Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 62 of 328
Found at i:17127217 original size:4 final size:4
Alignment explanation
Indices: 17127135--17127206 Score: 90
Period size: 4 Copynumber: 18.0 Consensus size: 4
17127125 TGGGATATGC
* * * *
17127135 AATG TATG AATG AATG CATG AATG AATG CATG AATG AATG CATG AATG
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG
* *
17127183 AATG CATG AATG AATG CATG AATG
1 AATG AATG AATG AATG AATG AATG
17127207 TCAAATGAAT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.42, C:0.07, G:0.25, T:0.26
Consensus pattern (4 bp):
AATG
Found at i:17128934 original size:37 final size:38
Alignment explanation
Indices: 17128834--17128935 Score: 95
Period size: 37 Copynumber: 2.6 Consensus size: 38
17128824 ATATATTTGG
17128834 TAATAATAATA--TAAAATAATAA-TATGTACATAAAAA
1 TAATAATAATATCTAAAATAA-AAGTATGTACATAAAAA
* *
17128870 TAAATATATATATATGCATATAATAAAAGTATGTA-ATAATAA
1 T-AATA-ATA-ATAT-C-TAAAATAAAAGTATGTACATAAAAA
*
17128912 TAATAATAATATCTACAATAAAAG
1 TAATAATAATATCTAAAATAAAAG
17128936 AAAATATTAG
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
36 1 0.02
37 14 0.25
38 4 0.07
39 7 0.13
40 3 0.05
41 4 0.07
42 9 0.16
43 13 0.24
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.32
Consensus pattern (38 bp):
TAATAATAATATCTAAAATAAAAGTATGTACATAAAAA
Found at i:17130421 original size:27 final size:28
Alignment explanation
Indices: 17130341--17130422 Score: 130
Period size: 27 Copynumber: 2.9 Consensus size: 28
17130331 GGTTTCTTAT
17130341 TTTTTTTTTGGGGTTAGGTTTTTCTTTTTC
1 TTTTTTTTTGGGGTTAGG-TTTT-TTTTTC
*
17130371 TTTTTTTTTAGGGTTAGGTTTTTTTTTC
1 TTTTTTTTTGGGGTTAGGTTTTTTTTTC
17130399 -TTTTTTTTGGGGTTAGGTTTTTTT
1 TTTTTTTTTGGGGTTAGGTTTTTTT
17130423 GGGGGGATTA
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
27 23 0.46
28 6 0.12
29 4 0.08
30 17 0.34
ACGTcount: A:0.05, C:0.04, G:0.21, T:0.71
Consensus pattern (28 bp):
TTTTTTTTTGGGGTTAGGTTTTTTTTTC
Found at i:17130957 original size:35 final size:35
Alignment explanation
Indices: 17130911--17130987 Score: 145
Period size: 35 Copynumber: 2.2 Consensus size: 35
17130901 AACGGCGCTG
*
17130911 TTTTCATAAACAGTTTATTTGAAACCCTTTTTCTT
1 TTTTCTTAAACAGTTTATTTGAAACCCTTTTTCTT
17130946 TTTTCTTAAACAGTTTATTTGAAACCCTTTTTCTT
1 TTTTCTTAAACAGTTTATTTGAAACCCTTTTTCTT
17130981 TTTTCTT
1 TTTTCTT
17130988 TCTTACCAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.22, C:0.17, G:0.05, T:0.56
Consensus pattern (35 bp):
TTTTCTTAAACAGTTTATTTGAAACCCTTTTTCTT
Found at i:17138592 original size:17 final size:16
Alignment explanation
Indices: 17138572--17138609 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 16
17138562 TTTTTTTATA
17138572 TTTAAAATTTAGTTGTT
1 TTTAAAATTTAG-TGTT
17138589 TTTAAAAATTTAGTGTT
1 TTT-AAAATTTAGTGTT
17138606 TTTA
1 TTTA
17138610 TTTTTTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 1 0.05
17 10 0.50
18 9 0.45
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (16 bp):
TTTAAAATTTAGTGTT
Found at i:17138598 original size:18 final size:17
Alignment explanation
Indices: 17138575--17138609 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
17138565 TTTTATATTT
17138575 AAAATTTAGTTGTTTTTA
1 AAAATTTAG-TGTTTTTA
17138593 AAAATTTAGTGTTTTTA
1 AAAATTTAGTGTTTTTA
17138610 TTTTTTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (17 bp):
AAAATTTAGTGTTTTTA
Found at i:17144256 original size:15 final size:14
Alignment explanation
Indices: 17144232--17144275 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
17144222 AAGCCTATTC
*
17144232 TTTCTTCTTTGATT
1 TTTCTTCTTTAATT
17144246 TTTCTTTCTTTAATT
1 TTTC-TTCTTTAATT
*
17144261 TTCCTTCTTTTAATT
1 TTTCTTC-TTTAATT
17144276 CCTTATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 7 0.27
15 19 0.73
ACGTcount: A:0.11, C:0.16, G:0.02, T:0.70
Consensus pattern (14 bp):
TTTCTTCTTTAATT
Found at i:17146706 original size:30 final size:30
Alignment explanation
Indices: 17146672--17146731 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
17146662 TATTTTATTA
*
17146672 TTAATTTTGTTATTATTTTAAAGGTATTTG
1 TTAATTTTATTATTATTTTAAAGGTATTTG
*
17146702 TTAATTTTATTATTATTTTAGAGGTATTTG
1 TTAATTTTATTATTATTTTAAAGGTATTTG
17146732 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.00, G:0.13, T:0.60
Consensus pattern (30 bp):
TTAATTTTATTATTATTTTAAAGGTATTTG
Found at i:17163903 original size:28 final size:27
Alignment explanation
Indices: 17163863--17163919 Score: 96
Period size: 28 Copynumber: 2.1 Consensus size: 27
17163853 CCTAAAAAAT
*
17163863 TAAGTAAGTAACTAGGTAGTTTATATA
1 TAAGCAAGTAACTAGGTAGTTTATATA
17163890 TAAGCAAGCTAACTAGGTAGTTTATATA
1 TAAGCAAG-TAACTAGGTAGTTTATATA
17163918 TA
1 TA
17163920 TTTTATAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (27 bp):
TAAGCAAGTAACTAGGTAGTTTATATA
Found at i:17164501 original size:2 final size:2
Alignment explanation
Indices: 17164494--17164527 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17164484 TGGTTCTATG
17164494 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17164528 TTTTGAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17167178 original size:29 final size:29
Alignment explanation
Indices: 17167145--17167203 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
17167135 AAAGATAGAG
*
17167145 AGATTAAATT-TCTGAAAATAAGAATAAAA
1 AGATTAAATTCT-TGAAAATAAAAATAAAA
17167174 AGATTAAATTCTTGAAAATAAAAATAAAA
1 AGATTAAATTCTTGAAAATAAAAATAAAA
17167203 A
1 A
17167204 AAACTAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.27
Consensus pattern (29 bp):
AGATTAAATTCTTGAAAATAAAAATAAAA
Found at i:17168572 original size:22 final size:22
Alignment explanation
Indices: 17168547--17168590 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17168537 AATTATTAAC
* *
17168547 ATAATGAATTTTAATTAATTTT
1 ATAATAAATTCTAATTAATTTT
*
17168569 ATAATAAATTCTGATTAATTTT
1 ATAATAAATTCTAATTAATTTT
17168591 GGTCATTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (22 bp):
ATAATAAATTCTAATTAATTTT
Found at i:17168764 original size:21 final size:21
Alignment explanation
Indices: 17168735--17168776 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17168725 CATTAATTCA
17168735 TAATATAA-TTAATTTTAATTT
1 TAATATAATTTAA-TTTAATTT
*
17168756 TAATCTAATTTAATTTAATTT
1 TAATATAATTTAATTTAATTT
17168777 GGGTTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATATAATTTAATTTAATTT
Found at i:17176342 original size:22 final size:19
Alignment explanation
Indices: 17176309--17176355 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
17176299 AAATATGATA
17176309 ATTATTAATATATAATTATATCT
1 ATTA-TAATATAT-ATTA-AT-T
17176332 ATTATAATATATATTAATT
1 ATTATAATATATATTAATT
17176351 ATTAT
1 ATTAT
17176356 CAACTTTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 4 0.17
22 8 0.33
23 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTATAATATATATTAATT
Found at i:17176351 original size:16 final size:15
Alignment explanation
Indices: 17176311--17176352 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
17176301 ATATGATAAT
17176311 TATTAATATATAATTA
1 TATTAAT-TATAATTA
17176327 TATCT-ATTATAATATA
1 TAT-TAATTATAAT-TA
17176343 TATTAATTAT
1 TATTAATTAT
17176353 TATCAACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.30
16 15 0.65
17 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTAATTATAATTA
Found at i:17177018 original size:25 final size:24
Alignment explanation
Indices: 17176987--17177047 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
17176977 AATTTTTCTC
*
17176987 TTAAATTTTAAATTTTATTTAATTA
1 TTAAATTTTAAA-TTTATTGAATTA
* *
17177012 TTTAATTTTTCAATTTATTGAATTA
1 -TTAAATTTTAAATTTATTGAATTA
17177037 TTAATATTTTA
1 TTAA-ATTTTA
17177048 TATTAATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 4 0.14
25 15 0.52
26 10 0.34
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
TTAAATTTTAAATTTATTGAATTA
Found at i:17177060 original size:25 final size:25
Alignment explanation
Indices: 17177007--17177060 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
17176997 AATTTTATTT
* *
