Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 194 of 226
Found at i:58539792 original size:41 final size:40
Alignment explanation
Indices: 58539747--58539832 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
58539737 AGCGGCGCTT
* *
58539747 TTAGCGGCGTTTGGACAAAAAACGCCAC-TAATAATCGAGCA
1 TTAGCGGCATTT-GACAAAAAACGCCACAAAAT-ATCGAGCA
* * *
58539788 TTAGCGGCATTTTACGAAAAACGCCGCAAAATATCGAGCA
1 TTAGCGGCATTTGACAAAAAACGCCACAAAATATCGAGCA
58539828 TTAGC
1 TTAGC
58539833 TGCGCTACAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
40 25 0.64
41 14 0.36
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (40 bp):
TTAGCGGCATTTGACAAAAAACGCCACAAAATATCGAGCA
Found at i:58540179 original size:114 final size:113
Alignment explanation
Indices: 58539874--58540220 Score: 559
Period size: 113 Copynumber: 3.1 Consensus size: 113
58539864 AGCATTAGCA
* *
58539874 GCGTTTTACAAAAAGCGCCGCAATAGAGTCACAAAGAACGACGCCGTTTTCATATATTTGGGAAC
1 GCGTTTTACAAAAAGCGCCGCAATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAAC
* * *
58539939 ATTAGTGGCGGTTTTTCCCAAGCGCGGCTAAAACTCCGTTCTTCAGCG
66 ATTAGTGGCGGTTTTGCCCAAGCGCCGCTAATACTCCGTTCTTCAGCG
* *
58539987 GCGTTTTATAAAAAGCGCCGCAATGGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAAC
1 GCGTTTTACAAAAAGCGCCGCAATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAAC
*
58540052 ATTAGTGGCGGTTTTGCCCAAGCGCCGCTAATACTCCATTCTTCAGCG
66 ATTAGTGGCGGTTTTGCCCAAGCGCCGCTAATACTCCGTTCTTCAGCG
* *
58540100 GCGTTTTACAAAAAGCGTCGCAAATAGAGTAACACAGAACGACACCGTTTTCATATATTTGGGAA
1 GCGTTTTACAAAAAGCGCCGC-AATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAA
* * *
58540165 CACTAGTGGCGGTTTTTGCCCAAACGCCGCTAATAATCCGTTCTTCAGCG
65 CATTAGTGGCGG-TTTTGCCCAAGCGCCGCTAATACTCCGTTCTTCAGCG
58540215 GCGTTT
1 GCGTTT
58540221 GGCATTAAGC
Statistics
Matches: 216, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
113 124 0.57
114 52 0.24
115 40 0.19
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (113 bp):
GCGTTTTACAAAAAGCGCCGCAATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAAC
ATTAGTGGCGGTTTTGCCCAAGCGCCGCTAATACTCCGTTCTTCAGCG
Found at i:58540384 original size:41 final size:40
Alignment explanation
Indices: 58540330--58540445 Score: 90
Period size: 41 Copynumber: 2.9 Consensus size: 40
58540320 GATGCTCCGC
* * * *
58540330 TCTAAAGCAGCGTTTATGGAGAATCGCCGCTAATGTTCTGG
1 TCTATAGCGGCGTTTATGGAGAATCGCCGCTAATCTT-GGG
** *
58540371 TCTATAGCGGCGTTCCTGGAGAAGT-GCCGGTAACTCTTGGG
1 TCTATAGCGGCGTTTATGGAGAA-TCGCCGCTAA-TCTTGGG
* * * * *
58540412 TCTTTAGCGGCGTTTGTGTAAAAACGCCGCTAAT
1 TCTATAGCGGCGTTTATGGAGAATCGCCGCTAAT
58540446 TAGAAATATT
Statistics
Matches: 58, Mismatches: 14, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
40 1 0.02
41 53 0.91
42 4 0.07
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (40 bp):
TCTATAGCGGCGTTTATGGAGAATCGCCGCTAATCTTGGG
Found at i:58542871 original size:16 final size:16
Alignment explanation
Indices: 58542850--58542880 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
58542840 ATTTTCCCTA
58542850 TTCTAAAATCCCTAAG
1 TTCTAAAATCCCTAAG
58542866 TTCTAAAATCCCTAA
1 TTCTAAAATCCCTAA
58542881 CTCATAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.32
Consensus pattern (16 bp):
TTCTAAAATCCCTAAG
Found at i:58544079 original size:28 final size:28
Alignment explanation
Indices: 58544023--58544076 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 28
58544013 TAATAGATAA
58544023 TTTTATTTGTATTAACAATTTTTAAAAT
1 TTTTATTTGTATTAACAATTTTTAAAAT
58544051 TTTTA-TTGTATTAACAATTTTTAAAA
1 TTTTATTTGTATTAACAATTTTTAAAA
58544077 ATTACATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (28 bp):
TTTTATTTGTATTAACAATTTTTAAAAT
Found at i:58544091 original size:27 final size:27
Alignment explanation
Indices: 58544032--58544091 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
58544022 ATTTTATTTG
* ** *
58544032 TATTAACAATTTTTAAAATTTTTATTG
1 TATTAACAATTTTTAAAAATTACATTA
58544059 TATTAACAATTTTTAAAAATTACATTA
1 TATTAACAATTTTTAAAAATTACATTA
*
58544086 TTTTAA
1 TATTAA
58544092 TAAAAAAACA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (27 bp):
TATTAACAATTTTTAAAAATTACATTA
Found at i:58544486 original size:14 final size:14
Alignment explanation
Indices: 58544464--58544503 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
58544454 TATGACACCA
*
58544464 AATATATTTTAAAC
1 AATAAATTTTAAAC
58544478 AATAAATTTTAAAC
1 AATAAATTTTAAAC
* *
58544492 ATTAAAGTTTAA
1 AATAAATTTTAA
58544504 TTTTAAACAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (14 bp):
AATAAATTTTAAAC
Found at i:58550521 original size:21 final size:21
Alignment explanation
Indices: 58550495--58550545 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
58550485 CTACAACTTA
* *
58550495 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
58550516 AAGCAGAGGCAGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
*
58550537 AAGCTGAGG
1 AAGCAGAGG
58550546 TTCAACAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.18, G:0.43, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCGAGAG
Found at i:58550582 original size:87 final size:87
Alignment explanation
Indices: 58550429--58550626 Score: 249
Period size: 87 Copynumber: 2.3 Consensus size: 87
58550419 ACATAACTTA
* * * *
58550429 AAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTT
1 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAACTACAACTT
*
58550494 AAAGCAGATGCGGCAGCGAGAG
66 AAAGAAGATGCGGCAGCGAGAG
* * *
58550516 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATG-AGCAACTGCAAC-AGTAG
1 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAG-AACTCCAACTA-CAA
58550578 CTTAAAGAAGATGCGGCAGCGAGAG
63 CTTAAAGAAGATGCGGCAGCGAGAG
* * *
58550603 AAGCAGCGGCTGCAGCGAGGGAAG
1 AAGCAGAGGCAGCAGCGAGAGAAG
58550627 TAGAGGCTGC
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
86 3 0.03
87 89 0.92
88 5 0.05
ACGTcount: A:0.38, C:0.18, G:0.32, T:0.11
Consensus pattern (87 bp):
AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAACTACAACTT
AAAGAAGATGCGGCAGCGAGAG
Found at i:58550619 original size:21 final size:21
Alignment explanation
Indices: 58550593--58550651 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
58550583 AGAAGATGCG
* *
58550593 GCAGCGAGAGAAGCAGCGGCT
1 GCAGCGAGGGAAGCAGAGGCT
*
58550614 GCAGCGAGGGAAGTAGAGGCT
1 GCAGCGAGGGAAGCAGAGGCT
58550635 GCAGCGAGGGAAGCAGA
1 GCAGCGAGGGAAGCAGA
58550652 ACAGCATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.31, C:0.19, G:0.46, T:0.05
Consensus pattern (21 bp):
GCAGCGAGGGAAGCAGAGGCT
Found at i:58550881 original size:14 final size:14
Alignment explanation
Indices: 58550862--58550888 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
58550852 TATAGATTTT
58550862 GTTAGATTTGGTTG
1 GTTAGATTTGGTTG
58550876 GTTAGATTTGGTT
1 GTTAGATTTGGTT
58550889 TCTTCTGATT
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:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (14 bp):
GTTAGATTTGGTTG
Found at i:58551017 original size:43 final size:43
Alignment explanation
Indices: 58550956--58551090 Score: 218
Period size: 43 Copynumber: 3.1 Consensus size: 43
58550946 CAAAATTAGC
* *
58550956 GGCGTTTTTTGGCTAAGCGTCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTAGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
58550999 GGCGTTTTTCGTCTAAGCGCCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTAGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
58551042 GGCGTTTTTAGGCTAAGCGCCGCTAAAGACCATGGTCTATA-T
1 GGCGTTTTTAGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
58551084 CGGCGTT
1 -GGCGTT
58551091 GCAAAGAAAA
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
42 1 0.01
43 85 0.99
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (43 bp):
GGCGTTTTTAGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
Found at i:58551439 original size:15 final size:16
Alignment explanation
Indices: 58551414--58551443 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
58551404 CATTTTAACC
58551414 CAAATTAAAAATAATA
1 CAAATTAAAAATAATA
58551430 CAAA-TAAAAATAAT
1 CAAATTAAAAATAAT
58551444 GTCAGATCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (16 bp):
CAAATTAAAAATAATA
Found at i:58552399 original size:24 final size:24
Alignment explanation
Indices: 58552372--58552422 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 24
58552362 AACAGATGGA
58552372 AAACCAGAAA-CAAAGCAAGAATCT
1 AAACCAGAAACCAAA-CAAGAATCT
58552396 AAACCAGAAACCAAACAAGAATCT
1 AAACCAGAAACCAAACAAGAATCT
58552420 AAA
1 AAA
58552423 GAAGTTGAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.61, C:0.22, G:0.10, T:0.08
