Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 191 of 204
Found at i:56355476 original size:17 final size:18
Alignment explanation
Indices: 56355432--56355476 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 18
56355422 GTCAGCAATA
56355432 ATTTTT-TAT-TTTATAT
1 ATTTTTATATATTTATAT
56355448 ATTTTTA-A-ATTTAT-T
1 ATTTTTATATATTTATAT
56355463 ATTTTTATATATTT
1 ATTTTTATATATTT
56355477 TTGTTGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
15 8 0.32
16 13 0.52
17 4 0.16
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTTATATATTTATAT
Found at i:56358641 original size:23 final size:23
Alignment explanation
Indices: 56358597--56358639 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
56358587 ACCTTCTTTT
56358597 GTAACCATTAATTTTATTTTTAA
1 GTAACCATTAATTTTATTTTTAA
*
56358620 GTAACCTTTAA-TTTATTTTT
1 GTAACCATTAATTTTATTTTT
56358640 TATGGTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.56
Consensus pattern (23 bp):
GTAACCATTAATTTTATTTTTAA
Found at i:56362450 original size:2 final size:2
Alignment explanation
Indices: 56362443--56362475 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
56362433 TGGTTGGACT
56362443 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
56362476 GATGTTAGTA
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:56366249 original size:29 final size:29
Alignment explanation
Indices: 56366168--56366256 Score: 81
Period size: 31 Copynumber: 3.0 Consensus size: 29
56366158 GGTTAAATCA
* *
56366168 AAATTAAAGTTTCAAGTATATATTTGAACC
1 AAATTAAAG-TTCAAGTATATAATTGCACC
* * *
56366198 ACAATTAGAATTTCACG-AGTATAATTGCATC
1 A-AATTA-AAGTTCAAGTA-TATAATTGCACC
*
56366229 AAATTAAAGTTCATGTATATAATTGCAC
1 AAATTAAAGTTCAAGTATATAATTGCAC
56366257 ATTAAATCAA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
29 17 0.36
30 8 0.17
31 20 0.43
32 2 0.04
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (29 bp):
AAATTAAAGTTCAAGTATATAATTGCACC
Found at i:56380167 original size:22 final size:21
Alignment explanation
Indices: 56380142--56380184 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
56380132 AAGGTCACCG
* *
56380142 TACATATCACTTCCTCCACATA
1 TACAAATCACATCC-CCACATA
*
56380164 TACAAATCTCATCCCCACATA
1 TACAAATCACATCCCCACATA
56380185 CAGATATAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (21 bp):
TACAAATCACATCCCCACATA
Found at i:56381536 original size:16 final size:15
Alignment explanation
Indices: 56381516--56381558 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
56381506 AAATTTTACA
*
56381516 AATTAAAAAATAATT
1 AATTAAAAAATAAAT
56381531 ATATT-AAAAATAAAT
1 A-ATTAAAAAATAAAT
56381546 AATATAAAAAATA
1 AAT-TAAAAAATA
56381559 TGATTTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 2 0.08
15 12 0.50
16 10 0.42
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AATTAAAAAATAAAT
Found at i:56384439 original size:127 final size:125
Alignment explanation
Indices: 56384161--56384574 Score: 555
Period size: 127 Copynumber: 3.3 Consensus size: 125
56384151 GATAAAATCA
* * * * * * * *
56384161 AAGCAGGATGATTTATCAAAAGGATTTTTGAAGTCGCGCCCACGTGTACGCGCTTTTGCTATAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * *
56384226 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAATT-TAAAAACGCTTC
66 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTAAAAAAACGCTTC
* * * *
56384285 AAGCAGGATGTTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGAAGCACTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * *
56384350 TGGTCCTAAAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTTAAAAAAAACGCTTC
66 AGGTCCTGAAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTT-AAAAAAACGCTTC
* *
56384412 AAGTAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGGGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* *
56384477 AGGTCCTGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAG-TATAAAAAACGCTGC
66 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTA-AAAAAACGCTTC
* *
56384537 AAGCAGGATGCTATT-TGAGAAGAATTTTTGAAAACGCG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCG
56384575 AAGAATTTGT
Statistics
Matches: 254, Mismatches: 31, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
124 63 0.25
125 78 0.31
126 34 0.13
127 79 0.31
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (125 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTAAAAAAACGCTTC
Found at i:56385920 original size:19 final size:19
Alignment explanation
Indices: 56385892--56385929 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
56385882 CTAATCATAC
56385892 AACAGCTTTAAC-AACTACT
1 AACAGCTTT-ACTAACTACT
*
56385911 AACAGTTTTACTAACTACT
1 AACAGCTTTACTAACTACT
56385930 CTAACAAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.39, C:0.24, G:0.05, T:0.32
Consensus pattern (19 bp):
AACAGCTTTACTAACTACT
Found at i:56386352 original size:21 final size:21
Alignment explanation
Indices: 56386326--56386365 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
56386316 ATTTACACCT
56386326 TTCATAAACGTCATTATTTTA
1 TTCATAAACGTCATTATTTTA
*
56386347 TTCATAAATGTCATTATTT
1 TTCATAAACGTCATTATTT
56386366 AAAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (21 bp):
TTCATAAACGTCATTATTTTA
Found at i:56389068 original size:120 final size:120
Alignment explanation
Indices: 56388853--56389069 Score: 326
Period size: 120 Copynumber: 1.8 Consensus size: 120
56388843 TTGATATCAC
* * * * *
56388853 TGATTAATTTTCTAACCGTGGATATTTTCTGAAAAGTTAAATGAGTGACAATAAAATGTGTTCCA
1 TGATTAATCTTCTAACCGTGGATACTTTCCGAAAAGATAAATGAGTGACAATAAAATGTATTCCA
*
56388918 TTTTCGTGAGCGGGATTAAAAATTATTTTTTTCGGGTATCCATCATCGGTAATAG
66 TTTTCGTGAACGGGATTAAAAATTATTTTTTTCGGGTATCCATCATCGGTAATAG
* * *
56388973 TGATTAATCTTCTAACTGTGGATGCTTTCCGAAAAGATAAATGATTGACAATAAAATGTATTCCA
1 TGATTAATCTTCTAACCGTGGATACTTTCCGAAAAGATAAATGAGTGACAATAAAATGTATTCCA
* *
56389038 TTTTCGTGAATGGAGATTAATAATTATTTTTT
66 TTTTCGTGAACGG-GATTAAAAATTATTTTTT
56389070 AATTATTTGA
Statistics
Matches: 85, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
120 68 0.80
121 17 0.20
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (120 bp):
TGATTAATCTTCTAACCGTGGATACTTTCCGAAAAGATAAATGAGTGACAATAAAATGTATTCCA
TTTTCGTGAACGGGATTAAAAATTATTTTTTTCGGGTATCCATCATCGGTAATAG
Found at i:56391981 original size:72 final size:72
Alignment explanation
Indices: 56391864--56392252 Score: 553
Period size: 72 Copynumber: 5.4 Consensus size: 72
56391854 GAGGAAAAGT
56391864 ACCATTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATG
1 ACCATTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATG
56391929 GAATTTG
66 GAATTTG
** * * * *
56391936 ACCATTTAATTGATTTTCTGAAACATCAAACTCCTCCAAAGATGATAACTGCCCTATAGACGAGG
1 ACCATTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATG
56392001 GAATTTG
66 GAATTTG
* * * *
56392008 GCCGTTTAACTGATTTTCTGAGACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATG
1 ACCATTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATG
*
56392073 GAATTGG
66 GAATTTG
** * * * *
56392080 ACCATTTAATTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACAAGG
1 ACCATTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATG
56392145 GAATTTG
66 GAATTTG
* * * * * *
56392152 GCCGTTTAATTGATTTTTTGAAACATCAAACAACTTCAGAGATGATAACTCCCATGTAGACAATG
1 ACCATTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATG
56392217 GAATTTG
66 GAATTTG
* *
56392224 ACCATTTAATTGATTTACTGAAAGATCAA
1 ACCATTTAATTGATTTTCTGAAACATCAA
56392253 GCTGAGTAAC
Statistics
Matches: 272, Mismatches: 45, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 272 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (72 bp):
ACCATTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATG
GAATTTG
Found at i:56392086 original size:144 final size:144
Alignment explanation
Indices: 56391868--56392252 Score: 671
Period size: 144 Copynumber: 2.7 Consensus size: 144
56391858 AAAAGTACCA
56391868 TTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATGGAAT
1 TTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATGGAAT
* *
56391933 TTGACCATTTAATTGATTTTCTGAAACATCAAACTCCTCCAAAGATGATAACTGCCCTATAGACG
66 TTGACCATTTAATTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACA
56391998 AGGGAATTTGGCCG
131 AGGGAATTTGGCCG
* *
56392012 TTTAACTGATTTTCTGAGACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATGGAAT
1 TTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATGGAAT
*
56392077 TGGACCATTTAATTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACA
66 TTGACCATTTAATTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACA
56392142 AGGGAATTTGGCCG
131 AGGGAATTTGGCCG
* * * *
56392156 TTTAATTGATTTTTTGAAACATCAAACAACTTCAGAGATGATAACTCCCATGTAGACAATGGAAT
1 TTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATGGAAT
* *
56392221 TTGACCATTTAATTGATTTACTGAAAGATCAA
66 TTGACCATTTAATTGATTTTCTGAAACATCAA
56392253 GCTGAGTAAC
Statistics
Matches: 227, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
144 227 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (144 bp):
TTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATGGAAT
TTGACCATTTAATTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACA
AGGGAATTTGGCCG
Found at i:56393540 original size:27 final size:26
Alignment explanation
Indices: 56393483--56393540 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
56393473 TTTAGGTCTT
*
56393483 AAAAGCTAATGGAGGAAAAAAGAAAG
1 AAAAGCTAAAGGAGGAAAAAAGAAAG
*
56393509 TAAAGCTAAAGGA-GAAAAAAGAGAAGG
1 AAAAGCTAAAGGAGGAAAAAAGA-AA-G
56393536 AAAAG
1 AAAAG
56393541 AAAATGGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 9 0.33
26 13 0.48
27 5 0.19
ACGTcount: A:0.62, C:0.03, G:0.28, T:0.07
Consensus pattern (26 bp):
AAAAGCTAAAGGAGGAAAAAAGAAAG
Found at i:56396552 original size:15 final size:16
Alignment explanation
Indices: 56396532--56396564 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
56396522 GGAGAGAGAA
56396532 AAAATAATAA-AAAAT
1 AAAATAATAACAAAAT
56396547 AAAATAATAACAAAAT
1 AAAATAATAACAAAAT
56396563 AA
1 AA
56396565 TAACATATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAATAATAACAAAAT
Found at i:56399916 original size:19 final size:16
Alignment explanation
