Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 128 of 444
Found at i:33478922 original size:55 final size:55
Alignment explanation
Indices: 33478851--33478954 Score: 199
Period size: 55 Copynumber: 1.9 Consensus size: 55
33478841 GCGAGCTCAA
33478851 ATTATATAGCACTATGTGTGCGAGCTGATTTTATAGCACTAAGTGTGCGAATTTG
1 ATTATATAGCACTATGTGTGCGAGCTGATTTTATAGCACTAAGTGTGCGAATTTG
*
33478906 ATTATATAGCATTATGTGTGCGAGCTGATTTTATAGCACTAAGTGTGCG
1 ATTATATAGCACTATGTGTGCGAGCTGATTTTATAGCACTAAGTGTGCG
33478955 GATTCACTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (55 bp):
ATTATATAGCACTATGTGTGCGAGCTGATTTTATAGCACTAAGTGTGCGAATTTG
Found at i:33479672 original size:18 final size:15
Alignment explanation
Indices: 33479634--33479664 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
33479624 TGGCCATAGT
33479634 TGTA-TTATGTATGA
1 TGTAGTTATGTATGA
33479648 TGTAGTTATGTATGA
1 TGTAGTTATGTATGA
33479663 TG
1 TG
33479665 AAATAGTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (15 bp):
TGTAGTTATGTATGA
Found at i:33486763 original size:27 final size:27
Alignment explanation
Indices: 33486679--33486832 Score: 173
Period size: 27 Copynumber: 5.5 Consensus size: 27
33486669 GACGAGAATG
* * *
33486679 GCACTAAGTGTGCAAGCTGGAAATATATG
1 GCACTAAGTGTGCGAGCT-G-ATTATATA
*
33486708 GCACTAAGTGTGCGAGCTCAAATTATATA
1 GCACTAAGTGTGCGAGCT--GATTATATA
* *
33486737 GCACTATGTGTGCGAGCTGATTTTATA
1 GCACTAAGTGTGCGAGCTGATTATATA
**
33486764 GCACTAAGTGTGCGAATTTGATTATATA
1 GCACTAAGTGTGCG-AGCTGATTATATA
* *
33486792 GCACTATGTGTGCGAGCTGATTTTATA
1 GCACTAAGTGTGCGAGCTGATTATATA
33486819 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
33486833 GATTCACTAT
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
27 43 0.41
28 23 0.22
29 40 0.38
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTGATTATATA
Found at i:33486800 original size:55 final size:55
Alignment explanation
Indices: 33486729--33486832 Score: 208
Period size: 55 Copynumber: 1.9 Consensus size: 55
33486719 GCGAGCTCAA
33486729 ATTATATAGCACTATGTGTGCGAGCTGATTTTATAGCACTAAGTGTGCGAATTTG
1 ATTATATAGCACTATGTGTGCGAGCTGATTTTATAGCACTAAGTGTGCGAATTTG
33486784 ATTATATAGCACTATGTGTGCGAGCTGATTTTATAGCACTAAGTGTGCG
1 ATTATATAGCACTATGTGTGCGAGCTGATTTTATAGCACTAAGTGTGCG
33486833 GATTCACTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (55 bp):
ATTATATAGCACTATGTGTGCGAGCTGATTTTATAGCACTAAGTGTGCGAATTTG
Found at i:33488483 original size:132 final size:131
Alignment explanation
Indices: 33488245--33488484 Score: 293
Period size: 132 Copynumber: 1.8 Consensus size: 131
33488235 AAAGGCGATG
* * * * *
33488245 TTCGATATTTGGCAATTCATAGAATCGTGCCTATCGTGTTGGGTTGCAATTTCTCGTTTGTTCAA
1 TTCGATATTTGGCAATTCAGAGAATCGTGCCTATCGTGCTGGGTTACAATTTCTCGCTTGTCCAA
* * ** *
33488310 AATAATCAAAAGTCCCTTTTGAATTTCACTTATGTTTTCTAAAAACTCTTCAAAACGAAGGTAAT
66 AATAATCAAAAGTCCCTTTAGAATTTCACTAATACTCTCTAAAAACTCTTCAAAACGAAGGTAAT
33488375 A
131 A
* * * * *
33488376 TTCGATGTTTGGCAATTCGGAGAATCGTGAGCTATCGTGCTGGGTTACGATTTCTTGCTTGTCCA
1 TTCGATATTTGGCAATTCAGAGAATCGTG-CCTATCGTGCTGGGTTACAATTTCTCGCTTGTCCA
* * *
33488441 AAATGATC-GAAGATTCCTTTAGAATTTCACTAATACTCTCTAAA
65 AAATAATCAAAAG-TCCCTTTAGAATTTCACTAATACTCTCTAAA
33488485 TTTGAAAATA
Statistics
Matches: 89, Mismatches: 18, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
131 29 0.33
132 60 0.67
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.37
Consensus pattern (131 bp):
TTCGATATTTGGCAATTCAGAGAATCGTGCCTATCGTGCTGGGTTACAATTTCTCGCTTGTCCAA
AATAATCAAAAGTCCCTTTAGAATTTCACTAATACTCTCTAAAAACTCTTCAAAACGAAGGTAAT
A
Found at i:33489947 original size:40 final size:40
Alignment explanation
Indices: 33489887--33490074 Score: 263
Period size: 40 Copynumber: 4.7 Consensus size: 40
33489877 ACTACTTGCT
*
33489887 CAAATGCCTTCGGGACTTAGCCTGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
33489927 CAAATGCCTTTGGGATTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
33489967 CAAATGCCTTCGTGACTTAGCCCGGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
33490007 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
*
33490046 CAAATACCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
33490075 CATCCAAATA
Statistics
Matches: 130, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
38 1 0.01
39 32 0.25
40 96 0.74
41 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:33491952 original size:179 final size:179
Alignment explanation
Indices: 33491642--33492002 Score: 668
Period size: 179 Copynumber: 2.0 Consensus size: 179
33491632 ATTCCAACTT
*
33491642 CAACTCAGATTCTTTACTACTTAACACGAAAGCAAGGTAGGCTTCATATCCTTTTCTCATATACC
1 CAACTCAGATTCTTTACTACTCAACACGAAAGCAAGGTAGGCTTCATATCCTTTTCTCATATACC
33491707 TTTGAGCCATCATTGAGGTAATCACAACCGACGGAGTATTCAACTCACTTGAATCAATCAGGAGA
66 TTTGAGCCATCATTGAGGTAATCACAACCGACGGAGTATTCAACTCACTTGAATCAATCAGGAGA
*
33491772 ATCTCACCATCTGAGAATTTCAATTCGATGTACTTGCTACCACAATTTA
131 ATCTCACCATCTGAGAATTTCAATTCGATATACTTGCTACCACAATTTA
33491821 CAACTCAGATTCTTTACTACTCAACACGAAAGCAAGGTAGGCTTCATATCCTTTTCTCATATACC
1 CAACTCAGATTCTTTACTACTCAACACGAAAGCAAGGTAGGCTTCATATCCTTTTCTCATATACC
* * *
33491886 TTTGAGCCATCATTGAGGTAATCACAACTGACGGAGTATTCAACTCACTTGAATTAATCCGGAGA
66 TTTGAGCCATCATTGAGGTAATCACAACCGACGGAGTATTCAACTCACTTGAATCAATCAGGAGA
*
33491951 ATCTCACCATCTGAGCATTTCAATTCGATATACTTGCTACCACAATTTA
131 ATCTCACCATCTGAGAATTTCAATTCGATATACTTGCTACCACAATTTA
33492000 CAA
1 CAA
33492003 TCACATCATG
Statistics
Matches: 176, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
179 176 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (179 bp):
CAACTCAGATTCTTTACTACTCAACACGAAAGCAAGGTAGGCTTCATATCCTTTTCTCATATACC
TTTGAGCCATCATTGAGGTAATCACAACCGACGGAGTATTCAACTCACTTGAATCAATCAGGAGA
ATCTCACCATCTGAGAATTTCAATTCGATATACTTGCTACCACAATTTA
Found at i:33497831 original size:22 final size:21
Alignment explanation
Indices: 33497790--33497833 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
33497780 TTACAAAAAA
*
33497790 TATCGATATCATTTTAGTAGG
1 TATCGATATCATTCTAGTAGG
33497811 TATCGATACTCATTGCT-GTAGG
1 TATCGATA-TCATT-CTAGTAGG
33497833 T
1 T
33497834 GAAGTTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 11 0.55
23 1 0.05
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (21 bp):
TATCGATATCATTCTAGTAGG
Found at i:33499740 original size:20 final size:19
Alignment explanation
Indices: 33499715--33499754 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
33499705 AATCGGGCCA
*
33499715 TAAAAAAATTTCGTTCAAAT
1 TAAAAAAA-TTCATTCAAAT
*
33499735 TAAAAACATTCATTCAAAT
1 TAAAAAAATTCATTCAAAT
33499754 T
1 T
33499755 CATAATGTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (19 bp):
TAAAAAAATTCATTCAAAT
Found at i:33501796 original size:48 final size:48
Alignment explanation
Indices: 33501753--33501880 Score: 193
Period size: 48 Copynumber: 2.7 Consensus size: 48
33501743 TCATATCGGT
** *
33501753 GCCGATGCCATGTCATAGACATGGTCTTACACTAGCACACATATCACC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAAC
* * *
33501801 GCTGAAGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAAC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAAC
*
33501849 GCCGATACCATGTCCCAGACATGGTCTTACAC
1 GCCGATGCCATGTCCCAGACATGGTCTTACAC
33501881 GTGATCTCAT
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 71 1.00
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAAC
Found at i:33502316 original size:3 final size:3
Alignment explanation
Indices: 33502308--33502368 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
33502298 ATGAAATTGC
33502308 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
33502356 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
33502369 CATGAACTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:33504808 original size:29 final size:32
Alignment explanation
Indices: 33504756--33504819 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
33504746 ACAGTCTATA
33504756 TTTTTATAATTTTTAAAAGATT-AAAT-TAAT
1 TTTTTATAATTTTTAAAAGATTAAAATATAAT
** *
33504786 TTTTTATAA-TTTTAAGGGGTTAAAATATAAT
1 TTTTTATAATTTTTAAAAGATTAAAATATAAT
33504817 TTT
1 TTT
33504820 ATTTTTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 9 0.31
30 13 0.45
31 7 0.24
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (32 bp):
TTTTTATAATTTTTAAAAGATTAAAATATAAT
Found at i:33505533 original size:15 final size:15
Alignment explanation
Indices: 33505513--33505545 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
33505503 GAATTATCTT
33505513 TCCCATACACATAAC
1 TCCCATACACATAAC
*
33505528 TCCCATATACATAAC
1 TCCCATACACATAAC
33505543 TCC
1 TCC
