Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 62 of 145
Found at i:20409238 original size:106 final size:105
Alignment explanation
Indices: 20409121--20409328 Score: 380
Period size: 106 Copynumber: 2.0 Consensus size: 105
20409111 ATTGGATCCG
*
20409121 GTAAGGAAGATACAACATTTATTATTATTATTTTTGTAGATTTGCTCTCTCTATCTATATTTTTT
1 GTAAGGAAGATACAACATTTATTATTATTATTTTTGCAGATTTGCTCTCTCTATCTATA-TTTTT
20409186 TGTTGAGATTGGGTTAGTTTTTTAGATTGTTTTCTTCTCCA
65 TGTTGAGATTGGGTTAGTTTTTTAGATTGTTTTCTTCTCCA
* *
20409227 GTAAGGAAGATACAACCTTTATTATTATTTTTTTTGCAGATTTGCTCTCTCTATCTATATTTTTT
1 GTAAGGAAGATACAACATTTATTATTATTATTTTTGCAGATTTGCTCTCTCTATCTATATTTTTT
20409292 GTTGAGATTGGGTTAGTTTTTTAGATTGTTTTCTTCT
66 GTTGAGATTGGGTTAGTTTTTTAGATTGTTTTCTTCT
20409329 TCTTCACCGT
Statistics
Matches: 99, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
105 43 0.43
106 56 0.57
ACGTcount: A:0.22, C:0.11, G:0.15, T:0.52
Consensus pattern (105 bp):
GTAAGGAAGATACAACATTTATTATTATTATTTTTGCAGATTTGCTCTCTCTATCTATATTTTTT
GTTGAGATTGGGTTAGTTTTTTAGATTGTTTTCTTCTCCA
Found at i:20409970 original size:103 final size:104
Alignment explanation
Indices: 20409777--20409984 Score: 382
Period size: 103 Copynumber: 2.0 Consensus size: 104
20409767 TCTTGCTATT
*
20409777 TGCAGAGATTGATTATCTATTTAATTTTACATTCTTTTATTATTTTTTCTACTTCATTTTGAATA
1 TGCAGAGATTGATTATCTATTTAATTTTACATTCTTTTATTAGTTTTTCTACTTCATTTTGAATA
*
20409842 ATTTTATTTTCTATTTTTCGTGTTTGTTTTATTAGCATC
66 ATTTTATTTTCTATTTTCCGTGTTTGTTTTATTAGCATC
*
20409881 TGCAGAGATTGATTATCTATTTAATTTTACATTCTTTTATT-GTTTTTCTACTTCTTTTTGAATA
1 TGCAGAGATTGATTATCTATTTAATTTTACATTCTTTTATTAGTTTTTCTACTTCATTTTGAATA
20409945 ATTTTATTTTCTATTTTCCGTGTTTGTTTTATTAGCATC
66 ATTTTATTTTCTATTTTCCGTGTTTGTTTTATTAGCATC
20409984 T
1 T
20409985 AACTCAGCCA
Statistics
Matches: 101, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
103 60 0.59
104 41 0.41
ACGTcount: A:0.21, C:0.11, G:0.09, T:0.59
Consensus pattern (104 bp):
TGCAGAGATTGATTATCTATTTAATTTTACATTCTTTTATTAGTTTTTCTACTTCATTTTGAATA
ATTTTATTTTCTATTTTCCGTGTTTGTTTTATTAGCATC
Found at i:20411661 original size:23 final size:23
Alignment explanation
Indices: 20411605--20411662 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
20411595 TTCAACTCAA
**
20411605 GAACATGGCCACAATAAAAACAG
1 GAACATGGCCTTAATAAAAACAG
*
20411628 GAACATGGCCTTAATAAAAATAG
1 GAACATGGCCTTAATAAAAACAG
20411651 GAACATGGCCTT
1 GAACATGGCCTT
20411663 CATTTGTCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.17
Consensus pattern (23 bp):
GAACATGGCCTTAATAAAAACAG
Found at i:20413395 original size:39 final size:40
Alignment explanation
Indices: 20413352--20413456 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
20413342 TTCCATTATG
20413352 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
20413391 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
20413436 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
20413457 ACACCTCTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:20413450 original size:45 final size:44
Alignment explanation
Indices: 20413350--20413459 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
20413340 TTTTCCATTA
20413350 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
20413389 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
20413434 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
20413460 CCTCTATTCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:20413459 original size:16 final size:16
Alignment explanation
Indices: 20413438--20413486 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
20413428 TTGATTTGCT
20413438 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
20413454 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
* *
20413470 ATTACGCCTCTAATCC
1 ATTACACCTCTATTCC
20413486 A
1 A
20413487 ACACAGCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.27, C:0.37, G:0.02, T:0.35
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:20417965 original size:25 final size:24
Alignment explanation
Indices: 20417936--20418022 Score: 111
Period size: 25 Copynumber: 3.5 Consensus size: 24
20417926 TACCAGTTTT
* *
20417936 AGCTCTTATGAGCTTACCGATACTC
1 AGCTCGTATGAGCTTACCGTTA-TC
20417961 AGCTCGTATGAGCTTACCGTTATTC
1 AGCTCGTATGAGCTTACCGTTA-TC
* * *
20417986 AGCTCGGAGGAGCTTACCGTTAAC
1 AGCTCGTATGAGCTTACCGTTATC
20418010 AGCTCGTATGAGC
1 AGCTCGTATGAGC
20418023 ATACATGTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
24 12 0.22
25 42 0.78
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (24 bp):
AGCTCGTATGAGCTTACCGTTATC
Found at i:20430460 original size:21 final size:21
Alignment explanation
Indices: 20430429--20430501 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
20430419 ACTGTTGTTG
*
20430429 AGAAGTAAGTTGCTGCTGCAGA
1 AGAAG-AAGTTGTTGCTGCAGA
* *
20430451 AGAGGAAGTTGTTGCTGCGGA
1 AGAAGAAGTTGTTGCTGCAGA
*
20430472 A-AATGAAGTTGTTGCTGAAGA
1 AGAA-GAAGTTGTTGCTGCAGA
20430493 AGAAGAAGT
1 AGAAGAAGT
20430502 AGCTAAAGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.02
21 36 0.84
22 6 0.14
ACGTcount: A:0.34, C:0.08, G:0.34, T:0.23
Consensus pattern (21 bp):
AGAAGAAGTTGTTGCTGCAGA
Found at i:20448835 original size:78 final size:78
Alignment explanation
Indices: 20448705--20448861 Score: 228
Period size: 78 Copynumber: 2.0 Consensus size: 78
20448695 TGCATCCAGA
* *
20448705 GAAAGGTTTCACAGTGAAAAAAAGGAACTATATTGGTTTTAATGTGCTTATTCGTCAGGTTACTG
1 GAAAGGTTTCACAGTGAAAAAAAGCAACTATATTGGTTTTAATGTGCGTATTCGTCAGGTTACTG
20448770 AAACTCTCAATTG
66 AAACTCTCAATTG
* * **
20448783 GAAAGGTTTCACATTGAAAGAAAGCAACTATATTGGTTTT-ATG-GCACGTATTCGTCAGGTTGT
1 GAAAGGTTTCACAGTGAAAAAAAGCAACTATATTGGTTTTAATGTG--CGTATTCGTCAGGTTAC
20448846 TGAAACTCTCAATTG
64 TGAAACTCTCAATTG
20448861 G
1 G
20448862 GATTTGTTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
76 1 0.01
77 3 0.04
78 67 0.94
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (78 bp):
GAAAGGTTTCACAGTGAAAAAAAGCAACTATATTGGTTTTAATGTGCGTATTCGTCAGGTTACTG
AAACTCTCAATTG
Found at i:20455422 original size:78 final size:78
Alignment explanation
Indices: 20455292--20455448 Score: 242
Period size: 78 Copynumber: 2.0 Consensus size: 78
20455282 TGCATCCAGA
* ** *
20455292 GAAAGGTTTCACAGTGAAAAAAAGGAACTATATTGGTTTTATGGTGCTTATTCGTCAGGTTACTG
1 GAAAGGTTTCACAGTGAAAAAAAGCAACTATATTGGTTTTATGGCACGTATTCGTCAGGTTACTG
20455357 AAACTCTCAATTG
66 AAACTCTCAATTG
* * **
20455370 GAAAGGTTTCACATTGAAAGAAAGCAACTATATTGGTTTTATGGCACGTATTCGTCAGGTTGTTG
1 GAAAGGTTTCACAGTGAAAAAAAGCAACTATATTGGTTTTATGGCACGTATTCGTCAGGTTACTG
20455435 AAACTCTCAATTG
66 AAACTCTCAATTG
20455448 G
1 G
20455449 GATTTGTTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 71 1.00
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.33
Consensus pattern (78 bp):
GAAAGGTTTCACAGTGAAAAAAAGCAACTATATTGGTTTTATGGCACGTATTCGTCAGGTTACTG
AAACTCTCAATTG
Found at i:20472527 original size:11 final size:11
Alignment explanation
Indices: 20472513--20472544 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
20472503 TATTTTTTAA
20472513 TTTTAAAATAC
1 TTTTAAAATAC
20472524 TTTTAAAATAC
1 TTTTAAAATAC
20472535 TTTTAAAATA
1 TTTTAAAATA
20472545 AATTTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:20472565 original size:27 final size:26
Alignment explanation
Indices: 20472535--20472596 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
20472525 TTTAAAATAC
* *
20472535 TTTTAAAATAAATTTTTTATTTTTTAT
1 TTTTAAAAT-AATTTTTTAATGTTTAT
*
20472562 TTTTAAAATACTTTTTTAATGTTTAT
1 TTTTAAAATAATTTTTTAATGTTTAT
*
20472588 TTTAAAAAT
1 TTTTAAAAT
20472597 GGGCCGGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 22 0.71
27 9 0.29
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTTAAAATAATTTTTTAATGTTTAT
Found at i:20472743 original size:80 final size:82
Alignment explanation
Indices: 20472638--20472795 Score: 230
Period size: 80 Copynumber: 2.0 Consensus size: 82
20472628 TTCCCGGGCC
* * **
20472638 GGGCCTAGGCAAAATTTTAGACCCATATTTCGGGCCGGGCCGGG-CCGGGCCTAGGAGGCGGGCC
1 GGGCCTAGGCAAAATTTCAGACCCATATTTCAGGCCGGGCCGGGCCCGGGCCTAGGAGGCAAGCC
20472702 -AAAAATTTTTTCCGGT
66 AAAAAATTTTTTCCGGT
* * * *
20472718 GGGCCTGGGTAAAATTTCAGGCCCATATTTCAGGTCGGGCCGGGCCCGGGCCTAGGAGGCAAGCC
1 GGGCCTAGGCAAAATTTCAGACCCATATTTCAGGCCGGGCCGGGCCCGGGCCTAGGAGGCAAGCC
20472783 AAAAAATTTTTTC
66 AAAAAATTTTTTC
20472796 GAGCTCGGCC
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
80 38 0.56
81 18 0.26
82 12 0.18
ACGTcount: A:0.22, C:0.25, G:0.32, T:0.22
Consensus pattern (82 bp):
GGGCCTAGGCAAAATTTCAGACCCATATTTCAGGCCGGGCCGGGCCCGGGCCTAGGAGGCAAGCC
AAAAAATTTTTTCCGGT
Found at i:20474615 original size:5 final size:5
Alignment explanation
Indices: 20474593--20474673 Score: 56
Period size: 5 Copynumber: 15.6 Consensus size: 5
20474583 TTTTATTGAA
* * ** *
20474593 TTTAT CTTTAT CTTTAT TTTAT TTTAT TTTAGT TTTTT TTTGT TCAAG
1 TTTAT -TTTAT -TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT
* *
20474641 CTTGT TTTAT TTT-T ATTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT -TTTAT TTTAT TTTAT TTT
20474674 TGCAGAATAA
Statistics
Matches: 59, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
4 1 0.02
5 42 0.71
6 16 0.27
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:20491341 original size:75 final size:74
Alignment explanation
Indices: 20491208--20491386 Score: 252
Period size: 75 Copynumber: 2.4 Consensus size: 74
20491198 TATATATCGA
* *
20491208 GCATTAGCGGCGCTTTTTGAAAAACACCACAAAAAATTAAGAACAACGCCGTCGTTTTATGTTGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCACAAAAAATTAAGAACAACGCCGCCGTTTTATGTTGA
20491273 GCTTTAGTG
66 GCTTTAGTG
* * * * *
20491282 GTATTAGAGGCACTTTTTGAAAAACGCCGTA-AAAAAATTCAGCACAACGCCGCCGTTTTATGTT
1 GCATTAGCGGCGCTTTTTGAAAAACGCC--ACAAAAAATTAAGAACAACGCCGCCGTTTTATGTT
20491346 GAGCTTTAGTG
64 GAGCTTTAGTG
* *
20491357 GCATTAGCGGTGCTTCTTGAAAAACGCCAC
1 GCATTAGCGGCGCTTTTTGAAAAACGCCAC
20491387 TATAGATCAA
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
73 1 0.01
74 24 0.27
75 64 0.71
76 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (74 bp):
GCATTAGCGGCGCTTTTTGAAAAACGCCACAAAAAATTAAGAACAACGCCGCCGTTTTATGTTGA
GCTTTAGTG
Found at i:20491646 original size:7 final size:7
Alignment explanation
Indices: 20491634--20491728 Score: 50
Period size: 7 Copynumber: 13.3 Consensus size: 7
20491624 CAGATTATAT
