Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 181 of 205
Found at i:53820224 original size:54 final size:55
Alignment explanation
Indices: 53820038--53820255 Score: 324
Period size: 54 Copynumber: 4.1 Consensus size: 55
53820028 CACGTGAGCC
* *
53820038 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG-AA
*
53820093 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAG--A---AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAA
* *
53820144 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
53820198 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
53820253 AAG
1 AAG
53820256 TAGAAATTGA
Statistics
Matches: 150, Mismatches: 6, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
50 14 0.09
51 34 0.23
52 1 0.01
54 52 0.35
55 37 0.25
56 6 0.04
57 6 0.04
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (55 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
Found at i:53820253 original size:14 final size:14
Alignment explanation
Indices: 53820234--53820268 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
53820224 GAGTTGATTT
53820234 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
**
53820248 TTGAAAAGTAGAAA
1 TTGAAAAACAGAAA
53820262 TTGAAAA
1 TTGAAAA
53820269 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:53820500 original size:85 final size:87
Alignment explanation
Indices: 53820356--53820605 Score: 294
Period size: 85 Copynumber: 2.8 Consensus size: 87
53820346 AACAAAAATT
* * *
53820356 AAAAACAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
53820421 TTGATTTGAAAAG-TAGAATT-AG
65 TTGATTTGAAAAGATAG-ATTAAA
* * * *
53820443 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
53820506 TTGATTTTTGAAAAGCATAGATTGAAAA
65 TTGA--TTTGAAAAG-ATAGATT--AAA
*
53820534 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
53820598 GTTGATTT
64 GTTGATTT
53820606 CTGAAAAACA
Statistics
Matches: 138, Mismatches: 13, Indels: 20
0.81 0.08 0.12
Matches are distributed among these distances:
84 3 0.02
85 33 0.24
87 32 0.23
88 3 0.02
89 3 0.02
91 28 0.20
93 33 0.24
95 3 0.02
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (87 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTGAAAAGATAGATTAAA
Found at i:53820538 original size:192 final size:191
Alignment explanation
Indices: 53820202--53820626 Score: 515
Period size: 192 Copynumber: 2.3 Consensus size: 191
53820192 AATTAAAAGG
*
53820202 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAGTAGAAATTGAA
1 CTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAAAACAGAAATTGAAAAGCAGAAATTGAA
* *
53820267 AATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTTTGAAACA
65 AATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGA--TTTTTTGAAACA
53820332 CAGAAATTAAAAAAAACAAAAATTAAAAACAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGA
128 CAGAAATTAAAAAAAACAAAAATTAAAAACAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGA
* ** *
53820396 CTCAACTCACCTCTTGCAATATGAGTTGA-TTTGAAAAGTAG-AATTAGTAAAGCAGAAATTGAA
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAGAAATT-GAAAAGCAGAAATTGAA
*
53820459 AATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATAAGTTGA-TTTTTGAAA-AGC
65 AATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTGAAACA-C
* * * * * * *
53820522 ATAGATT-GAAAAAA-AAACA-T------A-AA-TTGAAAATACCTCAGCATGTGAGCC-GAGG
129 AGAAATTAAAAAAAACAAAAATTAAAAACAGAATTTGAAAAGACCTCAGCGTGTG-GCCTGAGA
* *
53820574 CTCAACTCACCTCTTGCAATATGAGTTGATTTCTGAAAAACAAAAATT-AAAAG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTT-TGAAAAACAGAAATTGAAAAG
53820627 GCTTAACTCA
Statistics
Matches: 206, Mismatches: 19, Indels: 27
0.82 0.08 0.11
Matches are distributed among these distances:
178 51 0.25
179 11 0.05
180 8 0.04
181 4 0.02
186 1 0.00
187 4 0.02
188 7 0.03
189 15 0.07
191 4 0.02
192 73 0.35
194 28 0.14
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (191 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAGAAATTGAAAAGCAGAAATTGAAA
ATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTGAAACACAG
AAATTAAAAAAAACAAAAATTAAAAACAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGA
Found at i:53820542 original size:18 final size:18
Alignment explanation
Indices: 53820516--53820551 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53820506 TTGATTTTTG
* *
53820516 AAAAGCATAGATTGAAAA
1 AAAAACATAAATTGAAAA
53820534 AAAAACATAAATTGAAAA
1 AAAAACATAAATTGAAAA
53820552 TACCTCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.06, G:0.11, T:0.17
Consensus pattern (18 bp):
AAAAACATAAATTGAAAA
Found at i:53820593 original size:93 final size:88
Alignment explanation
Indices: 53820356--53820612 Score: 301
Period size: 93 Copynumber: 2.9 Consensus size: 88
53820346 AACAAAAATT
* * *
53820356 AAAAACAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
53820421 TTGA--TTTGAAAAGTAGAATTAG
65 TTGATTTTTGAAAAGTAGAATTAA
* * * *
53820443 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
53820506 TTGATTTTTGAAAAGCATAG-ATTGAAAA
65 TTGATTTTTGAAAAG--TAGAATT---AA
*
53820534 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
*
53820598 GTTGATTTCTGAAAA
64 GTTGATTTTTGAAAA
53820613 ACAAAAATTA
Statistics
Matches: 144, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
84 3 0.02
85 33 0.23
87 32 0.22
88 3 0.02
89 3 0.02
91 25 0.17
93 42 0.29
95 3 0.02
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (88 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTTTGAAAAGTAGAATTAA
Found at i:53820945 original size:193 final size:192
Alignment explanation
Indices: 53820570--53821177 Score: 1126
Period size: 193 Copynumber: 3.2 Consensus size: 192
53820560 CATGTGAGCC
** *
53820570 GAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTCTGAAAAACAAAAATTAAAAGGCTTAACT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTT-TGAAAAACAAAAATTAAAAGGCTTAACT
53820635 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
65 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
* *
53820700 AACTCATTTCTCGCAATATGAGTTGATTTTTTTTTAAAATTTAAAAATACCTCAACGTGTCTT
130 AACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAATTTAAAAATACCTCAACGTGTCTT
53820763 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
*
53820828 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCTGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
53820893 ACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTT-AAAAATTTAAAAATACCTCAACGTGTCTT
*
53820956 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAATAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
*
53821021 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACATCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
53821086 ACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAATTTAAAAATACCTCAACGTGTCTT
53821148 GAGGCTCAACTCATTTCTCGCAATATGAGT
1 GAGGCTCAACTCATTTCTCGCAATATGAGT
53821178 CAATTTAAAA
Statistics
Matches: 405, Mismatches: 9, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
192 184 0.45
193 221 0.55
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.31
Consensus pattern (192 bp):
GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
ACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAATTTAAAAATACCTCAACGTGTCTT
Found at i:53821160 original size:70 final size:70
Alignment explanation
Indices: 53821010--53821555 Score: 512
Period size: 70 Copynumber: 7.7 Consensus size: 70
53821000 AAAAATTAAA
* ** * * * * * **
53821010 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAA-CTAAAAATACATCGGCGT
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTAAAA-AAAAATTTAAAAATACCTCAACGT
53821073 GCCCCG
65 GCCCCG
* ****
53821079 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAATTTAAAAATACCTCAACGTG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTAAAAAAAAATTTAAAAATACCTCAACGTG
* **
53821144 TCTTG
66 CCCCG
* * * * **
53821149 AGGCTCAACTCATTTCTCGCAATATGAG-TCAATTTAAAACATAAA-CTAAAAATACCTCGGCGT
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTAAAA-AAAAATTTAAAAATACCTCAACGT
53821212 GCCCCG
65 GCCCCG
* ***
53821218 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTAAAAAAAAATTTAAAAATACCTCAACGTG
* **
53821283 TCTTG
66 CCCCG
* * * * **
53821288 AGGCTCAACTCATTTCTCGCAATATGAG-TCAATTTAAAACATAAA-CTAAAAATACCTCGGCGT
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTAAAA-AAAAATTTAAAAATACCTCAACGT
53821351 GCCCCG
65 GCCCCG
* ***
53821357 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTAAAAAAAAATTTAAAAATACCTCAACGTG
53821422 CCCCG
66 CCCCG
* * *
53821427 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTAT
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT-AAAAA-AAAATTTAAAA---AT-AC-CT
* **
53821492 CAACGTGTCTTG
59 CAACGTGCCCCG
*
53821504 AGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTAAAAACAAAAATTAAAA
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTAAAAA-AAAATTTAAAA
53821556 GGCTTAACTC
Statistics
Matches: 386, Mismatches: 76, Indels: 24
0.79 0.16 0.05
Matches are distributed among these distances:
69 139 0.36
70 170 0.44
71 2 0.01
72 10 0.03
75 18 0.05
76 5 0.01
77 42 0.11
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (70 bp):
AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTAAAAAAAAATTTAAAAATACCTCAACGTG
CCCCG
Found at i:53821196 original size:139 final size:139
Alignment explanation
Indices: 53821010--53821455 Score: 820
Period size: 139 Copynumber: 3.2 Consensus size: 139
53821000 AAAAATTAAA
* ** *
53821010 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACATCGGCGTGC
1 AGGCTCAACTCATTTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGC
*
53821075 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAATTTAAAAATACCTCAA
66 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAA
53821140 CGTGTCTTG
131 CGTGTCTTG
53821149 AGGCTCAACTCATTTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGC
1 AGGCTCAACTCATTTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGC
53821214 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAA
66 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAA
53821279 CGTGTCTTG
131 CGTGTCTTG
53821288 AGGCTCAACTCATTTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGC
1 AGGCTCAACTCATTTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGC
53821353 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAA
66 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAA
* **
53821418 CGTGCCCCG
131 CGTGTCTTG
53821427 AGGCTCAACTCATTTCTCGCAATATGAGT
1 AGGCTCAACTCATTTCTCGCAATATGAGT
53821456 TGATTTTGAA
Statistics
Matches: 299, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 299 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (139 bp):
AGGCTCAACTCATTTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGC
CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAA
CGTGTCTTG
Found at i:53829830 original size:16 final size:16
Alignment explanation
Indices: 53829809--53829909 Score: 62
Period size: 18 Copynumber: 6.0 Consensus size: 16
53829799 TTTTTCCTTT
53829809 TTTTTTAAAACACGAA
1 TTTTTTAAAACACGAA
*
53829825 TTTTTTAAAATACAAGAA
1 TTTTTT-AAA-ACACGAA
*
53829843 --TTTTAGAAACACAAA
1 TTTTTTA-AAACACGAA
*
53829858 TTTTTAAAAAAACACGAA
1 TTTTT--TAAAACACGAA
** *
53829876 AATTTTGAAACACGAGA
1 TTTTTTAAAACACGA-A
*
53829893 TTTCTTTGAAACACGAA
1 TTT-TTTAAAACACGAA
53829910 AATTTATGAA
Statistics
Matches: 65, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
15 6 0.09
16 20 0.31
17 9 0.14
18 29 0.45
19 1 0.02
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.32
Consensus pattern (16 bp):
TTTTTTAAAACACGAA
Found at i:53829853 original size:33 final size:34
Alignment explanation
Indices: 53829811--53829895 Score: 95
Period size: 33 Copynumber: 2.5 Consensus size: 34
53829801 TTTCCTTTTT
* * *
53829811 TTTTA-AAACACGAATTTTTTAAAATACA-AGAA
1 TTTTAGAAACACGAATTTTTAAAAAAACACAAAA
*
53829843 TTTTAGAAACACAAATTTTTAAAAAAACACGAAAA
1 TTTTAGAAACACGAATTTTTAAAAAAACAC-AAAA
53829878 TTTT-GAAACACGAGATTT
1 TTTTAGAAACACGA-ATTT
53829896 CTTTGAAACA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
32 5 0.11
33 20 0.45
34 8 0.18
35 11 0.25
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (34 bp):
TTTTAGAAACACGAATTTTTAAAAAAACACAAAA
Found at i:53829921 original size:17 final size:17
Alignment explanation
Indices: 53829867--53830218 Score: 203
Period size: 17 Copynumber: 19.9 Consensus size: 17
53829857 ATTTTTAAAA
53829867 AAACACGAAAA-TTTTG
1 AAACACGAAAATTTTTG
* *
53829883 AAACACGAGATTTCTTTG
1 AAACACGAAAATT-TTTG
*
53829901 AAACACGAAAATTTATG
1 AAACACGAAAATTTTTG
** *
53829918 AAACACGGTCAATTTCTTA
1 AAACAC-GAAAATTT-TTG
*
53829937 AAACACGAAAGTTTTTG
1 AAACACGAAAATTTTTG
* **
53829954 AAAAACGGGAATTTTTTTTTG
1 AAACAC--GAA--AATTTTTG
*
53829975 AAACACGAAAAATTTTG
1 AAACACGAAAATTTTTG
*
53829992 AAACACCG-GAA-TTTTG
1 AAACA-CGAAAATTTTTG
** *
53830008 AAAACACGAGGATTTTTT
1 -AAACACGAAAATTTTTG
* **
53830026 AAATACGAAAA-ACTTG
1 AAACACGAAAATTTTTG
*
53830042 AAAACAAGAAAATTTTTG
1 -AAACACGAAAATTTTTG
* *
53830060 AAATACGAAAATTTTAG
1 AAACACGAAAATTTTTG
53830077 AAACACGAAAATTTTTG
1 AAACACGAAAATTTTTG
*
53830094 AAACAC-AGAAGTTTTTAG
1 AAACACGA-AAATTTTT-G
*
53830112 AAAACACGAAAAATTTTG
1 -AAACACGAAAATTTTTG
* **
53830130 AAA-ATTGGAATTTTTTTG
1 AAACA--CGAAAATTTTTG
*
53830148 AAAACACGAGAATTTTTG
1 -AAACACGAAAATTTTTG
*
53830166 AAAAACATGAAAATTTTTG
1 --AAACACGAAAATTTTTG
* **
53830185 CAACACGGGAATTTTTG
1 AAACACGAAAATTTTTG
53830202 AAAACACGAAAAATTTT
1 -AAACACG-AAAATTTT
53830219 CCGATTTTTA
Statistics
Matches: 253, Mismatches: 58, Indels: 47
0.71 0.16 0.13
Matches are distributed among these distances:
16 20 0.08
17 111 0.44
18 59 0.23
19 50 0.20
20 2 0.01
21 11 0.04
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (17 bp):
AAACACGAAAATTTTTG
Found at i:53829990 original size:21 final size:21
Alignment explanation
Indices: 53829948--53829990 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
53829938 AACACGAAAG
** *
53829948 TTTTTGAAAAACGGGAATTTT
1 TTTTTGAAAAACGAAAAATTT
*
53829969 TTTTTGAAACACGAAAAATTT
1 TTTTTGAAAAACGAAAAATTT
53829990 T
1 T
53829991 GAAACACCGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (21 bp):
TTTTTGAAAAACGAAAAATTT
Found at i:53830169 original size:36 final size:35
Alignment explanation
Indices: 53830041--53830169 Score: 136
Period size: 36 Copynumber: 3.7 Consensus size: 35
53830031 CGAAAAACTT
* **
53830041 GAAAACAAGAAAATTTTTGAAATAC-GAAAATTTTA
1 GAAAACACGAAAATTTTTGAAA-ACAGAAGTTTTTA
53830076 G-AAACACGAAAATTTTTGAAACACAGAAGTTTTTA
1 GAAAACACGAAAATTTTTGAAA-ACAGAAGTTTTTA
* ** * *
53830111 GAAAACACGAAAAATTTTGAAAATTGGAATTTTTTT
1 GAAAACACGAAAATTTTTGAAAA-CAGAAGTTTTTA
*
53830147 GAAAACACGAGAATTTTTGAAAA
1 GAAAACACGAAAATTTTTGAAAA
53830170 ACATGAAAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
34 21 0.26
35 11 0.14
36 48 0.60
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (35 bp):
GAAAACACGAAAATTTTTGAAAACAGAAGTTTTTA
Found at i:53830170 original size:19 final size:18
Alignment explanation
Indices: 53829809--53830210 Score: 172
Period size: 17 Copynumber: 22.8 Consensus size: 18
53829799 TTTTTCCTTT
*
53829809 TTTTTTAAAACAC--GAA
1 TTTTTGAAAACACGAGAA
* * *
53829825 TTTTTTAAAATACAAGAA
1 TTTTTGAAAACACGAGAA
*
53829843 TTTTAG-AAACAC-A-AA
1 TTTTTGAAAACACGAGAA
*
53829858 TTTTTAAAAAAACACGA-AA
1 TTTTT--GAAAACACGAGAA
* *
53829877 ATTTTG-AAACACGAGAT
1 TTTTTGAAAACACGAGAA
*
53829894 TTCTTTG-AAACACGAAAA
1 TT-TTTGAAAACACGAGAA
*
53829912 TTTATG-AAACACG-GTCAA
1 TTTTTGAAAACACGAG--AA
53829930 TTTCTT-AAAACACGA-AA
1 TTT-TTGAAAACACGAGAA
*
53829947 GTTTTTGAAAA-ACGGGAA
1 -TTTTTGAAAACACGAGAA
*
53829965 TTTTTTTTTG-AAACACGAAAA
1 ----TTTTTGAAAACACGAGAA
*
53829986 ATTTTG-AAACACCG-GAA
1 TTTTTGAAAACA-CGAGAA
*
53830003 -TTTTGAAAACACGAGGA
1 TTTTTGAAAACACGAGAA
* *
53830020 TTTTT-TAAATACGA-AA
1 TTTTTGAAAACACGAGAA
*** * *
53830036 AACTTGAAAACAAGAAAA
1 TTTTTGAAAACACGAGAA
* *
53830054 TTTTTG-AAATACGAAAA
1 TTTTTGAAAACACGAGAA
* *
53830071 TTTTAG-AAACACGAAAA
1 TTTTTGAAAACACGAGAA
53830088 TTTTTG-AAACAC-AGAA
1 TTTTTGAAAACACGAGAA
*
53830104 GTTTTTAGAAAACACGAAAA
1 -TTTTT-GAAAACACGAGAA
* **
53830124 ATTTTGAAAA-TTG-GAA
1 TTTTTGAAAACACGAGAA
53830140 TTTTTTTGAAAACACGAGAA
1 --TTTTTGAAAACACGAGAA
* *
53830160 TTTTTGAAAAACATGAAAA
1 TTTTTG-AAAACACGAGAA
* *
53830179 TTTTTG-CAACACGGGAA
1 TTTTTGAAAACACGAGAA
53830196 TTTTTGAAAACACGA
1 TTTTTGAAAACACGA
53830211 AAAATTTTCC
Statistics
Matches: 294, Mismatches: 56, Indels: 70
0.70 0.13 0.17
Matches are distributed among these distances:
15 6 0.02
16 36 0.12
17 110 0.37
18 80 0.27
19 42 0.14
20 9 0.03
21 11 0.04
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (18 bp):
TTTTTGAAAACACGAGAA
Found at i:53830362 original size:20 final size:22
Alignment explanation
Indices: 53830322--53830364 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
53830312 TGTTACCTTA
53830322 TTTTTGAAAAACACGAGAAATT
1 TTTTTGAAAAACACGAGAAATT
*
53830344 TTTTTG-AAGACACGA-AAATT
1 TTTTTGAAAAACACGAGAAATT
53830364 T
1 T
53830365 CGAAACCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 8 0.40
22 6 0.30
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (22 bp):
TTTTTGAAAAACACGAGAAATT
Found at i:53830559 original size:17 final size:18
Alignment explanation
Indices: 53830533--53830578 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
53830523 ATTATTTTTA
*
53830533 ATAAAATAAAATAAAAAT
1 ATAAATTAAAATAAAAAT
*
53830551 -TAAATTAAATTAAAAAT
1 ATAAATTAAAATAAAAAT
53830568 ATAAATATAAA
1 ATAAAT-TAAA
53830579 TATGCATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 15 0.62
18 5 0.21
19 4 0.17
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAAATTAAAATAAAAAT
Found at i:53830720 original size:9 final size:9
Alignment explanation
Indices: 53830706--53830769 Score: 58
Period size: 9 Copynumber: 6.8 Consensus size: 9
53830696 CGAATTGAAC
53830706 CTTTTTTTT
1 CTTTTTTTT
*
53830715 CTTTTTTTC
1 CTTTTTTTT
53830724 CTTCTTTTTT
1 CTT-TTTTTT
53830734 CCTTCTCTTTTT
1 -CTT-T-TTTTT
*
53830746 CTTCTTTTT
1 CTTTTTTTT
*
53830755 CTTTTCTTT
1 CTTTTTTTT
53830764 -TTTTTT
1 CTTTTTT
53830770 CTCTGCTGGG
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
8 5 0.11
9 23 0.50
10 5 0.11
11 8 0.17
12 5 0.11
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:53830761 original size:11 final size:10
Alignment explanation
Indices: 53830707--53830771 Score: 67
Period size: 11 Copynumber: 6.0 Consensus size: 10
53830697 GAATTGAACC
53830707 TTTTTTTTCT
1 TTTTTTTTCT
53830717 TTTTTTCCTTCT
1 TTTTTT--TTCT
*
53830729 TTTTTCCTTCT
1 TTTTT-TTTCT
*
53830740 CTTTTTCTTCT
1 -TTTTTTTTCT
53830751 TTTTCTTTTCT
1 TTTT-TTTTCT
53830762 TTTTTTTTCT
1 TTTTTTTTCT
53830772 CTGCTGGGCC
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
10 16 0.33
11 18 0.38
12 14 0.29
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:53830766 original size:22 final size:21
Alignment explanation
Indices: 53830707--53830771 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 21
53830697 GAATTGAACC
53830707 TTTTTTTTCTTTTTTTCCTTCT
1 TTTTTTTTCTTTTTTT-CTTCT
* *
53830729 TTTTTCCTTCTCTTTTTCTTCT
1 TTTTT-TTTCTTTTTTTCTTCT
53830751 TTTTCTTTTCTTTTTTT-TTCT
1 TTTT-TTTTCTTTTTTTCTTCT
53830772 CTGCTGGGCC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 4 0.11
22 23 0.62
23 10 0.27
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTTTCTTTTTTTCTTCT
Found at i:53831060 original size:17 final size:19
Alignment explanation
Indices: 53831025--53831063 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
53831015 TGTTATAATA
*
53831025 TTTTTTATTATTTCTTTTC
1 TTTTTCATTATTTCTTTTC
53831044 TTTTTCATT-TTTC-TTTC
1 TTTTTCATTATTTCTTTTC
53831061 TTT
1 TTT
53831064 CTTCTTCCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 8 0.42
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTCATTATTTCTTTTC
