Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 123 of 189
Found at i:34969911 original size:15 final size:16
Alignment explanation
Indices: 34969891--34969923 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
34969881 TAACTTATTC
34969891 TTTCAAGTT-ATTTAT
1 TTTCAAGTTGATTTAT
*
34969906 TTTCAATTTGATTTAT
1 TTTCAAGTTGATTTAT
34969922 TT
1 TT
34969924 CTAACATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.64
Consensus pattern (16 bp):
TTTCAAGTTGATTTAT
Found at i:34979719 original size:38 final size:37
Alignment explanation
Indices: 34979650--34979722 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
34979640 TTTTCATAAT
* *
34979650 TTCACTTTTTCACTTTTAATCACTATTCAATTCAAAA
1 TTCACTTTTCCACTTTTAATCAATATTCAATTCAAAA
34979687 TTCACTTTTCCA-TTTTCAAGTCAATATTCAATTCAA
1 TTCACTTTTCCACTTTT-AA-TCAATATTCAATTCAA
34979723 TTCAATTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.32, C:0.22, G:0.01, T:0.45
Consensus pattern (37 bp):
TTCACTTTTCCACTTTTAATCAATATTCAATTCAAAA
Found at i:34979890 original size:23 final size:23
Alignment explanation
Indices: 34979857--34979932 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
34979847 ATAAGTGCCA
34979857 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
34979880 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
34979903 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
34979926 CACTGAT
1 CACTGAT
34979933 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:34980414 original size:30 final size:30
Alignment explanation
Indices: 34980380--34980438 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
34980370 TCCTTGACTC
34980380 AAACTTTGGCAAAATTACAATTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
* * * *
34980410 AAACTTTTGCATATTTACACTTTTGCCCC
1 AAACTTTGGCAAAATTACAATTTTGCCCC
34980439 AAAGCTCGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCCCCT
Found at i:34981445 original size:14 final size:14
Alignment explanation
Indices: 34981418--34981452 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
34981408 TAGCCTAGAT
34981418 TAATTAATTTAACA
1 TAATTAATTTAACA
34981432 TAACTTAA-TTAACA
1 TAA-TTAATTTAACA
34981446 TAATTAA
1 TAATTAA
34981453 CCTTTTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 12 0.60
15 4 0.20
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATTAATTTAACA
Found at i:34983524 original size:61 final size:61
Alignment explanation
Indices: 34983449--34983567 Score: 177
Period size: 61 Copynumber: 2.0 Consensus size: 61
34983439 ATCACATTAT
* * * *
34983449 TATTAAATTGATAAAATATTATCTAGATATAA-ATTAAATTAAATTAAATATCTCATATGGA
1 TATTAAATTAATAAAATACTATCTAAATA-AATATTAAATTAAATTAAATATATCATATGGA
*
34983510 TATTAAATTAATAAAATACTATCTAAATAAATATTAAATTAAATTTAATATATCATAT
1 TATTAAATTAATAAAATACTATCTAAATAAATATTAAATTAAATTAAATATATCATAT
34983568 TAATATATAG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
60 2 0.04
61 50 0.96
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.40
Consensus pattern (61 bp):
TATTAAATTAATAAAATACTATCTAAATAAATATTAAATTAAATTAAATATATCATATGGA
Found at i:34983547 original size:31 final size:30
Alignment explanation
Indices: 34983449--34983551 Score: 93
Period size: 31 Copynumber: 3.4 Consensus size: 30
34983439 ATCACATTAT
* *
34983449 TATTAAATTGATAAAATATTATCTAGATATAA
1 TATTAAATTAATAAAATA-TATCTAAATA-AA
* * * **
34983481 -ATTAAATTAAATTAAATATCTC-ATATGGA
1 TATTAAATT-AATAAAATATATCTAAATAAA
34983510 TATTAAATTAATAAAATACTATCTAAATAAA
1 TATTAAATTAATAAAATA-TATCTAAATAAA
34983541 TATTAAATTAA
1 TATTAAATTAA
34983552 ATTTAATATA
Statistics
Matches: 56, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
29 9 0.16
30 14 0.25
31 26 0.46
32 7 0.12
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (30 bp):
TATTAAATTAATAAAATATATCTAAATAAA
Found at i:34988441 original size:12 final size:12
Alignment explanation
Indices: 34988424--34988448 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34988414 GGTGTTCATT
34988424 CGGTTAACCGAC
1 CGGTTAACCGAC
34988436 CGGTTAACCGAC
1 CGGTTAACCGAC
34988448 C
1 C
34988449 CGAAATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:34988628 original size:9 final size:9
Alignment explanation
Indices: 34988610--34988649 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
34988600 TTTGGTTAAA
34988610 AATTAACCG
1 AATTAACCG
*
34988619 AATTACCCG
1 AATTAACCG
*
34988628 AATTACCCG
1 AATTAACCG
34988637 AATTAACCG
1 AATTAACCG
34988646 AATT
1 AATT
34988650 GAATCACTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:35003093 original size:9 final size:9
Alignment explanation
Indices: 35003075--35003150 Score: 116
Period size: 9 Copynumber: 8.4 Consensus size: 9
35003065 GTAGTGATTC
*
35003075 AATTCAGTT
1 AATTCGGTT
35003084 AATTCGGTT
1 AATTCGGTT
*
35003093 AATTCGGGT
1 AATTCGGTT
*
35003102 AATCCGGTT
1 AATTCGGTT
35003111 AATTCGGTT
1 AATTCGGTT
*
35003120 AATTCAGTT
1 AATTCGGTT
35003129 AATTCGGTT
1 AATTCGGTT
35003138 AATTCGGTT
1 AATTCGGTT
35003147 AATT
1 AATT
35003151 TTTAACCAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 60 1.00
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:35005639 original size:15 final size:16
Alignment explanation
Indices: 35005619--35005652 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
35005609 TAAATATTAT
35005619 AAAATAAAAAT-AAAC
1 AAAATAAAAATCAAAC
*
35005634 AAAATAAACATCAAAC
1 AAAATAAAAATCAAAC
35005650 AAA
1 AAA
35005653 TGCCATCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAATAAAAATCAAAC
Found at i:35009432 original size:14 final size:14
Alignment explanation
Indices: 35009413--35009452 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
35009403 TTGTTTGGCA
35009413 GTAAAATGTTTTCT
1 GTAAAATGTTTTCT
*
35009427 GTAAAATGATTTCT
1 GTAAAATGTTTTCT
*
35009441 GGAAAATGTTTT
1 GTAAAATGTTTT
35009453 ACTTTTCTGG
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:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (14 bp):
GTAAAATGTTTTCT
Found at i:35009461 original size:20 final size:20
Alignment explanation
Indices: 35009436--35009495 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
35009426 TGTAAAATGA
35009436 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGTTTTACT
35009456 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGTTTTACT
* *
35009476 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGTTTTACT
35009496 GGAAAATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.27, C:0.10, G:0.13, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGTTTTACT
Found at i:35009511 original size:14 final size:15
Alignment explanation
Indices: 35009415--35009511 Score: 56
Period size: 20 Copynumber: 6.0 Consensus size: 15
35009405 GTTTGGCAGT
*
35009415 AAAATG-TTTTCTGT
1 AAAATGATTTTCTGG
35009429 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
35009443 AAAATGTTTTACTTTTCTGG
1 AAAATG----A-TTTTCTGG
*
35009463 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
35009483 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
35009498 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
35009512 TGTTTGGTAA
Statistics
Matches: 71, Mismatches: 5, Indels: 14
0.79 0.06 0.16
Matches are distributed among these distances:
14 26 0.37
15 11 0.15
16 1 0.01
18 1 0.01
20 32 0.45
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.45
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:35009566 original size:32 final size:31
Alignment explanation
Indices: 35009488--35009572 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 31
35009478 TCTGTAAAAT
* *
35009488 GATTTACTGGAAAATATTTTCTGGTGTTTGGTA
1 GATTT-CT-GAAAATATTTTCTGCTGTTTGGCA
* * *
35009521 AATCTGTGTAAAATATTTTCTGCTGTTTGGCA
1 GATTTCTG-AAAATATTTTCTGCTGTTTGGCA
35009553 GATTTCCTGAAAATATTTTC
1 GATTT-CTGAAAATATTTTC
35009573 CGGAAAAGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
31 1 0.02
32 36 0.86
33 5 0.12
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.45
Consensus pattern (31 bp):
GATTTCTGAAAATATTTTCTGCTGTTTGGCA
Found at i:35009624 original size:14 final size:14
Alignment explanation
Indices: 35009605--35009632 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35009595 ATTTTACATA
35009605 TATTAATATATATT
1 TATTAATATATATT
35009619 TATTAATATATATT
1 TATTAATATATATT
35009633 AATAAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTAATATATATT
Found at i:35009905 original size:71 final size:72
Alignment explanation
Indices: 35009821--35009963 Score: 252
Period size: 71 Copynumber: 2.0 Consensus size: 72
35009811 ATAATAATAT
*
35009821 TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGT-CTAGTACATAATATTACA
1 TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCCAAGTACATAATATTACA
35009885 CCACATA
66 CCACATA
* *
35009892 TATCCAAATACATAATTAATGGTACACCACATAGTAAGAACATTGTCCAAGTGCATAATATTACA
1 TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCCAAGTACATAATATTACA
35009957 CCACATA
66 CCACATA
35009964 AATGTATCAA
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
71 45 0.66
72 23 0.34
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.27
Consensus pattern (72 bp):
TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCCAAGTACATAATATTACA
CCACATA
Found at i:35010946 original size:27 final size:28
Alignment explanation
Indices: 35010907--35010982 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 28
35010897 TTCAACCATT
* *
35010907 TCAATATCCAACAAGCTTAAAACATA-A
1 TCAATATCCAACAAACTCAAAACATATA
* *
35010934 TCAATATCTAACAAACTCAAGACATATA
1 TCAATATCCAACAAACTCAAAACATATA
*
35010962 TCAAAATCCAACAAACT-AAAA
1 TCAATATCCAACAAACTCAAAA
35010983 TTTCAATATC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
27 25 0.61
28 16 0.39
ACGTcount: A:0.54, C:0.22, G:0.03, T:0.21
