Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 132 of 161
Found at i:41222655 original size:17 final size:18
Alignment explanation
Indices: 41222623--41222657 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
41222613 AAAACCCTAG
41222623 CTTTTTCTCCTTTCTTTCT
1 CTTTTTCT-CTTTCTTTCT
41222642 CTTTTTCT-TTTCTTTC
1 CTTTTTCTCTTTCTTTC
41222658 GTTCCTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (18 bp):
CTTTTTCTCTTTCTTTCT
Found at i:41222711 original size:27 final size:28
Alignment explanation
Indices: 41222633--41222711 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 28
41222623 CTTTTTCTCC
*
41222633 TTTCTTTCTCTTTTTC-TTTTC-TTTCG
1 TTTCTTTTTCTTTTTCGTTTTCATTTCG
*
41222659 TTCCTTTTT-TGTTTTCG-TTTCAATTT-G
1 TTTCTTTTTCT-TTTTCGTTTTC-ATTTCG
*
41222686 TTTCTTTTTCTATTTCGTTTTCATTT
1 TTTCTTTTTCTTTTTCGTTTTCATTT
41222712 TATTTTTTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
25 1 0.02
26 16 0.37
27 18 0.42
28 8 0.19
ACGTcount: A:0.05, C:0.18, G:0.06, T:0.71
Consensus pattern (28 bp):
TTTCTTTTTCTTTTTCGTTTTCATTTCG
Found at i:41222719 original size:13 final size:13
Alignment explanation
Indices: 41222703--41222728 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41222693 TTCTATTTCG
41222703 TTTTCATTTTATT
1 TTTTCATTTTATT
41222716 TTTTCATTTTATT
1 TTTTCATTTTATT
41222729 ATTATTTCAA
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:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTCATTTTATT
Found at i:41222720 original size:19 final size:19
Alignment explanation
Indices: 41222698--41222735 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
41222688 TCTTTTTCTA
*
41222698 TTTCGTTTTCATT-TTATTT
1 TTTCATTTT-ATTATTATTT
41222717 TTTCATTTTATTATTATTT
1 TTTCATTTTATTATTATTT
41222736 CAATTACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.74
Consensus pattern (19 bp):
TTTCATTTTATTATTATTT
Found at i:41225413 original size:41 final size:39
Alignment explanation
Indices: 41225285--41225415 Score: 101
Period size: 41 Copynumber: 3.3 Consensus size: 39
41225275 TTTGGCACAT
* * *
41225285 AGTGCCTCATTGAATAAT-TCGAAGTAATAATTTGACACCC
1 AGTGTCTCATCGAATAATCT-GAAGT-ATAAATTGACACCC
* * *
41225325 AGTGTCTCATC-AACTAAACCGAAG--TAAATTGGCACCC
1 AGTGTCTCATCGAA-TAATCTGAAGTATAAATTGACACCC
* *
41225362 AGT-ACGTCATCGAATTAATCTGAAGTATTAAATTGACACCT
1 AGTGTC-TCATCGAA-TAATCTGAAGTA-TAAATTGACACCC
41225403 AGTGTCTCATCGA
1 AGTGTCTCATCGA
41225416 CTCAATGTCG
Statistics
Matches: 70, Mismatches: 13, Indels: 15
0.71 0.13 0.15
Matches are distributed among these distances:
36 1 0.01
37 19 0.27
38 10 0.14
39 2 0.03
40 16 0.23
41 21 0.30
42 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (39 bp):
AGTGTCTCATCGAATAATCTGAAGTATAAATTGACACCC
Found at i:41226358 original size:11 final size:12
Alignment explanation
Indices: 41226333--41226365 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
41226323 TTTCAATTAT
41226333 TTTCTTTTTCTA
1 TTTCTTTTTCTA
41226345 TTTCTTTTTC-A
1 TTTCTTTTTCTA
41226356 TTTCATTTTT
1 TTTC-TTTTT
41226366 TTGTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTCTTTTTCTA
Found at i:41229362 original size:19 final size:20
Alignment explanation
Indices: 41229327--41229372 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
41229317 ATCATGTTCA
41229327 TATTTTTAACATAATTTAAT
1 TATTTTTAACATAATTTAAT
41229347 TATTTTTATA-AT-ATTTAAT
1 TATTTTTA-ACATAATTTAAT
41229366 TATTTTT
1 TATTTTT
41229373 CGACAAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.56
20 10 0.40
21 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTTTAACATAATTTAAT
Found at i:41242818 original size:25 final size:26
Alignment explanation
Indices: 41242790--41242840 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
41242780 AAACTGTACT
41242790 TATTGGTTA-AGTAAAAAAAT-TATGA
1 TATT-GTTATAGTAAAAAAATATATGA
* *
41242815 TATTTTTATGGTAAAAAAATATATGA
1 TATTGTTATAGTAAAAAAATATATGA
41242841 ATCTAGTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 3 0.14
25 14 0.64
26 5 0.23
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (26 bp):
TATTGTTATAGTAAAAAAATATATGA
Found at i:41244497 original size:26 final size:27
Alignment explanation
Indices: 41244463--41244524 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
41244453 AGGGGTAAAA
*
41244463 CGGTAATTTTACCCCTCGA-GGTATTTT
1 CGGTCATTTTACCCCTCGAGGGT-TTTT
* *
41244490 -GGTCATTTTATCCTTCGAGGGTTTTT
1 CGGTCATTTTACCCCTCGAGGGTTTTT
41244516 CGGTCATTT
1 CGGTCATTT
41244525 AACAACCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 19 0.63
27 11 0.37
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.45
Consensus pattern (27 bp):
CGGTCATTTTACCCCTCGAGGGTTTTT
Found at i:41252371 original size:19 final size:20
Alignment explanation
Indices: 41252347--41252386 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
41252337 TAGAGAACAA
41252347 TTTTAAAT-TTAAACTTATT
1 TTTTAAATATTAAACTTATT
41252366 TTTTAAATAATTAAACTTATT
1 TTTTAAAT-ATTAAACTTATT
41252387 CGAGTTGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
21 11 0.58
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTAAATATTAAACTTATT
Found at i:41255199 original size:12 final size:12
Alignment explanation
Indices: 41255182--41255206 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41255172 GCAAAAGAAG
41255182 AAAATAACAAAA
1 AAAATAACAAAA
41255194 AAAATAACAAAA
1 AAAATAACAAAA
41255206 A
1 A
41255207 GGAGGACTTT
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:0.08, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAATAACAAAA
Found at i:41256099 original size:22 final size:22
Alignment explanation
Indices: 41256074--41256121 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
41256064 TATTAGCTTA
41256074 ATTTTAAATCAAA-TTAG-TTTTT
1 ATTTT-AA-CAAATTTAGCTTTTT
*
41256096 ATTTTGACAAATTTAGCTTTTT
1 ATTTTAACAAATTTAGCTTTTT
41256118 ATTT
1 ATTT
41256122 CTAATATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 4 0.17
21 5 0.22
22 14 0.61
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (22 bp):
ATTTTAACAAATTTAGCTTTTT
Found at i:41268938 original size:124 final size:125
Alignment explanation
Indices: 41268738--41269084 Score: 554
Period size: 124 Copynumber: 2.8 Consensus size: 125
41268728 TTTCGAGTTA
* *
41268738 ACGTTTCTGATCAAATAGTATAAAATCGCTTCTAGCTGGGTGCTATTTGAGAAGAATTTGTGAAA
1 ACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAA
* * *
41268803 TCGCGCTCTCGTGGATGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAA-TTTTTTTTG
66 TCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGGAAGAAATAATTTTTTTTTG
* *
41268862 ACGTTTTTGAGGAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAA
1 ACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAA
* *
41268927 TCACGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGGAATAAATAATTTTTTTTTG
66 TCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGGAAGAAATAATTTTTTTTTG
* * *
41268987 ACGTTTCTGAGCAAATAGTATAAAA-CACTTCTAGCAGGATGCTATTTGAGAAGAATTTGTAAAA
1 ACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAA
* *
41269051 TTGCGCCCTCGTGGACGCGGTTTTGCTACAGTAG
66 TCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
41269085 CATGTTTAGG
Statistics
Matches: 205, Mismatches: 17, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
124 173 0.84
125 32 0.16
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (125 bp):
ACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAA
TCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGGAAGAAATAATTTTTTTTTG
Found at i:41272173 original size:64 final size:64
Alignment explanation
Indices: 41272095--41272223 Score: 249
Period size: 64 Copynumber: 2.0 Consensus size: 64
41272085 TTTTTTCAAT
*
41272095 TATTTGTACAAATTAATTAAGCTCGTGTTATTACATCAAATAATATCAAAATAACTCAAAAAAA
1 TATTTGTACAAATTAATTAAGCTCATGTTATTACATCAAATAATATCAAAATAACTCAAAAAAA
41272159 TATTTGTACAAATTAATTAAGCTCATGTTATTACATCAAATAATATCAAAATAACTCAAAAAAA
1 TATTTGTACAAATTAATTAAGCTCATGTTATTACATCAAATAATATCAAAATAACTCAAAAAAA
41272223 T
1 T
41272224 TTCTATTTTA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.33
Consensus pattern (64 bp):
TATTTGTACAAATTAATTAAGCTCATGTTATTACATCAAATAATATCAAAATAACTCAAAAAAA
Found at i:41272680 original size:18 final size:18
Alignment explanation
Indices: 41272642--41272681 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
41272632 GACTCGGAAA
*
41272642 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGCT
*
41272660 AGGATACATATAAGTGCT
1 AGGATACATATAAGGGCT
41272678 AGGA
1 AGGA
41272682 AACGCACCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.07, G:0.28, T:0.25
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:41273557 original size:20 final size:20
Alignment explanation
Indices: 41273520--41273557 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41273510 TTTATTTTTA
*
41273520 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
41273540 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
41273558 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:41274457 original size:12 final size:13
Alignment explanation
Indices: 41274440--41274473 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
41274430 TTTACGATAT
41274440 AAAAAAATTTTAAA
1 AAAAAAATTTT-AA
41274454 AAAAATAATTTTAA
1 AAAAA-AATTTTAA
41274468 AAAAAA
1 AAAAAA
41274474 TAATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 12 0.63
15 6 0.32
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAAAATTTTAA
Found at i:41274481 original size:16 final size:15
Alignment explanation
Indices: 41274440--41274480 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
41274430 TTTACGATAT
41274440 AAAAA-AATTTTAAA
1 AAAAATAATTTTAAA
41274454 AAAAATAATTTTAAA
1 AAAAATAATTTTAAA
41274469 AAAAATAATTTT
1 AAAAATAATTTT
41274481 TTTTAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAATAATTTTAAA
Found at i:41274560 original size:11 final size:11
Alignment explanation
Indices: 41274548--41274600 Score: 63
Period size: 11 Copynumber: 4.7 Consensus size: 11