Indices: 56399875--56399925 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
56399865 TTTACAAATT
56399875 AAAAATAATTATAAAA
1 AAAAATAATTATAAAA
*
56399891 AAGAATAATTATATTAAA
1 AAAAATAATTATA--AAA
56399909 AATAAATAA-TATAAAA
1 AA-AAATAATTATAAAA
56399925 A
1 A
56399926 TATAATATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
16 16 0.53
18 9 0.30
19 5 0.17
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (16 bp):
AAAAATAATTATAAAA
Found at i:56399932 original size:16 final size:17
Alignment explanation
Indices: 56399895--56399932 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
56399885 ATAAAAAAGA
*
56399895 ATAATTATATTAAAAAT
1 ATAATAATATTAAAAAT
56399912 A-AATAATA-TAAAAAT
1 ATAATAATATTAAAAAT
56399927 ATAATA
1 ATAATA
56399933 TGAATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 10 0.53
17 1 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAATAATATTAAAAAT
Found at i:56404067 original size:72 final size:72
Alignment explanation
Indices: 56403986--56404298 Score: 475
Period size: 72 Copynumber: 4.3 Consensus size: 72
56403976 AAAAGTACCA
* * * * *
56403986 TTTAATTGATTTTTTGAAACATCAAA-TACCTCCAAAGATGATAACTCCCCTATAGACAATGGAA
1 TTTAATTGATTGTATGAAACATCAAACT-CCTCCAAAGATGACAACTGCCCTATAGACAAGGGAA
* *
56404050 TTTGACCA
65 TTTGGCCG
* *
56404058 TTTAATTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACAAGGGAAT
1 TTTAATTGATTGTATGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACAAGGGAAT
56404123 TTGGCCG
66 TTGGCCG
* * *
56404130 TTTAATTGATTGTATGAAACATCAAACTTCTTCAGAGATGACAACTGCCCTATAGACAAGGGAAT
1 TTTAATTGATTGTATGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACAAGGGAAT
56404195 TTGGCCG
66 TTGGCCG
*
56404202 TTTAACTGATTGTATGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACAAGGGAAT
1 TTTAATTGATTGTATGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACAAGGGAAT
56404267 TTGGCCG
66 TTGGCCG
* *
56404274 TTTAATTGATTGGATGAAAGATCAA
1 TTTAATTGATTGTATGAAACATCAA
56404299 GCTGAGTAAC
Statistics
Matches: 222, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
72 221 1.00
73 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (72 bp):
TTTAATTGATTGTATGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACAAGGGAAT
TTGGCCG
Found at i:56405760 original size:4 final size:4
Alignment explanation
Indices: 56405751--56405792 Score: 75
Period size: 4 Copynumber: 10.5 Consensus size: 4
56405741 AGTTTATCCT
*
56405751 ATAA ATAA ATAA ATAA ATAA ATAA ATAG ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
56405793 CGTGTAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:56408580 original size:24 final size:24
Alignment explanation
Indices: 56408553--56408598 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
56408543 AAGTTGAGAA
56408553 GCAAGTCTATGGAGTAAGTCCCCC
1 GCAAGTCTATGGAGTAAGTCCCCC
*
56408577 GCAAGTGTATGGAGTAAGTCCC
1 GCAAGTCTATGGAGTAAGTCCC
56408599 ACTCCCACGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (24 bp):
GCAAGTCTATGGAGTAAGTCCCCC
Found at i:56408772 original size:23 final size:24
Alignment explanation
Indices: 56408730--56408781 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
56408720 TTCGTATAAA
*
56408730 ATATCAAATTATTCACATGT-ATT
1 ATATCAAATTATTCAAATGTCATT
* *
56408753 ATATGAAATTATTTAAATGTCATT
1 ATATCAAATTATTCAAATGTCATT
56408777 A-ATCA
1 ATATCA
56408782 TTATATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (24 bp):
ATATCAAATTATTCAAATGTCATT
Found at i:56416333 original size:75 final size:75
Alignment explanation
Indices: 56416242--56416394 Score: 288
Period size: 75 Copynumber: 2.0 Consensus size: 75
56416232 TACCCAATCA
* *
56416242 TTTGCTTTATAAAGATCCGCAGAACTCAAATCAAGGTACTGCAAGGAAGAAAGTCCAGAAACCCA
1 TTTGCTTCAGAAAGATCCGCAGAACTCAAATCAAGGTACTGCAAGGAAGAAAGTCCAGAAACCCA
56416307 TTGAAGACTT
66 TTGAAGACTT
56416317 TTTGCTTCAGAAAGATCCGCAGAACTCAAATCAAGGTACTGCAAGGAAGAAAGTCCAGAAACCCA
1 TTTGCTTCAGAAAGATCCGCAGAACTCAAATCAAGGTACTGCAAGGAAGAAAGTCCAGAAACCCA
56416382 TTGAAGACTT
66 TTGAAGACTT
56416392 TTT
1 TTT
56416395 TATTTGAGAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (75 bp):
TTTGCTTCAGAAAGATCCGCAGAACTCAAATCAAGGTACTGCAAGGAAGAAAGTCCAGAAACCCA
TTGAAGACTT
Found at i:56419442 original size:3 final size:3
Alignment explanation
Indices: 56419434--56419482 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
56419424 TATCTTAAAA
56419434 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
56419482 T
1 T
56419483 TCGCTCTTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:56423144 original size:61 final size:60
Alignment explanation
Indices: 56423039--56423154 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 60
56423029 GGGAAAGTGT
* *
56423039 ACTATATTGTAATCACCATTCATTTGCAAAATCTCAATATTGTATCGGAATCACCATGAAA
1 ACTATATTGAAATCACCATTCATTTGCAAAATCTCAATACTGTAT-GGAATCACCATGAAA
* * * *
56423100 ACTATATTGAAATTATCATTCATTTGCAAAATCAT-AGTACTGTATGGGATCACCA
1 ACTATATTGAAATCACCATTCATTTGCAAAATC-TCAATACTGTATGGAATCACCA
56423155 CAATAGTGAG
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
60 9 0.19
61 38 0.79
62 1 0.02
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (60 bp):
ACTATATTGAAATCACCATTCATTTGCAAAATCTCAATACTGTATGGAATCACCATGAAA
Found at i:56423276 original size:34 final size:34
Alignment explanation
Indices: 56423210--56423276 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
56423200 CTATATTGGA
* *
56423210 ATCACCATTCATTTACATTTACGAAATTAATTTT
1 ATCACCATTCATTTACATTTACAAAATCAATTTT
* *
56423244 ATCACCATTCATTTGCATTTGCAAAATCAATTT
1 ATCACCATTCATTTACATTTACAAAATCAATTT
56423277 CGTAGTCTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.42
Consensus pattern (34 bp):
ATCACCATTCATTTACATTTACAAAATCAATTTT
Found at i:56423794 original size:25 final size:25
Alignment explanation
Indices: 56423746--56423794 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
56423736 AATGTTATAT
* *
56423746 TAATAATATTAATATTAGATAAAAA
1 TAATAATATTAATATTAAACAAAAA
*
56423771 TAATTATATTAATATTAAACAAAA
1 TAATAATATTAATATTAAACAAAA
56423795 TAAAAAAAAC
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:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
TAATAATATTAATATTAAACAAAAA
Found at i:56424319 original size:31 final size:31
Alignment explanation
Indices: 56424284--56424342 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
56424274 TTAATATAAA
56424284 ATTTAAATTTATTATTATATTT-TTTGAAAAT
1 ATTTAAATTTATTA-TATATTTCTTTGAAAAT
* *
56424315 ATTTATATTTTTTATATATTTCTTTGAA
1 ATTTAAATTTATTATATATTTCTTTGAA
56424343 CTTTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (31 bp):
ATTTAAATTTATTATATATTTCTTTGAAAAT
Found at i:56427724 original size:72 final size:72
Alignment explanation
Indices: 56427633--56428109 Score: 665
Period size: 72 Copynumber: 6.6 Consensus size: 72
56427623 AAAGTACCAG
*
56427633 TTAATTGATTTTCTGAAACATCAAA-TACCTCCAAAGATGATAACTGCCCTATAGACAAGGGAAT
1 TTAATTGATTTTCTGAAACATCAAACT-CCTCCAAAGATGACAACTGCCCTATAGACAAGGGAAT
56427697 TTGGCCGT
65 TTGGCCGT
* * ** * * *
56427705 TTAACTGATTTTTTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATGGG-AT
1 TTAATTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACAA-GGGAAT
* *
56427769 TTGACCAT
65 TTGGCCGT
56427777 TTAATTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACAAGGGAATT
1 TTAATTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACAAGGGAATT
56427842 TGGCCGT
66 TGGCCGT
* * *
56427849 TTAATTGATTTTCTGAAGCAACAAACTTCTCCAAAGATGACAACTGCCCTATAGACAAGGGAATT
1 TTAATTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACAAGGGAATT
56427914 TGGCCGT
66 TGGCCGT
* ** * * * *
56427921 TTAATTGATTGTT-TGAAACAACAAACAACTTCAAAGACGATAACTCCCCTATAGACAATGGG-A
1 TTAATTGATT-TTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACAA-GGGAA
* *
56427984 TTTGACCAT
64 TTTGGCCGT
*
56427993 TTAACTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACAAGGGAATT
1 TTAATTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACAAGGGAATT
56428058 TGGCCGT
66 TGGCCGT
* *
56428065 TTAATTGATTTTCTGAAGCAACAAACTCCTCCAAAGATGACAACT
1 TTAATTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACT
56428110 CCTCCAAAGA
Statistics
Matches: 356, Mismatches: 42, Indels: 14
0.86 0.10 0.03
Matches are distributed among these distances:
71 8 0.02
72 340 0.96
73 8 0.02
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.28
Consensus pattern (72 bp):
TTAATTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACAAGGGAATT
TGGCCGT
Found at i:56428007 original size:216 final size:216
Alignment explanation
Indices: 56427633--56428109 Score: 857
Period size: 216 Copynumber: 2.2 Consensus size: 216
56427623 AAAGTACCAG
* * *
56427633 TTAATTGATTTTCTGAAACATCAAA-TACCTCCAAAGATGATAACTGCCCTATAGACAAGGGAAT
1 TTAATTGATTTTCTGAAGCAACAAACT-CCTCCAAAGATGACAACTGCCCTATAGACAAGGGAAT
* * *
56427697 TTGGCCGTTTAACTGATTTTTTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACA
65 TTGGCCGTTTAACTGATTGTTTGAAACAACAAACAACTTCAAAGACGATAACTCCCCTATAGACA
*
56427762 ATGGGATTTGACCATTTAATTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCT
130 ATGGGATTTGACCATTTAACTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCT
56427827 ATAGACAAGGGAATTTGGCCGT
195 ATAGACAAGGGAATTTGGCCGT
*
56427849 TTAATTGATTTTCTGAAGCAACAAACTTCTCCAAAGATGACAACTGCCCTATAGACAAGGGAATT
1 TTAATTGATTTTCTGAAGCAACAAACTCCTCCAAAGATGACAACTGCCCTATAGACAAGGGAATT
*
56427914 TGGCCGTTTAATTGATTGTTTGAAACAACAAACAACTTCAAAGACGATAACTCCCCTATAGACAA
66 TGGCCGTTTAACTGATTGTTTGAAACAACAAACAACTTCAAAGACGATAACTCCCCTATAGACAA
56427979 TGGGATTTGACCATTTAACTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTA
131 TGGGATTTGACCATTTAACTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTA
56428044 TAGACAAGGGAATTTGGCCGT
196 TAGACAAGGGAATTTGGCCGT
56428065 TTAATTGATTTTCTGAAGCAACAAACTCCTCCAAAGATGACAACT
1 TTAATTGATTTTCTGAAGCAACAAACTCCTCCAAAGATGACAACT
56428110 CCTCCAAAGA
Statistics
Matches: 250, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
216 249 1.00
217 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.28
Consensus pattern (216 bp):
TTAATTGATTTTCTGAAGCAACAAACTCCTCCAAAGATGACAACTGCCCTATAGACAAGGGAATT
TGGCCGTTTAACTGATTGTTTGAAACAACAAACAACTTCAAAGACGATAACTCCCCTATAGACAA
TGGGATTTGACCATTTAACTGATTTTCTGAAACATCAAACTCCTCCAAAGATGACAACTGCCCTA
