Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 15 of 32
Found at i:2228244 original size:25 final size:25
Alignment explanation
Indices: 2228208--2228257 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2228198 TGTGCGGACC
*
2228208 CTACCATTAATCCGAGTCAGAATCT
1 CTACCATCAATCCGAGTCAGAATCT
*
2228233 CTACCATCAATCCGTGTCAGAATCT
1 CTACCATCAATCCGAGTCAGAATCT
2228258 AAAACGGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.28
Consensus pattern (25 bp):
CTACCATCAATCCGAGTCAGAATCT
Found at i:2230123 original size:13 final size:14
Alignment explanation
Indices: 2230105--2230134 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2230095 ACTACGTAAT
2230105 AAAAAAAA-GAAAA
1 AAAAAAAAGGAAAA
2230118 AAAAAAAAGGAAAA
1 AAAAAAAAGGAAAA
2230132 AAA
1 AAA
2230135 TAGGTATAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGGAAAA
Found at i:2230124 original size:14 final size:14
Alignment explanation
Indices: 2230105--2230134 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2230095 ACTACGTAAT
2230105 AAAAAAAAGAAAAA
1 AAAAAAAAGAAAAA
*
2230119 AAAAAAAGGAAAAA
1 AAAAAAAAGAAAAA
2230133 AA
1 AA
2230135 TAGGTATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAAA
Found at i:2231022 original size:15 final size:17
Alignment explanation
Indices: 2231002--2231044 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
2230992 ATTAATTAAT
2231002 ATATTAT-TTAAA-ATA
1 ATATTATATTAAATATA
2231017 ATATTATATTAAATATA
1 ATATTATATTAAATATA
*
2231034 AAATTAATATT
1 ATATT-ATATT
2231045 TTATTTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 5 0.21
17 7 0.29
18 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATTATATTAAATATA
Found at i:2231026 original size:17 final size:19
Alignment explanation
Indices: 2231006--2231045 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
2230996 ATTAATATAT
*
2231006 TATTTAAA-ATAATATT-A
1 TATTTAAATATAAAATTAA
2231023 TA-TTAAATATAAAATTAA
1 TATTTAAATATAAAATTAA
2231041 TATTT
1 TATTT
2231046 TATTTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 5 0.26
17 9 0.47
18 3 0.16
19 2 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATTTAAATATAAAATTAA
Found at i:2231263 original size:4 final size:4
Alignment explanation
Indices: 2231254--2231284 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
2231244 AACAAAGATA
*
2231254 AAAT AAAT AAGT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
2231285 AATTTGCCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2232247 original size:13 final size:13
Alignment explanation
Indices: 2232229--2232254 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2232219 AAAAAAATAT
2232229 ATAAATCTATAAA
1 ATAAATCTATAAA
2232242 ATAAATCTATAAA
1 ATAAATCTATAAA
2232255 TATATAAAAA
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:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAATCTATAAA
Found at i:2232252 original size:21 final size:20
Alignment explanation
Indices: 2232218--2232264 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
2232208 TTTTTTAGGT
*
2232218 TAAAAAAATATATAAATCTA
1 TAAAAAAATATATAAATATA
*
2232238 TAAAATAAATCTATAAATATA
1 TAAAA-AAATATATAAATATA
2232259 TAAAAA
1 TAAAAA
2232265 GATTAATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAAAAATATATAAATATA
Found at i:2232326 original size:29 final size:29
Alignment explanation
Indices: 2232284--2232343 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
2232274 AGAAATTATT
2232284 TTTTATATATTAT-AATAATAATAAAATAAA
1 TTTTATATATTATAAATAA-AAT-AAATAAA
* *
2232314 TTTTA-ATTTTATAAATAAAATTAATAAA
1 TTTTATATATTATAAATAAAATAAATAAA
2232342 TT
1 TT
2232344 AATATTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 8 0.30
29 9 0.33
30 10 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTTATATATTATAAATAAAATAAATAAA
Found at i:2234004 original size:26 final size:27
Alignment explanation
Indices: 2233949--2234005 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
2233939 ATACATTAAT
* * *
2233949 ATTTAAAAATTTTTCATTAATTTATCA
1 ATTTAAAAATTTTTCAATAATATATAA
2233976 ATTT-AAAATTTTT-AATAATAATATAA
1 ATTTAAAAATTTTTCAATAAT-ATATAA
2234002 ATTT
1 ATTT
2234006 TATCTTGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 5 0.19
26 17 0.65
27 4 0.15
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTTAAAAATTTTTCAATAATATATAA
Found at i:2234436 original size:19 final size:19
Alignment explanation
Indices: 2234370--2234442 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 19
2234360 TCATTAAAAT
2234370 TTTTAAATAAATATACTTTAAA
1 TTTTAAATAAA-ATA--TTAAA
2234392 TTTTAATATAAAATATTAAA
1 TTTTAA-ATAAAATATTAAA
**
2234412 AATTAAATAAAATA-TAATA
1 TTTTAAATAAAATATTAA-A
2234431 TTTTAAA-AAAAT
1 TTTTAAATAAAAT
2234443 TATTTGGGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 8 0.18
19 14 0.31
20 9 0.20
22 9 0.20
23 5 0.11
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTTAAATAAAATATTAAA
Found at i:2234721 original size:3 final size:3
Alignment explanation
Indices: 2234713--2234741 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2234703 TGCTTCAAAA
2234713 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2234742 AAAAAAAGAG
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2243482 original size:17 final size:17
Alignment explanation
Indices: 2243460--2243497 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
2243450 TATTTGAATA
2243460 TTACAGGAACGGCATGC
1 TTACAGGAACGGCATGC
2243477 TTACAGGAACGGCATGC
1 TTACAGGAACGGCATGC
2243494 TTAC
1 TTAC
2243498 TCTTCCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (17 bp):
TTACAGGAACGGCATGC
Found at i:2246199 original size:29 final size:24
Alignment explanation
Indices: 2246140--2246188 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2246130 TGTGCTATAT
2246140 ATATCAATAGTATATGAAATTTAA
1 ATATCAATAGTATATGAAATTTAA
*
2246164 ATATCAATAGTGTATGAAATTTAA
1 ATATCAATAGTATATGAAATTTAA
2246188 A
1 A
2246189 GCTTGAATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (24 bp):
ATATCAATAGTATATGAAATTTAA
Found at i:2246557 original size:2 final size:2
Alignment explanation
Indices: 2246550--2246579 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2246540 CAGTCGCCCA
2246550 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2246580 ACTGAAGCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2248261 original size:24 final size:23
Alignment explanation
Indices: 2248217--2248261 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2248207 TATTTTAAAA
**
2248217 TTTGAATTATTTTAATGTTATTT
1 TTTGAATTATTTTAAAATTATTT
*
2248240 TTTGTATTATATTTAAAATTAT
1 TTTGAATTAT-TTTAAAATTAT
2248262 CAAATTTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (23 bp):
TTTGAATTATTTTAAAATTATTT
Found at i:2249701 original size:4 final size:5
Alignment explanation
Indices: 2249669--2249717 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
2249659 ATTTTTAAAA
* *
2249669 AAATT AAATT AAAAAT AAA-T ATA-T AAATT -AATT AAATT AAATT AAATT
1 AAATT AAATT -AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT
2249717 A
1 A
