Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 130 of 144
Found at i:40464569 original size:19 final size:18
Alignment explanation
Indices: 40464516--40464569 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 18
40464506 AAAACCACTT
* *
40464516 TCATTTCTA-AATGTTTC
1 TCATTTCTATAATTTTTG
*
40464533 TCATTTCTCTAA-TTTTG
1 TCATTTCTATAATTTTTG
40464550 TCATTTCTATATATTTTTG
1 TCATTTCTATA-ATTTTTG
40464569 T
1 T
40464570 TTATTTGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 21 0.70
18 3 0.10
19 6 0.20
ACGTcount: A:0.20, C:0.15, G:0.06, T:0.59
Consensus pattern (18 bp):
TCATTTCTATAATTTTTG
Found at i:40472730 original size:22 final size:25
Alignment explanation
Indices: 40472705--40472756 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 25
40472695 TTATACAAAA
40472705 AGCACAGATGTGCT-A-AA-CAGAG
1 AGCACAGATGTGCTAATAATCAGAG
**
40472727 AGCATTGATGTGCTAATAATCAGAG
1 AGCACAGATGTGCTAATAATCAGAG
40472752 AGCAC
1 AGCAC
40472757 GCTAAGGATC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 12 0.50
23 1 0.04
24 2 0.08
25 9 0.38
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (25 bp):
AGCACAGATGTGCTAATAATCAGAG
Found at i:40473667 original size:27 final size:26
Alignment explanation
Indices: 40473617--40473673 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
40473607 AAATCCCAAA
* *
40473617 TTTTCTTTCTTTCCTTCCCTTTTTCT
1 TTTTCTTTCTTTCCTCCCCTTTTTCG
40473643 TTTTCTTTCCTTT-CTCCCCTGTTTTCG
1 TTTTCTTT-CTTTCCTCCCCT-TTTTCG
40473670 TTTT
1 TTTT
40473674 GCTTCTCTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.00, C:0.30, G:0.04, T:0.67
Consensus pattern (26 bp):
TTTTCTTTCTTTCCTCCCCTTTTTCG
Found at i:40473726 original size:5 final size:5
Alignment explanation
Indices: 40473716--40473747 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
40473706 TTTGTTCTTT
40473716 TATAA TATAA TATAA TAT-A TATAA TAT-A TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATA
40473748 CTTAACTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 8 0.32
5 17 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TATAA
Found at i:40473739 original size:9 final size:9
Alignment explanation
Indices: 40473716--40473747 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
40473706 TTTGTTCTTT
40473716 TATAATATAA
1 TATAATAT-A
40473726 TATAATATA
1 TATAATATA
40473735 TATAATATA
1 TATAATATA
40473744 TATA
1 TATA
40473748 CTTAACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TATAATATA
Found at i:40474561 original size:21 final size:21
Alignment explanation
Indices: 40474535--40474576 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
40474525 CAACCCAATC
*
40474535 ATAAAAATTACTAATAATTTA
1 ATAAAAATTACAAATAATTTA
40474556 ATAAAAATTACAAATAATTTA
1 ATAAAAATTACAAATAATTTA
40474577 TGTGTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (21 bp):
ATAAAAATTACAAATAATTTA
Found at i:40474643 original size:9 final size:9
Alignment explanation
Indices: 40474625--40474673 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
40474615 GTAGTGATTC
*
40474625 AATTCAGGT
1 AATTCGGGT
40474634 AATTCGGGT
1 AATTCGGGT
*
40474643 AATTCGGTT
1 AATTCGGGT
40474652 AATTCGGGT
1 AATTCGGGT
*
40474661 AATTCGGAT
1 AATTCGGGT
40474670 AATT
1 AATT
40474674 TAGTTGATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (9 bp):
AATTCGGGT
Found at i:40475189 original size:62 final size:59
Alignment explanation
Indices: 40475102--40475235 Score: 182
Period size: 62 Copynumber: 2.2 Consensus size: 59
40475092 TCCAAAAATA
* * *
40475102 ATATTATTTTAAT-AGATTTAATATTAAATTTAA-CTTAATGTTTATCTTGTAGATAAATATT
1 ATATTAATTTAATAAGATTAAATATTAAATTTAATC-TAATATTTATC-T-T-GATAAATATT
*
40475163 CTATTAATTTAATAAGATTAAATATTAAATTTAATCTAATATTTATCTTGATAAATATT
1 ATATTAATTTAATAAGATTAAATATTAAATTTAATCTAATATTTATCTTGATAAATATT
40475222 ATATTAATTTAATA
1 ATATTAATTTAATA
40475236 TTAAAGTGAT
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
59 23 0.35
60 1 0.02
61 12 0.18
62 29 0.44
63 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (59 bp):
ATATTAATTTAATAAGATTAAATATTAAATTTAATCTAATATTTATCTTGATAAATATT
Found at i:40486168 original size:10 final size:10
Alignment explanation
Indices: 40486155--40486201 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
40486145 TTATATTATT
40486155 ATAATTTAAA
1 ATAATTTAAA
*
40486165 ATAAGTTAAA
1 ATAATTTAAA
*
40486175 ATAATATAACA
1 ATAATTTAA-A
40486186 A-AATTTTAAA
1 ATAA-TTTAAA
40486196 ATAATT
1 ATAATT
40486202 ACTTACAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (10 bp):
ATAATTTAAA
Found at i:40486195 original size:21 final size:23
Alignment explanation
Indices: 40486170--40486220 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
40486160 TTAAAATAAG
40486170 TTAAAATAA-TA-TAACAAAATT
1 TTAAAATAATTACTAACAAAATT
* *
40486191 TTAAAATAATTACTTACAAATTT
1 TTAAAATAATTACTAACAAAATT
40486214 TTAAAAT
1 TTAAAAT
40486221 TAAGAGACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 9 0.35
22 2 0.08
23 15 0.58
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (23 bp):
TTAAAATAATTACTAACAAAATT
Found at i:40490222 original size:19 final size:18
Alignment explanation
Indices: 40490200--40490244 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
40490190 TAATCATATG
40490200 TTTAGTTATA-TTTTTTTAA
1 TTTAGTT-TAGTTTTTTT-A
*
40490219 TTTAATTTAGTTTTTTTA
1 TTTAGTTTAGTTTTTTTA
40490237 TTTAGTTT
1 TTTAGTTT
40490245 TTCAGATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (18 bp):
TTTAGTTTAGTTTTTTTA
Found at i:40494143 original size:61 final size:61
Alignment explanation
Indices: 40494048--40494229 Score: 364
Period size: 61 Copynumber: 3.0 Consensus size: 61
40494038 TAGCTAAAAA
40494048 AATGTTGCCCACGGTCATTATTAACCAAAGTCTCATCATTTGCATAAGAGACACGTCGAAC
1 AATGTTGCCCACGGTCATTATTAACCAAAGTCTCATCATTTGCATAAGAGACACGTCGAAC
40494109 AATGTTGCCCACGGTCATTATTAACCAAAGTCTCATCATTTGCATAAGAGACACGTCGAAC
1 AATGTTGCCCACGGTCATTATTAACCAAAGTCTCATCATTTGCATAAGAGACACGTCGAAC
40494170 AATGTTGCCCACGGTCATTATTAACCAAAGTCTCATCATTTGCATAAGAGACACGTCGAA
1 AATGTTGCCCACGGTCATTATTAACCAAAGTCTCATCATTTGCATAAGAGACACGTCGAA
40494230 AATTATTTGC
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 121 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.26
Consensus pattern (61 bp):
AATGTTGCCCACGGTCATTATTAACCAAAGTCTCATCATTTGCATAAGAGACACGTCGAAC
Found at i:40500900 original size:18 final size:17
Alignment explanation
Indices: 40500877--40500913 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
40500867 CTACCAAATG
40500877 AAACTCTAAATAATGCTA
1 AAACTCTAAATAAT-CTA
*
40500895 AAACTCTAATTAATCTA
1 AAACTCTAAATAATCTA
40500912 AA
1 AA
40500914 TAAGAAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (17 bp):
AAACTCTAAATAATCTA
Found at i:40503341 original size:44 final size:42
Alignment explanation
Indices: 40503280--40503443 Score: 145
Period size: 44 Copynumber: 3.8 Consensus size: 42
40503270 TCCAATATGT
*
40503280 AATTATGTGTAAGACCATGTCTGGGACGTTGGCATCGATTTG
1 AATTACGTGTAAGACCATGTCTGGGACGTTGGCATCGATTTG
* * *
40503322 TAATTTACGTGTAAGACCATGTCTGGGACATCGGCATCGTATATG
1 -AA-TTACGTGTAAGACCATGTCTGGGACGTTGGCATCG-ATTTG
* * * * * *
40503367 AGTT-TGTGTACGACCCTGTCGGGGACAG-TGGCATTGATAGTTG
1 AATTACGTGTAAGACCATGTCTGGGAC-GTTGGCATCGAT--TTG
* *
40503410 -ATTACATGTAAGACCATGTCTGAGACGTTGGCAT
1 AATTACGTGTAAGACCATGTCTGGGACGTTGGCAT
40503444 TGTACGAGCT
Statistics
Matches: 94, Mismatches: 20, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
41 2 0.02
42 27 0.29
43 28 0.30
44 33 0.35
45 4 0.04
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.31
Consensus pattern (42 bp):
AATTACGTGTAAGACCATGTCTGGGACGTTGGCATCGATTTG
Found at i:40506793 original size:13 final size:14
Alignment explanation
Indices: 40506770--40506817 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 14
40506760 TAAGTCCATC
*
40506770 ACAGAAACAGATAT
1 ACAGAATCAGATAT
*
40506784 -CAGAATCAGATGT
1 ACAGAATCAGATAT
*
40506797 ACAGAAT-AGATAA
1 ACAGAATCAGATAT
40506810 ACAGAATC
1 ACAGAATC
40506818 CTACCCTCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 22 0.79
14 6 0.21
ACGTcount: A:0.52, C:0.15, G:0.17, T:0.17
Consensus pattern (14 bp):
ACAGAATCAGATAT
Found at i:40511631 original size:16 final size:17
Alignment explanation
Indices: 40511612--40511651 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
40511602 TTGAAAAGAA
40511612 AAATAATTT-AAAACTT
1 AAATAATTTAAAAACTT
*
40511628 AAAT-TTTTAAAAACTT
1 AAATAATTTAAAAACTT
40511644 AAA-AATTT
1 AAATAATTT
40511652 GGAGAAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATAATTTAAAAACTT
Found at i:40511967 original size:57 final size:57
Alignment explanation
Indices: 40511869--40512059 Score: 244
Period size: 57 Copynumber: 3.4 Consensus size: 57
40511859 ATACAAACTA
* *
40511869 CAGAGAATATTT-ACTATTCA-TGTGTCTTTTCTTGTAGGGAATATTTACTGTTTTCAC
1 CAGAGAATATTTCA-TGTTCACT-TGTCTTTTCTTGTAGGGAATATTTACTGTTTTCGC
* * * * *
40511926 CAGAGAAAATTTCCTGTTCACTTGTCCTTTCTTGTAAGGAATATTTACAG-TTTCTGC
1 CAGAGAATATTTCATGTTCACTTGTCTTTTCTTGTAGGGAATATTTACTGTTTTC-GC
* *
40511983 CATAGAATATTTCATGTTCACTTGTCTTTTCTTGCAGGGAATATTTACTGTTTTCGC
1 CAGAGAATATTTCATGTTCACTTGTCTTTTCTTGTAGGGAATATTTACTGTTTTCGC
*
40512040 TAGAGAATATTTCATGTTCA
1 CAGAGAATATTTCATGTTCA
