Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 88 of 126
Found at i:17325564 original size:17 final size:17
Alignment explanation
Indices: 17325542--17325576 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
17325532 ACAACATATA
*
17325542 TATCTTTGATAATTTAT
1 TATCTTAGATAATTTAT
*
17325559 TATCTTAGATATTTTAT
1 TATCTTAGATAATTTAT
17325576 T
1 T
17325577 TATAATTAAT
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:0.29, C:0.06, G:0.06, T:0.60
Consensus pattern (17 bp):
TATCTTAGATAATTTAT
Found at i:17327935 original size:2 final size:2
Alignment explanation
Indices: 17327928--17327962 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
17327918 TATTCTACTT
* *
17327928 TA TA TA TA CA GA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17327963 TTATCTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:17330199 original size:15 final size:15
Alignment explanation
Indices: 17330161--17330189 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17330151 GAATAGAAAG
17330161 AAGAAA-AAAAATGA
1 AAGAAAGAAAAATGA
17330175 AAGAAAGAAAAATGA
1 AAGAAAGAAAAATGA
17330190 GAAGTAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (15 bp):
AAGAAAGAAAAATGA
Found at i:17331101 original size:42 final size:42
Alignment explanation
Indices: 17331046--17331131 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
17331036 CCTTTTGTCA
17331046 CTGGATTGTTTTAATATAATGTATAAATTTGTTTAAAGTTGT
1 CTGGATTGTTTTAATATAATGTATAAATTTGTTTAAAGTTGT
17331088 CTGGATTGTTTTAATATAATGTATAAATTTGTTTAAAGTTGT
1 CTGGATTGTTTTAATATAATGTATAAATTTGTTTAAAGTTGT
17331130 CT
1 CT
17331132 AACTTTTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.50
Consensus pattern (42 bp):
CTGGATTGTTTTAATATAATGTATAAATTTGTTTAAAGTTGT
Found at i:17331120 original size:23 final size:23
Alignment explanation
Indices: 17331051--17331121 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 23
17331041 TGTCACTGGA
17331051 TTGTTTTAATATAATGTATAAAT
1 TTGTTTTAATATAATGTATAAAT
* **
17331074 TTG-TTTAA-AGT--TGTCTGGA-
1 TTGTTTTAATA-TAATGTATAAAT
17331093 TTGTTTTAATATAATGTATAAAT
1 TTGTTTTAATATAATGTATAAAT
17331116 TTGTTT
1 TTGTTT
17331122 AAAGTTGTCT
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
19 3 0.08
20 11 0.31
21 2 0.06
22 11 0.31
23 9 0.25
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (23 bp):
TTGTTTTAATATAATGTATAAAT
Found at i:17333448 original size:18 final size:20
Alignment explanation
Indices: 17333425--17333463 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
17333415 TTCTTCTATC
17333425 TTCTTTT-TCCTTT-TACTT
1 TTCTTTTCTCCTTTGTACTT
*
17333443 TTCTTTTCTCTTTTGTACTT
1 TTCTTTTCTCCTTTGTACTT
17333463 T
1 T
17333464 ATTATACGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 5 0.28
20 6 0.33
ACGTcount: A:0.05, C:0.21, G:0.03, T:0.72
Consensus pattern (20 bp):
TTCTTTTCTCCTTTGTACTT
Found at i:17336951 original size:2 final size:2
Alignment explanation
Indices: 17336944--17336972 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17336934 CCAGTATCTT
17336944 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 T
17336973 TTAGGTGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17339728 original size:3 final size:3
Alignment explanation
Indices: 17339720--17339751 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
17339710 GCCATCTTGT
17339720 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
17339752 AAATATACTT
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:0.66, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:17339796 original size:7 final size:7
Alignment explanation
Indices: 17339786--17339810 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17339776 ATGAAAATGA
17339786 AAAAGAT
1 AAAAGAT
17339793 AAAAGAT
1 AAAAGAT
17339800 AAAAGAT
1 AAAAGAT
17339807 AAAA
1 AAAA
17339811 AAAAAAAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAGAT
Found at i:17339817 original size:14 final size:14
Alignment explanation
Indices: 17339785--17339818 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
17339775 TATGAAAATG
*
17339785 AAAAAGATAAAAGA
1 AAAAAGATAAAAAA
*
17339799 TAAAAGATAAAAAA
1 AAAAAGATAAAAAA
17339813 AAAAAG
1 AAAAAG
17339819 GGAGGAAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (14 bp):
AAAAAGATAAAAAA
Found at i:17346510 original size:32 final size:32
Alignment explanation
Indices: 17346469--17346531 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
17346459 AAAACCTACT
*
17346469 TATAACCTAAAGTAGGACCACATAATTCTATC
1 TATAACCTAAAGTAGGACCAAATAATTCTATC
17346501 TATAACCTAAAGTAGGACCAAATAATTCTAT
1 TATAACCTAAAGTAGGACCAAATAATTCTAT
17346532 GGCCATGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.29
Consensus pattern (32 bp):
TATAACCTAAAGTAGGACCAAATAATTCTATC
Found at i:17349675 original size:17 final size:18
Alignment explanation
Indices: 17349646--17349681 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
17349636 TTTAGTAGTA
*
17349646 AATATTAAAAATATTTAT
1 AATATTAAAAATAATTAT
17349664 AATATT-AAAATAATTAT
1 AATATTAAAAATAATTAT
17349681 A
1 A
17349682 TTTTAGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATATTAAAAATAATTAT
Found at i:17349870 original size:16 final size:17
Alignment explanation
Indices: 17349851--17349887 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
17349841 ATATAATTCT
17349851 ATAATTATATT-AAATA
1 ATAATTATATTAAAATA
17349867 ATAATTATATTAAAATA
1 ATAATTATATTAAAATA
17349884 ATAA
1 ATAA
17349888 AAATATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATTATATTAAAATA
Found at i:17350177 original size:16 final size:18
Alignment explanation
Indices: 17350142--17350178 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
17350132 AATTTGAGTC
*
17350142 AAATTACAACATATTTTA
1 AAATTACAACATATTATA
17350160 AAATTA-AA-ATATTATA
1 AAATTACAACATATTATA
17350176 AAA
1 AAA
17350179 CTTTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 2 0.11
18 6 0.33
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATTACAACATATTATA
Found at i:17350477 original size:13 final size:14
Alignment explanation
Indices: 17350452--17350479 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17350442 TAAAAAATTT
17350452 AAAAATTATTTTTC
1 AAAAATTATTTTTC
17350466 AAAAATTATTTTTC
1 AAAAATTATTTTTC
17350480 TTAGAACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
AAAAATTATTTTTC
Found at i:17351663 original size:25 final size:25
Alignment explanation
Indices: 17351635--17351688 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
17351625 ACATATATAT
*
17351635 AATTCTTTAAAAGTTATGTACAAAA
1 AATTCTTTAAAAGTTAGGTACAAAA
*
17351660 AATTCTTTAAAAGTTAGGTGCAAAA
1 AATTCTTTAAAAGTTAGGTACAAAA
17351685 AATT
1 AATT
17351689 AATTTACTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.35
Consensus pattern (25 bp):
AATTCTTTAAAAGTTAGGTACAAAA
Found at i:17351782 original size:2 final size:2
Alignment explanation
Indices: 17351775--17351800 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17351765 ATTCCCTTAA
17351775 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
17351801 GTTCCAGCCA
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:17353933 original size:33 final size:33
Alignment explanation
Indices: 17353891--17353958 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
17353881 CAACACCCAA
*
17353891 AAGTAAGACTAGACTTGTCTTCATTTCTACTCG
1 AAGTAAGACTAGACTTGTCTTCATTCCTACTCG
17353924 AAGTAAGACTAGACTTGTCTTCATTCCTACTCG
1 AAGTAAGACTAGACTTGTCTTCATTCCTACTCG
17353957 AA
1 AA
17353959 CCCCCTGCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (33 bp):
AAGTAAGACTAGACTTGTCTTCATTCCTACTCG
Found at i:17357254 original size:30 final size:30
Alignment explanation
Indices: 17357213--17357269 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
17357203 CAAATTGTTT
17357213 AAAAATGAAATAA-AAATAAAATTATTTGAA
1 AAAAATGAAATAATAAA-AAAATTATTTGAA
* *
17357243 AAAAATTAAATAATAAAATAATTATTT
1 AAAAATGAAATAATAAAAAAATTATTT
17357270 TTGGTTGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.32
Consensus pattern (30 bp):
AAAAATGAAATAATAAAAAAATTATTTGAA
Found at i:17357569 original size:2 final size:2
Alignment explanation
Indices: 17357564--17357592 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17357554 TGTGTGTGTC
17357564 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 T
17357593 TAGTAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17360289 original size:199 final size:199
Alignment explanation
Indices: 17359945--17360343 Score: 762
Period size: 199 Copynumber: 2.0 Consensus size: 199
17359935 GAATACAAAG
*
17359945 AAAAAGAGAAAAAGATATATTAGTTTTAGCTATGCTTTGTAAAAGGAGATTAAAGGCAAATTAGA
1 AAAAAGAGAAAAAGATATATTAGTTGTAGCTATGCTTTGTAAAAGGAGATTAAAGGCAAATTAGA
17360010 GGGCCCAAAATCAAAAGCCTGATTCATTTTATTTATTGTGAAGACCAAGACCATCCCAGCACGAC
66 GGGCCCAAAATCAAAAGCCTGATTCATTTTATTTATTGTGAAGACCAAGACCATCCCAGCACGAC
*
17360075 TTTCCTGTCGGAGTTGAATCCTGCAATTTCATCAATTCCCACAGCCATGAACATGATGCAACTGC
131 TTTCCTCTCGGAGTTGAATCCTGCAATTTCATCAATTCCCACAGCCATGAACATGATGCAACTGC
17360140 GTTA
196 GTTA
17360144 AAAAAGAGAAAAAGATATATTAGTTGTAGCTATGCTTTGTAAAAGGAGATTAAAGGCAAATTAGA
1 AAAAAGAGAAAAAGATATATTAGTTGTAGCTATGCTTTGTAAAAGGAGATTAAAGGCAAATTAGA
*
17360209 GGGCCCAAAATCAAAAGCTTGATTCATTTTATTTATTGTGAAGACCAAGACCATCCCAGCACGAC
66 GGGCCCAAAATCAAAAGCCTGATTCATTTTATTTATTGTGAAGACCAAGACCATCCCAGCACGAC
*
17360274 TTTCCTCTTGGAGTTGAATCCTGCAATTTCATCAATTCCCACAGCCATGAACATGATGCAACTGC
131 TTTCCTCTCGGAGTTGAATCCTGCAATTTCATCAATTCCCACAGCCATGAACATGATGCAACTGC
17360339 GTTA
196 GTTA
17360343 A
1 A
17360344 TTTTTCTTAA
Statistics
Matches: 196, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
199 196 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (199 bp):
AAAAAGAGAAAAAGATATATTAGTTGTAGCTATGCTTTGTAAAAGGAGATTAAAGGCAAATTAGA
GGGCCCAAAATCAAAAGCCTGATTCATTTTATTTATTGTGAAGACCAAGACCATCCCAGCACGAC
TTTCCTCTCGGAGTTGAATCCTGCAATTTCATCAATTCCCACAGCCATGAACATGATGCAACTGC
GTTA
Found at i:17363061 original size:15 final size:16
Alignment explanation
