Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 77 of 182
Found at i:23341550 original size:21 final size:21
Alignment explanation
Indices: 23341526--23341578 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
23341516 CATTATTTCT
*
23341526 AATCTCACCGCTACAGTACCC
1 AATCTCACCGCTACAGTAACC
*
23341547 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
23341568 AATCTCACCGC
1 AATCTCACCGC
23341579 CACCGCTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.40, G:0.09, T:0.21
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:23342204 original size:10 final size:10
Alignment explanation
Indices: 23342170--23342203 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
23342160 TCCAAGAGTT
23342170 TATACATATA
1 TATACATATA
*
23342180 TATACCTATA
1 TATACATATA
*
23342190 TATATATATA
1 TATACATATA
23342200 TATA
1 TATA
23342204 TTCGCACCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (10 bp):
TATACATATA
Found at i:23354921 original size:25 final size:26
Alignment explanation
Indices: 23354866--23354926 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 26
23354856 CAATTAGATC
* *
23354866 CATTTTATGAT-AAAATTATTTACTAT
1 CATTTT-TGATAAAAATTATTAAATAT
23354892 C-TTTTTGATAAAAATTATTAAAT-T
1 CATTTTTGATAAAAATTATTAAATAT
23354916 CATTTTT-ATAA
1 CATTTTTGATAA
23354927 TTCCTGTCGG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
24 10 0.32
25 20 0.65
26 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (26 bp):
CATTTTTGATAAAAATTATTAAATAT
Found at i:23357613 original size:20 final size:20
Alignment explanation
Indices: 23357584--23357629 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
23357574 TAAATAGAAC
23357584 AAGACACAATTAATTAAGTT
1 AAGACACAATTAATTAAGTT
* **
23357604 AAGACCCAATTAATTCGGTT
1 AAGACACAATTAATTAAGTT
23357624 AAGACA
1 AAGACA
23357630 AGACACATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (20 bp):
AAGACACAATTAATTAAGTT
Found at i:23367087 original size:24 final size:24
Alignment explanation
Indices: 23367046--23367094 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
23367036 TTTTACAGAA
* *
23367046 CTAAAAAAAATAAATAAATGAAAC
1 CTAAAAAAAAGAAATAAAAGAAAC
* *
23367070 CTAAAAAAACGAACTAAAAGAAAC
1 CTAAAAAAAAGAAATAAAAGAAAC
23367094 C
1 C
23367095 CTAGCCCTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.67, C:0.14, G:0.06, T:0.12
Consensus pattern (24 bp):
CTAAAAAAAAGAAATAAAAGAAAC
Found at i:23369990 original size:3 final size:3
Alignment explanation
Indices: 23369984--23370008 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
23369974 TAACAAAAAA
23369984 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
23370009 CAAATTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:23370532 original size:22 final size:22
Alignment explanation
Indices: 23370488--23370532 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
23370478 TTTTATAATT
* *
23370488 TTTTTATTTATAGAATTTAAAA
1 TTTTTATTTATAGAAGTAAAAA
23370510 TTTTTATTTATA-AAGTAACAAA
1 TTTTTATTTATAGAAGTAA-AAA
23370532 T
1 T
23370533 GTTAACTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (22 bp):
TTTTTATTTATAGAAGTAAAAA
Found at i:23383078 original size:54 final size:54
Alignment explanation
Indices: 23382996--23383129 Score: 225
Period size: 54 Copynumber: 2.5 Consensus size: 54
23382986 CCTATCACCA
*
23382996 TGGTCC-AGTTGCAAAGCCACCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
1 TGGTCCTA-TTGCAAAGCCTCCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
23383050 TGGTCCTATTGCAAAGCCTCCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
1 TGGTCCTATTGCAAAGCCTCCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
* *
23383104 TGGTCCTATTGCAAAGTCTCCTACAG
1 TGGTCCTATTGCAAAGCCTCCCACAG
23383130 CATTAACTCC
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
54 75 0.99
55 1 0.01
ACGTcount: A:0.17, C:0.35, G:0.21, T:0.27
Consensus pattern (54 bp):
TGGTCCTATTGCAAAGCCTCCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
Found at i:23383158 original size:54 final size:54
Alignment explanation
Indices: 23382996--23383158 Score: 159
Period size: 54 Copynumber: 3.0 Consensus size: 54
23382986 CCTATCACCA
* * * * * *
23382996 TGGTCC-AGTTGCAAAGCCACCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
1 TGGTCCTA-TTGCAAAGCCTCCCACAGCATCAACTCCGGTTCCAGCACAGGCTCC
* * * * *
23383050 TGGTCCTATTGCAAAGCCTCCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
1 TGGTCCTATTGCAAAGCCTCCCACAGCATCAACTCCGGTTCCAGCACAGGCTCC
* * * *
23383104 TGGTCCTATTGCAAAGTCTCCTACAGCATTAACTCCAGG-TCCAGCACAGTCTCC
1 TGGTCCTATTGCAAAGCCTCCCACAGCATCAACTCC-GGTTCCAGCACAGGCTCC
23383158 T
1 T
23383159 TATCACCATG
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
54 94 0.97
55 3 0.03
ACGTcount: A:0.18, C:0.36, G:0.20, T:0.26
Consensus pattern (54 bp):
TGGTCCTATTGCAAAGCCTCCCACAGCATCAACTCCGGTTCCAGCACAGGCTCC
Found at i:23383857 original size:29 final size:29
Alignment explanation
Indices: 23383825--23383881 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
23383815 TTTTTTTAAA
23383825 AATTTATTAAATTATTCAAAATT-TTATTT
1 AATTTATTAAATTATT-AAAATTGTTATTT
* * *
23383854 AATTTGTTGAATTGTTAAAATTGTTATT
1 AATTTATTAAATTATTAAAATTGTTATT
23383882 GTATAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (29 bp):
AATTTATTAAATTATTAAAATTGTTATTT
Found at i:23386576 original size:31 final size:30
Alignment explanation
Indices: 23386538--23386601 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
23386528 AATGTTAGGC
* *
23386538 AAAAAATTATGTGAATAGGTTAATTTTAGAA
1 AAAAAATTACGGGAATAGGTT-ATTTTAGAA
* *
23386569 AAAAAATTGCGGGAATAGGTTATTTTTGAA
1 AAAAAATTACGGGAATAGGTTATTTTAGAA
23386599 AAA
1 AAA
23386602 CACTTCTAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 11 0.38
31 18 0.62
ACGTcount: A:0.47, C:0.02, G:0.19, T:0.33
Consensus pattern (30 bp):
AAAAAATTACGGGAATAGGTTATTTTAGAA
Found at i:23386961 original size:16 final size:15
Alignment explanation
Indices: 23386934--23386972 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
23386924 TATCATTTCA
23386934 ATATATAATTTAAAT
1 ATATATAATTTAAAT
23386949 ATATATAAATTTAAAT
1 ATATAT-AATTTAAAT
23386965 ATAT-TAAT
1 ATATATAAT
23386973 AATATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.13
15 7 0.30
16 13 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATATATAATTTAAAT
Found at i:23386978 original size:11 final size:11
Alignment explanation
Indices: 23386962--23386998 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
23386952 TATAAATTTA
23386962 AATATATTAAT
1 AATATATTAAT
*
23386973 AATATATAAAT
1 AATATATTAAT
23386984 -A-ATATTAAT
1 AATATATTAAT
23386993 AATATA
1 AATATA
23386999 GAATTTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 7 0.32
10 2 0.09
11 13 0.59
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AATATATTAAT
Found at i:23386990 original size:20 final size:19
Alignment explanation
Indices: 23386944--23386998 Score: 71
Period size: 20 Copynumber: 3.0 Consensus size: 19
23386934 ATATATAATT
*
23386944 TAAATATA-T-ATAA-ATT
1 TAAATATATTAATAATATA
23386960 TAAATATATTAATAATATA
1 TAAATATATTAATAATATA
23386979 TAAATAATATTAATAATATA
1 TAAAT-ATATTAATAATATA
23386999 GAATTTTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
16 8 0.24
17 1 0.03
18 4 0.12
19 7 0.21
20 14 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAATATATTAATAATATA
Found at i:23389167 original size:14 final size:14
Alignment explanation
Indices: 23389148--23389181 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
23389138 ATTTTTATTG
23389148 CTTTTTCTTC-GTAT
1 CTTTTT-TTCAGTAT
23389162 CTTTTTTTCAGTAT
1 CTTTTTTTCAGTAT
23389176 CTTTTT
1 CTTTTT
23389182 GGTACCGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.16
14 16 0.84
ACGTcount: A:0.09, C:0.18, G:0.06, T:0.68
Consensus pattern (14 bp):
CTTTTTTTCAGTAT
Found at i:23390199 original size:44 final size:45
Alignment explanation
Indices: 23389972--23390212 Score: 166
Period size: 44 Copynumber: 5.4 Consensus size: 45
23389962 CGCTCTGCTA
* * * * * *
23389972 CAACTTCAGGGAGATATGATT-ATTAACTTTTAATGTGTTCCACTG
1 CAACTTCAGGGAGATAAGATTCATCATC-TTCAATCTGCTCCACTG
* * ** * *
23390017 CAATTTCAGAGAGATAAGATTCGCCATTTTCAATCTGCCCCACTG
1 CAACTTCAGGGAGATAAGATTCATCATCTTCAATCTGCTCCACTG
* * * * * * *
23390062 CAACTTCAGGGGGATAAGATTTAT-TTATTCAGTCTACTCCGCTG
1 CAACTTCAGGGAGATAAGATTCATCATCTTCAATCTGCTCCACTG
* * * * * * *
23390106 TAACTTCAGGGAGATAGGATT-ATTAGCTTTAATCTGCTCTATTG
1 CAACTTCAGGGAGATAAGATTCATCATCTTCAATCTGCTCCACTG
* * *
23390150 TAACTTCAGGGAGATAAGATTCGTCATCTTCAGTCTG-TCCACTG
1 CAACTTCAGGGAGATAAGATTCATCATCTTCAATCTGCTCCACTG
* *
23390194 CAACTTTAGGGGGATAAGA
1 CAACTTCAGGGAGATAAGA
23390213 CTTGCTATCT
Statistics
Matches: 146, Mismatches: 47, Indels: 7
0.73 0.23 0.04
Matches are distributed among these distances:
43 2 0.01
44 84 0.58
45 59 0.40
46 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (45 bp):
CAACTTCAGGGAGATAAGATTCATCATCTTCAATCTGCTCCACTG
Found at i:23390754 original size:89 final size:89
Alignment explanation
Indices: 23390571--23390791 Score: 250
Period size: 89 Copynumber: 2.5 Consensus size: 89
23390561 GAGGCAAGGT
* * *
23390571 TGGTG-CTGTCGATCTGCTTCGCTGCCAGTACAGGAAGACAAG-TCTACTATCTTCAGTCTACTC
1 TGGTGTCT-TCGATCTACTTCGCTGCCAGTACAGGAAGGCAAGATATACTATCTTCAGTCTACTC
* *
23390634 CGCTGCAAACTCAAGGAGGTCAGGC
65 CACTGCAAACTCAAGGAGGTCAGAC
* * * *
23390659 TGGTGTCTTTGATCTACTTCACTGCCAGTACAGGAAGGCGAGATATACTATCTTCAGTCTGCTCC
1 TGGTGTCTTCGATCTACTTCGCTGCCAGTACAGGAAGGCAAGATATACTATCTTCAGTCTACTCC
* * * * *
23390724 ATTGTAAAGTTAGGGAGG-CAAGAC
66 ACTGCAAACTCAAGGAGGTC-AGAC
* * *
23390748 TTGTGTCTTCGATCTACTTTGCTGCCAGTATAGGAAGGCAAGAT
1 TGGTGTCTTCGATCTACTTCGCTGCCAGTACAGGAAGGCAAGAT
23390792 CTGCTATTTT
Statistics
Matches: 110, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
88 35 0.32
89 75 0.68
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.29
Consensus pattern (89 bp):
TGGTGTCTTCGATCTACTTCGCTGCCAGTACAGGAAGGCAAGATATACTATCTTCAGTCTACTCC
ACTGCAAACTCAAGGAGGTCAGAC
Found at i:23390807 original size:45 final size:45
Alignment explanation
Indices: 23390753--23391660 Score: 1160
Period size: 45 Copynumber: 20.0 Consensus size: 45
23390743 AAGACTTGTG
* * * *
23390753 TCTTCGATCTACTTTGCTGCCAGTATAGGAAGGCAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* *