2249718 TATATATCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
4 10 0.26
5 24 0.63
6 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AAATT
Found at i:2250067 original size:7 final size:7
Alignment explanation
Indices: 2250055--2250093 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
2250045 ATTATAATAC
2250055 AAAAATT
1 AAAAATT
2250062 AAAAATT
1 AAAAATT
2250069 AAAAATAT
1 AAAAAT-T
*
2250077 TAAAATT
1 AAAAATT
2250084 -AAAATT
1 AAAAATT
2250090 AAAA
1 AAAA
2250094 TTTTAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
6 6 0.21
7 17 0.59
8 6 0.21
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAAAATT
Found at i:2250717 original size:20 final size:21
Alignment explanation
Indices: 2250674--2250728 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
2250664 TCTCAAATAA
*
2250674 AATTAAAAAAAATAAATTATTT
1 AATTAAATAAAATAAA-TATTT
2250696 AATTAAATAAAATAAA-ATTT
1 AATTAAATAAAATAAATATTT
* *
2250716 AAATAAATTAAAT
1 AATTAAATAAAAT
2250729 TTAATTACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 15 0.50
22 15 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AATTAAATAAAATAAATATTT
Found at i:2250723 original size:15 final size:16
Alignment explanation
Indices: 2250698--2250732 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2250688 AATTATTTAA
2250698 TTAAATAAAATAAAAT
1 TTAAATAAAATAAAAT
*
2250714 TTAAAT-AAATTAAAT
1 TTAAATAAAATAAAAT
2250729 TTAA
1 TTAA
2250733 TTACATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAAATAAAATAAAAT
Found at i:2250741 original size:35 final size:32
Alignment explanation
Indices: 2250683--2250751 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 32
2250673 AAATTAAAAA
2250683 AAATAAATTATTTAATTAAATAAAATAAAATTT
1 AAATAAATTATTTAATTAAAT-AAATAAAATTT
* *
2250716 AAATAAATTAAATTTAATTACATAAATTAAATTT
1 AAATAAATT--ATTTAATTAAATAAATAAAATTT
2250750 AA
1 AA
2250752 TCCATTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
33 9 0.28
34 12 0.38
35 11 0.34
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
AAATAAATTATTTAATTAAATAAATAAAATTT
Found at i:2251428 original size:19 final size:19
Alignment explanation
Indices: 2251401--2251444 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2251391 AAGTGTATGC
**
2251401 AATTAATTTTTTATAAATA
1 AATTAATTTAATATAAATA
* *
2251420 AATTTATTTAATATAAATT
1 AATTAATTTAATATAAATA
2251439 AATTAA
1 AATTAA
2251445 ATTTTATTTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTAATTTAATATAAATA
Found at i:2251471 original size:16 final size:18
Alignment explanation
Indices: 2251441--2251478 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2251431 TATAAATTAA
*
2251441 TTAAATTTTATTTAAT-T
1 TTAAATTTTAATTAATCT
2251458 TTAAA-TTTAATTAATCT
1 TTAAATTTTAATTAATCT
2251475 TTAA
1 TTAA
2251479 TCGAATCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
TTAAATTTTAATTAATCT
Found at i:2255881 original size:6 final size:6
Alignment explanation
Indices: 2255859--2255893 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
2255849 TGTATTACTG
*
2255859 TCTTTT TCCTTT T-TTTT TCTTTT TCTTTT TCTTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
2255894 CCCGGGGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TCTTTT
Found at i:2255881 original size:17 final size:17
Alignment explanation
Indices: 2255859--2255894 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
2255849 TGTATTACTG
2255859 TCTTTTTCCTTTTT-TTT
1 TCTTTTT-CTTTTTCTTT
2255876 TCTTTTTCTTTTTCTTT
1 TCTTTTTCTTTTTCTTT
2255893 TC
1 TC
2255895 CCGGGGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TCTTTTTCTTTTTCTTT
Found at i:2256164 original size:14 final size:15
Alignment explanation
Indices: 2256145--2256200 Score: 71
Period size: 14 Copynumber: 3.8 Consensus size: 15
2256135 CGAATAAGTC
2256145 TTTATTTATATTTA-
1 TTTATTTATATTTAG
*
2256159 TTTATTTATTTTTGAG
1 TTTATTTATATTT-AG
2256175 TTT-TTTATATTTAG
1 TTTATTTATATTTAG
*
2256189 TTTATTTTTATT
1 TTTATTTATATT
2256201 AAATTTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
14 17 0.47
15 16 0.44
16 3 0.08
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.73
Consensus pattern (15 bp):
TTTATTTATATTTAG
Found at i:2256207 original size:29 final size:29
Alignment explanation
Indices: 2256149--2256209 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
2256139 TAAGTCTTTA
* * *
2256149 TTTATATTTATTTATTTATTTTTGAGTTT
1 TTTATATTTATTTATTTATTATTAAATTT
2256178 TTTATATTTAGTTTATTT-TTATTAAATTT
1 TTTATATTTA-TTTATTTATTATTAAATTT
2256207 TTT
1 TTT
2256210 TGAAATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (29 bp):
TTTATATTTATTTATTTATTATTAAATTT
Found at i:2256278 original size:75 final size:74
Alignment explanation
Indices: 2256154--2256314 Score: 178
Period size: 75 Copynumber: 2.1 Consensus size: 74
2256144 CTTTATTTAT
* * * ** * * *
2256154 ATTTATTTATTTATTTTTGAGTTTTTTATATTTAGTTTATTTTTATTAAATTTTTTTGAAATTTT
1 ATTTATTTA--TATTTTTAAGTTTTTTATATTTAATTTATTATTATTAAAAATTTTTAAAACTGT
*
2256219 ATTAAAATTTG
64 ATTAAAATTCG
* * *
2256230 ATTTATTTATATTTTTAAGTTTTTTTATATTTAATTTGTTATTGTTAAAAATTTTTAAAACTGTG
1 ATTTATTTATATTTTTAAG-TTTTTTATATTTAATTTATTATTATTAAAAATTTTTAAAACTGTA
2256295 TTAAAATTCG
65 TTAAAATTCG
*
2256305 ATTTACTTAT
1 ATTTATTTAT
2256315 TGATAGGTGT
Statistics
Matches: 71, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
74 9 0.13
75 53 0.75
76 9 0.13
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (74 bp):
ATTTATTTATATTTTTAAGTTTTTTATATTTAATTTATTATTATTAAAAATTTTTAAAACTGTAT
TAAAATTCG
Found at i:2256548 original size:18 final size:18
Alignment explanation
Indices: 2256501--2256551 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
2256491 TATTTAATTA
*
2256501 AAATTAAAAAATAAAAAT
1 AAATTAAAAAATATAAAT
** * *
2256519 TTATTTATAAATATAAAT
1 AAATTAAAAAATATAAAT
2256537 AAATTAAAAAATATA
1 AAATTAAAAAATATA
2256552 TTATTCAAAC
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATTAAAAAATATAAAT
Found at i:2256867 original size:19 final size:21
Alignment explanation
Indices: 2256837--2256878 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
2256827 CCGGCTTGAG
2256837 TTTTATTTTTTATAA-TTAAA
1 TTTTATTTTTTATAATTTAAA
2256857 TTTTA-TTTTTATAATTTAAA
1 TTTTATTTTTTATAATTTAAA
2256877 TT
1 TT
2256879 GATTTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATTTTTTATAATTTAAA
Found at i:2256883 original size:19 final size:19
Alignment explanation
Indices: 2256843--2256883 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2256833 TGAGTTTTAT
*
2256843 TTTTTATAATTAAATTTTA
1 TTTTTATAATTAAATTTGA
2256862 TTTTTATAATTTAAA-TTGA
1 TTTTTATAA-TTAAATTTGA
2256881 TTT
1 TTT
2256884 AATTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTTATAATTAAATTTGA
Found at i:2256938 original size:20 final size:20
Alignment explanation
Indices: 2256881--2256939 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
2256871 TTTAAATTGA
* *
2256881 TTTAATTTAAA-ATAATAAT
1 TTTAATTTAAATTTAATTAT
* *
2256900 TATAAATTAAAATTT-ATTAT
1 T-TTAATTTAAATTTAATTAT
2256920 TTTAATTTAAATTTAATTAT
1 TTTAATTTAAATTTAATTAT
