Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 19 of 175
Found at i:5088485 original size:20 final size:20
Alignment explanation
Indices: 5088408--5088503 Score: 70
Period size: 20 Copynumber: 4.6 Consensus size: 20
5088398 TTATTTTTTT
* * *
5088408 CTTTCTTTTTCCTTCCCTCC
1 CTTTCTTTTTCTTTCCTTTC
5088428 CTCTTCTTCTTCTCCTTTCCTTTC
1 CT-TTCTT-TT-T-CTTTCCTTTC
* * *
5088452 CTTTCTTCTCCTTTCCTTTT
1 CTTTCTTTTTCTTTCCTTTC
5088472 CTTTCTTTTTCTTT-CTTCTC
1 CTTTCTTTTTCTTTCCTT-TC
5088492 C-TTCTTTCTTCT
1 CTTTCTTT-TTCT
5088504 CCTCCAGCCG
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
19 9 0.15
20 29 0.48
21 5 0.08
22 3 0.05
23 6 0.10
24 9 0.15
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (20 bp):
CTTTCTTTTTCTTTCCTTTC
Found at i:5088487 original size:10 final size:10
Alignment explanation
Indices: 5088434--5088498 Score: 62
Period size: 10 Copynumber: 6.6 Consensus size: 10
5088424 CTCCCTCTTC
*
5088434 TTCTTCTCCT
1 TTCTTTTCCT
*
5088444 TTCCTTTCCT
1 TTCTTTTCCT
*
5088454 TTCTTCTCCT
1 TTCTTTTCCT
5088464 TTCCTTTT-CT
1 TT-CTTTTCCT
*
5088474 TTCTTTTTCT
1 TTCTTTTCCT
*
5088484 TTCTTCTCC-
1 TTCTTTTCCT
5088493 TTCTTT
1 TTCTTT
5088499 CTTCTCCTCC
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
9 10 0.22
10 31 0.69
11 4 0.09
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (10 bp):
TTCTTTTCCT
Found at i:5088490 original size:13 final size:13
Alignment explanation
Indices: 5088452--5088506 Score: 56
Period size: 13 Copynumber: 3.9 Consensus size: 13
5088442 CTTTCCTTTC
5088452 CTTTCTTCTCCTTT
1 CTTTCTTCTCC-TT
**
5088466 CCTTTTCTTTCTTTTT
1 -C-TTTC-TTCTCCTT
5088482 CTTTCTTCTCCTT
1 CTTTCTTCTCCTT
5088495 CTTTCTTCTCCT
1 CTTTCTTCTCCT
5088507 CCAGCCGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 18 0.53
14 4 0.12
15 2 0.06
16 6 0.18
17 4 0.12
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (13 bp):
CTTTCTTCTCCTT
Found at i:5088585 original size:27 final size:27
Alignment explanation
Indices: 5088539--5088604 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
5088529 ATAAGGGCTA
* * *
5088539 GTGCCGCCTGTGGCAGTGGCACCTTTG
1 GTGCCGCCTGTGCCACTGGCACCTCTG
*
5088566 GTGCCGCCTTTGCCACTGGCACCTCTG
1 GTGCCGCCTGTGCCACTGGCACCTCTG
5088593 GTGCCGCCTGTG
1 GTGCCGCCTGTG
5088605 GCAGGCCCTC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.06, C:0.35, G:0.33, T:0.26
Consensus pattern (27 bp):
GTGCCGCCTGTGCCACTGGCACCTCTG
Found at i:5089188 original size:27 final size:29
Alignment explanation
Indices: 5089158--5089217 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 29
5089148 TGTCTTCTGC
*
5089158 GGTTAGGATTTTGG-GTTATT-GGTTTAG
1 GGTTAGGATTTTGGTGTTATTAAGTTTAG
* *
5089185 GGTTAGGGTTTTGGTGTTTTTAAGTTTAG
1 GGTTAGGATTTTGGTGTTATTAAGTTTAG
5089214 GGTT
1 GGTT
5089218 TTAGAGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 13 0.46
28 5 0.18
29 10 0.36
ACGTcount: A:0.13, C:0.00, G:0.37, T:0.50
Consensus pattern (29 bp):
GGTTAGGATTTTGGTGTTATTAAGTTTAG
Found at i:5089426 original size:96 final size:96
Alignment explanation
Indices: 5089203--5089540 Score: 348
Period size: 96 Copynumber: 3.5 Consensus size: 96
5089193 TTTTGGTGTT
* * * * ** ** *
5089203 TTTA-AGTTT-AGGGTTTT-AGAGAAAAATTAAATAAATAAGGGTTTAGGGTTTGTCAATTAAAT
1 TTTAGAGTTTAAGGTTTTTAAGA-AAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAAAT
* *
5089265 TAATTATAAATTTTT-CAAAATTGGATT-AGG
65 TAATTATAAATTTTTAAAAAATTAGATTAAGG
* * * * * *
5089295 TTTCGTGTTTATTGTTTTTTAAGAAAAAATTAATTAAATTAGGGTTTAGGGTTACTTGAGTAATT
1 TTTAGAGTTTA-AGGTTTTTAAGAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAAAT
5089360 TAATTA-AAATTTTTTAAAAAATTAGATTAAGG
65 TAATTATAAA-TTTTTAAAAAATTAGATTAAGG
* * *
5089392 TTTAGAG-TTAAGAGTTTTTAAGGAAAAATCAATTAAATTAGGGTTCAGGATTACTTGAGTAAAT
1 TTTAGAGTTTAAG-GTTTTTAAGAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAAAT
* *
5089456 TAATTATAAATTTTTATAAAATTAGATTAGGG
65 TAATTATAAATTTTTAAAAAATTAGATTAAGG
* * * *
5089488 TTTAGTGTTTAAGGTTTTTAAGTAAAAACTCAAATAAATTAGGGTTTGGGGTT
1 TTTAGAGTTTAAGGTTTTTAAG-AAAAAATCAATTAAATTAGGGTTTAGGGTT
5089541 TAGGGTTACT
Statistics
Matches: 202, Mismatches: 33, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
92 3 0.01
93 4 0.02
94 3 0.01
95 50 0.25
96 102 0.50
97 40 0.20
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (96 bp):
TTTAGAGTTTAAGGTTTTTAAGAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAAATT
AATTATAAATTTTTAAAAAATTAGATTAAGG
Found at i:5090961 original size:21 final size:22
Alignment explanation
Indices: 5090914--5090962 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
5090904 TTTTGTCCAA
*
5090914 CTTCCAGCGGGGGTTGTGGTTG
1 CTTCCGGCGGGGGTTGTGGTTG
*
5090936 C-TCCGGCGGGGGTTTTGGTT-
1 CTTCCGGCGGGGGTTGTGGTTG
5090956 CTTCCGG
1 CTTCCGG
5090963 TTGGGGATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.02, C:0.22, G:0.43, T:0.33
Consensus pattern (22 bp):
CTTCCGGCGGGGGTTGTGGTTG
Found at i:5093116 original size:22 final size:21
Alignment explanation
Indices: 5093091--5093139 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
5093081 TCTTTTAAAT
* *
5093091 AGAAATTTGAGAGGAATTTGAG
1 AGAAATTAGAGA-GAAATTGAG
5093113 AGAATATTAGAGAGAAATTGAG
1 AGAA-ATTAGAGAGAAATTGAG
5093135 AGAAA
1 AGAAA
5093140 GGATTTAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 16 0.67
23 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (21 bp):
AGAAATTAGAGAGAAATTGAG
Found at i:5093135 original size:10 final size:10
Alignment explanation
Indices: 5093091--5093139 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 10
5093081 TCTTTTAAAT
5093091 AGAAATTTGAG
1 AGAAA-TTGAG
*
5093102 AGGAATTTGAG
1 A-GAAATTGAG
5093113 AGAATATTAGAG
1 AGAA-ATT-GAG
5093125 AGAAATTGAG
1 AGAAATTGAG
5093135 AGAAA
1 AGAAA
5093140 GGATTTAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
10 11 0.33
11 12 0.36
12 10 0.30
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (10 bp):
AGAAATTGAG
Found at i:5094284 original size:16 final size:16
Alignment explanation
Indices: 5094263--5094318 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
5094253 CGTTTGGTTC
5094263 ACTGTAATGGAATAGA
1 ACTGTAATGGAATAGA
*
5094279 ACTGTAATTGAATAGA
1 ACTGTAATGGAATAGA
*
5094295 ATTGTAATGGAATA-A
1 ACTGTAATGGAATAGA
5094310 AGCTGTAAT
1 A-CTGTAAT
5094319 CAGTAATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 2 0.06
16 33 0.94
ACGTcount: A:0.43, C:0.05, G:0.21, T:0.30
Consensus pattern (16 bp):
ACTGTAATGGAATAGA
Found at i:5094576 original size:58 final size:58
Alignment explanation
Indices: 5094497--5094620 Score: 178
Period size: 58 Copynumber: 2.1 Consensus size: 58
5094487 TTTTAATAAG
* *
5094497 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACCATATT-TTAACATA
1 ATTATTATTAAAAATAATTTAAT-AAAATAATAAATAATTTAACAAAATTCTTAACATA
* * * *
5094555 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAAAATTCTTAATATA
1 ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAACATA
5094613 ATTATTAT
1 ATTATTAT
5094621 ATGAATTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 22 0.37
58 37 0.63
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (58 bp):
ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAACATA
Found at i:5098117 original size:21 final size:21
Alignment explanation
Indices: 5098092--5098165 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
5098082 AATTTTGAGG
5098092 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
5098113 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
5098134 ATAT--AATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
5098151 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
5098166 ATATATGATT
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.08
19 22 0.43
21 25 0.49
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:5098135 original size:40 final size:37
Alignment explanation
Indices: 5098091--5098172 Score: 112
Period size: 40 Copynumber: 2.2 Consensus size: 37
5098081 TAATTTTGAG
5098091 GATATGCAATCTTAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATG--ATATGCAATCTTAGA-AT
**
5098131 GATATATAATCTTAGATATGATATGCAATCTTAGAAT
1 GATATGCAATCTTAGATATGATATGCAATCTTAGAAT
5098168 -ATATG
1 GATATG
5098173 ATTTTGTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
36 4 0.10
37 2 0.05
38 15 0.38
40 18 0.46
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.38
Consensus pattern (37 bp):
GATATGCAATCTTAGATATGATATGCAATCTTAGAAT
Found at i:5098141 original size:19 final size:19
Alignment explanation
Indices: 5098098--5098165 Score: 100
Period size: 19 Copynumber: 3.5 Consensus size: 19
5098088 GAGGATATGC
5098098 AATCTTAGATATGATATAT
1 AATCTTAGATATGATATAT
5098117 GCAATCTTAGATATGATATAT
1 --AATCTTAGATATGATATAT
**
5098138 AATCTTAGATATGATATGC
1 AATCTTAGATATGATATAT
5098157 AATCTTAGA
1 AATCTTAGA
5098166 ATATATGATT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 26 0.58
21 19 0.42
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (19 bp):
AATCTTAGATATGATATAT
Found at i:5098775 original size:25 final size:25
Alignment explanation
Indices: 5098724--5098775 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
5098714 AATTTTGTTA
**
5098724 ATGTAATTATTATTATTATTTTCAT
1 ATGTAATTATTATTATTATTAGCAT
5098749 ATGTAATTATTATTATT-TTAGCTAT
1 ATGTAATTATTATTATTATTAGC-AT
5098774 AT
1 AT
5098776 ATATATGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.58
Consensus pattern (25 bp):
ATGTAATTATTATTATTATTAGCAT
Found at i:5099365 original size:19 final size:19
