Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 132 of 335
Found at i:39187059 original size:6 final size:6
Alignment explanation
Indices: 39187050--39187119 Score: 63
Period size: 6 Copynumber: 11.0 Consensus size: 6
39187040 TAGGAATAGC
*
39187050 AAAATA AAAATA AAAATA AAAATA AAAATA TTAAAAGT- -ATATA AAAATTA
1 AAAATA AAAATA AAAATA AAAATA AAAATA --AAAA-TA AAAATA AAAA-TA
39187100 AAATATA AAAATTA AAAATA
1 AAA-ATA AAAA-TA AAAATA
39187120 TAAGTATAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
4 1 0.02
5 2 0.04
6 29 0.54
7 16 0.30
8 5 0.09
9 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.24
Consensus pattern (6 bp):
AAAATA
Found at i:39187097 original size:31 final size:31
Alignment explanation
Indices: 39187059--39187121 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
39187049 CAAAATAAAA
*
39187059 ATAAAAATAAAAATA-AAAATATTAAAAGTAT
1 ATAAAAATAAAAATATAAAA-ATTAAAAATAT
*
39187090 ATAAAAATTAAAATATAAAAATTAAAAATAT
1 ATAAAAATAAAAATATAAAAATTAAAAATAT
39187121 A
1 A
39187122 AGTATAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (31 bp):
ATAAAAATAAAAATATAAAAATTAAAAATAT
Found at i:39187125 original size:37 final size:36
Alignment explanation
Indices: 39187053--39187127 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 36
39187043 GAATAGCAAA
39187053 ATAAAAATAAAAATAAAAATAAAAATATTAAAAGTAT
1 ATAAAAATAAAAATAAAAATAAAAATATT-AAAGTAT
39187090 ATAAAAATTAAAATATAAAAATTAAAAATA-T-AAGTAT
1 ATAAAAA-TAAAA-ATAAAAA-TAAAAATATTAAAGTAT
39187127 A
1 A
39187128 AGAATACTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
37 14 0.40
38 5 0.14
39 8 0.23
40 8 0.23
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.27
Consensus pattern (36 bp):
ATAAAAATAAAAATAAAAATAAAAATATTAAAGTAT
Found at i:39187173 original size:22 final size:20
Alignment explanation
Indices: 39187155--39187206 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 20
39187145 AACTAATTAG
39187155 TAAAATAAAAATAAATAATA
1 TAAAATAAAAATAAATAATA
*
39187175 TAACAATTAAAAATAAATAAAA
1 TAA-AA-TAAAAATAAATAATA
39187197 TAAAATAAAA
1 TAAAATAAAA
39187207 TTGGGGTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 8 0.28
21 4 0.14
22 17 0.59
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (20 bp):
TAAAATAAAAATAAATAATA
Found at i:39187376 original size:30 final size:30
Alignment explanation
Indices: 39187333--39187389 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
39187323 ATGTGAAATC
* *
39187333 CCACACGCCCGTGTGGCCAGGCCGTGTGCT
1 CCACACACCCGTGTGGCCAGACCGTGTGCT
* *
39187363 CCACACACTCGTGTGGTCAGACCGTGT
1 CCACACACCCGTGTGGCCAGACCGTGT
39187390 AGCTGTTCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.14, C:0.37, G:0.30, T:0.19
Consensus pattern (30 bp):
CCACACACCCGTGTGGCCAGACCGTGTGCT
Found at i:39191315 original size:26 final size:26
Alignment explanation
Indices: 39191285--39191363 Score: 103
Period size: 26 Copynumber: 3.2 Consensus size: 26
39191275 TGAAATTCCC
*
39191285 ATCATAGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
39191311 ATCATGGTAA-A--T-GCTAACCCATT
1 ATCATGG-AACATTTACCTAACCCATT
39191334 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
39191360 ATCA
1 ATCA
39191364 ATTTGTATCA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
22 2 0.04
23 18 0.40
24 1 0.02
25 1 0.02
26 21 0.47
27 2 0.04
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:39193519 original size:27 final size:28
Alignment explanation
Indices: 39193474--39193547 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 28
39193464 GAATATCCAA
*
39193474 CCCAAACACACTCGGAATAAT-ATAAATCCT
1 CCCAAACACAC-C--AATAATAATAAAGCCT
*
39193504 -CCATAACACACCAAT-ATAATATAGCCT
1 CCCA-AACACACCAATAATAATAAAGCCT
39193531 CCCAAACACACCAATAA
1 CCCAAACACACCAATAA
39193548 GGCATTAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
26 2 0.05
27 21 0.55
28 4 0.11
29 4 0.11
30 7 0.18
ACGTcount: A:0.46, C:0.32, G:0.04, T:0.18
Consensus pattern (28 bp):
CCCAAACACACCAATAATAATAAAGCCT
Found at i:39194536 original size:20 final size:18
Alignment explanation
Indices: 39194511--39194551 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
39194501 TTCTTTTTCC
*
39194511 TTTACTTTAGTTTTATTCTA
1 TTTACTTTA-ATTTATT-TA
39194531 TTTACTTTAATTTATTTA
1 TTTACTTTAATTTATTTA
39194549 TTT
1 TTT
39194552 TATTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 6 0.30
20 9 0.45
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTACTTTAATTTATTTA
Found at i:39194566 original size:14 final size:14
Alignment explanation
Indices: 39194511--39194567 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
39194501 TTCTTTTTCC
39194511 TTTACTTTAGTTTTAT
1 TTTA-TTTA-TTTTAT
* * *
39194527 TCTATTTACTTTAA
1 TTTATTTATTTTAT
39194541 TTTATTTATTTTAT
1 TTTATTTATTTTAT
*
39194555 TTTATTTGTTTTA
1 TTTATTTATTTTA
39194568 CATTAATAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 27 0.79
15 4 0.12
16 3 0.09
ACGTcount: A:0.21, C:0.05, G:0.04, T:0.70
Consensus pattern (14 bp):
TTTATTTATTTTAT
Found at i:39210138 original size:29 final size:28
Alignment explanation
Indices: 39210106--39210173 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
39210096 ATAATATCAT
39210106 TATAATTTAATTATCATAAATTCA-T-ATTA
1 TATAATTTAATT-T-ATAAA-TCATTAATTA
* *
39210135 TATAAATTATATTTATATATCATTAATTA
1 TATAATTTA-ATTTATAAATCATTAATTA
39210164 TATAATTTAA
1 TATAATTTAA
39210174 AACAAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
27 3 0.09
28 6 0.18
29 21 0.64
30 3 0.09
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (28 bp):
TATAATTTAATTTATAAATCATTAATTA
Found at i:39210139 original size:15 final size:14
Alignment explanation
Indices: 39210106--39210168 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
39210096 ATAATATCAT
*
39210106 TATAATTTA-ATTA
1 TATAAATTATATTA
39210119 TCATAAATTCATATTA
1 T-ATAAATT-ATATTA
39210135 TATAAATTATATTTA
1 TATAAATTATA-TTA
*
39210150 TATATCATTA-ATTA
1 TATA-AATTATATTA
39210164 TATAA
1 TATAA
39210169 TTTAAAACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
13 1 0.02
14 16 0.38
15 16 0.38
16 9 0.21
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (14 bp):
TATAAATTATATTA
Found at i:39210306 original size:17 final size:18
Alignment explanation
Indices: 39210271--39210306 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
39210261 TATTGTTCTA
*
39210271 TAATTCAACTTTTATCCT
1 TAATTCAACTTTAATCCT
39210289 TAATTCAA-TTTAATCCT
1 TAATTCAACTTTAATCCT
39210306 T
1 T
39210307 TTTTCTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTCAACTTTAATCCT
Found at i:39215552 original size:26 final size:26
Alignment explanation
Indices: 39215516--39215599 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
39215506 CATGAAATTC
39215516 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
39215542 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
39215568 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
39215594 TTATCA
1 TTATCA
39215600 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:39219433 original size:26 final size:26
Alignment explanation
Indices: 39219404--39219457 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
39219394 TCAAACATGC
39219404 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGT-AATTTAACACCTAGGGGT
* *
39219430 ATTTCGGTAATTTATCTACCTAGGGGT
1 ATTTAGGTAATTTAAC-ACCTAGGGGT
39219457 A
1 A
39219458 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.29
26 7 0.29
27 10 0.42
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (26 bp):
ATTTAGGTAATTTAACACCTAGGGGT
Found at i:39220971 original size:26 final size:26
Alignment explanation
Indices: 39220935--39221018 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
39220925 CATGAAATTC
39220935 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
39220961 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
39220987 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
39221013 TTATCA
1 TTATCA
39221019 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:39221533 original size:106 final size:106
Alignment explanation
Indices: 39221348--39221543 Score: 349
Period size: 106 Copynumber: 1.8 Consensus size: 106
39221338 GGGCGTTACA
* *
39221348 AATGTTTTGGCTGAAAATGATATTTTTAGATTTCACGATTTCAAAAGCTAGGATTAAATTTCTGA
1 AATGTTTTGGCTGAAAATGATATTTTCAGATTTCACGATTTCAAAAGCTAGAATTAAATTTCTGA
39221413 GTTTTTAAAACAAACTAATGTAATTTCCAAAATAACATGTC
66 GTTTTTAAAACAAACTAATGTAATTTCCAAAATAACATGTC
*
39221454 AATGTTTTGGCTGAAAATGATATTTTCAGATTTCCCGATTTCAAAAGCTAGAATTAAACTTT-TG
1 AATGTTTTGGCTGAAAATGATATTTTCAGATTTCACGATTTCAAAAGCTAGAATTAAA-TTTCTG
39221518 AGTTTTTAAAACAAACTAATGTAATT
65 AGTTTTTAAAACAAACTAATGTAATT
39221544 CCTCCGGATT
Statistics
Matches: 86, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
106 83 0.97
107 3 0.03
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.38
Consensus pattern (106 bp):
AATGTTTTGGCTGAAAATGATATTTTCAGATTTCACGATTTCAAAAGCTAGAATTAAATTTCTGA
GTTTTTAAAACAAACTAATGTAATTTCCAAAATAACATGTC
Found at i:39222688 original size:24 final size:24
Alignment explanation
Indices: 39222637--39222694 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
39222627 AATAAATTTC
*
39222637 AATATATATTTATTTAAAAAATTC
1 AATATATATTTATTTAAAAAATTA
* *
39222661 AATATATATTTATTT-TAATATATA
1 AATATATATTTATTTAAAAAAT-TA
39222685 AATATATATT
1 AATATATATT
39222695 CCCCTCATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 4 0.13
24 26 0.87
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
AATATATATTTATTTAAAAAATTA
Found at i:39225500 original size:26 final size:26
Alignment explanation
Indices: 39225463--39225598 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
39225453 TGATACAAAT
* *
