Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 1 of 106
Found at i:12 original size:7 final size:7
Alignment explanation
Indices: 1--60 Score: 86
Period size: 7 Copynumber: 8.7 Consensus size: 7
1 AACCCCA
1 AACCCCA
8 AACCCCA
1 AACCCCA
*
15 ACCCCCA
1 AACCCCA
*
22 ACCCCCA
1 AACCCCA
29 AACCCC-
1 AACCCCA
*
35 AACCCCC
1 AACCCCA
42 AACCCCA
1 AACCCCA
49 AACCCCA
1 AACCCCA
56 AACCC
1 AACCC
61 TAAAACTAGC
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
6 6 0.12
7 43 0.88
ACGTcount: A:0.37, C:0.63, G:0.00, T:0.00
Consensus pattern (7 bp):
AACCCCA
Found at i:60 original size:21 final size:20
Alignment explanation
Indices: 1--56 Score: 103
Period size: 21 Copynumber: 2.8 Consensus size: 20
1 AACCCCAAACCCCAACCCCC
1 AACCCCAAACCCCAACCCCC
21 AACCCCCAAACCCCAACCCCC
1 AA-CCCCAAACCCCAACCCCC
42 AACCCCAAACCCCAA
1 AACCCCAAACCCCAA
57 ACCCTAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.43
21 20 0.57
ACGTcount: A:0.38, C:0.62, G:0.00, T:0.00
Consensus pattern (20 bp):
AACCCCAAACCCCAACCCCC
Found at i:16039 original size:69 final size:69
Alignment explanation
Indices: 15840--16019 Score: 272
Period size: 69 Copynumber: 2.6 Consensus size: 69
15830 TATGAAATGC
* *
15840 ATGTATGCCAAGTTG-TATTGTATGTGATGTAGATTCCATATACTACAAGAGATAAGAATGAAAA
1 ATGTATGCTAAGTTGCTATTGTATGTGATGTAGATTCCATATACTACAAGAGATAAGAATGAGAA
*
15904 CATG
66 CATA
* * * * *
15908 ATATATGCTAAGTTGCTATTGTATATGATGTAGATTCCATATACTGCACGAGATAAGAATGAGCA
1 ATGTATGCTAAGTTGCTATTGTATGTGATGTAGATTCCATATACTACAAGAGATAAGAATGAGAA
15973 CATA
66 CATA
*
15977 ATGTTTGCTAAGTTGCTATTGTATGTGATGTAGATTCCATATA
1 ATGTATGCTAAGTTGCTATTGTATGTGATGTAGATTCCATATA
16020 TTATATGAGA
Statistics
Matches: 100, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
68 13 0.13
69 87 0.87
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (69 bp):
ATGTATGCTAAGTTGCTATTGTATGTGATGTAGATTCCATATACTACAAGAGATAAGAATGAGAA
CATA
Found at i:16061 original size:69 final size:69
Alignment explanation
Indices: 15840--16097 Score: 254
Period size: 69 Copynumber: 3.8 Consensus size: 69
15830 TATGAAATGC
* * *
15840 ATGTATGCCAAGTTG-TATTGTATGTGATGTAGATTCCATATACTACAAGAGATAAGAATGAAAA
1 ATGTATGCCAAGTTGCTATTGTATGTGATGTAGATTCCATATACTACATGAGAGAAGAATGAGAA
15904 CATG
66 CATG
* * * * * * *
15908 ATATATGCTAAGTTGCTATTGTATATGATGTAGATTCCATATACTGCACGAGATAAGAATGAGCA
1 ATGTATGCCAAGTTGCTATTGTATGTGATGTAGATTCCATATACTACATGAGAGAAGAATGAGAA
*
15973 CATA
66 CATG
* * * * *
15977 ATGTTTGCTAAGTTGCTATTGTATGTGATGTAGATTCCATATATTATATGAGACGAA-AATGAGT
1 ATGTATGCCAAGTTGCTATTGTATGTGATGTAGATTCCATATACTACATGAGA-GAAGAATGAGA
*
16041 ATATG
65 ACATG
* * * * ** *
16046 ATGTATACCATGTTGC-AATGGATGTGATG-ATGATTCCACCTACTATATGAGA
1 ATGTATGCCAAGTTGCTATTGTATGTGATGTA-GATTCCATATACTACATGAGA
16098 CGAATACAAA
Statistics
Matches: 159, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
67 1 0.01
68 42 0.26
69 114 0.72
70 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (69 bp):
ATGTATGCCAAGTTGCTATTGTATGTGATGTAGATTCCATATACTACATGAGAGAAGAATGAGAA
CATG
Found at i:18927 original size:42 final size:42
Alignment explanation
Indices: 18874--18958 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
18864 TCGTAAGTAG
* *
18874 GGTCATCGCACTCAACATCTTCTAAGACAACAGTTGTGGCAT
1 GGTCATCGCACTCAACATCTTCTAACACAACAGTTATGGCAT
* * * *
18916 GGTCATTGCACTGAACCTCTTCTAACACAATAGTTATGGCAT
1 GGTCATCGCACTCAACATCTTCTAACACAACAGTTATGGCAT
18958 G
1 G
18959 TTCTGTACTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (42 bp):
GGTCATCGCACTCAACATCTTCTAACACAACAGTTATGGCAT
Found at i:19645 original size:21 final size:21
Alignment explanation
Indices: 19619--19672 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
19609 CAGGTTACAC
19619 CGGGTTAGGGTACTCAATAAA
1 CGGGTTAGGGTACTCAATAAA
*
19640 CGGGTTTGGGTACTCAATAAA
1 CGGGTTAGGGTACTCAATAAA
* *
19661 CTGGTTCGGGTA
1 CGGGTTAGGGTA
19673 GTGAAATCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (21 bp):
CGGGTTAGGGTACTCAATAAA
Found at i:20546 original size:28 final size:28
Alignment explanation
Indices: 20514--20571 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
20504 ATAACTTGTA
* *
20514 ATGTCTTTTAGCACATGCACTTTATATT
1 ATGTCTTTTAACACATACACTTTATATT
* *
20542 ATGTCTTTTAATACATACATTTTATATT
1 ATGTCTTTTAACACATACACTTTATATT
20570 AT
1 AT
20572 AACTAGTTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (28 bp):
ATGTCTTTTAACACATACACTTTATATT
Found at i:20678 original size:41 final size:40
Alignment explanation
Indices: 20577--20778 Score: 246
Period size: 40 Copynumber: 5.0 Consensus size: 40
20567 ATTATAACTA
*
20577 GTTGTTTGGATATTTAT-TTTAGTTATTTAAGTTTATGTTGTT
1 GTTGTTTGGATATTTGTGTTTAGTTATTTAAGTTTA---TGTT
* *
20619 GTTGTTTGGATATATGTGTTTGGTTATTTAAGTTTATGTT
1 GTTGTTTGGATATTTGTGTTTAGTTATTTAAGTTTATGTT
* *
20659 ATTTGTTTGGATCTTTGTGTTTAGTTATTTAAGTTTATGTT
1 -GTTGTTTGGATATTTGTGTTTAGTTATTTAAGTTTATGTT
* * * * *
20700 GTTATTTGGATATTTATGTATAGTT-TTTAAGTTTATATC
1 GTTGTTTGGATATTTGTGTTTAGTTATTTAAGTTTATGTT
* *
20739 GTTGTATGGATATTTGTTTTTAGTTATTTAAGTTTATGTT
1 GTTGTTTGGATATTTGTGTTTAGTTATTTAAGTTTATGTT
20779 TAAGATCTTT
Statistics
Matches: 136, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 32 0.24
40 36 0.26
41 36 0.26
42 15 0.11
43 17 0.12
ACGTcount: A:0.20, C:0.01, G:0.20, T:0.59
Consensus pattern (40 bp):
GTTGTTTGGATATTTGTGTTTAGTTATTTAAGTTTATGTT
Found at i:20749 original size:39 final size:40
Alignment explanation
Indices: 20577--20775 Score: 204
Period size: 41 Copynumber: 4.9 Consensus size: 40
20567 ATTATAACTA
* * *
20577 GTTGTTTGGATATTTAT-TTTAGTTATTTAAGTTTATGTTGTT
1 GTTGTTTGGATATTTGTGTTTAGTTATTTAAGTTTA---TATC
* * * *
20619 GTTGTTTGGATATATGTGTTTGGTTATTTAAGTTTATGTTA
1 GTTGTTTGGATATTTGTGTTTAGTTATTTAAGTTTAT-ATC
* * * *
20660 TTTGTTTGGATCTTTGTGTTTAGTTATTTAAGTTTATGTT
1 GTTGTTTGGATATTTGTGTTTAGTTATTTAAGTTTATATC
* * *
20700 GTTATTTGGATATTTATGTATAGTT-TTTAAGTTTATATC
1 GTTGTTTGGATATTTGTGTTTAGTTATTTAAGTTTATATC
* *
20739 GTTGTATGGATATTTGTTTTTAGTTATTTAAGTTTAT
1 GTTGTTTGGATATTTGTGTTTAGTTATTTAAGTTTAT
20776 GTTTAAGATC
Statistics
Matches: 131, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
39 32 0.24
40 33 0.25
41 34 0.26
42 15 0.11
43 17 0.13
ACGTcount: A:0.20, C:0.01, G:0.20, T:0.59
Consensus pattern (40 bp):
GTTGTTTGGATATTTGTGTTTAGTTATTTAAGTTTATATC
Found at i:20771 original size:79 final size:81
Alignment explanation
Indices: 20575--20778 Score: 252
Period size: 79 Copynumber: 2.5 Consensus size: 81
20565 ATATTATAAC
* * * *
20575 TAGTTGTTTGGATATTT-ATTTTAGTTATTTAAGTTTATGTTGTTGTTGTTTGGATATATGTGTT
1 TAGTTGTTTGGATATTTGTTTTTAGTTATTTAAGTTTA---TGTTGTTATTTGGATATATATGTA
* *
20639 TGGTTATTTAAGTTTATGT
63 TAGTTATTTAAGTTTATGA
* * * *
20658 TATTTGTTTGGATCTTTGTGTTTAGTTATTTAAGTTTATGTTGTTATTTGGATATTTATGTATAG
1 TAGTTGTTTGGATATTTGTTTTTAGTTATTTAAGTTTATGTTGTTATTTGGATATATATGTATAG
20723 TT-TTTAAGTTTAT-A
66 TTATTTAAGTTTATGA
* *
20737 TCGTTGTATGGATATTTGTTTTTAGTTATTTAAGTTTATGTT
1 TAGTTGTTTGGATATTTGTTTTTAGTTATTTAAGTTTATGTT
20779 TAAGATCTTT
Statistics
Matches: 105, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
79 37 0.35
80 11 0.10
81 24 0.23
83 15 0.14
84 18 0.17
ACGTcount: A:0.20, C:0.01, G:0.20, T:0.59
Consensus pattern (81 bp):
TAGTTGTTTGGATATTTGTTTTTAGTTATTTAAGTTTATGTTGTTATTTGGATATATATGTATAG
TTATTTAAGTTTATGA
Found at i:21718 original size:22 final size:22
Alignment explanation
Indices: 21688--21740 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
21678 ACTAGCCATG
21688 CAATGCCTAATATCCATTCACA
1 CAATGCCTAATATCCATTCACA
*
