Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 37 of 163
Found at i:9801051 original size:35 final size:35
Alignment explanation
Indices: 9801012--9801108 Score: 124
Period size: 35 Copynumber: 2.7 Consensus size: 35
9801002 AATCGATTTT
9801012 AAATTTATTTTAAATTTAAATTTATTTTTAAATTA
1 AAATTTATTTTAAATTTAAATTTATTTTTAAATTA
* * * *
9801047 AAATTTGTTTTAAAATTTAAATTTA-ATTTAAGTTC
1 AAATTTATTTT-AAATTTAAATTTATTTTTAAATTA
*
9801082 AAATTTATTTTTAAATTTAAAGTTATT
1 AAATTTA-TTTTAAATTTAAATTTATT
9801109 GTAAATTTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
35 35 0.67
36 17 0.33
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (35 bp):
AAATTTATTTTAAATTTAAATTTATTTTTAAATTA
Found at i:9801822 original size:3 final size:3
Alignment explanation
Indices: 9801814--9801891 Score: 84
Period size: 3 Copynumber: 25.0 Consensus size: 3
9801804 AATAGGGAAC
* * *
9801814 TAA TAA TAA TAA TTAA TAA TAA TAAA TAA TAT TAA TAA CAA CAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
**
9801861 TAA TAA TAA TTT TAA TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
9801892 AATCTGAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
3 55 0.86
4 9 0.14
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:9801832 original size:13 final size:12
Alignment explanation
Indices: 9801814--9801891 Score: 84
Period size: 13 Copynumber: 6.2 Consensus size: 12
9801804 AATAGGGAAC
9801814 TAATAATAATAA
1 TAATAATAATAA
9801826 TTAATAATAATAAA
1 -TAATAATAAT-AA
*
9801840 TAATATTAATAA
1 TAATAATAATAA
* *
9801852 CAACAATAATAA
1 TAATAATAATAA
**
9801864 TAATAATTTTAA
1 TAATAATAATAA
9801876 TAATAAATAATAA
1 TAAT-AATAATAA
9801889 TAA
1 TAA
9801892 AATCTGAAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
12 23 0.43
13 28 0.53
14 2 0.04
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.35
Consensus pattern (12 bp):
TAATAATAATAA
Found at i:9802948 original size:29 final size:29
Alignment explanation
Indices: 9802915--9803121 Score: 135
Period size: 29 Copynumber: 7.1 Consensus size: 29
9802905 CAAAAGTTAT
* *
9802915 ATTTTTACCCTTGAACTTTCTAAAATTCC
1 ATTTTTACCCTCGAACTTTCAAAAATTCC
** *
9802944 ATTTTTGACCC-CGAGTTTTTCAAAAATTACG
1 ATTTTT-ACCCTCGA-ACTTTCAAAAATT-CC
*
9802975 A--TTTACCC-CTAAACTTTTC-AAAATTCC
1 ATTTTTACCCTC-GAAC-TTTCAAAAATTCC
* **
9803002 ATTTATGA-CCTCGATTTTTTCAAAAATTCC
1 ATTT-TTACCCTCGA-ACTTTCAAAAATTCC
* * *
9803032 ATTTTTACCCCCAAACTTTCTAAAATTCC
1 ATTTTTACCCTCGAACTTTCAAAAATTCC
* *
9803061 A-TTTTAACCTCG-ATTTTCCAAAAATTACC
1 ATTTTTACCCTCGAACTTT-CAAAAATT-CC
*
9803090 A-TTTTACCCTTGAACTTTCAAAAATTCC
1 ATTTTTACCCTCGAACTTTCAAAAATTCC
9803118 ATTT
1 ATTT
9803122 ATGACCTTGA
Statistics
Matches: 135, Mismatches: 27, Indels: 32
0.70 0.14 0.16
Matches are distributed among these distances:
27 6 0.04
28 29 0.21
29 61 0.45
30 37 0.27
31 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (29 bp):
ATTTTTACCCTCGAACTTTCAAAAATTCC
Found at i:9803011 original size:58 final size:58
Alignment explanation
Indices: 9802917--9803156 Score: 281
Period size: 58 Copynumber: 4.1 Consensus size: 58
9802907 AAAGTTATAT
* * * * *
9802917 TTTTACCCTTGAACTTTCTAAAATTCCATTTTTGACCCCGAGTTTTTCAAAAATTACGA
1 TTTTACCCCTAAACTTTCTAAAATTCCATTTATGACCTCGA-TTTTTCAAAAATTACCA
9802976 -TTTACCCCTAAACTTT-TCAAAATTCCATTTATGACCTCGATTTTTTCAAAAATT-CCA
1 TTTTACCCCTAAACTTTCT-AAAATTCCATTTATGACCTCGA-TTTTTCAAAAATTACCA
* * *
9803033 TTTTTACCCCCAAACTTTCTAAAATTCCATTT-TAACCTCGATTTTCCAAAAATTACCA
1 -TTTTACCCCTAAACTTTCTAAAATTCCATTTATGACCTCGATTTTTCAAAAATTACCA
* * * * * *
9803091 TTTTACCCTTGAACTTTCAAAAATTCCATTTATGACCTTGATTCTTCCAAAAAGTACCA
1 TTTTACCCCTAAACTTTCTAAAATTCCATTTATGACCTCGATT-TTTCAAAAATTACCA
9803150 TTTTACC
1 TTTTACC
9803157 ACCGGATGTC
Statistics
Matches: 158, Mismatches: 16, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
57 42 0.27
58 67 0.42
59 48 0.30
60 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.40
Consensus pattern (58 bp):
TTTTACCCCTAAACTTTCTAAAATTCCATTTATGACCTCGATTTTTCAAAAATTACCA
Found at i:9803142 original size:29 final size:28
Alignment explanation
Indices: 9802993--9803142 Score: 90
Period size: 29 Copynumber: 5.2 Consensus size: 28
9802983 CTAAACTTTT
*
9802993 CAAAATTCCATTTATGACCTCGATTTTTTC
1 CAAAATTCCATTT-TGACCTCGA-TTCTTC
* * * * **
9803023 AAAAATTCCATTTTTACCCCCAAACTTTC
1 CAAAATTCCATTTTGACCTCGATTC-TTC
* *
9803052 TAAAATTCCATTTTAACCTCGATT-TTC
1 CAAAATTCCATTTTGACCTCGATTCTTC
* *
9803079 CAAAAATTACCATTTT-ACCCTTGA-ACTTTC
1 C-AAAATT-CCATTTTGA-CCTCGATTC-TTC
* *
9803109 AAAAATTCCATTTATGACCTTGATTCTTC
1 CAAAATTCCATTT-TGACCTCGATTCTTC
9803138 CAAAA
1 CAAAA
9803143 AGTACCATTT
Statistics
Matches: 92, Mismatches: 19, Indels: 19
0.71 0.15 0.15
Matches are distributed among these distances:
27 3 0.03
28 13 0.14
29 59 0.64
30 17 0.18
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.39
Consensus pattern (28 bp):
CAAAATTCCATTTTGACCTCGATTCTTC
Found at i:9803142 original size:116 final size:118
Alignment explanation
Indices: 9802928--9803153 Score: 316
Period size: 116 Copynumber: 1.9 Consensus size: 118
9802918 TTTACCCTTG
* * *
9802928 AACTTTCTAAAATTCCATTTTTGACCCCGAGTTTTTCAAAAATTACGATTTACCCCTAAACTTTT
1 AACTTTCTAAAATTCCATTTTTAACCCCGAGTTTTCCAAAAATTACCATTTACCCCTAAACTTTT
* * *
9802993 CAAAATTCCATTTATGACCTCGATTTTTTCAAAAA-TTCCATTTTTACCCCCA
66 CAAAATTCCATTTATGACCTCGATTCTTCCAAAAAGTACCATTTTTACCCCCA
* * *
9803045 AACTTTCTAAAATTCCA-TTTTAACCTCGA-TTTTCCAAAAATTACCATTTTACCCTTGAAC-TT
1 AACTTTCTAAAATTCCATTTTTAACCCCGAGTTTTCCAAAAATTACCA-TTTACCCCTAAACTTT
*
9803107 TCAAAAATTCCATTTATGACCTTGATTCTTCCAAAAAGTACCATTTT
65 TC-AAAATTCCATTTATGACCTCGATTCTTCCAAAAAGTACCATTTT
9803154 ACCACCGGAT
Statistics
Matches: 96, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
115 19 0.20
116 52 0.54
117 25 0.26
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (118 bp):
AACTTTCTAAAATTCCATTTTTAACCCCGAGTTTTCCAAAAATTACCATTTACCCCTAAACTTTT
CAAAATTCCATTTATGACCTCGATTCTTCCAAAAAGTACCATTTTTACCCCCA
Found at i:9803249 original size:28 final size:28
Alignment explanation
Indices: 9803197--9803258 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
9803187 CTCAATTTCC
9803197 CCAAAATTACCATTTTGCCCCCGAGTGA-
1 CCAAAATTACCATTTTGCCCCCGAGT-AT
* *
9803225 CCAAAATTACCATTTTGCTCTCGAGTAT
1 CCAAAATTACCATTTTGCCCCCGAGTAT
9803253 CCAAAA
1 CCAAAA
9803259 ATCACATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 1 0.03
28 30 0.97
ACGTcount: A:0.32, C:0.29, G:0.11, T:0.27
Consensus pattern (28 bp):
CCAAAATTACCATTTTGCCCCCGAGTAT
Found at i:9810689 original size:6 final size:6
Alignment explanation
Indices: 9810678--9810756 Score: 58
Period size: 6 Copynumber: 13.7 Consensus size: 6
9810668 AGCCCAACAG
* * * *
9810678 AATTTA AATTT- ATTTTA AAATTA AATTTA CA-TAA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * *
9810723 -ATTATA AATTGA AGTTTA AATTTA AAATTA AATT
1 AATT-TA AATTTA AATTTA AATTTA AATTTA AATT
9810757 AATGTTCAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
4 3 0.06
5 8 0.15
6 40 0.74
7 3 0.06
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (6 bp):
AATTTA
Found at i:9810703 original size:17 final size:17
Alignment explanation
Indices: 9810681--9810756 Score: 68
Period size: 17 Copynumber: 4.4 Consensus size: 17
9810671 CCAACAGAAT
*
9810681 TTAAATTTATTTTAAAA
1 TTAAATTTATTATAAAA
*
9810698 TTAAATTTA-CATAAAA
1 TTAAATTTATTATAAAA
9810714 TTTAAATTTATTAT-AAA
1 -TTAAATTTATTATAAAA
*
9810731 TTGAAGTTTAAATT-TAAAA
1 TT-AAATTT--ATTATAAAA
9810750 TTAAATT
1 TTAAATT
9810757 AATGTTCAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
16 7 0.15
17 26 0.54
18 7 0.15
19 8 0.17
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (17 bp):
TTAAATTTATTATAAAA
Found at i:9811459 original size:28 final size:28
Alignment explanation
Indices: 9811424--9811483 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
9811414 ATAATGCTTA
*
9811424 ATAA-TAATACT-GTTATTAATAATAACC
1 ATAATTAATACTAATTA-TAATAATAACC
* *
9811451 ATAATTAATATTAATTATAATAATAACT
1 ATAATTAATACTAATTATAATAATAACC
9811479 ATAAT
1 ATAAT
9811484 ATTTAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 4 0.14
28 21 0.75
29 3 0.11
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.40
Consensus pattern (28 bp):
ATAATTAATACTAATTATAATAATAACC
Found at i:9811464 original size:22 final size:24
Alignment explanation
Indices: 9811437--9811494 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 24
9811427 ATAATACTGT
*
9811437 TATTAATAATAACCATAA-T-TAA
1 TATTAATAATAACAATAACTATAA
* *
9811459 TATTAATTATAATAATAACTATAA
1 TATTAATAATAACAATAACTATAA
9811483 TATTTAATAATA
1 TA-TTAATAATA
9811495 TTTAATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 15 0.52
23 1 0.03
24 5 0.17
25 8 0.28
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.41
Consensus pattern (24 bp):
TATTAATAATAACAATAACTATAA
Found at i:9811494 original size:10 final size:10
Alignment explanation
Indices: 9811479--9811504 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
9811469 AATAATAACT
9811479 ATAATATTTA
1 ATAATATTTA
9811489 ATAATATTTA
1 ATAATATTTA
9811499 ATAATA
1 ATAATA
9811505 ANNNNNNNNN
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
ATAATATTTA
Found at i:9817286 original size:17 final size:18
Alignment explanation
Indices: 9817264--9817300 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
9817254 ATTCTTTTGA
9817264 TGAGATTGATTTGT-AAT
1 TGAGATTGATTTGTGAAT
*
9817281 TGAGATTGCTTTGTGAAT
1 TGAGATTGATTTGTGAAT
9817299 TG
1 TG
9817301 GTTCAAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.24, C:0.03, G:0.27, T:0.46
Consensus pattern (18 bp):
TGAGATTGATTTGTGAAT
Found at i:9836387 original size:55 final size:55
Alignment explanation
Indices: 9836314--9836455 Score: 187
Period size: 55 Copynumber: 2.6 Consensus size: 55
9836304 ATTAAATGTG
** *
9836314 CAACATAACAATCGATTTAAACATATAAACAATCAATTCAAAATAAATAATATTC
1 CAACATAACAATAAATTTAAACATATAAACAATCAATTCAAAATAAACAATATTC
* * * *
9836369 CAACATAACAATAAATTTAAATATATATACAATCAATTCAAAATAAACAGTATTT