Found at i:53831061 original size:22 final size:22
Alignment explanation
Indices: 53831035--53831094 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 22
53831025 TTTTTTATTA
*
53831035 TTTCTTTTCTTTTTCAT-TTTTC
1 TTTC-TTTCTTCTTCATCTTTTC
*
53831057 TTTCTTTCTTCTTCCTCTTTTC
1 TTTCTTTCTTCTTCATCTTTTC
*
53831079 TTATTCCTTCTTCTTC
1 -T-TTCTTTCTTCTTC
53831095 CTTCCTTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 10 0.31
22 9 0.28
23 1 0.03
24 12 0.38
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTCTTTCTTCTTCATCTTTTC
Found at i:53831080 original size:14 final size:13
Alignment explanation
Indices: 53831035--53831108 Score: 53
Period size: 14 Copynumber: 5.5 Consensus size: 13
53831025 TTTTTTATTA
53831035 TTTCTT-TT-CTT
1 TTTCTTCTTCCTT
* *
53831046 TTTCATTTTTCTTT
1 TTTC-TTCTTCCTT
53831060 CTTTCTTCTTCCTCT
1 -TTTCTTCTTCCT-T
*
53831075 TTTCTTATTCCTT
1 TTTCTTCTTCCTT
*
53831088 CTTCTTCCTTCCTT
1 TTTCTT-CTTCCTT
*
53831102 CTTCTTC
1 TTTCTTC
53831109 AAAGTCTAGC
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
11 4 0.08
12 2 0.04
13 9 0.18
14 31 0.61
15 5 0.10
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTCTTCTTCCTT
Found at i:53831093 original size:35 final size:35
Alignment explanation
Indices: 53831037--53831105 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
53831027 TTTTATTATT
* * * *
53831037 TCTTTTCTTTTTCATTTTTCTTTCTTTCTTCTTCC
1 TCTTTTCTTATTCATTCTTCTTCCTTCCTTCTTCC
*
53831072 TCTTTTCTTATTCCTTCTTCTTCCTTCCTTCTTC
1 TCTTTTCTTATTCATTCTTCTTCCTTCCTTCTTC
53831106 TTCAAAGTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (35 bp):
TCTTTTCTTATTCATTCTTCTTCCTTCCTTCTTCC
Found at i:53831515 original size:29 final size:29
Alignment explanation
Indices: 53831482--53831592 Score: 91
Period size: 30 Copynumber: 3.7 Consensus size: 29
53831472 TGTAATTTTT
*
53831482 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
53831511 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
53831541 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* *
53831570 GGAAAAGTTTAGGGGTCAAAATG
1 AGAAAA-TTTA-GGGTTAAAATG
53831593 CAGTTTTTAT
Statistics
Matches: 67, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
29 14 0.21
30 51 0.76
31 2 0.03
ACGTcount: A:0.45, C:0.03, G:0.23, T:0.29
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:53831537 original size:30 final size:30
Alignment explanation
Indices: 53831497--53831592 Score: 131
Period size: 30 Copynumber: 3.2 Consensus size: 30
53831487 ATTTAGGATT
*
53831497 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
53831527 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
53831557 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
53831587 AAAATG
1 AAAATG
53831593 CAGTTTTTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.04
30 55 0.96
ACGTcount: A:0.45, C:0.03, G:0.24, T:0.28
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:53831901 original size:33 final size:33
Alignment explanation
Indices: 53831822--53831904 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
53831812 AGATAGTCCG
* * * *
53831822 CTAGGACAGTAAACACATAATAAAAATAGTCTT
1 CTAGGACAGTAAACACAAAACAAAAATAATCTA
* * *
53831855 CT-GAGACAATAAACACAAAACAGAGATAATCTA
1 CTAG-GACAGTAAACACAAAACAAAAATAATCTA
53831888 CTAGGACAGTAAACACA
1 CTAGGACAGTAAACACA
53831905 GAATAAAGAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
32 1 0.03
33 38 0.95
34 1 0.03
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (33 bp):
CTAGGACAGTAAACACAAAACAAAAATAATCTA
Found at i:53832856 original size:11 final size:11
Alignment explanation
Indices: 53832818--53832860 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
53832808 ATGTGAGAAA
53832818 AAAAATTATAT
1 AAAAATTATAT
*
53832829 AATAAATTTATAA
1 AA-AAA-TTATAT
*
53832842 AAAAATGATAT
1 AAAAATTATAT
53832853 AAAAATTA
1 AAAAATTA
53832861 AATGTGATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 13 0.50
12 6 0.23
13 7 0.27
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
AAAAATTATAT
Found at i:53837901 original size:19 final size:20
Alignment explanation
Indices: 53837873--53837917 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
53837863 ACATTTATAA
* *
53837873 AAAAACTATTTTAATAATT-
1 AAAAATTATTTAAATAATTC
*
53837892 AAAAATTATTTAAATTATTC
1 AAAAATTATTTAAATAATTC
53837912 AAAAAT
1 AAAAAT
53837918 ATAAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAATTATTTAAATAATTC
Found at i:53840944 original size:18 final size:20
Alignment explanation
Indices: 53840921--53840966 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
53840911 TAATAATAAC
53840921 AAATAAAGAAAGAA-AAA-G
1 AAATAAAGAAAGAACAAATG
53840939 AAAT-AA-AAAGAACAAATG
1 AAATAAAGAAAGAACAAATG
53840957 AAA-AAAGAAA
1 AAATAAAGAAA
53840967 ATCAGAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 6 0.25
17 5 0.21
18 10 0.42
19 3 0.12
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (20 bp):
AAATAAAGAAAGAACAAATG
Found at i:53840999 original size:21 final size:22
Alignment explanation
Indices: 53840959--53841004 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
53840949 AACAAATGAA
*
53840959 AAAAGAAAATCAGAAAGGAAAG
1 AAAAGAAAAACAGAAAGGAAAG
*
53840981 AAAAGAAAAAC-GGAAGGAAAG
1 AAAAGAAAAACAGAAAGGAAAG
53841002 AAA
1 AAA
53841005 GAAGAAAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.70, C:0.04, G:0.24, T:0.02
Consensus pattern (22 bp):
AAAAGAAAAACAGAAAGGAAAG
Found at i:53852924 original size:3 final size:3
Alignment explanation
Indices: 53852916--53852940 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
53852906 GCCCTCTTGA
53852916 CTG CTG CTG CTG CTG CTG CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG C
53852941 CCCATCTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.32, T:0.32
Consensus pattern (3 bp):
CTG
Found at i:53857428 original size:20 final size:20
Alignment explanation
Indices: 53857382--53857430 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
53857372 ATGAAAATAG
**
53857382 ACATATAAGAAATTTAGAAAA
1 ACATATAA-AAAGCTAGAAAA
*
53857403 A-TTATAAAAAGCTAGAAAA
1 ACATATAAAAAGCTAGAAAA
53857422 ACATATAAA
1 ACATATAAA
53857431 TTATTAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 11 0.48
20 11 0.48
21 1 0.04
ACGTcount: A:0.63, C:0.06, G:0.08, T:0.22
Consensus pattern (20 bp):
ACATATAAAAAGCTAGAAAA
Found at i:53857631 original size:11 final size:10
Alignment explanation
Indices: 53857601--53857690 Score: 60
Period size: 10 Copynumber: 8.6 Consensus size: 10
53857591 TTACTTGAAA
53857601 TTTAAATATT
1 TTTAAATATT
***
53857611 TTTTTTTATT
1 TTTAAATATT
53857621 TTTATAATATT
1 TTTA-AATATT
53857632 TTTAAAT-TT
1 TTTAAATATT
53857641 TTTAAAT-TT
1 TTTAAATATT
*
53857650 ATAATTATATATT
1 -T--TTAAATATT
53857663 TTTAAAT-TT
1 TTTAAATATT
53857672 TATTAAAAATATT
1 T-TT--AAATATT
53857685 TTTAAA
1 TTTAAA
53857691 ATTATATATT
Statistics
Matches: 63, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
9 14 0.22
10 24 0.38
11 8 0.13
12 12 0.19
13 5 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTAAATATT
Found at i:53857673 original size:23 final size:22
Alignment explanation
Indices: 53857639--53857706 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
53857629 ATTTTTAAAT
53857639 TTTTTAAATTTATAATTATATA
1 TTTTTAAATTTATAATTATATA
*
53857661 TTTTTAAATTT-T-ATTAAAAATA
1 TTTTTAAATTTATAATT--ATATA
*
53857683 TTTTTAAAATTATATATTATATA
1 TTTTTAAATTTATA-ATTATATA
53857706 T
1 T
53857707 GATTTTTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 3 0.08
21 1 0.03
22 25 0.66
23 6 0.16
25 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTTAAATTTATAATTATATA
Found at i:53860063 original size:25 final size:27
Alignment explanation
Indices: 53860035--53860093 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
53860025 GTGTAATATA
*
53860035 CACGAGCTGA-GAATCAGTAAGCTC-T
1 CACGAGCTGACAAATCAGTAAGCTCAT
*
53860060 CACGAGCT-ACAAATCGGTAAGCTCAT
1 CACGAGCTGACAAATCAGTAAGCTCAT
53860086 -ACGAGCTG
1 CACGAGCTG
53860094 TGTGTGTCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 1 0.03
25 27 0.93
26 1 0.03
ACGTcount: A:0.32, C:0.25, G:0.24, T:0.19
Consensus pattern (27 bp):
CACGAGCTGACAAATCAGTAAGCTCAT
Found at i:53866549 original size:15 final size:13
Alignment explanation
Indices: 53866518--53866543 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53866508 ATGTAGGGGA
53866518 CACATGGCCATGT
1 CACATGGCCATGT
53866531 CACATGGCCATGT
1 CACATGGCCATGT
53866544 GTCACACACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (13 bp):
CACATGGCCATGT
Found at i:53867349 original size:21 final size:21
Alignment explanation
Indices: 53867323--53867365 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
53867313 ATACATGTAT
*
53867323 GCTCATACGAGCTGTGAATCG
1 GCTCATACGAGCTGAGAATCG
*
53867344 GCTCATACGAGTTGAGAATCG
1 GCTCATACGAGCTGAGAATCG
53867365 G
1 G
53867366 TAAGCTCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (21 bp):
GCTCATACGAGCTGAGAATCG
Found at i:53873489 original size:24 final size:24
Alignment explanation
Indices: 53873462--53873538 Score: 95
Period size: 24 Copynumber: 3.2 Consensus size: 24
53873452 GTGCTTTCTA
53873462 GTTAAGTGCT-TTTCGGAGCTTCCC
1 GTTAAGTGCTCTTT-GGAGCTTCCC
*
53873486 GTTAAGTGCTCTTTGGAGCTACCC
1 GTTAAGTGCTCTTTGGAGCTTCCC
*
53873510 GATATAG-GCTCTTTGTGAGCTTCCC
1 GTTA-AGTGCTCTTTG-GAGCTTCCC
53873535 GTTA
1 GTTA
53873539 TTAAGCCCGA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
24 30 0.65
25 16 0.35
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.36
Consensus pattern (24 bp):
GTTAAGTGCTCTTTGGAGCTTCCC
Found at i:53876622 original size:22 final size:22
Alignment explanation
Indices: 53876578--53876636 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
53876568 ATGAATGTTG
*
53876578 TTTAAATTTATCACATATTATTAT
1 TTTAAATTTAT--CATATAATTAT
53876602 TTTAAATTTATCATATAATTAT
1 TTTAAATTTATCATATAATTAT
*
53876624 TTTAAGTTT-TCAT
