Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 63 of 344
Found at i:20356372 original size:28 final size:29
Alignment explanation
Indices: 20356317--20356394 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 29
20356307 TAGGCACTTC
*
20356317 CACACGGGTA-ATCCACACGCCATTGTGTGA
1 CACACGGGTAGA-CTACACGCC-TTGTGTGA
20356347 CACACGGGTAGACTACACGCCTGTGTGTGA
1 CACACGGGTAGACTACACGCCT-TGTGTGA
*
20356377 CACACGAGTAGACTACAC
1 CACACGGGTAGACTACAC
20356395 CCCCGTGTGT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 1 0.02
30 42 0.95
31 1 0.02
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.18
Consensus pattern (29 bp):
CACACGGGTAGACTACACGCCTTGTGTGA
Found at i:20361700 original size:40 final size:37
Alignment explanation
Indices: 20361634--20361768 Score: 143
Period size: 35 Copynumber: 3.7 Consensus size: 37
20361624 CATGGCAAAG
20361634 TGTGAAATGTAGGTATGGTA--TCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTTCATCCATACTGAGT
20361669 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATT-TC--ATCCATACTGAGT
** * ** *
20361709 TAAGAAACGTAGGTATGACATTTC--CCATACCGAGT
1 TGTGAAATGTAGGTATGGTATTTCATCCATACTGAGT
* *
20361744 TGTAAAATGTAGGTACGGTATTTCA
1 TGTGAAATGTAGGTATGGTATTTCA
20361769 ATGAGGAAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 11
0.77 0.12 0.10
Matches are distributed among these distances:
35 47 0.58
38 2 0.02
39 2 0.02
40 30 0.37
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.33
Consensus pattern (37 bp):
TGTGAAATGTAGGTATGGTATTTCATCCATACTGAGT
Found at i:20366983 original size:9 final size:9
Alignment explanation
Indices: 20366954--20366990 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
20366944 TGAGTTTTCG
20366954 AATTCGAAT
1 AATTCGAAT
*
20366963 AACTCGAAT
1 AATTCGAAT
20366972 AATTCGAAT
1 AATTCGAAT
*
20366981 AATTCAAAT
1 AATTCGAAT
20366990 A
1 A
20366991 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:20367904 original size:5 final size:5
Alignment explanation
Indices: 20367894--20367919 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
20367884 GAACAAATAT
20367894 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
20367920 ATTCCATCTC
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:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:20368019 original size:5 final size:5
Alignment explanation
Indices: 20368009--20368034 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
20367999 CTCGAAAATT
20368009 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
20368035 CGAATGCTCA
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:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:20370391 original size:40 final size:37
Alignment explanation
Indices: 20370329--20370459 Score: 128
Period size: 35 Copynumber: 3.6 Consensus size: 37
20370319 GCAAAGTGTG
*
20370329 AAATGTAGGTATGGTA--TCATCCATACTGAGTTGTA
1 AAATGTAGGTATGGTATTTCATCCATACAGAGTTGTA
* *
20370364 AAATGTAGGTATGGTATTATCAAATCCATACAGGGTT-AA
1 AAATGTAGGTATGGTATT-TC--ATCCATACAGAGTTGTA
* ** *
20370403 GAAACGTAGGTATGACATTTC--CCATACCGAGTTGTA
1 -AAATGTAGGTATGGTATTTCATCCATACAGAGTTGTA
20370439 AAATGTAGGTATGGTATTTCA
1 AAATGTAGGTATGGTATTTCA
20370460 ATGAGGAAAA
Statistics
Matches: 76, Mismatches: 12, Indels: 15
0.74 0.12 0.15
Matches are distributed among these distances:
35 43 0.57
36 1 0.01
38 2 0.03
39 3 0.04
40 27 0.36
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (37 bp):
AAATGTAGGTATGGTATTTCATCCATACAGAGTTGTA
Found at i:20380939 original size:170 final size:171
Alignment explanation
Indices: 20380654--20381000 Score: 633
Period size: 170 Copynumber: 2.0 Consensus size: 171
20380644 GACTTCTTTG
*
20380654 GGAAGAGAAATGCATGGTCATGGAACCAAAATTCTAGATGATAGAACATAGGGAGAGAAGCCATT
1 GGAAGAGAAATGCATGGTCATGGAACCAAAATTCAAGATGATAGAACATAGGGAGAGAAGCCATT
* *
20380719 GTATGCCCAGTATCGCAATGAGATAGTTCCCCTTAATCTTAATTATCTCTTGTTGCAAAACACTT
66 GTATGCCCAGTATCCCAATGAGATAGTTCCCCTTAATCTTAATCATCTCTTGTTGCAAAACACTT
*
20380784 ACATTCTTTTGCAATTGTGTAATGATCTCATCCCCC-CCAT
131 ACATCCTTTTGCAATTGTGTAATGATCTCATCCCCCTCCAT
*
20380824 GGAAGAGAAATGCATGGTCATGGAATCAAAATTCAAGATGATAGAACATAGGGAGAGAAGCCATT
1 GGAAGAGAAATGCATGGTCATGGAACCAAAATTCAAGATGATAGAACATAGGGAGAGAAGCCATT
*
20380889 GTATGCCTAGTATCCCAATGAGATAGTTCCCCTTAATCTTAATCATCTCTTGTTGCAAAACACTT
66 GTATGCCCAGTATCCCAATGAGATAGTTCCCCTTAATCTTAATCATCTCTTGTTGCAAAACACTT
20380954 ACATCCTTTTGCAATTGTGTAATGATCTCATCCCCCTCCAT
131 ACATCCTTTTGCAATTGTGTAATGATCTCATCCCCCTCCAT
20380995 GGAAGA
1 GGAAGA
20381001 TCGTTGAAGC
Statistics
Matches: 170, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
170 160 0.94
171 10 0.06
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Consensus pattern (171 bp):
GGAAGAGAAATGCATGGTCATGGAACCAAAATTCAAGATGATAGAACATAGGGAGAGAAGCCATT
GTATGCCCAGTATCCCAATGAGATAGTTCCCCTTAATCTTAATCATCTCTTGTTGCAAAACACTT
ACATCCTTTTGCAATTGTGTAATGATCTCATCCCCCTCCAT
Found at i:20383449 original size:11 final size:11
Alignment explanation
Indices: 20383433--20383459 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
20383423 ATGCTCTGGA
20383433 TAATATTAAGG
1 TAATATTAAGG
20383444 TAATATTAAGG
1 TAATATTAAGG
20383455 TAATA
1 TAATA
20383460 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (11 bp):
TAATATTAAGG
Found at i:20384610 original size:21 final size:21
Alignment explanation
Indices: 20384584--20384625 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
20384574 AAAGTAGCAG
20384584 CAAGGAAAGCAGAGGCAACAA
1 CAAGGAAAGCAGAGGCAACAA
*
20384605 CAAGGACAGCAGAGGCAACAA
1 CAAGGAAAGCAGAGGCAACAA
20384626 AAAAATATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.21, G:0.29, T:0.00
Consensus pattern (21 bp):
CAAGGAAAGCAGAGGCAACAA
Found at i:20392562 original size:26 final size:25
Alignment explanation
Indices: 20392528--20392579 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
20392518 AACGAATTCA
20392528 AAATGACTT-GTTCATGATCGTAAAT
1 AAATGACTTAGTT-ATGATCGTAAAT
*
20392553 AAATGAACTTAGGTTGTGATCGTAAAT
1 AAATG-ACTTA-GTTATGATCGTAAAT
20392580 CCACTAGCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 5 0.22
26 4 0.17
27 11 0.48
28 3 0.13
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.35
Consensus pattern (25 bp):
AAATGACTTAGTTATGATCGTAAAT
Found at i:20392615 original size:36 final size:36
Alignment explanation
Indices: 20392568--20392651 Score: 107
Period size: 36 Copynumber: 2.3 Consensus size: 36
20392558 AACTTAGGTT
* * *
20392568 GTGATCGTAAATCCACT-AGCCTTAATAATATTAGTC
1 GTGATCGTAAAT-CAATGAGCCTTAATAACATCAGTC
*
20392604 GTGATCGTAAATCAATGAGCCTTAATAGCATCAGTC
1 GTGATCGTAAATCAATGAGCCTTAATAACATCAGTC
*
20392640 GTGATCATAAAT
1 GTGATCGTAAAT
20392652 TAGTGAACTA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
35 3 0.07
36 39 0.93
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (36 bp):
GTGATCGTAAATCAATGAGCCTTAATAACATCAGTC
Found at i:20392787 original size:134 final size:134
Alignment explanation
Indices: 20392604--20393194 Score: 697
Period size: 134 Copynumber: 4.4 Consensus size: 134
20392594 AATATTAGTC
* * ** * * **
20392604 GTGATCGTAAATCAATGAGCCTTAATAGCATCAGTCGTGATCATAAATTAGTGAACTATTTGAAT
1 GTGATCATAAATCAACGAGCCTTAATAATATCAGTCGTGATCGTAAATCAGCAAACTATTTGAAT
* * * *
20392669 GGAGTTGCAATTGTAAAT-AAGCTTACTCAGAAGAACTTGTTCATGATCATAAATTAATGAACTT
66 GGAGTTGCGATCGTAAATCAA-CTAACTCAGAAGAACTTGTTCATGATCATAAATCAATGAACTT
20392733 AGGTT
130 AGGTT
* * * * * *
20392738 TTGATCATAAATCAACAAGCCTTAATAATAGT-AGTCGTGATCGTAAATTAGCGAACTGTTTAAA
1 GTGATCATAAATCAACGAGCCTTAATAATA-TCAGTCGTGATCGTAAATCAGCAAACTATTTGAA
* * * *
20392802 TGAAGTTGTGATCATAAATCAACTAACTTAGAAGAACTTGTTCATGATCGA-AAATCAATGAACT
65 TGGAGTTGCGATCGTAAATCAACTAACTCAGAAGAACTTGTTCATGATC-ATAAATCAATGAACT
20392866 TAGGTT
129 TAGGTT
* * * * *
20392872 GTGATCATTAATTAGCGAGCCTTAACAATATCAGTCGTGATCGTAAATCAACAAACTATTTGAAT
1 GTGATCATAAATCAACGAGCCTTAATAATATCAGTCGTGATCGTAAATCAGCAAACTATTTGAAT
* * *
20392937 GGAGTTGCGATCGTAAATCAACTAATTCAAAAGAACTTGTTCATGATTATAAATCAATGAACTTA
66 GGAGTTGCGATCGTAAATCAACTAACTCAGAAGAACTTGTTCATGATCATAAATCAATGAACTTA
20393002 GGTT
131 GGTT
* * * * *
20393006 GTGATCATAAATCAACGAGCCTTAACAATATTAGTTGTGATCATAAATCAGCAAACTGTTTGAAT
1 GTGATCATAAATCAACGAGCCTTAATAATATCAGTCGTGATCGTAAATCAGCAAACTATTTGAAT
* * * * *
20393071 GGAGTTGTGATTGTAAATCAACTAACTCA-AATGGAA-TTGTTTATGATCGTAAATCAATAAACT
66 GGAGTTGCGATCGTAAATCAACTAACTCAGAA--GAACTTGTTCATGATCATAAATCAATGAACT
20393134 TAGGTT
129 TAGGTT
* * * * *
20393140 GTAATCATAAATCAGCGAGCCTTAATAATATCAGTCATGATCGCAAATCAACAAA
1 GTGATCATAAATCAACGAGCCTTAATAATATCAGTCGTGATCGTAAATCAGCAAA
20393195 TTGTTTAATA
Statistics
Matches: 390, Mismatches: 60, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
133 4 0.01
134 379 0.97
135 7 0.02
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (134 bp):
GTGATCATAAATCAACGAGCCTTAATAATATCAGTCGTGATCGTAAATCAGCAAACTATTTGAAT
GGAGTTGCGATCGTAAATCAACTAACTCAGAAGAACTTGTTCATGATCATAAATCAATGAACTTA
GGTT
Found at i:20393065 original size:268 final size:267
Alignment explanation
Indices: 20392633--20393194 Score: 768
Period size: 268 Copynumber: 2.1 Consensus size: 267
20392623 CCTTAATAGC
* * *** * *
20392633 ATCAGTCGTGATCATAAATTAGTGAACTATTTGAATGGAGTTGCAATTGTAAATAAGCTTACTCA
1 ATCAGTCGTGATCGTAAATCAACAAACTATTTGAATGGAGTTGCAATCGTAAATAAGCTAACTCA
* * *
20392698 GAAGAACTTGTTCATGATCATAAATTAATGAACTTAGGTTTTGATCATAAATCAACAAGCCTTAA
66 AAAGAACTTGTTCATGATCATAAATCAATGAACTTAGGTTGTGATCATAAATCAACAAGCCTTAA
* * * *
20392763 TAATAGTAGTCGTGATCGTAAATTAGCGAACTGTTTAAATGAAGTTGTGATCATAAATCAACTAA
131 CAATAGTAGTCGTGATCATAAATCAGCAAACTGTTTAAATGAAGTTGTGATCATAAATCAACTAA
* * * * *
20392828 CTTAGAA-GAACTTGTTCATGATCGAAAATCAATGAACTTAGGTTGTGATCATTAATTAGCGAGC
196 CTCA-AAGGAA-TTGTTCATGATCGAAAATCAATAAACTTAGGTTGTAATCATAAATCAGCGAGC
20392892 CTTAACAAT
259 CTTAACAAT
* *
20392901 ATCAGTCGTGATCGTAAATCAACAAACTATTTGAATGGAGTTGCGATCGTAAATCAA-CTAATTC
1 ATCAGTCGTGATCGTAAATCAACAAACTATTTGAATGGAGTTGCAATCGTAAAT-AAGCTAACTC
* *
20392965 AAAAGAACTTGTTCATGATTATAAATCAATGAACTTAGGTTGTGATCATAAATCAACGAGCCTTA
65 AAAAGAACTTGTTCATGATCATAAATCAATGAACTTAGGTTGTGATCATAAATCAACAAGCCTTA
* * * * **
20393030 ACAATATTAGTTGTGATCATAAATCAGCAAACTGTTTGAATGGAGTTGTGATTGTAAATCAACTA
130 ACAATAGTAGTCGTGATCATAAATCAGCAAACTGTTTAAATGAAGTTGTGATCATAAATCAACTA
* *
20393095 ACTCAAATGGAATTGTTTATGATCGTAAATCAATAAACTTAGGTTGTAATCATAAATCAGCGAGC
195 ACTCAAA-GGAATTGTTCATGATCGAAAATCAATAAACTTAGGTTGTAATCATAAATCAGCGAGC
*
20393160 CTTAATAAT
259 CTTAACAAT
* *
20393169 ATCAGTCATGATCGCAAATCAACAAA
