Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold66
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: 4623749
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 850 characters in sequence are not A, C, G, or T
File 9 of 26
Found at i:1478099 original size:30 final size:30
Alignment explanation
Indices: 1478050--1478122 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
1478040 TTAAAATATT
* * *
1478050 TTATATTTATATAATTTTAATATATTAATAA
1 TTATATTTAAATAAATTTAAAATATTAAT-A
*
1478081 TT-TATTTAAATAAATTTAAAATATTTATA
1 TTATATTTAAATAAATTTAAAATATTAATA
*
1478110 TTATATTTTAATA
1 TTATATTTAAATA
1478123 TAATCAGCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 3 0.08
30 31 0.86
31 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TTATATTTAAATAAATTTAAAATATTAATA
Found at i:1488723 original size:22 final size:22
Alignment explanation
Indices: 1488665--1488724 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
1488655 TAATTTAATT
* *
1488665 TATTTTATATATATTTATGTTA
1 TATTTTAAATATTTTTATGTTA
* *
1488687 T-TTGTATATTATTTTTATGTTA
1 TATTTTA-AATATTTTTATGTTA
1488709 TATTTTAAATATTTTT
1 TATTTTAAATATTTTT
1488725 TATAAATACA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
21 4 0.13
22 22 0.73
23 4 0.13
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (22 bp):
TATTTTAAATATTTTTATGTTA
Found at i:1490319 original size:19 final size:19
Alignment explanation
Indices: 1490281--1490321 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1490271 TTATATCAAA
*
1490281 ATTAAATAAAAATTATAAT
1 ATTAAATAAAAATTAGAAT
1490300 ATTAAAT-AAAATTAAGAAT
1 ATTAAATAAAAATT-AGAAT
1490319 ATT
1 ATT
1490322 TAAAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
ATTAAATAAAAATTAGAAT
Found at i:1491219 original size:2 final size:2
Alignment explanation
Indices: 1491206--1491239 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1491196 AGGAATAGAT
*
1491206 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1491240 GAAAGCAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1496538 original size:2 final size:2
Alignment explanation
Indices: 1496531--1496570 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1496521 TACAACATAG
1496531 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1496571 GAATTAACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1496846 original size:4 final size:4
Alignment explanation
Indices: 1496810--1496865 Score: 67
Period size: 4 Copynumber: 14.0 Consensus size: 4
1496800 TTGCTTTGGA
* * * * *
1496810 ATAT GTAT ATAC ATAT GTAC ATAT ATAT GTAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1496858 ATAT ATAT
1 ATAT ATAT
1496866 GGAACAATTG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (4 bp):
ATAT
Found at i:1496865 original size:12 final size:12
Alignment explanation
Indices: 1496810--1496861 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
1496800 TTGCTTTGGA
*
1496810 ATATGTATATAC
1 ATATGTATATAT
*
1496822 ATATGTACATAT
1 ATATGTATATAT
1496834 ATATGTATATAT
1 ATATGTATATAT
*
1496846 ATATATATATAT
1 ATATGTATATAT
1496858 ATAT
1 ATAT
1496862 ATATGGAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (12 bp):
ATATGTATATAT
Found at i:1497289 original size:2 final size:2
Alignment explanation
Indices: 1497282--1497318 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1497272 ATGCAAATTG
1497282 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1497319 CCCACTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1497430 original size:24 final size:23
Alignment explanation
Indices: 1497403--1497450 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 23
1497393 AATATAATAT
1497403 TTATA-TTAAATATATTATTATTAA
1 TTATATTTAAA-ATATTA-TATTAA
1497427 TTATATTTAAAATATTATATTAA
1 TTATATTTAAAATATTATATTAA
1497450 T
1 T
1497451 ATTATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.30
24 11 0.48
25 5 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTATATTTAAAATATTATATTAA
Found at i:1497467 original size:35 final size:35
Alignment explanation
Indices: 1497414--1497483 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
1497404 TATATTAAAT
1497414 ATATTATTATTAATTATATTTAAA-ATATTATATTA
1 ATATTATTATTAATTATA-TTAAATATATTATATTA
*
1497449 ATATTATT-TTTATATATATTAAATATATTATATTA
1 ATATTATTATTAAT-TATATTAAATATATTATATTA
1497484 TTAAATTCAG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 9 0.28
35 23 0.72
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (35 bp):
ATATTATTATTAATTATATTAAATATATTATATTA
Found at i:1497644 original size:18 final size:18
Alignment explanation
Indices: 1497623--1497658 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1497613 TTGAGCATTC
1497623 ATTTAATCAATTTTTTAA
1 ATTTAATCAATTTTTTAA
* *
1497641 ATTTATTTAATTTTTTAA
1 ATTTAATCAATTTTTTAA
1497659 TTAGAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTAATCAATTTTTTAA
Found at i:1501973 original size:14 final size:15
Alignment explanation
Indices: 1501954--1501987 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1501944 TATTAAAATA
1501954 TATTATATTTAT-TT
1 TATTATATTTATATT
*
1501968 TATTATCTTTATATT
1 TATTATATTTATATT
1501983 TATTA
1 TATTA
1501988 AACGCACTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTATATTTATATT
Found at i:1503050 original size:23 final size:22
Alignment explanation
Indices: 1503024--1503078 Score: 85
Period size: 23 Copynumber: 2.5 Consensus size: 22
1503014 AATTATTTAA
1503024 TATTTTATTTTA-AAAATAATTAT
1 TATTTTATTTTATAAAAT-ATT-T
1503047 TATTTTATTTTATAAAATATTT
1 TATTTTATTTTATAAAATATTT
1503069 TATTTTATTT
1 TATTTTATTT
1503079 AAATTTTAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.35
23 15 0.48
24 5 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTTATTTTATAAAATATTT
Found at i:1503899 original size:3 final size:3
Alignment explanation
Indices: 1503891--1503921 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1503881 TGACGGTCCC
1503891 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1503922 GTTGGGCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:1508649 original size:19 final size:18
Alignment explanation
Indices: 1508625--1508673 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
1508615 GTATAAATAT
*
1508625 TAAATTATTTTTATTTGTA
1 TAAATTATTTTTATAT-TA
1508644 TAAATT-TTTTTATATTA
1 TAAATTATTTTTATATTA
*
1508661 TTAA-TATTTTTAT
1 TAAATTATTTTTAT
1508674 CTAAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 12 0.44
18 8 0.30
19 6 0.22
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TAAATTATTTTTATATTA
Found at i:1509898 original size:18 final size:18
Alignment explanation
Indices: 1509865--1509899 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1509855 TAAATATCAT
*
1509865 GGATGATGGCGTTGATGC
1 GGATGATGGCGATGATGC
*
1509883 GGATGATGGTGATGATG
1 GGATGATGGCGATGATG
1509900 TTGATTCTGA
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:0.20, C:0.06, G:0.46, T:0.29
Consensus pattern (18 bp):
GGATGATGGCGATGATGC
Found at i:1510523 original size:21 final size:21
Alignment explanation
Indices: 1510497--1510539 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1510487 AAAAAATTAT
*
1510497 TTTTATAA-TAATATTTATATA
1 TTTTATAATTAA-ATTTAAATA
1510518 TTTTATAATTAAATTTAAATA
1 TTTTATAATTAAATTTAAATA
1510539 T
1 T
1510540 AAAATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTATAATTAAATTTAAATA
Found at i:1511255 original size:22 final size:20
Alignment explanation