1 TTTAAATTTATCAT
53876637 GTATCATTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 18 0.55
24 11 0.33
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAAATTTATCATATAATTAT
Found at i:53880647 original size:3 final size:3
Alignment explanation
Indices: 53880639--53880668 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
53880629 TGTCTATCAA
53880639 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
53880669 TTTCTCTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:53883253 original size:21 final size:21
Alignment explanation
Indices: 53883229--53883268 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53883219 CGTATAAGAA
* *
53883229 ATTAATTTATTAGAGAAATGC
1 ATTAATTTATCAGAAAAATGC
53883250 ATTAATTTATCAGAAAAAT
1 ATTAATTTATCAGAAAAAT
53883269 AAAATACCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (21 bp):
ATTAATTTATCAGAAAAATGC
Found at i:53887182 original size:20 final size:20
Alignment explanation
Indices: 53887145--53887183 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53887135 GGCACTCTCC
*
53887145 ATGAAACAAATTACTAAAAA
1 ATGAAACAAAATACTAAAAA
* *
53887165 ATGACACAAAATAGTAAAA
1 ATGAAACAAAATACTAAAA
53887184 GGGTGGAGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.64, C:0.10, G:0.08, T:0.18
Consensus pattern (20 bp):
ATGAAACAAAATACTAAAAA
Found at i:53894247 original size:36 final size:36
Alignment explanation
Indices: 53894207--53894278 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
53894197 CTTGAAGCAA
*
53894207 TTGGCACTGCTCTTAAGCATTGCTTCTAGCACTACT
1 TTGGCACTGCTCTAAAGCATTGCTTCTAGCACTACT
53894243 TTGGCACTGCTCTAAAGCATTGCTTCTAGCACTACT
1 TTGGCACTGCTCTAAAGCATTGCTTCTAGCACTACT
53894279 CAGTTTACTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.35
Consensus pattern (36 bp):
TTGGCACTGCTCTAAAGCATTGCTTCTAGCACTACT
Found at i:53895984 original size:9 final size:9
Alignment explanation
Indices: 53895967--53896021 Score: 83
Period size: 9 Copynumber: 6.1 Consensus size: 9
53895957 TGAGTTTTCG
53895967 AATTCGAAT
1 AATTCGAAT
*
53895976 AACTCGAAT
1 AATTCGAAT
*
53895985 AATTTGAAT
1 AATTCGAAT
53895994 AATTCGAAT
1 AATTCGAAT
*
53896003 AATTTGAAT
1 AATTCGAAT
53896012 AATTCGAAT
1 AATTCGAAT
53896021 A
1 A
53896022 TCAAACTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 40 1.00
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (9 bp):
AATTCGAAT
Found at i:53895993 original size:18 final size:18
Alignment explanation
Indices: 53895967--53896021 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
53895957 TGAGTTTTCG
* *
53895967 AATTCGAATAACTCGAAT
1 AATTTGAATAATTCGAAT
53895985 AATTTGAATAATTCGAAT
1 AATTTGAATAATTCGAAT
53896003 AATTTGAATAATTCGAAT
1 AATTTGAATAATTCGAAT
53896021 A
1 A
53896022 TCAAACTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (18 bp):
AATTTGAATAATTCGAAT
Found at i:53896270 original size:30 final size:31
Alignment explanation
Indices: 53896235--53896294 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
53896225 AAACCTTTTA
*
53896235 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
53896265 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
53896295 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:53896562 original size:9 final size:9
Alignment explanation
Indices: 53896548--53896576 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
53896538 AATTTCACAT
53896548 TTTATATTA
1 TTTATATTA
53896557 TTTATATTA
1 TTTATATTA
53896566 TTTATATTA
1 TTTATATTA
53896575 TT
1 TT
53896577 GAATTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTATATTA
Found at i:53898550 original size:164 final size:164
Alignment explanation
Indices: 53898279--53898681 Score: 716
Period size: 164 Copynumber: 2.5 Consensus size: 164
53898269 TTTATTTTGG
*
53898279 TTGCTCTTGTTGAGAGTCGAACTCAAGACCTCCCGCTTACTAAACGGATGCTCTAACCAACTGAG
1 TTGCTCTTGTTGAGAGTCGAACTCAAGACCTCCCGCTTACTAAACGGGTGCTCTAACCAACTGAG
* ** *
53898344 CTACAAGAGCCTTGTTGATAGCTGAATCGAAAGTAATTTAAAGATTCATGACTAAAGTAGATTAC
66 CTACAAGAGCCTTGTTGAGAGCCCAATCGAAAGTAATTTAAAGATTCATAACTAAAGTAGATTAC
* **
53898409 ATGTCAGAACTCAAAATAGAAAATGAAACACAGT
131 ATGTCAGAACTCAAAATAGAAAATAAAACACAAA
53898443 TTGCTCTTGTTGAGAGTCGAACTCAAGACCTCCCGCTTACTAAACGGGTGCTCTAACCAACTGAG
1 TTGCTCTTGTTGAGAGTCGAACTCAAGACCTCCCGCTTACTAAACGGGTGCTCTAACCAACTGAG
* *
53898508 CTACAAGAGCCTTGTTGAGAGCCCAATCGAAATTATTTTAAAGATTCATAACTAAAGTAGATTAC
66 CTACAAGAGCCTTGTTGAGAGCCCAATCGAAAGTAATTTAAAGATTCATAACTAAAGTAGATTAC
53898573 ATGTCAGAACTCAAAATAGAAAATAAAACACAAA
131 ATGTCAGAACTCAAAATAGAAAATAAAACACAAA
53898607 TTGCTCTTGTTGAGAGTCGAACTCAAGACCTCCCGCTTACTAAACGGGTGCTCTAACCAACTGAG
1 TTGCTCTTGTTGAGAGTCGAACTCAAGACCTCCCGCTTACTAAACGGGTGCTCTAACCAACTGAG
53898672 CTACAAGAGC
66 CTACAAGAGC
53898682 TGCTTCGTAA
Statistics
Matches: 229, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
164 229 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (164 bp):
TTGCTCTTGTTGAGAGTCGAACTCAAGACCTCCCGCTTACTAAACGGGTGCTCTAACCAACTGAG
CTACAAGAGCCTTGTTGAGAGCCCAATCGAAAGTAATTTAAAGATTCATAACTAAAGTAGATTAC
ATGTCAGAACTCAAAATAGAAAATAAAACACAAA
Found at i:53905291 original size:27 final size:26
Alignment explanation
Indices: 53905236--53905298 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
53905226 TTTAAAGCAC
* *
53905236 AAAAGTATATATACATAAATATTTAA
1 AAAAGTATATAAAAATAAATATTTAA
*
53905262 AAAAGTATCATAAAAATAAA-ATTATTA
1 AAAAGTAT-ATAAAAATAAATATT-TAA
53905289 AAAA-TATATA
1 AAAAGTATATA
53905299 GATAATATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 3 0.09
26 14 0.44
27 15 0.47
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (26 bp):
AAAAGTATATAAAAATAAATATTTAA
Found at i:53910378 original size:6 final size:6
Alignment explanation
Indices: 53910361--53910398 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
53910351 AAGCATGTTA
*
53910361 TATCTG TTTCTG TATCTG TATCTG TATTCTG TATCTG T
1 TATCTG TATCTG TATCTG TATCTG TA-TCTG TATCTG T
53910399 TTTTGGAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.13, C:0.16, G:0.16, T:0.55
Consensus pattern (6 bp):
TATCTG
Found at i:53910392 original size:19 final size:18
Alignment explanation
Indices: 53910361--53910398 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
53910351 AAGCATGTTA
53910361 TATCTGTTTCTGTATCTG
1 TATCTGTTTCTGTATCTG
53910379 TATCTGTATTCTGTATCTG
1 TATCTGT-TTCTGTATCTG
53910398 T
1 T
53910399 TTTTGGAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.13, C:0.16, G:0.16, T:0.55
Consensus pattern (18 bp):
TATCTGTTTCTGTATCTG
Found at i:53912097 original size:50 final size:50
Alignment explanation
Indices: 53911973--53912219 Score: 237
Period size: 50 Copynumber: 4.8 Consensus size: 50
53911963 GATAATAACA
* ** * * * *
53911973 TGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATGTTTCCTGT-AC
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATATCAG
* * **
53912022 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCAG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATATCAG
* * * *
53912072 TGCCCATGCCATGTCCCAGACATGGTCTTACGA-GGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTAC-ATGGGACCTCTCATATCAG
*
53912122 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAACCTCATTGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCAT-A--TCA---G
* * * *
53912178 TGCCAATGCCATGGCTCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCT
53912220 TTACCCAAAT
Statistics
Matches: 162, Mismatches: 27, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
49 40 0.25
50 81 0.50
51 1 0.01
53 2 0.01
56 38 0.23
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATATCAG
Found at i:53919842 original size:49 final size:49
Alignment explanation
Indices: 53919722--53919848 Score: 148
Period size: 49 Copynumber: 2.6 Consensus size: 49
53919712 GGTAAAGAGA
* * * * *
53919722 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGACATGAGCA-CGACAAGAAAAC
* * * *
53919772 TCCCATGTAAGACCATATCTGGGATATGACATTAGCA-GTACAAGAAAAT
1 TCCCATGTAAGACCATGTCTGGGACATGACATGAGCACG-ACAAGAAAAC
53919821 TCCCATGTAAGACCATGTCTGGGACATG
1 TCCCATGTAAGACCATGTCTGGGACATG
53919849 GCTTTGGCAT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
48 1 0.02
49 32 0.49
50 32 0.49
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (49 bp):
TCCCATGTAAGACCATGTCTGGGACATGACATGAGCACGACAAGAAAAC
Found at i:53922522 original size:31 final size:31
Alignment explanation
Indices: 53922480--53922571 Score: 123
Period size: 31 Copynumber: 3.0 Consensus size: 31
53922470 AGGCCAAGTT
*
53922480 GGGCTTGTGGGCCCACACGGGCATGCCACAC
1 GGGCATGTGGGCCCACACGGGCATGCCACAC
*
53922511 GGGTATGTGGGCCCACACGGGCAAT-CCACAC
1 GGGCATGTGGGCCCACACGGGC-ATGCCACAC
* * *
53922542 GGGCATGTGGGCCCAAACAGGCAAGCCACA
1 GGGCATGTGGGCCCACACGGGCATGCCACA
53922572 TGGCCACGTG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
30 1 0.02
31 50 0.94
32 2 0.04
ACGTcount: A:0.23, C:0.33, G:0.34, T:0.11
Consensus pattern (31 bp):
GGGCATGTGGGCCCACACGGGCATGCCACAC
Found at i:53922583 original size:31 final size:31
Alignment explanation
Indices: 53922486--53922584 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 31
53922476 AGTTGGGCTT
* * * ** *
53922486 GTGGGCCCACACGGGCATGCCACACGGGTAT
1 GTGGGCCCAAACAGGCAAGCCACACGGCCAC
* * * * *
53922517 GTGGGCCCACACGGGCAATCCACACGGGCAT
1 GTGGGCCCAAACAGGCAAGCCACACGGCCAC
*
53922548 GTGGGCCCAAACAGGCAAGCCACATGGCCAC
1 GTGGGCCCAAACAGGCAAGCCACACGGCCAC
53922579 GTGGGC
1 GTGGGC
53922585 TCATATTTCT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.22, C:0.33, G:0.34, T:0.10
Consensus pattern (31 bp):
GTGGGCCCAAACAGGCAAGCCACACGGCCAC
Found at i:53924205 original size:37 final size:37
Alignment explanation
Indices: 53924150--53924222 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 37
53924140 CTTTGAGAGG
53924150 GTTGAATCTTAACGTTTTG-GTAGAAACCTTAAGGGA
1 GTTGAATCTTAACGTTTTGAGTAGAAACCTTAAGGGA
* *
53924186 GTTGCAATCTTAA-GATTTTGATTAGAAATCTTAAGGG
1 GTTG-AATCTTAACG-TTTTGAGTAGAAACCTTAAGGG
