Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 56 of 210
Found at i:16991703 original size:19 final size:19
Alignment explanation
Indices: 16991656--16991749 Score: 91
Period size: 19 Copynumber: 4.8 Consensus size: 19
16991646 TTAATTTTTA
*
16991656 ATAAAAAATTTTATTAAAATTT
1 ATAAAAAA--TTA-TAAAAATT
*
16991678 ATTAAAAATTATAAAAATT
1 ATAAAAAATTATAAAAATT
* *
16991697 TTAAAAAATCATAAAAATT
1 ATAAAAAATTATAAAAATT
** *
16991716 ATAAAATTTTATAAAAATC
1 ATAAAAAATTATAAAAATT
16991735 AT-AAAAATTATAAAA
1 ATAAAAAATTATAAAA
16991750 TACATCAAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
18 11 0.18
19 39 0.65
20 3 0.05
22 7 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAAAAAATTATAAAAATT
Found at i:16991711 original size:28 final size:29
Alignment explanation
Indices: 16991659--16991749 Score: 132
Period size: 28 Copynumber: 3.1 Consensus size: 29
16991649 ATTTTTAATA
* *
16991659 AAAAATTTTATTAAAATTTATTAAAAATTAT
1 AAAAATTTTA-TAAAAATCA-TAAAAATTAT
16991690 AAAAATTTTA-AAAAATCATAAAAATTAT
1 AAAAATTTTATAAAAATCATAAAAATTAT
16991718 -AAAATTTTATAAAAATCATAAAAATTAT
1 AAAAATTTTATAAAAATCATAAAAATTAT
16991746 AAAA
1 AAAA
16991750 TACATCAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
27 9 0.16
28 28 0.50
29 9 0.16
31 10 0.18
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (29 bp):
AAAAATTTTATAAAAATCATAAAAATTAT
Found at i:16991759 original size:28 final size:28
Alignment explanation
Indices: 16991680--16991760 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
16991670 TAAAATTTAT
**
16991680 TAAAAATTATAAAAATTTTA-AAAAATCA
1 TAAAAATTAT-AAAATTACATAAAAATCA
**
16991708 TAAAAATTATAAAATTTTATAAAAATCA
1 TAAAAATTATAAAATTACATAAAAATCA
16991736 TAAAAATTATAAAA-TACATCAAAAA
1 TAAAAATTATAAAATTACAT-AAAAA
16991761 GACCCTTTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
27 12 0.24
28 37 0.76
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (28 bp):
TAAAAATTATAAAATTACATAAAAATCA
Found at i:16991965 original size:18 final size:18
Alignment explanation
Indices: 16991925--16991968 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
16991915 GGGCGATAAT
16991925 TTTTTATATTTTTTACAA
1 TTTTTATATTTTTTACAA
*
16991943 ATTTTATATTTCTTTAC-A
1 TTTTTATATTT-TTTACAA
16991961 TTTTTATA
1 TTTTTATA
16991969 AATTCTTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTTATATTTTTTACAA
Found at i:16992080 original size:26 final size:27
Alignment explanation
Indices: 16992050--16992112 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 27
16992040 AAATTCTCTA
* *
16992050 ATTTTTAAT-AAATTTAAAT-ATTTTT
1 ATTTTTTATAAAAGTTAAATAATTTTT
16992075 ATTTTTTATAAAAGTTAAATAATTTTT
1 ATTTTTTATAAAAGTTAAATAATTTTT
16992102 ATAATTTTTAT
1 AT--TTTTTAT
16992113 TGATTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 8 0.25
26 9 0.28
27 8 0.25
29 7 0.22
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (27 bp):
ATTTTTTATAAAAGTTAAATAATTTTT
Found at i:16994469 original size:15 final size:16
Alignment explanation
Indices: 16994451--16994481 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
16994441 CTCCCAATCC
16994451 CTCTTCTCTTC-CTTT
1 CTCTTCTCTTCTCTTT
16994466 CTCTTCTCTTCTCTTT
1 CTCTTCTCTTCTCTTT
16994482 TTCATGGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (16 bp):
CTCTTCTCTTCTCTTT
Found at i:16999346 original size:6 final size:6
Alignment explanation
Indices: 16999335--16999385 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
16999325 ATATTGCAAG
*
16999335 TTTCCA TTTCCA TTTTCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA
16999383 TTT
1 TTT
16999386 TTTGGAAACC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.16, C:0.29, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTCCA
Found at i:17008167 original size:14 final size:13
Alignment explanation
Indices: 17008147--17008178 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
17008137 TATAAATACT
17008147 AAATAAAATAATA
1 AAATAAAATAATA
17008160 ATAATAAAATAATA
1 A-AATAAAATAATA
17008174 AAATA
1 AAATA
17008179 TCATTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
AAATAAAATAATA
Found at i:17010392 original size:27 final size:27
Alignment explanation
Indices: 17010348--17010413 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
17010338 TTAACCCATG
** *
17010348 TTTAATGTCCTGGCAGACTATCCCGTA
1 TTTAATGTCCCAGCAGACTACCCCGTA
* * *
17010375 TTTAATGTCCCAGTAGACTACCCCTTG
1 TTTAATGTCCCAGCAGACTACCCCGTA
*
17010402 TTTATTGTCCCA
1 TTTAATGTCCCA
17010414 ATGAACTATA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.36
Consensus pattern (27 bp):
TTTAATGTCCCAGCAGACTACCCCGTA
Found at i:17013025 original size:13 final size:13
Alignment explanation
Indices: 17013007--17013033 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17012997 AAAGTCAACC
17013007 ATATAAGAAGTTA
1 ATATAAGAAGTTA
17013020 ATATAAGAAGTTA
1 ATATAAGAAGTTA
17013033 A
1 A
17013034 AATCAAGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.30
Consensus pattern (13 bp):
ATATAAGAAGTTA
Found at i:17013687 original size:9 final size:9
Alignment explanation
Indices: 17013675--17013715 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
17013665 TCAATTAGGT
17013675 TAATTCGGG
1 TAATTCGGG
*
17013684 TAATTCGGT
1 TAATTCGGG
17013693 TAATTCGGG
1 TAATTCGGG
*
17013702 TAATTCGGT
1 TAATTCGGG
17013711 TAATT
1 TAATT
17013716 TTTAACCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.41
Consensus pattern (9 bp):
TAATTCGGG
Found at i:17013693 original size:18 final size:18
Alignment explanation
Indices: 17013667--17013715 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
17013657 TGTATGATTC
*
17013667 AATTAGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
17013685 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
17013703 AATTCGGTTAATT
1 AATTCGGTTAATT
17013716 TTTAACCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.41
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:17018767 original size:6 final size:6
Alignment explanation
Indices: 17018758--17018790 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
17018748 TTCTTGGTAT
17018758 TGGGAA TGGGAA TGGGAA TGGGAA TGGGAA TGG
1 TGGGAA TGGGAA TGGGAA TGGGAA TGGGAA TGG
17018791 AGTTGAGGAT
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:0.30, C:0.00, G:0.52, T:0.18
Consensus pattern (6 bp):
TGGGAA
Found at i:17020286 original size:16 final size:16
Alignment explanation
Indices: 17020267--17020301 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
17020257 TAATTGAAAT
17020267 GTGTTAGAATTTTAGG
1 GTGTTAGAATTTTAGG
17020283 GTGTTAGAATTTTAGG
1 GTGTTAGAATTTTAGG
17020299 GTG
1 GTG
17020302 GTGCCACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.34, T:0.43
Consensus pattern (16 bp):
GTGTTAGAATTTTAGG
Found at i:17020551 original size:18 final size:18
Alignment explanation
Indices: 17020528--17020564 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17020518 TAACAAAGTG
17020528 TGTATAATAAA-ATTAAAA
1 TGTATAA-AAATATTAAAA
17020546 TGTATAAAAATATTAAAA
1 TGTATAAAAATATTAAAA
17020564 T
1 T
17020565 AAAAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
TGTATAAAAATATTAAAA
Found at i:17021856 original size:8 final size:8
Alignment explanation
Indices: 17021838--17021886 Score: 55
Period size: 8 Copynumber: 6.1 Consensus size: 8
17021828 TTTTTAAAAT
17021838 ATTTA-AA
1 ATTTATAA
17021845 ATTTATAA
1 ATTTATAA
17021853 ATTTATGAA
1 ATTTAT-AA
* *
17021862 AATTAAAA
1 ATTTATAA
17021870 ATTTATAA
1 ATTTATAA
*
17021878 ATATATAA
1 ATTTATAA
17021886 A
1 A
17021887 AGAACTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
7 5 0.14
8 24 0.69
9 6 0.17
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (8 bp):
ATTTATAA
Found at i:17028447 original size:16 final size:16
Alignment explanation
Indices: 17028423--17028494 Score: 72
Period size: 16 Copynumber: 4.5 Consensus size: 16
17028413 CGTTTGGTTC
*
17028423 ATTGGAATGGAATAGA
1 ATTGTAATGGAATAGA
*
17028439 ATTGTAATGGAATAGG
1 ATTGTAATGGAATAGA
* *
17028455 ACTGTAATGGAATAAA
1 ATTGTAATGGAATAGA
* * *
17028471 ACTGTGATGGGATAGA
1 ATTGTAATGGAATAGA
*
17028487 GTTGTAAT
1 ATTGTAAT
17028495 CAGTGATTCA
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.39, C:0.03, G:0.29, T:0.29
Consensus pattern (16 bp):
ATTGTAATGGAATAGA
Found at i:17028554 original size:62 final size:62
Alignment explanation
Indices: 17028457--17028599 Score: 277
Period size: 62 Copynumber: 2.3 Consensus size: 62
17028447 GGAATAGGAC
