAATTCCTTTTA-TTTCATAAGTTTTTCATTTTTT-TTTGAAATTT
628706 CTCTATTTCT
Statistics
Matches: 178, Mismatches: 27, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
163 45 0.25
164 124 0.70
165 3 0.02
166 6 0.03
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (166 bp):
AAAATTCCTTTTATTTCATAAGTTTTTCATTTTTTTTTGAAATTTACCTTGTTTTCGAAATACAA
AGTTTTCTACTTCGTAAATATTTTGAGGGAGATTTTTCTTAGCTCATAATTATTAAAATTCATAA
AATATCATCATTTAATTCACAGTAAATTAGTTTTAA
Found at i:633723 original size:2 final size:2
Alignment explanation
Indices: 633716--633746 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
633706 GTGCCAAGTG
633716 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
633747 ATGAATGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:634454 original size:17 final size:18
Alignment explanation
Indices: 634423--634457 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
634413 TTTCAACATA
634423 AAAAAGGACTCCAATTTT
1 AAAAAGGACTCCAATTTT
634441 AAAAAGGACT-CAATTTT
1 AAAAAGGACTCCAATTTT
634458 GTTCACACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (18 bp):
AAAAAGGACTCCAATTTT
Found at i:635171 original size:8 final size:8
Alignment explanation
Indices: 635160--635227 Score: 52
Period size: 8 Copynumber: 8.1 Consensus size: 8
635150 AATTAAAATT
635160 TATATAAA
1 TATATAAA
635168 TATA-AAA
1 TATATAAA
*
635175 TAT-TTAA
1 TATATAAA
635182 TA-ATATAA
1 TATATA-AA
635190 TATAATAAAA
1 TAT-AT-AAA
635200 TATATAAATA
1 TATAT-AA-A
635210 TAATATAAA
1 T-ATATAAA
635219 TATATAAA
1 TATATAAA
635227 T
1 T
635228 TATCAAATCT
Statistics
Matches: 50, Mismatches: 2, Indels: 16
0.74 0.03 0.24
Matches are distributed among these distances:
7 11 0.22
8 16 0.32
9 7 0.14
10 11 0.22
11 5 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TATATAAA
Found at i:635173 original size:17 final size:16
Alignment explanation
Indices: 635153--635229 Score: 50
Period size: 17 Copynumber: 4.5 Consensus size: 16
635143 ATTAACGAAT
*
635153 TAAAATTTATATAAATA
1 TAAAATTAATA-AAATA
*
635170 TAAAA-TATTTAATAATA
1 TAAAATTA-ATAA-AATA
*
635187 TAATA-TAATAAAATA
1 TAAAATTAATAAAATA
635202 TATAAATATAATATAAATA
1 TA-AAAT-TAATA-AAATA
635221 TATAAATTA
1 TA-AAATTA
635230 TCAAATCTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
15 6 0.12
16 7 0.14
17 17 0.35
18 7 0.14
19 12 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAATTAATAAAATA
Found at i:635188 original size:23 final size:26
Alignment explanation
Indices: 635161--635235 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 26
635151 ATTAAAATTT
*
635161 ATATAAATATAAAATAT-T-TA-ATA
1 ATATAAATATAAAATATATAAATATA
635184 ATATAATATAATAAAATATATAAATATA
1 ATATAA-AT-ATAAAATATATAAATATA
635212 ATATAAATATATAAAT-TATCAAAT
1 ATATAAATATA-AAATATAT-AAAT
635236 CTTATAAATG
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
23 6 0.14
24 2 0.05
25 9 0.20
26 7 0.16
27 11 0.25
28 9 0.20
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (26 bp):
ATATAAATATAAAATATATAAATATA
Found at i:635191 original size:5 final size:5
Alignment explanation
Indices: 635181--635225 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
635171 AAAATATTTA
*
635181 ATAAT ATAAT ATAAT AAAAT AT-AT A-AAT ATAAT ATAA- AT-AT ATAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
635226 ATTATCAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
3 1 0.03
4 10 0.29
5 23 0.68
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:635223 original size:13 final size:13
Alignment explanation
Indices: 635161--635225 Score: 57
Period size: 13 Copynumber: 5.1 Consensus size: 13
635151 ATTAAAATTT
*
635161 ATATAAATATAAA
1 ATATAAATATATA
*
635174 ATATTTAATAATATA
1 ATA-TAAAT-ATATA
635189 ATAT-AATA-A-A
1 ATATAAATATATA
635199 ATATATAA-ATATA
1 ATATA-AATATATA
635212 ATATAAATATATA
1 ATATAAATATATA
635225 A
1 A
635226 ATTATCAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
10 5 0.12
11 2 0.05
12 6 0.14
13 18 0.42
14 5 0.12
15 7 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATATAAATATATA
Found at i:635598 original size:16 final size:16
Alignment explanation
Indices: 635574--635617 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
635564 ATCGATTCGA
* *
635574 AACTTAAAATGATCTG
1 AACTCAAAATGATCCG
635590 AACTCAAAATGATCCG
1 AACTCAAAATGATCCG
635606 AACTCAAAATGA
1 AACTCAAAATGA