41274538 AAATATGGAT
*
41274548 TTGAGAGAAATT
1 TTGAGAGAAA-A
*
41274560 TTGA-AGGAAA
1 TTGAGAGAAAA
41274570 TTGAGAGAAAA
1 TTGAGAGAAAA
41274581 TTGAGAGGAAAA
1 TTGAGA-GAAAA
41274593 TTGAGAGA
1 TTGAGAGA
41274601 GGATTAGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
10 4 0.11
11 17 0.47
12 15 0.42
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (11 bp):
TTGAGAGAAAA
Found at i:41274593 original size:23 final size:22
Alignment explanation
Indices: 41274548--41274600 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
41274538 AAATATGGAT
*
41274548 TTGAGAGAAATTTTGAAGGAAA
1 TTGAGAGAAATATTGAAGGAAA
41274570 TTGAGAGAAA-ATTGAGAGGAAAA
1 TTGAGAGAAATATTGA-AGG-AAA
41274593 TTGAGAGA
1 TTGAGAGA
41274601 GGATTAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 4 0.14
22 13 0.46
23 11 0.39
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (22 bp):
TTGAGAGAAATATTGAAGGAAA
Found at i:41274603 original size:14 final size:12
Alignment explanation
Indices: 41274567--41274599 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
41274557 ATTTTGAAGG
41274567 AAATTGAGA-GA
1 AAATTGAGAGGA
41274578 AAATTGAGAGGA
1 AAATTGAGAGGA
41274590 AAATTGAGAG
1 AAATTGAGAG
41274600 AGGATTAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.52, C:0.00, G:0.30, T:0.18
Consensus pattern (12 bp):
AAATTGAGAGGA
Found at i:41275399 original size:21 final size:21
Alignment explanation
Indices: 41275373--41275434 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
41275363 ATTTAATATT
41275373 TTTCTTTTATATTCTTTTAAC
1 TTTCTTTTATATTCTTTTAAC
* * *
41275394 TTTCTTTTTTATTATTTT-CC
1 TTTCTTTTATATTCTTTTAAC
* *
41275414 TCTCTTTTCTATTTCTTTTAA
1 TTTCTTTTATA-TTCTTTTAA
41275435 TGTATTTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 10 0.31
21 22 0.69
ACGTcount: A:0.15, C:0.16, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTCTTTTATATTCTTTTAAC
Found at i:41275499 original size:27 final size:29
Alignment explanation
Indices: 41275445--41275499 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
41275435 TGTATTTTTT
41275445 CTATATTTTTTATTTGTTAAAACTAATTC
1 CTATATTTTTTATTTGTTAAAACTAATTC
*
41275474 CTATA-TTTTTATTTTTTAAAAC-AATT
1 CTATATTTTTTATTTGTTAAAACTAATT
41275500 TAACTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 4 0.16
28 16 0.64
29 5 0.20
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (29 bp):
CTATATTTTTTATTTGTTAAAACTAATTC
Found at i:41288814 original size:4 final size:4
Alignment explanation
Indices: 41288805--41288837 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
41288795 ATATAGATAT
41288805 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
41288838 CCCGCACGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:41296285 original size:26 final size:26
Alignment explanation
Indices: 41296233--41296286 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
41296223 TTTATTTAAA
* * *
41296233 TATAATTAAATAATAATTATAACTAT
1 TATAAATAAATAATAAATAAAACTAT
* *
41296259 TATAAATAAATATTAAATAAAATTAT
1 TATAAATAAATAATAAATAAAACTAT
41296285 TA
1 TA
41296287 ATACTTATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (26 bp):
TATAAATAAATAATAAATAAAACTAT
Found at i:41296301 original size:33 final size:34
Alignment explanation
Indices: 41296224--41296302 Score: 85
Period size: 33 Copynumber: 2.4 Consensus size: 34
41296214 AAGGATAATT
41296224 TTATTTA-AATATAATTAAATAATAATTATAACTA
1 TTATTTATAA-ATAATTAAATAATAATTATAACTA
**
41296258 TTATAAATAAAT-ATTAAATAA-AATTATTAA-TA
1 TTATTTATAAATAATTAAATAATAATTA-TAACTA
41296290 CTTATTTATAAAT
1 -TTATTTATAAAT
41296303 CCTCTAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
32 7 0.18
33 22 0.58
34 7 0.18
35 2 0.05
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (34 bp):
TTATTTATAAATAATTAAATAATAATTATAACTA
Found at i:41302489 original size:2 final size:2
Alignment explanation
Indices: 41302482--41302520 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
41302472 CGGATATGTA
* *
41302482 TG TG TG TG TG TG TG TA TA TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
41302521 CTGTACAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.05, C:0.00, G:0.44, T:0.51
Consensus pattern (2 bp):
TG
Found at i:41302503 original size:16 final size:16
Alignment explanation
Indices: 41302478--41302512 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
41302468 AATACGGATA
*
41302478 TGTATGTGTGTGTGTG
1 TGTATATGTGTGTGTG
41302494 TGTATATGTGTGTGTG
1 TGTATATGTGTGTGTG
41302510 TGT
1 TGT
41302513 GTGTGTGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.09, C:0.00, G:0.40, T:0.51
Consensus pattern (16 bp):
TGTATATGTGTGTGTG
Found at i:41302503 original size:18 final size:18
Alignment explanation
Indices: 41302480--41302514 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
41302470 TACGGATATG
41302480 TATGTGTGTGTGTGTGTA
1 TATGTGTGTGTGTGTGTA
41302498 TATGTGTGTGTGTGTGT
1 TATGTGTGTGTGTGTGT
41302515 GTGTGTCTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.09, C:0.00, G:0.40, T:0.51
Consensus pattern (18 bp):
TATGTGTGTGTGTGTGTA
Found at i:41302818 original size:29 final size:29
Alignment explanation
Indices: 41302780--41302906 Score: 123
Period size: 29 Copynumber: 4.1 Consensus size: 29
41302770 GGACTATATA
41302780 AATCGATAATGATTGAAATACATCAAAAT
1 AATCGATAATGATTGAAATACATCAAAAT
41302809 AATCGATAATGATTGAAATACATCAAAAT
1 AATCGATAATGATTGAAATACATCAAAAT
* * * *
41302838 ACATC-AAAATGAAATTAAAATA-TTAAAATTTATAT
1 A-ATCGATAATG--ATTGAAATACAT-CAA---A-AT
41302873 AAATCGATAATGATTGAAATACATCAAAAT
1 -AATCGATAATGATTGAAATACATCAAAAT
41302903 AATC
1 AATC
41302907 TAAAAATATT
Statistics
Matches: 79, Mismatches: 8, Indels: 22
0.72 0.07 0.20
Matches are distributed among these distances:
29 39 0.49
30 6 0.08
31 11 0.14
34 11 0.14
35 6 0.08
36 6 0.08
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.29
Consensus pattern (29 bp):
AATCGATAATGATTGAAATACATCAAAAT
Found at i:41304506 original size:49 final size:49
Alignment explanation
Indices: 41304452--41304555 Score: 145
Period size: 49 Copynumber: 2.1 Consensus size: 49
41304442 TCATGTGTTA
* * ** * *
41304452 TAATTTTATACAGTGTTGAGTTTTTTATTCATGATATTGAACTCAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
*
41304501 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
41304550 TAATTT
1 TAATTT
41304556 GTTTTTTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.51
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
Found at i:41305729 original size:44 final size:41
Alignment explanation
Indices: 41305681--41305779 Score: 92
Period size: 44 Copynumber: 2.3 Consensus size: 41
41305671 AGTATTATAT
41305681 ATTATGATTTTAGTAAATTCATATAAGAATAAGAATT-TTATTAA
1 ATTAT-ATTTTAGTAAATT-ATAT-AGAATAAGAATTATT-TTAA
* ** *
41305725 ATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAA
1 A-T-TATATT-TTAGTAAATTATATAGAATAAGAATTATTTTAA
41305769 ATTATATTTTA
1 ATTATATTTTA
41305780 TAGTATTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
41 3 0.06
42 6 0.13
43 1 0.02
44 15 0.32
45 10 0.21
46 12 0.26
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (41 bp):
ATTATATTTTAGTAAATTATATAGAATAAGAATTATTTTAA
Found at i:41305768 original size:26 final size:28
Alignment explanation
Indices: 41305714--41305795 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 28
41305704 TAAGAATAAG
* * *
41305714 AATTTTATTAAATTATATATTATTATTA
1 AATTATATTTAATAATATATTATTATTA
41305742 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTTAATAATATATTATTATTA
* *
41305768 AATTATATTTTATAGTATTATATATTAT
1 AATTATATTTAATAATA-TAT-TATTAT
41305796 GATTTTATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 18 0.40
27 6 0.13
28 16 0.36
29 4 0.09
30 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (28 bp):
AATTATATTTAATAATATATTATTATTA
Found at i:41305793 original size:110 final size:115
Alignment explanation
Indices: 41305627--41305875 Score: 361
Period size: 110 Copynumber: 2.2 Consensus size: 115
41305617 AATAAAGTAG
*
41305627 ATTA-TAAATTATATTTAAAAATAATTATTTAAATTATATTTTATAGTATTATATATTATGA-TT
1 ATTATTAAATTATATTTAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATTT
*
41305690 -TTAGTAAATTC-AT-ATAAGA-A-TAAGAATTTTATTAAATTATATATT
66 ATTAGTAAATTCAATAATAAGATATTAACAATTTTATTAAATTATATATT
41305735 ATTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATT
1 ATTATTAAATTATATTTAATAATAATTA-TTTAAATTATATTTTATAGTATTATATATTATGA-T
*
41305800 TTATTAGTAAATTCATATAATAATATTTATTAACAATTTTATTAAATTATATATT
64 TTATTAGTAAATTCA-ATAATAAGA--TATTAACAATTTTATTAAATTATATATT
*
41305855 -TTATTAAATTATATTTTATAA
1 ATTATTAAATTATATTTAATAA
41305876 CAGTTATGTT
Statistics
Matches: 125, Mismatches: 4, Indels: 13
0.88 0.03 0.09
Matches are distributed among these distances:
108 4 0.03
109 22 0.18
110 34 0.27
112 2 0.02
113 11 0.09
115 2 0.02
116 5 0.04
119 21 0.17
120 24 0.19
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (115 bp):
ATTATTAAATTATATTTAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATTT
ATTAGTAAATTCAATAATAAGATATTAACAATTTTATTAAATTATATATT
Found at i:41305873 original size:15 final size:17
Alignment explanation
Indices: 41305835--41305868 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41305825 TTTATTAACA
41305835 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
41305852 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
41305869 TTTATAACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:41315656 original size:19 final size:18
Alignment explanation
Indices: 41315633--41315692 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
41315623 AAAAAAAAGC
41315633 AAAATAATAAAAATCAAA
1 AAAATAATAAAAATCAAA
*
41315651 ATAAATAATAATAAT-AAA
1 A-AAATAATAAAAATCAAA
*
41315669 AGAGAGTAA-AAAAATCAAA
1 A-A-AATAATAAAAATCAAA
41315688 AAAAT
1 AAAAT
41315693 CAAAATGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 2 0.06
18 12 0.35
19 20 0.59
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.18
Consensus pattern (18 bp):
AAAATAATAAAAATCAAA
