Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 21 of 167
Found at i:6317972 original size:15 final size:15
Alignment explanation
Indices: 6317930--6317979 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
6317920 ATAACTTTGA
*
6317930 ATGCAAATG-ATGCG
1 ATGCAAATGCATGAG
6317944 ATG-AAATGCTATGAG
1 ATGCAAATGC-ATGAG
6317959 ATGCAAATGCATGA-
1 ATGCAAATGCATGAG
6317973 ATGCAAA
1 ATGCAAA
6317980 AAGGACATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.31
15 11 0.34
16 6 0.19
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.22
Consensus pattern (15 bp):
ATGCAAATGCATGAG
Found at i:6321871 original size:10 final size:10
Alignment explanation
Indices: 6321849--6321932 Score: 61
Period size: 10 Copynumber: 8.6 Consensus size: 10
6321839 TATTTTACAT
6321849 ATAAAATATA
1 ATAAAATATA
* *
6321859 ATATAATAAA
1 ATAAAATATA
6321869 ATAAAA-ATA
1 ATAAAATATA
*
6321878 A-AAAAGA-A
1 ATAAAATATA
6321886 ATAAAA-ATA
1 ATAAAATATA
* *
6321895 A-AAAACAGA
1 ATAAAATATA
6321904 ATAAATATATA
1 ATAAA-ATATA
6321915 TATAAATATATA
1 -ATAAA-ATATA
6321927 ATAAAA
1 ATAAAA
6321933 GAAATTTTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
8 11 0.18
9 13 0.22
10 17 0.28
11 8 0.13
12 11 0.18
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.24
Consensus pattern (10 bp):
ATAAAATATA
Found at i:6321877 original size:6 final size:6
Alignment explanation
Indices: 6321866--6321898 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
6321856 ATAATATAAT
*
6321866 AAAATA AAAATA AAAA-A GAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
6321899 ACAGAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (6 bp):
AAAATA
Found at i:6321889 original size:17 final size:17
Alignment explanation
Indices: 6321867--6321899 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
6321857 TAATATAATA
6321867 AAATAAAAATAAAAAAG
1 AAATAAAAATAAAAAAG
6321884 AAATAAAAATAAAAAA
1 AAATAAAAATAAAAAA
6321900 CAGAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (17 bp):
AAATAAAAATAAAAAAG
Found at i:6321898 original size:18 final size:18
Alignment explanation
Indices: 6321867--6321908 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
6321857 TAATATAATA
6321867 AAATAAAAATAAAAA-AG
1 AAATAAAAATAAAAACAG
6321884 AAATAAAAATAAAAAACAG
1 AAATAAAAAT-AAAAACAG
6321903 -AATAAA
1 AAATAAA
6321909 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.43
18 11 0.48
19 2 0.09
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.12
Consensus pattern (18 bp):
AAATAAAAATAAAAACAG
Found at i:6323812 original size:18 final size:18
Alignment explanation
Indices: 6323789--6323823 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
6323779 ACAAAGTGAA
6323789 AATAG-AGCAAAATGTGGG
1 AATAGAAGC-AAATGTGGG
6323807 AATAGAAGCAAATGTGG
1 AATAGAAGCAAATGTGG
6323824 TGGTTATTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.46, C:0.06, G:0.31, T:0.17
Consensus pattern (18 bp):
AATAGAAGCAAATGTGGG
Found at i:6324906 original size:24 final size:24
Alignment explanation
Indices: 6324874--6324919 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
6324864 AGAATGGGTC
6324874 TGCTGGTCTAGTGGTTAAGATGTG
1 TGCTGGTCTAGTGGTTAAGATGTG
6324898 TGCTGGTCTAGTGGTTAAGATG
1 TGCTGGTCTAGTGGTTAAGATG
6324920 GTTAACAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.09, G:0.37, T:0.37
Consensus pattern (24 bp):
TGCTGGTCTAGTGGTTAAGATGTG
Found at i:6329501 original size:20 final size:21
Alignment explanation
Indices: 6329461--6329502 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
6329451 TCTCACTAGA
6329461 TAAAATTATTTTTTAATTTTT
1 TAAAATTATTTTTTAATTTTT
6329482 TAAAATTATTTTTTAATTTTT
1 TAAAATTATTTTTTAATTTTT
6329503 GGTGCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TAAAATTATTTTTTAATTTTT
Found at i:6330000 original size:18 final size:18
Alignment explanation
Indices: 6329977--6330017 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
6329967 TCTAAAGCAA
*
6329977 ATTTTAAAATCCAAACTG
1 ATTTTAAAACCCAAACTG
* *
6329995 ATTTTAAAGCCCAATCTG
1 ATTTTAAAACCCAAACTG
6330013 ATTTT
1 ATTTT
6330018 GATTTCAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (18 bp):
ATTTTAAAACCCAAACTG
Found at i:6335046 original size:9 final size:9
Alignment explanation
Indices: 6335032--6335064 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
6335022 AAAAGGACAA
*
6335032 CAACAACAG
1 CAACAATAG
6335041 CAACAATAG
1 CAACAATAG
6335050 CAACAATAG
1 CAACAATAG
6335059 CAACAA
1 CAACAA
6335065 AAGAACAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.58, C:0.27, G:0.09, T:0.06
Consensus pattern (9 bp):
CAACAATAG
Found at i:6337398 original size:22 final size:22
Alignment explanation
Indices: 6337372--6337456 Score: 86
Period size: 22 Copynumber: 3.9 Consensus size: 22
6337362 GCCTCTCCTT
6337372 TTTCTTTTCTTTTCTTTTTTTG
1 TTTCTTTTCTTTTCTTTTTTTG
*
6337394 TTTCTTTT-TCCTTCTTTTTTTG
1 TTTCTTTTCT-TTTCTTTTTTTG
* * *
6337416 TTGT-TTTTTTTTTGTGTTTTCT-
1 TT-TCTTTTCTTTTCT-TTTTTTG
6337438 TTTCTTTTCTTTTCTTTTT
1 TTTCTTTTCTTTTCTTTTT
6337457 GTTTTTTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
21 6 0.12
22 39 0.75
23 7 0.13
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (22 bp):
TTTCTTTTCTTTTCTTTTTTTG
Found at i:6337437 original size:39 final size:37
Alignment explanation
Indices: 6337371--6337464 Score: 104
Period size: 39 Copynumber: 2.5 Consensus size: 37
6337361 GGCCTCTCCT
*
6337371 TTTTCTTTTCT-TTTCTTTTTTTGTTTCTTTT-TCCTTC
1 TTTTCTTTT-TGTTTTTTTTTTTGTTTCTTTTCT-CTTC
*
6337408 TTTT-TTTGTTGTTTTTTTTTTGTGTTTTCTTTTCTTTTC
1 TTTTCTTT-TTGTTTTTTTTTT-TG-TTTCTTTTCTCTTC
6337447 TTTTCTTTTTGTTTTTTT
1 TTTTCTTTTTGTTTTTTT
6337465 AAGGTGAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
36 4 0.08
37 14 0.29
38 2 0.04
39 25 0.51
40 4 0.08
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (37 bp):
TTTTCTTTTTGTTTTTTTTTTTGTTTCTTTTCTCTTC
Found at i:6337461 original size:5 final size:5
Alignment explanation
Indices: 6337371--6337455 Score: 59
Period size: 5 Copynumber: 16.8 Consensus size: 5
6337361 GGCCTCTCCT
* * * *
6337371 TTTTC TTTTC TTTTC TTTTTT TGTTTC TTTT- TCCTTC TTTTT TTGTTG
1 TTTTC TTTTC TTTTC -TTTTC T-TTTC TTTTC T-TTTC TTTTC TT-TTC
* *
6337419 TTTT- TTTT- TTGTG TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
6337456 TGTTTTTTTA
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
4 8 0.12
5 44 0.68
6 13 0.20
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:6340142 original size:15 final size:16
Alignment explanation
Indices: 6340112--6340144 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
6340102 TAATGCAAAT
*
6340112 AATGCGATGCAATGCA
1 AATGCGATGAAATGCA
6340128 AATGC-ATGAAATGCA
1 AATGCGATGAAATGCA
6340143 AA
1 AA
6340145 AGAAAGGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.18
Consensus pattern (16 bp):
AATGCGATGAAATGCA
Found at i:6342240 original size:24 final size:25
Alignment explanation
Indices: 6342186--6342241 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
6342176 TATTTAAAGG
* * *
6342186 TTTAGAATAGATACTATAAAAGCAA
1 TTTAAAATAAATAATATAAAAGCAA
6342211 TTTAAAATAAATAATATAAAA-CAA
1 TTTAAAATAAATAATATAAAAGCAA
6342235 TTTAAAA
1 TTTAAAA
6342242 ATCATTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.30
Consensus pattern (25 bp):
TTTAAAATAAATAATATAAAAGCAA
Found at i:6342570 original size:26 final size:27
Alignment explanation
Indices: 6342513--6342584 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 27
6342503 ATCACATATA
*
6342513 ATAAAAATAGTTTAAAGTAAATAACAT
1 ATAAAAATAGTTTAAAATAAATAACAT
*
6342540 ATAAAAATA-TTTAAAATAAATAATAT
1 ATAAAAATAGTTTAAAATAAATAACAT
* **
6342566 GT-AAAGGAGTTTAAAATAA
1 ATAAAAATAGTTTAAAATAA
6342585 CTGATGCGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
25 4 0.10
26 26 0.67
27 9 0.23
ACGTcount: A:0.60, C:0.01, G:0.08, T:0.31
Consensus pattern (27 bp):
ATAAAAATAGTTTAAAATAAATAACAT
Found at i:6342880 original size:17 final size:17
Alignment explanation
Indices: 6342860--6342893 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6342850 TAAAATAATC
*
6342860 TAAAGTAAAGAATATAT
1 TAAAATAAAGAATATAT
*
6342877 TAAAATAAATAATATAT
1 TAAAATAAAGAATATAT
6342894 GGGAAATAAA
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:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (17 bp):
TAAAATAAAGAATATAT
Found at i:6347610 original size:56 final size:56
Alignment explanation
Indices: 6347524--6347636 Score: 208
Period size: 56 Copynumber: 2.0 Consensus size: 56
6347514 AACCATCCAA
*
6347524 AGGGCTCTCCACTCGACGTCTTCTTCTTAGAGATTTCGAAGGAAAAATAGATAGCT
1 AGGGCTCTCCACTCGACATCTTCTTCTTAGAGATTTCGAAGGAAAAATAGATAGCT
*
6347580 AGGGCTCTCCACTCGACATCTTCTTCTTAGAGATTTCGGAGGAAAAATAGATAGCT
1 AGGGCTCTCCACTCGACATCTTCTTCTTAGAGATTTCGAAGGAAAAATAGATAGCT
6347636 A
1 A
6347637 TCTATTTTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (56 bp):
AGGGCTCTCCACTCGACATCTTCTTCTTAGAGATTTCGAAGGAAAAATAGATAGCT
Found at i:6354974 original size:26 final size:27
Alignment explanation
Indices: 6354914--6354974 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
6354904 AATTGAGTTT
* *
6354914 GTTTATTTTAGTTTATGTAGTTATTTA
1 GTTTATTTTAATTTATGTAGTTACTTA
* *
6354941 -TTTCTTTTAATTTAT-TTGTTACTTA
1 GTTTATTTTAATTTATGTAGTTACTTA
*
6354966 GTTTTTTTT
1 GTTTATTTT
6354975 TAAAACTGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 8 0.29
26 20 0.71
ACGTcount: A:0.18, C:0.03, G:0.10, T:0.69
Consensus pattern (27 bp):
GTTTATTTTAATTTATGTAGTTACTTA
Found at i:6360413 original size:19 final size:18
Alignment explanation
Indices: 6360386--6360423 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
6360376 TTGTTTAATT
6360386 TATAGATTTTTTAAATTAA
1 TATAGA-TTTTTAAATTAA
*
6360405 TATATATTTTTAAATTAA
1 TATAGATTTTTAAATTAA
6360423 T
1 T
6360424 TTATTAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
TATAGATTTTTAAATTAA
Found at i:6363417 original size:29 final size:29
Alignment explanation
Indices: 6363377--6363439 Score: 81
Period size: 33 Copynumber: 2.0 Consensus size: 29
6363367 GATACCATTA
*
6363377 AAAATATATATAATCTAAAGAATATACAAAATT
1 AAAATATATAT-ATAT-AA-AAT-TACAAAATT
6363410 AAAATATATATATATAAAATTACAAAATT
1 AAAATATATATATATAAAATTACAAAATT
6363439 A
1 A
6363440 TAAAATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 10 0.34
30 3 0.10
31 2 0.07
32 3 0.10
33 11 0.38
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (29 bp):
AAAATATATATATATAAAATTACAAAATT
Found at i:6363815 original size:22 final size:22
Alignment explanation
Indices: 6363765--6363819 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
6363755 CCCAACTAAT
*
6363765 CTAGCCCAATACCCTAAACCAAC
1 CTAGCCCAATA-CCTAAAACAAC
*
6363788 CTAGCCCAAT-CCTAAAACTAC
1 CTAGCCCAATACCTAAAACAAC
6363809 CTGAGCCCAAT
1 CT-AGCCCAAT
6363820 TTACAAACCC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 11 0.38
22 8 0.28
23 10 0.34
ACGTcount: A:0.36, C:0.40, G:0.07, T:0.16
Consensus pattern (22 bp):
CTAGCCCAATACCTAAAACAAC
Found at i:6367553 original size:21 final size:22
Alignment explanation
Indices: 6367527--6367568 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
6367517 TGACCTTTCC
*
6367527 AAGGTATGGG-TAGGTATGGGA
1 AAGGTATGGGCAAGGTATGGGA
6367548 AAGGTATGGGCAAGGTATGGG
1 AAGGTATGGGCAAGGTATGGG
6367569 GTATGGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.29, C:0.02, G:0.48, T:0.21
Consensus pattern (22 bp):
AAGGTATGGGCAAGGTATGGGA
Found at i:6367554 original size:11 final size:10
Alignment explanation
Indices: 6367527--6367568 Score: 57
Period size: 11 Copynumber: 4.0 Consensus size: 10
6367517 TGACCTTTCC
6367527 AAGGTATGGG
1 AAGGTATGGG
*
6367537 TAGGTATGGG
1 AAGGTATGGG
6367547 AAAGGTATGGG
1 -AAGGTATGGG
6367558 CAAGGTATGGG
1 -AAGGTATGGG
6367569 GTATGGGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.29, C:0.02, G:0.48, T:0.21
Consensus pattern (10 bp):
AAGGTATGGG
Found at i:6371319 original size:11 final size:11
Alignment explanation
Indices: 6371292--6371345 Score: 74
Period size: 11 Copynumber: 5.0 Consensus size: 11
6371282 TGACCTTTCC
6371292 AAGGTATGGG-
1 AAGGTATGGGA
*
6371302 TAGGTATGGGA
1 AAGGTATGGGA
*
6371313 AAGGTATGGGC
1 AAGGTATGGGA
*
6371324 AAGGTATGGGC
1 AAGGTATGGGA
6371335 AAGGTATGGGA
1 AAGGTATGGGA
6371346 TATATTCTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
10 9 0.23
11 30 0.77
ACGTcount: A:0.30, C:0.04, G:0.46, T:0.20
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:6376692 original size:19 final size:19
Alignment explanation
Indices: 6376668--6376704 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
6376658 TGCAATTTTG
6376668 ATTTTTCTATTGTTCTCAA
1 ATTTTTCTATTGTTCTCAA
6376687 ATTTTTCTATTGTTCTCA
1 ATTTTTCTATTGTTCTCA
6376705 CTCTTGGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.19, C:0.16, G:0.05, T:0.59
Consensus pattern (19 bp):
ATTTTTCTATTGTTCTCAA
Found at i:6378049 original size:19 final size:19
Alignment explanation
Indices: 6378025--6378061 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
6378015 TGCAATTTTG
6378025 ATTTTTCTATTGTTCTCAA
1 ATTTTTCTATTGTTCTCAA
6378044 ATTTTTCTATTGTTCTCA
1 ATTTTTCTATTGTTCTCA
6378062 CTCTTGGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.19, C:0.16, G:0.05, T:0.59
Consensus pattern (19 bp):
ATTTTTCTATTGTTCTCAA
Found at i:6379395 original size:13 final size:14
Alignment explanation
Indices: 6379379--6379407 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6379369 CTAATTAAAA
