Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 135 of 150
Found at i:40526495 original size:26 final size:27
Alignment explanation
Indices: 40526459--40526510 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
40526449 CAAAAAAATT
40526459 TGTTGTTTTTTC-TTTACTATTTTTGC
1 TGTTGTTTTTTCGTTTACTATTTTTGC
* *
40526485 TGTTTTTTTTTCGTTTTTCTATTTTT
1 TGTTGTTTTTTCG-TTTACTATTTTT
40526511 TTTATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 11 0.50
28 11 0.50
ACGTcount: A:0.06, C:0.10, G:0.10, T:0.75
Consensus pattern (27 bp):
TGTTGTTTTTTCGTTTACTATTTTTGC
Found at i:40529851 original size:26 final size:26
Alignment explanation
Indices: 40529790--40529852 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
40529780 TCTGACCCAT
*
40529790 AGCTCGTGTAAACAGACCCATTTCAC
1 AGCTCGTGTGAACAGACCCATTTCAC
40529816 AGCTCGTGTGAACAGACCCATTTCAC
1 AGCTCGTGTGAACAGACCCATTTCAC
40529842 AGCTCGTGTGA
1 AGCTCGTGTGA
40529853 GCACTATTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (26 bp):
AGCTCGTGTGAACAGACCCATTTCAC
Found at i:40540141 original size:30 final size:30
Alignment explanation
Indices: 40539906--40540157 Score: 201
Period size: 30 Copynumber: 8.4 Consensus size: 30
40539896 TCATTGACGA
* *
40539906 ATGAAAAGGGATAGCTTCGGCTATC-AATA
1 ATGAAAAGGGATGGCTTCGGCTATCAAATT
* * * * *
40539935 ATGAAAAGGGATTG-TGACGACCATAAAATT
1 ATGAAAAGGGATGGCT-TCGGCTATCAAATT
* ** *
40539965 ATGAAAAGGGATGGCTTTGGCTATCGTACT
1 ATGAAAAGGGATGGCTTCGGCTATCAAATT
*
40539995 ATGAAAAGGGATGGCTTCGGCTATC-GATCT
1 ATGAAAAGGGATGGCTTCGGCTATCAAAT-T
*
40540025 ATGAAAAGGGATGGCTTTGGCTATCAAATT
1 ATGAAAAGGGATGGCTTCGGCTATCAAATT
* * **
40540055 ATGAAAAGGGAT-G-TTGACGACCATCAAACA
1 ATGAAAAGGGATGGCTT--CGGCTATCAAATT
* * * * *
40540085 ATAAAAATGGATGG-TGACGACCATCAAATT
1 ATGAAAAGGGATGGCT-TCGGCTATCAAATT
*
40540115 ATGAAAAGGGATGGCTTCGGTTATCAAATT
1 ATGAAAAGGGATGGCTTCGGCTATCAAATT
*
40540145 ACGAAAAGGGATG
1 ATGAAAAGGGATG
40540158 TGTCAACCAT
Statistics
Matches: 176, Mismatches: 37, Indels: 19
0.76 0.16 0.08
Matches are distributed among these distances:
28 3 0.02
29 20 0.11
30 147 0.84
31 6 0.03
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.25
Consensus pattern (30 bp):
ATGAAAAGGGATGGCTTCGGCTATCAAATT
Found at i:40542620 original size:29 final size:29
Alignment explanation
Indices: 40542587--40542650 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
40542577 TAATCCACCA
40542587 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
40542616 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
40542646 CCCAA
1 CCCAA
40542651 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:40542624 original size:30 final size:30
Alignment explanation
Indices: 40542594--40542650 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
40542584 CCACCCAACT
40542594 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
40542623 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
40542651 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:40547791 original size:21 final size:20
Alignment explanation
Indices: 40547767--40547815 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
40547757 ATTTTATCCA
**
40547767 TTTTTATTTAATTAGTTTAT
1 TTTTTATTTAATTACATTAT
40547787 TTTTTATTCTAATTACATTA-
1 TTTTTATT-TAATTACATTAT
40547807 TTTTTATTT
1 TTTTTATTT
40547816 TTAAGGTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 1 0.04
20 16 0.62
21 9 0.35
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTTATTTAATTACATTAT
Found at i:40547910 original size:26 final size:25
Alignment explanation
Indices: 40547871--40547920 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
40547861 ATTTTCTTTA
* *
40547871 AAAAAATTGTAATATATAACTAAAC
1 AAAAAATTGTAATAAAAAACTAAAC
*
40547896 AAAAAATTTTGAATAAAAAACTAAA
1 AAAAAATTGT-AATAAAAAACTAAA
40547921 ATAAAATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (25 bp):
AAAAAATTGTAATAAAAAACTAAAC
Found at i:40550403 original size:22 final size:22
Alignment explanation
Indices: 40550378--40550426 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
40550368 AATACTTTAA
*
40550378 AAAAAATTATTTTTTTATTT-TT
1 AAAAAATT-TTTTTGTATTTATT
* *
40550400 AAAATATTTTTTTGTGTTTATT
1 AAAAAATTTTTTTGTATTTATT
40550422 AAAAA
1 AAAAA
40550427 CCGGGCCGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (22 bp):
AAAAAATTTTTTTGTATTTATT
Found at i:40550419 original size:19 final size:20
Alignment explanation
Indices: 40550380--40550419 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
40550370 TACTTTAAAA
*
40550380 AAAATTATTTTTTTATTTTT
1 AAAATTATTTTTTTATGTTT
*
40550400 AAAA-TATTTTTTTGTGTTT
1 AAAATTATTTTTTTATGTTT
40550419 A
1 A
40550420 TTAAAAACCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (20 bp):
AAAATTATTTTTTTATGTTT
Found at i:40564743 original size:5 final size:5
Alignment explanation
Indices: 40564733--40564761 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
40564723 GATCTCTCCT
40564733 CACCC CACCC CACCC CACCC CACCC CACC
1 CACCC CACCC CACCC CACCC CACCC CACC
40564762 AACCCCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.79, G:0.00, T:0.00
Consensus pattern (5 bp):
CACCC
Found at i:40570858 original size:41 final size:40
Alignment explanation
Indices: 40570813--40570890 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
40570803 ACAATTCTTG
*
40570813 ATTTAATTTAA-TATTTTCTCATAAAAATG-ATAAAAATGACA
1 ATTT-ATTTAACTATTTT-T-ATAAAAACGTATAAAAATGACA
40570854 ATTTATTTAATCTATTTTTATAAAAACGTATAAAAAT
1 ATTTATTTAA-CTATTTTTATAAAAACGTATAAAAAT
40570891 TCTTAAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
40 14 0.42
41 13 0.39
42 6 0.18
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.42
Consensus pattern (40 bp):
ATTTATTTAACTATTTTTATAAAAACGTATAAAAATGACA
Found at i:40570916 original size:20 final size:20
Alignment explanation
Indices: 40570874--40570919 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
40570864 TCTATTTTTA
*
40570874 TAAAAACGTATAAAAATTCT
1 TAAAAACGTATAAAAAGTCT
*
40570894 TAAAAACTTAT-AAAAGTCAT
1 TAAAAACGTATAAAAAGTC-T
40570914 TAAAAA
1 TAAAAA
40570920 TAAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.59, C:0.09, G:0.04, T:0.28
Consensus pattern (20 bp):
TAAAAACGTATAAAAAGTCT
Found at i:40571060 original size:21 final size:21
Alignment explanation
Indices: 40571043--40571092 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
40571033 TTTATAAATA
*
40571043 ATATAAAAATTATAATAAGGT
1 ATATAAAAATTATAATAAGAT
*
40571064 ATATAGAAATTATAA-AAG-T
1 ATATAAAAATTATAATAAGAT
40571083 -TATAAAAATT
1 ATATAAAAATT
40571093 TAAAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 9 0.33
19 1 0.04
20 3 0.11
21 14 0.52
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (21 bp):
ATATAAAAATTATAATAAGAT
Found at i:40571098 original size:8 final size:9
Alignment explanation
Indices: 40571029--40571107 Score: 63
Period size: 9 Copynumber: 8.6 Consensus size: 9
40571019 AAAATTTCCC
*
40571029 AAAATTTAT
1 AAAAATTAT
40571038 AAATAA-TAT
1 AAA-AATTAT
40571047 AAAAATTAT
1 AAAAATTAT
*
40571056 AATAAGGTATAT
1 AA-AA-AT-TAT
*
40571068 AGAAATTAT
1 AAAAATTAT
*
40571077 AAAAGTTAT
1 AAAAATTAT
40571086 AAAAATT-T
1 AAAAATTAT
*
40571094 AAAAATTTT
1 AAAAATTAT
40571103 AAAAA
1 AAAAA
40571108 ATAATCATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
8 10 0.18
9 36 0.63
10 4 0.07
11 3 0.05
12 4 0.07
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:40571230 original size:14 final size:15
Alignment explanation
Indices: 40571211--40571246 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
40571201 GTTCCTCTCC
40571211 TTTTTATTTAT-AAA
1 TTTTTATTTATAAAA
*
40571225 TTTTTATTTTTAAAA
1 TTTTTATTTATAAAA
40571240 TTTTTAT
1 TTTTTAT
40571247 CTCCAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTATTTATAAAA
Found at i:40571662 original size:10 final size:10
Alignment explanation
Indices: 40571647--40571839 Score: 69
Period size: 10 Copynumber: 19.4 Consensus size: 10
40571637 CCAGTTCAAG
*
40571647 TTTTTATGAT
1 TTTTTATAAT
40571657 TTTTTATAAT
1 TTTTTATAAT
*
40571667 TTTTTA-AAG
1 TTTTTATAAT
*
40571676 TTTATATTAATT
1 TTTTTA-TAA-T
*
40571688 TTTTTATGAT
1 TTTTTATAAT
* *
40571698 TTTTTAAGAAA
1 TTTTT-ATAAT
* *
40571709 CTTTTATATGT
1 TTTTTATA-AT
*
40571720 TTTTTATAAA
1 TTTTTATAAT
* *
