Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 131 of 214
Found at i:39888019 original size:21 final size:21
Alignment explanation
Indices: 39887971--39888036 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
39887961 AATTAATTAT
39887971 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
39887993 --AAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
*
39888012 AAAAAATTAGAATATTCATAC
1 AAAAAATTACAATATTCATAC
39888033 AAAA
1 AAAA
39888037 TACTAATCCA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
19 17 0.41
20 2 0.05
21 22 0.54
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Found at i:39889165 original size:19 final size:19
Alignment explanation
Indices: 39889138--39889174 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39889128 CAAATTATAT
*
39889138 TTATATAAAATTAATAATA
1 TTATATAAAAATAATAATA
*
39889157 TTATTTAAAAATAATAAT
1 TTATATAAAAATAATAAT
39889175 GAAAAAATAA
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTATATAAAAATAATAATA
Found at i:39889431 original size:6 final size:6
Alignment explanation
Indices: 39889420--39889444 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
39889410 TTATGATGAT
39889420 TAATTA TAATTA TAATTA TAATTA T
1 TAATTA TAATTA TAATTA TAATTA T
39889445 TTGAATATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATTA
Found at i:39890567 original size:23 final size:23
Alignment explanation
Indices: 39890539--39890590 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
39890529 GGATGCCACT
39890539 TTGCATCGAAGTGCCACTAACAC
1 TTGCATCGAAGTGCCACTAACAC
* * *
39890562 TTGCATCGTAGTGTCACTATCAC
1 TTGCATCGAAGTGCCACTAACAC
39890585 TTGCAT
1 TTGCAT
39890591 GCATAGAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (23 bp):
TTGCATCGAAGTGCCACTAACAC
Found at i:39892299 original size:15 final size:15
Alignment explanation
Indices: 39892276--39892333 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 15
39892266 GTTAGGACAC
*
39892276 AACGTATTGAATTCT
1 AACGCATTGAATTCT
39892291 AACGCATTGAATTCT
1 AACGCATTGAATTCT
** *
39892306 AACG--TTGTGTCCT
1 AACGCATTGAATTCT
39892319 AACGCATTGAATTCT
1 AACGCATTGAATTCT
39892334 CGATAATGAG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
13 10 0.29
15 24 0.71
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (15 bp):
AACGCATTGAATTCT
Found at i:39895388 original size:14 final size:15
Alignment explanation
Indices: 39895357--39895393 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
39895347 AAATCTAGAG
*
39895357 AAATTAAATTATGTA
1 AAATTAAAATATGTA
39895372 AAATTAAAATA-GTA
1 AAATTAAAATATGTA
39895386 AAATTAAA
1 AAATTAAA
39895394 TTTTAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (15 bp):
AAATTAAAATATGTA
Found at i:39896132 original size:125 final size:125
Alignment explanation
Indices: 39895919--39896287 Score: 576
Period size: 125 Copynumber: 3.0 Consensus size: 125
39895909 TTAGGTCCAA
* * ** * *
39895919 GAAGAAATAATTTCGAGTTGACGTTTCTGATCAAATAGTATAAAATCGCTTCTAGCATAATGATG
1 GAAGAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTA
* *
39895984 TTTGATAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCTTG
66 TTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATG
* *
39896044 GAAGAAATAATTTTGAGTTGACATTTCTAAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTA
1 GAAGAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTA
* *
39896109 TTTAAGAAGAATTTGTGAAATCGCGCCCTTGTGGACGCGCTTTTGCTACAGTAGGTCATG
66 TTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATG
* * * *
39896169 GAAGAAATAATTTCGAGTTTACTTTTCTGAGAAAATAGTATAAAATCGCTTCTAGCAGGATACTA
1 GAAGAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTA
* *
39896234 TTTGAGAAGAATTTGTGAAAGCACGCCCTCGTGGACGCGCTTTTGCTACAGTAG
66 TTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
39896288 CATGTTTGGG
Statistics
Matches: 222, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
125 222 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (125 bp):
GAAGAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTA
TTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATG
Found at i:39899528 original size:64 final size:64
Alignment explanation
Indices: 39899449--39899585 Score: 172
Period size: 64 Copynumber: 2.2 Consensus size: 64
39899439 ATCAAATAAA
* *
39899449 TTTAAGTTAAGGGTTACAG-TTTTTAAGTTCTA-GTTTAAAGTTTAAAAGTTAAGGGTTAAGGGT
1 TTTAAGTTAAGGGTTA-AGATTTTTAAGTT-GAGGGTTAAAGTTTAAAAGTTAAGGGTTAAGGGT
39899512 T
64 T
** ** *
39899513 TTTAAGTTAAGGGTTAAGATTTTTAAGTTGAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAAGATTTTTAAGTTGAGGGTTAAAGTTTAAAAGTTAAGGGTTAAGGGTT
39899577 TTTAA-TTAA
1 TTTAAGTTAA
39899586 ATTAGTTAGG
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
63 7 0.11
64 57 0.89
ACGTcount: A:0.29, C:0.01, G:0.26, T:0.44
Consensus pattern (64 bp):
TTTAAGTTAAGGGTTAAGATTTTTAAGTTGAGGGTTAAAGTTTAAAAGTTAAGGGTTAAGGGTT
Found at i:39899647 original size:68 final size:67
Alignment explanation
Indices: 39899532--39900530 Score: 953
Period size: 68 Copynumber: 14.8 Consensus size: 67
39899522 AGGGTTAAGA
* *
39899532 TTTTTAAGTTGAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAG-TTAG
1 TTTTTAAGTTAAGGGTTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTAAATTAGTTTAG
39899595 GG
66 GG
* * ** * ** *
39899597 TTTTTAAGTTTAAGGGTTTAGGATTTTTAATTAAATTAGTTTAAGGTTTTTAAGTT-AA-GGGGT
1 TTTTTAAG-TTAAGGGTTTAGGGTTTTTAATTTAA-GGGTTTAGGGTTTTTAA-TTAAATTAGTT
39899660 TAGGG
63 TAGGG
* * * ** **
39899665 TTTTTAAATTTAAGGGTTTAGTGTTTTTAATTAAATTAGTTTAGGGTTTTTAAGTT-AAGGAG-T
1 TTTTT-AAGTTAAGGGTTTAGGGTTTTTAATTTAA-GGGTTTAGGGTTTTTAA-TTAAATTAGTT
*
39899728 TAAGG
63 TAGGG
* ** ** *
39899733 TTTTTAAGTTTAAGGGTTTAGGGTTTTTAATTAAATTAGTTTAGGGTTTTTAAGTT-AA-GGGCT
1 TTTTTAAG-TTAAGGGTTTAGGGTTTTTAATTTAA-GGGTTTAGGGTTTTTAA-TTAAATTAGTT
39899796 TAGGG
63 TAGGG
* * **
39899801 TTTTTAATTTTAAGGGTTTAGGATTTTTAATTTAAGGG-TTAGGGTTTTTAAGTT-AA-GGGTTT
1 TTTTTAA-GTTAAGGGTTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAA-TTAAATTAGTTT
39899863 AGGG
64 AGGG
** *
39899867 TTTTTAA-TTAA-ATTAGTTAGGGTTTTTAAGTTTAAGGGTTTAGAGTTTTTAATTAAATTAGTT
1 TTTTTAAGTTAAGGGT--TTAGGGTTTTTAA-TTTAAGGGTTTAGGGTTTTTAATTAAATTAGTT
39899930 TAGGG
63 TAGGG
* * *
39899935 TTTTTAAGTTAAGGG-TTAGGATTTTTAAATTTAAGGGTCTATGGTTTTTAATTAAATTAGTTTA
1 TTTTTAAGTTAAGGGTTTAGGGTTTTT-AATTTAAGGGTTTAGGGTTTTTAATTAAATTAGTTTA
39899999 GGG
65 GGG
* *
39900002 TTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTTAAAGGTTTAGGGTTTTTAATTAAATTAGTTTA
1 TTTTTAAGTTAAGGGTTTAGGGTTTTTAA-TTTAAGGGTTTAGGGTTTTTAATTAAATTAGTTTA
39900067 GGG
65 GGG
*
39900070 TTTTTAAGTTAAGGGTTATGGTTTAGGGTTTTTATTTTTAAGGGTTTAGGGTTTTTAATTAAATT
1 TTTTTAAGTTAA--G----GGTTTAGGGTTTTTA-ATTTAAGGGTTTAGGGTTTTTAATTAAATT
39900135 AGTTTAGGG
59 AGTTTAGGG
* * *
39900144 TTTTTAAGTTAAGGGCTTAGGGTTTTTAATTGTAAGGGTTTAGGGTTTTTAATTTAA--AGGTTA
1 TTTTTAAGTTAAGGGTTTAGGGTTTTTAATT-TAAGGGTTTAGGGTTTTTAATTAAATTAGTTTA
39900207 GGG
65 GGG
* * *
39900210 TTTTAAAGTTAAGGGTTTAAGGTTTTTAATTTTAAGGGGTTAGGGTTTTTAATTAAATTAGTTTA
1 TTTTTAAGTTAAGGGTTTAGGGTTTTTAA-TTTAAGGGTTTAGGGTTTTTAATTAAATTAGTTTA
39900275 GGG
65 GGG
* * *
39900278 TTTTTAAGTTAAGGG-TTAGAGTTTTTATGTTTAAGGGTTTATGGTTTTTAATTAAATTAGTTTA
1 TTTTTAAGTTAAGGGTTTAGGGTTTTTA-ATTTAAGGGTTTAGGGTTTTTAATTAAATTAGTTTA
39900342 GGG
65 GGG
* * ** * * *
39900345 TTTTTAAGTTATGGGTTTATGGTTTTTAATTTTAAGGGTTTAGAATTTTTAATTTAA--GGGTTA
1 TTTTTAAGTTAAGGGTTTAGGGTTTTTAA-TTTAAGGGTTTAGGGTTTTTAATTAAATTAGTTTA
*
39900408 GAG
65 GGG
** * * * * * **
39900411 TTTTTAAGTTAAAAG-TTAAGGTTTTTAAGTTAAGGATTTAGTGTTTTTAATTTTAA-GGGTTTA
1 TTTTTAAGTTAAGGGTTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAA-TTAAATTAGTTTA
*
39900474 GGA
65 GGG
** * * *
39900477 TTTTTAA-TTAAATTAGTTTAGAGTTTTTAAGTTAAGGGTTGAGGGTTTTTAATT
1 TTTTTAAGTT-AA-GGGTTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATT
39900531 TTAAGAATTT
Statistics
Matches: 806, Mismatches: 88, Indels: 78
0.83 0.09 0.08
Matches are distributed among these distances:
63 1 0.00
64 22 0.03
65 39 0.05
66 140 0.17
67 165 0.20
68 364 0.45
69 10 0.01
70 1 0.00
72 1 0.00
74 63 0.08
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.49
Consensus pattern (67 bp):
TTTTTAAGTTAAGGGTTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTAAATTAGTTTAG
GG
Found at i:39900534 original size:23 final size:22
Alignment explanation
Indices: 39899497--39900550 Score: 879
Period size: 23 Copynumber: 46.9 Consensus size: 22
39899487 AGTTTAAAAG
* *
39899497 TTAAGGGTTAAGGGTTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAT
* * *
39899519 TTAAGGG-TTAAGATTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAT
* *
39899540 TTGAGGG-TTAGGGTTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAT
39899561 TTAAGGGTTTAGGGTTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* **
39899583 TAAATTAG-TTAGGGTTTTTAAGT
1 TTAA-GGGTTTAGGGTTTTTAA-T
*
39899606 TTAAGGGTTTAGGATTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* ** * *
39899628 TAAATTAGTTTAAGGTTTTTAAG
1 TTAA-GGGTTTAGGGTTTTTAAT
*
39899651 TTAAGGGGTTAGGGTTTTTAAAT
1 TTAAGGGTTTAGGGTTTTT-AAT
*
39899674 TTAAGGGTTTAGTGTTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* ** *
39899696 TAAATTAGTTTAGGGTTTTTAAG
1 TTAA-GGGTTTAGGGTTTTTAAT
*
39899719 TTAAGGAG-TTAAGGTTTTTAAGT
1 TTAAGG-GTTTAGGGTTTTTAA-T
39899742 TTAAGGGTTTAGGGTTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* ** *
39899764 TAAATTAGTTTAGGGTTTTTAAG
1 TTAA-GGGTTTAGGGTTTTTAAT
*
39899787 TTAAGGGCTTAGGGTTTTTAATT
1 TTAAGGGTTTAGGGTTTTTAA-T
*
39899810 TTAAGGGTTTAGGATTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
*
39899832 TTAAGGG-TTAGGGTTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAT
39899853 TTAAGGGTTTAGGGTTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* **
39899875 TAAATTAG-TTAGGGTTTTTAAGT
1 TTAA-GGGTTTAGGGTTTTTAA-T
*
39899898 TTAAGGGTTTAGAGTTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* ** *
39899920 TAAATTAGTTTAGGGTTTTTAAG
1 TTAA-GGGTTTAGGGTTTTTAAT
*
39899943 TTAAGGG-TTAGGATTTTTAAAT
1 TTAAGGGTTTAGGGTTTTT-AAT
* *
39899965 TTAAGGGTCTATGGTTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* ** *
39899987 TAAATTAGTTTAGGGTTTTTAAG
1 TTAA-GGGTTTAGGGTTTTTAAT
*
39900010 TTAAGGGGTTAGGGTTTTTAAGT
1 TTAAGGGTTTAGGGTTTTTAA-T
*
39900033 TTAAAGGTTTAGGGTTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* ** *
39900055 TAAATTAGTTTAGGGTTTTTAAG
1 TTAA-GGGTTTAGGGTTTTTAAT
*
39900078 TTAAGGGTTATGGTTTAGGGTTTTTATTT
1 TTAA--G----GGTTTAGGGTTTTTA-AT
39900107 TTAAGGGTTTAGGGTTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* ** *
39900129 TAAATTAGTTTAGGGTTTTTAAG
1 TTAA-GGGTTTAGGGTTTTTAAT
*
39900152 TTAAGGGCTTAGGGTTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
39900174 TGTAAGGGTTTAGGGTTTTTAAT
1 T-TAAGGGTTTAGGGTTTTTAAT
* * *
39900197 TTAAAGG-TTAGGGTTTTAAAG
1 TTAAGGGTTTAGGGTTTTTAAT
*
39900218 TTAAGGGTTTAAGGTTTTTAATT
1 TTAAGGGTTTAGGGTTTTTAA-T
*
39900241 TTAAGGGGTTAGGGTTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* ** *
39900263 TAAATTAGTTTAGGGTTTTTAAG
1 TTAA-GGGTTTAGGGTTTTTAAT
* *
39900286 TTAAGGG-TTAGAGTTTTTATGT
1 TTAAGGGTTTAGGGTTTTTA-AT
*
39900308 TTAAGGGTTTATGGTTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* ** *
39900330 TAAATTAGTTTAGGGTTTTTAAG
1 TTAA-GGGTTTAGGGTTTTTAAT
* *
39900353 TTATGGGTTTATGGTTTTTAATT
1 TTAAGGGTTTAGGGTTTTTAA-T
**
39900376 TTAAGGGTTTAGAATTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* *
39900398 TTAAGGG-TTAGAGTTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAT
** * *
39900419 TTAAAAG-TTAAGGTTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAT
* *
39900440 TTAAGGATTTAGTGTTTTTAATT
1 TTAAGGGTTTAGGGTTTTTAA-T
*
39900463 TTAAGGGTTTAGGATTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* ** * *