39225463 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
39225489 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
39225515 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
39225541 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
39225567 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
39225593 TGATAA
1 TGATAA
39225599 GAATATCATG
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:39227622 original size:134 final size:137
Alignment explanation
Indices: 39227381--39227664 Score: 520
Period size: 134 Copynumber: 2.1 Consensus size: 137
39227371 GAGTAGTCTC
39227381 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
39227446 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCT-TGGCCCAGTA-C
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
39227509 ACTGTTA
131 ACTGTTA
*
39227516 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
39227580 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
39227645 ACTGTTA
131 ACTGTTA
**
39227652 CCTGAATGGGCTT
1 CCCAAATGGGCTT
39227665 AGGCCCAATG
Statistics
Matches: 144, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
134 95 0.66
135 30 0.21
136 19 0.13
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:39231455 original size:26 final size:26
Alignment explanation
Indices: 39231418--39231552 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
39231408 TGATACAAAT
*
39231418 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
39231444 TGATAATGGGTTAGGTAAATGTT-CA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
39231469 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
39231495 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
39231521 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
39231547 TGATAA
1 TGATAA
39231553 GAATTCATGT
Statistics
Matches: 104, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
25 24 0.23
26 80 0.77
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:39231473 original size:51 final size:52
Alignment explanation
Indices: 39231418--39231552 Score: 245
Period size: 51 Copynumber: 2.6 Consensus size: 52
39231408 TGATACAAAT
39231418 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATG-TTCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
39231469 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
* *
39231521 TGATAATGGGTTAGGTAAATGTTTCATGATAA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAA
39231553 GAATTCATGT
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
51 47 0.58
52 34 0.42
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.36
Consensus pattern (52 bp):
TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
Found at i:39233572 original size:133 final size:136
Alignment explanation
Indices: 39233333--39233615 Score: 509
Period size: 133 Copynumber: 2.1 Consensus size: 136
39233323 GAGTAGTCTC
39233333 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
39233398 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCT-TGGCCCAGT-CA
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACA
39233461 CTGTTA
131 CTGTTA
*
39233467 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
39233531 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTA-C
39233596 ACTGTTA
130 ACTGTTA
**
39233603 CCTGAATGGGCTT
1 CCCAAATGGGCTT
39233616 AGGCCCAATG
Statistics
Matches: 143, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
133 95 0.66
134 29 0.20
136 19 0.13
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (136 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACA
CTGTTA
Found at i:39238033 original size:13 final size:13
Alignment explanation
Indices: 39238015--39238048 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
39238005 GTCTTGATTC
39238015 TTAAAATTAAAAA
1 TTAAAATTAAAAA
39238028 TTAAAATTTAAAAA
1 TTAAAA-TTAAAAA
*
39238042 TAAAAAT
1 TTAAAAT
39238049 ATTTAAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TTAAAATTAAAAA
Found at i:39245648 original size:18 final size:19
Alignment explanation
Indices: 39245599--39245648 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
39245589 TATAATATAA
39245599 TTATTTAATTAATAAATATC
1 TTATTTAA-TAATAAATATC
39245619 TT-TTATAAAATAATAAATAT-
1 TTATT-T--AATAATAAATATC
39245639 TTATTTAATA
1 TTATTTAATA
39245649 TCTAATACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
18 4 0.15
19 2 0.08
20 6 0.23
21 12 0.46
22 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATTTAATAATAAATATC
Found at i:39245819 original size:19 final size:21
Alignment explanation
Indices: 39245773--39245819 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 21
39245763 TATAATAAAT
* *
39245773 TAATTTAATATCATTTATTAC
1 TAATTAAATATCATATATTAC
39245794 TAA-TAAATAT-ATATATTA-
1 TAATTAAATATCATATATTAC
39245812 TAATTAAA
1 TAATTAAA
39245820 ATCTAAGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.13
19 11 0.48
20 6 0.26
21 3 0.13
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (21 bp):
TAATTAAATATCATATATTAC
Found at i:39247564 original size:30 final size:30
Alignment explanation
Indices: 39247479--39247596 Score: 132
Period size: 30 Copynumber: 3.9 Consensus size: 30
39247469 AAAAAATTAT
* * *
39247479 ATTTTGACGCCTAAACTTTTCATAAATTAT-
1 ATTTTAACCCCTAAACTTTTCTTAAATT-TC
39247509 ATTTTAACCCCTAAACTTTTCTTAAATTTC
1 ATTTTAACCCCTAAACTTTTCTTAAATTTC
*
39247539 ATTTTAACCCCTAAACTTTAT-TTAAACTTC
1 ATTTTAACCCCTAAACTTT-TCTTAAATTTC
* ** *
39247569 ACTTCGACCCCTAAACTTTCCTTAAATT
1 ATTTTAACCCCTAAACTTTTCTTAAATT
39247597 ACAATTTGAC
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
29 1 0.01
30 74 0.97
31 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.42
Consensus pattern (30 bp):
ATTTTAACCCCTAAACTTTTCTTAAATTTC
Found at i:39248279 original size:37 final size:37
Alignment explanation
Indices: 39248212--39248292 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 37
39248202 GTTAGTGAGA
* * *
39248212 TGGGGTAGTTTATGTTGGGTTTGAAATATTAAGTTAG
1 TGGGTTAGTCTATGTTGGGCTTGAAATATTAAGTTAG
* *
39248249 TGGGTTAGTCTATGTTGGGCTTGGATTATTAAGTTAG
1 TGGGTTAGTCTATGTTGGGCTTGAAATATTAAGTTAG
39248286 TGGGTTA
1 TGGGTTA
39248293 AGGTTGGTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.21, C:0.02, G:0.33, T:0.43
Consensus pattern (37 bp):
TGGGTTAGTCTATGTTGGGCTTGAAATATTAAGTTAG
Found at i:39248661 original size:14 final size:15
Alignment explanation
Indices: 39248637--39248665 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39248627 TATATCATGT
39248637 ATATATATATTTTTA
1 ATATATATATTTTTA
39248652 ATAT-TATATTTTTA
1 ATATATATATTTTTA
39248666 TGTACCTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATATATATTTTTA
Found at i:39248758 original size:26 final size:27
Alignment explanation
Indices: 39248700--39248760 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
39248690 TATCACATTG
39248700 TTCATACATTTTATTATATGAGTATAT
1 TTCATACATTTTATTATATGAGTATAT
*
39248727 AT-ATAC-TTTTA-TATAT-AGTATTATT
1 TTCATACATTTTATTATATGAGTA-TA-T
39248752 TTCATACAT
1 TTCATACAT
39248761 CATTATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
23 4 0.14
24 7 0.25
25 7 0.25
26 8 0.29
27 2 0.07
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.52
Consensus pattern (27 bp):
TTCATACATTTTATTATATGAGTATAT
Found at i:39248831 original size:22 final size:22
Alignment explanation
Indices: 39248804--39248871 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
39248794 TATTATCATT
39248804 TATTTTAATATTATTATGTATA
1 TATTTTAATATTATTATGTATA
* *
39248826 TATTTTAACATTACTA-GTTATA
1 TATTTTAATATTATTATG-TATA
* *
39248848 TATTTTTACTA-TCTTATGTATA
1 TA-TTTTAATATTATTATGTATA
39248870 TA
1 TA
39248872 CTTCAAACAC
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.03
22 29 0.78
23 7 0.19
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (22 bp):
TATTTTAATATTATTATGTATA
Found at i:39250146 original size:136 final size:136
Alignment explanation
Indices: 39249902--39250323 Score: 772
Period size: 136 Copynumber: 3.1 Consensus size: 136
39249892 CATTGGGCCT
** * * *
39249902 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGATACTGGGCTAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
39249967 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
39250032 ATATGC
131 ATATGC
39250038 AAGCCCATTTGGGTAACAGTGATACTGGGCTAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGATACTGGGCTAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
39250103 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
39250168 ATATGC
131 ATATGC
*
39250174 AAGCCCATTTGGGTAACAGTGATACTGGGCTAAAACCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGATACTGGGCTAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
39250239 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AA
39250304 CATATGC
130 CATATGC
39250311 AAGCCCATTTGGG
1 AAGCCCATTTGGG
39250324 GAGTATACTC
Statistics
Matches: 278, Mismatches: 7, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
136 256 0.92
137 22 0.08
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (136 bp):
AAGCCCATTTGGGTAACAGTGATACTGGGCTAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
ATATGC
Found at i:39252168 original size:25 final size:26
Alignment explanation
Indices: 39252099--39252181 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
39252089 ACATGAATTC
39252099 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
39252125 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
39252151 TTATCATG-AACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
39252176 TTATCA
1 TTATCA
39252182 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
25 22 0.39
26 34 0.61
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:39256180 original size:136 final size:136