23390798 TTTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * * *
23390843 TCTTCGATCTACTTTGCTGCCATTACAAGAAAACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * *
23390888 TCTTCGATCTACTTCACTGCCAGTACAGGAAGACTAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * * *
23390933 TCTTTGATCTACTTCGCTGCCAATACAGGAGGATAAGATTTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * *
23390978 TCTTCGATTTACTTCGCTGCCAGTATAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
*
23391023 TCTTCGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
*
23391068 TCTTCGATCTACTTTGCTGCCAATACAGGAAGACAAGATCTACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACA-G--G--AAG----ACAAGATCTGCTA
* *
23391122 TCTTCGATCTACTTCGCTGCCAATATAGAAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* *
23391167 TCTTTGATCTACTTCGCTACCAATACAGGAAGACAAGAT-TCGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCT-GCTA
*
23391212 TCTTCGATCTACTTCGCTTGCCAATACAGGAAGACAAAATCTGCTA
1 TCTTCGATCTACTTCGC-TGCCAATACAGGAAGACAAGATCTGCTA
* ** * * *** * * *
23391258 TTTTTAACCTACTCCGCTGCTGCT-CAGGGAGATAAG-GCTAG-TA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCT-GCTA
* *
23391301 TCTTCGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGTTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * *
23391346 TCTTCGATCTACTTCGCTACCAATACAGGAAGACATGATCTGTTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * * **
23391391 TCTTCAATCTATTTCGCTGTCTTTACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* *
23391436 TCTTCGATCTACTTCGCTGCCAATACAGGAAGATAAGATCTTCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * * *
23391481 TCTTTGATCTACTTTGCTGCCAATACAGGAAGATAAGATCTGTTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* *
23391526 TCTTCGATCTACTTCGCTGCCAATACAAGAAGACAAGATATGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
23391571 TCTTCGATCTACTTCGCTGCC-ATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
*
23391615 TCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
23391660 T
1 T
23391661 TTTTTTAACC
Statistics
Matches: 746, Mismatches: 100, Indels: 34
0.85 0.11 0.04
Matches are distributed among these distances:
43 20 0.03
44 63 0.08
45 579 0.78
46 37 0.05
47 1 0.00
48 1 0.00
49 3 0.00
50 3 0.00
53 1 0.00
54 38 0.05
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (45 bp):
TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
Found at i:23393742 original size:14 final size:14
Alignment explanation
Indices: 23393723--23393756 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
23393713 ATTTTTATTA
23393723 CTTTTTCTTC-GTAT
1 CTTTTT-TTCAGTAT
23393737 CTTTTTTTCAGTAT
1 CTTTTTTTCAGTAT
23393751 CTTTTT
1 CTTTTT
23393757 GGTACCGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.16
14 16 0.84
ACGTcount: A:0.09, C:0.18, G:0.06, T:0.68
Consensus pattern (14 bp):
CTTTTTTTCAGTAT
Found at i:23396670 original size:21 final size:21
Alignment explanation
Indices: 23396646--23396699 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
23396636 CAGCGGTGGT
*
23396646 GGTGAGATTAGTTATTGTAGC
1 GGTGAGATTAGATATTGTAGC
* * *
23396667 GGTGTGATTGGATATTGTAGT
1 GGTGAGATTAGATATTGTAGC
23396688 GGTGAGATTAGA
1 GGTGAGATTAGA
23396700 AACAGCGGTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.02, G:0.37, T:0.37
Consensus pattern (21 bp):
GGTGAGATTAGATATTGTAGC
Found at i:23399940 original size:22 final size:22
Alignment explanation
Indices: 23399898--23399941 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
23399888 ATTTTAAGTA
*
23399898 ATAATATTTCTAAATTATAATT
1 ATAATATTTCTAAAGTATAATT
*
23399920 ATAATTATTTTTAAAGT-TAATT
1 ATAA-TATTTCTAAAGTATAATT
23399942 TAAATGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
ATAATATTTCTAAAGTATAATT
Found at i:23401673 original size:3 final size:3
Alignment explanation
Indices: 23401665--23401694 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
23401655 TAGAAATAGA
23401665 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
23401695 TGTAATCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:23407492 original size:24 final size:26
Alignment explanation
Indices: 23407460--23407510 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 26
23407450 TATATGGGTC
23407460 TCACATATTTTTATTA-TACT-TAATT
1 TCACATATTTTTA-TACTACTATAATT
23407485 TCAC-TATTTTTATACTACTATAATT
1 TCACATATTTTTATACTACTATAATT
23407510 T
1 T
23407511 GTTTTTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 2 0.08
24 12 0.50
25 10 0.42
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (26 bp):
TCACATATTTTTATACTACTATAATT
Found at i:23407575 original size:16 final size:16
Alignment explanation
Indices: 23407554--23407591 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
23407544 TTTGGTTCGC
23407554 TGTAATGGAATACAGG
1 TGTAATGGAATACAGG
* *
23407570 TGTAATGTAATAGAGG
1 TGTAATGGAATACAGG
23407586 TGTAAT
1 TGTAAT
23407592 AGGTAATCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.37, C:0.03, G:0.29, T:0.32
Consensus pattern (16 bp):
TGTAATGGAATACAGG
Found at i:23407852 original size:18 final size:17
Alignment explanation
Indices: 23407825--23407941 Score: 59
Period size: 18 Copynumber: 7.0 Consensus size: 17
23407815 TTATTATTAA
23407825 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
*
23407842 ATATGAATTTACTAAAAT
1 ATAT-AATTTAATAAAAT
* * *
23407860 -CATAATAT-ATAATACT
1 ATATAATTTAATAA-AAT
* *
23407876 ATAAAATATAATTTAAAAT
1 ATATAATTTAA--TAAAAT
* *
23407895 A-ATTA-TT-AT-TAA-
1 ATATAATTTAATAAAAT
*
23407907 ATATAATTTAACAAAAAT
1 ATATAATTTAA-TAAAAT
23407925 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
23407942 TCTTAGTATT
Statistics
Matches: 72, Mismatches: 16, Indels: 24
0.64 0.14 0.21
Matches are distributed among these distances:
12 1 0.01
13 5 0.07
14 3 0.04
15 4 0.06
16 7 0.10
17 20 0.28
18 26 0.36
19 3 0.04
20 3 0.04
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.39
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:23407977 original size:120 final size:119
Alignment explanation
Indices: 23407841--23408078 Score: 449
Period size: 120 Copynumber: 2.0 Consensus size: 119
23407831 TTTAATAAAA
23407841 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
23407906 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
66 AATATAATTTAACAAAAATATATAATTTAAT-AAATTCTTAGTATTAAATATTCT
*
23407961 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTGAAATAATTATTATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
*
23408026 AATATAATTTAACATAAATATATAATTTAATAAATTCTTAGTATTAAATATTC
66 AATATAATTTAACAAAAATATATAATTTAATAAATTCTTAGTATTAAATATTC
23408079 GGGTTTTTTT
Statistics
Matches: 116, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
119 22 0.19
120 94 0.81
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (119 bp):
TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
AATATAATTTAACAAAAATATATAATTTAATAAATTCTTAGTATTAAATATTCT
Found at i:23408059 original size:59 final size:58
Alignment explanation
Indices: 23407863--23408051 Score: 195
Period size: 59 Copynumber: 3.2 Consensus size: 58
23407853 CTAAAATCAT
*
23407863 AATATATAATACTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAACAAA
1 AATATATAATACTATAAAATATAATTT-AAATAATTATTATTAAATATAATTTAACATA
* * * * * * * **
23407922 AATATATAAT-TTAATAAAATTCTTAGTATTAAAT-ATTCTTATATGAATTTACTAAAATCAT-
1 AATATATAATACT-ATAAAA-T-ATAAT-TTAAATAATTATTAT-TAAATATAATTTAA-CATA
23407983 AATATATAATACTATAAAATATAATTTGAAATAATTATTATTAAATATAATTTAACATA
1 AATATATAATACTATAAAATATAATTT-AAATAATTATTATTAAATATAATTTAACATA
23408042 AATATATAAT
1 AATATATAAT
23408052 TTAATAAATT
Statistics
Matches: 101, Mismatches: 19, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
58 6 0.06
59 42 0.42
60 16 0.16
61 32 0.32
62 5 0.05
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (58 bp):
AATATATAATACTATAAAATATAATTTAAATAATTATTATTAAATATAATTTAACATA
Found at i:23408144 original size:120 final size:119
Alignment explanation
Indices: 23407842--23408117 Score: 355
Period size: 120 Copynumber: 2.3 Consensus size: 119
23407832 TTAATAAAAT
* * * * *
23407842 ATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTAA
1 ATATGAATTTACTAAAA-CATAATATAAAAAAATAAAAAATATAATTTGAAATAATTATTATTAA
**
23407907 ATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCTT
65 ATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCGG
* * * *
23407962 ATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTGAAATAATTATTATTAA
1 ATATGAATTTACTAAAA-CATAATATAAAAAAATAAAAAATATAATTTGAAATAATTATTATTAA
*
23408027 ATATAATTTAACATAAATATATAATTTAAT-AAATTCTTAGTATTAAATATTCGG
65 ATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCGG
* ** *
23408081 GT-T-TTTTTAC-AAAA-ATATTATAAAAAAATAAAAAATA
1 ATATGAATTTACTAAAACATAATATAAAAAAATAAAAAATA
23408118 ACTAAAATGT
Statistics
Matches: 144, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
114 18 0.12
116 4 0.03
117 5 0.03
118 1 0.01
119 23 0.16
120 93 0.65
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (119 bp):
ATATGAATTTACTAAAACATAATATAAAAAAATAAAAAATATAATTTGAAATAATTATTATTAAA
TATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCGG
Found at i:23408293 original size:27 final size:27
Alignment explanation
Indices: 23408227--23408302 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
23408217 GCCTGATCAG
* *
23408227 GCCAATTAAATTGGCGGCACCAAAGGT
1 GCCAAATAAATTGGTGGCACCAAAGGT
*
23408254 GCCAAATAAATTGGTGGCACCAATGGT
1 GCCAAATAAATTGGTGGCACCAAAGGT
*
23408281 GCCAAAGT-CATTGGTGGCACCA
1 GCCAAA-TAAATTGGTGGCACCA
23408303 TGTTTGGCAC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 43 0.98
28 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (27 bp):
GCCAAATAAATTGGTGGCACCAAAGGT
Found at i:23408428 original size:19 final size:18
Alignment explanation
Indices: 23408401--23408470 Score: 79
Period size: 19 Copynumber: 3.8 Consensus size: 18
23408391 TAACTTATTT
*
23408401 TTTTTATTTAATAACTTTA
1 TTTTAATTTAATAAC-TTA
23408420 TTTTAATTTAATAAAC-TA
1 TTTTAATTTAAT-AACTTA
* *
23408438 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACT-TA
23408457 TTTTAATTTAATAA
1 TTTTAATTTAATAA
23408471 ACTATTAAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
17 3 0.07
18 12 0.28
19 25 0.58
20 3 0.07
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTAATTTAATAACTTA
Found at i:23408430 original size:37 final size:37
Alignment explanation
Indices: 23408406--23408476 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
23408396 TATTTTTTTT
*
23408406 ATTTAATAACTTTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
23408443 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
23408477 AAGTAATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:23408721 original size:19 final size:19
Alignment explanation
Indices: 23408694--23408763 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
23408684 TCAACTCAAT
*
23408694 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
23408713 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
23408731 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
23408750 TTTTAATTTAATAA
1 TTTTAATTTAATAA
23408764 AATATTAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:23408744 original size:37 final size:37
Alignment explanation
Indices: 23408699--23408769 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
23408689 TCAATTTTTT
*
23408699 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
23408736 ATTTAATAACTCTATTTTAATTTAATAAAATATT
1 ATTTAATAACTCTATTTTAATTTAATAAAATATT
23408770 AAGTAATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
Found at i:23409063 original size:17 final size:18
Alignment explanation
Indices: 23409035--23409107 Score: 105
Period size: 18 Copynumber: 4.1 Consensus size: 18
23409025 AGTATTATTT
23409035 AATAGTTTATTAAATTAA
1 AATAGTTTATTAAATTAA
*
23409053 AATAG-TTATTAAATGAA
1 AATAGTTTATTAAATTAA
23409070 AATAGTTTATTAAATTAA
1 AATAGTTTATTAAATTAA
*
23409088 AATAGAGTTATTAAA-TAA
1 AATAG-TTTATTAAATTAA
23409106 AA
1 AA
23409108 AAATGAGTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
17 16 0.32
18 26 0.52
19 8 0.16
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.38
Consensus pattern (18 bp):
AATAGTTTATTAAATTAA
Found at i:23409077 original size:35 final size:36
Alignment explanation
Indices: 23409035--23409108 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 36
23409025 AGTATTATTT
*
23409035 AATAGTTTATTAAATTAAAAT-AGTTATTAAATGAA
1 AATAGTTTATTAAATTAAAATAAGTTATTAAATAAA
23409070 AATAGTTTATTAAATTAAAATAGAGTTATTAAATAAA
1 AATAGTTTATTAAATTAAAATA-AGTTATTAAATAAA
23409107 AA
1 AA
23409109 AATGAGTTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 21 0.58
37 15 0.42
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (36 bp):
AATAGTTTATTAAATTAAAATAAGTTATTAAATAAA
Found at i:23409369 original size:37 final size:37
Alignment explanation
Indices: 23409327--23409397 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
23409317 AGTATTACTT
23409327 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
23409364 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
23409398 AAAAAAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.39
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:23409402 original size:19 final size:19
Alignment explanation
Indices: 23409333--23409401 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
23409323 ACTTAATAGT
23409333 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
23409352 TTATTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAG
23409370 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
23409389 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
23409402 AAATGAGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 20 0.47
19 23 0.53
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:23409498 original size:294 final size:294
Alignment explanation
Indices: 23408787--23409761 Score: 1582
Period size: 292 Copynumber: 3.3 Consensus size: 294
23408777 ACTTAATTTT
* *
23408787 TTAAATTAAAATAGGGTTATTAAATAAAAAATTGAGTTGAAGGGGAATAAAAAGAAAATAATAAA
1 TTAAATTAAAATAGAGTTATTAAATAAAAAAATGAGTTGAAGGGGAATAAAAAGAAAATAATAAA
*
23408852 TAAGGAGGGCTTAGAAGGCAATTAGCCACATTTCAATTTTAGTGCGCACAGCAACAGCAATTCAC
66 TAAGGAGGGCTTAGAAGGCAATTAGCCACATTTCAATTTTAGTGCGCACAGCAGCAGCAATTCAC
*
23408917 TTTCAAAATTTAAAATGGTAAATTTGCATGTCAGGTCCTTAAAACTGCAAATGGTCACTTAATTA
131 TTTCAAAATTCAAAATGGTAAATTTGCATGTCAGGTCCTTAAAACTGCAAATGGTCACTTAATTA
* * *
23408982 GAATTCTCTCATTTAATAACTCTATTTTAATTTAAAAAAATAAAGTATTATTTAATAGTTTATTA
196 GAATTCTCTCATTTAATAACTCTATTTTAATTTTAAAAAATTAAGTATTACTTAATAGTTTATTA
*
23409047 AATTAAAAT--AGTTATTAAATGAAAATAGTTTA
261 AATTAAAATAGAGTTATTAAATGAGAATAGTTTA
23409079 TTAAATTAAAATAGAGTTATTAAATAAAAAAATGAGTTGAAGGGGAATAAAAAGAAAATAATAAA
1 TTAAATTAAAATAGAGTTATTAAATAAAAAAATGAGTTGAAGGGGAATAAAAAGAAAATAATAAA
23409144 TAAGGAGGGCTTAGAAGGCAATTAGCCACATTTCAATTTTAGTGCGCACAGCAGCAGCAATTCAC
66 TAAGGAGGGCTTAGAAGGCAATTAGCCACATTTCAATTTTAGTGCGCACAGCAGCAGCAATTCAC
23409209 TTTCAAAATTCAAAATGGTAAATTTGCATGTCAGGTCCTTAAAACTGCAAATGGTCACTTAATTA
131 TTTCAAAATTCAAAATGGTAAATTTGCATGTCAGGTCCTTAAAACTGCAAATGGTCACTTAATTA
23409274 GAATTCTCTCATTTAATAACTCTATTTTAATTTTAAAAAATTAAGTATTACTTAATAGTTTATTA
196 GAATTCTCTCATTTAATAACTCTATTTTAATTTTAAAAAATTAAGTATTACTTAATAGTTTATTA
23409339 AATTAAAATAGAGTTATTAAATGAGAATAGTTTA
261 AATTAAAATAGAGTTATTAAATGAGAATAGTTTA
23409373 TTAAATTAAAATAGAGTTATTAAATAAAAAAATGAGTTGAAGGGGAATAAAAAGAAAATAATAAA
1 TTAAATTAAAATAGAGTTATTAAATAAAAAAATGAGTTGAAGGGGAATAAAAAGAAAATAATAAA
23409438 TAAGGAGGGCTTAGAAGGCAATTAGCCACATTTCAATTTTAGTGCGCACAGCAGCAGCAATTCAC
66 TAAGGAGGGCTTAGAAGGCAATTAGCCACATTTCAATTTTAGTGCGCACAGCAGCAGCAATTCAC
* * * *
23409503 TTTCAAAATTCAAAATGGTAAATTTCAAAATGGTAAATTTGCATGTTAGGTCTTTGAAACTGCAG
131 --T-----TTC---A----AAA-TTCAAAATGGTAAATTTGCATGTCAGGTCCTTAAAACTGCAA
*
23409568 ATGGTCACTTAATTAGAATTCTCTCATTTAATAACTCTATTTTAATTTAATAAAATATTAAG---
181 ATGGTCACTTAATTAGAATTCTCTCATTTAATAACTCTATTTTAATTT--TAAAAAATTAAGTAT
* *
23409630 TACTTAATATTTTATTATATTAAAATAGAGTTATTAAATGAGAATAGTTTA
244 TACTTAATAGTTTATTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
* * * *
23409681 TTAAATTAAAAAAGAGTTATTAAATAAAAAAATAAGTTAAAGGGAAATAAAAAGAAAATAATAAA
1 TTAAATTAAAATAGAGTTATTAAATAAAAAAATGAGTTGAAGGGGAATAAAAAGAAAATAATAAA
*
23409746 TAAGGAGGACTTAGAA
66 TAAGGAGGGCTTAGAA
23409762 AGTAATTACA
Statistics
Matches: 644, Mismatches: 20, Indels: 22
0.94 0.03 0.03
Matches are distributed among these distances:
292 262 0.41
294 152 0.24
296 1 0.00
301 3 0.00
304 1 0.00
308 128 0.20
309 86 0.13
311 11 0.02
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.32
Consensus pattern (294 bp):
TTAAATTAAAATAGAGTTATTAAATAAAAAAATGAGTTGAAGGGGAATAAAAAGAAAATAATAAA
TAAGGAGGGCTTAGAAGGCAATTAGCCACATTTCAATTTTAGTGCGCACAGCAGCAGCAATTCAC
TTTCAAAATTCAAAATGGTAAATTTGCATGTCAGGTCCTTAAAACTGCAAATGGTCACTTAATTA
GAATTCTCTCATTTAATAACTCTATTTTAATTTTAAAAAATTAAGTATTACTTAATAGTTTATTA
AATTAAAATAGAGTTATTAAATGAGAATAGTTTA
Found at i:23409531 original size:15 final size:15
Alignment explanation
Indices: 23409511--23409542 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
23409501 ACTTTCAAAA
23409511 TTCAAAATGGTAAAT
1 TTCAAAATGGTAAAT
23409526 TTCAAAATGGTAAAT
1 TTCAAAATGGTAAAT
23409541 TT
1 TT
23409543 GCATGTTAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (15 bp):
TTCAAAATGGTAAAT
Found at i:23409663 original size:19 final size:19
Alignment explanation
Indices: 23409641--23409709 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
23409631 ACTTAATATT
*
23409641 TTATTATATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
23409660 TTATTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAG
*
23409678 TTATTAAATTAAAAAAGAG
1 TTATTAAATTAAAATAGAG
23409697 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
23409710 AAATAAGTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
18 19 0.46
19 22 0.54
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:23409682 original size:37 final size:37
Alignment explanation
Indices: 23409635--23409705 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
23409625 TTAAGTACTT
* * *
23409635 AATATTTTATTATATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAAAAGAGTTATTAAATGAG
23409672 AATAGTTTATTAAATTAAAAAAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAAAAGAGTTATTAAAT
23409706 AAAAAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAAAAGAGTTATTAAATGAG
Found at i:23409710 original size:18 final size:18
Alignment explanation
Indices: 23409650--23409711 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
23409640 TTTATTATAT
*
23409650 TAAAATAGAGTTATTAAA
1 TAAAAAAGAGTTATTAAA
* * *
23409668 TGAGAATAG-TTTATTAAA
1 T-AAAAAAGAGTTATTAAA
23409686 TTAAAAAAGAGTTATTAAA
1 -TAAAAAAGAGTTATTAAA
23409705 TAAAAAA
1 TAAAAAA
23409712 ATAAGTTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
18 21 0.58
19 15 0.42
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.32
Consensus pattern (18 bp):
TAAAAAAGAGTTATTAAA
Found at i:23409718 original size:20 final size:19
Alignment explanation
Indices: 23409678--23409719 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
23409668 TGAGAATAGT
* *
23409678 TTATTAAATTAAAAAAGAG
1 TTATTAAATAAAAAAAAAG
23409697 TTATTAAATAAAAAAATAAG
1 TTATTAAATAAAAAAA-AAG
23409717 TTA
1 TTA
23409720 AAGGGAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (19 bp):
TTATTAAATAAAAAAAAAG
Found at i:23409820 original size:26 final size:27
Alignment explanation
Indices: 23409784--23409834 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
23409774 CTTTTTTTTC
*
23409784 CTTTGGCACCA-TGGTGCCGCCAATGA
1 CTTTGGCACCATTGGTGCCACCAATGA
23409810 CTTTGGCACCATTGGTGCCACCAAT
1 CTTTGGCACCATTGGTGCCACCAAT
23409835 TTAATTGGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.20, C:0.31, G:0.24, T:0.25
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCACCAATGA
Found at i:23409917 original size:23 final size:23
Alignment explanation
Indices: 23409891--23409935 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
23409881 GTTTTTTTTA
23409891 TATATTTTAGTAAATAAAAAAAC
1 TATATTTTAGTAAATAAAAAAAC
*
23409914 TATATTTTGGTAAATAAAAAAA
1 TATATTTTAGTAAATAAAAAAA
23409936 AGTTATAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (23 bp):
TATATTTTAGTAAATAAAAAAAC
Found at i:23423808 original size:21 final size:21
Alignment explanation
Indices: 23423781--23423835 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
23423771 ACAGCGGTAG
*
23423781 CAGTGAGATTAGTTACTGTAA
1 CAGTGAGATTAGATACTGTAA
* * *
23423802 CGGTGAGATTGGATACTGTAG