40512060 TGCATCTTTT
Statistics
Matches: 114, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
56 4 0.04
57 105 0.92
58 5 0.04
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (57 bp):
CAGAGAATATTTCATGTTCACTTGTCTTTTCTTGTAGGGAATATTTACTGTTTTCGC
Found at i:40513373 original size:174 final size:175
Alignment explanation
Indices: 40513072--40513421 Score: 657
Period size: 174 Copynumber: 2.0 Consensus size: 175
40513062 ATTTGTTTGA
*
40513072 AAAATATTGTGAGGATTTTTGTGTAGCAGTCTGTGAAGACACTTCTATTTCTTTTGGAAAAACAT
1 AAAATATTGTGAGGATTTTTGTGTAGCAGTCTGTGAAGACACTGCTATTTCTTTTGGAAAAACAT
*
40513137 CTTGGAGAGATGTCTCTTTTAAAACATTTTTTGAGAGATTTTGGTTTGTGTAAAACAATCTCTTT
66 CTTGGAGAGATGTCTCTTTTAAAACATTTTTTGAGAGATTTTGGTTTGTGTAAAAAAATCTCTTT
40513202 ATTTTTTGAAATCTTTGCCGCTTTAGGAGCAATTTGTTTAAGAGG
131 ATTTTTTGAAATCTTTGCCGCTTTAGGAGCAATTTGTTTAAGAGG
*
40513247 AAAA-ATTGTGAGGATTTTTGTGTAGCAGTCTGTGAAGATACTGCTATTTCTTTTGGAAAAACAT
1 AAAATATTGTGAGGATTTTTGTGTAGCAGTCTGTGAAGACACTGCTATTTCTTTTGGAAAAACAT
40513311 CTTGGAGAGATGTCTCTTTTAAAACATTTTTTGAGAGATTTTGGTTTGTGTAAAAAAATCTCTTT
66 CTTGGAGAGATGTCTCTTTTAAAACATTTTTTGAGAGATTTTGGTTTGTGTAAAAAAATCTCTTT
*
40513376 ATTTTTTGAAATCTTTGCCGCTTTAGGAGCAATTTGTTTGAGAGG
131 ATTTTTTGAAATCTTTGCCGCTTTAGGAGCAATTTGTTTAAGAGG
40513421 A
1 A
40513422 GTTTCCTCTG
Statistics
Matches: 171, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
174 167 0.98
175 4 0.02
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (175 bp):
AAAATATTGTGAGGATTTTTGTGTAGCAGTCTGTGAAGACACTGCTATTTCTTTTGGAAAAACAT
CTTGGAGAGATGTCTCTTTTAAAACATTTTTTGAGAGATTTTGGTTTGTGTAAAAAAATCTCTTT
ATTTTTTGAAATCTTTGCCGCTTTAGGAGCAATTTGTTTAAGAGG
Found at i:40520519 original size:57 final size:57
Alignment explanation
Indices: 40520431--40520572 Score: 216
Period size: 57 Copynumber: 2.5 Consensus size: 57
40520421 GAAAAAATGA
*
40520431 TGCAAGAAAAGATGC-A-TGAACAGGAAATATTCTCTGGAGAAAATAGTAAATATTCCC
1 TGCAAGAAAAGA--CAAGTGAACAGGAAATATTCTCTGGAGAAAACAGTAAATATTCCC
* * *
40520488 TGCAATAGAAGACAAGTGAACAGGAAATATTCTCTGGCGAAAACAGTAAATATTCCC
1 TGCAAGAAAAGACAAGTGAACAGGAAATATTCTCTGGAGAAAACAGTAAATATTCCC
40520545 TGCAAGAAAAGACAAGTGAACAGGAAAT
1 TGCAAGAAAAGACAAGTGAACAGGAAAT
40520573 CGGTAAATAT
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
55 1 0.01
56 1 0.01
57 75 0.97
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (57 bp):
TGCAAGAAAAGACAAGTGAACAGGAAATATTCTCTGGAGAAAACAGTAAATATTCCC
Found at i:40520592 original size:42 final size:42
Alignment explanation
Indices: 40520533--40520614 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
40520523 GGCGAAAACA
40520533 GTAAATATTCCCTGCAAGAAAAGACAAGTGAACAGGAAATCG
1 GTAAATATTCCCTGCAAGAAAAGACAAGTGAACAGGAAATCG
*
40520575 GTAAATATTCCCTGCAAGAAAAGACAAGTGTACAGGAAAT
1 GTAAATATTCCCTGCAAGAAAAGACAAGTGAACAGGAAAT
40520615 ATTCTCTGGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (42 bp):
GTAAATATTCCCTGCAAGAAAAGACAAGTGAACAGGAAATCG
Found at i:40520647 original size:99 final size:99
Alignment explanation
Indices: 40520476--40520656 Score: 335
Period size: 99 Copynumber: 1.8 Consensus size: 99
40520466 GGAGAAAATA
* *
40520476 GTAAATATTCCCTGCAATAGAAGACAAGTGAACAGGAAATATTCTCTGGCGAAAACAGTAAATAT
1 GTAAATATTCCCTGCAAGAAAAGACAAGTGAACAGGAAATATTCTCTGGCGAAAACAGTAAATAT
40520541 TCCCTGCAAGAAAAGACAAGTGAACAGGAAATCG
66 TCCCTGCAAGAAAAGACAAGTGAACAGGAAATCG
*
40520575 GTAAATATTCCCTGCAAGAAAAGACAAGTGTACAGGAAATATTCTCTGGCGAAAACAGTAAATAT
1 GTAAATATTCCCTGCAAGAAAAGACAAGTGAACAGGAAATATTCTCTGGCGAAAACAGTAAATAT
40520640 TCCCTGCAAGAAAAGAC
66 TCCCTGCAAGAAAAGAC
40520657 GCATGAATAG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 79 1.00
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.20
Consensus pattern (99 bp):
GTAAATATTCCCTGCAAGAAAAGACAAGTGAACAGGAAATATTCTCTGGCGAAAACAGTAAATAT
TCCCTGCAAGAAAAGACAAGTGAACAGGAAATCG
Found at i:40521132 original size:37 final size:36
Alignment explanation
Indices: 40521054--40521145 Score: 98
Period size: 37 Copynumber: 2.4 Consensus size: 36
40521044 TTAAATTTTA
40521054 TATTAAAATAATCACTTTAATATTAAATTAATAAAATAC
1 TATTAAAATAAT-A--TTAATATTAAATTAATAAAATAC
* *
40521093 TATTAAGATAAGTATTAA-ATTAAATATAATATTAA-AC
1 TATTAAAATAA-TATTAATATTAAAT-TAATA-AAATAC
40521130 TATTAAAATAATATTA
1 TATTAAAATAATATTA
40521146 TTTTTGGAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
36 12 0.26
37 21 0.45
38 2 0.04
39 11 0.23
40 1 0.02
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (36 bp):
TATTAAAATAATATTAATATTAAATTAATAAAATAC
Found at i:40521596 original size:19 final size:20
Alignment explanation
Indices: 40521574--40521613 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
40521564 TTTAATTAAT
*
40521574 TTGATT-AATTTAATTTTTC
1 TTGATTAAAATTAATTTTTC
40521593 TTGATTAAAATTAATTTTTC
1 TTGATTAAAATTAATTTTTC
40521613 T
1 T
40521614 AAAAATCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (20 bp):
TTGATTAAAATTAATTTTTC
Found at i:40522768 original size:16 final size:16
Alignment explanation
Indices: 40522747--40522780 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40522737 TTATGCATGC
*
40522747 AAAATATAAAAGACAT
1 AAAATACAAAAGACAT
*
40522763 AAAATACAAAATACAT
1 AAAATACAAAAGACAT
40522779 AA
1 AA
40522781 TAGTGAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.09, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAATACAAAAGACAT
Found at i:40539097 original size:26 final size:27
Alignment explanation
Indices: 40539054--40539107 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
40539044 TTTTTTATAT
*
40539054 ATTTTATAATTTATATATACATATACAC
1 ATTTTATAA-TTACATATACATATACAC
*
40539082 ATTTTATAA-TACATATATATATACAC
1 ATTTTATAATTACATATACATATACAC
40539108 GTACATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 15 0.62
28 9 0.38
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (27 bp):
ATTTTATAATTACATATACATATACAC
Found at i:40539350 original size:29 final size:29
Alignment explanation
Indices: 40539316--40539371 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
40539306 CATATTTTCG
40539316 TATA-TTCTACAA-TTCACATATATATATTA
1 TATATTTC-ACAATTTCA-ATATATATATTA
*
40539345 TATATTTCACAATTTTAATATATATAT
1 TATATTTCACAATTTCAATATATATAT
40539372 ACATACTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (29 bp):
TATATTTCACAATTTCAATATATATATTA
Found at i:40540796 original size:29 final size:30
Alignment explanation
Indices: 40540757--40540813 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
40540747 AACACTTTTA
*
40540757 AATTTTAATTTCT-CTATTTTTAATTTAAAG
1 AATTTTAATTTATACTA-TTTTAATTTAAAG
40540787 AATTTT-ATTTATACTATTTTAATTTAA
1 AATTTTAATTTATACTATTTTAATTTAA
40540814 TAATTAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (30 bp):
AATTTTAATTTATACTATTTTAATTTAAAG
Found at i:40548497 original size:21 final size:20
Alignment explanation
Indices: 40548473--40548516 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
40548463 GAAAAAGATG
40548473 TCTTAAAAAACTTCTTGTTTT
1 TCTTAAAAAAC-TCTTGTTTT
* *
40548494 TCTTAGAAATCTCTTGTTTT
1 TCTTAAAAAACTCTTGTTTT
40548514 TCT
1 TCT
40548517 CTCGATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.23, C:0.16, G:0.07, T:0.55
Consensus pattern (20 bp):
TCTTAAAAAACTCTTGTTTT
Found at i:40552718 original size:7 final size:7
Alignment explanation
Indices: 40552706--40552730 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40552696 TTTATACTCT
40552706 TTTAAAA
1 TTTAAAA
40552713 TTTAAAA
1 TTTAAAA
40552720 TTTAAAA
1 TTTAAAA
40552727 TTTA
1 TTTA
40552731 GTCTTTGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
TTTAAAA
Found at i:40552986 original size:25 final size:25
Alignment explanation
Indices: 40552952--40552999 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
40552942 AAAATGAAAA
40552952 CTTTAAAATTAAAAAAATAAAAACT
1 CTTTAAAATTAAAAAAATAAAAACT
*
40552977 CTTTAAAATTCAAAAAATAAAAA
1 CTTTAAAATTAAAAAAATAAAAA
40553000 TAAAATTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (25 bp):
CTTTAAAATTAAAAAAATAAAAACT
Found at i:40553256 original size:16 final size:16
Alignment explanation
Indices: 40553235--40553267 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
40553225 GGTTCAAAGC
*
40553235 AAATAAATTATTAAAA
1 AAATAAACTATTAAAA
40553251 AAATAAACTATTAAAA
1 AAATAAACTATTAAAA
40553267 A
1 A
40553268 TAGATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATAAACTATTAAAA
Found at i:40553432 original size:17 final size:17
Alignment explanation
Indices: 40553412--40553444 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40553402 TGAATTTTGT
40553412 AAAT-TTTTATATTTTTA
1 AAATCTTTT-TATTTTTA
40553429 AAATCTTTTTATTTTT
1 AAATCTTTTTATTTTT
40553445 TATTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
AAATCTTTTTATTTTTA
Found at i:40554071 original size:22 final size:22
Alignment explanation
Indices: 40554043--40554084 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
40554033 TTTAATTTTC
40554043 ATTTTTTAAATTTTAAAAAAGT
1 ATTTTTTAAATTTTAAAAAAGT
* *
40554065 ATTTTTTTATTTTTAAAAAA
1 ATTTTTTAAATTTTAAAAAA
40554085 TTATAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
ATTTTTTAAATTTTAAAAAAGT
Found at i:40554096 original size:24 final size:21
Alignment explanation
Indices: 40554053--40554106 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
