Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, whole genome shotgun sequence
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: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 29 of 100
Found at i:5327085 original size:66 final size:67
Alignment explanation
Indices: 5327004--5327130 Score: 161
Period size: 66 Copynumber: 1.9 Consensus size: 67
5326994 AATCATCAAC
*
5327004 AATTTAATAACAAATAAGTT-ATAACTTA-ATAGTAAAATA-TTTATAAATTAGGAGTAAATTAA
1 AATTTAATAACAAATAA-TTGATAACTTAGA-AGCAAAATATTTTATAAATTAGGAGTAAATTAA
5327066 AGCT
64 AGCT
* * * * *
5327070 AATTTAATAATAAATAATTGATAATTTAGAAGCATACTATTTTATAAATTAGTAGTAAATT
1 AATTTAATAACAAATAATTGATAACTTAGAAGCAAAATATTTTATAAATTAGGAGTAAATT
5327131 GTTAATAACA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
65 2 0.04
66 29 0.56
67 21 0.40
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.38
Consensus pattern (67 bp):
AATTTAATAACAAATAATTGATAACTTAGAAGCAAAATATTTTATAAATTAGGAGTAAATTAAAG
CT
Found at i:5327094 original size:22 final size:22
Alignment explanation
Indices: 5326931--5327097 Score: 60
Period size: 22 Copynumber: 7.5 Consensus size: 22
5326921 TAATTTATTT
*
5326931 ATTGATAAATTAATAATAAATTA
1 ATTGATAATTTAATAATAAA-TA
5326954 ATT-ATAAATTT-ATAATAAAT-
1 ATTGAT-AATTTAATAATAAATA
* * *
5326974 ATTTAGTAATTTAGCA-AAAAAATC
1 ATTGA-TAATTTA--ATAATAAATA
** * *
5326998 ATCAACAATTTAATAACAAATA
1 ATTGATAATTTAATAATAAATA
* *
5327020 AGTT-ATAACTTAATAGTAAA-A
1 A-TTGATAATTTAATAATAAATA
* * ** *
5327041 TATTTATAAATTAGGAGTAAATTA
1 -ATTGATAATTTAATAATAAA-TA
* *
5327065 A-AGCTAATTTAATAATAAATA
1 ATTGATAATTTAATAATAAATA
5327086 ATTGATAATTTA
1 ATTGATAATTTA
5327098 GAAGCATACT
Statistics
Matches: 106, Mismatches: 24, Indels: 29
0.67 0.15 0.18
Matches are distributed among these distances:
20 3 0.03
21 14 0.13
22 63 0.59
23 21 0.20
24 5 0.05
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (22 bp):
ATTGATAATTTAATAATAAATA
Found at i:5327618 original size:21 final size:21
Alignment explanation
Indices: 5327491--5327610 Score: 95
Period size: 21 Copynumber: 5.9 Consensus size: 21
5327481 AGAGCTTATT
* * * *
5327491 AAAATTTTATAAAAAATTAGC
1 AAAATTATATCAAAAGTTACC
* *
5327512 AAAATTGTATCAATAGTTACC
1 AAAATTATATCAAAAGTTACC
* *
5327533 AAAATTATATCATAAGTTACG
1 AAAATTATATCAAAAGTTACC
* * *
5327554 AAAATTATATCGAAGGTCACC
1 AAAATTATATCAAAAGTTACC
* *
5327575 AAAATTTTATTAAAA--T--C
1 AAAATTATATCAAAAGTTACC
5327592 AAAATTATATCAAAAGTTA
1 AAAATTATATCAAAAGTTA
5327611 TTAAAATTTA
Statistics
Matches: 75, Mismatches: 21, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
17 14 0.19
19 1 0.01
21 60 0.80
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (21 bp):
AAAATTATATCAAAAGTTACC
Found at i:5332345 original size:34 final size:34
Alignment explanation
Indices: 5332281--5332345 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 34
5332271 AAAAATACAT
* * **
5332281 TTTCGGATAATTGCAATGCTTTTTGAAAATGTAC
1 TTTCAGATAATTGCAATACTTTTCCAAAATGTAC
5332315 TTTCAGATAATTGCAATAC-TTTCCATAAATG
1 TTTCAGATAATTGCAATACTTTTCCA-AAATG
5332346 AATTTTCGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
33 4 0.15
34 22 0.85
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (34 bp):
TTTCAGATAATTGCAATACTTTTCCAAAATGTAC
Found at i:5337693 original size:17 final size:17
Alignment explanation
Indices: 5337671--5337725 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
5337661 TAATATTATG
5337671 AAAAATTCAAAATTTTA
1 AAAAATTCAAAATTTTA
* **
5337688 AAAAATTTTAAAAAATT-
1 AAAAA-TTCAAAATTTTA
5337705 AAAAATTCAAAAATTTTA
1 AAAAATTC-AAAATTTTA
5337723 AAA
1 AAA
5337726 TTTTGTAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
16 2 0.07
17 16 0.55
18 11 0.38
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAATTCAAAATTTTA
Found at i:5337694 original size:10 final size:10
Alignment explanation
Indices: 5337679--5337704 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5337669 TGAAAAATTC
5337679 AAAATTTTAA
1 AAAATTTTAA
5337689 AAAATTTTAA
1 AAAATTTTAA
5337699 AAAATT
1 AAAATT
5337705 AAAAATTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:5337700 original size:9 final size:9
Alignment explanation
Indices: 5337679--5337813 Score: 73
Period size: 9 Copynumber: 14.9 Consensus size: 9
5337669 TGAAAAATTC
5337679 AAAATTTTAA
1 AAAATTTT-A
5337689 AAAATTTTA
1 AAAATTTTA
*
5337698 AAAA-ATTA
1 AAAATTTTA
*
5337706 AAAA-TTCA
1 AAAATTTTA
5337714 AAAATTTT-
1 AAAATTTTA
*
5337722 AAAATTTTG
1 AAAATTTTA
*
5337731 TAAA-TTTA
1 AAAATTTTA
*
5337739 ATAAA-TATA
1 A-AAATTTTA
** *
5337748 AATTTTTTTG
1 AA-AATTTTA
5337758 AAAATTTTGA
1 AAAATTTT-A
* *
5337768 AAATTTTTT
1 AAAATTTTA
*
5337777 GAAATTTTA
1 AAAATTTTA
*
5337786 AAAATTTTTTG
1 AAAA--TTTTA
5337797 AAAATTTTA
1 AAAATTTTA
5337806 AAAATTTT
1 AAAATTTT
5337814 CAAAGAATAA
Statistics
Matches: 94, Mismatches: 23, Indels: 17
0.70 0.17 0.13
Matches are distributed among these distances:
8 25 0.27
9 42 0.45
10 19 0.20
11 8 0.09
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.46
Consensus pattern (9 bp):
AAAATTTTA
Found at i:5337781 original size:19 final size:20
Alignment explanation
Indices: 5337751--5337813 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
5337741 AAATATAAAT
*
5337751 TTTTTTGAAAATTTTGAAAA
1 TTTTTTGAAAATTTTAAAAA
5337771 TTTTTTG-AAATTTTAAAAA
1 TTTTTTGAAAATTTTAAAAA
5337790 TTTTTTGAAAATTTTAAAAA
1 TTTTTTGAAAATTTTAAAAA
5337810 TTTT
1 TTTT
5337814 CAAAGAATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 18 0.44
20 23 0.56
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (20 bp):
TTTTTTGAAAATTTTAAAAA
Found at i:5338685 original size:19 final size:18
Alignment explanation
Indices: 5338659--5338697 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5338649 TTTTTCATAA
5338659 AATTTTATAT-ATTTTTTT
1 AATTTT-TATGATTTTTTT
5338677 AATTTTTATGATTTTTTT
1 AATTTTTATGATTTTTTT
5338695 AAT
1 AAT
5338698 GTTGACGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
AATTTTTATGATTTTTTT
Found at i:5343275 original size:18 final size:18
Alignment explanation
Indices: 5343252--5343286 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5343242 AATAATATAT
* *
5343252 AAAAAATAAGAAAAATTC
1 AAAAAAAAAAAAAAATTC
5343270 AAAAAAAAAAAAAAATT
1 AAAAAAAAAAAAAAATT
5343287 TCTACCTGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (18 bp):
AAAAAAAAAAAAAAATTC
Found at i:5343810 original size:18 final size:19
Alignment explanation
Indices: 5343789--5343831 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
5343779 TGAGACTATT
**
5343789 TTTTTTGTATTCTGA-CCC
1 TTTTTTGTAAGCTGACCCC
*
5343807 TTTTTTTTAAGCTGACCCC
1 TTTTTTGTAAGCTGACCCC
5343826 TTTTTT
1 TTTTTT
5343832 TTCTTCTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.12, C:0.21, G:0.09, T:0.58
Consensus pattern (19 bp):
TTTTTTGTAAGCTGACCCC
Found at i:5344180 original size:7 final size:7
Alignment explanation
Indices: 5344164--5344203 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
5344154 CCATCCTCGA
5344164 TTTT-TT
1 TTTTGTT
5344170 TTTTGTT
1 TTTTGTT
5344177 TTTTGTT
1 TTTTGTT
*
5344184 TTTTTTT
1 TTTTGTT
*
5344191 TTTTGTA
1 TTTTGTT
5344198 TTTTGT
1 TTTTGT
5344204 ATTATTTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
6 4 0.13
7 26 0.87
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.88
Consensus pattern (7 bp):
TTTTGTT
Found at i:5344190 original size:21 final size:21
Alignment explanation
Indices: 5344164--5344203 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5344154 CCATCCTCGA
*
5344164 TTTTTTTTTTGTTTTTTGTTT
1 TTTTTTTTTTGTATTTTGTTT
5344185 TTTTTTTTTTGTATTTTGT
1 TTTTTTTTTTGTATTTTGT
5344204 ATTATTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.88
Consensus pattern (21 bp):
TTTTTTTTTTGTATTTTGTTT
Found at i:5344211 original size:21 final size:21
Alignment explanation
Indices: 5344166--5344211 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
5344156 ATCCTCGATT
* * *
5344166 TTTTTTTTGTTTTTTGTTTTT
1 TTTTTTTTGTATTTTGTATTA
5344187 TTTTTTTTGTATTTTGTATTA
1 TTTTTTTTGTATTTTGTATTA
5344208 TTTT
1 TTTT
5344212 CTTGATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.07, C:0.00, G:0.09, T:0.85
Consensus pattern (21 bp):
TTTTTTTTGTATTTTGTATTA
Found at i:5344235 original size:14 final size:13
Alignment explanation
Indices: 5344163--5344249 Score: 59
Period size: 14 Copynumber: 6.3 Consensus size: 13
5344153 GCCATCCTCG
5344163 ATTTTTTTTTTGT
1 ATTTTTTTTTTGT
*
5344176 -TTTTTGTTTTTTT
1 ATTTTT-TTTTTGT
*
5344189 TTTTTTGTATTTTGT
1 ATTTTT-T-TTTTGT
* *
5344204 ATTATTTTCTTGAT
1 ATTTTTTTTTTG-T
5344218 ATTTTTTTTCTTGT
1 ATTTTTTTT-TTGT
* *
5344232 ATTTCATATTTTGT
1 ATTT-TTTTTTTGT
5344246 ATTT
1 ATTT
5344250 ATATTTCATA
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
12 5 0.08
13 10 0.17
14 29 0.49
15 15 0.25
ACGTcount: A:0.11, C:0.03, G:0.08, T:0.77
Consensus pattern (13 bp):
ATTTTTTTTTTGT
Found at i:5344255 original size:13 final size:13
Alignment explanation
Indices: 5344196--5344268 Score: 51
Period size: 13 Copynumber: 5.5 Consensus size: 13
5344186 TTTTTTTTTG
5344196 TATTTTGTA-TTA
1 TATTTTGTATTTA
* *
5344208 TTTTCTTGATATTTT
1 TATT-TTG-TATTTA
*
5344223 TTTTCTTGTATTTCA
1 TATT-TTGTATTT-A
5344238 TATTTTGTATTTA
1 TATTTTGTATTTA
**
5344251 TATTTCATATTTA
1 TATTTTGTATTTA
5344264 T-TTTT
1 TATTTT
5344269 TTTTTGGACA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
12 6 0.12
13 16 0.32
14 15 0.30
15 13 0.26
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.70
Consensus pattern (13 bp):
TATTTTGTATTTA
Found at i:5344893 original size:11 final size:11
Alignment explanation
Indices: 5344877--5344915 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
5344867 TTATTCATTG
5344877 ATAAATTAATA
1 ATAAATTAATA
*
5344888 ATAAATTAATT
1 ATAAATTAATA
*
5344899 ATAAATTTATA
1 ATAAATTAATA
5344910 ATAAAT
1 ATAAAT
5344916 CTTTAGTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATAAATTAATA
Found at i:5345033 original size:22 final size:22
Alignment explanation
Indices: 5344873--5345072 Score: 92
Period size: 22 Copynumber: 9.1 Consensus size: 22
5344863 TAATTTATTC
* *
5344873 ATTGATAAATTAATAATAAATT
1 ATTGATAATTTAGTAATAAATT
5344895 AATT-ATAAATTTA-TAATAAATCT
1 -ATTGAT-AATTTAGTAATAAAT-T
*
5344918 -TT-AGTAATTTAGTAA-AAAAT
1 ATTGA-TAATTTAGTAATAAATT
* *
