Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 134 of 163
Found at i:43514200 original size:24 final size:24
Alignment explanation
Indices: 43514151--43514202 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
43514141 AATCAAAGTC
* *
43514151 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
* *
43514175 AAATATATTATACTCATACATACT
1 AAATATATTATACTAATAAATACT
43514199 AAAT
1 AAAT
43514203 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:43518179 original size:24 final size:24
Alignment explanation
Indices: 43518164--43518215 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
43518154 AATTAAAGTC
43518164 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
43518188 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
43518212 AAAT
1 AAAT
43518216 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:43533178 original size:2 final size:2
Alignment explanation
Indices: 43533171--43533199 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43533161 AAATTATGTG
43533171 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
43533200 GTGTGTGTGT
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:43534179 original size:41 final size:41
Alignment explanation
Indices: 43534134--43534278 Score: 254
Period size: 41 Copynumber: 3.5 Consensus size: 41
43534124 GACTTTAAGT
43534134 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
*
43534175 CTAGCAGGCTACGTGCCGATGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
43534216 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
*
43534257 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTACGTGCCGGTGA
43534279 ATATGTTAAA
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 99 1.00
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (41 bp):
CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:43538425 original size:20 final size:19
Alignment explanation
Indices: 43538389--43538426 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
43538379 ATAAATAAGT
43538389 ATTTTCAAATTACAAATTA
1 ATTTTCAAATTACAAATTA
43538408 ATTTATCAATATTA-AAATT
1 ATTT-TCAA-ATTACAAATT
43538427 TTAAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTTCAAATTACAAATTA
Found at i:43546650 original size:17 final size:17
Alignment explanation
Indices: 43546613--43546660 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
43546603 GAATTTAGAA
*
43546613 GAATTTT-TGAATTAGT
1 GAATTTTGTGATTTAGT
*
43546629 GAATTTTGTGATTTATT
1 GAATTTTGTGATTTAGT
43546646 GAATTTTGTGATTTA
1 GAATTTTGTGATTTA
43546661 AAAAGAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (17 bp):
GAATTTTGTGATTTAGT
Found at i:43547804 original size:46 final size:46
Alignment explanation
Indices: 43547751--43547890 Score: 208
Period size: 46 Copynumber: 3.0 Consensus size: 46
43547741 CCATGGCAAA
* *
43547751 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACTATACTCAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
* * *
43547797 TTGTGAAAAGTAGGTATGATGTTTTAGTGAAGAAAACCATATTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
* * *
43547843 TAGTGAAAAGTAAGTATGGTGTTTGAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
43547889 TT
1 TT
43547891 ATAGCATTGT
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 83 1.00
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.31
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
Found at i:43548388 original size:12 final size:12
Alignment explanation
Indices: 43548371--43548400 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
43548361 ATTTTCGATA
43548371 TGAATTAACTAT
1 TGAATTAACTAT
43548383 TGAATTAACTAT
1 TGAATTAACTAT
43548395 TGAATT
1 TGAATT
43548401 GGTTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (12 bp):
TGAATTAACTAT
Found at i:43549283 original size:22 final size:23
Alignment explanation
Indices: 43549245--43549289 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
43549235 AGTCAGGTAA
*
43549245 TGTAATATCTCGAAAATTACTAC
1 TGTAATATCCCGAAAATTACTAC
43549268 TGTAATA-CCCGAAAATTACTAC
1 TGTAATATCCCGAAAATTACTAC
43549290 AATAAGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (23 bp):
TGTAATATCCCGAAAATTACTAC
Found at i:43549734 original size:228 final size:228
Alignment explanation
Indices: 43549322--43549779 Score: 774
Period size: 228 Copynumber: 2.0 Consensus size: 228
43549312 ATAGTAAAAT
43549322 AAGGAAATAAAGTGACAAAAAGGGAAATTTTGAGTTATGGCAACATTGAGAATTATATTATGACA
1 AAGGAAATAAAGTGACAAAAAGGGAAATTTTGAGTTATGGCAACATTGAGAATTATATTATGACA
*
43549387 TTAATTCAAGAAAGTATTAAATCGCAAAAGTGAGAAAAGTTTTGTTACCCAAGAGTAAATACTTA
66 TTAATTCAAGAAAGGATTAAATCGCAAAAGTGAGAAAAGTTTTGTTACCCAAGAGTAAATACTTA
* * *
43549452 AAAGTTGAGGGGTTAAAGTGTAAATATGAAAAAGTTGAAGGACCAATGGTGTAAATATTTTAAGG
131 AAAGTTGAGGGGTTAAAGTGTAAATATGAAAAACTTAAAGGACCAATAGTGTAAATATTTTAAGG
43549517 GTGGAATAATCTAGAAACTAAGAAAAATGGATG
196 GTGGAATAATCTAGAAACTAAGAAAAATGGATG
43549550 AAGGAAATAAAGTGACAAAAAGGGAAATTTTGAGTTATGGCAACATTGAGAATTATATTATGACA
1 AAGGAAATAAAGTGACAAAAAGGGAAATTTTGAGTTATGGCAACATTGAGAATTATATTATGACA
* *
43549615 TTAATTCATGAAAGGATTAAATCGCAAAAGTGAGAAAAGTTTTGTTGCCCAAGAGTTAAATAC-T
66 TTAATTCAAGAAAGGATTAAATCGCAAAAGTGAGAAAAGTTTTGTTACCCAAGAG-TAAATACTT
* * * *
43549679 CAAATTTGAGGGGTTAAAGTGTAAATATGAAAAACTTAAAGGGCCAATAGTGTAAATCTTTTAAG
130 AAAAGTTGAGGGGTTAAAGTGTAAATATGAAAAACTTAAAGGACCAATAGTGTAAATATTTTAAG
* * * *
43549744 GGTTGCATAATCTAGAAACTAAGGAAAGTGGATG
195 GGTGGAATAATCTAGAAACTAAGAAAAATGGATG
43549778 AA
1 AA
43549780 TTAGGGCCAA
Statistics
Matches: 215, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
228 208 0.97
229 7 0.03
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (228 bp):
AAGGAAATAAAGTGACAAAAAGGGAAATTTTGAGTTATGGCAACATTGAGAATTATATTATGACA
TTAATTCAAGAAAGGATTAAATCGCAAAAGTGAGAAAAGTTTTGTTACCCAAGAGTAAATACTTA
AAAGTTGAGGGGTTAAAGTGTAAATATGAAAAACTTAAAGGACCAATAGTGTAAATATTTTAAGG
GTGGAATAATCTAGAAACTAAGAAAAATGGATG
Found at i:43558452 original size:23 final size:23
Alignment explanation
Indices: 43558421--43558473 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
43558411 AGTGTTCTTG
43558421 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCAGCTACAT
* *
43558444 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCAGCTACAT
43558467 ATCAGTG
1 ATCAGTG
43558474 TGGCTTTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCAGCTACAT
Found at i:43560390 original size:13 final size:13
Alignment explanation
Indices: 43560372--43560405 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
43560362 TGATTGGTTA
*
43560372 GTCCAGTGGAACT
1 GTCCAGCGGAACT
43560385 GTCCAGCGGAACT
1 GTCCAGCGGAACT
43560398 GTCCAGCG
1 GTCCAGCG
43560406 TGGTAGGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.29, G:0.32, T:0.18
Consensus pattern (13 bp):
GTCCAGCGGAACT
Found at i:43563115 original size:20 final size:21
Alignment explanation
Indices: 43563082--43563122 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
43563072 TTAAACTGAA
43563082 AAGATAAAAATATT-TTTTGT
1 AAGATAAAAATATTGTTTTGT
* *
43563102 AAGATTAAATTATTGTTTTGT
1 AAGATAAAAATATTGTTTTGT
43563123 TTATTTTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (21 bp):
AAGATAAAAATATTGTTTTGT
Found at i:43564894 original size:25 final size:25
Alignment explanation
Indices: 43564843--43564895 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
43564833 ACTTTAGCGC
* ***
43564843 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTACTAGCACGGCAGT
43564868 GCTCTCTGATTACTAGCACGGCAGT
1 GCTCTCTGATTACTAGCACGGCAGT
43564893 GCT
1 GCT
43564896 ATCTATTTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.34
Consensus pattern (25 bp):
GCTCTCTGATTACTAGCACGGCAGT
Found at i:43564938 original size:22 final size:23
Alignment explanation
Indices: 43564890--43564946 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
43564880 CTAGCACGGC
* *
43564890 AGTGCTATCTATTTAGCACATGT
1 AGTGCTCTCTGTTTAGCACATGT
*
43564913 -GTGCTCTCTGTTTAGCAC-TTT
1 AGTGCTCTCTGTTTAGCACATGT
43564934 AGTGCTCTCTGTT
1 AGTGCTCTCTGTT
43564947 CATTAGCACA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (23 bp):
AGTGCTCTCTGTTTAGCACATGT
Found at i:43567533 original size:1 final size:1
Alignment explanation
Indices: 43567527--43567557 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
43567517 GGAGATAAAT
43567527 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
43567558 GCACTTGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:43568173 original size:25 final size:25
Alignment explanation
Indices: 43568124--43568173 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
43568114 ATTTTTTTAA
*
43568124 ATTTATTTTCAATTTATTAGGATAT
1 ATTTATTTTCAATATATTAGGATAT
*
43568149 ATTTATTTT-AATATATGTAGTATAT
1 ATTTATTTTCAATATAT-TAGGATAT
43568174 TTGATGTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (25 bp):
ATTTATTTTCAATATATTAGGATAT
Found at i:43573853 original size:22 final size:20
Alignment explanation
Indices: 43573812--43573859 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 20
43573802 CATATTATTT
43573812 TTTAATTTATTTTTTAAATA
1 TTTAATTTATTTTTTAAATA
43573832 TTTATATTATATTATTTT-AATA
1 TTTA-ATT-TATT-TTTTAAATA
43573854 TTTAAT
1 TTTAAT
43573860 AAAATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.16
21 5 0.20
22 12 0.48
23 4 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTAATTTATTTTTTAAATA
Found at i:43575432 original size:27 final size:24
Alignment explanation
Indices: 43575370--43575433 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 24
43575360 CAAAATCGAA
*
43575370 AATAATTTCATTTATTTTTACTCT
1 AATAATTTAATTTATTTTTACTCT
* * *
43575394 -ATATTTTTATTTATTTTTTTATTCTT
1 AATAATTTAATTTA--TTTTTACTC-T
43575420 AATAATTTAATTTA
1 AATAATTTAATTTA
43575434 AGTATTCCAC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 11 0.35
25 8 0.26
26 1 0.03
27 11 0.35
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (24 bp):
AATAATTTAATTTATTTTTACTCT
Found at i:43577080 original size:42 final size:41
Alignment explanation
Indices: 43577004--43577296 Score: 354
Period size: 42 Copynumber: 7.0 Consensus size: 41
43576994 ACGTCGATAA
*
43577004 CTTTTGCGGCGCTTACATAAAGAAACGCCGCTAAAGCTCATGTT
1 CTTTAGCGGCGCTTA-A-AAA-AAACGCCGCTAAAGCTCATGTT
* *
43577048 CTTTAGCGGCGCTTAGAAAAAAACGCCCCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-AAAAAAACGCCGCTAAAGCTCATGTT
* * *
43577090 CTTTAGCGACGCTTAAAATAAACGTCGCTAAAGCTCATGTT