40554043 ATTTTTTAAA
*
40554053 TTTTAAAAAAGTATTTTTTTAT
1 TTTTAAAAAAGTATTATTTT-T
*
40554075 TTTTAAAAAATTATAATATTTTT
1 TTTTAAAAAAGTAT--TATTTTT
40554098 TATTTAAAA
1 T-TTTAAAA
40554107 TATAATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 13 0.48
23 2 0.07
24 12 0.44
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTAAAAAAGTATTATTTTT
Found at i:40554127 original size:24 final size:25
Alignment explanation
Indices: 40554070--40554127 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
40554060 AAAGTATTTT
* *
40554070 TTTATTTTTAAAAAATTATAATATTT
1 TTTA-TTTTAAAAAATAATAATATTA
*
40554096 TTTA-TTTAAAATATAATAA-ATTA
1 TTTATTTTAAAAAATAATAATATTA
40554119 TTTATTTTA
1 TTTATTTTA
40554128 CTTTTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 7 0.25
24 17 0.61
26 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TTTATTTTAAAAAATAATAATATTA
Found at i:40555576 original size:30 final size:30
Alignment explanation
Indices: 40555532--40555603 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
40555522 TTTCTAAAAC
40555532 TTAAAAAT-ATTTTTTATACTTTT-TAATTT
1 TTAAAAATAATTTTTT-TACTTTTATAATTT
*
40555561 TTAAAAATAATTTTTTTATTTTTATAATTT
1 TTAAAAATAATTTTTTTACTTTTATAATTT
40555591 TTAAAAACTAATT
1 TTAAAAA-TAATT
40555604 AAATGTTGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 14 0.36
30 20 0.51
31 5 0.13
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (30 bp):
TTAAAAATAATTTTTTTACTTTTATAATTT
Found at i:40564446 original size:9 final size:9
Alignment explanation
Indices: 40564412--40564510 Score: 71
Period size: 9 Copynumber: 10.8 Consensus size: 9
40564402 TTTCCATAAG
40564412 AATATTA-A
1 AATATTATA
*
40564420 AAAATTATAA
1 AATATTAT-A
*
40564430 AAGAATTATA
1 AA-TATTATA
40564440 AATATTATA
1 AATATTATA
40564449 AATATTA-A
1 AATATTATA
40564457 AAT-TTATA
1 AATATTATA
*
40564465 TATACTTATTA
1 AATA-TTA-TA
40564476 AA-ATTATTA
1 AATATTA-TA
*
40564485 AAAATTATA
1 AATATTATA
*
40564494 AAAACTTATA
1 AATA-TTATA
40564504 AATATTA
1 AATATTA
40564511 AGGTTAAATA
Statistics
Matches: 77, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
7 3 0.04
8 13 0.17
9 30 0.39
10 22 0.29
11 9 0.12
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (9 bp):
AATATTATA
Found at i:40564474 original size:29 final size:29
Alignment explanation
Indices: 40564420--40564510 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
40564410 AGAATATTAA
* *
40564420 AAAATTATAAAAGAATTATAAATA-TTA-T
1 AAAATTATTAAA-AATTATAAAAACTTATT
* * *
40564448 -AAA-TATTAAAATTTATATATACTTATT
1 AAAATTATTAAAAATTATAAAAACTTATT
40564475 AAAATTATTAAAAATTATAAAAACTTA-T
1 AAAATTATTAAAAATTATAAAAACTTATT
40564503 AAATATTA
1 AAA-ATTA
40564511 AGGTTAAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
25 9 0.17
26 9 0.17
27 4 0.08
28 7 0.13
29 23 0.44
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (29 bp):
AAAATTATTAAAAATTATAAAAACTTATT
Found at i:40564503 original size:10 final size:9
Alignment explanation
Indices: 40564415--40564510 Score: 63
Period size: 10 Copynumber: 10.4 Consensus size: 9
40564405 CCATAAGAAT
40564415 ATTA-AAAA
1 ATTATAAAA
40564423 ATTATAAAAGA
1 ATTAT-AAA-A
*
40564434 ATTATAAAT
1 ATTATAAAA
*
40564443 ATTATAAAT
1 ATTATAAAA
40564452 A-T-TAAAA
1 ATTATAAAA
* *
40564459 TTTATATATA
1 ATTATA-AAA
* *
40564469 CTTATTAAA
1 ATTATAAAA
40564478 ATTATTAAAA
1 ATTA-TAAAA
40564488 ATTATAAAA
1 ATTATAAAA
*
40564497 ACTTATAAAT
1 A-TTATAAAA
40564507 ATTA
1 ATTA
40564511 AGGTTAAATA
Statistics
Matches: 70, Mismatches: 10, Indels: 15
0.74 0.11 0.16
Matches are distributed among these distances:
7 4 0.06
8 6 0.09
9 26 0.37
10 28 0.40
11 6 0.09
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (9 bp):
ATTATAAAA
Found at i:40565154 original size:10 final size:11
Alignment explanation
Indices: 40565106--40565166 Score: 70
Period size: 11 Copynumber: 5.5 Consensus size: 11
40565096 ATTATTCTAG
*
40565106 ATTTTTTTAAA
1 ATTTTTTTAGA
40565117 ATTTTTTTA-A
1 ATTTTTTTAGA
* * *
40565127 CTTTCTTTATGT
1 ATTTTTTTA-GA
40565139 ATTTTTTTAGA
1 ATTTTTTTAGA
40565150 ATTTTTTTAGA
1 ATTTTTTTAGA
40565161 ATTTTT
1 ATTTTT
40565167 ATATTTTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
10 8 0.19
11 27 0.64
12 7 0.17
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.67
Consensus pattern (11 bp):
ATTTTTTTAGA
Found at i:40565227 original size:19 final size:19
Alignment explanation
Indices: 40565188--40565256 Score: 77
Period size: 20 Copynumber: 3.6 Consensus size: 19
40565178 AAAATATAAA
* *
40565188 ATTTGGAATTTTATAAA-T
1 ATTTTGAATTTTAAAAATT
* *
40565206 ATTTTGACTTTTAAAAGTT
1 ATTTTGAATTTTAAAAATT
*
40565225 ATTTTGAATTTTTAAAAATG
1 ATTTTGAA-TTTTAAAAATT
40565245 ATTTTGAATTTT
1 ATTTTGAATTTT
40565257 TTTTTTGTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 13 0.31
19 12 0.29
20 17 0.40
ACGTcount: A:0.35, C:0.01, G:0.10, T:0.54
Consensus pattern (19 bp):
ATTTTGAATTTTAAAAATT
Found at i:40566335 original size:20 final size:22
Alignment explanation
Indices: 40566298--40566338 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
40566288 GAATAAATTT
40566298 ATATGTTTTTATAAAATTTTAA
1 ATATGTTTTTATAAAATTTTAA
*
40566320 ATAT-TTTTTAT-TAATTTTA
1 ATATGTTTTTATAAAATTTTA
40566339 TAATTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
ATATGTTTTTATAAAATTTTAA
Found at i:40567324 original size:2 final size:2
Alignment explanation
Indices: 40567317--40567341 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40567307 GATTGAAATG
40567317 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
40567342 CCCCTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:40567641 original size:6 final size:6
Alignment explanation
Indices: 40567630--40567654 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40567620 TATTTTTTTA
40567630 TTTAAT TTTAAT TTTAAT TTTAAT T
1 TTTAAT TTTAAT TTTAAT TTTAAT T
40567655 ATAAAACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTAAT
Found at i:40569820 original size:17 final size:16
Alignment explanation
Indices: 40569798--40569829 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
40569788 TCTCTTTTTC
40569798 TCTTTCTTTCTTTATTT
1 TCTTTCTTT-TTTATTT
40569815 TCTTTCTTTTTTATT
1 TCTTTCTTTTTTATT
40569830 AAAAGCACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (16 bp):
TCTTTCTTTTTTATTT
Found at i:40572865 original size:12 final size:12
Alignment explanation
Indices: 40572828--40572867 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
40572818 ACCGACGAAT
40572828 AAAACAAAAACC
1 AAAACAAAAACC
* **
40572840 AAAACCAAGCCC
1 AAAACAAAAACC
40572852 AAAACAAAAACC
1 AAAACAAAAACC
40572864 AAAA
1 AAAA
40572868 TCGAAAACTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.70, C:0.28, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAACAAAAACC
Found at i:40575845 original size:18 final size:18
Alignment explanation
Indices: 40575822--40575861 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
40575812 GTTGAATTTT
40575822 ATAATTTGAATAAGTCAA
1 ATAATTTGAATAAGTCAA
* *
40575840 ATAATTTGGATAATTCAA
1 ATAATTTGAATAAGTCAA
40575858 ATAA
1 ATAA
40575862 AAAATTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (18 bp):
ATAATTTGAATAAGTCAA
Found at i:40575991 original size:20 final size:20
Alignment explanation
Indices: 40575932--40575992 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
40575922 TTTCAACAAA
40575932 AATTA-CAAAATAGTTCAAAAT
1 AATTATCAAAA-A-TTCAAAAT
*
40575953 AATTTTCAAAAATTCAAAAT
1 AATTATCAAAAATTCAAAAT
*
40575973 AATTAT-AATAATTCTAAAAT
1 AATTATCAAAAATTC-AAAAT
40575993 TTATATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 7 0.20
20 18 0.51
21 5 0.14
22 5 0.14
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.34
Consensus pattern (20 bp):
AATTATCAAAAATTCAAAAT
Found at i:40576037 original size:11 final size:11
Alignment explanation
Indices: 40576001--40576050 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
40575991 ATTTATATTT
40576001 TTTATAAAAA-A
1 TTTA-AAAAATA
*
40576012 TTT-AAAAGTA
1 TTTAAAAAATA
40576022 TTTTAAAAAATA
1 -TTTAAAAAATA
40576034 TTTAAAAAATA
1 TTTAAAAAATA
*
40576045 TATAAA
1 TTTAAA
40576051 GAAAGTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 4 0.12
10 1 0.03
11 22 0.67
12 6 0.18
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
TTTAAAAAATA
Found at i:40585097 original size:9 final size:9
Alignment explanation
Indices: 40585083--40585115 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
40585073 ATAACAAAGG
40585083 AAATAAGAA
1 AAATAAGAA
40585092 AAATAAGAA
1 AAATAAGAA
*
40585101 AAATAAAAA
1 AAATAAGAA
40585110 AAATAA
1 AAATAA
40585116 AGGATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (9 bp):
AAATAAGAA
Found at i:40585690 original size:3 final size:3
Alignment explanation
Indices: 40585677--40585717 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
40585667 CAAAATTTGG
40585677 AAT AAT AAAT AAT AAT -AT AAT AAT -AT AAT AAT ATAT AAT AA
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AA
40585718 AAATTAAGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 4 0.12
3 24 0.71
4 6 0.18
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:40585698 original size:8 final size:8
