Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
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: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 2 of 54
Found at i:540772 original size:73 final size:73
Alignment explanation
Indices: 540554--540773 Score: 359
Period size: 73 Copynumber: 3.0 Consensus size: 73
540544 TGTGCATAAG
* * *
540554 TTTTAGGGTATTAAGGCATGTTTTCGGTAATGTTGTTACCTTTGGTTGTCTGCTCAATTTAATGT
1 TTTTAGGGTATTAAAGCATGTTTTCGGTTATGTTGTTACCTTTGGTTTTCTGCTCAATTTAATGT
*
540619 ATAATGTG
66 ATAATGTA
* * * *
540627 TTTTAGGGTATTGAAGCATGTTTTTGGTTATGTTGTTACCTTTGGTTTGCTGCTCAATTTAATGC
1 TTTTAGGGTATTAAAGCATGTTTTCGGTTATGTTGTTACCTTTGGTTTTCTGCTCAATTTAATGT
*
540692 ACAATGTA
66 ATAATGTA
540700 TTTTAGGGTATTAAAGCATGTTTTCGGTTATGTTGTTACCTTTGGTTTTCTGCTCAATTTAATGT
1 TTTTAGGGTATTAAAGCATGTTTTCGGTTATGTTGTTACCTTTGGTTTTCTGCTCAATTTAATGT
540765 ATAATGTA
66 ATAATGTA
540773 T
1 T
540774 GGAGACAGGA
Statistics
Matches: 133, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 133 1.00
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.48
Consensus pattern (73 bp):
TTTTAGGGTATTAAAGCATGTTTTCGGTTATGTTGTTACCTTTGGTTTTCTGCTCAATTTAATGT
ATAATGTA
Found at i:564376 original size:21 final size:21
Alignment explanation
Indices: 564337--564376 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
564327 ACTGGAGCTC
**
564337 CCATTTGGTAAAGTTGTAGTG
1 CCATTTGGTAAAGCAGTAGTG
*
564358 CCATTTGGTATAGCAGTAG
1 CCATTTGGTAAAGCAGTAG
564377 ATGTTCTGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.35
Consensus pattern (21 bp):
CCATTTGGTAAAGCAGTAGTG
Found at i:565910 original size:23 final size:25
Alignment explanation
Indices: 565880--565930 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
565870 CAGAAACCAT
*
565880 AAAACCCTAAAAAAGA-AGC-AAGA
1 AAAACCCTAAAAAACACAGCTAAGA
*
565903 AAAACCCTTAAAAACACAGCTAAGA
1 AAAACCCTAAAAAACACAGCTAAGA
565928 AAA
1 AAA
565931 CAAAAAGTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 14 0.58
24 3 0.12
25 7 0.29
ACGTcount: A:0.63, C:0.20, G:0.10, T:0.08
Consensus pattern (25 bp):
AAAACCCTAAAAAACACAGCTAAGA
Found at i:579068 original size:40 final size:41
Alignment explanation
Indices: 579010--579089 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
579000 TTATGAAAAA
*
579010 CACCAATCGTGGCGAGGTTG-AAAACCCCACTAAGGTGAAT
1 CACCAATCGTGGCAAGGTTGAAAAACCCCACTAAGGTGAAT
*
579050 CACCAATCTTGGCAAGGTTGAAAAACCCCACTAAGGTGAA
1 CACCAATCGTGGCAAGGTTGAAAAACCCCACTAAGGTGAA
579090 AAATAGCCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
40 18 0.49
41 19 0.51
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (41 bp):
CACCAATCGTGGCAAGGTTGAAAAACCCCACTAAGGTGAAT
Found at i:579426 original size:29 final size:30
Alignment explanation
Indices: 579397--579451 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 30
579387 AAAAGTATTA
*
579397 AAATAAAAT-AAGAAAA-GAATCCTAATTT
1 AAATAAAATAAAGAAAATAAATCCTAATTT
*
579425 AAATAGAATAAAGAAAATAAATCCTAA
1 AAATAAAATAAAGAAAATAAATCCTAA
579452 ATCAACTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 8 0.35
29 7 0.30
30 8 0.35
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.22
Consensus pattern (30 bp):
AAATAAAATAAAGAAAATAAATCCTAATTT
Found at i:581736 original size:40 final size:41
Alignment explanation
Indices: 581681--581760 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 41
581671 TTATGAAAAA
581681 CACCAATCGTGGCAAGGTTG-AAAACCCCACTAAGGTGAAT
1 CACCAATCGTGGCAAGGTTGAAAAACCCCACTAAGGTGAAT
*
581721 CACCAATCTTGGCAAGGTTGAAAAACCCCACTAAGGTGAA
1 CACCAATCGTGGCAAGGTTGAAAAACCCCACTAAGGTGAA
581761 AAATAGCCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 19 0.50
41 19 0.50
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.17
Consensus pattern (41 bp):
CACCAATCGTGGCAAGGTTGAAAAACCCCACTAAGGTGAAT
Found at i:591574 original size:10 final size:10
Alignment explanation
Indices: 591561--591586 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
591551 GAAAACGATA
591561 AAAAAATAAT
1 AAAAAATAAT
591571 AAAAAATAAT
1 AAAAAATAAT
591581 AAAAAA
1 AAAAAA
591587 ACAGCTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATAAT
Found at i:593709 original size:23 final size:23
Alignment explanation
Indices: 593671--593725 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
593661 TTTAATTGAT
593671 TTAGGAGTTATTTTCTT-TATTCTA
1 TTAGGA-TTATTTTCTTAT-TTCTA
* *
593695 TTAGGATTCTTTTCTTATTTTTA
1 TTAGGATTATTTTCTTATTTCTA
593718 TTAGGATT
1 TTAGGATT
593726 TTAATACTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 21 0.75
24 7 0.25
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.60
Consensus pattern (23 bp):
TTAGGATTATTTTCTTATTTCTA
Found at i:593860 original size:36 final size:36
Alignment explanation
Indices: 593813--593957 Score: 194
Period size: 36 Copynumber: 4.1 Consensus size: 36
593803 ATTTTGTTAA
*
593813 TTATTTTAATTGTATTAGACAACTAGAAGTAGAGTT
1 TTATTCTAATTGTATTAGACAACTAGAAGTAGAGTT
* *
593849 TTATTCTAATTGTATTAGGCAACTAAAAGTA-A---
1 TTATTCTAATTGTATTAGACAACTAGAAGTAGAGTT
593881 TTATTCTAATTGTATTAGGA-AACTAGAAGTAGAGTT
1 TTATTCTAATTGTATTA-GACAACTAGAAGTAGAGTT
*
593917 TTATTCTAATTGTATTA-AGCAACTAGAAGTAAAGTT
1 TTATTCTAATTGTATTAGA-CAACTAGAAGTAGAGTT
593953 TTATT
1 TTATT
593958 AGGATGTGGG
Statistics
Matches: 96, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
32 27 0.28
33 2 0.02
34 1 0.01
35 1 0.01
36 65 0.68
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (36 bp):
TTATTCTAATTGTATTAGACAACTAGAAGTAGAGTT
Found at i:593919 original size:68 final size:68
Alignment explanation
Indices: 593810--593948 Score: 235
Period size: 68 Copynumber: 2.0 Consensus size: 68
593800 AATATTTTGT
* *
593810 TAATTATTTTAATTGTATTAGACAACTAGAAGTAGAGTTTTATTCTAATTGTATTAGGCAACTAA
1 TAATTATTCTAATTGTATTAGACAACTAGAAGTAGAGTTTTATTCTAATTGTATTAAGCAACTAA
593875 AAG
66 AAG
593878 TAATTATTCTAATTGTATTAGGA-AACTAGAAGTAGAGTTTTATTCTAATTGTATTAAGCAACTA
1 TAATTATTCTAATTGTATTA-GACAACTAGAAGTAGAGTTTTATTCTAATTGTATTAAGCAACTA
*
593942 GAAG
65 AAAG
593946 TAA
1 TAA
593949 AGTTTTATTA
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
68 65 0.97
69 2 0.03
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (68 bp):
TAATTATTCTAATTGTATTAGACAACTAGAAGTAGAGTTTTATTCTAATTGTATTAAGCAACTAA
AAG
Found at i:594284 original size:50 final size:50
Alignment explanation
Indices: 594209--594307 Score: 198
Period size: 50 Copynumber: 2.0 Consensus size: 50
594199 CTGCAGGTCT
594209 AGGCATAAGGAATGCAACAGAAAACTTTGAACAGATCCTGAGACAGATGC
1 AGGCATAAGGAATGCAACAGAAAACTTTGAACAGATCCTGAGACAGATGC
594259 AGGCATAAGGAATGCAACAGAAAACTTTGAACAGATCCTGAGACAGATG
1 AGGCATAAGGAATGCAACAGAAAACTTTGAACAGATCCTGAGACAGATG
594308 TAAACGTACT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.16
Consensus pattern (50 bp):
AGGCATAAGGAATGCAACAGAAAACTTTGAACAGATCCTGAGACAGATGC
Found at i:594353 original size:65 final size:65
Alignment explanation
Indices: 594279--594406 Score: 238
Period size: 65 Copynumber: 2.0 Consensus size: 65
594269 AATGCAACAG
*
594279 AAAACTTTGAACAGATCCTGAGACAGATGTAAACGTACTTACAATCCTTCATGTAAATGTGTTAA
1 AAAACTTTGAACAGATCCTGAGACAGATGCAAACGTACTTACAATCCTTCATGTAAATGTGTTAA
*
594344 AAAACTTTGAACAGATCCTGAGACAGATGCAAACGTACTTACAATCCTTTATGTAAATGTGTT
1 AAAACTTTGAACAGATCCTGAGACAGATGCAAACGTACTTACAATCCTTCATGTAAATGTGTT
594407 TAATTTTCCC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.30
Consensus pattern (65 bp):
AAAACTTTGAACAGATCCTGAGACAGATGCAAACGTACTTACAATCCTTCATGTAAATGTGTTAA
Found at i:603799 original size:51 final size:51
Alignment explanation
Indices: 603760--603855 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 51
603750 GGTTCATCCC
* *
603760 AAAATGGAAAGGTAGATTCACCTCCAACATCGAAAAAGAAGGAAAAAACCA
1 AAAATGGAAAGGTAGAATCACCTCCAACATCCAAAAAGAAGGAAAAAACCA
* *
603811 AAAATGGAAAGGTAGAATCCCCTGCAACATCCAAAAAG-AGGAAAA
1 AAAATGGAAAGGTAGAATCACCTCCAACATCCAAAAAGAAGGAAAA
603856 GAAAGTTCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 7 0.17
51 34 0.83
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (51 bp):
AAAATGGAAAGGTAGAATCACCTCCAACATCCAAAAAGAAGGAAAAAACCA
Found at i:606753 original size:2 final size:2
Alignment explanation
Indices: 606748--606800 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
606738 TTTTTTCTTT
606748 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
606790 TA TA TA TA TA T
1 TA TA TA TA TA T
606801 TTATTTAGGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:610272 original size:16 final size:18
Alignment explanation
Indices: 610239--610279 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
610229 TCTTAAAGTC
610239 TTTCTCTTTCTGTCTTCT
1 TTTCTCTTTCTGTCTTCT
*