635618 CTCGGATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.48, C:0.18, G:0.11, T:0.23
Consensus pattern (16 bp):
AACTCAAAATGATCCG
Found at i:636404 original size:16 final size:16
Alignment explanation
Indices: 636379--636419 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
636369 TAAACCCAAT
*
636379 TGACCCGAATCTATAA
1 TGACCTGAATCTATAA
636395 TGACCTGAATCTATAA
1 TGACCTGAATCTATAA
636411 TGACCTGAA
1 TGACCTGAA
636420 CCCGATTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.27
Consensus pattern (16 bp):
TGACCTGAATCTATAA
Found at i:639567 original size:28 final size:28
Alignment explanation
Indices: 639536--639589 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
639526 TTATATATTT
639536 TTTAAATTAT-TATATAAATACAATTTTA
1 TTTAAATTATATATA-AAATACAATTTTA
* *
639564 TTTATATTATATATAAAATATAATTT
1 TTTAAATTATATATAAAATACAATTT
639590 AAAATAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
TTTAAATTATATATAAAATACAATTTTA
Found at i:641588 original size:67 final size:66
Alignment explanation
Indices: 641402--641589 Score: 200
Period size: 67 Copynumber: 2.8 Consensus size: 66
641392 ATCACCGGCA
* * * *
641402 CCCCAACATAATAGAGAATGCCACCAACATCACTAAAACGAGTGATGGATGGGAGGGATGACCAA
1 CCCCAACGTAAT-GAGAA-GCCACCAACATCACCAAAAAGAGTGATGGATGGTAGGGATGACCAA
641467 CAT
64 CAT
* ** * * *
641470 -CCCAATGTGGTGACGAAAGCCCCCAACATCACCCAAAAGAGTGATGGATGGTAGGCG-TGACTA
1 CCCCAACGTAATGA-G-AAGCCACCAACATCACCAAAAAGAGTGATGGATGGTAGG-GATGACCA
*
641533 ACGT
63 ACAT
*
641537 CCCCAACGTAATGGAGAAGCCACCAATATCACCAAAAAGAGTGATGGATGGTA
1 CCCCAACGTAAT-GAGAAGCCACCAACATCACCAAAAAGAGTGATGGATGGTA
641590 CTTGTGTGAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
66 2 0.02
67 82 0.84
68 12 0.12
69 2 0.02
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (66 bp):
CCCCAACGTAATGAGAAGCCACCAACATCACCAAAAAGAGTGATGGATGGTAGGGATGACCAACA
T
Found at i:646906 original size:66 final size:65
Alignment explanation
Indices: 646781--646926 Score: 157
Period size: 66 Copynumber: 2.2 Consensus size: 65
646771 GCAACTTTCA
* * * * * *
646781 TCCCTATTGGTTTTGCCATATAGAGTAGTGGTGTAGCAACTATAAAACTGTGCTTAGTTGCTCTT
1 TCCC-ATTGGTTTTACCATATAGAGTAGTAGTGCAGCAACTACAAAACTATGCTCAGTTGCTCTT
*
646846 AT
65 -G
* * * **
646848 TCCCATTGGTTTTATCATGTAGAGTAGTAGTGCAGCAACTCCAGGACTATGCTCAGTTGCTCTTG
1 TCCCATTGGTTTTACCATATAGAGTAGTAGTGCAGCAACTACAAAACTATGCTCAGTTGCTCTTG
646913 TCGCCATTGGTTTT
1 TC-CCATTGGTTTT
646927 GCAAAGCAGT
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
65 2 0.03
66 60 0.91
67 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (65 bp):
TCCCATTGGTTTTACCATATAGAGTAGTAGTGCAGCAACTACAAAACTATGCTCAGTTGCTCTTG
Found at i:650252 original size:310 final size:308
Alignment explanation
Indices: 649513--650435 Score: 1438
Period size: 308 Copynumber: 3.0 Consensus size: 308
649503 AGGGTGGACG
* *
649513 AGGTACCGTTAGAAAGATAACTTGATGAAGGTCAATCTAAAAATATTTTAAAAATCCTAAAAAAT
1 AGGTACCGTTAGAAAGATGACTTGATGAAGGTCGATCTAAAAATATTTTAAAAATCCTAAAAAAT
* * * *
649578 TATTTTTCAGGAGGAATAAATTCTTAAAATCACATTAAGTATGCTACTAGCAGAGCATACTAGAA
66 CACTTTTCAGGAGGAATAAATTCTTAAAATCACGTTAAGTATGCTACTAGCAGAGCATACTAGAG
* *
649643 AAATGGTGTGTCAAACTTTGAAAAATCACCCTAGACTCGTTTAATATCAAAAAATTATAAATGAT
131 AAATGGTGTGTCAAACTTTGAAAAATCACCCTAGACTCATTTAATATCAAAAATTTATAAATGAT
* * * *
649708 ACCTTTTCGGAAAGGAAATTTCGTGAAAGTTTTTGGAAAAATATTTGAAAAGTTTGGAAAAATCA
196 ACCTTTTCGAAAAGGAAATTTCATGAAAGTTTTTGGAAAAATATTTGAAAATTTTGAAAAAATCA
* * * *
649773 TCTAGTAGGCATAAATGGTCCAACCAAAATGCACTTTGTTGATTCTAG
261 TCTAGTAGGCCTAAATGGTCCAACCAAAATGCACTTTGCTGATTCCAA
* *
649821 AGGTACCGTTAGAAAGATGACTTGATGAGGGTCGATCT-AAAATTTTTTCAAAAATCCTAAAAAA
1 AGGTACCGTTAGAAAGATGACTTGATGAAGGTCGATCTAAAAATATTTT-AAAAATCCTAAAAAA
* * * * *
649885 TCGCTTTCCAGGAGGAATAAATTCTTGAAATCATGTTATGTATGCTACTAGCAGAGCATACTAGA
65 TCACTTTTCAGGAGGAATAAATTCTTAAAATCACGTTAAGTATGCTACTAGCAGAGCATACTAGA
* * *
649950 GAAATGGTGTGTCAAACTTTGAAAAATCACCTTAGACTCATTTAGTGTCAAAAATTTATAAATGA
130 GAAATGGTGTGTCAAACTTTGAAAAATCACCCTAGACTCATTTAATATCAAAAATTTATAAATGA
*
650015 TACCTTTTCGAAAAGGAAATTTCATGAAAGTTTTTGTAAAAATATTTGAAAATTTTGAAAAAAAA
195 TACCTTTTCGAAAAGGAAATTTCATGAAAGTTTTTGGAAAAATATTTGAAAATTTTG--AAAAAA
* *
650080 TCATCTAGTAGGCCTAAATGGTCCAACCATAATGCACTTTGCTGTTTCCAA
258 TCATCTAGTAGGCCTAAATGGTCCAACCAAAATGCACTTTGCTGATTCCAA