1 CAGTGAGATTAGATACTGTAA
23423823 CAGTGAGATTAGA
1 CAGTGAGATTAGA
23423836 AACAATGGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (21 bp):
CAGTGAGATTAGATACTGTAA
Found at i:23424779 original size:113 final size:113
Alignment explanation
Indices: 23424581--23424806 Score: 416
Period size: 113 Copynumber: 2.0 Consensus size: 113
23424571 CCATCTATGG
*
23424581 CCCCAATACAATCCTTTAAAATAAATACAAGTAATGAGATAAAGGTTAGAACTAATTTATATTTT
1 CCCCAATACAATCCTTTAAAATAAATACAAGTAATGAGATAAAGGTTAGAAATAATTTATATTTT
23424646 AAAAATATAAAGATTGTGTAAATTTCACCTTAAAGTGAGACCAATATC
66 AAAAATATAAAGATTGTGTAAATTTCACCTTAAAGTGAGACCAATATC
*
23424694 CCCCAATACAATCCTTTAAAATAAATACAAGTAATGAGATAAATGTTAGAAATAATTTATATTTT
1 CCCCAATACAATCCTTTAAAATAAATACAAGTAATGAGATAAAGGTTAGAAATAATTTATATTTT
* *
23424759 AAAAATATAAAGATTGTGTAAATTTTACCTTAAAGTGAGGCCAATATC
66 AAAAATATAAAGATTGTGTAAATTTCACCTTAAAGTGAGACCAATATC
23424807 TTGTATCATG
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 109 1.00
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (113 bp):
CCCCAATACAATCCTTTAAAATAAATACAAGTAATGAGATAAAGGTTAGAAATAATTTATATTTT
AAAAATATAAAGATTGTGTAAATTTCACCTTAAAGTGAGACCAATATC
Found at i:23425164 original size:113 final size:113
Alignment explanation
Indices: 23424966--23425191 Score: 416
Period size: 113 Copynumber: 2.0 Consensus size: 113
23424956 CCATCTATGG
*
23424966 CCCCAATACAATCCTTTAAAATAAATACAAGTAATGAGATAAAGGTTAGAACTAATTTATATTTT
1 CCCCAATACAATCCTTTAAAATAAATACAAGTAATGAGATAAAGGTTAGAAATAATTTATATTTT
23425031 AAAAATATAAAGATTGTGTAAATTTCACCTTAAAGTGAGACCAATATC
66 AAAAATATAAAGATTGTGTAAATTTCACCTTAAAGTGAGACCAATATC
*
23425079 CCCCAATACAATCCTTTAAAATAAATACAAGTAATGAGATAAATGTTAGAAATAATTTATATTTT
1 CCCCAATACAATCCTTTAAAATAAATACAAGTAATGAGATAAAGGTTAGAAATAATTTATATTTT
* *
23425144 AAAAATATAAAGATTGTGTAAATTTTACCTTAAAGTGAGGCCAATATC
66 AAAAATATAAAGATTGTGTAAATTTCACCTTAAAGTGAGACCAATATC
23425192 TTGTATCATG
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 109 1.00
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (113 bp):
CCCCAATACAATCCTTTAAAATAAATACAAGTAATGAGATAAAGGTTAGAAATAATTTATATTTT
AAAAATATAAAGATTGTGTAAATTTCACCTTAAAGTGAGACCAATATC
Found at i:23425253 original size:385 final size:385
Alignment explanation
Indices: 23424543--23425267 Score: 1450
Period size: 385 Copynumber: 1.9 Consensus size: 385
23424533 TTTGACAAGA
23424543 AAGCAAAATGTATGCTTTTATGTGTTTTCCATCTATGGCCCCAATACAATCCTTTAAAATAAATA
1 AAGCAAAATGTATGCTTTTATGTGTTTTCCATCTATGGCCCCAATACAATCCTTTAAAATAAATA
23424608 CAAGTAATGAGATAAAGGTTAGAACTAATTTATATTTTAAAAATATAAAGATTGTGTAAATTTCA
66 CAAGTAATGAGATAAAGGTTAGAACTAATTTATATTTTAAAAATATAAAGATTGTGTAAATTTCA
23424673 CCTTAAAGTGAGACCAATATCCCCCAATACAATCCTTTAAAATAAATACAAGTAATGAGATAAAT
131 CCTTAAAGTGAGACCAATATCCCCCAATACAATCCTTTAAAATAAATACAAGTAATGAGATAAAT
23424738 GTTAGAAATAATTTATATTTTAAAAATATAAAGATTGTGTAAATTTTACCTTAAAGTGAGGCCAA
196 GTTAGAAATAATTTATATTTTAAAAATATAAAGATTGTGTAAATTTTACCTTAAAGTGAGGCCAA
23424803 TATCTTGTATCATGTCGAACATGGTTCGGTATTTCCTCGAATTGACATTCAGTGGGTTTAATCGT
261 TATCTTGTATCATGTCGAACATGGTTCGGTATTTCCTCGAATTGACATTCAGTGGGTTTAATCGT
23424868 GTCTATTCTCATTCGAGCAAATATATGCAACATATCAGTAAAAATTCGACTAACAGTTTC
326 GTCTATTCTCATTCGAGCAAATATATGCAACATATCAGTAAAAATTCGACTAACAGTTTC
23424928 AAGCAAAATGTATGCTTTTATGTGTTTTCCATCTATGGCCCCAATACAATCCTTTAAAATAAATA
1 AAGCAAAATGTATGCTTTTATGTGTTTTCCATCTATGGCCCCAATACAATCCTTTAAAATAAATA
23424993 CAAGTAATGAGATAAAGGTTAGAACTAATTTATATTTTAAAAATATAAAGATTGTGTAAATTTCA
66 CAAGTAATGAGATAAAGGTTAGAACTAATTTATATTTTAAAAATATAAAGATTGTGTAAATTTCA
23425058 CCTTAAAGTGAGACCAATATCCCCCAATACAATCCTTTAAAATAAATACAAGTAATGAGATAAAT
131 CCTTAAAGTGAGACCAATATCCCCCAATACAATCCTTTAAAATAAATACAAGTAATGAGATAAAT
23425123 GTTAGAAATAATTTATATTTTAAAAATATAAAGATTGTGTAAATTTTACCTTAAAGTGAGGCCAA
196 GTTAGAAATAATTTATATTTTAAAAATATAAAGATTGTGTAAATTTTACCTTAAAGTGAGGCCAA
23425188 TATCTTGTATCATGTCGAACATGGTTCGGTATTTCCTCGAATTGACATTCAGTGGGTTTAATCGT
261 TATCTTGTATCATGTCGAACATGGTTCGGTATTTCCTCGAATTGACATTCAGTGGGTTTAATCGT
23425253 GTCTATTCTCATTCG
326 GTCTATTCTCATTCG
23425268 GACTAACAGT
Statistics
Matches: 340, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
385 340 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (385 bp):
AAGCAAAATGTATGCTTTTATGTGTTTTCCATCTATGGCCCCAATACAATCCTTTAAAATAAATA
CAAGTAATGAGATAAAGGTTAGAACTAATTTATATTTTAAAAATATAAAGATTGTGTAAATTTCA
CCTTAAAGTGAGACCAATATCCCCCAATACAATCCTTTAAAATAAATACAAGTAATGAGATAAAT
GTTAGAAATAATTTATATTTTAAAAATATAAAGATTGTGTAAATTTTACCTTAAAGTGAGGCCAA
TATCTTGTATCATGTCGAACATGGTTCGGTATTTCCTCGAATTGACATTCAGTGGGTTTAATCGT
GTCTATTCTCATTCGAGCAAATATATGCAACATATCAGTAAAAATTCGACTAACAGTTTC
Found at i:23434193 original size:44 final size:44
Alignment explanation
Indices: 23434099--23434216 Score: 123
Period size: 44 Copynumber: 2.7 Consensus size: 44
23434089 TAAATTGAGA
* ** *
23434099 AAGACCATAGTTGAAAGATATTATGGCATCATGATATAATGAGT
1 AAGACCATAGCTGAAAGACGTTATGGCATCATGATATAATGACT
* *
23434143 AAGACCATGGCTG-AAGACGTTATGGCATCATGGTA-AATAGGACT
1 AAGACCATAGCTGAAAGACGTTATGGCATCATGATATAAT--GACT
* * *
23434187 ATGACCATAGCTGAAAGACGCTATGACATC
1 AAGACCATAGCTGAAAGACGTTATGGCATC
23434217 CTTTGAAAGT
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
42 3 0.05
43 19 0.31
44 25 0.41
45 14 0.23
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (44 bp):
AAGACCATAGCTGAAAGACGTTATGGCATCATGATATAATGACT
Found at i:23434493 original size:27 final size:27
Alignment explanation
Indices: 23434436--23434508 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
23434426 CCTATGTGAT
* * ** * *
23434436 GTTAAATACAAGATAATCCGACGGGAT
1 GTTAAATACAGGATAGTCTAACGAGAC
23434463 GTTAAATACAGGATAGTCTAACGAGAC
1 GTTAAATACAGGATAGTCTAACGAGAC
* *
23434490 GTTAAATATAGGCTAGTCT
1 GTTAAATACAGGATAGTCT
23434509 GTGGAGACAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (27 bp):
GTTAAATACAGGATAGTCTAACGAGAC
Found at i:23437772 original size:44 final size:44
Alignment explanation
Indices: 23437678--23437795 Score: 123
Period size: 44 Copynumber: 2.7 Consensus size: 44
23437668 TAAATTGAGA
* ** *
23437678 AAGACCATAGTTGAAAGATATTATGGCATCATGATATAATGAGT
1 AAGACCATAGCTGAAAGACGTTATGGCATCATGATATAATGACT
* *
23437722 AAGACCATGGCTG-AAGACGTTATGGCATCATGGTA-AATAGGACT
1 AAGACCATAGCTGAAAGACGTTATGGCATCATGATATAAT--GACT
* * *
23437766 ATGACCATAGCTGAAAGACGCTATGACATC
1 AAGACCATAGCTGAAAGACGTTATGGCATC
23437796 CTTTGAAAGT
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
42 3 0.05
43 19 0.31
44 25 0.41
45 14 0.23
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (44 bp):
AAGACCATAGCTGAAAGACGTTATGGCATCATGATATAATGACT
Found at i:23438072 original size:27 final size:27
Alignment explanation
Indices: 23438015--23438087 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
23438005 CCTATGTGAT
* * ** * *
23438015 GTTAAATACAAGATAATCCGACGGGAT
1 GTTAAATACAGGATAGTCTAACGAGAC
23438042 GTTAAATACAGGATAGTCTAACGAGAC
1 GTTAAATACAGGATAGTCTAACGAGAC
* *
23438069 GTTAAATATAGGCTAGTCT
1 GTTAAATACAGGATAGTCT
23438088 GTGGAGACAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (27 bp):
GTTAAATACAGGATAGTCTAACGAGAC
Found at i:23439892 original size:87 final size:86
Alignment explanation
Indices: 23439796--23439960 Score: 233
Period size: 87 Copynumber: 1.9 Consensus size: 86
23439786 TTTTAAATTT
* *
23439796 GGTGAATTCATCAAGTCCGTCTCAATAGGACCACCCAAA-CTCTAGGATATGAACTCATTAAGAT
1 GGTGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACCT-TAGGATATGAACTCATTAAGAG
23439860 TAAGAAACTCAACCTCACATGTC
65 TAAGAAA-TCAACCTCACATGTC
* * * * *
23439883 GGTGAATTCATCAAGTCCATCTTAATAGGACCACGCAAACCTTGGGGTATGAATTCATTAAGAGT
1 GGTGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACCTTAGGATATGAACTCATTAAGAGT
*
23439948 AATAAATCAACCT
66 AAGAAATCAACCT
23439961 TATGCATGTA
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
86 7 0.10
87 60 0.87
88 2 0.03
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.25
Consensus pattern (86 bp):
GGTGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACCTTAGGATATGAACTCATTAAGAGT
AAGAAATCAACCTCACATGTC
Found at i:23443922 original size:90 final size:90
Alignment explanation
Indices: 23443825--23444103 Score: 423
Period size: 90 Copynumber: 3.1 Consensus size: 90
23443815 GCATATTGAA
* * *
23443825 TTGTATAAATATTTTCTTGATTTTCGATAGTATATCGTAACTTATACTAATTGAATTCGTTTGAT
1 TTGTATAAATATTTTCTTGATTTTCGATAGTATATCGTAACTTATATTGATTGAATTCATTTGAT
23443890 TGACCAAATTATGCAACTTGTATAT
66 TGACCAAATTATGCAACTTGTATAT
* *
23443915 TTGTATAAATATTTGCTTGATTTTCGATAGTATATAGTAACTTATATTGATTGAATTCATTTGAT
1 TTGTATAAATATTTTCTTGATTTTCGATAGTATATCGTAACTTATATTGATTGAATTCATTTGAT
* *
23443980 TGATCAGATTATGCAACTTGTATAT
66 TGACCAAATTATGCAACTTGTATAT
* *
23444005 TTGTATAAATATTTTCTTGATTTCCGATAGTATATCGTAACTTGATATTGATTGAATTCATATGA
1 TTGTATAAATATTTTCTTGATTTTCGATAGTATATCGTAACTT-ATATTGATTGAATTCATTTGA
* *** *
23444070 TTTAGTGAATTATGCAAGTTGTATAT
65 TTGACCAAATTATGCAACTTGTATAT
23444096 TTGTATAA
1 TTGTATAA
23444104 CTCACCATTG
Statistics
Matches: 171, Mismatches: 17, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
90 123 0.72
91 48 0.28
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (90 bp):
TTGTATAAATATTTTCTTGATTTTCGATAGTATATCGTAACTTATATTGATTGAATTCATTTGAT
TGACCAAATTATGCAACTTGTATAT
Found at i:23444026 original size:46 final size:46
Alignment explanation
Indices: 23443885--23444026 Score: 111
Period size: 46 Copynumber: 3.1 Consensus size: 46
23443875 TTGAATTCGT
* * *
23443885 TTGATTGACCAAATTATGCAACTTGTATATTTGTATAAATATTTGC
1 TTGATTGATCAGATTATGCAACTTGTATATTTGTATAAATATTTTC
* * **
23443931 TTGATTTTCGAT-AG-TATATAGTAAC-T-TATA-TTG-ATTGAAT-TCAT-
1 TTGA--TT-GATCAGAT-TAT-GCAACTTGTATATTTGTA-TAAATATTTTC
23443975 TTGATTGATCAGATTATGCAACTTGTATATTTGTATAAATATTTTC
1 TTGATTGATCAGATTATGCAACTTGTATATTTGTATAAATATTTTC
23444021 TTGATT
1 TTGATT
23444027 TCCGATAGTA
Statistics
Matches: 71, Mismatches: 11, Indels: 28
0.65 0.10 0.25
Matches are distributed among these distances:
41 7 0.10
42 8 0.11
43 5 0.07
44 11 0.15
45 5 0.07
46 17 0.24
47 5 0.07
48 7 0.10
49 6 0.08
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.47
Consensus pattern (46 bp):
TTGATTGATCAGATTATGCAACTTGTATATTTGTATAAATATTTTC
Found at i:23447528 original size:40 final size:40
Alignment explanation
Indices: 23447468--23447567 Score: 155
Period size: 40 Copynumber: 2.5 Consensus size: 40
23447458 CTATACTCTA