*
20491634 GGTTTAG
1 GGTTTAA
20491641 GGTTTAA
1 GGTTTAA
20491648 GGTTTAA
1 GGTTTAA
20491655 GGTTTAA
1 GGTTTAA
20491662 GAG-TTACTA
1 G-GTTTA--A
*
20491671 -TTTTAA
1 GGTTTAA
*
20491677 GGTTTAT
1 GGTTTAA
* *
20491684 GGATTATG
1 GGTTTA-A
*
20491692 GGTTTAG
1 GGTTTAA
* *
20491699 GGATTAT
1 GGTTTAA
*
20491706 GGTTTAT
1 GGTTTAA
*
20491713 GGTTTAT
1 GGTTTAA
20491720 GGTTTAA
1 GGTTTAA
20491727 GG
1 GG
20491729 GTTGGGGTTT
Statistics
Matches: 71, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
6 1 0.01
7 60 0.85
8 9 0.13
9 1 0.01
ACGTcount: A:0.23, C:0.01, G:0.31, T:0.45
Consensus pattern (7 bp):
GGTTTAA
Found at i:20491653 original size:14 final size:14
Alignment explanation
Indices: 20491634--20491731 Score: 56
Period size: 14 Copynumber: 6.8 Consensus size: 14
20491624 CAGATTATAT
20491634 GGTTTAGGGTTTAA
1 GGTTTAGGGTTTAA
*
20491648 GGTTTAAGGTTTAA
1 GGTTTAGGGTTTAA
*
20491662 GAGTTACTA--TTTTAA
1 G-GTT--TAGGGTTTAA
* * *
20491677 GGTTTATGGATTATG
1 GGTTTAGGGTTTA-A
* *
20491692 GGTTTAGGGATTAT
1 GGTTTAGGGTTTAA
* *
20491706 GGTTTATGGTTTAT
1 GGTTTAGGGTTTAA
20491720 GGTTTAAGGGTT
1 GGTTT-AGGGTT
20491732 GGGGTTTAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 13
0.74 0.11 0.14
Matches are distributed among these distances:
12 2 0.03
14 37 0.55
15 26 0.39
17 2 0.03
ACGTcount: A:0.22, C:0.01, G:0.31, T:0.46
Consensus pattern (14 bp):
GGTTTAGGGTTTAA
Found at i:20491695 original size:15 final size:14
Alignment explanation
Indices: 20491677--20491725 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
20491667 ACTATTTTAA
20491677 GGTTTATGGATTAT
1 GGTTTATGGATTAT
*
20491691 GGGTTTAGGGATTAT
1 -GGTTTATGGATTAT
*
20491706 GGTTTATGGTTTAT
1 GGTTTATGGATTAT
20491720 GGTTTA
1 GGTTTA
20491726 AGGGTTGGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.49
Consensus pattern (14 bp):
GGTTTATGGATTAT
Found at i:20492884 original size:20 final size:20
Alignment explanation
Indices: 20492861--20493006 Score: 97
Period size: 20 Copynumber: 7.3 Consensus size: 20
20492851 TACTTTGACA
*
20492861 CCCCTGATTGCACTTACATG
1 CCCCTGATTGCACTTACGTG
* *
20492881 CCCCT-ATTTGTACTTTA-GTA
1 CCCCTGA-TTGCAC-TTACGTG
*
20492901 CCCCTGATTGCACTTACATG
1 CCCCTGATTGCACTTACGTG
* * *
20492921 CCCCT-ATTTGTA-TTTCGGTA
1 CCCCTGA-TTGCACTTAC-GTG
20492941 CCCCTGATTGCACTTACGTG
1 CCCCTGATTGCACTTACGTG
* *
20492961 CCCCTGTTTGTACTT-CG-G
1 CCCCTGATTGCACTTACGTG
* *
20492979 CACCCTTGGTTGCACTTCCGTG
1 C-CCC-TGATTGCACTTACGTG
20493001 CCCCTG
1 CCCCTG
20493007 GTTATACTCT
Statistics
Matches: 97, Mismatches: 17, Indels: 24
0.70 0.12 0.17
Matches are distributed among these distances:
18 2 0.02
19 13 0.13
20 67 0.69
21 13 0.13
22 2 0.02
ACGTcount: A:0.14, C:0.34, G:0.17, T:0.35
Consensus pattern (20 bp):
CCCCTGATTGCACTTACGTG
Found at i:20493006 original size:40 final size:40
Alignment explanation
Indices: 20492751--20493006 Score: 278
Period size: 40 Copynumber: 6.4 Consensus size: 40
20492741 TGACTGACTA
* *
20492751 CACTTACATGCCCTTGTTTGTACTTCGGTACCCCTGATTG
1 CACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGATTG
* * ** *
20492791 CACTTACGTGCCCATGTTTGAACTTCAATACCCCTAATTG
1 CACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGATTG
* * *** * **
20492831 CACTTATGTTCCCCTACATGTACTTTGACACCCCTGATTG
1 CACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGATTG
* * **
20492871 CACTTACATGCCCCTATTTGTACTTTAGTACCCCTGATTG
1 CACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGATTG
* * *
20492911 CACTTACATGCCCCTATTTGTATTTCGGTACCCCTGATTG
1 CACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGATTG
* * *
20492951 CACTTACGTGCCCCTGTTTGTACTTCGGCACCCTTGGTTG
1 CACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGATTG
*
20492991 CACTTCCGTGCCCCTG
1 CACTTACGTGCCCCTG
20493007 GTTATACTCT
Statistics
Matches: 181, Mismatches: 35, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 181 1.00
ACGTcount: A:0.17, C:0.32, G:0.16, T:0.35
Consensus pattern (40 bp):
CACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGATTG
Found at i:20494554 original size:30 final size:30
Alignment explanation
Indices: 20494514--20494580 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
20494504 GTGTCTCAAC
*
20494514 TGTGTATGACACACAGCCATGCGACACGAT
1 TGTGTGTGACACACAGCCATGCGACACGAT
* * *
20494544 TGTGTGTGACATAGAGCCATGCGACACGGT
1 TGTGTGTGACACACAGCCATGCGACACGAT
*
20494574 CGTGTGT
1 TGTGTGT
20494581 CCCCTGTATG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (30 bp):
TGTGTGTGACACACAGCCATGCGACACGAT
Found at i:20499790 original size:6 final size:6
Alignment explanation
Indices: 20499779--20499812 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
20499769 TTTTTGAGTA
20499779 AGTAGG AGTAGG AGTAGG AGTAGG AGTAGG AGTA
1 AGTAGG AGTAGG AGTAGG AGTAGG AGTAGG AGTA
20499813 ATAGTATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.47, T:0.18
Consensus pattern (6 bp):
AGTAGG
Found at i:20499818 original size:18 final size:18
Alignment explanation
Indices: 20499779--20499818 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
20499769 TTTTTGAGTA
*
20499779 AGTAGGAGTAGGAGTAGG
1 AGTAGGAGTAGGAGTAAG
*
20499797 AGTAGGAGTAGGAGTAAT
1 AGTAGGAGTAGGAGTAAG
20499815 AGTA
1 AGTA
20499819 TATTTTTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.42, T:0.20
Consensus pattern (18 bp):
AGTAGGAGTAGGAGTAAG
Found at i:20501230 original size:14 final size:15
Alignment explanation
Indices: 20501213--20501241 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20501203 GTGGCAAGTC
20501213 AATTATTCA-TCATG
1 AATTATTCATTCATG
20501227 AATTATTCATTCATG
1 AATTATTCATTCATG
20501242 TGCTCCAAAA
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:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (15 bp):
AATTATTCATTCATG
Found at i:20514903 original size:5 final size:5
Alignment explanation
Indices: 20514893--20514918 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
20514883 GATATTTCTA
20514893 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
20514919 TCGTTCTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:20516963 original size:20 final size:20
Alignment explanation
Indices: 20516940--20516978 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
20516930 ATGTAAATTA
20516940 ATTTTATAATATACTTTTTT
1 ATTTTATAATATACTTTTTT
20516960 ATTTTATAATATACTTTTT
1 ATTTTATAATATACTTTTT
20516979 GACCACGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTTATAATATACTTTTTT
Found at i:20522316 original size:177 final size:177
Alignment explanation
Indices: 20522020--20522362 Score: 668
Period size: 177 Copynumber: 1.9 Consensus size: 177
20522010 GAAGAATGAG
*
20522020 CATGACAAACAGTATCAGCAGTTCCTGGACACACTGAAGCAATTACAGATCAACATTCTTTTAGT
1 CATGACAAACAGTATCAGCAGTTCCTGGACACACTGAAGCAATTACAGATCAACATTCCTTTAGT
20522085 AGATGCTCTGGTACAAATTCCAAGTTATGGGAAATTTATGAAAGACCTCTTGCCCAAGAAGAAGA
66 AGATGCTCTGGTACAAATTCCAAGTTATGGGAAATTTATGAAAGACCTCTTGCCCAAGAAGAAGA
20522150 AGCTCACTGATATTGAAACTATTGCACTCATAGAAGCAATTACAGAT
131 AGCTCACTGATATTGAAACTATTGCACTCATAGAAGCAATTACAGAT
*
20522197 CATGACAAACAGTATCAGGAGTTCCTGGACACACTGAAGCAATTACAGATCAACATTCCTTTAGT
1 CATGACAAACAGTATCAGCAGTTCCTGGACACACTGAAGCAATTACAGATCAACATTCCTTTAGT
20522262 AGATGCTCTGGTACAAATTCCAAGTTATGGGAAATTTATGAAAGACCTCTTGCCCAAGAAGAAGA
66 AGATGCTCTGGTACAAATTCCAAGTTATGGGAAATTTATGAAAGACCTCTTGCCCAAGAAGAAGA
20522327 AGCTCACTGATATTGAAACTATTGCACTCATAGAAG
131 AGCTCACTGATATTGAAACTATTGCACTCATAGAAG
20522363 GTTGTACTGT
Statistics
Matches: 164, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
177 164 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (177 bp):
CATGACAAACAGTATCAGCAGTTCCTGGACACACTGAAGCAATTACAGATCAACATTCCTTTAGT
AGATGCTCTGGTACAAATTCCAAGTTATGGGAAATTTATGAAAGACCTCTTGCCCAAGAAGAAGA
AGCTCACTGATATTGAAACTATTGCACTCATAGAAGCAATTACAGAT
Found at i:20527766 original size:21 final size:21
Alignment explanation
Indices: 20527750--20527790 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20527740 GCTGCTACAG
*
20527750 AAGAGGAAGTTATTGCTAAAA
1 AAGAAGAAGTTATTGCTAAAA
*
20527771 AAGAAGAAGTTGTTGC-AAAA
1 AAGAAGAAGTTATTGCTAAAA
20527791 GGGAAGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.49, C:0.05, G:0.24, T:0.22
Consensus pattern (21 bp):
AAGAAGAAGTTATTGCTAAAA
Found at i:20535148 original size:160 final size:160
Alignment explanation
Indices: 20534884--20535845 Score: 1915
Period size: 160 Copynumber: 6.0 Consensus size: 160
20534874 GAAATAGAAT
20534884 AGTAAAATTACGTTCCCATAGAAAATTGATTTTCAAAACTAGTAACACTGCTACTACTGTGAGGG
1 AGTAAAATTACGTTCCCATAGAAAATTGATTTTCAAAACTAGTAACACTGCTACTACTGTGAGGG
20534949 TTGCAGATTGACAGAGAGATAGAGTGAGGATGGTAAGGGTCGGGGTACCTCCAAAATGACAGAAA
66 TTGCAGATTGACAGAGAGATAGAGTGAGGATGGTAAGGGTCGGGGTACCTCCAAAATGACAGAAA
20535014 AGGCAATGAGATTCCGAATCATTCTCCTCC
131 AGGCAATGAGATTCCGAATCATTCTCCTCC
20535044 AGTAAAATTACGTTCCCATAGAAAATTGATTTTCAAAACTAGTAACACTGCTACTACTGTGAGGG
1 AGTAAAATTACGTTCCCATAGAAAATTGATTTTCAAAACTAGTAACACTGCTACTACTGTGAGGG
20535109 TTGCAGATTGACAGAGAGATAGAGTGAGGATGGTAAGGGTCGGGGTACCTCCAAAATGACAGAAA
66 TTGCAGATTGACAGAGAGATAGAGTGAGGATGGTAAGGGTCGGGGTACCTCCAAAATGACAGAAA
20535174 AGGCAATGAGATTCCGAATCATTCTCCTCC
131 AGGCAATGAGATTCCGAATCATTCTCCTCC
20535204 AGTAAAATTACGTTCCCATAGAAAATTGATTTTCAAAACTAGTAACACTGCTACTACTGTGAGGG
1 AGTAAAATTACGTTCCCATAGAAAATTGATTTTCAAAACTAGTAACACTGCTACTACTGTGAGGG
20535269 TTGCAGATTGACAGAGAGATAGAGTGAGGATGGTAAGGGTCGGGGTACCTCCAAAATGACAGAAA
66 TTGCAGATTGACAGAGAGATAGAGTGAGGATGGTAAGGGTCGGGGTACCTCCAAAATGACAGAAA
20535334 AGGCAATGAGATTCCGAATCATTCTCCTCC
131 AGGCAATGAGATTCCGAATCATTCTCCTCC
20535364 AGTAAAATTACGTTCCCATAGAAAATTGATTTTCAAAACTAGTAACACTGCTACTACTGTGAGGG
1 AGTAAAATTACGTTCCCATAGAAAATTGATTTTCAAAACTAGTAACACTGCTACTACTGTGAGGG
20535429 TTGCAGATTGACAGAGAGATAGAGTGAGGATGGTAAGGGTCGGGGTACCTCCAAAATGACAGAAA
66 TTGCAGATTGACAGAGAGATAGAGTGAGGATGGTAAGGGTCGGGGTACCTCCAAAATGACAGAAA
20535494 AGGCAATGAGATTCCGAATCATTCTCCTCC
131 AGGCAATGAGATTCCGAATCATTCTCCTCC
20535524 AGTAAAATTACGTTCCCATAGAAAATTGATTTTCAAAACTAGTAACACTGCTACTACTGTGAGGG
1 AGTAAAATTACGTTCCCATAGAAAATTGATTTTCAAAACTAGTAACACTGCTACTACTGTGAGGG
*
20535589 TTGCAGATTGACAGAGAGATAGAGTGAGGATGGTAAGGGTCGGGGTGCCTCCAAAATGACAGAAA
66 TTGCAGATTGACAGAGAGATAGAGTGAGGATGGTAAGGGTCGGGGTACCTCCAAAATGACAGAAA
20535654 AGGCAATGAGATTCCGAATCATTCTCCTCC