610257 TTTCT-TTTCT-TTTTCT
1 TTTCTCTTTCTGTCTTCT
610273 TTTCTCT
1 TTTCTCT
610280 CTCTCCACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 10 0.48
17 6 0.29
18 5 0.24
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTCTCTTTCTGTCTTCT
Found at i:627260 original size:121 final size:121
Alignment explanation
Indices: 627086--627328 Score: 423
Period size: 121 Copynumber: 2.0 Consensus size: 121
627076 AAGCTGGTTT
* * *
627086 CCACCAAACCCCACACAGAATTTTCATCCACCAATAGCTTACGTTGAAGCAAAATGATTGATTTG
1 CCACCAAACCCAACACAGAATTCTCATCCACCAACAGCTTACGTTGAAGCAAAATGATTGATTTG
*
627151 TTACATCGATCTGACAAGGAGAATGCTTTCATTCTTAAAGTTGGACACCAACTTAA
66 TTACATCGATCTCACAAGGAGAATGCTTTCATTCTTAAAGTTGGACACCAACTTAA
*
627207 CCACCAAACCCAACACTGAATTCTCATCCACCAACAGCTTACGTTGAAGCAAAATGATTGATTTG
1 CCACCAAACCCAACACAGAATTCTCATCCACCAACAGCTTACGTTGAAGCAAAATGATTGATTTG
* *
627272 TTACATTGATCTCACAGGGAGAATGCTTTCATTCTTAAAGTTGGACACCAACTTAA
66 TTACATCGATCTCACAAGGAGAATGCTTTCATTCTTAAAGTTGGACACCAACTTAA
627328 C
1 C
627329 ATGTTCACAA
Statistics
Matches: 115, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 115 1.00
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (121 bp):
CCACCAAACCCAACACAGAATTCTCATCCACCAACAGCTTACGTTGAAGCAAAATGATTGATTTG
TTACATCGATCTCACAAGGAGAATGCTTTCATTCTTAAAGTTGGACACCAACTTAA
Found at i:638892 original size:17 final size:19
Alignment explanation
Indices: 638855--638893 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
638845 GCAAGAACAA
638855 AAACACAACAATAATGGAAC
1 AAACACAACAATAAT-GAAC
638875 AAACACAACAA-AAT-AAC
1 AAACACAACAATAATGAAC
638892 AA
1 AA
638894 GATGAGGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
19 3 0.16
20 11 0.58
ACGTcount: A:0.67, C:0.21, G:0.05, T:0.08
Consensus pattern (19 bp):
AAACACAACAATAATGAAC
Found at i:640234 original size:172 final size:172
Alignment explanation
Indices: 639940--640270 Score: 495
Period size: 172 Copynumber: 1.9 Consensus size: 172
639930 ACCTTGAAAG
*
639940 ATTTATCACACCCTAAAACTTCCTAGCGCTTCCAAATTTAGTCCCTAACCAAAAAAAAAAAGTAG
1 ATTTATCACACCCTAAAACTTCCTAGCGCTTCCAAATTTAGTCCCTAACCAAAAAAAAAAAGAAG
* **
640005 AGTTCCAATCAATTTTCAACATCCCCAAGTTTTGCTTTTCACTGAAATGGCTTCCAAGATAGCTA
66 AGGTCCAATCAATTTTCAACATCCCCAAGTTTTGCTTTTCACTGAAAAAGCTTCCAAGATAGCTA
*
640070 AACATGCATCCTACATTAAACAAGGAAAAAAAAAACCATAAAT
131 AACATGCATCCTACACTAAACAA-GAAAAAAAAAACCATAAAT
** * * * * *
640113 ATTTATCACACTTTGAAACTTCCTAGTGCTTCCGAATTTAGTCCCTAACC-AAAACAAGAAGAAG
1 ATTTATCACACCCTAAAACTTCCTAGCGCTTCCAAATTTAGTCCCTAACCAAAAAAAAAAAGAAG
* * *
640177 AGGTCTAATCCATTTTCAACATCCCCAAGTTTTGCTTTTCACTGAAACAAG-TTCCAAGATTGCT
66 AGGTCCAATCAATTTTCAACATCCCCAAGTTTTGCTTTTCACTGAAA-AAGCTTCCAAGATAGCT
640241 AAACATGCATCCTACACTAAACAAGAAAAA
130 AAACATGCATCCTACACTAAACAAGAAAAA
640271 TACCACCACA
Statistics
Matches: 142, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
171 6 0.04
172 90 0.63
173 46 0.32
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (172 bp):
ATTTATCACACCCTAAAACTTCCTAGCGCTTCCAAATTTAGTCCCTAACCAAAAAAAAAAAGAAG
AGGTCCAATCAATTTTCAACATCCCCAAGTTTTGCTTTTCACTGAAAAAGCTTCCAAGATAGCTA
AACATGCATCCTACACTAAACAAGAAAAAAAAAACCATAAAT
Found at i:642512 original size:2 final size:2
Alignment explanation
Indices: 642505--642557 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
642495 CATGGTGGAA
642505 AT 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 AT
*
642547 AT GT AT AT AT A
1 AT AT AT AT AT A
642558 CACACACTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:676076 original size:17 final size:18
Alignment explanation
Indices: 676051--676088 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
676041 TATCAGGTTG
676051 TTTGCAGTTAG-TTTGTT
1 TTTGCAGTTAGCTTTGTT
* *
676068 TTTGTAGTTTGCTTTGTT
1 TTTGCAGTTAGCTTTGTT
676086 TTT
1 TTT
676089 CTTTCCCCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.08, C:0.05, G:0.21, T:0.66
Consensus pattern (18 bp):
TTTGCAGTTAGCTTTGTT
Found at i:677332 original size:22 final size:25
Alignment explanation
Indices: 677285--677332 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
677275 GGATACGGTT
677285 TTTGCTTATGGTCGAGCCTTTTAGA
1 TTTGCTTATGGTCGAGCCTTTTAGA
*
677310 TTTGC-TATGGTTGAG-C-TTTAGA
1 TTTGCTTATGGTCGAGCCTTTTAGA
677332 T
1 T
677333 CAATAAAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 1 0.05
24 9 0.41
25 5 0.23
ACGTcount: A:0.17, C:0.12, G:0.25, T:0.46
Consensus pattern (25 bp):
TTTGCTTATGGTCGAGCCTTTTAGA
Found at i:677406 original size:24 final size:21
Alignment explanation
Indices: 677373--677418 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 21
677363 CTTTAAATTT
677373 TTTGCATGGTTGAGCCTCTTAGA
1 TTTGCATGGTTGAG-CT-TTAGA
677396 TTTGCTATGGTTGAGCTTTAGA
1 TTTGC-ATGGTTGAGCTTTAGA
677418 T
1 T
677419 CAATAAAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 7 0.32
24 9 0.41
ACGTcount: A:0.17, C:0.13, G:0.26, T:0.43
Consensus pattern (21 bp):
TTTGCATGGTTGAGCTTTAGA
Found at i:677441 original size:86 final size:86
Alignment explanation
Indices: 677283--677469 Score: 329
Period size: 86 Copynumber: 2.2 Consensus size: 86
677273 TTGGATACGG
* *
677283 TTTTTGCTTATGGTCGAGCCTTTTAGATTTGCTATGGTTGAGCTTTAGATCAATAAAGCATGAGT
1 TTTTTGC--ATGGTTGAGCCTCTTAGATTTGCTATGGTTGAGCTTTAGATCAATAAAGCATGAGT
*
677348 TTCAAGTTATTTCTGCTTTAAAT
64 TTAAAGTTATTTCTGCTTTAAAT
677371 TTTTTGCATGGTTGAGCCTCTTAGATTTGCTATGGTTGAGCTTTAGATCAATAAAGCATGAGTTT
1 TTTTTGCATGGTTGAGCCTCTTAGATTTGCTATGGTTGAGCTTTAGATCAATAAAGCATGAGTTT
677436 AAAGTTATTTCTGCTTTAAAT
66 AAAGTTATTTCTGCTTTAAAT
677457 TTTTTGCATGGTT
1 TTTTTGCATGGTT
677470 TCACACGACA
Statistics
Matches: 96, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
86 89 0.93
88 7 0.07
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.45
Consensus pattern (86 bp):
TTTTTGCATGGTTGAGCCTCTTAGATTTGCTATGGTTGAGCTTTAGATCAATAAAGCATGAGTTT
AAAGTTATTTCTGCTTTAAAT
Found at i:689297 original size:11 final size:11
Alignment explanation
Indices: 689281--689321 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
689271 AATGTTATGA
689281 TTTTGGGCCAC
1 TTTTGGGCCAC
**
689292 TTTTGGGATAC
1 TTTTGGGCCAC
689303 TTTTGGGCCAC
1 TTTTGGGCCAC
*
689314 TTTAGGGC
1 TTTTGGGC
689322 TTTATTGGGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.12, C:0.20, G:0.29, T:0.39
Consensus pattern (11 bp):
TTTTGGGCCAC
Found at i:689331 original size:21 final size:21
Alignment explanation
Indices: 689280--689333 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
689270 TAATGTTATG
*
689280 ATTTTGGGCCACTTTTGGGAT
1 ATTTTGGGCCACTTTAGGGAT
*
689301 ACTTTTGGGCCACTTTAGGGCT
1 A-TTTTGGGCCACTTTAGGGAT
689323 -TTATTGGGCCA
1 ATT-TTGGGCCA
689334 GCTTGTGGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 2 0.07
21 9 0.31
22 18 0.62
ACGTcount: A:0.15, C:0.19, G:0.28, T:0.39
Consensus pattern (21 bp):
ATTTTGGGCCACTTTAGGGAT
Found at i:695071 original size:2 final size:2
Alignment explanation
Indices: 695064--695102 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
695054 TTAATTACTG
695064 AT AT AT AT 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 AT AT AT AT A
695103 AGTATTTCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:697495 original size:13 final size:13
Alignment explanation
Indices: 697479--697503 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
697469 AGAAGGAAAA
697479 GAAAGAAAGGAAG
1 GAAAGAAAGGAAG
697492 GAAAGAAAGGAA
1 GAAAGAAAGGAA
697504 AATCATAGAA
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:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (13 bp):
GAAAGAAAGGAAG
Found at i:698585 original size:2 final size:2
Alignment explanation
Indices: 698578--698610 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
698568 TTCTTCCCTC
698578 AT 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 AT A
698611 AGCAATTAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:698730 original size:20 final size:20
Alignment explanation
Indices: 698707--698745 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
698697 GAAAAAGGAA
*
698707 AAAAAATGGAAGAAAAGAAC
1 AAAAAAGGGAAGAAAAGAAC
*
698727 AAAAAAGGGAAGGAAAGAA
1 AAAAAAGGGAAGAAAAGAA
698746 AGGAAGAGAG
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:0.69, C:0.03, G:0.26, T:0.03
Consensus pattern (20 bp):
AAAAAAGGGAAGAAAAGAAC
Found at i:707789 original size:6 final size:6
Alignment explanation
Indices: 707778--707816 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
707768 CTTCTGCTAT
** *
707778 ATCCTC ATCCTC ATCCTC CCCCTC ATCATC ATCCTC ATC
1 ATCCTC ATCCTC ATCCTC ATCCTC ATCCTC ATCCTC ATC
707817 ATCCTCCCCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.51, G:0.00, T:0.31