* * *
23447468 TGTTTGTCGTGTTTCAGTTGGATCAGCTCTTATGAGCTTC
1 TGTTTGGCGTGTTTCGGTTGGACCAGCTCTTATGAGCTTC
*
23447508 TGTTTGGCATGTTTCGGTTGGACCAGCTCTTATGAGCTTC
1 TGTTTGGCGTGTTTCGGTTGGACCAGCTCTTATGAGCTTC
*
23447548 TGTTTGGGGTGTTTCGGTTG
1 TGTTTGGCGTGTTTCGGTTG
23447568 ATTTGACGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.10, C:0.16, G:0.30, T:0.44
Consensus pattern (40 bp):
TGTTTGGCGTGTTTCGGTTGGACCAGCTCTTATGAGCTTC
Found at i:23450016 original size:12 final size:11
Alignment explanation
Indices: 23449994--23450034 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
23449984 AATTTCCTTG
23449994 AGCTTCTTTTC
1 AGCTTCTTTTC
23450005 AGCTTCCTTTTC
1 AGCTT-CTTTTC
23450017 AGC-TCTTTT-
1 AGCTTCTTTTC
*
23450026 AGCTGCTTT
1 AGCTTCTTT
23450035 GGCTGCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 3 0.11
10 9 0.33
11 6 0.22
12 9 0.33
ACGTcount: A:0.10, C:0.27, G:0.12, T:0.51
Consensus pattern (11 bp):
AGCTTCTTTTC
Found at i:23455299 original size:20 final size:18
Alignment explanation
Indices: 23455275--23455322 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 18
23455265 ATTTTTTCAT
*
23455275 AAAAAATTATTTATTTTTA
1 AAAAAATTACTT-TTTTTA
*
23455294 ATAAAAGTATACTTTTTTTA
1 A-AAAAAT-TACTTTTTTTA
23455314 AAAAAATTA
1 AAAAAATTA
23455323 AAAAAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
18 2 0.08
19 6 0.25
20 12 0.50
21 4 0.17
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
AAAAAATTACTTTTTTTA
Found at i:23488389 original size:88 final size:88
Alignment explanation
Indices: 23488236--23488809 Score: 806
Period size: 88 Copynumber: 6.5 Consensus size: 88
23488226 CAGTGAAGAG
* * * * * **
23488236 AGCAGATCTTACCTTTCTGCACTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCTCATTGGG
1 AGCAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGG
* * * *
23488301 TTGCAGCGGAACAGGTTAGAAAT
66 TTGCAGTGGAGCAGGCTAAAAAT
* *
23488324 AGCAGATCTTGCCTTCCTACACCGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGGG
1 AGCAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGG
* *
23488389 TTGCAGCGGAGCAGGCTAAAAAG
66 TTGCAGTGGAGCAGGCTAAAAAT
* * * * *
23488412 AGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATTGAAGATACCAACCTTGCCTCCCTGGG
1 AGCAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGG
* *
23488477 TTGCAGTGGAGTAGGTTAAAAAT
66 TTGCAGTGGAGCAGGCTAAAAAT
* * * *
23488500 AGCAGATCTTGCTTTCCTACACCGACAGTGAAGCAAATCGAAGACACCAGCCTTGCCTCACTGGG
1 AGCAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGG
*
23488565 TTGTAGTGGAGCAGGCTAAAAAT
66 TTGCAGTGGAGCAGGCTAAAAAT
* * * * * * * *
23488588 AGTAGATCTTGCATTCCTACACCGAAAGCGAAGCAGATCAAAGACACCAGCATTACCTCCCTGGG
1 AGCAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGG
23488653 TTGCAGTGGAGCAGGCTAAAAAT
66 TTGCAGTGGAGCAGGCTAAAAAT
* *
23488676 AGCAGATCTTGCCTTCCTGCACCGATAGTGAAGCAGATCGAAGACACCAGCCTTACCTCCCTGGG
1 AGCAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGG
23488741 TTGCAGTGGAGCAGGCTAAAAAT
66 TTGCAGTGGAGCAGGCTAAAAAT
*
23488764 AGCAGATCTTGCCTTCCTGCACCGATAGTGAAGCAGATCGAAGACA
1 AGCAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACA
23488810 TCTAGTTTTA
Statistics
Matches: 433, Mismatches: 53, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 433 1.00
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.21
Consensus pattern (88 bp):
AGCAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGG
TTGCAGTGGAGCAGGCTAAAAAT
Found at i:23488423 original size:44 final size:44
Alignment explanation
Indices: 23488375--23488517 Score: 135
Period size: 44 Copynumber: 3.2 Consensus size: 44
23488365 AGACACCAGC
* *
23488375 CTTGCCTTCCTGGGTTGCAGCGGAGCAGGCTAAAAAGAGCAGAT
1 CTTGCCTTCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
*** * * * * * *
23488419 CTTGCCTTCCTGCACTGACAGCGAAGCAGATTGAAGATACCA-AC
1 CTTGCCTTCCTGGGTTG-CAGCGGAGCAGGTTAAAAATAGCAGAT
* * *
23488463 CTTGCCTCCCTGGGTTGCAGTGGAGTAGGTTAAAAATAGCAGAT
1 CTTGCCTTCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
*
23488507 CTTGCTTTCCT
1 CTTGCCTTCCT
23488518 ACACCGACAG
Statistics
Matches: 72, Mismatches: 25, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
43 17 0.24
44 38 0.53
45 17 0.24
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.25
Consensus pattern (44 bp):
CTTGCCTTCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
Found at i:23488923 original size:45 final size:44
Alignment explanation
Indices: 23488817--23488934 Score: 150
Period size: 44 Copynumber: 2.7 Consensus size: 44
23488807 ACATCTAGTT
** *
23488817 TTATCCCCCTGAAGTTGCAGTGGAGCAGACTGAATAAGCAGGTC
1 TTATCCCCCTGAAGTTGCAGTGGAGCAGACCCAATAAGCAGATC
*
23488861 TTATCCCCCTGAAGTTGCAGTGGGGCAGACCCAA-AATGGC-GAATC
1 TTATCCCCCTGAAGTTGCAGTGGAGCAGACCCAATAA--GCAG-ATC
*
23488906 TTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 TTATCCCCCTGAAGTTGCAGTGGAGCAGA
23488935 TTTAAGCATA
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
43 2 0.03
44 32 0.49
45 31 0.48
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (44 bp):
TTATCCCCCTGAAGTTGCAGTGGAGCAGACCCAATAAGCAGATC
Found at i:23488999 original size:44 final size:44
Alignment explanation
Indices: 23488902--23489022 Score: 131
Period size: 44 Copynumber: 2.8 Consensus size: 44
23488892 CAAAATGGCG
* * * *
23488902 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTTAAGCATAT
1 AATCTTATCTCCCTGAAGTTGTAGTAGAGCAGATTTAAGAATAC
* * *
23488946 AATCCTATCTCCCTAAAGTTGTAGTAGAGCGGA-TTAA-AATCAC
1 AATCTTATCTCCCTGAAGTTGTAGTAGAGCAGATTTAAGAAT-AC
*
23488989 AGATCTTATCTCTCTGAAGTTGTAG-AGAGCAGAT
1 A-ATCTTATCTCCCTGAAGTTGTAGTAGAGCAGAT
23489023 CACATCTAGT
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
42 2 0.03
43 13 0.21
44 48 0.76
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGTAGTAGAGCAGATTTAAGAATAC
Found at i:23489272 original size:44 final size:44
Alignment explanation
Indices: 23489175--23489285 Score: 134
Period size: 44 Copynumber: 2.5 Consensus size: 44
23489165 GAAGATGGCG
* * *
23489175 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCACTGGAGCAGATTAAAACCAAT
* *
23489219 AATCCTATCTCCCTGAAGTTGCACTGGAGCAGATTAAAATCACA-
1 AATCTTATCTCCCTGAAGTTGCACTGGAGCAGATTAAAACCA-AT
* * *
23489263 GATCTTATCTCTCTAAAGTTGCA
1 AATCTTATCTCCCTGAAGTTGCA
23489286 GAGAGCAGAT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 56 0.98
45 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCACTGGAGCAGATTAAAACCAAT
Found at i:23489411 original size:45 final size:43
Alignment explanation
Indices: 23489304--23489510 Score: 189
Period size: 45 Copynumber: 4.7 Consensus size: 43
23489294 ATCGTATCTG
* * * * *
23489304 GTCTTATCTCTCTGAAGTTGTAGAGGAGTAGACTGAATAAGCA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTCAAAAAGCA
* * *
23489347 GGTCTTATCTCCCTAAAGTTGCAGTGGAGTAGACCCAAGAAAACGA
1 -GTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTCAA-AAAGC-A
*
23489393 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAATAAAGCAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTCAA-AAAGC-A
* * * * * *
23489438 GTCTTATCCCCCTGAAATTGCAGTGGGGCAGACTAAATAAAGAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTCAA-AAAGCA
* * * *
23489482 ATCCTATCTCCCTAAAGTTGTAGTGGAGT
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGT
23489511 GGATTAGAAT
Statistics
Matches: 134, Mismatches: 27, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
44 53 0.40
45 80 0.60
46 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (43 bp):
GTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTCAAAAAGCA
Found at i:23489490 original size:89 final size:89
Alignment explanation
Indices: 23489308--23489509 Score: 223
Period size: 89 Copynumber: 2.3 Consensus size: 89
23489298 TATCTGGTCT
* * * * * *
23489308 TATCTCTCTGAAGTTGTAGAGGAGTAGACTGAATAAGCAGGTCTTATCTCCCTAAAGTTGCAGTG
1 TATCTCCCTGAAGTTGTAGTGGAGCAGACTCAATAAGCAAGTCTTATCCCCCTAAAGTTGCAGTG
* * *
23489373 GAGTAGACCCAAGAAAACGAGTCT
66 GAGCAGACCCAAGAAAACGAATCC
*
23489397 TATCTCCCTGAAGTTGCAGTGGAGCAGACTCAATAAAGCAAGTCTTATCCCCCTGAAA-TTGCAG
1 TATCTCCCTGAAGTTGTAGTGGAGCAGACTCAAT-AAGCAAGTCTTATCCCCCT-AAAGTTGCAG
* *
23489461 TGGGGCAGA-CTAA-ATAAA-GAAATCC
64 TGGAGCAGACCCAAGA-AAACG-AATCC
*
23489486 TATCTCCCTAAAGTTGTAGTGGAG
1 TATCTCCCTGAAGTTGTAGTGGAG
23489510 TGGATTAGAA
Statistics
Matches: 95, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
88 2 0.02
89 60 0.63
90 30 0.32
91 3 0.03
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (89 bp):
TATCTCCCTGAAGTTGTAGTGGAGCAGACTCAATAAGCAAGTCTTATCCCCCTAAAGTTGCAGTG
GAGCAGACCCAAGAAAACGAATCC
Found at i:23490226 original size:5 final size:5
Alignment explanation
Indices: 23490216--23490241 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
23490206 ATATACTGAT
23490216 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
23490242 GTGAAAGACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:23504317 original size:17 final size:17
Alignment explanation
Indices: 23504295--23504352 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 17
23504285 ATGTAATAAC
23504295 TTTCATAAACATATGCT
1 TTTCATAAACATATGCT
*
23504312 TTTCAT-ATCATA---T
1 TTTCATAAACATATGCT
23504325 TTTCATATAACATATGCAT
1 TTTCATA-AACATATGC-T
*
23504344 TTCCATAAA
1 TTTCATAAA
23504353 AAATCATCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 11
0.70 0.07 0.24
Matches are distributed among these distances:
13 7 0.22
15 5 0.16
16 5 0.16
17 6 0.19
18 2 0.06
19 7 0.22
ACGTcount: A:0.36, C:0.17, G:0.03, T:0.43
Consensus pattern (17 bp):
TTTCATAAACATATGCT
Found at i:23504716 original size:25 final size:24
Alignment explanation
Indices: 23504682--23504733 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
23504672 AAGTTCAAGT
23504682 GAGCCATATCAGGAAGCTCACAAA
1 GAGCCATATCAGGAAGCTCACAAA
* *
23504706 GAGCCTATATCAGGATGCTCATAAA
1 GAGCC-ATATCAGGAAGCTCACAAA
23504731 GAG
1 GAG
23504734 TTGCGGTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.17
Consensus pattern (24 bp):
GAGCCATATCAGGAAGCTCACAAA
Found at i:23512197 original size:37 final size:38
Alignment explanation
Indices: 23512146--23512253 Score: 106
Period size: 37 Copynumber: 2.9 Consensus size: 38
23512136 ATTTCAAAAA
*
23512146 TAATA-TTATTTTAATAGTTTAATATTAAATTTAAT-T
1 TAATACTTATCTTAATAGTTTAATATTAAATTTAATAT
*
23512182 TAATACTTATCTTAATAGTATT-TTATT-AATTTAATAT