33505546 TAACTAGGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.39, G:0.00, T:0.24
Consensus pattern (15 bp):
TCCCATACACATAAC
Found at i:33513487 original size:18 final size:18
Alignment explanation
Indices: 33513464--33513498 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
33513454 CCGGCGCCCC
33513464 CTCTCTCCTT-TCCTTTTT
1 CTCTCT-CTTATCCTTTTT
33513482 CTCTCTCTTATCCTTTT
1 CTCTCTCTTATCCTTTT
33513499 CTTTTCTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.60
Consensus pattern (18 bp):
CTCTCTCTTATCCTTTTT
Found at i:33514272 original size:23 final size:21
Alignment explanation
Indices: 33514237--33514308 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
33514227 TTAATTTTAA
*
33514237 AAAATTTGAAATATATATTTG
1 AAAATTTTAAATATATATTTG
* * *
33514258 AAATGTTTTATAATATATTTTTT
1 AAA-ATTTTA-AATATATATTTG
*
33514281 AAAATTTTAAATATATATTCTT
1 AAAATTTTAAATATATATT-TG
33514303 AAAATT
1 AAAATT
33514309 ATTTTTTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
21 12 0.29
22 17 0.40
23 13 0.31
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (21 bp):
AAAATTTTAAATATATATTTG
Found at i:33514293 original size:21 final size:21
Alignment explanation
Indices: 33514237--33514360 Score: 93
Period size: 21 Copynumber: 6.1 Consensus size: 21
33514227 TTAATTTTAA
* * *
33514237 AAAATTTGAAATATATATTTG
1 AAAATTTTAAATATATTTTTT
*
33514258 AAATGTTTTATAATATATTTTTT
1 AAA-ATTTTA-AATATATTTTTT
*
33514281 AAAATTTTAAATATATATTCTT
1 AAAATTTTAAATATAT-TTTTT
33514303 AAAA--TT--AT-T-TTTTTT
1 AAAATTTTAAATATATTTTTT
33514318 -AAATTTTAAATAT-TATTTTT
1 AAAATTTTAAATATAT-TTTTT
* *
33514338 GAAATTTTAAATATATTGTTT
1 AAAATTTTAAATATATTTTTT
33514359 AA
1 AA
33514361 TAATATAAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
14 3 0.04
15 4 0.05
16 3 0.04
17 1 0.01
18 4 0.05
19 2 0.02
20 7 0.08
21 28 0.34
22 18 0.22
23 13 0.16
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (21 bp):
AAAATTTTAAATATATTTTTT
Found at i:33514343 original size:35 final size:36
Alignment explanation
Indices: 33514275--33514343 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
33514265 TTATAATATA
33514275 TTTTTTAAAATTTTAAATATATATTCTTAAAATTAT
1 TTTTTTAAAATTTTAAATATATATTCTTAAAATTAT
* * *
33514311 TTTTTTTAAATTTTAAATAT-TATTTTTGAAATT
1 TTTTTTAAAATTTTAAATATATATTCTTAAAATT
33514344 TTAAATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 11 0.37
36 19 0.63
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (36 bp):
TTTTTTAAAATTTTAAATATATATTCTTAAAATTAT
Found at i:33514479 original size:10 final size:9
Alignment explanation
Indices: 33514416--33514475 Score: 52
Period size: 10 Copynumber: 6.4 Consensus size: 9
33514406 TTGTTATTAG
33514416 TTTTATAATA
1 TTTTA-AATA
33514426 TTTTAAATA
1 TTTTAAATA
33514435 --TTAAATA
1 TTTTAAATA
* *
33514442 TTTTTAATTTG
1 -TTTTAA-ATA
33514453 TTTTATAATA
1 TTTTA-AATA
33514463 TTTTAAATA
1 TTTTAAATA
33514472 TTTT
1 TTTT
33514476 TAAAATATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
7 7 0.17
9 12 0.29
10 20 0.49
11 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (9 bp):
TTTTAAATA
Found at i:33514552 original size:22 final size:23
Alignment explanation
Indices: 33514509--33514553 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
33514499 ATGACCTTTC
* *
33514509 AAATTTATTTTTTATAATATTTT
1 AAATGTATATTTTATAATATTTT
33514532 AAATGTATATTTTA-AATATTTT
1 AAATGTATATTTTATAATATTTT
33514554 CTAATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
AAATGTATATTTTATAATATTTT
Found at i:33514561 original size:30 final size:26
Alignment explanation
Indices: 33514527--33514605 Score: 77
Period size: 30 Copynumber: 2.7 Consensus size: 26
33514517 TTTTTATAAT
*
33514527 ATTTTAAATGTATATTTTAAATATTTTCTA
1 ATTTTAAAT-TA-ATTTTAAA-ATTAT-TA
33514557 ATTTTAAATATAATTTTTATAAATTATTA
1 ATTTTAAAT-TAA-TTTTA-AAATTATTA
33514586 ATTTTTAAATTAATTTTAAA
1 A-TTTTAAATTAATTTTAAA
33514606 GATATTCAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
27 2 0.05
28 5 0.11
29 7 0.16
30 28 0.64
31 2 0.05
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (26 bp):
ATTTTAAATTAATTTTAAAATTATTA
Found at i:33516001 original size:13 final size:14
Alignment explanation
Indices: 33515959--33516003 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
33515949 AATAAATGAT
33515959 TAAAGTATATTATAA
1 TAAAGTA-ATTATAA
33515974 TAATA-TAA-TATAA
1 TAA-AGTAATTATAA
33515987 TAAAGTAATTA-AA
1 TAAAGTAATTATAA
33516000 TAAA
1 TAAA
33516004 ACAAATAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 1 0.04
13 17 0.63
14 3 0.11
15 5 0.19
16 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (14 bp):
TAAAGTAATTATAA
Found at i:33516066 original size:12 final size:12
Alignment explanation
Indices: 33516048--33516081 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
33516038 GAACAGGGAA
33516048 AGAAAGAAAAAG
1 AGAAAGAAAAAG
*
33516060 GGAAAGAAAAAG
1 AGAAAGAAAAAG
*
33516072 AAAAAGAAAA
1 AGAAAGAAAA
33516082 TTTAGGGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AGAAAGAAAAAG
Found at i:33518477 original size:18 final size:19
Alignment explanation
Indices: 33518454--33518492 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
33518444 TGGAATTAAG
*
33518454 AATTGAAATGTGA-ATTGA
1 AATTGAAATATGAGATTGA
*
33518472 AATTGAGATATGAGATTGA
1 AATTGAAATATGAGATTGA
33518491 AA
1 AA
33518493 GCTTGAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (19 bp):
AATTGAAATATGAGATTGA
Found at i:33519884 original size:23 final size:23
Alignment explanation
Indices: 33519858--33519907 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 23
33519848 TGATGTTGGT
33519858 GATATTTTATAATTATTTAATTA
1 GATATTTTATAATTATTTAATTA
*
33519881 GATA----ATAATTATTTATTTA
1 GATATTTTATAATTATTTAATTA
33519900 -ATATTTTA
1 GATATTTTA
33519908 ATAAGATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 9
0.69 0.03 0.28
Matches are distributed among these distances:
18 3 0.14
19 14 0.64
22 1 0.05
23 4 0.18
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
GATATTTTATAATTATTTAATTA
Found at i:33521484 original size:123 final size:123
Alignment explanation
Indices: 33521265--33521603 Score: 597
Period size: 123 Copynumber: 2.8 Consensus size: 123
33521255 GAATTATGTG
*
33521265 AAATGAAATATGGATGTGTAATGATTATTGATGTATGTGTGTATGAGTATTTGAATGGTACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
*
33521330 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
33521388 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
33521453 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
* * * * *
33521511 AAATGAAATATGGATGTGTAATGATTATTGATTTATGTGTGCATGAGCAATTGAATGATACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
* *
33521576 GCTAAGTCCCGAAGACATTTATGCTAGT
66 GCTAAGTCCCGAAGGCAATTATGCTAGT
33521604 AATTATATCT
Statistics
Matches: 207, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 207 1.00
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.34
Consensus pattern (123 bp):
AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
Found at i:33521641 original size:40 final size:40
Alignment explanation
Indices: 33521572--33521815 Score: 292
Period size: 40 Copynumber: 6.1 Consensus size: 40
33521562 TGAATGATAC
* * * * **
33521572 CCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* * * * *
33521612 CTGGGTTAAGACCCGAAGGCAATTGTGCTAG-TGACTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTG-TTATAT
*
33521652 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
*
33521692 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* *
33521732 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* * ** *
33521772 CCGGGCTAAGACCCGAGGGCATTCGTGCGTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
33521812 CCGG
1 CCGG
33521816 TTGTATTCCG
Statistics
Matches: 180, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
40 178 0.99
41 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
Found at i:33524847 original size:21 final size:21
Alignment explanation
Indices: 33524823--33524867 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
33524813 AAATATCTGA
33524823 TAAATAAATTGGTAACTCCGG
1 TAAATAAATTGGTAACTCCGG
33524844 TAAATAAATTGGTAACTCCGG
1 TAAATAAATTGGTAACTCCGG
33524865 TAA
1 TAA
33524868 TGCTCTGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (21 bp):
TAAATAAATTGGTAACTCCGG
Found at i:33527304 original size:30 final size:29
Alignment explanation
Indices: 33527263--33527364 Score: 116
Period size: 30 Copynumber: 3.4 Consensus size: 29
33527253 GTTGCTCTGG
* *
33527263 GTGAAATGAACTCGAACTGCCTATGTCCGA
1 GTGATATGAACTCGAACCGCC-ATGTCCGA
*