Consensus pattern (6 bp):
ATCCTC
Found at i:707809 original size:24 final size:24
Alignment explanation
Indices: 707782--707831 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
707772 TGCTATATCC
*
707782 TCATCCTCATCCTCC-CCCTCATCA
1 TCATCCTCATCATCCTCCC-CATCA
707806 TCATCCTCATCATCCTCCCCATCA
1 TCATCCTCATCATCCTCCCCATCA
707830 TC
1 TC
707832 TGCCATGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.18, C:0.52, G:0.00, T:0.30
Consensus pattern (24 bp):
TCATCCTCATCATCCTCCCCATCA
Found at i:707817 original size:12 final size:12
Alignment explanation
Indices: 707782--707853 Score: 58
Period size: 12 Copynumber: 6.0 Consensus size: 12
707772 TGCTATATCC
*
707782 TCATCCTCATCC
1 TCATCCTCATCA
**
707794 TCCCCCTCATCA
1 TCATCCTCATCA
707806 TCATCCTCATCA
1 TCATCCTCATCA
* *
707818 TCCTCCCCATCA
1 TCATCCTCATCA
*
707830 TC-TGCCAT-GTCA
1 TCAT-CC-TCATCA
707842 TCATCCTCATCA
1 TCATCCTCATCA
707854 CCCATATCAT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
11 2 0.04
12 43 0.93
13 1 0.02
ACGTcount: A:0.19, C:0.47, G:0.03, T:0.31
Consensus pattern (12 bp):
TCATCCTCATCA
Found at i:707865 original size:36 final size:36
Alignment explanation
Indices: 707803--707871 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
707793 CTCCCCCTCA
* *
707803 TCATCATCCTCATCATCCTCCCCATCATCTGCCATG
1 TCATCATCCTCATCACCCTCACCATCATCTGCCATG
*
707839 TCATCATCCTCATCACCCAT-ATCATCATCTGCC
1 TCATCATCCTCATCACCC-TCACCATCATCTGCC
707872 CTATTCTCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 28 0.97
37 1 0.03
ACGTcount: A:0.22, C:0.43, G:0.04, T:0.30
Consensus pattern (36 bp):
TCATCATCCTCATCACCCTCACCATCATCTGCCATG
Found at i:716046 original size:17 final size:17
Alignment explanation
Indices: 715997--716046 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
715987 AAAGAAAGAA
*
715997 AGGAAGAGAGATAGAGAG
1 AGGAAGAGA-AAAGAGAG
716015 A-G-AGA-AAAAGA-AG
1 AGGAAGAGAAAAGAGAG
716028 AGGAAGAGAAAAGAGAG
1 AGGAAGAGAAAAGAGAG
716045 AG
1 AG
716047 AAGTGGAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
13 3 0.11
14 5 0.19
15 4 0.15
16 9 0.33
17 5 0.19
18 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.40, T:0.02
Consensus pattern (17 bp):
AGGAAGAGAAAAGAGAG
Found at i:716479 original size:22 final size:23
Alignment explanation
Indices: 716450--716497 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
716440 TGAATGTCAT
*
716450 AAATA-TTTTTATTTCAAGAA-A
1 AAATATTTTTTATTGCAAGAACA
716471 AAATAATTTTTTATTGCAAGAACA
1 AAAT-ATTTTTTATTGCAAGAACA
716495 AAA
1 AAA
716498 AAAAACATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 4 0.17
22 1 0.04
23 14 0.61
24 4 0.17
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (23 bp):
AAATATTTTTTATTGCAAGAACA
Found at i:716832 original size:2 final size:2
Alignment explanation
Indices: 716825--716854 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
716815 ATGAAAGCTA
716825 CT CT 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 CT CT
716855 TTGGCTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:717408 original size:25 final size:24
Alignment explanation
Indices: 717379--717428 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
717369 CCCAATTCTT
717379 ATTTTT-TAAAAAAATGAATTTCAA
1 ATTTTTATAAAAAAATGAATTT-AA
* *
717403 ATTTTTATATAAAAATTAATTTAA
1 ATTTTTATAAAAAAATGAATTTAA
717427 AT
1 AT
717429 GAATATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
ATTTTTATAAAAAAATGAATTTAA
Found at i:717675 original size:41 final size:41
Alignment explanation
Indices: 717630--717717 Score: 140
Period size: 41 Copynumber: 2.1 Consensus size: 41
717620 ATTATAATAG
**
717630 AAAAATGGAACTTTGGGTTATAAATTTTGCCATGAAATAAC
1 AAAAATGGAACTTTGGGTTATAAATTAAGCCATGAAATAAC
*
717671 AAAAATGGAACTTTGGGTTATAAATTAAGCTATGAAATAAC
1 AAAAATGGAACTTTGGGTTATAAATTAAGCCATGAAATAAC
717712 ATAAAA
1 A-AAAA
717718 ATTTTAGTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
41 39 0.91
42 4 0.09
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.30
Consensus pattern (41 bp):
AAAAATGGAACTTTGGGTTATAAATTAAGCCATGAAATAAC
Found at i:721040 original size:194 final size:190
Alignment explanation
Indices: 720630--721052 Score: 560
Period size: 194 Copynumber: 2.2 Consensus size: 190
720620 CCTGCAATCC
* * * * *
720630 TTATCTGGAAACAGATTGGTTTAAAGGATGCGTAAGTTAAAGTCTAACCCCAGACCGATTGATTT
1 TTATCAGGAAACAGATTGGTTTAAGGGATGCATAAGTTGAAGTCTAACCCCAGACCCATTGATTT
* * * * *
720695 CAGGTGCTATAGTGCAAAATGGGTGCTTGGGTCACTGGTTATTTCATACTTTTGCAGGTCATGGA
66 CAGCTGCCATAGTGCAAAATGGGTGCTTGGATCACCGGTTATTTCATACTTTTACAGGTCATGGA
* * * * *
720760 CTGGCCTGGATGTCAAACAATGTGTAATATTCCAACCCATTTGGCCATTTCTGTTGTTTT
131 CTGACCTGCATGTCAAACAATGTGTAAGATTCCAACCCATTTGGCCATTTCTATTCTTTT
* ** * * *
720820 TTATAAGGGGACAGATTTGG-TTAAGGGATGCATAAGTTGAAGTCTAAGCCCAGCCCCATTGCTT
1 TTATCAGGAAACAGA-TTGGTTTAAGGGATGCATAAGTTGAAGTCTAACCCCAGACCCATTGATT
* * **
720884 TGAGCTGCCACCATGAGTGCAAAATGGGTGGTTGGATTGCCGGTTATTTCATACTTTTACAGGTC
65 TCAGCTG---CCAT-AGTGCAAAATGGGTGCTTGGATCACCGGTTATTTCATACTTTTACAGGTC
720949 ATGGACTGACCTGCATGTCAAACAATGTGTAAGATTCCAACCCATTTGGCCATTTCTATTCTTTT
126 ATGGACTGACCTGCATGTCAAACAATGTGTAAGATTCCAACCCATTTGGCCATTTCTATTCTTTT
*
721014 TTATCAGGAAACAGATTGGTTTAAGGGATGCAGAAGTTG
1 TTATCAGGAAACAGATTGGTTTAAGGGATGCATAAGTTG
721053 CCACGTGGCT
Statistics
Matches: 198, Mismatches: 29, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
190 53 0.27
191 4 0.02
193 7 0.04
194 134 0.68
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (190 bp):
TTATCAGGAAACAGATTGGTTTAAGGGATGCATAAGTTGAAGTCTAACCCCAGACCCATTGATTT
CAGCTGCCATAGTGCAAAATGGGTGCTTGGATCACCGGTTATTTCATACTTTTACAGGTCATGGA
CTGACCTGCATGTCAAACAATGTGTAAGATTCCAACCCATTTGGCCATTTCTATTCTTTT
Found at i:734999 original size:117 final size:116
Alignment explanation
Indices: 734762--734978 Score: 291
Period size: 117 Copynumber: 1.9 Consensus size: 116
734752 TAGAGATTAA
* *
734762 CAACATAAATGCAACCAACACTGTTGATGTTAAGGATTTTCCCTGGCTTGGGGTATGCAATGCAC
1 CAACATAAATGCAACCAACACTGTTGATGTGAAGCATTTTCCCTGGCTTGGGGTATGCAATGCAC
* *
734827 TTCAATGCTTTGCATCTAACATTAACACCAGATAAGAGGAAAGCAATACTAT
66 -ACAATGCTTTGCATCTAACAATAACACCAGATAAGAGGAAAGCAATACTAT
* * * * *
734879 CAACATACATGCAACCAATACTGTTGATGTGAAGCATTTTCCGTGGCTTGGGGTATGC-CT-TA-
1 CAACATAAATGCAACCAACACTGTTGATGTGAAGCATTTTCCCTGGCTTGGGGTATGCAATGCAC
*
734941 ACAATTCTTTGCATCTCAA-AAT-ACACCAGATAAGAGGA
66 ACAATGCTTTGCATCT-AACAATAACACCAGATAAGAGGA
734979 TTGCAGCGCA
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
112 16 0.18
113 16 0.18
114 2 0.02
115 1 0.01
116 1 0.01
117 53 0.60
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (116 bp):
CAACATAAATGCAACCAACACTGTTGATGTGAAGCATTTTCCCTGGCTTGGGGTATGCAATGCAC
ACAATGCTTTGCATCTAACAATAACACCAGATAAGAGGAAAGCAATACTAT
Found at i:736308 original size:16 final size:16
Alignment explanation
Indices: 736283--736315 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
736273 TTCAAAAAAA
736283 AATAAAAATAAATAAT
1 AATAAAAATAAATAAT
*
736299 AATAATAATAAATAAT
1 AATAAAAATAAATAAT
736315 A
1 A
736316 TATATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AATAAAAATAAATAAT
Found at i:736320 original size:2 final size:2
Alignment explanation
Indices: 736313--736346 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
736303 ATAATAAATA
736313 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
736347 TTAGAAAGTT
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:738020 original size:102 final size:102
Alignment explanation
Indices: 737844--738046 Score: 334
Period size: 102 Copynumber: 2.0 Consensus size: 102
737834 AAAAGACAGG
*
737844 ACTTTGGTGTAAATTCACTGTAATTGCTATGAGGAAAGCAAGTAGGATCACTGCTTCGTTCCCCT
1 ACTTTGGTGTAAATTCACCGTAATTGCTATGAGGAAAGCAAGTAGGATCACTGCTTCGTTCCCCT
*
737909 TTAATCTGCAAAATTTAATCTTTGAATGATGTCTCTA
66 TTAATCTGCAAAATTGAATCTTTGAATGATGTCTCTA
* *** * *
737946 ACTTTGGTGTAAATTCACCGTAATTGGTATGAGGAAAGGGTGTAGGATCATTGCTTGGTTCCCCT
1 ACTTTGGTGTAAATTCACCGTAATTGCTATGAGGAAAGCAAGTAGGATCACTGCTTCGTTCCCCT
738011 TTAATCTGCAAAATTGAATCTTTGAATGATGTCTCT
66 TTAATCTGCAAAATTGAATCTTTGAATGATGTCTCT
738047 TATTAATGGA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 93 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (102 bp):
ACTTTGGTGTAAATTCACCGTAATTGCTATGAGGAAAGCAAGTAGGATCACTGCTTCGTTCCCCT
TTAATCTGCAAAATTGAATCTTTGAATGATGTCTCTA
Found at i:743058 original size:30 final size:30
Alignment explanation
Indices: 742988--743058 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 30
742978 ACGTTTAAAC
*
742988 AAATCTTTAAATTTTTATTTTGAATCAAAT
1 AAATCTTTATATTTTTATTTTGAATCAAAT
* *
743018 AAATTTTTATATTTTTATTTTGAGTCAAAT
