Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold289
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: 700734
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:479277 original size:21 final size:19
Alignment explanation
Indices: 479253--479308 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
479243 TTCAACAATT
*
479253 TGTATTGATACAAACAGTAAA
1 TGTATCGATACAAA-AGT-AA
* *
479274 TGTATCGATACATAAGTAT
1 TGTATCGATACAAAAGTAA
479293 TGTATCGATACAAAAG
1 TGTATCGATACAAAAG
479309 CTACCATGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.52
20 3 0.10
21 12 0.39
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (19 bp):
TGTATCGATACAAAAGTAA
Found at i:483485 original size:24 final size:24
Alignment explanation
Indices: 483458--483556 Score: 65
Period size: 24 Copynumber: 3.9 Consensus size: 24
483448 AACATAAGCA
483458 ATATAATATAAATGATAGAAATAC
1 ATATAATATAAATGATAGAAATAC
* * * *
483482 ATATTACAAAAATAAT-ATAAATAATAGAA
1 ATA-TA-ATATA-AATGATAGA-AAT--AC
* *
483511 ACATAATATAGATGATAGAAATAC
1 ATATAATATAAATGATAGAAATAC
* *
483535 ATATGATATAAATGATATAAAT
1 ATATAATATAAATGATAGAAAT
483557 GATAAAAACA
Statistics
Matches: 54, Mismatches: 14, Indels: 14
0.66 0.17 0.17
Matches are distributed among these distances:
24 22 0.41
25 2 0.04
26 12 0.22
27 13 0.24
28 2 0.04
29 3 0.06
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (24 bp):
ATATAATATAAATGATAGAAATAC
Found at i:483518 original size:20 final size:20
Alignment explanation
Indices: 483493--483531 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
483483 TATTACAAAA
483493 ATAATATAAATAATAGAAAC
1 ATAATATAAATAATAGAAAC
* *
483513 ATAATATAGATGATAGAAA
1 ATAATATAAATAATAGAAA
483532 TACATATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.26
Consensus pattern (20 bp):
ATAATATAAATAATAGAAAC
Found at i:483520 original size:53 final size:53
Alignment explanation
Indices: 483460--483569 Score: 157
Period size: 53 Copynumber: 2.1 Consensus size: 53
483450 CATAAGCAAT
* *
483460 ATAATATAAATGATAGAAATACATATTACAAAAATAATATAAATAATAGAAAC
1 ATAATATAAATGATAGAAATACATATGACAAAAATAATATAAATAATAAAAAC
* * * * *
483513 ATAATATAGATGATAGAAATACATATGATATAAATGATATAAATGATAAAAAC
1 ATAATATAAATGATAGAAATACATATGACAAAAATAATATAAATAATAAAAAC
483566 ATAA
1 ATAA
483570 GTAACATAAC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.60, C:0.05, G:0.08, T:0.27
Consensus pattern (53 bp):
ATAATATAAATGATAGAAATACATATGACAAAAATAATATAAATAATAAAAAC
Found at i:486280 original size:41 final size:41
Alignment explanation
Indices: 486226--486353 Score: 102
Period size: 41 Copynumber: 3.3 Consensus size: 41
486216 AAAAATAAAG
486226 TTAAACTTC-TATAAATAAAAATAAATCATATCTTAAAAAAT
1 TTAAA-TTCATATAAATAAAAATAAATCATATCTTAAAAAAT
* *
486267 TTAAATTCATAT-AAT---CAT--A-CATA---AAAATAAAT
1 TTAAATTCATATAAATAAAAATAAATCATATCTTAAA-AAAT
*
486299 TTAAA-T-ATTTACATATAAAAATAAATCATATCTTAAAAAAT
1 TTAAATTCATATA-A-ATAAAAATAAATCATATCTTAAAAAAT
486340 TTAAATTCATATAA
1 TTAAATTCATATAA
486354 TTTTTTTAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 31
0.64 0.06 0.30
Matches are distributed among these distances:
30 3 0.05
31 4 0.06
32 10 0.15
33 2 0.03
34 4 0.06
35 1 0.02
36 2 0.03
37 2 0.03
38 1 0.02
39 4 0.06
40 6 0.09
41 17 0.26
42 5 0.08
43 4 0.06
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (41 bp):
TTAAATTCATATAAATAAAAATAAATCATATCTTAAAAAAT
Found at i:486297 original size:73 final size:73
Alignment explanation
Indices: 486158--486354 Score: 246
Period size: 73 Copynumber: 2.7 Consensus size: 73
486148 AAATCAAACT
* *
486158 AATAT-TACAAATAAAAATAAAAT-ATATCTT-AAAAATTTAAACTT-GTATAAGCAAATTAAAA
1 AATATCTACAAATAAAAAT-AAATCATATCTTAAAAAATTTAAA-TTCATATAATCAAATTAAAA
486219 AATAAAGTTA
64 AATAAAGTTA
*
486229 AACT-TCTATAAATAAAAATAAATCATATCTTAAAAAATTTAAATTCATATAATCATACA-T-AA
1 AA-TATCTACAAATAAAAATAAATCATATCTTAAAAAATTTAAATTCATATAATCA-A-ATTAAA
*
486291 AAATAAATTTA
63 AAATAAAGTTA
* *
486302 AATATTTACATATAAAAATAAATCATATCTTAAAAAATTTAAATTCATATAAT
1 AATATCTACAAATAAAAATAAATCATATCTTAAAAAATTTAAATTCATATAAT
486355 TTTTTTAAAC
Statistics
Matches: 111, Mismatches: 7, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
71 7 0.06
72 23 0.21
73 78 0.70
74 2 0.02
75 1 0.01
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.34
Consensus pattern (73 bp):
AATATCTACAAATAAAAATAAATCATATCTTAAAAAATTTAAATTCATATAATCAAATTAAAAAA
TAAAGTTA
Found at i:487729 original size:10 final size:11
Alignment explanation
Indices: 487706--487740 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
487696 GTGTTTCAAA
487706 AAATTTAAATTT
1 AAATTT-AATTT
487718 AAATTT-ATTT
1 AAATTTAATTT
487728 AAATTTAATTT
1 AAATTTAATTT
487739 AA
1 AA
487741 TCAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:487729 original size:16 final size:15
Alignment explanation
Indices: 487708--487739 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
487698 GTTTCAAAAA
487708 ATTTAAATTTAAATTT
1 ATTTAAATTT-AATTT
487724 ATTTAAATTTAATTT
1 ATTTAAATTTAATTT
487739 A
1 A
487740 ATCAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTAAATTTAATTT
Found at i:487797 original size:15 final size:15
Alignment explanation
Indices: 487743--487823 Score: 58
Period size: 15 Copynumber: 5.3 Consensus size: 15
487733 TAATTTAATC
*
487743 AAAAATTAAAAT-TA
1 AAAAATTTAAATATA
487757 AAATAATTTAAACTCA-A
1 AAA-AATTTAAA-T-ATA
*
487774 AATAATTTAAATATA
1 AAAAATTTAAATATA
*
487789 AAAAATTTAAACTCTA
1 AAAAATTTAAA-TATA
* * *
487805 AAAAGTGTGAATATA
1 AAAAATTTAAATATA
487820 AAAA
1 AAAA
487824 TATGCATGCC
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
14 4 0.08
15 26 0.49
16 20 0.38
17 3 0.06
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.30
Consensus pattern (15 bp):
AAAAATTTAAATATA
Found at i:487799 original size:31 final size:32
Alignment explanation
Indices: 487746--487807 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
487736 TTTAATCAAA
487746 AATTAAAATTAAAATAATTTAAACTC-AAAAT
1 AATTAAAATTAAAATAATTTAAACTCTAAAAT
*
487777 AATTTAAATATAAAA-AATTTAAACTCTAAAA
1 AATTAAAAT-TAAAATAATTTAAACTCTAAAA
487808 AGTGTGAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 19 0.68
32 9 0.32
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (32 bp):
AATTAAAATTAAAATAATTTAAACTCTAAAAT
Found at i:487806 original size:16 final size:16
Alignment explanation
Indices: 487743--487808 Score: 68
Period size: 16 Copynumber: 4.2 Consensus size: 16
487733 TAATTTAATC
*
487743 AAAAA-TTAAAAT-TA
1 AAAAATTTAAACTCTA
487757 AAATAATTTAAACTC-A
1 AAA-AATTTAAACTCTA
*
487773 AAATAATTTAAA-TATA
1 AAA-AATTTAAACTCTA
487789 AAAAATTTAAACTCTA
1 AAAAATTTAAACTCTA
487805 AAAA
1 AAAA
487809 GTGTGAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
14 3 0.07
15 11 0.25
16 30 0.68
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAATTTAAACTCTA
Found at i:487818 original size:31 final size:31
Alignment explanation
Indices: 487751--487823 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
487741 TCAAAAATTA
*
487751 AAAT-TAAAATAATTTAAACTCAAAATAATTT
1 AAATATAAAA-AATTTAAACTCAAAATAATGT
*
487782 AAATATAAAAAATTTAAACTCTAAAA-AGTGT
1 AAATATAAAAAATTTAAACTC-AAAATAATGT
*
487813 GAATATAAAAA
1 AAATATAAAAA
487824 TATGCATGCC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 28 0.76
32 9 0.24
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.30
Consensus pattern (31 bp):
AAATATAAAAAATTTAAACTCAAAATAATGT
Found at i:500173 original size:23 final size:21
Alignment explanation
Indices: 500140--500226 Score: 70
Period size: 21 Copynumber: 4.1 Consensus size: 21
500130 ACAAAAAAAA
* *
500140 TTTGTCTAAGTCATTTCGTTTCT
1 TTTGTCCAAGTCATTTC-TCT-T
*
500163 TTTGTCCAAGTTATTTCTCTT
1 TTTGTCCAAGTCATTTCTCTT
***
500184 TTTGTCCAAGTTGCTTCTCTT
1 TTTGTCCAAGTCATTTCTCTT
* *
500205 TTTGT-CAACTCACTTC-CTT
1 TTTGTCCAAGTCATTTCTCTT
500224 TTT
1 TTT
500227 TCCTTGTGAG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
19 6 0.11
20 8 0.14
21 25 0.45
22 2 0.04
23 15 0.27
ACGTcount: A:0.13, C:0.22, G:0.10, T:0.55
Consensus pattern (21 bp):
TTTGTCCAAGTCATTTCTCTT
Found at i:500188 original size:21 final size:21
Alignment explanation
Indices: 500162--500226 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
500152 ATTTCGTTTC
*
500162 TTTTGTCCAAGTTATTTCTCT
1 TTTTGTCCAAGTTACTTCTCT
*
500183 TTTTGTCCAAGTTGCTTCTCT
1 TTTTGTCCAAGTTACTTCTCT
* *
500204 TTTTGT-CAACTCACTTC-CT
1 TTTTGTCCAAGTTACTTCTCT
500223 TTTT
1 TTTT
500227 TCCTTGTGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 6 0.15
20 8 0.21
21 25 0.64
ACGTcount: A:0.12, C:0.23, G:0.09, T:0.55
Consensus pattern (21 bp):
TTTTGTCCAAGTTACTTCTCT
Found at i:502316 original size:20 final size:20
Alignment explanation
Indices: 502293--502348 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
502283 AAGTACCCAG
**
502293 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCATCA
* * *
502313 ATGTGTCGATACATGCATGA
1 ATGTATCGATACATTCATCA
502333 ATGTATCGATACATTC
1 ATGTATCGATACATTC
502349 TGTATTTTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTCATCA
Found at i:506782 original size:12 final size:12
Alignment explanation
Indices: 506767--506796 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
506757 GCTATTGATG
506767 AAGCTATTCCAT
1 AAGCTATTCCAT
506779 AAGCTATTCCAT
1 AAGCTATTCCAT
506791 AAGCTA
1 AAGCTA
506797 ATTGTCCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (12 bp):
AAGCTATTCCAT
Found at i:512227 original size:22 final size:22
Alignment explanation
Indices: 512165--512216 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
512155 ATCAATCGTT
**
512165 TTTCTCCCCCTTAATCAAAAAA
1 TTTCTCCCCCTTAATCAAAGCA
512187 TTTCTCCCCCTTAATCAAAGCA
1 TTTCTCCCCCTTAATCAAAGCA
512209 TTTCTCCC
1 TTTCTCCC
512217 TCTTTGTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.27, C:0.37, G:0.02, T:0.35