39900485 TAAATTAGTTTAGAGTTTTTAAG
1 TTAA-GGGTTTAGGGTTTTTAAT
*
39900508 TTAAGGGTTGAGGGTTTTTAATT
1 TTAAGGGTTTAGGGTTTTTAA-T
** *
39900531 TTAAGAATTTAGGGGTTTTA
1 TTAAGGGTTTAGGGTTTTTA
39900551 GGTAATAACT
Statistics
Matches: 814, Mismatches: 177, Indels: 81
0.76 0.17 0.08
Matches are distributed among these distances:
21 126 0.15
22 266 0.33
23 403 0.50
27 1 0.00
28 14 0.02
29 4 0.00
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (22 bp):
TTAAGGGTTTAGGGTTTTTAAT
Found at i:39900542 original size:45 final size:43
Alignment explanation
Indices: 39899497--39900550 Score: 814
Period size: 45 Copynumber: 23.5 Consensus size: 43
39899487 AGTTTAAAAG
* * * *
39899497 TTAAGGGTTAAGGGTTTTTAAGTTAAGGGTTAAGATTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAT
*
39899540 TTGAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAT
* ** *
39899583 TAAATTAG-TTAGGGTTTTTAAGTTTAAGGGTTTAGGATTTTTAAT
1 TTAA-GGGTTTAGGGTTTTTAAG-TTAAGGG-TTAGGGTTTTTAAT
* ** *
39899628 TAAATTAGTTTAAGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAAT
1 TTAA-GGGTTTAGGGTTTTTAAGTTAA-GGGTTAGGGTTTTT-AAT
* * * *
39899674 TTAAGGGTTTAGTGTTTTTAA-TTAAATTAGTTTAGGGTTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAGTT-AA--GGGTTAGGGTTTTTAAT
*
39899719 TTAAGGAG-TTAAGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAAT
1 TTAAGG-GTTTAGGGTTTTTAAG-TTAAGGG-TTAGGGTTTTTAAT
* **
39899764 TAAATTAGTTTAGGGTTTTTAAGTTAAGGGCTTAGGGTTTTTAATT
1 TTAA-GGGTTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAA-T
* * *
39899810 TTAAGGGTTTAGGATTTTTAATTTAAGGGTTAGGGTTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAT
**
39899853 TTAAGGGTTTAGGGTTTTTAA-TTAAATTAGTTAGGGTTTTTAAGT
1 TTAAGGGTTTAGGGTTTTTAAGTT-AA-GGGTTAGGGTTTTTAA-T
* * * *
39899898 TTAAGGGTTTAGAGTTTTTAA-TTAAATTAGTTTAGGGTTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAGTT-AA--GGGTTAGGGTTTTTAAT
* * *
39899943 TTAAGGG-TTAGGATTTTTAAATTTAAGGGTCTATGGTTTTTAAT
1 TTAAGGGTTTAGGGTTTTT-AAGTTAAGGGT-TAGGGTTTTTAAT
* **
39899987 TAAATTAGTTTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGT
1 TTAA-GGGTTTAGGGTTTTTAAGTTAA-GGGTTAGGGTTTTTAA-T
* * * *
39900033 TTAAAGGTTTAGGGTTTTTAA-TTAAATTAGTTTAGGGTTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAGTT-AA--GGGTTAGGGTTTTTAAT
**
39900078 TTAAGGGTTATGGTTTAGGGTTTTTATTTTTAAGGGTTTAGGGTTTTTAAT
1 TTAA--G----GGTTTAGGGTTTTTA-AGTTAAGGG-TTAGGGTTTTTAAT
* **
39900129 TAAATTAGTTTAGGGTTTTTAAGTTAAGGGCTTAGGGTTTTTAAT
1 TTAA-GGGTTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAT
* * * *
39900174 TGTAAGGGTTTAGGGTTTTTAATTTAAAGGTTAGGGTTTTAAAG
1 T-TAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAT
* *
39900218 TTAAGGGTTTAAGGTTTTTAATTTTAAGGGGTTAGGGTTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAA-GTTAA-GGGTTAGGGTTTTTAAT
* ** * *
39900263 TAAATTAGTTTAGGGTTTTTAAGTTAAGGGTTAGAGTTTTTATGT
1 TTAA-GGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTA-AT
* * * *
39900308 TTAAGGGTTTATGGTTTTTAA-TTAAATTAGTTTAGGGTTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAGTT-AA--GGGTTAGGGTTTTTAAT
* * * **
39900353 TTATGGGTTTATGGTTTTTAATTTTAAGGGTTTAGAATTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAA-GTTAAGGG-TTAGGGTTTTTAAT
* ** * *
39900398 TTAAGGG-TTAGAGTTTTTAAGTTAAAAGTTAAGGTTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAT
* * * *
39900440 TTAAGGATTTAGTGTTTTTAATTTTAAGGGTTTAGGATTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAA-GTTAAGGG-TTAGGGTTTTTAAT
* ** *
39900485 TAAATTAGTTTAGAGTTTTTAAGTTAAGGGTTGAGGGTTTTTAATT
1 TTAA-GGGTTTAGGGTTTTTAAGTTAAGGGTT-AGGGTTTTTAA-T
** *
39900531 TTAAGAATTTAGGGGTTTTA
1 TTAAGGGTTTAGGGTTTTTA
39900551 GGTAATAACT
Statistics
Matches: 817, Mismatches: 140, Indels: 106
0.77 0.13 0.10
Matches are distributed among these distances:
42 38 0.05
43 81 0.10
44 137 0.17
45 358 0.44
46 163 0.20
47 4 0.00
50 1 0.00
51 31 0.04
52 2 0.00
53 2 0.00
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (43 bp):
TTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAT
Found at i:39901861 original size:20 final size:20
Alignment explanation
Indices: 39901824--39901861 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39901814 TTTATTTTTA
*
39901824 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
39901844 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
39901862 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:39902861 original size:11 final size:11
Alignment explanation
Indices: 39902847--39902923 Score: 61
Period size: 11 Copynumber: 6.9 Consensus size: 11
39902837 TTAAATATGG
39902847 ATTTGAGAGAA
1 ATTTGAGAGAA
**
39902858 ATTTG-GAAGGG
1 ATTTGAG-AGAA
39902869 ATTTGAGAGCAA
1 ATTTGAGAG-AA
39902881 A-TTGAGAGGAA
1 ATTTGAGA-GAA
39902892 ATTT-AGAGAA
1 ATTTGAGAGAA
* *
39902902 AATTAAGAGGAA
1 ATTTGAGA-GAA
39902914 ATTTGAGAGA
1 ATTTGAGAGA
39902924 GGATTAGTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
10 7 0.13
11 31 0.60
12 14 0.27
ACGTcount: A:0.44, C:0.01, G:0.30, T:0.25
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:39902904 original size:22 final size:23
Alignment explanation
Indices: 39902869--39902923 Score: 85
Period size: 22 Copynumber: 2.4 Consensus size: 23
39902859 TTTGGAAGGG
* *
39902869 ATTTGAGAGCAAATTGAGAGGAA
1 ATTTGAGAGAAAATTAAGAGGAA
39902892 ATTT-AGAGAAAATTAAGAGGAA
1 ATTTGAGAGAAAATTAAGAGGAA
39902914 ATTTGAGAGA
1 ATTTGAGAGA
39902924 GGATTAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.47, C:0.02, G:0.27, T:0.24
Consensus pattern (23 bp):
ATTTGAGAGAAAATTAAGAGGAA
Found at i:39903473 original size:23 final size:24
Alignment explanation
Indices: 39903447--39903496 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
39903437 AAGTTTCTCA
39903447 AATTAT-ATT-TATACAAAATTATT
1 AATTATCATTATATACAAAATT-TT
*
39903470 AATTATCATTATATACAAAGTTTT
1 AATTATCATTATATACAAAATTTT
39903494 AAT
1 AAT
39903497 GAAAAAGACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 6 0.25
24 8 0.33
25 10 0.42
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (24 bp):
AATTATCATTATATACAAAATTTT
Found at i:39906124 original size:26 final size:26
Alignment explanation
Indices: 39906053--39906124 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 26
39906043 TATGGGCTAG
* *
39906053 TTTGACAA-TGCTTTTAAAAAGTGAT
1 TTTGAAAAGTGCTTTTAAAAAATGAT
* * *
39906078 TTTGAAAAGTGACGTGT-AAAAATGCT
1 TTTGAAAAGTG-CTTTTAAAAAATGAT
*
39906104 TTTGAGAAGTGCTTTTAAAAA
1 TTTGAAAAGTGCTTTTAAAAA
39906125 GTTTGGTTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
25 10 0.28
26 23 0.64
27 3 0.08
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.36
Consensus pattern (26 bp):
TTTGAAAAGTGCTTTTAAAAAATGAT
Found at i:39912950 original size:5 final size:5
Alignment explanation
Indices: 39912940--39913023 Score: 168
Period size: 5 Copynumber: 16.8 Consensus size: 5
39912930 TACTGTTCAT
39912940 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
39912990 TATTA TATTA TATTA TATTA TATTA TATTA TATT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATT
39913024 GACAATTGAA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 79 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:39915997 original size:31 final size:31
Alignment explanation
Indices: 39915934--39915999 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
39915924 AAGTTGTGGA
* * *
39915934 TTTAGTCCCTGTATTTTTTGAATTTATCAAT
1 TTTAGTCCCTATACTTTTTGAATTTATAAAT
*
39915965 TTTAGTCTCTATACTTTTTGAATTT-TGAAAT
1 TTTAGTCCCTATACTTTTTGAATTTAT-AAAT
39915996 TTTA
1 TTTA
39916000 ATCTAGACCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.56
Consensus pattern (31 bp):
TTTAGTCCCTATACTTTTTGAATTTATAAAT
Found at i:39921420 original size:25 final size:25
Alignment explanation
Indices: 39921371--39921434 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
39921361 TTTAATTGAA
* **
39921371 TTTTAATAAATTTATATATTTTTAT-
1 TTTTAA-AATTTTATATATAATTATC
39921396 TTATTAAAATTTTATATATAATTATC
1 TT-TTAAAATTTTATATATAATTATC
*
39921422 TTTTAACATTTTA
1 TTTTAAAATTTTA
39921435 AATGTTTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 27 0.82
26 6 0.18
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTTAAAATTTTATATATAATTATC
Found at i:39927268 original size:9 final size:9
Alignment explanation
Indices: 39927254--39927281 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
39927244 AAACAATTCG
39927254 ATAATATAA
1 ATAATATAA
39927263 ATAATATAA
1 ATAATATAA
39927272 ATAATATAA
1 ATAATATAA
39927281 A
1 A
39927282 ATGTGAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
ATAATATAA
Found at i:39927574 original size:30 final size:31
Alignment explanation
Indices: 39927535--39927594 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
39927525 GGAGGTGGGA
*
39927535 TGGGAAGGGAATAAAAGTTTTAGGG-GAAAAG
1 TGGGAAGGGAATAAAAATTTT-GGGAGAAAAG
*
39927566 TGGG-AGGGAGTAAAAATTTTGGGAGAAAA
1 TGGGAAGGGAATAAAAATTTTGGGAGAAAA
39927595 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 19 0.73
31 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGGGAGAAAAG
Found at i:39927914 original size:9 final size:9
Alignment explanation
Indices: 39927897--39927927 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
39927887 TCGAGTTGAT
39927897 TCGAATAAC
1 TCGAATAAC
*
39927906 TCGATTAAC
1 TCGAATAAC
39927915 TCGAATAAC
1 TCGAATAAC
39927924 TCGA
1 TCGA
39927928 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:39934512 original size:49 final size:50
Alignment explanation
Indices: 39934410--39934601 Score: 260
Period size: 49 Copynumber: 3.8 Consensus size: 50
39934400 ATTTGGGTAA
*
39934410 AGAGGTCCCATGTAAGACCATGTGTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
39934460 AGAGGTCCCATGTAAGACCATGTCT-GGATATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
39934509 AGAGGTCCCCTGTAAGACCATGTCTAGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
39934559 AGAACATCTCATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
39934602 TGTTATTATC
Statistics
Matches: 124, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
49 46 0.37
50 46 0.37
51 32 0.26
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:39934544 original size:99 final size:101
Alignment explanation
Indices: 39934410--39934601 Score: 271
Period size: 99 Copynumber: 1.9 Consensus size: 101
39934400 ATTTGGGTAA
* * * * **
39934410 AGAGGTCCCATGTAAGACCATGTGTGGGACATGGCATTGGCACCGAGATGAG-AGGTCCCATGTA
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATGGGCACCGACATGAGAACATCCCATGTA
*
39934474 AGACCATGTCT-GGATATGGCGTTGGCACCGAGATG
66 AGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* *
39934509 AGAGGTCCCCTGTAAGACCATGTCTAGGACATGGCATGGGCACCGACATGAGAACATCTCATGTA
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATGGGCACCGACATGAGAACATCCCATGTA
* *
39934574 AGACCATGTTTGGGACATGGCTTTGGCA
66 AGACCATGTCTGGGACATGGCGTTGGCA
39934602 TGTTATTATC
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
99 47 0.59
100 19 0.24
101 14 0.17
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (101 bp):
AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATGGGCACCGACATGAGAACATCCCATGTA
AGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:39936850 original size:20 final size:21
Alignment explanation
Indices: 39936807--39936851 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
39936797 GTAAGGTGTT
*
39936807 AATATGCATAATGGAATAATA
1 AATATGCATAACGGAATAATA
39936828 AATATG-ATAACGTGAATAA-A
1 AATATGCATAACG-GAATAATA
39936848 AATA
1 AATA
39936852 ATATGAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.56, C:0.04, G:0.13, T:0.27
Consensus pattern (21 bp):
AATATGCATAACGGAATAATA
Found at i:39937213 original size:22 final size:23
Alignment explanation