Alignment explanation
Indices: 39255936--39256357 Score: 772
Period size: 136 Copynumber: 3.1 Consensus size: 136
39255926 CATTGGGCCT
** * * *
39255936 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGATACTGGGCTAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
39256001 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
39256066 ATATGC
131 ATATGC
39256072 AAGCCCATTTGGGTAACAGTGATACTGGGCTAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGATACTGGGCTAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
39256137 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
39256202 ATATGC
131 ATATGC
*
39256208 AAGCCCATTTGGGTAACAGTGATACTGGGCTAAAACCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGATACTGGGCTAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
39256273 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AA
39256338 CATATGC
130 CATATGC
39256345 AAGCCCATTTGGG
1 AAGCCCATTTGGG
39256358 GAGATACTCA
Statistics
Matches: 278, Mismatches: 7, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
136 256 0.92
137 22 0.08
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (136 bp):
AAGCCCATTTGGGTAACAGTGATACTGGGCTAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
ATATGC
Found at i:39258173 original size:26 final size:26
Alignment explanation
Indices: 39258137--39258220 Score: 159
Period size: 26 Copynumber: 3.2 Consensus size: 26
39258127 CATGATATTC
39258137 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
39258163 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
39258189 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
39258215 TTATCA
1 TTATCA
39258221 ATTTGTATCA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 57 1.00
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:39262059 original size:4 final size:4
Alignment explanation
Indices: 39262052--39262081 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
39262042 TCATTTATTT
39262052 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TT
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TT
39262082 GCATATCCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.53
Consensus pattern (4 bp):
TTCA
Found at i:39269597 original size:44 final size:44
Alignment explanation
Indices: 39269489--39269648 Score: 205
Period size: 44 Copynumber: 3.6 Consensus size: 44
39269479 TATGCCTAAA
* *
39269489 AAAAAAGATCAATGTGAAATCCCGAAAAGGGCGTCTTGGTTAAC
1 AAAAAAGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGGTTAAC
* *
39269533 AAAAAAAGATCAAGGTGAAAACCCGATAAGGGTGTCTTGGTTAAC
1 -AAAAAAGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGGTTAAC
* * *
39269578 AAAAAAGATAAAGGTGAAAACCCGAAAAAGGCGTCTTGATTAAC
1 AAAAAAGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGGTTAAC
* * *
39269622 ACAAAAGAT-TAGGATGAAAACCTGAAA
1 AAAAAAGATCAAGG-TGAAAACCCGAAA
39269649 GGACTTTCTA
Statistics
Matches: 102, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
43 3 0.03
44 59 0.58
45 40 0.39
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.18
Consensus pattern (44 bp):
AAAAAAGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGGTTAAC
Found at i:39270564 original size:76 final size:78
Alignment explanation
Indices: 39270445--39270665 Score: 279
Period size: 76 Copynumber: 2.8 Consensus size: 78
39270435 TCTGTTCGTT
* * *
39270445 AAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
* **
39270510 TT-CT-TTTGAAA
66 TTACTCATAAAAA
* * * *
39270521 AAAATCGACTCATATTGCGAGAAGTGAGTTGAACCTCAGGACACGCTGAGGTAATTTT-AATTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT-ATTTTCAATTTC
39270585 TTTACTCATAAAAA
65 TTTACTCATAAAAA
*
39270599 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACACGCTGAGGTATTTTCAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTCAATT
39270663 TCT
63 TCT
39270666 GTTTTCAAAA
Statistics
Matches: 123, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
76 54 0.44
77 9 0.07
78 37 0.30
79 5 0.04
80 18 0.15
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (78 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
TTACTCATAAAAA
Found at i:39270628 original size:78 final size:76
Alignment explanation
Indices: 39270445--39270709 Score: 267
Period size: 76 Copynumber: 3.5 Consensus size: 76
39270435 TCTGTTCGTT
* * *
39270445 AAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGCTGAGGTATTTTCAATTTCT
* **
39270510 TTCTTTTGAAA
66 TTCTATAAAAA
* * * *
39270521 AAAATCGACTCATATTGCGAGAAGTGAGTTGAACCTCAGGACACGCTGAGGTAATTTT-AATTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGCTGAGGT-ATTTTCAATTTC
39270585 TTTACTCATAAAAA
65 TTT-CT-ATAAAAA
* **
39270599 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGC-TCACACGCTGAGGTATTTTCAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAACC-T--CAAGACACGCTGAGGTATTTTCAATT
*
39270663 TCTGTT-T-T---CA
63 TCT-TTCTATAAAAA
*
39270673 AAAATCAACTCATATTTG-GAGAGGTGAGTTGATCCTC
1 AAAATCAACTCATA-TTGCGAGAGGTGAGTTGAACCTC
39270710 GGGCCACATG
Statistics
Matches: 162, Mismatches: 18, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
71 1 0.01
73 1 0.01
74 31 0.19
75 3 0.02
76 54 0.33
77 8 0.05
78 36 0.22
79 7 0.04
80 18 0.11
81 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (76 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGCTGAGGTATTTTCAATTTCT
TTCTATAAAAA
Found at i:39270698 original size:74 final size:74
Alignment explanation
Indices: 39270445--39270744 Score: 213
Period size: 74 Copynumber: 4.0 Consensus size: 74
39270435 TCTGTTCGTT
* ** ***
39270445 AAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG--ACACGTTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCCACACGCCAAGGTATTTTCAATTT
* *
39270508 CTTTCTTTTGAAA
66 C--TATTTT--CA
* * * * **
39270521 AAAATCGACTCATATTGCGAGAAGTGAGTTGAACCTCAGG--ACACGCTGAGGTAATTTT-AATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCCACACGCCAAGGT-ATTTTCAATT
39270583 T-T-TTTACTCATAAAAA
65 TCTATTT--TC------A
* **
39270599 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACACGCTGAGGTATTTTCAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGC-CACACGCCAAGGTATTTTCAATT
*
39270663 TCTGTTTTCA
65 TCTATTTTCA
* * *
39270673 AAAATCAACTCATATTTG-GAGAGGTGAGTTGATCCTCGGGCCACATGCCAATGTATTTTCAATT
1 AAAATCAACTCATA-TTGCGAGAGGTGAGTTGAGCCTCGGGCCACACGCCAAGGTATTTTCAATT
39270737 TCTATTTT
65 TCTATTTT
39270745 TAATTTCCGT
Statistics
Matches: 189, Mismatches: 18, Indels: 36
0.78 0.07 0.15
Matches are distributed among these distances:
72 3 0.02
73 1 0.01
74 59 0.31
75 6 0.03
76 51 0.27
77 7 0.04
78 34 0.18
79 5 0.03
80 19 0.10
81 1 0.01
82 3 0.02
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (74 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCCACACGCCAAGGTATTTTCAATTT
CTATTTTCA
Found at i:39270989 original size:77 final size:78
Alignment explanation
Indices: 39270774--39270996 Score: 315
Period size: 80 Copynumber: 2.9 Consensus size: 78
39270764 ATATATATAT
39270774 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTCAAT
*
39270839 TTCTGTTTTTCAAAA
66 TTCTGTCTTTC--AA
* * * * *
39270854 AAAAATAAACTCATATTACGAGAGGTGAATTGAGGCTCGGGTCACATGCCGAGATATTTTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTCAAT
39270919 TTCTGTCTTTC-A
66 TTCTGTCTTTCAA
* * * * *
39270931 AAAAATCAACTCATATTGCGAGAGTTGAGTTAAGCCTCAGGTCACACGCTGAGGTA-TTTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTCAAT
39270995 TT
66 TT
39270997 TTTTTTGCTT
Statistics
Matches: 127, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
76 10 0.08
77 47 0.37
80 70 0.55
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (78 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTCAAT
TTCTGTCTTTCAA
Found at i:39271306 original size:30 final size:29
Alignment explanation
Indices: 39271272--39271357 Score: 102
Period size: 30 Copynumber: 2.9 Consensus size: 29
39271262 AAAAATAAAA
**
39271272 AAATTATATTTTGACCCCTAAACTTTTTGT
1 AAATT-TATTTTGACCCCTAAACTTTTCCT
* *
39271302 AAATTGTATTTTAACCTCTAAACTTTTCCT
1 AAATT-TATTTTGACCCCTAAACTTTTCCT
39271332 AAATTTCATTTTGACCCCTAAA-TTTT
1 AAATTT-ATTTTGACCCCTAAACTTTT
39271358 ATTTAAACTT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 5 0.10
30 43 0.90
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.47
Consensus pattern (29 bp):
AAATTTATTTTGACCCCTAAACTTTTCCT
Found at i:39271383 original size:60 final size:60
Alignment explanation
Indices: 39271272--39271417 Score: 147
Period size: 60 Copynumber: 2.5 Consensus size: 60
39271262 AAAAATAAAA
* * * * * *
39271272 AAATTATATTTTGACCCCTAAACTTTT-TGTAAATTGTATTTTAACCTCTAAACTTTTCC-T
1 AAATTACATTTTGACCCCTAAA-TTTTATGTAAATTGCACTTCAACCCCTAAA-ATTTCCTT
* *
39271332 AAATTTCATTTTGACCCCTAAATTTTATTTAAACTT-CACTTCAACCCCTAAAATTTCCTT
1 AAATTACATTTTGACCCCTAAATTTTATGTAAA-TTGCACTTCAACCCCTAAAATTTCCTT
* *
39271392 AAATTACAATTTGA-CCCTAATTTTTA
1 AAATTACATTTTGACCCCTAAATTTTA
39271418 AAAAATTACA
Statistics
Matches: 72, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
59 20 0.28
60 50 0.69
61 2 0.03
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.44
Consensus pattern (60 bp):
AAATTACATTTTGACCCCTAAATTTTATGTAAATTGCACTTCAACCCCTAAAATTTCCTT
Found at i:39272064 original size:36 final size:37
Alignment explanation
Indices: 39272011--39272084 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
39272001 GTTAGTGAGA
*
39272011 TAGGGTAGTTTGTGTTGGG-TTGAAATATTAAGTTAG
1 TAGGGTAGTCTGTGTTGGGCTTGAAATATTAAGTTAG
* * * *
39272047 TAGGTTAGTCTGTGTTGGGCTTGGATTGTTAAGTTAG
1 TAGGGTAGTCTGTGTTGGGCTTGAAATATTAAGTTAG
39272084 T
1 T
39272085 GGGCTGGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
36 17 0.53
37 15 0.47
ACGTcount: A:0.20, C:0.03, G:0.34, T:0.43