Indices: 1511224--1511275 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
1511214 TTTTATATTT
*
1511224 AAAATTATTTATAAATTAATAA
1 AAAATAATTTAT-AATTAA-AA
1511246 AAAATAATTT-TAATTAAAA
1 AAAATAATTTATAATTAAAA
*
1511265 TAAATAATTTA
1 AAAATAATTTA
1511276 ATTCGTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 11 0.41
20 6 0.22
21 1 0.04
22 9 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATAATTTATAATTAAAA
Found at i:1511878 original size:39 final size:40
Alignment explanation
Indices: 1511794--1511878 Score: 101
Period size: 39 Copynumber: 2.2 Consensus size: 40
1511784 AAACAAATAT
1511794 ATTTTA-A-TTTTAATTTAATTATAAAATATTAATATAAA
1 ATTTTATATTTTTAATTTAATTATAAAATATTAATATAAA
*
1511832 A-TATATATTTTTAATATT-ATTAT-AAATATTTAA-ATAAA
1 ATTTTATATTTTTAAT-TTAATTATAAAATA-TTAATATAAA
1511870 ATTTTATAT
1 ATTTTATAT
1511879 CGATTTAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
37 3 0.08
38 13 0.32
39 22 0.55
40 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (40 bp):
ATTTTATATTTTTAATTTAATTATAAAATATTAATATAAA
Found at i:1513446 original size:16 final size:16
Alignment explanation
Indices: 1513425--1513479 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
1513415 AATAAATATC
1513425 ATAAAATTTATATAAT
1 ATAAAATTTATATAAT
1513441 ATAAAATATTATAT-AT
1 ATAAAAT-TTATATAAT
*
1513457 -TTAAATTTATATAAAT
1 ATAAAATTTATAT-AAT
1513473 ATAAAAT
1 ATAAAAT
1513480 ATTTTAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
14 6 0.18
15 5 0.15
16 11 0.33
17 11 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAAAATTTATATAAT
Found at i:1513472 original size:25 final size:26
Alignment explanation
Indices: 1513439--1513493 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
1513429 AATTTATATA
* *
1513439 ATATAAAATATTATATA-TTTAAATT
1 ATATAAAATATAAAATATTTTAAATT
1513464 -TATATAAATATAAAATATTTTAAATT
1 ATATA-AAATATAAAATATTTTAAATT
1513490 ATAT
1 ATAT
1513494 TTAACGTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 4 0.16
25 10 0.40
26 8 0.32
27 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATATAAAATATAAAATATTTTAAATT
Found at i:1514551 original size:3 final size:3
Alignment explanation
Indices: 1514545--1514571 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1514535 TTTTTGTGCA
1514545 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1514572 TTGTTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1519373 original size:17 final size:17
Alignment explanation
Indices: 1519344--1519388 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
1519334 TTTAATATTT
1519344 TATTAAA-AAATTTAAA
1 TATTAAATAAATTTAAA
1519360 TATTAAATAAATTTTAAA
1 TATTAAATAAA-TTTAAA
1519378 T-TTAAATAAAT
1 TATTAAATAAAT
1519389 AATTGATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.30
17 12 0.44
18 7 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TATTAAATAAATTTAAA
Found at i:1526663 original size:18 final size:19
Alignment explanation
Indices: 1526642--1526710 Score: 70
Period size: 18 Copynumber: 3.5 Consensus size: 19
1526632 TTAAAATTTT
1526642 AAAATTAATTAA-ATTAAA
1 AAAATTAATTAATATTAAA
1526660 AAAATTAATTGAATTGATTAAA
1 AAAATTAATT-AA-T-ATTAAA
*
1526682 AAAA-TATTTAATATTAAA
1 AAAATTAATTAATATTAAA
*
1526700 ATAATTGAATT
1 AAAATT-AATT
1526711 GAATTTAAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
18 19 0.45
19 4 0.10
20 5 0.12
21 4 0.10
22 10 0.24
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (19 bp):
AAAATTAATTAATATTAAA
Found at i:1526981 original size:9 final size:9
Alignment explanation
Indices: 1526967--1527004 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1526957 TTAATTTTAA
1526967 AATTAAATT
1 AATTAAATT
1526976 AATTAAATTT
1 AATTAAA-TT
*
1526986 AATTAATTT
1 AATTAAATT
1526995 AATT-AATT
1 AATTAAATT
1527003 AA
1 AA
1527005 ATCAACTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 5 0.19
9 13 0.50
10 8 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
AATTAAATT
Found at i:1527776 original size:22 final size:21
Alignment explanation
Indices: 1527746--1527803 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
1527736 TAAATATGAT
*
1527746 AAATTATATAAAATATGAGATA
1 AAATAATATAAAATATGAGA-A
1527768 AAATAATATATAAA-ATGAGAA
1 AAATAATATA-AAATATGAGAA
*
1527789 TAATAAT-TAAAATAT
1 AAATAATATAAAATAT
1527804 AATATAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 3 0.09
20 4 0.12
21 7 0.22
22 15 0.47
23 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (21 bp):
AAATAATATAAAATATGAGAA
Found at i:1527780 original size:12 final size:12
Alignment explanation
Indices: 1527750--1527826 Score: 59
Period size: 12 Copynumber: 6.3 Consensus size: 12
1527740 TATGATAAAT
1527750 TATATAAAAT-A
1 TATATAAAATAA
*
1527761 TGAGATAAAATAA
1 T-ATATAAAATAA
*
1527774 TATATAAAATGA
1 TATATAAAATAA
*
1527786 GA-ATAATAATTAA
1 TATATAA-AA-TAA
* *
1527799 AATATAATATAA
1 TATATAAAATAA
*
1527811 TATAAAAAATAA
1 TATATAAAATAA
1527823 TATA
1 TATA
1527827 AACACGATTA
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
11 5 0.10
12 36 0.71
13 6 0.12
14 4 0.08
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (12 bp):
TATATAAAATAA
Found at i:1527816 original size:17 final size:17
Alignment explanation
Indices: 1527775--1527827 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
1527765 ATAAAATAAT
*
1527775 ATATAAAATGAGAATAATA
1 ATATAAAAT-ATAAT-ATA
1527794 AT-TAAAATATAATATA
1 ATATAAAATATAATATA
*
1527810 ATATAAAAAATAATATA
1 ATATAAAATATAATATA
1527827 A
1 A
1527828 ACACGATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 5 0.16
17 18 0.58
18 6 0.19
19 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (17 bp):
ATATAAAATATAATATA
Found at i:1527914 original size:32 final size:32
Alignment explanation
Indices: 1527853--1527914 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
1527843 TATAAACATG
*
1527853 TCAAAATTTATATAAAATATATTATTATTATA
1 TCAAAATTTATATAAAATATAATATTATTATA
*
1527885 TCAAAATTTATATAAATTTATAATA-TATTA
1 TCAAAATTTATATAAA-ATATAATATTATTA
1527915 AATATGATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 21 0.78
33 6 0.22
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (32 bp):
TCAAAATTTATATAAAATATAATATTATTATA
Found at i:1528562 original size:27 final size:24
Alignment explanation
Indices: 1528531--1528591 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 24
1528521 ATTCACTTGT
*
1528531 TAAATTAAAATGATAATTATAATATAA
1 TAAATTAAAAT-ATAA-TATAAAAT-A
1528558 TAAATTAAAATATAATATAAAATA
1 TAAATTAAAATATAATATAAAATA
*
1528582 TAAAATAAAA
1 TAAATTAAAA
1528592 AAATTAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 10 0.31
25 7 0.22
26 4 0.12
27 11 0.34
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
TAAATTAAAATATAATATAAAATA
Found at i:1528569 original size:15 final size:15
Alignment explanation
Indices: 1528545--1528574 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1528535 TTAAAATGAT
*
1528545 AATTATAATATAATA
1 AATTAAAATATAATA
1528560 AATTAAAATATAATA
1 AATTAAAATATAATA
1528575 TAAAATATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATTAAAATATAATA
Found at i:1528578 original size:12 final size:12
Alignment explanation
Indices: 1528536--1528591 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 12
1528526 CTTGTTAAAT
1528536 TAAAATGATAAT-
1 TAAAAT-ATAATA
*
1528548 TATAATATAATAAA
1 TAAAATATAAT--A
1528562 TTAAAATATAATA
1 -TAAAATATAATA
*
1528575 TAAAATATAAAA
1 TAAAATATAATA
1528587 TAAAA
1 TAAAA