Indices: 17363015--17363063 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
17363005 TTTTAAAACA
17363015 ATGGTTTTTGTTAATAT
1 ATGGTTTTTGTTAA-AT
*
17363032 AT-ATTTTT-TTGAAAT
1 ATGGTTTTTGTT-AAAT
17363047 -TGGTTTTTGTTAAAT
1 ATGGTTTTTGTTAAAT
17363062 AT
1 AT
17363064 AATTAATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 9
0.70 0.05 0.24
Matches are distributed among these distances:
14 1 0.04
15 13 0.50
16 10 0.38
17 2 0.08
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (16 bp):
ATGGTTTTTGTTAAAT
Found at i:17364013 original size:27 final size:27
Alignment explanation
Indices: 17363975--17364029 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
17363965 TTGACTATAC
17363975 TTATAGAATCTGAATATTATTGTTTTT
1 TTATAGAATCTGAATATTATTGTTTTT
17364002 TTATAGAATCTGAATATTATTGTTTTT
1 TTATAGAATCTGAATATTATTGTTTTT
17364029 T
1 T
17364030 ATAACTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.04, G:0.11, T:0.56
Consensus pattern (27 bp):
TTATAGAATCTGAATATTATTGTTTTT
Found at i:17364895 original size:21 final size:21
Alignment explanation
Indices: 17364849--17364889 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17364839 TTTTATAATT
**
17364849 CTAAAGTAAACTTTTTTAAAA
1 CTAAAGTAAACAATTTTAAAA
17364870 CTAAAGTAAACAATTTTAAA
1 CTAAAGTAAACAATTTTAAA
17364890 CATAAAAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (21 bp):
CTAAAGTAAACAATTTTAAAA
Found at i:17366372 original size:15 final size:17
Alignment explanation
Indices: 17366353--17366400 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
17366343 AAAGAAAAGG
*
17366353 GGAAAAACAAAAAAG-A
1 GGAAAAAAAAAAAAGAA
17366369 -GAAAAAAAATAAAAGAA
1 GGAAAAAAAA-AAAAGAA
*
17366386 GGAAAAATAAAAAAG
1 GGAAAAAAAAAAAAG
17366401 TAGTTTGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 8 0.30
16 5 0.19
17 6 0.22
18 8 0.30
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (17 bp):
GGAAAAAAAAAAAAGAA
Found at i:17366382 original size:18 final size:18
Alignment explanation
Indices: 17366355--17366392 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
17366345 AGAAAAGGGG
17366355 AAAAACAAAA-AAGAGAAA
1 AAAAACAAAAGAAG-GAAA
*
17366373 AAAAATAAAAGAAGGAAA
1 AAAAACAAAAGAAGGAAA
17366391 AA
1 AA
17366393 TAAAAAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (18 bp):
AAAAACAAAAGAAGGAAA
Found at i:17366399 original size:17 final size:16
Alignment explanation
Indices: 17366347--17366400 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
17366337 ATAAAGAAAG
* *
17366347 AAAAGGGGAAAAACAA
1 AAAAGAGGAAAAAAAA
17366363 AAAAGA-GAAAAAAAA
1 AAAAGAGGAAAAAAAA
*
17366378 TAAAAGAAGGAAAAATAA
1 -AAAAG-AGGAAAAAAAA
17366396 AAAAG
1 AAAAG
17366401 TAGTTTGGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 8 0.25
16 10 0.31
17 6 0.19
18 8 0.25
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.04
Consensus pattern (16 bp):
AAAAGAGGAAAAAAAA
Found at i:17369113 original size:21 final size:22
Alignment explanation
Indices: 17369087--17369128 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17369077 AGCTAATTTA
17369087 TCTTTTT-GCATTCTTTCTTTG
1 TCTTTTTCGCATTCTTTCTTTG
* *
17369108 TCTTTTTCTCTTTCTTTCTTT
1 TCTTTTTCGCATTCTTTCTTT
17369129 TAATTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.02, C:0.21, G:0.05, T:0.71
Consensus pattern (22 bp):
TCTTTTTCGCATTCTTTCTTTG
Found at i:17370015 original size:3 final size:3
Alignment explanation
Indices: 17370007--17370068 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
17369997 GAAATGTTTG
*
17370007 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A A-A ATTA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
*
17370051 AAA AT- ATA AT- ATA ATA AT
1 ATA ATA ATA ATA ATA ATA AT
17370069 TTTTTATTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 8 0.16
3 41 0.80
4 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:17372559 original size:21 final size:20
Alignment explanation
Indices: 17372535--17372586 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
17372525 GTAATTTTTT
*
17372535 TTTTAATTTTTTGAATTATTA
1 TTTTAATTTTTT-AAGTATTA
* *
17372556 TTTTAATATTTTACGTATTA
1 TTTTAATTTTTTAAGTATTA
17372576 TTTTAAATTTT
1 TTTT-AATTTT
17372587 ATCATTAGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (20 bp):
TTTTAATTTTTTAAGTATTA
Found at i:17378542 original size:371 final size:368
Alignment explanation
Indices: 17376290--17378705 Score: 1878
Period size: 368 Copynumber: 6.6 Consensus size: 368
17376280 GAAGTACTTG
* * * * ** * *
17376290 TGTCACGGACTTAAAGAAGAGTCATTAATCTCACATTGAACATAATAGGAGGGTCACTGGGGTAT
1 TGTCACGGACCTAAGGAAGAGTCCTGAATCTCACATCAAACATAATAAGAGGGTCACTAGGGTAT
* ** * *
17376355 AAAAGGGTTCACACCACCTTTTTCTTGTGAGGTACCTTTTATAGGATAAAA-TCATGAGGCC-AA
66 AAAAGGGTTCACACCACCTCTACCTTGTGAGGCACCTTTTGTAGGATAAAACT-ATGAGGCCAAA
* * * * ** ** * * **
17376418 GGGGACCAAAGTGGACAATACCTCATAAGGGTGTGAACCGTGACAGATAGGCTGATTTGAGACAC
130 GGGG-CCAGAGCGAACAATACCTCACAAGGGTGTGAACTATG-GTGGTAGGCTGATCTGAGACGT
* * * * * *
17376483 CGAATGAGTAGATGCCCAGGTCTCAGAGTCGCGCGGGTTTGAAGCTTAAGTCTCAACTCGTGACA
193 CGGATGAGTGGATGCCCAGGTCTTAGAGTC-AGCAGGTTTGAAGCTTAAGTCTCGACTCGTGACA
* * * *
17376548 AGTGGTATCAAAGCTAGCCCTAAACCGTTCGATCCATGTCAAGTGCCTCGAGGAAGGTAGGCAGG
257 AGTGGTATCAAAGCTAGCCCTAAACCATTCGATCCACGTCAAGCGCCTCGAGGGAGGTAGGCAGG
* *
17376613 GTGGTCAGCCTCCGTGAC-AAGAGTGTCACGAGGTTGGGTGGGTGAGAA
322 GTGGCCAGCCTCCGTGACGAAGA-CGTCACGAGGTTGGGT-GGTGAGAA
* * * * ** *
17376661 TGTCACAGACCTAAGAAAGAGT--T-TATCTTACATTGAACATAATAGGAGGGTCACTAGGGTAT
1 TGTCACGGACCTAAGGAAGAGTCCTGAATCTCACATCAAACATAATAAGAGGGTCACTAGGGTAT
* * * * * * ** *
17376723 AAAAGGGTTCACACCACCTCTTCCTTGTGAGACACCTTTTGTAAGATAAAATTGTAAGGTTAAGG
66 AAAAGGGTTCACACCACCTCTACCTTGTGAGGCACCTTTTGTAGGATAAAACTATGAGGCCAAAG
* * * * * * * **
17376788 GGGCTAGAGTGGATAATACCTCACAAGGGTGTAAATTATGGTAGGTAGGTTGATCTGAGATATCG
131 GGGCCAGAGCGAACAATACCTCACAAGGGTGTGAACTATGGT-GGTAGGCTGATCTGAGACGTCG
* * ** * *
17376853 GATGAGTGGATGCCCAGGTC-TCGAAGTGAAGTGGGTTGGAAACTTAAGTCTCGACT--T-----
195 GATGAGTGGATGCCCAGGTCTTAG-AGT-CAGCAGGTTTGAAGCTTAAGTCTCGACTCGTGACAA
* * * * ** * ** *
17376910 GT-GTATCAAAGCCAGCCCTAAATCGTTCGATTCACGTCTGGCACCTCGAAAGAGGTAGGCATGG
258 GTGGTATCAAAGCTAGCCCTAAACCATTCGATCCACGTCAAGCGCCTCGAGGGAGGTAGGCAGGG
* * * * *
17376974 TGGCCAGCTTCCGTGATGAAGATGTCACGAGATTAGGTGAG-GAAGAA
323 TGGCCAGCCTCCGTGACGAAGACGTCACGAGGTTGGGTG-GTG-AGAA
* * * *
17377021 TGTCACGGACCTAAGGAAGAGTCCCGAATC-CTACATCGAACATAATAAAAAGGTCACTAGGGTA
1 TGTCACGGACCTAAGGAAGAGTCCTGAATCTC-ACATCAAACATAATAAGAGGGTCACTAGGGTA
* * * * *
17377085 TAAAAGGGTTCATACCACCTCAACCTTGTGAGGCACTTTTTGTAGGA-CAAAC-GTGAGGCCAAA
65 TAAAAGGGTTCACACCACCTCTACCTTGTGAGGCACCTTTTGTAGGATAAAACTATGAGGCCAAA
* * * * * ** * *
17377148 GGGGCCAGAGTGGACAATACCTCATAAGGGTGTAAACTGTGACAGATAGGCTGATCT-AGATGTC
130 GGGGCCAGAGCGAACAATACCTCACAAGGGTGTGAACTATG-GTGGTAGGCTGATCTGAGACGTC
* * * * * * *
17377212 GGATGAGTAGATGCTCGGGT-TTCAGAGTCGTGTAGG-TTCAGAGCTTAAGTCTCGA-TATGTGA
194 GGATGAGTGGATGCCCAGGTCTT-AGAGTC-AGCAGGTTTGA-AGCTTAAGTCTCGACT-CGTGA
*** * * * * * * *
17377274 CAAGTGGTATGTGAGCCAGCCCTAAACCGTTCGATCCATGCCTAGCACCTCGAGGAAGGTAGGCA
255 CAAGTGGTATCAAAGCTAGCCCTAAACCATTCGATCCACGTCAAGCGCCTCGAGGGAGGTAGGCA
* * * * * *
17377339 AGGTGGCCAGCTTTCGTGACGAAGGACGTCACGATGTTAGGTTAGG-AAGAA
320 GGGTGGCCAGCCTCCGTGACGAA-GACGTCACGAGGTT-GGGT-GGTGAGAA
* * * * *
17377390 TGTCACGAACCTAAGGAAGAGTCTTGAATCCCACATCAAACATAATAAGAGGGTTAGTAGGGTAT
1 TGTCACGGACCTAAGGAAGAGTCCTGAATCTCACATCAAACATAATAAGAGGGTCACTAGGGTAT
** * * * * * * * * *
17377455 AAAAAAGTTTACACTATCTCTGCCTTGTGAGGTACCTTTTGTAGGATAAAATTGTTAGGCCAGAG
66 AAAAGGGTTCACACCACCTCTACCTTGTGAGGCACCTTTTGTAGGATAAAACTATGAGGCCAAAG
* * * * * * * * * *
17377520 AGGCCAAAGC-AGACAATACCTCACAAAGGTGTGAACCATAGTTGGAAGGCTAATCTGGGATGCC
131 GGGCCAGAGCGA-ACAATACCTCACAAGGGTGTGAACTAT-GGTGGTAGGCTGATCTGAGACGTC
* * * * * *
17377584 AGATGAGTGGATG-CCAGGT-TTCGAAGTCA-CACGAGTTTGAAGCTTAAGTCTTGACCCGGGAT
194 GGATGAGTGGATGCCCAGGTCTTAG-AGTCAGCA-G-GTTTGAAGCTTAAGTCTCGACTCGTGAC
* * * * *
17377646 AAGTGGTATTAAAG-TCAGCCATAAACTATTCGATCCACGTCGAGCGTCTCGAGGGAGGTAGGCA
256 AAGTGGTATCAAAGCT-AGCCCTAAACCATTCGATCCACGTCAAGCGCCTCGAGGGAGGTAGGCA
* *
17377710 GGGTGGTCAGCCTCCGTGACG-AGAGCGTCACGAGGTTGAGG-GGTGAAAA
320 GGGTGGCCAGCCTCCGTGACGAAGA-CGTCACGAGGTTG-GGTGGTGAGAA
* * * * * *
17377759 TGTCATGGACCTAAGAAAGAGTCTTAAATCTCACACCAAACATAATAGGAGGGTCACT-GGGTAT
1 TGTCACGGACCTAAGGAAGAGTCCTGAATCTCACATCAAACATAATAAGAGGGTCACTAGGGTAT
* * *
17377823 AAAAGGGTTCACATCACCTCAACCTTGTAAGGCACCTTTTGTAGGAT--AACTATGAGGCC-AAG
66 AAAAGGGTTCACACCACCTCTACCTTGTGAGGCACCTTTTGTAGGATAAAACTATGAGGCCAAAG
* *
17377885 AGGGCCAGAGC-AGACAATACCTCACAAGGGTGTGAA-TCATGGTAGGTAGGCTGATTTGAAACG
131 -GGGCCAGAGCGA-ACAATACCTCACAAGGGTGTGAACT-ATGGT-GGTAGGCTGATCTGAGACG
* * * * * *
17377948 TCGGATGAGTGGATGTCCAGATCCTAGAGCCA-CACGAGTTTGGAGCTTAAGTCTCGACCCGTGA
192 TCGGATGAGTGGATGCCCAGGTCTTAGAGTCAGCA-G-GTTTGAAGCTTAAGTCTCGACTCGTGA
* * * * *
17378012 CAAGTGATATCAGAGCTAGCCCTAAACCATTCGATCCACGTCGAGCGTCTCGATGGA-GTAGGCA
255 CAAGTGGTATCAAAGCTAGCCCTAAACCATTCGATCCACGTCAAGCGCCTCGAGGGAGGTAGGCA
* * ** * * * *
17378076 GGGTGGTCAGCCTCTGTGATTAGGGCATCATGAGGTTGGGTGGGTGAGAA
320 GGGTGGCCAGCCTCCGTGACGAAGACGTCACGAGGTTGGGT-GGTGAGAA
** * *
17378126 TGTCATAGACCTAAGGAAGAGTCCTGAATCTCACATCAAACATAATAAAAGGGTCACTGGGGTAT
1 TGTCACGGACCTAAGGAAGAGTCCTGAATCTCACATCAAACATAATAAGAGGGTCACTAGGGTAT
* * *
17378191 AAAAGGGTTCACACCACCTCTTCTTTGTGAGGCACCTTTTGTAGGATAAAACCATGAGGCCAAAG
66 AAAAGGGTTCACACCACCTCTACCTTGTGAGGCACCTTTTGTAGGATAAAACTATGAGGCCAAAG
** * * * ** * **
17378256 GGGTTAGAGCGAACAATACCTCACAAAGGTATGAACTGTGGTGGTTAAACTGATCTGGGACGTTA
131 GGGCCAGAGCGAACAATACCTCACAAGGGTGTGAACTATGGTGG-TAGGCTGATCTGAGACGTCG
* * * * *
17378321 GATAAGTGGATGCTC-GAGTCTTAGAGTCATGCAGGTTCGAAGTTTAAGTCTCGACTCATGACAA
195 GATGAGTGGATGCCCAG-GTCTTAGAGTCA-GCAGGTTTGAAGCTTAAGTCTCGACTCGTGACAA
* ** * **
17378385 GTGGTATCAGAGCTAGCCCTAAACCATTCGATCCACACCAAGTGCCTTAAGGGAGGTAGGCAGGG
258 GTGGTATCAAAGCTAGCCCTAAACCATTCGATCCACGTCAAGCGCCTCGAGGGAGGTAGGCAGGG