131 AGGCAATGAGATTCCGAATCATTCTCCTCC
20535684 AGTAAAATTACGTTCCCATAGAAAATTGATTTTCAAAACTAGTAACACTGCTACTACTGTGAGGG
1 AGTAAAATTACGTTCCCATAGAAAATTGATTTTCAAAACTAGTAACACTGCTACTACTGTGAGGG
20535749 TTGCAGATTGACAGAGAGATAGAGTGAGGATGGTAAGGGTCGGGGTACCTCCAAAATGACAGAAA
66 TTGCAGATTGACAGAGAGATAGAGTGAGGATGGTAAGGGTCGGGGTACCTCCAAAATGACAGAAA
20535814 AGGCAATGAGATTCCGAATCATTCTCCTCC
131 AGGCAATGAGATTCCGAATCATTCTCCTCC
20535844 AG
1 AG
20535846 GTCTGGGATC
Statistics
Matches: 800, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 800 1.00
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.24
Consensus pattern (160 bp):
AGTAAAATTACGTTCCCATAGAAAATTGATTTTCAAAACTAGTAACACTGCTACTACTGTGAGGG
TTGCAGATTGACAGAGAGATAGAGTGAGGATGGTAAGGGTCGGGGTACCTCCAAAATGACAGAAA
AGGCAATGAGATTCCGAATCATTCTCCTCC
Found at i:20541895 original size:32 final size:32
Alignment explanation
Indices: 20541851--20541927 Score: 138
Period size: 32 Copynumber: 2.4 Consensus size: 32
20541841 ATTATAGTAT
20541851 AACATA-ATATAAATATTATAAAAAATTATAA
1 AACATAGATATAAATATTATAAAAAATTATAA
*
20541882 AACATAGATATAAATATTATAAACAATTATAA
1 AACATAGATATAAATATTATAAAAAATTATAA
20541914 AACATAGATATAAA
1 AACATAGATATAAA
20541928 AAGATGAGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 6 0.14
32 38 0.86
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (32 bp):
AACATAGATATAAATATTATAAAAAATTATAA
Found at i:20542863 original size:61 final size:61
Alignment explanation
Indices: 20542768--20542884 Score: 207
Period size: 61 Copynumber: 1.9 Consensus size: 61
20542758 AATTAATCAC
* *
20542768 ATTAATATTATATTAATAAAATATTATCTAGATAAATATTAAATTAAATTTAATATCTCAT
1 ATTAATATTACATTAATAAAATACTATCTAGATAAATATTAAATTAAATTTAATATCTCAT
*
20542829 ATTAATATTACATTAATAAAATACTATCTAGATAAATATTAAATTTAATTTAATAT
1 ATTAATATTACATTAATAAAATACTATCTAGATAAATATTAAATTAAATTTAATAT
20542885 TAAATTCATT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (61 bp):
ATTAATATTACATTAATAAAATACTATCTAGATAAATATTAAATTAAATTTAATATCTCAT
Found at i:20544254 original size:71 final size:71
Alignment explanation
Indices: 20544112--20544244 Score: 187
Period size: 71 Copynumber: 1.9 Consensus size: 71
20544102 TCTATCGACG
* * * * *
20544112 CCTTGAGGACTTCTACTGAAACAAGTCAAGTTAGTAGCCAAAGTTCAACATCTCCTACACTTCTA
1 CCTTAAGGACTTCTACTAAAACAAGTCAAGTCAGTAGCAAAAGTTCAACATCCCCTACACTTCTA
20544177 CCGATA
66 CCGATA
* *
20544183 CCTTAAGGACTTCTAAC-AAAACAATTCAAGTCAGTAGCAAAAGTTCAGCATCCCCTACACTT
1 CCTTAAGGACTTCT-ACTAAAACAAGTCAAGTCAGTAGCAAAAGTTCAACATCCCCTACACTT
20544245 TTATTGATAC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 52 0.96
72 2 0.04
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.26
Consensus pattern (71 bp):
CCTTAAGGACTTCTACTAAAACAAGTCAAGTCAGTAGCAAAAGTTCAACATCCCCTACACTTCTA
CCGATA
Found at i:20556071 original size:18 final size:18
Alignment explanation
Indices: 20556048--20556085 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
20556038 CCGAGTGGGT
*
20556048 CACATGAGCATGTGGGCC
1 CACATGAGCATGTGAGCC
*
20556066 CACATGGGCATGTGAGCC
1 CACATGAGCATGTGAGCC
20556084 CA
1 CA
20556086 TTATTACTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.32, T:0.16
Consensus pattern (18 bp):
CACATGAGCATGTGAGCC
Found at i:20568628 original size:50 final size:50
Alignment explanation
Indices: 20568500--20568741 Score: 175
Period size: 50 Copynumber: 4.7 Consensus size: 50
20568490 GTTAATAACA
* * * ** * *
20568500 TGCCAAAGTCATGTCGCAGACATGGTCTTACATGGGATGTTTCCTATAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * **
20568549 AGCCAATGCCATATCCCA-TCTATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGAC-ATGGTCTTACATGGGACCTCTCATATCGG
* * ** * *
20568599 TGCCCATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
** * * **
20568649 TGCCAACACCATGTCCCAAACATGGTCTTACGTGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
20568705 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
20568742 TCCCATTCCC
Statistics
Matches: 148, Mismatches: 35, Indels: 13
0.76 0.18 0.07
Matches are distributed among these distances:
48 2 0.01
49 35 0.24
50 76 0.51
51 1 0.01
53 1 0.01
56 33 0.22
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:20569289 original size:56 final size:50
Alignment explanation
Indices: 20569170--20569302 Score: 140
Period size: 56 Copynumber: 2.5 Consensus size: 50
20569160 TTCATCCCTT
* * **
20569170 ATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTTGGTGCCAACACC
1 ATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTTAATGCCAACACC
* **
20569220 ATGTCCCAAACATGGTCTTACGTGGGACCTCTCATAACCTCAATAATGCCAATGCC
1 ATGTCCCAGACATGGTCTTACGTGGGACCTCTCAT---CT---TAATGCCAACACC
*
20569276 ATGTCCCAGACATGGTCTTACATGGGA
1 ATGTCCCAGACATGGTCTTACGTGGGA
20569303 TCCCATTCCC
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
50 32 0.47
53 2 0.03
56 34 0.50
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.26
Consensus pattern (50 bp):
ATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTTAATGCCAACACC
Found at i:20569671 original size:561 final size:561
Alignment explanation
Indices: 20568609--20569732 Score: 2248
Period size: 561 Copynumber: 2.0 Consensus size: 561
20568599 TGCCCATGCC
20568609 ATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTTGGTGCCAACACCATGTCCCAAACATGG
1 ATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTTGGTGCCAACACCATGTCCCAAACATGG
20568674 TCTTACGTGGGACCTCTCATAACCTCAATAATGCCAATGCCATGTCCCAGACATGGTCTTACATG
66 TCTTACGTGGGACCTCTCATAACCTCAATAATGCCAATGCCATGTCCCAGACATGGTCTTACATG
20568739 GGATCCCATTCCCTTAATGTCATGACATTTGTATCAGATACATTCTTAATGTTTCAACGAGACAT
131 GGATCCCATTCCCTTAATGTCATGACATTTGTATCAGATACATTCTTAATGTTTCAACGAGACAT
20568804 TTTAACACTAATTCTCTATCATCTCATACTTGAGTCCACATTAAATAATTTCATAAAATAAGTAC
196 TTTAACACTAATTCTCTATCATCTCATACTTGAGTCCACATTAAATAATTTCATAAAATAAGTAC
20568869 ATAATTGCTGGAAAATAACAACATTAATAATAATTATTGAAATATTGCATTTATTTACCGTAAAC
261 ATAATTGCTGGAAAATAACAACATTAATAATAATTATTGAAATATTGCATTTATTTACCGTAAAC
20568934 TTACCTCAGTACAAAATACGATCAAATCTAGTAACCTAGTCCTCAATCTTTTTCTTTCCCCGATC
326 TTACCTCAGTACAAAATACGATCAAATCTAGTAACCTAGTCCTCAATCTTTTTCTTTCCCCGATC
20568999 TAACTCCAGATTTTGTTCTTCTTGATATATAATAGAAAATTTATCTTATTTAATACTCACATTCA
391 TAACTCCAGATTTTGTTCTTCTTGATATATAATAGAAAATTTATCTTATTTAATACTCACATTCA
20569064 TCAAAACAATCCTTGACTCGAAATTTAGCAAAATTACGATTTTGCCTCTAAAATTTTGCATATTT
456 TCAAAACAATCCTTGACTCGAAATTTAGCAAAATTACGATTTTGCCTCTAAAATTTTGCATATTT
20569129 ACATTTCTGCCCCAAAGCTCAAAAATTAAACTTCATCCCTT
521 ACATTTCTGCCCCAAAGCTCAAAAATTAAACTTCATCCCTT
20569170 ATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTTGGTGCCAACACCATGTCCCAAACATGG
1 ATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTTGGTGCCAACACCATGTCCCAAACATGG
20569235 TCTTACGTGGGACCTCTCATAACCTCAATAATGCCAATGCCATGTCCCAGACATGGTCTTACATG
66 TCTTACGTGGGACCTCTCATAACCTCAATAATGCCAATGCCATGTCCCAGACATGGTCTTACATG
20569300 GGATCCCATTCCCTTAATGTCATGACATTTGTATCAGATACATTCTTAATGTTTCAACGAGACAT
131 GGATCCCATTCCCTTAATGTCATGACATTTGTATCAGATACATTCTTAATGTTTCAACGAGACAT
20569365 TTTAACACTAATTCTCTATCATCTCATACTTGAGTCCACATTAAATAATTTCATAAAATAAGTAC
196 TTTAACACTAATTCTCTATCATCTCATACTTGAGTCCACATTAAATAATTTCATAAAATAAGTAC
20569430 ATAATTGCTGGAAAATAACAACATTAATAATAATTATTGAAATATTGCATTTATTTACCGTAAAC
261 ATAATTGCTGGAAAATAACAACATTAATAATAATTATTGAAATATTGCATTTATTTACCGTAAAC
20569495 TTACCTCAGTACAAAATACGATCAAATCTAGTAACCTAGTCCTCAATCTTTTTCTTTCCCCGATC
326 TTACCTCAGTACAAAATACGATCAAATCTAGTAACCTAGTCCTCAATCTTTTTCTTTCCCCGATC
20569560 TAACTCCAGATTTTGTTCTTCTTGATATATAATAGAAAATTTATCTTATTTAATACTCACATTCA
391 TAACTCCAGATTTTGTTCTTCTTGATATATAATAGAAAATTTATCTTATTTAATACTCACATTCA
20569625 TCAAAACAATCCTTGACTCGAAATTTAGCAAAATTACGATTTTGCCTCTAAAATTTTGCATATTT
456 TCAAAACAATCCTTGACTCGAAATTTAGCAAAATTACGATTTTGCCTCTAAAATTTTGCATATTT
20569690 ACATTTCTGCCCCAAAGCTCAAAAATTAAACTTCATCCCTT
521 ACATTTCTGCCCCAAAGCTCAAAAATTAAACTTCATCCCTT
20569731 AT
1 AT
20569733 TCTTATGTTT
Statistics
Matches: 563, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
561 563 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.34
Consensus pattern (561 bp):
ATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTTGGTGCCAACACCATGTCCCAAACATGG
TCTTACGTGGGACCTCTCATAACCTCAATAATGCCAATGCCATGTCCCAGACATGGTCTTACATG
GGATCCCATTCCCTTAATGTCATGACATTTGTATCAGATACATTCTTAATGTTTCAACGAGACAT
TTTAACACTAATTCTCTATCATCTCATACTTGAGTCCACATTAAATAATTTCATAAAATAAGTAC
ATAATTGCTGGAAAATAACAACATTAATAATAATTATTGAAATATTGCATTTATTTACCGTAAAC
TTACCTCAGTACAAAATACGATCAAATCTAGTAACCTAGTCCTCAATCTTTTTCTTTCCCCGATC
TAACTCCAGATTTTGTTCTTCTTGATATATAATAGAAAATTTATCTTATTTAATACTCACATTCA
TCAAAACAATCCTTGACTCGAAATTTAGCAAAATTACGATTTTGCCTCTAAAATTTTGCATATTT
ACATTTCTGCCCCAAAGCTCAAAAATTAAACTTCATCCCTT
Found at i:20579424 original size:28 final size:28
Alignment explanation
Indices: 20579381--20579435 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
20579371 GAGTAAGGAT
20579381 TAAGGAAATCACTGAATCAACATAATCA
1 TAAGGAAATCACTGAATCAACATAATCA
* *
20579409 TAAGGAAATCATTGAATCTACATAATC
1 TAAGGAAATCACTGAATCAACATAATC
20579436 CTGGACTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.25
Consensus pattern (28 bp):
TAAGGAAATCACTGAATCAACATAATCA
Found at i:20580464 original size:31 final size:30
Alignment explanation
Indices: 20580409--20580468 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
20580399 AGTTACAAAA
* * *
20580409 TAGTCATCCAACTATTCCACTTTTTCTTTTT
1 TAGTCACCCAACTATTCAAATTTTT-TTTTT
*
20580440 TAGTCACCCAACTATTTAAATTTTTTTTT
1 TAGTCACCCAACTATTCAAATTTTTTTTT
20580469 AATCACCAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.23, C:0.22, G:0.03, T:0.52
Consensus pattern (30 bp):
TAGTCACCCAACTATTCAAATTTTTTTTTT
Found at i:20580484 original size:26 final size:28
Alignment explanation
Indices: 20580435--20580487 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
20580425 CCACTTTTTC
* *
20580435 TTTTTTAGTCACCCAACTATTTAAATTT
1 TTTTTTAATCACCCAACTAGTTAAATTT
20580463 TTTTTTAATCA-CCAACT-GTTAAATT
1 TTTTTTAATCACCCAACTAGTTAAATT
20580488 ACTAACGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 7 0.30
27 6 0.26
28 10 0.43
ACGTcount: A:0.30, C:0.17, G:0.04, T:0.49
Consensus pattern (28 bp):
TTTTTTAATCACCCAACTAGTTAAATTT
Found at i:20582789 original size:113 final size:114
Alignment explanation
Indices: 20582630--20582857 Score: 449
Period size: 113 Copynumber: 2.0 Consensus size: 114
