Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 53 of 292
Found at i:15420030 original size:28 final size:28
Alignment explanation
Indices: 15419988--15420062 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 28
15419978 TGGCCTATTT
* *
15419988 AGGCCCAATCTCATTCATATGGCCCATC
1 AGGCCCAAACACATTCATATGGCCCATC
* *
15420016 AGGCCTAAACACATTCATATGGCCCGTC
1 AGGCCCAAACACATTCATATGGCCCATC
*
15420044 AGGCCCAAGCACATTCATA
1 AGGCCCAAACACATTCATA
15420063 GTCATGCAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.21
Consensus pattern (28 bp):
AGGCCCAAACACATTCATATGGCCCATC
Found at i:15421865 original size:43 final size:43
Alignment explanation
Indices: 15421774--15421873 Score: 114
Period size: 43 Copynumber: 2.3 Consensus size: 43
15421764 ATATCCCGGA
* ** * *
15421774 TATGGTCTTACATATTATCACATATCGATGCCAATAGCCCAGC
1 TATGGTCTTACACAAAATCAAATAGCGATGCCAATAGCCCAGC
*
15421817 TATGGTCTTACACAAAATCAAATAGCGATGCCAAT-GTCCTAGAC
1 TATGGTCTTACACAAAATCAAATAGCGATGCCAATAG-CCCAG-C
15421861 -ATGGTCTTACACA
1 TATGGTCTTACACA
15421874 TAGTCATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
42 1 0.02
43 47 0.96
44 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (43 bp):
TATGGTCTTACACAAAATCAAATAGCGATGCCAATAGCCCAGC
Found at i:15440711 original size:26 final size:23
Alignment explanation
Indices: 15440652--15440718 Score: 62
Period size: 26 Copynumber: 2.7 Consensus size: 23
15440642 TATTACATGC
*
15440652 CTCTTTGTGAGCATTCCTGATATG
1 CTCTTTGTGAGC-TTCCTGATAAG
*
15440676 CTCTTCGTGAGCTTCCTGATTAAAAG
1 CTCTTTGTGAGCTTCCTGA-T--AAG
* *
15440702 TTCTTTGTGAACTTCCT
1 CTCTTTGTGAGCTTCCT
15440719 ATTTTAAACT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 7 0.20
24 12 0.34
26 16 0.46
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (23 bp):
CTCTTTGTGAGCTTCCTGATAAG
Found at i:15442552 original size:26 final size:24
Alignment explanation
Indices: 15442522--15442611 Score: 96
Period size: 26 Copynumber: 3.7 Consensus size: 24
15442512 AGACTCACCA
15442522 CAGCTCGTATGAGCTTACTGATATAT
1 CAGCTCGTATGAGCTTACTGAT-T-T
*
15442548 CAGCTCGTAAGAGCTTACT-ATTTT
1 CAGCTCGTATGAGCTTACTGA-TTT
* *
15442572 CAGCTCAT-TGGAGCTTACCG-TTT
1 CAGCTCGTAT-GAGCTTACTGATTT
15442595 CAGCTCGTATGAGCTTA
1 CAGCTCGTATGAGCTTA
15442612 GTATTCAGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
23 17 0.31
24 17 0.31
25 2 0.04
26 19 0.35
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.34
Consensus pattern (24 bp):
CAGCTCGTATGAGCTTACTGATTT
Found at i:15442861 original size:20 final size:20
Alignment explanation
Indices: 15442838--15442914 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
15442828 GTGTTTATAT
*
15442838 GGATGAATTACTGTTAATAC
1 GGATGAACTACTGTTAATAC
* * *
15442858 GGATGAATTACTTTTATTAC
1 GGATGAACTACTGTTAATAC
* * * *
15442878 CGATGAACAACTATTTATAC
1 GGATGAACTACTGTTAATAC
15442898 GGATGAACTACTAGTTA
1 GGATGAACTACT-GTTA
15442915 TATGAATAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (20 bp):
GGATGAACTACTGTTAATAC
Found at i:15444622 original size:18 final size:18
Alignment explanation
Indices: 15444596--15444630 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
15444586 ATATATTAAG
15444596 CCAAGTACCCAACCCAAC
1 CCAAGTACCCAACCCAAC
*
15444614 CCAATTACCCAACCCAA
1 CCAAGTACCCAACCCAA
15444631 TCATAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.49, G:0.03, T:0.09
Consensus pattern (18 bp):
CCAAGTACCCAACCCAAC
Found at i:15444623 original size:13 final size:13
Alignment explanation
Indices: 15444607--15444631 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15444597 CAAGTACCCA
15444607 ACCCAACCCAATT
1 ACCCAACCCAATT
15444620 ACCCAACCCAAT
1 ACCCAACCCAAT
15444632 CATAAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:15444697 original size:20 final size:20
Alignment explanation
Indices: 15444659--15444697 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
15444649 ATTTAATAAA
**
15444659 TAAAAATAAAAATCTAAAAC
1 TAAAAATAAAAATAAAAAAC
*
15444679 TAAAACTAAAAATAAAAAA
1 TAAAAATAAAAATAAAAAA
15444698 ACATATAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAAAC
Found at i:15444731 original size:9 final size:9
Alignment explanation
Indices: 15444717--15444793 Score: 57
Period size: 9 Copynumber: 8.6 Consensus size: 9
15444707 TTTATACAAA
15444717 TAATTCGAT
1 TAATTCGAT
15444726 TAATTCGAT
1 TAATTCGAT
* **
15444735 TAATTTGGG
1 TAATTCGAT
* *
15444744 TAATTTGGT
1 TAATTCGAT
* *
15444753 CAATTTGAT
1 TAATTCGAT
*
15444762 TAATTCGGT
1 TAATTCGAT
15444771 TAATTC-AGT
1 TAATTCGA-T
*
15444780 TAATTCGGT
1 TAATTCGAT
15444789 TAATT
1 TAATT
15444794 TTATACTTAT
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
9 55 1.00
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.47
Consensus pattern (9 bp):
TAATTCGAT
Found at i:15444747 original size:18 final size:18
Alignment explanation
Indices: 15444725--15444794 Score: 77
Period size: 18 Copynumber: 3.9 Consensus size: 18
15444715 AATAATTCGA
*
15444725 TTAATTCGATTAATTTGG
1 TTAATTCGGTTAATTTGG
* * * *
15444743 GTAATTTGGTCAATTTGA
1 TTAATTCGGTTAATTTGG
**
15444761 TTAATTCGGTTAATTCAG
1 TTAATTCGGTTAATTTGG
15444779 TTAATTCGGTTAATTT
1 TTAATTCGGTTAATTT
15444795 TATACTTATT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.49
Consensus pattern (18 bp):
TTAATTCGGTTAATTTGG
Found at i:15444757 original size:27 final size:27
Alignment explanation
Indices: 15444727--15444794 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
15444717 TAATTCGATT
**
15444727 AATTCGATTAATTTGGGTAATTTGGTC
1 AATTCGATTAATTTGGGTAATTCAGTC
* * * *
15444754 AATTTGATTAATTCGGTTAATTCAGTT
1 AATTCGATTAATTTGGGTAATTCAGTC
*
15444781 AATTCGGTTAATTT
1 AATTCGATTAATTT
15444795 TATACTTATT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.28, C:0.07, G:0.18, T:0.47
Consensus pattern (27 bp):
AATTCGATTAATTTGGGTAATTCAGTC
Found at i:15444784 original size:36 final size:36
Alignment explanation
Indices: 15444718--15444794 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
15444708 TTATACAAAT
* ** *
15444718 AATTCGATTAATTCGATTAATTTGGGTAATTTGGTC
1 AATTTGATTAATTCGATTAATTCAGGTAATTCGGTC
* * *
15444754 AATTTGATTAATTCGGTTAATTCAGTTAATTCGGTT
1 AATTTGATTAATTCGATTAATTCAGGTAATTCGGTC
15444790 AATTT
1 AATTT
15444795 TATACTTATT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.47
Consensus pattern (36 bp):
AATTTGATTAATTCGATTAATTCAGGTAATTCGGTC
Found at i:15445656 original size:376 final size:376
Alignment explanation
Indices: 15444963--15445712 Score: 1464
Period size: 376 Copynumber: 2.0 Consensus size: 376
15444953 GTTAATTCAA
*
15444963 TTAAGATAAAGCTTCAGATTAGTCAACTTTGTTTCTACGCCTTTATTGTCGAGGTAAGTTTGTGT
1 TTAAGATAAAGCTTCAGATTAGTCAACTTTGTTTCTACGCCTTTATTATCGAGGTAAGTTTGTGT
15445028 TATTTTATAATGTTTTAATGCTATCTTTTGAGCTATAGGTAAATTGTGGATTGTTATGTAAATAA
66 TATTTTATAATGTTTTAATGCTATCTTTTGAGCTATAGGTAAATTGTGGATTGTTATGTAAATAA
15445093 TTAATGCAAATCCAACGACGTTACGAAAACTATCGAGCCCCGTTAGAACTTTAGGAATTCGTAGG
131 TTAATGCAAATCCAACGACGTTACGAAAACTATCGAGCCCCGTTAGAACTTTAGGAATTCGTAGG
*
15445158 ATACAAATGACATGTCATTAAGGTTTTCATGTTTCAGGTGCTGGTCTTGAATGTCTTACCGATGG
196 ATACAAATGACATGTCATTAAGGTTTTCATGTTTCAGGTGCTGGTCTTGAATGTCCTACCGATGG
*
15445223 CTGAGGTCCAGCATGTGTTGTGGATACTTCACAGCTCGTGTAAGCAGCATCGTGTAGCTTACATT
261 CTGAGGTCCAACATGTGTTGTGGATACTTCACAGCTCGTGTAAGCAGCATCGTGTAGCTTACATT
15445288 CCGACCCACAACTCATGTGAGCAGGCCCAATTCACAGCTCATGTAACATAG
326 CCGACCCACAACTCATGTGAGCAGGCCCAATTCACAGCTCATGTAACATAG
15445339 TTAAGATAAAGCTTCAGATTAGTCAACTTTGTTTCTACGCCTTTATTATCGAGGTAAGTTTGTGT
1 TTAAGATAAAGCTTCAGATTAGTCAACTTTGTTTCTACGCCTTTATTATCGAGGTAAGTTTGTGT
15445404 TATTTTATAATGTTTTAATGCTATCTTTTGAGCTATAGGTAAATTGTGGATTGTTATGTAAATAA
66 TATTTTATAATGTTTTAATGCTATCTTTTGAGCTATAGGTAAATTGTGGATTGTTATGTAAATAA
15445469 TTAATGCAAATCCAACGACGTTACGAAAACTATCGAGCCCCGTTAGAACTTTAGGAATTCGTAGG
131 TTAATGCAAATCCAACGACGTTACGAAAACTATCGAGCCCCGTTAGAACTTTAGGAATTCGTAGG
15445534 ATACAAATGACATGTCATTAAGGTTTTCATGTTTCAGGTGCTGGTCTTGAATGTCCTACCGATGG
196 ATACAAATGACATGTCATTAAGGTTTTCATGTTTCAGGTGCTGGTCTTGAATGTCCTACCGATGG
*
15445599 CTGAGGTCCAACATGTGTTGTGGATACTTCACAGCTCGTGTGAGCAGCATCGTGTAGCTTACATT
261 CTGAGGTCCAACATGTGTTGTGGATACTTCACAGCTCGTGTAAGCAGCATCGTGTAGCTTACATT
15445664 CCGACCCACAACTCATGTGAGCAGGCCCAATTCACAGCTCATGTAACAT
326 CCGACCCACAACTCATGTGAGCAGGCCCAATTCACAGCTCATGTAACAT
15445713 CCCGAATTAG
Statistics
Matches: 370, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
376 370 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (376 bp):
TTAAGATAAAGCTTCAGATTAGTCAACTTTGTTTCTACGCCTTTATTATCGAGGTAAGTTTGTGT
TATTTTATAATGTTTTAATGCTATCTTTTGAGCTATAGGTAAATTGTGGATTGTTATGTAAATAA
TTAATGCAAATCCAACGACGTTACGAAAACTATCGAGCCCCGTTAGAACTTTAGGAATTCGTAGG
ATACAAATGACATGTCATTAAGGTTTTCATGTTTCAGGTGCTGGTCTTGAATGTCCTACCGATGG
CTGAGGTCCAACATGTGTTGTGGATACTTCACAGCTCGTGTAAGCAGCATCGTGTAGCTTACATT
CCGACCCACAACTCATGTGAGCAGGCCCAATTCACAGCTCATGTAACATAG
Found at i:15447805 original size:28 final size:28
Alignment explanation
Indices: 15447736--15447836 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
15447726 GACAAGATTG
* * * *
15447736 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
15447766 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
15447794 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
15447823 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
15447837 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:15452281 original size:46 final size:45
Alignment explanation
Indices: 15452231--15452401 Score: 170