1528592 AAATTAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
11 5 0.14
12 21 0.57
13 1 0.03
15 10 0.27
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (12 bp):
TAAAATATAATA
Found at i:1534802 original size:22 final size:22
Alignment explanation
Indices: 1534777--1534831 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1534767 ATTATTTAAA
*
1534777 AATATTAAAATATTTT-TATATT
1 AATATTTAAATATTTTATA-ATT
*
1534799 AATATTTATATATTTTATAATT
1 AATATTTAAATATTTTATAATT
1534821 AA-ATTTAAATA
1 AATATTTAAATA
1534832 AAAAATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.28
22 19 0.66
23 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AATATTTAAATATTTTATAATT
Found at i:1537492 original size:16 final size:16
Alignment explanation
Indices: 1537439--1537494 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
1537429 TCTGAATTTT
*
1537439 AATTTAATTAATTTATA
1 AATTTAATAAATTTA-A
**
1537456 AATTTTAA-AAAAATAA
1 AA-TTTAATAAATTTAA
*
1537472 TATTTAATAAATTTAA
1 AATTTAATAAATTTAA
1537488 AATTTAA
1 AATTTAA
1537495 ATCCTTTCAA
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
15 5 0.17
16 14 0.47
17 6 0.20
18 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTAATAAATTTAA
Found at i:1538921 original size:22 final size:22
Alignment explanation
Indices: 1538888--1538937 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1538878 AATGAGAGCT
**
1538888 TCTTC-TCTTTTCATGTTTTTC
1 TCTTCTTCTTTTCACATTTTTC
1538909 TCTTCTTCTTTTCACATTTTTC
1 TCTTCTTCTTTTCACATTTTTC
1538931 TCTTCTT
1 TCTTCTT
1538938 TTGAGCTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.06, C:0.26, G:0.02, T:0.66
Consensus pattern (22 bp):
TCTTCTTCTTTTCACATTTTTC
Found at i:1544811 original size:15 final size:15
Alignment explanation
Indices: 1544791--1544824 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1544781 TTTAAGTTTG
1544791 AATTGAATTCACTTC
1 AATTGAATTCACTTC
* *
1544806 AATTGAATTGATTTC
1 AATTGAATTCACTTC
1544821 AATT
1 AATT
1544825 CTTAATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (15 bp):
AATTGAATTCACTTC
Found at i:1549237 original size:13 final size:13
Alignment explanation
Indices: 1549219--1549244 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1549209 TTTTATTTTT
1549219 AAATATATAATAA
1 AAATATATAATAA
1549232 AAATATATAATAA
1 AAATATATAATAA
1549245 TTTTTTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATATATAATAA
Found at i:1549699 original size:27 final size:27
Alignment explanation
Indices: 1549659--1549710 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1549649 GGTTCTTAAC
*
1549659 CTCACTTATGAAATTAAAAAAATTTTA
1 CTCACTTATAAAATTAAAAAAATTTTA
*
1549686 CTCACTTATAAAATTAAAATAATTT
1 CTCACTTATAAAATTAAAAAAATTT
1549711 CATCGTTAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (27 bp):
CTCACTTATAAAATTAAAAAAATTTTA
Found at i:1549882 original size:2 final size:2
Alignment explanation
Indices: 1549875--1549910 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1549865 TATGATTGAA
1549875 AT AT AT AT 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 AT AT AT AT
1549911 CCTTATTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1551718 original size:16 final size:16
Alignment explanation
Indices: 1551686--1551758 Score: 62
Period size: 16 Copynumber: 4.6 Consensus size: 16
1551676 TATACTATAA
*
1551686 TTATATT-TAAAATATT
1 TTATATTATATAA-ATT
1551702 TTATATTATATAAATT
1 TTATATTATATAAATT
* *
1551718 TTA-ATATATATTATTT
1 TTATAT-TATATAAATT
*
1551734 TTATATTATATTATATT
1 TTATATTATA-TAAATT
1551751 TTA-ATTAT
1 TTATATTAT
1551759 TTGTTTATCA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
15 2 0.04
16 33 0.70
17 12 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATATTATATAAATT
Found at i:1552061 original size:10 final size:10
Alignment explanation
Indices: 1552046--1552076 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1552036 AAAGAAAATG
1552046 AAAAAAGAAA
1 AAAAAAGAAA
1552056 AAAAAAGAAA
1 AAAAAAGAAA
*
1552066 AGAAAAGAAA
1 AAAAAAGAAA
1552076 A
1 A
1552077 CCCTAATCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:1552459 original size:17 final size:18
Alignment explanation
Indices: 1552437--1552470 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1552427 TATTATTAAA
1552437 TTAAA-TAAAATTATTTT
1 TTAAATTAAAATTATTTT
*
1552454 TTAAATTTAAATTATTT
1 TTAAATTAAAATTATTT
1552471 ATATTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAAATTAAAATTATTTT
Found at i:1553854 original size:16 final size:16
Alignment explanation
Indices: 1553817--1553856 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1553807 TATATATAAT
1553817 TTTTATGTAAATATGA
1 TTTTATGTAAATATGA
* *
1553833 -TTTATGTTAATTTGA
1 TTTTATGTAAATATGA
1553848 TTTTATGTA
1 TTTTATGTA
1553857 TTATTTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (16 bp):
TTTTATGTAAATATGA
Found at i:1554330 original size:2 final size:2
Alignment explanation
Indices: 1554323--1554354 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1554313 TGTTACACGA
1554323 AT AT 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 AT AT
1554355 GTAACTTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1554635 original size:2 final size:2
Alignment explanation
Indices: 1554630--1554664 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1554620 TTGGTTTAAA
1554630 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1554665 ACCAAATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1556052 original size:18 final size:18
Alignment explanation
Indices: 1556026--1556061 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1556016 TTATTTTCGC
1556026 TTTTATTTTTGTTGGTTT
1 TTTTATTTTTGTTGGTTT
* *
1556044 TTTTCTTTTTTTTGGTTT
1 TTTTATTTTTGTTGGTTT
1556062 GGTTTTTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.03, C:0.03, G:0.14, T:0.81
Consensus pattern (18 bp):
TTTTATTTTTGTTGGTTT
Found at i:1563075 original size:34 final size:37
Alignment explanation
Indices: 1563030--1563106 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 37
1563020 TAGTTTTAAA
*
1563030 TATAAATAAT-AAA-AC-AT-ATATTATTAATTATAT
1 TATAAATAATAAAACACAATAATAATATTAATTATAT
1563063 TATAAATAAATAAAACACAAATAATAATATTAATTATAT
1 TATAAAT-AATAAAACAC-AATAATAATATTAATTATAT
1563102 TATAA
1 TATAA
1563107 TCGAATAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
33 7 0.19
34 3 0.08
35 3 0.08
36 2 0.05
38 2 0.05
39 20 0.54
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (37 bp):
TATAAATAATAAAACACAATAATAATATTAATTATAT
Found at i:1567014 original size:4 final size:4
Alignment explanation
Indices: 1567005--1567038 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
1566995 AGTTTATTCT
1567005 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1567039 CTTACTTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1567729 original size:12 final size:12
Alignment explanation
Indices: 1567716--1567779 Score: 71
Period size: 12 Copynumber: 5.6 Consensus size: 12
1567706 AAATATTATG
*
1567716 ATATAAAATATG
1 ATATAAAATATA
*
1567728 ATATAAAAAATA
1 ATATAAAATATA
1567740 AT-TAAAATATA
1 ATATAAAATATA
* *
1567751 AAATATAATATA
1 ATATAAAATATA
1567763 ATATAAAA-AT-
1 ATATAAAATATA
1567773 ATATAAA
1 ATATAAA
1567780 TTAACTTAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
10 7 0.16
11 11 0.25
12 26 0.59
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (12 bp):
ATATAAAATATA
Found at i:1567745 original size:23 final size:23
Alignment explanation
