Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 169 of 279
Found at i:56167551 original size:30 final size:32
Alignment explanation
Indices: 56167510--56167597 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 32
56167500 TAGAAACAGT
56167510 ACATA-AA-TCTTAAAAGTTAACAATGAC-A-
1 ACATAGAAGTCTTAAAAGTTAACAATGACAAC
**
56167538 ACATAGAAGTCTTAAAAGTTTAA-AAAAACAAC
1 ACATAGAAGTCTTAAAAG-TTAACAATGACAAC
* *
56167570 ACAAAGTAAGTCTTGAAAGTTAACAATG
1 ACATAG-AAGTCTTAAAAGTTAACAATG
56167598 GTAGAACATA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
28 5 0.11
29 2 0.04
30 13 0.28
31 5 0.11
32 9 0.19
33 13 0.28
ACGTcount: A:0.52, C:0.12, G:0.11, T:0.24
Consensus pattern (32 bp):
ACATAGAAGTCTTAAAAGTTAACAATGACAAC
Found at i:56168826 original size:23 final size:22
Alignment explanation
Indices: 56168798--56168861 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
56168788 AACATGAAAT
* *
56168798 TTTGTGAAACCTTTGTGGCGTAA
1 TTTGTGAAGCCTTTGTGGCAT-A
* *
56168821 TTTGTGACGCCTTTGTAGCATA
1 TTTGTGAAGCCTTTGTGGCATA
56168843 TTCTGTGAAGCCTTTGTGG
1 TT-TGTGAAGCCTTTGTGG
56168862 TCTGGTTAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 3 0.09
23 31 0.91
ACGTcount: A:0.17, C:0.16, G:0.27, T:0.41
Consensus pattern (22 bp):
TTTGTGAAGCCTTTGTGGCATA
Found at i:56171428 original size:89 final size:89
Alignment explanation
Indices: 56171277--56171454 Score: 356
Period size: 89 Copynumber: 2.0 Consensus size: 89
56171267 CTCCAACATG
56171277 AAGCACACAAAACATGCATTCAATTACATCTCATACTTATCATTCAAGTATACCATTTCTCAAGT
1 AAGCACACAAAACATGCATTCAATTACATCTCATACTTATCATTCAAGTATACCATTTCTCAAGT
56171342 CATTTAACAACCTAACCATTCCAA
66 CATTTAACAACCTAACCATTCCAA
56171366 AAGCACACAAAACATGCATTCAATTACATCTCATACTTATCATTCAAGTATACCATTTCTCAAGT
1 AAGCACACAAAACATGCATTCAATTACATCTCATACTTATCATTCAAGTATACCATTTCTCAAGT
56171431 CATTTAACAACCTAACCATTCCAA
66 CATTTAACAACCTAACCATTCCAA
56171455 CTATCATAAT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.39, C:0.27, G:0.04, T:0.29
Consensus pattern (89 bp):
AAGCACACAAAACATGCATTCAATTACATCTCATACTTATCATTCAAGTATACCATTTCTCAAGT
CATTTAACAACCTAACCATTCCAA
Found at i:56177113 original size:74 final size:74
Alignment explanation
Indices: 56176986--56177123 Score: 190
Period size: 74 Copynumber: 1.9 Consensus size: 74
56176976 ACCAGTTTTA
* * *
56176986 TTTTACTTTAATATTTTGACCGAAAGGTGAAGATTAGGGCTAAAAGTGGAAATGAAAGTCTTCTT
1 TTTTACTTTAATAATTCGACCGAAAGGTGAAGATTAGGGCTAAAAGTGGAAATG-AAGGCTTCTT
56177051 CCATCGTGTT
65 CCATCGTGTT
** *
56177061 TTTTA-TTTAATAATTCGACCGAAAGGT-ATCTATTAGGGGTAAAAGTGGAAATGAAGGCTTCTT
1 TTTTACTTTAATAATTCGACCGAAAGGTGA-AGATTAGGGCTAAAAGTGGAAATGAAGGCTTCTT
56177124 ATAGATGACG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
73 10 0.18
74 41 0.73
75 5 0.09
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.36
Consensus pattern (74 bp):
TTTTACTTTAATAATTCGACCGAAAGGTGAAGATTAGGGCTAAAAGTGGAAATGAAGGCTTCTTC
CATCGTGTT
Found at i:56177268 original size:9 final size:8
Alignment explanation
Indices: 56177241--56177281 Score: 66
Period size: 8 Copynumber: 5.1 Consensus size: 8
56177231 GTTTCGTAAA
56177241 TTTAAA-T
1 TTTAAATT
56177248 TTTAAATT
1 TTTAAATT
56177256 TTTAAATTT
1 TTTAAA-TT
56177265 TTTAAATT
1 TTTAAATT
56177273 TTTAAATT
1 TTTAAATT
56177281 T
1 T
56177282 AAGTTTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 6 0.19
8 18 0.56
9 8 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTTAAATT
Found at i:56177269 original size:17 final size:17
Alignment explanation
Indices: 56177247--56177281 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
56177237 TAAATTTAAA
56177247 TTTTAAATTTTTAAATT
1 TTTTAAATTTTTAAATT
56177264 TTTTAAATTTTTAAATT
1 TTTTAAATTTTTAAATT
56177281 T
1 T
56177282 AAGTTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTAAATTTTTAAATT
Found at i:56179951 original size:72 final size:75
Alignment explanation
Indices: 56179817--56179953 Score: 190
Period size: 72 Copynumber: 1.9 Consensus size: 75
56179807 CATGGTTAAA
* * *
56179817 GTTCGAATGTATGATACAAGTTTATTGAGCTGAACTTAATATTATGAATTTCATATATATATATG
1 GTTCGAATATATGATACAAGTTTATTGAGCTGAACTTAATAGTATGAATTTCATATACATATATG
56179882 TGTGTGTGTG
66 TGTGTGTGTG
* * * *
56179892 GTTCGAATATAT-ATTCAAG-TTCTTGAGCTGAATTTAAT-GTATGAATTTTATATACATATATG
1 GTTCGAATATATGATACAAGTTTATTGAGCTGAACTTAATAGTATGAATTTCATATACATATATG
56179954 GTTCGAATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
72 21 0.38
73 17 0.31
74 6 0.11
75 11 0.20
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (75 bp):
GTTCGAATATATGATACAAGTTTATTGAGCTGAACTTAATAGTATGAATTTCATATACATATATG
TGTGTGTGTG
Found at i:56180197 original size:41 final size:40
Alignment explanation
Indices: 56180140--56180253 Score: 174
Period size: 41 Copynumber: 2.8 Consensus size: 40
56180130 TGAGATTTTT
56180140 AGACTTTACGTCTAGCATGCTTAATGCCGGTGAAATATTTC
1 AGACTTTACGTCTAGCA-GCTTAATGCCGGTGAAATATTTC
56180181 AGACTTTACGTCTAGCAGACTTAATGCCGGTGAAATATTTC
1 AGACTTTACGTCTAGCAG-CTTAATGCCGGTGAAATATTTC
* * *
56180222 AGACCTTAAGTCTAGCAGGTTTAATGCCGGTG
1 AGACTTTACGTCTAGCA-GCTTAATGCCGGTG
56180254 TATTGAATCA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
40 1 0.01
41 66 0.97
42 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (40 bp):
AGACTTTACGTCTAGCAGCTTAATGCCGGTGAAATATTTC
Found at i:56184969 original size:41 final size:42
Alignment explanation
Indices: 56184854--56184969 Score: 182
Period size: 41 Copynumber: 2.8 Consensus size: 42
56184844 ACTGGCACTT
* * *
56184854 AGCCTGCTAGACATAAAGTTTGAAATGTTTCA-CTGGCGTCA
1 AGCCTGCTAGACATAAAGTCTAAAATGTTTCACCTGGCATCA
56184895 AGCCTGCTAGACATAAAGTCTAAAATGTTTCACCT-GCATCA
1 AGCCTGCTAGACATAAAGTCTAAAATGTTTCACCTGGCATCA
*
56184936 AGCCTGCTAGACTTAAAGTCTAAAATGTTTCACC
1 AGCCTGCTAGACATAAAGTCTAAAATGTTTCACC
56184970 GACAATAAAC
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 68 0.97
42 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28
Consensus pattern (42 bp):
AGCCTGCTAGACATAAAGTCTAAAATGTTTCACCTGGCATCA
Found at i:56186052 original size:16 final size:16
Alignment explanation
Indices: 56186033--56186070 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
56186023 AACATTTACA
56186033 CTTTTTACAATTTAAT
1 CTTTTTACAATTTAAT
56186049 CTTTTTACAATTTAAT
1 CTTTTTACAATTTAAT
56186065 CTTTTT
1 CTTTTT
56186071 TGCTCAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (16 bp):
CTTTTTACAATTTAAT
Found at i:56186571 original size:19 final size:20
Alignment explanation
Indices: 56186534--56186577 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
56186524 CTTTTGTTTT
56186534 ATTTAGTTATCATTATACTA
1 ATTTAGTTATCATTATACTA
* *
56186554 ATTTA-TTATTATTTTACTA
1 ATTTAGTTATCATTATACTA
56186573 ATTTA
1 ATTTA
56186578 ACCTTTACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTTAGTTATCATTATACTA
Found at i:56186815 original size:14 final size:15
Alignment explanation
Indices: 56186796--56186824 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
56186786 TCACAAAACT
56186796 TTCACACAT-ATAAA
1 TTCACACATAATAAA
56186810 TTCACACATAATAAA
1 TTCACACATAATAAA
56186825 CATAGAAAAA
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:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:56188974 original size:2 final size:2
Alignment explanation
Indices: 56188967--56189014 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
56188957 CAAACAAGGG
56188967 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
56189009 GA GA GA
1 GA GA GA
56189015 ATTCCATTAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:56196557 original size:13 final size:13
Alignment explanation
Indices: 56196535--56196567 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
56196525 CCCCATATAC
*
56196535 AGATAAATATAAT
1 AGATACATATAAT
56196548 AGATACATATAAT
1 AGATACATATAAT
56196561 AGATACA
1 AGATACA
56196568 AATATACAGA
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:0.58, C:0.06, G:0.09, T:0.27
Consensus pattern (13 bp):
AGATACATATAAT
Found at i:56204045 original size:27 final size:26
Alignment explanation
Indices: 56204015--56204071 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
56204005 AATTTCGAGG
*
56204015 TTTACAATTTT-TAATTTTTATTAATT
1 TTTAC-ATTTTCTAACTTTTATTAATT
*
56204041 ATTTACATTTTCTCACTTTTATTAATT
1 -TTTACATTTTCTAACTTTTATTAATT
56204068 TTTA
1 TTTA
56204072 TTATTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTACATTTTCTAACTTTTATTAATT
Found at i:56204227 original size:22 final size:23
Alignment explanation
Indices: 56204188--56204230 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
56204178 TTTAAAAAAT
*
56204188 AAAACATAATATAATATTTATCA
1 AAAAAATAATATAATATTTATCA
*
56204211 AAAAAATAA-ATATTATTTAT
1 AAAAAATAATATAATATTTAT
56204231 TTGATTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAAAATAATATAATATTTATCA
Found at i:56204381 original size:86 final size:84
Alignment explanation
Indices: 56204263--56204484 Score: 192
Period size: 86 Copynumber: 2.6 Consensus size: 84
56204253 ATGATATGTT
* * * * * * *
56204263 TTTAGCGGCATTTTTGCGAGAAGCGTCGCTAAAGGTTTGTTCTATAGCGACATTTGTGATAAAAA
1 TTTAGCGGCATTTGTG-GAAAAGCGCCACTAAAGGTATGGTCTATAGCGACATTTGTG-GAAAAA
56204328 ACGCCGCTAAAGATCATGGTC
64 ACGCCGCTAAAGATCATGGTC
** * * * *
56204349 TTTAGCGGCATTTGTGGTAAAAGCGCCACTAAAGAACATGGTCTTTAGCGGCGTTTGTGGGAAAA
1 TTTAGCGGCATTTGTGG-AAAAGCGCCACTAAAG-GTATGGTCTATAGCGACATTTGTGGAAAAA
*** * *
56204414 GTTCCGCTAAAGGTCGTGGTC
64 ACGCCGCTAAAGATCATGGTC
* * * *
56204435 TATAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGGTCCTGGTCTTTAGCG
1 TTTAGCGGCATTTGTGG-AAAAGCGCCACTAAAGGT-ATGGTCTATAGCG
56204485 GCGTTTATTT
Statistics
Matches: 109, Mismatches: 24, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
85 1 0.01
86 91 0.83
87 17 0.16
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (84 bp):
TTTAGCGGCATTTGTGGAAAAGCGCCACTAAAGGTATGGTCTATAGCGACATTTGTGGAAAAAAC
GCCGCTAAAGATCATGGTC
Found at i:56204485 original size:86 final size:86
Alignment explanation
Indices: 56204331--56204490 Score: 248
Period size: 86 Copynumber: 1.9 Consensus size: 86
56204321 ATAAAAAACG
* *
56204331 CCGCTAAAGATCATGGTCTTTAGCGGCATTTGTGGTAAAAGCGCCACTAAAGAACATGGTCTTTA