1 CTTTAGCGGCGCTTAAAAAAAACGCCGCTAAAGCTCATGTT
* * * *
43577131 CTTTAGCGGCGCTTTGGAAGAAAAC-CCCCTAAAGATCATGTT
1 CTTTAGCGGCGC-TT-AAAAAAAACGCCGCTAAAGCTCATGTT
* * *
43577173 CTTTAGCGACGCTTAAAATAAACGTCGCTAAAGCTCATGTT
1 CTTTAGCGGCGCTTAAAAAAAACGCCGCTAAAGCTCATGTT
* *
43577214 CTTTAGCGGCGCTTAGAAAAAAACGCCCCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-AAAAAAACGCCGCTAAAGCTCATGTT
* * *
43577256 CTTTAGCGACGCTTAAAATAAACGTCGCTAAAGCTCATGTT
1 CTTTAGCGGCGCTTAAAAAAAACGCCGCTAAAGCTCATGTT
43577297 ACTAATTTTG
Statistics
Matches: 212, Mismatches: 33, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
40 6 0.03
41 85 0.40
42 97 0.46
43 9 0.04
44 15 0.07
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (41 bp):
CTTTAGCGGCGCTTAAAAAAAACGCCGCTAAAGCTCATGTT
Found at i:43577123 original size:83 final size:83
Alignment explanation
Indices: 43577026--43577296 Score: 499
Period size: 83 Copynumber: 3.3 Consensus size: 83
43577016 TTACATAAAG
*
43577026 AAACGCCGCTAAAGCTCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCCCTAAAGATCATGTTC
1 AAACGTCGCTAAAGCTCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCCCTAAAGATCATGTTC
43577091 TTTAGCGACGCTTAAAAT
66 TTTAGCGACGCTTAAAAT
* *
43577109 AAACGTCGCTAAAGCTCATGTTCTTTAGCGGCGCTTTGGAAGAAAAC-CCCCTAAAGATCATGTT
1 AAACGTCGCTAAAGCTCATGTTCTTTAGCGGCGC-TTAGAAAAAAACGCCCCTAAAGATCATGTT
43577173 CTTTAGCGACGCTTAAAAT
65 CTTTAGCGACGCTTAAAAT
43577192 AAACGTCGCTAAAGCTCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCCCTAAAGATCATGTTC
1 AAACGTCGCTAAAGCTCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCCCTAAAGATCATGTTC
43577257 TTTAGCGACGCTTAAAAT
66 TTTAGCGACGCTTAAAAT
43577275 AAACGTCGCTAAAGCTCATGTT
1 AAACGTCGCTAAAGCTCATGTT
43577297 ACTAATTTTG
Statistics
Matches: 181, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
82 10 0.06
83 161 0.89
84 10 0.06
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (83 bp):
AAACGTCGCTAAAGCTCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCCCTAAAGATCATGTTC
TTTAGCGACGCTTAAAAT
Found at i:43577685 original size:21 final size:21
Alignment explanation
Indices: 43577655--43577694 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
43577645 TTCTTTTGAA
*
43577655 CCTCTGCTTCTCTCGCTGCGG
1 CCTCTACTTCTCTCGCTGCGG
43577676 CCTCTACTTCTCTCGCTGC
1 CCTCTACTTCTCTCGCTGC
43577695 TTCTCTCGCT
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:0.03, C:0.45, G:0.17, T:0.35
Consensus pattern (21 bp):
CCTCTACTTCTCTCGCTGCGG
Found at i:43577695 original size:33 final size:33
Alignment explanation
Indices: 43577658--43577725 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
43577648 TTTTGAACCT
* *
43577658 CTGCTTCTCTCGCTGCGGCCTCTACTTCTCTCG
1 CTGCTTCTCTCGCTGCGACATCTACTTCTCTCG
43577691 CTGCTTCTCTCGCTGCGACATCTACTTCTCTCG
1 CTGCTTCTCTCGCTGCGACATCTACTTCTCTCG
43577724 CT
1 CT
43577726 ATAGCCTCTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.06, C:0.41, G:0.16, T:0.37
Consensus pattern (33 bp):
CTGCTTCTCTCGCTGCGACATCTACTTCTCTCG
Found at i:43577699 original size:12 final size:12
Alignment explanation
Indices: 43577682--43577706 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43577672 GCGGCCTCTA
43577682 CTTCTCTCGCTG
1 CTTCTCTCGCTG
43577694 CTTCTCTCGCTG
1 CTTCTCTCGCTG
43577706 C
1 C
43577707 GACATCTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.44, G:0.16, T:0.40
Consensus pattern (12 bp):
CTTCTCTCGCTG
Found at i:43590133 original size:114 final size:113
Alignment explanation
Indices: 43589830--43590138 Score: 300
Period size: 115 Copynumber: 2.7 Consensus size: 113
43589820 ATGCATGGTT
* * * *
43589830 AAGACCAAAACTCTGCGTTTTGGTTAATACATTTTCCGGCGCTTATCAAAAAGCGCCGCTAATAC
1 AAGA-CAAAACGCAGCGTTTTGGTTAATATATTTTGCGGCGCTTATC-AAAAGCGCCGCTAATAC
* * * *** *
43589895 AATGCTTTAGCGGCGATTTCTCGTGAACGCCACTAATTCCAGTATACATC
64 TATGATTTAGCGGCGATATCTCAAAAACGCCACTAATTCCAATATACATC
* * * * * * *
43589945 AAGACTTAAACGCTGCGTTTTTGTTAATATCTTTTGCGGCGCTTATAAAAAAGAGCCGCTAATAA
1 AAGAC-AAAACGCAGCGTTTTGGTTAATATATTTTGCGGCGCTTAT-CAAAAGCGCCGCTAATAC
* *
43590010 TAT-ACTTTAGCGGCGATATC-CAAAAAGCGCCACTAATTCTAATATACCTC
64 TATGA-TTTAGCGGCGATATCTCAAAAA-CGCCACTAATTCCAATATACATC
* * * * *
43590060 ATGTA-AAAACGCAGCGTTTTGGTGAGTATATTTTGCGGCGCTTCTGCACAAGCGCCGCTAATAC
1 AAG-ACAAAACGCAGCGTTTTGGTTAATATATTTTGCGGCGCTTAT-CAAAAGCGCCGCTAATAC
43590124 TATGATTTAGCGGCG
64 TATGATTTAGCGGCG
43590139 TTTCTTTATA
Statistics
Matches: 157, Mismatches: 31, Indels: 13
0.78 0.15 0.06
Matches are distributed among these distances:
114 64 0.41
115 92 0.59
116 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (113 bp):
AAGACAAAACGCAGCGTTTTGGTTAATATATTTTGCGGCGCTTATCAAAAGCGCCGCTAATACTA
TGATTTAGCGGCGATATCTCAAAAACGCCACTAATTCCAATATACATC
Found at i:43607501 original size:15 final size:15
Alignment explanation
Indices: 43607481--43607510 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43607471 TCCAAATTGT
*
43607481 TTGTTGAAGCTTCCA
1 TTGTTGAAGATTCCA
43607496 TTGTTGAAGATTCCA
1 TTGTTGAAGATTCCA
43607511 GAAAACATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (15 bp):
TTGTTGAAGATTCCA
Found at i:43610422 original size:20 final size:20
Alignment explanation
Indices: 43610397--43610436 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
43610387 AAATATTTTC
43610397 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
* *
43610417 AGTAAATTATTTTTCAGAAA
1 AGTAAATCATTTTCCAGAAA
43610437 TTATTTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (20 bp):
AGTAAATCATTTTCCAGAAA
Found at i:43615909 original size:30 final size:31
Alignment explanation
Indices: 43615849--43615918 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
43615839 ATACACAAAT
43615849 AATTTTATGTGTATGACTGAATCAAAATCAA
1 AATTTTATGTGTATGACTGAATCAAAATCAA
* * * *
43615880 AATTTTATGTTTATGATTGCA-CCAAATCAA
1 AATTTTATGTGTATGACTGAATCAAAATCAA
43615910 AA-TTTATGT
1 AATTTTATGT
43615919 ATCAAATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 7 0.20
30 10 0.29
31 18 0.51
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (31 bp):
AATTTTATGTGTATGACTGAATCAAAATCAA
Found at i:43619931 original size:8 final size:8
Alignment explanation
Indices: 43619920--43619987 Score: 50
Period size: 8 Copynumber: 8.8 Consensus size: 8
43619910 CTTTTATACA
43619920 TATATATT
1 TATATATT
*
43619928 TATAAATT
1 TATATATT
* *
43619936 TTTTTATT
1 TATATATT
* *
43619944 TTTTTATT
1 TATATATT
43619952 TAT-T-TT
1 TATATATT
* *
43619958 TATTTTTT
1 TATATATT
43619966 TATATATT
1 TATATATT
43619974 TATATATT
1 TATATATT
*
43619982 TTTATA
1 TATATA
43619988 GATTTATATT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
6 5 0.10
7 2 0.04
8 43 0.86
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
TATATATT
Found at i:43619959 original size:18 final size:18
Alignment explanation
Indices: 43619936--43620012 Score: 84
Period size: 18 Copynumber: 4.2 Consensus size: 18
43619926 TTTATAAATT
*
43619936 TTTTTATTTTTTTATTTA
1 TTTTTATTTTTTTATATA
43619954 TTTTTATTTTTTTATATA
1 TTTTTATTTTTTTATATA
* * *
43619972 TTTATATATTTTTATAGA
1 TTTTTATTTTTTTATATA
*
43619990 TTTATATTTGTTATTA-ATA
1 TTTTTATTT-TT-TTATATA
43620009 TTTT
1 TTTT
43620013 ATTAATAAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
18 40 0.80
19 7 0.14
20 3 0.06
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.73
Consensus pattern (18 bp):
TTTTTATTTTTTTATATA
Found at i:43619962 original size:26 final size:26
Alignment explanation
Indices: 43619933--43619986 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
43619923 ATATTTATAA
* * *
43619933 ATTTTTTTATTTTTTTATTTATTTTT
1 ATTTTTTTATATATTTATATATTTTT
43619959 ATTTTTTTATATATTTATATATTTTT
1 ATTTTTTTATATATTTATATATTTTT
43619985 AT
1 AT
43619987 AGATTTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (26 bp):
ATTTTTTTATATATTTATATATTTTT
Found at i:43619987 original size:10 final size:10
Alignment explanation
Indices: 43619919--43619992 Score: 66
Period size: 10 Copynumber: 7.8 Consensus size: 10
43619909 TCTTTTATAC
*
43619919 ATATATATTT
1 ATATATTTTT
*
43619929 ATAAATTTTT
1 ATATATTTTT
* *
43619939 TTATTTTTTT
1 ATATATTTTT
*
43619949 ATTTATTTTT
1 ATATATTTTT
43619959 AT-T-TTTTT
1 ATATATTTTT
43619967 ATATA--TTT
1 ATATATTTTT
43619975 ATATATTTTT
1 ATATATTTTT
*
43619985 ATAGATTT
1 ATATATTT
43619993 ATATTTGTTA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
8 15 0.29
9 2 0.04
10 34 0.67
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.70
Consensus pattern (10 bp):
ATATATTTTT
Found at i:43620013 original size:46 final size:46
Alignment explanation
Indices: 43619920--43620014 Score: 109
Period size: 46 Copynumber: 2.1 Consensus size: 46
43619910 CTTTTATACA
* ** * * * *
43619920 TATATATTTATAAATTTTTTTATTTTTTTATTTATTTTTATTTTTT
1 TATATATTTATAAATTTTTATAGATTTATATTTATTATTAATATTT
* *
43619966 TATATATTTATATATTTTTATAGATTTATATTTGTTATTAATATTT
1 TATATATTTATAAATTTTTATAGATTTATATTTATTATTAATATTT
43620012 TAT
1 TAT
43620015 TAATAAGTGA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.69
Consensus pattern (46 bp):
TATATATTTATAAATTTTTATAGATTTATATTTATTATTAATATTT
Found at i:43620224 original size:16 final size:17
Alignment explanation
Indices: 43620203--43620236 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
43620193 GTTTCTCTTA
43620203 TATCTCT-GTCTTTTAT
1 TATCTCTAGTCTTTTAT
*
43620219 TATCTCTATTCTTTTAT
1 TATCTCTAGTCTTTTAT
43620236 T
1 T
43620237 TCATAACAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.15, C:0.18, G:0.03, T:0.65
Consensus pattern (17 bp):
TATCTCTAGTCTTTTAT
Found at i:43622874 original size:112 final size:113
Alignment explanation
Indices: 43622662--43622882 Score: 270
Period size: 112 Copynumber: 2.0 Consensus size: 113
43622652 CAGTGAAAGT
* * *
43622662 ATATAAGAATTATTTTGAAGTGATTTGAATTTAATATTAAAATCTAATTAATAGATAAATTATTT
1 ATATAAGAATTATTGTGAAGTGATTTGAATATAATATTAAAATCTAATTAATAGATAAATTAGTT
* * *
43622727 AATTCAAAAGTTAATTCTTTGAAAAATCGTAATAA-TAATTTTTTTAA
66 AATTCAAAAGCTAATTATTTGAAAAAGCGTAATAATTAATTTTTTTAA
* ** *
43622774 ATATAATAATTATTGTGAAGTGATTTGAGA-ATAATATTAATTTTTAATTAATAGATAAATT-GT
1 ATATAAGAATTATTGTGAAGTGATTTGA-ATATAATATTAAAATCTAATTAATAGATAAATTAGT
* * *
43622837 TAAGTTGAAAAGCTAATTATTT-TAAAAGCAGTGATAATTAATTTTT
65 TAA-TTCAAAAGCTAATTATTTGAAAAAGC-GTAATAATTAATTTTT
43622883 AATTTTTTTT
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
111 9 0.10
112 74 0.80
113 9 0.10