33527293 GTGATATGAACTCGAACCGTCCATGTCCGG
1 GTGATATGAACTCGAACCG-CCATGTCCGA
**
33527323 GTGATATGAACTTAAACCGCCCATGTCC-A
1 GTGATATGAACTCGAACCG-CCATGTCCGA
33527352 GGTGATATGAACT
1 -GTGATATGAACT
33527365 GCTCTGGGAC
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
30 61 0.97
31 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.25
Consensus pattern (29 bp):
GTGATATGAACTCGAACCGCCATGTCCGA
Found at i:33530324 original size:22 final size:21
Alignment explanation
Indices: 33530297--33530348 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
33530287 AAATATTTAA
*
33530297 ATATTTTATATTATTAAAAAAT
1 ATATTTTAAATT-TTAAAAAAT
*
33530319 ATATTTAAAATTTTAAAAAAT
1 ATATTTTAAATTTTAAAAAAT
33530340 A-ATTTTAAA
1 ATATTTTAAA
33530349 AATATATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 7 0.26
21 10 0.37
22 10 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATTTTAAATTTTAAAAAAT
Found at i:33530334 original size:21 final size:21
Alignment explanation
Indices: 33530310--33530383 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
33530300 TTTTATATTA
33530310 TTAAAAAATATATTTAAAATT
1 TTAAAAAATATATTTAAAATT
33530331 TTAAAAAATA-A--T----TT
1 TTAAAAAATATATTTAAAATT
* *
33530345 TAAAAATATATATTTAAAATT
1 TTAAAAAATATATTTAAAATT
33530366 TT-AAAAATATATTATAAA
1 TTAAAAAATATATT-TAAA
33530384 GCATTTCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 16
0.67 0.07 0.26
Matches are distributed among these distances:
14 10 0.24
15 1 0.02
17 1 0.02
18 1 0.02
20 11 0.27
21 17 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAAAATATATTTAAAATT
Found at i:33530389 original size:23 final size:22
Alignment explanation
Indices: 33530340--33530397 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
33530330 TTTAAAAAAT
*
33530340 AATTTTAAAAATATATATTTAA
1 AATTTTAAAAATATATATATAA
33530362 AATTTTAAAAATATAT-TATAA
1 AATTTTAAAAATATATATATAA
*
33530383 AGCATTTCAAAAATA
1 A--ATTTTAAAAATA
33530398 AATTTCAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 5 0.16
22 16 0.50
23 11 0.34
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (22 bp):
AATTTTAAAAATATATATATAA
Found at i:33530440 original size:24 final size:23
Alignment explanation
Indices: 33530412--33530461 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
33530402 TCAAGTTTTT
*
33530412 TAAAATCAATAATAAACAAATAAA
1 TAAAATAAATAA-AAACAAATAAA
**
33530436 TAAAATAAATAAGGACAAATAAA
1 TAAAATAAATAAAAACAAATAAA
33530459 TAA
1 TAA
33530462 GGACAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (23 bp):
TAAAATAAATAAAAACAAATAAA
Found at i:33530457 original size:14 final size:14
Alignment explanation
Indices: 33530438--33530472 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
33530428 CAAATAAATA
33530438 AAATAAATAAGGAC
1 AAATAAATAAGGAC
33530452 AAATAAATAAGGAC
1 AAATAAATAAGGAC
33530466 AAATAAA
1 AAATAAA
33530473 AAACTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.69, C:0.06, G:0.11, T:0.14
Consensus pattern (14 bp):
AAATAAATAAGGAC
Found at i:33532251 original size:27 final size:26
Alignment explanation
Indices: 33532214--33532328 Score: 131
Period size: 27 Copynumber: 4.3 Consensus size: 26
33532204 AGCATGGCTG
*
33532214 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGTCA
33532240 CCAGATACAGATAATCGTGGCAGAGTCA
1 CCAGA-ACAGATAAT-GTGGCAGAGTCA
* *
33532268 CCAGAACAGATATATGTGGTAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGTCA
* * * *
33532295 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGTCA
33532322 CCAGAAC
1 CCAGAAC
33532329 GCTTCCTCCA
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
26 5 0.06
27 55 0.71
28 18 0.23
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGTCA
Found at i:33532273 original size:54 final size:54
Alignment explanation
Indices: 33532214--33532328 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 54
33532204 AGCATGGCTG
* *
33532214 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGTCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
** * * *
33532268 CCAGAACAGATATATGTGGTAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
33532322 CCAGAAC
1 CCAGAAC
33532329 GCTTCCTCCA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
54 36 0.68
55 17 0.32
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:33533966 original size:26 final size:26
Alignment explanation
Indices: 33533930--33534039 Score: 168
Period size: 26 Copynumber: 4.2 Consensus size: 26
33533920 CATGAAATTC
33533930 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
33533956 TTATCATGAAATATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
33533982 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
33534008 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
33534034 TTATCA
1 TTATCA
33534040 ATTTGTACCA
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
26 77 0.97
27 2 0.03
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:33535009 original size:11 final size:11
Alignment explanation
Indices: 33534993--33535043 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
33534983 AAAAAACTAT
33534993 TTTTCTTACTG
1 TTTTCTTACTG
*
33535004 TTTTCTTACTT
1 TTTTCTTACTG
* *
33535015 TTTTTTTATTG
1 TTTTCTTACTG
* *
33535026 TTTTCTTGCTA
1 TTTTCTTACTG
33535037 TTTTCTT
1 TTTTCTT
33535044 GTTATTTTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.08, C:0.14, G:0.06, T:0.73
Consensus pattern (11 bp):
TTTTCTTACTG
Found at i:33535040 original size:22 final size:23
Alignment explanation
Indices: 33534988--33535061 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 23
33534978 TGCAAAAAAA
33534988 ACTATTTTTCTTACTGTTTTCTT
1 ACTATTTTTCTTACTGTTTTCTT
* *
33535011 ACT-TTTTTTTTATTGTTTTCTT
1 ACTATTTTTCTTACTGTTTTCTT
* ** *
33535033 GCTA-TTTTCTTGTTATTTT-TT
1 ACTATTTTTCTTACTGTTTTCTT
33535054 ACTATTTT
1 ACTATTTT
33535062 GCTACCATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
21 5 0.12
22 34 0.81
23 3 0.07
ACGTcount: A:0.12, C:0.12, G:0.05, T:0.70
Consensus pattern (23 bp):
ACTATTTTTCTTACTGTTTTCTT
Found at i:33539467 original size:2 final size:2
Alignment explanation
Indices: 33539460--33539492 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
33539450 TAAAGAACAT
33539460 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
33539493 TTGACATATT
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:33541080 original size:314 final size:314
Alignment explanation
Indices: 33540511--33541143 Score: 1230
Period size: 314 Copynumber: 2.0 Consensus size: 314
33540501 AGGATTAGTT
33540511 TTTGATTTGTACTTGATGTAATGGCTAATGTATTAGTTAGTTTTAGTTTGAAATTTAACTTGTAT
1 TTTGATTTGTACTTGATGTAATGGCTAATGTATTAGTTAGTTTTAGTTTGAAATTTAACTTGTAT
*
33540576 TAGTGGTGTATTGGTGGGAGCAGTTACATTGTTAGGTAACTGTCCAATTTGTTTTTATAACTTAC
66 TAGTGGTGTATTGGTAGGAGCAGTTACATTGTTAGGTAACTGTCCAATTTGTTTTTATAACTTAC
33540641 ATATATTTTGAATTATCAATGAAATGACATGAGATTTTTTCATCATCTTTGTTGTTCAAACTTAT
131 ATATATTTTGAATTATCAATGAAATGACATGAGATTTTTTCATCATCTTTGTTGTTCAAACTTAT
33540706 TACTCTCTCATTCATTTTTGCTTTGGTTTTCACTTTGTTTTGCAAATACAAATTTGCTTTGTGTT
196 TACTCTCTCATTCATTTTTGCTTTGGTTTTCACTTTGTTTTGCAAATACAAATTTGCTTTGTGTT
*
33540771 TCTGATACATTGTTGCTGTCAATGTTCTTACAAATGGTAATCAGAGCCTAAGTC
261 TCTGATACATTGTTGCTGTCAATGTTCCTACAAATGGTAATCAGAGCCTAAGTC
33540825 TTTGATTTGTACTTGATGTAATGGCTAATGTATTAGTTAGTTTTAGTTTGAAATTTAACTTGTAT
1 TTTGATTTGTACTTGATGTAATGGCTAATGTATTAGTTAGTTTTAGTTTGAAATTTAACTTGTAT
* *
33540890 TAGTGGTGTATTGGTAGGAGCAGTTACATTGTTCGGTAACTGTCCAGTTTGTTTTTATAACTTAC
66 TAGTGGTGTATTGGTAGGAGCAGTTACATTGTTAGGTAACTGTCCAATTTGTTTTTATAACTTAC
33540955 ATATATTTTGAATTATCAATGAAATGACATGAGATTTTTTCATCATCTTTGTTGTTCAAACTTAT
131 ATATATTTTGAATTATCAATGAAATGACATGAGATTTTTTCATCATCTTTGTTGTTCAAACTTAT
33541020 TACTCTCTCATTCATTTTTGCTTTGGTTTTCACTTTGTTTTGCAAATACAAATTTGCTTTGTGTT
196 TACTCTCTCATTCATTTTTGCTTTGGTTTTCACTTTGTTTTGCAAATACAAATTTGCTTTGTGTT
33541085 TCTGATACATTGTTGCTGTCAATGTTCCTACAAATGGTAATCAGAGCCTAAGTC
261 TCTGATACATTGTTGCTGTCAATGTTCCTACAAATGGTAATCAGAGCCTAAGTC
33541139 TTTGA
1 TTTGA
33541144 GGGCCTCTGT
Statistics
Matches: 315, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
314 315 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (314 bp):
TTTGATTTGTACTTGATGTAATGGCTAATGTATTAGTTAGTTTTAGTTTGAAATTTAACTTGTAT
TAGTGGTGTATTGGTAGGAGCAGTTACATTGTTAGGTAACTGTCCAATTTGTTTTTATAACTTAC
ATATATTTTGAATTATCAATGAAATGACATGAGATTTTTTCATCATCTTTGTTGTTCAAACTTAT
TACTCTCTCATTCATTTTTGCTTTGGTTTTCACTTTGTTTTGCAAATACAAATTTGCTTTGTGTT
TCTGATACATTGTTGCTGTCAATGTTCCTACAAATGGTAATCAGAGCCTAAGTC
Found at i:33547053 original size:13 final size:13
Alignment explanation
Indices: 33547037--33547102 Score: 89