Consensus pattern (37 bp):
TAGGGTAGTCTGTGTTGGGCTTGAAATATTAAGTTAG
Found at i:39272464 original size:14 final size:15
Alignment explanation
Indices: 39272440--39272468 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39272430 TATATCATGT
39272440 ATATATATATTTTTA
1 ATATATATATTTTTA
39272455 ATAT-TATATTTTTA
1 ATATATATATTTTTA
39272469 TGTACATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATATATATTTTTA
Found at i:39272695 original size:22 final size:22
Alignment explanation
Indices: 39272669--39272736 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
39272659 TTTCAATATT
39272669 TATTTTATATATATTATGTATA
1 TATTTTATATATATTATGTATA
* *
39272691 TATTTTA-ACATTACTA-GTTATA
1 TATTTTATATA-TATTATG-TATA
*
39272713 TATTTT-TACTATCTTATGTATA
1 TATTTTATA-TATATTATGTATA
39272735 TA
1 TA
39272737 CTTCAAACAC
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
21 3 0.08
22 31 0.86
23 2 0.06
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (22 bp):
TATTTTATATATATTATGTATA
Found at i:39282325 original size:16 final size:16
Alignment explanation
Indices: 39282296--39282338 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
39282286 GTGGCCGGAG
39282296 CTCTC-CCCTT-TCCC
1 CTCTCTCCCTTCTCCC
*
39282310 CTCTCTTCCTTCTCCC
1 CTCTCTCCCTTCTCCC
*
39282326 TTCTCTCCCTTCT
1 CTCTCTCCCTTCT
39282339 TTCTTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 5 0.21
15 4 0.17
16 15 0.62
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (16 bp):
CTCTCTCCCTTCTCCC
Found at i:39283354 original size:2 final size:2
Alignment explanation
Indices: 39283302--39283345 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
39283292 AGTATATGTT
39283302 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39283342 TA TA
1 TA TA
39283346 GGCATATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39294304 original size:17 final size:17
Alignment explanation
Indices: 39294282--39294316 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
39294272 CATGAATCTG
39294282 AACAATAAGATGATGGA
1 AACAATAAGATGATGGA
39294299 AACAATAAGATGATGGA
1 AACAATAAGATGATGGA
39294316 A
1 A
39294317 GAAGTGTGCG
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:0.54, C:0.06, G:0.23, T:0.17
Consensus pattern (17 bp):
AACAATAAGATGATGGA
Found at i:39295920 original size:71 final size:70
Alignment explanation
Indices: 39295821--39295996 Score: 214
Period size: 71 Copynumber: 2.5 Consensus size: 70
39295811 CTTTTCAAGG
*
39295821 AAAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTC-AAGACACGTTGAGGTACTTTTAATTT
1 AAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCGAAGA-ACGCTGAGGTACTTTTAATTT
*
39295884 TTGTTTT
64 ATGTTTT
** * *
39295891 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGAACGCTGAGGTATTTTTAGTTTA
1 -AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAAGAACGCTGAGGTACTTTTAATTTA
39295956 TGTTTT
65 TGTTTT
** * *
39295962 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
39295997 TTTAATTTTT
Statistics
Matches: 93, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
69 31 0.33
71 58 0.62
72 4 0.04
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (70 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAAGAACGCTGAGGTACTTTTAATTTAT
GTTTT
Found at i:39296117 original size:72 final size:71
Alignment explanation
Indices: 39295996--39296183 Score: 234
Period size: 72 Copynumber: 2.6 Consensus size: 71
39295986 GAGTTAAGCC
* * * * *
39295996 TTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC
1 TTTTCAATTTTTGTTTTT-AAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGACACGA
39296060 TGAGGTA
65 TGAGGTA
** *
39296067 TTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGATACGA
1 TTTTCAATTTTTGT-TTTTAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGACACGA
39296132 TGAGGTA
65 TGAGGTA
* * *
39296139 ATTTCAATTTCTGTTTGTCAAGAATCAACTCATATTGCGAGAGGT
1 TTTTCAATTTTTGTTT-TTAA-AATCAACTCATATTGCGAGAGGT
39296184 GGGTTGAACC
Statistics
Matches: 100, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
71 6 0.06
72 69 0.69
73 25 0.25
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (71 bp):
TTTTCAATTTTTGTTTTTAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGACACGAT
GAGGTA
Found at i:39296246 original size:199 final size:193
Alignment explanation
Indices: 39295821--39296284 Score: 583
Period size: 199 Copynumber: 2.4 Consensus size: 193
39295811 CTTTTCAAGG
* * *
39295821 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTACTTTT-AATTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA-TTTTCAATTTT
* * * * *
39295885 TGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGAACGCTGAGGTATTTTT
65 TGTTTTCAAAATCAACTCATATTGCGAGAAGTAAGTTGAGCCTCGAGGAACGATGAGGTAATTTC
* ** **
39295950 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
130 AATTTATGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTACTTTTTC
* * *
39296014 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTT
* ** *
39296079 GTGTTTTAATTTCAACTCATATTGCGAGAGGTAAGTTGAGCCTC-AGGATACGATGAGGTAATTT
66 GT-TTTCAAAATCAACTCATATTGCGAGAAGTAAGTTGAGCCTCGAGGA-ACGATGAGGTAATTT
* *
39296143 CAATTTCTGTTTGTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAA-CCTTTTAATTTCTAC
129 CAATTTATGTTT-T--A-AATCAACTCATATTGCGAGAGGTGAGTT-AAGCCTTTTAATTT-TAC
39296207 TTTTTC
188 TTTTTC
* * * * *
39296213 AAAATCAGCTCATATTACGAGAGGTGAGTTGAGCCTCAGGTCACGCCGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTT
39296278 GTTTTCA
66 GTTTTCA
39296285 TTATTATGTT
Statistics
Matches: 232, Mismatches: 30, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
192 4 0.02
193 59 0.25
194 58 0.25
195 1 0.00
197 1 0.00
198 40 0.17
199 69 0.30
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (193 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTT
GTTTTCAAAATCAACTCATATTGCGAGAAGTAAGTTGAGCCTCGAGGAACGATGAGGTAATTTCA
ATTTATGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTACTTTTTC
Found at i:39296377 original size:14 final size:14
Alignment explanation
Indices: 39296358--39296384 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39296348 TCGAGGTATT
39296358 TTCAAATTCTGTTA
1 TTCAAATTCTGTTA
39296372 TTCAAATTCTGTT
1 TTCAAATTCTGTT
39296385 TTTAATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.52
Consensus pattern (14 bp):
TTCAAATTCTGTTA
Found at i:39296475 original size:14 final size:14
Alignment explanation
Indices: 39296456--39296490 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
39296446 CGCTGAGGTA
* *
39296456 TTTTCAATTTCTGC
1 TTTTCAATTCCTAC
39296470 TTTTCAATTCCTAC
1 TTTTCAATTCCTAC
39296484 TTTTCAA
1 TTTTCAA
39296491 AAAAATCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.20, C:0.23, G:0.03, T:0.54
Consensus pattern (14 bp):
TTTTCAATTCCTAC
Found at i:39296681 original size:55 final size:55
Alignment explanation
Indices: 39296621--39296772 Score: 252
Period size: 55 Copynumber: 2.7 Consensus size: 55
39296611 TGAGGTATTC
*
39296621 TTAATTTTTGTTGTTTCAAAAATCAACTCATGTTGCGAGAGGTGAGTTAAGCCTT
1 TTAATTTCTGTTGTTTCAAAAATCAACTCATGTTGCGAGAGGTGAGTTAAGCCTT
39296676 TTAATTTCTGTTGTTTCAAAAATCAACTCATGTTGCGAGAGGTGAGTTAAGCCTT
1 TTAATTTCTGTTGTTTCAAAAATCAACTCATGTTGCGAGAGGTGAGTTAAGCCTT
* *
39296731 TTAATTTCTGTT-TTTCAAAAAAATCAACTCATATTACGAGAG
1 TTAATTTCTGTTGTTTC--AAAAATCAACTCATGTTGCGAGAG
39296773 AGTCAATTCA
Statistics
Matches: 92, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
54 4 0.04
55 66 0.72
56 22 0.24
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (55 bp):
TTAATTTCTGTTGTTTCAAAAATCAACTCATGTTGCGAGAGGTGAGTTAAGCCTT
Found at i:39298123 original size:16 final size:16
Alignment explanation
Indices: 39298094--39298136 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
39298084 ATGGCCGGAG
39298094 CTCTC-CCCTT-TCCC
1 CTCTCTCCCTTCTCCC
*
39298108 CTCTCTTCCTTCTCCC
1 CTCTCTCCCTTCTCCC
39298124 CTCTCTCCCTTCT
1 CTCTCTCCCTTCT
39298137 TTCTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 5 0.20
15 4 0.16
16 16 0.64
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (16 bp):
CTCTCTCCCTTCTCCC
Found at i:39299120 original size:15 final size:14
Alignment explanation
Indices: 39299091--39299124 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
39299081 TTGATATTAG
*
39299091 TATATGTTTATATA
1 TATATCTTTATATA
39299105 TATATCTTTAATATA
1 TATATCTTT-ATATA
39299120 TATAT
1 TATAT
39299125 ATATAGGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (14 bp):
TATATCTTTATATA
Found at i:39301860 original size:3 final size:3
Alignment explanation
Indices: 39301847--39301922 Score: 125
Period size: 3 Copynumber: 25.3 Consensus size: 3
39301837 GATAATAGAA
*
39301847 AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
39301895 AAT AAT AAT AAT AAT AAT GGT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
39301923 TAAATTAATA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:39302065 original size:3 final size:3
Alignment explanation
Indices: 39302050--39302164 Score: 96
Period size: 3 Copynumber: 39.7 Consensus size: 3
39302040 AAATATATAT
* * *
39302050 ATA ATA GTA ATA ATA A-A AAA ATA ATA GTA ATA ATA ATTA A-A A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
* * * * * * *
39302093 ATG ATA ATA A-A GTA A-A ATG ATA ATA ATA CTA ATG TTA ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39302139 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
39302165 CAATTTTAAT
Statistics
Matches: 88, Mismatches: 19, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
2 9 0.10
3 76 0.86
4 3 0.03
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:39302176 original size:10 final size:10
Alignment explanation
Indices: 39302161--39302186 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