1 TAATACTTATCTTAATAGT-TTAATATTAAATTTAATAT
23512219 TAA-AGTCATTATCTTAAT-G-TTAA-ATTAAATTTAAT
1 TAATA--C-TTATCTTAATAGTTTAATATTAAATTTAAT
23512254 GTTTATCTTA
Statistics
Matches: 61, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
36 19 0.31
37 28 0.46
38 4 0.07
39 10 0.16
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (38 bp):
TAATACTTATCTTAATAGTTTAATATTAAATTTAATAT
Found at i:23513604 original size:23 final size:23
Alignment explanation
Indices: 23513578--23513638 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
23513568 TATGAAGTTT
*
23513578 TTGTGGTATATTCTGAAATGCCC
1 TTGTGGCATATTCTGAAATGCCC
*
23513601 TTGTGGCATATTCTGCAATG-CC
1 TTGTGGCATATTCTGAAATGCCC
23513623 TTG-GAGACATATTCTG
1 TTGTG-G-CATATTCTG
23513639 TAACTCTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 1 0.03
22 6 0.18
23 27 0.79
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (23 bp):
TTGTGGCATATTCTGAAATGCCC
Found at i:23513672 original size:23 final size:23
Alignment explanation
Indices: 23513585--23513674 Score: 83
Period size: 23 Copynumber: 3.9 Consensus size: 23
23513575 TTTTTGTGGT
* * *
23513585 ATATTCTGAAATGCCCTTGTGGC
1 ATATTCTGCAATGCCTTTGTGAC
* *
23513608 ATATTCTGCAATGCCTTGGAGAC
1 ATATTCTGCAATGCCTTTGTGAC
* *
23513631 ATATTCTGTAACT-CTTTTGTGAC
1 ATATTCTGCAA-TGCCTTTGTGAC
* *
23513654 GTATTCTGCAATGTCTTTGTG
1 ATATTCTGCAATGCCTTTGTG
23513675 GTAAGTTTTG
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
22 1 0.02
23 50 0.96
24 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (23 bp):
ATATTCTGCAATGCCTTTGTGAC
Found at i:23518504 original size:41 final size:41
Alignment explanation
Indices: 23518367--23518496 Score: 152
Period size: 41 Copynumber: 3.2 Consensus size: 41
23518357 GGCTTTATGT
* * * * *
23518367 CGGTGATTTATATCAGGCTCTGAGCCTAACAGGTTTCATGC
1 CGGTGAATTATATCAGGCTTTGAGCCTAGCAGGCTTCGTGC
* * * *
23518408 CGGTGAATTACATCAAGCCTTGAGCCTAGCAGGCTTTGTGC
1 CGGTGAATTATATCAGGCTTTGAGCCTAGCAGGCTTCGTGC
* * *
23518449 CGCTGTATTATATCAGGCTTTGAGCCTAGCAAGCTTCGTGC
1 CGGTGAATTATATCAGGCTTTGAGCCTAGCAGGCTTCGTGC
23518490 CGGTGAA
1 CGGTGAA
23518497 CTGTATCATG
Statistics
Matches: 71, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (41 bp):
CGGTGAATTATATCAGGCTTTGAGCCTAGCAGGCTTCGTGC
Found at i:23519584 original size:21 final size:21
Alignment explanation
Indices: 23519555--23519596 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
23519545 CGGTCTGAGA
* *
23519555 ACACAGGTGTTTGGAGTAGCC
1 ACACAGGTGTGTGGAATAGCC
*
23519576 ACACGGGTGTGTGGAATAGCC
1 ACACAGGTGTGTGGAATAGCC
23519597 GCATAACCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (21 bp):
ACACAGGTGTGTGGAATAGCC
Found at i:23525924 original size:12 final size:12
Alignment explanation
Indices: 23525907--23525936 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
23525897 TAGGCAACTT
*
23525907 TTTTTTTTGCGG
1 TTTTTTTTGCGC
23525919 TTTTTTTTGCGC
1 TTTTTTTTGCGC
23525931 TTTTTT
1 TTTTTT
23525937 GCTTCTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.10, G:0.17, T:0.73
Consensus pattern (12 bp):
TTTTTTTTGCGC
Found at i:23526899 original size:20 final size:20
Alignment explanation
Indices: 23526874--23526918 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
23526864 TAATCACCCT
23526874 TTAAACCTATCCAAAACACA
1 TTAAACCTATCCAAAACACA
**
23526894 TTAAACCTATCCTTAACACA
1 TTAAACCTATCCAAAACACA
23526914 TTAAA
1 TTAAA
23526919 ACATGCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (20 bp):
TTAAACCTATCCAAAACACA
Found at i:23527760 original size:40 final size:41
Alignment explanation
Indices: 23527716--23527828 Score: 149
Period size: 40 Copynumber: 2.8 Consensus size: 41
23527706 ATTCATCTAA
*
23527716 CTATTTTCATATAACCAATTCATATAATCATTCCATAT-AT
1 CTATTTTCATATAATCAATTCATATAATCATTCCATATAAT
* ***
23527756 CTATTTCCATATAATCAATTCATATAATCATTTTTTATAAT
1 CTATTTTCATATAATCAATTCATATAATCATTCCATATAAT
*
23527797 C-ATTTTCCATATAATCGATTCATATAATCATT
1 CTATTTT-CATATAATCAATTCATATAATCATT
23527829 TTTCACATAG
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
40 37 0.58
41 27 0.42
ACGTcount: A:0.36, C:0.18, G:0.01, T:0.45
Consensus pattern (41 bp):
CTATTTTCATATAATCAATTCATATAATCATTCCATATAAT
Found at i:23527783 original size:13 final size:13
Alignment explanation
Indices: 23527721--23527826 Score: 90
Period size: 13 Copynumber: 7.9 Consensus size: 13
23527711 TCTAACTATT
*
23527721 TTCATATAACCAA
1 TTCATATAATCAA
23527734 TTCATATAATC-A
1 TTCATATAATCAA
*
23527746 TTCCATAT-ATCTAT
1 TT-CATATAATC-AA
23527760 TTCCATATAATCAA
1 TT-CATATAATCAA
*
23527774 TTCATATAATCAT
1 TTCATATAATCAA
** *
23527787 TTTTTATAATCATT
1 TTCATATAATCA-A
*
23527801 TTCCATATAATCGA
1 TT-CATATAATCAA
23527815 TTCATATAATCA
1 TTCATATAATCA
23527827 TTTTTCACAT
Statistics
Matches: 76, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
12 6 0.08
13 44 0.58
14 16 0.21
15 10 0.13
ACGTcount: A:0.38, C:0.18, G:0.01, T:0.43
Consensus pattern (13 bp):
TTCATATAATCAA
Found at i:23527811 original size:28 final size:28
Alignment explanation
Indices: 23527718--23527857 Score: 105
Period size: 28 Copynumber: 5.1 Consensus size: 28
23527708 TCATCTAACT
* *
23527718 ATTTT-CATATAACCAATTCATATAATC
1 ATTTTCCATATAATCGATTCATATAATC
*
23527745 A--TTCCATAT-ATCTATTTCCATATAATC
1 ATTTTCCATATAATCGA-TT-CATATAATC
* **
23527772 A-ATT-CATATAATC-ATTTTTTATAATC
1 ATTTTCCATATAATCGA-TTCATATAATC
23527798 ATTTTCCATATAATCGATTCATATAATC
1 ATTTTCCATATAATCGATTCATATAATC
* * * * *
23527826 ATTTTTCACATAGTTGATTCATATAAAC
1 ATTTTCCATATAATCGATTCATATAATC
23527854 ATTT
1 ATTT
23527858 GAAATATTCA
Statistics
Matches: 93, Mismatches: 12, Indels: 15
0.77 0.10 0.12
Matches are distributed among these distances:
25 5 0.05
26 15 0.16
27 22 0.24
28 50 0.54
29 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.02, T:0.45
Consensus pattern (28 bp):
ATTTTCCATATAATCGATTCATATAATC
Found at i:23527818 original size:41 final size:40
Alignment explanation
Indices: 23527718--23527831 Score: 151
Period size: 41 Copynumber: 2.9 Consensus size: 40
23527708 TCATCTAACT
* ***
23527718 ATTTT-CATATAACCAATTCATATAATCATTCCATATATC
1 ATTTTCCATATAATCAATTCATATAATCATTTTTTATATC
23527757 -TATTTCCATATAATCAATTCATATAATCATTTTTTATAATC
1 AT-TTTCCATATAATCAATTCATATAATCATTTTTTAT-ATC
*
23527798 ATTTTCCATATAATCGATTCATATAATCATTTTT
1 ATTTTCCATATAATCAATTCATATAATCATTTTT
23527832 CACATAGTTG
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 3 0.05
40 27 0.41
41 34 0.52
42 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.01, T:0.46
Consensus pattern (40 bp):
ATTTTCCATATAATCAATTCATATAATCATTTTTTATATC
Found at i:23529379 original size:35 final size:35
Alignment explanation
Indices: 23529327--23529393 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
23529317 ACTTGATGCC
* *
23529327 ATAGTGTCTTTCAACTATTATCTTACTCATTTTCT
1 ATAGTGCCTTTCAACTATGATCTTACTCATTTTCT
* *
23529362 ATAGTGCCTTT-ATACTATGGTCTTATTCATTT
1 ATAGTGCCTTTCA-ACTATGATCTTACTCATTT
23529394 CCATCATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 1 0.04
35 26 0.96
ACGTcount: A:0.22, C:0.18, G:0.09, T:0.51
Consensus pattern (35 bp):
ATAGTGCCTTTCAACTATGATCTTACTCATTTTCT
Found at i:23529454 original size:45 final size:45
Alignment explanation
Indices: 23529413--23529522 Score: 114
Period size: 45 Copynumber: 2.4 Consensus size: 45
23529403 TTCCATAGTT
*
23529413 TCTTTC-ACATATGATCTTACACGTTTAAATCGTGATGCCATAGCG
1 TCTTTCAAC-TATGATCTTACACGTTTAAATCATGATGCCATAGCG
* * * * * *
23529458 TCTTTCAACTATGGTTTTACTCGTTTGATTCATGATGCCATAACG
1 TCTTTCAACTATGATCTTACACGTTTAAATCATGATGCCATAGCG
* * *
23529503 TCTTTCGACCATGGTCTTAC
1 TCTTTCAACTATGATCTTAC
23529523 TCGTATTTCA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 52 0.96
46 2 0.04
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (45 bp):
TCTTTCAACTATGATCTTACACGTTTAAATCATGATGCCATAGCG
Found at i:23529523 original size:45 final size:45
Alignment explanation
Indices: 23529427--23529526 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 45
23529417 TCACATATGA
* * * *
23529427 TCTTACACGTTTAAATCGTGATGCCATAGCGTCTTTCAACTATGG
1 TCTTACTCGTTTAAATCATGATGCCATAACGTCTTTCAACCATGG
* * * *
23529472 TTTTACTCGTTTGATTCATGATGCCATAACGTCTTTCGACCATGG
1 TCTTACTCGTTTAAATCATGATGCCATAACGTCTTTCAACCATGG
23529517 TCTTACTCGT
1 TCTTACTCGT
23529527 ATTTCAACCA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (45 bp):
TCTTACTCGTTTAAATCATGATGCCATAACGTCTTTCAACCATGG
Found at i:23530314 original size:15 final size:15
Alignment explanation
Indices: 23530291--23530322 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
23530281 TCAATTAGGC
23530291 TTTTGTTTTGTTTAA
1 TTTTGTTTTGTTTAA
*
23530306 TTTTTTTTTGTTTAA
1 TTTTGTTTTGTTTAA
23530321 TT
1 TT
23530323 ATCAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (15 bp):
TTTTGTTTTGTTTAA
Found at i:23531057 original size:27 final size:27
Alignment explanation
Indices: 23531019--23531073 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
23531009 ATTTTCAAAC
23531019 ATAACCTTTAATTTACTTAACATTACA
1 ATAACCTTTAATTTACTTAACATTACA
23531046 ATAACCTTTAATTTACTTAACATTACA
1 ATAACCTTTAATTTACTTAACATTACA
23531073 A
1 A
23531074 CTTAGTCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (27 bp):
ATAACCTTTAATTTACTTAACATTACA
Found at i:23533852 original size:22 final size:23
Alignment explanation
Indices: 23533827--23533884 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
23533817 TACCAATAGT
*
23533827 AATAATAAAATAAAGATAAAT-A
1 AATAATAAAATAAAGAGAAATAA
*
23533849 AATAA-ATAAATAACGAGAAATAA
1 AATAATA-AAATAAAGAGAAATAA
23533872 AATAATAAAATAA
1 AATAATAAAATAA
23533885 TAAAATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 1 0.03
22 17 0.55
23 12 0.39
24 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (23 bp):
AATAATAAAATAAAGAGAAATAA
Found at i:23533878 original size:8 final size:8
Alignment explanation
Indices: 23533867--23533891 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
23533857 AATAACGAGA
23533867 AATAAAAT
1 AATAAAAT
23533875 AATAAAAT
1 AATAAAAT
23533883 AATAAAAT
1 AATAAAAT
23533891 A
1 A
23533892 TATCAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:23539002 original size:26 final size:26
Alignment explanation
Indices: 23538949--23539030 Score: 78
Period size: 26 Copynumber: 3.2 Consensus size: 26
23538939 GCACACCGCA