17177007 AATTATTTAATTTTTCAATTTATTG
1 AATTATTTAATTTTTCAATTAATTA
17177032 AATTA-TTAATATTTT-ATATTAATTA
1 AATTATTTAAT-TTTTCA-ATTAATTA
17177057 AATT
1 AATT
17177061 TTGAGAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
AATTATTTAATTTTTCAATTAATTA
Found at i:17179888 original size:22 final size:22
Alignment explanation
Indices: 17179863--17179906 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17179853 AATTATTAAA
* *
17179863 ATAATTAATTTTAATTAGTTTT
1 ATAATAAATTTTAATTAATTTT
*
17179885 ATAATAAATTTTGATTAATTTT
1 ATAATAAATTTTAATTAATTTT
17179907 GGTCATTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
ATAATAAATTTTAATTAATTTT
Found at i:17180071 original size:22 final size:22
Alignment explanation
Indices: 17180043--17180087 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
17180033 TTTATGTGTA
*
17180043 TTAATTTATAATATAA-TTAATT
1 TTAATTT-TAATACAATTTAATT
17180065 TTAATTTTAATACAATTTAATT
1 TTAATTTTAATACAATTTAATT
17180087 T
1 T
17180088 GGGTTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTTTAATACAATTTAATT
Found at i:17190525 original size:25 final size:25
Alignment explanation
Indices: 17190497--17190548 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
17190487 TATGTGAGTA
*
17190497 AATTCTATGATATTTATTGCTTAAG
1 AATTCTATGATATTTATTGCATAAG
17190522 AATTCTATGATATTTATTGCATAAG
1 AATTCTATGATATTTATTGCATAAG
17190547 AA
1 AA
17190549 ATTGACATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.44
Consensus pattern (25 bp):
AATTCTATGATATTTATTGCATAAG
Found at i:17190816 original size:20 final size:20
Alignment explanation
Indices: 17190791--17190841 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
17190781 CGGTTAAGGG
17190791 CACGGGCGTGTCCCAAGCCA
1 CACGGGCGTGTCCCAAGCCA
17190811 CACGGGCGTGTCCCAAGCCA
1 CACGGGCGTGTCCCAAGCCA
17190831 CACGGGCGTGT
1 CACGGGCGTGT
17190842 GTGACTACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.18, C:0.37, G:0.33, T:0.12
Consensus pattern (20 bp):
CACGGGCGTGTCCCAAGCCA
Found at i:17194703 original size:17 final size:16
Alignment explanation
Indices: 17194683--17194717 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
17194673 ATTTAAGTAA
17194683 TAGTTTAATTTTGATTG
1 TAGTTTAATTTTG-TTG
17194700 TAGTTTAATTTTGTTG
1 TAGTTTAATTTTGTTG
17194716 TA
1 TA
17194718 CGCTATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.23, C:0.00, G:0.17, T:0.60
Consensus pattern (16 bp):
TAGTTTAATTTTGTTG
Found at i:17196737 original size:20 final size:20
Alignment explanation
Indices: 17196712--17196773 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 20
17196702 AATTAAATTC
17196712 TAAAAGATAAATACAAATAAA
1 TAAAAGATAAATA-AAATAAA
*
17196733 T-AAAGATAATTAAAGAT-AA
1 TAAAAGATAAATAAA-ATAAA
17196752 TAAAAGATAAATGAAAATAAA
1 TAAAAGATAAAT-AAAATAAA
17196773 T
1 T
17196774 CCTAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
19 5 0.14
20 23 0.66
21 7 0.20
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.23
Consensus pattern (20 bp):
TAAAAGATAAATAAAATAAA
Found at i:17196741 original size:10 final size:10
Alignment explanation
Indices: 17196714--17196773 Score: 63
Period size: 10 Copynumber: 6.0 Consensus size: 10
17196704 TTAAATTCTA
17196714 AAAGATAAAT
1 AAAGATAAAT
17196724 ACAA-ATAAAT
1 A-AAGATAAAT
*
17196734 AAAGATAATT
1 AAAGATAAAT
17196744 AAAGAT-AAT
1 AAAGATAAAT
17196753 AAAAGATAAAT
1 -AAAGATAAAT
17196764 GAAA-ATAAAT
1 -AAAGATAAAT
17196774 CCTAAAATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
9 4 0.09
10 31 0.72
11 8 0.19
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:17196762 original size:30 final size:30
Alignment explanation
Indices: 17196714--17196771 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
17196704 TTAAATTCTA
*
17196714 AAAGATAAATACAAATAAAT-AAAGATAATT
1 AAAGATAAATAAAAATAAATGAAA-ATAATT
17196744 AAAGAT-AATAAAAGATAAATGAAAATAA
1 AAAGATAAATAAAA-ATAAATGAAAATAA
17196772 ATCCTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 6 0.24
30 16 0.64
31 3 0.12
ACGTcount: A:0.69, C:0.02, G:0.09, T:0.21
Consensus pattern (30 bp):
AAAGATAAATAAAAATAAATGAAAATAATT
Found at i:17198764 original size:15 final size:15
Alignment explanation
Indices: 17198744--17198790 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
17198734 ACCCAAACAA
17198744 AATAAAGTAATAAAT
1 AATAAAGTAATAAAT
* *
17198759 AATAAAATAA-AATAA
1 AATAAAGTAATAA-AT
*
17198774 AATAAAGTAATGAAT
1 AATAAAGTAATAAAT
17198789 AA
1 AA
17198791 ATATATAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
14 2 0.08
15 22 0.88
16 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (15 bp):
AATAAAGTAATAAAT
Found at i:17198769 original size:5 final size:5
Alignment explanation
Indices: 17198759--17198825 Score: 68
Period size: 5 Copynumber: 13.4 Consensus size: 5
17198749 AGTAATAAAT
* *
17198759 AATAA AATAA AATAA AATAA AGTAA TGAATAA ATATAT AA-AA AATAA
1 AATAA AATAA AATAA AATAA AATAA --AATAA A-ATAA AATAA AATAA
17198806 AATAA AAT-A AA-AA AATAA AA
1 AATAA AATAA AATAA AATAA AA
17198826 ATTGGGTTGC
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
4 9 0.17
5 35 0.67
6 4 0.08
7 4 0.08
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:17200976 original size:40 final size:40
Alignment explanation
Indices: 17200921--17200998 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 40
17200911 ATCAACAAAT
17200921 GGTGATTGGATGCGTGTCAGGAGGTATTAGGCATTCCTAA
1 GGTGATTGGATGCGTGTCAGGAGGTATTAGGCATTCCTAA
*
17200961 GGTGATTGGATGCGTGTCAGGAGGTGTTAGGCATTCCT
1 GGTGATTGGATGCGTGTCAGGAGGTATTAGGCATTCCT
17200999 TTTATATAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.19, C:0.13, G:0.37, T:0.31
Consensus pattern (40 bp):
GGTGATTGGATGCGTGTCAGGAGGTATTAGGCATTCCTAA
Found at i:17201399 original size:29 final size:28
Alignment explanation
Indices: 17201361--17201428 Score: 91
Period size: 29 Copynumber: 2.4 Consensus size: 28
17201351 TAAAAAGTGG
* *
17201361 AAAAACTAAATCCTTAAAAATAAGAATA
1 AAAAAATAAATCCTTAAAAATAAAAATA
**
17201389 AAAAAATTAAATTGTTAAAAATAAAAATA
1 AAAAAA-TAAATCCTTAAAAATAAAAATA
17201418 AAAAAATAAAT
1 AAAAAATAAAT
17201429 TTCAAATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 10 0.29
29 25 0.71
ACGTcount: A:0.69, C:0.04, G:0.03, T:0.24
Consensus pattern (28 bp):
AAAAAATAAATCCTTAAAAATAAAAATA
Found at i:17201444 original size:29 final size:29
Alignment explanation
Indices: 17201376--17201434 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
17201366 CTAAATCCTT
* *
17201376 AAAAATAAGAATAAAAAAATTAAATTGTT
1 AAAAATAAAAATAAAAAAATTAAATTGTC
17201405 AAAAATAAAAATAAAAAAA-TAAATT-TC
1 AAAAATAAAAATAAAAAAATTAAATTGTC
17201432 AAA
1 AAA
17201435 TATACGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 4 0.14
28 6 0.21
29 18 0.64
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (29 bp):
AAAAATAAAAATAAAAAAATTAAATTGTC
Found at i:17207089 original size:33 final size:33
Alignment explanation
Indices: 17207048--17207114 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
17207038 ACTGTAAGTA
17207048 AAAATCTAACCATATTGCTCATTCAAATGATTT
1 AAAATCTAACCATATTGCTCATTCAAATGATTT
17207081 AAAATCTAACCATATTGCTCATTCAAATGATTT
1 AAAATCTAACCATATTGCTCATTCAAATGATTT
17207114 A
1 A
17207115 TCCATTGTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.36
Consensus pattern (33 bp):
AAAATCTAACCATATTGCTCATTCAAATGATTT
Found at i:17213511 original size:45 final size:45
Alignment explanation
Indices: 17213454--17213545 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
17213444 GTAGAGAAAA
* *
17213454 TTAATGTCAATGAGGAGGTTGATAGCCAGCTAGCAAGTGAGAAGC
1 TTAATGTCAATGAGGAGGTTAACAGCCAGCTAGCAAGTGAGAAGC
*
17213499 TTAATGTCAATGAGGAGGTTAACAGTCAGCTAGCAAGTGAGAAGC
1 TTAATGTCAATGAGGAGGTTAACAGCCAGCTAGCAAGTGAGAAGC
17213544 TT
1 TT
17213546 TGTTCTGCAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.24
Consensus pattern (45 bp):
TTAATGTCAATGAGGAGGTTAACAGCCAGCTAGCAAGTGAGAAGC
Found at i:17219655 original size:15 final size:16
Alignment explanation
Indices: 17219625--17219663 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
17219615 TAGTAAAAAT