Consensus pattern (28 bp):
TCAATATCCAACAAACTCAAAACATATA
Found at i:35012489 original size:15 final size:16
Alignment explanation
Indices: 35012469--35012501 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
35012459 AGTACCACTT
35012469 AAAATGAAAGCA-TGA
1 AAAATGAAAGCATTGA
35012484 AAAATGAAAGCATTGA
1 AAAATGAAAGCATTGA
35012500 AA
1 AA
35012502 GTACCACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.61, C:0.06, G:0.18, T:0.15
Consensus pattern (16 bp):
AAAATGAAAGCATTGA
Found at i:35015089 original size:28 final size:27
Alignment explanation
Indices: 35015057--35015124 Score: 97
Period size: 25 Copynumber: 2.6 Consensus size: 27
35015047 AAGCTTTAAG
35015057 GAATGGAAAATGTCTGCTGCTTAGA-AGA
1 GAATGGAAAATGTCT-CTGCTTAGAGA-A
35015085 GAATGGAAAATG--TCTGCTTAGAGAA
1 GAATGGAAAATGTCTCTGCTTAGAGAA
35015110 GAATGGAAAATGTCT
1 GAATGGAAAATGTCT
35015125 TACCAATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
25 22 0.59
26 2 0.05
27 1 0.03
28 12 0.32
ACGTcount: A:0.38, C:0.09, G:0.28, T:0.25
Consensus pattern (27 bp):
GAATGGAAAATGTCTCTGCTTAGAGAA
Found at i:35023218 original size:15 final size:15
Alignment explanation
Indices: 35023198--35023229 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
35023188 ATGAATATTC
*
35023198 TAAAATTTATTAAAT
1 TAAAATTAATTAAAT
35023213 TAAAATTAATTAAAT
1 TAAAATTAATTAAAT
35023228 TA
1 TA
35023230 TATCCCACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAAATTAATTAAAT
Found at i:35025001 original size:6 final size:6
Alignment explanation
Indices: 35024984--35025013 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
35024974 TTAAGTGGAT
35024984 TAAAAC TAAAAAC TAAAAC TAAAAC TAAAA
1 TAAAAC T-AAAAC TAAAAC TAAAAC TAAAA
35025014 TCACCGTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAC
Found at i:35025914 original size:46 final size:46
Alignment explanation
Indices: 35025858--35025951 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
35025848 ATGAATTCTT
35025858 ATGAAATTTGCTGTGCCATATCCTCTTTGCGTTCCTCAAATGGCAG
1 ATGAAATTTGCTGTGCCATATCCTCTTTGCGTTCCTCAAATGGCAG
35025904 ATGAAATTTGCTGTGCCATATCCTCTTTGCGTTCCTCAAATGGCAG
1 ATGAAATTTGCTGTGCCATATCCTCTTTGCGTTCCTCAAATGGCAG
35025950 AT
1 AT
35025952 TGTGATTTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.35
Consensus pattern (46 bp):
ATGAAATTTGCTGTGCCATATCCTCTTTGCGTTCCTCAAATGGCAG
Found at i:35030138 original size:76 final size:76
Alignment explanation
Indices: 35029986--35030137 Score: 270
Period size: 76 Copynumber: 2.0 Consensus size: 76
35029976 GCAAAACCTC
*
35029986 AGTTTCAAATGCTGGACTCCAAACTGAGTATAGGGAGAAAGGGGGGCCAGTGAGTGTTAAAAAAA
1 AGTTTCAAATGCTGGACTCCAAACTGAGTATAGGGAGAAAGGGCGGCCAGTGAGTGTTAAAAAAA
*
35030051 GGGAAAAAAAA
66 GGAAAAAAAAA
*
35030062 AGTTTCAACTGCTGGACTCCAAACTGAGTATAGGGAGAAAGGGCGGCCAGTGAGTGTT-AAAAAA
1 AGTTTCAAATGCTGGACTCCAAACTGAGTATAGGGAGAAAGGGCGGCCAGTGAGTGTTAAAAAAA
35030126 GGAAAAAAAAA
66 GGAAAAAAAAA
35030137 A
1 A
35030138 AAAGAAACAA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
75 17 0.23
76 56 0.77
ACGTcount: A:0.42, C:0.12, G:0.29, T:0.17
Consensus pattern (76 bp):
AGTTTCAAATGCTGGACTCCAAACTGAGTATAGGGAGAAAGGGCGGCCAGTGAGTGTTAAAAAAA
GGAAAAAAAAA
Found at i:35042338 original size:17 final size:19
Alignment explanation
Indices: 35042316--35042359 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 19
35042306 GTTAATATAA
35042316 TTTTTAA-AATTTTAAA-T-
1 TTTTTAATAA-TTTAAAGTG
35042333 TTTTTAATAATTTAAAGTG
1 TTTTTAATAATTTAAAGTG
35042352 TTTTTAAT
1 TTTTTAAT
35042360 TAGGATGTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 13 0.54
18 3 0.12
19 8 0.33
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTTAATAATTTAAAGTG
Found at i:35047810 original size:36 final size:35
Alignment explanation
Indices: 35047735--35047812 Score: 84
Period size: 36 Copynumber: 2.2 Consensus size: 35
35047725 AAGTTTTGTT
* ** ***
35047735 AAAATAATTTAGGGTTAGGTTTTTAGGGTTTTGTT
1 AAAATAATTTAGGGTTAGGATTTTAGGAATTTAAA
*
35047770 AAAATAATTTAGGGTTTTGGATTTTAGGAATTTAAA
1 AAAATAATTTAGGG-TTAGGATTTTAGGAATTTAAA
35047806 AAAATAA
1 AAAATAA
35047813 ATCAAGATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
35 14 0.40
36 21 0.60
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (35 bp):
AAAATAATTTAGGGTTAGGATTTTAGGAATTTAAA
Found at i:35047902 original size:34 final size:33
Alignment explanation
Indices: 35047830--35047905 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 33
35047820 TTTAGTGTTA
35047830 TTTTTT-AAAAATTAATTAAATTAGGGTTTAAG
1 TTTTTTAAAAAATTAATTAAATTAGGGTTTAAG
*
35047862 TATTTTAAATAAATTAATTAAATTAGGGTTT-AG
1 TTTTTTAAA-AAATTAATTAAATTAGGGTTTAAG
*
35047895 TTTTTTTAAAA
1 TTTTTTAAAAA
35047906 TAATATTGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
32 7 0.18
33 11 0.28
34 21 0.54
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (33 bp):
TTTTTTAAAAAATTAATTAAATTAGGGTTTAAG
Found at i:35048107 original size:126 final size:126
Alignment explanation
Indices: 35047977--35048234 Score: 412
Period size: 126 Copynumber: 2.0 Consensus size: 126
35047967 TTTTTTATAG
* * *
35047977 TAGTTCCTGAAAAAATAATTTTGAGAATAC-TGTTCTTAACAAATAGTATGAAAAACGCTTCAAG
1 TAGTTCCTGAAAAAATAATTTTGAGAAGACGT-TTCTAAACAAATAGTATCAAAAACGCTTCAAG
* * *
35048041 CAGGATGCATTGTCAGCAAAATT-ATTGAAAAAAGCTCCCATGTGGACGCTCTTTTTCTACAA
65 CAGGATGCACTGTCAGCAAAATTGA-TGAAAAAAGCTCCCATGTCGACACTCTTTTTCTACAA
*
35048103 TAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTAAACAAATAGTGTCAAAAACGCTTCAAGC
1 TAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTAAACAAATAGTATCAAAAACGCTTCAAGC
*
35048168 AGGATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCATGTCGACACTCTTTTTCTACAG
66 AGGATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCATGTCGACACTCTTTTTCTACAA
35048229 TAGTTC
1 TAGTTC
35048235 ATGTTTGGCT
Statistics
Matches: 122, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
126 120 0.98
127 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (126 bp):
TAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTAAACAAATAGTATCAAAAACGCTTCAAGC
AGGATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCATGTCGACACTCTTTTTCTACAA
Found at i:35051723 original size:18 final size:18
Alignment explanation
Indices: 35051702--35051737 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
35051692 AAAAGGAAAT
**
35051702 ATATAAGGTTTAGGATAC
1 ATATAAGGGCTAGGATAC
35051720 ATATAAGGGCTAGGATAC
1 ATATAAGGGCTAGGATAC
35051738 GCACCTGGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.28
Consensus pattern (18 bp):
ATATAAGGGCTAGGATAC
Found at i:35053323 original size:19 final size:20
Alignment explanation
Indices: 35053301--35053339 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
35053291 ATTAATTAAA
*
35053301 ATTATATAA-ATGAAAAAAT
1 ATTAAATAATATGAAAAAAT
*
35053320 ATTAAATAATATTAAAAAAT
1 ATTAAATAATATGAAAAAAT
35053340 TAAAATTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
ATTAAATAATATGAAAAAAT
Found at i:35053323 original size:25 final size:24
Alignment explanation
Indices: 35053274--35053325 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
35053264 ATTGTTATAA
* *
35053274 AAAATTATAAAATACAAATTAATT
1 AAAATTATAAAATAAAAAATAATT
35053298 AAAATTATATAAATGAAAAAAT-ATT
1 AAAATTATA-AAAT-AAAAAATAATT
35053323 AAA
1 AAA
35053326 TAATATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.38
25 10 0.42
26 5 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (24 bp):
AAAATTATAAAATAAAAAATAATT
Found at i:35053564 original size:29 final size:30
Alignment explanation
Indices: 35053502--35053565 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
35053492 ATTAATTAAA
35053502 GAGAGCGTTGAGAAATTTAAGGAGAAATTT
1 GAGAGCGTTGAGAAATTTAAGGAGAAATTT
* *
35053532 GAGAGCTTTGAGAAA-TTAGGGAGAAATTT
1 GAGAGCGTTGAGAAATTTAAGGAGAAATTT
35053561 GAGAG
1 GAGAG
35053566 TTTTTTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 18 0.56
30 14 0.44
ACGTcount: A:0.39, C:0.03, G:0.33, T:0.25
Consensus pattern (30 bp):
GAGAGCGTTGAGAAATTTAAGGAGAAATTT
Found at i:35054102 original size:23 final size:23
Alignment explanation
Indices: 35054072--35054117 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
35054062 TAGCGGTTAG
35054072 AAAATTGATTGCAATATTGATAA
1 AAAATTGATTGCAATATTGATAA
35054095 AAAATTGATTGCAATATTGATAA
1 AAAATTGATTGCAATATTGATAA
35054118 TATATTACGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (23 bp):
AAAATTGATTGCAATATTGATAA
Found at i:35058084 original size:22 final size:22
Alignment explanation
Indices: 35058056--35058100 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
35058046 GTTTTGGTAC
35058056 AGGTAAGTTCGTATAAGGATTA
1 AGGTAAGTTCGTATAAGGATTA
35058078 AGGTAAGTTCGTATAAGGATTA
1 AGGTAAGTTCGTATAAGGATTA
35058100 A
1 A
35058101 CTTGTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (22 bp):
AGGTAAGTTCGTATAAGGATTA
Found at i:35064369 original size:37 final size:35
Alignment explanation
Indices: 35064326--35064413 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
35064316 TTCTGATTTA
* *
35064326 CATGTTAAACATGTTA-ATATTCTGATGTTCCGATTCG
1 CATGTTAAGCATGCTATAT-TTCTGA--TTCCGATTCG
* *
35064363 CGTGTTAAGCATGCTATATTTCTGATTCTGATTCG
1 CATGTTAAGCATGCTATATTTCTGATTCCGATTCG
35064398 CATGTTAAGCATGCTA
1 CATGTTAAGCATGCTA
35064414 CTGTGATAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
35 24 0.53
37 19 0.42
38 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (35 bp):
CATGTTAAGCATGCTATATTTCTGATTCCGATTCG
Found at i:35064404 original size:35 final size:36
Alignment explanation
Indices: 35064315--35064413 Score: 112
Period size: 37 Copynumber: 2.8 Consensus size: 36
35064305 AGTTATTGAT
** * *
35064315 GTTCTGATTTACATGTTAAACATGTTAATATTCTGA
1 GTTCTGATTCGCATGTTAAGCATGCTAATATTCTGA
