Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 127 of 172
Found at i:42335525 original size:23 final size:23
Alignment explanation
Indices: 42335500--42335578 Score: 79
Period size: 23 Copynumber: 3.3 Consensus size: 23
42335490 AATATTCAAA
*
42335500 ATTTTAAAAATAATTTAAAAATA-
1 ATTTTAAAAAT-ATTTAAATATAG
* * *
42335523 ATTTTTAAAATTTTTAAATATAT
1 ATTTTAAAAATATTTAAATATAG
*
42335546 ATATTATAAAATATTTCAAATATAG
1 ATTTTA-AAAATATTT-AAATATAG
42335571 ATTTTAAA
1 ATTTTAAA
42335579 TTTTTTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
22 9 0.20
23 14 0.31
24 10 0.22
25 12 0.27
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (23 bp):
ATTTTAAAAATATTTAAATATAG
Found at i:42335604 original size:10 final size:9
Alignment explanation
Indices: 42335591--42335694 Score: 50
Period size: 10 Copynumber: 11.2 Consensus size: 9
42335581 TTTTAAAATT
42335591 AATAACAAAA
1 AATAA-AAAA
*
42335601 AATAAATAA
1 AATAAAAAA
*
42335610 AAT-AAATA
1 AATAAAAAA
* *
42335618 CA-AAATAA
1 AATAAAAAA
42335626 AATAAGAAAA
1 AATAA-AAAA
*
42335636 AATATAAAA
1 AATAAAAAA
**
42335645 CTTAAAAAA
1 AATAAAAAA
*
42335654 ATTAAAGAAA
1 AATAAA-AAA
* *
42335664 AAGACAAAA
1 AATAAAAAA
*
42335673 GATAATAAAA
1 AATAA-AAAA
42335683 AAGTAAAAAA
1 AA-TAAAAAA
42335693 AA
1 AA
42335695 AGTGAAAGAT
Statistics
Matches: 68, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
8 8 0.12
9 28 0.41
10 29 0.43
11 3 0.04
ACGTcount: A:0.76, C:0.04, G:0.05, T:0.15
Consensus pattern (9 bp):
AATAAAAAA
Found at i:42339407 original size:20 final size:20
Alignment explanation
Indices: 42339382--42339425 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
42339372 TAAGATACGG
42339382 TGAAGG-AAAAGAAATAACTT
1 TGAAGGTAAAAGAAATAA-TT
**
42339402 TGAAGGTAAAATTAATAATT
1 TGAAGGTAAAAGAAATAATT
42339422 TGAA
1 TGAA
42339426 TTCATTTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.52, C:0.02, G:0.18, T:0.27
Consensus pattern (20 bp):
TGAAGGTAAAAGAAATAATT
Found at i:42340204 original size:31 final size:31
Alignment explanation
Indices: 42340160--42340218 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
42340150 AATTTGGACC
*
42340160 AAAATAAATTTTAAGTGCTGAAGTGAATCTT
1 AAAATAAAGTTTAAGTGCTGAAGTGAATCTT
* * *
42340191 AAAATTAAGTTTAAGTGCTTAATTGAAT
1 AAAATAAAGTTTAAGTGCTGAAGTGAAT
42340219 AAAAAATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.37
Consensus pattern (31 bp):
AAAATAAAGTTTAAGTGCTGAAGTGAATCTT
Found at i:42344838 original size:18 final size:19
Alignment explanation
Indices: 42344811--42344860 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
42344801 TTTATTACAT
*
42344811 TTTA-TTTTTGTTTT-TAG
1 TTTATTTTTTGTTTTCTAA
42344828 TTTATTTTTTGTTTTCTAA
1 TTTATTTTTTGTTTTCTAA
42344847 TTT-TTCTTTTGTTT
1 TTTATT-TTTTGTTT
42344861 GCTTTTGGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 4 0.14
18 12 0.41
19 13 0.45
ACGTcount: A:0.10, C:0.04, G:0.08, T:0.78
Consensus pattern (19 bp):
TTTATTTTTTGTTTTCTAA
Found at i:42349922 original size:22 final size:21
Alignment explanation
Indices: 42349897--42349939 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
42349887 CATTATTAAC
*
42349897 ATAATGAATTTTAATTAATTTT
1 ATAATAAATTTTAATT-ATTTT
*
42349919 ATAATAAATTTTGATTATTTT
1 ATAATAAATTTTAATTATTTT
42349940 CGACAGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
ATAATAAATTTTAATTATTTT
Found at i:42352294 original size:19 final size:18
Alignment explanation
Indices: 42352270--42352315 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
42352260 TTTGTTTTAC
*
42352270 TTTCTTTTTATTTTTTATT
1 TTTCTTTTTA-TGTTTATT
42352289 TTTCTTTTTATGTTTATT
1 TTTCTTTTTATGTTTATT
*
42352307 TTTATTTTT
1 TTTCTTTTT
42352316 TTAGACTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.83
Consensus pattern (18 bp):
TTTCTTTTTATGTTTATT
Found at i:42352316 original size:7 final size:6
Alignment explanation
Indices: 42352274--42352315 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
42352264 TTTTACTTTC
* *
42352274 TTTTTA TTTTTTA TTTTTC TTTTTA TGTTTA TTTTTA TTTTT
1 TTTTTA -TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
42352316 TTAGACTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:42352351 original size:25 final size:25
Alignment explanation
Indices: 42352305--42352352 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
42352295 TTTATGTTTA
* *
42352305 TTTTTATTTTTTTAGACTTATTTCT
1 TTTTTATCTTTTGAGACTTATTTCT
42352330 TTTTTATCTTTTGA-ACTATATTT
1 TTTTTATCTTTTGAGACT-TATTT
42352353 AATTTTATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.19, C:0.08, G:0.04, T:0.69
Consensus pattern (25 bp):
TTTTTATCTTTTGAGACTTATTTCT
Found at i:42352358 original size:25 final size:25
Alignment explanation
Indices: 42352304--42352358 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
42352294 TTTTATGTTT
* * *
42352304 ATTTTTATTTTTTTAGACTTATTTC
1 ATTTTTATCTTTTGAGACTTATTTA
*
42352329 TTTTTTATCTTTTGA-ACTATATTTA
1 ATTTTTATCTTTTGAGACT-TATTTA
42352354 ATTTT
1 ATTTT
42352359 ATGTTTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (25 bp):
ATTTTTATCTTTTGAGACTTATTTA
Found at i:42355993 original size:25 final size:25
Alignment explanation
Indices: 42355909--42355985 Score: 136
Period size: 25 Copynumber: 3.1 Consensus size: 25
42355899 GAAAGCTNGT
42355909 TCATGTGAGCTGTATAACGGGAAGC
1 TCATGTGAGCTGTATAACGGGAAGC
*
42355934 TCATGTGAGCTATATAACGGGAAGC
1 TCATGTGAGCTGTATAACGGGAAGC
*
42355959 TCATGTGAGCTGTATAACAGGAAGC
1 TCATGTGAGCTGTATAACGGGAAGC
42355984 TC
1 TC
42355986 TTGCGAGCCA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.25
Consensus pattern (25 bp):
TCATGTGAGCTGTATAACGGGAAGC
Found at i:42356007 original size:25 final size:25
Alignment explanation
Indices: 42355979--42356101 Score: 106
Period size: 25 Copynumber: 4.9 Consensus size: 25
42355969 TGTATAACAG
*
42355979 GAAGCTCTTGCGAGCCAAATATCGA
1 GAAGCTCTTGAGAGCCAAATATCGA
** * *
42356004 GAAGCTCAAGAGAGCC-ATTAATCGG
1 GAAGCTCTTGAGAGCCAAAT-ATCGA
* * * *
42356029 GAAGCTCGTGAAAGCTAAATAAT-GG
1 GAAGCTCTTGAGAGCCAAAT-ATCGA
* * *
42356054 GAAACTCTTAAGAGCCAAGTATCGA
1 GAAGCTCTTGAGAGCCAAATATCGA
42356079 GAAGCTCTTGAGAGCCAAATATC
1 GAAGCTCTTGAGAGCCAAATATC
42356102 AGGACGCTTA
Statistics
Matches: 75, Mismatches: 20, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
24 4 0.05
25 66 0.88
26 5 0.07
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (25 bp):
GAAGCTCTTGAGAGCCAAATATCGA
Found at i:42356008 original size:50 final size:50
Alignment explanation
Indices: 42355909--42356011 Score: 143
Period size: 50 Copynumber: 2.1 Consensus size: 50
42355899 GAAAGCTNGT
* * * * *
42355909 TCATGTGAGCTGTATAACGGGAAGCTCATGTGAGCTATATAACGGGAAGC
1 TCATGTGAGCTGTATAACAGGAAGCTCATGCGAGCCAAATAACGAGAAGC
* *
42355959 TCATGTGAGCTGTATAACAGGAAGCTCTTGCGAGCCAAATATCGAGAAGC
1 TCATGTGAGCTGTATAACAGGAAGCTCATGCGAGCCAAATAACGAGAAGC
42356009 TCA
1 TCA
42356012 AGAGAGCCAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.23
Consensus pattern (50 bp):
TCATGTGAGCTGTATAACAGGAAGCTCATGCGAGCCAAATAACGAGAAGC
Found at i:42362569 original size:31 final size:30
Alignment explanation
Indices: 42362534--42362610 Score: 73
Period size: 31 Copynumber: 2.5 Consensus size: 30
42362524 GTTAAAGATA
42362534 AAATTGATACTCGAATTTATTTATTTCTCCT
1 AAATTGATACTCGAATTT-TTTATTTCTCCT
* * * * * *
42362565 AAATTGGTACTTGTGATTTTTTTTTTGTTCT
1 AAATTGATACTCG-AATTTTTTATTTCTCCT
*
42362596 AGATTGATACTCGAA
1 AAATTGATACTCGAA
42362611 CTTGTATTAG
Statistics
Matches: 35, Mismatches: 10, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.86
32 4 0.11
ACGTcount: A:0.26, C:0.12, G:0.13, T:0.49
Consensus pattern (30 bp):
AAATTGATACTCGAATTTTTTATTTCTCCT
Found at i:42363098 original size:191 final size:193
Alignment explanation
Indices: 42362739--42363114 Score: 477
Period size: 192 Copynumber: 2.0 Consensus size: 193
42362729 GAAAAATAAT
* ** * * *
42362739 GAGGTATAAGAGGACGTCACGTGGCAGTGTGCGATTAGCTAGCACTGCCACGTCAGCAAAAAAAT
1 GAGGTATAAGAGGACGTCACGCGGCAGCATGCGATTAGCTAACAATACCACGTCAGC-AAAAAAT
* ** ** * **
42362804 TAACGTTCTTAGTCTCAGGTATCAATATAGTGGACAAAAAAAAGTTTGGGTATCAATCTGGGAAA
65 TAACGTTCTTAGTCTCAAGTATCAATATAGCAGACAAAAAAAAGTTTGAATATAAATCTGAAAAA
* * * *
42362869 AAAAATCATAAGTATCAATTTGGGAGAAATGGACAAATTCGAGTACCAATTTTATTAAGAAAAG
130 AAAAACCATAAGTATAAATTTGGGAGAAATGAACAAATTCGAATACCAATTTTATTAAGAAAAG
* * *
42362933 GAGGTATAAGAGGACGTCACGCGGCGGCATGTGATTGGCTAACAATACCACGTCAGC-AAAAATT
1 GAGGTATAAGAGGACGTCACGCGGCAGCATGCGATTAGCTAACAATACCACGTCAGCAAAAAATT