1 CAACATAACAATAAATTTAAACATATAAACAATCAATTCAAAATAAACAATATTC
* *
9836424 C-ACTATAACAATAATTTTAAGCATATAAACAA
1 CAAC-ATAACAATAAATTTAAACATATAAACAA
9836456 AACAAAATGT
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
54 2 0.03
55 73 0.97
ACGTcount: A:0.54, C:0.15, G:0.02, T:0.29
Consensus pattern (55 bp):
CAACATAACAATAAATTTAAACATATAAACAATCAATTCAAAATAAACAATATTC
Found at i:9838472 original size:23 final size:23
Alignment explanation
Indices: 9838421--9838477 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
9838411 CGTCCATCCT
* *
9838421 TGCTGACTGGAGCTTTTAGAAAC
1 TGCTGACTGGACCTTCTAGAAAC
* * *
9838444 TACTGATTGGACCTTCTAGAAGC
1 TGCTGACTGGACCTTCTAGAAAC
9838467 TGCTGACTGGA
1 TGCTGACTGGA
9838478 TGCCACATCA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (23 bp):
TGCTGACTGGACCTTCTAGAAAC
Found at i:9838796 original size:20 final size:20
Alignment explanation
Indices: 9838773--9838811 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9838763 AAAATAAATA
9838773 TAAATTAAAAATT-TAAAAAG
1 TAAA-TAAAAATTATAAAAAG
*
9838793 TAAATATAAATTATAAAAA
1 TAAATAAAAATTATAAAAA
9838812 TTTAAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (20 bp):
TAAATAAAAATTATAAAAAG
Found at i:9838797 original size:26 final size:27
Alignment explanation
Indices: 9838762--9838830 Score: 106
Period size: 28 Copynumber: 2.6 Consensus size: 27
9838752 TTGATGAGAA
9838762 AAAAATAAATATAAA-T-TAAAAATTT
1 AAAAATAAATATAAATTATAAAAATTT
9838787 AAAAAGTAAATATAAATTATAAAAATTT
1 AAAAA-TAAATATAAATTATAAAAATTT
9838815 AAAACATAAATATAAA
1 AAAA-ATAAATATAAA
9838831 AATATATTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
25 5 0.12
26 10 0.25
27 1 0.03
28 23 0.57
29 1 0.03
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (27 bp):
AAAAATAAATATAAATTATAAAAATTT
Found at i:9838982 original size:19 final size:19
Alignment explanation
Indices: 9838958--9838996 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
9838948 AGTTAATAAT
*
9838958 AAGTTAATTATAAAATTCA
1 AAGTTAATGATAAAATTCA
*
9838977 AAGTTAATGGTAAAATTCA
1 AAGTTAATGATAAAATTCA
9838996 A
1 A
9838997 TTAAATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.33
Consensus pattern (19 bp):
AAGTTAATGATAAAATTCA
Found at i:9840944 original size:19 final size:19
Alignment explanation
Indices: 9840904--9840946 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
9840894 GATTGATGAG
*
9840904 AAAAAGTAAATATAAGTTAT
1 AAAAAGTAAATATAAG-AAT
9840924 AAAAAGTTAAATATAA-AAT
1 AAAAAG-TAAATATAAGAAT
9840943 AAAA
1 AAAA
9840947 TTTTAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 6 0.29
21 9 0.43
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (19 bp):
AAAAAGTAAATATAAGAAT
Found at i:9846585 original size:8 final size:8
Alignment explanation
Indices: 9846572--9846596 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
9846562 CACAACTGAG
9846572 TCATACTA
1 TCATACTA
9846580 TCATACTA
1 TCATACTA
9846588 TCATACTA
1 TCATACTA
9846596 T
1 T
9846597 GTTTTCTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (8 bp):
TCATACTA
Found at i:9856068 original size:17 final size:17
Alignment explanation
Indices: 9856046--9856084 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
9856036 AGGTGGAGAA
* *
9856046 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
9856063 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
9856080 CTTGT
1 CTTGT
9856085 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:9856557 original size:148 final size:148
Alignment explanation
Indices: 9856289--9856570 Score: 492
Period size: 148 Copynumber: 1.9 Consensus size: 148
9856279 TTGATTCAAT
* * *
9856289 TTTTCGACATTAGTGAATCTTCTTCTCCTCTGCCCGTGGTTTTTTCCCGAAAGGGTTTCCACGTA
1 TTTTCGACATTAGTAAATCCTCTTCTCCTCTGCCCGTGATTTTTTCCCGAAAGGGTTTCCACGTA
*
9856354 AAATCTGTGTGTTCTTTCTTTTCGTTTTCTTTGCGATATTTATTCATTATCGTCATTTAAATCTT
66 AAATCTGTGTGTTCTTTCTTTTCGTTTTCCTTGCGATATTTATTCATTATCGTCATTTAAATCTT
9856419 ATCAAATATAGTATTCCA
131 ATCAAATATAGTATTCCA
* *
9856437 TTTTCGACATTAGTAAATCCTCTTCTCCTCTGCCTGTGATTTTTTCCTGAAAGGGTTTCCACGTA
1 TTTTCGACATTAGTAAATCCTCTTCTCCTCTGCCCGTGATTTTTTCCCGAAAGGGTTTCCACGTA
* *
9856502 AAATCTGTGTGTTTTTTCTTTTCGTTTTCCTTGCGATATTTATTCATTGTCGTCATTTAAATCTT
66 AAATCTGTGTGTTCTTTCTTTTCGTTTTCCTTGCGATATTTATTCATTATCGTCATTTAAATCTT
9856567 ATCA
131 ATCA
9856571 GCGAGTTTTC
Statistics
Matches: 126, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
148 126 1.00
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (148 bp):
TTTTCGACATTAGTAAATCCTCTTCTCCTCTGCCCGTGATTTTTTCCCGAAAGGGTTTCCACGTA
AAATCTGTGTGTTCTTTCTTTTCGTTTTCCTTGCGATATTTATTCATTATCGTCATTTAAATCTT
ATCAAATATAGTATTCCA
Found at i:9856698 original size:17 final size:17
Alignment explanation
Indices: 9856649--9856698 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
9856639 ACATAGATCG
9856649 CAAAGATGCAAACTC-TC
1 CAAAGATGC-AACTCATC
*
9856666 CAAAGGTGCAAGCTCAT-
1 CAAAGATGCAA-CTCATC
9856683 CAAAGATGCGAACTCA
1 CAAAGATGC-AACTCA
9856699 CTAACAGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 2 0.07
17 23 0.82
18 3 0.11
ACGTcount: A:0.40, C:0.26, G:0.18, T:0.16
Consensus pattern (17 bp):
CAAAGATGCAACTCATC
Found at i:9856747 original size:34 final size:34
Alignment explanation
Indices: 9856649--9856747 Score: 99
Period size: 34 Copynumber: 2.9 Consensus size: 34
9856639 ACATAGATCG
* * *
9856649 CAAAGATGCAAACTCTCCAAAGGTGCAAGCTCAT
1 CAAAGATGCAAACTCACCAAAAGTGCGAGCTCAT
* * * **
9856683 CAAAGATGCGAACTCACTAACAGTATGAGCTCAT
1 CAAAGATGCAAACTCACCAAAAGTGCGAGCTCAT
* * *
9856717 CAATGCTGCAAAGTCACCAAAAGTGCGAGCT
1 CAAAGATGCAAACTCACCAAAAGTGCGAGCT
9856748 TATACGTGCG
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.18
Consensus pattern (34 bp):
CAAAGATGCAAACTCACCAAAAGTGCGAGCTCAT
Found at i:9857619 original size:21 final size:21
Alignment explanation
Indices: 9857594--9857633 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
9857584 TATTTATGAG
9857594 AAAAAGTAAATATAAATTATA
1 AAAAAGTAAATATAAATTATA
*
9857615 AAAAATTAAATATAAATTA
1 AAAAAGTAAATATAAATTA
9857634 AAATTTTAAA
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:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (21 bp):
AAAAAGTAAATATAAATTATA
Found at i:9859495 original size:21 final size:19
Alignment explanation
Indices: 9859469--9859510 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
9859459 TAGTTTTCAA
*
9859469 TGTAACTATGTTAATTTAGTT
1 TGTAACT-TGTTAACTTA-TT
9859490 TGTAACTTGTTAACTTATT
1 TGTAACTTGTTAACTTATT
9859509 TG
1 TG
9859511 GTTATGATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.26, C:0.07, G:0.14, T:0.52
Consensus pattern (19 bp):
TGTAACTTGTTAACTTATT
Found at i:9861773 original size:23 final size:23
Alignment explanation
Indices: 9861747--9861790 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
9861737 CGATGTGGCG
9861747 GTGTTTTCTTCTATTTGGCAATC
1 GTGTTTTCTTCTATTTGGCAATC
9861770 GTGTTTTCTTCTATTTGGCAA
1 GTGTTTTCTTCTATTTGGCAA
9861791 AAACGATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.14, C:0.16, G:0.18, T:0.52
Consensus pattern (23 bp):
GTGTTTTCTTCTATTTGGCAATC
Found at i:9862308 original size:33 final size:32
Alignment explanation
Indices: 9862257--9862321 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
9862247 TTGTTCAGTG
*
9862257 ATAAACTTTATAAGTTTCAAGTTGATTAGTAT
1 ATAAACTTTATAAGTTTCAAGCTGATTAGTAT
*
9862289 ATAAACTTTTGTAAGTTTCAAGCTGATTAGTAT
1 ATAAAC-TTTATAAGTTTCAAGCTGATTAGTAT
9862322 GAGGATTCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 6 0.20
33 24 0.80
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (32 bp):
ATAAACTTTATAAGTTTCAAGCTGATTAGTAT
Found at i:9863127 original size:23 final size:22
Alignment explanation
Indices: 9863100--9863142 Score: 77
Period size: 22 Copynumber: 1.9 Consensus size: 22
9863090 TGTTTGATTA
9863100 ATAAAAAAAAGTAAATATAAATT
1 ATAAAAAAAA-TAAATATAAATT
9863123 ATAAAAAAAATAAATATAAA
1 ATAAAAAAAATAAATATAAA
9863143 AAATTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (22 bp):
ATAAAAAAAATAAATATAAATT
Found at i:9863142 original size:15 final size:16
Alignment explanation
Indices: 9863116--9863145 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9863106 AAAAGTAAAT
9863116 ATAAATTATAAAAAAA
1 ATAAATTATAAAAAAA
9863132 ATAAA-TATAAAAAA
1 ATAAATTATAAAAAA
9863146 TTATTTTGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
ATAAATTATAAAAAAA
Found at i:9887080 original size:20 final size:21
Alignment explanation
Indices: 9887052--9887094 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
9887042 TACATGATTG
9887052 ATGAGAAAAAG-TAAATATAA
1 ATGAGAAAAAGTTAAATATAA
*
9887072 ATGATAAAAAGTTAAATATAA
1 ATGAGAAAAAGTTAAATATAA
9887093 AT
1 AT
9887095 TAAAATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.26
Consensus pattern (21 bp):
ATGAGAAAAAGTTAAATATAA
Found at i:9893139 original size:23 final size:23
Alignment explanation
Indices: 9893109--9893163 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
9893099 ACGTGGCGTC
* *
9893109 CAGTCAGCAGTTTCTAGAAGATT
1 CAGTCAGCAGCTTCCAGAAGATT
*
9893132 CAGTCAGCAGCTTCCAGAAGGTT
1 CAGTCAGCAGCTTCCAGAAGATT
*
9893155 TAGTCAGCA
1 CAGTCAGCA
9893164 AGGATGGACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (23 bp):
CAGTCAGCAGCTTCCAGAAGATT
Found at i:9904798 original size:15 final size:15
Alignment explanation
Indices: 9904773--9904815 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
9904763 AAAATATTAA
9904773 ATTGAAATATTATAAT
1 ATTG-AATATTATAAT
*
9904789 ATTGAATATTATACT
1 ATTGAATATTATAAT
*
9904804 ATTCAATATTAT
1 ATTGAATATTAT
9904816 TAAACACACA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (15 bp):
ATTGAATATTATAAT
Found at i:9904869 original size:16 final size:16
Alignment explanation
Indices: 9904848--9904885 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
9904838 TTATATTTAA
9904848 TAATATAATAAATAAT
1 TAATATAATAAATAAT
* *
9904864 TAATATAATTAATTAT
1 TAATATAATAAATAAT
9904880 T-ATATA
1 TAATATA