Period size: 13 Copynumber: 5.1 Consensus size: 13
33547027 TTTAAACTAA
*
33547037 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
*
33547050 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
*
33547063 ACTTTTTC-ACAGC
1 AC-TTTTCAAAAGC
33547076 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
33547089 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
33547102 A
1 A
33547103 TTGCCAAACT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
12 5 0.11
13 37 0.80
14 4 0.09
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:33550576 original size:2 final size:2
Alignment explanation
Indices: 33550569--33550609 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
33550559 CTTGTAAATT
33550569 TA TA TA TA 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 TA TA TA TA T
33550610 TACTAATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33552674 original size:13 final size:13
Alignment explanation
Indices: 33552656--33552681 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33552646 TTCAAAAACT
33552656 TTAACGATTTTAC
1 TTAACGATTTTAC
33552669 TTAACGATTTTAC
1 TTAACGATTTTAC
33552682 AAATTGGTAC
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:0.08, T:0.46
Consensus pattern (13 bp):
TTAACGATTTTAC
Found at i:33552914 original size:20 final size:19
Alignment explanation
Indices: 33552891--33552930 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
33552881 TTAGTTTTAA
33552891 TTAATCTTAATTAATTAAGT
1 TTAATCTTAA-TAATTAAGT
* *
33552911 TTAATTTTAATAATTTAGT
1 TTAATCTTAATAATTAAGT
33552930 T
1 T
33552931 ATTAATTAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (19 bp):
TTAATCTTAATAATTAAGT
Found at i:33553644 original size:5 final size:5
Alignment explanation
Indices: 33553625--33553662 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
33553615 ATAAATAAGA
33553625 ATATT AT-TAT ATATT ATATT ATATT ATA-T ATATT ATAT
1 ATATT ATAT-T ATATT ATATT ATATT ATATT ATATT ATAT
33553663 AAATAGGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 5 0.17
5 24 0.80
6 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:33553945 original size:2 final size:2
Alignment explanation
Indices: 33553940--33553966 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33553930 ATTATATACG
33553940 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 T
33553967 GAGAATCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33554411 original size:13 final size:13
Alignment explanation
Indices: 33554395--33554422 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
33554385 CGATCTCTTC
33554395 TGGGTATTCTATA
1 TGGGTATTCTATA
33554408 TGGGTATTCTATA
1 TGGGTATTCTATA
33554421 TG
1 TG
33554423 TTCTTTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.25, T:0.46
Consensus pattern (13 bp):
TGGGTATTCTATA
Found at i:33556720 original size:12 final size:13
Alignment explanation
Indices: 33556699--33556735 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
33556689 ATAAATAAGA
33556699 ATAT-TATTATAT
1 ATATATATTATAT
33556711 AT-TATATTATAT
1 ATATATATTATAT
33556723 -TATATATTATAT
1 ATATATATTATAT
33556735 A
1 A
33556736 AATACGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.09
12 20 0.91
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATATATATTATAT
Found at i:33561849 original size:16 final size:16
Alignment explanation
Indices: 33561828--33561862 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
33561818 TTTAAAAATT
*
33561828 AATAACCTAAATTCGA
1 AATAACCCAAATTCGA
*
33561844 AATAACCCAAATTCTA
1 AATAACCCAAATTCGA
33561860 AAT
1 AAT
33561863 GAATCCAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.26
Consensus pattern (16 bp):
AATAACCCAAATTCGA
Found at i:33562416 original size:2 final size:2
Alignment explanation
Indices: 33562411--33562439 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33562401 CCTTATTTAT
33562411 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 T
33562440 GTATGTATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33567547 original size:2 final size:2
Alignment explanation
Indices: 33567540--33567583 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
33567530 ATGTTTTTCG
*
33567540 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33567582 TA
1 TA
33567584 CTCCAGTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33567708 original size:22 final size:22
Alignment explanation
Indices: 33567682--33567745 Score: 92
Period size: 22 Copynumber: 2.8 Consensus size: 22
33567672 GAAATACTAC
33567682 ATATACATGTAAATATATCTCA
1 ATATACATGTAAATATATCTCA
33567704 ATATACATGTAAATATATCTCA
1 ATATACATGTAAATATATCTCA
*
33567726 ATTATATCTATATAAATATA
1 A-TATA-C-ATGTAAATATA
33567746 AGTTTTAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
22 23 0.61
23 4 0.11
24 1 0.03
25 10 0.26
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (22 bp):
ATATACATGTAAATATATCTCA
Found at i:33569437 original size:17 final size:16
Alignment explanation
Indices: 33569411--33569442 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
33569401 AAATGAATAG
33569411 TAATTTTAATATTTTA
1 TAATTTTAATATTTTA
33569427 TAATATTTAATATTTT
1 TAAT-TTTAATATTTT
33569443 TTAAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TAATTTTAATATTTTA
Found at i:33569815 original size:29 final size:30
Alignment explanation
Indices: 33569772--33569853 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 30
33569762 AAAAATGAAT
*
33569772 TAAATCAAAATTTCATGTATAAAACTACACA
1 TAAATC-AAAGTTCATGTATAAAACTACACA
* * * *
33569803 -AAATCAAAGTTCATTTATGACATTACACA
1 TAAATCAAAGTTCATGTATAAAACTACACA
**
33569832 TTGGATCAAAGTTCATGTATAA
1 -TAAATCAAAGTTCATGTATAA
33569854 TTTTAATATT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
29 19 0.47
30 5 0.12
31 16 0.40
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.32
Consensus pattern (30 bp):
TAAATCAAAGTTCATGTATAAAACTACACA
Found at i:33570192 original size:9 final size:9
Alignment explanation
Indices: 33570142--33570234 Score: 66
Period size: 9 Copynumber: 9.9 Consensus size: 9
33570132 AATAATAAAA
*
33570142 AATTTCTAT
1 AATTTTTAT
33570151 AATTTTTTAT
1 AA-TTTTTAT
33570161 AATGTTTT-T
1 AAT-TTTTAT
33570170 AACTTTTTAAAT
1 AA-TTTTT--AT
33570182 AATTTTTAT
1 AATTTTTAT
*
33570191 AA-TTGTAT
1 AATTTTTAT
33570199 -ATTTTATAT
1 AATTTT-TAT
*
33570208 AAATTTTAT
1 AATTTTTAT
*
33570217 ATTTTTTTAT
1 A-ATTTTTAT
33570227 AATTTTTA
1 AATTTTTA
33570235 ATACATTTTA
Statistics
Matches: 67, Mismatches: 7, Indels: 20
0.71 0.07 0.21
Matches are distributed among these distances:
7 1 0.01
8 7 0.10
9 27 0.40
10 24 0.36
11 5 0.07
12 3 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (9 bp):
AATTTTTAT
Found at i:33570321 original size:10 final size:10
Alignment explanation
Indices: 33570306--33570339 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
33570296 TAACATATAA
33570306 ATAATATGTT
1 ATAATATGTT
33570316 ATAATATGTT
1 ATAATATGTT
33570326 ATAATAT-TT
1 ATAATATGTT
33570335 ATAAT
1 ATAAT
33570340 TTTTCTATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (10 bp):
ATAATATGTT
Found at i:33575214 original size:23 final size:23
Alignment explanation
Indices: 33575187--33575231 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
33575177 GCTAGATTTT
33575187 TCCTAAACATTATCACTAAATAA
1 TCCTAAACATTATCACTAAATAA
*
33575210 TCCTAAATATTATCACTAAATA
1 TCCTAAACATTATCACTAAATA
33575232 TTATCATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (23 bp):
TCCTAAACATTATCACTAAATAA
Found at i:33575230 original size:13 final size:13
Alignment explanation
Indices: 33575189--33575242 Score: 69
Period size: 13 Copynumber: 4.4 Consensus size: 13
33575179 TAGATTTTTC
*
33575189 CTAAACATTATCA
1 CTAAATATTATCA
33575202 CTAAATA--ATC-
1 CTAAATATTATCA
33575212 CTAAATATTATCA
1 CTAAATATTATCA
33575225 CTAAATATTATCA
1 CTAAATATTATCA
*
33575238 TTAAA
1 CTAAA
33575243 CAATTCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 7 0.19
11 3 0.08
12 3 0.08
13 23 0.64
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:33575821 original size:14 final size:14
Alignment explanation
Indices: 33575802--33575828 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33575792 AATATATACT
33575802 TTTATTTATTTTTA
1 TTTATTTATTTTTA
33575816 TTTATTTATTTTT
1 TTTATTTATTTTT
33575829 TCAAACGTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTATTTTTA
Found at i:33578078 original size:13 final size:13
Alignment explanation
Indices: 33578060--33578087 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
33578050 GAAGCACGAC
33578060 TCACACGGGCGTG