1 ATCAGTCGTGATCGTAAATCAACAAA
20393195 TTGTTTAATA
Statistics
Matches: 257, Mismatches: 34, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
267 2 0.01
268 250 0.97
269 5 0.02
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (267 bp):
ATCAGTCGTGATCGTAAATCAACAAACTATTTGAATGGAGTTGCAATCGTAAATAAGCTAACTCA
AAAGAACTTGTTCATGATCATAAATCAATGAACTTAGGTTGTGATCATAAATCAACAAGCCTTAA
CAATAGTAGTCGTGATCATAAATCAGCAAACTGTTTAAATGAAGTTGTGATCATAAATCAACTAA
CTCAAAGGAATTGTTCATGATCGAAAATCAATAAACTTAGGTTGTAATCATAAATCAGCGAGCCT
TAACAAT
Found at i:20395819 original size:17 final size:17
Alignment explanation
Indices: 20395797--20395834 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
20395787 TTTATTTTCC
20395797 ATTCTGGACACGAACCT
1 ATTCTGGACACGAACCT
20395814 ATTCTGGACACGAACCT
1 ATTCTGGACACGAACCT
20395831 ATTC
1 ATTC
20395835 AGTGCAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (17 bp):
ATTCTGGACACGAACCT
Found at i:20396121 original size:11 final size:11
Alignment explanation
Indices: 20396105--20396132 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
20396095 GTCGCCTCTT
20396105 CCTTCGTTCTA
1 CCTTCGTTCTA
20396116 CCTTCGTTCTA
1 CCTTCGTTCTA
20396127 CCTTCG
1 CCTTCG
20396133 CCTCCCGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.39, G:0.11, T:0.43
Consensus pattern (11 bp):
CCTTCGTTCTA
Found at i:20399663 original size:18 final size:17
Alignment explanation
Indices: 20399635--20399669 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20399625 ATTATTAAGA
*
20399635 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
20399652 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
20399670 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:20399721 original size:120 final size:120
Alignment explanation
Indices: 20399585--20399806 Score: 435
Period size: 120 Copynumber: 1.9 Consensus size: 120
20399575 TTGGTCCAAT
*
20399585 TCATATATTATGATTTGAGTCAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTAT
1 TCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTAT
20399650 ATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTA
66 ATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTA
20399705 TCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTAT
1 TCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTAT
20399770 ATATTTTAATTAAAATATATTTAATAATAATTATGTT
66 ATATTTTAATTAAAATATATTTAATAATAATTATGTT
20399807 TAAATATGAT
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 101 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (120 bp):
TCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTAT
ATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTA
Found at i:20399783 original size:18 final size:17
Alignment explanation
Indices: 20399755--20399789 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20399745 ATTATTAAGA
*
20399755 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
20399772 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
20399790 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:20400019 original size:44 final size:45
Alignment explanation
Indices: 20399954--20400044 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
20399944 ACCTCTATTC
* * *
20399954 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
20399998 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
20400043 CA
1 CA
20400045 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:20400046 original size:16 final size:16
Alignment explanation
Indices: 20400025--20400093 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
20400015 GATTAGCTAT
20400025 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
20400041 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
20400058 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
20400074 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
20400090 TACA
1 TACA
20400094 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:20400067 original size:33 final size:32
Alignment explanation
Indices: 20400025--20400093 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
20400015 GATTAGCTAT
20400025 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
20400058 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
20400090 TACA
1 TACA
20400094 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:20402935 original size:33 final size:33
Alignment explanation
Indices: 20402898--20402965 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
20402888 CAAGCATCCA
20402898 CTAATCTATCAATTAAGGATAAATGAAAACTAT
1 CTAATCTATCAATTAAGGATAAATGAAAACTAT
*
20402931 CTAATCTATCAATTAAGGGTAAATGAAAACTAT
1 CTAATCTATCAATTAAGGATAAATGAAAACTAT
20402964 CT
1 CT
20402966 TTGAGCACAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (33 bp):
CTAATCTATCAATTAAGGATAAATGAAAACTAT
Found at i:20409244 original size:20 final size:21
Alignment explanation
Indices: 20409197--20409246 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
20409187 ATGCCACATC
20409197 AGTATTCTTATCCTGAATTTCA
1 AGTATT-TTATCCTGAATTTCA
* *
20409219 AG-ATTTTATTCTGAATTT-T
1 AGTATTTTATCCTGAATTTCA
20409238 AGTATTTTA
1 AGTATTTTA
20409247 ATTTGGATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.08
20 18 0.72
21 3 0.12
22 2 0.08
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (21 bp):
AGTATTTTATCCTGAATTTCA
Found at i:20410040 original size:153 final size:150
Alignment explanation
Indices: 20409753--20410068 Score: 346
Period size: 160 Copynumber: 2.0 Consensus size: 150
20409743 AAAAAAATAA
* *
20409753 ATAATAATTACAGCATTACTTATATAAACAATAAATGATTACATATACGATAAAAATAAAATTAT
1 ATAATAATTACAGCATTACTTATATAAACAATAAATGATTACATATACAATAAAAATAAAAATAT
* *
20409818 TATACATATTATTATTTTATTACTGAAATTATACTTAACATATTTTTAGTAACGTTATAAATATC
66 TATACATATTATTATTTTATTACTGAAATTATACTTAACATATTTTTAATAAC-TTAT--ACATC
20409883 AAATAATCCAAAATTTTATTTAT
128 AAATAATCCAAAATTTTATTTAT
* * * * *
20409906 ATAATAATTACATCATTATTTATATAAACAATAAGTGATTGCATATGCAATAAAAATAAATTTAA
1 ATAATAATTACAGCATTACTTATATAAACAATAAATGATTACATATACAAT---AA-AAA--TAA
* * * * * *
20409971 AAATATTATACATTTTGTTGTTTTATTATTGAAATTATACTTTAACATGTTTTTAATAATTTCAT
60 AAATATTATACATATTATTATTTTATTACTGAAATTATAC-TTAACATATTTTTAATAACTT-AT
* *
20410036 AAATATAAAATAATCCAAAATTTTCA-TTAT
123 --ACATCAAATAATCCAAAATTTT-ATTTAT
20410066 ATA
1 ATA
20410069 CAATTTTTAG
Statistics
Matches: 139, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
153 45 0.32
156 2 0.01
157 3 0.02
159 40 0.29
160 48 0.35
161 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (150 bp):
ATAATAATTACAGCATTACTTATATAAACAATAAATGATTACATATACAATAAAAATAAAAATAT
TATACATATTATTATTTTATTACTGAAATTATACTTAACATATTTTTAATAACTTATACATCAAA
TAATCCAAAATTTTATTTAT
Found at i:20412904 original size:22 final size:23
Alignment explanation
Indices: 20412875--20412929 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
20412865 TTTCAACTTT
* *
20412875 CTTAATTAAGTTTTAA-TAAATCA
1 CTTAATTAAG-TCTAATTAAACCA
20412898 -TTAATTAAGTCTAATTAAACCA
1 CTTAATTAAGTCTAATTAAACCA
20412920 CTTAATTAAG
1 CTTAATTAAG
20412930 CATAACCTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 4 0.14
22 15 0.54
23 9 0.32
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (23 bp):
CTTAATTAAGTCTAATTAAACCA
Found at i:20413682 original size:12 final size:12
Alignment explanation
Indices: 20413665--20413689 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20413655 TGTGAAAAAT
20413665 AAAATAAAATAA
1 AAAATAAAATAA
20413677 AAAATAAAATAA
1 AAAATAAAATAA
20413689 A
1 A
20413690 GAACACACAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:20420432 original size:13 final size:13
Alignment explanation
Indices: 20420414--20420439 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20420404 TATGAAAAAT
20420414 AAAATAAAATAAA
1 AAAATAAAATAAA
20420427 AAAATAAAATAAA
1 AAAATAAAATAAA
20420440 GAACACACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAATAAAATAAA
Found at i:20439828 original size:45 final size:45
Alignment explanation
Indices: 20439764--20439853 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
20439754 TGAGGAAGAA
20439764 ATCTACTATTTATAAATGATTAATTTAAATTTATTTAGATTTATT
1 ATCTACTATTTATAAATGATTAATTTAAATTTATTTAGATTTATT
20439809 ATCTACTATTTATAAATGATTAATTTAAATTTATTTAGATTTATT
1 ATCTACTATTTATAAATGATTAATTTAAATTTATTTAGATTTATT
20439854 CCTATTAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (45 bp):
ATCTACTATTTATAAATGATTAATTTAAATTTATTTAGATTTATT
Found at i:20440388 original size:24 final size:24
Alignment explanation
Indices: 20440361--20440407 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
20440351 GTTAGTATAT
20440361 GTTAAAATATAATTTATTTCTAAA
1 GTTAAAATATAATTTATTTCTAAA
*
20440385 GTTAATATATAATTTATTTCTAA
1 GTTAAAATATAATTTATTTCTAA
20440408 TAAAATCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (24 bp):
GTTAAAATATAATTTATTTCTAAA
Found at i:20446850 original size:20 final size:20
Alignment explanation
Indices: 20446825--20446870 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
20446815 AGACCTCAAT
*
20446825 TTCTCAAAATCTCTTTTTGG
1 TTCTCAAAATCTCATTTTGG
*
20446845 TTCTCAACATCTCATTTTGG
1 TTCTCAAAATCTCATTTTGG
20446865 TTCTCA
1 TTCTCA
20446871 GCTTTTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.24, G:0.09, T:0.48
Consensus pattern (20 bp):
TTCTCAAAATCTCATTTTGG
Found at i:20448772 original size:24 final size:25
Alignment explanation
Indices: 20448738--20448795 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
20448728 TCTTACTACA
* **
20448738 TCAATATCCATTTCATGCATTTC-T
1 TCAATAACCATTTCATAAATTTCAT
20448762 TCAATAACCATTTCATAAATTTCATT
1 TCAATAACCATTTCATAAATTTCA-T
20448788 TCAATAAC
1 TCAATAAC
20448796 TTTTTCTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 20 0.69
26 9 0.31
ACGTcount: A:0.34, C:0.22, G:0.02, T:0.41
Consensus pattern (25 bp):
TCAATAACCATTTCATAAATTTCAT
Found at i:20449376 original size:14 final size:15
Alignment explanation
Indices: 20449357--20449390 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
20449347 TTTAATGAGA
20449357 TATTTTATTATTA-T
1 TATTTTATTATTATT
20449371 TATTTTATTATTATT
1 TATTTTATTATTATT
20449386 TATTT
1 TATTT
20449391 AGTATAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTTTATTATTATT
Found at i:20451564 original size:12 final size:13
Alignment explanation
Indices: 20451546--20451577 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
20451536 TTGATATCTC
20451546 AATTTCAATTCAT
1 AATTTCAATTCAT
20451559 -ATTTCAATTCAT