* * * *
17378450 TGGCCAACCTCTGTGACGAAGACGTCATGAGGTTGGGTGGAAGAGAA
323 TGGCCAGCCTCCGTGACGAAGACGTCACGAGGTTGGGTGG-TGAGAA
* ** * * * *
17378497 TGTCATGGACCTAAAAAAGAGTCCTGAATCCCACATCAAACATAAT-AGAAAGGTCA-TTGAAGT
1 TGTCACGGACCTAAGGAAGAGTCCTGAATCTCACATCAAACATAATAAG-AGGGTCACTAG-GGT
* * * * ** * **
17378560 ATAAAAAGGTTCATACCATCTCTACCTTGTGAGGTACCTTTTGTAAAACAAAACTATGAGATC-A
64 ATAAAAGGGTTCACACCACCTCTACCTTGTGAGGCACCTTTTGTAGGATAAAACTATGAGGCCAA
* ** * ** * *
17378624 GGGGGTTAGAGC-AGATAATACCTCACAAGGGTGTGAACCCTGGCAGGTAGGCTGATCTGAGACT
129 AGGGGCCAGAGCGA-ACAATACCTCACAAGGGTGTGAACTATGG-TGGTAGGCTGATCTGAGACG
* *
17378688 TTGCATGAGTGGATGCCC
192 TCGGATGAGTGGATGCCC
17378706 GGGTATCGGA
Statistics
Matches: 1637, Mismatches: 339, Indels: 139
0.77 0.16 0.07
Matches are distributed among these distances:
359 5 0.00
360 147 0.09
361 61 0.04
362 4 0.00
363 72 0.04
365 6 0.00
366 106 0.06
367 148 0.09
368 338 0.21
369 173 0.11
370 238 0.15
371 317 0.19
372 22 0.01
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (368 bp):
TGTCACGGACCTAAGGAAGAGTCCTGAATCTCACATCAAACATAATAAGAGGGTCACTAGGGTAT
AAAAGGGTTCACACCACCTCTACCTTGTGAGGCACCTTTTGTAGGATAAAACTATGAGGCCAAAG
GGGCCAGAGCGAACAATACCTCACAAGGGTGTGAACTATGGTGGTAGGCTGATCTGAGACGTCGG
ATGAGTGGATGCCCAGGTCTTAGAGTCAGCAGGTTTGAAGCTTAAGTCTCGACTCGTGACAAGTG
GTATCAAAGCTAGCCCTAAACCATTCGATCCACGTCAAGCGCCTCGAGGGAGGTAGGCAGGGTGG
CCAGCCTCCGTGACGAAGACGTCACGAGGTTGGGTGGTGAGAA
Found at i:17384241 original size:2 final size:2
Alignment explanation
Indices: 17384234--17384258 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17384224 TTCAAATAAC
17384234 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 T
17384259 TCTCTTTTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17385091 original size:2 final size:2
Alignment explanation
Indices: 17385046--17385078 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17385036 GTGCGCGTTT
17385046 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
17385079 TCTAAGATAT
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:17386384 original size:12 final size:12
Alignment explanation
Indices: 17386367--17386394 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
17386357 ATAACATTGC
17386367 TATTTGAATATT
1 TATTTGAATATT
17386379 TATTTGAATATT
1 TATTTGAATATT
17386391 TATT
1 TATT
17386395 GGTGTTTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (12 bp):
TATTTGAATATT
Found at i:17387772 original size:27 final size:27
Alignment explanation
Indices: 17387705--17387784 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 27
17387695 ATTTATTAAA
* **
17387705 ATTAAAAT-TAAAATAGCATATTTATT
1 ATTAAAATATAAAAAATAATATTTATT
*
17387731 ATTAAAATATTAAAAATAATATTTATT
1 ATTAAAATATAAAAAATAATATTTATT
* * *
17387758 ATT-AAGTCATAAAAAGTATTATTTATT
1 ATTAAAAT-ATAAAAAATAATATTTATT
17387785 TTATTATTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
26 11 0.25
27 33 0.75
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (27 bp):
ATTAAAATATAAAAAATAATATTTATT
Found at i:17389062 original size:29 final size:27
Alignment explanation
Indices: 17389029--17389095 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 27
17389019 ATTAATTAAA
*
17389029 ATTAATATATATTTATTGAAAAAATATAT
1 ATTAATATATATTTA-TAAAAAAAT-TAT
17389058 ATTAATATATATTTATAAAAAAATTAT
1 ATTAATATATATTTATAAAAAAATTAT
* *
17389085 CTAAATATATA
1 ATTAATATATA
17389096 AGATAAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 12 0.34
28 8 0.23
29 15 0.43
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (27 bp):
ATTAATATATATTTATAAAAAAATTAT
Found at i:17390188 original size:13 final size:14
Alignment explanation
Indices: 17390162--17390191 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
17390152 GTTCATTTTT
17390162 TTTAATGTATTTAA
1 TTTAATGTATTTAA
17390176 TTTAATG-ATTTAA
1 TTTAATGTATTTAA
17390189 TTT
1 TTT
17390192 TATTATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (14 bp):
TTTAATGTATTTAA
Found at i:17390193 original size:14 final size:15
Alignment explanation
Indices: 17390161--17390193 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
17390151 AGTTCATTTT
17390161 TTTTAATGTATTTAA
1 TTTTAATGTATTTAA
17390176 -TTTAATG-ATTTAA
1 TTTTAATGTATTTAA
17390189 TTTTA
1 TTTTA
17390194 TTATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTAATGTATTTAA
Found at i:17392423 original size:4 final size:4
Alignment explanation
Indices: 17392406--17392436 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
17392396 AATTTTTGTT
*
17392406 TTTA TTTG TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
17392437 TATCTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:17398228 original size:30 final size:29
Alignment explanation
Indices: 17398173--17398232 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
17398163 CCATGGAGAA
* *
17398173 TTTAAAAGAAATTGCTTATCTAAAAATTT
1 TTTAAAAGAAATTCCTTATCAAAAAATTT
*
17398202 TTTAAAAGTAAATTCCTTA-CAAAAAAATT
1 TTTAAAAG-AAATTCCTTATCAAAAAATTT
17398231 TT
1 TT
17398233 CACTTATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (29 bp):
TTTAAAAGAAATTCCTTATCAAAAAATTT
Found at i:17403339 original size:16 final size:16
Alignment explanation
Indices: 17403313--17403368 Score: 64
Period size: 15 Copynumber: 3.6 Consensus size: 16
17403303 CCCAAATACC
17403313 AATTA-AAAAATAATT
1 AATTATAAAAATAATT
17403328 AATTATAAAAATAA-T
1 AATTATAAAAATAATT
**
17403343 -ATGGTAAAAATTAATT
1 AATTATAAAAA-TAATT
17403359 AATTATAAAA
1 AATTATAAAA
17403369 GGACATATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 8 0.24
15 9 0.27
16 9 0.27
17 7 0.21
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (16 bp):
AATTATAAAAATAATT
Found at i:17403414 original size:2 final size:2
Alignment explanation
Indices: 17403407--17403453 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
17403397 ATCACCTAAA
* * *
17403407 AT AT AT AT AC AC AT GT 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
17403449 AT AT A
1 AT AT A
17403454 AGATACGAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:17413675 original size:23 final size:22
Alignment explanation
Indices: 17413622--17413675 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
17413612 TTAAAAATGG
* * *
17413622 ATTATTTCCAAAAAATATATAA
1 ATTATTTTCAAAAAATAAAAAA
17413644 ATTAGTTTTCAAAAAATACAAAAA
1 ATTA-TTTTCAAAAAATA-AAAAA
17413668 ATTATTTT
1 ATTATTTT
17413676 TATCAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 16 0.59
24 7 0.26
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (22 bp):
ATTATTTTCAAAAAATAAAAAA
Found at i:17413762 original size:15 final size:15
Alignment explanation
Indices: 17413744--17413789 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
17413734 AAGAAAAGGG
17413744 GAAAAACAA-AAAAGA
1 GAAAAA-AATAAAAGA
17413759 GAAAAAAATAAAAGA
1 GAAAAAAATAAAAGA
*
17413774 -AGGAAAAATAAAAGA
1 GA-AAAAAATAAAAGA
17413789 G
1 G
17413790 TAGTTTGGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 3 0.11
15 24 0.89
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.04
Consensus pattern (15 bp):
GAAAAAAATAAAAGA
Found at i:17416470 original size:17 final size:17
Alignment explanation
Indices: 17416448--17416482 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
17416438 ATTAATTATA
*
17416448 AATAAAATATCTAAGAT
1 AATAAAATATCAAAGAT
*
17416465 AATAAATTATCAAAGAT
1 AATAAAATATCAAAGAT
17416482 A
1 A
17416483 TATATGTTGT
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:0.60, C:0.06, G:0.06, T:0.29
Consensus pattern (17 bp):
AATAAAATATCAAAGAT
Found at i:17422337 original size:10 final size:10
Alignment explanation
Indices: 17422322--17422346 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
17422312 GCTATAAAGT
17422322 AATTAATGAA
1 AATTAATGAA
17422332 AATTAATGAA
1 AATTAATGAA
17422342 AATTA
1 AATTA
17422347 TTAACATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (10 bp):
AATTAATGAA
Found at i:17423937 original size:59 final size:57
Alignment explanation
Indices: 17423647--17424183 Score: 644
Period size: 59 Copynumber: 9.1 Consensus size: 57
17423637 TTTTGTGTAG
* * *
17423647 GGAAAATTGATACTTTCAACTTTTCCCC-AAAATATTTTTTAGAAATTTTAATTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT-GAAAATTTATTTTTAA
* * * *
17423704 GGAAAATTGATATTTTCAACTTTTCCTCAAAAAAAACTTTTTTCTTGAACATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCC-C--CAAAAA-TATTTT-TTGAAAATTTATTTTTAA
** *
17423766 GGAAAATTGATACTTTCAACTTTTTTCCAAAAATGTTTTTTGAAAATTTATTTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTA-TTTTTAA
* *
17423824 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT-ATTTTTTGAAAATTTATTTTTAA
* * * *
17423882 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAGATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT-GAAAATTT-ATTTTTAA
* *
17423941 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCCTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT--ATTTTTTGAAAATTTATTTTTAA
* * *
17424000 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTCTTTTTTTGAAATTTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-T-ATTTTTTGAAAATTTATTTTTAA
* * *
17424059 GAAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAA-TTT-ATTTTTAA
* ** *
17424118 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCCTTTTTTGAAATTTTATTTTTAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA--TATTTTTTGAAAATTTATTTTT-AA
17424178 GGAAAA
1 GGAAAA
17424184 AAATAAAACA
Statistics
Matches: 418, Mismatches: 44, Indels: 33
0.84 0.09 0.07
Matches are distributed among these distances:
57 51 0.12
58 93 0.22
59 193 0.46
60 18 0.04
61 21 0.05
62 40 0.10
63 2 0.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (57 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTAA
Found at i:17423984 original size:177 final size:175
Alignment explanation
Indices: 17423647--17424183 Score: 753
Period size: 177 Copynumber: 3.0 Consensus size: 175
17423637 TTTTGTGTAG
* * * * *