* * * * *
42362997 AACGTTGTTAGTCTTAAGTATCGATATAGCAGACAGAAAAAATTTTGAATATAAATCT-AAAAAA
66 AACGTTCTTAGTCTCAAGTATCAATATAGCAGACAAAAAAAAGTTTGAATATAAATCTGAAAAAA
* *
42363061 AAAACCATAAGTATAAATTTGGGAGAAGTGAACAAATTCGAATACTAATTTTAT
131 AAAACCATAAGTATAAATTTGGGAGAAATGAACAAATTCGAATACCAATTTTAT
42363115 ATTTAACCCT
Statistics
Matches: 154, Mismatches: 28, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
191 52 0.34
192 54 0.35
194 48 0.31
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (193 bp):
GAGGTATAAGAGGACGTCACGCGGCAGCATGCGATTAGCTAACAATACCACGTCAGCAAAAAATT
AACGTTCTTAGTCTCAAGTATCAATATAGCAGACAAAAAAAAGTTTGAATATAAATCTGAAAAAA
AAAACCATAAGTATAAATTTGGGAGAAATGAACAAATTCGAATACCAATTTTATTAAGAAAAG
Found at i:42367382 original size:20 final size:20
Alignment explanation
Indices: 42367357--42367399 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
42367347 AAAATTATAC
42367357 TTTTAAAACTA-ATTTAATTT
1 TTTTAAAA-TATATTTAATTT
*
42367377 TTTTAAAATATTTTTAATTT
1 TTTTAAAATATATTTAATTT
42367397 TTT
1 TTT
42367400 AATTTATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTAAAATATATTTAATTT
Found at i:42369988 original size:23 final size:23
Alignment explanation
Indices: 42369961--42370005 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
42369951 CCCGTTACAT
*
42369961 GGCTCTTTGTGAGCTTCCTGATA
1 GGCTCTTCGTGAGCTTCCTGATA
42369984 GGCTCTTCGTGAGCTTCCTGAT
1 GGCTCTTCGTGAGCTTCCTGAT
42370006 TAAAAGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.27, T:0.38
Consensus pattern (23 bp):
GGCTCTTCGTGAGCTTCCTGATA
Found at i:42370098 original size:23 final size:26
Alignment explanation
Indices: 42370070--42370127 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
42370060 AGCCCGGATA
42370070 AGCTTCCTGA-TAA-G-CTCTTTGTG
1 AGCTTCCTGATTAATGACTCTTTGTG
*
42370093 AGCTTCCCGATTAATGACTCTTTGTG
1 AGCTTCCTGATTAATGACTCTTTGTG
42370119 AGCTTCCTG
1 AGCTTCCTG
42370128 TTATATGGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 9 0.30
24 3 0.10
25 1 0.03
26 17 0.57
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (26 bp):
AGCTTCCTGATTAATGACTCTTTGTG
Found at i:42376240 original size:21 final size:21
Alignment explanation
Indices: 42376181--42376241 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
42376171 GATTATATGA
* * *
42376181 ATTGGATTGAATATTGATTAT
1 ATTGAATTGATTATTGAATAT
42376202 ATTGAATTGATT-TATGAATAT
1 ATTGAATTGATTAT-TGAATAT
42376223 ATGTGAATTG-TTATTGAAT
1 AT-TGAATTGATTATTGAAT
42376242 TGAAATTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.03
21 25 0.74
22 8 0.24
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (21 bp):
ATTGAATTGATTATTGAATAT
Found at i:42377019 original size:45 final size:45
Alignment explanation
Indices: 42376955--42377149 Score: 300
Period size: 45 Copynumber: 4.3 Consensus size: 45
42376945 CTGTTACCGC
*
42376955 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATTTTGT
1 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* *
42377000 TACTGCTACTATTACCGATTCGACACTTTGTGTGTCGAATATTGT
1 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
*
42377045 TACTGCTACTGTTACCGATTCGGCACTGTGTGTGTCGAATATTGT
1 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* * * * *
42377090 TACTGTTACCGTTACCGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
*
42377135 TACTGTTACTGTTAC
1 TACTGCTACTGTTAC
42377150 TATTACTGTT
Statistics
Matches: 137, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 137 1.00
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.41
Consensus pattern (45 bp):
TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
Found at i:42377140 original size:6 final size:6
Alignment explanation
Indices: 42377129--42377171 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
42377119 GTGTGTTGAA
*
42377129 TACTGT TACTGT TACTGT TACTAT TACTGT TACTGT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT T
42377172 CCGGATTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.51
Consensus pattern (6 bp):
TACTGT
Found at i:42377358 original size:18 final size:18
Alignment explanation
Indices: 42377335--42377617 Score: 189
Period size: 18 Copynumber: 15.3 Consensus size: 18
42377325 AAAGGTATAA
*
42377335 AATAATTGATTATTACTG
1 AATAATTGATTGTTACTG
42377353 AATAATTGATTGTTACTG
1 AATAATTGATTGTTACTG
* *
42377371 GATAATTGACTGTTACT-
1 AATAATTGATTGTTACTG
*
42377388 AGAT-ATTAGACTGTTACTG
1 A-ATAATT-GATTGTTACTG
* * *
42377407 AATAACTGAATATTACTG
1 AATAATTGATTGTTACTG
**
42377425 AATAATTGATCATTACTG
1 AATAATTGATTGTTACTG
* *
42377443 AATAACTGATTGTCACTG
1 AATAATTGATTGTTACTG
* *
42377461 AATGAA-TGACTGCTACTG
1 AAT-AATTGATTGTTACTG
* *
42377479 AATAACTTAATAGTTACTG
1 AATAA-TTGATTGTTACTG
42377498 AAT-ATCTGATT-TTACTG
1 AATAAT-TGATTGTTACTG
*
42377515 AATAATTGACTGTTACTGG
1 AATAATTGATTGTTACT-G
* *
42377534 ATAACCGATCAATTGATCGATACTG
1 ---A---AT-AATTGATTGTTACTG
* * * *
42377559 AATAACTGGTTATTATTG
1 AATAATTGATTGTTACTG
*
42377577 AATAATTGATTGTTACCG
1 AATAATTGATTGTTACTG
* *
42377595 AATAACTGACTGTTACTG
1 AATAATTGATTGTTACTG
42377613 AATAA
1 AATAA
42377618 ATAATTATTC
Statistics
Matches: 206, Mismatches: 41, Indels: 36
0.73 0.14 0.13
Matches are distributed among these distances:
17 19 0.09
18 152 0.74
19 19 0.09
22 2 0.01
25 3 0.01
26 11 0.05
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
AATAATTGATTGTTACTG
Found at i:42381888 original size:317 final size:320
Alignment explanation
Indices: 42381294--42381976 Score: 848
Period size: 317 Copynumber: 2.1 Consensus size: 320
42381284 CAACGGTTTT
*
42381294 CTAATAGGG-AGGCTTTATGCTTATTCGATAATTGTGGCATTGCCAACGTTGTCCATGTAGGTTG
1 CTAATAGGGCA-GCTTTATGCTTATTCGATAATTGTGGCATTGCCAACGTTGTCCATGTAGGTTC
* *
42381358 TTACATTTTATTAAAGAGAGAACATATATTCAGTAATGGAGTCCTTCTGTGGTGGGGGAAGGGCA
65 TTACATTTTATTAAAGAAAGAACATATATTCAGTAATGGAGTCCTTCTATGGTGGGGGAAGGGCA
* * * *
42381423 AGGGCAGTCTACTCGTTGTCAGGTTGCAATAAGAAATGAAAACTAGTCATTGGAGGGAACACAAG
130 AGGGCAGTCTACTCCTTGTCAGGTTGAAACAAGAAACGAAAACTAGTCATTGGAGGGAACACAAG
** * * *
42381488 GCTAGAGGAGAGTGGCTTTGCATACGAGCCTTACTCTATAGGCTCATCAGAGTGCTACAGCTAGC
195 GCTAGAGGAGAGTGGCTTCACATAAGAGCCTTACTCTATAGGCACATCAGAGTGCTACAACTAGC
* *
42381553 ACTTTGAAGCCCGCTGAAAAACAGATG--TGCTCTACTAGCGCGCAATGG-TTTGAAGCTTTG
260 ACTTTGAAGCCAGCTGAAAAACAGATGCTTG--CTACTAGCGCGCAATGGTTTTCAAGCTTTG
* * * *** * ** *
42381613 CTGATAGGGCAGCTTTATGCTTATTCAATAATTGTGGTATTGCCTTGGATTTTCTGTTTAGGTTC
1 CTAATAGGGCAGCTTTATGCTTATTCGATAATTGTGGCATTGCCAACG-TTGTCCATGTAGGTTC
*
42381678 TTACATTTTATTAAATAAAGAACATATATTCAGTAATGGAGTCCTTAC-ATGGTGGGGGAAGGGC
65 TTACATTTTATTAAAGAAAGAACATATATTCAGTAATGGAGTCCTT-CTATGGTGGGGGAAGGGC
** * * *
42381742 AAGGGCAG-C-A-TCCTTGTTGGGTTGAAACAAGAAACGGAAACTAGTCGTTGGAGGGAACACGA
129 AAGGGCAGTCTACTCCTTGTCAGGTTGAAACAAGAAACGAAAACTAGTCATTGGAGGGAACACAA
* * * * *
42381804 GGCTTGTGGA-ATGTGG-TTCCACATAAGAGCCTTACTCTATAGTG-ACGTTAGTGTGCTACAAC
194 GGCTAGAGGAGA-GTGGCTT-CACATAAGAGCCTTACTCTATAG-GCACATCAGAGTGCTACAAC
* * * *
42381866 TAGCACTTTGAAGCCAGCTGAAAAACTGATGCTTGCTATTGGTGCGCAATGGTTTTCAAGCTTTG
256 TAGCACTTTGAAGCCAGCTGAAAAACAGATGCTTGCTACTAGCGCGCAATGGTTTTCAAGCTTTG
*
42381931 CTAATAGGGCAGCTTTATTGCTTATTCGATAATTGTGCCATTGCCA
1 CTAATAGGGCAGCTTTA-TGCTTATTCGATAATTGTGGCATTGCCA
42381977 GCATTTTCCA
Statistics
Matches: 310, Mismatches: 44, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
316 3 0.01
317 131 0.42
318 29 0.09
319 67 0.22
320 79 0.25
321 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (320 bp):
CTAATAGGGCAGCTTTATGCTTATTCGATAATTGTGGCATTGCCAACGTTGTCCATGTAGGTTCT
TACATTTTATTAAAGAAAGAACATATATTCAGTAATGGAGTCCTTCTATGGTGGGGGAAGGGCAA
GGGCAGTCTACTCCTTGTCAGGTTGAAACAAGAAACGAAAACTAGTCATTGGAGGGAACACAAGG
CTAGAGGAGAGTGGCTTCACATAAGAGCCTTACTCTATAGGCACATCAGAGTGCTACAACTAGCA
CTTTGAAGCCAGCTGAAAAACAGATGCTTGCTACTAGCGCGCAATGGTTTTCAAGCTTTG
Found at i:42384202 original size:14 final size:15
Alignment explanation
Indices: 42384183--42384211 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42384173 GATTTGCAAC
42384183 AGTTAAATT-TATTA
1 AGTTAAATTATATTA
42384197 AGTTAAATTATATTA
1 AGTTAAATTATATTA
42384212 TTTTCAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
AGTTAAATTATATTA
Found at i:42387829 original size:28 final size:28
Alignment explanation
Indices: 42387782--42387835 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
42387772 AGTCTCTTCA
*
42387782 TGTTAAAAATTCTATTCATTTAATTATC
1 TGTTAAAAATTCTATCCATTTAATTATC
*
42387810 TGTTAAAAATT-TCATCCATTTTATTA
1 TGTTAAAAATTCT-ATCCATTTAATTA