Found at i:41315718 original size:21 final size:21
Alignment explanation
Indices: 41315679--41315718 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
41315669 AGAGAGTAAA
*
41315679 AAAATCAAAAAAATCAAAATG
1 AAAATCAAAAAAAGCAAAATG
* *
41315700 AAAATGAAAAAAAGGAAAA
1 AAAATCAAAAAAAGCAAAA
41315719 AATAAAAAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.75, C:0.05, G:0.10, T:0.10
Consensus pattern (21 bp):
AAAATCAAAAAAAGCAAAATG
Found at i:41315822 original size:56 final size:55
Alignment explanation
Indices: 41315718--41315827 Score: 150
Period size: 56 Copynumber: 2.0 Consensus size: 55
41315708 AAAAAGGAAA
* * *
41315718 AAATAAAAAAGGAGAGGCCCAGGCGAAAACCCGCAAAGGGCTCTTTGAGTCCAAG
1 AAATAAAAAAGGAGAGGCCAAGGCGAAAACCCGCAAAGGGCACTTTGAGACCAAG
* *
41315773 AAATGAAAAATGGAGAGGCCAAGGTGAAAACCCGCAAAGGGCAAC-TTGAGACCAA
1 AAAT-AAAAAAGGAGAGGCCAAGGCGAAAACCCGCAAAGGGC-ACTTTGAGACCAA
41315828 AGGGTATTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
55 4 0.08
56 43 0.90
57 1 0.02
ACGTcount: A:0.43, C:0.20, G:0.27, T:0.10
Consensus pattern (55 bp):
AAATAAAAAAGGAGAGGCCAAGGCGAAAACCCGCAAAGGGCACTTTGAGACCAAG
Found at i:41317158 original size:89 final size:88
Alignment explanation
Indices: 41317008--41317309 Score: 523
Period size: 89 Copynumber: 3.4 Consensus size: 88
41316998 AATCACAAGC
41317008 CCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAGCCCTAGTTCCCTGACCAGCAGT
1 CCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAGCCCTAGTTCCCTGACCAGCAGT
*
41317073 GGAATAGGTGGAAGAATGTAAAT
66 GGAATAGGTGGAAGAATGTAAGT
*
41317096 CCTAGTTCCCTGACCAGCAGTTGGAATAGGTGGAAGACTGTAAGTCCTAGTTCCCTGACCAGCAG
1 CCTAGTTCCCTGACCAGCAG-TGGAATAGGTGGAAGACTGTAAGCCCTAGTTCCCTGACCAGCAG
*
41317161 TTGGAATAGGTGGAAGAATGTAAGC
65 -TGGAATAGGTGGAAGAATGTAAGT
* *
41317186 CCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTAAGCCCTAGTTCCCTCACCAGCAGT
1 CCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAGCCCTAGTTCCCTGACCAGCAGT
*
41317251 GGAATAGGTGGAAGATTGTAAGT
66 GGAATAGGTGGAAGAATGTAAGT
*
41317274 CCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGA
1 CCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGA
41317310 TTGCATTTCC
Statistics
Matches: 203, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
88 77 0.38
89 84 0.41
90 42 0.21
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (88 bp):
CCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAGCCCTAGTTCCCTGACCAGCAGT
GGAATAGGTGGAAGAATGTAAGT
Found at i:41317310 original size:44 final size:44
Alignment explanation
Indices: 41317004--41317312 Score: 510
Period size: 44 Copynumber: 7.0 Consensus size: 44
41316994 GTGAAATCAC
*
41317004 AAGCCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGT
1 AAGCCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGT
*
41317048 AAGCCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGAATGT
1 AAGCCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGT
** *
41317092 AAATCCTAGTTCCCTGACCAGCAGTTGGAATAGGTGGAAGACTGT
1 AAGCCCTAGTTCCCTGACCAGCAG-TGGAATAGGTGGAAGATTGT
* *
41317137 AAGTCCTAGTTCCCTGACCAGCAGTTGGAATAGGTGGAAGAATGT
1 AAGCCCTAGTTCCCTGACCAGCAG-TGGAATAGGTGGAAGATTGT
41317182 AAGCCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGT
1 AAGCCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGT
*
41317226 AAGCCCTAGTTCCCTCACCAGCAGTGGAATAGGTGGAAGATTGT
1 AAGCCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGT
* *
41317270 AAGTCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
1 AAGCCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
41317313 CATTTCCTAG
Statistics
Matches: 252, Mismatches: 12, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
44 167 0.66
45 85 0.34
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (44 bp):
AAGCCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGT
Found at i:41317484 original size:87 final size:87
Alignment explanation
Indices: 41317331--41317491 Score: 268
Period size: 87 Copynumber: 1.9 Consensus size: 87
41317321 AGTCCTAGCT
* * * *
41317331 CTCTGAACAGCAGTGAATTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTATTGGAGCAG
1 CTCTGAACAACAGTGAAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAACAG
41317396 ATCAAAGACCCCAGGCTTGTCA
66 ATCAAAGACCCCAGGCTTGTCA
*
41317418 CTCTGAACAACAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAACAG
1 CTCTGAACAACAGTGAAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAACAG
*
41317483 ATCGAAGAC
66 ATCAAAGAC
41317492 TCTAATCCTA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 68 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (87 bp):
CTCTGAACAACAGTGAAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAACAG
ATCAAAGACCCCAGGCTTGTCA
Found at i:41319104 original size:3 final size:3
Alignment explanation
Indices: 41319096--41319140 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
41319086 TAATATTTTC
* *
41319096 ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ACTC A-T ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT
41319141 GATACTATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 1 0.03
3 33 0.92
4 2 0.06
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:41319114 original size:15 final size:15
Alignment explanation
Indices: 41319096--41319151 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
41319086 TAATATTTTC
41319096 ATTATTATTATTGTT
1 ATTATTATTATTGTT
*
41319111 ATTATTATTATTATT
1 ATTATTATTATTGTT
*
41319126 ACTCATATTATTATTGAT
1 A-T--TATTATTATTGTT
*
41319144 ACTATTAT
1 ATTATTAT
41319152 ATTTAGTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 21 0.62
16 1 0.03
18 12 0.35
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (15 bp):
ATTATTATTATTGTT
Found at i:41321913 original size:29 final size:29
Alignment explanation
Indices: 41321879--41321983 Score: 210
Period size: 29 Copynumber: 3.6 Consensus size: 29
41321869 ACAAAATGAT
41321879 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATTTCA
41321908 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATTTCA
41321937 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATTTCA
41321966 AACATAAGTGACTAAAAT
1 AACATAAGTGACTAAAAT
41321984 ATAATTTGAG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 76 1.00
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (29 bp):
AACATAAGTGACTAAAATGTAACATTTCA
Found at i:41324650 original size:10 final size:10
Alignment explanation
Indices: 41324637--41324661 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41324627 GAGCTGATTT
41324637 TGGACAAGGC
1 TGGACAAGGC
41324647 TGGACAAGGC
1 TGGACAAGGC
41324657 TGGAC
1 TGGAC
41324662 GGTTTTGGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.20, G:0.40, T:0.12
Consensus pattern (10 bp):
TGGACAAGGC
Found at i:41326320 original size:14 final size:13
Alignment explanation
Indices: 41326301--41326340 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
41326291 TTGATTGCCA
41326301 GTAAAATATTTTT
1 GTAAAATATTTTT
41326314 CGTAAAATGATTTTT
1 -GTAAAAT-ATTTTT
*
41326329 GGAAAATATTTT
1 GTAAAATATTTT
41326341 ACTTTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 5 0.21
14 13 0.54
15 6 0.25
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (13 bp):
GTAAAATATTTTT
Found at i:41326440 original size:32 final size:32
Alignment explanation
Indices: 41326365--41326443 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
41326355 TGATTTACTG
* ** **
41326365 GAAAATATTTTCTGGTGTTTGATTGAATCTGT
1 GAAAATATTTTCTGCTGTTTGACAGAATCCCT
*
41326397 GTAAAATATTTTCTGCTGTTTGACAGATTCCCT
1 G-AAAATATTTTCTGCTGTTTGACAGAATCCCT
41326430 GAAAATATTTTCTG
1 GAAAATATTTTCTG
41326444 AAAAAGTTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
32 14 0.35
33 26 0.65
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (32 bp):
GAAAATATTTTCTGCTGTTTGACAGAATCCCT
Found at i:41326478 original size:20 final size:20
Alignment explanation
Indices: 41326453--41326504 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
41326443 GAAAAAGTTG
41326453 TTTTTACATATATT-AATAAA
1 TTTTTACATATATTAAAT-AA
* *
41326473 TTTTT--ATATTTTAAATTA
1 TTTTTACATATATTAAATAA
41326491 TTTTTACATATATT
1 TTTTTACATATATT
41326505 GCAATGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
18 12 0.46
19 3 0.12
20 11 0.42
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTACATATATTAAATAA
Found at i:41334977 original size:18 final size:18
Alignment explanation
Indices: 41334954--41335020 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
41334944 TTTTTTAAAA
41334954 TATAAATTTTAGAATTTT
1 TATAAATTTTAGAATTTT
41334972 TATAAATATTTTA-AA-TTT
1 TAT-AA-ATTTTAGAATTTT
*
41334990 TAAAAATTATTTAGAATTTT
1 TATAAA-T-TTTAGAATTTT
*
41335010 TTTATAATTTT
1 TATA-AATTTT
41335021 TGTTGAGAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
16 1 0.03
17 3 0.08
18 12 0.31
19 9 0.23
20 12 0.31
21 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TATAAATTTTAGAATTTT
Found at i:41335000 original size:19 final size:20
Alignment explanation
Indices: 41334945--41335010 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 20
41334935 AAAGTATACT
41334945 TTTTTAAAATATAAATTTTAGAA
1 TTTTTAAAA-AT--ATTTTAGAA
*
41334968 TTTTTATAAATATTTTA-AA
1 TTTTTAAAAATATTTTAGAA
41334987 -TTTTAAAAAT-TATTTAGAA
1 TTTTTAAAAATAT-TTTAGAA
41335006 TTTTT
1 TTTTT
41335011 TTATAATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 1 0.03
18 13 0.34
19 4 0.11
20 10 0.26
22 2 0.05
23 8 0.21
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTTTAAAAATATTTTAGAA
Found at i:41336060 original size:20 final size:20
Alignment explanation
Indices: 41336016--41336108 Score: 61
Period size: 20 Copynumber: 4.8 Consensus size: 20
41336006 ATCTCAACAA
*
41336016 AAAAATATCAAAATAATTT-T
1 AAAAATTTCAAAAT-ATTTAT
*
41336036 CAAAATTTCAAAATATTTAT
1 AAAAATTTCAAAATATTTAT
* *
41336056 AAAAAATTCCAAAGA-ATATA-
1 -AAAAATTTCAAA-ATATTTAT
* *
41336076 AAAAATTT--AAATTTTTTT
1 AAAAATTTCAAAATATTTAT
*
41336094 AAAAATTTCCAAATA
1 AAAAATTTCAAAATA