17423647 GGAAAATTGATACTTTCAACTTTTCCCCAAAATAT-TTTTTAGAAATTTTAATTTCAAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAA-ATCTTTTTTGAAATTTTATTTTTAAGAAAAAT
* * * * *
17423711 TGATATTTTCAACTTTTCCTCAAAAAAAACTTTTTTCTTGAACATTT-ATTTTTAAGGAAAATTG
65 TGATACTTTCAACTTTTCC-CAAAAAATA--TTTTT-TGGAA-TTTTGATTTTCAAGGAAAATTG
* *
17423775 ATACTTTCAACTTTT-TTCCAAAAAT--GTTTTTTGAAAATTTATTTTTTAA
125 ATACTTTCAACTTTTCCT-CAAAAATCCCTTTTTTGAAAATTTATTTTTTAA
*
17423824 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTGAAAATTTATTTTTAAGAAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAT-CTTTTTTGAAATTTTATTTTTAAGAAAAAT
*
17423889 TGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAGATTTTGATTTTCAAGGAAAATTGATAC
65 TGATACTTTCAACTTTTCCCAAAAAATATTTTTTGGA-ATTTTGATTTTCAAGGAAAATTGATAC
17423954 TTTCAACTTTTCCTCAAAAATCCCTTTTTTGAAAATTTA-TTTTTAA
129 TTTCAACTTTTCCTCAAAAATCCCTTTTTTGAAAATTTATTTTTTAA
17424000 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTCTTTTTTTGAAATTTTATTTTTAAGAAAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA-TC-TTTTTTGAAATTTTATTTTTAAGAAAAA
* *
17424065 TTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAAATTTTGATTTTCAAGGAAAATTGATA
64 TTGATACTTTCAACTTTTCCCAAAAAATATTTTTTG-GAATTTTGATTTTCAAGGAAAATTGATA
* * *
17424130 CTTTCAACTTTTCCTCAAAAACCCCTTTTTTGAAATTTTATTTTTAAA
128 CTTTCAACTTTTCCTCAAAAATCCCTTTTTTGAAAATTTATTTTTTAA
17424178 GGAAAA
1 GGAAAA
17424184 AAATAAAACA
Statistics
Matches: 329, Mismatches: 20, Indels: 21
0.89 0.05 0.06
Matches are distributed among these distances:
174 6 0.02
175 44 0.13
176 44 0.13
177 180 0.55
178 55 0.17
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (175 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTGAAATTTTATTTTTAAGAAAAATT
GATACTTTCAACTTTTCCCAAAAAATATTTTTTGGAATTTTGATTTTCAAGGAAAATTGATACTT
TCAACTTTTCCTCAAAAATCCCTTTTTTGAAAATTTATTTTTTAA
Found at i:17424191 original size:5 final size:5
Alignment explanation
Indices: 17424183--17424269 Score: 54
Period size: 5 Copynumber: 16.8 Consensus size: 5
17424173 TTAAAGGAAA
* *
17424183 AAAAT AAAAC AAAAT AAAAGT GAGAAAA AAAAT AAAAT -AAAT AAAAT
1 AAAAT AAAAT AAAAT AAAA-T -A-AAAT AAAAT AAAAT AAAAT AAAAT
** *
17424230 --AAT AAAGG AAAGT AAAAAT AAAAAT AAAAT AAATAT AAAA
1 AAAAT AAAAT AAAAT -AAAAT -AAAAT AAAAT AAA-AT AAAA
17424270 AGAATATTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
3 3 0.05
4 4 0.06
5 38 0.58
6 17 0.26
7 1 0.02
8 3 0.05
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:17424300 original size:4 final size:4
Alignment explanation
Indices: 17424293--17424325 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
17424283 AACCTAATCT
17424293 AATA AAT- AA-A AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AATA AAT
17424326 TCAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 4 0.15
4 23 0.85
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:17424314 original size:18 final size:19
Alignment explanation
Indices: 17424207--17424320 Score: 64
Period size: 18 Copynumber: 6.2 Consensus size: 19
17424197 TAAAAGTGAG
17424207 AAAAA-AAATAAAATAAAT
1 AAAAATAAATAAAATAAAT
**
17424225 -AAAAT-AATAAAGGAAAGT
1 AAAAATAAATAAAATAAA-T
17424243 AAAAATAAAAATAAAATAAAT
1 AAAAAT--AAATAAAATAAAT
*
17424264 ATAAAA-AGAAT--ATTAAAT
1 A-AAAATA-AATAAAATAAAT
** **
17424282 AAACCT-AATCTAATAAAT
1 AAAAATAAATAAAATAAAT
17424300 AAAAATAAAT-AAATAAAT
1 AAAAATAAATAAAATAAAT
17424318 AAA
1 AAA
17424321 TAAATTCAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 24
0.68 0.10 0.22
Matches are distributed among these distances:
16 3 0.04
17 15 0.21
18 28 0.38
19 9 0.12
20 3 0.04
21 2 0.03
22 13 0.18
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.21
Consensus pattern (19 bp):
AAAAATAAATAAAATAAAT
Found at i:17424882 original size:9 final size:10
Alignment explanation
Indices: 17424859--17424884 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
17424849 TTCCCAAAAA
17424859 AAAAATCTCC
1 AAAAATCTCC
17424869 AAAAATCTCC
1 AAAAATCTCC
17424879 AAAAAT
1 AAAAAT
17424885 TTTCTGCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAAATCTCC
Found at i:17425389 original size:17 final size:17
Alignment explanation
Indices: 17425342--17425390 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
17425332 AAAATAATAA
*
17425342 TAATAAAGATAAAAAAT
1 TAATAAAAATAAAAAAT
**
17425359 TAA-AAATGTAAAAAAAT
1 TAATAAAAAT-AAAAAAT
17425376 TAATAAAAATAAAAA
1 TAATAAAAATAAAAA
17425391 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 4 0.15
17 18 0.69
18 4 0.15
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (17 bp):
TAATAAAAATAAAAAAT
Found at i:17425402 original size:5 final size:6
Alignment explanation
Indices: 17425337--17425401 Score: 51
Period size: 6 Copynumber: 10.2 Consensus size: 6
17425327 TACATAAAAT
* * *
17425337 AATAAT AATAAA GATAAAA AATTAAA AATGTAAA AA-AATT AATAAA AATAAA
1 AATAAA AATAAA AAT-AAA AA-TAAA AA--TAAA AATAA-A AATAAA AATAAA
17425389 AATAAA AATAAA A
1 AATAAA AATAAA A
17425402 TGAAGAGAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
5 2 0.04
6 28 0.58
7 11 0.23
8 7 0.15
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (6 bp):
AATAAA
Found at i:17425754 original size:42 final size:41
Alignment explanation
Indices: 17425622--17426084 Score: 638
Period size: 42 Copynumber: 11.1 Consensus size: 41
17425612 TTTGACCAAA
* * *
17425622 GCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAA-GTAAATT
*
17425665 GCTCCTCTAAACAAAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
17425706 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATT
* * * *
17425748 GCTCCTCTAAATAGAGGTACCACAACTTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
*
17425790 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
17425831 GCTCCTCTAAATAGAGGCACCACGACTTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
* * * *
17425873 GCTCCTCTAAATAGAGGCACCATGACTTTTGAAAAATAATTT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
*
17425915 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
17425956 GCTCCTCTAAACAGAGGCACCACAACTTTGGAAAAGTGAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
* *
17425998 GCTCCTCTAAACAGAGGGACCACGACTTTGGAAAATTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
* * *
17426040 GTTCCTTTAAACAGAGGCATCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
17426082 GCT
1 GCT
17426085 TCTTAACAAT
Statistics
Matches: 379, Mismatches: 37, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
41 115 0.30
42 232 0.61
43 32 0.08
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:17425824 original size:83 final size:82
Alignment explanation
Indices: 17425622--17426084 Score: 638
Period size: 83 Copynumber: 5.5 Consensus size: 82
17425612 TTTGACCAAA
* * * *
17425622 GCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACATAAATTGCTCCTCTAAACAAAGGCACCA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAA-GTAAATTGCTCCTCTAAACAGAGGCACCA
*
17425687 CGACTTTGAAAAGTAAATT
64 CGACTTTGGAAAGTAAATT
* *
17425706 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCTCCTCTAAATAGAGGTACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
17425771 AACTTTTGGAAAGTAAATT
65 GAC-TTTGGAAAGTAAATT
* *
17425790 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATAGCTCCTCTAAATAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
17425855 ACTTTTGGAAAGTAAATT
66 AC-TTTGGAAAGTAAATT
* * * *
17425873 GCTCCTCTAAATAGAGGCACCATGACTTTTGAAAAATAATTTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
* *
17425938 GACTTTGAAAAATAAATT
65 GACTTTGGAAAGTAAATT
* * *
17425956 GCTCCTCTAAACAGAGGCACCACAACTTTGGAAAAGTGAATTGCTCCTCTAAACAGAGGGACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
17426021 GACTTTGGAAAATTAAATT
65 GACTTTGG-AAAGTAAATT
* * *
17426040 GTTCCTTTAAACAGAGGCATCACGACTTTGGAAAAGTAAATTGCT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCT
17426085 TCTTAACAAT
Statistics
Matches: 341, Mismatches: 33, Indels: 10
0.89 0.09 0.03
Matches are distributed among these distances:
82 3 0.01
83 176 0.52
84 161 0.47
85 1 0.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (82 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
ACTTTGGAAAGTAAATT
Found at i:17425847 original size:125 final size:124
Alignment explanation
Indices: 17425622--17426084 Score: 660
Period size: 125 Copynumber: 3.7 Consensus size: 124
17425612 TTTGACCAAA
* * * *
17425622 GCTCCTCTAAACAGAGGCTCAACGAC-TTTGAGAAACATAAATTGCTCCTCTAAACAAAGGCACC
1 GCTCCTCTAAATAGAGGCACCACGACTTTTG-GAAA-ATAAATTGCTCCTCTAAACAGAGGCACC
17425686 ACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATT
64 ACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATT
* * *
17425748 GCTCCTCTAAATAGAGGTACCACAACTTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAATAGAGGCACCACGACTTTTGGAAAATAAATTGCTCCTCTAAACAGAGGCACCAC
* * *
17425813 GACTTTGAAAAGTAAATAGCTCCTCTAAATAGAGGCACCACGACTTTTGGAAAGTAAATT
66 GACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
* * *
17425873 GCTCCTCTAAATAGAGGCACCATGACTTTTGAAAAATAATTTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAATAGAGGCACCACGACTTTTGGAAAATAAATTGCTCCTCTAAACAGAGGCACCAC
* * *
17425938 GACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTGGAAAAGTGAATT
66 GACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
* * * * *
17425998 GCTCCTCTAAACAGAGGGACCACGAC-TTTGGAAAATTAAATTGTTCCTTTAAACAGAGGCATCA
1 GCTCCTCTAAATAGAGGCACCACGACTTTTGGAAAA-TAAATTGCTCCTCTAAACAGAGGCACCA
17426062 CGACTTTGGAAAAGTAAATTGCT
65 CGACTTT-GAAAAGTAAATTGCT
17426085 TCTTAACAAT
Statistics
Matches: 301, Mismatches: 31, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
124 11 0.04
125 243 0.81
126 43 0.14
127 4 0.01
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (124 bp):
GCTCCTCTAAATAGAGGCACCACGACTTTTGGAAAATAAATTGCTCCTCTAAACAGAGGCACCAC
GACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:17427362 original size:11 final size:10
Alignment explanation
Indices: 17427346--17427414 Score: 88
Period size: 10 Copynumber: 6.9 Consensus size: 10