Period size: 46 Copynumber: 3.7 Consensus size: 45
15452221 TTGAGCATCT
*
15452231 GAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTTC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATGTCC
* * * *
15452277 GAACTCGTTGAGTTGAGTCCAAGTTC-GTGA-GATG-TAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGATGCGAA-T--G--TCC
* *
15452324 GAACTCGTTGA-TTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATGTCC
* *
15452369 GAGCTCGTTGAGTTGAGTTCGAGTTCACTTAGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTAGG
15452402 GGCGGGTTAC
Statistics
Matches: 102, Mismatches: 13, Indels: 21
0.75 0.10 0.15
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 17 0.17
46 56 0.55
47 16 0.16
49 4 0.04
50 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (45 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGATGCGAATGTCC
Found at i:15454813 original size:18 final size:20
Alignment explanation
Indices: 15454786--15454827 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
15454776 TATAGACTCA
15454786 ATATAAAAC-TAAACAT-AT
1 ATATAAAACTTAAACATCAT
* *
15454804 ATATATAACTTAATCATCAT
1 ATATAAAACTTAAACATCAT
15454824 ATAT
1 ATAT
15454828 GCATGCAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 6 0.30
20 6 0.30
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (20 bp):
ATATAAAACTTAAACATCAT
Found at i:15464029 original size:130 final size:129
Alignment explanation
Indices: 15463752--15464075 Score: 312
Period size: 130 Copynumber: 2.5 Consensus size: 129
15463742 GTGAAATTCC
* * * * *
15463752 AAGGAGATATTCGATTATTTTGGGCAAATGAAAAAGTGCAACCCAGCATGATAGGGCTCGATTCT
1 AAGGA-ATATTCGATTGTTTTGGACAAATGAAAAAGCGCAACCCAGCACGATAGGGCACGATTCT
* ** * *
15463817 CAAATCGCCAAACATCGAACATCTCCTTCATTTTGAAAGATTTTAGAAAATGTGAGTGAAGTTCC
65 CAAATCACCAAACATCGAACATCTCCTTCATTTTGAAAGATTTTAGAAAACATGAATGAAG-ACC
*
15463882 G
129 A
* * * * *
15463883 AAGGGATCTTCAATTGTTTTGGACCAATAAAAAAGCGCAACCCAGCACGATAGGGCACGATTCTC
1 AAGGAATATTCGATTGTTTTGGACAAATGAAAAAGCGCAACCCAGCACGATAGGGCACGATTCTC
* ** * * *
15463948 AAATCACCAAACATTGAACATCAT-CTTTGTTTT-TAAGGTTTTTGATAAACATGAATGTAA-AC
66 AAATCACCAAACATCGAACATC-TCCTTCATTTTGAAAGATTTTAGA-AAACATGAATG-AAGAC
15464010 CTA
128 C-A
* * * * * * *
15464013 AAGGAATATTCGATTGTTTTAGACAAACGAGAAATCACAACCCAGCACGATAAGGCATGATTC
1 AAGGAATATTCGATTGTTTTGGACAAATGAAAAAGCGCAACCCAGCACGATAGGGCACGATTC
15464076 CCGAATTGTC
Statistics
Matches: 155, Mismatches: 34, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
129 11 0.07
130 137 0.88
131 7 0.05
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (129 bp):
AAGGAATATTCGATTGTTTTGGACAAATGAAAAAGCGCAACCCAGCACGATAGGGCACGATTCTC
AAATCACCAAACATCGAACATCTCCTTCATTTTGAAAGATTTTAGAAAACATGAATGAAGACCA
Found at i:15464204 original size:129 final size:130
Alignment explanation
Indices: 15464018--15464348 Score: 400
Period size: 130 Copynumber: 2.6 Consensus size: 130
15464008 ACCTAAAGGA
* * * * * * * *
15464018 ATATTCGATTGTTTTAGACAAACGAGAAATCACAACCCAGCACGATAAGGCATGATTCC-CGAAT
1 ATATTCGATTATTTTAAACAAACGCGAAATTACAACCCAACACGTTAGGGCACGATTCCACGAAT
* * *
15464082 TGTCAAACACCGAGTATTACCTTCGTTTTAAAGGATTTTTAGAAGACCTGAGTGAAATTTTGAAA
66 TGTCAAACACCGAGTATCACCTTCG-TTTAAAGGA-TTTTAAAAGACATGAGTGAAATTTTG-AA
15464147 G-G
128 GTG
* * *
15464149 ATATTTGATTATTTTAAAC-AA-TCGAAATTGCAACCCAACACGTTAGGGCACGATTCCACGAAT
1 ATATTCGATTATTTTAAACAAACGCGAAATTACAACCCAACACGTTAGGGCACGATTCCACGAAT
* * * * * *
15464212 TGCCAAATACCGTGTATCGCCTTCGTTTAAGGGATTTTAAAATACATGAGTGAAATTTTGAAGTG
66 TGTCAAACACCGAGTATCACCTTCGTTTAAAGGATTTTAAAAGACATGAGTGAAATTTTGAAGTG
* * *
15464277 ATATTCGATTATTTTGAGCAAACGCGAAATTACAACCCAACACGTTAGGGCACGATTCCGCGAAT
1 ATATTCGATTATTTTAAACAAACGCGAAATTACAACCCAACACGTTAGGGCACGATTCCACGAAT
15464342 TGTCAAA
66 TGTCAAA
15464349 TATCAAATCT
Statistics
Matches: 169, Mismatches: 27, Indels: 9
0.82 0.13 0.04
Matches are distributed among these distances:
127 3 0.02
128 40 0.24
129 38 0.22
130 72 0.43
131 16 0.09
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (130 bp):
ATATTCGATTATTTTAAACAAACGCGAAATTACAACCCAACACGTTAGGGCACGATTCCACGAAT
TGTCAAACACCGAGTATCACCTTCGTTTAAAGGATTTTAAAAGACATGAGTGAAATTTTGAAGTG
Found at i:15471263 original size:44 final size:45
Alignment explanation
Indices: 15471214--15471375 Score: 166
Period size: 46 Copynumber: 3.5 Consensus size: 45
15471204 TATGCGTGTT
*
15471214 GATGCATGTCCCAGACATGTCTTACACTAGCACT-ACTCTTA-GTC
1 GATGCATGTCCCAGACATGTCTTACACTAGCACTCA-TCTTATGCC
* * * ** *
15471258 GATGCATGTCCCATACATGTCTTACTCTGGCACTCATAATATGGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTTAT-GCC
* * * *
15471304 GAAGCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTGGATGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCACTCATCT-TATGCC
15471350 GATGCCATGTCCCAGACATGGTCTTA
1 GATG-CATGTCCCAGACAT-GTCTTA
15471376 TACTGGTGCA
Statistics
Matches: 94, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
44 34 0.36
45 1 0.01
46 37 0.39
47 16 0.17
48 6 0.06
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTTATGCC
Found at i:15471512 original size:15 final size:17
Alignment explanation
Indices: 15471492--15471523 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
15471482 TATAACTTAA
15471492 CAATTC-AT-ACAATAT
1 CAATTCAATGACAATAT
15471507 CAATTCAATGACAATAT
1 CAATTCAATGACAATAT
15471524 GAATACAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (17 bp):
CAATTCAATGACAATAT
Found at i:15476071 original size:42 final size:43
Alignment explanation
Indices: 15475966--15476072 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 43
15475956 TGTGTTATCA
* ** *
15475966 TGTAAGACCATGTCTGGGACGTTGGCATCGACTTCTGTTTTACG
1 TGTAAGACCATGTCTGGGACATCAGCATCGAC-TCTGATTTACG
* *
15476010 TGAAAGACCATGTTTGGGACATCAGCATCGTA-TCTGATTT-CG
1 TGTAAGACCATGTCTGGGACATCAGCATCG-ACTCTGATTTACG
*
15476052 TGTAAGACCCTGTCTGGGACA
1 TGTAAGACCATGTCTGGGACA
15476073 GTGGCATCGA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
42 20 0.38
43 7 0.13
44 25 0.47
45 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATCAGCATCGACTCTGATTTACG
Found at i:15476080 original size:42 final size:43
Alignment explanation
Indices: 15475966--15476127 Score: 129
Period size: 43 Copynumber: 3.8 Consensus size: 43
15475956 TGTGTTATCA
*
15475966 TGTAAGACCATGTCTGGGAC-GTTGGCATCG-ACTTCTGTTTTACG
1 TGTAAGACCATGTCTGGGACAG-TGGCATCGTA--TCTGATTTACG
* * *
15476010 TGAAAGACCATGTTTGGGACA-TCAGCATCGTATCTGATTT-CG
1 TGTAAGACCATGTCTGGGACAGT-GGCATCGTATCTGATTTACG
* * *
15476052 TGTAAGACCCTGTCTGGGACAGTGGCATCGATATTTGA-TTACA
1 TGTAAGACCATGTCTGGGACAGTGGCATCG-TATCTGATTTACG
* * * *
15476095 TATAAGACCACGTCTAGGAC-GTTGGCATTGTAT
1 TGTAAGACCATGTCTGGGACAG-TGGCATCGTAT
15476128 ATGTTCTTTG
Statistics
Matches: 96, Mismatches: 15, Indels: 16
0.76 0.12 0.13
Matches are distributed among these distances:
42 32 0.33
43 39 0.41
44 24 0.25
45 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACAGTGGCATCGTATCTGATTTACG
Found at i:15476652 original size:22 final size:22
Alignment explanation
Indices: 15476623--15476665 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
15476613 GGAAGAATAA
15476623 AGAAATGAA-AAAAAAAAAGAG
1 AGAAATGAAGAAAAAAAAAGAG
*
15476644 AGAATATGAAGAAAAACAAAGA
1 AGAA-ATGAAGAAAAAAAAAGA
15476666 AAAGAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 5 0.26
23 10 0.53
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.07
Consensus pattern (22 bp):
AGAAATGAAGAAAAAAAAAGAG
Found at i:15477871 original size:29 final size:29
Alignment explanation
Indices: 15477838--15477920 Score: 166
Period size: 29 Copynumber: 2.9 Consensus size: 29
15477828 GTGACGAGAT
15477838 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
15477867 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
15477896 TGGCACTAAGTGTGCATGCTGGAAA
1 TGGCACTAAGTGTGCATGCTGGAAA
15477921 AAATACGGCA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:15477960 original size:59 final size:58
Alignment explanation
Indices: 15477834--15477969 Score: 159
Period size: 59 Copynumber: 2.3 Consensus size: 58
15477824 TACGGTGACG
* * *
15477834 AGAT-TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAAAATACGGCACTAAGTGTGCATGCTCGAA
* **
15477891 ATATATGGCACTAAGTGTGCATGCTGGAAAAAATACGGCACTGGGTGTGCGA-GCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGG-AAAAATACGGCACTAAGTGTGC-ATGCTCGAA
* * *
15477950 GGGTATGGCACTATGTGTGC
1 AGATATGGCACTAAGTGTGC
15477970 GGGCTTAAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
57 3 0.05
58 22 0.33
59 40 0.61
60 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.25
Consensus pattern (58 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAAAATACGGCACTAAGTGTGCATGCTCGAA
Found at i:15484585 original size:19 final size:17
Alignment explanation
Indices: 15484556--15484606 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
15484546 ATAAAGAAAT
15484556 GAAAA-AAAAAAAAAGA
1 GAAAAGAAAAAAAAAGA
*
15484572 GAATATGAAGAAAAACAA-A
1 GAA-AAGAA-AAAAA-AAGA
15484591 GAAAAGAAAAAAAAAG
1 GAAAAGAAAAAAAAAG
15484607 TGTTCATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
16 5 0.18
17 6 0.21
18 6 0.21
19 9 0.32
20 2 0.07
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (17 bp):
GAAAAGAAAAAAAAAGA
Found at i:15485838 original size:30 final size:29
Alignment explanation
Indices: 15485766--15485830 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
15485756 TGACGAGATT
* *
15485766 GGCACTAAGTGTGCATGCTGGAAATATAT
1 GGCACTAAGTGTGCATGCTGGAAAAATAC