21710 CAATACCTAATATCCATTCACA
1 CAATGCCTAATATCCATTCACA
*
21732 TAATGCCTA
1 CAATGCCTA
21741 TAAACAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.30, G:0.04, T:0.28
Consensus pattern (22 bp):
CAATGCCTAATATCCATTCACA
Found at i:26249 original size:2 final size:2
Alignment explanation
Indices: 26242--26271 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
26232 TCGAAGGTGC
26242 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26272 NCACAACGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26283 original size:111 final size:110
Alignment explanation
Indices: 26161--26382 Score: 417
Period size: 111 Copynumber: 2.0 Consensus size: 110
26151 AGTTGTCATG
26161 TCACAACGGAATTTTCATCTTGTATTGCTGTGAACTTGGTTTTGATTCAACTGATCACAGATGCA
1 TCACAACGGAATTTTCATCTTGTATTGCTGTGAACTTGGTTTTGATTCAACTGATCACAGATGCA
*
26226 TCTAGATCGAAGGTGCATATATATATATATATATATATATATATA
66 TCTAGATCGAAGGTACATATATATATATATATATATATATATATA
26271 TNCACAACGGAATTTTCATCTTGTATTGCTGTGAACTTGGTTTTGATTCAACTGATCACAGATGC
1 T-CACAACGGAATTTTCATCTTGTATTGCTGTGAACTTGGTTTTGATTCAACTGATCACAGATGC
*
26336 ATCTAGATCGAAGGTATATATATATATATATATATATATATATATA
65 ATCTAGATCGAAGGTACATATATATATATATATATATATATATATA
26382 T
1 T
26383 ATGTAGCCTG
Statistics
Matches: 109, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
110 1 0.01
111 108 0.99
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (110 bp):
TCACAACGGAATTTTCATCTTGTATTGCTGTGAACTTGGTTTTGATTCAACTGATCACAGATGCA
TCTAGATCGAAGGTACATATATATATATATATATATATATATATA
Found at i:26357 original size:2 final size:2
Alignment explanation
Indices: 26350--26384 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
26340 AGATCGAAGG
26350 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26385 GTAGCCTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40724 original size:6 final size:6
Alignment explanation
Indices: 40681--40722 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
40671 GGGTTTAAAC
* *
40681 TCCCAC TCCCAA TCCCAA TCCCAA TCCCAA TCCCAA GCCCAA
1 TCCCAA TCCCAA TCCCAA TCCCAA TCCCAA TCCCAA TCCCAA
40723 GCAGAGCAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.31, C:0.52, G:0.02, T:0.14
Consensus pattern (6 bp):
TCCCAA
Found at i:42066 original size:2 final size:2
Alignment explanation
Indices: 42059--42087 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42049 TCACTCAGCT
42059 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 T
42088 ATGTATTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:44879 original size:2 final size:2
Alignment explanation
Indices: 44872--44901 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
44862 CATAGGTTGT
44872 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
44902 AATACAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:50997 original size:3 final size:3
Alignment explanation
Indices: 50989--51016 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
50979 ACTAAATGGC
50989 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
51017 CACCGTGTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:51652 original size:58 final size:57
Alignment explanation
Indices: 51562--51676 Score: 180
Period size: 58 Copynumber: 2.0 Consensus size: 57
51552 TTTTCCATGG
*
51562 ATGTTAAGTAAACATTCTTTTATAGAGAGAGAGAGAGAG-GAGGTAAAGACCAAACCT
1 ATGTTAAGTAAACAATCTTTTATAGAGAGAGAGAGAGAGAG-GGTAAAGACCAAACCT
51619 NATGTTAAGTAAACAATC-TTTATTAGAGAGAGAGAGAGAGAGGGTAAAGACCAAACCT
1 -ATGTTAAGTAAACAATCTTTTA-TAGAGAGAGAGAGAGAGAGGGTAAAGACCAAACCT
51677 TTAAAAATTT
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
57 4 0.07
58 49 0.91
59 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.24, T:0.22
Consensus pattern (57 bp):
ATGTTAAGTAAACAATCTTTTATAGAGAGAGAGAGAGAGAGGGTAAAGACCAAACCT
Found at i:53474 original size:2 final size:2
Alignment explanation
Indices: 53469--53493 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53459 AGAAAAAAGC
53469 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
53494 AATAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54403 original size:2 final size:2
Alignment explanation
Indices: 54398--54430 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
54388 CAACTTGCTT
54398 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54431 GTATTCACAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55419 original size:29 final size:29
Alignment explanation
Indices: 55370--55441 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
55360 AGAAGCTGAT
* *
55370 AGAGAA-AAGCTGGACATGAATAAGTACA
1 AGAGAAGAAGCTGTACAAGAATAAGTACA
* * *
55398 GGGGAAGAAGCTGTACAAGAATAGGTACA
1 AGAGAAGAAGCTGTACAAGAATAAGTACA
*
55427 AGAGAAGAAGGTGTA
1 AGAGAAGAAGCTGTA
55442 TGTGAACAGG
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
28 4 0.11
29 31 0.89
ACGTcount: A:0.46, C:0.08, G:0.32, T:0.14
Consensus pattern (29 bp):
AGAGAAGAAGCTGTACAAGAATAAGTACA
Found at i:67055 original size:22 final size:22
Alignment explanation
Indices: 67027--67073 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
67017 CTAAGAATAG
67027 ACGAAACTCGGTATCGTACCTA
1 ACGAAACTCGGTATCGTACCTA
67049 ACGAAACTCGGTATCGTACCTA
1 ACGAAACTCGGTATCGTACCTA
67071 ACG
1 ACG
67074 GTACACTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (22 bp):
ACGAAACTCGGTATCGTACCTA
Found at i:73933 original size:2 final size:2
Alignment explanation
Indices: 73926--73953 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
73916 TAATGATTAT
73926 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
73954 ANTTGTCACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:74030 original size:101 final size:100
Alignment explanation
Indices: 73855--74055 Score: 393
Period size: 101 Copynumber: 2.0 Consensus size: 100
73845 TGCTGCTTGC
73855 TTGTCACCTTTTGAAAGGGAAGGGCTTGTGGTTATGTCCATACCTAAACGAATGATGATGATAAT
1 TTGTCACCTTTTGAAAGGGAAGGGCTTGTGGTTATGTCCATACCTAAACGAATGATGATGATAAT
73920 GATTATTATATATATATATATATATATATATATAA
66 GATTATTATATATATATATATATATATATATATAA
73955 NTTGTCACCTTTTGAAAGGGAAGGGCTTGTGGTTATGTCCATACCTAAACGAATGATGATGATAA
1 -TTGTCACCTTTTGAAAGGGAAGGGCTTGTGGTTATGTCCATACCTAAACGAATGATGATGATAA
74020 TGATTATTATATATATATATATATATATATATATAA
65 TGATTATTATATATATATATATATATATATATATAA
74056 GTTATAACTA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 100 1.00
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (100 bp):
TTGTCACCTTTTGAAAGGGAAGGGCTTGTGGTTATGTCCATACCTAAACGAATGATGATGATAAT
GATTATTATATATATATATATATATATATATATAA
Found at i:74034 original size:2 final size:2
Alignment explanation
Indices: 74027--74054 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
74017 TAATGATTAT
74027 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
74055 AGTTATAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:75998 original size:2 final size:2
Alignment explanation
Indices: 75991--76017 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
75981 TGCATGTTTT
75991 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
76018 TCAAATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:81957 original size:40 final size:40
Alignment explanation
Indices: 81881--81959 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 40
81871 TTGACTATTT
* * * *
81881 TTCACCTTAATGGGGTTTTTAACCTTGCCAATATTGGTGA
1 TTCACCTTAATGGAGTTTTCAACCTCGCCAAGATTGGTGA
* * *
81921 TTCACCTTAGTGGAGTTTTCAACCTCGTCACGATTGGTG
1 TTCACCTTAATGGAGTTTTCAACCTCGCCAAGATTGGTG
81960 TCTTTCACAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (40 bp):