Alignment explanation
Indices: 40585678--40585716 Score: 64
Period size: 8 Copynumber: 5.1 Consensus size: 8
40585668 AAAATTTGGA
40585678 ATAATAA-
1 ATAATAAT
40585685 ATAATAAT
1 ATAATAAT
40585693 ATAATAAT
1 ATAATAAT
40585701 ATAATAAT
1 ATAATAAT
40585709 AT-ATAAT
1 ATAATAAT
40585716 A
1 A
40585717 AAAATTAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 13 0.42
8 18 0.58
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATAATAAT
Found at i:40590314 original size:17 final size:19
Alignment explanation
Indices: 40590278--40590314 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
40590268 TGTTTGGAGT
*
40590278 AAATGGCTTGAATGGTATA
1 AAATGGCTTGAATGGCATA
40590297 AAATGG-TT-AATGGCATA
1 AAATGGCTTGAATGGCATA
40590314 A
1 A
40590315 TTTAATAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 2 0.12
19 6 0.35
ACGTcount: A:0.41, C:0.05, G:0.24, T:0.30
Consensus pattern (19 bp):
AAATGGCTTGAATGGCATA
Found at i:40596927 original size:21 final size:22
Alignment explanation
Indices: 40596877--40596927 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
40596867 TTTATTATTA
40596877 TTTTC-TTTTTCTTTAACAATT
1 TTTTCTTTTTTCTTTAACAATT
** * *
40596898 TTTAGTTTTTTTTTTCA-AATT
1 TTTTCTTTTTTCTTTAACAATT
40596919 TTTTCTTTT
1 TTTTCTTTT
40596928 CATTTTTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.16, C:0.10, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTCTTTTTTCTTTAACAATT
Found at i:40598912 original size:17 final size:17
Alignment explanation
Indices: 40598890--40598922 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40598880 AATACTTTGT
*
40598890 ATTTTTGTCGTTGCAAA
1 ATTTTTGCCGTTGCAAA
40598907 ATTTTTGCCGTTGCAA
1 ATTTTTGCCGTTGCAA
40598923 GTTCTCTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.45
Consensus pattern (17 bp):
ATTTTTGCCGTTGCAAA
Found at i:40600459 original size:98 final size:98
Alignment explanation
Indices: 40600290--40600485 Score: 383
Period size: 98 Copynumber: 2.0 Consensus size: 98
40600280 AGATGGAGCT
40600290 AAAGAAGACAAGGGGAATAAGTCAGAAAAATAAAATGGGGGATTCTTGTCCTGTTATTTATTTAA
1 AAAGAAGACAAGGGGAATAAGTCAGAAAAATAAAATGGGGGATTCTTGTCCTGTTATTTATTTAA
40600355 TTATTTTTAGGTCTTTAGGAATTTATTTCTTTC
66 TTATTTTTAGGTCTTTAGGAATTTATTTCTTTC
40600388 AAAGAAGACAAGGGGAATAAGTCAGAAAAATAAAATGGGGGATTCTTGTCCTGTTATTTATTTAA
1 AAAGAAGACAAGGGGAATAAGTCAGAAAAATAAAATGGGGGATTCTTGTCCTGTTATTTATTTAA
*
40600453 TTATTTTTTGGTCTTTAGGAATTTATTTCTTTC
66 TTATTTTTAGGTCTTTAGGAATTTATTTCTTTC
40600486 GTAATTAGGA
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 97 1.00
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.39
Consensus pattern (98 bp):
AAAGAAGACAAGGGGAATAAGTCAGAAAAATAAAATGGGGGATTCTTGTCCTGTTATTTATTTAA
TTATTTTTAGGTCTTTAGGAATTTATTTCTTTC
Found at i:40601047 original size:137 final size:137
Alignment explanation
Indices: 40600801--40601071 Score: 524
Period size: 137 Copynumber: 2.0 Consensus size: 137
40600791 CTTTCATAAG
40600801 TATGTTTTAATAAATGAATGTTTAGAGATATTCTTGTTACTGAGATAGTTTGTATGCAAGTATGA
1 TATGTTTTAATAAATGAATGTTTAGAGATATTCTTGTTACTGAGATAGTTTGTATGCAAGTATGA
* *
40600866 ATGATGATTTTATCTAAGTGAAAGTATGTTATCATGAAGAATGGAATGCTTGTATGATCTTAGCC
66 ATGATGATTTTATCTAAGTGAAAGTATGTTATCATGAAGAATGGAATGCTTGTATAATATTAGCC
40600931 TTAGTAA
131 TTAGTAA
40600938 TATGTTTTAATAAATGAATGTTTAGAGATATTCTTGTTACTGAGATAGTTTGTATGCAAGTATGA
1 TATGTTTTAATAAATGAATGTTTAGAGATATTCTTGTTACTGAGATAGTTTGTATGCAAGTATGA
40601003 ATGATGATTTTATCTAAGTGAAAGTATGTTATCATGAAGAATGGAATGCTTGTATAATATTAGCC
66 ATGATGATTTTATCTAAGTGAAAGTATGTTATCATGAAGAATGGAATGCTTGTATAATATTAGCC
40601068 TTAG
131 TTAG
40601072 CAATGTTTGC
Statistics
Matches: 132, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 132 1.00
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.40
Consensus pattern (137 bp):
TATGTTTTAATAAATGAATGTTTAGAGATATTCTTGTTACTGAGATAGTTTGTATGCAAGTATGA
ATGATGATTTTATCTAAGTGAAAGTATGTTATCATGAAGAATGGAATGCTTGTATAATATTAGCC
TTAGTAA
Found at i:40602788 original size:11 final size:11
Alignment explanation
Indices: 40602772--40602807 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
40602762 CTTCATTCAT
*
40602772 ATCCCTCAATC
1 ATCCCTCAAGC
40602783 ATCCCTCAAGC
1 ATCCCTCAAGC
*
40602794 ATCCATCAAGC
1 ATCCCTCAAGC
40602805 ATC
1 ATC
40602808 ATTCTCTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.31, C:0.42, G:0.06, T:0.22
Consensus pattern (11 bp):
ATCCCTCAAGC
Found at i:40604504 original size:20 final size:19
Alignment explanation
Indices: 40604478--40604545 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
40604468 GCCACATGTG
40604478 CAAACAGGGGTATCGAAGTA
1 CAAACAGGGGTA-CGAAGTA
* * * * *
40604498 TAAACAGTGGCACGTATGTG
1 CAAACAGGGGTACG-AAGTA
40604518 CAAACAGGGGTACCGAAGTA
1 CAAACAGGGGTA-CGAAGTA
40604538 CAAACAGG
1 CAAACAGG
40604546 AGCACGTATG
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
19 2 0.06
20 32 0.89
21 2 0.06
ACGTcount: A:0.38, C:0.18, G:0.29, T:0.15
Consensus pattern (19 bp):
CAAACAGGGGTACGAAGTA
Found at i:40604528 original size:40 final size:40
Alignment explanation
Indices: 40604473--40604557 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
40604463 ATTTAGCCAC
* *
40604473 ATGTGCAAACAGGGGTATCGAAGTATAAACAGTG-GCACGT
1 ATGTGCAAACAGGGGTACCGAAGTACAAACAG-GAGCACGT
40604513 ATGTGCAAACAGGGGTACCGAAGTACAAACAGGAGCACGT
1 ATGTGCAAACAGGGGTACCGAAGTACAAACAGGAGCACGT
40604553 ATGTG
1 ATGTG
40604558 AAAATATTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
39 1 0.02
40 41 0.98
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.18
Consensus pattern (40 bp):
ATGTGCAAACAGGGGTACCGAAGTACAAACAGGAGCACGT
Found at i:40605754 original size:19 final size:19
Alignment explanation
Indices: 40605730--40605769 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
40605720 GTAAGATAAG
40605730 AAATCTAAATGTACTTACT
1 AAATCTAAATGTACTTACT
40605749 AAATCTAAATGTACTTACT
1 AAATCTAAATGTACTTACT
40605768 AA
1 AA
40605770 GCTCTTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (19 bp):
AAATCTAAATGTACTTACT
Found at i:40613015 original size:25 final size:28
Alignment explanation
Indices: 40612986--40613037 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 28
40612976 TCTATTAGTA
40612986 AAGGTTAATATA-GTA-AAT-TAACAAT
1 AAGGTTAATATATGTATAATATAACAAT
40613011 AAGGTTAATATATGTATAATATAACAA
1 AAGGTTAATATATGTATAATATAACAA
40613038 ATTAAAATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 12 0.50
26 3 0.12
27 3 0.12
28 6 0.25
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.33
Consensus pattern (28 bp):
AAGGTTAATATATGTATAATATAACAAT
Found at i:40614952 original size:41 final size:40
Alignment explanation
Indices: 40614923--40615039 Score: 162
Period size: 41 Copynumber: 2.9 Consensus size: 40
40614913 GTGAATTAAT
*
40614923 TCAGACTTTAAGTCTAGCAGGCTACGTGCCGGTGATCTGAA
1 TCAG-CTTTAAGCCTAGCAGGCTACGTGCCGGTGATCTGAA
* *
40614964 TCAGGTTATAAACCTAGCAGGCTACGTGCCGGTGATCTGAA
1 TCAGCTT-TAAGCCTAGCAGGCTACGTGCCGGTGATCTGAA
* *
40615005 TCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGA
1 TCA-GCTTTAAGCCTAGCAGGCTACGTGCCGGTGA
40615040 ATATGTTAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
40 2 0.03
41 63 0.94
42 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (40 bp):
TCAGCTTTAAGCCTAGCAGGCTACGTGCCGGTGATCTGAA
Found at i:40620142 original size:97 final size:96
Alignment explanation
Indices: 40619975--40620163 Score: 270
Period size: 97 Copynumber: 2.0 Consensus size: 96
40619965 TAAATGTCGT
** * *
40619975 ACACCATTGTATTGGACCGAGCTCAGTGAAAATAAGATACACGGGGTTGATTTGATTAAAGAGAC
1 ACACCATTGTATTGGACCGAGCTCAGCAAAAATAAGATACAAGGGGTCGATTTGATTAAAGAGAC
*
40620040 CGAACAGAAAGTGAAAGTGATTCGGGANCCGA
66 CGAACAAAAAGTGAAAGTGATTCGGGA-CCGA
* * * * *
40620072 ACACCTTTGTATTGGACTGAGCTGAGCAAAAATAAGATTCAAGTGGTCGATTTGATTAAAGAGAC
1 ACACCATTGTATTGGACCGAGCTCAGCAAAAATAAGATACAAGGGGTCGATTTGATTAAAGAGAC
*
40620137 TGAACAAAAAGTGAAAGTGATTCGGGA
66 CGAACAAAAAGTGAAAGTGATTCGGGA
40620164 TAGTCTGAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
97 81 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (96 bp):
ACACCATTGTATTGGACCGAGCTCAGCAAAAATAAGATACAAGGGGTCGATTTGATTAAAGAGAC
CGAACAAAAAGTGAAAGTGATTCGGGACCGA
Found at i:40621029 original size:25 final size:28
Alignment explanation
Indices: 40621000--40621051 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 28
40620990 TATATTAGTA
40621000 AAGGTTAATATA-GTA-AAT-TAACAAT
1 AAGGTTAATATATGTATAATATAACAAT
40621025 AAGGTTAATATATGTATAATATAACAA
1 AAGGTTAATATATGTATAATATAACAA
40621052 ATTAAAATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 12 0.50
26 3 0.12
27 3 0.12
28 6 0.25
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.33
Consensus pattern (28 bp):
AAGGTTAATATATGTATAATATAACAAT
Found at i:40622856 original size:41 final size:41
Alignment explanation
Indices: 40622811--40622996 Score: 354
Period size: 41 Copynumber: 4.5 Consensus size: 41
40622801 GACTTTAAGT
40622811 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
40622852 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
40622893 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
*
40622934 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAGC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