1 AAATCTTTATATTTTTATTTTGAATCAAAT
*
743048 AAATCCTTATA
1 AAATCTTTATA
743059 ACTAATGATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (30 bp):
AAATCTTTATATTTTTATTTTGAATCAAAT
Found at i:761298 original size:32 final size:32
Alignment explanation
Indices: 761257--761321 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
761247 AATTAACAAA
761257 TCTTTTAATTCTTATCTGTAAAAGACCATAAT
1 TCTTTTAATTCTTATCTGTAAAAGACCATAAT
*
761289 TCTTTTAATTCTTTTCTGTAAAAGACCATAAT
1 TCTTTTAATTCTTATCTGTAAAAGACCATAAT
761321 T
1 T
761322 GATTAAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.32, C:0.15, G:0.06, T:0.46
Consensus pattern (32 bp):
TCTTTTAATTCTTATCTGTAAAAGACCATAAT
Found at i:761586 original size:106 final size:105
Alignment explanation
Indices: 761386--761704 Score: 460
Period size: 106 Copynumber: 3.0 Consensus size: 105
761376 GTATAGAAGC
* * *
761386 AGCAATTCTACTATCTTACCAATCTGTGAGCCATGGATTGAACTCAACTCTATCACCACTCCTGT
1 AGCAATTCTACTTTCTTACCAATCTGTGAGCCATGGATTGAACT-TACTCTATCACCATTCCTGT
* *
761451 TAACCTCAGCCAGGGTAAAGGTTCAGTTTTACAAGTTAACAG
65 TAACTTCAACCA-GGTAAAGGTTCAGTTTTACAAGTTAACAG
* *
761493 CGCAATTCTACTTTCTTACCAATCTGTGAGCCATGGATTGCACTTACTCTATCACCATTCCTGTT
1 AGCAATTCTACTTTCTTACCAATCTGTGAGCCATGGATTGAACTTACTCTATCACCATTCCTGTT
*
761558 AACTTCAACCAGAGTAAAGGTTCAGTTTTGCAAGTTAACAG
66 AACTTCAACCAG-GTAAAGGTTCAGTTTTACAAGTTAACAG
* * * * *
761599 AGCAATTCTACTTTCGTACCAATCTGTGAACCATGGATTGAACCTACTCTATCACAATTCCGGTT
1 AGCAATTCTACTTTCTTACCAATCTGTGAGCCATGGATTGAACTTACTCTATCACCATTCCTGTT
*
761664 AACTT-AATCCAGGATAAAGGTTCAGCTTTACAAGTTAACAG
66 AACTTCAA-CCAGG-TAAAGGTTCAGTTTTACAAGTTAACAG
761705 GCATCTTCCT
Statistics
Matches: 192, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
105 4 0.02
106 147 0.77
107 41 0.21
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (105 bp):
AGCAATTCTACTTTCTTACCAATCTGTGAGCCATGGATTGAACTTACTCTATCACCATTCCTGTT
AACTTCAACCAGGTAAAGGTTCAGTTTTACAAGTTAACAG
Found at i:763502 original size:21 final size:21
Alignment explanation
Indices: 763478--763520 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
763468 TCACAAAAAT
* *
763478 AAATAATTTAAAGCAAAGAAA
1 AAATAATTAAAAGAAAAGAAA
* *
763499 AAATTATTAAAATAAAAGAAA
1 AAATAATTAAAAGAAAAGAAA
763520 A
1 A
763521 TAAAATGACT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (21 bp):
AAATAATTAAAAGAAAAGAAA
Found at i:763548 original size:124 final size:117
Alignment explanation
Indices: 763310--763548 Score: 329
Period size: 119 Copynumber: 2.0 Consensus size: 117
763300 CTTTTCCCTT
* *
763310 TCTCCAGGTTTTGACATTTTTCCCTTTTTTTTCTTTTATCCCAAAAATAAAATAATTTAAAGCAC
1 TCTCCAGGTTTTGACATTTTTCCCTTTTTTTTCTTTTATCACAAAAATAAAATAATTTAAAGCAA
* *
763375 AGAAAAAATAATTAAAATAAAATAAAATGACTCAATTTTTTTCATTTTTTTA
66 AGAAAAAATAATTAAAATAAAATAAAATGACTCAAATTTTTTCAATTTTTTA
*
763427 TCTCCAGGTTTTGATATTTTT-CCTTTTTTTTCCTTCTTTAATCACAAAAAT-AAATAATTTAAA
1 TCTCCAGGTTTTGACATTTTTCCCTTTTTTTT-C-T-TTT-ATCACAAAAATAAAATAATTTAAA
*
763490 GCAAAGAAAAAATTATTAAAATAAAAGAAAATAAAATGACTCAAATTTTTTCAATTTTT
62 GCAAAGAAAAAATAATTAAAAT-----AAAATAAAATGACTCAAATTTTTTCAATTTTT
763549 ATTAAAAAAA
Statistics
Matches: 107, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
116 10 0.09
117 21 0.20
118 1 0.01
119 35 0.33
120 10 0.09
124 30 0.28
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.42
Consensus pattern (117 bp):
TCTCCAGGTTTTGACATTTTTCCCTTTTTTTTCTTTTATCACAAAAATAAAATAATTTAAAGCAA
AGAAAAAATAATTAAAATAAAATAAAATGACTCAAATTTTTTCAATTTTTTA
Found at i:764739 original size:22 final size:21
Alignment explanation
Indices: 764701--764741 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
764691 TTAAAAAATT
764701 TTAAATTTACGTTATAATTCA
1 TTAAATTTACGTTATAATTCA
*
764722 TTAAATTATATGTTATAATT
1 TTAAATT-TACGTTATAATT
764742 ACAATTTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (21 bp):
TTAAATTTACGTTATAATTCA
Found at i:771684 original size:22 final size:22
Alignment explanation
Indices: 771642--771686 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
771632 AAAATATTTC
**
771642 TCTTCAAAAATCAGAGGTGATT
1 TCTTCAAAAATCAGACATGATT
771664 TCTTCAGAAAATCA-ACATGATT
1 TCTTCA-AAAATCAGACATGATT
771686 T
1 T
771687 AAAGAAACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (22 bp):
TCTTCAAAAATCAGACATGATT
Found at i:774806 original size:31 final size:33
Alignment explanation
Indices: 774771--774831 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
774761 CATTACAATG
774771 TAATTAATAATCAT-AG-TT-TCATTAATTAATT
1 TAATTAATAAT-ATGAGTTTGTCATTAATTAATT
*
774802 TAATTAATTATATGAGTTTGTCATTAATTA
1 TAATTAATAATATGAGTTTGTCATTAATTA
774832 TATGAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 2 0.08
31 12 0.46
32 2 0.08
33 10 0.38
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (33 bp):
TAATTAATAATATGAGTTTGTCATTAATTAATT
Found at i:775020 original size:17 final size:17
Alignment explanation
Indices: 774990--775040 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
774980 AAATAGAAAA
* *
774990 TAAA-TATATTTATATT
1 TAAAGTATATATATACT
775006 TAAAGTATATATATACT
1 TAAAGTATATATATACT
*
775023 AAAAGTATTAGTATATAC
1 TAAAGTA-TA-TATATAC
775041 ATAATATAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 4 0.14
17 16 0.55
18 2 0.07
19 7 0.24
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (17 bp):
TAAAGTATATATATACT
Found at i:780753 original size:5 final size:5
Alignment explanation
Indices: 780743--780768 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
780733 GATTTTTATG
780743 TATAT TATAT TATAT TATAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT T
780769 TTAATTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:787135 original size:4 final size:4
Alignment explanation
Indices: 787119--787213 Score: 54
Period size: 4 Copynumber: 24.5 Consensus size: 4
787109 CGTAAGCATG
* * * *
787119 ATGT ATG- ATGT ATGT ATGC ATGT AAGT A--T ATGT ATGT ATGG ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * **
787164 ATGT ATGAA AAGT ATAT ATGT AGGG ATGT ATAA ATGT ATGT ATG- ATGT
1 ATGT ATG-T ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
787212 AT
1 AT
787214 TTGTGCAAGT
Statistics
Matches: 66, Mismatches: 20, Indels: 10
0.69 0.21 0.10
Matches are distributed among these distances:
2 2 0.03
3 6 0.09
4 56 0.85
5 2 0.03
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.39
Consensus pattern (4 bp):
ATGT
Found at i:787139 original size:22 final size:23
Alignment explanation
Indices: 787114--787171 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
787104 AATTACGTAA
787114 GCATG-ATGTATGATGTATGTAT
1 GCATGCATGTATGATGTATGTAT
* *
787136 GCATGTAAGTAT-ATGTATGTAT
1 GCATGCATGTATGATGTATGTAT
*
787158 GGATGCATGTATGA
1 GCATGCATGTATGA
787172 AAAGTATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 24 0.80
23 6 0.20
ACGTcount: A:0.29, C:0.05, G:0.28, T:0.38
Consensus pattern (23 bp):
GCATGCATGTATGATGTATGTAT
Found at i:794136 original size:122 final size:123
Alignment explanation
Indices: 793918--794153 Score: 395
Period size: 122 Copynumber: 1.9 Consensus size: 123
793908 ACATCCCCGA
**
793918 AAAATGCATAACATAAGATTAGATCTCACAACATACTAGCACAAGTGAAAGAACAATGCCTTTGC
1 AAAATGCATAACATAAGAGCAGATCTCACAACATACTAGCACAAGTGAAAGAACAATGCCTTTGC
*
793983 TTCGAAATCGGTTTATGGCTTTATTCTATTACTACAAGCTTCGAACCTAAACATCCTG
66 TTCGAAATCGGTTTATGGCTTTATGCTATTACTACAAGCTTCGAACCTAAACATCCTG
*
794041 AAAATGCATAACATGAGAGCAGATCTCACAACATACTAGCACAAGTG-AAGAACAATGCCTTT-C
1 AAAATGCATAACATAAGAGCAGATCTCACAACATACTAGCACAAGTGAAAGAACAATGCCTTTGC
* *
794104 TTTGGAAATCGGTTTATGGCTTTATGCTATTACTACAAGCTTCTAACCTA
66 -TTCGAAATCGGTTTATGGCTTTATGCTATTACTACAAGCTTCGAACCTA
794154 GTTTTCTCCA
Statistics
Matches: 106, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
121 1 0.01
122 61 0.58
123 44 0.42
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (123 bp):
AAAATGCATAACATAAGAGCAGATCTCACAACATACTAGCACAAGTGAAAGAACAATGCCTTTGC
TTCGAAATCGGTTTATGGCTTTATGCTATTACTACAAGCTTCGAACCTAAACATCCTG
Found at i:804140 original size:40 final size:39
Alignment explanation
Indices: 804086--804162 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 39
804076 AAAGTATAGC
804086 ATGATGATGCTTCATCATCAACACTTTATACCTATAACA
1 ATGATGATGCTTCATCATCAACACTTTATACCTATAACA
804125 ATGATGTATGCTTCATCATCAACACTTTATACCTATAA
1 ATGATG-ATGCTTCATCATCAACACTTTATACCTATAA
804163 AAACTCTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
39 6 0.16
40 31 0.84
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (39 bp):
ATGATGATGCTTCATCATCAACACTTTATACCTATAACA
Found at i:810981 original size:29 final size:26
Alignment explanation
Indices: 810922--810984 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 26