Indices: 1567716--1567779 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
1567706 AAATATTATG
1567716 ATATAAAATATGATATAAAAAATA
1 ATATAAAATAT-ATATAAAAAATA
* * *
1567740 AT-TAAAATATAAAATATAATATA
1 ATATAAAATAT-ATATAAAAAATA
1567763 ATATAAAA-ATATATAAA
1 ATATAAAATATATATAAA
1567780 TTAACTTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 5 0.15
23 21 0.64
24 7 0.21
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
ATATAAAATATATATAAAAAATA
Found at i:1567745 original size:37 final size:35
Alignment explanation
Indices: 1567693--1567771 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
1567683 CAGAGAAAAA
* * * *
1567693 ATAAAAAATACTTAAATATTATGATATAAAATATGAT
1 ATAAAAAATAATTAAA-A-TATAAAATAAAATATAAT
*
1567730 ATAAAAAATAATTAAAATATAAAATATAATATAAT
1 ATAAAAAATAATTAAAATATAAAATAAAATATAAT
1567765 ATAAAAA
1 ATAAAAA
1567772 TATATAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 21 0.57
36 1 0.03
37 15 0.41
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.32
Consensus pattern (35 bp):
ATAAAAAATAATTAAAATATAAAATAAAATATAAT
Found at i:1567771 original size:25 final size:27
Alignment explanation
Indices: 1567743--1567809 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
1567733 AAAAATAATT
1567743 AAAATATAAAATATAA--T-ATAATATA
1 AAAATATAAAATATAACTTAAT-ATATA
1567768 AAAATATATAAAT-TAACTTAATATATA
1 AAAATATA-AAATATAACTTAATATATA
*
1567795 AAAATATCAAATATA
1 AAAATATAAAATATA
1567810 TATTATCAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
25 11 0.31
26 8 0.22
27 15 0.42
28 2 0.06
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (27 bp):
AAAATATAAAATATAACTTAATATATA
Found at i:1567772 original size:18 final size:18
Alignment explanation
Indices: 1567722--1567775 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
1567712 TATGATATAA
*
1567722 AATATGATATAAAAA-AT
1 AATATAATATAAAAATAT
*
1567739 AAT-TAAAATATAAAATAT
1 AATATAATATA-AAAATAT
1567757 AATATAATATAAAAATAT
1 AATATAATATAAAAATAT
1567775 A
1 A
1567776 TAAATTAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 5 0.16
17 7 0.23
18 13 0.42
19 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
AATATAATATAAAAATAT
Found at i:1568270 original size:2 final size:2
Alignment explanation
Indices: 1568263--1568288 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1568253 TAATAAAGGA
1568263 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
1568289 CACATGCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1570822 original size:16 final size:16
Alignment explanation
Indices: 1570800--1570837 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1570790 TAATTGATTC
1570800 AAATTTAAAATAATTT
1 AAATTTAAAATAATTT
*
1570816 GAATTTAAAATAATTT
1 AAATTTAAAATAATTT
1570832 AAATTT
1 AAATTT
1570838 GATTAATCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
AAATTTAAAATAATTT
Found at i:1570883 original size:11 final size:11
Alignment explanation
Indices: 1570867--1570891 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1570857 CTGATTAACC
1570867 TGAATCTAAAA
1 TGAATCTAAAA
1570878 TGAATCTAAAA
1 TGAATCTAAAA
1570889 TGA
1 TGA
1570892 TTAAAAACGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (11 bp):
TGAATCTAAAA
Found at i:1572310 original size:18 final size:17
Alignment explanation
Indices: 1572278--1572316 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1572268 CAAATCAAAG
*
1572278 ATTTTTTAAATATATAA
1 ATTTTTTAAAAATATAA
*
1572295 ATTTTTTAAAAAATATAT
1 ATTTTTT-AAAAATATAA
1572313 ATTT
1 ATTT
1572317 ATACCAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTTTAAAAATATAA
Found at i:1577564 original size:2 final size:2
Alignment explanation
Indices: 1577557--1577583 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1577547 GAACAAAAAG
1577557 TA 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 T
1577584 GAACTTCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1578640 original size:26 final size:27
Alignment explanation
Indices: 1578602--1578654 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
1578592 AATATTTTAA
* *
1578602 ATTTTTTTATTAATTTAA-AAATAAAT
1 ATTTTTTTATTAAATTAATAAAAAAAT
1578628 ATTTTATTT-TTAAATTAATAAAAAAAT
1 ATTTT-TTTATTAAATTAATAAAAAAAT
1578655 TTAAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTTTTTTATTAAATTAATAAAAAAAT
Found at i:1578704 original size:21 final size:20
Alignment explanation
Indices: 1578656--1578713 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
1578646 TAAAAAAATT
* **
1578656 TAAAATTAATTAAAATTAAA
1 TAAAAATAATTATGATTAAA
*
1578676 TAAAAATAAATTTTGATTAAA
1 TAAAAAT-AATTATGATTAAA
* *
1578697 TTAGAATAATTATGATT
1 TAAAAATAATTATGATT
1578714 TTTAATTAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (20 bp):
TAAAAATAATTATGATTAAA
Found at i:1579763 original size:24 final size:24
Alignment explanation
Indices: 1579736--1579796 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
1579726 TAATATTATT
1579736 TATAAATATTTAAATTTAATTT-AA
1 TATAAATATTTAAATTT-ATTTAAA
*
1579760 TATAAA-ATATAAAATTTATTTAAA
1 TATAAATAT-TTAAATTTATTTAAA
*
1579784 TTTATAATATTTA
1 TATA-AATATTTA
1579797 TAAATAAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
23 6 0.20
24 18 0.60
25 4 0.13
26 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TATAAATATTTAAATTTATTTAAA
Found at i:1579831 original size:13 final size:13
Alignment explanation
Indices: 1579808--1579842 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
1579798 AAATAAGTAA
1579808 TTTAAATATATATT
1 TTTAAATATAT-TT
1579822 TTTAAA-ATATTT
1 TTTAAATATATTT
1579834 TTTAAATAT
1 TTTAAATAT
1579843 TTATAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.40
13 6 0.30
14 6 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTAAATATATTT
Found at i:1580698 original size:21 final size:21
Alignment explanation
Indices: 1580655--1580695 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
1580645 AACCACAAAA
1580655 ATTTAAATTATTTAAAAATTT
1 ATTTAAATTATTTAAAAATTT
1580676 ATTT-AATTATTTAAAAATTT
1 ATTTAAATTATTTAAAAATTT
1580696 TATATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTAAATTATTTAAAAATTT
Found at i:1584515 original size:2 final size:2
Alignment explanation
Indices: 1584508--1584534 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1584498 AATTTAACAT
1584508 TA 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 T
1584535 CATTCTCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1588204 original size:17 final size:19
Alignment explanation
Indices: 1588164--1588204 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
1588154 CAATAACATG
1588164 TTAA-TAAAAATATATATA
1 TTAATTAAAAATATATATA
*
1588182 TTAATTAAAAA-AT-TATT
1 TTAATTAAAAATATATATA
1588199 TTAATT
1 TTAATT
1588205 TTTTTATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 9 0.43
18 6 0.29
19 6 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAATTAAAAATATATATA
Found at i:1589876 original size:23 final size:23
Alignment explanation
Indices: 1589849--1589893 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1589839 ATATTTATTT
1589849 AAATT-TTAATAAATAAAAATTAA
1 AAATTATTAA-AAATAAAAATTAA
* *
1589872 AAATTATTTAAAATTAAAATTA
1 AAATTATTAAAAATAAAAATTA
1589894 TATTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATTATTAAAAATAAAAATTAA
Found at i:1589982 original size:25 final size:25
Alignment explanation
Indices: 1589932--1590000 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
1589922 TTACTCAACC