Consensus pattern (22 bp):
TTTCTCCCCCTTAATCAAAGCA
Found at i:512275 original size:73 final size:74
Alignment explanation
Indices: 512186--512332 Score: 278
Period size: 73 Copynumber: 2.0 Consensus size: 74
512176 TAATCAAAAA
*
512186 ATTTCTCCCCCTTAATCAAAGCATTTCTCCCTCTTTGTCAAATCTT-AAAAATTTATTTTCAATA
1 ATTTCTCCCCCTTAATCAAAGCATTTCTCCCCCTTTGTCAAATCTTAAAAAATTTATTTTCAATA
512250 AAAATATTT
66 AAAATATTT
512259 ATTTCTCCCCCTTAATCAAAGCATTTCTCCCCCTTTGTCAAATCTTAAAAAATTTATTTTCAATA
1 ATTTCTCCCCCTTAATCAAAGCATTTCTCCCCCTTTGTCAAATCTTAAAAAATTTATTTTCAATA
512324 AAAATATTT
66 AAAATATTT
512333 CTCCCCCTTT
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
73 45 0.62
74 27 0.38
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.41
Consensus pattern (74 bp):
ATTTCTCCCCCTTAATCAAAGCATTTCTCCCCCTTTGTCAAATCTTAAAAAATTTATTTTCAATA
AAAATATTT
Found at i:514591 original size:13 final size:13
Alignment explanation
Indices: 514573--514598 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
514563 CATTTTGGAA
514573 TGTATCGATACAT
1 TGTATCGATACAT
514586 TGTATCGATACAT
1 TGTATCGATACAT
514599 CTTGTGTGTA
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:514716 original size:13 final size:13
Alignment explanation
Indices: 514698--514722 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
514688 ACATTTGGTC
514698 ATGTATCGATACA
1 ATGTATCGATACA
514711 ATGTATCGATAC
1 ATGTATCGATAC
514723 TGTGCAATCT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:519325 original size:21 final size:19
Alignment explanation
Indices: 519288--519329 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
519278 GAATCATGTA
*
519288 AATTCTTGTTTTTTTAGCT
1 AATTCTTATTTTTTTAGCT
519307 AATTCATTATTTTTATTAGCT
1 AATTC-TTATTTTT-TTAGCT
519328 AA
1 AA
519330 CTTTTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
21 8 0.40
ACGTcount: A:0.26, C:0.10, G:0.07, T:0.57
Consensus pattern (19 bp):
AATTCTTATTTTTTTAGCT
Found at i:521316 original size:12 final size:12
Alignment explanation
Indices: 521299--521339 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
521289 TCCTCTATAT
521299 AAAAAAATAAAA
1 AAAAAAATAAAA
* **
521311 AAAAAACTAAGG
1 AAAAAAATAAAA
521323 AAAAAAATAAAA
1 AAAAAAATAAAA
521335 AAAAA
1 AAAAA
521340 TAGAAAGGAG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.85, C:0.02, G:0.05, T:0.07
Consensus pattern (12 bp):
AAAAAAATAAAA
Found at i:521347 original size:25 final size:24
Alignment explanation
Indices: 521299--521348 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
521289 TCCTCTATAT
*
521299 AAAAAAATAAAAAAAAAACTAAGG
1 AAAAAAATAAAAAAAAAACAAAGG
*
521323 AAAAAAATAAAAAAAAATAGAAAGG
1 AAAAAAATAAAAAAAAA-ACAAAGG
521348 A
1 A
521349 GTCCAGATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.80, C:0.02, G:0.10, T:0.08
Consensus pattern (24 bp):
AAAAAAATAAAAAAAAAACAAAGG
Found at i:522503 original size:28 final size:28
Alignment explanation
Indices: 522438--523338 Score: 1041
Period size: 28 Copynumber: 31.4 Consensus size: 28
522428 TGTTCATCTC
* *
522438 TTCAAAGCCCAAAAGTTAGTGGCACCCCT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCCT
*
522467 TTCAAAGCTCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
522495 TTCAAAGCTCACAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
522523 TTCAAAGCCCACAACTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * *
522552 TTCAAAGCCCACAAGTTAGTGGCATCAT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
522580 TTCAAAGCCCACACGAGTC-GATGGCAACTCCT
1 TTCAAAGCCCACA--AGTCAG-TGGC-AC-CCT
* *
522612 TTCAAAGCCCACGAGTCAGTGGCAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGC-AC-CCT
*
522642 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
522670 TTCAAAGCCCACAAGTCAGTGACACCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
522698 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
522726 TTCAAAACCCACAAGTCAGTAGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
522754 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
522782 TTCAATGCCCACGAGTCAGTGGCAACTCCT
1 TTCAAAGCCCACAAGTCAGTGGC-AC-CCT
* *
522812 TTCAATGCCCACGAA-TCAGTGGCAACTCTT
1 TTCAAAGCCCAC-AAGTCAGTGGC-AC-CCT
* *
522842 TTCAAAGCCCACGAGTCAGTGGCAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGC-AC-CCT
* * *
522872 TTCAAAGCCCACGAGTCAGTGACACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
522901 TTCAAAGCCCACAACTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
522929 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
522957 TTTAAAGCCCACAAGTCAGTAGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
*
522986 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
523014 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
523042 TTCAAAGTCCACACAAGTCAGTGGCACCTT
1 TTCAAAG-CC-CACAAGTCAGTGGCACCCT
* *
523072 TTCAAAGCCCACAAGTCAGTGGCAATCTT
1 TTCAAAGCCCACAAGTCAGTGGC-ACCCT
* * * *
523101 TTCAAAGCCCATAAGTCATTAGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
523130 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
523158 TTCAAAGCCAAGAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
523186 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * * * *
523215 TTCAACGCCTACAAGTTAGTAGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
523243 TTCAAAGTCCACAAGTTAGTGGTACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
523271 TTCAAAGCCTACAAGTAAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
523299 TTCAAAGCCCACAGGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
523328 TTCAAAGCCCA
1 TTCAAAGCCCA
523339 TAAGCTAGTT
Statistics
Matches: 760, Mismatches: 94, Indels: 36
0.85 0.11 0.04
Matches are distributed among these distances:
28 412 0.54
29 186 0.24
30 145 0.19
31 3 0.00
32 14 0.02
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:522555 original size:57 final size:57
Alignment explanation
Indices: 522438--523434 Score: 1066
Period size: 57 Copynumber: 17.2 Consensus size: 57
522428 TGTTCATCTC
* * *
522438 TTCAAAGCCCAAAAGTTAGTGGCACCCCTTTCAAAGCTCACAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * *
522495 TTCAAAGCTCACAAGTCAATGGCACCCTTTCAAAGCCCACAACTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * *
522552 TTCAAAGCCCACAAGTTAGTGGCATCATTTCAAAGCCCACACGAGTC-GATGGCAACTCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACA--AGTCAG-TGGC-ACTCCT
* *
522612 TTCAAAGCCCACGAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGC-AC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* *
522670 TTCAAAGCCCACAAGTCAGTGACACCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * *
522726 TTCAAAACCCACAAGTCAGTAGCATCCTTTCAAAGCCCACAAGTTAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * *
522782 TTCAATGCCCACGAGTCAGTGGCAACTCCTTTCAATGCCCACGAA-TCAGTGGCAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGC-AC-CCTTTCAAAGCCCAC-AAGTCAGTGGC-ACTCCT
* * * * *
522842 TTCAAAGCCCACGAGTCAGTGGCAACTCTTTTCAAAGCCCACGAGTCAGTGACACTCTT
1 TTCAAAGCCCACAAGTCAGTGGC-AC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* *
522901 TTCAAAGCCCACAACTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * *
522957 TTTAAAGCCCACAAGTCAGTAGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
*
523014 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGTCCACACAAGTCAGTGGCAC-CTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGCACTCCT
* * * * * *
523072 TTCAAAGCCCACAAGTCAGTGGCAATCTTTTCAAAGCCCATAAGTCATTAGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGC-ACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * *
523130 TTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCAAGAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * * *
523186 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAACGCCTACAAGTTAGTAGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * * *
523243 TTCAAAGTCCACAAGTTAGTGGTACCCTTTCAAAGCCTACAAGTAAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * *** *
523299 TTCAAAGCCCACAGGTCAGTGGCACTCTTTTCAAAGCCCATAAG-CTAGTTATAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTC-AG-TGGCACTCCT
* * * * *
523358 TTCAAAGCCCACACGAGTCGGTGGCAACTCTTTTCAAAGCCCACACGAGTCGGTAGCAACTCTT
1 TTCAAAGCCCACA--AGTCAGTGGC-AC-CCTTTCAAAGCCCACA--AGTCAGTGGC-ACTCCT
523422 TTCAAAGCCCACA
1 TTCAAAGCCCACA
523435 CAAGTTAGTG
Statistics
Matches: 803, Mismatches: 100, Indels: 67
0.83 0.10 0.07
Matches are distributed among these distances:
56 229 0.29
57 241 0.30
58 118 0.15
59 64 0.08
60 83 0.10
61 10 0.01
62 33 0.04
63 2 0.00
64 22 0.03
65 1 0.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (57 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
Found at i:522583 original size:85 final size:85
Alignment explanation
Indices: 522438--523449 Score: 1138
Period size: 85 Copynumber: 11.6 Consensus size: 85
522428 TGTTCATCTC
* * * * * *
522438 TTCAAAGCCCAAAAGTTAGTGGCACCCCTTTCAAAGCTCACAAGTCAGTGGCACCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
* *
522503 TCACAAGTCAATGGCACCCT
66 CCACAAGTCAGTGGCACCCT
* * *
522523 TTCAAAGCCCACAACTCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCATCATTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
522588 CCACACGAGTC-GATGGCAACTCCT
66 CCACA--AGTCAG-TGGC-AC-CCT
*
522612 TTCAAAGCCCACGAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGC-ACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAG
* *
522677 CCCACAAGTCAGTGACACCTT
65 CCCACAAGTCAGTGGCACCCT
* * *
522698 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAACCCACAAGTCAGTAGCATCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
* *
522762 CCACAAGTTAGTGGCATCCT
66 CCACAAGTCAGTGGCACCCT
* * * * *
522782 TTCAATGCCCACGAGTCAGTGGCAACTCCTTTCAATGCCCACGAA-TCAGTGGCAACTCTTTTCA
1 TTCAAAGCCCACAAGTCAGTGGC-ACTCTTTTCAAAGCCCAC-AAGTCAGTGGC-A-TCCTTTCA
* *