1 AATTTCAATTCAT
20451571 AATTTCA
1 AATTTCA
20451578 CTTTCTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTTCAATTCAT
Found at i:20454800 original size:24 final size:23
Alignment explanation
Indices: 20454773--20454818 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
20454763 GCAATGTATT
20454773 TTTTTTCATAT-TTCTTTGTTTTAA
1 TTTTTT-ATATATTCTTT-TTTTAA
*
20454797 TTTTTTATGTATTCTTTTTTTA
1 TTTTTTATATATTCTTTTTTTA
20454819 TGATTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (23 bp):
TTTTTTATATATTCTTTTTTTAA
Found at i:20457437 original size:3 final size:3
Alignment explanation
Indices: 20457431--20457504 Score: 57
Period size: 3 Copynumber: 25.3 Consensus size: 3
20457421 TCAGTTAATT
* * *
20457431 TTA TTA TTA TT- TATA TTCA TTA TTA TTA TTA CTA TTA CTA CTA TT-
1 TTA TTA TTA TTA T-TA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
20457476 GTA TT- TT- TTA CTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
20457505 ACTATTAAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
2 6 0.10
3 48 0.83
4 4 0.07
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:20457619 original size:3 final size:3
Alignment explanation
Indices: 20457611--20457831 Score: 127
Period size: 3 Copynumber: 73.3 Consensus size: 3
20457601 ACTTTTACCT
* *
20457611 TTA TTA TTA TTA TT- TTA TTA TCTA TTTA TTTA TATC TTT TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA T-TA -TTA -TTA T-TA TTA TTA T-TA
* * * *
20457657 CTT- TTA -AA TT- TTA -TA TTA TTTA TTT TTA TTA TTT TTA CTA TTA
1 -TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
* * *
20457700 TTA TTA GCGTA TTA TTA TTCT TTA TT- TTA TTA TT- GTA TTA TTA TTA
1 TTA TTA --TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * **
20457746 TTA TTA TTA TTA TTA TTA TTA TTA TCA TCA TCA -AA TTA AT- TTA GCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
20457792 TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA GTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
20457832 ATCTCTTTCT
Statistics
Matches: 170, Mismatches: 30, Indels: 36
0.72 0.13 0.15
Matches are distributed among these distances:
2 14 0.08
3 134 0.79
4 18 0.11
5 4 0.02
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:20457729 original size:29 final size:26
Alignment explanation
Indices: 20457682--20457770 Score: 99
Period size: 26 Copynumber: 3.3 Consensus size: 26
20457672 TTATTTATTT
*
20457682 TTATTATTTTTACTATTATTATTAGCGTA
1 TTATTATTTTTA-TTTTATTATTA--GTA
20457711 TTATTATTCTTTATTTTATTATT-GTA
1 TTATTATT-TTTATTTTATTATTAGTA
* *
20457737 TTATTATTATTATTATTATTATTATTA
1 TTATTATTTTTATT-TTATTATTAGTA
20457764 TTATTAT
1 TTATTAT
20457771 CATCATCAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
25 5 0.09
26 19 0.35
27 9 0.17
29 17 0.31
30 4 0.07
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.65
Consensus pattern (26 bp):
TTATTATTTTTATTTTATTATTAGTA
Found at i:20458066 original size:18 final size:18
Alignment explanation
Indices: 20458045--20458086 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
20458035 GGTCCTATTA
*
20458045 TTTTATTTTACTCTTTA-
1 TTTTTTTTTACTCTTTAG
*
20458062 TTTTTTTTTATTCTTTAG
1 TTTTTTTTTACTCTTTAG
20458080 TTTTTTT
1 TTTTTTT
20458087 ATCTATTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTTTTTTACTCTTTAG
Found at i:20464818 original size:45 final size:45
Alignment explanation
Indices: 20464754--20465339 Score: 213
Period size: 45 Copynumber: 13.2 Consensus size: 45
20464744 GAATTCACAG
20464754 ATCTTATCTCCATGAGGTAGTAATGGAGCAGATCGAAGACAGTGA
1 ATCTTATCTCCATGAGGTAGTAATGGAGCAGATCGAAGACAGTGA
* * * * *
20464799 ATCTTATCTCCTTCAGGTAGTAAGGGAGCAGATTC-AAGCCACT-A
1 ATCTTATCTCCATGAGGTAGTAATGGAGCAGA-TCGAAGACAGTGA
** * * * * * ** *
20464843 GCCTTGTCTCCCTGA-GCAGTAGTGGAGCAG-GCTGAAGATTGTAA
1 ATCTTATCTCCATGAGGTAGTAATGGAGCAGATC-GAAGACAGTGA
* * ** * *
20464887 ATCTTATCTCCATGAGGTAGCAATAGAGCAGATTAAAGACGGCGA
1 ATCTTATCTCCATGAGGTAGTAATGGAGCAGATCGAAGACAGTGA
* * * ** * *
20464932 ATCTTATCTCCTTGAGGTAGCAAGGGAGCAGATTTAAGCCACT-A
1 ATCTTATCTCCATGAGGTAGTAATGGAGCAGATCGAAGACAGTGA
* * * * * * **
20464976 GTCGTGTCTCTC-TGA-GCAGTAGTGGAGCAG-GCTGAAGATTGT-A
1 ATCTTATCTC-CATGAGGTAGTAATGGAGCAGATC-GAAGACAGTGA
* * *
20465019 GATCTTATCTCTATGAGGTAGCAATGGAGCAGATCGAAGAC-GACGA
1 -ATCTTATCTCCATGAGGTAGTAATGGAGCAGATCGAAGACAG-TGA
* * * * *** * *
20465065 ATCTTATTTCCTTGAGGTAGCAAGGGAGCAGATTTCAGCCACT-A
1 ATCTTATCTCCATGAGGTAGTAATGGAGCAGATCGAAGACAGTGA
** * * * * * **
20465109 GCCTTGTCTCCCTGA-GCAGCAGTGGAGCAAGAT-GAAGATTGT-A
1 ATCTTATCTCCATGAGGTAGTAATGGAGC-AGATCGAAGACAGTGA
* * * *
20465152 GATCTTATCTCCATGAGGTAGCAATGGAGCAGATTGAAGACGGAGA
1 -ATCTTATCTCCATGAGGTAGTAATGGAGCAGATCGAAGACAGTGA
* * * ** * *
20465198 ATCTTATCTCCTTGAGGTAGCAAGGGAGCAGATTTAAGCCACT--
1 ATCTTATCTCCATGAGGTAGTAATGGAGCAGATCGAAGACAGTGA
* * * **
20465241 AGCTTTATCTCCCA-GA-GCAGTAATGGAGCAG-GCTGAAGATTGT-A
1 ATC-TTATCT-CCATGAGGTAGTAATGGAGCAGATC-GAAGACAGTGA
* * * * * *
20465285 GATCTCATCTGCATAAGGTAGTAATGGAACAGATCGAAGACGGCGA
1 -ATCTTATCTCCATGAGGTAGTAATGGAGCAGATCGAAGACAGTGA
20465331 ATCTTATCT
1 ATCTTATCT
20465340 TGGTAGCAAG
Statistics
Matches: 384, Mismatches: 128, Indels: 58
0.67 0.22 0.10
Matches are distributed among these distances:
41 1 0.00
43 66 0.17
44 89 0.23
45 221 0.58
46 7 0.02
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (45 bp):
ATCTTATCTCCATGAGGTAGTAATGGAGCAGATCGAAGACAGTGA
Found at i:20464992 original size:133 final size:133
Alignment explanation
Indices: 20464752--20465406 Score: 960
Period size: 133 Copynumber: 5.0 Consensus size: 133
20464742 GTGAATTCAC
* * * *
20464752 AGATCTTATCTCCATGAGGTAGTAATGGAGCAGATCGAAGACAGTGAATCTTATCTCCTTCAGGT
1 AGATCTTATCTCCATGAGGTAGCAATGGAGCAGATCGAAGACGGCGAATCTTATCTCCTTGAGGT
* *
20464817 AGTAAGGGAGCAGATTCAAGCCACTAGCCTTGTCTCCCTGAGCAGTAGTGGAGCAGGCTGAAGAT
66 AGCAAGGGAGCAGATTTAAGCCACTAGCCTTGTCTCCCTGAGCAGTAGTGGAGCAGGCTGAAGAT
20464882 TGT
131 TGT
* * **
20464885 AAATCTTATCTCCATGAGGTAGCAATAGAGCAGATTAAAGACGGCGAATCTTATCTCCTTGAGGT
1 AGATCTTATCTCCATGAGGTAGCAATGGAGCAGATCGAAGACGGCGAATCTTATCTCCTTGAGGT
* * *
20464950 AGCAAGGGAGCAGATTTAAGCCACTAGTCGTGTCTCTCTGAGCAGTAGTGGAGCAGGCTGAAGAT
66 AGCAAGGGAGCAGATTTAAGCCACTAGCCTTGTCTCCCTGAGCAGTAGTGGAGCAGGCTGAAGAT
20465015 TGT
131 TGT
* * *
20465018 AGATCTTATCTCTATGAGGTAGCAATGGAGCAGATCGAAGACGACGAATCTTATTTCCTTGAGGT
1 AGATCTTATCTCCATGAGGTAGCAATGGAGCAGATCGAAGACGGCGAATCTTATCTCCTTGAGGT
* * * *
20465083 AGCAAGGGAGCAGATTTCAGCCACTAGCCTTGTCTCCCTGAGCAGCAGTGGAGCAAGATGAAGAT
66 AGCAAGGGAGCAGATTTAAGCCACTAGCCTTGTCTCCCTGAGCAGTAGTGGAGCAGGCTGAAGAT
20465148 TGT
131 TGT
* *
20465151 AGATCTTATCTCCATGAGGTAGCAATGGAGCAGATTGAAGACGGAGAATCTTATCTCCTTGAGGT
1 AGATCTTATCTCCATGAGGTAGCAATGGAGCAGATCGAAGACGGCGAATCTTATCTCCTTGAGGT
* * * *
20465216 AGCAAGGGAGCAGATTTAAGCCACTAGCTTTATCTCCCAGAGCAGTAATGGAGCAGGCTGAAGAT
66 AGCAAGGGAGCAGATTTAAGCCACTAGCCTTGTCTCCCTGAGCAGTAGTGGAGCAGGCTGAAGAT
20465281 TGT
131 TGT
* * * * *
20465284 AGATCTCATCTGCATAAGGTAGTAATGGAACAGATCGAAGACGGCGAATCTTA--T-CTT--GGT
1 AGATCTTATCTCCATGAGGTAGCAATGGAGCAGATCGAAGACGGCGAATCTTATCTCCTTGAGGT
* ** *
20465344 AGCAAGGGAGCAGATTCAAGCCACTAGCCTTGTCTCCCTGAGTTGTAGTGGAGCAGGTTGAAG
66 AGCAAGGGAGCAGATTTAAGCCACTAGCCTTGTCTCCCTGAGCAGTAGTGGAGCAGGCTGAAG
20465407 TTACAAGTCT
Statistics
Matches: 467, Mismatches: 55, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
128 58 0.12
130 3 0.01
131 1 0.00
133 405 0.87
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (133 bp):
AGATCTTATCTCCATGAGGTAGCAATGGAGCAGATCGAAGACGGCGAATCTTATCTCCTTGAGGT
AGCAAGGGAGCAGATTTAAGCCACTAGCCTTGTCTCCCTGAGCAGTAGTGGAGCAGGCTGAAGAT
TGT
Found at i:20465443 original size:44 final size:44
Alignment explanation
Indices: 20465376--20465628 Score: 267
Period size: 45 Copynumber: 5.6 Consensus size: 44
20465366 ACTAGCCTTG
* * *
20465376 TCTCCCTG-AGTTGTAGTGGAGCAGGTTGAAGTTACAAGTCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTTA
* * *
20465419 TCTCCCTGAAGTTGCAG-GGAAGCAGACTGAAGATATCGAATCTTA
1 TCTCCCTGAAGTTGCAGTGG-AGCAGATTGAAGTTA-CAAATCTTA
20465464 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCACAAACCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAAT-------CTTA
* * *
20465515 TCTCCCTGAAGTTGCAATGGAGCAGGTTGAAGTTACAAGTCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTTA
* * * * *
20465559 TCTCCCTAAAGTTGCAGCGGAGCAGACTGAAGATAGCAAATCTCA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTA-CAAATCTTA
*
20465604 TCTCCCTGAAGTTACAGTGGAGCAG
1 TCTCCCTGAAGTTGCAGTGGAGCAG
20465629 TGGAACAGAT
Statistics
Matches: 175, Mismatches: 23, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
43 10 0.06
44 56 0.32
45 66 0.38
46 2 0.01
51 41 0.23
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (44 bp):
TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTTA
Found at i:20465712 original size:148 final size:140
Alignment explanation
Indices: 20465409--20465734 Score: 332
Period size: 140 Copynumber: 2.3 Consensus size: 140
20465399 GGTTGAAGTT
* * * * *
20465409 ACAAGTCTTATCTCCCTGAAGTTGCAG-GGAAGCAGACTGAAGATATCGAATCTTATCTCCCTGA
1 ACAAATCTTATCTCCCTAAAGTTGCAGCGG-AGCAGACTGAAGATAGCAAATCTCATCTCCCTGA
* * * *
20465473 AGTTGCAGTGGAGCAGATTGAAGTTACAAATCACAAACCTTATCTCCCTGAAGTTGCAATGGAGC
65 AGTTACAGTGGAGCAGATGGAAGTTACAAATCACAAACCTTATCTCCCTGAAGTTACAATAGAGC
* ** **
20465538 AGGTTGAAGTT
130 AAGTCAAAGCC
*
20465549 ACAAGTCTTATCTCCCTAAAGTTGCAGCGGAGCAGACTGAAGATAGCAAATCTCATCTCCCTGAA
1 ACAAATCTTATCTCCCTAAAGTTGCAGCGGAGCAGACTGAAGATAGCAAATCTCATCTCCCTGAA
* ** * *
20465614 GTTACAGTGGAGCAG-TGGAACAGATTGAAACTACAAGTTACGGATCTTATCTCTCTGAAGTTAC
66 GTTACAGTGGAGCAGATGG-A-AG-TT---AC-A-AA-TCACAAACCTTATCTCCCTGAAGTTAC
*
20465678 AGTAGAGCAAGTCAAAGCC
122 AATAGAGCAAGTCAAAGCC
* * *
20465697 ATAAATCTTATCTCCCTAAAGGTGCAGCGAAGCAGACT
1 ACAAATCTTATCTCCCTAAAGTTGCAGCGGAGCAGACT
20465735 AAAACCACAA
Statistics
Matches: 153, Mismatches: 23, Indels: 12
0.81 0.12 0.06
Matches are distributed among these distances:
139 2 0.01
140 73 0.48
141 4 0.03
142 2 0.01
145 2 0.01
146 1 0.01
147 2 0.01
148 67 0.44
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (140 bp):
ACAAATCTTATCTCCCTAAAGTTGCAGCGGAGCAGACTGAAGATAGCAAATCTCATCTCCCTGAA
GTTACAGTGGAGCAGATGGAAGTTACAAATCACAAACCTTATCTCCCTGAAGTTACAATAGAGCA
AGTCAAAGCC
Found at i:20467096 original size:16 final size:16
Alignment explanation
Indices: 20467071--20467101 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20467061 AATCAGATAA
*
20467071 TTTTATTATTATTTAC
1 TTTTACTATTATTTAC