40571730 ATTTTAAACAT
1 TTTTTATA-AT
*
40571741 GTTTTATTAA-
1 TTTTTA-TAAT
40571751 -TTTTATAAT
1 TTTTTATAAT
* *
40571760 TTATTAGAAT
1 TTTTTATAAT
** *
40571770 TTACTA-GA-
1 TTTTTATAAT
40571778 TTTTTAT-A-
1 TTTTTATAAT
40571786 TTTTTATAA-
1 TTTTTATAAT
* *
40571795 TATTTATAAG
1 TTTTTATAAT
*
40571805 TTTTTATTAT
1 TTTTTATAAT
40571815 TTTTTATAAAT
1 TTTTTAT-AAT
* *
40571826 TTTATATCAT
1 TTTTTATAAT
40571836 TTTT
1 TTTT
40571840 AATATCTTTA
Statistics
Matches: 135, Mismatches: 35, Indels: 26
0.69 0.18 0.13
Matches are distributed among these distances:
8 15 0.11
9 22 0.16
10 60 0.44
11 32 0.24
12 6 0.04
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.62
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:40574971 original size:42 final size:42
Alignment explanation
Indices: 40574920--40575047 Score: 125
Period size: 42 Copynumber: 3.0 Consensus size: 42
40574910 CCGAAGGCTG
* *
40574920 AACAGAAGCTCATGAA-AGCTAAATAGAAACCCATAAGGGTTG
1 AACAGAAGCTCAT-AAGAGCTAAACAGAAACCCATAAGGGTTA
* *
40574962 AAC-GAAAGCTCGTAAGAGCTGAACAGAAACCCATAAGGGTTA
1 AACAG-AAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTA
* * * * * * *
40575004 AACAGAAGCTCAAAAGGGCTGAACGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTA
40575046 AA
1 AA
40575048 TATTAGAAGC
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 3 0.04
42 68 0.94
43 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.16
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTA
Found at i:40574998 original size:21 final size:21
Alignment explanation
Indices: 40574916--40574998 Score: 62
Period size: 21 Copynumber: 4.0 Consensus size: 21
40574906 AAGCCCGAAG
* *
40574916 GCTGAACAGAAGCTCATGAA-A
1 GCTGAACAGAAACCCAT-AAGA
* * *
40574937 GCTAAATAGAAACCCATAAGG
1 GCTGAACAGAAACCCATAAGA
* * *
40574958 GTTGAAC-GAAAGCTCGTAAGA
1 GCTGAACAGAAA-CCCATAAGA
40574979 GCTGAACAGAAACCCATAAG
1 GCTGAACAGAAACCCATAAG
40574999 GGTTAAACAG
Statistics
Matches: 45, Mismatches: 14, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
20 6 0.13
21 35 0.78
22 4 0.09
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.14
Consensus pattern (21 bp):
GCTGAACAGAAACCCATAAGA
Found at i:40575007 original size:21 final size:21
Alignment explanation
Indices: 40574939--40575010 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
40574929 TCATGAAAGC
*
40574939 TAAATAGAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGGGT
* * * * *
40574960 TGAAC-GAAAGCTCGTAAGAGC
1 TAAACAGAAA-CCCATAAGGGT
*
40574981 TGAACAGAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGGGT
40575002 TAAACAGAA
1 TAAACAGAA
40575011 GCTCAAAAGG
Statistics
Matches: 38, Mismatches: 11, Indels: 4
0.72 0.21 0.08
Matches are distributed among these distances:
20 4 0.11
21 30 0.79
22 4 0.11
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (21 bp):
TAAACAGAAACCCATAAGGGT
Found at i:40575036 original size:21 final size:21
Alignment explanation
Indices: 40574944--40575036 Score: 62
Period size: 21 Copynumber: 4.4 Consensus size: 21
40574934 AAAGCTAAAT
* * *
40574944 AGAAACCCATAAGGGTTGAAC
1 AGAAACTCAAAAGGGCTGAAC
** *
40574965 -GAAAGCTCGTAAGAGCTGAAC
1 AGAAA-CTCAAAAGGGCTGAAC
* * * *
40574986 AGAAACCCATAAGGGTTAAAC
1 AGAAACTCAAAAGGGCTGAAC
*
40575007 AGAAGCTCAAAAGGGCTGAAC
1 AGAAACTCAAAAGGGCTGAAC
*
40575028 GGAAACTCA
1 AGAAACTCA
40575037 TATGAGTTAA
Statistics
Matches: 54, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 4 0.07
21 46 0.85
22 4 0.07
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (21 bp):
AGAAACTCAAAAGGGCTGAAC
Found at i:40584131 original size:7 final size:7
Alignment explanation
Indices: 40584121--40584152 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
40584111 TTATTTTTAT
40584121 TTATTAG
1 TTATTAG
40584128 TTATTAG
1 TTATTAG
40584135 TTATTAG
1 TTATTAG
*
40584142 TTATTAT
1 TTATTAG
40584149 TTAT
1 TTAT
40584153 ATATTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.62
Consensus pattern (7 bp):
TTATTAG
Found at i:40584162 original size:14 final size:14
Alignment explanation
Indices: 40584104--40584163 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
40584094 AGTTTATCTA
40584104 TTTATTT-TTA-TT
1 TTTATTTATTAGTT
40584116 TTTATTTATTAGTT
1 TTTATTTATTAGTT
* *
40584130 ATTAGTTATTAGTT
1 TTTATTTATTAGTT
*
40584144 ATTATTTATATA-TT
1 TTTATTTAT-TAGTT
40584158 TTTATT
1 TTTATT
40584164 ATAATTATAC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
12 7 0.17
13 3 0.07
14 29 0.71
15 2 0.05
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (14 bp):
TTTATTTATTAGTT
Found at i:40584162 original size:17 final size:18
Alignment explanation
Indices: 40584142--40584179 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
40584132 TAGTTATTAG
*
40584142 TTATTAT-TTATATATTT
1 TTATTATATTATACATTT
40584159 TTATTATAATTATACATTT
1 TTATTAT-ATTATACATTT
40584178 TT
1 TT
40584180 TCTTTCACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATTATATTATACATTT
Found at i:40584480 original size:15 final size:15
Alignment explanation
Indices: 40584452--40584492 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
40584442 TTTGATTGCA
40584452 AGTAAAAT-ATTTTT
1 AGTAAAATGATTTTT
*
40584466 CGTAAAATGATTTTT
1 AGTAAAATGATTTTT
40584481 AG-AAAATG-TTTT
1 AGTAAAATGATTTT
40584493 ACTTTTCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.17
14 13 0.54
15 7 0.29
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.46
Consensus pattern (15 bp):
AGTAAAATGATTTTT
Found at i:40586400 original size:19 final size:20
Alignment explanation
Indices: 40586373--40586410 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
40586363 TTATGATAAT
* *
40586373 TATATTTTA-ATAGTTAAAA
1 TATAATTTATATAATTAAAA
40586392 TATAATTTATATAATTAAA
1 TATAATTTATATAATTAAA
40586411 TTAAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TATAATTTATATAATTAAAA
Found at i:40586975 original size:20 final size:18
Alignment explanation
Indices: 40586943--40586994 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
40586933 ATTTCATGTT
40586943 ATTTTTTAAATTTTTATG
1 ATTTTTTAAATTTTTATG
40586961 ATTTTTTATATATTTTTA--
1 ATTTTTTA-A-ATTTTTATG
*
40586979 A-TTTTTAAATATTTAT
1 ATTTTTTAAATTTTTAT
40586995 TGACATTACA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
15 6 0.20
16 1 0.03
17 6 0.20
18 9 0.30
19 1 0.03
20 7 0.23
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
ATTTTTTAAATTTTTATG
Found at i:40592218 original size:24 final size:24
Alignment explanation
Indices: 40592165--40592218 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
40592155 TTCGTAGGCC
* * * *
40592165 AAATAAATTATGCTAATAAATGCT
1 AAATATATTATACCAATAAATACT
40592189 AAATATATTATACCAATAAATACT
1 AAATATATTATACCAATAAATACT
40592213 AAATAT
1 AAATAT
40592219 TCTAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATATATTATACCAATAAATACT
Found at i:40593374 original size:15 final size:15
Alignment explanation
Indices: 40593340--40593374 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
40593330 GCCCATTAAA
*
40593340 CAAATAAATAAAGCC
1 CAAATAAATAAAACC
*
40593355 TAAATAAATAAAACC
1 CAAATAAATAAAACC
40593370 CAAAT
1 CAAAT
40593375 CCAATAAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.63, C:0.17, G:0.03, T:0.17
Consensus pattern (15 bp):
CAAATAAATAAAACC
Found at i:40594574 original size:4 final size:4
Alignment explanation
Indices: 40594567--40594628 Score: 83
Period size: 4 Copynumber: 16.0 Consensus size: 4
40594557 ATATGTTTGT
* * *
40594567 TTTA TTTA TTTA TTTA CTTA TTTA TTTA TTTA TTTA TTCA TTCA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
40594615 TTTA -TTA TTT- TTTA
1 TTTA TTTA TTTA TTTA
40594629 AAATATTCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
3 6 0.12
4 46 0.88
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:40601714 original size:2 final size:2
Alignment explanation
Indices: 40601707--40601731 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40601697 CTCCAACTTC
40601707 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 A
40601732 AAAGCTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40607092 original size:3 final size:3
Alignment explanation
Indices: 40607084--40607134 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
40607074 ATTTCATATC