9904886 TTAGAACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATATAATAAATAAT
Found at i:9904956 original size:23 final size:23
Alignment explanation
Indices: 9904917--9904961 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
9904907 AAATATGTAT
*
9904917 TAAAATTTATAAATATATAATAA
1 TAAAATTTATAAATATAAAATAA
*
9904940 TAAATATTTAT-AGTATAAAATA
1 TAAA-ATTTATAAATATAAAATA
9904962 TTATTATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TAAAATTTATAAATATAAAATAA
Found at i:9905612 original size:21 final size:21
Alignment explanation
Indices: 9905588--9905645 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
9905578 ATCTTCTTGG
*
9905588 TGAGTTGGGGCAGCTTCCTAC
1 TGAGTTGGGGTAGCTTCCTAC
*
9905609 TGAGTTGGGGTAG-TCTCTTAC
1 TGAGTTGGGGTAGCT-TCCTAC
*
9905630 TGAGTTTGGGTAGCTT
1 TGAGTTGGGGTAGCTT
9905646 GTTGTTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.14, C:0.16, G:0.34, T:0.36
Consensus pattern (21 bp):
TGAGTTGGGGTAGCTTCCTAC
Found at i:9910523 original size:184 final size:183
Alignment explanation
Indices: 9910170--9910559 Score: 525
Period size: 184 Copynumber: 2.1 Consensus size: 183
9910160 TTGTCTCTTT
* *
9910170 CCTAAGGCAAT-TAGTATGCAAATGGCAAACAATAAATTTACAAAAATCCAAACCTGCAATTCAG
1 CCTAAGGCTATATA-TATGCACATGGCAAACAATAAATTTACAAAAATCCAAACCTGCAATTCAG
* * *
9910234 TTTGATATAAACAACAATCATATTTCAATGAACATTTAAAATACTCATAAATTATATTTGAATAA
65 TTTGATACAAACAACAATCATATTTCAATCAACATTTAAAATACTCATAAATCATATTTGAATAA
* * * *
9910299 TTTGATGACATACACAATTTTAAATAATTCAATAAAAAATGATTTGTCATTAAA
130 TTTAATGACATACACAATTTCAAATAATTCAATAAAAAATGATTTATCACTAAA
* * * * *
9910353 CTCTAAGGTTATCTATATGCACATGGCAGACCATAAGTTTACAAAAATCCAAACCTGCAATTCAG
1 C-CTAAGGCTATATATATGCACATGGCAAACAATAAATTTACAAAAATCCAAACCTGCAATTCAG
* * ** *
9910418 TTTGGTACAAACAATAATCATATTTCAATCAACATTTAAAAAATA-TGTTGAATCATATTTGAAT
65 TTTGATACAAACAACAATCATATTTCAATCAACATTT--AAAATACTCATAAATCATATTTGAAT
* *
9910482 AATTTAATGACATACACAGTTTCAAATAATTCAAT-AAAAATGTTTTATCACTAAA
128 AATTTAATGACATACACAATTTCAAATAATTCAATAAAAAATGATTTATCACTAAA
*
9910537 CCTAAGGCTATATGTATGCACAT
1 CCTAAGGCTATATATATGCACAT
9910560 AACAAAGCAT
Statistics
Matches: 180, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
183 20 0.11
184 105 0.58
185 49 0.27
186 6 0.03
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (183 bp):
CCTAAGGCTATATATATGCACATGGCAAACAATAAATTTACAAAAATCCAAACCTGCAATTCAGT
TTGATACAAACAACAATCATATTTCAATCAACATTTAAAATACTCATAAATCATATTTGAATAAT
TTAATGACATACACAATTTCAAATAATTCAATAAAAAATGATTTATCACTAAA
Found at i:9911128 original size:21 final size:21
Alignment explanation
Indices: 9911102--9911142 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9911092 TAACGTGGCA
*
9911102 AGTTAACTGGCCACATCAACT
1 AGTTAACTGACCACATCAACT
*
9911123 AGTTAACTGACCACGTCAAC
1 AGTTAACTGACCACATCAAC
9911143 ATTACCATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (21 bp):
AGTTAACTGACCACATCAACT
Found at i:9912491 original size:20 final size:21
Alignment explanation
Indices: 9912452--9912491 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9912442 TTAATGGCTC
**
9912452 AGTGACTAAAAGGTTAATATA
1 AGTGACTAAAAGCATAATATA
9912473 AGTGACTAAAA-CATAATAT
1 AGTGACTAAAAGCATAATAT
9912492 TTCAAACATA
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:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (21 bp):
AGTGACTAAAAGCATAATATA
Found at i:9926318 original size:15 final size:15
Alignment explanation
Indices: 9926298--9926335 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
9926288 AATATTTTAA
*
9926298 AATATTATAATATTG
1 AATATTATAATATTC
*
9926313 AATATTATAGTATTC
1 AATATTATAATATTC
9926328 AATATTAT
1 AATATTAT
9926336 TAAACATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (15 bp):
AATATTATAATATTC
Found at i:9926406 original size:18 final size:18
Alignment explanation
Indices: 9926383--9926421 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
9926373 TAATAAATAC
9926383 TTAATATAATTA-ATTATT
1 TTAATA-AATTATATTATT
*
9926401 TTAATAAATTATTTTATT
1 TTAATAAATTATATTATT
9926419 TTA
1 TTA
9926422 TAACTTTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAATAAATTATATTATT
Found at i:9926558 original size:14 final size:14
Alignment explanation
Indices: 9926494--9926562 Score: 52
Period size: 14 Copynumber: 4.6 Consensus size: 14
9926484 ATATCATTGA
9926494 AAATATTT-ATAAT
1 AAATATTTAATAAT
9926507 -AATATTTTAATAAT
1 AAATA-TTTAATAAT
*
9926521 AAATATGTATTATGATTTAT
1 AAATA--T-TTA--A-TAAT
9926541 AAATATTTAATAAT
1 AAATATTTAATAAT
9926555 AAATATTT
1 AAATATTT
9926563 TATAGTGTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
12 4 0.09
13 3 0.07
14 16 0.36
15 5 0.11
16 1 0.02
17 6 0.13
18 1 0.02
19 1 0.02
20 8 0.18
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (14 bp):
AAATATTTAATAAT
Found at i:9927212 original size:21 final size:21
Alignment explanation
Indices: 9927186--9927244 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
9927176 GGGCAGCATC
* *
9927186 TTGTTGGTGTGTTGGGGCAAT
1 TTGTTGATGAGTTGGGGCAAT
*
9927207 TTGTTGATGAGTTGGGGCAAC
1 TTGTTGATGAGTTGGGGCAAT
** *
9927228 TTCCTGTTGAGTTGGGG
1 TTGTTGATGAGTTGGGG
9927245 TAGTCTCTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.12, C:0.08, G:0.41, T:0.39
Consensus pattern (21 bp):
TTGTTGATGAGTTGGGGCAAT
Found at i:9927259 original size:21 final size:21
Alignment explanation
Indices: 9927235--9927284 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
9927225 AACTTCCTGT
*
9927235 TGAGTTGGGGTAGTCTCTTGC
1 TGAGTTGGGGTAGCCTCTTGC
*
9927256 TGAGTTGGGGTAGCCTGTTGC
1 TGAGTTGGGGTAGCCTCTTGC
*
9927277 TGAATTGG
1 TGAGTTGG
9927285 AGCAACCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.12, C:0.12, G:0.40, T:0.36
Consensus pattern (21 bp):
TGAGTTGGGGTAGCCTCTTGC
Found at i:9927721 original size:164 final size:163
Alignment explanation
Indices: 9927451--9927775 Score: 562
Period size: 164 Copynumber: 2.0 Consensus size: 163
9927441 ATGGTGGCCT
* * *
9927451 ATTTCTTGCATTTACTACACTTCATTTCAACCTTTCTCTTGGCCTACTAGCTGGCCTTCTTAGTG
1 ATTTCTTGCATTTACTACACTTCATTTCAACC-TTCTCTTGGCCTACCAGCTGGCCTTCTTAATC
9927516 TAGTAGGCAGTTTTGGCAGCATGTTTAGCATAGACTCCCATTGCTTAGGACCCCTTATTGACCTT
65 TAGTAGGCAGTTTTGGCAGCATGTTTAGCATAGACTCCCATTGCTTAGGACCCCTTATTGACCTT
9927581 ATGAAGTAGGAGTAAATGGCAAGATGAGTTTACC
130 ATGAAGTAGGAGTAAATGGCAAGATGAGTTTACC
*
9927615 ATTTCTTGCATTTACTACACTTCATTTCAAAACC-TCTCTTGGCCTACCCGCTGGCCTTCTTAAT
1 ATTTCTTGCATTTACTACACTTCATTTC--AACCTTCTCTTGGCCTACCAGCTGGCCTTCTTAAT
*
9927679 CTAGTAGGCAGTTTTGGCAGCATGTTTGGCATAGACTCCCATTGCTTAGGACCCCTTATTGACCT
64 CTAGTAGGCAGTTTTGGCAGCATGTTTAGCATAGACTCCCATTGCTTAGGACCCCTTATTGACCT
*
9927744 TATGAAGTTGGAGTAAATGGCAAGATGAGTTT
129 TATGAAGTAGGAGTAAATGGCAAGATGAGTTT
9927776 GCTTGGTGTA
Statistics
Matches: 153, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
164 149 0.97
166 4 0.03
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.35
Consensus pattern (163 bp):
ATTTCTTGCATTTACTACACTTCATTTCAACCTTCTCTTGGCCTACCAGCTGGCCTTCTTAATCT
AGTAGGCAGTTTTGGCAGCATGTTTAGCATAGACTCCCATTGCTTAGGACCCCTTATTGACCTTA
TGAAGTAGGAGTAAATGGCAAGATGAGTTTACC
Found at i:9932780 original size:21 final size:21
Alignment explanation
Indices: 9932752--9932825 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
9932742 CTACAACTTA
9932752 AAGCGGAGGCAGCAACGAGGG
1 AAGCGGAGGCAGCAACGAGGG
*
9932773 AAGTGGAGGCAGCAACGAGGG
1 AAGCGGAGGCAGCAACGAGGG
* *
9932794 AAGCGAAGGCAGCAGCGAGGG
1 AAGCGGAGGCAGCAACGAGGG
*
9932815 AAGCAGAGGCA
1 AAGCGGAGGCA
9932826 ACAAGAAAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.35, C:0.18, G:0.46, T:0.01
Consensus pattern (21 bp):
AAGCGGAGGCAGCAACGAGGG
Found at i:9933189 original size:43 final size:43
Alignment explanation
Indices: 9933128--9933442 Score: 300
Period size: 43 Copynumber: 7.3 Consensus size: 43
9933118 ATCTGTTAAT
* * * *
9933128 TTTAGCGACGTTTGTGGGAAAAGCGTAGCTAAAGACAATGTTC
1 TTTAGCGGCGTTTTTGGGAAAAGCGTCGCTAAAGACCATGTTC
* * *
9933171 TTTAGCGGTGTTTTTGGGATAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTTTGGGAAAAGCGTCGCTAAAGACCATGTTC
* ** * * *
9933214 TTTAGCAGCGTTTACGGGAAATGCGCCGCTAAATACCATGTTC
1 TTTAGCGGCGTTTTTGGGAAAAGCGTCGCTAAAGACCATGTTC
* * * *
9933257 TTTGGC-G-GTGTTTGCAGAGAAAGTG-CTGCTAAAGACCATGTT-
1 TTTAGCGGCGTTTTTG-GGA-AAAGCGTC-GCTAAAGACCATGTTC
* * *
9933299 TTTAGTGGCGTTCTTGGTG-AAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTTTGG-GAAAAGCGTCGCTAAAGACCATGTTC
* * **
9933342 TTTAGCGACGTTTGTGGTTAAAGCG-CTGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTTTGGGAAAAGCGTC-GCTAAAGACCATGTTC
* *
9933385 TTTAGTGGCGTTTTTAGGAAAAGCGTCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTTTGGGAAAAGCGTCGCTAAAGACCATGTTC
*
9933428 TATAGCGGCGTTTTT
1 TTTAGCGGCGTTTTT
9933443 CCTAATAAAC
Statistics
Matches: 220, Mismatches: 41, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
41 4 0.02
42 29 0.13
43 180 0.82
44 7 0.03
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTTTGGGAAAAGCGTCGCTAAAGACCATGTTC
Found at i:9933342 original size:128 final size:129
Alignment explanation
Indices: 9933155--9933439 Score: 330
Period size: 128 Copynumber: 2.2 Consensus size: 129
9933145 GAAAAGCGTA
* *
9933155 GCTAAAGACAATGTTCTTTAGCGGTGTTTTTGGGATAAGCGCCGCTAAAGACCATGTTCTTTAGC
1 GCTAAAGACAATGTTCTTTAGCGGCGTTCTTGGGATAAGCGCCGCTAAAGACCATGTTCTTTAGC
*
9933220 -AGCGTTTACGG-GAAATGCGCCGCTAAATACCATGTTCTTTGGCGGTGTTTGCAGAGAAAGTGC
66 GA-CGTTTACGGTGAAA-GCGCCGCTAAAGACCATGTTCTTTGGCGGTGTTTGCAGAGAAAGTGC
9933283 T
129 T
* *
9933284 GCTAAAGACCATGTT-TTTAGTGGCGTTCTTGGTGA-AAGCGCCGCTAAAGACCATGTTCTTTAG
1 GCTAAAGACAATGTTCTTTAGCGGCGTTCTTGG-GATAAGCGCCGCTAAAGACCATGTTCTTTAG
** * * * * * ** *
9933347 CGACGTTTGTGGTTAAAGCGCTGCTAAAGACCATGTTCTTTAGTGGCGTTTTTAG-GAAA-AGCG
65 CGACGTTTACGGTGAAAGCGCCGCTAAAGACCATGTTCTTTGGCGGTGTTTGCAGAGAAAGTGC-
9933410 T
129 T
* *
9933411 CGCTAAAGACCATGTTCTATAGCGGCGTT
1 -GCTAAAGACAATGTTCTTTAGCGGCGTT
9933440 TTTCCTAATA
Statistics
Matches: 133, Mismatches: 17, Indels: 12
0.82 0.10 0.07
Matches are distributed among these distances:
126 2 0.02
127 5 0.04
128 96 0.72
129 30 0.23
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.31
Consensus pattern (129 bp):
GCTAAAGACAATGTTCTTTAGCGGCGTTCTTGGGATAAGCGCCGCTAAAGACCATGTTCTTTAGC
GACGTTTACGGTGAAAGCGCCGCTAAAGACCATGTTCTTTGGCGGTGTTTGCAGAGAAAGTGCT
Found at i:9949081 original size:55 final size:55
Alignment explanation
Indices: 9949005--9949136 Score: 165
Period size: 55 Copynumber: 2.4 Consensus size: 55
9948995 ATTTGGATTG
* * * * *
9949005 AATCGATTGTTATGCTGGAATATTGCTTCATTTGAATCGATTGTTTTTATGTTTA
1 AATCAATTGTCATGTTGGAATATTGCTACATTTGAATCGATTGTTTATATGTTTA
* * *
9949060 AATCAATTGTCATGTTGGAATATTGCTACTTTTGAATTGATTGTTTATATTTTTA
1 AATCAATTGTCATGTTGGAATATTGCTACATTTGAATCGATTGTTTATATGTTTA
* * *
9949115 AATCAATTATCATATTGAAATA
1 AATCAATTGTCATGTTGGAATA
9949137 CTTTTATGTA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 66 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.48
Consensus pattern (55 bp):
AATCAATTGTCATGTTGGAATATTGCTACATTTGAATCGATTGTTTATATGTTTA
Found at i:9951286 original size:29 final size:29
Alignment explanation
Indices: 9951204--9951399 Score: 172
Period size: 30 Copynumber: 6.8 Consensus size: 29
9951194 GTAAGTCCTT
* **
9951204 AAACTATCCAAAAATTATATTTTGACCCCC
1 AAACT-TCCAAAAATTACATTTTGACCCTA
* * * *
9951234 GAGCTTCTCCAAAATTACATTTTTTACCCTA
1 AAACTTC-CAAAAATTACA-TTTTGACCCTA
* *
9951265 AAACTTCCAAAAATTACATTTTCACCCTTG
1 AAACTTCCAAAAATTACATTTTGACCC-TA
*
9951295 AAACTTCTAAAAATT-CATTTTGACCC-A
1 AAACTTCCAAAAATTACATTTTGACCCTA
*
9951322 AAACTTCC-AAAATTACATTTTTA-CCTCA
1 AAACTTCCAAAAATTACATTTTGACCCT-A
*
9951350 AAA-TTCCAAAAA-TACAATTTTGA-CCTG
1 AAACTTCCAAAAATTAC-ATTTTGACCCTA
9951377 AAACTTCCAAAAATTATCATTTT
1 AAACTTCCAAAAATTA-CATTTT
9951400 ACCTCGATGT
Statistics
Matches: 136, Mismatches: 19, Indels: 23
0.76 0.11 0.13
Matches are distributed among these distances:
26 8 0.06
27 24 0.18
28 26 0.19
29 27 0.20
30 38 0.28
31 13 0.10
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTGACCCTA
Found at i:9951352 original size:28 final size:28
Alignment explanation
Indices: 9951241--9951404 Score: 142
Period size: 27 Copynumber: 5.8 Consensus size: 28
9951231 CCCGAGCTTC
9951241 TCCAAAATTACATTTTTTACC-CTAAAACT
1 TCCAAAATTACA-TTTTTACCTC-AAAACT
* **
9951270 TCCAAAAATTACATTTTCACCCTTGAAACT
1 TCC-AAAATTACATTTTTA-CCTCAAAACT
* *
9951300 TCTAAAAATT-CATTTTGACC-CAAAACT
1 TC-CAAAATTACATTTTTACCTCAAAACT
9951327 TCCAAAATTACATTTTTACCTCAAAA-T
1 TCCAAAATTACATTTTTACCTCAAAACT
* * *
9951354 TCCAAAAATACAATTTTGACCT-GAAACT
1 TCCAAAATTAC-ATTTTTACCTCAAAACT
9951382 TCCAAAAATTATCA-TTTTACCTC
1 TCC-AAAATTA-CATTTTTACCTC
9951405 GATGTCCAAA
Statistics
Matches: 110, Mismatches: 14, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
26 6 0.05
27 30 0.27
28 27 0.25
29 22 0.20
30 25 0.23
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (28 bp):
TCCAAAATTACATTTTTACCTCAAAACT
Found at i:9951427 original size:56 final size:56
Alignment explanation
Indices: 9951241--9951522 Score: 204
Period size: 56 Copynumber: 5.0 Consensus size: 56
9951231 CCCGAGCTTC
* * * * *
9951241 TCCAAAATTACATTTTTTACCCTAAAACTTCCAAAAATTA-CATTTTCACCCTTGAAACT-
1 TCCAAAAATCCATTTTTGACCC-GAAACTTCCAAAAATTACCATTTT-ACCCTCG--A-TG
* * * *
9951300 TCTAAAAATTCA-TTTTGACCCAAAACTTCC-AAAATTA-CATTTTTA-CCTCAAAAT-
1 TCCAAAAATCCATTTTTGACCCGAAACTTCCAAAAATTACCA-TTTTACCCTC--GATG
* * * *
9951354 TCCAAAAATACAATTTTGACCTGAAACTTCCAAAAATTATCATTTTA-CCTCGATG
1 TCCAAAAATCCATTTTTGACCCGAAACTTCCAAAAATTACCATTTTACCCTCGATG
* **
9951409 TCCAAAAACTCCATTTTTGAACCGAAACTTTTAAAAATTACCATTTTACCCTCGAGTG
1 TCCAAAAA-TCCATTTTTGACCCGAAACTTCCAAAAATTACCATTTTACCCTCGA-TG
* * **
9951467 TCCAAGAATTCCGTTTTTGATCCCG-ATTTTCCTAAAAATTACCATTTTACCCTCGA
1 TCCAA-AAATCCATTTTTGA-CCCGAAACTTCC-AAAAATTACCATTTTACCCTCGA
9951523 ATATCTAAAA
Statistics
Matches: 185, Mismatches: 25, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
54 13 0.07
55 28 0.15
56 58 0.31
57 21 0.11
58 28 0.15
59 37 0.20
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (56 bp):
TCCAAAAATCCATTTTTGACCCGAAACTTCCAAAAATTACCATTTTACCCTCGATG
Found at i:9951476 original size:29 final size:30
Alignment explanation
Indices: 9951440--9951522 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 30
9951430 CCGAAACTTT
9951440 TAAAAATTACCATTTTACCCTCGAGTGTCC
1 TAAAAATTACCATTTTACCCTCGAGTGTCC
* * * * *
9951470 -AAGAATT-CCGTTTTTGATCC-CGATTTTCC
1 TAAAAATTACC-ATTTT-ACCCTCGAGTGTCC
9951499 TAAAAATTACCATTTTACCCTCGA
1 TAAAAATTACCATTTTACCCTCGA
9951523 ATATCTAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
28 2 0.05
29 20 0.50
30 16 0.40
31 2 0.05
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (30 bp):
TAAAAATTACCATTTTACCCTCGAGTGTCC
Found at i:9951512 original size:59 final size:58
Alignment explanation
Indices: 9951381--9951522 Score: 168
Period size: 59 Copynumber: 2.5 Consensus size: 58
9951371 GACCTGAAAC
*
9951381 TTCC-AAAAATTATCATTTTA-CCTCGATGTCCAAAAACTCCATTTTTGAACCGAAACT
1 TTCCTAAAAATTACCATTTTACCCTCGATGTCCAAAAACTCCATTTTTGAACCG-AACT
* * * * *
9951438 TT--TAAAAATTACCATTTTACCCTCGAGTGTCCAAGAATTCCGTTTTTGATCCCG-ATT
1 TTCCTAAAAATTACCATTTTACCCTCGA-TGTCCAAAAACTCCATTTTTGA-ACCGAACT
9951495 TTCCTAAAAATTACCATTTTACCCTCGA
1 TTCCTAAAAATTACCATTTTACCCTCGA
9951523 ATATCTAAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
56 15 0.21
57 12 0.16
58 19 0.26
59 27 0.37
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (58 bp):
TTCCTAAAAATTACCATTTTACCCTCGATGTCCAAAAACTCCATTTTTGAACCGAACT
Found at i:9953569 original size:54 final size:55
Alignment explanation
Indices: 9953467--9953579 Score: 158
Period size: 54 Copynumber: 2.1 Consensus size: 55
9953457 GTCATAAAAG
* * * *
9953467 TATTTCAACATGACAATTGATTTAAATATATAAACAATCGATTCAAAAGAAGCAA
1 TATTCCAACATGAAAATTGATTTAAACATATAAACAATCGATTAAAAAGAAGCAA
*
9953522 TATTCCAACATGAAAAATTGATTTAAACA-A-AAATAATCGATTAAAAAGAAGCAA
1 TATTCCAACATG-AAAATTGATTTAAACATATAAACAATCGATTAAAAAGAAGCAA
9953576 TATT
1 TATT
9953580 TCAGCATAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
54 26 0.50
55 12 0.23
56 14 0.27
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.28
Consensus pattern (55 bp):
TATTCCAACATGAAAATTGATTTAAACATATAAACAATCGATTAAAAAGAAGCAA
Found at i:9954409 original size:20 final size:19
Alignment explanation
Indices: 9954371--9954413 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
9954361 AATATTTATT
*
9954371 TAATATTTTAATTAAAATAA
1 TAATATTTTAATAAAAAT-A
9954391 TAATATTTT-ATAAACAATA
1 TAATATTTTAATAAA-AATA
9954410 TAAT
1 TAAT
9954414 TATATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATATTTTAATAAAAATA
Found at i:9954897 original size:23 final size:21
Alignment explanation
Indices: 9954871--9954924 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
9954861 AAAAGGCAAA
*
9954871 AAATAAATGGCATAAAAAACAAC
1 AAATAAAT-ACAT-AAAAACAAC
*
9954894 AAATAAAATACATAAAAACAAT
1 AAAT-AAATACATAAAAACAAC
9954916 AAATAAATA
1 AAATAAATA
9954925 AGATTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 5 0.18
22 12 0.43
23 7 0.25
24 4 0.14
ACGTcount: A:0.70, C:0.09, G:0.04, T:0.17
Consensus pattern (21 bp):
AAATAAATACATAAAAACAAC
Found at i:9954993 original size:26 final size:27
Alignment explanation
Indices: 9954964--9955031 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 27
9954954 AAAAAATGAA
9954964 TAACAAATAAATAAATA-AATAAAAAT
1 TAACAAATAAATAAATATAATAAAAAT
* * *
9954990 TAACTACTAAATAAA-ATAATATAAAT
1 TAACAAATAAATAAATATAATAAAAAT
*
9955016 TATATAAA-AAATAAAT
1 TA-ACAAATAAATAAAT
9955032 GGGACCAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
25 1 0.03
26 30 0.91
27 2 0.06
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (27 bp):
TAACAAATAAATAAATATAATAAAAAT
Found at i:9955168 original size:5 final size:5
Alignment explanation
Indices: 9955152--9955196 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
9955142 TACAAATTAG
* *
9955152 AAATA GAAATA AAATA AAATA AAACTA AATTC AAATA AAATA AAA
1 AAATA -AAATA AAATA AAATA AAA-TA AAATA AAATA AAATA AAA
9955197 ATTATAAGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
5 25 0.74
6 9 0.26
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:9955180 original size:16 final size:15
Alignment explanation
Indices: 9955152--9955196 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
9955142 TACAAATTAG
9955152 AAATAGAAATAAAATA
1 AAATA-AAATAAAATA
* *
9955168 AAATAAAACTAAATTC
1 AAATAAAA-TAAAATA
9955184 AAATAAAATAAAA
1 AAATAAAATAAAA
9955197 ATTATAAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (15 bp):
AAATAAAATAAAATA
Found at i:9961401 original size:56 final size:56
Alignment explanation
Indices: 9961339--9961446 Score: 173
Period size: 56 Copynumber: 1.9 Consensus size: 56
9961329 ATAGCCATTG
*
9961339 ATATTAAATCTTTA-TTTTCTCATATCTGAATCCAAAAGAAAATGCCAAAAAAACCC
1 ATATTAAATCTTTATTTTTC-CATATCTGAACCCAAAAGAAAATGCCAAAAAAACCC
* *
9961395 ATATTAAATTTTTATTTTTCCATATCTGAACCCAAAAGAAAATGCTAAAAAA
1 ATATTAAATCTTTATTTTTCCATATCTGAACCCAAAAGAAAATGCCAAAAAA
9961447 GAATCTAGAG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
56 43 0.90
57 5 0.10
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.32
Consensus pattern (56 bp):
ATATTAAATCTTTATTTTTCCATATCTGAACCCAAAAGAAAATGCCAAAAAAACCC
Found at i:9963652 original size:20 final size:19
Alignment explanation
Indices: 9963614--9963656 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
9963604 TAATATTTAT
*
9963614 TAATATTTTAATTAAAATAA
1 TAATATTTTAATAAAAAT-A
9963634 TAATATTTT-ATAAACAATA
1 TAATATTTTAATAAA-AATA
9963653 TAAT
1 TAAT
9963657 TATATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATATTTTAATAAAAATA
Found at i:9964156 original size:9 final size:9
Alignment explanation
Indices: 9964138--9964295 Score: 64
Period size: 9 Copynumber: 16.9 Consensus size: 9
9964128 CATTAAAAAC
9964138 AAATAAATA
1 AAATAAATA
*
9964147 AAATACATA
1 AAATAAATA
9964156 AAA-ACAAT-
1 AAATA-AATA
9964164 AAATAAATA
1 AAATAAATA
*
9964173 AGATTAAATA
1 A-AATAAATA
9964183 AAGGCA-AGAATA
1 AA---ATA-AATA