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.43
Consensus pattern (113 bp):
ATATAAGAATTATTGTGAAGTGATTTGAATATAATATTAAAATCTAATTAATAGATAAATTAGTT
AATTCAAAAGCTAATTATTTGAAAAAGCGTAATAATTAATTTTTTTAA
Found at i:43627612 original size:44 final size:43
Alignment explanation
Indices: 43627384--43627671 Score: 169
Period size: 44 Copynumber: 6.7 Consensus size: 43
43627374 TTTTTTGTCT
* *** *
43627384 GCTCCACTGCAACTTCAGGGAGATAAG--ACTGGATGCGATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATACTGGCTTTAATCC
* * * *
43627425 GCTCTACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TACTGGCTTTAATCC
* ** *** * * *
43627469 TCTCCACTATAACTTCAGGGAGATAAGATTCACAATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-T-ACTGGCTTTAATCC
* * * *
43627514 GCCCCCACTGCAACTTCAGGGGGATAAG--ACTAG--TTACGATCT
1 G-CTCCACTGCAACTTCAGGGAGATAAGATACTGGCTTTA--ATCC
* * *
43627556 GCT-CTCTGCAACTTCAGAGAGATAAGAT-CTGTCATTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATACTGGC--TTTAATCC
* * * *
43627599 GCTCCGCTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TACTGGCTTTAATCC
*
43627643 GCTCCACTACAACTTCAGGGAGATAAGAT
1 GCTCCACTGCAACTTCAGGGAGATAAGAT
43627672 TCGCCATCTT
Statistics
Matches: 188, Mismatches: 43, Indels: 30
0.72 0.16 0.11
Matches are distributed among these distances:
40 22 0.12
41 28 0.15
42 7 0.04
43 7 0.04
44 87 0.46
45 12 0.06
46 25 0.13
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (43 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATACTGGCTTTAATCC
Found at i:43627614 original size:130 final size:131
Alignment explanation
Indices: 43627387--43627628 Score: 319
Period size: 130 Copynumber: 1.9 Consensus size: 131
43627377 TTTGTCTGCT
* * * *
43627387 CCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGGGAGATAGG
1 CCACTGCAACTTCAGGGAGATAAGACTAGATACGATCTGCTCTACTGCAACTTCAGAGAGATAAG
* ** *
43627452 ATTATTGGCTTTAATCTTCTCCACTATAACTTCAGGGAGATAAGATTCACAATCTTCAGTCTGCC
66 ATTACTGGCTTTAATCCGCTCCACTACAACTTCAGGGAGATAAGATTCACAATCTTCAGTCTGCC
43627517 C
131 C
* *
43627518 CCACTGCAACTTCAGGGGGATAAGACTAGTTACGATCTGCTCT-CTGCAACTTCAGAGAGATAAG
1 CCACTGCAACTTCAGGGAGATAAGACTAGATACGATCTGCTCTACTGCAACTTCAGAGAGATAAG
* * * *
43627582 A-T-CTGTCATTTTAATCCGCTCCGCTGCAACTTCAGGGAGATAGGATT
66 ATTACTGGC--TTTAATCCGCTCCACTACAACTTCAGGGAGATAAGATT
43627629 ATTGGCTTTA
Statistics
Matches: 95, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
128 3 0.03
129 1 0.01
130 52 0.55
131 39 0.41
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (131 bp):
CCACTGCAACTTCAGGGAGATAAGACTAGATACGATCTGCTCTACTGCAACTTCAGAGAGATAAG
ATTACTGGCTTTAATCCGCTCCACTACAACTTCAGGGAGATAAGATTCACAATCTTCAGTCTGCC
C
Found at i:43629347 original size:11 final size:11
Alignment explanation
Indices: 43629328--43629360 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
43629318 TGCCTCTCAT
43629328 TTTTC-TTTTC
1 TTTTCTTTTTC
43629338 TTTTCTTTTTC
1 TTTTCTTTTTC
43629349 TTTTCATTTTTC
1 TTTTC-TTTTTC
43629361 ATCATTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 5 0.24
11 10 0.48
12 6 0.29
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:43629396 original size:14 final size:14
Alignment explanation
Indices: 43629379--43629425 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
43629369 TATTTTTTCG
43629379 ATTTTGATTTTTTT
1 ATTTTGATTTTTTT
*
43629393 ATTTTGATTTTGATT
1 ATTTTGATTTT-TTT
*
43629408 -TTTTGATTTTTTA
1 ATTTTGATTTTTTT
43629421 ATTTT
1 ATTTT
43629426 TTTTAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 1 0.04
14 25 0.89
15 2 0.07
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (14 bp):
ATTTTGATTTTTTT
Found at i:43629435 original size:8 final size:8
Alignment explanation
Indices: 43629380--43629427 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
43629370 ATTTTTTCGA
43629380 TTTTGATT
1 TTTTGATT
*
43629388 TTTT--TA
1 TTTTGATT
43629394 TTTTGA--
1 TTTTGATT
43629400 TTTTGATT
1 TTTTGATT
43629408 TTTTGATT
1 TTTTGATT
*
43629416 TTTTAATT
1 TTTTGATT
43629424 TTTT
1 TTTT
43629428 TTAATTTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
6 11 0.32
8 23 0.68
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (8 bp):
TTTTGATT
Found at i:43629443 original size:28 final size:27
Alignment explanation
Indices: 43629380--43629435 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 27
43629370 ATTTTTTCGA
* *
43629380 TTTTGATTTTTTTATTTTGATTTTGATT
1 TTTTGATTTTTTAATTTT-ATTTTAATT
43629408 TTTTGATTTTTTAATTTT-TTTTAATT
1 TTTTGATTTTTTAATTTTATTTTAATT
43629434 TT
1 TT
43629436 CTTTGATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 9 0.35
28 17 0.65
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (27 bp):
TTTTGATTTTTTAATTTTATTTTAATT
Found at i:43630249 original size:25 final size:25
Alignment explanation
Indices: 43630196--43630261 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
43630186 AAGAGAATCC
* *
43630196 AAAAGAATAAAAGAATAATTATTCG
1 AAAAGAATAAAAGAATAATTACTCA
*
43630221 AAAAGAATGAAAGAAT-ATTAGCTCA
1 AAAAGAATAAAAGAATAATTA-CTCA
43630246 AAAATGAATACAAAGA
1 AAAA-GAATA-AAAGA
43630262 TTTATTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
24 4 0.12
25 21 0.62
26 4 0.12
27 5 0.15
ACGTcount: A:0.61, C:0.06, G:0.14, T:0.20
Consensus pattern (25 bp):
AAAAGAATAAAAGAATAATTACTCA
Found at i:43636146 original size:12 final size:11
Alignment explanation
Indices: 43636131--43636178 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 11
43636121 TATAGGCATA
43636131 ATAATAAATAAT
1 ATAAT-AATAAT
43636143 ATAATAATAAT
1 ATAATAATAAT
*
43636154 -TAAT-ATAAC
1 ATAATAATAAT
43636163 ATAATTAATAAT
1 ATAA-TAATAAT
43636175 ATAA
1 ATAA
43636179 AAAATTGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
9 4 0.13
10 7 0.23
11 7 0.23
12 13 0.42
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:43636148 original size:15 final size:15
Alignment explanation
Indices: 43636128--43636178 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
43636118 ACGTATAGGC
43636128 ATAATAATAAATAAT
1 ATAATAATAAATAAT
*
43636143 ATAATAATAATTAAT
1 ATAATAATAAATAAT
*
43636158 ATAACATAATTAATAAT
1 AT-A-ATAATAAATAAT
43636175 ATAA
1 ATAA
43636179 AAAATTGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 17 0.55
16 2 0.06
17 12 0.39
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAATAATAAATAAT
Found at i:43648763 original size:105 final size:106
Alignment explanation
Indices: 43648624--43648837 Score: 412
Period size: 105 Copynumber: 2.0 Consensus size: 106
43648614 TTATAAGGAG
43648624 AATGCATGATTTAAAAGTTTAGGGTTAGTACTAGAAGTAGATATTGTATAAAAAAATAATATTTA
1 AATGCATGATTTAAAAGTTTAGGGTTAGTACTAGAAGTAGATATTGTATAAAAAAATAATATTTA
43648689 TTTATATTTATGTTTTTAATTATTAAATTTTATTTGACTTC
66 TTTATATTTATGTTTTTAATTATTAAATTTTATTTGACTTC
43648730 AATGCATGATTT-AAAGTTTAGGGTTAGTACTAGAAGTAGATATTGTATAAAAAAATAATATTTA
1 AATGCATGATTTAAAAGTTTAGGGTTAGTACTAGAAGTAGATATTGTATAAAAAAATAATATTTA
*
43648794 TTTATATTTATGTTTTTAATTATTAAATTTTTTTTGACTTC
66 TTTATATTTATGTTTTTAATTATTAAATTTTATTTGACTTC
43648835 AAT
1 AAT
43648838 TAAAATTAAA
Statistics
Matches: 107, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
105 95 0.89
106 12 0.11
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.47
Consensus pattern (106 bp):
AATGCATGATTTAAAAGTTTAGGGTTAGTACTAGAAGTAGATATTGTATAAAAAAATAATATTTA
TTTATATTTATGTTTTTAATTATTAAATTTTATTTGACTTC
Found at i:43664367 original size:109 final size:108
Alignment explanation
Indices: 43664227--43664569 Score: 547
Period size: 109 Copynumber: 3.2 Consensus size: 108
43664217 CGGCACCAGA
*
43664227 ATACGAAAAAAAT-AAAAAAAATTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGGGG
1 ATACGAAAAAAGTAAAAAAAAATTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGGGG
* *
43664291 AAATTTTTTTTTCACTGTTTTCGTGTTAATAGCAGGTATCAGT
66 AAATTTTTTTTTCACTTTTTTCGTGTCAATAGCAGGTATCAGT
* *
43664334 ATACGAAAAAAGTTAAAAAAAAATTTGGTGGTGGCCTGCCAATGGCCGACACCACCTTTTTT-GT
1 ATACGAAAAAAG-TAAAAAAAAATTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGGG
*
43664398 GATAATTTTTTTTTC-CTTTTTTTGTGTCAATAGCAGGTATCAGT
65 GA-AATTTTTTTTTCACTTTTTTCGTGTCAATAGCAGGTATCAGT
43664442 ATACGAAAAAAG-AAAAAAAAATTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGTGG
1 ATACGAAAAAAGTAAAAAAAAATTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTG-GG
*
43664506 G--ATTTTTTTTT-ACTTTTTTCGTGTCAATAGCATGTATCAGT
65 GAAATTTTTTTTTCACTTTTTTCGTGTCAATAGCAGGTATCAGT
43664547 ATACGAAAAAAGTAAAAAAAAAT
1 ATACGAAAAAAGTAAAAAAAAAT
43664570 CCCACAAAAA
Statistics
Matches: 219, Mismatches: 10, Indels: 15
0.90 0.04 0.06
Matches are distributed among these distances:
105 49 0.22
106 57 0.26
107 11 0.05
108 44 0.20
109 58 0.26
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (108 bp):
ATACGAAAAAAGTAAAAAAAAATTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGGGG
AAATTTTTTTTTCACTTTTTTCGTGTCAATAGCAGGTATCAGT
Found at i:43664493 original size:106 final size:106
Alignment explanation
Indices: 43664227--43664569 Score: 546
Period size: 106 Copynumber: 3.2 Consensus size: 106
43664217 CGGCACCAGA
* *
43664227 ATACGAAAAAAAT-AAAAAAAATTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGGGG
1 ATACGAAAAAAGTAAAAAAAAATTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTT-GTG
* *
43664291 AAATTTTTTTTTCACTGTTTTCGTGTTAATAGCAGGTATCAGT
65 AAATTTTTTTTTC-CTTTTTTCGTGTCAATAGCAGGTATCAGT
*
43664334 ATACGAAAAAAGTTAAAAAAAAATTTGGTGGTGGCCTGCCAATGGCCGACACCACCTTTTTTGTG
1 ATACGAAAAAAG-TAAAAAAAAATTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGTG
*
43664399 ATAATTTTTTTTTCCTTTTTTTGTGTCAATAGCAGGTATCAGT
65 A-AATTTTTTTTTCCTTTTTTCGTGTCAATAGCAGGTATCAGT
*
43664442 ATACGAAAAAAG-AAAAAAAAATTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGTGG
1 ATACGAAAAAAGTAAAAAAAAATTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGTGA
* * *
43664506 GATTTTTTTTTACTTTTTTCGTGTCAATAGCATGTATCAGT
66 AATTTTTTTTTCCTTTTTTCGTGTCAATAGCAGGTATCAGT
43664547 ATACGAAAAAAGTAAAAAAAAAT
1 ATACGAAAAAAGTAAAAAAAAAT
43664570 CCCACAAAAA
Statistics
Matches: 220, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
105 49 0.22
106 60 0.27
107 11 0.05
108 42 0.19
109 58 0.26
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (106 bp):
ATACGAAAAAAGTAAAAAAAAATTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGTGA
AATTTTTTTTTCCTTTTTTCGTGTCAATAGCAGGTATCAGT
Found at i:43667082 original size:103 final size:105
Alignment explanation