810912 AGTTTATTAT
*
810922 ATTTAAAATAATAATATAAAAATTTA
1 ATTTAAAATAATAAAATAAAAATTTA
810948 A-TTAAAAGTAATAAAAATAAAAATTTAA
1 ATTTAAAA-TAAT-AAAATAAAAATTT-A
810976 ATTTAAAAT
1 ATTTAAAAT
810985 TTTTAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 6 0.19
26 5 0.16
27 12 0.38
28 3 0.09
29 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
ATTTAAAATAATAAAATAAAAATTTA
Found at i:812309 original size:27 final size:27
Alignment explanation
Indices: 812251--812310 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
812241 GACTCAACGA
* *
812251 CGGAGGAGAACTCGCCGGTGTCAATGT
1 CGGAGGAGAACTCGCCGGTGCCAATGC
* ** *
812278 AGGAGGAGAACTTTCCGGTGCCGATGC
1 CGGAGGAGAACTCGCCGGTGCCAATGC
812305 CGGAGG
1 CGGAGG
812311 GGTAGACATT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.40, T:0.17
Consensus pattern (27 bp):
CGGAGGAGAACTCGCCGGTGCCAATGC
Found at i:812397 original size:45 final size:45
Alignment explanation
Indices: 812333--812438 Score: 196
Period size: 45 Copynumber: 2.4 Consensus size: 45
812323 TGGAGAACTC
812333 GCCGGGGATTGAACCGGGGCCT-TCGAAGAAGCAGGCGGAGTCGCA
1 GCCGGGGATTGAACCGGGG-CTGTCGAAGAAGCAGGCGGAGTCGCA
812378 GCCGGGGATTGAACCGGGGCTGTCGAAGAAGCAGGCGGAGTCGCA
1 GCCGGGGATTGAACCGGGGCTGTCGAAGAAGCAGGCGGAGTCGCA
812423 GCCGGGGATTGAACCG
1 GCCGGGGATTGAACCG
812439 ATGGGGGCGT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
44 2 0.03
45 58 0.97
ACGTcount: A:0.22, C:0.24, G:0.43, T:0.11
Consensus pattern (45 bp):
GCCGGGGATTGAACCGGGGCTGTCGAAGAAGCAGGCGGAGTCGCA
Found at i:813465 original size:106 final size:106
Alignment explanation
Indices: 813355--813549 Score: 286
Period size: 106 Copynumber: 1.8 Consensus size: 106
813345 TTAAATAAGT
*
813355 TTATAAATCACAAGTCCATGTTCTCAACTTAAAATACATACTTGATAAGT-AGTGAAAAATCC-A
1 TTATAAATCACAAGTCCACGTTCTCAACTTAAAATACATACTTGATAAGTGA-TGAAAAA-CCTA
* * *
813418 TGCCCCATCTTATCTCTCATTAATGTCCATAGTTTAAGTACGC
64 TACCCCATCTCATATCTCATTAATGTCCATAGTTTAAGTACGC
* **
813461 TTATAAATCACGAGTCCACGTTCTCAACTTAAAATACATGTTTGATAAGTGATGAAAAACCTATA
1 TTATAAATCACAAGTCCACGTTCTCAACTTAAAATACATACTTGATAAGTGATGAAAAACCTATA
*
813526 TCCCATCTCATATCTCATTAATGT
66 CCCCATCTCATATCTCATTAATGT
813550 AAGATTCGTA
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
105 2 0.03
106 76 0.96
107 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.33
Consensus pattern (106 bp):
TTATAAATCACAAGTCCACGTTCTCAACTTAAAATACATACTTGATAAGTGATGAAAAACCTATA
CCCCATCTCATATCTCATTAATGTCCATAGTTTAAGTACGC
Found at i:813657 original size:24 final size:24
Alignment explanation
Indices: 813630--813676 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
813620 TTTATATTTT
* *
813630 TATCCAAATTCAATTAAATATTAG
1 TATCAAAATTCAATTAAAAATTAG
813654 TATCAAAATTCAATTAAAAATTA
1 TATCAAAATTCAATTAAAAATTA
813677 ATCTTTGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.36
Consensus pattern (24 bp):
TATCAAAATTCAATTAAAAATTAG
Found at i:814131 original size:19 final size:18
Alignment explanation
Indices: 814093--814131 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
814083 CATTATATAT
814093 ATTATTAATAAAATTTAA
1 ATTATTAATAAAATTTAA
814111 ATTATTAAATTAAAA-TTAA
1 ATTATT-AA-TAAAATTTAA
814130 AT
1 AT
814132 CATAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 8 0.42
20 5 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTATTAATAAAATTTAA
Found at i:814425 original size:2 final size:2
Alignment explanation
Indices: 814418--814461 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
814408 AATGAAAGAA
* *
814418 AT AT AT AT AT AT AT AT AT AA AT AA AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
814459 AT A
1 AT A
814462 GAATTTATAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:815557 original size:3 final size:3
Alignment explanation
Indices: 815549--815597 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
815539 CGGAAATGTG
* * *
815549 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GTT GGT GTT GGT GTT GGT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
815597 G
1 G
815598 CAAGTGGGGG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.61, T:0.39
Consensus pattern (3 bp):
GGT
Found at i:816836 original size:18 final size:18
Alignment explanation
Indices: 816803--816837 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
816793 AGATCATGTT
* *
816803 CGTGATCGTGATAGGGAA
1 CGTGATCGGGACAGGGAA
816821 CGTGATCGGGACAGGGA
1 CGTGATCGGGACAGGGA
816838 TAAGGATCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.14, G:0.43, T:0.17
Consensus pattern (18 bp):
CGTGATCGGGACAGGGAA
Found at i:824398 original size:15 final size:15
Alignment explanation
Indices: 824380--824428 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
824370 TTATGCCATT
*
824380 TTCATTTTCCTCTTC
1 TTCATTTTCTTCTTC
* *
824395 TTCATTCTCTTCCTC
1 TTCATTTTCTTCTTC
*
824410 TTCCTTTTCTTCTTC
1 TTCATTTTCTTCTTC
824425 TTCA
1 TTCA
824429 GACTCATCCT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.06, C:0.35, G:0.00, T:0.59
Consensus pattern (15 bp):
TTCATTTTCTTCTTC
Found at i:824439 original size:30 final size:30
Alignment explanation
Indices: 824384--824440 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
824374 GCCATTTTCA
** *
824384 TTTTCCTCTTCTTCATTCTCTTCCTCTTCC
1 TTTTCCTCTTCTTCAGACTCATCCTCTTCC
*
824414 TTTTCTTCTTCTTCAGACTCATCCTCT
1 TTTTCCTCTTCTTCAGACTCATCCTCT
824441 GAATCAGGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.07, C:0.37, G:0.02, T:0.54
Consensus pattern (30 bp):
TTTTCCTCTTCTTCAGACTCATCCTCTTCC
Found at i:828932 original size:15 final size:15
Alignment explanation
Indices: 828912--828943 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
828902 AATCCGACCG
828912 AAACCATAGATTTCA
1 AAACCATAGATTTCA
828927 AAACCATAGATTTCA
1 AAACCATAGATTTCA
828942 AA
1 AA
828944 TATTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (15 bp):
AAACCATAGATTTCA
Found at i:839779 original size:71 final size:68
Alignment explanation
Indices: 839658--839789 Score: 165
Period size: 71 Copynumber: 1.9 Consensus size: 68
839648 AGTAAATATT
* * ** *
839658 TTAATTAATTTATCCGAATCATATATTATATGTCGGTTTCTTTCATATTTTTGGACTCATAGTCA
1 TTAATTAATTTATCCGAATCATATACTATATGCCAATTTCCTTCATATTTTTGGACTCATAGTCA
839723 ATC
66 ATC
* * *
839726 TTAATTAATTTTATCCGAATCGTGTATACTATATGCCAATTTCCTTCTTATTTTTGGATTCATA
1 TTAATTAA-TTTATCCGAATC--ATATACTATATGCCAATTTCCTTCATATTTTTGGACTCATA
839790 ATCTCGTTCA
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
68 8 0.15
69 12 0.23
71 33 0.62
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (68 bp):
TTAATTAATTTATCCGAATCATATACTATATGCCAATTTCCTTCATATTTTTGGACTCATAGTCA
ATC
Found at i:843068 original size:39 final size:40
Alignment explanation
Indices: 843019--843097 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
843009 TATGAAGCAA
843019 CTTATTTCCAATTGAATTCGAA-GACCCA-TCTGAGGATTTC
1 CTTATTTCCAATTGAATTC-AATGACCCACT-TGAGGATTTC
843059 CTTA-TTCCAATTGAATTCAATGACCCACTTGAGGATTTC
1 CTTATTTCCAATTGAATTCAATGACCCACTTGAGGATTTC
843098 AGGTTGACTA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
38 2 0.05
39 30 0.81
40 5 0.14
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (40 bp):
CTTATTTCCAATTGAATTCAATGACCCACTTGAGGATTTC
Found at i:858419 original size:3 final size:3
Alignment explanation
Indices: 858413--858438 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
858403 CCACCGCTAG
858413 CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CA
858439 TACCTACCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:873542 original size:13 final size:13
Alignment explanation
Indices: 873524--873548 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
873514 TAAAAAAAAA
873524 TTAGAGAGAGAAT
1 TTAGAGAGAGAAT
873537 TTAGAGAGAGAA
1 TTAGAGAGAGAA
873549 GCTTTCAAGC
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:0.48, C:0.00, G:0.32, T:0.20
Consensus pattern (13 bp):
TTAGAGAGAGAAT
Found at i:873798 original size:29 final size:28
Alignment explanation
Indices: 873760--873822 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
873750 GGTAATAGAA
* *
873760 AAAAAGTATATAAAAATAGATACAAAAG
1 AAAAAGTATACAAAAATAAATACAAAAG
* * *
873788 AAAAAGTTATACGAGAATAAATACAAGAG
1 AAAAAG-TATACAAAAATAAATACAAAAG
873817 AAAAAG
1 AAAAAG
873823 CTGTACATGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.65, C:0.05, G:0.14, T:0.16
Consensus pattern (28 bp):
AAAAAGTATACAAAAATAAATACAAAAG
Found at i:883023 original size:23 final size:23
Alignment explanation
Indices: 882997--883044 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
882987 TAGGAATAGT
*
882997 TTTTTAA-AAAAATTATTTACTAA
1 TTTTTAATAAAAA-TATTTAATAA