Indices: 39937188--39937247 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
39937178 ATAAAAAAAA
*
39937188 CATATAATTATGTATATATAT-T
1 CATATAATTATGTATATAGATAT
* **
39937210 CATAAAAAAATGTATATAGATAT
1 CATATAATTATGTATATAGATAT
*
39937233 -ATATAGTTATGTATA
1 CATATAATTATGTATA
39937248 AAAATATGAG
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (23 bp):
CATATAATTATGTATATAGATAT
Found at i:39938060 original size:15 final size:15
Alignment explanation
Indices: 39938040--39938070 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
39938030 TGCATATAAG
39938040 AGAAAATAAATAAAA
1 AGAAAATAAATAAAA
39938055 AGAAAATAAATAAAA
1 AGAAAATAAATAAAA
39938070 A
1 A
39938071 AGGGGAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (15 bp):
AGAAAATAAATAAAA
Found at i:39939810 original size:28 final size:28
Alignment explanation
Indices: 39939774--39939833 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
39939764 GAAAGAAAGG
*
39939774 AAATTATATATGAA-AATAAATTTAAAAT
1 AAATAATATATGAATAA-AAATTTAAAAT
* *
39939802 AAATAATATATGAATGAAAATTTGAAAT
1 AAATAATATATGAATAAAAATTTAAAAT
39939830 AAAT
1 AAAT
39939834 TAAAAATACG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (28 bp):
AAATAATATATGAATAAAAATTTAAAAT
Found at i:39940202 original size:18 final size:18
Alignment explanation
Indices: 39940171--39940205 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39940161 ATAGATAAAT
39940171 AAACATATAAACTAATAC
1 AAACATATAAACTAATAC
39940189 AAACA-ATAATACTAATA
1 AAACATATAA-ACTAATA
39940206 ATTATAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.23
Consensus pattern (18 bp):
AAACATATAAACTAATAC
Found at i:39940231 original size:15 final size:15
Alignment explanation
Indices: 39940202--39940241 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
39940192 CAATAATACT
* *
39940202 AATAATTATAGTAAC
1 AATAATAATATTAAC
*
39940217 ATTAATAATATTAAC
1 AATAATAATATTAAC
39940232 AATAATAATA
1 AATAATAATA
39940242 AACAATAGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (15 bp):
AATAATAATATTAAC
Found at i:39948891 original size:23 final size:23
Alignment explanation
Indices: 39948857--39948905 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
39948847 TTCATATATA
*
39948857 TTTTAAAAAATATTATTCAGGTT
1 TTTTAAAAAATATTATTCAAGTT
* *
39948880 TTTTAAATAATATTATTTAAGTT
1 TTTTAAAAAATATTATTCAAGTT
39948903 TTT
1 TTT
39948906 CATTACATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (23 bp):
TTTTAAAAAATATTATTCAAGTT
Found at i:39949375 original size:39 final size:39
Alignment explanation
Indices: 39949247--39949381 Score: 119
Period size: 40 Copynumber: 3.4 Consensus size: 39
39949237 CGTTTGGACA
* * *
39949247 AAAAACGCCACTAAAAAATAAGCATTAGCGGCGCTTATAT
1 AAAAACGCCGCT-AAAAATAAGCATTAGCGGCGCTTTTTT
** * * * *
39949287 AAAAACGCCGCTAAAGGTCGAGAACTAGCGGCGCTTTTTG
1 AAAAACGCCGCTAAAAAT-AAGCATTAGCGGCGCTTTTTT
* * * *
39949327 GAAACCGCCGCTAAAAATAAGCATTAGTGGCGTTTTTTT
1 AAAAACGCCGCTAAAAATAAGCATTAGCGGCGCTTTTTT
*
39949366 AAAAGCGCCGC-AAAAA
1 AAAAACGCCGCTAAAAA
39949382 GTCTAAGCCC
Statistics
Matches: 73, Mismatches: 21, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
38 5 0.07
39 28 0.38
40 40 0.55
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATAAGCATTAGCGGCGCTTTTTT
Found at i:39949477 original size:41 final size:41
Alignment explanation
Indices: 39949418--39949658 Score: 367
Period size: 41 Copynumber: 5.9 Consensus size: 41
39949408 GAGTTTTTGG
*
39949418 GGCCTTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTCT
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT
*
39949459 GGCCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTCT
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT
*
39949500 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTTT
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT
* * *
39949541 GACCTTTAACGGCGTTTTTAAAAAAGCGCCGCTAATGCT-T
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT
* * * *
39949581 CGGCCTTTAGCAGCTTTTTTTAAAAAGCGCCGCTAATGCTCG
1 -GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT
*
39949623 GGCCTTTAGCGGCGTTTTTGAAAAAGCACCGCTAAT
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
39949659 AATAATAAAA
Statistics
Matches: 181, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
40 1 0.01
41 180 0.99
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.30
Consensus pattern (41 bp):
GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT
Found at i:39950763 original size:7 final size:7
Alignment explanation
Indices: 39950753--39950786 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
39950743 TAAGGTTTAA
39950753 GGGTTAG
1 GGGTTAG
39950760 GGGTTAG
1 GGGTTAG
*
39950767 GGGTTTG
1 GGGTTAG
*
39950774 GGGTTTG
1 GGGTTAG
39950781 GGGTTA
1 GGGTTA
39950787 AGAGTTAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.09, C:0.00, G:0.56, T:0.35
Consensus pattern (7 bp):
GGGTTAG
Found at i:39952002 original size:143 final size:142
Alignment explanation
Indices: 39951663--39952189 Score: 681
Period size: 143 Copynumber: 3.7 Consensus size: 142
39951653 ATTCCAAATG
* * * * *
39951663 AAAAACGCCGCAAAAGGTAAGCAATAGCGACGTTTTT-TAAAAAACGCCACAAAA-ATAATTTTA
1 AAAAACGCCACAATAGATAAGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAATA-AAATTTA
* * ** *
39951726 -TTTT--AAAAATAGCGCCATTTTATATAGCAAAACAGTGTCGTTTTATTCCAAATAAAATAATT
65 CTTTTAAAAAAATAGCACCATTTT-TTTA--AATTCA--CTCGTTTTATTCCAAATAAAATAATT
* *
39951788 TTTTGCCGCGTTTTTATAAA
125 TTTTGCGGCGTTTGTAT--A
*
39951808 AAAAACGCCGCAATAGATAAGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAATAAAATTTAC
1 AAAAACGCCACAATAGATAAGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAATAAAATTTAC
*
39951873 TTTTAAAAAAATAGCGCCATTTTTTTTAAATTCACTCGTTTTATTCCAAATAAAATAATTTTTTG
66 TTTTAAAAAAATAGCACCA-TTTTTTTAAATTCACTCGTTTTATTCCAAATAAAATAATTTTTTG
*
39951938 CGGCGTTTGTGTA
130 CGGCGTTTGTATA
*
39951951 AAAAACGCCACAATAGATAAGCAATAGCGGCGTTTTTATAAAAAATGCCACAAAATAAAATTTAC
1 AAAAACGCCACAATAGATAAGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAATAAAATTTAC
* * * *
39952016 TTTTAAAAAAATAGAATCATTTTTTTAAATTCTCTCG-TTTATTCCAAATAAAATAATTTTTTAC
66 TTTTAAAAAAATAGCACCATTTTTTTAAATTCACTCGTTTTATTCCAAATAAAATAATTTTTTGC
*
39952080 GGCATTTGTATA
131 GGCGTTTGTATA
* ** *
39952092 AAAAAC-ACAGCAATAGATAAAAAATAGCGGCGTTTTTATAAAAAAACGCTACAAAATAAAATTT
1 AAAAACGCCA-CAATAGATAAGCAATAGCGGCGTTTTTAT-AAAAAACGCCACAAAATAAAATTT
39952156 ACTTTTAAAAAAATAGCACCATTTTTTTAAATTC
64 ACTTTTAAAAAAATAGCACCATTTTTTTAAATTC
39952190 CCCACCCCCT
Statistics
Matches: 347, Mismatches: 27, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
140 2 0.01
141 69 0.20
142 71 0.20
143 80 0.23
145 73 0.21
146 23 0.07
147 9 0.03
149 16 0.05
150 4 0.01
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.32
Consensus pattern (142 bp):
AAAAACGCCACAATAGATAAGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAATAAAATTTAC
TTTTAAAAAAATAGCACCATTTTTTTAAATTCACTCGTTTTATTCCAAATAAAATAATTTTTTGC
GGCGTTTGTATA
Found at i:39952225 original size:21 final size:20
Alignment explanation
Indices: 39952199--39952243 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
39952189 CCCCACCCCC
*
39952199 TCCCCCCGAAATCCCCAACTT
1 TCCCCCCAAAATCCCCAA-TT
* *
39952220 TCCCCCTAAAATCCCTAATT
1 TCCCCCCAAAATCCCCAATT
39952240 TCCC
1 TCCC
39952244 ACGTCCAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.24, C:0.49, G:0.02, T:0.24
Consensus pattern (20 bp):
TCCCCCCAAAATCCCCAATT
Found at i:39955470 original size:12 final size:12
Alignment explanation
Indices: 39955453--39955482 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
39955443 ATTTATCACC
39955453 AATTTGCTTTAA
1 AATTTGCTTTAA
39955465 AATTTGCTTTAA
1 AATTTGCTTTAA
39955477 AATTTG
1 AATTTG
39955483 ATCTGTCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (12 bp):
AATTTGCTTTAA
Found at i:39956776 original size:43 final size:43
Alignment explanation
Indices: 39956701--39956809 Score: 146
Period size: 43 Copynumber: 2.5 Consensus size: 43
39956691 TAAAGATTAT
* * * * *
39956701 GTTTTTAGCGGCGTTTGTGATAAAAAGTGCCGCTAAAGGTTTTG
1 GTTTTTAGCGGCGTTTGTGGT-AAAAGCGCCGCTAAAAGTCTTA
39956745 GTTTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAAGTCTTA
1 GTTTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAAGTCTTA
* *
39956788 GTCTTTAGCAGCGTTTGTGGTA
1 GTTTTTAGCGGCGTTTGTGGTA
39956810 GGTCTTGGTC
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
43 38 0.66
44 20 0.34
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.36
Consensus pattern (43 bp):
GTTTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAAGTCTTA
Found at i:39958916 original size:30 final size:30
Alignment explanation
Indices: 39958852--39958909 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
39958842 TATTTAAGTT
*
39958852 AATTAAGTTATTCGGATCAACTTGAATAAA
1 AATTAAGTTATTCGGATCAACTCGAATAAA
* * *
39958882 AATTAAGTTTTTCGGTTTAACTCGAATA
1 AATTAAGTTATTCGGATCAACTCGAATA
39958910 TGAATTACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (30 bp):
AATTAAGTTATTCGGATCAACTCGAATAAA
Found at i:39959406 original size:29 final size:30
Alignment explanation
Indices: 39959347--39959410 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
39959337 ATTGGAATTG
* **
39959347 AATTTTAAAATATGAAAAGTAAAGAGTCTA
1 AATTCTAAAATATGAAAAGTAAAGAAACTA
* *
39959377 AATTCTAAAATAT-AAAATTATAGAAACTA
1 AATTCTAAAATATGAAAAGTAAAGAAACTA
39959406 AATTC
1 AATTC
39959411 CAAATCTACA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.55, C:0.06, G:0.08, T:0.31
Consensus pattern (30 bp):
AATTCTAAAATATGAAAAGTAAAGAAACTA
Found at i:39960156 original size:18 final size:18
Alignment explanation
Indices: 39960103--39960156 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
39960093 ATTCACCTAA
* *
39960103 ACCCAATCCAAACCCAAAT
1 ACCCAA-CCCAACCCAATT
*
39960122 ATCCAACCCAACCCAATT
1 ACCCAACCCAACCCAATT
39960140 ACCCAACCCAACCCAAT
1 ACCCAACCCAACCCAAT
39960157 CATAAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 26 0.84
19 5 0.16
ACGTcount: A:0.43, C:0.46, G:0.00, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAATT
Found at i:39960192 original size:6 final size:6
Alignment explanation
Indices: 39960184--39960233 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
39960174 ATTTAATAAA
* *
39960184 TAAAAA TAAAAT TATAAAAC TAAAAC TAAAAC TAAAAC TAAAATC TAAAA
1 TAAAAC TAAAAC TA-AAA-C TAAAAC TAAAAC TAAAAC TAAAA-C TAAAA
39960234 GTCTAAACAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
6 25 0.64
7 12 0.31
8 2 0.05
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.22
Consensus pattern (6 bp):
TAAAAC
Found at i:39960233 original size:7 final size:6
Alignment explanation
Indices: 39960198--39960233 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
39960188 AATAAAATTA
39960198 TAAAAC TAAAAC TAAAAC TAAAAC TAAAATC TAAAA
1 TAAAAC TAAAAC TAAAAC TAAAAC TAAAA-C TAAAA
39960234 GTCTAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.67, C:0.14, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAC
Found at i:39960373 original size:27 final size:27
Alignment explanation
Indices: 39960308--39960383 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
39960298 GTAGTGATTC
* *
39960308 AATTCGGTTAATTCGGGTAATTCGGGT
1 AATTCAGTTAATTCGGTTAATTCGGGT
*
39960335 AATTCAGTTAATTCAGTTAATTCGGGT
1 AATTCAGTTAATTCGGTTAATTCGGGT
* *
39960362 AATT-TGTATAATTTGGTTAATT
1 AATTCAGT-TAATTCGGTTAATT
39960384 TTTAACCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 2 0.05
27 40 0.95
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (27 bp):
AATTCAGTTAATTCGGTTAATTCGGGT
Found at i:39960384 original size:9 final size:9
Alignment explanation
Indices: 39960308--39960383 Score: 73
Period size: 9 Copynumber: 8.4 Consensus size: 9
39960298 GTAGTGATTC