40607084 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
40607132 ATT
1 ATT
40607135 GCTTTTATAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:40607356 original size:15 final size:17
Alignment explanation
Indices: 40607345--40607382 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
40607335 ACGTATATAC
40607345 TTATATTTTATATATCT
1 TTATATTTTATATATCT
*
40607362 TTGTATTTTATA-ATCT
1 TTATATTTTATATATCT
*
40607378 ATATA
1 TTATA
40607383 CATATGCATG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (17 bp):
TTATATTTTATATATCT
Found at i:40608001 original size:112 final size:112
Alignment explanation
Indices: 40607714--40608157 Score: 524
Period size: 112 Copynumber: 4.0 Consensus size: 112
40607704 TTCAAAAAAG
* * * * * *
40607714 AAAAT-TTTTCTAAATGAGGCAATATTTAGCATTT-AGAAATTCGAGAAAACGTGTCCTAAGGTG
1 AAAATATTTTCAAAATAAGGCAATATTTTGCGTTTGAGAAATTCGAGAAAACATGCCCTAAGGTG
* * *
40607777 CTGTGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTT
66 CTGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
* * *
40607824 AAAAAATTTT-AAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTG
1 AAAATATTTTCAAAATAAGGCAATATTTTGCGTTTGAGAAATTCGAGAAAACATGCCCTAAGGTG
* * *
40607888 CTGGGTGTCGATTTTTCTCATTAAACCAAATGGTTAAATATTCTTTT
66 CTGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
* *
40607935 AAAATATTTTCAAAATAAGGCAATGTTTTGTGTTTGAGAAATTCGAGAAAACATGCCCTAAGGTG
1 AAAATATTTTCAAAATAAGGCAATATTTTGCGTTTGAGAAATTCGAGAAAACATGCCCTAAGGTG
*
40608000 CTGGGTGTCGATTTTTCTCATTCAACCAAATGACTAAATATCCTTTT
66 CTGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
* * ** ** * * * *
40608047 AAAA-A-TTTCGAAGTAAGATAATATTTTGCGTTTG-GAAATTTAAGGAAACGTGCCCTAATGCG
1 AAAATATTTTCAAAATAAGGCAATATTTTGCGTTTGAGAAATTCGAGAAAACATGCCCTAAGGTG
* ** * * * *
40608109 CTGGGTTTCGATTTTTC-CATTTGACCAAATAGCCAAATATTCTCTT
66 CTGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
40608155 AAA
1 AAA
40608158 TCTTAATCCA
Statistics
Matches: 289, Mismatches: 42, Indels: 8
0.85 0.12 0.02
Matches are distributed among these distances:
108 25 0.09
109 38 0.13
110 46 0.16
111 81 0.28
112 99 0.34
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (112 bp):
AAAATATTTTCAAAATAAGGCAATATTTTGCGTTTGAGAAATTCGAGAAAACATGCCCTAAGGTG
CTGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
Found at i:40612308 original size:17 final size:17
Alignment explanation
Indices: 40612288--40612329 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
40612278 AAAAATTTTC
* *
40612288 AAATTTTAAAATAATTT
1 AAATTTCAAAATAACTT
40612305 AAA-TTCAAAATAACTT
1 AAATTTCAAAATAACTT
40612321 AAATTTCAA
1 AAATTTCAA
40612330 CCAATTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTTCAAAATAACTT
Found at i:40618506 original size:3 final size:3
Alignment explanation
Indices: 40618498--40618526 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
40618488 TTTGAGACAC
40618498 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
40618527 AACATGGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:40618631 original size:2 final size:2
Alignment explanation
Indices: 40618626--40618656 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40618616 TCTCTTTTTT
40618626 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
40618657 CCTTTTTTAA
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:40631916 original size:18 final size:19
Alignment explanation
Indices: 40631883--40631926 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
40631873 ACAGCACCTA
*
40631883 AACAGTAATCAGTAACGGT
1 AACAGTAATCAGTAACAGT
*
40631902 AGCAGTAAT-AGTAACAGT
1 AACAGTAATCAGTAACAGT
40631920 AACAGTA
1 AACAGTA
40631927 TTCAACACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.20
Consensus pattern (19 bp):
AACAGTAATCAGTAACAGT
Found at i:40631920 original size:6 final size:6
Alignment explanation
Indices: 40631883--40631926 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
40631873 ACAGCACCTA
* * *
40631883 AACAGT AATCAGT AACGGT AGCAGT AATAGT AACAGT AACAGT A
1 AACAGT AA-CAGT AACAGT AACAGT AACAGT AACAGT AACAGT A
40631927 TTCAACACAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.20
Consensus pattern (6 bp):
AACAGT
Found at i:40631961 original size:39 final size:39
Alignment explanation
Indices: 40631912--40632004 Score: 132
Period size: 39 Copynumber: 2.4 Consensus size: 39
40631902 AGCAGTAATA
* * **
40631912 GTAACAGTAACAGTATTCAACACATAAAGTGCTGAATTT
1 GTAACAGTAACAGTATTCAACACACAAAGTACTGAATCG
* *
40631951 GTAGCAGTAACAGTATTCAACACACAAAGTATTGAATCG
1 GTAACAGTAACAGTATTCAACACACAAAGTACTGAATCG
40631990 GTAACAGTAACAGTA
1 GTAACAGTAACAGTA
40632005 GTCGGCATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (39 bp):
GTAACAGTAACAGTATTCAACACACAAAGTACTGAATCG
Found at i:40632250 original size:40 final size:40
Alignment explanation
Indices: 40632204--40632290 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 40
40632194 AATTCATTAC
* *
40632204 TTCAGTAA-TCTCACAGTTCAATGCAGTACACATAACAATA
1 TTCAGTAACT-TCACAATTCAATGCAGTACACAAAACAATA
** *
40632244 TTCAGTAACTTCACAATTCAATTTAGTACTCAAAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
40632284 TTCAGTA
1 TTCAGTA
40632291 TTCCATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
40 40 0.98
41 1 0.02
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (40 bp):
TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
Found at i:40634958 original size:27 final size:27
Alignment explanation
Indices: 40634914--40634966 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
40634904 GACAACCAAA
*
40634914 TTTTCCTTTTTCTTTTTCTTTCTTTCT
1 TTTTCCTTTTTCTCTTTCTTTCTTTCT
*
40634941 TTTTCCTTCTTTC-CTTTCTTTGTTTC
1 TTTTCCTT-TTTCTCTTTCTTTCTTTC
40634967 GTTCTACTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.74
Consensus pattern (27 bp):
TTTTCCTTTTTCTCTTTCTTTCTTTCT
Found at i:40635213 original size:18 final size:19
Alignment explanation
Indices: 40635190--40635225 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
40635180 ATTATCTATC
40635190 TAATAAATATCT-TTTAAA
1 TAATAAATATCTATTTAAA
40635208 TAATAAATATCTATTTAA
1 TAATAAATATCTATTTAA
40635226 TATACAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATAAATATCTATTTAAA
Found at i:40636109 original size:17 final size:17
Alignment explanation
Indices: 40636087--40636121 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40636077 TTCGAATAGC
* *
40636087 TGTTTCTTTTCTTCTTT
1 TGTTTCATTTATTCTTT
40636104 TGTTTCATTTATTCTTT
1 TGTTTCATTTATTCTTT
40636121 T
1 T
40636122 ATTTTATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.14, G:0.06, T:0.74
Consensus pattern (17 bp):
TGTTTCATTTATTCTTT
Found at i:40636173 original size:8 final size:8
Alignment explanation
Indices: 40636147--40636180 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
40636137 GTATTAGTTA
40636147 ATAATAAT
1 ATAATAAT
* *
40636155 ATATTATT
1 ATAATAAT
40636163 ATAATAAT
1 ATAATAAT
40636171 ATAATAAT
1 ATAATAAT
40636179 AT
1 AT
40636181 TTAATTCACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
ATAATAAT
Found at i:40636228 original size:5 final size:5
Alignment explanation
Indices: 40636218--40636247 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
40636208 TTATAAGAAA
40636218 TTATT TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT
40636248 ACAAGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:40642474 original size:45 final size:45
Alignment explanation
Indices: 40642420--40642506 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
40642410 CAGTAATAGT
* * *
40642420 AACAGTATTCAACACACAAAGTTTTGAATCTGTAACAGTAACGGC
1 AACAGTATTCAACACACAAAGTATCGAATCAGTAACAGTAACGGC
40642465 AACAGTATTCAACACACAAAGTATCGAATCAGTAACAGTAAC
1 AACAGTATTCAACACACAAAGTATCGAATCAGTAACAGTAAC
40642507 AATAGTCGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.22
Consensus pattern (45 bp):
AACAGTATTCAACACACAAAGTATCGAATCAGTAACAGTAACGGC
Found at i:40642755 original size:40 final size:40
Alignment explanation
Indices: 40642710--40642796 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 40
40642700 AATTCATAAC
* *
40642710 TTCAGTAA-TCTCACAGTTCAATACAGTACACATAACAATA
1 TTCAGTAACT-TCACAATTCAATACAGTACACAAAACAATA
* *
40642750 TTCAGTAACTTCACAATTCAATTCAGTACTCAAAACAATA
1 TTCAGTAACTTCACAATTCAATACAGTACACAAAACAATA
*
40642790 TTTAGTA
1 TTCAGTA