Indices: 43666906--43667218 Score: 308
Period size: 103 Copynumber: 3.0 Consensus size: 105
43666896 CAATTTTTTT
* * * * *
43666906 TTACTTTTTTCATATACTCATACCTGCTATTGACACGAAAAAAGTAAAAAAAAATTTCGACAAAA
1 TTACTTTTTTCATATACTCATACATGATATTGACACGAAAAAAATAAAAAAAAATTCCCACAAAA
* *
43666971 AAGGTGGTGCCGGCCATTGGTAGGCCACCA-CAAAAAAAA
66 AAGGTGGTGCCAGCCATTGGCAGGCCACCATCAAAAAAAA
* * *
43667010 TTACTTTTTTCGTATACTGATACATGATATTGACATGAAAAAAAT-AAAAAAAATTCCCACAAAA
1 TTACTTTTTTCATATACTCATACATGATATTGACACGAAAAAAATAAAAAAAAATTCCCACAAAA
* *****
43667074 AAGTTGGTGCCAGCCATTGGCAGGCCACCATCAAATTTTTTTT
66 AAGGTGGTGCCAGCCATTGGCAGGCCACCATCAAA---AAAAA
* * * ** *
43667117 TTCACTTTTTTCATATACTGATACCTGCTATAAACACGAAAAAAGTGAAAAAAAAATTTCCC-CA
1 TT-ACTTTTTTCATATACTCATACATGATATTGACACGAAAAAAAT-AAAAAAAAA-TTCCCACA
* * * * *
43667181 AAAAAGGTGGTGCCGGTCATTGACAGGTCACCACCAAA
63 AAAAAGGTGGTGCCAGCCATTGGCAGGCCACCATCAAA
43667219 TTTTTTTTCT
Statistics
Matches: 172, Mismatches: 29, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
103 44 0.26
104 43 0.25
107 2 0.01
108 36 0.21
110 42 0.24
111 5 0.03
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.27
Consensus pattern (105 bp):
TTACTTTTTTCATATACTCATACATGATATTGACACGAAAAAAATAAAAAAAAATTCCCACAAAA
AAGGTGGTGCCAGCCATTGGCAGGCCACCATCAAAAAAAA
Found at i:43667213 original size:110 final size:107
Alignment explanation
Indices: 43666871--43667226 Score: 418
Period size: 110 Copynumber: 3.3 Consensus size: 107
43666861 GGGTGTTACA
* * *
43666871 GTGCCGGCCATTGGCATGCCACCACCAA-TTTTTTTTTACTTTTTTCATATACTCATACCTGCTA
1 GTGCCGGCCATTGGCAGGCCACCACAAATTTTTTTTTTACTTTTTTCATATACTGATACCTGCTA
**
43666935 TTGACACGAAAAAAGTAAAAAAAAATTTCGACAAAAAAGGTG
66 TTGACACGAAAAAAGTAAAAAAAAATTTCCCCAAAAAAGGTG
* ***** * * *
43666977 GTGCCGGCCATTGGTAGGCCACCACAAA---AAAAATTACTTTTTTCGTATACTGATACATGATA
1 GTGCCGGCCATTGGCAGGCCACCACAAATTTTTTTTTTACTTTTTTCATATACTGATACCTGCTA
* * *
43667039 TTGACATGAAAAAAAT-AAAAAAAA-TTCCCACAAAAAAGTTG
66 TTGACACGAAAAAAGTAAAAAAAAATTTCCC-CAAAAAAGGTG
*
43667080 GTGCCAGCCATTGGCAGGCCACCATCAAATTTTTTTTTTCACTTTTTTCATATACTGATACCTGC
1 GTGCCGGCCATTGGCAGGCCACCA-CAAATTTTTTTTTT-ACTTTTTTCATATACTGATACCTGC
**
43667145 TATAAACACGAAAAAAGTGAAAAAAAAATTTCCCCAAAAAAGGTG
64 TATTGACACGAAAAAAGT-AAAAAAAAATTTCCCCAAAAAAGGTG
* * *
43667190 GTGCCGGTCATTGACAGGTCACCACCAAATTTTTTTT
1 GTGCCGGCCATTGGCAGGCCACCA-CAAATTTTTTTT
43667227 CTTTTTTTCG
Statistics
Matches: 204, Mismatches: 37, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
102 3 0.01
103 40 0.20
104 43 0.21
106 25 0.12
107 2 0.01
108 36 0.18
110 50 0.25
111 5 0.02
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (107 bp):
GTGCCGGCCATTGGCAGGCCACCACAAATTTTTTTTTTACTTTTTTCATATACTGATACCTGCTA
TTGACACGAAAAAAGTAAAAAAAAATTTCCCCAAAAAAGGTG
Found at i:43668525 original size:110 final size:108
Alignment explanation
Indices: 43668386--43669354 Score: 795
Period size: 109 Copynumber: 8.6 Consensus size: 108
43668376 AATTTATTTT
** *
43668386 TTTTGGTGGTGGCCTGCCAATGGTTGGCACAACCTTTTTTGTAGGAA-TTTTTTTTTACTTTTTT
1 TTTTGGTGGTGG-CTGCCAATGGCCGGCACCACCTTTTTTGT-GGAATTTTTTTTTTACTTTTTT
* * *
43668450 AGTGTCAAAAAAAGGTATCAGTATACGAAAAAAGTAAAAAAAAAAA
64 CGTGTCAAAAGAAGGTATTAGTATACGAAAAAAGT-AAAAAAAAAA
*
43668496 TTTTGGTTGTGGCTAGCCAATGGCCGGCACCACCTTTTTTGTGGCAAAATTTTTTTTTGATTACT
1 TTTTGGTGGTGGCT-GCCAATGGCCGGCACCACCTTTTTTGTGG---AA-TTTTTTTT--TTACT
* *
43668561 TTTTTCGTGTCAATAGCAGGTATTAGTATACGGAAAAAA-TAAAAAAAAAATA
59 TTTTTCGTGTCAAAAGAAGGTATTAGTATAC-GAAAAAAGT-AAAAAAAAA-A
* ** *
43668613 TTTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGTGGAAAATTTTTTTGAAATTTTTT
1 TTTTGGTGGTGG-CTGCCAATGGCCGGCACCACCTTTTTTGTGG-AATTTTTTTTTTACTTTTTT
* * * * *
43668678 TGTGGCAATAGCAGTTATTAGTATACGAAAAAAGTAAAAAAAAATA
64 CGTGTCAAAAGAAGGTATTAGTATACGAAAAAAGTAAAAAAAAA-A
* *
43668724 TTTTGGTGGTGGCCTGCCAATGGCCGACACCACCTTTTTTATGAGAA-TTTTTTTTTACTTTTTT
1 TTTTGGTGGTGG-CTGCCAATGGCCGGCACCACCTTTTTTGTG-GAATTTTTTTTTTACTTTTTT
* *
43668788 TGTGTCAATAGCAA-GTATTAGTATACGAAAAAAGT-AAAAAAAAA
64 CGTGTCAAAAG-AAGGTATTAGTATACGAAAAAAGTAAAAAAAAAA
* * ** ** ** * *
43668832 -TTTGGTGGTAGCCTACCAAAAATTTATTTTGGTGGTGGC-CTGCC--AATGGCCGGCAACATCT
1 TTTTGGTGGT-GGCTGCC----A---A---T-G-GCCGGCACCACCTTTTTTG-TGG--A-AT-T
* *
43668893 TTTTTGTGAGAATTTTTTTTTACTTTTTTAGTGTCAAAAGAAGGTATCAGTATACGAAAAAAGT-
48 TTT-------------TTTTTACTTTTTTCGTGTCAAAAGAAGGTATTAGTATACGAAAAAAGTA
43668957 AAAAAAAAA
100 AAAAAAAAA
* * * * *
43668966 TTGTTGGT-G-GCCTGGCAATGGCCGGTACCACCTTTTTTGTGGGATTTTTTTTTTACTTTTTTT
1 TT-TTGGTGGTGGCTGCCAATGGCCGGCACCACCTTTTTTGTGGAATTTTTTTTTTACTTTTTTC
* *
43669029 GTGTCAATAA-CAGTTATTAGTATACGAAAAAAGTAAAAAAAAAATTA
65 GTGTCAA-AAGAAGGTATTAGTATACGAAAAAAGT-AAAAAAAAA--A
*
43669076 TTTTGGTGGTGGCTTGCCAATTGCCGGCACCACCTTTTTTGTGAGAATTTTTTTTTTACTTTTTT
1 TTTTGGTGGTGGC-TGCCAATGGCCGGCACCACCTTTTTTGTG-GAATTTTTTTTTTACTTTTTT
* *
43669141 CGTGTCAATAGCAGGTATTAGTA-ACTGAAAAAAGTAAAAAAAAAA
64 CGTGTCAAAAGAAGGTATTAGTATAC-GAAAAAAGTAAAAAAAAAA
* *
43669186 -TTTGGTGGTGGCCTACCAATGGCCGGCACCACCTTTTTTGTGGGAATTTTTTTTTTACATTTTT
1 TTTTGGTGGTGG-CTGCCAATGGCCGGCACCACCTTTTTTGT-GGAATTTTTTTTTTACTTTTTT
* *
43669250 CGTGTCAATAGCAA-GTATCAGTATACGAAAAAAGTAAAAAAAAAA
64 CGTGTCAAAAG-AAGGTATTAGTATACGAAAAAAGTAAAAAAAAAA
* *
43669295 -TTT-GTGGTGGCCTGCCAATAGCCGGCACAACCTTTTTTGTAGGAATTTTTTTTTTACTTT
1 TTTTGGTGGTGG-CTGCCAATGGCCGGCACCACCTTTTTTGT-GGAATTTTTTTTTTACTTT
43669355 GACATGAAAA
Statistics
Matches: 718, Mismatches: 74, Indels: 136
0.77 0.08 0.15
Matches are distributed among these distances:
106 41 0.06
107 15 0.02
108 62 0.09
109 115 0.16
110 89 0.12
111 65 0.09
112 72 0.10
113 47 0.07
114 15 0.02
115 3 0.00
116 44 0.06
117 50 0.07
118 7 0.01
119 8 0.01
120 2 0.00
121 7 0.01
122 4 0.01
123 3 0.00
124 2 0.00
126 1 0.00
129 1 0.00
133 7 0.01
134 51 0.07
135 2 0.00
136 5 0.01
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.37
Consensus pattern (108 bp):
TTTTGGTGGTGGCTGCCAATGGCCGGCACCACCTTTTTTGTGGAATTTTTTTTTTACTTTTTTCG
TGTCAAAAGAAGGTATTAGTATACGAAAAAAGTAAAAAAAAAA
Found at i:43668895 original size:134 final size:134
Alignment explanation
Indices: 43668722--43668967 Score: 413
Period size: 134 Copynumber: 1.8 Consensus size: 134
43668712 TAAAAAAAAA
*
43668722 TATTTTGGTGGTGGCCTGCCAATGGCCGACACCACCTTTTTTATGAGAATTTTTTTTTACTTTTT
1 TATTTTGGTGGTGGCCTGCCAATGGCCGACAACACCTTTTTTATGAGAATTTTTTTTTACTTTTT
* * *
43668787 TTGTGTCAATAGCAA-GTATTAGTATACGAAAAAAGTAAAAAAAAATTTGGTGGTAGCCTACCAA
66 TAGTGTCAAAAG-AAGGTATCAGTATACGAAAAAAGTAAAAAAAAATTTGGTGGTAGCCTACCAA
43668851 AAATT
130 AAATT
* * *
43668856 TATTTTGGTGGTGGCCTGCCAATGGCCGGCAACATCTTTTTTGTGAGAATTTTTTTTTACTTTTT
1 TATTTTGGTGGTGGCCTGCCAATGGCCGACAACACCTTTTTTATGAGAATTTTTTTTTACTTTTT
43668921 TAGTGTCAAAAGAAGGTATCAGTATACGAAAAAAGTAAAAAAAAATT
66 TAGTGTCAAAAGAAGGTATCAGTATACGAAAAAAGTAAAAAAAAATT
43668968 GTTGGTGGCC
Statistics
Matches: 104, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
133 2 0.02
134 102 0.98
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.37
Consensus pattern (134 bp):
TATTTTGGTGGTGGCCTGCCAATGGCCGACAACACCTTTTTTATGAGAATTTTTTTTTACTTTTT
TAGTGTCAAAAGAAGGTATCAGTATACGAAAAAAGTAAAAAAAAATTTGGTGGTAGCCTACCAAA
AATT
Found at i:43669049 original size:240 final size:244
Alignment explanation
Indices: 43668611--43669071 Score: 689
Period size: 240 Copynumber: 1.9 Consensus size: 244
43668601 AAAAAAAAAA
*
43668611 TATTTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGTGGAAAATTTTTTTGAAATTTT
1 TATTTTGGTGGTGGCCTGCCAATGGCCGGCAACACCTTTTTTGTGGAAAATTTTTTTGAAATTTT
* * * * *
43668676 TTTGTGGCAATAGCAGTTATTAGTATACGAAAAAAGTAAAAAAAAATATTTTGGTGGTGGCCTGC
66 TTAGTGGCAAAAGAAGGTATCAGTATACGAAAAAAGTAAAAAAAAATA-TTTGGTGGTGGCCTGC
*
43668741 CAATGGCCGACACCACCTTTTTTATGAGAATTTTTTTTTACTTTTTTTGTGTCAATAGCAAGTAT
130 CAATGGCCGACACCACCTTTTTTATGAGAATTTTTTTTTACTTTTTTTGTGTCAATAACAAGTAT
43668806 TAGTATACGAAAAAAGTAAAAAAAAATTTGGTGGTAGCCTACCAAAAATT
195 TAGTATACGAAAAAAGTAAAAAAAAATTTGGTGGTAGCCTACCAAAAATT
* * ** *
43668856 TATTTTGGTGGTGGCCTGCCAATGGCCGGCAACATCTTTTTTGT-GAGAATTTTTTTTTACTTTT
1 TATTTTGGTGGTGGCCTGCCAATGGCCGGCAACACCTTTTTTGTGGAAAATTTTTTTGAAATTTT
* * *
43668920 TTAGTGTCAAAAGAAGGTATCAGTATACGAAAAAAGT-AAAAAAAA-A-TTGTTGGTGGCCTGGC
66 TTAGTGGCAAAAGAAGGTATCAGTATACGAAAAAAGTAAAAAAAAATATTTGGTGGTGGCCTGCC
** * * *
43668982 AATGGCCGGTACCACCTTTTTTGTGGGATTTTTTTTTTACTTTTTTTGTGTCAATAAC-AGTTAT
131 AATGGCCGACACCACCTTTTTTATGAGAATTTTTTTTTACTTTTTTTGTGTCAATAACAAG-TAT
43669046 TAGTATACGAAAAAAGTAAAAAAAAA
195 TAGTATACGAAAAAAGTAAAAAAAAA
43669072 ATTATTTTGG
Statistics
Matches: 195, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
239 2 0.01
240 95 0.49
242 1 0.01
243 8 0.04
244 47 0.24
245 42 0.22
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.37
Consensus pattern (244 bp):
TATTTTGGTGGTGGCCTGCCAATGGCCGGCAACACCTTTTTTGTGGAAAATTTTTTTGAAATTTT
TTAGTGGCAAAAGAAGGTATCAGTATACGAAAAAAGTAAAAAAAAATATTTGGTGGTGGCCTGCC
AATGGCCGACACCACCTTTTTTATGAGAATTTTTTTTTACTTTTTTTGTGTCAATAACAAGTATT
AGTATACGAAAAAAGTAAAAAAAAATTTGGTGGTAGCCTACCAAAAATT
Found at i:43669389 original size:108 final size:109
Alignment explanation
Indices: 43669168--43669389 Score: 252
Period size: 108 Copynumber: 2.0 Consensus size: 109
43669158 TTAGTAACTG
* * *
43669168 AAAAAAGTAAAAAAAAAATTTGGTGGTGGCCTACCAATGGCCGGCACCACCTTTTTTGTGGGAAT
1 AAAAAAGTAAAAAAAAAATTTGGTGGTGGCCTACCAATAGCCGGCACAACCTTTTTTGTAGGAAT
** * ** * * ** ** * *
43669233 TTTTTTTTTACATTTTTCGTGTCAATAGCAAGTATCAGTATACG
66 TTTTTTTTTACATTTGACATGAAAAAAGAAAAAAAAAATATACA
*
43669277 AAAAAAGTAAAAAAAAAATTT-GTGGTGGCCTGCCAATAGCCGGCACAACCTTTTTTGTAGGAAT
1 AAAAAAGTAAAAAAAAAATTTGGTGGTGGCCTACCAATAGCCGGCACAACCTTTTTTGTAGGAAT
43669341 TTTTTTTTTAC-TTTGACATGAAAAAAGTAAAAAAAAAAT-TCACA
66 TTTTTTTTTACATTTGACATGAAAAAAG-AAAAAAAAAATAT-ACA
43669385 AAAAA
1 AAAAA
43669390 GGTGGTGTCG
Statistics
Matches: 94, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
107 11 0.12
108 62 0.66
109 21 0.22
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (109 bp):
AAAAAAGTAAAAAAAAAATTTGGTGGTGGCCTACCAATAGCCGGCACAACCTTTTTTGTAGGAAT
TTTTTTTTTACATTTGACATGAAAAAAGAAAAAAAAAATATACA
Found at i:43671642 original size:47 final size:46
Alignment explanation
Indices: 43671586--43671676 Score: 146
Period size: 47 Copynumber: 2.0 Consensus size: 46
43671576 GGGTGCAGGC
* * *
43671586 CTGTGAATGGCCGGCACCCAGTACATTAAAAAATTTCGAGTTTTATT
1 CTGTCAATGGCCGGCACCCAATACAGT-AAAAATTTCGAGTTTTATT
43671633 CTGTCAATGGCCGGCACCCAATACAGTAAAAATTTCGAGTTTTA