5344938 ATCGATAATTTAATAATAAATT
1 ATTGATAATTTAGTAATAAATT
* * * *
5344960 AATT-ATAACTTAATAGTAAAAT
1 -ATTGATAATTTAGTAATAAATT
* * * *
5344982 ATTTATAAATAAG-AGTAAATT
1 ATTGATAATTTAGTAATAAATT
** *
5345003 AAAGTTAATTTAGTAATAAATT
1 ATTGATAATTTAGTAATAAATT
* *
5345025 ATTGATAATTT-GAAAGTATATT
1 ATTGATAATTTAGTAA-TAAATT
** *
5345047 ACTTTTTAAATTAGTAATAAATT
1 A-TTGATAATTTAGTAATAAATT
5345070 ATT
1 ATT
5345073 AATTACATAA
Statistics
Matches: 134, Mismatches: 30, Indels: 27
0.70 0.16 0.14
Matches are distributed among these distances:
20 1 0.01
21 43 0.32
22 63 0.47
23 24 0.18
24 3 0.02
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (22 bp):
ATTGATAATTTAGTAATAAATT
Found at i:5345105 original size:22 final size:22
Alignment explanation
Indices: 5344873--5345124 Score: 88
Period size: 22 Copynumber: 11.5 Consensus size: 22
5344863 TAATTTATTC
* *
5344873 ATTGATAAATTAATAATAAATT
1 ATTGATAATTTAATAGTAAATT
*
5344895 AATT-ATAAATTT-ATAATAAATCT
1 -ATTGAT-AATTTAATAGTAAAT-T
* * *
5344918 -TT-AGTAATTTAGTA-AAAAAT
1 ATTGA-TAATTTAATAGTAAATT
* *
5344938 ATCGATAATTTAATAATAAATT
1 ATTGATAATTTAATAGTAAATT
* *
5344960 AATT-ATAACTTAATAGTAAAAT
1 -ATTGATAATTTAATAGTAAATT
* * *
5344982 ATTTATAA-ATAAGAGTAAATT
1 ATTGATAATTTAATAGTAAATT
** * * *
5345003 AAAGTTAATTTAGTAATAAATT
1 ATTGATAATTTAATAGTAAATT
*
5345025 ATTGATAATTTGAA-AGTATATT
1 ATTGATAATTT-AATAGTAAATT
** * * *
5345047 ACTTTTTAAATTAGTAATAAATT
1 A-TTGATAATTTAATAGTAAATT
* * **
5345070 ATTAATTACATAATAGTAAATT
1 ATTGATAATTTAATAGTAAATT
* * * *
5345092 AATGATAATTTAATTGTCAATC
1 ATTGATAATTTAATAGTAAATT
*
5345114 ATTAATAATTT
1 ATTGATAATTT
5345125 TTTTATTCTT
Statistics
Matches: 164, Mismatches: 52, Indels: 27
0.67 0.21 0.11
Matches are distributed among these distances:
20 1 0.01
21 38 0.23
22 100 0.61
23 25 0.15
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (22 bp):
ATTGATAATTTAATAGTAAATT
Found at i:5345480 original size:42 final size:42
Alignment explanation
Indices: 5345434--5345551 Score: 102
Period size: 42 Copynumber: 2.9 Consensus size: 42
5345424 AGAGCTTATT
* *
5345434 AAAATTTTATAAAAAATTATCAAAATTGTATC-AATAGTTACC
1 AAAATTTTATAAAAAATTATCAAAATTATATCGAA-AGTCACC
* * * * * *
5345476 AAAATTATATCATAAGTTATGAAAATTATATCGAAGGTCACC
1 AAAATTTTATAAAAAATTATCAAAATTATATCGAAAGTCACC
* *
5345518 AAAATTTTAT-TAAAA-TA--AAAATTATATCAAAAGT
1 AAAATTTTATAAAAAATTATCAAAATTATATCGAAAGT
5345552 TATTAAATTT
Statistics
Matches: 61, Mismatches: 14, Indels: 6
0.75 0.17 0.07
Matches are distributed among these distances:
38 15 0.25
40 2 0.03
41 2 0.03
42 40 0.66
43 2 0.03
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.34
Consensus pattern (42 bp):
AAAATTTTATAAAAAATTATCAAAATTATATCGAAAGTCACC
Found at i:5345493 original size:21 final size:21
Alignment explanation
Indices: 5345454--5345507 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
5345444 AAAAAATTAT
*
5345454 CAAAATTGTATCAATAGTTAC
1 CAAAATTATATCAATAGTTAC
*
5345475 CAAAATTATATC-ATAAGTTAT
1 CAAAATTATATCAAT-AGTTAC
*
5345496 GAAAATTATATC
1 CAAAATTATATC
5345508 GAAGGTCACC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.35
Consensus pattern (21 bp):
CAAAATTATATCAATAGTTAC
Found at i:5346395 original size:12 final size:12
Alignment explanation
Indices: 5346380--5346405 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5346370 TCTTGATGTT
5346380 GATCTTGATCAG
1 GATCTTGATCAG
5346392 GATCTTGATCAG
1 GATCTTGATCAG
5346404 GA
1 GA
5346406 CAACGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (12 bp):
GATCTTGATCAG
Found at i:5347973 original size:18 final size:18
Alignment explanation
Indices: 5347924--5347975 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
5347914 AAATAATAGT
*
5347924 ATGAAATAAAATATTTCTA
1 ATGAAATAAAATA-TTATA
* *
5347943 ATAAAAT-ATATATTATA
1 ATGAAATAAAATATTATA
*
5347960 TTGAAATAAAATATTA
1 ATGAAATAAAATATTA
5347976 CATAAAATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
17 9 0.35
18 11 0.42
19 6 0.23
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (18 bp):
ATGAAATAAAATATTATA
Found at i:5350313 original size:34 final size:34
Alignment explanation
Indices: 5350235--5350318 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 34
5350225 AAAAAATTAC
* * * *
5350235 TTCCAAAAAT-ACATTTATGGATAATTGCAATGCT
1 TTCCAAAAATGA-ATTTCTAGATAACTGCAATACT
* *
5350269 TTCTAAAAATGTATTTCTAGATAACTGCAATACT
1 TTCCAAAAATGAATTTCTAGATAACTGCAATACT
*
5350303 TTCCATAAATGAATTT
1 TTCCAAAAATGAATTT
5350319 TCGATATAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (34 bp):
TTCCAAAAATGAATTTCTAGATAACTGCAATACT
Found at i:5350353 original size:33 final size:33
Alignment explanation
Indices: 5350309--5350373 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
5350299 TACTTTCCAT
*
5350309 AAATGAATTTTCGATATA-ATTA-AGAAGTTTTCG
1 AAATAAATTTTC-A-ATACATTAGAGAAGTTTTCG
5350342 AAATAAATTTTCAATACATTAGAGAAGTTTTC
1 AAATAAATTTTCAATACATTAGAGAAGTTTTC
5350374 AAAAATTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 3 0.10
32 5 0.17
33 21 0.72
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (33 bp):
AAATAAATTTTCAATACATTAGAGAAGTTTTCG
Found at i:5350663 original size:2 final size:2
Alignment explanation
Indices: 5350656--5350694 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
5350646 TCTGTTGGCT
* *
5350656 TA TA TA TA AA TA GA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5350695 CACATGTTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:5351046 original size:32 final size:32
Alignment explanation
Indices: 5350985--5351048 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
5350975 TTGTCTTTTC
* *
5350985 TTTCTTTCTTTATATTTATATTTTTTTTCTTT
1 TTTCTTTCTTTATATATATATTTTCTTTCTTT
* *
5351017 TTTCTTTCTTTATATATGTCTTTTCTTTCTTT
1 TTTCTTTCTTTATATATATATTTTCTTTCTTT
5351049 CTTCATATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.11, C:0.12, G:0.02, T:0.75
Consensus pattern (32 bp):
TTTCTTTCTTTATATATATATTTTCTTTCTTT
Found at i:5351226 original size:26 final size:26
Alignment explanation
Indices: 5351197--5351249 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
5351187 AGGTTGGATA
5351197 TGATAACAAAGGAAAGAAGTAGAAAT
1 TGATAACAAAGGAAAGAAGTAGAAAT
5351223 TGATAACAAAGGAAAGAAGTAGAAAT
1 TGATAACAAAGGAAAGAAGTAGAAAT
5351249 T
1 T
5351250 CTTTTTCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.57, C:0.04, G:0.23, T:0.17
Consensus pattern (26 bp):
TGATAACAAAGGAAAGAAGTAGAAAT
Found at i:5351392 original size:58 final size:58
Alignment explanation
Indices: 5351277--5351392 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 58
5351267 GAATTGTTGA
** * *
5351277 AAAAAATTGAGGGGCTACTTAATCCAAATGAGCTTCTGTTAGGAAATCATCGGGAAAT
1 AAAAAATTGAGGGGCTACTTAATCCAAATGAGCTTCTGTTAAAAAATAATCGAGAAAT
*
5351335 AAAAAATTGAGGGG-TCACTTAATCCAAATGAGCTTCTGTTAAAAAATAATTGAGAAAT
1 AAAAAATTGAGGGGCT-ACTTAATCCAAATGAGCTTCTGTTAAAAAATAATCGAGAAAT
5351393 CAACACGCAC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
57 1 0.02
58 51 0.98
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (58 bp):
AAAAAATTGAGGGGCTACTTAATCCAAATGAGCTTCTGTTAAAAAATAATCGAGAAAT
Found at i:5351433 original size:18 final size:18
Alignment explanation
Indices: 5351389--5351433 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
5351379 AATAATTGAG
5351389 AAATCAACACGCACACACA
1 AAAT-AACACGCACACACA
* * *
5351408 ACACAACACGCACACGCA
1 AAATAACACGCACACACA
5351426 AAATAACA
1 AAATAACA
5351434 AATTCAAATC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.53, C:0.36, G:0.07, T:0.04
Consensus pattern (18 bp):
AAATAACACGCACACACA
Found at i:5351489 original size:74 final size:74
Alignment explanation
Indices: 5351411--5351554 Score: 198
Period size: 74 Copynumber: 1.9 Consensus size: 74
5351401 ACACACAACA
* * * *
5351411 CAACACGCACACGCAAAATAACAAATTCAAATCAAAAATAAAAATATAAAAATATATTTGTTTCG
1 CAACACCCACACACAAAATAACAAACTCAAATCAAAAATAAAAATATAAAAATATACTTGTTTCG
5351476 ACCTACACG
66 ACCTACACG
* ** * * *
5351485 CAACACCCACACATAAAATAGTAAGCTCAAATCAAGAATAAAAATATAAAAATATACTTGTTTGG
1 CAACACCCACACACAAAATAACAAACTCAAATCAAAAATAAAAATATAAAAATATACTTGTTTCG
5351550 ACCTA
66 ACCTA
5351555 ATTCAAAATA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.51, C:0.19, G:0.08, T:0.22
Consensus pattern (74 bp):
CAACACCCACACACAAAATAACAAACTCAAATCAAAAATAAAAATATAAAAATATACTTGTTTCG
ACCTACACG
Found at i:5351659 original size:19 final size:20
Alignment explanation
Indices: 5351635--5351673 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5351625 AAAACTCCTT
5351635 ACTCAA-TACTTAATCAAAA
1 ACTCAACTACTTAATCAAAA
* *
5351654 ACTCAACTCCTTACTCAAAA
1 ACTCAACTACTTAATCAAAA
5351674 CTTAACAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (20 bp):
ACTCAACTACTTAATCAAAA
Found at i:5351662 original size:31 final size:31
Alignment explanation
Indices: 5351627--5351690 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
5351617 AATCTCCAAA
*
5351627 AACTCCTTACTCAATACTTAATC-AAAAACTC
1 AACTCCTTACTCAAAACTTAA-CAAAAAACTC
5351658 AACTCCTTACTCAAAACTTAACAAAAAACTC
1 AACTCCTTACTCAAAACTTAACAAAAAACTC
5351689 AA
1 AA
5351691 TTACACAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (31 bp):
AACTCCTTACTCAAAACTTAACAAAAAACTC
Found at i:5353439 original size:24 final size:24
Alignment explanation
Indices: 5353407--5353454 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5353397 CATTCTTCCT
5353407 TTCTTTCCTAAATAATGTAAGTAA
1 TTCTTTCCTAAATAATGTAAGTAA
5353431 TTCTTTCCTAAATAATGTAAGTAA
1 TTCTTTCCTAAATAATGTAAGTAA
5353455 AAAAACATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (24 bp):
TTCTTTCCTAAATAATGTAAGTAA
Found at i:5357517 original size:27 final size:27
Alignment explanation
Indices: 5357476--5357564 Score: 101
Period size: 27 Copynumber: 3.3 Consensus size: 27
5357466 ACTTGCCAAT
*
5357476 TTCCCAACCAACCCCTTCAAAACCAGA
1 TTCCCAACCAGCCCCTTCAAAACCAGA
* *
5357503 TTCCCACCCAGCCCCTTCAAAACTAGA
1 TTCCCAACCAGCCCCTTCAAAACCAGA
* *
5357530 -ACCTCAAACAG-CCCTTCAAAACCAGA
1 TTCC-CAACCAGCCCCTTCAAAACCAGA
*
5357556 TTCTCAACC
1 TTCCCAACC
5357565 TACCCAACCT
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
26 20 0.40
27 30 0.60
ACGTcount: A:0.35, C:0.43, G:0.06, T:0.17
Consensus pattern (27 bp):
TTCCCAACCAGCCCCTTCAAAACCAGA
Found at i:5361053 original size:15 final size:15
Alignment explanation