17427336 TTTGAATCTT
17427346 TTTTTTTTTC
1 TTTTTTTTTC
*
17427356 -ATTTTTTTC
1 TTTTTTTTTC
*
17427365 -ATTTTTTTC
1 TTTTTTTTTC
17427374 TTCTTTTTTTC
1 TT-TTTTTTTC
17427385 TTTTTTTTTTC
1 -TTTTTTTTTC
17427396 TTTTTTTTTC
1 TTTTTTTTTC
17427406 TTTTTTTTT
1 TTTTTTTTT
17427415 TCATCATCTT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
9 17 0.31
10 19 0.35
11 16 0.30
12 2 0.04
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:17427369 original size:21 final size:20
Alignment explanation
Indices: 17427345--17427418 Score: 105
Period size: 21 Copynumber: 3.6 Consensus size: 20
17427335 ATTTGAATCT
17427345 TTTTTTTTTTCATTTTTTTC
1 TTTTTTTTTTCATTTTTTTC
*
17427365 ATTTTTTTCTTC-TTTTTTTC
1 -TTTTTTTTTTCATTTTTTTC
*
17427385 TTTTTTTTTTCTTTTTTTTTC
1 TTTTTTTTTTC-ATTTTTTTC
17427406 TTTTTTTTTTCAT
1 TTTTTTTTTTCAT
17427419 CATCTTTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.21
20 9 0.19
21 29 0.60
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTTTTTTCATTTTTTTC
Found at i:17427380 original size:29 final size:28
Alignment explanation
Indices: 17427346--17427414 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 28
17427336 TTTGAATCTT
17427346 TTTTTTTTTCATTTTTTTC-ATTTTTTTC
1 TTTTTTTTTC-TTTTTTTCTATTTTTTTC
*
17427374 TTCTTTTTTTCTTTTTTTTTTCTTTTTTTTTC
1 TT-TTTTTTTC---TTTTTTTCTATTTTTTTC
17427406 TTTTTTTTT
1 TTTTTTTTT
17427415 TCATCATCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 2 0.06
29 8 0.23
31 15 0.43
32 10 0.29
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (28 bp):
TTTTTTTTTCTTTTTTTCTATTTTTTTC
Found at i:17427388 original size:27 final size:27
Alignment explanation
Indices: 17427344--17427443 Score: 89
Period size: 28 Copynumber: 3.7 Consensus size: 27
17427334 AATTTGAATC
**
17427344 TTTTTT-TTTTTCATTTTTTTCAT-TT
1 TTTTTTCTTTTTTTTTTTTTTCATCTT
**
17427369 TTTTCTTCTTTTTTTCTTTTTTTTTTCTT
1 TTTT-TTCTTTTTTT-TTTTTTTCATCTT
**
17427398 TTTTTT-TCTTTTTTTTTTCATCATCTT
1 TTTTTTCT-TTTTTTTTTTTTTCATCTT
17427425 TTTTTCTCTTTTTTTTTTT
1 TTTTT-TCTTTTTTTTTTT
17427444 CTCATTTTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
25 4 0.07
26 2 0.03
27 20 0.33
28 27 0.45
29 7 0.12
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (27 bp):
TTTTTTCTTTTTTTTTTTTTTCATCTT
Found at i:17427415 original size:11 final size:11
Alignment explanation
Indices: 17427366--17427442 Score: 93
Period size: 11 Copynumber: 6.6 Consensus size: 11
17427356 ATTTTTTTCA
*
17427366 TTTTTTTCTTC
1 TTTTTTTCTTT
17427377 TTTTTTTCTTT
1 TTTTTTTCTTT
17427388 TTTTTTTC-TT
1 TTTTTTTCTTT
17427398 TTTTTTTCTTT
1 TTTTTTTCTTT
17427409 TTTTTTTCATCATCT
1 TTTTTTTC-T--T-T
17427424 TTTTTTCTCTTT
1 TTTTTT-TCTTT
17427436 TTTTTTT
1 TTTTTTT
17427443 TCTCATTTTT
Statistics
Matches: 59, Mismatches: 1, Indels: 12
0.82 0.01 0.17
Matches are distributed among these distances:
10 10 0.17
11 29 0.49
12 8 0.14
13 1 0.02
14 1 0.02
15 8 0.14
16 2 0.03
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:17427429 original size:1 final size:1
Alignment explanation
Indices: 17427344--17427415 Score: 63
Period size: 1 Copynumber: 72.0 Consensus size: 1
17427334 AATTTGAATC
** ** * * * * *
17427344 TTTTTTTTTTTCATTTTTTTCATTTTTTTCTTCTTTTTTTCTTTTTTTTTTCTTTTTTTTTCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
17427409 TTTTTTT
1 TTTTTTT
17427416 CATCATCTTT
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:17427452 original size:11 final size:11
Alignment explanation
Indices: 17427346--17427439 Score: 63
Period size: 10 Copynumber: 8.6 Consensus size: 11
17427336 TTTGAATCTT
*
17427346 TTTTTTTTTCA
1 TTTTTTTCTCA
17427357 -TTTTTT-TCA
1 TTTTTTTCTCA
17427366 TTTTTTTCTTC-
1 TTTTTTTC-TCA
**
17427377 TTTTTTTCTTT
1 TTTTTTTCTCA
*
17427388 TTTTTTTCT-T
1 TTTTTTTCTCA
**
17427398 TTTTTTTCTTT
1 TTTTTTTCTCA
17427409 TTTTTTTCATCA
1 TTTTTTTC-TCA
17427421 TCTTTTTTTCTC-
1 --TTTTTTTCTCA
17427433 TTTTTTT
1 TTTTTTT
17427440 TTTTCTCATT
Statistics
Matches: 72, Mismatches: 3, Indels: 17
0.78 0.03 0.18
Matches are distributed among these distances:
9 3 0.04
10 30 0.42
11 26 0.36
12 3 0.04
13 2 0.03
14 8 0.11
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTTCTCA
Found at i:17431600 original size:59 final size:59
Alignment explanation
Indices: 17431350--17431972 Score: 749
Period size: 59 Copynumber: 10.4 Consensus size: 59
17431340 TTGTGTAGGT
* * * *
17431350 AAAATTGATACTTTCAACTTTTCCC-CAAAATATTTTTTAGGAAGTTTTTAATTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTT-GGAAATTTTGATTTTCAAGG
* * * * * *
17431409 AATAATTGATATTTTTCAACTTTTCCTCAAAAAAAAACTTTTTCTTGAACAATTT-ATTTTTAAG
1 AA-AATTGATA-CTTTCAACTTTTCC-C-TAAAAATA-TTTTT-TGGAA-ATTTTGATTTTCAAG
*
17431473 A
59 G
* * * * *
17431474 AAAATTGGATACTTTCAACATTTTCCCCAAAAATGTTTTTTTTTGAAAATTTGATTTTTTAAGG
1 AAAATT-GATACTTTCAAC-TTTTCCCTAAAAA--TATTTTTTGGAAATTTTGA-TTTTCAAGG
* * *
17431538 AAAATTGATACTTTCAGCTTTTCCCTAAAAATATCTTTTGGAGATTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTTGATTTTCAAGG
* * * *
17431597 AAAATTGATACTTTCAACTTTT-CCTCAAAAATCCTTTTTT-GAAAATTT-ATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCCT-AAAAAT-ATTTTTTGGAAATTTTGATTTTCAAGG
*
17431655 AAAATTGATACTTTCAAC-TTTCCCTAAAAATATTTTTTGGAGATTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTTGATTTTCAAGG
17431713 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATA--TTTTTTGGAAATTTTGATTTTCAAGG
17431774 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTTGATTTTCAAGG
** * * *
17431833 AAAATTGATACTTTCAACTTTT-CCTCAAAAACCCTTTTTTTGAAATTTT-ATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCCT-AAAAA-TATTTTTTGGAAATTTTGATTTTCAAGG
*
17431892 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTTGATTTTGAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTTGATTTTCAAGG
17431951 AAAATTGATACTTTCAACTTTT
1 AAAATTGATACTTTCAACTTTT
17431973 TCTCAAAAAC
Statistics
Matches: 493, Mismatches: 45, Indels: 52
0.84 0.08 0.09
Matches are distributed among these distances:
56 6 0.01
57 15 0.03
58 75 0.15
59 175 0.35
60 44 0.09
61 71 0.14
62 18 0.04
63 22 0.04
64 36 0.07
65 27 0.05
66 4 0.01
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTTGATTTTCAAGG
Found at i:17431784 original size:236 final size:239
Alignment explanation
Indices: 17431350--17431981 Score: 857
Period size: 236 Copynumber: 2.6 Consensus size: 239
17431340 TTGTGTAGGT
* * * *
17431350 AAAATTGATACTTTCAACTTTTCCCCAAAATA---TTTTTTAGGAAGTTT-TTAATTTCAAGGAA
1 AAAATTGATACTTTCAACTTTTCCTCAAAA-ACCCTTTTTTTGAAAATTTATT--TTT-AA-GAA
* * * * * * * *
17431411 TAATTGATATTTTTCAACTTTTCCTCAAAAAAAAACTTTTTCTTGAACAATTT-ATTTTTAAGAA
61 AAATTGATA-CTTTCAACTTTTCC-C-TAAAAATA-TTTTT-TGGAA-ATTTTGATTTTCAAGGA
* * *
17431475 AAATTGGATACTTTCAACATTTTCCCCAAAAATGTTTTTTTTTGAAAATTTGATTTTTTAAGGAA
120 AAATT-GATACTTTCAAC-TTTTCCCCAAAAATATTTTTTTTGGAAAATTTGATTTTTCAAGGAA
* *
17431540 AATTGATACTTTCAGCTTTTCCCTAAAAATATCTTTTGGAGATTTTGATTTTCAAGG
183 AATTGATACTTTCAACTTTTCCCTAAAAATATCTTTTGGAAATTTTGATTTTCAAGG
*
17431597 AAAATTGATACTTTCAACTTTTCCTCAAAAATCC-TTTTTTGAAAATTTATTTTTAAGAAAAATT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTATTTTTAAGAAAAATT
*
17431661 GATACTTTCAAC-TTTCCCTAAAAATATTTTTTGGAGATTTTGATTTTCAAGGAAAATTGATACT
66 GATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTTGATTTTCAAGGAAAATTGATACT
* *
17431725 TTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTTGA-TTTTCAAGGAAAATTGATACTTTC
131 TTCAACTTTTCCCCAAAAATATTTTTTTTGGAAAATTTGATTTTTCAAGGAAAATTGATACTTTC
*
17431789 AACTTTTCCCTAAAAATATTTTTTGGAAATTTTGATTTTCAAGG
196 AACTTTTCCCTAAAAATATCTTTTGGAAATTTTGATTTTCAAGG
*
17431833 AAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAATTTTATTTTTAAGAAAAATT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTATTTTTAAGAAAAATT
*
17431898 GATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTTGATTTTGAAGGAAAATTGATACT
66 GATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTTGATTTTCAAGGAAAATTGATACT
* *
17431963 TTCAACTTTTTCTCAAAAA
131 TTCAACTTTTCCCCAAAAA
17431982 CGCCTTTTTT
Statistics
Matches: 350, Mismatches: 28, Indels: 23
0.87 0.07 0.06
Matches are distributed among these distances:
236 97 0.28
237 71 0.20
238 82 0.23
239 17 0.05
240 5 0.01
241 6 0.02
242 1 0.00
243 5 0.01
244 7 0.02
245 11 0.03
246 3 0.01
247 32 0.09
248 11 0.03
249 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (239 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTATTTTTAAGAAAAATT
GATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTTGATTTTCAAGGAAAATTGATACT
TTCAACTTTTCCCCAAAAATATTTTTTTTGGAAAATTTGATTTTTCAAGGAAAATTGATACTTTC
AACTTTTCCCTAAAAATATCTTTTGGAAATTTTGATTTTCAAGG
Found at i:17432022 original size:5 final size:5
Alignment explanation
Indices: 17432014--17432101 Score: 60
Period size: 5 Copynumber: 17.8 Consensus size: 5
17432004 TTAAAAGAAA
* * *
17432014 AAAAT AAAAC AAAAT AAAAGT GAGA- AAAA- AAAAT AAAAT -AAAT -AAAT
1 AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* *
17432061 -AAAT AAAAG AAAGT AAAAAT AAAAAT AAAAT AAATAT AAAA
1 AAAAT AAAAT AAAAT -AAAAT -AAAAT AAAAT AAA-AT AAAA
17432102 AGAATATTAA
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
4 18 0.26
5 32 0.47
6 18 0.26
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:17432077 original size:22 final size:22
Alignment explanation
Indices: 17432013--17432102 Score: 74
Period size: 22 Copynumber: 4.0 Consensus size: 22
17432003 TTTAAAAGAA
* *
17432013 AAAAATAAAACAAAATAAAAGT
1 AAAAATAAAAGAAAATAAAAAT
* *
17432035 GAGAAAAAAAAATAAAATAAATAA-
1 -A-AAAATAAAAGAAAATAAA-AAT
* *
17432059 ATAAATAAAAGAAAGTAAAAAT
1 AAAAATAAAAGAAAATAAAAAT
*
17432081 AAAAATAAAATAAATATAAAAA
1 AAAAATAAAAGAAA-ATAAAAA
17432103 GAATATTAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
21 2 0.04
22 26 0.49
23 8 0.15
24 16 0.30
25 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.16
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAAAAAT
Found at i:17432164 original size:11 final size:11
Alignment explanation
Indices: 17432050--17432164 Score: 58