17219625 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
17219642 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
17219657 ATAATTT
1 ATAATTT
17219664 TTAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:17220829 original size:17 final size:16
Alignment explanation
Indices: 17220809--17220845 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 16
17220799 TTTTTTATAA
17220809 TTTTTTAAAAATTTGAT
1 TTTTTTAAAAA-TTGAT
17220826 TTTTTTAAAAATTGAT
1 TTTTTTAAAAATTGAT
17220842 TTTT
1 TTTT
17220846 ATATATAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTTTTAAAAATTGAT
Found at i:17222448 original size:23 final size:23
Alignment explanation
Indices: 17222401--17222638 Score: 190
Period size: 24 Copynumber: 10.0 Consensus size: 23
17222391 GTTAAAAGGA
* *
17222401 TCACATAACAGTTTACAAAAGGGGT
1 TCACATAACA-TTCAC-TAAGGGGT
* *
17222426 TCACATATCGTTCACTAAGGGGT
1 TCACATAACATTCACTAAGGGGT
**
17222449 TCGTATAACATTCACTAAGGGGT
1 TCACATAACATTCACTAAGGGGT
*
17222472 TCACACAACATTCACTAAGGGGT
1 TCACATAACATTCACTAAGGGGT
* *
17222495 TGGCACA-AATATTCATTAAGGGGT
1 T--CACATAACATTCACTAAGGGGT
** * *
17222519 TGGCATAAATATTCACTGAGGGGT
1 TCACAT-AACATTCACTAAGGGGT
* *
17222543 TCGCATAACATTCACTGAGGGGT
1 TCACATAACATTCACTAAGGGGT
**
17222566 TTGCATAACATTCACTAAGGGGGT
1 TCACATAACATTCACTAA-GGGGT
**
17222590 TTGCATAACATTCACTAAGGGGGT
1 TCACATAACATTCACTAA-GGGGT
** * *
17222614 TTGCATAAATATTCATTAAGGGGT
1 TCACAT-AACATTCACTAAGGGGT
17222638 T
1 T
17222639 TGGCTTATCC
Statistics
Matches: 184, Mismatches: 23, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
22 2 0.01
23 79 0.43
24 81 0.44
25 22 0.12
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (23 bp):
TCACATAACATTCACTAAGGGGT
Found at i:17222514 original size:24 final size:23
Alignment explanation
Indices: 17222436--17222640 Score: 194
Period size: 24 Copynumber: 8.7 Consensus size: 23
17222426 TCACATATCG
* * *
17222436 TTCACTAAGGGGTTCGTATAACA
1 TTCACTAAGGGGTTTGCAAAACA
** *
17222459 TTCACTAAGGGGTTCACACAACA
1 TTCACTAAGGGGTTTGCAAAACA
* *
17222482 TTCACTAAGGGGTTGGCACAAATA
1 TTCACTAAGGGGTTTGCA-AAACA
* * *
17222506 TTCATTAAGGGGTTGGCATAAATA
1 TTCACTAAGGGGTTTGCA-AAACA
* * *
17222530 TTCACTGAGGGGTTCGCATAACA
1 TTCACTAAGGGGTTTGCAAAACA
* *
17222553 TTCACTGAGGGGTTTGCATAACA
1 TTCACTAAGGGGTTTGCAAAACA
*
17222576 TTCACTAAGGGGGTTTGCATAACA
1 TTCACTAA-GGGGTTTGCAAAACA
*
17222600 TTCACTAAGGGGGTTTGCATAAATA
1 TTCACTAA-GGGGTTTGCA-AAACA
*
17222625 TTCATTAAGGGGTTTG
1 TTCACTAAGGGGTTTG
17222641 GCTTATCCGA
Statistics
Matches: 160, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
23 68 0.43
24 82 0.51
25 10 0.06
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (23 bp):
TTCACTAAGGGGTTTGCAAAACA
Found at i:17222603 original size:94 final size:95
Alignment explanation
Indices: 17222436--17222638 Score: 275
Period size: 94 Copynumber: 2.1 Consensus size: 95
17222426 TCACATATCG
*
17222436 TTCACTAAGGGGTTCGTATAACATTCACTAAGGGGTTCACACAACATTCACTAAGGGGTTGGCAC
1 TTCACTAAGGGGTTCGCATAACATTCACTAAGGGGTTCACACAACATTCACTAAGGGGTTGGCAC
* *
17222501 AAATATTCATTAA-GGGGTTGGCATAAATA
66 AAACATTCACTAAGGGGGTTGGCATAAATA
* * ** * *
17222530 TTCACTGAGGGGTTCGCATAACATTCACTGAGGGGTTTGCATAACATTCACTAAGGGGGTTTGCA
1 TTCACTAAGGGGTTCGCATAACATTCACTAAGGGGTTCACACAACATTCACTAA-GGGGTTGGCA
* *
17222595 -TAACATTCACTAAGGGGGTTTGCATAAATA
65 CAAACATTCACTAAGGGGGTTGGCATAAATA
*
17222625 TTCATTAAGGGGTT
1 TTCACTAAGGGGTT
17222639 TGGCTTATCC
Statistics
Matches: 94, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
94 58 0.62
95 36 0.38
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (95 bp):
TTCACTAAGGGGTTCGCATAACATTCACTAAGGGGTTCACACAACATTCACTAAGGGGTTGGCAC
AAACATTCACTAAGGGGGTTGGCATAAATA
Found at i:17222717 original size:43 final size:43
Alignment explanation
Indices: 17222643--17222766 Score: 176
Period size: 43 Copynumber: 2.8 Consensus size: 43
17222633 GGGGTTTGGC
17222643 TTATCCGATGATGCATTATGTGTATGCCAATATAGTTGCTTCGAT
1 TTATCCGATGATGCA--ATGTGTATGCCAATATAGTTGCTTCGAT
* * * *
17222688 TTATCTGATGATGCAATGTGTATACCAATATAGTTGCTTTGGT
1 TTATCCGATGATGCAATGTGTATGCCAATATAGTTGCTTCGAT
* *
17222731 TTATCCGATGATGCACTGTGTATGCCAGTATAGTTG
1 TTATCCGATGATGCAATGTGTATGCCAATATAGTTG
17222767 TTCCAGTATA
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
43 57 0.80
45 14 0.20
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.40
Consensus pattern (43 bp):
TTATCCGATGATGCAATGTGTATGCCAATATAGTTGCTTCGAT
Found at i:17228039 original size:50 final size:50
Alignment explanation
Indices: 17227960--17228236 Score: 464
Period size: 50 Copynumber: 5.5 Consensus size: 50
17227950 CCATGGCAAC
* *
17227960 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
17228010 AAGTGATAAGTGATAGCTTCGGCTGCACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
17228060 AAGTGATAAGTGATAGCTTCGGCAACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
17228110 AAGTGATAAGTGATAGCTTCGACTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
17228160 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
17228210 CAAGTAAAAAGTGGTAGCTTCGGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
17228237 CTGATCAATG
Statistics
Matches: 213, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
50 191 0.90
51 22 0.10
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:17228256 original size:31 final size:31
Alignment explanation
Indices: 17228215--17228298 Score: 114
Period size: 31 Copynumber: 2.7 Consensus size: 31
17228205 AATGACAAGT
17228215 AAAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAA-TGGTAGCTTCGGCTACCTGATCAATG
* *
17228247 AAAAATGGTAGCTCCGGCTACCTGATCAGTG
1 AAAAATGGTAGCTTCGGCTACCTGATCAATG
* * *
17228278 AATAGTGATAGCTTCGGCTAC
1 AAAAATGGTAGCTTCGGCTAC
17228299 AAGTGACAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 41 0.89
32 5 0.11
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAAATGGTAGCTTCGGCTACCTGATCAATG
Found at i:17238228 original size:2 final size:2
Alignment explanation
Indices: 17238223--17238258 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
17238213 ATACACACAC
17238223 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17238259 TACCACTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17244687 original size:31 final size:31
Alignment explanation
Indices: 17244642--17244712 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
17244632 TTTGTGAAAT
* * *
17244642 TATACATATTAAATTTTAATTTTGGTTCAAA
1 TATACACATGAAATTTTAATTTTGATTCAAA
* * *
17244673 TATAGACATGAAATTTTGATTTTGATTCAAT
1 TATACACATGAAATTTTAATTTTGATTCAAA
17244704 TATACACAT
1 TATACACAT
17244713 TTAAAGAAAC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.45
Consensus pattern (31 bp):
TATACACATGAAATTTTAATTTTGATTCAAA
Found at i:17247569 original size:27 final size:26
Alignment explanation
Indices: 17247539--17247595 Score: 60
Period size: 27 Copynumber: 2.1 Consensus size: 26
17247529 TTTATTTTGA
* * *
17247539 ATTTGAGAATTGGGTTATAATTAGTTT
1 ATTTGA-AATTGGGTAATAATGAGTAT
*
17247566 ATTTTGAATTTGGGTAATAATGAGTAT
1 A-TTTGAAATTGGGTAATAATGAGTAT
17247593 ATT
1 ATT
17247596 ATTTGGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
26 2 0.08
27 18 0.72
28 5 0.20
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (26 bp):
ATTTGAAATTGGGTAATAATGAGTAT
Found at i:17247915 original size:24 final size:23
Alignment explanation
Indices: 17247901--17247947 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
17247891 AATGAATTGT
17247901 TAATT-TAAAATTAAAATATTTA
1 TAATTATAAAATTAAAATATTTA
17247923 TAATTATAAAATTTAAAATTATTTA
1 TAATTATAAAA-TTAAAA-TATTTA
17247948 AATCTGTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.23
23 5 0.23
24 6 0.27
25 6 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TAATTATAAAATTAAAATATTTA
Found at i:17247927 original size:15 final size:15
Alignment explanation
Indices: 17247902--17247944 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
17247892 ATGAATTGTT
17247902 AATTTAAAATTA-AA
1 AATTTAAAATTATAA
*
17247916 ATATTTATAATTATAA
1 A-ATTTAAAATTATAA
17247932 AATTTAAAATTAT