TTCACCTTAATGGAGTTTTCAACCTCGCCAAGATTGGTGA
Found at i:84060 original size:9 final size:9
Alignment explanation
Indices: 84046--84084 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
84036 GCACGATTAA
*
84046 TAACACGTT
1 TAACACGAT
84055 TAACACGAT
1 TAACACGAT
*
84064 TAACACGCT
1 TAACACGAT
84073 TAACACGAT
1 TAACACGAT
84082 TAA
1 TAA
84085 ATAAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.41, C:0.23, G:0.10, T:0.26
Consensus pattern (9 bp):
TAACACGAT
Found at i:84069 original size:18 final size:18
Alignment explanation
Indices: 84046--84084 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
84036 GCACGATTAA
*
84046 TAACACGTTTAACACGAT
1 TAACACGCTTAACACGAT
84064 TAACACGCTTAACACGAT
1 TAACACGCTTAACACGAT
84082 TAA
1 TAA
84085 ATAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.23, G:0.10, T:0.26
Consensus pattern (18 bp):
TAACACGCTTAACACGAT
Found at i:87598 original size:2 final size:2
Alignment explanation
Indices: 87593--87642 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
87583 CAGCTCTCTT
87593 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
87635 TA TA TA TA
1 TA TA TA TA
87643 CAAAAAAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:87695 original size:2 final size:2
Alignment explanation
Indices: 87688--87731 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
87678 NNNNNNNNNN
87688 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
87730 TA
1 TA
87732 GTGAAAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:92321 original size:16 final size:16
Alignment explanation
Indices: 92302--92334 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
92292 TAATTTTACG
*
92302 TGAGAATAGAATGAAA
1 TGAGAATAGAATAAAA
92318 TGAGAATAGAATAAAA
1 TGAGAATAGAATAAAA
92334 T
1 T
92335 AAATATTATG
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:0.58, C:0.00, G:0.21, T:0.21
Consensus pattern (16 bp):
TGAGAATAGAATAAAA
Found at i:92529 original size:22 final size:21
Alignment explanation
Indices: 92502--92562 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 21
92492 TTTTTTATTT
92502 TTTAAATATTAATATT-ATAA
1 TTTAAATATTAATATTAATAA
92522 TTATTAAAATATTAATAATTAATAA
1 -T-TT-AAATATTAAT-ATTAATAA
*
92547 TTTAAATATCAATATT
1 TTTAAATATTAATATT
92563 TTAGTATAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
21 4 0.11
22 11 0.31
23 12 0.34
24 4 0.11
25 4 0.11
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTAAATATTAATATTAATAA
Found at i:94606 original size:3 final size:3
Alignment explanation
Indices: 94598--94622 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
94588 TTTTGTGACA
94598 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
94623 GAACAATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:105794 original size:19 final size:20
Alignment explanation
Indices: 105756--105796 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
105746 CTTGTTTGAC
*
105756 TAAACGAATTAAATAAATTT
1 TAAACAAATTAAATAAATTT
105776 TAAACAAATTAAA-AAATTT
1 TAAACAAATTAAATAAATTT
105795 TA
1 TA
105797 TTTAAAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (20 bp):
TAAACAAATTAAATAAATTT
Found at i:107379 original size:39 final size:39
Alignment explanation
Indices: 107309--107404 Score: 138
Period size: 39 Copynumber: 2.5 Consensus size: 39
107299 TAAGTATGAA
* * *
107309 ATCTGTTTAATAGCCTTATCTAATTTTTGTTTCACTGAT
1 ATCTGTTTAATAGCCATAACTAATTTCTGTTTCACTGAT
* *
107348 ATCTGTTTAATAGCCATAACTTATTTCTGTTTCGCTGAT
1 ATCTGTTTAATAGCCATAACTAATTTCTGTTTCACTGAT
*
107387 CTCTGTTTAATAGCCATA
1 ATCTGTTTAATAGCCATA
107405 TCCATTATTG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (39 bp):
ATCTGTTTAATAGCCATAACTAATTTCTGTTTCACTGAT
Found at i:114365 original size:2 final size:2
Alignment explanation
Indices: 114353--114388 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
114343 CTATCCTATC
114353 AT AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
114389 CGTACNNNNN
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:115450 original size:2 final size:2
Alignment explanation
Indices: 115443--115477 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
115433 NNNNNNNNNN
115443 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
115478 GTTCACTCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:121684 original size:4 final size:4
Alignment explanation
Indices: 121675--121699 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
121665 CACTACCCTC
121675 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
121700 CGTAAGGGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:124729 original size:3 final size:3
Alignment explanation
Indices: 124721--124747 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
124711 TTAAGGAAGG
124721 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
124748 GTTAGTCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:154362 original size:25 final size:24
Alignment explanation
Indices: 154334--154381 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
154324 GGTTCTATGT
*
154334 TGGAGCTCATCACCTTGTTCTCCTA
1 TGGAACTCATCACCTTGTT-TCCTA
**
154359 TGGAACTCATTGCCTTGTTTCCT
1 TGGAACTCATCACCTTGTTTCCT
154382 TGTTTCTCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.15, C:0.29, G:0.17, T:0.40
Consensus pattern (24 bp):
TGGAACTCATCACCTTGTTTCCTA
Found at i:167821 original size:34 final size:34
Alignment explanation
Indices: 167768--167837 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
167758 TAAAATTTAT
* * * *
167768 CAATAAATGTTACATGTCAAGGTCAAAAGTTCAA
1 CAATAAATGTCACACGTCAAAGCCAAAAGTTCAA
*
167802 CAATAGATGTCACACGTCAAAGCCAAAAGTTCAA
1 CAATAAATGTCACACGTCAAAGCCAAAAGTTCAA
167836 CA
1 CA
167838 TCATGTCATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.21
Consensus pattern (34 bp):
CAATAAATGTCACACGTCAAAGCCAAAAGTTCAA
Found at i:175070 original size:2 final size:2
Alignment explanation
Indices: 175063--175098 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
175053 TCAGTTTTAA
175063 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
175099 TGACTTAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:194580 original size:2 final size:2
Alignment explanation
Indices: 194573--194600 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
194563 ACCATTGAAA
194573 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
194601 CGAACAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:195266 original size:18 final size:18
Alignment explanation
Indices: 195243--195288 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
195233 GATTTTTGAC
*
195243 AAACAAAATTGGTAAGAG
1 AAACAAAACTGGTAAGAG
195261 AAACAAAACTGGTAAGAG
1 AAACAAAACTGGTAAGAG
195279 AAACAAAACT
1 AAACAAAACT
195289 CTAAGCCTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.59, C:0.11, G:0.17, T:0.13
Consensus pattern (18 bp):
AAACAAAACTGGTAAGAG
Found at i:202565 original size:3 final size:3
Alignment explanation
Indices: 202551--202582 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
202541 CGATTAGGGT
*
202551 TTC TTC TCC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
202583 TTTTTCCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:203346 original size:2 final size:2
Alignment explanation
Indices: 203339--203384 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
203329 ATACATAAAC
*
203339 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
203381 AT AT
1 AT AT
203385 TTTATGTGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:207042 original size:19 final size:19