9964195 TAAATAACATAA
1 -AAATAA-AT-A
*
9964207 AAATGAATA
1 AAATAAATA
9964216 ACAATAAAT-
1 A-AATAAATA
9964225 AAATAAAT-
1 AAATAAATA
*
9964233 AAA-ACA-A
1 AAATAAATA
9964240 AAATAAATAA
1 AAATAAAT-A
9964250 AAATTAAATA
1 AAA-TAAATA
9964260 CTAAATAAAATA
1 --AAAT-AAATA
*
9964272 ATATAAATA
1 AAATAAATA
*
9964281 ATAT-AA-A
1 AAATAAATA
9964288 AAATAAAT
1 AAATAAAT
9964296 GGGACCAAAT
Statistics
Matches: 116, Mismatches: 10, Indels: 46
0.67 0.06 0.27
Matches are distributed among these distances:
7 9 0.08
8 23 0.20
9 28 0.24
10 26 0.22
11 15 0.13
12 13 0.11
13 2 0.02
ACGTcount: A:0.70, C:0.04, G:0.03, T:0.22
Consensus pattern (9 bp):
AAATAAATA
Found at i:9964156 original size:13 final size:14
Alignment explanation
Indices: 9964138--9964230 Score: 75
Period size: 14 Copynumber: 6.7 Consensus size: 14
9964128 CATTAAAAAC
9964138 AAATAAATAA-AAT
1 AAATAAATAACAAT
*
9964151 ACATAAA-AACAAT
1 AAATAAATAACAAT
* *
9964164 AAATAAATAAGATT
1 AAATAAATAACAAT
** *
9964178 AAATAAA-GGCAAG
1 AAATAAATAACAAT
*
9964191 AATATAAATAACATAA
1 AA-ATAAATAACA-AT
*
9964207 AAATGAATAACAAT
1 AAATAAATAACAAT
9964221 AAATAAATAA
1 AAATAAATAA
9964231 ATAAAACAAA
Statistics
Matches: 60, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
12 2 0.03
13 18 0.30
14 26 0.43
15 11 0.18
16 3 0.05
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.20
Consensus pattern (14 bp):
AAATAAATAACAAT
Found at i:9964217 original size:15 final size:15
Alignment explanation
Indices: 9964194--9964259 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
9964184 AGGCAAGAAT
9964194 ATAAATAACATAAAA
1 ATAAATAACATAAAA
* *
9964209 ATGAATAACA-ATAA
1 ATAAATAACATAAAA
9964223 ATAAATAA-ATAAAA
1 ATAAATAACATAAAA
*
9964237 CAAAAATAA-ATAAAA
1 -ATAAATAACATAAAA
9964252 ATTAAATA
1 A-TAAATA
9964260 CTAAATAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
13 1 0.02
14 14 0.33
15 27 0.64
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.21
Consensus pattern (15 bp):
ATAAATAACATAAAA
Found at i:9964225 original size:74 final size:76
Alignment explanation
Indices: 9964076--9964259 Score: 186
Period size: 74 Copynumber: 2.4 Consensus size: 76
9964066 TAATGGCATA
* **
9964076 AAAT-ATAAAA-AAATAA-AAATAAAAATTGAATAAAAGGCAAAAATATAAATGGCATTAAAAAC
1 AAATAATAAAACAAA-AATAAATAAAAATTAAAT-AAAGGCAAAAATATAAATAACATTAAAAAC
9964138 AAATAAATAAAAT
64 AAATAAATAAAAT
* * * **
9964151 ACAT-A-AAAACAATAAATAAAT-AAGATTAAATAAAGGCAAGAATATAAATAACA-TAAAAATG
1 AAATAATAAAACAA-AAATAAATAAAAATTAAATAAAGGCAAAAATATAAATAACATTAAAAACA
9964212 AATAACA-ATAAAT
65 AATAA-ATA-AAAT
9964225 AAATAAATAAAACAAAAATAAATAAAAATTAAATA
1 AAAT-AATAAAACAAAAATAAATAAAAATTAAATA
9964260 CTAAATAAAA
Statistics
Matches: 90, Mismatches: 10, Indels: 16
0.78 0.09 0.14
Matches are distributed among these distances:
73 12 0.13
74 31 0.34
75 16 0.18
76 14 0.16
77 17 0.19
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (76 bp):
AAATAATAAAACAAAAATAAATAAAAATTAAATAAAGGCAAAAATATAAATAACATTAAAAACAA
ATAAATAAAAT
Found at i:9964231 original size:33 final size:33
Alignment explanation
Indices: 9964194--9964281 Score: 99
Period size: 33 Copynumber: 2.7 Consensus size: 33
9964184 AGGCAAGAAT
* * *
9964194 ATAAATAACATAAAAATGAATAACAA-TAAATAA
1 ATAAATAAAATAAAAATAAATAAAAATTAAAT-A
*
9964227 ATAAATAAAACAAAAATAAATAAAAATTAAATA
1 ATAAATAAAATAAAAATAAATAAAAATTAAATA
* *
9964260 CTAAATAAAAT-AATATAAATAA
1 ATAAATAAAATAAAAATAAATAA
9964282 TATAAAAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
32 10 0.21
33 32 0.68
34 5 0.11
ACGTcount: A:0.72, C:0.05, G:0.01, T:0.23
Consensus pattern (33 bp):
ATAAATAAAATAAAAATAAATAAAAATTAAATA
Found at i:9964265 original size:37 final size:37
Alignment explanation
Indices: 9964224--9964295 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
9964214 TAACAATAAA
*
9964224 TAAATAAATAAAACAAAAATAA-ATAAAAATTAAATAC
1 TAAATAAA-AAAACAAAAATAATATAAAAAATAAATAC
* * *
9964261 TAAATAAAATAATATAAATAATATAAAAAATAAAT
1 TAAATAAAAAAACAAAAATAATATAAAAAATAAAT
9964296 GGGACCAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 10 0.33
37 20 0.67
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (37 bp):
TAAATAAAAAAACAAAAATAATATAAAAAATAAATAC
Found at i:9964313 original size:4 final size:4
Alignment explanation
Indices: 9964138--9964295 Score: 78
Period size: 4 Copynumber: 38.0 Consensus size: 4
9964128 CATTAAAAAC
* * *
9964138 AAAT AAAT AAAAT ACAT AAAA ACAAT AAAT AAAT AAGATT AAAT AAAGG
1 AAAT AAAT -AAAT AAAT AAAT A-AAT AAAT AAAT AA-A-T AAAT AAA-T
* * *
9964187 CAAG AATAT AAAT AACAT -AA- AAAT GAAT AACAAT AAAT AAAT AAAT
1 AAAT AA-AT AAAT AA-AT AAAT AAAT AAAT -A-AAT AAAT AAAT AAAT
* *
9964233 AAA- ACAA- AAAT AAAT AAA- AATT AAAT -ACT AAAT AAAAT AATAT AAAT
1 AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AA-AT AAAT
9964280 AATAT AAA- AAAT AAAT
1 AA-AT AAAT AAAT AAAT
9964296 GGGACCAAAT
Statistics
Matches: 121, Mismatches: 14, Indels: 38
0.70 0.08 0.22
Matches are distributed among these distances:
3 13 0.11
4 73 0.60
5 29 0.24
6 6 0.05
ACGTcount: A:0.70, C:0.04, G:0.03, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:9964432 original size:29 final size:30
Alignment explanation
Indices: 9964361--9964432 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
9964351 TAAATGAGGC
*
9964361 AAAATTAAATAAAGGACTAAATTGAAAACA
1 AAAATAAAATAAAGGACTAAATTGAAAACA
* * * *
9964391 CAAATACATTAAAGGTAC-AAATT-AGAACA
1 AAAATAAAATAAAGG-ACTAAATTGAAAACA
9964420 AAAATAAAATAAA
1 AAAATAAAATAAA
9964433 ATAAAATTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
29 15 0.45
30 16 0.48
31 2 0.06
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.19
Consensus pattern (30 bp):
AAAATAAAATAAAGGACTAAATTGAAAACA
Found at i:9973207 original size:54 final size:56
Alignment explanation
Indices: 9973103--9973208 Score: 173
Period size: 54 Copynumber: 1.9 Consensus size: 56
9973093 ATAGCCATTG
9973103 ATATTAAATCTTTATTTTCTCATATCTGAATCCAAAAGAAAATGCCAAAAAAAACC
1 ATATTAAATCTTTATTTTCTCATATCTGAATCCAAAAGAAAATGCCAAAAAAAACC
*
9973159 ATATTAAAT-TTTATTTT-TCCATATCTGAA-CCAAAAGAAAATGCTAAAAAA
1 ATATTAAATCTTTATTTTCT-CATATCTGAATCCAAAAGAAAATGCCAAAAAA
9973209 GAATCTAGAG
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
54 21 0.44
55 18 0.38
56 9 0.19
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (56 bp):
ATATTAAATCTTTATTTTCTCATATCTGAATCCAAAAGAAAATGCCAAAAAAAACC
Found at i:9975429 original size:20 final size:19
Alignment explanation
Indices: 9975391--9975433 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
9975381 AATATTTATT
*
9975391 TAATATTTTAATTAAAATAA
1 TAATATTTTAATAAAAAT-A
9975411 TAATATTTT-ATAAACAATA
1 TAATATTTTAATAAA-AATA
9975430 TAAT
1 TAAT
9975434 TATATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATATTTTAATAAAAATA
Found at i:9975934 original size:9 final size:9
Alignment explanation
Indices: 9975916--9976077 Score: 79
Period size: 9 Copynumber: 17.9 Consensus size: 9
9975906 CATTAAAAAC
9975916 AAATAAATA
1 AAATAAATA
*
9975925 AAATACATA
1 AAATAAATA
*
9975934 AAAAACAAT-
1 AAATA-AATA
9975943 AAATAAATA
1 AAATAAATA
*
9975952 AGATTAAATA
1 A-AATAAATA
*** *
9975962 AAGGCAAGA
1 AAATAAATA
*
9975971 ATATAAATA
1 AAATAAATA
*
9975980 ACAT-AA-A
1 AAATAAATA
9975987 AAA-AAATAA
1 AAATAAAT-A
9975996 CAAATAAAT-
1 -AAATAAATA
9976005 AAATAAATA
1 AAATAAATA
*
9976014 AAA-CAA-A
1 AAATAAATA
9976021 AAATAAATAA
1 AAATAAAT-A
9976031 AAATTAAATA
1 AAA-TAAATA
9976041 CTAAATAAAATA
1 --AAAT-AAATA
*
9976053 ATATAAATA
1 AAATAAATA
*
9976062 ATATAAA-A
1 AAATAAATA
9976070 AAATAAAT
1 AAATAAAT
9976078 GGGACCAAAT
Statistics
Matches: 116, Mismatches: 20, Indels: 34
0.68 0.12 0.20
Matches are distributed among these distances:
7 9 0.08
8 24 0.21
9 44 0.38
10 21 0.18
11 10 0.09
12 8 0.07
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (9 bp):
AAATAAATA
Found at i:9975965 original size:75 final size:79
Alignment explanation
Indices: 9975858--9976072 Score: 210
Period size: 75 Copynumber: 2.7 Consensus size: 79
9975848 GGCATAAAAT
* * ** *
9975858 ATAAAA-AAATAA-AAATAAAAATTGAATAAAAGGCAAAAATATAAATGGCATTAAAAACAAATA
1 ATAAAACAAAAAATAAATAAAAATTAAAT-AAAGGCAAAAATATAAATAACA-TAAAAAAAAATA
* *
9975921 A-ATA-AAATACAT-A
64 ACAAATAAATAAATAA
* * *
9975934 A-AAAACAATAAATAAAT-AAGATTAAATAAAGGCAAGAATATAAATAACATAAAAAAAAATAAC
1 ATAAAACAAAAAATAAATAAAAATTAAATAAAGGCAAAAATATAAATAACATAAAAAAAAATAAC
9975997 AAATAAATAAATAA
66 AAATAAATAAATAA
*** *
9976011 ATAAAACAAAAAATAAATAAAAATTAAATACTAAATAAAATAATATAAATAATATAAAAAAA
1 ATAAAACAAAAAATAAATAAAAATTAAATA--AAGGCAAA-AATATAAATAACATAAAAAAA
9976073 TAAATGGGAC
Statistics
Matches: 112, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
74 12 0.11
75 25 0.22
76 20 0.18
77 6 0.05
78 15 0.13
79 10 0.09
81 4 0.04
82 20 0.18
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.20
Consensus pattern (79 bp):
ATAAAACAAAAAATAAATAAAAATTAAATAAAGGCAAAAATATAAATAACATAAAAAAAAATAAC
AAATAAATAAATAA
Found at i:9976014 original size:34 final size:34
Alignment explanation
Indices: 9975973--9976070 Score: 110
Period size: 34 Copynumber: 2.8 Consensus size: 34
9975963 AGGCAAGAAT
*
9975973 ATAAATAACATAAAAAA-AAATAACAAA-TAAATAA
1 ATAAATAAAATAAAAAATAAATAA-AAATTAAAT-A
*
9976007 ATAAATAAAACAAAAAATAAATAAAAATTAAATA
1 ATAAATAAAATAAAAAATAAATAAAAATTAAATA
*
9976041 CTAAATAAAATAATATAAATAATATAAAAA
1 ATAAATAAAATAA-A-AAATAA-ATAAAAA
9976071 AATAAATGGG
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
34 30 0.55
35 12 0.22
36 6 0.11
37 7 0.13
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.21
Consensus pattern (34 bp):
ATAAATAAAATAAAAAATAAATAAAAATTAAATA
Found at i:9976095 original size:4 final size:4
Alignment explanation
Indices: 9975916--9976077 Score: 88
Period size: 4 Copynumber: 40.0 Consensus size: 4
9975906 CATTAAAAAC
* * *
9975916 AAAT AAAT AAAAT ACAT AAA- AAA- CAAT AAAT AAAT AAGATT AAAT AAAGG
1 AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-A-T AAAT AAA-T
* * *
9975966 CAAG AATAT AAAT AACAT AAA- AAA- AAAT -AAC AAAT AAAT AAAT AAAT