1 CCGCTAAAGATCATGGTCTATAGCGGCATTTGTGGAAAAAGCGCCACTAAAGAACATGGTCTTTA
56204396 GCGGCGTTTGTGGGAAAAGTT
66 GCGGCGTTTGTGGGAAAAGTT
* * * ** *
56204417 CCGCTAAAGGTCGTGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGGTCCTGGTCTTTA
1 CCGCTAAAGATCATGGTCTATAGCGGCATTTGTGGAAAAAGCGCCACTAAAGAACATGGTCTTTA
56204482 GCGGCGTTT
66 GCGGCGTTT
56204491 ATTTCCAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 66 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (86 bp):
CCGCTAAAGATCATGGTCTATAGCGGCATTTGTGGAAAAAGCGCCACTAAAGAACATGGTCTTTA
GCGGCGTTTGTGGGAAAAGTT
Found at i:56204487 original size:43 final size:43
Alignment explanation
Indices: 56204323--56204490 Score: 210
Period size: 43 Copynumber: 3.9 Consensus size: 43
56204313 CATTTGTGAT
* * *
56204323 AAAAAACGCCGCTAAAGATCATGGTCTTTAGCGGCATTTGTGG
1 AAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGG
* *
56204366 TAAAAGCGCCACTAAAGAACATGGTCTTTAGCGGCGTTTGTGG
1 AAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGG
* ** * * * *
56204409 GAAAAGTTCCGCTAAAGGTCGTGGTCTATAGCGGCGTTTGTGG
1 AAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGG
* *
56204452 AAAAAGCGCCACTAAAGGTCCTGGTCTTTAGCGGCGTTT
1 AAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTT
56204491 ATTTCCAAAA
Statistics
Matches: 106, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 106 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (43 bp):
AAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGG
Found at i:56204809 original size:18 final size:20
Alignment explanation
Indices: 56204781--56204818 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
56204771 TTAATTAAGA
56204781 AATTAAATAAAT-ATATTTT
1 AATTAAATAAATAATATTTT
56204800 AATT-AATAAATAATATTTT
1 AATTAAATAAATAATATTTT
56204819 TTTAGAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTAAATAAATAATATTTT
Found at i:56208029 original size:22 final size:22
Alignment explanation
Indices: 56207999--56208040 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
56207989 TGCAGTTCTT
*
56207999 ATTTTTATACGTGTATATATGA
1 ATTTGTATACGTGTATATATGA
* *
56208021 ATTTGTATATGTGTGTATAT
1 ATTTGTATACGTGTATATAT
56208041 AAATAATGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (22 bp):
ATTTGTATACGTGTATATATGA
Found at i:56211209 original size:26 final size:26
Alignment explanation
Indices: 56211173--56211227 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
56211163 TCTTCAATGA
56211173 TTAATTTCTAACCGGTTTTTTGGTGG
1 TTAATTTCTAACCGGTTTTTTGGTGG
*
56211199 TTAATTTCTAACCGGTTTTTTTGTGG
1 TTAATTTCTAACCGGTTTTTTGGTGG
56211225 TTA
1 TTA
56211228 TTAGTGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.16, C:0.11, G:0.20, T:0.53
Consensus pattern (26 bp):
TTAATTTCTAACCGGTTTTTTGGTGG
Found at i:56215037 original size:54 final size:54
Alignment explanation
Indices: 56214973--56215079 Score: 155
Period size: 54 Copynumber: 2.0 Consensus size: 54
56214963 TTTGAACAGT
* *
56214973 AGTCTCCCCCT-AAGCAGTAGCTT-CCCTTCGAACAATGGTGTTTTCTGGAATAAC
1 AGTCTCCCCCTGAA-CAATAACTTCCCCTT-GAACAATGGTGTTTTCTGGAATAAC
*
56215027 AGTCTTCCCCTGAACAATAACTTCCCCTTGAACAATGGTGTTTTCTGGAATAA
1 AGTCTCCCCCTGAACAATAACTTCCCCTTGAACAATGGTGTTTTCTGGAATAA
56215080 AGTTTTCAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
54 41 0.85
55 7 0.15
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (54 bp):
AGTCTCCCCCTGAACAATAACTTCCCCTTGAACAATGGTGTTTTCTGGAATAAC
Found at i:56238074 original size:23 final size:23
Alignment explanation
Indices: 56238059--56238104 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
56238049 GTTTGCGAAT
* *
56238059 GTTAAATGAACATGTTCGTAAAC
1 GTTAAATGAAAATGTTCGCAAAC
*
56238082 GTTAAATGAAAATGTTCACAAAC
1 GTTAAATGAAAATGTTCGCAAAC
56238105 AATAAACCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.28
Consensus pattern (23 bp):
GTTAAATGAAAATGTTCGCAAAC
Found at i:56238110 original size:23 final size:23
Alignment explanation
Indices: 56238061--56238110 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
56238051 TTGCGAATGT
* ** **
56238061 TAAATGAACATGTTCGTAAACGT
1 TAAATGAAAATGTTCACAAACAA
56238084 TAAATGAAAATGTTCACAAACAA
1 TAAATGAAAATGTTCACAAACAA
56238107 TAAA
1 TAAA
56238111 CCAACCAAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (23 bp):
TAAATGAAAATGTTCACAAACAA
Found at i:56244632 original size:16 final size:18
Alignment explanation
Indices: 56244609--56244648 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
56244599 TTTTTATTTT
56244609 TATTTTGAT-AATTTAAA
1 TATTTTGATGAATTTAAA
*
56244626 T-TTTTGATGATTTTAAA
1 TATTTTGATGAATTTAAA
56244643 TATTTT
1 TATTTT
56244649 TTATAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 7 0.35
17 9 0.45
18 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (18 bp):
TATTTTGATGAATTTAAA
Found at i:56244642 original size:17 final size:17
Alignment explanation
Indices: 56244609--56244662 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
56244599 TTTTTATTTT
56244609 TATTTTGATAATTTAAA
1 TATTTTGATAATTTAAA
*
56244626 T-TTTTGATGATTTTAAA
1 TATTTTGAT-AATTTAAA
* *
56244643 TATTTTTTATAATTTTAA
1 TA-TTTTGATAATTTAAA
56244661 TA
1 TA
56244663 AAAATTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 7 0.23
17 9 0.30
18 8 0.27
19 6 0.20
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
TATTTTGATAATTTAAA
Found at i:56259219 original size:25 final size:23
Alignment explanation
Indices: 56259175--56259235 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
56259165 ATTTTAATTC
*
56259175 ATTTAATAATATAATATCATTATA
1 ATTTAATTATATAATATCA-TATA
56259199 ATTTAATTATCATAA-ATTCATATA
1 ATTTAATTAT-ATAATA-TCATATA
*
56259223 ATATAAATTATAT
1 AT-TTAATTATAT
56259236 TTAAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATTATATAATATCATATA
Found at i:56259224 original size:35 final size:33
Alignment explanation
Indices: 56259183--56259266 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 33
56259173 TCATTTAATA
* *
56259183 ATATAATATCATTATAATTTAATTATCATAAATT
1 ATATAATATAATTAT-ATTTAAATATCATAAATT
*
56259217 CATATAATATAAATTATATTTAAATATCATTAATT
1 -ATATAATAT-AATTATATTTAAATATCATAAATT
56259252 ATATATATATAATTA
1 ATATA-ATATAATTA
56259267 AACAAATAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
34 10 0.23
35 29 0.66
36 5 0.11
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (33 bp):
ATATAATATAATTATATTTAAATATCATAAATT
Found at i:56263556 original size:43 final size:43
Alignment explanation
Indices: 56263471--56263556 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 43
56263461 AATCATGACA
* * * *
56263471 ACTTTACGTAAAAGTATTTATGATAAAATATATTTAATTTTTT
1 ACTTTACATAAAAGTATCTATAAGAAAATATATTTAATTTTTT
56263514 ACTTTACCATAAAAGTATCTATAAGAAAATATATTTAATTTTT
1 ACTTTA-CATAAAAGTATCTATAAGAAAATATATTTAATTTTT
56263557 CTACATTCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
43 6 0.16
44 32 0.84
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (43 bp):
ACTTTACATAAAAGTATCTATAAGAAAATATATTTAATTTTTT
Found at i:56264731 original size:34 final size:34
Alignment explanation
Indices: 56264688--56264809 Score: 111
Period size: 34 Copynumber: 3.6 Consensus size: 34
56264678 CAATATGGCG
*
56264688 TGCTTATAACATATCAATATGGTAGCAATTGATA
1 TGCTTATAACATATCAATATGGTAGCAATTAATA
* * *
56264722 TGCTCATAACAGT-TCCATATGGTAGCAAATAATA
1 TGCTTATAACA-TATCAATATGGTAGCAATTAATA
*** * * *
56264756 TGCTTATAATGGATTAATACGGTGGCAATTAATA
1 TGCTTATAACATATCAATATGGTAGCAATTAATA
* * *
56264790 TACTGATAACAAATCAATAT
1 TGCTTATAACATATCAATAT
56264810 CCTAGTAAAA
Statistics
Matches: 66, Mismatches: 20, Indels: 4
0.73 0.22 0.04
Matches are distributed among these distances:
34 65 0.98
35 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (34 bp):
TGCTTATAACATATCAATATGGTAGCAATTAATA
Found at i:56268564 original size:19 final size:20
Alignment explanation
Indices: 56268540--56268585 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
56268530 ACATATTGCC
56268540 TTAGATTACGTCAAAGGCA-
1 TTAGATTACGTCAAAGGCAT
*
56268559 TTAGATTATGTCAAAGGCAT
1 TTAGATTACGTCAAAGGCAT
56268579 TTAGATT
1 TTAGATT
56268586 GGGTTCAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (20 bp):
TTAGATTACGTCAAAGGCAT
Found at i:56271129 original size:18 final size:18
Alignment explanation
Indices: 56271108--56271163 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
56271098 AAATTGTGAT
*
56271108 AAAATTAAAATTTATTAA
1 AAAATTAAAATATATTAA
56271126 AAAATTACAAA-ATACTTAA
1 AAAATTA-AAATATA-TTAA
*
56271145 AAAATAAAAATATATTAA
1 AAAATTAAAATATATTAA
56271163 A
1 A
56271164 GTTATTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 17 0.52
19 16 0.48
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATTAAAATATATTAA
Found at i:56271672 original size:24 final size:24
Alignment explanation
Indices: 56271644--56271692 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
56271634 ATATGAGTAC
56271644 AATATATTA--TAT-AAATTATATA
1 AATATATTATTTATGAAATT-TATA
56271666 AATATATTATTTATGAAATTTATA
1 AATATATTATTTATGAAATTTATA
56271690 AAT
1 AAT
56271693 GATCTATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.38
24 10 0.42
25 5 0.21
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
AATATATTATTTATGAAATTTATA
Found at i:56273485 original size:22 final size:22
Alignment explanation
Indices: 56273460--56273504 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
56273450 TGTTATAACT
56273460 TTTTTTTATTTACCAAAATATA
1 TTTTTTTATTTACCAAAATATA
56273482 TTTTTTTATTTACCAAAATATA
1 TTTTTTTATTTACCAAAATATA
56273504 T
1 T
56273505 CAAAAACAAA
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:0.36, C:0.09, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTTTTATTTACCAAAATATA
Found at i:56273688 original size:18 final size:19
Alignment explanation
Indices: 56273643--56273720 Score: 104
Period size: 19 Copynumber: 4.2 Consensus size: 19
56273633 TATTCTCCTT
* *
56273643 TAACTCTTTTTTTATTTAA
1 TAACTCTATTTTAATTTAA
56273662 TAACTCTATTTTAATTTAA
1 TAACTCTATTTTAATTTAA
* * *
56273681 TAA-GCTATTCTCATTTAA
1 TAACTCTATTTTAATTTAA
56273699 TAACTCTATTTTAATTTAA
1 TAACTCTATTTTAATTTAA
56273718 TAA
1 TAA