6379379 TTTTA-AGAAATTT
1 TTTTATAGAAATTT
6379392 TTTTATAGAAATTT
1 TTTTATAGAAATTT
6379406 TT
1 TT
6379408 CTCAAAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTTTATAGAAATTT
Found at i:6400858 original size:17 final size:16
Alignment explanation
Indices: 6400818--6400862 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
6400808 ACTTAATCAT
6400818 TTTAATATTAAATTAA
1 TTTAATATTAAATTAA
* *
6400834 TATAAATATTAGATTAAA
1 T-TTAATATTAAATT-AA
6400852 TTTAATATTAA
1 TTTAATATTAA
6400863 CTCTTATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 1 0.04
17 19 0.83
18 3 0.13
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
TTTAATATTAAATTAA
Found at i:6407244 original size:16 final size:16
Alignment explanation
Indices: 6407223--6407256 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
6407213 TAGTTATTAC
6407223 TTGAGAACAACTCCTG
1 TTGAGAACAACTCCTG
*
6407239 TTGAGAACAACTCTTG
1 TTGAGAACAACTCCTG
6407255 TT
1 TT
6407257 TGGAATAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (16 bp):
TTGAGAACAACTCCTG
Found at i:6408644 original size:16 final size:16
Alignment explanation
Indices: 6408618--6408673 Score: 71
Period size: 15 Copynumber: 3.6 Consensus size: 16
6408608 TAACGAAGAG
*
6408618 TGATC-AAAATATAAA
1 TGATCTAAAATAGAAA
6408633 TGATCTAAAATAGAAA
1 TGATCTAAAATAGAAA
*
6408649 TGA-CCAAAATAGAAA
1 TGATCTAAAATAGAAA
*
6408664 TTATCTAAAA
1 TGATCTAAAA
6408674 CATTTTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
15 18 0.51
16 17 0.49
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.25
Consensus pattern (16 bp):
TGATCTAAAATAGAAA
Found at i:6415787 original size:5 final size:5
Alignment explanation
Indices: 6415773--6415804 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
6415763 TTGTGTGTTC
6415773 TTTA- TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
6415805 TTCACAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:6422578 original size:5 final size:5
Alignment explanation
Indices: 6422568--6422599 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
6422558 TTGTGTGTTC
6422568 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
6422600 TTCACACTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:6422582 original size:9 final size:9
Alignment explanation
Indices: 6422568--6422598 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
6422558 TTGTGTGTTC
6422568 TTTATTTTA
1 TTTATTTTA
6422577 TTTATTTTA
1 TTTATTTTA
6422586 TTTTATTTTA
1 -TTTATTTTA
6422596 TTT
1 TTT
6422599 TTTCACACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:6425760 original size:21 final size:21
Alignment explanation
Indices: 6425734--6425774 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6425724 AGACGAGCAA
* *
6425734 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
6425755 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
6425775 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:6432472 original size:16 final size:17
Alignment explanation
Indices: 6432441--6432473 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6432431 TTCATTAGTA
6432441 TATAGCAATCATTTCAT
1 TATAGCAATCATTTCAT
*
6432458 TATATCAAT-ATTTCAT
1 TATAGCAATCATTTCAT
6432474 GCACCATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.45
Consensus pattern (17 bp):
TATAGCAATCATTTCAT
Found at i:6432821 original size:46 final size:46
Alignment explanation
Indices: 6432759--6433262 Score: 857
Period size: 46 Copynumber: 11.0 Consensus size: 46
6432749 TTTGACATGA
* * * * * *
6432759 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* ** *** *
6432805 TACCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
6432851 TGCCATGTTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
6432897 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
6432943 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
6432989 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
6433035 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
6433081 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
6433127 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
6433173 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
6433219 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
6433263 AGAGCACACT
Statistics
Matches: 442, Mismatches: 15, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
45 4 0.01
46 438 0.99
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:6446219 original size:23 final size:24
Alignment explanation
Indices: 6446180--6446227 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
6446170 TTTATTTGAT
6446180 AATATGTTTTGATATAACAAATTAA
1 AATATGTTTTGATATAA-AAATTAA
*
6446205 AATAT-TTTTGA-ATAAAAGTTAA
1 AATATGTTTTGATATAAAAATTAA
6446227 A
1 A
6446228 GTTGAACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 4 0.18
24 6 0.27
25 5 0.23
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (24 bp):
AATATGTTTTGATATAAAAATTAA
Found at i:6448117 original size:16 final size:17
Alignment explanation
Indices: 6448085--6448117 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6448075 ATAGATATAA
6448085 AAATAGTAATTTAGAAT
1 AAATAGTAATTTAGAAT
*
6448102 AAATAG-AATTTCGAAT
1 AAATAGTAATTTAGAAT
6448118 TTAAAGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33
Consensus pattern (17 bp):
AAATAGTAATTTAGAAT
Found at i:6451216 original size:18 final size:19
Alignment explanation
Indices: 6451168--6451220 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 19
6451158 ACAATATATA
* *
6451168 ATATATAATAACAAAAATT
1 ATATATAAGAATAAAAATT
* *
6451187 -TATAAAAGAATAATAATT
1 ATATATAAGAATAAAAATT
6451205 ATATATAA-AATAAAAA
1 ATATATAAGAATAAAAA
6451221 AATATATTGG
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
18 21 0.78
19 6 0.22
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
ATATATAAGAATAAAAATT
Found at i:6451510 original size:18 final size:17
Alignment explanation
Indices: 6451470--6451540 Score: 60
Period size: 16 Copynumber: 4.2 Consensus size: 17
6451460 ACCTTTAATG
* *
6451470 ATAATAATATAT-AGAT
1 ATAAAAATATATAATAT
6451486 A-AAAAATATATAATAGT
1 ATAAAAATATATAATA-T
*
6451503 ATAAAAATAACATAATAT
1 ATAAAAAT-ATATAATAT
6451521 A-AAATAAT-TATAATAT
1 ATAAA-AATATATAATAT
6451537 ATAA
1 ATAA
6451541 TATGAAAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
15 9 0.20
16 11 0.24
17 7 0.16
18 11 0.24
19 7 0.16
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (17 bp):
ATAAAAATATATAATAT
Found at i:6456760 original size:29 final size:30
Alignment explanation
Indices: 6456718--6456788 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 30
6456708 GTGACCTCGT
* *
6456718 TAAAAGGAAA-CTTTTGTGGCAATCTCTA-
1 TAAAAGAAAACCTTTTATGGCAATCTCTAG
*
6456746 TTAAAGAAAACC-TTTATGGCAATCTCTAG
1 TAAAAGAAAACCTTTTATGGCAATCTCTAG
*
6456775 TAAAAGAAATCCTT
1 TAAAAGAAAACCTT
6456789 CATACGATCT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 23 0.66
29 11 0.31
30 1 0.03
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (30 bp):
TAAAAGAAAACCTTTTATGGCAATCTCTAG
Found at i:6456798 original size:28 final size:29
Alignment explanation
Indices: 6456739--6456837 Score: 87
Period size: 28 Copynumber: 3.5 Consensus size: 29
6456729 TTTTGTGGCA
* * * * *
6456739 ATCTCTA-TTAAAGAAAACCTTTATGGCA
1 ATCTCTAGTAAAAGAAATCCTTCATGACG
6456767 ATCTCTAGTAAAAGAAATCCTTCAT-ACG
1 ATCTCTAGTAAAAGAAATCCTTCATGACG
* * *
6456795 ATCTCT-GTTAATATAAATCCTTCATGACT
1 ATCTCTAG-TAAAAGAAATCCTTCATGACG
*
6456824 ATCTCTATTAAAAG
1 ATCTCTAGTAAAAG
6456838 GAAACATTTG
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
27 1 0.02
28 29 0.52
29 26 0.46
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.34
Consensus pattern (29 bp):
ATCTCTAGTAAAAGAAATCCTTCATGACG
Found at i:6464059 original size:32 final size:32
Alignment explanation
Indices: 6464006--6464083 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
6463996 CCACACCTCA
* * *
6464006 GTGTAGCCCACATGCCTAATTTGGCCTAGCCC
1 GTGTGGCCCACACGCCCAATTTGGCCTAGCCC
*
6464038 GTGTGGCCCACACGCCCAATTTGGCCTAGCTC
1 GTGTGGCCCACACGCCCAATTTGGCCTAGCCC
*
6464070 TTGTGGCCCACACG
1 GTGTGGCCCACACG
6464084 GCCACCCTCC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.17, C:0.36, G:0.24, T:0.23
Consensus pattern (32 bp):
GTGTGGCCCACACGCCCAATTTGGCCTAGCCC
Found at i:6480014 original size:16 final size:16
Alignment explanation
Indices: 6479986--6480024 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
6479976 ATTTAATCTA
6479986 AATATAA-ATATAAAT
1 AATATAATATATAAAT
* *
6480001 AATTTAATATATAATT
1 AATATAATATATAAAT
6480017 AATATAAT
1 AATATAAT
6480025 TTTTTATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATAATATATAAAT
Found at i:6480032 original size:21 final size:20
Alignment explanation
Indices: 6479986--6480042 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
6479976 ATTTAATCTA
6479986 AATATAAATATAA-ATAATTT
1 AATATAAA-ATAATATAATTT
*
6480006 AATATATAATTAATATAATTT
1 AATATA-AAATAATATAATTT
**
6480027 TTTATAAAATAATATA
1 AATATAAAATAATATA
6480043 TTTGGACTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATAAAATAATATAATTT
Found at i:6486770 original size:14 final size:15
Alignment explanation
Indices: 6486749--6486783 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6486739 AAAATAAGTG
*
6486749 TTGAAAAATTAAATA
1 TTGAAAATTTAAATA
*
6486764 TTGAAAATTTAAGTA
1 TTGAAAATTTAAATA
6486779 TTGAA
1 TTGAA
6486784 TTTAAGTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.37
Consensus pattern (15 bp):
TTGAAAATTTAAATA
Found at i:6486952 original size:24 final size:24
Alignment explanation
Indices: 6486923--6486976 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
6486913 TTTTCTTTAT
6486923 TCTAAA-GAAAAATCAAATTTTAAA
1 TCTAAACG-AAAATCAAATTTTAAA
6486947 TCTAAACGAAAATCAAATTTTAAA
1 TCTAAACGAAAATCAAATTTTAAA
*
6486971 CCTAAA
1 TCTAAA
6486977 ATTTTTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.28
Consensus pattern (24 bp):
TCTAAACGAAAATCAAATTTTAAA
Found at i:6493995 original size:129 final size:128
Alignment explanation
Indices: 6493858--6494116 Score: 437
Period size: 129 Copynumber: 2.0 Consensus size: 128
6493848 CTAAATTAAC
* *
6493858 AAAAAAAATGAGATGACCAAAATATGAACGACCACTATTTAGAGTAACTAACGAGATAGTTTGCC
1 AAAAAAAATGAGATGACCAAAATAGGAACGACCACTATTTAGAGTAACTAACGAGATAGTATGCC
*
6493923 CTTTATTTTACTAATAAATAAATGCATTAATATACTAAATTAATTTCATATTTATTTTCTCAGA
66 CTTTATTTTACTAAGAAATAAATGCATT-ATATACTAAATTAATTTCATATTTATTTTCTCAGA
* * *
6493987 AAAAAAAATGGGATGACCAAAATAGGAACGACCACTATTTAGAGTGACTAACGGGATAGTATGCC
1 AAAAAAAATGAGATGACCAAAATAGGAACGACCACTATTTAGAGTAACTAACGAGATAGTATGCC
* *
6494052 CTTTGTTTTACTAAGAAATAAATGTATTATATACTAAATTAATTTCATATTTATTTTCTCAGA
66 CTTTATTTTACTAAGAAATAAATGCATTATATACTAAATTAATTTCATATTTATTTTCTCAGA
6494115 AA
1 AA
6494117 CTTGGGAGGA
Statistics
Matches: 122, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
128 37 0.30
129 85 0.70
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (128 bp):
AAAAAAAATGAGATGACCAAAATAGGAACGACCACTATTTAGAGTAACTAACGAGATAGTATGCC
CTTTATTTTACTAAGAAATAAATGCATTATATACTAAATTAATTTCATATTTATTTTCTCAGA
Found at i:6500096 original size:25 final size:24
Alignment explanation
Indices: 6500059--6500112 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
6500049 ACACAAATAC
6500059 AGCTCTTTATGAGCGTCCTGATAT
1 AGCTCTTTATGAGCGTCCTGATAT
*
6500083 ATGCTCTTCT-TGAGCTTCCTGATAT
1 A-GCTCTT-TATGAGCGTCCTGATAT
6500108 AGCTC
1 AGCTC
6500113 ACTTGAACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 5 0.19
25 21 0.78
26 1 0.04
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.39
Consensus pattern (24 bp):
AGCTCTTTATGAGCGTCCTGATAT
Found at i:6500117 original size:23 final size:25
Alignment explanation
Indices: 6500068--6500133 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 25
6500058 CAGCTCTTTA
*
6500068 TGAGCGTCCTGATATATGCTCTTCT
1 TGAGCGTCCTGATATATGCTCTACT
*
6500093 TGAGCTTCCTGATATA-GCTC-ACT
1 TGAGCGTCCTGATATATGCTCTACT
* * *
6500116 TGAACATCCTGTTATATG
1 TGAGCGTCCTGATATATG
6500134 GCTATCCAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 15 0.43
24 5 0.14
25 15 0.43
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (25 bp):
TGAGCGTCCTGATATATGCTCTACT
Found at i:6504110 original size:14 final size:15
Alignment explanation
Indices: 6504082--6504110 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6504072 TGGCCAATTA
6504082 AAAATTTTTAGCAAT
1 AAAATTTTTAGCAAT
6504097 AAAATTTTTA-CAAT
1 AAAATTTTTAGCAAT
6504111 TTAGTCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (15 bp):
AAAATTTTTAGCAAT
Found at i:6509179 original size:11 final size:11
Alignment explanation
Indices: 6509163--6509207 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
6509153 GGATTGTAGT
6509163 TATTTTATTAA
1 TATTTTATTAA
*
6509174 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
6509187 TATTTTATTAT
1 TATTTTATTAA
6509198 TATTTTATTA
1 TATTTTATTA
6509208 GTATATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:6509213 original size:24 final size:25
Alignment explanation
Indices: 6509159--6509213 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
6509149 GCTAGGATTG
6509159 TAGT-TATTTTATTAATATTTTAAT
1 TAGTATATTTTATTAATATTTTAAT
* *
6509183 AAG-ATATTTTATTATTATTTT-AT
1 TAGTATATTTTATTAATATTTTAAT
6509206 TAGTATAT
1 TAGTATAT
6509214 AAAGAAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (25 bp):
TAGTATATTTTATTAATATTTTAAT