Alignment explanation
Indices: 5099343--5099379 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5099333 AGGCTTTTGT
* *
5099343 TATATTTATTATTGCATTG
1 TATATTTAATATAGCATTG
5099362 TATATTTAATATAGCATT
1 TATATTTAATATAGCATT
5099380 ACATCATTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.54
Consensus pattern (19 bp):
TATATTTAATATAGCATTG
Found at i:5099740 original size:98 final size:98
Alignment explanation
Indices: 5099619--5099813 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
5099609 CTAAAAACAA
* *
5099619 TAAAGGAAATATTCCAAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
5099684 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
* *
5099717 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
5099782 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
5099814 ATTTTATTGT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:5103533 original size:32 final size:32
Alignment explanation
Indices: 5103492--5103554 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
5103482 TACTTTAAAG
*
5103492 ATGTTCAAAACACACTTGTTTCCTTTTGAGTA
1 ATGTTCAAAACACACTTGTTGCCTTTTGAGTA
5103524 ATGTTCAAAACACACTTGTTGCCTTTTGAGT
1 ATGTTCAAAACACACTTGTTGCCTTTTGAGT
5103555 GGGATTTGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (32 bp):
ATGTTCAAAACACACTTGTTGCCTTTTGAGTA
Found at i:5104162 original size:20 final size:19
Alignment explanation
Indices: 5104115--5104162 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
5104105 GTTCAGATTT
5104115 AAAAAAAACAAAAAAACAA
1 AAAAAAAACAAAAAAACAA
*
5104134 AAACAAAAACAAAAAAATAA
1 AAA-AAAAACAAAAAAACAA
5104154 AAAATAAAA
1 AAAA-AAAA
5104163 GTGAAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.88, C:0.08, G:0.00, T:0.04
Consensus pattern (19 bp):
AAAAAAAACAAAAAAACAA
Found at i:5105577 original size:44 final size:43
Alignment explanation
Indices: 5105498--5105709 Score: 126
Period size: 44 Copynumber: 4.8 Consensus size: 43
5105488 GCCACCAAGC
* * * * *
5105498 CTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGAT
1 CTTGTCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-TGTAGAT
* *
5105542 CTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAGAT
1 CTTGTCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATG-TAGAT
* * * *** *
5105586 CTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAAG-C
1 CTTGTC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--ATGTAGAT
* * * * * *
5105630 CTTGTCTCACTCAGCAGCAGCGGAGAAGGTTGAAGATTGTAGAT
1 CTTGTCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-TGTAGAT
* *
5105674 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA
1 CTTGTCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA
5105710 CGGCGGATCT
Statistics
Matches: 121, Mismatches: 36, Indels: 22
0.68 0.20 0.12
Matches are distributed among these distances:
42 5 0.04
43 9 0.07
44 96 0.79
45 8 0.07
46 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (43 bp):
CTTGTCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGTAGAT
Found at i:5105665 original size:132 final size:131
Alignment explanation
Indices: 5105428--5105816 Score: 661
Period size: 132 Copynumber: 2.9 Consensus size: 131
5105418 CTGTATTGAC
5105428 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
1 AGTGGAGCAGATCGAAGACGGCG-ATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
* *
5105493 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTGTCTCCCTAAGCA
65 CAAGCCTTGTCTCCCTCAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
5105558 GT
130 GT
* *
5105560 AGTGGAGCAGATCGAAGATGACAGATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
1 AGTGGAGCAGATCGAAGACGGC-GATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
*
5105625 CAAGCCTTGTCTCACTCAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
65 CAAGCCTTGTCTCCCTCAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
5105690 GT
130 GT
*
5105692 AGTGGAGCAGATCGAAGACGGCGGATCTTATCTTTCTAAGATAGTGGGAAGCAGATTTAAGCCAC
1 AGTGGAGCAGATCGAAGACGGC-GATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
* * * *
5105757 TAAGCCTTGTCTCCCTCAACAGCAGCAGAGAAGGTTGAAGATTGTAGATCCTATCTCCCT
65 CAAGCCTTGTCTCCCTCAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCT
5105817 GAAGTTGCAG
Statistics
Matches: 242, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
132 241 1.00
133 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (131 bp):
AGTGGAGCAGATCGAAGACGGCGATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACC
AAGCCTTGTCTCCCTCAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
T
Found at i:5105849 original size:44 final size:43
Alignment explanation
Indices: 5105801--5106358 Score: 349
Period size: 44 Copynumber: 12.9 Consensus size: 43
5105791 TTGAAGATTG
* **
5105801 TAGATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACC
1 TAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC
* * * *** *
5105844 TTAGATCTTATCTCTCTGAAGTTGTAG-AGAGCAGA-TCGCATC
1 -TAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC
* *
5105886 TAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC
1 TAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AACC
* * * * **
5105930 AAG-TCTTATC-CTCCTAAAGTTGCAGTGGGGCAGACTGAAGATGGC
1 TAGATCTTATCTC-CCTGAAGTTGCAGTGGAGCAGA-TTAA-A-ACC
* *
5105975 AAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC
1 TAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC
* *
5106017 GATA-ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACC
1 --TAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC
* * * *** *
5106061 TTAGATCTTATCTCTCTGAAGTTACAG-AGAGCAGA-TCGCATC
1 -TAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC
* * * * *
5106103 -AAATCTTATCTCTCTAAAGTTGCAGTGGAGCAGACTAAGTAAGC
1 TAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AACC
* * * **
5106147 AAG-TCTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGC
1 TAGATCTTATCTC-CCTGAAGTTGCAGTGGAGCAGA-TTAA-A-ACC
*
5106192 AAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC
1 TAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC
* * *
5106234 GATA-ATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACC
1 --TAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC
* ** *** *
5106278 TTAGATCTTATCTCTCTGAAGTTGCA-AAGAGCAGA-TCGCATC
1 -TAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC
* * *
5106320 TAG-TCTTATCTCACTGAAGTTGCAGTGAAGCAGACTAAA
1 TAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
5106359 TAAGCAAGTC
Statistics
Matches: 403, Mismatches: 84, Indels: 56
0.74 0.15 0.10
Matches are distributed among these distances:
40 62 0.15
41 26 0.06
42 15 0.04
43 25 0.06
44 203 0.50
45 70 0.17
46 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (43 bp):
TAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC
Found at i:5106047 original size:217 final size:217
Alignment explanation
Indices: 5105804--5106409 Score: 1068
Period size: 217 Copynumber: 2.8 Consensus size: 217
5105794 AAGATTGTAG
* *
5105804 ATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGT
1 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGC
*
5105869 AGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGT
66 AGAGAGCAGATCGCATCTAGTCTTATCTCACTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGT
*
5105934 CTTATCCTCCTAAAGTTGCAGTGGGGCAGACTGAAGATGGCAAGTCTTATCTCCCTGAAGTTGCA
131 CTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAGTCTTATCTCCCTGAAGTTGCA
*
5105999 GTGGAGCAGATTAAAGCCGATA
196 GTGGAGCAGATTAAAACCGATA
*
5106021 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTAC
1 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGC
* * * *
5106086 AGAGAGCAGATCGCATCAAATCTTATCTCTCTAAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGT
66 AGAGAGCAGATCGCATCTAGTCTTATCTCACTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGT
5106151 CTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAGTCTTATCTCCCTGAAGTTGCA
131 CTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAGTCTTATCTCCCTGAAGTTGCA
5106216 GTGGAGCAGATTAAAACCGATA
196 GTGGAGCAGATTAAAACCGATA
*
5106238 ATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGC
1 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGC
* * *
5106303 AAAGAGCAGATCGCATCTAGTCTTATCTCACTGAAGTTGCAGTGAAGCAGACTAAATAAGCAAGT
66 AGAGAGCAGATCGCATCTAGTCTTATCTCACTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGT
* *
5106368 CTTATCCTCCTGAAGTTGTAGTGAGGCAGACTGAAGATGGCA
131 CTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCA
5106410 CTAATTCCTA
Statistics
Matches: 369, Mismatches: 20, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
217 369 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (217 bp):
ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGC
AGAGAGCAGATCGCATCTAGTCTTATCTCACTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGT
CTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAGTCTTATCTCCCTGAAGTTGCA
GTGGAGCAGATTAAAACCGATA
Found at i:5106600 original size:21 final size:21
Alignment explanation
Indices: 5106575--5106693 Score: 135
Period size: 19 Copynumber: 5.9 Consensus size: 21
5106565 AATTTTGAGG
5106575 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
5106596 ATATGCAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
5106615 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
5106636 GTAT--AATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
5106653 ATATGCAATCTTAGAATAT-AT
1 ATATGCAATCTTAG-ATATGAT