39302151 ATAATAATAA
39302161 TAATCAATTT
1 TAATCAATTT
39302171 TAATCAATTT
1 TAATCAATTT
39302181 TAATCA
1 TAATCA
39302187 TAATGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (10 bp):
TAATCAATTT
Found at i:39304083 original size:2 final size:2
Alignment explanation
Indices: 39304078--39304103 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39304068 TTGCATTTTC
39304078 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
39304104 ATTTTGATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39306755 original size:26 final size:26
Alignment explanation
Indices: 39306717--39306800 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
39306707 CATGAAATTC
* *
39306717 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
39306743 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
39306769 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
39306795 TTATCA
1 TTATCA
39306801 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.35
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:39307662 original size:30 final size:30
Alignment explanation
Indices: 39307626--39307719 Score: 170
Period size: 30 Copynumber: 3.1 Consensus size: 30
39307616 AGCCTTTGCT
39307626 ACCACCAACTCCACTAGCCACACTTGCTCC
1 ACCACCAACTCCACTAGCCACACTTGCTCC
39307656 ACCACCAACTCCACTAGCCACACTTGCTCC
1 ACCACCAACTCCACTAGCCACACTTGCTCC
* *
39307686 ACTACCTACTCCACTAGCCACACTTGCTCC
1 ACCACCAACTCCACTAGCCACACTTGCTCC
39307716 ACCA
1 ACCA
39307720 TCACTTATAC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.27, C:0.49, G:0.06, T:0.18
Consensus pattern (30 bp):
ACCACCAACTCCACTAGCCACACTTGCTCC
Found at i:39308310 original size:27 final size:25
Alignment explanation
Indices: 39308203--39308340 Score: 92
Period size: 25 Copynumber: 5.7 Consensus size: 25
39308193 TTTTTTTTGT
* *
39308203 TATTAT-TATAT-TTTTTAATATTA
1 TATTATGTATATATATTTAATACTA
** *
39308226 TATTA--TATATATATTCTTTTAATA
1 TATTATGTATATATATT-TAATACTA
* * * *
39308250 TATTAGGTATAT-T-CTAAATTCTA
1 TATTATGTATATATATTTAATACTA
*
39308273 TATTACGTATATATATATT-ATACTA
1 TATTATGTATATATAT-TTAATACTA
* *
39308298 TTTTATGTATATATCTTTAATACTA
1 TATTATGTATATATATTTAATACTA
*
39308323 TATTATTTATATATATTT
1 TATTATGTATATATATTT
39308341 TTTTCCTACA
Statistics
Matches: 87, Mismatches: 20, Indels: 14
0.72 0.17 0.12
Matches are distributed among these distances:
22 5 0.06
23 22 0.25
24 14 0.16
25 40 0.46
26 6 0.07
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.57
Consensus pattern (25 bp):
TATTATGTATATATATTTAATACTA
Found at i:39308409 original size:25 final size:24
Alignment explanation
Indices: 39308359--39308422 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 24
39308349 CATGTTATCT
*
39308359 TATGTATATATTTTAATTATATTATG
1 TATGTAT-T-TTTTAACTATATTATG
39308385 TATGTATTTTTTACACTATATTATG
1 TATGTATTTTTTA-ACTATATTATG
**
39308410 TACATATTTTTTA
1 TATGTATTTTTTA
39308423 TATCTATTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.15
25 22 0.65
26 7 0.21
ACGTcount: A:0.31, C:0.05, G:0.06, T:0.58
Consensus pattern (24 bp):
TATGTATTTTTTAACTATATTATG
Found at i:39308509 original size:25 final size:24
Alignment explanation
Indices: 39308481--39308536 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
39308471 GTTATATTTT
*
39308481 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
39308506 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
39308529 CACTATTA
1 CACTATTA
39308537 CTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:39309671 original size:17 final size:15
Alignment explanation
Indices: 39309641--39309680 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
39309631 ATTAAAAATA
39309641 TTAAATAAATGAATT
1 TTAAATAAATGAATT
39309656 TTAAATTAATATGAATT
1 TTAAA-TAA-ATGAATT
39309673 TT-AATAAA
1 TTAAATAAA
39309681 AAAAATACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 1 0.04
15 8 0.35
16 5 0.22
17 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (15 bp):
TTAAATAAATGAATT
Found at i:39314951 original size:17 final size:19
Alignment explanation
Indices: 39314909--39314951 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
39314899 GCTATAAAAA
*
39314909 ATAATTAAGTGTGAAACCT
1 ATAATTAAGTGTGAAAACT
*
39314928 ATAATTAAGT-TTAAAACT
1 ATAATTAAGTGTGAAAACT
39314946 -TAATTA
1 ATAATTA
39314952 GTAATTGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 6 0.27
19 10 0.45
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (19 bp):
ATAATTAAGTGTGAAAACT
Found at i:39316491 original size:21 final size:21
Alignment explanation
Indices: 39316467--39316506 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
39316457 ATTTTAATCC
* *
39316467 TTTATTTAGTAATTTTTTCGA
1 TTTAGTTAGTAAATTTTTCGA
*
39316488 TTTAGTTATTAAATTTTTC
1 TTTAGTTAGTAAATTTTTC
39316507 AAATTTAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.62
Consensus pattern (21 bp):
TTTAGTTAGTAAATTTTTCGA
Found at i:39317493 original size:3 final size:3
Alignment explanation
Indices: 39317474--39317507 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
39317464 TTGTTCTTTT
*
39317474 TTA TT- TTA TTT TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
39317508 CTTTTTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (3 bp):
TTA
Found at i:39318276 original size:21 final size:21
Alignment explanation
Indices: 39318252--39318322 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
39318242 GTCCCTGGTC
39318252 CACACGGGTGTGTGTCTTAGT
1 CACACGGGTGTGTGTCTTAGT
* **
39318273 CACAC-GGTCGTGTGCCTCTCTT
1 CACACGGGT-GTGTGTCT-TAGT
* *
39318295 CACACGAGTGTGT-TCCTTTGT
1 CACACGGGTGTGTGT-CTTAGT
39318316 CACACGG
1 CACACGG
39318323 CCGTGTGCCC
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 3 0.08
21 20 0.53
22 13 0.34
23 2 0.05
ACGTcount: A:0.14, C:0.28, G:0.27, T:0.31
Consensus pattern (21 bp):
CACACGGGTGTGTGTCTTAGT
Found at i:39318300 original size:22 final size:22
Alignment explanation
Indices: 39318272--39318342 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
39318262 TGTGTCTTAG
39318272 TCACACGGTCGTGTGCCTCTCT
1 TCACACGGTCGTGTGCCTCTCT
*
39318294 TCACACGAGT-GTGTTCCT-T-T
1 TCACACG-GTCGTGTGCCTCTCT
* * *
39318314 GTCACACGGCCGTGTGCCCCTCC
1 -TCACACGGTCGTGTGCCTCTCT
39318337 TCACAC
1 TCACAC
39318343 AAGCTTTTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
20 2 0.05
21 14 0.36
22 21 0.54
23 2 0.05
ACGTcount: A:0.13, C:0.38, G:0.21, T:0.28
Consensus pattern (22 bp):
TCACACGGTCGTGTGCCTCTCT
Found at i:39318300 original size:43 final size:43
Alignment explanation
Indices: 39318252--39318342 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
39318242 GTCCCTGGTC
* * * *
39318252 CACACGGGTGTGTGT-CTTAGTCACACGGTCGTGTGCCTCTCTT
1 CACACGAGTGTGT-TCCTTAGTCACACGGCCGTGTGCCCCTCCT
*
39318295 CACACGAGTGTGTTCCTTTGTCACACGGCCGTGTGCCCCTCCT
1 CACACGAGTGTGTTCCTTAGTCACACGGCCGTGTGCCCCTCCT
39318338 CACAC
1 CACAC
39318343 AAGCTTTTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 1 0.02
43 41 0.98
ACGTcount: A:0.13, C:0.34, G:0.24, T:0.29
Consensus pattern (43 bp):
CACACGAGTGTGTTCCTTAGTCACACGGCCGTGTGCCCCTCCT
Found at i:39323323 original size:36 final size:37
Alignment explanation
Indices: 39323283--39323354 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
39323273 TACTTGTTAT
39323283 CAACTAATGTTTATT-GTAAAATTACATTTACATTAC
1 CAACTAATGTTTATTAGTAAAATTACATTTACATTAC
39323319 CAACTAATGTTTATTAGTAAAATTACATTTACATTA
1 CAACTAATGTTTATTAGTAAAATTACATTTACATTA
39323355 AAAATCTATC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 15 0.43
37 20 0.57
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (37 bp):
CAACTAATGTTTATTAGTAAAATTACATTTACATTAC
Found at i:39323369 original size:31 final size:34
Alignment explanation
Indices: 39323298--39323369 Score: 78
Period size: 37 Copynumber: 2.1 Consensus size: 34
39323288 AATGTTTATT
* *
39323298 GTAAAATTACATTTACATTACCAACTAATGTTTATTA
1 GTAAAATTACATTTACATTA-CAAC-AA-GTCTATCA
39323335 GTAAAATTACATTTACATTA-AA-AA-TCTATCA
1 GTAAAATTACATTTACATTACAACAAGTCTATCA
39323366 GTAA
1 GTAA
39323370 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
31 9 0.27
33 2 0.06
35 2 0.06
37 20 0.61
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (34 bp):
GTAAAATTACATTTACATTACAACAAGTCTATCA
Found at i:39327216 original size:29 final size:29
Alignment explanation
Indices: 39327180--39327244 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
39327170 ATGTGGCATA
39327180 AGTGTGTATGGCCATTTGTAGGGCACACG
1 AGTGTGTATGGCCATTTGTAGGGCACACG
39327209 AGTGTGTATGGCCATTTGTAGGGCACACG
1 AGTGTGTATGGCCATTTGTAGGGCACACG
*
39327238 GGTGTGT
1 AGTGTGT
39327245 GTGTTGGCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.18, C:0.15, G:0.37, T:0.29
Consensus pattern (29 bp):
AGTGTGTATGGCCATTTGTAGGGCACACG
Found at i:39327836 original size:20 final size:20
Alignment explanation
Indices: 39327813--39327851 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39327803 TGTGATACCT
*
39327813 ACTAAATGAGTATGATCTGC
1 ACTAAATGAATATGATCTGC
**
39327833 ACTATCTGAATATGATCTG
1 ACTAAATGAATATGATCTG
39327852 AATCTGTATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (20 bp):
ACTAAATGAATATGATCTGC
Found at i:39330536 original size:25 final size:25
Alignment explanation
Indices: 39330494--39330548 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
39330484 TATTAAATAT
*
39330494 TAAAATAATAATATAAATATTCTTTC
1 TAAAATAATAATAAAAATATT-TTTC
39330520 TAAAA-AATAATAAAAATATTTTTC
1 TAAAATAATAATAAAAATATTTTTC
39330544 -AAAAT
1 TAAAAT
39330549 TTTTTAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 4 0.15
24 4 0.15
25 14 0.52
26 5 0.19
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (25 bp):
TAAAATAATAATAAAAATATTTTTC