Found at i:6511088 original size:46 final size:46
Alignment explanation
Indices: 6511020--6511246 Score: 260
Period size: 46 Copynumber: 4.9 Consensus size: 46
6511010 GTGTGCTCTC
* *
6511020 TGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACA
* *
6511066 TGATATGAAATATGTAAAACCATGGTTGAAAGACACCATGGCAACA
1 TGATATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * * * *
6511112 TGATATGAAATGTGTAAAACCATGGATGAAAGATATCATGGCAACG
1 TGATATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * * *
6511158 TGACATGAAA-A-GAATAAGATCATGGTTGAGAGATACCATAGCAACA
1 TGATATGAAATATG--TAAGACCATGGTTGAAAGATACCATGGCAACA
*** **
6511204 TGACGGGAAATAAATAAGACCATGGTTGAAAGATACCATGGCA
1 TGATATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCA
6511247 NNNNNNNNNN
Statistics
Matches: 153, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
44 1 0.01
46 151 0.99
47 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (46 bp):
TGATATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACA
Found at i:6516278 original size:32 final size:32
Alignment explanation
Indices: 6516188--6516316 Score: 152
Period size: 32 Copynumber: 4.0 Consensus size: 32
6516178 ACAACTTGAA
* *
6516188 ACTTGAAAAGGTTATGTACACTTTGTATGTAC
1 ACTTGAAAAGGTTAGGTACACTTTGTGTGTAC
*
6516220 ACTTGAAAAGGTTATGTACACTTTGTGTGTAC
1 ACTTGAAAAGGTTAGGTACACTTTGTGTGTAC
* * *
6516252 ACTTGGAAAGGTTAGGTATACTTTGTGTATAC
1 ACTTGAAAAGGTTAGGTACACTTTGTGTGTAC
** *
6516284 -CATATGAAAAGGAAAGGTATACTTTGTGTGTAC
1 AC-T-TGAAAAGGTTAGGTACACTTTGTGTGTAC
6516317 CACTCAGAAA
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
31 1 0.01
32 60 0.70
33 25 0.29
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (32 bp):
ACTTGAAAAGGTTAGGTACACTTTGTGTGTAC
Found at i:6519666 original size:43 final size:43
Alignment explanation
Indices: 6519501--6519667 Score: 153
Period size: 43 Copynumber: 3.9 Consensus size: 43
6519491 ATAAGCTCGC
* * * *
6519501 ACAATGCC-ATATCCCAGATATGGTCTTATATGTTATCAT-AT
1 ACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCATAAT
** * * * * *
6519542 ATTGATGTCACTGTCTCAGACATGGTCTTACACGAAATCATAAT
1 A-CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCATAAT
**
6519586 ATGATGCCAATGTCCCAGACATGGTCTTACACT-TAATC-TCAAT
1 ACAATGCCAATGTCCCAGACATGGTCTTACA-TGTAATCAT-AAT
*
6519629 ACAATGCCAATGTCCTAGACATGGTCTTACATGTAATCA
1 ACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCA
6519668 CATCTCGATA
Statistics
Matches: 100, Mismatches: 19, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
41 1 0.01
42 6 0.06
43 90 0.90
44 3 0.03
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (43 bp):
ACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCATAAT
Found at i:6521482 original size:16 final size:16
Alignment explanation
Indices: 6521447--6521481 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
6521437 TTATTTTTTC
6521447 TTTTATGATTTTGGAA
1 TTTTATGATTTTGGAA
*
6521463 TTTTATGGTTTTGG-A
1 TTTTATGATTTTGGAA
6521478 TTTT
1 TTTT
6521482 TGTATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.17, C:0.00, G:0.20, T:0.63
Consensus pattern (16 bp):
TTTTATGATTTTGGAA
Found at i:6521901 original size:20 final size:19
Alignment explanation
Indices: 6521856--6521893 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
6521846 CATCCAAACA
*
6521856 CCAGAAAGGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
6521875 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
6521894 TTCAGAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (19 bp):
CCAGAAAAGTAAATCATTT
Found at i:6522209 original size:26 final size:26
Alignment explanation
Indices: 6522179--6522241 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 26
6522169 TTATGTCTCA
*
6522179 TAAATTTCGATTTTT-CTTTTCTCAAT
1 TAAATTTTGATTTTTACTTTTC-CAAT
* *
6522205 TAAATTTTG-TTTTTAGTTTTCCACT
1 TAAATTTTGATTTTTACTTTTCCAAT
6522230 TAAATTTTGATT
1 TAAATTTTGATT
6522242 ACACTAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 17 0.53
26 15 0.47
ACGTcount: A:0.24, C:0.11, G:0.06, T:0.59
Consensus pattern (26 bp):
TAAATTTTGATTTTTACTTTTCCAAT
Found at i:6522329 original size:21 final size:22
Alignment explanation
Indices: 6522295--6522336 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
6522285 TTAAAGAATT
*
6522295 TTATATTTAAGTTTTGAGATTA
1 TTATATTTAAGTTTCGAGATTA
*
6522317 TTAT-TTTGAGTTTCGAGATT
1 TTATATTTAAGTTTCGAGATT
6522337 TAATTTTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.26, C:0.02, G:0.17, T:0.55
Consensus pattern (22 bp):
TTATATTTAAGTTTCGAGATTA
Found at i:6528141 original size:28 final size:28
Alignment explanation
Indices: 6528071--6528141 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
6528061 TTTTCCTTAT
*
6528071 TTTAGTCACTTTAA-ATTTTTTTATCAA
1 TTTAGTCACTTTAATTTTTTTTTATCAA
*
6528098 TTTAATCACTTTAATTTTTTTTTATCAA
1 TTTAGTCACTTTAATTTTTTTTTATCAA
*
6528126 TTTAGTCACTCTAATT
1 TTTAGTCACTTTAATT
6528142 AAGATAATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 13 0.33
28 26 0.67
ACGTcount: A:0.28, C:0.13, G:0.03, T:0.56
Consensus pattern (28 bp):
TTTAGTCACTTTAATTTTTTTTTATCAA
Found at i:6529154 original size:19 final size:20
Alignment explanation
Indices: 6529126--6529163 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
6529116 TTTCAGCAGC
6529126 AGAAGCAAGAAGCAGCAAGG
1 AGAAGCAAGAAGCAGCAAGG
*
6529146 AGAAG-AAGAAGGAGCAAG
1 AGAAGCAAGAAGCAGCAAG
6529164 AAAAAAAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.53, C:0.11, G:0.37, T:0.00
Consensus pattern (20 bp):
AGAAGCAAGAAGCAGCAAGG
Found at i:6529190 original size:14 final size:14
Alignment explanation
Indices: 6529149--6529191 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
6529139 AGCAAGGAGA
6529149 AGAAGAAGGAGCAAG
1 AGAAGAAGGAG-AAG
* *
6529164 AAAAAAAGGAGAAG
1 AGAAGAAGGAGAAG
*
6529178 AGAAGAAGAAGAAG
1 AGAAGAAGGAGAAG
6529192 GTCCCCAACC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.63, C:0.02, G:0.35, T:0.00
Consensus pattern (14 bp):
AGAAGAAGGAGAAG
Found at i:6529252 original size:27 final size:27
Alignment explanation
Indices: 6529217--6529282 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
6529207 AAACAAACGA
* *
6529217 GGTGCCGCCTTTGCCAGAGGCACAACC
1 GGTGCCGCCTCTGCCAGAGGCACAAAC
*
6529244 GGTGTCGCCTCTGCCAGAGGCACAAAC
1 GGTGCCGCCTCTGCCAGAGGCACAAAC
6529271 GGTGCCGCCTCT
1 GGTGCCGCCTCT
6529283 AGCACTCCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.17, C:0.36, G:0.30, T:0.17
Consensus pattern (27 bp):
GGTGCCGCCTCTGCCAGAGGCACAAAC
Found at i:6529359 original size:17 final size:18
Alignment explanation
Indices: 6529327--6529360 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6529317 TTTTTGCCAA
*
6529327 TTTTTTTTTAGCTTTTTG
1 TTTTTTTTTAGATTTTTG
6529345 TTTTTTTTTA-ATTTTT
1 TTTTTTTTTAGATTTTT
6529361 AAACAGATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.82
Consensus pattern (18 bp):
TTTTTTTTTAGATTTTTG
Found at i:6530042 original size:15 final size:15
Alignment explanation
Indices: 6530022--6530052 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6530012 CTTGTCCAAA
6530022 GCTAATAACAACTTT
1 GCTAATAACAACTTT
6530037 GCTAATAACAACTTT
1 GCTAATAACAACTTT
6530052 G
1 G
6530053 GAATTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (15 bp):
GCTAATAACAACTTT
Found at i:6531498 original size:16 final size:18
Alignment explanation
Indices: 6531462--6531495 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
6531452 CGGAAAAAAA
6531462 AAAAGAAAAAAGGTTAGG
1 AAAAGAAAAAAGGTTAGG
6531480 AAAA-AAAAAAGGTTAG
1 AAAAGAAAAAAGGTTAG
6531496 AAATACAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.65, C:0.00, G:0.24, T:0.12
Consensus pattern (18 bp):
AAAAGAAAAAAGGTTAGG
Found at i:6539015 original size:13 final size:13
Alignment explanation
Indices: 6538997--6539024 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6538987 AACCCAAAAA
6538997 AAAAGTGGTTGGT
1 AAAAGTGGTTGGT
6539010 AAAAGTGGTTGGT
1 AAAAGTGGTTGGT
6539023 AA
1 AA
6539025 GGTAAGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (13 bp):
AAAAGTGGTTGGT
Found at i:6543768 original size:19 final size:20
Alignment explanation
Indices: 6543746--6543786 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
6543736 TTGAAATTTA
* *
6543746 TTTAAT-ATTTTTTATAAAT
1 TTTAATAATATTTTAAAAAT
6543765 TTTAATAATATTTTAAAAAT
1 TTTAATAATATTTTAAAAAT
6543785 TT
1 TT
6543787 ATAAAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAATAATATTTTAAAAAT
Found at i:6543787 original size:19 final size:19
Alignment explanation
Indices: 6543745--6543787 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
6543735 TTTGAAATTT
*
6543745 ATTTAATATTTTTTATAAA
1 ATTTAATATATTTTATAAA
*
6543764 TTTTAATAATATTTTA-AAA
1 ATTTAAT-ATATTTTATAAA
6543783 ATTTA
1 ATTTA
6543788 TAAAAAATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTAATATATTTTATAAA
Found at i:6549447 original size:73 final size:72
Alignment explanation
Indices: 6549350--6549506 Score: 242
Period size: 73 Copynumber: 2.2 Consensus size: 72
6549340 TGATATTTTT
*
6549350 ATTTCTGTTTTTAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCAGGACACGCTGAGGT
1 ATTTCTGTTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
*
6549415 ATTTTCA
66 ATGTTCA
* * * *
6549422 ATTTCTGTTTTTCAAAAATCGACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGG
1 ATTTCTGTTTTT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
6549487 TATGTTCA
65 TATGTTCA
*
6549495 ATTTTTGTTTTT
1 ATTTCTGTTTTT
6549507 TAATTTATGT
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
72 12 0.16
73 65 0.84
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (72 bp):
ATTTCTGTTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
ATGTTCA
Found at i:6549874 original size:73 final size:72
Alignment explanation
Indices: 6549777--6549933 Score: 242
Period size: 73 Copynumber: 2.2 Consensus size: 72
6549767 TGATATTTTT
*
6549777 ATTTCTGTTTTTAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCAGGACACGCTGAGGT
1 ATTTCTGTTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
*
6549842 ATTTTCA
66 ATGTTCA
* * * *
6549849 ATTTCTGTTTTTCAAAAATCGACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGG
1 ATTTCTGTTTTT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
6549914 TATGTTCA
65 TATGTTCA
*
6549922 ATTTTTGTTTTT
1 ATTTCTGTTTTT
6549934 TAATTTATGT
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
72 12 0.16
73 65 0.84
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (72 bp):
ATTTCTGTTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
ATGTTCA
Found at i:6549900 original size:427 final size:427
Alignment explanation
Indices: 6549105--6549959 Score: 1692
Period size: 427 Copynumber: 2.0 Consensus size: 427
6549095 TTTTTTTGTT
6549105 TTTGTTTTTCTTCTTTCTTCTATATTCTAACATATATCTATATACATATATATTATATTATTAAG
1 TTTGTTTTTCTTCTTTCTTCTATATTCTAACATATATCTATATACATATATATTATATTATTAAG
6549170 CAAAAATAAAAAATATATATATATAATGTTTACTTTTTCGGCCACCGTGCACGGGTATTTTTATT
66 CAAAAATAAAAAATATATATATATAATGTTTACTTTTTCGGCCACCGTGCACGGGTATTTTTATT
6549235 CATGCATGACATATACAAGTACTCCAGTAGAGCAAGAAATTTTGAATGATAGTTATACTGGATCA
131 CATGCATGACATATACAAGTACTCCAGTAGAGCAAGAAATTTTGAATGATAGTTATACTGGATCA
6549300 AGGAAAAGACCCTTGAGTTCCACCAGATGATTTGTTATTCTGATATTTTTATTTCTGTTTTTAAA
196 AGGAAAAGACCCTTGAGTTCCACCAGATGATTTGTTATTCTGATATTTTTATTTCTGTTTTTAAA
6549365 AATCAACTCATATTGCGAGATGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGT
261 AATCAACTCATATTGCGAGATGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGT
6549430 TTTTCAAAAATCGACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATGTTCA
326 TTTTCAAAAATCGACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATGTTCA
*
6549495 ATTTTTGTTTTTTAATTTATGTTTAAAAAAAATCAAC
391 ATTTTTGTTTTTTAATTTATGTCTAAAAAAAATCAAC
6549532 TTTGTTTTTCTTCTTTCTTCTATATTCTAACATATATCTATATACATATATATTATATTATTAAG
1 TTTGTTTTTCTTCTTTCTTCTATATTCTAACATATATCTATATACATATATATTATATTATTAAG
6549597 CAAAAATAAAAAATATATATATATAATGTTTACTTTTTCGGCCACCGTGCACGGGTATTTTTATT
66 CAAAAATAAAAAATATATATATATAATGTTTACTTTTTCGGCCACCGTGCACGGGTATTTTTATT
6549662 CATGCATGACATATACAAGTACTCCAGTAGAGCAAGAAATTTTGAATGATAGTTATACTGGATCA
131 CATGCATGACATATACAAGTACTCCAGTAGAGCAAGAAATTTTGAATGATAGTTATACTGGATCA
6549727 AGGAAAAGACCCTTGAGTTCCACCAGATGATTTGTTATTCTGATATTTTTATTTCTGTTTTTAAA
196 AGGAAAAGACCCTTGAGTTCCACCAGATGATTTGTTATTCTGATATTTTTATTTCTGTTTTTAAA
6549792 AATCAACTCATATTGCGAGATGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGT
261 AATCAACTCATATTGCGAGATGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGT
6549857 TTTTCAAAAATCGACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATGTTCA
326 TTTTCAAAAATCGACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATGTTCA
*
6549922 ATTTTTGTTTTTTAATTTATGTCTAAAAAAACTCAAC
391 ATTTTTGTTTTTTAATTTATGTCTAAAAAAAATCAAC
6549959 T
1 T
6549960 CATATTGCGA
Statistics
Matches: 426, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
427 426 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.39
Consensus pattern (427 bp):
TTTGTTTTTCTTCTTTCTTCTATATTCTAACATATATCTATATACATATATATTATATTATTAAG
CAAAAATAAAAAATATATATATATAATGTTTACTTTTTCGGCCACCGTGCACGGGTATTTTTATT
CATGCATGACATATACAAGTACTCCAGTAGAGCAAGAAATTTTGAATGATAGTTATACTGGATCA
AGGAAAAGACCCTTGAGTTCCACCAGATGATTTGTTATTCTGATATTTTTATTTCTGTTTTTAAA
AATCAACTCATATTGCGAGATGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGT
TTTTCAAAAATCGACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATGTTCA
ATTTTTGTTTTTTAATTTATGTCTAAAAAAAATCAAC
Found at i:6550058 original size:73 final size:77
Alignment explanation
Indices: 6549947--6550168 Score: 272
Period size: 81 Copynumber: 2.9 Consensus size: 77
6549937 TTTATGTCTA
* *
6549947 AAAAAACTCAACTCATATTGCGAGAGGTGAATTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
1 AAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
6550012 TCTG-TT-TG-TC
65 TCTGCTTCTGTTC
* * * * *
6550022 -AAAAATCAACTCATATTGTGAGATGTGAGTTAAGCCTCAGGGCACGCTGAGTTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
*
6550086 TTGCTTCTGCTTTTC
66 CTGCTTCTG---TTC
* * *
6550101 AAAAAAATCAACACATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTGTTTTCAATT
1 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
6550166 TCT
65 TCT
6550169 ATTTTTTTCA
Statistics
Matches: 122, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
73 54 0.44
74 7 0.06
75 2 0.02
79 2 0.02
81 57 0.47
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (77 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
CTGCTTCTGTTC
Found at i:6550067 original size:160 final size:154
Alignment explanation
Indices: 6549789--6550168 Score: 553
Period size: 160 Copynumber: 2.4 Consensus size: 154
6549779 TTCTGTTTTT
*
6549789 AAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* * * *
6549854 TGTTTTTCAAAAATCGACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATGT
66 TGTTTGTCAAAAATCAACTCATATTGTGAGAGGTGAGTTAAGCCTCAGGGCACGCTGAGGTATGT
* * *
6549919 TCAATTTTTGTTTTTTAATTTATGTCTAA
131 TCAATTTTTG-CTTCT-ACTT-T-TC-AA
* *
6549948 AAAAACTCAACTCATATTGCGAGAGGTGAATTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
1 AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
* * *
6550013 CTGTTTGTCAAAAATCAACTCATATTGTGAGATGTGAGTTAAGCCTCAGGGCACGCTGAGTTATT
65 CTGTTTGTCAAAAATCAACTCATATTGTGAGAGGTGAGTTAAGCCTCAGGGCACGCTGAGGTATG
*
6550078 TTCAATTTTTGCTTCTGCTTTTCAA
130 TTCAATTTTTGCTTCTACTTTTCAA
* * *
6550103 AAAAATCAACACATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTGTTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
6550168 T
66 T
6550169 ATTTTTTTCA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
154 56 0.28
155 7 0.03
156 2 0.01
157 1 0.00
158 2 0.01
159 8 0.04
160 125 0.62
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (154 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
TGTTTGTCAAAAATCAACTCATATTGTGAGAGGTGAGTTAAGCCTCAGGGCACGCTGAGGTATGT
TCAATTTTTGCTTCTACTTTTCAA
Found at i:6550308 original size:88 final size:89
Alignment explanation
Indices: 6550103--6550316 Score: 247
Period size: 89 Copynumber: 2.4 Consensus size: 89
6550093 TGCTTTTCAA
* * * **
6550103 AAAAATCAACACATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTGTTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGATATTTTCAAAATC
*
6550168 TATTTTTTTCAATTTACATTTTTC
66 TAGTTTTTTCAATTTACATTTTTC
* * * * **
6550192 AAAAATTAACTTATATTGTGAGAGGTGAGTTGAGCCTCGGGTTACGTGTCGAGATATTTTCAAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGT-T-GAGATATTTTCAAAA
*
6550257 TCT-GTTTTTTGAA-TT-C-TGTTTTC
64 TCTAGTTTTTTCAATTTACAT-TTTTC
*
6550280 AAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
6550317 TAGCTCACGT
Statistics
Matches: 105, Mismatches: 17, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
87 1 0.01
88 39 0.37
89 42 0.40
90 9 0.09
91 14 0.13
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (89 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGATATTTTCAAAATC
TAGTTTTTTCAATTTACATTTTTC
Found at i:6550366 original size:88 final size:87
Alignment explanation
Indices: 6550103--6550412 Score: 263
Period size: 88 Copynumber: 3.5 Consensus size: 87
6550093 TGCTTTTCAA
* * * *
6550103 AAAAATCAACACATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGT-TGAGGTGTTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGTGTGAGATATTTTCAATTT
* *
6550167 CTATTTTTTTCAATT-TACATTTTTC
66 -T-TGTTTTTCAATTCT--AGTTTTC
* * * * * **
6550192 AAAAATTAACTTATATTGTGAGAGGTGAGTTGAGCCTCGGGTTACGTGTCGAGATATTTTCAAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGTGT-GAGATATTTTCAATT
* *
6550257 TCTGTTTTTTGAATTCT-GTTTTC
65 TTTG-TTTTTCAATTCTAGTTTTC
* * * * *
6550280 AAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTTAGCTCACGTGCTGAGCTATTCTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGTG-TGAGATATTTTCAATT
6550345 TTTGTTTTT-AATGTCTAGTTTT-
65 TTTGTTTTTCAAT-TCTAGTTTTC
* * * **
6550367 AAAGAGTCAATTTATATTGCGAGAAATGAGTTGAG-CTCAGGATCAC
1 AAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCAC
6550413 ATGCCGAGTA
Statistics
Matches: 176, Mismatches: 36, Indels: 19
0.76 0.16 0.08
Matches are distributed among these distances:
86 3 0.02
87 15 0.09
88 93 0.53
89 42 0.24
90 10 0.06
91 13 0.07
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (87 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGTGTGAGATATTTTCAATTT
TTGTTTTTCAATTCTAGTTTTC
Found at i:6552186 original size:17 final size:16
Alignment explanation
Indices: 6552145--6552189 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
6552135 AATATATACA
*
6552145 TATATATATATTATTG
1 TATATATATATTTTTG
*
6552161 T-TATGTATATTTTTAG
1 TATATATATATTTTT-G
6552177 TATATATATATTT
1 TATATATATATTT
6552190 GTGAAGTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 11 0.46
16 3 0.12
17 10 0.42
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (16 bp):
TATATATATATTTTTG
Found at i:6552453 original size:22 final size:23
Alignment explanation
Indices: 6552428--6552507 Score: 58
Period size: 23 Copynumber: 3.4 Consensus size: 23
6552418 TGTATATATC
*
6552428 GTATATGTTTTATATA-TATTAT
1 GTATATATTTTATATACTATTAT
* *
6552450 GTATACATTTTCA-ATATTATTA-
1 GTATATATTTT-ATATACTATTAT
*
6552472 GTTATATTTTTTATATACTATTCCAT
1 G-TATATATTTTATATACTATT--AT
*
6552498 GTACATATTT
1 GTATATATTT
6552508 CCATTTCATC
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
22 14 0.32
23 21 0.48
25 8 0.18
26 1 0.02
ACGTcount: A:0.31, C:0.07, G:0.06, T:0.55
Consensus pattern (23 bp):
GTATATATTTTATATACTATTAT
Found at i:6552493 original size:23 final size:22
Alignment explanation
Indices: 6552414--6552493 Score: 56
Period size: 23 Copynumber: 3.5 Consensus size: 22
6552404 ATTTCTAATG
* *
6552414 TATATGTATATATCGTATATGTTT
1 TATATATAT-TAT-GTATATTTTT
*
6552438 TATATATATTATGTATACATTTT
1 TATATATATTATGTATA-TTTTT
*
6552461 CA-ATATTATTA-GTTATATTTTT
1 TATATA-TATTATG-TATATTTTT
6552483 TATATACTATT
1 TATATA-TATT
6552494 CCATGTACAT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
22 14 0.31
23 23 0.51
24 8 0.18
ACGTcount: A:0.33, C:0.05, G:0.06, T:0.56
Consensus pattern (22 bp):
TATATATATTATGTATATTTTT
Found at i:6552676 original size:20 final size:19
Alignment explanation
Indices: 6552625--6552676 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 19
6552615 TTTATTATTA
*
6552625 ATATTAGTATATATATTTT
1 ATATTAGTATACATATTTT
*
6552644 ATTATTCTTGTATACATATTTT
1 A-TA-T-TAGTATACATATTTT
6552666 ATATATAGTAT
1 ATAT-TAGTAT
6552677 TATTTTCGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 1 0.04
20 8 0.31
21 3 0.12
22 14 0.54
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (19 bp):
ATATTAGTATACATATTTT
Found at i:6552828 original size:11 final size:11
Alignment explanation
Indices: 6552797--6552836 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
6552787 TACATTTTTT
6552797 TATAT-TTAT-
1 TATATATTATG
6552806 TATATATATATG
1 TATATAT-TATG
6552818 TATATATTATG
1 TATATATTATG
6552829 TATATATT
1 TATATATT
6552837 TTAACATTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.18
10 1 0.04
11 15 0.54
12 7 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (11 bp):
TATATATTATG
Found at i:6553033 original size:22 final size:23
Alignment explanation
Indices: 6553008--6553110 Score: 70
Period size: 23 Copynumber: 4.4 Consensus size: 23
6552998 TGTATATATC
*
6553008 GTATATGTTTTATATA-TATTAT
1 GTATATATTTTATATACTATTAT
*
6553030 GTATATATTTTCA-ATATTATTA-
1 GTATATATTTT-ATATACTATTAT
*
6553052 GTTATATTTTTTATATACTATTCCAT
1 G-TATATATTTTATATACTATT--AT
* * *
6553078 GTACATATTTCCATAT-CATCTTAT
1 GTATATATTT-TATATAC-TATTAT
6553102 GTATATATT
1 GTATATATT
6553111 CTTAAACATT
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
22 15 0.23
23 22 0.34
24 10 0.16
25 9 0.14
26 8 0.12
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (23 bp):
GTATATATTTTATATACTATTAT
Found at i:6553253 original size:580 final size:579
Alignment explanation
Indices: 6552210--6554042 Score: 2770
Period size: 580 Copynumber: 3.1 Consensus size: 579
6552200 ATCAATAGTT
* * * *
6552210 ATTTTTTTATATTGTTATTATTTTTAATACT-TATATATTATGTATATATTTTAATACTAC-A-T
1 ATTTTTTTATA-T-TTATTATATAT-ATA-TGTATATATTATGTATATATTTTAACATTACTAGT
* *
6552272 TATATATATA-TATTTATGTTATGTATATATTTCTAATATTATATATTAAGTATTTCTAATATCC
62 TATATTTTTACT-TTTATGTTATGTATATATTTCTAATATTATATATTAAGTATTTCTAATATCC
*
6552336 TTATTATTTATATCCATATACGTACGTATCTATGTAGCGTATTAATAAGTTCCTTTTATATTGCT
126 TTATTATTTATATCCATATACGTACGTATCTATATAGCGTATTAATAAGTTCCTTTTATATTGCT
*
6552401 ATCATTTCTAATGTATATGTATATATCGTATATGTTTTATATATATTATGTATACATTTTCAATA
191 ATCATTTCTAATGTATATGTATATATCGTATATGTTTTATATATATTATGTATATATTTTCAATA
6552466 TTATTAGTTATATTTTTTATATACTATTCCATGTACATATTTCCATTTCATCTTATGTATATATT
256 TTATTAGTTATATTTTTTATATACTATTCCATGTACATATTTCCATTTCATCTTATGTATATATT
6552531 CTTAAACATTATTATATGTATATGTATATTTTTAATACCATATTTTGTATATATTATCATTACAT
321 CTTAAACATTATTATATGTATATGTATATTTTTAATACCATATTTTGTATATATTATCATTACAT
6552596 TTATTTTATTCCTACTATATTTATTATTAATATTAGTATATATATTTTATTATTCTTGTATACAT
386 TTATTTTATTCCTACTATATTTATTATTAATATTAGTATATATATTTTATTATTCTTGTATACAT
6552661 ATTTTATATATAGTATTATTTTCGTATATCATTATATTTATTATTATACCTATTATTTTCACTAT
451 ATTTTATATATAGTATTATTTTCGTATATCATTATATTTATTATTATACCTATTATTTTCACTAT
6552726 TATCACTTATTATTTTATTTTAATATTATTATGTATATATTTTTCATATATGTCATGTACATAC
516 TATCACTTATTATTTTATTTTAATATTATTATGTATATATTTTTCATATATGTCATGTACATAC
6552790 ATTTTTTTATATTTATTATATATATATGTATATATTATGTATATATTTTAACATTACTAGTTATA
1 ATTTTTTTATATTTATTATATATATATGTATATATTATGTATATATTTTAACATTACTAGTTATA
6552855 TTTTTACTTTTTATGTTATGTATATATTTCTAATATTATATATTAAGTATTTCTAATATCCTTAT
66 TTTTTAC-TTTTATGTTATGTATATATTTCTAATATTATATATTAAGTATTTCTAATATCCTTAT
6552920 TATTTATATCCATATACGTACGTATCTATATAGCGTATTAATAAGTTCCTTTTATATTGCTATCA
130 TATTTATATCCATATACGTACGTATCTATATAGCGTATTAATAAGTTCCTTTTATATTGCTATCA
6552985 TTTCTAATGTATATGTATATATCGTATATGTTTTATATATATTATGTATATATTTTCAATATTAT
195 TTTCTAATGTATATGTATATATCGTATATGTTTTATATATATTATGTATATATTTTCAATATTAT
*
6553050 TAGTTATATTTTTTATATACTATTCCATGTACATATTTCCATATCATCTTATGTATATATTCTTA
260 TAGTTATATTTTTTATATACTATTCCATGTACATATTTCCATTTCATCTTATGTATATATTCTTA
*
6553115 AACATTATTATATGTATATGTATATTTTTAATACCATATTTTGTATATATTATTATTACATTTAT
325 AACATTATTATATGTATATGTATATTTTTAATACCATATTTTGTATATATTATCATTACATTTAT
*
6553180 TTTATTCCTACTATATTTATTATTAATATTAGTATATATATTTTATTATTCTTGTATACACATTT
390 TTTATTCCTACTATATTTATTATTAATATTAGTATATATATTTTATTATTCTTGTATACATATTT
6553245 TATATATAGTATTATTTTCGTATATCATTATATTTATTATTATACCTATTATTTTCACTATTATC
455 TATATATAGTATTATTTTCGTATATCATTATATTTATTATTATACCTATTATTTTCACTATTATC
* *
6553310 ACTTATCATTTTATTTTAATATTATTATGTATATATTTTTCATATATGTCATATACATAC
520 ACTTATTATTTTATTTTAATATTATTATGTATATATTTTTCATATATGTCATGTACATAC
** * *
6553370 ATTTTTCAATATTTATTTTATACATATATGTATATATTATGCATATATTTTAACATTACTAGTTA
1 ATTTTTTTATATTTA--TTATATATATATGTATATATTATGTATATATTTTAACATTACTAGTTA
* * * * * *
6553435 TATTTTTAC---TATCTTAGGTATATACTTCAAACACTATATA-T-AGTATATTTCTAACACTAT
64 TATTTTTACTTTTATGTTATGTATATATTTCTAATATTATATATTAAG--TATTTCT-A-A-TA-
* ** * * * ** **
6553495 TAC-TATTCATATATATATATATATTTTACGTACATACTCTAAATA-CACTCATTGTTTCCGTTT
123 TCCTTATT-AT-T-TATATCCATA---TACGTACGTA-TCTATATAGC-GT-ATT-AATAAG-TT
* * * * *
6553558 CATGTTTA-ATT-CTAGT-ATTACGT--T-TAATATCGCATATATC-TTTATTGTTTT-CA-ATA
177 CCT-TTTATATTGCTA-TCATTTC-TAATGT-ATAT-GTATATATCGTATA-TGTTTTATATATA
* * *
6553614 TTATTGTCACACTTATATTTGATTCAATATATTTCTAGCTCTGATTTTTTATATACTATTCCATG
236 TTA-TGT---A--TATA-TT--TTCAATAT-TAT-TAGTTAT-ATTTTTTATATACTATTCCATG
6553679 TACATATTTCCATTTCATCTTATGTATATATTCTTAAACATTATTATATGTATATGTATATTTTT
289 TACATATTTCCATTTCATCTTATGTATATATTCTTAAACATTATTATATGTATATGTATATTTTT
6553744 AATACCATATTTTGTATATATTATCATTACATTTATTTTATTCCTACTATATTTATTATTAATAT
354 AATACCATATTTTGTATATATTATCATTACATTTATTTTATTCCTACTATATTTATTATTAATAT
6553809 TAGTATATATATTTTATTATTCTTGTATACATATTTTATATATAGTATTATTTTCGTATATCATT
419 TAGTATATATATTTTATTATTCTTGTATACATATTTTATATATAGTATTATTTTCGTATATCATT
6553874 ATATTTATTATTATACCTATTATTTTCACTATTATCACTTATTATTTTATTTTAATATTATTATG
484 ATATTTATTATTATACCTATTATTTTCACTATTATCACTTATTATTTTATTTTAATATTATTATG
6553939 TATATATTTTTCATATATGTCATGTACATAC
549 TATATATTTTTCATATATGTCATGTACATAC
6553970 ATTTTTTTATATTTATTATATATATATGTATATATTATGTATATATTTTAACATTACTAGTTATA
1 ATTTTTTTATATTTATTATATATATATGTATATATTATGTATATATTTTAACATTACTAGTTATA
6554035 TTTTTACT
66 TTTTTACT
6554043 ATCTTAGGTA
Statistics
Matches: 1160, Mismatches: 50, Indels: 67
0.91 0.04 0.05
Matches are distributed among these distances:
576 3 0.00
577 31 0.03
578 42 0.04
579 11 0.01
580 524 0.45
581 7 0.01
582 59 0.05
583 1 0.00
584 8 0.01
587 10 0.01
588 15 0.01
589 15 0.01
590 23 0.02
591 9 0.01
592 5 0.00
594 4 0.00
595 2 0.00
597 8 0.01
598 57 0.05
599 5 0.00
600 321 0.28
ACGTcount: A:0.32, C:0.10, G:0.05, T:0.54
Consensus pattern (579 bp):
ATTTTTTTATATTTATTATATATATATGTATATATTATGTATATATTTTAACATTACTAGTTATA