* * *
1589932 AAAAAATTAT-TAATTTAATATATT
1 AAAAAATTATATTATATAAAATATT
*
1589956 AAAAAATTATATTATATAAAATTTT
1 AAAAAATTATATTATATAAAATATT
1589981 AAAATATATTAATATTATAT
1 AAAA-A-ATT-ATATTATAT
1590001 TTCAATTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 10 0.27
25 14 0.38
26 1 0.03
27 3 0.08
28 9 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
AAAAAATTATATTATATAAAATATT
Found at i:1590622 original size:33 final size:34
Alignment explanation
Indices: 1590557--1590629 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 34
1590547 TTAAAAAATT
*
1590557 TTAAAAATAATATTCATTCTTAATATTATT-AAA
1 TTAAAAATAATATTCATTCTTAATATCATTAAAA
*
1590590 TTAAAAATAATATTTATTCTTAATA-CAGTTAAAA
1 TTAAAAATAATATTCATTCTTAATATCA-TTAAAA
1590624 TTAAAA
1 TTAAAA
1590630 TAGAGAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 1 0.03
33 26 0.72
34 9 0.25
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (34 bp):
TTAAAAATAATATTCATTCTTAATATCATTAAAA
Found at i:1590810 original size:23 final size:25
Alignment explanation
Indices: 1590769--1590817 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
1590759 TTGAATTATT
1590769 ATTTAAATAATAAAAATTATT-TAA
1 ATTTAAATAATAAAAATTATTATAA
* *
1590793 ATTT-AATTATAAATATTATTATAA
1 ATTTAAATAATAAAAATTATTATAA
1590817 A
1 A
1590818 ATAATTACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTTAAATAATAAAAATTATTATAA
Found at i:1590822 original size:23 final size:23
Alignment explanation
Indices: 1590778--1590824 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1590768 TATTTAAATA
*
1590778 ATAAAAATTATTTAAATTTAATT
1 ATAAAAATTATTTAAATATAATT
*
1590801 ATAAATATTATTATAAA-ATAATT
1 ATAAAAATTATT-TAAATATAATT
1590824 A
1 A
1590825 CTTCCTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATAAAAATTATTTAAATATAATT
Found at i:1592881 original size:20 final size:20
Alignment explanation
Indices: 1592830--1592884 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1592820 AAATATAAAT
1592830 AATATAAATATTAA-AATTTA
1 AATATAAATA-TAATAATTTA
* *
1592850 TATAAAAATATAATAATTTA
1 AATATAAATATAATAATTTA
*
1592870 AATATAATTATAATA
1 AATATAAATATAATA
1592885 CTAACAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATATAAATATAATAATTTA
Found at i:1593362 original size:29 final size:30
Alignment explanation
Indices: 1593324--1593389 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
1593314 TTTTTTTATT
* *
1593324 TTTATATATTTTA-AAATGATAATAATTTA-A
1 TTTA-ATATTATATAAAT-ATAATAATTAATA
*
1593354 TTTAATATTATATAAATATTATAATTAATA
1 TTTAATATTATATAAATATAATAATTAATA
1593384 TTTAAT
1 TTTAAT
1593390 TTAAATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 16 0.52
30 15 0.48
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (30 bp):
TTTAATATTATATAAATATAATAATTAATA
Found at i:1593412 original size:11 final size:11
Alignment explanation
Indices: 1593347--1593414 Score: 61
Period size: 11 Copynumber: 6.1 Consensus size: 11
1593337 AAATGATAAT
1593347 AATTTAATTT-
1 AATTTAATTTA
*
1593357 AATATT-ATATA
1 AAT-TTAATTTA
*
1593368 AATATTATAATTA
1 AAT-TTA-ATTTA
1593381 ATATTTAATTTA
1 A-ATTTAATTTA
1593393 AATTT-ATTTA
1 AATTTAATTTA
1593403 AATTTAATTTA
1 AATTTAATTTA
1593414 A
1 A
1593415 TTGATTTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
10 16 0.33
11 18 0.38
12 5 0.10
13 7 0.15
14 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:1593424 original size:21 final size:22
Alignment explanation
Indices: 1593378--1593421 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1593368 AATATTATAA
*
1593378 TTAATATTTAATTTAAATTTAT
1 TTAATATTTAATTTAAATTGAT
1593400 TTAA-ATTTAATTT-AATTGAT
1 TTAATATTTAATTTAAATTGAT
1593420 TT
1 TT
1593422 TAATCATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 9 0.43
22 4 0.19
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TTAATATTTAATTTAAATTGAT
Found at i:1595198 original size:22 final size:20
Alignment explanation
Indices: 1595173--1595243 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
1595163 TCTTTCTTGG
* *
1595173 TAAATTTTATTGTGATTATATT
1 TAAATTTTATTAT-ATT-TATA
* *
1595195 TAAAATATATTATATTTATA
1 TAAATTTTATTATATTTATA
*
1595215 TAAATTTTAATATA-TTA-A
1 TAAATTTTATTATATTTATA
*
1595233 TAATTTTTATT
1 TAAATTTTATT
1595244 TTATAAATTT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 10 0.25
19 3 0.08
20 14 0.35
21 3 0.08
22 10 0.25
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TAAATTTTATTATATTTATA
Found at i:1595235 original size:18 final size:18
Alignment explanation
Indices: 1595214--1595262 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 18
1595204 TTATATTTAT
1595214 ATAAATTTTAATATATTA
1 ATAAATTTTAATATATTA
*
1595232 AT-AATTTT--TAT-TTT
1 ATAAATTTTAATATATTA
*
1595246 ATAAATTTTAAAATATT
1 ATAAATTTTAATATATT
1595263 TAATTTTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
14 4 0.16
15 9 0.36
17 8 0.32
18 4 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATAAATTTTAATATATTA
Found at i:1595250 original size:32 final size:31
Alignment explanation
Indices: 1595207--1595269 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 31
1595197 AAATATATTA
*
1595207 TATTTATATAAATTTTAATATATTAATAATTTT
1 TATTTATATAAATTTTAAAATATT--TAATTTT
1595240 TATTT-TATAAATTTTAAAATATTTAATTTT
1 TATTTATATAAATTTTAAAATATTTAATTTT
1595270 ATGTCAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.24
32 17 0.59
33 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (31 bp):
TATTTATATAAATTTTAAAATATTTAATTTT
Found at i:1595254 original size:15 final size:16
Alignment explanation
Indices: 1595204--1595255 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
1595194 TTAAAATATA
1595204 TTATATTTATATAAATT
1 TTATATTT-TATAAATT
*
1595221 TTAATATATTA-ATAATT
1 TT-ATATTTTATA-AATT
1595238 TT-TATTTTATAAATT
1 TTATATTTTATAAATT
1595253 TTA
1 TTA
1595256 AAATATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
15 12 0.41
16 2 0.07
17 10 0.34
18 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATATTTTATAAATT
Found at i:1596498 original size:9 final size:9
Alignment explanation
Indices: 1596484--1596508 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1596474 TAAAATTTAA
1596484 ATTTAATAT
1 ATTTAATAT
1596493 ATTTAATAT
1 ATTTAATAT
1596502 ATTTAAT
1 ATTTAAT
1596509 TTAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTTAATAT
Found at i:1597489 original size:29 final size:29
Alignment explanation
Indices: 1597402--1597500 Score: 146
Period size: 29 Copynumber: 3.4 Consensus size: 29
1597392 ATCAAGCTTT
1597402 TAAAACATAATTTATTTCTGCAAACTACA
1 TAAAACATAATTTATTTCTGCAAACTACA
* * *
1597431 TTAAAACATAATTTGTTTCTGAAAATTACA
1 -TAAAACATAATTTATTTCTGCAAACTACA
1597461 TAAAACATAATTTATTT-TCGCAAACTACA
1 TAAAACATAATTTATTTCT-GCAAACTACA
1597490 TAAAACATAAT
1 TAAAACATAAT
1597501 AATATAATAC
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
28 1 0.02
29 35 0.56
30 26 0.42
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.35
Consensus pattern (29 bp):
TAAAACATAATTTATTTCTGCAAACTACA
Found at i:1597517 original size:23 final size:24
Alignment explanation
Indices: 1597491--1597537 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
1597481 CAAACTACAT
1597491 AAAACATAATAAT-ATAATACAAC
1 AAAACATAATAATAATAATACAAC
1597514 AAAACATAATAATAATAATACAAC
1 AAAACATAATAATAATAATACAAC
1597538 GATAAACGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.66, C:0.13, G:0.00, T:0.21
Consensus pattern (24 bp):
AAAACATAATAATAATAATACAAC