1 CTGTCAATGGCCGGCACCCAATACAGTAAAAATTTCGAGTTTTA
43671677 CTGTACTGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 17 0.41
47 24 0.59
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.30
Consensus pattern (46 bp):
CTGTCAATGGCCGGCACCCAATACAGTAAAAATTTCGAGTTTTATT
Found at i:43672519 original size:2 final size:2
Alignment explanation
Indices: 43672512--43672539 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43672502 AAACCCAGAG
43672512 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
43672540 CTCGTATGTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:43674775 original size:24 final size:24
Alignment explanation
Indices: 43674739--43674787 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
43674729 ACCGTCATGG
43674739 ACACCGGCAACAACTCCTGGTGTA
1 ACACCGGCAACAACTCCTGGTGTA
*
43674763 ACACCGGCTACAACTCCTGGTGTA
1 ACACCGGCAACAACTCCTGGTGTA
43674787 A
1 A
43674788 GAAGCTATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.33, G:0.20, T:0.18
Consensus pattern (24 bp):
ACACCGGCAACAACTCCTGGTGTA
Found at i:43676111 original size:3 final size:3
Alignment explanation
Indices: 43676103--43676133 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
43676093 ATTAATTTGC
43676103 ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
43676134 GATACCTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:43681037 original size:6 final size:6
Alignment explanation
Indices: 43681026--43681052 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
43681016 CCATCGATTC
43681026 GAGTGA GAGTGA GAGTGA GAGTGA GAG
1 GAGTGA GAGTGA GAGTGA GAGTGA GAG
43681053 AATCGAGGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.52, T:0.15
Consensus pattern (6 bp):
GAGTGA
Found at i:43681870 original size:56 final size:60
Alignment explanation
Indices: 43681793--43681905 Score: 155
Period size: 57 Copynumber: 1.9 Consensus size: 60
43681783 AAAGAAGAAA
* *
43681793 AAATTATTTTTTTAGGTGCTGG-CTGTCAATGGCCGGCACCCAGTAC-G-AAAAAAAGGG
1 AAATTATTTTTTTAGGTGCTGGCCTGTAAATGGCCGGCACCCAATACAGTAAAAAAAGGG
*
43681850 AAATT-TTTTTTT-GTGTGCTGGCCTGTAAATGGTCGGCACCCAATACAGTAAAAAAA
1 AAATTATTTTTTTAG-GTGCTGGCCTGTAAATGGCCGGCACCCAATACAGTAAAAAAA
43681906 ATTCGAGTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
55 1 0.02
56 14 0.29
57 26 0.53
58 1 0.02
59 7 0.14
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (60 bp):
AAATTATTTTTTTAGGTGCTGGCCTGTAAATGGCCGGCACCCAATACAGTAAAAAAAGGG
Found at i:43682259 original size:111 final size:112
Alignment explanation
Indices: 43682123--43682334 Score: 300
Period size: 111 Copynumber: 1.9 Consensus size: 112
43682113 CCACCACCAA
* ** * *
43682123 ATTTTTTTTGTACTTTTTTTGTATACTGATACTTGATACTGACACAAAAAAAAGT-AAAATTTTT
1 ATTTTTTTTGTACCTTTTTCATATACTGATACCTGATACTGACACAAAAAAAAGTAAAAATTTGT
*
43682187 TTACTGTATTAGGTGCCGACCATTGACAGGCCAGAACCCAAAAAAAG
66 TTACTGTACTAGGTGCCGACCATTGACAGGCCAGAACCCAAAAAAAG
* *
43682234 ATTTTTTTTTTACCTTTTTCATATACTGATACCTGATACTGACACGAAAAAAAGTAAAAAAAATT
1 ATTTTTTTTGTACCTTTTTCATATACTGATACCTGATACTGACACAAAAAAAAGT---AAAAATT
* *
43682299 TGTTTACTGTACTGGGTGCCGGCCATTGACAGGCCA
63 TGTTTACTGTACTAGGTGCCGACCATTGACAGGCCA
43682335 ACACTCAAAT
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
111 49 0.56
115 38 0.44
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (112 bp):
ATTTTTTTTGTACCTTTTTCATATACTGATACCTGATACTGACACAAAAAAAAGTAAAAATTTGT
TTACTGTACTAGGTGCCGACCATTGACAGGCCAGAACCCAAAAAAAG
Found at i:43683757 original size:109 final size:108
Alignment explanation
Indices: 43683355--43683770 Score: 561
Period size: 110 Copynumber: 3.8 Consensus size: 108
43683345 GACACCAGAG
** * *
43683355 TACGAAAAAAAGTAAAAAAAAA-AATTTTGGGTGTTGGCCTGTCAATGGCCGGCACCCAGTATAG
1 TACG-AAAAAAGTAAAAAAAAATTTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAG
43683419 TAA-TTTTTTTTACTTTTTTTCGTGTT-AGTATCAGGTATCAGTA
65 TAATTTTTTTTTACTTTTTTTCGT-TTCAGTATCAGGTATCAGTA
* * *
43683462 TACGAAAAAAGTAAAAAAAAAAATTTTTTGGGTGCTGACCTGTCAATGGCCGGCTCCCAGTACAG
1 TACGAAAAAAGT-AAAAAAAAATTTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAG
* ** * *
43683527 TGATTTTTTTTTACTTTTTTTTATTGTCAGTATCAGGTATCAATG
65 TAATTTTTTTTTACTTTTTTTCGTT-TCAGTATCAGGTATCAGTA
* * * *
43683572 TACGAAAAAAGTAAAAAAAATATTTTTTTGGATGCTTGCCTGTCAATGGCCAGCACACAGTACAG
1 TACGAAAAAAGTAAAAAAAA-ATTTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAG
43683637 TAAATTTTTTTTTTAC-TTTTTTCGTTTCAGTATCAGGTATCAGTA
65 T-AA-TTTTTTTTTACTTTTTTTCGTTTCAGTATCAGGTATCAGTA
* *
43683682 TACGAAAAAAGTAAAAAAAAATTTTTTTGAGTGCTGGCTTGTCAATGGCCGGCACCCAGTACAGT
1 TACGAAAAAAGTAAAAAAAAATTTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAG-
*
43683747 TAATTTTTTTTTCCTTTTTTTCGT
65 TAATTTTTTTTTACTTTTTTTCGT
43683771 ACTGGGTGCC
Statistics
Matches: 269, Mismatches: 30, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
106 8 0.03
107 13 0.05
108 49 0.18
109 76 0.28
110 103 0.38
111 9 0.03
112 11 0.04
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.38
Consensus pattern (108 bp):
TACGAAAAAAGTAAAAAAAAATTTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAGT
AATTTTTTTTTACTTTTTTTCGTTTCAGTATCAGGTATCAGTA
Found at i:43686397 original size:29 final size:29
Alignment explanation
Indices: 43686355--43686410 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
43686345 TTTCCTTTCG
43686355 CTGTTAAATTTAAATGCACTTACATATCA
1 CTGTTAAATTTAAATGCACTTACATATCA
43686384 CTGTTAAATTTAAATGCACTTACATAT
1 CTGTTAAATTTAAATGCACTTACATAT
43686411 TGCAGGCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (29 bp):
CTGTTAAATTTAAATGCACTTACATATCA
Found at i:43688915 original size:34 final size:33
Alignment explanation
Indices: 43688859--43688924 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 33
43688849 ATCACCTTTA
* * *
43688859 AACCCAACTCCTCACAGCTCACCATCAACCAGC
1 AACCCAAATCCTAACAACTCACCATCAACCAGC
43688892 AACCCATAATCCTAACAACTCACCATCAACCAG
1 AACCCA-AATCCTAACAACTCACCATCAACCAG
43688925 TAATCCCCCT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 6 0.21
34 23 0.79
ACGTcount: A:0.38, C:0.44, G:0.05, T:0.14
Consensus pattern (33 bp):
AACCCAAATCCTAACAACTCACCATCAACCAGC
Found at i:43693117 original size:42 final size:42
Alignment explanation
Indices: 43692962--43693117 Score: 152
Period size: 42 Copynumber: 3.7 Consensus size: 42
43692952 TCTCACGAGC
* * * * *
43692962 TTCTGTT-AACTCATATGAGTTTCTGTTTAACCCTAATGGGT
1 TTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGGT
* * * * *
43693003 TTCCGTTCAGCTCTTTTGAGCTTCAGTTTAACCCTTACGGGT
1 TTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGGT
* ** *
43693045 TTTTGTTCAGCTCTTATGAGCTTCCATTCAACTCTTATGGGT
1 TTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGGT
* * *
43693087 TTCTGTTTAGCACTTATGTGCTTCTGTTCAA
1 TTCTGTTCAGCTCTTATGAGCTTCTGTTCAA
43693118 ACTTCAGGCT
Statistics
Matches: 92, Mismatches: 22, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
41 6 0.07
42 86 0.93
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.44
Consensus pattern (42 bp):
TTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGGT
Found at i:43708284 original size:19 final size:19
Alignment explanation
Indices: 43708260--43708301 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
43708250 TTCATGAATA
43708260 CACAAT-TCATATTTCAATT
1 CACAATCTCAT-TTTCAATT
*
43708279 CACAATCTCATTTTCATTT
1 CACAATCTCATTTTCAATT
43708298 CACA
1 CACA
43708302 TATAATATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.40
Consensus pattern (19 bp):
CACAATCTCATTTTCAATT
Found at i:43708464 original size:40 final size:39
Alignment explanation
Indices: 43708405--43708544 Score: 133
Period size: 40 Copynumber: 3.6 Consensus size: 39
43708395 AACACATCAG
* *
43708405 TTTGGCACCTAGTGCCTCATCGGATAATTCGAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGATAA-TCGAAGTAATAA
* * * *
43708445 TTTGACACCCAGTGTCTCATCGGCTAAACCAAAGT-A-AA
1 TTTGACACCCAGTGCCTCATCGGAT-AATCGAAGTAATAA
* *
43708483 -TTGGCACCCAGTGCCTCATCGAATTAATCTGAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGA-TAATC-GAAGTAATAA
* *
43708523 TTTGACACCCAATGTCTCATCG
1 TTTGACACCCAGTGCCTCATCG
43708545 ACTCGAAGTC
Statistics
Matches: 79, Mismatches: 15, Indels: 11
0.75 0.14 0.10
Matches are distributed among these distances:
37 22 0.28
38 7 0.09
39 2 0.03
40 28 0.35
41 20 0.25
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (39 bp):
TTTGACACCCAGTGCCTCATCGGATAATCGAAGTAATAA
Found at i:43708542 original size:41 final size:41
Alignment explanation
Indices: 43708434--43708545 Score: 124
Period size: 37 Copynumber: 2.8 Consensus size: 41
43708424 TCGGATAATT
*
43708434 CGAAGTAATAATTTGACACCCAGTGTCTCATCG-GCTAAAC
1 CGAAGTAATAATTTGACACCCAGTGTCTCATCGAACTAAAC
* * * * *
43708474 CAAAGT-A-AA-TTGGCACCCAGTGCCTCATCGAATTAATC
1 CGAAGTAATAATTTGACACCCAGTGTCTCATCGAACTAAAC
* *
43708512 TGAAGTAATAATTTGACACCCAATGTCTCATCGA
1 CGAAGTAATAATTTGACACCCAGTGTCTCATCGA
43708546 CTCGAAGTCA
Statistics
Matches: 57, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
37 19 0.33
38 10 0.18
39 2 0.04
40 7 0.12
41 19 0.33
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (41 bp):
CGAAGTAATAATTTGACACCCAGTGTCTCATCGAACTAAAC
Found at i:43709450 original size:20 final size:20
Alignment explanation
Indices: 43709425--43709464 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
43709415 AAGGCCGTGG
43709425 CTTTCTCCTTCCTTTCTTTC
1 CTTTCTCCTTCCTTTCTTTC
* *
43709445 CTTTCTCTTTTCTTTCTTTC
1 CTTTCTCCTTCCTTTCTTTC
43709465 TTTTTATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (20 bp):
CTTTCTCCTTCCTTTCTTTC
Found at i:43709454 original size:15 final size:15
Alignment explanation
Indices: 43709437--43709469 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
43709427 TTCTCCTTCC
43709437 TTTCTTTCCTTTCTCT
1 TTTCTTT-CTTTCTCT
43709453 TTTCTTTCTTTCT-T
1 TTTCTTTCTTTCTCT
43709467 TTT
1 TTT
43709470 ATTTATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 6 0.35
16 7 0.41
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTCTTTCTTTCTCT
Found at i:43709484 original size:5 final size:5
Alignment explanation
Indices: 43709474--43709507 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
43709464 CTTTTTATTT
43709474 ATATA ATATA ATATA ATATA ATATA ATAT- ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA
43709508 CTTAATACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:43710381 original size:16 final size:16