* *
23538949 GCTC-TTATGAGCGTCCCG-TTATATG
1 GCTCTTTATGAGCTTCCCGATTA-AAG
* *
23538974 GCTCTTTGTGGGCTTCCCGATTAAAG
1 GCTCTTTATGAGCTTCCCGATTAAAG
* * *
23539000 GCTCCTTATGAGCTTCCTGATTAATG
1 GCTCTTTATGAGCTTCCCGATTAAAG
23539026 GCTCT
1 GCTCT
23539031 CCAGAGCTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
25 4 0.09
26 38 0.84
27 3 0.07
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (26 bp):
GCTCTTTATGAGCTTCCCGATTAAAG
Found at i:23541654 original size:43 final size:40
Alignment explanation
Indices: 23541588--23541699 Score: 109
Period size: 41 Copynumber: 2.7 Consensus size: 40
23541578 AACTCGTACA
* * * *
23541588 ATGCCATATCCCGGATATGGTCTTACATGTTAATGCATAT-TG
1 ATGCCATGTCCCAGATATGGTCTTACACG--AAT-CATATACG
* *
23541630 ATGCCACTGTCCCAGATAGGGTCTTATACGAATCATATACG
1 ATGCCA-TGTCCCAGATATGGTCTTACACGAATCATATACG
*
23541671 ATGCCAATGTCCCAGACATGGTCTTACAC
1 ATGCC-ATGTCCCAGATATGGTCTTACAC
23541700 ATTTTCTTAC
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
40 5 0.09
41 28 0.48
42 7 0.12
43 18 0.31
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (40 bp):
ATGCCATGTCCCAGATATGGTCTTACACGAATCATATACG
Found at i:23542242 original size:184 final size:184
Alignment explanation
Indices: 23541916--23542430 Score: 744
Period size: 184 Copynumber: 2.8 Consensus size: 184
23541906 TTAGCAATGA
* * * * * *
23541916 ATATCAATATATCC-AACAATTCGGTACTGTATAACCATTCATGAATCAAGATCGGCAATATATA
1 ATATCCATATA-CCAAACAATTCGGCAATGTATAACCATACACGAATCAAGATCGACAATATATA
*
23541980 ATCATACACAAATCAAATTCGACATCCTATATTCATAAAAAATTCACTATCAACAATATATAACC
65 ATCATACACAAATCAAATTCGACATCCTATATTCATAAAAAATTCACTATCGACAATATATAACC
*
23542045 AAGTACGAATTAATTTCAGTAATGTACAACCTTGTACGAATCAAGTCAGCAACTT
130 AAGTACAAATTAATTTCAGTAATGTACAACCTTGTACGAATCAAGTCAGCAACTT
* *
23542100 ATATCCATATACCAAACAATTTGGCAATGTATAACCATAAACGAATCAAGATCGACAATATATAA
1 ATATCCATATACCAAACAATTCGGCAATGTATAACCATACACGAATCAAGATCGACAATATATAA
* * *
23542165 TCATACACAAATTAAATTCGACATCCTATATTCATAAACAATTCACTATCGGCAATATATAACCA
66 TCATACACAAATCAAATTCGACATCCTATATTCATAAAAAATTCACTATCGACAATATATAACCA
* *
23542230 AGTACAAATTAATTTTAGTAATGTACAACCTTGTACGAATCAATTCAGCAACTT
131 AGTACAAATTAATTTCAGTAATGTACAACCTTGTACGAATCAAGTCAGCAACTT
* * * * *
23542284 ATATCCATATAACAAACAATTCGGCAATGTATAACCATACACAAATCAAGTTCGATAATGTATAA
1 ATATCCATATACCAAACAATTCGGCAATGTATAACCATACACGAATCAAGATCGACAATATATAA
* * * * * * * *
23542349 TCAAATACAAATCCAATTCGGCATCCTATATACATAAAGAATTCAATATCGAAAATATATAACCA
66 TCATACACAAATCAAATTCGACATCCTATATTCATAAAAAATTCACTATCGACAATATATAACCA
* *
23542414 TGTACAATTTAATTTCA
131 AGTACAAATTAATTTCA
23542431 ACAAGGTAAA
Statistics
Matches: 295, Mismatches: 35, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
183 2 0.01
184 293 0.99
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (184 bp):
ATATCCATATACCAAACAATTCGGCAATGTATAACCATACACGAATCAAGATCGACAATATATAA
TCATACACAAATCAAATTCGACATCCTATATTCATAAAAAATTCACTATCGACAATATATAACCA
AGTACAAATTAATTTCAGTAATGTACAACCTTGTACGAATCAAGTCAGCAACTT
Found at i:23542317 original size:91 final size:91
Alignment explanation
Indices: 23542033--23542320 Score: 260
Period size: 91 Copynumber: 3.1 Consensus size: 91
23542023 TCACTATCAA
* *
23542033 CAATATATAACCAAGTACGAATTAATTTCAGTAATGTACAACCTTGTACGAATCAAGTCAGCAAC
1 CAATATATAACCAAGTACGAATTAATTTTAGTAATGTACAACCTTGTACGAATCAATTCAGCAAC
* *
23542098 TTATATCCATATACCAAACAATTTGG
66 TTATATCCATATAACAAACAATTCGG
* * * ** * * * * * * ** * *
23542124 CAATGTATAACCATA-AACGAATCAA-GATCGACAATATATAATCATACACAAATTAAATTC-GA
1 CAATATATAACCA-AGTACGAATTAATTTTAG-TAATGTACAACCTTGTACGAA-TCAATTCAG-
* * * * *
23542186 CATCCTATATTCATA-AACAATTCACTATCGG
62 CAACTTATATCCATATAACAA-ACAAT-TCGG
*
23542217 CAATATATAACCAAGTACAAATTAATTTTAGTAATGTACAACCTTGTACGAATCAATTCAGCAAC
1 CAATATATAACCAAGTACGAATTAATTTTAGTAATGTACAACCTTGTACGAATCAATTCAGCAAC
23542282 TTATATCCATATAACAAACAATTCGG
66 TTATATCCATATAACAAACAATTCGG
*
23542308 CAATGTATAACCA
1 CAATATATAACCA
23542321 TACACAAATC
Statistics
Matches: 141, Mismatches: 46, Indels: 20
0.68 0.22 0.10
Matches are distributed among these distances:
90 1 0.01
91 54 0.38
92 43 0.30
93 41 0.29
94 2 0.01
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (91 bp):
CAATATATAACCAAGTACGAATTAATTTTAGTAATGTACAACCTTGTACGAATCAATTCAGCAAC
TTATATCCATATAACAAACAATTCGG
Found at i:23542322 original size:30 final size:30
Alignment explanation
Indices: 23542099--23542371 Score: 115
Period size: 31 Copynumber: 8.9 Consensus size: 30
23542089 GTCAGCAACT
* *
23542099 TATATCCATATACCAAA-CAATTTGGCAATG
1 TATAACCATATA-CAAATCAATTCGGCAATG
* * * * *
23542129 TATAACCATAAACGAATCAAGATCGACAATA
1 TATAACCATATACAAATCAA-TTCGGCAATG
* * * * *
23542160 TATAATCATACACAAATTAAATTCGAC-ATCC
1 TATAACCATATACAAA-TCAATTCGGCAAT-G
** * * * *
23542191 TATATTCATAAACAATTCACTATCGGCAATA
1 TATAACCATATACAAATCAAT-TCGGCAATG
* ** *
23542222 TATAACCA-AGTACAAATTAATTTTAGTAATG
1 TATAACCATA-TACAAATCAA-TTCGGCAATG
* * * * *
23542253 TACAACCTTGTACGAATCAATTCAGCAACT-
1 TATAACCATATACAAATCAATTCGGCAA-TG
*
23542283 TATATCCATATAACAAA-CAATTCGGCAATG
1 TATAACCATAT-ACAAATCAATTCGGCAATG
* **
23542313 TATAACCATACACAAATCAAGTTCGATAATG
1 TATAACCATATACAAATCAA-TTCGGCAATG
* *
23542344 TATAATCAAATACAAATCCAATTCGGCA
1 TATAACCATATACAAAT-CAATTCGGCA
23542372 TCCTATATAC
Statistics
Matches: 176, Mismatches: 52, Indels: 29
0.68 0.20 0.11
Matches are distributed among these distances:
29 9 0.05
30 54 0.31
31 104 0.59
32 9 0.05
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (30 bp):
TATAACCATATACAAATCAATTCGGCAATG
Found at i:23550310 original size:22 final size:22
Alignment explanation
Indices: 23550277--23550319 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
23550267 CAATGCCTAT
*
23550277 TTACAGTTTAAT-ATAAAAAAC
1 TTACAGTCTAATAATAAAAAAC
23550298 TTACTAGTCTAATAATAAAAAA
1 TTAC-AGTCTAATAATAAAAAA
23550320 ATTAAAAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 7 0.37
23 8 0.42
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (22 bp):
TTACAGTCTAATAATAAAAAAC
Found at i:23554416 original size:13 final size:13
Alignment explanation
Indices: 23554398--23554422 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23554388 AGTAATAATA
23554398 AAATAAATAAATC
1 AAATAAATAAATC
23554411 AAATAAATAAAT
1 AAATAAATAAAT
23554423 TACGAGAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAATAAATC
Found at i:23555193 original size:20 final size:20
Alignment explanation
Indices: 23555170--23555213 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
23555160 TGAGGCGTAC
23555170 TCTTATCTTGTTTTACTCTT
1 TCTTATCTTGTTTTACTCTT
*
23555190 TCTTATCTTGTTTTACTGTT
1 TCTTATCTTGTTTTACTCTT
23555210 TCTT
1 TCTT
23555214 CTACTAAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.09, C:0.18, G:0.07, T:0.66
Consensus pattern (20 bp):
TCTTATCTTGTTTTACTCTT
Found at i:23566220 original size:18 final size:18
Alignment explanation
Indices: 23566197--23566234 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
23566187 TGTTAGTGGA
*
23566197 AGATCGGAAGGTCCCGCT
1 AGATCGGAAGATCCCGCT
*
23566215 AGATCGGAAGATCCTGCT
1 AGATCGGAAGATCCCGCT
23566233 AG
1 AG
23566235 GGTAGTGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.24, G:0.32, T:0.18
Consensus pattern (18 bp):
AGATCGGAAGATCCCGCT
Found at i:23574150 original size:16 final size:17
Alignment explanation
Indices: 23574129--23574166 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
23574119 TTCTTTAGGG
*
23574129 ATTTTACT-TTTATTTT
1 ATTTTACTATATATTTT
23574145 ATTTTACTACTATATTTT
1 ATTTTACTA-TATATTTT
23574163 ATTT
1 ATTT
23574167 AAATAAGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTACTATATATTTT
Found at i:23580415 original size:3 final size:3
Alignment explanation
Indices: 23580407--23580439 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
23580397 TCACACCAGG
23580407 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
23580440 AATTTTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:23580818 original size:25 final size:26
Alignment explanation
Indices: 23580774--23580827 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
23580764 AAGTGGAAAT
*
23580774 AAAAAAAGAAAATAGGTGAAACAGAA
1 AAAAAAAGAAAACAGGTGAAACAGAA
* *
23580800 AAAAAAAG-AAACAGTTGAAATAGAA
1 AAAAAAAGAAAACAGGTGAAACAGAA
23580825 AAA
1 AAA
23580828 TAAATAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 17 0.68
26 8 0.32
ACGTcount: A:0.70, C:0.04, G:0.17, T:0.09
Consensus pattern (26 bp):
AAAAAAAGAAAACAGGTGAAACAGAA
Found at i:23580949 original size:13 final size:12
Alignment explanation
Indices: 23580916--23580942 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
23580906 TGTATCTGTC
23580916 AAATCTTAATTT
1 AAATCTTAATTT
23580928 AAATCTTAATTT
1 AAATCTTAATTT
23580940 AAA
1 AAA
23580943 ATATTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (12 bp):
AAATCTTAATTT
Found at i:23581032 original size:39 final size:39
Alignment explanation
Indices: 23580980--23581055 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
23580970 AAAAATAAAG
* *
23580980 GGGAAGCTTGTGACTGGCAACACCTATAAATTTTTTTAA
1 GGGAAGCCTGTGACTAGCAACACCTATAAATTTTTTTAA
*
23581019 GGGAAGCCTGTGACTAGCGACACCTATAAATTTTTTT
1 GGGAAGCCTGTGACTAGCAACACCTATAAATTTTTTT
23581056 CTTTCTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (39 bp):
GGGAAGCCTGTGACTAGCAACACCTATAAATTTTTTTAA
Found at i:23581428 original size:21 final size:20
Alignment explanation
Indices: 23581391--23581430 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
23581381 TTTCTTAGTC
*
23581391 TCATTTTAACTCTGTTTAGA
1 TCATTTTAACTCAGTTTAGA
*
23581411 TCATTTGTAGCTCAGTTTAG
1 TCATTT-TAACTCAGTTTAG
23581431 TTGTGATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.47
Consensus pattern (20 bp):
TCATTTTAACTCAGTTTAGA
Found at i:23583162 original size:18 final size:18
Alignment explanation
Indices: 23583139--23583174 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
23583129 TAAAAGGCAT
23583139 GACAACTTTGAAGCTTGG
1 GACAACTTTGAAGCTTGG
23583157 GACAACTTTGAAGCTTGG
1 GACAACTTTGAAGCTTGG
23583175 TTTGGACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (18 bp):
GACAACTTTGAAGCTTGG
Found at i:23586014 original size:26 final size:25
Alignment explanation
Indices: 23585960--23586026 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