** *
650131 AGGTATTGTTAGAAAGATGACTTGATGATGGTCGATCTAAAAATATTTTAAAAATCCTAAAAAAT
1 AGGTACCGTTAGAAAGATGACTTGATGAAGGTCGATCTAAAAATATTTTAAAAATCCTAAAAAAT
*
650196 CACTTTTCAAGAGGAATAAATTCTTAAAATCACGTTAAGTATGCTACTAGCAGAGCATACTAGAG
66 CACTTTTCAGGAGGAATAAATTCTTAAAATCACGTTAAGTATGCTACTAGCAGAGCATACTAGAG
* *
650261 AAATGGTGTGTCAAACTTTGAAAAATCACCCTAGACTCATTCAATATCAAAAATTCATAAATGAT
131 AAATGGTGTGTCAAACTTTGAAAAATCACCCTAGACTCATTTAATATCAAAAATTTATAAATGAT
*
650326 ACCTTTTCAAAAAGGAAATTTCATGAAAGTTTTTGGAAAAATATTTGAAAAATTTT-AAAAAATC
196 ACCTTTTCGAAAAGGAAATTTCATGAAAGTTTTTGGAAAAATATTTG-AAAATTTTGAAAAAATC
* *
650390 GTCTAGTAGGCCTAAATGGTCCAACTC-GAATGCACTTTGCTGATTC
260 ATCTAGTAGGCCTAAATGGTCCAAC-CAAAATGCACTTTGCTGATTC
650436 TAGGAGTTTT
Statistics
Matches: 560, Mismatches: 49, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
307 9 0.02
308 268 0.48
309 1 0.00
310 265 0.47
311 17 0.03
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.31
Consensus pattern (308 bp):
AGGTACCGTTAGAAAGATGACTTGATGAAGGTCGATCTAAAAATATTTTAAAAATCCTAAAAAAT
CACTTTTCAGGAGGAATAAATTCTTAAAATCACGTTAAGTATGCTACTAGCAGAGCATACTAGAG
AAATGGTGTGTCAAACTTTGAAAAATCACCCTAGACTCATTTAATATCAAAAATTTATAAATGAT
ACCTTTTCGAAAAGGAAATTTCATGAAAGTTTTTGGAAAAATATTTGAAAATTTTGAAAAAATCA
TCTAGTAGGCCTAAATGGTCCAACCAAAATGCACTTTGCTGATTCCAA
Found at i:651331 original size:20 final size:19
Alignment explanation
Indices: 651306--651358 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
651296 CATTTTAGAC
*
651306 ATGTATTGATACATTCACTT
1 ATGTATTGATACATT-ACCT
* *
651326 ATGTATCGATATATTACCT
1 ATGTATTGATACATTACCT
*
651345 ATTATATTGATACA
1 A-TGTATTGATACA
651359 ATTTGTTGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (19 bp):
ATGTATTGATACATTACCT
Found at i:652448 original size:81 final size:81
Alignment explanation
Indices: 652330--652546 Score: 258
Period size: 81 Copynumber: 2.7 Consensus size: 81
652320 ATCTATATTC
* * * *
652330 TAGAAATAAAAACAGGATTGGAGTATCCCCTCAGAAATAGTTAGGTTGGAGTATCCCTGA-AAAT
1 TAGAAGTAAAAATAGGATTGGAGTATCCCCTCAGAAATAGTGAGGTTGGAGTATCCC-CATAAAT
652394 -GAAAAATTTGATATTTT
65 AG-AAAATTTGATATTTT
* * ** * * *
652411 TAGGAGTAAAAATAGGATTGAAGTATCCCCTTGGAAATGGTGGGGTTGGAGTATCCCCATAGATA
1 TAGAAGTAAAAATAGGATTGGAGTATCCCCTCAGAAATAGTGAGGTTGGAGTATCCCCATAAATA
652476 GAAAATTTGATATTTT
66 GAAAATTTGATATTTT
* * * * *
652492 TAGAAGTAAAAATAAGATTGGAGTATCCCCTCAAAAATGGTGGGGTTGAAGTATC
1 TAGAAGTAAAAATAGGATTGGAGTATCCCCTCAGAAATAGTGAGGTTGGAGTATC
652547 TTCTTTTAAT
Statistics
Matches: 116, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
80 1 0.01
81 114 0.98
82 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.29
Consensus pattern (81 bp):
TAGAAGTAAAAATAGGATTGGAGTATCCCCTCAGAAATAGTGAGGTTGGAGTATCCCCATAAATA
GAAAATTTGATATTTT
Found at i:652457 original size:160 final size:159
Alignment explanation
Indices: 652189--652546 Score: 386
Period size: 160 Copynumber: 2.2 Consensus size: 159
652179 AAAATTGGGG
* *
652189 TTGGAGTATCCCCTCAAAGATGGTAGGGTTAGAGTATCCTTGAGATGAAAAAGTTAATATTTTGA
1 TTGGAGTATCCCCTCAAA-ATGGTAGGGTTAGAGTATCCCTGAAATGAAAAAGTTAATATTTTGA
* * * * * *
652254 AAGTAAAAACGGGGTTGGAGTATTCCTTTGGAAATGATGGGGTTGGAGTATCTCCAAT-GGT-GA
65 AAGTAAAAACAGGATTGAAGTATCCCCTTGGAAATGATGGGGTTGGAGTATC-CCAATAGATAG-
*
652317 AAAATCT-ATA-TTCTAGAAATAAAAACAGGA
128 AAAATCTGATATTTCTAGAAATAAAAACAAGA
* * * *
652347 TTGGAGTATCCCCTCAGAAATAGTTA-GGTTGGAGTATCCCTGAAAATGAAAAATTTGATATTTT
1 TTGGAGTATCCCCTCA-AAAT-GGTAGGGTTAGAGTATCCCTG-AAATGAAAAAGTTAATATTTT
* * * * *
652411 TAGGAGTAAAAATAGGATTGAAGTATCCCCTTGGAAATGGTGGGGTTGGAGTATCCCCATAGATA
63 GA-AAGTAAAAACAGGATTGAAGTATCCCCTTGGAAATGATGGGGTTGGAGTATCCCAATAGATA
* * * *
652476 GAAAATTTGATATTTTTAGAAGTAAAAATAAGA
127 GAAAATCTGATATTTCTAGAAATAAAAACAAGA
*
652509 TTGGAGTATCCCCTCAAAAATGGTGGGGTT-GAAGTATC
1 TTGGAGTATCCCCTC-AAAATGGTAGGGTTAG-AGTATC
652547 TTCTTTTAAT
Statistics
Matches: 165, Mismatches: 24, Indels: 18
0.80 0.12 0.09
Matches are distributed among these distances:
158 32 0.19
159 28 0.17
160 52 0.32
161 7 0.04
162 45 0.27
163 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.30
Consensus pattern (159 bp):
TTGGAGTATCCCCTCAAAATGGTAGGGTTAGAGTATCCCTGAAATGAAAAAGTTAATATTTTGAA
AGTAAAAACAGGATTGAAGTATCCCCTTGGAAATGATGGGGTTGGAGTATCCCAATAGATAGAAA
ATCTGATATTTCTAGAAATAAAAACAAGA
Found at i:654713 original size:20 final size:20
Alignment explanation