1 AAAT AA-AT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * *
9976013 AAA- ACAAA AAAT AAAT AAA- AATT AAAT -ACT AAAT AAAAT AATAT AAAT
1 AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AA-AT AAAT
*
9976061 AATAT AAAA AAAT AAAT
1 AA-AT AAAT AAAT AAAT
9976078 GGGACCAAAT
Statistics
Matches: 125, Mismatches: 17, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
3 18 0.14
4 76 0.61
5 28 0.22
6 3 0.02
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:9978248 original size:7 final size:7
Alignment explanation
Indices: 9978225--9978256 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
9978215 ATGGAAACAA
9978225 AAATG-G
1 AAATGAG
9978231 AAATG-G
1 AAATGAG
9978237 AAATGAG
1 AAATGAG
9978244 AAATGAG
1 AAATGAG
9978251 AAATGA
1 AAATGA
9978257 TTTATTTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 11 0.44
7 14 0.56
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.16
Consensus pattern (7 bp):
AAATGAG
Found at i:9984737 original size:15 final size:16
Alignment explanation
Indices: 9984712--9984749 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
9984702 ATAAAAATTG
*
9984712 AATAAAAGGCA-AAAA
1 AATAAATGGCATAAAA
*
9984727 TATAAATGGCATAAAA
1 AATAAATGGCATAAAA
9984743 AATAAAT
1 AATAAAT
9984750 AAAATACATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.66, C:0.05, G:0.11, T:0.18
Consensus pattern (16 bp):
AATAAATGGCATAAAA
Found at i:9984744 original size:60 final size:58
Alignment explanation
Indices: 9984680--9984828 Score: 131
Period size: 61 Copynumber: 2.5 Consensus size: 58
9984670 CATTAATGGC
* * **
9984680 AAAAACTATAAAAAATAAAAAAATAAAAATTGAATAAAAGGCAAAAATATAAATGGCAT
1 AAAAAATATAAAAAATAAAAAAATAAAAATTAAAT-AAAGGCAAAAATATAAATAACAT
* * *
9984739 AAAAAATA-AATAAAATACATAAAAA-ATAAGATTAAATAAAGGCAAGAATATAGATAACAT
1 AAAAAATATAA-AAAATA-A-AAAAATA-AAAATTAAATAAAGGCAAAAATATAAATAACAT
* *
9984799 AAAAAAATGAATAACAAATAAATAAATAAA
1 -AAAAAAT--ATAAAAAATAAAAAAATAAA
9984829 TAAAACAATA
Statistics
Matches: 72, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
58 2 0.03
59 13 0.18
60 21 0.29
61 26 0.36
62 2 0.03
63 6 0.08
64 2 0.03
ACGTcount: A:0.69, C:0.05, G:0.07, T:0.19
Consensus pattern (58 bp):
AAAAAATATAAAAAATAAAAAAATAAAAATTAAATAAAGGCAAAAATATAAATAACAT
Found at i:9984751 original size:4 final size:4
Alignment explanation
Indices: 9984737--9984886 Score: 78
Period size: 4 Copynumber: 36.8 Consensus size: 4
9984727 TATAAATGGC
* **
9984737 ATAA A-AA ATAA ATAAA ATAC ATAA A-AA ATAA GATTAA ATAA AGGCA
1 ATAA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA -A-TAA ATAA A-TAA
* * * * *
9984783 AGAA TATAG ATAA CATAA AAAA ATGA AT-A ACAA ATAA ATAA ATAA ATAA
1 ATAA -ATAA ATAA -ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* * *
9984832 A-ACA ATAA ATAA ATAA A-AA TTAA AT-A CTAA ATAA GATAA TATAA ACAA
1 ATA-A ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA -ATAA -ATAA ATAA
9984880 ATAA ATA
1 ATAA ATA
9984887 GGACCAAATG
Statistics
Matches: 112, Mismatches: 20, Indels: 28
0.70 0.12 0.17
Matches are distributed among these distances:
3 13 0.12
4 73 0.65
5 23 0.21
6 3 0.03
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:9985004 original size:30 final size:29
Alignment explanation
Indices: 9984950--9985024 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
9984940 ACTAAATAAG
* *
9984950 ACAAAATTAAATAAAGGACTAAATTGAAA
1 ACAAAAATAAATAAAGGACTAAATTAAAA
**
9984979 ACTCAAATAAATTAAAGGTAC-AAATTAAAA
1 ACAAAAATAAA-TAAAGG-ACTAAATTAAAA
9985009 ACAAAAATAAAATAAA
1 ACAAAAAT-AAATAAA
9985025 ATAAAACTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
29 8 0.22
30 24 0.65
31 5 0.14
ACGTcount: A:0.65, C:0.08, G:0.07, T:0.20
Consensus pattern (29 bp):
ACAAAAATAAATAAAGGACTAAATTAAAA
Found at i:9985020 original size:5 final size:5
Alignment explanation
Indices: 9985012--9985051 Score: 62
Period size: 5 Copynumber: 7.8 Consensus size: 5
9985002 ATTAAAAACA
*
9985012 AAAAT AAAAT AAAAT AAAACT AAATT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT AAAAT AAAA
9985052 ATTACAGGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 28 0.88
6 4 0.12
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:9985030 original size:16 final size:16
Alignment explanation
Indices: 9985006--9985051 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
9984996 GTACAAATTA
*
9985006 AAAACAAAAATAAAAT
1 AAAATAAAAATAAAAT
* *
9985022 AAAATAAAACTAAATT
1 AAAATAAAAATAAAAT
9985038 AAAAT-AAAATAAAA
1 AAAATAAAAATAAAA
9985052 ATTACAGGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAATAAAAATAAAAT
Found at i:9985030 original size:21 final size:21
Alignment explanation
Indices: 9985006--9985051 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
9984996 GTACAAATTA
9985006 AAAACAAAAATAAAATAAAAT
1 AAAACAAAAATAAAATAAAAT
* *
9985027 AAAACTAAATTAAAATAAAAT
1 AAAACAAAAATAAAATAAAAT
9985048 AAAA
1 AAAA
9985052 ATTACAGGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.17
Consensus pattern (21 bp):
AAAACAAAAATAAAATAAAAT
Found at i:9990540 original size:59 final size:60
Alignment explanation
Indices: 9990369--9990541 Score: 190
Period size: 59 Copynumber: 2.9 Consensus size: 60
9990359 ATTAGACAAA
** * * * *
9990369 AAAAAAAACTTAGATACCAAATTAAGAAAAAGTG-GAAGTTCAAGTATCAAATTGGGTTC
1 AAAAAAAGTTTAGGTACCAAATTAAAAAAAAGTGTCAAGTTCAAGTACCAAATTGGGTTC
* * * *
9990428 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAAAATGTCAAATTCAGGTACCAAATTTGG-TC
1 AAAAAAAGTTTAGGTACCAAATTA--AAAAAAAGTGTCAAGTTCAAGTACCAAATTGGGTTC
* *
9990489 AAAAAAAGTTTAGGTACCAAATTAAAAAAAAGTGTTAAG-TCTAAATACCAAAT
1 AAAAAAAGTTTAGGTACCAAATTAAAAAAAAGTGTCAAGTTC-AAGTACCAAAT
9990542 GTTTTATTAA
Statistics
Matches: 95, Mismatches: 15, Indels: 8
0.81 0.13 0.07
Matches are distributed among these distances:
58 2 0.02
59 42 0.44
61 34 0.36
62 17 0.18
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.24
Consensus pattern (60 bp):
AAAAAAAGTTTAGGTACCAAATTAAAAAAAAGTGTCAAGTTCAAGTACCAAATTGGGTTC
Found at i:9990975 original size:17 final size:17
Alignment explanation
Indices: 9990953--9990986 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9990943 ATTATTGTTT
* *
9990953 ACGTTTTATCTTTATCA
1 ACGTTTCATCTTCATCA
9990970 ACGTTTCATCTTCATCA
1 ACGTTTCATCTTCATCA
9990987 GTAGTTTGAA
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:0.24, C:0.24, G:0.06, T:0.47
Consensus pattern (17 bp):
ACGTTTCATCTTCATCA
Found at i:9991781 original size:22 final size:22
Alignment explanation
Indices: 9991756--9991797 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
9991746 TTTTTTTGGA
*
9991756 TAGTGTATATTCATGTTCTTTC
1 TAGTGGATATTCATGTTCTTTC
9991778 TAGTGGATATTCATGTTCTT
1 TAGTGGATATTCATGTTCTT
9991798 CCTCTCTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.12, G:0.17, T:0.52
Consensus pattern (22 bp):
TAGTGGATATTCATGTTCTTTC
Found at i:10001064 original size:59 final size:57
Alignment explanation
Indices: 10000983--10001095 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 57
10000973 TGTGTGGCAC
*
10000983 CCATTTCAATCATGTAATTTAGAAG-AATCAATTTTTGAAGTTTCTAGTATGTGTGCTAT
1 CCATTTCAATCAAGTAATTTAGAAGAAAT-AATTTTTGAAGTTTCTA--ATGTGTGCTAT
10001042 CCATTTCAATCAAGTAATTTAGAAGAAAATAATTTTTGAAGTTTCTAATGTGTG
1 CCATTTCAATCAAGTAATTTAGAAG-AAATAATTTTTGAAGTTTCTAATGTGTG
10001096 GGTTTTAGCA
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
58 7 0.14
59 24 0.47
60 17 0.33
61 3 0.06
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.41
Consensus pattern (57 bp):
CCATTTCAATCAAGTAATTTAGAAGAAATAATTTTTGAAGTTTCTAATGTGTGCTAT
Found at i:10002554 original size:55 final size:55
Alignment explanation
Indices: 10002478--10002609 Score: 165
Period size: 55 Copynumber: 2.4 Consensus size: 55
10002468 ATTTGGATTG
* * * * *
10002478 AATCGATTGTTATGCTGGAATATTGCTTCATTTGAATCGATTGTTTTTATGTTTA
1 AATCAATTGTCATGTTGGAATATTGCTACATTTGAATCGATTGTTTATATGTTTA
* * *
10002533 AATCAATTGTCATGTTGGAATATTGCTACTTTTGAATTGATTGTTTATATTTTTA
1 AATCAATTGTCATGTTGGAATATTGCTACATTTGAATCGATTGTTTATATGTTTA
* * *
10002588 AATCAATTATCATATTGAAATA
1 AATCAATTGTCATGTTGGAATA
10002610 CTTTTATGTA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 66 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.48
Consensus pattern (55 bp):
AATCAATTGTCATGTTGGAATATTGCTACATTTGAATCGATTGTTTATATGTTTA
Found at i:10004736 original size:29 final size:29
Alignment explanation
Indices: 10004686--10004942 Score: 169
Period size: 29 Copynumber: 9.0 Consensus size: 29
10004676 GTAAGTCCTT
*
10004686 AAACTATCCAAAAATTATATTTTGACCC-C
1 AAACT-TCCAAAAATTACATTTTGACCCTC
* * * * *
10004715 GAGCTTCTCCAAAATTACATTTTTTACCCTA
1 AAACTTC-CAAAAATTACA-TTTTGACCCTC
* *
10004746 AAACTTCCAAAAATTACATTTTCACCCTT
1 AAACTTCCAAAAATTACATTTTGACCCTC
* *
10004775 GAACTTCCAAAAATTCCATTTTGACCC-C
1 AAACTTCCAAAAATTACATTTTGACCCTC
*
10004803 AAAACTTCCAAAAATTACATTTTTACCCTC
1 -AAACTTCCAAAAATTACATTTTGACCCTC
* *
10004833 AAA-TTTCAAAAATCA-ATTTTGA-CCT-
1 AAACTTCCAAAAATTACATTTTGACCCTC
* *
10004858 GAACTTCC-AAAATT-TATTTT-ACCCTC
1 AAACTTCCAAAAATTACATTTTGACCCTC
* * * *
10004884 GAA-TGTCCAAAAAACTCCATTTTTGACCC-G
1 AAACT-TCC-AAAAATTACA-TTTTGACCCTC
**
10004914 AAACTTTTAAAAATTACCATTTT-ACCCTC
1 AAACTTCCAAAAATTA-CATTTTGACCCTC
10004943 GGGTGTCCAA
Statistics
Matches: 177, Mismatches: 33, Indels: 36
0.72 0.13 0.15
Matches are distributed among these distances:
24 1 0.01
25 16 0.09
26 12 0.07
27 6 0.03
28 21 0.12
29 83 0.47
30 28 0.16
31 10 0.06
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTGACCCTC
Found at i:10004813 original size:58 final size:57
Alignment explanation
Indices: 10004686--10005004 Score: 228
Period size: 59 Copynumber: 5.5 Consensus size: 57
10004676 GTAAGTCCTT
* * * * *
10004686 AAACTATCCAAAAATTATATTTTGACCC-CGAGCTTCTCCAAAATTACATTTTTTACCCTA
1 AAACT-TCCAAAAATTACATTTT-ACCCTCGAACTTC-CAAAAATTCCATTTTTGACCC-A
*
10004746 AAACTTCCAAAAATTACATTTTCACCCTTGAACTTCCAAAAATTCCA-TTTTGACCCCA
1 AAACTTCCAAAAATTACATTTT-ACCCTCGAACTTCCAAAAATTCCATTTTTGA-CCCA