1 TCACACGGGCGTG
33578073 TCACACGGGCGTG
1 TCACACGGGCGTG
33578086 TC
1 TC
33578088 CCTGCCGAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.32, G:0.36, T:0.18
Consensus pattern (13 bp):
TCACACGGGCGTG
Found at i:33587001 original size:96 final size:96
Alignment explanation
Indices: 33586835--33587016 Score: 256
Period size: 96 Copynumber: 1.9 Consensus size: 96
33586825 GTGTCCGAGG
* * * ***
33586835 AAGTCTGTCATCGATGGGAATGATAGAGCAGATACGGAGCCCAAGAAGCTTAGTTCGAGCAAGGG
1 AAGTCTGTCATCGAAGGGAATGATAGAGCAGACAAGGAGCCCAAGAAGCTTAGAAAGAGCAAGGG
*
33586900 GAAAGCTGAAGCCAAGAGGGCAAAGATAAGC
66 GAAAGCCGAAGCCAAGAGGGCAAAGATAAGC
* * * *
33586931 AAGTCTGTCATCGAAGGGAATGATGGAGCAGACAATGAGCCTAAGAAGCTTGGAAAGAGCAAGGG
1 AAGTCTGTCATCGAAGGGAATGATAGAGCAGACAAGGAGCCCAAGAAGCTTAGAAAGAGCAAGGG
*
33586996 TAAAGCCGAAGCCAAGAGGGC
66 GAAAGCCGAAGCCAAGAGGGC
33587017 TAAAAGGAGC
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
96 74 1.00
ACGTcount: A:0.37, C:0.16, G:0.33, T:0.14
Consensus pattern (96 bp):
AAGTCTGTCATCGAAGGGAATGATAGAGCAGACAAGGAGCCCAAGAAGCTTAGAAAGAGCAAGGG
GAAAGCCGAAGCCAAGAGGGCAAAGATAAGC
Found at i:33597288 original size:5 final size:5
Alignment explanation
Indices: 33597278--33597304 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
33597268 TGAAAAGGAA
33597278 AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA
33597305 TTTATTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:33597423 original size:13 final size:13
Alignment explanation
Indices: 33597405--33597448 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
33597395 CTAGATTTTT
33597405 ACTAAATATTATC
1 ACTAAATATTATC
33597418 ACTAAATA--AT-
1 ACTAAATATTATC
*
33597428 TCTAAATATTATC
1 ACTAAATATTATC
33597441 ACTAAATA
1 ACTAAATA
33597449 ATTCAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.27
11 2 0.08
12 2 0.08
13 15 0.58
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (13 bp):
ACTAAATATTATC
Found at i:33597436 original size:23 final size:23
Alignment explanation
Indices: 33597406--33597457 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
33597396 TAGATTTTTA
33597406 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
33597429 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
33597452 CAAAAT
1 CTAAAT
33597458 TTAAAAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:33597827 original size:17 final size:18
Alignment explanation
Indices: 33597805--33597838 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33597795 ACAACTGCAA
33597805 TTAAAT-TATAATTATTT
1 TTAAATGTATAATTATTT
*
33597822 TTAAATGTATACTTATT
1 TTAAATGTATAATTATT
33597839 CAAACTTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TTAAATGTATAATTATTT
Found at i:33597914 original size:20 final size:19
Alignment explanation
Indices: 33597877--33597915 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
33597867 TTAATAATTC
* *
33597877 TAAATTAAATATTGTAAAT
1 TAAATTAAATAATATAAAT
33597896 TAAATGTAAATAATATAAAT
1 TAAAT-TAAATAATATAAAT
33597916 GAAGGAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
TAAATTAAATAATATAAAT
Found at i:33597957 original size:2 final size:2
Alignment explanation
Indices: 33597952--33597979 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33597942 TTTTTCTCAA
33597952 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
33597980 TAAATAGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33602567 original size:21 final size:21
Alignment explanation
Indices: 33602519--33602568 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
33602509 GAAGCTCAAA
*
33602519 AGAGCTAAACAAAAACCCATT
1 AGAGTTAAACAAAAACCCATT
* *
33602540 AGGGTTAAACAAAAACTCATAT
1 AGAGTTAAACAAAAACCCAT-T
33602562 A-AGTTAA
1 AGAGTTAA
33602569 CTAAAGCTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.52, C:0.16, G:0.12, T:0.20
Consensus pattern (21 bp):
AGAGTTAAACAAAAACCCATT
Found at i:33615520 original size:27 final size:28
Alignment explanation
Indices: 33615464--33615533 Score: 124
Period size: 27 Copynumber: 2.5 Consensus size: 28
33615454 AAACTTGTAC
33615464 AGCACTAAGTGTGCGAGTTTGATCATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
33615492 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
33615519 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
33615534 GACTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 24 0.59
28 17 0.41
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:33615544 original size:27 final size:27
Alignment explanation
Indices: 33615464--33615545 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
33615454 AAACTTGTAC
* *
33615464 AGCACTAAGTGTGCGAGTTTGA-TCATAT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
33615492 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
33615519 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
33615546 GCTTTTGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
26 1 0.02
27 30 0.61
28 18 0.37
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:33633535 original size:21 final size:21
Alignment explanation
Indices: 33633511--33633564 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
33633501 ATAAGTGCTA
*
33633511 AACGGAAACCCATAAGG-GTTG
1 AACGGAAACCCA-AAGGAGCTG
*
33633532 AACGGAAGCCCAAAGGAGCTG
1 AACGGAAACCCAAAGGAGCTG
*
33633553 AACAGAAACCCA
1 AACGGAAACCCA
33633565 CAAAGGTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (21 bp):
AACGGAAACCCAAAGGAGCTG
Found at i:33633604 original size:42 final size:42
Alignment explanation
Indices: 33633493--33633627 Score: 110
Period size: 42 Copynumber: 3.2 Consensus size: 42
33633483 AAGTTTGCAC
* * * * * * *
33633493 AGAAGCACATAAGTGCTAAACGGAAACCCATAAGGGTTGAAC
1 AGAAGCTCAAAAGAGCTAAACGAAAACCCATAAAGGTTAAAT
* * * * *
33633535 GGAAGCCCAAAGGAGCTGAAC-AGAAACCCACAAAGGTTAAAT
1 AGAAGCTCAAAAGAGCTAAACGA-AAACCCATAAAGGTTAAAT
* *
33633577 AGAAGCTCAAAAGAGCTAAACGAAAACCTATTAAGGTTAAAT
1 AGAAGCTCAAAAGAGCTAAACGAAAACCCATAAAGGTTAAAT
* *
33633619 GGAAACTCA
1 AGAAGCTCA
33633628 TATGAGTTAA
Statistics
Matches: 71, Mismatches: 20, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
42 70 0.99
43 1 0.01
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (42 bp):
AGAAGCTCAAAAGAGCTAAACGAAAACCCATAAAGGTTAAAT
Found at i:33639259 original size:13 final size:13
Alignment explanation
Indices: 33639241--33639304 Score: 85
Period size: 13 Copynumber: 4.9 Consensus size: 13
33639231 AGTTTGGCAA
33639241 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
33639254 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
33639267 TG-TTGTGAAAAAG
1 TGCTTTTG-AAAAG
*
33639280 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
33639293 TGCTTTTGAAAA
1 TGCTTTTGAAAA
33639305 ATTTGGTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
12 4 0.09
13 35 0.81
14 4 0.09
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:33639284 original size:26 final size:27
Alignment explanation
Indices: 33639241--33639305 Score: 98
Period size: 26 Copynumber: 2.5 Consensus size: 27
33639231 AGTTTGGCAA
*
33639241 TGCTTTTG-AAAAGTGCTTTTGAGAAG
1 TGCTTGTGAAAAAGTGCTTTTGAGAAG
33639267 TG-TTGTGAAAAAGTGCTTTTGAGAAG
1 TGCTTGTGAAAAAGTGCTTTTGAGAAG
*
33639293 TGCTTTTGAAAAA
1 TGCTTGTGAAAAA
33639306 TTTGGTTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
25 4 0.11
26 22 0.63
27 9 0.26
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (27 bp):
TGCTTGTGAAAAAGTGCTTTTGAGAAG
Found at i:33641126 original size:61 final size:63
Alignment explanation
Indices: 33641012--33641136 Score: 148
Period size: 62 Copynumber: 2.0 Consensus size: 63
33641002 TCAATTTGTA
* * * * *
33641012 TTAGATATTATAAATATTTAAGTTTATTTTTTACCTAATTATTATTTAGATACTA-TTTATAT
1 TTAGATATTACAAATATTAAACTTTATTTTTTACCTAATTAATATTTAAATACTACTTTATAT
* * *
33641074 TTAGATATTACAATTATTAAACTTTA-TTTTTA-TTAAATTAATATTTAAATACTACTTTGTAT
1 TTAGATATTACAAATATTAAACTTTATTTTTTACCT-AATTAATATTTAAATACTACTTTATAT
33641136 T
1 T
33641137 ACTTTATCAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
60 1 0.02
61 23 0.43
62 29 0.55
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.54
Consensus pattern (63 bp):
TTAGATATTACAAATATTAAACTTTATTTTTTACCTAATTAATATTTAAATACTACTTTATAT
Found at i:33642443 original size:14 final size:14
Alignment explanation
Indices: 33642400--33642448 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
33642390 ATTATATTTT
33642400 TAAATTAAAAAAAA
1 TAAATTAAAAAAAA
* *
33642414 TGAAATTAAGAGAAA
1 T-AAATTAAAAAAAA
* *
33642429 TATATTAAAATAAA
1 TAAATTAAAAAAAA
33642443 TAAATT
1 TAAATT
33642449 CAGATTTTGA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (14 bp):