20582620 TTCCATATAA
20582630 TATATTTTAACTTTTTAATGTTAAATATTTATATAATATATTATTGTAATCAACTTTAATATAAC
1 TATATTTTAACTTTTTAATGTTAAATATTTATATAATATATTATTGTAATCAACTTTAATATAAC
20582695 ATTAAATGTAATATTGATATATTTTCAACTTTCTTTTTTTAGATGATAG
66 ATTAAATGTAATATTGATATATTTTCAACTTTCTTTTTTTAGATGATAG
20582744 TATATTTTAAC-TTTTAATGTTAAATATTTATATAATATATTATTGTAATCAACTTTAATATAAC
1 TATATTTTAACTTTTTAATGTTAAATATTTATATAATATATTATTGTAATCAACTTTAATATAAC
20582808 ATTAAATGTAATATTGATATATTTTCAACTTTCTTTTTTTAGATGATAG
66 ATTAAATGTAATATTGATATATTTTCAACTTTCTTTTTTTAGATGATAG
20582857 T
1 T
20582858 TTTTAATATA
Statistics
Matches: 114, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
113 103 0.90
114 11 0.10
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (114 bp):
TATATTTTAACTTTTTAATGTTAAATATTTATATAATATATTATTGTAATCAACTTTAATATAAC
ATTAAATGTAATATTGATATATTTTCAACTTTCTTTTTTTAGATGATAG
Found at i:20585192 original size:14 final size:14
Alignment explanation
Indices: 20585173--20585200 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20585163 TTGGAATGAA
20585173 GATTAAATTTCATG
1 GATTAAATTTCATG
20585187 GATTAAATTTCATG
1 GATTAAATTTCATG
20585201 AATTTCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
GATTAAATTTCATG
Found at i:20585210 original size:14 final size:14
Alignment explanation
Indices: 20585174--20585204 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
20585164 TGGAATGAAG
*
20585174 ATTAAATTTCATGG
1 ATTAAATTTCATGA
20585188 ATTAAATTTCATGA
1 ATTAAATTTCATGA
20585202 ATT
1 ATT
20585205 TCATTTTCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (14 bp):
ATTAAATTTCATGA
Found at i:20585684 original size:24 final size:25
Alignment explanation
Indices: 20585622--20585684 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
20585612 AGCGCCCCGT
*
20585622 TAGCTCTCTC-GAGCTTCCTGTTATA
1 TAGCTCT-TCGGAGCTTCCCGTTATA
*
20585647 TAGTTCTT-GAGAGCTTCCCGTTA-A
1 TAGCTCTTCG-GAGCTTCCCGTTATA
20585671 TAGCTCTTCGGAGC
1 TAGCTCTTCGGAGC
20585685 ATCTCAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 13 0.41
25 19 0.59
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (25 bp):
TAGCTCTTCGGAGCTTCCCGTTATA
Found at i:20592696 original size:17 final size:17
Alignment explanation
Indices: 20592674--20592714 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
20592664 ATGAGTTCAT
*
20592674 ATGATTTTAGTTATTAG
1 ATGATTTTAGTTATTAC
*
20592691 ATGATTTTAGTTCTTAC
1 ATGATTTTAGTTATTAC
20592708 ATGATTT
1 ATGATTT
20592715 AGGGATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.27, C:0.05, G:0.15, T:0.54
Consensus pattern (17 bp):
ATGATTTTAGTTATTAC
Found at i:20593395 original size:25 final size:26
Alignment explanation
Indices: 20593367--20593430 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
20593357 ATAGTTCTTA
20593367 TGAGCTTCCCGATT-TTGGCTCTTCG
1 TGAGCTTCCCGATTATTGGCTCTTCG
* *
20593392 TGAGCTTTCCG-TTAATTGGCTCTTTG
1 TGAGCTTCCCGATT-ATTGGCTCTTCG
*
20593418 TGAGCTTCTCGAT
1 TGAGCTTCCCGAT
20593431 AAGGCTCGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 2 0.06
25 10 0.31
26 19 0.59
27 1 0.03
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.42
Consensus pattern (26 bp):
TGAGCTTCCCGATTATTGGCTCTTCG
Found at i:20593848 original size:11 final size:11
Alignment explanation
Indices: 20593832--20593862 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
20593822 TATCTCTATT
20593832 ATTTGAAATGC
1 ATTTGAAATGC
20593843 ATTTGAAATGC
1 ATTTGAAATGC
20593854 ATTTGAAAT
1 ATTTGAAAT
20593863 ACATGACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (11 bp):
ATTTGAAATGC
Found at i:20596144 original size:18 final size:16
Alignment explanation
Indices: 20596123--20596210 Score: 78
Period size: 15 Copynumber: 5.6 Consensus size: 16
20596113 TCTTTCTAGT
20596123 TTATTTTTATTTATTAAA
1 TTATTTTTATTT-TT-AA
*
20596141 TTA-TTTT-TCTTTAA
1 TTATTTTTATTTTTAA
20596155 TTAATTTTTATTTTTAA
1 TT-ATTTTTATTTTTAA
*
20596172 --ATTTATTATTTTTCA
1 TTATTT-TTATTTTTAA
*
20596187 TTATTTTTA-TATTAA
1 TTATTTTTATTTTTAA
20596202 TTATTTTTA
1 TTATTTTTA
20596211 ATTATTTTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
14 8 0.14
15 25 0.42
16 9 0.15
17 14 0.24
18 3 0.05
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTTTTATTTTTAA
Found at i:20596164 original size:33 final size:31
Alignment explanation
Indices: 20596123--20596224 Score: 101
Period size: 33 Copynumber: 3.4 Consensus size: 31
20596113 TCTTTCTAGT
20596123 TTATTTTTATTTATTAAATTATTTTTCTTTAA
1 TTATTTTTATTTATTAAATTATTTTT-TTTAA
* *
20596155 TTAATTTTTATTT-TTAAATTTATTATTTTTCA
1 TT-ATTTTTATTTATTAAA-TTATTTTTTTTAA
20596187 TTATTTTTA--TATT-AATTA---TTTTTAA
1 TTATTTTTATTTATTAAATTATTTTTTTTAA
20596212 TTATTTTTCATTT
1 TTATTTTT-ATTT
20596225 TCTCTAGCCT
Statistics
Matches: 61, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
25 14 0.23
26 1 0.02
28 4 0.07
29 3 0.05
30 2 0.03
31 7 0.11
32 13 0.21
33 17 0.28
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (31 bp):
TTATTTTTATTTATTAAATTATTTTTTTTAA
Found at i:20596194 original size:25 final size:25
Alignment explanation
Indices: 20596162--20596219 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
20596152 TAATTAATTT
* *
20596162 TTATTTTTAAATTTATTATTTTTCA
1 TTATTTTTAAATTAATTATTTTTAA
*
20596187 TTATTTTTATATTAATTATTTTTAA
1 TTATTTTTAAATTAATTATTTTTAA
20596212 TTATTTTT
1 TTATTTTT
20596220 CATTTTCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (25 bp):
TTATTTTTAAATTAATTATTTTTAA
Found at i:20597367 original size:15 final size:16
Alignment explanation
Indices: 20597342--20597371 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20597332 TTAATTTTTT
20597342 AAATCATTTTAATTAC
1 AAATCATTTTAATTAC
20597358 AAAT-ATTTTAATTA
1 AAATCATTTTAATTA
20597372 GTTTTCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATCATTTTAATTAC
Found at i:20608149 original size:48 final size:47
Alignment explanation
Indices: 20608076--20608167 Score: 114
Period size: 48 Copynumber: 1.9 Consensus size: 47
20608066 TACTTTGCCT
*
20608076 AAAAAGGGGAAAGGACCAAGATGAAAACCCACAAAGGGCGCTTTTAA
1 AAAAAGGAGAAAGGACCAAGATGAAAACCCACAAAGGGCGCTTTTAA
* ***
20608123 AAAAAGGAGAGAGAGACCAA-AGTGAAAACTTGCAAAGGGCGCTTT
1 AAAAAGGAGAAAG-GACCAAGA-TGAAAACCCACAAAGGGCGCTTT
20608168 GAGCCGAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
47 12 0.32
48 26 0.68
ACGTcount: A:0.46, C:0.15, G:0.27, T:0.12
Consensus pattern (47 bp):
AAAAAGGAGAAAGGACCAAGATGAAAACCCACAAAGGGCGCTTTTAA
Found at i:20610077 original size:44 final size:44
Alignment explanation
Indices: 20609438--20610064 Score: 907
Period size: 44 Copynumber: 14.2 Consensus size: 44
20609428 ATCACAAAGC
* *
20609438 CCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATTGTAAGC
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
*
20609482 CCTATCTCCCTGACCAGCAGTGGAATAGGCTGAAGATTGTAAGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
* * * *
20609526 CCTAGCTCCCTGAACAGCAGTGGAATAGGTCGAAGATTGTAAGC
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
* *
20609570 CCTATCTCCCTGACCATCAGTGGAATAGGCTGAAGATTGTAAGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
* * * * * *
20609614 CCTAGCTCCCTGAACAGCAGTGGAATAAGTCGAAGATGGTAAGC
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
* *
20609658 CCTATCTCCCTGACTAGTAGTGGAATAGGTTGAAGATTGTAAGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
* * * * *
20609702 CCTATCTCCCTGACCAACAGTGGAATAGATCGAAGATGGTAAGC
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
** * *
20609746 CCTATCTCCCTGAATAGCAGTGGAATAGGTCGAAAATTGTAAGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
* * * *
20609790 CCTAGCTCCCTGAACAGCAGTGGAATAGGTCGAAGATGGTAAG-
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
* *
20609833 CCATATCTCCCTAACCAGCAGTGGAATAGGTTGAAGATCGTAAGT
1 CC-TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
20609878 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
20609922 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
**
20609966 CCTATCTCTTTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
20610010 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGT-AGAT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAG-T
*
20610054 CCTGTCTCCCT
1 CCTATCTCCCT
20610065 AAGCAGTAGT
Statistics
Matches: 520, Mismatches: 60, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
43 4 0.01
44 514 0.99
45 2 0.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (44 bp):
CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
Found at i:20614637 original size:48 final size:48
Alignment explanation
Indices: 20614585--20614676 Score: 114
Period size: 47 Copynumber: 1.9 Consensus size: 48
20614575 CACGATTTTC
*
20614585 ATTATGTGGCAGTATACCTACAATTTTGGTGGC-TTGTCCACAATATTG
1 ATTAT-TGGCAGTATACCTACAATTTTGGTGACATTGTCCACAATATTG
* * * * *
20614633 ATTATTGGCAGTTTATCTCCGATTTTGGTGACATTGTTCACAAT
1 ATTATTGGCAGTATACCTACAATTTTGGTGACATTGTCCACAAT
20614677 TTGGTGTGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
47 22 0.59
48 15 0.41
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (48 bp):
ATTATTGGCAGTATACCTACAATTTTGGTGACATTGTCCACAATATTG
Found at i:20616350 original size:20 final size:20
Alignment explanation
Indices: 20616311--20616350 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20616301 TTTGGACTAA
*
20616311 GGACTAAATCCTAATAAATT
1 GGACTAAATCCGAATAAATT
20616331 GGACTAAAT-CGAATAGAATT
1 GGACTAAATCCGAATA-AATT
20616351 AAAAACTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (20 bp):
GGACTAAATCCGAATAAATT
Found at i:20618573 original size:19 final size:19
Alignment explanation
Indices: 20618546--20618589 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
20618536 TTTATGTTTT
20618546 ATTTA-TTTATTTACTTA-A
1 ATTTATTTTATTT-CTTATA
*
20618564 ATTTATTTTATTTTTTATA
1 ATTTATTTTATTTCTTATA
20618583 ATTTATT
1 ATTTATT
20618590 AATGCGGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTATTTTATTTCTTATA
Found at i:20627585 original size:20 final size:20
Alignment explanation
Indices: 20627560--20627598 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20627550 TTATAAACCG
20627560 AATCAAACCATACCTTTCTA
1 AATCAAACCATACCTTTCTA
*
20627580 AATCAAACCATATCTTTCT
1 AATCAAACCATACCTTTCT
20627599 GAGACCTTCG
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:0.38, C:0.28, G:0.00, T:0.33