15485795 GGCACTAAGTGTGCATGCTGGAAAAAATAC
1 GGCACTAAGTGTGCATGCTGG-AAAAATAC
15485825 GGCACT
1 GGCACT
15485831 GGGTGTGCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
29 21 0.64
30 12 0.36
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (29 bp):
GGCACTAAGTGTGCATGCTGGAAAAATAC
Found at i:15489311 original size:48 final size:47
Alignment explanation
Indices: 15489255--15489482 Score: 216
Period size: 48 Copynumber: 4.9 Consensus size: 47
15489245 CACATGGTAG
* *
15489255 GATGCCAATGCCATATTCCAGATATGGTCTTACATGGGATCACATATC
1 GATGCCAATGCCAT-GTCCAGACATGGTCTTACATGGGATCACATATC
* * * **
15489303 GATGCCAATGCCATGTCCAAAAAATGGTCTTACATGGGATCATAGGTC
1 GATGCCAATGCCATGTCC-AGACATGGTCTTACATGGGATCACATATC
*
15489351 GATGCCAATGTCATGTCCTAGACATGGTCTTACATGGGATCACATATC
1 GATGCCAATGCCATGTCC-AGACATGGTCTTACATGGGATCACATATC
* * * ** *
15489399 GATG---TTG--ATAGCCCAG-CTATGGTCTTACACGAAATTACATATC
1 GATGCCAATGCCAT-GTCCAGAC-ATGGTCTTACATGGGATCACATATC
* *
15489442 GATGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATC
1 GATGCCAATGCCATGT-CCAGACATGGTCTTACATGGGATC
15489483 GCACATAACC
Statistics
Matches: 143, Mismatches: 27, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
42 1 0.01
43 29 0.20
44 3 0.02
45 2 0.01
46 1 0.01
47 4 0.03
48 102 0.71
49 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (47 bp):
GATGCCAATGCCATGTCCAGACATGGTCTTACATGGGATCACATATC
Found at i:15490599 original size:13 final size:13
Alignment explanation
Indices: 15490578--15490625 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
15490568 CCGTGTGAGT
*
15490578 CACACGGCCTGGC
1 CACATGGCCTGGC
15490591 CACATGGCCTGGC
1 CACATGGCCTGGC
15490604 CACATGGCCTGGC
1 CACATGGCCTGGC
*
15490617 CATATGGCC
1 CACATGGCC
15490626 GTGTGACCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.17, C:0.40, G:0.29, T:0.15
Consensus pattern (13 bp):
CACATGGCCTGGC
Found at i:15491965 original size:19 final size:19
Alignment explanation
Indices: 15491941--15491978 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
15491931 GTGCGTTTGT
15491941 GCTATATTTAAATTGGCAA
1 GCTATATTTAAATTGGCAA
15491960 GCTATATTTAAATTGGCAA
1 GCTATATTTAAATTGGCAA
15491979 AGTGTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (19 bp):
GCTATATTTAAATTGGCAA
Found at i:15492037 original size:26 final size:26
Alignment explanation
Indices: 15492006--15492056 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
15491996 ACTGTAGATG
15492006 GCATTATTGATGTATTGTGTTTGTAA
1 GCATTATTGATGTATTGTGTTTGTAA
15492032 GCATTATTGATGTATTGTGTTTGTA
1 GCATTATTGATGTATTGTGTTTGTA
15492057 TGACAGAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.22, C:0.04, G:0.24, T:0.51
Consensus pattern (26 bp):
GCATTATTGATGTATTGTGTTTGTAA
Found at i:15496870 original size:46 final size:45
Alignment explanation
Indices: 15496817--15496992 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 45
15496807 TATTTGGGCA
15496817 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *** * *
15496863 TCCGAACTCATTGAGTTGAGTCTGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
15496910 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
15496956 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
15496993 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 67 0.63
47 30 0.28
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:15496972 original size:93 final size:93
Alignment explanation
Indices: 15496813--15496984 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
15496803 AGGATATTTG
* *
15496813 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCATTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAG
*
15496878 TTGAGTCTGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * *
15496906 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAG
15496971 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
15496985 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:15504148 original size:4 final size:4
Alignment explanation
Indices: 15504139--15504181 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
15504129 ATATAAACAT
15504139 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
15504182 AAGAAACCGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:15509067 original size:53 final size:53
Alignment explanation
Indices: 15509007--15509113 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
15508997 GAAAAAACTG
*
15509007 ACGTATTATTAATACCATAAATTGGAAAAATATCAAATTAATAATTATGTGCT
1 ACGTATTATTAATACCATAAATTAGAAAAATATCAAATTAATAATTATGTGCT
15509060 ACGTATTATTAATACCATAAATTAGAAAAATATCAAATTAATAATTATGTGCT
1 ACGTATTATTAATACCATAAATTAGAAAAATATCAAATTAATAATTATGTGCT
15509113 A
1 A
15509114 TATACCATTA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (53 bp):
ACGTATTATTAATACCATAAATTAGAAAAATATCAAATTAATAATTATGTGCT
Found at i:15513538 original size:16 final size:17
Alignment explanation
Indices: 15513514--15513546 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
15513504 TATAATATGT
15513514 ACTACTATTAT-ATATA
1 ACTACTATTATGATATA
*
15513530 ACTATTATTATGATATA
1 ACTACTATTATGATATA
15513547 GATTATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.45
Consensus pattern (17 bp):
ACTACTATTATGATATA
Found at i:15513722 original size:17 final size:17
Alignment explanation
Indices: 15513700--15513735 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
15513690 CAACTAGTAT
15513700 ATTAATAAATAATAATA
1 ATTAATAAATAATAATA
* *
15513717 ATTAATAATTAATATTA
1 ATTAATAAATAATAATA
15513734 AT
1 AT
15513736 GTACTACTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTAATAAATAATAATA
Found at i:15516549 original size:15 final size:15
Alignment explanation
Indices: 15516529--15516558 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
15516519 CCTCACAGTC
15516529 GTAATGCAAGAATAA
1 GTAATGCAAGAATAA
15516544 GTAATGCAAGAATAA
1 GTAATGCAAGAATAA
15516559 CTTAGGCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (15 bp):
GTAATGCAAGAATAA
Found at i:15526690 original size:25 final size:26
Alignment explanation
Indices: 15526654--15526702 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
15526644 AATACTTATC
15526654 TTAATAGTATTATATTAAT-TTAATA
1 TTAATAGTATTATATTAATATTAATA
*
15526679 TTAA-AGTGATTATCTTAATATTAA
1 TTAATAGT-ATTATATTAATATTAA
15526703 ATTTAATCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 14 0.67
26 4 0.19
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (26 bp):
TTAATAGTATTATATTAATATTAATA
Found at i:15526758 original size:69 final size:67
Alignment explanation
Indices: 15526622--15526759 Score: 195
Period size: 69 Copynumber: 2.0 Consensus size: 67
15526612 TATTTTAATA
* * *
15526622 TATCTAATATTAAATTAAATTTAATACTTATCTTAATAGTATTATATTAATTTAATATTAAAGTG
1 TATCTAATATTAAATTAAATCTAATACTTATCTTAATAGTATTATATTAATTTAATAGTAAACTG
15526687 AT
66 AT
* ** *
15526689 TATCTTAATATTAAATTTAATCTAATTTTTATCTTTATCAGTATTATATTAATTTAATAGTAAAC
1 TATC-TAATATTAAATTAAATCTAATACTTATCTTAAT-AGTATTATATTAATTTAATAGTAAAC
15526754 TGAT
64 TGAT
15526758 TA
1 TA
15526760 AGTTTAATCA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
67 4 0.06
68 28 0.45
69 30 0.48
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (67 bp):
TATCTAATATTAAATTAAATCTAATACTTATCTTAATAGTATTATATTAATTTAATAGTAAACTG
AT
Found at i:15531320 original size:48 final size:48
Alignment explanation
Indices: 15531249--15531440 Score: 208
Period size: 48 Copynumber: 4.0 Consensus size: 48
15531239 TACTCAGGAG
* * * **
15531249 TCTCGCACACTAAGTGCTCATATCATGGCCCGAAGCCATCTCAATGTA
1 TCTCGCACCCTAAGTGATAATATCATGGCCCGAAGCCAAATCAATGTA
* * *
15531297 TCTCGCACCCGAAGTGATAATATCATGGCCC-AAACCAAATCAATGAA
1 TCTCGCACCCTAAGTGATAATATCATGGCCCGAAGCCAAATCAATGTA
* * ** *
15531344 GCTCACACCCTAAGT-ATCAATATCATGGCTTGAAGCCAAATCAATATA
1 TCTCGCACCCTAAGTGAT-AATATCATGGCCCGAAGCCAAATCAATGTA
* * * *
15531392 ACTCGCACCCAAAGTGCTAATATCATGTCCCGAAGCCAAATCAATGTA
1 TCTCGCACCCTAAGTGATAATATCATGGCCCGAAGCCAAATCAATGTA
15531440 T
1 T
15531441 TCCCTAATGA
Statistics
Matches: 116, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
46 2 0.02
47 35 0.30
48 78 0.67
49 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (48 bp):
TCTCGCACCCTAAGTGATAATATCATGGCCCGAAGCCAAATCAATGTA
Found at i:15547201 original size:44 final size:44
Alignment explanation
Indices: 15547135--15547227 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
15547125 AGCACCGAAC
* * * *
15547135 TGCATCATTGAATAAACTGAAGTAGGGTAAACTGGTACGTAAAG
1 TGCATCATCGAATAAACCGAAGTAGGATAAACTGGCACGTAAAG
* * *
15547179 TGCATCATCGAATAGACCGAAGTAGGATAACCTGGCATGTAAAG
1 TGCATCATCGAATAAACCGAAGTAGGATAAACTGGCACGTAAAG
15547223 TGCAT
1 TGCAT
15547228 TCTGGAGCTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.24
Consensus pattern (44 bp):
TGCATCATCGAATAAACCGAAGTAGGATAAACTGGCACGTAAAG
Found at i:15554964 original size:29 final size:29
Alignment explanation
Indices: 15554931--15554994 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
15554921 AAATAAGTTG
* *
15554931 ATCTTTATCCAACCAATTTCAAATATTTA
1 ATCTTTATCCAACCAACTTCAAATATTCA
* *
15554960 ATCTTTATCCAGCCAACTTCAAATCTTCA
1 ATCTTTATCCAACCAACTTCAAATATTCA
15554989 ATCTTT
1 ATCTTT
15554995 CAATCTACCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.41
Consensus pattern (29 bp):
ATCTTTATCCAACCAACTTCAAATATTCA
Found at i:15574668 original size:22 final size:22
Alignment explanation
Indices: 15574640--15574684 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
15574630 CATAAATGAG
15574640 AAGTGATGAATTCTTTTGGGCT
1 AAGTGATGAATTCTTTTGGGCT