522846 AAGCCCACGAGTCAGTGGCAACTCTT
62 AAGCCCACAAGTCAGTGGC-AC-CCT
* * *
522872 TTCAAAGCCCACGAGTCAGTGACACTCTTTTCAAAGCCCACAACTCAGTGGCATCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
522937 CCACAAGTCAGTGGCACCCT
66 CCACAAGTCAGTGGCACCCT
* *
522957 TTTAAAGCCCACAAGTCAGTAGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
523022 CCACAAGTCAGTGGCACCCT
66 CCACAAGTCAGTGGCACCCT
*
523042 TTCAAAGTCCACACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCAATCTTTTCAA
1 TTCAAAG-CC-CACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGC-ATCCTTTCAA
* * * *
523106 AGCCCATAAGTCATTAGCACTCTT
63 AGCCCACAAGTCAGTGGCAC-CCT
* * * * *
523130 TTCAAAGCCCACAAGTTAGTGGCA-TCCTTTCAAAGCCAAGAAGTCAGTGGCACCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
*
523194 CCACAAGTCAGTGGCACTCTT
66 CCACAAGTCAGTGGCAC-CCT
* * * * * * * * *
523215 TTCAACGCCTACAAGTTAGTAGCA-TCCTTTCAAAGTCCACAAGTTAGTGGTACCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
* *
523279 CTACAAGTAAGTGGCACCCT
66 CCACAAGTCAGTGGCACCCT
* * *** *
523299 TTCAAAGCCCACAGGTCAGTGGCACTCTTTTCAAAGCCCATAAG-CTAGTTATAACTCTTTTCAA
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTC-AG-TGGCA-TCCTTTCAA
* *
523363 AGCCCACACGAGTCGGTGGCAACTCTT
63 AGCCCACA--AGTCAGTGGC-AC-CCT
* * *
523390 TTCAAAGCCCACACGAGTCGGTAGCAACTCTTTTCAAAGCCCACACAAGTTAGTGGCATC
1 TTCAAAGCCCACA--AGTCAGTGGC-ACTCTTTTCAAAG-CC-CACAAGTCAGTGGCATC
523450 TTTGTTTAAA
Statistics
Matches: 793, Mismatches: 100, Indels: 59
0.83 0.11 0.06
Matches are distributed among these distances:
84 94 0.12
85 270 0.34
86 113 0.14
87 95 0.12
88 45 0.06
89 58 0.07
90 70 0.09
91 15 0.02
93 7 0.01
94 15 0.02
95 4 0.01
96 7 0.01
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (85 bp):
TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
CCACAAGTCAGTGGCACCCT
Found at i:523582 original size:45 final size:47
Alignment explanation
Indices: 523521--523631 Score: 127
Period size: 49 Copynumber: 2.4 Consensus size: 47
523511 ATTGCTAGCA
* *
523521 TTGAATCAGCATATTGG-CACCTTT-ATTAGCCCAATGTCATTGGCC
1 TTGAATCAGCACATTGGCCACCTTTCATTAGCCCAATGTCACTGGCC
* * *
523566 TTGAATCAGCACATTGGTCCACTTTTCCCTTAGCCCAATGTCGCTGGCC
1 TTGAATCAGCACATTGG-CCACCTTT-CATTAGCCCAATGTCACTGGCC
**
523615 TTGAATTGGCACATTGG
1 TTGAATCAGCACATTGG
523632 TACTCCTCTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
45 16 0.29
47 6 0.11
49 33 0.60
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (47 bp):
TTGAATCAGCACATTGGCCACCTTTCATTAGCCCAATGTCACTGGCC
Found at i:524621 original size:20 final size:20
Alignment explanation
Indices: 524596--524663 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
524586 TACCCAGATT
524596 TATCGATACATTTTTCAATG
1 TATCGATACATTTTTCAATG
* * *
524616 TATCGATACATGTATGAATG
1 TATCGATACATTTTTCAATG
* *
524636 TATCGATACATTCTTCAATT
1 TATCGATACATTTTTCAATG
524656 TATCGATA
1 TATCGATA
524664 TATTCCATCT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (20 bp):
TATCGATACATTTTTCAATG
Found at i:525641 original size:22 final size:23
Alignment explanation
Indices: 525616--525662 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
525606 TTTTAATATG
525616 TCCAGCATTTAATTGAATG-TTA
1 TCCAGCATTTAATTGAATGATTA
* * *
525638 TCCATCATTTCATTGTATGATTA
1 TCCAGCATTTAATTGAATGATTA
525661 TC
1 TC
525663 ACATATTCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.45
Consensus pattern (23 bp):
TCCAGCATTTAATTGAATGATTA
Found at i:535062 original size:24 final size:24
Alignment explanation
Indices: 535030--535077 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
535020 AGATATATAC
535030 ATATATATATATATAATGCAAAAA
1 ATATATATATATATAATGCAAAAA
* * *
535054 ATATGTATATTTATAATGCGAAAA
1 ATATATATATATATAATGCAAAAA
535078 TATTAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.35
Consensus pattern (24 bp):
ATATATATATATATAATGCAAAAA
Found at i:537685 original size:64 final size:64
Alignment explanation
Indices: 537603--538128 Score: 308
Period size: 64 Copynumber: 8.3 Consensus size: 64
537593 GGTTAAACTC
* * *
537603 TTTTGACTTGTTCGGAAAGAGACAAGTTTGAC-TTTGAACTTATAT-TGAAAGACACAGGTTCAA
1 TTTTGACTTGTTCAGAAAGAGACAAGTTTGACTTTTG-ACTTAT-TCAGAAAGATACAGGTTCAA
537666 A
64 A
* * ** * * * * *
537667 TTTTGAATTGTTCAGAAAGAGATAAGTTTGACTCCTCACCTATTCAAAAAAATATAGGTTCAACA
1 TTTTGACTTGTTCAGAAAGAGACAAGTTTGACTTTTGACTTATTCAGAAAGATACAGGTTCAA-A
* * * * * **
537732 -TTTGACTTATTTAGAATGAAACAAGTTTGACTTTTGACCTATTCAGAAAGATACAGGTTTGAA
1 TTTTGACTTGTTCAGAAAGAGACAAGTTTGACTTTTGACTTATTCAGAAAGATACAGGTTCAAA
* * * * * ** **
537795 TTTTAACTTGTTTAAAAAGAGACAAGTTTGACTTTTAACTTATTCAAAAAGATACAACTTC-GT
1 TTTTGACTTGTTCAGAAAGAGACAAGTTTGACTTTTGACTTATTCAGAAAGATACAGGTTCAAA
* * * *
537858 TTTTGACTTGTTCAGAACGAGA-AAGTTTGACTTTTGACTTATT-TGAAA-AAACAAGGGTCCAA
1 TTTTGACTTGTTCAGAAAGAGACAAGTTTGACTTTTGACTTATTCAGAAAGATAC-A-GGTTCAA
537920 A
64 A
* * ** * * * * *
537921 TTTTGAGTAGTTCATTAATATACAAGTTTGACTTTTGACTTATAT-AGAAA-AGCACAAGTCCAA
1 TTTTGACTTGTTCAGAAAGAGACAAGTTTGACTTTTGACTTAT-TCAGAAAGA-TACAGGTTCAA
537984 A
64 A
* * * * * * * * *
537985 TTTTGACTTGTTCAAAAAGAGATAAAG-TTAACTTTTAACCTATT-TGAAA-AAACATG-TCTAT
1 TTTTGACTTGTTCAGAAAGAGA-CAAGTTTGACTTTTGACTTATTCAGAAAGATACAGGTTC-AA
538046 A
64 A
* * * * * * * * *
538047 TTTTGACTTGTT-TGAAAGGGGACAAGTTTGAGTTTTGAGC-TATTTAAAAAAACATAGGTCCAA
1 TTTTGACTTGTTCAGAAA-GAGACAAGTTTGACTTTTGA-CTTATTCAGAAAGATACAGGTTCAA
538110 A
64 A
*
538111 TTTTGACTTGTTTAGAAA
1 TTTTGACTTGTTCAGAAA
538129 AAAAAAATAG
Statistics
Matches: 351, Mismatches: 92, Indels: 37
0.73 0.19 0.08
Matches are distributed among these distances:
60 3 0.01
61 11 0.03
62 55 0.16
63 45 0.13
64 218 0.62
65 17 0.05
66 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (64 bp):
TTTTGACTTGTTCAGAAAGAGACAAGTTTGACTTTTGACTTATTCAGAAAGATACAGGTTCAAA
Found at i:537896 original size:31 final size:32
Alignment explanation
Indices: 537602--537900 Score: 147
Period size: 32 Copynumber: 9.4 Consensus size: 32
537592 GGGTTAAACT
* **
537602 CTTTTGACTTGTTCGGAAAGAGACAAGTTTGA
1 CTTTTGACTTATTCAAAAAGAGACAAGTTTGA
** * * **
537634 C-TTTGAACTTATAT-TGAAAGACACAGGTTCAA
1 CTTTTG-ACTTAT-TCAAAAAGAGACAAGTTTGA
* * * * *
537666 ATTTTGAATTGTTCAGAAAGAGATAAGTTTGA
1 CTTTTGACTTATTCAAAAAGAGACAAGTTTGA
** * * * * * * **
537698 CTCCTCACCTATTCAAAAAAATATAGGTTCAA
1 CTTTTGACTTATTCAAAAAGAGACAAGTTTGA
* * * * *
537730 CATTTGACTTATTTAGAATGAAACAAGTTTGA
1 CTTTTGACTTATTCAAAAAGAGACAAGTTTGA
* * * *
537762 CTTTTGACCTATTCAGAAAGATACAGGTTTGA
1 CTTTTGACTTATTCAAAAAGAGACAAGTTTGA
* * * *
537794 ATTTTAACTTGTTTAAAAAGAGACAAGTTTGA
1 CTTTTGACTTATTCAAAAAGAGACAAGTTTGA
* * * *
537826 CTTTTAACTTATTCAAAAAGATACAACTTCG-
1 CTTTTGACTTATTCAAAAAGAGACAAGTTTGA
* * * *
537857 TTTTTGACTTGTTCAGAACGAGA-AAGTTTGA
1 CTTTTGACTTATTCAAAAAGAGACAAGTTTGA
537888 CTTTTGACTTATT
1 CTTTTGACTTATT
537901 TGAAAAAACA
Statistics
Matches: 190, Mismatches: 72, Indels: 11
0.70 0.26 0.04
Matches are distributed among these distances:
30 5 0.03
31 33 0.17
32 147 0.77
33 5 0.03
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (32 bp):
CTTTTGACTTATTCAAAAAGAGACAAGTTTGA
Found at i:538072 original size:126 final size:131
Alignment explanation
Indices: 537942--538189 Score: 321
Period size: 126 Copynumber: 1.9 Consensus size: 131
537932 TCATTAATAT
* *
537942 ACAAGTTTGACTTTTGA-CTTATATAGAAAAGCACAAGTCCAAATTTTGACTTGTTCA-AAAAGA
1 ACAAGTTTGACTTTTGAGC-TATATAAAAAAACACAAGTCCAAATTTTGACTTGTTCAGAAAA-A
* * *
538005 GATAA-A-G-TTAACTTTTAACCTATTTGAAAAAACAT-G-TCTATATTTTGACTTGTTTGAAAG
64 AAAAATAGGTTTAACTTTTAACCTATTTGAAAAAACATAGATCTAAATTTTGACTTGTTTGAAAG
538065 GGG
129 GGG
* * * * *
538068 ACAAGTTTGAGTTTTGAGCTATTTAAAAAAACATAGGTCCAAATTTTGACTTGTTTAGAAAAAAA
1 ACAAGTTTGACTTTTGAGCTATATAAAAAAACACAAGTCCAAATTTTGACTTGTTCAGAAAAAAA
* *
538133 AAATAGGTTTTACTTTTAACCTATTTGAAAAGACATAGATCTAAATTTTGACTTGTT
66 AAATAGGTTTAACTTTTAACCTATTTGAAAAAACATAGATCTAAATTTTGACTTGTT
538190 CAAAAGGATA
Statistics
Matches: 103, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
126 52 0.50
127 6 0.06
128 1 0.01
129 26 0.25
130 1 0.01
131 17 0.17
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (131 bp):
ACAAGTTTGACTTTTGAGCTATATAAAAAAACACAAGTCCAAATTTTGACTTGTTCAGAAAAAAA
AAATAGGTTTAACTTTTAACCTATTTGAAAAAACATAGATCTAAATTTTGACTTGTTTGAAAGGG
G
Found at i:538179 original size:67 final size:63
Alignment explanation
Indices: 537944--538189 Score: 194
Period size: 67 Copynumber: 3.8 Consensus size: 63
537934 ATTAATATAC
* * * * * *
537944 AAGTTTGACTTTTGACTTATATAGAAAAGCACA-AGTCCAAATTTTGACTTG-TTCAAAAAGAGA
1 AAGTTTGACTTTTAACCTAT-TTGAAAA-AACATAGTCTAAATTTTGACTTGTTTGAAAAA-A-A
*
538007 TA
62 AA
* * **** *
538009 AAG-TTAACTTTTAACCTATTTGAAAAAACAT-GTCTATATTTTGACTTGTTTGAAAGGGGAC
1 AAGTTTGACTTTTAACCTATTTGAAAAAACATAGTCTAAATTTTGACTTGTTTGAAAAAAAAA
* * * * *
538070 AAGTTTGAGTTTTGAGCTATTTAAAAAAACATAGGTCCAAATTTTGACTTGTTTAGAAAAAAAAA
1 AAGTTTGACTTTTAACCTATTTGAAAAAACATA-GTCTAAATTTTGACTTGTTT-GAAAAAAAAA
* *
538135 ATAGGTTTTACTTTTAACCTATTTGAAAAGACATAGATCTAAATTTTGACTTGTT
1 A-A-GTTTGACTTTTAACCTATTTGAAAAAACATAG-TCTAAATTTTGACTTGTT
538190 CAAAAGGATA
Statistics
Matches: 139, Mismatches: 33, Indels: 16
0.74 0.18 0.09
Matches are distributed among these distances:
61 3 0.02
62 41 0.29
63 11 0.08
64 31 0.22
65 9 0.06
66 2 0.01
67 42 0.30
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.37
Consensus pattern (63 bp):
AAGTTTGACTTTTAACCTATTTGAAAAAACATAGTCTAAATTTTGACTTGTTTGAAAAAAAAA
Found at i:543008 original size:21 final size:20
Alignment explanation
Indices: 542957--543013 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
542947 GAATATTCGT
* *
542957 GTGTAGTATCGATACATAGG
1 GTGTGGTATCGATACATAGC
*
542977 GTGTGGTATCGATACCTAGC
1 GTGTGGTATCGATACATAGC
*
542997 GTGATTGTATCGATACA
1 GTG-TGGTATCGATACA
543014 AACCTTAGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (20 bp):
GTGTGGTATCGATACATAGC