42387836 GAATTAATCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 22 0.96
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.50
Consensus pattern (28 bp):
TGTTAAAAATTCTATCCATTTAATTATC
Found at i:42392117 original size:14 final size:13
Alignment explanation
Indices: 42392095--42392125 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
42392085 AGTTTGGCAA
42392095 TTTTTTATTTTAT
1 TTTTTTATTTTAT
42392108 TTTTTATATTTTAT
1 TTTTT-TATTTTAT
42392122 TTTT
1 TTTT
42392126 ATACAAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTATTTTAT
Found at i:42392124 original size:13 final size:13
Alignment explanation
Indices: 42392094--42392128 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
42392084 AAGTTTGGCA
42392094 ATTTTT-TATTTT
1 ATTTTTATATTTT
42392106 ATTTTTTATATTTT
1 A-TTTTTATATTTT
42392120 ATTTTTATA
1 ATTTTTATA
42392129 CAAAGATACC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.05
13 13 0.62
14 7 0.33
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTTTTATATTTT
Found at i:42393754 original size:24 final size:24
Alignment explanation
Indices: 42393706--42393767 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
42393696 ACCTATTTGT
* *
42393706 TTGAACCGTTATATCAATCATTTC
1 TTGAACCATTATATCAATCAGTTC
* *
42393730 TTGAACCATTATATCGATTAGTTC
1 TTGAACCATTATATCAATCAGTTC
* *
42393754 TTGGACTATTATAT
1 TTGAACCATTATAT
42393768 TGATCAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (24 bp):
TTGAACCATTATATCAATCAGTTC
Found at i:42397286 original size:31 final size:31
Alignment explanation
Indices: 42397251--42397313 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
42397241 TTCATGGAGC
*
42397251 TAAGGTCCAAAATATGGAAGAAACAGGTGTT
1 TAAGGTCCAAAATATAGAAGAAACAGGTGTT
42397282 TAAGGTCCAAAATATAGAAGAAACAGGTGTT
1 TAAGGTCCAAAATATAGAAGAAACAGGTGTT
42397313 T
1 T
42397314 CCACAACTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.10, G:0.24, T:0.24
Consensus pattern (31 bp):
TAAGGTCCAAAATATAGAAGAAACAGGTGTT
Found at i:42407622 original size:8 final size:8
Alignment explanation
Indices: 42407609--42407640 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
42407599 TAAATTTGAC
42407609 TTTTTTTA
1 TTTTTTTA
42407617 TTTTTTTA
1 TTTTTTTA
42407625 TTTTTTTA
1 TTTTTTTA
42407633 TTTTTTTA
1 TTTTTTTA
42407641 AGTTTGAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTA
Found at i:42409542 original size:32 final size:32
Alignment explanation
Indices: 42409506--42409624 Score: 154
Period size: 32 Copynumber: 3.8 Consensus size: 32
42409496 AAATGAGTGG
42409506 TTTTGTGAAATGATAACAAATATCAACTTTCA
1 TTTTGTGAAATGATAACAAATATCAACTTTCA
*
42409538 TTTTGTGAAATGCTAACAAAT-TACAAC-TTCAA
1 TTTTGTGAAATGATAACAAATAT-CAACTTTC-A
* *
42409570 TTTTGTAAAATGATAACAAATATCAACTTTAA
1 TTTTGTGAAATGATAACAAATATCAACTTTCA
* *
42409602 TTTTGTTAAATGATGAC-AATATC
1 TTTTGTGAAATGATAACAAATATC
42409625 CCTCTGAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
31 10 0.13
32 64 0.83
33 3 0.04
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (32 bp):
TTTTGTGAAATGATAACAAATATCAACTTTCA
Found at i:42412605 original size:42 final size:42
Alignment explanation
Indices: 42412541--42412622 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
42412531 TTTTTGAGGC
*
42412541 TTTTCATAACTCAACATCAAAGACGAAGTGTTTTCTCAAAAT
1 TTTTCATAACTCAACATCAAAGACCAAGTGTTTTCTCAAAAT
* *
42412583 TTTTCATAATTCAACATGAAAGACCAAGTGTTTTCTCAAA
1 TTTTCATAACTCAACATCAAAGACCAAGTGTTTTCTCAAA
42412623 TGATTTTGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (42 bp):
TTTTCATAACTCAACATCAAAGACCAAGTGTTTTCTCAAAAT
Found at i:42413911 original size:30 final size:30
Alignment explanation
Indices: 42413877--42413939 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
42413867 ACTTATTTTA
42413877 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
42413907 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
42413937 TTG
1 TTG
42413940 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.03, G:0.16, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:42413952 original size:30 final size:30
Alignment explanation
Indices: 42413877--42413956 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
42413867 ACTTATTTTA
**
42413877 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTAAGTTATTATTTTAAAGGCAT
** *
42413907 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTAAGTTATTATTTTAAAGGCAT
*
42413937 TTGCTT-GTTAAGTTA-TATTT
1 TTG-TTAATTAAGTTATTATTT
42413957 ATCTTAGTGT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 5 0.11
30 38 0.84
31 2 0.04
ACGTcount: A:0.24, C:0.04, G:0.15, T:0.57
Consensus pattern (30 bp):
TTGTTAATTAAGTTATTATTTTAAAGGCAT
Found at i:42414076 original size:11 final size:11
Alignment explanation
Indices: 42414060--42414089 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
42414050 TATATATATT
42414060 TAAAAATTATA
1 TAAAAATTATA
*
42414071 TAAAAATAATA
1 TAAAAATTATA
42414082 TAAAAATT
1 TAAAAATT
42414090 TAATACGGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:42416531 original size:12 final size:12
Alignment explanation
Indices: 42416514--42416548 Score: 63
Period size: 11 Copynumber: 3.0 Consensus size: 12
42416504 TGTTCATAAT
42416514 TTTAATATTAAA
1 TTTAATATTAAA
42416526 TTTAATATT-AA
1 TTTAATATTAAA
42416537 TTTAATATTAAA
1 TTTAATATTAAA
42416549 GTGATTATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:42427276 original size:43 final size:44
Alignment explanation
Indices: 42427229--42427311 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
42427219 TCTTTCTATT
* *
42427229 ATTATTAGGTATCTTATT-TATTTCTTTATTGTTTATTATTATG
1 ATTATTAGGTATCTTATTCTATTTATTTACTGTTTATTATTATG
* * *
42427272 ATTATTAGTTATTTTATTCTCTTTATTTACTGTTTATTAT
1 ATTATTAGGTATCTTATTCTATTTATTTACTGTTTATTAT
42427312 CTATTTTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
43 16 0.47
44 18 0.53
ACGTcount: A:0.23, C:0.06, G:0.07, T:0.64
Consensus pattern (44 bp):
ATTATTAGGTATCTTATTCTATTTATTTACTGTTTATTATTATG
Found at i:42430015 original size:20 final size:21
Alignment explanation
Indices: 42429972--42430017 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
42429962 ACTGTTTTGT
42429972 TATGGG-CCAACTGTATTGAA
1 TATGGGCCCAACTGTATTGAA
*
42429992 -ATGGGCCCAACTGTGTT-AA
1 TATGGGCCCAACTGTATTGAA
42430011 TATGGGC
1 TATGGGC
42430018 AAGGCCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGGGCCCAACTGTATTGAA
Found at i:42436633 original size:29 final size:30
Alignment explanation
Indices: 42436600--42436659 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
42436590 TTCGATCCAA
*
42436600 TGTGTAATGTTACACAT-TAACTTTGATTT
1 TGTGTAATGTTACACATGAAACTTTGATTT
* * *
42436629 TGTGTAATTTTATACATGAAATTTTGATTT
1 TGTGTAATGTTACACATGAAACTTTGATTT
42436659 T
1 T
42436660 ATTCAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.52
Consensus pattern (30 bp):
TGTGTAATGTTACACATGAAACTTTGATTT
Found at i:42438997 original size:14 final size:14
Alignment explanation
Indices: 42438961--42439003 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
42438951 ACTAAAAAAC
*
42438961 AAATTCAAGAATAAAA
1 AAATTCAA-AAT-TAA
42438977 AAATTCAAAATTAA
1 AAATTCAAAATTAA
*
42438991 AATTTCAAAATTA
1 AAATTCAAAATTA
42439004 GATAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 14 0.56
15 3 0.12
16 8 0.32
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (14 bp):
AAATTCAAAATTAA
Found at i:42439072 original size:31 final size:31
Alignment explanation
Indices: 42439033--42439101 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
42439023 AATTAAAAGG
* * *
42439033 TGAA-AGATCGATTGAATAAACAAATGGATA
1 TGAATAGATCAATCGAATAAACAAATAGATA
42439063 TGAATAGATCAATCGAATAAACAAATAGATA
1 TGAATAGATCAATCGAATAAACAAATAGATA
42439094 TGAATAGA
1 TGAATAGA
42439102 AGATAGTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.23
Consensus pattern (31 bp):
TGAATAGATCAATCGAATAAACAAATAGATA
Found at i:42445225 original size:12 final size:12
Alignment explanation
Indices: 42445208--42445232 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42445198 GAAGATGAGA
42445208 AGAACAAATCAG
1 AGAACAAATCAG
42445220 AGAACAAATCAG
1 AGAACAAATCAG
42445232 A
1 A
42445233 CAAGAAAAGA
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:0.60, C:0.16, G:0.16, T:0.08
Consensus pattern (12 bp):
AGAACAAATCAG
Found at i:42449629 original size:20 final size:20
Alignment explanation
Indices: 42449601--42449648 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
42449591 GTCCAATTTT
*
42449601 TTATTTTTAAAAATAATTAA