*
883020 TTTTTAATTAAAATATTTAATAA
1 TTTTTAATAAAAATATTTAATAA
883043 TT
1 TT
883045 AAAAATAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTTAATAAAAATATTTAATAA
Found at i:897007 original size:13 final size:14
Alignment explanation
Indices: 896982--897044 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
896972 ATTTAAAAAA
896982 TTAATTATAAAATT
1 TTAATTATAAAATT
896996 TTAATTA-AAAATT
1 TTAATTATAAAATT
*
897009 TTACACTTTAAAAAATT
1 TTA-A--TTATAAAATT
** *
897026 AAAATAATAAAATT
1 TTAATTATAAAATT
897040 TTAAT
1 TTAAT
897045 AACAAAAATC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
13 9 0.23
14 19 0.49
16 4 0.10
17 7 0.18
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAATTATAAAATT
Found at i:904725 original size:37 final size:37
Alignment explanation
Indices: 904654--904725 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
904644 TTTGATGTGG
**
904654 TTTTGAGACCTTATTAAGTCAAAATAATTTTTCATGA
1 TTTTGAGACCTTATTAAGTCAAAATAATACTTCATGA
* * *
904691 TTTTGGGATCTTATTATGTCAAAATAATACTTCAT
1 TTTTGAGACCTTATTAAGTCAAAATAATACTTCAT
904726 TAATGAGATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (37 bp):
TTTTGAGACCTTATTAAGTCAAAATAATACTTCATGA
Found at i:909885 original size:29 final size:28
Alignment explanation
Indices: 909853--909908 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
909843 CATTATTCTC
909853 TTGTAC-TTGTTCACGTATAACTTCTTTTT
1 TTGTACATT-TTCACGTATAACTT-TTTTT
*
909882 TTGTACATTTTCACGTATACCTTTTTT
1 TTGTACATTTTCACGTATAACTTTTTT
909909 CTATTACCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 4 0.16
29 19 0.76
30 2 0.08
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.55
Consensus pattern (28 bp):
TTGTACATTTTCACGTATAACTTTTTTT
Found at i:910127 original size:13 final size:12
Alignment explanation
Indices: 910109--910139 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
910099 CCTCCAAAGC
910109 TTCTCTCTCTAAA
1 TTCTCTCTCT-AA
910122 TTCTCTCTCTAA
1 TTCTCTCTCTAA
910134 TTCTCT
1 TTCTCT
910140 TTTATTTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (12 bp):
TTCTCTCTCTAA
Found at i:926408 original size:16 final size:17
Alignment explanation
Indices: 926383--926421 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
926373 TGTCTAGCGA
926383 AAAATATATTT-TTTTG
1 AAAATATATTTATTTTG
926399 ATAAAT-TATTTATTTTG
1 A-AAATATATTTATTTTG
926416 AAAATA
1 AAAATA
926422 GATGAACCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
AAAATATATTTATTTTG
Found at i:929066 original size:13 final size:13
Alignment explanation
Indices: 929048--929072 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
929038 AACTCTCAAG
929048 CAATAATTTAGTT
1 CAATAATTTAGTT
929061 CAATAATTTAGT
1 CAATAATTTAGT
929073 GATACAGGAT
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
CAATAATTTAGTT
Found at i:934484 original size:89 final size:89
Alignment explanation
Indices: 934407--934575 Score: 223
Period size: 89 Copynumber: 1.9 Consensus size: 89
934397 TTTCAGTCGG
* * * * * *
934407 CGACACTAGCCAGAAGCCCCAGTTCTCTCTAGAACC-AGTGGCACAGTAACCCATATCTTCTCTC
1 CGACACAAGCCAGAAGCCCCAGCTCTCTCTAGAACCGA-CGGCACAGGAACCCAGATATTCTCTC
934471 TCTAGCTTCTTCCTTTTCCAACCGA
65 TCTAGCTTCTTCCTTTTCCAACCGA
* * * *
934496 TGATACAAGCCCGAAGCCCCAGCTCTCTCTAGAACCGACGGCACAGGAACCCAGATATTCTCTTT
1 CGACACAAGCCAGAAGCCCCAGCTCTCTCTAGAACCGACGGCACAGGAACCCAGATATTCTCTCT
*
934561 CTTGCTTCTTCCTTT
66 CTAGCTTCTTCCTTT
934576 AGCCGGCGGC
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
89 67 0.99
90 1 0.01
ACGTcount: A:0.23, C:0.35, G:0.15, T:0.27
Consensus pattern (89 bp):
CGACACAAGCCAGAAGCCCCAGCTCTCTCTAGAACCGACGGCACAGGAACCCAGATATTCTCTCT
CTAGCTTCTTCCTTTTCCAACCGA
Found at i:935206 original size:24 final size:25
Alignment explanation
Indices: 935156--935213 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
935146 GCAAAATTTC
***
935156 AAATTTTCAACGGAATTTATGTTGG
1 AAATTTTCAACGGAATTTATAACGG
*
935181 AAATTTTCAACGG-ATTTCTAACGG
1 AAATTTTCAACGGAATTTATAACGG
*
935205 AATTTTTCA
1 AAATTTTCA
935214 TTGGAAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 15 0.54
25 13 0.46
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (25 bp):
AAATTTTCAACGGAATTTATAACGG
Found at i:935223 original size:37 final size:35
Alignment explanation
Indices: 935160--935231 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 35
935150 AATTTCAAAT
*
935160 TTTCAACGGAATTTATGTTGGAAATTTTCAACGGA
1 TTTCAACGGAATTTATATTGGAAATTTTCAACGGA
*
935195 TTTCTAACGGAATTTTTCATTGGAAATTTTCAACGGA
1 TTTC-AACGGAATTTAT-ATTGGAAATTTTCAACGGA
935232 AAGTATTACC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 4 0.12
36 11 0.33
37 18 0.55
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (35 bp):
TTTCAACGGAATTTATATTGGAAATTTTCAACGGA
Found at i:935232 original size:13 final size:13
Alignment explanation
Indices: 935179--935233 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
935169 AATTTATGTT
935179 GGAAATTTTCAAC
1 GGAAATTTTCAAC
935192 GG--A-TTTCTAAC
1 GGAAATTTTC-AAC
* **
935203 GGAATTTTTCATT
1 GGAAATTTTCAAC
935216 GGAAATTTTCAAC
1 GGAAATTTTCAAC
935229 GGAAA
1 GGAAA
935234 GTATTACCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
10 4 0.12
11 6 0.19
13 18 0.56
14 4 0.12
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.35
Consensus pattern (13 bp):
GGAAATTTTCAAC
Found at i:940014 original size:16 final size:16
Alignment explanation
Indices: 939986--940028 Score: 70
Period size: 15 Copynumber: 2.7 Consensus size: 16
939976 ATTTTATTAT
939986 ATTAAAAATATATAAAA
1 ATTAAAAA-ATATAAAA
940003 ATTAAAAAATATAAAA
1 ATTAAAAAATATAAAA
940019 A-TAAAAAATA
1 ATTAAAAAATA
940029 ATTGATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.35
16 9 0.35
17 8 0.31
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
ATTAAAAAATATAAAA
Found at i:947918 original size:40 final size:40
Alignment explanation
Indices: 947879--947975 Score: 167
Period size: 40 Copynumber: 2.4 Consensus size: 40
947869 ACCATAGCTT
*
947879 AACTTAAACAACATAATGAGGATTATGTATACAAAAGCTTTC
1 AACTTAAAC--CATAATGAAGATTATGTATACAAAAGCTTTC
947921 AACTTAAACCATAATGAAGATTATGTATACAAAAGCTTTC
1 AACTTAAACCATAATGAAGATTATGTATACAAAAGCTTTC
947961 AACTTAAACCATAAT
1 AACTTAAACCATAAT
947976 CCTCATTATG
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
40 45 0.83
42 9 0.17
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.29
Consensus pattern (40 bp):
AACTTAAACCATAATGAAGATTATGTATACAAAAGCTTTC
Found at i:947984 original size:40 final size:40
Alignment explanation
Indices: 947900--947985 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
947890 CATAATGAGG
* *
947900 ATTATGTATACAAAAGCTTTCAACTTAAACCATAATGAAG
1 ATTATGTATACAAAAGCTTTCAACTTAAACCATAATCAAC
**
947940 ATTATGTATACAAAAGCTTTCAACTTAAACCATAATCCTC
1 ATTATGTATACAAAAGCTTTCAACTTAAACCATAATCAAC
947980 ATTATG
1 ATTATG
947986 AGCTTTGTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (40 bp):
ATTATGTATACAAAAGCTTTCAACTTAAACCATAATCAAC
Found at i:951737 original size:28 final size:29
Alignment explanation
Indices: 951698--951779 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 29
951688 CAAAGAAAAG
951698 CTGTATATGAATAGGTATAAGAGAAGAAA
1 CTGTATATGAATAGGTATAAGAGAAGAAA
* * *
951727 TTGTAT-TGAATAGATATAAGAGAAGAAG
1 CTGTATATGAATAGGTATAAGAGAAGAAA
* * *
951755 CTGTATGTGAACAGGTACAAGAGAA
1 CTGTATATGAATAGGTATAAGAGAA
951780 TAAGGTAAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 25 0.56
29 20 0.44
ACGTcount: A:0.45, C:0.05, G:0.26, T:0.24
Consensus pattern (29 bp):
CTGTATATGAATAGGTATAAGAGAAGAAA
Found at i:951777 original size:29 final size:28
Alignment explanation
Indices: 951687--951779 Score: 100
Period size: 28 Copynumber: 3.3 Consensus size: 28
951677 ATAGAAGCTA
951687 ACAA-AGAA-AAGCTGTATATGAATAGGT
1 ACAAGAGAAGAAGCTGTAT-TGAATAGGT
* ** *
951714 ATAAGAGAAGAAATTGTATTGAATAGAT
1 ACAAGAGAAGAAGCTGTATTGAATAGGT
* *
951742 ATAAGAGAAGAAGCTGTATGTGAACAGGT
1 ACAAGAGAAGAAGCTGTAT-TGAATAGGT
951771 ACAAGAGAA
1 ACAAGAGAA
951780 TAAGGTAAAG
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
27 3 0.06
28 29 0.54
29 22 0.41
ACGTcount: A:0.48, C:0.05, G:0.25, T:0.22
Consensus pattern (28 bp):
ACAAGAGAAGAAGCTGTATTGAATAGGT
Found at i:954167 original size:34 final size:34
Alignment explanation
Indices: 954099--954167 Score: 79
Period size: 34 Copynumber: 2.0 Consensus size: 34
954089 TCAATTTGAG
**
954099 AAGATAAAAGGAGAGAATTAAGGAGATATGGGAA
1 AAGATAAAAGGAGAGAATTAAGGAGATAAAGGAA
*
954133 AAGATAAAGAAGGAGAGGATTAA-G-GATAAAGGAA
1 AAGAT-AA-AAGGAGAGAATTAAGGAGATAAAGGAA
954167 A
1 A
954168 TTGCAATTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
34 14 0.47
35 3 0.10
36 13 0.43