Indices: 654688--654759 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
654678 TCAAAAACCC
654688 ATAATGTATCGATACAATGA
1 ATAATGTATCGATACAATGA
*
654708 ATAATGTATCTATAC-AT--
1 ATAATGTATCGATACAATGA
*
654725 AT--TGTACCGATACAATGAA
1 ATAATGTATCGATACAATG-A
* *
654744 ATAAGGTATCAATACA
1 ATAATGTATCGATACA
654760 TTTTGGTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
15 9 0.22
16 2 0.05
17 2 0.05
19 4 0.10
20 14 0.35
21 9 0.22
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (20 bp):
ATAATGTATCGATACAATGA
Found at i:654743 original size:35 final size:36
Alignment explanation
Indices: 654687--654760 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 36
654677 GTCAAAAACC
* * *
654687 CATAATGTATCGATACAATG-AATAATGTATCTATA
1 CATAATGTACCGATACAATGAAATAAGGTATCAATA
*
654722 CATATTGTACCGATACAATGAAATAAGGTATCAATA
1 CATAATGTACCGATACAATGAAATAAGGTATCAATA
654758 CAT
1 CAT
654761 TTTGGTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
35 18 0.53
36 16 0.47
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (36 bp):
CATAATGTACCGATACAATGAAATAAGGTATCAATA
Found at i:657287 original size:28 final size:30
Alignment explanation
Indices: 657234--657296 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 30
657224 AGAATAATAT
* *
657234 TTTTTAATATATTAATTTAATTATTA-AAA
1 TTTTTAATATATTAATTAAATAATTAGAAA
*
657263 TTTTT-ATATATTGAA-TAAATAATTAGATA
1 TTTTTAATATATT-AATTAAATAATTAGAAA
657292 TTTTT
1 TTTTT
657297 GTACACACCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 15 0.52
29 14 0.48
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (30 bp):
TTTTTAATATATTAATTAAATAATTAGAAA
Found at i:657680 original size:50 final size:51
Alignment explanation
Indices: 657553--657686 Score: 207
Period size: 50 Copynumber: 2.6 Consensus size: 51
657543 TTTTACTGTT
* *
657553 TGTATCGATACATTATTCATTGTATCGATACATTCTGGGTTTTTACCTAGA
1 TGTATCGATACATTATTCATTGTATCGATACATTCTGGGATTTTACCCAGA
*
657604 TGTATCGATACATTCTTCATTGTATCGATACATTCT-GGATTTTACCCAGA
1 TGTATCGATACATTATTCATTGTATCGATACATTCTGGGATTTTACCCAGA
* * *
657654 TGTATCGATACATTGTTCAATATATCGATACAT
1 TGTATCGATACATTATTCATTGTATCGATACAT
657687 GTAGGTAAAT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 42 0.55
51 35 0.45
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (51 bp):
TGTATCGATACATTATTCATTGTATCGATACATTCTGGGATTTTACCCAGA
Found at i:658621 original size:20 final size:21
Alignment explanation
Indices: 658576--658621 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
658566 TGTTAATAGC
658576 CCATG-TTCATGCATTTTGAG
1 CCATGTTTCATGCATTTTGAG
* *
658596 CTATGTTTCATGCATTTTTA-
1 CCATGTTTCATGCATTTTGAG
658616 CCATGT
1 CCATGT
658622 CCAGCACCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.46
Consensus pattern (21 bp):
CCATGTTTCATGCATTTTGAG
Found at i:661110 original size:20 final size:19
Alignment explanation
Indices: 661071--661111 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
661061 ACAAGGTAAC
*
661071 TAAATAAATATAAATTGTA
1 TAAATAAATATAAATGGTA
*
661090 TAAATAATTATAAAATGGTA
1 TAAATAAATAT-AAATGGTA
661110 TA
1 TA
661112 GACATTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (19 bp):
TAAATAAATATAAATGGTA
Found at i:662126 original size:16 final size:16
Alignment explanation
Indices: 662105--662146 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
662095 CCCAATTGAT
662105 CCGAATCCGA-AATGAC
1 CCGAAT-CGAGAATGAC
*
662121 CCGAATCTAGAATGAC
1 CCGAATCGAGAATGAC
662137 CCGAACTCGA
1 CCGAA-TCGA
662147 TTAATCCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 2 0.09
16 17 0.77
17 3 0.14
ACGTcount: A:0.36, C:0.31, G:0.19, T:0.14
Consensus pattern (16 bp):
CCGAATCGAGAATGAC
Found at i:662164 original size:69 final size:69
Alignment explanation
Indices: 662048--662186 Score: 208
Period size: 69 Copynumber: 2.0 Consensus size: 69
662038 TAAACCCAAT
* *
662048 TGACCCGAATCCAGAATGACCCGAACTCGATTAATCTGAGTGATAAACCCAATTGA-TCCGAATC
1 TGACCCGAATCCAGAATGACCCGAACTCGATTAATCCGAATGATAAACCCAATTGACT-CGAATC
662112 CGAAA
65 CGAAA
* * * *
662117 TGACCCGAATCTAGAATGACCCGAACTCGATTAATCCGAATGTTAAACTCGATTGACTCGAATCC
1 TGACCCGAATCCAGAATGACCCGAACTCGATTAATCCGAATGATAAACCCAATTGACTCGAATCC
662182 GAAA
66 GAAA
662186 T
1 T
662187 TACGAGAACC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
69 62 0.98
70 1 0.02
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22