1 TTATATTTAAAAATAATTAA
* * *
42449621 TTTTATTTAATACTAATTAA
1 TTATATTTAAAAATAATTAA
42449641 TTATATTT
1 TTATATTT
42449649 GACTACAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATATTTAAAAATAATTAA
Found at i:42449812 original size:23 final size:27
Alignment explanation
Indices: 42449763--42449815 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
42449753 TTATTGATAT
42449763 AAATAATATAATATATAAACCAAATGAA
1 AAATAATATAATATATAAACC-AATGAA
42449791 AAATAATAT-AT-TATAAA-C-ATGAA
1 AAATAATATAATATATAAACCAATGAA
42449814 AA
1 AA
42449816 CAAGTCAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 7 0.28
25 1 0.04
26 6 0.24
27 2 0.08
28 9 0.36
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (27 bp):
AAATAATATAATATATAAACCAATGAA
Found at i:42452274 original size:20 final size:21
Alignment explanation
Indices: 42452249--42452307 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
42452239 AAAAATATAA
42452249 ATTTTGGATTTTTTATAAA-T
1 ATTTTGGATTTTTTATAAATT
* * *
42452269 ATTTT-GAATTTTGAAAAATT
1 ATTTTGGATTTTTTATAAATT
*
42452289 ATTTTGAATTTTTTTATAA
1 ATTTTGGA-TTTTTTATAA
42452308 TTTTTGTTGA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 10 0.34
20 11 0.38
21 1 0.03
22 7 0.24
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (21 bp):
ATTTTGGATTTTTTATAAATT
Found at i:42453103 original size:27 final size:27
Alignment explanation
Indices: 42453065--42453118 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
42453055 TGACAATTGG
*
42453065 CATTGTCACAACTTAAGCACGATGTAT
1 CATTGTCACAACTCAAGCACGATGTAT
42453092 CATTGTCACAACTCAAGCACGATGTAT
1 CATTGTCACAACTCAAGCACGATGTAT
42453119 TTAGAGTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (27 bp):
CATTGTCACAACTCAAGCACGATGTAT
Found at i:42457587 original size:48 final size:48
Alignment explanation
Indices: 42457535--42457631 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
42457525 TAAACTGTTA
42457535 GTTCTAGTGCTTATGACGATTCCGGATTTGTGGAATCACTCATTTTCT
1 GTTCTAGTGCTTATGACGATTCCGGATTTGTGGAATCACTCATTTTCT
42457583 GTTCTAGTGCTTATGACGATTCCGGATTTGTGGAATCACTCATTTTCT
1 GTTCTAGTGCTTATGACGATTCCGGATTTGTGGAATCACTCATTTTCT
42457631 G
1 G
42457632 CCTCATTCTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (48 bp):
GTTCTAGTGCTTATGACGATTCCGGATTTGTGGAATCACTCATTTTCT
Found at i:42467867 original size:12 final size:12
Alignment explanation
Indices: 42467850--42467916 Score: 50
Period size: 12 Copynumber: 5.5 Consensus size: 12
42467840 GTTTTTTAAA
42467850 AAAATAATATAT
1 AAAATAATATAT
*
42467862 AAAATAAAAAGTATGT
1 AAAAT---AA-TATAT
*
42467878 AAAATAATTTAT
1 AAAATAATATAT
42467890 AAAATAAT-TAT
1 AAAATAATATAT
*
42467901 ATAAT-ATATA-
1 AAAATAATATAT
42467911 AAAATA
1 AAAATA
42467917 TCAATTTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
10 6 0.14
11 9 0.20
12 16 0.36
13 2 0.05
15 2 0.05
16 9 0.20
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (12 bp):
AAAATAATATAT
Found at i:42468034 original size:12 final size:12
Alignment explanation
Indices: 42468017--42468041 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42468007 TTTTAAAATT
42468017 ATGAATAATATA
1 ATGAATAATATA
42468029 ATGAATAATATA
1 ATGAATAATATA
42468041 A
1 A
42468042 AACATAAATA
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:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATGAATAATATA
Found at i:42468098 original size:11 final size:11
Alignment explanation
Indices: 42468082--42468127 Score: 56
Period size: 11 Copynumber: 3.9 Consensus size: 11
42468072 TATACATAAC
42468082 ATATAATAAAA
1 ATATAATAAAA
*
42468093 AAATAATAAGTAA
1 ATATAATAA--AA
42468106 TATATAATAAAA
1 -ATATAATAAAA
42468118 ATATAATAAA
1 ATATAATAAA
42468128 TGTTATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 18 0.60
12 2 0.07
13 2 0.07
14 8 0.27
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (11 bp):
ATATAATAAAA
Found at i:42468112 original size:25 final size:25
Alignment explanation
Indices: 42468077--42468161 Score: 93
Period size: 25 Copynumber: 3.4 Consensus size: 25
42468067 TACGATATAC
*
42468077 ATAACATATAATAAAAAAATAATAA
1 ATAATATATAATAAAAAAATAATAA
* *
42468102 GTAATATATAATAAAAATATAATAA
1 ATAATATATAATAAAAAAATAATAA
**
42468127 ATGTTATATAATAAAATAAA-ATATAA
1 ATAATATATAATAAAA-AAATA-ATAA
42468153 AT-ATATATA
1 ATAATATATA
42468162 GGAAAATAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
25 42 0.84
26 8 0.16
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (25 bp):
ATAATATATAATAAAAAAATAATAA
Found at i:42474666 original size:17 final size:18
Alignment explanation
Indices: 42474632--42474667 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42474622 TTAATTTTCC
*
42474632 CTTTTTCTTTTCTCATTT
1 CTTTTTCTTTCCTCATTT
42474650 CTTTTTCTTTCCT-ATTT
1 CTTTTTCTTTCCTCATTT
42474667 C
1 C
42474668 GTTCCACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (18 bp):
CTTTTTCTTTCCTCATTT
Found at i:42474776 original size:23 final size:23
Alignment explanation
Indices: 42474744--42474811 Score: 59
Period size: 23 Copynumber: 2.8 Consensus size: 23
42474734 TACTTAATTA
*
42474744 ATAATTAATATAATATATTATAA-T
1 ATAATAAATAT-ATATATTA-AAGT
*
42474768 -TAATAAATATCTTATACTTAAAGT
1 ATAATAAATAT-ATATA-TTAAAGT
42474792 ATAAGTAAATATATATATTA
1 ATAA-TAAATATATATATTA
42474812 CATTTGTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
23 15 0.42
24 7 0.19
25 7 0.19
26 7 0.19
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (23 bp):
ATAATAAATATATATATTAAAGT
Found at i:42474782 original size:18 final size:19
Alignment explanation
Indices: 42474744--42474788 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
42474734 TACTTAATTA
42474744 ATAATTAATATAATATATT
1 ATAATTAATATAATATATT
*
42474763 ATAATTAATA-AATATCTT
1 ATAATTAATATAATATATT
*
42474781 ATACTTAA
1 ATAATTAA
42474789 AGTATAAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATTAATATAATATATT
Found at i:42476423 original size:17 final size:16
Alignment explanation
Indices: 42476390--42476420 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42476380 GCGCTGAAAC
42476390 ATATTATGTCAAAAAG
1 ATATTATGTCAAAAAG
*
42476406 ATATTGTGTCAAAAA
1 ATATTATGTCAAAAA
42476421 AGAACAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.32
Consensus pattern (16 bp):
ATATTATGTCAAAAAG
Found at i:42479563 original size:24 final size:24
Alignment explanation
Indices: 42479535--42479580 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
42479525 TCAAAATGCA
*
42479535 ATTTTTATTTTTTAAAATTTTTTT
1 ATTTTTATTTTTTAAAAATTTTTT
42479559 ATTTTTATTTTTTAAAAATTTT
1 ATTTTTATTTTTTAAAAATTTT
42479581 GAAAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (24 bp):
ATTTTTATTTTTTAAAAATTTTTT
Found at i:42480852 original size:10 final size:11
Alignment explanation
Indices: 42480826--42480852 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
42480816 ACTATTAGTA
42480826 ATTTTTTAAAT
1 ATTTTTTAAAT
42480837 ATTTTTTAAAT
1 ATTTTTTAAAT
42480848 ATTTT
1 ATTTT
42480853 ACTATACTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTTTTAAAT
Found at i:42483338 original size:14 final size:16
Alignment explanation
Indices: 42483314--42483345 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42483304 TATTTAAAAG
42483314 ATAACATTAAAA-GAA
1 ATAACATTAAAATGAA
42483329 ATAA-ATTAAAATGAA
1 ATAACATTAAAATGAA
42483344 AT
1 AT
42483346 GAAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.25
Consensus pattern (16 bp):
ATAACATTAAAATGAA
Found at i:42499675 original size:17 final size:18
Alignment explanation
Indices: 42499653--42499696 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
42499643 TCAACAGTTG
42499653 TATTTA-AAAAATAATTA
1 TATTTATAAAAATAATTA
* *
42499670 TATTTATCAAAATAATTG
1 TATTTATAAAAATAATTA
42499688 TATTTATAA
1 TATTTATAA
42499697 TGCATCTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
TATTTATAAAAATAATTA
Found at i:42500409 original size:33 final size:33
Alignment explanation
Indices: 42500367--42500432 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
42500357 AAAATAAGTT
42500367 TAAAAATATAAAATCTTCAATTAGTTATGAAAA
1 TAAAAATATAAAATCTTCAATTAGTTATGAAAA
*
42500400 TAAAAATATAAAATCTTCTATTAGTTATGAAAA
1 TAAAAATATAAAATCTTCAATTAGTTATGAAAA
42500433 ATTAGTAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (33 bp):
TAAAAATATAAAATCTTCAATTAGTTATGAAAA
Found at i:42500632 original size:31 final size:31
Alignment explanation
Indices: 42500570--42500634 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
42500560 TCTAATAGTG