Found at i:1599879 original size:2 final size:2
Alignment explanation
Indices: 1599872--1599902 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1599862 TATAGTAAGC
1599872 TA TA TA 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 T
1599903 GAATGAAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1600248 original size:2 final size:2
Alignment explanation
Indices: 1600241--1600280 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1600231 ATAGTAAGTG
1600241 AT AT AT AT AT AT 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 AT AT AT AT AT AT
1600281 GAATGAAAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1600495 original size:376 final size:371
Alignment explanation
Indices: 1599766--1601004 Score: 1580
Period size: 376 Copynumber: 3.3 Consensus size: 371
1599756 AAATGATTAA
* *
1599766 TCACTCGCTTTCAAGTTTAAAGTATTCTTTTTACAAATTGACTAGTTATAGACTTGGAT-GATCA
1 TCACTCGCTTTCAAGTTTAAA-TATTCTTTTTACAAATTGACTAGTTATAGGCTT-CATCGATCA
* *
1599830 TATTTGTTTGTGTGTGATGTGGACTAATTTAATATAGTAA--G-------CTATATATATATATA
64 TCTTTGTTTGTGTGTGATGTGGACTAATTTAATATAGTAAGTGTATATATATATATATATATATA
*
1599886 TATATATATATATATATGAATGAAAGCTTCATCTCATTAAAACAAGAAATCCT-TTATTATTATT
129 TATATATATATATATATGAATGAAAGCTTCATCTCACTAAAACAA-AAATCCTCTT-TTATTATT
1599950 ATT-TCTTTTTTAATTTTTTCCAATCCTCTCTCATCTTTGGTTTTTTTTTCACACTTTTATGATT
192 ATTAT-TTTTTTAATTTTTTCCAATCCTCTCTCATCTTTGG--TTTTTTTCACACTTTTA-GATT
* *
1600014 TTTTTTATCTTCATCTTAGGAGTAGTATTTTTGAAATGCAATAACTAAATGAGTTAACATTGATT
253 TTTTTTATTTTCATCTTAGGAG-AGTATTTTTGAAATGCAATAACTAAATGAGTTAACATTGATC
* * *
1600079 TTAAATTCTAAATATCATTACTGAATTAAAAATCTATCTAAATTAGAATGGTTGG
317 TTAGATTATAAATATCATTACTGAATTAAAAATCTATCTAAATTAGAATAGTTGG
* * *
1600134 TCACTCGCTTTCAAGTTTATAATATTCTTTTTACAGATTGACTAGTTATAGGCTTCGTCGGTCAT
1 TCACTCGCTTTCAAGTTTA-AATATTCTTTTTACAAATTGACTAGTTATAGGCTTCATCGATCAT
*
1600199 CTTTGTTTGTATGTGATGTGGACTAATTTAATATAGTAAGTGATATATATATATATATATATATA
65 CTTTGTTTGTGTGTGATGTGGACTAATTTAATATAGTAAGTG-TATATATATATATATATATATA
*
1600264 TATATATATATATATATGAATGAAAGCTTCATCTCACTAAAATAAAAATCCTCTTTTAATTATTA
129 TATATATATATATATATGAATGAAAGCTTCATCTCACTAAAACAAAAATCCTCTTTT-ATTATTA
*
1600329 TTATTCTTTTAATTTTTTCCAATCCTCTCTCATCTTTGGTTTTTTTCCACACTTTTACGA-TTTT
193 TTATTTTTTTAATTTTTTCCAATCCTCTCTCATCTTTGGTTTTTTT-CACACTTTTA-GATTTTT
* * * * * *
1600393 TTTATTTTCATCTTAGAAGCAGTATTTTTGAAATACAATAATTAAATGAGTTAATAGTAATCTTA
256 TTTATTTTCATCTTAGGAG-AGTATTTTTGAAATGCAATAACTAAATGAGTTAACATTGATCTTA
* * * *
1600458 GATTATAAATATAATTACTGAATTGAAAATCTATCTAAATCAGAATAATTGG
320 GATTATAAATATCATTACTGAATTAAAAATCTATCTAAATTAGAATAGTTGG
* * *
1600510 TCACTTGCTTTTAAGTTTATAATATTTTTTTTACAAATTGACTAGTTATA-GCTTTCATCGATCA
1 TCACTCGCTTTCAAGTTTA-AATATTCTTTTTACAAATTGACTAGTTATAGGC-TTCATCGATCA
* *
1600574 TCTTTGTTTGTGTGTGATGTGGGCTAATTTAATATAGTAAGTAATATATATATATATATATATAT
64 TCTTTGTTTGTGTGTGATGTGGACTAATTTAATATAGTAAGT-GTATATATATATATATATATAT
* * *
1600639 ATATATATATATATATATGAATGAAAGCTTCATTTCACTCAAACAAGAATCCTTCTTTTATTATT
128 ATATATATATATATATATGAATGAAAGCTTCATCTCACTAAAACAAAAATCC-TCTTTTATTATT
* * * *
1600704 ATTATTTTTTTAATTTTATT-TAATCC-CTTTCATCTTTGATTTTTTTCACACTTTTATATTTTT
192 ATTATTTTTTTAATTTT-TTCCAATCCTCTCTCATCTTTGGTTTTTTTCACACTTTTAGATTTTT
* * * *
1600767 TTTATTTTCATTTTAGGAGAGGTATTTTT-AAATGCAATACCTCAAGGAGTTAACATTGATCTTA
256 TTTATTTTCATCTTAGGAGA-GTATTTTTGAAATGCAATAACTAAATGAGTTAACATTGATCTTA
* * * * * *
1600831 GATTATAAGTATCATTAGTGAATTAAAAATTTACCTAAATTAAAATAGTTGA
320 GATTATAAATATCATTACTGAATTAAAAATCTATCTAAATTAGAATAGTTGG
* * * * * *
1600883 TTACTCGTTTTCAAGTTTGAAATATT-TTTTTGATAAATT-ATCTAATTATAAGCTTAATCGATC
1 TCACTCGCTTTCAAGTTT-AAATATTCTTTTT-ACAAATTGA-CTAGTTATAGGCTTCATCGATC
* * * * * * *
1600946 ATTTTTATTTATGTGTGATATAGATTAATTTAATATAATAAGTGTATATATATATATAT
63 ATCTTTGTTTGTGTGTGATGTGGACTAATTTAATATAGTAAGTGTATATATATATATAT
1601005 GAATGAAAGT
Statistics
Matches: 763, Mismatches: 82, Indels: 48
0.85 0.09 0.05
Matches are distributed among these distances:
367 1 0.00
368 92 0.12
369 2 0.00
370 1 0.00
372 21 0.03
373 149 0.20
374 42 0.06
375 20 0.03
376 303 0.40
377 29 0.04
378 102 0.13
379 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.46
Consensus pattern (371 bp):
TCACTCGCTTTCAAGTTTAAATATTCTTTTTACAAATTGACTAGTTATAGGCTTCATCGATCATC
TTTGTTTGTGTGTGATGTGGACTAATTTAATATAGTAAGTGTATATATATATATATATATATATA
TATATATATATATATGAATGAAAGCTTCATCTCACTAAAACAAAAATCCTCTTTTATTATTATTA
TTTTTTTAATTTTTTCCAATCCTCTCTCATCTTTGGTTTTTTTCACACTTTTAGATTTTTTTTAT
TTTCATCTTAGGAGAGTATTTTTGAAATGCAATAACTAAATGAGTTAACATTGATCTTAGATTAT
AAATATCATTACTGAATTAAAAATCTATCTAAATTAGAATAGTTGG
Found at i:1600624 original size:2 final size:2
Alignment explanation
Indices: 1600617--1600656 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1600607 ATAGTAAGTA
1600617 AT AT AT AT AT AT 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 AT AT AT AT AT AT
1600657 GAATGAAAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1607064 original size:32 final size:32
Alignment explanation
Indices: 1607026--1607108 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 32
1607016 TGAATTCGGG
* *
1607026 TCATTTC-GAGTTCGGATTATTTCGAGTTCAGA
1 TCATTTCGGA-TTCGGATCATTTCGAGTTCAAA
*
1607058 TCATTTCGGATTCGGATCATTTCGGGTTCAAA
1 TCATTTCGGATTCGGATCATTTCGAGTTCAAA
* *
1607090 TTATTTCGGATTCGAATCA
1 TCATTTCGGATTCGGATCA
1607109 ATCGGGTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
32 43 0.96
33 2 0.04
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (32 bp):
TCATTTCGGATTCGGATCATTTCGAGTTCAAA
Found at i:1607098 original size:16 final size:16
Alignment explanation
Indices: 1607026--1607098 Score: 74
Period size: 16 Copynumber: 4.6 Consensus size: 16
1607016 TGAATTCGGG
* *
1607026 TCATTTCGAGTTCGGA
1 TCATTTCGGGTTCAGA
* *
1607042 TTATTTCGAGTTCAGA
1 TCATTTCGGGTTCAGA
* *
1607058 TCATTTCGGATTCGGA
1 TCATTTCGGGTTCAGA
*
1607074 TCATTTCGGGTTCAAA
1 TCATTTCGGGTTCAGA
*
1607090 TTATTTCGG
1 TCATTTCGG
1607099 ATTCGAATCA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (16 bp):
TCATTTCGGGTTCAGA
Found at i:1610883 original size:5 final size:5
Alignment explanation
Indices: 1610869--1610947 Score: 61
Period size: 5 Copynumber: 15.4 Consensus size: 5
1610859 AAGTTAAGTT
* * * *
1610869 ATTTA A-TTA ATTTAA ATTTA ATTAA ATTTAA ATATA ATTTTT ATTCA
1 ATTTA ATTTA ATTT-A ATTTA ATTTA ATTT-A ATTTA A-TTTA ATTTA
* * *
1610916 AATTA ATTTA ATTTA AATTA ATTTA AATTA AT
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA AT
1610948 AAAAATATTT
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
4 4 0.07
5 40 0.71
6 12 0.21
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (5 bp):
ATTTA
Found at i:1610961 original size:28 final size:29
Alignment explanation
Indices: 1610926--1610985 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
1610916 AATTAATTTA
*
1610926 ATTTAAA-TTAATT-TAAATTAATAAAAAT
1 ATTTAAATTTAATTATAAAAT-ATAAAAAT
*
1610954 ATTTAAATTTAATTATAAAATATAAAATT
1 ATTTAAATTTAATTATAAAATATAAAAAT
1610983 ATT
1 ATT
1610986 AATACAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.25
29 16 0.57
30 5 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
ATTTAAATTTAATTATAAAATATAAAAAT
Found at i:1610962 original size:43 final size:43
Alignment explanation
Indices: 1610868--1610972 Score: 101
Period size: 43 Copynumber: 2.4 Consensus size: 43
1610858 AAAGTTAAGT
***
1610868 TATTT-AATTAATTTAAATTTAATTAAATTTAAATATAATTTT
1 TATTTAAATTAATTTAAATTTAATTAAATTTAAATATAATAAA
*