Found at i:545677 original size:80 final size:80
Alignment explanation
Indices: 545544--545711 Score: 223
Period size: 80 Copynumber: 2.1 Consensus size: 80
545534 CTTTCACCTT
* * * * * *
545544 ATTTTTACTTTCAAAACATTGAATTTTTCATCTTCGAGGATCTTCCAATCCCACCATCTTCGAG-
1 ATTTTTACTTCCAAAACACTGAATTTTTCATCTCCAAGAATCTTCCAACCCCACCATCTTCGAGA
*
545608 GGAATACTTCAACCCC
66 GG-ATACTCCAACCCC
545624 ATTTTTACTTCCAAAACACTGAATTTTTCATCTCCAAGAATAC-TCCAACCCCACCATCTTCGAG
1 ATTTTTACTTCCAAAACACTGAATTTTTCATCTCCAAGAAT-CTTCCAACCCCACCATCTTCGAG
* *
545688 AGGATACTCCAATCCT
65 AGGATACTCCAACCCC
545704 ATTTTTAC
1 ATTTTTAC
545712 ACTAAAATTT
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
80 74 0.96
81 3 0.04
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (80 bp):
ATTTTTACTTCCAAAACACTGAATTTTTCATCTCCAAGAATCTTCCAACCCCACCATCTTCGAGA
GGATACTCCAACCCC
Found at i:548650 original size:68 final size:68
Alignment explanation
Indices: 548541--548673 Score: 248
Period size: 68 Copynumber: 2.0 Consensus size: 68
548531 GCTTACTAGT
* *
548541 AGAAATGACTAAGTAGGGTGGCTGATATTAAATGCTATGGTGGCTGGCTAGTGCTCAGGAATGGA
1 AGAAATGAATAAGTAGGGTGGCTGATATTAAATGCTATGGTGGCTAGCTAGTGCTCAGGAATGGA
548606 AGC
66 AGC
548609 AGAAATGAATAAGTAGGGTGGCTGATATTAAATGCTATGGTGGCTAGCTAGTGCTCAGGAATGGA
1 AGAAATGAATAAGTAGGGTGGCTGATATTAAATGCTATGGTGGCTAGCTAGTGCTCAGGAATGGA
548674 TAGGGTGCTA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.31, C:0.11, G:0.33, T:0.26
Consensus pattern (68 bp):
AGAAATGAATAAGTAGGGTGGCTGATATTAAATGCTATGGTGGCTAGCTAGTGCTCAGGAATGGA
AGC
Found at i:551409 original size:11 final size:11
Alignment explanation
Indices: 551389--551425 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
551379 AATTTTTCTA
551389 TTTTTGAAAAT
1 TTTTTGAAAAT
*
551400 TTTTTTAAAAT
1 TTTTTGAAAAT
551411 TTTTCTGAAAAT
1 TTTT-TGAAAAT
551423 TTT
1 TTT
551426 GAAAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (11 bp):
TTTTTGAAAAT
Found at i:551414 original size:12 final size:12
Alignment explanation
Indices: 551389--551425 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
551379 AATTTTTCTA
551389 TTTTTGAAAATT
1 TTTTTGAAAATT
551401 TTTTT-AAAATT
1 TTTTTGAAAATT
*
551412 TTTCTGAAAATT
1 TTTTTGAAAATT
551424 TT
1 TT
551426 GAAAAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (12 bp):
TTTTTGAAAATT
Found at i:552829 original size:17 final size:19
Alignment explanation
Indices: 552802--552840 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
552792 AAAAAGTCAT
552802 AAAAATGAATA-AAAAAAG
1 AAAAATGAATAGAAAAAAG
*
552820 AAAAAT-AATAGAAATAAG
1 AAAAATGAATAGAAAAAAG
552838 AAA
1 AAA
552841 CAGCTTTCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (19 bp):
AAAAATGAATAGAAAAAAG
Found at i:557377 original size:52 final size:52
Alignment explanation
Indices: 557299--557420 Score: 226
Period size: 52 Copynumber: 2.3 Consensus size: 52
557289 CGAAATATGA
557299 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
**
557351 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
557403 AAATTTGCCTGCATGTAT
1 AAATTTGCCTGCATGTAT
557421 TGTCGTAACG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
Found at i:560572 original size:52 final size:52
Alignment explanation
Indices: 560487--560611 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
560477 ATATGAAAAG
* *
560487 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
560539 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
560591 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
560612 AAGATCAGTG
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:560624 original size:52 final size:51
Alignment explanation
Indices: 560487--560631 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
560477 ATATGAAAAG
*
560487 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
560539 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
560591 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
560632 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:560726 original size:13 final size:13
Alignment explanation
Indices: 560708--560732 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
560698 CAAAAAAATA
560708 TGTATCGATACAT
1 TGTATCGATACAT
560721 TGTATCGATACA
1 TGTATCGATACA
560733 ACATTTTATG
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:560728 original size:33 final size:33
Alignment explanation
Indices: 560686--560752 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
560676 AGTAGCTTAA
560686 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
560719 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
560752 A
1 A
560753 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:561095 original size:13 final size:13
Alignment explanation
Indices: 561077--561101 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
561067 CAAAGATCAG
561077 TGTATCGATACAA
1 TGTATCGATACAA
561090 TGTATCGATACA
1 TGTATCGATACA
561102 TTTAAGTGAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:561193 original size:13 final size:13
Alignment explanation
Indices: 561175--561199 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
561165 TGTATCGAGA
561175 TGTATCGATACAT
1 TGTATCGATACAT
561188 TGTATCGATACA
1 TGTATCGATACA
561200 ACACTTTATG
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:562092 original size:156 final size:156
Alignment explanation
Indices: 561901--562317 Score: 480
Period size: 155 Copynumber: 2.7 Consensus size: 156
561891 ATTTTAGTAA
* * * ** * *
561901 TTTTCTTAAAACCGAGTCCTAGGTTATCACCAGGTCTGTTTTTATGCCGAAGGTGGGTATTTAAG
1 TTTTC-TAGAACCAAGTCCTAGGTTGTCACCAGGTC-AATTTTATGCCAAAGGTGGGTATTTAGG
* * *
561966 ATAGGTTCATCTCATCTATAATCCTTTTCAGGTCCTTTAGGGGTATCAAGTATTTCTACGTCAAA
64 ATAGGTTCATCTCATCTATAATTCTTTTCAAGTCCTTTAGGGGTACCAAGTATTTCTACGTCAAA
* *
562031 AGTACCCTCTAAGGGCGTTTTCATAA-T
129 ACTACCCTCTAAGGGCATTTTCATAATT
* * ** **
562058 TTTTCTAGAACCAAGTCCTAGGTTGTCACTAGGTCCACTTTTATGCCAAATTTGGACATTTAGGA
1 TTTTCTAGAACCAAGTCCTAGGTTGTCACCAGGT-CAATTTTATGCCAAAGGTGGGTATTTAGGA
* * * * * *
562123 TAGGTTCATCTCATTTATAATTCTTTTTATGT-CTTTAGGGGTACCAGGTATTTCTATGTCGAAA
65 TAGGTTCATCTCATCTATAATTCTTTTCAAGTCCTTTAGGGGTACCAAGTATTTCTACGTCAAAA
* * *
562187 CTATCCTTTAAGGGCATTTTTATAATT
130 CTACCCTCTAAGGGCATTTTCATAATT
* * *
562214 TTTTCT-GAATCAAGTCTTAGGTTGTCACCGAGTTCAATTTTATGCCAAAGGTGGGTATTTAGGA
1 TTTTCTAGAACCAAGTCCTAGGTTGTCACC-AGGTCAATTTTATGCCAAAGGTGGGTATTTAGGA
* * *
562278 TAGGTTCATCCCATCTATAATTCTTTCCAAGTCCTCTAGG
65 TAGGTTCATCTCATCTATAATTCTTTTCAAGTCCTTTAGG
562318 ATCTCCGGGT
Statistics
Matches: 216, Mismatches: 40, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
155 120 0.56
156 90 0.42
157 6 0.03
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (156 bp):
TTTTCTAGAACCAAGTCCTAGGTTGTCACCAGGTCAATTTTATGCCAAAGGTGGGTATTTAGGAT
AGGTTCATCTCATCTATAATTCTTTTCAAGTCCTTTAGGGGTACCAAGTATTTCTACGTCAAAAC
TACCCTCTAAGGGCATTTTCATAATT
Found at i:563852 original size:2 final size:2
Alignment explanation
Indices: 563847--563879 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
563837 TTTAAAAATG
563847 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
563880 TTAATCTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:564594 original size:140 final size:141
Alignment explanation
Indices: 564333--564611 Score: 488
Period size: 140 Copynumber: 2.0 Consensus size: 141
564323 TTGTAATTAG
*
564333 AGATTACGGAGGGTTGATGGTCGGGGGCCCTTCGGTTATCATTAATAGATTACATGATGCCACCA
1 AGATTACGGAGGGTTGATGGTCGGGGGCCCTTCGGTTATCATTAATAGAGTACATGATG-C-CCA
*
564398 TTTCAGATGCAATGGCAGCAGTCAAAGCTCTAGAGGTTTCTGCACAAGCACAGATGGGCTATGGG
64 TTTCAGATGCAATGGCAGCAGTCAAAGCTCTAGAGGTTTCTGCACAAGCACAGATGGGCTATGAG
564463 CGAATCGTCTTAC
129 CGAATCGTCTTAC
* *
564476 AGATTACGGAGGGTTGATGGTCGGGGGCCCTTTGGTTATTATTAATAGAGTACATGATG-CCATT
1 AGATTACGGAGGGTTGATGGTCGGGGGCCCTTCGGTTATCATTAATAGAGTACATGATGCCCATT
*
564540 TCAGATGCAATGGCAGCAGTCAAAGCTCTAGAGGTTTCTTCACAAGCACAGATGGGCTATGAGCG
66 TCAGATGCAATGGCAGCAGTCAAAGCTCTAGAGGTTTCTGCACAAGCACAGATGGGCTATGAGCG
564605 AATCGTC
131 AATCGTC
564612 CTTAGGAGGC
Statistics
Matches: 131, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
140 75 0.57
143 56 0.43
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (141 bp):
AGATTACGGAGGGTTGATGGTCGGGGGCCCTTCGGTTATCATTAATAGAGTACATGATGCCCATT
TCAGATGCAATGGCAGCAGTCAAAGCTCTAGAGGTTTCTGCACAAGCACAGATGGGCTATGAGCG
AATCGTCTTAC
Found at i:564936 original size:18 final size:18
Alignment explanation
Indices: 564915--564959 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
564905 TAATTCGTAT
564915 TATATTAATTTTA-ATTTA
1 TATATTAATTTTATA-TTA
*
564933 TATATTTATTTTATATTA
1 TATATTAATTTTATATTA
*
564951 TATTTTAAT
1 TATATTAAT
564960 AATTTTATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TATATTAATTTTATATTA
Found at i:565545 original size:16 final size:15
Alignment explanation
Indices: 565520--565549 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
565510 AATAAAATAT
565520 TTAAATAAATTATAC
1 TTAAATAAATTATAC
565535 TTAATATAAATTATA
1 TTAA-ATAAATTATA
565550 AAATATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAAATAAATTATAC
Found at i:567343 original size:25 final size:24
Alignment explanation
Indices: 567294--567347 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
567284 TTAATTTTTA
*
567294 AAAATATTATTTTGTGATGATAAT
1 AAAATATTATTTTGTAATGATAAT
*
567318 ATAAATATTATTTTTTAAT-ATAAAT
1 A-AAATATTATTTTGTAATGAT-AAT
567343 AAAAT
1 AAAAT
567348 TTTAAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (24 bp):
AAAATATTATTTTGTAATGATAAT
Found at i:567349 original size:19 final size:19
Alignment explanation
Indices: 567314--567350 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
567304 TTTGTGATGA
**
567314 TAATATAAATATTATTTTT
1 TAATATAAATAAAATTTTT
567333 TAATATAAATAAAATTTT