TAGACAAGGGAATTTGGCCGT
Found at i:56434446 original size:20 final size:20
Alignment explanation
Indices: 56434423--56434476 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
56434413 CATAGAACAC
** *
56434423 AATAATAATGACGTAATTAT
1 AATAATAATGACCAAATAAT
*
56434443 AATAATAATCACCAAATAAT
1 AATAATAATGACCAAATAAT
*
56434463 AATAACAATGACCA
1 AATAATAATGACCA
56434477 TATTAATTAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.56, C:0.13, G:0.06, T:0.26
Consensus pattern (20 bp):
AATAATAATGACCAAATAAT
Found at i:56434543 original size:3 final size:3
Alignment explanation
Indices: 56434524--56434571 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
56434514 AATTAAACAC
* * * *
56434524 TAA TAA AAA TGA TAA TAA TAA -AA TAA TAA TAA TAG TGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
56434571 T
1 T
56434572 GAAATGTATA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:56435172 original size:15 final size:15
Alignment explanation
Indices: 56435147--56435181 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
56435137 GACTCTGTTT
*
56435147 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
56435161 TAATTAATATTAAGA
1 TAATTAATATTAAGA
56435176 TAATTA
1 TAATTA
56435182 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:56435224 original size:10 final size:10
Alignment explanation
Indices: 56435206--56435253 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
56435196 ATTTTAGGAT
56435206 TTTAT-TTTA
1 TTTATCTTTA
56435215 TTTATCTTTA
1 TTTATCTTTA
56435225 TTTATCTTTA
1 TTTATCTTTA
* ** *
56435235 ATTAAATGTA
1 TTTATCTTTA
56435245 TTTATCTTT
1 TTTATCTTT
56435254 TAGGAATTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
9 5 0.17
10 25 0.83
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:56452399 original size:18 final size:20
Alignment explanation
Indices: 56452368--56452410 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
56452358 TTTTTTGGAC
* *
56452368 ATTTTTAAATTTTTATATAT
1 ATTTTTAAATTTTTAAAAAT
56452388 ATTTTT-AA-TTTTAAAAAT
1 ATTTTTAAATTTTTAAAAAT
56452406 ATTTT
1 ATTTT
56452411 AGACTTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 13 0.62
19 2 0.10
20 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTTTAAATTTTTAAAAAT
Found at i:56453459 original size:27 final size:28
Alignment explanation
Indices: 56453401--56453468 Score: 93
Period size: 27 Copynumber: 2.4 Consensus size: 28
56453391 AAATAAAAAA
*
56453401 TAACTAAAAGTATTATAACTTTTTTTTATT
1 TAAC-AAAA-TATTATAACATTTTTTTATT
*
56453431 TACCAAAATATTATAA-ATTTTTTTATT
1 TAACAAAATATTATAACATTTTTTTATT
56453458 TAACAAAATAT
1 TAACAAAATAT
56453469 ACAAAAAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.57
28 8 0.23
29 4 0.11
30 3 0.09
ACGTcount: A:0.43, C:0.07, G:0.01, T:0.49
Consensus pattern (28 bp):
TAACAAAATATTATAACATTTTTTTATT
Found at i:56453903 original size:27 final size:26
Alignment explanation
Indices: 56453868--56453923 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 26
56453858 GTTACATTTT
56453868 AATCCTTTGGCACCATTGGTGCCGCC
1 AATCCTTTGGCACCATTGGTGCCGCC
*
56453894 AATCTCTTTGGCACCTTTGGTGCCGCC
1 AATC-CTTTGGCACCATTGGTGCCGCC
56453921 AAT
1 AAT
56453924 GTGATTAGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.16, C:0.32, G:0.21, T:0.30
Consensus pattern (26 bp):
AATCCTTTGGCACCATTGGTGCCGCC
Found at i:56455407 original size:18 final size:17
Alignment explanation
Indices: 56455380--56455416 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
56455370 TTTCATGTTT
56455380 TTTTTAATATTTATGAA
1 TTTTTAATATTTATGAA
*
56455397 TTTTTATATATTTTTGAA
1 TTTTTA-ATATTTATGAA
56455415 TT
1 TT
56455417 CTTTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (17 bp):
TTTTTAATATTTATGAA
Found at i:56455717 original size:17 final size:17
Alignment explanation
Indices: 56455697--56455729 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
56455687 CATATTAAAA
56455697 AAATGTAAA-AAATTAAT
1 AAAT-TAAATAAATTAAT
56455714 AAATTAAATAAATTAA
1 AAATTAAATAAATTAA
56455730 AAGACTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
AAATTAAATAAATTAAT
Found at i:56455829 original size:9 final size:9
Alignment explanation
Indices: 56455789--56455832 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
56455779 AGAATTATTT
56455789 AAAAATTCAA
1 AAAAATT-AA
56455799 AAAAATTATA
1 AAAAATTA-A
*
56455809 AGAAATTTAA
1 A-AAAATTAA
56455819 AAAAATTAA
1 AAAAATTAA
56455828 AAAAA
1 AAAAA
56455833 AACAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 13 0.43
10 11 0.37
11 6 0.20
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (9 bp):
AAAAATTAA
Found at i:56455833 original size:10 final size:10
Alignment explanation
Indices: 56455789--56455843 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
56455779 AGAATTATTT
*
56455789 AAAAATTCAA
1 AAAAATTAAA
*
56455799 AAAAATTATA
1 AAAAATTAAA
* *
56455809 AGAAATTTAA
1 AAAAATTAAA
56455819 AAAAATTAAA
1 AAAAATTAAA
**
56455829 AAAAAACAAA
1 AAAAATTAAA
56455839 AAAAA
1 AAAAA
56455844 AACTATAGTA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:56457951 original size:24 final size:24
Alignment explanation
Indices: 56457918--56457966 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
56457908 TCATAATATT
* *
56457918 AAGTGATGTTTTAGAAAGGTCATA
1 AAGTGATGTTTCAAAAAGGTCATA
*
56457942 AAGTGTTGTTTCAAAAAGGTCATA
1 AAGTGATGTTTCAAAAAGGTCATA
56457966 A
1 A
56457967 TATTAAGTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (24 bp):
AAGTGATGTTTCAAAAAGGTCATA
Found at i:56458771 original size:25 final size:25
Alignment explanation
Indices: 56458723--56458771 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
56458713 AATTTTATAT
* *
56458723 TAATAATATTAATATTAGATAAAAA
1 TAATAATATTAATATTAAACAAAAA
*
56458748 TAATTATATTAATATTAAACAAAA
1 TAATAATATTAATATTAAACAAAA
56458772 TAAAAAAAAA
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:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
TAATAATATTAATATTAAACAAAAA
Found at i:56459157 original size:17 final size:16
Alignment explanation
Indices: 56459138--56459168 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56459128 GGGCTTCCTT
*
56459138 TTTTTTAGAAAGACGA
1 TTTTTGAGAAAGACGA
56459154 TTTTTGAGAAAGACG
1 TTTTTGAGAAAGACG
56459169 TGCATGCCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.35
Consensus pattern (16 bp):
TTTTTGAGAAAGACGA
Found at i:56464604 original size:44 final size:44
Alignment explanation
Indices: 56464541--56464630 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
56464531 TCAAGGAAAA
56464541 TTCTAATTAATTGCACTTAGTTTTCCACAAAATGTAATATGAAT
1 TTCTAATTAATTGCACTTAGTTTTCCACAAAATGTAATATGAAT
56464585 TTCTAATTAATTGCACTTAGTTTTCCACAAAATGTAATATGAAT
1 TTCTAATTAATTGCACTTAGTTTTCCACAAAATGTAATATGAAT
56464629 TT
1 TT
56464631 GGATTATTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (44 bp):
TTCTAATTAATTGCACTTAGTTTTCCACAAAATGTAATATGAAT
Found at i:56471826 original size:28 final size:27
Alignment explanation
Indices: 56471793--56471848 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 27
56471783 ACATATATTG
56471793 TTAAATTTATGTGTTTCTAGAAAAATTT
1 TTAAATTTATGTGTTTCTAG-AAAATTT
56471821 TTAAATTTATGTGTTTCTAGAAAATTT
1 TTAAATTTATGTGTTTCTAGAAAATTT
56471848 T
1 T
56471849 GTGAGGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.52
Consensus pattern (27 bp):
TTAAATTTATGTGTTTCTAGAAAATTT
Found at i:56477788 original size:18 final size:19
Alignment explanation
Indices: 56477725--56477835 Score: 79
Period size: 18 Copynumber: 5.8 Consensus size: 19
56477715 AATAAAATAA
56477725 TATAAAAACATT-T-AAAAT
1 TATAAAAA-ATTATAAAAAT
* *
56477743 TAGAAAAAAGTTATAAAAAG
1 TATAAAAAA-TTATAAAAAT
*
56477763 CAT-AAAAATTATAAAAAAT
1 TATAAAAAATTAT-AAAAAT
*
56477782 TGT-AAAAATTATAAAAAT
1 TATAAAAAATTATAAAAAT
* *
56477800 TATAAAATA-TATAGAAAT
1 TATAAAAAATTATAAAAAT
*
56477818 ATAGAAAAAAATTATAAA
1 -TA-TAAAAAATTATAAA
56477836 TTTTCATAAA
Statistics
Matches: 72, Mismatches: 13, Indels: 13
0.73 0.13 0.13
Matches are distributed among these distances:
17 1 0.01
18 29 0.40
19 27 0.38
20 10 0.14
21 5 0.07
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (19 bp):
TATAAAAAATTATAAAAAT
Found at i:56477795 original size:28 final size:29
Alignment explanation
Indices: 56477725--56477806 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 29
56477715 AATAAAATAA
* *
56477725 TATAAAAA-CATTTAAAATTAGAAAAAAGT
1 TATAAAAAGCA-TAAAAATTATAAAAAAGT
56477754 TATAAAAAGCATAAAAATTATAAAAAA-T
1 TATAAAAAGCATAAAAATTATAAAAAAGT
* **
56477782 TGTAAAAATTATAAAAATTATAAAA
1 TATAAAAAGCATAAAAATTATAAAA
56477807 TATATAGAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
28 23 0.49
29 22 0.47
30 2 0.04
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (29 bp):
TATAAAAAGCATAAAAATTATAAAAAAGT
Found at i:56477955 original size:10 final size:10
Alignment explanation
Indices: 56477920--56477971 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
56477910 ACAAGAAACA
56477920 TTTTATAATT
1 TTTTATAATT
*
56477930 TTTCTATAACT
1 TTT-TATAATT
*
56477941 TTTTATTATT
1 TTTTATAATT
56477951 TTTTAT--TT
1 TTTTATAATT
*
56477959 TTTTATCATT
1 TTTTATAATT
56477969 TTT
1 TTT
56477972 CGTCATATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
8 8 0.22
10 19 0.53
11 9 0.25
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTATAATT
Found at i:56481320 original size:39 final size:40
Alignment explanation
Indices: 56481266--56481349 Score: 152
Period size: 39 Copynumber: 2.1 Consensus size: 40
56481256 CAAGGAAGGG
56481266 TGTGTTGTGATTGAATCCCAATGGTGGCCGAATCCAAGA-
1 TGTGTTGTGATTGAATCCCAATGGTGGCCGAATCCAAGAT
*
56481305 TGTGTTGTGATTGAATCCCAATGGTGGTCGAATCCAAGAT
1 TGTGTTGTGATTGAATCCCAATGGTGGCCGAATCCAAGAT
56481345 TGTGT
1 TGTGT
56481350 GTGCCGTGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 38 0.88
40 5 0.12
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (40 bp):
TGTGTTGTGATTGAATCCCAATGGTGGCCGAATCCAAGAT
Found at i:56481339 original size:17 final size:17
Alignment explanation
Indices: 56481278--56481339 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
56481268 TGTTGTGATT
*
56481278 GAATCCCAATGGTGGCC
1 GAATCCCAATGGTGGTC
* *