53924223 GGATTGTAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 5 0.16
37 13 0.41
38 14 0.44
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.36
Consensus pattern (37 bp):
GTTGAATCTTAACGTTTTGAGTAGAAACCTTAAGGGA
Found at i:53925914 original size:10 final size:10
Alignment explanation
Indices: 53925860--53925927 Score: 50
Period size: 10 Copynumber: 6.3 Consensus size: 10
53925850 TATATACTTA
53925860 AATTAATAATT
1 AATTAAT-ATT
*
53925871 AATTAATTTT
1 AATTAATATT
53925881 AATTAAT-TT
1 AATTAATATT
53925890 AATTAAACATAATT
1 AATT--A-AT-ATT
53925904 AATTAATATT
1 AATTAATATT
53925914 AGACTTAAT-TT
1 A-A-TTAATATT
53925925 AAT
1 AAT
53925928 AAAGTTAATG
Statistics
Matches: 49, Mismatches: 1, Indels: 16
0.74 0.02 0.24
Matches are distributed among these distances:
9 7 0.14
10 14 0.29
11 14 0.29
12 8 0.16
14 6 0.12
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (10 bp):
AATTAATATT
Found at i:53926319 original size:60 final size:60
Alignment explanation
Indices: 53926248--53926367 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
53926238 GGTGCATTAC
53926248 CTACTAGGATTTTTTCCATTAGTGCAGTGATTTTGTCATGACTAGTATTTTTTTGAATTG
1 CTACTAGGATTTTTTCCATTAGTGCAGTGATTTTGTCATGACTAGTATTTTTTTGAATTG
53926308 CTACTAGGATTTTTTCCATTAGTGCAGTGATTTTGTCATGACTAGTATTTTTTTGAATTG
1 CTACTAGGATTTTTTCCATTAGTGCAGTGATTTTGTCATGACTAGTATTTTTTTGAATTG
53926368 ATGGAATAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (60 bp):
CTACTAGGATTTTTTCCATTAGTGCAGTGATTTTGTCATGACTAGTATTTTTTTGAATTG
Found at i:53928172 original size:40 final size:41
Alignment explanation
Indices: 53928077--53928215 Score: 129
Period size: 41 Copynumber: 3.4 Consensus size: 41
53928067 CTTCGGTGGC
* * * * **
53928077 TTTAGTGGCGTTTTTGAAAAAGCGCCGCTAATGGTCTGGGT
1 TTTAGTGGCATTTTTCAAGAAGCGCGGCTAATGGTAGGGGT
* * ** * * *
53928118 TTTAGCGGCGTTTTTGTAGATGCGTC-GCT-ATGTTGGGGGT
1 TTTAGTGGCATTTTTCAAGAAGCG-CGGCTAATGGTAGGGGT
*
53928158 TTTAGTGGCATTTTTCAAGAAGCGCGGCTAATGGTAGTGGT
1 TTTAGTGGCATTTTTCAAGAAGCGCGGCTAATGGTAGGGGT
53928199 TTTAGTGGCATTTTTCA
1 TTTAGTGGCATTTTTCA
53928216 GGTTCACCGC
Statistics
Matches: 80, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 1 0.01
40 30 0.38
41 48 0.60
42 1 0.01
ACGTcount: A:0.17, C:0.13, G:0.32, T:0.38
Consensus pattern (41 bp):
TTTAGTGGCATTTTTCAAGAAGCGCGGCTAATGGTAGGGGT
Found at i:53928285 original size:16 final size:15
Alignment explanation
Indices: 53928252--53928306 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 15
53928242 TAATTGGGTT
*
53928252 ATTATTT-ATATT-A
1 ATTATTTAAAATTGA
53928265 ATTATTTAAAATTGA
1 ATTATTTAAAATTGA
**
53928280 ACTTATTTCTAATTGA
1 A-TTATTTAAAATTGA
53928296 A-TATTTAAAAT
1 ATTATTTAAAAT
53928307 CTTTAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
13 7 0.21
14 12 0.35
15 2 0.06
16 13 0.38
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (15 bp):
ATTATTTAAAATTGA
Found at i:53928620 original size:14 final size:15
Alignment explanation
Indices: 53928594--53928631 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
53928584 GGGGTTTATA
53928594 TATGGATTTAGGGAT
1 TATGGATTTAGGGAT
53928609 TATGGA-TTAGGGAT
1 TATGGATTTAGGGAT
53928623 TATGG-TTTA
1 TATGGATTTA
53928632 ATTAAGGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (15 bp):
TATGGATTTAGGGAT
Found at i:53929004 original size:22 final size:22
Alignment explanation
Indices: 53928979--53929044 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 22
53928969 GATTTAAGAT
53928979 TTAGGGGTTAGGGGTTTAGAGG
1 TTAGGGGTTAGGGGTTTAGAGG
** * *
53929001 TTAGATGTTAGTGGTTAAGA-G
1 TTAGGGGTTAGGGGTTTAGAGG
*
53929022 TTAGGGATTTA-GGGTTTAG-GG
1 TTAGGG-GTTAGGGGTTTAGAGG
53929043 TT
1 TT
53929045 TTAGGGGTCG
Statistics
Matches: 33, Mismatches: 9, Indels: 5
0.70 0.19 0.11
Matches are distributed among these distances:
21 14 0.42
22 19 0.58
ACGTcount: A:0.21, C:0.00, G:0.41, T:0.38
Consensus pattern (22 bp):
TTAGGGGTTAGGGGTTTAGAGG
Found at i:53929251 original size:19 final size:18
Alignment explanation
Indices: 53929222--53929275 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
53929212 GGACCAAATT
*
53929222 ATAAGAAATAAAATTAAA
1 ATAAAAAATAAAATTAAA
* *
53929240 ATAGAAAAATAAAAATGAA
1 ATA-AAAAATAAAATTAAA
53929259 ATAAAAACACTAAAATT
1 ATAAAAA-A-TAAAATT
53929276 TTGAATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.24
19 16 0.55
20 6 0.21
ACGTcount: A:0.70, C:0.04, G:0.06, T:0.20
Consensus pattern (18 bp):
ATAAAAAATAAAATTAAA
Found at i:53929330 original size:47 final size:50
Alignment explanation
Indices: 53929260--53929361 Score: 142
Period size: 50 Copynumber: 2.1 Consensus size: 50
53929250 AAAAATGAAA
53929260 TAAAAACACTAAAATTTTGAA-TTTTATCTA-AT-TTTTATAAATATTACT
1 TAAAAACACTAAAATTTTGAATTTTTA-CTACATATTTTATAAATATTACT
53929308 TAAAAA-ACTAAAATTTAT-AATTTTTACTACTATATTTTATAAATATTACT
1 TAAAAACACTAAAATTT-TGAATTTTTACTAC-ATATTTTATAAATATTACT
53929358 TAAA
1 TAAA
53929362 CAAAACTATG
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
47 15 0.31
48 12 0.24
49 2 0.04
50 20 0.41
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.45
Consensus pattern (50 bp):
TAAAAACACTAAAATTTTGAATTTTTACTACATATTTTATAAATATTACT
Found at i:53930086 original size:47 final size:50
Alignment explanation
Indices: 53930016--53930117 Score: 133
Period size: 50 Copynumber: 2.1 Consensus size: 50
53930006 AAAAATGAAA
*
53930016 TAAAAACACTAAAATTTTGAA-TTTTATCTA-ATA-TTTATAACTATTACT
1 TAAAAACACTAAAATTTTGAATTTTTA-CTACATATTTTATAAATATTACT
53930064 TAAAAA-ACTAAAATTTAT-AATTTTTACTACTATATTTTATAAATATTACT
1 TAAAAACACTAAAATTT-TGAATTTTTACTAC-ATATTTTATAAATATTACT
53930114 TAAA
1 TAAA
53930118 CAAAACTATG
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
47 15 0.31
48 12 0.25
49 3 0.06
50 18 0.38
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.44
Consensus pattern (50 bp):
TAAAAACACTAAAATTTTGAATTTTTACTACATATTTTATAAATATTACT
Found at i:53930115 original size:50 final size:48
Alignment explanation
Indices: 53930016--53930117 Score: 129
Period size: 47 Copynumber: 2.1 Consensus size: 48
53930006 AAAAATGAAA
*
53930016 TAAAAACACTAAAATTTTGAATTTTATCTAATATTTATAACTATTACT
1 TAAAAACACTAAAATTTTGAATTTTATCTAATATTTATAAATATTACT
53930064 TAAAAA-ACTAAAATTTAT-AATTTT-TACTACTATATTTTATAAATATTACT
1 TAAAAACACTAAAATTT-TGAATTTTAT-CTA--ATA-TTTATAAATATTACT
53930114 TAAA
1 TAAA
53930118 CAAAACTATG
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
46 1 0.02
47 19 0.40
48 7 0.15
49 3 0.06
50 18 0.38
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.44
Consensus pattern (48 bp):
TAAAAACACTAAAATTTTGAATTTTATCTAATATTTATAAATATTACT
Found at i:53931235 original size:14 final size:14
Alignment explanation
Indices: 53931216--53931242 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53931206 AAGGTTTTTC
53931216 AGTTAATCATCTTT
1 AGTTAATCATCTTT
53931230 AGTTAATCATCTT
1 AGTTAATCATCTT
53931243 GCTGTTCGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (14 bp):
AGTTAATCATCTTT
Found at i:53931491 original size:22 final size:22
Alignment explanation
Indices: 53931459--53931502 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
53931449 CATTTGATTA
53931459 ATTGTTGTAGCCAATGCAAATT
1 ATTGTTGTAGCCAATGCAAATT
*
53931481 ATTGTTTTAGCCAATGCAAATT
1 ATTGTTGTAGCCAATGCAAATT
53931503 TTATTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.39
Consensus pattern (22 bp):
ATTGTTGTAGCCAATGCAAATT
Found at i:53931942 original size:52 final size:53
Alignment explanation
Indices: 53931883--53932063 Score: 151
Period size: 54 Copynumber: 3.4 Consensus size: 53
53931873 TTATTTTAAA
* ** *
53931883 AATACATAACATACATAATATATTAAAACCTATAT-TTTTAA-TATATATATAT
1 AATACATAACTTACATAATATATTAAAACCTATATATAATAACT-TACATATAT
* *
53931935 AATACATAACTTACATAACTTATATTGAAACTTATATATAATAACTTACATATAT
1 AATACATAACTTACATAA--TATATTAAAACCTATATATAATAACTTACATATAT
* *
53931990 AATGCATAACTTACATAATA-ACTTACATAA-CT-TATATAGA-AACTTATATATA-
1 AATACATAACTTACATAATATA-TTA-A-AACCTATATATA-ATAACTTACATATAT
*
53932042 AACTTGCATAACTTACATAATA
1 AA--TACATAACTTACATAATA
53932064 ACATAACAAC
Statistics
Matches: 109, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
52 20 0.18
53 21 0.19
54 36 0.33
55 31 0.28
56 1 0.01
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.37
Consensus pattern (53 bp):
AATACATAACTTACATAATATATTAAAACCTATATATAATAACTTACATATAT
Found at i:53932012 original size:12 final size:12
Alignment explanation
Indices: 53931995--53932019 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53931985 TATATAATGC
53931995 ATAACTTACATA
1 ATAACTTACATA
53932007 ATAACTTACATA
1 ATAACTTACATA
53932019 A
1 A
53932020 CTTATATAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:53932019 original size:9 final size:9
Alignment explanation
Indices: 53932007--53932239 Score: 79
Period size: 9 Copynumber: 26.9 Consensus size: 9
53931997 AACTTACATA
53932007 ATAACTTAC
1 ATAACTTAC
*
53932016 ATAACTTAT
1 ATAACTTAC
*
53932025 ATAGAAACTTATAT
1 AT---AAC-T-TAC
*
53932039 ATAAACTTGC
1 ATAA-CTTAC
53932049 ATAACTTAC
1 ATAACTTAC
*
53932058 ATAA-TAAC
1 ATAACTTAC
*
53932066 ATAACAACTTAG
1 AT---AACTTAC
53932078 ATAA--TAC
1 ATAACTTAC
* *
53932085 ATATCCTAC
1 ATAACTTAC
53932094 ATAACTTAC
1 ATAACTTAC
53932103 ATAACTTAC
1 ATAACTTAC
53932112 ATAA--TAC
1 ATAACTTAC
**
53932119 ACCACTTAC
1 ATAACTTAC
53932128 AT-A---A-
1 ATAACTTAC
*
53932132 ATAACTTGC
1 ATAACTTAC
53932141 ATAA--TAC
1 ATAACTTAC
* * *
53932148 AGAGCCTAC
1 ATAACTTAC
*
53932157 ATAACTTAT
1 ATAACTTAC
*
53932166 AAAACTTAC
1 ATAACTTAC
53932175 ATAA--TAC
1 ATAACTTAC
**
53932182 ACCACTTAC
1 ATAACTTAC
53932191 ATAA--TAC
1 ATAACTTAC
*
53932198 ATTACTTAC
1 ATAACTTAC
53932207 ATAACTTAC
1 ATAACTTAC
*
53932216 ATTA--TAC
1 ATAACTTAC
*
53932223 ACAACTTAC
1 ATAACTTAC
53932232 ATAACTTA
1 ATAACTTA
53932240 ATTAATATTA
Statistics
Matches: 162, Mismatches: 35, Indels: 54
0.65 0.14 0.22
Matches are distributed among these distances:
4 2 0.01
5 2 0.01
7 30 0.19
8 6 0.04
9 98 0.60
10 5 0.03
11 5 0.03
12 8 0.05
13 1 0.01
14 5 0.03
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.31
Consensus pattern (9 bp):
ATAACTTAC
Found at i:53932035 original size:21 final size:21
Alignment explanation
Indices: 53931975--53932023 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
53931965 CTTATATATA
*
53931975 ATAACTTACATATATAA--TGC
1 ATAACTTACATA-ATAACTTAC
53931995 ATAACTTACATAATAACTTAC
1 ATAACTTACATAATAACTTAC
53932016 ATAACTTA
1 ATAACTTA
53932024 TATAGAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.15
20 12 0.46
21 10 0.38
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (21 bp):
ATAACTTACATAATAACTTAC
Found at i:53932062 original size:54 final size:54
Alignment explanation
Indices: 53931992--53932117 Score: 148
Period size: 54 Copynumber: 2.3 Consensus size: 54
53931982 ACATATATAA
* * * * *
53931992 TGCATAACTTACATAATAACTTACATAACTTATATAGAAACTTAT-ATATA-AACT
1 TGCATAACTTACATAATAACATA-ACAACTTAGATA-AAACATATCATACATAACT
* *
53932046 TGCATAACTTACATAATAACATAACAACTTAGATAATACATATCCTACATAACT
1 TGCATAACTTACATAATAACATAACAACTTAGATAAAACATATCATACATAACT
*
53932100 TACATAACTTACATAATA
1 TGCATAACTTACATAATA
53932118 CACCACTTAC
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
52 6 0.10
53 13 0.21
54 43 0.69
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (54 bp):
TGCATAACTTACATAATAACATAACAACTTAGATAAAACATATCATACATAACT
Found at i:53932115 original size:63 final size:63
Alignment explanation
Indices: 53932060--53932194 Score: 166
Period size: 63 Copynumber: 2.2 Consensus size: 63
53932050 TAACTTACAT
* * *
53932060 AATAACAT-AACAACTTAG-ATAATACATATCCTACATAACTTACATAACTTACATAATACACC
1 AATAACATAAACAACTT-GCATAATACAGAGCCTACATAACTTACAAAACTTACATAATACACC
* * * *
53932122 ACTTACATAAATAACTTGCATAATACAGAGCCTACATAACTTATAAAACTTACATAATACACC
1 AATAACATAAACAACTTGCATAATACAGAGCCTACATAACTTACAAAACTTACATAATACACC
* *
53932185 ACTTACATAA
1 AATAACATAA
53932195 TACATTACTT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
62 7 0.11
63 57 0.89
ACGTcount: A:0.47, C:0.22, G:0.03, T:0.27
Consensus pattern (63 bp):
AATAACATAAACAACTTGCATAATACAGAGCCTACATAACTTACAAAACTTACATAATACACC
Found at i:53932119 original size:25 final size:25
Alignment explanation
Indices: 53932071--53932217 Score: 60
Period size: 25 Copynumber: 6.0 Consensus size: 25
53932061 ATAACATAAC
* * *
53932071 AACTTAGATAATACATATCCTACAT
1 AACTTACATAATACATAACTTACAT
*
53932096 AACTTACATAACTTACATAA--TACAC
1 AACTTACATAA--TACATAACTTACAT
* *
53932121 CACTTACAT-A-A-ATAACTTGCAT
1 AACTTACATAATACATAACTTACAT
* * * *
53932143 AA--TACAGAGCCTACATAACTTATAA
1 AACTTACATA--ATACATAACTTACAT
**
53932168 AACTTACATAATACACCACTTACAT
1 AACTTACATAATACATAACTTACAT
*
53932193 AA--TACATTACTTACATAACTTACAT
1 AACTTACA-TA-ATACATAACTTACAT
53932218 TATACACAAC
Statistics
Matches: 88, Mismatches: 21, Indels: 26
0.65 0.16 0.19
Matches are distributed among these distances:
20 8 0.09
21 1 0.01
22 4 0.05
23 4 0.05
24 4 0.05
25 56 0.64
27 11 0.12
ACGTcount: A:0.45, C:0.22, G:0.03, T:0.30
Consensus pattern (25 bp):
AACTTACATAATACATAACTTACAT
Found at i:53932125 original size:16 final size:15
Alignment explanation
Indices: 53932106--53932210 Score: 70
Period size: 16 Copynumber: 6.7 Consensus size: 15
53932096 AACTTACATA
53932106 ACTTACATAATACACC
1 ACTTACATAATACA-C
*
53932122 ACTTACATAA-ATA-
1 ACTTACATAATACAC
* *
53932135 ACTTGCATAATACAG
1 ACTTACATAATACAC
* * *
53932150 AGCCTACATAACTTATAAA
1 A-CTTACATAA--TA-CAC
53932169 ACTTACATAATACACC
1 ACTTACATAATACA-C
*
53932185 ACTTACATAATACATT
1 ACTTACATAATACA-C
53932201 ACTTACATAA
1 ACTTACATAA
53932211 CTTACATTAT
Statistics
Matches: 70, Mismatches: 12, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
13 9 0.13
14 2 0.03
15 4 0.06
16 43 0.61
18 10 0.14
19 2 0.03
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.29
Consensus pattern (15 bp):
ACTTACATAATACAC
Found at i:53932213 original size:41 final size:41
Alignment explanation
Indices: 53932154--53932235 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
53932144 ATACAGAGCC
* *
53932154 TACATAACTTATAAAACTTACATAATACACCACTTACATAA
1 TACATAACTTACAAAACTTACATAATACACAACTTACATAA
* * *
53932195 TACATTACTTACATAACTTACATTATACACAACTTACATAA
1 TACATAACTTACAAAACTTACATAATACACAACTTACATAA
53932236 CTTAATTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (41 bp):
TACATAACTTACAAAACTTACATAATACACAACTTACATAA
Found at i:53932222 original size:25 final size:25
Alignment explanation
Indices: 53932185--53932262 Score: 92
Period size: 25 Copynumber: 3.3 Consensus size: 25
53932175 ATAATACACC
*
53932185 ACTTACATAATACATTACTTACATA
1 ACTTACATTATACATTACTTACATA
**
53932210 ACTTACATTATACACAACTTACATA
1 ACTTACATTATACATTACTTACATA
*
53932235 ACTTA-ATTA-ATATTA--TACATA
1 ACTTACATTATACATTACTTACATA
53932256 ACTTACA
1 ACTTACA
53932263 GCCAGGATAC
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
21 11 0.24
22 1 0.02
23 3 0.07
24 4 0.09
25 27 0.59
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (25 bp):
ACTTACATTATACATTACTTACATA
Found at i:53934019 original size:21 final size:21
Alignment explanation
Indices: 53933995--53934048 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
53933985 CAACAACTTA
*
53933995 AAGCAGAGGCTGCAGCAAAAG
1 AAGCAGAGGCTGCAACAAAAG
*
53934016 AAGCAGAGGCTACAACAAAAG
1 AAGCAGAGGCTGCAACAAAAG
53934037 AAGCAGAGGCTG
1 AAGCAGAGGCTG
53934049 TAGCGAGGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.44, C:0.19, G:0.31, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCTGCAACAAAAG
Found at i:53934444 original size:43 final size:43
Alignment explanation
Indices: 53934392--53934525 Score: 166
Period size: 43 Copynumber: 3.1 Consensus size: 43
53934382 GTCACAACAA
* * *
53934392 TAGCGGCGTTTGTGGTAGAA-G-AGCTGCTAAAGAACATGGCCTT
1 TAGCGGCGTTTGTGGGA-AATGCA-CCGCTAAAGAACATGACCTT
53934435 TAGCGGCGTTTGTGGGAAATGCACCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGGGAAATGCACCGCTAAAGAACATGACCTT
* ** *
53934478 TAGCGGCGTTTTTATGAAA-GCACCGCTAAAGAACATCACCTT
1 TAGCGGCGTTTGTGGGAAATGCACCGCTAAAGAACATGACCTT
53934520 TAGCGG
1 TAGCGG
53934526 TGATGACAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
42 30 0.37
43 51 0.62
44 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAATGCACCGCTAAAGAACATGACCTT
Found at i:53935786 original size:18 final size:17
Alignment explanation
Indices: 53935754--53935795 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
53935744 TAATAATTAT
53935754 TTAAAAATTATAAAAATA
1 TTAAAAATTATAAAAA-A
53935772 TTAAAAATT-TCAAAAAA
1 TTAAAAATTAT-AAAAAA
53935789 -TAAAAAT
1 TTAAAAAT
53935796 ATTGATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.30
17 2 0.09
18 14 0.61
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
TTAAAAATTATAAAAAA
Found at i:53935805 original size:25 final size:25
Alignment explanation
Indices: 53935737--53935814 Score: 70
Period size: 25 Copynumber: 3.0 Consensus size: 25
53935727 ACACATAAGT
53935737 AAAATATTAATAATTATTTA-AAAATTATA
1 AAAATATTAA-AA--ATTTATAAAA--ATA
53935766 AAAATATTAAAAATTTCA-AAAAATA
1 AAAATATTAAAAATTT-ATAAAAATA
* *
53935791 AAAATATTGATAATTTATAAAAAT
1 AAAATATTAAAAATTTATAAAAAT
53935815 TATACATAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
24 1 0.02
25 23 0.51
26 4 0.09
27 5 0.11
28 2 0.04
29 10 0.22
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (25 bp):
AAAATATTAAAAATTTATAAAAATA
Found at i:53936764 original size:30 final size:30
Alignment explanation
Indices: 53936730--53936813 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
53936720 TTTTTTAAAA
*
53936730 TTAAATATATTTT-T-ATATTTTAAAAATGAT
1 TTAAATA-ATTTTGTAAT-TTTTAAAAATAAT
53936760 TTAAATAATTTTGTAATTTTTAAAAATAAT
1 TTAAATAATTTTGTAATTTTTAAAAATAAT
** *
53936790 TT-TTTAATTTTTTTAATTTTTAAA
1 TTAAATAA-TTTTGTAATTTTTAAA
53936814 TTTAAAAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 8 0.17
30 37 0.79
31 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (30 bp):
TTAAATAATTTTGTAATTTTTAAAAATAAT
Found at i:53936786 original size:21 final size:21
Alignment explanation
Indices: 53936762--53936801 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
53936752 AAAATGATTT
53936762 AAATAATTTTGTAATTTTTAA
1 AAATAATTTTGTAATTTTTAA
*
53936783 AAATAATTTTTTAATTTTT
1 AAATAATTTTGTAATTTTT
53936802 TTAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
AAATAATTTTGTAATTTTTAA
Found at i:53938837 original size:12 final size:12
Alignment explanation
Indices: 53938820--53938855 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
53938810 AGAGAGAATG
53938820 ATGAATGAGAGA
1 ATGAATGAGAGA
53938832 ATGAATGAGAGA
1 ATGAATGAGAGA
53938844 ATGAATGAGAGA
1 ATGAATGAGAGA
53938856 TGAGTGTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (12 bp):
ATGAATGAGAGA
Found at i:53938841 original size:27 final size:27
Alignment explanation
Indices: 53938795--53938847 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
53938785 CAAGAGAAAA
53938795 GAATAGAGATATGGAAGAGAGAATGAT
1 GAATAGAGATATGGAAGAGAGAATGAT
53938822 GAATGAGAGA-AT-GAATGAGAGAATGA
1 GAAT-AGAGATATGGAA-GAGAGAATGA
53938848 ATGAGAGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 3 0.12
27 16 0.67
28 5 0.21
ACGTcount: A:0.49, C:0.00, G:0.34, T:0.17
Consensus pattern (27 bp):
GAATAGAGATATGGAAGAGAGAATGAT
Found at i:53940141 original size:31 final size:32
Alignment explanation
Indices: 53940106--53940168 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
53940096 CTTTTCAGAC
* *
53940106 TTTGAGCAAACTTTTCTTTGCT-TTTTATTCT
1 TTTGAACAAACTTATCTTTGCTCTTTTATTCT
*
53940137 TTTGAACAAACTTATCTTTGTTCTTTTATTCT
1 TTTGAACAAACTTATCTTTGCTCTTTTATTCT
53940169 CTCTCTCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 19 0.68
32 9 0.32
ACGTcount: A:0.19, C:0.16, G:0.08, T:0.57
Consensus pattern (32 bp):
TTTGAACAAACTTATCTTTGCTCTTTTATTCT
Found at i:53940901 original size:11 final size:11