39960308 AATTCGGTT
1 AATTCGGTT
*
39960317 AATTCGGGT
1 AATTCGGTT
*
39960326 AATTCGGGT
1 AATTCGGTT
*
39960335 AATTCAGTT
1 AATTCGGTT
*
39960344 AATTCAGTT
1 AATTCGGTT
*
39960353 AATTCGGGT
1 AATTCGGTT
*
39960362 AATT-TGTAT
1 AATTCGGT-T
*
39960371 AATTTGGTT
1 AATTCGGTT
39960380 AATT
1 AATT
39960384 TTTAACCAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
8 1 0.02
9 54 0.95
10 2 0.04
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:39964666 original size:41 final size:41
Alignment explanation
Indices: 39964617--39964766 Score: 210
Period size: 41 Copynumber: 3.6 Consensus size: 41
39964607 GACTTTAAGT
39964617 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
39964658 CTAGCAGGCTACGTGCCGATGATCTGAATCTGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
* * * **
39964699 CTAGCAGGCTACGTACCGGTGATCTGAATCAAGCTATAAGT
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
39964740 CTAGCAGGCTATGTGCCGTTGAATCTG
1 CTAGCAGGCTACGTGCCGGTG-ATCTG
39964767 TTTTAATTAA
Statistics
Matches: 96, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 91 0.95
42 5 0.05
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (41 bp):
CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:39971532 original size:12 final size:12
Alignment explanation
Indices: 39971515--39971567 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
39971505 TCGAATAAGC
39971515 ATGTATATATAT
1 ATGTATATATAT
39971527 ATGTATATATAT
1 ATGTATATATAT
*
39971539 AATGCTAGAATATAT
1 -ATG-TA-TATATAT
**
39971554 ATACATATATAT
1 ATGTATATATAT
39971566 AT
1 AT
39971568 AAGTTATTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 20 0.59
13 4 0.12
14 4 0.12
15 6 0.18
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (12 bp):
ATGTATATATAT
Found at i:39972278 original size:41 final size:41
Alignment explanation
Indices: 39972229--39972369 Score: 219
Period size: 41 Copynumber: 3.4 Consensus size: 41
39972219 GACTTTAAGT
*
39972229 CTAGCAGGCTACGTGCCGGTGATCTGAATCAAGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
39972270 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
* * * **
39972311 CTAGCAGGCTACGTACCGGTGATCTAAATCAGGCTATAAGT
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
*
39972352 CTAGCAGGCTATGTGCCG
1 CTAGCAGGCTACGTGCCG
39972370 TTGAATCTAT
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 92 1.00
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:39973157 original size:24 final size:24
Alignment explanation
Indices: 39973130--39973176 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
39973120 TTCATGTGAA
39973130 CATAGACTCATTCAGCTT-TAATTT
1 CATA-ACTCATTCAGCTTCTAATTT
*
39973154 CATATCTCATTCAGCTTCTAATT
1 CATAACTCATTCAGCTTCTAATT
39973177 CAATTTACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.28, C:0.23, G:0.06, T:0.43
Consensus pattern (24 bp):
CATAACTCATTCAGCTTCTAATTT
Found at i:39973977 original size:46 final size:46
Alignment explanation
Indices: 39973910--39974094 Score: 325
Period size: 46 Copynumber: 4.0 Consensus size: 46
39973900 ACATTGTTAT
* * *
39973910 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTAGTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
* *
39973956 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAT
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
39974002 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
39974048 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
39974094 A
1 A
39974095 CTTTGCCATG
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 133 1.00
ACGTcount: A:0.29, C:0.28, G:0.10, T:0.34
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
Found at i:39975367 original size:16 final size:17
Alignment explanation
Indices: 39975321--39975368 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
39975311 AAATTCTTTT
*
39975321 TAAACCACAAAATTCAA
1 TAAATCACAAAATTCAA
*
39975338 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAA
*
39975355 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
39975369 TTCTAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 7 0.25
17 21 0.75
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.25
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:39977889 original size:12 final size:11
Alignment explanation
Indices: 39977872--39977904 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
39977862 AGCATGCATG
39977872 CATACATAGATA
1 CATACATAG-TA
39977884 CATACATAGTA
1 CATACATAGTA
39977895 CATACA-AGTA
1 CATACATAGTA
39977905 TTTGCAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 4 0.19
11 8 0.38
12 9 0.43
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.24
Consensus pattern (11 bp):
CATACATAGTA
Found at i:39978069 original size:151 final size:149
Alignment explanation
Indices: 39977758--39978064 Score: 348
Period size: 151 Copynumber: 2.0 Consensus size: 149
39977748 AATATATTTG
* *
39977758 CAAGTTGCATAAGACCTCAAGAATGTATGGGAAAATAGCATTATACTAAATGTATGGGACCCATG
1 CAAG-TGCATAAGACCTCAAGAATGTATGGGAAAACAACATTATACTAAATGTATGGGACCCATG
* * * * * * *
39977823 AAACCTTCATTTACACAGATATATAGAAGCAAGCAAGCAAGCATGCATGCATACATAGATACATA
65 AAACCTTCATTTACACACACACACAGAACCAAGCAAGCAAGCATGCATGCATACATACACACATA
* *
39977888 CATAGTACATACAAGTATTTG
130 CATAGTACATAC-AGTATATA
* *
39977909 CAAGTTGCATAAGACCTCAAGAATGTATGGGAAAACAACATTATACTAAATGTATTGGACCTATG
1 CAAG-TGCATAAGACCTCAAGAATGTATGGGAAAACAACATTATACTAAATGTATGGGACCCATG
* * * *
39977974 AAGCCTTCATTTACATACACACACAGACATCCATA-CATGCAAGCATGCATGCATGCATTCACAC
65 AAACCTTCATTTACACACACACACAGA-A-CCA-AGCAAGCAAGCATGCATGCATACA-T-ACAC
* *
39978038 ATATACATATGTACGTAC-GTATATA
125 ACATACATA-GTACATACAGTATATA
39978063 CA
1 CA
39978065 TGCATGCATA
Statistics
Matches: 131, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
151 82 0.63
152 1 0.01
153 22 0.17
154 9 0.07
155 10 0.08
156 7 0.05
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.25
Consensus pattern (149 bp):
CAAGTGCATAAGACCTCAAGAATGTATGGGAAAACAACATTATACTAAATGTATGGGACCCATGA
AACCTTCATTTACACACACACACAGAACCAAGCAAGCAAGCATGCATGCATACATACACACATAC
ATAGTACATACAGTATATA
Found at i:39978257 original size:94 final size:94
Alignment explanation
Indices: 39978093--39978282 Score: 301
Period size: 94 Copynumber: 2.0 Consensus size: 94
39978083 TATCTAAAAG
* *
39978093 TATTTGTAAGTTGCATAAGACCTCAAGAATGTATGGGAAAACAGAATTATACTAAATGTATTGGA
1 TATTTGCAAGTTGCATAAGACCTCAAGAATGTATGGGAAAACAGAATTATACTAAATGTATGGGA
*
39978158 CCTATGAAACCTTCATTTACAAACATACA
66 CCTATGAAACCTTAATTTACAAACATACA
* *
39978187 TATTTGCAAGTTGCATAAGACCTCAAGAATGTATGGGACAACA-ACATTATGCTAAATGTATGGG
1 TATTTGCAAGTTGCATAAGACCTCAAGAATGTATGGGAAAACAGA-ATTATACTAAATGTATGGG
* *
39978251 ATCTATGAAACCTTAATTTACATACATACA
65 ACCTATGAAACCTTAATTTACAAACATACA
39978281 TA
1 TA
39978283 CGTACATACG
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
93 1 0.01
94 87 0.99
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (94 bp):
TATTTGCAAGTTGCATAAGACCTCAAGAATGTATGGGAAAACAGAATTATACTAAATGTATGGGA
CCTATGAAACCTTAATTTACAAACATACA
Found at i:39979499 original size:31 final size:31
Alignment explanation
Indices: 39979398--39979508 Score: 111
Period size: 31 Copynumber: 3.6 Consensus size: 31
39979388 TTGCATTTTG
* *
39979398 GAAAA-TTTGGAAAATTTTCATTTCTCCCTT
1 GAAAATTTTTGAAAATTTTCATTTTTCCCTT
* * * *
39979428 GAAAAGTTTAGAAAATTTTAATTAGGTTCCC-T
1 GAAAATTTTTGAAAATTTTCATT--TTTCCCTT
39979460 -AAAATTTTTGAAAATTTTCATTTTTCCCTT
1 GAAAATTTTTGAAAATTTTCATTTTTCCCTT
* *
39979490 GAAATTTTTTGAAATTTTT
1 GAAAATTTTTGAAAATTTT
39979509 AATTAAACTC
Statistics
Matches: 66, Mismatches: 10, Indels: 9
0.78 0.12 0.11
Matches are distributed among these distances:
29 5 0.08
30 6 0.09
31 50 0.76
32 1 0.02
33 4 0.06
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.47
Consensus pattern (31 bp):
GAAAATTTTTGAAAATTTTCATTTTTCCCTT
Found at i:39983233 original size:12 final size:12
Alignment explanation
Indices: 39983216--39983240 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39983206 GCACCAGTTT
39983216 CTCATTTATACC
1 CTCATTTATACC
39983228 CTCATTTATACC
1 CTCATTTATACC
39983240 C
1 C
39983241 CTAGCTGGAC
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:0.24, C:0.36, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCATTTATACC
Found at i:39990375 original size:3 final size:3
Alignment explanation
Indices: 39990367--39990392 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39990357 TGTGTTAAAA
39990367 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
39990393 ATAATACTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:39991532 original size:35 final size:35
Alignment explanation
Indices: 39991466--39991532 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
39991456 CAAACACCAG
*
39991466 AAAATATTTTCCAGTAAATCATTTTACAAAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAAAAAAGT
39991501 AAAACATTTTCCAG-AAATCATTTTACAAAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAAAAAA
39991533 CATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 18 0.58
35 13 0.42
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAAAAAAGT
Found at i:39991539 original size:14 final size:14
Alignment explanation
Indices: 39991501--39991540 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
39991491 ACAAAAAAGT
* *
39991501 AAAACATTTTCCAG
1 AAAACATTTTACAA
*
39991515 AAATCATTTTACAA
1 AAAACATTTTACAA
39991529 AAAACATTTTAC
1 AAAACATTTTAC
39991541 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAA
Found at i:39994165 original size:3 final size:3
Alignment explanation
Indices: 39994130--39994213 Score: 64
Period size: 3 Copynumber: 27.3 Consensus size: 3
39994120 ATAAGAAAAC
* * * * *
39994130 ATA ATA CTA ACA ATA GTA TTA ATA A-A TATA ATA ATA ATA GTA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
*
39994174 GATA ATA ATG ATA ATA ATA ATA ATA ACTAA ATA ATA ATA A
1 -ATA ATA ATA ATA ATA ATA ATA ATA A-T-A ATA ATA ATA A
39994214 AAAATTGCTA
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
2 2 0.03
3 56 0.88
4 4 0.06
5 2 0.03
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:39995801 original size:44 final size:44
Alignment explanation
Indices: 39995695--39996675 Score: 417
Period size: 44 Copynumber: 22.8 Consensus size: 44
39995685 AATTCCTCGG
* * * *
39995695 TCTGTTCCACTGTAATCTCAGGGAGATAAGA-CC-TGA-TGCGA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTCAA
* ** * *
39995736 TCTACTCTGCTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAA
1 TCTGCTCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTCAA
* * * * * *
39995780 TCCGCTCCACTGTAATCTCAGAGAGATAGGAT--TACTAGCTTCGA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTCAA
* * *
39995824 TCTACTCCACTGTAATCTCAGGGAGATAAGA-CC-TGA-TACAA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTCAA
* * * *
39995865 TCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAA
1 TCTGCTCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTCAA
* * *
39995909 TCTGCTCCACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTCAA
* * * *
39995953 TTTGCTCCGCTATAATCTCAGGGAGATAAGAT-CTGAAATT-TTTCGA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT----TTATTTCAA
* * ** * *
39995999 TCTGTTCCACTGTAATCTCAGGGAAATAAGA-CC--TGGTGCGA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTCAA
* * * *
39996040 TCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAA
1 TCTGCTCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTCAA
* * * *
39996084 TCTGCTCCACTGTAATATCAGGGAGATAGGAT--TACTAGCTTCAA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTCAA
* ** **
39996128 TCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-CTGAAATTCTTCGG
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-T-TTCAA
* * ** * *