15574662 AAGTGATGAATTCTTTTGGGCT
1 AAGTGATGAATTCTTTTGGGCT
15574684 A
1 A
15574685 TGTAACTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.40
Consensus pattern (22 bp):
AAGTGATGAATTCTTTTGGGCT
Found at i:15577772 original size:12 final size:12
Alignment explanation
Indices: 15577754--15577783 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
15577744 ATTAACACCT
15577754 CACTAAACTAAC
1 CACTAAACTAAC
*
15577766 TACTAAACTAAC
1 CACTAAACTAAC
15577778 CACTAA
1 CACTAA
15577784 CTCCATCATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (12 bp):
CACTAAACTAAC
Found at i:15577952 original size:24 final size:26
Alignment explanation
Indices: 15577901--15577953 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
15577891 TTTTTGGAGA
*
15577901 AAAAAGGAGAGAGTCTCGAATACAAG
1 AAAAAGGAGAGACTCTCGAATACAAG
*
15577927 AAAAA-GAGAGACTTTCG-ATACAAG
1 AAAAAGGAGAGACTCTCGAATACAAG
15577951 AAA
1 AAA
15577954 TACACGAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.40
25 10 0.40
26 5 0.20
ACGTcount: A:0.53, C:0.11, G:0.23, T:0.13
Consensus pattern (26 bp):
AAAAAGGAGAGACTCTCGAATACAAG
Found at i:15578256 original size:3 final size:3
Alignment explanation
Indices: 15578233--15578690 Score: 131
Period size: 3 Copynumber: 152.0 Consensus size: 3
15578223 GAGAAGAGTG
* * *
15578233 TTA TTT TTA ATA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
15578280 TTA TTA CTT- TTA CTA TTA TT- CTA TATA CTA TTA CTGA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA T-TA TTA TTA -TTA -TTA TTA TTA
* * * * * * *
15578327 TTA TTA ATA GTAA CGTA ATA GTA TTT TTA TTA TT- TTA TTA TT- TTT
1 TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
15578372 TTA CCTTT TTA TTA CTA TTA TTA TTAA CTTA CTA TTA TTA TTT TTA TCA
1 TTA --TTA TTA TTA TTA TTA TTA TT-A -TTA TTA TTA TTA TTA TTA TTA
* * * * *
15578421 ATA -TA GTA TTA TT- TTC TT- TT- TTT TTA -TA TTA TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * * * *
15578464 GCA CGTA -TA TTA TTA TTA GTGTA TCA TTG TTA TTT TCTA TT- TTA TTA
1 TTA -TTA TTA TTA TTA TTA -T-TA TTA TTA TTA TTA T-TA TTA TTA TTA
* *
15578511 TTA CTT- TTA -TA CTA TTG TT- TCTA TTA TTA TTA TT- TTCA TT- TT-
1 TTA -TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TT-A TTA TTA
*
15578553 TCTA TT- TTA TTA TTA CTT- TTA -TA CTA TTA TT- TCTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
* * * *
15578597 TT- TTCA TTA CTTCCG TTA TTA TTA TCA TTA TTT TCTA TTA TCA TTA
1 TTA TT-A TTA -TT--A TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
* *
15578643 ATA TGTCG TT- TGT- TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-T-A TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
15578688 TTA
1 TTA
15578691 ACACTATTAT
Statistics
Matches: 341, Mismatches: 65, Indels: 98
0.68 0.13 0.19
Matches are distributed among these distances:
2 46 0.13
3 251 0.74
4 35 0.10
5 9 0.03
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:15578403 original size:28 final size:27
Alignment explanation
Indices: 15578350--15578403 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
15578340 CGTAATAGTA
* ***
15578350 TTTTTATTATTTTATTATTTTTTTACC
1 TTTTTATTATATTATTATTAACTTACC
15578377 TTTTTATTACTATTATTATTAACTTAC
1 TTTTTATTA-TATTATTATTAACTTAC
15578404 TATTATTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTTATTATATTATTATTAACTTACC
Found at i:15578543 original size:23 final size:23
Alignment explanation
Indices: 15578509--15578565 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
15578499 TCTATTTTAT
15578509 TATTACTT-TTATACT-ATTGTTTC
1 TATTA-TTATTATACTCATT-TTTC
**
15578532 TATTATTATTATTTTCATTTTTC
1 TATTATTATTATACTCATTTTTC
15578555 TATT-TTATTAT
1 TATTATTATTAT
15578566 TACTTTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 9 0.30
23 18 0.60
24 3 0.10
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.67
Consensus pattern (23 bp):
TATTATTATTATACTCATTTTTC
Found at i:15578562 original size:54 final size:54
Alignment explanation
Indices: 15578496--15578604 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
15578486 ATCATTGTTA
*
15578496 TTTTCTATTTTATTATTACTTTTATACTATTGTTTCTATTATTATTATTTTCAT
1 TTTTCTATTTTATTATTACTTTTATACTATTATTTCTATTATTATTATTTTCAT
15578550 TTTTCTATTTTATTATTACTTTTATACTATTATTTCTATTATTATTATTTTCAT
1 TTTTCTATTTTATTATTACTTTTATACTATTATTTCTATTATTATTATTTTCAT
15578604 T
1 T
15578605 ACTTCCGTTA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.23, C:0.09, G:0.01, T:0.67
Consensus pattern (54 bp):
TTTTCTATTTTATTATTACTTTTATACTATTATTTCTATTATTATTATTTTCAT
Found at i:15579115 original size:125 final size:127
Alignment explanation
Indices: 15578933--15579194 Score: 325
Period size: 125 Copynumber: 2.1 Consensus size: 127
15578923 ATTTTTCAAG
* * ** *
15578933 TAAAGGCAATATTCGATACTTGGAAATTCGAGAAATCGTGTCCTAATGTACTAGGTTTCGGTTTT
1 TAAAGGCAATATTCGATACTTAGAAATTCGAGAAATCGTGCCCTAACATACTAGGTTTCGATTTT
* * *
15578998 TCGTTTGATCTAAGCAACCGATTATCC-TTTTAAAA-TAAAATACATGAGTTTTAAAT-AACA
66 CCGTTTGATCTAAACAACCGAATATCCTTTTTAAAATTAAAATACATGAGTTTTAAATGAA-A
* * * *
15579058 TAAAGGCAATATTCCG-TATTTAGAAATTCGAGTAGTCGTGCCCTAACATACTGGGTTTCGATTT
1 TAAAGGCAATATT-CGATACTTAGAAATTCGAGAAATCGTGCCCTAACATACTAGGTTTCGATTT
* * * *
15579122 TCCGTTTGATCTAAATATCCGAATATCCTTTTTAAAATTTAAATACATGTGTTTTAAATGAAA
65 TCCGTTTGATCTAAACAACCGAATATCCTTTTTAAAATTAAAATACATGAGTTTTAAATGAAA
15579185 TAGAAGGCAA
1 TA-AAGGCAA
15579195 GCTCATAATC
Statistics
Matches: 116, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
125 75 0.65
126 10 0.09
127 22 0.19
128 9 0.08
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (127 bp):
TAAAGGCAATATTCGATACTTAGAAATTCGAGAAATCGTGCCCTAACATACTAGGTTTCGATTTT
CCGTTTGATCTAAACAACCGAATATCCTTTTTAAAATTAAAATACATGAGTTTTAAATGAAA
Found at i:15583970 original size:2 final size:2
Alignment explanation
Indices: 15583963--15583988 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15583953 ACAACACTTA
15583963 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
15583989 TATTTGCACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15587394 original size:60 final size:60
Alignment explanation
Indices: 15587304--15587417 Score: 210
Period size: 60 Copynumber: 1.9 Consensus size: 60
15587294 CATGACACAT
*
15587304 ATATAGGTAATGAAAAAGGAAATTACCATCATGGCCTAGGTGAATTCATAGCGATGGCAC
1 ATATAGGTAATGAAAAAGGAAATTACCATCATGGCCTAGATGAATTCATAGCGATGGCAC
*
15587364 ATATAGGTAATGAAAAAGGAAATTACCATCATGGCCTAGATGGATTCATAGCGA
1 ATATAGGTAATGAAAAAGGAAATTACCATCATGGCCTAGATGAATTCATAGCGA
15587418 GAAGTATGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (60 bp):
ATATAGGTAATGAAAAAGGAAATTACCATCATGGCCTAGATGAATTCATAGCGATGGCAC
Found at i:15593593 original size:93 final size:93
Alignment explanation
Indices: 15593480--15593651 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
15593470 CGCCCATAAG
* *
15593480 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTAAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTAAACTCA
15593545 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
15593573 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTAAACTCA
15593638 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
15593652 TTAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTAAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:15593667 original size:46 final size:47
Alignment explanation
Indices: 15593473--15593648 Score: 211
Period size: 46 Copynumber: 3.8 Consensus size: 47
15593463 TGTAACCCGC
* * *
15593473 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG-GCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCAT
* *
15593519 CCATAAGTGAACTCGGACTAAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-G-C-A-TTCGCAT
* *
15593569 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA-CATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCAT
15593612 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
15593649 TGCTTAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.56
47 28 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (47 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCAT
Found at i:15597142 original size:2 final size:2
Alignment explanation
Indices: 15597135--15597168 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
15597125 GTTAGTGGAC
*
15597135 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15597169 GTAGGTGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:15598951 original size:40 final size:40
Alignment explanation
Indices: 15598891--15599058 Score: 187
Period size: 40 Copynumber: 4.2 Consensus size: 40
15598881 CGGGATTTAA
* ** *
15598891 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTCGCACAATTGCCTTCGGGTCTTAGC
* *** *
15598931 CCGGATTTGGTAACTTGCACAATTGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCACAATTGCCTTCGGGTCTTAGC
15598971 CCGGATATAACAACTCGCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCAC-AATTGCCTTCGGGTCTTAGC
* * * *
15599011 CCGGATATAATC-ACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAA-CAACTCGCACAATTGCCTTCGGGTCTTAGC
15599051 CCGGATAT
1 CCGGATAT
15599059 CATTCAAATG
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.02
40 104 0.95
41 3 0.03
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CCGGATATAACAACTCGCACAATTGCCTTCGGGTCTTAGC
Found at i:15599038 original size:80 final size:80
Alignment explanation
Indices: 15598877--15599058 Score: 215
Period size: 80 Copynumber: 2.3 Consensus size: 80
15598867 AATTCACGTA
* * * * **