Alignment explanation
Indices: 43710360--43710390 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43710350 AGTAAAAATA
*
43710360 ATATAATATTTATAAT
1 ATATAACATTTATAAT
43710376 ATATAACATTTATAA
1 ATATAACATTTATAA
43710391 ATAAGACTTT
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATAACATTTATAAT
Found at i:43722321 original size:100 final size:100
Alignment explanation
Indices: 43722194--43722393 Score: 400
Period size: 100 Copynumber: 2.0 Consensus size: 100
43722184 CATAAATTGT
43722194 TGAGATCCAATTAAAGGATGAAAAAAATATGAAATTAAATATTATTGAGTATAGTTTATTATAGA
1 TGAGATCCAATTAAAGGATGAAAAAAATATGAAATTAAATATTATTGAGTATAGTTTATTATAGA
43722259 AGAAACTGTGTAAGTAATGGAATTGTAAACCATGA
66 AGAAACTGTGTAAGTAATGGAATTGTAAACCATGA
43722294 TGAGATCCAATTAAAGGATGAAAAAAATATGAAATTAAATATTATTGAGTATAGTTTATTATAGA
1 TGAGATCCAATTAAAGGATGAAAAAAATATGAAATTAAATATTATTGAGTATAGTTTATTATAGA
43722359 AGAAACTGTGTAAGTAATGGAATTGTAAACCATGA
66 AGAAACTGTGTAAGTAATGGAATTGTAAACCATGA
43722394 GATATAATAA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (100 bp):
TGAGATCCAATTAAAGGATGAAAAAAATATGAAATTAAATATTATTGAGTATAGTTTATTATAGA
AGAAACTGTGTAAGTAATGGAATTGTAAACCATGA
Found at i:43725128 original size:74 final size:74
Alignment explanation
Indices: 43725039--43725208 Score: 340
Period size: 74 Copynumber: 2.3 Consensus size: 74
43725029 TTTATATTAA
43725039 TGTTTTGTGAGTTTTTAGTAATATAAAATTATTTTGTTAAATATTTTTAGTAAATAATTTATTAT
1 TGTTTTGTGAGTTTTTAGTAATATAAAATTATTTTGTTAAATATTTTTAGTAAATAATTTATTAT
43725104 AAATTGTTG
66 AAATTGTTG
43725113 TGTTTTGTGAGTTTTTAGTAATATAAAATTATTTTGTTAAATATTTTTAGTAAATAATTTATTAT
1 TGTTTTGTGAGTTTTTAGTAATATAAAATTATTTTGTTAAATATTTTTAGTAAATAATTTATTAT
43725178 AAATTGTTG
66 AAATTGTTG
43725187 TGTTTTGTGAGTTTTTAGTAAT
1 TGTTTTGTGAGTTTTTAGTAAT
43725209 GTAATTTAAA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 96 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (74 bp):
TGTTTTGTGAGTTTTTAGTAATATAAAATTATTTTGTTAAATATTTTTAGTAAATAATTTATTAT
AAATTGTTG
Found at i:43725144 original size:41 final size:41
Alignment explanation
Indices: 43725082--43725207 Score: 126
Period size: 42 Copynumber: 3.2 Consensus size: 41
43725072 TTGTTAAATA
43725082 TTTTTAGTAAATAATTTATTATAAATTGTTGTGTTTTGTGAG
1 TTTTTAGTAAATAA-TTATTATAAATTGTTGTGTTTTGTGAG
* * ***
43725124 TTTTTAG----TAA-TA-TA-AAATTATTTTGTTAAAT-A-
1 TTTTTAGTAAATAATTATTATAAATTGTTGTGTTTTGTGAG
43725156 TTTTTAGTAAATAATTTATTATAAATTGTTGTGTTTTGTGAG
1 TTTTTAGTAAATAA-TTATTATAAATTGTTGTGTTTTGTGAG
43725198 TTTTTAGTAA
1 TTTTTAGTAA
43725208 TGTAATTTAA
Statistics
Matches: 64, Mismatches: 10, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
32 7 0.11
33 1 0.02
34 12 0.19
35 2 0.03
36 5 0.08
38 5 0.08
39 2 0.03
40 12 0.19
41 1 0.02
42 17 0.27
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (41 bp):
TTTTTAGTAAATAATTATTATAAATTGTTGTGTTTTGTGAG
Found at i:43725345 original size:27 final size:27
Alignment explanation
Indices: 43725307--43725390 Score: 123
Period size: 27 Copynumber: 3.1 Consensus size: 27
43725297 ATTTTGGTCA
* *
43725307 ACCAGTCGCGCCTGTCAGATAGGCTTC
1 ACCAGTCGCGCCTATCAGATAGGCTCC
*
43725334 ACCAGTTGCGCCTATCAGATAGGCTCC
1 ACCAGTCGCGCCTATCAGATAGGCTCC
* *
43725361 ACCAGTCGCGCCTACCAGATAGGCGCC
1 ACCAGTCGCGCCTATCAGATAGGCTCC
43725388 ACC
1 ACC
43725391 TACCTCATAC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.21, C:0.37, G:0.24, T:0.18
Consensus pattern (27 bp):
ACCAGTCGCGCCTATCAGATAGGCTCC
Found at i:43727423 original size:40 final size:40
Alignment explanation
Indices: 43727368--43727448 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
43727358 TATACAAGAA
43727368 GTTTCCAGTAATGCCTATAACTATGGGTAAATGTAGAGTT
1 GTTTCCAGTAATGCCTATAACTATGGGTAAATGTAGAGTT
43727408 GTTTCCAGTAATGCCTATAACTATGGGTAAATGTAGAGTT
1 GTTTCCAGTAATGCCTATAACTATGGGTAAATGTAGAGTT
43727448 G
1 G
43727449 CCTAAGTCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (40 bp):
GTTTCCAGTAATGCCTATAACTATGGGTAAATGTAGAGTT
Found at i:43729500 original size:22 final size:24
Alignment explanation
Indices: 43729448--43729502 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
43729438 TTATAAAAAA
*
43729448 TTATAAAATTTTTTTATAAAGTGTC
1 TTAT-AAATTTTTTTATAAACTGTC
* *
43729473 TAATAAATTTTTTTA-ACACT-TC
1 TTATAAATTTTTTTATAAACTGTC
43729495 TTATAAAT
1 TTATAAAT
43729503 AATTTACCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 9 0.35
23 3 0.12
24 11 0.42
25 3 0.12
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (24 bp):
TTATAAATTTTTTTATAAACTGTC
Found at i:43731728 original size:57 final size:57
Alignment explanation
Indices: 43731643--43731752 Score: 220
Period size: 57 Copynumber: 1.9 Consensus size: 57
43731633 TTCTCCCAAA
43731643 AAAATAATAAAATAATAAATACATGTATCATTCAAAATGGAAGTAGGTAATTGGAAT
1 AAAATAATAAAATAATAAATACATGTATCATTCAAAATGGAAGTAGGTAATTGGAAT
43731700 AAAATAATAAAATAATAAATACATGTATCATTCAAAATGGAAGTAGGTAATTG
1 AAAATAATAAAATAATAAATACATGTATCATTCAAAATGGAAGTAGGTAATTG
43731753 AGTGGAACAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (57 bp):
AAAATAATAAAATAATAAATACATGTATCATTCAAAATGGAAGTAGGTAATTGGAAT
Found at i:43732152 original size:19 final size:17
Alignment explanation
Indices: 43732115--43732148 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
43732105 CAAAAAGGTA
*
43732115 AAAGTAAAGAAAATTTC
1 AAAGTAAAAAAAATTTC
43732132 AAAGTAAAAAATAATTT
1 AAAGTAAAAAA-AATTT
43732149 TCAAGAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.26
Consensus pattern (17 bp):
AAAGTAAAAAAAATTTC
Found at i:43732479 original size:19 final size:17
Alignment explanation
Indices: 43732442--43732475 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
43732432 CAAAAAGGTA
*
43732442 AAAGTAAAGAAAATTTC
1 AAAGTAAAAAAAATTTC
43732459 AAAGTAAAAAATAATTT
1 AAAGTAAAAAA-AATTT
43732476 TCAAGAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.26
Consensus pattern (17 bp):
AAAGTAAAAAAAATTTC
Found at i:43732550 original size:327 final size:327
Alignment explanation
Indices: 43731956--43732610 Score: 1310
Period size: 327 Copynumber: 2.0 Consensus size: 327
43731946 GAAATTTCTG
43731956 GCATACAAAACTCAACCAATTTTACTGATTTATGTAATTTTACAATCACTCAACTAAATGAAAAT
1 GCATACAAAACTCAACCAATTTTACTGATTTATGTAATTTTACAATCACTCAACTAAATGAAAAT
43732021 TTTTTGTTTAATCATTGAATTAGAGCCTTTGATCACAAGACTAAACTAGAGGTTATTTGAACCCA
66 TTTTTGTTTAATCATTGAATTAGAGCCTTTGATCACAAGACTAAACTAGAGGTTATTTGAACCCA
43732086 ATCCAAAACTTCACCTGTCCAAAAAGGTAAAAGTAAAGAAAATTTCAAAGTAAAAAATAATTTTC
131 ATCCAAAACTTCACCTGTCCAAAAAGGTAAAAGTAAAGAAAATTTCAAAGTAAAAAATAATTTTC
43732151 AAGAAATGGGGCCTTAAGATGTGGACTGCAAAGCTGCGTAGGGGATGGGATAATAAGGCAAATTA
196 AAGAAATGGGGCCTTAAGATGTGGACTGCAAAGCTGCGTAGGGGATGGGATAATAAGGCAAATTA
43732216 GAGAGCAAAAGTTGGAAGCAAGGTTTAATGGTGGTGGCCCCCCTCATTTTGGGCATATGTTTCAG
261 GAGAGCAAAAGTTGGAAGCAAGGTTTAATGGTGGTGGCCCCCCTCATTTTGGGCATATGTTTCAG
43732281 CA
326 CA
43732283 GCATACAAAACTCAACCAATTTTACTGATTTATGTAATTTTACAATCACTCAACTAAATGAAAAT
1 GCATACAAAACTCAACCAATTTTACTGATTTATGTAATTTTACAATCACTCAACTAAATGAAAAT
43732348 TTTTTGTTTAATCATTGAATTAGAGCCTTTGATCACAAGACTAAACTAGAGGTTATTTGAACCCA
66 TTTTTGTTTAATCATTGAATTAGAGCCTTTGATCACAAGACTAAACTAGAGGTTATTTGAACCCA
43732413 ATCCAAAACTTCACCTGTCCAAAAAGGTAAAAGTAAAGAAAATTTCAAAGTAAAAAATAATTTTC
131 ATCCAAAACTTCACCTGTCCAAAAAGGTAAAAGTAAAGAAAATTTCAAAGTAAAAAATAATTTTC
43732478 AAGAAATGGGGCCTTAAGATGTGGACTGCAAAGCTGCGTAGGGGATGGGATAATAAGGCAAATTA
196 AAGAAATGGGGCCTTAAGATGTGGACTGCAAAGCTGCGTAGGGGATGGGATAATAAGGCAAATTA
43732543 GAGAGCAAAAGTTGGAAGCAAGGTTTAATGGTGGTGGCCCCCCTCATTTTGGGCATATGTTTCAG
261 GAGAGCAAAAGTTGGAAGCAAGGTTTAATGGTGGTGGCCCCCCTCATTTTGGGCATATGTTTCAG
43732608 CA
326 CA
43732610 G
1 G
43732611 TTATCCATTT
Statistics
Matches: 328, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
327 328 1.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (327 bp):
GCATACAAAACTCAACCAATTTTACTGATTTATGTAATTTTACAATCACTCAACTAAATGAAAAT
TTTTTGTTTAATCATTGAATTAGAGCCTTTGATCACAAGACTAAACTAGAGGTTATTTGAACCCA
ATCCAAAACTTCACCTGTCCAAAAAGGTAAAAGTAAAGAAAATTTCAAAGTAAAAAATAATTTTC
AAGAAATGGGGCCTTAAGATGTGGACTGCAAAGCTGCGTAGGGGATGGGATAATAAGGCAAATTA
GAGAGCAAAAGTTGGAAGCAAGGTTTAATGGTGGTGGCCCCCCTCATTTTGGGCATATGTTTCAG
CA
Found at i:43736471 original size:15 final size:15
Alignment explanation
Indices: 43736438--43736471 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
43736428 AGACACTGTC
*
43736438 AAAACACAAAAAAAG
1 AAAACACAAAAAAAA
43736453 AAAACACAAAAAAAA
1 AAAACACAAAAAAAA
43736468 AAAA
1 AAAA
43736472 AATCCCCCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (15 bp):
AAAACACAAAAAAAA
Found at i:43736775 original size:1 final size:1
Alignment explanation
Indices: 43736771--43736796 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
43736761 TTTTTCTCTC
43736771 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
43736797 CTATTTTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:43739716 original size:24 final size:23
Alignment explanation
Indices: 43739685--43739729 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
43739675 TACATGTGAA
43739685 AATAATGAAA-TAAATAAATAAAC
1 AATAATGAAATTAAA-AAATAAAC
43739708 AATACATGAAATTAAAAAATAA
1 AATA-ATGAAATTAAAAAATAA
43739730 CTCTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 4 0.20
24 12 0.60
25 4 0.20
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.22
Consensus pattern (23 bp):
AATAATGAAATTAAAAAATAAAC
Found at i:43748030 original size:16 final size:16
Alignment explanation
Indices: 43748009--43748045 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
43747999 TAACTAGCAT
43748009 AATAAAATATTTAAAA
1 AATAAAATATTTAAAA
*
43748025 AAT-AAATATTTTAAA
1 AATAAAATATTTAAAA
43748040 AATAAA
1 AATAAA
43748046 TACATAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAAAATATTTAAAA
Found at i:43748033 original size:15 final size:15
Alignment explanation
Indices: 43748013--43748047 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
43748003 TAGCATAATA
43748013 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
*
43748028 AAATATTTTAAAAAT
1 AAATATTTAAAAAAT
43748043 AAATA
1 AAATA
43748048 CATAGCAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:43751849 original size:20 final size:20
Alignment explanation
Indices: 43751824--43751865 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
43751814 GGCTCTATAT
43751824 AAATAACTTA-AAGTTAATTA
1 AAATAACTTAGAA-TTAATTA
43751844 AAATAACTTAGAATTAATTA