20467087 TTTTACTATTATTTA
1 TTTTACTATTATTTA
20467102 TATTCATTAT
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:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTACTATTATTTAC
Found at i:20467267 original size:3 final size:3
Alignment explanation
Indices: 20467259--20467453 Score: 104
Period size: 3 Copynumber: 64.3 Consensus size: 3
20467249 ACTTTTACCT
20467259 TTA TTA TTA TTA TTA TT- TTA TTA TCTA TTTA TTTA TATA TT- TTCA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA -TTA T-TA TTA TT-A
* * *
20467304 TATA CTT- TTA -AA TT- TTA -TA TTA TT- TATA TTTA TT- TTT TTA CTA
1 T-TA -TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA TTA TTA TTA TTA
* *
20467347 TTA TTA TTA GCGTA TTA TTA TTCT TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA --TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
* * * **
20467395 TTA TTA TTA TTA TTA TTA TCA -AA TTA AT- TTA GCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
20467441 TTT TTA GTA TTA T
1 TTA TTA TTA TTA T
20467454 ATCTCTTTCT
Statistics
Matches: 149, Mismatches: 22, Indels: 42
0.70 0.10 0.20
Matches are distributed among these distances:
2 16 0.11
3 109 0.73
4 18 0.12
5 6 0.04
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:20467692 original size:13 final size:14
Alignment explanation
Indices: 20467671--20467700 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
20467661 TATTTTACTC
20467671 TTTATTTTTATTTA
1 TTTATTTTTATTTA
20467685 TTTA-TTTTATTTA
1 TTTATTTTTATTTA
20467698 TTT
1 TTT
20467701 TTTAGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTATTTTTATTTA
Found at i:20470411 original size:30 final size:30
Alignment explanation
Indices: 20470329--20470433 Score: 106
Period size: 30 Copynumber: 3.5 Consensus size: 30
20470319 TTTGCATCGT
* *
20470329 ATCTG-ATTCTGTATCTGCATTTGTGTCTGA
1 ATCTGTATT-TGTATATGCATCTGTGTCTGA
* * *
20470359 ATCTAT-TTTTTATTTTTGCATCTGTGTCTGA
1 ATCTGTATTTGTA--TATGCATCTGTGTCTGA
20470390 ATCTGTATTTGTATATGCATCTGTGTCTGA
1 ATCTGTATTTGTATATGCATCTGTGTCTGA
* *
20470420 ATTTGTATCTGTAT
1 ATCTGTATTTGTAT
20470434 CTATTACTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
29 3 0.05
30 34 0.55
31 20 0.32
32 5 0.08
ACGTcount: A:0.18, C:0.13, G:0.17, T:0.51
Consensus pattern (30 bp):
ATCTGTATTTGTATATGCATCTGTGTCTGA
Found at i:20470435 original size:24 final size:24
Alignment explanation
Indices: 20470373--20470435 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
20470363 ATTTTTTATT
* * *
20470373 TTTGCATCTGTGTCTGAATCTGTA
1 TTTGTATCTGTATCTGAATCTGAA
* * **
20470397 TTTGTATATGCATCTGTGTCTGAA
1 TTTGTATCTGTATCTGAATCTGAA
20470421 TTTGTATCTGTATCT
1 TTTGTATCTGTATCT
20470436 ATTACTATCT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.49
Consensus pattern (24 bp):
TTTGTATCTGTATCTGAATCTGAA
Found at i:20477049 original size:24 final size:24
Alignment explanation
Indices: 20477017--20477089 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
20477007 GATGAGATAC
20477017 CAACCTTTTCATTGCTATCCTTTT
1 CAACCTTTTCATTGCTATCCTTTT
**
20477041 CAACCTTTTCATTGCTATATTTTT
1 CAACCTTTTCATTGCTATCCTTTT
*
20477065 CAACCTTTTCATTTGTTATCCTTTT
1 CAACCTTTTCA-TTGCTATCCTTTT
20477090 TGGATAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
24 33 0.77
25 10 0.23
ACGTcount: A:0.18, C:0.25, G:0.04, T:0.53
Consensus pattern (24 bp):
CAACCTTTTCATTGCTATCCTTTT
Found at i:20478750 original size:3 final size:3
Alignment explanation
Indices: 20478742--20478773 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
20478732 ATCTAGTTTT
*
20478742 TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
20478774 GGATTAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:20479000 original size:19 final size:18
Alignment explanation
Indices: 20478976--20479011 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20478966 ATAAAACCCT
20478976 AATCGAATATATCAATTTA
1 AATCG-ATATATCAATTTA
*
20478995 AATCGATTTATCAATTT
1 AATCGATATATCAATTT
20479012 TTCCAATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.42
Consensus pattern (18 bp):
AATCGATATATCAATTTA
Found at i:20488990 original size:9 final size:9
Alignment explanation
Indices: 20488976--20489025 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
20488966 ATAAGTATAA
20488976 AATTAACCG
1 AATTAACCG
*
20488985 AATTAATCG
1 AATTAACCG
*
20488994 AATTACCCG
1 AATTAACCG
* *
20489003 AATTACCCA
1 AATTAACCG
20489012 AATTAACCG
1 AATTAACCG
20489021 AATTA
1 AATTA
20489026 TTTGTATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:20489056 original size:6 final size:6
Alignment explanation
Indices: 20489045--20489097 Score: 79
Period size: 6 Copynumber: 8.5 Consensus size: 6
20489035 AATTATATGT
*
20489045 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA
20489095 TTT
1 TTT
20489098 ATTAAATTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
6 34 0.79
7 8 0.19
8 1 0.02
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:20491222 original size:25 final size:27
Alignment explanation
Indices: 20491201--20491251 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
20491191 ATGTTTTTCT
*
20491201 ATTTTTTAAAATTTT-TATTTTTAATA
1 ATTTTTGAAAATTTTATATTTTTAATA
*
20491227 ATTTTTGGAAATTTTATATTTTTAA
1 ATTTTTGAAAATTTTATATTTTTAA
20491252 ATTATTTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (27 bp):
ATTTTTGAAAATTTTATATTTTTAATA
Found at i:20491223 original size:15 final size:16
Alignment explanation
Indices: 20491203--20491232 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20491193 GTTTTTCTAT
20491203 TTTTTAA-AATTTTTA
1 TTTTTAATAATTTTTA
20491218 TTTTTAATAATTTTT
1 TTTTTAATAATTTTT
20491233 GGAAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTAATAATTTTTA
Found at i:20493779 original size:22 final size:23
Alignment explanation
Indices: 20493749--20493798 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
20493739 TATTTAAACA
*
20493749 TATTTAAATATATTATAT-TTA-T
1 TATTAAAATAT-TTATATGTTATT
20493771 TATTAAAATATTTATATGTTATT
1 TATTAAAATATTTATATGTTATT
20493794 TATTA
1 TATTA
20493799 GTTTGTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 6 0.24
22 13 0.52
23 6 0.24
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TATTAAAATATTTATATGTTATT
Found at i:20502906 original size:59 final size:61
Alignment explanation
Indices: 20502772--20502918 Score: 194
Period size: 59 Copynumber: 2.4 Consensus size: 61
20502762 TCTAATATTT
* **
20502772 TTATT-AATTAATATTTTAATAATAAATATATTAAAAATGTTATTAAATTATATATTATTGTTT
1 TTATTAAATT-ATA-TTTAATAATAATTATATTAAAAATG-TATTAAATTATATATTATTGTAA
*
20502835 TTATTAAATTATATTTAATAATAATTATATTAAAATATG-ATTAAATTATTTATTA-T-TAA
1 TTATTAAATTATATTTAATAATAATTATATTAAAA-ATGTATTAAATTATATATTATTGTAA
20502894 TTATTAAATTATATTTAATAATAAT
1 TTATTAAATTATATTTAATAATAAT
20502919 CTTATTAGAA
Statistics
Matches: 78, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
59 26 0.33
60 1 0.01
61 15 0.19
62 21 0.27
63 11 0.14
64 4 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (61 bp):
TTATTAAATTATATTTAATAATAATTATATTAAAAATGTATTAAATTATATATTATTGTAA
Found at i:20505708 original size:27 final size:23
Alignment explanation
Indices: 20505652--20505708 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
20505642 ATATTTAAAA
20505652 TAATAAAAATAATTTTAAAATAC
1 TAATAAAAATAATTTTAAAATAC
*
20505675 AATATAAAAATAAATTTTCCAAAAATAC
1 TA-ATAAAAAT-AATTTT---AAAATAC
20505703 TAATAA
1 TAATAA
20505709 GGATTATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 1 0.04
24 8 0.30
25 6 0.22
27 4 0.15
28 8 0.30
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (23 bp):
TAATAAAAATAATTTTAAAATAC
Found at i:20511565 original size:15 final size:15
Alignment explanation
Indices: 20511545--20511573 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20511535 ATTGAAGTTC
20511545 AACTTTAAATTTATA
1 AACTTTAAATTTATA
20511560 AACTTTAAATTTAT
1 AACTTTAAATTTAT
20511574 CAAGCGCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (15 bp):
AACTTTAAATTTATA
Found at i:20514169 original size:8 final size:8
Alignment explanation
Indices: 20514164--20514198 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
20514154 TGTTTTATTA
20514164 TATTATAT
1 TATTATAT
20514172 TATTATAT
1 TATTATAT
* *
20514180 TAATATGT
1 TATTATAT
20514188 TATTATAT
1 TATTATAT
20514196 TAT
1 TAT
20514199 ATACTTAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (8 bp):
TATTATAT
Found at i:20516405 original size:663 final size:663
Alignment explanation
Indices: 20515127--20516452 Score: 2064
Period size: 663 Copynumber: 2.0 Consensus size: 663
20515117 TCCAATACAC
* *
20515127 TGGTGATCGACATCTCCTACCATATAGAGCTTCATATGGTGCAATTTGAATACTTGATTGGAAAC
1 TGGTGATCGACATCTCCTACCATATAGAGCTTCATATGGTGCAATTTGAATACCTGATTGGAAAA
* * *
20515192 TATTATTATATACAAATTCGGCTAATGGTAAGTAACGTTCCCAACCTGATTCAAAATCAATGATA
66 TATTATTATACACAAATTCGGCTAACGGTAAGTAACATTCCCAACCTGATTCAAAATCAATGATA
* * * * **
20515257 TAAGATCGAAGCATGTCTTCTAAAATCTAATGACTCGTTCTGACTGTTTATCGGTTTGTGGATGA
131 CAAGATCAAAGCATGTCTTCAAAAATATAATGACTCGTTCTGACTGTCCATCGGTTTGTGGATGA
* *
20515322 AAAGCTATACTAAAATGAAGTCGAGTACCAAGAGACTCAAGCAACTGTTTCCAAAACCTCGATGT
196 AAAGCTATACTAAAATGAAGTCGAGTACCAAGAGACTCAAGCAACTATTTCAAAAACCTCGATGT
** * * *
20515387 AAATTGTGGATCTCGATTAGAGATTATCGATACAAGAATTTCATGTAGTCTTACAATTTCCTGGA
261 AAACCGTGGATCTCGATCAGAGATTATCGATACAAGAATTCCATGTAGTCTCACAATTTCCTGGA
* *
20515452 TGTAAGTTTCTGCAAGTTTCTGAAGTAGCCAATCCATTCTAACTACTATAAAATGGGTTGACTTT
326 TATAAGTTTCTGCAAGTTTCTGAAGTAGCCAATCCATTCTAACTACTATAAAATGGGCTGACTTT
** * * *
20515517 CTAAGGCGGTTAACAATAACCTAAATAGTATTTTTCTTACTTACTGACAATGGTAATCCAATTAC
391 CTAAACCGGTCAACAATAACCCAAATAGTATTTTTCTTACTTACTGACAACGGTAATCCAATTAC
* *
20515582 AAAATTCATTGTGATACAGTCCCATTTCTACTCAAAAATATTAATAGGCTGAAGTAATCCAGTTG
456 AAAATCCATTGTGATACAGTCCCATTTCCACTCAAAAATATTAATAGGCTGAAGTAATCCAGTTG
** *
20515647 GCACCTGATGCTCAGCTTTGACTCATTGTCATGTCAAACATTTAGCCACGAATTCCACTATATCC
521 GCACCTGATAATCAGCTTTGACTCATTGACATGTCAAACATTTAGCCACGAATTCCACTATATCC
* * *
20515712 CTCTTCATACTTGGCCACCAATATAATTCCCATAAATCACGGTACATTTTTGTTTCTTCAGGATG
586 CTCTTCATACATGGCCACCAATACAATTCCCATAAATCACGGTACATTTTTGTTTCTCCAGGATG
20515777 AAATGCGAATGGA
651 AAATGCGAATGGA
*
20515790 TGGTGATCGACATCTCCTACCATATAGAGCTTCATATTGTGTC-ATTTGAATACCTGATTGGAAA
1 TGGTGATCGACATCTCCTACCATATAGAGCTTCATATGGTG-CAATTTGAATACCTGATTGGAAA
*
20515854 ATATTATTATACACAAATTCGGCTAACGGTAAGTAACATTCCCAACCTGATTCAAAATCAATTAT
65 ATATTATTATACACAAATTCGGCTAACGGTAAGTAACATTCCCAACCTGATTCAAAATCAATGAT