Indices: 5361033--5361073 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
5361023 TTTAGCTGTT
*
5361033 GAAGAAGAAGACGAC
1 GAAGAAGAAGAAGAC
*
5361048 GAAGAAGAAGAAGAG
1 GAAGAAGAAGAAGAC
*
5361063 GAAGATGAAGA
1 GAAGAAGAAGA
5361074 GCAGATGGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.56, C:0.05, G:0.37, T:0.02
Consensus pattern (15 bp):
GAAGAAGAAGAAGAC
Found at i:5362097 original size:12 final size:13
Alignment explanation
Indices: 5362073--5362100 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5362063 TTGTTTCGTA
5362073 AAAAATAATTTTT
1 AAAAATAATTTTT
5362086 AAAAATAATTTTT
1 AAAAATAATTTTT
5362099 AA
1 AA
5362101 GAAAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAAAATAATTTTT
Found at i:5362196 original size:14 final size:15
Alignment explanation
Indices: 5362179--5362210 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5362169 TTTGTTATTT
5362179 AATTT-TTTTTTAAA
1 AATTTATTTTTTAAA
5362193 AATTTATTTTTTAAA
1 AATTTATTTTTTAAA
5362208 AAT
1 AAT
5362211 AATATTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTTATTTTTTAAA
Found at i:5362275 original size:26 final size:26
Alignment explanation
Indices: 5362217--5362288 Score: 98
Period size: 25 Copynumber: 2.9 Consensus size: 26
5362207 AAATAATATT
*
5362217 AATA-TTACTATTAAAATAT-TGTAAA
1 AATATTTATTATTAAAATATAT-TAAA
5362242 AA-ATTTATTATTAAAATATATTAAA
1 AATATTTATTATTAAAATATATTAAA
5362267 AATATTTATTATTAAAAT-TATT
1 AATATTTATTATTAAAATATATT
5362289 CATATTAAAC
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
24 1 0.02
25 26 0.60
26 16 0.37
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (26 bp):
AATATTTATTATTAAAATATATTAAA
Found at i:5362281 original size:16 final size:16
Alignment explanation
Indices: 5362260--5362307 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
5362250 TATTAAAATA
5362260 TATTAAAAATATTTAT
1 TATTAAAAATATTTAT
* *
5362276 TATTAAAATTATTCA-
1 TATTAAAAATATTTAT
*
5362291 TATTAAACAATAATTAT
1 TATTAAA-AATATTTAT
5362308 ATTTTAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (16 bp):
TATTAAAAATATTTAT
Found at i:5362463 original size:18 final size:18
Alignment explanation
Indices: 5362430--5362479 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
5362420 AATATATTAA
5362430 ATTAATAATA--TTATTT
1 ATTAATAATATTTTATTT
5362446 ATTAATAATATTTTATTT
1 ATTAATAATATTTTATTT
5362464 ATTAAT-ATATTATTAT
1 ATTAATAATATT-TTAT
5362480 AATATTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.32
17 5 0.16
18 16 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTAATAATATTTTATTT
Found at i:5362483 original size:28 final size:27
Alignment explanation
Indices: 5362435--5362555 Score: 121
Period size: 28 Copynumber: 4.5 Consensus size: 27
5362425 ATTAAATTAA
5362435 TAATATTATTTATTAATAATATTTTATTTAT
1 TAATA-TA-TTATT-ATAATA-TTTATTTAT
*
5362466 TAATATATTATTATAATATTTATTAAT
1 TAATATATTATTATAATATTTATTTAT
5362493 T-A-A-ATTA--ATAATA-TTATTTAT
1 TAATATATTATTATAATATTTATTTAT
5362514 TAATATATTATACTATAATATTT-TTTAT
1 TAATATATTAT--TATAATATTTATTTAT
*
5362542 TAATATAATATTAT
1 TAATATATTATTAT
5362556 TTATAAATAA
Statistics
Matches: 79, Mismatches: 3, Indels: 21
0.77 0.03 0.20
Matches are distributed among these distances:
21 8 0.10
22 7 0.09
23 1 0.01
24 8 0.10
25 1 0.01
26 4 0.05
27 9 0.11
28 27 0.34
29 7 0.09
30 2 0.03
31 5 0.06
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (27 bp):
TAATATATTATTATAATATTTATTTAT
Found at i:5362507 original size:66 final size:68
Alignment explanation
Indices: 5362392--5362522 Score: 205
Period size: 66 Copynumber: 1.9 Consensus size: 68
5362382 TTTATATTAA
*
5362392 TTATTAATATATTATAATATAATTTATTAATATATTAAATTAATAATATTATTTATTAATAATAT
1 TTATTAATATATTAT-ATATAATATATTAATATATTAAATTAATAATATTATTTATTAAT-ATAT
5362457 TTTAT
64 TTTAT
*
5362462 TTATTAATATATTAT-TATAATAT-TTATTA-ATTAAATTAATAATATTATTTATTAATATATT
1 TTATTAATATATTATATATAATATATTAATATATTAAATTAATAATATTATTTATTAATATATT
5362523 ATACTATAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
65 5 0.08
66 27 0.46
67 5 0.08
68 7 0.12
70 15 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (68 bp):
TTATTAATATATTATATATAATATATTAATATATTAAATTAATAATATTATTTATTAATATATTT
TAT
Found at i:5362550 original size:18 final size:18
Alignment explanation
Indices: 5362527--5362573 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
5362517 TATATTATAC
* *
5362527 TATAATATTTTTTATTAA
1 TATAATATTATTTATAAA
5362545 TATAATATTATTTATAAA
1 TATAATATTATTTATAAA
5362563 TA-AA-ATTATTT
1 TATAATATTATTT
5362574 CCAAAAGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 7 0.26
17 2 0.07
18 18 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATAATATTATTTATAAA
Found at i:5362563 original size:66 final size:66
Alignment explanation
Indices: 5362393--5362553 Score: 182
Period size: 66 Copynumber: 2.3 Consensus size: 66
5362383 TTATATTAAT
* *
5362393 TATTAATATATTATAATATAATTTATTAATATATTAAATTAATAATATTATTTATTAATAATATT
1 TATTAATATA-T-TAATATAATAT-TTATTA-ATTAAATTAATAATATTATTTATTAATAATATT
*
5362458 TTATT
62 TTATA
*
5362463 TATTAATATATTATTATAATATTTATTAATTAAATTAATAATATTATTTATTAAT-ATATTATAC
1 TATTAATATATTAATATAATATTTATTAATTAAATTAATAATATTATTTATTAATAATATT-T--
5362527 TATAA
63 TAT-A
* *
5362532 TATT-TTTTATTAATATAATATT
1 TATTAATATATTAATATAATATT
5362554 ATTTATAAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
65 5 0.06
66 28 0.35
67 5 0.06
68 27 0.34
69 5 0.06
70 10 0.12
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.55
Consensus pattern (66 bp):
TATTAATATATTAATATAATATTTATTAATTAAATTAATAATATTATTTATTAATAATATTTTAT
A
Found at i:5362943 original size:2 final size:2
Alignment explanation
Indices: 5362938--5362965 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5362928 TTTTTTGTAA
5362938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5362966 TAACTGCATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5367006 original size:1 final size:1
Alignment explanation
Indices: 5367000--5367029 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
5366990 ATTTAATGGC
5367000 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5367030 CCTATACTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5373157 original size:4 final size:4
Alignment explanation
Indices: 5373150--5373205 Score: 58
Period size: 4 Copynumber: 14.0 Consensus size: 4
5373140 GTGTGTGTCC
* * * * *
5373150 ATAT ATAT ATAT ATAT ATAT ATAT ATTT ATTT ATTT ATTT ATTT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
5373198 TTAT ATAT
1 ATAT ATAT
5373206 CACATTTGCA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (4 bp):
ATAT
Found at i:5383593 original size:25 final size:26
Alignment explanation
Indices: 5383565--5383615 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
5383555 ATTCCTTCTG
*
5383565 AAAATC-AAAGAATTTTGAGAGAAAA
1 AAAATCAAAAGAATTTTGAAAGAAAA
*
5383590 AAAATCAAAAGAATTTTTAAAGAAAA
1 AAAATCAAAAGAATTTTGAAAGAAAA
5383616 TTGATGGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.63, C:0.04, G:0.12, T:0.22
Consensus pattern (26 bp):
AAAATCAAAAGAATTTTGAAAGAAAA
Found at i:5386560 original size:25 final size:26
Alignment explanation
Indices: 5386515--5386565 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
5386505 ATTGTAGATA
*
5386515 CCCATTTTAGTCTGGGCCCAATTAGG
1 CCCATTTTAGTCTGGGCCCAACTAGG
5386541 CCCATTTT-GT-TCGGGCCCAACTAGG
1 CCCATTTTAGTCT-GGGCCCAACTAGG
5386566 TCAATTATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 1 0.04
25 14 0.61
26 8 0.35
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (26 bp):
CCCATTTTAGTCTGGGCCCAACTAGG
Found at i:5386604 original size:3 final size:3
Alignment explanation
Indices: 5386596--5386664 Score: 88
Period size: 3 Copynumber: 23.7 Consensus size: 3
5386586 CCAATTAGAT
*
5386596 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
5386643 TTA ATG TTA TTT TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
5386665 TTTTTTCTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 4 0.07
3 52 0.93
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5387277 original size:49 final size:49
Alignment explanation
Indices: 5387202--5387305 Score: 129
Period size: 48 Copynumber: 2.1 Consensus size: 49
5387192 GGCTTTGAAT
* * * * *
5387202 TTTTTGGTGGAGTTTCTGTTGATTTTCTAGAAATTGAT-GAGTTCTCAG
1 TTTTTGGTGGAATTTCTGGTGATTTTCCAGAAATCGATGGAATTCTCAG
* *
5387250 TTTTTGGTTGAATTTTTGGTGACTTTTCCAGAAATCGATGGAATTCTCAG
1 TTTTTGGTGGAATTTCTGGTGA-TTTTCCAGAAATCGATGGAATTCTCAG
5387300 TTTTTG
1 TTTTTG
5387306 ATTAAAGTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
48 18 0.38
49 14 0.30
50 15 0.32
ACGTcount: A:0.19, C:0.10, G:0.23, T:0.48
Consensus pattern (49 bp):
TTTTTGGTGGAATTTCTGGTGATTTTCCAGAAATCGATGGAATTCTCAG
Found at i:5387542 original size:5 final size:5
Alignment explanation
Indices: 5387532--5387566 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
5387522 TCCTTTTTTC
5387532 TATTT TATTT TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT
5387567 CTAACCTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:5387577 original size:31 final size:32
Alignment explanation
Indices: 5387542--5387602 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
5387532 TATTTTATTT
*
5387542 TATTTTATTTT-ATTTTATTTTA-TTTCTAACC
1 TATTTT-TTTTCATTTTATATTATTTTCTAACC
*
5387573 TATTTTTTTTCTTTTTATATTATTTTCTAA
1 TATTTTTTTTCATTTTATATTATTTTCTAA
5387603 AAAAAAACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 4 0.15
31 15 0.58
32 7 0.27
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.70
Consensus pattern (32 bp):
TATTTTTTTTCATTTTATATTATTTTCTAACC
Found at i:5397849 original size:7 final size:7
Alignment explanation
Indices: 5397827--5397860 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
5397817 CTTGATTCTA
5397827 AAAAAAT
1 AAAAAAT
5397834 AATAAAAAT
1 -A-AAAAAT
5397843 AAAAAAT
1 AAAAAAT
5397850 AAAAAAT
1 AAAAAAT
5397857 AAAA
1 AAAA
5397861 GAAAGAGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 17 0.68
8 2 0.08
9 6 0.24
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAAAT
Found at i:5397921 original size:9 final size:8
Alignment explanation
Indices: 5397905--5397943 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
5397895 CGATTTGAAC
5397905 AAAAAAAT
1 AAAAAAAT
5397913 AATAAAAAT
1 AA-AAAAAT
5397922 AAAAAAAT
1 AAAAAAAT