1 AAATAACTTAGAATTAATTA
43751864 AA
1 AA
43751866 TTTTTATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
AAATAACTTAGAATTAATTA
Found at i:43752330 original size:7 final size:7
Alignment explanation
Indices: 43752284--43752386 Score: 52
Period size: 7 Copynumber: 14.9 Consensus size: 7
43752274 CTTGAACCCC
43752284 AAGGTTT
1 AAGGTTT
43752291 -AGGTCTT
1 AAGGT-TT
* *
43752298 GAGATTT
1 AAGGTTT
*
43752305 AAGATTT
1 AAGGTTT
* *
43752312 AGGGTTC
1 AAGGTTT
*
43752319 GAGGTTT
1 AAGGTTT
43752326 AAGGTTT
1 AAGGTTT
*
43752333 -ATGTTT
1 AAGGTTT
43752339 AAGGTTT
1 AAGGTTT
43752346 AAGGATTT
1 AAGG-TTT
*
43752354 -AGAGTTC
1 AAG-GTTT
*
43752361 AGGGTTT
1 AAGGTTT
*
43752368 -ACGTTT
1 AAGGTTT
*
43752374 AAGGTTC
1 AAGGTTT
43752381 AAGGTT
1 AAGGTT
43752387 CGGGGTTACG
Statistics
Matches: 71, Mismatches: 18, Indels: 14
0.69 0.17 0.14
Matches are distributed among these distances:
6 13 0.18
7 50 0.70
8 8 0.11
ACGTcount: A:0.25, C:0.05, G:0.29, T:0.41
Consensus pattern (7 bp):
AAGGTTT
Found at i:43752340 original size:13 final size:13
Alignment explanation
Indices: 43752322--43752346 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43752312 AGGGTTCGAG
43752322 GTTTAAGGTTTAT
1 GTTTAAGGTTTAT
43752335 GTTTAAGGTTTA
1 GTTTAAGGTTTA
43752347 AGGATTTAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (13 bp):
GTTTAAGGTTTAT
Found at i:43752353 original size:42 final size:42
Alignment explanation
Indices: 43752284--43752368 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 42
43752274 CTTGAACCCC
* *
43752284 AAGGTTTAGGTCTTGAGATTTAAGATTTAGGGTTC-GAGGTTT
1 AAGGTTTAGGTCTTAAGATTTAAGATTTAGAGTTCAG-GGTTT
* *
43752326 AAGGTTTATGT-TTAAGGTTTAAGGATTTAGAGTTCAGGGTTT
1 AAGGTTTAGGTCTTAAGATTTAA-GATTTAGAGTTCAGGGTTT
43752368 A
1 A
43752369 CGTTTAAGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
41 9 0.24
42 27 0.73
43 1 0.03
ACGTcount: A:0.26, C:0.04, G:0.29, T:0.41
Consensus pattern (42 bp):
AAGGTTTAGGTCTTAAGATTTAAGATTTAGAGTTCAGGGTTT
Found at i:43757192 original size:36 final size:36
Alignment explanation
Indices: 43757147--43757383 Score: 249
Period size: 36 Copynumber: 6.0 Consensus size: 36
43757137 GGTAGCTTTA
*
43757147 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
43757183 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
43757219 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGTT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAA--G-T
43757258 AGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -G-C-TA--T--ACTTATCTGATCAAGTGAAAAAGTGATAAGT
* * *
43757301 GTTATACTTATCTGATCAAGAGACAAAGTGATAAGTGGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAA---GT
43757340 AGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GC--TA--T--ACTTATCTGATCAAGTGAAAAAGTGATAAGT
43757383 G
1 G
43757384 TGGTAGTGTA
Statistics
Matches: 172, Mismatches: 9, Indels: 34
0.80 0.04 0.16
Matches are distributed among these distances:
36 95 0.55
38 2 0.01
39 3 0.02
40 4 0.02
41 1 0.01
42 6 0.03
43 3 0.02
44 3 0.02
46 55 0.32
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (36 bp):
GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:43757203 original size:21 final size:20
Alignment explanation
Indices: 43757175--43757240 Score: 52
Period size: 21 Copynumber: 3.5 Consensus size: 20
43757165 AGTGAAAAAG
43757175 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
* **
43757195 TGATCAAGTG--A-A--AAAG
1 TGAT-AAGTGCTATACTTATC
43757211 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
43757231 TGATCAAGTG
1 TGAT-AAGTG
43757241 ACAAAGTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 13
0.63 0.12 0.25
Matches are distributed among these distances:
15 5 0.15
16 5 0.15
17 1 0.03
18 2 0.06
19 1 0.03
20 9 0.27
21 10 0.30
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
TGATAAGTGCTATACTTATC
Found at i:43757268 original size:118 final size:118
Alignment explanation
Indices: 43757111--43757337 Score: 382
Period size: 118 Copynumber: 1.9 Consensus size: 118
43757101 TTTGAGTACT
* *
43757111 TCTGATCAAGAGATAAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAATGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
43757176 GATAAGTGCTATACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTATACTTA
66 GATAAGTGCTATACTTATCTGATCAAGAGAAAAAGTGATAAGTGCTATACTTA
* * *
43757229 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAATGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
* *
43757294 GATAAGTGTTATACTTATCTGATCAAGAGACAAAGTGATAAGTG
66 GATAAGTGCTATACTTATCTGATCAAGAGAAAAAGTGATAAGTG
43757338 GTAGCTTTAG
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
118 101 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30
Consensus pattern (118 bp):
TCTGATCAAGAGACAAAATGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTATACTTATCTGATCAAGAGAAAAAGTGATAAGTGCTATACTTA
Found at i:43757384 original size:82 final size:82
Alignment explanation
Indices: 43757183--43757384 Score: 359
Period size: 82 Copynumber: 2.5 Consensus size: 82
43757173 AGTGATAAGT
* * *
43757183 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTATACTTATCTGATCAAGTGACAAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTATACTTATCTGATCAAGAGACAAAGT
*
43757248 GATAAGTGTTAGCCTTA
66 GATAAGTGGTAGCCTTA
43757265 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTATACTTATCTGATCAAGAGACAAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTATACTTATCTGATCAAGAGACAAAGT
*
43757330 GATAAGTGGTAGCTTTA
66 GATAAGTGGTAGCCTTA
43757347 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGT
43757385 GGTAGTGTAT
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 115 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (82 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTATACTTATCTGATCAAGAGACAAAGT
GATAAGTGGTAGCCTTA
Found at i:43773477 original size:35 final size:37
Alignment explanation
Indices: 43773429--43773498 Score: 99
Period size: 35 Copynumber: 1.9 Consensus size: 37
43773419 TCCCCACTAT
* * *
43773429 TTTAAATTCAAAGCTATTATTATAA-ATTT-TTTTGC
1 TTTAAAATAAAAGCTATTACTATAATATTTATTTTGC
43773464 TTTAAAATAAAAGCTATTACTATAATATTTATTTT
1 TTTAAAATAAAAGCTATTACTATAATATTTATTTT
43773499 TAGTAATCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 22 0.73
36 4 0.13
37 4 0.13
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (37 bp):
TTTAAAATAAAAGCTATTACTATAATATTTATTTTGC
Found at i:43774781 original size:39 final size:39
Alignment explanation
Indices: 43774696--43774783 Score: 92
Period size: 39 Copynumber: 2.3 Consensus size: 39
43774686 TAAAAAGATT
* * * *
43774696 AATAAAAAAT-AAAATAACTTGAAAATAATATATTTATT
1 AATAAAAAATAAAAAAAACTTGAAAATAACATATTCATA
*
43774734 AATTAAAAATAAAAAAAAGCTTG-AAATAACAT-TTCATAA
1 AATAAAAAATAAAAAAAA-CTTGAAAATAACATATTCAT-A
43774773 AATAAAAAATA
1 AATAAAAAATA
43774784 CAAATGTGCT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
38 13 0.32
39 24 0.59
40 4 0.10
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (39 bp):
AATAAAAAATAAAAAAAACTTGAAAATAACATATTCATA
Found at i:43777825 original size:42 final size:42
Alignment explanation
Indices: 43777731--43777827 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
43777721 GGCAAAAAAA
* * * *
43777731 CTAGGCAAGCTTTCCGCACAGTTGTCAGGAAAGCTCGTCTAG
1 CTAGGCGAGCTTTCCGCACAATTGTCAAGAAAGCTCGTCCAG
* * *
43777773 CTAGGTGAGCTTTCTGCACAATTGTCAAGAAAGCTTGTCCAG
1 CTAGGCGAGCTTTCCGCACAATTGTCAAGAAAGCTCGTCCAG
*
43777815 -TTGGACGAGCTTT
1 CTAGG-CGAGCTTT
43777828 TACTGATATG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 3 0.07
42 42 0.93
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.28
Consensus pattern (42 bp):
CTAGGCGAGCTTTCCGCACAATTGTCAAGAAAGCTCGTCCAG
Found at i:43787904 original size:17 final size:17
Alignment explanation
Indices: 43787884--43787920 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
43787874 AATTTTTGAA
*
43787884 TTAGTGAATTCTGTGAT
1 TTAGTGAATTCTATGAT
*
43787901 TTAGTGAATTTTATGAT
1 TTAGTGAATTCTATGAT
43787918 TTA
1 TTA
43787921 AAAAGAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.27, C:0.03, G:0.19, T:0.51
Consensus pattern (17 bp):
TTAGTGAATTCTATGAT
Found at i:43789029 original size:46 final size:46
Alignment explanation
Indices: 43788958--43789051 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
43788948 CCATGGAAAA
* *
43788958 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAATCATACTGAG
1 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAG
*
43789004 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGGAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAG
43789050 TT
1 TT
43789052 ATAGCATTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAG
Found at i:43790998 original size:15 final size:16
Alignment explanation
Indices: 43790978--43791016 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
43790968 ATGTTAGAAA
43790978 TGTAAAATTAT-ATTT
1 TGTAAAATTATAATTT
43790993 TGTAAAA-TATAATTT
1 TGTAAAATTATAATTT
43791008 T-T-AAATTAT
1 TGTAAAATTAT
43791017 GCAAATTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.14
14 7 0.32
15 12 0.55
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (16 bp):
TGTAAAATTATAATTT
Found at i:43795019 original size:21 final size:21
Alignment explanation
Indices: 43794995--43795035 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
43794985 TCAAAGAAAA
*
43794995 CAAACACTTGGGGTTGTACAT
1 CAAACACTTGGGGCTGTACAT
43795016 CAAACACTTGGGGCTGTACA
1 CAAACACTTGGGGCTGTACA
43795036 AGGTAAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (21 bp):
CAAACACTTGGGGCTGTACAT
Found at i:43797341 original size:16 final size:17
Alignment explanation
Indices: 43797320--43797352 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
43797310 AATTTTAAAA
*
43797320 AATTCTATTAT-ATATC
1 AATTCTAATATGATATC
43797336 AATTCTAATATGATATC
1 AATTCTAATATGATATC
43797353 CTTAATAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.45
Consensus pattern (17 bp):
AATTCTAATATGATATC
Found at i:43797451 original size:21 final size:21
Alignment explanation
Indices: 43797427--43797482 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
43797417 CACCATTGTT
*
43797427 TCTAATCTCACCGCTACAGTA
1 TCTAATCTCACCGCTACAATA
*
43797448 TCTAATCTCACCGCTATAATA
1 TCTAATCTCACCGCTACAATA
*
43797469 ACTAATCTCACCGC
1 TCTAATCTCACCGC
43797483 CACCGCTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.34, G:0.07, T:0.29