*
20515919 ACAAGCTCAAAGCATGTCTTCAAAAATATGAATGACTCGTTCTGACTGTCCATCGGTTTGTGGAT
130 ACAAGATCAAAGCATGTCTTCAAAAATAT-AATGACTCGTTCTGACTGTCCATCGGTTTGTGGAT
* *
20515984 GAAAAGCTATACTAAAATGCAGTCGAGTACCAAGAGACTCATGCAACTATTTCAAAAACCTCGAT
194 GAAAAGCTATACTAAAATGAAGTCGAGTACCAAGAGACTCAAGCAACTATTTCAAAAACCTCGAT
* * * **
20516049 GTAAACCGTGGATCTTGATCAGATATTATCGATACATGAATTCCATGTAGTCTCACAATTTTTTG
259 GTAAACCGTGGATCTCGATCAGAGATTATCGATACAAGAATTCCATGTAGTCTCACAATTTCCTG
* * *
20516114 GATATAAGTTTCTGCAAGTTTCTGAAGT-GACCAATCCATTTTGACTGCTATAAAATGGGCTGAC
324 GATATAAGTTTCTGCAAGTTTCTGAAGTAG-CCAATCCATTCTAACTACTATAAAATGGGCTGAC
* * *
20516178 TTTGTAAACCTGTCAACAATAACCCAAATAGTATTTTTCTTACTTACT-ACAACGGTAATCCAGT
388 TTTCTAAACCGGTCAACAATAACCCAAATAGTATTTTTCTTACTTACTGACAACGGTAATCCAAT
** *
20516242 TACAAAATCCATTGTGATACAGTCCCATTTCCACTCAGGAATATTAATAGGCTGAAGTAATCTAG
453 TACAAAATCCATTGTGATACAGTCCCATTTCCACTCAAAAATATTAATAGGCTGAAGTAATCCAG
* *
20516307 TTGGCACCTGATAATCAGCTTTGACTCGTTGACATGTCACACATTTAGCCACGAATTCCACTATA
518 TTGGCACCTGATAATCAGCTTTGACTCATTGACATGTCAAACATTTAGCCACGAATTCCACTATA
* * * *
20516372 TCCCTCTTCATACATGGCCACTAATACAATTCCCGTTAATCATGGTACATTTTTGTTTCTCCAGG
583 TCCCTCTTCATACATGGCCACCAATACAATTCCCATAAATCACGGTACATTTTTGTTTCTCCAGG
* *
20516437 ATGTAATGTGAATGGA
648 ATGAAATGCGAATGGA
20516453 CTGTCATGTG
Statistics
Matches: 600, Mismatches: 60, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
663 351 0.58
664 249 0.41
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (663 bp):
TGGTGATCGACATCTCCTACCATATAGAGCTTCATATGGTGCAATTTGAATACCTGATTGGAAAA
TATTATTATACACAAATTCGGCTAACGGTAAGTAACATTCCCAACCTGATTCAAAATCAATGATA
CAAGATCAAAGCATGTCTTCAAAAATATAATGACTCGTTCTGACTGTCCATCGGTTTGTGGATGA
AAAGCTATACTAAAATGAAGTCGAGTACCAAGAGACTCAAGCAACTATTTCAAAAACCTCGATGT
AAACCGTGGATCTCGATCAGAGATTATCGATACAAGAATTCCATGTAGTCTCACAATTTCCTGGA
TATAAGTTTCTGCAAGTTTCTGAAGTAGCCAATCCATTCTAACTACTATAAAATGGGCTGACTTT
CTAAACCGGTCAACAATAACCCAAATAGTATTTTTCTTACTTACTGACAACGGTAATCCAATTAC
AAAATCCATTGTGATACAGTCCCATTTCCACTCAAAAATATTAATAGGCTGAAGTAATCCAGTTG
GCACCTGATAATCAGCTTTGACTCATTGACATGTCAAACATTTAGCCACGAATTCCACTATATCC
CTCTTCATACATGGCCACCAATACAATTCCCATAAATCACGGTACATTTTTGTTTCTCCAGGATG
AAATGCGAATGGA
Found at i:20519539 original size:42 final size:41
Alignment explanation
Indices: 20519413--20519540 Score: 125
Period size: 44 Copynumber: 3.0 Consensus size: 41
20519403 AGGATTCTGT
*
20519413 TATTTGATTTCGTGTAAGACCACGTCTGGGACATTGGCATCG
1 TATTTGATTTCGTGTAAGACCATGTCTGGGACA-TGGCATCG
* * * *
20519455 -ACTTCTGTTTTATGTGTAAGACCATGTCTAGGACATCAGCATCG
1 TA-TT-TGATTT-CGTGTAAGACCATGTCTGGGACAT-GGCATCG
*
20519499 TATTTGATTTCGTGTAAGACTC-TGTCTGGGATAGTGGCATCG
1 TATTTGATTTCGTGTAAGAC-CATGTCTGGGACA-TGGCATCG
20519541 ATGTCTAATT
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
41 1 0.01
42 26 0.38
43 13 0.19
44 28 0.41
45 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (41 bp):
TATTTGATTTCGTGTAAGACCATGTCTGGGACATGGCATCG
Found at i:20522324 original size:78 final size:78
Alignment explanation
Indices: 20522191--20522348 Score: 262
Period size: 78 Copynumber: 2.0 Consensus size: 78
20522181 TGTGAGAAAA
* * *
20522191 GATTGTGAAGCCTATTTTGCTTCTGTAATTGATTCGAGAATGTCAGAAAAAAAATTTGAATTTGT
1 GATTGTGAAGCATATTTTGCTTATGTAATTCATTCGAGAATGTCAGAAAAAAAATTTGAATTTGT
20522256 ACCTGTTGTCTGT
66 ACCTGTTGTCTGT
*
20522269 GATTGTGAAGCATATTTTGCTTATGTAATTCATTCGAGAATGTCAGAAAAGAAATTTGAATTTGT
1 GATTGTGAAGCATATTTTGCTTATGTAATTCATTCGAGAATGTCAGAAAAAAAATTTGAATTTGT
**
20522334 GTCTGTTGTCTGT
66 ACCTGTTGTCTGT
20522347 GA
1 GA
20522349 GTTCCCTGAT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (78 bp):
GATTGTGAAGCATATTTTGCTTATGTAATTCATTCGAGAATGTCAGAAAAAAAATTTGAATTTGT
ACCTGTTGTCTGT
Found at i:20530351 original size:6 final size:6
Alignment explanation
Indices: 20530314--20530348 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
20530304 CAAAAATTTT
*
20530314 ACATTC ACATTC ACATTC ACATTC ACATTA ACATT
1 ACATTC ACATTC ACATTC ACATTC ACATTC ACATT
20530349 AACTTGAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (6 bp):
ACATTC
Found at i:20530567 original size:14 final size:14
Alignment explanation
Indices: 20530543--20530575 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
20530533 AAAACCCTAA
20530543 TTTTC-CCTTTTTC
1 TTTTCTCCTTTTTC
*
20530556 TTTTCTCCTTTTTT
1 TTTTCTCCTTTTTC
20530570 TTTTCT
1 TTTTCT
20530576 TTCCTATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTCCTTTTTC
Found at i:20530647 original size:8 final size:8
Alignment explanation
Indices: 20530642--20530676 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
20530632 TGTTTTATTA
20530642 TATTATAT
1 TATTATAT
20530650 TATTATAT
1 TATTATAT
*
20530658 TAATATAT
1 TATTATAT
20530666 TATTATAT
1 TATTATAT
20530674 TAT
1 TAT
20530677 ATACTTAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTATAT
Found at i:20530654 original size:13 final size:13
Alignment explanation
Indices: 20530636--20530678 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 13
20530626 CTTTTATGTT
20530636 TTATTATATTATA
1 TTATTATATTATA
20530649 TTATTATATTAATATA
1 TTATTATA-T--TATA
20530665 TTATTATATTATA
1 TTATTATATTATA
20530678 T
1 T
20530679 ACTTAAGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 13 0.48
14 1 0.04
15 1 0.04
16 12 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATTATATTATA
Found at i:20538167 original size:14 final size:15
Alignment explanation
Indices: 20538148--20538186 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
20538138 TGAAAATGAG
*
20538148 TAAAATATAA-CATT
1 TAAAATATAAGCAAT
*
20538162 TAAAATATAAGTAAT
1 TAAAATATAAGCAAT
20538177 TAAAATATAA
1 TAAAATATAA
20538187 TCTAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (15 bp):
TAAAATATAAGCAAT
Found at i:20539104 original size:5 final size:5
Alignment explanation
Indices: 20539096--20539120 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
20539086 TAAAAAAAAA
20539096 AAACT AAACT AAACT AAACT AAACT
1 AAACT AAACT AAACT AAACT AAACT
20539121 CAAGCAGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
AAACT
Found at i:20543876 original size:31 final size:31
Alignment explanation
Indices: 20543809--20543869 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
20543799 CTTAACAACC
**
20543809 CAGTGACTTAAATAAAAGCTTTTGAATAGTT
1 CAGTGACTTAAATAAAAGCTTTCAAATAGTT
*
20543840 CAGTGACTTAAAT-GAAGACTTTCAAATAGT
1 CAGTGACTTAAATAAAAG-CTTTCAAATAGT
20543870 CTAGTGATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 3 0.12
31 23 0.88
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.33
Consensus pattern (31 bp):
CAGTGACTTAAATAAAAGCTTTCAAATAGTT
Found at i:20547075 original size:27 final size:26
Alignment explanation
Indices: 20547018--20547130 Score: 95
Period size: 27 Copynumber: 4.2 Consensus size: 26
20547008 GTCCTAGTGA
*
20547018 ACTATCCTGTATTTACTATCCCAGT-AG
1 ACTATCCTGTATTTA-TGTCCCA-TCAG
*
20547045 ACTATCCTGTATTTATTGTCCCATCAT
1 ACTATCCTGTATTTA-TGTCCCATCAG
* * *
20547072 ACTATCTCATGT-TTGATGTCCTATCGG
1 ACTATC-C-TGTATTTATGTCCCATCAG
* *
20547099 ACTATCCCGTGTTTAATGTCCCATCAG
1 ACTATCCTGTATTT-ATGTCCCATCAG
20547126 ACTAT
1 ACTAT
20547131 TTACGATGTC
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
25 2 0.03
26 4 0.06
27 57 0.81
28 4 0.06
29 3 0.04
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.39
Consensus pattern (26 bp):
ACTATCCTGTATTTATGTCCCATCAG
Found at i:20547310 original size:45 final size:46
Alignment explanation
Indices: 20547207--20547339 Score: 169
Period size: 45 Copynumber: 2.9 Consensus size: 46
20547197 AAACTATCAA
* * * *
20547207 ATGATGTCATAGTGTCTTTCAGCTATGGTCTTAGTCTTGTTTCTATC
1 ATGATGCCATAGCGTCTTTCAGCTATGGTCTTAATCAT-TTTCTATC
* * * *
20547254 ATGATGCCATAGCGTCTTTTAGTTATGTTCTTACTCATTTT-TATC
1 ATGATGCCATAGCGTCTTTCAGCTATGGTCTTAATCATTTTCTATC
*
20547299 ATGATGCCATAGCATCTTTCAGCTATGGTCTTAATCATTTT
1 ATGATGCCATAGCGTCTTTCAGCTATGGTCTTAATCATTTT
20547340 AGGTATATAA
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
45 40 0.54
46 3 0.04
47 31 0.42
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.46
Consensus pattern (46 bp):
ATGATGCCATAGCGTCTTTCAGCTATGGTCTTAATCATTTTCTATC
Found at i:20548414 original size:18 final size:19
Alignment explanation
Indices: 20548372--20548419 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
20548362 AGATGATGAA
20548372 ATTCATTCATCTTTTCCCATTC
1 ATTCA-TCATCTTTTCCC--TC
20548394 ATTCATCATCTTTTCCC-C
1 ATTCATCATCTTTTCCCTC
20548412 ATTC-TCAT
1 ATTCATCAT
20548420 TTCATTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.15
18 5 0.19
21 12 0.46
22 5 0.19
ACGTcount: A:0.19, C:0.33, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTCATCATCTTTTCCCTC
Found at i:20548423 original size:25 final size:24
Alignment explanation
Indices: 20548372--20548438 Score: 79
Period size: 25 Copynumber: 2.9 Consensus size: 24
20548362 AGATGATGAA
20548372 ATTCATTCATCTTTT-CCCA-TTC
1 ATTCATTCATCTTTTCCCCATTTC
20548394 ATTCA-TCATCTTTTCCCCATTCTC
1 ATTCATTCATCTTTTCCCCATT-TC
*
20548418 ATTTCATTC-TCTTTTCTCCAT
1 A-TTCATTCATCTTTTCCCCAT
20548439 CTTTACAACT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
21 9 0.23
22 9 0.23
23 1 0.03
24 3 0.08
25 15 0.38
26 2 0.05
ACGTcount: A:0.16, C:0.33, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTCATTCATCTTTTCCCCATTTC
Found at i:20548735 original size:34 final size:36
Alignment explanation
Indices: 20548692--20548759 Score: 122
Period size: 34 Copynumber: 1.9 Consensus size: 36
20548682 AAAGAAATAT
20548692 TTAAAGAGTAGAAGAAGAAAGC-TGATT-CAAGCAG
1 TTAAAGAGTAGAAGAAGAAAGCTTGATTCCAAGCAG
20548726 TTAAAGAGTAGAAGAAGAAAGCTTGATTCCAAGC
1 TTAAAGAGTAGAAGAAGAAAGCTTGATTCCAAGC
20548760 TTTGGTTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 22 0.69
35 5 0.16
36 5 0.16
ACGTcount: A:0.46, C:0.10, G:0.25, T:0.19
Consensus pattern (36 bp):
TTAAAGAGTAGAAGAAGAAAGCTTGATTCCAAGCAG
Found at i:20559638 original size:15 final size:15
Alignment explanation
Indices: 20559618--20559647 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20559608 TTATAATTTA
*
20559618 ATTTAATTTTTAAAT
1 ATTTAATTATTAAAT
20559633 ATTTAATTATTAAAT
1 ATTTAATTATTAAAT
20559648 TGAATTTGAG
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTAATTATTAAAT
Found at i:20562496 original size:6 final size:6
Alignment explanation
Indices: 20562485--20562511 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
20562475 TGTGTACCGC
20562485 TACTGT TACTGT TACTGT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TAC