Consensus pattern (24 bp):
AAACCAGAAACCAAACAAGAATCT
Found at i:58557411 original size:23 final size:24
Alignment explanation
Indices: 58557358--58557413 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
58557348 ACGAATATAC
*
58557358 TAAAATATTAAAATAAATATTTTT
1 TAAAATATAAAAATAAATATTTTT
* * *
58557382 AATAAAT-TAAAAATATATTTTTTT
1 TA-AAATATAAAAATAAATATTTTT
58557406 TAAAATAT
1 TAAAATAT
58557414 CTTTATACTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
23 4 0.16
24 17 0.68
25 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TAAAATATAAAAATAAATATTTTT
Found at i:58558400 original size:60 final size:60
Alignment explanation
Indices: 58558328--58558556 Score: 277
Period size: 59 Copynumber: 3.8 Consensus size: 60
58558318 TTTTTGCGTA
* * *
58558328 ATACCTGAACTTGACACTTTTTTCTAATTTGATATCTATACTTTTTTTGGGCCCAATTT-
1 ATACCTAAACTTGACACTTTTTTCTAATTTGATACCTAAACTTTTTTTGGGCCCAATTTG
* * *
58558387 AGTACCTAAACTTGACACTTTTTCCTAATTTAATACCTAAAC-TTTTTTGAGCCCAATTTG
1 A-TACCTAAACTTGACACTTTTTTCTAATTTGATACCTAAACTTTTTTTGGGCCCAATTTG
* * *
58558447 ATACCTGAACTTGACA-TTTTTTCCTAATTTGGTACCTAAACCTTTTTTTGGCCCCAATTTG
1 ATACCTAAACTTGACACTTTTTT-CTAATTTGATACCTAAA-CTTTTTTTGGGCCCAATTTG
* * *
58558508 ATACCTAAACTTGGCATTTTTTTTCTAATTTGGTACC-AAAGCTTTTTTT
1 ATACCTAAACTTGACA-CTTTTTTCTAATTTGATACCTAAA-CTTTTTTT
58558557 TTTAGGTTCA
Statistics
Matches: 148, Mismatches: 15, Indels: 12
0.85 0.09 0.07
Matches are distributed among these distances:
58 5 0.03
59 46 0.31
60 37 0.25
61 41 0.28
62 13 0.09
63 6 0.04
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (60 bp):
ATACCTAAACTTGACACTTTTTTCTAATTTGATACCTAAACTTTTTTTGGGCCCAATTTG
Found at i:58558417 original size:31 final size:30
Alignment explanation
Indices: 58558382--58558487 Score: 87
Period size: 31 Copynumber: 3.5 Consensus size: 30
58558372 TTTTGGGCCC
58558382 AATTTAGTACCTAAACTTGACACTTTTTCCT
1 AATTTAGTACCTAAACTTGACA-TTTTTCCT
* * *
58558413 AATTTAATACCTAAACTT----TTTTGAGCCC
1 AATTTAGTACCTAAACTTGACATTTT--TCCT
*
58558441 AATTT-GATACCTGAACTTGACATTTTTTCCT
1 AATTTAG-TACCTAAACTTGACA-TTTTTCCT
*
58558472 AATTTGGTACCTAAAC
1 AATTTAGTACCTAAAC
58558488 CTTTTTTTGG
Statistics
Matches: 58, Mismatches: 8, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
26 4 0.07
28 17 0.29
31 32 0.55
32 1 0.02
33 4 0.07
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.41
Consensus pattern (30 bp):
AATTTAGTACCTAAACTTGACATTTTTCCT
Found at i:58558997 original size:29 final size:30
Alignment explanation
Indices: 58558951--58559020 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
58558941 AAAAGATTAG
*
58558951 GTACCAAAATTAGGAAAAAGA-GTCAAGTTTAA
1 GTACC-AAATTA-GAAAAA-ATGTCAAATTTAA
*
58558983 GTACCAAATTA-AAAAAATGTCAAATTTAG
1 GTACCAAATTAGAAAAAATGTCAAATTTAA
58559012 GTACCAAAT
1 GTACCAAAT
58559021 GTGGTATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 1 0.03
29 23 0.66
31 6 0.17
32 5 0.14
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.24
Consensus pattern (30 bp):
GTACCAAATTAGAAAAAATGTCAAATTTAA
Found at i:58563069 original size:28 final size:27
Alignment explanation
Indices: 58563015--58563072 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
58563005 AAAAGATATT
58563015 AAAAAATTATAATTTTATACCTTTTTTA
1 AAAAAATTATAATTTTATA-CTTTTTTA
*
58563043 AAAAAATTGATAATTTTTTA-TTCTTTTA
1 AAAAAATT-ATAATTTTATACTT-TTTTA
58563071 AA
1 AA
58563073 TTTTAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 2 0.07
28 15 0.56
29 10 0.37
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (27 bp):
AAAAAATTATAATTTTATACTTTTTTA
Found at i:58563632 original size:78 final size:78
Alignment explanation
Indices: 58563503--58563659 Score: 233
Period size: 78 Copynumber: 2.0 Consensus size: 78
58563493 AACGATAAGT
* * * * **
58563503 GTCAATTTCAATTATGGAATAAAGTTTAGGTGCTCATTTCGACCAAAAAAATGTTTAGGTTGATA
1 GTCAATTCCAATTATGGAATAAAGTTTAGGTACCCATTTCGACCAAAAAAATATTTAGGTACATA
58563568 ACTCAAACAAATG
66 ACTCAAACAAATG
* * *
58563581 GTCAATTCCAATTATGGAATAAAGTTTAGGTACCCGTTTTGACCAAAAAAATATTTAGGTACCTA
1 GTCAATTCCAATTATGGAATAAAGTTTAGGTACCCATTTCGACCAAAAAAATATTTAGGTACATA
58563646 ACTCAAACAAATG
66 ACTCAAACAAATG
58563659 G
1 G
58563660 CATAGTTTAA
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (78 bp):
GTCAATTCCAATTATGGAATAAAGTTTAGGTACCCATTTCGACCAAAAAAATATTTAGGTACATA
ACTCAAACAAATG
Found at i:58565349 original size:23 final size:23
Alignment explanation
Indices: 58565282--58565352 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
58565272 AAATCCATTA
* *
58565282 ATCGAGAAGCTCCGGATAACCATGT
1 ATCGAGAAGCTCCGGAGAGCCA--T
* * ** *
58565307 ATCGGGAAGTTCAAGCGAGCCAT
1 ATCGAGAAGCTCCGGAGAGCCAT
58565330 ATCGAGAAGCTCCGGAGAGCCAT
1 ATCGAGAAGCTCCGGAGAGCCAT
58565353 TAATCAGAAA
Statistics
Matches: 34, Mismatches: 12, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
23 19 0.56
25 15 0.44
ACGTcount: A:0.31, C:0.24, G:0.28, T:0.17
Consensus pattern (23 bp):
ATCGAGAAGCTCCGGAGAGCCAT
Found at i:58565412 original size:25 final size:25
Alignment explanation
Indices: 58565276--58565412 Score: 79
Period size: 25 Copynumber: 5.5 Consensus size: 25
58565266 CTACGAAAAT
* * * *
58565276 CCATTAATCGAGAAGCTCCGGATAA
1 CCATTAATCGGGAAGCTCCGAAGAG
*
58565301 CCATGT-ATCGGGAAG-TTC-AAGCGAG
1 CCAT-TAATCGGGAAGCTCCGAA--GAG
* *
58565326 CCA-T-ATCGAGAAGCTCCGGAGAG
1 CCATTAATCGGGAAGCTCCGAAGAG
* * * *
58565349 CCATTAATCAGAAAGCTCACAAAAAG
1 CCATTAATCGGGAAGCTC-CGAAGAG
*
58565375 CCTTTAATCGGGAAGCTCCGAAGAG
1 CCATTAATCGGGAAGCTCCGAAGAG
58565400 CCATATAAT-GGGA
1 CCAT-TAATCGGGA
58565413 CACTCATAAG
Statistics
Matches: 83, Mismatches: 20, Indels: 18
0.69 0.17 0.15
Matches are distributed among these distances:
23 16 0.19
24 5 0.06
25 38 0.46
26 24 0.29
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (25 bp):
CCATTAATCGGGAAGCTCCGAAGAG
Found at i:58567052 original size:30 final size:31
Alignment explanation
Indices: 58566995--58567061 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
58566985 TGCCTTAATG
* * ** *
58566995 TAAATATTCAAAATTTATAGGGTC-AAAATA
1 TAAATATGCAAAATTTAAAGGAACAAAAACA
*
58567025 TAAATATGGAAAATTTAAAGGAACAAAAACA
1 TAAATATGCAAAATTTAAAGGAACAAAAACA
58567056 TAAATA
1 TAAATA
58567062 ACTTAAATGT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.57, C:0.06, G:0.10, T:0.27
Consensus pattern (31 bp):
TAAATATGCAAAATTTAAAGGAACAAAAACA
Found at i:58571620 original size:24 final size:24
Alignment explanation
Indices: 58571588--58571738 Score: 83
Period size: 25 Copynumber: 6.1 Consensus size: 24
58571578 TTCAGGTTGT
*
58571588 ATAA-CAAGAAGCTCATAAGAGCC
1 ATAATCAAGAAGCTCAGAAGAGCC
*
58571611 ATAATCAAGAAGCTCATG-CGAGCC
1 ATAATCAAGAAGCTCA-GAAGAGCC
** * * *
58571635 AATAAT-GGGTACCTCCGAAGAGCC
1 -ATAATCAAGAAGCTCAGAAGAGCC
** * *
58571659 ATTAATCGGGAAGCTCCGGAGAGCC
1 A-TAATCAAGAAGCTCAGAAGAGCC
*
58571684 ATTAATCAAGAAGCTCACAAAGAGCC
1 A-TAATCAAGAAGCTCA-GAAGAGCC
* * *
58571710 TTTAATCGAGAAGCTCCAGAAAAGCC
1 -ATAATCAAGAAGCT-CAGAAGAGCC
58571736 ATA
1 ATA
58571739 CATTGGGACG
Statistics
Matches: 98, Mismatches: 21, Indels: 16
0.73 0.16 0.12
Matches are distributed among these distances:
23 6 0.06
24 30 0.31
25 36 0.37
26 24 0.24
27 2 0.02
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (24 bp):
ATAATCAAGAAGCTCAGAAGAGCC
Found at i:58571681 original size:25 final size:25
Alignment explanation
Indices: 58571647--58571737 Score: 110
Period size: 26 Copynumber: 3.6 Consensus size: 25
58571637 TAATGGGTAC
*
58571647 CTCCGAAGAGCCATTAATCGGGAAG
1 CTCCGAAGAGCCATTAATCGAGAAG
* *
58571672 CTCCGGAGAGCCATTAATCAAGAAG
1 CTCCGAAGAGCCATTAATCGAGAAG
* *
58571697 CTCACAAAGAGCCTTTAATCGAGAAG
1 CTC-CGAAGAGCCATTAATCGAGAAG
*
58571723 CTCCAGAAAAGCCAT
1 CTCC-GAAGAGCCAT
58571738 ACATTGGGAC
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
25 26 0.48
26 28 0.52
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.16
Consensus pattern (25 bp):
CTCCGAAGAGCCATTAATCGAGAAG
Found at i:58574144 original size:25 final size:25
Alignment explanation
Indices: 58574125--58574172 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
58574115 AAGCTCTTTT
58574125 GAGCTGAATAACGAGAAGCTCATGC
1 GAGCTGAATAACGAGAAGCTCATGC
*
58574150 GAGCTGAATAACGGGAAGCTCAT
1 GAGCTGAATAACGAGAAGCTCAT
58574173 AAGAGCTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.19, G:0.29, T:0.17
Consensus pattern (25 bp):
GAGCTGAATAACGAGAAGCTCATGC
Found at i:58574178 original size:25 final size:25
Alignment explanation
Indices: 58574125--58574179 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
58574115 AAGCTCTTTT
**
58574125 GAGCTGAATAACGAGAAGCTCATGC
1 GAGCTGAATAACGAGAAGCTCATAA