56273721 ACTATTAAGT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
18 15 0.30
19 35 0.70
ACGTcount: A:0.35, C:0.12, G:0.01, T:0.53
Consensus pattern (19 bp):
TAACTCTATTTTAATTTAA
Found at i:56273700 original size:37 final size:37
Alignment explanation
Indices: 56273656--56273726 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
56273646 CTCTTTTTTT
*
56273656 ATTTAATAACTCTATTTTAATTTAATAAGCTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
56273693 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
56273727 AAGTAATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:56273981 original size:18 final size:18
Alignment explanation
Indices: 56273944--56274012 Score: 84
Period size: 19 Copynumber: 3.7 Consensus size: 18
56273934 TCAACTCAAT
* *
56273944 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAA-ACTA
56273963 TTTTAATTTAATAAACTA
1 TTTTAATTTAATAAACTA
* *
56273981 TTCTCATTTAATAAATCTA
1 TTTTAATTTAATAAA-CTA
56274000 TTTTAATTTAATA
1 TTTTAATTTAATA
56274013 TAATATTAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.37
19 27 0.63
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTAATTTAATAAACTA
Found at i:56274325 original size:37 final size:37
Alignment explanation
Indices: 56274278--56274348 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
56274268 AGTATGACTT
*
56274278 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGCTTATTAAATTAAAATAGAGTTATTAAATGAG
56274315 AATAGCTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGCTTATTAAATTAAAATAGAGTTATTAAAT
56274349 AATAAAAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.49, C:0.01, G:0.11, T:0.38
Consensus pattern (37 bp):
AATAGCTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:56274326 original size:18 final size:19
Alignment explanation
Indices: 56274284--56274348 Score: 96
Period size: 19 Copynumber: 3.5 Consensus size: 19
56274274 ACTTAATAGT
56274284 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
56274303 TTATTAAATGAGAATAG-C
1 TTATTAAATTAAAATAGAG
56274321 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
56274340 TTATTAAAT
1 TTATTAAAT
56274349 AATAAAAAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.38
19 24 0.62
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:56274475 original size:27 final size:27
Alignment explanation
Indices: 56274426--56274503 Score: 106
Period size: 27 Copynumber: 2.9 Consensus size: 27
56274416 ACTTTTTTTC
56274426 CTTTGGCACCA-TGGTGCCGCCAATGA
1 CTTTGGCACCATTGGTGCCGCCAATGA
* *
56274452 CTTTGGCACCATTGGTGCCACCAATTTA
1 CTTTGGCACCATTGGTGCCGCCAA-TGA
*
56274480 -TTTGGCACCTTTGGTGCCGCCAAT
1 CTTTGGCACCATTGGTGCCGCCAAT
56274504 TTAATTGGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.26
27 32 0.70
28 2 0.04
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.29
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCGCCAATGA
Found at i:56274504 original size:27 final size:26
Alignment explanation
Indices: 56274427--56274512 Score: 102
Period size: 27 Copynumber: 3.2 Consensus size: 26
56274417 CTTTTTTTCC
* *
56274427 TTTGGCACCATGGTGCCGCCAA-TGA
1 TTTGGCACCTTGGTGCCGCCAATTTA
*
56274452 CTTTGGCACCATTGGTGCCACCAATTTA
1 -TTTGGCACC-TTGGTGCCGCCAATTTA
56274480 TTTGGCACCTTTGGTGCCGCCAATTTA
1 TTTGGCACC-TTGGTGCCGCCAATTTA
*
56274507 ATTGGC
1 TTTGGC
56274513 CTGATCAGGT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
26 9 0.17
27 41 0.79
28 2 0.04
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (26 bp):
TTTGGCACCTTGGTGCCGCCAATTTA
Found at i:56274583 original size:24 final size:24
Alignment explanation
Indices: 56274550--56274597 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
56274540 TTTGTTTTTT
56274550 TATATATTTTGGTAAATAAAAAAA
1 TATATATTTTGGTAAATAAAAAAA
*
56274574 TATATTTTTTGGTAAATAAAAAAA
1 TATATATTTTGGTAAATAAAAAAA
56274598 AGTTATAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (24 bp):
TATATATTTTGGTAAATAAAAAAA
Found at i:56285325 original size:16 final size:17
Alignment explanation
Indices: 56285286--56285325 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
56285276 TTTTATAACA
56285286 TAAT-AAATTATTATTT
1 TAATAAAATTATTATTT
56285302 TAATAAAATT-TTATTT
1 TAATAAAATTATTATTT
56285318 TAATAAAA
1 TAATAAAA
56285326 AAATTTAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATAAAATTATTATTT
Found at i:56285551 original size:16 final size:18
Alignment explanation
Indices: 56285528--56285568 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
56285518 ATTATGTCTA
56285528 TATAAAATA-T-AATTAT
1 TATAAAATATTAAATTAT
*
56285544 TTTAAAATATTAAATTAT
1 TATAAAATATTAAATTAT
56285562 TATAAAA
1 TATAAAA
56285569 AATATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 8 0.38
17 1 0.05
18 12 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAAAATATTAAATTAT
Found at i:56285561 original size:18 final size:16
Alignment explanation
Indices: 56285528--56285581 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 16
56285518 ATTATGTCTA
56285528 TATAAAATATAATTAT
1 TATAAAATATAATTAT
*
56285544 TTTAAAATATTAAATTAT
1 TATAAAATA-T-AATTAT
* *
56285562 TATAAAAAAT-ATTTT
1 TATAAAATATAATTAT
56285577 TATAA
1 TATAA
56285582 TATTTTACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
15 9 0.28
16 8 0.25
17 2 0.06
18 13 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATAAAATATAATTAT
Found at i:56286131 original size:2 final size:2
Alignment explanation
Indices: 56286124--56286148 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56286114 TGGTAAGCCC
56286124 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
56286149 ACATCACCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:56290899 original size:20 final size:21
Alignment explanation
Indices: 56290862--56290900 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
56290852 ACATAAAATC
*
56290862 GTTAAATGGTATCTATACTAG
1 GTTAAATGGTATCGATACTAG
56290883 GTTAAAT-GTATCGATACT
1 GTTAAATGGTATCGATACT
56290901 TTAAGCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (21 bp):
GTTAAATGGTATCGATACTAG
Found at i:56297055 original size:72 final size:70
Alignment explanation
Indices: 56296937--56297080 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 70
56296927 TAGAAAAGAA
* *
56296937 AGAAACATATGAAACGAAACAGAGAAGGAAAAAGGGGGAAAGAAAAAGAGAAAGAAAAAAAGAGA
1 AGAAACATATGAAACGAAACAGAGAAGGAAAAAGGGAGAAACAAAAAGAG--AGAAAAAAAGAGA
*
56297002 GAAGCTT
64 AAAGCTT
*
56297009 AGAAACATATGAAACGGAACAGAGAAGGAAAAAGGGAGAAACAAAAAGAGAGAAAAAAAGAGAAA
1 AGAAACATATGAAACGAAACAGAGAAGGAAAAAGGGAGAAACAAAAAGAGAGAAAAAAAGAGAAA
*
56297074 AGGTT
66 AGCTT
56297079 AG
1 AG
56297081 GGTTTTAAGG
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
70 20 0.30
72 47 0.70
ACGTcount: A:0.61, C:0.06, G:0.28, T:0.06
Consensus pattern (70 bp):
AGAAACATATGAAACGAAACAGAGAAGGAAAAAGGGAGAAACAAAAAGAGAGAAAAAAAGAGAAA
AGCTT
Found at i:56304203 original size:19 final size:19
Alignment explanation
Indices: 56304168--56304205 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
56304158 CCTAAATGAT
*
56304168 TTTAAATTGTTTTTAAAAC
1 TTTAAATTGTTTCTAAAAC
56304187 TTTAAATAT-TTTCTAAAAC
1 TTTAAAT-TGTTTCTAAAAC
56304206 ATATTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (19 bp):
TTTAAATTGTTTCTAAAAC
Found at i:56306273 original size:19 final size:20
Alignment explanation
Indices: 56306251--56306292 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
56306241 TTATTTAGGA
56306251 ATTTATATT-ATTATAT-CAT
1 ATTTA-ATTAATTATATACAT
*
56306270 ATTTAATTAATTTTATACAT
1 ATTTAATTAATTATATACAT
56306290 ATT
1 ATT
56306293 AAAGCAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 3 0.15
19 11 0.55
20 6 0.30
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTAATTAATTATATACAT
Found at i:56308637 original size:30 final size:30
Alignment explanation
Indices: 56308559--56308645 Score: 83
Period size: 30 Copynumber: 2.9 Consensus size: 30
56308549 TATTTATTTT
*
56308559 TATTTTTT-AAA-TTTTAAAATACTTTTAAAA
1 TATTTTTTAAAATTTTTTAAA-A-TTTTAAAA
*
56308589 TACTTTTTTTAAATTTTTT-AAATTTTAAAA
1 TA-TTTTTTAAAATTTTTTAAAATTTTAAAA
56308619 T-TTTTTTAAAATACTTTTTAAAATTTT
1 TATTTTTTAAAAT--TTTTTAAAATTTT
56308646 TTTAATTTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
28 10 0.20
30 16 0.33
31 14 0.29
32 5 0.10
33 4 0.08
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (30 bp):
TATTTTTTAAAATTTTTTAAAATTTTAAAA
Found at i:56308637 original size:40 final size:40
Alignment explanation
Indices: 56308560--56308686 Score: 200
Period size: 40 Copynumber: 3.1 Consensus size: 40
56308550 ATTTATTTTT
* *
56308560 ATTTTTTAAATTTTAAAATACTTTTAAAATACTTTTTTTAA
1 ATTTTTTAAATTTTAAAATATTTTTAAAATAC-TTTTTAAA
*
56308601 ATTTTTTAAATTTTAAAATTTTTTTAAAATACTTTTTAAA
1 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTAAA
* *
56308641 ATTTTTTTAATTTTAAAATATTTTTAAAATGCTTTTTAAA
1 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTAAA
56308681 ATTTTT
1 ATTTTT
56308687 ATTTTAATTT
Statistics
Matches: 80, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 50 0.62
41 30 0.38
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (40 bp):
ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTAAA
Found at i:56308655 original size:29 final size:29
Alignment explanation
Indices: 56308622--56308679 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
56308612 TTTAAAATTT
*
56308622 TTTTAAAATACTTTTTAAAAT-TTTTTTAA
1 TTTTAAAATA-TTTTTAAAATGCTTTTTAA
56308651 TTTTAAAATATTTTTAAAATGCTTTTTAA
1 TTTTAAAATATTTTTAAAATGCTTTTTAA
56308680 AATTTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (29 bp):
TTTTAAAATATTTTTAAAATGCTTTTTAA
Found at i:56308678 original size:12 final size:11
Alignment explanation
Indices: 56308570--56308686 Score: 76
Period size: 11 Copynumber: 11.3 Consensus size: 11
56308560 ATTTTTTAAA
*
56308570 TTTTAAAATAC
1 TTTTAAAATAT
56308581 TTTTAAAATACTT
1 TTTTAAAATA--T
*
56308594 TTTTTAAAT-T
1 TTTTAAAATAT
56308604 TTTT--AA-A-
1 TTTTAAAATAT
*
56308611 TTTTAAAATTT
1 TTTTAAAATAT
56308622 TTTTAAAATACT
1 TTTTAAAATA-T
56308634 TTTTAAAAT-T
1 TTTTAAAATAT
*
56308644 TTTT----TAA
1 TTTTAAAATAT
56308651 TTTTAAAATAT
1 TTTTAAAATAT
*