*
40622975 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTACGTGCCGGTGA
40622997 ATATGTTAAA
Statistics
Matches: 143, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 143 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:40642315 original size:6 final size:6
Alignment explanation
Indices: 40642304--40642336 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
40642294 TTAATTCTAT
40642304 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
40642337 GGATTTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:40642342 original size:18 final size:18
Alignment explanation
Indices: 40642304--40642342 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
40642294 TTAATTCTAT
**
40642304 TTTTTATTTTTATTTTTA
1 TTTTTATTTTTATTTGGA
40642322 TTTTTATTTTTATTTGGA
1 TTTTTATTTTTATTTGGA
40642340 TTT
1 TTT
40642343 CATTATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.79
Consensus pattern (18 bp):
TTTTTATTTTTATTTGGA
Found at i:40644847 original size:3 final size:3
Alignment explanation
Indices: 40644839--40644886 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
40644829 TTTTTAAAAC
40644839 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
40644887 CAATGGATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:40660917 original size:29 final size:30
Alignment explanation
Indices: 40660872--40660954 Score: 87
Period size: 29 Copynumber: 2.7 Consensus size: 30
40660862 GAATTTGATC
* * *
40660872 AAATCAAAATTTCATGTATAAAATTGCTCA-
1 AAATC-AAAGTTCATGTATAAAATTACACAT
* *
40660902 GAATCAAAGTTCATGTATACAATTACACATT
1 AAATCAAAGTTCATGTATAAAATTACACA-T
*
40660933 AAATCATAGTTCATGTATAAAA
1 AAATCAAAGTTCATGTATAAAA
40660955 AAAATCTAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
29 20 0.47
30 4 0.09
31 19 0.44
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATTACACAT
Found at i:40661626 original size:34 final size:33
Alignment explanation
Indices: 40661577--40661640 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
40661567 ATTAAAATTA
* **
40661577 AAAATTGATCGAATAAACCAATTAAACTAAACAT
1 AAAATTGATCAAATAAAAAAATTAAA-TAAACAT
*
40661611 AAAATTGATTAAATAAAAAAATTAAATAAA
1 AAAATTGATCAAATAAAAAAATTAAATAAA
40661641 TCGAAATTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 4 0.15
34 22 0.85
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.25
Consensus pattern (33 bp):
AAAATTGATCAAATAAAAAAATTAAATAAACAT
Found at i:40661820 original size:21 final size:21
Alignment explanation
Indices: 40661769--40661824 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
40661759 AATAGCGGTG
*
40661769 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
** * *
40661790 ATGGTAAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
40661811 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
40661825 AACAATGGTG
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.07, G:0.34, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:40665275 original size:14 final size:13
Alignment explanation
Indices: 40665243--40665272 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
40665233 GGAAAATTAC
40665243 TTTTGAGAAGTGT
1 TTTTGAGAAGTGT
40665256 TTTTGAGAAGTGT
1 TTTTGAGAAGTGT
40665269 TTTT
1 TTTT
40665273 TGAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (13 bp):
TTTTGAGAAGTGT
Found at i:40670288 original size:45 final size:41
Alignment explanation
Indices: 40670211--40670308 Score: 108
Period size: 45 Copynumber: 2.3 Consensus size: 41
40670201 ATATGTTTTC
* *
40670211 TCGTGTAAGACCACGTCTGGGACGATGACATCGATATATGTGGT
1 TCGTGTAAGACCACGTCTAGGACGATGACATCG-TAT-T-TGAT
* *
40670255 TACGTGTAAGACCATGTCTAGGAC-ATTGGCATCGTATTTGAT
1 T-CGTGTAAGACCACGTCTAGGACGA-TGACATCGTATTTGAT
40670297 TCGTGTAAGACC
1 TCGTGTAAGACC
40670309 CTGTTCGGGA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
41 11 0.23
42 4 0.08
43 1 0.02
44 5 0.10
45 27 0.56
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (41 bp):
TCGTGTAAGACCACGTCTAGGACGATGACATCGTATTTGAT
Found at i:40672112 original size:35 final size:35
Alignment explanation
Indices: 40672066--40672136 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
40672056 GAATAGAAGA
40672066 TAAGATGAATGGCAAAGCATACACATGTTTTGTAC
1 TAAGATGAATGGCAAAGCATACACATGTTTTGTAC
40672101 TAAGATGAATGGCAAAGCATACACATGTTTTGTAC
1 TAAGATGAATGGCAAAGCATACACATGTTTTGTAC
40672136 T
1 T
40672137 TAAATGGGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.30
Consensus pattern (35 bp):
TAAGATGAATGGCAAAGCATACACATGTTTTGTAC
Found at i:40672646 original size:64 final size:64
Alignment explanation
Indices: 40672540--40672667 Score: 220
Period size: 64 Copynumber: 2.0 Consensus size: 64
40672530 ATTTCGAGCC
* *
40672540 GTGTTTTATATGGTAATGCCTTGTAACCTTATTTCGGTAACGGATACGGGTTATGAGTGTTACA
1 GTGTTTTATATGGTAATGCCTTGTAACCCTATTTCGGCAACGGATACGGGTTATGAGTGTTACA
* *
40672604 GTGTTTTATATGGTAATGCCTTGTAACCCTATTTTGGCAACGGATACGGGTTATGGGTGTTACA
1 GTGTTTTATATGGTAATGCCTTGTAACCCTATTTCGGCAACGGATACGGGTTATGAGTGTTACA
40672668 ATTATAATTC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (64 bp):
GTGTTTTATATGGTAATGCCTTGTAACCCTATTTCGGCAACGGATACGGGTTATGAGTGTTACA
Found at i:40672765 original size:40 final size:41
Alignment explanation
Indices: 40672719--40672806 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 41
40672709 AATTCATTAC
* * * *
40672719 TTCAGTAATTTCACAGTTCAATGCAGTAC-ACATAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACTAAAAAACAATA
**
40672759 TTCAGTAACTTCACAATTCAATTTAGTACTAAAAAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACTAAAAAACAATA
40672800 TTCAGTA
1 TTCAGTA
40672807 TTCCATAATG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
40 25 0.61
41 16 0.39
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (41 bp):
TTCAGTAACTTCACAATTCAATGCAGTACTAAAAAACAATA
Found at i:40678351 original size:10 final size:9
Alignment explanation
Indices: 40678330--40678390 Score: 52
Period size: 10 Copynumber: 6.3 Consensus size: 9
40678320 TTTATCATTA
40678330 TTTATAATAT
1 TTTATAA-AT
*
40678340 TTTTTACAATT
1 TTTATA-AA-T
40678351 TTTATAAA-
1 TTTATAAAT
*
40678359 TTTATACTAT
1 TTTATA-AAT
40678369 TTTATAAAAT
1 TTTAT-AAAT
40678379 TTTATAAAT
1 TTTATAAAT
40678388 TTT
1 TTT
40678391 TTTGTATTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
8 6 0.14
9 8 0.19
10 20 0.48
11 8 0.19
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTATAAAT
Found at i:40678363 original size:29 final size:28
Alignment explanation
Indices: 40678329--40678389 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
40678319 TTTTATCATT
* *
40678329 ATTTATAATATTTTTTACAATTTTTATAA
1 ATTTATAATATTTTATA-AAATTTTATAA
*
40678358 ATTTATACTATTTTATAAAATTTTATAA
1 ATTTATAATATTTTATAAAATTTTATAA
40678386 ATTT
1 ATTT
40678390 TTTTGTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (28 bp):
ATTTATAATATTTTATAAAATTTTATAA
Found at i:40678363 original size:39 final size:37
Alignment explanation
Indices: 40678320--40678430 Score: 98
Period size: 39 Copynumber: 2.9 Consensus size: 37
40678310 TCTACCTAAT
40678320 TTTATCATTATTTATAATATTTTTTACAATTTTTATAAA
1 TTTAT-ATTATTTATAATATTTTTTA-AATTTTTATAAA
* * * * **
40678359 TTTATACTATTTTATAAAATTTTATAAATTTTTTTGTA
1 TTTATATTA-TTTATAATATTTTTTAAATTTTTATAAA
*
40678397 TTTCTATATATTTCATAAT-TTTTTTATAATTTTT
1 TTTATAT-TATTT-ATAATATTTTTTA-AATTTTT
40678431 GTGATTATAT
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
38 26 0.45
39 32 0.55
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (37 bp):
TTTATATTATTTATAATATTTTTTAAATTTTTATAAA
Found at i:40678389 original size:19 final size:20
Alignment explanation
Indices: 40678317--40678390 Score: 66
Period size: 19 Copynumber: 3.8 Consensus size: 20
40678307 TCATCTACCT
*
40678317 AATTTTAT-CATTATTTATAA
1 AATTTTATACAAT-TTTATAA
* *
40678337 TATTTTTTACAATTTT-TATA
1 AATTTTATACAATTTTATA-A
*
40678357 AA-TTTATACTATTTTATAA
1 AATTTTATACAATTTTATAA
40678376 AATTTTATA-AATTTT
1 AATTTTATACAATTTT
40678391 TTTGTATTTC
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
19 21 0.49
20 19 0.44
21 3 0.07
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (20 bp):
AATTTTATACAATTTTATAA
Found at i:40678398 original size:29 final size:28
Alignment explanation
Indices: 40678366--40678421 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
40678356 AAATTTATAC
*
40678366 TATTT-TATAAAATTTTATAAATTTTTTTG
1 TATTTCTAT-AAATTTCAT-AATTTTTTTG
*
40678395 TATTTCTATATATTTCATAATTTTTTT
1 TATTTCTATAAATTTCATAATTTTTTT
40678422 ATAATTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.38
29 12 0.50
30 3 0.12
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (28 bp):
TATTTCTATAAATTTCATAATTTTTTTG
Found at i:40678417 original size:37 final size:35
Alignment explanation
Indices: 40678376--40678466 Score: 87
Period size: 39 Copynumber: 2.5 Consensus size: 35
40678366 TATTTTATAA
*
40678376 AATTTTATAAATTTTTTTGTATT-TCTATATAT-TTCAT
1 AATTTT-TAAATTTTTTTG-ATTATATATAT-TGTTC-T
*
40678413 AATTTTTTTATAATTTTTGTGATTATATATATTGTTCT
1 AA--TTTTTA-AATTTTTTTGATTATATATATTGTTCT
40678451 AATTTTTAAATTTTTT
1 AATTTTTAAATTTTTT
40678467 ATATATTTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
35 7 0.15
36 6 0.13
37 2 0.04
38 9 0.20
39 22 0.48