1 AATTTAAAATTAT
17247945 TTAAATCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 21 0.84
16 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTTAAAATTATAA
Found at i:17249269 original size:2 final size:2
Alignment explanation
Indices: 17249258--17249288 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
17249248 TTTACTTACA
17249258 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17249289 TTTTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:17250292 original size:12 final size:13
Alignment explanation
Indices: 17250268--17250292 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17250258 AATTTTATGA
17250268 TTTTTAAATTTTT
1 TTTTTAAATTTTT
17250281 TTTTTAAATTTT
1 TTTTTAAATTTT
17250293 AAAATGACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTAAATTTTT
Found at i:17251372 original size:22 final size:22
Alignment explanation
Indices: 17251347--17251391 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
17251337 AATTTATCAT
17251347 TATATCTATTTATAAAAGAGAA
1 TATATCTATTTATAAAAGAGAA
17251369 TATATCTATTTATAAAAGAGAA
1 TATATCTATTTATAAAAGAGAA
17251391 T
1 T
17251392 GGTTTATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (22 bp):
TATATCTATTTATAAAAGAGAA
Found at i:17255389 original size:15 final size:15
Alignment explanation
Indices: 17255369--17255399 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17255359 TTGTTCTTCA
17255369 AATATATATATATAT
1 AATATATATATATAT
*
17255384 AATATATATGTATAT
1 AATATATATATATAT
17255399 A
1 A
17255400 TGAAGTTGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
AATATATATATATAT
Found at i:17257342 original size:2 final size:2
Alignment explanation
Indices: 17257335--17257359 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17257325 ACCACTAAAC
17257335 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
17257360 AATCAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17258710 original size:27 final size:27
Alignment explanation
Indices: 17258680--17258731 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
17258670 ACATTTTCAA
17258680 TTTT-TAAAATATAGAAAAT-GAAAATTG
1 TTTTCTAAAA-AT-GAAAATGGAAAATTG
17258707 TTTTCTAAAAATGAAAATGGAAAAT
1 TTTTCTAAAAATGAAAATGGAAAAT
17258732 GAAATAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 6 0.26
27 12 0.52
28 5 0.22
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.35
Consensus pattern (27 bp):
TTTTCTAAAAATGAAAATGGAAAATTG
Found at i:17260677 original size:24 final size:24
Alignment explanation
Indices: 17260650--17260696 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
17260640 TTATTAATTT
17260650 TATG-TTATTT-TAATTTCTTTTAAA
1 TATGTTTATTTGT-ATTT-TTTTAAA
17260674 TATGTTTATTTGTATTTTTTTAA
1 TATGTTTATTTGTATTTTTTTAA
17260697 CAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 10 0.48
25 10 0.48
26 1 0.05
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (24 bp):
TATGTTTATTTGTATTTTTTTAAA
Found at i:17261130 original size:10 final size:10
Alignment explanation
Indices: 17261115--17261142 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
17261105 TCACTTTAGT
17261115 TTTCATGTTA
1 TTTCATGTTA
17261125 TTTCATGTTA
1 TTTCATGTTA
17261135 TTTCATGT
1 TTTCATGT
17261143 ATTATTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.61
Consensus pattern (10 bp):
TTTCATGTTA
Found at i:17268088 original size:24 final size:24
Alignment explanation
Indices: 17268060--17268111 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
17268050 TTCATAGATA
* *
17268060 AAATAAATTGTGCTAACAAATACT
1 AAATAAATTATACTAACAAATACT
* * *
17268084 AAATATATTATACTAATACATACT
1 AAATAAATTATACTAACAAATACT
17268108 AAAT
1 AAAT
17268112 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAACAAATACT
Found at i:17268931 original size:2 final size:2
Alignment explanation
Indices: 17268924--17268959 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
17268914 TGGTTAACCG
17268924 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17268960 TTTGTTGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17269357 original size:30 final size:31
Alignment explanation
Indices: 17269298--17269363 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
17269288 ATTAGTAAAG
*
17269298 ATAAAATTATACTTTAACCTCTCTAAAAATA
1 ATAAAATTATAATTTAACCTCTCTAAAAATA
* * * *
17269329 ATAAAATTTTAATTTAA-TTCTTTAAAAATT
1 ATAAAATTATAATTTAACCTCTCTAAAAATA
17269359 ATAAA
1 ATAAA
17269364 GATATAGGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (31 bp):
ATAAAATTATAATTTAACCTCTCTAAAAATA
Found at i:17276691 original size:25 final size:26
Alignment explanation
Indices: 17276663--17276722 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
17276653 GATTCTCTGG
* *
17276663 AGCTAGTGTTTGCAGCATTTA-ACCA
1 AGCTAGTGTTAGCAGCATTTATACAA
* * *
17276688 AGCTAATGTTAGCAGCCTTTATTCAA
1 AGCTAGTGTTAGCAGCATTTATACAA
17276714 AGCTAGTGT
1 AGCTAGTGT
17276723 CTAATTGCCT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 18 0.64
26 10 0.36
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (26 bp):
AGCTAGTGTTAGCAGCATTTATACAA
Found at i:17283392 original size:12 final size:12
Alignment explanation
Indices: 17283375--17283400 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17283365 TCACTCAACC
17283375 AAAATTCAAAAA
1 AAAATTCAAAAA
17283387 AAAATTCAAAAA
1 AAAATTCAAAAA
17283399 AA
1 AA
17283401 TTTAAAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAATTCAAAAA
Found at i:17283693 original size:15 final size:15
Alignment explanation
Indices: 17283669--17283698 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17283659 AATTTCACTT
*
17283669 GATTTGATTCGATTC
1 GATTTAATTCGATTC
17283684 GATTTAATTCGATTC
1 GATTTAATTCGATTC
17283699 AACTCAGATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (15 bp):
GATTTAATTCGATTC
Found at i:17285621 original size:28 final size:28
Alignment explanation
Indices: 17285572--17285626 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
17285562 CTTATTAAAA
* *
17285572 TAAAATTCAAAGATGTATTAATATCAAC
1 TAAAATTAAAAGATATATTAATATCAAC
*
17285600 TAAAATGTAAAAGATATA-TAATTTCAA
1 TAAAAT-TAAAAGATATATTAATATCAA
17285627 AAATTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (28 bp):
TAAAATTAAAAGATATATTAATATCAAC
Found at i:17285837 original size:17 final size:17
Alignment explanation
Indices: 17285814--17285853 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
17285804 TTTTTAGGGT
17285814 TTTTTTTCAATTTTGATA
1 TTTTTTTCAATTTTGA-A
*
17285832 TTTTTTTGAATTTTGAA
1 TTTTTTTCAATTTTGAA
17285849 TTTTT
1 TTTTT
17285854 ATTTTTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (17 bp):
TTTTTTTCAATTTTGAA
Found at i:17286957 original size:10 final size:10
Alignment explanation
Indices: 17286942--17286992 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
17286932 TTCTAAAATC
17286942 TTAAAAATAA
1 TTAAAAATAA
17286952 TTAAAAAT-A
1 TTAAAAATAA
*
17286961 TTAAAAATAT
1 TTAAAAATAA
*
17286971 TTTAAAATAA
1 TTAAAAATAA
17286981 TTTTAAAAATAA
1 --TTAAAAATAA
17286993 AAATTCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 9 0.26
10 16 0.47
12 9 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
TTAAAAATAA
Found at i:17286964 original size:19 final size:19
Alignment explanation
Indices: 17286922--17286979 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
17286912 AAAAAATTTC
* *
17286922 TTAACAATAATTCTAAAATC
1 TTAAAAATAATT-TAAAATA
*
17286942 TTAAAAATAATTAAAAATA
1 TTAAAAATAATTTAAAATA
*
17286961 TTAAAAATATTTTAAAATA
1 TTAAAAATAATTTAAAATA
17286980 ATTTTAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 22 0.67
20 11 0.33
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAAAAATAATTTAAAATA
Found at i:17288604 original size:22 final size:22
Alignment explanation
Indices: 17288542--17288604 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 22
17288532 CTCCGATTAT
* * * *
17288542 TAGCACCTTAGTACTCTCCGTT
1 TAGCACATTAGTGCTCTCTGTA
*
17288564 TAGCACATTCGTGCTCTCTGTA
1 TAGCACATTAGTGCTCTCTGTA
*
17288586 TAGCACTTTAGTGCTCTCT
1 TAGCACATTAGTGCTCTCT