* *
35064351 TGTTCCGATTCGCGTGTTAAGCATGCT-ATATTTCTGA
1 -GTTCTGATTCGCATGTTAAGCATGCTAATA-TTCTGA
35064388 -TTCTGATTCGCATGTTAAGCATGCTA
1 GTTCTGATTCGCATGTTAAGCATGCTA
35064414 CTGTGATAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
35 23 0.44
36 3 0.06
37 26 0.50
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.41
Consensus pattern (36 bp):
GTTCTGATTCGCATGTTAAGCATGCTAATATTCTGA
Found at i:35070373 original size:30 final size:29
Alignment explanation
Indices: 35070339--35070400 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
35070329 AGGCTAAATA
** *
35070339 AGGCCTATAGGTTGATTTTGAAATTTATTT
1 AGGCCTATAGGCCGATTTT-AAAATTATTT
*
35070369 AGGCCTTTAGGCCGATTTTAAAATTATTT
1 AGGCCTATAGGCCGATTTTAAAATTATTT
35070398 AGG
1 AGG
35070401 AAAATAGGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (29 bp):
AGGCCTATAGGCCGATTTTAAAATTATTT
Found at i:35071899 original size:22 final size:22
Alignment explanation
Indices: 35071857--35071899 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
35071847 ATAAAATATC
*
35071857 GAAATATGCCAAGTACGTAAAG
1 GAAATATGCCAAGTACATAAAG
*
35071879 GAAATTATGTCAAG-ACATAAA
1 GAAA-TATGCCAAGTACATAAA
35071900 AAGTTGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.21
Consensus pattern (22 bp):
GAAATATGCCAAGTACATAAAG
Found at i:35076470 original size:40 final size:40
Alignment explanation
Indices: 35076422--35076497 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
35076412 TAAAAAATTC
*
35076422 ATTTTGAATTAAATAGTTTGTGTTATTTGAGTTAATTCAA
1 ATTTTGAATTAAATAGTTTGAGTTATTTGAGTTAATTCAA
*
35076462 ATTTTGAATTAAATAGTTTGAGTTGTTTGAGTTAAT
1 ATTTTGAATTAAATAGTTTGAGTTATTTGAGTTAAT
35076498 CAAGTTATTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.32, C:0.01, G:0.17, T:0.50
Consensus pattern (40 bp):
ATTTTGAATTAAATAGTTTGAGTTATTTGAGTTAATTCAA
Found at i:35086692 original size:19 final size:20
Alignment explanation
Indices: 35086668--35086706 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
35086658 TAGATTTACC
*
35086668 GAATAAAAGAAGGA-GAGAA
1 GAATAAAAAAAGGAGGAGAA
35086687 GAATAAAAAAAGGAGGAGAA
1 GAATAAAAAAAGGAGGAGAA
35086707 TTAGCATGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.64, C:0.00, G:0.31, T:0.05
Consensus pattern (20 bp):
GAATAAAAAAAGGAGGAGAA
Found at i:35094656 original size:14 final size:14
Alignment explanation
Indices: 35094620--35094649 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
35094610 CTTTATGTTT
*
35094620 TATAAATATAATAA
1 TATAATTATAATAA
35094634 TATAATTATAATAA
1 TATAATTATAATAA
35094648 TA
1 TA
35094650 ACATTATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TATAATTATAATAA
Found at i:35099071 original size:17 final size:17
Alignment explanation
Indices: 35099046--35099079 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
35099036 ATAATAAGCA
* *
35099046 AAGTTTAATATTTAAAT
1 AAGTATAATATATAAAT
35099063 AAGTATAATATATAAAT
1 AAGTATAATATATAAAT
35099080 TCTACTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
AAGTATAATATATAAAT
Found at i:35099972 original size:41 final size:41
Alignment explanation
Indices: 35099918--35100121 Score: 282
Period size: 41 Copynumber: 5.0 Consensus size: 41
35099908 TTAATTAAAA
* * *
35099918 CAGATTCAACGGCACTTAGCCTGCTAAGCTTAAAGTCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
* *
35099960 CAGATCACCGGCACTTAGTCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
* *
35100001 CAGTTCACCGGCACTTAGCCTGCTAGGCTTAAAGCTTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
** *
35100042 CAGATCGTCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
* * *
35100083 CAGTTCACCGGCACTTAGCTTGCTAGGCTTTAAGCCTGA
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGA
35100122 ATTGATTCAC
Statistics
Matches: 142, Mismatches: 20, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 138 0.97
42 4 0.03
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
Found at i:35100065 original size:82 final size:83
Alignment explanation
Indices: 35099922--35100121 Score: 316
Period size: 82 Copynumber: 2.4 Consensus size: 83
35099912 TTAAAACAGA
* * *
35099922 TTCAACGGCACTTAGCCTGCTAAGCTTAAAG-TCTGATTCAGATCACCGGCACTTAGTCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCTCTGATTCAGATCACCGGCACTTAGCCTGCTAG
35099986 GCTTATAGCCTGATTCAG
66 GCTTATAGCCTGATTCAG
**
35100004 TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCT-TGATTCAGATCGTCGGCACTTAGCCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCTCTGATTCAGATCACCGGCACTTAGCCTGCTAG
35100068 GCTTATAGCCTGATTCAG
66 GCTTATAGCCTGATTCAG
* *
35100086 TTCACCGGCACTTAGCTTGCTAGGCTTTAAGC-CTGA
1 TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCTCTGA
35100122 ATTGATTCAC
Statistics
Matches: 109, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
82 108 0.99
83 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (83 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCTCTGATTCAGATCACCGGCACTTAGCCTGCTAG
GCTTATAGCCTGATTCAG
Found at i:35100146 original size:41 final size:41
Alignment explanation
Indices: 35099922--35100151 Score: 216
Period size: 41 Copynumber: 5.6 Consensus size: 41
35099912 TTAAAACAGA
* * * * * *
35099922 TTCAACGGCACTTAGCCTGCTAAGCTTAAAGTCTGATTCAG
1 TTCACCGGCAATTAGCTTGCTAGGCTTATAGCCTGATTCAG
* *
35099963 ATCACCGGCACTTAG-TCTGCTAGGCTTATAGCCTGATTCAG
1 TTCACCGGCAATTAGCT-TGCTAGGCTTATAGCCTGATTCAG
* * * *
35100004 TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCTTGATTCAG
1 TTCACCGGCAATTAGCTTGCTAGGCTTATAGCCTGATTCAG
* ** * *
35100045 ATCGTCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
1 TTCACCGGCAATTAGCTTGCTAGGCTTATAGCCTGATTCAG
* *
35100086 TTCACCGGCACTTAGCTTGCTAGGCTT-TAAGCCTGAATTGA-
1 TTCACCGGCAATTAGCTTGCTAGGCTTAT-AGCCTG-ATTCAG
*
35100127 TTCACTGGCAATATA-CTTGCTAGGC
1 TTCACCGGCAAT-TAGCTTGCTAGGC
35100152 GCTGAGCCTG
Statistics
Matches: 162, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
40 1 0.01
41 155 0.96
42 6 0.04
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.30
Consensus pattern (41 bp):
TTCACCGGCAATTAGCTTGCTAGGCTTATAGCCTGATTCAG
Found at i:35100148 original size:123 final size:123
Alignment explanation
Indices: 35099927--35100151 Score: 314
Period size: 123 Copynumber: 1.8 Consensus size: 123
35099917 ACAGATTCAA
*
35099927 CGGCACTTAGCCTGCTAAGCTTAAAGTCTGATTCAGATCACCGGCACTTAGTCTGCTAGGCTTAT
1 CGGCACTTAGCCTGCTAAGCTTAAAGCCTGATTCAGATCACCGGCACTTAGTCTGCTAGGCTTAT
*
35099992 AGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTAAAGCTTGATTCAGATCGT
66 AGCCTGATTCAGTTCACCGGCAATTAGCCTGCTAGGCTTAAAGCTTGATTCAGATCGT
* * *
35100050 CGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAG-CTTGCTAGGCTT-
1 CGGCACTTAGCCTGCTAAGCTTAAAGCCTGATTCAGATCACCGGCACTTAGTC-TGCTAGGCTTA
* * *
35100113 TAAGCCTGAATTGA-TTCACTGGCAATATA-CTTGCTAGGC
65 T-AGCCTG-ATTCAGTTCACCGGCAAT-TAGCCTGCTAGGC
35100152 GCTGAGCCTG
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
122 2 0.02
123 82 0.91
124 6 0.07
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (123 bp):
CGGCACTTAGCCTGCTAAGCTTAAAGCCTGATTCAGATCACCGGCACTTAGTCTGCTAGGCTTAT
AGCCTGATTCAGTTCACCGGCAATTAGCCTGCTAGGCTTAAAGCTTGATTCAGATCGT
Found at i:35100160 original size:82 final size:81
Alignment explanation
Indices: 35099922--35100162 Score: 240
Period size: 82 Copynumber: 2.9 Consensus size: 81
35099912 TTAAAACAGA
* * * * *
35099922 TTCAACGGCACTTAGCCTGCTAAGCTTAAAGTCTGATTCAGATCAC-CGGCACTTAGTCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT-AGATC-CTCGGCAATTAGCCTGCTAG
* *
35099986 GCTTATAGCCTGATTCAG
64 GCCTAGAGCCTGATTCAG
* * *
35100004 TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCTTGATTCAGATCGTCGGCACTTAGCCTGCTAGG
1 TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT-AGATCCTCGGCAATTAGCCTGCTAGG
* *
35100069 CTTATAGCCTGATTCAG
65 CCTAGAGCCTGATTCAG
* * *
35100086 TTCACCGGCACTTAGCTTGCTAGGCTTTAAGCCTGAATT-GATTCACT-GGCAATATA-CTTGCT
1 TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTG-ATTAGA-TC-CTCGGCAAT-TAGCCTGCT
35100148 AGGCGCT-GAGCCTGA
62 AGGC-CTAGAGCCTGA
35100163 ATACGCAATT
Statistics
Matches: 139, Mismatches: 14, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
81 2 0.01
82 130 0.94
83 7 0.05
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.29
Consensus pattern (81 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTAGATCCTCGGCAATTAGCCTGCTAGGC
CTAGAGCCTGATTCAG
Found at i:35102517 original size:19 final size:19
Alignment explanation
Indices: 35102495--35102555 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
35102485 GTGTGGGTTT
*
35102495 ATGCACCTCGTGTGCCAAG
1 ATGCACCTCATGTGCCAAG
* * *
35102514 ATGCTCTTCATGTGCCAGG
1 ATGCACCTCATGTGCCAAG
* * * *
35102533 ATGCGCTTCAAGTGCCAGG
1 ATGCACCTCATGTGCCAAG
35102552 ATGC
1 ATGC
35102556 GTTTCGTGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.25
Consensus pattern (19 bp):
ATGCACCTCATGTGCCAAG
Found at i:35102566 original size:19 final size:19
Alignment explanation
Indices: 35102505--35102568 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
35102495 ATGCACCTCG
*
35102505 TGTGCCAAGATGC-TCTTCA
1 TGTGCCAGGATGCGT-TTCA
*
35102524 TGTGCCAGGATGCGCTTCA
1 TGTGCCAGGATGCGTTTCA
* *
35102543 AGTGCCAGGATGCGTTTCG
1 TGTGCCAGGATGCGTTTCA
35102562 TGTGCCA
1 TGTGCCA
35102569 ATATGCACTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (19 bp):
TGTGCCAGGATGCGTTTCA
Found at i:35103045 original size:24 final size:24
Alignment explanation
Indices: 35103018--35103067 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
35103008 ACTATTTAAT
*
35103018 AATATCAAATAATCAAATATTCTC
1 AATATCAAATAATCAAAGATTCTC
*
35103042 AATATCAAATAATCGAAGATTCTC
1 AATATCAAATAATCAAAGATTCTC
35103066 AA
1 AA
35103068 CACTCCTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30