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (35 bp):
AATTTTTAAATTTTTTTGATTATATATATTGTTCT
Found at i:40678444 original size:39 final size:39
Alignment explanation
Indices: 40678378--40678457 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
40678368 TTTTATAAAA
* *
40678378 TTTTATAAATTTTTTTGTATTTCTATATAT-TTCATAATTT
1 TTTTATAAATTTTTGTGTATTTATATAT-TGTTC-TAATTT
40678418 TTTTAT-AATTTTTGTG-ATTATATATATTGTTCTAATTT
1 TTTTATAAATTTTTGTGTATT-TATATATTGTTCTAATTT
40678456 TT
1 TT
40678458 AAATTTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
38 12 0.33
39 18 0.50
40 6 0.17
ACGTcount: A:0.26, C:0.04, G:0.05, T:0.65
Consensus pattern (39 bp):
TTTTATAAATTTTTGTGTATTTATATATTGTTCTAATTT
Found at i:40680827 original size:17 final size:17
Alignment explanation
Indices: 40680805--40680838 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40680795 ATATGGAAAA
*
40680805 TAATCTTAGAAGATTTG
1 TAATCTGAGAAGATTTG
*
40680822 TAATCTGATAAGATTTG
1 TAATCTGAGAAGATTTG
40680839 ATTTTGTAAT
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:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (17 bp):
TAATCTGAGAAGATTTG
Found at i:40682939 original size:17 final size:17
Alignment explanation
Indices: 40682919--40682956 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
40682909 TAGGTGCAAT
*
40682919 ATATATAAAATAATAGA
1 ATATATAAAATAATAAA
*
40682936 ATATGTAAAATAATAAA
1 ATATATAAAATAATAAA
40682953 ATAT
1 ATAT
40682957 TTACAATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
ATATATAAAATAATAAA
Found at i:40685477 original size:17 final size:16
Alignment explanation
Indices: 40685439--40685469 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
40685429 GAGTATAGTA
40685439 AAATATTTTAAAAAAT
1 AAATATTTTAAAAAAT
40685455 AAATATTTTAAAAAA
1 AAATATTTTAAAAAA
40685470 AGAGATATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATATTTTAAAAAAT
Found at i:40686064 original size:28 final size:28
Alignment explanation
Indices: 40686032--40686090 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
40686022 GGGTCTTTAT
40686032 AAAGGCTTATTTTCGTAA-ATTTTAAAAA
1 AAAGGCTTATTTTCGTAATA-TTTAAAAA
* *
40686060 AAAGGTTTATTTTTGTAATATTTAAAAA
1 AAAGGCTTATTTTCGTAATATTTAAAAA
40686088 AAA
1 AAA
40686091 TGACCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (28 bp):
AAAGGCTTATTTTCGTAATATTTAAAAA
Found at i:40688513 original size:41 final size:40
Alignment explanation
Indices: 40688455--40688652 Score: 216
Period size: 41 Copynumber: 4.8 Consensus size: 40
40688445 GATTTTTAAA
* *
40688455 CCTTTAGCGGCATTTTTATTTGAGCGCCGCTAATGCTCGG
1 CCTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGG
* * *
40688495 ATCTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATCCTATGG
1 -CCTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCT-CGG
* ** *
40688537 CCGTTAGCGGCGTTTTTGCCTAAGCGCCGCTAATGCTCGG
1 CCTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGG
* * * * *
40688577 ATCTTTAGTGGCGTATTTATCTGAGCGCCTCTAATTCTCTGG
1 -CCTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTC-GG
* *
40688619 CCTTTAGCGGCGTTTATATCTAAGCGCCGCTAAT
1 CCTTTAGCGGCGTTTTTATCTGAGCGCCGCTAAT
40688653 AATTACAAAA
Statistics
Matches: 127, Mismatches: 27, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
40 2 0.02
41 121 0.95
42 4 0.03
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.34
Consensus pattern (40 bp):
CCTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGG
Found at i:40688596 original size:82 final size:82
Alignment explanation
Indices: 40688477--40688652 Score: 271
Period size: 82 Copynumber: 2.1 Consensus size: 82
40688467 TTTTTATTTG
*
40688477 AGCGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATCCTATGGCCGTT
1 AGCGCCGCTAATGCTCGGATCTTTAGCGGCGTATTTATCTGAGCGCCGCTAATCCTATGGCCGTT
* *
40688542 AGCGGCGTTTTTGCCTA
66 AGCGGCGTTTATACCTA
* * * * *
40688559 AGCGCCGCTAATGCTCGGATCTTTAGTGGCGTATTTATCTGAGCGCCTCTAATTCTCTGGCCTTT
1 AGCGCCGCTAATGCTCGGATCTTTAGCGGCGTATTTATCTGAGCGCCGCTAATCCTATGGCCGTT
*
40688624 AGCGGCGTTTATATCTA
66 AGCGGCGTTTATACCTA
40688641 AGCGCCGCTAAT
1 AGCGCCGCTAAT
40688653 AATTACAAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 85 1.00
ACGTcount: A:0.16, C:0.26, G:0.25, T:0.32
Consensus pattern (82 bp):
AGCGCCGCTAATGCTCGGATCTTTAGCGGCGTATTTATCTGAGCGCCGCTAATCCTATGGCCGTT
AGCGGCGTTTATACCTA
Found at i:40700485 original size:21 final size:20
Alignment explanation
Indices: 40700459--40700527 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 20
40700449 CAACAACTTA
*
40700459 AAGCAGAGGTGGCAGCGAGGG
1 AAGCAGAGGT-GCAGCGAGAG
*
40700480 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGG-TGCAGCGAGAG
* *
40700501 AAGTAGAGGAAGCAGCGAGAG
1 AAGCAGAGG-TGCAGCGAGAG
40700522 AAGCAG
1 AAGCAG
40700528 CGATAGAAGC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 39 0.98
22 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.43, T:0.04
Consensus pattern (20 bp):
AAGCAGAGGTGCAGCGAGAG
Found at i:40700526 original size:12 final size:12
Alignment explanation
Indices: 40700492--40700539 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
40700482 GCAGAGGCTA
40700492 CAGCGAGAGAAG
1 CAGCGAGAGAAG
*
40700504 TA--GAG-GAAG
1 CAGCGAGAGAAG
40700513 CAGCGAGAGAAG
1 CAGCGAGAGAAG
*
40700525 CAGCGATAGAAG
1 CAGCGAGAGAAG
40700537 CAG
1 CAG
40700540 AGGTTCAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
9 5 0.17
10 3 0.10
11 3 0.10
12 19 0.63
ACGTcount: A:0.42, C:0.15, G:0.40, T:0.04
Consensus pattern (12 bp):
CAGCGAGAGAAG
Found at i:40701009 original size:43 final size:42
Alignment explanation
Indices: 40700962--40701053 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
40700952 ATCAAATAGT
*
40700962 GGCGTTTGTGAAATAAGCGCCGCTAAAGAACACTACTGTTAGC
1 GGCGTTTGTG-AACAAGCGCCGCTAAAGAACACTACTGTTAGC
* * * * *
40701005 GGCGTTTTTGACCAAGCGCCGCTATAGAACATTACTTTTAGC
1 GGCGTTTGTGAACAAGCGCCGCTAAAGAACACTACTGTTAGC
*
40701047 GGTGTTT
1 GGCGTTT
40701054 TCTTCCTAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 33 0.79
43 9 0.21
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (42 bp):
GGCGTTTGTGAACAAGCGCCGCTAAAGAACACTACTGTTAGC
Found at i:40701074 original size:85 final size:84
Alignment explanation
Indices: 40700975--40701269 Score: 371
Period size: 85 Copynumber: 3.5 Consensus size: 84
40700965 GTTTGTGAAA
* * *
40700975 TAAGCGCCGCTAAAGAACACT-A-CTGTTAGCGGCGTTTTTGACCAAGCGCCGCTATAGAACATT
1 TAAGCGCCGCTAAAGAACA-TGATCT-TTAGCGGCGTTTTTTACCAAGCGCCGCTAAAGAACATG
**
40701038 A-CTTTTAGCGGTGTTTTCTTCC
64 ATC-TTTAGCGGCATTTT-TTCC
* * * *
40701060 TAAGCGCCGTTAAAGAACGTGATCTTTAGCGGCATTTTTTCCCAAGCGCCGCTAAAGAACATGAT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACCAAGCGCCGCTAAAGAACATGAT
40701125 CTTTAGCGGCATTTTTTCC
66 CTTTAGCGGCATTTTTTCC
* * *
40701144 CAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCGTAAGCGCCGCTAAAGAACATGA
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTAC-CAAGCGCCGCTAAAGAACATGA
*
40701209 TCTTTAGTGGCATTTATTTCC
65 TCTTTAGCGGCATTT-TTTCC
* **
40701230 TTAGCGCCGCTAAAGAACATGATCTTTAGCGATGTTTTTT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
40701270 TCTGTAAGCG
Statistics
Matches: 185, Mismatches: 20, Indels: 9
0.86 0.09 0.04
Matches are distributed among these distances:
84 42 0.23
85 99 0.54
86 44 0.24
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.32
Consensus pattern (84 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACCAAGCGCCGCTAAAGAACATGAT
CTTTAGCGGCATTTTTTCC
Found at i:40701077 original size:43 final size:42
Alignment explanation
Indices: 40700975--40701288 Score: 357
Period size: 42 Copynumber: 7.4 Consensus size: 42
40700965 GTTTGTGAAA
*
40700975 TAAGCGCCGCTAAAGAACACT-A-CTGTTAGCGGCGTTTTTGACC
1 TAAGCGCCGCTAAAGAACA-TGATCT-TTAGCGGCGTTTTT-TCC
* * *
40701018 -AAGCGCCGCTATAGAACATTA-CTTTTAGCGGTGTTTTCTTCC
1 TAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTT-TTCC
* * *
40701060 TAAGCGCCGTTAAAGAACGTGATCTTTAGCGGCATTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
* *
40701102 CAAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
* *
40701144 CAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCG
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTTCC
* *
40701187 TAAGCGCCGCTAAAGAACATGATCTTTAGTGGCATTTATTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTCC
* ** *
40701230 TTAGCGCCGCTAAAGAACATGATCTTTAGCGATGTTTTTTTCTG
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTTC-C
*
40701274 TAAGCGCCGCAAAAG
1 TAAGCGCCGCTAAAG
40701289 TTAGCGACGT
Statistics
Matches: 236, Mismatches: 26, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
41 1 0.00
42 112 0.47
43 106 0.45
44 17 0.07
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
Found at i:40701268 original size:127 final size:127
Alignment explanation
Indices: 40700976--40701268 Score: 380
Period size: 127 Copynumber: 2.3 Consensus size: 127
40700966 TTTGTGAAAT
** * *
40700976 AAGCGCCGCTAAAGAACACT-A-CTGTTAGCGGCGTTTTTGACCAAGCGCCGCTATAGAACATTA
1 AAGCGCCGCTAAAGAACA-TGATCT-TTAGCGATGTTTTTGACCAAGCGCCGCTAAAGAACATGA
* * *
40701039 CTTTTAGCGGTGTTTTCTTCCTAAGCGCCGTTAAAGAACGTGATCTTTAGCGGCATTTTTTCCC
64 CTTTTAGCGGCGTTTTCTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTCCC
*
40701103 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCAT-TTTTT-CCCAAGCGCCGCTAAAGAACATGA
1 AAGCGCCGCTAAAGAACATGATCTTTAGC-G-ATGTTTTTGACCAAGCGCCGCTAAAGAACATGA
* * *
40701166 -TCTTTAGCGGCGTTTTTTTCGTAAGCGCCGCTAAAGAACATGATCTTTAGTGGCATTTATTTCC
64 CT-TTTAGCGGCGTTTTCTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTT-TTTCC
*
40701230 T
127 C
*
40701231 TAGCGCCGCTAAAGAACATGATCTTTAGCGATGTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGATGTTTTT
40701269 TTCTGTAAGC
Statistics
Matches: 146, Mismatches: 13, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
126 4 0.03
127 101 0.69
128 41 0.28
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (127 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGATGTTTTTGACCAAGCGCCGCTAAAGAACATGACT
TTTAGCGGCGTTTTCTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTCCC
Found at i:40706548 original size:149 final size:149
Alignment explanation
Indices: 40706273--40706570 Score: 524
Period size: 149 Copynumber: 2.0 Consensus size: 149
40706263 AACGGTGAAC
* **
40706273 AATAAATACAAGCTAACTTTGATGGTGAAAATGAAGATGAAAGGCAATATTTAATAGAGCGAGTG
1 AATAAATACAAGCTAACTTTGATGGTGAAAATGAAGATGAAAGGCAACATCCAATAGAGCGAGTG
* * * *
40706338 CAAAATGAGCAACAAGTAGCTGAACTAACAAATTGATCGTCCTGAACGTAACAAGAGGAGACCTC
66 CAAAATGAGCAACAAGTAGCTGAACCAACAAATTGATAGTCCTGAAAGTAACAAGAAGAGACCTC
40706403 CATGGATGGAGAATTTTAT
131 CATGGATGGAGAATTTTAT
40706422 AATAAATACAAGCTAACTTTGATGGTGAAAATGAAGATGAAAGGCAACATCCAATAGAGCGAGTG
1 AATAAATACAAGCTAACTTTGATGGTGAAAATGAAGATGAAAGGCAACATCCAATAGAGCGAGTG
*
40706487 CAAAATGAGCAACAAGTAGCTGAACCAACAAATTGATAGTCCTTAAAGTAACAAGAAGAGACCTC
66 CAAAATGAGCAACAAGTAGCTGAACCAACAAATTGATAGTCCTGAAAGTAACAAGAAGAGACCTC
40706552 CATGGATGGAGAATTTTAT
131 CATGGATGGAGAATTTTAT
40706571 GGTAGAGGGA
Statistics
Matches: 141, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
149 141 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.22
Consensus pattern (149 bp):
AATAAATACAAGCTAACTTTGATGGTGAAAATGAAGATGAAAGGCAACATCCAATAGAGCGAGTG
CAAAATGAGCAACAAGTAGCTGAACCAACAAATTGATAGTCCTGAAAGTAACAAGAAGAGACCTC
CATGGATGGAGAATTTTAT
Found at i:40710715 original size:220 final size:221
Alignment explanation
Indices: 40710327--40710764 Score: 860
Period size: 220 Copynumber: 2.0 Consensus size: 221
40710317 GGGAAGTGAC
40710327 TTAGTCATCATATCTGTAGGATTTTCATGAGTACTAAGTTTGCTCACAACAATATCACCACGAGC
1 TTAGTCATCATATCTGTAGGATTTTCATGAGTACTAAGTTTGCTCACAACAATATCACCACGAGC
40710392 AATAATATCACGAACAAAATGATAACAAACATCAATGTGTTTTGTTCTCTCATGAAACATTTGAT
66 AATAATATCACGAACAAAATGATAACAAACATCAATGTGTTTTGTTCTCTCATGAAACATTTGAT
40710457 CTTTTGTAAGAAAGATGACACTTTCACTGTCACAAAATACTGTACTGATTTGAATGTCTTTATTG
131 CTTTTGTAAGAAAGATGACACTTTCACTGTCACAAAATACTGTACTGATTTGAATGTCTTTATTG
40710522 AGTTCACTAAAGAGTCCCTTCAAGTT
196 AGTTCACTAAAGAGTCCCTTCAAGTT
40710548 TTAGT-ATCATATCTGTAGGATTTTCATGAGTACTAAGTTTGCTCACAACAATATCACCACGAGC
1 TTAGTCATCATATCTGTAGGATTTTCATGAGTACTAAGTTTGCTCACAACAATATCACCACGAGC
*
40710612 AATAATATCACGAACAAAATGATAACAAACGTCAATGTGTTTTGTTCTCTCATGAAACATTTGAT
66 AATAATATCACGAACAAAATGATAACAAACATCAATGTGTTTTGTTCTCTCATGAAACATTTGAT
40710677 CTTTTGTAAGAAAGATGACACTTTCACTGTCACAAAATACTGTACTGATTTGAATGTCTTTATTG
131 CTTTTGTAAGAAAGATGACACTTTCACTGTCACAAAATACTGTACTGATTTGAATGTCTTTATTG
40710742 AGTTCACTAAAGAGTCCCTTCAA
196 AGTTCACTAAAGAGTCCCTTCAA
40710765 CCAAATGGAT
Statistics
Matches: 216, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
220 211 0.98
221 5 0.02
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (221 bp):
TTAGTCATCATATCTGTAGGATTTTCATGAGTACTAAGTTTGCTCACAACAATATCACCACGAGC
AATAATATCACGAACAAAATGATAACAAACATCAATGTGTTTTGTTCTCTCATGAAACATTTGAT
CTTTTGTAAGAAAGATGACACTTTCACTGTCACAAAATACTGTACTGATTTGAATGTCTTTATTG
AGTTCACTAAAGAGTCCCTTCAAGTT
Found at i:40721338 original size:18 final size:18
Alignment explanation
Indices: 40721315--40721407 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
40721305 CCCAACTACT
*
40721315 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
40721333 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
40721351 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
*
40721369 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
40721387 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
40721405 GTA
1 GTA
40721408 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:40721367 original size:36 final size:36
Alignment explanation
Indices: 40721315--40721407 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
40721305 CCCAACTACT
*
40721315 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
40721351 GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
40721387 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
40721408 AACGGTCGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:40723817 original size:17 final size:18
Alignment explanation
Indices: 40723788--40723824 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
40723778 TTTTGGTACA
40723788 TAACAAAATTTATA-TTT
1 TAACAAAATTTATAGTTT
40723805 TAACACAAA-TTATAGTTT
1 TAACA-AAATTTATAGTTT
40723823 TA
1 TA
40723825 TTAACTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (18 bp):
TAACAAAATTTATAGTTT
Found at i:40725147 original size:31 final size:31
Alignment explanation
Indices: 40725073--40725147 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
40725063 TGTTTTGGCC
* *
40725073 CAATTCAATCCTTAATGTTATCAAGCATTCC
1 CAATTCAATCCTTAACGTTATCAAGCATTCA
* * *
40725104 CAATTTAGTCCTTAACGTTATC-AGTCGTTCA
1 CAATTCAATCCTTAACGTTATCAAG-CATTCA
*
40725135 CGATTCAATCCTT
1 CAATTCAATCCTT
40725148 TGGGCATTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 2 0.06
31 33 0.94
ACGTcount: A:0.28, C:0.25, G:0.09, T:0.37
Consensus pattern (31 bp):
CAATTCAATCCTTAACGTTATCAAGCATTCA
Found at i:40727821 original size:46 final size:46
Alignment explanation
Indices: 40727754--40727846 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
40727744 TGTGTTTGAA
40727754 TGATGTTTTAAATCTCTTGAATGTGTGCCCAAATGGTATGGATGGT
1 TGATGTTTTAAATCTCTTGAATGTGTGCCCAAATGGTATGGATGGT
40727800 TGATGTTTTAAATCTCTTGAATGTGTGCCCAAATGGTATGGATGGT
1 TGATGTTTTAAATCTCTTGAATGTGTGCCCAAATGGTATGGATGGT
40727846 T
1 T
40727847 AGGTATGGCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.40
Consensus pattern (46 bp):
TGATGTTTTAAATCTCTTGAATGTGTGCCCAAATGGTATGGATGGT
Found at i:40728871 original size:22 final size:22
Alignment explanation
Indices: 40728843--40728885 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
40728833 GAGGGTAGCA
* *
40728843 TTCTGCATTTGTATTTGATATG
1 TTCTGCATCTGTATCTGATATG
40728865 TTCTGCATCTGTATCTGATAT
1 TTCTGCATCTGTATCTGATAT
40728886 ACTCCGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (22 bp):
TTCTGCATCTGTATCTGATATG
Found at i:40737457 original size:4 final size:4
Alignment explanation
Indices: 40737448--40737755 Score: 616
Period size: 4 Copynumber: 77.0 Consensus size: 4
40737438 AAGATACATA
40737448 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
40737496 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
40737544 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
40737592 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
40737640 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
40737688 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
40737736 TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG
40737756 NNNNNNNNNN
Statistics
Matches: 304, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 304 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:40740513 original size:7 final size:7
Alignment explanation
Indices: 40740501--40740535 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
40740491 AACTTTTCAA
40740501 CATTTTT
1 CATTTTT
40740508 -ATTTTT
1 CATTTTT
40740514 CA-TTTT
1 CATTTTT
40740520 CATTTTT
1 CATTTTT
40740527 CATTTTT
1 CATTTTT
40740534 CA
1 CA
40740536 CACACTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 12 0.46
7 14 0.54
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:40740519 original size:13 final size:13
Alignment explanation
Indices: 40740501--40740533 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
40740491 AACTTTTCAA
40740501 CATTTTTATTTTT
1 CATTTTTATTTTT
*
40740514 CATTTTCATTTTT
1 CATTTTTATTTTT
40740527 CATTTTT
1 CATTTTT
40740534 CACACACTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (13 bp):
CATTTTTATTTTT
Found at i:40741426 original size:15 final size:15
Alignment explanation
Indices: 40741393--40741425 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
40741383 TGGCCTCTCC
40741393 TTTT-CTTCTTCTTT
1 TTTTCCTTCTTCTTT
40741407 TTTTCCTTCTCTCTTT
1 TTTTCCTTCT-TCTTT
40741423 TTT
1 TTT
40741426 CATTTTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 5 0.29
16 8 0.47
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCCTTCTTCTTT
Found at i:40741489 original size:6 final size:6
Alignment explanation
Indices: 40741422--40741508 Score: 70
Period size: 6 Copynumber: 14.7 Consensus size: 6
40741412 CTTCTCTCTT
* * * * **
40741422 TTTTCA TTTTCA TTTTCA TTTTGA CTTTGA TTTTGA TTTTTC TTTTGA
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA
* * *