2256940 AAAAGTATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 12 0.39
20 18 0.58
21 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTAATTTAAATTTAATTAT
Found at i:2262637 original size:12 final size:13
Alignment explanation
Indices: 2262621--2262670 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 13
2262611 AATAATTAAA
2262621 AATTAATTTTTAT
1 AATTAATTTTTAT
*
2262634 -ATTAATATTTAT
1 AATTAATTTTTAT
* *
2262646 AATTAAATTTTAA
1 AATTAATTTTTAT
*
2262659 AAAT-ATTTTTAT
1 AATTAATTTTTAT
2262671 TATATAAATA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
12 17 0.59
13 12 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTAATTTTTAT
Found at i:2265684 original size:2 final size:2
Alignment explanation
Indices: 2265677--2265706 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2265667 GTTTATACAA
2265677 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
2265707 TGAATCGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2265783 original size:16 final size:17
Alignment explanation
Indices: 2265757--2265789 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2265747 ATTTTTATTA
2265757 ATTATTAAAAAAATAAT
1 ATTATTAAAAAAATAAT
2265774 ATTA-TAAAAAAATAAT
1 ATTATTAAAAAAATAAT
2265790 TTTTTAATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATTATTAAAAAAATAAT
Found at i:2267193 original size:22 final size:23
Alignment explanation
Indices: 2267163--2267208 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
2267153 TTCAAAATTT
2267163 TTTACTTTTAA-AATATTA-TAAA
1 TTTACTTTTAATAAT-TTATTAAA
*
2267185 TTTATTTTTAATAATTTATTAAA
1 TTTACTTTTAATAATTTATTAAA
2267208 T
1 T
2267209 AAATATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTACTTTTAATAATTTATTAAA
Found at i:2267355 original size:28 final size:28
Alignment explanation
Indices: 2267322--2267401 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 28
2267312 TAAAATATCA
2267322 AAAATAATTAAAATATAATATAATATAT
1 AAAATAATTAAAATATAATATAATATAT
* * *
2267350 AAAATAATTTAAATATAAAATAATTTAT
1 AAAATAATTAAAATATAATATAATATAT
* *
2267378 -AATTATATTAAAAT-TTATATAATA
1 AAAATA-ATTAAAATATAATATAATA
2267402 ATATTATTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
27 11 0.26
28 32 0.74
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
AAAATAATTAAAATATAATATAATATAT
Found at i:2267366 original size:18 final size:18
Alignment explanation
Indices: 2267342--2267391 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 18
2267332 AAATATAATA
2267342 TAATATATAAAATAA-TT
1 TAATATATAAAATAATTT
2267359 TAA-ATATAAAATAATTT
1 TAATATATAAAATAATTT
2267376 ATAATTATATTAAAAT
1 -TAA-TATA-TAAAAT
2267392 TTATATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 11 0.39
17 5 0.18
18 3 0.11
20 3 0.11
21 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATATATAAAATAATTT
Found at i:2267367 original size:16 final size:17
Alignment explanation
Indices: 2267336--2267376 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
2267326 TAATTAAAAT
*
2267336 ATAATATAATATATAAA
1 ATAATTTAATATATAAA
2267353 ATAATTTAA-ATATAAA
1 ATAATTTAATATATAAA
2267369 ATAATTTA
1 ATAATTTA
2267377 TAATTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAATTTAATATATAAA
Found at i:2267419 original size:31 final size:31
Alignment explanation
Indices: 2267363--2267460 Score: 118
Period size: 31 Copynumber: 3.3 Consensus size: 31
2267353 ATAATTTAAA
*
2267363 TATAAAATAAT-TTA-TAATTATATTAAAATT
1 TATATAATAATATTATTAA-TATATTAAAATT
2267393 TATATAATAATATTATTAATATATTAAAATT
1 TATATAATAATATTATTAATATATTAAAATT
* *
2267424 TATAT-A-AATATTATT-ATATGTTAAAATA
1 TATATAATAATATTATTAATATATTAAAATT
2267452 TAT-TAATAA
1 TATATAATAA
2267461 AATATAAATA
Statistics
Matches: 61, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
27 1 0.02
28 15 0.25
29 11 0.18
30 11 0.18
31 20 0.33
32 3 0.05
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (31 bp):
TATATAATAATATTATTAATATATTAAAATT
Found at i:2271578 original size:2 final size:2
Alignment explanation
Indices: 2271571--2271605 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2271561 CAATTTACAG
*
2271571 AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2271606 GAATCTCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2273715 original size:2 final size:2
Alignment explanation
Indices: 2273708--2273738 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2273698 GCTTTAATGT
2273708 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
2273739 TATCTGAGAC
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:2274428 original size:15 final size:15
Alignment explanation
Indices: 2274377--2274435 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
2274367 TATTTAAATA
*
2274377 TAAAATAAA-ATATT
1 TAAATTAAATATATT
*
2274391 TAAATATATAAT-TTTT
1 TAAAT-TA-AATATATT
2274407 TAAATTAAATATATT
1 TAAATTAAATATATT
*
2274422 TATATTAAATATAT
1 TAAATTAAATATAT
2274436 ATTCGATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
14 7 0.19
15 20 0.54
16 10 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAATTAAATATATT
Found at i:2278692 original size:15 final size:17
Alignment explanation
Indices: 2278672--2278703 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
2278662 AATTTTTAAT
2278672 TTTTTAA-A-ATATCTA
1 TTTTTAACATATATCTA
2278687 TTTTTAACATATATCTA
1 TTTTTAACATATATCTA
2278704 AATTTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTTAACATATATCTA
Found at i:2279513 original size:13 final size:13
Alignment explanation
Indices: 2279491--2279524 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2279481 TCTGTATTTC
*
2279491 TTTTTCTTTCTTT
1 TTTTTTTTTCTTT
2279504 TTTTTTTTTCTTT
1 TTTTTTTTTCTTT
2279517 TTTCTTTT
1 TTT-TTTT
2279525 GGCATTGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTCTTT
Found at i:2283277 original size:14 final size:14
Alignment explanation
Indices: 2283240--2283278 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2283230 ATTTTATATT
*
2283240 TATTATTTTAAAAA
1 TATTATTTTTAAAA
* *
2283254 TTTTATTTTTAATA
1 TATTATTTTTAAAA
2283268 TATTATTTTTA
1 TATTATTTTTA
2283279 TAAAATTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTATTTTTAAAA
Found at i:2283343 original size:36 final size:35
Alignment explanation
Indices: 2283262--2283343 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 35
2283252 AATTTTATTT
2283262 TTAATA-TATTATTTTTATAAAATTAAAAAAATAAA
1 TTAATATTA-TATTTTTATAAAATTAAAAAAATAAA
* * * *
2283297 ATATTAATTATATTTTTATAATATATAAAAAAATTAA
1 TTAAT-ATTATATTTTTATAAAAT-TAAAAAAATAAA
2283334 TTAATATTAT
1 TTAATATTAT
2283344 TACGTATTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
35 3 0.08
36 19 0.50
37 16 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (35 bp):
TTAATATTATATTTTTATAAAATTAAAAAAATAAA
Found at i:2284439 original size:20 final size:21
Alignment explanation
Indices: 2284405--2284446 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
2284395 TTTTATTATT
2284405 AATTATTATAAATATAATAAA
1 AATTATTATAAATATAATAAA
*
2284426 AATTATTA-AAATATATTAAA
1 AATTATTATAAATATAATAAA
2284446 A
1 A