* * * *
10004804 AAACTTCCAAAAATTACATTTTTACCCTC-AAATTTCAAAAA-T-CAATTTTGA-CCT
1 AAACTTCCAAAAATTACA-TTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCA
* * * *
10004858 GAACTTCC-AAAATT-TATTTTACCCTCGAA-TGTCCAAAAAACTCCATTTTTGACCCG
1 AAACTTCCAAAAATTACATTTTACCCTCGAACT-TCC-AAAAATTCCATTTTTGACCCA
** ** * *
10004914 AAACTTTTAAAAATTACCATTTTACCCTCG-GGTGTCCAAGAATTCCGTTTTTGATCCC-
1 AAACTTCCAAAAATTA-CATTTTACCCTCGAACT-TCCAAAAATTCCATTTTTGA-CCCA
* **
10004972 GATTTTCCTAAAAATTACCATTTTACCCTCGAA
1 AAACTTCC-AAAAATTA-CATTTTACCCTCGAA
10005005 TATCTAAATG
Statistics
Matches: 212, Mismatches: 30, Indels: 34
0.77 0.11 0.12
Matches are distributed among these distances:
51 11 0.05
52 5 0.02
53 11 0.05
54 10 0.05
55 10 0.05
56 14 0.07
57 16 0.08
58 46 0.22
59 78 0.37
60 11 0.05
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (57 bp):
AAACTTCCAAAAATTACATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCA
Found at i:10016207 original size:17 final size:17
Alignment explanation
Indices: 10016185--10016218 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
10016175 ATTATTGTTT
* *
10016185 ACGTTTTATCTTTATCA
1 ACGTTTCATCTTCATCA
10016202 ACGTTTCATCTTCATCA
1 ACGTTTCATCTTCATCA
10016219 GTAGTTTGAA
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:0.24, C:0.24, G:0.06, T:0.47
Consensus pattern (17 bp):
ACGTTTCATCTTCATCA
Found at i:10017013 original size:22 final size:22
Alignment explanation
Indices: 10016988--10017029 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
10016978 TTTTATTGGA
*
10016988 TAGTGTATATTCATGTTCTTTC
1 TAGTGGATATTCATGTTCTTTC
10017010 TAGTGGATATTCATGTTCTT
1 TAGTGGATATTCATGTTCTT
10017030 CCTCTCTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.12, G:0.17, T:0.52
Consensus pattern (22 bp):
TAGTGGATATTCATGTTCTTTC
Found at i:10026240 original size:59 final size:57
Alignment explanation
Indices: 10026159--10026271 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 57
10026149 TGTGTGGCAC
*
10026159 CCATTTCAATCATGTAATTTAGAAG-AATCAATTTTTGAAGTTTCTAGTATGTGTGCTAT
1 CCATTTCAATCAAGTAATTTAGAAGAAAT-AATTTTTGAAGTTTCTA--ATGTGTGCTAT
10026218 CCATTTCAATCAAGTAATTTAGAAGAAAATAATTTTTGAAGTTTCTAATGTGTG
1 CCATTTCAATCAAGTAATTTAGAAG-AAATAATTTTTGAAGTTTCTAATGTGTG
10026272 GGTTTTAGCA
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
58 7 0.14
59 24 0.47
60 17 0.33
61 3 0.06
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.41
Consensus pattern (57 bp):
CCATTTCAATCAAGTAATTTAGAAGAAATAATTTTTGAAGTTTCTAATGTGTGCTAT
Found at i:10027582 original size:55 final size:55
Alignment explanation
Indices: 10027506--10027637 Score: 165
Period size: 55 Copynumber: 2.4 Consensus size: 55
10027496 ATTTGGATTG
* * * * *
10027506 AATCGATTGTTATGCTGGAATATTGCTTCATTTGAATCGATTGTTTTTATGTTTA
1 AATCAATTGTCATGTTGGAATATTGCTACATTTGAATCGATTGTTTATATGTTTA
* * *
10027561 AATCAATTGTCATGTTGGAATATTGCTACTTTTGAATTGATTGTTTATATTTTTA
1 AATCAATTGTCATGTTGGAATATTGCTACATTTGAATCGATTGTTTATATGTTTA
* * *
10027616 AATCAATTATCATATTGAAATA
1 AATCAATTGTCATGTTGGAATA
10027638 CTTTTATGTA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 66 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.48
Consensus pattern (55 bp):
AATCAATTGTCATGTTGGAATATTGCTACATTTGAATCGATTGTTTATATGTTTA
Found at i:10029864 original size:59 final size:60
Alignment explanation
Indices: 10029722--10029991 Score: 254
Period size: 59 Copynumber: 4.5 Consensus size: 60
10029712 GTAAGTCCTT
* * * * * * * *
10029722 AAACTATCCAAAAATTA-TATTTTGACCCCCGAGCT-TCTCCAAAATTACATTTTTTACCCTA
1 AAACT-TCCAAAAATTACCATTTTTACCCTCGAACTGTC-CAAAAATTCCATTTTTGACCC-G
10029783 AAACTTCCAAAAATTA-CATTTTTACCCTCGAACT-TCCAAAAATTCCA-TTTTGACCCTG
1 AAACTTCCAAAAATTACCATTTTTACCCTCGAACTGTCCAAAAATTCCATTTTTGACCC-G
* *
10029841 AAACTTCCAAAAATTATCATTTTTACCCTCGAA-TGTCCAAAAAACTCCATTTTTGACCCG
1 AAACTTCCAAAAATTACCATTTTTACCCTCGAACTGTCC-AAAAATTCCATTTTTGACCCG
** * * *
10029901 AAACTTTTAAAAATTACCA-TTTTACCCTCG-AGTGTCCAAGAATTCCGTTTTTGATCCCG
1 AAACTTCCAAAAATTACCATTTTTACCCTCGAACTGTCCAAAAATTCCATTTTTGA-CCCG
**
10029960 -ATTTTCCTAAAAATTACCA-TTTTACCCTCGAA
1 AAACTTCC-AAAAATTACCATTTTTACCCTCGAA
10029992 TATCTAAAAT
Statistics
Matches: 182, Mismatches: 19, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
58 44 0.24
59 70 0.38
60 54 0.30
61 14 0.08
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.34
Consensus pattern (60 bp):
AAACTTCCAAAAATTACCATTTTTACCCTCGAACTGTCCAAAAATTCCATTTTTGACCCG
Found at i:10029882 original size:29 final size:29
Alignment explanation
Indices: 10029723--10029991 Score: 176
Period size: 29 Copynumber: 9.1 Consensus size: 29
10029713 TAAGTCCTTA
* * *
10029723 AACTATCCAAAAATTATATTTTGACCCCCG
1 AACT-TCCAAAAATTACATTTTTACCCTCG
* * **
10029753 AGCTTCTCCAAAATTACATTTTTTACCCTAA
1 AACTTC-CAAAAATTACA-TTTTTACCCTCG
10029784 AACTTCCAAAAATTACATTTTTACCCTCG
1 AACTTCCAAAAATTACATTTTTACCCTCG
* *
10029813 AACTTCCAAAAATTCCATTTTGACCCT-G
1 AACTTCCAAAAATTACATTTTTACCCTCG
10029841 AAACTTCCAAAAATTATCATTTTTACCCTCG
1 -AACTTCCAAAAATTA-CATTTTTACCCTCG
* *
10029872 AA-TGTCCAAAAAACTCCATTTTTGA-CC-CG
1 AACT-TCC-AAAAATTACATTTTT-ACCCTCG
**
10029901 AAACTTTTAAAAATTACCA-TTTTACCCTCG
1 -AACTTCCAAAAATTA-CATTTTTACCCTCG
* * * * *
10029931 -AGTGTCCAAGAATTCCGTTTTTGATCC-CG
1 AACT-TCCAAAAATTACATTTTT-ACCCTCG
**
10029960 ATTTTCCTAAAAATTACCA-TTTTACCCTCG
1 AACTTCC-AAAAATTA-CATTTTTACCCTCG
10029990 AA
1 AA
10029992 TATCTAAAAT
Statistics
Matches: 184, Mismatches: 35, Indels: 40
0.71 0.14 0.15
Matches are distributed among these distances:
28 5 0.03
29 85 0.46
30 71 0.39
31 23 0.12
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.34
Consensus pattern (29 bp):
AACTTCCAAAAATTACATTTTTACCCTCG
Found at i:10032045 original size:55 final size:55
Alignment explanation
Indices: 10031942--10032055 Score: 158
Period size: 55 Copynumber: 2.1 Consensus size: 55
10031932 GTCATAAAAG
* * * * *
10031942 TATTTCAACATGACAATTGATTTAAATATATAAACAATCAATTCAAAAGAAGCAA
1 TATTCCAACATGAAAATTGATTTAAACATAAAAACAATCAATTAAAAAGAAGCAA
*
10031997 TATTCCAACATGAAAATTGATTTAAACA-AAAAACTAATCGATTAAAAAGAAGCAA
1 TATTCCAACATGAAAATTGATTTAAACATAAAAAC-AATCAATTAAAAAGAAGCAA
10032052 TATT
1 TATT
10032056 TCAGCATAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 5 0.10
55 47 0.90
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.28
Consensus pattern (55 bp):
TATTCCAACATGAAAATTGATTTAAACATAAAAACAATCAATTAAAAAGAAGCAA
Found at i:10032891 original size:20 final size:19
Alignment explanation
Indices: 10032853--10032895 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
10032843 AATATTTATT
*
10032853 TAATATTTTAATTAAAATAA
1 TAATATTTTAATAAAAAT-A
10032873 TAATATTTT-ATAAACAATA
1 TAATATTTTAATAAA-AATA
10032892 TAAT
1 TAAT
10032896 TATATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATATTTTAATAAAAATA
Found at i:10033392 original size:13 final size:14
Alignment explanation
Indices: 10033374--10033420 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 14
10033364 CATAAAAAAC
10033374 AAATAAATAA-AAT
1 AAATAAATAACAAT
*
10033387 ACATAAA-AACAAT
1 AAATAAATAACAAT
* *
10033400 AAATAAATAAGATT
1 AAATAAATAACAAT
10033414 AAATAAA
1 AAATAAA
10033421 AGCAAGAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 2 0.07
13 15 0.54
14 11 0.39
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (14 bp):
AAATAAATAACAAT
Found at i:10033421 original size:26 final size:24
Alignment explanation
Indices: 10033365--10033475 Score: 64
Period size: 26 Copynumber: 4.3 Consensus size: 24
10033355 AATAAATGGC
*
10033365 ATAAAAAACAAATAAATAAAATAC
1 ATAAAAAACAAATAAATAAAATAA
* *
10033389 ATAAAAACAATAAATAAATAAGATTAA
1 AT-AAAA-AACAAATAAATAA-AATAA
* *
10033416 ATAAAAGCAA-GAATACAAAAAACATAA
1 ATAAAA--AACAAATA-AATAAA-ATAA
*
10033443 AAAATGAATAACAAATAAAT-AAATAA
1 ATAA--AA-AACAAATAAATAAAATAA
10033469 ATAAAAA
1 ATAAAAA
10033476 TTAACTACTA
Statistics
Matches: 67, Mismatches: 11, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
23 1 0.01
24 4 0.06
25 4 0.06
26 28 0.42
27 20 0.30
28 4 0.06
29 6 0.09
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.17
Consensus pattern (24 bp):
ATAAAAAACAAATAAATAAAATAA
Found at i:10033480 original size:26 final size:27
Alignment explanation
Indices: 10033451--10033518 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 27
10033441 AAAAAATGAA
10033451 TAACAAATAAATAAATA-AATAAAAAT
1 TAACAAATAAATAAATATAATAAAAAT
* * *
10033477 TAACTACTAAATAAA-ATAATATAAAT
1 TAACAAATAAATAAATATAATAAAAAT
*
10033503 TATATAAA-AAATAAAT
1 TA-ACAAATAAATAAAT
10033519 GGGACCAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
25 1 0.03
26 30 0.91
27 2 0.06
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (27 bp):
TAACAAATAAATAAATATAATAAAAAT
Found at i:10033536 original size:4 final size:4
Alignment explanation
Indices: 10033365--10033518 Score: 52
Period size: 4 Copynumber: 37.5 Consensus size: 4
10033355 AATAAATGGC
* * *
10033365 ATAA A-AA ACAA ATAA ATAAA ATAC ATAA AAACA ATAA ATAA ATAA GATTAA
1 ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATA-A ATAA ATAA ATAA -A-TAA
* * * * *
10033416 ATAA A-AGCA AGAA TACAA AAAA CATAA A-AA ATGA AT-A ACAA ATAA
1 ATAA ATA--A ATAA -ATAA ATAA -ATAA ATAA ATAA ATAA ATAA ATAA
* * * *
10033461 ATAA ATAA ATAA A-AA TTAA CT-A CTAA ATAAA ATAA TATAA ATTAT ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA -ATAA A-TAA ATAA
10033510 A-AA ATAA AT
1 ATAA ATAA AT
10033519 GGGACCAAAT
Statistics
Matches: 116, Mismatches: 16, Indels: 36
0.69 0.10 0.21
Matches are distributed among these distances:
3 17 0.15
4 67 0.58
5 28 0.24
6 4 0.03
ACGTcount: A:0.70, C:0.06, G:0.03, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:10033655 original size:5 final size:5
Alignment explanation
Indices: 10033639--10033683 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
10033629 TACAAATTAG
* *
10033639 AAATA GAAATA AAATA AAATA AAACTA AATTC AAATA AAATA AAA
1 AAATA -AAATA AAATA AAATA AAA-TA AAATA AAATA AAATA AAA