* *
42500570 ACTTAAATAAAAATTTCTGAATAATTTAATA
1 ACTTAAATAAAAATTTCTAAATAATTCAATA
* *
42500601 ACTTAAATGAAAACTTTC-AAATAGTTCAATA
1 ACTTAAAT-AAAAATTTCTAAATAATTCAATA
42500632 ACT
1 ACT
42500635 ATTTTATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 21 0.72
32 8 0.28
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (31 bp):
ACTTAAATAAAAATTTCTAAATAATTCAATA
Found at i:42516554 original size:13 final size:13
Alignment explanation
Indices: 42516538--42516570 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
42516528 CAATGCTTTT
42516538 GAAAAGTGCTATA
1 GAAAAGTGCTATA
*
42516551 GAAAAGTGCTATT
1 GAAAAGTGCTATA
42516564 GAAAAGT
1 GAAAAGT
42516571 TTGGTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.45, C:0.06, G:0.24, T:0.24
Consensus pattern (13 bp):
GAAAAGTGCTATA
Found at i:42522142 original size:22 final size:23
Alignment explanation
Indices: 42522085--42522142 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
42522075 GTGATTATAT
* *
42522085 TTTATTTCTATTTCCACAGGGTAG
1 TTTAGTTCTA-TTCCACAAGGTAG
*
42522109 GTTAGTTC-ATTCCACAAGGTAG
1 TTTAGTTCTATTCCACAAGGTAG
42522131 TTTA-TTCTATTC
1 TTTAGTTCTATTC
42522143 TGTGACTGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 3 0.10
22 19 0.66
23 1 0.03
24 6 0.21
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.45
Consensus pattern (23 bp):
TTTAGTTCTATTCCACAAGGTAG
Found at i:42526342 original size:19 final size:19
Alignment explanation
Indices: 42526291--42526361 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
42526281 AAAAATTACA
* * *
42526291 AAAAATCAAAGTAATTTTC
1 AAAATTCAAAATAATTTTT
*
42526310 AAAATTTGAAAATAATTTTT
1 AAAA-TTCAAAATAATTTTT
*
42526330 AAAATTCAAAAT-ATTTAT
1 AAAATTCAAAATAATTTTT
42526348 AGAAATTCTAAAAT
1 A-AAATTC-AAAAT
42526362 TTATATTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
18 6 0.14
19 17 0.40
20 20 0.47
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:42526363 original size:18 final size:19
Alignment explanation
Indices: 42526318--42526366 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
42526308 TCAAAATTTG
*
42526318 AAAATAATTTTTA-AAATTC
1 AAAAT-ATTTATAGAAATTC
42526337 AAAATATTTATAGAAATTC
1 AAAATATTTATAGAAATTC
*
42526356 TAAA-ATTTATA
1 AAAATATTTATA
42526367 TTTTTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (19 bp):
AAAATATTTATAGAAATTC
Found at i:42526390 original size:19 final size:18
Alignment explanation
Indices: 42526357--42526403 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
42526347 TAGAAATTCT
*
42526357 AAAATTTATATTTTTTAA
1 AAAATTTAAATTTTTTAA
42526375 AAAATTATAAATTTTTTAA
1 AAAATT-TAAATTTTTTAA
*
42526394 AAAATCTAAA
1 AAAATTTAAA
42526404 AAAATATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAATTTAAATTTTTTAA
Found at i:42526403 original size:18 final size:19
Alignment explanation
Indices: 42526357--42526398 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
42526347 TAGAAATTCT
*
42526357 AAAATT-TATATTTTTTAA
1 AAAATTATAAATTTTTTAA
42526375 AAAATTATAAATTTTTTAA
1 AAAATTATAAATTTTTTAA
42526394 AAAAT
1 AAAAT
42526399 CTAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AAAATTATAAATTTTTTAA
Found at i:42526427 original size:20 final size:21
Alignment explanation
Indices: 42526394--42526434 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
42526384 AATTTTTTAA
42526394 AAAATCTAAAAAAAT-ATAAT
1 AAAATCTAAAAAAATAATAAT
* *
42526414 AAAATTTAATAAAATAATAAT
1 AAAATCTAAAAAAATAATAAT
42526435 TTTAGAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAATCTAAAAAAATAATAAT
Found at i:42526754 original size:21 final size:21
Alignment explanation
Indices: 42526730--42526769 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
42526720 ACCTTTTCTA
42526730 AAGTTAAAA-GTCAAAACTATC
1 AAGTTAAAAGGT-AAAACTATC
42526751 AAGTTAAAAGGTAAAACTA
1 AAGTTAAAAGGTAAAACTA
42526770 CTTTGTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (21 bp):
AAGTTAAAAGGTAAAACTATC
Found at i:42529500 original size:48 final size:48
Alignment explanation
Indices: 42529429--42529712 Score: 216
Period size: 48 Copynumber: 5.9 Consensus size: 48
42529419 AGGGTAAATT
* *
42529429 GCCGATG-CATGTCCCAGATATGGTCTTACACTGGCTCACATGTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCGAG
* * *** ** * *
42529476 GCCGATGCCATATCCCAAACATGGTCTTACACTAGCTTTTAACTCAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCGAG
** * * * * * *
42529524 ATCGATGCCATGTCCCAGTCATGATCTTACACTGGCTCTCATAAT-GTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-GTCGAG
* * * * *
42529572 GTCGATGCCATATCTCAGACATGGTCTTACACTAG-TACACATGTCAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCT-CACATGTCGAG
* * * * * * * *
42529620 ACCGATGCCATCTCCCAGACAAGGTCTTAAACTGGCTCTCATAAT-GTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-GTCGAG
*
42529668 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATGTC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTC
42529713 ACCTAAATAC
Statistics
Matches: 174, Mismatches: 56, Indels: 13
0.72 0.23 0.05
Matches are distributed among these distances:
47 10 0.06
48 161 0.93
49 3 0.02
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.27
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCGAG
Found at i:42529710 original size:96 final size:96
Alignment explanation
Indices: 42529430--42529713 Score: 356
Period size: 96 Copynumber: 3.0 Consensus size: 96
42529420 GGGTAAATTG
* * * *
42529430 CCGATG-CATGTCCCAGATATGGTCTTACACTGGCTCACAT-GTCGAGGCCGATGCCATATCCCA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCCGATGCCATATCCCA
* **** **
42529493 AACATGGTCTTACACTAGCTTTTAACTCAATA
65 GACATGGTCTTACACTAGCACACATGTCAATA
* * * * *
42529525 TCGATGCCATGTCCCAGTCATGATCTTACACTGGCTCTCATAATGTGGTCGATGCCATATCTCAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCCATATCCCAG
*
42529590 ACATGGTCTTACACTAGTACACATGTCAATA
66 ACATGGTCTTACACTAGCACACATGTCAATA
* * * *
42529621 CCGATGCCATCTCCCAGACAAGGTCTTAAACTGGCTCTCATAATGTGGCCGATGCCATGTCCCAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCCATATCCCAG
42529686 ACATGGTCTTACACTAGCACACATGTCA
66 ACATGGTCTTACACTAGCACACATGTCA
42529714 CCTAAATACT
Statistics
Matches: 160, Mismatches: 27, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
95 5 0.03
96 154 0.96
97 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (96 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCCATATCCCAG
ACATGGTCTTACACTAGCACACATGTCAATA
Found at i:42530306 original size:30 final size:30
Alignment explanation
Indices: 42530270--42530326 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
42530260 ACCAAGATTC
42530270 ATTTTCTTCCATAAAAATTCAGCAAAATTT
1 ATTTTCTTCCATAAAAATTCAGCAAAATTT
42530300 ATTTTCTTCCATAAAAATTCAGCAAAA
1 ATTTTCTTCCATAAAAATTCAGCAAAA
42530327 AACATAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.37
Consensus pattern (30 bp):
ATTTTCTTCCATAAAAATTCAGCAAAATTT
Found at i:42532040 original size:41 final size:40
Alignment explanation
Indices: 42531969--42532047 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 40
42531959 TGTCGTAACT
**
42531969 TATGGTGTGTAGGGATGGATGGGTCAATTTTATTCCCCATA
1 TATGGTGTGTAGGGATGGATAAGTCAATTTTA-TCCCCATA
*
42532010 TATGGTGTGTAGGGATTGG-TAAGTCGATTTTATCCCCA
1 TATGGTGTGTAGGGA-TGGATAAGTCAATTTTATCCCCA
42532048 CATGGTGTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 6 0.18
41 25 0.74
42 3 0.09
ACGTcount: A:0.22, C:0.13, G:0.29, T:0.37
Consensus pattern (40 bp):
TATGGTGTGTAGGGATGGATAAGTCAATTTTATCCCCATA
Found at i:42539135 original size:41 final size:41
Alignment explanation
Indices: 42539078--42539155 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
42539068 TACTGTACCT
42539078 TATGGTGTGTAGGGATGAATGGGTCGATTTTATTCCCCATA
1 TATGGTGTGTAGGGATGAATGGGTCGATTTTATTCCCCATA
** *
42539119 TATGGTGTGTAGGGATGGGTGGGTTGATTTTATTCCC
1 TATGGTGTGTAGGGATGAATGGGTCGATTTTATTCCC
42539156 ACATGGTGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.18, C:0.10, G:0.33, T:0.38
Consensus pattern (41 bp):
TATGGTGTGTAGGGATGAATGGGTCGATTTTATTCCCCATA
Found at i:42541195 original size:22 final size:22
Alignment explanation
Indices: 42541170--42541214 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
42541160 AGCTCTAAAA
42541170 CCCATAAAATGTCTAAAATTTT
1 CCCATAAAATGTCTAAAATTTT
42541192 CCCATAAAATGTCTAAAATTTT
1 CCCATAAAATGTCTAAAATTTT
42541214 C
1 C
42541215 GGTGGTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.36
Consensus pattern (22 bp):
CCCATAAAATGTCTAAAATTTT