5397930 AAAAAGAA-
1 AAAAA-AAT
5397938 AAAAAA
1 AAAAAA
5397944 GTTTAAGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 1 0.03
8 18 0.62
9 10 0.34
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:5397925 original size:17 final size:16
Alignment explanation
Indices: 5397905--5397943 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
5397895 CGATTTGAAC
5397905 AAAAAAATAATAAA-AA
1 AAAAAAATAA-AAAGAA
5397921 TAAAAAAATAAAAAGAA
1 -AAAAAAATAAAAAGAA
5397938 AAAAAA
1 AAAAAA
5397944 GTTTAAGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (16 bp):
AAAAAAATAAAAAGAA
Found at i:5397930 original size:14 final size:14
Alignment explanation
Indices: 5397907--5397942 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
5397897 ATTTGAACAA
*
5397907 AAAAATAATAAAAAT
1 AAAAA-AATAAAAAG
5397922 AAAAAAATAAAAAG
1 AAAAAAATAAAAAG
5397936 AAAAAAA
1 AAAAAAA
5397943 AGTTTAAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (14 bp):
AAAAAAATAAAAAG
Found at i:5398992 original size:89 final size:87
Alignment explanation
Indices: 5398899--5399367 Score: 404
Period size: 89 Copynumber: 5.3 Consensus size: 87
5398889 TGATTCTTAA
* * * *
5398899 TTTCATTTCGATAATTTATTTTTGACCTTAATTCAGTCCTGGTTGCTTTCTAATGACTTGTGGTT
1 TTTCATTTCGATCATTTATTTTTGACCTCAATTCAGTCCTGGTCGCTTTCTAATGACTCGTGGTT
* *
5398964 TTGTCTTGGTCACATGATTCATGG
66 TT-TC-CGATCACATGATTCATGG
* * * * *
5398988 TTTCA-TTCTGATCATTTATTTTTAACATCGACTT-AGTTCTGGTCGACTTTTTAATGACTCGTG
1 TTTCATTTC-GATCATTTATTTTTGACCTC-AATTCAGTCCTGGTCG-CTTTCTAATGACTCGTG
* * * *
5399051 GTTTCATTCTGACCACATAATTCGTGG
63 GTTT--TTCCGATCACATGATTCATGG
* * * * *
5399078 TTTCATTTCGATCGTTTATTTTTGACCTCGACTC-GATCCTGATCGCTTTCTAATGACTCGTGAT
1 TTTCATTTCGATCATTTATTTTTGACCTCAATTCAG-TCCTGGTCGCTTTCTAATGACTCGTGGT
* *
5399142 TTTGTCCCAATCACATGATTCATAG
65 TTT-T-CCGATCACATGATTCATGG
* ** * *
5399167 TTTCATCTCGATCATTTATTTTCAACCTCGATTCAATCCTGGTCGACTTTCTAATGACTCGTGGT
1 TTTCATTTCGATCATTTATTTTTGACCTCAATTCAGTCCTGGTCG-CTTTCTAATGACTCGTGGT
5399232 TTCATTCCGATCACATGATTCATGG
65 TT--TTCCGATCACATGATTCATGG
* * *
5399257 TTT--TGTTCGATCATTTATTTTCGACC-CAATT---T--TGGTCACTTTCTAATGACTTGTGGT
1 TTTCAT-TTCGATCATTTATTTTTGACCTCAATTCAGTCCTGGTCGCTTTCTAATGACTCGTGGT
* *
5399314 TTCATCTC-AGTCACATGATTCGTGG
65 TT-TTC-CGA-TCACATGATTCATGG
*
5399339 TTTCATTTCGATAATTTATTTTTGACCTC
1 TTTCATTTCGATCATTTATTTTTGACCTC
5399368 TACTTTGTCT
Statistics
Matches: 311, Mismatches: 49, Indels: 45
0.77 0.12 0.11
Matches are distributed among these distances:
81 3 0.01
82 38 0.12
83 24 0.08
84 2 0.01
85 1 0.00
87 1 0.00
88 9 0.03
89 120 0.39
90 105 0.34
91 6 0.02
92 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (87 bp):
TTTCATTTCGATCATTTATTTTTGACCTCAATTCAGTCCTGGTCGCTTTCTAATGACTCGTGGTT
TTTCCGATCACATGATTCATGG
Found at i:5399079 original size:90 final size:91
Alignment explanation
Indices: 5398899--5399430 Score: 403
Period size: 89 Copynumber: 6.0 Consensus size: 91
5398889 TGATTCTTAA
* * * * * *
5398899 TTTCATT-TCGATAATTTATTTTTGACCT-TAATTCAGTCCTGGTTG-CTTTCTAATGACTTGTG
1 TTTCATTCTCGATCATTTATTTTTAACCTCGACTT-AGTCCTGGTCGACTTTCTAATGACTCGTG
* *
5398961 GTTT--TGTCTTGGTCACATGATTCATGG
65 GTTTCAT-TC-CGATCACATGATTCATGG
* * *
5398988 TTTCATTCT-GATCATTTATTTTTAACATCGACTTAGTTCTGGTCGACTTTTTAATGACTCGTGG
1 TTTCATTCTCGATCATTTATTTTTAACCTCGACTTAGTCCTGGTCGACTTTCTAATGACTCGTGG
* * * *
5399052 TTTCATTCTGACCACATAATTCGTGG
66 TTTCATTCCGATCACATGATTCATGG
* * * *
5399078 TTTCATT-TCGATCGTTTATTTTTGACCTCGAC-TCGATCCTGATCG-CTTTCTAATGACTCGTG
1 TTTCATTCTCGATCATTTATTTTTAACCTCGACTTAG-TCCTGGTCGACTTTCTAATGACTCGTG
* ** * * *
5399140 ATTTTGTCCCAATCACATGATTCATAG
65 GTTTCATTCCGATCACATGATTCATGG
* *
5399167 TTTCA-TCTCGATCATTTATTTTCAACCTCGA-TTCAATCCTGGTCGACTTTCTAATGACTCGTG
1 TTTCATTCTCGATCATTTATTTTTAACCTCGACTT-AGTCCTGGTCGACTTTCTAATGACTCGTG
5399230 GTTTCATTCCGATCACATGATTCATGG
65 GTTTCATTCCGATCACATGATTCATGG
** * *
5399257 TTT--TGT-TCGATCATTTATTTTCGACC-C-AATT--T--TGGTC-ACTTTCTAATGACTTGTG
1 TTTCAT-TCTCGATCATTTATTTTTAACCTCGACTTAGTCCTGGTCGACTTTCTAATGACTCGTG
* *
5399312 GTTTCATCTCAG-TCACATGATTCGTGG
65 GTTTCAT-TCCGATCACATGATTCATGG
* * * * * * * * * *
5399339 TTTCATT-TCGATAATTTATTTTTGACCTCTACTTTGTCTTGGTAG-CTTTTTATTGATTCATGG
1 TTTCATTCTCGATCATTTATTTTTAACCTCGACTTAGTCCTGGTCGACTTTCTAATGACTCGTGG
* * *
5399402 TTTC-GTCTCGATCACAGGATTCGTGG
66 TTTCATTC-CGATCACATGATTCATGG
5399428 TTT
1 TTT
5399431 TGCCCCAATC
Statistics
Matches: 359, Mismatches: 58, Indels: 52
0.77 0.12 0.11
Matches are distributed among these distances:
82 41 0.11
83 27 0.08
84 2 0.01
85 4 0.01
87 4 0.01
88 5 0.01
89 160 0.45
90 113 0.31
91 2 0.01
92 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.45
Consensus pattern (91 bp):
TTTCATTCTCGATCATTTATTTTTAACCTCGACTTAGTCCTGGTCGACTTTCTAATGACTCGTGG
TTTCATTCCGATCACATGATTCATGG
Found at i:5399211 original size:179 final size:179
Alignment explanation
Indices: 5398899--5399282 Score: 481
Period size: 179 Copynumber: 2.2 Consensus size: 179
5398889 TGATTCTTAA
* * * * * * *
5398899 TTTCATTTCGATAATTTATTTTTGACCTTAATTCAGTCCTGGTTGCTTTCTAATGACTTGTGGTT
1 TTTCATTTCGATCATTTATTTTTGACCTCAACTCAGTCCTGATCGCTTTCTAATGACTCGTGATT
**** * * * *
5398964 TTGTCTTGGTCACATGATTCATGGTTTCATTCTGATCATTTATTTTTAACATCGACTTAGTTCTG
66 TTGTCCCAATCACATGATTCATAGTTTCATTCTGATCATTTATTTTCAACATCGACTTAATCCTG
* * *
5399029 GTCGACTTTTTAATGACTCGTGGTTTCATTCTGACCACATAATTCGTGG
131 GTCGACTTTCTAATGACTCGTGGTTTCATTCCGACCACATAATTCATGG
* *
5399078 TTTCATTTCGATCGTTTATTTTTGACCTCGACTC-GATCCTGATCGCTTTCTAATGACTCGTGAT
1 TTTCATTTCGATCATTTATTTTTGACCTCAACTCAG-TCCTGATCGCTTTCTAATGACTCGTGAT
*
5399142 TTTGTCCCAATCACATGATTCATAGTTTCA-TCTCGATCATTTATTTTCAACCTCGA-TTCAATC
65 TTTGTCCCAATCACATGATTCATAGTTTCATTCT-GATCATTTATTTTCAACATCGACTT-AATC
* *
5399205 CTGGTCGACTTTCTAATGACTCGTGGTTTCATTCCGATCACATGATTCATGG
128 CTGGTCGACTTTCTAATGACTCGTGGTTTCATTCCGACCACATAATTCATGG
*
5399257 TTT--TGTTCGATCATTTATTTTCGACC
1 TTTCAT-TTCGATCATTTATTTTTGACC
5399283 CAATTTTGGT
Statistics
Matches: 176, Mismatches: 25, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
177 1 0.01
178 25 0.14
179 150 0.85
ACGTcount: A:0.20, C:0.21, G:0.15, T:0.44
Consensus pattern (179 bp):
TTTCATTTCGATCATTTATTTTTGACCTCAACTCAGTCCTGATCGCTTTCTAATGACTCGTGATT
TTGTCCCAATCACATGATTCATAGTTTCATTCTGATCATTTATTTTCAACATCGACTTAATCCTG
GTCGACTTTCTAATGACTCGTGGTTTCATTCCGACCACATAATTCATGG
Found at i:5399945 original size:3 final size:3
Alignment explanation
Indices: 5399931--5400004 Score: 82
Period size: 3 Copynumber: 25.7 Consensus size: 3
5399921 ATTAGATTTT
* * * *
5399931 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA CTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
5399979 CTA TTA TTA TT- TTA TT- TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5400005 TTCTTATGTT
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
2 6 0.09
3 58 0.91
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:5400826 original size:5 final size:5
Alignment explanation
Indices: 5400818--5400859 Score: 57
Period size: 5 Copynumber: 7.8 Consensus size: 5
5400808 CTTTTTTCCA
5400818 ATTTT ATTTT ATTTTCT AATTTT ATTTT ATTTT ATTTT ATTT
1 ATTTT ATTTT A-TTT-T -ATTTT ATTTT ATTTT ATTTT ATTT
5400860 CTAATCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 25 0.74
6 4 0.12
7 4 0.12
8 1 0.03
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:5400838 original size:18 final size:18
Alignment explanation
Indices: 5400811--5400850 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
5400801 AGGTTTTCTT
5400811 TTTTCCAATTTTATTTTA
1 TTTTCCAATTTTATTTTA
*
5400829 TTTTCTAATTTTATTTTA
1 TTTTCCAATTTTATTTTA
5400847 TTTT
1 TTTT
5400851 ATTTTATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTCCAATTTTATTTTA
Found at i:5400883 original size:28 final size:28
Alignment explanation
Indices: 5400818--5400873 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
5400808 CTTTTTTCCA
5400818 ATTTTATTTTATTTTCTAATTTTATTTT
1 ATTTTATTTTATTTTCTAATTTTATTTT
*
5400846 ATTTTATTTTA-TTTCTAATCTTTTTTTT
1 ATTTTATTTTATTTTCTAAT-TTTATTTT
5400874 TGTTTCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (28 bp):
ATTTTATTTTATTTTCTAATTTTATTTT
Found at i:5402658 original size:20 final size:22
Alignment explanation
Indices: 5402619--5402665 Score: 80
Period size: 20 Copynumber: 2.2 Consensus size: 22
5402609 CTTGAAATTA
5402619 ATAAAATATTATTTTATTAAAT
1 ATAAAATATTATTTTATTAAAT
5402641 ATAAAATATTA-TTT-TTAAAT
1 ATAAAATATTATTTTATTAAAT
5402661 ATAAA
1 ATAAA
5402666 TATAAACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 11 0.44
21 3 0.12
22 11 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAAAATATTATTTTATTAAAT
Found at i:5402682 original size:16 final size:16
Alignment explanation
Indices: 5402661--5402722 Score: 79
Period size: 16 Copynumber: 3.8 Consensus size: 16
5402651 ATTTTTAAAT
*
5402661 ATAAATATAAACTTAA
1 ATAAATATAAAATTAA
* *
5402677 ATAAATATAAAAAATAT
1 ATAAATAT-AAAATTAA
5402694 ATAAATATAAAATTAA
1 ATAAATATAAAATTAA
5402710 ATAAATAATAAAA
1 ATAAAT-ATAAAA
5402723 ATATATATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
16 20 0.51
17 19 0.49
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAATATAAAATTAA
Found at i:5402699 original size:17 final size:16
Alignment explanation
Indices: 5402659--5402729 Score: 79
Period size: 17 Copynumber: 4.3 Consensus size: 16
5402649 TTATTTTTAA
**
5402659 ATATAAATATAAACTT
1 ATATAAATATAAAAAT
*
5402675 AAATAAATATAAAAAAT
1 ATATAAATAT-AAAAAT
*
5402692 ATATAAATATAAAATT
1 ATATAAATATAAAAAT
*
5402708 AAATAAATAATAAAAAT
1 ATATAAAT-ATAAAAAT
5402725 ATATA
1 ATATA
5402730 TTTTCTAGGT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
16 21 0.47
17 24 0.53
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (16 bp):
ATATAAATATAAAAAT
Found at i:5402701 original size:33 final size:35
Alignment explanation
Indices: 5402659--5402730 Score: 121
Period size: 33 Copynumber: 2.1 Consensus size: 35
5402649 TTATTTTTAA
*
5402659 ATATAAATATAAACTTAAATAAAT-ATAAAAA-AT
1 ATATAAATATAAAATTAAATAAATAATAAAAATAT
5402692 ATATAAATATAAAATTAAATAAATAATAAAAATAT
1 ATATAAATATAAAATTAAATAAATAATAAAAATAT
5402727 ATAT
1 ATAT
5402731 TTTCTAGGTC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 23 0.64
34 7 0.19
35 6 0.17
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (35 bp):