39996174 TCTGTTCCACTGTAATCTCAGGGAAATAAGA-CC--TGGTGCGA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTCAA
* * *
39996215 TCTGCTCTACTTTAA-CTTCAGAGAGATAAGATCC----TTT-AA
1 TCTGCTCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTCAA
* * * *
39996254 TCCGCTCCACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTCAA
* * * *
39996298 TTTGCTCCGCTATAATCTCAGGGAGATAAGAT-CTGAAATT-TTTCGA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT----TTATTTCAA
* * ** * *
39996344 TCTGTTCCACTGTAATCTCAGGGAAATAAGA-CC--TGGTGCGA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTCAA
* * * *
39996385 TCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAA
1 TCTGCTCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTCAA
* * * * *
39996429 TCTGCTCCACTGTAATATTAGGGAGATAGGAT--TACTAGCTTCAA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTCAA
* ** **
39996473 TCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-CTGAAATTCTTCGG
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-T-TTCAA
* * ** * *
39996519 TCTGTTCCACTGTAATCTCAGGGAAATAAGA-CC--TGGTGCGA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTCAA
* * *
39996560 TCTGCTCTACTTTAA-CTTCAGAGAGATAAGATCC----TTT-AA
1 TCTGCTCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTCAA
* * * *
39996599 TCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATA-TTCAA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGA-TCCTTTATTTCAA
** *
39996643 TCTGCTCCGTTGTAATATCAGGGAGATAAGATC
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATC
39996676 TGCAATTCTT
Statistics
Matches: 698, Mismatches: 175, Indels: 132
0.69 0.17 0.13
Matches are distributed among these distances:
39 51 0.07
40 14 0.02
41 164 0.23
42 16 0.02
43 18 0.03
44 297 0.43
45 8 0.01
46 126 0.18
48 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (44 bp):
TCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTCAA
Found at i:39996000 original size:175 final size:175
Alignment explanation
Indices: 39995818--39996720 Score: 1466
Period size: 175 Copynumber: 5.2 Consensus size: 175
39995808 GGATTACTAG
** * * * *
39995818 CTTCGATCTACTCCACTGTAATCTCAGGGAGATAAGACCTGATACAATCTACTCTACTGTAACTT
1 CTTCGATCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTT
39995883 CAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGC
66 CAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGC
* *
39995948 TTCAATTTGCTCCGCTATAATCTCAGGGAGATAAGATCTGAAATT
131 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
*
39995993 TTTCGATCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTT
1 CTTCGATCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTT
*
39996058 CAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATATCAGGGAGATAGGATTACTAGC
66 CAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGC
39996123 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
131 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
* * *
39996168 CTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTTTAACTT
1 CTTCGATCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTT
*
39996233 CAGAGAGATAAGATCC-----TTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGC
66 CAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGC
* *
39996293 TTCAATTTGCTCCGCTATAATCTCAGGGAGATAAGATCTGAAATT
131 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
*
39996338 TTTCGATCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTT
1 CTTCGATCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTT
* *
39996403 CAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATATTAGGGAGATAGGATTACTAGC
66 CAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGC
39996468 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
131 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
* * *
39996513 CTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTTTAACTT
1 CTTCGATCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTT
* **
39996578 CAGAGAGATAAGATCC-----TTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATA
66 CAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGC
* * *
39996638 TTCAATCTGCTCCGTTGTAATATCAGGGAGATAAGATCTGCAATT
131 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
* *
39996683 CTTCGGTCTGTTCCACCGTAATCTCAGGGAAATAAGAC
1 CTTCGATCTGTTCCACTGTAATCTCAGGGAAATAAGAC
39996721 TTGTATAATG
Statistics
Matches: 683, Mismatches: 40, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
170 280 0.41
175 403 0.59
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (175 bp):
CTTCGATCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTT
CAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGC
TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
Found at i:39996334 original size:345 final size:345
Alignment explanation
Indices: 39995829--39996720 Score: 1577
Period size: 345 Copynumber: 2.6 Consensus size: 345
39995819 TTCGATCTAC
* * * * * *
39995829 TCCACTGTAATCTCAGGGAGATAAGACCTGATACAATCTACTCTACTGTAACTTCAGAGAGATAA
1 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTTTAACTTCAGAGAGATAA
*
39995894 GATCCTTTATTTTAATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATTTGCT
66 GATCC-----TTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATTTGCT
39995959 CCGCTATAATCTCAGGGAGATAAGATCTGAAATTTTTCGATCTGTTCCACTGTAATCTCAGGGAA
126 CCGCTATAATCTCAGGGAGATAAGATCTGAAATTTTTCGATCTGTTCCACTGTAATCTCAGGGAA
39996024 ATAAGACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGC
191 ATAAGACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGC
39996089 TCCACTGTAATATCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA
256 TCCACTGTAATATCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA
39996154 TAAGATCTGAAATTCTTCGGTCTGT
321 TAAGATCTGAAATTCTTCGGTCTGT
39996179 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTTTAACTTCAGAGAGATAA
1 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTTTAACTTCAGAGAGATAA
39996244 GATCCTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATTTGCTCCGCT
66 GATCCTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATTTGCTCCGCT
39996309 ATAATCTCAGGGAGATAAGATCTGAAATTTTTCGATCTGTTCCACTGTAATCTCAGGGAAATAAG
131 ATAATCTCAGGGAGATAAGATCTGAAATTTTTCGATCTGTTCCACTGTAATCTCAGGGAAATAAG
39996374 ACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCAC
196 ACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCAC
*
39996439 TGTAATATTAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
261 TGTAATATCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
39996504 TCTGAAATTCTTCGGTCTGT
326 TCTGAAATTCTTCGGTCTGT
39996524 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTTTAACTTCAGAGAGATAA
1 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTTTAACTTCAGAGAGATAA
** * *
39996589 GATCCTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATATTCAATCTGCTCCGTT
66 GATCCTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATTTGCTCCGCT
* * * * * *
39996654 GTAATATCAGGGAGATAAGATCTGCAATTCTTCGGTCTGTTCCACCGTAATCTCAGGGAAATAAG
131 ATAATCTCAGGGAGATAAGATCTGAAATTTTTCGATCTGTTCCACTGTAATCTCAGGGAAATAAG
39996719 AC
196 AC
39996721 TTGTATAATG
Statistics
Matches: 524, Mismatches: 18, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
345 460 0.88
350 64 0.12
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (345 bp):
TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTTTAACTTCAGAGAGATAA
GATCCTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATTTGCTCCGCT
ATAATCTCAGGGAGATAAGATCTGAAATTTTTCGATCTGTTCCACTGTAATCTCAGGGAAATAAG
ACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCAC
TGTAATATCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
TCTGAAATTCTTCGGTCTGT
Found at i:39996502 original size:129 final size:129
Alignment explanation
Indices: 39995695--39996508 Score: 561
Period size: 129 Copynumber: 6.3 Consensus size: 129
39995685 AATTCCTCGG
* * **
39995695 TCTGTTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAA-CTTCAGAG
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATGCAATCTACTCCACTGTAATC-TCAGAG
* * * *
39995759 AGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGAGAGATAGGATTACTAGCTTCGA
65 AGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAA
* * *
39995824 TCTACTCCACTGTAATCTCAGGGAGATAAGACCTGATACAATCTACTCTACTGTAA-CTTCAGAG
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATGCAATCTACTCCACTGTAATC-TCAGAG
*
39995888 AGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAA
65 AGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAA
* * * * * * **
39995953 TTTGCTCCGCTATAATCTCAGGGAGATAAGATCTGAAATTTTTCGATCTGTTCCACTGTAATCTC
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGACCTG--A---TGCAATCTACTCCACTGTAATCTC
* * ** *** * * * *
39996018 AGGGAAATAAGA-CC--TGGTGCGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTA
61 AGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT--TACTA
* *
39996078 -TTTTAA
123 GCTTCAA
* * * * * * *
39996084 TCTGCTCCACTGTAATATCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAG
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGA--CCT-GATGCAATCTACTCCACTGTAATCTCAG
* ** ** * * * *
39996149 GGAGATAAGAT-CTGAAATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGA--CCT-GG
63 AGAGATAAGATCCT-TTATT-TT-AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGC
* *
39996210 TGCGA
125 TTCAA
* * * * ** *
39996215 TCTGCTCTACTTTAA-CTTCAGAGAGATAAGATCCT--T-TAATCCGCTCCACTGTAATCTCAGG
1 TCTGCTCCACTGTAATC-TCAGGGAGATAAGA-CCTGATGCAATCTACTCCACTGTAATCTCAGA
* * * * * * * * *
39996276 GAGATAGGAT--TACTAGCTTCAATTTGCTCCGCTATAATCTCAGGGAGATAAGATCTGA-AATT
64 GAGATAAGATCCT-TTA-TTTTAATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-G
* *
39996338 TTTCGA
124 CTTCAA
* * * * *
39996344 TCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAA-CTTCAGAG
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATGCAATCTACTCCACTGTAATC-TCAGAG
* * *
39996408 AGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATATTAGGGAGATAGGATTACTAGCTTCAA
65 AGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAA
* *
39996473 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGA
39996509 AATTCTTCGG
Statistics
Matches: 532, Mismatches: 116, Indels: 74
0.74 0.16 0.10
Matches are distributed among these distances:
124 26 0.05
125 3 0.01
126 32 0.06
127 1 0.00
128 3 0.01
129 248 0.47
130 9 0.02
131 144 0.27
132 5 0.01
133 6 0.01
134 53 0.10
135 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (129 bp):
TCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATGCAATCTACTCCACTGTAATCTCAGAGA
GATAAGATCCTTTATTTTAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAA
Found at i:40003230 original size:3 final size:3
Alignment explanation
Indices: 40003195--40003278 Score: 64
Period size: 3 Copynumber: 27.3 Consensus size: 3
40003185 ATAAGAAAAC
* * * * *
40003195 ATA ATA CTA AAA ATA GTA TTA ATA A-A TATA ATA ATA ATA GTA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
*
40003239 GATA ATA ATG ATA ATA ATA ATA ATA ACTAA ATA ATA ATA A
1 -ATA ATA ATA ATA ATA ATA ATA ATA A-T-A ATA ATA ATA A
40003279 AAAATTGCTA
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
2 2 0.03
3 56 0.88
4 4 0.06
5 2 0.03
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:40005989 original size:21 final size:21
Alignment explanation
Indices: 40005963--40006016 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
40005953 CGGGCTAGGC
*
40005963 CAAGCTCGAACCTTAAATGTT
1 CAAGCTCGAACCTTAAACGTT
40005984 CAAGCTCGAACCTTAAACGTT
1 CAAGCTCGAACCTTAAACGTT
* *
40006005 TAAGCTTGAACC
1 CAAGCTCGAACC
40006017 CGGCCCATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (21 bp):
CAAGCTCGAACCTTAAACGTT
Found at i:40006566 original size:33 final size:33
Alignment explanation