Consensus pattern (20 bp):
AATCAAACCATACCTTTCTA
Found at i:20628637 original size:21 final size:21
Alignment explanation
Indices: 20628587--20628630 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
20628577 GGGTCTACAC
* *
20628587 GCCCATGTGAAGGCCACACGT
1 GCCCCTGTGAAAGCCACACGT
20628608 GCCCCTGTGAAAGCCACACGT
1 GCCCCTGTGAAAGCCACACGT
20628629 GC
1 GC
20628631 TTGTGTGCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.36, G:0.27, T:0.14
Consensus pattern (21 bp):
GCCCCTGTGAAAGCCACACGT
Found at i:20631054 original size:14 final size:15
Alignment explanation
Indices: 20631027--20631055 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20631017 AAATAAAAAT
20631027 TAAAACCAAATAATA
1 TAAAACCAAATAATA
20631042 TAAAACC-AATAATA
1 TAAAACCAAATAATA
20631056 AAAGTCCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAAACCAAATAATA
Found at i:20631569 original size:14 final size:14
Alignment explanation
Indices: 20631552--20631581 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20631542 TCTTTCTCTC
20631552 TTTTCGTTTCTTTT
1 TTTTCGTTTCTTTT
*
20631566 TTTTCTTTTCTTTT
1 TTTTCGTTTCTTTT
20631580 TT
1 TT
20631582 ATATTATTAA
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:0.00, C:0.13, G:0.03, T:0.83
Consensus pattern (14 bp):
TTTTCGTTTCTTTT
Found at i:20632207 original size:3 final size:3
Alignment explanation
Indices: 20632199--20632250 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
20632189 TTCAGTTTAA
* * * * *
20632199 TAT TAT TAT TAT TAC TAG TAT TAT TAT TAT TAC TAT TAT TAG TAG TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20632247 TAT T
1 TAT T
20632251 TTTTTATCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:20632220 original size:18 final size:18
Alignment explanation
Indices: 20632199--20632239 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
20632189 TTCAGTTTAA
20632199 TATTATTATTATTACTAG
1 TATTATTATTATTACTAG
*
20632217 TATTATTATTATTACTAT
1 TATTATTATTATTACTAG
20632235 TATTA
1 TATTA
20632240 GTAGTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (18 bp):
TATTATTATTATTACTAG
Found at i:20632354 original size:21 final size:24
Alignment explanation
Indices: 20632300--20632354 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 24
20632290 TTATTATGTG
20632300 GTATTATTTTAAGTTTTCCATATAT
1 GTATTATTTTAAG-TTTCCATATAT
20632325 -TATTA-TTTAA-TTT-CATA-AT
1 GTATTATTTTAAGTTTCCATATAT
20632344 GTATTATTTTA
1 GTATTATTTTA
20632355 TATATATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 2 0.07
20 9 0.32
21 7 0.25
23 5 0.18
24 5 0.18
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.58
Consensus pattern (24 bp):
GTATTATTTTAAGTTTCCATATAT
Found at i:20636552 original size:14 final size:14
Alignment explanation
Indices: 20636533--20636566 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
20636523 CAAAATGAAA
*
20636533 GTGGAAGATCTTAT
1 GTGGAAGACCTTAT
20636547 GTGGAAGACCTTAT
1 GTGGAAGACCTTAT
*
20636561 CTGGAA
1 GTGGAA
20636567 TAGCATTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (14 bp):
GTGGAAGACCTTAT
Found at i:20636653 original size:15 final size:14
Alignment explanation
Indices: 20636631--20636682 Score: 59
Period size: 16 Copynumber: 3.4 Consensus size: 14
20636621 CAGATTCAAT
20636631 AAAAAAAAGAAGAAC
1 AAAAAAAA-AAGAAC
20636646 AGAAAAAAAAAGAAC
1 A-AAAAAAAAAGAAC
20636661 AAAAAACAAAAAGAAAC
1 -AAAAA-AAAAAG-AAC
20636678 AAAAA
1 AAAAA
20636683 TCTCTACCGG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
15 11 0.33
16 19 0.58
17 3 0.09
ACGTcount: A:0.83, C:0.08, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGAAC
Found at i:20636678 original size:17 final size:15
Alignment explanation
Indices: 20636631--20636682 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
20636621 CAGATTCAAT
*
20636631 AAAAAAAAGAAGAAC
1 AAAAAAAAAAAGAAC
*
20636646 AGAAAAAAAAAGAAC
1 AAAAAAAAAAAGAAC
20636661 AAAAAACAAAAAGAAAC
1 AAAAAA-AAAAAG-AAC
20636678 AAAAA
1 AAAAA
20636683 TCTCTACCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
15 18 0.56
16 6 0.19
17 8 0.25
ACGTcount: A:0.83, C:0.08, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAGAAC
Found at i:20638678 original size:88 final size:87
Alignment explanation
Indices: 20638494--20638697 Score: 284
Period size: 88 Copynumber: 2.3 Consensus size: 87
20638484 ATCTCATCTC
* * * * * *
20638494 ATCTCCCTAAGCAGCAGTGAAGTAGGTTAAAAATAGCAGATCTTTTCTTCATGTATTGGTAGCGA
1 ATCTCCCTGA-CAGTAGTGGAGTAGGTTAAAAATAGCAGATCTTGTCTTCATGTATCGGCAGCGA
20638559 AATAGATCGAAGACACCAGCCTT
65 AATAGATCGAAGACACCAGCCTT
*
20638582 ATCTCCCTGATCAGTAGTGGAGTAGGTTAAAAATAGCAGATCTTGTCTTCCTGTATCGGCAGCGA
1 ATCTCCCTGA-CAGTAGTGGAGTAGGTTAAAAATAGCAGATCTTGTCTTCATGTATCGGCAGCGA
*
20638647 AGTAGATCGAAGAC-CTCAGCCTT
65 AATAGATCGAAGACAC-CAGCCTT
*
20638670 ATCTCCCTGGACAGTAGTGGAATAGGTT
1 ATCTCCCT-GACAGTAGTGGAGTAGGTT
20638698 GAAGATTGTA
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
87 1 0.01
88 101 0.97
89 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (87 bp):
ATCTCCCTGACAGTAGTGGAGTAGGTTAAAAATAGCAGATCTTGTCTTCATGTATCGGCAGCGAA
ATAGATCGAAGACACCAGCCTT
Found at i:20638859 original size:44 final size:44
Alignment explanation
Indices: 20638796--20639147 Score: 302
Period size: 44 Copynumber: 8.0 Consensus size: 44
20638786 TTAAGCCGCC
* * *
20638796 AGTCCTACCTTCCTGGACAGTAGTGGAATAGGTTGAAGATTGTA
1 AGTCCTATCTCCCTAGACAGTAGTGGAATAGGTTGAAGATTGTA
* * *
20638840 AGTCTTATCTCCCTAGACAGCAGTGGAATAGGTTGAAGGTTGTA
1 AGTCCTATCTCCCTAGACAGTAGTGGAATAGGTTGAAGATTGTA
* *
20638884 AGTCCTATCTCCCTGGACTGTAGTGGAATAGGTTGAAGATTGT-
1 AGTCCTATCTCCCTAGACAGTAGTGGAATAGGTTGAAGATTGTA
* ** ** ** *
20638927 AGATCCTGTCTCCCTA-AGCAGTAGTGGAGCAAATCAAAGATGGTGA
1 AG-TCCTATCTCCCTAGA-CAGTAGTGGAATAGGTTGAAGATTGT-A
* * * ** * * * *****
20638973 A-TCTTATCTTCATAGGGTAGTAG-GGAAGCAGATTTAAG-CCACC
1 AGTCCTATCTCCCTA-GACAGTAGTGGAA-TAGGTTGAAGATTGTA
* * *
20639016 AGTCCTATCTCCCTGGACAGCAATGGAATAGGTTGAAGATTGTA
1 AGTCCTATCTCCCTAGACAGTAGTGGAATAGGTTGAAGATTGTA
*
20639060 AGTCCTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGTA
1 AGTCCTATCTCCCTAGACAGTAGTGGAATAGGTTGAAGATTGTA
*
20639104 AGTCCTATATCCC-AGGACAGTAGTGGAATAGGTTGAAGATTGTA
1 AGTCCTATCTCCCTA-GACAGTAGTGGAATAGGTTGAAGATTGTA
20639148 GATCCTGTCT
Statistics
Matches: 241, Mismatches: 56, Indels: 22
0.76 0.18 0.07
Matches are distributed among these distances:
43 15 0.06
44 213 0.88
45 12 0.05
46 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (44 bp):
AGTCCTATCTCCCTAGACAGTAGTGGAATAGGTTGAAGATTGTA
Found at i:20638975 original size:220 final size:220
Alignment explanation
Indices: 20638669--20639249 Score: 883
Period size: 220 Copynumber: 2.6 Consensus size: 220
20638659 ACCTCAGCCT
* * * *
20638669 TATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGTAGATCATGTCTGCCTAAACAATAGTGG
1 TATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
* * * * *
20638734 AACAGATAAAAGACGGTGAATCTTATCTTCCCAATGTAGTAGGGAAGTAGATTTAAGCCGCCAGT
66 AGCAGATCAAAGATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCGCCAGT
* * * *
20638799 CCTACCTTCCTGGACAGTAGTGGAATAGGTTGAAGATTGTAAGTCTTATCTCCCTAGACAGCAGT
131 CCTACCTCCCTGGACAGCAATGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTAGACAGCAGT
*
20638864 GGAATAGGTTGAAGGTTGTAAGTCC
196 GGAATAGGTTGAAGATTGTAAGTCC
*
20638889 TATCTCCCTGGACTGTAGTGGAATAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
1 TATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
* ** * *
20638954 AGCAAATCAAAGATGGTGAATCTTATCTTCATAGGGTAGTAGGGAAGCAGATTTAAGCCACCAGT
66 AGCAGATCAAAGATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCGCCAGT
* * *
20639019 CCTATCTCCCTGGACAGCAATGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGACAGTAGT
131 CCTACCTCCCTGGACAGCAATGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTAGACAGCAGT
20639084 GGAATAGGTTGAAGATTGTAAGTCC
196 GGAATAGGTTGAAGATTGTAAGTCC
* * ** *
20639109 TATATCCCAGGACAGTAGTGGAATAGGTTGAAGATTGTAGATCCTGTCTCTTTAAGCAGTAGTGA
1 TATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
* *
20639174 AGCAGATCAAAGATGGTGAATCTTATCTACCCAAGGTAGTAGGGAAGCAGATTTAAGCCGCCAGC
66 AGCAGATCAAAGATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCGCCAGT
*
20639239 CCTATCTCCCT
131 CCTACCTCCCT
20639250 AGTTGCAGTG
Statistics
Matches: 325, Mismatches: 36, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
220 325 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (220 bp):
TATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
AGCAGATCAAAGATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCGCCAGT
CCTACCTCCCTGGACAGCAATGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTAGACAGCAGT
GGAATAGGTTGAAGATTGTAAGTCC
Found at i:20639187 original size:88 final size:88
Alignment explanation
Indices: 20639016--20639187 Score: 188
Period size: 88 Copynumber: 2.0 Consensus size: 88
20639006 TTAAGCCACC
* * *
20639016 AGTCCTATCTCCCTGGACAGCAATGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGACAGT
1 AGTCCTATATCCCAGGACAGCAATGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTAGACAGT
* * **
20639081 AGTGGAATAGGTTGAAGATTGTA
66 AGTGGAACAGATCAAAGATTGTA
* * * **
20639104 AGTCCTATATCCCAGGACAGTAGTGGAATAGGTTGAAGATTGT-AGATCCTGTCTCTTTA-AGCA
1 AGTCCTATATCCCAGGACAGCAATGGAATAGGTTGAAGATTGTAAG-TCCTATCTCCCTAGA-CA
20639167 GTAGT-GAAGCAGATCAAAGAT
64 GTAGTGGAA-CAGATCAAAGAT
20639188 GGTGAATCTT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
87 6 0.09
88 63 0.91
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (88 bp):
AGTCCTATATCCCAGGACAGCAATGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTAGACAGT
AGTGGAACAGATCAAAGATTGTA
Found at i:20639971 original size:18 final size:18
Alignment explanation
Indices: 20639945--20639979 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20639935 TACCTGCACA
*
20639945 CAAACAAACAACAAAGAG
1 CAAACAAACAAAAAAGAG
*
20639963 CAAAGAAACAAAAAAGA
1 CAAACAAACAAAAAAGA
20639980 ACGCAGCAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.17, G:0.11, T:0.00
Consensus pattern (18 bp):
CAAACAAACAAAAAAGAG
Found at i:20640846 original size:3 final size:3
Alignment explanation
Indices: 20640838--20640886 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
20640828 TTCAGTTTAA
* * * *
20640838 TAT TAT TAT TAC TAG TAT TAT TAT TAT TAC TAT TAT TAT TAG TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20640886 T