40642797 TTCCATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
40 40 0.98
41 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (40 bp):
TTCAGTAACTTCACAATTCAATACAGTACACAAAACAATA
Found at i:40643570 original size:17 final size:17
Alignment explanation
Indices: 40643548--40643582 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40643538 GAATGGTCTC
* *
40643548 TGTTTCTTTTCTTCTTT
1 TGTTTCATTTATTCTTT
40643565 TGTTTCATTTATTCTTT
1 TGTTTCATTTATTCTTT
40643582 T
1 T
40643583 ATTTTATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.14, G:0.06, T:0.74
Consensus pattern (17 bp):
TGTTTCATTTATTCTTT
Found at i:40649308 original size:18 final size:18
Alignment explanation
Indices: 40649287--40649341 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
40649277 CTGTTTTTGT
*
40649287 TATGATTTTCTGTTGAGA
1 TATGATTTTCTATTGAGA
*
40649305 TATGATTTCCTATTGAGA
1 TATGATTTTCTATTGAGA
40649323 TATGATTTTCTATTGAGA
1 TATGATTTTCTATTGAGA
40649341 T
1 T
40649342 TTGTTGCTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.49
Consensus pattern (18 bp):
TATGATTTTCTATTGAGA
Found at i:40654871 original size:18 final size:18
Alignment explanation
Indices: 40654850--40654904 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
40654840 CTGTTTTTGT
40654850 TATGATTTTCTGTTGAGA
1 TATGATTTTCTGTTGAGA
*
40654868 TATGATTTCCTGTTGAGA
1 TATGATTTTCTGTTGAGA
*
40654886 TATGATTTTCTATTGAGA
1 TATGATTTTCTGTTGAGA
40654904 T
1 T
40654905 TTGTTGCTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.24, C:0.07, G:0.20, T:0.49
Consensus pattern (18 bp):
TATGATTTTCTGTTGAGA
Found at i:40662558 original size:32 final size:32
Alignment explanation
Indices: 40662517--40662577 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
40662507 GGCCCATTTT
40662517 TATTTTAAAAAT-TTTAAAAAATTAAAAAAAAG
1 TATTTTAAAAATATTT-AAAAATTAAAAAAAAG
*
40662549 TATTTTAAAAATATTTTAAAATTAAAAAA
1 TATTTTAAAAATATTTAAAAATTAAAAAA
40662578 TTAAAAAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 24 0.89
33 3 0.11
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (32 bp):
TATTTTAAAAATATTTAAAAATTAAAAAAAAG
Found at i:40662579 original size:40 final size:40
Alignment explanation
Indices: 40662530--40662620 Score: 141
Period size: 38 Copynumber: 2.3 Consensus size: 40
40662520 TTTAAAAATT
* *
40662530 TTAAAAAATTAAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAATTAAAAAAAAGTATGTAAAAAATATTTTAAAA
40662570 TTAAAAAATT--AAAAAAGTATGTAAAAAATATTTTAAAA
1 TTAAAAAATTAAAAAAAAGTATGTAAAAAATATTTTAAAA
*
40662608 TTAAAAAAATAAA
1 TTAAAAAATTAAA
40662621 TATATTTATT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
38 35 0.76
40 11 0.24
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (40 bp):
TTAAAAAATTAAAAAAAAGTATGTAAAAAATATTTTAAAA
Found at i:40663470 original size:2 final size:2
Alignment explanation
Indices: 40663463--40663508 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
40663453 ATTAAATTTA
* * *
40663463 AT AT AT AT AT AT AT AT AT AT AA AA AT TT A- 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 AT
40663504 AT AT A
1 AT AT A
40663509 ACCATGGTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:40667595 original size:10 final size:10
Alignment explanation
Indices: 40667566--40667595 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
40667556 AAAATATAAA
*
40667566 ATATATATAT
1 ATATATATAC
40667576 ATATATATAC
1 ATATATATAC
40667586 ATATATATAC
1 ATATATATAC
40667596 TCTTATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATATAC
Found at i:40667665 original size:2 final size:2
Alignment explanation
Indices: 40667658--40667740 Score: 70
Period size: 2 Copynumber: 44.0 Consensus size: 2
40667648 GTTCACAAGC
* *
40667658 AT AT AT AT AT AT AT AT GT AT AT -T TT AT AT AT ACT -T AT -T A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * *
40667697 AT -T CT A- AC AT AC 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 AT
40667737 AT AT
1 AT AT
40667741 TATCTTATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
1 6 0.09
2 60 0.90
3 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40669573 original size:26 final size:25
Alignment explanation
Indices: 40669498--40669574 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 25
40669488 ACCGCATCTC
*
40669498 TTATGAGCGTCCCGATATATGGCTCT
1 TTATGAGCTTCCCGATAT-TGGCTCT
* *
40669524 TCA-GAGCTTCTCGAT-TTAAAGGCTCTT
1 TTATGAGCTTCCCGATATT---GGCTC-T
40669551 TTATGAGCTTCCCGATATTGGCTC
1 TTATGAGCTTCCCGATATTGGCTC
40669575 GCATAATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
23 1 0.03
24 1 0.03
25 10 0.25
26 12 0.30
27 3 0.08
28 11 0.28
29 2 0.05
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.36
Consensus pattern (25 bp):
TTATGAGCTTCCCGATATTGGCTCT
Found at i:40669658 original size:25 final size:25
Alignment explanation
Indices: 40669553--40669665 Score: 79
Period size: 26 Copynumber: 4.5 Consensus size: 25
40669543 AGGCTCTTTT
* *
40669553 ATGAGCTTCCCGATAT-TGGCTCGC
1 ATGAGCTTCCCGTTATATGGCTCGA
* ** *
40669577 ATAATTTTCCCGTTTTAATGGCTC-A
1 ATGAGCTTCCCGTTAT-ATGGCTCGA
*
40669602 CATGAGCTTCTCGTTATATGGCTCGA
1 -ATGAGCTTCCCGTTATATGGCTCGA
* * *
40669628 AAGAGCTTCCCGTTTATAT-GCTTGT
1 ATGAGCTTCCCG-TTATATGGCTCGA
40669653 ATGAGCATTCCCG
1 ATGAGC-TTCCCG
40669666 AATATGAATT
Statistics
Matches: 67, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
24 11 0.16
25 26 0.39
26 30 0.45
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.35
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATATGGCTCGA
Found at i:40670337 original size:14 final size:15
Alignment explanation
Indices: 40670305--40670337 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40670295 TATGATAATG
*
40670305 TATGATTTGAGATAA
1 TATGATTGGAGATAA
40670320 TATGATTGGAGA-AA
1 TATGATTGGAGATAA
40670334 TATG
1 TATG
40670338 CATATAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.36
Consensus pattern (15 bp):
TATGATTGGAGATAA
Found at i:40672545 original size:23 final size:24
Alignment explanation
Indices: 40672505--40672552 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
40672495 GTTTGAGATT
40672505 ATTCTAAAAAATATTATATTATAA
1 ATTCTAAAAAATATTATATTATAA
*
40672529 ATTCTAAAAAATA-TATATTGTAA
1 ATTCTAAAAAATATTATATTATAA
40672552 A
1 A
40672553 AATAATTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
ATTCTAAAAAATATTATATTATAA
Found at i:40676994 original size:13 final size:13
Alignment explanation
Indices: 40676976--40677000 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40676966 GTGAATATTT
40676976 CTGTGATTTTGAC
1 CTGTGATTTTGAC
40676989 CTGTGATTTTGA
1 CTGTGATTTTGA
40677001 GTATATTCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.12, G:0.24, T:0.48
Consensus pattern (13 bp):
CTGTGATTTTGAC
Found at i:40682943 original size:2 final size:2
Alignment explanation
Indices: 40682936--40682968 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
40682926 TTGATTCTCT
40682936 TA 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 TA T
40682969 TTTGGGTTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40716127 original size:11 final size:10
Alignment explanation
Indices: 40716098--40716166 Score: 50
Period size: 10 Copynumber: 6.5 Consensus size: 10
40716088 AAATTTATTT
40716098 ATAATTAAAA
1 ATAATTAAAA
*
40716108 ATAAATAAAA
1 ATAATTAAAA
40716118 ATATATTAAAAA
1 ATA-ATT-AAAA
*
40716130 AGTATTTAAATA
1 A-TAATTAAA-A
*
40716142 ATAATTTAAAC
1 ATAA-TTAAAA
*
40716153 A-AATTAAAC
1 ATAATTAAAA
40716162 ATAAT
1 ATAAT
40716167 AATTTCGCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
9 7 0.15
10 17 0.35
11 8 0.17
12 14 0.29
13 2 0.04
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (10 bp):
ATAATTAAAA
Found at i:40716785 original size:147 final size:147
Alignment explanation
Indices: 40716491--40716775 Score: 326
Period size: 147 Copynumber: 1.9 Consensus size: 147
40716481 AATTTGTACA
* **
40716491 TATTATAATTTACCATAAAGTCAGTTACACATTTAAGGTTTAAGGTTATGTATCATTAATATAAA
1 TATTATAATTTACCATAAAGTCAGTTACACATTTAAGGTTTAAGCTTACATATCATTAATAT-AA
* ** * *
40716556 AAAATGTACATTATAATGTCATAATTGTAGATAAGGTGACATATAATTAATAATCTATCTTAACT
65 AAAATATACATTATAATAACATAATTGTA-ATAAGGTGACATATAATTAATAATCTACCTAAACT
40716621 ATATAATGGTAACTGTATG
129 ATATAATGGTAACTGTATG
* * ** *