* *
5106674 GATTTTGTAATCTTAGATAT
1 -A-TATGCAATCTTAGATAT
5106694 TTAATTTGTA
Statistics
Matches: 85, Mismatches: 4, Indels: 17
0.80 0.04 0.16
Matches are distributed among these distances:
17 3 0.04
19 40 0.47
20 4 0.05
21 22 0.26
22 5 0.06
23 11 0.13
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.40
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:5106618 original size:40 final size:39
Alignment explanation
Indices: 5106574--5106693 Score: 163
Period size: 38 Copynumber: 3.0 Consensus size: 39
5106564 TAATTTTGAG
5106574 GATATGCAATCTTAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATATG-AATCTTAGATAT
*
5106614 GATATGCAATCTTAGATATGATGTAT-AATCTTAGATAT
1 GATATGCAATCTTAGATATGATATATGAATCTTAGATAT
*
5106652 GATATGCAATCTTAGAATAT-ATGATTTTGTAATCTTAGATAT
1 GATATGCAATCTTAG-ATATGAT-A-TATG-AATCTTAGATAT
5106694 TTAATTTGTA
Statistics
Matches: 72, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
38 29 0.40
39 4 0.06
40 27 0.38
42 12 0.17
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (39 bp):
GATATGCAATCTTAGATATGATATATGAATCTTAGATAT
Found at i:5106620 original size:19 final size:19
Alignment explanation
Indices: 5106574--5106667 Score: 143
Period size: 19 Copynumber: 4.8 Consensus size: 19
5106564 TAATTTTGAG
5106574 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5106593 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
5106614 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
5106633 GATGTATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5106652 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
5106668 ATATATGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
19 48 0.72
21 19 0.28
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:5107266 original size:25 final size:25
Alignment explanation
Indices: 5107215--5107266 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
5107205 AATTTTGTTA
**
5107215 ATGTAATTATTATTATTATTTTCAT
1 ATGTAATTATTATTATTATTAGCAT
5107240 ATGTAATTATTATTATT-TTAGCTAT
1 ATGTAATTATTATTATTATTAGC-AT
5107265 AT
1 AT
5107267 ATATATGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.58
Consensus pattern (25 bp):
ATGTAATTATTATTATTATTAGCAT
Found at i:5107854 original size:19 final size:19
Alignment explanation
Indices: 5107832--5107868 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5107822 AGGCCTTTGT
* *
5107832 TATATTTATTATTGCATTG
1 TATATTTAATATAGCATTG
5107851 TATATTTAATATAGCATT
1 TATATTTAATATAGCATT
5107869 ACATCATTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.54
Consensus pattern (19 bp):
TATATTTAATATAGCATTG
Found at i:5108228 original size:98 final size:98
Alignment explanation
Indices: 5108108--5108302 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
5108098 CTAAAAACAA
* *
5108108 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
5108173 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
* *
5108206 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTGACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
5108271 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
5108303 ATTTTATTGT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:5109922 original size:26 final size:26
Alignment explanation
Indices: 5109891--5109940 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
5109881 TTTACAAACC
5109891 AAACCCAAAACAAACACAATTCAAAT
1 AAACCCAAAACAAACACAATTCAAAT
*
5109917 AAACCCAAAACAAACCCAATTCAA
1 AAACCCAAAACAAACACAATTCAA
5109941 TTACAAAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.60, C:0.30, G:0.00, T:0.10
Consensus pattern (26 bp):
AAACCCAAAACAAACACAATTCAAAT
Found at i:5110366 original size:11 final size:11
Alignment explanation
Indices: 5110352--5110385 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5110342 GTTTTTTTTT
5110352 GGAATTTTAGG
1 GGAATTTTAGG
5110363 GGAATTTTAGG
1 GGAATTTTAGG
**
5110374 GGTTTTTTAGG
1 GGAATTTTAGG
5110385 G
1 G
5110386 CATTTCAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (11 bp):
GGAATTTTAGG
Found at i:5111087 original size:17 final size:16
Alignment explanation
Indices: 5111061--5111092 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
5111051 CTTATATATT
5111061 TTTTTATATTTTTATA
1 TTTTTATATTTTTATA
5111077 TTTTTACTATTTTTAT
1 TTTTTA-TATTTTTAT
5111093 TTATCCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTATATTTTTATA
Found at i:5111091 original size:9 final size:8
Alignment explanation
Indices: 5111061--5111092 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
5111051 CTTATATATT
5111061 TTTTTATA
1 TTTTTATA
5111069 TTTTTATA
1 TTTTTATA
5111077 TTTTTACTA
1 TTTTTA-TA
5111086 TTTTTAT
1 TTTTTAT
5111093 TTATCCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTATA
Found at i:5114495 original size:20 final size:21
Alignment explanation
Indices: 5114440--5114496 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 21
5114430 TTAACATGGT
5114440 AATAAC-A-ATAATAAAATAA
1 AATAACAACATAATAAAATAA
*
5114459 AATAACTACATAA-AAAAT-A
1 AATAACAACATAATAAAATAA
5114478 AATAA-AACATAGATAAAAT
1 AATAACAACATA-ATAAAAT
5114497 TTAAAATGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
18 5 0.15
19 13 0.39
20 11 0.33
21 4 0.12
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.21
Consensus pattern (21 bp):
AATAACAACATAATAAAATAA
Found at i:5117985 original size:7 final size:7
Alignment explanation
Indices: 5117973--5118022 Score: 100
Period size: 7 Copynumber: 7.1 Consensus size: 7
5117963 ATTATATCAT
5117973 TTTATTA
1 TTTATTA
5117980 TTTATTA
1 TTTATTA
5117987 TTTATTA
1 TTTATTA
5117994 TTTATTA
1 TTTATTA
5118001 TTTATTA
1 TTTATTA
5118008 TTTATTA
1 TTTATTA
5118015 TTTATTA
1 TTTATTA
5118022 T
1 T
5118023 GTCCTTTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTATTA
Found at i:5118190 original size:6 final size:6
Alignment explanation
Indices: 5118179--5118224 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
5118169 GTTATTCTAC
* * *
5118179 TATTAA TATTAA TATTAA TATTAA TATTAT TATTAT TATTAT TATT
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATT
5118225 TACTTATTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (6 bp):
TATTAA
Found at i:5118211 original size:3 final size:3
Alignment explanation
Indices: 5118179--5118224 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
5118169 GTTATTCTAC
* * * *
5118179 TAT TAA TAT TAA TAT TAA TAT TAA TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5118225 TACTTATTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:5118352 original size:4 final size:4
Alignment explanation
Indices: 5118343--5118368 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5118333 TGTTTTATCT
5118343 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
5118369 ATTATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:5118998 original size:107 final size:107
Alignment explanation
Indices: 5118819--5119012 Score: 318
Period size: 107 Copynumber: 1.8 Consensus size: 107
5118809 AATAATAAGG
* *
5118819 CAATGTTTTGCGTTTGAAAATTCGAGAAAACGTACCCTAATGGGTTGGGTTTCGATTTTTTCGTT
1 CAATGTTTTGCGTTTGAAAATTCGAGAAAACGTACCCTAATGGGCTGGGTTTCGATTTTCTCGTT
5118884 CGACCAAATAGCCAAAAATCCTTATAAAATTTCAAAATAAAA
66 CGACCAAATAGCCAAAAATCCTTATAAAATTTCAAAATAAAA
* *
5118926 CAATGTTTTGCGTTTGAAAATTTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGA-TTTCTCGT
1 CAATGTTTTGCGTTTGAAAA-TTCGAGAAAACGTACCCTAATGGGCTGGGTTTCGATTTTCTCGT
* *
5118990 TGGACCAAATAGCCAAATATCCT
65 TCGACCAAATAGCCAAAAATCCT
5119013 CTTGAATCTT
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
107 48 0.60
108 32 0.40
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (107 bp):
CAATGTTTTGCGTTTGAAAATTCGAGAAAACGTACCCTAATGGGCTGGGTTTCGATTTTCTCGTT
CGACCAAATAGCCAAAAATCCTTATAAAATTTCAAAATAAAA
Found at i:5124046 original size:44 final size:44
Alignment explanation
Indices: 5123983--5124070 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
5123973 CCCCCAACAT
*
5123983 GTTTCACAGTCCTACAAACATTGTATAAACCTAATAACCACCCA
1 GTTTCACAGTCCTACAAACATTATATAAACCTAATAACCACCCA
5124027 GTTTCACAGTCCTACAAACATTATATAAACCTAATAACCACCCA
1 GTTTCACAGTCCTACAAACATTATATAAACCTAATAACCACCCA
5124071 ACAAAAAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.40, C:0.30, G:0.06, T:0.25
Consensus pattern (44 bp):
GTTTCACAGTCCTACAAACATTATATAAACCTAATAACCACCCA
Found at i:5126424 original size:2 final size:2
Alignment explanation
Indices: 5126417--5126459 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5126407 ATGTACATGG
5126417 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5126459 G
1 G
5126460 GGCGGGAAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5128760 original size:12 final size:12
Alignment explanation
Indices: 5128745--5128777 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
5128735 ATAAATAATT
5128745 AATTAAATTAGA
1 AATTAAATTAGA
*
5128757 AATTAAATTGGA
1 AATTAAATTAGA
5128769 AATTAAATT
1 AATTAAATT
5128778 TAGATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (12 bp):
AATTAAATTAGA
Found at i:5136674 original size:30 final size:30
Alignment explanation
Indices: 5136619--5136680 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
5136609 CACTAAGCAA
5136619 GTTTTATATACATGTATCATCCATTT-CAT
1 GTTTTATATACATGTATCATCCATTTCCAT
5136648 GTTTTAATATATCATGTAAT-AT-CATTTCCAT
1 GTTTT-ATATA-CATGT-ATCATCCATTTCCAT
5136679 GT
1 GT
5136681 ATTTCATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 5 0.17
30 10 0.34
31 12 0.41
32 2 0.07