17288605 ATTCAATAGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.17, C:0.29, G:0.16, T:0.38
Consensus pattern (22 bp):
TAGCACATTAGTGCTCTCTGTA
Found at i:17290059 original size:13 final size:13
Alignment explanation
Indices: 17290041--17290102 Score: 88
Period size: 13 Copynumber: 4.8 Consensus size: 13
17290031 AGTTTGGCAA
17290041 TACTTTTGAAAAG
1 TACTTTTGAAAAG
17290054 TACTTTTGAAAAG
1 TACTTTTGAAAAG
* * *
17290067 TGCTGTGGAAAAG
1 TACTTTTGAAAAG
*
17290080 TGCTTTTGAAAAG
1 TACTTTTGAAAAG
17290093 TACTTTTGAA
1 TACTTTTGAA
17290103 GTTTGGTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (13 bp):
TACTTTTGAAAAG
Found at i:17291270 original size:27 final size:26
Alignment explanation
Indices: 17291230--17291344 Score: 131
Period size: 27 Copynumber: 4.3 Consensus size: 26
17291220 AGCATGGCTG
* *
17291230 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
17291256 CCAGATACAAATAATTGTGGCAGAGCCA
1 CCAGA-ACAGATAA-TGTGGCAGAGCCA
*
17291284 CCAGAATAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
17291311 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
17291338 CCAGAAC
1 CCAGAAC
17291345 GCTTCCTCCA
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
26 5 0.07
27 54 0.71
28 17 0.22
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:17291295 original size:54 final size:54
Alignment explanation
Indices: 17291230--17291344 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
17291220 AGCATGGCTG
*
17291230 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAAATAATTGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAAATAATTGTGGCAGAGCCA
* * * * *
17291284 CCAGAATAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAAATAATTGTGGCAGAGCCA
17291338 CCAGAAC
1 CCAGAAC
17291345 GCTTCCTCCA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
54 35 0.66
55 18 0.34
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAAATAATTGTGGCAGAGCCA
Found at i:17291750 original size:8 final size:8
Alignment explanation
Indices: 17291734--17291763 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
17291724 CTCAAAATAC
17291734 CGGCTTTT
1 CGGCTTTT
*
17291742 CGGCATTT
1 CGGCTTTT
17291750 CGGCTTTT
1 CGGCTTTT
17291758 CGGCTT
1 CGGCTT
17291764 ATGCCGATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.03, C:0.27, G:0.27, T:0.43
Consensus pattern (8 bp):
CGGCTTTT
Found at i:17300704 original size:2 final size:2
Alignment explanation
Indices: 17300697--17300727 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17300687 TATGGAGTAT
17300697 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17300728 TATTAAAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17307248 original size:22 final size:22
Alignment explanation
Indices: 17307209--17307260 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
17307199 TGAAATTCAT
*
17307209 AATATATAAAAAAATTTAAAGTA
1 AATA-ATAAAAAAATTTAAAATA
* * *
17307232 AATAATAAAACATTTTAAAATG
1 AATAATAAAAAAATTTAAAATA
17307254 AATAATA
1 AATAATA
17307261 CATAAAGCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (22 bp):
AATAATAAAAAAATTTAAAATA
Found at i:17307320 original size:52 final size:49
Alignment explanation
Indices: 17307223--17307320 Score: 115
Period size: 52 Copynumber: 1.9 Consensus size: 49
17307213 TATAAAAAAA
* * * *
17307223 TTTAAAGTAAATAATAAAACATTTTAAAATGAATAATACATAAAGCGAG
1 TTTAAAATAAATAATAAAAAATTTTAAAATCAATAATACACAAAGCGAG
* *
17307272 TTTAAAATAAATAATGTAAAAGAATTTTAAAATCTATATTACACAAAGC
1 TTTAAAATAAATAA--TAAAA-AATTTTAAAATCAATAATACACAAAGC
17307321 AAATTAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
49 13 0.32
51 5 0.12
52 22 0.55
ACGTcount: A:0.54, C:0.07, G:0.08, T:0.31
Consensus pattern (49 bp):
TTTAAAATAAATAATAAAAAATTTTAAAATCAATAATACACAAAGCGAG
Found at i:17307634 original size:13 final size:13
Alignment explanation
Indices: 17307614--17307646 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
17307604 TAAAATAGTT
17307614 TAAAATAAATAAA
1 TAAAATAAATAAA
*
17307627 TGAAATAAATAAA
1 TAAAATAAATAAA
17307640 TAAAATA
1 TAAAATA
17307647 TCAAAGAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (13 bp):
TAAAATAAATAAA
Found at i:17316652 original size:40 final size:40
Alignment explanation
Indices: 17316525--17316654 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
17316515 ATGCTGGAAA
* *
17316525 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
17316565 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
17316605 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
17316645 TTATATCCGG
1 TTATATCCGG
17316655 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:17316653 original size:80 final size:79
Alignment explanation
Indices: 17316488--17316654 Score: 196
Period size: 80 Copynumber: 2.1 Consensus size: 79
17316478 AAATTGAATG
* *
17316488 ATATCCGGGCTAAGTCCCGAAGACATTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCAA
1 ATATCCGGGCTAAGACCCGAAGACATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCAA
17316553 TTGTGCTAGTGGCT
66 TTGTGCTAGTGGCT
* * * ** *
17316567 ACATCCGGGCTAAGACCCGAAGGCATTCGTGC-GAGTCATTCTATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGACATT-ATGCTG-GAAATTATATCCGGGCTAAGACCCGAAGGC
*
17316631 -ATTCGTGC-ACGTGGTT
64 AATT-GTGCTA-GTGGCT
17316647 ATATCCGG
1 ATATCCGG
17316655 TTGTATTCCG
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
79 29 0.39
80 45 0.61
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGACATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCAA
TTGTGCTAGTGGCT
Found at i:17320169 original size:13 final size:13
Alignment explanation
Indices: 17320151--17320178 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17320141 TCGCCTTGGG
17320151 GTGCGCCAGTGTT
1 GTGCGCCAGTGTT
17320164 GTGCGCCAGTGTT
1 GTGCGCCAGTGTT
17320177 GT
1 GT
17320179 TGTGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.21, G:0.39, T:0.32
Consensus pattern (13 bp):
GTGCGCCAGTGTT
Found at i:17324704 original size:40 final size:40
Alignment explanation
Indices: 17324577--17324706 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
17324567 ATGCTGGAAA
* *
17324577 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
17324617 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
17324657 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
17324697 TTATATCCGG
1 TTATATCCGG
17324707 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:17324705 original size:80 final size:79
Alignment explanation
Indices: 17324540--17324706 Score: 196
Period size: 80 Copynumber: 2.1 Consensus size: 79
17324530 GAATTGAATG
* *
17324540 ATATCCGGGCTAAGTCCCGAAGACATTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCAA
1 ATATCCGGGCTAAGACCCGAAGACATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCAA
17324605 TTGTGCTAGTGGCT
66 TTGTGCTAGTGGCT
* * * ** *
17324619 ACATCCGGGCTAAGACCCGAAGGCATTCGTGC-GAGTCATTCTATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGACATT-ATGCTG-GAAATTATATCCGGGCTAAGACCCGAAGGC
*
17324683 -ATTCGTGC-ACGTGGTT
64 AATT-GTGCTA-GTGGCT
17324699 ATATCCGG
1 ATATCCGG
17324707 TTGTATTCCG
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
79 29 0.39
80 45 0.61
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGACATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCAA
TTGTGCTAGTGGCT
Found at i:17327905 original size:27 final size:26
Alignment explanation
Indices: 17327870--17327981 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
17327860 AGCATGGCTG
* *
17327870 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
17327896 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
17327924 CCAGAACAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
17327951 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
17327978 CCAG
1 CCAG
17327982 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 53 0.70
28 17 0.22
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:17327962 original size:54 final size:54
Alignment explanation
Indices: 17327870--17327981 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