Alignment explanation
Indices: 207008--207056 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
206998 GGGAGTCTCA
*
207008 TAATTTGATTTGATTTAGTC
1 TAATTTGAGTT-ATTTAGTC
* *
207028 TATTTTGAGTTATTTCGTC
1 TAATTTGAGTTATTTAGTC
207047 TAATTTGAGT
1 TAATTTGAGT
207057 GATTCGGGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.22, C:0.06, G:0.16, T:0.55
Consensus pattern (19 bp):
TAATTTGAGTTATTTAGTC
Found at i:214185 original size:21 final size:21
Alignment explanation
Indices: 214152--214193 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
214142 GGCAGCAAGT
*
214152 TTCTTGCTACAGCGAAG-TTCA
1 TTCTCGCTACAGC-AAGATTCA
*
214173 TTCTCGCTGCAGCAAGATTCA
1 TTCTCGCTACAGCAAGATTCA
214194 GGCGGCCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (21 bp):
TTCTCGCTACAGCAAGATTCA
Found at i:229259 original size:24 final size:24
Alignment explanation
Indices: 229227--229275 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
229217 AGAATCCAGG
229227 TTCCTTCTGCATTAAACTGTTCTA
1 TTCCTTCTGCATTAAACTGTTCTA
229251 TTCCTTCTGCATTAAACTGTTCTA
1 TTCCTTCTGCATTAAACTGTTCTA
229275 T
1 T
229276 GTATGAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.47
Consensus pattern (24 bp):
TTCCTTCTGCATTAAACTGTTCTA
Found at i:251800 original size:76 final size:76
Alignment explanation
Indices: 251710--251861 Score: 268
Period size: 76 Copynumber: 2.0 Consensus size: 76
251700 AACAGTGGTA
* * *
251710 AAATTAACAGTAAAAGAAGGTTTATTGATGTAAAGGAAAAGGAGTGCCTCTGTAATTTTGCTTCA
1 AAATTAACAGTAAAAGAAGGTTTATTGATGTAAAAGAAAAGGAGAGCCTCAGTAATTTTGCTTCA
251775 TTCAAAGGGGT
66 TTCAAAGGGGT
*
251786 AAATTAACAGTAAAAGAAGTTTTATTGATGTAAAAGAAAAGGAGAGCCTCAGTAATTTTGCTTCA
1 AAATTAACAGTAAAAGAAGGTTTATTGATGTAAAAGAAAAGGAGAGCCTCAGTAATTTTGCTTCA
251851 TTCAAAGGGGT
66 TTCAAAGGGGT
251862 GAGAGAAGGT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (76 bp):
AAATTAACAGTAAAAGAAGGTTTATTGATGTAAAAGAAAAGGAGAGCCTCAGTAATTTTGCTTCA
TTCAAAGGGGT
Found at i:253167 original size:7 final size:7
Alignment explanation
Indices: 253155--253184 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
253145 GGACTCGATT
253155 TCTCTGC
1 TCTCTGC
253162 TCTCTGC
1 TCTCTGC
253169 TCTCTGC
1 TCTCTGC
253176 TCTCTGC
1 TCTCTGC
253183 TC
1 TC
253185 ACACAGAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.43, G:0.13, T:0.43
Consensus pattern (7 bp):
TCTCTGC
Found at i:277022 original size:2 final size:2
Alignment explanation
Indices: 277015--277040 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
277005 ACACAATCAG
277015 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
277041 AAACCAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:280805 original size:4 final size:4
Alignment explanation
Indices: 280796--280825 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
280786 ATGAAGATTT
280796 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TT
280826 GGGAGTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTTG
Found at i:285655 original size:3 final size:3
Alignment explanation
Indices: 285641--285679 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
285631 ATTAACTCTC
*
285641 CTT CTC CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
285680 GGCCAACAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:285933 original size:2 final size:2
Alignment explanation
Indices: 285926--285957 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
285916 TTTAAATGTG
285926 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
285958 CTTTAAGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:286300 original size:15 final size:15
Alignment explanation
Indices: 286266--286300 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
286256 ACACTGACCC
286266 AAAAACAAAATAAAA
1 AAAAACAAAATAAAA
* *
286281 GAAAATAAAATAAAA
1 AAAAACAAAATAAAA
286296 AAAAA
1 AAAAA
286301 GCGCAAAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.86, C:0.03, G:0.03, T:0.09
Consensus pattern (15 bp):
AAAAACAAAATAAAA
Found at i:290017 original size:2 final size:2
Alignment explanation
Indices: 290010--290053 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
290000 ACATGGGTAC
290010 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
290052 AT
1 AT
290054 GTTGGACACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:307226 original size:40 final size:41
Alignment explanation
Indices: 307156--307238 Score: 132
Period size: 40 Copynumber: 2.0 Consensus size: 41
307146 TCAATTACCG
307156 AAGTCGAATACTTTCAATCACCTCAGTTAGACAAGTTCTGT
1 AAGTCGAATACTTTCAATCACCTCAGTTAGACAAGTTCTGT
* **
307197 AAGTCGAATAC-TTCTATCACCTTTGTTAGACAAGTTCTGT
1 AAGTCGAATACTTTCAATCACCTCAGTTAGACAAGTTCTGT
307237 AA
1 AA
307239 TGTCACCTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 28 0.72
41 11 0.28
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.34
Consensus pattern (41 bp):
AAGTCGAATACTTTCAATCACCTCAGTTAGACAAGTTCTGT
Found at i:313516 original size:2 final size:2
Alignment explanation
Indices: 313509--313534 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
313499 CAGGTGCATT
313509 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
313535 ATGGCATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:316866 original size:2 final size:2
Alignment explanation
Indices: 316859--316890 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
316849 TGGCAAATGA
316859 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
316891 TATTTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:317189 original size:2 final size:2
Alignment explanation
Indices: 317182--317216 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
317172 AATCATGTGT
*
317182 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
317217 CCACGATCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:331386 original size:17 final size:18
Alignment explanation
Indices: 331343--331386 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
331333 CAAAGAAAAG
* *
331343 CGAGAGGAGAGAGAGATA
1 CGAGAAGAGAGAGAGACA
331361 CGAGAAAGAGAGAGAGACA
1 CGAG-AAGAGAGAGAGACA
331380 -GAGAAGA
1 CGAGAAGA
331387 CACAAGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 4 0.17
18 7 0.30
19 12 0.52
ACGTcount: A:0.50, C:0.07, G:0.41, T:0.02
Consensus pattern (18 bp):
CGAGAAGAGAGAGAGACA
Found at i:336457 original size:30 final size:30
Alignment explanation
Indices: 336423--336481 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
336413 GACATCTAAT
** *
336423 GCACCTTCACCAACTGTCCAATCTTCTCAG
1 GCACCTTCACCAACAATCCAAACTTCTCAG
336453 GCACCTTCACCAACAATCCAAACTTCTCA
1 GCACCTTCACCAACAATCCAAACTTCTCA
336482 ACCGGTATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.29, C:0.41, G:0.07, T:0.24
Consensus pattern (30 bp):
GCACCTTCACCAACAATCCAAACTTCTCAG
Found at i:354679 original size:14 final size:14
Alignment explanation
Indices: 354660--354698 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
354650 TAATCTTGGT
354660 TTGATTTGCAGATA
1 TTGATTTGCAGATA
354674 TTGATTTGCAGATA
1 TTGATTTGCAGATA
354688 TTGATTTGCAG
1 TTGATTTGCAG
354699 GTATACATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.44
Consensus pattern (14 bp):
TTGATTTGCAGATA
Found at i:357139 original size:22 final size:22
Alignment explanation
Indices: 357113--357155 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
357103 GACATGTGGC
357113 GGCAATAAAGTCAACAAGAGGT
1 GGCAATAAAGTCAACAAGAGGT
357135 GGCAATAAAGTCAACAAGAGG
1 GGCAATAAAGTCAACAAGAGG