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (30 bp):
GTTTTATATACATGTATCATCCATTTCCAT
Found at i:5136920 original size:50 final size:50
Alignment explanation
Indices: 5136859--5136972 Score: 140
Period size: 50 Copynumber: 2.3 Consensus size: 50
5136849 ATTGGTATGT
* * *
5136859 TCTCACGAGCTGTGAATC-AGTAAGCTTATACAAGCTAAGAATCAGTAAGC
1 TCTCACAAGCTGTAAATCGA-TAAGCTCATACAAGCTAAGAATCAGTAAGC
* * *
5136909 TCTCACAAGCTGTAAATCGATAAGCTCATACGAGCTGAGAATCGGTAAGC
1 TCTCACAAGCTGTAAATCGATAAGCTCATACAAGCTAAGAATCAGTAAGC
**
5136959 TCTCATGAGCTGTA
1 TCTCACAAGCTGTA
5136973 GTGCGTCTGC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 54 0.98
51 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (50 bp):
TCTCACAAGCTGTAAATCGATAAGCTCATACAAGCTAAGAATCAGTAAGC
Found at i:5136960 original size:25 final size:25
Alignment explanation
Indices: 5136866--5136960 Score: 97
Period size: 25 Copynumber: 3.8 Consensus size: 25
5136856 TGTTCTCACG
* *
5136866 AGCTGTGAATCAGTAAGCTTATACA
1 AGCTGAGAATCAGTAAGCTCATACA
*
5136891 AGCTAAGAATCAGTAAGCTC-TCACA
1 AGCTGAGAATCAGTAAGCTCAT-ACA
*
5136916 AGCTGTA-AATC-GATAAGCTCATACG
1 AGCTG-AGAATCAG-TAAGCTCATACA
*
5136941 AGCTGAGAATCGGTAAGCTC
1 AGCTGAGAATCAGTAAGCTC
5136961 TCATGAGCTG
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
24 3 0.05
25 53 0.90
26 3 0.05
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (25 bp):
AGCTGAGAATCAGTAAGCTCATACA
Found at i:5136968 original size:25 final size:25
Alignment explanation
Indices: 5136859--5136970 Score: 95
Period size: 25 Copynumber: 4.5 Consensus size: 25
5136849 ATTGGTATGT
* *
5136859 TCTCACGAGCTGTGAATCAGTAAGC
1 TCTCACGAGCTGAGAATCGGTAAGC
* * * *
5136884 T-TATACAAGCTAAGAATCAGTAAGC
1 TCT-CACGAGCTGAGAATCGGTAAGC
* *
5136909 TCTCACAAGCTGTA-AATCGATAAGC
1 TCTCACGAGCTG-AGAATCGGTAAGC
5136934 TCAT-ACGAGCTGAGAATCGGTAAGC
1 TC-TCACGAGCTGAGAATCGGTAAGC
*
5136959 TCTCATGAGCTG
1 TCTCACGAGCTG
5136971 TAGTGCGTCT
Statistics
Matches: 70, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
24 3 0.04
25 64 0.91
26 3 0.04
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (25 bp):
TCTCACGAGCTGAGAATCGGTAAGC
Found at i:5145556 original size:10 final size:11
Alignment explanation
Indices: 5145536--5145568 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5145526 ATTTTTCCTA
5145536 GGATGTGAATT
1 GGATGTGAATT
5145547 GGAT-TGAATT
1 GGATGTGAATT
*
5145557 GAATGTGAATT
1 GGATGTGAATT
5145568 G
1 G
5145569 TATTAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (11 bp):
GGATGTGAATT
Found at i:5145562 original size:21 final size:21
Alignment explanation
Indices: 5145538--5145579 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5145528 TTTTCCTAGG
*
5145538 ATGTGAATTGGATTGAATTGA
1 ATGTGAATTGGATTAAATTGA
*
5145559 ATGTGAATTGTATTAAATTGA
1 ATGTGAATTGGATTAAATTGA
5145580 GCTAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (21 bp):
ATGTGAATTGGATTAAATTGA
Found at i:5151009 original size:22 final size:22
Alignment explanation
Indices: 5150968--5151018 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
5150958 AATTTTTAAT
5150968 TTTAAAAAATAGAGAAACTAAA
1 TTTAAAAAATAGAGAAACTAAA
5150990 TTTATAAAAATA-A-AAGACTAAA
1 TTTA-AAAAATAGAGAA-ACTAAA
5151012 TTCTAAA
1 TT-TAAA
5151019 TATACAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 2 0.08
22 15 0.58
23 9 0.35
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (22 bp):
TTTAAAAAATAGAGAAACTAAA
Found at i:5154181 original size:30 final size:30
Alignment explanation
Indices: 5154121--5154182 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
5154111 AGTTTATATC
* *
5154121 TTTATAATTTTTAAATGATTAAATTAAATT
1 TTTATAATTTTTAAATGACTAAAATAAATT
* *
5154151 TTTATCATTTTTAGA-GACTAAAATATAATT
1 TTTATAATTTTTAAATGACTAAAATA-AATT
5154181 TT
1 TT
5154183 ACCAAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (30 bp):
TTTATAATTTTTAAATGACTAAAATAAATT
Found at i:5154835 original size:19 final size:19
Alignment explanation
Indices: 5154793--5154832 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
5154783 TCACTCCCCC
5154793 CTTCTCTTCTTTCACCTTT
1 CTTCTCTTCTTTCACCTTT
5154812 CTTCTC-TCTTT-ACCCTTT
1 CTTCTCTTCTTTCA-CCTTT
5154830 CTT
1 CTT
5154833 TCTGCCGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 1 0.05
18 13 0.65
19 6 0.30
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.57
Consensus pattern (19 bp):
CTTCTCTTCTTTCACCTTT
Found at i:5174943 original size:16 final size:16
Alignment explanation
Indices: 5174922--5174955 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5174912 CTTCAACCTC
*
5174922 TCATTTCCTTCTCATT
1 TCATTTCCTCCTCATT
5174938 TCATTTCCTCCTCATT
1 TCATTTCCTCCTCATT
5174954 TC
1 TC
5174956 CTCTCCGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.00, T:0.53
Consensus pattern (16 bp):
TCATTTCCTCCTCATT
Found at i:5175852 original size:13 final size:11
Alignment explanation
Indices: 5175824--5175857 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
5175814 ATTTTTTTCT
5175824 CATATATTGTA
1 CATATATTGTA
5175835 CATATATTGTA
1 CATATATTGTA
5175846 CATATATTGTA
1 CATATATTGTA
5175857 C
1 C
5175858 TAATTCCTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (11 bp):
CATATATTGTA
Found at i:5176681 original size:321 final size:321
Alignment explanation
Indices: 5176097--5176739 Score: 1241
Period size: 321 Copynumber: 2.0 Consensus size: 321
5176087 TAACCTCAAG
5176097 AGTTACCTTCATTCAGGGAGTGCTATGGTTGTTACGCCTATGAGTAATACAAGATAGGTCATAAG
1 AGTTACCTTCATTCAGGGAGTGCTATGGTTGTTACGCCTATGAGTAATACAAGATAGGTCATAAG
*
5176162 AAGTATTTTAAGTGTTAGAATGAATTCCACCTATTATTATATATACTAGATGGATGTTTCTGACA
66 AAGTATTTTAAGTGCTAGAATGAATTCCACCTATTATTATATATACTAGATGGATGTTTCTGACA
5176227 TCTGAAATTGCTTATTGTAAATCAATGACTCTTTTAAGTTTAGAATTTGATGTATGAGGACTATC
131 TCTGAAATTGCTTATTGTAAATCAATGACTCTTTTAAGTTTAGAATTTGATGTATGAGGACTATC
*
5176292 TTTTCGTATCTATGTTTCTTTTGTTGTTTAAGTTGCAATATAGATCTTTCTCTCTGAGACAAATA
196 TTTTCATATCTATGTTTCTTTTGTTGTTTAAGTTGCAATATAGATCTTTCTCTCTGAGACAAATA
5176357 CATACTCAAGGAGAGGTGTATGCACACATGCATGTAATTACATGTTATTCTTGTTTACCAC
261 CATACTCAAGGAGAGGTGTATGCACACATGCATGTAATTACATGTTATTCTTGTTTACCAC
* *
5176418 AGTTACCTTCATTCAGGGAGTGCTATGGTTGTTACGTCTATGAGTAATACAAGATATGTCATAAG
1 AGTTACCTTCATTCAGGGAGTGCTATGGTTGTTACGCCTATGAGTAATACAAGATAGGTCATAAG
5176483 AAGTATTTTAAGTGCTAGAATGAATTCCACCTATTATTATATATACTAGATGGATGTTTCTGACA
66 AAGTATTTTAAGTGCTAGAATGAATTCCACCTATTATTATATATACTAGATGGATGTTTCTGACA
5176548 TCTGAAATTGCTTATTGTAAATCAATGACTCTTTTAAGTTTAGAATTTGATGTATGAGGACTATC
131 TCTGAAATTGCTTATTGTAAATCAATGACTCTTTTAAGTTTAGAATTTGATGTATGAGGACTATC
*
5176613 TTTTCATATCTATGTTTCTTTTGTTGTTTAAGTTGCAATATAGATCTTTCTCTCTGAGACAGATA
196 TTTTCATATCTATGTTTCTTTTGTTGTTTAAGTTGCAATATAGATCTTTCTCTCTGAGACAAATA
5176678 CATACTCAAGGAGAGGTGTATGCACACATGCATGTAATTACATGTTATTCTTGTTTACCAC
261 CATACTCAAGGAGAGGTGTATGCACACATGCATGTAATTACATGTTATTCTTGTTTACCAC
5176739 A
1 A
5176740 CTGTGTCTGT
Statistics
Matches: 317, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
321 317 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (321 bp):
AGTTACCTTCATTCAGGGAGTGCTATGGTTGTTACGCCTATGAGTAATACAAGATAGGTCATAAG
AAGTATTTTAAGTGCTAGAATGAATTCCACCTATTATTATATATACTAGATGGATGTTTCTGACA
TCTGAAATTGCTTATTGTAAATCAATGACTCTTTTAAGTTTAGAATTTGATGTATGAGGACTATC
TTTTCATATCTATGTTTCTTTTGTTGTTTAAGTTGCAATATAGATCTTTCTCTCTGAGACAAATA
CATACTCAAGGAGAGGTGTATGCACACATGCATGTAATTACATGTTATTCTTGTTTACCAC
Found at i:5177410 original size:20 final size:20
Alignment explanation
Indices: 5177385--5177424 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5177375 AATATTTTCC
* *
5177385 AGTAAATCATTTTACAGAAA
1 AGTAAAACACTTTACAGAAA
*
5177405 AGTAAAACACTTTCCAGAAA
1 AGTAAAACACTTTACAGAAA
5177425 TTATTTTACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (20 bp):
AGTAAAACACTTTACAGAAA
Found at i:5185728 original size:376 final size:375
Alignment explanation
Indices: 5185036--5185789 Score: 1463
Period size: 376 Copynumber: 2.0 Consensus size: 375
5185026 AATGGAAACC
*
5185036 ATTTAAAATCATACTAGGCAGCTTGGACATAACATATATGCTTAGTATATGAAAAGCAACAAGAC
1 ATTTAAAATCATACTAGGCAGCTTGGACATAACATATATGCTGAGTATATGAAAAGCAACAAGAC
5185101 ATTAACATGACAAAACCAGCACTTGTAAATCACATAATTGATATAAAGTAAAATCTAGAAGACAT
66 ATTAACATGACAAAACCAGCACTTGTAAATCACATAATTGATATAAAGTAAAATCTAGAAGACAT
*
5185166 TGAAATGTTGCAAATGCATCATATCAGTCTTCCTCTTTGCTGAAATAGAAAAGATATAACCCAGA
131 TGAAATGTTGAAAATGCATCATATCAGTCTTCCTCTTTGCTGAAATAGAAAAGATATAACCCAGA
*
5185231 TAAGATAAGCATTAACTTATCTATACAAGTAAAATTCAAGAACATGCAAATAACTCAACCCGACG
196 TAAGATAAGCATTAACTTATCTATACAAGTAAAACTCAAGAACATGCAAATAACTCAACCCGACG
*
5185296 AGTAAGGCAATATTGACACTGTGTAATCACATAGGATTGCCGAATACATGATCATGTAAAACGAC
261 AGTAAGGCAATATTGACACTGTGTAATCACATAGGATTGCCGAATACATAATCATGTAAAACGAC
5185361 TTACCTCTCAAGAGTTTGGTTTTTCCTTAGCTGCATGCGTGAAAAATTCG
326 TTACCTCTCAAGAGTTTGGTTTTTCCTTAGCTGCATGCGTGAAAAATTCG
5185411 ATTTAAAATCATACTAGGCAGCTTGGACATAACATATATGCTGAGTATATGAAAAGCAACAAGAC
1 ATTTAAAATCATACTAGGCAGCTTGGACATAACATATATGCTGAGTATATGAAAAGCAACAAGAC
5185476 ATTAACATGACAAAACCAGCACTTGTAAATCACATAATTGATATACAAGTAAAATCTAGAAGACA
66 ATTAACATGACAAAACCAGCACTTGTAAATCACATAATTGATATA-AAGTAAAATCTAGAAGACA
5185541 TTGAAATGTTGAAAATGCATCATATCAGTCTTCCTCTTTGCTGAAATAGAAAAGATATAACCCAG
130 TTGAAATGTTGAAAATGCATCATATCAGTCTTCCTCTTTGCTGAAATAGAAAAGATATAACCCAG
5185606 ATAAGATAAGCATTAACTTATCTATACAAGTAAAACTCAAGAACATGCAAATAACTCAACCCGAC
195 ATAAGATAAGCATTAACTTATCTATACAAGTAAAACTCAAGAACATGCAAATAACTCAACCCGAC