Consensus pattern (24 bp):
AATATCAAATAATCAAAGATTCTC
Found at i:35107604 original size:8 final size:9
Alignment explanation
Indices: 35107583--35107607 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
35107573 TTTTTGAAAA
35107583 AAAAATCCC
1 AAAAATCCC
35107592 AAAAATCCC
1 AAAAATCCC
35107601 AAAAATC
1 AAAAATC
35107608 GGATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.28, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAATCCC
Found at i:35109566 original size:589 final size:589
Alignment explanation
Indices: 35108450--35110806 Score: 4705
Period size: 589 Copynumber: 4.0 Consensus size: 589
35108440 CAAATTCATA
35108450 ACTTGTTAATGATATATATATGTATGTTCATGACATAAATAGGTTGAAACGTTTAGATGGTTGAA
1 ACTTGTTAATGATATATATATGTATGTTCATGACATAAATAGGTTGAAACGTTTAGATGGTTGAA
35108515 ATGGATGAATTTTGATATGTTGAACGTGTAATGTATAGGAATTTATGATGCAAGAGAATAAAATT
66 ATGGATGAATTTTGATATGTTGAACGTGTAATGTATAGGAATTTATGATGCAAGAGAATAAAATT
35108580 GAGCATATGGAAATGGTTAGAATGCTGAAATGGTTGAATTGATATAAATTTTGAATTGAATGAGT
131 GAGCATATGGAAATGGTTAGAATGCTGAAATGGTTGAATTGATATAAATTTTGAATTGAATGAGT
35108645 GATTTGAATAGGTACCATTTAGACCATTTGAAAACAAACGATCATGTCGGGTTGTTAACATTGTG
196 GATTTGAATAGGTACCATTTAGACCATTTGAAAACAAACGATCATGTCGGGTTGTTAACATTGTG
35108710 ACGAAATCAAGTCAGTGAGTTGCATCACGACGAGGAACCCTTGAAGTCGTGTCAACTTGATAAAT
261 ACGAAATCAAGTCAGTGAGTTGCATCACGACGAGGAACCCTTGAAGTCGTGTCAACTTGATAAAT
35108775 TGCAAAATTTACATTTTGGTCCTAATTCAACCTCGGGTTATCAAAAGAGCTTTCATAATCTCGTA
326 TGCAAAATTTACATTTTGGTCCTAATTCAACCTCGGGTTATCAAAAGAGCTTTCATAATCTCGTA
35108840 TAAGACTTGGATTTGATTGAAAAACAAATTGTGATTGCGTAATGTGGTTAGTGGCACATATAAAA
391 TAAGACTTGGATTTGATTGAAAAACAAATTGTGATTGCGTAATGTGGTTAGTGGCACATATAAAA
*
35108905 GGGTAAATGGATTTGTAGTTGCTCTGGCAATGAATGTGGCACCCCGTAGCTTGGACCCAACAACT
456 GGGTAAATGGATTTGTAGTTGCTCCGGCAATGAATGTGGCACCCCGTAGCTTGGACCCAACAACT
35108970 GCGTTGGGTATGGTGTGTTACAATTACATTAAAAAATCCAATAATCTCCCAATTGGACTATATAT
521 GCGTTGGGTATGGTGTGTTACAATTACATTAAAAAATCCAATAATCTCCCAATTGGACTATATAT
35109035 ATAT
586 ATAT
35109039 ACTTGTTAATGATATATATATGTATGTTCATGACATAAATAGGTTGAAACGTTTAGATGGTTGAA
1 ACTTGTTAATGATATATATATGTATGTTCATGACATAAATAGGTTGAAACGTTTAGATGGTTGAA
35109104 ATGGATGAATTTTGATATGTTGAACGTGTAATGTATAGGAATTTATGATGCAAGAGAATAAAATT
66 ATGGATGAATTTTGATATGTTGAACGTGTAATGTATAGGAATTTATGATGCAAGAGAATAAAATT
35109169 GAGCATATGGAAATGGTTAGAATGCTGAAATGGTTGAATTGATATAAATTTTGAATTGAATGAGT
131 GAGCATATGGAAATGGTTAGAATGCTGAAATGGTTGAATTGATATAAATTTTGAATTGAATGAGT
35109234 GATTTGAATAGGTACCATTTAGACCATTTGAAAACAAACGATCATGTCGGGTTGTTAACATTGTG
196 GATTTGAATAGGTACCATTTAGACCATTTGAAAACAAACGATCATGTCGGGTTGTTAACATTGTG
35109299 ACGAAATCAAGTCAGTGAGTTGCATCACGACGAGGAACCCTTGAAGTCGTGTCAACTTGATAAAT
261 ACGAAATCAAGTCAGTGAGTTGCATCACGACGAGGAACCCTTGAAGTCGTGTCAACTTGATAAAT
35109364 TGCAAAATTTACATTTTGGTCCTAATTCAACCTCGGGTTATCAAAAGAGCTTTCATAATCTCGTA
326 TGCAAAATTTACATTTTGGTCCTAATTCAACCTCGGGTTATCAAAAGAGCTTTCATAATCTCGTA
35109429 TAAGACTTGGATTTGATTGAAAAACAAATTGTGATTGCGTAATGTGGTTAGTGGCACATATAAAA
391 TAAGACTTGGATTTGATTGAAAAACAAATTGTGATTGCGTAATGTGGTTAGTGGCACATATAAAA
35109494 GGGTAAATGGATTTGTAGTTGCTCCGGCAATGAATGTGGCACCCCGTAGCTTGGACCCAACAACT
456 GGGTAAATGGATTTGTAGTTGCTCCGGCAATGAATGTGGCACCCCGTAGCTTGGACCCAACAACT
35109559 GCGTTGGGTATGGTGTGTTACAATTACATTAAAAAATCCAATAATCTCCCAATTGGACTATATAT
521 GCGTTGGGTATGGTGTGTTACAATTACATTAAAAAATCCAATAATCTCCCAATTGGACTATATAT
35109624 ATAT
586 ATAT
35109628 ACTTGTTAATGATATATATATGTATGTTCATGACATAAATAGGTTGAAACGTTTAGATGGTTGAA
1 ACTTGTTAATGATATATATATGTATGTTCATGACATAAATAGGTTGAAACGTTTAGATGGTTGAA
35109693 ATGGATGAATTTTGATATGTTGAACGTGTAATGTATAGGAATTTATGATGCAAGAGAATAAAATT
66 ATGGATGAATTTTGATATGTTGAACGTGTAATGTATAGGAATTTATGATGCAAGAGAATAAAATT
35109758 GAGCATATGGAAATGGTTAGAATGCTGAAATGGTTGAATTGATATAAATTTTGAATTGAATGAGT
131 GAGCATATGGAAATGGTTAGAATGCTGAAATGGTTGAATTGATATAAATTTTGAATTGAATGAGT
35109823 GATTTGAATAGGTACCATTTAGACCATTTGAAAACAAACGATCATGTCGGGTTGTTAACATTGTG
196 GATTTGAATAGGTACCATTTAGACCATTTGAAAACAAACGATCATGTCGGGTTGTTAACATTGTG
35109888 ACGAAATCAAGTCAGTGAGTTGCATCACGACGAGGAACCCTTGAAGTCGTGTCAACTTGATAAAT
261 ACGAAATCAAGTCAGTGAGTTGCATCACGACGAGGAACCCTTGAAGTCGTGTCAACTTGATAAAT
35109953 TGCAAAATTTACATTTTGGTCCTAATTCAACCTCGGGTTATCAAAAGAGCTTTCATAATCTCGTA
326 TGCAAAATTTACATTTTGGTCCTAATTCAACCTCGGGTTATCAAAAGAGCTTTCATAATCTCGTA
35110018 TAAGACTTGGATTTGATTGAAAAACAAATTGTGATTGCGTAATGTGGTTAGTGGCACATATAAAA
391 TAAGACTTGGATTTGATTGAAAAACAAATTGTGATTGCGTAATGTGGTTAGTGGCACATATAAAA
35110083 GGGTAAATGGATTTGTAGTTGCTCCGGCAATGAATGTGGCACCCCGTAGCTTGGACCCAACAACT
456 GGGTAAATGGATTTGTAGTTGCTCCGGCAATGAATGTGGCACCCCGTAGCTTGGACCCAACAACT
35110148 GCGTTGGGTATGGTGTGTTACAATTACATTAAAAAATCCAATAATCTCCCAATTGGACTATATAT
521 GCGTTGGGTATGGTGTGTTACAATTACATTAAAAAATCCAATAATCTCCCAATTGGACTATATAT
35110213 ATAT
586 ATAT
35110217 ACTTGTTAATGATATATATATGTATGTTCATGACATAAATAGGTTGAAACGTTTAGATGGTTGAA
1 ACTTGTTAATGATATATATATGTATGTTCATGACATAAATAGGTTGAAACGTTTAGATGGTTGAA
35110282 ATGGATGAATTTTGATATGTTGAACGTGTAATGTATAGGAATTTATGATGCAAGAGAATAAAATT
66 ATGGATGAATTTTGATATGTTGAACGTGTAATGTATAGGAATTTATGATGCAAGAGAATAAAATT
35110347 GAGCATATGGAAATGGTTAGAATGCTGAAATGGTTGAATTGATATAAATTTTGAATTGAATGAGT
131 GAGCATATGGAAATGGTTAGAATGCTGAAATGGTTGAATTGATATAAATTTTGAATTGAATGAGT
35110412 GATTTGAATAGGTACCATTTAGACCATTTGAAAACAAACGATCATGTCGGGTTGTTAACATTGTG
196 GATTTGAATAGGTACCATTTAGACCATTTGAAAACAAACGATCATGTCGGGTTGTTAACATTGTG
35110477 ACGAAATCAAGTCAGTGAGTTGCATCACGACGAGGAACCCTTGAAGTCGTGTCAACTTGATAAAT
261 ACGAAATCAAGTCAGTGAGTTGCATCACGACGAGGAACCCTTGAAGTCGTGTCAACTTGATAAAT
35110542 TGCAAAATTTACATTTTGGTCCTAATTCAACCTCGGGTTATCAAAAGAGCTTTCATAATCTCGTA
326 TGCAAAATTTACATTTTGGTCCTAATTCAACCTCGGGTTATCAAAAGAGCTTTCATAATCTCGTA
35110607 TAAGACTTGGATTTGATTGAAAAACAAATTGTGATTGCGTAATGTGGTTAGTGGCACATATAAAA
391 TAAGACTTGGATTTGATTGAAAAACAAATTGTGATTGCGTAATGTGGTTAGTGGCACATATAAAA
35110672 GGGTAAATGGATTTGTAGTTGCTCCGGCAATGAATGTGGCACCCCGTAGCTTGGACCCAACAACT
456 GGGTAAATGGATTTGTAGTTGCTCCGGCAATGAATGTGGCACCCCGTAGCTTGGACCCAACAACT
35110737 GCGTTGGGTATGGTGTGTTACAATTACATTAAAAAATCCAATAATCTCCCAATTGGACTATATAT
521 GCGTTGGGTATGGTGTGTTACAATTACATTAAAAAATCCAATAATCTCCCAATTGGACTATATAT
35110802 ATAT
586 ATAT
35110806 A
1 A
35110807 TACTTATCAC
Statistics
Matches: 1767, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
589 1767 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (589 bp):
ACTTGTTAATGATATATATATGTATGTTCATGACATAAATAGGTTGAAACGTTTAGATGGTTGAA
ATGGATGAATTTTGATATGTTGAACGTGTAATGTATAGGAATTTATGATGCAAGAGAATAAAATT
GAGCATATGGAAATGGTTAGAATGCTGAAATGGTTGAATTGATATAAATTTTGAATTGAATGAGT
GATTTGAATAGGTACCATTTAGACCATTTGAAAACAAACGATCATGTCGGGTTGTTAACATTGTG
ACGAAATCAAGTCAGTGAGTTGCATCACGACGAGGAACCCTTGAAGTCGTGTCAACTTGATAAAT
TGCAAAATTTACATTTTGGTCCTAATTCAACCTCGGGTTATCAAAAGAGCTTTCATAATCTCGTA
TAAGACTTGGATTTGATTGAAAAACAAATTGTGATTGCGTAATGTGGTTAGTGGCACATATAAAA
GGGTAAATGGATTTGTAGTTGCTCCGGCAATGAATGTGGCACCCCGTAGCTTGGACCCAACAACT
GCGTTGGGTATGGTGTGTTACAATTACATTAAAAAATCCAATAATCTCCCAATTGGACTATATAT
ATAT
Found at i:35116566 original size:22 final size:22
Alignment explanation
Indices: 35116532--35116586 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
35116522 TTAATAAATG
35116532 TTTTTATA-A-TTCTCT-AATTT
1 TTTTTATATATTTCT-TGAATTT
35116552 TTTTTATATATTTCTTGAATTT
1 TTTTTATATATTTCTTGAATTT
* *
35116574 TATTTATTTATTT
1 TTTTTATATATTT
35116587 ATAAATCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 8 0.27
21 2 0.07
22 20 0.67
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTTATATATTTCTTGAATTT
Found at i:35117091 original size:24 final size:24
Alignment explanation
Indices: 35117064--35117110 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
35117054 ATTATTATTT
*
35117064 TAAT-TAATATTTTTAATTGATAAA
1 TAATATAATA-TTTTAATTAATAAA
*
35117088 TAATATATTATTTTAATTAATAA
1 TAATATAATATTTTAATTAATAA
35117111 CTCTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TAATATAATATTTTAATTAATAAA
Found at i:35117109 original size:20 final size:19
Alignment explanation
Indices: 35117054--35117110 Score: 55
Period size: 20 Copynumber: 3.1 Consensus size: 19
35117044 TATTATTATT
35117054 ATTATTATTTTAATTAAT-
1 ATTATTATTTTAATTAATA
* * * *
35117072 ATTTTTA-ATTGATAAATA
1 ATTATTATTTTAATTAATA
35117090 ATATATTATTTTAATTAATA
1 AT-TATTATTTTAATTAATA
35117110 A
1 A
35117111 CTCTTTTATT
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
17 7 0.25
18 8 0.29
19 4 0.14
20 9 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
ATTATTATTTTAATTAATA
Found at i:35117181 original size:31 final size:29
Alignment explanation
Indices: 35117121--35117181 Score: 68
Period size: 31 Copynumber: 2.0 Consensus size: 29
35117111 CTCTTTTATT
*
35117121 TATAAAATAAAATAATAAATATGTAATTA
1 TATAAAATAAAATAATAAATATATAATTA
* * *
35117150 TATAATAATAGAAATATTATATATATCATTA
1 TATAA-AATA-AAATAATAAATATATAATTA
35117181 T
1 T
35117182 CTTAAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 5 0.19
30 4 0.15
31 17 0.65
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (29 bp):
TATAAAATAAAATAATAAATATATAATTA
Found at i:35117240 original size:20 final size:18
Alignment explanation
Indices: 35117215--35117251 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 18
35117205 ACTCCTTTAT
35117215 TTATATAAATAAAATAATAA
1 TTATAT-AATAAAA-AATAA
35117235 TTATATAATAAAAAATA
1 TTATATAATAAAAAATA
35117252 TTTTTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 7 0.41
20 6 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TTATATAATAAAAAATAA
Found at i:35117260 original size:20 final size:20
Alignment explanation
Indices: 35117212--35117259 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
35117202 ATAACTCCTT
35117212 TATTTATATAAATAAAATAA
1 TATTTATATAAATAAAATAA
*
35117232 TAATTATAT-AATAAAA-AA
1 TATTTATATAAATAAAATAA