Alignment explanation
Indices: 53940872--53940925 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
53940862 AATTATTAAC
53940872 ATATTGAATTTT
1 ATATT-AATTTT
53940884 A-ATTAATTTT
1 ATATTAATTTT
53940894 ATATTAATTTT
1 ATATTAATTTT
*
53940905 -TCATAAATTTT
1 AT-ATTAATTTT
53940916 GAT-TTAATTT
1 -ATATTAATTT
53940926 CGACAGATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
10 8 0.22
11 26 0.72
12 1 0.03
13 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (11 bp):
ATATTAATTTT
Found at i:53940905 original size:22 final size:23
Alignment explanation
Indices: 53940872--53940925 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
53940862 AATTATTAAC
*
53940872 ATATTGAA-TTTTAATTAATTTT-
1 ATATT-AATTTTTAATAAATTTTG
*
53940894 ATATTAATTTTTCATAAATTTTG
1 ATATTAATTTTTAATAAATTTTG
53940917 AT-TTAATTT
1 ATATTAATTT
53940926 CGACAGATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 2 0.07
22 24 0.86
23 2 0.07
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (23 bp):
ATATTAATTTTTAATAAATTTTG
Found at i:53960242 original size:21 final size:20
Alignment explanation
Indices: 53960205--53960247 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
53960195 TTATTCCTTA
53960205 TTATTTTTTATATTTTATCTG
1 TTATTTTTTATATTTTA-CTG
*
53960226 TTATTTTTT-TGTGTTTACTG
1 TTATTTTTTATAT-TTTACTG
53960246 TT
1 TT
53960248 GCTACTGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.14, C:0.05, G:0.09, T:0.72
Consensus pattern (20 bp):
TTATTTTTTATATTTTACTG
Found at i:53970290 original size:43 final size:43
Alignment explanation
Indices: 53970229--53970352 Score: 212
Period size: 43 Copynumber: 2.9 Consensus size: 43
53970219 TACCATCGAC
*
53970229 CGCAGCATGAATACTTAGTTCAATGGAAGGGACTTCCTAACAG
1 CGCAGCATGAATACTTAGTTCGATGGAAGGGACTTCCTAACAG
*
53970272 CGCAGTATGAATACTTAGTTCGATGGAAGGGACTTCCTAACAG
1 CGCAGCATGAATACTTAGTTCGATGGAAGGGACTTCCTAACAG
* *
53970315 TGCGGCATGAATACTTAGTTCGATGGAAGGGACTTCCT
1 CGCAGCATGAATACTTAGTTCGATGGAAGGGACTTCCT
53970353 GACATCGAAG
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 76 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (43 bp):
CGCAGCATGAATACTTAGTTCGATGGAAGGGACTTCCTAACAG
Found at i:53972370 original size:13 final size:13
Alignment explanation
Indices: 53972352--53972384 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
53972342 CACTTATTAC
53972352 TTTTATTTAATAA
1 TTTTATTTAATAA
53972365 TTTTATTTAATAA
1 TTTTATTTAATAA
53972378 TTTTATT
1 TTTTATT
53972385 ACTCTTGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTATTTAATAA
Found at i:53977300 original size:45 final size:45
Alignment explanation
Indices: 53977233--53977360 Score: 116
Period size: 45 Copynumber: 2.8 Consensus size: 45
53977223 CGCCTAAAAC
* *
53977233 GAGTAAGACCATAACTAAAAGATGTTATGATATTAT-G-ATAAAGAT
1 GAGTAAGACCATAACTAAAAGATGCTATGATATCATGGAAT-AA-AT
** ** *
53977278 GAGTAAGACCATAGGTGTAAGATGCTATGGTATCATGGAATAAAT
1 GAGTAAGACCATAACTAAAAGATGCTATGATATCATGGAATAAAT
** * * *
53977323 GAGTAAGACCATGGCTAAAACATACTATGACATCATGG
1 GAGTAAGACCATAACTAAAAGATGCTATGATATCATGG
53977361 TAAACATGAC
Statistics
Matches: 66, Mismatches: 15, Indels: 4
0.78 0.18 0.05
Matches are distributed among these distances:
45 61 0.92
46 3 0.05
47 2 0.03
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (45 bp):
GAGTAAGACCATAACTAAAAGATGCTATGATATCATGGAATAAAT
Found at i:53977557 original size:27 final size:27
Alignment explanation
Indices: 53977478--53977558 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
53977468 CATCATAAAA
* *
53977478 AGTCCAACGAGACATTAAATACA-GGAT
1 AGTCTAACGGGACATTAAATA-AGGGAT
* * * *
53977505 AGCCTAATGGGACATTAAACATGGGAT
1 AGTCTAACGGGACATTAAATAAGGGAT
*
53977532 AGTCTAACGGGACACTAAATAAGGGAT
1 AGTCTAACGGGACATTAAATAAGGGAT
53977559 GGTTCGTCAA
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (27 bp):
AGTCTAACGGGACATTAAATAAGGGAT
Found at i:53987303 original size:5 final size:5
Alignment explanation
Indices: 53987293--53987348 Score: 112
Period size: 5 Copynumber: 11.2 Consensus size: 5
53987283 AAAAGGTTTT
53987293 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
53987343 TAATA T
1 TAATA T
53987349 CAACTTTGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 51 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:53996813 original size:18 final size:18
Alignment explanation
Indices: 53996799--53996854 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
53996789 CACAGTTTGG
53996799 CAAATTAATACAGTTTAC
1 CAAATTAATACAGTTTAC
*
53996817 CATATTAATACA-TATTAC
1 CAAATTAATACAGT-TTAC
* * *
53996835 AAAATTAACACAGTTCAC
1 CAAATTAATACAGTTTAC
53996853 CA
1 CA
53996855 TAATGATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
17 1 0.03
18 28 0.93
19 1 0.03
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (18 bp):
CAAATTAATACAGTTTAC
Found at i:53997187 original size:32 final size:31
Alignment explanation
Indices: 53997146--53997220 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 31
53997136 TGACCCATAT
*
53997146 ATGCTTATATATGATATATATAATCA-AGACCC
1 ATGCATATATATGATATATATAA-CATA-ACCC
*
53997178 -TCGCATATATATTATATATATAACATAACCC
1 AT-GCATATATATGATATATATAACATAACCC
53997209 ATGCATATATAT
1 ATGCATATATAT
53997221 ATTACATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
31 17 0.45
32 21 0.55
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (31 bp):
ATGCATATATATGATATATATAACATAACCC
Found at i:54001627 original size:23 final size:24
Alignment explanation
Indices: 54001584--54001628 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
54001574 AGCTAAGTTC
54001584 ATAAATACTATCTTAGTTCTCTCT
1 ATAAATACTATCTTAGTTCTCTCT
*
54001608 ATAAATAGTATC-TAGTTCTCT
1 ATAAATACTATCTTAGTTCTCT
54001629 ATCTTCCCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (24 bp):
ATAAATACTATCTTAGTTCTCTCT
Found at i:54011240 original size:22 final size:22
Alignment explanation
Indices: 54011212--54011255 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
54011202 ATGATGGCTA
54011212 TAAATACTCATCAATTTCGAGG
1 TAAATACTCATCAATTTCGAGG
54011234 TAAATACTCATCAATTTCGAGG
1 TAAATACTCATCAATTTCGAGG
54011256 CAATCCTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (22 bp):
TAAATACTCATCAATTTCGAGG
Found at i:54014441 original size:19 final size:19
Alignment explanation
Indices: 54014417--54014455 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
54014407 TAATATAAGC
*
54014417 CCACCCAACAGAGATTAGG
1 CCACCCAACAGAGATCAGG
54014436 CCACCCAACAGAGATCAGG
1 CCACCCAACAGAGATCAGG
54014455 C
1 C
54014456 TATACTTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.36, G:0.21, T:0.08
Consensus pattern (19 bp):
CCACCCAACAGAGATCAGG
Found at i:54029606 original size:17 final size:17
Alignment explanation
Indices: 54029593--54029628 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
54029583 TGTTCATATG
*
54029593 AAATTACAGTTCATACC
1 AAATGACAGTTCATACC
*
54029610 AAATGACAGTTCATTCC
1 AAATGACAGTTCATACC
54029627 AA
1 AA
54029629 TTAATAGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (17 bp):
AAATGACAGTTCATACC
Found at i:54037574 original size:50 final size:50
Alignment explanation
Indices: 54037448--54037789 Score: 378
Period size: 50 Copynumber: 6.9 Consensus size: 50
54037438 GATAATAACA
* * *
54037448 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA--TGTT-TC-CTGTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTC-G--G
* * * * * *
54037497 TGCCAATGTCATATCCTAGATATGGTCTTACATGGAAGTCCTCATAT-T-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGG--GACCTCTTATCTCGG
* * *
54037547 TGCCCATGTCATGTCCCAGACATGGTCTT--ATGAGGAACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG-GG-ACCTCTTATCTCGG
* *
54037597 TGCCAACGCCATGTCTCAGACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
*
54037647 TGCCAATGCCATGTCCCAGACATGGTCTTATATGGGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
*
54037697 TGCCAACT-CCATGTCCCAGATATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAA-TGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
* * *
54037747 TGCCAATTCCATGTCTCAAACATGGTCTTACATGGGACCTCTT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
54037790 TACCCAAATG
Statistics
Matches: 250, Mismatches: 29, Indels: 27
0.82 0.09 0.09
Matches are distributed among these distances:
47 1 0.00
48 9 0.04
49 33 0.13
50 196 0.78
51 4 0.02
52 4 0.02
53 2 0.01
54 1 0.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
Found at i:54039172 original size:24 final size:23
Alignment explanation
Indices: 54039137--54039181 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
54039127 GTTCAACTTC
*
54039137 ATAAATATTATCTTACTTCTCTCT
1 ATAAATACTATC-TACTTCTCTCT
*
54039161 ATAAATACTATCTAGTTCTCT
1 ATAAATACTATCTACTTCTCT
54039182 ATCTTCCCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.31, C:0.20, G:0.02, T:0.47
Consensus pattern (23 bp):
ATAAATACTATCTACTTCTCTCT
Found at i:54059917 original size:39 final size:39
Alignment explanation
Indices: 54059872--54059991 Score: 129
Period size: 39 Copynumber: 3.1 Consensus size: 39
54059862 CAAGAGGACA
54059872 TTGTTGTTGAGAAGGAAATTGATGCTGTAGAAGAAGAAG
1 TTGTTGTTGAGAAGGAAATTGATGCTGTAGAAGAAGAAG
*
54059911 TTGTTG-T-CGAAGCGAAAATTGATGCTGTAGAAGAAGAAG
1 TTGTTGTTGAGAAG-G-AAATTGATGCTGTAGAAGAAGAAG
* * * * * *
54059950 TTGTTGTCGA-AGCGGAAGTTGTTGCTGAAGAAGAAAAAG
1 TTGTTGTTGAGA-AGGAAATTGATGCTGTAGAAGAAGAAG
54059989 TTG
1 TTG
54059992 CTGAGAATGA
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
37 4 0.06
38 2 0.03
39 59 0.87
40 2 0.03
41 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.33, T:0.28
Consensus pattern (39 bp):
TTGTTGTTGAGAAGGAAATTGATGCTGTAGAAGAAGAAG
Found at i:54059967 original size:18 final size:18
Alignment explanation
Indices: 54059907--54059973 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
54059897 TGTAGAAGAA
54059907 GAAGTTGTTGTCGAAGCG
1 GAAGTTGTTGTCGAAGCG
* * * **
54059925 AAAATTGATGCTGTAGAAGAA