56481295 GAATCCAAGATGTGTTGTGATT
1 GAATCCCA-ATG-G-TG-G-TC
56481317 GAATCCCAATGGTGGTC
1 GAATCCCAATGGTGGTC
56481334 GAATCC
1 GAATCC
56481340 AAGATTGTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
17 14 0.40
18 4 0.11
19 3 0.09
20 3 0.09
21 4 0.11
22 7 0.20
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (17 bp):
GAATCCCAATGGTGGTC
Found at i:56487805 original size:28 final size:28
Alignment explanation
Indices: 56487774--56487832 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
56487764 ATATTTAGAC
* *
56487774 TTTAATTTCGTAT-TTTTAATTTTAAGAA
1 TTTAATTCCATATATTTTAATTTTAA-AA
56487802 TTT-ATTCCATATATTTTAATTTTAAAA
1 TTTAATTCCATATATTTTAATTTTAAAA
56487829 TTTA
1 TTTA
56487833 GGTGCAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 12 0.44
28 15 0.56
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (28 bp):
TTTAATTCCATATATTTTAATTTTAAAA
Found at i:56490207 original size:17 final size:17
Alignment explanation
Indices: 56490185--56490218 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
56490175 TCATAGTTGA
56490185 ACTCTCTAAACTTTTTC
1 ACTCTCTAAACTTTTTC
56490202 ACTCTCTAAACTTTTTC
1 ACTCTCTAAACTTTTTC
56490219 TATATAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (17 bp):
ACTCTCTAAACTTTTTC
Found at i:56494702 original size:12 final size:12
Alignment explanation
Indices: 56494681--56494730 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
56494671 AAAAACGAAA
*
56494681 TGATTAAAAACT
1 TGATGAAAAACT
* *
56494693 TGATGGAAAATT
1 TGATGAAAAACT
*
56494705 TTATGAAAAGACT
1 TGATGAAAA-ACT
56494718 TGATGAAAAACT
1 TGATGAAAAACT
56494730 T
1 T
56494731 AAAAAGAACT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
12 20 0.67
13 10 0.33
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:56500514 original size:20 final size:22
Alignment explanation
Indices: 56500489--56500535 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
56500479 ATACCTTGGG
*
56500489 AAATTA-AAATAAATT-TAAGA
1 AAATTATAAATAAATTATAAAA
*
56500509 AAATTATAATTAAATTATAAAA
1 AAATTATAAATAAATTATAAAA
56500531 AAATT
1 AAATT
56500536 TGTTGAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 6 0.26
21 8 0.35
22 9 0.39
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
AAATTATAAATAAATTATAAAA
Found at i:56504199 original size:37 final size:37
Alignment explanation
Indices: 56504152--56504226 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
56504142 TAAGAAACTA
56504152 AAAAAAAATTAAAGAAAATTATAAGAAAATTTTATCT
1 AAAAAAAATTAAAGAAAATTATAAGAAAATTTTATCT
56504189 AAAAAAAATTAAAGAAAATTATAAGAAAATTTTATCT
1 AAAAAAAATTAAAGAAAATTATAAGAAAATTTTATCT
56504226 A
1 A
56504227 TTTTTATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (37 bp):
AAAAAAAATTAAAGAAAATTATAAGAAAATTTTATCT
Found at i:56504218 original size:11 final size:11
Alignment explanation
Indices: 56504156--56504219 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 11
56504146 AAACTAAAAA
56504156 AAAATTA-AAG
1 AAAATTATAAG
56504166 AAAATTATAAG
1 AAAATTATAAG
*
56504177 AAAATTTTATCTAAAA
1 AAAA--TTA--T-AAG
56504193 AAAATTA-AAG
1 AAAATTATAAG
56504203 AAAATTATAAG
1 AAAATTATAAG
56504214 AAAATT
1 AAAATT
56504220 TTATCTATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
10 16 0.36
11 16 0.36
13 3 0.07
14 3 0.07
15 1 0.02
16 6 0.13
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (11 bp):
AAAATTATAAG
Found at i:56504324 original size:9 final size:9
Alignment explanation
Indices: 56504289--56504354 Score: 62
Period size: 9 Copynumber: 7.3 Consensus size: 9
56504279 ATCTTTAAAA
56504289 TTTTAAA-T
1 TTTTAAATT
*
56504297 TTCTAAATT
1 TTTTAAATT
* *
56504306 TTATATATT
1 TTTTAAATT
*
56504315 TTTTTAATT
1 TTTTAAATT
*
56504324 TTTTAAAATA
1 TTTT-AAATT
*
56504334 TTTTAGATT
1 TTTTAAATT
56504343 TTTTAAATT
1 TTTTAAATT
56504352 TTT
1 TTT
56504355 AAAAAGTGGC
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
8 6 0.13
9 32 0.71
10 7 0.16
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTAAATT
Found at i:56504337 original size:45 final size:45
Alignment explanation
Indices: 56504259--56504353 Score: 113
Period size: 45 Copynumber: 2.1 Consensus size: 45
56504249 AGCTTACTTT
56504259 TTTTATATATTTTTTTGAAAATCTTTAAAATTTTA-AATTTCTAAA
1 TTTTATATATTTTTTT-AAAATCTTTAAAATTTTAGAATTTCTAAA
* * * *
56504304 TTTTATATATTTTTTT-AATTTTTTAAAATATTTTAGATTTTTTAAA
1 TTTTATATATTTTTTTAAAATCTTT-AAA-ATTTTAGAATTTCTAAA
56504350 TTTT
1 TTTT
56504354 TAAAAAGTGG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
43 6 0.14
44 3 0.07
45 22 0.51
46 12 0.28
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (45 bp):
TTTTATATATTTTTTTAAAATCTTTAAAATTTTAGAATTTCTAAA
Found at i:56504355 original size:27 final size:28
Alignment explanation
Indices: 56504289--56504358 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 28
56504279 ATCTTTAAAA
* *
56504289 TTTTAAATTTCT-AAATTTTATATATTT
1 TTTTAAATTTTTAAAATTTTATAGATTT
*
56504316 TTTTAATTTTTTAAAATATTT-TAGA-TT
1 TTTTAAATTTTTAAAAT-TTTATAGATTT
56504343 TTTTAAATTTTTAAAA
1 TTTTAAATTTTTAAAA
56504359 AGTGGCATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 27 0.73
28 7 0.19
29 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (28 bp):
TTTTAAATTTTTAAAATTTTATAGATTT
Found at i:56504357 original size:8 final size:8
Alignment explanation
Indices: 56504277--56504357 Score: 54
Period size: 8 Copynumber: 9.4 Consensus size: 8
56504267 ATTTTTTTGA
*
56504277 AAATCTTT
1 AAATTTTT
*
56504285 AAAATTTT
1 AAATTTTT
*
56504293 AAATTTCT
1 AAATTTTT
56504301 AAATTTTAT
1 AAATTTT-T
*
56504310 ATATTTTTTT
1 A-A-ATTTTT
*
56504320 AATTTTTT
1 AAATTTTT
56504328 AAAATATTTT
1 -AAAT-TTTT
*
56504338 AGATTTTTT
1 A-AATTTTT
56504347 AAATTTTT
1 AAATTTTT
56504355 AAA
1 AAA
56504358 AAGTGGCATA
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
8 33 0.57
9 12 0.21
10 9 0.16
11 4 0.07
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.58
Consensus pattern (8 bp):
AAATTTTT
Found at i:56504701 original size:2 final size:2
Alignment explanation
Indices: 56504694--56504724 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
56504684 CCATAAAACT
56504694 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 T
56504725 TAGCATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56508216 original size:4 final size:4
Alignment explanation
Indices: 56508207--56508231 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
56508197 AAAGTAAAAG
56508207 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
56508232 GTAATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:56511685 original size:14 final size:15
Alignment explanation
Indices: 56511666--56511694 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
56511656 ATAAAGCCAA
56511666 TTCACT-TTACTTCC
1 TTCACTGTTACTTCC
56511680 TTCACTGTTACTTCC
1 TTCACTGTTACTTCC
56511695 ATTATTTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.14, C:0.34, G:0.03, T:0.48
Consensus pattern (15 bp):
TTCACTGTTACTTCC
Found at i:56517320 original size:18 final size:18
Alignment explanation
Indices: 56517297--56517333 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
56517287 AATTTTTTTG
*
56517297 TTAAATATATAATTTATT
1 TTAAATAAATAATTTATT
*
56517315 TTAAATAAATTATTTATT
1 TTAAATAAATAATTTATT
56517333 T
1 T
56517334 ATTTTAATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAAATAAATAATTTATT
Found at i:56517323 original size:22 final size:22
Alignment explanation
Indices: 56517298--56517340 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
56517288 ATTTTTTTGT
56517298 TAAA-TATATAATTTATTTTAAA
1 TAAATTAT-TAATTTATTTTAAA
*
56517320 TAAATTATTTATTTATTTTAA
1 TAAATTATTAATTTATTTTAA
56517341 TACCTTACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TAAATTATTAATTTATTTTAAA
Found at i:56520392 original size:13 final size:13
Alignment explanation
Indices: 56520376--56520409 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
56520366 TATGCTTTTA
56520376 TTTATATTTATAT
1 TTTATATTTATAT
56520389 TTTA-ACTTTATAT
1 TTTATA-TTTATAT
56520402 TTTATATT
1 TTTATATT
56520410 AGTATAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.05
13 17 0.89
14 1 0.05
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTATATTTATAT
Found at i:56524664 original size:72 final size:72
Alignment explanation
Indices: 56524517--56524664 Score: 197
Period size: 72 Copynumber: 2.1 Consensus size: 72
56524507 GAGGAAAAGT
* * **
56524517 ACCATTTAATTGATTTTCTGATACATCGAAGAACTTCAAAGATGATAACTCCCCTATAGACAATG
1 ACCATTTAATTGATTTTCTGAAACATCAAAGAACTTCAAAGACCATAACTCCCCTATAGACAATG
**
56524582 GAATTTG
66 GAATGGG
* * * **
56524589 ACCATTTAATTGATTTTTTGAAACATCAAAGAATTTCAAAGACCATAACTCCCCTATGGATGATG
1 ACCATTTAATTGATTTTCTGAAACATCAAAGAACTTCAAAGACCATAACTCCCCTATAGACAATG
56524654 GAATGGG
66 GAATGGG
56524661 ACCA
1 ACCA
56524665 GAAATTTTGT
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (72 bp):
ACCATTTAATTGATTTTCTGAAACATCAAAGAACTTCAAAGACCATAACTCCCCTATAGACAATG
GAATGGG
Found at i:56526521 original size:8 final size:8
Alignment explanation
Indices: 56526443--56526522 Score: 61
Period size: 9 Copynumber: 9.1 Consensus size: 8
56526433 ATTTAAAGAA
56526443 TTTACATTT
1 TTTA-ATTT
56526452 TTTAAATTT
1 TTT-AATTT
56526461 TTTAAATTT
1 TTT-AATTT
* *
56526470 CTAAATTT
1 TTTAATTT
56526478 TTATATATTT
1 TT-TA-ATTT
56526488 TTTGAATTT
1 TTT-AATTT
* *
56526497 TTAAATAT
1 TTTAATTT
56526505 TTTAGATTT
1 TTTA-ATTT
56526514 TTTAATTT
1 TTTAATTT
56526522 T
1 T
56526523 AAAATGTGAC
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
8 18 0.31
9 32 0.55
10 8 0.14
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (8 bp):
TTTAATTT
Found at i:56530197 original size:14 final size:14
Alignment explanation
Indices: 56530180--56530208 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
56530170 TCATCATTTG
56530180 CCTATAACCAAAAC
1 CCTATAACCAAAAC
56530194 CCTATAACCAAAAC
1 CCTATAACCAAAAC
56530208 C
1 C
56530209 ATGCTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.38, G:0.00, T:0.14
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:56537386 original size:18 final size:19
Alignment explanation
Indices: 56537365--56537402 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