*
58574150 GAGCTGAATAACGGGAAGCTCATAA
1 GAGCTGAATAACGAGAAGCTCATAA
58574175 GAGCT
1 GAGCT
58574180 ATGGTATGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.16
Consensus pattern (25 bp):
GAGCTGAATAACGAGAAGCTCATAA
Found at i:58578854 original size:21 final size:21
Alignment explanation
Indices: 58578828--58578870 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
58578818 GGTTCGCTGT
*
58578828 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
58578849 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
58578870 A
1 A
58578871 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:58578870 original size:16 final size:16
Alignment explanation
Indices: 58578851--58578883 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
58578841 TGTATTGGAT
*
58578851 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
58578867 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
58578883 T
1 T
58578884 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:58578928 original size:45 final size:44
Alignment explanation
Indices: 58578862--58578956 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
58578852 GGATTAGAGG
* *
58578862 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
58578907 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
58578951 TGTAAT
1 TGTAAT
58578957 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:58579139 original size:18 final size:17
Alignment explanation
Indices: 58579118--58579152 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
58579108 TTATTATTTA
*
58579118 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
58579136 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
58579153 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:58579146 original size:28 final size:27
Alignment explanation
Indices: 58579076--58579148 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
58579066 TTTATTATCA
*
58579076 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
58579104 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
58579131 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
58579149 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:58579265 original size:144 final size:147
Alignment explanation
Indices: 58579037--58579308 Score: 487
Period size: 144 Copynumber: 1.9 Consensus size: 147
58579027 ATGATTATTG
58579037 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
*
58579102 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
58579167 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
*
58579186 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
58579248 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
58579309 ATATTCTTAT
Statistics
Matches: 121, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
144 92 0.76
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:58579283 original size:18 final size:17
Alignment explanation
Indices: 58579262--58579296 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
58579252 TTATTATTAA
*
58579262 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
58579280 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
58579297 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:58579340 original size:54 final size:54
Alignment explanation
Indices: 58579282--58579460 Score: 128
Period size: 55 Copynumber: 3.1 Consensus size: 54
58579272 ATTAAAATAT
*
58579282 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAACC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
** * * * * *
58579336 ATAATATATGATACTGTAAAATAT-AAAATAACATAATTATTATTAAATAT-AATATAATTAAAA
1 ATAAT-T-T-A-A---TAAAAT-TCTTAATAA-TTAA-TATTCTT--ATATGAAT-TTACTCAAA
*
58579399 TAT
53 -AC
*
58579402 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
58579456 ATAAT
1 ATAAT
58579461 ATATGATTAT
Statistics
Matches: 91, Mismatches: 18, Indels: 32
0.65 0.13 0.23
Matches are distributed among these distances:
54 10 0.11
55 11 0.12
56 4 0.04
57 7 0.08
58 5 0.05
59 11 0.12
61 11 0.12
62 5 0.05
63 7 0.08
64 4 0.04
65 11 0.12
66 5 0.05
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (54 bp):
ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
Found at i:58579342 original size:61 final size:61
Alignment explanation
Indices: 58579277--58579464 Score: 190
Period size: 61 Copynumber: 3.1 Consensus size: 61
58579267 TTTTAATTAA
*
58579277 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAACCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * * *
58579338 AATATATGATACT-GTAAAA-T-ATAA-AATAACATAATTATTAT-TAAATATAAT-ATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAATAATTA-AT-ATTCTTATATGAATTTACTCA-AATCAT
58579397 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
58579458 AATATAT
1 AATATAT
58579465 GATTATAACT
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
58 6 0.06
59 29 0.31
60 16 0.17
61 37 0.39
62 6 0.06
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
Found at i:58579375 original size:120 final size:120
Alignment explanation
Indices: 58579245--58579467 Score: 419
Period size: 120 Copynumber: 1.9 Consensus size: 120
58579235 ATCATATTTA
* *
58579245 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
58579310 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
58579365 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
58579430 TATTCTTATATGAATTTACTCAAATCATAATATATGAT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGAT
58579468 TATAACTAAT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 100 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
Found at i:58579403 original size:18 final size:17
Alignment explanation
Indices: 58579382--58579416 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
58579372 TTATTATTAA
58579382 ATATAATATAATTAAAAT
1 ATATAATATAA-TAAAAT
*
58579400 ATATAATTTAATAAAAT
1 ATATAATATAATAAAAT
58579417 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATAATAAAAT
Found at i:58579493 original size:15 final size:15
Alignment explanation
Indices: 58579461--58579509 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 15
58579451 AAATCATAAT
*
58579461 ATATGATTATAACT-A
1 ATATGATT-TAATTAA
58579476 ATATGATTTAATTAAA
1 ATATGATTTAATT-AA
58579492 TATATGATTTAATTAA
1 -ATATGATTTAATTAA
58579508 AT
1 AT
58579510 TTAAAATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 4 0.13
15 10 0.33
16 3 0.10
17 13 0.43
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (15 bp):
ATATGATTTAATTAA
Found at i:58579504 original size:17 final size:17
Alignment explanation
Indices: 58579476--58579509 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
58579466 ATTATAACTA
58579476 ATATGATTTAATTAAAT
1 ATATGATTTAATTAAAT
58579493 ATATGATTTAATTAAAT
1 ATATGATTTAATTAAAT
58579510 TTAAAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
ATATGATTTAATTAAAT
Found at i:58579652 original size:93 final size:91
Alignment explanation
Indices: 58579542--58579735 Score: 275
Period size: 93 Copynumber: 2.1 Consensus size: 91
58579532 GATTATAGTT
* * *
58579542 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTAT-ATAATAATATATAATTTC
* *
58579605 ATAAAATTCTTGATAATAAAAATTTTCTTA
64 ATAAAATTCTT-AAAAT-AAAATGTTCTTA
* *
58579635 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAGTGATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
58579700 AAAATTCTTAAAATAAAATGTTCTTA
66 AAAATTCTTAAAATAAAATGTTCTTA
58579726 TATGAATTTA
1 TATGAATTTA
58579736 CTAAAATCAA
Statistics
Matches: 92, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
91 21 0.23
92 4 0.04
93 63 0.68
94 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (91 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
AAAATTCTTAAAATAAAATGTTCTTA
Found at i:58579727 original size:47 final size:45
Alignment explanation
Indices: 58579592--58579732 Score: 115
Period size: 47 Copynumber: 3.1 Consensus size: 45
58579582 ATTTAATAAT
* *
58579592 AATATATAATTTCATAAAATTCTTGATAATAAAAATTTTCTTATATG
1 AATATATAATTTCATAAAATTCTT-AAAAT-AAAATATTCTTATATG
* * ** * * **
58579639 AATTTATACAATT--TAAAATAATTAATATTAAATATAATTATATAG
1 AATATATA-ATTTCATAAAATTCTTAAAATAAAATATTCTTATAT-G
* *
58579684 TGATATATAATTTCATAAAATTCTTAAAATAAAATGTTCTTATATG
1 -AATATATAATTTCATAAAATTCTTAAAATAAAATATTCTTATATG
58579730 AAT
1 AAT
58579733 TTACTAAAAT
Statistics
Matches: 68, Mismatches: 21, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
44 11 0.16
45 9 0.13
46 15 0.22
47 30 0.44
48 3 0.04
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (45 bp):
AATATATAATTTCATAAAATTCTTAAAATAAAATATTCTTATATG
Found at i:58582960 original size:23 final size:25