357156 ATGAGAGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.14, G:0.28, T:0.12
Consensus pattern (22 bp):
GGCAATAAAGTCAACAAGAGGT
Found at i:358410 original size:15 final size:14
Alignment explanation
Indices: 358392--358421 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
358382 AAAAAAAAAA
*
358392 TTTTAAAAATGTTC
1 TTTTTAAAATGTTC
358406 TTTTTAAAATGTTC
1 TTTTTAAAATGTTC
358420 TT
1 TT
358422 ATTGCAGGCT
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:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (14 bp):
TTTTTAAAATGTTC
Found at i:359693 original size:23 final size:23
Alignment explanation
Indices: 359663--359712 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
359653 GCATTTGGCT
*
359663 AGCAATGGATTTTTATATGGAAA
1 AGCAATGGATTTTTATAGGGAAA
359686 AGCAATGGATTTTTATAGGGAAA
1 AGCAATGGATTTTTATAGGGAAA
359709 AGCA
1 AGCA
359713 GGTTTTCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.30
Consensus pattern (23 bp):
AGCAATGGATTTTTATAGGGAAA
Found at i:372223 original size:107 final size:106
Alignment explanation
Indices: 372036--372264 Score: 273
Period size: 107 Copynumber: 2.2 Consensus size: 106
372026 ATTAAGTTGT
* * * *
372036 GCCTAATTAACTAAA-TTATTTAATTAAATCATTGGACCTAATTAATTAAATTATTTAATTAAGT
1 GCCTAATTGATTAAATTTGTTTAATTAAATCATTGGACCTAATTAATTAAATTATTTAATTAAAT
*
372100 CATTAGGTCTAATTAATTAAATTAAACAATTAAGTTATTGG
66 CATTAGGTCTAATTAATTAAATTAAACAATTAAGTTATTGA
* * * * * *
372141 GTCTAATTGATTAAATTTGTTTAATTAAGTCATTGGGCCTAGTTGATTAAAATTGTTTAATTAAA
1 GCCTAATTGATTAAATTTGTTTAATTAAATCATTGGACCTAATTAATT-AAATTATTTAATTAAA
** * ***
372206 TTGTT-GGGCTTAATTAATTAAATTATTTAATTAAGTTATTGA
65 TCATTAGGTC-TAATTAATTAAATTAAACAATTAAGTTATTGA
372248 GCCTAATTGATTAAATT
1 GCCTAATTGATTAAATT
372265 AAACAATTAA
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
105 12 0.12
106 30 0.29
107 61 0.59
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.44
Consensus pattern (106 bp):
GCCTAATTGATTAAATTTGTTTAATTAAATCATTGGACCTAATTAATTAAATTATTTAATTAAAT
CATTAGGTCTAATTAATTAAATTAAACAATTAAGTTATTGA
Found at i:372241 original size:142 final size:139
Alignment explanation
Indices: 372009--372284 Score: 376
Period size: 142 Copynumber: 2.0 Consensus size: 139
371999 TCTCAAACAC
*
372009 TTGATTAAAATTGTTTAATTAAGTTGTGCCTAATTAACTAAATTATTTAATTAAATCATTGGACC
1 TTGATTAAAATTGTTTAATTAAGTTGGGCCTAATTAACTAAATTATTTAATTAAATCATTGGACC
*
372074 TAATTAATTAAATTATTTAATTAAGTCATT-AGGTCTAATTAATTAAATTAAACAATTAAGTT-A
66 TAATTAATTAAATTATTTAATTAAGTCATTGA-GCCTAATTAATTAAATTAAACAATTAAGTTAA
372137 TTGGGTCTAA
130 TTGGGTCTAA
* * * * * **
372147 TTGATTAAATTTGTTTAATTAAGTCATTGGGCCTAGTTGATTAAAATTGTTTAATTAAATTGTTG
1 TTGATTAAAATTGTTTAATTAAG---TTGGGCCTAATTAACT-AAATTATTTAATTAAATCATTG
* * * *
372212 GGCTTAATTAATTAAATTATTTAATTAAGTTATTGAGCCTAATTGATTAAATTAAACAATTAAGT
62 GACCTAATTAATTAAATTATTTAATTAAGTCATTGAGCCTAATTAATTAAATTAAACAATTAAGT
372277 TAATTGGG
127 TAATTGGG
372285 CTTATAAAGG
Statistics
Matches: 119, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
138 22 0.18
141 12 0.10
142 78 0.66
143 7 0.06
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (139 bp):
TTGATTAAAATTGTTTAATTAAGTTGGGCCTAATTAACTAAATTATTTAATTAAATCATTGGACC
TAATTAATTAAATTATTTAATTAAGTCATTGAGCCTAATTAATTAAATTAAACAATTAAGTTAAT
TGGGTCTAA
Found at i:372273 original size:35 final size:35
Alignment explanation
Indices: 372016--372285 Score: 249
Period size: 35 Copynumber: 7.7 Consensus size: 35
372006 CACTTGATTA
* * *
372016 AAATTGTTTAATTAAG---TTGTGCCTAATTAACT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
* * *
372048 AAATTATTTAATTAAATCATTGGACCTAATTAATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
* * *
372083 AAATTATTTAATTAAGTCATTAGGTCTAATTAATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
*** * *
372118 AAATTAAACAATTAAGTTATTGGGTCTAATTGATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
* * * *
372153 AAATTTGTTTAATTAAGTCATTGGGCCTAGTTGATT
1 AAA-TTATTTAATTAAGTTATTGGGCCTAATTAATT
* * * *
372189 AAAATTGTTTAATTAAATTGTTGGGCTTAATTAATT
1 -AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
* *
372225 AAATTATTTAATTAAGTTATTGAGCCTAATTGATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
***
372260 AAATTAAACAATTAAGTTAATTGGGC
1 AAATTATTTAATTAAGTT-ATTGGGC
372286 TTATAAAGGA
Statistics
Matches: 194, Mismatches: 38, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
32 14 0.07
35 120 0.62
36 57 0.29
37 3 0.02
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.43
Consensus pattern (35 bp):
AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
Found at i:378381 original size:13 final size:13
Alignment explanation
Indices: 378363--378388 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
378353 GAGCAAGTTG
378363 TGATAAATCTATA
1 TGATAAATCTATA
378376 TGATAAATCTATA
1 TGATAAATCTATA
378389 ACGTCAAGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
TGATAAATCTATA
Found at i:383311 original size:16 final size:16
Alignment explanation
Indices: 383290--383321 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
383280 AAACATGATG
383290 AATTTATTATTTATTT
1 AATTTATTATTTATTT
*
383306 AATTTATTTTTTATTT
1 AATTTATTATTTATTT
383322 GAGTTTGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
AATTTATTATTTATTT
Found at i:385826 original size:2 final size:2
Alignment explanation
Indices: 385819--385848 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
385809 ATTAATTATC
385819 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
385849 GTCTTCTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:386534 original size:23 final size:23
Alignment explanation
Indices: 386508--386553 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
386498 ATACAATAAC
*
386508 CTTATCCTAATATAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
386531 CTTATCCTAATAGAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
386554 TGTTATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (23 bp):
CTTATCCTAATAGAATTAGGAAT
Found at i:390925 original size:23 final size:23
Alignment explanation
Indices: 390899--390944 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
390889 ATACAATAAC
*
390899 CTTATCCTAATATAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
390922 CTTATCCTAATAGAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
390945 TATTATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (23 bp):
CTTATCCTAATAGAATTAGGAAT
Found at i:396046 original size:22 final size:22
Alignment explanation
Indices: 395996--396047 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
395986 AATACAGCAT
* **
395996 ACGAAATTATTTACTTTTTCTG
1 ACGAAATTATGTACTTTTTCCA
**
396018 ATAAAATTATGTACTTTTTCCA
1 ACGAAATTATGTACTTTTTCCA
396040 ACGAAATT
1 ACGAAATT
396048 TTTCGTTGAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (22 bp):
ACGAAATTATGTACTTTTTCCA
Found at i:399144 original size:30 final size:29
Alignment explanation
Indices: 399083--399155 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
399073 CCATGTTGAA
*
399083 AAAAAAATATTGTTGTTACAGGTTATGTT
1 AAAAAAATATTGTTGTTACAGCTTATGTT
399112 AAAAAAATATTGTTGTTACACGCTATAT-TT
1 AAAAAAATATTGTTGTTACA-GCT-TATGTT
* *
399142 AAAAACATCTTGTT
1 AAAAAAATATTGTT
399156 ACACTTTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 20 0.51
30 16 0.41
31 3 0.08
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (29 bp):
AAAAAAATATTGTTGTTACAGCTTATGTT
Found at i:408182 original size:26 final size:26
Alignment explanation
Indices: 408130--408185 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