15598877 CCTTCGGGATTTA-ACCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGATTTGG
1 CCTTCGGGACTTAGCCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCGGATATAA
* *
15598941 TAACTTGCACAATTG
66 TAACTAGCACAAATG
* ** *
15598956 CCTTCGGGTCTTAGCCCGGATATAACAACTCGCACGAA-TGCCTTCGGGTCTTAGCCCGGATATA
1 CCTTCGGGACTTAGCCCGGATATAACAACAAGCAC-AATTGCCTTCGGGTCTTAACCCGGATATA
* *
15599020 ATCACTAGCATAAATG
65 ATAACTAGCACAAATG
15599036 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
15599059 CATTCAAATG
Statistics
Matches: 86, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
79 11 0.13
80 73 0.85
81 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCGGATATAA
TAACTAGCACAAATG
Found at i:15603519 original size:39 final size:39
Alignment explanation
Indices: 15603476--15603562 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
15603466 CCGGCAATTA
15603476 GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACAAG
1 GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACAAG
* *
15603515 GCCTGCTAGGTATAAACCTGAATTTATCACCGGCACGAG
1 GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACAAG
15603554 GCCTGCTAG
1 GCCTGCTAG
15603563 ACATTAAGTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.22
Consensus pattern (39 bp):
GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACAAG
Found at i:15607164 original size:43 final size:41
Alignment explanation
Indices: 15607060--15607228 Score: 144
Period size: 43 Copynumber: 4.0 Consensus size: 41
15607050 ACAATAGCTC
* * **
15607060 ATACAATGCC-ATATCCCAGATATGGTCTTACATGTCGTCA
1 ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCA
* * ** * *
15607100 CATATCGATGCCACTACCCCAG-CGAGGGTCTTACATGAAATCA
1 -ATA-CAATGCCAATGTCCCAGAC-ATGGTCTTACATGTAATCA
* * *
15607143 TATAACGATGCCAATGTCCCAGACATAGTCTTACACGTAATCGCA
1 -AT-ACAATGCCAATGTCCCAGACATGGTCTTACATGTAAT--CA
15607188 ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCA
1 ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCA
15607229 CATCTCGGTA
Statistics
Matches: 102, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
41 5 0.05
42 6 0.06
43 85 0.83
44 4 0.04
45 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (41 bp):
ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCA
Found at i:15607880 original size:22 final size:20
Alignment explanation
Indices: 15607855--15607897 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
15607845 CATCAAGATA
15607855 TCATCAATTAAAACTCAAAAAT
1 TCATCAA-T-AAACTCAAAAAT
* *
15607877 TCATTAATAAATTCAAAAAT
1 TCATCAATAAACTCAAAAAT
15607897 T
1 T
15607898 AAGCTACGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 12 0.63
21 1 0.05
22 6 0.32
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (20 bp):
TCATCAATAAACTCAAAAAT
Found at i:15610725 original size:39 final size:39
Alignment explanation
Indices: 15610671--15610942 Score: 490
Period size: 39 Copynumber: 7.0 Consensus size: 39
15610661 AAGACACTGA
15610671 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
15610710 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
15610749 AAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
15610788 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
15610827 AAATGTATCCGGACTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
15610866 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
15610905 AAATGTATCCGGGTTAAAGTCCCGCAGGCTTTGTGCTG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
15610943 ATAATATAAT
Statistics
Matches: 223, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 223 1.00
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.23
Consensus pattern (39 bp):
AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
Found at i:15617547 original size:21 final size:21
Alignment explanation
Indices: 15617521--15617567 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
15617511 AGTTAGGGTT
15617521 TGAAATCAACAGAACAATGTA
1 TGAAATCAACAGAACAATGTA
*
15617542 TGAAATCAACATAACAATGTA
1 TGAAATCAACAGAACAATGTA
15617563 TGAAA
1 TGAAA
15617568 AGTAAGAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.21
Consensus pattern (21 bp):
TGAAATCAACAGAACAATGTA
Found at i:15619115 original size:6 final size:6
Alignment explanation
Indices: 15619106--15619135 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
15619096 TGATAAGATT
15619106 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC
15619136 TTCTCTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CCCTTC
Found at i:15625674 original size:25 final size:26
Alignment explanation
Indices: 15625640--15625699 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
15625630 CACCAACACA
* * *
15625640 CTGCCAGTAA-AATATCACAGCAGAG
1 CTGCCAGTAACAATAACACAACAAAG
*
15625665 CTGCCAGTAACAATAACGCAACAAAG
1 CTGCCAGTAACAATAACACAACAAAG
15625691 CTGCCAGTA
1 CTGCCAGTA
15625700 TCAGTATATG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.40, C:0.27, G:0.18, T:0.15
Consensus pattern (26 bp):
CTGCCAGTAACAATAACACAACAAAG
Found at i:15628814 original size:17 final size:16
Alignment explanation
Indices: 15628776--15628818 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
15628766 TCAACAATCG
15628776 CTAAATAAAATTAGAAA
1 CTAAA-AAAATTAGAAA
15628793 CTAAAAAAATATA-AAA
1 CTAAAAAAAT-TAGAAA
15628809 CTTAAAAAAA
1 C-TAAAAAAA
15628819 ATCTAACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.21
Consensus pattern (16 bp):
CTAAAAAAATTAGAAA
Found at i:15629780 original size:15 final size:15
Alignment explanation
Indices: 15629760--15629789 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15629750 TTCATTGTTA
*
15629760 TGTCTTTAGTATTTT
1 TGTCTTTAATATTTT
15629775 TGTCTTTAATATTTT
1 TGTCTTTAATATTTT
15629790 GCATGCGTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.67
Consensus pattern (15 bp):
TGTCTTTAATATTTT
Found at i:15630971 original size:25 final size:26
Alignment explanation
Indices: 15630921--15630973 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
15630911 AACTGTAAAG
15630921 AGAAAATTATCTAAAGAAATTATTTT
1 AGAAAATTATCTAAAGAAATTATTTT
* *
15630947 AGAAAATT-TCTAGAGATAATTTTTTT
1 AGAAAATTATCTAAAGA-AATTATTTT
15630973 A
1 A
15630974 TATACAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (26 bp):
AGAAAATTATCTAAAGAAATTATTTT
Found at i:15639730 original size:21 final size:21
Alignment explanation
Indices: 15639706--15639748 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
15639696 CCTCATTGGC
*
15639706 AAGGTTTTAGTTCTCATGGTT
1 AAGGCTTTAGTTCTCATGGTT
* *
15639727 AAGGCTTTCGTTCTCGTGGTT
1 AAGGCTTTAGTTCTCATGGTT
15639748 A
1 A
15639749 TGTTTATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.14, G:0.26, T:0.44
Consensus pattern (21 bp):
AAGGCTTTAGTTCTCATGGTT
Found at i:15643156 original size:40 final size:40
Alignment explanation
Indices: 15643096--15643233 Score: 156
Period size: 40 Copynumber: 3.5 Consensus size: 40
15643086 CGGATGATAA
* * * * * *
15643096 CCGGACTAAGATCCAAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACTATAT
*
15643136 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACTATAT
**
15643176 CCGGGCTAAGTTCCGAAGGCATTTGTGCGAGTTG-CTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGACTATAT
15643216 CC-GGCTAA-ATCCCGAAGG
1 CCGGGCTAAGA-CCCGAAGG
15643234 TACTTGGGTT
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
39 13 0.15
40 70 0.83
41 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACTATAT
Found at i:15643233 original size:39 final size:40
Alignment explanation
Indices: 15643111--15643233 Score: 160
Period size: 40 Copynumber: 3.1 Consensus size: 40
15643101 CTAAGATCCA
* * * *
15643111 AAGGCATTTATGCTAGTGATTATATCCGGGCTAAGA-CCCG
1 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAA-ATCCCG
* *
15643151 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTTCCG
1 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAATCCCG
*
15643191 AAGGCATTTGTGCGAGTTGCTATATCC-GGCTAAATCCCG
1 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAATCCCG
15643230 AAGG
1 AAGG
15643234 TACTTGGGTT
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
39 14 0.19
40 59 0.81
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (40 bp):
AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAATCCCG
Found at i:15645788 original size:83 final size:84
Alignment explanation
Indices: 15645636--15645818 Score: 269
Period size: 83 Copynumber: 2.2 Consensus size: 84
15645626 TCTTTGCTTG
* * *
15645636 GAAACAAAACAATATCGAATAAAATCTTGTTAAACGGCGCAAATAAATCCCAAAATAGATTTTAT
1 GAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGCGCAAATAAATCCCAAAATAGATTTTAT
15645701 TTAATTCTATTCTAATTTA
66 TTAATTCTATTCTAATTTA
* * ** * *
15645720 GAAACAAAATAAAATCAAATAAAGTCTTGTTAAATGG-GGGAATAAATTCCGAAATAGATTTTAT
1 GAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGCGCAAATAAATCCCAAAATAGATTTTAT
*
15645784 TTAATTCTATTCTAATTTT
66 TTAATTCTATTCTAATTTA
15645803 GAAACAAAATAAAATC
1 GAAACAAAATAAAATC
15645819 TTGTTAAACG
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
83 57 0.64
84 32 0.36
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.32
Consensus pattern (84 bp):
GAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGCGCAAATAAATCCCAAAATAGATTTTAT
TTAATTCTATTCTAATTTA
Found at i:15649325 original size:3 final size:3
Alignment explanation
Indices: 15649317--15649360 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
15649307 AAAGAGCAAA
15649317 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