ATATAAATATAAAATTAAATAAATAATAAAAATAT
Found at i:5403707 original size:31 final size:30
Alignment explanation
Indices: 5403668--5403728 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 30
5403658 ATATAATTTG
5403668 AAAATTCAAAATACAAATTATACATTTTAT
1 AAAATTCAAAATACAAATTATACATTTTAT
* *
5403698 AAAAGTTCAAGATACAAATTATATATTTTAT
1 AAAA-TTCAAAATACAAATTATACATTTTAT
5403729 TTAATTAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAATTCAAAATACAAATTATACATTTTAT
Found at i:5413027 original size:28 final size:28
Alignment explanation
Indices: 5412976--5413029 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
5412966 CACGAATTGC
*
5412976 AAAAGCTGAAGAAATAGTCAAATGAAGT
1 AAAAGCTGAAGAAATAGACAAATGAAGT
*
5413004 AAAAGCTGAAGTAAATA-ACTAATGAA
1 AAAAGCTGAAG-AAATAGACAAATGAA
5413030 TAGTCAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.19
Consensus pattern (28 bp):
AAAAGCTGAAGAAATAGACAAATGAAGT
Found at i:5413884 original size:187 final size:187
Alignment explanation
Indices: 5413641--5414733 Score: 1234
Period size: 187 Copynumber: 5.8 Consensus size: 187
5413631 GAGCAAAACT
* * * * * *
5413641 CCTTCAATATTTCGCTACTCAAATTTTAAGACGATTAGTAAAGGCATTTATTCTAGAAAAATACC
1 CCTTCAATATTCCACTACTCAAATTTTAAGATGGTTAGTGAAGGTATTTATTCTAGAAAAATACC
* * *
5413706 TTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTTAGAACAAACGCCTTC
66 TTCAATAATTCTTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTGAGAACAAACGCCTTC
* * * *
5413771 AATAA-TTTCATATTAAAAAT-TTTTAGGATTATTAAATGCATATTCTAGTGAAAAATG
131 AATAATTTTC-TTTTAAAAATATTTGA-GATTATTAAATGCATCTTCTATTGAAAAATG
* * * * * *
5413828 CCTTCAATATACCATTACTTAAATTTTAAGATAGTAAGTTAAGGTATTTATTCTAGAAAAATACC
1 CCTTCAATATTCCACTACTCAAATTTTAAGATGGTTAGTGAAGGTATTTATTCTAGAAAAATACC
* *
5413893 TTCAATAATTCTTTTTAAATTT-TGTACATAATTATTGAAGGTGTTTTTTGAGAACAAACACCTT
66 TTCAATAATTCTTTTT-AATTTATGTACATAATTATTGAAGGTATTTTTTGAGAACAAACGCCTT
* *
5413957 CAATAATTTTCTTTTAAAAATATTTGGGATTATTAAAAT-CATCTTCTATTGAAAAACG
130 CAATAATTTTCTTTTAAAAATATTTGAGATTATT-AAATGCATCTTCTATTGAAAAATG
* * ** *
5414015 CCTTCGATATTTCACTACTCAAATTTTAAGACAGTTAGTGAAGG-AGTTTATTCTAGAAAAATGC
1 CCTTCAATATTCCACTACTCAAATTTTAAGATGGTTAGTGAAGGTA-TTTATTCTAGAAAAATAC
** * * * *
5414079 CTTCGTTGATTCTTTTTAATTTATGTACATAATTATTCAAGGTATTTTTTGAAAACAAATGCCTT
65 CTTCAATAATTCTTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTGAGAACAAACGCCTT
* * * *
5414144 CAATAATTTTCGTTTAAAAATATTTGAGATTATTAAATACGTTTTCTATTGAAAAATG
130 CAATAATTTTCTTTTAAAAATATTTGAGATTATTAAATGCATCTTCTATTGAAAAATG
* * * * * *
5414202 CCTTCAATATTCCATTACTCAAATATTAAGATGGTTAGTGAATGTGTTTATTTTAGAAAAATGCC
1 CCTTCAATATTCCACTACTCAAATTTTAAGATGGTTAGTGAAGGTATTTATTCTAGAAAAATACC
* * * * *
5414267 TTCATTGATTGTTTTTAATTTATGTACATAATTATTGAAGGTGTTTTTTGAGAACAAATGCCTTC
66 TTCAATAATTCTTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTGAGAACAAACGCCTTC
* ** * *
5414332 AATAATTTTCTTTTAAAAATATTTGAGATTATTAAAGGTGTCTTCTAGTGAAAAATA
131 AATAATTTTCTTTTAAAAATATTTGAGATTATTAAATGCATCTTCTATTGAAAAATG
* * * * * * * *
5414389 TCTTCAACATACCAGTACTCAAAATTTAATATGGTTAGTGAAGGTGTTTATTCTAGAAAAACACC
1 CCTTCAATATTCCACTACTCAAATTTTAAGATGGTTAGTGAAGGTATTTATTCTAGAAAAATACC
* * * *
5414454 TTTAATAATTCCTTTTAAATTT-TGTACATAATTATTGAAGGTGTTTTTTTTAGAACAAACGCCA
66 TTCAATAATT-CTTTTTAATTTATGTACATAATTATTGAAGGT-ATTTTTTGAGAACAAACGCC-
* *
5414518 TT-AATAA-TTTCTTTTTAAAAATATTTGAGATTATTAAAGGCATCTTCTATTGAAAAACG
128 TTCAATAATTTTC-TTTTAAAAATATTTGAGATTATTAAATGCATCTTCTATTGAAAAATG
* * * * * * * *
5414577 CTTTCAATATTCGACTACTCAAATTTTAAGATGGTTAGTGAATGTGTTTATTCCAGTAAAATGCT
1 CCTTCAATATTCCACTACTCAAATTTTAAGATGGTTAGTGAAGGTATTTATTCTAGAAAAATACC
* * * * * * * * *
5414642 TTCACTAATTCATTTTT-ATTTTTTTACGTAATTATTGAAGGTTTTTTTTTTATAACAAACACTT
66 TTCAATAATTC-TTTTTAATTTATGTACATAATTATTGAAGG-TATTTTTTGAGAACAAACGCCT
*
5414706 TCAATAATTTT-TTTAAAAAAATATTTGA
129 TCAATAATTTTCTTT-TAAAAATATTTGA
5414734 AAAATGCCTT
Statistics
Matches: 776, Mismatches: 112, Indels: 35
0.84 0.12 0.04
Matches are distributed among these distances:
186 10 0.01
187 557 0.72
188 203 0.26
189 6 0.01
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (187 bp):
CCTTCAATATTCCACTACTCAAATTTTAAGATGGTTAGTGAAGGTATTTATTCTAGAAAAATACC
TTCAATAATTCTTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTGAGAACAAACGCCTTC
AATAATTTTCTTTTAAAAATATTTGAGATTATTAAATGCATCTTCTATTGAAAAATG
Found at i:5414363 original size:62 final size:62
Alignment explanation
Indices: 5414110--5414372 Score: 155
Period size: 62 Copynumber: 4.2 Consensus size: 62
5414100 TATGTACATA
* * * * *
5414110 ATTATTCAAGGTATTTTTTGAAAACAAATGCCTTCAATAATTTTCGTTTAAAAATATTTGA-G
1 ATTATTAAAGGTGTTTTTTGAGAA-AAATGCCTTCAATAATTTTCTTTTAAAAATATTAGATG
*** * ** *
5414172 ATTATTAAATACGTTTTCTAT-TGAAAAATGCCTTCAAT-A--TTCCATTACTCAAATATTAAGA
1 ATTATTAAAGGTGTTTT-T-TGAGAAAAATGCCTTCAATAATTTTCTTTTA--AAAATATT-AGA
5414233 TG
61 TG
* * * * * * * * ** * *
5414235 GTTAGTGAATGTGTTTATTTTAGAAAAATGCCTTCATTGATTGT-TTTT-AATTTATGTACATA
1 ATTATTAAAGGTGTTT-TTTGAGAAAAATGCCTTCAATAATTTTCTTTTAAAAATAT-TAGATG
* *
5414297 ATTATTGAAGGTGTTTTTTGAGAACAAATGCCTTCAATAATTTTCTTTTAAAAATATTTGA-G
1 ATTATTAAAGGTGTTTTTTGAGAA-AAATGCCTTCAATAATTTTCTTTTAAAAATATTAGATG
5414359 ATTATTAAAGGTGT
1 ATTATTAAAGGTGT
5414373 CTTCTAGTGA
Statistics
Matches: 147, Mismatches: 39, Indels: 30
0.68 0.18 0.14
Matches are distributed among these distances:
59 6 0.04
61 15 0.10
62 77 0.52
63 38 0.26
64 8 0.05
65 2 0.01
66 1 0.01
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (62 bp):
ATTATTAAAGGTGTTTTTTGAGAAAAATGCCTTCAATAATTTTCTTTTAAAAATATTAGATG
Found at i:5414723 original size:561 final size:561
Alignment explanation
Indices: 5413641--5414733 Score: 1446
Period size: 561 Copynumber: 1.9 Consensus size: 561
5413631 GAGCAAAACT
* * *
5413641 CCTTCAATATTTCGCTACTCAAATTTTAAGACGATTAGTAAAGGCATTTATTCTAGAAAAATACC
1 CCTTCAATATTCCACTACTCAAATATTAAGACGATTAGTAAAGGCATTTATTCTAGAAAAATACC
*
5413706 TTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTTAGAACAAACGCCTTC
66 TTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTGAGAACAAACGCCTTC
* * * *
5413771 AATAATTTCATATTAAAAATTTTTAGGATTATTAAATGCATATTCTAGTGAAAAATGCCTTCAAT
131 AATAATTTCATATTAAAAATTTTGAGGATTATTAAAGGCATATTCTAGTGAAAAATACCTTCAAC
* * * * *
5413836 ATACCATTACTTAAATTTTAAGATAGTAAGTTAAGGTATTTATTCTAGAAAAATACCTTCAATAA
196 ATACCAGTACTCAAAATTTAAGATAGTAAGTGAAGGTATTTATTCTAGAAAAACACCTTCAATAA
*
5413901 TTCTTTTTAAATTTTGTACATAATTATTGAAGGTGTTTTTTGAGAACAAACACCTTCAATAATTT
261 TTCCTTTTAAATTTTGTACATAATTATTGAAGGTGTTTTTTGAGAACAAACACCTTCAATAATTT
* * *
5413966 TCTTTTAAAAATATTTGGGATTATTAAAATCATCTTCTATTGAAAAACGCCTTCGATATTTCACT
326 TCTTTTAAAAATATTTGAGATTATTAAAAGCATCTTCTATTGAAAAACGCCTTCAATATTTCACT
* ** *
5414031 ACTCAAATTTTAAGACAGTTAGTGAAGGAGTTTATTCTAGAAAAATGCCTTCGTTGATTCTTTTT
391 ACTCAAATTTTAAGACAGTTAGTGAAGGAGTTTATTCCAGAAAAATGCCTTCACTAATTCTTTTT
**
5414096 AATTTATGTACATAATTATTCAAGGTATTTTTTGAAAACAAATGCCTTCAATAATTTTCGTTT-A
456 AATTTATGTACATAATTATTCAAGGTATTTTTTGAAAACAAACACCTTCAATAATTTTC-TTTAA
5414160 AAAATATTTGAGATTATTAAATACGTTTTCTATTGAAAAATG
520 AAAATATTTGAGATTATTAAATACGTTTTCTATTGAAAAATG
* * * * * ** * *
5414202 CCTTCAATATTCCATTACTCAAATATTAAGATGGTTAGTGAATGTGTTTATTTTAGAAAAATGCC
1 CCTTCAATATTCCACTACTCAAATATTAAGACGATTAGTAAAGGCATTTATTCTAGAAAAATACC
* * ** * *
5414267 TTCATTGATTGTTTTTAATTTATGTACATAATTATTGAAGGTGTTTTTTGAGAACAAATGCCTTC
66 TTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTGAGAACAAACGCCTTC
* ** * *
5414332 AATAATTTTC-TTTTAAAAATATTTGA-GATTATTAAAGGTGTCTTCTAGTGAAAAATATCTTCA
131 AATAA-TTTCATATTAAAAAT-TTTGAGGATTATTAAAGGCATATTCTAGTGAAAAATACCTTCA
* * * * *
5414395 ACATACCAGTACTCAAAATTTAATATGGTTAGTGAAGGTGTTTATTCTAGAAAAACACCTTTAAT
194 ACATACCAGTACTCAAAATTTAAGATAGTAAGTGAAGGTATTTATTCTAGAAAAACACCTTCAAT
* *
5414460 AATTCCTTTTAAATTTTGTACATAATTATTGAAGGTGTTTTTTTTAGAACAAACGCCATT-AATA
259 AATTCCTTTTAAATTTTGTACATAATTATTGAAGGTG-TTTTTTGAGAACAAACACC-TTCAATA
* *
5414524 A-TTTCTTTTTAAAAATATTTGAGATTATTAAAGGCATCTTCTATTGAAAAACGCTTTCAATA-T
322 ATTTTC-TTTTAAAAATATTTGAGATTATTAAAAGCATCTTCTATTGAAAAACGCCTTCAATATT
** * * * *
5414587 TCGACTACTCAAATTTTAAGATGGTTAGTGAATGTGTTTATTCCAGTAAAATGCTTTCACTAATT
386 TC-ACTACTCAAATTTTAAGACAGTTAGTGAAGGAGTTTATTCCAGAAAAATGCCTTCACTAATT
* * * * * * * *
5414652 CATTTTT-ATTTTTTTACGTAATTATTGAAGGTTTTTTTTTTATAACAAACACTTTCAATAATTT
450 C-TTTTTAATTTATGTACATAATTATTCAAGG-TATTTTTTGAAAACAAACACCTTCAATAATTT
5414716 T-TTTAAAAAAATATTTGA
513 TCTTT-AAAAAATATTTGA
5414734 AAAATGCCTT
Statistics
Matches: 456, Mismatches: 66, Indels: 18
0.84 0.12 0.03
Matches are distributed among these distances:
561 256 0.56
562 154 0.34
563 46 0.10
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (561 bp):
CCTTCAATATTCCACTACTCAAATATTAAGACGATTAGTAAAGGCATTTATTCTAGAAAAATACC
TTCACTAATTCCTTTTAATTTATGTACATAATTATTGAAGGTATTTTTTGAGAACAAACGCCTTC
AATAATTTCATATTAAAAATTTTGAGGATTATTAAAGGCATATTCTAGTGAAAAATACCTTCAAC
ATACCAGTACTCAAAATTTAAGATAGTAAGTGAAGGTATTTATTCTAGAAAAACACCTTCAATAA
TTCCTTTTAAATTTTGTACATAATTATTGAAGGTGTTTTTTGAGAACAAACACCTTCAATAATTT
TCTTTTAAAAATATTTGAGATTATTAAAAGCATCTTCTATTGAAAAACGCCTTCAATATTTCACT
ACTCAAATTTTAAGACAGTTAGTGAAGGAGTTTATTCCAGAAAAATGCCTTCACTAATTCTTTTT
AATTTATGTACATAATTATTCAAGGTATTTTTTGAAAACAAACACCTTCAATAATTTTCTTTAAA
AAATATTTGAGATTATTAAATACGTTTTCTATTGAAAAATG
Found at i:5414814 original size:100 final size:101
Alignment explanation
Indices: 5414634--5414827 Score: 268
Period size: 100 Copynumber: 1.9 Consensus size: 101
5414624 TTATTCCAGT
* * ** *
5414634 AAAATGCTTTCACTAATTCATTTTTATTTTTTTACGTAATTATTGAAGGTTTTTTTTTTATAACA
1 AAAATGCCTTCACTAATTCATTTTTATTTTTTTACATAATTATTGAAGGTCATTTTTTTAGAACA
5414699 AACACTTTCAATAATTT-TTTTAAAAAAATATTTGA
66 AACACTTTCAATAATTTCTTTTAAAAAAATATTTGA
* *
5414734 AAAATGCCTTCACTAATTCGTTTTTATTTTTTTTACATAATTATTGAAGG-CATTTTTTTAGAAT
1 AAAATGCCTTCACTAATTCATTTTTA-TTTTTTTACATAATTATTGAAGGTCATTTTTTTAGAAC
*
5414798 AAACACCTTT-ATTAATTTCCTTTTAAAAAA
65 AAACA-CTTTCAATAATTT-CTTTTAAAAAA
5414828 TTTTGAGATT
Statistics
Matches: 82, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
100 46 0.56
101 26 0.32
102 10 0.12
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.48
Consensus pattern (101 bp):
AAAATGCCTTCACTAATTCATTTTTATTTTTTTACATAATTATTGAAGGTCATTTTTTTAGAACA
AACACTTTCAATAATTTCTTTTAAAAAAATATTTGA
Found at i:5425240 original size:7 final size:7