40716640 TATTATAATTTGA-CATAAAGTTAGTTGCATGTTTAGGGTTTAAGCTTACATATCATTAATAT-A
1 TATTATAATTT-ACCATAAAGTCAGTTACACATTTAAGGTTTAAGCTTACATATCATTAATATAA
* * * *
40716703 AAAATATACATTATAATAACATAGTTGT-AT-AGAGTGATACATATCATTTATTATCTACCTAAA
65 AAAATATACATTATAATAACATAATTGTAATAAG-GTG--ACATATAATTAATAATCTACCTAAA
*
40716766 TTATATAATG
127 CTATATAATG
40716776 TCAATTGTAT
Statistics
Matches: 114, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
144 2 0.02
145 5 0.04
147 54 0.47
149 52 0.46
150 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (147 bp):
TATTATAATTTACCATAAAGTCAGTTACACATTTAAGGTTTAAGCTTACATATCATTAATATAAA
AAATATACATTATAATAACATAATTGTAATAAGGTGACATATAATTAATAATCTACCTAAACTAT
ATAATGGTAACTGTATG
Found at i:40722114 original size:15 final size:15
Alignment explanation
Indices: 40722094--40722122 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40722084 AATTATTGTT
40722094 TAAATAAATTTTTAA
1 TAAATAAATTTTTAA
40722109 TAAATAAATTTTTA
1 TAAATAAATTTTTA
40722123 CATATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAATAAATTTTTAA
Found at i:40727310 original size:3 final size:3
Alignment explanation
Indices: 40727302--40727341 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
40727292 GCTCAGTTAA
40727302 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
40727342 TATAACCACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:40734257 original size:40 final size:40
Alignment explanation
Indices: 40734213--40734299 Score: 124
Period size: 39 Copynumber: 2.2 Consensus size: 40
40734203 ACGTAACCCT
* *
40734213 GATTTGCTT-CCACGTCAGCAAATCGCGCTTACGTGGACGC
1 GATTTGCTTGCCACGTAAG-AAATCGCGCTGACGTGGACGC
*
40734253 GATTTG-TTGCCACGTAAGTAATCGCGCTGACGTGGACGC
1 GATTTGCTTGCCACGTAAGAAATCGCGCTGACGTGGACGC
40734292 GATTTGCT
1 GATTTGCT
40734300 GACACGTCCC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
39 27 0.64
40 15 0.36
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.28
Consensus pattern (40 bp):
GATTTGCTTGCCACGTAAGAAATCGCGCTGACGTGGACGC
Found at i:40745901 original size:15 final size:16
Alignment explanation
Indices: 40745883--40745915 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
40745873 CTAAATTTCA
40745883 ATTTTTTA-AAATAAT
1 ATTTTTTAGAAATAAT
*
40745898 ATTTTTTAGAATTAAT
1 ATTTTTTAGAAATAAT
40745914 AT
1 AT
40745916 CTACTCATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
ATTTTTTAGAAATAAT
Found at i:40749301 original size:32 final size:32
Alignment explanation
Indices: 40749242--40749302 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
40749232 TGTATAATTA
40749242 TATTAAATTATTTAAATATTATCTAAAATATT
1 TATTAAATTATTTAAATATTATCTAAAATATT
*
40749274 TATTTAATT-TTT-AATATTAAGTCTAAAAT
1 TATTAAATTATTTAAATATT-A-TCTAAAAT
40749303 GAACATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 6 0.23
31 4 0.15
32 16 0.62
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (32 bp):
TATTAAATTATTTAAATATTATCTAAAATATT
Found at i:40750023 original size:14 final size:15
Alignment explanation
Indices: 40750004--40750036 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40749994 ACTAACATAT
*
40750004 TTTGA-CCTTTTTAA
1 TTTGACCCTATTTAA
40750018 TTTGACCCTATTTAA
1 TTTGACCCTATTTAA
40750033 TTTG
1 TTTG
40750037 TGAATTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.55
Consensus pattern (15 bp):
TTTGACCCTATTTAA
Found at i:40750507 original size:16 final size:18
Alignment explanation
Indices: 40750462--40750502 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
40750452 AAGCTGTTTA
40750462 TATATATATTAATAAATT
1 TATATATATTAATAAATT
*
40750480 TATATATATTAATAATTT
1 TATATATATTAATAAATT
40750498 TATAT
1 TATAT
40750503 TTTAAGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATATATATTAATAAATT
Found at i:40751773 original size:32 final size:32
Alignment explanation
Indices: 40751732--40751792 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
40751722 TGTCAGTCAT
40751732 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
40751764 TTCAATATCCAACAAGCTTAAAACATAAT
1 TTCAATATCCAACAAGCTTAAAACATAAT
40751793 CAATATCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.26
Consensus pattern (32 bp):
TTCAATATCCAACAAGCTTAAAACATAATAAA
Found at i:40751799 original size:27 final size:30
Alignment explanation
Indices: 40751732--40751805 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 30
40751722 TGTCAGTCAT
40751732 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAAC--AATAAA
40751764 TTCAATATCCAACAAGCTTAAAAC-AT-AA
1 TTCAATATCCAACAAGCTTAAAACAATAAA
*
40751792 -TCAATATCTAACAA
1 TTCAATATCCAACAA
40751806 ATTCAAGACA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 13 0.32
28 2 0.05
29 2 0.05
32 24 0.59
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.26
Consensus pattern (30 bp):
TTCAATATCCAACAAGCTTAAAACAATAAA
Found at i:40755324 original size:15 final size:15
Alignment explanation
Indices: 40755306--40755338 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
40755296 TAACGTTAAC
40755306 AATAATAATAATGAT
1 AATAATAATAATGAT
40755321 AATAATAATAATGAT
1 AATAATAATAATGAT
40755336 AAT
1 AAT
40755339 GATACAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (15 bp):
AATAATAATAATGAT
Found at i:40757880 original size:17 final size:17
Alignment explanation
Indices: 40757858--40757910 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
40757848 TCTTCAACAG
40757858 ACAGATGCAAAATCCAA
1 ACAGATGCAAAATCCAA
*
40757875 ACAGAT--TAAA--CAA
1 ACAGATGCAAAATCCAA
*
40757888 ACATATGCAAAATCCAA
1 ACAGATGCAAAATCCAA
40757905 ACAGAT
1 ACAGAT
40757911 TCTTCAACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
13 8 0.29
15 6 0.21
17 14 0.50
ACGTcount: A:0.55, C:0.21, G:0.09, T:0.15
Consensus pattern (17 bp):
ACAGATGCAAAATCCAA
Found at i:40757896 original size:30 final size:30
Alignment explanation
Indices: 40757853--40757911 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
40757843 AAGATTCTTC
*
40757853 AACAGACAGATGCAAAATCCAAACAGATTA
1 AACAAACAGATGCAAAATCCAAACAGATTA
*
40757883 AACAAACATATGCAAAATCCAAACAGATT
1 AACAAACAGATGCAAAATCCAAACAGATT
40757912 CTTCAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.54, C:0.20, G:0.10, T:0.15
Consensus pattern (30 bp):
AACAAACAGATGCAAAATCCAAACAGATTA
Found at i:40758761 original size:32 final size:32
Alignment explanation
Indices: 40758720--40758782 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
40758710 GGCTTATTTT
40758720 TATTTTAAAAAT-TTTTAAAAATTAAAAAAAAG
1 TATTTTAAAAATATTTT-AAAATTAAAAAAAAG
40758752 TATTTTAAAAATATTTTAAAATTAAAAAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAAAA
40758783 TTAAAAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 26 0.87
33 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (32 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAAAG
Found at i:40758791 original size:40 final size:40
Alignment explanation
Indices: 40758736--40758940 Score: 324
Period size: 40 Copynumber: 5.1 Consensus size: 40
40758726 AAAAATTTTT
40758736 AAAAATTAAAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
1 AAAAATT--AAAAAAGTATTTTAAAAATATTTTAAAATTAAA
*
40758778 AAAAATTAAAAAAGTATTTTAAAAAGATTTTAAAATTAAA
1 AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
*
40758818 AAAAATTAAAAAAGTATTTTAAAAAGATTTTAAAATT--A
1 AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
40758856 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
1 AAAAATT-AAAAAAGTATTTTAAAAATATTTTAAAATTAAA
* * *
40758897 AAAAATTTAAAAAGTATGTAAAAAATATTTTAAAATTAAA
1 AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
40758937 AAAA
1 AAAA
40758941 TAAATATATT
Statistics
Matches: 155, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
38 8 0.05
39 29 0.19
40 103 0.66
41 8 0.05
42 7 0.05
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (40 bp):
AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
Found at i:40758817 original size:79 final size:78
Alignment explanation
Indices: 40758734--40758940 Score: 285
Period size: 79 Copynumber: 2.6 Consensus size: 78
40758724 TTAAAAATTT
40758734 TTAAAAATTAAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAATT-AAAAAAGTATTTT
1 TTAAAAA--AAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTT
40758798 AAAAAGATTTTAAAA
64 AAAAAGATTTTAAAA
*