41336109 ATAATTTTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
16 1 0.02
17 4 0.07
18 8 0.14
19 11 0.20
20 17 0.30
21 14 0.25
22 1 0.02
ACGTcount: A:0.56, C:0.08, G:0.01, T:0.35
Consensus pattern (20 bp):
AAAAATTTCAAAATATTTAT
Found at i:41336104 original size:38 final size:39
Alignment explanation
Indices: 41336037--41336111 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 39
41336027 AATAATTTTC
41336037 AAAATTTCAAAATATTTATAAAAAATTCCAAAGAATATAA
1 AAAATTT-AAAATATTTATAAAAAATTCCAAAGAATATAA
* * * *
41336077 AAAATTT-AAATTTTTTTAAAAATTTCCAAATAATA
1 AAAATTTAAAATATTTATAAAAAATTCCAAAGAATA
41336112 ATTTTGAGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 24 0.77
40 7 0.23
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.36
Consensus pattern (39 bp):
AAAATTTAAAATATTTATAAAAAATTCCAAAGAATATAA
Found at i:41337188 original size:21 final size:21
Alignment explanation
Indices: 41337158--41337197 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
41337148 TTATTTTTAA
41337158 TATTAATATAAATTTTAAATT
1 TATTAATATAAATTTTAAATT
* **
41337179 TATTAGTATATTTTTTAAA
1 TATTAATATAAATTTTAAA
41337198 AAATATTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
TATTAATATAAATTTTAAATT
Found at i:41337259 original size:20 final size:18
Alignment explanation
Indices: 41337234--41337273 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
41337224 TTTTAAATTA
41337234 TTTATTATTAATAATATTTT
1 TTTATT-TTAAT-ATATTTT
*
41337254 TTTATTTTTATATATTTT
1 TTTATTTTAATATATTTT
41337272 TT
1 TT
41337274 AAATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 4 0.21
20 6 0.32
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTTAATATATTTT
Found at i:41337262 original size:9 final size:9
Alignment explanation
Indices: 41337247--41337284 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
41337237 ATTATTAATA
41337247 ATATTTTTT
1 ATATTTTTT
41337256 -TATTTTTAT
1 ATATTTTT-T
41337265 ATATTTTTT
1 ATATTTTTT
*
41337274 AAATTTTTT
1 ATATTTTTT
41337283 AT
1 AT
41337285 TATATTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 7 0.28
9 11 0.44
10 7 0.28
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
ATATTTTTT
Found at i:41337271 original size:17 final size:17
Alignment explanation
Indices: 41337203--41337274 Score: 60
Period size: 16 Copynumber: 4.2 Consensus size: 17
41337193 TTAAAAAATA
41337203 TTTATTTTTATATA-TT
1 TTTATTTTTATATATTT
* * *
41337219 TTAAATTTTA-A-ATTA
1 TTTATTTTTATATATTT
*
41337234 TTTATTATTAATAATATTTT
1 TTTATT-TTTAT-ATA-TTT
41337254 TTTATTTTTATATATTT
1 TTTATTTTTATATATTT
41337271 TTTA
1 TTTA
41337275 AATTTTTTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
14 1 0.02
15 6 0.14
16 11 0.26
17 7 0.17
18 4 0.10
19 5 0.12
20 8 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATTTTTATATATTT
Found at i:41337280 original size:26 final size:26
Alignment explanation
Indices: 41337147--41337285 Score: 81
Period size: 26 Copynumber: 5.2 Consensus size: 26
41337137 GTGAGGGATA
* *
41337147 TTTATTTTTA-ATATTAATATAAATTT
1 TTTATTTTTATATATT-TTTTAAATTT
** * *
41337173 TAAATTTATTAGTATATTTTTTAAAAAATA
1 TTTATTT-TTA-TATATTTTTT--AAATTT
41337203 TTTATTTTTATATA--TTTTAAATTT
1 TTTATTTTTATATATTTTTTAAATTT
** **
41337227 TAAATTATTTAT-TA-TTAATAATATTTT
1 TTTATT-TTTATATATTTTTTAA-A-TTT
41337254 TTTATTTTTATATATTTTTTAAATTT
1 TTTATTTTTATATATTTTTTAAATTT
41337280 TTTATT
1 TTTATT
41337286 ATATTCATCT
Statistics
Matches: 84, Mismatches: 18, Indels: 22
0.68 0.15 0.18
Matches are distributed among these distances:
24 10 0.12
25 9 0.11
26 24 0.29
27 13 0.15
28 11 0.13
29 8 0.10
30 9 0.11
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (26 bp):
TTTATTTTTATATATTTTTTAAATTT
Found at i:41339904 original size:5 final size:5
Alignment explanation
Indices: 41339894--41339930 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
41339884 AAAGAATAAT
*
41339894 AAATA AAAT- AACTA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA
41339931 ACTAACTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 3 0.10
5 26 0.90
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:41339910 original size:24 final size:24
Alignment explanation
Indices: 41339883--41339928 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
41339873 ACTAATAGTA
41339883 AAAAGAATAAT-AAATAAAATAACT
1 AAAAGAA-AATAAAATAAAATAACT
*
41339907 AAAATAAAATAAAATAAAATAA
1 AAAAGAAAATAAAATAAAATAA
41339929 AAACTAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (24 bp):
AAAAGAAAATAAAATAAAATAACT
Found at i:41344804 original size:22 final size:22
Alignment explanation
Indices: 41344779--41344821 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41344769 TTTGCCCAAC
**
41344779 TTTAAAAATTATTTTGAGAGAT
1 TTTAAAAAGAATTTTGAGAGAT
*
41344801 TTTAAAGAGAATTTTGAGAGA
1 TTTAAAAAGAATTTTGAGAGA
41344822 GAAAATGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.40
Consensus pattern (22 bp):
TTTAAAAAGAATTTTGAGAGAT
Found at i:41345409 original size:22 final size:21
Alignment explanation
Indices: 41345384--41345436 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 21
41345374 CAGTACTAAA
* *
41345384 AAAAACGAAAAGTAATAATAAT
1 AAAAACGAAAAATAATAA-AAC
**
41345406 AAAAATAAAAAATAATAAAAC
1 AAAAACGAAAAATAATAAAAC
*
41345427 AAAAAGGAAA
1 AAAAACGAAA
41345437 GGGAAGGGAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.13
Consensus pattern (21 bp):
AAAAACGAAAAATAATAAAAC
Found at i:41346332 original size:9 final size:9
Alignment explanation
Indices: 41346318--41346351 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
41346308 AGTGACCCCT
41346318 ATTTTTTAA
1 ATTTTTTAA
41346327 ATTTTTTTTAA
1 A--TTTTTTAA
41346338 ATTTTTTAA
1 ATTTTTTAA
41346347 ATTTT
1 ATTTT
41346352 AAAAACAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 14 0.61
11 9 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:41346335 original size:11 final size:11
Alignment explanation
Indices: 41346319--41346344 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
41346309 GTGACCCCTA
41346319 TTTTTTAAATT
1 TTTTTTAAATT
41346330 TTTTTTAAATT
1 TTTTTTAAATT
41346341 TTTT
1 TTTT
41346345 AAATTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTAAATT
Found at i:41348560 original size:41 final size:41
Alignment explanation
Indices: 41348515--41348610 Score: 124
Period size: 41 Copynumber: 2.4 Consensus size: 41
41348505 AGAACACCAA
*
41348515 CATTAAACCTGCTAGACA-TAAAGTCTGAAATATTTCACCGG
1 CATTAAACCTACTAGA-AGTAAAGTCTGAAATATTTCACCGG
* *
41348556 CATTAAGCCTACTAGAAGTAAAGTCTGAAATATTTCACTGG
1 CATTAAACCTACTAGAAGTAAAGTCTGAAATATTTCACCGG
* *
41348597 TATT-AAGCTACTAG
1 CATTAAACCTACTAG
41348611 GCACAGAGCT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 9 0.19
41 39 0.81
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (41 bp):
CATTAAACCTACTAGAAGTAAAGTCTGAAATATTTCACCGG
Found at i:41348901 original size:62 final size:61
Alignment explanation
Indices: 41348820--41349003 Score: 178
Period size: 63 Copynumber: 3.0 Consensus size: 61
41348810 CATATGTATA
* * *
41348820 ATTATATATAATTATTAACATTAAGTTCAGCTCAAAGAAACTTGTATCTTACATTCGAACCTC
1 ATTATATATATTTA-TAACATTAAGTTCAACTCAAAGAAA-TTGTATCTTACATTCGAACCAC
* * * * *
41348883 -TTATATATATTTCATAACATTACA-TTCAATTCAAAGACATTGCATCATATATTCGAACCAC
1 ATTATATATATTT-ATAACATTA-AGTTCAACTCAAAGAAATTGTATCTTACATTCGAACCAC
* *
41348944 ATATTTATACAATTTATAACATTAAGTTCAACTCAAA-AAATTTGTAT-TATACATTCGAAC
1 AT-TATATA-TATTTATAACATTAAGTTCAACTCAAAGAAA-TTGTATCT-TACATTCGAAC
41349004 ATCATCATAT
Statistics
Matches: 98, Mismatches: 15, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
61 18 0.18
62 35 0.36
63 41 0.42
64 4 0.04
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (61 bp):
ATTATATATATTTATAACATTAAGTTCAACTCAAAGAAATTGTATCTTACATTCGAACCAC
Found at i:41353889 original size:22 final size:22
Alignment explanation
Indices: 41353864--41353911 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
41353854 ATGTCATGCG
41353864 AACCTTGCTAAAATATCATGTA
1 AACCTTGCTAAAATATCATGTA
* * * *
41353886 AACCTTGTTATAATTTCATGTG
1 AACCTTGCTAAAATATCATGTA
41353908 AACC
1 AACC
41353912 CTATTATGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (22 bp):
AACCTTGCTAAAATATCATGTA
Found at i:41353963 original size:33 final size:33
Alignment explanation
Indices: 41353920--41354022 Score: 127
Period size: 33 Copynumber: 3.1 Consensus size: 33
41353910 CCCTATTATG
*
41353920 ATGTGTGAACCTATGTTGTGTGACTGCTATGTA
1 ATGTGTGAACCTATGTTGTGTGACTACTATGTA
* *
41353953 AT-TTTCGAACCTATGTTGTGTGACTACTATGTG
1 ATGTGT-GAACCTATGTTGTGTGACTACTATGTA
* * * *
41353986 ATGTGTGAACCTATGCTATGTGACTTCTATGTG
1 ATGTGTGAACCTATGTTGTGTGACTACTATGTA
41354019 ATGT
1 ATGT
41354023 ACGAACTCTA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
32 2 0.03
33 57 0.93
34 2 0.03
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (33 bp):
ATGTGTGAACCTATGTTGTGTGACTACTATGTA
Found at i:41354159 original size:18 final size:18
Alignment explanation
Indices: 41354019--41354304 Score: 253
Period size: 18 Copynumber: 16.3 Consensus size: 18
41354009 CTTCTATGTG
* *
41354019 ATGTACGAACTCTA-CTA
1 ATGTGCGAACCCTACCTA
* *
41354036 ATGTGCAAACCCTACCTT
1 ATGTGCGAACCCTACCTA
** *
41354054 ACATGCAAACCCTACC-A
1 ATGTGCGAACCCTACCTA
*
41354071 ATGTGCGAGCCCTACCTA
1 ATGTGCGAACCCTACCTA
* * *
41354089 AAGTGTGAACCCTA-TTA
1 ATGTGCGAACCCTACCTA
* * *
41354106 TTGTGTGAACCCTTCCTA
1 ATGTGCGAACCCTACCTA
* * *
41354124 AAGTGCAAACCTTA-CTA
1 ATGTGCGAACCCTACCTA
* *
41354141 ATGTGTGAACCCTTCCTA
1 ATGTGCGAACCCTACCTA
* *
41354159 AAGTGCAAACCCTA-CTA
1 ATGTGCGAACCCTACCTA
*
41354176 ATGTGCAAACCCTACCTA
1 ATGTGCGAACCCTACCTA
*
41354194 ATGTGCGAACCCTTCCTA
1 ATGTGCGAACCCTACCTA
* *
41354212 AAGTGCAAACCCTA-CTA
1 ATGTGCGAACCCTACCTA
41354229 ATGTGCGAACCCTACCTA
1 ATGTGCGAACCCTACCTA
* *
41354247 ATGTGCGAATCCAACCTA
1 ATGTGCGAACCCTACCTA
* * *
41354265 AAGTGTGAACTCTA-CTA
1 ATGTGCGAACCCTACCTA
41354282 ATGTGCGAACCCTACCTA
1 ATGTGCGAACCCTACCTA
41354300 ATGTG
1 ATGTG
41354305 TGAGCCTAAC
Statistics
Matches: 210, Mismatches: 52, Indels: 13