Found at i:39332382 original size:25 final size:25
Alignment explanation
Indices: 39332354--39332410 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
39332344 CACTTATCAA
39332354 AGTTTAAGT-GTGAAACTAAAAACAG
1 AGTTTAAGTAG-GAAACTAAAAACAG
* *
39332379 AGTTTAAGTAGGAAATTAAAAATAG
1 AGTTTAAGTAGGAAACTAAAAACAG
*
39332404 AATTTAA
1 AGTTTAA
39332411 CTGGGAGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.51, C:0.04, G:0.18, T:0.28
Consensus pattern (25 bp):
AGTTTAAGTAGGAAACTAAAAACAG
Found at i:39333313 original size:20 final size:20
Alignment explanation
Indices: 39333276--39333313 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39333266 TGTGGATTCC
**
39333276 ACACGCCCGTGTGGCTTGGG
1 ACACGCCCGTGTCCCTTGGG
39333296 ACACGCCCGTGTCCCTTG
1 ACACGCCCGTGTCCCTTG
39333314 TCCGTGGAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.37, G:0.32, T:0.21
Consensus pattern (20 bp):
ACACGCCCGTGTCCCTTGGG
Found at i:39337763 original size:59 final size:59
Alignment explanation
Indices: 39337671--39337790 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
39337661 CGTTTGGGTT
39337671 AGATGTGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAGAGATGTGTGCC
1 AGATGTGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAGAGATGTGTGCC
39337730 AGATGTGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAGAGATGTGTGCC
1 AGATGTGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAGAGATGTGTGCC
39337789 AG
1 AG
39337791 TGTAAGATCA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23
Consensus pattern (59 bp):
AGATGTGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAGAGATGTGTGCC
Found at i:39337803 original size:48 final size:47
Alignment explanation
Indices: 39337730--39337957 Score: 259
Period size: 48 Copynumber: 4.9 Consensus size: 47
39337720 GATGTGTGCC
*
39337730 AGATGTGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAG
1 AGATGTGTGCCAGTGTAAGA-CATGTATGGGACATGGCATCGGCGTAG
* *
39337778 AGATGTGTGCCAGTGTAAGATCATGTTTGGGACATGGCATCGACGTAG
1 AGATGTGTGCCAGTGTAAGA-CATGTATGGGACATGGCATCGGCGTAG
* * * * * **
39337826 AGATGAGTGCTAGTGTAAGACATATCTGGGACAT-GCATCGGCCTCT
1 AGATGTGTGCCAGTGTAAGACATGTATGGGACATGGCATCGGCGTAG
** *
39337872 AGATGTAAGCCAGTGTAAGACATGTATAGGACAT-GCATCGGC-TACG
1 AGATGTGTGCCAGTGTAAGACATGTATGGGACATGGCATCGGCGTA-G
**
39337918 AGACATGT--CAGTGTAAGACATGTATGGGACATGGCATCGG
1 AGATGTGTGCCAGTGTAAGACATGTATGGGACATGGCATCGG
39337958 TAACTTGACC
Statistics
Matches: 153, Mismatches: 25, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
44 23 0.15
45 8 0.05
46 47 0.31
47 12 0.08
48 63 0.41
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (47 bp):
AGATGTGTGCCAGTGTAAGACATGTATGGGACATGGCATCGGCGTAG
Found at i:39340090 original size:3 final size:3
Alignment explanation
Indices: 39340082--39340128 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
39340072 TATATACACG
39340082 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
39340129 GATTGTACAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:39340946 original size:3 final size:3
Alignment explanation
Indices: 39340938--39340971 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
39340928 TGGTGTAGAG
39340938 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
39340972 GATATTCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:39341804 original size:3 final size:3
Alignment explanation
Indices: 39341796--39341824 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
39341786 TAGATTATGG
39341796 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
39341825 TCCATATGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:39343859 original size:21 final size:20
Alignment explanation
Indices: 39343835--39343883 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
39343825 AACTCGTAAT
* *
39343835 CTTAAATCCTAAACCTTAAAC
1 CTTAAATCCCAAACC-AAAAC
39343856 CTTAAATCCCAAACCAAAAC
1 CTTAAATCCCAAACCAAAAC
39343876 CTTAAATC
1 CTTAAATC
39343884 AGGGTTTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.24
Consensus pattern (20 bp):
CTTAAATCCCAAACCAAAAC
Found at i:39345796 original size:32 final size:32
Alignment explanation
Indices: 39345738--39345798 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
39345728 AAACTCGAAT
* * *
39345738 TTCGAGTTAATCAAATCGAGTCGTTTGAATTA
1 TTCGAGTAAATCAAATCAAGTAGTTTGAATTA
39345770 TTCGAGTAAATTCAAAT-AAGTAGTTTGAA
1 TTCGAGTAAA-TCAAATCAAGTAGTTTGAA
39345799 CCGAGTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 19 0.76
33 6 0.24
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (32 bp):
TTCGAGTAAATCAAATCAAGTAGTTTGAATTA
Found at i:39345904 original size:19 final size:19
Alignment explanation
Indices: 39345882--39345937 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
39345872 CAAAAATTAA
39345882 AAAAATTCAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
39345901 -AAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
39345919 AAAAATTCCAAAT-TTTAT
1 AAAAATTCAAAATATTTAT
39345937 A
1 A
39345938 TTTTAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
17 4 0.12
18 19 0.56
19 11 0.32
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:39345933 original size:34 final size:33
Alignment explanation
Indices: 39345895--39345958 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
39345885 AATTCAAAAT
*
39345895 AATTTTAAAATTCAAAATATTTATAAAAATTCCA
1 AATTTTAAAATTCAAAA-AATTATAAAAATTCCA
* * *
39345929 AATTTTATATTTTAAAAAATTATAAAAATT
1 AATTTTAAAATTCAAAAAATTATAAAAATT
39345959 AAATATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 12 0.46
34 14 0.54
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (33 bp):
AATTTTAAAATTCAAAAAATTATAAAAATTCCA
Found at i:39351329 original size:20 final size:21
Alignment explanation
Indices: 39351280--39351331 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
39351270 ATGTGGAAAA
*
39351280 TAAATAAATAATTCATGAAGT
1 TAAATAAATAACTCATGAAGT
* * *
39351301 TAAAAAAATAACTC-TTAATT
1 TAAATAAATAACTCATGAAGT
39351321 TAAATAAATAA
1 TAAATAAATAA
39351332 ACATAATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.33
Consensus pattern (21 bp):
TAAATAAATAACTCATGAAGT
Found at i:39352168 original size:27 final size:27
Alignment explanation
Indices: 39352138--39352189 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
39352128 TATTATTAAA
* *
39352138 TATTTATAAATT-GTAATATATATTTAT
1 TATTTAAAAATTAGT-ATAAATATTTAT
39352165 TATTTAAAAATTAGTATAAATATTT
1 TATTTAAAAATTAGTATAAATATTT
39352190 TCTATAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (27 bp):
TATTTAAAAATTAGTATAAATATTTAT
Found at i:39352417 original size:18 final size:17
Alignment explanation
Indices: 39352385--39352420 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
39352375 TGTTTTAAAA
39352385 AATTAAATAAAAATATT
1 AATTAAATAAAAATATT
*
39352402 AATTAATATAATAATATT
1 AATTAA-ATAAAAATATT
39352420 A
1 A
39352421 GGCTTAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTAAATAAAAATATT
Found at i:39353275 original size:107 final size:107
Alignment explanation
Indices: 39353089--39353337 Score: 498
Period size: 107 Copynumber: 2.3 Consensus size: 107
39353079 CTTTTATTAA
39353089 AATAATTGTATTTTTTATAAATTATTTTATCTCAATTAATCTAAAATAATATGAGATAATCAAAA
1 AATAATTGTATTTTTTATAAATTATTTTATCTCAATTAATCTAAAATAATATGAGATAATCAAAA
39353154 TTAATAGGGTTTAATTAATAATATGAGATAATAATAATTATT
66 TTAATAGGGTTTAATTAATAATATGAGATAATAATAATTATT
39353196 AATAATTGTATTTTTTATAAATTATTTTATCTCAATTAATCTAAAATAATATGAGATAATCAAAA
1 AATAATTGTATTTTTTATAAATTATTTTATCTCAATTAATCTAAAATAATATGAGATAATCAAAA
39353261 TTAATAGGGTTTAATTAATAATATGAGATAATAATAATTATT
66 TTAATAGGGTTTAATTAATAATATGAGATAATAATAATTATT
39353303 AATAATTGTATTTTTTATAAATTATTTTATCTCAA
1 AATAATTGTATTTTTTATAAATTATTTTATCTCAA
39353338 ATGAAGAGAT
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 142 1.00
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (107 bp):
AATAATTGTATTTTTTATAAATTATTTTATCTCAATTAATCTAAAATAATATGAGATAATCAAAA
TTAATAGGGTTTAATTAATAATATGAGATAATAATAATTATT
Found at i:39354357 original size:16 final size:17
Alignment explanation
Indices: 39354331--39354362 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
39354321 TTAATTGAAA
39354331 AATATAAATTTTATTAT
1 AATATAAATTTTATTAT
39354348 AATA-AAATTTTATTA
1 AATATAAATTTTATTA
39354363 CTTTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATAAATTTTATTAT
Found at i:39355591 original size:7 final size:7
Alignment explanation
Indices: 39355579--39355606 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
39355569 TAACATAGTT
39355579 ATATTTA
1 ATATTTA
39355586 ATATTTA
1 ATATTTA
39355593 ATATTTA
1 ATATTTA
39355600 ATATTTA
1 ATATTTA
39355607 TTAATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATATTTA
Found at i:39361926 original size:25 final size:25
Alignment explanation
Indices: 39361898--39361947 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
39361888 AAGCAATGAA
39361898 GAATACAT-TACATTGGGGCAACTTT
1 GAATACATAT-CATTGGGGCAACTTT
*
39361923 GAATATATATCATTGGGGCAACTTT
1 GAATACATATCATTGGGGCAACTTT
39361948 TTTAACTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (25 bp):
GAATACATATCATTGGGGCAACTTT
Found at i:39375410 original size:3 final size:3
Alignment explanation
Indices: 39375402--39375734 Score: 184
Period size: 3 Copynumber: 110.0 Consensus size: 3
39375392 AAAAGAAAAT
* * *
39375402 ATA ATA ATA ATA ATA ATA ATG ATG ATG ATA A-A GATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
* * * * * * *
39375447 ATA GTA ATA AAA ATG ATT GTA ATA ATA ATG GTA ATA ATA ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
* * * * *
39375493 GTA ATA ATA ATA CATTA ATA AGA ATA ATG ATA GTA CATTA ATA ATA ACA