2284447 TTTAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTATTATAAATATAATAAA
Found at i:2284455 original size:19 final size:20
Alignment explanation
Indices: 2284414--2284460 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
2284404 TAATTATTAT
*
2284414 AAATATAATAAAAATTATTA
1 AAATATAATAAAAATTATAA
*
2284434 AAATAT-ATTAAAATT-TAA
1 AAATATAATAAAAATTATAA
2284452 AAA-ATAATA
1 AAATATAATA
2284461 TATGATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 2 0.09
18 7 0.30
19 8 0.35
20 6 0.26
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATATAATAAAAATTATAA
Found at i:2284522 original size:20 final size:20
Alignment explanation
Indices: 2284497--2284566 Score: 70
Period size: 20 Copynumber: 3.3 Consensus size: 20
2284487 TATTATGTTA
2284497 ATTATATTTAAATATATTAT
1 ATTATATTTAAATATATTAT
*
2284517 ATTATATTT-ATTATATTATT
1 ATTATATTTAAATATATTA-T
*
2284537 TTTATATTTATTAAATATATTAT
1 ATTATA--T-TTAAATATATTAT
2284560 AATTATA
1 -ATTATA
2284567 ATATATTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
19 8 0.20
20 15 0.38
22 1 0.03
23 3 0.08
24 13 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTATATTTAAATATATTAT
Found at i:2284537 original size:32 final size:32
Alignment explanation
Indices: 2284466--2284533 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
2284456 TAATATATGA
2284466 TATATATTAAATATAATATATTATTATGTTAAT
1 TATAT-TTAAATATAATATATTATTATGTTAAT
*
2284499 TATATTTAAATATATTATATTA-TAT-TT-AT
1 TATATTTAAATATAATATATTATTATGTTAAT
2284528 TATATT
1 TATATT
2284534 ATTTTTATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
29 8 0.24
30 2 0.06
31 3 0.09
32 16 0.47
33 5 0.15
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (32 bp):
TATATTTAAATATAATATATTATTATGTTAAT
Found at i:2284557 original size:13 final size:13
Alignment explanation
Indices: 2284539--2284604 Score: 57
Period size: 13 Copynumber: 5.0 Consensus size: 13
2284529 ATATTATTTT
2284539 TATATTTATTAAA
1 TATATTTATTAAA
2284552 TATATTATAATTATAA
1 TATATT-T-ATTA-AA
*
2284568 TATATTT-TTGAA
1 TATATTTATTAAA
2284580 TA-A-TTATTTAAA
1 TATATTTA-TTAAA
*
2284592 TATATTAATTAAA
1 TATATTTATTAAA
2284605 ATTATTTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
10 2 0.05
11 1 0.02
12 10 0.23
13 14 0.33
14 3 0.07
15 5 0.12
16 8 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (13 bp):
TATATTTATTAAA
Found at i:2284566 original size:11 final size:11
Alignment explanation
Indices: 2284495--2284571 Score: 63
Period size: 10 Copynumber: 7.2 Consensus size: 11
2284485 ATTATTATGT
2284495 TAATTATATT-
1 TAATTATATTA
*
2284505 TAAATATATTA
1 TAATTATATTA
2284516 T-ATTATATT-
1 TAATTATATTA
2284525 T-ATTATATTA
1 TAATTATATTA
**
2284535 TTTTTATATTTA
1 TAATTATA-TTA
*
2284547 TTAAATATATTA
1 -TAATTATATTA
*
2284559 TAATTATAATA
1 TAATTATATTA
2284570 TA
1 TA
2284572 TTTTTGAATA
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
9 9 0.17
10 17 0.31
11 17 0.31
12 6 0.11
13 5 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TAATTATATTA
Found at i:2284574 original size:29 final size:29
Alignment explanation
Indices: 2284400--2284629 Score: 96
Period size: 29 Copynumber: 8.2 Consensus size: 29
2284390 TTTTTTTTTA
* * *
2284400 TTATT-AAT-TATTATAAATATAATAAAAA
1 TTATTAAATATATTATAATTATAAT-ATAT
* * *
2284428 TTATTAAAATATATTAAAATTTAAAAAATAAT
1 TTATT-AAATATATTATAA-TTATAATAT-AT
* * *
2284460 ATATGATATATATTA-AA-TATAATATA-
1 TTATTAAATATATTATAATTATAATATAT
** *
2284486 TTATTATGT-TAATTATATTTA-AATATAT
1 TTATTAAATAT-ATTATAATTATAATATAT
* * **
2284514 TATATTATATTTATTAT-ATTATTTTTATAT
1 T-TATTAAATATATTATAATTA-TAATATAT
2284544 TTATTAAATATATTATAATTATAATATAT
1 TTATTAAATATATTATAATTATAATATAT
*
2284573 TT-TTGAATA-ATTAT--TTA-AATATAT
1 TTATTAAATATATTATAATTATAATATAT
* *
2284597 TAATTAAA-ATTATTTTAAATT-TAATAT-T
1 TTATTAAATA-TATTAT-AATTATAATATAT
2284625 TTATT
1 TTATT
2284630 TTTTATTAAA
Statistics
Matches: 153, Mismatches: 28, Indels: 42
0.69 0.13 0.19
Matches are distributed among these distances:
24 9 0.06
25 8 0.05
26 14 0.09
27 13 0.08
28 28 0.18
29 40 0.26
30 16 0.10
31 17 0.11
32 8 0.05
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (29 bp):
TTATTAAATATATTATAATTATAATATAT
Found at i:2284588 original size:43 final size:44
Alignment explanation
Indices: 2284467--2284589 Score: 118
Period size: 41 Copynumber: 2.9 Consensus size: 44
2284457 AATATATGAT
*
2284467 ATATATTA-AA-TATAATATATTATTATG-TTAATTATAT-TTAA
1 ATATATTATAATTATAATATATTATT-TGATTAATTATTTATTAA
* **
2284508 ATATATTAT-ATTAT-ATTTATTATATT-ATTTTTATATTTATTAA
1 ATATATTATAATTATAATATATTAT-TTGATTAAT-TATTTATTAA
*
2284551 ATATATTATAATTATAATATATT-TTTGAATAATTATTTA
1 ATATATTATAATTATAATATATTATTTGATTAATTATTTA
2284590 AATATATTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
41 21 0.32
42 8 0.12
43 21 0.32
44 9 0.14
45 6 0.09
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (44 bp):
ATATATTATAATTATAATATATTATTTGATTAATTATTTATTAA
Found at i:2284998 original size:2 final size:2
Alignment explanation
Indices: 2284986--2285027 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
2284976 GCCAAAGATA
2284986 AG AG AG A- AG AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2285026 AG
1 AG
2285028 GGAAGGCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2288307 original size:2 final size:2
Alignment explanation
Indices: 2288300--2288336 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2288290 CTAATTTACT
2288300 TA TA TA 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 TA TA TA T
2288337 TTGAATAGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2289825 original size:2 final size:2
Alignment explanation
Indices: 2289818--2289843 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2289808 AGTAAAGGGG
2289818 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
2289844 ACCTGTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2293307 original size:67 final size:67
Alignment explanation
Indices: 2293168--2293300 Score: 248
Period size: 67 Copynumber: 2.0 Consensus size: 67
2293158 TAGCTACAGC
* *
2293168 ATTATTAATTATTCTATTTCCATGTCCAAACTAATGTCAATTTGTTGCCATATATTTATGTTATA
1 ATTATTAATTATCCTATTTCCATGTCCAAACTAATGTCAATTTGTTGCCATATATTTATGCTATA
2293233 CA
66 CA
2293235 ATTATTAATTATCCTATTTCCATGTCCAAACTAATGTCAATTTGTTGCCATATATTTATGCTATA
1 ATTATTAATTATCCTATTTCCATGTCCAAACTAATGTCAATTTGTTGCCATATATTTATGCTATA
2293300 C
66 C
2293301 GTTTATTTCT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.31, C:0.17, G:0.08, T:0.45
Consensus pattern (67 bp):
ATTATTAATTATCCTATTTCCATGTCCAAACTAATGTCAATTTGTTGCCATATATTTATGCTATA
CA
Found at i:2293769 original size:19 final size:19
Alignment explanation
Indices: 2293745--2293783 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2293735 AATAAAAAGT
2293745 GCTTCTTCTTACAACCTAA
1 GCTTCTTCTTACAACCTAA
2293764 GCTTCTTCTTACAACCTAA
1 GCTTCTTCTTACAACCTAA
2293783 G
1 G
2293784 GCACCCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.31, G:0.08, T:0.36
Consensus pattern (19 bp):
GCTTCTTCTTACAACCTAA
Found at i:2310653 original size:22 final size:22