408120 CATAGTTAAT
**
408130 AATATCATACAATACGTAATATGTAA
1 AATATCATACAATACGTAATACATAA
* * *
408156 AATATCATACGATATGTGATACATAA
1 AATATCATACAATACGTAATACATAA
408182 AATA
1 AATA
408186 CAAATAATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (26 bp):
AATATCATACAATACGTAATACATAA
Found at i:408722 original size:45 final size:45
Alignment explanation
Indices: 408671--408757 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
408661 CTAGCCAAAC
*
408671 TTAATTATTTTGATATATTTCTTTCCTAAAATGATAATGTTTGAT
1 TTAATTATTTTGATATATTTCTTTCCTAAAACGATAATGTTTGAT
408716 TTAATTATTTTGATATATTTCTTTCCTAAAACGATAATGTTT
1 TTAATTATTTTGATATATTTCTTTCCTAAAACGATAATGTTT
408758 AAAGTTATGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (45 bp):
TTAATTATTTTGATATATTTCTTTCCTAAAACGATAATGTTTGAT
Found at i:411122 original size:57 final size:54
Alignment explanation
Indices: 411006--411167 Score: 155
Period size: 57 Copynumber: 2.8 Consensus size: 54
410996 CTTGATATTT
** * *
411006 AGCAAATAATTAGATATTGTTTCCTTTAAGCTTTTGTTATTTGCTTTCATATTA
1 AGCAAATAATTAGATATTGTTTCCGCTAAGCTTTTGTTATTTGCTTTCAAACTA
411060 AGCAAATAATTAGATATTGTTTATTCCGCTAAGCTTTTGTTATTTGC-TTCGAAACTA
1 AGCAAATAATTAGATATTG--T-TTCCGCTAAGCTTTTGTTATTTGCTTTC-AAACTA
* * *
411117 TGCAAATAATAATTAAATCTTGTTTCCGCTAATCAAGCTTTTGTTATTTGC
1 AGC--A-AATAATTAGATATTGTTTCCGC---T-AAGCTTTTGTTATTTGC
411168 AAAATACAGT
Statistics
Matches: 90, Mismatches: 7, Indels: 15
0.80 0.06 0.13
Matches are distributed among these distances:
54 19 0.21
56 4 0.04
57 34 0.38
58 1 0.01
59 1 0.01
60 14 0.16
61 17 0.19
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (54 bp):
AGCAAATAATTAGATATTGTTTCCGCTAAGCTTTTGTTATTTGCTTTCAAACTA
Found at i:412279 original size:22 final size:22
Alignment explanation
Indices: 412251--412300 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
412241 ATTATTTGCA
412251 AAAGAAATTGCAAGTTAATATT
1 AAAGAAATTGCAAGTTAATATT
*
412273 AAAGAAATTGCAAGTTAATTTT
1 AAAGAAATTGCAAGTTAATATT
*
412295 GAAGAA
1 AAAGAA
412301 CCCTTTCCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.50, C:0.04, G:0.16, T:0.30
Consensus pattern (22 bp):
AAAGAAATTGCAAGTTAATATT
Found at i:418756 original size:16 final size:16
Alignment explanation
Indices: 418724--418762 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
418714 ATATATATAT
*
418724 ATATACATGTACGTGC
1 ATATACATGTACATGC
*
418740 ATATACATGTATATGC
1 ATATACATGTACATGC
*
418756 ACATACA
1 ATATACA
418763 GAAGGAGGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (16 bp):
ATATACATGTACATGC
Found at i:431391 original size:70 final size:69
Alignment explanation
Indices: 431292--431431 Score: 192
Period size: 70 Copynumber: 2.0 Consensus size: 69
431282 TTTACATATA
* * * * *
431292 TGAAAAAATAACTGTTAGAGATTATTAAATATATATTACCATTAATTGATT-GCAAATAGGAAAA
1 TGAAAAAAAAACTATTAAAGATCATTAAATATATATTACCATTAATTGATTAG-AAATAAGAAAA
431356 ATAGT
65 ATAGT
* *
431361 TGAAAAAAAAAGCTATTAAAGATCATTAAATATATATTACCATTACTTGATTAGAAATAAGAGAA
1 TGAAAAAAAAA-CTATTAAAGATCATTAAATATATATTACCATTAATTGATTAGAAATAAGAAAA
431426 ATAGT
65 ATAGT
431431 T
1 T
431432 AAGAATTAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
69 10 0.16
70 51 0.82
71 1 0.02
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.32
Consensus pattern (69 bp):
TGAAAAAAAAACTATTAAAGATCATTAAATATATATTACCATTAATTGATTAGAAATAAGAAAAA
TAGT
Found at i:439149 original size:20 final size:21
Alignment explanation
Indices: 439111--439149 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
439101 TGAAAAGGAT
*
439111 AAAATGAATTATTATAAATAA
1 AAAATAAATTATTATAAATAA
*
439132 AAAATAAATTGTTA-AAAT
1 AAAATAAATTATTATAAAT
439150 GTTTTAAGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (21 bp):
AAAATAAATTATTATAAATAA
Found at i:441700 original size:10 final size:10
Alignment explanation
Indices: 441685--441711 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
441675 GTTCCTTTGT
441685 CTACAATTGC
1 CTACAATTGC
441695 CTACAATTGC
1 CTACAATTGC
441705 CTACAAT
1 CTACAAT
441712 ATTGGGATTA
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:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (10 bp):
CTACAATTGC
Found at i:446377 original size:22 final size:24
Alignment explanation
Indices: 446352--446411 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 24
446342 AATTTAAATA
446352 TTAATATTTTAA-ATTAAT-TGTT
1 TTAATATTTTAATATTAATATGTT
* * *
446374 TTAA-AATTAAATATTAATATTTT
1 TTAATATTTTAATATTAATATGTT
446397 TTAAT-TTTTAATATT
1 TTAATATTTTAATATT
446412 TTAAGTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 5 0.17
22 10 0.33
23 15 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TTAATATTTTAATATTAATATGTT
Found at i:449097 original size:84 final size:84
Alignment explanation
Indices: 448946--449154 Score: 276
Period size: 84 Copynumber: 2.5 Consensus size: 84
448936 TTCTATCATG
* * * * *
448946 TCCACGCCACCTTCAGGTTCCAAAGGTGAGAGCACAAGTGGCATTCGAGTTCCCGATGCTGCAAA
1 TCCACACCACCTTCAGGTTCCAAAGGTGAGAGCACAAGTGACATTCGACTTACAGATGCTGCAAA
*
449011 ACCTAGAACCCCCAGCACT
66 ACCTAGAACCACCAGCACT
* * * * **
449030 TCCCCACCGCCTTCAGGTTCCAAAGGTGATAGCACAAGTGACATTGGACTTACAGATGCTGTGAA
1 TCCACACCACCTTCAGGTTCCAAAGGTGAGAGCACAAGTGACATTCGACTTACAGATGCTGCAAA
449095 ACCTAGAACCACCAGCACT
66 ACCTAGAACCACCAGCACT
**
449114 TCCACACCACCTTCAGGTTCCGGAGGT-AGGAGCACAAGTGA
1 TCCACACCACCTTCAGGTTCCAAAGGTGA-GAGCACAAGTGA
449155 GGCTCCAAAT
Statistics
Matches: 107, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
83 1 0.01
84 106 0.99
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19
Consensus pattern (84 bp):
TCCACACCACCTTCAGGTTCCAAAGGTGAGAGCACAAGTGACATTCGACTTACAGATGCTGCAAA
ACCTAGAACCACCAGCACT
Found at i:449646 original size:20 final size:19
Alignment explanation
Indices: 449604--449646 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
449594 GATCAAATTA
*
449604 TCTAGTCTTAAGAGTGTTC
1 TCTAGTCTTAAGAGTGATC
*
449623 TCTATTCTTAAGAGTGGATC
1 TCTAGTCTTAAGAGT-GATC
449643 TCTA
1 TCTA
449647 CTGTTTATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (19 bp):
TCTAGTCTTAAGAGTGATC
Found at i:452194 original size:66 final size:65
Alignment explanation
Indices: 452123--452249 Score: 201
Period size: 62 Copynumber: 2.0 Consensus size: 65
452113 AAAAAATTTT
452123 AATTG-ATTGAATGGTTTCATTAAAATAATACTTGTTAT-ATTTT-ATAGTATTG-AT-ATTTAA
1 AATTGTATTGAATGGTTTCATTAAAATAATACTTGTTATAATTTTAATAGTATTGTATAATTTAA
*
452183 ANATTGTATTGAATGGTTTCATTAAAATAATACTTGTTTTAATTTTAATAGTATTGTATAATTTA
1 A-ATTGTATTGAATGGTTTCATTAAAATAATACTTGTTATAATTTTAATAGTATTGTATAATTTA
452248 A
65 A
452249 A
1 A
452250 TATTAACATT
Statistics
Matches: 60, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
60 1 0.02
61 4 0.07
62 32 0.53
63 5 0.08
64 9 0.15
65 2 0.03
66 7 0.12
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.48
Consensus pattern (65 bp):
AATTGTATTGAATGGTTTCATTAAAATAATACTTGTTATAATTTTAATAGTATTGTATAATTTAA
Found at i:454923 original size:23 final size:23
Alignment explanation
Indices: 454893--454939 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
454883 CCCACGGTTC
454893 TAATGTCGTGACGATGTTGGCTT
1 TAATGTCGTGACGATGTTGGCTT
454916 TAATGTCGTGACGATGTTGGCTT
1 TAATGTCGTGACGATGTTGGCTT
454939 T
1 T
454940 CTTCTGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.13, G:0.30, T:0.40
Consensus pattern (23 bp):
TAATGTCGTGACGATGTTGGCTT
Found at i:456611 original size:2 final size:2
Alignment explanation
Indices: 456606--456633 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