17028457 TGTAATGGAATAAAACTGTGATGGGATAGAGTTGTAATCAGTGATTCAATTGTTTGGTTGAA
1 TGTAATGGAATAAAACTGTGATGGGATAGAGTTGTAATCAGTGATTCAATTGTTTGGTTGAA
17028519 TGTAATGGAATAAAACTGTGATGGGATAGAGTTGTAATCAGTGATTCAATTGTTTGGTTGAA
1 TGTAATGGAATAAAACTGTGATGGGATAGAGTTGTAATCAGTGATTCAATTGTTTGGTTGAA
*
17028581 TGTAATGGAATAGAACTGT
1 TGTAATGGAATAAAACTGT
17028600 AATAGTATTA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 80 1.00
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (62 bp):
TGTAATGGAATAAAACTGTGATGGGATAGAGTTGTAATCAGTGATTCAATTGTTTGGTTGAA
Found at i:17032588 original size:9 final size:9
Alignment explanation
Indices: 17032574--17032650 Score: 102
Period size: 9 Copynumber: 8.4 Consensus size: 9
17032564 TTTGGTTAAA
17032574 AATTACCCG
1 AATTACCCG
17032583 AATTACCCG
1 AATTACCCG
*
17032592 AATTAACCG
1 AATTACCCG
17032601 AATTACCCG
1 AATTACCCG
*
17032610 AATTAACCG
1 AATTACCCG
17032619 AATTA-CCG
1 AATTACCCG
*
17032627 AAAAATACCCG
1 --AATTACCCG
17032638 AATTACCCG
1 AATTACCCG
17032647 AATT
1 AATT
17032651 TTTTTTATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
8 3 0.05
9 50 0.83
10 4 0.07
11 3 0.05
ACGTcount: A:0.40, C:0.27, G:0.10, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:17032606 original size:27 final size:27
Alignment explanation
Indices: 17032573--17032650 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
17032563 TTTTGGTTAA
17032573 AAATTACCCGAATTACCCGAATTAACCG
1 AAATTACCCGAATTACCCGAATT-ACCG
*
17032601 -AATTACCCGAATTAACCGAATTACCG
1 AAATTACCCGAATTACCCGAATTACCG
*
17032627 AAAAATACCCGAATTACCCGAATT
1 -AAATTACCCGAATTACCCGAATT
17032651 TTTTTTATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
26 4 0.09
27 21 0.47
28 20 0.44
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.22
Consensus pattern (27 bp):
AAATTACCCGAATTACCCGAATTACCG
Found at i:17037831 original size:18 final size:18
Alignment explanation
Indices: 17037808--17037884 Score: 88
Period size: 18 Copynumber: 4.4 Consensus size: 18
17037798 CAAGGTCACG
*
17037808 ATCAATAGCGTCACTATC
1 ATCAATAACGTCACTATC
* *
17037826 ATCAATAATGTCACTAGC
1 ATCAATAACGTCACTATC
*
17037844 ATCAATATCGTCACTATC
1 ATCAATAACGTCACTATC
*
17037862 ATCAATATCG--A-TATC
1 ATCAATAACGTCACTATC
17037877 ATCAATAA
1 ATCAATAA
17037885 GAAAACCCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
15 11 0.21
16 1 0.02
18 40 0.77
ACGTcount: A:0.39, C:0.23, G:0.08, T:0.30
Consensus pattern (18 bp):
ATCAATAACGTCACTATC
Found at i:17040381 original size:24 final size:21
Alignment explanation
Indices: 17040318--17040389 Score: 99
Period size: 21 Copynumber: 3.3 Consensus size: 21
17040308 AACTGAGTTA
*
17040318 GACAAAAAGAGAAGCAACTTG
1 GACAAAAAGAGAAGTAACTTG
17040339 GACAAAAAGAGAAGTAACTTG
1 GACAAAAAGAGAAGTAACTTG
*
17040360 GACAAAAAGAAACGAAGTAACTTC
1 GACAAAAAG--A-GAAGTAACTTG
17040384 GACAAA
1 GACAAA
17040390 TCTTTTTTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
21 29 0.63
23 1 0.02
24 16 0.35
ACGTcount: A:0.54, C:0.14, G:0.21, T:0.11
Consensus pattern (21 bp):
GACAAAAAGAGAAGTAACTTG
Found at i:17043153 original size:7 final size:7
Alignment explanation
Indices: 17043141--17043166 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
17043131 TATTGAATAA
17043141 TATTTTG
1 TATTTTG
17043148 TATTTTG
1 TATTTTG
17043155 TATTTTG
1 TATTTTG
17043162 TATTT
1 TATTT
17043167 AATTATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (7 bp):
TATTTTG
Found at i:17051177 original size:12 final size:12
Alignment explanation
Indices: 17051154--17051187 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
17051144 TATATATTTT
17051154 AAAATT-ATATA
1 AAAATTAATATA
17051165 AAAATTAATATA
1 AAAATTAATATA
*
17051177 AAAAGTAATAT
1 AAAATTAATAT
17051188 GGGTGGGCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:17057937 original size:30 final size:30
Alignment explanation
Indices: 17057903--17057961 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
17057893 TACGAGCTTT
17057903 GGGGCAAAAGTGTAAATATGCAAAAGTTTA
1 GGGGCAAAAGTGTAAATATGCAAAAGTTTA
* * *
17057933 GGGGCAAAATTGTAAATTTGCCAAAGTTT
1 GGGGCAAAAGTGTAAATATGCAAAAGTTT
17057962 GAGTCAAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.27
Consensus pattern (30 bp):
GGGGCAAAAGTGTAAATATGCAAAAGTTTA
Found at i:17058433 original size:23 final size:23
Alignment explanation
Indices: 17058403--17058447 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
17058393 GTGTTATTGA
*
17058403 TCAGTGGTAGTTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
17058426 TCAGTGGTAGCTTCGGCTACAT
1 TCAGTGGTAGCTTCGGCTACAT
17058448 ATAAGTGTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.36
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:17058454 original size:23 final size:23
Alignment explanation
Indices: 17058405--17058454 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
17058395 GTTATTGATC
* * *
17058405 AGTGGTAGTTTCGGCTACATTTC
1 AGTGGTAGCTTCGGCTACATATA
17058428 AGTGGTAGCTTCGGCTACATATA
1 AGTGGTAGCTTCGGCTACATATA
17058451 AGTG
1 AGTG
17058455 TGGCACTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (23 bp):
AGTGGTAGCTTCGGCTACATATA
Found at i:17077975 original size:5 final size:5
Alignment explanation
Indices: 17077965--17077995 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
17077955 CTTTTTTTAT
17077965 TTAAA TTAAA TTAAA TT-AA TTAAA TTAAA TT
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TT
17077996 GTAAATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (5 bp):
TTAAA
Found at i:17077987 original size:14 final size:14
Alignment explanation
Indices: 17077968--17077995 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17077958 TTTTTATTTA
17077968 AATTAAATTAAATT
1 AATTAAATTAAATT
17077982 AATTAAATTAAATT
1 AATTAAATTAAATT
17077996 GTAAATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTAAATTAAATT
Found at i:17081054 original size:15 final size:16
Alignment explanation
Indices: 17081023--17081059 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
17081013 AAAGTGCTGG
17081023 AAATAATAAAATAAAA
1 AAATAATAAAATAAAA
*
17081039 AAATAA-AAAGTAAAA
1 AAATAATAAAATAAAA
17081054 AAATAA
1 AAATAA
17081060 GTAGGCAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (16 bp):
AAATAATAAAATAAAA
Found at i:17092586 original size:27 final size:27
Alignment explanation
Indices: 17092552--17092615 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
17092542 CATTTCAATT
17092552 CCTA-GGGGTGTA-ACAG-TCATTTTAC
1 CCTATGGGG-GTATACAGATCATTTTAC
* *
17092577 CCTATGGGGGTATTCGGATCATTTTAC
1 CCTATGGGGGTATACAGATCATTTTAC
17092604 CCTATGGGGGTA
1 CCTATGGGGGTA
17092616 CTTTGGTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 7 0.21
26 6 0.18
27 21 0.62
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (27 bp):
CCTATGGGGGTATACAGATCATTTTAC
Found at i:17095359 original size:17 final size:16
Alignment explanation
Indices: 17095293--17095359 Score: 55
Period size: 17 Copynumber: 4.1 Consensus size: 16
17095283 CATTCATAGT
*
17095293 TCACAATTAATATAGC
1 TCACAATTAATAGAGC
*
17095309 TCACAATTCAACAGAGC
1 TCACAATT-AATAGAGC
* *
17095326 TCACACA-TAGTATAGC
1 TCACA-ATTAATAGAGC
*
17095342 TCACAATTCAGTAGAGC
1 TCACAATT-AATAGAGC
17095359 T
1 T
17095360 AGCATAGTAG
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
15 1 0.02
16 19 0.46
17 20 0.49
18 1 0.02
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (16 bp):
TCACAATTAATAGAGC
Found at i:17106670 original size:17 final size:18
Alignment explanation
Indices: 17106638--17106671 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
17106628 GGAAGTGTTG
17106638 TGCTTTGTTGGATGATGT
1 TGCTTTGTTGGATGATGT
*
17106656 TGCTTT-TTTGATGATG
1 TGCTTTGTTGGATGATG
17106672 AATATTTGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.12, C:0.06, G:0.29, T:0.53
Consensus pattern (18 bp):
TGCTTTGTTGGATGATGT
Found at i:17108562 original size:26 final size:26
Alignment explanation
Indices: 17108528--17108579 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
17108518 TGATTGAAAC
*
17108528 ACATTAATTACAACACAATTCAAAAT
1 ACATGAATTACAACACAATTCAAAAT
17108554 ACATGAATTACAACACAATTCAAAAT
1 ACATGAATTACAACACAATTCAAAAT
17108580 TAAACATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.54, C:0.19, G:0.02, T:0.25
Consensus pattern (26 bp):
ACATGAATTACAACACAATTCAAAAT
Found at i:17116309 original size:30 final size:30
Alignment explanation
Indices: 17116273--17116354 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