15649361 AATGCCAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:15649715 original size:17 final size:16
Alignment explanation
Indices: 15649693--15649739 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
15649683 TTATGAATTT
15649693 TTTTTAAAATTTGTTAA
1 TTTTTAAAATTT-TTAA
**
15649710 TTTTTAAAAAAATTTAA
1 TTTTT-AAAATTTTTAA
15649727 TTTTTAAAATTTT
1 TTTTTAAAATTTT
15649740 GATGAACTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 6 0.24
17 14 0.56
18 5 0.20
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
TTTTTAAAATTTTTAA
Found at i:15650078 original size:21 final size:21
Alignment explanation
Indices: 15650045--15650092 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
15650035 TTTAATTATA
* * *
15650045 TTATAATTATTTATTAGATGT
1 TTATTATTATTTAATAGATAT
* *
15650066 TTATTATTTTTTAATATATAT
1 TTATTATTATTTAATAGATAT
15650087 TTATTA
1 TTATTA
15650093 AATTAATTCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
TTATTATTATTTAATAGATAT
Found at i:15665839 original size:27 final size:27
Alignment explanation
Indices: 15665809--15665863 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
15665799 GAGTCATTTG
15665809 TCTTTATCATAAATGACTTGATTACCA
1 TCTTTATCATAAATGACTTGATTACCA
* **
15665836 TCTTTGTGGTAAATGACTTGATTACCA
1 TCTTTATCATAAATGACTTGATTACCA
15665863 T
1 T
15665864 TTGATTGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (27 bp):
TCTTTATCATAAATGACTTGATTACCA
Found at i:15671923 original size:37 final size:37
Alignment explanation
Indices: 15671870--15671991 Score: 199
Period size: 37 Copynumber: 3.3 Consensus size: 37
15671860 TATAAAAGAA
* * *
15671870 GTCTTACCCAGACATAATCTCCATACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
15671907 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
*
15671944 GTCTTACTCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
*
15671981 GTCTCACCCGG
1 GTCTTACCCGG
15671992 AACATATTCC
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 79 1.00
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.27
Consensus pattern (37 bp):
GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
Found at i:15672148 original size:49 final size:49
Alignment explanation
Indices: 15672093--15672404 Score: 554
Period size: 49 Copynumber: 6.4 Consensus size: 49
15672083 TTTTACATTA
*
15672093 GCCATTAGGCCTTATCACATATACATACACTTTCACATCCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
15672142 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
15672191 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
15672240 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* *
15672289 GCCATTAGGCCTCATCACATATACAT-CCCTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* * *
15672337 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCGCATTG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
15672386 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTTATCACA
15672405 CATATATGTA
Statistics
Matches: 253, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
48 46 0.18
49 207 0.82
ACGTcount: A:0.29, C:0.33, G:0.09, T:0.29
Consensus pattern (49 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
Found at i:15676274 original size:14 final size:14
Alignment explanation
Indices: 15676257--15676290 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
15676247 AAGATTTTTG
*
15676257 AATTATAATTTATT
1 AATTATAATTAATT
15676271 AATTATAATTAATT
1 AATTATAATTAATT
*
15676285 AGTTAT
1 AATTAT
15676291 TAGCTCAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
AATTATAATTAATT
Found at i:15679808 original size:20 final size:20
Alignment explanation
Indices: 15679783--15679821 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
15679773 CTTACTTCAG
15679783 ATAAAAGCATT-ATTATTAAT
1 ATAAAA-CATTAATTATTAAT
*
15679803 ATAAAACTTTAATTATTAA
1 ATAAAACATTAATTATTAA
15679822 CAAACGTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (20 bp):
ATAAAACATTAATTATTAAT
Found at i:15690110 original size:71 final size:69
Alignment explanation
Indices: 15689907--15690120 Score: 392
Period size: 69 Copynumber: 3.1 Consensus size: 69
15689897 TGTACCACGT
* *
15689907 CATCACCTGAAAATTTATATAATTTTTTTTTTAATTTTCAAGTGATGGTGTAGCATAATCACAAA
1 CATCACCTGAAAATTTATATAATATTTTTTTTAATTTTCAAGTGATGGTGTAGCACAATCACAAA
15689972 GTGC
66 GTGC
15689976 CATCACCTGAAAATTTATATAATATTTTTTTTAATTTTCAAGTGATGGTGTAGCACAATCACAAA
1 CATCACCTGAAAATTTATATAATATTTTTTTTAATTTTCAAGTGATGGTGTAGCACAATCACAAA
15690041 GTGC
66 GTGC
15690045 CATCACCTGAAAATTTATATAATATATATTTTTTAATTTTCAAGTGATGGTGTAGCACAATCACA
1 CATCACCTGAAAATTTATATAATAT-T-TTTTTTAATTTTCAAGTGATGGTGTAGCACAATCACA
15690110 AAGTGC
64 AAGTGC
15690116 CATCA
1 CATCA
15690121 TCAAACTTTT
Statistics
Matches: 141, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
69 92 0.65
70 1 0.01
71 48 0.34
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (69 bp):
CATCACCTGAAAATTTATATAATATTTTTTTTAATTTTCAAGTGATGGTGTAGCACAATCACAAA
GTGC
Found at i:15691225 original size:17 final size:17
Alignment explanation
Indices: 15691203--15691235 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
15691193 GCAAACAAAA
15691203 AAGTCA-AACAGAAAACC
1 AAGTCAGAA-AGAAAACC
15691220 AAGTCAGAAAGAAAAC
1 AAGTCAGAAAGAAAAC
15691236 ATACCTCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.61, C:0.18, G:0.15, T:0.06
Consensus pattern (17 bp):
AAGTCAGAAAGAAAACC
Found at i:15694870 original size:15 final size:15
Alignment explanation
Indices: 15694850--15694879 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
15694840 CCGTCAACAA
15694850 AGGCTATGTTCATCT
1 AGGCTATGTTCATCT
15694865 AGGCTATGTTCATCT
1 AGGCTATGTTCATCT
15694880 CTAACCTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (15 bp):
AGGCTATGTTCATCT
Found at i:15706274 original size:24 final size:22
Alignment explanation
Indices: 15706235--15706280 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
15706225 AGCAGGTATG
15706235 TTTTTGTTTTATTGAACATTAAT
1 TTTTTGTTTTATTGAAC-TTAAT
15706258 TTTTTGTTGTT-TATGAACTTAAT
1 TTTTTGTT-TTAT-TGAACTTAAT
15706281 ACATAGTCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.24, C:0.04, G:0.11, T:0.61
Consensus pattern (22 bp):
TTTTTGTTTTATTGAACTTAAT
Found at i:15712697 original size:38 final size:38
Alignment explanation
Indices: 15712650--15712728 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
15712640 TTTCCCAAAC
* **
15712650 ATATAAGGGTTCACATAAATATAAGGTTTTGCATACAT
1 ATATAAGGGTTCACATAAATATAAGGGTTCACATACAT
** *
15712688 ATATAAGGGTTTGCATACATATAAGGGTTCACATACAT
1 ATATAAGGGTTCACATAAATATAAGGGTTCACATACAT
15712726 ATA
1 ATA
15712729 AGAGTTTGCT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.33
Consensus pattern (38 bp):
ATATAAGGGTTCACATAAATATAAGGGTTCACATACAT
Found at i:15712713 original size:56 final size:55
Alignment explanation
Indices: 15712648--15712801 Score: 175
Period size: 56 Copynumber: 2.7 Consensus size: 55
15712638 TATTTCCCAA
**
15712648 ACATATAAGGGTTCACATAAATATAAGGTTTTGCATACATATATAAGGGTTTGCAT
1 ACATATAAGGGTTCACATAAATATAAGG-TTTGCATACATATATAAGGGTTCACAT
* * *
15712704 ACATATAAGGGTTCACATACATATAAGAGTTTGCTTACATATATAGGGGTTCACAT
1 ACATATAAGGGTTCACATAAATATAAG-GTTTGCATACATATATAAGGGTTCACAT
* * *
15712760 ACATATGAGGATTTC-CATACATATATAGGGGTTTGCATACAT
1 ACATATAAGG-GTTCACATA-A-ATATA-AGGTTTGCATACAT
15712802 TGCATACATA
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
56 62 0.75
57 4 0.05
58 16 0.19
59 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (55 bp):
ACATATAAGGGTTCACATAAATATAAGGTTTGCATACATATATAAGGGTTCACAT
Found at i:15712742 original size:18 final size:18
Alignment explanation
Indices: 15712648--15712801 Score: 137
Period size: 18 Copynumber: 8.2 Consensus size: 18
15712638 TATTTCCCAA
**
15712648 ACATATAAGGGTTCACAT
1 ACATATAAGGGTTTGCAT
* *
15712666 AAATATAAGGTTTTGCAT
1 ACATATAAGGGTTTGCAT
15712684 ACATATATAAGGGTTTGCAT
1 AC--ATATAAGGGTTTGCAT
**
15712704 ACATATAAGGGTTCACAT
1 ACATATAAGGGTTTGCAT
* *
15712722 ACATATAAGAGTTTGCTT
1 ACATATAAGGGTTTGCAT
**
15712740 ACATATATAGGGGTTCACAT
1 ACATATA-A-GGGTTTGCAT
* * *
15712760 ACATATGAGGATTTCCAT
1 ACATATAAGGGTTTGCAT
15712778 ACATATATAGGGGTTTGCAT
1 ACATATA-A-GGGTTTGCAT
15712798 ACAT
1 ACAT
15712802 TGCATACATA
Statistics
Matches: 107, Mismatches: 23, Indels: 10
0.76 0.16 0.07
Matches are distributed among these distances:
18 63 0.59
19 3 0.03
20 41 0.38
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (18 bp):
ACATATAAGGGTTTGCAT
Found at i:15712748 original size:38 final size:37
Alignment explanation
Indices: 15712688--15712801 Score: 142
Period size: 38 Copynumber: 3.1 Consensus size: 37
15712678 TTGCATACAT
15712688 ATATAAGGGTTTGCATACATATA-A-GGGTTCACATAC
1 ATATAA-GGTTTGCATACATATATAGGGGTTCACATAC
*
15712724 ATATAAGAGTTTGCTTACATATATAGGGGTTCACATAC
1 ATATAAG-GTTTGCATACATATATAGGGGTTCACATAC
* * **
15712762 ATATGAGGATTTCCATACATATATAGGGGTTTGCATAC
1 ATATAAGG-TTTGCATACATATATAGGGGTTCACATAC
15712800 AT
1 AT
15712802 TGCATACATA
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
35 1 0.01
36 20 0.29
37 2 0.03
38 45 0.66
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.33
Consensus pattern (37 bp):
ATATAAGGTTTGCATACATATATAGGGGTTCACATAC
Found at i:15714162 original size:39 final size:39
Alignment explanation
Indices: 15714117--15714217 Score: 157
Period size: 39 Copynumber: 2.6 Consensus size: 39
15714107 GCTCTGATGA
* *
15714117 GCTTCAGTTAGCCTTCGGGCTTTTGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCTGTTTAGCACTTATGT
*
15714156 GTTTCAGTTAGCCTTCGGGCTTCTGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCTGTTTAGCACTTATGT
* *
15714195 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
15714218 AAATCACGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.12, C:0.23, G:0.25, T:0.41
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCTGTTTAGCACTTATGT
Found at i:15725442 original size:46 final size:47
Alignment explanation
Indices: 15725366--15725460 Score: 122
Period size: 46 Copynumber: 2.0 Consensus size: 47
15725356 ATTGTCACAT
* * *
15725366 ATCACACACTGAAGCCATAGTCCTGCTATGGTTTTACACGG-ATCAC
1 ATCACACACCGAAGCCATAGTCCAGATATGGTTTTACACGGAATCAC
* *
15725412 ATCACACACCGATGCCATA-TCCCAGATATGGTTTTATACGGAATCAC
1 ATCACACACCGAAGCCATAGT-CCAGATATGGTTTTACACGGAATCAC
15725459 AT
1 AT
15725461 TATCATGTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
45 1 0.02
46 34 0.81
47 7 0.17
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (47 bp):
ATCACACACCGAAGCCATAGTCCAGATATGGTTTTACACGGAATCAC
Found at i:15725495 original size:53 final size:51
Alignment explanation
Indices: 15725418--15725552 Score: 150
Period size: 53 Copynumber: 2.6 Consensus size: 51
15725408 TCACATCACA
* * * *
15725418 CACCGATGCCATATCCCAGATATGGTTTTATAC-GGAATCACAT-TATCA-TG
1 CACCAATGCCATAGCCCAGCTATGGTCTTATACGGGAA-CACATATA-CATTG
15725468 TCACACATATGCCATAGCCCAGCTATGGTCTTATACGGGAACACATATCACATTG
1 -CAC-CA-ATGCCATAGCCCAGCTATGGTCTTATACGGGAACACATAT-ACATTG
*
15725523 CACCAATGCCATAGCCTAGCTATGGTCTTA
1 CACCAATGCCATAGCCCAGCTATGGTCTTA
15725553 AATGGGCGCA
Statistics
Matches: 73, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
51 3 0.04
52 25 0.34
53 32 0.44
54 10 0.14
55 3 0.04
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (51 bp):
CACCAATGCCATAGCCCAGCTATGGTCTTATACGGGAACACATATACATTG
Found at i:15730945 original size:23 final size:23
Alignment explanation
Indices: 15730909--15730959 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
15730899 TCGTTGTTTA
*
15730909 ATATTTTTATCTTTATAAACTTG
1 ATATTTTTATCTTTATAAAATTG
*
15730932 TTATTTGTTA-CTTTATAAAATTG
1 ATATTT-TTATCTTTATAAAATTG
15730955 ATATT
1 ATATT
15730960 ATTTTTTCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (23 bp):
ATATTTTTATCTTTATAAAATTG
Found at i:15735007 original size:111 final size:113
Alignment explanation
Indices: 15734863--15735087 Score: 355
Period size: 111 Copynumber: 2.0 Consensus size: 113
15734853 CTTTTTATCA
* * * *
15734863 AATTAAGTATTCAATCGATAAATTTTCTTAACGAAAATTTCAAACAAACATATTATCATGCTTTA
1 AATTAAGGATTCAAACGATAAAATTTCTTAACGAAAATTTCAAACAAACATATTATCATGCTGTA
* *
15734928 GACATT-AA-AATAATAAAATAATTATTGTGACCTCAGATTTGTGGTC
66 GACATTAAATAATAATAAAATAATTATTATGACCTCAGATTTATGGTC
*
15734974 AATTAAGGATTCAAACGATAAAATTTCTTAACGAAAGTTTCAAACAAACATATTATCATGCTGTA
1 AATTAAGGATTCAAACGATAAAATTTCTTAACGAAAATTTCAAACAAACATATTATCATGCTGTA
*
15735039 GACATTAAAATAATAATAAAATAATTATTATGACCTCGGATTTATGGTC
66 GACATT-AAATAATAATAAAATAATTATTATGACCTCAGATTTATGGTC
15735088 CCGAAATCAC
Statistics
Matches: 103, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
111 66 0.64
113 2 0.02
114 35 0.34
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (113 bp):
AATTAAGGATTCAAACGATAAAATTTCTTAACGAAAATTTCAAACAAACATATTATCATGCTGTA
GACATTAAATAATAATAAAATAATTATTATGACCTCAGATTTATGGTC
Found at i:15736401 original size:27 final size:27
Alignment explanation
Indices: 15736363--15736419 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
15736353 TCTGCCAGGG
15736363 AAGTTGCAGATGCAATTTTAAATTTGT
1 AAGTTGCAGATGCAATTTTAAATTTGT
*
15736390 AAGTTGCAGATGCAATTTTTAATTTGT
1 AAGTTGCAGATGCAATTTTAAATTTGT
15736417 AAG
1 AAG
15736420 GCGATAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.40
Consensus pattern (27 bp):
AAGTTGCAGATGCAATTTTAAATTTGT
Found at i:15740136 original size:96 final size:96
Alignment explanation
Indices: 15739959--15740136 Score: 277
Period size: 96 Copynumber: 1.9 Consensus size: 96
15739949 TATTCTCTTG
* * * *
15739959 TTGGATATTTAATTGGACATTGGAAACCCTTATGATCTTTTGAACTACACCAATAACATTGCACA
1 TTGGATATTTAATTGGACATCGAAAACCCTCATGATCTTTTAAACTACACCAATAACATTGCACA
* *
15740024 AAAGGTGATAGCTCAATATTTTTCTCTCTAT
66 AAAGGTGAGAGATCAATATTTTTCTCTCTAT
*
15740055 TTGGATATTTAATTGGACATCGAAAACCCTCATGATCTTTTAAACTACACCAATAACATTTCACA
1 TTGGATATTTAATTGGACATCGAAAACCCTCATGATCTTTTAAACTACACCAATAACATTGCACA
15740120 ACAA-GTGAGAGATCAAT
66 A-AAGGTGAGAGATCAAT
15740137 CGAACTGGTC
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
96 72 0.97
97 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (96 bp):
TTGGATATTTAATTGGACATCGAAAACCCTCATGATCTTTTAAACTACACCAATAACATTGCACA
AAAGGTGAGAGATCAATATTTTTCTCTCTAT
Found at i:15740764 original size:20 final size:17
Alignment explanation
Indices: 15740734--15740786 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 17
15740724 CAACCCAAAA
15740734 TTTTTTT-TATTTTTTCT
1 TTTTTTTGTATTTTTT-T
15740751 TTTCTTTTCGTATTTTCTTT
1 TTT-TTTT-GTATTTT-TTT
15740771 TTTTTTTGTACTTTTT
1 TTTTTTTGTA-TTTTT
15740787 GATCACTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
17 3 0.10
18 8 0.26
19 8 0.26
20 10 0.32
21 2 0.06
ACGTcount: A:0.06, C:0.09, G:0.04, T:0.81
Consensus pattern (17 bp):
TTTTTTTGTATTTTTTT
Found at i:15740766 original size:19 final size:20
Alignment explanation
Indices: 15740744--15740786 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
15740734 TTTTTTTTAT
15740744 TTTTTCTTTTCTTTTCGTA-
1 TTTTTCTTTTCTTTTCGTAC
* *
15740763 -TTTTCTTTTTTTTTTGTAC
1 TTTTTCTTTTCTTTTCGTAC
15740782 TTTTT
1 TTTTT
15740787 GATCACTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 16 0.80
20 4 0.20
ACGTcount: A:0.05, C:0.12, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTTCTTTTCGTAC
Found at i:15745358 original size:20 final size:20
Alignment explanation
Indices: 15745335--15745376 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
15745325 TATTTTTATT
* *
15745335 TATTTAATAAATAAAATTTA
1 TATTTAACAAATAAAAATTA
*
15745355 TATTTAACATATAAAAATTA
1 TATTTAACAAATAAAAATTA
15745375 TA
1 TA
15745377 AATAATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
TATTTAACAAATAAAAATTA
Found at i:15745650 original size:16 final size:16
Alignment explanation
Indices: 15745629--15745659 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15745619 ATATTACCAT
*
15745629 TATTTAATTTTAAAAA
1 TATTTAATATTAAAAA
15745645 TATTTAATATTAAAA
1 TATTTAATATTAAAA
15745660 TAATAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTAATATTAAAAA
Found at i:15747185 original size:18 final size:20
Alignment explanation
Indices: 15747162--15747208 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
15747152 TTATAAAATA
15747162 AATATAA-ATTGTT-TTTAT
1 AATATAATATTGTTATTTAT
*
15747180 AATATATATATTTTTATTTAT
1 AATATA-ATATTGTTATTTAT
15747201 AATATAAT
1 AATATAAT
15747209 TTTAAAACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 6 0.24
19 1 0.04
20 7 0.28
21 11 0.44
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
AATATAATATTGTTATTTAT
Found at i:15752743 original size:3 final size:3
Alignment explanation
Indices: 15752735--15752763 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
15752725 TAGGTGATAA
15752735 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
15752764 AATGCATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:15757803 original size:28 final size:28
Alignment explanation
Indices: 15757705--15757803 Score: 101
Period size: 28 Copynumber: 3.5 Consensus size: 28
15757695 TCACAAATTG
* * * *
15757705 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGAGTTC-GACTATATA
* * * *
15757734 ACACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTCGACTATATA
15757762 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGTTCGACTATAT-A
15757790 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
15757804 GGCTTATTAC
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.73
29 15 0.25
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTCGACTATATA
Found at i:15775433 original size:86 final size:86
Alignment explanation
Indices: 15775283--15775449 Score: 325
Period size: 86 Copynumber: 1.9 Consensus size: 86
15775273 CCTTGTACAA
15775283 GAAAGCGTGGAAAGCAAAGAAAAAGCTAGTTGCACGATTATTAAATGTCATAACAATCTACATAG
1 GAAAGCGTGGAAAGCAAAGAAAAAGCTAGTTGCACGATTATTAAATGTCATAACAATCTACATAG
15775348 GTGGTTATTTATGGTCGAGGT
66 GTGGTTATTTATGGTCGAGGT
*
15775369 GAAAGCGTGGAAAGCAAAGAAAAAGCTAGTTGCACGATTATTAAATGTCATAACAATCTGCATAG
1 GAAAGCGTGGAAAGCAAAGAAAAAGCTAGTTGCACGATTATTAAATGTCATAACAATCTACATAG
15775434 GTGGTTATTTATGGTC
66 GTGGTTATTTATGGTC
15775450 AAACAACTCA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 80 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (86 bp):
GAAAGCGTGGAAAGCAAAGAAAAAGCTAGTTGCACGATTATTAAATGTCATAACAATCTACATAG
GTGGTTATTTATGGTCGAGGT
Found at i:15785150 original size:31 final size:31
Alignment explanation
Indices: 15785107--15785179 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
15785097 AAACAATAGC
* * *
15785107 TTTTATATTTTCATCTTTTAT-AATTTATTTTT
1 TTTTAT-TTTTCATATTTTATAAAATT-TTATT
*
15785139 TTTTATTTTTCATATTTTTTAAAATTTTATT
1 TTTTATTTTTCATATTTTATAAAATTTTATT
15785170 TTTTATTTTT
1 TTTTATTTTT
15785180 AATAATTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 26 0.72
32 10 0.28
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (31 bp):
TTTTATTTTTCATATTTTATAAAATTTTATT
Found at i:15785172 original size:32 final size:32
Alignment explanation