Alignment explanation
Indices: 58582912--58582959 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
58582902 AGTTGTAAAG
58582912 AGAAAATTATCTAAAGAGATTATTTT
1 AGAAAATTATCT-AAGAGATTATTTT
58582938 AGAAAATT-TCT-AGAGA-TATTTT
1 AGAAAATTATCTAAGAGATTATTTT
58582960 TCTTATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
25 3 0.14
26 8 0.36
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (25 bp):
AGAAAATTATCTAAGAGATTATTTT
Found at i:58584592 original size:40 final size:40
Alignment explanation
Indices: 58584546--58584655 Score: 211
Period size: 40 Copynumber: 2.8 Consensus size: 40
58584536 CATCAATATT
58584546 AAACATTTATACATTATATCATGACATTAATGAACCTATG
1 AAACATTTATACATTATATCATGACATTAATGAACCTATG
*
58584586 ACACATTTATACATTATATCATGACATTAATGAACCTATG
1 AAACATTTATACATTATATCATGACATTAATGAACCTATG
58584626 AAACATTTATACATTATATCATGACATTAA
1 AAACATTTATACATTATATCATGACATTAA
58584656 ATAACCATAT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 68 1.00
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.35
Consensus pattern (40 bp):
AAACATTTATACATTATATCATGACATTAATGAACCTATG
Found at i:58590329 original size:5 final size:5
Alignment explanation
Indices: 58590319--58590371 Score: 54
Period size: 5 Copynumber: 10.0 Consensus size: 5
58590309 GTCTACCTGC
58590319 AAAAT AAAAT AAAAT AGAAAT AAGAA- AAAAT AAAAAT AAAAAT AAAAT
1 AAAAT AAAAT AAAAT A-AAAT AA-AAT AAAAT -AAAAT -AAAAT AAAAT
*
58590367 GAAAT
1 AAAAT
58590372 GTGTAATTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
4 2 0.05
5 23 0.53
6 18 0.42
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:58590341 original size:16 final size:16
Alignment explanation
Indices: 58590320--58590371 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
58590310 TCTACCTGCA
58590320 AAATAAAATAAAATAG
1 AAATAAAATAAAATAG
*
58590336 AAATAAGAA-AAAATAA
1 AAATAA-AATAAAATAG
58590352 AAATAAAAATAAAAT-G
1 AAAT-AAAATAAAATAG
58590368 AAAT
1 AAAT
58590372 GTGTAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 22 0.71
17 9 0.29
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (16 bp):
AAATAAAATAAAATAG
Found at i:58596311 original size:13 final size:13
Alignment explanation
Indices: 58596293--58596319 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58596283 GTAAAATATT
58596293 TCACATCATCAGG
1 TCACATCATCAGG
58596306 TCACATCATCAGG
1 TCACATCATCAGG
58596319 T
1 T
58596320 GATTATATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.26
Consensus pattern (13 bp):
TCACATCATCAGG
Found at i:58600596 original size:61 final size:61
Alignment explanation
Indices: 58600501--58600621 Score: 188
Period size: 61 Copynumber: 2.0 Consensus size: 61
58600491 TTTGGGAAGT
* * * *
58600501 GAAACTAATTGACATACCAACTATCGTTTTGTTTCATTGTTGGGGGAATTAAGTTAAAAGG
1 GAAACTAATTGACACACCAACTAACGTTTTGTTTCACTGTTGGGGGAATTAAATTAAAAGG
* *
58600562 GAAACTAATTGACACACCAAGTAACGTTTTGTTTCACTGTTTGGGGAATTAAATTAAAAG
1 GAAACTAATTGACACACCAACTAACGTTTTGTTTCACTGTTGGGGGAATTAAATTAAAAG
58600622 AGCAACTTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (61 bp):
GAAACTAATTGACACACCAACTAACGTTTTGTTTCACTGTTGGGGGAATTAAATTAAAAGG
Found at i:58604076 original size:31 final size:29
Alignment explanation
Indices: 58604033--58604122 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 29
58604023 AATATATTTA
*
58604033 TTTTTTAAATTTTTTTAATTTTAAAATACT
1 TTTTTTATATTTTTTTAATTTTAAAATA-T
58604063 TTTTTTAT-TATTTTTTAATTTTAAAATAT
1 TTTTTTATAT-TTTTTTAATTTTAAAATAT
**
58604092 TTTTAAAATACTTTTTTTAATTTTTAAAATA
1 TTTT-TTATA-TTTTTTTAA-TTTTAAAATA
58604123 AATTTTTGGT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
29 6 0.12
30 27 0.52
31 8 0.15
32 11 0.21
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (29 bp):
TTTTTTATATTTTTTTAATTTTAAAATAT
Found at i:58604094 original size:17 final size:17
Alignment explanation
Indices: 58604022--58604097 Score: 61
Period size: 17 Copynumber: 4.7 Consensus size: 17
58604012 CAGATATAAT
* * *
58604022 AAATATATTTATTTTTT
1 AAATATTTTTAATTTTA
*
58604039 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
*
58604056 AAATA-CTTT--TTTTA
1 AAATATTTTTAATTTTA
**
58604070 TTAT-TTTTTAATTTTA
1 AAATATTTTTAATTTTA
58604086 AAATATTTTTAA
1 AAATATTTTTAA
58604098 AATACTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
14 10 0.23
16 10 0.23
17 24 0.55
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:58604128 original size:21 final size:21
Alignment explanation
Indices: 58604090--58604129 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
58604080 ATTTTAAAAT
**
58604090 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
58604111 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
58604130 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:58604136 original size:22 final size:21
Alignment explanation
Indices: 58604089--58604147 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
58604079 AATTTTAAAA
* *
58604089 TATTTTTAAAAT-ACTTTTTT
1 TATTTTTAAAATAAATTTTTG
58604109 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAATAAATTTTT-G
58604132 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
58604148 GGGCCGGGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.33
22 14 0.42
23 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:58605319 original size:37 final size:37
Alignment explanation
Indices: 58605229--58605305 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 37
58605219 TGTAGTGGAT
*
58605229 ACAAGCTT-GAAAATTAAGTCGAATAAAATTAAGTCAA
1 ACAAGCTTCG-AAATTAAGTCGAATAAAAATAAGTCAA
58605266 ACAAGCTTCGAAATTAAGTCGAATAAAAATAAGTCAA
1 ACAAGCTTCGAAATTAAGTCGAATAAAAATAAGTCAA
58605303 ACA
1 ACA
58605306 TTTGCTATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.22
Consensus pattern (37 bp):
ACAAGCTTCGAAATTAAGTCGAATAAAAATAAGTCAA
Found at i:58608090 original size:31 final size:31
Alignment explanation
Indices: 58608049--58608121 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
58608039 CACCGTAAAA
* * *
58608049 ATTTGAAGCAAATAACCCATTTCGGTATTTC
1 ATTTGTAGCAAACAACCCATTTCGGTAATTC
* *
58608080 TTTTGTAGCAAACGACCCATTTCGGTAATTC
1 ATTTGTAGCAAACAACCCATTTCGGTAATTC
58608111 ATTTGTA-CAAA
1 ATTTGTAGCAAA
58608122 ACGTACCATT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 4 0.11
31 32 0.89
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (31 bp):
ATTTGTAGCAAACAACCCATTTCGGTAATTC
Found at i:58608124 original size:31 final size:32
Alignment explanation
Indices: 58608063--58608132 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 32
58608053 GAAGCAAATA
* *
58608063 ACCCATTTCGGTATTTCTTTTGTAGCAAACG-
1 ACCCATTTCGGTAATTCATTTGTAGCAAACGT
58608094 ACCCATTTCGGTAATTCATTTGTA-CAAAACGT
1 ACCCATTTCGGTAATTCATTTGTAGC-AAACGT
58608126 A-CCATTT
1 ACCCATTT
58608133 TGATAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 1 0.03
31 33 0.94
32 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (32 bp):
ACCCATTTCGGTAATTCATTTGTAGCAAACGT
Found at i:58615486 original size:13 final size:14
Alignment explanation
Indices: 58615455--58615489 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
58615445 AAATAACTAA
58615455 AATTTTATATTGAT
1 AATTTTATATTGAT
*
58615469 AATTTTATATT-TT
1 AATTTTATATTGAT
58615482 AATTTTAT
1 AATTTTAT
58615490 TATGCACACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
AATTTTATATTGAT
Found at i:58616655 original size:32 final size:31
Alignment explanation
Indices: 58616601--58616661 Score: 113
Period size: 31 Copynumber: 1.9 Consensus size: 31
58616591 ATTTTTTGAC
58616601 ATAATTTGATCTTTATACTTTTATAATGTCA
1 ATAATTTGATCTTTATACTTTTATAATGTCA
58616632 ATAATTTGATCTTTATACTTTTTATAATGT
1 ATAATTTGATCTTTATAC-TTTTATAATGT
58616662 TATTAGTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 18 0.62
32 11 0.38
ACGTcount: A:0.31, C:0.08, G:0.07, T:0.54
Consensus pattern (31 bp):
ATAATTTGATCTTTATACTTTTATAATGTCA
Found at i:58626951 original size:72 final size:74
Alignment explanation
Indices: 58626836--58627006 Score: 204
Period size: 74 Copynumber: 2.3 Consensus size: 74
58626826 AATAAGAATA
* * *
58626836 AAATAAAGGAAAAATGCAAAAAAAAAAAGAGAGTAGGAAATAAAATGAAGGAAGAAATTGC-TAA
1 AAAT-AAGG-AAAATGCAAAAAAAAAAAGAGAGAAGGAAATAAAATAAAGGAA-AAATTGCAAAA
58626900 GTATAGGAAATG
63 GTATAGGAAATG
*
58626912 AAATAAGGAAAATGCAAAAAAAAAAA-A-AGAAGGAAATAAAATAAAGGAAAAATTTCAAAAAAG
1 AAATAAGGAAAATGCAAAAAAAAAAAGAGAGAAGGAAATAAAATAAAGGAAAAATTGC--AAAAG
58626975 TATAGGAAATG
64 TATAGGAAATG
* * * *
58626986 GAATAGGGGAAATGTAAAAAA
1 AAATAAGGAAAATGCAAAAAA
58627007 TGGAGATGTA
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
71 6 0.07
72 20 0.24
73 1 0.01