17327860 AGCATGGCTG
* *
17327870 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
17327924 CCAGAACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
17327978 CCAG
1 CCAG
17327982 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:17335730 original size:27 final size:26
Alignment explanation
Indices: 17335695--17335806 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
17335685 AGCATGGCTG
* *
17335695 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
17335721 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
17335749 CCAGAACAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
17335776 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
17335803 CCAG
1 CCAG
17335807 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 53 0.70
28 17 0.22
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:17335787 original size:54 final size:54
Alignment explanation
Indices: 17335695--17335806 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
17335685 AGCATGGCTG
* *
17335695 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
17335749 CCAGAACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
17335803 CCAG
1 CCAG
17335807 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:17346405 original size:30 final size:29
Alignment explanation
Indices: 17346362--17346422 Score: 113
Period size: 30 Copynumber: 2.1 Consensus size: 29
17346352 CAAGTAGCCG
17346362 AAGCTAGTTAAATCACACACTTAGTGCCA
1 AAGCTAGTTAAATCACACACTTAGTGCCA
17346391 AAGCTAGTTTAAATCACACACTTAGTGCCA
1 AAGCTAG-TTAAATCACACACTTAGTGCCA
17346421 AA
1 AA
17346423 ACTTCCATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (29 bp):
AAGCTAGTTAAATCACACACTTAGTGCCA
Found at i:17349168 original size:3 final size:3
Alignment explanation
Indices: 17349160--17349188 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
17349150 TTACTATTTT
17349160 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
17349189 TTCACACTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:17349980 original size:59 final size:59
Alignment explanation
Indices: 17349915--17350032 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
17349905 TAACTAAAGT
*
17349915 CTTTATTTCTTTCTATTCTTCTTTATTAAAAAAAATCATTTTCTGATCTTCATAATTGG
1 CTTTATTTCTTTCTATACTTCTTTATTAAAAAAAATCATTTTCTGATCTTCATAATTGG
17349974 CTTTATTTCTTTCTATACTTCTTTATTAAAAAAAATCATTTTCTGATCTTCATAATTGG
1 CTTTATTTCTTTCTATACTTCTTTATTAAAAAAAATCATTTTCTGATCTTCATAATTGG
17350033 AAAATATTAC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.28, C:0.15, G:0.05, T:0.52
Consensus pattern (59 bp):
CTTTATTTCTTTCTATACTTCTTTATTAAAAAAAATCATTTTCTGATCTTCATAATTGG
Found at i:17352011 original size:40 final size:39
Alignment explanation
Indices: 17351942--17352078 Score: 120
Period size: 37 Copynumber: 3.5 Consensus size: 39
17351932 CCAGTTTGGT
* *
17351942 ACCCAGTGCCTCATCGGA-TAATTCAAAGTAATAATTTGAC
1 ACCCAGTGCCTCATC-GACTAAATCGAAGTAATAA-TTGAC
*
17351982 ACCCAGT-CTCTCATCGACTAAATCGAAGT-A-AATTGGC
1 ACCCAGTGC-CTCATCGACTAAATCGAAGTAATAATTGAC
* * * *
17352019 ACCCAGTGCCTCATCCAATTAATCCGAAGTAGTAAATTGAC
1 ACCCAGTGCCTCATCGACTAAAT-CGAAGTAAT-AATTGAC
* *
17352060 ACCTAGTGTCTCATCGACT
1 ACCCAGTGCCTCATCGACT
17352079 CGAAGTCGAA
Statistics
Matches: 78, Mismatches: 12, Indels: 13
0.76 0.12 0.13
Matches are distributed among these distances:
37 22 0.28
38 9 0.12
39 4 0.05
40 22 0.28
41 21 0.27
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (39 bp):
ACCCAGTGCCTCATCGACTAAATCGAAGTAATAATTGAC
Found at i:17352271 original size:2 final size:2
Alignment explanation
Indices: 17352264--17352333 Score: 76
Period size: 2 Copynumber: 35.5 Consensus size: 2
17352254 TTCATTCTAG
*
17352264 AT AT AT AT AT AT AT AT AT AT AT AT AT ACC A- AT -T CA- AT -T CAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT -AT AT AT -AT
17352305 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17352334 CCAATTCAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 14
0.80 0.01 0.19
Matches are distributed among these distances:
1 4 0.07
2 54 0.90
3 2 0.03
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:17352312 original size:43 final size:43
Alignment explanation
Indices: 17352252--17352346 Score: 167
Period size: 43 Copynumber: 2.3 Consensus size: 43
17352242 TACAAAAATT
17352252 AATTC-ATTC-TAGATATATATATATATATATATATATATACC
1 AATTCAATTCATAGATATATATATATATATATATATATATACC
*
17352293 AATTCAATTCATATATATATATATATATATATATATATATACC
1 AATTCAATTCATAGATATATATATATATATATATATATATACC
17352336 AATTCAATTCA
1 AATTCAATTCA
17352347 ATCATTCAAT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
41 5 0.10
42 4 0.08
43 42 0.82
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.43
Consensus pattern (43 bp):
AATTCAATTCATAGATATATATATATATATATATATATATACC
Found at i:17353155 original size:27 final size:26
Alignment explanation
Indices: 17353093--17353167 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 26
17353083 TTTATTTACT
17353093 TATTATAATATATAATATAATATATG
1 TATTATAATATATAATATAATATATG
17353119 TACTTAATAAT-TA-AGATATAATATTATAG
1 TA-TT-ATAATATATA-ATATAATA-TAT-G
17353148 TATTATAATATATATATATA
1 TATTATAATATATA-ATATA
17353168 TTTTTTTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
26 3 0.07
27 17 0.41
28 12 0.29
29 9 0.22
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (26 bp):
TATTATAATATATAATATAATATATG
Found at i:17353610 original size:23 final size:23
Alignment explanation
Indices: 17353576--17353619 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
17353566 AGACATGATC
*
17353576 GGTGCAAATGAAAGTGGCACTTT
1 GGTGCAAATGAAAGTGACACTTT
* *
17353599 GGTGCAATTGAATGTGACACT
1 GGTGCAAATGAAAGTGACACT
17353620 AATGGCACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.27
Consensus pattern (23 bp):
GGTGCAAATGAAAGTGACACTTT
Found at i:17356100 original size:26 final size:26
Alignment explanation
Indices: 17356043--17356103 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
17356033 TAACCGGAGC
* * *
17356043 TCCTGATTAAAGGCTCTTCGTGAGCT
1 TCCTGATTAAAAGCTCTTCGTAAACT
* * *
17356069 TTCTGATTAAAAGTTCTTTGTAAACT
1 TCCTGATTAAAAGCTCTTCGTAAACT
17356095 TCCTGATTA
1 TCCTGATTA
17356104 TGGCTCTTAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (26 bp):
TCCTGATTAAAAGCTCTTCGTAAACT
Found at i:17357971 original size:61 final size:61
Alignment explanation
Indices: 17357904--17358045 Score: 166
Period size: 60 Copynumber: 2.4 Consensus size: 61
17357894 ATTAGAGTTA
* *
17357904 ACTGGGCCTTAGCCCATATCAATATTAATTTGGGCCATAGCCCT-TTACAATATC-AGAGTAT
1 ACTGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAA-ATCGAGA-TAT
* * * *
17357965 ACTGGGCC-TAGCTCATATCAGTATCAATCTGGGCCGTAGCCCTATTACAAGTCGAGATAT
1 ACTGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAATCGAGATAT
* *
17358025 ATTGGGCCTT-GCCTATATCAA
1 ACTGGGCCTTAGCCCATATCAA
17358046 CACAGTTGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
60 50 0.74
61 18 0.26
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (61 bp):
ACTGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAATCGAGATAT
Found at i:17360636 original size:43 final size:43
Alignment explanation
Indices: 17360494--17360637 Score: 150
Period size: 43 Copynumber: 3.3 Consensus size: 43
17360484 CATCAAAATG
* * *
17360494 TGATATTCGGGCCTC-GGCCTAGCAAGCTTTAA-GCTGGTGAACAA
1 TGATA-TCGGGCTTCGGGCCTAGCAGGCTATAATGCTGGTG-A-AA
* * * *
17360538 T-ATTATCGGGCTACGGGCCTAGTAGGCTATAATGTTGGTGAGA
1 TGA-TATCGGGCTTCGGGCCTAGCAGGCTATAATGCTGGTGAAA
* *
17360581 TAATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAAA
1 TGATATCGGGCTTCGGGCCTAGCAGGCTATAATGCTGGTGAAA
17360624 TGATATCGGGCTTC
1 TGATATCGGGCTTC
17360638 AAGCATAGCA
Statistics
Matches: 83, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
43 58 0.70
44 19 0.23
45 6 0.07
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (43 bp):
TGATATCGGGCTTCGGGCCTAGCAGGCTATAATGCTGGTGAAA
Found at i:17360647 original size:43 final size:43
Alignment explanation
Indices: 17360561--17360649 Score: 115
Period size: 43 Copynumber: 2.1 Consensus size: 43