56308662 TTTTAAAATGCT
1 TTTTAAAAT-AT
56308674 TTTTAAAAT-T
1 TTTTAAAATAT
56308684 TTT
1 TTT
56308687 ATTTTAATTT
Statistics
Matches: 85, Mismatches: 7, Indels: 29
0.70 0.06 0.24
Matches are distributed among these distances:
6 1 0.01
7 8 0.09
8 2 0.02
9 2 0.02
10 14 0.16
11 30 0.35
12 20 0.24
13 8 0.09
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:56310383 original size:152 final size:152
Alignment explanation
Indices: 56310126--56310716 Score: 1069
Period size: 152 Copynumber: 3.9 Consensus size: 152
56310116 TGTCATGGAT
* * *
56310126 GGTATTTTAAATGTGAAATATGGAGATGAGGGTTGATTTGGTTGGAGGATACTCTGAAGCTGAG-
1 GGTATCTTAAGTGTGAAATATGGAGATGAGGGTTGATTTGGTTGGAGGATACTATGAAGCTG-GT
* * *
56310190 CACAATGT-AAAGTTCGGATATCTTTTGGCCTTCACCACCTCCATGCTTTCGTGGAGTGTGATTG
65 GACAATGTGAAA-TTCGGATTTCCTTTGGCCTTCACCACCTCCATGCTTTCGTGGAGTGTGATTG
56310254 ATCTATTTCTTTGCTGTCATGTTC
129 ATCTATTTCTTTGCTGTCATGTTC
*
56310278 AGTATCTTAAGTGTGAAATATGGAGATGAGGGTTGATTTGGTTGGAGGATACTATGAAGCTGGTG
1 GGTATCTTAAGTGTGAAATATGGAGATGAGGGTTGATTTGGTTGGAGGATACTATGAAGCTGGTG
56310343 ACAATGTGAAATTCGGATTTCCTTTGGCCTTCACCACCTCCATGCTTTCGTGGAGTGTGATTGAT
66 ACAATGTGAAATTCGGATTTCCTTTGGCCTTCACCACCTCCATGCTTTCGTGGAGTGTGATTGAT
56310408 CTATTTCTTTGCTGTCATGTTC
131 CTATTTCTTTGCTGTCATGTTC
56310430 GGTATCTTAAGTGTGAAATATGGAGATGAGGGTTGATTTGGTTGGAGGATACTATGAAGCTGGTG
1 GGTATCTTAAGTGTGAAATATGGAGATGAGGGTTGATTTGGTTGGAGGATACTATGAAGCTGGTG
56310495 ACAATGTGAAATTCGGATTTCCTTTGGCCTTCACCACCTCCATGCTTTCGTGGAGTGTGATTGAT
66 ACAATGTGAAATTCGGATTTCCTTTGGCCTTCACCACCTCCATGCTTTCGTGGAGTGTGATTGAT
56310560 CTATTTCTTTGCTGTCATGTTC
131 CTATTTCTTTGCTGTCATGTTC
56310582 GGTATCTTAAGTGTGAAATATGGAGATGAGGGTTGATTTGGTTGGAGGATACTATGAAGCTGGTG
1 GGTATCTTAAGTGTGAAATATGGAGATGAGGGTTGATTTGGTTGGAGGATACTATGAAGCTGGTG
* *
56310647 ACAATGTGAAATTCGGATTTCCTTTGGCCTTTACCACCTCCATGCTTTCGTGGAATGTGATTGAT
66 ACAATGTGAAATTCGGATTTCCTTTGGCCTTCACCACCTCCATGCTTTCGTGGAGTGTGATTGAT
56310712 CTATT
131 CTATT
56310717 GCTAAAAAAT
Statistics
Matches: 427, Mismatches: 10, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
151 1 0.00
152 423 0.99
153 3 0.01
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.37
Consensus pattern (152 bp):
GGTATCTTAAGTGTGAAATATGGAGATGAGGGTTGATTTGGTTGGAGGATACTATGAAGCTGGTG
ACAATGTGAAATTCGGATTTCCTTTGGCCTTCACCACCTCCATGCTTTCGTGGAGTGTGATTGAT
CTATTTCTTTGCTGTCATGTTC
Found at i:56320452 original size:14 final size:15
Alignment explanation
Indices: 56320430--56320506 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
56320420 CAATCAAACA
56320430 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
56320444 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
56320459 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
56320479 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
56320493 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
56320507 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:56320471 original size:20 final size:20
Alignment explanation
Indices: 56320446--56320485 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
56320436 AATATTTTCC
*
56320446 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
56320466 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
56320486 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:56320491 original size:34 final size:35
Alignment explanation
Indices: 56320434--56320500 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
56320424 CAAACACCAG
*
56320434 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
56320469 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
56320501 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:56322415 original size:138 final size:138
Alignment explanation
Indices: 56322167--56322439 Score: 485
Period size: 138 Copynumber: 2.0 Consensus size: 138
56322157 GAGATGCGTT
* *
56322167 TTGCAGTTATGTCTTTTAAGTAGTTTCCTATAGAGTATTAATGGAGATGATTGGCATTTCTTAAT
1 TTGCAGTTATGTCTTTTAAGTAGTTCCCTATAGAGTATTAATGGAGATGATTGCCATTTCTTAAT
56322232 TCCATTGAGTGCAATTCAAGTGAATTCAATATTTTCTAGCTTGTACCAATGTGTCAAATTT-CTC
66 TCCATTGAGTGCAATTCAAGTGAATTCAATATTTTCTAGCTTGTACCAATGTGTCAAATTTCCT-
56322296 AAGAAACTA
130 AAGAAACTA
* *
56322305 TTGCAGTTATGTCTTTTAGGTAGTTCCCTGTAGAGTATTAATGGAGATGATTGCCATTTCTTAAT
1 TTGCAGTTATGTCTTTTAAGTAGTTCCCTATAGAGTATTAATGGAGATGATTGCCATTTCTTAAT
*
56322370 TCCATTGAGTGCAATTCGAGTGAATTCAATATTTTCTAGCTTGTACCAATGTGTCAAATTTCCTA
66 TCCATTGAGTGCAATTCAAGTGAATTCAATATTTTCTAGCTTGTACCAATGTGTCAAATTTCCTA
56322435 AGAAA
131 AGAAA
56322440 TTGTAAAAGA
Statistics
Matches: 129, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
138 127 0.98
139 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.40
Consensus pattern (138 bp):
TTGCAGTTATGTCTTTTAAGTAGTTCCCTATAGAGTATTAATGGAGATGATTGCCATTTCTTAAT
TCCATTGAGTGCAATTCAAGTGAATTCAATATTTTCTAGCTTGTACCAATGTGTCAAATTTCCTA
AGAAACTA
Found at i:56322753 original size:30 final size:28
Alignment explanation
Indices: 56322699--56322793 Score: 76
Period size: 28 Copynumber: 3.4 Consensus size: 28
56322689 AAATTATTAA
56322699 AATATTAATATAAA-ATAT-TATAATTTTT
1 AATATT-AT-TAAACATATATATAATTTTT
56322727 AATATTATTAAACATACATATATAATTATTT
1 AATATTATTAAACAT--ATATATAATT-TTT
*
56322758 -ATA-T-TTAATCATATA-ATAATTTATT
1 AATATTATTAAACATATATATAATTT-TT
*
56322783 AATATAATTAA
1 AATATTATTAA
56322794 TATAATTTAT
Statistics
Matches: 56, Mismatches: 2, Indels: 18
0.74 0.03 0.24
Matches are distributed among these distances:
24 1 0.02
25 8 0.14
26 10 0.18
27 4 0.07
28 17 0.30
29 3 0.05
30 10 0.18
31 3 0.05
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (28 bp):
AATATTATTAAACATATATATAATTTTT
Found at i:56322796 original size:25 final size:25
Alignment explanation
Indices: 56322768--56322825 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
56322758 ATATTTAATC
56322768 ATATAATAATT-TATTAATATAATTA
1 ATATAATAATTATATTAATA-AATTA
* *
56322793 ATATAATTTATTATTTTAATAAATTA
1 ATATAA-TAATTATATTAATAAATTA
56322819 AT-TAATA
1 ATATAATA
56322826 TTTCAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 1 0.04
25 9 0.32
26 11 0.39
27 7 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
ATATAATAATTATATTAATAAATTA
Found at i:56322812 original size:22 final size:22
Alignment explanation
Indices: 56322746--56322821 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
56322736 AAACATACAT
*
56322746 ATATAA-TTATTTATATTTAATCAT
1 ATATAATTTA-TTAT-TTTAAT-AA
* * *
56322770 ATAATAATTTATTAATATAATTA
1 AT-ATAATTTATTATTTTAATAA
56322793 ATATAATTTATTATTTTAATAA
1 ATATAATTTATTATTTTAATAA
56322815 AT-TAATT
1 ATATAATT
56322822 AATATTTCAA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
21 5 0.12
22 19 0.44
23 2 0.05
24 7 0.16
25 7 0.16
26 3 0.07
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATAATTTATTATTTTAATAA
Found at i:56328381 original size:18 final size:21
Alignment explanation
Indices: 56328334--56328392 Score: 61
Period size: 24 Copynumber: 2.8 Consensus size: 21
56328324 TCTTTATAAT
56328334 ATTTTTAAAAATATAAATTTTGAA
1 ATTTTTAAAAAT-T--ATTTTGAA
*
56328358 ATTTTTATAAA-TATTTTG-A
1 ATTTTTAAAAATTATTTTGAA
56328377 A-TTTTAAAAATTATTT
1 ATTTTTAAAAATTATTT
56328393 AAATTTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 8 0.25
19 7 0.22
20 6 0.19
22 1 0.03
24 10 0.31
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
ATTTTTAAAAATTATTTTGAA
Found at i:56338154 original size:22 final size:22
Alignment explanation
Indices: 56338127--56338179 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
56338117 GCAATATAAT
56338127 AACAAAATAG-CAACAAAACAAC
1 AACAAAATAGCCAAC-AAACAAC
* *
56338149 ATCAAAAT-GCCAACAAACGAC
1 AACAAAATAGCCAACAAACAAC
56338170 AACAAAATAG
1 AACAAAATAG
56338180 TAGTAAACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.62, C:0.23, G:0.08, T:0.08
Consensus pattern (22 bp):
AACAAAATAGCCAACAAACAAC
Found at i:56338175 original size:21 final size:22
Alignment explanation
Indices: 56338099--56338179 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 22
56338089 ACATCTAAAC
* * *
56338099 AACAATAACAAAATAGGAGCAA
1 AACAACAACAAAATAGCAACAA
* * *
56338121 TATAATAACAAAATAGCAACAA
1 AACAACAACAAAATAGCAACAA
*
56338143 AACAACATCAAAAT-GCCAAC-A
1 AACAACAACAAAATAG-CAACAA
*
56338164 AACGACAACAAAATAG
1 AACAACAACAAAATAG
56338180 TAGTAAACAA
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
21 14 0.30
22 33 0.70
ACGTcount: A:0.62, C:0.19, G:0.09, T:0.11
Consensus pattern (22 bp):
AACAACAACAAAATAGCAACAA
Found at i:56338910 original size:2 final size:2
Alignment explanation
Indices: 56338903--56338928 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
56338893 GTGATTTCAG
56338903 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
56338929 CTTTACTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:56347678 original size:3 final size:3
Alignment explanation
Indices: 56347670--56347707 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
56347660 GTTTGCTCGT
56347670 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
56347708 TGAAAATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:56349086 original size:20 final size:19
Alignment explanation
Indices: 56349044--56349086 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
56349034 ATATTATTTG
**
56349044 ATAAAATTTTTAAAAAATT
1 ATAAAATTTTTAAAAAACA
*
56349063 ATAAATATTTTTAAAATACA
1 ATAAA-ATTTTTAAAAAACA
56349083 ATAA
1 ATAA
56349087 TTTTTCAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAAATTTTTAAAAAACA
Found at i:56352235 original size:729 final size:727
Alignment explanation
Indices: 56350838--56353032 Score: 3770
Period size: 729 Copynumber: 3.0 Consensus size: 727
56350828 TAGCATTGTT
*
56350838 ATATAATTTAATGTCCATTTAGGG-TTTACAGGTTAAAAATCTGAAAATCTAAGAGTCATATTTA
1 ATATAATTTAATGTCCATTTAGGGTTTTGCAGGTTAAAAATCTGAAAATCTAAGAGTCATATTTA
*
56350902 GCTTTTGGATGCTTCATTTTCTGAAAGCAAAATCATTGTAATCCTATTAATATCACATGTTGTTT
66 GCTTTTGGATGCTTCATTTTCTGAAAGCAAAATCATTGTAATTCTATTAATATCACA---TGTTT
56350967 TGTCCAATCATATTATTATTTTGAATTTTAAGTTCTTGAAATATTATTTTCCTTTGATCTGAATA
128 TGTCCAATCATATTATTATTTTGAATTTTAAGTTCTTGAAATATTATTTTCCTTTGATCTGAATA