5185671 GAGTAAGGCAATATTGACACTGTGTAATCACATAGGATTGCCGAATACATAATCATGTAAAACGA
260 GAGTAAGGCAATATTGACACTGTGTAATCACATAGGATTGCCGAATACATAATCATGTAAAACGA
5185736 CTTACCTCTCAAGAGTTTGGTTTTTCCTTAGCTGCATGCGTGAAAAATTCG
325 CTTACCTCTCAAGAGTTTGGTTTTTCCTTAGCTGCATGCGTGAAAAATTCG
5185787 ATT
1 ATT
5185790 GCCAAGCAAG
Statistics
Matches: 374, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
375 109 0.29
376 265 0.71
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (375 bp):
ATTTAAAATCATACTAGGCAGCTTGGACATAACATATATGCTGAGTATATGAAAAGCAACAAGAC
ATTAACATGACAAAACCAGCACTTGTAAATCACATAATTGATATAAAGTAAAATCTAGAAGACAT
TGAAATGTTGAAAATGCATCATATCAGTCTTCCTCTTTGCTGAAATAGAAAAGATATAACCCAGA
TAAGATAAGCATTAACTTATCTATACAAGTAAAACTCAAGAACATGCAAATAACTCAACCCGACG
AGTAAGGCAATATTGACACTGTGTAATCACATAGGATTGCCGAATACATAATCATGTAAAACGAC
TTACCTCTCAAGAGTTTGGTTTTTCCTTAGCTGCATGCGTGAAAAATTCG
Found at i:5186984 original size:23 final size:24
Alignment explanation
Indices: 5186934--5186984 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
5186924 TGGATACAAG
5186934 TTTAGTATTGATTTTGGAAAATTCT
1 TTTAGTATTGATTTT-GAAAATTCT
*
5186959 TTTAGTATTG-TTGTT-AAAATTTT
1 TTTAGTATTGATT-TTGAAAATTCT
5186982 TTT
1 TTT
5186985 TTGAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 10 0.42
24 2 0.08
25 12 0.50
ACGTcount: A:0.25, C:0.02, G:0.14, T:0.59
Consensus pattern (24 bp):
TTTAGTATTGATTTTGAAAATTCT
Found at i:5190955 original size:31 final size:32
Alignment explanation
Indices: 5190920--5190987 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
5190910 AAAATTAGAT
* *
5190920 TAAATTGTGATTAAAAT-AAAAT-TTAAATACA
1 TAAATTG-CATTAAAATAAAAATATTAAATAAA
*
5190951 TAAA-TGCATTAAATTAAAAATATTAAATAAA
1 TAAATTGCATTAAAATAAAAATATTAAATAAA
5190982 TAAATT
1 TAAATT
5190988 ATTTAGTAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 7 0.23
30 7 0.23
31 16 0.52
32 1 0.03
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.35
Consensus pattern (32 bp):
TAAATTGCATTAAAATAAAAATATTAAATAAA
Found at i:5191661 original size:26 final size:27
Alignment explanation
Indices: 5191629--5191686 Score: 86
Period size: 26 Copynumber: 2.2 Consensus size: 27
5191619 CAACCAAAAC
5191629 CTAATTTTAA-TTTATTTATACAT-TTT
1 CTAATTTTAATTTTA-TTATACATATTT
5191655 CTAATTTTAATTTTATTATACATATTT
1 CTAATTTTAATTTTATTATACATATTT
5191682 -TAATT
1 CTAATT
5191687 GTATATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 23 0.77
27 7 0.23
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (27 bp):
CTAATTTTAATTTTATTATACATATTT
Found at i:5202309 original size:41 final size:41
Alignment explanation
Indices: 5202253--5202485 Score: 297
Period size: 41 Copynumber: 5.7 Consensus size: 41
5202243 TTAATATAAA
* * * *
5202253 CAGATTCACTGGCACTTAGCTTGTTAGGCTTAAAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* * *
5202295 CAGATCACCAGCACTTAGCCTGCTAGGCTTATAGCCTAATC
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* * * *
5202336 CAGTTCACCGGCACTTAGCGTGCTAGGCTTATAGCCTAATC
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* * *
5202377 CAGTTCACCAGCACTTAGCCTGCTAGGTTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
5202418 CA-ATTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
5202459 TAGATCACCGGCACTTAGCCTGCTAGG
1 CAGATCACCGGCACTTAGCCTGCTAGG
5202486 TTTTAAAACC
Statistics
Matches: 169, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
41 164 0.97
42 5 0.03
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
Found at i:5202476 original size:123 final size:123
Alignment explanation
Indices: 5202264--5202485 Score: 329
Period size: 123 Copynumber: 1.8 Consensus size: 123
5202254 AGATTCACTG
* * *
5202264 GCACTTAGCTTGTTAGGCTTAAAGCCTGATTCAGATCACCAGCACTTAGCCTGCTAGGCTTATAG
1 GCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCACCAGCACTTAGCCTGCTAGGCTTATAA
* *
5202329 CCTAATCCAGTTCACCGGCACTTAGCGTGCTAGGCTTATAGCCTAATCCAGTTCACCA
66 CCTAATCCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTAATCCAGTTCACCA
* * *
5202387 GCACTTAGCCTGCTAGGTTTATAGCCTGATTCA-ATTCACCGGCACTTAGCCTGCTAGGCTTATA
1 GCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGA-TCACCAGCACTTAGCCTGCTAGGCTTATA
* **
5202451 ACCTGATTTAGATCACCGGCACTTAGCCTGCTAGG
65 ACCTAATCCAGATCACCGGCACTTAGCCTGCTAGG
5202486 TTTTAAAACC
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
122 1 0.01
123 86 0.99
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (123 bp):
GCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCACCAGCACTTAGCCTGCTAGGCTTATAA
CCTAATCCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTAATCCAGTTCACCA
Found at i:5208903 original size:27 final size:26
Alignment explanation
Indices: 5208872--5208939 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 26
5208862 TAATTTAAAT
5208872 TATATGTATATATGTTTACAAAATATG
1 TATATGTATATATGTTTA-AAAATATG
* *
5208899 TATATATAAGTAAAT-TTTAAAAATATG
1 TATATGT-A-TATATGTTTAAAAATATG
* *
5208926 AATATGCATATATG
1 TATATGTATATATG
5208940 AAACATGTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
25 4 0.12
26 1 0.03
27 18 0.56
28 5 0.16
29 4 0.12
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (26 bp):
TATATGTATATATGTTTAAAAATATG
Found at i:5209329 original size:7 final size:7
Alignment explanation
Indices: 5209298--5209344 Score: 51
Period size: 8 Copynumber: 6.4 Consensus size: 7
5209288 ATATGCGTAT
5209298 ATATATA
1 ATATATA
5209305 GATATAATA
1 -ATAT-ATA
5209314 ATAT-TA
1 ATATATA
*
5209320 ATATTTA
1 ATATATA
5209327 ATATAATA
1 ATAT-ATA
5209335 ATATATA
1 ATATATA
5209342 ATA
1 ATA
5209345 CTAATAATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
6 6 0.17
7 12 0.34
8 14 0.40
9 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (7 bp):
ATATATA
Found at i:5209338 original size:15 final size:16
Alignment explanation
Indices: 5209306--5209352 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
5209296 ATATATATAG
* *
5209306 ATATAATAATATTAAT
1 ATATAATACTAATAAT
*
5209322 ATTTAATA-TAATAAT
1 ATATAATACTAATAAT
5209337 ATATAATACTAATAAT
1 ATATAATACTAATAAT
5209353 CATACAGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATAATACTAATAAT
Found at i:5209349 original size:21 final size:21
Alignment explanation
Indices: 5209306--5209350 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
5209296 ATATATATAG
*
5209306 ATATAATAATATTAATATTTA
1 ATATAATAATATTAATATCTA
5209327 ATATAATAATATATAATA-CTA
1 ATATAATAATAT-TAATATCTA
5209348 ATA
1 ATA
5209351 ATCATACAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATAATAATATTAATATCTA
Found at i:5217217 original size:40 final size:40
Alignment explanation
Indices: 5217162--5217247 Score: 163
Period size: 40 Copynumber: 2.1 Consensus size: 40
5217152 GTTCGCCAAA
5217162 AGCTTCTTTAAAAATTTAACGAATTGGGCATCTACGAAAG
1 AGCTTCTTTAAAAATTTAACGAATTGGGCATCTACGAAAG
*
5217202 AGCTTCTTTAAAAATTTAACGAATTGGGCATCTATGAAAG
1 AGCTTCTTTAAAAATTTAACGAATTGGGCATCTACGAAAG
5217242 AGCTTC
1 AGCTTC
5217248 AATAAACAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (40 bp):
AGCTTCTTTAAAAATTTAACGAATTGGGCATCTACGAAAG
Found at i:5219191 original size:18 final size:19
Alignment explanation
Indices: 5219150--5219191 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
5219140 AAATAAAAGA
*
5219150 AAAATTAGAAAACAAAACT
1 AAAATTAGAAAACAAAAAT
*
5219169 TAAATTA-AAAACAAAAAT
1 AAAATTAGAAAACAAAAAT
5219187 AAAAT
1 AAAAT
5219192 GTAATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.19
Consensus pattern (19 bp):
AAAATTAGAAAACAAAAAT
Found at i:5219672 original size:16 final size:17
Alignment explanation
Indices: 5219645--5219716 Score: 66
Period size: 17 Copynumber: 4.4 Consensus size: 17
5219635 AAAAAGTATT
5219645 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
5219662 TTAAAAA-ATTTT---A
1 TTAAAAATATTTTAAAA
*
5219675 --AAAAGTATTTTAAAAAA
1 TTAAAAATATTTT--AAAA
5219692 TTTAAAAATATTTTAAAA
1 -TTAAAAATATTTTAAAA
5219710 TTAAAAA
1 TTAAAAA
5219717 AAGTATTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 18
0.69 0.03 0.28
Matches are distributed among these distances:
11 4 0.09
12 5 0.11
13 1 0.02
16 5 0.11
17 15 0.34
18 4 0.09
20 10 0.23
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:5219675 original size:10 final size:11
Alignment explanation
Indices: 5219635--5219740 Score: 81
Period size: 12 Copynumber: 10.4 Consensus size: 11
5219625 CAAAAATTAA
5219635 AAAAAGTATTTT
1 AAAAA-TATTTT
5219647 AAAAATATTTT
1 AAAAATATTTT
5219658 --AAA-A--TT
1 AAAAATATTTT
5219664 AAAAA-ATTTT
1 AAAAATATTTT
5219674 AAAAAGTATTTT
1 AAAAA-TATTTT
5219686 AAAAA-A-TTT
1 AAAAATATTTT
5219695 AAAAATATTTT
1 AAAAATATTTT
**
5219706 --AAA-ATTAA
1 AAAAATATTTT
5219714 AAAAAGTATTTT
1 AAAAA-TATTTT
*
5219726 AAAAGTATTTT
1 AAAAATATTTT
5219737 AAAA
1 AAAA
5219741 TTAAAAAATA
Statistics
Matches: 77, Mismatches: 5, Indels: 25
0.72 0.05 0.23
Matches are distributed among these distances:
6 2 0.03
8 8 0.10
9 14 0.18
10 12 0.16
11 19 0.25
12 22 0.29
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:5219745 original size:48 final size:47
Alignment explanation
Indices: 5219644--5219750 Score: 153
Period size: 48 Copynumber: 2.2 Consensus size: 47
5219634 AAAAAAGTAT
5219644 TTTAAAAATATTTTAAAATTAAAAAATTTTAAAAAGTATTTTAAAAAA
1 TTTAAAAATATTTTAAAATTAAAAAATTTTAAAAAGTATTTT-AAAAA
*
5219692 TTTAAAAATATTTTAAAATTAAAAAAAGTATTTTAAAAGTATTTT-AAAA
1 TTTAAAAATATTTTAAAATT-AAAAAA-T-TTTAAAAAGTATTTTAAAAA
*
5219741 TTAAAAAATA
1 TTTAAAAATA
5219751 AAAATTATTA
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
48 20 0.37
49 19 0.35