Alignment explanation
Indices: 2310605--2310653 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
2310595 TTTATGTGTA
* * * *
2310605 AAATTTAAGTATTTTTAATATT
1 AAATTTAAATAATTTAAAAATT
*
2310627 TAATTTAAATAATTTAAAAATT
1 AAATTTAAATAATTTAAAAATT
2310649 AAATT
1 AAATT
2310654 AATTTTTTTA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
AAATTTAAATAATTTAAAAATT
Found at i:2311376 original size:13 final size:13
Alignment explanation
Indices: 2311358--2311382 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2311348 ATTTATCACA
2311358 GAAAAATAAAAAT
1 GAAAAATAAAAAT
2311371 GAAAAATAAAAA
1 GAAAAATAAAAA
2311383 ACTTATTGTT
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:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
GAAAAATAAAAAT
Found at i:2315924 original size:19 final size:20
Alignment explanation
Indices: 2315900--2315945 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 20
2315890 AATTAAGATC
2315900 TATTTATAATTGAATAA-TT
1 TATTTATAATTGAATAAGTT
*
2315919 TA-TT-TAATTTAATAAGTT
1 TATTTATAATTGAATAAGTT
2315937 TGATTTATA
1 T-ATTTATA
2315946 TTATATCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
17 10 0.45
18 5 0.23
19 3 0.14
20 2 0.09
21 2 0.09
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (20 bp):
TATTTATAATTGAATAAGTT
Found at i:2321198 original size:6 final size:6
Alignment explanation
Indices: 2321187--2321211 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2321177 GTGTACGTTG
2321187 CCCTGT CCCTGT CCCTGT CCCTGT C
1 CCCTGT CCCTGT CCCTGT CCCTGT C
2321212 TCTACAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.52, G:0.16, T:0.32
Consensus pattern (6 bp):
CCCTGT
Found at i:2321289 original size:2 final size:2
Alignment explanation
Indices: 2321282--2321311 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2321272 TTTCAAGGTA
2321282 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2321312 GAAGTGGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2323444 original size:23 final size:23
Alignment explanation
Indices: 2323396--2323445 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2323386 CCCTTAATTC
**
2323396 TTAACCTATATCTAATTATTCGT
1 TTAACCTATATCTAATTATTAAT
*
2323419 TTAACCTATGTCTAATT-TCTAAT
1 TTAACCTATATCTAATTAT-TAAT
2323442 TTAA
1 TTAA
2323446 AAAATATATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.32, C:0.16, G:0.04, T:0.48
Consensus pattern (23 bp):
TTAACCTATATCTAATTATTAAT
Found at i:2323793 original size:2 final size:2
Alignment explanation
Indices: 2323786--2323819 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2323776 AAATACTACA
* *
2323786 AT AT AT AT AC AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2323820 GTGTGCCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2325358 original size:21 final size:21
Alignment explanation
Indices: 2325334--2325384 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
2325324 GTAATTTTAG
*
2325334 TAATAAAACATATGA-TTTTTT
1 TAATAAAA-ATATAATTTTTTT
*
2325355 TAAT-CAAATATAATTTTTTT
1 TAATAAAAATATAATTTTTTT
2325375 TAAATAAAAA
1 T-AATAAAAA
2325385 ATATTATAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 5 0.21
20 9 0.38
21 7 0.29
22 3 0.12
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (21 bp):
TAATAAAAATATAATTTTTTT
Found at i:2325505 original size:22 final size:20
Alignment explanation
Indices: 2325477--2325519 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 20
2325467 ATTAATATGC
2325477 TTATTAATTTGTAATATTATTA
1 TTATTAATTT-TAA-ATTATTA
2325499 TTATTAATTTTAAATTATTA
1 TTATTAATTTTAAATTATTA
2325519 T
1 T
2325520 ATTTTGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.38
21 3 0.14
22 10 0.48
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTATTAATTTTAAATTATTA
Found at i:2325522 original size:22 final size:22
Alignment explanation
Indices: 2325463--2325522 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
2325453 CAAATTTTTA
* *
2325463 TTAAATTAATATGCTTATTAATT
1 TTAAATTATTAT-ATTATTAATT
2325486 TGT-AA-TATTATTATTATTAATT
1 T-TAAATTATTA-TATTATTAATT
2325508 TTAAATTATTATATT
1 TTAAATTATTATATT
2325523 TTGAAAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
21 1 0.03
22 20 0.65
23 9 0.29
24 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (22 bp):
TTAAATTATTATATTATTAATT
Found at i:2326085 original size:12 final size:12
Alignment explanation
Indices: 2326068--2326109 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
2326058 AATAATAATA
2326068 ATTTAATAAATT
1 ATTTAATAAATT
2326080 ATTTAA-AAA-T
1 ATTTAATAAATT
*
2326090 ATTTTAATAATTT
1 A-TTTAATAAATT
2326103 ATTTAAT
1 ATTTAAT
2326110 TTTAACAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 2 0.08
11 8 0.31
12 14 0.54
13 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTTAATAAATT
Found at i:2326095 original size:23 final size:23
Alignment explanation
Indices: 2326064--2326108 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2326054 GTAAAATAAT
2326064 AATAATTTAATAAATTATTTAAA
1 AATAATTTAATAAATTATTTAAA
* *
2326087 AATATTTTAATAATTTATTTAA
1 AATAATTTAATAAATTATTTAA
2326109 TTTTAACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AATAATTTAATAAATTATTTAAA
Found at i:2326101 original size:31 final size:29
Alignment explanation
Indices: 2326063--2326126 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
2326053 AGTAAAATAA
2326063 TAATAATTTAATAAATTATTTAAAAATATTT
1 TAATAATTTAATAAA-T-TTTAAAAATATTT
* * *
2326094 TAATAATTTATTTAATTTTAACAATATTT
1 TAATAATTTAATAAATTTTAAAAATATTT
2326123 TAAT
1 TAAT
2326127 TGAATTATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 16 0.53
30 1 0.03
31 13 0.43
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
TAATAATTTAATAAATTTTAAAAATATTT
Found at i:2329037 original size:22 final size:22
Alignment explanation
Indices: 2328999--2329043 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
2328989 TTAAAAAGTT
2328999 ATTTTTAATTAATATTTAAATA
1 ATTTTTAATTAATATTTAAATA
2329021 ATTTTATAATTAA-ATTTAAATA
1 ATTTT-TAATTAATATTTAAATA
2329043 A
1 A
2329044 ATATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTTTAATTAATATTTAAATA
Found at i:2329050 original size:23 final size:23
Alignment explanation
Indices: 2329004--2329050 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
2328994 AAGTTATTTT
*
2329004 TAATTAATATTTAAATAATTTTA
1 TAATTAATATTTAAATAATATTA
2329027 TAATTAA-ATTTAAATAAATATTA
1 TAATTAATATTTAAAT-AATATTA
2329050 T
1 T
2329051 TATTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATTAATATTTAAATAATATTA
Found at i:2329267 original size:22 final size:20
Alignment explanation
Indices: 2329242--2329290 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
2329232 TAAATTTTTT
2329242 TATTTTAGATTGATAAAAATAA
1 TATTTTAGA-T-ATAAAAATAA
*
2329264 TATTTT-TATATAAAAATAA
1 TATTTTAGATATAAAAATAA
2329283 TATATTTA
1 TAT-TTTA
2329291 TTTAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 13 0.54
20 4 0.17
21 1 0.04
22 6 0.25
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (20 bp):
TATTTTAGATATAAAAATAA