TTTTTACTTTTATGTTATGTATATATTTCTAATATTATATATTAAGTATTTCTAATATCCTTATT
ATTTATATCCATATACGTACGTATCTATATAGCGTATTAATAAGTTCCTTTTATATTGCTATCAT
TTCTAATGTATATGTATATATCGTATATGTTTTATATATATTATGTATATATTTTCAATATTATT
AGTTATATTTTTTATATACTATTCCATGTACATATTTCCATTTCATCTTATGTATATATTCTTAA
ACATTATTATATGTATATGTATATTTTTAATACCATATTTTGTATATATTATCATTACATTTATT
TTATTCCTACTATATTTATTATTAATATTAGTATATATATTTTATTATTCTTGTATACATATTTT
ATATATAGTATTATTTTCGTATATCATTATATTTATTATTATACCTATTATTTTCACTATTATCA
CTTATTATTTTATTTTAATATTATTATGTATATATTTTTCATATATGTCATGTACATAC
Found at i:6553688 original size:600 final size:597
Alignment explanation
Indices: 6552477--6554262 Score: 2832
Period size: 580 Copynumber: 3.0 Consensus size: 597
6552467 TATTAGTTAT
6552477 ATTTTTTATATACTATTCCATGTACATATTTCCATTTCATCTTATGTATATATTCTTAAACATTA
1 ATTTTTTATATACTATTCCATGTACATATTTCCATTTCATCTTATGTATATATTCTTAAACATTA
6552542 TTATATGTATATGTATATTTTTAATACCATATTTTGTATATATTATCATTACATTTATTTTATTC
66 TTATATGTATATGTATATTTTTAATACCATATTTTGTATATATTATCATTACATTTATTTTATTC
6552607 CTACTATATTTATTATTAATATTAGTATATATATTTTATTATTCTTGTATACATATTTTATATAT
131 CTACTATATTTATTATTAATATTAGTATATATATTTTATTATTCTTGTATACATATTTTATATAT
6552672 AGTATTATTTTCGTATATCATTATATTTATTATTATACCTATTATTTTCACTATTATCACTTATT
196 AGTATTATTTTCGTATATCATTATATTTATTATTATACCTATTATTTTCACTATTATCACTTATT
6552737 ATTTTATTTTAATATTATTATGTATATATTTTTCATATATGTCATGTACATACATTTTTTTATAT
261 ATTTTATTTTAATATTATTATGTATATATTTTTCATATATGTCATGTACATACATTTTTTTATAT
6552802 TTATTATATATATATGTATATATTATGTATATATTTTAACATTACTAGTTATATTTTTACTTTTT
326 TTATTATATATATATGTATATATTATGTATATATTTTAACATTACTAGTTATATTTTTAC----T
* * * * * * *
6552867 ATGTTATGTATATATTTCTAATA-T-TATATATTAAGTATTTCT-A-A-TA-TCCTTATT-AT-T
387 ATCTTAGGTATATACTTCAAACACTATATATAGT-A-TATTTCTAACACTATTAC-TATTCATAT
** * * * ** ** *
6552924 -TATATCCATA---TACGTACGTA-TCTATATAGC-GT-ATT-AATAAG-TTCCT-TTTATATTG
449 ATATATATATATTTTACGTACATACTCTAAATA-CACTCATTGTTTCCGTTTCATGTTTA-ATT-
* * * *
6552979 CTA-TCATTTC-TAATGT-ATAT-GTATATATC-GTATATGTTTTATATATATTA-TGT---A--
511 CTAGT-ATTACGT--T-TAATATCGCATATATCTTTAT-TGTTTT-CA-ATATTATTGTCACACT
* * *
6553033 TATA-TT--TTCAATAT-TATTAGTTAT-
569 TATATTTGATTCAATATATTTTAGCTCTG
*
6553057 ATTTTTTATATACTATTCCATGTACATATTTCCATATCATCTTATGTATATATTCTTAAACATTA
1 ATTTTTTATATACTATTCCATGTACATATTTCCATTTCATCTTATGTATATATTCTTAAACATTA
*
6553122 TTATATGTATATGTATATTTTTAATACCATATTTTGTATATATTATTATTACATTTATTTTATTC
66 TTATATGTATATGTATATTTTTAATACCATATTTTGTATATATTATCATTACATTTATTTTATTC
*
6553187 CTACTATATTTATTATTAATATTAGTATATATATTTTATTATTCTTGTATACACATTTTATATAT
131 CTACTATATTTATTATTAATATTAGTATATATATTTTATTATTCTTGTATACATATTTTATATAT
*
6553252 AGTATTATTTTCGTATATCATTATATTTATTATTATACCTATTATTTTCACTATTATCACTTATC
196 AGTATTATTTTCGTATATCATTATATTTATTATTATACCTATTATTTTCACTATTATCACTTATT
* **
6553317 ATTTTATTTTAATATTATTATGTATATATTTTTCATATATGTCATATACATACATTTTTCAATAT
261 ATTTTATTTTAATATTATTATGTATATATTTTTCATATATGTCATGTACATACATTTTTTTATAT
* *
6553382 TTATTTTATACATATATGTATATATTATGCATATATTTTAACATTACTAGTTATATTTTTACTAT
326 TTA--TTATATATATATGTATATATTATGTATATATTTTAACATTACTAGTTATATTTTTACTAT
6553447 CTTAGGTATATACTTCAAACACTATATATAGTATATTTCTAACACTATTACTATTCATATATATA
389 CTTAGGTATATACTTCAAACACTATATATAGTATATTTCTAACACTATTACTATTCATATATATA
6553512 TATATATTTTACGTACATACTCTAAATACACTCATTGTTTCCGTTTCATGTTTAATTCTAGTATT
454 TATATATTTTACGTACATACTCTAAATACACTCATTGTTTCCGTTTCATGTTTAATTCTAGTATT
6553577 ACGTTTAATATCGCATATATCTTTATTGTTTTCAATATTATTGTCACACTTATATTTGATTCAAT
519 ACGTTTAATATCGCATATATCTTTATTGTTTTCAATATTATTGTCACACTTATATTTGATTCAAT
6553642 ATATTTCTAGCTCTG
584 ATATTT-TAGCTCTG
6553657 ATTTTTTATATACTATTCCATGTACATATTTCCATTTCATCTTATGTATATATTCTTAAACATTA
1 ATTTTTTATATACTATTCCATGTACATATTTCCATTTCATCTTATGTATATATTCTTAAACATTA
6553722 TTATATGTATATGTATATTTTTAATACCATATTTTGTATATATTATCATTACATTTATTTTATTC
66 TTATATGTATATGTATATTTTTAATACCATATTTTGTATATATTATCATTACATTTATTTTATTC
6553787 CTACTATATTTATTATTAATATTAGTATATATATTTTATTATTCTTGTATACATATTTTATATAT
131 CTACTATATTTATTATTAATATTAGTATATATATTTTATTATTCTTGTATACATATTTTATATAT
6553852 AGTATTATTTTCGTATATCATTATATTTATTATTATACCTATTATTTTCACTATTATCACTTATT
196 AGTATTATTTTCGTATATCATTATATTTATTATTATACCTATTATTTTCACTATTATCACTTATT
6553917 ATTTTATTTTAATATTATTATGTATATATTTTTCATATATGTCATGTACATACATTTTTTTATAT
261 ATTTTATTTTAATATTATTATGTATATATTTTTCATATATGTCATGTACATACATTTTTTTATAT
6553982 TTATTATATATATATGTATATATTATGTATATATTTTAACATTACTAGTTATATTTTTACTATCT
326 TTATTATATATATATGTATATATTATGTATATATTTTAACATTACTAGTTATATTTTTACTATCT
6554047 TAGGTATATACTTCAAACACTATATATAGTATATTTCTAACACTATTACTATTCATATATATATA
391 TAGGTATATACTTCAAACACTATATATAGTATATTTCTAACACTATTACTATTCATATATATATA
6554112 TATATTTTACGTACATACTCTAAATACACTCATTGTTTCCGTTTCATGTTTAATTCTAGTATTAC
456 TATATTTTACGTACATACTCTAAATACACTCATTGTTTCCGTTTCATGTTTAATTCTAGTATTAC
6554177 GTTTAATATCGCATATATCTTTATTGTTTTCAATATTATTGTCACACTTATATTTGATTCAATAT
521 GTTTAATATCGCATATATCTTTATTGTTTTCAATATTATTGTCACACTTATATTTGATTCAATAT
6554242 ATTTTTAGCTCTG
586 A-TTTTAGCTCTG
*
6554255 -TCTTTTAT
1 ATTTTTTAT
6554263 TTATTTTTAT
Statistics
Matches: 1125, Mismatches: 43, Indels: 59
0.92 0.04 0.05
Matches are distributed among these distances:
578 26 0.02
579 3 0.00
580 329 0.29
581 6 0.01
582 59 0.05
583 1 0.00
584 8 0.01
587 10 0.01
588 15 0.01
589 12 0.01
590 23 0.02
591 12 0.01
592 5 0.00
594 4 0.00
595 2 0.00
597 15 0.01
598 266 0.24
599 8 0.01
600 321 0.29
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.53
Consensus pattern (597 bp):
ATTTTTTATATACTATTCCATGTACATATTTCCATTTCATCTTATGTATATATTCTTAAACATTA
TTATATGTATATGTATATTTTTAATACCATATTTTGTATATATTATCATTACATTTATTTTATTC
CTACTATATTTATTATTAATATTAGTATATATATTTTATTATTCTTGTATACATATTTTATATAT
AGTATTATTTTCGTATATCATTATATTTATTATTATACCTATTATTTTCACTATTATCACTTATT
ATTTTATTTTAATATTATTATGTATATATTTTTCATATATGTCATGTACATACATTTTTTTATAT
TTATTATATATATATGTATATATTATGTATATATTTTAACATTACTAGTTATATTTTTACTATCT
TAGGTATATACTTCAAACACTATATATAGTATATTTCTAACACTATTACTATTCATATATATATA
TATATTTTACGTACATACTCTAAATACACTCATTGTTTCCGTTTCATGTTTAATTCTAGTATTAC
GTTTAATATCGCATATATCTTTATTGTTTTCAATATTATTGTCACACTTATATTTGATTCAATAT
ATTTTAGCTCTG
Found at i:6553856 original size:20 final size:19
Alignment explanation
Indices: 6553805--6553856 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 19
6553795 TTTATTATTA
*
6553805 ATATTAGTATATATATTTT
1 ATATTAGTATACATATTTT
*
6553824 ATTATTCTTGTATACATATTTT
1 A-TA-T-TAGTATACATATTTT
6553846 ATATATAGTAT
1 ATAT-TAGTAT
6553857 TATTTTCGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 1 0.04
20 8 0.31
21 3 0.12
22 14 0.54
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (19 bp):
ATATTAGTATACATATTTT
Found at i:6554008 original size:11 final size:11
Alignment explanation
Indices: 6553977--6554016 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
6553967 TACATTTTTT
6553977 TATAT-TTAT-
1 TATATATTATG
6553986 TATATATATATG
1 TATATAT-TATG
6553998 TATATATTATG
1 TATATATTATG
6554009 TATATATT
1 TATATATT
6554017 TTAACATTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.18
10 1 0.04
11 15 0.54
12 7 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (11 bp):
TATATATTATG
Found at i:6563418 original size:16 final size:16
Alignment explanation
Indices: 6563397--6563447 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
6563387 GGTTCATTAG
*
6563397 AATGGAATAGAGCTGT
1 AATGGAATAGAACTGT
*
6563413 AATGGAATAGAACTAT
1 AATGGAATAGAACTGT
*
6563429 AATAGAATAGAACTGT
1 AATGGAATAGAACTGT
6563445 AAT
1 AAT
6563448 TAGTAATTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.47, C:0.06, G:0.22, T:0.25
Consensus pattern (16 bp):
AATGGAATAGAACTGT
Found at i:6587887 original size:18 final size:17
Alignment explanation
Indices: 6587864--6587919 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 17
6587854 GTATTTTATA
6587864 TATAAAATCATTAAAAAT
1 TATAAAAT-ATTAAAAAT
*
6587882 TATAAAAT-TATAGGAAAT
1 TATAAAATAT-TA-AAAAT
*
6587900 CATAAAATATATAAAAAT
1 TATAAAATAT-TAAAAAT
6587918 TA
1 TA
6587920 GGCCTAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 1 0.03
17 2 0.06
18 24 0.77
19 4 0.13
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (17 bp):
TATAAAATATTAAAAAT
Found at i:6588183 original size:14 final size:14
Alignment explanation
Indices: 6588164--6588192 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6588154 AATATATTTA
6588164 ATTTTTTAAAAAAT
1 ATTTTTTAAAAAAT
6588178 ATTTTTTAAAAAAT
1 ATTTTTTAAAAAAT
6588192 A
1 A
6588193 AAATCTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTTTTTAAAAAAT
Found at i:6588195 original size:19 final size:20
Alignment explanation
Indices: 6588173--6588216 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
6588163 AATTTTTTAA
*
6588173 AAAATATTTTTTAA-AAAAT
1 AAAATATTGTTTAACAAAAT
* *
6588192 AAAATCTTGTTTAACTAAAT
1 AAAATATTGTTTAACAAAAT
6588212 AAAAT
1 AAAAT
6588217 GTGCATAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (20 bp):
AAAATATTGTTTAACAAAAT
Found at i:6590634 original size:18 final size:18
Alignment explanation
Indices: 6590611--6590694 Score: 55
Period size: 18 Copynumber: 4.6 Consensus size: 18
6590601 ATCCTAATTC
6590611 TAAAAAAATATAAAAATA
1 TAAAAAAATATAAAAATA
* ** *
6590629 TAAAAAACACA-AATATTTT
1 TAAAAAA-ATATAA-AAATA
* * *
6590648 TAAAAATATATAATAATT
1 TAAAAAAATATAAAAATA
*
6590666 TTAAAAAATATATAAAA-A
1 TAAAAAAATATA-AAAATA
6590684 TAAAAAAATAT
1 TAAAAAAATAT
6590695 TTTCAAAAAA
Statistics
Matches: 48, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
18 33 0.69
19 15 0.31
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAAAATATAAAAATA
Found at i:6590666 original size:20 final size:20
Alignment explanation
Indices: 6590605--6590680 Score: 70
Period size: 18 Copynumber: 4.0 Consensus size: 20
6590595 AATTTGATCC
*
6590605 TAATTCTAAAAAA-ATATAA
1 TAATTTTAAAAAATATATAA
* * * *
6590624 -AAATATAAAAAACACA-AA
1 TAATTTTAAAAAATATATAA
*
6590642 T-ATTTTTAAAAATATATAA
1 TAATTTTAAAAAATATATAA
6590661 TAATTTTAAAAAATATATAA
1 TAATTTTAAAAAATATATAA
6590681 AAATAAAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
18 22 0.50
19 5 0.11
20 17 0.39
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
TAATTTTAAAAAATATATAA
Found at i:6590691 original size:20 final size:20
Alignment explanation
Indices: 6590649--6590691 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
6590639 AAATATTTTT
* ***
6590649 AAAAATATATAATAATTTTA
1 AAAAATATATAAAAATAAAA
6590669 AAAAATATATAAAAATAAAA
1 AAAAATATATAAAAATAAAA
6590689 AAA
1 AAA
6590692 TATTTTCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAATATATAAAAATAAAA
Found at i:6590727 original size:30 final size:29
Alignment explanation
Indices: 6590648--6590717 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
6590638 CAAATATTTT
* *
6590648 TAAAAATATATAATAATTTTAAAAAATATA
1 TAAAAATA-AAAAAAATTTTAAAAAATATA
6590678 TAAAAATAAAAAAATATTTTCAAAAAAT-TA
1 TAAAAATAAAAAAA-ATTTT-AAAAAATATA
*
6590708 TAATAATAAA
1 TAAAAATAAA
6590718 TTTAAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 4 0.11
30 24 0.69
31 7 0.20
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (29 bp):
TAAAAATAAAAAAAATTTTAAAAAATATA
Found at i:6593160 original size:125 final size:125
Alignment explanation
Indices: 6592938--6593162 Score: 353
Period size: 125 Copynumber: 1.8 Consensus size: 125
6592928 TGGCAATTTC
* * * *
6592938 ATATGTAGTTAGTTTATTTAAGATCGAAGTGTATAATTTTAAAAATAAAAATAAATTCAAATTAC
1 ATATGTAGTTAATTTATTTAAGATCAAAATGTATAATTTTAAAAATAAAAAGAAATTCAAATTAC
*
6593003 AATGATATCACTAAATATGACATCCTATACTTGATCTGATTGTTGAATATTCAGATTTAA
66 AATAATATCACTAAATATGACATCCTATACTTGATCTGATTGTTGAATATTCAGATTTAA
* **
6593063 ATATGTAGTTAATTTCTTTAAGATCAAAATGTATAATTTTAAAAATGGAAAGAAA-TCTAAATTA
1 ATATGTAGTTAATTTATTTAAGATCAAAATGTATAATTTTAAAAATAAAAAGAAATTC-AAATTA
*
6593127 CAATAATATCACTAAATGTGACATCCTATACTTGAT
65 CAATAATATCACTAAATATGACATCCTATACTTGAT
6593163 TTAATTTTTG
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
124 2 0.02
125 88 0.98
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (125 bp):
ATATGTAGTTAATTTATTTAAGATCAAAATGTATAATTTTAAAAATAAAAAGAAATTCAAATTAC
AATAATATCACTAAATATGACATCCTATACTTGATCTGATTGTTGAATATTCAGATTTAA
Found at i:6595753 original size:156 final size:156
Alignment explanation
Indices: 6595407--6596501 Score: 1638
Period size: 156 Copynumber: 7.0 Consensus size: 156
6595397 TAGCTACTTG
* * *
6595407 TTCAGTGAAGAACAACACGAGGCAATAATGTTACATTGAATGCAACTATGCATTGCAAAGTGTTT
1 TTCAGTGAAGAACAACACGAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTTT
** * *
6595472 CAAATTTGCCAAGTGATAAGAGAAATTCCAAAA-AAAAATCTAATGTCCTTAAAAGTATATTCGC
66 CACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCGC
* * * *
6595536 CAATTTTATAAAAAATATTGTCGTCT
131 CGATTTTATAGAAAATATCGCCGTCT
6595562 TTCAGTGAAGAACAACACGAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTTT
1 TTCAGTGAAGAACAACACGAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTTT
* * *
6595627 CACTTTTCCCAAGTGATAAGAGAAATTCTAAAAGAAAAATCTAATGTCTTTCAAAGTAGATTCGC
66 CACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCGC
*
6595692 CGATTTTATAGAAAATATCGCCATCT
131 CGATTTTATAGAAAATATCGCCGTCT
* * * * *
6595718 TTCAGTGAAGAACAACACAAGGCAATAATGATACACTGCATACAACTATGTATTACAAAGTATTT
1 TTCAGTGAAGAACAACACGAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTTT
* * * *
6595783 CACTTTTGCCAAGTGATAAAGAGATATTCGAAAAGAAAAATCTAATGTATTTAAAAGTAGATTCA
66 CACTTTTGCCAAGTGAT-AAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCG
**
6595848 CCGATTTTATAGAAAATATCGCCACCT