74 49 0.58
75 4 0.05
76 4 0.05
ACGTcount: A:0.63, C:0.02, G:0.20, T:0.14
Consensus pattern (74 bp):
AAATAAGGAAAATGCAAAAAAAAAAAGAGAGAAGGAAATAAAATAAAGGAAAAATTGCAAAAGTA
TAGGAAATG
Found at i:58629049 original size:16 final size:16
Alignment explanation
Indices: 58629028--58629061 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58629018 AAAGTCTAAA
* *
58629028 TTTGATTTATCAATAT
1 TTTGATATAACAATAT
58629044 TTTGATATAACAATAT
1 TTTGATATAACAATAT
58629060 TT
1 TT
58629062 AAAATTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (16 bp):
TTTGATATAACAATAT
Found at i:58630763 original size:31 final size:28
Alignment explanation
Indices: 58630727--58630783 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 28
58630717 ACTCTCTCAA
*
58630727 CAAAAATTACAAATTAATTTAAAATAATTTT
1 CAAAAATT-CAAAAT-ATTTAAAA-AATTTT
58630758 CAAAAATTCAAAATATTTAAAAAATT
1 CAAAAATTCAAAATATTTAAAAAATT
58630784 ACCAAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 4 0.16
29 8 0.32
30 5 0.20
31 8 0.32
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (28 bp):
CAAAAATTCAAAATATTTAAAAAATTTT
Found at i:58630828 original size:21 final size:21
Alignment explanation
Indices: 58630804--58630863 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
58630794 TATTTTTTTT
*
58630804 AAAATTTATAAAATTTATAAA
1 AAAATTTAAAAAATTTATAAA
*
58630825 AAAATTCTAAAAAATATAT-AA
1 AAAATT-TAAAAAATTTATAAA
58630846 AAAA-TTAAAAAATTTATA
1 AAAATTTAAAAAATTTATA
58630864 GATCAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 11 0.32
20 1 0.03
21 12 0.35
22 10 0.29
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATTTAAAAAATTTATAAA
Found at i:58630958 original size:13 final size:13
Alignment explanation
Indices: 58630940--58630964 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58630930 TTTAGCAATG
58630940 CTTTTGAAAAGTA
1 CTTTTGAAAAGTA
58630953 CTTTTGAAAAGT
1 CTTTTGAAAAGT
58630965 TTAATTTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (13 bp):
CTTTTGAAAAGTA
Found at i:58636520 original size:41 final size:41
Alignment explanation
Indices: 58636418--58636534 Score: 143
Period size: 41 Copynumber: 3.0 Consensus size: 41
58636408 CCTGATCGGA
* *
58636418 TAATTCGAAGTAATAAATTGACACCCAGTGTCTCATCG-GC
1 TAATTCGAAGTAGTAAATTGACACCCAGTGTCTCATCGAAC
** ** *
58636458 TAAACCG-A--AGTAAATTGACACCCAGTACCTCATCGAAT
1 TAATTCGAAGTAGTAAATTGACACCCAGTGTCTCATCGAAC
58636496 TAATTCGAAGTAGTAAATTGACACCCAGTGTCTCATCGA
1 TAATTCGAAGTAGTAAATTGACACCCAGTGTCTCATCGA
58636535 CTCGAAGTCG
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
37 24 0.39
38 5 0.08
39 2 0.03
40 5 0.08
41 26 0.42
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (41 bp):
TAATTCGAAGTAGTAAATTGACACCCAGTGTCTCATCGAAC
Found at i:58637424 original size:4 final size:4
Alignment explanation
Indices: 58637415--58637473 Score: 63
Period size: 4 Copynumber: 15.2 Consensus size: 4
58637405 AAGGCCGTGG
*
58637415 CTTT CTTT C-TT CTTT CTCTT -TTT CTTT CCTTT TTTT C-TT -TTT CTTT
1 CTTT CTTT CTTT CTTT CT-TT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT
58637461 CTTT CTTT CTTT C
1 CTTT CTTT CTTT C
58637474 CAATTTCGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
3 9 0.19
4 32 0.68
5 6 0.13
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:58637440 original size:19 final size:19
Alignment explanation
Indices: 58637416--58637470 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 19
58637406 AGGCCGTGGC
58637416 TTTCTTTCTTCTTTCTCTT
1 TTTCTTTCTTCTTTCTCTT
*
58637435 TTTCTTTCCTT-TTTTTCTT
1 TTTCTTT-CTTCTTTCTCTT
58637454 TTTCTTTCTTTCTTTCT
1 TTTCTTTC-TTCTTTCT
58637471 TTCCAATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 1 0.03
19 23 0.74
20 7 0.23
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTCTTTCTTCTTTCTCTT
Found at i:58645430 original size:41 final size:41
Alignment explanation
Indices: 58645317--58645433 Score: 109
Period size: 41 Copynumber: 3.0 Consensus size: 41
58645307 CCTGATCAGA
* * * * *
58645317 TAATTCGAAGTAATAAATTGACACACAGTCTCTCATCG-GT
1 TAATCCGAAGTAGTAAATTGACACCCAGTGTCTCATCGAAT
* ** *
58645357 TAAACC-AA--AGTAAATT-AGCACCCAAAGCCTCATCGAAT
1 TAATCCGAAGTAGTAAATTGA-CACCCAGTGTCTCATCGAAT
58645395 TAATCCGAAGTAGTAAATTGACACCCAGTGTCTCATCGA
1 TAATCCGAAGTAGTAAATTGACACCCAGTGTCTCATCGA
58645434 CTCGAAGTCG
Statistics
Matches: 58, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
36 1 0.02
37 19 0.33
38 6 0.10
39 4 0.07
40 4 0.07
41 23 0.40
42 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (41 bp):
TAATCCGAAGTAGTAAATTGACACCCAGTGTCTCATCGAAT
Found at i:58646335 original size:6 final size:6
Alignment explanation
Indices: 58646311--58646398 Score: 72
Period size: 6 Copynumber: 14.3 Consensus size: 6
58646301 AGGCCGTGAC
* * * *
58646311 TTTCTT TCTTCTT TCTCTT TTTC-T TTCCTT TTTCTT TTTC-T TTCCTG
1 TTTCTT T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* *
58646358 TTTCGTT TTGCTTT GTTTCTT TTTCTT TTTCTA TTTCTT TT
1 TTTC-TT TTTC-TT -TTTCTT TTTCTT TTTCTT TTTCTT TT
58646399 ATTTATTTGT
Statistics
Matches: 64, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
5 8 0.12
6 39 0.61
7 14 0.22
8 3 0.05
ACGTcount: A:0.01, C:0.20, G:0.05, T:0.74
Consensus pattern (6 bp):
TTTCTT
Found at i:58646341 original size:17 final size:17
Alignment explanation
Indices: 58646311--58646356 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
58646301 AGGCCGTGAC
58646311 TTTCTTTCTTCTTTCTCTT
1 TTTCTTTC--CTTTCTCTT
*
58646330 TTTCTTTCCTTTTTCTT
1 TTTCTTTCCTTTCTCTT
58646347 TTTCTTTCCT
1 TTTCTTTCCT
58646357 GTTTCGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 18 0.69
19 8 0.31
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTCTTTCCTTTCTCTT
Found at i:58646345 original size:23 final size:23
Alignment explanation
Indices: 58646310--58646353 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
58646300 AAGGCCGTGA
58646310 CTTTCTTTCTTCTTTCTCTTTTT
1 CTTTCTTTCTTCTTTCTCTTTTT
*
58646333 CTTTCCTTT-TTCTTTTTCTTT
1 CTTT-CTTTCTTCTTTCTCTTT
58646354 CCTGTTTCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (23 bp):
CTTTCTTTCTTCTTTCTCTTTTT
Found at i:58646361 original size:17 final size:17
Alignment explanation
Indices: 58646326--58646385 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
58646316 TTCTTCTTTC
*
58646326 TCTTTTTCTTTCCTTTT
1 TCTTTTTCTTTCCTGTT
58646343 TCTTTTTCTTTCCTGTT
1 TCTTTTTCTTTCCTGTT
*
58646360 TCGTTTTGC-TT--TGTT
1 TC-TTTTTCTTTCCTGTT
58646375 TCTTTTTCTTT
1 TCTTTTTCTTT
58646386 TTCTATTTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
14 5 0.13
15 8 0.21
17 20 0.53
18 5 0.13
ACGTcount: A:0.00, C:0.20, G:0.07, T:0.73
Consensus pattern (17 bp):
TCTTTTTCTTTCCTGTT
Found at i:58646681 original size:15 final size:15
Alignment explanation
Indices: 58646661--58646690 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
58646651 CAATTAGCTT
58646661 CGTAAATATTTTTAA
1 CGTAAATATTTTTAA
58646676 CGTAAATATTTTTAA
1 CGTAAATATTTTTAA
58646691 AAAATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (15 bp):
CGTAAATATTTTTAA
Found at i:58650249 original size:17 final size:17
Alignment explanation
Indices: 58650223--58650283 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
58650213 CCATATATAA
*
58650223 TAAATATTTTTATTTTT
1 TAAATTTTTTTATTTTT
*
58650240 TAAATTTTTTTAATTTT
1 TAAATTTTTTTATTTTT
*
58650257 AAATTATTTTTTTATTTTT
1 TAA--ATTTTTTTATTTTT
*
58650276 TTAATTTT
1 TAAATTTT
58650284 AAAATATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 22 0.61
19 14 0.39
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TAAATTTTTTTATTTTT
Found at i:58650273 original size:27 final size:28
Alignment explanation
Indices: 58650232--58650306 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 28
58650222 ATAAATATTT
58650232 TTATTTTTTAAATTTTTTTAATTTTAAA
1 TTATTTTTTAAATTTTTTTAATTTTAAA
*
58650260 TTATTTTTT-TATTTTTTTAATTTTAAA
1 TTATTTTTTAAATTTTTTTAATTTTAAA
* *
58650287 ATATTTTTAAAATATTTTTT
1 TTATTTTTTAAAT-TTTTTT
58650307 TTATTTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
27 24 0.59
28 11 0.27
29 6 0.15
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (28 bp):
TTATTTTTTAAATTTTTTTAATTTTAAA
Found at i:58650275 original size:9 final size:9
Alignment explanation
Indices: 58650229--58650283 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
58650219 ATAATAAATA
58650229 TTTTT-ATT
1 TTTTTAATT
*
58650237 TTTTAAATT
1 TTTTTAATT
58650246 TTTTTAATT
1 TTTTTAATT
*
58650255 TTAAATT-ATT
1 TT--TTTAATT
58650265 TTTTT-ATT
1 TTTTTAATT
58650273 TTTTTAATT
1 TTTTTAATT
58650282 TT
1 TT
58650284 AAAATATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