1 T
20640887 TTTTTATCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:20640859 original size:18 final size:18
Alignment explanation
Indices: 20640838--20640884 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
20640828 TTCAGTTTAA
20640838 TATTATTATTACTAGTAT
1 TATTATTATTACTAGTAT
*
20640856 TATTATTATTACTATTAT
1 TATTATTATTACTAGTAT
*
20640874 TATTAGTATTA
1 TATTATTATTA
20640885 TTTTTTTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (18 bp):
TATTATTATTACTAGTAT
Found at i:20648222 original size:20 final size:20
Alignment explanation
Indices: 20648199--20648254 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
20648189 CAAATGCTCT
20648199 TTTAAATCAATTCATTATTA
1 TTTAAATCAATTCATTATTA
* **
20648219 TTTAAATCGATTGTTTATTA
1 TTTAAATCAATTCATTATTA
*
20648239 TTTGAATCAATTCATT
1 TTTAAATCAATTCATT
20648255 GTGGTTTAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (20 bp):
TTTAAATCAATTCATTATTA
Found at i:20662825 original size:4 final size:4
Alignment explanation
Indices: 20662816--20662860 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
20662806 TATCAAAAAG
* * * *
20662816 TGTA TGTA TGCA TGTA TGCA TGTA TGCA TGTA TGCA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
20662861 ATTTTATTCA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.42
Consensus pattern (4 bp):
TGTA
Found at i:20662832 original size:8 final size:8
Alignment explanation
Indices: 20662819--20662857 Score: 78
Period size: 8 Copynumber: 4.9 Consensus size: 8
20662809 CAAAAAGTGT
20662819 ATGTATGC
1 ATGTATGC
20662827 ATGTATGC
1 ATGTATGC
20662835 ATGTATGC
1 ATGTATGC
20662843 ATGTATGC
1 ATGTATGC
20662851 ATGTATG
1 ATGTATG
20662858 TATATTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (8 bp):
ATGTATGC
Found at i:20665972 original size:86 final size:86
Alignment explanation
Indices: 20665823--20665994 Score: 328
Period size: 86 Copynumber: 2.0 Consensus size: 86
20665813 GGAAGTGACT
20665823 TAGTCATCATATCTGCAGGATTTTCATGAGTATTAATTTTACTCACAACAATATCACCACGAGCA
1 TAGTCATCATATCTGCAGGATTTTCATGAGTATTAATTTTACTCACAACAATATCACCACGAGCA
20665888 ATAATATCACGAACAAAATGA
66 ATAATATCACGAACAAAATGA
20665909 TAGTCATCATATCTGCAGGATTTTCATGAGTATTAATTTTACTCACAACCAATATCACC-CGAGC
1 TAGTCATCATATCTGCAGGATTTTCATGAGTATTAATTTTACTCACAA-CAATATCACCACGAGC
20665973 AATAATATCACGAACAAAATGA
65 AATAATATCACGAACAAAATGA
20665995 CATCAAAAAT
Statistics
Matches: 85, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
86 75 0.88
87 10 0.12
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (86 bp):
TAGTCATCATATCTGCAGGATTTTCATGAGTATTAATTTTACTCACAACAATATCACCACGAGCA
ATAATATCACGAACAAAATGA
Found at i:20671513 original size:39 final size:39
Alignment explanation
Indices: 20671470--20671586 Score: 119
Period size: 39 Copynumber: 3.0 Consensus size: 39
20671460 GAGTCTCCTG
* * **
20671470 CTTCAACTTCACTGCTTAACAGTGCTAAACTGGACTCTA
1 CTTCAACTTCACTGGTTAACAATGCTAAACCAGACTCTA
* * *
20671509 CTTCATA-TTCACCGGTTAACACTGCTAATCCAGACTCTA
1 CTTCA-ACTTCACTGGTTAACAATGCTAAACCAGACTCTA
* * * *
20671548 CTTCTACTTCACTGGTTATCAATGCTAAGCCAGAATCTA
1 CTTCAACTTCACTGGTTAACAATGCTAAACCAGACTCTA
20671587 AAGCTAGTCT
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
38 1 0.02
39 62 0.97
40 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (39 bp):
CTTCAACTTCACTGGTTAACAATGCTAAACCAGACTCTA
Found at i:20673042 original size:39 final size:39
Alignment explanation
Indices: 20672999--20673115 Score: 119
Period size: 39 Copynumber: 3.0 Consensus size: 39
20672989 GAGTCTCCTG
* * **
20672999 CTTCAACTTCACTGCTTAACAGTGCTAAACTGGACTCTA
1 CTTCAACTTCACTGGTTAACAATGCTAAACCAGACTCTA
* * *
20673038 CTTCATA-TTCACCGGTTAACACTGCTAATCCAGACTCTA
1 CTTCA-ACTTCACTGGTTAACAATGCTAAACCAGACTCTA
* * * *
20673077 CTTCTACTTCACTGGTTATCAATGCTAAGCCAGAATCTA
1 CTTCAACTTCACTGGTTAACAATGCTAAACCAGACTCTA
20673116 AAGCTAGTCT
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
38 1 0.02
39 62 0.97
40 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (39 bp):
CTTCAACTTCACTGGTTAACAATGCTAAACCAGACTCTA
Found at i:20680276 original size:30 final size:29
Alignment explanation
Indices: 20680233--20680290 Score: 107
Period size: 30 Copynumber: 2.0 Consensus size: 29
20680223 AAGGAAATAA
20680233 ATCCTAATTCCTAAGAATCAGTAATTGAT
1 ATCCTAATTCCTAAGAATCAGTAATTGAT
20680262 ATCCTAATTTCCTAAGAATCAGTAATTGA
1 ATCCTAA-TTCCTAAGAATCAGTAATTGA
20680291 GATTAGTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.34
Consensus pattern (29 bp):
ATCCTAATTCCTAAGAATCAGTAATTGAT
Found at i:20684970 original size:3 final size:3
Alignment explanation
Indices: 20684962--20685014 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
20684952 TTGCACCGCG
* * *
20684962 ATA ATA ATA ATG ATA ATA ATG ATA ATA ATA ATA ATA TTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20685010 ATA AT
1 ATA AT
20685015 TGTTTATTGC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:20687993 original size:194 final size:195
Alignment explanation
Indices: 20687653--20688041 Score: 771
Period size: 194 Copynumber: 2.0 Consensus size: 195
20687643 AAATTTTTTG
20687653 TTGGTATCAATTTCACATTTTATTTTTAAAATAACTTTTAATAAAAAATCACATTTTTTACATTT
1 TTGGTATCAATTTCACATTTTATTTTTAAAATAACTTTTAATAAAAAATCACATTTTTTACATTT
20687718 AATATATTTTTTAATTTAAAAATACATGGTGACAAGAATCAGAAGATGATTGAAGCAACTAAGCA
66 AATATATTTTTTAATTTAAAAATACATGGTGACAAGAATCAGAAGATGATTGAAGCAACTAAGCA
20687783 AACAAAGAAGCGAACTCGTATATAAAAGATTAATGAATAAATTATGAGAGGATTAAAGTTAATAA
131 AACAAAGAAGCGAACTCGTATATAAAAGATTAATGAATAAATTATGAGAGGATTAAAGTTAATAA
20687848 TTGGTATCAA-TTCACATTTTATTTTTAAAATAACTTTTAATAAAAAATCACATTTTTTACATTT
1 TTGGTATCAATTTCACATTTTATTTTTAAAATAACTTTTAATAAAAAATCACATTTTTTACATTT
20687912 AATATATTTTTTAATTTAAAAATACATGGTGACAAGAATCAGAAGATGATTGAAGCAACTAAGCA
66 AATATATTTTTTAATTTAAAAATACATGGTGACAAGAATCAGAAGATGATTGAAGCAACTAAGCA
20687977 AACAAAGAAGCGAACTCGTATATAAAAGATTAATGAATAAATTATGAGAGGATTAAAGTTAATAA
131 AACAAAGAAGCGAACTCGTATATAAAAGATTAATGAATAAATTATGAGAGGATTAAAGTTAATAA
20688042 CAAATTTGAT
Statistics
Matches: 194, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
194 184 0.95
195 10 0.05
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (195 bp):
TTGGTATCAATTTCACATTTTATTTTTAAAATAACTTTTAATAAAAAATCACATTTTTTACATTT
AATATATTTTTTAATTTAAAAATACATGGTGACAAGAATCAGAAGATGATTGAAGCAACTAAGCA
AACAAAGAAGCGAACTCGTATATAAAAGATTAATGAATAAATTATGAGAGGATTAAAGTTAATAA
Found at i:20692673 original size:18 final size:18
Alignment explanation
Indices: 20692647--20692685 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
20692637 CCAAGGAAAA
20692647 TAAGAAAAAGCTATAATC
1 TAAGAAAAAGCTATAATC
*
20692665 TAAGGAAAAGCTATAATC
1 TAAGAAAAAGCTATAATC
20692683 TAA
1 TAA
20692686 TTGTTCTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.23
Consensus pattern (18 bp):
TAAGAAAAAGCTATAATC
Found at i:20699360 original size:18 final size:18
Alignment explanation
Indices: 20699333--20699371 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
20699323 AAAGCCATTC
*
20699333 ATTCATACATTTAGGTAA
1 ATTCACACATTTAGGTAA
20699351 ATTCACACATTTAGGTAA
1 ATTCACACATTTAGGTAA
20699369 ATT
1 ATT
20699372 GCATCTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (18 bp):
ATTCACACATTTAGGTAA
Found at i:20717026 original size:92 final size:91
Alignment explanation
Indices: 20716869--20717077 Score: 278
Period size: 92 Copynumber: 2.3 Consensus size: 91
20716859 TTGATTTTAG
* * *
20716869 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
20716934 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
20716961 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
20717025 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
20717053 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
20717078 GTTATAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 71 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:20717040 original size:24 final size:25
Alignment explanation
Indices: 20717005--20717052 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
20716995 TTATGAAATT
20717005 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
20717029 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
20717053 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:20717248 original size:16 final size:16
Alignment explanation
Indices: 20717227--20717268 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
20717217 TTATTAAATT
*
20717227 ATATATTTTAATTATA
1 ATATATTTTAATAATA
20717243 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
20717258 AT-TATGTTTAA
1 ATATAT-TTTAA
20717269 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:20717253 original size:15 final size:15
Alignment explanation
Indices: 20717218--20717259 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
20717208 TTAAGAATTT
*
20717218 TATTAAATTAT-ATA
1 TATTTAATTATAATA
20717232 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
20717246 TATTTAATAATAAT
1 TATTTAATTATAAT
20717260 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:20717496 original size:45 final size:44
Alignment explanation
Indices: 20717413--20717502 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
20717403 ACCTCTATTC
*
20717413 CATTCAACCAAACACAAGATTACTATTACGCCTGTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
* *
20717457 CATTCAACCAAACA-ATTGATTTGCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACA-AGA-TTACTATTACGCCTCTATTCCATTA
20717502 C
1 C
20717503 GCCTCTAATC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 16 0.39
45 24 0.59
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
Found at i:20717503 original size:16 final size:16
Alignment explanation
Indices: 20717482--20717546 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
20717472 TTGATTTGCT
*
20717482 ATTACGCCTCTATTCC
1 ATTACGCCTCTAATCC
*
20717498 ATTACGCCTCTAATCT
1 ATTACGCCTCTAATCC
20717514 ATTACGCCTCTAATCC
1 ATTACGCCTCTAATCC
*
20717530 ATTACGCCTCTATTCC
1 ATTACGCCTCTAATCC
20717546 A
1 A
20717547 ATACAGCGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.23, C:0.35, G:0.06, T:0.35
Consensus pattern (16 bp):
ATTACGCCTCTAATCC
Found at i:20717521 original size:32 final size:32
Alignment explanation
Indices: 20717480--20717541 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