1 TAATATAAATAAAATTTT
567351 AAACAAATAT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATATAAATAAAATTTTT
Found at i:567623 original size:29 final size:32
Alignment explanation
Indices: 567562--567625 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
567552 ATTTTATCAA
* *
567562 TATTTTTTTAACTAGTATATATCTTATTTAAT
1 TATTTTTTTAACTAGTATATATCATATTAAAT
*
567594 TATTTTTTTAAGTA-TATATAT-ATA-TAAAT
1 TATTTTTTTAACTAGTATATATCATATTAAAT
567623 TAT
1 TAT
567626 ATACATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 7 0.24
30 2 0.07
31 7 0.24
32 13 0.45
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (32 bp):
TATTTTTTTAACTAGTATATATCATATTAAAT
Found at i:567628 original size:15 final size:15
Alignment explanation
Indices: 567608--567639 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
567598 TTTTTAAGTA
*
567608 TATATATATATAAAT
1 TATATACATATAAAT
567623 TATATACATATAAAT
1 TATATACATATAAAT
567638 TA
1 TA
567640 AATTTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
TATATACATATAAAT
Found at i:568505 original size:13 final size:15
Alignment explanation
Indices: 568472--568519 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
568462 TGTAATGAAA
568472 TATATTTATATATAT
1 TATATTTATATATAT
* *
568487 TATATTTATGTATTT
1 TATATTTATATATAT
* * *
568502 TATTTTTTTATAAAT
1 TATATTTATATATAT
568517 TAT
1 TAT
568520 CACGTCATCC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TATATTTATATATAT
Found at i:569237 original size:13 final size:13
Alignment explanation
Indices: 569221--569271 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
569211 ATAAGAATCG
*
569221 AAAATAATTATTA
1 AAAATAATTAATA
569234 AAAAT-ATTAAATA
1 AAAATAATT-AATA
569247 AAAATATATATAATA
1 AAAATA-AT-TAATA
569262 ATAAATAATT
1 A-AAATAATT
569272 TAAAATTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
12 3 0.09
13 13 0.41
14 1 0.03
15 9 0.28
16 6 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAAATAATTAATA
Found at i:569329 original size:13 final size:14
Alignment explanation
Indices: 569302--569340 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
569292 AATTATGTTT
569302 ATATTAAATAATAAA
1 ATATTAAA-AATAAA
569317 ATA-TAAAAATAAA
1 ATATTAAAAATAAA
*
569330 TTATTAAAAAT
1 ATATTAAAAAT
569341 TATATTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 8 0.36
14 11 0.50
15 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATATTAAAAATAAA
Found at i:569342 original size:63 final size:66
Alignment explanation
Indices: 569237--569358 Score: 180
Period size: 63 Copynumber: 1.9 Consensus size: 66
569227 ATTATTAAAA
*
569237 ATATTAAATAAAAATATATATAATAATAAATAATTTAAAATTATATTTA-ACTAAAAATTATGTT
1 ATATTAAATAAAAATATATATAATAATAAATAATTAAAAATTATATTTATACTAAAAATTATGTT
569301 T
66 T
* *
569302 ATATTAAATAATAAA-ATATA-AA-AATAAATTATTAAAAATTATATTTATATTAAAAAT
1 ATATTAAATAA-AAATATATATAATAATAAATAATTAAAAATTATATTTATACTAAAAAT
569359 AAATTAATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
63 23 0.44
64 10 0.19
65 16 0.31
66 3 0.06
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (66 bp):
ATATTAAATAAAAATATATATAATAATAAATAATTAAAAATTATATTTATACTAAAAATTATGTT
T
Found at i:569382 original size:63 final size:62
Alignment explanation
Indices: 569244--569385 Score: 153
Period size: 63 Copynumber: 2.3 Consensus size: 62
569234 AAAATATTAA
* * * * ** *
569244 ATAAAAATATATATAATAATAAATAATTTAAAATTATATTTAACTAAAAATTATGTTTATAT
1 ATAAATATAAATATAAAAATAAATAATTAAAAATTATATTTAACTAAAAATTAAATTAATAT
* *
569306 -TAAATAATAAAATATAAAAATAAATTATTAAAAATTATATTTATATTAAAAA-TAAATTAATAA
1 ATAAAT-AT-AAATATAAAAATAAATAATTAAAAATTATATTTA-ACTAAAAATTAAATTAAT-A
569369 T
62 T
569370 ATAAATATAAATATAA
1 ATAAATATAAATATAA
569386 TAAAAAGTAG
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
61 4 0.06
62 2 0.03
63 44 0.67
64 11 0.17
65 5 0.08
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.39
Consensus pattern (62 bp):
ATAAATATAAATATAAAAATAAATAATTAAAAATTATATTTAACTAAAAATTAAATTAATAT
Found at i:570793 original size:15 final size:16
Alignment explanation
Indices: 570757--570796 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
570747 TTTAATGTTT
*
570757 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
570774 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
570789 ATAAAATT
1 ATAAAATT
570797 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:570799 original size:16 final size:17
Alignment explanation
Indices: 570757--570799 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
570747 TTTAATGTTT
*
570757 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
570774 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
570789 ATAAAATTTAT
1 ATAAAATTTAT
570800 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:571741 original size:17 final size:19
Alignment explanation
Indices: 571719--571754 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
571709 ATACTACTTT
571719 AAATAT-ACA-AAAAATAA
1 AAATATGACATAAAAATAA
571736 AAATATGACATAAAAATAA
1 AAATATGACATAAAAATAA
571755 TTAAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 3 0.18
19 8 0.47
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (19 bp):
AAATATGACATAAAAATAA
Found at i:571763 original size:22 final size:22
Alignment explanation
Indices: 571727--571779 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
571717 TTAAATATAC
*
571727 AAAA-AATAAAAATATGACATA
1 AAAATAATAAAAATATAACATA
* *
571748 AAAATAATTAAAATATAATATA
1 AAAATAATAAAAATATAACATA
571770 AAAATGAATA
1 AAAAT-AATA
571780 TGACACGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 4 0.15
22 19 0.73
23 3 0.12
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (22 bp):
AAAATAATAAAAATATAACATA
Found at i:572161 original size:15 final size:15
Alignment explanation
Indices: 572141--572196 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
572131 TATAAATATT
*
572141 TTTTTCTTTATTTCC
1 TTTTTCTTTTTTTCC
572156 TTTTTCTTTTTTTCTC
1 TTTTTCTTTTTTTC-C
* *
572172 TTTCTTTTTTTTTTCT
1 TTT-TTCTTTTTTTCC
572188 TTTTTCTTT
1 TTTTTCTTT
572197 GTTCTTTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
15 18 0.51
16 7 0.20
17 10 0.29
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTCTTTTTTTCC
Found at i:572173 original size:25 final size:24
Alignment explanation
Indices: 572139--572192 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
572129 TATATAAATA
572139 TTTTTTTCTTTATTTCCTTTTTCT
1 TTTTTTTCTTTATTTCCTTTTTCT
* **
572163 TTTTTTCTCTTTCTTTTTTTTTTCT
1 TTTTTT-TCTTTATTTCCTTTTTCT
572188 TTTTT
1 TTTTT
572193 CTTTGTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTTTTTCTTTATTTCCTTTTTCT
Found at i:572207 original size:4 final size:4
Alignment explanation
Indices: 572143--572227 Score: 74
Period size: 4 Copynumber: 22.8 Consensus size: 4
572133 TAAATATTTT
* * * *
572143 TTTC TTTA TTTC CTT- TTTC TTT- TTT- TCTC TTTC TTT- TTTT TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
* *
572187 TTT- TTTC TTT- GTTC TTTC TTTC TTTC TTTA TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
572228 TTTGGCTGAA
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
3 15 0.23
4 50 0.77
ACGTcount: A:0.02, C:0.18, G:0.01, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:574305 original size:22 final size:22
Alignment explanation
Indices: 574279--574322 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
574269 TAAAAATTTT
* * *
574279 ATATTTTTTTAATTATTGATTA
1 ATATTTATTTAATCATTAATTA
574301 ATATTTATTTAATCATTAATTA
1 ATATTTATTTAATCATTAATTA
574323 CTAAAATCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
ATATTTATTTAATCATTAATTA
Found at i:574989 original size:12 final size:11
Alignment explanation
Indices: 574971--575024 Score: 65
Period size: 12 Copynumber: 4.8 Consensus size: 11
574961 ATGTTAATGT
574971 TTATATTTATA
1 TTATATTTATA
574982 TCTATATTTATA
1 T-TATATTTATA
574994 TTATTATTTATA
1 TTA-TATTTATA
*
575006 ATATATTTA-A
1 TTATATTTATA
*
575016 TTAAATTTA
1 TTATATTTA
575025 GTATCACGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
10 8 0.21
11 9 0.24
12 21 0.55
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TTATATTTATA
Found at i:575002 original size:24 final size:22
Alignment explanation
Indices: 574974--575018 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
574964 TTAATGTTTA
*
574974 TATTTATATCTATATTTATATTAT
1 TATTTATA-ATATATTTA-ATTAT
574998 TATTTATAATATATTTAATTA
1 TATTTATAATATATTTAATTA
575019 AATTTAGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 8 0.40
24 8 0.40
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTATAATATATTTAATTAT
Found at i:575544 original size:28 final size:26
Alignment explanation
Indices: 575512--575578 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
575502 ATATTTTATA
* *
575512 ATTAAATTTAAATAAAATTTTTTTAATT
1 ATTAAATATAAAT-AAA-GTTTTTAATT
**
575540 ATTAAATATAAATTTAGTTTTTAATT
1 ATTAAATATAAATAAAGTTTTTAATT
575566 ATTAAATATAAAT
1 ATTAAATATAAAT
575579 TCAAGTTGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 22 0.63
27 1 0.03
28 12 0.34
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (26 bp):
ATTAAATATAAATAAAGTTTTTAATT
Found at i:576952 original size:19 final size:20
Alignment explanation
Indices: 576916--576953 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
576906 TAATTATATA
*
576916 TTTTTTATTCTCCTTTTTTC
1 TTTTTTATTCTCCATTTTTC
*
576936 TTTTTT-TTCTTCATTTTT
1 TTTTTTATTCTCCATTTTT
576954 TATTTAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTATTCTCCATTTTTC
Found at i:576952 original size:20 final size:20
Alignment explanation
Indices: 576916--576954 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
576906 TAATTATATA
*
576916 TTTTTTATTCTCCTTTTTTC
1 TTTTTTATTCTCATTTTTTC
576936 TTTTTT-TTCTTCATTTTTT
1 TTTTTTATTC-TCATTTTTT
576955 ATTTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTATTCTCATTTTTTC
Found at i:577119 original size:49 final size:49
Alignment explanation
Indices: 577051--577162 Score: 172
Period size: 49 Copynumber: 2.3 Consensus size: 49
577041 AGTTACTATA
* * *
577051 TAATTAAATTAAATATAAGTTTAAAATATTTAGCATGCATAATATAACT
1 TAATTAAATTTAATATAAGTTTAAAATATTAAGCATGCAAAATATAACT
577100 TAATTAGAATTTAAT-TAAGTTTAAAATATTAAGCATGCAAAATATAACT
1 TAATTA-AATTTAATATAAGTTTAAAATATTAAGCATGCAAAATATAACT
577149 TAATTAAAATTTAA
1 TAATT-AAATTTAA
577163 CAGTAATTAA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
49 50 0.86
50 8 0.14
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.38
Consensus pattern (49 bp):
TAATTAAATTTAATATAAGTTTAAAATATTAAGCATGCAAAATATAACT
Found at i:582421 original size:2 final size:2
Alignment explanation
Indices: 582414--582439 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
582404 CCTTCTCCTC
582414 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
582440 GTCCCTTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:586588 original size:10 final size:10
Alignment explanation
Indices: 586573--586634 Score: 52
Period size: 11 Copynumber: 5.7 Consensus size: 10
586563 TTAATTTTAT
586573 AATAATTAAA
1 AATAATTAAA
586583 AATAATTTTAAA
1 AATAA--TTAAA
* *
586595 ATTAAATATAA
1 AATAATTA-AA
586606 AATCAATTAAA
1 AAT-AATTAAA
*
586617 AATGAATAAAA
1 AAT-AATTAAA
586628 AATAATT
1 AATAATT
586635 TTTCTATTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
10 10 0.24
11 18 0.44
12 13 0.32
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (10 bp):
AATAATTAAA
Found at i:586963 original size:2 final size:2
Alignment explanation
Indices: 586956--586989 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
586946 AAAACTCATA
586956 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
586990 GTGTGTGTGT
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:598499 original size:32 final size:33
Alignment explanation
Indices: 598440--598503 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
598430 ACAAGTCAAT
*
598440 GTATCGATAAATTTTATGATGTATCGATACAAC
1 GTATCGATAAATATTATGATGTATCGATACAAC
* *
598473 GTATCGATACATATTGTG-TGTATCGATACAA
1 GTATCGATAAATATTATGATGTATCGATACAA
598504 GTTTGGCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
GTATCGATAAATATTATGATGTATCGATACAAC
Found at i:598614 original size:20 final size:20
Alignment explanation
Indices: 598589--598639 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
598579 ATCAATACAA
*
598589 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * *
598609 TGTATCGATACATTTAAATG
1 TGTATCGATACAATGAAATC
598629 TGTATCGATAC
1 TGTATCGATAC
598640 TTTTCAGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:600613 original size:20 final size:21
Alignment explanation
Indices: 600574--600626 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
600564 GCTGCTAGTG
*
600574 TGGGGGCTGCTCGGTTGCGACC
1 TGGGGG-TGCTCGGTCGCGACC
600596 TGGGGGTGC-CGGTCGCGACC
1 TGGGGGTGCTCGGTCGCGACC
600616 TGGTGGGTGCT
1 TGG-GGGTGCT
600627 GCCTAAGAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 13 0.46
21 9 0.32
22 6 0.21
ACGTcount: A:0.04, C:0.25, G:0.49, T:0.23
Consensus pattern (21 bp):
TGGGGGTGCTCGGTCGCGACC
Found at i:601077 original size:13 final size:13
Alignment explanation
Indices: 601059--601096 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
601049 TATAATCCCT
* *
601059 TGTATCGATATAG
1 TGTATCGATACAA
601072 TGTATCGATACAA
1 TGTATCGATACAA
601085 TGTATCGATACA
1 TGTATCGATACA
601097 GAGAATGCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:604508 original size:13 final size:13
Alignment explanation
Indices: 604490--604515 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
604480 TACACCAATT
604490 ATGTATCGATACA
1 ATGTATCGATACA
604503 ATGTATCGATACA
1 ATGTATCGATACA
604516 CCAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:604534 original size:34 final size:32
Alignment explanation
Indices: 604472--604536 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
604462 TAGCCAAACT
**
604472 TGTATCGATACACCAATTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
604504 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
604537 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.29
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:608594 original size:15 final size:15
Alignment explanation
Indices: 608576--608614 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
608566 TAAAAATGTC
608576 CAAAAT-AAGGAAGCT
1 CAAAATGAA-GAAGCT
608591 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
608606 CCAAATGAA
1 CAAAATGAA
608615 ATTGATGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.54, C:0.15, G:0.18, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:610598 original size:20 final size:20
Alignment explanation
Indices: 610555--610601 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
610545 AAATCTTTTG
610555 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
610576 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
610596 CAAAAT
1 CAAAAT
610602 CAGCTTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:612918 original size:20 final size:22
Alignment explanation
Indices: 612895--612949 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
612885 ACAATTCAAA
* *
612895 GTATCGATACATGTTG-CA-AT
1 GTATCGATACATGTAGAAATAT
612915 GTATCGATACATG-AGAAATAT
1 GTATCGATACATGTAGAAATAT
612936 GTATCGATACATGT
1 GTATCGATACATGT
612950 CATTGGGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 14 0.47
21 15 0.50
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.33
Consensus pattern (22 bp):
GTATCGATACATGTAGAAATAT
Found at i:613015 original size:13 final size:13
Alignment explanation
Indices: 612997--613022 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
612987 TACACCAAGT
612997 ATGTATCGATACA
1 ATGTATCGATACA
613010 ATGTATCGATACA
1 ATGTATCGATACA
613023 CCAAAAAAAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:614769 original size:13 final size:13
Alignment explanation
Indices: 614751--614777 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
614741 ACATTTTATG
614751 ATGTATCGATACA
1 ATGTATCGATACA
614764 ATGTATCGATACA
1 ATGTATCGATACA
614777 A
1 A
614778 GTTTGGCTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:614856 original size:20 final size:21
Alignment explanation
Indices: 614809--614861 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
614799 GCCAATGACT
**
614809 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
614830 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
614850 TGTATCGATACA
1 TGTATCGATACA
614862 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:614867 original size:13 final size:13
Alignment explanation
Indices: 614849--614877 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
614839 ACATTTGGTC
614849 ATGTATCGATACA
1 ATGTATCGATACA
614862 ATGTATCGATACA
1 ATGTATCGATACA
614875 ATG
1 ATG
614878 CAATCTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:614888 original size:20 final size:20
Alignment explanation
Indices: 614863--614913 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
614853 ATCGATACAA
*
614863 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * *
614883 TGTATCGATACATTTAAATG
1 TGTATCGATACAATGAAATC
614903 TGTATCGATAC
1 TGTATCGATAC
614914 TTTTCAGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:623647 original size:20 final size:21
Alignment explanation
Indices: 623600--623652 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
623590 GCCAATGACT
**
623600 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
623621 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
623641 TGTATCGATACA
1 TGTATCGATACA
623653 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:623658 original size:13 final size:13
Alignment explanation
Indices: 623640--623668 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
623630 ACATTTGGTC
623640 ATGTATCGATACA
1 ATGTATCGATACA
623653 ATGTATCGATACA
1 ATGTATCGATACA
623666 ATG
1 ATG
623669 CAATCTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:623679 original size:20 final size:20
Alignment explanation
Indices: 623654--623704 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
623644 ATCGATACAA
*
623654 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * *
623674 TGTATCGATACATTTAAATG
1 TGTATCGATACAATGAAATC
623694 TGTATCGATAC
1 TGTATCGATAC
623705 TTTTCAGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:625322 original size:12 final size:12
Alignment explanation
Indices: 625305--625334 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
625295 AGTCAACTTC
625305 ATCATCATCATT
1 ATCATCATCATT
*
625317 ATCATCATCTTT
1 ATCATCATCATT
625329 ATCATC
1 ATCATC
625335 TTTGATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (12 bp):
ATCATCATCATT
Found at i:632659 original size:52 final size:52
Alignment explanation
Indices: 632589--632709 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
632579 GAAAATTTAT
*
632589 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
632641 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
632693 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
632710 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:632722 original size:52 final size:51
Alignment explanation
Indices: 632589--632729 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
632579 GAAAATTTAT
632589 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
632641 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
632693 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
632730 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:632736 original size:13 final size:13
Alignment explanation