1 ATA ATA ATA ATA -A-TA ATA ATA ATA ATA ATA ATA -A-TA ATA ATA ATA
* * *
39375542 ATA ATA A-A A-A ATA ATA GAAA ATA ATA ATA ATA A-A CTA AGGA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA A-TA ATA
* * * * * *
39375586 ATA ATA ATA CTA ACA ATA AT- ATAA ATA ATA ATA AAA ACA ACA AGA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA
* * * *
39375631 GA-A ATA GTA ACA ATA ATA GTA ATA AAA ATA ATA A-A AGTA ATA ATA
1 -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
* *
39375676 ATA ATA ACA ATA ATA A-A ATTA ATA ATA A-A ATA A-A ATTA ATCA ATT
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA A-TA AT-A ATA
*
39375721 TTA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA
39375735 GTAAATTAAC
Statistics
Matches: 254, Mismatches: 52, Indels: 48
0.72 0.15 0.14
Matches are distributed among these distances:
2 19 0.07
3 208 0.82
4 23 0.09
5 4 0.02
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:39375724 original size:27 final size:26
Alignment explanation
Indices: 39375642--39375749 Score: 101
Period size: 27 Copynumber: 3.9 Consensus size: 26
39375632 AAATAGTAAC
* * *
39375642 AATAATAGTAATAAAAATAATAAAAGT
1 AATAATA-AAATAAAATTAATAAAATT
39375669 AATAATAATAATAACAA-TAATAAAATT
1 AATAATAA-AATAA-AATTAATAAAATT
**
39375696 AATAATAAAATAAAATTAATCAATTTT
1 AATAATAAAATAAAATTAAT-AAAATT
39375723 AATAATAAAATAGTAAATTAACTAAAA
1 AATAATAAAATA--AAATTAA-TAAAA
39375750 AGGATTAAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
25 2 0.03
26 9 0.13
27 45 0.66
28 2 0.03
29 9 0.13
30 1 0.01
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (26 bp):
AATAATAAAATAAAATTAATAAAATT
Found at i:39380024 original size:22 final size:22
Alignment explanation
Indices: 39379958--39380024 Score: 57
Period size: 22 Copynumber: 2.9 Consensus size: 22
39379948 CTTATTTATT
* *
39379958 TATTTTATTATTATA-AT-ATA
1 TATTTTATTATAATAGATAACA
39379978 TATATTTACTTAATAATTAAGATAACA
1 TAT-TTTA-TT-ATAA-T-AGATAACA
39380005 TATTTTATTATAATAGATAA
1 TATTTTATTATAATAGATAA
39380025 ATTAAATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
20 3 0.08
21 4 0.11
22 8 0.21
23 4 0.11
24 5 0.13
25 3 0.08
26 6 0.16
27 5 0.13
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (22 bp):
TATTTTATTATAATAGATAACA
Found at i:39383192 original size:46 final size:46
Alignment explanation
Indices: 39383125--39383601 Score: 646
Period size: 46 Copynumber: 10.7 Consensus size: 46
39383115 TGGCAACCTG
*
39383125 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTAATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
39383171 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-----TG---
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
*
39383209 TGTGTAAGACCATGGTTGAAAGATACAATGGCAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
* * *
39383255 TGTGTAAGACCATGGTTGAAAGATACTATGGCAACTTGATATGAGA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
*
39383301 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAGA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
39383347 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG---TG---
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
* *
39383387 TGT-T-AGACCATAGTTGAAAGATACCATGGCAACCTGATATGATA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
*
39383431 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAGA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
* * *
39383477 TGTGTCAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
* ** * *
39383523 AGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG-AAA
* * *
39383569 TGAGTAAGACCATAGTTGAAAGACACCATGGCA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCA
39383602 TCACGTCAAA
Statistics
Matches: 392, Mismatches: 22, Indels: 34
0.88 0.05 0.08
Matches are distributed among these distances:
38 66 0.17
39 1 0.00
40 3 0.01
41 4 0.01
43 4 0.01
44 3 0.01
45 2 0.01
46 309 0.79
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.23
Consensus pattern (46 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
Found at i:39383211 original size:84 final size:84
Alignment explanation
Indices: 39383076--39383557 Score: 694
Period size: 84 Copynumber: 5.5 Consensus size: 84
39383066 AGTGTGCTCT
39383076 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGT
39383141 TGAAAGATACCATGGCAAC
66 TGAAAGATACCATGGCAAC
*
39383160 CTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGT
*
39383225 TGAAAGATACAATGGCAAC
66 TGAAAGATACCATGGCAAC
* *
39383244 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACTATGGCAACTTGATATGAGATGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC-----CT--G-TGTGTAAG
39383309 ACCATGGTTGAAAGATACCATGGCAAC
58 ACCATGGTTGAAAGATACCATGGCAAC
* * *
39383336 CTGATATGAGATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTTAGACCATAGT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGT
39383401 TGAAAGATACCATGGCAAC
66 TGAAAGATACCATGGCAAC
* *
39383420 CTGATATGATATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAGATGTGTCAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-----T--G-TGTGTAAG
39383485 ACCATGGTTGAAAGATACCATGGCAAC
58 ACCATGGTTGAAAGATACCATGGCAAC
* * * **
39383512 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
39383558 ATGACAGAAA
Statistics
Matches: 362, Mismatches: 20, Indels: 24
0.89 0.05 0.06
Matches are distributed among these distances:
84 205 0.57
85 1 0.00
87 1 0.00
89 2 0.01
91 2 0.01
92 151 0.42
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.24
Consensus pattern (84 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGT
TGAAAGATACCATGGCAAC
Found at i:39383312 original size:130 final size:127
Alignment explanation
Indices: 39383086--39383601 Score: 616
Period size: 130 Copynumber: 3.9 Consensus size: 127
39383076 CTGATATGAA
39383086 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC--TGTGTGTAAGACCATGGTTGAAAGAT
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTGTAAGACCATGGTTGAAAGAT
*
39383149 ACCATGGCAACCTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-T-G
66 ACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCATAG
*
39383209 -TGTGTAAGACCATGGTTGAAAGATACAATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG---TG---TGTGTAAGACCATGGTTG
* * *
39383273 AAAGATACTATGGCAACTTGATATGAGATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCT
60 AAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-
39383338 GATATGAG
124 ---AT-AG
*
39383346 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGT-T-AGACCATAGTTGAAAGAT
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTGTAAGACCATGGTTGAAAGAT
*
39383409 ACCATGGCAACCTGATATGATATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
66 ACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC----AT-
39383474 AG
126 AG
* * * **
39383476 ATGTGTCAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG---TG---TGTGTAAGACCATGGTTG
* * * * *
39383541 AAAGATACCATGGCAACATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACCATGGCA
60 AAAGATACCATGGCAACCTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
39383602 TCACGTCAAA
Statistics
Matches: 347, Mismatches: 21, Indels: 35
0.86 0.05 0.09
Matches are distributed among these distances:
122 35 0.10
127 2 0.01
130 196 0.56
131 1 0.00
132 3 0.01
133 2 0.01
135 3 0.01
136 1 0.00
137 3 0.01
138 101 0.29
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (127 bp):
ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTGTAAGACCATGGTTGAAAGAT
ACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCATAG
Found at i:39383362 original size:176 final size:175
Alignment explanation
Indices: 39383076--39383557 Score: 771
Period size: 176 Copynumber: 2.8 Consensus size: 175
39383066 AGTGTGCTCT
*
39383076 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC----CT--G-TGTGTAAGA
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACTGATATGAGATGTGTAAGA
*
39383134 CCATGGTTGAAAGATACCATGGCAACCTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCA
66 CCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCA
*
39383199 TGGCAACCTGTGTGTAAGACCATGGTTGAAAGATACAATGGCAAC
131 TGGCAACCTGTGTGTAAGACCATAGTTGAAAGATACAATGGCAAC
*
39383244 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACTATGGCAACTTGATATGAGATGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC-TGATATGAGATGTGTAAG
*
39383309 ACCATGGTTGAAAGATACCATGGCAACCTGATATGAGATGTGTAAGACCATGGTTGAAAGATACC
65 ACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACC
* *
39383374 ATGGCAACCTGTGTGTTAGACCATAGTTGAAAGATACCATGGCAAC
130 ATGGCAACCTGTGTGTAAGACCATAGTTGAAAGATACAATGGCAAC
* *
39383420 CTGATATGATATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAGATGTGTCAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA-CTGATATGAGATGTGTAAG
* * * **
39383485 ACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTGAAAGATACC
65 ACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACC
39383550 ATGGCAAC
130 ATGGCAAC
39383558 ATGACAGAAA
Statistics
Matches: 289, Mismatches: 16, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
168 45 0.16
173 1 0.00
175 1 0.00
176 241 0.83
177 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.24
Consensus pattern (175 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACTGATATGAGATGTGTAAGA
CCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCA
TGGCAACCTGTGTGTAAGACCATAGTTGAAAGATACAATGGCAAC
Found at i:39383907 original size:23 final size:25
Alignment explanation
Indices: 39383862--39383908 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
39383852 AATAAATATA
*
39383862 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
39383887 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