17360551 CGGGCCTAGT
** * ** *
17360561 AGGCTATAATGTTGGTGAGATAATATCGGGCTTCGGGCCTAGC
1 AGGCTATAATGCCGGTGAAATAATATCGGGCTTCAAGCATAGC
*
17360604 AGGCTATAATGCCGGTGAAATGATATCGGGCTTCAAGCATAGC
1 AGGCTATAATGCCGGTGAAATAATATCGGGCTTCAAGCATAGC
17360647 AGG
1 AGG
17360650 TGAAATACCG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (43 bp):
AGGCTATAATGCCGGTGAAATAATATCGGGCTTCAAGCATAGC
Found at i:17365181 original size:60 final size:60
Alignment explanation
Indices: 17365058--17365195 Score: 145
Period size: 60 Copynumber: 2.3 Consensus size: 60
17365048 GAGTTAACTA
*
17365058 GGCCTTAGCCCATATCAATATTAATCTGGGTCATAACCCATTACAATATCAGAGTATACTG
1 GGCC-TAGCCCATATCAATATCAATCTGGGTCATAACCCATTACAATATCAGAGTATACTG
* * * * * * *
17365119 GGCCTAGCTCATATCAGTATCAATTTGGGTCGTAGCCCTATTACAAGT-TGAGA-TATATTG
1 GGCCTAGCCCATATCAATATCAATCTGGGTCATAACCC-ATTACAA-TATCAGAGTATACTG
* *
17365179 GGCCTTGCCCACATCAA
1 GGCCTAGCCCATATCAA
17365196 CACAGTTGGC
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
60 47 0.75
61 15 0.24
62 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (60 bp):
GGCCTAGCCCATATCAATATCAATCTGGGTCATAACCCATTACAATATCAGAGTATACTG
Found at i:17372541 original size:19 final size:19
Alignment explanation
Indices: 17372517--17372553 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
17372507 ATCTCTTAAT
*
17372517 AAATTCGTTGTTATCTTAG
1 AAATTCGTTATTATCTTAG
17372536 AAATTCGTTATTATCTTA
1 AAATTCGTTATTATCTTA
17372554 AGTTGAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (19 bp):
AAATTCGTTATTATCTTAG
Found at i:17373217 original size:42 final size:41
Alignment explanation
Indices: 17373137--17373222 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 41
17373127 TTTGAATTAA
17373137 TTTATGGAAGACATTACTTAAATTATCATTCAATTTTTTTT
1 TTTATGGAAGACATTACTTAAATTATCATTCAATTTTTTTT
**
17373178 TTTATGGAAGACATTAC-TAAGGATTATCATTCGCTTTTTTTT
1 TTTATGGAAGACATTACTTAA--ATTATCATTCAATTTTTTTT
17373220 TTT
1 TTT
17373223 TATTAAGGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
40 3 0.07
41 17 0.41
42 21 0.51
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.51
Consensus pattern (41 bp):
TTTATGGAAGACATTACTTAAATTATCATTCAATTTTTTTT
Found at i:17377510 original size:16 final size:17
Alignment explanation
Indices: 17377491--17377525 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17377481 AAACGAAATG
*
17377491 ATGAAAAT-AAAAGAAA
1 ATGAAAATGAAAAAAAA
17377507 ATGAAAATGAAAAAAAA
1 ATGAAAATGAAAAAAAA
17377524 AT
1 AT
17377526 CTAATCTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.14
Consensus pattern (17 bp):
ATGAAAATGAAAAAAAA
Found at i:17377738 original size:15 final size:16
Alignment explanation
Indices: 17377710--17377750 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
17377700 AAAAGAAAAT
17377710 AAAATGAAATTTTTGA
1 AAAATGAAATTTTTGA
17377726 AAAATGAAATTTTTGA
1 AAAATGAAATTTTTGA
17377742 AAAAT-AAAT
1 AAAATGAAAT
17377751 AATTTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (16 bp):
AAAATGAAATTTTTGA
Found at i:17382219 original size:265 final size:264
Alignment explanation
Indices: 17381741--17382267 Score: 946
Period size: 265 Copynumber: 2.0 Consensus size: 264
17381731 ATGATATGTT
*
17381741 AGTGCTAGCTTGGAGTGCAACACGATATCCTAACTTCACATTGTACCAACCATTTTTAGAAAAAT
1 AGTGCTAGCTTGGAGTGCAACACGATATCCTAACTTCACATTGTACCAACCATCTTTAGAAAAAT
*
17381806 GCCATATAAGTTGGTCTAGTGGCCTAGAATACGAAAGAGGGATACTAAAAATTTTCTTAGCATCT
66 GCCATATAAGTTGGTCTAGTGGCCTAGAATACGAAAGAGGAATACTAAAAATTTTCTTAGCATCT
* * * *
17381871 TGAGGTGCTAAGAGACCTTTAATTGTAATGACTCGGTTTCCAACGATGTTGAAAATTGCGATTTT
131 TAAGGTGCTAAGAGACCCTTAATTGTAATGACTCGGTTTCCAACGATGTTGAAAAATGCGATTTC
17381936 GGAGTCTCACTTGCATAAACTGAGTTTGCAAATATAAAATAAGAATATTTACATTAGAAAAATAT
196 GGAGTCTCACTTGCATAAACTGAGTTTGCAAATATAAAATAAGAATATTTACATTAG-AAAATAT
17382001 ATTAG
260 ATTAG
* *
17382006 AGTGTTAGCTTGGAGTGCAACACGATATCCTAACTTCACATTGTCCCAACCATCTTTAGAAAAAT
1 AGTGCTAGCTTGGAGTGCAACACGATATCCTAACTTCACATTGTACCAACCATCTTTAGAAAAAT
17382071 GCCATATAAGTTGGTCTAGTGGCCTAGAATACGAAAGAGGAATACTAAAAATTTTCTTAGCATCT
66 GCCATATAAGTTGGTCTAGTGGCCTAGAATACGAAAGAGGAATACTAAAAATTTTCTTAGCATCT
* *
17382136 TAAGGTGCTAAGAGACCCTTAATTGTAATGACTCGGTTTCCAATGATGTTGAAAAATGCTATTTC
131 TAAGGTGCTAAGAGACCCTTAATTGTAATGACTCGGTTTCCAACGATGTTGAAAAATGCGATTTC
*
17382201 GGAGTCTCACTTGCATAAACTGAGTTTGTAAATATAAAATAAGAATATTTACATTAGAAAATATA
196 GGAGTCTCACTTGCATAAACTGAGTTTGCAAATATAAAATAAGAATATTTACATTAGAAAATATA
17382266 TT
261 TT
17382268 GAAGTTCGGT
Statistics
Matches: 251, Mismatches: 11, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
264 10 0.04
265 241 0.96
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (264 bp):
AGTGCTAGCTTGGAGTGCAACACGATATCCTAACTTCACATTGTACCAACCATCTTTAGAAAAAT
GCCATATAAGTTGGTCTAGTGGCCTAGAATACGAAAGAGGAATACTAAAAATTTTCTTAGCATCT
TAAGGTGCTAAGAGACCCTTAATTGTAATGACTCGGTTTCCAACGATGTTGAAAAATGCGATTTC
GGAGTCTCACTTGCATAAACTGAGTTTGCAAATATAAAATAAGAATATTTACATTAGAAAATATA
TTAG
Found at i:17384986 original size:15 final size:15
Alignment explanation
Indices: 17384954--17384982 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17384944 ATTTTCAGTG
17384954 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
17384969 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
17384983 ATTTTCTTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:17386169 original size:43 final size:43
Alignment explanation
Indices: 17386105--17386276 Score: 135
Period size: 43 Copynumber: 4.0 Consensus size: 43
17386095 CATAGGATTT
17386105 TCGATATGTG-TTCTC-ATGTAAGACCACGTCTAGGACGTTGGCA
1 TCGATATGTGATT-TCGA-GTAAGACCACGTCTAGGACGTTGGCA
* * * * * *
17386148 TCGATATGTAATTTCGAGTAAGACTATGTTTGGGACATTGGCA
1 TCGATATGTGATTTCGAGTAAGACCACGTCTAGGACGTTGGCA
*
17386191 TCG-TAATTGTGA-TTCGTGTAAGACC-CTGTC-AGGACAG-TGGCA
1 TCGAT-A-TGTGATTTCGAGTAAGACCAC-GTCTAGGAC-GTTGGCA
* * *
17386233 TCGACATGTGATTAC-ATGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATGTGATTTCGA-GTAAGACCACGTCTAGGACGTTGGCA
17386276 T
1 T
17386277 TGTACGATAT
Statistics
Matches: 100, Mismatches: 17, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
41 5 0.05
42 28 0.28
43 60 0.60
44 7 0.07
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (43 bp):
TCGATATGTGATTTCGAGTAAGACCACGTCTAGGACGTTGGCA
Found at i:17396874 original size:12 final size:12
Alignment explanation
Indices: 17396857--17396886 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
17396847 CTCACACGCT
17396857 CGTGTGCTAGGC
1 CGTGTGCTAGGC
*
17396869 CGTGTGCTAGGT
1 CGTGTGCTAGGC
17396881 CGTGTG
1 CGTGTG
17396887 AAAACTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.20, G:0.43, T:0.30
Consensus pattern (12 bp):
CGTGTGCTAGGC
Found at i:17400855 original size:59 final size:58
Alignment explanation
Indices: 17400781--17400917 Score: 176
Period size: 53 Copynumber: 2.4 Consensus size: 58
17400771 CGGATATTGT
* * *
17400781 TACTGTTACTATTACTATTACTGTTTCGGATTTGTTCCGATAAGTTACTCTGTGTACCG
1 TACTGTTACTGTTACTATTACTGTTT-GAATTTGTTCCGATAAGGTACTCTGTGTACCG
*
17400840 TACTGTTACTGTTACTATT-C----TGAATTTGTTCCGATGAGGTACTCTGTGTACCG
1 TACTGTTACTGTTACTATTACTGTTTGAATTTGTTCCGATAAGGTACTCTGTGTACCG
* *
17400893 TACTGCTACTGTTACTGTTACTGTT
1 TACTGTTACTGTTACTATTACTGTT
17400918 ACTGTTCCGG
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
53 46 0.69
54 2 0.03
58 1 0.01
59 18 0.27
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.44
Consensus pattern (58 bp):
TACTGTTACTGTTACTATTACTGTTTGAATTTGTTCCGATAAGGTACTCTGTGTACCG
Found at i:17400908 original size:6 final size:6
Alignment explanation
Indices: 17400893--17400923 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
17400883 CTGTGTACCG
*
17400893 TACTGC TACTGT TACTGT TACTGT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT T
17400924 CCGGCTTCGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:17401099 original size:18 final size:18
Alignment explanation
Indices: 17401037--17401106 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 18
17401027 GGAAAGATTG
17401037 ACTGTTACTGAATAATTTA
1 ACTGTTACTGAATAA-TTA
* * *