1 GAAGTTG-T--TGTCGAAGCG
54059946 GAAGTTGTTGTCGAAGCG
1 GAAGTTGTTGTCGAAGCG
54059964 GAAGTTGTTG
1 GAAGTTGTTG
54059974 CTGAAGAAGA
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
18 22 0.61
19 1 0.03
20 1 0.03
21 12 0.33
ACGTcount: A:0.30, C:0.07, G:0.34, T:0.28
Consensus pattern (18 bp):
GAAGTTGTTGTCGAAGCG
Found at i:54060004 original size:17 final size:18
Alignment explanation
Indices: 54059970--54060006 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
54059960 AGCGGAAGTT
54059970 GTTGCTGAAGAAGAAAAA
1 GTTGCTGAAGAAGAAAAA
54059988 GTTGCTG-AGAATGAAAAA
1 GTTGCTGAAGAA-GAAAAA
54060006 G
1 G
54060007 AAAAAGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.46, C:0.05, G:0.30, T:0.19
Consensus pattern (18 bp):
GTTGCTGAAGAAGAAAAA
Found at i:54063727 original size:30 final size:30
Alignment explanation
Indices: 54063692--54063764 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
54063682 GCTACAGGGG
*
54063692 ACACACGACCATGTTAGCTGGCCGTGTGTC
1 ACACACGGCCATGTTAGCTGGCCGTGTGTC
54063722 ACACACGGCCATGTTAGCTGGCCGTGTGTC
1 ACACACGGCCATGTTAGCTGGCCGTGTGTC
54063752 ACACACGGCCATG
1 ACACACGGCCATG
54063765 ACACACGCCC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.21, C:0.32, G:0.27, T:0.21
Consensus pattern (30 bp):
ACACACGGCCATGTTAGCTGGCCGTGTGTC
Found at i:54069194 original size:5 final size:5
Alignment explanation
Indices: 54069184--54069334 Score: 302
Period size: 5 Copynumber: 30.2 Consensus size: 5
54069174 AAAAGGTTTT
54069184 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
54069234 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
54069284 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
54069334 T
1 T
54069335 CAACTTTGTT
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 146 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:54077480 original size:17 final size:17
Alignment explanation
Indices: 54077468--54077569 Score: 78
Period size: 17 Copynumber: 5.9 Consensus size: 17
54077458 TTTTCATATG
54077468 AAATAACAGTTCATACC
1 AAATAACAGTTCATACC
* *
54077485 AAATGACAGTTCATTCC
1 AAATAACAGTTCATACC
* * *
54077502 AATTAACAGTTCAGAAC
1 AAATAACAGTTCATACC
* * *
54077519 ACATAATAGTTACATTCC
1 AAATAACAGTT-CATACC
* * * * *
54077537 ACATAATATTTCATGCA
1 AAATAACAGTTCATACC
54077554 AAATAACAGTTCATAC
1 AAATAACAGTTCATAC
54077570 TCTATAATAA
Statistics
Matches: 64, Mismatches: 20, Indels: 2
0.74 0.23 0.02
Matches are distributed among these distances:
17 51 0.80
18 13 0.20
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (17 bp):
AAATAACAGTTCATACC
Found at i:54078630 original size:33 final size:34
Alignment explanation
Indices: 54078562--54078651 Score: 112
Period size: 33 Copynumber: 2.6 Consensus size: 34
54078552 CATATATGCT
* *
54078562 TATATATGATATATATAATCA-AGACCCAAGTATA
1 TATATATTATATATATAA-CATAGACCCAAGCATA
*
54078596 TATATATTATATATATAACATA-ACCCATGCATA
1 TATATATTATATATATAACATAGACCCAAGCATA
*
54078629 TATATATTACATATATACACATA
1 TATATATTATATATATA-ACATA
54078652 TCTTTTTAGT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
33 27 0.54
34 23 0.46
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (34 bp):
TATATATTATATATATAACATAGACCCAAGCATA
Found at i:54086537 original size:85 final size:85
Alignment explanation
Indices: 54086394--54086572 Score: 358
Period size: 85 Copynumber: 2.1 Consensus size: 85
54086384 GGCCGACCAT
54086394 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
54086459 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
54086479 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
54086544 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
54086564 GAGCATGGG
1 GAGCATGGG
54086573 CAATAAAATA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 94 1.00
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:54094482 original size:25 final size:29
Alignment explanation
Indices: 54094447--54094532 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 29
54094437 CATATTTATG
54094447 GAAAGTCAAAGATATGGGTATC-AA-A-T
1 GAAAGTCAAAGATATGGGTATCAAATATT
54094473 -AAAGTCAAAGATATGGGTATCAAATATT
1 GAAAGTCAAAGATATGGGTATCAAATATT
*
54094501 GGAAAGTCAAAGATATGGGTATCGAGATATT
1 -GAAAGTCAAAGATATGGGTATC-AAATATT
54094532 G
1 G
54094533 GCATAAGAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
25 21 0.40
26 2 0.04
27 1 0.02
28 1 0.02
30 22 0.42
31 6 0.11
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (29 bp):
GAAAGTCAAAGATATGGGTATCAAATATT
Found at i:54094509 original size:30 final size:30
Alignment explanation
Indices: 54094445--54094533 Score: 125
Period size: 25 Copynumber: 3.1 Consensus size: 30
54094435 TCCATATTTA
54094445 TGGAAAGTCAAAGATATGGGTATC-AA-A-
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
54094472 T--AAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
54094500 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
54094531 TGG
1 TGG
54094534 CATAAGAAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
25 21 0.38
26 2 0.04
27 2 0.04
28 1 0.02
30 21 0.38
31 8 0.15
ACGTcount: A:0.42, C:0.07, G:0.26, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:54096811 original size:271 final size:271
Alignment explanation
Indices: 54096328--54096872 Score: 1081
Period size: 271 Copynumber: 2.0 Consensus size: 271
54096318 ACCAGGTTAT
54096328 GGTATATGCGATTGGGACATGCTGGTGAAAAAGCTTTCCAGAGTTTGGCAAAGCAAGGCTTGTTG
1 GGTATATGCGATTGGGACATGCTGGTGAAAAAGCTTTCCAGAGTTTGGCAAAGCAAGGCTTGTTG
54096393 AAAGGTGAAAATTCTTGCAAATTGGAATTCTGTGAAAATTGTGTTCTGGGCAAGCAGATGAGGAT
66 AAAGGTGAAAATTCTTGCAAATTGGAATTCTGTGAAAATTGTGTTCTGGGCAAGCAGATGAGGAT
54096458 AAAATTTGGTTCAGCAATTCACAATACAAAAAGAATTCTGGACTACGTTCACAGTGATGTATGGG
131 AAAATTTGGTTCAGCAATTCACAATACAAAAAGAATTCTGGACTACGTTCACAGTGATGTATGGG
54096523 GACCTACTAAAGTGGCTTCTTTGGGAGGTATGCACTATTTTGTTACTTTTGTTGATGATTATTCA
196 GACCTACTAAAGTGGCTTCTTTGGGAGGTATGCACTATTTTGTTACTTTTGTTGATGATTATTCA
54096588 AGAAAAGTATG
261 AGAAAAGTATG
54096599 GGTATATGCGATTGGGACATGCTGGTGAAAAAGCTTTCCAGAGTTTGGCAAAGCAAGGCTTGTTG
1 GGTATATGCGATTGGGACATGCTGGTGAAAAAGCTTTCCAGAGTTTGGCAAAGCAAGGCTTGTTG
54096664 AAAGGTGAAAATTCTTGCAAATTGGAATTCTGTGAAAATTGTGTTCTGGGCAAGCAGATGAGGAT
66 AAAGGTGAAAATTCTTGCAAATTGGAATTCTGTGAAAATTGTGTTCTGGGCAAGCAGATGAGGAT
*
54096729 AAAATTTGGTTCAGCAATTCACAATACAAAAAGAATTCTGGACTACGTTCACAGTGATGTGTGGG
131 AAAATTTGGTTCAGCAATTCACAATACAAAAAGAATTCTGGACTACGTTCACAGTGATGTATGGG
54096794 GACCTACTAAAGTGGCTTCTTTGGGAGGTATGCACTATTTTGTTACTTTTGTTGATGATTATTCA
196 GACCTACTAAAGTGGCTTCTTTGGGAGGTATGCACTATTTTGTTACTTTTGTTGATGATTATTCA
54096859 AGAAAAGTATG
261 AGAAAAGTATG
54096870 GGT
1 GGT
54096873 GTATCAAATG
Statistics
Matches: 273, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
271 273 1.00
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.31
Consensus pattern (271 bp):
GGTATATGCGATTGGGACATGCTGGTGAAAAAGCTTTCCAGAGTTTGGCAAAGCAAGGCTTGTTG
AAAGGTGAAAATTCTTGCAAATTGGAATTCTGTGAAAATTGTGTTCTGGGCAAGCAGATGAGGAT
AAAATTTGGTTCAGCAATTCACAATACAAAAAGAATTCTGGACTACGTTCACAGTGATGTATGGG
GACCTACTAAAGTGGCTTCTTTGGGAGGTATGCACTATTTTGTTACTTTTGTTGATGATTATTCA
AGAAAAGTATG
Found at i:54099403 original size:15 final size:15
Alignment explanation
Indices: 54099383--54099462 Score: 74
Period size: 15 Copynumber: 5.3 Consensus size: 15
54099373 TTTATGGAAA
54099383 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
54099398 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
54099412 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
54099428 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
54099442 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
54099458 ATCAA
1 ATCAA
54099463 GATTTTGGCA
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
14 9 0.18
15 31 0.63
16 9 0.18
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:54099412 original size:30 final size:30
Alignment explanation
Indices: 54099376--54099462 Score: 156
Period size: 30 Copynumber: 2.9 Consensus size: 30
54099366 ATCCATATTT
*
54099376 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
54099406 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
54099436 TTGGAAAGTCAAAGATATGGGTATCAA
1 ATGGAAAGTCAAAGATATGGGTATCAA
54099463 GATTTTGGCA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.46, C:0.07, G:0.23, T:0.24
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:54109356 original size:56 final size:56
Alignment explanation
Indices: 54109294--54109404 Score: 204
Period size: 56 Copynumber: 2.0 Consensus size: 56
54109284 GTTTTAAACG
*
54109294 GTATATATTTTGCAAACATTCTACAAATTTTCTTTCATACATCCATTGTGTTAACA
1 GTATATATTTTGCAAACATTCTACAAATTTTCTTTCATACATCAATTGTGTTAACA
*
54109350 GTATATATTTTGCAAACATTCTATAAATTTTCTTTCATACATCAATTGTGTTAAC
1 GTATATATTTTGCAAACATTCTACAAATTTTCTTTCATACATCAATTGTGTTAAC
54109405 GAAATCTCGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.44
Consensus pattern (56 bp):
GTATATATTTTGCAAACATTCTACAAATTTTCTTTCATACATCAATTGTGTTAACA
Found at i:54116108 original size:23 final size:23
Alignment explanation
Indices: 54116082--54116125 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
54116072 TGTGTAACTT
*
54116082 TTCATCTTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
54116105 TTCATATTCAAGTCTCTTCAC
1 TTCATATTCAAGTCTCTTCAC
54116126 ATTTCTAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.32, G:0.05, T:0.43
Consensus pattern (23 bp):
TTCATATTCAAGTCTCTTCACTC
Found at i:54121020 original size:14 final size:15
Alignment explanation
Indices: 54120994--54121030 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
54120984 AAATAAAGAT
54120994 AAATATTT-G-ATAA
1 AAATATTTGGAATAA
54121007 AAA-ATTTGGAATAA
1 AAATATTTGGAATAA
54121021 AAATATTTGG
1 AAATATTTGG
54121031 GCTTCGATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 4 0.19
13 4 0.19
14 7 0.33
15 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.35
Consensus pattern (15 bp):
AAATATTTGGAATAA
Done.