*
35117250 TATTTTTATA
1 TATTTATATA
35117260 TTTATCATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 9 0.38
19 7 0.29
20 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TATTTATATAAATAAAATAA
Found at i:35117276 original size:89 final size:93
Alignment explanation
Indices: 35117102--35117283 Score: 230
Period size: 89 Copynumber: 2.0 Consensus size: 93
35117092 ATATTATTTT
* *
35117102 AATTAATAACTCTTTTATTTATAAAATAAAATAATAAATATGTAATTATATAATAATAGAAATAT
1 AATTAATAACTCCTTTATTTATAAAATAAAATAATAAATATATAATTATATAATAAT--AAATAT
35117167 TATATATATCATTATCTTAAAAATATTTGA
64 TATATATATCATTATCTTAAAAATATTTGA
* * *
35117197 AATTAATAACTCCTTTATTTATATAAATAAAATAATAATTATATAA-TA-A-AA-AAT-ATTTTT
1 AATTAATAACTCCTTTATTTATA-AAATAAAATAATAAATATATAATTATATAATAATAAATATT
* * *
35117257 ATATTTATCATTATGTTAAATATATTT
65 ATATATATCATTATCTTAAAAATATTT
35117284 TATTTTTTAA
Statistics
Matches: 78, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
89 28 0.36
92 3 0.04
93 2 0.03
94 1 0.01
95 24 0.31
96 20 0.26
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (93 bp):
AATTAATAACTCCTTTATTTATAAAATAAAATAATAAATATATAATTATATAATAATAAATATTA
TATATATCATTATCTTAAAAATATTTGA
Found at i:35117727 original size:13 final size:13
Alignment explanation
Indices: 35117709--35117733 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35117699 TAATATATTT
35117709 ATTAATTAAAAAC
1 ATTAATTAAAAAC
35117722 ATTAATTAAAAA
1 ATTAATTAAAAA
35117734 TAAAAAACTT
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:35119180 original size:8 final size:9
Alignment explanation
Indices: 35119149--35119177 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
35119139 ATATGGCCCC
35119149 TTTAAAATT
1 TTTAAAATT
35119158 TTTAAAATT
1 TTTAAAATT
35119167 TTTAAAATT
1 TTTAAAATT
35119176 TT
1 TT
35119178 AAATTACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTAAAATT
Found at i:35122050 original size:17 final size:19
Alignment explanation
Indices: 35122028--35122062 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
35122018 CTAAAATAGT
35122028 AACAAAA-TTA-ACAATAA
1 AACAAAAGTTATACAATAA
35122045 AACAAAAGTTATACAATA
1 AACAAAAGTTATACAATA
35122063 TCCAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (19 bp):
AACAAAAGTTATACAATAA
Found at i:35122155 original size:19 final size:19
Alignment explanation
Indices: 35122128--35122176 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
35122118 TGAAAAAAAC
* *
35122128 AACAATAAAATAGCAACAA
1 AACAGTAAAACAGCAACAA
*
35122147 AACAGTAAAAACAGCAAGAA
1 AACAGT-AAAACAGCAACAA
*
35122167 AATAGTAAAA
1 AACAGTAAAA
35122177 AAATAATAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.67, C:0.12, G:0.10, T:0.10
Consensus pattern (19 bp):
AACAGTAAAACAGCAACAA
Found at i:35122162 original size:20 final size:20
Alignment explanation
Indices: 35122134--35122177 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
35122124 AAACAACAAT
*
35122134 AAAATAGCAACAAAACAGTA
1 AAAACAGCAACAAAACAGTA
* *
35122154 AAAACAGCAAGAAAATAGTA
1 AAAACAGCAACAAAACAGTA
35122174 AAAA
1 AAAA
35122178 AATAATAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.68, C:0.11, G:0.11, T:0.09
Consensus pattern (20 bp):
AAAACAGCAACAAAACAGTA
Found at i:35123035 original size:19 final size:19
Alignment explanation
Indices: 35123007--35123043 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35122997 CAATTAAGTT
* *
35123007 AAATTTAAATTGTTTTTTA
1 AAATTAAAATAGTTTTTTA
35123026 AAATTAAAATAGTTTTTT
1 AAATTAAAATAGTTTTTT
35123044 CATTCATAAA
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:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
AAATTAAAATAGTTTTTTA
Found at i:35128223 original size:33 final size:33
Alignment explanation
Indices: 35128180--35128308 Score: 105
Period size: 33 Copynumber: 3.6 Consensus size: 33
35128170 CAGATGCGGT
*
35128180 GGAATTAGCACTTAGCAACCACCAATGAATAGG
1 GGAATCAGCACTTAGCAACCACCAATGAATAGG
* *
35128213 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGG
1 GGAATCAGCACTTAGCAA-CCAC---CA-A--T-GAATA-GG
*
35128255 TGGAATCAGCACTTAGCAACCACCAATGAATCGG
1 -GGAATCAGCACTTAGCAACCACCAATGAATAGG
* **
35128289 GAAATCAGCACACAGCAACC
1 GGAATCAGCACTTAGCAACC
35128309 CCTTTATATG
Statistics
Matches: 77, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
33 34 0.44
34 5 0.06
35 3 0.04
36 1 0.01
37 2 0.03
38 2 0.03
39 2 0.03
40 1 0.01
41 4 0.05
42 5 0.06
43 18 0.23
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAATAGG
Found at i:35128228 original size:75 final size:76
Alignment explanation
Indices: 35128136--35128310 Score: 271
Period size: 76 Copynumber: 2.3 Consensus size: 76
35128126 CAACCCCTTG
* * * *
35128136 GGGGAATCAGCACTTAGCAACCCCC-TTCACATTTCAGATGCGGTGGAATTAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACC
35128200 ACCAATGAATA
66 ACCAATGAATA
35128211 GGGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACC
*
35128276 ACCAATGAATC
66 ACCAATGAATA
* **
35128287 GGGAAATCAGCACACAGCAACCCC
1 GGGGAATCAGCACTTAGCAACCCC
35128311 TTTATATGCA
Statistics
Matches: 91, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
75 25 0.27
76 66 0.73
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.19
Consensus pattern (76 bp):
GGGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACC
ACCAATGAATA
Found at i:35129660 original size:36 final size:36
Alignment explanation
Indices: 35129613--35129694 Score: 128
Period size: 36 Copynumber: 2.3 Consensus size: 36
35129603 ATGGTCTGAC
* *
35129613 TCTTCTTCCTCAACCGCATTTTCTTCCTCACCTGCA
1 TCTTCTTCCTCAACCGCATCTTCTTCCTCACCTACA
*
35129649 TCTTCTTCCTCAACTGCATCTTCTTCCTCACCTACA
1 TCTTCTTCCTCAACCGCATCTTCTTCCTCACCTACA
*
35129685 ACTTCTTCCT
1 TCTTCTTCCT
35129695 TGGTCACATC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.15, C:0.41, G:0.04, T:0.40
Consensus pattern (36 bp):
TCTTCTTCCTCAACCGCATCTTCTTCCTCACCTACA
Found at i:35129689 original size:18 final size:18
Alignment explanation
Indices: 35129613--35129694 Score: 112
Period size: 18 Copynumber: 4.6 Consensus size: 18
35129603 ATGGTCTGAC
35129613 TCTTCTTCCTCAACC-GCA
1 TCTTCTTCCTC-ACCTGCA
*
35129631 TTTTCTTCCTCACCTGCA
1 TCTTCTTCCTCACCTGCA
*
35129649 TCTTCTTCCTCAACTGCA
1 TCTTCTTCCTCACCTGCA
*
35129667 TCTTCTTCCTCACCTACA
1 TCTTCTTCCTCACCTGCA
*
35129685 ACTTCTTCCT
1 TCTTCTTCCT
35129695 TGGTCACATC
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
17 3 0.05
18 54 0.95
ACGTcount: A:0.15, C:0.41, G:0.04, T:0.40
Consensus pattern (18 bp):
TCTTCTTCCTCACCTGCA
Found at i:35133893 original size:24 final size:24
Alignment explanation
Indices: 35133866--35133911 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
35133856 AAACCTAATT
35133866 CTAATCAAAGTC-AAATATATTACG
1 CTAAT-AAAGTCTAAATATATTACG
*
35133890 CTAATAAATTCTAAATATATTA
1 CTAATAAAGTCTAAATATATTA
35133912 TACTCATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (24 bp):
CTAATAAAGTCTAAATATATTACG
Found at i:35133920 original size:24 final size:24
Alignment explanation
Indices: 35133878--35133929 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
35133868 AATCAAAGTC
* *
35133878 AAATATATTACGCTAATAAATTCT
1 AAATATATTACACTAATAAATACT
* *
35133902 AAATATATTATACTCATAAATACT
1 AAATATATTACACTAATAAATACT
35133926 AAAT
1 AAAT
35133930 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATATATTACACTAATAAATACT
Found at i:35136636 original size:22 final size:22
Alignment explanation
Indices: 35136605--35136649 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
35136595 TTTGTACTTA
*
35136605 TGGATTGAAGAAATAAGTGAAG
1 TGGATCGAAGAAATAAGTGAAG
*
35136627 TGGATCGAAGAAATGAGTGAAG
1 TGGATCGAAGAAATAAGTGAAG
35136649 T
1 T
35136650 AGTAACTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.33, T:0.22
Consensus pattern (22 bp):
TGGATCGAAGAAATAAGTGAAG
Found at i:35139048 original size:25 final size:26
Alignment explanation
Indices: 35139027--35139076 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
35139017 CAAAAAAACT
* *
35139027 AAAATCTAACCTAAAAA-GAAAAGAG
1 AAAACCTAAACTAAAAATGAAAAGAG
35139052 AAAACCTAAACTAAAAATGAAAAGA
1 AAAACCTAAACTAAAAATGAAAAGA
35139077 ATAGAAACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.66, C:0.12, G:0.10, T:0.12
Consensus pattern (26 bp):
AAAACCTAAACTAAAAATGAAAAGAG
Found at i:35143068 original size:12 final size:12
Alignment explanation
Indices: 35143017--35143071 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
35143007 TTTCTTTTGT
35143017 TTCTTTTTCTAA-
1 TTCTTTTTC-AAC
* *
35143029 TTCATTTTC-TC
1 TTCTTTTTCAAC
35143040 TTCTTTCTTCAAC
1 TTCTTT-TTCAAC
*
35143053 TTCTTTTTCAAT
1 TTCTTTTTCAAC
35143065 TTCTTTT
1 TTCTTTT
35143072 CTGTTTCACA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
11 5 0.14
12 23 0.66
13 7 0.20
ACGTcount: A:0.13, C:0.22, G:0.00, T:0.65
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:35143078 original size:17 final size:18
Alignment explanation
Indices: 35143053--35143090 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
35143043 TTTCTTCAAC
* *
35143053 TTCTTTTTCA-ATTTCTT
1 TTCTGTTTCACATTCCTT
35143070 TTCTGTTTCACATTCCTT
1 TTCTGTTTCACATTCCTT
35143088 TTC
1 TTC
35143091 ACTCTCTCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.24, G:0.03, T:0.63
Consensus pattern (18 bp):
TTCTGTTTCACATTCCTT
Found at i:35146819 original size:23 final size:20
Alignment explanation
Indices: 35146767--35146819 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
35146757 CCACGTCTTT
*
35146767 TTCTTTTGTTTCTTTTTCTAA
1 TTCTTTT-TCTCTTTTTCTAA
*
35146788 TTCATTTTCTCTTATTTCTCAA
1 TTCTTTTTCTCTT-TTTCT-AA
35146810 CTTCTTTTTC
1 -TTCTTTTTC
35146820 ATTTTTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 5 0.19
21 11 0.42
22 2 0.08
23 8 0.31