17401056 ATTGTTACTGTAT-ATCTG
1 ACTGTTACTGAATAAT-TA
* * *
17401074 ATTTTTACTGAATAATTC
1 ACTGTTACTGAATAATTA
17401092 ACTGTTACTGAATAA
1 ACTGTTACTGAATAA
17401107 CCGATCAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
17 1 0.02
18 27 0.66
19 13 0.32
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (18 bp):
ACTGTTACTGAATAATTA
Found at i:17401136 original size:18 final size:18
Alignment explanation
Indices: 17401113--17401168 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
17401103 ATAACCGATC
17401113 AATTGATTGATACTGAAT
1 AATTGATTGATACTGAAT
*
17401131 AATTGATT-ATTATTGAAT
1 AATTGATTGA-TACTGAAT
* *
17401149 AATTGATTGTTACCGAAT
1 AATTGATTGATACTGAAT
17401167 AA
1 AA
17401169 CTGACTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 1 0.03
18 31 0.97
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.41
Consensus pattern (18 bp):
AATTGATTGATACTGAAT
Found at i:17401167 original size:36 final size:36
Alignment explanation
Indices: 17401113--17401195 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 36
17401103 ATAACCGATC
* * * * *
17401113 AATTGATTGATACTGAATAATTGATTATTATTGAAT
1 AATTGATTGTTACCGAATAACTGACTATTATTAAAT
17401149 AATTGATTGTTACCGAATAACTGACTATTATTAAAT
1 AATTGATTGTTACCGAATAACTGACTATTATTAAAT
* *
17401185 AAATAATTGTT
1 AATTGATTGTT
17401196 CTGATTGACT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (36 bp):
AATTGATTGTTACCGAATAACTGACTATTATTAAAT
Found at i:17406465 original size:3 final size:3
Alignment explanation
Indices: 17406457--17406487 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
17406447 TTCCATACCA
17406457 TCC TCC TCC TCC TCC -CC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
17406488 TTCTTCGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
TCC
Found at i:17406477 original size:14 final size:14
Alignment explanation
Indices: 17406458--17406485 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17406448 TCCATACCAT
17406458 CCTCCTCCTCCTCC
1 CCTCCTCCTCCTCC
17406472 CCTCCTCCTCCTCC
1 CCTCCTCCTCCTCC
17406486 TCTTCTTCGA
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:0.00, C:0.71, G:0.00, T:0.29
Consensus pattern (14 bp):
CCTCCTCCTCCTCC
Found at i:17410117 original size:4 final size:4
Alignment explanation
Indices: 17410108--17410149 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
17410098 TATAAACCAA
* * *
17410108 ATAC ATAC ATAC ATAC ATAC ATCC AGAC ATAC ATAT ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
17410150 TTATGAACAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.48, C:0.24, G:0.02, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:17411667 original size:37 final size:37
Alignment explanation
Indices: 17411617--17411695 Score: 158
Period size: 37 Copynumber: 2.1 Consensus size: 37
17411607 TTTAGCAAAA
17411617 TCATGTATCTGACTCAATTATTGGTAATGACAAAGAC
1 TCATGTATCTGACTCAATTATTGGTAATGACAAAGAC
17411654 TCATGTATCTGACTCAATTATTGGTAATGACAAAGAC
1 TCATGTATCTGACTCAATTATTGGTAATGACAAAGAC
17411691 TCATG
1 TCATG
17411696 AGAGACTGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (37 bp):
TCATGTATCTGACTCAATTATTGGTAATGACAAAGAC
Found at i:17421724 original size:34 final size:34
Alignment explanation
Indices: 17421686--17421752 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
17421676 TTTTCATCTT
17421686 CTTTCTCTCTTTCTCAAGCAAATCTCATTCCTCA
1 CTTTCTCTCTTTCTCAAGCAAATCTCATTCCTCA
*
17421720 CTTTCTCTCTTTCTCAGGCAAATCTCATTCCTC
1 CTTTCTCTCTTTCTCAAGCAAATCTCATTCCTC
17421753 TTCGCAGGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.18, C:0.36, G:0.04, T:0.42
Consensus pattern (34 bp):
CTTTCTCTCTTTCTCAAGCAAATCTCATTCCTCA
Found at i:17422539 original size:25 final size:25
Alignment explanation
Indices: 17422510--17422560 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
17422500 ACTCTGACAG
17422510 TGGCAGTGACACCCACCAATTCTGA
1 TGGCAGTGACACCCACCAATTCTGA
17422535 TGGCAGTGACACCCACCAATTCTGA
1 TGGCAGTGACACCCACCAATTCTGA
17422560 T
1 T
17422561 ATAGGAAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (25 bp):
TGGCAGTGACACCCACCAATTCTGA
Found at i:17423227 original size:6 final size:6
Alignment explanation
Indices: 17423216--17423268 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
17423206 GAAGATATTA
* *
17423216 TTTTAT TTTTAT TTTTAT TTCTGT TTTTA- -TTTAT TTTTA- TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
*
17423261 TTTAAT TT
1 TTTTAT TT
17423269 ATTAATTAGG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
4 4 0.10
5 5 0.13
6 30 0.77
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:17423229 original size:11 final size:11
Alignment explanation
Indices: 17423216--17423268 Score: 63
Period size: 11 Copynumber: 4.7 Consensus size: 11
17423206 GAAGATATTA
17423216 TTTTATTTTTAT
1 TTTTA-TTTTAT
*
17423228 TTTTATTTCTGT
1 TTTTATTT-TAT
17423240 TTTTA-TTTAT
1 TTTTATTTTAT
17423250 TTTTATTTTAT
1 TTTTATTTTAT
*
17423261 TTTAATTT
1 TTTTATTT
17423269 ATTAATTAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
10 7 0.19
11 17 0.47
12 12 0.33
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:17423844 original size:29 final size:28
Alignment explanation
Indices: 17423812--17423874 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 28
17423802 ATTTATTTTG
17423812 TTATTCTAATAATATTATTAT-TTATCTAT
1 TTATT-TAATAATATTATTATATT-TCTAT
** *
17423841 TTATATTTCTACTATTATTATATTTCTAT
1 TTAT-TTAATAATATTATTATATTTCTAT
17423870 TTATT
1 TTATT
17423875 ATATTTCTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
28 1 0.03
29 25 0.86
30 3 0.10
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (28 bp):
TTATTTAATAATATTATTATATTTCTAT
Found at i:17423855 original size:15 final size:16
Alignment explanation
Indices: 17423823--17423883 Score: 65
Period size: 15 Copynumber: 3.9 Consensus size: 16
17423813 TATTCTAATA
*
17423823 ATATTATTATTTAT-CT
1 ATATTA-TATTTCTACT
17423839 AT-TTATATTTCTACT
1 ATATTATATTTCTACT
17423854 ATTATTATATTTCTA-T
1 A-TATTATATTTCTACT
*
17423870 TTATTATATTTCTA
1 ATATTATATTTCTA
17423884 TTTCTATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
14 6 0.15
15 19 0.47
16 4 0.10
17 11 0.28
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (16 bp):
ATATTATATTTCTACT
Found at i:17423860 original size:32 final size:32
Alignment explanation
Indices: 17423815--17423883 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
17423805 TATTTTGTTA
17423815 TTCTAATAATATTAT-TATT-TATCTATTTATAT
1 TTCTAATAATATTATAT-TTCTATCTA-TTATAT
* * *
17423847 TTCTACTATTATTATATTTCTATTTATTATAT
1 TTCTAATAATATTATATTTCTATCTATTATAT
17423879 TTCTA
1 TTCTA
17423884 TTTCTATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 26 0.81
33 6 0.19
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (32 bp):
TTCTAATAATATTATATTTCTATCTATTATAT
Found at i:17423884 original size:15 final size:15
Alignment explanation
Indices: 17423841--17423886 Score: 74
Period size: 15 Copynumber: 2.9 Consensus size: 15
17423831 ATTTATCTAT
17423841 TTATATTTCTACTATTA
1 TTATATTTCTA-T-TTA
17423858 TTATATTTCTATTTA
1 TTATATTTCTATTTA
17423873 TTATATTTCTATTT
1 TTATATTTCTATTT
17423887 CTATTTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 17 0.59
16 1 0.03
17 11 0.38
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATATTTCTATTTA
Found at i:17424034 original size:3 final size:3
Alignment explanation
Indices: 17424026--17424188 Score: 222
Period size: 3 Copynumber: 53.7 Consensus size: 3
17424016 TTTAAAACTT
17424026 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
17424074 TTA TTA TTA TTA TTA TTA TGTA TTA ATA TCA TTA TT- TT- TTA TATA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA T-TA
* * * *
17424119 TTA TATA TTA TTA TTA TTA TTA TTA CTA TTA GTA CTA TTA TTA TTT
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17424165 TCTA TTA TTA TTA TTA TTA TTA TT
1 T-TA TTA TTA TTA TTA TTA TTA TT
17424189 TATAGTATAT
Statistics
Matches: 144, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
2 4 0.03
3 129 0.90
4 11 0.08
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Done.