TAAATTAAAAAAAA
Found at i:33652474 original size:21 final size:21
Alignment explanation
Indices: 33652450--33652514 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
33652440 AAGTCTAGCT
*
33652450 GAAGCACATAAGTGCTAAACG
1 GAAGCACACAAGTGCTAAACG
*
33652471 GAAGC-C-CGAAG-GCT-AACT
1 GAAGCACAC-AAGTGCTAAACG
*
33652489 GAAGCACACAAGTGTTAAACG
1 GAAGCACACAAGTGCTAAACG
33652510 GAAGC
1 GAAGC
33652515 CTGAAGGCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
18 8 0.23
19 7 0.20
20 7 0.20
21 13 0.37
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.12
Consensus pattern (21 bp):
GAAGCACACAAGTGCTAAACG
Found at i:33652491 original size:39 final size:39
Alignment explanation
Indices: 33652432--33652532 Score: 157
Period size: 39 Copynumber: 2.6 Consensus size: 39
33652422 ATCGTGATCT
* * *
33652432 GAAGCCCGAAGTCTAGCTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
*
33652471 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGTTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
*
33652510 GAAGCCTGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
33652533 TGATCAGAGC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.37, C:0.23, G:0.27, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
Found at i:33656037 original size:23 final size:23
Alignment explanation
Indices: 33656007--33656060 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
33655997 ATTATAAAAG
33656007 AATGAGTGAGCTTATGAAAGCTC
1 AATGAGTGAGCTTATGAAAGCTC
33656030 AATGAGTGAGCTTATGAAAGCTC
1 AATGAGTGAGCTTATGAAAGCTC
*
33656053 AGTGAGTG
1 AATGAGTG
33656061 CTCAAACATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (23 bp):
AATGAGTGAGCTTATGAAAGCTC
Found at i:33658853 original size:32 final size:31
Alignment explanation
Indices: 33658788--33658854 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
33658778 ACTTTAAATT
* * *
33658788 ATTAATTCTAATTATTTTAATATTTTATTTA
1 ATTAATTCTAATTATTTTAATATCTAATCTA
33658819 ATTAATTCCTAATTA-TTTAATTATCTAATCTA
1 ATTAATT-CTAATTATTTTAA-TATCTAATCTA
33658851 ATTA
1 ATTA
33658855 CGGTTTCCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 12 0.39
32 19 0.61
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.55
Consensus pattern (31 bp):
ATTAATTCTAATTATTTTAATATCTAATCTA
Found at i:33660120 original size:46 final size:46
Alignment explanation
Indices: 33660053--33660142 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
33660043 TTTAGTTTTC
* *
33660053 TGAGCAAAAATAAAAAGTGAAACAAAGAATGAAATGTATGAAATAG
1 TGAGCAAAAATAAAAAATGAAACAAAGAATGAAATGGATGAAATAG
*
33660099 TGAGCAAAAATAAAAAATGAAACAGAGAATGAAATGGATGAAAT
1 TGAGCAAAAATAAAAAATGAAACAAAGAATGAAATGGATGAAAT
33660143 GATGTTATGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.59, C:0.04, G:0.20, T:0.17
Consensus pattern (46 bp):
TGAGCAAAAATAAAAAATGAAACAAAGAATGAAATGGATGAAATAG
Found at i:33666152 original size:30 final size:30
Alignment explanation
Indices: 33666113--33666170 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
33666103 CACGGGCTGG
* *
33666113 CACATGGGCGTGTGGCCAACCCGTGTGGCT
1 CACACGGGCGTGTGCCCAACCCGTGTGGCT
*
33666143 CACACGGGCGTGTGCCCAGCCCGTGTGG
1 CACACGGGCGTGTGCCCAACCCGTGTGG
33666171 AAGTGCCTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.12, C:0.33, G:0.38, T:0.17
Consensus pattern (30 bp):
CACACGGGCGTGTGCCCAACCCGTGTGGCT
Found at i:33669332 original size:15 final size:16
Alignment explanation
Indices: 33669312--33669341 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33669302 TATATATGTA
33669312 TTATTT-TTTTCTTTT
1 TTATTTATTTTCTTTT
33669327 TTATTTATTTTCTTT
1 TTATTTATTTTCTTT
33669342 CTTTTTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (16 bp):
TTATTTATTTTCTTTT
Found at i:33670390 original size:16 final size:15
Alignment explanation
Indices: 33670369--33670412 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
33670359 ATAAAAATTG
33670369 AAATAAAACTAAAA-A
1 AAATAAAA-TAAAATA
33670384 CAAATAAAAATAAAATA
1 -AAAT-AAAATAAAATA
33670401 AAATAAAATAAA
1 AAATAAAATAAA
33670413 TGGACTCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 8 0.31
16 13 0.50
17 5 0.19
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16
Consensus pattern (15 bp):
AAATAAAATAAAATA
Found at i:33670400 original size:5 final size:5
Alignment explanation
Indices: 33670369--33670412 Score: 54
Period size: 5 Copynumber: 8.4 Consensus size: 5
33670359 ATAAAAATTG
33670369 AAATA AAACTA AAA-A CAAATAA AAATA AAATA AAATA AAATA AA
1 AAATA AAA-TA AAATA -AAAT-A AAATA AAATA AAATA AAATA AA
33670413 TGGACTCCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 1 0.03
5 24 0.69
6 9 0.26
7 1 0.03
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16
Consensus pattern (5 bp):
AAATA
Found at i:33672022 original size:14 final size:14
Alignment explanation
Indices: 33672004--33672032 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
33671994 AATAAAGCAG
33672004 TAAAAATAA-ATAA
1 TAAAAATAAGATAA
33672017 TAAAAATAAGATAA
1 TAAAAATAAGATAA
33672031 TA
1 TA
33672033 TGAAATAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.24
Consensus pattern (14 bp):
TAAAAATAAGATAA
Found at i:33674114 original size:27 final size:28
Alignment explanation
Indices: 33674057--33674126 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
33674047 AAATTTGTAC
**
33674057 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
*
33674085 AGCACTATGTGTGCG-AGCTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
33674112 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
33674127 GACTTATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 24 0.63
28 14 0.37
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:33674135 original size:27 final size:27
Alignment explanation
Indices: 33674057--33674138 Score: 103
Period size: 27 Copynumber: 3.0 Consensus size: 27
33674047 AAATTTGTAC
* *
33674057 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGGACTT-ATTATAT
* *
33674085 AGCACTATGTGTGC-GAGCTGATTATAT
1 AGCACTAAGTGTGCGGA-CTTATTATAT
33674112 AGCACTAAGTGTGCGGACTTATTATAT
1 AGCACTAAGTGTGCGGACTTATTATAT
33674139 GCTTTTGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
27 30 0.65
28 16 0.35
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.34
Consensus pattern (27 bp):
AGCACTAAGTGTGCGGACTTATTATAT
Found at i:33682035 original size:27 final size:28
Alignment explanation
Indices: 33681978--33682047 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
33681968 AAATTTGTAC
**
33681978 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
*
33682006 AGCACTATGTGTGCG-AGCTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
33682033 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
33682048 GACTTATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 24 0.63
28 14 0.37
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:33682056 original size:27 final size:27
Alignment explanation
Indices: 33681978--33682059 Score: 103
Period size: 27 Copynumber: 3.0 Consensus size: 27
33681968 AAATTTGTAC
* *
33681978 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGGACTT-ATTATAT
* *
33682006 AGCACTATGTGTGC-GAGCTGATTATAT
1 AGCACTAAGTGTGCGGA-CTTATTATAT
33682033 AGCACTAAGTGTGCGGACTTATTATAT
1 AGCACTAAGTGTGCGGACTTATTATAT
33682060 GCTTTTGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
27 30 0.65
28 16 0.35
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.34
Consensus pattern (27 bp):
AGCACTAAGTGTGCGGACTTATTATAT
Found at i:33686211 original size:38 final size:39
Alignment explanation
Indices: 33686169--33686256 Score: 124
Period size: 40 Copynumber: 2.3 Consensus size: 39
33686159 GTCCAACCCA
* *
33686169 ACACACCATGTA-GGGATAAAATCGACCCACCCATCCCT
1 ACACACCATATAGGGGATAAAATCAACCCACCCATCCCT
* *
33686207 ACACACCATATATGGGGATACAATCAACCCATCCATCCCT
1 ACACACCATATA-GGGGATAAAATCAACCCACCCATCCCT
33686247 ACACACCATA
1 ACACACCATA
33686257 AGGTACTGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 11 0.25
40 33 0.75
ACGTcount: A:0.36, C:0.36, G:0.10, T:0.17
Consensus pattern (39 bp):
ACACACCATATAGGGGATAAAATCAACCCACCCATCCCT
Found at i:33689583 original size:28 final size:29
Alignment explanation
Indices: 33689548--33689606 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
33689538 ATTACTATTT
33689548 TTTTATTATATAG-CGATAAATTGAGGAA
1 TTTTATTATATAGTCGATAAATTGAGGAA
*
33689576 TTTTATTATCTAGTCGATAAATTGAGGAA
1 TTTTATTATATAGTCGATAAATTGAGGAA
33689605 TT
1 TT
33689607 GTTTTTAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 12 0.41
29 17 0.59
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (29 bp):