Period size: 11 Copynumber: 10.0 Consensus size: 11
17432040 AAAAAAATAA
17432050 AATAAATAAAT
1 AATAAATAAAT
*
17432061 AAATAAAAGAAAGT
1 -AAT-AAATAAA-T
17432075 AA-AAATAAA-
1 AATAAATAAAT
17432084 AATAAAATAAAT
1 AAT-AAATAAAT
*
17432096 -ATAAAAAGAAT
1 AATAAATA-AAT
*
17432107 ATTAAATAAACCT
1 AATAAATAAA--T
*
17432120 AATCTAATAAAT
1 AAT-AAATAAAT
* *
17432132 AAAAAACAAAT
1 AATAAATAAAT
*
17432143 AA-AATAAAAAT
1 AATAA-ATAAAT
17432154 AATAAATAAAT
1 AATAAATAAAT
17432165 TCAAAAAAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 25
0.68 0.10 0.22
Matches are distributed among these distances:
9 2 0.03
10 6 0.08
11 40 0.51
12 13 0.16
13 11 0.14
14 7 0.09
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:17433196 original size:41 final size:43
Alignment explanation
Indices: 17433151--17433243 Score: 138
Period size: 41 Copynumber: 2.2 Consensus size: 43
17433141 ATATATACAT
* *
17433151 AAAAAAATAATAATAATAATAAAGATAAAAA-AAAATGTAA-A-
1 AAAAAAATAATAATAAAAATAAAAATAAAAATAAAATG-AAGAG
17433192 AAAAAAATAATAATAAAAATAAAAATAAAAATAAAATGAAGAG
1 AAAAAAATAATAATAAAAATAAAAATAAAAATAAAATGAAGAG
17433235 AAAAAAATA
1 AAAAAAATA
17433244 TATATAGACT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 31 0.66
42 7 0.15
43 9 0.19
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.17
Consensus pattern (43 bp):
AAAAAAATAATAATAAAAATAAAAATAAAAATAAAATGAAGAG
Found at i:17433198 original size:6 final size:6
Alignment explanation
Indices: 17433153--17433227 Score: 82
Period size: 6 Copynumber: 12.7 Consensus size: 6
17433143 ATATACATAA
* * * *
17433153 AAAAAT AATAAT AATAAT AAAGAT AAAAA- AAAATGT AAAAA- AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA-AT AAAAAT AAAAAT
*
17433200 AATAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
17433228 TGAAGAGAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
5 9 0.16
6 45 0.78
7 4 0.07
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.19
Consensus pattern (6 bp):
AAAAAT
Found at i:17434014 original size:2 final size:2
Alignment explanation
Indices: 17434009--17434043 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
17433999 GTGCGTGTTT
17434009 TA 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 TA T
17434044 TCTAAGAGAT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17435578 original size:24 final size:24
Alignment explanation
Indices: 17435550--17435598 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
17435540 TTGAAAAATT
17435550 AATATTAATGTTAATTTGCGAATA
1 AATATTAATGTTAATTTGCGAATA
*
17435574 AATATTAATGTTAATTTGCGGATA
1 AATATTAATGTTAATTTGCGAATA
17435598 A
1 A
17435599 TTTTAAACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.14, T:0.41
Consensus pattern (24 bp):
AATATTAATGTTAATTTGCGAATA
Found at i:17435955 original size:17 final size:17
Alignment explanation
Indices: 17435933--17435966 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
17435923 TTATTAATTA
17435933 GAAATTAA-AAAATAAAT
1 GAAATTAACAAAA-AAAT
17435950 GAAATTAACAAAAAAAT
1 GAAATTAACAAAAAAAT
17435967 TTTGGATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21
Consensus pattern (17 bp):
GAAATTAACAAAAAAAT
Found at i:17436236 original size:2 final size:2
Alignment explanation
Indices: 17436229--17436261 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17436219 TTCTTTACTA
17436229 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
17436262 GACACACACA
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:17436502 original size:14 final size:14
Alignment explanation
Indices: 17436464--17436504 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
17436454 TAAAATCAAA
* *
17436464 ATTTATTTAATAAA
1 ATTTATTTAATTAT
17436478 ATTTA-TT-ATTAT
1 ATTTATTTAATTAT
17436490 ATTTATTTAATTAT
1 ATTTATTTAATTAT
17436504 A
1 A
17436505 CAAAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 8 0.35
13 4 0.17
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTATTTAATTAT
Found at i:17441347 original size:26 final size:24
Alignment explanation
Indices: 17441301--17441353 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
17441291 AAGAAAATTA
* *
17441301 TTTTTATTTATTTTTCTTGAGTTT
1 TTTTTATTTATTTTTCATGAGATT
*
17441325 TTTTTTTTTATTTTGATCATGAGATT
1 TTTTTATTTATTTT--TCATGAGATT
17441351 TTT
1 TTT
17441354 CATTTTGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 13 0.54
26 11 0.46
ACGTcount: A:0.15, C:0.04, G:0.09, T:0.72
Consensus pattern (24 bp):
TTTTTATTTATTTTTCATGAGATT
Found at i:17443157 original size:15 final size:16
Alignment explanation
Indices: 17443131--17443160 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17443121 ATATTAAAAG
17443131 TTTTATAATATTTTAA
1 TTTTATAATATTTTAA
17443147 TTTTA-AATATTTTA
1 TTTTATAATATTTTA
17443161 TAATTCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTATAATATTTTAA
Found at i:17443635 original size:22 final size:22
Alignment explanation
Indices: 17443567--17443637 Score: 56
Period size: 22 Copynumber: 3.1 Consensus size: 22
17443557 AAATATATAA
* *
17443567 ATAATATATTTAATATAATTTAAT
1 ATAAT-TATTTAATATTA-TAAAT
*
17443591 AATAAATACTTTCAAT-TTA-AAAT
1 -ATAATTA-TTT-AATATTATAAAT
17443614 ATAATTATTTAATATTATAAAT
1 ATAATTATTTAATATTATAAAT
17443636 AT
1 AT
17443638 TTTTAATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
20 3 0.08
21 6 0.16
22 12 0.32
23 3 0.08
24 2 0.05
25 9 0.24
26 3 0.08
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (22 bp):
ATAATTATTTAATATTATAAAT
Found at i:17443821 original size:15 final size:15
Alignment explanation
Indices: 17443745--17443839 Score: 55
Period size: 15 Copynumber: 5.6 Consensus size: 15
17443735 TAGTTTTAGT
17443745 TTTTAATATTAATATAA
1 TTTTAATATTAAT-T-A
17443762 TATTATAATATTAAATATTA
1 T-TT-TAATATT--A-ATTA
*
17443782 TTATTAAAATCTAATTAA
1 TT-TTAATAT-TAATT-A
17443800 TTTTTAATATTAATTA
1 -TTTTAATATTAATTA
* *
17443816 TTTTAATAATAAATA
1 TTTTAATATTAATTA
*
17443831 ATTTAATAT
1 TTTTAATAT
17443840 ATTTTAATAA
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
15 20 0.32
16 1 0.02
17 9 0.14
18 10 0.16
19 15 0.24
20 4 0.06
21 2 0.03
22 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTTAATATTAATTA
Found at i:17443830 original size:22 final size:21
Alignment explanation
Indices: 17443804--17443868 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 21
17443794 AATTAATTTT
17443804 TAATATTAATTATTTTAATAA
1 TAATATTAATTATTTTAATAA
17443825 TAAATAATTTAATATATTTTAATAA
1 T-AAT-A-TTAAT-TATTTTAATAA
* *
17443850 TTATATAAAATTATTTTAA
1 TAATAT-TAATTATTTTAA
17443869 CAAAAATCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
21 1 0.03
22 12 0.32
23 5 0.14
24 7 0.19
25 12 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATATTAATTATTTTAATAA
Found at i:17445726 original size:16 final size:16
Alignment explanation
Indices: 17445705--17445745 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
17445695 TTTTGAAGAA
*
17445705 TTTAAAATGAGGAT-AT
1 TTTAAAATGA-CATCAT
17445721 TTTAAAAT-ACATCAT
1 TTTAAAATGACATCAT
17445736 TTTAAAATGA
1 TTTAAAATGA
17445746 TTGAATTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.09
15 11 0.50
16 9 0.41
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (16 bp):
TTTAAAATGACATCAT
Found at i:17449349 original size:2 final size:2
Alignment explanation
Indices: 17449330--17449367 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
17449320 TCAAAGTGTC
* *
17449330 TA TA TT TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17449368 CACTCACACC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:17456131 original size:9 final size:8
Alignment explanation
Indices: 17456114--17456140 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
17456104 TCAAATGCTC
17456114 AATAAAAA
1 AATAAAAA
17456122 AATAAAAA
1 AATAAAAA
17456130 AATAAAAA
1 AATAAAAA
17456138 AAT
1 AAT
17456141 GCCTTATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
AATAAAAA
Found at i:17460009 original size:16 final size:16
Alignment explanation
Indices: 17459985--17460023 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
17459975 ACCAACTATT
*
17459985 TATTATAAAAAATAAA
1 TATTTTAAAAAATAAA
* *
17460001 TATTTTAAAAATTATA
1 TATTTTAAAAAATAAA
17460017 TATTTTA
1 TATTTTA
17460024 TCTCGCCAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATTTTAAAAAATAAA
Found at i:17465547 original size:4 final size:4
Alignment explanation
Indices: 17465532--17465748 Score: 51
Period size: 4 Copynumber: 52.0 Consensus size: 4
17465522 ATTTAGTAAT
* *
17465532 ATTA ATTTA ATTA ATTA TACTTT ATT- ATTA TATTA ATTAA ATACA ATTA
1 ATTA A-TTA ATTA ATTA -A-TTA ATTA ATTA -ATTA ATT-A AT-TA ATTA
* * * * * *
17465581 AATA ATTA CTT- ATTG ATTA ATTA GTATTA GTTA AATA A-TA TTTA A-TA
1 ATTA ATTA ATTA ATTA ATTA ATTA --ATTA ATTA ATTA ATTA ATTA ATTA
* * **
17465628 ATATT ATT- ATTA ATTTA ATTA A-T- ATTA ATATC A-TA A-TA ATTA AGAA
1 AT-TA ATTA ATTA A-TTA ATTA ATTA ATTA AT-TA ATTA ATTA ATTA ATTA
* *
17465674 ATGTC ATTA ATTAA ATTA ATTA GTATTCAA ATTA ATTA AAT- ATTA ATTA
1 AT-TA ATTA ATT-A ATTA ATTA --ATT--A ATTA ATTA ATTA ATTA ATTA
17465723 ATTA A-TA ATATCA ATTA ACTTA ATTA
1 ATTA ATTA AT-T-A ATTA A-TTA ATTA
17465749 TATTTCAAAT
Statistics
Matches: 159, Mismatches: 24, Indels: 60
0.65 0.10 0.25
Matches are distributed among these distances:
2 1 0.01
3 25 0.16
4 80 0.50
5 37 0.23
6 15 0.09
8 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (4 bp):
ATTA
Found at i:17465799 original size:53 final size:53
Alignment explanation
Indices: 17465679--17465892 Score: 147
Period size: 53 Copynumber: 3.9 Consensus size: 53
17465669 AAGAAATGTC
* *
17465679 ATTAATTAAATTAATTAGTA-TTCAAATTAATTA-AATATTAATT-AATTAATA
1 ATTAATTAAATTAATTA-TATTTCAAATTAAATATAATTTTAATTAAATTAATA
* *
17465730 ATATCAATTAACTTAATTATATTTCAAATTAAATATAATTTTTATTAAATT-ATA
1 AT-T-AATTAAATTAATTATATTTCAAATTAAATATAATTTTAATTAAATTAATA
* * ** *
17465784 ATTAATAAATATTAATTGTAATTATCTAATCATTTTATATTAATTATAATTAAATTAATA
1 ATTAATTAA-ATTAATTAT-ATT-TC-AA--ATTAAATA-TAATTTTAATTAAATTAATA