Indices: 632718--632742 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
632708 CAAAGATCAG
632718 TGTATCGATACAA
1 TGTATCGATACAA
632731 TGTATCGATACA
1 TGTATCGATACA
632743 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:632824 original size:13 final size:13
Alignment explanation
Indices: 632806--632830 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
632796 ACAAAAAATA
632806 TGTATCGATACAT
1 TGTATCGATACAT
632819 TGTATCGATACA
1 TGTATCGATACA
632831 ACATTTTATG
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:632826 original size:32 final size:33
Alignment explanation
Indices: 632785--632850 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
632775 AGTAGCTTAA
632785 ATTGTATCGATACAA-AAAATATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
***
632817 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
632850 A
1 A
632851 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAACAAAATATGTATCGATAC
Found at i:638909 original size:19 final size:19
Alignment explanation
Indices: 638857--638916 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
638847 GGAGAAGATA
638857 GAGATAATTGTTTAAGGGG
1 GAGATAATTGTTTAAGGGG
* * *
638876 GAGA-ATTTTTTTAAGGAG
1 GAGATAATTGTTTAAGGGG
*
638894 GAGATAATCGTTTAAGGGG
1 GAGATAATTGTTTAAGGGG
638913 GAGA
1 GAGA
638917 ATTTTTGAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.33, C:0.02, G:0.35, T:0.30
Consensus pattern (19 bp):
GAGATAATTGTTTAAGGGG
Found at i:639526 original size:21 final size:19
Alignment explanation
Indices: 639479--639533 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
639469 TTTGTATCAT
*
639479 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
639498 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
639517 ACAAATTGTATCGATAC
1 AC--ATTGTATCGATAC
639534 GTGAAACTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 18 0.58
21 13 0.42
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:639602 original size:13 final size:13
Alignment explanation
Indices: 639581--639611 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
639571 CGATACATGG
*
639581 TACAATGTATCGA
1 TACATTGTATCGA
639594 TACATTGTATCGA
1 TACATTGTATCGA
639607 TACAT
1 TACAT
639612 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:639612 original size:33 final size:32
Alignment explanation
Indices: 639565--639631 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
639555 CTATCATTAT
*
639565 TTGTTTCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
639598 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
639631 T
1 T
639632 AGCTTGTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:644091 original size:20 final size:20
Alignment explanation
Indices: 644062--644113 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
644052 TATTGATACT
*
644062 TATCAGTACATTCACAAATG
1 TATCAATACATTCACAAATG
* **
644082 TATCTATACATTCACTCATG
1 TATCAATACATTCACAAATG
644102 TATCAATACATT
1 TATCAATACATT
644114 TGTGTCTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.37
Consensus pattern (20 bp):
TATCAATACATTCACAAATG
Found at i:655159 original size:25 final size:25
Alignment explanation
Indices: 655109--655155 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
655099 AACAAAAAAG
*
655109 TAATAAAATATTAATAATATAATAA
1 TAATAAAATAGTAATAATATAATAA
655134 TAATAAAATAGTAATAAT-TAAT
1 TAATAAAATAGTAATAATATAAT
655156 TAATTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (25 bp):
TAATAAAATAGTAATAATATAATAA
Found at i:655425 original size:25 final size:25
Alignment explanation
Indices: 655396--655447 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
655386 ATGCTTTTAC
655396 TTTCATGCATATTTTCA-TGCATGCA
1 TTTCATGCA-ATTTTCATTGCATGCA
* *
655421 TTTCATGTAATTTTCATTTCATGCA
1 TTTCATGCAATTTTCATTGCATGCA
655446 TT
1 TT
655448 ATATTTCATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (25 bp):
TTTCATGCAATTTTCATTGCATGCA
Found at i:655443 original size:29 final size:29
Alignment explanation
Indices: 655408--655563 Score: 123
Period size: 29 Copynumber: 5.6 Consensus size: 29
655398 TCATGCATAT
*
655408 TTTCATGCATGCATTTCATGTAATTTTCA
1 TTTCATGCATGCATTTCACGTAATTTTCA
** * * *
655437 TTTCATGCATTATATTTCATG-CA-TTACA
1 TTTCATGCA-TGCATTTCACGTAATTTTCA
*
655465 TTTCATGCATGCATTTCACATAATTTTCA
1 TTTCATGCATGCATTTCACGTAATTTTCA
*
655494 -TT--T-CATGCATTTCA--TACA-TTACA
1 TTTCATGCATGCATTTCACGTA-ATTTTCA
* * *
655517 TTTCATGCATGCATGTCACCTAATGTTCA
1 TTTCATGCATGCATTTCACGTAATTTTCA
*
655546 TTTCATGCATGCTTTTCA
1 TTTCATGCATGCATTTCA
655564 AAAACATTTC
Statistics
Matches: 100, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
23 6 0.06
24 3 0.03
25 11 0.11
26 2 0.02
27 17 0.17
28 17 0.17
29 35 0.35
30 9 0.09
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.45
Consensus pattern (29 bp):
TTTCATGCATGCATTTCACGTAATTTTCA
Found at i:655508 original size:14 final size:14
Alignment explanation
Indices: 655396--655508 Score: 76
Period size: 14 Copynumber: 8.1 Consensus size: 14
655386 ATGCTTTTAC
*
655396 TTTCATGCATAT--
1 TTTCATGCATTTCA
*
655408 TTTCATGCA-TGCA
1 TTTCATGCATTTCA
*
655421 TTTCATGTAATTTTCA
1 TTTCATG-CA-TTTCA
655437 TTTCATGCATTAT-A
1 TTTCATGCATT-TCA
*
655451 TTTCATGCATTACA
1 TTTCATGCATTTCA
*
655465 TTTCATGCA-TGCA
1 TTTCATGCATTTCA
*
655478 TTTCACAT-AATTTTCA
1 TTT--CATGCA-TTTCA
655494 TTTCATGCATTTCA
1 TTTCATGCATTTCA
655508 T
1 T
655509 ACATTACATT
Statistics
Matches: 79, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
12 9 0.11
13 13 0.16
14 35 0.44
15 6 0.08
16 16 0.20
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.48
Consensus pattern (14 bp):
TTTCATGCATTTCA
Found at i:655515 original size:52 final size:52
Alignment explanation
Indices: 655408--655555 Score: 197
Period size: 52 Copynumber: 2.8 Consensus size: 52
655398 TCATGCATAT
** *
655408 TTTCATGCATGCATTTCATGTAATTTTCATTTCATGCATTATATTTCATGCATTACA
1 TTTCATGCATGCATTTCACATAATTTTCATTTCATGC-----ATTTCATACATTACA
655465 TTTCATGCATGCATTTCACATAATTTTCATTTCATGCATTTCATACATTACA
1 TTTCATGCATGCATTTCACATAATTTTCATTTCATGCATTTCATACATTACA
* * *
655517 TTTCATGCATGCATGTCACCTAATGTTCATTTCATGCAT
1 TTTCATGCATGCATTTCACATAATTTTCATTTCATGCAT
655556 GCTTTTCAAA
Statistics
Matches: 85, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
52 50 0.59
57 35 0.41
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.45
Consensus pattern (52 bp):
TTTCATGCATGCATTTCACATAATTTTCATTTCATGCATTTCATACATTACA
Found at i:655601 original size:15 final size:13
Alignment explanation
Indices: 655580--655613 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
655570 TTTCATGCAT
655580 TGCATTGCATTTCA
1 TGCATTGC-TTTCA
655594 TAGCATTGCTTTCA
1 T-GCATTGCTTTCA
655608 TGCATT
1 TGCATT
655614 AAAGCTACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 7 0.37
15 7 0.37
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.44
Consensus pattern (13 bp):
TGCATTGCTTTCA
Found at i:656433 original size:15 final size:15
Alignment explanation
Indices: 656413--656448 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
656403 CAGCAGAATC
656413 GAAAAGAAAAAGAAA
1 GAAAAGAAAAAGAAA
* *
656428 GAAAAGAAATAGCAA
1 GAAAAGAAAAAGAAA
656443 GAAAAG
1 GAAAAG
656449 GTCACAACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.72, C:0.03, G:0.22, T:0.03
Consensus pattern (15 bp):
GAAAAGAAAAAGAAA
Found at i:656804 original size:22 final size:22
Alignment explanation
Indices: 656747--656803 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
656737 AAAATATATC
*
656747 AGCAGCAAACG-AAATCAGCAAT
1 AGCAGCAAA-GAAAAGCAGCAAT
656769 AGCAGCAAAGAAAAGCAGCAA-
1 AGCAGCAAAGAAAAGCAGCAAT
656790 A-CAGCAAAGGAAAA
1 AGCAGCAAA-GAAAA
656804 AAAATAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 7 0.22
21 7 0.22
22 18 0.56
ACGTcount: A:0.56, C:0.19, G:0.21, T:0.04
Consensus pattern (22 bp):
AGCAGCAAAGAAAAGCAGCAAT
Found at i:668716 original size:35 final size:36
Alignment explanation
Indices: 668677--668745 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
668667 TAGATAGTGT
* **
668677 GAAAAAATATTATGTATAAAAAAAAGAA-AAAAAGG
1 GAAAAAATATAAAATATAAAAAAAAGAAGAAAAAGG
668712 GAAAAAATATAAAATATAAAAAAAAGAAGAAAAA
1 GAAAAAATATAAAATATAAAAAAAAGAAGAAAAA
668746 AATTGAACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 25 0.83
36 5 0.17
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (36 bp):
GAAAAAATATAAAATATAAAAAAAAGAAGAAAAAGG
Found at i:670157 original size:42 final size:42
Alignment explanation
Indices: 670098--670885 Score: 347
Period size: 42 Copynumber: 18.8 Consensus size: 42
670088 GCCTACCTTT
* * * * *
670098 AGTCTACCTGTTGGCTTTGACCCTAGAGACTACCTTATCTAA
1 AGTCTGCCTGTCGGCTTTGACCTTAGAGACTTCCTCATCTAA
* * * * * *
670140 AGTCTACCTGTCGGCTTTGACCTTGGAGACTTTCTTACCCTTCA
1 AGTCTGCCTGTCGGCTTTGACCTTAGAGACTTCCTCA-TC-TAA
** * * *
670184 A-TCTGCCTGTCAACTTTGACCTTGGAGACTTTCCT-ACCCT-T
1 AGTCTGCCTGTCGGCTTTGACCTTAGAGAC-TTCCTCA-TCTAA
** * *
670225 AGTCTGCCTGTCAACTTTGACCCTAGAGACTACCTCATCTAA
1 AGTCTGCCTGTCGGCTTTGACCTTAGAGACTTCCTCATCTAA
* * * ** * * * *
670267 AGTTTACCTATCGGCTTTGACCCCAAAGATTTTCCT-ACCCT-T
1 AGTCTGCCTGTCGGCTTTGACCTTAGAGA-CTTCCTCA-TCTAA
* * * * *
670309 AGTCTGCTTGTCGACTTTGACCCTAGAAACTGT-CTCATTTAA
1 AGTCTGCCTGTCGGCTTTGACCTTAGAGACT-TCCTCATCTAA
** * * **
670351 AGTCTGCCTGTTAGCTTTGACCTTGGAGACTTTCTCACTCTTT
1 AGTCTGCCTGTCGGCTTTGACCTTAGAGACTTCCTCA-TCTAA
* * * *
670394 AGTCTGCCTGTCAGCTTTGACCCTAGAGACTGCCTCA-CATCA
1 AGTCTGCCTGTCGGCTTTGACCTTAGAGACTTCCTCATC-TAA
* * ** * * **
670436 AGTCAGCCTGTCGGCATTT-ACCTTGGAGACTTTTTTACCCTTC
1 AGTCTGCCTGTCGGC-TTTGACCTTAGAGACTTCCTCA-TCTAA
* *
670479 AGTCT-CCTTGTCAGCTTTGACCTTAGAGACTACCTCATCTAA
1 AGTCTGCC-TGTCGGCTTTGACCTTAGAGACTTCCTCATCTAA
* * * * **
670521 AGTCTGTCTGTCGGCTTTGACCTTAGAGACTTTCTTACCTTTC
1 AGTCTGCCTGTCGGCTTTGACCTTAGAGACTTCCTCATC-TAA
* * *
670564 ATTCTGCCTATCGGCTTTGACCTT-GAAGACTGCCTCATCTAA