Indices: 40006529--40006593 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
40006519 CTAGGATTAG
40006529 TCGAATTAAATTGAACTTTAAACTTCAAAATGT
1 TCGAATTAAATTGAACTTTAAACTTCAAAATGT
*
40006562 TCGAATTAAATTGATCTTTAAACTTCAAAATG
1 TCGAATTAAATTGAACTTTAAACTTCAAAATG
40006594 GTTTAATTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (33 bp):
TCGAATTAAATTGAACTTTAAACTTCAAAATGT
Found at i:40006969 original size:24 final size:24
Alignment explanation
Indices: 40006923--40006969 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
40006913 TTTTTTTTCA
*
40006923 AATCGACTTTAGTTGAGTAAATTG
1 AATCGACTTTAGTTCAGTAAATTG
*
40006947 AATCGACTTT-GATTCAGTCAATT
1 AATCGACTTTAG-TTCAGTAAATT
40006970 TTATTTAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (24 bp):
AATCGACTTTAGTTCAGTAAATTG
Found at i:40013695 original size:25 final size:25
Alignment explanation
Indices: 40013658--40013743 Score: 68
Period size: 25 Copynumber: 3.3 Consensus size: 25
40013648 CATAATTGAA
**
40013658 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATATATTGATTTTGTATATT
* *
40013683 ATGAAATATATTGATTATGAATATT
1 ATGAAATATATTGATTTTGTATATT
40013708 GAATTG-AATATATGTGATATTGTGTATA-T
1 --A-TGAAATATAT-TGAT-TT-TGTATATT
40013737 ATGAAAT
1 ATGAAAT
40013744 TGAGACATTG
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
25 21 0.44
26 2 0.04
27 12 0.25
28 6 0.12
29 2 0.04
30 5 0.10
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.44
Consensus pattern (25 bp):
ATGAAATATATTGATTTTGTATATT
Found at i:40014125 original size:27 final size:27
Alignment explanation
Indices: 40014095--40014149 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
40014085 TGAAATGAAT
*
40014095 ATGAGACGAGAAATGAAATATGAAATA
1 ATGAAACGAGAAATGAAATATGAAATA
* ** *
40014122 ATGAAATGAGATGTGAATTATGAAATA
1 ATGAAACGAGAAATGAAATATGAAATA
40014149 A
1 A
40014150 AATCGAGTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.22, T:0.24
Consensus pattern (27 bp):
ATGAAACGAGAAATGAAATATGAAATA
Found at i:40018285 original size:56 final size:56
Alignment explanation
Indices: 40018149--40018285 Score: 154
Period size: 56 Copynumber: 2.4 Consensus size: 56
40018139 AAATGGAAGT
** *
40018149 ATAAGTAATATCGAATTTAAATA-TTAAAAAATAAAAGAATAATAAATAAATAGGTAA
1 ATAAGTAATATTAAATTTAAGTATTTAAAAAATAAAAGAATAATAAATAAATA-G-AA
** * *
40018206 A-ACAAAAATATTAAATTTAAGTATTTAAAAAGTAAAAGAATAAATAAATGAATA-AA
1 ATA-AGTAATATTAAATTTAAGTATTTAAAAAATAAAAGAAT-AATAAATAAATAGAA
40018262 ATAAGTAATATTAAATTTAAGTAT
1 ATAAGTAATATTAAATTTAAGTAT
40018286 ATGAGAAATA
Statistics
Matches: 67, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
56 23 0.34
57 17 0.25
58 16 0.24
59 11 0.16
ACGTcount: A:0.61, C:0.01, G:0.08, T:0.30
Consensus pattern (56 bp):
ATAAGTAATATTAAATTTAAGTATTTAAAAAATAAAAGAATAATAAATAAATAGAA
Found at i:40019904 original size:44 final size:43
Alignment explanation
Indices: 40019854--40020542 Score: 190
Period size: 45 Copynumber: 15.3 Consensus size: 43
40019844 ATTTTAACCT
* *
40019854 ACTGCAACTTTAGGGGTATAAA-ACTTGTAGTTTTAATCTACTCC
1 ACTGCAACTTTAGGGG-A-AAAGACTTGTAGCTTCAATCTACTCC
*
40019898 ACTGCAACTTCA-GGGAAAAGACTTGTAGCTTCAATCTACTCC
1 ACTGCAACTTTAGGGGAAAAGACTTGTAGCTTCAATCTACTCC
* * * * ** *
40019940 ACTGCAACTTTAGAGAGGTAAGATCTGTAACTTGTATCTTTAATATGTTAC
1 ACTGCAACTTTAG-G-GG-AA-A--AG--ACTTGTAGCTTCAATCTACTCC
* * * ** * *
40019991 ACTACAACTTTAGGGAGATACGATTTGCTATGGTAAATTTAATCCGAC-CC
1 ACTGCAACTTTAGGG-GAAAAGA----CT-T-GTAGCTTCAAT-CTACTCC
* * * * * **
40020041 ACTACAACTTCAGAGGTATAGGA-TT-TATTTTCAATCTACTCC
1 ACTGCAACTTTAG-GGGAAAAGACTTGTAGCTTCAATCTACTCC
* * * * *
40020083 GCTGCAA-TTTCAGGGAGATAAGACTTGTAGATTTAATCTTGCTCC
1 ACTGCAACTTT-AGGG-GAAAAGACTTGTAGCTTCAATC-TACTCC
* * * * *
40020128 ACTGCAACTTTAGAGAGATAAGATTTGTAACTTTAATCTACTCC
1 ACTGCAACTTTAG-GGGAAAAGACTTGTAGCTTCAATCTACTCC
* * * * * *
40020172 ACTGCAACTTCAGGGAGATAAGATTTGT-GACTTCAATCTGCGCT
1 ACTGCAACTTTAGGG-GAAAAGACTTGTAG-CTTCAATCTACTCC
* * * * * * *
40020216 ACAGCAATTTTAGAGTGATAAGATTTGCTATCTTCAATCTGCTCC
1 ACTGCAACTTTAG-GGGAAAAGACTTG-TAGCTTCAATCTACTCC
* * ** * * *
40020261 ACTGCAACTTCAGGGAGATAAGTTTTGCTATCTTCAATTTGCTCC
1 ACTGCAACTTTAGGG-GAAAAGACTTG-TAGCTTCAATCTACTCC
* * * * * *
40020306 ACTGCAACTTTAGGGAGATAAGATTTGTGGTTTTAATCTGCTCC
1 ACTGCAACTTTAGGG-GAAAAGACTTGTAGCTTCAATCTACTCC
* * * *
40020350 ACTGCAACTTCAGGGAGATAAGA-TTGGT-GACTTCAATCTGCTCT
1 ACTGCAACTTTAGGG-GAAAAGACTT-GTAG-CTTCAATCTACTCC
* * * * ** *
40020394 ACTGCAATTTTAGAGTGATAAGATTTGCTATATTCAATCTGCTCC
1 ACTGCAACTTTAG-GGGAAAAGACTTG-TAGCTTCAATCTACTCC
* * * * * * *
40020439 ACCGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTGCTCC
1 ACTGCAACTTTAG-GGGAAAAGACTTG-TAGCTTCAATCTACTCC
* * * * * * * * *
40020484 ACTGCAACTTCAAGGAGATAAGATTTGTGGTTTTAATTTGCTCC
1 ACTGCAACTT-TAGGGGAAAAGACTTGTAGCTTCAATCTACTCC
40020528 ACTGCAACTTTAGGG
1 ACTGCAACTTTAGGG
40020543 AGATAAGATT
Statistics
Matches: 511, Mismatches: 94, Indels: 81
0.74 0.14 0.12
Matches are distributed among these distances:
41 10 0.02
42 53 0.10
43 12 0.02
44 171 0.33
45 189 0.37
46 9 0.02
47 1 0.00
48 3 0.01
49 4 0.01
50 29 0.06
51 30 0.06
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (43 bp):
ACTGCAACTTTAGGGGAAAAGACTTGTAGCTTCAATCTACTCC
Found at i:40019934 original size:42 final size:44
Alignment explanation
Indices: 40019854--40019949 Score: 135
Period size: 42 Copynumber: 2.2 Consensus size: 44
40019844 ATTTTAACCT
* * *
40019854 ACTGCAACTTTAGGGGTATAAAACTTGTAGTTTTAATCTACTCC
1 ACTGCAACTTCAGGGGTATAAAACTTGTAGCTTCAATCTACTCC
40019898 ACTGCAACTTCA-GGG-A-AAAGACTTGTAGCTTCAATCTACTCC
1 ACTGCAACTTCAGGGGTATAAA-ACTTGTAGCTTCAATCTACTCC
40019940 ACTGCAACTT
1 ACTGCAACTT
40019950 TAGAGAGGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
41 3 0.06
42 31 0.65
43 3 0.06
44 11 0.23
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (44 bp):
ACTGCAACTTCAGGGGTATAAAACTTGTAGCTTCAATCTACTCC
Found at i:40020148 original size:45 final size:44
Alignment explanation
Indices: 40020070--40020554 Score: 483
Period size: 45 Copynumber: 10.9 Consensus size: 44
40020060 AGGATTTATT
* * *
40020070 TTCAATCTACTCCGCTGCAA-TTTCAGGGAGATAAGACTTGTAGA
1 TTCAATCTGCTCCACTGCAACTTT-AGGGAGATAAGATTTGTAGA
* *
40020114 TTTAATCTTGCTCCACTGCAACTTTAGAGAGATAAGATTTGTA-A
1 TTCAATC-TGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAGA
* * *
40020158 CTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGT-GA
1 -TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAGA
* * * * * * **
40020202 CTTCAATCTGCGCTACAGCAATTTTAGAGTGATAAGATTTGCTATC
1 -TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTG-TAGA
* * **
40020248 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGTTTTGCTATC
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTG-TAGA
* * *
40020293 TTCAATTTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTGGT
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAGA
* * *
40020337 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGT-GA
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAGA
* * * * *
40020380 CTTCAATCTGCTCTACTGCAATTTTAGAGTGATAAGATTTGCTATA
1 -TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTG-TAGA
* * * **
40020426 TTCAATCTGCTCCACCGCAACTTCAGAGAGATAAGATTTGCTATC
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTG-TAGA
* * * *
40020471 TTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTGGT
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAGA
* *
40020515 TTTAATTTGCTCCACTGCAACTTTAGGGAGATAAGATTTG
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTG
40020555 CCATGATAAC
Statistics
Matches: 370, Mismatches: 62, Indels: 18
0.82 0.14 0.04
Matches are distributed among these distances:
43 1 0.00
44 179 0.48
45 186 0.50
46 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (44 bp):
TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAGA
Found at i:40020178 original size:89 final size:88
Alignment explanation
Indices: 40019854--40020554 Score: 553
Period size: 89 Copynumber: 7.8 Consensus size: 88
40019844 ATTTTAACCT
* * * ** *
40019854 ACTGCAACTTTAG-GGGTATAAAACTTGTAGTTTTAATCTACTCCACTGCAACTTCAGGGA-A-A
1 ACTGCAACTTTAGAGAG-ATAAGATTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATA
* * *
40019916 AGACTTGTAGCTTCAATCTACTCC
65 AGATTTGTAGATTCAATCTGCTCC
* * * * * * *
40019940 ACTGCAACTTTAGAGAGGTAAGATCTGTAACTTGTATCTTTAATATGTTACACTACAACTTTAGG
1 ACTGCAACTTTAGAGAGATAAGA----T---TTGTAACTTTAATCTGCTCCACTGCAACTTCAGG
* * *
40020005 GAGATACGATTTGCTATGGTAAATTTAATCCGAC-CC
59 GAGATAAGATTTG-TA--G---ATTCAATCTG-CTCC
* * * * * * *
40020041 ACTACAACTTCAGAG-GTATAGGA-TT-T-ATTTTCAATCTACTCCGCTGCAATTTCAGGGAGAT
1 ACTGCAACTTTAGAGAG-ATAAGATTTGTAACTTT-AATCTGCTCCACTGCAACTTCAGGGAGAT
* *
40020102 AAGACTTGTAGATTTAATCTTGCTCC
64 AAGATTTGTAGATTCAATC-TGCTCC
*
40020128 ACTGCAACTTTAGAGAGATAAGATTTGTAACTTTAATCTACTCCACTGCAACTTCAGGGAGATAA
1 ACTGCAACTTTAGAGAGATAAGATTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
* *
40020193 GATTTGT-GACTTCAATCTGCGCT
66 GATTTGTAGA-TTCAATCTGCTCC
* * * * *
40020216 ACAGCAATTTTAGAGTGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATA
1 ACTGCAACTTTAGAGAGATAAGATTTG-TAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATA
* ** *
40020281 AGTTTTGCTATCTTCAATTTGCTCC
65 AGATTTG-TAGATTCAATCTGCTCC
* ***
40020306 ACTGCAACTTTAGGGAGATAAGATTTGTGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
1 ACTGCAACTTTAGAGAGATAAGATTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
* *
40020371 GATTGGT-GACTTCAATCTGCTCT
66 GATTTGTAGA-TTCAATCTGCTCC
* * * * *
40020394 ACTGCAATTTTAGAGTGATAAGATTTGCTATA-TTCAATCTGCTCCACCGCAACTTCAGAGAGAT
1 ACTGCAACTTTAGAGAGATAAGATTTG-TA-ACTTTAATCTGCTCCACTGCAACTTCAGGGAGAT
**
40020458 AAGATTTGCTATCTTCAATCTGCTCC
64 AAGATTTG-TAGATTCAATCTGCTCC
* *** * *
40020484 ACTGCAACTTCA-AGGAGATAAGATTTGTGGTTTTAATTTGCTCCACTGCAACTTTAGGGAGATA
1 ACTGCAACTTTAGA-GAGATAAGATTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATA
40020548 AGATTTG
65 AGATTTG
40020555 CCATGATAAC
Statistics
Matches: 486, Mismatches: 93, Indels: 69
0.75 0.14 0.11
Matches are distributed among these distances:
86 26 0.05
87 23 0.05
88 69 0.14
89 195 0.40
90 73 0.15
91 5 0.01
92 28 0.06
93 30 0.06
94 1 0.00
95 6 0.01
96 2 0.00
98 1 0.00
100 1 0.00
101 25 0.05
102 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (88 bp):
ACTGCAACTTTAGAGAGATAAGATTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
GATTTGTAGATTCAATCTGCTCC
Found at i:40020276 original size:178 final size:179
Alignment explanation
Indices: 40020070--40020554 Score: 735
Period size: 178 Copynumber: 2.7 Consensus size: 179
40020060 AGGATTTATT
* * * * ** *
40020070 TTCAATCTACTCCGCTGCAATTTCAGGGAGATAAGACTTG-TAGATTTAATCTTGCTCCACTGCA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTTGCTCCACTGCA
*** *
40020134 ACTTTAGAGAGATAAGATTTGTAACTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTG
66 ACTTTAGAGAGATAAGATTTGTGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG
*
40020199 TGACTTCAATCTGCGCTACAGCAATTTTAGAGTGATAAGATTTGCTATC
131 TGACTTCAATCTGCGCTACAGCAATTTTAGAGTGATAAGATTTGCTATA
*
40020248 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGTTTTGCTATCTTCAAT-TTGCTCCACTGCA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTTGCTCCACTGCA
* *
40020312 ACTTTAGGGAGATAAGATTTGTGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGG
66 ACTTTAGAGAGATAAGATTTGTGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG
* *
40020377 TGACTTCAATCTGCTCTACTGCAATTTTAGAGTGATAAGATTTGCTATA
131 TGACTTCAATCTGCGCTACAGCAATTTTAGAGTGATAAGATTTGCTATA
* *
40020426 TTCAATCTGCTCCACCGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATC-TGCTCCACTGCA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTTGCTCCACTGCA
* * *
40020490 ACTTCA-AGGAGATAAGATTTGTGGTTTTAATTTGCTCCACTGCAACTTTAGGGAGATAAGATTT