56351032 TGGCTTGTTTCCCTTACATGGGAAAGTCAGCAAGGAATTTTATCTGGTTATTCTTTTTCTTTTTT
193 TGGCTTGTTTCCCTTACATGGGAAAGTCAGCAAGGAATTTTATCTGGTTATTCTTTTTCTTTTTT
56351097 CTTTTGATTTTTGAAGGCAAAAACTGTATTGGGATAAAACAAGAACAAATTTAAATAATTGAATT
258 CTTTTGATTTTTGAAGGCAAAAACTGTATTGGGATAAAACAAGAACAAATTTAAATAATTGAATT
56351162 ATTAAGATATATTATTTTAATTTATATGGAAACTTTGTCTAATATTTCCCTTATATGTCTAATTT
323 ATTAAGATATATTATTTTAATTTATATGGAAACTTTGTCTAATATTTCCCTTATATGTCTAATTT
56351227 TATCTAATCGTGTTTGTTGTTCGGATTTGCATAATTCACCAAAAAAAAAAAAGCAACTAACAGAA
388 TATCTAATCGTGTTTGTTGTTCGGATTTGCATAATTCACCAAAAAAAAAAAAGCAACTAACAGAA
56351292 GTAAGAAGCTTAGAAAGTACTTTGGAGAAGCTTTTGACATATTAATTACGAGCTATGCCATTGTT
453 GTAAGAAGCTTAGAAAGTACTTTGGAGAAGCTTTTGACATATTAATTACGAGCTATGCCATTGTT
56351357 GCTGGAATCTTTTTCTTAACAATTCCTATGTGTTGTTTATATCTATTTTTAATTCTTTTGTTCTT
518 GCTGGAATCTTTTTCTTAACAATTCCTATGTGTTGTTTATATCTATTTTTAATTCTTTTGTTCTT
56351422 TACATATAACTTAGTTGGTATTGATGAAACAGAGTTTTTGGCTCGAAAGAGTGAGTGGGAAGAAA
583 TACATATAACTTAGTTGGTATTGATGAAACAGAGTTTTTGGCTCGAAAGAGTGAGTGGGAAGAAA
56351487 TGTTACATGCTGTCACCCAGGGACCTCTCCATTATATGGAGTGACACCCCAGATTATTGGAGATG
648 TGTTACATGCTGTCACCCAGGGACCTCTCCATTATATGGAGTGACACCCCAGATTATTGGAGATG
56351552 GGTGTCTATACCCGA
713 GGTGTCTATACCCGA
56351567 ATATAATTTAATGTCCATTTAGGGTTTTGCAGGTTAAAAATCTGAAAATCTAAGAGTCATATTTA
1 ATATAATTTAATGTCCATTTAGGGTTTTGCAGGTTAAAAATCTGAAAATCTAAGAGTCATATTTA
56351632 GCTTTTGGATGCTTCATTTTCTGAAAGCAAAATCATTGTAATTCTATTAATATCACATGTTTTGT
66 GCTTTTGGATGCTTCATTTTCTGAAAGCAAAATCATTGTAATTCTATTAATATCACATGTTTTGT
56351697 CCAATCATATTATTATTTTGAATTTTAAGTTCTTGAAATATTATTTTCCTTTGATCTGAATATGG
131 CCAATCATATTATTATTTTGAATTTTAAGTTCTTGAAATATTATTTTCCTTTGATCTGAATATGG
**
56351762 CTTGTTTCCCTTACATGGGAAAAAAACAGCAAGGAATTTTATCTGGTTATTCTTTTTCTTTTTTC
196 CTTGTTTCCCTTACATGGG--AAAGTCAGCAAGGAATTTTATCTGGTTATTCTTTTTCTTTTTTC
56351827 TTTTGATTTTTGAAGGCAAAAACTGTATTGGGATAAAACAAGAACAAATTTAAATAATTGAATTA
259 TTTTGATTTTTGAAGGCAAAAACTGTATTGGGATAAAACAAGAACAAATTTAAATAATTGAATTA
56351892 TTAAGATATATTATTTTAATTTATATGGAAACTTTGTCTAATATTTCCCTTATATGTCTAATTTT
324 TTAAGATATATTATTTTAATTTATATGGAAACTTTGTCTAATATTTCCCTTATATGTCTAATTTT
*
56351957 ATCTAATCGTGTTTGTTGTTCGGAATTGCATAATTCACCAAAAAAAAAAAAGCAACTAACAGAAG
389 ATCTAATCGTGTTTGTTGTTCGGATTTGCATAATTCACCAAAAAAAAAAAAGCAACTAACAGAAG
56352022 TAAGAAGCTTAGAAAGTACTTTGGAGAAGCTTTTGACATATTAATTACGAGCTATGCCATTGTTG
454 TAAGAAGCTTAGAAAGTACTTTGGAGAAGCTTTTGACATATTAATTACGAGCTATGCCATTGTTG
56352087 CTGGAATCTTTTTCTTAACAATTCCTATGTGTTGTTTATATCTATTTTTAATTCTTTTGTTCTTT
519 CTGGAATCTTTTTCTTAACAATTCCTATGTGTTGTTTATATCTATTTTTAATTCTTTTGTTCTTT
56352152 ACATATAACTTAGTTGGTATTGATGAAACAGAGTTTTTGGCTCGAAAGAGTGAGTGGGAAGAAAT
584 ACATATAACTTAGTTGGTATTGATGAAACAGAGTTTTTGGCTCGAAAGAGTGAGTGGGAAGAAAT
56352217 GTTACATGCTGTCACCCAGGGACCTCTCCATTATATGGAGTGACACCCCAGATTATTGGAGATGG
649 GTTACATGCTGTCACCCAGGGACCTCTCCATTATATGGAGTGACACCCCAGATTATTGGAGATGG
56352282 GTGTCTATACCCGA
714 GTGTCTATACCCGA
**** * * * * * * * * *
56352296 GGCCAGGTTT-TTCTCTCCTCCTTGCCATGCTGGTTG--GGTGT--AAA--TGATAA-C-AATAG
1 ATATA-ATTTAATGTC-CAT--TT---AGGGT-TTTGCAGGT-TAAAAATCTGAAAATCTAAGA-
* ** * ** * * * * * *
56352352 GATGCTTATCCATCTTTTAAATTCAAAATAATTGAAAATCTTTTAAGAG-AAAAT-ACTTG--CT
56 G-T-CATATTTAGCTTTTGGATGC---TTCATT-----T-TCTGAA-AGCAAAATCA-TTGTAAT
56352413 TCTATTAATATCACATGTTTTGTCCAATCATATTATTATTTTGAATTTTAAGTTCTTGAAATATT
108 TCTATTAATATCACATGTTTTGTCCAATCATATTATTATTTTGAATTTTAAGTTCTTGAAATATT
56352478 ATTTTCCTTTGATCTGAATATGGCTTGTTTCCCTTACATGGGAAAGTCAGCAAGGAATTTTATCT
173 ATTTTCCTTTGATCTGAATATGGCTTGTTTCCCTTACATGGGAAAGTCAGCAAGGAATTTTATCT
56352543 GGTTATTCTTTTTCTTTTTTCTTTTGATTTTTGAAGGCAAAAACTGTATTGGGATAAAACAAGAA
238 GGTTATTCTTTTTCTTTTTTCTTTTGATTTTTGAAGGCAAAAACTGTATTGGGATAAAACAAGAA
56352608 CAAATTTAAATAATTGAATTATTAAGATATATTATTTTAATTTATATGGAAACTTTGTCTAATAT
303 CAAATTTAAATAATTGAATTATTAAGATATATTATTTTAATTTATATGGAAACTTTGTCTAATAT
56352673 TTCCCTTATATGTCTAATTTTATCTAATCGTGTTTGTTGTTCGGATTTGCATAATTCACCAAAAA
368 TTCCCTTATATGTCTAATTTTATCTAATCGTGTTTGTTGTTCGGATTTGCATAATTCACCAAAAA
56352738 AAAAAAAGCAACTAACAGAAGTAAGAAGCTTAGAAAGTACTTTGGAGAAGCTTTTGACATATTAA
433 AAAAAAAGCAACTAACAGAAGTAAGAAGCTTAGAAAGTACTTTGGAGAAGCTTTTGACATATTAA
56352803 TTACGAGCTATGCCATTGTTGCTGGAATCTTTTTCTTAACAATTCCTATGTGTTGTTTATATCTA
498 TTACGAGCTATGCCATTGTTGCTGGAATCTTTTTCTTAACAATTCCTATGTGTTGTTTATATCTA
56352868 TTTTTAATTCTTTTGTTCTTTACATATAACTTAGTTGGTATTGATGAAACAGAGTTTTTGGCTCG
563 TTTTTAATTCTTTTGTTCTTTACATATAACTTAGTTGGTATTGATGAAACAGAGTTTTTGGCTCG
56352933 AAAGAGTGAGTGGGAAGAAATGTTACATGCTGTCACCCAGGGACCTCTCCATTATATGGAGTGAC
628 AAAGAGTGAGTGGGAAGAAATGTTACATGCTGTCACCCAGGGACCTCTCCATTATATGGAGTGAC
56352998 ACCCCAGATTATTGGAGATGGGTGTCTATACCCGA
693 ACCCCAGATTATTGGAGATGGGTGTCTATACCCGA
56353033 GGCCAGGTTT
Statistics
Matches: 1407, Mismatches: 33, Indels: 44
0.95 0.02 0.03
Matches are distributed among these distances:
727 92 0.07
729 541 0.38
730 102 0.07
731 6 0.00
732 15 0.01
733 3 0.00
734 3 0.00
735 8 0.01
736 3 0.00
737 510 0.36
739 108 0.08
740 2 0.00
741 12 0.01
742 2 0.00
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (727 bp):
ATATAATTTAATGTCCATTTAGGGTTTTGCAGGTTAAAAATCTGAAAATCTAAGAGTCATATTTA
GCTTTTGGATGCTTCATTTTCTGAAAGCAAAATCATTGTAATTCTATTAATATCACATGTTTTGT
CCAATCATATTATTATTTTGAATTTTAAGTTCTTGAAATATTATTTTCCTTTGATCTGAATATGG
CTTGTTTCCCTTACATGGGAAAGTCAGCAAGGAATTTTATCTGGTTATTCTTTTTCTTTTTTCTT
TTGATTTTTGAAGGCAAAAACTGTATTGGGATAAAACAAGAACAAATTTAAATAATTGAATTATT
AAGATATATTATTTTAATTTATATGGAAACTTTGTCTAATATTTCCCTTATATGTCTAATTTTAT
CTAATCGTGTTTGTTGTTCGGATTTGCATAATTCACCAAAAAAAAAAAAGCAACTAACAGAAGTA
AGAAGCTTAGAAAGTACTTTGGAGAAGCTTTTGACATATTAATTACGAGCTATGCCATTGTTGCT
GGAATCTTTTTCTTAACAATTCCTATGTGTTGTTTATATCTATTTTTAATTCTTTTGTTCTTTAC
ATATAACTTAGTTGGTATTGATGAAACAGAGTTTTTGGCTCGAAAGAGTGAGTGGGAAGAAATGT
TACATGCTGTCACCCAGGGACCTCTCCATTATATGGAGTGACACCCCAGATTATTGGAGATGGGT
GTCTATACCCGA
Found at i:56352839 original size:737 final size:737
Alignment explanation
Indices: 56350945--56353150 Score: 3837
Period size: 737 Copynumber: 3.0 Consensus size: 737
56350935 CATTGTAATC
56350945 CTATTAATATCACATGTTGTTTTGTCCAATCATATTATTATTTTGAATTTTAAGTTCTTGAAATA
1 CTATTAATATCACA---TGTTTTGTCCAATCATATTATTATTTTGAATTTTAAGTTCTTGAAATA
56351010 TTATTTTCCTTTGATCTGAATATGGCTTGTTTCCCTTACATGGGAAAGTCAGCAAGGAATTTTAT
63 TTATTTTCCTTTGATCTGAATATGGCTTGTTTCCCTTACATGGGAAAGTCAGCAAGGAATTTTAT
56351075 CTGGTTATTCTTTTTCTTTTTTCTTTTGATTTTTGAAGGCAAAAACTGTATTGGGATAAAACAAG
128 CTGGTTATTCTTTTTCTTTTTTCTTTTGATTTTTGAAGGCAAAAACTGTATTGGGATAAAACAAG
56351140 AACAAATTTAAATAATTGAATTATTAAGATATATTATTTTAATTTATATGGAAACTTTGTCTAAT
193 AACAAATTTAAATAATTGAATTATTAAGATATATTATTTTAATTTATATGGAAACTTTGTCTAAT
56351205 ATTTCCCTTATATGTCTAATTTTATCTAATCGTGTTTGTTGTTCGGATTTGCATAATTCACCAAA
258 ATTTCCCTTATATGTCTAATTTTATCTAATCGTGTTTGTTGTTCGGATTTGCATAATTCACCAAA
56351270 AAAAAAAAAGCAACTAACAGAAGTAAGAAGCTTAGAAAGTACTTTGGAGAAGCTTTTGACATATT
323 AAAAAAAAAGCAACTAACAGAAGTAAGAAGCTTAGAAAGTACTTTGGAGAAGCTTTTGACATATT
56351335 AATTACGAGCTATGCCATTGTTGCTGGAATCTTTTTCTTAACAATTCCTATGTGTTGTTTATATC
388 AATTACGAGCTATGCCATTGTTGCTGGAATCTTTTTCTTAACAATTCCTATGTGTTGTTTATATC
56351400 TATTTTTAATTCTTTTGTTCTTTACATATAACTTAGTTGGTATTGATGAAACAGAGTTTTTGGCT
453 TATTTTTAATTCTTTTGTTCTTTACATATAACTTAGTTGGTATTGATGAAACAGAGTTTTTGGCT
56351465 CGAAAGAGTGAGTGGGAAGAAATGTTACATGCTGTCACCCAGGGACCTCTCCATTATATGGAGTG
518 CGAAAGAGTGAGTGGGAAGAAATGTTACATGCTGTCACCCAGGGACCTCTCCATTATATGGAGTG
**** * * * *
56351530 ACACCCCAGATTATTGGAGATGGGTGTCTATACCCGAATATA-ATTTAATGTC-CAT--TT---A
583 ACACCCCAGATTATTGGAGATGGGTGTCTATACCCGAGGCCAGGTTT-TTCTCTCCTCCTTGCCA
* * * * * * ** * ** * *
56351588 GGGT-TTTGCAGGT-TAAAAATCTGA-AA-ATCTAAGA-GTCATATTTAGCTTTTGGATGC---T
647 TGCTGGTTG--GGTGT--AAA--TGATAACA-ATAGGATG-CTTATCCATCTTTTAAATTCAAAA
* * * *
56351645 TCATT-----T-TCTGAA-AGCAAAAT-CATTGTAATT
704 TAATTGAAAATCTTTTAAGAG-AAAATAC-TTG--CTT
56351675 CTATTAATATCACATGTTTTGTCCAATCATATTATTATTTTGAATTTTAAGTTCTTGAAATATTA
1 CTATTAATATCACATGTTTTGTCCAATCATATTATTATTTTGAATTTTAAGTTCTTGAAATATTA
**
56351740 TTTTCCTTTGATCTGAATATGGCTTGTTTCCCTTACATGGGAAAAAAACAGCAAGGAATTTTATC
66 TTTTCCTTTGATCTGAATATGGCTTGTTTCCCTTACATGGG--AAAGTCAGCAAGGAATTTTATC
56351805 TGGTTATTCTTTTTCTTTTTTCTTTTGATTTTTGAAGGCAAAAACTGTATTGGGATAAAACAAGA
129 TGGTTATTCTTTTTCTTTTTTCTTTTGATTTTTGAAGGCAAAAACTGTATTGGGATAAAACAAGA
56351870 ACAAATTTAAATAATTGAATTATTAAGATATATTATTTTAATTTATATGGAAACTTTGTCTAATA
194 ACAAATTTAAATAATTGAATTATTAAGATATATTATTTTAATTTATATGGAAACTTTGTCTAATA
*
56351935 TTTCCCTTATATGTCTAATTTTATCTAATCGTGTTTGTTGTTCGGAATTGCATAATTCACCAAAA
259 TTTCCCTTATATGTCTAATTTTATCTAATCGTGTTTGTTGTTCGGATTTGCATAATTCACCAAAA
56352000 AAAAAAAAGCAACTAACAGAAGTAAGAAGCTTAGAAAGTACTTTGGAGAAGCTTTTGACATATTA
324 AAAAAAAAGCAACTAACAGAAGTAAGAAGCTTAGAAAGTACTTTGGAGAAGCTTTTGACATATTA
56352065 ATTACGAGCTATGCCATTGTTGCTGGAATCTTTTTCTTAACAATTCCTATGTGTTGTTTATATCT
389 ATTACGAGCTATGCCATTGTTGCTGGAATCTTTTTCTTAACAATTCCTATGTGTTGTTTATATCT
56352130 ATTTTTAATTCTTTTGTTCTTTACATATAACTTAGTTGGTATTGATGAAACAGAGTTTTTGGCTC
454 ATTTTTAATTCTTTTGTTCTTTACATATAACTTAGTTGGTATTGATGAAACAGAGTTTTTGGCTC
56352195 GAAAGAGTGAGTGGGAAGAAATGTTACATGCTGTCACCCAGGGACCTCTCCATTATATGGAGTGA
519 GAAAGAGTGAGTGGGAAGAAATGTTACATGCTGTCACCCAGGGACCTCTCCATTATATGGAGTGA
56352260 CACCCCAGATTATTGGAGATGGGTGTCTATACCCGAGGCCAGGTTTTTCTCTCCTCCTTGCCATG
584 CACCCCAGATTATTGGAGATGGGTGTCTATACCCGAGGCCAGGTTTTTCTCTCCTCCTTGCCATG
56352325 CTGGTTGGGTGTAAATGATAACAATAGGATGCTTATCCATCTTTTAAATTCAAAATAATTGAAAA
649 CTGGTTGGGTGTAAATGATAACAATAGGATGCTTATCCATCTTTTAAATTCAAAATAATTGAAAA
56352390 TCTTTTAAGAGAAAATACTTGCTT
714 TCTTTTAAGAGAAAATACTTGCTT
56352414 CTATTAATATCACATGTTTTGTCCAATCATATTATTATTTTGAATTTTAAGTTCTTGAAATATTA
1 CTATTAATATCACATGTTTTGTCCAATCATATTATTATTTTGAATTTTAAGTTCTTGAAATATTA
56352479 TTTTCCTTTGATCTGAATATGGCTTGTTTCCCTTACATGGGAAAGTCAGCAAGGAATTTTATCTG
66 TTTTCCTTTGATCTGAATATGGCTTGTTTCCCTTACATGGGAAAGTCAGCAAGGAATTTTATCTG
56352544 GTTATTCTTTTTCTTTTTTCTTTTGATTTTTGAAGGCAAAAACTGTATTGGGATAAAACAAGAAC
131 GTTATTCTTTTTCTTTTTTCTTTTGATTTTTGAAGGCAAAAACTGTATTGGGATAAAACAAGAAC
56352609 AAATTTAAATAATTGAATTATTAAGATATATTATTTTAATTTATATGGAAACTTTGTCTAATATT
196 AAATTTAAATAATTGAATTATTAAGATATATTATTTTAATTTATATGGAAACTTTGTCTAATATT