Consensus pattern (21 bp):
TCTAATCTCACCGCTACAATA
Found at i:43801812 original size:1 final size:1
Alignment explanation
Indices: 43801806--43801871 Score: 132
Period size: 1 Copynumber: 66.0 Consensus size: 1
43801796 AAATTTCTAC
43801806 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
43801871 A
1 A
43801872 CCTAAAGCAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:43815514 original size:36 final size:35
Alignment explanation
Indices: 43815448--43815518 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 35
43815438 GCATCCCACA
* *
43815448 AAGACTCAATTACTGGATTCTTTAACTTCCCAAGT
1 AAGACTCAATTACCGGATTCTTTAAATTCCCAAGT
43815483 AAGACTCAACTTACC-GAGTTCTTTAAATTCCCAAGT
1 AAGACTCAA-TTACCGGA-TTCTTTAAATTCCCAAGT
43815519 TTTTTTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
35 11 0.34
36 21 0.66
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.32
Consensus pattern (35 bp):
AAGACTCAATTACCGGATTCTTTAAATTCCCAAGT
Found at i:43821553 original size:82 final size:82
Alignment explanation
Indices: 43821416--43821577 Score: 315
Period size: 82 Copynumber: 2.0 Consensus size: 82
43821406 ATACATTTAA
43821416 AATTATGTCTACAATTATTCATTAATTACCTCGTACTTTAAATCAACTTGATAATTAATAACAAT
1 AATTATGTCTACAATTATTCATTAATTACCTCGTACTTTAAATCAACTTGATAATTAATAACAAT
43821481 AAGCAATATTTCAATCT
66 AAGCAATATTTCAATCT
*
43821498 AATTATGTCTACAATTATTCATTAATTATCTCGTACTTTAAATCAACTTGATAATTAATAACAAT
1 AATTATGTCTACAATTATTCATTAATTACCTCGTACTTTAAATCAACTTGATAATTAATAACAAT
43821563 AAGCAATATTTCAAT
66 AAGCAATATTTCAAT
43821578 ATTTTATTTA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.40
Consensus pattern (82 bp):
AATTATGTCTACAATTATTCATTAATTACCTCGTACTTTAAATCAACTTGATAATTAATAACAAT
AAGCAATATTTCAATCT
Found at i:43821689 original size:97 final size:98
Alignment explanation
Indices: 43821581--43821775 Score: 365
Period size: 98 Copynumber: 2.0 Consensus size: 98
43821571 TTTCAATATT
*
43821581 TTATTTAATTGTATTCATACCTTATTTCACTATCT-AATTTTATTGGATTTTTCAGCAACAACAA
1 TTATTTAATTGTATTCATACCTTATTTCACTATCTAAATTTTATTGGATTTTTCAACAACAACAA
43821645 TTATAATAACTAATTTTATAAAATTGTATTCAA
66 TTATAATAACTAATTTTATAAAATTGTATTCAA
*
43821678 TTATTTAATTGTATTCATACCTTATTTCACTTTCTAAATTTTATTGGATTTTTCAACAACAACAA
1 TTATTTAATTGTATTCATACCTTATTTCACTATCTAAATTTTATTGGATTTTTCAACAACAACAA
43821743 TTATAATAACTAATTTTATAAAATTGTATTCAA
66 TTATAATAACTAATTTTATAAAATTGTATTCAA
43821776 ATTAACTCAT
Statistics
Matches: 95, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
97 34 0.36
98 61 0.64
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (98 bp):
TTATTTAATTGTATTCATACCTTATTTCACTATCTAAATTTTATTGGATTTTTCAACAACAACAA
TTATAATAACTAATTTTATAAAATTGTATTCAA
Found at i:43822448 original size:105 final size:105
Alignment explanation
Indices: 43822266--43822474 Score: 400
Period size: 105 Copynumber: 2.0 Consensus size: 105
43822256 ACTTTTCACA
43822266 TATACTATATCATTCGAGATTAATTTTATCAGTAATTTATTTCATTTGCCCTTATTAACTTGACT
1 TATACTATATCATTCGAGATTAATTTTATCAGTAATTTATTTCATTTGCCCTTATTAACTTGACT
43822331 CGGACTCTGACAGATACGCGGATTCCACCCAAACACACCC
66 CGGACTCTGACAGATACGCGGATTCCACCCAAACACACCC
* *
43822371 TATACTATATCATTCGAGATTAATTTTATTAGTAATTTATTTCATTTGCCCTTCTTAACTTGACT
1 TATACTATATCATTCGAGATTAATTTTATCAGTAATTTATTTCATTTGCCCTTATTAACTTGACT
43822436 CGGACTCTGACAGATACGCGGATTCCACCCAAACACACC
66 CGGACTCTGACAGATACGCGGATTCCACCCAAACACACC
43822475 AGAATATCCA
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 102 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.35
Consensus pattern (105 bp):
TATACTATATCATTCGAGATTAATTTTATCAGTAATTTATTTCATTTGCCCTTATTAACTTGACT
CGGACTCTGACAGATACGCGGATTCCACCCAAACACACCC
Found at i:43828914 original size:25 final size:25
Alignment explanation
Indices: 43828877--43828931 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
43828867 GAACCTTAGC
* * *
43828877 GTGCTTTTTGATTATTAGCACGTTA
1 GTGCTATTCGATTATTAGCACATTA
43828902 GTGCTATTCGATTATTAGCACATTA
1 GTGCTATTCGATTATTAGCACATTA
43828927 GTGCT
1 GTGCT
43828932 CTCCGTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.44
Consensus pattern (25 bp):
GTGCTATTCGATTATTAGCACATTA
Found at i:43828944 original size:22 final size:22
Alignment explanation
Indices: 43828916--43828978 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
43828906 TATTCGATTA
43828916 TTAGCACATTAGTGCTCTCCGT
1 TTAGCACATTAGTGCTCTCCGT
* * *
43828938 TTAGCACATTTGTTCTCTCTGT
1 TTAGCACATTAGTGCTCTCCGT
* *
43828960 ATAGCACTTTAGTGCTCTC
1 TTAGCACATTAGTGCTCTC
43828979 TGATTATTAG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.17, C:0.25, G:0.16, T:0.41
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCCGT
Found at i:43830347 original size:20 final size:21
Alignment explanation
Indices: 43830310--43830349 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
43830300 CATGGTGTGA
*
43830310 TTTTAAAAAATAGTTTAATTT
1 TTTTAAAAAATAGATTAATTT
*
43830331 TTTTTAAAAATA-ATTAATT
1 TTTTAAAAAATAGATTAATT
43830350 GTTAACGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
TTTTAAAAAATAGATTAATTT
Found at i:43831721 original size:18 final size:18
Alignment explanation
Indices: 43831671--43831729 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 18
43831661 ATATACGAAC
*
43831671 TATATATAT-TTAAAACA
1 TATATATATATTAACACA
*
43831688 TTTATA-ATA-T-ACACA
1 TATATATATATTAACACA
43831703 TATATATATATTAACACA
1 TATATATATATTAACACA
43831721 TATATATAT
1 TATATATAT
43831730 GCGTACCTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
15 9 0.26
16 6 0.17
17 6 0.17
18 14 0.40
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.42
Consensus pattern (18 bp):
TATATATATATTAACACA
Found at i:43831723 original size:16 final size:16
Alignment explanation
Indices: 43831671--43831729 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
43831661 ATATACGAAC
*
43831671 TATATATATTTAAAACA
1 TATATATA-TTAACACA
* *
43831688 TTTATA-ATATACACATA
1 TATATATAT-TA-ACACA
43831705 TATATATATTAACACA
1 TATATATATTAACACA
43831721 TATATATAT
1 TATATATAT
43831730 GCGTACCTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
15 1 0.03
16 16 0.47
17 15 0.44
18 2 0.06
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.42
Consensus pattern (16 bp):
TATATATATTAACACA
Found at i:43833435 original size:30 final size:32
Alignment explanation
Indices: 43833370--43833457 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 32
43833360 TAAAAAGATT
* * *
43833370 AAAAT-ATTTTTTTATAATTTTTATTTTCT--
1 AAAATAATTTTTATATATTTTTTATTTTTTAA
43833399 -AAATAA-TTTTA-ATGA-TTTTTATTTTTTAA
1 AAAATAATTTTTATAT-ATTTTTTATTTTTTAA
43833428 AAAATAATTTTTATATATTTTTTATTTTTT
1 AAAATAATTTTTATATATTTTTTATTTTTT
43833458 TAANNNNNNN
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
27 13 0.27
28 9 0.18
29 1 0.02
30 6 0.12
31 6 0.12
32 14 0.29
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (32 bp):
AAAATAATTTTTATATATTTTTTATTTTTTAA
Found at i:43849813 original size:25 final size:24
Alignment explanation
Indices: 43849783--43849888 Score: 106
Period size: 25 Copynumber: 4.3 Consensus size: 24
43849773 ATGTAATCAA
43849783 GAAGCTCTTTCGAGCCATGTAACGG
1 GAAGCTCTTTCGAGCCAT-TAACGG
*
43849808 GAAGCTCATGT-GAGCCATATAACGG
1 GAAGCTC-TTTCGAGCCAT-TAACGG
* *
43849833 GAAGCTCTTGCGAGCCAATTATCGG
1 GAAGCTCTTTCGAGCC-ATTAACGG
* * * *
43849858 GAAGCTCATACGAGCCATAAATGG
1 GAAGCTCTTTCGAGCCATTAACGG
43849882 GAAGCTC
1 GAAGCTC
43849889 AAGAAAGCCA
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
24 13 0.19
25 51 0.75
26 4 0.06
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (24 bp):
GAAGCTCTTTCGAGCCATTAACGG
Found at i:43849859 original size:50 final size:49
Alignment explanation
Indices: 43849783--43849937 Score: 150
Period size: 49 Copynumber: 3.1 Consensus size: 49
43849773 ATGTAATCAA
* * **
43849783 GAAGCTCTTTCGAGCC-ATGTAACGGGAAGCTCATGTGAGCCATATAACGG
1 GAAGCTCTTGCGAGCCAAT-TATCGGGAAGCTCATACGAGCCATA-AACGG
*
43849833 GAAGCTCTTGCGAGCCAATTATCGGGAAGCTCATACGAGCCATAAATGG
1 GAAGCTCTTGCGAGCCAATTATCGGGAAGCTCATACGAGCCATAAACGG
** ** * * * ** *
43849882 GAAGCTCAAGAAAGCCAAATATCGGGAAGCTCAAAAGAGCTGTAATCGG
1 GAAGCTCTTGCGAGCCAATTATCGGGAAGCTCATACGAGCCATAAACGG
43849931 GAAGCTC
1 GAAGCTC
43849938 ATGTAAGCCA
Statistics
Matches: 88, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
49 49 0.56
50 37 0.42
51 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (49 bp):
GAAGCTCTTGCGAGCCAATTATCGGGAAGCTCATACGAGCCATAAACGG
Found at i:43849913 original size:25 final size:24
Alignment explanation
Indices: 43849805--43849915 Score: 84
Period size: 25 Copynumber: 4.5 Consensus size: 24
43849795 AGCCATGTAA
** * *
43849805 CGGGAAGCTCATGTGAGCCATATAA
1 CGGGAAGCTCA-ACGAGCCAAATAT
** *
43849830 CGGGAAGCTCTTGCGAGCCAATTAT
1 CGGGAAGCTC-AACGAGCCAAATAT
43849855 CGGGAAGCTCATACGAGCCATAA-AT
1 CGGGAAGCTCA-ACGAGCCA-AATAT
43849880 -GGGAAGCTCAA-GAAAGCCAAATAT
1 CGGGAAGCTCAACG--AGCCAAATAT
43849904 CGGGAAGCTCAA
1 CGGGAAGCTCAA
43849916 AAGAGCTGTA
Statistics
Matches: 71, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
22 1 0.01
23 3 0.04
24 17 0.24
25 49 0.69
26 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.27, T:0.17
Consensus pattern (24 bp):
CGGGAAGCTCAACGAGCCAAATAT
Found at i:43854472 original size:13 final size:13
Alignment explanation
Indices: 43854454--43854478 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43854444 GGCATAATTT
43854454 TTAAAAATTAAAA
1 TTAAAAATTAAAA
43854467 TTAAAAATTAAA
1 TTAAAAATTAAA
43854479 TAAAAAAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TTAAAAATTAAAA
Found at i:43863278 original size:19 final size:19
Alignment explanation
Indices: 43863254--43863291 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
43863244 GTCCATTTAT
43863254 ATACCTGAA-TGTACCAAAC
1 ATACCT-AAGTGTACCAAAC
43863273 ATACCTAAGTGTACCAAAC
1 ATACCTAAGTGTACCAAAC
43863292 GTTATACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (19 bp):
ATACCTAAGTGTACCAAAC
Found at i:43895459 original size:22 final size:23
Alignment explanation
Indices: 43895415--43895459 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
43895405 GTATTCAAAT
* *
43895415 CTTATTCTATCAATTCTCTCAAC
1 CTTATTCTATCAATTCACGCAAC
*
43895438 CTTATTC-ATCTATTCACGCAAC
1 CTTATTCTATCAATTCACGCAAC
43895460 TATTTTATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.27, C:0.31, G:0.02, T:0.40
Consensus pattern (23 bp):
CTTATTCTATCAATTCACGCAAC
Done.