17116263 AATATCTCGG
17116273 TACCCATATCTTTGACTTTCCAATATTTGA
1 TACCCATATCTTTGACTTTCCAATATTTGA
* *
17116303 TACCCATATCTTTGACTTTCTATTATTTGA
1 TACCCATATCTTTGACTTTCCAATATTTGA
*
17116333 TACCCATATCTTTGATTTTCCA
1 TACCCATATCTTTGACTTTCCA
17116355 TAAATATGGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.24, C:0.23, G:0.06, T:0.46
Consensus pattern (30 bp):
TACCCATATCTTTGACTTTCCAATATTTGA
Found at i:17116316 original size:15 final size:15
Alignment explanation
Indices: 17116273--17116348 Score: 57
Period size: 15 Copynumber: 5.1 Consensus size: 15
17116263 AATATCTCGG
17116273 TACCCATATCTTTGA
1 TACCCATATCTTTGA
** *
17116288 CTTTCCA-ATATTTGA
1 -TACCCATATCTTTGA
17116303 TACCCATATCTTTGA
1 TACCCATATCTTTGA
** * *
17116318 CTTTCTAT-TATTTGA
1 -TACCCATATCTTTGA
17116333 TACCCATATCTTTGA
1 TACCCATATCTTTGA
17116348 T
1 T
17116349 TTTCCATAAA
Statistics
Matches: 43, Mismatches: 14, Indels: 7
0.67 0.22 0.11
Matches are distributed among these distances:
14 8 0.19
15 27 0.63
16 8 0.19
ACGTcount: A:0.25, C:0.22, G:0.07, T:0.46
Consensus pattern (15 bp):
TACCCATATCTTTGA
Found at i:17120971 original size:30 final size:30
Alignment explanation
Indices: 17120935--17121016 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
17120925 AATATCTCGG
17120935 TACCCATATCTTTGACTTTCCAATATTTGA
1 TACCCATATCTTTGACTTTCCAATATTTGA
* *
17120965 TACCCATATCTTTGACTTTCTATTATTTGA
1 TACCCATATCTTTGACTTTCCAATATTTGA
*
17120995 TACCCATATCTTTGATTTTCCA
1 TACCCATATCTTTGACTTTCCA
17121017 TAAATATGGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.24, C:0.23, G:0.06, T:0.46
Consensus pattern (30 bp):
TACCCATATCTTTGACTTTCCAATATTTGA
Found at i:17120978 original size:15 final size:15
Alignment explanation
Indices: 17120935--17121010 Score: 57
Period size: 15 Copynumber: 5.1 Consensus size: 15
17120925 AATATCTCGG
17120935 TACCCATATCTTTGA
1 TACCCATATCTTTGA
** *
17120950 CTTTCCA-ATATTTGA
1 -TACCCATATCTTTGA
17120965 TACCCATATCTTTGA
1 TACCCATATCTTTGA
** * *
17120980 CTTTCTAT-TATTTGA
1 -TACCCATATCTTTGA
17120995 TACCCATATCTTTGA
1 TACCCATATCTTTGA
17121010 T
1 T
17121011 TTTCCATAAA
Statistics
Matches: 43, Mismatches: 14, Indels: 7
0.67 0.22 0.11
Matches are distributed among these distances:
14 8 0.19
15 27 0.63
16 8 0.19
ACGTcount: A:0.25, C:0.22, G:0.07, T:0.46
Consensus pattern (15 bp):
TACCCATATCTTTGA
Found at i:17129392 original size:72 final size:72
Alignment explanation
Indices: 17129275--17129438 Score: 206
Period size: 72 Copynumber: 2.3 Consensus size: 72
17129265 CGAAGTATGT
* * * * *
17129275 TTTTATCAATAGTTATTTATGCTTGGTTTTTGGATATTGAATTTATGTTTTACATATTTATGT-G
1 TTTTATCAATAGTTGTTTATGCTTGGTCTTTAGATATTGAATTTATGTTCTACATATTT-TGTAC
17129339 T-AATCTAG
65 TAAAT-TAG
* * * * *
17129347 TTTTATTAATAGTTGTTTGTGTTTGGTCTTTAGATATTGAATTTATGTTCTACTTATTTTTTACT
1 TTTTATCAATAGTTGTTTATGCTTGGTCTTTAGATATTGAATTTATGTTCTACATATTTTGTACT
17129412 AAATTAG
66 AAATTAG
17129419 TTTTATCAATAGTTGTTTAT
1 TTTTATCAATAGTTGTTTAT
17129439 ATGTGATTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
71 2 0.03
72 73 0.94
73 3 0.04
ACGTcount: A:0.24, C:0.05, G:0.14, T:0.56
Consensus pattern (72 bp):
TTTTATCAATAGTTGTTTATGCTTGGTCTTTAGATATTGAATTTATGTTCTACATATTTTGTACT
AAATTAG
Found at i:17131220 original size:13 final size:13
Alignment explanation
Indices: 17131202--17131226 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17131192 CTAATTACAA
17131202 ATATTTAATTATT
1 ATATTTAATTATT
17131215 ATATTTAATTAT
1 ATATTTAATTAT
17131227 AGTTTATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATATTTAATTATT
Found at i:17131251 original size:19 final size:19
Alignment explanation
Indices: 17131214--17131251 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
17131204 ATTTAATTAT
*
17131214 TATATTTAATTATAGTTTA
1 TATATTTAATTATAATTTA
17131233 TATATTCTAATTA-AATTTA
1 TATATT-TAATTATAATTTA
17131252 ATAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (19 bp):
TATATTTAATTATAATTTA
Found at i:17131502 original size:13 final size:13
Alignment explanation
Indices: 17131481--17131528 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
17131471 ACACTCAAAA
17131481 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
17131494 TTCTCAAAACCAC
1 TTTTCAAAAGCAC
* *
17131507 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
17131520 TTTTCAAAA
1 TTTTCAAAA
17131529 ATAAGGAAGA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:17137680 original size:31 final size:31
Alignment explanation
Indices: 17137626--17137687 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
17137616 AATAACAATC
* *
17137626 CAATGACTTCAATAAAAACTTTTGAATAGTT
1 CAATAACTTAAATAAAAACTTTTGAATAGTT
* *
17137657 CAATAACTTAAATCAAAATTTTTGAATAGTT
1 CAATAACTTAAATAAAAACTTTTGAATAGTT
17137688 TAATGACCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (31 bp):
CAATAACTTAAATAAAAACTTTTGAATAGTT
Found at i:17137706 original size:31 final size:32
Alignment explanation
Indices: 17137639--17137708 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
17137629 TGACTTCAAT
* * *
17137639 AAAAACTTTTGAATAGTTCAATAACTTAAATC
1 AAAAATTTTTGAATAGTTCAATAACTCAAAAC
* *
17137671 -AAAATTTTTGAATAGTTTAATGAC-CAAAAC
1 AAAAATTTTTGAATAGTTCAATAACTCAAAAC
17137701 AAAAATTT
1 AAAAATTT
17137709 ATAATTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (32 bp):
AAAAATTTTTGAATAGTTCAATAACTCAAAAC
Found at i:17138108 original size:13 final size:13
Alignment explanation
Indices: 17138090--17138120 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
17138080 ATTTAGTATT
17138090 TATATAATAAATA
1 TATATAATAAATA
17138103 TATATAATAAATA
1 TATATAATAAATA
17138116 TATAT
1 TATAT
17138121 TTTTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TATATAATAAATA
Found at i:17139043 original size:19 final size:19
Alignment explanation
Indices: 17139019--17139065 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
17139009 CTAACCAAAA
17139019 TTTTACAACATTT-TTTTTC
1 TTTTACAAC-TTTATTTTTC
*
17139038 TTTTACAACTTTATTTTTT
1 TTTTACAACTTTATTTTTC
17139057 TTCTTACAA
1 TT-TTACAA
17139066 AAATATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 3 0.12
19 16 0.64
20 6 0.24
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTACAACTTTATTTTTC
Found at i:17139552 original size:25 final size:28
Alignment explanation
Indices: 17139524--17139581 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 28
17139514 AATTTATACT
* *
17139524 AATATTTA-A-TAATATTTAAGT-TTAA
1 AATATTTAGATTAATATTAAACTCTTAA
17139549 AATA-TTAGATTAATATTAAACTCTTAA
1 AATATTTAGATTAATATTAAACTCTTAA
17139576 AATATT
1 AATATT
17139582 AAACATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 3 0.11
25 5 0.19
26 10 0.37
27 8 0.30
28 1 0.04
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (28 bp):
AATATTTAGATTAATATTAAACTCTTAA
Found at i:17142422 original size:26 final size:25
Alignment explanation
Indices: 17142379--17142436 Score: 89
Period size: 26 Copynumber: 2.3 Consensus size: 25
17142369 CTCACCCCAG
*
17142379 TTTTACCCCAGTAAAATTTTTATAA
1 TTTTACCCCAGTAAAATTTTGATAA
*
17142404 TTTTACCCCTAGTAAAATTTTGATGA
1 TTTTACCCC-AGTAAAATTTTGATAA
17142430 TTTTACC
1 TTTTACC
17142437 ATCGATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 9 0.30
26 21 0.70
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (25 bp):
TTTTACCCCAGTAAAATTTTGATAA
Found at i:17142445 original size:26 final size:26
Alignment explanation
Indices: 17142379--17142449 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
17142369 CTCACCCCAG
*
17142379 TTTTACCCC-AGTAAAATTTTTATAA
1 TTTTACCCCGAGTAAAATTTTGATAA
* *
17142404 TTTTACCCCTAGTAAAATTTTGATGA
1 TTTTACCCCGAGTAAAATTTTGATAA
*
17142430 TTTTACCATCGA-TAAAATTT
1 TTTTACC-CCGAGTAAAATTT
17142450 AGAGAAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
25 9 0.22
26 29 0.73
27 2 0.05
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (26 bp):
TTTTACCCCGAGTAAAATTTTGATAA
Found at i:17146801 original size:73 final size:73
Alignment explanation
Indices: 17146690--17146852 Score: 204
Period size: 73 Copynumber: 2.2 Consensus size: 73
17146680 ACTAAAATTA
* * * *
17146690 CTCAAACGAGTAATGTCTACTGATTCC-ATTGAAAGTGCTCAAACGAGAAATATCTACTGATTCT
1 CTCAAACGAGCAATATCGACT-AATCCTATTGAAAGTGCTCAAACGAGAAATATCTACTGATTCT
17146754 ACTGAAAGTG
65 ACTG-AAGTG
* * * * * *
17146764 TTC-AATGAGCAATATCGACTAATCCTATTGAATGTGCTCAAATGAGCAATGTCTACTGATTCTA
1 CTCAAACGAGCAATATCGACTAATCCTATTGAAAGTGCTCAAACGAGAAATATCTACTGATTCTA
17146828 CTGAAGTG
66 CTGAAGTG