ACGTcount: A:0.11, C:0.21, G:0.02, T:0.66
Consensus pattern (20 bp):
TTCTTTTTCTCTTTTTCTAA
Found at i:35151265 original size:6 final size:6
Alignment explanation
Indices: 35151254--35151281 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
35151244 CACTGATCTT
35151254 CCCTTC CCCTTC CCCTTC CCCTTC CCCT
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCT
35151282 ATCCTTGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CCCTTC
Found at i:35153869 original size:22 final size:24
Alignment explanation
Indices: 35153819--35153869 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 24
35153809 TTGCAATGCT
35153819 TTTATATTTTAATAATTGAATATTA
1 TTTATATTTTAAT-ATTGAATATTA
35153844 -TTATATATTTAAT-TTG-AT-TTA
1 TTTATAT-TTTAATATTGAATATTA
35153865 TTTAT
1 TTTAT
35153870 TTATAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
21 3 0.12
22 6 0.25
23 3 0.12
24 6 0.25
25 6 0.25
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (24 bp):
TTTATATTTTAATATTGAATATTA
Found at i:35154080 original size:34 final size:35
Alignment explanation
Indices: 35154027--35154093 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
35154017 CAAACACCAG
* *
35154027 AAAATATTTTTCAGCAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGCAAATCATTTTACAGAAAAGT
*
35154062 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGCAAATCATTTTACAGAAAA
35154094 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGCAAATCATTTTACAGAAAAGT
Found at i:35154085 original size:14 final size:14
Alignment explanation
Indices: 35154062--35154101 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
35154052 ACAGAAAAGT
*
35154062 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
35154076 AAATCATTTTACGG
1 AAAACATTTTACAG
35154090 AAAACATTTTAC
1 AAAACATTTTAC
35154102 TGACAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:35162817 original size:41 final size:41
Alignment explanation
Indices: 35162789--35162931 Score: 196
Period size: 41 Copynumber: 3.5 Consensus size: 41
35162779 TGATTCAGAA
*
35162789 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTATTT
* *
35162830 CACCAGCATTAAGCCTGCTAGATGTAAAGTCTGAATTATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTATTT
* * *
35162871 CACTGGCACTAAGCTTGCTAGACGTAAAGTCTGAATTATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTATTT
* ** *
35162912 GACTAGCATTAAGTCTGCTA
1 CACCGGCATTAAGCCTGCTA
35162932 AGCACAGAGC
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 89 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTATTT
Found at i:35166020 original size:75 final size:75
Alignment explanation
Indices: 35165881--35166085 Score: 266
Period size: 75 Copynumber: 2.7 Consensus size: 75
35165871 AAAGAAAAGG
* * * * * *
35165881 ATTCATGGCATTGCCTTCGATAGAATATCCATTGAATTGGCAGATCGAGGTACATGAAATATGAC
1 ATTCATGACGTTGCCTTCGATAGAATATCCATTGAACTGGCAGATCGTGGTACATAAAACATGAC
*
35165946 TCTATACTGA
66 TCTATAATGA
* ** * * *
35165956 ATTTATGGTGTTGCCTTCGATGGAATATCCTTTGAACTGGTAGATCGTGGTACATAAAACATGAC
1 ATTCATGACGTTGCCTTCGATAGAATATCCATTGAACTGGCAGATCGTGGTACATAAAACATGAC
35166021 TCTATAATGA
66 TCTATAATGA
* * *
35166031 ATTCATGACGTTGCCTTCGATACAAAATGCATTGAACTGGCAGATCGTGGTACAT
1 ATTCATGACGTTGCCTTCGATAGAATATCCATTGAACTGGCAGATCGTGGTACAT
35166086 GAATAATGGT
Statistics
Matches: 110, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 110 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (75 bp):
ATTCATGACGTTGCCTTCGATAGAATATCCATTGAACTGGCAGATCGTGGTACATAAAACATGAC
TCTATAATGA
Found at i:35176235 original size:26 final size:27
Alignment explanation
Indices: 35176205--35176257 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
35176195 CCACCACTGA
*
35176205 ATCGGGG-AATCAGCACTTAGCAACCC
1 ATCGGGGAAATCAGCACATAGCAACCC
35176231 ATCGGGGAAATCAGCACATAGCAACCC
1 ATCGGGGAAATCAGCACATAGCAACCC
35176258 CCTTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.34, C:0.30, G:0.23, T:0.13
Consensus pattern (27 bp):
ATCGGGGAAATCAGCACATAGCAACCC
Found at i:35176443 original size:26 final size:27
Alignment explanation
Indices: 35176414--35176466 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
35176404 ACCAATGAAA
*
35176414 TCGGGG-AATCAGCACTTAGCAACCCC
1 TCGGGGAAATCAGCACATAGCAACCCC
35176440 TCGGGGAAATCAGCACATAGCAACCCC
1 TCGGGGAAATCAGCACATAGCAACCCC
35176467 CTTTCACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.30, C:0.34, G:0.23, T:0.13
Consensus pattern (27 bp):
TCGGGGAAATCAGCACATAGCAACCCC
Found at i:35176477 original size:105 final size:103
Alignment explanation
Indices: 35176174--35176544 Score: 591
Period size: 105 Copynumber: 3.6 Consensus size: 103
35176164 TAGCCGTTAT
** * *
35176174 TGGTGGATCCCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCATCGGGGA
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
*
35176239 AATCAGCACATAGCAACCCCCTTTTTATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
*
35176277 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
35176342 AATCAGCACATAGCAACCCCCCTTTTCATTTCAAAGATA
66 AATCAGCACATAGCAA-CCCCCTTTTCATTTCAAAGATA
35176381 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATG-AATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
*
35176446 AAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
65 AAATCAGCACATAGCAACCCCCTTT-TCATTTCAAAGATA
* * * **
35176486 TGGTGGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
35176545 TTTATATACA
Statistics
Matches: 251, Mismatches: 13, Indels: 7
0.93 0.05 0.03
Matches are distributed among these distances:
103 76 0.30
104 86 0.34
105 88 0.35
106 1 0.00
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.20
Consensus pattern (103 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
Found at i:35176906 original size:29 final size:29
Alignment explanation
Indices: 35176873--35176936 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
35176863 TAATCCACCA
35176873 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
35176902 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
35176932 CCCAA
1 CCCAA
35176937 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:35176910 original size:30 final size:30
Alignment explanation
Indices: 35176880--35176936 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
35176870 CCACCCAACT
35176880 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
35176909 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
35176937 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:35185107 original size:14 final size:14
Alignment explanation
Indices: 35185084--35185117 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
35185074 TTATGCCTAA
35185084 ATTTAAATTTTAAT
1 ATTTAAATTTTAAT
*
35185098 ATTTACATTTTAAT
1 ATTTAAATTTTAAT
*
35185112 TTTTAA
1 ATTTAA
35185118 CGTAATTTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTAAATTTTAAT
Found at i:35197273 original size:25 final size:25
Alignment explanation
Indices: 35197208--35197277 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
35197198 CGTATTGCCC
* * *
35197208 CATAGCTCGTATGAGCTTATCGATT
1 CATAGCTCGTATGAGCATACCAATT
* * *
35197233 TACAGCTCG-AGAGAGCATACCAATT
1 CATAGCTCGTA-TGAGCATACCAATT
35197258 CATAGCTCGTATGAGCATAC
1 CATAGCTCGTATGAGCATAC
35197278 ATGTATAGGA
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
24 1 0.03
25 32 0.94
26 1 0.03
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (25 bp):
CATAGCTCGTATGAGCATACCAATT
Found at i:35198909 original size:120 final size:120
Alignment explanation
Indices: 35198691--35198928 Score: 413
Period size: 120 Copynumber: 2.0 Consensus size: 120
35198681 CCCCTGCAAC
* *
35198691 TTTGGAATTTTTCAATGCTTTCTTAAAAATTCTCTGAGTTCCTGATTTAGTCTCGACTTGTTTCT
1 TTTGAAATTTTTCAATGCTTTCTGAAAAATTCTCTGAGTTCCTGATTTAGTCTCGACTTGTTTCT
*
35198756 AACATGTATTTAGGGCCTCGAGGTCTCGTATAAGGGACAATATGTATGATTTTGA
66 AACATGTATTTAGGGCCTCGAGGGCTCGTATAAGGGACAATATGTATGATTTTGA
*
35198811 TTTGAAATTTTTCAATGCTTTCTGAAAAATTCTCTGAGTTCTTGATTTAGTCTCGACTTGTTTCT
1 TTTGAAATTTTTCAATGCTTTCTGAAAAATTCTCTGAGTTCCTGATTTAGTCTCGACTTGTTTCT
* * *
35198876 AACCTGTATTTAGGGCCTTGAGGGCTTGTATAAGGGACAATATGTATGATTTT
66 AACATGTATTTAGGGCCTCGAGGGCTCGTATAAGGGACAATATGTATGATTTT
35198929 AATTGGTTTT
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 111 1.00
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.42
Consensus pattern (120 bp):
TTTGAAATTTTTCAATGCTTTCTGAAAAATTCTCTGAGTTCCTGATTTAGTCTCGACTTGTTTCT
AACATGTATTTAGGGCCTCGAGGGCTCGTATAAGGGACAATATGTATGATTTTGA
Found at i:35201684 original size:40 final size:44
Alignment explanation
Indices: 35201639--35201737 Score: 125
Period size: 44 Copynumber: 2.3 Consensus size: 44
35201629 TCATATTACT
*
35201639 TTAATTAA-TTAAATATA-AA-ATAATAATTTAATA-TTATCAC
1 TTAATTAATTTAAATATACAATATAAAAATTTAATATTTATCAC
* * *
35201679 TTAATTAATTTAAATGTACAATATAAAAATTTATTATTTATCTC
1 TTAATTAATTTAAATATACAATATAAAAATTTAATATTTATCAC
*
35201723 TTATTTAATTTAAAT
1 TTAATTAATTTAAAT
35201738 TAATTAGAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
40 8 0.16
41 8 0.16
42 2 0.04
43 12 0.24
44 20 0.40
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.47
Consensus pattern (44 bp):
TTAATTAATTTAAATATACAATATAAAAATTTAATATTTATCAC
Found at i:35206368 original size:10 final size:10
Alignment explanation
Indices: 35206353--35206379 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
35206343 TTAAGTTTAG
35206353 TGTGTTTAAA
1 TGTGTTTAAA
35206363 TGTGTTTAAA
1 TGTGTTTAAA
35206373 TGTGTTT
1 TGTGTTT
35206380 GTTAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (10 bp):
TGTGTTTAAA
Found at i:35208114 original size:12 final size:12
Alignment explanation
Indices: 35208099--35208123 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35208089 GATCCCTATA