ACGTcount: A:0.55, C:0.00, G:0.32, T:0.13
Consensus pattern (34 bp):
AAGATAAAAGGAGAGAATTAAGGAGATAAAGGAA
Found at i:958491 original size:22 final size:22
Alignment explanation
Indices: 958464--958530 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
958454 TTAACCAGGA
958464 AAGCGCAATGGCATTGCATTGG
1 AAGCGCAATGGCATTGCATTGG
958486 AAGCGCAATGGCATTGCATTGG
1 AAGCGCAATGGCATTGCATTGG
958508 AAGCGCAATGGCATTGCATTGG
1 AAGCGCAATGGCATTGCATTGG
958530 A
1 A
958531 CCCATAAGTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.22
Consensus pattern (22 bp):
AAGCGCAATGGCATTGCATTGG
Found at i:960331 original size:32 final size:32
Alignment explanation
Indices: 960285--960348 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
960275 ACCCTTCAAA
**
960285 GTTTCAAAAGTTTATAATTTTTTCCTTATTTT
1 GTTTCAAAAGTTTATAATTTTACCCTTATTTT
960317 GTTTCAAATA-TTTATAATTTTACCCTTATTTT
1 GTTTCAAA-AGTTTATAATTTTACCCTTATTTT
960349 TAAAAAGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.27, C:0.11, G:0.05, T:0.58
Consensus pattern (32 bp):
GTTTCAAAAGTTTATAATTTTACCCTTATTTT
Found at i:970755 original size:10 final size:10
Alignment explanation
Indices: 970712--970772 Score: 59
Period size: 10 Copynumber: 5.6 Consensus size: 10
970702 ATTTTTTTCA
970712 TTTCTTTTTCT
1 TTTCTTTTT-T
970723 TTTCTCTTTTT
1 TTTCT-TTTTT
970734 TCTTCTTCTTTTT
1 T-TTC-T-TTTTT
970747 TTTCTTTTTT
1 TTTCTTTTTT
* *
970757 TTTCTGTGTT
1 TTTCTTTTTT
970767 TTTCTT
1 TTTCTT
970773 CTTCCTCCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
10 18 0.41
11 8 0.18
12 10 0.23
13 8 0.18
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.80
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:970758 original size:13 final size:14
Alignment explanation
Indices: 970706--970759 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 14
970696 ATGCCCATTT
970706 TTTTCATTTCTTTTTC
1 TTTTC-TTT-TTTTTC
*
970722 TTTTCTCTTTTTTC
1 TTTTCTTTTTTTTC
970736 TTCTTCTTTTTTTTC
1 TT-TTCTTTTTTTTC
970751 TTTT-TTTTT
1 TTTTCTTTTT
970760 CTGTGTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 5 0.14
14 10 0.29
15 15 0.43
16 5 0.14
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTCTTTTTTTTC
Found at i:970920 original size:24 final size:25
Alignment explanation
Indices: 970850--970922 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 25
970840 TCTCTCTTTT
* *
970850 TCTTTCTTTTCTTCTTTTTCCTTCTC
1 TCTTTCTTCT-TTCTTTTTCTTTCTC
* * * *
970876 TCATTC-TCCTTCCTTTCCTTTCTC
1 TCTTTCTTCTTTCTTTTTCTTTCTC
970900 -CTTTCTTCTTTCTTTTTCTTTCT
1 TCTTTCTTCTTTCTTTTTCTTTCT
970923 TTTCTCCTCG
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
23 4 0.11
24 26 0.72
25 1 0.03
26 5 0.14
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (25 bp):
TCTTTCTTCTTTCTTTTTCTTTCTC
Found at i:975613 original size:15 final size:15
Alignment explanation
Indices: 975593--975623 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
975583 ATAACAATAT
975593 AAAAATTTTTAGTGA
1 AAAAATTTTTAGTGA
975608 AAAAATTTTTAGTGA
1 AAAAATTTTTAGTGA
975623 A
1 A
975624 CTTCAACACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (15 bp):
AAAAATTTTTAGTGA
Found at i:980451 original size:22 final size:22
Alignment explanation
Indices: 980423--980474 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
980413 CGATATTTGT
* *
980423 GCATTGCGTGACTAGTTTTTAG
1 GCATTGCATGACTAATTTTTAG
*
980445 GCATTGCATTACTAATTTTTAG
1 GCATTGCATGACTAATTTTTAG
980467 GCATTGCA
1 GCATTGCA
980475 GGATTGATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.40
Consensus pattern (22 bp):
GCATTGCATGACTAATTTTTAG
Found at i:980486 original size:23 final size:22
Alignment explanation
Indices: 980423--980487 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
980413 CGATATTTGT
*
980423 GCATTGC-GTGACTAGTTTTTAG
1 GCATTGCAG-GACTAATTTTTAG
**
980445 GCATTGCATTACTAATTTTTAG
1 GCATTGCAGGACTAATTTTTAG
* *
980467 GCATTGCAGGATTGATTTTTA
1 GCATTGCAGGACTAATTTTTA
980488 AGTATTATGT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.23, C:0.12, G:0.22, T:0.43
Consensus pattern (22 bp):
GCATTGCAGGACTAATTTTTAG
Found at i:980652 original size:22 final size:22
Alignment explanation
Indices: 980600--980669 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
980590 ACTTAGGCAT
* * *
980600 TGCCTAAAAATCAGTCGCATAA
1 TGCCTAAAAATCAATCACACAA
*
980622 TACCTAAAAATCAATCACACAA
1 TGCCTAAAAATCAATCACACAA
* **
980644 TGCC-AAAAACCAATCACGTAA
1 TGCCTAAAAATCAATCACACAA
980665 TGCCT
1 TGCCT
980670 GAATATTAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 18 0.46
22 21 0.54
ACGTcount: A:0.44, C:0.27, G:0.09, T:0.20
Consensus pattern (22 bp):
TGCCTAAAAATCAATCACACAA
Found at i:985047 original size:14 final size:13
Alignment explanation
Indices: 985030--985085 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 13
985020 TTATATATTT
985030 TTTTTATTATACTA
1 TTTTTATTATA-TA
*
985044 TTTTTATTTTATA
1 TTTTTATTATATA
*
985057 -TATT-TT-TATA
1 TTTTTATTATATA
985067 TTTTTATTATTATA
1 TTTTTATTA-TATA
985081 TTTTT
1 TTTTT
985086 TCATAAGCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 4 0.11
11 5 0.14
12 5 0.14
13 2 0.06
14 19 0.54
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTTATTATATA
Found at i:985060 original size:23 final size:23
Alignment explanation
Indices: 985036--985081 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
985026 ATTTTTTTTA
985036 TTATACTATTTTTATTTTATATAT
1 TTATA-TATTTTTATTTTATATAT
*
985060 TTTTATATTTTTATTATTATAT
1 TTATATATTTTTATT-TTATAT
985082 TTTTTCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
TTATATATTTTTATTTTATATAT
Found at i:985077 original size:17 final size:15
Alignment explanation
Indices: 985017--985065 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 15
985007 GTGAACAAAA
985017 ATTTTATATATTTTT
1 ATTTTATATATTTTT
*
985032 TTTATTATACTATTTTT
1 ATT-TTATA-TATTTTT
985049 ATTTTATATATTTTT
1 ATTTTATATATTTTT
985064 AT
1 AT
985066 ATTTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 11 0.37
16 10 0.33
17 9 0.30
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTATATATTTTT
Found at i:985085 original size:23 final size:23
Alignment explanation
Indices: 985042--985086 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
985032 TTTATTATAC
985042 TATTTTTATTTTATATATTTTTA
1 TATTTTTATTTTATATATTTTTA
985065 TATTTTTATTATTATAT-TTTTT
1 TATTTTTATT-TTATATATTTTT
985087 CATAAGCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (23 bp):
TATTTTTATTTTATATATTTTTA
Found at i:985332 original size:11 final size:10
Alignment explanation
Indices: 985298--985341 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
985288 TATGTTTGAA
985298 TTATTATTAT
1 TTATTATTAT
* *
985308 TTTTTATCAT
1 TTATTATTAT
985318 TTATTATTTAT
1 TTATTA-TTAT
985329 TTATTATT-T
1 TTATTATTAT
985338 TTAT
1 TTAT
985342 CAAGTAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 5 0.17
10 15 0.52
11 9 0.31
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (10 bp):
TTATTATTAT
Found at i:987252 original size:37 final size:37
Alignment explanation
Indices: 987162--987520 Score: 478
Period size: 37 Copynumber: 9.8 Consensus size: 37
987152 TTTTTTTCTT
* * * *
987162 AAATGAATTCCTCAAAATTGAGGCAATGCGACTTTTAA
1 AAATGAACTCCTCAAAACTGAGGCAACGAGACTTTT-A
* *
987200 AAATGAACTCTTCAAAACTGAGGCCACGAGACTTTTA
1 AAATGAACTCCTCAAAACTGAGGCAACGAGACTTTTA
* * *
987237 AAATAAACTCCTCAAAACTGAGGCAATGGGACTTTTA
1 AAATGAACTCCTCAAAACTGAGGCAACGAGACTTTTA
* *
987274 AAATGAACTCCTCAAAATTGAGGCAACGAGACTTTGA
1 AAATGAACTCCTCAAAACTGAGGCAACGAGACTTTTA
987311 AAATGAACTCCTCAAAACTGAGGCAACGCA-ACCTTTTA
1 AAATGAACTCCTCAAAACTGAGGCAACG-AGA-CTTTTA
*
987349 AAATGAACTCCTCAAAATTGAGGCAACGAGAC-TTTA
1 AAATGAACTCCTCAAAACTGAGGCAACGAGACTTTTA
*
987385 AAATGAAACT--T-AAAATTGAGGCAACGAGAC-TTTA
1 AAATG-AACTCCTCAAAACTGAGGCAACGAGACTTTTA
* * *
987419 AAATGAACTCCTCAAAATTGAGGTAACGAGACTTTAA
1 AAATGAACTCCTCAAAACTGAGGCAACGAGACTTTTA
*
987456 AAATGAACTCCTCAAAACTGAGGCAACGAGACTTTAA
1 AAATGAACTCCTCAAAACTGAGGCAACGAGACTTTTA
*
987493 AAATGAACTCCTCAAAACTGAGGTAACG
1 AAATGAACTCCTCAAAACTGAGGCAACG
987521 CAACCTTTTT
Statistics
Matches: 289, Mismatches: 24, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
33 4 0.01
34 28 0.10
35 2 0.01
36 27 0.09
37 164 0.57
38 64 0.22
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (37 bp):
AAATGAACTCCTCAAAACTGAGGCAACGAGACTTTTA
Found at i:987480 original size:182 final size:187
Alignment explanation
Indices: 987162--987529 Score: 566
Period size: 182 Copynumber: 2.0 Consensus size: 187
987152 TTTTTTTCTT
* * * * *
987162 AAATGAATTCCTCAAAATTGAGGCAATGCGACTTTTAAAAATGAACTCTTCAAAACTGAGGCCAC