56352674 TCCCTTATATGTCTAATTTTATCTAATCGTGTTTGTTGTTCGGATTTGCATAATTCACCAAAAAA
261 TCCCTTATATGTCTAATTTTATCTAATCGTGTTTGTTGTTCGGATTTGCATAATTCACCAAAAAA
56352739 AAAAAAGCAACTAACAGAAGTAAGAAGCTTAGAAAGTACTTTGGAGAAGCTTTTGACATATTAAT
326 AAAAAAGCAACTAACAGAAGTAAGAAGCTTAGAAAGTACTTTGGAGAAGCTTTTGACATATTAAT
56352804 TACGAGCTATGCCATTGTTGCTGGAATCTTTTTCTTAACAATTCCTATGTGTTGTTTATATCTAT
391 TACGAGCTATGCCATTGTTGCTGGAATCTTTTTCTTAACAATTCCTATGTGTTGTTTATATCTAT
56352869 TTTTAATTCTTTTGTTCTTTACATATAACTTAGTTGGTATTGATGAAACAGAGTTTTTGGCTCGA
456 TTTTAATTCTTTTGTTCTTTACATATAACTTAGTTGGTATTGATGAAACAGAGTTTTTGGCTCGA
56352934 AAGAGTGAGTGGGAAGAAATGTTACATGCTGTCACCCAGGGACCTCTCCATTATATGGAGTGACA
521 AAGAGTGAGTGGGAAGAAATGTTACATGCTGTCACCCAGGGACCTCTCCATTATATGGAGTGACA
56352999 CCCCAGATTATTGGAGATGGGTGTCTATACCCGAGGCCAGGTTTTTCTCTCCTCCTTGCCATGCT
586 CCCCAGATTATTGGAGATGGGTGTCTATACCCGAGGCCAGGTTTTTCTCTCCTCCTTGCCATGCT
56353064 GGTTGGGTGTAAATGATAACAATAGGATGCTTATCCATCTTTTAAATTCAAAATAATTGAAAATC
651 GGTTGGGTGTAAATGATAACAATAGGATGCTTATCCATCTTTTAAATTCAAAATAATTGAAAATC
56353129 TTTTAAGAGAAAATACTTGCTT
716 TTTTAAGAGAAAATACTTGCTT
56353151 ATTCATCTTT
Statistics
Matches: 1420, Mismatches: 31, Indels: 43
0.95 0.02 0.03
Matches are distributed among these distances:
727 92 0.06
729 514 0.36
730 19 0.01
731 3 0.00
732 21 0.01
733 5 0.00
734 3 0.00
735 8 0.01
736 3 0.00
737 628 0.44
739 108 0.08
740 1 0.00
741 12 0.01
742 3 0.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (737 bp):
CTATTAATATCACATGTTTTGTCCAATCATATTATTATTTTGAATTTTAAGTTCTTGAAATATTA
TTTTCCTTTGATCTGAATATGGCTTGTTTCCCTTACATGGGAAAGTCAGCAAGGAATTTTATCTG
GTTATTCTTTTTCTTTTTTCTTTTGATTTTTGAAGGCAAAAACTGTATTGGGATAAAACAAGAAC
AAATTTAAATAATTGAATTATTAAGATATATTATTTTAATTTATATGGAAACTTTGTCTAATATT
TCCCTTATATGTCTAATTTTATCTAATCGTGTTTGTTGTTCGGATTTGCATAATTCACCAAAAAA
AAAAAAGCAACTAACAGAAGTAAGAAGCTTAGAAAGTACTTTGGAGAAGCTTTTGACATATTAAT
TACGAGCTATGCCATTGTTGCTGGAATCTTTTTCTTAACAATTCCTATGTGTTGTTTATATCTAT
TTTTAATTCTTTTGTTCTTTACATATAACTTAGTTGGTATTGATGAAACAGAGTTTTTGGCTCGA
AAGAGTGAGTGGGAAGAAATGTTACATGCTGTCACCCAGGGACCTCTCCATTATATGGAGTGACA
CCCCAGATTATTGGAGATGGGTGTCTATACCCGAGGCCAGGTTTTTCTCTCCTCCTTGCCATGCT
GGTTGGGTGTAAATGATAACAATAGGATGCTTATCCATCTTTTAAATTCAAAATAATTGAAAATC
TTTTAAGAGAAAATACTTGCTT
Found at i:56354275 original size:9 final size:9
Alignment explanation
Indices: 56354261--56354294 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
56354251 AAATTTCAAG
*
56354261 TCGAATAAC
1 TCGAATAAA
*
56354270 TCGAATAAT
1 TCGAATAAA
56354279 TCGAATAAA
1 TCGAATAAA
56354288 TCGAATA
1 TCGAATA
56354295 TCAAACTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (9 bp):
TCGAATAAA
Found at i:56361215 original size:15 final size:15
Alignment explanation
Indices: 56361165--56361215 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
56361155 TATAATAATT
*
56361165 AATATTAATAATATA
1 AATATTAATATTATA
*
56361180 AATATAAATATTA-A
1 AATATTAATATTATA
* *
56361194 ATTTATTATTATTATA
1 A-ATATTAATATTATA
56361210 AATATT
1 AATATT
56361216 TTCTTTTTAG
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
14 2 0.07
15 24 0.86
16 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTAATATTATA
Found at i:56365246 original size:26 final size:25
Alignment explanation
Indices: 56365208--56365272 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
56365198 CCCTTAACAT
*
56365208 ATTATATCAATTTAGTAATTAATATA
1 ATTATATCAATTTAAT-ATTAATATA
** *
56365234 ATTATATTTATTTAATATTAATATT
1 ATTATATCAATTTAATATTAATATA
*
56365259 ATTAATATAAATTT
1 ATT-ATATCAATTT
56365273 TAAATTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 11 0.34
26 21 0.66
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (25 bp):
ATTATATCAATTTAATATTAATATA
Found at i:56367504 original size:19 final size:19
Alignment explanation
Indices: 56367480--56367519 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
56367470 TCATGCAAGA
56367480 TTTAGATTTAGG-TTTTATT
1 TTTAGA-TTAGGATTTTATT
56367499 TTTAGATTAGGATTTTTATT
1 TTTAGATTAGGA-TTTTATT
56367519 T
1 T
56367520 ATGCAAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 6 0.32
20 8 0.42
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (19 bp):
TTTAGATTAGGATTTTATT
Found at i:56367509 original size:46 final size:47
Alignment explanation
Indices: 56367439--56367530 Score: 127
Period size: 46 Copynumber: 2.0 Consensus size: 47
56367429 AAAAAATTGG
56367439 GATTGTAGGTTTTTTTTAAATTAGGA-TTTT-TTCATGCAAGATTTA
1 GATTGTAGGTTTTTTTTAAATTAGGATTTTTATTCATGCAAGATTTA
* *
56367484 GATT-TAGGTTTTATTTTTAGATTAGGATTTTTATTTATGCAAGATTT
1 GATTGTAGG-TTT-TTTTTAAATTAGGATTTTTATTCATGCAAGATTT
56367531 GGCTAACCCC
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
44 4 0.10
45 7 0.17
46 13 0.32
47 4 0.10
48 13 0.32
ACGTcount: A:0.26, C:0.03, G:0.17, T:0.53
Consensus pattern (47 bp):
GATTGTAGGTTTTTTTTAAATTAGGATTTTTATTCATGCAAGATTTA
Found at i:56370418 original size:44 final size:44
Alignment explanation
Indices: 56370355--56370443 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
56370345 TATTTCGTAT
56370355 ATTCGATTTTCGAATTAATTACAGCAAATAAATGAGTAAAGATA
1 ATTCGATTTTCGAATTAATTACAGCAAATAAATGAGTAAAGATA
56370399 ATTCGATTTTCGAATTAATTACAGCAAATAAATGAGTAAAGATA
1 ATTCGATTTTCGAATTAATTACAGCAAATAAATGAGTAAAGATA
56370443 A
1 A
56370444 AGTTCATCGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.31
Consensus pattern (44 bp):
ATTCGATTTTCGAATTAATTACAGCAAATAAATGAGTAAAGATA
Found at i:56374010 original size:26 final size:25
Alignment explanation
Indices: 56373972--56374036 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
56373962 CCCTTAACAT
*
56373972 ATTATATCAATTTAGTAATTAATATA
1 ATTATATCAATTTAAT-ATTAATATA
** *
56373998 ATTATATTTATTTAATATTAATATT
1 ATTATATCAATTTAATATTAATATA
*
56374023 ATTAATATAAATTT
1 ATT-ATATCAATTT
56374037 TAAATTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 11 0.34
26 21 0.66
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (25 bp):
ATTATATCAATTTAATATTAATATA
Found at i:56378649 original size:31 final size:32
Alignment explanation
Indices: 56378613--56378677 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
56378603 CTTAGATAAT
56378613 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
56378644 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
56378676 TT
1 TT
56378678 GTAATTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:56379240 original size:12 final size:12
Alignment explanation
Indices: 56379223--56379276 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 12
56379213 TTCTTTAAAT
56379223 AAAAGCAAAAAA
1 AAAAGCAAAAAA
56379235 AAAAGC---AAA
1 AAAAGCAAAAAA
*
56379244 AACAGC--AAAA
1 AAAAGCAAAAAA
56379254 AAAA-CAAAAAA
1 AAAAGCAAAAAA
56379265 AAAAGCAAAAAA
1 AAAAGCAAAAAA
56379277 GCGCAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
9 9 0.25
10 6 0.17
11 8 0.22
12 13 0.36
ACGTcount: A:0.81, C:0.11, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAGCAAAAAA
Found at i:56379244 original size:9 final size:9
Alignment explanation
Indices: 56379232--56379326 Score: 55
Period size: 9 Copynumber: 9.8 Consensus size: 9
56379222 TAAAAGCAAA
56379232 AAAAAAAGC
1 AAAAAAAGC
*
56379241 AAAAACAGC
1 AAAAAAAGC
*
56379250 AAAAAAAAC
1 AAAAAAAGC
56379259 AAAAAAAAAAGC
1 ---AAAAAAAGC
*
56379271 AAAAAAGCGC
1 AAAAAA-AGC
*
56379281 AAAAAAGAGT
1 AAAAAA-AGC
**
56379291 AAAAAGCGC
1 AAAAAAAGC
**
56379300 AAAAAAAATAA
1 -AAAAAAA-GC
56379311 AAAAAAAGC
1 AAAAAAAGC
56379320 AAAAAAA
1 AAAAAAA
56379327 AAGCGCAAAA
Statistics
Matches: 64, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
9 29 0.45
10 27 0.42
12 8 0.12
ACGTcount: A:0.77, C:0.11, G:0.11, T:0.02
Consensus pattern (9 bp):
AAAAAAAGC
Found at i:56379244 original size:10 final size:10
Alignment explanation
Indices: 56379231--56379327 Score: 74
Period size: 10 Copynumber: 9.8 Consensus size: 10
56379221 ATAAAAGCAA
56379231 AAAAAAAAGC
1 AAAAAAAAGC
*
56379241 -AAAAACAGC
1 AAAAAAAAGC
56379250 AAAAAAAA-C
1 AAAAAAAAGC
56379259 AAAAAAAAAAGC
1 --AAAAAAAAGC
**
56379271 AAAAAAGCGC
1 AAAAAAAAGC
*
56379281 AAAAAAGAG-
1 AAAAAAAAGC
* **
56379290 TAAAAAGCGC
1 AAAAAAAAGC
**
56379300 AAAAAAAATA
1 AAAAAAAAGC
56379310 AAAAAAAAGC
1 AAAAAAAAGC
56379320 AAAAAAAA
1 AAAAAAAA
56379328 AGCGCAAAAA
Statistics
Matches: 68, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
9 16 0.24
10 43 0.63
11 8 0.12
12 1 0.01
ACGTcount: A:0.77, C:0.10, G:0.10, T:0.02
Consensus pattern (10 bp):
AAAAAAAAGC
Found at i:56379250 original size:21 final size:21
Alignment explanation
Indices: 56379223--56379276 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
56379213 TTCTTTAAAT
*
56379223 AAAAGCAAAAAAAA-AAGCAAA
1 AAAAGCAAAAAAAACAA-AAAA
*
56379244 AACAGCAAAAAAAACAAAAAA
1 AAAAGCAAAAAAAACAAAAAA
56379265 AAAAGCAAAAAA
1 AAAAGCAAAAAA
56379277 GCGCAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.81, C:0.11, G:0.07, T:0.00
Consensus pattern (21 bp):
AAAAGCAAAAAAAACAAAAAA
Found at i:56379363 original size:13 final size:13
Alignment explanation
Indices: 56379347--56379378 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
56379337 AAGAGAGAGT
*
56379347 AAAAAGCGCAAAA
1 AAAAAGCACAAAA
56379360 AAAAAGCACAAAA
1 AAAAAGCACAAAA
56379373 AAAAAG
1 AAAAAG
56379379 TTGCCTACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.75, C:0.12, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAGCACAAAA
Found at i:56392361 original size:19 final size:19
Alignment explanation
Indices: 56392337--56392374 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
56392327 TGCTTCAATA
*
56392337 TGGTGTAGTACTAATTATG
1 TGGTGTAATACTAATTATG
*
56392356 TGGTGTAATACTAGTTATG
1 TGGTGTAATACTAATTATG
56392375 GACTTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.42
Consensus pattern (19 bp):
TGGTGTAATACTAATTATG
Found at i:56397029 original size:14 final size:14
Alignment explanation
Indices: 56397010--56397042 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
56397000 TTTTCTTAAT
*
56397010 AATAATTATAAATA
1 AATAATAATAAATA
56397024 AATAATAATAAATA
1 AATAATAATAAATA
56397038 AATAA
1 AATAA
56397043 ATTAAAACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAATAATAAATA
Found at i:56397929 original size:18 final size:18
Alignment explanation
Indices: 56397906--56397943 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
56397896 TTCAATTAAG
*
56397906 TCTTTCATT-AAGTGTTTT
1 TCTTTC-TTCAAGTATTTT
56397924 TCTTTCTTCAAGTATTTT
1 TCTTTCTTCAAGTATTTT
56397942 TC
1 TC
56397944 ATTTAGTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.61
Consensus pattern (18 bp):
TCTTTCTTCAAGTATTTT
Found at i:56404953 original size:22 final size:22
Alignment explanation
Indices: 56404928--56404970 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
56404918 AAACAAAAAC
56404928 CCTTACACCCATCAAATCCTAA
1 CCTTACACCCATCAAATCCTAA
* * *
56404950 CCTTTCACCTATCACATCCTA
1 CCTTACACCCATCAAATCCTA
56404971 GTTTTCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.42, G:0.00, T:0.28
Consensus pattern (22 bp):
CCTTACACCCATCAAATCCTAA
Found at i:56407233 original size:18 final size:18
Alignment explanation
Indices: 56407210--56407247 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
56407200 AGAACTAAAT
*
56407210 GAAAAATACTTGAA-GAAA
1 GAAAAACACTT-AATGAAA
56407228 GAAAAACACTTAATGAAA
1 GAAAAACACTTAATGAAA
56407246 GA
1 GA
56407248 CTTAATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (18 bp):
GAAAAACACTTAATGAAA
Found at i:56418700 original size:16 final size:19
Alignment explanation
Indices: 56418670--56418729 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 19
56418660 AAAATAAAAT
56418670 TTAA-ATATTATATAATTTA
1 TTAATATATTA-ATAATTTA
56418689 TTAA-A-A-TAATAAATTATA
1 TTAATATATTAAT-AATT-TA
56418707 TTAATTATATTAATAATTTA
1 TTAA-TATATTAATAATTTA
56418727 TTA
1 TTA
56418730 TATGGCTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.06
17 6 0.17
18 7 0.20
19 5 0.14
20 6 0.17
21 5 0.14
22 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAATATATTAATAATTTA
Found at i:56418721 original size:25 final size:25
Alignment explanation
Indices: 56418676--56418732 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
56418666 AAATTTAAAT
56418676 ATTATA-TAATTTATTAAAATAATAA
1 ATTATATTAATTTATT-AAATAATAA
**
56418701 ATTATATTAATTATATT-AATAATTT
1 ATTATATTAATT-TATTAAATAATAA
56418726 ATTATAT
1 ATTATAT
56418733 GGCTAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 19 0.68
26 5 0.18
27 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTATATTAATTTATTAAATAATAA
Found at i:56421051 original size:21 final size:19
Alignment explanation
Indices: 56421009--56421052 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
56420999 TTTTGAAAAA
* *
56421009 TTTATGATTTTTAATTATT
1 TTTATGATTTTAAATAATT
56421028 TTTATAGATTTTAAAATAATT
1 TTTAT-GATTTT-AAATAATT
56421049 TTTA
1 TTTA
56421053 GCCTAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 6 0.29
21 10 0.48
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTATGATTTTAAATAATT
Found at i:56430370 original size:294 final size:294
Alignment explanation
Indices: 56429923--56430514 Score: 1132
Period size: 294 Copynumber: 2.0 Consensus size: 294
56429913 AAACGGGCTT
*
56429923 ATTTTTTTTTGTCTAAGCCTATTTTTTGGGCCTAATATTTTTGCCCAAACCCTCCCAAATTTCGG
1 ATTTTTTTTTGTCTAAGCCTATTTTTTGAGCCTAATATTTTTGCCCAAACCCTCCCAAATTTCGG
56429988 ACAAACCTTCGAGCCTGGACAAATAGCCTGACACTTGAATTGGTGTAGTGCTTAGTAAATGTCTA
66 ACAAACCTTCGAGCCTGGACAAATAGCCTGACACTTGAATTGGTGTAGTGCTTAGTAAATGTCTA
56430053 ACAGTTTCTTAGTTCTCAACCCATTTTAATTTCCAGAAATTAATCACTTTCAACAATCTTTGATG
131 ACAGTTTCTTAGTTCTCAACCCATTTTAATTTCCAGAAATTAATCACTTTCAACAATCTTTGATG
**
56430118 TTTAGATGGGTGTCTGAACATGTTTTACTTCCAATCCCGACAAAGAAAAGGGATCATTCGTATTC
196 TTTAGATAAGTGTCTGAACATGTTTTACTTCCAATCCCGACAAAGAAAAGGGATCATTCGTATTC
56430183 AAAGTTTTCATGTTTACGCTTTTCATATACTGGC
261 AAAGTTTTCATGTTTACGCTTTTCATATACTGGC
56430217 ATTTTTTTTTGTCTAAGCCTATTTTTTGAGCCTAATATTTTTGCCCAAACCCTCCCAAATTTCGG
1 ATTTTTTTTTGTCTAAGCCTATTTTTTGAGCCTAATATTTTTGCCCAAACCCTCCCAAATTTCGG
56430282 ACAAACCTTCGAGCCTGGACAAATAGCCTGACACTTGAATTGGTGTAGTGCTTAGTAAATGTC-A
66 ACAAACCTTCGAGCCTGGACAAATAGCCTGACACTTGAATTGGTGTAGTGCTTAGTAAATGTCTA
56430346 ACAGTTTCTTAGTTCTCTAACCCATTTTAATTTCCAGAAATTAATCACTTTCAACAATCTTTGAT
131 ACAGTTTCTTAGTTCTC-AACCCATTTTAATTTCCAGAAATTAATCACTTTCAACAATCTTTGAT
56430411 GTTTAGATAAGTGTCTGAACATGTTTTACTTCCAATCCCGACAAAGAAAAGGGATCATTCGTATT
195 GTTTAGATAAGTGTCTGAACATGTTTTACTTCCAATCCCGACAAAGAAAAGGGATCATTCGTATT
*
56430476 TAAAGTTTTCATGTTTACGCTTTTCATATACTGGC
260 CAAAGTTTTCATGTTTACGCTTTTCATATACTGGC
56430511 ATTT
1 ATTT
56430515 CTGATAATTT
Statistics
Matches: 293, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
293 18 0.06
294 275 0.94
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (294 bp):
ATTTTTTTTTGTCTAAGCCTATTTTTTGAGCCTAATATTTTTGCCCAAACCCTCCCAAATTTCGG
ACAAACCTTCGAGCCTGGACAAATAGCCTGACACTTGAATTGGTGTAGTGCTTAGTAAATGTCTA
ACAGTTTCTTAGTTCTCAACCCATTTTAATTTCCAGAAATTAATCACTTTCAACAATCTTTGATG
TTTAGATAAGTGTCTGAACATGTTTTACTTCCAATCCCGACAAAGAAAAGGGATCATTCGTATTC
AAAGTTTTCATGTTTACGCTTTTCATATACTGGC
Found at i:56431224 original size:13 final size:13
Alignment explanation
Indices: 56431208--56431237 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
56431198 TTGTATTGCA
*
56431208 TGTTTGATTTTCT
1 TGTTTGATTTCCT
56431221 TGTTTGATTTCCT
1 TGTTTGATTTCCT
56431234 TGTT
1 TGTT
56431238 AACCCCTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.10, G:0.17, T:0.67
Consensus pattern (13 bp):
TGTTTGATTTCCT
Found at i:56434871 original size:23 final size:21
Alignment explanation
Indices: 56434845--56434885 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
56434835 AATTAAATTA
56434845 TATATATTATGATTTTAGTAT
1 TATATATTATGATTTTAGTAT
56434866 TATATATTATGATTTTAGTA
1 TATATATTATGATTTTAGTA
56434886 AATTCATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (21 bp):
TATATATTATGATTTTAGTAT
Found at i:56435219 original size:16 final size:16
Alignment explanation
Indices: 56435200--56435243 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
56435190 TCTATTCCAT
*
56435200 TATTCCATTACGCATC
1 TATTCCATTACACATC
*
56435216 TATTCCATTCCACATC
1 TATTCCATTACACATC
56435232 TATTCCATTACA
1 TATTCCATTACA
56435244 GCGAACCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.39
Consensus pattern (16 bp):
TATTCCATTACACATC
Found at i:56435740 original size:18 final size:16
Alignment explanation
Indices: 56435715--56435757 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 16
56435705 AGGCCTTTTT
*
56435715 ATTAAATTATTTATGTA
1 ATTAAATTATTT-TATA
56435732 ATATAAATTATTTTATA
1 AT-TAAATTATTTTATA
56435749 ATTAAATTA
1 ATTAAATTA
56435758 ATTGTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 7 0.29
17 7 0.29
18 10 0.42
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTAAATTATTTTATA
Found at i:56448713 original size:31 final size:31
Alignment explanation
Indices: 56448678--56448747 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
56448668 ATTATAAAAT
* *
56448678 AGTCATTAAACTTTTTAAAAGTTGTCATTTA
1 AGTCATTAAACTATTGAAAAGTTGTCATTTA
** * *
56448709 AGTCATTAAACTATTGAAATTTTTTTATTTA
1 AGTCATTAAACTATTGAAAAGTTGTCATTTA
56448740 AGTCATTA
1 AGTCATTA
56448748 CGCTATTAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (31 bp):
AGTCATTAAACTATTGAAAAGTTGTCATTTA
Found at i:56448766 original size:31 final size:31
Alignment explanation
Indices: 56448704--56448764 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
56448694 AAAAGTTGTC
56448704 ATTTAAGTCATTAAACTATTGAAATTTTTTT
1 ATTTAAGTCATTAAACTATTGAAATTTTTTT
** *
56448735 ATTTAAGTCATTACGCTATT-AAGTTTTTTT
1 ATTTAAGTCATTAAACTATTGAAATTTTTTT
56448765 TAAGTTCAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.52
Consensus pattern (31 bp):
ATTTAAGTCATTAAACTATTGAAATTTTTTT
Found at i:56452176 original size:62 final size:62
Alignment explanation
Indices: 56452105--56452230 Score: 218
Period size: 62 Copynumber: 2.0 Consensus size: 62
56452095 TTGAAGTTTA
* *
56452105 TTTTGAAAAATAGACAAATAAATATTAGGTTGAATCAAATTATAAAGTATTTA-AGTTAAAAG
1 TTTTGAAAAATAGAAAAATAAATATTAGGTTGAATCAAATTATAAAGCA-TTACAGTTAAAAG
56452167 TTTTGAAAAATAGAAAAATAAATATTAGGTTGAATCAAATTATAAAGCATTACAGTTAAAAG
1 TTTTGAAAAATAGAAAAATAAATATTAGGTTGAATCAAATTATAAAGCATTACAGTTAAAAG
56452229 TT
1 TT
56452231 CGGGAAGTAC
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
61 3 0.05
62 58 0.95
ACGTcount: A:0.50, C:0.04, G:0.13, T:0.33
Consensus pattern (62 bp):
TTTTGAAAAATAGAAAAATAAATATTAGGTTGAATCAAATTATAAAGCATTACAGTTAAAAG
Found at i:56453072 original size:23 final size:23
Alignment explanation
Indices: 56453045--56453098 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
56453035 TTTAATATGT
* *
56453045 TATTTAA-AAAAATATTTTTATTA
1 TATTTAATAAAAA-AATTTAATTA
56453068 TATTTGAATAAAAAAATTTAATTA
1 TATTT-AATAAAAAAATTTAATTA
56453092 TATTTAA
1 TATTTAA
56453099 CAAATTGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.26
24 15 0.56
25 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TATTTAATAAAAAAATTTAATTA
Found at i:56460798 original size:29 final size:29
Alignment explanation
Indices: 56460735--56460799 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
56460725 GAGAAGAAGT
* *
56460735 ATAAACATATTGGGTCATTTACGTAAAAA
1 ATAAAAATATTGGGCCATTTACGTAAAAA
* *
56460764 GTAAAAATATTGGGCCATTTA-TTAAAAA
1 ATAAAAATATTGGGCCATTTACGTAAAAA
56460792 ATGAAAAA
1 AT-AAAAA
56460800 GAAAGGATGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 7 0.23
29 23 0.77
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (29 bp):
ATAAAAATATTGGGCCATTTACGTAAAAA
Found at i:56463802 original size:114 final size:113
Alignment explanation
Indices: 56463675--56464094 Score: 606
Period size: 114 Copynumber: 3.7 Consensus size: 113
56463665 ATCGCAACTG
* * * * ** *
56463675 AAAAAACCTAAGCCTAACGACGCTGTTTTGTGAGCTTTTGTTGATTTAGCGGCGTTTTTAAGAAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTATGAAA
* *
56463740 GCGCCGCTAATGCTCAGGGCTTTAGCAGCGTTTTAGAGGAAGCGCCGCA
66 GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG-GGAAGCGCCGCA
* * * *
56463789 AAAAAACCTAAGCCCAACGATGCCGTTTTGTGAACTTTCGGGGATTTAGCGGCGTTTTTAGGAAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTATGAAA
56463854 GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGGAAGCGCCGCA
66 GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTT-GGGAAGCGCCGCA
* *
56463903 AAAAAACCTAAGCCCAACGACGCTGTTTTCTGAGCTTTCGGGGATTTTGCGGCGTTTTTATGAAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTATGAAA
* *
56463968 GCGCAGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCT
66 GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGG-AAGCGCCGCA
** * * * *
56464017 AAATCACCTTAGTCAAACGACGCCATTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTATGAAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTATGAAA
56464082 GCGCCGCTAATGC
66 GCGCCGCTAATGC
56464095 GCGCTAAAAA
Statistics
Matches: 277, Mismatches: 27, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
113 3 0.01
114 273 0.99
115 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.28
Consensus pattern (113 bp):
AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTATGAAA
GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAGCGCCGCA
Found at i:56464369 original size:15 final size:15
Alignment explanation
Indices: 56464349--56464379 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
56464339 CATATTTTAA
56464349 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
56464364 GGTTTAGGGATTATG
1 GGTTTAGGGAGTATG
56464379 G
1 G
56464380 ATTAGGTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:56465791 original size:21 final size:22
Alignment explanation
Indices: 56465760--56465801 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
56465750 CCCCCCTCCG
56465760 AAATCCCCAACTTTCCACCCTA
1 AAATCCCCAACTTTCCACCCTA
*
56465782 AAAT-CCCAACTTTCCCCCCT
1 AAATCCCCAACTTTCCACCCT
56465802 CCTAAACGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.29, C:0.48, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATCCCCAACTTTCCACCCTA
Found at i:56467443 original size:66 final size:66
Alignment explanation
Indices: 56467337--56467462 Score: 243
Period size: 66 Copynumber: 1.9 Consensus size: 66
56467327 CATTTCAGAG
*
56467337 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA
1 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGACTACCAGTCCAGGCTAAATCCCCTGCAAGA
56467402 T
66 T
56467403 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGACTACCAGTCCAGGCTAAATCCCCTG
1 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGACTACCAGTCCAGGCTAAATCCCCTG
56467463 TAATATAAAC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.26, C:0.38, G:0.18, T:0.17
Consensus pattern (66 bp):
AGCACACTCCCGCGAACCTCATCCTTACAGCGGGACTACCAGTCCAGGCTAAATCCCCTGCAAGA
T
Found at i:56467677 original size:57 final size:60
Alignment explanation
Indices: 56467584--56467731 Score: 214
Period size: 57 Copynumber: 2.5 Consensus size: 60
56467574 ACCCTAATTC
* * *
56467584 GGATTACCCGTCCGGGCTAAATCCATTTTCCACATATTCTTCGGGAGGGCTATATC-A-A
1 GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGGGAGGGCTATATCGATA
56467642 -GATCACCCGTCCGGGCTAGAT-CTTTTTCACACATATTCTTCGGGAGGGCTATATCAGGATA
1 GGATCACCCGTCCGGGCTAGATCCTTTTTC-CACATATTCTTCGGGAGGGCTATATC--GATA
56467703 GGATCACCCGTCCGGGCTAGATCCTTTTT
1 GGATCACCCGTCCGGGCTAGATCCTTTTT
56467732 ACCGTCAATT
Statistics
Matches: 80, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
56 6 0.08
57 45 0.56
60 1 0.01
61 1 0.01
62 21 0.26
63 6 0.08
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (60 bp):
GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGGGAGGGCTATATCGATA
Found at i:56472680 original size:6 final size:6
Alignment explanation
Indices: 56472655--56472717 Score: 56
Period size: 6 Copynumber: 10.2 Consensus size: 6
56472645 CATTCTTCTC
* ** *
56472655 CCCTTT CCCCTT CTCC-TT CCCTTT CCCCTAC CCCTTT CCCTTA CCCTTT
1 CCCTTT CCCTTT C-CCTTT CCCTTT -CCCTTT CCCTTT CCCTTT CCCTTT
56472704 CCCTTT CCCGTTT C
1 CCCTTT CCC-TTT C
56472718 GAAGCCTACA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
5 2 0.04
6 34 0.74
7 10 0.22
ACGTcount: A:0.03, C:0.54, G:0.02, T:0.41
Consensus pattern (6 bp):
CCCTTT
Found at i:56472689 original size:13 final size:12
Alignment explanation
Indices: 56472673--56472706 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
56472663 CCTTCTCCTT
56472673 CCCTTTCCCCTA
1 CCCTTTCCCCTA
*
56472685 CCCCTTTCCCTTA
1 -CCCTTTCCCCTA
56472698 CCCTTTCCC
1 CCCTTTCCC
56472707 TTTCCCGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.06, C:0.59, G:0.00, T:0.35
Consensus pattern (12 bp):
CCCTTTCCCCTA
Found at i:56475008 original size:20 final size:20
Alignment explanation
Indices: 56474983--56475022 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
56474973 AATATTTTCT
*
56474983 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
56475003 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
56475023 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:56475025 original size:34 final size:35
Alignment explanation
Indices: 56474971--56475037 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
56474961 CAAACACCAG
* *
56474971 AAAATATTTTCTAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
56475006 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
56475038 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:56475029 original size:14 final size:14
Alignment explanation
Indices: 56475006--56475045 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
56474996 ACAGAAAAGT
*
56475006 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
56475020 AAATCATTTTACGG
1 AAAACATTTTACAG
56475034 AAAACATTTTAC
1 AAAACATTTTAC
56475046 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:56476126 original size:25 final size:24
Alignment explanation
Indices: 56476090--56476173 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 24
56476080 ACAGCTTTAT
*
56476090 GAGCTT-CTCGATTTGCAGCTCGTGA
1 GAGCTTAC-CGATTT-CAGCTTGTGA
56476115 GAGCTTACCGATTCTCAGCTTGT-A
1 GAGCTTACCGATT-TCAGCTTGTGA
*
56476139 TGAGCTTACCGATTCACAGCTTGTGA
1 -GAGCTTACCGATT-TCAGCTTGTGA
*
56476165 GAGCATACC
1 GAGCTTACC
56476174 AATTCATAGC
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
24 1 0.02
25 48 0.92
26 3 0.06
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.30
Consensus pattern (24 bp):
GAGCTTACCGATTTCAGCTTGTGA
Found at i:56476159 original size:50 final size:49
Alignment explanation
Indices: 56476081--56476178 Score: 126
Period size: 50 Copynumber: 2.0 Consensus size: 49
56476071 GGACACACCA
** * *
56476081 CAGCTTTATGAGCTTCTCGATTTGCAGCTCGTGAGAGCTTACCGATTCT
1 CAGCTTTATGAGCTTCTCGATTCACAGCTCGTGAGAGCATACCAATTCT
*
56476130 CAGCTTGTATGAGCTTAC-CGATTCACAGCTTGTGAGAGCATACCAATTC
1 CAGCTT-TATGAGCTT-CTCGATTCACAGCTCGTGAGAGCATACCAATTC
56476179 ATAGCTCATA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 6 0.14
50 35 0.83
51 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.32
Consensus pattern (49 bp):
CAGCTTTATGAGCTTCTCGATTCACAGCTCGTGAGAGCATACCAATTCT
Found at i:56476178 original size:25 final size:25
Alignment explanation
Indices: 56476105--56476184 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 25
56476095 TCTCGATTTG
* *
56476105 CAGCTCGTGAGAGCTTACCGATTCT
1 CAGCTTGTGAGAGCTTACCGATTCA
56476130 CAGCTTGT-ATGAGCTTACCGATTCA
1 CAGCTTGTGA-GAGCTTACCGATTCA
* *
56476155 CAGCTTGTGAGAGCATACCAATTCA
1 CAGCTTGTGAGAGCTTACCGATTCA
*
56476180 TAGCT
1 CAGCT
56476185 CATATAAGCA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
24 1 0.02
25 46 0.96
26 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (25 bp):
CAGCTTGTGAGAGCTTACCGATTCA
Found at i:56483055 original size:4 final size:4
Alignment explanation
Indices: 56483046--56483086 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
56483036 TACAAAATTC
* *
56483046 TAAA TAAA TAAA TAAA TAAA TAAA TTTAA TAAA TTAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA -TAAA TAAA TAAA TAAA
56483087 AAAACTCATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 29 0.91
5 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (4 bp):
TAAA
Found at i:56489852 original size:31 final size:30
Alignment explanation
Indices: 56489817--56489911 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 30
56489807 AATTTATCAT
56489817 ATTAATAAAATCATATTTAGATAAATATTAA
1 ATTAATAAAAT-ATATTTAGATAAATATTAA
* * * *
56489848 ATTAAATTAAATAT-CTTATATTAATATTAA
1 ATT-AATAAAATATATTTAGATAAATATTAA
* *
56489878 ATTAATAAAATACTATCTGGATAAATATTAA
1 ATTAATAAAATA-TATTTAGATAAATATTAA
56489909 ATT
1 ATT
56489912 CATTAAAACA
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
29 8 0.16
30 17 0.33
31 19 0.37
32 7 0.14
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (30 bp):
ATTAATAAAATATATTTAGATAAATATTAA
Found at i:56493906 original size:34 final size:35
Alignment explanation
Indices: 56493830--56493910 Score: 98
Period size: 34 Copynumber: 2.3 Consensus size: 35
56493820 ATAAAAATTG
56493830 AATTAATTATAAATAAATAAATTTAAAATATTTATC
1 AATTAA-TATAAATAAATAAATTTAAAATATTTATC
*
56493866 ATTTAATAT-AATAAAT-AATTTAAAATGATTATAT-
1 AATTAATATAAATAAATAAATTTAAAAT-ATT-TATC
56493900 AATTAAT-TAAA
1 AATTAATATAAA
56493911 ATATTTATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
33 11 0.28
34 18 0.45
35 6 0.15
36 5 0.12
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (35 bp):
AATTAATATAAATAAATAAATTTAAAATATTTATC
Found at i:56493911 original size:21 final size:20
Alignment explanation
Indices: 56493876--56493921 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
56493866 ATTTAATATA
56493876 ATAAATAATTTAAAATGATTAT
1 ATAAATAATTTAAAAT-ATT-T
*
56493898 ATAATTAA-TTAAAATATTT
1 ATAAATAATTTAAAATATTT
56493917 ATAAA
1 ATAAA
56493922 AATGTCATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 5 0.23
20 3 0.14
21 7 0.32
22 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
ATAAATAATTTAAAATATTT
Found at i:56497182 original size:23 final size:22
Alignment explanation
Indices: 56497139--56497196 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
56497129 AAATGGTATC
* *
56497139 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
56497160 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
56497183 TGCATATCATATCT
1 TACAAATCATATCT
56497197 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Done.