66 ACTTTAGA-GAGATAAGATTTGTGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT
40020554 G
130 G
40020555 CCATGATAAC
Statistics
Matches: 279, Mismatches: 25, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
178 272 0.97
179 7 0.03
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (179 bp):
TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTTGCTCCACTGCA
ACTTTAGAGAGATAAGATTTGTGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG
TGACTTCAATCTGCGCTACAGCAATTTTAGAGTGATAAGATTTGCTATA
Found at i:40032466 original size:19 final size:20
Alignment explanation
Indices: 40032439--40032492 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
40032429 ATCGAATTTT
*
40032439 AATATTAAAAAAATAAA-AG
1 AATAATAAAAAAATAAATAG
*
40032458 AATAATAAATAAATAAATAG
1 AATAATAAAAAAATAAATAG
*
40032478 AA-AAAACAAAAAATA
1 AATAATA-AAAAAATA
40032493 TTAAATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.19
Consensus pattern (20 bp):
AATAATAAAAAAATAAATAG
Found at i:40032530 original size:4 final size:4
Alignment explanation
Indices: 40032521--40032546 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
40032511 AAAGTAAAAG
40032521 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
40032547 ATAAGTAATA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:40032557 original size:64 final size:63
Alignment explanation
Indices: 40032420--40032570 Score: 180
Period size: 64 Copynumber: 2.4 Consensus size: 63
40032410 GAAGGGAAGT
* *
40032420 ATAAGTAATATCGAATTTTAA-TATTAAAAAAATAAAAGAATAATAAATAAATAAATAGAAAAA
1 ATAAGTAATAT-TAAATTTAAGTATTAAAAAAATAAAAGAATAATAAATAAATAAATAGAAAAA
* ** * * *
40032483 ACAAAAAATATTAAATTTAAGTATTTACAAAGTAAAAGAATAAATAAATAAATAAATA-AATAAA
1 ATAAGTAATATTAAATTTAAGTATTAAAAAAATAAAAGAAT-AATAAATAAATAAATAGAA-AAA
*
40032547 ATAAGTAATATTAAATTGAAGTAT
1 ATAAGTAATATTAAATTTAAGTAT
40032571 ATGAGAAATA
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
62 7 0.10
63 27 0.37
64 39 0.53
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (63 bp):
ATAAGTAATATTAAATTTAAGTATTAAAAAAATAAAAGAATAATAAATAAATAAATAGAAAAA
Found at i:40033778 original size:21 final size:21
Alignment explanation
Indices: 40033752--40033793 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40033742 GCAGAGTAGT
*
40033752 TGGTGGTGGC-AGGCTAGGGTG
1 TGGTGGCGGCTAGG-TAGGGTG
40033773 TGGTGGCGGCTAGGTAGGGTG
1 TGGTGGCGGCTAGGTAGGGTG
40033794 CGGCGCTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.10, C:0.10, G:0.57, T:0.24
Consensus pattern (21 bp):
TGGTGGCGGCTAGGTAGGGTG
Found at i:40035417 original size:13 final size:14
Alignment explanation
Indices: 40035399--40035428 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
40035389 CAATTTTTGG
40035399 GTTTTGA-TCTCGA
1 GTTTTGATTCTCGA
40035412 GTTTTGATTCTCGA
1 GTTTTGATTCTCGA
40035426 GTT
1 GTT
40035429 CAATTTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.13, C:0.13, G:0.23, T:0.50
Consensus pattern (14 bp):
GTTTTGATTCTCGA
Found at i:40035442 original size:19 final size:20
Alignment explanation
Indices: 40035413--40035454 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
40035403 TGATCTCGAG
*
40035413 TTTTGATTCTCGAGTTCAAT
1 TTTTGATTCTCGAGTCCAAT
*
40035433 TTTTGA-TCTCTAGTCCAAT
1 TTTTGATTCTCGAGTCCAAT
40035452 TTT
1 TTT
40035455 CAAGTTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.52
Consensus pattern (20 bp):
TTTTGATTCTCGAGTCCAAT
Found at i:40038775 original size:53 final size:53
Alignment explanation
Indices: 40038712--40038817 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
40038702 ACAGGGTATC
*
40038712 AACATATTTAACTACAATTAATTATCATTAATAATAAGGTTAAATTTGGCATT
1 AACATATTTAACTAAAATTAATTATCATTAATAATAAGGTTAAATTTGGCATT
40038765 AACATATTTAACTAAAATTAATTATCATTAATAATAAGGTTAAATTTGGCATT
1 AACATATTTAACTAAAATTAATTATCATTAATAATAAGGTTAAATTTGGCATT
40038818 TTCATCTACT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (53 bp):
AACATATTTAACTAAAATTAATTATCATTAATAATAAGGTTAAATTTGGCATT
Found at i:40040289 original size:21 final size:22
Alignment explanation
Indices: 40040255--40040295 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
40040245 CATGTACTTC
40040255 ATTTTGACATAATTTCATCCTT
1 ATTTTGACATAATTTCATCCTT
*
40040277 ATTTTGA-ATAATTTGATCC
1 ATTTTGACATAATTTCATCC
40040296 ATGCCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49
Consensus pattern (22 bp):
ATTTTGACATAATTTCATCCTT
Found at i:40045875 original size:18 final size:18
Alignment explanation
Indices: 40045852--40045894 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
40045842 GAATAGATTT
40045852 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
40045870 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
40045888 TTAATTA
1 TTAATTA
40045895 TACCTTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:40049322 original size:3 final size:3
Alignment explanation
Indices: 40049314--40049345 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
40049304 TATGCTACCA
40049314 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
40049346 GTGTTTGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:40049822 original size:22 final size:22
Alignment explanation
Indices: 40049797--40049851 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
40049787 TAGGAAGCAA
* *
40049797 AATGTAGATTAGTAGGCACCGT
1 AATGCAGATCAGTAGGCACCGT
*
40049819 AATGCAGATCAGTAGGCATCGT
1 AATGCAGATCAGTAGGCACCGT
* *
40049841 AGTGCAAATCA
1 AATGCAGATCA
40049852 CGTACAGGCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (22 bp):
AATGCAGATCAGTAGGCACCGT
Found at i:40055885 original size:20 final size:20
Alignment explanation
Indices: 40055860--40055905 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
40055850 ATAAAATCAC
*
40055860 ATAATAACA-ATTTAAAGTAA
1 ATAATAA-AGATTTAAAATAA
*
40055880 ATAATAAAGATTTAAAATGA
1 ATAATAAAGATTTAAAATAA
40055900 ATAATA
1 ATAATA
40055906 TGAAATGCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (20 bp):
ATAATAAAGATTTAAAATAA
Found at i:40057041 original size:3 final size:3
Alignment explanation
Indices: 40057033--40057081 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
40057023 TAATGTTCGT
40057033 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
40057081 A
1 A
40057082 ATACAAAGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:40058105 original size:44 final size:44
Alignment explanation
Indices: 40058057--40058383 Score: 161
Period size: 44 Copynumber: 7.4 Consensus size: 44
40058047 AAGATTCGCT
* *
40058057 ATCTTTGATCTACTCCACTACTGCTTAGGGAGACAGGATCTACA
1 ATCTTTAATCTACTCCACTACTGCTTAGGGAGATAGGATCTACA
* * ***
40058101 ATCTTTAACCTACTCCACTACTGCTCAGGGAGATAGGA-CTGGT
1 ATCTTTAATCTACTCCACTACTGCTTAGGGAGATAGGATCTACA
** * * * *
40058144 GGCTTAAATCTACTTCC-CTACTACCTT-GGGAAGATAAGAT-TCACC
1 ATCTTTAATCTAC-TCCACTACT-GCTTAGGG-AGATAGGATCT-ACA
* * * * *
40058189 ATCTTTGATCTGCTTCACTACTGTTTAGGGAGACAGGATCTACA
1 ATCTTTAATCTACTCCACTACTGCTTAGGGAGATAGGATCTACA
* * * ** * *
40058233 TTCTTCAACCTACTCCACTGTTGCTCAGGGAGATAGGAT-T--G
1 ATCTTTAATCTACTCCACTACTGCTTAGGGAGATAGGATCTACA
* * * * * *
40058274 ATGGCTTAAATCTGCTTCC-CTACTACCTT-GGGAATATAAGAT-TCACC
1 AT--CTTTAATCTAC-TCCACTACT-GCTTAGGG-AGATAGGATCT-ACA
* * * *
40058321 GTCTTTGATCTACTCCACTACAGCTTAGGGAGACAGGATCTACA
1 ATCTTTAATCTACTCCACTACTGCTTAGGGAGATAGGATCTACA
* *
40058365 ATCTTCAACCTACTCCACT
1 ATCTTTAATCTACTCCACT
40058384 GTTGCTCAGA
Statistics
Matches: 199, Mismatches: 65, Indels: 38
0.66 0.22 0.13
Matches are distributed among these distances:
41 1 0.01
43 34 0.17
44 130 0.65
45 33 0.17
47 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (44 bp):
ATCTTTAATCTACTCCACTACTGCTTAGGGAGATAGGATCTACA
Found at i:40058284 original size:132 final size:132
Alignment explanation
Indices: 40058047--40058392 Score: 557
Period size: 132 Copynumber: 2.6 Consensus size: 132
40058037 CCAGGGAAAG
* * *
40058047 AAGATTCGCTATCTTTGATCTACTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTTAACCT
1 AAGATTCACCATCTTTGATCTACTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCT
** *
40058112 ACTCCACTACTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTACTTCCCTACTACCTTGGGAAG
66 ACTCCACTGTTGCTCAGGGAGATAGGACTGATGGCTTAAATCTACTTCCCTACTACCTTGGGAAG
40058177 AT
131 AT
* * * *
40058179 AAGATTCACCATCTTTGATCTGCTTCACTACTGTTTAGGGAGACAGGATCTACATTCTTCAACCT
1 AAGATTCACCATCTTTGATCTACTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCT
* * *
40058244 ACTCCACTGTTGCTCAGGGAGATAGGATTGATGGCTTAAATCTGCTTCCCTACTACCTTGGGAAT
66 ACTCCACTGTTGCTCAGGGAGATAGGACTGATGGCTTAAATCTACTTCCCTACTACCTTGGGAAG
40058309 AT
131 AT
* *
40058311 AAGATTCACCGTCTTTGATCTACTCCACTACAGCTTAGGGAGACAGGATCTACAATCTTCAACCT
1 AAGATTCACCATCTTTGATCTACTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCT
40058376 ACTCCACTGTTGCTCAG
66 ACTCCACTGTTGCTCAG
40058393 AGAGGTAAGG
Statistics
Matches: 195, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
132 195 1.00
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.30
Consensus pattern (132 bp):
AAGATTCACCATCTTTGATCTACTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCT
ACTCCACTGTTGCTCAGGGAGATAGGACTGATGGCTTAAATCTACTTCCCTACTACCTTGGGAAG
AT
Found at i:40059837 original size:6 final size:6
Alignment explanation
Indices: 40059826--40059860 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
40059816 GGCCTCTCTC
40059826 CTTTTT CTTTTT CTTTTT -TTTTT C-TTTT CTTTTT C
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT C
40059861 ATCATTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 10 0.37
6 17 0.63
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
CTTTTT
Found at i:40059847 original size:11 final size:11
Alignment explanation
Indices: 40059826--40059860 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
40059816 GGCCTCTCTC
40059826 CTTTTTCTTTTT
1 CTTTTT-TTTTT
40059838 CTTTTTTTTTT
1 CTTTTTTTTTT
*
40059849 CTTTTCTTTTT
1 CTTTTTTTTTT
40059860 C
1 C
40059861 ATCATTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:40059853 original size:16 final size:17
Alignment explanation
Indices: 40059827--40059859 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
40059817 GCCTCTCTCC
40059827 TTTTTCTTTTTCTTTTT
1 TTTTTCTTTTTCTTTTT
40059844 TTTTTC-TTTTCTTTTT
1 TTTTTCTTTTTCTTTTT
40059860 CATCATTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTCTTTTTCTTTTT
Found at i:40059894 original size:35 final size:35
Alignment explanation
Indices: 40059862--40059930 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
40059852 TTCTTTTTCA
40059862 TCATTTTCA-TTT-TTTATTTTTTGAAATATTTTT
1 TCATTTTCATTTTGTTTATTTTTTGAAATATTTTT
* * *
40059895 TGATTTTGATTTTGTTTTTTTTTTGAAATATTTTT
1 TCATTTTCATTTTGTTTATTTTTTGAAATATTTTT
40059930 T
1 T
40059931 GATCAGATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 7 0.23
34 3 0.10
35 21 0.68
ACGTcount: A:0.19, C:0.03, G:0.07, T:0.71
Consensus pattern (35 bp):
TCATTTTCATTTTGTTTATTTTTTGAAATATTTTT
Found at i:40072086 original size:18 final size:20
Alignment explanation
Indices: 40072060--40072097 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
40072050 AAACTACAAC
*
40072060 TCTACAAAAC-ATGGTTTTT
1 TCTACAAAACTAAGGTTTTT
40072079 TCTA-AAAACTAAGGTTTTT
1 TCTACAAAACTAAGGTTTTT
40072098 CGTAAATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (20 bp):
TCTACAAAACTAAGGTTTTT
Found at i:40077044 original size:27 final size:27
Alignment explanation
Indices: 40077013--40077083 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
40077003 TGTTCCGACC
40077013 CACAGCTCGTGTGAGCAG-GCTAATTTT
1 CACAGCTCGTGTGAGCAGAGC-AATTTT
* * *
40077040 TACAGCTTGTGTGAGCAGAGCCATTTT
1 CACAGCTCGTGTGAGCAGAGCAATTTT
*
40077067 CATAGCTCGTGTGAGCA
1 CACAGCTCGTGTGAGCA
40077084 TACATGTACA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