40741470 TTTT-C TTCTT-T TTTTGT TTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TT-TTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
40741509 TTTTTGGATT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
5 4 0.06
6 65 0.94
ACGTcount: A:0.11, C:0.08, G:0.09, T:0.71
Consensus pattern (6 bp):
TTTTGA
Found at i:40746313 original size:3 final size:3
Alignment explanation
Indices: 40746305--40746341 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
40746295 CAAATAAAAC
*
40746305 TAA TAA TAA TAA TTAA TAA TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
40746342 ATGCTAATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:40746350 original size:22 final size:22
Alignment explanation
Indices: 40746296--40746343 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
40746286 ATAAAATGGC
40746296 AAATAA-AACTAATAATAATAAT
1 AAATAATAA-TAATAATAATAAT
* *
40746318 TAATAATAATAATAATGATAAT
1 AAATAATAATAATAATAATAAT
40746340 AAAT
1 AAAT
40746344 GCTAATACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATAATAATAATAATAATAAT
Found at i:40747157 original size:16 final size:15
Alignment explanation
Indices: 40747125--40747162 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
40747115 TGAAACAAAC
40747125 AAAAAAGAAAAAGAA
1 AAAAAAGAAAAAGAA
40747140 AAATAAAGAAAATA-AA
1 AAA-AAAGAAAA-AGAA
40747156 AAAAAAG
1 AAAAAAG
40747163 CCAGAATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 13 0.62
17 1 0.05
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (15 bp):
AAAAAAGAAAAAGAA
Found at i:40748286 original size:50 final size:50
Alignment explanation
Indices: 40748147--40748287 Score: 149
Period size: 50 Copynumber: 2.8 Consensus size: 50
40748137 CAAAGTCAGG
* * * * *
40748147 GAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTG-ACCGTCTGG
1 GAAGCAAGATTCGCTGTTGTAGCTTCAATCTATTCCACTGCAACGTATGA
* * * * ** *
40748196 GGAGTAAGATTCGCTGTTGTAGCTTCAATATTTTTAACTGCAATGTATGA
1 GAAGCAAGATTCGCTGTTGTAGCTTCAATCTATTCCACTGCAACGTATGA
**
40748246 GAAGCAAGATTCATTGTTGTAGCTTCAATCTATTCCACTGCA
1 GAAGCAAGATTCGCTGTTGTAGCTTCAATCTATTCCACTGCA
40748288 TCTCTAGGAA
Statistics
Matches: 72, Mismatches: 19, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
49 33 0.46
50 39 0.54
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (50 bp):
GAAGCAAGATTCGCTGTTGTAGCTTCAATCTATTCCACTGCAACGTATGA
Found at i:40748465 original size:44 final size:44
Alignment explanation
Indices: 40748414--40748739 Score: 134
Period size: 44 Copynumber: 7.5 Consensus size: 44
40748404 CACTCTACTG
* *
40748414 CAACTTCAGAGAGATAAGATCTATT-ATTTTAATCCGCTCCACTA
1 CAACTTCAGAGAGATAAGAT-TATTGACTTCAATCCGCTCCACTA
* * * * * *
40748458 CAACTTCAGGGAGATAGGATTATTGGCTTCAATCTGTTCCACTG
1 CAACTTCAGAGAGATAAGATTATTGACTTCAATCCGCTCCACTA
* * * * *
40748502 CAACCTCAGAGAGATAAGA-T-TTGCTTCTTCGATCTG-TCCCACTG
1 CAACTTCAGAGAGATAAGATTATTG--ACTTCAATCCGCT-CCACTA
* * ** * * * *
40748546 CAACTTCAGGGGGATAAGACCTGCTT-AC-TCAGTCTGCTCCGCTG
1 CAACTTCAGAGAGATAAGA--TTATTGACTTCAATCCGCTCCACTA
* ** * * ** *
40748590 CAACCTT-AGGGAGATAAGA--CCTGA-TGCGATCAACTCTACTA
1 CAA-CTTCAGAGAGATAAGATTATTGACTTCAATCCGCTCCACTA
* *
40748631 TAACTTCAGAGAGATAAGATTTATT-ACTTTAATCCGCTCCACTA
1 CAACTTCAGAGAGATAAGA-TTATTGACTTCAATCCGCTCCACTA
* * * * ** *
40748675 CAACTTCAGGGAGATAGGATTATCGGCTTCAATCTACTCCACTG
1 CAACTTCAGAGAGATAAGATTATTGACTTCAATCCGCTCCACTA
* * *
40748719 TAACCTCAGGGAGATAAGATT
1 CAACTTCAGAGAGATAAGATT
40748740 TGCCATCTTC
Statistics
Matches: 211, Mismatches: 53, Indels: 36
0.70 0.18 0.12
Matches are distributed among these distances:
40 5 0.02
41 22 0.10
42 3 0.01
43 11 0.05
44 163 0.77
45 5 0.02
48 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (44 bp):
CAACTTCAGAGAGATAAGATTATTGACTTCAATCCGCTCCACTA
Found at i:40748705 original size:217 final size:218
Alignment explanation
Indices: 40748323--40748913 Score: 959
Period size: 217 Copynumber: 2.7 Consensus size: 218
40748313 TTAGTCTGCT
* * * * * * *
40748323 CCACTGCAACTTTAGGGGAATAAGACTTGATTTCTCAGTCTGCTCCGCTGTAAACTCAGGAAGAT
1 CCACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCGCTGCAACCTCAGGAAGAT
* * *
40748388 AAGACTTGGTGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTATTTTAATCCGCTC
66 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
* **
40748453 CACTACAACTTCAGGGAGATAGGATTATTGGCTTCAATCTGTTCCACTGCAACCTCAGAGAGATA
131 CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTACTCCACTGCAACCTCAGAGAGATA
*
40748518 AGATTTG-CTTCTTCGATCTGTC
196 AGATTTGCCATCTTCGATCTGTC
* *
40748540 CCACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCGCTGCAACCTTAGGGAGAT
1 CCACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCGCTGCAACCTCAGGAAGAT
* ** *
40748605 AAGACCTGATGCGATCAACTCTACTATAACTTCAGAGAGATAAGATTTATTACTTTAATCCGCTC
66 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
* *
40748670 CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTACTCCACTGTAACCTCAGGGAGATA
131 CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTACTCCACTGCAACCTCAGAGAGATA
40748735 AGATTTGCCATCTTCGATCTGTC
196 AGATTTGCCATCTTCGATCTGTC
*
40748758 CCACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCGCTGCAACCTCAAGAAGAT
1 CCACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCGCTGCAACCTCAGGAAGAT
40748823 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
66 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
*
40748888 CACTACAACCTCAGGGAGATAGGATT
131 CACTACAACTTCAGGGAGATAGGATT
40748914 TGTTGCTTAA
Statistics
Matches: 343, Mismatches: 30, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
217 181 0.53
218 162 0.47
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.27
Consensus pattern (218 bp):
CCACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCGCTGCAACCTCAGGAAGAT
AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTACTCCACTGCAACCTCAGAGAGATA
AGATTTGCCATCTTCGATCTGTC
Found at i:40749052 original size:129 final size:129
Alignment explanation
Indices: 40748899--40749257 Score: 558
Period size: 129 Copynumber: 2.8 Consensus size: 129
40748889 ACTACAACCT
* * * *
40748899 CAGGGAGATAGGATTTGTTG-CTTAAATATGCTTCCTTACACTTGAAGATAAGATTCATCGTCTT
1 CAGGGATATAGGACTTG-TGACTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTT
* * *
40748963 CGATCTGCTCCACTACTGCTTAGGGAGACAAGGTCTGTAATTTTCTAACCTATTCCACTGCTGAC
65 CGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
* * *
40749028 TAGGGATATAGGACTTGTGACTTAAATCTGCTTCCTTACAGTTGAAGATAAGATTCGCCGTCTTC
1 CAGGGATATAGGACTTGTGACTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTC
* * * *
40749093 GATCTGCTCCGCTACTGCTTAGGGAGACAAGATATGTAATTTCCCAACCTATTTCGCTGCTGAC
66 GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
*
40749157 CAGGGATATAGGACTTGTGACATAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTC
1 CAGGGATATAGGACTTGTGACTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTC
*
40749222 GATCTGCTCCACTATTGCTTAGGGAGACAAGATCTG
66 GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTG
40749258 CTATATTCAC
Statistics
Matches: 208, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
128 2 0.01
129 206 0.99
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (129 bp):
CAGGGATATAGGACTTGTGACTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTC
GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
Found at i:40750536 original size:7 final size:7
Alignment explanation
Indices: 40750524--40750558 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
40750514 AACTTTTCAA
40750524 CATTTTT
1 CATTTTT
40750531 -ATTTTT
1 CATTTTT
40750537 CA-TTTT
1 CATTTTT
40750543 CATTTTT
1 CATTTTT
40750550 CATTTTT
1 CATTTTT
40750557 CA
1 CA
40750559 CACACTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 12 0.46
7 14 0.54
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:40750542 original size:13 final size:13
Alignment explanation
Indices: 40750524--40750556 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
40750514 AACTTTTCAA
40750524 CATTTTTATTTTT
1 CATTTTTATTTTT
*
40750537 CATTTTCATTTTT
1 CATTTTTATTTTT
40750550 CATTTTT
1 CATTTTT
40750557 CACACACTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (13 bp):
CATTTTTATTTTT
Found at i:40751449 original size:15 final size:15
Alignment explanation
Indices: 40751416--40751448 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
40751406 TGGCCTCTCC
40751416 TTTT-CTTCTTCTTT
1 TTTTCCTTCTTCTTT
40751430 TTTTCCTTCTCTCTTT
1 TTTTCCTTCT-TCTTT
40751446 TTT
1 TTT
40751449 CATTTTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 5 0.29
16 8 0.47
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCCTTCTTCTTT
Found at i:40751512 original size:6 final size:6
Alignment explanation
Indices: 40751445--40751531 Score: 70
Period size: 6 Copynumber: 14.7 Consensus size: 6
40751435 CTTCTCTCTT
* * * * **
40751445 TTTTCA TTTTCA TTTTCA TTTTGA CTTTGA TTTTGA TTTTTC TTTTGA
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA
* * *
40751493 TTTT-C TTCTT-T TTTTGT TTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TT-TTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
40751532 TTTTTGGATT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
5 4 0.06
6 65 0.94
ACGTcount: A:0.11, C:0.08, G:0.09, T:0.71
Consensus pattern (6 bp):
TTTTGA
Done.