8 14 0.36
9 18 0.46
10 5 0.13
11 2 0.05
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTAATT
Found at i:58650333 original size:20 final size:20
Alignment explanation
Indices: 58650269--58650347 Score: 76
Period size: 20 Copynumber: 4.1 Consensus size: 20
58650259 ATTATTTTTT
*
58650269 TATTTTTT-TAATTTTAAAA
1 TATTTTTTAAAATTTTAAAA
****
58650288 TA-TTTTTAAAATATTTTTTT
1 TATTTTTTAAAAT-TTTAAAA
58650308 TATTTTTT--AATTTTAAAA
1 TATTTTTTAAAATTTTAAAA
58650326 TATTTTTTAAAATTTTAAAA
1 TATTTTTTAAAATTTTAAAA
58650346 TA
1 TA
58650348 AAATTTTGAT
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
18 16 0.35
19 8 0.17
20 17 0.37
21 5 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTTAAAATTTTAAAA
Found at i:58650333 original size:39 final size:38
Alignment explanation
Indices: 58650253--58650338 Score: 138
Period size: 38 Copynumber: 2.2 Consensus size: 38
58650243 ATTTTTTTAA
*
58650253 TTTTAAATTATTTTTTTATTTTTTTAATTTTAAAATAT
1 TTTTAAAATATTTTTTTATTTTTTTAATTTTAAAATAT
58650291 TTTTAAAATATTTTTTT-TATTTTTTAATTTTAAAATATT
1 TTTTAAAATATTTTTTTAT-TTTTTTAATTTTAAAATA-T
58650330 TTTTAAAAT
1 TTTTAAAAT
58650339 TTTAAAATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
37 1 0.02
38 34 0.76
39 10 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (38 bp):
TTTTAAAATATTTTTTTATTTTTTTAATTTTAAAATAT
Found at i:58650341 original size:26 final size:27
Alignment explanation
Indices: 58650291--58650343 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
58650281 TTTAAAATAT
* **
58650291 TTTTAAAATATTTTTTTTATTTTTTAA
1 TTTTAAAATATTTTTTTAAAATTTTAA
58650318 TTTTAAAATA-TTTTTTAAAATTTTAA
1 TTTTAAAATATTTTTTTAAAATTTTAA
58650344 AATAAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTAAAATATTTTTTTAAAATTTTAA
Found at i:58662570 original size:21 final size:20
Alignment explanation
Indices: 58662530--58662570 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
58662520 TAACTTTTTC
*
58662530 AAATATAATATTATTTTAAT
1 AAATATAATATTAATTTAAT
*
58662550 AAATTTAATATTTAATTTAAT
1 AAATATAATA-TTAATTTAAT
58662571 TTAATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AAATATAATATTAATTTAAT
Found at i:58662637 original size:30 final size:30
Alignment explanation
Indices: 58662601--58662698 Score: 117
Period size: 30 Copynumber: 3.2 Consensus size: 30
58662591 TATTTTATTA
58662601 ATTTAATATTAATGTGAGTTATTAAATTTG
1 ATTTAATATTAATGTGAGTTATTAAATTTG
* * * ** *
58662631 ATTTAATATTTATCTTGATATTATTTTA-TTA
1 ATTTAATATTAAT-GTGA-GTTATTAAATTTG
58662662 ATTTAATATTAATGTGAGTTATTAAATTTG
1 ATTTAATATTAATGTGAGTTATTAAATTTG
58662692 ATTTAAT
1 ATTTAAT
58662699 TTTTATCTTG
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
29 6 0.11
30 24 0.45
31 17 0.32
32 6 0.11
ACGTcount: A:0.36, C:0.01, G:0.09, T:0.54
Consensus pattern (30 bp):
ATTTAATATTAATGTGAGTTATTAAATTTG
Found at i:58662650 original size:61 final size:61
Alignment explanation
Indices: 58662558--58662735 Score: 311
Period size: 61 Copynumber: 2.9 Consensus size: 61
58662548 ATAAATTTAA
* *
58662558 TATTTAATTTAATTTAATTTTTTATCTTGATAGTATTTTATTAATTTAATATTAATGTGAGT
1 TATTAAATTTGATTTAA-TTTTTATCTTGATAGTATTTTATTAATTTAATATTAATGTGAGT
* *
58662620 TATTAAATTTGATTTAATATTTATCTTGATATTATTTTATTAATTTAATATTAATGTGAGT
1 TATTAAATTTGATTTAATTTTTATCTTGATAGTATTTTATTAATTTAATATTAATGTGAGT
58662681 TATTAAATTTGATTTAATTTTTATCTTGATAGTATTTTATTAATTTAATATTAAT
1 TATTAAATTTGATTTAATTTTTATCTTGATAGTATTTTATTAATTTAATATTAAT
58662736 CTAAGTAATT
Statistics
Matches: 110, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
61 95 0.86
62 15 0.14
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (61 bp):
TATTAAATTTGATTTAATTTTTATCTTGATAGTATTTTATTAATTTAATATTAATGTGAGT
Found at i:58666230 original size:19 final size:19
Alignment explanation
Indices: 58666203--58666239 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
58666193 TTGAACTTAG
* *
58666203 TAAATCTTAATTGATTAAT
1 TAAAACTTAATTAATTAAT
58666222 TAAAACTTAATTAATTAA
1 TAAAACTTAATTAATTAA
58666240 ACATTAAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (19 bp):
TAAAACTTAATTAATTAAT
Found at i:58667086 original size:41 final size:42
Alignment explanation
Indices: 58667035--58667128 Score: 147
Period size: 42 Copynumber: 2.3 Consensus size: 42
58667025 TATATTTAAA
58667035 AATTTTAATTTTTATTAAAAA-ATATAAA-AAAATATTTTTT
1 AATTTTAATTTTTATTAAAAACATATAAATAAAATATTTTTT
* * *
58667075 AATTTTAAATTTTATTAAAAACTTATAAATAACATATTTTTT
1 AATTTTAATTTTTATTAAAAACATATAAATAAAATATTTTTT
58667117 AATTTTAATTTT
1 AATTTTAATTTT
58667129 AATTTTTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 20 0.42
41 6 0.12
42 22 0.46
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (42 bp):
AATTTTAATTTTTATTAAAAACATATAAATAAAATATTTTTT
Found at i:58667129 original size:41 final size:39
Alignment explanation
Indices: 58667035--58667129 Score: 136
Period size: 40 Copynumber: 2.3 Consensus size: 39
58667025 TATATTTAAA
58667035 AATTTTAATTTTTATTAAAAAATATAAAAAAATATTTTTT
1 AATTTTAA-TTTTATTAAAAAATATAAAAAAATATTTTTT
* *
58667075 AATTTTAAATTTTATTAAAAACTTATAAATAACATATTTTTT
1 AATTTT-AATTTTATTAAAAA-ATATAAA-AAAATATTTTTT
58667117 AATTTTAATTTTA
1 AATTTTAATTTTA
58667130 ATTTTTTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
40 18 0.36
41 15 0.30
42 17 0.34
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (39 bp):
AATTTTAATTTTATTAAAAAATATAAAAAAATATTTTTT
Found at i:58667193 original size:28 final size:28
Alignment explanation
Indices: 58667132--58667203 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 28
58667122 TAATTTTAAT
*
58667132 TTTTTATTATTTTTAAAAGTTTTAAATTA
1 TTTTTA-TATTTTTAAAAGTTTTAAAATA
58667161 TTTTTACTATTTTTAAAA-TTTTAAAATA
1 TTTTTA-TATTTTTAAAAGTTTTAAAATA
58667189 TTTTTATATTGTTTA
1 TTTTTATATT-TTTA
58667204 TAATATTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
27 4 0.10
28 19 0.47
29 17 0.43
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (28 bp):
TTTTTATATTTTTAAAAGTTTTAAAATA
Found at i:58667295 original size:19 final size:20
Alignment explanation
Indices: 58667271--58667328 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
58667261 ATTTTTATAA
58667271 TTTTTTAT-AA-TTTATATG
1 TTTTTTATAAATTTTATATG
*
58667289 TTGTTTTCTAAATTTTATATG
1 TT-TTTTATAAATTTTATATG
*
58667310 TTTTTT-TGAATTTTTATAT
1 TTTTTTAT-AAATTTTATAT
58667329 ATTTATTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 2 0.06
19 6 0.18
20 16 0.47
21 10 0.29
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (20 bp):
TTTTTTATAAATTTTATATG
Found at i:58667305 original size:21 final size:20
Alignment explanation
Indices: 58667281--58667339 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
58667271 TTTTTTATAA
58667281 TTTATATGTTGTTTTCT-AAAT
1 TTTATATGTT-TTTT-TGAAAT
*
58667302 TTTATATGTTTTTTTGAATT
1 TTTATATGTTTTTTTGAAAT
*
58667322 TTTATATATTTATTTTGA
1 TTTATATGTTT-TTTTGA
58667340 TTTATATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.03
20 17 0.50
21 16 0.47
ACGTcount: A:0.24, C:0.02, G:0.08, T:0.66
Consensus pattern (20 bp):
TTTATATGTTTTTTTGAAAT
Found at i:58667324 original size:20 final size:20
Alignment explanation
Indices: 58667301--58667353 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
58667291 GTTTTCTAAA
*
58667301 TTTTATATGTTTTTTTGAAT
1 TTTTATATATTTTTTTGAAT
58667321 TTTTATATATTTATTTTG-AT
1 TTTTATATATTT-TTTTGAAT
*
58667341 TTATATATATTTT
1 TTTTATATATTTT
58667354 AATGTGTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 1 0.03
20 24 0.80
21 5 0.17
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.70
Consensus pattern (20 bp):
TTTTATATATTTTTTTGAAT
Found at i:58674190 original size:19 final size:19
Alignment explanation
Indices: 58674168--58674216 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
58674158 ATTAGAATTT
58674168 TTTTATAAAAA-ATAATAAA
1 TTTTATAAAAACATAA-AAA
58674187 TTTTAATAAAAACATAAAAA
1 TTTT-ATAAAAACATAAAAA
**
58674207 AATTATAAAA
1 TTTTATAAAA
58674217 TTTTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 10 0.38
20 12 0.46
21 4 0.15
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TTTTATAAAAACATAAAAA
Found at i:58674225 original size:29 final size:30
Alignment explanation
Indices: 58674174--58674242 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
58674164 ATTTTTTTAT
58674174 AAAAAATAATAAATTTTAATAAAAA-CATA
1 AAAAAATAATAAATTTTAATAAAAATCATA
* *
58674203 AAAAAATTATAAAATTTT-TTAAAAATCATA
1 AAAAAATAAT-AAATTTTAATAAAAATCATA
*
58674233 AAAAATTAAT
1 AAAAAATAAT
58674243 GACCTTTAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.44
30 19 0.56
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (30 bp):
AAAAAATAATAAATTTTAATAAAAATCATA