456596 TTCGAGAGAA
456606 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
456634 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:456689 original size:2 final size:2
Alignment explanation
Indices: 456682--456707 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
456672 TTCGAGAGTA
456682 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
456708 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:456712 original size:2 final size:2
Alignment explanation
Indices: 456707--456731 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
456697 TCTCTCTCTC
456707 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
456732 GTAGATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:477668 original size:43 final size:43
Alignment explanation
Indices: 477607--477697 Score: 164
Period size: 43 Copynumber: 2.1 Consensus size: 43
477597 ATTGAGCAAA
*
477607 AAAAAGATGAGCTGGAGTTGAAACTTGGATTAGGAAATCAAGG
1 AAAAAGATGAGCTGGAGTTGAAACTTAGATTAGGAAATCAAGG
*
477650 AAAAAGATGAGCTGGAGTTGAAATTTAGATTAGGAAATCAAGG
1 AAAAAGATGAGCTGGAGTTGAAACTTAGATTAGGAAATCAAGG
477693 AAAAA
1 AAAAA
477698 CATAGAGTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.46, C:0.05, G:0.27, T:0.21
Consensus pattern (43 bp):
AAAAAGATGAGCTGGAGTTGAAACTTAGATTAGGAAATCAAGG
Found at i:485043 original size:64 final size:64
Alignment explanation
Indices: 484963--485088 Score: 200
Period size: 64 Copynumber: 2.0 Consensus size: 64
484953 CAGGTGATCA
484963 ATGAACAACCAGATTTTGTAT-GTAAAACCACAGGTCGATATCATCAATATAAGATAAATGATTG
1 ATGAACAACCAGATTTTGTATCG-AAAACCACAGGTCGATATCATCAATATAAGATAAATGATTG
* * **
485027 ATGAACAACCGGATTTTGTATCGAAAACCACATGTTTATATCATCAATATAAGATAAATGAT
1 ATGAACAACCAGATTTTGTATCGAAAACCACAGGTCGATATCATCAATATAAGATAAATGAT
485089 ACGATCATTC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
64 56 0.98
65 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.29
Consensus pattern (64 bp):
ATGAACAACCAGATTTTGTATCGAAAACCACAGGTCGATATCATCAATATAAGATAAATGATTG
Found at i:492097 original size:58 final size:58
Alignment explanation
Indices: 492029--492145 Score: 207
Period size: 58 Copynumber: 2.0 Consensus size: 58
492019 CATTGTGGTT
*
492029 CCTATTTTATTGTTAATGGTAGTTTTCCATTTCATGTTGTTGGAGGTTGTGTCTCCAC
1 CCTATTTTATTGTTAATGGTAGTTTTCCATTTCATGTTATTGGAGGTTGTGTCTCCAC
* *
492087 CCTATTTTATTGTTAGTGGTAGTTTTCTATTTCATGTTATTGGAGGTTGTGTCTCCAC
1 CCTATTTTATTGTTAATGGTAGTTTTCCATTTCATGTTATTGGAGGTTGTGTCTCCAC
492145 C
1 C
492146 TTTCCACTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.49
Consensus pattern (58 bp):
CCTATTTTATTGTTAATGGTAGTTTTCCATTTCATGTTATTGGAGGTTGTGTCTCCAC
Found at i:509849 original size:233 final size:231
Alignment explanation
Indices: 509442--509867 Score: 617
Period size: 233 Copynumber: 1.8 Consensus size: 231
509432 TCATATCATC
* * *
509442 GTACTAATGTCTCGTAGGCAGCCATCTAAAAGCTTTCAGATTTCTACATTAACCCAGAATTCAGA
1 GTACTAATGTCTCGTAGGCAGCCATCCAAAAACTTTCAGATTTCTACATTAAACCAGAATTCAGA
* * *
509507 CTGGTTTTTTGGCTGTCCTGGTATGTCCTACTTCAAATGTACTTATATCACCAGTTCTAATTCCA
66 CAGGTTTTTTGGCTGTCCTGGTATGTCCTACTTCAAATGTACTTATATCACCAATTCGAATTCCA
* * *
509572 ACACGACGAACACTTGCTTTCAACATTCAAGCTCCTACTCAACCATGACAATCTAATGTAAAACA
131 ACACAACGAACACTTGCTTTCAACATTCAAGCCCCTACTCAACCATGACAAGCTAATGTAAAACA
509637 AAATGTGTTTTTTCCTCATACCTTAGTACAAAGAAT
196 AAATGTGTTTTTTCCTCATACCTTAGTACAAAGAAT
* *
509673 GTACTAATGTCTTGCT-GGCAGCCATCCAAAAACTTTCAGATTTCTATA-TAAACCAGGAATTTC
1 GTACTAATGTCTCG-TAGGCAGCCATCCAAAAACTTTCAGATTTCTACATTAAACCA-GAA-TTC
* *
509736 AGACAGGTTTCTTTGGCTG-CTCTGGTATGTCCTACTTCGAGTGTACTTATATCACCAAATT-GA
63 AGACAGGTTT-TTTGGCTGTC-CTGGTATGTCCTACTTCAAATGTACTTATATCACC-AATTCGA
* * * *
509799 ATTCCGACACAATGGACACTTGCTTTCAACATTCAAGCCCCTAGTCAACCATGACAAGCTAATGT
125 ATTCCAACACAACGAACACTTGCTTTCAACATTCAAGCCCCTACTCAACCATGACAAGCTAATGT
509864 AAAA
190 AAAA
509868 GGGAGAAACT
Statistics
Matches: 172, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
230 6 0.03
231 45 0.26
232 14 0.08
233 104 0.60
234 3 0.02
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (231 bp):
GTACTAATGTCTCGTAGGCAGCCATCCAAAAACTTTCAGATTTCTACATTAAACCAGAATTCAGA
CAGGTTTTTTGGCTGTCCTGGTATGTCCTACTTCAAATGTACTTATATCACCAATTCGAATTCCA
ACACAACGAACACTTGCTTTCAACATTCAAGCCCCTACTCAACCATGACAAGCTAATGTAAAACA
AAATGTGTTTTTTCCTCATACCTTAGTACAAAGAAT
Found at i:516558 original size:30 final size:30
Alignment explanation
Indices: 516479--516578 Score: 85
Period size: 30 Copynumber: 3.4 Consensus size: 30
516469 TTTTAAAAAA
* * * *
516479 AAATTAAATATATCTTTATATATTTATTAT
1 AAATTAAATAAATTTTTATATTTTTATTTT
** * **
516509 -GTTTAATTAAATTCGTATATTTTTATTTT
1 AAATTAAATAAATTTTTATATTTTTATTTT
*
516538 AAATTAAATAAATTTTTATATTTTTATCTT
1 AAATTAAATAAATTTTTATATTTTTATTTT
* *
516568 GAATCAAATAA
1 AAATTAAATAA
516579 TCGCATTAGG
Statistics
Matches: 52, Mismatches: 17, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
29 20 0.38
30 32 0.62
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (30 bp):
AAATTAAATAAATTTTTATATTTTTATTTT
Found at i:516561 original size:29 final size:29
Alignment explanation
Indices: 516479--516561 Score: 69
Period size: 29 Copynumber: 2.8 Consensus size: 29
516469 TTTTAAAAAA
* *
516479 AAATTAAATATATCTTTATATATTTATTAT
1 AAATTAAATAAATTTTTATAT-TTTATTAT
** * ** *
516509 -GTTTAATTAAATTCGTATATTTTTATTTT
1 AAATTAAATAAATTTTTATA-TTTTATTAT
516538 AAATTAAATAAATTTTTATATTTT
1 AAATTAAATAAATTTTTATATTTT
516562 TATCTTGAAT
Statistics
Matches: 38, Mismatches: 13, Indels: 5
0.68 0.23 0.09
Matches are distributed among these distances:
29 23 0.61
30 15 0.39
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (29 bp):
AAATTAAATAAATTTTTATATTTTATTAT
Found at i:517685 original size:27 final size:27
Alignment explanation
Indices: 517633--517685 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
517623 ATTTAATTTT
* *
517633 TAAAATATTAATAATTTATAATTTAAG
1 TAAAATATTAATAATTAAAAATTTAAG
517660 TAAAATATTAATAA-TAAAAATATTAA
1 TAAAATATTAATAATTAAAAAT-TTAA
517686 TAATTAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
TAAAATATTAATAATTAAAAATTTAAG
Found at i:517732 original size:26 final size:26
Alignment explanation
Indices: 517692--517742 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
517682 TTAATAATTA
517692 ATAATTTAAATATTAATATTTTATTT
1 ATAATTTAAATATTAATATTTTATTT
*
517718 ATAATTT-AATCATTAATGTTTTATT
1 ATAATTTAAAT-ATTAATATTTTATT
517743 AGAAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (26 bp):
ATAATTTAAATATTAATATTTTATTT
Found at i:523289 original size:1 final size:1
Alignment explanation
Indices: 523283--523343 Score: 59
Period size: 1 Copynumber: 61.0 Consensus size: 1
523273 CACATAAATT
* * * * * * *
523283 AAAAAAAAAATAAATAAATAAAAAAAATAAAAAAATAAAAAAAATAAAAAAATAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
523344 TCGGGATGGC
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (1 bp):
A
Found at i:523307 original size:17 final size:17
Alignment explanation
Indices: 523285--523344 Score: 111
Period size: 17 Copynumber: 3.5 Consensus size: 17
523275 CATAAATTAA
*
523285 AAAAAAAATAAATAAAT
1 AAAAAAAATAAAAAAAT
523302 AAAAAAAATAAAAAAAT
1 AAAAAAAATAAAAAAAT
523319 AAAAAAAATAAAAAAAT
1 AAAAAAAATAAAAAAAT
523336 AAAAAAAAT
1 AAAAAAAAT
523345 CGGGATGGCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (17 bp):
AAAAAAAATAAAAAAAT
Found at i:523312 original size:9 final size:9
Alignment explanation
Indices: 523285--523344 Score: 90
Period size: 8 Copynumber: 7.0 Consensus size: 9
523275 CATAAATTAA