1610910 TATTCAAATTAATTT-AATTTAAATT-AATTTAAAT-TAATAAAAA
1 TATTTAAATTAATTTAAATTT-AATTAAATTTAAATATAAT--AAA
1610953 TATTTAAATTTAATTATAAA
1 TATTTAAA-TTAATT-TAAA
1610973 ATATAAAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
41 4 0.08
42 18 0.35
43 20 0.39
44 6 0.12
45 1 0.02
46 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.50
Consensus pattern (43 bp):
TATTTAAATTAATTTAAATTTAATTAAATTTAAATATAATAAA
Found at i:1611440 original size:12 final size:13
Alignment explanation
Indices: 1611422--1611455 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
1611412 ATATTATATA
1611422 ATTATATTTAAAT
1 ATTATATTTAAAT
1611435 -TTATA-TTAAAT
1 ATTATATTTAAAT
1611446 ATTATATTTA
1 ATTATATTTA
1611456 TAAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.32
12 10 0.53
13 3 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTATATTTAAAT
Found at i:1611642 original size:18 final size:18
Alignment explanation
Indices: 1611602--1611642 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1611592 ATTTCGATGA
* *
1611602 GATTAAATTTAATTATAT
1 GATTAAACTTAATTAAAT
*
1611620 AATTAAACTTAATTAAAT
1 GATTAAACTTAATTAAAT
1611638 GATTA
1 GATTA
1611643 TTGCATAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (18 bp):
GATTAAACTTAATTAAAT
Found at i:1627017 original size:4 final size:4
Alignment explanation
Indices: 1627008--1627046 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
1626998 GTTATTTTTC
* * *
1627008 ATAT ATAT ATAT ATAT ATAT ATAT TTAT TTAT ATTT ATA
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATA
1627047 GATTTTGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (4 bp):
ATAT
Found at i:1627017 original size:6 final size:6
Alignment explanation
Indices: 1627008--1627046 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1626998 GTTATTTTTC
* * *
1627008 ATATAT ATATAT ATATAT ATATAT TTATTT ATATTT ATA
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATA
1627047 GATTTTGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
ATATAT
Found at i:1627021 original size:10 final size:10
Alignment explanation
Indices: 1627008--1627046 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1626998 GTTATTTTTC
1627008 ATATATATAT
1 ATATATATAT
1627018 ATATATATAT
1 ATATATATAT
* *
1627028 ATATTTATTT
1 ATATATATAT
*
1627038 ATATTTATA
1 ATATATATA
1627047 GATTTTGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
ATATATATAT
Found at i:1627161 original size:2 final size:2
Alignment explanation
Indices: 1627154--1627186 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1627144 CACTCATTGG
1627154 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1627187 GTATTCGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1631101 original size:31 final size:30
Alignment explanation
Indices: 1631066--1631130 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 30
1631056 ATTTTTTTAT
* *
1631066 ATAAAATTTTTAATATTATTATTAATA-ATTA
1 ATAAAATTTTTAA-ATT-TTATAAACAGATTA
1631097 ATAAAATTTTTAAATTTTATAAACAGATTA
1 ATAAAATTTTTAAATTTTATAAACAGATTA
1631127 ATAA
1 ATAA
1631131 TAATAATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 7 0.23
30 11 0.35
31 13 0.42
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (30 bp):
ATAAAATTTTTAAATTTTATAAACAGATTA
Found at i:1631384 original size:20 final size:20
Alignment explanation
Indices: 1631361--1631405 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1631351 AAAATTTTTA
*
1631361 AATATTTAAATTTAAATAAT
1 AATATTTAAATATAAATAAT
**
1631381 AATATTTTTATATAAATAAT
1 AATATTTAAATATAAATAAT
1631401 AATAT
1 AATAT
1631406 AAATCAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATATTTAAATATAAATAAT
Found at i:1632206 original size:44 final size:42
Alignment explanation
Indices: 1632127--1632221 Score: 113
Period size: 42 Copynumber: 2.2 Consensus size: 42
1632117 CGTTGAGAGC
*
1632127 TTATTTTAATATTTAAAATAATATAAAAAATAAAAAAATTATTT
1 TTATATTAATATTTAAAATAATATAAAAAAT-AAAAAATTA-TT
* *
1632171 TTATATTAATATTTATAATTAA-A-AATAAATAAAAAATTATT
1 TTATATTAATATTTA-AAATAATATAAAAAATAAAAAATTATT
1632212 TTATTATTAA
1 TTA-TATTAA
1632222 AATAATAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
41 5 0.11
42 15 0.33
43 6 0.13
44 15 0.33
45 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (42 bp):
TTATATTAATATTTAAAATAATATAAAAAATAAAAAATTATT
Found at i:1633456 original size:24 final size:24
Alignment explanation
Indices: 1633429--1633486 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
1633419 TGATTTGCAT
1633429 GAGTGATCCATGATTCTAGTTTCG
1 GAGTGATCCATGATTCTAGTTTCG
1633453 GAGTGATCCATGATTCTAGTTTCG
1 GAGTGATCCATGATTCTAGTTTCG
*
1633477 GAATGATCCA
1 GAGTGATCCA
1633487 CCCAGATCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (24 bp):
GAGTGATCCATGATTCTAGTTTCG
Found at i:1636597 original size:16 final size:16
Alignment explanation
Indices: 1636544--1636608 Score: 69
Period size: 16 Copynumber: 4.0 Consensus size: 16
1636534 AATAAAATAC
1636544 GTATTAAGATTATATTT
1 GTATTAA-ATTATATTT
* * *
1636561 TTGTTAAATTAAAATTT
1 GTATTAAATT-ATATTT
1636578 -TATTAAATTATATTT
1 GTATTAAATTATATTT
*
1636593 GTATTAATTTATATTT
1 GTATTAAATTATATTT
1636609 ATGTTTATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
15 5 0.12
16 25 0.62
17 10 0.25
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (16 bp):
GTATTAAATTATATTT
Found at i:1636618 original size:16 final size:16
Alignment explanation
Indices: 1636574--1636634 Score: 65
Period size: 16 Copynumber: 4.0 Consensus size: 16
1636564 TTAAATTAAA
*
1636574 ATTT-TATTAAATTAT
1 ATTTATATTAATTTAT
*
1636589 ATTTGTATTAATTTAT
1 ATTTATATTAATTTAT
* *
1636605 ATTTATGTTTATTTA-
1 ATTTATATTAATTTAT
1636620 ATTT-TATTAATTTAT
1 ATTTATATTAATTTAT
1636635 TATGCTGTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
14 8 0.21
15 8 0.21
16 22 0.58
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
ATTTATATTAATTTAT
Found at i:1636813 original size:28 final size:28
Alignment explanation
Indices: 1636770--1636858 Score: 78
Period size: 28 Copynumber: 3.2 Consensus size: 28
1636760 AGATTAATTC
*
1636770 ATTTTAAA-TTCAAATTTTAATTTAATTA
1 ATTTTAAATTTTAAATTTTAATTTAA-TA
* *
1636798 A-TTTATATATTT-AATTAGT-ATTTAATA
1 ATTTTAAAT-TTTAAATT-TTAATTTAATA
*
1636825 ATTTTAAATTTTAAATTTTAATATTTATA
1 ATTTTAAATTTTAAATTTTAAT-TTAATA
1636854 ATTTT
1 ATTTT
1636859 TTTCTAACTC
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
27 12 0.25
28 23 0.48
29 13 0.27
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (28 bp):
ATTTTAAATTTTAAATTTTAATTTAATA
Found at i:1636856 original size:15 final size:15
Alignment explanation
Indices: 1636816--1636858 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1636806 ATTTAATTAG
1636816 TATTTAATAATTTTAA
1 TATTT-ATAATTTTAA
1636832 -ATTT-TAAATTTTAA
1 TATTTAT-AATTTTAA
1636846 TATTTATAATTTT
1 TATTTATAATTTT
1636859 TTTCTAACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 1 0.04
14 8 0.33
15 14 0.58
16 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTTATAATTTTAA
Found at i:1637146 original size:23 final size:25
Alignment explanation
Indices: 1637119--1637186 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 25
1637109 TTGTAATGTG
*
1637119 ATTTAATAGTTATTATTTTA-TAAT
1 ATTTAATAATTATTATTTTATTAAT
* * *
1637143 -TTTAAGATTTTTTA-TTTATTAAT
1 ATTTAATAATTATTATTTTATTAAT
1637166 ATTT-ATAATTATTA-TTTATTA
1 ATTTAATAATTATTATTTTATTA
1637187 CAATTAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
22 4 0.11