0.76 0.19 0.05
Matches are distributed among these distances:
17 93 0.44
18 117 0.56
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (18 bp):
ATGTGCGAACCCTACCTA
Found at i:41354173 original size:88 final size:88
Alignment explanation
Indices: 41354033--41354300 Score: 297
Period size: 88 Copynumber: 3.0 Consensus size: 88
41354023 ACGAACTCTA
* * ** * * * *
41354033 CTAATGTGCAAACCCTACCTTACATGCAAACCCTACC-AATGTGCGAGCCCTACCTAAAGTGTGA
1 CTAAAGTGCAAACCCTA-CTAATGTGCGAACCCTACCTAAAGTGCAAACCCTACCTAAAGTGTGA
* * *
41354097 ACCCTATTATTGTGTGAACCCTTC
65 ACCCTACTAATGTGCGAACCCTTC
* * * * **
41354121 CTAAAGTGCAAACCTTACTAATGTGTGAACCCTTCCTAAAGTGCAAACCCTA-CTAATGTGCAAA
1 CTAAAGTGCAAACCCTACTAATGTGCGAACCCTACCTAAAGTGCAAACCCTACCTAAAGTGTGAA
41354185 CCCTACCTAATGTGCGAACCCTTC
66 CCCTA-CTAATGTGCGAACCCTTC
* * * *
41354209 CTAAAGTGCAAACCCTACTAATGTGCGAACCCTACCTAATGTGCGAATCCAACCTAAAGTGTGAA
1 CTAAAGTGCAAACCCTACTAATGTGCGAACCCTACCTAAAGTGCAAACCCTACCTAAAGTGTGAA
* *
41354274 CTCTACTAATGTGCGAACCCTAC
66 CCCTACTAATGTGCGAACCCTTC
41354297 CTAA
1 CTAA
41354301 TGTGTGAGCC
Statistics
Matches: 148, Mismatches: 29, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
87 27 0.18
88 108 0.73
89 13 0.09
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (88 bp):
CTAAAGTGCAAACCCTACTAATGTGCGAACCCTACCTAAAGTGCAAACCCTACCTAAAGTGTGAA
CCCTACTAATGTGCGAACCCTTC
Found at i:41354204 original size:53 final size:53
Alignment explanation
Indices: 41354019--41354304 Score: 285
Period size: 53 Copynumber: 5.4 Consensus size: 53
41354009 CTTCTATGTG
* * * * * *
41354019 ATGTACGAACTCTA-CTAATGTGCAAACCCTACCTTACA-TGCAAACCCTACCA
1 ATGTGCGAACCCTACCTAATGTGCGAACCCTTCC-TAAAGTGCAAACCCTACTA
* * * ** ** *
41354071 ATGTGCGAGCCCTACCTAAAGTGTGAACCCTAT--TATTGTGTGAACCCTTCCTA
1 ATGTGCGAACCCTACCTAATGTGCGAACCCT-TCCTAAAGTGCAAACCC-TACTA
* * * *
41354124 AAGTGCAAACCTTA-CTAATGTGTGAACCCTTCCTAAAGTGCAAACCCTACTA
1 ATGTGCGAACCCTACCTAATGTGCGAACCCTTCCTAAAGTGCAAACCCTACTA
*
41354176 ATGTGCAAACCCTACCTAATGTGCGAACCCTTCCTAAAGTGCAAACCCTACTA
1 ATGTGCGAACCCTACCTAATGTGCGAACCCTTCCTAAAGTGCAAACCCTACTA
* ** ** *
41354229 ATGTGCGAACCCTACCTAATGTGCGAATCCAACCTAAAGTGTGAACTCTACTA
1 ATGTGCGAACCCTACCTAATGTGCGAACCCTTCCTAAAGTGCAAACCCTACTA
41354282 ATGTGCGAACCCTACCTAATGTG
1 ATGTGCGAACCCTACCTAATGTG
41354305 TGAGCCTAAC
Statistics
Matches: 194, Mismatches: 33, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
51 3 0.02
52 49 0.25
53 142 0.73
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (53 bp):
ATGTGCGAACCCTACCTAATGTGCGAACCCTTCCTAAAGTGCAAACCCTACTA
Found at i:41354307 original size:35 final size:35
Alignment explanation
Indices: 41354024--41354300 Score: 279
Period size: 35 Copynumber: 7.9 Consensus size: 35
41354014 ATGTGATGTA
* * *
41354024 CGAACTCTACTAATGTGCAAACCCTACCTTACA-TG
1 CGAACCCTACTAATGTGCGAACCCTACC-TAAAGTG
* * *
41354059 CAAACCCTACCAATGTGCGAGCCCTACCTAAAGTG
1 CGAACCCTACTAATGTGCGAACCCTACCTAAAGTG
* * * * *
41354094 TGAACCCTATTATTGTGTGAACCCTTCCTAAAGTG
1 CGAACCCTACTAATGTGCGAACCCTACCTAAAGTG
* * * *
41354129 CAAACCTTACTAATGTGTGAACCCTTCCTAAAGTG
1 CGAACCCTACTAATGTGCGAACCCTACCTAAAGTG
* * *
41354164 CAAACCCTACTAATGTGCAAACCCTACCTAATGTG
1 CGAACCCTACTAATGTGCGAACCCTACCTAAAGTG
* * * *
41354199 CGAACCCTTCCTAAAGTGCAAACCCTA-CTAATGTG
1 CGAACCC-TACTAATGTGCGAACCCTACCTAAAGTG
* *
41354234 CGAACCCTACCTAATGTGCGAATCCAACCTAAAGTG
1 CGAACCCTA-CTAATGTGCGAACCCTACCTAAAGTG
* *
41354270 TGAACTCTACTAATGTGCGAACCCTACCTAA
1 CGAACCCTACTAATGTGCGAACCCTACCTAA
41354301 TGTGTGAGCC
Statistics
Matches: 201, Mismatches: 37, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
34 4 0.02
35 166 0.83
36 31 0.15
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.25
Consensus pattern (35 bp):
CGAACCCTACTAATGTGCGAACCCTACCTAAAGTG
Found at i:41354321 original size:53 final size:53
Alignment explanation
Indices: 41354064--41354348 Score: 233
Period size: 53 Copynumber: 5.4 Consensus size: 53
41354054 ACATGCAAAC
* * * * * **
41354064 CCTACCAATGTGCGAGCCCTACCTAAAGTGTGAACCCT-A-TTATTGTGTGAA
1 CCTACTAATGTGCGAACCCTACCTAATGTGCGAACCCTAACCTAAAGTGTGAA
* * * * * * **
41354115 CCCTTCCTAAAGTGCAAACCTTA-CTAATGTGTGAACCCT-TCCTAAAGTGCAAA
1 -CC-TACTAATGTGCGAACCCTACCTAATGTGCGAACCCTAACCTAAAGTGTGAA
* * **
41354168 CCCTACTAATGTGCAAACCCTACCTAATGTGCGAACCCT-TCCTAAAGTGCAAA
1 -CCTACTAATGTGCGAACCCTACCTAATGTGCGAACCCTAACCTAAAGTGTGAA
*
41354221 CCCTACTAATGTGCGAACCCTACCTAATGTGCGAATCC-AACCTAAAGTGTGAA
1 -CCTACTAATGTGCGAACCCTACCTAATGTGCGAACCCTAACCTAAAGTGTGAA
* * *
41354274 CTCTACTAATGTGCGAACCCTACCTAATGTGTG-AGCCTAACCAAAAGTGTGAA
1 C-CTACTAATGTGCGAACCCTACCTAATGTGCGAACCCTAACCTAAAGTGTGAA
* *
41354327 GCCTACCTTATGTGTGAACCCT
1 -CCTA-CTAATGTGCGAACCCT
41354349 GCTATGTTGT
Statistics
Matches: 198, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
52 37 0.19
53 146 0.74
54 15 0.08
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.25
Consensus pattern (53 bp):
CCTACTAATGTGCGAACCCTACCTAATGTGCGAACCCTAACCTAAAGTGTGAA
Found at i:41354341 original size:18 final size:18
Alignment explanation
Indices: 41354061--41354348 Score: 221
Period size: 18 Copynumber: 16.3 Consensus size: 18
41354051 CTTACATGCA
*
41354061 AACCCTACC-AATGTGCG
1 AACCCTACCTAATGTGTG
* *
41354078 AGCCCTACCTAAAGTGTG
1 AACCCTACCTAATGTGTG
* *
41354096 AACCCTA-TTATTGTGTG
1 AACCCTACCTAATGTGTG
* * **
41354113 AACCCTTCCTAAAGTGCA
1 AACCCTACCTAATGTGTG
*
41354131 AACCTTA-CTAATGTGTG
1 AACCCTACCTAATGTGTG
* * **
41354148 AACCCTTCCTAAAGTGCA
1 AACCCTACCTAATGTGTG
**
41354166 AACCCTA-CTAATGTGCA
1 AACCCTACCTAATGTGTG
*
41354183 AACCCTACCTAATGTGCG
1 AACCCTACCTAATGTGTG
* * **
41354201 AACCCTTCCTAAAGTGCA
1 AACCCTACCTAATGTGTG
*
41354219 AACCCTA-CTAATGTGCG
1 AACCCTACCTAATGTGTG
*
41354236 AACCCTACCTAATGTGCG
1 AACCCTACCTAATGTGTG
* * *
41354254 AATCCAACCTAAAGTGTG
1 AACCCTACCTAATGTGTG
* *
41354272 AACTCTA-CTAATGTGCG
1 AACCCTACCTAATGTGTG
41354289 AACCCTACCTAATGTGTG
1 AACCCTACCTAATGTGTG
* * *
41354307 -AGCCTAACCAAAAGTGTG
1 AACCCT-ACCTAATGTGTG
* *
41354325 AAGCCTACCTTATGTGTG
1 AACCCTACCTAATGTGTG
41354343 AACCCT
1 AACCCT
41354349 GCTATGTTGT
Statistics
Matches: 213, Mismatches: 50, Indels: 15
0.77 0.18 0.05
Matches are distributed among these distances:
17 82 0.38
18 126 0.59
19 5 0.02
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (18 bp):
AACCCTACCTAATGTGTG
Found at i:41354374 original size:17 final size:18
Alignment explanation
Indices: 41354352--41354386 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
41354342 GAACCCTGCT
41354352 ATGTTGT-TATGCGAACC
1 ATGTTGTATATGCGAACC
41354369 ATGTTGTATATGCGAACC
1 ATGTTGTATATGCGAACC
41354387 CTACTATGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (18 bp):
ATGTTGTATATGCGAACC
Found at i:41357940 original size:21 final size:21
Alignment explanation
Indices: 41357900--41357940 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41357890 TTTTGCCTAA
*
41357900 AATATGAATTGGACTGAATTG
1 AATATGAATTGGACTAAATTG
* *
41357921 AATATGAATTGTATTAAATT
1 AATATGAATTGGACTAAATT
41357941 TAGTTAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.39
Consensus pattern (21 bp):
AATATGAATTGGACTAAATTG
Found at i:41358308 original size:24 final size:24
Alignment explanation
Indices: 41358262--41358314 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
41358252 TGAAAGTGAG
* *
41358262 TCCCGTTATTAGCCCTCTCGAGCT
1 TCCCGTTAATAGCCCTCTCGAGCA
*
41358286 TCCCGTTAATAGCTCT-TCGGAGCA
1 TCCCGTTAATAGCCCTCTC-GAGCA
41358310 TCCCG
1 TCCCG
41358315 ATTGGTTGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.15, C:0.36, G:0.19, T:0.30
Consensus pattern (24 bp):
TCCCGTTAATAGCCCTCTCGAGCA
Found at i:41358558 original size:25 final size:25
Alignment explanation
Indices: 41358521--41358574 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
41358511 TTTTCTGAAT
**
41358521 ATGGCTCTTATGAGCTTCCCATTAC
1 ATGGCTCACATGAGCTTCCCATTAC
* * *
41358546 ATGGCTCACATGAGGTTCCTATTAT
1 ATGGCTCACATGAGCTTCCCATTAC
41358571 ATGG
1 ATGG
41358575 ATCGAGAGAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.35
Consensus pattern (25 bp):
ATGGCTCACATGAGCTTCCCATTAC
Found at i:41360540 original size:5 final size:5
Alignment explanation
Indices: 41360530--41360607 Score: 68
Period size: 5 Copynumber: 14.8 Consensus size: 5
41360520 AGTATATCTT
* *
41360530 ATATC ATATC ATATC ATATC ATATC ATATTGG AT-TAC ATATC GTATC
1 ATATC ATATC ATATC ATATC ATATC ATA-T-C ATAT-C ATATC ATATC
* *
41360577 ATATC ATATCTC ATATC ATAAC AGATC ATAT
1 ATATC ATA--TC ATATC ATATC ATATC ATAT
41360608 ATTACCCCCA
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
5 50 0.85
6 2 0.03
7 7 0.12
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38
Consensus pattern (5 bp):
ATATC
Found at i:41360553 original size:27 final size:27
Alignment explanation
Indices: 41360523--41360607 Score: 80
Period size: 32 Copynumber: 3.0 Consensus size: 27
41360513 TTATCGAAGT
41360523 ATATCTTATATCATATCATATCATATC
1 ATATCTTATATCATATCATATCATATC
* *
41360550 ATATCATATTGGATTACATATCGTATCATATC
1 ATATCTTA-T--A-T-CATATCATATCATATC
* * *
41360582 ATATCTCATATCATAACAGATCATAT
1 ATATCTTATATCATATCATATCATAT
41360608 ATTACCCCCA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
27 19 0.41
28 2 0.04
29 1 0.02
30 1 0.02
31 2 0.04
32 21 0.46
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.40
Consensus pattern (27 bp):
ATATCTTATATCATATCATATCATATC
Found at i:41364067 original size:41 final size:41
Alignment explanation
Indices: 41364007--41364146 Score: 181
Period size: 41 Copynumber: 3.4 Consensus size: 41
41363997 ACAAGTTACA
** * * *
41364007 TGATACAACACACCGGCATGAAGCTTGCTAGGCTCAAGGCT
1 TGATACATTACACCGGCATGAAGCCTGCTAGGTTCAAGACT
* * *
41364048 TGATATATTACACCAGCATGAAGCCTACTAGGTTCAAGACT
1 TGATACATTACACCGGCATGAAGCCTGCTAGGTTCAAGACT
* * *
41364089 TGATACATTACACTGGCACGAAGCCTGCTAGGTTCAAGACC
1 TGATACATTACACCGGCATGAAGCCTGCTAGGTTCAAGACT
41364130 TGATACATTACACCGGC
1 TGATACATTACACCGGC
41364147 GCAAAACCTA
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 84 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.23