20562512 CCTTACGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:20569315 original size:16 final size:16
Alignment explanation
Indices: 20569296--20569327 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
20569286 TCAACGACTG
20569296 ACAAATTATTGGGTAA
1 ACAAATTATTGGGTAA
20569312 ACAAATTATTGGGTAA
1 ACAAATTATTGGGTAA
20569328 TTTACATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ACAAATTATTGGGTAA
Found at i:20586003 original size:46 final size:48
Alignment explanation
Indices: 20585899--20586018 Score: 145
Period size: 48 Copynumber: 2.5 Consensus size: 48
20585889 TGTCTTCGAC
** * * *
20585899 ATGGACTTACATGAATTATTCCTATCTCCAATGCCATATATATATAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATATAAT
* * *
20585947 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCCATATA-A-CTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATATAAT
*
20585993 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
20586019 CTGTCCTGTC
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
46 27 0.44
47 1 0.02
48 34 0.55
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (48 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATATAAT
Found at i:20591684 original size:34 final size:34
Alignment explanation
Indices: 20591639--20591708 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
20591629 GGATAAACCA
20591639 ACGATAAGTGTGCCCAGCACTAGTCAAATAATCG
1 ACGATAAGTGTGCCCAGCACTAGTCAAATAATCG
* *
20591673 ACGATACGTGTGCCCAGCACTAGTCGAATAATCG
1 ACGATAAGTGTGCCCAGCACTAGTCAAATAATCG
20591707 AC
1 AC
20591709 AAGATTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (34 bp):
ACGATAAGTGTGCCCAGCACTAGTCAAATAATCG
Found at i:20592763 original size:16 final size:17
Alignment explanation
Indices: 20592723--20592785 Score: 76
Period size: 16 Copynumber: 3.7 Consensus size: 17
20592713 AATAGTATTA
20592723 ACATATATATTA-TATAAT
1 ACATATAT-TTATTAT-AT
*
20592741 ACTTATATTTATTATAT
1 ACATATATTTATTATAT
*
20592758 A-GTATATTTATTATAT
1 ACATATATTTATTATAT
20592774 ACATATATTTAT
1 ACATATATTTAT
20592786 GCCATGACCG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
16 15 0.38
17 15 0.38
18 10 0.25
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (17 bp):
ACATATATTTATTATAT
Found at i:20599715 original size:20 final size:20
Alignment explanation
Indices: 20599679--20599717 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
20599669 GTATGTGTTC
*
20599679 GGATGTTGTGTATATATTTG
1 GGATGTTGTGTAGATATTTG
20599699 GGATGTTAG-GTAGATATTT
1 GGATGTT-GTGTAGATATTT
20599718 AAGCACCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (20 bp):
GGATGTTGTGTAGATATTTG
Found at i:20601341 original size:24 final size:24
Alignment explanation
Indices: 20601305--20601354 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
20601295 AATACAATCA
*
20601305 AAACTCACCGTTTGATTTAAGCCT
1 AAACTCACCGTTTGATTAAAGCCT
* *
20601329 AAACTCACTGTTTTATTAAAGCCT
1 AAACTCACCGTTTGATTAAAGCCT
20601353 AA
1 AA
20601355 GACCCAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (24 bp):
AAACTCACCGTTTGATTAAAGCCT
Found at i:20603017 original size:13 final size:13
Alignment explanation
Indices: 20602999--20603023 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20602989 CCTTGTTAAA
20602999 ATAAAATAAAATG
1 ATAAAATAAAATG
20603012 ATAAAATAAAAT
1 ATAAAATAAAAT
20603024 AAAAGTAAAA
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:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
ATAAAATAAAATG
Found at i:20613720 original size:37 final size:36
Alignment explanation
Indices: 20613639--20613773 Score: 103
Period size: 37 Copynumber: 3.6 Consensus size: 36
20613629 CTTCACTCAA
* * *
20613639 TATAACAGTAGAATTTGATCAATTAAACATC-TGTCAG
1 TATAACAGTAGGATTTGCTCAGTTAAAC-TCAT-TCAG
* *
20613676 TAGAACAGTAGGATTTGCTCAGTTAAACTCCATTTAG
1 TATAACAGTAGGATTTGCTCAGTTAAACT-CATTCAG
* * * * *
20613713 TATAACAGTATGATTTTCT-TGATTGAGCTTCATTCAG
1 TATAACAGTAGGATTTGCTCAG-TTAAAC-TCATTCAG
*
20613750 TATAACAGTAAGATTTGGCTCAGT
1 TATAACAGTAGGATTT-GCTCAGT
20613774 AGAACGTATC
Statistics
Matches: 77, Mismatches: 15, Indels: 11
0.75 0.15 0.11
Matches are distributed among these distances:
36 2 0.03
37 69 0.90
38 5 0.06
39 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (36 bp):
TATAACAGTAGGATTTGCTCAGTTAAACTCATTCAG
Found at i:20616362 original size:16 final size:16
Alignment explanation
Indices: 20616341--20616376 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
20616331 GTTCAAATTG
20616341 TTTTGTTAGTTTTTAA
1 TTTTGTTAGTTTTTAA
20616357 TTTTGTTAGTTTTTAA
1 TTTTGTTAGTTTTTAA
20616373 TTTT
1 TTTT
20616377 TCTTTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.17, C:0.00, G:0.11, T:0.72
Consensus pattern (16 bp):
TTTTGTTAGTTTTTAA
Found at i:20619864 original size:63 final size:63
Alignment explanation
Indices: 20619760--20619929 Score: 241
Period size: 63 Copynumber: 2.7 Consensus size: 63
20619750 TGCTAGGCCA
* * * *
20619760 TGTGACTCACTGTTTGCCATTAAGAACCATACGGGCTAGAGACACAGGCATGTGTCTAGGTCG
1 TGTGACTCACTGTTTGCCATTAAGGACCACACGGGCCAGAGACACAAGCATGTGTCTAGGTCG
* * * * *
20619823 TGTGACTCACTATTTTCCATTAAGGACCACATGGGCCAGAGACACAAGCGTGTGTCTAGGTTG
1 TGTGACTCACTGTTTGCCATTAAGGACCACACGGGCCAGAGACACAAGCATGTGTCTAGGTCG
* *
20619886 TGTGACTCACTGTTTGCCTTTAAGGACCACACGAGCCAGAGACA
1 TGTGACTCACTGTTTGCCATTAAGGACCACACGGGCCAGAGACA
20619930 GGGGCGTATG
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 93 1.00
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (63 bp):
TGTGACTCACTGTTTGCCATTAAGGACCACACGGGCCAGAGACACAAGCATGTGTCTAGGTCG
Found at i:20622385 original size:23 final size:23
Alignment explanation
Indices: 20622359--20622438 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 23
20622349 CAGCTTGTAT
*
20622359 GAGCTTACCAATTCAGCTCATCA
1 GAGCTTACCATTTCAGCTCATCA
** *
20622382 GAGCTTACTGTTTCAGCTCGTCA
1 GAGCTTACCATTTCAGCTCATCA
* * *
20622405 AAGCTTACCATTTTAGCTTAAT-A
1 GAGCTTACCATTTCAGC-TCATCA
20622428 GAGCTTACCAT
1 GAGCTTACCAT
20622439 CCATCAACTT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
23 43 0.96
24 2 0.04
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.33
Consensus pattern (23 bp):
GAGCTTACCATTTCAGCTCATCA
Found at i:20622461 original size:26 final size:26
Alignment explanation
Indices: 20622428--20622486 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
20622418 TAGCTTAATA
20622428 GAGCTTACCATCCATCAACTTAGGAG
1 GAGCTTACCATCCATCAACTTAGGAG
* ** *
20622454 GAGCTTACCGTTTATCAGCTTAGGAG
1 GAGCTTACCATCCATCAACTTAGGAG
*
20622480 AAGCTTA
1 GAGCTTA
20622487 TCGATCATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (26 bp):
GAGCTTACCATCCATCAACTTAGGAG
Found at i:20629949 original size:26 final size:26
Alignment explanation
Indices: 20629919--20629977 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
20629909 CAGCTTAATA
*
20629919 GAGCTTACCGTCCATCAGCTCAGGAG
1 GAGCTTACCGTCCATCAACTCAGGAG
* **
20629945 GAGCTTACTGTTTATCAACTCAGGAG
1 GAGCTTACCGTCCATCAACTCAGGAG
*
20629971 AAGCTTA
1 GAGCTTA
20629978 TTGATCATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (26 bp):
GAGCTTACCGTCCATCAACTCAGGAG
Found at i:20633793 original size:20 final size:20
Alignment explanation
Indices: 20633746--20633833 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
20633736 TTATATAGGA
*
20633746 TTGCACTTCGGTG-C-CTTT
1 TTGCACTTCGGTGTCTCTAT
*
20633764 GTTACACTTCGGTGTCTCTAT
1 -TTGCACTTCGGTGTCTCTAT
*
20633785 TTGCACTTCGGTGCCTCTGA-
1 TTGCACTTCGGTGTCTCT-AT
* *
20633805 TCGCACAATC-GTGTCTCTAT
1 TTGCAC-TTCGGTGTCTCTAT
20633825 TTGCACTTC
1 TTGCACTTC
20633834 AGTGCCTGTC
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
19 15 0.27
20 34 0.62
21 6 0.11
ACGTcount: A:0.12, C:0.28, G:0.19, T:0.40
Consensus pattern (20 bp):
TTGCACTTCGGTGTCTCTAT
Found at i:20635199 original size:42 final size:42
Alignment explanation
Indices: 20635136--20635299 Score: 195
Period size: 42 Copynumber: 3.7 Consensus size: 42
20635126 CTTCGTTTTC
** *
20635136 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACAT-A
* *
20635179 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATA
20635220 TCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC---AT--C-T-TCACATA
*
20635269 TCGATGCCATAGCCCAGCTATAGTCTTACAC
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC
20635300 GAATCACATA
Statistics
Matches: 105, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
41 2 0.02
42 63 0.60
43 1 0.01
45 2 0.02
48 1 0.01
49 36 0.34
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.29
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATA
Found at i:20635286 original size:91 final size:93
Alignment explanation
Indices: 20635171--20635389 Score: 252
Period size: 91 Copynumber: 2.4 Consensus size: 93
20635161 TTACACATCT
*
20635171 TCACATAATGATGCCATAGCCCAGCTATGGTCTTACAC-ATAT-TCATATAT-C-GATGCCATAG
1 TCACAT-ATGATGCCATAGCCCAGCTATGGTCTTACACGA-ATCACATATATACTGATGCCATAG
* *
20635232 CCCAGCTATGGTCTTACAC-GTAATCACATA
64 CCCAGATATGATCTTACACAGTAA-CACATA
* * *
20635262 TCACATATCGATGCCATAGCCCAGCTATAGTCTTACACGAATCACATATCTCACTGATGCCATAT
1 TCACATAT-GATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATAT-ACTGATGCCATAG
* *
20635327 CCCAGATATGATCTTATACAGTAACATATA
64 CCCAGATATGATCTTACACAGTAACACATA
* * *
20635357 TCACA-CTGATGCCATATCCCAGATATGGTCTTA
1 TCACATATGATGCCATAGCCCAGCTATGGTCTTA
20635390 TACGGAAATC
Statistics
Matches: 109, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
90 2 0.02
91 36 0.33
92 7 0.06
93 23 0.21
94 2 0.02
95 35 0.32
96 4 0.04
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (93 bp):
TCACATATGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATATACTGATGCCATAGCC
CAGATATGATCTTACACAGTAACACATA
Found at i:20635392 original size:47 final size:47
Alignment explanation
Indices: 20635222--20635389 Score: 205
Period size: 47 Copynumber: 3.6 Consensus size: 47
20635212 TTCATATATC
* *
20635222 GATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATAT
1 GATGCCATAGCCCAGATATGGTCTTACACGTAATCACATATCACA-CT
* * *
20635270 CGATGCCATAGCCCAGCTATAGTCTTACACG-AATCACATATCTCACT
1 -GATGCCATAGCCCAGATATGGTCTTACACGTAATCACATATCACACT
* * * *
20635317 GATGCCATATCCCAGATATGATCTTATACAGTAA-CATATATCACACT
1 GATGCCATAGCCCAGATATGGTCTTACAC-GTAATCACATATCACACT
*
20635364 GATGCCATATCCCAGATATGGTCTTA
1 GATGCCATAGCCCAGATATGGTCTTA
20635390 TACGGAAATC
Statistics
Matches: 106, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
46 24 0.23
47 38 0.36
48 15 0.14