40758813 TTAAAAAAAATTAAAAAAGTATTTTAAAAAGATTTTAAAATT--AAAAAATTAAAAAAAGTATTT
1 TT-AAAAAAA--AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAAGTATTT
*
40758876 TAAAAATATTTTAAAA
63 TAAAAAGATTTTAAAA
* *
40758892 TTAAAAAAAATTTAAAAAGTATGTAAAAAATATTTTAAAATTAAAAAAA
1 TTAAAAAAAA---AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAA
40758941 TAAATATATT
Statistics
Matches: 114, Mismatches: 5, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
76 1 0.01
78 17 0.15
79 57 0.50
80 34 0.30
81 5 0.04
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (78 bp):
TTAAAAAAAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAA
AAAGATTTTAAAA
Found at i:40758932 original size:10 final size:11
Alignment explanation
Indices: 40758720--40758891 Score: 65
Period size: 11 Copynumber: 16.9 Consensus size: 11
40758710 GGCTTATTTT
40758720 TATTTTAAAAA
1 TATTTTAAAAA
40758731 T-TTTTAAAAA
1 TATTTTAAAAA
***
40758741 T-TAAAAAAAA
1 TATTTTAAAAA
40758751 GTATTTTAAAAA
1 -TATTTTAAAAA
40758763 TATTTT--AAA
1 TATTTTAAAAA
40758772 -A--TTAAAAA
1 TATTTTAAAAA
* * *
40758780 AAATTAAAAAA
1 TATTTTAAAAA
40758791 GTATTTTAAAAA
1 -TATTTTAAAAA
*
40758803 GATTTT--AAA
1 TATTTTAAAAA
40758812 -A--TTAAAAA
1 TATTTTAAAAA
* * *
40758820 AAATTAAAAAA
1 TATTTTAAAAA
40758831 GTATTTTAAAAA
1 -TATTTTAAAAA
*
40758843 GATTTT--AAA
1 TATTTTAAAAA
40758852 -A--TTAAAAA
1 TATTTTAAAAA
**
40758860 -ATTAAAAAAA
1 TATTTTAAAAA
40758870 GTATTTTAAAAA
1 -TATTTTAAAAA
40758882 TATTTTAAAA
1 TATTTTAAAA
40758892 TTAAAAAAAA
Statistics
Matches: 121, Mismatches: 20, Indels: 40
0.67 0.11 0.22
Matches are distributed among these distances:
6 6 0.05
8 13 0.11
9 11 0.09
10 21 0.17
11 40 0.33
12 30 0.25
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:40765480 original size:32 final size:31
Alignment explanation
Indices: 40765439--40765516 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
40765429 GAATGTACTG
*
40765439 AGCTC-TCAAAAATTTTGAAAAATTTTCATTA
1 AGCTCTTCAAAAATTTTGAAAAATCTT-ATTA
* * *
40765470 GGCTCTTCAAAATTTTTGGAAAATCTTATTA
1 AGCTCTTCAAAAATTTTGAAAAATCTTATTA
* *
40765501 AGCCCTCCAAAAATTT
1 AGCTCTTCAAAAATTT
40765517 GGGAATATTC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 20 0.53
32 18 0.47
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (31 bp):
AGCTCTTCAAAAATTTTGAAAAATCTTATTA
Found at i:40766414 original size:2 final size:2
Alignment explanation
Indices: 40766401--40766442 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
40766391 AAAAAGAAAA
*
40766401 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
40766442 A
1 A
40766443 CACCTTTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40766414 original size:10 final size:10
Alignment explanation
Indices: 40766395--40766442 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
40766385 ACATTGAAAA
*
40766395 AGAAAAAGAG
1 AGAAAGAGAG
40766405 AGAAAGAGAG
1 AGAAAGAGAG
40766415 AG--AGAGAG
1 AGAAAGAGAG
*
40766423 AGAGAGAGAG
1 AGAAAGAGAG
40766433 AG-AAGAGAG
1 AGAAAGAGAG
40766442 A
1 A
40766443 CACCTTTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
8 8 0.24
9 7 0.21
10 19 0.56
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (10 bp):
AGAAAGAGAG
Found at i:40782942 original size:29 final size:30
Alignment explanation
Indices: 40782879--40782943 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
40782869 GAAAATTCTC
40782879 ATTAAACCTCCAAAATTTTTGAAAAAATTAA
1 ATTAAACCTCCAAAATTTTTGAAAAAA-TAA
* *
40782910 ATTAAACCT-CAAATTTTTTTAAAAAA-AA
1 ATTAAACCTCCAAAATTTTTGAAAAAATAA
40782938 GATTAA
1 -ATTAA
40782944 TTAAGCTCCC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 2 0.06
29 5 0.16
30 15 0.48
31 9 0.29
ACGTcount: A:0.52, C:0.11, G:0.03, T:0.34
Consensus pattern (30 bp):
ATTAAACCTCCAAAATTTTTGAAAAAATAA
Found at i:40792210 original size:22 final size:23
Alignment explanation
Indices: 40792169--40792214 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
40792159 AAGCCCGCCC
40792169 ATATTATTATTTTTTAAATATTT
1 ATATTATTATTTTTTAAATATTT
40792192 ATATTA-TATTATTTT-AATATTT
1 ATATTATTATT-TTTTAAATATTT
40792214 A
1 A
40792215 ATAAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
ATATTATTATTTTTTAAATATTT
Found at i:40796075 original size:33 final size:34
Alignment explanation
Indices: 40795972--40796076 Score: 115
Period size: 34 Copynumber: 3.1 Consensus size: 34
40795962 AAACTCATGT
* * * *
40795972 TAAGCAAGTTTATTGCTACTGTAATGATTTGTTA
1 TAAGCATGATTATTGCTACCGTATTGATTTGTTA
* * *
40796006 TAAGCATGATAATT-CTTACCATATTGATTTGCTA
1 TAAGCATGATTATTGC-TACCGTATTGATTTGTTA
*
40796040 TAAGCATG-TTATTGCTACCGTATTGATCTGTTA
1 TAAGCATGATTATTGCTACCGTATTGATTTGTTA
40796073 TAAG
1 TAAG
40796077 TATGTCATAT
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
33 24 0.41
34 34 0.59
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (34 bp):
TAAGCATGATTATTGCTACCGTATTGATTTGTTA
Found at i:40797964 original size:29 final size:31
Alignment explanation
Indices: 40797914--40797974 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 31
40797904 ATACATTTGA
*
40797914 ACCACAATAAAAATTCTGTGTA-CATAATTGT
1 ACCACAATAAAAATTCTATGTATCA-AATTGT
*
40797945 ACCA-AATTAAAATT-TATGTATCAAATTGT
1 ACCACAATAAAAATTCTATGTATCAAATTGT
40797974 A
1 A
40797975 TACTGAGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 12 0.44
30 11 0.41
31 4 0.15
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.34
Consensus pattern (31 bp):
ACCACAATAAAAATTCTATGTATCAAATTGT
Found at i:40807646 original size:36 final size:35
Alignment explanation
Indices: 40807606--40807704 Score: 157
Period size: 36 Copynumber: 2.8 Consensus size: 35
40807596 TAGTTTTAGC
40807606 TACACTTATCTGATCAGGAAACAAAGTGATAGTGGT
1 TACACTTATCTGATCA-GAAACAAAGTGATAGTGGT
40807642 TACACTTATCTGATCAG-AACAAAGTGATAGTGGT
1 TACACTTATCTGATCAGAAACAAAGTGATAGTGGT
40807676 TAACACTTATTCTGATCAGAAAC-AAGTGA
1 T-ACACTTA-TCTGATCAGAAACAAAGTGA
40807705 NNNNNNNNNN
Statistics
Matches: 60, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
34 18 0.30
35 8 0.13
36 31 0.52
37 3 0.05
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (35 bp):
TACACTTATCTGATCAGAAACAAAGTGATAGTGGT
Found at i:40809578 original size:34 final size:34
Alignment explanation
Indices: 40809539--40809604 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
40809529 AGTATGAAAG
*
40809539 TATAAATAAAACATATGTACGATATATGAATACA
1 TATAAATAAAACATATGGACGATATATGAATACA
** *
40809573 TATAAATAAAATGTATGGATGATATATGAATA
1 TATAAATAAAACATATGGACGATATATGAATA
40809605 AATGTATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.32
Consensus pattern (34 bp):
TATAAATAAAACATATGGACGATATATGAATACA
Found at i:40812347 original size:41 final size:40
Alignment explanation
Indices: 40812297--40812376 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 40
40812287 AAACTAGCAG
**
40812297 TTTAACAATTTATATGCAAGGAACTAGCAAAAAATCAACAA
1 TTTAACAATTTATATGCAACAAACTAGC-AAAAATCAACAA
* *
40812338 TTTAGCAATTTATATGCAACAAATTAGCAAAAATCAACA
1 TTTAACAATTTATATGCAACAAACTAGCAAAAATCAACA
40812377 CGAAATAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
40 11 0.31
41 24 0.69
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (40 bp):
TTTAACAATTTATATGCAACAAACTAGCAAAAATCAACAA
Found at i:40814675 original size:15 final size:15
Alignment explanation
Indices: 40814655--40814689 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
40814645 GAAGTAAATG
40814655 TGATAACATTAGGAT
1 TGATAACATTAGGAT
40814670 TGATAACATTAGGAT
1 TGATAACATTAGGAT
40814685 TGATA
1 TGATA
40814690 GCGACACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (15 bp):
TGATAACATTAGGAT
Found at i:40820457 original size:36 final size:36
Alignment explanation
Indices: 40820404--40820472 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
40820394 NNNNNNNNNN
*
40820404 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCACT
1 TATCACTTTGTCACTTGATCAGATAAGTGTAGCACT
*
40820440 TATCACTTTTTCACTTGATCAGATAAGTGTAGC
1 TATCACTTTGTCACTTGATCAGATAAGTGTAGC
40820473 TAAAGCTACC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (36 bp):
TATCACTTTGTCACTTGATCAGATAAGTGTAGCACT
Found at i:40824164 original size:55 final size:55
Alignment explanation
Indices: 40824085--40824195 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
40824075 TTTTCTTAAA
* *