Alignment explanation
Indices: 5425230--5425255 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5425220 TAATTTTTTT
5425230 ATCATAA
1 ATCATAA
5425237 ATCATAA
1 ATCATAA
5425244 ATCATAA
1 ATCATAA
5425251 ATCAT
1 ATCAT
5425256 GTGGAGTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (7 bp):
ATCATAA
Found at i:5425858 original size:104 final size:103
Alignment explanation
Indices: 5425735--5426056 Score: 355
Period size: 104 Copynumber: 3.0 Consensus size: 103
5425725 ATATTTTTAT
* *
5425735 AAAAACATATTTGAATAAAAGCTTTACCAACAGATTGGAAGGCAATCTTTTAAAAGATAGAGTTT
1 AAAAAAATATTTAAATAAAAGCTTTACCAACAGATTGGAAGGCAATCTTTTAAAA-ATAGAGTTT
5425800 TACTAACATATTGGAAAACTTTATAATTTTATTTATTTC
65 TACTAACATATTGGAAAACTTTATAATTTTATTTATTTC
* * * * *
5425839 AAAAAAATATTTAAATAAAAGCCTTAACAATAGATTGGAAGGCAATAATTTTTTTTTTAAAAAAA
1 AAAAAAATATTTAAATAAAAGCTTTACCAACAGATTGGAAGGC---AA----TCTTTTAAAAATA
* * *
5425904 AAGGTTTTACCAACATATT-GAAAAATCTTATAATTTTATTTATTTC
59 GA-GTTTTACTAACATATTGGAAAACT-TTATAATTTTATTTATTTC
* * *
5425950 -AAAAAA-ATTTAAATAAAAGCTTTACCAACAGATTGAAAGGTAATCATTTTTAAAAAATAGGGT
1 AAAAAAATATTTAAATAAAAGCTTTACCAACAGATTGGAAGGCAATC--TTTT-AAAAATAGAGT
* * *
5426013 TTCACTAACATATTGGAAGACCTTATAATTTTATTTATTT-
63 TTTACTAACATATTGGAAAACTTTATAATTTTATTTATTTC
5426053 AAAA
1 AAAA
5426057 TATATATACA
Statistics
Matches: 180, Mismatches: 24, Indels: 28
0.78 0.10 0.12
Matches are distributed among these distances:
102 1 0.01
104 77 0.43
105 10 0.06
106 2 0.01
107 2 0.01
109 30 0.17
110 15 0.08
111 43 0.24
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.36
Consensus pattern (103 bp):
AAAAAAATATTTAAATAAAAGCTTTACCAACAGATTGGAAGGCAATCTTTTAAAAATAGAGTTTT
ACTAACATATTGGAAAACTTTATAATTTTATTTATTTC
Found at i:5426723 original size:21 final size:21
Alignment explanation
Indices: 5426697--5426739 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5426687 GTATTTTATT
*
5426697 TATTATTCATTTTCATATATC
1 TATTATTCATTTGCATATATC
5426718 TATTATTCATTTGCATATATC
1 TATTATTCATTTGCATATATC
5426739 T
1 T
5426740 GTCATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.14, G:0.02, T:0.56
Consensus pattern (21 bp):
TATTATTCATTTGCATATATC
Found at i:5426750 original size:21 final size:21
Alignment explanation
Indices: 5426705--5426750 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5426695 TTTATTATTC
* * *
5426705 ATTTTCATATATCTATTATTC
1 ATTTGCATATATCTATCATTA
*
5426726 ATTTGCATATATCTGTCATTA
1 ATTTGCATATATCTATCATTA
5426747 ATTT
1 ATTT
5426751 ACCTACGCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.54
Consensus pattern (21 bp):
ATTTGCATATATCTATCATTA
Found at i:5429744 original size:12 final size:12
Alignment explanation
Indices: 5429729--5429759 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5429719 GAATTAAGAA
5429729 AAAAAAAGAAAG
1 AAAAAAAGAAAG
*
5429741 AAAAAGAGAAAG
1 AAAAAAAGAAAG
5429753 AAAAAAA
1 AAAAAAA
5429760 AATTGATGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAG
Found at i:5432043 original size:18 final size:17
Alignment explanation
Indices: 5432020--5432076 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 17
5432010 TTGTTTGTCT
5432020 TATTTATTTATTTGTTTA
1 TATTTATTTATTT-TTTA
*
5432038 TATTTATTT-TTTTCTA
1 TATTTATTTATTTTTTA
*
5432054 TATATT-TTTAATTTTT-
1 TAT-TTATTTATTTTTTA
5432070 TATTTAT
1 TATTTAT
5432077 CTAGTTCTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
15 2 0.06
16 13 0.39
17 9 0.27
18 9 0.27
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (17 bp):
TATTTATTTATTTTTTA
Found at i:5432888 original size:107 final size:104
Alignment explanation
Indices: 5432653--5432886 Score: 296
Period size: 103 Copynumber: 2.2 Consensus size: 104
5432643 TCAATATATA
* *
5432653 TTTATAAAAACATATTTGAATAAAAGCCTTACCAACATATTGGAAGGCAATCTTTAAAAAATATG
1 TTTA-AAAAACATATTTAAATAAAAGCCTTACCAACAGATTGGAAGGCAATCTTTAAAAAATATG
* * *
5432718 GTTATATCAACATATTGAAAAACCTTATAATTTTATTTAT
65 ATTATACCAACATATTGAAAAACCTTATAATTTTATGTAT
*
5432758 TTTAAAAAA-ATATTTAAATAAAAGCCTTACCAACAGATTGTAAGGCAATCATTTTTTAAAAAAT
1 TTTAAAAAACATATTTAAATAAAAGCCTTACCAACAGATTGGAAGGCAATC----TTTAAAAAAT
* * *
5432822 GTGATTTTACCAATATATTGAAAAACCTTATAA-TTT-TGT-T
62 ATGATTATACCAACATATTGAAAAACCTTATAATTTTATGTAT
*
5432862 TTTAAAAATACATATATAAATAAAA
1 TTTAAAAA-ACATATTTAAATAAAA
5432887 AGTCTTATTA
Statistics
Matches: 113, Mismatches: 10, Indels: 11
0.84 0.07 0.08
Matches are distributed among these distances:
103 38 0.34
104 14 0.12
105 7 0.06
106 16 0.14
107 38 0.34
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (104 bp):
TTTAAAAAACATATTTAAATAAAAGCCTTACCAACAGATTGGAAGGCAATCTTTAAAAAATATGA
TTATACCAACATATTGAAAAACCTTATAATTTTATGTAT
Found at i:5433643 original size:97 final size:95
Alignment explanation
Indices: 5433422--5433713 Score: 557
Period size: 95 Copynumber: 3.1 Consensus size: 95
5433412 AGTTAATATT
5433422 ACCCTCCAAGTCTGTAAGCATCGCTTGTGTTCAAACTTCAAAGTTTGGCGTGTTTGAATTAATCA
1 ACCCTCCAAGTCTGTAAGCATCGCTTGTGTTCAAACTTCAAAGTTTGGCGTGTTTGAATTAATCA
5433487 CGTTAACCTTGACCCCAGTCTCCACGAATG
66 CGTTAACCTTGACCCCAGTCTCCACGAATG
*
5433517 ACCCTCCAAGTCTGTAAGCATCGCTTGTGTTCAAACTTCAAAGTTTGGCGTGTTTGAATTAAAAA
1 ACCCTCCAAGTCTGTAAGCATCGCTTGTGTTCAAACTTCAAAGTTTGGCGTGTTTGAATT--AAT
5433582 CACGTTAACCTTGACCCCAGTCTCCACGAATG
64 CACGTTAACCTTGACCCCAGTCTCCACGAATG
5433614 ACCCTCCAAGTCTGTAAGCATCGCTTGTGTTCAAACTTCAAAGTTTGGCGTGTTTGAATTAATCA
1 ACCCTCCAAGTCTGTAAGCATCGCTTGTGTTCAAACTTCAAAGTTTGGCGTGTTTGAATTAATCA
5433679 CGTTAACCTTGACCCCAGTCTCCACGAATG
66 CGTTAACCTTGACCCCAGTCTCCACGAATG
5433709 ACCCT
1 ACCCT
5433714 AGTCTCTGCG
Statistics
Matches: 193, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
95 99 0.51
97 94 0.49
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (95 bp):
ACCCTCCAAGTCTGTAAGCATCGCTTGTGTTCAAACTTCAAAGTTTGGCGTGTTTGAATTAATCA
CGTTAACCTTGACCCCAGTCTCCACGAATG
Found at i:5442621 original size:2 final size:2
Alignment explanation
Indices: 5442614--5442645 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5442604 CTTAGGCCTC
*
5442614 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5442646 TTGCGATCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5442881 original size:21 final size:21
Alignment explanation
Indices: 5442845--5442929 Score: 93
Period size: 21 Copynumber: 4.0 Consensus size: 21
5442835 ATAATATAAG
*
5442845 TAAAATTTGA-TAACTTTTGA
1 TAAAATTTTAGTAACTTTTGA
*
5442865 TAAAATTTTAGTAACTTTCGA
1 TAAAATTTTAGTAACTTTTGA
* *
5442886 TACAATTTTGGTAA-TTATTGA
1 TAAAATTTTAGTAACTT-TTGA
*
5442907 TAAAATTTTAGTAATCTCTTGA
1 TAAAATTTTAGTAA-CTTTTGA
5442929 T
1 T
5442930 GTAGTTTTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
20 11 0.21
21 36 0.68
22 5 0.09
23 1 0.02
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (21 bp):
TAAAATTTTAGTAACTTTTGA
Found at i:5443339 original size:22 final size:22
Alignment explanation
Indices: 5443280--5443416 Score: 105
Period size: 22 Copynumber: 6.2 Consensus size: 22
5443270 ATTATTAGCA
**
5443280 ATTTACTACTAAGCTAT-AAGTG
1 ATTTACTACTAAATTATCAA-TG
* * * *
5443302 ATATATTATTAAATTATCAATA
1 ATTTACTACTAAATTATCAATG
* *
5443324 ATTTACTACTAAATTAGCATTG
1 ATTTACTACTAAATTATCAATG
* *
5443346 ATTTACTATTAAATTATGAATG
1 ATTTACTACTAAATTATCAATG
* * *
5443368 ATTTATTACTAAGTTATGAATG
1 ATTTACTACTAAATTATCAATG
* * * *
5443390 ATTTATTATTCAATTATTAATG
1 ATTTACTACTAAATTATCAATG
5443412 ATTTA
1 ATTTA
5443417 TTAAGAAATT
Statistics
Matches: 91, Mismatches: 23, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
22 89 0.98
23 2 0.02
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.45
Consensus pattern (22 bp):
ATTTACTACTAAATTATCAATG
Found at i:5443414 original size:66 final size:65
Alignment explanation
Indices: 5443344--5443469 Score: 148
Period size: 66 Copynumber: 1.9 Consensus size: 65
5443334 AAATTAGCAT
** * * *
5443344 TGATTTACTATTAAATTA-TGAATGATTTATTACTAAGTTATGAA-TGATTTATTATTCAATTAT
1 TGATTTACTAAGAAATTATTG-ATGATTTATAACAAAGTTAT-AACTGATTTACTATT-AATTAT
5443407 TAA
63 TAA
* *
5443410 TGATTTATTAAGAAATTATTGATGATTTGTAACAAAGTTATAACTGATTTACTATTAATT
1 TGATTTACTAAGAAATTATTGATGATTTATAACAAAGTTATAACTGATTTACTATTAATT
5443470 TGTGGATGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
65 6 0.12
66 43 0.84
67 2 0.04
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (65 bp):
TGATTTACTAAGAAATTATTGATGATTTATAACAAAGTTATAACTGATTTACTATTAATTATTAA
Found at i:5443417 original size:11 final size:11
Alignment explanation
Indices: 5443359--5443420 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
5443349 TACTATTAAA
*
5443359 TTATGAATGAT
1 TTATTAATGAT
* * *
5443370 TTATTACTAAG
1 TTATTAATGAT
*
5443381 TTATGAATGAT
1 TTATTAATGAT
* * *
5443392 TTATTATTCAA
1 TTATTAATGAT
5443403 TTATTAATGAT
1 TTATTAATGAT
5443414 TTATTAA
1 TTATTAA
5443421 GAAATTATTG
Statistics
Matches: 36, Mismatches: 15, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.37, C:0.03, G:0.10, T:0.50
Consensus pattern (11 bp):
TTATTAATGAT
Found at i:5443417 original size:22 final size:22
Alignment explanation
Indices: 5443300--5443437 Score: 127
Period size: 22 Copynumber: 6.3 Consensus size: 22
5443290 AAGCTATAAG
* *
5443300 TGATATATTATTAAATTATCAA
1 TGATTTATTATTAAATTATGAA
* * * *
5443322 TAATTTACTACTAAATTA-GCAT
1 TGATTTATTATTAAATTATG-AA
*
5443344 TGATTTACTATTAAATTATGAA
1 TGATTTATTATTAAATTATGAA
* *
5443366 TGATTTATTACTAAGTTATGAA
1 TGATTTATTATTAAATTATGAA
* *
5443388 TGATTTATTATTCAATTATTAA
1 TGATTTATTATTAAATTATGAA
**
5443410 TGATTTATTAAGAAATTATTG-A
1 TGATTTATTATTAAATTA-TGAA
5443432 TGATTT
1 TGATTT
5443438 GTAACAAAGT
Statistics
Matches: 93, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
22 91 0.98
23 2 0.02
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (22 bp):
TGATTTATTATTAAATTATGAA
Found at i:5443419 original size:44 final size:44
Alignment explanation
Indices: 5443258--5443416 Score: 160
Period size: 44 Copynumber: 3.6 Consensus size: 44
5443248 GTTATCATTA
* ** *
5443258 ATTTATTATTATATTATTAGCAATTTACTACTAAGCTAT-AAGTG
1 ATTTATTATTAAATTATTAATAATTTACTACTAAGTTATGAA-TG
* * * *
5443302 ATATATTATTAAATTATCAATAATTTACTACTAAATTA-GCATTG
1 ATTTATTATTAAATTATTAATAATTTACTACTAAGTTATG-AATG
* * * *
5443346 ATTTACTATTAAATTATGAATGATTTATTACTAAGTTATGAATG
1 ATTTATTATTAAATTATTAATAATTTACTACTAAGTTATGAATG
* *
5443390 ATTTATTATTCAATTATTAATGATTTA
1 ATTTATTATTAAATTATTAATAATTTA