Found at i:58674430 original size:20 final size:22
Alignment explanation
Indices: 58674402--58674446 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
58674392 GAAATTTATA
* *
58674402 TTTCTTTAC-ATTTTATATAAT
1 TTTCTTTACTACTTTATAAAAT
58674423 TTTC-TTACTACTTTATAAAAT
1 TTTCTTTACTACTTTATAAAAT
58674444 TTT
1 TTT
58674447 ATAGTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTCTTTACTACTTTATAAAAT
Found at i:58674475 original size:60 final size:60
Alignment explanation
Indices: 58674395--58674524 Score: 147
Period size: 59 Copynumber: 2.2 Consensus size: 60
58674385 TTTTTATGAA
* * * * *
58674395 ATTTATATTTCTTTACATTTTATATAATTTTCTTACTA-CTTTATAAAATTTTATAGTTTTT
1 ATTTATATTTCTATACA-TTT-TAGAATTTTCTTACGATCTTTATAAAATTTTACAATTTTT
* * *
58674456 -TTTATATTTCTATATATTTTAGAATTTTTTTACGATTTTTATAAAATTTTACAATTTTT
1 ATTTATATTTCTATACATTTTAGAATTTTCTTACGATCTTTATAAAATTTTACAATTTTT
*
58674515 ATATATATTT
1 ATTTATATTT
58674525 TACGATTTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
58 13 0.22
59 23 0.40
60 22 0.38
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (60 bp):
ATTTATATTTCTATACATTTTAGAATTTTCTTACGATCTTTATAAAATTTTACAATTTTT
Found at i:58674505 original size:20 final size:20
Alignment explanation
Indices: 58674482--58674537 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
58674472 TTTTAGAATT
58674482 TTTTTACGATTTTTATAAAA
1 TTTTTACGATTTTTATAAAA
* *
58674502 -TTTTACAATTTTTAT-ATA
1 TTTTTACGATTTTTATAAAA
58674520 TATTTTACGATTTTTATA
1 T-TTTTACGATTTTTATA
58674538 TTTTTTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.07
19 14 0.47
20 14 0.47
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (20 bp):
TTTTTACGATTTTTATAAAA
Found at i:58674526 original size:30 final size:29
Alignment explanation
Indices: 58674434--58674526 Score: 82
Period size: 30 Copynumber: 3.1 Consensus size: 29
58674424 TTCTTACTAC
* * *
58674434 TTTATAAAATTTTATAGTTTTTTTTATAT
1 TTTATAAAATTTTACAATTTTTTATATAT
* * *
58674463 TTCTAT-ATATTTTAGAATTTTTT-TACGATT
1 TT-TATAAAATTTTACAATTTTTTATA-TA-T
58674493 TTTATAAAATTTTACAATTTTTATATATAT
1 TTTATAAAATTTTACAATTTTT-TATATAT
58674523 TTTA
1 TTTA
58674527 CGATTTTTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
28 2 0.04
29 20 0.39
30 25 0.49
31 2 0.04
32 2 0.04
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (29 bp):
TTTATAAAATTTTACAATTTTTTATATAT
Found at i:58674538 original size:20 final size:20
Alignment explanation
Indices: 58674483--58674538 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
58674473 TTTAGAATTT
58674483 TTTTACGATTTTTATA-AAA
1 TTTTACGATTTTTATATAAA
* *
58674502 TTTTACAATTTTTATATATA
1 TTTTACGATTTTTATATAAA
58674522 TTTTACGATTTTTATAT
1 TTTTACGATTTTTATAT
58674539 TTTTTATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (20 bp):
TTTTACGATTTTTATATAAA
Found at i:58674581 original size:10 final size:9
Alignment explanation
Indices: 58674454--58674598 Score: 64
Period size: 9 Copynumber: 15.6 Consensus size: 9
58674444 TTTATAGTTT
58674454 TTTTTAT-A
1 TTTTTATAA
*
58674462 TTTCTAT-A
1 TTTTTATAA
*
58674470 TATTTTAGAA
1 T-TTTTATAA
*
58674480 TTTTTTTACGA
1 TTTTTATA--A
58674491 TTTTTATAAA
1 TTTTTAT-AA
* *
58674501 ATTTTACAA
1 TTTTTATAA
58674510 TTTTTATATA
1 TTTTTATA-A
**
58674520 TATTTTACGA
1 T-TTTTATAA
*
58674530 TTTTTATAT
1 TTTTTATAA
58674539 TTTTTATTAAA
1 TTTTTA-T-AA
* *
58674550 ATTTAATAA
1 TTTTTATAA
* *
58674559 TATTTATAG
1 TTTTTATAA
58674568 TTTTTATTAA
1 TTTTTA-TAA
*
58674578 -TTTTA-AT
1 TTTTTATAA
58674585 TTTTTATAA
1 TTTTTATAA
58674594 TTTTT
1 TTTTT
58674599 TTCTAATTTT
Statistics
Matches: 99, Mismatches: 26, Indels: 23
0.67 0.18 0.16
Matches are distributed among these distances:
7 1 0.01
8 13 0.13
9 51 0.52
10 16 0.16
11 17 0.17
12 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:58707764 original size:25 final size:22
Alignment explanation
Indices: 58707706--58707765 Score: 57
Period size: 25 Copynumber: 2.5 Consensus size: 22
58707696 TGCAACCACT
58707706 TTTTATATTAAAATATTTTTTTA
1 TTTT-TATTAAAATATTTTTTTA
* * *
58707729 CTTTAAATAAAATATTATCATTTTA
1 TTTTTATTAAAATATT-T--TTTTA
58707754 TTTTTATTAAAA
1 TTTTTATTAAAA
58707766 ATACATACAG
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
22 10 0.36
23 4 0.14
25 14 0.50
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTTATTAAAATATTTTTTTA
Found at i:58707858 original size:27 final size:27
Alignment explanation
Indices: 58707827--58707880 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
58707817 CCCAAGACCA
*
58707827 GTCACGCCTGTCAGATAGGCACCACTG
1 GTCACGCCTGACAGATAGGCACCACTG
* *
58707854 GTCACGCCTGACAGGTAGGCGCCACTG
1 GTCACGCCTGACAGATAGGCACCACTG
58707881 CCTCTCCCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.20, C:0.33, G:0.30, T:0.17
Consensus pattern (27 bp):
GTCACGCCTGACAGATAGGCACCACTG
Found at i:58708122 original size:59 final size:59
Alignment explanation
Indices: 58708021--58708134 Score: 201
Period size: 59 Copynumber: 1.9 Consensus size: 59
58708011 TTTTTATAAT
* *
58708021 TATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGGTATAAATTGTTGTGTTTGTAA
1 TATTTTAAAATTAATTTATTAGTAATTTAGGATAATGGTATAAATTGTTGTGTTTGTAA
*
58708080 TATTTTAAAATTAATTTATTAGTAATTTAGGATAATGTTATAAATTGTTGTGTTT
1 TATTTTAAAATTAATTTATTAGTAATTTAGGATAATGGTATAAATTGTTGTGTTT
58708135 AGTTTAGTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (59 bp):
TATTTTAAAATTAATTTATTAGTAATTTAGGATAATGGTATAAATTGTTGTGTTTGTAA
Found at i:58708313 original size:27 final size:27
Alignment explanation
Indices: 58708275--58708331 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
58708265 ATTTTGTTCA
** *
58708275 ACCAGTCGCGCCTGTCAGATAGGCTCC
1 ACCAGTCGCGCCTACCAGATAGGCGCC
58708302 ACCAGTCGCGCCTACCAGATAGGCGCC
1 ACCAGTCGCGCCTACCAGATAGGCGCC
58708329 ACC
1 ACC
58708332 TACCCCATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.21, C:0.40, G:0.25, T:0.14
Consensus pattern (27 bp):
ACCAGTCGCGCCTACCAGATAGGCGCC
Found at i:58710748 original size:10 final size:10
Alignment explanation
Indices: 58710716--58710749 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
58710706 ACCCAAGAAG
58710716 TGACTCAAAA
1 TGACTCAAAA
*
58710726 TGATTCGAAAA
1 TGACTC-AAAA
58710737 TGACTCAAAA
1 TGACTCAAAA
58710747 TGA
1 TGA
58710750 TGTTTCAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (10 bp):
TGACTCAAAA
Found at i:58712777 original size:19 final size:18
Alignment explanation
Indices: 58712739--58712777 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
58712729 TATTGATATC
*
58712739 TTTATATTTAATTCATTT
1 TTTATATTTAATTCAGTT
*
58712757 TTTATTATTTAATTTAGTT
1 TTTA-TATTTAATTCAGTT
58712776 TT
1 TT
58712778 GATTCTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTATATTTAATTCAGTT
Found at i:58712797 original size:6 final size:6
Alignment explanation
Indices: 58712786--58712814 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
58712776 TTGATTCTAA
58712786 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
58712815 AAAATTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:58713606 original size:13 final size:13
Alignment explanation
Indices: 58713588--58713612 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58713578 GAAGTGTGGC
58713588 AACATCAATTGGT
1 AACATCAATTGGT
58713601 AACATCAATTGG
1 AACATCAATTGG
58713613 CATATTCGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
AACATCAATTGGT
Found at i:58717099 original size:20 final size:20
Alignment explanation
Indices: 58717074--58717114 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
58717064 GTACACAATT
*
58717074 TCAATGGGTTGGCCAAGATG
1 TCAATGGGTTCGCCAAGATG
58717094 TCAATGGGTTCGCCAAGATG
1 TCAATGGGTTCGCCAAGATG
58717114 T
1 T
58717115 GGATGAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (20 bp):
TCAATGGGTTCGCCAAGATG
Found at i:58718887 original size:66 final size:66
Alignment explanation
Indices: 58718806--58718933 Score: 186
Period size: 66 Copynumber: 1.9 Consensus size: 66
58718796 GCATATTGCT
* * * *
58718806 CAACTTAAAGCGGAGGCAGTATCGAGAGAAGTAGAGGCTCAA-AGAAAATATGAAGAACTCCAAG
1 CAACTTAAAGCGGAGGCAGCAGCGAGAGAAGCAGAGGC-AAATAGAAAATATGAAGAACTCCAAG
58718870 TA
65 TA
* *
58718872 CAACTTAAAGCGGAGGCAGCAGCGAGGGAAGCAGAGGCAAATAGAAAATATGACGAACTCCA
1 CAACTTAAAGCGGAGGCAGCAGCGAGAGAAGCAGAGGCAAATAGAAAATATGAAGAACTCCA
58718934 GCTACAGCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 2 0.04
66 53 0.96
ACGTcount: A:0.43, C:0.17, G:0.27, T:0.12
Consensus pattern (66 bp):
CAACTTAAAGCGGAGGCAGCAGCGAGAGAAGCAGAGGCAAATAGAAAATATGAAGAACTCCAAGT
A
Found at i:58719371 original size:43 final size:42
Alignment explanation