56537355 AATGGTGTTA
56537365 ATAAAAAAAATAA-AAATT
1 ATAAAAAAAATAAGAAATT
* *
56537383 ATAAAATAATTAAGAAATT
1 ATAAAAAAAATAAGAAATT
56537402 A
1 A
56537403 AATAAAAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (19 bp):
ATAAAAAAAATAAGAAATT
Found at i:56541201 original size:29 final size:29
Alignment explanation
Indices: 56541152--56541208 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
56541142 CAACGGTGCC
* *
56541152 TTCGAACCAATAACTCAGATATCACTTGG
1 TTCGAACCAACAACTCAGATACCACTTGG
* *
56541181 TTCGAACCAACAGCTCGGATACCACTTG
1 TTCGAACCAACAACTCAGATACCACTTG
56541209 TCACGGGGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (29 bp):
TTCGAACCAACAACTCAGATACCACTTGG
Found at i:56543466 original size:13 final size:14
Alignment explanation
Indices: 56543450--56543483 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
56543440 TATGCTTTTA
56543450 TTTATATTTT-AAT
1 TTTATATTTTAAAT
56543463 TTTA-ATTTTAAAT
1 TTTATATTTTAAAT
56543476 TTTATATT
1 TTTATATT
56543484 AATATAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.26
13 11 0.58
14 3 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTATATTTTAAAT
Found at i:56546165 original size:118 final size:123
Alignment explanation
Indices: 56546015--56546251 Score: 319
Period size: 118 Copynumber: 2.0 Consensus size: 123
56546005 AAAGATCTGG
* *
56546015 AAAGGACCTTCCTTGTGACATGTGGCACACACTTACATG-T-TC-TC-TTTT-T-T-CATTTCAT
1 AAAGGACCTTCCTTGTGACACGTGCCACACACTTACATGTTCTCATCTTTTTCTGTACATTTCAT
* *
56546073 -AAAACAGGTTAAAATTCAGTTTTGGTCCTTTTAATATGTGTAAATTTAAAATTTAGGTCC
66 GAAAA-AGGCTAAAATTCAG--TTGGTACTTTTAATATGTGTAAATTTAAAATTTAGGTCC
*
56546133 AAAGGACCTTCCTTTTGACACGTGCCACACACTTACATGTTCTCATCTTTTTCTGTAGCATTTCA
1 AAAGGACCTTCCTTGTGACACGTGCCACACACTTACATGTTCTCATCTTTTTCTGTA-CATTTCA
* *
56546198 TGAAAAAGGCTAAATTTCAGTTGGTACTTTTAATATGTTTAAATTTAAAATTTA
65 TGAAAAAGGCTAAAATTCAGTTGGTACTTTTAATATGTGTAAATTTAAAATTTA
56546252 ATTCATATAC
Statistics
Matches: 103, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
118 36 0.35
119 1 0.01
120 2 0.02
121 2 0.02
122 4 0.04
123 1 0.01
124 33 0.32
126 20 0.19
127 4 0.04
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.40
Consensus pattern (123 bp):
AAAGGACCTTCCTTGTGACACGTGCCACACACTTACATGTTCTCATCTTTTTCTGTACATTTCAT
GAAAAAGGCTAAAATTCAGTTGGTACTTTTAATATGTGTAAATTTAAAATTTAGGTCC
Found at i:56546356 original size:16 final size:16
Alignment explanation
Indices: 56546322--56546355 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
56546312 CTTGACATGC
56546322 TTTTCTTTTCTTTTCT
1 TTTTCTTTTCTTTTCT
56546338 TTTTCTTTT-TTTT-T
1 TTTTCTTTTCTTTTCT
56546352 TTTT
1 TTTT
56546356 TGCAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 4 0.22
16 9 0.50
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTCTTTTCTTTTCT
Found at i:56556672 original size:19 final size:18
Alignment explanation
Indices: 56556650--56556692 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
56556640 CACCCATATC
56556650 TTTTTTTTAAATATATTAA
1 TTTTTTTTAAATAT-TTAA
* *
56556669 TTTTATTTCAATATTTAA
1 TTTTTTTTAAATATTTAA
56556687 TATTTT
1 T-TTTT
56556693 AATTTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTTTTAAATATTTAA
Found at i:56558290 original size:6 final size:6
Alignment explanation
Indices: 56558281--56558319 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
56558271 TTATTTATAT
* * *
56558281 TTTAAA TTTAAA TTTAAA TTCAAA TTCAAA TTCAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
56558320 TATTATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:56558296 original size:12 final size:12
Alignment explanation
Indices: 56558281--56558319 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
56558271 TTATTTATAT
*
56558281 TTTAAATTTAAA
1 TTTAAATTCAAA
56558293 TTTAAATTCAAA
1 TTTAAATTCAAA
*
56558305 TTCAAATTCAAA
1 TTTAAATTCAAA
56558317 TTT
1 TTT
56558320 TATTATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (12 bp):
TTTAAATTCAAA
Found at i:56562102 original size:72 final size:72
Alignment explanation
Indices: 56561976--56562116 Score: 228
Period size: 72 Copynumber: 2.0 Consensus size: 72
56561966 GAGGAAAAGT
* * *
56561976 ACCATTTAGTTGATTATCTGTAACATCAAAGAACTTCAAAGATGATAACTCCCCTATAGACAATG
1 ACCACTTAATTGATTATCTGAAACATCAAAGAACTTCAAAGATGATAACTCCCCTATAGACAATG
56562041 GAATTTG
66 GAATTTG
* * *
56562048 ACCACTTAATTGATTTTCTGAAACATCAAAGAACTTCAAAGATGATAACTCCCCTATCGACACTG
1 ACCACTTAATTGATTATCTGAAACATCAAAGAACTTCAAAGATGATAACTCCCCTATAGACAATG
56562113 GAAT
66 GAAT
56562117 GGGACCAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.29
Consensus pattern (72 bp):
ACCACTTAATTGATTATCTGAAACATCAAAGAACTTCAAAGATGATAACTCCCCTATAGACAATG
GAATTTG
Found at i:56563779 original size:17 final size:16
Alignment explanation
Indices: 56563757--56563814 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 16
56563747 ATTTTTAAAG
*
56563757 TTTTAAATTTCTAAATT
1 TTTTAAATTT-TAAATA
56563774 TTTTAAATTTTAAAATA
1 TTTTAAATTTT-AAATA
56563791 TTTTAAATTTTTAAA-A
1 TTTTAAA-TTTTAAATA
56563807 GTTTTAAA
1 -TTTTAAA
56563815 ATGTGACATA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
16 2 0.05
17 31 0.84
18 4 0.11
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTTAAATTTTAAATA
Found at i:56563782 original size:9 final size:9
Alignment explanation
Indices: 56563748--56563816 Score: 54
Period size: 9 Copynumber: 8.0 Consensus size: 9
56563738 TTTCTGGAAA
56563748 TTTTTAAA-
1 TTTTTAAAT
*
56563756 GTTTTAAA-
1 TTTTTAAAT
*
56563764 TTTCTAAAT
1 TTTTTAAAT
56563773 TTTTTAAA-
1 TTTTTAAAT
*
56563781 TTTTAAAAT
1 TTTTTAAAT
*
56563790 ATTTTAAAT
1 TTTTTAAAT
* *
56563799 TTTTAAAAG
1 TTTTTAAAT
*
56563808 TTTTAAAAT
1 TTTTTAAAT
56563817 GTGACATATA
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
8 20 0.42
9 28 0.58
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:56563802 original size:8 final size:8
Alignment explanation
Indices: 56563745--56563805 Score: 77
Period size: 8 Copynumber: 7.4 Consensus size: 8
56563735 TAATTTCTGG
56563745 AAATTTTT
1 AAATTTTT
*
56563753 AAAGTTTT
1 AAATTTTT
*
56563761 AAATTTCT
1 AAATTTTT
56563769 AAATTTTTT
1 AAA-TTTTT
*
56563778 AAATTTTA
1 AAATTTTT
56563786 AAATATTTT
1 AAAT-TTTT
56563795 AAATTTTT
1 AAATTTTT
56563803 AAA
1 AAA
56563806 AGTTTTAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
8 31 0.69
9 14 0.31
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (8 bp):
AAATTTTT
Found at i:56564743 original size:15 final size:16
Alignment explanation
Indices: 56564715--56564744 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
56564705 CCCAAATTTA
56564715 CCCAATAGCCCAAACT
1 CCCAATAGCCCAAACT
56564731 CCCAATA-CCCAAAC
1 CCCAATAGCCCAAAC
56564745 CATACCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.47, G:0.03, T:0.10
Consensus pattern (16 bp):
CCCAATAGCCCAAACT
Found at i:56566170 original size:16 final size:16
Alignment explanation
Indices: 56566151--56566184 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
56566141 ATATTTTATA
56566151 ATTTATGTATACATAT
1 ATTTATGTATACATAT
*
56566167 ATTTATGTCTACATAT
1 ATTTATGTATACATAT
56566183 AT
1 AT
56566185 ATTTTTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (16 bp):
ATTTATGTATACATAT
Found at i:56566187 original size:101 final size:96
Alignment explanation
Indices: 56566079--56566261 Score: 233
Period size: 101 Copynumber: 1.9 Consensus size: 96
56566069 CTTTATATTT
* *
56566079 TATATATTTTATAA-CTTCATACGCGTATATATATATACATACATACTCATATATTTTTTTATAT
1 TATATATTTT-TAATCTTCATAAGCGTATATATATATACATACATACT--TATA--TATTT-TAT
*
56566143 ATTTTATAATTTATGTATACATATATTTATGTCTACA
60 ATTTTATAATTTATATATACATATATTTATGTCTACA
* * ** *
56566180 TATATATTTTTAATCTTTATAAGTGTATATATATATATTTACGTACTTATATATTTTATATTTTA
1 TATATATTTTTAATCTTCATAAGCGTATATATATATACATACATACTTATATATTTTATATTTTA
56566245 TAATTTATATATACATA
66 TAATTTATATATACATA
56566262 CATATTTTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
96 25 0.34
97 4 0.05
99 4 0.05
100 3 0.04
101 37 0.51
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (96 bp):
TATATATTTTTAATCTTCATAAGCGTATATATATATACATACATACTTATATATTTTATATTTTA
TAATTTATATATACATATATTTATGTCTACA
Found at i:56566369 original size:29 final size:29
Alignment explanation
Indices: 56566337--56566395 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
56566327 TTTTTTAAAC
56566337 TTTGTTATATATACACATACATAGATTTT
1 TTTGTTATATATACACATACATAGATTTT
56566366 TTTGTTATATATACACATACATAGATTTT
1 TTTGTTATATATACACATACATAGATTTT
56566395 T
1 T
56566396 ACTTTTACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (29 bp):
TTTGTTATATATACACATACATAGATTTT
Found at i:56569677 original size:18 final size:18
Alignment explanation
Indices: 56569651--56569686 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
56569641 CATACATCCA
*
56569651 TAAATAATTACAAATTTT
1 TAAACAATTACAAATTTT
*
56569669 TAAACAATTACTAATTTT
1 TAAACAATTACAAATTTT
56569687 CTTTGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAACAATTACAAATTTT
Found at i:56577098 original size:2 final size:2
Alignment explanation
Indices: 56577091--56577116 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
56577081 GATTTTAATA
56577091 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
56577117 TCATAGATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56579057 original size:23 final size:20
Alignment explanation
Indices: 56579016--56579066 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 20
56579006 TTTTAGATTT
56579016 TTTTTAAATTTTCTTTATATA
1 TTTTTAAATTTTCTTTATA-A
56579037 TTCTTTAGAATTTT-TTCTATAA
1 TT-TTTA-AATTTTCTT-TATAA
56579059 TTTTTAAA
1 TTTTTAAA
56579067 AAATATGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 2 0.07
21 6 0.22
22 9 0.33
23 10 0.37
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTTAAATTTTCTTTATAA
Found at i:56579792 original size:29 final size:31
Alignment explanation
Indices: 56579752--56579809 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
56579742 TTTAATGTAC
* *
56579752 AATTGTATACATGAA-CTTTAATT-TGGTAT
1 AATTATATACATGAAGCTCTAATTGTGGTAT
56579781 AATTATATACATGAAGCTCTAATTGTGGT
1 AATTATATACATGAAGCTCTAATTGTGGT
56579810 TTAAATGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 14 0.56