17146836 CTCAAACGAGCAATATC
1 CTCAAACGAGCAATATC
17146853 TACTGCTACT
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
72 11 0.15
73 62 0.83
74 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (73 bp):
CTCAAACGAGCAATATCGACTAATCCTATTGAAAGTGCTCAAACGAGAAATATCTACTGATTCTA
CTGAAGTG
Found at i:17146847 original size:36 final size:36
Alignment explanation
Indices: 17146690--17147037 Score: 223
Period size: 37 Copynumber: 9.7 Consensus size: 36
17146680 ACTAAAATTA
* * * *
17146690 CTCAAACGAGTAATGTCTACTGATTCCATTGAAAGTG
1 CTCAAACGAGCAATATCTACTGATTCTACTG-AAGTG
*
17146727 CTCAAACGAGAAATATCTACTGATTCTACTGAAAGTG
1 CTCAAACGAGCAATATCTACTGATTCTACTG-AAGTG
* * * * * *
17146764 TTC-AATGAGCAATATCGACTAATCCTATTGAATGTG
1 CTCAAACGAGCAATATCTACTGATTCTACTGAA-GTG
* *
17146800 CTCAAATGAGCAATGTCTACTGATTCTACTGAAGTG
1 CTCAAACGAGCAATATCTACTGATTCTACTGAAGTG
17146836 CTCAAACGAGCAATATCTACTG---CTACTGAAAGTG
1 CTCAAACGAGCAATATCTACTGATTCTACTG-AAGTG
* * * *
17146870 CT-TAACAAGCAGTATCTACTGATCCTACTGAA-T-
1 CTCAAACGAGCAATATCTACTGATTCTACTGAAGTG
* * * * * * *
17146903 CT---GCTAGCAATGTCTATTGATTCGAATG-CGTG
1 CTCAAACGAGCAATATCTACTGATTCTACTGAAGTG
* ** * *
17146935 CTCAAACAAGCGGTATCTATTGATTCTATTGCATAGTTG
1 CTCAAACGAGCAATATCTACTGATTCTACTG-A-AG-TG
* * *
17146974 CTTAAACGAGCAATATCCACTGATTATACTGAATGCTTG
1 CTCAAACGAGCAATATCTACTGATTCTACTGAA-G--TG
* *
17147013 CTCAAACGAGCATTATCCACTGATT
1 CTCAAACGAGCAATATCTACTGATT
17147038 ATATTGAATA
Statistics
Matches: 245, Mismatches: 49, Indels: 32
0.75 0.15 0.10
Matches are distributed among these distances:
31 19 0.08
32 2 0.01
33 24 0.10
34 8 0.03
35 23 0.09
36 55 0.22
37 60 0.24
38 3 0.01
39 51 0.21
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30
Consensus pattern (36 bp):
CTCAAACGAGCAATATCTACTGATTCTACTGAAGTG
Found at i:17146886 original size:33 final size:33
Alignment explanation
Indices: 17146792--17146890 Score: 92
Period size: 36 Copynumber: 2.9 Consensus size: 33
17146782 CTAATCCTAT
** *
17146792 TGAATGTGCTCAAATGAGCAATGTCTACTGATTCTAC
1 TGAA-GTGCTCAAACAAGCAATATCTACTG---CTAC
*
17146829 TGAAGTGCTCAAACGAGCAATATCTACTGCTAC
1 TGAAGTGCTCAAACAAGCAATATCTACTGCTAC
* *
17146862 TGAAAGTGCT-TAACAAGCAGTATCTACTG
1 TG-AAGTGCTCAAACAAGCAATATCTACTG
17146891 ATCCTACTGA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
33 22 0.39
34 7 0.12
36 23 0.41
37 4 0.07
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (33 bp):
TGAAGTGCTCAAACAAGCAATATCTACTGCTAC
Found at i:17147014 original size:39 final size:39
Alignment explanation
Indices: 17146971--17147046 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
17146961 TATTGCATAG
*
17146971 TTGCTTAAACGAGCAATATCCACTGATTATACTGAATGC
1 TTGCTCAAACGAGCAATATCCACTGATTATACTGAATGC
* *
17147010 TTGCTCAAACGAGCATTATCCACTGATTATATTGAAT
1 TTGCTCAAACGAGCAATATCCACTGATTATACTGAAT
17147047 AAGATTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (39 bp):
TTGCTCAAACGAGCAATATCCACTGATTATACTGAATGC
Found at i:17155563 original size:54 final size:54
Alignment explanation
Indices: 17155503--17155608 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 54
17155493 AGCCCACACG
*
17155503 GGCGTGTGAACCAAGTCAGTGAGTCACACGGGCT-AGCACACGGGTT-GACACATC
1 GGCGTGTGAACCAAGTCAATGAGTCACACGGG-TGAGCACAC-GGTTGGACACATC
* *
17155557 GGCGTGTGAACTAAGTCAATGAGTTACACGGGTGAGCACACGGTTGGACACA
1 GGCGTGTGAACCAAGTCAATGAGTCACACGGGTGAGCACACGGTTGGACACA
17155609 CGGGTATGTG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
53 5 0.11
54 42 0.89
ACGTcount: A:0.27, C:0.23, G:0.32, T:0.18
Consensus pattern (54 bp):
GGCGTGTGAACCAAGTCAATGAGTCACACGGGTGAGCACACGGTTGGACACATC
Found at i:17155667 original size:19 final size:19
Alignment explanation
Indices: 17155645--17155683 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
17155635 ATGTTAGAGC
*
17155645 CACACAGTCTAGGCTCTGT
1 CACACAGCCTAGGCTCTGT
* *
17155664 CACACGGCCTGGGCTCTGT
1 CACACAGCCTAGGCTCTGT
17155683 C
1 C
17155684 TTACGGCCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.36, G:0.26, T:0.23
Consensus pattern (19 bp):
CACACAGCCTAGGCTCTGT
Found at i:17158028 original size:20 final size:20
Alignment explanation
Indices: 17157985--17158032 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
17157975 AAAAAGTATT
*
17157985 TTTTGTTAAAATATAAATTC
1 TTTTGTTAAAATATAAATTA
17158005 TTTTGTTAAAA-AT-AATTA
1 TTTTGTTAAAATATAAATTA
*
17158023 TATT-TTAAAA
1 TTTTGTTAAAA
17158033 GAAATAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 6 0.23
18 7 0.27
19 2 0.08
20 11 0.42
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (20 bp):
TTTTGTTAAAATATAAATTA
Found at i:17162420 original size:39 final size:39
Alignment explanation
Indices: 17162366--17162446 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
17162356 TCACAAAAAC
17162366 AAAGTTAAATAAATTAGGGTGTTACAACTCTACCCCTCT
1 AAAGTTAAATAAATTAGGGTGTTACAACTCTACCCCTCT
17162405 AAAGTTAAATAAATTAGGGTGTTACAACTCTACCCCTCT
1 AAAGTTAAATAAATTAGGGTGTTACAACTCTACCCCTCT
17162444 AAA
1 AAA
17162447 AGAAATTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (39 bp):
AAAGTTAAATAAATTAGGGTGTTACAACTCTACCCCTCT
Found at i:17163908 original size:412 final size:414
Alignment explanation
Indices: 17163142--17163966 Score: 1465
Period size: 412 Copynumber: 2.0 Consensus size: 414
17163132 GACTAACTAT
* * *
17163142 AGAAAATCCTCCTAACTCCTTCGGAAATCAATCGCACAACTCCAAAGCATATCCTCCAGTATTTT
1 AGAAAATCCTCCTAACTCCCTCGGAAATCAATCGCACAACTCCAAAGCATATCCTCCAGTATCTG
17163207 AATCACCCTTTCAGATTAACTATCGGTCTGAGGATGGAATGCAGTACTAAAGCCCAATCTCGAAC
66 AATCACCCTTTCAGATTAACTATCGGTCTGAGGATGGAATGCAGTACTAAAGCCCAATCTCGAAC
17163272 CCAAAGTCTCATGAAGTTTTTTTCCAAAACCGAGAAGTGAAACGAGGATCTCTATCAGAAATTAT
131 CCAAAGTCTCATGAAGTTTTTTTCCAAAACCGAGAAGTGAAACGAGGATCTCTATCAGAAATTAT
** * *
17163337 CAAAATTGGAACCCCGTGAAGCTTTACAATCTCAGAAATGTAGAGCTTGGCCAACTTTTGCAGTA
196 CAAAACCGGAACCCCGTGAAGCCTTACAATCTCAGAAATATAGAGCTTGGCCAACTTTTGCAGTA
17163402 AATAATTTGTCCAAACTGGAATGAAATGGGTGGACTTGGTTAACTGATCCACGATGACCCAAACA
261 AATAATTTGTCCAAACTGGAATGAAATGGGTGGACTTGGTTAACTGATCCACGATGACCCAAACA
17163467 AAATCCTTCTTAGTAGGTGTTAAAGGCAACCCACTAACGAAGTCCATAGTTACATGTTCCCATTT
326 AAATCCTTCTTAGTAGGTGTTAAAGGCAACCCACTAACGAAGTCCATAGTTACATGTTCCCATTT
17163532 CCATAAGGGAATCTTAACGAGTTA
391 CCATAAGGGAATCTTAACGAGTTA
*
17163556 AGAAAATTCTCCTAACTCCCTCGGAAATCAATCGCACAACTCCAAAGCATATCCTCCAGTATCTG
1 AGAAAATCCTCCTAACTCCCTCGGAAATCAATCGCACAACTCCAAAGCATATCCTCCAGTATCTG
* * * *
17163621 AATCACCCTTTTAGATTGATTATCGGTCTGAGGATGGAATG-AGTACTAAAGTCCAATCTCGAAC
66 AATCACCCTTTCAGATTAACTATCGGTCTGAGGATGGAATGCAGTACTAAAGCCCAATCTCGAAC
*
17163685 CCAAAGTCTCATGAAG-TTTTTTCCAAAATCGAGAAGTGAAACGAGGATCTCTATCAGAAATTAT
131 CCAAAGTCTCATGAAGTTTTTTTCCAAAACCGAGAAGTGAAACGAGGATCTCTATCAGAAATTAT
* *
17163749 CAAAACCGGAACCCCGTGAAGCCTTACAATCTCAGAAATATAGAGCTTGTCCAACTTTTGCAGTG
196 CAAAACCGGAACCCCGTGAAGCCTTACAATCTCAGAAATATAGAGCTTGGCCAACTTTTGCAGTA
* *
17163814 AATAATTTGTTCGAACTGGAATGAAATGGGTGGACTTGGTTAACTGATCCACGATGACCCAAACA
261 AATAATTTGTCCAAACTGGAATGAAATGGGTGGACTTGGTTAACTGATCCACGATGACCCAAACA
*
17163879 AAATCCTTCTTAGTAGGTGTTAAAGGCAACCCACTAACGAAGTCTATAGTTACATGTTCCCATTT
326 AAATCCTTCTTAGTAGGTGTTAAAGGCAACCCACTAACGAAGTCCATAGTTACATGTTCCCATTT
*
17163944 TCATAAGGGAATCTTAACGAGTT
391 CCATAAGGGAATCTTAACGAGTT
17163967 GGAGCAAACC
Statistics
Matches: 392, Mismatches: 19, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
412 255 0.65
413 38 0.10
414 99 0.25
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (414 bp):
AGAAAATCCTCCTAACTCCCTCGGAAATCAATCGCACAACTCCAAAGCATATCCTCCAGTATCTG
AATCACCCTTTCAGATTAACTATCGGTCTGAGGATGGAATGCAGTACTAAAGCCCAATCTCGAAC
CCAAAGTCTCATGAAGTTTTTTTCCAAAACCGAGAAGTGAAACGAGGATCTCTATCAGAAATTAT
CAAAACCGGAACCCCGTGAAGCCTTACAATCTCAGAAATATAGAGCTTGGCCAACTTTTGCAGTA
AATAATTTGTCCAAACTGGAATGAAATGGGTGGACTTGGTTAACTGATCCACGATGACCCAAACA
AAATCCTTCTTAGTAGGTGTTAAAGGCAACCCACTAACGAAGTCCATAGTTACATGTTCCCATTT
CCATAAGGGAATCTTAACGAGTTA
Found at i:17166428 original size:12 final size:11
Alignment explanation
Indices: 17166410--17166441 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
17166400 TATTCTTGCC
17166410 TAAATCTTGAG
1 TAAATCTTGAG
17166421 TAAAATCTTGAG
1 T-AAATCTTGAG
17166433 TAAATCTTG
1 TAAATCTTG
17166442 TCAATCTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (11 bp):
TAAATCTTGAG
Found at i:17167357 original size:91 final size:91
Alignment explanation
Indices: 17167248--17167420 Score: 301
Period size: 91 Copynumber: 1.9 Consensus size: 91
17167238 TGCAAACATT