35208099 AAGAAAGTGATC
1 AAGAAAGTGATC
35208111 AAGAAAGTGATC
1 AAGAAAGTGATC
35208123 A
1 A
35208124 TTCATCTGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.24, T:0.16
Consensus pattern (12 bp):
AAGAAAGTGATC
Found at i:35214191 original size:24 final size:25
Alignment explanation
Indices: 35214163--35214218 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
35214153 TTAATATTGT
35214163 TTTCTCTCATCCCATAATCTT-TCTA
1 TTTCTCTCA-CCCATAATCTTCTCTA
*
35214188 -TTCTCTCACCCTTAATCTTCTCTA
1 TTTCTCTCACCCATAATCTTCTCTA
35214212 TTTCTCT
1 TTTCTCT
35214219 TATTTTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 10 0.36
24 12 0.43
25 6 0.21
ACGTcount: A:0.16, C:0.34, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTCTCTCACCCATAATCTTCTCTA
Found at i:35215487 original size:13 final size:13
Alignment explanation
Indices: 35215464--35215495 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
35215454 AGGCAAGGCT
35215464 ACTGTTCGTTGATC
1 ACTG-TCGTTGATC
35215478 ACTGTCGTTGATC
1 ACTGTCGTTGATC
35215491 ACTGT
1 ACTGT
35215496 AGTCGTGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.41
Consensus pattern (13 bp):
ACTGTCGTTGATC
Found at i:35219003 original size:35 final size:35
Alignment explanation
Indices: 35218957--35219028 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
35218947 GTTATGGTCG
35218957 AATCCAGAAGTGTTACAAAGAAGGGTTTCGAAACT
1 AATCCAGAAGTGTTACAAAGAAGGGTTTCGAAACT
*
35218992 AATCCGGAAGTGTTACAAAGAAGGGTTTCGAAACT
1 AATCCAGAAGTGTTACAAAGAAGGGTTTCGAAACT
35219027 AA
1 AA
35219029 CTTTACTTCG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (35 bp):
AATCCAGAAGTGTTACAAAGAAGGGTTTCGAAACT
Found at i:35228103 original size:44 final size:43
Alignment explanation
Indices: 35228055--35228274 Score: 131
Period size: 47 Copynumber: 4.9 Consensus size: 43
35228045 AATATTAATT
35228055 ATTTTAAATTGTATAAATTCATATAAAAAAATTTATTATCAAGA
1 ATTTTAAATT-TATAAATTCATATAAAAAAATTTATTATCAAGA
* * * * * * **
35228099 ATTTTATGAAATTATATA-TCATTATTAAATTATATTTAATATTAATT
1 ATTTTA--AATTTATAAATTCA-TA-TAAA-AAAATTTATTATCAAGA
*
35228146 ATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAAGA
1 ATTTTAAATT-TATAAATTCATATAAAAAAATTTATTATCAAGA
* * * * * **
35228190 ATTTTATGAAATTATATATT-ATTATTAAATTATATTTAATAAT-AATT
1 ATTTTA--AATTTATAAATTCA-TA-TAAA-AAAATTT-ATTATCAAGA
* *
35228237 ATTTTAAATTATACAAATTCATATAAGAAAATTTATTA
1 ATTTTAAATT-TATAAATTCATATAAAAAAATTTATTA
35228275 GTTATAATTA
Statistics
Matches: 129, Mismatches: 32, Indels: 31
0.67 0.17 0.16
Matches are distributed among these distances:
43 3 0.02
44 32 0.25
45 28 0.22
46 28 0.22
47 34 0.26
48 4 0.03
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (43 bp):
ATTTTAAATTTATAAATTCATATAAAAAAATTTATTATCAAGA
Found at i:35228105 original size:91 final size:91
Alignment explanation
Indices: 35227976--35228274 Score: 508
Period size: 91 Copynumber: 3.3 Consensus size: 91
35227966 TTGATTTTAG
* * *
35227976 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAA-AAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
*
35228041 ATTTAATATTAATTATTTTAAATTGTA
65 ATTTAATATTAATTATTTTAAATTATA
35228068 TAAATTCATATAAAAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAAAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
35228133 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
* *
35228159 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAAAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
35228224 TTTAATAATAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
* *
35228250 CAAATTCATATAAGAAAATTTATTA
1 TAAATTCATATAAAAAAATTTATTA
35228275 GTTATAATTA
Statistics
Matches: 199, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
91 186 0.93
92 13 0.07
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAAAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATATTAATTATTTTAAATTATA
Found at i:35228214 original size:101 final size:92
Alignment explanation
Indices: 35228160--35228351 Score: 176
Period size: 101 Copynumber: 2.0 Consensus size: 92
35228150 TAAATTATAT
35228160 AAATTCATATAAGAAAATTTATTA-TCAAGAATT-TTATGA--AATTATATATTATTATTAAATT
1 AAATTCATATAAGAAAATTTATTAGT-AAGAATTATT-TGATTAATTATATA-TATTATTAAATT
* *
35228221 ATATTTAATAATAATTATTTTAAATTATAC
63 ATATTTAATATTAATTATTTTAAATTATAT
* * * *
35228251 AAATTCATATAAGAAAATTTATTAGTTATAATTATTTTCAATTTTATTAAATCATATATTTTAAT
1 AAATTCATATAAGAAAATTTATTAGTAAGAATTA-TTT-GA-TTAATT--AT-ATATA--TT-AT
* *
35228316 TAAAATATATTTAATATTAATTATTTCAAATTATAT
57 TAAATTATATTTAATATTAATTATTTTAAATTATAT
35228352 TTTATAGTAT
Statistics
Matches: 80, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
91 29 0.36
92 2 0.03
93 3 0.04
96 3 0.04
98 4 0.05
99 3 0.04
100 2 0.03
101 34 0.43
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.48
Consensus pattern (92 bp):
AAATTCATATAAGAAAATTTATTAGTAAGAATTATTTGATTAATTATATATATTATTAAATTATA
TTTAATATTAATTATTTTAAATTATAT
Found at i:35228355 original size:59 final size:58
Alignment explanation
Indices: 35228291--35228489 Score: 145
Period size: 59 Copynumber: 3.3 Consensus size: 58
35228281 ATTATTTTCA
35228291 ATTTTATTA-AATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTAT
1 ATTTTA-TAGAATCATATATTTTAATTAAAATATATTTAATA-TAATTATCTT-AAATTAT
* * * ** * * * ** * *
35228350 ATTTTATAGTATCATATATTATGATTTTAGTA-AATTCATATAAGAATCTTGATTATTAAGA
1 ATTTTATAGAATCATATATTTTAATTAAAATATATTTAATATAATTATCTT-A-AATT-A-T
* *
35228411 ATTTTATTA-AATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTAT
1 ATTTTA-TAGAATCATATATTTTAATTAAAATATATTTAAT-ATAATTATCTTAAATTAT
* *
35228470 CTTTTATAGTATCATATATT
1 ATTTTATAGAATCATATATT
35228490 ATGATTTGAG
Statistics
Matches: 101, Mismatches: 30, Indels: 18
0.68 0.20 0.12
Matches are distributed among these distances:
57 5 0.05
58 13 0.13
59 40 0.40
60 2 0.02
61 25 0.25
62 8 0.08
63 8 0.08
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (58 bp):
ATTTTATAGAATCATATATTTTAATTAAAATATATTTAATATAATTATCTTAAATTAT
Found at i:35228419 original size:120 final size:120
Alignment explanation
Indices: 35228290--35228553 Score: 458
Period size: 120 Copynumber: 2.2 Consensus size: 120
35228280 AATTATTTTC
* *
35228290 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
* * *
35228354 TATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATCTTGATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
35228410 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
35228475 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
35228530 AATTTTATTAAATTATATATTTTA
1 AATTTTATTAAATTATATATTTTA
35228554 TAGTATCGTA
Statistics
Matches: 137, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
120 135 0.99
121 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:35228439 original size:18 final size:17
Alignment explanation
Indices: 35228411--35228445 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35228401 ATTATTAAGA
*
35228411 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
35228428 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
35228446 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:35228547 original size:59 final size:59
Alignment explanation
Indices: 35228364--35228547 Score: 155
Period size: 66 Copynumber: 3.1 Consensus size: 59
35228354 TATAGTATCA
* * *
35228364 TATATTATGATTTTAGTAAATTCATATAAGAATCTTGATTATTAAGAATTTTATTAAAT
1 TATATTATGATTTAAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
* * ** * * *
35228423 TATA-TAT--TTTAATTAAAAT-ATAT-TTAATAATAATTATGTTA-AATTATCTTTTATAGTAT
1 TATATTATGATTTAAGTAAATTCATATAAGAATATTAATTAT-TAAGAATT-T-TATTA-A--AT
*
35228482 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 --TATATTATGATTTAAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
35228543 TATAT
1 TATAT
35228548 ATTTTATAGT
Statistics
Matches: 93, Mismatches: 18, Indels: 28
0.67 0.13 0.20
Matches are distributed among these distances:
54 13 0.14
55 7 0.08
56 13 0.14
57 1 0.01
58 3 0.03
59 11 0.12
61 6 0.06
62 3 0.03
63 1 0.01
64 13 0.14
65 7 0.08
66 15 0.16
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (59 bp):
TATATTATGATTTAAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
Found at i:35228566 original size:78 final size:78
Alignment explanation
Indices: 35228471--35228644 Score: 305
Period size: 78 Copynumber: 2.2 Consensus size: 78
35228461 TTAAATTATC
35228471 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTT
1 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTT
35228536 ATTAAATTATATA
66 ATTAAATTATATA
* *
35228549 TTTTATAGTATCGTATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTT
1 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTT
35228614 ATTAAATTATATA
66 ATTAAATTATATA
* *
35228627 TTTTA-ATTATAATATATT
1 TTTTATAGTATCATATATT
35228645 TAATAATAAT
Statistics
Matches: 91, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
77 10 0.11
78 81 0.89
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (78 bp):
TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTT
ATTAAATTATATA
Found at i:35228643 original size:16 final size:16
Alignment explanation
Indices: 35228622--35228663 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
35228612 TTATTAAATT
*
35228622 ATATATTTTAATTATA
1 ATATATTTTAATAATA
35228638 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
35228653 AT-TATGTTTAA
1 ATATAT-TTTAA
35228664 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:35228648 original size:15 final size:15
Alignment explanation
Indices: 35228613--35228654 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
35228603 TTAAGAATTT
*
35228613 TATTAAATTAT-ATA
1 TATTTAATTATAATA
35228627 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
35228641 TATTTAATAATAAT
1 TATTTAATTATAAT