30 7 0.28
31 4 0.16
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (31 bp):
AATTATATACATGAAGCTCTAATTGTGGTAT
Found at i:56580026 original size:29 final size:30
Alignment explanation
Indices: 56579979--56580037 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
56579969 GAATTGGATC
*
56579979 AAATCAAAATTTCTTGTATAAAATTGCACA
1 AAATCAAAATTTCATGTATAAAATTGCACA
*
56580009 AAATCAAAA-TTCATGTATACAATTGCACA
1 AAATCAAAATTTCATGTATAAAATTGCACA
56580038 TTAAACAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTGCACA
Found at i:56584609 original size:28 final size:27
Alignment explanation
Indices: 56584571--56584631 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
56584561 TATAGGTAAT
*
56584571 AAAA-AAATAAACAG-ATTAAAAATTATA
1 AAAATAAATAAA-AGTATTAAAAAAT-TA
*
56584598 AAAATAAATAAAAGTTTTAAAAAATTA
1 AAAATAAATAAAAGTATTAAAAAATTA
56584625 AAAATAA
1 AAAATAA
56584632 TTTAATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 15 0.50
28 15 0.50
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (27 bp):
AAAATAAATAAAAGTATTAAAAAATTA
Found at i:56585900 original size:2 final size:2
Alignment explanation
Indices: 56585893--56585918 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
56585883 TTAAGCATTG
56585893 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
56585919 ATGACCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56595661 original size:21 final size:21
Alignment explanation
Indices: 56595637--56595676 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
56595627 TAACTCTAGC
56595637 ATTTATAAAA-TTTATAATTAA
1 ATTT-TAAAACTTTATAATTAA
*
56595658 ATTTTAAAACTTTTTAATT
1 ATTTTAAAACTTTATAATT
56595677 CTTAAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTTAAAACTTTATAATTAA
Found at i:56604556 original size:17 final size:17
Alignment explanation
Indices: 56604531--56604564 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
56604521 TTGAATGAGA
* *
56604531 TTATCTTTTTGTTAAAT
1 TTATATTTTGGTTAAAT
56604548 TTATATTTTGGTTAAAT
1 TTATATTTTGGTTAAAT
56604565 CAAATCAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.09, T:0.62
Consensus pattern (17 bp):
TTATATTTTGGTTAAAT
Found at i:56609680 original size:30 final size:31
Alignment explanation
Indices: 56609646--56609703 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
56609636 TTATTTTATG
56609646 TAAAAATAATCTT-AAAAAATAATACAAATT
1 TAAAAATAATCTTAAAAAAATAATACAAATT
56609676 TAAAAATAATCTTAAAAAAATAATACAA
1 TAAAAATAATCTTAAAAAAATAATACAA
56609704 GTGAGTCGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (31 bp):
TAAAAATAATCTTAAAAAAATAATACAAATT
Found at i:56611176 original size:79 final size:79
Alignment explanation
Indices: 56611045--56611199 Score: 301
Period size: 79 Copynumber: 2.0 Consensus size: 79
56611035 GTTGAAGAAG
*
56611045 GGAAAAGGTTAGAGAAAAATGCAGGGCAAAGTCATTGCGATCTATTCTACCATTTATCCAACACC
1 GGAAAAGGTTAGAGAAAAATGCAGGGCAAAGTCATTGCAATCTATTCTACCATTTATCCAACACC
56611110 ATGCCCTAAACCAT
66 ATGCCCTAAACCAT
56611124 GGAAAAGGTTAGAGAAAAATGCAGGGCAAAGTCATTGCAATCTATTCTACCATTTATCCAACACC
1 GGAAAAGGTTAGAGAAAAATGCAGGGCAAAGTCATTGCAATCTATTCTACCATTTATCCAACACC
56611189 ATGCCCTAAAC
66 ATGCCCTAAAC
56611200 ATTAATATGT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 75 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (79 bp):
GGAAAAGGTTAGAGAAAAATGCAGGGCAAAGTCATTGCAATCTATTCTACCATTTATCCAACACC
ATGCCCTAAACCAT
Found at i:56617366 original size:69 final size:69
Alignment explanation
Indices: 56617008--56617384 Score: 304
Period size: 69 Copynumber: 5.5 Consensus size: 69
56616998 TCGTTTTCTT
* * * * * * *
56617008 CAAGAAAAAGAGC-CGCCTGTTGCTGGACATGAAGAACCGTCTGAAATGCTAAATAAACGATC-T
1 CAAGAAAATGAGCTC-CATGTTGCTGGACATGAAGAGCCATCGGAAATGCTAGATAAAC-AGCGT
*
56617071 CTACTC
64 CAACTC
* * * ** * * * * *
56617077 CAAGAAAAAGAGC-CACCTGTCGCTGGACACAAAGAACCGTCAGAAATGCTAGATCAACTA-CCT
1 CAAGAAAATGAGCTC-CATGTTGCTGGACATGAAGAGCCATCGGAAATGCTAGATAAAC-AGCGT
** *
56617140 CTCCTG
64 CAACTC
* * *
56617146 CAAGGAAAA-GAGC-CACATGTTCCTGGAGATGAAGAGCCGTCGGAAATGCTAGATAAACAAG-G
1 CAA-GAAAATGAGCTC-CATGTTGCTGGACATGAAGAGCCATCGGAAATGCTAGATAAAC-AGCG
*
56617208 TCGAA-AC
63 TC-AACTC
* * *
56617215 AAAGAAAATGAGCTCCATGTTGCCGGACATGAAGAGCCATCGGAAGTGCTAGATAAAC-GACGTC
1 CAAGAAAATGAGCTCCATGTTGCTGGACATGAAGAGCCATCGGAAATGCTAGATAAACAG-CGTC
*
56617279 GACTC
65 AACTC
* * * *
56617284 CAAGAAAATGAGCTCCATGTTGATGGACATGAAGAGCCCTCGGAAATACTAGATCAACAGCGTCA
1 CAAGAAAATGAGCTCCATGTTGCTGGACATGAAGAGCCATCGGAAATGCTAGATAAACAGCGTCA
56617349 ACTC
66 ACTC
*
56617353 CAAGAAAATGAGCTCCATGTTGCTGGAAATGA
1 CAAGAAAATGAGCTCCATGTTGCTGGACATGA
56617385 GCTAGATAAA
Statistics
Matches: 255, Mismatches: 43, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
67 1 0.00
68 7 0.03
69 240 0.94
70 7 0.03
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.18
Consensus pattern (69 bp):
CAAGAAAATGAGCTCCATGTTGCTGGACATGAAGAGCCATCGGAAATGCTAGATAAACAGCGTCA
ACTC
Found at i:56617450 original size:123 final size:123
Alignment explanation
Indices: 56617262--56617507 Score: 323
Period size: 123 Copynumber: 2.0 Consensus size: 123
56617252 CATCGGAAGT
* ** * * *
56617262 GCTAGATAAACGACGTCGACTCCAAGAAAATGAGCTCCATGTTGATGGACATGAAGAGCCCTCGG
1 GCTAGATAAACGAAGTCGACTCCAAGAAAACAAACTCCATGTTGACGGACATGAAGAGCCATCGG
* * *
56617327 AAATACTAGATCAAC-AGCGTCAACTCCAAGAAAATGAGCTCCATGTTGCTGGAAATGA
66 AAATACTAGATAAACGA-CGTCAACTCCAAGAAAATGAGCTCCAAGTTGATGGAAATGA
* ** *
56617385 GCTAGATAAACGAAGTCGACTCCAAGAAAACAAACTCCGTGTTTCCGGGCATGAAGAGCCATCGG
1 GCTAGATAAACGAAGTCGACTCCAAGAAAACAAACTCCATGTTGACGGACATGAAGAGCCATCGG
* * * *
56617450 AAATGCTAGATAAACGACGTCGACTCCTAGAAAATGAGCTCCAAGTTGATGGACATGA
66 AAATACTAGATAAACGACGTCAACTCCAAGAAAATGAGCTCCAAGTTGATGGAAATGA
56617508 ACAGCCCGTA
Statistics
Matches: 105, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
123 104 0.99
124 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (123 bp):
GCTAGATAAACGAAGTCGACTCCAAGAAAACAAACTCCATGTTGACGGACATGAAGAGCCATCGG
AAATACTAGATAAACGACGTCAACTCCAAGAAAATGAGCTCCAAGTTGATGGAAATGA
Found at i:56617679 original size:129 final size:129
Alignment explanation
Indices: 56617437--56617986 Score: 710
Period size: 129 Copynumber: 4.3 Consensus size: 129
56617427 TTCCGGGCAT
* * * * * *
56617437 GAAGAGCCATCGGAAATGCTAGATAAACGACGTCGACTCCTAGA-AAATGAGCTCCAAGTTGATG
1 GAAGAGCCCTCGAAAATGCTAGATAAAAGACGTCGAATCCAAGAGAAA-GAACTCCAAGTTGATG
* * * * * *
56617501 GACATGAACAGCCCGT-AGAAATGCTAGATAAATGGCTTCGACTCCAAGAACATGTCAATGGACA
65 GACATGAAGAGCCC-TCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATCGATGGACA
*
56617565 T
129 C
* * * *
56617566 GAAGAGCCCTCGAAAATGCTAAATAAAAGAGGACGAATCCAAGATAAAGAACTCCAAGTTGATGG
1 GAAGAGCCCTCGAAAATGCTAGATAAAAGACGTCGAATCCAAGAGAAAGAACTCCAAGTTGATGG
** * *
56617631 ACACCAAGAGCCCTCAGAAATGCTAGATAAACGACGTCAACTCAAAGAACATATCGATGGACAC
66 ACATGAAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATCGATGGACAC
* * * *
56617695 GAAGAGCCTTGGCAAATGCTAGATAAAAGACGTC-AACTCCAAGAGAAAAAACTCCAAGTTGATG
1 GAAGAGCCCTCGAAAATGCTAGATAAAAGACGTCGAA-TCCAAGAGAAAGAACTCCAAGTTGATG
* * *
56617759 GACATGAAGAACCCTCAGAAATGCTAGATAAACGGCGTCGACTTAAAGAATATATCGATGGACAC
65 GACATGAAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATCGATGGACAC
* * * * * *
56617824 GAAGGGCTCTCAAAAAAGCTAGATAAAATACGTCGACTCCAAGAGAAAGAACTCCAAGTTGATGG
1 GAAGAGCCCTCGAAAATGCTAGATAAAAGACGTCGAATCCAAGAGAAAGAACTCCAAGTTGATGG
*
56617889 ACATGAAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATTGATGGACAC
66 ACATGAAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATCGATGGACAC
* * *
56617953 GAAGAGCCCTTGGAAATGCTAGATAAAAGGCGTC
1 GAAGAGCCCTCGAAAATGCTAGATAAAAGACGTC
56617987 AACTCGAGGA
Statistics
Matches: 360, Mismatches: 57, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
128 3 0.01
129 353 0.98
130 4 0.01
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.17
Consensus pattern (129 bp):
GAAGAGCCCTCGAAAATGCTAGATAAAAGACGTCGAATCCAAGAGAAAGAACTCCAAGTTGATGG
ACATGAAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATCGATGGACAC
Found at i:56617712 original size:60 final size:61
Alignment explanation
Indices: 56617518--56618187 Score: 411
Period size: 60 Copynumber: 10.6 Consensus size: 61
56617508 ACAGCCCGTA
* * * * * * * *
56617518 GAAATGCTAGATAAATGGCTTCGACTCCAAGAACAT-GTCAATGGACATGAAGAGCCCTCG
1 GAAATGCTAGATAAAAGACGTCGACTCAAAGAAAATCATCGATGGACACGAAGAGCCCTCG
* * * * * * * *
56617578 AAAATGCTAAATAAAAGAGGACGAATCCAAGATAAAGAACTCCAAGTTGATGGACACCAAGAGCC
1 GAAATGCTAGATAAAAGACGTCGACT-CAA-A-GAA-AA-T-C-A-TCGATGGACACGAAGAGCC
*
56617643 CTCA
58 CTCG
* * * *
56617647 GAAATGCTAGATAAACGACGTCAACTCAAAGAACAT-ATCGATGGACACGAAGAG-CCTTG
1 GAAATGCTAGATAAAAGACGTCGACTCAAAGAAAATCATCGATGGACACGAAGAGCCCTCG
* * * *
56617706 GCAAATGCTAGATAAAAGACGTCAACTCCAAGAGAAAAAACTCCAAGTTGATGGACATGAAGAAC
1 G-AAATGCTAGATAAAAGACGTCGACT-CAA-AG--AAAA-T-C-A-TCGATGGACACGAAGAGC
*
56617771 CCTCA
57 CCTCG
* * * * * * *
56617776 GAAATGCTAGATAAACGGCGTCGACTTAAAGAATAT-ATCGATGGACACGAAGGGCTCTCA
1 GAAATGCTAGATAAAAGACGTCGACTCAAAGAAAATCATCGATGGACACGAAGAGCCCTCG
* * * * *
56617836 AAAAAGCTAGATAAAATACGTCGACTCCAAGAGAAAGAACTCCAAGTTGATGGACATGAAGAGCC
1 GAAATGCTAGATAAAAGACGTCGACT-CAA-AG-AA-AA-T-C-A-TCGATGGACACGAAGAGCC
*
56617901 CTCA
58 CTCG
* * * * *
56617905 GAAATGCTAGATAAACGGCGTCGACTCAAAGAACAT-ATTGATGGACACGAAGAGCCCTTG
1 GAAATGCTAGATAAAAGACGTCGACTCAAAGAAAATCATCGATGGACACGAAGAGCCCTCG
* * * * * * *
56617965 GAAATGCTAGATAAAAGGCGTCAACTCGAGGAAAAT-GTTGATGGACAC-AGAGAGCCCTCA
1 GAAATGCTAGATAAAAGACGTCGACTCAAAGAAAATCATCGATGGACACGA-AGAGCCCTCG
* * * * *
56618025 AAAATGCTAGATAAAAGACATCGACTCCAAGAAAATGAGCTCCAAGTTGATGGACATGAAGAGCC
1 GAAATGCTAGATAAAAGACGTCGACTCAAAG-AAA--A--T-C-A-TCGATGGACACGAAGAGCC
56618090 CTCG
58 CTCG
* * **
56618094 GAAATGCTAGATAAACGACGTCGACTCCAAGAAAATGTTC-ATGGACACGAAGAGCCCTCG
1 GAAATGCTAGATAAAAGACGTCGACTCAAAGAAAATCATCGATGGACACGAAGAGCCCTCG
* * *
56618154 GAAATGCTAGATAAAAGACTTAGACTCCAAGAAA
1 GAAATGCTAGATAAAAGACGTCGACTCAAAGAAA
56618188 TTGAGCTCCG
Statistics
Matches: 476, Mismatches: 94, Indels: 80
0.73 0.14 0.12
Matches are distributed among these distances:
59 5 0.01
60 241 0.51
61 14 0.03
62 5 0.01
63 5 0.01
64 9 0.02
65 9 0.02
66 5 0.01