*
17167248 GGTGATTTATCCACAAATTTACTAGCAGCTTTTATTTGCAAACCCATTGTGCATTCACAACCTAT
1 GGTGATTTATCCACAAATTTACTAGCAGCTTTTATCTGCAAACCCATTGTGCATTCACAACCTAT
17167313 TGGCAACATATTAACCTACAAACACA
66 TGGCAACATATTAACCTACAAACACA
* * *
17167339 GGTGGTTTATCCATAAATTTACTAGCAGCTTTTATCTGCAAACCCATTGTGCATTCATAACCTAT
1 GGTGATTTATCCACAAATTTACTAGCAGCTTTTATCTGCAAACCCATTGTGCATTCACAACCTAT
*
17167404 TGGCAGCATATTAACCT
66 TGGCAACATATTAACCT
17167421 GCAACACTAA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 77 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (91 bp):
GGTGATTTATCCACAAATTTACTAGCAGCTTTTATCTGCAAACCCATTGTGCATTCACAACCTAT
TGGCAACATATTAACCTACAAACACA
Found at i:17167423 original size:45 final size:45
Alignment explanation
Indices: 17167284--17167424 Score: 115
Period size: 45 Copynumber: 3.1 Consensus size: 45
17167274 AGCTTTTATT
* *
17167284 TGCAAACCCATTGTGCATTCACAACCTATTGGCAACATATTAACC
1 TGCAAACCCATTGTGCATTCATAACCTATTGGCAGCATATTAACC
* * * ** * ** * * * *
17167329 TACAAACACAGGTGGTTTATCCATAAATTTACTAGCAGC-T-TTTATC
1 TGCAAACCCA--TTGTGCATTCAT-AACCTATTGGCAGCATATTAACC
17167375 TGCAAACCCATTGTGCATTCATAACCTATTGGCAGCATATTAACC
1 TGCAAACCCATTGTGCATTCATAACCTATTGGCAGCATATTAACC
17167420 TGCAA
1 TGCAA
17167425 CACTAATGGT
Statistics
Matches: 65, Mismatches: 26, Indels: 10
0.64 0.26 0.10
Matches are distributed among these distances:
43 10 0.15
44 9 0.14
45 17 0.26
46 12 0.18
47 8 0.12
48 9 0.14
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.30
Consensus pattern (45 bp):
TGCAAACCCATTGTGCATTCATAACCTATTGGCAGCATATTAACC
Found at i:17168702 original size:20 final size:20
Alignment explanation
Indices: 17168677--17168716 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17168667 CGTAAAATGA
*
17168677 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
17168697 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
17168717 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:17168706 original size:34 final size:34
Alignment explanation
Indices: 17168663--17168728 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
17168653 CAGTAAAATA
*
17168663 TTTTCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCGTAAAATGATTTACTGGAAAATATTTTAC
17168696 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATGATTTACTGGAAAATATTTT
17168729 CTGGTGTTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.40
35 13 0.43
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.47
Consensus pattern (34 bp):
TTTTCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:17168732 original size:14 final size:15
Alignment explanation
Indices: 17168657--17168732 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
17168647 GATTGCCAGT
*
17168657 AAAAT-ATTTTC-GT
1 AAAATGATTTTCTGG
17168670 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
17168684 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
17168704 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
17168719 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
17168733 TGTTAGATTG
Statistics
Matches: 50, Mismatches: 5, Indels: 15
0.71 0.07 0.21
Matches are distributed among these distances:
13 9 0.18
14 16 0.32
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:17171137 original size:29 final size:30
Alignment explanation
Indices: 17171105--17171168 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
17171095 ATTAAAAAGA
* *
17171105 TAAA-ATAAGTGACCAAAATGAAAATTTAC
1 TAAAGATAAGTGACCAAAATAAAAAATTAC
* * *
17171134 TAAAGTTAGGTGACCGAAATAAAAAATTAC
1 TAAAGATAAGTGACCAAAATAAAAAATTAC
17171164 TAAAG
1 TAAAG
17171169 TTGGGTGACT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.23
Consensus pattern (30 bp):
TAAAGATAAGTGACCAAAATAAAAAATTAC
Found at i:17171164 original size:30 final size:30
Alignment explanation
Indices: 17171113--17171183 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
17171103 GATAAAATAA
* *
17171113 GTGACCAAAATGAAAATTTACTAAAGTTAG
1 GTGACCAAAATAAAAAATTACTAAAGTTAG
* *
17171143 GTGACCGAAATAAAAAATTACTAAAGTTGG
1 GTGACCAAAATAAAAAATTACTAAAGTTAG
*
17171173 GTGACTAAAAT
1 GTGACCAAAAT
17171184 GAAAGTACAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.25
Consensus pattern (30 bp):
GTGACCAAAATAAAAAATTACTAAAGTTAG
Found at i:17173261 original size:19 final size:20
Alignment explanation
Indices: 17173239--17173293 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
17173229 ATCTCGTATA
17173239 TTTTTACATTTTTA-TAATT
1 TTTTTACATTTTTATTAATT
* *
17173258 TTTTTA-AATTTTATTTATT
1 TTTTTACATTTTTATTAATT
* *
17173277 TATTTACATTTTCATTA
1 TTTTTACATTTTTATTA
17173294 TTATCTTGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 6 0.21
19 15 0.54
20 7 0.25
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTACATTTTTATTAATT
Found at i:17173925 original size:43 final size:43
Alignment explanation
Indices: 17173877--17174170 Score: 363
Period size: 43 Copynumber: 6.8 Consensus size: 43
17173867 TTTTAGGAAT
*
17173877 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * **
17173920 AAACGCCGCTATAGATCAAGAGCTTTAACGGAGCTTTTTGCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
17173963 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTCTCCCAA
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * ** **
17174006 AAATGTCGCTATAGATCAAGAGCTTTAGCTACGCTTTTTGCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
17174049 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTCCCCAA
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * *
17174092 AAACGCCGCTATAGCTCGAGGCCTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * *
17174135 AAACGTCGCTATAGCTCGAGACCTTTAGCGACGCTT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTT
17174171 CTCGTAAAAA
Statistics
Matches: 212, Mismatches: 39, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 212 1.00
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:17173979 original size:86 final size:86
Alignment explanation
Indices: 17173877--17174184 Score: 413
Period size: 86 Copynumber: 3.6 Consensus size: 86
17173867 TTTTAGGAAT
* *
17173877 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGAG
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTATAGATCAAGAG
*
17173942 CTTTAACGGA-GCTTTTTGCAC
66 CTTTAGC-GACGCTTTTTGCAC
* * *
17173963 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTCTCCCAAAAATGTCGCTATAGATCAAGAG
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTATAGATCAAGAG
*
17174028 CTTTAGCTACGCTTTTTGCAC
66 CTTTAGCGACGCTTTTTGCAC
* * *
17174049 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTCCCCAAAAACGCCGCTATAGCTCGAG-G
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTATAGATCAAGAG
**
17174113 CCTTTAGCGACGCTTTTCCCAC
66 -CTTTAGCGACGCTTTTTGCAC
* * * * * **
17174135 AAACGTCGCTATAGCTCGAGACCTTTAGCGACGCTTCTCGTAAAAACGCC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAAAAACGCC
17174185 ACTAAAAACA
Statistics
Matches: 196, Mismatches: 24, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
85 2 0.01
86 194 0.99
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (86 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTATAGATCAAGAG
CTTTAGCGACGCTTTTTGCAC
Found at i:17175503 original size:2 final size:2
Alignment explanation
Indices: 17175496--17175546 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
17175486 CCAACAACTT
17175496 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17175538 GA GA GA GA G
1 GA GA GA GA G
17175547 GGGAAAAATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17175754 original size:20 final size:20
Alignment explanation
Indices: 17175729--17175768 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
17175719 TTAGAATTTA
17175729 AAATAATAAATTAATAACAC
1 AAATAATAAATTAATAACAC
17175749 AAATAATAAATTAATAACAC
1 AAATAATAAATTAATAACAC
17175769 GTACTTGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (20 bp):
AAATAATAAATTAATAACAC
Found at i:17177941 original size:14 final size:14
Alignment explanation
Indices: 17177922--17177970 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
17177912 AACCTTAAAT
17177922 CCCTAACTCTTAAC
1 CCCTAACTCTTAAC
17177936 CCCTAACGTC-TAAC
1 CCCTAAC-TCTTAAC
*
17177950 CCCTAAACCCTTAAC
1 CCCT-AACTCTTAAC
*
17177965 CACTAA
1 CCCTAA
17177971 ACCTTAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.33, C:0.43, G:0.02, T:0.22
Consensus pattern (14 bp):
CCCTAACTCTTAAC
Found at i:17178010 original size:14 final size:14
Alignment explanation