523285 AAAAAAAAT
1 AAAAAAAAT
*
523294 -AAATAAAT
1 AAAAAAAAT
523302 AAAAAAAAT
1 AAAAAAAAT
523311 -AAAAAAAT
1 AAAAAAAAT
523319 AAAAAAAAT
1 AAAAAAAAT
523328 -AAAAAAAT
1 AAAAAAAAT
523336 AAAAAAAAT
1 AAAAAAAAT
523345 CGGGATGGCT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
8 23 0.50
9 23 0.50
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:523320 original size:25 final size:25
Alignment explanation
Indices: 523287--523342 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 25
523277 TAAATTAAAA
*
523287 AAAAAATAAATAAATAAAAAAAATA
1 AAAAAATAAAAAAATAAAAAAAATA
523312 AAAAAATAAAAAAA-ATAAAAAAATA
1 AAAAAATAAAAAAATA-AAAAAAATA
523337 AAAAAA
1 AAAAAA
523343 ATCGGGATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 1 0.03
25 28 0.97
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (25 bp):
AAAAAATAAAAAAATAAAAAAAATA
Found at i:524290 original size:13 final size:13
Alignment explanation
Indices: 524267--524300 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
524257 TTTGGAGGCT
524267 TAAAA-AAAATAA
1 TAAAATAAAATAA
524279 TAAAATAAAATAA
1 TAAAATAAAATAA
524292 TAATAATAA
1 TAA-AATAA
524301 TAATTAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 10 0.50
14 5 0.25
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAATAAAATAA
Found at i:524293 original size:16 final size:17
Alignment explanation
Indices: 524269--524303 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
524259 TGGAGGCTTA
524269 AAAAAAATAATAA-AAT
1 AAAAAAATAATAATAAT
*
524285 AAAATAATAATAATAAT
1 AAAAAAATAATAATAAT
524302 AA
1 AA
524304 TTAATGATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAAAATAATAATAAT
Found at i:524365 original size:8 final size:8
Alignment explanation
Indices: 524352--524385 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
524342 TTTAAATAAA
524352 AAAAATAT
1 AAAAATAT
524360 AAAAATAT
1 AAAAATAT
524368 AAAAATAT
1 AAAAATAT
524376 AAAAATAT
1 AAAAATAT
524384 AA
1 AA
524386 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAAATAT
Found at i:531851 original size:50 final size:50
Alignment explanation
Indices: 531793--531903 Score: 168
Period size: 50 Copynumber: 2.2 Consensus size: 50
531783 TAATTAGATG
* * *
531793 AAAATATTTTTGAGTTTTGCTTACATAGCTCAGGAGTCAGCGTTGCATTT
1 AAAATATTTTTGAGTTTTGATTACATAGCTCAGAAATCAGCGTTGCATTT
* *
531843 AAAATATTTTTGAGTTTTGATTACATATCTCAGAAATCAGGGTTGCATTT
1 AAAATATTTTTGAGTTTTGATTACATAGCTCAGAAATCAGCGTTGCATTT
*
531893 AAAATTTTTTT
1 AAAATATTTTT
531904 TTTCATGTCT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (50 bp):
AAAATATTTTTGAGTTTTGATTACATAGCTCAGAAATCAGCGTTGCATTT
Found at i:537303 original size:2 final size:2
Alignment explanation
Indices: 537296--537346 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
537286 CCAATCGGAA
*
537296 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
537338 AT AT TT AT A
1 AT AT AT AT A
537347 AGCACAACTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:544299 original size:29 final size:28
Alignment explanation
Indices: 544218--544300 Score: 80
Period size: 29 Copynumber: 3.0 Consensus size: 28
544208 GAACAAATAG
*
544218 AATAAAAATA-AAAT-ATAAATAAATATA
1 AATAAAAATATAAATAATAAATAAA-AAA
* * * *
544245 AATAATAATATAAACAAAAAAGAAAACAA
1 AATAAAAATATAAATAATAAATAAAA-AA
*
544274 AATAAAAATATATATAATAAATAAAAA
1 AATAAAAATATAAATAATAAATAAAAA
544301 TTATTTATAT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
27 9 0.21
28 5 0.12
29 29 0.67
ACGTcount: A:0.75, C:0.02, G:0.01, T:0.22
Consensus pattern (28 bp):
AATAAAAATATAAATAATAAATAAAAAA
Found at i:549308 original size:55 final size:53
Alignment explanation
Indices: 549248--549351 Score: 129
Period size: 52 Copynumber: 1.9 Consensus size: 53
549238 ATTATCTTCA
* *
549248 AATTATCATTATAACTATTATTTATAGTATTTTA-AATTTCAAAATATTTTTCTTT
1 AATTATCATTAT---TATTATTTATAATATTATATAATTTCAAAATATTTTTCTTT
* * *
549303 AATTATTATTATTATTATTTATAATATTATATAATTTTAAATTATTTTT
1 AATTATCATTATTATTATTTATAATATTATATAATTTCAAAATATTTTT
549352 AATAAAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
52 17 0.40
53 15 0.35
55 11 0.26
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.58
Consensus pattern (53 bp):
AATTATCATTATTATTATTTATAATATTATATAATTTCAAAATATTTTTCTTT
Found at i:550528 original size:15 final size:15
Alignment explanation
Indices: 550505--550535 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
550495 TGGGATAGAA
*
550505 AAGTTAATAATAAAT
1 AAGTAAATAATAAAT
550520 AAGTAAATAATAAAT
1 AAGTAAATAATAAAT
550535 A
1 A
550536 CTAAAACGTG
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:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (15 bp):
AAGTAAATAATAAAT
Found at i:556551 original size:81 final size:80
Alignment explanation
Indices: 556419--556664 Score: 298
Period size: 81 Copynumber: 3.0 Consensus size: 80
556409 CTATTGGTAT
* * * *
556419 ATAATATTGATTTTTTTGTACCAATCAAAAATTAATTATTGGTAATTCAATTTATTTCTAAATAA
1 ATAATATTCATATTTTTG-ACCAATCAAAAATTAATTATTGGTCATTCAATTTATCTCTAAATAA
556484 ATCAAAATAATTTAGAG
65 AT-AAAATAATTTAGAG
* * *
556501 ATAATATTTATATTTTTGA-CATATCAAAAATTAATTATTAGTCATCCAATTTATCTCTAAATAA
1 ATAATATTCATATTTTTGACCA-ATCAAAAATTAATTATTGGTCATTCAATTTATCTCTAAATAA
* * *
556565 ATAAAAAATATTTAAAA
65 ATAAAATA-ATTTAGAG
* * * *
556582 ATAATATTCATATTTTTTACCAATCAAAATTTAATTATTGGTCATTTAATTTATCTCT-AATAAT
1 ATAATATTCATATTTTTGACCAATCAAAAATTAATTATTGGTCATTCAATTTATCTCTAAATAAA
* *
556646 TATATTAATTTAGAG
66 TAAAATAATTTAGAG
556661 ATAA
1 ATAA
556665 AAGTCAAATT
Statistics
Matches: 140, Mismatches: 21, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
79 10 0.07
80 16 0.11
81 96 0.69
82 18 0.13
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (80 bp):
ATAATATTCATATTTTTGACCAATCAAAAATTAATTATTGGTCATTCAATTTATCTCTAAATAAA
TAAAATAATTTAGAG
Found at i:556945 original size:17 final size:17
Alignment explanation
Indices: 556925--556957 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
556915 GAGGCATTCA
556925 AAGATTG-GAAGCATTTG
1 AAGATTGAG-AGCATTTG
556942 AAGATTGAGAGCATTT
1 AAGATTGAGAGCATTT
556958 CAGAGATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.30
Consensus pattern (17 bp):
AAGATTGAGAGCATTTG
Found at i:557080 original size:33 final size:33
Alignment explanation
Indices: 557042--557107 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
557032 CAAAGTTCGT
557042 AATCAAGATACTGTGTTCATAATCAAGATTAAG
1 AATCAAGATACTGTGTTCATAATCAAGATTAAG
*
557075 AATCAAGATACTGTGTTTATAATCAAGATTAAG
1 AATCAAGATACTGTGTTCATAATCAAGATTAAG
557108 TCGTCAAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (33 bp):
AATCAAGATACTGTGTTCATAATCAAGATTAAG
Found at i:568336 original size:23 final size:21
Alignment explanation
Indices: 568301--568362 Score: 56
Period size: 23 Copynumber: 2.9 Consensus size: 21
568291 ATATTTTATT
568301 TTTAATAA-T-TTATTGAAAA
1 TTTAATAATTATTATTGAAAA
*
568320 TATTAATAAATTATTATTTTAAAA
1 T-TTAAT-AATTATTA-TTGAAAA
*
568344 TTTAATGATTATCTATTGA
1 TTTAATAATTAT-TATTGA
568363 TTTTATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
19 1 0.03
20 5 0.15
21 2 0.06
22 9 0.26
23 10 0.29
24 7 0.21
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (21 bp):
TTTAATAATTATTATTGAAAA
Found at i:568851 original size:2 final size:2
Alignment explanation
Indices: 568846--568881 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
568836 ACACACACAC
568846 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
568882 CTAACAGTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.