67 5 0.01
68 13 0.03
69 160 0.34
70 5 0.01
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (61 bp):
GAAATGCTAGATAAAAGACGTCGACTCAAAGAAAATCATCGATGGACACGAAGAGCCCTCG
Found at i:56617973 original size:189 final size:189
Alignment explanation
Indices: 56617753--56618170 Score: 588
Period size: 189 Copynumber: 2.2 Consensus size: 189
56617743 AAACTCCAAG
* * * * * * *
56617753 TTGATGGACATGAAGAACCCTCAGAAATGCTAGATAAACGGCGTCGACTTAAAGAATATATCGAT
1 TTGATGGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGGCGTCAACTCAAAGAAAATATCGAT
* * * *
56617818 GGACAC-GAAGGGCTCTCAAAAAAGCTAGATAAAATACGTCGACTCCAAGAGAAA-GAACTCCAA
66 GGACACAG-AGAGCCCTCAAAAAAGCTAGATAAAAGACATCGACTCCAAGA-AAATGAACTCCAA
* *
56617881 GTTGATGGACATGAAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATA
129 GTTGATGGACATGAAGAGCCCTCAGAAATGCTAGATAAACGACGTCGACTCAAAGAAAATA
* * * * *
56617942 TTGATGGACACGAAGAGCCCTTGGAAATGCTAGATAAAAGGCGTCAACTCGAGGAAAATGTTGAT
1 TTGATGGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGGCGTCAACTCAAAGAAAATATCGAT
* *
56618007 GGACACAGAGAGCCCTCAAAAATGCTAGATAAAAGACATCGACTCCAAGAAAATGAGCTCCAAGT
66 GGACACAGAGAGCCCTCAAAAAAGCTAGATAAAAGACATCGACTCCAAGAAAATGAACTCCAAGT
* * *
56618072 TGATGGACATGAAGAGCCCTCGGAAATGCTAGATAAACGACGTCGACTCCAAGAAAATG
131 TGATGGACATGAAGAGCCCTCAGAAATGCTAGATAAACGACGTCGACTCAAAGAAAATA
*
56618131 TTCATGGACACGAAGAGCCCTCGGAAATGCTAGATAAAAG
1 TTGATGGACACGAAGAGCCCTCGGAAATGCTAGATAAAAG
56618171 ACTTAGACTC
Statistics
Matches: 202, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
188 3 0.01
189 198 0.98
190 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (189 bp):
TTGATGGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGGCGTCAACTCAAAGAAAATATCGAT
GGACACAGAGAGCCCTCAAAAAAGCTAGATAAAAGACATCGACTCCAAGAAAATGAACTCCAAGT
TGATGGACATGAAGAGCCCTCAGAAATGCTAGATAAACGACGTCGACTCAAAGAAAATA
Found at i:56618079 original size:258 final size:254
Alignment explanation
Indices: 56617493--56618125 Score: 697
Period size: 258 Copynumber: 2.5 Consensus size: 254
56617483 ATGAGCTCCA
* * * * * * * * * * *
56617493 AGTTGATGGACATGAACAGCCCGT-AGAAATGCTAGATAAATGGCTTCGACTCCAAGAACATGTC
1 AGTTGATGGACAAGAAGAACCC-TCAAAAATGCTAGATAAAAGACATCGACTCAAAAAATATATC
* * * * * *
56617557 AATGGACATGAAGAGCCCTCGAAAATGCTAAATAAAAGAGGACGAATCCAAGATAAAGAACTCCA
65 GATGGACATGAAGAGCCCTCGAAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCA
56617622 AGTTGATGGACACCAAGAGCCCTCAGAAATGCTAGATAAACGACGTCAACTCAAAGAACATATCG
130 AGTTGATGGACACCAAGAGCCCTCAGAAATGCTAGATAAACGACGTCAACTCAAAGAACATATCG
56617687 ATGGACACGAAGAGCCTTGGCAAATGCTAGATAAAAGACGTCAACTCCAAGAGAAAAAACT
195 ATGGACACGAAGAGCCTTGGCAAATGCTAGATAAAAGACGTCAACTCC-AGAGAAAAAACT
* * * * * * *
56617748 CCAAGTTGATGGACATGAAGAACCCTCAGAAATGCTAGATAAACGGCGTCGACTTAAAGAATATA
1 ---AGTTGATGGACAAGAAGAACCCTCAAAAATGCTAGATAAAAGACATCGACTCAAAAAATATA
* * * * * *
56617813 TCGATGGACACGAAGGGCTCTCAAAAAAGCTAGATAAAATACGTCGACTCCAAGAGAAAGAACTC
63 TCGATGGACATGAAGAGCCCTCGAAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTC
** * *
56617878 CAAGTTGATGGACATGAAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATAT
128 CAAGTTGATGGACACCAAGAGCCCTCAGAAATGCTAGATAAACGACGTCAACTCAAAGAACATAT
* * *
56617943 TGATGGACACGAAGAGCCCTTGG-AAATGCTAGATAAAAGGCGTCAACT-C-GAG-GAAAA-T
193 CGATGGACACGAAGAG-CCTTGGCAAATGCTAGATAAAAGACGTCAACTCCAGAGAAAAAACT
*
56618001 -GTTGATGGACACAG-AGAGCCCTCAAAAATGCTAGATAAAAGACATCGACTCCAAGAAAATGAG
1 AGTTGATGGACA-AGAAGAACCCTCAAAAATGCTAGATAAAAGACATCGACT-CAA-AAAAT-A-
* * *
56618064 CTCCAAGTTGATGGACATGAAGAGCCCTCGGAAATGCTAGATAAACGACGTCGACTCCAAGA
61 -T---A-TCGATGGACATGAAGAGCCCTCGAAAATGCTAGATAAAAGACGTCGACTCCAAGA
56618126 AAATGTTCAT
Statistics
Matches: 319, Mismatches: 44, Indels: 24
0.82 0.11 0.06
Matches are distributed among these distances:
249 42 0.13
250 3 0.01
251 4 0.01
252 1 0.00
253 1 0.00
254 5 0.02
255 3 0.01
257 3 0.01
258 251 0.79
259 6 0.02
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.17
Consensus pattern (254 bp):
AGTTGATGGACAAGAAGAACCCTCAAAAATGCTAGATAAAAGACATCGACTCAAAAAATATATCG
ATGGACATGAAGAGCCCTCGAAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAA
GTTGATGGACACCAAGAGCCCTCAGAAATGCTAGATAAACGACGTCAACTCAAAGAACATATCGA
TGGACACGAAGAGCCTTGGCAAATGCTAGATAAAAGACGTCAACTCCAGAGAAAAAACT
Found at i:56618172 original size:129 final size:129
Alignment explanation
Indices: 56617942--56618256 Score: 411
Period size: 129 Copynumber: 2.4 Consensus size: 129
56617932 AAAGAACATA
* * * * * * *
56617942 TTGATGGACACGAAGAGCCCTTGGAAATGCTAGATAAAAGGCGTCAACTCGAGGAAAATGTTGAT
1 TTGATGGACATGAAGAGCCCTTGGAAATGCTAGATAAACGACGTCGACTCCAAGAAAATGTTCAT
*
56618007 GGACACAGAGAGCCCTCAAAAATGCTAGATAAAAGACATCGACTCCAAGAAAATGAGCTCCAAG
66 GGACACAGAGAGCCCTCAAAAATGCTAGATAAAAGACATAGACTCCAAGAAAATGAGCTCCAAG
*
56618071 TTGATGGACATGAAGAGCCCTCGGAAATGCTAGATAAACGACGTCGACTCCAAGAAAATGTTCAT
1 TTGATGGACATGAAGAGCCCTTGGAAATGCTAGATAAACGACGTCGACTCCAAGAAAATGTTCAT
** * * **
56618136 GGACAC-GAAGAGCCCTCGGAAATGCTAGATAAAAGACTTAGACTCCAAGAAATTGAGCTCCGTG
66 GGACACAG-AGAGCCCTCAAAAATGCTAGATAAAAGACATAGACTCCAAGAAAATGAGCTCCAAG
* * * * *
56618200 TTGCTAGACAT-AGAGAACTCTTTGAAATGCTAGATAAACGACGTCGACTCCAA-AAAA
1 TTGATGGACATGA-AGAGCCCTTGGAAATGCTAGATAAACGACGTCGACTCCAAGAAAA
56618257 CTAAGCTCCA
Statistics
Matches: 163, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
128 6 0.04
129 157 0.96
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.19
Consensus pattern (129 bp):
TTGATGGACATGAAGAGCCCTTGGAAATGCTAGATAAACGACGTCGACTCCAAGAAAATGTTCAT
GGACACAGAGAGCCCTCAAAAATGCTAGATAAAAGACATAGACTCCAAGAAAATGAGCTCCAAG
Found at i:56618467 original size:186 final size:186
Alignment explanation
Indices: 56618135--56618480 Score: 444
Period size: 186 Copynumber: 1.9 Consensus size: 186
56618125 AAAATGTTCA
* * *
56618135 TGGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACTTAGACTCCAAGAAATTGAGCTCCGTG
1 TGGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACATAGACTCCAAGAAAATGAGCTCCATG
** *
56618200 TTGCTAGACATAGAGAACTCTTTGAAATGCTAGATAAACGACGTCGACTCCAAAAAACTAAGCTC
66 TTGCTAGACATAGAGAACTCTCGGAAATGCTAGATAAACGACGTCGACTCCAAAAAACTAAGCAC
*
56618265 CATGTTGTTAGACATGAAGAGCCCTCGAAAATGCTAGAAAATGAGCTTCATGTTGC
131 CATATTGTTAGACATGAAGAGCCCTCGAAAATGCTAGAAAATGAGCTTCATGTTGC
* * * * * *
56618321 TGGACATGAAGAGCCCTCGGAAATGCTAGATAAACGGCATCGACTCCGAGAAAATGGGCTCCATG
1 TGGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACATAGACTCCAAGAAAATGAGCTCCATG
* * * * ** *
56618386 TTTCTGGACAT-GAAGAGC-CGTCGGAAATGCTAGATAAACGACGTCGACTCCAAGAAGTTGAGC
66 TTGCTAGACATAG-AGAACTC-TCGGAAATGCTAGATAAACGACGTCGACTCCAAAAAACTAAGC
* * * *
56618449 ACCCTATTTTTGGACATGAAGAGCCGTCGAAA
129 ACCATATTGTTAGACATGAAGAGCCCTCGAAA
56618481 GGGCTAGATA
Statistics
Matches: 134, Mismatches: 24, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
185 2 0.01
186 132 0.99
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (186 bp):
TGGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACATAGACTCCAAGAAAATGAGCTCCATG
TTGCTAGACATAGAGAACTCTCGGAAATGCTAGATAAACGACGTCGACTCCAAAAAACTAAGCAC
CATATTGTTAGACATGAAGAGCCCTCGAAAATGCTAGAAAATGAGCTTCATGTTGC
Found at i:56618657 original size:138 final size:136
Alignment explanation
Indices: 56618315--56618651 Score: 363
Period size: 138 Copynumber: 2.4 Consensus size: 136
56618305 ATGAGCTTCA
* ** * *
56618315 TGTTGCTGGACATGAAGAGCCCTCGGAAATGCTAGATAAACGGCATCGACTCCGAGAAAATGG-G
1 TGTTGCTGGACATGAAGAGCCATC-GAAATGCTAGATAAACAACATCTACTCCAAGAAAA-GGAG
* * * * **
56618379 CTCCATGTTTCTGGACATGAAGAGCCGTCGGAAATGCTAGATAAACGACGTCGACTCCAAGAAGT
64 -TCCATGTTGCTGGACATGAAGAGCCGTCAGAAATGCCAGATAAACCACGTCGACTCCAAGAAAA
*
56618444 TGAGCACCC
128 GGAGCACCC
* ** * * * ** *
56618453 TATTTTTGGACATGAAGAGCCGTCGAAAGGGCTAGATAACCTCCGTCTACTCCAAGAAAAGGAGT
1 TGTTGCTGGACATGAAGAGCCATCGAAA-TGCTAGATAAACAACATCTACTCCAAGAAAAGGAGT
* *
56618518 CCACTGTTGCTGGACATGAAG-GACCGTCAGAAATGCCAGATAAACCACTTCTACTCCAAGAAAA
65 CCA-TGTTGCTGGACATGAAGAG-CCGTCAGAAATGCCAGATAAACCACGTCGACTCCAAGAAAA
*
56618582 GGAGCCCCC
128 GGAGCACCC
*
56618591 TGTTGCTGGACATGAAGAGCCATCAGAAATTCTAGATAAACAACATCTACTCCAAGGAAAA
1 TGTTGCTGGACATGAAGAGCCATC-GAAATGCTAGATAAACAACATCTACTCCAA-GAAAA
56618652 CAGTCCCCTG
Statistics
Matches: 162, Mismatches: 31, Indels: 11
0.79 0.15 0.05
Matches are distributed among these distances:
137 11 0.07
138 142 0.88
139 9 0.06
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.20
Consensus pattern (136 bp):
TGTTGCTGGACATGAAGAGCCATCGAAATGCTAGATAAACAACATCTACTCCAAGAAAAGGAGTC
CATGTTGCTGGACATGAAGAGCCGTCAGAAATGCCAGATAAACCACGTCGACTCCAAGAAAAGGA
GCACCC
Found at i:56618660 original size:69 final size:68
Alignment explanation
Indices: 56618315--56618719 Score: 325
Period size: 69 Copynumber: 5.9 Consensus size: 68
56618305 ATGAGCTTCA
* * * * * *
56618315 TGTTGCTGGACATGAAGAGCCCTCGGAAATGCTAGATAAACGGCATCGACTCCGAGAAAATG-GG
1 TGTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGATAAACGACATCTACTCCAAGAAAA-GAGT
*
56618379 CTCCA
65 C-CCC
* * * * **
56618384 TGTTTCTGGACATGAAGAGCCGTCGGAAATGCTAGATAAACGACGTCGACTCCAAGAAGTTGAG-
1 TGTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGATAAACGACATCTACTCCAAGAA-AAGAGT
56618448 CACCC
65 C-CCC
* ** * * ** *
56618453 TATTTTTGGACATGAAGAGCCGTC-GAAAGGGCTAGATAACCTCCGTCTACTCCAAGAAAAGGAG
1 TGTTGCTGGACATGAAGAGCCGTCAGAAA-TGCTAGATAAACGACATCTACTCCAAGAAAA-GAG
*
56618517 TCCAC
64 TCCCC
* * *
56618522 TGTTGCTGGACATGAAG-GACCGTCAGAAATGCCAGATAAACCACTTCTACTCCAAGAAAAGGAG
1 TGTTGCTGGACATGAAGAG-CCGTCAGAAATGCTAGATAAACGACATCTACTCCAAGAAAA-GAG
*
56618586 CCCCC
64 TCCCC
* * * *
56618591 TGTTGCTGGACATGAAGAGCCATCAGAAATTCTAGATAAACAACATCTACTCCAAGGAAAACAGT
1 TGTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGATAAACGACATCTACTCCAA-GAAAAGAGT
56618656 CCCC
65 CCCC
* ** * ** ** * *
56618660 TGGTT-TTGGACACAAAGAACCACCAGAGTTGCTCGATAAACGACATGTACTCCAAGAAAA
1 T-GTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGATAAACGACATCTACTCCAAGAAAA
56618720 AGAACCGCAT
Statistics
Matches: 278, Mismatches: 48, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
68 10 0.04
69 253 0.91
70 15 0.05
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.20
Consensus pattern (68 bp):
TGTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGATAAACGACATCTACTCCAAGAAAAGAGTC