50 1 0.02
51 14 0.26
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (47 bp):
TTTAAAAATATTTTAAAATTAAAAAATTTTAAAAAGTATTTTAAAAA
Found at i:5230740 original size:22 final size:21
Alignment explanation
Indices: 5230705--5230745 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
5230695 ACTTATACTT
5230705 TTAAATTCTACAAATATAAAGA
1 TTAAATTCTACAAA-ATAAAGA
5230727 TTAAATTCCT-CAAAATAAA
1 TTAAATT-CTACAAAATAAA
5230746 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 11 0.61
23 2 0.11
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (21 bp):
TTAAATTCTACAAAATAAAGA
Found at i:5232261 original size:10 final size:10
Alignment explanation
Indices: 5232246--5232273 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
5232236 ACTGTAAAAA
5232246 AAAGTGTTGT
1 AAAGTGTTGT
5232256 AAAGTGTTGT
1 AAAGTGTTGT
5232266 AAAGTGTT
1 AAAGTGTT
5232274 AAAAATATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (10 bp):
AAAGTGTTGT
Found at i:5242849 original size:17 final size:17
Alignment explanation
Indices: 5242824--5242863 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
5242814 ATAATAAGAA
* **
5242824 GTTATAATAAAATTAAT
1 GTTAAAATAAAAAAAAT
5242841 GTTAAAATAAAAAAAAT
1 GTTAAAATAAAAAAAAT
5242858 GTTAAA
1 GTTAAA
5242864 TTAATTACAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (17 bp):
GTTAAAATAAAAAAAAT
Found at i:5246255 original size:9 final size:9
Alignment explanation
Indices: 5246238--5246274 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
5246228 TGAGTTTTCG
5246238 AATTCGAAT
1 AATTCGAAT
*
5246247 AACTCGAAT
1 AATTCGAAT
*
5246256 AATTCAAAT
1 AATTCGAAT
5246265 AATTCGAAT
1 AATTCGAAT
5246274 A
1 A
5246275 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5246969 original size:15 final size:16
Alignment explanation
Indices: 5246949--5246981 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5246939 AATTCCAAAA
5246949 TACATTT-TATATTTT
1 TACATTTATATATTTT
5246964 TACATTTAATATATTTT
1 TACATTT-ATATATTTT
5246981 T
1 T
5246982 TAATTCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (16 bp):
TACATTTATATATTTT
Found at i:5247318 original size:5 final size:5
Alignment explanation
Indices: 5247308--5247335 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
5247298 GAAAATTTTT
5247308 GATTC GATTC GATTC GATTC GATTC GAT
1 GATTC GATTC GATTC GATTC GATTC GAT
5247336 CGAATGCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (5 bp):
GATTC
Found at i:5250786 original size:9 final size:9
Alignment explanation
Indices: 5250772--5250874 Score: 118
Period size: 9 Copynumber: 11.4 Consensus size: 9
5250762 TTTGGTTAAA
5250772 AATTAACCG
1 AATTAACCG
*
5250781 AATTAACCA
1 AATTAACCG
*
5250790 AATTACCCG
1 AATTAACCG
*
5250799 AATTAACTG
1 AATTAACCG
5250808 AATTATA-CG
1 AATTA-ACCG
*
5250817 AATTAATCG
1 AATTAACCG
5250826 AATTAACCG
1 AATTAACCG
5250835 AATTAACCG
1 AATTAACCG
* *
5250844 AATTACCCA
1 AATTAACCG
*
5250853 AATTACCCG
1 AATTAACCG
*
5250862 AATTTACCG
1 AATTAACCG
5250871 AATT
1 AATT
5250875 GAATCACTAC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
8 1 0.01
9 78 0.98
10 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:5251844 original size:20 final size:20
Alignment explanation
Indices: 5251821--5251867 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
5251811 AGTACCATAA
*
5251821 TGCAAACATGGGAACCAAAG
1 TGCAAACAAGGGAACCAAAG
* *
5251841 TGCAAAAAAGGGCACCAAAG
1 TGCAAACAAGGGAACCAAAG
*
5251861 TGAAAAC
1 TGCAAAC
5251868 TATAAGTATC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.19, G:0.23, T:0.09
Consensus pattern (20 bp):
TGCAAACAAGGGAACCAAAG
Found at i:5258509 original size:27 final size:26
Alignment explanation
Indices: 5258478--5258551 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 26
5258468 CGTATTCGTG
*
5258478 AGAAGTTCGTTAAGACTATCTAGTGT
1 AGAAGTTCGTTAAGACTATCTAATGT
* * *
5258504 GGGAAGTT-GATCAAAACTATCTAATGT
1 -AGAAGTTCG-TTAAGACTATCTAATGT
* *
5258531 AGAAGTCCGTTAGGACTATCT
1 AGAAGTTCGTTAAGACTATCT
5258552 TGTAAATGTG
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
26 15 0.42
27 21 0.58
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (26 bp):
AGAAGTTCGTTAAGACTATCTAATGT
Found at i:5259087 original size:28 final size:28
Alignment explanation
Indices: 5259022--5259089 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
5259012 AGGTGTTCCG
* *
5259022 TGTCACGACATCCCTGACAGTTTACTGT
1 TGTCGCGACATCCCTGACAGTTTACCGT
*
5259050 TGTCGCGACATCCCTGGCAGTTTACCGT
1 TGTCGCGACATCCCTGACAGTTTACCGT
* *
5259078 TTTCGTGACATC
1 TGTCGCGACATC
5259090 GAAAGAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.18, C:0.29, G:0.21, T:0.32
Consensus pattern (28 bp):
TGTCGCGACATCCCTGACAGTTTACCGT
Found at i:5262204 original size:17 final size:18
Alignment explanation
Indices: 5262182--5262218 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
5262172 TAGGGTTTTT
5262182 ATAATAATAAA-AA-TAAA
1 ATAAT-ATAAAGAACTAAA
5262199 ATAATATAAAGAACTAAA
1 ATAATATAAAGAACTAAA
5262217 AT
1 AT
5262219 TCAAGAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 7 0.39
18 6 0.33
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (18 bp):
ATAATATAAAGAACTAAA
Found at i:5263582 original size:54 final size:54
Alignment explanation
Indices: 5263482--5263588 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 54
5263472 ATTGAAAACC
* * *
5263482 TTGTTCTAGAAAACACCATTGTTCAAAAGGAAGCTACTATTAAGGGGGAGACTG
1 TTGTTCCAGAAAACACAATTGTTCAAAAGGAAGCTACTATTAAGGGGAAGACTG
*
5263536 TTGTTCCAGAAAACACAATTGTTCAAAAGGAAGCTACTGA-TCAGGGGAAGACT
1 TTGTTCCAGAAAACACAATTGTTCAAAAGGAAGCTACT-ATTAAGGGGAAGACT
5263589 AATATTTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 47 0.98
55 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.24
Consensus pattern (54 bp):
TTGTTCCAGAAAACACAATTGTTCAAAAGGAAGCTACTATTAAGGGGAAGACTG
Found at i:5281927 original size:30 final size:30
Alignment explanation
Indices: 5281888--5281944 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
5281878 TTTTACAAAT
5281888 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
5281918 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
5281945 AACAACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:5282840 original size:21 final size:20
Alignment explanation
Indices: 5282790--5282840 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
5282780 ATTCAAAAAC
*
5282790 TAAATAAAATTATAAAAATTA
1 TAAAT-AAATTACAAAAATTA
*
5282811 -ATAACAAATTACAGAAAATTA
1 TA-AATAAATTACA-AAAATTA
5282832 TAAATAAAT
1 TAAATAAAT
5282841 ACCATAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
20 8 0.33
21 15 0.62
22 1 0.04
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (20 bp):
TAAATAAATTACAAAAATTA
Found at i:5282886 original size:10 final size:11
Alignment explanation
Indices: 5282863--5282887 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5282853 AAAATGTTAG
5282863 AAATTATAAAA
1 AAATTATAAAA
5282874 AAATTATAAAA
1 AAATTATAAAA
5282885 AAA
1 AAA
5282888 AATTGTTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATTATAAAA
Found at i:5284351 original size:17 final size:18
Alignment explanation
Indices: 5284325--5284359 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5284315 AATTATTCCC
5284325 TTTTTCTTGAAATTTTTA
1 TTTTTCTTGAAATTTTTA
*
5284343 TTTTT-TTGAGATTTTTA
1 TTTTTCTTGAAATTTTTA
5284360 CAAGTAGGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.20, C:0.03, G:0.09, T:0.69
Consensus pattern (18 bp):
TTTTTCTTGAAATTTTTA
Found at i:5285192 original size:42 final size:42
Alignment explanation
Indices: 5285119--5285275 Score: 174
Period size: 42 Copynumber: 3.7 Consensus size: 42
5285109 TCGTGTTTAC
* * * *
5285119 TTTCCGTTTAGCTCTCACGAGCTTCTATTTAACTCATATGAG
1 TTTCCGTTTAGCTCTCATGAGCTTCTGTTTAACCCTTATGAG
* * *
5285161 TTTCCGTTCAGCTCT-ATTGAGTTTCTGTTTAACCCTTATGGG
1 TTTCCGTTTAGCTCTCA-TGAGCTTCTGTTTAACCCTTATGAG
* * * *
5285203 TTTCCGTTAAGCTTTTATGAGCTTCTGTTCAACCCTTA-GAGG
1 TTTCCGTTTAGCTCTCATGAGCTTCTGTTTAACCCTTATGA-G
*
5285245 TTTCTGTTTAGCTCTCATGAGCTTCTGTTTA
1 TTTCCGTTTAGCTCTCATGAGCTTCTGTTTA
5285276 GCCTTCGGGC
Statistics
Matches: 95, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
41 2 0.02
42 92 0.97
43 1 0.01
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (42 bp):
TTTCCGTTTAGCTCTCATGAGCTTCTGTTTAACCCTTATGAG
Found at i:5285270 original size:21 final size:21
Alignment explanation
Indices: 5285119--5285277 Score: 97
Period size: 21 Copynumber: 7.6 Consensus size: 21
5285109 TCGTGTTTAC
* * *
5285119 TTTCCGTTTAGCTCTCACGAG
1 TTTCTGTTTAGCTCTTATGAG
* * * *
5285140 CTTCTATTTAACTCATATGAG
1 TTTCTGTTTAGCTCTTATGAG
* *
5285161 TTTCCGTTCAGCTC-TATTGAG
1 TTTCTGTTTAGCTCTTA-TGAG
* * *
5285182 TTTCTGTTTAACCCTTATGGG
1 TTTCTGTTTAGCTCTTATGAG
* * *
5285203 TTTCCGTTAAGCTTTTATGAG
1 TTTCTGTTTAGCTCTTATGAG
* * * *
5285224 CTTCTGTTCAACCCTTA-GAGG
1 TTTCTGTTTAGCTCTTATGA-G
*
5285245 TTTCTGTTTAGCTCTCATGAG
1 TTTCTGTTTAGCTCTTATGAG
*
5285266 CTTCTGTTTAGC
1 TTTCTGTTTAGC
5285278 CTTCGGGCTT
Statistics
Matches: 99, Mismatches: 35, Indels: 8
0.70 0.25 0.06
Matches are distributed among these distances:
20 4 0.04
21 91 0.92
22 4 0.04
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.43
Consensus pattern (21 bp):
TTTCTGTTTAGCTCTTATGAG
Found at i:5287667 original size:2 final size:2
Alignment explanation
Indices: 5287660--5287704 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
5287650 TACAATAGAT