20717470 AATTGATTTG
*
20717480 CTATTACGCCTCTATTCCATTACGCCTCTAAT
1 CTATTACGCCTCTAATCCATTACGCCTCTAAT
20717512 CTATTACGCCTCTAATCCATTACGCCTCTA
1 CTATTACGCCTCTAATCCATTACGCCTCTA
20717542 TTCCAATACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.23, C:0.35, G:0.06, T:0.35
Consensus pattern (32 bp):
CTATTACGCCTCTAATCCATTACGCCTCTAAT
Found at i:20725437 original size:6 final size:6
Alignment explanation
Indices: 20725426--20725451 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
20725416 CTGGTACAAG
20725426 TTTGAA TTTGAA TTTGAA TTTGAA TT
1 TTTGAA TTTGAA TTTGAA TTTGAA TT
20725452 GCTACACGAA
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:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (6 bp):
TTTGAA
Found at i:20740009 original size:3 final size:3
Alignment explanation
Indices: 20740001--20740028 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
20739991 AAAGATCCTA
20740001 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
20740029 TCCCATAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:20742403 original size:27 final size:27
Alignment explanation
Indices: 20742362--20742533 Score: 188
Period size: 27 Copynumber: 6.4 Consensus size: 27
20742352 GTAATGGGCC
* *
20742362 TAAAATGATTGAAATACCCTTGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
*
20742389 TAAAATGACTAAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
*
20742416 TAAAATGA-TCAAAATACCCTCGAAGGG
1 TAAAATGACT-GAAATACCCTCGAAGGG
* *
20742443 TAAAATGA-TCGAAATACCCCCGAAGGA
1 TAAAATGACT-GAAATACCCTCGAAGGG
* **
20742470 TAAAATAACTGAAATACCGGCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
* * *
20742497 TAAGATGACCGAAATACTC-CGAAAGGG
1 TAAAATGACTGAAATACCCTCG-AAGGG
20742524 TAAAATGACT
1 TAAAATGACT
20742534 ATTATACCAC
Statistics
Matches: 125, Mismatches: 17, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
26 3 0.02
27 121 0.97
28 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.19
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCTCGAAGGG
Found at i:20742541 original size:81 final size:81
Alignment explanation
Indices: 20742362--20742531 Score: 216
Period size: 81 Copynumber: 2.1 Consensus size: 81
20742352 GTAATGGGCC
* ** * * * *
20742362 TAAAATGATTGAAATACCCTTGAAGGGTAAAATGACTAAAATACCCTCGAAGGGTAAAATGATCA
1 TAAAATGATCGAAATACCCCCGAAGGATAAAATAACTAAAATACCCGCGAAGGGTAAAATGACCA
20742427 AAATACCCTCGAAGGG
66 AAATACCCTCGAAGGG
* * * *
20742443 TAAAATGATCGAAATACCCCCGAAGGATAAAATAACTGAAATACCGGCGAAGGGTAAGATGACCG
1 TAAAATGATCGAAATACCCCCGAAGGATAAAATAACTAAAATACCCGCGAAGGGTAAAATGACCA
*
20742508 AAATACTC-CGAAAGGG
66 AAATACCCTCG-AAGGG
20742524 TAAAATGA
1 TAAAATGA
20742532 CTATTATACC
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
80 2 0.03
81 74 0.97
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.18
Consensus pattern (81 bp):
TAAAATGATCGAAATACCCCCGAAGGATAAAATAACTAAAATACCCGCGAAGGGTAAAATGACCA
AAATACCCTCGAAGGG
Found at i:20742928 original size:28 final size:28
Alignment explanation
Indices: 20742897--20742957 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
20742887 CCCACACTAG
* *
20742897 TACTGCTTAGGGCTCAAGCCTAGACTGT
1 TACTGCTTAGGGATCAAGCCCAGACTGT
* *
20742925 TACTGCTTAGGGATCAGGCCCAGATTGT
1 TACTGCTTAGGGATCAAGCCCAGACTGT
20742953 TACTG
1 TACTG
20742958 TATGTCGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (28 bp):
TACTGCTTAGGGATCAAGCCCAGACTGT
Found at i:20745432 original size:199 final size:199
Alignment explanation
Indices: 20745092--20745489 Score: 796
Period size: 199 Copynumber: 2.0 Consensus size: 199
20745082 TCCAAGGTAG
20745092 GAGGGTGTTTTTGGTTTAAGTGTTATAAGAGGGCGTTTATACCTTAGCTTTTAATTAACTAACTT
1 GAGGGTGTTTTTGGTTTAAGTGTTATAAGAGGGCGTTTATACCTTAGCTTTTAATTAACTAACTT
20745157 TGGGGTCATGCTTGTTTCTATGTGGGCGTTCGTGGAAATAGCACTCTTCTCGTAAACAGGTGTGT
66 TGGGGTCATGCTTGTTTCTATGTGGGCGTTCGTGGAAATAGCACTCTTCTCGTAAACAGGTGTGT
20745222 AATCACACTCTCTCTCAACTGCAAATCGGTAAAAGCCGAAAAGCAAGAAAATACGGTGTTGAGAC
131 AATCACACTCTCTCTCAACTGCAAATCGGTAAAAGCCGAAAAGCAAGAAAATACGGTGTTGAGAC
20745287 CATA
196 CATA
20745291 GAGGGTGTTTTTGGTTTAAGTGTTATAAGAGGGCGTTTATACCTTAGCTTTTAATTAACTAACTT
1 GAGGGTGTTTTTGGTTTAAGTGTTATAAGAGGGCGTTTATACCTTAGCTTTTAATTAACTAACTT
20745356 TGGGGTCATGCTTGTTTCTATGTGGGCGTTCGTGGAAATAGCACTCTTCTCGTAAACAGGTGTGT
66 TGGGGTCATGCTTGTTTCTATGTGGGCGTTCGTGGAAATAGCACTCTTCTCGTAAACAGGTGTGT
20745421 AATCACACTCTCTCTCAACTGCAAATCGGTAAAAGCCGAAAAGCAAGAAAATACGGTGTTGAGAC
131 AATCACACTCTCTCTCAACTGCAAATCGGTAAAAGCCGAAAAGCAAGAAAATACGGTGTTGAGAC
20745486 CATA
196 CATA
20745490 TGGGCATGCG
Statistics
Matches: 199, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
199 199 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.32
Consensus pattern (199 bp):
GAGGGTGTTTTTGGTTTAAGTGTTATAAGAGGGCGTTTATACCTTAGCTTTTAATTAACTAACTT
TGGGGTCATGCTTGTTTCTATGTGGGCGTTCGTGGAAATAGCACTCTTCTCGTAAACAGGTGTGT
AATCACACTCTCTCTCAACTGCAAATCGGTAAAAGCCGAAAAGCAAGAAAATACGGTGTTGAGAC
CATA
Found at i:20745630 original size:27 final size:27
Alignment explanation
Indices: 20745592--20745840 Score: 276
Period size: 27 Copynumber: 9.3 Consensus size: 27
20745582 GTAATGGGCC
*
20745592 TAAAATGACAGAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
*
20745619 TAAAATGACAGAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
*
20745646 TAAAATGA-TCGAAATACACTCGAAGGG
1 TAAAATGACT-GAAATACCCTCGAAGGG
*
20745673 TAAAATGACTGAAATACCCTTGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
* *
20745700 TAAAATGACTGAAATACCCTCAAAAGG
1 TAAAATGACTGAAATACCCTCGAAGGG
*
20745727 TAAAATGA-TGAAAATACCTTC-AAGGG
1 TAAAATGACTG-AAATACCCTCGAAGGG
* * *
20745753 TAAAATGACCGAAATACCTTTGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
* * *
20745780 TAAAATAACCGAAATACCC-CTGAAAGG
1 TAAAATGACTGAAATACCCTC-GAAGGG
* *
20745807 TAAGATGA-TCGAAATACTCC-CGAAGGA
1 TAAAATGACT-GAAATAC-CCTCGAAGGG
20745834 TAAAATG
1 TAAAATG
20745841 GCTATTATAC
Statistics
Matches: 193, Mismatches: 21, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
26 23 0.12
27 166 0.86
28 4 0.02
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.19
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCTCGAAGGG
Found at i:20745729 original size:81 final size:80
Alignment explanation
Indices: 20745592--20745840 Score: 324
Period size: 81 Copynumber: 3.1 Consensus size: 80
20745582 GTAATGGGCC
* *
20745592 TAAAATGACAGAAATACCCTCGAAGGGTAAAATGACAGAAATACCCTCGAAGGGTAAAATGATCG
1 TAAAATGACAGAAATACCCTTGAAGGGTAAAATGACAGAAATACCCTCGAAAGGTAAAATGATCG
20745657 AAATACACTCGAAGGG
66 AAATAC-CTCGAAGGG
* * *
20745673 TAAAATGACTGAAATACCCTTGAAGGGTAAAATGACTGAAATACCCTCAAAAGGTAAAATGAT-G
1 TAAAATGACAGAAATACCCTTGAAGGGTAAAATGACAGAAATACCCTCGAAAGGTAAAATGATCG
20745737 AAAATACCTTC-AAGGG
66 -AAATACC-TCGAAGGG
* * * * *
20745753 TAAAATGACCGAAATACCTTTGAAGGGTAAAATAACCGAAATACCC-CTGAAAGGTAAGATGATC
1 TAAAATGACAGAAATACCCTTGAAGGGTAAAATGACAGAAATACCCTC-GAAAGGTAAAATGATC
* *
20745817 GAAATACTCCCGAAGGA
65 GAAATAC-CTCGAAGGG
20745834 TAAAATG
1 TAAAATG
20745841 GCTATTATAC
Statistics
Matches: 149, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
79 1 0.01
80 69 0.46
81 79 0.53
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.19
Consensus pattern (80 bp):
TAAAATGACAGAAATACCCTTGAAGGGTAAAATGACAGAAATACCCTCGAAAGGTAAAATGATCG
AAATACCTCGAAGGG
Found at i:20745851 original size:107 final size:108
Alignment explanation
Indices: 20745592--20745823 Score: 301
Period size: 107 Copynumber: 2.2 Consensus size: 108
20745582 GTAATGGGCC
* * * * *
20745592 TAAAATGACAGAAATACCCTCGAAGGGTAAAATGA-CAGAAATACCCTCGAAGGGTAAAATGATC
1 TAAAATGACTGAAATACCCTCAAAAGGTAAAATGATGA-AAATACCCTCGAAGGGTAAAATGACC
* * * *
20745656 GAAATACACTCGAAGGGTAAAATGACTGAAATACCCTTGAAGGG
65 GAAATACACTCGAAGGGTAAAATAACCGAAATACCCCTGAAAGG
*
20745700 TAAAATGACTGAAATACCCTCAAAAGGTAAAATGATGAAAATACCTTC-AAGGGTAAAATGACCG
1 TAAAATGACTGAAATACCCTCAAAAGGTAAAATGATGAAAATACCCTCGAAGGGTAAAATGACCG
*
20745764 AAATAC-CTTTGAAGGGTAAAATAACCGAAATACCCCTGAAAGG
66 AAATACAC-TCGAAGGGTAAAATAACCGAAATACCCCTGAAAGG
*
20745807 TAAGATGA-TCGAAATAC
1 TAAAATGACT-GAAATAC
20745824 TCCCGAAGGA
Statistics
Matches: 109, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
106 2 0.02
107 65 0.60
108 41 0.38
109 1 0.01
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.19
Consensus pattern (108 bp):
TAAAATGACTGAAATACCCTCAAAAGGTAAAATGATGAAAATACCCTCGAAGGGTAAAATGACCG
AAATACACTCGAAGGGTAAAATAACCGAAATACCCCTGAAAGG
Found at i:20746219 original size:28 final size:28
Alignment explanation
Indices: 20746188--20746252 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
20746178 TTTCTGTATT
*
20746188 GGGCT-AGTGCCCACACTGTTACTACTTA
1 GGGCTCAG-GCCCACACTATTACTACTTA
*
20746216 GGGCTCAGGCCCAGACTATTACTACTTA
1 GGGCTCAGGCCCACACTATTACTACTTA
*
20746244 AGGCTCAGG
1 GGGCTCAGG
20746253 TCCAGATTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 31 0.94
29 2 0.06
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (28 bp):
GGGCTCAGGCCCACACTATTACTACTTA
Found at i:20746265 original size:28 final size:28
Alignment explanation
Indices: 20746196--20746266 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
20746186 TTGGGCTAGT
* *
20746196 GCCCACACTGTTACTACTTAGGGCTCAG
1 GCCCAGACTGTTACTACTTAAGGCTCAG
*
20746224 GCCCAGACTATTACTACTTAAGGCTCAG
1 GCCCAGACTGTTACTACTTAAGGCTCAG
* *
20746252 GTCCAGATTGTTACT
1 GCCCAGACTGTTACT
20746267 GTATGTCGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (28 bp):
GCCCAGACTGTTACTACTTAAGGCTCAG
Found at i:20747834 original size:20 final size:19
Alignment explanation
Indices: 20747810--20747855 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
20747800 AGTTTCGGTA
*
20747810 AAATTATTGTAAAA-AATAT
1 AAATTATTATAAAATAAT-T
20747829 ATAATTATTATAAAATAATT
1 A-AATTATTATAAAATAATT
20747849 AAATTAT
1 AAATTAT
20747856 ACTTAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.29
20 14 0.58
21 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
AAATTATTATAAAATAATT
Found at i:20747903 original size:22 final size:23
Alignment explanation
Indices: 20747878--20747920 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
20747868 AAAAATTTTA
20747878 ATTTTAATTAATTTT-ATAATAT
1 ATTTTAATTAATTTTGATAATAT
*
20747900 ATTTTTATTAATTTTGATAAT
1 ATTTTAATTAATTTTGATAAT
20747921 TTTCGACAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