10033684 ATTATAAGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
5 25 0.74
6 9 0.26
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:10033667 original size:16 final size:15
Alignment explanation
Indices: 10033639--10033683 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
10033629 TACAAATTAG
10033639 AAATAGAAATAAAATA
1 AAATA-AAATAAAATA
* *
10033655 AAATAAAACTAAATTC
1 AAATAAAA-TAAAATA
10033671 AAATAAAATAAAA
1 AAATAAAATAAAA
10033684 ATTATAAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (15 bp):
AAATAAAATAAAATA
Found at i:10041419 original size:55 final size:56
Alignment explanation
Indices: 10041343--10041475 Score: 160
Period size: 55 Copynumber: 2.4 Consensus size: 56
10041333 ATTTGGATTG
* * * * *
10041343 AATCGATTGTTATGCTGGAATATTGCTTCATTTGAATCGATTGTTTTTA-TGTTTA
1 AATCAATTGTCATGTTGGAATATTGCTACATTTGAATCGATTGTTTATATTGTTTA
* * *
10041398 AATCAATTGTCATGTTGGAATATTGCTACTTTTGAATTGATTGTTTATATTTTTTA
1 AATCAATTGTCATGTTGGAATATTGCTACATTTGAATCGATTGTTTATATTGTTTA
* * *
10041454 AATCAATTATCATATTGAAATA
1 AATCAATTGTCATGTTGGAATA
10041476 CTTTTATGTA
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
55 42 0.64
56 24 0.36
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.48
Consensus pattern (56 bp):
AATCAATTGTCATGTTGGAATATTGCTACATTTGAATCGATTGTTTATATTGTTTA
Found at i:10043702 original size:58 final size:57
Alignment explanation
Indices: 10043560--10043827 Score: 209
Period size: 58 Copynumber: 4.5 Consensus size: 57
10043550 GTAAGTCCTT
* * * * * * *
10043560 AAACTATCCAAAAATTATATTTTGACCCCCGAGCTTCTCCAAAATTACATTTTTTTACCCTA
1 AAACT-TCCAAAAATTACATTTT-ACCCTCGAACTTCT-AAAAATTCCA--TTTTGACCCCA
*
10043622 AAACTTCCAAAAAATTACATTTTCACCCTTGAACTTCTAAAAATTCCATTTTGACCCCA
1 AAACTTCC-AAAAATTACATTTT-ACCCTCGAACTTCTAAAAATTCCATTTTGACCCCA
* * * **
10043681 AAACTTCCAAAAATTACATTTTTACCCTCAAAATTCCAAAAATTCCAATTTTGA-CCTT
1 AAACTTCCAAAAATTACA-TTTTACCCTCGAACTTCTAAAAATTCC-ATTTTGACCCCA
* * * * * *
10043739 GAACTTCCAAAAAATTATCATTTTA-CCTCGAA-TGTCAAAAAACTCCATTTTTAACCCG
1 AAACTTCC-AAAAATTA-CATTTTACCCTCGAACT-TCTAAAAATTCCATTTTGACCCCA
**
10043797 AAACTTTTAAAAATTACCATTTTACCCTCGA
1 AAACTTCCAAAAATTA-CATTTTACCCTCGA
10043828 GTGTCCAAGA
Statistics
Matches: 172, Mismatches: 26, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
57 22 0.13
58 67 0.39
59 41 0.24
60 2 0.01
61 11 0.06
62 29 0.17
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (57 bp):
AAACTTCCAAAAATTACATTTTACCCTCGAACTTCTAAAAATTCCATTTTGACCCCA
Found at i:10043766 original size:29 final size:29
Alignment explanation
Indices: 10043556--10043762 Score: 164
Period size: 29 Copynumber: 6.9 Consensus size: 29
10043546 CCCTGTAAGT
*
10043556 CCTTAAACTATCCAAAAATTATATTTTGAC
1 CCTTAAACT-TCCAAAAATTACATTTTGAC
*** * * *
10043586 CCCCGAGCTTCTCCAAAATTACATTTTTTTAC
1 CCTTAAACTTC-CAAAAATTACA--TTTTGAC
* *
10043618 CCTAAAACTTCCAAAAAATTACATTTTCAC
1 CCTTAAACTTCC-AAAAATTACATTTTGAC
* * *
10043648 CCTTGAACTTCTAAAAATTCCATTTTGAC
1 CCTTAAACTTCCAAAAATTACATTTTGAC
** *
10043677 CCCAAAACTTCCAAAAATTACATTTTTAC
1 CCTTAAACTTCCAAAAATTACATTTTGAC
* * *
10043706 CCTCAAAATTCCAAAAATTCCAATTTTGA-
1 CCTTAAACTTCCAAAAATTAC-ATTTTGAC
*
10043735 CCTTGAACTTCCAAAAAATTATCATTTT
1 CCTTAAACTTCC-AAAAATTA-CATTTT
10043763 ACCTCGAATG
Statistics
Matches: 137, Mismatches: 33, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
29 66 0.48
30 47 0.34
31 2 0.01
32 22 0.16
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (29 bp):
CCTTAAACTTCCAAAAATTACATTTTGAC
Found at i:10045932 original size:55 final size:55
Alignment explanation
Indices: 10045838--10045969 Score: 167
Period size: 55 Copynumber: 2.4 Consensus size: 55
10045828 GTCATAAAAG
* * * * * *
10045838 TATTTCAACATGACAATTGATTTAAATATATAAACAATCGATTCAAAAGAAGCAA
1 TATTTCAACATGAAAATCGATTTAAACAAAAAAACAATCGATTAAAAAGAAGCAA
* *
10045893 TATTCCAACATGAAAATCGATTTAAACAAAAAAATAATCGATTAAAAAGAAGCAA
1 TATTTCAACATGAAAATCGATTTAAACAAAAAAACAATCGATTAAAAAGAAGCAA
*
10045948 TATTTCAGCAT-AACAATCGATT
1 TATTTCAACATGAA-AATCGATT
10045970 CAATCCAAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
54 2 0.03
55 64 0.97
ACGTcount: A:0.50, C:0.14, G:0.09, T:0.27
Consensus pattern (55 bp):
TATTTCAACATGAAAATCGATTTAAACAAAAAAACAATCGATTAAAAAGAAGCAA
Found at i:10046784 original size:20 final size:19
Alignment explanation
Indices: 10046746--10046788 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
10046736 AATATTTATT
*
10046746 TAATATTTTAATTAAAATAA
1 TAATATTTTAATAAAAAT-A
10046766 TAATATTTT-ATAAACAATA
1 TAATATTTTAATAAA-AATA
10046785 TAAT
1 TAAT
10046789 TATATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATATTTTAATAAAAATA
Found at i:10047374 original size:26 final size:27
Alignment explanation
Indices: 10047345--10047412 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 27
10047335 AAAAAATGAA
10047345 TAACAAATAAATAAATA-AATAAAAAT
1 TAACAAATAAATAAATATAATAAAAAT
* * *
10047371 TAACTACTAAATAAA-ATAATATAAAT
1 TAACAAATAAATAAATATAATAAAAAT
*
10047397 TATATAAA-AAATAAAT
1 TA-ACAAATAAATAAAT
10047413 GGGACCAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
25 1 0.03
26 30 0.91
27 2 0.06
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (27 bp):
TAACAAATAAATAAATATAATAAAAAT
Found at i:10047549 original size:5 final size:5
Alignment explanation
Indices: 10047533--10047577 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
10047523 GTACAATTAG
* *
10047533 AAATA GAAATA AAATA AAATA AAACTA AATTC AAATA AAATA AAA
1 AAATA -AAATA AAATA AAATA AAA-TA AAATA AAATA AAATA AAA
10047578 ATTATAAGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
5 25 0.74
6 9 0.26
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:10047561 original size:16 final size:15
Alignment explanation
Indices: 10047533--10047577 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
10047523 GTACAATTAG
10047533 AAATAGAAATAAAATA
1 AAATA-AAATAAAATA
* *
10047549 AAATAAAACTAAATTC
1 AAATAAAA-TAAAATA
10047565 AAATAAAATAAAA
1 AAATAAAATAAAA
10047578 ATTATAAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (15 bp):
AAATAAAATAAAATA
Found at i:10047677 original size:18 final size:18
Alignment explanation
Indices: 10047654--10047702 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
10047644 CAATCGAAGG
10047654 ATTAAATTAAAAAATAAA
1 ATTAAATTAAAAAATAAA
** *
10047672 ATTAAAGGGAAAAATTAAA
1 ATTAAA-TTAAAAAATAAA
*
10047691 ATTGAATTAAAA
1 ATTAAATTAAAA
10047703 TTAAAAAGGA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (18 bp):
ATTAAATTAAAAAATAAA
Found at i:10053818 original size:57 final size:57
Alignment explanation
Indices: 10053754--10053862 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 57
10053744 ATAGCCATTG
*
10053754 ATATTAAATCTTTA-TTTTCTCATATCTGAATCCAAAAGAAAATGCCAAAAAAAACCC
1 ATATTAAATCTTTATTTTTC-CATATCTGAACCCAAAAGAAAATGCCAAAAAAAACCC
* *
10053811 ATATTAAATTTTTATTTTTCCATATCTGAACCCAAAAGAAAATGCTAAAAAA
1 ATATTAAATCTTTATTTTTCCATATCTGAACCCAAAAGAAAATGCCAAAAAA
10053863 GAATCTAGAG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
57 43 0.90
58 5 0.10
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.32
Consensus pattern (57 bp):
ATATTAAATCTTTATTTTTCCATATCTGAACCCAAAAGAAAATGCCAAAAAAAACCC
Found at i:10056093 original size:20 final size:19
Alignment explanation
Indices: 10056055--10056097 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
10056045 AATATTTATT
*
10056055 TAATATTTTAATTAAAATAA
1 TAATATTTTAATAAAAAT-A
10056075 TAATATTTT-ATAAACAATA
1 TAATATTTTAATAAA-AATA
10056094 TAAT
1 TAAT
10056098 TATATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATATTTTAATAAAAATA
Found at i:10056598 original size:9 final size:9
Alignment explanation
Indices: 10056580--10056740 Score: 66
Period size: 9 Copynumber: 16.9 Consensus size: 9
10056570 CATTAAAAAC
10056580 AAATAAATA
1 AAATAAATA
*
10056589 AAATACATA
1 AAATAAATA
*
10056598 AAAAACAAT-
1 AAATA-AATA
10056607 AAATAAATA
1 AAATAAATA
*
10056616 AGATTAAATA
1 A-AATAAATA
10056626 AAGGCA-AGAATA
1 AA---ATA-AATA
10056638 TAAATAACATAA
1 -AAATAA-AT-A
*
10056650 AAATGAATAA
1 AAATAAAT-A
10056660 CAAATAAAT-
1 -AAATAAATA
10056669 AAATAAATA
1 AAATAAATA
*
10056678 AAA-CAA-A
1 AAATAAATA
10056685 AAATAAATAA
1 AAATAAAT-A
10056695 AAATTAAATA
1 AAA-TAAATA
10056705 CTAAATAAAATA
1 --AAAT-AAATA
*
10056717 ATATAAATA
1 AAATAAATA
*
10056726 ATAT-AA-A
1 AAATAAATA
10056733 AAATAAAT
1 AAATAAAT
10056741 GGGACCAAAT
Statistics
Matches: 118, Mismatches: 12, Indels: 44
0.68 0.07 0.25
Matches are distributed among these distances:
7 8 0.07
8 19 0.16
9 30 0.25
10 24 0.20
11 22 0.19
12 13 0.11
13 2 0.02
ACGTcount: A:0.71, C:0.04, G:0.03, T:0.22
Consensus pattern (9 bp):
AAATAAATA
Found at i:10056660 original size:15 final size:15
Alignment explanation
Indices: 10056637--10056704 Score: 61
Period size: 15 Copynumber: 4.5 Consensus size: 15
10056627 AGGCAAGAAT
10056637 ATAAATAACATAAAA
1 ATAAATAACATAAAA
*
10056652 ATGAATAACA-AATAA
1 ATAAATAACATAA-AA
10056667 ATAAATAA-ATAAAACA
1 ATAAATAACAT-AAA-A
*
10056683 AAAAATAA-ATAAAA
1 ATAAATAACATAAAA
10056697 ATTAAATA
1 A-TAAATA
10056705 CTAAATAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
14 5 0.11
15 27 0.61
16 12 0.27
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.21
Consensus pattern (15 bp):
ATAAATAACATAAAA
Found at i:10056664 original size:11 final size:10
Alignment explanation
Indices: 10056634--10056726 Score: 53
Period size: 11 Copynumber: 8.5 Consensus size: 10
10056624 TAAAGGCAAG
*
10056634 AATATAAATA
1 AATAAAAATA
*
10056644 ACATAAAAATG
1 A-ATAAAAATA
10056655 AATAACAAATA
1 AATAA-AAATA
10056666 AATAAATAAATAA
1 AAT-AA-AAAT-A
*
10056679 AACAAAAAATA
1 AA-TAAAAATA
10056690 AATAAAAATTA
1 AATAAAAA-TA
*
10056701 AATACTAAATA
1 AATA-AAAATA
*
10056712 AA-ATAATATA
1 AATA-AAAATA
10056722 AATAA
1 AATAA
10056727 TATAAAAAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
10 18 0.28
11 29 0.45
12 13 0.20
13 5 0.08
ACGTcount: A:0.72, C:0.04, G:0.01, T:0.23
Consensus pattern (10 bp):
AATAAAAATA
Done.