23 29 0.81
24 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (25 bp):
ATTTAATAATTATTATTTTATTAAT
Found at i:1637179 original size:16 final size:17
Alignment explanation
Indices: 1637133--1637179 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
1637123 AATAGTTATT
1637133 ATTTTATAATT-TTAAG
1 ATTTTATAATTATTAAG
* * *
1637149 ATTTTTTATTTATTAAT
1 ATTTTATAATTATTAAG
1637166 A-TTTATAATTATTA
1 ATTTTATAATTATTA
1637180 TTTATTACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
ATTTTATAATTATTAAG
Found at i:1637244 original size:20 final size:21
Alignment explanation
Indices: 1637213--1637261 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
1637203 TATTCATTAT
1637213 ATATATATATGATCAAA-ATAA
1 ATATA-ATATGATCAAATATAA
*
1637234 ATATAATATGATTAAATATAA
1 ATATAATATGATCAAATATAA
1637255 AT-TAATA
1 ATATAATA
1637262 ATTATAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (21 bp):
ATATAATATGATCAAATATAA
Found at i:1637250 original size:19 final size:21
Alignment explanation
Indices: 1637213--1637256 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1637203 TATTCATTAT
1637213 ATATATATATGATCAAAATAA
1 ATATATATATGATCAAAATAA
*
1637234 ATATA-ATATGATTAAATATAA
1 ATATATATATGATCAAA-ATAA
1637255 AT
1 AT
1637257 TAATAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (21 bp):
ATATATATATGATCAAAATAA
Found at i:1638350 original size:17 final size:17
Alignment explanation
Indices: 1638330--1638387 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
1638320 TAAGATTTGA
1638330 ATTAAAAATATATTTTT
1 ATTAAAAATATATTTTT
* *
1638347 ATTAAATATTTATTTTAT
1 ATTAAAAATATATTTT-T
* *
1638365 TTTAAAAA-ATAATTTT
1 ATTAAAAATATATTTTT
1638381 -TTAAAAA
1 ATTAAAAA
1638388 ATAAAAAATC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 7 0.21
16 1 0.03
17 19 0.56
18 7 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTAAAAATATATTTTT
Found at i:1641313 original size:68 final size:68
Alignment explanation
Indices: 1641204--1641340 Score: 256
Period size: 68 Copynumber: 2.0 Consensus size: 68
1641194 AAACTCAACT
* *
1641204 TATAAATAATTCTATTCTTAATGTAATAATAAATTTTACTTTTAATTGTAAACTTATTCTAAGAT
1 TATAAACAATTCTATTCTTAATGTAATAATAAAATTTACTTTTAATTGTAAACTTATTCTAAGAT
1641269 ACA
66 ACA
1641272 TATAAACAATTCTATTCTTAATGTAATAATAAAATTTACTTTTAATTGTAAACTTATTCTAAGAT
1 TATAAACAATTCTATTCTTAATGTAATAATAAAATTTACTTTTAATTGTAAACTTATTCTAAGAT
1641337 ACA
66 ACA
1641340 T
1 T
1641341 GAACAATAAG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (68 bp):
TATAAACAATTCTATTCTTAATGTAATAATAAAATTTACTTTTAATTGTAAACTTATTCTAAGAT
ACA
Found at i:1641827 original size:2 final size:2
Alignment explanation
Indices: 1641822--1641848 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1641812 AAAAAAGGCA
1641822 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1641849 AAGAAACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1642007 original size:23 final size:24
Alignment explanation
Indices: 1641981--1642037 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
1641971 AATAAAAATA
*
1641981 TTTATAAATA-TTAAGATATTA-AT
1 TTTAAAAATATTTAA-ATATTATAT
1642004 TTTAAAAATATTTAAATATTATAT
1 TTTAAAAATATTTAAATATTATAT
1642028 TTTAAAAATA
1 TTTAAAAATA
1642038 AATATATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTAAAAATATTTAAATATTATAT
Found at i:1642078 original size:18 final size:20
Alignment explanation
Indices: 1642055--1642094 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
1642045 AAATCAATTA
*
1642055 AATTATCAAAA-ACTTT-TT
1 AATTATAAAAATACTTTATT
1642073 AATTATAAAAATACTTTATT
1 AATTATAAAAATACTTTATT
1642093 AA
1 AA
1642095 CAAGTGGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 5 0.26
20 4 0.21
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTATAAAAATACTTTATT
Found at i:1643375 original size:22 final size:22
Alignment explanation
Indices: 1643331--1643372 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1643321 ATAATAAGAA
1643331 TTTAATTAATTTTAAAATTAAT
1 TTTAATTAATTTTAAAATTAAT
1643353 TTTAATT-ATTATT-AAATTAA
1 TTTAATTAATT-TTAAAATTAA
1643373 ATTATTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTAATTAATTTTAAAATTAAT
Found at i:1645471 original size:19 final size:23
Alignment explanation
Indices: 1645431--1645495 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 23
1645421 TGATTTAAAA
1645431 TTATATAAGATAATAT--ATAATTT
1 TTATAT-A-ATAATATAAATAATTT
1645454 TTAT-T-AT-ATA-AAATAATTT
1 TTATATAATAATATAAATAATTT
1645473 TTATATAATAATATAAATAATTT
1 TTATATAATAATATAAATAATTT
1645496 ATTTTTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
18 3 0.08
19 13 0.36
20 1 0.03
21 2 0.06
22 4 0.11
23 13 0.36
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TTATATAATAATATAAATAATTT
Found at i:1648909 original size:51 final size:56
Alignment explanation
Indices: 1648807--1648914 Score: 138
Period size: 56 Copynumber: 2.0 Consensus size: 56
1648797 ATTATATAAT
*
1648807 TTATATTATATAAAAAATAAATATATAATATTTTAATATAAATATTAAAAAATATA
1 TTATATTATATAAAAAATAAATATATAATATTTTAATATAAATATAAAAAAATATA
* *
1648863 TTAT-TTATAGTAGAAAATAAA-ATAT-ATTTTTTAA-A-AAAT-TAAAAAAATATA
1 TTATATTATA-TAAAAAATAAATATATAATATTTTAATATAAATATAAAAAAATATA
1648914 T
1 T
1648915 AATACGATTG
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
51 12 0.25
52 4 0.08
53 1 0.02
54 8 0.17
55 9 0.19
56 14 0.29
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (56 bp):
TTATATTATATAAAAAATAAATATATAATATTTTAATATAAATATAAAAAAATATA
Found at i:1648984 original size:16 final size:16
Alignment explanation
Indices: 1648963--1648995 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1648953 AAATTTATAT
1648963 TTTAAATTAAAT-TAAA
1 TTTAAA-TAAATATAAA
1648979 TTTAAATAAATATAAA
1 TTTAAATAAATATAAA
1648995 T
1 T
1648996 AATATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAAATAAATATAAA
Found at i:1649618 original size:3 final size:3
Alignment explanation
Indices: 1649612--1649676 Score: 85
Period size: 3 Copynumber: 21.7 Consensus size: 3
1649602 CAGCACCATG
* * * * *
1649612 TTC TTC TTC TTA TTC TTC TTC ATC ATC ATC TTC ATC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1649660 TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TT
1649677 GGCTTCCAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.08, C:0.31, G:0.00, T:0.62
Consensus pattern (3 bp):
TTC
Found at i:1652812 original size:31 final size:32
Alignment explanation
Indices: 1652769--1652831 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
1652759 GAATATGATC
1652769 CGAATATATTAATGTGTTAAA-ATATATATAAA
1 CGAATATATTAATGTG-TAAACATATATATAAA
*
1652801 CGAATA-ATTAATGTGTAAACATTTATATAAA
1 CGAATATATTAATGTGTAAACATATATATAAA
1652832 ATTTTAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 4 0.14
31 19 0.66
32 6 0.21
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.37
Consensus pattern (32 bp):
CGAATATATTAATGTGTAAACATATATATAAA
Found at i:1652868 original size:19 final size:20
Alignment explanation
Indices: 1652843--1652905 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
1652833 TTTTAATATT
1652843 TTAAATATATAAAAAAAATA
1 TTAAATATATAAAAAAAATA
*
1652863 -TAAATACGATATAAAAAAATAA
1 TTAAATA-TATA-AAAAAAAT-A
1652885 TTAAA-ATATAATATAAAAATA
1 TTAAATATATAA-A-AAAAATA
1652906 ATTATGATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
19 6 0.17
20 4 0.11
21 13 0.37
22 8 0.23
23 4 0.11
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (20 bp):
TTAAATATATAAAAAAAATA
Done.