Consensus pattern (41 bp):
TGATACATTACACCGGCATGAAGCCTGCTAGGTTCAAGACT
Found at i:41364157 original size:82 final size:82
Alignment explanation
Indices: 41364007--41364166 Score: 185
Period size: 82 Copynumber: 2.0 Consensus size: 82
41363997 ACAAGTTACA
* * * * * ** *
41364007 TGATACAACACACCGGCATGAAGCTTGCTAGGCTCAAGGCTTGATATATTACACCAGCATGAAGC
1 TGATACAACACACCGGCACGAAGCCTGCTAGGCTCAAGACCTGATACATTACACCAGCACAAAAC
*
41364072 CTACTAGGTTCAAGACT
66 CTACTAGGCTCAAGACT
** * * * *
41364089 TGATACATTACACTGGCACGAAGCCTGCTAGGTTCAAGACCTGATACATTACACCGGCGCAAAAC
1 TGATACAACACACCGGCACGAAGCCTGCTAGGCTCAAGACCTGATACATTACACCAGCACAAAAC
41364154 CTACTAGGCTCAA
66 CTACTAGGCTCAA
41364167 AGCCTGATTT
Statistics
Matches: 63, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
82 63 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (82 bp):
TGATACAACACACCGGCACGAAGCCTGCTAGGCTCAAGACCTGATACATTACACCAGCACAAAAC
CTACTAGGCTCAAGACT
Found at i:41364161 original size:41 final size:41
Alignment explanation
Indices: 41364034--41364174 Score: 131
Period size: 41 Copynumber: 3.4 Consensus size: 41
41364024 ATGAAGCTTG
* * * * * ** *
41364034 CTAGGCTCAAGGCTTGATATATTACACCAGCATGAAGCCTA
1 CTAGGTTCAAGACCTGATACATTACACCGGCACAAAACCTA
* * * * *
41364075 CTAGGTTCAAGACTTGATACATTACACTGGCACGAAGCCTG
1 CTAGGTTCAAGACCTGATACATTACACCGGCACAAAACCTA
*
41364116 CTAGGTTCAAGACCTGATACATTACACCGGCGCAAAACCTA
1 CTAGGTTCAAGACCTGATACATTACACCGGCACAAAACCTA
*
41364157 CTAGGCTCAA-AGCCTGAT
1 CTAGGTTCAAGA-CCTGAT
41364175 TTCACACATC
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 1 0.01
41 84 0.99
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (41 bp):
CTAGGTTCAAGACCTGATACATTACACCGGCACAAAACCTA
Found at i:41367081 original size:20 final size:20
Alignment explanation
Indices: 41367058--41367123 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
41367048 GGTATTAAAA
41367058 TACAAACAAGGGTACCGAAG
1 TACAAACAAGGGTACCGAAG
* * * *
41367078 TACAAATAGGGGCA-CGTATG
1 TACAAACAAGGGTACCG-AAG
*
41367098 TGCAAACAAGGGTACCGAAG
1 TACAAACAAGGGTACCGAAG
41367118 TACAAA
1 TACAAA
41367124 TAGGGGCACA
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
19 2 0.06
20 30 0.88
21 2 0.06
ACGTcount: A:0.42, C:0.18, G:0.26, T:0.14
Consensus pattern (20 bp):
TACAAACAAGGGTACCGAAG
Found at i:41367139 original size:40 final size:40
Alignment explanation
Indices: 41367060--41367145 Score: 154
Period size: 40 Copynumber: 2.1 Consensus size: 40
41367050 TATTAAAATA
**
41367060 CAAACAAGGGTACCGAAGTACAAATAGGGGCACGTATGTG
1 CAAACAAGGGTACCGAAGTACAAATAGGGGCACAAATGTG
41367100 CAAACAAGGGTACCGAAGTACAAATAGGGGCACAAATGTG
1 CAAACAAGGGTACCGAAGTACAAATAGGGGCACAAATGTG
41367140 CAAACA
1 CAAACA
41367146 TTCAATAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.42, C:0.19, G:0.27, T:0.13
Consensus pattern (40 bp):
CAAACAAGGGTACCGAAGTACAAATAGGGGCACAAATGTG
Found at i:41367926 original size:24 final size:21
Alignment explanation
Indices: 41367862--41367915 Score: 85
Period size: 19 Copynumber: 2.7 Consensus size: 21
41367852 TCTTCAAGGA
*
41367862 TATGTAATCTTAGATATGA--
1 TATGCAATCTTAGATATGATT
41367881 TATGCAATCTTAGATATGATT
1 TATGCAATCTTAGATATGATT
41367902 TATGCAATCTTAGA
1 TATGCAATCTTAGA
41367916 AGATATGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.56
21 14 0.44
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (21 bp):
TATGCAATCTTAGATATGATT
Found at i:41368271 original size:3 final size:3
Alignment explanation
Indices: 41368257--41368303 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
41368247 ATTAAGTTAC
* * *
41368257 TAT TAT TCT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAG TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
41368304 CTATATATAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:41368460 original size:17 final size:17
Alignment explanation
Indices: 41368418--41368461 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
41368408 CATAACTTTT
*
41368418 ATATACA-TATATATAC
1 ATATACATTTTATATAC
*
41368434 ATTTACATTTTATATAC
1 ATATACATTTTATATAC
*
41368451 ATATATATTTT
1 ATATACATTTT
41368462 TTTATTTCCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:41368687 original size:28 final size:30
Alignment explanation
Indices: 41368628--41368687 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
41368618 TATTTGTTTA
* *
41368628 TATATATGTAATTATCTTTTTCATAATCTG
1 TATATATGTAATAATCTTTTTCATAATATG
41368658 TATATATGTATATAAT-TTTTT-AT-ATATG
1 TATATATGTA-ATAATCTTTTTCATAATATG
41368686 TA
1 TA
41368688 CATGTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 6 0.22
29 2 0.07
30 15 0.56
31 4 0.15
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (30 bp):
TATATATGTAATAATCTTTTTCATAATATG
Found at i:41370251 original size:3 final size:3
Alignment explanation
Indices: 41370243--41370284 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
41370233 GTATATATAG
* * *
41370243 TAA TAA TAA TAA TAA TGA TGA TAA TAA TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
41370285 CTTAATAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:41370292 original size:20 final size:20
Alignment explanation
Indices: 41370267--41370326 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
41370257 ATGATGATAA
41370267 TAATAACAATAATAATAACT
1 TAATAACAATAATAATAACT
* *
41370287 TAATAACAAGAA-AATCAAATT
1 TAATAACAATAATAAT--AACT
*
41370308 TAATAAAAATAAATAATAA
1 TAATAACAAT-AATAATAA
41370327 ATAAAAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
19 3 0.09
20 11 0.34
21 13 0.41
22 2 0.06
23 3 0.09
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.27
Consensus pattern (20 bp):
TAATAACAATAATAATAACT
Found at i:41370631 original size:23 final size:24
Alignment explanation
Indices: 41370601--41370647 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
41370591 AAATTAAATC
41370601 TCTAAGATTACA-AAATCATATCT
1 TCTAAGATTACATAAATCATATCT
*
41370624 TCTAAGATTGCATAAATCATATCT
1 TCTAAGATTACATAAATCATATCT
41370648 AAGATTGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.36
Consensus pattern (24 bp):
TCTAAGATTACATAAATCATATCT
Found at i:41370645 original size:24 final size:24
Alignment explanation
Indices: 41370601--41370666 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 24
41370591 AAATTAAATC
*
41370601 TCTAAGATTACA-AAATCATATCT
1 TCTAAGATTGCATAAATCATATCT
41370624 TCTAAGATTGCATAAATCATA---
1 TCTAAGATTGCATAAATCATATCT
41370645 TCTAAGATTGCAT--ATCATATCT
1 TCTAAGATTGCATAAATCATATCT
41370667 AAGATTACAT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 6 0.16
21 13 0.34
23 11 0.29
24 8 0.21
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (24 bp):
TCTAAGATTGCATAAATCATATCT
Found at i:41370650 original size:21 final size:21
Alignment explanation
Indices: 41370601--41370677 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 21
41370591 AAATTAAATC
41370601 TCTAAGATTACA-AAATCATA
1 TCTAAGATTACATAAATCATA
*
41370621 TCTTCTAAGATTGCATAAATCATA
1 ---TCTAAGATTACATAAATCATA
*
41370645 TCTAAGATTGCAT--ATCATA
1 TCTAAGATTACATAAATCATA
41370664 TCTAAGATTACATA
1 TCTAAGATTACATA
41370678 TCCTTGAAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
19 18 0.36
21 13 0.26
23 11 0.22
24 8 0.16
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.35
Consensus pattern (21 bp):
TCTAAGATTACATAAATCATA
Found at i:41371394 original size:44 final size:44
Alignment explanation
Indices: 41371344--41371462 Score: 152
Period size: 44 Copynumber: 2.7 Consensus size: 44
41371334 TCTGCTATTC
* * *
41371344 TCAACCTACTCTACTGCTGCTCAGGGAGATAGGA-TTCACAATCT
1 TCAACCTATTCCACTGCTGCTCAGGGAGATAGGACCT-ACAATCT
*
41371388 TCAACCTATTCCACTGCTGAC-CAGGGAGATAGTACCTACAATCT
1 TCAACCTATTCCACTGCTG-CTCAGGGAGATAGGACCTACAATCT
* *
41371432 TCAATCTATTCCACTACTGCTCAGGGAGATA
1 TCAACCTATTCCACTGCTGCTCAGGGAGATA
41371463 AAATTCCTAC
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 63 0.95
45 2 0.03
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.27
Consensus pattern (44 bp):
TCAACCTATTCCACTGCTGCTCAGGGAGATAGGACCTACAATCT
Found at i:41371513 original size:68 final size:68
Alignment explanation
Indices: 41371404--41371530 Score: 177
Period size: 68 Copynumber: 1.9 Consensus size: 68
41371394 TATTCCACTG
* *
41371404 CTGACCAGGGAGATAGTACCTACAATCTTCAATCTATTCCACTACTG-CTCAGGGAGATAAAATT
1 CTGACCAGGGAGATAGGACCTACAATCTTCAACCTATTCCACTACTGAC-CAGGGAGATAAAATT
41371468 CCTA
65 CCTA
* * *
41371472 CTGACCAGGGAGATAGGA-TTCACAATCTTTAACCTATTCCACTGCTGACCAGGGAGATA
1 CTGACCAGGGAGATAGGACCT-ACAATCTTCAACCTATTCCACTACTGACCAGGGAGATA
41371531 GGGCTGGGGT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
67 1 0.02
68 50 0.96
69 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (68 bp):
CTGACCAGGGAGATAGGACCTACAATCTTCAACCTATTCCACTACTGACCAGGGAGATAAAATTC
CTA
Found at i:41371652 original size:88 final size:88
Alignment explanation
Indices: 41371532--41371845 Score: 497
Period size: 88 Copynumber: 3.6 Consensus size: 88
41371522 AGGGAGATAG
* * * * *
41371532 GGCTGGGGTCATCGGTCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
*
41371597 TCCGTTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
*
41371620 GGCTAGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
* *
41371685 TCCACTGCAACCCGGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* *
41371708 GGCTGGTGTCTTTGATCTGATTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
**
41371773 TCCGCTGCAA--CAGATAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
41371794 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCT
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCT
41371846 TTCTTCGATC
Statistics
Matches: 208, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
86 58 0.28
88 150 0.72
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (88 bp):
GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
TCCGCTGCAACCCAGGGAGGCAA
Found at i:41371937 original size:44 final size:44
Alignment explanation
Indices: 41371828--41372334 Score: 470