130 CCGATTTTATAGAAAATATCGCCGTCT
* *
6595875 TTCAGTGAAGAACAACACGAGGCAATAATGTTACACTGAATGCAACTATGTATTGTAAAGTGTTT
1 TTCAGTGAAGAACAACACGAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTTT
* *
6595940 CACTTTTGCCAAGTGATAAGGGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGGTTCGC
66 CACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCGC
* *
6596005 CAATTTTATAGAAAATAAT-GTCGTCT
131 CGATTTTATAGAAAAT-ATCGCCGTCT
* * * *
6596031 TTCAGTGAAGAACAACACGAAGCAATAATGTTACACTGCATGCAATTATGTTTTGTAAAGTGTTT
1 TTCAGTGAAGAACAACACGAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTTT
* * *
6596096 CACTTTTGCCAAGTGATGAGAGATATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCGT
66 CACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCGC
6596161 CGATTTTATAGAAAATATCGCCGTCT
131 CGATTTTATAGAAAATATCGCCGTCT
* * * *
6596187 TTCAGTGAAGAACAACATGAGGCAATAATGTTATACTACATGTAACTATGTATTGCAAAGTGTTT
1 TTCAGTGAAGAACAACACGAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTTT
* * *
6596252 CAATTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAACCTGATGTCTTTAAAAGTAGATTCGC
66 CACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCGC
*
6596317 CGATTTTATAGAAAATATCACCGTCT
131 CGATTTTATAGAAAATATCGCCGTCT
* * * *
6596343 TTCAGT-ACATAACAACACAAGGCAATAATGTTACACTACATGCAACTTTGTATTGCAAAGTGTT
1 TTCAGTGA-AGAACAACACGAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTT
* *
6596407 TCACTTTTTCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTATATTCG
65 TCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCG
* * *
6596472 TCGATTTTGTAGAAAATATCGCTGTCT
130 CCGATTTTATAGAAAATATCGCCGTCT
6596499 TTC
1 TTC
6596502 TACACATGTT
Statistics
Matches: 850, Mismatches: 85, Indels: 9
0.90 0.09 0.01
Matches are distributed among these distances:
155 94 0.11
156 611 0.72
157 145 0.17
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.30
Consensus pattern (156 bp):
TTCAGTGAAGAACAACACGAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTTT
CACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCGC
CGATTTTATAGAAAATATCGCCGTCT
Found at i:6596261 original size:312 final size:312
Alignment explanation
Indices: 6595407--6599095 Score: 4861
Period size: 312 Copynumber: 12.0 Consensus size: 312
6595397 TAGCTACTTG
* * * *
6595407 TTCAGTGAAGAACAACACGAGGCAATAATGTTACATTGAATGCAACTATGCATTGCAAAGTGTTT
1 TTCAGTGAAGAACAACACAAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTTT
** * *
6595472 CAAATTTGCCAAGTGATAAGAGAAATTCCAAAA-AAAAATCTAATGTCCTTAAAAGTATATTCGC
66 CACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCGC
* * * * *
6595536 CAATTTTATAAAAAATATTGTCGTCTTTCAGTGAAGAACAACACGAGGCAATAATGTTACACTGC
131 CGATTTTATAGAAAATATCGCCGTCTTTCAGTGAAGAACAACACGAGGCAATAATGTTACACTAC
* *
6595601 ATGCAACTATGTATTGCAAAGTGTTTCACTTTTCCCAAGTGATAAGAGAAATTCTAAAAGAAAAA
196 ATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAA
* *
6595666 TCTAATGTCTTTCAAAGTAGATTCGCCGATTTTATAGAAAATATCGCCATCT
261 TCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGCCGTCT
* * * *
6595718 TTCAGTGAAGAACAACACAAGGCAATAATGATACACTGCATACAACTATGTATTACAAAGTATTT
1 TTCAGTGAAGAACAACACAAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTTT
* * * *
6595783 CACTTTTGCCAAGTGATAAAGAGATATTCGAAAAGAAAAATCTAATGTATTTAAAAGTAGATTCA
66 CACTTTTGCCAAGTGAT-AAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCG
**
6595848 CCGATTTTATAGAAAATATCGCCACCTTTCAGTGAAGAACAACACGAGGCAATAATGTTACACTG
130 CCGATTTTATAGAAAATATCGCCGTCTTTCAGTGAAGAACAACACGAGGCAATAATGTTACACT-
* *
6595913 A-ATGCAACTATGTATTGTAAAGTGTTTCACTTTTGCCAAGTGATAAGGGAAATTCCAAAAGAAA
194 ACATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAA
* * *
6595977 AATCTAATGTCTTTAAAAGTAGGTTCGCCAATTTTATAGAAAATAAT-GTCGTCT
259 AATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAAT-ATCGCCGTCT
* * *
6596031 TTCAGTGAAGAACAACACGAA-GCAATAATGTTACACTGCATGCAATTATGTTTTGTAAAGTGTT
1 TTCAGTGAAGAACAACAC-AAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTT
* *
6596095 TCACTTTTGCCAAGTGATGAGAGATATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCG
65 TCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCG
* * *
6596160 TCGATTTTATAGAAAATATCGCCGTCTTTCAGTGAAGAACAACATGAGGCAATAATGTTATACTA
130 CCGATTTTATAGAAAATATCGCCGTCTTTCAGTGAAGAACAACACGAGGCAATAATGTTACACTA
* *
6596225 CATGTAACTATGTATTGCAAAGTGTTTCAATTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAA
195 CATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAA
* * *
6596290 ACCTGATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCACCGTCT
260 ATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGCCGTCT
* * *
6596343 TTCAGT-ACATAACAACACAAGGCAATAATGTTACACTACATGCAACTTTGTATTGCAAAGTGTT
1 TTCAGTGA-AGAACAACACAAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTT
* *
6596407 TCACTTTTTCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTATATTCG
65 TCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCG
* * * ** *
6596472 TCGATTTTGTAGAAAATATCGCTGTCTTTC--T----------AC-A--C----ATGTTATGCTG
130 CCGATTTTATAGAAAATATCGCCGTCTTTCAGTGAAGAACAACACGAGGCAATAATGTTACACTA
* * *
6596518 CATACAACTATGTATTGCAAAGTGTTTCACTTTTTCCAAGTGATAAGAGAAATT-CATAAAG-AC
195 CATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCA-AAAGAAA
*
6596581 AATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGCTGTCT
259 AATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGCCGTCT
* * * * * *
6596635 TTCAGTGTAGAACAACACGAGGTAGTAATGTTACATTG-AGTCCAACTATGTATTGCAAAGTGTT
1 TTCAGTGAAGAACAACACAAGGCAATAATGTTACACTGCA-TGCAACTATGTATTGCAAAGTGTT
* * *
6596699 TCA-TTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATATCTTTAAATGTAGATACG
65 TCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCG
* * * * *
6596763 TCAATTTTATAGAAAATATCGCAGTCTTTCAGTGAAGAACAACACGAGGCAATAATGTTACATTG
130 CCGATTTTATAGAAAATATCGCCGTCTTTCAGTGAAGAACAACACGAGGCAATAATGTTACACTA
* *
6596828 CATGCAACTATGTATTGCAAAGTGTTTCATTTTTGCCAAGTGATAAGAGAAATTTCAAAAGAAAA
195 CATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAA
* * *
6596893 ATCTAATGTCTTTAAAAGTAGATTCGCCAATTTTATAGAAAATATAGTCGTCT
260 ATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGCCGTCT
* *
6596946 TTCAGTGTAGAACAACACGAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTTT
1 TTCAGTGAAGAACAACACAAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTTT
* * * * * *
6597011 CACTTTTGCTAAGTGATAAGAGAAACTCCAAAATAACATTCTAATGTCTTTAAAAGTAGATTCGT
66 CACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCGC
* ***
6597076 CGATTTTATAAAAAATATCATTGTCTTTCAGTGAAGAACAACACGAGGCAATAATGTTACACTGA
131 CGATTTTATAGAAAATATCGCCGTCTTTCAGTGAAGAACAACACGAGGCAATAATGTTACACT-A
*
6597141 -ATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGCGAAATTCCAAAAGAAAA
195 CATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAA
* * * **
6597205 ACCTAATGTATTTAAAAGTAGATTCGACGATTTTATAGAAAATATAACCGTCT
260 ATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGCCGTCT
* *
6597258 TTCCA-T-ACAGAACAACACGAGGCAATAATGTTACACTGAATGCAACTATGTATTGCAAAGTGT
1 TT-CAGTGA-AGAACAACACAAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGT
* * *
6597321 TTCACTTTTGCCAAGTGATAAGAGAAATTTCAAAAAAAAAATCTAATGTCTTTAAAAGTAGATTG
64 TTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTC
* * * * *
6597386 GTCGATTTTATAGAAAATATCGTCGTCTTTCAATGTAGAACAACACGAGGCAATAATGCTACACT
129 GCCGATTTTATAGAAAATATCGCCGTCTTTCAGTGAAGAACAACACGAGGCAATAATGTTACACT
* *
6597451 ACATGCAACTATGTATTACAAAGTGTTTCACTTTTTCCAAGTGATAAGAGAAATTCCAAAAGAAA
194 ACATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAA
* * * *
6597516 AATCTAATGTCTTTAAAAGTATATTTGCCGATTTTATAGAAAATATTGCTGTCT
259 AATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGCCGTCT
* * * * * * **
6597570 TTCAATGCAGAACAACGCGAGGCAATAATGTTACACTACATACAACTATGTATTTTAAAGTGTTT
1 TTCAGTGAAGAACAACACAAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTTT
* *
6597635 CACTTTTGCCAAGTAATAAGAGAAATTCCAAAATAAAAATCTAATGTCTTTAAAAGTAGATTCGC
66 CACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCGC
* * * * ** *
6597700 CAATTTTATAGAAAATATCGCAGTTTTTTCAATGAAGAACAACATAAAGCAATAATGTTACACTA
131 CGATTTTATAGAAAATATCGCCG-TCTTTCAGTGAAGAACAACACGAGGCAATAATGTTACACTA
6597765 CATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAA
195 CATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAA
* * * * *
6597830 ATCTAATGTTTTTAAAAGTAGGTTCGCCCG-TTTTATAGAAAATATCACTGTTT
260 ATCTAATGTCTTTAAAAGTAGATTCG-CCGATTTTATAGAAAATATCGCCGTCT
* * * * *
6597883 TTCAGTGAAGAAGAACA-GAGGCAATAATGTTACATTGCATGTAACTATGTATTACAAAGTGTTT
1 TTCAGTGAAGAACAACACAAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTTT
* * * *
6597947 CACTTTGGCCAAGTGATAAGATAAATTGCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCGT
66 CACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCGC
* * * *
6598012 CGATTTTATAGAAAATTTCGTCGTCTTTTAGTGAAGAATAACACGAGGCAATAATGTTACACTTA
131 CGATTTTATAGAAAATATCGCCGTCTTTCAGTGAAGAACAACACGAGGCAATAATGTTACAC-TA
*
6598077 -ATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAATGATAAGAGAAATTCCAAAAGAAAA
195 CATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAA
* ** * * *
6598141 ACCTAATGTCTTTAAAAGTAGATTAACCGGTTTTACAGAAAATATCGTCGTCAT
260 ATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGCCGTC-T
* * * *
6598195 TT-AATGAAGAACAAC-CGAGGCAATAATGTTACCCTGCATGCAACTATGTATTACAAAGTGTTT
1 TTCAGTGAAGAACAACACAAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTTT
* * *
6598258 CGCTTTTGCCAAGTAATAATAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCGC
66 CACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCGC
* * * * *
6598323 C-ATTTTATAGAAAATATCGTCATTTTTCAGTAAAGAACAACACGAGGCAATAATGTTACACTGC
131 CGATTTTATAGAAAATATCGCCGTCTTTCAGTGAAGAACAACACGAGGCAATAATGTTACACTAC
* *
6598387 ATGCAACTATGTATTGCAAAGTTTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAG
196 ATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAA
** ** *
6598452 TCTAATGTCTTTAAAAGTAGATTTACC-AGTTTTATAGAAAATATCATCGTTT
261 TCTAATGTCTTTAAAAGTAGATTCGCCGA-TTTTATAGAAAATATCGCCGTCT
* * * * *
6598504 TTCAGTGGAGAACAACGC-GGGACAATAACGTTACATTGCATGCAACTATGTATTGCAAAGTGTT
1 TTCAGTGAAGAACAACACAAGG-CAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTT
*
6598568 TCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTTG
65 TCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCG
* ** * * *
6598633 CCAATTTTATAGAAAATATTACCATCTTTCAGTGAAGAACAACACG-GGACAATAACGTTACATT
130 CCGATTTTATAGAAAATATCGCCGTCTTTCAGTGAAGAACAACACGAGG-CAATAATGTTACACT
* *
6598697 GCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAAAGAAATTCCAAAAGAAA
194 ACATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAA
* * * * *
6598762 AATCTAATGTCTTTAAAAG-AGATTAGTCAATTTTATAGAAAATATTGCCATCT
259 AATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGCCGTCT
* * * * *
6598815 TTCAATGAAGAGCAACACGAGGCAATAATGTTACATTGCATGCAATTATGTATTGCAAAGTGTTT
1 TTCAGTGAAGAACAACACAAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTTT
* * *
6598880 CATTTTTGCCAAGTGATACGAGAAATTCCAAAAGAAAAATCTAATGTTTTTAAAAGTAGA-----
66 CACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCGC
* * * *
6598940 --A---TATAG------T---CGTCTTTCAATGCAGAACAACACGAGGCAATAATATTACACTGC
131 CGATTTTATAGAAAATATCGCCGTCTTTCAGTGAAGAACAACACGAGGCAATAATGTTACACTAC
** * * *
6598991 ATGCAACTATGTATTGCAAAGTGTTTCACTTTTTTCAAATGAGAAGTGAAATTCCAAAAGAAAAA
196 ATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAA
* * * * **
6599056 TCTGACGTTTTTAAAAATAGATTAACCGATTTTATAGAAA
261 TCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAA
6599096 GTATTACCAT
Statistics
Matches: 3002, Mismatches: 318, Indels: 134
0.87 0.09 0.04
Matches are distributed among these distances:
291 84 0.03
292 215 0.07
293 85 0.03
295 1 0.00
297 1 0.00
299 1 0.00
300 1 0.00
301 5 0.00
303 2 0.00
304 2 0.00
306 1 0.00
309 4 0.00
310 240 0.08
311 682 0.23
312 1255 0.42
313 416 0.14
314 7 0.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (312 bp):
TTCAGTGAAGAACAACACAAGGCAATAATGTTACACTGCATGCAACTATGTATTGCAAAGTGTTT
CACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCGC
CGATTTTATAGAAAATATCGCCGTCTTTCAGTGAAGAACAACACGAGGCAATAATGTTACACTAC
ATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAA
TCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGCCGTCT
Found at i:6596376 original size:468 final size:469
Alignment explanation
Indices: 6595407--6598939 Score: 4321
Period size: 468 Copynumber: 7.6 Consensus size: 469
6595397 TAGCTACTTG
* *
6595407 TTCAGTGAAGAACAACACGAGGCAATAATGTTACATTGAATGCAACTATGCATTGCAAAGTGTTT
1 TTCAGTGAAGAACAACACGAGGCAATAATGTTACACTGAATGCAACTATGTATTGCAAAGTGTTT
** *
6595472 CAAATTTGCCAAGTGATAAGAGAAATTCCAAAA-AAAAATCTAATGTCCTTAAAAGTATATTCGC
66 CACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTATATTCGC
* * *
6595536 CAATTTTATAAAAAATATTGTCGTCTTTCAGTGAAGAACAACACGAGGCAATAATGTTACACTGC
131 CAATTTTATAGAAAATAATGTCGTCTTTCAGTGAAGAACAACACGAAGCAATAATGTTACACTGC
*
6595601 ATGCAACTATGTATTGCAAAGTGTTTCACTTTTCCCAAGTGATAAGAGAAATTCTAAAAGAAAAA
196 ATGCAACTATGTATTGCAAAGTGTTTCACTTTTCCCAAGTGATAAGAGAAATTCCAAAAGAAAAA
*
6595666 TCTAATGTCTTTCAAAGTAGATTCGCCGATTTTATAGAAAATATCGCCATCTTTCAGTGAAGAAC
261 TCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGCCATCTTTCAGTGAAGAAC
* *
6595731 AACACAAGGCAATAATGATACACTGCATACAACTATGTATTACAAAGTATTTCACTTTTGCCAAG
326 AACACAAGGCAATAATGATACACTACATACAACTATGTATTACAAAGTATTTCAATTTTGCCAAG
* * *