39383909 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:39385966 original size:3 final size:3
Alignment explanation
Indices: 39385952--39386011 Score: 93
Period size: 3 Copynumber: 20.0 Consensus size: 3
39385942 TGGTAACCTT
* * *
39385952 TTC TTT TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC ATC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
39386000 TTC TTC TTC TTC
1 TTC TTC TTC TTC
39386012 AGTAGTGTAG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:39393654 original size:5 final size:6
Alignment explanation
Indices: 39393626--39393659 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
39393616 TAATGCATAG
39393626 TTTTCT TGTTTCTT TTTTCT TTTTCT TTTTCT TT
1 TTTTCT T-TTTC-T TTTTCT TTTTCT TTTTCT TT
39393660 AAAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 16 0.62
7 8 0.31
8 2 0.08
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:39397739 original size:25 final size:25
Alignment explanation
Indices: 39397683--39397757 Score: 84
Period size: 24 Copynumber: 3.0 Consensus size: 25
39397673 ATGTTAACAA
39397683 AATATTCAAAAT-ATATTTTAT-ATT
1 AATATT-AAAATAATATTTTATAATT
*
39397707 AATATTAATATAATATTTTATAATT
1 AATATTAAAATAATATTTTATAATT
*
39397732 AA-ATTTAAAATAATATATTTGTAATT
1 AATA-TTAAAATAATAT-TTTATAATT
39397758 TTTTGTATTG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
23 4 0.09
24 16 0.36
25 16 0.36
26 8 0.18
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (25 bp):
AATATTAAAATAATATTTTATAATT
Found at i:39398614 original size:20 final size:21
Alignment explanation
Indices: 39398586--39398632 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
39398576 AAAGCCATAT
*
39398586 GAAACAGAAAGAA-AAAAAGA
1 GAAAGAGAAAGAAGAAAAAGA
**
39398606 GAAAGAGAAAGAAGAAAGGGA
1 GAAAGAGAAAGAAGAAAAAGA
39398627 GAAAGA
1 GAAAGA
39398633 AGGTTCAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.68, C:0.02, G:0.30, T:0.00
Consensus pattern (21 bp):
GAAAGAGAAAGAAGAAAAAGA
Found at i:39403778 original size:53 final size:53
Alignment explanation
Indices: 39403697--39403847 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
39403687 CTTACACGGT
* *
39403697 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
* *
39403752 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCATATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
39403805 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
39403848 GCGCACTTAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.01
53 80 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:39408556 original size:18 final size:18
Alignment explanation
Indices: 39408521--39408564 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
39408511 TAGGAATGTG
*
39408521 CAAAAAAATAAATTAAAT
1 CAAAAAAATAAATCAAAT
**
39408539 CAAAAAAATGGATCAAAT
1 CAAAAAAATAAATCAAAT
39408557 -AAAAAAAT
1 CAAAAAAAT
39408565 TTTATTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.18
Consensus pattern (18 bp):
CAAAAAAATAAATCAAAT
Found at i:39408823 original size:22 final size:22
Alignment explanation
Indices: 39408798--39408849 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
39408788 CCAACTTAAT
* *
39408798 AATTAATTTAATTATAAAATTA
1 AATTAAATTAATTAAAAAATTA
*
39408820 AATTAAATTACTTAAAAAATTA
1 AATTAAATTAATTAAAAAATTA
39408842 AATCTAAA
1 AAT-TAAA
39408850 AACAAAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
AATTAAATTAATTAAAAAATTA
Found at i:39409986 original size:22 final size:21
Alignment explanation
Indices: 39409958--39410001 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
39409948 AATCTGAGTT
*
39409958 TGCTTCTTGGCACAGGTTTTTC
1 TGCTTCTTGGCAC-GGTGTTTC
39409980 TGCTTCTTGGCACGGTGTTTC
1 TGCTTCTTGGCACGGTGTTTC
39410001 T
1 T
39410002 TCCATACTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.07, C:0.23, G:0.25, T:0.45
Consensus pattern (21 bp):
TGCTTCTTGGCACGGTGTTTC
Found at i:39414281 original size:50 final size:50
Alignment explanation
Indices: 39414224--39414471 Score: 316
Period size: 50 Copynumber: 4.9 Consensus size: 50
39414214 AACGAAGCTC
* * * *
39414224 TCTGGTACGCATAGTAGCCTGTACTTAGTACTACATATGCGACCTAACAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
* * *
39414274 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACAGGTGACCTAACTA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
* * * * * * *
39414324 TCTGATACACGTAGTAGCCTGCACTTAGTACTACATACGTGATCGAAGCTA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAA-CAA
* * *
39414375 TCGGGTACACATAGTAGCCTGCACTTAGCACTACACATGCGACCTAACAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
* *
39414425 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAA
39414472 AACCATCTTA
Statistics
Matches: 170, Mismatches: 27, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
50 129 0.76
51 41 0.24
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (50 bp):
TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
Found at i:39414409 original size:101 final size:100
Alignment explanation
Indices: 39414235--39414468 Score: 333
Period size: 101 Copynumber: 2.3 Consensus size: 100
39414225 CTGGTACGCA
* * * * * *
39414235 TAGTAGCCTGTACTTAGTACTACATATGCGACCTAACAATCTGGTACACGTAGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACATACGTGACCGAACAATCGGGTACACATAGTAGCCTGCACTT
* * *
39414300 AGTACTACACAGGTGACCTAACTATCTGATACACG
66 AGCACTACACAGGCGACCTAACAATCTGATACACG
* *
39414335 TAGTAGCCTGCACTTAGTACTACATACGTGATCGAAGCTATCGGGTACACATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACATACGTGACCGAA-CAATCGGGTACACATAGTAGCCTGCACT
* *
39414400 TAGCACTACACATGCGACCTAACAATCTGGTACACG
65 TAGCACTACACAGGCGACCTAACAATCTGATACACG
*
39414436 TAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACATACGTGACC
39414469 TAAAACCATC
Statistics
Matches: 118, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
100 31 0.26
101 87 0.74
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (100 bp):
TAGTAGCCTGCACTTAGTACTACATACGTGACCGAACAATCGGGTACACATAGTAGCCTGCACTT
AGCACTACACAGGCGACCTAACAATCTGATACACG
Found at i:39419018 original size:13 final size:13
Alignment explanation
Indices: 39418974--39419030 Score: 57
Period size: 13 Copynumber: 4.6 Consensus size: 13
39418964 AATATATTTA
*
39418974 AACCCAAGTACCC
1 AACCCAATTACCC
*
39418987 AACTCAA-TA--C
1 AACCCAATTACCC
*
39418997 AACCCAATTACTC
1 AACCCAATTACCC
*
39419010 AACCTAATTACCC
1 AACCCAATTACCC
39419023 AACCCAAT
1 AACCCAAT
39419031 AATAAAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
10 7 0.19
11 2 0.06
12 2 0.06
13 25 0.69
ACGTcount: A:0.42, C:0.39, G:0.02, T:0.18
Consensus pattern (13 bp):
AACCCAATTACCC
Found at i:39419047 original size:16 final size:16
Alignment explanation
Indices: 39419028--39419064 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
39419018 TACCCAACCC
* *
39419028 AATAATAAAAATTACA
1 AATAATAAAAAATAAA
39419044 AATAATAAAAAATAAA
1 AATAATAAAAAATAAA
39419060 AATAA
1 AATAA
39419065 AAATCTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (16 bp):
AATAATAAAAAATAAA
Found at i:39422782 original size:17 final size:17
Alignment explanation
Indices: 39422762--39422822 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
39422752 ATTTCAAAAC
39422762 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
* ***
39422779 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
*
39422798 CTTATGTAATGCTTTTAA
1 -TTATGTAATGTTTTTAA
39422816 TTATGTA
1 TTATGTA
39422823 GTGATTCAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 16 0.50
18 4 0.12
19 3 0.09
20 9 0.28
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:39422801 original size:37 final size:36
Alignment explanation
Indices: 39422754--39422831 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 36
39422744 ATATGTTAAT
*
39422754 TTCAAAACTTATGTAATGTTTTTAATTATGTAGTGA
1 TTCAAAACTTATGTAATGCTTTTAATTATGTAGTGA
39422790 TTCAAAGACTTATGTAATGCTTTTAATTATGTAGTGA
1 TTCAAA-ACTTATGTAATGCTTTTAATTATGTAGTGA
39422827 TTCAA
1 TTCAA
39422832 TTCAGTTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
36 6 0.15
37 34 0.85
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (36 bp):
TTCAAAACTTATGTAATGCTTTTAATTATGTAGTGA
Found at i:39422844 original size:9 final size:9
Alignment explanation
Indices: 39422830--39422860 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
39422820 GTAGTGATTC
39422830 AATTCAGTT
1 AATTCAGTT
39422839 AATTCAGTT
1 AATTCAGTT
*
39422848 AATTCGGTT
1 AATTCAGTT
39422857 AATT
1 AATT
39422861 TTTAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (9 bp):
AATTCAGTT
Found at i:39424850 original size:16 final size:15
Alignment explanation
Indices: 39424826--39424883 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
39424816 GTAGTTTAGA
39424826 AGAATAGAAAAAGAAG
1 AGAA-AGAAAAAGAAG
*
39424842 AGAACAGAAAAGGAATG
1 AGAA-AGAAAAAGAA-G
* *
39424859 A-AAGGAAAAAGAAA
1 AGAAAGAAAAAGAAG
39424873 AGAAAGAAAAA
1 AGAAAGAAAAA
39424884 AGAGAAGCAG
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
14 1 0.03
15 16 0.47
16 15 0.44
17 2 0.06
ACGTcount: A:0.71, C:0.02, G:0.24, T:0.03
Consensus pattern (15 bp):
AGAAAGAAAAAGAAG
Found at i:39425004 original size:31 final size:29
Alignment explanation
Indices: 39424934--39425005 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
39424924 AAGGAAAAGG
* *
39424934 AAAA-TAGG-TTGTGTTTATGGTTTGAAA
1 AAAATTAGGATTGTGCTTAGGGTTTGAAA
39424961 AAAATTAGGATTGTGCTTAGGGTTTGAAA
1 AAAATTAGGATTGTGCTTAGGGTTTGAAA
39424990 AAAATTAAGAGATTGT
1 AAAATT-AG-GATTGT
39425006 ATTTGGGGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 4 0.10
28 4 0.10
29 23 0.59
30 2 0.05
31 6 0.15
ACGTcount: A:0.38, C:0.01, G:0.25, T:0.36
Consensus pattern (29 bp):
AAAATTAGGATTGTGCTTAGGGTTTGAAA
Done.