* * *
17465844 A--AA-TAATATCAATTAAATTT-AAATTAAATATCATTTTTATATTAAATTA
1 ATTAATTAA-ATTAATTATATTTCAAATTAAATAT-AATTTTA-ATTAAATTA
17465893 TATTTATTTT
Statistics
Matches: 129, Mismatches: 19, Indels: 29
0.73 0.11 0.16
Matches are distributed among these distances:
50 1 0.01
51 13 0.10
52 17 0.13
53 35 0.27
54 16 0.12
55 7 0.05
56 5 0.04
57 9 0.07
58 8 0.06
59 14 0.11
60 4 0.03
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.47
Consensus pattern (53 bp):
ATTAATTAAATTAATTATATTTCAAATTAAATATAATTTTAATTAAATTAATA
Found at i:17470932 original size:167 final size:167
Alignment explanation
Indices: 17470736--17471070 Score: 616
Period size: 167 Copynumber: 2.0 Consensus size: 167
17470726 ATTTCACCAT
*
17470736 CATAATTAAAAACAAAGAAACAGAAAGGCAATCCATTCACCAATCAAGTCCTATTAATTAATTAG
1 CATAATTAAAAACAAAGAAACAGAAAGGCAATCCATTCACCAATCAAGTCCCATTAATTAATTAG
*
17470801 TAAACCCTAATTCTAGAAGAAATTGAAACTTGATCAGGCAGTTCTTGAACTCTTTCACTTGTTTT
66 TAAACCCTAATTCTAGAAGAAATCGAAACTTGATCAGGCAGTTCTTGAACTCTTTCACTTGTTTT
17470866 TCCTGAAAGATATAAGAACTGGATATATGTTCTTAAA
131 TCCTGAAAGATATAAGAACTGGATATATGTTCTTAAA
*
17470903 CATAATTAAAAACAAAGAAACAGAAAGGCAATTCATTCACCAATCAAGTCCCATTAATTAATTAG
1 CATAATTAAAAACAAAGAAACAGAAAGGCAATCCATTCACCAATCAAGTCCCATTAATTAATTAG
*
17470968 TAAACCCTAATTCTAGAAGAAATCGAAACTTGATCAGGCAGTTCTTGGACTCTTTCACTTGTTTT
66 TAAACCCTAATTCTAGAAGAAATCGAAACTTGATCAGGCAGTTCTTGAACTCTTTCACTTGTTTT
* *
17471033 TCCTGATAGATATAAGAACTGGATATATTTTCTTAAA
131 TCCTGAAAGATATAAGAACTGGATATATGTTCTTAAA
17471070 C
1 C
17471071 GCTTCAAAAT
Statistics
Matches: 162, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
167 162 1.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (167 bp):
CATAATTAAAAACAAAGAAACAGAAAGGCAATCCATTCACCAATCAAGTCCCATTAATTAATTAG
TAAACCCTAATTCTAGAAGAAATCGAAACTTGATCAGGCAGTTCTTGAACTCTTTCACTTGTTTT
TCCTGAAAGATATAAGAACTGGATATATGTTCTTAAA
Found at i:17472987 original size:20 final size:20
Alignment explanation
Indices: 17472949--17472987 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17472939 TATAGCTTTG
*
17472949 GTTCTTCAATGTAAACTGTA
1 GTTCTTCAATGCAAACTGTA
*
17472969 GTTCTTCAATGCAATCTGT
1 GTTCTTCAATGCAAACTGT
17472988 GGGATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (20 bp):
GTTCTTCAATGCAAACTGTA
Found at i:17478861 original size:20 final size:20
Alignment explanation
Indices: 17478824--17478859 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17478814 AATGTATCCA
17478824 ATTAAAATAGATATTTTTAT
1 ATTAAAATAGATATTTTTAT
17478844 ATTAAAAT-G-TATTTTT
1 ATTAAAATAGATATTTTT
17478860 TTTATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.44
19 1 0.06
20 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (20 bp):
ATTAAAATAGATATTTTTAT
Found at i:17479030 original size:34 final size:34
Alignment explanation
Indices: 17478992--17479059 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
17478982 AAATTAAAAA
* *
17478992 TAAACTAAGTTAATGTTACGAATAGTTTTTTTTT
1 TAAACTAAGTTAATGTTACAAATAGCTTTTTTTT
17479026 TAAACTAAGTTAATGTTACAAATAGCTTTTTTTT
1 TAAACTAAGTTAATGTTACAAATAGCTTTTTTTT
17479060 ATTATATCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (34 bp):
TAAACTAAGTTAATGTTACAAATAGCTTTTTTTT
Found at i:17479555 original size:15 final size:15
Alignment explanation
Indices: 17479535--17479572 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
17479525 GTTTGGATTG
*
17479535 AAGGAAAGGAAAAGA
1 AAGGAAAGAAAAAGA
*
17479550 AAGGAAAGAAAAATA
1 AAGGAAAGAAAAAGA
17479565 AAGGAAAG
1 AAGGAAAG
17479573 TAATGGAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (15 bp):
AAGGAAAGAAAAAGA
Found at i:17479580 original size:25 final size:25
Alignment explanation
Indices: 17479539--17479587 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
17479529 GGATTGAAGG
*
17479539 AAAGGAAAAGAAAGGAAAGAAAAAT
1 AAAGGAAAAGAAAGGAAACAAAAAT
*
17479564 AAAGG-AAAGTAATGGAAACAAAAA
1 AAAGGAAAAG-AAAGGAAACAAAAA
17479588 AAGCATTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.69, C:0.02, G:0.22, T:0.06
Consensus pattern (25 bp):
AAAGGAAAAGAAAGGAAACAAAAAT
Found at i:17483234 original size:4 final size:4
Alignment explanation
Indices: 17483225--17483249 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
17483215 TAAATGGCTA
17483225 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
17483250 TAGAGTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:17486992 original size:41 final size:41
Alignment explanation
Indices: 17486928--17487012 Score: 134
Period size: 41 Copynumber: 2.1 Consensus size: 41
17486918 AAAAGTCAAT
* *
17486928 TATTTCAGTTTGACTTATGAAGCCACCAATGAATATGTGTC
1 TATTTCAGTTTGACTTATCAAGCCACCAATGAACATGTGTC
* *
17486969 TATTTCAGTTTGATTTATCAAGCCACCAATGAACATGTTTC
1 TATTTCAGTTTGACTTATCAAGCCACCAATGAACATGTGTC
17487010 TAT
1 TAT
17487013 GTATTTATGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (41 bp):
TATTTCAGTTTGACTTATCAAGCCACCAATGAACATGTGTC
Found at i:17487035 original size:2 final size:2
Alignment explanation
Indices: 17487030--17487072 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
17487020 TGTGTGTGTG
*
17487030 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17487072 T
1 T
17487073 TTTTGCTAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:17490096 original size:5 final size:5
Alignment explanation
Indices: 17490086--17490141 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
17490076 AATAATTTAA
*
17490086 AATAT AATAT -A-AT AATAT AATAT GAATAT AATA- AA-AT AATAT AAAAAT
1 AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT AATAT -AATAT
17490134 AATAT AAT
1 AATAT AAT
17490142 TTAAAATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
3 3 0.07
4 6 0.14
5 25 0.58
6 9 0.21
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (5 bp):
AATAT
Found at i:17490115 original size:11 final size:10
Alignment explanation
Indices: 17490086--17490141 Score: 57
Period size: 11 Copynumber: 5.8 Consensus size: 10
17490076 AATAATTTAA
17490086 AATATAATAT
1 AATATAATAT
17490096 -A-ATAATAT
1 AATATAATAT
17490104 AATATGAATAT
1 AATAT-AATAT
17490115 AATA-AA-AT
1 AATATAATAT
*
17490123 AATATAAAAAT
1 AATAT-AATAT
17490134 AATATAAT
1 AATATAAT
17490142 TTAAAATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
8 13 0.33
9 4 0.10
10 6 0.15
11 16 0.41
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (10 bp):
AATATAATAT
Found at i:17490115 original size:19 final size:18
Alignment explanation
Indices: 17490086--17490141 Score: 80
Period size: 19 Copynumber: 3.2 Consensus size: 18
17490076 AATAATTTAA
17490086 AATATAATATAATAATAT
1 AATATAATATAATAATAT
*
17490104 AATATGAATATAATAAAAT
1 AATAT-AATATAATAATAT
17490123 AATATAA-A-AATAATAT
1 AATATAATATAATAATAT
17490139 AAT
1 AAT
17490142 TTAAAATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 10 0.29
17 1 0.03
18 7 0.20
19 17 0.49
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
AATATAATATAATAATAT
Found at i:17490137 original size:24 final size:24
Alignment explanation
Indices: 17490086--17490141 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
17490076 AATAATTTAA
* *
17490086 AATATAATATAATAATATAATATG
1 AATATAATAAAATAATATAAAATG
17490110 AATATAATAAAATAATATAAAAAT-
1 AATATAATAAAATAATAT-AAAATG
17490134 AATATAAT
1 AATATAAT
17490142 TTAAAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (24 bp):
AATATAATAAAATAATATAAAATG
Found at i:17490279 original size:32 final size:32
Alignment explanation
Indices: 17490243--17490325 Score: 98
Period size: 30 Copynumber: 2.7 Consensus size: 32
17490233 TTTATTTACA
*
17490243 ACATGATATAAATACATGAATTTTAATATTTT
1 ACATGATATAAATATATGAATTTTAATATTTT
* * *
17490275 ACATG--ATACATATATAAATTTTGATATTTT
1 ACATGATATAAATATATGAATTTTAATATTTT
* *
17490305 ATATAATATAAATATATGAAT
1 ACATGATATAAATATATGAAT
17490326 CATTAAATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
30 24 0.59
32 17 0.41
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (32 bp):
ACATGATATAAATATATGAATTTTAATATTTT
Found at i:17494855 original size:21 final size:21
Alignment explanation
Indices: 17494825--17494875 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
17494815 ATATTTTTTA
17494825 AATA-TTTATATTTAAAAAAT
1 AATATTTTATATTTAAAAAAT
*
17494845 AATATTTTATATTTTAAAAAT
1 AATATTTTATATTTAAAAAAT
17494866 AATATTTTAT
1 AATATTTTAT
17494876 TAATTTCGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATTTTATATTTAAAAAAT
Found at i:17499925 original size:18 final size:17
Alignment explanation
Indices: 17499891--17499929 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 17
17499881 ATATCTTACG
17499891 TAAATTTTTTAAAAAGA
1 TAAATTTTTTAAAAAGA
17499908 TAAA-TTTTTAAATTAAGA
1 TAAATTTTTTAAA--AAGA
17499926 TAAA
1 TAAA
17499930 AAAGATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.40
17 4 0.20
18 8 0.40
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
TAAATTTTTTAAAAAGA
Found at i:17502730 original size:38 final size:39
Alignment explanation
Indices: 17502676--17502750 Score: 134
Period size: 38 Copynumber: 1.9 Consensus size: 39
17502666 AATCTCACTC
17502676 GAACATAATAGAAATGTCACTGGGGTATAT-AAGGGTGT
1 GAACATAATAGAAATGTCACTGGGGTATATAAAGGGTGT
*
17502714 GAACATAATAGGAATGTCACTGGGGTATATAAAGGGT
1 GAACATAATAGAAATGTCACTGGGGTATATAAAGGGT
17502751 TCACACCACC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 29 0.83
39 6 0.17
ACGTcount: A:0.37, C:0.08, G:0.29, T:0.25
Consensus pattern (39 bp):
GAACATAATAGAAATGTCACTGGGGTATATAAAGGGTGT
Found at i:17502826 original size:24 final size:24
Alignment explanation
Indices: 17502794--17502845 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
17502784 AGGGTGTGAA
17502794 ACGTAGCGGTTAAGCTGATTTGGG
1 ACGTAGCGGTTAAGCTGATTTGGG
17502818 ACGTAGCGGTTAAGCTGATTTGGG
1 ACGTAGCGGTTAAGCTGATTTGGG
17502842 ACGT
1 ACGT
17502846 TGAAAGGGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.21, C:0.13, G:0.37, T:0.29
Consensus pattern (24 bp):
ACGTAGCGGTTAAGCTGATTTGGG
Found at i:17504811 original size:134 final size:136