27 35 0.95
28 2 0.05
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.30
Consensus pattern (27 bp):
CACAGCTCGTGTGAGCAGAGCAATTTT
Found at i:40083130 original size:6 final size:6
Alignment explanation
Indices: 40083085--40083154 Score: 52
Period size: 6 Copynumber: 11.2 Consensus size: 6
40083075 TGCCAGAAGC
* * * * *
40083085 AAATAA AAGAAAA AAATTAGA AAACAA AAATTA AACTAA AAATAA AAAAATA
1 AAATAA AA-ATAA AAA-TA-A AAATAA AAATAA AAATAA AAATAA AAATA-A
40083137 AAAT-A AAATAA AAATAA A
1 AAATAA AAATAA AAATAA A
40083155 TGGCTAAATT
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
5 5 0.10
6 29 0.59
7 11 0.22
8 4 0.08
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:40084057 original size:26 final size:26
Alignment explanation
Indices: 40084028--40084103 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 26
40084018 CACCAATATC
* * *
40084028 GCAGCAAAACTGCCAGTAATAGTGAT
1 GCAGCAAAGCTGCCAGTAACAGTAAT
* *
40084054 GCAGCAATGCTGCTAGTAACAGTAAT
1 GCAGCAAAGCTGCCAGTAACAGTAAT
*
40084080 GCAGCAAAGCTTCCAGTAACAGTA
1 GCAGCAAAGCTGCCAGTAACAGTA
40084104 TATGTGGCAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAGTAACAGTAAT
Found at i:40084122 original size:27 final size:26
Alignment explanation
Indices: 40084040--40084124 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
40084030 AGCAAAACTG
* * * **
40084040 CCAGTAATAGTGATGCAGCAATGCTG
1 CCAGTAACAGTAATGCAGCAAAGCCA
* **
40084066 CTAGTAACAGTAATGCAGCAAAGCTT
1 CCAGTAACAGTAATGCAGCAAAGCCA
**
40084092 CCAGTAACAGTATATGTGGCAAAGCCA
1 CCAGTAACAGTA-ATGCAGCAAAGCCA
40084119 CCAGTA
1 CCAGTA
40084125 GAGTATACTT
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 32 0.67
27 16 0.33
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.21
Consensus pattern (26 bp):
CCAGTAACAGTAATGCAGCAAAGCCA
Found at i:40084194 original size:32 final size:32
Alignment explanation
Indices: 40084158--40084239 Score: 92
Period size: 36 Copynumber: 2.4 Consensus size: 32
40084148 ATCCCACCCC
40084158 ATGCAGTATGTCATGCCATATAATATACGTGT
1 ATGCAGTATGTCATGCCATATAATATACGTGT
* * * *
40084190 ATGCAGTATGTCATACATGTCATTTATTATATGTGT
1 ATGCAGTATG---T-CATGCCATATAATATACGTGT
40084226 ATGCAGTATGTCAT
1 ATGCAGTATGTCAT
40084240 ACTCAATAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
32 13 0.31
33 1 0.02
35 1 0.02
36 27 0.64
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.39
Consensus pattern (32 bp):
ATGCAGTATGTCATGCCATATAATATACGTGT
Found at i:40084362 original size:27 final size:27
Alignment explanation
Indices: 40084318--40084406 Score: 144
Period size: 27 Copynumber: 3.3 Consensus size: 27
40084308 TATAACAGTT
* *
40084318 ATTTTACCCTTTGAGGGTAATTC-AGTC
1 ATTTTACCCTTCGGGGGTAATTCGA-TC
40084345 ATTTTACCCTTCGGGGGTAATTCGATC
1 ATTTTACCCTTCGGGGGTAATTCGATC
40084372 ATTTTACCCTTCGGGGGTAATTCGATC
1 ATTTTACCCTTCGGGGGTAATTCGATC
40084399 ATTTTACC
1 ATTTTACC
40084407 ATGATTCGCA
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
27 58 0.98
28 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.39
Consensus pattern (27 bp):
ATTTTACCCTTCGGGGGTAATTCGATC
Found at i:40085901 original size:14 final size:14
Alignment explanation
Indices: 40085882--40085912 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
40085872 TGATTGTTTT
*
40085882 TAATCTAAATTTAC
1 TAATCTAAATTAAC
40085896 TAATCTAAATTAAC
1 TAATCTAAATTAAC
40085910 TAA
1 TAA
40085913 GAATGCAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:40087313 original size:15 final size:16
Alignment explanation
Indices: 40087289--40087322 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
40087279 CACCGTATTA
40087289 TATTTAATATT-AAAT
1 TATTTAATATTAAAAT
*
40087304 TATTTTATATTAAAAT
1 TATTTAATATTAAAAT
40087320 TAT
1 TAT
40087323 ACAAGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTAATATTAAAAT
Found at i:40088257 original size:12 final size:13
Alignment explanation
Indices: 40088233--40088262 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
40088223 ACTTCTTCAA
40088233 TTCTCTCTCAAAT
1 TTCTCTCTCAAAT
40088246 TTCTCTCT-AAAT
1 TTCTCTCTCAAAT
40088258 TTCTC
1 TTCTC
40088263 AAAGCTCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.20, C:0.30, G:0.00, T:0.50
Consensus pattern (13 bp):
TTCTCTCTCAAAT
Found at i:40091390 original size:13 final size:13
Alignment explanation
Indices: 40091372--40091400 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
40091362 GCTGTTTCGA
40091372 TTTCTTTATTTAT
1 TTTCTTTATTTAT
40091385 TTTCTTTATTTAT
1 TTTCTTTATTTAT
40091398 TTT
1 TTT
40091401 TGTGCCGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTCTTTATTTAT
Found at i:40096969 original size:16 final size:18
Alignment explanation
Indices: 40096948--40096986 Score: 64
Period size: 16 Copynumber: 2.3 Consensus size: 18
40096938 AATTATCTTG
40096948 ATTTAAACT-AAAA-TAA
1 ATTTAAACTAAAAATTAA
40096964 ATTTAAACTAAAAATTAA
1 ATTTAAACTAAAAATTAA
40096982 ATTTA
1 ATTTA
40096987 TTATTATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.43
17 4 0.19
18 8 0.38
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTTAAACTAAAAATTAA
Found at i:40100680 original size:15 final size:16
Alignment explanation
Indices: 40100656--40100689 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
40100646 CACCGTATTA
40100656 TATTTAATATT-AAAT
1 TATTTAATATTAAAAT
*
40100671 TATTTTATATTAAAAT
1 TATTTAATATTAAAAT
40100687 TAT
1 TAT
40100690 ATAAGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTAATATTAAAAT
Found at i:40101961 original size:14 final size:14
Alignment explanation
Indices: 40101942--40101972 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
40101932 TGATTGTTTT
*
40101942 TAATCTAAATTTAC
1 TAATCTAAATTAAC
40101956 TAATCTAAATTAAC
1 TAATCTAAATTAAC
40101970 TAA
1 TAA
40101973 GAACGCAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:40107396 original size:14 final size:14
Alignment explanation
Indices: 40107377--40107407 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
40107367 TGATTATTGT
*
40107377 TAATCTAAATTTAC
1 TAATCTAAATTAAC
40107391 TAATCTAAATTAAC
1 TAATCTAAATTAAC
40107405 TAA
1 TAA
40107408 GTACGCTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:40109080 original size:12 final size:11
Alignment explanation
Indices: 40109037--40109083 Score: 67
Period size: 11 Copynumber: 4.2 Consensus size: 11
40109027 ACACATTATT
*
40109037 TCTCAAGTTTC
1 TCTCAAATTTC
40109048 TCTCAAATTTC
1 TCTCAAATTTC
*
40109059 TGTCAAATTTC
1 TCTCAAATTTC
40109070 TCTCTAAATTTC
1 TCTC-AAATTTC
40109082 TC
1 TC
40109084 AAAGCTCTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
11 23 0.72
12 9 0.28
ACGTcount: A:0.23, C:0.26, G:0.04, T:0.47
Consensus pattern (11 bp):
TCTCAAATTTC
Found at i:40109319 original size:25 final size:24
Alignment explanation
Indices: 40109268--40109318 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
40109258 TTCAATATTA
* *
40109268 TTTAATACTTTTTATTTATGTAAT
1 TTTAATAATTTTTATTTATATAAT
40109292 TTTAATTAATTTTTATTT-TATAAT
1 TTTAA-TAATTTTTATTTATATAAT
40109316 TTT
1 TTT
40109319 TTATATTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTAATAATTTTTATTTATATAAT
Found at i:40110042 original size:28 final size:28
Alignment explanation
Indices: 40110011--40110065 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
40110001 TGAGTGGGCC
40110011 ACACGAGCATGCGGGCCCACACGGGCAT
1 ACACGAGCATGCGGGCCCACACGGGCAT
* * *
40110039 ACACGGGCGTGTGGGCCCACACGGGCA
1 ACACGAGCATGCGGGCCCACACGGGCA
40110066 CAGACGAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.22, C:0.35, G:0.36, T:0.07
Consensus pattern (28 bp):
ACACGAGCATGCGGGCCCACACGGGCAT
Found at i:40110078 original size:28 final size:28
Alignment explanation
Indices: 40110006--40110083 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 28
40109996 TGGGCTGAGT
* * *
40110006 GGGC-CACACGAGCATGCGGGCCCACAC
1 GGGCACACACGAACGTGTGGGCCCACAC
* **
40110033 GGGCATACACGGGCGTGTGGGCCCACAC
1 GGGCACACACGAACGTGTGGGCCCACAC
* * *
40110061 GGGCACAGACGAATGTGTAGGCC
1 GGGCACACACGAACGTGTGGGCC
40110084 TATTTTTACT
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 4 0.10
28 36 0.90
ACGTcount: A:0.22, C:0.32, G:0.37, T:0.09
Consensus pattern (28 bp):
GGGCACACACGAACGTGTGGGCCCACAC
Found at i:40113701 original size:18 final size:18
Alignment explanation
Indices: 40113678--40113720 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
40113668 GCCAGGTGCA
* *
40113678 TATCCTTGCTCTTATATG
1 TATCCTTACCCTTATATG
*
40113696 TATCCTAACCCTTATATG
1 TATCCTTACCCTTATATG
*
40113714 TTTCCTT
1 TATCCTT
40113721 TTCCCAGTCT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.19, C:0.26, G:0.07, T:0.49
Consensus pattern (18 bp):
TATCCTTACCCTTATATG
Found at i:40114232 original size:94 final size:93
Alignment explanation
Indices: 40114071--40114265 Score: 318
Period size: 94 Copynumber: 2.1 Consensus size: 93
40114061 AACATTGATT
* *
40114071 TTTTTAATATATTTTTACAAAATGTTTTTATATTATTTCATTTAATAAAATAAAAGTTGTTTTTA
1 TTTTTAATATATTTGTACAAAATGTTTTTATATTATTTCATTTAATAAAATAAAAGTTGTGTTTA
*
40114136 ATATTTTAATAATAATTTATTTTTTTATA
66 ATATTTTAATAATAATTTA-TATTTTATA
* * *
40114165 TTTTTAATATATTTGTACACACTGTTTTTATATTATTTTATTTAATAAAATAAAAGTTGTGTTTA
1 TTTTTAATATATTTGTACAAAATGTTTTTATATTATTTCATTTAATAAAATAAAAGTTGTGTTTA
*
40114230 ATATTTTAATAGTAATTTATATTTTATA
66 ATATTTTAATAATAATTTATATTTTATA
40114258 TTTTTAAT
1 TTTTTAAT
40114266 CAAATAGAAG
Statistics
Matches: 94, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
93 16 0.17
94 78 0.83
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.57
Consensus pattern (93 bp):
TTTTTAATATATTTGTACAAAATGTTTTTATATTATTTCATTTAATAAAATAAAAGTTGTGTTTA
ATATTTTAATAATAATTTATATTTTATA
Found at i:40116025 original size:38 final size:39
Alignment explanation
Indices: 40115946--40116025 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 39
40115936 GTGTAGTGGG
*
40115946 GGAGTGTTGGAGTGATTTTAGGAGGAAAAAAATATGAGATT
1 GGAGTGTTGGAGTGATTTTAGAAGG--AAAAATATGAGATT
*
40115987 GGAGTGTTGGAGTGATTTTAGAAGG-AAAATATGGGATT
1 GGAGTGTTGGAGTGATTTTAGAAGGAAAAATATGAGATT
40116025 G
1 G
40116026 TGGAGTTATC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 13 0.35
41 24 0.65
ACGTcount: A:0.34, C:0.00, G:0.36, T:0.30
Consensus pattern (39 bp):
GGAGTGTTGGAGTGATTTTAGAAGGAAAAATATGAGATT
Found at i:40125716 original size:17 final size:18
Alignment explanation
Indices: 40125684--40125718 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
40125674 TGTGGTCAGC
40125684 CCGTGTGGAAATGCTCAAG
1 CCGTGTGG-AATGCTCAAG
40125703 CCGTGTGG-ATGCTCAA
1 CCGTGTGGAATGCTCAA
40125719 AATAACTCAT
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:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (18 bp):
CCGTGTGGAATGCTCAAG
Found at i:40129153 original size:15 final size:15
Alignment explanation
Indices: 40129133--40129214 Score: 67
Period size: 15 Copynumber: 5.5 Consensus size: 15
40129123 AGAAACATTT
40129133 TAATAAAAAGAATAA
1 TAATAAAAAGAATAA
*
40129148 TAATAAAAATAATAA
1 TAATAAAAAGAATAA
* *
40129163 CAATAATAA-AATAGA
1 TAATAAAAAGAATA-A
* ** **
40129178 AAATAACGAGAATGC
1 TAATAAAAAGAATAA
*
40129193 TAATAAAAATAATAA
1 TAATAAAAAGAATAA
40129208 TAATAAA
1 TAATAAA
40129215 TAAATAAATA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
14 4 0.08
15 44 0.86
16 3 0.06
ACGTcount: A:0.68, C:0.04, G:0.06, T:0.22
Consensus pattern (15 bp):
TAATAAAAAGAATAA
Found at i:40129221 original size:17 final size:17
Alignment explanation
Indices: 40129199--40129231 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40129189 ATGCTAATAA
40129199 AAAT-AATAATAATAAAT
1 AAATAAATAA-AATAAAT
40129216 AAATAAATAAAATAAA
1 AAATAAATAAAATAAA
40129232 CAATGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAATAAAATAAAT
Done.