Indices: 58719324--58719552 Score: 253
Period size: 42 Copynumber: 5.4 Consensus size: 42
58719314 GGAAAAATGT
* * *
58719324 CGCTAAAGGTCATGTTTTTTGGCGGCATTTGTGAGGAAAGCGC
1 CGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTG-GGAAAGCGC
* * * * *
58719367 CGCTAAAGGTCATATTCTTTAGTGGTGTTTTTGGAAAAGCGC
1 CGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAGCGC
*
58719409 CGCTAAAAGTCATGTTCTTTAGCGGCGTTTGTGGGAAAGCGC
1 CGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAGCGC
* * * *
58719451 CACTAAAAGTCATGTTC-TTAACAGCGTTTGTGGGAAAGCGC
1 CGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAGCGC
* * * * *
58719492 CGCTGAAGGTCATATTCTTTAGTGGCATTTGTGGGGAAAGCAC
1 CGCTAAAGGTCATGTTCTTTAGCGGCGTTTGT-GGGAAAGCGC
* *
58719535 CGTTAAAGGCCATGTTCT
1 CGCTAAAGGTCATGTTCT
58719553 ATAACGACAT
Statistics
Matches: 154, Mismatches: 30, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
41 35 0.23
42 70 0.45
43 49 0.32
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (42 bp):
CGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAGCGC
Found at i:58719524 original size:83 final size:84
Alignment explanation
Indices: 58719324--58719532 Score: 249
Period size: 83 Copynumber: 2.5 Consensus size: 84
58719314 GGAAAAATGT
* * * * *
58719324 CGCTAAAGGTCATGTTTTTTGGCGGCATTTGTGAGGAAAGCGCCGCTAAAGGTCATATTCTTTAG
1 CGCTAAAGGTCATGTTCTTTAGCGGCATTTGTG-GGAAAGCGCCACTAAAAGTCATATTCTTTAA
** * *
58719389 TGGTGTTTTTGGAAAAGCGC
65 CAGCGTTTGTGGAAAAGCGC
* * *
58719409 CGCTAAAAGTCATGTTCTTTAGCGGCGTTTGTGGGAAAGCGCCACTAAAAGTCATGTTC-TTAAC
1 CGCTAAAGGTCATGTTCTTTAGCGGCATTTGTGGGAAAGCGCCACTAAAAGTCATATTCTTTAAC
*
58719473 AGCGTTTGTGGGAAAGCGC
66 AGCGTTTGTGGAAAAGCGC
* * *
58719492 CGCTGAAGGTCATATTCTTTAGTGGCATTTGTGGGGAAAGC
1 CGCTAAAGGTCATGTTCTTTAGCGGCATTTGT-GGGAAAGC
58719533 ACCGTTAAAG
Statistics
Matches: 105, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
83 45 0.43
84 31 0.30
85 29 0.28
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (84 bp):
CGCTAAAGGTCATGTTCTTTAGCGGCATTTGTGGGAAAGCGCCACTAAAAGTCATATTCTTTAAC
AGCGTTTGTGGAAAAGCGC
Found at i:58721838 original size:21 final size:21
Alignment explanation
Indices: 58721788--58721839 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
58721778 CAATTCTGAA
*
58721788 AATTTTAAAATATCTTAAAAT
1 AATTTTAAAATAACTTAAAAT
* * *
58721809 AAATATAAAATAAGTTAAAAT
1 AATTTTAAAATAACTTAAAAT
*
58721830 ATTTTTAAAA
1 AATTTTAAAA
58721840 ATAATTTGAT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
AATTTTAAAATAACTTAAAAT
Found at i:58722135 original size:11 final size:11
Alignment explanation
Indices: 58722097--58722135 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
58722087 TGAGGTCAAC
*
58722097 ATATTTTAAAA
1 ATATATTAAAA
*
58722108 ATATATAAAAA
1 ATATATTAAAA
58722119 AT-TATTAAAA
1 ATATATTAAAA
58722129 ATATATT
1 ATATATT
58722136 GAAGGTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATATATTAAAA
Found at i:58722219 original size:32 final size:31
Alignment explanation
Indices: 58722154--58722224 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 31
58722144 AATTTGTTGA
* *
58722154 ATTTTTAACATAATTTTAATATTTTATATTT
1 ATTTTTAACATAATTTTAATATTTTAGAATT
* * *
58722185 ATTTTTAATATACTTTTTAATTTTTTAGAATT
1 ATTTTTAACATA-ATTTTAATATTTTAGAATT
*
58722217 ATTGTTAA
1 ATTTTTAA
58722225 GAATTTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 11 0.33
32 22 0.67
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (31 bp):
ATTTTTAACATAATTTTAATATTTTAGAATT
Found at i:58725034 original size:18 final size:18
Alignment explanation
Indices: 58725011--58725048 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
58725001 GCACACGGGC
*
58725011 GTGTGGCTTGGCCTTGTG
1 GTGTGGCTTGGCCGTGTG
58725029 GTGTGGCTTGGCCGTGTG
1 GTGTGGCTTGGCCGTGTG
58725047 GT
1 GT
58725049 ACAAGTCAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.47, T:0.37
Consensus pattern (18 bp):
GTGTGGCTTGGCCGTGTG
Found at i:58726475 original size:21 final size:21
Alignment explanation
Indices: 58726436--58726477 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
58726426 TTTGCCTAAG
* *
58726436 ATATGAATTGGATTGAATTGA
1 ATATGAATTAGATTAAATTGA
*
58726457 ATATGAATTATATTAAATTGA
1 ATATGAATTAGATTAAATTGA
58726478 GTTAAATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (21 bp):
ATATGAATTAGATTAAATTGA
Found at i:58726969 original size:26 final size:26
Alignment explanation
Indices: 58726940--58727012 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
58726930 CTCGATGTAT
58726940 GGCTTTTCGTGAGCTTCCTGATTAAA
1 GGCTTTTCGTGAGCTTCCTGATTAAA
*
58726966 GGCTCTTT-GTGAGCTTCCTGATTAAT
1 GGCT-TTTCGTGAGCTTCCTGATTAAA
* **
58726992 GGC-TCTCCAGAGCTTCCTGAT
1 GGCTTTTCGTGAGCTTCCTGAT
58727013 ATGGCTCGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 2 0.05
25 12 0.29
26 24 0.59
27 3 0.07
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.37
Consensus pattern (26 bp):
GGCTTTTCGTGAGCTTCCTGATTAAA
Found at i:58727078 original size:25 final size:25
Alignment explanation
Indices: 58726951--58727093 Score: 66
Period size: 25 Copynumber: 5.8 Consensus size: 25
58726941 GCTTTTCGTG
* * *
58726951 AGCTTCCTGATTAAAGGCTCTTTGTG
1 AGCTTCCCGATTAATGGCTCTTTG-A
* **
58726977 AGCTTCCTGATTAATGGCTC-TCCA
1 AGCTTCCCGATTAATGGCTCTTTGA
* *
58727001 GAGCTTCCTGA-T-ATGGCTCGCTTGA
1 -AGCTTCCCGATTAATGGCTC-TTTGA
* * * *
58727026 A-CTTCCC-AATATATAGCTATCT-A
1 AGCTTCCCGATTA-ATGGCTCTTTGA
58727049 GAGCTTCCCGATTAATGGCTCTTTGA
1 -AGCTTCCCGATTAATGGCTCTTTGA
* *
58727075 AGCTACCCG-TTATTGGCTC
1 AGCTTCCCGATTAATGGCTC
58727094 GCATGAGCTT
Statistics
Matches: 90, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
22 1 0.01
23 14 0.16
24 13 0.14
25 39 0.43
26 23 0.26
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (25 bp):
AGCTTCCCGATTAATGGCTCTTTGA
Found at i:58730556 original size:23 final size:23
Alignment explanation
Indices: 58730530--58730605 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
58730520 ATAAGTGCAA
58730530 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
58730553 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
58730576 CACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
58730599 CACTGAT
1 CACTGAT
58730606 CAATAACACT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:58732805 original size:12 final size:12
Alignment explanation
Indices: 58732788--58732813 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
58732778 CATGGTTAAA
58732788 CAAGTCAGTGAC
1 CAAGTCAGTGAC
58732800 CAAGTCAGTGAC
1 CAAGTCAGTGAC
58732812 CA
1 CA
58732814 TAACGTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.27, G:0.23, T:0.15
Consensus pattern (12 bp):
CAAGTCAGTGAC
Found at i:58743305 original size:16 final size:16
Alignment explanation
Indices: 58743266--58743328 Score: 58
Period size: 15 Copynumber: 4.0 Consensus size: 16
58743256 TCACATTAGA
*
58743266 AATATAATTAGTTAGTT
1 AATATAATTA-TTTGTT
*
58743283 AA-GTAATTATTTGTT
1 AATATAATTATTTGTT
**
58743298 AATATAATT-TTTGCC
1 AATATAATTATTTGTT
*
58743313 AAAATAATTATTTGTT
1 AATATAATTATTTGTT
58743329 GACATAATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
15 19 0.53
16 15 0.42
17 2 0.06
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (16 bp):
AATATAATTATTTGTT
Found at i:58747070 original size:15 final size:15
Alignment explanation
Indices: 58747050--58747080 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
58747040 ATTAAAACGC
*
58747050 ATTATCTTTTTATTT
1 ATTATCTTTCTATTT
58747065 ATTATCTTTCTATTT
1 ATTATCTTTCTATTT
58747080 A
1 A
58747081 AAAATTAGAA
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:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTATCTTTCTATTT
Found at i:58749123 original size:21 final size:22
Alignment explanation
Indices: 58749097--58749142 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
58749087 TTGTATTCAC
*
58749097 AAAAAATAATATTATTTATATTTA
1 AAAAAAT-A-ATTATATATATTTA
58749121 AAAAAATAAATTATATATATTT
1 AAAAAAT-AATTATATATATTT
58749143 TACTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAAAATAATTATATATATTTA
Found at i:58749133 original size:23 final size:25
Alignment explanation
Indices: 58749080--58749142 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
58749070 TCTTAAATTT
* *
58749080 ATATTATTTGTATTCACAAAAAATA
1 ATATTATTTATATTTACAAAAAATA
58749105 ATATTATTTATATTTA-AAAAAATA
1 ATATTATTTATATTTACAAAAAATA
*
58749129 A-ATTATATATATTT
1 ATATTATTTATATTT
58749143 TACTTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 12 0.34
24 9 0.26
25 14 0.40
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (25 bp):
ATATTATTTATATTTACAAAAAATA
Done.