Indices: 17177993--17178034 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
17177983 AACCCTTAAA
17177993 CCATAATCCCTAAT
1 CCATAATCCCTAAT
17178007 CCATAATCCCTAAAT
1 CCATAATCCCT-AAT
*
17178022 CCATACTCCCTAA
1 CCATAATCCCTAA
17178035 ACCTTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.36, C:0.38, G:0.00, T:0.26
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:17178022 original size:15 final size:15
Alignment explanation
Indices: 17177989--17178035 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
17177979 TCCCAACCCT
17177989 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
17178003 T-AATCCATAATCCC
1 TAAATCCATAATCCC
*
17178017 TAAATCCATACTCCC
1 TAAATCCATAATCCC
17178032 TAAA
1 TAAA
17178036 CCTTAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 2 0.07
14 12 0.40
15 16 0.53
ACGTcount: A:0.40, C:0.34, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:17178271 original size:15 final size:14
Alignment explanation
Indices: 17178210--17178313 Score: 75
Period size: 15 Copynumber: 6.9 Consensus size: 14
17178200 ACCTTTGAAT
* *
17178210 CCCTAAACCCTAAAT
1 CCCT-AACCCTTAAC
17178225 CCCTAACTCTCTTAAC
1 CCCTAAC-C-CTTAAC
*
17178241 CCCTAA-CATCTAAC
1 CCCTAACCCT-TAAC
17178255 CCCTAAACCCTTAAC
1 CCCT-AACCCTTAAC
*
17178270 CCTCTAACCCCTAAAC
1 CC-CTAA-CCCTTAAC
*
17178286 CCTTAACCCTCTAAC
1 CCCTAACCCT-TAAC
*
17178301 CCCTAAACCTTAA
1 CCCTAACCCTTAA
17178314 ATCTCAACCC
Statistics
Matches: 72, Mismatches: 9, Indels: 17
0.73 0.09 0.17
Matches are distributed among these distances:
13 1 0.01
14 19 0.26
15 29 0.40
16 23 0.32
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.23
Consensus pattern (14 bp):
CCCTAACCCTTAAC
Found at i:17178275 original size:23 final size:23
Alignment explanation
Indices: 17178249--17178330 Score: 123
Period size: 23 Copynumber: 3.7 Consensus size: 23
17178239 ACCCCTAACA
17178249 TCTAACCCCTAAACCCTTAACCC
1 TCTAACCCCTAAACCCTTAACCC
17178272 TCTAACCCCTAAACCCTTAACCC
1 TCTAACCCCTAAACCCTTAACCC
**
17178295 TCTAACCCCTAAA-CCTTAAATC
1 TCTAACCCCTAAACCCTTAACCC
*
17178317 TC-AACCCTTAAACC
1 TCTAACCCCTAAACC
17178331 ATAATCCCTA
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.16
22 10 0.18
23 36 0.65
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.23
Consensus pattern (23 bp):
TCTAACCCCTAAACCCTTAACCC
Found at i:17178717 original size:41 final size:41
Alignment explanation
Indices: 17178656--17178816 Score: 279
Period size: 41 Copynumber: 3.9 Consensus size: 41
17178646 TAAAATGTTT
17178656 TTAGCGGCGCTT-TTCTAAAAACGCCGCTAAAGGCCCCAGCA
1 TTAGCGGCGCTTCTTC-AAAAACGCCGCTAAAGGCCCCAGCA
17178697 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCCAGCA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCCAGCA
* *
17178738 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCCAGCA
*
17178779 TTAGCGGCGCTTCTTTAAAAACGCCGCTAAAGGCCCCA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCCA
17178817 AAAACTCAGA
Statistics
Matches: 114, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
41 111 0.97
42 3 0.03
ACGTcount: A:0.27, C:0.32, G:0.22, T:0.19
Consensus pattern (41 bp):
TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCCAGCA
Found at i:17185762 original size:27 final size:27
Alignment explanation
Indices: 17185732--17185786 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
17185722 ATTATCAAAA
*
17185732 TTAATTAAAATTCAA-TATTTTAATAAT
1 TTAAGTAAAATTCAATTATTTT-ATAAT
* *
17185759 TTAAGTACAATTTAATTATTTTATAAT
1 TTAAGTAAAATTCAATTATTTTATAAT
17185786 T
1 T
17185787 ATATTATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (27 bp):
TTAAGTAAAATTCAATTATTTTATAAT
Found at i:17189946 original size:9 final size:9
Alignment explanation
Indices: 17189929--17189965 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
17189919 TGAGTTTTCG
17189929 AATTCGAAT
1 AATTCGAAT
*
17189938 AACTCGAAT
1 AATTCGAAT
17189947 AATTCGAAT
1 AATTCGAAT
17189956 AATTCGAAT
1 AATTCGAAT
17189965 A
1 A
17189966 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:17190042 original size:21 final size:21
Alignment explanation
Indices: 17190001--17190043 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
17189991 ACCCCAAACT
* *
17190001 CTCAAACCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTCTTCC
17190022 CTCAAAAC-TTTTACTCCTTCC
1 CTCAAAACTTTTTACT-CTTCC
17190043 C
1 C
17190044 GCTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.37, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTTACTCTTCC
Found at i:17195129 original size:20 final size:20
Alignment explanation
Indices: 17195106--17195143 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17195096 TTACTAATTT
* *
17195106 ATTTTACATTAAACATAAAC
1 ATTTGACATCAAACATAAAC
17195126 ATTTGACATCAAACATAA
1 ATTTGACATCAAACATAA
17195144 GGAAAACCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.32
Consensus pattern (20 bp):
ATTTGACATCAAACATAAAC
Found at i:17195520 original size:5 final size:4
Alignment explanation
Indices: 17195469--17195536 Score: 57
Period size: 4 Copynumber: 15.8 Consensus size: 4
17195459 AAATTTTTGT
* *
17195469 TTTC TTTC TTTC TTTC TTT- TTGTT TTTC TCTTC TCTTC TCTTA TTTC
1 TTTC TTTC TTTC TTTC TTTC TT-TC TTTC T-TTC T-TTC T-TTC TTTC
17195516 TTTTC TTTC TTTCC TTTC TTT
1 -TTTC TTTC TTT-C TTTC TTT
17195537 TTCAGCTGCT
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
3 2 0.04
4 31 0.55
5 23 0.41
ACGTcount: A:0.01, C:0.24, G:0.01, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:17198394 original size:22 final size:20
Alignment explanation
Indices: 17198369--17198417 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
17198359 ATAAAATATT
*
17198369 TTTATATTTACTTTTTAAAATC
1 TTTATATTTA-TATTT-AAATC
*
17198391 TTTATAATTTATATTTAAATT
1 TTTAT-ATTTATATTTAAATC
17198412 TTTATA
1 TTTATA
17198418 ATTTTCTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.04
21 9 0.38
22 9 0.38
23 5 0.21
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTATATTTATATTTAAATC
Found at i:17198427 original size:22 final size:22
Alignment explanation
Indices: 17198366--17198429 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
17198356 AATATAAAAT
* *
17198366 ATTTTTAT-ATTTACTTTTTAAA
1 ATTTTTATAATTTTCTATTT-AA
* *
17198388 ATCTTTATAA-TTTATATTTAA
1 ATTTTTATAATTTTCTATTTAA
17198409 ATTTTTATAATTTTCTATTTA
1 ATTTTTATAATTTTCTATTTA
17198430 CTTTTTTTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 11 0.32
22 22 0.65
23 1 0.03
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTTTTATAATTTTCTATTTAA
Found at i:17199204 original size:30 final size:28
Alignment explanation
Indices: 17199168--17199248 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 28
17199158 TTAAAATATT
*
17199168 TTTATATTTTCTTTTTAGAAATTTTTTAAA
1 TTTATATTTACTTTTTA-AAA-TTTTTAAA
17199198 TTTATATTTACTTTTTAAAATTTTTAAA
1 TTTATATTTACTTTTTAAAATTTTTAAA
* *
17199226 TATTCT-TTTGACTTTTTATAATT
1 T-TTATATTT-ACTTTTTAAAATT
17199249 AGAACTAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
28 12 0.26
29 18 0.39
30 16 0.35
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTATATTTACTTTTTAAAATTTTTAAA
Found at i:17199241 original size:28 final size:30
Alignment explanation
Indices: 17199168--17199243 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
17199158 TTAAAATATT
*
17199168 TTTATATTTTCTTTTTAGAAATTTTTTAAA
1 TTTATATTTACTTTTTAGAAATTTTTTAAA
17199198 TTTATATTTACTTTTTA-AAA-TTTTTAAA
1 TTTATATTTACTTTTTAGAAATTTTTTAAA
*
17199226 TATTCT-TTTGACTTTTTA
1 T-TTATATTT-ACTTTTTA
17199244 TAATTAGAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
28 12 0.29
29 14 0.33
30 16 0.38
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (30 bp):
TTTATATTTACTTTTTAGAAATTTTTTAAA
Found at i:17199488 original size:29 final size:30
Alignment explanation
Indices: 17199444--17199502 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
17199434 CAAAAGCTTG
* *
17199444 AGTGACTAAAACAAAA-AAAATTAATAGTT
1 AGTGACCAAAACAAAATAAAATGAATAGTT
* *
17199473 AGTGACCAAAATAAAATAAACTGAATAGTT
1 AGTGACCAAAACAAAATAAAATGAATAGTT
17199503 GGGTGACTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (30 bp):
AGTGACCAAAACAAAATAAAATGAATAGTT
Found at i:17199898 original size:16 final size:17
Alignment explanation
Indices: 17199872--17199903 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
17199862 AAATATACTA
17199872 AAAAAACAAAAACCTGC
1 AAAAAACAAAAACCTGC
17199889 AAAAAA-AAAAACCTG
1 AAAAAACAAAAACCTG