1 AGTCTGCCTGTCGGCTTTGACCTTAG-AGACTTCCTCATCTAA
* * * * * * **
670606 AATTTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTACCCTTC
1 AGTCTGCCTGTCGGCTTTGACCTTAGAGACTTCCTCA-TCTAA
* * * * * *
670649 AGTCTACCTGTCGACTTTGGCCCTGGAGACTACCTCATCTAA
1 AGTCTGCCTGTCGGCTTTGACCTTAGAGACTTCCTCATCTAA
* * * * **
670691 AGTCTGCTTGTCGGCTTTGACCTTAGAGACTTTCTTACCTTTC
1 AGTCTGCCTGTCGGCTTTGACCTTAGAGACTTCCTCATC-TAA
* * * * *
670734 ATTCTGCCTATCAGCTTTGACCCT-GAAGACTGCCTCATCTAA
1 AGTCTGCCTGTCGGCTTTGACCTTAG-AGACTTCCTCATCTAA
* * * * * **
670776 AATCTGCC--T--G---TGACCTTGGAGACTTTCTTACCCTTC
1 AGTCTGCCTGTCGGCTTTGACCTTAGAGACTTCCTCA-TCTAA
**
670812 AGTCTGCCTGTCGGCTTTGA-CTCGGGAGA-TTGCCTCATCTAA
1 AGTCTGCCTGTCGGCTTTGACCT-TAGAGACTT-CCTCATCTAA
* * * *
670854 AGTCTGCTTGTCAGCTTTGACCCTGGAGACTT
1 AGTCTGCCTGTCGGCTTTGACCTTAGAGACTT
670886 TTCAACCTTT
Statistics
Matches: 550, Mismatches: 157, Indels: 77
0.70 0.20 0.10
Matches are distributed among these distances:
35 14 0.03
36 10 0.02
38 2 0.00
40 2 0.00
41 13 0.02
42 298 0.54
43 203 0.37
44 8 0.01
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (42 bp):
AGTCTGCCTGTCGGCTTTGACCTTAGAGACTTCCTCATCTAA
Found at i:670254 original size:85 final size:86
Alignment explanation
Indices: 670140--670886 Score: 640
Period size: 85 Copynumber: 8.9 Consensus size: 86
670130 CCTTATCTAA
* * * ** * * * **
670140 AGTCTACCTGTCGGCTTTGACCTTGGAGACTTTCTTACCCTTCAA-TCTGCCTGTCAACTTTGAC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTACCTCA-TCTTAAAGTCTGCCTGTCGGCTTTGAC
670204 CTTGGAGACTTTCCTACCCTT-
65 CTTGGAGACTTTCCTACCCTTC
** * * *
670225 AGTCTGCCTGTCAACTTTGACCCTAGAGACTACCTCATC-TAAAGTTTACCTATCGGCTTTGACC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTACCTCATCTTAAAGTCTGCCTGTCGGCTTTGACC
**** *
670289 CCAAAGATTTTCCTACCCTT-
66 TTGGAGACTTTCCTACCCTTC
* * * ** **
670309 AGTCTGCTTGTCGACTTTGACCCTAGAAACTGTCTCAT-TTAAAGTCTGCCTGTTAGCTTTGACC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTACCTCATCTTAAAGTCTGCCTGTCGGCTTTGACC
* *
670373 TTGGAGACTTT-CTCACTCTTT
66 TTGGAGACTTTCCT-ACCCTTC
* * * * *
670394 AGTCTGCCTGTCAGCTTTGACCCTAGAGACTGCCTCA-CATCAAGTCAGCCTGTCGGCATTT-AC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTACCTCATCTTAAAGTCTGCCTGTCGGC-TTTGAC
**
670457 CTTGGAGACTTTTTTACCCTTC
65 CTTGGAGACTTTCCTACCCTTC
* * *
670479 AGTCT-CCTTGTCAGCTTTGACCTTAGAGACTACCTCATC-TAAAGTCTGTCTGTCGGCTTTGAC
1 AGTCTGCC-TGTCGGCTTTGACCCTAGAGACTACCTCATCTTAAAGTCTGCCTGTCGGCTTTGAC
* * *
670542 CTTAGAGACTTTCTTACCTTTC
65 CTTGGAGACTTTCCTACCCTTC
* * * * * *
670564 ATTCTGCCTATCGGCTTTGA-CCTTGAAGACTGCCTCATC-TAAAATTTGCCTGTCGGCTTTGAC
1 AGTCTGCCTGTCGGCTTTGACCCTAG-AGACTACCTCATCTTAAAGTCTGCCTGTCGGCTTTGAC
*
670627 CTTGGAGACTTTCTTACCCTTC
65 CTTGGAGACTTTCCTACCCTTC
* * * * *
670649 AGTCTACCTGTCGACTTTGGCCCTGGAGACTACCTCATC-TAAAGTCTGCTTGTCGGCTTTGACC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTACCTCATCTTAAAGTCTGCCTGTCGGCTTTGACC
* * *
670713 TTAGAGACTTTCTTACCTTTC
66 TTGGAGACTTTCCTACCCTTC
* * * * *
670734 ATTCTGCCTATCAGCTTTGACCCT-GAAGACTGCCTCATC-TAAAATCTGCC--T--G---TGAC
1 AGTCTGCCTGTCGGCTTTGACCCTAG-AGACTACCTCATCTTAAAGTCTGCCTGTCGGCTTTGAC
*
670790 CTTGGAGACTTTCTTACCCTTC
65 CTTGGAGACTTTCCTACCCTTC
* ** * * * *
670812 AGTCTGCCTGTCGGCTTTGACTCGGGAGATTGCCTCATC-TAAAGTCTGCTTGTCAGCTTTGACC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTACCTCATCTTAAAGTCTGCCTGTCGGCTTTGACC
*
670876 CTGGAGACTTT
66 TTGGAGACTTT
670887 TCAACCTTTT
Statistics
Matches: 540, Mismatches: 100, Indels: 44
0.79 0.15 0.06
Matches are distributed among these distances:
78 64 0.12
79 1 0.00
80 1 0.00
81 1 0.00
82 1 0.00
83 6 0.01
84 104 0.19
85 351 0.65
86 11 0.02
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.35
Consensus pattern (86 bp):
AGTCTGCCTGTCGGCTTTGACCCTAGAGACTACCTCATCTTAAAGTCTGCCTGTCGGCTTTGACC
TTGGAGACTTTCCTACCCTTC
Found at i:670572 original size:170 final size:170
Alignment explanation
Indices: 670185--670903 Score: 738
Period size: 170 Copynumber: 4.3 Consensus size: 170
670175 TACCCTTCAA
* * * * * *
670185 TCTGCCTGTCAACTTTGACCTTGGAGACTTTCCTACCCTTAGTCTGCCTGTCAACTTTGACCCTA
1 TCTGCTTGTCAGCTTTGACCTTGGAGACTTTCTTACCTTTAGTCTGCCTATCAGCTTTGACCCTA
* * * * **** * *
670250 G-AGACTACCTCATCTAAAGTTTA-CCTATCGGCTTTGACCCCAAAGATTTTCCTACCCTT-AGT
66 GAAGACTGCCTCATCTAAA-ATCAGCCTGTCGGCTTTGACCTTGGAGACTTTCTTACCCTTCAGT
* * * ** *
670312 CTGCTTGTCGACTTTGACCCTAGAAACTGTCTCATTTAAAG
130 CTACCTGTCGACTTTGACCCTAGAGACTACCTCATCTAAAG
* * * *
670353 TCTGCCTGTTAGCTTTGACCTTGGAGACTTTCTCACTCTTTAGTCTGCCTGTCAGCTTTGACCCT
1 TCTGCTTGTCAGCTTTGACCTTGGAGACTTTCTTAC-CTTTAGTCTGCCTATCAGCTTTGACCCT
* * *
670418 AG-AGACTGCCTCA-CATCAAGTCAGCCTGTCGGCATTT-ACCTTGGAGACTTTTTTACCCTTCA
65 AGAAGACTGCCTCATC-TAAAATCAGCCTGTCGGC-TTTGACCTTGGAGACTTTCTTACCCTTCA
*
670480 GTCT-CCTTGTC-AGCTTTGACCTTAGAGACTACCTCATCTAAAG
128 GTCTACC-TGTCGA-CTTTGACCCTAGAGACTACCTCATCTAAAG
* * * *
670523 TCTG-TCTGTCGGCTTTGACCTTAGAGACTTTCTTACCTTTCATTCTGCCTATCGGCTTTGA-CC
1 TCTGCT-TGTCAGCTTTGACCTTGGAGACTTTCTTACCTTT-AGTCTGCCTATCAGCTTTGACCC
* **
670586 TTGAAGACTGCCTCATCTAAAATTTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTACCCTTCAG
64 TAGAAGACTGCCTCATCTAAAATCAGCCTGTCGGCTTTGACCTTGGAGACTTTCTTACCCTTCAG
* *
670651 TCTACCTGTCGACTTTGGCCCTGGAGACTACCTCATCTAAAG
129 TCTACCTGTCGACTTTGACCCTAGAGACTACCTCATCTAAAG
* * *
670693 TCTGCTTGTCGGCTTTGACCTTAGAGACTTTCTTACCTTTCATTCTGCCTATCAGCTTTGACCCT
1 TCTGCTTGTCAGCTTTGACCTTGGAGACTTTCTTACCTTT-AGTCTGCCTATCAGCTTTGACCCT
*
670758 -GAAGACTGCCTCATCTAAAAT----CTG-C--CTGTGACCTTGGAGACTTTCTTACCCTTCAGT
65 AGAAGACTGCCTCATCTAAAATCAGCCTGTCGGCTTTGACCTTGGAGACTTTCTTACCCTTCAGT
* * * ** * *
670815 CTGCCTGTCGGCTTTGACTCGGGAGATTGCCTCATCTAAAG
130 CTACCTGTCGACTTTGACCCTAGAGACTACCTCATCTAAAG
* * *
670856 TCTGCTTGTCAGCTTTGACCCTGGAGACTTT-TCAACCTTTTGTCTGCC
1 TCTGCTTGTCAGCTTTGACCTTGGAGACTTTCT-TACCTTTAGTCTGCC
670904 CGTTGGCTTT
Statistics
Matches: 478, Mismatches: 56, Indels: 40
0.83 0.10 0.07
Matches are distributed among these distances:
162 7 0.01
163 99 0.21
165 1 0.00
166 3 0.01
168 35 0.07
169 78 0.16
170 247 0.52
171 8 0.02
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.35
Consensus pattern (170 bp):
TCTGCTTGTCAGCTTTGACCTTGGAGACTTTCTTACCTTTAGTCTGCCTATCAGCTTTGACCCTA
GAAGACTGCCTCATCTAAAATCAGCCTGTCGGCTTTGACCTTGGAGACTTTCTTACCCTTCAGTC
TACCTGTCGACTTTGACCCTAGAGACTACCTCATCTAAAG
Found at i:670624 original size:127 final size:128
Alignment explanation
Indices: 670111--670884 Score: 458
Period size: 127 Copynumber: 6.1 Consensus size: 128
670101 CTACCTGTTG
* * * *
670111 GCTTTGACCCTAGAGACTACCTTATCTAAAGTCTACCTGTCGGCTTTGACCTTGGAGACTTTCTT
1 GCTTTGACCTTAGAGACTACCTCATCTAAAGTCTACCTGTCGGCTTTGACCCTAGAGACTTTCTT
* * * * *
670176 ACCCTTCAATCTGCCTGTCAACTTTGACCTTGGAGACTTTCCT-ACCCT-TAGTCTGCCTGTCA
66 ACCCTTCAGTCTGCCTGTCGACTTTGACCTTGAAGAC-TGCCTCACCCTAAAGTCTGCCTGTCA
* * * * * * * *
670238 ACTTTGACCCTAGAGACTACCTCATCTAAAGTTTACCTATCGGCTTTGACCCCAAAGATTTTCCT
1 GCTTTGACCTTAGAGACTACCTCATCTAAAGTCTACCTGTCGGCTTTGACCCTAGAGACTTTCTT
* * * ** *
670303 ACCCTT-AGTCTGCTTGTCGACTTTGACCCTAGAA-ACTGTCTCA-TTTAAAGTCTGCCTGTTA
66 ACCCTTCAGTCTGCCTGTCGACTTTGA-CCTTGAAGACTGCCTCACCCTAAAGTCTGCCTGTCA
* ** ** * * * *
670364 GCTTTGACCTTGGAGACTTTCTCACTCTTTAGTCTGCCTGTCAGCTTTGACCCTAGAGAC-TGCC
1 GCTTTGACCTTAGAGACTACCTCA-TCTAAAGTCTACCTGTCGGCTTTGACCCTAGAGACTTTCT
* * * * * *** * **
670428 T-CACATCAAGTCAGCCTGTCGGCATTT-ACCTTGGAGACTTTTTTACCCTTCAGTCT-CCTTGT
65 TACCCTTC-AGTCTGCCTGTCGAC-TTTGACCTTGAAGACTGCCTCACCCTAAAGTCTGCC-TGT
670490 CA
127 CA
** *
670492 GCTTTGACCTTAGAGACTACCTCATCTAAAGTCTGTCTGTCGGCTTTGACCTTAGAGACTTTCTT
1 GCTTTGACCTTAGAGACTACCTCATCTAAAGTCTACCTGTCGGCTTTGACCCTAGAGACTTTCTT
* * * * * * * *
670557 ACCTTTCATTCTGCCTATCGGCTTTGACCTTGAAGACTGCCTCA-TCTAAAATTTGCCTGTCG
66 ACCCTTCAGTCTGCCTGTCGACTTTGACCTTGAAGACTGCCTCACCCTAAAGTCTGCCTGTCA
* ** * * ** * * * **
670619 GCTTTGACCTTGGAGACTTTCTTACCCTTCAGTCTACCTGTCGACTTTGGCCCTGGAGACTACCT
1 GCTTTGACCTTAGAGACTACCTCA-TCTAAAGTCTACCTGTCGGCTTTGACCCTAGAGACTTTCT
* * ** * * ** * * ** * *
670684 CA-TCTAAAGTCTGCTTGTCGGCTTTGACCTT-AGAGACTTTCTTACCTTTCATTCTGCCTATCA
65 TACCCTTCAGTCTGCCTGTCGACTTTGACCTTGA-AGACTGCCTCACCCTAAAGTCTGCCTGTCA
* * * * * *
670747 GCTTTGACCCT-GAAGACTGCCTCATCTAAA----ATCTG-C--CTGTGACCTTGGAGACTTTCT
1 GCTTTGACCTTAG-AGACTACCTCATCTAAAGTCTACCTGTCGGCTTTGACCCTAGAGACTTTCT
* * * * * *
670804 TACCCTTCAGTCTGCCTGTCGGCTTTGA-CTCGGGAGATTGCCTCA-TCTAAAGTCTGCTTGTCA
65 TACCCTTCAGTCTGCCTGTCGACTTTGACCT-TGAAGACTGCCTCACCCTAAAGTCTGCCTGTCA
* *
670867 GCTTTGACCCTGGAGACT
1 GCTTTGACCTTAGAGACT
670885 TTTCAACCTT
Statistics
Matches: 482, Mismatches: 143, Indels: 51
0.71 0.21 0.08
Matches are distributed among these distances:
120 46 0.10
121 29 0.06
122 1 0.00
123 4 0.01
125 7 0.01
126 61 0.13
127 209 0.43
128 122 0.25
129 3 0.01
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.35
Consensus pattern (128 bp):
GCTTTGACCTTAGAGACTACCTCATCTAAAGTCTACCTGTCGGCTTTGACCCTAGAGACTTTCTT
ACCCTTCAGTCTGCCTGTCGACTTTGACCTTGAAGACTGCCTCACCCTAAAGTCTGCCTGTCA
Found at i:670846 original size:78 final size:78
Alignment explanation
Indices: 670708--670860 Score: 216
Period size: 78 Copynumber: 2.0 Consensus size: 78
670698 TTGTCGGCTT
* * *
670708 TGACCTTAGAGACTTTCTTACCTTTCATTCTGCCTATCAGCTTTGACCCTGAAGACTGCCTCATC
1 TGACCTTAGAGACTTTCTTACCCTTCAGTCTGCCTATCAGCTTTGACCCGGAAGACTGCCTCATC
670773 TAAAATCTGCCTG
66 TAAAATCTGCCTG
* * * * * *
670786 TGACCTTGGAGACTTTCTTACCCTTCAGTCTGCCTGTCGGCTTTGACTCGGGAGATTGCCTCATC
1 TGACCTTAGAGACTTTCTTACCCTTCAGTCTGCCTATCAGCTTTGACCCGGAAGACTGCCTCATC
*
670851 TAAAGTCTGC
66 TAAAATCTGC
670861 TTGTCAGCTT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
78 65 1.00
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (78 bp):
TGACCTTAGAGACTTTCTTACCCTTCAGTCTGCCTATCAGCTTTGACCCGGAAGACTGCCTCATC
TAAAATCTGCCTG
Done.