Found at i:2329302 original size:19 final size:19
Alignment explanation
Indices: 2329254--2329296 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
2329244 TTTTAGATTG
*
2329254 ATAAAAATAATATTTTTAT
1 ATAAAAATAATATATTTAT
2329273 ATAAAAATAATATATTTAT
1 ATAAAAATAATATATTTAT
*
2329292 TTAAA
1 ATAAA
2329297 TTTAATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAAAAATAATATATTTAT
Found at i:2329329 original size:9 final size:8
Alignment explanation
Indices: 2329300--2329325 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2329290 ATTTAAATTT
2329300 AATTATAA
1 AATTATAA
2329308 AATTATAA
1 AATTATAA
2329316 AATTATAA
1 AATTATAA
2329324 AA
1 AA
2329326 ATTAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AATTATAA
Found at i:2329400 original size:26 final size:26
Alignment explanation
Indices: 2329339--2329398 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
2329329 AATATAAAAT
*
2329339 AATTTTAATAAAATAATTAATATTTTA
1 AATTTAAAT-AAATAATTAATATTTTA
2329366 AATTTAAATAAATAAATTAA-A-TTTA
1 AATTTAAATAAAT-AATTAATATTTTA
2329391 AATTTAAA
1 AATTTAAA
2329399 ATTTTTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 12 0.39
26 5 0.16
27 14 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AATTTAAATAAATAATTAATATTTTA
Found at i:2332271 original size:19 final size:21
Alignment explanation
Indices: 2332224--2332275 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 21
2332214 TAATAAATAA
2332224 TTAATAATATTAA-AAAATTAT
1 TTAAT-ATATTAATAAAATTAT
2332245 TTAA-ATATTAATAAAA-T-T
1 TTAATATATTAATAAAATTAT
2332263 TTAATATA-TAATA
1 TTAATATATTAATA
2332276 TGAGGGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 10 0.34
19 11 0.38
20 4 0.14
21 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAATATATTAATAAAATTAT
Found at i:2344104 original size:20 final size:19
Alignment explanation
Indices: 2344048--2344105 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
2344038 TTTAATAAAA
*
2344048 AAAAATTAAT-TTTTAAATT
1 AAAAA-TAATATTTTATATT
2344067 AAAAA-AATATTTTATATATT
1 AAAAATAATA-TTT-TATATT
2344087 ATAAAATAATATTTTATAT
1 A-AAAATAATATTTTATAT
2344106 ACAAATGGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
17 3 0.09
19 8 0.24
20 11 0.33
21 7 0.21
22 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAAATAATATTTTATATT
Found at i:2344834 original size:11 final size:11
Alignment explanation
Indices: 2344804--2344839 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2344794 AACGTACGAT
2344804 TATAATATTT-
1 TATAATATTTA
2344814 TA-AA-ATTTA
1 TATAATATTTA
2344823 TATAATATTTA
1 TATAATATTTA
2344834 TATAAT
1 TATAAT
2344840 TTTTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
8 4 0.17
9 4 0.17
10 4 0.17
11 11 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TATAATATTTA
Found at i:2345014 original size:19 final size:19
Alignment explanation
Indices: 2344948--2345014 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
2344938 TTTTATTAAT
* *
2344948 TATAAAAAATTAAAATATA
1 TATAATAAATTAAAATTTA
*
2344967 -AT-ATAAAATAAAATTTAA
1 TATAATAAATTAAAATTT-A
* *
2344985 AATAATTAATTAAAATTTA
1 TATAATAAATTAAAATTTA
2345004 TATAATAAATT
1 TATAATAAATT
2345015 TATTGACACA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
17 11 0.29
18 3 0.08
19 12 0.32
20 12 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TATAATAAATTAAAATTTA
Found at i:2347749 original size:14 final size:14
Alignment explanation
Indices: 2347730--2347758 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2347720 TAAGAGCGCA
2347730 TGTCAGCATGTGTT
1 TGTCAGCATGTGTT
2347744 TGTCAGCATGTGTT
1 TGTCAGCATGTGTT
2347758 T
1 T
2347759 CTTCTTCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.28, T:0.45
Consensus pattern (14 bp):
TGTCAGCATGTGTT
Found at i:2352384 original size:2 final size:2
Alignment explanation
Indices: 2352377--2352417 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
2352367 ACAATATCAC
* *
2352377 AT AT AT AT AT AT AT AT TT AT AT AT TT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2352418 GTATTTCCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:2352835 original size:12 final size:13
Alignment explanation
Indices: 2352818--2352843 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2352808 TGGAATTTAT
2352818 AAAAAAATAAGGA
1 AAAAAAATAAGGA
2352831 AAAAAAATAAGGA
1 AAAAAAATAAGGA
2352844 TGGGTCTAAG
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:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (13 bp):
AAAAAAATAAGGA
Found at i:2353177 original size:13 final size:12
Alignment explanation
Indices: 2353165--2353198 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
2353155 CAAATATAAT
2353165 TTTAAAAATTAA
1 TTTAAAAATTAA
*
2353177 TTTAATAAAATAA
1 TTTAA-AAATTAA
2353190 TTTAAAAAT
1 TTTAAAAAT
2353199 AAAGATCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TTTAAAAATTAA
Found at i:2354140 original size:15 final size:15
Alignment explanation
Indices: 2354107--2354234 Score: 80
Period size: 16 Copynumber: 8.9 Consensus size: 15
2354097 AATGAGTTTG
2354107 AATTT-AAAAATTT-
1 AATTTAAAAAATTTA
2354120 -ATTTAAAAAATTTA
1 AATTTAAAAAATTTA
2354134 AATTT----AA-TT-
1 AATTTAAAAAATTTA
* *
2354143 AA-TCAAAAAATTTC
1 AATTTAAAAAATTTA
*
2354157 AATTTTAAAAATTTA
1 AATTTAAAAAATTTA
* *
2354172 AATTTTAAATAGTTTA
1 AA-TTTAAAAAATTTA
*
2354188 AA-TTAAAAATAATTA
1 AATTTAAAAA-ATTTA
2354203 GAATTTAAAAAAATTTA
1 -AATTT-AAAAAATTTA
2354220 AATTTAAAAGAATTT
1 AATTTAAAA-AATTT
2354235 GAACTCAAGA
Statistics
Matches: 88, Mismatches: 11, Indels: 29
0.69 0.09 0.23
Matches are distributed among these distances:
8 1 0.01
9 2 0.02
10 2 0.02
11 2 0.02
12 6 0.07
13 10 0.11
14 8 0.09
15 22 0.25
16 24 0.27
17 6 0.07
18 5 0.06
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (15 bp):
AATTTAAAAAATTTA
Found at i:2354189 original size:16 final size:15
Alignment explanation
Indices: 2354148--2354234 Score: 70
Period size: 15 Copynumber: 5.5 Consensus size: 15
2354138 TAATTAATCA
*
2354148 AAAAATTTCAATTTT
1 AAAAATTTAAATTTT
2354163 AAAAATTTAAATTTT
1 AAAAATTTAAATTTT
*
2354178 AAATAGTTTAAA--TT
1 AAA-AATTTAAATTTT
*
2354192 AAAAATAATTAGAATTTAA
1 AAAAAT--TTA-AATTT-T
*
2354211 AAAAATTTAAATTTA
1 AAAAATTTAAATTTT
2354226 AAAGAATTT
1 AAA-AATTT
2354235 GAACTCAAGA
Statistics
Matches: 60, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
13 2 0.03
14 5 0.08
15 24 0.40
16 19 0.32
17 3 0.05
18 1 0.02
19 6 0.10
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.40
Consensus pattern (15 bp):
AAAAATTTAAATTTT
Found at i:2354458 original size:22 final size:22
Alignment explanation
Indices: 2354433--2354480 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
2354423 ATATATGATG
*
2354433 AAATAAAAATTTATCAAAAAGT
1 AAATAAAAATTTATAAAAAAGT
* * *
2354455 AAATTATATTTTATAAAAAAGT
1 AAATAAAAATTTATAAAAAAGT
2354477 AAAT
1 AAAT
2354481 TAATCATGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (22 bp):
AAATAAAAATTTATAAAAAAGT
Found at i:2355773 original size:143 final size:143
Alignment explanation
Indices: 2355619--2355909 Score: 528