17199904 TGGCGGCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.69, C:0.19, G:0.06, T:0.06
Consensus pattern (17 bp):
AAAAAACAAAAACCTGC
Found at i:17199934 original size:27 final size:27
Alignment explanation
Indices: 17199904--17199966 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
17199894 AAAAAACCTG
*
17199904 TGGCGGCACCAAAGGTGCCAAAGTGAT
1 TGGCGGCACCAAAGGTGCCAAAGAGAT
17199931 TGGCGGCACCAAAGGTGCCAAAGAGAT
1 TGGCGGCACCAAAGGTGCCAAAGAGAT
17199958 TGGCGGCAC
1 TGGCGGCAC
17199967 AGAACTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.29, C:0.24, G:0.35, T:0.13
Consensus pattern (27 bp):
TGGCGGCACCAAAGGTGCCAAAGAGAT
Found at i:17200458 original size:19 final size:19
Alignment explanation
Indices: 17200434--17200496 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
17200424 TCTAATTAAG
17200434 TAATAACTCTATTTTACTT
1 TAATAACTCTATTTTACTT
* * ** ***
17200453 TAATAAGTTTATTAAAAAG
1 TAATAACTCTATTTTACTT
*
17200472 CAATAACTCTATTTTACTT
1 TAATAACTCTATTTTACTT
17200491 TAATAA
1 TAATAA
17200497 ACTATTGCTT
Statistics
Matches: 28, Mismatches: 16, Indels: 0
0.64 0.36 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.44
Consensus pattern (19 bp):
TAATAACTCTATTTTACTT
Found at i:17200560 original size:18 final size:17
Alignment explanation
Indices: 17200531--17200565 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
17200521 GTAATGTTTC
*
17200531 AAAAAATGTTTTTAGGA
1 AAAAAATGTTTTAAGGA
17200548 AAAAAATGTTTTTAAGGA
1 AAAAAATG-TTTTAAGGA
17200566 GAAGTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (17 bp):
AAAAAATGTTTTAAGGA
Found at i:17201995 original size:27 final size:28
Alignment explanation
Indices: 17201964--17202028 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
17201954 TTTTTTTAGT
**
17201964 ATATTTTGATAAATAA-AAAAAATTATA
1 ATATTTTGATAAATAATAAAAAAAGATA
*
17201991 ATATTTTGGTAAATAATAAAAAAAGATA
1 ATATTTTGATAAATAATAAAAAAAGATA
*
17202019 ACATTTTGAT
1 ATATTTTGAT
17202029 TATTTTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 15 0.47
28 17 0.53
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.37
Consensus pattern (28 bp):
ATATTTTGATAAATAATAAAAAAAGATA
Found at i:17204087 original size:10 final size:10
Alignment explanation
Indices: 17204060--17204092 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
17204050 TAATATTCAT
*
17204060 AAAAATTATA
1 AAAAATTCTA
17204070 AAAAATTCTA
1 AAAAATTCTA
17204080 AAAAATTC-A
1 AAAAATTCTA
17204089 AAAA
1 AAAA
17204093 TATAAAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 5 0.23
10 17 0.77
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAATTCTA
Found at i:17204613 original size:28 final size:29
Alignment explanation
Indices: 17204557--17204618 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
17204547 TGTATATTTG
* ***
17204557 GAATTTAATCTCTAATTTTTTATTTTTAA
1 GAATTTAATCTATAATTTTTTAAAATTAA
17204586 GAATTTAATCTAT-ATTTTTTAAAATTAA
1 GAATTTAATCTATAATTTTTTAAAATTAA
*
17204614 AAATT
1 GAATT
17204619 CAAATCCAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 16 0.57
29 12 0.43
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (29 bp):
GAATTTAATCTATAATTTTTTAAAATTAA
Found at i:17211956 original size:46 final size:44
Alignment explanation
Indices: 17211887--17211975 Score: 160
Period size: 46 Copynumber: 2.0 Consensus size: 44
17211877 GGTATCAGAG
17211887 CCAGGTTGTAAATCGGCTGTAGATTATGGGTTTTATAAAAAAAA
1 CCAGGTTGTAAATCGGCTGTAGATTATGGGTTTTATAAAAAAAA
17211931 CCAGGTTGTAAAATTCGGCTGTAGATTATGGGTTTTATAAAAAAA
1 CCAGGTTGT-AAA-TCGGCTGTAGATTATGGGTTTTATAAAAAAA
17211976 TTTGGCTTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 9 0.21
45 3 0.07
46 31 0.72
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (44 bp):
CCAGGTTGTAAATCGGCTGTAGATTATGGGTTTTATAAAAAAAA
Found at i:17221715 original size:3 final size:3
Alignment explanation
Indices: 17221707--17221762 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
17221697 ACATGTTTCC
17221707 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17221755 ATT ATT AT
1 ATT ATT AT
17221763 ATACATATAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:17229129 original size:26 final size:25
Alignment explanation
Indices: 17229084--17229132 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
17229074 AAATGTCAAA
17229084 AAAAGTAGAAAGGCCAAAATTTGGG
1 AAAAGTAGAAAGGCCAAAATTTGGG
*
17229109 AAAAGTATGAGAA-GCCGAAATTTG
1 AAAAGTA-GA-AAGGCCAAAATTTG
17229133 AAAAAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 12 0.57
27 2 0.10
ACGTcount: A:0.47, C:0.08, G:0.27, T:0.18
Consensus pattern (25 bp):
AAAAGTAGAAAGGCCAAAATTTGGG
Found at i:17229138 original size:26 final size:25
Alignment explanation
Indices: 17229082--17229138 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
17229072 CAAAATGTCA
17229082 AAAAAAGTAGAAAGGCCAAAATTTG
1 AAAAAAGTAGAAAGGCCAAAATTTG
** *
17229107 GGAAAAGTATGAGAA-GCCGAAATTTG
1 AAAAAAGTA-GA-AAGGCCAAAATTTG
17229133 AAAAAA
1 AAAAAA
17229139 AAAGATAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
25 7 0.28
26 16 0.64
27 2 0.08
ACGTcount: A:0.54, C:0.07, G:0.23, T:0.16
Consensus pattern (25 bp):
AAAAAAGTAGAAAGGCCAAAATTTG
Found at i:17233710 original size:25 final size:24
Alignment explanation
Indices: 17233643--17233703 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
17233633 GGATGATATA
*
17233643 TCGA-CTTTTCATTGAGATCCTTT
1 TCGACCTTTTCATTGATATCCTTT
* *
17233666 TAGACTTTTTCATTGATATCCTTT
1 TCGACCTTTTCATTGATATCCTTT
17233690 TCGACCTTTTCATT
1 TCGACCTTTTCATT
17233704 TGTTATCTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 3 0.09
24 29 0.91
ACGTcount: A:0.18, C:0.21, G:0.10, T:0.51
Consensus pattern (24 bp):
TCGACCTTTTCATTGATATCCTTT
Found at i:17233715 original size:40 final size:40
Alignment explanation
Indices: 17233670--17233783 Score: 131
Period size: 40 Copynumber: 2.9 Consensus size: 40
17233660 TCCTTTTAGA
* * * *
17233670 CTTTTTCATTGATATCCTTTTCGACCTTTTCATTTGTTAT
1 CTTTTTCAATGACATCCTGTTCAACCTTTTCATTTGTTAT
*
17233710 CTTTTTGAATGACATCCTGTTCAACCTTTTCATTTGTTAT
1 CTTTTTCAATGACATCCTGTTCAACCTTTTCATTTGTTAT
* * * *
17233750 C-CTTTCGGATAACATCCTTTTCAACCTTTTCATT
1 CTTTTTC-AATGACATCCTGTTCAACCTTTTCATT
17233784 GGTTCAAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
39 3 0.05
40 60 0.95
ACGTcount: A:0.18, C:0.23, G:0.08, T:0.51
Consensus pattern (40 bp):
CTTTTTCAATGACATCCTGTTCAACCTTTTCATTTGTTAT
Found at i:17242757 original size:3 final size:3
Alignment explanation
Indices: 17242749--17242801 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
17242739 GCAGAAATAT
17242749 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
17242797 ATG AT
1 ATG AT
17242802 AAACAATCAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:17247227 original size:3 final size:3
Alignment explanation
Indices: 17247221--17247246 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17247211 TCTTTTTCCT
17247221 TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TC
17247247 TTCTTCTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
TCC
Found at i:17250026 original size:23 final size:23
Alignment explanation
Indices: 17249979--17250025 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
17249969 TATGGTTTAA
*
17249979 TTATTATATTTTTTATTGTTATT
1 TTATTATATTTTTTATTCTTATT
17250002 TTATTA-AGTTTTTTATTC-TATT
1 TTATTATA-TTTTTTATTCTTATT
17250024 TT
1 TT
17250026 TGCAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.72
Consensus pattern (23 bp):
TTATTATATTTTTTATTCTTATT
Found at i:17252813 original size:66 final size:66
Alignment explanation
Indices: 17252691--17252814 Score: 144
Period size: 66 Copynumber: 1.9 Consensus size: 66
17252681 TGTGATTATG
* **
17252691 TATTGAATTTTCATTATTGTATTAACTTAAATTATTTACATATATTTGCATTATATTTCTATTTT
1 TATTGAATTTTCATTATTGTATTAACTTAAATTATTTACATATACTTGCAAAATATTTCTATTTT
17252756 T
66 T
* * * * *
17252757 TATTGAATTTTCATTCTTGT-TTCAATTTCAATTATTTAGATGA-ACTTGTAAAATATTT
1 TATTGAATTTTCATTATTGTATT-AACTTAAATTATTTACAT-ATACTTGCAAAATATTT
17252815 GAATGAACTT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
65 2 0.04
66 45 0.94
67 1 0.02
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.55
Consensus pattern (66 bp):
TATTGAATTTTCATTATTGTATTAACTTAAATTATTTACATATACTTGCAAAATATTTCTATTTT
T
Found at i:17253447 original size:30 final size:30
Alignment explanation
Indices: 17253413--17253475 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
17253403 ACTTATTTTA
*