Found at i:42545958 original size:17 final size:18
Alignment explanation
Indices: 42545936--42545974 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
42545926 TAATTTTTAA
*
42545936 AAAAATAATAATAA-ATT
1 AAAAATAATAAAAACATT
*
42545953 AAAAATACTAAAAACATT
1 AAAAATAATAAAAACATT
42545971 AAAA
1 AAAA
42545975 TAAATGTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATAATAAAAACATT
Found at i:42546098 original size:17 final size:18
Alignment explanation
Indices: 42546072--42546106 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
42546062 CTAAAATAGT
42546072 AACAAAATTA-ACAATAA
1 AACAAAATTATACAATAA
*
42546089 AACAAGATTATACAATAA
1 AACAAAATTATACAATAA
42546107 CTAAACAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (18 bp):
AACAAAATTATACAATAA
Found at i:42550852 original size:27 final size:26
Alignment explanation
Indices: 42550783--42550867 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 26
42550773 TAATAATTAT
* * * *
42550783 TAAATATAATATAATAATATAACTAAA
1 TAAATA-AATAAAATAAAAAAAATAAA
*
42550810 TATA-AAATAAAATAAAAAGAAATAAA
1 TAAATAAATAAAATAAAAA-AAATAAA
* *
42550836 TAAATAAATAAAGTAAAGAAAATAGAA
1 TAAATAAATAAAATAAAAAAAATA-AA
42550863 TAAAT
1 TAAAT
42550868 TTAAAAGAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
25 10 0.21
26 15 0.32
27 22 0.47
ACGTcount: A:0.69, C:0.01, G:0.05, T:0.25
Consensus pattern (26 bp):
TAAATAAATAAAATAAAAAAAATAAA
Found at i:42551800 original size:6 final size:6
Alignment explanation
Indices: 42551768--42551806 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
42551758 TGTGTACCGC
* * *
42551768 TACTGC TACTGC TACTGT TACTGT TACTAT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TAC
42551807 GGTGTATTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.44
Consensus pattern (6 bp):
TACTGT
Found at i:42555426 original size:111 final size:111
Alignment explanation
Indices: 42555232--42555453 Score: 444
Period size: 111 Copynumber: 2.0 Consensus size: 111
42555222 CGGATTTATT
42555232 CACTTGTGACATTCATAGTGTAGCATACCTAAATCCTGAGTGAATGGTGGGCTATGTATGCGTGA
1 CACTTGTGACATTCATAGTGTAGCATACCTAAATCCTGAGTGAATGGTGGGCTATGTATGCGTGA
42555297 CTCATGCACTTTGATATAAGTAAAAGCCTGAGTTCAAATTGATAAA
66 CTCATGCACTTTGATATAAGTAAAAGCCTGAGTTCAAATTGATAAA
42555343 CACTTGTGACATTCATAGTGTAGCATACCTAAATCCTGAGTGAATGGTGGGCTATGTATGCGTGA
1 CACTTGTGACATTCATAGTGTAGCATACCTAAATCCTGAGTGAATGGTGGGCTATGTATGCGTGA
42555408 CTCATGCACTTTGATATAAGTAAAAGCCTGAGTTCAAATTGATAAA
66 CTCATGCACTTTGATATAAGTAAAAGCCTGAGTTCAAATTGATAAA
42555454 GAACTGAAAG
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 111 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.31
Consensus pattern (111 bp):
CACTTGTGACATTCATAGTGTAGCATACCTAAATCCTGAGTGAATGGTGGGCTATGTATGCGTGA
CTCATGCACTTTGATATAAGTAAAAGCCTGAGTTCAAATTGATAAA
Found at i:42565491 original size:4 final size:4
Alignment explanation
Indices: 42565484--42565553 Score: 140
Period size: 4 Copynumber: 17.5 Consensus size: 4
42565474 TTAAAAAAAA
42565484 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
42565532 ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC AT
42565554 GTTGGTGGTA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 66 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:42566407 original size:30 final size:30
Alignment explanation
Indices: 42566351--42566407 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
42566341 AGGCACTTCT
*
42566351 ACACGGGTGATCCACACGCTCGTGTGTGAC
1 ACACGGGTGATCCACACGCCCGTGTGTGAC
*
42566381 ACACGGGTAGA-CCACACGCCCTTGTGT
1 ACACGGGT-GATCCACACGCCCGTGTGT
42566408 CATGGCCATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.21, C:0.32, G:0.28, T:0.19
Consensus pattern (30 bp):
ACACGGGTGATCCACACGCCCGTGTGTGAC
Found at i:42571791 original size:22 final size:22
Alignment explanation
Indices: 42571750--42571793 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
42571740 TTCTTCTAAA
42571750 ATTATTTAAAATAATATAAAAT
1 ATTATTTAAAATAATATAAAAT
42571772 ATTATATTAATAA-AAT-TAAAAT
1 ATTAT-TTAA-AATAATATAAAAT
42571794 TAAAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 11 0.55
23 7 0.35
24 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTATTTAAAATAATATAAAAT
Found at i:42574946 original size:55 final size:55
Alignment explanation
Indices: 42574862--42574978 Score: 207
Period size: 55 Copynumber: 2.1 Consensus size: 55
42574852 GTTGTTTCTT
42574862 TTATACCATTCTTAAATTACTCATTAATCTTCATGAATTTTTAAATAAAAAATAA
1 TTATACCATTCTTAAATTACTCATTAATCTTCATGAATTTTTAAATAAAAAATAA
* *
42574917 TTATATCATTCTTAAATTACTCATTAATCTTCATGAATTTTTAAATAAAAGATAA
1 TTATACCATTCTTAAATTACTCATTAATCTTCATGAATTTTTAAATAAAAAATAA
42574972 TATATAC
1 T-TATAC
42574979 TTAAACACGT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
55 54 0.93
56 4 0.07
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.43
Consensus pattern (55 bp):
TTATACCATTCTTAAATTACTCATTAATCTTCATGAATTTTTAAATAAAAAATAA
Found at i:42574961 original size:29 final size:29
Alignment explanation
Indices: 42574873--42574962 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
42574863 TATACCATTC
42574873 TTAAATTACTCATTAATCTTCATGAATTT
1 TTAAATTACTCATTAATCTTCATGAATTT
*** * * *
42574902 TTAAA-TAAAAAATAAT-TAT-AT-CATTC
1 TTAAATTACTCATTAATCT-TCATGAATTT
42574928 TTAAATTACTCATTAATCTTCATGAATTT
1 TTAAATTACTCATTAATCTTCATGAATTT
42574957 TTAAAT
1 TTAAAT
42574963 AAAAGATAAT
Statistics
Matches: 44, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
26 8 0.18
27 11 0.25
28 11 0.25
29 14 0.32
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.46
Consensus pattern (29 bp):
TTAAATTACTCATTAATCTTCATGAATTT
Found at i:42590454 original size:155 final size:153
Alignment explanation
Indices: 42590229--42590527 Score: 365
Period size: 153 Copynumber: 1.9 Consensus size: 153
42590219 TGAAAGTTTA
* * * *
42590229 TCATCTTTATGCAGACGTTGATGTTGTCAAGCCTTCTTCCATCTTCCATCTGACCATGGTTGATC
1 TCATCTTTATGCAGACATTAATGATGTCAAGCCTTCTCCCATCTTCCATCTGACCATGGTTGATC
**
42590294 ACGGATTTTCCGCA-CTCAATG-GCACACATCCATCAGTTCATGAG-ACATGCATTCAGCTCAGC
66 ACGGA-TTT--G-ATCTCAATGAGCACACATCCATCAGTTCATG-GTACATGCATTCAGCAAAGC
42590356 CTCAGCACATATTTGTTGTGAATTTTTT
126 CTCAGCACATATTTGTTGTGAATTTTTT
* *
42590384 TCATCTTTATGCA-ACCATTAATGATGTCGATCCTTCTCCCA-CTTCCAGTCTGACCATGGTTGA
1 TCATCTTTATGCAGA-CATTAATGATGTCAAGCCTTCTCCCATCTTCCA-TCTGACCATGGTTGA
** * ** * *
42590447 TTGCGGATTTGATTTCCCTGAGCACATATCCATCATTTCATGGTACATGCATTCAGCAAAGCCTC
64 TCACGGATTTGATCTCAATGAGCACACATCCATCAGTTCATGGTACATGCATTCAGCAAAGCCTC
42590512 AGCACATATTTGTTGT
129 AGCACATATTTGTTGT
42590528 CAATAACTTT
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
151 1 0.01
152 6 0.05
153 54 0.44
154 10 0.08
155 53 0.43
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (153 bp):
TCATCTTTATGCAGACATTAATGATGTCAAGCCTTCTCCCATCTTCCATCTGACCATGGTTGATC
ACGGATTTGATCTCAATGAGCACACATCCATCAGTTCATGGTACATGCATTCAGCAAAGCCTCAG
CACATATTTGTTGTGAATTTTTT
Found at i:42596751 original size:31 final size:31
Alignment explanation
Indices: 42596716--42596781 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
42596706 AAAATTACTT
42596716 AATAACCCAATGACTTAAATAAAAACTTTCA
1 AATAACCCAATGACTTAAATAAAAACTTTCA
** * * *
42596747 AATAATTCACTGGCTTAAATGAAAACTTTCA
1 AATAACCCAATGACTTAAATAAAAACTTTCA
42596778 AATA
1 AATA
42596782 GTTCAATGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.48, C:0.17, G:0.06, T:0.29
Consensus pattern (31 bp):
AATAACCCAATGACTTAAATAAAAACTTTCA
Found at i:42602945 original size:38 final size:37
Alignment explanation
Indices: 42602861--42602933 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
42602851 GTAAAAAAAG
42602861 AAAGAAAAGAGAATTTTTGATTGATGTAGACAGTGCA
1 AAAGAAAAGAGAATTTTTGATTGATGTAGACAGTGCA
*
42602898 AAAGAAAAGAGAATTTTTTATTGATGTAGACAGTGC
1 AAAGAAAAGAGAATTTTTGATTGATGTAGACAGTGC
42602934 GAATGGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.29
Consensus pattern (37 bp):
AAAGAAAAGAGAATTTTTGATTGATGTAGACAGTGCA
Found at i:42603584 original size:19 final size:20
Alignment explanation
Indices: 42603544--42603582 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
42603534 AAGGAGTATG
*
42603544 TTCTGAAATGGAAAAAAAAA
1 TTCTGAAATAGAAAAAAAAA
42603564 TTCTGAAATAGAAAAAAAA
1 TTCTGAAATAGAAAAAAAA
42603583 TTTGGAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.62, C:0.05, G:0.13, T:0.21
Consensus pattern (20 bp):
TTCTGAAATAGAAAAAAAAA
Found at i:42605125 original size:3 final size:3
Alignment explanation
Indices: 42605117--42605152 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