Period size: 143 Copynumber: 2.0 Consensus size: 143
2355609 AACTTGAACC
* *
2355619 TAAAAAAACTTAAACTTGAAAAGGTTTAAACCTAAAAAAGTTCGAACTCAAATAAACCATAACAC
1 TAAAAAAACTTAAACTTGAAAAGGTTTAAACCTAAAAAAGTTCAAACCCAAATAAACCATAACAC
2355684 GAAAAGACCAAACCCGAATAGATCTAAATCCTAATAAATCCGAATCTTAAAAAACTTAAACTCAA
66 GAAAAGACCAAACCCGAATAGATCTAAATCCTAATAAATCCGAATCTTAAAAAACTTAAACTCAA
2355749 AATAATATAAACA
131 AATAATATAAACA
*
2355762 TAAAAAAACTTAAACTTGAAAAGGTTTAAATCTAAAAAAGTTCAAACCCAAATAAACCATAACAC
1 TAAAAAAACTTAAACTTGAAAAGGTTTAAACCTAAAAAAGTTCAAACCCAAATAAACCATAACAC
* *
2355827 GAAAAGATCAAACCCGAATAGATCTAAATCTTAATAAATCCGAATCTTAAAAAACTTAAACTCAA
66 GAAAAGACCAAACCCGAATAGATCTAAATCCTAATAAATCCGAATCTTAAAAAACTTAAACTCAA
*
2355892 AATAATATAAATA
131 AATAATATAAACA
2355905 TAAAA
1 TAAAA
2355910 TGACCCGATA
Statistics
Matches: 142, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
143 142 1.00
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.22
Consensus pattern (143 bp):
TAAAAAAACTTAAACTTGAAAAGGTTTAAACCTAAAAAAGTTCAAACCCAAATAAACCATAACAC
GAAAAGACCAAACCCGAATAGATCTAAATCCTAATAAATCCGAATCTTAAAAAACTTAAACTCAA
AATAATATAAACA
Found at i:2355775 original size:16 final size:16
Alignment explanation
Indices: 2355732--2355777 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
2355722 TCCGAATCTT
2355732 AAAAAACTTAAACTCA
1 AAAAAACTTAAACTCA
*
2355748 AAATAA-TATAAACAT-A
1 AAAAAACT-TAAAC-TCA
2355764 AAAAAACTTAAACT
1 AAAAAACTTAAACT
2355778 TGAAAAGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
15 2 0.08
16 21 0.84
17 2 0.08
ACGTcount: A:0.65, C:0.13, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAAACTTAAACTCA
Found at i:2360294 original size:26 final size:27
Alignment explanation
Indices: 2360252--2360302 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
2360242 AACTTACTTA
*
2360252 TATATTTTTATTATTTTTATATTATAT
1 TATATTTTAATTATTTTTATATTATAT
*
2360279 TATATTTTAATT-TTTTTATCTTAT
1 TATATTTTAATTATTTTTATATTAT
2360303 TATCAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (27 bp):
TATATTTTAATTATTTTTATATTATAT
Found at i:2360303 original size:24 final size:26
Alignment explanation
Indices: 2360246--2360305 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 26
2360236 AATTTTAACT
*
2360246 TACTTA-TATATTTTTATTATTTTTA
1 TACTTATTATATTTTAATTATTTTTA
*
2360271 TATTATATTATATTTTAATT-TTTTTA
1 TACT-TATTATATTTTAATTATTTTTA
2360297 T-CTTATTAT
1 TACTTATTAT
2360306 CAAAATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 6 0.20
25 4 0.13
26 9 0.30
27 11 0.37
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.68
Consensus pattern (26 bp):
TACTTATTATATTTTAATTATTTTTA
Found at i:2360733 original size:2 final size:2
Alignment explanation
Indices: 2360726--2360755 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2360716 GACTATACTA
2360726 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
2360756 TTGCGATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2361456 original size:4 final size:4
Alignment explanation
Indices: 2361449--2361473 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2361439 AACAACTGCT
2361449 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
2361474 ACTAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:2361642 original size:20 final size:22
Alignment explanation
Indices: 2361608--2361651 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
2361598 ACTTAAATAC
*
2361608 TTTTAATTT-ATTTTTTTATAA
1 TTTTAATTTAATTTTTATATAA
2361629 TTTT-ATTTAATTTTTATATAA
1 TTTTAATTTAATTTTTATATAA
2361650 TT
1 TT
2361652 ATCTTAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTAATTTAATTTTTATATAA
Found at i:2366508 original size:16 final size:15
Alignment explanation
Indices: 2366467--2366509 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
2366457 ATAATAATAT
2366467 TTAAATTTTAAATTA
1 TTAAATTTTAAATTA
* *
2366482 TTAATAATTTATATTA
1 TTAA-ATTTTAAATTA
2366498 TATAAATTTTAA
1 T-TAAATTTTAA
2366510 CATAATTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
15 4 0.18
16 15 0.68
17 3 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAAATTTTAAATTA
Found at i:2366508 original size:32 final size:33
Alignment explanation
Indices: 2366468--2366531 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
2366458 TAATAATATT
*
2366468 TAAATTTTAA-ATTATTA-ATAATTTATATTATA
1 TAAATTTTAACATAATTATAT-ATTTATATTATA
*
2366500 TAAATTTTAACATAATTATATATTTTTATTAT
1 TAAATTTTAACATAATTATATATTTATATTAT
2366532 TTTTATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 10 0.36
33 16 0.57
34 2 0.07
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (33 bp):
TAAATTTTAACATAATTATATATTTATATTATA
Found at i:2366557 original size:24 final size:23
Alignment explanation
Indices: 2366514--2366559 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
2366504 TTTTAACATA
2366514 ATTATATATTTTTATTATTTTTAT
1 ATTATATATTTTTA-TATTTTTAT
2366538 ATTATATTATATTTTA-ATTTTT
1 ATTATA-TAT-TTTTATATTTTT
2366560 TTATCGTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
24 12 0.60
25 3 0.15
26 5 0.25
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTATATATTTTTATATTTTTAT
Found at i:2366803 original size:4 final size:4
Alignment explanation
Indices: 2366794--2366818 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2366784 TAAATATTAA
2366794 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
2366819 TTGAATGGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:2367876 original size:20 final size:22
Alignment explanation
Indices: 2367849--2367890 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2367839 TTAAATACTT
2367849 TTAATTT-ATTTTT-TATAATT
1 TTAATTTAATTTTTATATAATT
*
2367869 TTATTTTAATTTTTATATAATT
1 TTAATTTAATTTTTATATAATT
2367891 ATCTTAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 6 0.32
22 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TTAATTTAATTTTTATATAATT
Found at i:2367892 original size:20 final size:20
Alignment explanation
Indices: 2367856--2367899 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
2367846 CTTTTAATTT
*
2367856 ATTTTTTATAATTTTATTTTA
1 ATTTTTTATAA-TTTATCTTA
2367877 ATTTTTATATAA-TTATCTTA
1 ATTTTT-TATAATTTATCTTA
2367897 ATT
1 ATT
2367900 GAATTTGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.48
21 6 0.29
22 5 0.24
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTTTTTATAATTTATCTTA
Found at i:2374123 original size:28 final size:28
Alignment explanation
Indices: 2374068--2374124 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
2374058 ATTCAAAAAT
** * *
2374068 ATATATTGACTGGACTTTTTAATCTATA
1 ATATATTGACTGGACTGATAAATATATA
*
2374096 ATATATTGACTTGACTGATAAATATATA
1 ATATATTGACTGGACTGATAAATATATA
2374124 A
1 A
2374125 AATAAAAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.42
Consensus pattern (28 bp):
ATATATTGACTGGACTGATAAATATATA
Found at i:2374864 original size:20 final size:21
Alignment explanation
Indices: 2374827--2374870 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
2374817 GAAACATTTT
*
2374827 AACATTTTTTTTACCTTAAAAG
1 AACATTTTTGTTA-CTTAAAAG