49 29 0.27
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.28
Consensus pattern (47 bp):
GATGCCATAGCCCAGATATGGTCTTACACGTAATCACATATCACACT
Found at i:20635446 original size:31 final size:31
Alignment explanation
Indices: 20635411--20635559 Score: 217
Period size: 31 Copynumber: 4.8 Consensus size: 31
20635401 CTTGTCACTT
*
20635411 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * * *
20635442 GTAGCCGGAGCTACAATTTTTCACTAATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * *
20635473 GTAGTCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
20635504 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
20635535 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
20635560 TGTCATTTGT
Statistics
Matches: 105, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 105 1.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:20635648 original size:50 final size:51
Alignment explanation
Indices: 20635535--20635663 Score: 197
Period size: 50 Copynumber: 2.5 Consensus size: 51
20635525 CACTGATCAG
* * * *
20635535 GTAGCCGAAGCTACCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAGATAAGT
*
20635586 GTAGCCGAAGCTATCACTTATCACTT-TCACTTATCTTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAGATAAGT
*
20635636 GTAGCCGGAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
20635664 TGCCATGGTC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
50 46 0.65
51 25 0.35
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAGATAAGT
Found at i:20640509 original size:42 final size:42
Alignment explanation
Indices: 20640446--20640609 Score: 161
Period size: 42 Copynumber: 3.7 Consensus size: 42
20640436 CTTCATTTTC
** * * * *
20640446 TCGATGCCATAGTTCAACTATGGTTTTATACATCTTCACGTA-A
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCA--TATA
20640489 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
* *
20640530 TCGATGCCATATCCCAGCTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC---AT---AT-TCATATA
20640579 TCGATGCCATAGCCCAGCTATGGTCTTACAC
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC
20640610 GAATCACATA
Statistics
Matches: 103, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
40 2 0.02
41 2 0.02
42 58 0.56
43 1 0.01
45 2 0.02
48 2 0.02
49 36 0.35
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
Found at i:20640702 original size:47 final size:47
Alignment explanation
Indices: 20640532--20640699 Score: 223
Period size: 47 Copynumber: 3.6 Consensus size: 47
20640522 TTCATATATC
* *
20640532 GATGCCATATCCCAGCTATGGTCTTACACGTAATCACATATCACATAT
1 GATGCCATATCCCAGATATGGTCTTACACGTAATCACATATCACA-CT
* * *
20640580 CGATGCCATAGCCCAGCTATGGTCTTACACG-AATCACATATCTCACT
1 -GATGCCATATCCCAGATATGGTCTTACACGTAATCACATATCACACT
* *
20640627 GATGCCATATCCCAGATATGGTCTTATACAGTAA-CATATATCACACT
1 GATGCCATATCCCAGATATGGTCTTACAC-GTAATCACATATCACACT
*
20640674 GATGCCATATCCCATATATGGTCTTA
1 GATGCCATATCCCAGATATGGTCTTA
20640700 TACGGAAATC
Statistics
Matches: 108, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
46 26 0.24
47 38 0.35
48 15 0.14
49 29 0.27
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (47 bp):
GATGCCATATCCCAGATATGGTCTTACACGTAATCACATATCACACT
Found at i:20640711 original size:95 final size:95
Alignment explanation
Indices: 20640490--20640699 Score: 256
Period size: 95 Copynumber: 2.3 Consensus size: 95
20640480 TTCACGTAAT
* * * *
20640490 GATGCCATAGCCCAGCTATGGTCTTACAC-ATAT-TCATATAT--C-GATGCCATATCCCAGCTA
1 GATGCCATAGCCCAGATATGGTCTTACACGA-ATCACATATCTCACTGATGCCATATCCCAGATA
20640550 TGGTCTTACACGTAATCACATATCACATATC
65 TGGTCTTACACGTAATCACATATCACATATC
*
20640581 GATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCACTGATGCCATATCCCAGATAT
1 GATGCCATAGCCCAGATATGGTCTTACACGAATCACATATCTCACTGATGCCATATCCCAGATAT
* * *
20640646 GGTCTTATACAGTAA-CATATATCACA-CT-
66 GGTCTTACAC-GTAATCACATATCACATATC
* *
20640674 GATGCCATATCCCATATATGGTCTTA
1 GATGCCATAGCCCAGATATGGTCTTA
20640700 TACGGAAATC
Statistics
Matches: 104, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
91 31 0.30
92 7 0.07
93 23 0.22
94 2 0.02
95 37 0.36
96 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (95 bp):
GATGCCATAGCCCAGATATGGTCTTACACGAATCACATATCTCACTGATGCCATATCCCAGATAT
GGTCTTACACGTAATCACATATCACATATC
Found at i:20640849 original size:50 final size:50
Alignment explanation
Indices: 20640782--20640877 Score: 156
Period size: 50 Copynumber: 1.9 Consensus size: 50
20640772 CACTCGTCAT
20640782 TTGTCCTTGATCAGATAAGTGTAGCCAAAGCTATCACTAATCACTTTCAC
1 TTGTCCTTGATCAGATAAGTGTAGCCAAAGCTATCACTAATCACTTTCAC
* ** *
20640832 TTGTCTTTGATCAGATAAGTGTAGCCGGAGCTATCACTTATCACTT
1 TTGTCCTTGATCAGATAAGTGTAGCCAAAGCTATCACTAATCACTT
20640878 GTTGCCATGG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (50 bp):
TTGTCCTTGATCAGATAAGTGTAGCCAAAGCTATCACTAATCACTTTCAC
Found at i:20652797 original size:20 final size:20
Alignment explanation
Indices: 20652721--20652798 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
20652711 ATGCTAACAA
*
20652721 AGGCACTGAAGTGCAAGCAG
1 AGGCACTGAAGTGCAATCAG
20652741 AGGCACTGAAGTGCAAAT-AG
1 AGGCACTGAAGTGC-AATCAG
* **
20652761 ACGCACCCAAGTGCAATCAG
1 AGGCACTGAAGTGCAATCAG
*
20652781 AGGCACGGAAGTGCAATC
1 AGGCACTGAAGTGCAATC
20652799 CCATACAAGC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
19 3 0.06
20 44 0.90
21 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.29, T:0.12
Consensus pattern (20 bp):
AGGCACTGAAGTGCAATCAG
Found at i:20655965 original size:32 final size:32
Alignment explanation
Indices: 20655920--20656000 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 32
20655910 GGACCCACAC
*
20655920 GCCCGTGTGGCCCACACAATCCAAATTGCCAT
1 GCCCGTGTGGCCCACACAACCCAAATTGCCAT
* * * *
20655952 GCCTGTGTGGCCCACACAGCCCGAATTGCCTT
1 GCCCGTGTGGCCCACACAACCCAAATTGCCAT
*
20655984 GCCCGTTTGGCCCACAC
1 GCCCGTGTGGCCCACAC
20656001 GGCCCTTACA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.19, C:0.40, G:0.22, T:0.20
Consensus pattern (32 bp):
GCCCGTGTGGCCCACACAACCCAAATTGCCAT
Found at i:20658061 original size:14 final size:15
Alignment explanation
Indices: 20658012--20658072 Score: 61
Period size: 16 Copynumber: 4.0 Consensus size: 15
20658002 TTTATTTAAG
*
20658012 TTTTGATAATAATAAT
1 TTTTTATAAT-ATAAT
*
20658028 TTTTTAGAATATAAAT
1 TTTTTATAATAT-AAT
*
20658044 TTTTAATAATATAA-
1 TTTTTATAATATAAT
*
20658058 TTTTTATATTATAAT
1 TTTTTATAATATAAT
20658073 AGCACAAGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
14 12 0.32
15 4 0.11
16 21 0.57
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
TTTTTATAATATAAT
Found at i:20659618 original size:71 final size:71
Alignment explanation
Indices: 20659528--20659955 Score: 473
Period size: 71 Copynumber: 6.0 Consensus size: 71
20659518 GAAATGATTT
* * * *
20659528 CACACATATTTGTCAGTTCTACCAACTAGCACAGGGCGCATTTATTGTCAGTTATACTGAACAGT
1 CACACATATTTGTCGGTTCTACCGACCAGCACAGGGCGCATTTATTGTCAGTTATACCGAACAGT
20659593 GCTGGG
66 GCTGGG
* * * *
20659599 CACACATATTTGTCGGTTCTACCGACTAGCGCAGGGCACATTTATTGTCAGTTATA-CTAACCAG
1 CACACATATTTGTCGGTTCTACCGACCAGCACAGGGCGCATTTATTGTCAGTTATACCGAA-CAG
*
20659663 TGTTGGG
65 TGCTGGG
* ** * * * *
20659670 CACACATATTTGTCGGTTCCACCGACCAAAATAGGGTGCATTTATTGTCGGTTATACCGACCAGT
1 CACACATATTTGTCGGTTCTACCGACCAGCACAGGGCGCATTTATTGTCAGTTATACCGAACAGT
20659735 GCTGGG
66 GCTGGG
* * * * * *
20659741 CACACATATTTGTCGCTTCTACCGACCAGCGCAGGGTGCATTTGTTTTCGGTTATACCG-ACAAG
1 CACACATATTTGTCGGTTCTACCGACCAGCACAGGGCGCATTTATTGTCAGTTATACCGAAC-AG
**
20659805 TATTGGG
65 TGCTGGG
* * * * *
20659812 CACACATATTTTTTGGTTTTACCGACCAGCACAGGGCGCATTTATTGTCAATTATACCGACCAGT
1 CACACATATTTGTCGGTTCTACCGACCAGCACAGGGCGCATTTATTGTCAGTTATACCGAACAGT
20659877 GCTGGG
66 GCTGGG
* * * * * * * * *
20659883 CACACATATTTTTTGGTTTTACTGACCAGCGCAGGGCGCATTTATTATCGGTTGTACCGACCAGT
1 CACACATATTTGTCGGTTCTACCGACCAGCACAGGGCGCATTTATTGTCAGTTATACCGAACAGT
*
20659948 GCTAGG
66 GCTGGG
20659954 CA
1 CA
20659956 TACTCATTGT
Statistics
Matches: 303, Mismatches: 50, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
70 3 0.01
71 297 0.98
72 3 0.01
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (71 bp):
CACACATATTTGTCGGTTCTACCGACCAGCACAGGGCGCATTTATTGTCAGTTATACCGAACAGT
GCTGGG
Found at i:20659671 original size:35 final size:35
Alignment explanation
Indices: 20659561--20659673 Score: 102
Period size: 35 Copynumber: 3.2 Consensus size: 35
20659551 AACTAGCACA
*
20659561 GGGCGCATTTATTGTCAGTTATACTGAA-CAGTGCT
1 GGGCACATTTATTGTCAGTTATACT-AACCAGTGCT
** * * ** * * *
20659596 GGGCACACATATTTGTCGGTTCTACCGACTAGCGCA
1 GGGCACATTTA-TTGTCAGTTATACTAACCAGTGCT
*
20659632 GGGCACATTTATTGTCAGTTATACTAACCAGTGTT
1 GGGCACATTTATTGTCAGTTATACTAACCAGTGCT
20659667 GGGCACA
1 GGGCACA
20659674 CATATTTGTC
Statistics
Matches: 56, Mismatches: 20, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
35 32 0.57
36 24 0.43
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (35 bp):
GGGCACATTTATTGTCAGTTATACTAACCAGTGCT
Found at i:20659800 original size:35 final size:35
Alignment explanation
Indices: 20659702--20659946 Score: 121
Period size: 36 Copynumber: 6.9 Consensus size: 35
20659692 CGACCAAAAT
* *
20659702 AGGGTGCATTTATTGTCGGTTATACCGACCAGTGC
1 AGGGTGCATTTATTTTCGGTTATACCGACCAGCGC
* ** ** * *
20659737 TGGGCACACATATTTGTCGCTTCTACCGACCAGCGC
1 AGGGTGCATTTATTT-TCGGTTATACCGACCAGCGC
* * ***
20659773 AGGGTGCATTTGTTTTCGGTTATACCGACAAGTAT
1 AGGGTGCATTTATTTTCGGTTATACCGACCAGCGC
* ** ** * * *
20659808 TGGGCACACATATTTTTTGGTTTTACCGACCAGCAC
1 AGGGTGCATTTA-TTTTCGGTTATACCGACCAGCGC
* * ** *
20659844 AGGGCGCATTTATTGTCAATTATACCGACCAGTGC
1 AGGGTGCATTTATTTTCGGTTATACCGACCAGCGC
* ** ** * * *
20659879 TGGGCACACATATTTTTTGGTTTTACTGACCAGCGC
1 AGGGTGCATTTA-TTTTCGGTTATACCGACCAGCGC
* * *
20659915 AGGGCGCATTTATTATCGGTTGTACCGACCAG
1 AGGGTGCATTTATTTTCGGTTATACCGACCAG
20659947 TGCTAGGCAT
Statistics
Matches: 145, Mismatches: 62, Indels: 6
0.68 0.29 0.03
Matches are distributed among these distances:
35 69 0.48
36 76 0.52
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.31
Consensus pattern (35 bp):
AGGGTGCATTTATTTTCGGTTATACCGACCAGCGC
Found at i:20659926 original size:213 final size:213
Alignment explanation
Indices: 20659528--20659955 Score: 527
Period size: 213 Copynumber: 2.0 Consensus size: 213
20659518 GAAATGATTT
* *
20659528 CACACATATTTGTCAGTTCTACCAACTAGCACAGGGCGCATTTATTGTCAGTTATACTGAACAGT
1 CACACATATTTGTCAGTTCTACCAACCAGCACAGGGCGCATTTATTGTCAGTTATACCGAACAGT
* * * * *
20659593 GCTGGGCACACATATTTGTCGGTTCTACCGACTAGCGCAGGGCACATTTATTGTCAGTTATACTA