TTTTATTATATAGTCGATAAATTGAGGAA
Found at i:33693279 original size:34 final size:34
Alignment explanation
Indices: 33693236--33693300 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
33693226 TGAGGGGTGT
33693236 TACAATTCTCTTGGTTATTATATCAATTTTGTGC
1 TACAATTCTCTTGGTTATTATATCAATTTTGTGC
33693270 TACAATTCTCTTGGTTATTATATCAATTTTG
1 TACAATTCTCTTGGTTATTATATCAATTTTG
33693301 AAAATACTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.51
Consensus pattern (34 bp):
TACAATTCTCTTGGTTATTATATCAATTTTGTGC
Found at i:33693928 original size:18 final size:19
Alignment explanation
Indices: 33693888--33693929 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
33693878 ACTTACTTAT
*
33693888 TAAAAACATTAAAAATTTG
1 TAAAAACATTAAAAATTTA
33693907 TAAAAA-ATTATAAAA-TTA
1 TAAAAACATTA-AAAATTTA
33693925 TAAAA
1 TAAAA
33693930 TTATTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
TAAAAACATTAAAAATTTA
Found at i:33694179 original size:27 final size:26
Alignment explanation
Indices: 33694095--33694196 Score: 80
Period size: 27 Copynumber: 3.7 Consensus size: 26
33694085 AAGTAAGTTC
* *
33694095 TACAATTTTCTATAAATTTTAATTATTTT
1 TACAATTTTTTAT-AA-TTTAA-AATTTT
* * *
33694124 TCCAATTTTTAAT-ATTTAAAATAAGTT
1 TACAATTTTTTATAATTTAAAAT--TTT
33694151 TACAATTTTTTATAATATTAAAATTTT
1 TACAATTTTTTATAAT-TTAAAATTTT
* *
33694178 TAAAATTTTTTACAATTTA
1 TACAATTTTTTATAATTTA
33694197 TTTTTACATT
Statistics
Matches: 59, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
25 2 0.03
26 8 0.14
27 30 0.51
28 2 0.03
29 17 0.29
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (26 bp):
TACAATTTTTTATAATTTAAAATTTT
Found at i:33697478 original size:56 final size:56
Alignment explanation
Indices: 33697418--33697721 Score: 493
Period size: 56 Copynumber: 5.4 Consensus size: 56
33697408 TCCCAGACAA
* *
33697418 GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAATGT
1 GGTCTTACTCGCACACATATATCGAAATCACATATCGATGCCAACGTATTAAACGT
* *
33697474 GGTCTTACTCGCACACATATATCGAAATCACATATCGATGCCAAC-TATTAAGCAT
1 GGTCTTACTCGCACACATATATCGAAATCACATATCGATGCCAACGTATTAAACGT
* * *
33697529 GGTCTTACTCGTACACATATATTGAAATCACATATCGATGCCAACGTATTAAATGT
1 GGTCTTACTCGCACACATATATCGAAATCACATATCGATGCCAACGTATTAAACGT
* *
33697585 GGTCTTACTCGCACACATATATCGAAATCACATATCGATGCCAACATATTAAACAT
1 GGTCTTACTCGCACACATATATCGAAATCACATATCGATGCCAACGTATTAAACGT
** *
33697641 GGTCTTACTCGCACACATATATCGAAATCACATATTAATGCCAATGTATTAAACGT
1 GGTCTTACTCGCACACATATATCGAAATCACATATCGATGCCAACGTATTAAACGT
33697697 GGTCTTACTCGCACACATATATCGA
1 GGTCTTACTCGCACACATATATCGA
33697722 TGCCATGGTC
Statistics
Matches: 228, Mismatches: 19, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
55 50 0.22
56 178 0.78
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.29
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATCGAAATCACATATCGATGCCAACGTATTAAACGT
Found at i:33697545 original size:111 final size:112
Alignment explanation
Indices: 33697418--33697721 Score: 529
Period size: 111 Copynumber: 2.7 Consensus size: 112
33697408 TCCCAGACAA
*
33697418 GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAATGTGGTCTTACT
1 GGTCTTACTCGCACACATATATCGAAATCACATATCGATGCCAACGTATTAAATGTGGTCTTACT
*
33697483 CGCACACATATATCGAAATCACATATCGATGCCAAC-TATTAAGCAT
66 CGCACACATATATCGAAATCACATATCGATGCCAACATATTAAACAT
* *
33697529 GGTCTTACTCGTACACATATATTGAAATCACATATCGATGCCAACGTATTAAATGTGGTCTTACT
1 GGTCTTACTCGCACACATATATCGAAATCACATATCGATGCCAACGTATTAAATGTGGTCTTACT
33697594 CGCACACATATATCGAAATCACATATCGATGCCAACATATTAAACAT
66 CGCACACATATATCGAAATCACATATCGATGCCAACATATTAAACAT
** * *
33697641 GGTCTTACTCGCACACATATATCGAAATCACATATTAATGCCAATGTATTAAACGTGGTCTTACT
1 GGTCTTACTCGCACACATATATCGAAATCACATATCGATGCCAACGTATTAAATGTGGTCTTACT
33697706 CGCACACATATATCGA
66 CGCACACATATATCGA
33697722 TGCCATGGTC
Statistics
Matches: 182, Mismatches: 10, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
111 98 0.54
112 84 0.46
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.29
Consensus pattern (112 bp):
GGTCTTACTCGCACACATATATCGAAATCACATATCGATGCCAACGTATTAAATGTGGTCTTACT
CGCACACATATATCGAAATCACATATCGATGCCAACATATTAAACAT
Found at i:33698575 original size:17 final size:18
Alignment explanation
Indices: 33698553--33698586 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
33698543 AACCCTAAGC
33698553 TTTTTTTCTTAT-TTTCT
1 TTTTTTTCTTATGTTTCT
*
33698570 TTTTTTTTTTATGTTTC
1 TTTTTTTCTTATGTTTC
33698587 AGTCATGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.06, C:0.09, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTTTTTCTTATGTTTCT
Found at i:33708813 original size:43 final size:43
Alignment explanation
Indices: 33708751--33708913 Score: 165
Period size: 43 Copynumber: 3.8 Consensus size: 43
33708741 AATGCCAACA
* * *
33708751 TCCCAGACGTGGTCATACATGTAATCAAATATCGATGCCACTG
1 TCCCAGACGTGGTCTTACACGAAATCAAATATCGATGCCACTG
* *
33708794 TCCCAGACAG-GGTCTTACATGAAATCAAATA-CGATGTCGA-TG
1 TCCCAGAC-GTGGTCTTACACGAAATCAAATATCGATG-CCACTG
* *
33708836 TCCCAGACATGGTCTTACACGTAAATCTCAA-ATCGATGCCAAC-G
1 TCCCAGACGTGGTCTTACACG-AAATC-AAATATCGATGCC-ACTG
* *
33708880 TCCCAAACGTGGTCTTACACGAAATCACATATCG
1 TCCCAGACGTGGTCTTACACGAAATCAAATATCG
33708914 GAATCCTATG
Statistics
Matches: 100, Mismatches: 11, Indels: 18
0.78 0.09 0.14
Matches are distributed among these distances:
42 26 0.26
43 45 0.45
44 29 0.29
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (43 bp):
TCCCAGACGTGGTCTTACACGAAATCAAATATCGATGCCACTG
Found at i:33710676 original size:25 final size:25
Alignment explanation
Indices: 33710634--33710682 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
33710624 TCTAACACTT
*
33710634 TTGGTATAAGTTAGAAATATTGGTA
1 TTGGTATAAGTTAAAAATATTGGTA
* *
33710659 TTGGTATAATTTAAAAATTTTGGT
1 TTGGTATAAGTTAAAAATATTGGT
33710683 TTGCCAAGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (25 bp):
TTGGTATAAGTTAAAAATATTGGTA
Found at i:33716622 original size:20 final size:20
Alignment explanation
Indices: 33716599--33716636 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
33716589 ATAAGTTTTA
33716599 TTTATCATTACAA-TATAATT
1 TTTAT-ATTACAATTATAATT
*
33716619 TTTATATTTCAATTATAA
1 TTTATATTACAATTATAA
33716637 ATTATTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTATATTACAATTATAATT
Found at i:33717121 original size:30 final size:30
Alignment explanation
Indices: 33717066--33717123 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
33717056 GTAGATTTTG
* *
33717066 AGTGTCTCTATAAAGATTATCTTTATCAAA
1 AGTGTCCCTATAAAGATTATATTTATCAAA
33717096 AGTGTCCCTATAAAGATT-TAATTTATCA
1 AGTGTCCCTATAAAGATTAT-ATTTATCA
33717124 TGAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (30 bp):
AGTGTCCCTATAAAGATTATATTTATCAAA
Found at i:33718464 original size:22 final size:22
Alignment explanation
Indices: 33718425--33718475 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
33718415 AATAACGTCT
*
33718425 AATTCAATTTATTCAAATAAATA
1 AATT-AATATATTCAAATAAATA
* *
33718448 AATTAATATATTTAAATATATA
1 AATTAATATATTCAAATAAATA
*
33718470 TATTAA
1 AATTAA
33718476 AAAGAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTAATATATTCAAATAAATA
Found at i:33722987 original size:19 final size:19
Alignment explanation
Indices: 33722960--33722999 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
33722950 TGAAAATGTG
*
33722960 TAAGTTATGCCTATAAATT
1 TAAGCTATGCCTATAAATT
*
33722979 TAAGCTATGCCTATGAATT
1 TAAGCTATGCCTATAAATT
33722998 TA
1 TA
33723000 TGAGGACATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (19 bp):
TAAGCTATGCCTATAAATT
Found at i:33725083 original size:25 final size:25
Alignment explanation
Indices: 33725052--33725117 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
33725042 ATTATCATGG
* * *
33725052 TTTTATCCATAGTTTTGTGGTTTTA
1 TTTTATCCACAATTTTATGGTTTTA
*
33725077 TTTTATCTACAATTTTATGGTTTTA
1 TTTTATCCACAATTTTATGGTTTTA
* *
33725102 TTTTGTCCACATTTTT
1 TTTTATCCACAATTTT
33725118 TGTGATTTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.61
Consensus pattern (25 bp):
TTTTATCCACAATTTTATGGTTTTA
Found at i:33726297 original size:15 final size:15
Alignment explanation
Indices: 33726247--33726298 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
33726237 ACGGATTCAC
*
33726247 ATAATTTTGAATTTT
1 ATAATTTTGAATATT
* *
33726262 ATAAGTTATAAATATT
1 ATAA-TTTTGAATATT
* *
33726278 TTAATTTTGAATATA
1 ATAATTTTGAATATT
33726293 ATAATT
1 ATAATT
33726299 CATTTTATTT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
ATAATTTTGAATATT
Found at i:33727669 original size:39 final size:40
Alignment explanation