5287660 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5287702 TC T
1 TC T
5287705 TTTCCTATGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5289329 original size:16 final size:14
Alignment explanation
Indices: 5289298--5289337 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
5289288 AAACATATTA
5289298 AATTAATTTTAATT
1 AATTAATTTTAATT
5289312 AATTAATTTCTCAATT
1 AATTAATTT-T-AATT
*
5289328 AAATAATTTT
1 AATTAATTTT
5289338 TTAAACCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 9 0.39
15 2 0.09
16 12 0.52
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTAATTTTAATT
Found at i:5298730 original size:19 final size:19
Alignment explanation
Indices: 5298706--5298753 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
5298696 AGCAATTTTA
5298706 CCACGTCAGCAAAGTGCAT
1 CCACGTCAGCAAAGTGCAT
* *
5298725 CCACGTTAGCAAAGTGTAT
1 CCACGTCAGCAAAGTGCAT
*
5298744 CAACGTCAGC
1 CCACGTCAGC
5298754 GCGTTTTGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (19 bp):
CCACGTCAGCAAAGTGCAT
Found at i:5303265 original size:22 final size:22
Alignment explanation
Indices: 5303217--5303265 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5303207 TAAGAATTAG
5303217 AAAAAAAATCGTAAAAATATAT
1 AAAAAAAATCGTAAAAATATAT
* * * *
5303239 CAAAAAAATTGTAAAATTTTAT
1 AAAAAAAATCGTAAAAATATAT
5303261 AAAAA
1 AAAAA
5303266 TAGTAAAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAAAAATCGTAAAAATATAT
Found at i:5303266 original size:19 final size:19
Alignment explanation
Indices: 5303242--5303283 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5303232 AATATATCAA
* **
5303242 AAAAATTGTAAAATTTTAT
1 AAAAATAGTAAAAAATTAT
5303261 AAAAATAGTAAAAAATTAT
1 AAAAATAGTAAAAAATTAT
5303280 AAAA
1 AAAA
5303284 TATATAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
AAAAATAGTAAAAAATTAT
Found at i:5303350 original size:56 final size:54
Alignment explanation
Indices: 5303250--5303355 Score: 135
Period size: 54 Copynumber: 1.9 Consensus size: 54
5303240 AAAAAAATTG
*
5303250 TAAAATTTTATAAAAATAGTAAAAAATTATAAAATATATAGAAATATAAAAAAA
1 TAAAATTTTATAAAAATAGTAAAAAATTATAAAATATAAAGAAATATAAAAAAA
* *
5303304 TAAAATTTTAT-AAAGTCGTAATAAAATTATACAAA-AGGTAAAGAAATATAAA
1 TAAAATTTTATAAAAATAGTAA-AAAATTATA-AAATA--TAAAGAAATATAAA
5303356 TTTTGTAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
53 8 0.18
54 21 0.47
55 3 0.07
56 13 0.29
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (54 bp):
TAAAATTTTATAAAAATAGTAAAAAATTATAAAATATAAAGAAATATAAAAAAA
Found at i:5303505 original size:9 final size:9
Alignment explanation
Indices: 5303491--5303545 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
5303481 TCATCAATTG
5303491 TTTTATAAT
1 TTTTATAAT
*
5303500 TTTTATAAAG
1 TTTTAT-AAT
*
5303510 TTTTACAAT
1 TTTTATAAT
*
5303519 TTTTTTATAT
1 TTTTATA-AT
*
5303529 TTTTATGAT
1 TTTTATAAT
5303538 TTTTATAA
1 TTTTATAA
5303546 AAAAATAATT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
9 22 0.61
10 14 0.39
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:5303514 original size:19 final size:18
Alignment explanation
Indices: 5303491--5303617 Score: 80
Period size: 19 Copynumber: 6.8 Consensus size: 18
5303481 TCATCAATTG
5303491 TTTTATAATTTTTATAAA
1 TTTTATAATTTTTATAAA
* * *
5303509 GTTTTACAATTTTTTTATAT
1 -TTTTATAATTTTTATA-AA
*
5303529 TTTTATGATTTTTATAAA
1 TTTTATAATTTTTATAAA
***
5303547 -AAAATAATTTTTCATAAA
1 TTTTATAATTTTT-ATAAA
5303565 TTTTA-AATTTTTATTAAAA
1 TTTTATAATTTTTA-T-AAA
*
5303584 TTTAATAA-TTTTACTAAA
1 TTTTATAATTTTTA-TAAA
* *
5303602 ATTTATTATTTATTAT
1 TTTTATAATTT-TTAT
5303618 GATTTTTAAT
Statistics
Matches: 81, Mismatches: 19, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
17 9 0.11
18 22 0.27
19 44 0.54
20 6 0.07
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTTATAATTTTTATAAA
Found at i:5303602 original size:55 final size:55
Alignment explanation
Indices: 5303495--5303602 Score: 132
Period size: 55 Copynumber: 2.0 Consensus size: 55
5303485 CAATTGTTTT
* * * *
5303495 ATAATTTTTATAAAGTTTTACAATTTTTTTATATTTTTATGATTTTTATAAAAAA
1 ATAATTTTTATAAAGTTTTACAATTTTTTTAAAATTTAATGAATTTTATAAAAAA
5303550 ATAATTTTTCATAAA-TTTTA-AATTTTTATTAAAATTTAAT-AATTTTACTAAAA
1 ATAATTTTT-ATAAAGTTTTACAATTTTT-TTAAAATTTAATGAATTTTA-TAAAA
5303603 TTTATTATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
54 13 0.28
55 28 0.61
56 5 0.11
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.54
Consensus pattern (55 bp):
ATAATTTTTATAAAGTTTTACAATTTTTTTAAAATTTAATGAATTTTATAAAAAA
Found at i:5304675 original size:14 final size:13
Alignment explanation
Indices: 5304651--5304680 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
5304641 TATTTTTTTC
5304651 ATTCATTATATCT
1 ATTCATTATATCT
5304664 ATTCACTTATATCT
1 ATTCA-TTATATCT
5304678 ATT
1 ATT
5304681 AATTTTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTCATTATATCT
Found at i:5317671 original size:26 final size:26
Alignment explanation
Indices: 5317595--5317840 Score: 195
Period size: 26 Copynumber: 9.4 Consensus size: 26
5317585 GAATAAAGTA
* * *
5317595 ATTATCTAACAGGCTTTGAGTCGGTG
1 ATTATTTAGCAGGCTTTGAGCCGGTG
* * * * * *
5317621 TTTATTTAGCGGGCCTAGACCCGGTT
1 ATTATTTAGCAGGCTTTGAGCCGGTG
* *
5317647 ATTATTTAGCAGGCTTTGAGTCGGTT
1 ATTATTTAGCAGGCTTTGAGCCGGTG
* * *
5317673 TTTATGTAGTAGGCTTTGAGCCGGTG
1 ATTATTTAGCAGGCTTTGAGCCGGTG
* * * * * *
5317699 ATTATTTAGTAAGCCTTAAACCAGTG
1 ATTATTTAGCAGGCTTTGAGCCGGTG
* *
5317725 ATTATTTAACAGGCTTTGAGCCGATG
1 ATTATTTAGCAGGCTTTGAGCCGGTG
* *
5317751 GTCATTTAGCAGGCTTTGAGCCGGTG
1 ATTATTTAGCAGGCTTTGAGCCGGTG
* * * *
5317777 TTTATTTAGTAGGTTTTGAGCTGGTG
1 ATTATTTAGCAGGCTTTGAGCCGGTG
* * * *
5317803 GTTATTTATCAGGCTTTAAGCCGGTA
1 ATTATTTAGCAGGCTTTGAGCCGGTG
5317829 ATTTATTTAGCA
1 A-TTATTTAGCA
5317841 AGTACCATGT
Statistics
Matches: 166, Mismatches: 53, Indels: 1
0.75 0.24 0.00
Matches are distributed among these distances:
26 157 0.95
27 9 0.05
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (26 bp):
ATTATTTAGCAGGCTTTGAGCCGGTG
Found at i:5327312 original size:17 final size:17
Alignment explanation
Indices: 5327286--5327333 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 17
5327276 GTCTTTCAAA
5327286 ATTTATATAATTTTT-AT
1 ATTTA-ATAATTTTTCAT
5327303 ATTTAGATAATTTTTCAT
1 ATTTA-ATAATTTTTCAT
5327321 ATATTAATAATTT
1 AT-TTAATAATTT
5327334 ATATTATCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 14 0.50
18 11 0.39
19 3 0.11
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
ATTTAATAATTTTTCAT
Found at i:5333846 original size:3 final size:3
Alignment explanation
Indices: 5333838--5333866 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5333828 TAACTTTCAT
5333838 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5333867 TAAATACCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5333989 original size:6 final size:7
Alignment explanation
Indices: 5333972--5333996 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5333962 TTAAAAACCC
5333972 TTTTTAA
1 TTTTTAA
5333979 TTTTTAA
1 TTTTTAA
5333986 TTTTTAA
1 TTTTTAA
5333993 TTTT
1 TTTT
5333997 GCATTATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTAA
Found at i:5334888 original size:22 final size:21
Alignment explanation
Indices: 5334858--5334902 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
5334848 ACACCAAAAC
* *
5334858 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCAGCG-TTTTTT
5334880 AGGCCTTTAGCAGCGTTTTTT
1 AGGCCTTTAGCAGCGTTTTTT
5334901 AG
1 AG
5334903 CGCCGCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.13, C:0.18, G:0.27, T:0.42
Consensus pattern (21 bp):
AGGCCTTTAGCAGCGTTTTTT
Found at i:5335045 original size:43 final size:43
Alignment explanation
Indices: 5334972--5335262 Score: 440
Period size: 43 Copynumber: 6.8 Consensus size: 43
5334962 GCGTCGCTAA
*
5334972 CTTTAGCGGCGC-TTTCCCACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
* * *
5335014 CTTTAGCGGCGCTTTTCCCACAAACGACGCTAAAGACCATGAT
1 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
*
5335057 CTTTAGCGACGCTTTTCCGACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
* *
5335100 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGAT
1 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
* * *
5335143 CTTTAGCGTCGCTTTTCCGACAAACGCCGCTAAAGACGATGAC
1 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
* * * *
5335186 TTTTAGCGACGCTTTTCCGACAAACGCCACTAAAGACCCTGAC
1 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
*
5335229 CTTTAGCGACGCTTTTCCCAAAAACGCCGCTAAA
1 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAA
5335263 ACATGGCTTT
Statistics
Matches: 226, Mismatches: 22, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
42 12 0.05
43 214 0.95
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.22
Consensus pattern (43 bp):
CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
Found at i:5340226 original size:39 final size:39
Alignment explanation
Indices: 5340183--5340267 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 39
5340173 TTGGGCCTAG
* *
5340183 TTTTTTGCGGCGCTTTTCTAAAAACGCCACTAATGCTCA
1 TTTTTAGCGGCGCTTTTCGAAAAACGCCACTAATGCTCA
* * * *
5340222 TTTTTAGCGGCGTTTTTCGAAAAGCGCCGCTAATGCTTA
1 TTTTTAGCGGCGCTTTTCGAAAAACGCCACTAATGCTCA
5340261 TTTTTAG
1 TTTTTAG
5340268 TGATTTTATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (39 bp):
TTTTTAGCGGCGCTTTTCGAAAAACGCCACTAATGCTCA
Found at i:5340699 original size:21 final size:21
Alignment explanation