66 ACTGGGCACACATATTTGTCGGTTCTACCGACCAGCACAGGGCACATTTATTGTCAATTATACCA
* * * *
20659658 ACCAGTGTTGGGCACACATATTTGTCGGTTCCACCGACCAAAATAGGGTGCATTTATTGTCGGTT
131 ACCAGTGCTGGGCACACATATTTGTCGGTTCCACCGACCAAAACAGGGCGCATTTATTATCGGTT
*
20659723 ATACCGACCAGTGCTGGG
196 ATACCGACCAGTGCTAGG
* * * * * *
20659741 CACACATATTTGTC-GCTTCTACCGACCAGCGCAGGGTGCATTTGTTTTCGGTTATACCG-ACAA
1 CACACATATTTGTCAG-TTCTACCAACCAGCACAGGGCGCATTTATTGTCAGTTATACCGAAC-A
* * * * *
20659804 GTATTGGGCACACATATTTTTTGGTTTTACCGACCAGCACAGGGCGCATTTATTGTCAATTATAC
64 GTACTGGGCACACATATTTGTCGGTTCTACCGACCAGCACAGGGCACATTTATTGTCAATTATAC
* * * ** * ***
20659869 CGACCAGTGCTGGGCACACATATTTTTTGGTTTTACTGACCAGCGCAGGGCGCATTTATTATCGG
129 CAACCAGTGCTGGGCACACATATTTGTCGGTTCCACCGACCAAAACAGGGCGCATTTATTATCGG
*
20659934 TTGTACCGACCAGTGCTAGG
194 TTATACCGACCAGTGCTAGG
20659954 CA
1 CA
20659956 TACTCATTGT
Statistics
Matches: 180, Mismatches: 33, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
212 3 0.02
213 177 0.98
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (213 bp):
CACACATATTTGTCAGTTCTACCAACCAGCACAGGGCGCATTTATTGTCAGTTATACCGAACAGT
ACTGGGCACACATATTTGTCGGTTCTACCGACCAGCACAGGGCACATTTATTGTCAATTATACCA
ACCAGTGCTGGGCACACATATTTGTCGGTTCCACCGACCAAAACAGGGCGCATTTATTATCGGTT
ATACCGACCAGTGCTAGG
Found at i:20659941 original size:142 final size:142
Alignment explanation
Indices: 20659528--20659943 Score: 544
Period size: 142 Copynumber: 2.9 Consensus size: 142
20659518 GAAATGATTT
* * * * *
20659528 CACACATATTTGTCAGTTCTACCAACTAGCACAGGGCGCATTTATTGTCAGTTATACTGAACAGT
1 CACACATATTTGTCGGTTCTACCGACCAGCACAGGGCGCATTTATTGTCAGTTATACCGACCAGT
* * * * **
20659593 GCTGGGCACACATATTTGTCGGTTCTACCGACTAGCGCAGGGCACATTTATTGTCAGTTATACTA
66 GCTGGGCACACATATTTGTCGGTTCTACCGACCAGCGCAGGGCGCATTTATTATCGGTTATACCG
* *
20659658 ACCAGTGTTGGG
131 ACAAGTATTGGG
* ** * * *
20659670 CACACATATTTGTCGGTTCCACCGACCAAAATAGGGTGCATTTATTGTCGGTTATACCGACCAGT
1 CACACATATTTGTCGGTTCTACCGACCAGCACAGGGCGCATTTATTGTCAGTTATACCGACCAGT
* * * *
20659735 GCTGGGCACACATATTTGTCGCTTCTACCGACCAGCGCAGGGTGCATTTGTTTTCGGTTATACCG
66 GCTGGGCACACATATTTGTCGGTTCTACCGACCAGCGCAGGGCGCATTTATTATCGGTTATACCG
20659800 ACAAGTATTGGG
131 ACAAGTATTGGG
* * * *
20659812 CACACATATTTTTTGGTTTTACCGACCAGCACAGGGCGCATTTATTGTCAATTATACCGACCAGT
1 CACACATATTTGTCGGTTCTACCGACCAGCACAGGGCGCATTTATTGTCAGTTATACCGACCAGT
* * * * *
20659877 GCTGGGCACACATATTTTTTGGTTTTACTGACCAGCGCAGGGCGCATTTATTATCGGTTGTACCG
66 GCTGGGCACACATATTTGTCGGTTCTACCGACCAGCGCAGGGCGCATTTATTATCGGTTATACCG
20659942 AC
131 AC
20659944 CAGTGCTAGG
Statistics
Matches: 233, Mismatches: 41, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
142 233 1.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (142 bp):
CACACATATTTGTCGGTTCTACCGACCAGCACAGGGCGCATTTATTGTCAGTTATACCGACCAGT
GCTGGGCACACATATTTGTCGGTTCTACCGACCAGCGCAGGGCGCATTTATTATCGGTTATACCG
ACAAGTATTGGG
Found at i:20669013 original size:34 final size:34
Alignment explanation
Indices: 20668962--20669049 Score: 90
Period size: 34 Copynumber: 2.6 Consensus size: 34
20668952 TGTACTGAAT
* *
20668962 TGGGCTAAGGCCTACACTGTTACTGCTGCTG-TA
1 TGGGTTAAGGCCCACACTGTTACTGCTGCTGATA
* * *
20668995 GTGGGTTAAGGCCCACACTGATATTTCTGCTGATA
1 -TGGGTTAAGGCCCACACTGTTACTGCTGCTGATA
*
20669030 TGGGCTTAA-GCCCAAACTGT
1 TGGG-TTAAGGCCCACACTGT
20669050 CCAACACTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
34 39 0.87
35 6 0.13
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.30
Consensus pattern (34 bp):
TGGGTTAAGGCCCACACTGTTACTGCTGCTGATA
Found at i:20672539 original size:42 final size:43
Alignment explanation
Indices: 20672493--20672573 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
20672483 GTAACTATGT
* * *
20672493 CTGGGACATTGGCATC-GTATTTAATTTCATGTAAGACCTTAC
1 CTGGGACAGTGGCATCAATATTTAATTACATGTAAGACCTTAC
*
20672535 CTGGGACAGTGGCATCAATATTTGATTACATGTAAGACC
1 CTGGGACAGTGGCATCAATATTTAATTACATGTAAGACC
20672574 ACGTCTGGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 15 0.44
43 19 0.56
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (43 bp):
CTGGGACAGTGGCATCAATATTTAATTACATGTAAGACCTTAC
Found at i:20672582 original size:43 final size:43
Alignment explanation
Indices: 20672491--20672592 Score: 113
Period size: 43 Copynumber: 2.4 Consensus size: 43
20672481 GTGTAACTAT
* * *
20672491 GTCTGGGACATTGGCATCGTATTTAATTTCATGTAAGACCTTAC
1 GTCTGGGACAGTGGCATCATATTTAATTACATGTAAGACC-TAC
*
20672535 --CTGGGACAGTGGCATCAATATTTGATTACATGTAAGACC-AC
1 GTCTGGGACAGTGGCATC-ATATTTAATTACATGTAAGACCTAC
20672576 GTCTGGGAC-GTTGGCAT
1 GTCTGGGACAG-TGGCAT
20672593 TGTATGAGCT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
41 2 0.04
42 16 0.32
43 32 0.64
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (43 bp):
GTCTGGGACAGTGGCATCATATTTAATTACATGTAAGACCTAC
Found at i:20675755 original size:42 final size:42
Alignment explanation
Indices: 20675709--20675813 Score: 129
Period size: 43 Copynumber: 2.5 Consensus size: 42
20675699 GTAACTATGT
* **
20675709 CTGGGACATTGGCATCGTATTTGATTTCATGTAAGACCTTGC
1 CTGGGACATTGGCATCGTATTTGATTACATGTAAGACCACGC
* * *
20675751 CTGGGACAGTGGCATCAATATTTGATTACATGTAAGACCACGT
1 CTGGGACATTGGCATC-GTATTTGATTACATGTAAGACCACGC
* *
20675794 CTGGGACGTTGGCATTGTAT
1 CTGGGACATTGGCATCGTAT
20675814 GAGCTTTTCG
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 18 0.35
43 34 0.65
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (42 bp):
CTGGGACATTGGCATCGTATTTGATTACATGTAAGACCACGC
Found at i:20678231 original size:25 final size:24
Alignment explanation
Indices: 20678190--20678238 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
20678180 GTAATGAGGG
20678190 GATAAGGGAGAAGATTTAGGAGCT
1 GATAAGGGAGAAGATTTAGGAGCT
*
20678214 GATAAGGGGGGAAGATTTAGGAGCT
1 GATAA-GGGAGAAGATTTAGGAGCT
20678239 AATCAAGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.35, C:0.04, G:0.41, T:0.20
Consensus pattern (24 bp):
GATAAGGGAGAAGATTTAGGAGCT
Found at i:20678253 original size:25 final size:24
Alignment explanation
Indices: 20678191--20678246 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
20678181 TAATGAGGGG
*
20678191 ATAAGGGAGAAGATTTAGGAGCTG
1 ATAAGGGAGAAGATTTAGGAGCTA
*
20678215 ATAAGGGGGGAAGATTTAGGAGCTA
1 ATAA-GGGAGAAGATTTAGGAGCTA
20678240 ATCAAGG
1 AT-AAGG
20678247 AGCAAGAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 4 0.14
25 22 0.79
26 2 0.07
ACGTcount: A:0.38, C:0.05, G:0.38, T:0.20
Consensus pattern (24 bp):
ATAAGGGAGAAGATTTAGGAGCTA
Found at i:20679751 original size:27 final size:27
Alignment explanation
Indices: 20679646--20679752 Score: 110
Period size: 27 Copynumber: 3.9 Consensus size: 27
20679636 AGGAAACATC
* *
20679646 CTGGTGGCTATGCCACAATTATCT-AAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
* *
20679673 CTGGTGGCTCTACCACATATTTCTGT-T
1 CTGGTGGCTCTGCCACAT-TATCTGTAT
*
20679700 CTAGTGGCTCTGCCACAATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
* *
20679728 CTGGTGACTCTGTCACATTATCTGT
1 CTGGTGGCTCTGCCACATTATCTGT
20679753 TCTAGCAGCC
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
26 2 0.03
27 48 0.73
28 16 0.24
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATTATCTGTAT
Found at i:20679752 original size:54 final size:54
Alignment explanation
Indices: 20679649--20679757 Score: 148
Period size: 54 Copynumber: 2.0 Consensus size: 54
20679639 AAACATCCTG
* *
20679649 GTGGCTATGCCACAATTATCTAATCTGGTGGCTCTACCACATATTTCTGTTCTA
1 GTGGCTATGCCACAATTATCTAATCTGGTGACTCTACCACATATATCTGTTCTA
* * **
20679703 GTGGCTCTGCCACAATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTTCTA
1 GTGGCTATGCCACAATTATCT-AATCTGGTGACTCTACCACATATATCTGTTCTA
20679757 G
1 G
20679758 CAGCCATGCT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
54 31 0.65
55 17 0.35
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (54 bp):
GTGGCTATGCCACAATTATCTAATCTGGTGACTCTACCACATATATCTGTTCTA
Found at i:20686027 original size:25 final size:25
Alignment explanation
Indices: 20685988--20686044 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
20685978 GTAAGGAGGG
20685988 GATAA-GGGAGAAGATTTAGGAGCT
1 GATAAGGGGAGAAGATTTAGGAGCT
20686012 GATAAGGGGAGAAGATTTAGGAGCT
1 GATAAGGGGAGAAGATTTAGGAGCT
20686037 GATCAAGG
1 GAT-AAGG
20686045 AGCAAGAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 5 0.16
25 22 0.71
26 4 0.13
ACGTcount: A:0.37, C:0.05, G:0.39, T:0.19
Consensus pattern (25 bp):
GATAAGGGGAGAAGATTTAGGAGCT
Found at i:20687483 original size:27 final size:26
Alignment explanation
Indices: 20687443--20687554 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
20687433 AGGAAGCGTC
*
20687443 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
20687470 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
20687497 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
20687525 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
20687551 CTGG
1 CTGG
20687555 CAGCAATGCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 7 0.09
27 52 0.68
28 17 0.22
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:20687547 original size:54 final size:54
Alignment explanation
Indices: 20687443--20687554 Score: 172
Period size: 54 Copynumber: 2.1 Consensus size: 54
20687433 AGGAAGCGTC
*
20687443 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
20687497 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
20687551 CTGG
1 CTGG
20687555 CAGCAATGCT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
54 35 0.66
55 18 0.34
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:20688928 original size:34 final size:34
Alignment explanation
Indices: 20688885--20688953 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
20688875 CATGTGGGGT
20688885 TTAAAACACCCATCCAGCCCTACACACCATATTA
1 TTAAAACACCCATCCAGCCCTACACACCATATTA
*
20688919 TTAAAACACCCATCCAGCCTTACACACCATATTA
1 TTAAAACACCCATCCAGCCCTACACACCATATTA
20688953 T
1 T
20688954 ACCAATGCGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.36, G:0.03, T:0.23
Consensus pattern (34 bp):
TTAAAACACCCATCCAGCCCTACACACCATATTA
Found at i:20694388 original size:16 final size:17
Alignment explanation
Indices: 20694369--20694401 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20694359 TTTTTCTTTC
20694369 GGGTTT-TTGTCATTTG
1 GGGTTTCTTGTCATTTG
*
20694385 GGGTTTCTTTTCATTTG
1 GGGTTTCTTGTCATTTG
20694402 TTTCTGAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.06, C:0.09, G:0.27, T:0.58
Consensus pattern (17 bp):
GGGTTTCTTGTCATTTG
Done.