6595796 TGATAAAGAGATATTCGAAAAGAAAAATCTAATGTATTTAAAAGTAGATTCACCGATTTTATAGA
391 TGATAAAGAGAAATTCCAAAAGAAAAACCTAATGTATTTAAAAGTAGATTCACCGATTTTATAGA
*
6595861 AAATATCGCCACCT
456 AAATATCACCACCT
*
6595875 TTCAGTGAAGAACAACACGAGGCAATAATGTTACACTGAATGCAACTATGTATTGTAAAGTGTTT
1 TTCAGTGAAGAACAACACGAGGCAATAATGTTACACTGAATGCAACTATGTATTGCAAAGTGTTT
* **
6595940 CACTTTTGCCAAGTGATAAGGGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGGTTCGC
66 CACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTATATTCGC
6596005 CAATTTTATAGAAAATAATGTCGTCTTTCAGTGAAGAACAACACGAAGCAATAATGTTACACTGC
131 CAATTTTATAGAAAATAATGTCGTCTTTCAGTGAAGAACAACACGAAGCAATAATGTTACACTGC
* * * * * *
6596070 ATGCAATTATGTTTTGTAAAGTGTTTCACTTTTGCCAAGTGATGAGAGATATTCCAAAAGAAAAA
196 ATGCAACTATGTATTGCAAAGTGTTTCACTTTTCCCAAGTGATAAGAGAAATTCCAAAAGAAAAA
* *
6596135 TCTAATGTCTTTAAAAGTAGATTCGTCGATTTTATAGAAAATATCGCCGTCTTTCAGTGAAGAAC
261 TCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGCCATCTTTCAGTGAAGAAC
** * * ** * *
6596200 AACATGAGGCAATAATGTTATACTACATGTAACTATGTATTGCAAAGTGTTTCAATTTTGCCAAG
326 AACACAAGGCAATAATGATACACTACATACAACTATGTATTACAAAGTATTTCAATTTTGCCAAG
* * *
6596265 TGAT-AAGAGAAATTCCAAAAGAAAAACCTGATGTCTTTAAAAGTAGATTCGCCGATTTTATAGA
391 TGATAAAGAGAAATTCCAAAAGAAAAACCTAATGTATTTAAAAGTAGATTCACCGATTTTATAGA
**
6596329 AAATATCACCGTCT
456 AAATATCACCACCT
* * *
6596343 TTCAGT-ACATAACAACACAAGGCAATAATGTTACACT-ACATGCAACTTTGTATTGCAAAGTGT
1 TTCAGTGA-AGAACAACACGAGGCAATAATGTTACACTGA-ATGCAACTATGTATTGCAAAGTGT
*
6596406 TTCACTTTTTCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTATATTC
64 TTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTATATTC
* * * **
6596471 GTCGATTTTGTAGAAAAT-ATCG-CTGTCTTTC--T----------AC--A-C----ATGTTATG
129 GCCAATTTTATAGAAAATAAT-GTC-GTCTTTCAGTGAAGAACAACACGAAGCAATAATGTTACA
* *
6596515 CTGCATACAACTATGTATTGCAAAGTGTTTCACTTTTTCCAAGTGATAAGAGAAATT-CATAAAG
192 CTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTCCCAAGTGATAAGAGAAATTCCA-AAAG
* ** *
6596579 -ACAATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGCTGTCTTTCAGTGT
256 AAAAATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGCCATCTTTCAGTGA
* * * * * * * * *
6596643 AGAACAACACGAGGTAGTAATGTTACATTGA-GTCCAACTATGTATTGCAAAGTGTTTC-ATTTT
321 AGAACAACACAAGGCAATAATGATACACT-ACATACAACTATGTATTACAAAGTATTTCAATTTT
* * * * * ** *
6596706 GCCAAGTGAT-AAGAGAAATTCCAAAAGAAAAATCTAATATCTTTAAATGTAGATACGTCAATTT
385 GCCAAGTGATAAAGAGAAATTCCAAAAGAAAAACCTAATGTATTTAAAAGTAGATTCACCGATTT
* *
6596770 TATAGAAAATATC-GCAGTCT
450 TATAGAAAATATCACCA-CCT
* *
6596790 TTCAGTGAAGAACAACACGAGGCAATAATGTTACATTGCATGCAACTATGTATTGCAAAGTGTTT
1 TTCAGTGAAGAACAACACGAGGCAATAATGTTACACTGAATGCAACTATGTATTGCAAAGTGTTT
* * *
6596855 CATTTTTGCCAAGTGATAAGAGAAATTTCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCGC
66 CACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTATATTCGC
* *
6596920 CAATTTTATAGAAAAT-ATAGTCGTCTTTCAGTGTAGAACAACACGAGGCAATAATGTTACACTG
131 CAATTTTATAGAAAATAAT-GTCGTCTTTCAGTGAAGAACAACACGAAGCAATAATGTTACACTG
* * * * *
6596984 CATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCTAAGTGATAAGAGAAACTCCAAAATAACA
195 CATGCAACTATGTATTGCAAAGTGTTTCACTTTTCCCAAGTGATAAGAGAAATTCCAAAAGAAAA
* * * ****
6597049 TTCTAATGTCTTTAAAAGTAGATTCGTCGATTTTATAAAAAATATCATTGTCTTTCAGTGAAGAA
260 ATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGCCATCTTTCAGTGAAGAA
* * * * * *
6597114 CAACACGAGGCAATAATGTTACACTGA-ATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCA
325 CAACACAAGGCAATAATGATACACT-ACATACAACTATGTATTACAAAGTATTTCAATTTTGCCA
*
6597178 AGTGAT-AAGCGAAATTCCAAAAGAAAAACCTAATGTATTTAAAAGTAGATTCGA-CGATTTTAT
389 AGTGATAAAGAGAAATTCCAAAAGAAAAACCTAATGTATTTAAAAGTAGATTC-ACCGATTTTAT
* **
6597241 AGAAAATATAACCGTCT
453 AGAAAATATCACCACCT
6597258 TTCCA-T-ACAGAACAACACGAGGCAATAATGTTACACTGAATGCAACTATGTATTGCAAAGTGT
1 TT-CAGTGA-AGAACAACACGAGGCAATAATGTTACACTGAATGCAACTATGTATTGCAAAGTGT
* * * *
6597321 TTCACTTTTGCCAAGTGATAAGAGAAATTTCAAAAAAAAAATCTAATGTCTTTAAAAGTAGATTG
64 TTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTATATTC
* * * * * *
6597386 GTCGATTTTATAGAAAAT-ATCGTCGTCTTTCAATGTAGAACAACACGAGGCAATAATGCTACAC
129 GCCAATTTTATAGAAAATAAT-GTCGTCTTTCAGTGAAGAACAACACGAAGCAATAATGTTACAC
* * *
6597450 TACATGCAACTATGTATTACAAAGTGTTTCACTTTTTCCAAGTGATAAGAGAAATTCCAAAAGAA
193 TGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTCCCAAGTGATAAGAGAAATTCCAAAAGAA
* * * ** * *
6597515 AAATCTAATGTCTTTAAAAGTATATTTGCCGATTTTATAGAAAATATTGCTGTCTTTCAATGCAG
258 AAATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGCCATCTTTCAGTGAAG
* * * ** * *
6597580 AACAACGCGAGGCAATAATGTTACACTACATACAACTATGTATTTTAAAGTGTTTCACTTTTGCC
323 AACAACACAAGGCAATAATGATACACTACATACAACTATGTATTACAAAGTATTTCAATTTTGCC
* * * * * *
6597645 AAGTAAT-AAGAGAAATTCCAAAATAAAAATCTAATGTCTTTAAAAGTAGATTCGCCAATTTTAT
388 AAGTGATAAAGAGAAATTCCAAAAGAAAAACCTAATGTATTTAAAAGTAGATTCACCGATTTTAT
* **
6597709 AGAAAATATC-GCAGTTTT
453 AGAAAATATCACCA--CCT
* ** *
6597727 TTCAATGAAGAACAACATAAAGCAATAATGTTACACT-ACATGCAACTATGTATTGCAAAGTGTT
1 TTCAGTGAAGAACAACACGAGGCAATAATGTTACACTGA-ATGCAACTATGTATTGCAAAGTGTT
* **
6597791 TCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTTTTTAAAAGTAGGTTCG
65 TCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTATATTCG
** ** * * * *
6597856 CCCGTTTTATAGAAAAT-ATCACTGTTTTTCAGTGAAGAAGAACA-GAGGCAATAATGTTACATT
130 CCAATTTTATAGAAAATAATGTC-GTCTTTCAGTGAAGAACAACACGAAGCAATAATGTTACACT
* * ** * *
6597919 GCATGTAACTATGTATTACAAAGTGTTTCACTTTGGCCAAGTGATAAGATAAATTGCAAAAGAAA
194 GCATGCAACTATGTATTGCAAAGTGTTTCACTTTTCCCAAGTGATAAGAGAAATTCCAAAAGAAA
* * * * *
6597984 AATCTAATGTCTTTAAAAGTAGATTCGTCGATTTTATAGAAAATTTCGTCGTCTTTTAGTGAAGA
259 AATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGCCATCTTTCAGTGAAGA
* * * * * * *
6598049 ATAACACGAGGCAATAATGTTACACTTA-ATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCC
324 ACAACACAAGGCAATAATGATACAC-TACATACAACTATGTATTACAAAGTATTTCAATTTTGCC
* * * * *
6598113 AAATGAT-AAGAGAAATTCCAAAAGAAAAACCTAATGTCTTTAAAAGTAGATTAACCGGTTTTAC
388 AAGTGATAAAGAGAAATTCCAAAAGAAAAACCTAATGTATTTAAAAGTAGATTCACCGATTTTAT
* ** *
6598177 AGAAAATATCGTCGTCAT
453 AGAAAATATC-ACCACCT
* * * *
6598195 TT-AATGAAGAACAAC-CGAGGCAATAATGTTACCCTGCATGCAACTATGTATTACAAAGTGTTT
1 TTCAGTGAAGAACAACACGAGGCAATAATGTTACACTGAATGCAACTATGTATTGCAAAGTGTTT
* * * *
6598258 CGCTTTTGCCAAGTAATAATAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTCGC
66 CACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTATATTCGC
* * * *
6598323 C-ATTTTATAGAAAAT-ATCGTCATTTTTCAGTAAAGAACAACACGAGGCAATAATGTTACACTG
131 CAATTTTATAGAAAATAAT-GTCGTCTTTCAGTGAAGAACAACACGAAGCAATAATGTTACACTG
* *
6598386 CATGCAACTATGTATTGCAAAGTTTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAA
195 CATGCAACTATGTATTGCAAAGTGTTTCACTTTTCCCAAGTGATAAGAGAAATTCCAAAAGAAAA
* ** ** * * *
6598451 GTCTAATGTCTTTAAAAGTAGATTTACC-AGTTTTATAGAAAATATCATCGTTTTTCAGTGGAGA
260 ATCTAATGTCTTTAAAAGTAGATTCGCCGA-TTTTATAGAAAATATCGCCATCTTTCAGTGAAGA
* * * * * * * * * *
6598515 ACAACGC-GGGACAATAACGTTACATTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCC
324 ACAACACAAGG-CAATAATGATACACTACATACAACTATGTATTACAAAGTATTTCAATTTTGCC
* * ** *
6598579 AAGTGAT-AAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTAGATTTGCCAATTTTAT
388 AAGTGATAAAGAGAAATTCCAAAAGAAAAACCTAATGTATTTAAAAGTAGATTCACCGATTTTAT
* *
6598643 AGAAAATATTACCATCT
453 AGAAAATATCACCACCT
* * *
6598660 TTCAGTGAAGAACAACACG-GGACAATAACGTTACATTGCATGCAACTATGTATTGCAAAGTGTT
1 TTCAGTGAAGAACAACACGAGG-CAATAATGTTACACTGAATGCAACTATGTATTGCAAAGTGTT
* * *
6598724 TCACTTTTGCCAAGTGATAAAAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAG-AGATTAG
65 TCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTATATTCG
* * * * * * * *
6598788 TCAATTTTATAGAAAATATTGCCATCTTTCAATGAAGAGCAACACGAGGCAATAATGTTACATTG
130 CCAATTTTATAGAAAATAATGTCGTCTTTCAGTGAAGAACAACACGAAGCAATAATGTTACACTG
* * * *
6598853 CATGCAATTATGTATTGCAAAGTGTTTCATTTTTGCCAAGTGATACGAGAAATTCCAAAAGAAAA
195 CATGCAACTATGTATTGCAAAGTGTTTCACTTTTCCCAAGTGATAAGAGAAATTCCAAAAGAAAA
*
6598918 ATCTAATGTTTTTAAAAGTAGA
260 ATCTAATGTCTTTAAAAGTAGA
6598940 ATATAGTCGT
Statistics
Matches: 2709, Mismatches: 297, Indels: 119
0.87 0.10 0.04
Matches are distributed among these distances:
446 1 0.00
447 219 0.08
448 112 0.04
449 62 0.02
453 1 0.00
454 1 0.00
456 2 0.00
459 2 0.00
462 1 0.00
465 41 0.02
466 437 0.16
467 362 0.13
468 1044 0.39
469 423 0.16
470 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (469 bp):
TTCAGTGAAGAACAACACGAGGCAATAATGTTACACTGAATGCAACTATGTATTGCAAAGTGTTT
CACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGAAAAATCTAATGTCTTTAAAAGTATATTCGC
CAATTTTATAGAAAATAATGTCGTCTTTCAGTGAAGAACAACACGAAGCAATAATGTTACACTGC
ATGCAACTATGTATTGCAAAGTGTTTCACTTTTCCCAAGTGATAAGAGAAATTCCAAAAGAAAAA
TCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGCCATCTTTCAGTGAAGAAC
AACACAAGGCAATAATGATACACTACATACAACTATGTATTACAAAGTATTTCAATTTTGCCAAG
TGATAAAGAGAAATTCCAAAAGAAAAACCTAATGTATTTAAAAGTAGATTCACCGATTTTATAGA
AAATATCACCACCT
Found at i:6596946 original size:156 final size:156
Alignment explanation
Indices: 6596515--6598939 Score: 3405
Period size: 156 Copynumber: 15.6 Consensus size: 156
6596505 ACATGTTATG
* *
6596515 CTGCATACAACTATGTATTGCAAAGTGTTTCACTTTTTCCAAGTGATAAGAGAAATT-CATAAAG
1 CTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCA-AAAG
*
6596579 -ACAATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCG-CTGTCTTTCAGTG
65 AAAAATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGTC-GTCTTTCAGTG
* * *
6596642 TAGAACAACACGAGGTAGTAATGTTACA
129 AAGAACAACACGAGGCAATAATGTTACA
* *
6596670 TTG-AGTCCAACTATGTATTGCAAAGTGTTTCA-TTTTGCCAAGTGATAAGAGAAATTCCAAAAG
1 CTGCA-TGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAG
* * * * *
6596733 AAAAATCTAATATCTTTAAATGTAGATACGTCAATTTTATAGAAAATATCG-CAGTCTTTCAGTG
65 AAAAATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGTC-GTCTTTCAGTG
6596797 AAGAACAACACGAGGCAATAATGTTACA
129 AAGAACAACACGAGGCAATAATGTTACA
* * *
6596825 TTGCATGCAACTATGTATTGCAAAGTGTTTCATTTTTGCCAAGTGATAAGAGAAATTTCAAAAGA
1 CTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGA
* * *
6596890 AAAATCTAATGTCTTTAAAAGTAGATTCGCCAATTTTATAGAAAATATAGTCGTCTTTCAGTGTA
66 AAAATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGTCGTCTTTCAGTGAA
6596955 GAACAACACGAGGCAATAATGTTACA
131 GAACAACACGAGGCAATAATGTTACA
* * *
6596981 CTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCTAAGTGATAAGAGAAACTCCAAAATA
1 CTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGA
* * * * * *
6597046 ACATTCTAATGTCTTTAAAAGTAGATTCGTCGATTTTATAAAAAATATCATTGTCTTTCAGTGAA
66 AAAATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGTCGTCTTTCAGTGAA
6597111 GAACAACACGAGGCAATAATGTTACA
131 GAACAACACGAGGCAATAATGTTACA
* *
6597137 CTGAATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGCGAAATTCCAAAAGA
1 CTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGA
* * * ***
6597202 AAAACCTAATGTATTTAAAAGTAGATTCGACGATTTTATAGAAAATATAACCGTCTTTCCA-T-A
66 AAAATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGTCGTCTTT-CAGTGA
6597265 CAGAACAACACGAGGCAATAATGTTACA
130 -AGAACAACACGAGGCAATAATGTTACA
* * *
6597293 CTGAATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTTCAAAAAA
1 CTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGA
* * * *
6597358 AAAATCTAATGTCTTTAAAAGTAGATTGGTCGATTTTATAGAAAATATCGTCGTCTTTCAATGTA
66 AAAATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGTCGTCTTTCAGTGAA
*
6597423 GAACAACACGAGGCAATAATGCTACA
131 GAACAACACGAGGCAATAATGTTACA
* * *
6597449 CTACATGCAACTATGTATTACAAAGTGTTTCACTTTTTCCAAGTGATAAGAGAAATTCCAAAAGA
1 CTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGA
* * * * *
6597514 AAAATCTAATGTCTTTAAAAGTATATTTGCCGATTTTATAGAAAATATTG-CTGTCTTTCAATGC
66 AAAATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGTC-GTCTTTCAGTGA
*
6597578 AGAACAACGCGAGGCAATAATGTTACA
130 AGAACAACACGAGGCAATAATGTTACA
* * ** * *
6597605 CTACATACAACTATGTATTTTAAAGTGTTTCACTTTTGCCAAGTAATAAGAGAAATTCCAAAATA
1 CTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGA
* * *
6597670 AAAATCTAATGTCTTTAAAAGTAGATTCGCCAATTTTATAGAAAATATCG-CAGTTTTTTCAATG
66 AAAATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGTC-G-TCTTTCAGTG
** *
6597734 AAGAACAACATAAAGCAATAATGTTACA
129 AAGAACAACACGAGGCAATAATGTTACA
*
6597762 CTACATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGA
1 CTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGA
* * * *
6597827 AAAATCTAATGTTTTTAAAAGTAGGTTCGCCCG-TTTTATAGAAAATATC-ACTGTTTTTCAGTG
66 AAAATCTAATGTCTTTAAAAGTAGATTCG-CCGATTTTATAGAAAATATCGTC-GTCTTTCAGTG
*
6597890 AAGAAGAACA-GAGGCAATAATGTTACA
129 AAGAACAACACGAGGCAATAATGTTACA
* * * * * *
6597917 TTGCATGTAACTATGTATTACAAAGTGTTTCACTTTGGCCAAGTGATAAGATAAATTGCAAAAGA
1 CTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGA
* * *
6597982 AAAATCTAATGTCTTTAAAAGTAGATTCGTCGATTTTATAGAAAATTTCGTCGTCTTTTAGTGAA
66 AAAATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGTCGTCTTTCAGTGAA
*
6598047 GAATAACACGAGGCAATAATGTTACA
131 GAACAACACGAGGCAATAATGTTACA
** *
6598073 CTTAATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAATGATAAGAGAAATTCCAAAAGA
1 CTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGA
* ** * * *
6598138 AAAACCTAATGTCTTTAAAAGTAGATTAACCGGTTTTACAGAAAATATCGTCGTCATTT-AATGA
66 AAAATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGTCGTC-TTTCAGTGA
*
6598202 AGAACAAC-CGAGGCAATAATGTTACC