CCC
Found at i:56621580 original size:82 final size:82
Alignment explanation
Indices: 56621494--56621656 Score: 290
Period size: 82 Copynumber: 2.0 Consensus size: 82
56621484 AACTCAAAAG
* *
56621494 ATTTCGATTTTTCCAAAGTAACCAGCATATTATTGAGAATAGAGTTTGTCAATCAATATTATTGA
1 ATTTCGATTTTTCCAAAGCAACCAGCATACTATTGAGAATAGAGTTTGTCAATCAATATTATTGA
56621559 GAAAAACCCATATCATT
66 GAAAAACCCATATCATT
* *
56621576 ATTTCGGTTTTTCCAAAGCAGCCAGCATACTATTGAGAATAGAGTTTGTCAATCAATATTATTGA
1 ATTTCGATTTTTCCAAAGCAACCAGCATACTATTGAGAATAGAGTTTGTCAATCAATATTATTGA
56621641 GAAAAACCCATATCAT
66 GAAAAACCCATATCAT
56621657 CAAAATGGTA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (82 bp):
ATTTCGATTTTTCCAAAGCAACCAGCATACTATTGAGAATAGAGTTTGTCAATCAATATTATTGA
GAAAAACCCATATCATT
Found at i:56622999 original size:35 final size:35
Alignment explanation
Indices: 56622953--56623024 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
56622943 CATGCATCGC
56622953 AAATGCCAAAAACCTCAATTTCCTTTTCTTTTTTT
1 AAATGCCAAAAACCTCAATTTCCTTTTCTTTTTTT
56622988 AAATGCCAAAAACCTCAATTTCCTTTTCTTTTTTT
1 AAATGCCAAAAACCTCAATTTCCTTTTCTTTTTTT
56623023 AA
1 AA
56623025 TTTTACTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (35 bp):
AAATGCCAAAAACCTCAATTTCCTTTTCTTTTTTT
Found at i:56629787 original size:29 final size:29
Alignment explanation
Indices: 56629747--56629802 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
56629737 AATATGTTAT
*
56629747 AAATTTGTATACACAAATTGTTGATTTAA
1 AAATTTGGATACACAAATTGTTGATTTAA
56629776 AAATTTGGATACACAAATTGTTGATTT
1 AAATTTGGATACACAAATTGTTGATTT
56629803 GTCTAATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (29 bp):
AAATTTGGATACACAAATTGTTGATTTAA
Found at i:56642083 original size:20 final size:20
Alignment explanation
Indices: 56642023--56642083 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
56642013 TCTTTTATGA
*
56642023 ATTATAACATCTTCAAA-AAT
1 ATTATAAC-TATTCAAATAAT
* **
56642043 ATATATAATTATTCATCTAAT
1 AT-TATAACTATTCAAATAAT
56642064 ATTATAACTATTCAAATAAT
1 ATTATAACTATTCAAATAAT
56642084 GAGAAAGGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
20 22 0.69
21 10 0.31
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTATAACTATTCAAATAAT
Found at i:56647037 original size:32 final size:33
Alignment explanation
Indices: 56646996--56647061 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
56646986 CGGCCCGTTT
* * *
56646996 TTAAAATAAATA-CCAAAAAATTATTTTAAAAA
1 TTAAAATAAAAATCAAAAAAAGTATTTTAAAAA
*
56647028 TTAAAATAAAAATTAAAAAAAGTATTTTAAAAA
1 TTAAAATAAAAATCAAAAAAAGTATTTTAAAAA
56647061 T
1 T
56647062 ATTTTAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 11 0.38
33 18 0.62
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.32
Consensus pattern (33 bp):
TTAAAATAAAAATCAAAAAAAGTATTTTAAAAA
Found at i:56647064 original size:11 final size:11
Alignment explanation
Indices: 56647044--56647150 Score: 56
Period size: 11 Copynumber: 10.4 Consensus size: 11
56647034 TAAAAATTAA
56647044 AAAAAGTATTTT
1 AAAAA-TATTTT
56647056 AAAAATATTTT
1 AAAAATATTTT
56647067 --AAA-A--TT
1 AAAAATATTTT
* *
56647073 AAAAA-AATTA
1 AAAAATATTTT
56647083 AAAAAGTATTTT
1 AAAAA-TATTTT
*
56647095 AAAAAAATTTT
1 AAAAATATTTT
56647106 --AAA-A-TTT
1 AAAAATATTTT
56647113 AAAAA-ATTTAAT
1 AAAAATATTT--T
*
56647125 AAAAGTATTTT
1 AAAAATATTTT
*
56647136 AAAAGTATTTT
1 AAAAATATTTT
56647147 AAAA
1 AAAA
56647151 TTAAAAAAAT
Statistics
Matches: 78, Mismatches: 5, Indels: 25
0.72 0.05 0.23
Matches are distributed among these distances:
6 2 0.03
7 3 0.04
8 6 0.08
9 10 0.13
10 8 0.10
11 27 0.35
12 18 0.23
13 4 0.05
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:56647089 original size:39 final size:39
Alignment explanation
Indices: 56647011--56647166 Score: 206
Period size: 39 Copynumber: 3.8 Consensus size: 39
56647001 ATAAATACCA
56647011 AAAAATTATTTTAAAAATTAAAATAAAAATTAAAAAAAGTATTTT
1 AAAAA-TATTTT-AAAATT--AA-AAAAATT-AAAAAAGTATTTT
56647056 AAAAATATTTTAAAATTAAAAAAATTAAAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAATTAAAAAAGTATTTT
* *
56647095 AAAAAAATTTTAAAATTTAAAAAATTTAATAAAAGTATTTT
1 AAAAATATTTTAAAA-TTAAAAAAATTAA-AAAAGTATTTT
*
56647136 AAAAGTATTTTAAAATTAAAAAAA-TAAAAAA
1 AAAAATATTTTAAAATTAAAAAAATTAAAAAA
56647167 TAATAAAAAT
Statistics
Matches: 104, Mismatches: 5, Indels: 11
0.87 0.04 0.09
Matches are distributed among these distances:
38 4 0.04
39 30 0.29
40 27 0.26
41 26 0.25
43 6 0.06
44 6 0.06
45 5 0.05
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (39 bp):
AAAAATATTTTAAAATTAAAAAAATTAAAAAAGTATTTT
Found at i:56647118 original size:17 final size:17
Alignment explanation
Indices: 56647053--56647121 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 17
56647043 AAAAAAGTAT
56647053 TTTAAAAATATTTTAAAA
1 TTTAAAAA-ATTTTAAAA
* **
56647071 TTAAAAAAATTAAAAAAGTA
1 TTTAAAAAATT-TTAAA--A
56647091 TTTTAAAAAAATTTTAAAA
1 -TTT-AAAAAATTTTAAAA
56647110 TTTAAAAAATTT
1 TTTAAAAAATTT
56647122 AATAAAAGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
17 12 0.30
18 13 0.32
19 1 0.03
20 1 0.03
21 5 0.12
22 8 0.20
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (17 bp):
TTTAAAAAATTTTAAAA
Found at i:56651678 original size:20 final size:18
Alignment explanation
Indices: 56651653--56651696 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
56651643 CAGAATTAAA
56651653 TTATATATTTTTACGATAGT
1 TTATATATTTTTA--ATAGT
*
56651673 TTATATCTTTTTAATAGT
1 TTATATATTTTTAATAGT
56651691 TTATAT
1 TTATAT
56651697 CTTTAGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.48
20 12 0.52
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.59
Consensus pattern (18 bp):
TTATATATTTTTAATAGT
Found at i:56651689 original size:18 final size:19
Alignment explanation
Indices: 56651653--56651700 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 19
56651643 CAGAATTAAA
*
56651653 TTATATATTTTTACGATAGT
1 TTATATCTTTTTAC-ATAGT
56651673 TTATATCTTTTTA-ATAGT
1 TTATATCTTTTTACATAGT
56651691 TTATATCTTT
1 TTATATCTTT
56651701 AGAATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 15 0.56
20 12 0.44
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.60
Consensus pattern (19 bp):
TTATATCTTTTTACATAGT
Found at i:56652801 original size:16 final size:16
Alignment explanation
Indices: 56652764--56652802 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
56652754 TTTGGTTCAC
*
56652764 TGTAATGAAATAGAAT
1 TGTAATAAAATAGAAT
* *
56652780 TATAATAAAATAGAGT
1 TGTAATAAAATAGAAT
56652796 TGTAATA
1 TGTAATA
56652803 TATTTTTTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.33
Consensus pattern (16 bp):
TGTAATAAAATAGAAT
Found at i:56654016 original size:37 final size:37
Alignment explanation
Indices: 56653913--56654131 Score: 381
Period size: 37 Copynumber: 6.0 Consensus size: 37
56653903 TACGTATGAT
* *
56653913 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
56653948 CACCTATCACTTTGTTTC-TGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
56653984 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
56654021 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
56654058 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
56654095 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
56654132 TAAAGCTATT
Statistics
Matches: 177, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
35 9 0.05
36 38 0.21
37 130 0.73
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:56654149 original size:46 final size:46
Alignment explanation
Indices: 56654095--56654342 Score: 354
Period size: 46 Copynumber: 5.3 Consensus size: 46
56654085 TAAGTGTAGC
**
56654095 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
56654141 TACTTATCACTTTGTCTCTTGATCAGATAAGTCTAGCCGAAGCTAT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT
**
56654187 CACTTATCACTTT-TCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
56654232 TACTTATCACTTTGTCTCTTGATCAGATAAGTCTAGCCGAAGCTAT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT
*
56654278 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT
56654330 CACTTATCACTTT
1 CACTTATCACTTT
56654343 CCACTTTCCA
Statistics
Matches: 180, Mismatches: 15, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
45 41 0.23
46 94 0.52
49 2 0.01
52 43 0.24
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (46 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:56654215 original size:91 final size:91
Alignment explanation
Indices: 56654095--56654342 Score: 397
Period size: 91 Copynumber: 2.6 Consensus size: 91
56654085 TAAGTGTAGC
56654095 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATTACTTATCACTTTGTCTCT
1 CACTTATCACTTT-TCTCTTGATCAGATAAGTGTAGCTAAAGCTATTACTTATCACTTTGTCTCT
56654160 TGATCAGATAAGTCTAGCCGAAGCTAT
65 TGATCAGATAAGTCTAGCCGAAGCTAT
56654187 CACTTATCACTTTTCTCTTGATCAGATAAGTGTAGCTAAAGCTATTACTTATCACTTTGTCTCTT
1 CACTTATCACTTTTCTCTTGATCAGATAAGTGTAGCTAAAGCTATTACTTATCACTTTGTCTCTT
56654252 GATCAGATAAGTCTAGCCGAAGCTAT
66 GATCAGATAAGTCTAGCCGAAGCTAT
** *
56654278 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
1 CACTTATCACTTTT--C---T--CTTGATCAGATAAGTGTAGCTAAAGCTATTACTTATCACTTT
56654343 CCACTTTCCA
Statistics
Matches: 146, Mismatches: 3, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
91 92 0.63
92 13 0.09
93 1 0.01
96 1 0.01
98 39 0.27
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (91 bp):
CACTTATCACTTTTCTCTTGATCAGATAAGTGTAGCTAAAGCTATTACTTATCACTTTGTCTCTT
GATCAGATAAGTCTAGCCGAAGCTAT
Found at i:56654299 original size:52 final size:52
Alignment explanation
Indices: 56654233--56654348 Score: 187
Period size: 52 Copynumber: 2.2 Consensus size: 52
56654223 TAAAGCTATT
* *
56654233 ACTTATCACTTTGTCTCTTGATCAGATAAGTCTAGCCGAAGCTATCACTTATC
1 ACTTTTCAC-TTGTCACTTGATCAGATAAGTCTAGCCGAAGCTATCACTTATC
*
56654286 ACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATC
1 ACTTTTCACTTGTCACTTGATCAGATAAGTCTAGCCGAAGCTATCACTTATC
*
56654338 ACTTTCCACTT
1 ACTTTTCACTT
56654349 TCCACTTTCC
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 51 0.86
53 8 0.14
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (52 bp):
ACTTTTCACTTGTCACTTGATCAGATAAGTCTAGCCGAAGCTATCACTTATC
Done.