2374849 AACATTTTTGTT-CTTAAAAG
1 AACATTTTTGTTACTTAAAAG
2374869 AA
1 AA
2374871 AGTTTTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
22 11 0.52
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (21 bp):
AACATTTTTGTTACTTAAAAG
Found at i:2376398 original size:14 final size:15
Alignment explanation
Indices: 2376358--2376402 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
2376348 TATATTTAAT
*
2376358 ATATTTTATAATAATA
1 ATATTTTATTAT-ATA
2376374 ATATTTATATTATATA
1 ATATTT-TATTATATA
2376390 AT-TTTTATTATAT
1 ATATTTTATTATAT
2376403 CATAATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 8 0.30
15 3 0.11
16 11 0.41
17 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATTTTATTATATA
Found at i:2378682 original size:21 final size:20
Alignment explanation
Indices: 2378657--2378702 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
2378647 ATTTATATTT
2378657 AATATATATAATTTTTTAAA
1 AATATATATAATTTTTTAAA
2378677 AA-ATATATAATTTTTTTAAA
1 AATATATATAA-TTTTTTAAA
2378697 AATATA
1 AATATA
2378703 AATTACCCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.33
20 13 0.54
21 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATATATATAATTTTTTAAA
Found at i:2378684 original size:19 final size:19
Alignment explanation
Indices: 2378660--2378706 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
2378650 TATATTTAAT
2378660 ATATATAATTTTTTAAAAA
1 ATATATAATTTTTTAAAAA
*
2378679 ATATATAATTTTTTTAAAA
1 ATATATAATTTTTTAAAAA
2378698 ATATA-AATT
1 ATATATAATT
2378707 ACCCGTATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATATAATTTTTTAAAAA
Found at i:2379899 original size:2 final size:2
Alignment explanation
Indices: 2379892--2379918 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2379882 CCTCCATGTC
2379892 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 A
2379919 AATTTGGACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2380623 original size:34 final size:34
Alignment explanation
Indices: 2380584--2380650 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
2380574 ATAAGTGAGA
* * *
2380584 GATTAAATTAGAAATAA-GATTTAATGAAAATTTT
1 GATTAAATTAAAAAAAACAATTT-ATGAAAATTTT
2380618 GATTAAATTAAAAAAAACAATTTATGAAAATTT
1 GATTAAATTAAAAAAAACAATTTATGAAAATTT
2380651 GAAAAGTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 25 0.86
35 4 0.14
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (34 bp):
GATTAAATTAAAAAAAACAATTTATGAAAATTTT
Found at i:2382010 original size:37 final size:37
Alignment explanation
Indices: 2381935--2382010 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
2381925 GTGGATTCAA
*
2381935 AATATTTTTATTCTAATTACTAATTAATAATAAAAAT
1 AATATTTTTATTCTAATTAATAATTAATAATAAAAAT
2381972 AATATTTTTATT-TAAATTTAATAA-T-ATAATAAATAAT
1 AATATTTTTATTCT-AA-TTAATAATTAATAATAAA-AAT
2382009 AA
1 AA
2382011 AATGAGTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
36 9 0.26
37 20 0.57
38 6 0.17
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (37 bp):
AATATTTTTATTCTAATTAATAATTAATAATAAAAAT
Found at i:2383209 original size:19 final size:19
Alignment explanation
Indices: 2383187--2383253 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
2383177 AACATGATTC
2383187 ATAAATATTATATAAATAA
1 ATAAATATTATATAAATAA
* *
2383206 ATAATTAAATTATAATAAAATAT
1 ATAA--ATATTAT-AT-AAATAA
* * *
2383229 ATAAATATAATATCAATAC
1 ATAAATATTATATAAATAA
2383248 ATAAAT
1 ATAAAT
2383254 TACCTTAATC
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
19 14 0.37
20 2 0.05
21 11 0.29
22 2 0.05
23 9 0.24
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAAATATTATATAAATAA
Found at i:2383214 original size:23 final size:22
Alignment explanation
Indices: 2383187--2383246 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 22
2383177 AACATGATTC
*
2383187 ATAAATATTATATAAATAAATAA
1 ATAAATATAATA-AAATAAATAA
* *
2383210 TTAAATTATAATAAAATATATAA
1 ATAAA-TATAATAAAATAAATAA
2383233 ATATAATATCAATA
1 ATA-AATAT-AATA
2383247 CATAAATTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
23 18 0.60
24 12 0.40
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
ATAAATATAATAAAATAAATAA
Found at i:2389132 original size:12 final size:12
Alignment explanation
Indices: 2389117--2389154 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
2389107 TTTTTAAAAT
2389117 TTTAAATTTAAA
1 TTTAAATTTAAA
2389129 TTTAAATTT-AA
1 TTTAAATTTAAA
*
2389140 TTTAATTTTATAA
1 TTTAAATTTA-AA
2389153 TT
1 TT
2389155 CGAATTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 10 0.43
12 9 0.39
13 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:2389143 original size:5 final size:6
Alignment explanation
Indices: 2389117--2389154 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
2389107 TTTTTAAAAT
*
2389117 TTTAAA TTTAAA TTTAAA TTT-AA TTTAAT TTTATAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA TT
2389155 CGAATTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 5 0.18
6 20 0.71
7 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:2389143 original size:17 final size:18
Alignment explanation
Indices: 2389121--2389154 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2389111 TAAAATTTTA
2389121 AATTTAAATTTA-AATTT
1 AATTTAAATTTATAATTT
*
2389138 AATTTAATTTTATAATT
1 AATTTAAATTTATAATT
2389155 CGAATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTTAAATTTATAATTT
Found at i:2389434 original size:17 final size:18
Alignment explanation
Indices: 2389395--2389435 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2389385 TTAATACGAT
*
2389395 TATTGAAAATATATTTTA
1 TATTAAAAATATATTTTA
2389413 TATTAAAAATA-ATTATTA
1 TATTAAAAATATATT-TTA
2389431 -ATTAA
1 TATTAA
2389436 TGTGATATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
TATTAAAAATATATTTTA
Found at i:2389711 original size:20 final size:22
Alignment explanation
Indices: 2389673--2389716 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
2389663 GAAATATTTT
*
2389673 AACATTTTTTTTACTTTAAAAG
1 AACATTTTTGTTACTTTAAAAG
2389695 AACATTTTTGTT-C-TTAAAAG
1 AACATTTTTGTTACTTTAAAAG
2389715 AA
1 AA
2389717 AGTTTTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
21 1 0.05
22 11 0.52
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (22 bp):
AACATTTTTGTTACTTTAAAAG
Found at i:2391349 original size:5 final size:5
Alignment explanation
Indices: 2391339--2391371 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
2391329 ATTAATACCA
2391339 ATATT ATATT ATATT ATATT ATA-T ATA-T ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT
2391372 TATAAATGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.30
5 19 0.70
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:2392606 original size:25 final size:24
Alignment explanation
Indices: 2392559--2392606 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2392549 TTAGATATAT
* *
2392559 TTTTAAAGAATATAAAATTATAAG
1 TTTTAAAAAATATAAAATCATAAG
*
2392583 TTTTAAAAAATATTAAATGCATAA
1 TTTTAAAAAATATAAAAT-CATAA
2392607 TATCTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (24 bp):
TTTTAAAAAATATAAAATCATAAG
Done.