40824085 TCCTTACATACAAGAAGGTTAGAAAGCTTACCATTTTACAAAATTTCCAGTTTCT
1 TCCTTACATACAAAAAGGTTAGAAAGCTTACCATCTTACAAAATTTCCAGTTTCT
40824140 TCCTTACATACAAAAAGGTTAGAAAGCTTACCATCTTACAAAATTTCCAGTTTCT
1 TCCTTACATACAAAAAGGTTAGAAAGCTTACCATCTTACAAAATTTCCAGTTTCT
40824195 T
1 T
40824196 AGGCTCAAAC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (55 bp):
TCCTTACATACAAAAAGGTTAGAAAGCTTACCATCTTACAAAATTTCCAGTTTCT
Found at i:40828095 original size:22 final size:22
Alignment explanation
Indices: 40828069--40828136 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 22
40828059 ATATCTAAAC
*
40828069 AATAACAACAAAATAGTAGCTA
1 AATAACAACAAAATAGTAGCAA
* * * *
40828091 TATAATAGCAAAATGGTAGCAA
1 AATAACAACAAAATAGTAGCAA
* *
40828113 AACAACAACAAAATAGTAGAAA
1 AATAACAACAAAATAGTAGCAA
40828135 AA
1 AA
40828137 AATTTAGGCA
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (22 bp):
AATAACAACAAAATAGTAGCAA
Found at i:40832494 original size:13 final size:13
Alignment explanation
Indices: 40832476--40832509 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
40832466 CTTCTATTAT
40832476 TTTTTATTTAATA
1 TTTTTATTTAATA
**
40832489 TTTTTATTTTTTA
1 TTTTTATTTAATA
40832502 TTTTTATT
1 TTTTTATT
40832510 AAAATTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTATTTAATA
Found at i:40835005 original size:32 final size:32
Alignment explanation
Indices: 40834964--40835028 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
40834954 CTTTTTATGG
40834964 GAAAATATTTAGACTCTACAAGCAGAGTTAGA
1 GAAAATATTTAGACTCTACAAGCAGAGTTAGA
40834996 GAAAATATTTAGACTCTACAAGCAGAGTTAGA
1 GAAAATATTTAGACTCTACAAGCAGAGTTAGA
40835028 G
1 G
40835029 GTTAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (32 bp):
GAAAATATTTAGACTCTACAAGCAGAGTTAGA
Found at i:40836469 original size:24 final size:24
Alignment explanation
Indices: 40836441--40836487 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
40836431 ATGAAATAAT
*
40836441 TAAAATTTTAAAAATTATTAAAAA
1 TAAAATATTAAAAATTATTAAAAA
* *
40836465 TAAAATATTGATAATTATTAAAA
1 TAAAATATTAAAAATTATTAAAA
40836488 TTATTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
TAAAATATTAAAAATTATTAAAAA
Found at i:40836471 original size:33 final size:33
Alignment explanation
Indices: 40836434--40836497 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
40836424 AAAATGTATG
40836434 AAATAATT-AAAATT-TTAAAAATTATTAAAAATA
1 AAAT-ATTGAAAATTATT-AAAATTATTAAAAATA
* *
40836467 AAATATTGATAATTATTAAAATTATTTAAAA
1 AAATATTGAAAATTATTAAAATTATTAAAAA
40836498 CATATACAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 3 0.11
33 22 0.81
34 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (33 bp):
AAATATTGAAAATTATTAAAATTATTAAAAATA
Found at i:40837814 original size:60 final size:60
Alignment explanation
Indices: 40837750--40837889 Score: 192
Period size: 59 Copynumber: 2.4 Consensus size: 60
40837740 GAATTAGAAA
* * *
40837750 TAAATTGATAAATTTTATAAATATCGAGAGTTAAATTTATTAAATTTTTAGAATCCGAAT
1 TAAATTGATCAATTTTATAAATATCAAGAGTTAAATTTATTAAATTTTTAAAATCCGAAT
* * * *
40837810 TAAATTGA-CAGTTTTATAAATATTAAGAGTTAAATTTATTGAATTTTTAAAATTCGAAT
1 TAAATTGATCAATTTTATAAATATCAAGAGTTAAATTTATTAAATTTTTAAAATCCGAAT
* *
40837869 TAAAATGATCAATTTTGTAAA
1 TAAATTGATCAATTTTATAAA
40837890 CATTGAGAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
59 51 0.74
60 18 0.26
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (60 bp):
TAAATTGATCAATTTTATAAATATCAAGAGTTAAATTTATTAAATTTTTAAAATCCGAAT
Found at i:40837903 original size:59 final size:59
Alignment explanation
Indices: 40837760--40837904 Score: 157
Period size: 59 Copynumber: 2.5 Consensus size: 59
40837750 TAAATTGATA
* ** * * *
40837760 AATTTTATAAATATCGAGAGTTAAATTTATTAAATTTTTAGAATCCGAATTAAATTGAC
1 AATTTTATAAACATTAAGAGATAAATTTATTAAATTTTTAAAATCCGAATTAAAATGAC
* * * * *
40837819 AGTTTTATAAATATTAAGAGTTAAATTTATTGAATTTTTAAAATTCGAATTAAAATGATC
1 AATTTTATAAACATTAAGAGATAAATTTATTAAATTTTTAAAATCCGAATTAAAATGA-C
* *
40837879 AATTTTGTAAACATTGAGA-ATAAATT
1 AATTTTATAAACATTAAGAGATAAATT
40837905 AGATTTAGGA
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
59 57 0.78
60 16 0.22
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.41
Consensus pattern (59 bp):
AATTTTATAAACATTAAGAGATAAATTTATTAAATTTTTAAAATCCGAATTAAAATGAC
Found at i:40843900 original size:19 final size:19
Alignment explanation
Indices: 40843876--40843915 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
40843866 TTCATGCACT
40843876 ATGATTATTTATGATCCCC
1 ATGATTATTTATGATCCCC
40843895 ATGATTATTTATGATCCCC
1 ATGATTATTTATGATCCCC
40843914 AT
1 AT
40843916 TTTGTCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (19 bp):
ATGATTATTTATGATCCCC
Found at i:40845159 original size:6 final size:6
Alignment explanation
Indices: 40845148--40845180 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
40845138 CAATAGATCT
40845148 AATTCA AATTCA AATTCA AATTCA AATTCA AAT
1 AATTCA AATTCA AATTCA AATTCA AATTCA AAT
40845181 CCATTGATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
AATTCA
Found at i:40847650 original size:17 final size:18
Alignment explanation
Indices: 40847617--40847650 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40847607 TCATAACAGT
*
40847617 TTTTATAATTTTTAAAAC
1 TTTTATAATTTTAAAAAC
40847635 TTTTA-AATTTTAAAAA
1 TTTTATAATTTTAAAAA
40847651 AATAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTATAATTTTAAAAAC
Found at i:40853807 original size:11 final size:11
Alignment explanation
Indices: 40853783--40853816 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
40853773 ATTGAATCAA
* *
40853783 TTTTATAATTT
1 TTTTAAAATAT
40853794 TTTTAAAATAT
1 TTTTAAAATAT
40853805 TTTTAAAATAT
1 TTTTAAAATAT
40853816 T
1 T
40853817 AATTTATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:40854749 original size:14 final size:14
Alignment explanation
Indices: 40854716--40854748 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40854706 CGTTGATTAA
*
40854716 AATTTTATTAAATT
1 AATTTTAATAAATT
40854730 AATTTTAATAAATT
1 AATTTTAATAAATT
40854744 -ATTTT
1 AATTTT
40854749 TTTTGAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
AATTTTAATAAATT
Found at i:40854972 original size:19 final size:19
Alignment explanation
Indices: 40854948--40854985 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40854938 AACCACTGTC
*
40854948 ACCCACTATAATCAAATTT
1 ACCCACCATAATCAAATTT
*
40854967 ACCCACCGTAATCAAATTT
1 ACCCACCATAATCAAATTT
40854986 GTTATTAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.29, G:0.03, T:0.29
Consensus pattern (19 bp):
ACCCACCATAATCAAATTT
Found at i:40855581 original size:28 final size:31
Alignment explanation
Indices: 40855522--40855579 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
40855512 GGGTTTGGGA
*
40855522 TGGGAGGAGAGTAAAAGTTTTGGGGGAAAAG
1 TGGGAGGAGAGTAAAAGTATTGGGGGAAAAG
40855553 TGGGA-GAGAGT-AAAGTATTGGGGGAAA
1 TGGGAGGAGAGTAAAAGTATTGGGGGAAA
40855580 GTAAAAAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 15 0.58
30 6 0.23
31 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.45, T:0.19
Consensus pattern (31 bp):
TGGGAGGAGAGTAAAAGTATTGGGGGAAAAG
Found at i:40860858 original size:3 final size:3
Alignment explanation
Indices: 40860773--40860840 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
40860763 TTGCATGCCC
40860773 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
40860821 TTG TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
40860841 TATCTTTCTT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:40880315 original size:92 final size:95
Alignment explanation
Indices: 40880090--40880359 Score: 252
Period size: 94 Copynumber: 2.9 Consensus size: 95
40880080 GATCCAAAAA
* ** * * * *
40880090 AAATCTATCATAGTAAATATTATTTCCCTGAAGTTGCAGTTGAGC-AGATTGAAGCTAAAAATCC
1 AAATCTACCATAGCGAATATTATCTCCCTGAAGTTGCAGTGGAGCAAGATTAAAACTAAAAATCC
*
40880154 TATACCCTTGAAGTTGCAGTAGGTCGGATT
66 TATACCCTTGAAGTTACAGTAGGTCGGATT
* * *
40880184 AAATCTACCATAGCGAATCTTATCCCCCTGAAGTTGCAGTGGAGCAAGA-TAAAACTACAAATTC
1 AAATCTACCATAGCGAATATTATCTCCCTGAAGTTGCAGTGGAGCAAGATTAAAACTA-AAAATC
* * *
40880248 C-ATTCCC-TGAAGTTACAGTGGGT-TGATT
65 CTATACCCTTGAAGTTACAGTAGGTCGGATT
* * * * *
40880276 GAAA-CTA-CAGTGGTGAATATTATCTCCCTGAAGTTGCAGTGGAGC-AGATTGAAGCTACAAAT
1 -AAATCTACCA-TAGCGAATATTATCTCCCTGAAGTTGCAGTGGAGCAAGATTAAAACTAAAAAT