1 AAATGAACTCCTCAAAATTGAGGCAACGAGACTTTTAAAAATGAACACTTCAAAACTGAGGCAAC
* * * *
987227 GAGACTTTTAAAATAAACTCCTCAAAACTGAGGCAATGGGACTTTTAAAATGAACTCCTCAAAAT
66 GAGACTTTTAAAATAAACTCCTCAAAACTGAGGCAACGAGACTTTAAAAATGAACTCCTCAAAAC
*
987292 TGAGGCAACGAGACTTTGAAAATGAACTCCTCAAAACTGAGGCAACGCAACCTTTTA
131 TGAGGCAACGAGACTTTAAAAATGAACTCCTCAAAACTGAGGCAACGCAACCTTTTA
*
987349 AAATGAACTCCTCAAAATTGAGGCAACGAGAC-TTT-AAAATGAA-ACTT-AAAATTGAGGCAAC
1 AAATGAACTCCTCAAAATTGAGGCAACGAGACTTTTAAAAATGAACACTTCAAAACTGAGGCAAC
* * *
987410 GAGAC-TTTAAAATGAACTCCTCAAAATTGAGGTAACGAGACTTTAAAAATGAACTCCTCAAAAC
66 GAGACTTTTAAAATAAACTCCTCAAAACTGAGGCAACGAGACTTTAAAAATGAACTCCTCAAAAC
*
987474 TGAGGCAACGAGACTTTAAAAATGAACTCCTCAAAACTGAGGTAACGCAACCTTTT
131 TGAGGCAACGAGACTTTAAAAATGAACTCCTCAAAACTGAGGCAACGCAACCTTTT
987530 TTCCTTTTTT
Statistics
Matches: 166, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
182 106 0.64
183 17 0.10
184 3 0.02
185 8 0.05
186 3 0.02
187 29 0.17
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (187 bp):
AAATGAACTCCTCAAAATTGAGGCAACGAGACTTTTAAAAATGAACACTTCAAAACTGAGGCAAC
GAGACTTTTAAAATAAACTCCTCAAAACTGAGGCAACGAGACTTTAAAAATGAACTCCTCAAAAC
TGAGGCAACGAGACTTTAAAAATGAACTCCTCAAAACTGAGGCAACGCAACCTTTTA
Found at i:993555 original size:14 final size:14
Alignment explanation
Indices: 993538--993585 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 14
993528 TTTCATTTCT
993538 TTTTTATTTTTTAA
1 TTTTTATTTTTTAA
*
993552 TTTTTATTATTTTTA
1 TTTTTATT-TTTTAA
*
993567 TTATATATTTTTTTAA
1 TT-TTTA-TTTTTTAA
993583 TTT
1 TTT
993586 ATTTTTTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 8 0.29
15 8 0.29
16 10 0.36
17 2 0.07
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTATTTTTTAA
Found at i:993564 original size:16 final size:15
Alignment explanation
Indices: 993544--993593 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
993534 TTCTTTTTTA
*
993544 TTTTTTAATTTTTAT
1 TTTTTTAATTTATAT
993559 TATTTTT-ATTATATAT
1 T-TTTTTAATT-TATAT
993575 TTTTTTAATTTAT-T
1 TTTTTTAATTTATAT
993589 TTTTT
1 TTTTT
993594 GTTTATGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.19
15 12 0.39
16 13 0.42
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTAATTTATAT
Found at i:993598 original size:12 final size:12
Alignment explanation
Indices: 993537--993599 Score: 56
Period size: 13 Copynumber: 5.0 Consensus size: 12
993527 TTTTCATTTC
*
993537 TTTTTTATTTTT
1 TTTTTTATTTAT
993549 TAATTTTTA-TTAT
1 T--TTTTTATTTAT
*
993562 TTTTATTATATAT
1 TTTT-TTATTTAT
993575 TTTTTTAATTTAT
1 TTTTTT-ATTTAT
*
993588 TTTTTTGTTTAT
1 TTTTTTATTTAT
993600 GATTTTAGTG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
11 3 0.07
12 11 0.26
13 22 0.52
14 6 0.14
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTTTATTTAT
Found at i:998753 original size:16 final size:15
Alignment explanation
Indices: 998722--998755 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
998712 ATTTGTAGAG
*
998722 TTATTTTATTATTTA
1 TTATTTTATTAATTA
998737 TTATTTATATTAATTA
1 TTATTT-TATTAATTA
998753 TTA
1 TTA
998756 AATAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATTTTATTAATTA
Found at i:1000863 original size:59 final size:61
Alignment explanation
Indices: 1000772--1000901 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 61
1000762 AAAGAAAAAC
* * * * * *
1000772 TTTTAAGCA-TTTTAAGCATTTTAAAGTGATTTTTGATATACATAG-AAAACCTTTGAGCG
1 TTTTGAGCATTTTTAAGCATTTTAAAGTCATTTTTGATACACAAAGAAAAACCTTTAAGCA
** * *
1000831 TTTTGAGCATTTTTAAGCA-TTTGGAGTCATTTTTGATACATAAAGAAAAACCTTTAAGTA
1 TTTTGAGCATTTTTAAGCATTTTAAAGTCATTTTTGATACACAAAGAAAAACCTTTAAGCA
1000891 TTTTGAGCATT
1 TTTTGAGCATT
1000902 CTTCGATAAG
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 28 0.47
60 31 0.53
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (61 bp):
TTTTGAGCATTTTTAAGCATTTTAAAGTCATTTTTGATACACAAAGAAAAACCTTTAAGCA
Found at i:1001132 original size:23 final size:23
Alignment explanation
Indices: 1001096--1001160 Score: 73
Period size: 22 Copynumber: 2.9 Consensus size: 23
1001086 GATTGATTTT
* *
1001096 TAAGTATTATGTGACTA-GTTGA
1 TAAGCATTACGTGACTAGGTTGA
*
1001118 TATGACATTACGTGAC-AGGTTGA
1 TAAG-CATTACGTGACTAGGTTGA
1001141 TAAGCATTACGTGACT-GGTT
1 TAAGCATTACGTGACTAGGTT
1001161 AGTAAGGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 19 0.53
23 17 0.47
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.35
Consensus pattern (23 bp):
TAAGCATTACGTGACTAGGTTGA
Found at i:1001184 original size:23 final size:23
Alignment explanation
Indices: 1001152--1001202 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1001142 AAGCATTACG
* * *
1001152 TGACTGGTTAGTAAGGTATTGTA
1 TGACTAGTTAGGAAGGCATTGTA
*
1001175 TGACTAGTTAGGAAGGCATTGTG
1 TGACTAGTTAGGAAGGCATTGTA
1001198 TGACT
1 TGACT
1001203 TAGGTATTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.25, C:0.08, G:0.31, T:0.35
Consensus pattern (23 bp):
TGACTAGTTAGGAAGGCATTGTA
Found at i:1001262 original size:22 final size:22
Alignment explanation
Indices: 1001229--1001288 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
1001219 ATCAGTTACG
*
1001229 CAATACCTAAAAACCAATCACA
1 CAATACCAAAAAACCAATCACA
* * * *
1001251 TAATTCCAAAAATCCAATGACA
1 CAATACCAAAAAACCAATCACA
*
1001273 CAATACCTAAAAACCA
1 CAATACCAAAAAACCA
1001289 GTAAAACAAT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.53, C:0.28, G:0.02, T:0.17
Consensus pattern (22 bp):
CAATACCAAAAAACCAATCACA
Found at i:1002049 original size:107 final size:107
Alignment explanation
Indices: 1001863--1002078 Score: 432
Period size: 107 Copynumber: 2.0 Consensus size: 107
1001853 GAACCAGAGC
1001863 TGTCGATGGAAGTGGAAAACCCCCATTTTGGTGCCCTTAGGCCACAGCTTTTGTGCAATGAATGA
1 TGTCGATGGAAGTGGAAAACCCCCATTTTGGTGCCCTTAGGCCACAGCTTTTGTGCAATGAATGA
1001928 GTTATGGCATTGATAGGGGAGAACCAGAGCTGTTGATGGTAG
66 GTTATGGCATTGATAGGGGAGAACCAGAGCTGTTGATGGTAG
1001970 TGTCGATGGAAGTGGAAAACCCCCATTTTGGTGCCCTTAGGCCACAGCTTTTGTGCAATGAATGA
1 TGTCGATGGAAGTGGAAAACCCCCATTTTGGTGCCCTTAGGCCACAGCTTTTGTGCAATGAATGA
1002035 GTTATGGCATTGATAGGGGAGAACCAGAGCTGTTGATGGTAG
66 GTTATGGCATTGATAGGGGAGAACCAGAGCTGTTGATGGTAG
1002077 TG
1 TG
1002079 GAAAACCCCC
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 109 1.00
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (107 bp):
TGTCGATGGAAGTGGAAAACCCCCATTTTGGTGCCCTTAGGCCACAGCTTTTGTGCAATGAATGA
GTTATGGCATTGATAGGGGAGAACCAGAGCTGTTGATGGTAG
Found at i:1004539 original size:21 final size:21
Alignment explanation
Indices: 1004473--1004541 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
1004463 GGCATCGCCT
* *
1004473 AAAAATCAGTCACGTAATGCC
1 AAAAACCAATCACGTAATGCC
* *** **
1004494 TAAAAACTAATCATAAAATATC
1 -AAAAACCAATCACGTAATGCC
1004516 AAAAACCAATCACGTAATGCC
1 AAAAACCAATCACGTAATGCC
1004537 AAAAA
1 AAAAA
1004542 ACCAGAGACG
Statistics
Matches: 33, Mismatches: 14, Indels: 1
0.69 0.29 0.02
Matches are distributed among these distances:
21 20 0.61
22 13 0.39
ACGTcount: A:0.54, C:0.20, G:0.07, T:0.19
Consensus pattern (21 bp):
AAAAACCAATCACGTAATGCC
Found at i:1004598 original size:22 final size:23
Alignment explanation
Indices: 1004564--1004643 Score: 76
Period size: 22 Copynumber: 3.6 Consensus size: 23
1004554 ATGATTAAGG
*
1004564 CACGCAATGCCTAAAAAT-CAAT
1 CACGCAATACCTAAAAATCCAAT
*
1004586 CTCGCAATACCT-AAAATCCAAT
1 CACGCAATACCTAAAAATCCAAT
* * *
1004608 GACACAATACCTAAAAA-CTAAT
1 CACGCAATACCTAAAAATCCAAT
* *
1004630 AAAGCAATACCTAA
1 CACGCAATACCTAA
1004644 TAAGTAATCG
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 5 0.11
22 38 0.81
23 4 0.09
ACGTcount: A:0.49, C:0.26, G:0.06, T:0.19
Consensus pattern (23 bp):
CACGCAATACCTAAAAATCCAAT
Found at i:1007566 original size:21 final size:23
Alignment explanation
Indices: 1007542--1007590 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 23
1007532 ATTTCAGTTT
1007542 TTTTTA-TTATAATTTATT-TTA
1 TTTTTATTTATAATTTATTATTA
*
1007563 -TTTTATTTATTATTTATTATTA
1 TTTTTATTTATAATTTATTATTA
1007585 TCTTTT
1 T-TTTT
1007591 GTTTGAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 5 0.22
21 11 0.48
22 3 0.13
24 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTTATTTATAATTTATTATTA
Found at i:1007583 original size:10 final size:10
Alignment explanation
Indices: 1007544--1007585 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
1007534 TTCAGTTTTT
*
1007544 TTTATTATAA
1 TTTATTATTA
1007554 TTTATT-TTA
1 TTTATTATTA
1007563 TTTTATTTATTA
1 -TTTA-TTATTA
1007575 TTTATTATTA
1 TTTATTATTA
1007585 T
1 T
1007586 CTTTTGTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
9 2 0.07
10 17 0.61
11 6 0.21
12 3 0.11
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTATTATTA
Done.