23585950 GACACACCGC
23585960 AGCTCTT-ATGAGCTTCTCGGTTAT
1 AGCTCTTGATGAGCTTCTCGGTTAT
* *
23585984 GGCTCTTGATGAGCTT-TCTGTTAATT
1 AGCTCTTGATGAGCTTCTCGGTT-A-T
23586010 AGCTCTTTG-TGAGCTTC
1 AGCTC-TTGATGAGCTTC
23586027 CCGATATAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
24 11 0.31
25 9 0.26
26 12 0.34
27 3 0.09
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.43
Consensus pattern (25 bp):
AGCTCTTGATGAGCTTCTCGGTTAT
Found at i:23590572 original size:21 final size:20
Alignment explanation
Indices: 23590530--23590573 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
23590520 TACTTTACAC
**
23590530 AAATTAATAAATTCCATATA
1 AAATTAATAAATTAAATATA
*
23590550 AAATATAATAAATTAAATTTA
1 AAAT-TAATAAATTAAATATA
23590571 AAA
1 AAA
23590574 AATTAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATTAATAAATTAAATATA
Found at i:23590593 original size:15 final size:14
Alignment explanation
Indices: 23590559--23590589 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
23590549 AAAATATAAT
23590559 AAATTAAATTTAAA
1 AAATTAAATTTAAA
23590573 AAATTAAATTTAAA
1 AAATTAAATTTAAA
23590587 AAA
1 AAA
23590590 ATTATTAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATTAAATTTAAA
Found at i:23591240 original size:24 final size:24
Alignment explanation
Indices: 23591212--23591263 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
23591202 TTAGTAAGTC
* *
23591212 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
23591236 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
23591260 AAAT
1 AAAT
23591264 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:23604074 original size:36 final size:35
Alignment explanation
Indices: 23603950--23604076 Score: 96
Period size: 36 Copynumber: 3.6 Consensus size: 35
23603940 ATGTATGTGA
* *
23603950 TTGTCAGTTTATCCGACTAACGCTGGGCGCAAATCT
1 TTGTCAGTTTATCCGACTAGCGCTAGG-GCAAATCT
* * * * *
23603986 TTGTCAATTTTTTCGATTA-CTGC-AGGGCACATCT
1 TTGTCAGTTTATCCGACTAGC-GCTAGGGCAAATCT
* * *
23604020 ACTATCGGTTTATCCGACTAGCGCTAGGTGCAAATCT
1 -TTGTCAGTTTATCCGACTAGCGCTAGG-GCAAATCT
* *
23604057 TTGTCGGTTTATTCGACTAG
1 TTGTCAGTTTATCCGACTAG
23604077 TGTTGGGCAC
Statistics
Matches: 69, Mismatches: 17, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
34 7 0.10
35 17 0.25
36 38 0.55
37 7 0.10
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.35
Consensus pattern (35 bp):
TTGTCAGTTTATCCGACTAGCGCTAGGGCAAATCT
Found at i:23604108 original size:40 final size:37
Alignment explanation
Indices: 23604057--23604164 Score: 119
Period size: 36 Copynumber: 2.9 Consensus size: 37
23604047 GTGCAAATCT
* *
23604057 TTGTCGGTTTATTCGACTAGTGTTGGGCACACATTTAACA
1 TTGTTGGTTTATTCGACTAGTGCTGGGCACACA---AACA
*
23604097 TTGTTGGTTTATTCGACTAGCGCTGGGCACA-AAACA
1 TTGTTGGTTTATTCGACTAGTGCTGGGCACACAAACA
* * * *
23604133 TTTTTGGTTTATCCGGCTAGTGCAGGGCACAC
1 TTGTTGGTTTATTCGACTAGTGCTGGGCACAC
23604165 CTATCGTCGG
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
36 30 0.51
39 1 0.02
40 28 0.47
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.34
Consensus pattern (37 bp):
TTGTTGGTTTATTCGACTAGTGCTGGGCACACAAACA
Found at i:23604140 original size:36 final size:36
Alignment explanation
Indices: 23604026--23604202 Score: 108
Period size: 36 Copynumber: 4.8 Consensus size: 36
23604016 ATCTACTATC
* ** * *
23604026 GGTTTATCCGACTAGCGCTAGGTGCAAATC-TTTGTC
1 GGTTTATCCGACTAGCGCTGGGCACAAAACATTT-TT
* * * *
23604062 GGTTTATTCGACTAGTGTTGGGCACACATTTAACATTGTT
1 GGTTTATCCGACTAGCGCTGGGCACA-A---AACATTTTT
*
23604102 GGTTTATTCGACTAGCGCTGGGCACAAAACATTTTT
1 GGTTTATCCGACTAGCGCTGGGCACAAAACATTTTT
* * * * ** *
23604138 GGTTTATCCGGCTAGTGCAGGGCAC--ACCTATCGTC
1 GGTTTATCCGACTAGCGCTGGGCACAAAAC-ATTTTT
* *
23604173 GGTTTATCCAACTAGCGCTGGGCGCAAAAC
1 GGTTTATCCGACTAGCGCTGGGCACAAAAC
23604203 TTGATTACGG
Statistics
Matches: 107, Mismatches: 26, Indels: 15
0.72 0.18 0.10
Matches are distributed among these distances:
34 2 0.02
35 23 0.21
36 49 0.46
37 3 0.03
39 1 0.01
40 27 0.25
41 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (36 bp):
GGTTTATCCGACTAGCGCTGGGCACAAAACATTTTT
Found at i:23605773 original size:21 final size:19
Alignment explanation
Indices: 23605731--23605773 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
23605721 AGGGACTTAA
23605731 TTAAATAAAATATAAAAGT
1 TTAAATAAAATATAAAAGT
* *
23605750 TTAAGATAATAATGTAAAATT
1 TTAA-ATAA-AATATAAAAGT
23605771 TTA
1 TTA
23605774 TTAAATGGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 4 0.20
21 12 0.60
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (19 bp):
TTAAATAAAATATAAAAGT
Found at i:23606495 original size:95 final size:95
Alignment explanation
Indices: 23606282--23606576 Score: 308
Period size: 95 Copynumber: 3.1 Consensus size: 95
23606272 GTACCGGTGG
* * * *
23606282 TGGATATCTTACTGATGGATAAGATCATGCATATATTGCGGATT-TTGCACAGCTAGTGTGAGCA
1 TGGATATCTTACCGATGGATAAGATCCTGCATATATTGCGGATTCTT-CACAGCTAGTGTAAGTA
* * *
23606346 ACATCGT-TATCGATTAATGTCCCGATTTAC
65 GCATCGTGTAACGATTAATGTCTCGATTTAC
* * * * * * *
23606376 TAGATACCTTATCGATGGCTAAGATCCTGCATATATTGTGGATTCTTCATAGCTCGTGTAAGTAG
1 TGGATATCTTACCGATGGATAAGATCCTGCATATATTGCGGATTCTTCACAGCTAGTGTAAGTAG
* *
23606441 CATTGTGTAAC-AGTTAATGTCTCGATTTAT
66 CATCGTGTAACGA-TTAATGTCTCGATTTAC
* * * * * * * * *
23606471 TGGATATCTTGCCAATGGATAAGATTCTGTATGTGTTGCAGATTCTTCACAGCTTGTGTAAATAG
1 TGGATATCTTACCGATGGATAAGATCCTGCATATATTGCGGATTCTTCACAGCTAGTGTAAGTAG
*
23606536 CATCGTGTAACGATTAACGTCTCGATTTAC
66 CATCGTGTAACGATTAATGTCTCGATTTAC
*
23606566 TGGATACCTTA
1 TGGATATCTTA
23606577 AATGTTCGGG
Statistics
Matches: 161, Mismatches: 36, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
94 56 0.35
95 104 0.65
96 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.36
Consensus pattern (95 bp):
TGGATATCTTACCGATGGATAAGATCCTGCATATATTGCGGATTCTTCACAGCTAGTGTAAGTAG
CATCGTGTAACGATTAATGTCTCGATTTAC
Found at i:23612511 original size:14 final size:16
Alignment explanation
Indices: 23612487--23612518 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
23612477 AAGATGATAT
23612487 GTTGAATTATAT-TTG
1 GTTGAATTATATCTTG
23612502 GTTG-ATTATATCTTG
1 GTTGAATTATATCTTG
23612517 GT
1 GT
23612519 ATGTGAATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.22, C:0.03, G:0.22, T:0.53
Consensus pattern (16 bp):
GTTGAATTATATCTTG
Found at i:23614682 original size:28 final size:28
Alignment explanation
Indices: 23614642--23614696 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
23614632 ATAATGTATG
*
23614642 GATAAATTTGATGGCTGTAGATTAACGT
1 GATAAATTTGATGGCTATAGATTAACGT
23614670 GATAAATTTGATGGCTATAGATTAACG
1 GATAAATTTGATGGCTATAGATTAACG
23614697 CAGATGATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.07, G:0.24, T:0.35
Consensus pattern (28 bp):
GATAAATTTGATGGCTATAGATTAACGT
Found at i:23615499 original size:11 final size:11
Alignment explanation
Indices: 23615483--23615527 Score: 72
Period size: 11 Copynumber: 4.1 Consensus size: 11
23615473 ATTAATCCTT
23615483 TCTCAATTTCC
1 TCTCAATTTCC
23615494 TCTCAATTTCC
1 TCTCAATTTCC
* *
23615505 TCTCAAATTGC
1 TCTCAATTTCC
23615516 TCTCAATTTCC
1 TCTCAATTTCC
23615527 T
1 T
23615528 TCCAAATTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.20, C:0.33, G:0.02, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:23615518 original size:22 final size:22
Alignment explanation
Indices: 23615483--23615543 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
23615473 ATTAATCCTT
*
23615483 TCTCAATTTCCTCTCAATTTCC
1 TCTCAAATTCCTCTCAATTTCC
*
23615505 TCTCAAATTGCTCTCAATTTCC
1 TCTCAAATTCCTCTCAATTTCC
*
23615527 T-TCCAAATTTCTCTCAA
1 TCT-CAAATTCCTCTCAA
23615544 ATCCATATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.23, C:0.33, G:0.02, T:0.43
Consensus pattern (22 bp):
TCTCAAATTCCTCTCAATTTCC
Found at i:23615525 original size:33 final size:33
Alignment explanation
Indices: 23615483--23615545 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
23615473 ATTAATCCTT
23615483 TCTCAATTTCC-TCTC-AATTTCCTCTCAAATTGC
1 TCTCAATTTCCTTC-CAAATTT-CTCTCAAATTGC
23615516 TCTCAATTTCCTTCCAAATTTCTCTCAAAT
1 TCTCAATTTCCTTCCAAATTTCTCTCAAAT
23615546 CCATATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 21 0.75
34 7 0.25
ACGTcount: A:0.24, C:0.32, G:0.02, T:0.43
Consensus pattern (33 bp):
TCTCAATTTCCTTCCAAATTTCTCTCAAATTGC
Found at i:23615561 original size:51 final size:51
Alignment explanation
Indices: 23615505--23615604 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 51
23615495 CTCAATTTCC
23615505 TCTCAAATTGCTCTCAA-TTTC-CTTCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAAATTGCTCTCAATTTTCTCTT--AAATTTCTCTCAAATCCATATTTAA
* * *
23615556 TCTCAACTTGCTCTCAATTTTCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAAATTGCTCTCAATTTTCTCTTAAATTTCTCTCAAATCCATATTT
23615605 TTAATTATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
51 37 0.84
52 4 0.09
53 3 0.07
ACGTcount: A:0.26, C:0.27, G:0.02, T:0.45
Consensus pattern (51 bp):
TCTCAAATTGCTCTCAATTTTCTCTTAAATTTCTCTCAAATCCATATTTAA
Found at i:23616753 original size:7 final size:7
Alignment explanation
Indices: 23616741--23616773 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
23616731 TAGTCGATTG
23616741 GTATTTA
1 GTATTTA
23616748 GTATTTA
1 GTATTTA
23616755 GTATTTA
1 GTATTTA
23616762 GTATTTA
1 GTATTTA
23616769 GTATT
1 GTATT
23616774 ATGTATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:23619737 original size:38 final size:39
Alignment explanation
Indices: 23619653--23619795 Score: 227
Period size: 38 Copynumber: 3.7 Consensus size: 39
23619643 ACCAAAAATT
*
23619653 TATTTTAAAAATAAAAAAATAAAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTAAAAAAT-AAAAAAAAGTATTTTAAAAA
23619694 TATTTTAAAATTAAAAAATAAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAATAAAAAAAAGTATTTTAAAAA
23619733 -ATTTTAAAATTAAAAAAT-AAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAATAAAAAAAAGTATTTTAAAAA
* *
23619770 TGTTTTAAAATTTAAAAATAAAAAAA
1 TATTTTAAAATTAAAAAATAAAAAAA
23619796 TAAATTTATT
Statistics
Matches: 97, Mismatches: 3, Indels: 6
0.92 0.03 0.06
Matches are distributed among these distances:
37 19 0.20
38 34 0.35
39 26 0.27
40 12 0.12
41 6 0.06
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (39 bp):
TATTTTAAAATTAAAAAATAAAAAAAAGTATTTTAAAAA
Done.