Indices: 15785137--15785198 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
15785127 TAATTTATTT
*
15785137 TTTTTTATTTTTCAT-ATTTTTTAAAATTTTA
1 TTTTTTATTTTTAATAATTTTTTAAAATTTTA
* *
15785168 TTTTTTATTTTTAATAATTATTTAAACTTTT
1 TTTTTTATTTTTAATAATTTTTTAAAATTTT
15785199 TAGATTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 14 0.52
32 13 0.48
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.69
Consensus pattern (32 bp):
TTTTTTATTTTTAATAATTTTTTAAAATTTTA
Found at i:15785221 original size:13 final size:13
Alignment explanation
Indices: 15785202--15785232 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
15785192 AACTTTTTAG
15785202 ATTTTTTTTAA-A
1 ATTTTTTTTAAGA
15785214 ATTTTTTTTAAGA
1 ATTTTTTTTAAGA
15785227 ATTTTT
1 ATTTTT
15785233 GAAAAATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (13 bp):
ATTTTTTTTAAGA
Found at i:15785281 original size:10 final size:10
Alignment explanation
Indices: 15785266--15785290 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
15785256 TATAAATTTC
15785266 AAAATATTGA
1 AAAATATTGA
15785276 AAAATATTGA
1 AAAATATTGA
15785286 AAAAT
1 AAAAT
15785291 CTGAAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (10 bp):
AAAATATTGA
Found at i:15785636 original size:12 final size:12
Alignment explanation
Indices: 15785619--15785643 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15785609 TAAAATTTGC
15785619 AAATATATATAT
1 AAATATATATAT
15785631 AAATATATATAT
1 AAATATATATAT
15785643 A
1 A
15785644 TAATTTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATATATATAT
Found at i:15785980 original size:37 final size:37
Alignment explanation
Indices: 15785937--15786011 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
15785927 TCGTGCCTGT
15785937 CAGATAAGCGCAAATGGTCGCGCTTGACAGGTAGGCG
1 CAGATAAGCGCAAATGGTCGCGCTTGACAGGTAGGCG
*
15785974 CAGATAAGCGCAACTGGTCGCGCTTGACAGGTAGGCG
1 CAGATAAGCGCAAATGGTCGCGCTTGACAGGTAGGCG
15786011 C
1 C
15786012 CACTGCCTGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.24, G:0.35, T:0.16
Consensus pattern (37 bp):
CAGATAAGCGCAAATGGTCGCGCTTGACAGGTAGGCG
Found at i:15786187 original size:11 final size:11
Alignment explanation
Indices: 15786173--15786238 Score: 51
Period size: 12 Copynumber: 5.7 Consensus size: 11
15786163 CACCGGAAGA
*
15786173 GAGAAGGAAAG
1 GAGAAGAAAAG
15786184 GAGAAGAAAAG
1 GAGAAGAAAAG
* *
15786195 AAGAGGAAGAAG
1 GAGAAGAA-AAG
*
15786207 AAGAAGAAGAAG
1 GAGAAGAA-AAG
*
15786219 AAGAAGAAGAAG
1 GAGAAGAA-AAG
*
15786231 AAGAAGAA
1 GAGAAGAA
15786239 GAAGAAAAGG
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
11 16 0.32
12 34 0.68
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (11 bp):
GAGAAGAAAAG
Found at i:15786198 original size:3 final size:3
Alignment explanation
Indices: 15786185--15786244 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
15786175 GAAGGAAAGG
*
15786185 AGA AGA A-A AGA AGA GGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
15786232 AGA AGA AGA AGA A
1 AGA AGA AGA AGA A
15786245 AAGGTAATGT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 52 0.96
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:15786481 original size:59 final size:59
Alignment explanation
Indices: 15786401--15786529 Score: 206
Period size: 59 Copynumber: 2.2 Consensus size: 59
15786391 GTAATTTTTT
* *
15786401 TTGTTT-TTTATAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATAATGTTATAAA
1 TTGTTTGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATAATATTATAAA
* *
15786459 TTGTTTGTTTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATATTATAAA
1 TTGTTTGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATAATATTATAAA
15786518 TTGTTGTGTTTA
1 TTGTT-TGTTTA
15786530 GTTTAGTATT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 6 0.09
59 53 0.83
60 5 0.08
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (59 bp):
TTGTTTGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATAATATTATAAA
Found at i:15786614 original size:31 final size:31
Alignment explanation
Indices: 15786577--15786675 Score: 100
Period size: 31 Copynumber: 3.3 Consensus size: 31
15786567 TTTTGTTAAA
15786577 TATTTTGTTAGTAATTTATTATAAATTGTTG
1 TATTTTGTTAGTAATTTATTATAAATTGTTG
* * * *
15786608 TGTTTTGTGAGT-TTTTAGTAATATAAA---AT-
1 TATTTTGTTAGTAATTTA-T--TATAAATTGTTG
15786637 TATTTTGTTAGTAATTTATTATAAATTGTTG
1 TATTTTGTTAGTAATTTATTATAAATTGTTG
15786668 TATTTTGT
1 TATTTTGT
15786676 GAGTTTTTAG
Statistics
Matches: 52, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
27 6 0.12
29 11 0.21
30 10 0.19
31 19 0.37
33 6 0.12
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (31 bp):
TATTTTGTTAGTAATTTATTATAAATTGTTG
Found at i:15786633 original size:33 final size:33
Alignment explanation
Indices: 15786596--15786696 Score: 99
Period size: 33 Copynumber: 3.2 Consensus size: 33
15786586 AGTAATTTAT
*
15786596 TATAAATTGTTGTGTTTTGTGAGTTTTTAGTAA
1 TATAAATTGTTGTATTTTGTGAGTTTTTAGTAA
* * *
15786629 TATAAA---AT-TATTTTGTTAGTAATTTA-T--
1 TATAAATTGTTGTATTTTGTGAGT-TTTTAGTAA
15786656 TATAAATTGTTGTATTTTGTGAGTTTTTAGTAA
1 TATAAATTGTTGTATTTTGTGAGTTTTTAGTAA
*
15786689 TGTAAATT
1 TATAAATT
15786697 AAAAATAATA
Statistics
Matches: 52, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
27 6 0.12
29 11 0.21
30 10 0.19
31 12 0.23
33 13 0.25
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.54
Consensus pattern (33 bp):
TATAAATTGTTGTATTTTGTGAGTTTTTAGTAA
Found at i:15786646 original size:60 final size:60
Alignment explanation
Indices: 15786577--15786694 Score: 218
Period size: 60 Copynumber: 2.0 Consensus size: 60
15786567 TTTTGTTAAA
*
15786577 TATTTTGTTAGTAATTTATTATAAATTGTTGTGTTTTGTGAGTTTTTAGTAATATAAAAT
1 TATTTTGTTAGTAATTTATTATAAATTGTTGTATTTTGTGAGTTTTTAGTAATATAAAAT
*
15786637 TATTTTGTTAGTAATTTATTATAAATTGTTGTATTTTGTGAGTTTTTAGTAATGTAAA
1 TATTTTGTTAGTAATTTATTATAAATTGTTGTATTTTGTGAGTTTTTAGTAATATAAA
15786695 TTAAAAATAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (60 bp):
TATTTTGTTAGTAATTTATTATAAATTGTTGTATTTTGTGAGTTTTTAGTAATATAAAAT
Found at i:15789018 original size:33 final size:33
Alignment explanation
Indices: 15788981--15789110 Score: 136
Period size: 33 Copynumber: 3.9 Consensus size: 33
15788971 ACTCATTTCT
*
15788981 ACCTGTATCCACCGCCATACTCCACTTCTCCTG
1 ACCTGTATCCACCGCCATACTCCACTCCTCCTG
* *
15789014 ACCTGTATCCACTGCCATACTCCACTCCTCTTG
1 ACCTGTATCCACCGCCATACTCCACTCCTCCTG
* ** * * *
15789047 ACTTGTATCCACCGCTGTACTCTATTCCTCCCG
1 ACCTGTATCCACCGCCATACTCCACTCCTCCTG
* * *
15789080 GCCCGTATCCACTGCTC-TACTCCACTCCTCC
1 ACCTGTATCCACCGC-CATACTCCACTCCTCC
15789111 CGGCTCAAGT
Statistics
Matches: 78, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.16, C:0.45, G:0.10, T:0.29
Consensus pattern (33 bp):
ACCTGTATCCACCGCCATACTCCACTCCTCCTG
Found at i:15789059 original size:66 final size:66
Alignment explanation
Indices: 15788984--15789109 Score: 166
Period size: 66 Copynumber: 1.9 Consensus size: 66
15788974 CATTTCTACC
* *
15788984 TGTATCCACCGCCATACTCCACTT-CTCCTGACCTGTATCCACTGC-CATACTCCACTCCTCTTG
1 TGTATCCACCGCCATACTCCA-TTCCTCCCGACCCGTATCCACTGCTC-TACTCCACTCCTCTTG
15789047 ACT
64 ACT
** * *
15789050 TGTATCCACCGCTGTACTCTATTCCTCCCGGCCCGTATCCACTGCTCTACTCCACTCCTC
1 TGTATCCACCGCCATACTCCATTCCTCCCGACCCGTATCCACTGCTCTACTCCACTCCTC
15789110 CCGGCTCAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 2 0.04
66 49 0.94
67 1 0.02
ACGTcount: A:0.16, C:0.44, G:0.10, T:0.30
Consensus pattern (66 bp):
TGTATCCACCGCCATACTCCATTCCTCCCGACCCGTATCCACTGCTCTACTCCACTCCTCTTGAC
T
Found at i:15789434 original size:77 final size:78
Alignment explanation
Indices: 15789307--15789514 Score: 292
Period size: 77 Copynumber: 2.7 Consensus size: 78
15789297 AATCACTTCA
* * * *
15789307 TATTTATGTAATGAATTTTTTTCCATTTTATTTATCGATTTTATGAGTTTTTTTTTTCAATTTAA
1 TATTTATGTAATGACTTTTTTGCCATTTTATTTATCAATTTTATGAGTTTTTTTTTGCAATTTAA
*
15789372 AT-GTCAACTTTG
66 ATAGTAAACTTTG
*
15789384 TATTTATGTAATGACTTTTTTGCCATTTTATTTATCAATTTTATGGGTTTTTTTTTGCAATTTAA
1 TATTTATGTAATGACTTTTTTGCCATTTTATTTATCAATTTTATGAGTTTTTTTTTGCAATTTAA
15789449 ATAGTAAACTTTG
66 ATAGTAAACTTTG
* * * * * * *
15789462 TATTTATGTAATGACTTTTTCGCTATTTCAGTAATTAATTTTAGGAGTTTTTT
1 TATTTATGTAATGACTTTTTTGCCATTTTATTTATCAATTTTATGAGTTTTTT
15789515 ACAATTTAAA
Statistics
Matches: 116, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
77 62 0.53
78 54 0.47
ACGTcount: A:0.25, C:0.08, G:0.11, T:0.56
Consensus pattern (78 bp):
TATTTATGTAATGACTTTTTTGCCATTTTATTTATCAATTTTATGAGTTTTTTTTTGCAATTTAA
ATAGTAAACTTTG
Found at i:15796400 original size:15 final size:15
Alignment explanation
Indices: 15796367--15796413 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
15796357 ACATATAACA
*
15796367 ATATAT-ATTATTAT
1 ATATATAATTACTAT
15796381 ATATATAATTACTAT
1 ATATATAATTACTAT
*
15796396 TTATATAA-TA-TAT
1 ATATATAATTACTAT
15796409 ATATA
1 ATATA
15796414 ATTCTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 7 0.24
14 8 0.28
15 14 0.48
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATATAATTACTAT
Found at i:15801375 original size:11 final size:10
Alignment explanation
Indices: 15801359--15801396 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
15801349 TTTAGTTTAA
15801359 TTAATTAAAGG
1 TTAATT-AAGG
15801370 TTAATTAA-G
1 TTAATTAAGG
*
15801379 TTAATTAAGA
1 TTAATTAAGG
15801389 TTAATTAA
1 TTAATTAA
15801397 AAGTTAAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 9 0.36
10 10 0.40
11 6 0.24
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (10 bp):
TTAATTAAGG
Done.