42605107 AAATAGATAT
*
42605117 TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
42605153 GAAATAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:42605295 original size:33 final size:33
Alignment explanation
Indices: 42605228--42605296 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
42605218 ACACTTGTAA
*
42605228 AAATATATATATAATTACTTAAAATTTAAGTAT
1 AAATATATATATAATTACTTAAAATTTAAATAT
*
42605261 AAATATATTTATAATTA-TTAATTAA-TTAAATAT
1 AAATATATATATAATTACTTAA--AATTTAAATAT
42605294 AAA
1 AAA
42605297 ATAAATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 4 0.12
33 26 0.81
34 2 0.06
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (33 bp):
AAATATATATATAATTACTTAAAATTTAAATAT
Found at i:42605926 original size:17 final size:18
Alignment explanation
Indices: 42605904--42605937 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
42605894 TAAATGAGTT
42605904 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
42605921 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
42605938 AAAAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:42607910 original size:17 final size:17
Alignment explanation
Indices: 42607873--42607910 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
42607863 TTATTTTTAT
*
42607873 TATTATTATCGTATTAC
1 TATTATTATCATATTAC
42607890 TATTATTATCATCATTA-
1 TATTATTATCAT-ATTAC
42607907 TATT
1 TATT
42607911 GTTTCTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.55
Consensus pattern (17 bp):
TATTATTATCATATTAC
Found at i:42609486 original size:21 final size:21
Alignment explanation
Indices: 42609462--42609514 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
42609452 TATATGTGTT
*
42609462 GTATCAGGTACCTCGTGTATC
1 GTATCAGGCACCTCGTGTATC
*
42609483 GTATCAGGCACCTCGTGTGTC
1 GTATCAGGCACCTCGTGTATC
* *
42609504 GTTTTAGGCAC
1 GTATCAGGCAC
42609515 TTTATGTGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32
Consensus pattern (21 bp):
GTATCAGGCACCTCGTGTATC
Found at i:42615008 original size:112 final size:113
Alignment explanation
Indices: 42614807--42615037 Score: 367
Period size: 112 Copynumber: 2.0 Consensus size: 113
42614797 AAATATAAAA
* * **
42614807 TTTTGGGGTCAAAGTTAAAATGCTTAAATTAAATTAGTACTTTTTTGAGGGGCCAAATTAAAAAA
1 TTTTGGGGCCAAAGTTAAAATGCTTAAATTAAATTACTACTTTTTAAAGGGGCCAAATTAAAAAA
* * *
42614872 AATCATTTGACCGACGTTTAAAAAAGG-TTAAATTG-ATTTTTTTTAAG
66 AATCATTTGACCAAAGTCTAAAAAAGGCTT-AATTGAATTTTTTTTAAG
42614919 TTTTGGGGCCAAAGTTAAAATGCTTAAATTAAATTACTACTTTTTAAAGGGGCCACAATTAAAAA
1 TTTTGGGGCCAAAGTTAAAATGCTTAAATTAAATTACTACTTTTTAAAGGGGCCA-AATTAAAAA
42614984 AAATCATTTGACCAAAGTCTAAAAAAGGCTTAATTGAATTTTTTTTAAG
65 AAATCATTTGACCAAAGTCTAAAAAAGGCTTAATTGAATTTTTTTTAAG
42615033 TTTTG
1 TTTTG
42615038 AGAGGGGCTA
Statistics
Matches: 109, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
112 51 0.47
113 39 0.36
114 19 0.17
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.37
Consensus pattern (113 bp):
TTTTGGGGCCAAAGTTAAAATGCTTAAATTAAATTACTACTTTTTAAAGGGGCCAAATTAAAAAA
AATCATTTGACCAAAGTCTAAAAAAGGCTTAATTGAATTTTTTTTAAG
Found at i:42616382 original size:19 final size:19
Alignment explanation
Indices: 42616355--42616405 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 19
42616345 AAAGTTTTAT
* *
42616355 TTTAATATTTTTCATAAGC
1 TTTACTATTTTTCACAAGC
*
42616374 TTTACTATTATTACACAAGC
1 TTTACTATT-TTTCACAAGC
*
42616394 TTTTCT-TTTTTC
1 TTTACTATTTTTC
42616406 TTTAACTTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 3 0.12
19 10 0.38
20 13 0.50
ACGTcount: A:0.25, C:0.16, G:0.04, T:0.55
Consensus pattern (19 bp):
TTTACTATTTTTCACAAGC
Found at i:42618215 original size:11 final size:11
Alignment explanation
Indices: 42618199--42618249 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
42618189 ATACGAAAAT
42618199 ATAAAAAGAAA
1 ATAAAAAGAAA
42618210 ATAAAAAGAAA
1 ATAAAAAGAAA
* *
42618221 ACAAATAAAAAGA
1 ATAAA-AAGAA-A
*
42618234 AAAAAAAGAAA
1 ATAAAAAGAAA
42618245 A-AAAA
1 ATAAAA
42618250 TTAGAGTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
10 4 0.12
11 17 0.50
12 8 0.24
13 5 0.15
ACGTcount: A:0.84, C:0.02, G:0.08, T:0.06
Consensus pattern (11 bp):
ATAAAAAGAAA
Found at i:42618228 original size:15 final size:15
Alignment explanation
Indices: 42618202--42618246 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
42618192 CGAAAATATA
42618202 AAAAGAAAATAAAAAG
1 AAAA-AAAATAAAAAG
*
42618218 AAAACAAATAAAAAG
1 AAAAAAAATAAAAAG
*
42618233 AAAAAAAAGAAAAA
1 AAAAAAAATAAAAA
42618247 AAATTAGAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.84, C:0.02, G:0.09, T:0.04
Consensus pattern (15 bp):
AAAAAAAATAAAAAG
Found at i:42618229 original size:26 final size:24
Alignment explanation
Indices: 42618194--42618250 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
42618184 TATATATACG
*
42618194 AAAATATAAAAAGAAAATAAAAAGAA
1 AAAAAATAAAAAG-AAA-AAAAAGAA
*
42618220 AACAAATAAAAAGAAAAAAAAGAA
1 AAAAAATAAAAAGAAAAAAAAGAA
42618244 AAAAAAT
1 AAAAAAT
42618251 TAGAGTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 14 0.50
25 3 0.11
26 11 0.39
ACGTcount: A:0.82, C:0.02, G:0.07, T:0.09
Consensus pattern (24 bp):
AAAAAATAAAAAGAAAAAAAAGAA
Found at i:42618908 original size:21 final size:21
Alignment explanation
Indices: 42618866--42618931 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 21
42618856 TTTTTATATA
* *
42618866 TTATTACTATTAT-TTTTATAT
1 TTATTACTAATATATATT-TAT
42618887 TTATTACTAATATATATTTAT
1 TTATTACTAATATATATTTAT
* *
42618908 TATAGTTACTACTATATATATAT
1 T-TA-TTACTAATATATATTTAT
42618931 T
1 T
42618932 ACGTATATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.42
22 5 0.13
23 17 0.45
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.58
Consensus pattern (21 bp):
TTATTACTAATATATATTTAT
Found at i:42619088 original size:22 final size:23
Alignment explanation
Indices: 42619051--42619096 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
42619041 TACACATGCA
*
42619051 TTTTTCATATTAATA-TATATATG
1 TTTTTAATATTAATATTAT-TATG
42619074 TTTTTAATATT-ATATTATTATG
1 TTTTTAATATTAATATTATTATG
42619096 T
1 T
42619097 ATATGTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (23 bp):
TTTTTAATATTAATATTATTATG
Found at i:42619115 original size:30 final size:28
Alignment explanation
Indices: 42619057--42619113 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
42619047 TGCATTTTTC
42619057 ATATTAATATATATATGTTTTTAATATT
1 ATATTAATATATATATGTTTTTAATATT
* *
42619085 ATATTATTATGTATATG-TTTTAATATT
1 ATATTAATATATATATGTTTTTAATATT
42619112 AT
1 AT
42619114 TAGCTATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 12 0.44
28 15 0.56
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (28 bp):
ATATTAATATATATATGTTTTTAATATT
Found at i:42619288 original size:21 final size:21
Alignment explanation
Indices: 42619247--42619288 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42619237 TCTAATATAA
* *
42619247 ATATATATATCATATAGGTTT
1 ATATACATATCATACAGGTTT
*
42619268 ATATACATATCATACATGTTT
1 ATATACATATCATACAGGTTT
42619289 CTTTATTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (21 bp):
ATATACATATCATACAGGTTT
Found at i:42624009 original size:75 final size:73
Alignment explanation
Indices: 42623886--42624101 Score: 297
Period size: 75 Copynumber: 2.9 Consensus size: 73
42623876 TCTGTTTTCT
* * * * *
42623886 AAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGAGGTACGCTGAGGTATTTTCAATTATTT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTACTG
*
42623951 TTTGTCAAAA
66 TTTGGC--AA
*
42623961 AAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTACTG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTACTG
42624026 TTTGGCAA
66 TTTGGCAA
* * * * * *
42624034 AAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTATTTTCGATTTCTG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTACTG
42624099 TTT
66 TTT
42624102 TTCAATTTAT
Statistics
Matches: 127, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
73 63 0.50
75 64 0.50
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (73 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTACTG
TTTGGCAA
Found at i:42624081 original size:73 final size:73
Alignment explanation
Indices: 42623886--42624101 Score: 283
Period size: 73 Copynumber: 2.9 Consensus size: 73
42623876 TCTGTTTTCT
* *
42623886 AAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGAGGTAC-GCTGAGGTATTTTCAATTATT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGG-ACAGCTGAGGTATTTTCAATTACT