Consensus pattern (69 bp):
TGACCCGAATCCAGAATGACCCGAACTCGATTAATCCGAATGATAAACCCAATTGACTCGAATCC
GAAA
Found at i:662204 original size:69 final size:69
Alignment explanation
Indices: 662060--662204 Score: 168
Period size: 69 Copynumber: 2.1 Consensus size: 69
662050 ACCCGAATCC
* * *
662060 AGAATGACCCGAACTCGATTAATCTGAGTGATAAACCCAATTGATCCGAATCCGAAATGACCCGA
1 AGAATGACCCGAACTCGATTAATCCGAATGATAAACCCAATTGATCCGAATCCGAAATGACCAGA
* *
662125 ATCT
66 ACCG
* * * * *
662129 AGAATGACCCGAACTCGATTAATCCGAATGTTAAACTCGATTGA-CTCGAATCCGAAATTACGAG
1 AGAATGACCCGAACTCGATTAATCCGAATGATAAACCCAATTGATC-CGAATCCGAAATGACCAG
662193 AACCCG
65 AA-CCG
662199 A-AATGA
1 AGAATGA
662205 GTCGAACCAA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
68 1 0.02
69 61 0.95
70 2 0.03
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (69 bp):
AGAATGACCCGAACTCGATTAATCCGAATGATAAACCCAATTGATCCGAATCCGAAATGACCAGA
ACCG
Found at i:662290 original size:15 final size:15
Alignment explanation
Indices: 662271--662310 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
662261 GAAAATTTTA
662271 AAACCCGAAATAACC
1 AAACCCGAAATAACC
* * *
662286 CAACCCGAAATGATC
1 AAACCCGAAATAACC
662301 AAACCCGAAA
1 AAACCCGAAA
662311 CTATTAAGCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.50, C:0.33, G:0.10, T:0.07
Consensus pattern (15 bp):
AAACCCGAAATAACC
Found at i:662654 original size:13 final size:13
Alignment explanation
Indices: 662636--662660 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
662626 ATTTTGCTTA
662636 GTATCGATACATT
1 GTATCGATACATT
662649 GTATCGATACAT
1 GTATCGATACAT
662661 CAAACTAACA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:662781 original size:73 final size:73
Alignment explanation
Indices: 662693--662836 Score: 198
Period size: 73 Copynumber: 2.0 Consensus size: 73
662683 CATTTTCATA
* * *
662693 GTTCATCACTATTCATTTATCAATACATCACTGTTCATCACTATACATTGAGCCCAACGGCTATA
1 GTTCATCACTATTCATATATCAATACATCAATATTCATCACTATACATTGAGCCCAACGGCTATA
662758 ATTTCACT
66 ATTTCACT
* * * * * * *
662766 GTTCATCATTGTTCATATATTAATACATCAATATTCATCACTGTACATTGAGCCTAATGGTTATA
1 GTTCATCACTATTCATATATCAATACATCAATATTCATCACTATACATTGAGCCCAACGGCTATA
662831 ATTTCA
66 ATTTCA
662837 AATACATATA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
73 61 1.00
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (73 bp):
GTTCATCACTATTCATATATCAATACATCAATATTCATCACTATACATTGAGCCCAACGGCTATA
ATTTCACT
Found at i:664900 original size:21 final size:21
Alignment explanation
Indices: 664874--664932 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
664864 TAATATTCTT
* *
664874 GAAAAGAAATTAAGTGAATTA
1 GAAAAGAAAATAAATGAATTA
664895 GAAAAGAAAATAAATGAATTA
1 GAAAAGAAAATAAATGAATTA
** *
664916 GAGGAGAAAAGAAATGA
1 GAAAAGAAAATAAATGA
664933 GTTGCAAGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.17
Consensus pattern (21 bp):
GAAAAGAAAATAAATGAATTA
Found at i:666151 original size:13 final size:13
Alignment explanation
Indices: 666133--666158 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
666123 CAATTTTTTG
666133 TGTATCGATACAT
1 TGTATCGATACAT
666146 TGTATCGATACAT
1 TGTATCGATACAT
666159 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:666224 original size:21 final size:21
Alignment explanation
Indices: 666197--666272 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
666187 CTGCCAAGAA
*
666197 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
* ****
666218 TTGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
666238 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
666259 ATGTATCGATACAT
1 ATGTATCGATACAT
666273 TGCAACATGT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 14 0.33
21 29 0.67
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:666244 original size:20 final size:20
Alignment explanation
Indices: 666219--666290 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
666209 ATCTTTTTTT
666219 TGTATCGATACATTGCAACA
1 TGTATCGATACATTGCAACA
****
666239 TGTATCGATACATCTTTTTCA
1 TGTATCGATACAT-TGCAACA
666260 TGTATCGATACATTGCAACA
1 TGTATCGATACATTGCAACA
666280 TGTATCGATAC
1 TGTATCGATAC
666291 TTTGAATTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTGCAACA
Found at i:666254 original size:41 final size:41
Alignment explanation
Indices: 666197--666290 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