17253413 TTGTTAATTTTGTTATTATTTTAAAGACGT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
17253443 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
17253473 TTG
1 TTG
17253476 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:17258677 original size:39 final size:37
Alignment explanation
Indices: 17258610--17258702 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
17258600 ACCAGAATGG
* *
17258610 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
17258649 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
17258686 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
17258703 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:17259042 original size:3 final size:3
Alignment explanation
Indices: 17259034--17259130 Score: 167
Period size: 3 Copynumber: 32.3 Consensus size: 3
17259024 GTCCATTCAC
17259034 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
17259082 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT ACT AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17259130 A
1 A
17259131 CTTACCTCAC
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:17260040 original size:14 final size:14
Alignment explanation
Indices: 17260021--17260066 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
17260011 TTTTTTTATT
17260021 ATAATAATAATTTA
1 ATAATAATAATTTA
*
17260035 ATAATACTAATTTA
1 ATAATAATAATTTA
17260049 ATAATAATAATTTA
1 ATAATAATAATTTA
17260063 ATAA
1 ATAA
17260067 CATTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAATAATTTA
Found at i:17260076 original size:28 final size:28
Alignment explanation
Indices: 17260011--17260077 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
17260001 TTTGTCAACT
*
17260011 TTTTTTTATTATAATAATAATTTAATAATA
1 TTTTTTTA--ATAATAATAATTTAATAACA
* **
17260041 CTAATTTAATAATAATAATTTAATAACA
1 TTTTTTTAATAATAATAATTTAATAACA
17260069 TTTTTTTAA
1 TTTTTTTAA
17260078 CACATAAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
28 25 0.83
30 5 0.17
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (28 bp):
TTTTTTTAATAATAATAATTTAATAACA
Found at i:17262996 original size:13 final size:14
Alignment explanation
Indices: 17262978--17263010 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
17262968 GTCTATTTTT
17262978 TTAAAATTA-AAAG
1 TTAAAATTATAAAG
*
17262991 TTAAAATTATTAAG
1 TTAAAATTATAAAG
17263005 TTAAAA
1 TTAAAA
17263011 GGTAAAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (14 bp):
TTAAAATTATAAAG
Found at i:17271332 original size:21 final size:22
Alignment explanation
Indices: 17271302--17271342 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
17271292 ATATCTAAAT
17271302 TACCACACACACATA-TATATA
1 TACCACACACACATACTATATA
*
17271323 TACCATACACACATACTATA
1 TACCACACACACATACTATA
17271343 AAACTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.24
Consensus pattern (22 bp):
TACCACACACACATACTATATA
Found at i:17276100 original size:21 final size:21
Alignment explanation
Indices: 17276074--17276132 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
17276064 CATGGTTTGC
*
17276074 CCACACGACTGTGTATCTCAG
1 CCACACGACTGTGTACCTCAG
* * *
17276095 CCACACGGCCGTGTCCCTCAG
1 CCACACGACTGTGTACCTCAG
*
17276116 CCATACGACTGTGTACC
1 CCACACGACTGTGTACC
17276133 CCGGTCACAC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.39, G:0.20, T:0.20
Consensus pattern (21 bp):
CCACACGACTGTGTACCTCAG
Found at i:17283489 original size:20 final size:20
Alignment explanation
Indices: 17283443--17283490 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
17283433 TGAACTAAAC
*
17283443 TTTAATTTAATTTTTGAGTAT
1 TTTAA-TTAATTTTGGAGTAT
*
17283464 TGTAATTAATTTTGGA-TAAT
1 TTTAATTAATTTTGGAGT-AT
17283484 TTTAATT
1 TTTAATT
17283491 TTTATCGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 18 0.78
21 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.58
Consensus pattern (20 bp):
TTTAATTAATTTTGGAGTAT
Found at i:17284654 original size:18 final size:18
Alignment explanation
Indices: 17284621--17284655 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17284611 ACGATGTGCC
*
17284621 AAACTATTTTCGTGCTTG
1 AAACTATTTTCATGCTTG
*
17284639 AAACTATTTTTATGCTT
1 AAACTATTTTCATGCTT
17284656 CCTGTTCTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (18 bp):
AAACTATTTTCATGCTTG
Found at i:17287105 original size:13 final size:13
Alignment explanation
Indices: 17287081--17287129 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
17287071 TTCAAGTTCT
17287081 GATATAGTTTCCAA
1 GATAT-GTTTCCAA
17287095 GATATGTTTCCAA
1 GATATGTTTCCAA
* * **
17287108 GTTATATTTTAAA
1 GATATGTTTCCAA
17287121 GATATGTTT
1 GATATGTTT
17287130 TACGCGTGCT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
13 24 0.83
14 5 0.17
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (13 bp):
GATATGTTTCCAA
Found at i:17289140 original size:26 final size:25
Alignment explanation
Indices: 17289110--17289184 Score: 114
Period size: 26 Copynumber: 2.9 Consensus size: 25
17289100 CCATATAACA
*
17289110 AAAAGCTCACGAAGAGCCTTTAAAT
1 AAAAGCTCACGAAGAGCCTTTAAAC
17289135 AGAAAGCTCACGAAGAGCCTTTAAAC
1 A-AAAGCTCACGAAGAGCCTTTAAAC
*
17289161 AAGAAGCTCACGAAGAGCCATTAA
1 AA-AAGCTCACGAAGAGCCTTTAA
17289185 TCAGGAGCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
25 2 0.04
26 44 0.96
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.16
Consensus pattern (25 bp):
AAAAGCTCACGAAGAGCCTTTAAAC
Found at i:17296411 original size:23 final size:23
Alignment explanation
Indices: 17296385--17296549 Score: 185
Period size: 23 Copynumber: 7.2 Consensus size: 23
17296375 ATAAGTGTCA
*
17296385 CACTGATATGTAGCTTAAGCTAC
1 CACTGATATGTAGCCTAAGCTAC
*
17296408 CACTAATATGTAGCCGT-AGCTAC
1 CACTGATATGTAGCC-TAAGCTAC
* *
17296431 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCTAAGCTAC
* *
17296454 CACTGATATTTAG-CTGTAGCTAC
1 CACTGATATGTAGCCT-AAGCTAC
* *
17296477 CACTGAAATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCTAAGCTAC
17296500 CACTGATATGTAGCC-ATAGCTAC
1 CACTGATATGTAGCCTA-AGCTAC
*
17296523 CACTGA-ATTGTAGCCGAAGCTAC
1 CACTGATA-TGTAGCCTAAGCTAC
17296546 CACT
1 CACT
17296550 AATCAATAAC
Statistics
Matches: 121, Mismatches: 14, Indels: 14
0.81 0.09 0.09
Matches are distributed among these distances:
22 3 0.02
23 115 0.95
24 3 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (23 bp):
CACTGATATGTAGCCTAAGCTAC
Found at i:17296452 original size:46 final size:46
Alignment explanation
Indices: 17296385--17296552 Score: 246
Period size: 46 Copynumber: 3.7 Consensus size: 46
17296375 ATAAGTGTCA
* **
17296385 CACTGATATGTAGCTTAAGCTACCACTAATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTAATATGTAGCCGTAGCTAC
* * *
17296431 CACTGAAATGTAGCCGAAGCTACCACTGATATTTAGCTGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTAATATGTAGCCGTAGCTAC
* * *
17296477 CACTGAAATGTAGCCAAAGCTACCACTGATATGTAGCCATAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTAATATGTAGCCGTAGCTAC
*
17296523 CACTGAATTGTAGCCGAAGCTACCACTAAT
1 CACTGAAATGTAGCCGAAGCTACCACTAAT
17296553 CAATAACACT
Statistics
Matches: 109, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 109 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTAATATGTAGCCGTAGCTAC
Found at i:17296468 original size:69 final size:69
Alignment explanation
Indices: 17296385--17296552 Score: 218
Period size: 69 Copynumber: 2.4 Consensus size: 69
17296375 ATAAGTGTCA
* **
17296385 CACTGATATGTAGCTTAAGCTACCACTAATATGTAGCCGTAGCTACCACTGAAATGTAGCCGA-A
1 CACTGATATTTAGCTTAAGCTACCACTAATATGTAGCCAAAGCTACCACTGAAATGTAGCC-ATA
17296449 GCTAC
65 GCTAC
*
17296454 CACTGATATTTAGCTGT-AGCTACCACTGAA-ATGTAGCCAAAGCTACCACTGATATGTAGCCAT
1 CACTGATATTTAGCT-TAAGCTACCACT-AATATGTAGCCAAAGCTACCACTGAAATGTAGCCAT
17296517 AGCTAC
64 AGCTAC
**
17296523 CACTGA-ATTGTAGCCGAAGCTACCACTAAT
1 CACTGATATT-TAGCTTAAGCTACCACTAAT
17296553 CAATAACACT
Statistics
Matches: 87, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
68 6 0.07
69 78 0.90
70 3 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (69 bp):
CACTGATATTTAGCTTAAGCTACCACTAATATGTAGCCAAAGCTACCACTGAAATGTAGCCATAG
CTAC
Found at i:17296804 original size:18 final size:17
Alignment explanation
Indices: 17296778--17296816 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
17296768 ATTTTCCTTC
17296778 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
17296795 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
17296813 CACA
1 CACA
17296817 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Done.