5443417 TTAAGAAATT
Statistics
Matches: 94, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
44 92 0.98
45 2 0.02
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.47
Consensus pattern (44 bp):
ATTTATTATTAAATTATTAATAATTTACTACTAAGTTATGAATG
Found at i:5443450 original size:22 final size:22
Alignment explanation
Indices: 5443356--5443460 Score: 65
Period size: 22 Copynumber: 4.8 Consensus size: 22
5443346 ATTTACTATT
* *
5443356 AAATTATGAATGATTTA-TTAC
1 AAATTATTAATGATTTAGTAAC
* * * *
5443377 TAAGTTATGAATGATTTATTATTC
1 -AAATTATTAATGATTTAGTA-AC
* *
5443401 -AATTATTAATGATTTATTAAG
1 AAATTATTAATGATTTAGTAAC
*
5443422 AAATTATTGATGATTT-GTAAC
1 AAATTATTAATGATTTAGTAAC
5443443 AAAGTTA-TAACTGATTTA
1 AAA-TTATTAA-TGATTTA
5443461 CTATTAATTT
Statistics
Matches: 66, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
21 8 0.12
22 56 0.85
23 1 0.02
24 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (22 bp):
AAATTATTAATGATTTAGTAAC
Found at i:5443534 original size:22 final size:22
Alignment explanation
Indices: 5443506--5443632 Score: 114
Period size: 22 Copynumber: 5.8 Consensus size: 22
5443496 AATAATTAAC
* * *
5443506 TAATTTACGATTAAACTATCAT
1 TAATTTACTATTAAATTATCAA
5443528 TAATTTACTATTAAATTATCAA
1 TAATTTACTATTAAATTATCAA
5443550 TAATTTAC-ATATAAATTATCAA
1 TAATTTACTAT-TAAATTATCAA
* * *
5443572 TGATTTACTATTATATTAT-TA
1 TAATTTACTATTAAATTATCAA
* *** *
5443593 TGCATTTACTATTTTGTTATCAT
1 T-AATTTACTATTAAATTATCAA
*
5443616 TAATTTACTATTTAATT
1 TAATTTACTATTAAATT
5443633 TTAGTTTATT
Statistics
Matches: 87, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
21 4 0.05
22 80 0.92
23 3 0.03
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (22 bp):
TAATTTACTATTAAATTATCAA
Found at i:5443822 original size:21 final size:21
Alignment explanation
Indices: 5443798--5443841 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5443788 AATTAAATTA
*
5443798 TTATTTTCGGTTGATTTTATT
1 TTATTTTCAGTTGATTTTATT
* *
5443819 TTATTTTCATTTTATTTTATT
1 TTATTTTCAGTTGATTTTATT
5443840 TT
1 TT
5443842 TTATTATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.73
Consensus pattern (21 bp):
TTATTTTCAGTTGATTTTATT
Found at i:5443830 original size:16 final size:16
Alignment explanation
Indices: 5443811--5443841 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5443801 TTTTCGGTTG
5443811 ATTTTATTTTATTTTC
1 ATTTTATTTTATTTTC
5443827 ATTTTATTTTATTTT
1 ATTTTATTTTATTTT
5443842 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTTTATTTTATTTTC
Found at i:5443853 original size:6 final size:5
Alignment explanation
Indices: 5443811--5443857 Score: 60
Period size: 5 Copynumber: 9.0 Consensus size: 5
5443801 TTTTCGGTTG
5443811 ATTTT ATTTT ATTTT CATTTT ATTTT ATTTT -TTATT ATTATT ATTTT
1 ATTTT ATTTT ATTTT -ATTTT ATTTT ATTTT ATT-TT ATT-TT ATTTT
5443858 TGGTTTCCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
4 2 0.05
5 24 0.62
6 13 0.33
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:5443854 original size:21 final size:21
Alignment explanation
Indices: 5443811--5443857 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
5443801 TTTTCGGTTG
5443811 ATTTTATTTTATTTTCATTTT
1 ATTTTATTTTATTTTCATTTT
5443832 ATTTTATTTT-TTATT-ATTATT
1 ATTTTATTTTATT-TTCATT-TT
5443853 ATTTT
1 ATTTT
5443858 TGGTTTCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (21 bp):
ATTTTATTTTATTTTCATTTT
Found at i:5444184 original size:11 final size:11
Alignment explanation
Indices: 5444168--5444195 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5444158 TGGAATTTCC
5444168 AAATTTCGGTT
1 AAATTTCGGTT
5444179 AAATTTCGGTT
1 AAATTTCGGTT
5444190 AAATTT
1 AAATTT
5444196 TTTCCAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.46
Consensus pattern (11 bp):
AAATTTCGGTT
Found at i:5460568 original size:11 final size:11
Alignment explanation
Indices: 5460552--5460577 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5460542 ACTAAGCTTG
5460552 AAAAAAATAAA
1 AAAAAAATAAA
5460563 AAAAAAATAAA
1 AAAAAAATAAA
5460574 AAAA
1 AAAA
5460578 GGATGACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:5461672 original size:43 final size:43
Alignment explanation
Indices: 5461625--5461728 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 43
5461615 GCCTCTTTGA
* * * *
5461625 AGAGGAGTAATTTATTTTC-CTTAAAGTTCTGTTGCTTCTATTT
1 AGAGGAGCAATTTATTTTCTC-AAAAGTTCTATTGCATCTATTT
* *
5461668 AGAGGAGCCATTTATTTTCTCAAAAGTTCTATTGCATCTGTTT
1 AGAGGAGCAATTTATTTTCTCAAAAGTTCTATTGCATCTATTT
*
5461711 AGAAGAGCAATTTATTTT
1 AGAGGAGCAATTTATTTT
5461729 AAAAGTTGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 51 0.98
44 1 0.02
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.44
Consensus pattern (43 bp):
AGAGGAGCAATTTATTTTCTCAAAAGTTCTATTGCATCTATTT
Found at i:5461783 original size:41 final size:42
Alignment explanation
Indices: 5461708--5461890 Score: 149
Period size: 44 Copynumber: 4.3 Consensus size: 42
5461698 ATTGCATCTG
* * *
5461708 TTTAGAAGAGC--AATTTATTTTAAAAGTTGTTGAGCCTTTA
1 TTTAGAAGAGCTTTATTTATTTTAAAAGTCGTTGAGCCTCTA
*
5461748 TTTA-AAGGAGCTTTATTTATTTT-AAAGTCGTTGAGCCTCTG
1 TTTAGAA-GAGCTTTATTTATTTTAAAAGTCGTTGAGCCTCTA
* * * **
5461789 TTTAGAAGAGCTTTACTTATTTTTTCAAAGTAGTTGAGTGTCTA
1 TTTAGAAGAGCTTTA-TT-TATTTTAAAAGTCGTTGAGCCTCTA
* * * * * *
5461833 ATTAGAGGAGCGTTGTTTATTTTCCCAAAGTCATTGAGCCTCTA
1 TTTAGAAGAGCTTTATTTATTTT--AAAAGTCGTTGAGCCTCTA
*
5461877 TTTAGAAGAACTTT
1 TTTAGAAGAGCTTT
5461891 GTTCATGTTT
Statistics
Matches: 112, Mismatches: 22, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
39 2 0.02
40 8 0.07
41 27 0.24
42 18 0.16
43 7 0.06
44 50 0.45
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (42 bp):
TTTAGAAGAGCTTTATTTATTTTAAAAGTCGTTGAGCCTCTA
Found at i:5461882 original size:44 final size:44
Alignment explanation
Indices: 5461737--5461935 Score: 154
Period size: 44 Copynumber: 4.6 Consensus size: 44
5461727 TTAAAAGTTG
* * *
5461737 TTGAGCCTTTATTTAAAGGAGCTTTATTTA-TTT-T-AAAGTCG
1 TTGAGCCTCTATTTAGAGGAGCTTTATTTATTTTCTCAAAGTCA
* * * *
5461778 TTGAGCCTCTGTTTAGAAGAGCTTTACTTATTTTTTCAAAGT-A
1 TTGAGCCTCTATTTAGAGGAGCTTTATTTATTTTCTCAAAGTCA
** * * * *
5461821 GTTGAGTGTCTAATTAGAGGAGCGTTGTTTATTTTCCCAAAGTCA
1 -TTGAGCCTCTATTTAGAGGAGCTTTATTTATTTTCTCAAAGTCA
* * * * * *
5461866 TTGAGCCTCTATTTAGAAGAACTTTGTTCATGTTTCTCAAAGGCG
1 TTGAGCCTCTATTTAGAGGAGCTTTATTTAT-TTTCTCAAAGTCA
* * *
5461911 TTAAGCCTCTACTTAAAGGAGCTTT
1 TTGAGCCTCTATTTAGAGGAGCTTT
5461936 CATCAAAATT
Statistics
Matches: 121, Mismatches: 31, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
41 25 0.21
42 3 0.02
43 1 0.01
44 61 0.50
45 31 0.26
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.41
Consensus pattern (44 bp):
TTGAGCCTCTATTTAGAGGAGCTTTATTTATTTTCTCAAAGTCA
Found at i:5462145 original size:10 final size:10
Alignment explanation
Indices: 5462130--5462214 Score: 59
Period size: 9 Copynumber: 8.2 Consensus size: 10
5462120 CATTTGCATT
*
5462130 TTTATTTTTA
1 TTTATTATTA
5462140 TTTATTATTA
1 TTTATTATTA
5462150 -TTATTATTA
1 TTTATTATTA
* *
5462159 -ATATATATTG
1 TTTAT-TATTA
5462169 TTT-TTATTA
1 TTTATTATTA
5462178 TTTATCTATTAA
1 TTTAT-TATT-A
*
5462190 TATATTTATTTA
1 TTTA-TTA-TTA
5462202 TTTATTATCTA
1 TTTATTAT-TA
5462213 TT
1 TT
5462215 AGTATATATA
Statistics
Matches: 60, Mismatches: 7, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
9 19 0.32
10 16 0.27
11 12 0.20
12 10 0.17
13 3 0.05
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.67
Consensus pattern (10 bp):
TTTATTATTA
Found at i:5462156 original size:16 final size:16
Alignment explanation
Indices: 5462130--5462214 Score: 57
Period size: 16 Copynumber: 5.1 Consensus size: 16
5462120 CATTTGCATT
*
5462130 TTTATTTTTATTTATTA
1 TTTATTATTA-TTATTA
*
5462147 -TTATTATTATTAATA
1 TTTATTATTATTATTA
* * *
5462162 TATATTGTTTTTATTA
1 TTTATTATTATTATTA
*
5462178 TTTATCTATTAATA-TA
1 TTTAT-TATTATTATTA
5462194 TTTATTTATTTATTATCTA
1 TTTA-TTA-TTATTAT-TA
5462213 TT
1 TT
5462215 AGTATATATA
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
15 5 0.10
16 31 0.61
17 11 0.22
19 4 0.08
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.67
Consensus pattern (16 bp):
TTTATTATTATTATTA
Found at i:5462250 original size:18 final size:18
Alignment explanation
Indices: 5462227--5462261 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5462217 TATATATATT
5462227 TTTATCTATTTTTTTTAC
1 TTTATCTATTTTTTTTAC
*
5462245 TTTATCTTTTTTTTTTA
1 TTTATCTATTTTTTTTA
5462262 TCAATATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTATCTATTTTTTTTAC
Found at i:5462991 original size:3 final size:3
Alignment explanation
Indices: 5462977--5463011 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
5462967 AGGTTTTTAT
5462977 TTA TTA TT- TTA TTA TTA TTA TTTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TT
5463012 CCTTAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:5463000 original size:13 final size:13
Alignment explanation
Indices: 5462977--5463011 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
5462967 AGGTTTTTAT
5462977 TTATTATTTTATTA
1 TTATTA-TTTATTA
5462991 TTATTATTTATTA
1 TTATTATTTATTA
5463004 TTATTATT
1 TTATTATT
5463012 CCTTAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTATTTATTA
Found at i:5463197 original size:63 final size:63
Alignment explanation
Indices: 5463129--5463278 Score: 189
Period size: 62 Copynumber: 2.4 Consensus size: 63
5463119 ATATTTTGGG
* * * * * * *
5463129 GGAAAAGTTGAAAGTATCGATTTTTTTTTGAAATTAAAAA-T-TTCAGAAAAAAACCATTTTTGA
1 GGAAAAGTTGAAAGTATCAATTTTTTCTTAAAAATAAAAATTATTAAGAAAAAAA-CA-GTTTAA
*
5463192 GGAAAAGTTGAAAGTACCAA-TTTTTCTTAAAAATAAAAATTATTAAGAAAAAAACAGTTTAA
1 GGAAAAGTTGAAAGTATCAATTTTTTCTTAAAAATAAAAATTATTAAGAAAAAAACAGTTTAA
5463254 GGAAAAGTTGAAAGTATCAATTTTT
1 GGAAAAGTTGAAAGTATCAATTTTT
5463279 CTTCTACAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
62 39 0.52
63 25 0.33
64 11 0.15
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (63 bp):
GGAAAAGTTGAAAGTATCAATTTTTTCTTAAAAATAAAAATTATTAAGAAAAAAACAGTTTAA
Found at i:5467285 original size:21 final size:19
Alignment explanation
Indices: 5467261--5467311 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
5467251 ATAATAGACA
5467261 ATTAATTATTATTAATATCAT
1 ATTAATTATTATT--TATCAT
5467282 ATTAATAATATTATTTATCAT