Period size: 44 Copynumber: 11.5 Consensus size: 44
41371818 CTGTCGGTGC
* * * *
41371828 AGGAAGGCAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-CTACCAATAT
* * * *
41371873 GGGAAGATAAGATCT-ATATCTTCGATCTGCTTCCTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCCTACCAATAT
* * * * * *
41371916 AGAAAGACAGGACCTGCTATCTTCAATCTACTTCAC-GCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-CTACCAATAT
* * * *
41371960 ATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-CTACCAATAT
* * *
41372005 GGGAAGACAAGATCTGC-GTCTTCGATCCACTTCCTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCCTACCAATAT
* * * * * * *
41372048 AGGAAGATAGGACCTGCTATCTTCAATCTACTTCATGCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCCTACCAATAT
* * * *
41372092 ATGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-CTACCAATAT
* * * *
41372137 GGGAAGACAAGATCTGC-ATCTTTGATCCACTTTCTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCCTACCAATAT
* * * * *
41372180 AGGAAGACATGACCTGCTATCTTCGATCTATTTCAC-GCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-CTACCAATAT
* *
41372224 ATGAAGACAAGATCTGCTTTCTTCGATCTACTCTGCC-ACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACT-T-CCTACCAATAT
* * *
41372269 GGGAAAACAAGATCTGC-ATCTTCGATCCACTTCCTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCCTACCAATAT
* *
41372312 AGGAAGACAGGACCTGCTATCTT
1 AGGAAGACAAGATCTGCTATCTT
41372335 TACTGATCTG
Statistics
Matches: 363, Mismatches: 88, Indels: 23
0.77 0.19 0.05
Matches are distributed among these distances:
42 2 0.01
43 84 0.23
44 199 0.55
45 77 0.21
46 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (44 bp):
AGGAAGACAAGATCTGCTATCTTCGATCTACTTCCTACCAATAT
Found at i:41371989 original size:132 final size:132
Alignment explanation
Indices: 41371830--41372334 Score: 823
Period size: 132 Copynumber: 3.8 Consensus size: 132
41371820 GTCGGTGCAG
* * * **
41371830 GAAGGCAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAGATCTATATCTT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
** *
41371895 CGATCTGCTTCCTACCAATATAGAAAGACAGGACCTGCTATCTTCAATCTACTTCACGCCAATAC
66 CGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCAATCTACTTCACGCCAATAC
41371960 AT
131 AT
* *
41371962 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCGTCTT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
* *
41372027 CGATCCACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCAATCTACTTCATGCCAATAC
66 CGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCAATCTACTTCACGCCAATAC
41372092 AT
131 AT
*
41372094 GAAGACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGATCTGCATCTT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
* * * * *
41372159 TGATCCACTTTCTACCAATATAGGAAGACATGACCTGCTATCTTCGATCTATTTCACGCCAATAC
66 CGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCAATCTACTTCACGCCAATAC
41372224 AT
131 AT
*
41372226 GAAGACAAGATCTGCTTTCTTCGATCTAC-TCTGCCACCAATATGGGAAAACAAGATCTGCATCT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTC-GCCACCAATATGGGAAGACAAGATCTGCATCT
41372290 TCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTT
65 TCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTT
41372335 TACTGATCTG
Statistics
Matches: 347, Mismatches: 25, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
131 1 0.00
132 346 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (132 bp):
GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
CGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCAATCTACTTCACGCCAATAC
AT
Found at i:41377186 original size:17 final size:17
Alignment explanation
Indices: 41377155--41377198 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
41377145 CATAACTTTT
*
41377155 ATATACA-TATATATAC
1 ATATACATTTTATATAC
*
41377171 ATTTACATTTTATATAC
1 ATATACATTTTATATAC
41377188 ATATACATTTT
1 ATATACATTTT
41377199 TTTATTCCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:41377327 original size:23 final size:23
Alignment explanation
Indices: 41377279--41377327 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
41377269 GTATGTTTTC
* *
41377279 TTATATTATTCTTCATAATTTTA
1 TTATATTATTCTTCATAAATTAA
*
41377302 TTATATATATTTTTC-TAAATTAA
1 TTATAT-TATTCTTCATAAATTAA
41377325 TTA
1 TTA
41377328 ATTTTAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (23 bp):
TTATATTATTCTTCATAAATTAA
Found at i:41384776 original size:15 final size:15
Alignment explanation
Indices: 41384756--41384812 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
41384746 TAAATTATAT
41384756 AATTAAATAATTAAA
1 AATTAAATAATTAAA
* *
41384771 AATTAATTAAATAAA
1 AATTAAATAATTAAA
*
41384786 ATATTAGAATAATT-AG
1 A-ATTA-AATAATTAAA
41384802 AATT-AATAATT
1 AATTAAATAATT
41384813 TTAGGTAGGA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 7 0.20
15 17 0.49
16 6 0.17
17 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (15 bp):
AATTAAATAATTAAA
Found at i:41384780 original size:32 final size:31
Alignment explanation
Indices: 41384742--41384808 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
41384732 CTGGAAGTCG
* *
41384742 TAATTAAATTATATAATTA-AATAATTAAAAAT
1 TAATTAAATAAAAT-ATTAGAATAATT-AAAAT
*
41384774 TAATTAAATAAAATATTAGAATAATTAGAAT
1 TAATTAAATAAAATATTAGAATAATTAAAAT
41384805 TAAT
1 TAAT
41384809 AATTTTAGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 12 0.39
32 19 0.61
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (31 bp):
TAATTAAATAAAATATTAGAATAATTAAAAT
Found at i:41392680 original size:29 final size:28
Alignment explanation
Indices: 41392634--41392688 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
41392624 TTAATTAACT
* * *
41392634 ATAAAAATTTTCATTTTAGGCACTTAAA
1 ATAAAAATTTGCAATTTAAGCACTTAAA
41392662 ATAAAAAGTTTGCAATTTAAGCACTTA
1 ATAAAAA-TTTGCAATTTAAGCACTTA
41392689 CATTATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (28 bp):
ATAAAAATTTGCAATTTAAGCACTTAAA
Found at i:41393196 original size:14 final size:15
Alignment explanation
Indices: 41393167--41393214 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
41393157 ATTTTTATTT
41393167 TATTTAATATTAATA
1 TATTTAATATTAATA
*
41393182 TATTT-ATATTTATATT
1 TATTTAATA-TTA-ATA
*
41393198 TATTTAACATTAATA
1 TATTTAATATTAATA
41393213 TA
1 TA
41393215 AATTTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
14 3 0.11
15 12 0.44
16 10 0.37
17 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTTAATATTAATA
Found at i:41400152 original size:112 final size:112
Alignment explanation
Indices: 41399955--41400180 Score: 443
Period size: 112 Copynumber: 2.0 Consensus size: 112
41399945 AAGTTCTGAG
41399955 CATTAGGGCAAGAGCATATATGTAACCTGTTTTATGTAAATAATTTTATTTTCTAGTGAAAGTTT
1 CATTAGGGCAAGAGCATATATGTAACCTGTTTTATGTAAATAATTTTATTTTCTAGTGAAAGTTT
41400020 TCTAAATGAAATTGAATCAGAATCGACGCCGCTTTGCATTCATGCAT
66 TCTAAATGAAATTGAATCAGAATCGACGCCGCTTTGCATTCATGCAT
41400067 CATTAGGGCAAGAGCATATATGTAACCTGTTTTATGTAAATAATTTTATTTTCTAGTGAAAGTTT
1 CATTAGGGCAAGAGCATATATGTAACCTGTTTTATGTAAATAATTTTATTTTCTAGTGAAAGTTT
*
41400132 TCTAAATGAAATTGAATCAGAATCGACGCCTCTTTGCATTCATGCAT
66 TCTAAATGAAATTGAATCAGAATCGACGCCGCTTTGCATTCATGCAT
41400179 CA
1 CA
41400181 CATTACATTG
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 113 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (112 bp):
CATTAGGGCAAGAGCATATATGTAACCTGTTTTATGTAAATAATTTTATTTTCTAGTGAAAGTTT
TCTAAATGAAATTGAATCAGAATCGACGCCGCTTTGCATTCATGCAT
Found at i:41408992 original size:44 final size:44
Alignment explanation
Indices: 41408912--41409147 Score: 172
Period size: 44 Copynumber: 5.1 Consensus size: 44
41408902 TAGATCACAT
* * *
41408912 CAGATTGAAGCCAGAAATCTTATCGCCTTGAGATTACAGCGGAG
1 CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAG
* * * *
41408956 CAGATTGAAGCTAGTAATCCTATCTCCCTGATATTACAGTGGAG
1 CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAG
** * *
41409000 CAGATT-AAAATA-AAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAG
1 CAGATTGAAGCTAGAA--ATCTTATCTCCCTGAGA-TTACAG-CG-G-AG
* * *
41409047 ATCACATCAGATTGAAGCCAGAAATCTTATCTCTCTGAGATTAGAGCGGAG
1 -------CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAG
* * * *
41409098 CAGGTTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAG
41409142 CAGATT
1 CAGATT
41409148 AAAACAAAAG
Statistics
Matches: 150, Mismatches: 26, Indels: 32
0.72 0.12 0.15
Matches are distributed among these distances:
42 1 0.01
43 5 0.03
44 104 0.69
45 1 0.01
46 1 0.01
47 2 0.01
51 2 0.01
52 1 0.01
53 1 0.01
54 26 0.17
55 4 0.03
56 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (44 bp):
CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAG
Found at i:41409026 original size:142 final size:141
Alignment explanation
Indices: 41408769--41409198 Score: 743
Period size: 142 Copynumber: 3.0 Consensus size: 141
41408759 AACAGCGGAG
*
41408769 CAGATTGAAGCTAGAAATCTTATCTCCTTGAGATTACAGCAGGAGCAGATTGAAGCTAGTAATCC
1 CAGATTGAAGCCAGAAATCTTATC-CCTTGAGATTACAGC-GGAGCAGATTGAAGCTAGTAATCC
*
41408834 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
64 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
41408899 GAGTAGATCACAT
129 GAGTAGATCACAT
41408912 CAGATTGAAGCCAGAAATCTTATCGCCTTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATC-CCTTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
*
41408977 ATCTCCCTGATATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
65 ATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
41409042 AGTAGATCACAT
130 AGTAGATCACAT
* * *
41409054 CAGATTGAAGCCAGAAATCTTATCTCTCTGAGATTAGAGCGGAGCAGGTTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCCCT-TGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
* * *
41409119 ATCTCCCTGAGATTACAGTGGAGCAGATTAAAACAAAAGATCTTATCTCGCTGAAGTTACAGTAG
65 ATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
41409184 AGTAGATCACAT
130 AGTAGATCACAT
41409196 CAG
1 CAG
41409199 GTCTTATCTC
Statistics
Matches: 275, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
141 2 0.01
142 235 0.85