130 AGAACAACACGAGGCAATAATGTTACA
* * * *
6598228 CTGCATGCAACTATGTATTACAAAGTGTTTCGCTTTTGCCAAGTAATAATAGAAATTCCAAAAGA
1 CTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGA
* * *
6598293 AAAATCTAATGTCTTTAAAAGTAGATTCGCC-ATTTTATAGAAAATATCGTCATTTTTCAGTAAA
66 AAAATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGTCGTCTTTCAGTGAA
6598357 GAACAACACGAGGCAATAATGTTACA
131 GAACAACACGAGGCAATAATGTTACA
*
6598383 CTGCATGCAACTATGTATTGCAAAGTTTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGA
1 CTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGA
* ** * * *
6598448 AAAGTCTAATGTCTTTAAAAGTAGATTTACC-AGTTTTATAGAAAATATCATCGTTTTTCAGTGG
66 AAAATCTAATGTCTTTAAAAGTAGATTCGCCGA-TTTTATAGAAAATATCGTCGTCTTTCAGTGA
* *
6598512 AGAACAACGCG-GGACAATAACGTTACA
130 AGAACAACACGAGG-CAATAATGTTACA
*
6598539 TTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGA
1 CTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGA
* * *** *
6598604 AAAATCTAATGTCTTTAAAAGTAGATTTGCCAATTTTATAGAAAATATTACCATCTTTCAGTGAA
66 AAAATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGTCGTCTTTCAGTGAA
*
6598669 GAACAACACG-GGACAATAACGTTACA
131 GAACAACACGAGG-CAATAATGTTACA
* *
6598695 TTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAAAGAAATTCCAAAAGA
1 CTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGA
* * * * * * *
6598760 AAAATCTAATGTCTTTAAAAG-AGATTAGTCAATTTTATAGAAAATATTGCCATCTTTCAATGAA
66 AAAATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGTCGTCTTTCAGTGAA
*
6598824 GAGCAACACGAGGCAATAATGTTACA
131 GAACAACACGAGGCAATAATGTTACA
* * * *
6598850 TTGCATGCAATTATGTATTGCAAAGTGTTTCATTTTTGCCAAGTGATACGAGAAATTCCAAAAGA
1 CTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGA
*
6598915 AAAATCTAATGTTTTTAAAAGTAGA
66 AAAATCTAATGTCTTTAAAAGTAGA
6598940 ATATAGTCGT
Statistics
Matches: 2053, Mismatches: 192, Indels: 49
0.89 0.08 0.02
Matches are distributed among these distances:
153 3 0.00
154 60 0.03
155 629 0.31
156 1215 0.59
157 144 0.07
158 2 0.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (156 bp):
CTGCATGCAACTATGTATTGCAAAGTGTTTCACTTTTGCCAAGTGATAAGAGAAATTCCAAAAGA
AAAATCTAATGTCTTTAAAAGTAGATTCGCCGATTTTATAGAAAATATCGTCGTCTTTCAGTGAA
GAACAACACGAGGCAATAATGTTACA
Found at i:6598986 original size:137 final size:137
Alignment explanation
Indices: 6598812--6599076 Score: 397
Period size: 137 Copynumber: 1.9 Consensus size: 137
6598802 AATATTGCCA
* * * *
6598812 TCTTTCAATGAAGAGCAACACGAGGCAATAATGTTACATTGCATGCAATTATGTATTGCAAAGTG
1 TCTTTCAATGAAGAACAACACGAGGCAATAATATTACACTGCATGCAACTATGTATTGCAAAGTG
* * * * *
6598877 TTTCA-TTTTTGCCAAGTGATACGAGAAATTCCAAAAGAAAAATCTAATGTTTTTAAAAGTAGAA
66 TTTCACTTTTT-CCAAATGAGAAGAGAAATTCCAAAAGAAAAATCTAACGTTTTTAAAAATAGAA
6598941 TATAGTCG
130 TATAGTCG
*
6598949 TCTTTCAATGCAGAACAACACGAGGCAATAATATTACACTGCATGCAACTATGTATTGCAAAGTG
1 TCTTTCAATGAAGAACAACACGAGGCAATAATATTACACTGCATGCAACTATGTATTGCAAAGTG
* * *
6599014 TTTCACTTTTTTCAAATGAGAAGTGAAATTCCAAAAGAAAAATCTGACGTTTTTAAAAATAGA
66 TTTCACTTTTTCCAAATGAGAAGAGAAATTCCAAAAGAAAAATCTAACGTTTTTAAAAATAGA
6599077 TTAACCGATT
Statistics
Matches: 114, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
137 109 0.96
138 5 0.04
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (137 bp):
TCTTTCAATGAAGAACAACACGAGGCAATAATATTACACTGCATGCAACTATGTATTGCAAAGTG
TTTCACTTTTTCCAAATGAGAAGAGAAATTCCAAAAGAAAAATCTAACGTTTTTAAAAATAGAAT
ATAGTCG
Found at i:6604502 original size:17 final size:17
Alignment explanation
Indices: 6604482--6604515 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6604472 AGGTTTAAGT
6604482 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
**
6604499 TTAAATTTTTTAATTAA
1 TTAAAAATTTTAATTAA
6604516 AAATCTATTT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:6606515 original size:34 final size:34
Alignment explanation
Indices: 6606431--6606570 Score: 138
Period size: 34 Copynumber: 4.0 Consensus size: 34
6606421 ATCACTTAAT
* **
6606431 ACATAGTATGCGAACCATCACATTATATGGTATG
1 ACATAGTATGCAAACCCCCACATTATATGGTATG
* **
6606465 ACAAAGTATGTGAACCCCCACATTATATGGTATG
1 ACATAGTATGCAAACCCCCACATTATATGGTATG
** *
6606499 ACATAGTATGCAAACCCCCATGTTATATAGTACATATG
1 ACATAGTATGCAAACCCCCACATTATAT-G---GTATG
*
6606537 ACATAGTATGCAAACCCCCA-AGTTATATAGTATG
1 ACATAGTATGCAAACCCCCACA-TTATATGGTATG
6606571 TGATTTAATA
Statistics
Matches: 88, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
34 57 0.65
35 1 0.01
38 30 0.34
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (34 bp):
ACATAGTATGCAAACCCCCACATTATATGGTATG
Found at i:6606546 original size:38 final size:38
Alignment explanation
Indices: 6606495--6606568 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
6606485 CATTATATGG
*
6606495 TATGACATAGTATGCAAACCCCCATGTTATATAGTACA
1 TATGACATAGTATGCAAACCCCCAAGTTATATAGTACA
6606533 TATGACATAGTATGCAAACCCCCAAGTTATATAGTA
1 TATGACATAGTATGCAAACCCCCAAGTTATATAGTA
6606569 TGTGATTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (38 bp):
TATGACATAGTATGCAAACCCCCAAGTTATATAGTACA
Found at i:6611485 original size:157 final size:157
Alignment explanation
Indices: 6611319--6611629 Score: 577
Period size: 157 Copynumber: 2.0 Consensus size: 157
6611309 TATAAGAATA
*
6611319 TTAATTATTAAGAATTTTATTAAATTATATATTTTAAGTATAATATATTTAATAATAATTATGTT
1 TTAATTATTAAGAATTTTATTAAATTATATATTTTAAGTAAAATATATTTAATAATAATTATGTT
*
6611384 TAAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACA
66 TAAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACA
6611449 ATAATAATTTACCAAAACAAATTTCTG
131 ATAATAATTTACCAAAACAAATTTCTG
* *
6611476 TTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATGTTTAATAATAATTATGTT
1 TTAATTATTAAGAATTTTATTAAATTATATATTTTAAGTAAAATATATTTAATAATAATTATGTT
6611541 TAAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACA
66 TAAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACA
*
6611606 ATAATCATTTACCAAAACAAATTT
131 ATAATAATTTACCAAAACAAATTT
6611630 ATGCTAAGGG
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 149 1.00
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.44
Consensus pattern (157 bp):
TTAATTATTAAGAATTTTATTAAATTATATATTTTAAGTAAAATATATTTAATAATAATTATGTT
TAAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACA
ATAATAATTTACCAAAACAAATTTCTG
Found at i:6611780 original size:16 final size:16
Alignment explanation
Indices: 6611759--6611826 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
6611749 GATTTGCTAT
* *
6611759 TACACCTTTAATCTAA
1 TACACCTCTAATCCAA
6611775 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
6611791 TACACTTCTAATCCAA
1 TACACCTCTAATCCAA
6611807 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
6611823 TACA
1 TACA
6611827 GCGAACCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.38, C:0.32, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:6614947 original size:22 final size:21
Alignment explanation
Indices: 6614912--6614960 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
6614902 GACGAATAAG
*
6614912 AAAATAGCACTAAAACAACAA
1 AAAATAACACTAAAACAACAA
*
6614933 TAAAATAACATTAAAACAACAA
1 -AAAATAACACTAAAACAACAA
6614955 AAAATA
1 AAAATA
6614961 GTAGCCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.69, C:0.14, G:0.02, T:0.14
Consensus pattern (21 bp):
AAAATAACACTAAAACAACAA
Found at i:6615910 original size:14 final size:14
Alignment explanation
Indices: 6615893--6615919 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6615883 TTTATATACT
6615893 TTTTTTAAATTTTA
1 TTTTTTAAATTTTA
6615907 TTTTTTAAATTTT
1 TTTTTTAAATTTT
6615920 TTTCAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTAAATTTTA
Found at i:6617080 original size:7 final size:7
Alignment explanation
Indices: 6617073--6617106 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
6617063 AATTAAAAAT
*
6617073 ATATAAT
1 ATATAAC
*
6617080 ATATAGC
1 ATATAAC
6617087 ATATAAC
1 ATATAAC
6617094 ATATAAC
1 ATATAAC
6617101 ATATAA
1 ATATAA
6617107 ATAATTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.32
Consensus pattern (7 bp):
ATATAAC
Found at i:6620572 original size:16 final size:16
Alignment explanation
Indices: 6620534--6620572 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
6620524 GATTTGATGA
* *
6620534 ATCTTAATTTAAATTG
1 ATCTAAATTTAAATTC
*
6620550 ATTTAAATTTAAATTC
1 ATCTAAATTTAAATTC
6620566 ATCTAAA
1 ATCTAAA
6620573 CTTGAAATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (16 bp):
ATCTAAATTTAAATTC
Found at i:6622611 original size:15 final size:16
Alignment explanation
Indices: 6622591--6622625 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
6622581 AATCTTTGAC
6622591 AATTAAAATAT-AATA
1 AATTAAAATATAAATA
*
6622606 AATTAAAATTTAAATA
1 AATTAAAATATAAATA
6622622 AATT
1 AATT
6622626 TAGATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTAAAATATAAATA
Found at i:6625979 original size:16 final size:17
Alignment explanation
Indices: 6625948--6625987 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
6625938 TGTATTTGAC
6625948 AATTTATTTAATAATTG
1 AATTTATTTAATAATTG
*
6625965 AATTTGTTT-ATAATT-
1 AATTTATTTAATAATTG
6625980 -ATTTATTT
1 AATTTATTT
6625988 TTATTATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 7 0.33
16 6 0.29
17 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (17 bp):
AATTTATTTAATAATTG
Found at i:6626452 original size:18 final size:18
Alignment explanation
Indices: 6626431--6626492 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 18
6626421 ACAATTTAAC
6626431 ATTTTTATATAATTTTTA
1 ATTTTTATATAATTTTTA
6626449 ATTTTTATAT--TTTCTGTA
1 ATTTTTATATAATTT-T-TA
6626467 ATTTTT-TATAGATATTTTAA
1 ATTTTTATATA-AT-TTTT-A
6626487 ATTTTT
1 ATTTTT
6626493 GAAGATTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
16 3 0.08
17 4 0.11
18 18 0.49
19 1 0.03
20 9 0.24
21 2 0.05
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (18 bp):
ATTTTTATATAATTTTTA
Found at i:6627315 original size:9 final size:9
Alignment explanation
Indices: 6627303--6627391 Score: 52
Period size: 10 Copynumber: 8.6 Consensus size: 9
6627293 CAAAAGATAC
6627303 AAAAAATTT
1 AAAAAATTT
*
6627312 AAAACATTT
1 AAAAAATTT
6627321 ATAAAAATTT
1 A-AAAAATTT
6627331 CAAAATTTATATTCT
1 -AAAA---A-ATT-T
*
6627346 AAAAAAATT
1 AAAAAATTT
6627355 ATAAAAATTCT
1 A-AAAAATT-T
6627366 AAAAAATGTAT
1 AAAAAAT-T-T
6627377 AAAAAAATTT
1 -AAAAAATTT
6627387 AAAAA
1 AAAAA
6627392 TTAAAATTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 22
0.70 0.05 0.24
Matches are distributed among these distances:
9 16 0.25
10 25 0.39
11 7 0.11
12 7 0.11
13 1 0.02
14 7 0.11
15 1 0.02
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (9 bp):
AAAAAATTT
Found at i:6627326 original size:18 final size:18
Alignment explanation
Indices: 6627304--6627393 Score: 62
Period size: 20 Copynumber: 4.8 Consensus size: 18
6627294 AAAAGATACA
6627304 AAAAATTTAAAACATTTAT
1 AAAAATTTAAAA-ATTTAT
*
6627323 AAAAATTTCAAAATTTAT
1 AAAAATTTAAAAATTTAT
*
6627341 ----ATTCTAAAAAAATTAT
1 AAAAATT-T-AAAAATTTAT
*
6627357 AAAAATTCTAAAAAATGTATAA
1 AAAAATT-T-AAAAAT-T-TAT
6627379 AAAAATTTAAAAATT
1 AAAAATTTAAAAATT
6627394 AAAATTTTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
14 3 0.05
15 1 0.02
16 8 0.14
18 6 0.10
19 12 0.21
20 17 0.29
21 2 0.03
22 9 0.16
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.34
Consensus pattern (18 bp):
AAAAATTTAAAAATTTAT
Found at i:6627366 original size:20 final size:20
Alignment explanation
Indices: 6627341--6627381 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
6627331 CAAAATTTAT
6627341 ATTCTAAAAAAAT-TATAAAA
1 ATTCT-AAAAAATGTATAAAA
6627361 ATTCTAAAAAATGTATAAAA
1 ATTCTAAAAAATGTATAAAA
6627381 A
1 A
6627382 AATTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.29
Consensus pattern (20 bp):
ATTCTAAAAAATGTATAAAA
Found at i:6631268 original size:24 final size:23
Alignment explanation
Indices: 6631241--6631296 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
6631231 AAAACGAATA
6631241 AATAATAAAAATCCTCAA-GTAAAT
1 AATAATAAAAA--CTCAAGGTAAAT
* *
6631265 AATATATATAAACTTAAGGTAAAT
1 AATA-ATAAAAACTCAAGGTAAAT
6631289 AATAATAA
1 AATAATAA
6631297 TACGATTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
23 7 0.26
24 14 0.52
25 6 0.22
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.29
Consensus pattern (23 bp):
AATAATAAAAACTCAAGGTAAAT
Found at i:6632666 original size:15 final size:15
Alignment explanation
Indices: 6632625--6632707 Score: 78
Period size: 15 Copynumber: 5.3 Consensus size: 15
6632615 GCCCGTTCGA
*
6632625 TTTTCTTCTCTGTTT
1 TTTTCTTCTTTGTTT
*
6632640 GTTTCTTCTTTGTTT
1 TTTTCTTCTTTGTTT
6632655 TTTTGCTT-TTTGTTT
1 TTTT-CTTCTTTGTTT
*
6632670 TCTGCTTCTTTTTTTGTTT
1 T-T--TTC-TTCTTTGTTT
*
6632689 TTTCCTTCTTTGTTT
1 TTTTCTTCTTTGTTT
6632704 TTTT
1 TTTT
6632708 GTATTTTGCG
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
15 36 0.64
16 6 0.11
17 1 0.02
18 5 0.09
19 8 0.14
ACGTcount: A:0.00, C:0.14, G:0.10, T:0.76
Consensus pattern (15 bp):
TTTTCTTCTTTGTTT
Found at i:6632685 original size:19 final size:19
Alignment explanation
Indices: 6632661--6632704 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
6632651 GTTTTTTTGC
*
6632661 TTTTTGTTTTCTGCTTCTT
1 TTTTTGTTTTCTCCTTCTT
*
6632680 TTTTTGTTTTTTCCTTCTT
1 TTTTTGTTTTCTCCTTCTT
6632699 TGTTTT
1 T-TTTT
6632705 TTTGTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.00, C:0.14, G:0.09, T:0.77
Consensus pattern (19 bp):
TTTTTGTTTTCTCCTTCTT
Done.