* *
40880338 CTTAT-CTCCTTGAAGTTGCAGT
64 CCTATAC-CCTTGAAGTTACAGT
40880360 GGAGCAAATT
Statistics
Matches: 144, Mismatches: 24, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
91 10 0.07
92 48 0.33
93 28 0.19
94 49 0.34
95 9 0.06
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (95 bp):
AAATCTACCATAGCGAATATTATCTCCCTGAAGTTGCAGTGGAGCAAGATTAAAACTAAAAATCC
TATACCCTTGAAGTTACAGTAGGTCGGATT
Found at i:40880358 original size:44 final size:44
Alignment explanation
Indices: 40880104--40880588 Score: 274
Period size: 44 Copynumber: 10.7 Consensus size: 44
40880094 CTATCATAGT
* * * *
40880104 AAATATTATTTCCCTGAAGTTGCAGTTGAGCAGATTGAAGCTAA
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAC
* * * * * *
40880148 AAATCCTATAC-CCTTGAAGTTGCAGTAGG-TCGGATTAAATCTACC
1 AAATCTTAT-CTCCCTGAAGTTGCAGT-GGAGCAGATTGAAGCTA-C
* * *
40880193 ATAGCGAATCTTATCCCCCTGAAGTTGCAGTGGAGCAAGA-TAAAACTAC
1 --A---AATCTTATCTCCCTGAAGTTGCAGTGGAGC-AGATTGAAGCTAC
* * ** *
40880242 AAAT-TCCAT-TCCCTGAAGTTACAGTGG-GTTGATTGAAACTAC
1 AAATCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAC
*
40880284 AGTGGTGAATATTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAC
1 A------AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAC
* * *
40880334 AAATCTTATCTCCTTGAAGTTGCAGTGGAGCAAATTAAAGCTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAC
* ** *
40880378 AAGTCTTATCTCTTTGAAGTTGCAGTGGAACAAGA-TGAAGCTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGC-AGATTGAAGCTAC
* * *
40880422 AAGTTTTATC-CCCTTGAAGTTGCAGTGGAACAAGA-TGAAGCTAC
1 AAATCTTATCTCCC-TGAAGTTGCAGTGGAGC-AGATTGAAGCTAC
** * * * * *
40880466 TGATCCTATGC-CCCTGAAGTTGCAGTGGTGTAGAATGAAGTTATAGTCAC
1 AAATCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-----CT-AC
*
40880516 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGA-TGAGGAC-AC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGC-AGATTGAAG-CTAC
* * *
40880560 AAATCCTATATCCTTGAAGTTGCAGTGGA
1 AAATCTTATCTCCCTGAAGTTGCAGTGGA
40880589 TTGGATTGAA
Statistics
Matches: 350, Mismatches: 57, Indels: 68
0.74 0.12 0.14
Matches are distributed among these distances:
41 2 0.01
42 10 0.03
43 21 0.06
44 201 0.57
45 7 0.02
46 1 0.00
47 2 0.01
48 5 0.01
49 24 0.07
50 72 0.21
51 5 0.01
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (44 bp):
AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAC
Found at i:40882397 original size:3 final size:3
Alignment explanation
Indices: 40882307--40882379 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
40882297 TTGCCCTTAC
40882307 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40882355 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
40882380 TATCTTTCTT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:40891093 original size:17 final size:17
Alignment explanation
Indices: 40891071--40891104 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40891061 TTTTAGTCAC
*
40891071 TTATTTTATTTTTTAAT
1 TTATTTTATTTCTTAAT
40891088 TTATTTTATTTCTTAAT
1 TTATTTTATTTCTTAAT
40891105 AGTTTTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TTATTTTATTTCTTAAT
Found at i:40899824 original size:22 final size:22
Alignment explanation
Indices: 40899796--40899862 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
40899786 TGTTGATAGT
*
40899796 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
40899818 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
40899840 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
40899862 A
1 A
40899863 TATATACCAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:40901869 original size:28 final size:30
Alignment explanation
Indices: 40901834--40901902 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
40901824 ATAAAAAATA
40901834 ACTAAAATATAATAA-AATTTTT-TTATTT
1 ACTAAAATATAATAATAATTTTTATTATTT
* *
40901862 A-TCAAAATATTATAATTATTTTTATTATTT
1 ACT-AAAATATAATAATAATTTTTATTATTT
40901892 ACTAAAATATA
1 ACTAAAATATA
40901903 TCAAAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 1 0.03
28 12 0.35
29 6 0.18
30 14 0.41
31 1 0.03
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
ACTAAAATATAATAATAATTTTTATTATTT
Found at i:40901986 original size:27 final size:27
Alignment explanation
Indices: 40901948--40902013 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
40901938 AGGTCAATGG
* **
40901948 CATTGGCGGCACCAAATGTGCCAAAGT
1 CATTGGCGGCACCAAAGGTGCCAAAAC
40901975 CATTGGCGGCACCAAAGGTGCCAAAAC
1 CATTGGCGGCACCAAAGGTGCCAAAAC
*
40902002 CATTAGCGGCAC
1 CATTGGCGGCAC
40902014 TACTCGTGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.15
Consensus pattern (27 bp):
CATTGGCGGCACCAAAGGTGCCAAAAC
Found at i:40902257 original size:3 final size:3
Alignment explanation
Indices: 40902251--40902282 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
40902241 AGTATTATTA
40902251 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
40902283 AGTATTAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:40903900 original size:86 final size:86
Alignment explanation
Indices: 40903755--40903928 Score: 330
Period size: 86 Copynumber: 2.0 Consensus size: 86
40903745 CTGTATGGGG
*
40903755 ATTACGATTCGTTGTATAACGAGTTTCAAGGTTGGATAGCTGGTATGCGGGAGTACGTACCAAGG
1 ATTACGATTCGTTGTATAACGAGTTTCAAGGTTGGATAGCTGCTATGCGGGAGTACGTACCAAGG
40903820 ACTGTGATTGAGTTGCAGACA
66 ACTGTGATTGAGTTGCAGACA
*
40903841 ATTACGATTCGTTGTATAACGAGTTTCAAGGTTGGATAGCTGCTATGCGGGAGTACGTACCGAGG
1 ATTACGATTCGTTGTATAACGAGTTTCAAGGTTGGATAGCTGCTATGCGGGAGTACGTACCAAGG
40903906 ACTGTGATTGAGTTGCAGACA
66 ACTGTGATTGAGTTGCAGACA
40903927 AT
1 AT
40903929 GCCATATTAC
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.29
Consensus pattern (86 bp):
ATTACGATTCGTTGTATAACGAGTTTCAAGGTTGGATAGCTGCTATGCGGGAGTACGTACCAAGG
ACTGTGATTGAGTTGCAGACA
Found at i:40914099 original size:44 final size:43
Alignment explanation
Indices: 40914049--40914203 Score: 131
Period size: 43 Copynumber: 3.6 Consensus size: 43
40914039 AATATTGAGA
*
40914049 AAGACCACGTCTGGGAC-GATGGCATTGATTTGAGATTTACGTGT
1 AAGACCACGTCTGGGACAG-TGGCATCGATTT-AGATTTACGTGT
* * * * *
40914093 AAGACCATGTCTGGGACATTGGCATCG-TATATGATTTGCGTAT
1 AAGACCACGTCTGGGACAGTGGCATCGATTTA-GATTTACGTGT
* * *
40914136 AAGACC-CTGTCTGGGACAGTGGCATCGATATTTGA-TTACATGC
1 AAGACCAC-GTCTGGGACAGTGGCATCGAT-TTAGATTTACGTGT
*
40914179 AAGACCTCGTCTGGGAC-GTAGGCAT
1 AAGACCACGTCTGGGACAGT-GGCAT
40914204 TGTACGATCT
Statistics
Matches: 90, Mismatches: 14, Indels: 15
0.76 0.12 0.13
Matches are distributed among these distances:
42 3 0.03
43 59 0.66
44 27 0.30
45 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (43 bp):
AAGACCACGTCTGGGACAGTGGCATCGATTTAGATTTACGTGT
Found at i:40914147 original size:43 final size:44
Alignment explanation
Indices: 40914049--40914172 Score: 137
Period size: 43 Copynumber: 2.8 Consensus size: 44
40914039 AATATTGAGA
* * * *
40914049 AAGACCACGTCTGGGAC-GATGGCATTGATTTGA-GATTTACGTGT
1 AAGACCATGTCTGGGACAG-TGGCATCGATAT-ATGATTTACGTAT
* *
40914093 AAGACCATGTCTGGGACATTGGCATCG-TATATGATTTGCGTAT
1 AAGACCATGTCTGGGACAGTGGCATCGATATATGATTTACGTAT
* *
40914136 AAGACCCTGTCTGGGACAGTGGCATCGATATTTGATT
1 AAGACCATGTCTGGGACAGTGGCATCGATATATGATT
40914173 ACATGCAAGA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
42 1 0.01
43 36 0.53
44 31 0.46
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (44 bp):
AAGACCATGTCTGGGACAGTGGCATCGATATATGATTTACGTAT
Found at i:40916111 original size:6 final size:6
Alignment explanation
Indices: 40916089--40916132 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
40916079 GCTATAATGT
* * * *
40916089 CACCCC CACGTC CACCTC TACCTC CACCTC TACCTC CACCTC CA
1 CACCTC CACCTC CACCTC CACCTC CACCTC CACCTC CACCTC CA
40916133 AAGGATCAAC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.18, C:0.61, G:0.02, T:0.18
Consensus pattern (6 bp):
CACCTC
Found at i:40916114 original size:12 final size:12
Alignment explanation
Indices: 40916099--40916130 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
40916089 CACCCCCACG
40916099 TCCACCTCTACC
1 TCCACCTCTACC
40916111 TCCACCTCTACC
1 TCCACCTCTACC
40916123 TCCACCTC
1 TCCACCTC
40916131 CAAAGGATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.16, C:0.59, G:0.00, T:0.25
Consensus pattern (12 bp):
TCCACCTCTACC
Done.