143 38 0.14
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (141 bp):
CAGATTGAAGCCAGAAATCTTATCCCTTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTA
TCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGA
GTAGATCACAT
Found at i:41409166 original size:44 final size:41
Alignment explanation
Indices: 41409118--41409225 Score: 101
Period size: 41 Copynumber: 2.6 Consensus size: 41
41409108 CTAGTAATCC
41409118 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAACAAAAGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGA-T--AACAAAAGATCT
* * * * ** *
41409162 TATCTCGCTGA-AGTTACAGTAGAGTAGATCACATCAGGTCT
1 TATCTCCCTGAGA-TTACAGTGGAGCAGATAACAAAAGATCT
*
41409203 TATCTCCATGAGATTACAGTGGA
1 TATCTCCCTGAGATTACAGTGGA
41409226 ATAGACCGAA
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
41 26 0.50
42 1 0.02
43 2 0.04
44 23 0.44
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (41 bp):
TATCTCCCTGAGATTACAGTGGAGCAGATAACAAAAGATCT
Found at i:41417877 original size:78 final size:78
Alignment explanation
Indices: 41417776--41417951 Score: 217
Period size: 78 Copynumber: 2.3 Consensus size: 78
41417766 TAAACATCAA
* * * * * * * **
41417776 CTCAAGGCCTGCTAAATACACACCGGCTCAAGGCCTGCTAAATACACACTAGCTCAAGGCCTGCT
1 CTCAAAGCCTACTAAATAAACACCGGCTCAAAGCCTGATAAATAAAAACTAGCTCAAAACCTGCT
* **
41417841 AAATAATCATTGG
66 AAATAAACACCGG
* *
41417854 CTCAAAGCCTACTAAATAAACACCGGCTCAAAGCTTGATAAATAAAAACTGGCTCAAAACCTGCT
1 CTCAAAGCCTACTAAATAAACACCGGCTCAAAGCCTGATAAATAAAAACTAGCTCAAAACCTGCT
41417919 AAATAAACACCGG
66 AAATAAACACCGG
*
41417932 CTCAAAGCCTATTAAATAAA
1 CTCAAAGCCTACTAAATAAA
41417952 GTACATTACG
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
78 83 1.00
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (78 bp):
CTCAAAGCCTACTAAATAAACACCGGCTCAAAGCCTGATAAATAAAAACTAGCTCAAAACCTGCT
AAATAAACACCGG
Found at i:41417951 original size:26 final size:26
Alignment explanation
Indices: 41417736--41417951 Score: 191
Period size: 26 Copynumber: 8.3 Consensus size: 26
41417726 TAGTACATGT
* *
41417736 TAAATAATCACCGACTCAAAGCCTAC
1 TAAATAAACACCGGCTCAAAGCCTAC
* * ** * *
41417762 TAGATAAACATCAACTCAAGGCCTGC
1 TAAATAAACACCGGCTCAAAGCCTAC
* * *
41417788 TAAATACACACCGGCTCAAGGCCTGC
1 TAAATAAACACCGGCTCAAAGCCTAC
* ** * *
41417814 TAAATACACACTAGCTCAAGGCCTGC
1 TAAATAAACACCGGCTCAAAGCCTAC
* **
41417840 TAAATAATCATTGGCTCAAAGCCTAC
1 TAAATAAACACCGGCTCAAAGCCTAC
*
41417866 TAAATAAACACCGGCTCAAAGCTTGA-
1 TAAATAAACACCGGCTCAAAGCCT-AC
* * * *
41417892 TAAATAAAAACTGGCTCAAAACCTGC
1 TAAATAAACACCGGCTCAAAGCCTAC
*
41417918 TAAATAAACACCGGCTCAAAGCCTAT
1 TAAATAAACACCGGCTCAAAGCCTAC
41417944 TAAATAAA
1 TAAATAAA
41417952 GTACATTACG
Statistics
Matches: 155, Mismatches: 33, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
26 154 0.99
27 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.20
Consensus pattern (26 bp):
TAAATAAACACCGGCTCAAAGCCTAC
Found at i:41420943 original size:57 final size:57
Alignment explanation
Indices: 41420875--41420988 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
41420865 AAAATTGGTA
41420875 ATTAAGTTAATAATGGTATAATAAGACAAAATTTAAAAGCTATTATCTTTTTTCTTT
1 ATTAAGTTAATAATGGTATAATAAGACAAAATTTAAAAGCTATTATCTTTTTTCTTT
41420932 ATTAAGTTAATAATGGTATAATAAGACAAAATTTAAAAGCTATTATCTTTTTTCTTT
1 ATTAAGTTAATAATGGTATAATAAGACAAAATTTAAAAGCTATTATCTTTTTTCTTT
41420989 CTTCTTGAAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (57 bp):
ATTAAGTTAATAATGGTATAATAAGACAAAATTTAAAAGCTATTATCTTTTTTCTTT
Found at i:41421418 original size:43 final size:44
Alignment explanation
Indices: 41421354--41421452 Score: 146
Period size: 43 Copynumber: 2.3 Consensus size: 44
41421344 CAGTGTTTAT
* **
41421354 GTGTAAGACCATAGATGGGCTATTGGCATCGATTTGAGATTT-C
1 GTGTAAGACCATAGATAGGCTATTGGCATCGATACGAGATTTCC
*
41421397 GTGTAAGACCATAGCTAGGCTATTGGCATCGATACGAGATTTCC
1 GTGTAAGACCATAGATAGGCTATTGGCATCGATACGAGATTTCC
*
41421441 ATGTAAGACCAT
1 GTGTAAGACCAT
41421453 GTCTGGGACA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 38 0.76
44 12 0.24
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (44 bp):
GTGTAAGACCATAGATAGGCTATTGGCATCGATACGAGATTTCC
Found at i:41425572 original size:92 final size:91
Alignment explanation
Indices: 41425417--41425595 Score: 245
Period size: 92 Copynumber: 2.0 Consensus size: 91
41425407 TGTAAAAAGT
* *
41425417 CCTCAAACTTTTTCAAAAAAAAATTAAACCCTTGCTTTTTTTTATTGCATTCAATTGGGTACTTG
1 CCTCAAACTTTTTCAAAAAAAAATTAAACCCCTGCTTTTTTTTATTGCATTCAATTGGATACTTG
* * *
41425482 AACTTTCAAAATGCATAAAAAAAGGC
66 AACTGTAAAAATGAATAAAAAAAGGC
* *
41425508 CCTCAAACTTTTTCAAGAAAAGTAATTAAGCCCCTGCTTTTTTTT-TTGCACTT-AATTGGATAC
1 CCTCAAACTTTTTCAA-AAAA-AAATTAAACCCCTGCTTTTTTTTATTGCA-TTCAATTGGATAC
*
41425571 TTGAACTGTAAAAATGAATTAAAAA
63 TTGAACTGTAAAAATGAATAAAAAA
41425596 GACCCTTTGA
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
91 16 0.21
92 39 0.51
93 22 0.29
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.36
Consensus pattern (91 bp):
CCTCAAACTTTTTCAAAAAAAAATTAAACCCCTGCTTTTTTTTATTGCATTCAATTGGATACTTG
AACTGTAAAAATGAATAAAAAAAGGC
Found at i:41425789 original size:29 final size:29
Alignment explanation
Indices: 41425734--41425789 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
41425724 CATTTAGAGT
** *
41425734 TATAAAAATTATTAAATTTTAATAAATAA
1 TATAAAAATTATTAAAAATTAAAAAATAA
41425763 TATAAAAA-TATTAAAAATTAGAAAAAT
1 TATAAAAATTATTAAAAATTA-AAAAAT
41425790 TGTTTTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (29 bp):
TATAAAAATTATTAAAAATTAAAAAATAA
Found at i:41426015 original size:20 final size:19
Alignment explanation
Indices: 41425990--41426161 Score: 73
Period size: 19 Copynumber: 8.9 Consensus size: 19
41425980 TTAGTACGAT
*
41425990 AATTTTTATACTTTTTTAC
1 AATTTTTATAATTTTTTAC
*
41426009 GAA-TTTTATATTTTCTTTAC
1 -AATTTTTATAATTT-TTTAC
* *
41426029 ATTTTTTATAATTTTCTTAT
1 AATTTTTATAATTTT-TTAC
* * ** * *
41426049 GA-CTTTATAAAATTTGAT
1 AATTTTTATAATTTTTTAC
* * *
41426067 AATTTTTTTCTATATTTCTA-
1 AATTTTTAT-AAT-TTTTTAC
* *
41426087 TATATTTTATAATTTTTTTAT
1 AAT-TTTTATAA-TTTTTTAC
* ** *
41426108 GATTTTTATAAAATTTTAT
1 AATTTTTATAATTTTTTAC
*
41426127 ATTTTTTAT-ATTTTTTAC
1 AATTTTTATAATTTTTTAC
41426145 AATTTTTATAATTTTTT
1 AATTTTTATAATTTTTT
41426162 TTCTAATTTT
Statistics
Matches: 111, Mismatches: 31, Indels: 21
0.68 0.19 0.13
Matches are distributed among these distances:
18 18 0.16
19 45 0.41
20 37 0.33
21 11 0.10
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTTTTATAATTTTTTAC
Found at i:41426101 original size:30 final size:28
Alignment explanation
Indices: 41426032--41426161 Score: 97
Period size: 29 Copynumber: 4.5 Consensus size: 28
41426022 TCTTTACATT
* * *
41426032 TTTTATAATTTTCT-TATGACTTTATAAAA
1 TTTTATAATTTTTTCTAT-A-TTTTTATAA
* *
41426061 TTTGATAATTTTTTTCTATATTTCTATATA
1 TTTTATAA-TTTTTTCTATATTTTTATA-A
41426091 TTTTATAATTTTTT-TATGATTTTTATAAAA
1 TTTTATAATTTTTTCTAT-ATTTTTAT--AA
* *
41426121 TTTTAT-ATTTTTTATAT-TTTTTACAA
1 TTTTATAATTTTTTCTATATTTTTATAA
41426147 TTTTTATAATTTTTT
1 -TTTTATAATTTTTT
41426162 TTCTAATTTT
Statistics
Matches: 85, Mismatches: 7, Indels: 19
0.77 0.06 0.17
Matches are distributed among these distances:
26 2 0.02
27 6 0.07
28 16 0.19
29 33 0.39
30 24 0.28
31 4 0.05
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (28 bp):
TTTTATAATTTTTTCTATATTTTTATAA
Found at i:41426112 original size:19 final size:19
Alignment explanation
Indices: 41426085--41426162 Score: 72
Period size: 20 Copynumber: 4.1 Consensus size: 19
41426075 TCTATATTTC
41426085 TATATATTTTATAATTTTTT
1 TATAT-TTTTATAATTTTTT
**
41426105 TATGATTTTTATAA-AATTT
1 TAT-ATTTTTATAATTTTTT
41426124 TATATTTTT-T-ATATTTTT
1 TATATTTTTATAAT-TTTTT
*
41426142 TACAATTTTTATAATTTTTT
1 TA-TATTTTTATAATTTTTT
41426162 T
1 T
41426163 TCTAATTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
16 1 0.02
17 1 0.02
18 11 0.23
19 12 0.26
20 18 0.38
21 4 0.09
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (19 bp):
TATATTTTTATAATTTTTT
Found at i:41426112 original size:29 final size:28
Alignment explanation
Indices: 41426032--41426162 Score: 124
Period size: 30 Copynumber: 4.5 Consensus size: 28
41426022 TCTTTACATT
* *
41426032 TTTTATAATTTTCTTATGACTTTATAAAA
1 TTTTATAATTTTTTTAT-ATTTTATAAAA
* *
41426061 TTTGATAATTTTTTTCTATATTTCTAT-ATA
1 TTTTATAA-TTTTTT-TATATTT-TATAAAA
41426091 TTTTATAATTTTTTTATGATTTTTATAAAA
1 TTTTATAATTTTTTTAT-A-TTTTATAAAA
* *
41426121 TTTTAT-A-TTTTTTATATTTTTTACAAT
1 TTTTATAATTTTTTTATATTTTATA-AAA
41426148 TTTTATAATTTTTTT
1 TTTTATAATTTTTTT
41426163 TCTAATTTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
26 6 0.07
27 9 0.11
28 12 0.14
29 24 0.28
30 28 0.33
31 6 0.07
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (28 bp):
TTTTATAATTTTTTTATATTTTATAAAA
Found at i:41426141 original size:37 final size:40
Alignment explanation
Indices: 41426080--41426155 Score: 104
Period size: 37 Copynumber: 2.0 Consensus size: 40
41426070 TTTTTTCTAT
**
41426080 ATTTCTATATATTTTATAATTTTTTTATGATTTTTATAAA
1 ATTTCTATATATTTTATAATTTTTTTACAATTTTTATAAA
*
41426120 ATTT-TATATTTTTTAT-A-TTTTTTACAATTTTTATAA
1 ATTTCTATATATTTTATAATTTTTTTACAATTTTTATAA
41426156 TTTTTTTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 17 0.52
38 1 0.03
39 11 0.33
40 4 0.12
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (40 bp):
ATTTCTATATATTTTATAATTTTTTTACAATTTTTATAAA
Found at i:41426162 original size:11 final size:10
Alignment explanation
Indices: 41426091--41426161 Score: 69
Period size: 9 Copynumber: 7.4 Consensus size: 10
41426081 TTTCTATATA
41426091 TTTTATAATTT
1 TTTTATAA-TT
*
41426102 TTTTATGA-T
1 TTTTATAATT
**
41426111 TTTTATAAAA
1 TTTTATAATT
41426121 TTTTAT-ATT
1 TTTTATAATT
41426130 TTTTAT-ATT
1 TTTTATAATT
*
41426139 TTTTACAA-T
1 TTTTATAATT
41426148 TTTTATAATT
1 TTTTATAATT
41426158 TTTT
1 TTTT
41426162 TTCTAATTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
9 31 0.62
10 12 0.24
11 7 0.14
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (10 bp):
TTTTATAATT
Done.