666187 CTGCCAAGAA
**
666197 ATGTATCGATACATCTTTTTTTTGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
666238 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
666279 ATGTATCGATAC
1 ATGTATCGATAC
666291 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:668753 original size:13 final size:13
Alignment explanation
Indices: 668735--668773 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
668725 ATAATCACCC
*
668735 TGTATCGATACAG
1 TGTATCGATACAA
668748 TGTATCGATACAA
1 TGTATCGATACAA
668761 TGTATCGATACAA
1 TGTATCGATACAA
668774 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:668784 original size:20 final size:20
Alignment explanation
Indices: 668759--668837 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
668749 GTATCGATAC
668759 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
668779 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
668804 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
668824 CATGTATCGATACA
1 AATGTATCGATACA
668838 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:674963 original size:13 final size:13
Alignment explanation
Indices: 674945--674970 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
674935 CAATTTTTTG
674945 TGTATCGATACAT
1 TGTATCGATACAT
674958 TGTATCGATACAT
1 TGTATCGATACAT
674971 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:675036 original size:21 final size:21
Alignment explanation
Indices: 675009--675084 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
674999 CTGCCAAGAA
*
675009 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
* ****
675030 TTGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
675050 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
675071 ATGTATCGATACAT
1 ATGTATCGATACAT
675085 TGCAACATGT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 14 0.33
21 29 0.67
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:675056 original size:20 final size:20
Alignment explanation
Indices: 675031--675102 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
675021 ATCTTTTTTT
675031 TGTATCGATACATTGCAACA
1 TGTATCGATACATTGCAACA
****
675051 TGTATCGATACATCTTTTTCA
1 TGTATCGATACAT-TGCAACA
675072 TGTATCGATACATTGCAACA
1 TGTATCGATACATTGCAACA
675092 TGTATCGATAC
1 TGTATCGATAC
675103 TTTGAATTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTGCAACA
Found at i:675066 original size:41 final size:41
Alignment explanation
Indices: 675009--675102 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
674999 CTGCCAAGAA
**
675009 ATGTATCGATACATCTTTTTTTTGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
675050 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
675091 ATGTATCGATAC
1 ATGTATCGATAC
675103 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:678131 original size:19 final size:21
Alignment explanation
Indices: 678093--678131 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
678083 ATTCCCTTGA
*
678093 AAATAACAATCGATGATTAGG
1 AAATAACAATCGAGGATTAGG
678114 AAATAA-AATCG-GGATTAG
1 AAATAACAATCGAGGATTAG
678132 AGTATCCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.49, C:0.08, G:0.21, T:0.23
Consensus pattern (21 bp):
AAATAACAATCGAGGATTAGG
Found at i:678410 original size:51 final size:51
Alignment explanation
Indices: 678263--678481 Score: 194
Period size: 51 Copynumber: 4.3 Consensus size: 51
678253 AATAACGAGG
* * * *
678263 TTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTAGAAATAAAATC-GAA
1 TTGGAGTATCCCCGATTATGAAAAATTAGTG-TTTTAGAAATAAAATCGGGA
* * * * * *
678314 GTTGGAATATCTCCAATTAAAGGAAAATTGGTGTTTT-GAAGATAAAA-CAGGGA
1 -TTGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTAGAA-ATAAAATC-GGGA
*
678367 TTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAATCGAGG-
1 TTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAATCG-GGA
* * * * * * *
678418 TTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAACCGGGG
1 TTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAATCGGGA
678469 TTGGAGTATCCCC
1 TTGGAGTATCCCC
678482 TCGGAGGTAA
Statistics
Matches: 137, Mismatches: 22, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
50 2 0.01
51 79 0.58
52 43 0.31
53 13 0.09
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (51 bp):
TTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAATCGGGA
Found at i:681097 original size:19 final size:18
Alignment explanation
Indices: 681069--681131 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
681059 AGCGATACAT
*
681069 TGTATTGATACAAACCTTA
1 TGTATCGATAC-AACCTTA
681088 TGTATCGATAC-A---T-
1 TGTATCGATACAACCTTA
681101 TGTATCGATACAACACTTA
1 TGTATCGATACAAC-CTTA
681120 TGTATCGATACA
1 TGTATCGATACA
681132 TTTTCTGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 11 0.30
14 2 0.05
17 1 0.03
18 1 0.03
19 22 0.59
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAACCTTA
Found at i:681102 original size:32 final size:32
Alignment explanation
Indices: 681061--681133 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
681051 AGCTTCGTAG
*
681061 CGATACATTGTATTGATACAA-ACCTTATGTAT
1 CGATACATTGTATCGATACAACA-CTTATGTAT
681093 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
681125 CGATACATT
1 CGATACATT
681134 TTCTGTTTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 38 0.97
33 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:681106 original size:13 final size:13
Alignment explanation
Indices: 681088--681112 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
681078 ACAAACCTTA
681088 TGTATCGATACAT
1 TGTATCGATACAT
681101 TGTATCGATACA
1 TGTATCGATACA
681113 ACACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:681160 original size:19 final size:19
Alignment explanation
Indices: 681100--681161 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
681090 TATCGATACA
681100 TTGTATCGATACAACACT-T
1 TTGTATCGATACAA-ACTGT
* **
681119 ATGTATCGATACATTTTCTGT
1 TTGTATCGATACA--AACTGT
681140 TTGTATCGATACAAACTGT
1 TTGTATCGATACAAACTGT
681159 TTG
1 TTG
681162 AAGTTCAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 19 0.56
20 2 0.06
21 13 0.38
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (19 bp):
TTGTATCGATACAAACTGT
Found at i:681279 original size:22 final size:23
Alignment explanation
Indices: 681238--681280 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
681228 ACAAAAATGT
*
681238 TTTTTTTATTTGTTAATTTTTAA
1 TTTTTTTATTTATTAATTTTTAA
*
681261 TTTTTTTA-TTATTATTTTTT
1 TTTTTTTATTTATTAATTTTT
681281 TTAATAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (23 bp):
TTTTTTTATTTATTAATTTTTAA
Found at i:681291 original size:12 final size:12
Alignment explanation
Indices: 681254--681296 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
681244 TATTTGTTAA
681254 TTTTTAAT-TTT
1 TTTTTAATATTT
*
681265 TTTATTATTATTT
1 TTT-TTAATATTT
681278 TTTTTAATAATTT
1 TTTTTAAT-ATTT
681291 TTTTTA
1 TTTTTA
681297 TCCTTTTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 3 0.11
12 8 0.30
13 16 0.59
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTAATATTT
Found at i:683586 original size:32 final size:32
Alignment explanation
Indices: 683550--683629 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
683540 GAAAGAAAGT
* *
683550 AAAAATAAAGAGAGAAAGAAAAAAAAAG-GAAC
1 AAAAATAAAGAAAAAAAGAAAAAAAAAGAG-AC
* * * *
683582 AAAAAGAAAAAAAAAAAGAAAAAAAGAGAGAG
1 AAAAATAAAGAAAAAAAGAAAAAAAAAGAGAC
*
683614 AAAAATAAAGATAAAA
1 AAAAATAAAGAAAAAA
683630 TCATAAAACA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 37 0.97
33 1 0.03
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.04
Consensus pattern (32 bp):
AAAAATAAAGAAAAAAAGAAAAAAAAAGAGAC
Found at i:683597 original size:12 final size:12
Alignment explanation
Indices: 683582--683629 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
683572 AAAAAGGAAC
683582 AAAAAGAAAAAA
1 AAAAAGAAAAAA
683594 AAAAAGAAAAAA
1 AAAAAGAAAAAA
* * *
683606 AGAGAGAGAAAA
1 AAAAAGAAAAAA
*
683618 ATAAAGATAAAA
1 AAAAAGA-AAAA
683630 TCATAAAACA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
12 26 0.90
13 3 0.10
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:683605 original size:20 final size:20
Alignment explanation
Indices: 683550--683608 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
683540 GAAAGAAAGT
* * *
683550 AAAAATAAAGAGAGAAAG-A
1 AAAAAAAAAGAAAAAAAGAA
*
683569 AAAAAAAAGGAACAAAAAGAA
1 AAAAAAAAAGAA-AAAAAGAA
683590 AAAAAAAAAGAAAAAAAGA
1 AAAAAAAAAGAAAAAAAGA
683609 GAGAGAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
19 9 0.27
20 12 0.36
21 12 0.36
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAGAAAAAAAGAA
Found at i:683617 original size:24 final size:23
Alignment explanation
Indices: 683560--683629 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 23
683550 AAAAATAAAG
*
683560 AGAGAAAGAAAAAAAAAGGAACAAA
1 AGAG-AAGAAAAAAAAA-GAAAAAA
683585 A-AGAA-AAAAAAAAAGAAAAAA
1 AGAGAAGAAAAAAAAAGAAAAAA
* *
683606 AGAGAGAGAAAAATAAAGATAAAA
1 AGAGA-AGAAAAAAAAAGAAAAAA
683630 TCATAAAACA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 7 0.18
22 12 0.31
23 3 0.08
24 16 0.41
25 1 0.03
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (23 bp):
AGAGAAGAAAAAAAAAGAAAAAA
Found at i:683618 original size:22 final size:22
Alignment explanation
Indices: 683568--683608 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
683558 AGAGAGAAAG
683568 AAAAAAAAAGGAACAAAAAGAA
1 AAAAAAAAAGGAACAAAAAGAA
683590 AAAAAAAAA-GAA-AAAAAGA
1 AAAAAAAAAGGAACAAAAAGA
683609 GAGAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 3 0.16
22 9 0.47
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAGGAACAAAAAGAA
Found at i:684224 original size:21 final size:21
Alignment explanation
Indices: 684200--684242 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
684190 TTTTTCATAA
684200 ATTAACAATTATTAATTTATC
1 ATTAACAATTATTAATTTATC
*
684221 ATTAATAATTATTAATTTATC
1 ATTAACAATTATTAATTTATC
684242 A
1 A
684243 ATAAAAGAAT
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:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTAACAATTATTAATTTATC
Found at i:684730 original size:4 final size:4
Alignment explanation
Indices: 684721--684754 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
684711 GCGACCTTGT
684721 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
684755 TCTCCTTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (4 bp):
TTAA
Found at i:684886 original size:2 final size:2
Alignment explanation
Indices: 684879--684907 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
684869 GCATTATTTG
684879 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
684908 ATTCATTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:685358 original size:30 final size:30
Alignment explanation
Indices: 685324--685391 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
685314 TATTATATTT
685324 AAATAAATTTTTAATCATTAATTTATACTC
1 AAATAAATTTTTAATCATTAATTTATACTC
* * * *
685354 AAATAAATTTTTAATCTTTAATTTGTATTT
1 AAATAAATTTTTAATCATTAATTTATACTC
685384 AAATAAAT
1 AAATAAAT
685392 CATAATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (30 bp):
AAATAAATTTTTAATCATTAATTTATACTC
Found at i:685411 original size:29 final size:30
Alignment explanation
Indices: 685286--685414 Score: 131
Period size: 29 Copynumber: 4.4 Consensus size: 30
685276 AAATTTTATT
* * *
685286 ATTT-TATTTAACTAAATATTTATAT-TTTT
1 ATTTATATTTAAATAAATTTTTA-ATCTTTA
*
685315 A-TTATATTTAAATAAATTTTTAATCATTA
1 ATTTATATTTAAATAAATTTTTAATCTTTA
* *
685344 ATTTATACTCAAATAAATTTTTAATCTTTA
1 ATTTATATTTAAATAAATTTTTAATCTTTA
* ** *
685374 ATTTGTATTTAAATAAA-TCATAATTTTTA
1 ATTTATATTTAAATAAATTTTTAATCTTTA
685403 ATTTATATTTAA
1 ATTTATATTTAA
685415 TTAAGTCCAT
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
28 4 0.05
29 40 0.48
30 39 0.47
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.54
Consensus pattern (30 bp):
ATTTATATTTAAATAAATTTTTAATCTTTA
Found at i:685523 original size:20 final size:21
Alignment explanation
Indices: 685474--685523 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
685464 TTGAATATAA
*
685474 TAAAAATA-ATAAAAATTTAT
1 TAAAAATATTTAAAAATTTAT
* *
685494 TTAAAA-ATTTAATAATTT-T
1 TAAAAATATTTAAAAATTTAT
685513 TAAAAATATTT
1 TAAAAATATTT
685524 TAATCAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAAATATTTAAAAATTTAT
Found at i:686059 original size:16 final size:16
Alignment explanation
Indices: 686038--686069 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
686028 TAAATTTTCG
686038 TATTTATAATATTTTT
1 TATTTATAATATTTTT
686054 TATTTATAATATTTTT
1 TATTTATAATATTTTT
686070 ATAATAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTTATAATATTTTT
Found at i:686317 original size:2 final size:2
Alignment explanation
Indices: 686310--686338 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
686300 TACTTGCATA
686310 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
686339 ATACACGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.