Alignment explanation
Indices: 17504662--17504935 Score: 516
Period size: 138 Copynumber: 2.0 Consensus size: 136
17504652 CGCAGAATTA
17504662 ATTGAAACTGCAATGCAGATATCTATGCTCCATGATACATACATAC-ATA-TATATATGTATATG
1 ATTGAAACTGCAATGCAGATATCTATGCTCCATGATACATACATACAATAGTATATATGTATATG
17504725 TACTAATTTTATTTTATTTTTACTGTTTTGTACTTTGAACTGACAGATTGAAGCCATTTTAATAT
66 TACTAATTTTATTTTATTTTTACTGTTTTGTACTTTGAACTGACAGATTGAAGCCATTTTAATAT
17504790 GGTCTT
131 GGTCTT
17504796 ATTGAAACTGCAATGCAGATATCTATGCTCCATGATACATACATACATATATGTATATATGTATA
1 ATTGAAACTGCAATGCAGATATCTATGCTCCATGATACATACATACA-ATA-GTATATATGTATA
17504861 TGTACTAATTTTATTTTATTTTTACTGTTTTGTACTTTGAACTGACAGATTGAAGCCATTTTAAT
64 TGTACTAATTTTATTTTATTTTTACTGTTTTGTACTTTGAACTGACAGATTGAAGCCATTTTAAT
17504926 ATGGTCTT
129 ATGGTCTT
17504934 AT
1 AT
17504936 GTGTATCCTA
Statistics
Matches: 136, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
134 46 0.34
136 3 0.02
138 87 0.64
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (136 bp):
ATTGAAACTGCAATGCAGATATCTATGCTCCATGATACATACATACAATAGTATATATGTATATG
TACTAATTTTATTTTATTTTTACTGTTTTGTACTTTGAACTGACAGATTGAAGCCATTTTAATAT
GGTCTT
Found at i:17504961 original size:138 final size:137
Alignment explanation
Indices: 17504685--17505112 Score: 503
Period size: 151 Copynumber: 3.0 Consensus size: 137
17504675 TGCAGATATC
17504685 TATGCTCCATGATACATACATAC--ATA-TATATATGTATATGTACTAATTTTATTTTATTTTTA
1 TATGCTCCATGATACATACATACATATATTATATATGTATATGTACTAATTTTATTTTATTTTTA
* * *
17504747 CTGTTTTGTACTTTGAACTGACAGATTGAAGCCATTTTAATATGGTCTTAT-TGAAACTGCAATG
66 CTGTTTTGTACTTTGAACTGACAGATTGAAGCCATTTTAATATGGTCTTATGTG-TA-TCCTAT-
* *
17504811 CA-G-AT-ATC
128 CATGTTTGA-G
17504819 TATGCTCCATGATACATACATACATATATGTATATATGTATATGTACTAATTTTATTTTATTTTT
1 TATGCTCCATGATACATACATACATATAT-TATATATGTATATGTACTAATTTTATTTTATTTTT
17504884 ACTGTTTTGTACTTTGAACTGACAGATTGAAGCCATTTTAATATGGTCTTATGTGTATCCTATCA
65 ACTGTTTTGTACTTTGAACTGACAGATTGAAGCCATTTTAATATGGTCTTATGTGTATCCTATCA
17504949 TGTTTGAG
130 TGTTTGAG
** * * * *
17504957 TATGC-AAATGAGAGTAGGGAAAATGACCCTATCATTACCATCATATATATGTATGTGTACTAAT
1 TATGCTCCAT--GA-T-----ACAT-A-CATA-CA-TA-TAT--TATATATGTATATGTACTAAT
* *
17505021 TTTATTTTATTTTTACTGTTTTGTACTTTGAACTGACAGATTGGAGCCATTTTTATATGGTCTTA
51 TTTATTTTATTTTTACTGTTTTGTACTTTGAACTGACAGATTGAAGCCATTTTAATATGGTCTTA
17505086 TGTGTATCCTATCATGTTTGAG
116 TGTGTATCCTATCATGTTTGAG
17505108 TATGC
1 TATGC
17505113 AAATAAGAGT
Statistics
Matches: 258, Mismatches: 14, Indels: 27
0.86 0.05 0.09
Matches are distributed among these distances:
134 23 0.09
136 5 0.02
137 7 0.03
138 94 0.36
139 5 0.02
140 1 0.00
145 3 0.01
146 1 0.00
147 3 0.01
148 2 0.01
149 2 0.01
150 2 0.01
151 110 0.43
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (137 bp):
TATGCTCCATGATACATACATACATATATTATATATGTATATGTACTAATTTTATTTTATTTTTA
CTGTTTTGTACTTTGAACTGACAGATTGAAGCCATTTTAATATGGTCTTATGTGTATCCTATCAT
GTTTGAG
Found at i:17505010 original size:151 final size:151
Alignment explanation
Indices: 17504849--17505153 Score: 565
Period size: 151 Copynumber: 2.0 Consensus size: 151
17504839 TACATATATG
17504849 TATATATGTATATGTACTAATTTTATTTTATTTTTACTGTTTTGTACTTTGAACTGACAGATTGA
1 TATATATGTATATGTACTAATTTTATTTTATTTTTACTGTTTTGTACTTTGAACTGACAGATTGA
*
17504914 AGCCATTTTAATATGGTCTTATGTGTATCCTATCATGTTTGAGTATGCAAATGAGAGTAGGGAAA
66 AGCCATTTTAATATGGTCTTATGTGTATCCTATCATGTTTGAGTATGCAAATAAGAGTAGGGAAA
17504979 ATGACCCTATCATTACCATCA
131 ATGACCCTATCATTACCATCA
* *
17505000 TATATATGTATGTGTACTAATTTTATTTTATTTTTACTGTTTTGTACTTTGAACTGACAGATTGG
1 TATATATGTATATGTACTAATTTTATTTTATTTTTACTGTTTTGTACTTTGAACTGACAGATTGA
* *
17505065 AGCCATTTTTATATGGTCTTATGTGTATCCTATCATGTTTGAGTATGCAAATAAGAGTAGGGGAA
66 AGCCATTTTAATATGGTCTTATGTGTATCCTATCATGTTTGAGTATGCAAATAAGAGTAGGGAAA
17505130 ATGACCCTATCATTACCATCA
131 ATGACCCTATCATTACCATCA
17505151 TAT
1 TAT
17505154 CTTCTGGAGA
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
151 149 1.00
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.42
Consensus pattern (151 bp):
TATATATGTATATGTACTAATTTTATTTTATTTTTACTGTTTTGTACTTTGAACTGACAGATTGA
AGCCATTTTAATATGGTCTTATGTGTATCCTATCATGTTTGAGTATGCAAATAAGAGTAGGGAAA
ATGACCCTATCATTACCATCA
Found at i:17505533 original size:2 final size:2
Alignment explanation
Indices: 17505526--17505577 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
17505516 ACTTGTTTTC
* * *
17505526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17505568 AT AT AT AT AT
1 AT AT AT AT AT
17505578 CCCGTTTGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:17507525 original size:2 final size:2
Alignment explanation
Indices: 17507518--17507544 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17507508 TAATTATAAT
17507518 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
17507545 TGTAAGTGGA
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:17514616 original size:11 final size:11
Alignment explanation
Indices: 17514602--17514643 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
17514592 AAATTTTAAG
17514602 TTATATTATTT
1 TTATATTATTT
17514613 TTATA-TATTTT
1 TTATATTA-TTT
*
17514624 TTATGTTATTT
1 TTATATTATTT
17514635 TTATATTAT
1 TTATATTAT
17514644 GTTTGAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 2 0.07
11 23 0.85
12 2 0.07
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (11 bp):
TTATATTATTT
Found at i:17515931 original size:125 final size:125
Alignment explanation
Indices: 17515709--17515960 Score: 479
Period size: 125 Copynumber: 2.0 Consensus size: 125
17515699 CAATTAAATG
17515709 TATTAAACATACCAAACCAGCAGCACAGGGTATCTTCTCTGATAGGAAGAAAATGACTCTTACAA
1 TATTAAACATACCAAACCAGCAGCACAGGGTATCTTCTCTGATAGGAAGAAAATGACTCTTACAA
*
17515774 TTATTTTATAGCTTGCGTTTTTCATTTGTTCTTTTCCTCTTCTAGCTGGAAATGAACCCT
66 TTATTGTATAGCTTGCGTTTTTCATTTGTTCTTTTCCTCTTCTAGCTGGAAATGAACCCT
17515834 TATTAAACATACCAAACCAGCAGCACAGGGTATC-TCTTCTGATAGGAAGAAAATGACTCTTACA
1 TATTAAACATACCAAACCAGCAGCACAGGGTATCTTC-TCTGATAGGAAGAAAATGACTCTTACA
17515898 ATTATTGTATAGCTTGCGTTTTTCATTTGTTCTTTTCCTCTTCTAGCTGGAAATGAACCCT
65 ATTATTGTATAGCTTGCGTTTTTCATTTGTTCTTTTCCTCTTCTAGCTGGAAATGAACCCT
17515959 TA
1 TA
17515961 GTCAAACCAT
Statistics
Matches: 125, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
124 2 0.02
125 123 0.98
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.36
Consensus pattern (125 bp):
TATTAAACATACCAAACCAGCAGCACAGGGTATCTTCTCTGATAGGAAGAAAATGACTCTTACAA
TTATTGTATAGCTTGCGTTTTTCATTTGTTCTTTTCCTCTTCTAGCTGGAAATGAACCCT
Found at i:17519911 original size:16 final size:18
Alignment explanation
Indices: 17519876--17519913 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
17519866 AACCAAATTA
*
17519876 TATATCTTTATTAGTTTT
1 TATATCTTTATTAATTTT
17519894 TATAT-TTT-TTAATTTT
1 TATATCTTTATTAATTTT
17519910 TATA
1 TATA
17519914 AAGTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
17 3 0.16
18 5 0.26
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (18 bp):
TATATCTTTATTAATTTT
Found at i:17520460 original size:2 final size:2
Alignment explanation
Indices: 17520453--17520500 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
17520443 AACGTTGGTT
* * *
17520453 TA TA TA TA TA CA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17520495 TA TA TA
1 TA TA TA
17520501 AGGTTTTAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17520675 original size:22 final size:23
Alignment explanation
Indices: 17520647--17520691 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
17520637 TAAGAAGAAT
17520647 ATTTGTTGA-CATTATTCAATTA
1 ATTTGTTGATCATTATTCAATTA
* *
17520669 ATTTGTTTATCTTTATTCAATTA
1 ATTTGTTGATCATTATTCAATTA
17520692 TATTATAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (23 bp):
ATTTGTTGATCATTATTCAATTA
Found at i:17526045 original size:30 final size:30
Alignment explanation
Indices: 17525960--17526038 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
17525950 ATTTATGTAC
*
17525960 AAATTAAAATTTTAAAGATTTATTTGGATAT
1 AAATTAAAA-ATTAAAGATTTATTTGGATAT
* * * *
17525991 AAATTAAAGATTAATGATTTATTTGGGTGT
1 AAATTAAAAATTAAAGATTTATTTGGATAT
17526021 AAATTAAAAATTAAAGAT
1 AAATTAAAAATTAAAGAT
17526039 ACATTTGAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 33 0.80
31 8 0.20
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.41
Consensus pattern (30 bp):
AAATTAAAAATTAAAGATTTATTTGGATAT
Found at i:17532449 original size:22 final size:22
Alignment explanation
Indices: 17532424--17532465 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17532414 ATCATTATAT
17532424 ATAAAACTCAAATATTTTTTCA
1 ATAAAACTCAAATATTTTTTCA
** *
17532446 ATAAATGTCAAATCTTTTTT
1 ATAAAACTCAAATATTTTTT
17532466 TATATAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.45
Consensus pattern (22 bp):
ATAAAACTCAAATATTTTTTCA
Found at i:17532481 original size:23 final size:22
Alignment explanation
Indices: 17532431--17532474 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17532421 TATATAAAAC
17532431 TCAAATATTTTTTCAATAAATG
1 TCAAATATTTTTTCAATAAATG
* *
17532453 TCAAATCTTTTTTTATATAAAT
1 TCAAATATTTTTTCA-ATAAAT
17532475 TTTAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (22 bp):
TCAAATATTTTTTCAATAAATG
Found at i:17533561 original size:2 final size:2
Alignment explanation
Indices: 17533536--17533578 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
17533526 GGATAGTGTT
*
17533536 TA TA T- TA TA T- TA TA TT TCA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
17533577 TA
1 TA
17533579 AACTTGATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 33 0.92
3 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:17534710 original size:17 final size:17
Alignment explanation
Indices: 17534688--17534722 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
17534678 AATTATAAAT
*
17534688 TTTTTTTATTACTCAAC
1 TTTTTTTAGTACTCAAC
17534705 TTTTTTTAGTACTCAAC
1 TTTTTTTAGTACTCAAC
17534722 T
1 T
17534723 AGATTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTTTTTAGTACTCAAC
Done.