Indices: 5340675--5340714 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5340665 TCTAAACCCC
5340675 TAAA-CCCTAACCCCTAAACTT
1 TAAATCCC-AACCCCTAAACTT
*
5340696 TAAATCCCAACCCTTAAAC
1 TAAATCCCAACCCCTAAAC
5340715 AATAAACCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAATCCCAACCCCTAAACTT
Found at i:5340933 original size:16 final size:17
Alignment explanation
Indices: 5340900--5340938 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
5340890 AAGAACACTA
5340900 TATTTAATATATTAAAT
1 TATTTAATATATTAAAT
5340917 TATTTAATATA-TAAAT
1 TATTTAATATATTAAAT
5340933 TATTTA
1 TATTTA
5340939 TAAAGAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATTTAATATATTAAAT
Found at i:5341175 original size:28 final size:29
Alignment explanation
Indices: 5341144--5341210 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 29
5341134 CCGCAACCCT
* * *
5341144 TAAACCCTAAATCTTAAAC-CATAAACTA
1 TAAACCATAAACCTTAAACTCATAAACCA
*
5341172 TAAACCAT-AACCTTAAACTCATAATCCA
1 TAAACCATAAACCTTAAACTCATAAACCA
*
5341200 TAAACCTTAAA
1 TAAACCATAAA
5341211 ATAGTAACTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
27 9 0.28
28 21 0.66
29 2 0.06
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (29 bp):
TAAACCATAAACCTTAAACTCATAAACCA
Found at i:5341208 original size:22 final size:23
Alignment explanation
Indices: 5341180--5341232 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
5341170 TATAAACCAT
*
5341180 AACCTTAAACTCA-TAATCCA-TA
1 AACCTTAAAATCAGTAA-CCATTA
*
5341202 AACCTTAAAAT-AGTAACTATTA
1 AACCTTAAAATCAGTAACCATTA
5341224 AACCTTAAA
1 AACCTTAAA
5341233 CTCTAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 3 0.11
22 24 0.89
ACGTcount: A:0.49, C:0.21, G:0.02, T:0.28
Consensus pattern (23 bp):
AACCTTAAAATCAGTAACCATTA
Found at i:5341210 original size:7 final size:7
Alignment explanation
Indices: 5341089--5341210 Score: 63
Period size: 7 Copynumber: 17.6 Consensus size: 7
5341079 TTTCAACCCC
5341089 TAAACCT
1 TAAACCT
5341096 TAAACCT
1 TAAACCT
* *
5341103 CAACCCT
1 TAAACCT
5341110 T-AACC-
1 TAAACCT
*
5341115 TATAACAT
1 TA-AACCT
*
5341123 TAAACCA
1 TAAACCT
*
5341130 TAAACCG
1 TAAACCT
* *
5341137 CAACCCT
1 TAAACCT
*
5341144 TAAACCC
1 TAAACCT
*
5341151 TAAATCT
1 TAAACCT
*
5341158 TAAACCA
1 TAAACCT
5341165 TAAA-CT
1 TAAACCT
*
5341171 ATAAACCA
1 -TAAACCT
5341179 T-AACCT
1 TAAACCT
*
5341185 TAAACTCA
1 TAAAC-CT
* *
5341193 TAATCCA
1 TAAACCT
5341200 TAAACCT
1 TAAACCT
5341207 TAAA
1 TAAA
5341211 ATAGTAACTA
Statistics
Matches: 83, Mismatches: 25, Indels: 14
0.68 0.20 0.11
Matches are distributed among these distances:
5 1 0.01
6 9 0.11
7 65 0.78
8 8 0.10
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.24
Consensus pattern (7 bp):
TAAACCT
Found at i:5341547 original size:19 final size:20
Alignment explanation
Indices: 5341521--5341566 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
5341511 ATAGAATTTT
5341521 AATT-AATA-TAAATAAACA
1 AATTAAATAGTAAATAAACA
* *
5341539 AATTAAATAGTAATTAGACA
1 AATTAAATAGTAAATAAACA
*
5341559 AATAAAAT
1 AATTAAAT
5341567 GTTTTTGCGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (20 bp):
AATTAAATAGTAAATAAACA
Found at i:5341630 original size:41 final size:41
Alignment explanation
Indices: 5341573--5341681 Score: 173
Period size: 41 Copynumber: 2.7 Consensus size: 41
5341563 AAATGTTTTT
* *
5341573 GCGGCGCTTTTCCAAAAACGCTGCTAAAGACCAGAGAATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAAACCAGAGAATTA
* *
5341614 GCGGCGCTTCTCCAAAAACGCCGCTAAAAACCAGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAAACCAGAGAATTA
*
5341655 GCGGCGCTTTTCTAAAAACGCCGCTAA
1 GCGGCGCTTTTCCAAAAACGCCGCTAA
5341682 TGTCCCGAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.18
Consensus pattern (41 bp):
GCGGCGCTTTTCCAAAAACGCCGCTAAAAACCAGAGAATTA
Found at i:5343138 original size:156 final size:157
Alignment explanation
Indices: 5342950--5343683 Score: 1026
Period size: 156 Copynumber: 4.6 Consensus size: 157
5342940 CGATACATAC
*
5342950 CGATATTGATCAAAACATA-CTAATAAATACATATC-CTGAGATACGAGAATGATTTTTGTTCCC
1 CGATATTGATAAAAACATATC-AATAAATACATATCTC-GAGATACGAGAATGATTTTTGTTCCC
* *
5343013 TGCATTTTCTCATGA-TTTTTTTTATTTTGAAAGATGTTTCGCATCATTTTATATTGTATCAATG
64 CGCATTTTCTCATCATTTTTTTTTATTTTGAAAGATGTTTCGCATCATTTTATATTGTATCAATG
** *
5343077 GATACAGATAAATACATACCGATATAAAT
129 GATACAGATCGATACATACCAATATAAAT
* * *
5343106 CGATATTGATCAAAACATATAAATAAATACATATCTCGAGATATGAGAATGATTTTTGTTCCCCG
1 CGATATTGATAAAAACATATCAATAAATACATATCTCGAGATACGAGAATGATTTTTGTTCCCCG
* *
5343171 CATTTTCTCGTCA-TTTTTTTTATTTTGAAAGATGTTTCGCATGATTTTATATTGTATCAATGGA
66 CATTTTCTCATCATTTTTTTTTATTTTGAAAGATGTTTCGCATCATTTTATATTGTATCAATGGA
* * *
5343235 TATAGATCGGTACATACCGATATAAAT
131 TACAGATCGATACATACCAATATAAAT
* * *
5343262 CGATATTGATAAACACATATCAATAAATACATATCTTGAGATACGAGAATGAGTTTTGTTCCCCG
1 CGATATTGATAAAAACATATCAATAAATACATATCTCGAGATACGAGAATGATTTTTGTTCCCCG
* * *
5343327 CATTTTCTCATCATTTTTTTTTATTTTGAAAGATGTTTCGCATGATTTCATATTGTATCAACGGA
66 CATTTTCTCATCATTTTTTTTTATTTTGAAAGATGTTTCGCATCATTTTATATTGTATCAATGGA
*
5343392 TGCAGATCGATACATACCAATATAAAT
131 TACAGATCGATACATACCAATATAAAT
* * ** *
5343419 CGATATTGATAAAAACATATTAATAAATACATATATTAAGATACGAGAATAATTTTTGTTCCCCG
1 CGATATTGATAAAAACATATCAATAAATACATATCTCGAGATACGAGAATGATTTTTGTTCCCCG
* * *
5343484 CATTTTTCTTATCAATTTTTTTTATTATTTTGAAAGATGTTCCGCATCATTTTATATTATATCAA
66 CA-TTTTCTCATC-A-TTTTTTT-TTATTTTGAAAGATGTTTCGCATCATTTTATATTGTATCAA
* *
5343549 TGGATACAGATCGATGCATACCAATATAAAA
127 TGGATACAGATCGATACATACCAATATAAAT
* * * * * *
5343580 CGGTATTGAAAAAAACATATCAATAAATACATATATCGAGATACAAGAATGATTTTTGTTTCCCA
1 CGATATTGATAAAAACATATCAATAAATACATATCTCGAGATACGAGAATGATTTTTGTTCCCCG
*
5343645 CATTTTCTCATCATTTTTTGTTTTATTTTAAAAGATGTT
66 CATTTTCTCATCA-TTTTT-TTTTATTTTGAAAGATGTT
5343684 AGTGAATTTG
Statistics
Matches: 521, Mismatches: 49, Indels: 13
0.89 0.08 0.02
Matches are distributed among these distances:
156 214 0.41
157 134 0.26
158 9 0.02
159 24 0.05
160 18 0.03
161 122 0.23
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (157 bp):
CGATATTGATAAAAACATATCAATAAATACATATCTCGAGATACGAGAATGATTTTTGTTCCCCG
CATTTTCTCATCATTTTTTTTTATTTTGAAAGATGTTTCGCATCATTTTATATTGTATCAATGGA
TACAGATCGATACATACCAATATAAAT
Found at i:5356579 original size:13 final size:13
Alignment explanation
Indices: 5356561--5356585 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5356551 GTGAATTAAT
5356561 GTGTGAAAATTTC
1 GTGTGAAAATTTC
5356574 GTGTGAAAATTT
1 GTGTGAAAATTT
5356586 TATCGTTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:5360955 original size:7 final size:6
Alignment explanation
Indices: 5360939--5361008 Score: 52
Period size: 6 Copynumber: 11.0 Consensus size: 6
5360929 AATGAGCAAG
* * *
5360939 AAAAGA AAAATGA AAAAGA AACA-A AAATGA AAAATGA AAAAGA AATTAAAA
1 AAAAGA AAAA-GA AAAAGA AAAAGA AAAAGA AAAA-GA AAAAGA AA--AAGA
*
5360990 GAAAAGA GAAAGA AAAAGA
1 -AAAAGA AAAAGA AAAAGA
5361009 GTGCGGGCAA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
5 3 0.06
6 27 0.54
7 15 0.30
8 3 0.06
9 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.07
Consensus pattern (6 bp):
AAAAGA
Found at i:5360970 original size:24 final size:23
Alignment explanation
Indices: 5360939--5360994 Score: 85
Period size: 24 Copynumber: 2.4 Consensus size: 23
5360929 AATGAGCAAG
5360939 AAAAGAAAAATGAAAAAGAAACA
1 AAAAGAAAAATGAAAAAGAAACA
**
5360962 AAAATGAAAAATGAAAAAGAAATT
1 AAAA-GAAAAATGAAAAAGAAACA
5360986 AAAAGAAAA
1 AAAAGAAAA
5360995 GAGAAAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 9 0.30
24 21 0.70
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.09
Consensus pattern (23 bp):
AAAAGAAAAATGAAAAAGAAACA
Found at i:5361006 original size:17 final size:17
Alignment explanation
Indices: 5360936--5361008 Score: 71
Period size: 17 Copynumber: 4.2 Consensus size: 17
5360926 TCGAATGAGC
*
5360936 AAGAAAAGAAAAATGAAA
1 AAGAAAA-AGAAATGAAA
5360954 AAGAAACAA-AAATGAAA
1 AAGAAA-AAGAAATGAAA
*
5360971 AATGAAAAAGAAAT-TAA
1 AA-GAAAAAGAAATGAAA
5360988 AAGAAAAGAGAAA-GAAA
1 AAGAAAA-AGAAATGAAA
5361005 AAGA
1 AAGA
5361009 GTGCGGGCAA
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.10
17 27 0.56
18 15 0.31
19 1 0.02
ACGTcount: A:0.75, C:0.01, G:0.16, T:0.07
Consensus pattern (17 bp):
AAGAAAAAGAAATGAAA
Found at i:5362816 original size:14 final size:13
Alignment explanation
Indices: 5362797--5362839 Score: 61
Period size: 14 Copynumber: 3.3 Consensus size: 13
5362787 GAAGCTGAAC
5362797 CTAACTTAGCTAG
1 CTAACTTAGCTAG
5362810 TCTAACTTAGCTAG
1 -CTAACTTAGCTAG
*
5362824 CTAACTCAGCT-G
1 CTAACTTAGCTAG
5362836 CTAA
1 CTAA
5362840 GACATTTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 5 0.18
13 10 0.36
14 13 0.46
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (13 bp):
CTAACTTAGCTAG
Found at i:5363309 original size:3 final size:3
Alignment explanation
Indices: 5363266--5363293 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5363256 GTGTTTGATG
5363266 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5363294 GTTCCCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5363523 original size:19 final size:18
Alignment explanation
Indices: 5363499--5363534 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5363489 ATTGTTTATG
*
5363499 GTTATTATTATTTATCGTC
1 GTTATTAATATTT-TCGTC
5363518 GTTATTAATATTTTCGT
1 GTTATTAATATTTTCGT
5363535 TTCTAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.22, C:0.08, G:0.11, T:0.58
Consensus pattern (18 bp):
GTTATTAATATTTTCGTC
Done.