ATTTTAATTAATTTTGATAATAT
Found at i:20757696 original size:22 final size:24
Alignment explanation
Indices: 20757671--20757714 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
20757661 CATGTATAGG
*
20757671 TGAACTTATAAT-GATG-TTTACT
1 TGAAATTATAATAGATGATTTACT
*
20757693 TGAAATTTTAATAGATGATTTA
1 TGAAATTATAATAGATGATTTA
20757715 GTATGTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 4 0.22
24 4 0.22
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (24 bp):
TGAAATTATAATAGATGATTTACT
Found at i:20758252 original size:23 final size:23
Alignment explanation
Indices: 20758226--20758271 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
20758216 GTGTTACACG
* *
20758226 GCCTGGCACACGGGCGTGTGACA
1 GCCTAGCAAACGGGCGTGTGACA
**
20758249 GCCTAGCAAACGTTCGTGTGACA
1 GCCTAGCAAACGGGCGTGTGACA
20758272 CGGTCGTGTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.28, G:0.33, T:0.17
Consensus pattern (23 bp):
GCCTAGCAAACGGGCGTGTGACA
Found at i:20759685 original size:17 final size:17
Alignment explanation
Indices: 20759663--20759701 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
20759653 AAAAATCACC
*
20759663 TAAAAATATTAAAATTA
1 TAAAAAAATTAAAATTA
20759680 TAAAAAAATTAAAATTA
1 TAAAAAAATTAAAATTA
20759697 -AAAAA
1 TAAAAA
20759702 CCCAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAAAAAATTAAAATTA
Found at i:20761113 original size:25 final size:26
Alignment explanation
Indices: 20761071--20761122 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
20761061 CACCATTGTT
*
20761071 ATTGTTTTTATTTTATTTTATTT-TTA
1 ATTGTTTTTATTTGATTTT-TTTATTA
*
20761097 ATTG-TTTTCTTTGATTTTTTTATTA
1 ATTGTTTTTATTTGATTTTTTTATTA
20761122 A
1 A
20761123 GAGTAGTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 3 0.13
25 16 0.70
26 4 0.17
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (26 bp):
ATTGTTTTTATTTGATTTTTTTATTA
Found at i:20765187 original size:25 final size:25
Alignment explanation
Indices: 20765150--20765202 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
20765140 TAATGTATCA
*
20765150 TTTTTTATGGGGAGTAATAACTTAT
1 TTTTTTATAGGGAGTAATAACTTAT
*
20765175 TTTTTTATAGGGAGTAATAATTTAT
1 TTTTTTATAGGGAGTAATAACTTAT
20765200 TTT
1 TTT
20765203 GCCCTCCACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.53
Consensus pattern (25 bp):
TTTTTTATAGGGAGTAATAACTTAT
Found at i:20766378 original size:44 final size:44
Alignment explanation
Indices: 20766324--20766466 Score: 268
Period size: 44 Copynumber: 3.2 Consensus size: 44
20766314 CTAGTATTGC
*
20766324 CTCCTGACCTCTACTAATTACTTAATTGGCGGATACTCACTTAT
1 CTCCTAACCTCTACTAATTACTTAATTGGCGGATACTCACTTAT
20766368 CTCCTAACCTCTACTAATTACTTAATTGGCGGATACTCACTTAT
1 CTCCTAACCTCTACTAATTACTTAATTGGCGGATACTCACTTAT
20766412 CTCCTAACCTCTACTAATTACTTAATTGGCGGATACTCACTTAT
1 CTCCTAACCTCTACTAATTACTTAATTGGCGGATACTCACTTAT
*
20766456 CTCCTGACCTC
1 CTCCTAACCTC
20766467 ACTTTCTCCA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 97 1.00
ACGTcount: A:0.25, C:0.29, G:0.10, T:0.36
Consensus pattern (44 bp):
CTCCTAACCTCTACTAATTACTTAATTGGCGGATACTCACTTAT
Found at i:20770462 original size:6 final size:6
Alignment explanation
Indices: 20770453--20770479 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
20770443 AACATTAATT
20770453 AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAA
20770480 AACCAAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:20770477 original size:22 final size:21
Alignment explanation
Indices: 20770435--20770481 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
20770425 AGAAAATCAC
* *
20770435 AAAAATAAAACATTAATTAAA
1 AAAAATAAAACATAAAATAAA
20770456 TAAAAATAAAA-ATAAAAATAAA
1 -AAAAATAAAACAT-AAAATAAA
20770478 AAAA
1 AAAA
20770482 CCAAATTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (21 bp):
AAAAATAAAACATAAAATAAA
Found at i:20776038 original size:24 final size:24
Alignment explanation
Indices: 20776011--20776057 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
20776001 AAAGTCAAAT
* *
20776011 ATATTATGCTAATAAATGCTAAAC
1 ATATTATACTAATAAATACTAAAC
*
20776035 ATATTATACTCATAAATACTAAA
1 ATATTATACTAATAAATACTAAA
20776058 TCTTCTAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (24 bp):
ATATTATACTAATAAATACTAAAC
Found at i:20780447 original size:23 final size:24
Alignment explanation
Indices: 20780421--20780476 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
20780411 AAACCTAATT
* *
20780421 CTAATAAATTC-AAATATATTATG
1 CTAATAAATGCTAAATATATTATC
20780444 CTAATAAATGCTAAATATATTATC
1 CTAATAAATGCTAAATATATTATC
*
20780468 CTCATAAAT
1 CTAATAAAT
20780477 ATTAAATCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (24 bp):
CTAATAAATGCTAAATATATTATC
Found at i:20780482 original size:24 final size:23
Alignment explanation
Indices: 20780421--20780483 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
20780411 AAACCTAATT
* *
20780421 CTAATAAATTCAAATATATTATG
1 CTAATAAATTTAAATATATTATC
*
20780444 CTAATAAATGCTAAATATATTATC
1 CTAATAAAT-TTAAATATATTATC
*
20780468 CTCATAAATATTAAAT
1 CTAATAAAT-TTAAAT
20780484 CTTCTAGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 9 0.27
24 24 0.73
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (23 bp):
CTAATAAATTTAAATATATTATC
Found at i:20780828 original size:7 final size:7
Alignment explanation
Indices: 20780816--20780847 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
20780806 GAAATGCTAC
20780816 AACATCG
1 AACATCG
20780823 AACATCG
1 AACATCG
20780830 AACATCG
1 AACATCG
20780837 AACATCG
1 AACATCG
20780844 AACA
1 AACA
20780848 GGTGAGGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.47, C:0.28, G:0.12, T:0.12
Consensus pattern (7 bp):
AACATCG
Found at i:20781225 original size:88 final size:88
Alignment explanation
Indices: 20781132--20781367 Score: 472
Period size: 88 Copynumber: 2.7 Consensus size: 88
20781122 ACTTTTTTTT
20781132 AATAATTTAAATTATTTTTAGTTTTTAAAAATGATATTTTGAAGTTTTAAAATTTTAAAACTTCA
1 AATAATTTAAATTATTTTTAGTTTTTAAAAATGATATTTTGAAGTTTTAAAATTTTAAAACTTCA
20781197 AAATATCATTTTTAAAAACTAAA
66 AAATATCATTTTTAAAAACTAAA
20781220 AATAATTTAAATTATTTTTAGTTTTTAAAAATGATATTTTGAAGTTTTAAAATTTTAAAACTTCA
1 AATAATTTAAATTATTTTTAGTTTTTAAAAATGATATTTTGAAGTTTTAAAATTTTAAAACTTCA
20781285 AAATATCATTTTTAAAAACTAAA
66 AAATATCATTTTTAAAAACTAAA
20781308 AATAATTTAAATTATTTTTAGTTTTTAAAAATGATATTTTGAAGTTTTAAAATTTTAAAA
1 AATAATTTAAATTATTTTTAGTTTTTAAAAATGATATTTTGAAGTTTTAAAATTTTAAAA
20781368 AATTAATTAA
Statistics
Matches: 148, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 148 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (88 bp):
AATAATTTAAATTATTTTTAGTTTTTAAAAATGATATTTTGAAGTTTTAAAATTTTAAAACTTCA
AAATATCATTTTTAAAAACTAAA
Found at i:20784881 original size:4 final size:4
Alignment explanation
Indices: 20784874--20784912 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
20784864 AAACCAAATT
* *
20784874 TTTA TTTA TTTA TTTA TATA TGTA TTTA TTTA -TTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
20784913 GTTTTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:20785239 original size:13 final size:12
Alignment explanation
Indices: 20785215--20785253 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
20785205 ATATGGATTA
20785215 TTGTTT-TTTAT
1 TTGTTTATTTAT
20785226 TTCGTTTATTTAT
1 TT-GTTTATTTAT
20785239 TTGTTTATATTAT
1 TTGTTTAT-TTAT
20785252 TT
1 TT
20785254 TTATGTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 10 0.40
13 13 0.52
ACGTcount: A:0.15, C:0.03, G:0.08, T:0.74
Consensus pattern (12 bp):
TTGTTTATTTAT
Found at i:20785284 original size:15 final size:15
Alignment explanation
Indices: 20785261--20785302 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
20785251 TTTTTATGTC
20785261 ATTGATGTATTTATT
1 ATTGATGTATTTATT
*
20785276 ATTGTTGTATTTATT
1 ATTGATGTATTTATT
20785291 ATT-ATAGTATTT
1 ATTGAT-GTATTT
20785303 GTACGTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 1 0.04
15 23 0.96
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.62
Consensus pattern (15 bp):
ATTGATGTATTTATT
Found at i:20797601 original size:89 final size:88
Alignment explanation
Indices: 20797493--20798046 Score: 314
Period size: 89 Copynumber: 6.4 Consensus size: 88
20797483 TCGCATCTAG
*
20797493 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAATTAAGTCTTATCCTCCTGAAGTTGCA
1 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTAAGAAATTAAGTCTTAT-CTCCTGAAGTTGCA
*
20797558 GTGAGGCAGACTGAAGATGGCAAA
65 GTGAGGCAGACTGAAGATCGCAAA
* ** ** *
20797582 TCTTATCTCTCTGAAGTTGCAATGGAGCAGGTTAAAGCCGA-TAATTC-TATCTTCCTGAAGTTG
1 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGACT-AAG-AAATTAAGTCTTATC-TCCTGAAGTTG
* * * ** *
20797645 CAGTGGAGTG--GA-TTAAAACCTTAGA
63 CAGT-GAG-GCAGACTGAAGATCGCAAA
* * * *
20797670 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CG-CATCT-AGTCTTATCTCCCTGAAGTTAC
1 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTAAGAAAT-TAAGTCTTATCT-CCTGAAGTTGC
* ** *
20797730 AGTG-GAGCAGACT-AAAAAAGCAAG
64 AGTGAG-GCAGACTGAAGATCGCAAA
**** *
20797754 TCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
1 TCTTATCTCT-CTGAAGTTGCAGTGGA-GCAGACT-AAGAAATTAAGTCTTATCT-CCTGAAGTT
* ** *
20797817 GCAGTGGGGCAGGTTAAAG-TCG-ATAA
62 GCAGTGAGGCAGACTGAAGATCGCA-AA
* ** * *
20797843 TCCTATCT-TCCTGAAGTTGCAGTGGAGTGGATTAA-AACCTT-AGATCTTATCTCTCTGAAGTT
1 TCTTATCTCT-CTGAAGTTGCAGTGGAGCAGACTAAGAA-ATTAAG-TCTTATCTC-CTGAAGTT
* * * *
20797905 GCAGAGA-GCAGA-TCG--CAT--CTAG
62 GCAGTGAGGCAGACT-GAAGATCGCAAA
* * * **
20797927 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCA
1 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTAAGAAATTAAGTCTTAT-CTCCTGAAGTTGCA
20797992 GTGAGGCAGACTGAAGAT-GACAAA
65 GTGAGGCAGACTGAAGATCG-CAAA
* *
20798016 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGA
1 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGA
20798047 TTAAAACCAA
Statistics
Matches: 351, Mismatches: 73, Indels: 82
0.69 0.14 0.16
Matches are distributed among these distances:
82 3 0.01
83 7 0.02
84 96 0.27
85 18 0.05
86 5 0.01
87 15 0.04
88 53 0.15
89 136 0.39
90 16 0.05
91 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (88 bp):
TCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTAAGAAATTAAGTCTTATCTCCTGAAGTTGCAG
TGAGGCAGACTGAAGATCGCAAA
Done.