35228655 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:35228923 original size:16 final size:16
Alignment explanation
Indices: 35228877--35228925 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
35228867 TTAATTTGCT
* *
35228877 ATTACGTCTCTATTCC
1 ATTACGCCTCTATTTC
*
35228893 ATTACACCTCTATTTC
1 ATTACGCCTCTATTTC
35228909 ATTACGCCTCTATTTC
1 ATTACGCCTCTATTTC
35228925 A
1 A
35228926 ATACAGCGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.22, C:0.31, G:0.04, T:0.43
Consensus pattern (16 bp):
ATTACGCCTCTATTTC
Found at i:35237599 original size:2 final size:2
Alignment explanation
Indices: 35237592--35237624 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35237582 TCCATCTACT
35237592 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
35237625 TCCACTTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:35244199 original size:16 final size:16
Alignment explanation
Indices: 35244178--35244208 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35244168 TCTTCAAGAA
*
35244178 AAGAAAGATTACGCCC
1 AAGAAAGAGTACGCCC
35244194 AAGAAAGAGTACGCC
1 AAGAAAGAGTACGCC
35244209 TACGCCCTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.10
Consensus pattern (16 bp):
AAGAAAGAGTACGCCC
Found at i:35246280 original size:25 final size:25
Alignment explanation
Indices: 35246189--35246282 Score: 77
Period size: 25 Copynumber: 3.8 Consensus size: 25
35246179 TCATGTACAT
35246189 GTATGCTCAT-ATGAGCTGTGAAAT-G
1 GTATGCTC-TCATGAGCTGT-AAATCG
* * *
35246214 GTATGCTCAC-TCGAGCTGTAGATCA
1 GTATGCTCTCAT-GAGCTGTAAATCG
* ** *
35246239 GTATGCTCTTACAAGCTATAAATCG
1 GTATGCTCTCATGAGCTGTAAATCG
35246264 GTATGCTCTCATGAGCTGT
1 GTATGCTCTCATGAGCTGT
35246283 GAAGTATCCG
Statistics
Matches: 51, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
24 4 0.08
25 47 0.92
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (25 bp):
GTATGCTCTCATGAGCTGTAAATCG
Found at i:35248526 original size:25 final size:25
Alignment explanation
Indices: 35248498--35248554 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
35248488 ACTTGTGAAG
35248498 CCTTTGTGGTGAGTCACCTATAAAA
1 CCTTTGTGGTGAGTCACCTATAAAA
* * *
35248523 CCTTTGTGGTGAGTCACTTGTAAAG
1 CCTTTGTGGTGAGTCACCTATAAAA
35248548 CCTTTGT
1 CCTTTGT
35248555 TGTAATAACC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (25 bp):
CCTTTGTGGTGAGTCACCTATAAAA
Found at i:35249889 original size:21 final size:21
Alignment explanation
Indices: 35249863--35249905 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
35249853 TTTGGGTGGA
**
35249863 TCAGCTCTTGCGAGCTTCTGT
1 TCAGCTCTCACGAGCTTCTGT
35249884 TCAGCTCTCACGAGCTTCTGT
1 TCAGCTCTCACGAGCTTCTGT
35249905 T
1 T
35249906 GGCGTGTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.12, C:0.30, G:0.21, T:0.37
Consensus pattern (21 bp):
TCAGCTCTCACGAGCTTCTGT
Found at i:35257119 original size:30 final size:31
Alignment explanation
Indices: 35257080--35257139 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
35257070 AGAGATGAGA
*
35257080 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
35257111 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
35257140 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:35257743 original size:18 final size:18
Alignment explanation
Indices: 35257720--35257766 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
35257710 TCGAGTTGAT
35257720 TCGAATAACTCGATTTAC
1 TCGAATAACTCGATTTAC
*
35257738 TCGAATAACTTGATTTAC
1 TCGAATAACTCGATTTAC
35257756 TCGAATAACTC
1 TCGAATAACTC
35257767 AATTCGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (18 bp):
TCGAATAACTCGATTTAC
Found at i:35262486 original size:21 final size:21
Alignment explanation
Indices: 35262460--35262502 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
35262450 ATTTGGTGGA
*
35262460 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTCACGAGCTTCTGT
35262481 TCAGCTCTCACGAGCTTCTGT
1 TCAGCTCTCACGAGCTTCTGT
35262502 T
1 T
35262503 GGCGTGTTCT
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:0.14, C:0.30, G:0.19, T:0.37
Consensus pattern (21 bp):
TCAGCTCTCACGAGCTTCTGT
Found at i:35263800 original size:50 final size:50
Alignment explanation
Indices: 35263730--35264113 Score: 380
Period size: 50 Copynumber: 7.7 Consensus size: 50
35263720 GGGTGTTACA
* *
35263730 TTTGTGGTGAGTCACCTGTAAAG-CTCTTGTGACAATTTACTTGGGAAGCC
1 TTTGTGGTGAGTCACCTGTAAAGCCT-TTGTGGCGATTTACTTGGGAAGCC
* * * * * *
35263780 TTTGTGGCGAGTTACTTGTAAAGCCCTTGTGACAATTTACTTGGGAAGCC
1 TTTGTGGTGAGTCACCTGTAAAGCCTTTGTGGCGATTTACTTGGGAAGCC
* * * * *
35263830 TTCGTGGTGAGTCACCTGTAAGGTCTTTGTGGTGATTTACTTGGGAAGCT
1 TTTGTGGTGAGTCACCTGTAAAGCCTTTGTGGCGATTTACTTGGGAAGCC
* * ** * *
35263880 TTTATGGCGAGTCACCCATAAAGCCTTTTTGGTGATTTACTT-GGAAGGCC
1 TTTGTGGTGAGTCACCTGTAAAGCCTTTGTGGCGATTTACTTGGGAA-GCC
* * * *
35263930 TTTGTGGTGAGTCACCTATAAAGCCTTTTTGGTGATTTACTTGGGAAACC
1 TTTGTGGTGAGTCACCTGTAAAGCCTTTGTGGCGATTTACTTGGGAAGCC
* * * *
35263980 TTTGTGGTGAGTCACCTGTAAAGCCTTTGTGACGATTTTCTTGGAAAACC
1 TTTGTGGTGAGTCACCTGTAAAGCCTTTGTGGCGATTTACTTGGGAAGCC
* * * * *
35264030 TTTGTGGTAACTCACTTGTAAAGCCTTTGTGGCAATTTATTTGGGAAGTCC
1 TTTGTGGTGAGTCACCTGTAAAGCCTTTGTGGCGATTTACTTGGGAAG-CC
** * *
35264081 -TTGT-GACAGGTTACCTGTAAAGCCTATGTGGCG
1 TTTGTGGTGA-GTCACCTGTAAAGCCTTTGTGGCG
35264114 TAATGCTTGG
Statistics
Matches: 279, Mismatches: 50, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
49 6 0.02
50 266 0.95
51 7 0.03
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (50 bp):
TTTGTGGTGAGTCACCTGTAAAGCCTTTGTGGCGATTTACTTGGGAAGCC
Found at i:35264058 original size:25 final size:25
Alignment explanation
Indices: 35263730--35264061 Score: 157
Period size: 25 Copynumber: 13.3 Consensus size: 25
35263720 GGGTGTTACA
* *
35263730 TTTGTGGTGAGTCACCTGTAAAG-C
1 TTTGTGGTGATTCACTTGTAAAGCC
*** * **
35263754 TCTTGTGACAATTTACTTGGGAAGCC
1 T-TTGTGGTGATTCACTTGTAAAGCC
*
35263780 TTTGTGGCGAGTT-ACTTGTAAAGCC
1 TTTGTGGTGA-TTCACTTGTAAAGCC
* *** * **
35263805 CTTGTGACAATTTACTTGGGAAGCC
1 TTTGTGGTGATTCACTTGTAAAGCC
* * * * *
35263830 TTCGTGGTGAGTCACCTGTAAGGTC
1 TTTGTGGTGATTCACTTGTAAAGCC
* ** *
35263855 TTTGTGGTGATTTACTTGGGAAGCT
1 TTTGTGGTGATTCACTTGTAAAGCC
* * * ***
35263880 TTTATGGCGAGTCACCCATAAAGCC
1 TTTGTGGTGATTCACTTGTAAAGCC
* * * *
35263905 TTTTTGGTGATTTACTTGGAAGGCC
1 TTTGTGGTGATTCACTTGTAAAGCC
* * *
35263930 TTTGTGGTGAGTCACCTATAAAGCC
1 TTTGTGGTGATTCACTTGTAAAGCC
* * *
35263955 TTTTTGGTGATTTACTTGGGAAA-CC
1 TTTGTGGTGATTCACTT-GTAAAGCC
* *
35263980 TTTGTGGTGAGTCACCTGTAAAGCC
1 TTTGTGGTGATTCACTTGTAAAGCC
** ** * *
35264005 TTTGTGACGATTTTCTTGGAAAACC
1 TTTGTGGTGATTCACTTGTAAAGCC
* *
35264030 TTTGTGGTAACTCACTTGTAAAGCC
1 TTTGTGGTGATTCACTTGTAAAGCC
35264055 TTTGTGG
1 TTTGTGG
35264062 CAATTTATTT
Statistics
Matches: 211, Mismatches: 91, Indels: 11
0.67 0.29 0.04
Matches are distributed among these distances:
24 7 0.03
25 197 0.93
26 7 0.03
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (25 bp):
TTTGTGGTGATTCACTTGTAAAGCC
Found at i:35266498 original size:40 final size:38
Alignment explanation
Indices: 35266434--35266622 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 38
35266424 ATCTAATGTT
* * *
35266434 CCATTTCATATATCTATTTCCATATAACCTATTCATATAA
1 CCATTTCATATAT-T-TTTTCATATAACCGATTCGTATAA
*
35266474 GCATTTCATATATCATTTTTCATATAACCGATTCGTATAA
1 CCATTTCATATAT--TTTTTCATATAACCGATTCGTATAA
* *
35266514 CCATTTCATATATTTATTTCCATATAACCAATACGTATAA
1 CCATTTCATATATTT-TTT-CATATAACCGATTCGTATAA
* *
35266554 CCATTTCATATATAATTTTTTATATAATCGATTCGTATAA
1 CCATTTCATATAT--TTTTTCATATAACCGATTCGTATAA
* *
35266594 ACATTTCGTATATTTATTTCCATATAACC
1 CCATTTCATATATTT-TTT-CATATAACC
35266623 AATCATATAT
Statistics
Matches: 126, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
38 4 0.03
39 6 0.05
40 110 0.87
41 4 0.03
42 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (38 bp):
CCATTTCATATATTTTTTCATATAACCGATTCGTATAA
Found at i:35266532 original size:80 final size:79
Alignment explanation
Indices: 35266434--35266631 Score: 288
Period size: 80 Copynumber: 2.5 Consensus size: 79
35266424 ATCTAATGTT
* * *
35266434 CCATTTCATATATCTATTTCCATATAACCTATTCATATAAGCATTTCATATATCATTTTTCATAT
1 CCATTTCATATATTTATTTCCATATAACC-ATTCATATAACCATTTCATATATAATTTTTCATAT
35266499 AACCGATTCGTATAA
65 AACCGATTCGTATAA
* * *
35266514 CCATTTCATATATTTATTTCCATATAACCAATACGTATAACCATTTCATATATAATTTTTTATAT
1 CCATTTCATATATTTATTTCCATATAACC-ATTCATATAACCATTTCATATATAATTTTTCATAT
*
35266579 AATCGATTCGTATAA
65 AACCGATTCGTATAA
* * *
35266594 ACATTTCGTATATTTATTTCCATATAACCAATCATATA
1 CCATTTCATATATTTATTTCCATATAACCATTCATATA
35266632 TAATTTTTTC
Statistics
Matches: 105, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
79 6 0.06
80 99 0.94
ACGTcount: A:0.35, C:0.18, G:0.04, T:0.43
Consensus pattern (79 bp):
CCATTTCATATATTTATTTCCATATAACCATTCATATAACCATTTCATATATAATTTTTCATATA
ACCGATTCGTATAA
Found at i:35266565 original size:13 final size:13
Alignment explanation
Indices: 35266434--35266565 Score: 90
Period size: 13 Copynumber: 9.9 Consensus size: 13
35266424 ATCTAATGTT
*
35266434 CCATTTCATATAT
1 CCATTTCATATAA
*
35266447 CTATTTCCATATAA
1 CCATTT-CATATAA
35266461 CC-TATTCATATAA
1 CCAT-TTCATATAA
*
35266474 GCATTTCATAT-A
1 CCATTTCATATAA
*
35266486 TCATTTTTCATATAA
1 CCA--TTTCATATAA
*
35266501 CCGA-TTCGTATAA
1 CC-ATTTCATATAA
*
35266514 CCATTTCATATAT
1 CCATTTCATATAA
**
35266527 TTATTTCCATATAA
1 CCATTT-CATATAA
* * *
35266541 CCAATACGTATAA
1 CCATTTCATATAA
35266554 CCATTTCATATA
1 CCATTTCATATA
35266566 TAATTTTTTA
Statistics
Matches: 90, Mismatches: 20, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
12 4 0.04
13 57 0.63
14 26 0.29
15 2 0.02
16 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (13 bp):
CCATTTCATATAA
Done.