Indices: 33727626--33727711 Score: 111
Period size: 39 Copynumber: 2.1 Consensus size: 40
33727616 TAAAAATTAT
* * *
33727626 ATATAATAAAATATTAATTATATTAAT-TTGTGTTTTTTA
1 ATATAATAAAACATTAATTATATTAATATAGTGTTCTTTA
* *
33727665 ATATAATAAAACATTTATTATATTTATGATAGTGTTCTTTA
1 ATATAATAAAACATTAATTATATTAAT-ATAGTGTTCTTTA
33727706 ATATAA
1 ATATAA
33727712 ATACTTTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 24 0.60
41 16 0.40
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (40 bp):
ATATAATAAAACATTAATTATATTAATATAGTGTTCTTTA
Found at i:33729676 original size:63 final size:63
Alignment explanation
Indices: 33729606--33729796 Score: 382
Period size: 63 Copynumber: 3.0 Consensus size: 63
33729596 ACCAAATACC
33729606 ATAAAATCATATCTCATAAAATCAGGATTTAAATAGGATATTATGTTTCTGATTTTAGGGGAG
1 ATAAAATCATATCTCATAAAATCAGGATTTAAATAGGATATTATGTTTCTGATTTTAGGGGAG
33729669 ATAAAATCATATCTCATAAAATCAGGATTTAAATAGGATATTATGTTTCTGATTTTAGGGGAG
1 ATAAAATCATATCTCATAAAATCAGGATTTAAATAGGATATTATGTTTCTGATTTTAGGGGAG
33729732 ATAAAATCATATCTCATAAAATCAGGATTTAAATAGGATATTATGTTTCTGATTTTAGGGGAG
1 ATAAAATCATATCTCATAAAATCAGGATTTAAATAGGATATTATGTTTCTGATTTTAGGGGAG
33729795 AT
1 AT
33729797 GATAAAGGAA
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 128 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (63 bp):
ATAAAATCATATCTCATAAAATCAGGATTTAAATAGGATATTATGTTTCTGATTTTAGGGGAG
Found at i:33730313 original size:92 final size:92
Alignment explanation
Indices: 33730150--33730332 Score: 312
Period size: 92 Copynumber: 2.0 Consensus size: 92
33730140 ATAGGGTTGT
* *
33730150 GTATATACATTCTCTCAACCTTTTTCTCTCTATTTCTTCACAAATGTATAATGCAATAATGTATA
1 GTATATACATTCTCTCAACCTTTTTCTCTCTATTTCTTCACAAATGTATAATGCAATAAGGCATA
33730215 ACTACTACTTCTAGAGAGATGATAACA
66 ACTACTACTTCTAGAGAGATGATAACA
33730242 GTATATACATTCTCTCAACCTTTTTCTCTCTATTTCTTCACAAATGTATAATGCAATAAGGCATA
1 GTATATACATTCTCTCAACCTTTTTCTCTCTATTTCTTCACAAATGTATAATGCAATAAGGCATA
* * * *
33730307 ATTACTAGTTGTTGAGAGATGATAAC
66 ACTACTACTTCTAGAGAGATGATAAC
33730333 TGTAGTCATC
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 85 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (92 bp):
GTATATACATTCTCTCAACCTTTTTCTCTCTATTTCTTCACAAATGTATAATGCAATAAGGCATA
ACTACTACTTCTAGAGAGATGATAACA
Found at i:33732859 original size:16 final size:16
Alignment explanation
Indices: 33732821--33732859 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
33732811 ATTACATGTG
33732821 AAAAATA-ATAAAATA
1 AAAAATATATAAAATA
**
33732836 AATTATATATAAAATA
1 AAAAATATATAAAATA
33732852 AAAAATAT
1 AAAAATAT
33732860 TCTACATTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAATATATAAAATA
Found at i:33739314 original size:2 final size:2
Alignment explanation
Indices: 33739278--33739305 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33739268 CTCTCTCTCT
33739278 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
33739306 GTCACACACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:33740837 original size:17 final size:16
Alignment explanation
Indices: 33740815--33740861 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 16
33740805 TTTTATGTGT
33740815 TTTTTAATTTATTATAA
1 TTTTTAATTT-TTATAA
33740832 TTTTTAAATTTTTATAA
1 TTTTT-AATTTTTATAA
33740849 TTTTATAATTTTT
1 TTTT-TAATTTTT
33740862 TTAAAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 22 0.79
18 6 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTAATTTTTATAA
Found at i:33747198 original size:16 final size:18
Alignment explanation
Indices: 33747179--33747211 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
33747169 TTATAAAGGT
33747179 TAATTAA-G-TAAAATAG
1 TAATTAATGATAAAATAG
33747195 TAATTAATGATAAAATA
1 TAATTAATGATAAAATA
33747212 AATAAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (18 bp):
TAATTAATGATAAAATAG
Found at i:33756144 original size:40 final size:40
Alignment explanation
Indices: 33756100--33756229 Score: 99
Period size: 40 Copynumber: 3.2 Consensus size: 40
33756090 ATAATAGAGA
33756100 TATTATATCGGTTCGAAAAATTTACATGCATAATGAATAC
1 TATTATATCGGTTCGAAAAATTTACATGCATAATGAATAC
** ** * **
33756140 TATTATATC-AAT--AAATATGATCATTTTAT-TATAAAAAAATA-
1 TATTATATCGGTTCGAAA-A--AT--TTACATGCAT-AATGAATAC
*
33756181 TATTACATCGGTTCGAAAAATTTACATGCATAATGAATAC
1 TATTATATCGGTTCGAAAAATTTACATGCATAATGAATAC
33756221 TATTATATC
1 TATTATATC
33756230 AATAAATATG
Statistics
Matches: 63, Mismatches: 16, Indels: 22
0.62 0.16 0.22
Matches are distributed among these distances:
37 3 0.05
38 1 0.02
39 11 0.17
40 21 0.33
41 12 0.19
42 11 0.17
43 1 0.02
44 3 0.05
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (40 bp):
TATTATATCGGTTCGAAAAATTTACATGCATAATGAATAC
Found at i:33756194 original size:81 final size:81
Alignment explanation
Indices: 33756099--33756264 Score: 323
Period size: 81 Copynumber: 2.0 Consensus size: 81
33756089 TATAATAGAG
*
33756099 ATATTATATCGGTTCGAAAAATTTACATGCATAATGAATACTATTATATCAATAAATATGATCAT
1 ATATTACATCGGTTCGAAAAATTTACATGCATAATGAATACTATTATATCAATAAATATGATCAT
33756164 TTTATTATAAAAAAAT
66 TTTATTATAAAAAAAT
33756180 ATATTACATCGGTTCGAAAAATTTACATGCATAATGAATACTATTATATCAATAAATATGATCAT
1 ATATTACATCGGTTCGAAAAATTTACATGCATAATGAATACTATTATATCAATAAATATGATCAT
33756245 TTTATTATAAAAAAAT
66 TTTATTATAAAAAAAT
33756261 ATAT
1 ATAT
33756265 AAAAAAATAT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 84 1.00
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (81 bp):
ATATTACATCGGTTCGAAAAATTTACATGCATAATGAATACTATTATATCAATAAATATGATCAT
TTTATTATAAAAAAAT
Found at i:33756267 original size:12 final size:12
Alignment explanation
Indices: 33756250--33756275 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
33756240 ATCATTTTAT
33756250 TATAAAAAAATA
1 TATAAAAAAATA
33756262 TATAAAAAAATA
1 TATAAAAAAATA
33756274 TA
1 TA
33756276 AAATTGCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
TATAAAAAAATA
Found at i:33759901 original size:69 final size:69
Alignment explanation
Indices: 33759784--33759937 Score: 229
Period size: 69 Copynumber: 2.2 Consensus size: 69
33759774 ATATATGATT
* * * *
33759784 GTTGAAATGTAAGATTATTTAGCATATTACTAGGTATATTATACTACCTTCTCTTTTTTT-TTTC
1 GTTGGAATGTAAGATTACTTAGCACATTACTAAGTATATTATACTACCTT-TCTTTTTTTATTTC
33759848 ATTTG
65 ATTTG
* *
33759853 GTTGGAATGTAAGATTACTTAGCACATTACTAAGTATATTATATTACCTTTTTTTTTTTATTTCA
1 GTTGGAATGTAAGATTACTTAGCACATTACTAAGTATATTATACTACCTTTCTTTTTTTATTTCA
33759918 TTTG
66 TTTG
*
33759922 GTTAGAATGTAAGATT
1 GTTGGAATGTAAGATT
33759938 TTGCTATTTG
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
68 8 0.10
69 69 0.90
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (69 bp):
GTTGGAATGTAAGATTACTTAGCACATTACTAAGTATATTATACTACCTTTCTTTTTTTATTTCA
TTTG
Found at i:33761868 original size:23 final size:23
Alignment explanation
Indices: 33761842--33761886 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
33761832 TCGGTATGTG
*
33761842 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
33761865 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
33761887 TTGAATTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:33766917 original size:22 final size:22
Alignment explanation
Indices: 33766853--33766917 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
33766843 AAAATAGAAA
33766853 CAGAGCATAAT-AGATATAGATG
1 CAGAGCAT-ATCAGATATAGATG
* * **
33766875 TAGAGCATATCAAATGCAGATG
1 CAGAGCATATCAGATATAGATG
*
33766897 CAGAGCATATCGGATATAGAT
1 CAGAGCATATCAGATATAGAT
33766918 TCAAAGTTCT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
21 2 0.06
22 31 0.94
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (22 bp):
CAGAGCATATCAGATATAGATG
Found at i:33768483 original size:69 final size:69
Alignment explanation
Indices: 33768386--33768579 Score: 266
Period size: 69 Copynumber: 2.8 Consensus size: 69
33768376 TAGTTTTCCT
* * * * *
33768386 TATGGAAAATGCCATACATACATTTCATAACTCAGTATGGAAAATACCATACCTACAG-ATCATA
1 TATGG-AAATACCATACCTACATATCATAGCTCGGTATGG-AAATACCATACCTACAGTATCATA
*
33768450 GCTCGG
64 GCTCAG
*
33768456 TATGGAAATACCATACCTACGTATCATAGCTCGGTATGGAAATACCATACCTAC-GTATCATAGC
1 TATGGAAATACCATACCTACATATCATAGCTCGGTATGGAAATACCATACCTACAGTATCATAGC
*
33768520 TTAG
66 TCAG
*
33768524 TATGGATAATACCATACCTACATATCATAGCTTGGTATGGAAATACCATACCTACA
1 TATGGA-AATACCATACCTACATATCATAGCTCGGTATGGAAATACCATACCTACA
33768580 TTTCACATTT
Statistics
Matches: 111, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
67 1 0.01
68 31 0.28
69 74 0.67
70 5 0.05
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (69 bp):
TATGGAAATACCATACCTACATATCATAGCTCGGTATGGAAATACCATACCTACAGTATCATAGC
TCAG
Done.