* *
42623950 TTTTGTCAAAA
64 GTTTGGC-AAA
* * *
42623961 AAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTACTG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA-GCTGAGGTATTTTCAATTACTG
42624026 TTTGGC-AA
65 TTTGGCAAA
* * *
42624034 AAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTATTTTCGATTTCTG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA-GCTGAGGTATTTTCAATTACTG
42624099 TTT
65 TTT
42624102 TTCAATTTAT
Statistics
Matches: 125, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
73 64 0.51
74 2 0.02
75 59 0.47
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (73 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAGCTGAGGTATTTTCAATTACTGT
TTGGCAAA
Found at i:42624221 original size:74 final size:74
Alignment explanation
Indices: 42624100--42624255 Score: 244
Period size: 74 Copynumber: 2.1 Consensus size: 74
42624090 CGATTTCTGT
*
42624100 TTTTCAATTTATGTTTTCAAAAATCAATGCATATTGCTAAAGGTGAATTGAGTCTCAGGTCGTAT
1 TTTTCAATTTATGTTTTCAAAAATCAATGCATATTGCTAAAGGTGAATTGAGCCTCAGGTC--AT
42624165 A-G-CGAGGTA
64 ACGCCGAGGTA
* * *
42624174 TTTTCAATTTATGTTTTCAAAAATTAATTCATATTGCTAGAGGTGAATTGAGCCTCAGGTCATAC
1 TTTTCAATTTATGTTTTCAAAAATCAATGCATATTGCTAAAGGTGAATTGAGCCTCAGGTCATAC
42624239 GCCGAGGTA
66 GCCGAGGTA
42624248 TTTTCAAT
1 TTTTCAAT
42624256 AGACGTTTTT
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
72 3 0.04
73 1 0.01
74 72 0.95
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (74 bp):
TTTTCAATTTATGTTTTCAAAAATCAATGCATATTGCTAAAGGTGAATTGAGCCTCAGGTCATAC
GCCGAGGTA
Found at i:42624395 original size:79 final size:78
Alignment explanation
Indices: 42624265--42624428 Score: 220
Period size: 79 Copynumber: 2.1 Consensus size: 78
42624255 TAGACGTTTT
* * ** * * *
42624265 TTTTCAATTTCTGCTTCTCAAAAAAAATTAACTCATATTGTGAGAGGTGAGTTGAGCCTTGGCTT
1 TTTTCAAGTTCTGCTTCTAAAAAAAAAACAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTC
*
42624330 ACACGCTGAGGTA
66 ACACGCTGAGGGA
* *
42624343 TTTTCAAGTTCTGCTTTTTAAAAAAAAAACAATTCATATTGCGAGAGGTGAGTTGAGCCTCGGCT
1 TTTTCAAGTTCTGC-TTCTAAAAAAAAAACAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCT
*
42624408 CGCACGCTGAGGGA
65 CACACGCTGAGGGA
42624422 TTTTCAA
1 TTTTCAA
42624429 TTTTTCGTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
78 13 0.18
79 61 0.82
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (78 bp):
TTTTCAAGTTCTGCTTCTAAAAAAAAAACAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTC
ACACGCTGAGGGA
Found at i:42641863 original size:13 final size:13
Alignment explanation
Indices: 42641836--42641868 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
42641826 TGTATTTTCA
42641836 TATTAT-TATTAT
1 TATTATATATTAT
*
42641848 TATTATATATTTT
1 TATTATATATTAT
42641861 TATTATAT
1 TATTATAT
42641869 GCACATACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTATATATTAT
Found at i:42643016 original size:33 final size:34
Alignment explanation
Indices: 42642979--42643044 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
42642969 AAATTTTAAT
42642979 ATTGAACTCGTA-TTTTTAAAAATCAAGACAACC
1 ATTGAACTCGTATTTTTTAAAAATCAAGACAACC
42643012 ATTGAACTCGTATTTTTTAAAAATCAAGACAAC
1 ATTGAACTCGTATTTTTTAAAAATCAAGACAAC
42643045 ACGTGTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 12 0.38
34 20 0.62
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (34 bp):
ATTGAACTCGTATTTTTTAAAAATCAAGACAACC
Found at i:42648835 original size:31 final size:26
Alignment explanation
Indices: 42648742--42648851 Score: 186
Period size: 26 Copynumber: 4.2 Consensus size: 26
42648732 TGGTACAAAT
42648742 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
42648768 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
42648794 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
42648820 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
42648846 TGATAA
1 TGATAA
42648852 GAATTTCATG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 78 0.98
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:42652918 original size:29 final size:28
Alignment explanation
Indices: 42652885--42652949 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
42652875 ATCTTATAAT
* *
42652885 TTGATTATTTTAATACTACAAGGGCTAAA
1 TTGATTA-TTTAATAATACAAGGACTAAA
* *
42652914 TTGATCTATTTAATAATAGAAGGACTAAT
1 TTGAT-TATTTAATAATACAAGGACTAAA
42652943 TTGATTA
1 TTGATTA
42652950 GATACCAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 2 0.06
29 27 0.87
30 2 0.06
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (28 bp):
TTGATTATTTAATAATACAAGGACTAAA
Found at i:42655082 original size:2 final size:2
Alignment explanation
Indices: 42655069--42655113 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
42655059 TCAATTCTTT
* * * *
42655069 TA TA TA TG TA TA TA TA TA CA TA TA TA CA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42655111 TA T
1 TA T
42655114 TATTTTTCAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:42656756 original size:10 final size:10
Alignment explanation
Indices: 42656741--42656765 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42656731 ATTTTTATTG
42656741 AATTAAATAT
1 AATTAAATAT
42656751 AATTAAATAT
1 AATTAAATAT
42656761 AATTA
1 AATTA
42656766 GTTAACATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AATTAAATAT
Found at i:42658276 original size:12 final size:12
Alignment explanation
Indices: 42658259--42658301 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
42658249 CTCTTAAACC
42658259 TATTTAAATTAA
1 TATTTAAATTAA
42658271 TATTTATAATTAA
1 TATTTA-AATTAA
*
42658284 -ATTTTAAATAAA
1 TA-TTTAAATTAA
42658296 TATTTA
1 TATTTA
42658302 TTAATTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TATTTAAATTAA
Found at i:42659705 original size:17 final size:17
Alignment explanation
Indices: 42659683--42659716 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
42659673 CTTACCTTCA
42659683 TTTTTTTTATTTTTTAT
1 TTTTTTTTATTTTTTAT
42659700 TTTTTTTTATTTTTTAT
1 TTTTTTTTATTTTTTAT
42659717 AAATGAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTTTTATTTTTTAT
Found at i:42670186 original size:21 final size:21
Alignment explanation
Indices: 42670162--42670217 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 21
42670152 TTAAATAATA
42670162 ATTAAAATTTATTAAGTATAT
1 ATTAAAATTTATTAAGTATAT
* *
42670183 ATT-AAGTAT-TTAAGTATAT
1 ATTAAAATTTATTAAGTATAT
42670202 ATATCAAAATTATATT
1 AT-T-AAAATT-TATT
42670218 TATCTTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
19 12 0.46
20 5 0.19
21 3 0.12
22 3 0.12
23 1 0.04
24 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (21 bp):
ATTAAAATTTATTAAGTATAT
Found at i:42683437 original size:14 final size:16
Alignment explanation
Indices: 42683414--42683452 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
42683404 ATAAGAAAAT
42683414 TATT-TAAATTT-TAA
1 TATTATAAATTTATAA
42683428 T-TTATAAATTTATAA
1 TATTATAAATTTATAA
42683443 TATTA-AAATT
1 TATTATAAATT
42683453 ATTTTATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.09
14 8 0.36
15 9 0.41
16 3 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATTATAAATTTATAA
Found at i:42683562 original size:21 final size:18
Alignment explanation
Indices: 42683538--42683585 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
42683528 GTTTAGTGAC
*
42683538 TTAAATTATTTTATTAAATAA
1 TTAAATAATTTT-TT-AA-AA
42683559 TT-AATAATTTTTTAAAA
1 TTAAATAATTTTTTAAAA
42683576 TTAAATAATT
1 TTAAATAATT
42683586 AAAATATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 4 0.16
18 9 0.36
19 2 0.08
20 8 0.32
21 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTAAATAATTTTTTAAAA
Found at i:42686802 original size:6 final size:6
Alignment explanation
Indices: 42686791--42686816 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
42686781 ACACCGTAGG
42686791 GTAACA GTAACA GTAACA GTAACA GT
1 GTAACA GTAACA GTAACA GTAACA GT
42686817 CATAATCAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
GTAACA
Found at i:42687748 original size:8 final size:8
Alignment explanation
Indices: 42687737--42687774 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
42687727 ATTATTTCTT
42687737 TTATTATA
1 TTATTATA
42687745 TTATTA-A
1 TTATTATA
*
42687752 GTATTATA
1 TTATTATA
42687760 TTATTATAA
1 TTATTAT-A
42687769 TTATTA
1 TTATTA
42687775 ATTTCTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 6 0.23
8 13 0.50
9 7 0.27
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (8 bp):
TTATTATA
Done.