1 ATTAAT--TATTATTTATCAT
5467303 -TTATATTAT
1 ATTA-ATTAT
5467312 CAATTATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
19 3 0.11
20 3 0.11
21 14 0.52
23 7 0.26
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTAATTATTATTTATCAT
Found at i:5469826 original size:24 final size:24
Alignment explanation
Indices: 5469773--5469828 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 24
5469763 AATATTTTAT
*
5469773 TAAATTTTTTTAATTACAATTACAA
1 TAAA-TTTTTTAATCACAATTACAA
*
5469798 T-AATTTTTTAATCACAATTATAA
1 TAAATTTTTTAATCACAATTACAA
5469821 TAAATTTT
1 TAAATTTT
5469829 ATTATTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 19 0.68
24 8 0.29
25 1 0.04
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (24 bp):
TAAATTTTTTAATCACAATTACAA
Found at i:5473958 original size:34 final size:34
Alignment explanation
Indices: 5473915--5473982 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
5473905 GAATGATAAT
5473915 CATAAATGTAAGGTTTCACAAATTTTATCATATA
1 CATAAATGTAAGGTTTCACAAATTTTATCATATA
5473949 CATAAATGTAAGGTTTCACAAATTTTATCATATA
1 CATAAATGTAAGGTTTCACAAATTTTATCATATA
5473983 ATTTACACCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (34 bp):
CATAAATGTAAGGTTTCACAAATTTTATCATATA
Found at i:5474547 original size:15 final size:14
Alignment explanation
Indices: 5474516--5474551 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5474506 TTACTTGATG
5474516 TTTTTGTTATTTAC
1 TTTTTGTTATTTAC
*
5474530 TTTTTGTTATTTGC
1 TTTTTGTTATTTAC
*
5474544 CTTTTGTT
1 TTTTTGTT
5474552 TCTTGTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.08, C:0.08, G:0.11, T:0.72
Consensus pattern (14 bp):
TTTTTGTTATTTAC
Found at i:5474578 original size:19 final size:18
Alignment explanation
Indices: 5474554--5474591 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5474544 CTTTTGTTTC
5474554 TTGTTTGTTATTTAT-TTTT
1 TTGTTT-TT-TTTATCTTTT
5474573 TTGTTTTTTTTATCTTTT
1 TTGTTTTTTTTATCTTTT
5474591 T
1 T
5474592 ATTATTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 7 0.39
19 6 0.33
ACGTcount: A:0.08, C:0.03, G:0.08, T:0.82
Consensus pattern (18 bp):
TTGTTTTTTTTATCTTTT
Found at i:5476898 original size:21 final size:21
Alignment explanation
Indices: 5476847--5476899 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
5476837 TAACTGCTGA
5476847 AATTTTGCACGTTCTACCTTC
1 AATTTTGCACGTTCTACCTTC
* *
5476868 -ATTCTAGCACGTTCT-TCTTC
1 AATT-TTGCACGTTCTACCTTC
5476888 AATTTTGGCACG
1 AATTTT-GCACG
5476900 CTCATGTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.19, C:0.26, G:0.13, T:0.42
Consensus pattern (21 bp):
AATTTTGCACGTTCTACCTTC
Found at i:5479329 original size:12 final size:12
Alignment explanation
Indices: 5479312--5479336 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5479302 TTCGTAAACG
5479312 TCTTTAGTAACA
1 TCTTTAGTAACA
5479324 TCTTTAGTAACA
1 TCTTTAGTAACA
5479336 T
1 T
5479337 ATCAAATAAG
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:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (12 bp):
TCTTTAGTAACA
Found at i:5482809 original size:71 final size:70
Alignment explanation
Indices: 5482719--5482855 Score: 211
Period size: 71 Copynumber: 1.9 Consensus size: 70
5482709 AGGTACAGAT
* * * * *
5482719 TCTCCAAAAAATGCCAATTAACATATCTTGATAGAAATTCAATACAAATTTAATGCTCATAAACA
1 TCTCCAAAAAATACCAATTAACATATCCTGATAAAAATCCAATACAAATTAAATGCTCATAAACA
5482784 ATGAC
66 ATGAC
*
5482789 TCTCCAAGAAAATACCAATTAACATATCCTGATAAAAATCCAATACGAATTAAATGCTCATAAAC
1 TCTCCAA-AAAATACCAATTAACATATCCTGATAAAAATCCAATACAAATTAAATGCTCATAAAC
5482854 AA
65 AA
5482856 CTTTACACAT
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
70 7 0.12
71 53 0.88
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.26
Consensus pattern (70 bp):
TCTCCAAAAAATACCAATTAACATATCCTGATAAAAATCCAATACAAATTAAATGCTCATAAACA
ATGAC
Found at i:5484282 original size:357 final size:356
Alignment explanation
Indices: 5483619--5485230 Score: 2054
Period size: 357 Copynumber: 4.5 Consensus size: 356
5483609 GAACATACCA
* * ** * * ** *
5483619 CCACACAAATTCTAACATTGTTATTAAAAGCGTATATCCAACAAAGACACCTTTAATAATTTATA
1 CCACACAAATTCTAACATTGTTATTGAAGGCGTATATTTAAGATAGATGCCTTTAATAATTTCTA
* *
5483684 TCACAGTTTGTAGTTAATTACTGAAGGCAGTTGCAGAAAACAACGCCTTCAATAATTTCTCTCAA
66 TCACAGTTTGTAGATAATAACTGAAGGCAGTTGCAGAAAACAACGCCTTCAATAATTTCTCTC--
* * * * * *
5483749 AAAAAAATTTT--TGGATTATTAAAGGCATCTTTTATTACGACAT-GCCTTCAATATACCACGGT
129 -AAAAAATTTTCACGAATTTTTAAAGGCATCTTTTATTA-TAAATCGCCTTCAATATACCACGAT
*
5483811 GGTAATGGAAGACGTTTATTAGAAAAGGCACCTTCAATATACCTTTAAACTTAGTAATCCATTAG
192 GGTAATGGAAGGCGTTTATTAGAAAAGGCACCTTCAATATACCTTTAAACTTAGTAATCCATTAG
* **
5483876 TGAAGGCATTTGTTAATAACAGACGCCTTCAAAAATTTTTTGTTAAATATTTTAAGAATTATTAA
257 TGAAGGCATTTGTTAATAACAGACACCTTC-AAAATTTTTCATTAAATATTTTAAGAATTATTAA
* *
5483941 AGGCGTTTTCTACTGTCAAATGCCTTCTATATACTG
321 AGACGTCTTCTACTGTCAAATGCCTTCTATATACTG
* * * *
5483977 TCACACAAATTCTAACATTGTTATTAAAAGTGTATATTTAAGATAGATGCCTTTAATAATTTCTA
1 CCACACAAATTCTAACATTGTTATTGAAGGCGTATATTTAAGATAGATGCCTTTAATAATTTCTA
* * * * * *
5484042 TCACAGTTTGTAGATAATAACTGAAGGCAATTGCAAAAAATAATGCCTTTAATAATTTCCCTCAA
66 TCACAGTTTGTAGATAATAACTGAAGGCAGTTGCAGAAAACAACGCCTTCAATAATTTCTCTCAA
* *
5484107 AAAATTTTAACGAATTTTTAAAGGCGTCTTTTATTATAAATCGCCTTCAATATACCACGATGGTA
131 AAAATTTTCACGAATTTTTAAAGGCATCTTTTATTATAAATCGCCTTCAATATACCACGATGGTA
* *
5484172 ATGAAAGGCGTTTATTAGAAAAGGCGCCTTCAATATACCTTTAAACTTAGTAATCCATTAGTGAA
196 ATGGAAGGCGTTTATTAGAAAAGGCACCTTCAATATACCTTTAAACTTAGTAATCCATTAGTGAA
* * * * *
5484237 GGCGTTTGTTAATAACATACACCTTCAAAATTTTCTCACTAAATATTTTAAAAATTATTAAATAC
261 GGCATTTGTTAATAACAGACACCTTCAAAATTTT-TCATTAAATATTTTAAGAATTATTAAAGAC
* *
5484302 GTCTTCTACTGTCAAATATCGTT-TATATACTG
325 GTCTTCTACTGTCAAAT-GCCTTCTATATACTG
** *
5484334 CCACACAAATTCTAACACCGTTATTGAAGGCGTATATTTAACATAGATGCCTTTAATAA-TTCAT
1 CCACACAAATTCTAACATTGTTATTGAAGGCGTATATTTAAGATAGATGCCTTTAATAATTTC-T
* * * ** * * * * *
5484398 ATCATAGTTTGTAAATAATAACTAAAAACGGTTACAGAAAACAGCACCTTCAATAATTTTTCTCA
65 ATCACAGTTTGTAGATAATAACTGAAGGCAGTTGCAGAAAACAACGCCTTCAATAATTTCTCTCA
* * * *
5484463 AAAAATTTTCACAAATTTTTAAAGGCATCTTTTATTATAAACCACCTTCAATATACCAAGATGGT
130 AAAAATTTTCACGAATTTTTAAAGGCATCTTTTATTATAAATCGCCTTCAATATACCACGATGGT
* * *
5484528 AATGGAAGGCGTTTATTAGAAAATGCACCTTCAATATACCTTTAAATTTAATAATCCATTAGTGA
195 AATGGAAGGCGTTTATTAGAAAAGGCACCTTCAATATACCTTTAAACTTAGTAATCCATTAGTGA
*
5484593 AGGCATTTGTTAATAACAGA-AGCCTTCAAAATTTTTCCAATAAATATTTTAAGAATTATTAAAG
260 AGGCATTTGTTAATAACAGACA-CCTTCAAAATTTTT-CATTAAATATTTTAAGAATTATTAAAG
* *
5484657 ACGTCTTCTACTGTCAAATGCCATATATATA-TCG
323 ACGTCTTCTACTGTCAAATGCCTTCTATATACT-G
** * * *
5484691 TTATACAAATTTTAACATTGTTATTGAAGGCGTATATTTAAGATAGATGCCTTTAATAATTCCTA
1 CCACACAAATTCTAACATTGTTATTGAAGGCGTATATTTAAGATAGATGCCTTTAATAATTTCTA
* ** ** *
5484756 TCACAATAAGTAGATAATAACTGAAGGCAGTTGCAGAAAACAACGATTTCAATAATTTCCCTCAA
66 TCACAGTTTGTAGATAATAACTGAAGGCAGTTGCAGAAAACAACGCCTTCAATAATTTCTCTCAA
** *
5484821 AAAATTTTCGTGAATTTTTAAAGGCATCTTTTATTATAAACCGCCTTCAATATACCACGATGGTA
131 AAAATTTTCACGAATTTTTAAAGGCATCTTTTATTATAAATCGCCTTCAATATACCACGATGGTA
* * * *
5484886 ATGGAATGTGTTTATTAGAAAAGGCACCTTCAATATACTTTTAAACTTAGTAATTCATTAGTGAA
196 ATGGAAGGCGTTTATTAGAAAAGGCACCTTCAATATACCTTTAAACTTAGTAATCCATTAGTGAA
* * * *
5484951 GGCATTTGTTAATAACAGACGCCTTCAAAATTTATTCTTTTAATATTTTGAGAATTATTAAATG-
261 GGCATTTGTTAATAACAGACACCTTCAAAATTT-TTCATTAAATATTTTAAGAATTATTAAA-GA
* * * * *
5485015 CATCTTTTACTGTAAAATACCTTCTATATACCG
324 CGTCTTCTACTGTCAAATGCCTTCTATATACTG
* * * * * *
5485048 CCACACAAATTCTAATACTGTTATTGAAGGCGTACATCTAAGAAAGATGCCTTTAATAATTACTA
1 CCACACAAATTCTAACATTGTTATTGAAGGCGTATATTTAAGATAGATGCCTTTAATAATTTCTA
* * * *
5485113 TCATAGTTTTGTAGATAATAACTGAAGGTAGTTGCAAAAAACAATGCCTTCAATAATTTCTCTCA
66 TCACAG-TTTGTAGATAATAACTGAAGGCAGTTGCAGAAAACAACGCCTTCAATAATTTCTCTCA
* ** *
5485178 AAAAATTTTTAC-AGATTAATAAAGGCGTCTTTTATTATAAATCGCCTTCAATA
130 AAAAATTTTCACGA-ATTTTTAAAGGCATCTTTTATTATAAATCGCCTTCAATA
5485231 AATTGTTATA
Statistics
Matches: 1081, Mismatches: 156, Indels: 34
0.85 0.12 0.03
Matches are distributed among these distances:
355 10 0.01
356 19 0.02
357 839 0.78
358 213 0.20
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (356 bp):
CCACACAAATTCTAACATTGTTATTGAAGGCGTATATTTAAGATAGATGCCTTTAATAATTTCTA
TCACAGTTTGTAGATAATAACTGAAGGCAGTTGCAGAAAACAACGCCTTCAATAATTTCTCTCAA
AAAATTTTCACGAATTTTTAAAGGCATCTTTTATTATAAATCGCCTTCAATATACCACGATGGTA
ATGGAAGGCGTTTATTAGAAAAGGCACCTTCAATATACCTTTAAACTTAGTAATCCATTAGTGAA
GGCATTTGTTAATAACAGACACCTTCAAAATTTTTCATTAAATATTTTAAGAATTATTAAAGACG
TCTTCTACTGTCAAATGCCTTCTATATACTG
Found at i:5494376 original size:43 final size:44
Alignment explanation
Indices: 5494289--5494380 Score: 132
Period size: 44 Copynumber: 2.1 Consensus size: 44
5494279 GAGAGAGGTT
** *
5494289 CATAATACATAGTTGTTTATATTACATTAGGCTCTGAAACCTTA
1 CATAATACATAACTGTTTATATTACATTAGGCTCAGAAACCTTA
* *
5494333 CATAATACATAACTGTTTATATTA-GTTAGGCTCAGAAATCTTA
1 CATAATACATAACTGTTTATATTACATTAGGCTCAGAAACCTTA
5494376 CATAA
1 CATAA
5494381 CAACAGACCA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 21 0.49
44 22 0.51
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (44 bp):
CATAATACATAACTGTTTATATTACATTAGGCTCAGAAACCTTA
Found at i:5507688 original size:1 final size:1
Alignment explanation
Indices: 5507682--5507708 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
5507672 CCAACTGGAG
5507682 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
5507709 CCTCTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5513087 original size:16 final size:16
Alignment explanation
Indices: 5513066--5513097 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5513056 AAAATCATCG
5513066 TAAATCATCATTATCA
1 TAAATCATCATTATCA
5513082 TAAATCATCATTATCA
1 TAAATCATCATTATCA
5513098 ATCAAAATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATCATCATTATCA
Found at i:5522740 original size:30 final size:30
Alignment explanation
Indices: 5522706--5522765 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
5522696 TACTTTCCAC
*
5522706 CTAAATAAATTATTAAATTTTAATTTATAT
1 CTAAATAAATCATTAAATTTTAATTTATAT
**
5522736 CTAAATAAATCATTATCTTTTAATTTATAT
1 CTAAATAAATCATTAAATTTTAATTTATAT
5522766 TTTAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (30 bp):
CTAAATAAATCATTAAATTTTAATTTATAT
Done.