Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, 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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 31 of 121
Found at i:5414228 original size:15 final size:15
Alignment explanation
Indices: 5414208--5414239 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5414198 TATACATTTC
5414208 TATATAT-A-AATAA
1 TATATATAATAATAA
5414221 TATATATAATAATAA
1 TATATATAATAATAA
5414236 TATA
1 TATA
5414240 ATGATAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 1 0.06
15 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TATATATAATAATAA
Found at i:5414404 original size:25 final size:24
Alignment explanation
Indices: 5414369--5414433 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 24
5414359 ATCTACGACT
* *
5414369 AATAATTTAAAATATGATAT-AATA
1 AATAATATAAAA-ATAATATAAATA
5414393 ATATAATATAAAAATAATATAAATA
1 A-ATAATATAAAAATAATATAAATA
5414418 AA-AATATAAAAATAAT
1 AATAATATAAAAATAAT
5414434 GATTTAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
23 14 0.38
24 8 0.22
25 15 0.41
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (24 bp):
AATAATATAAAAATAATATAAATA
Found at i:5414410 original size:16 final size:15
Alignment explanation
Indices: 5414389--5414432 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
5414379 AATATGATAT
5414389 AATAATATAATATAAA
1 AATAATATAA-ATAAA
5414405 AATAATATAAATAAA
1 AATAATATAAATAAA
*
5414420 AAT-ATAAAAATAA
1 AATAATATAAATAA
5414433 TGATTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 9 0.33
15 8 0.30
16 10 0.37
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAATATAAATAAA
Found at i:5414583 original size:25 final size:26
Alignment explanation
Indices: 5414513--5414584 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 26
5414503 GATACAAATT
5414513 ATAACATGTAATTTTTATATAAAATATA
1 ATAACATG-AATTTTTATAT-AAATATA
*
5414541 ATACGAACAT-AATATTTTATAT-GATATA
1 AT---AACATGAAT-TTTTATATAAATATA
5414569 ATAACATGAATTTTTA
1 ATAACATGAATTTTTA
5414585 GAACTAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
25 10 0.26
26 3 0.08
28 9 0.24
29 3 0.08
30 8 0.21
31 5 0.13
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (26 bp):
ATAACATGAATTTTTATATAAATATA
Found at i:5416506 original size:6 final size:6
Alignment explanation
Indices: 5416492--5416524 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5416482 GATAGAGAGA
*
5416492 TGGGG- TGGGAT TGGGGT TGGGGT TGGGGT TGGG
1 TGGGGT TGGGGT TGGGGT TGGGGT TGGGGT TGGG
5416525 AGGGGATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.03, C:0.00, G:0.67, T:0.30
Consensus pattern (6 bp):
TGGGGT
Found at i:5419980 original size:42 final size:42
Alignment explanation
Indices: 5419934--5420016 Score: 94
Period size: 42 Copynumber: 2.0 Consensus size: 42
5419924 ATAAGAGCGA
** * * * *
5419934 GACCTCCTTCTTCGCCTATAACTTATTGGTGACCTTGACTTG
1 GACCTCCACCTTCGCCGATAACTGATAGGTGACCTAGACTTG
**
5419976 GACCTTGACCTTCGCCGATAACTGATAGGTGACCTAGACTT
1 GACCTCCACCTTCGCCGATAACTGATAGGTGACCTAGACTT
5420017 TGATCTTGAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (42 bp):
GACCTCCACCTTCGCCGATAACTGATAGGTGACCTAGACTTG
Found at i:5420025 original size:42 final size:42
Alignment explanation
Indices: 5419943--5420071 Score: 134
Period size: 42 Copynumber: 3.1 Consensus size: 42
5419933 AGACCTCCTT
* * * * *
5419943 CTTCGCCTATAACTTATTGGTGACCTTGACTTGGACCTTGAC
1 CTTCGCCGATAACTAATAGGTGACCTTGACTTTGATCTTGAC
* * *
5419985 CTTCGCCGATAACTGATAGGTGACCTAGACTTTGATCTTGAT
1 CTTCGCCGATAACTAATAGGTGACCTTGACTTTGATCTTGAC
* * **
5420027 CTTCTCCGATAACTAATGGGTGATTTTGA-TTTGGATCTTGAC
1 CTTCGCCGATAACTAATAGGTGACCTTGACTTT-GATCTTGAC
5420069 CTT
1 CTT
5420072 GCACGAGGAG
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
41 3 0.04
42 69 0.96
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (42 bp):
CTTCGCCGATAACTAATAGGTGACCTTGACTTTGATCTTGAC
Found at i:5432399 original size:22 final size:22
Alignment explanation
Indices: 5432344--5432396 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
5432334 CAAGAGAAAT
*
5432344 GGGAAGAAAATAAAAACAAGAA
1 GGGAAGAAAAGAAAAACAAGAA
5432366 GGGAAGAAAAGAAAAA-AA-AA
1 GGGAAGAAAAGAAAAACAAGAA
5432386 GGGAAGGAAAA
1 GGGAA-GAAAA
5432397 AGAGAGAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 7 0.24
21 7 0.24
22 15 0.52
ACGTcount: A:0.68, C:0.02, G:0.28, T:0.02
Consensus pattern (22 bp):
GGGAAGAAAAGAAAAACAAGAA
Found at i:5442725 original size:3 final size:3
Alignment explanation
Indices: 5442717--5442748 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5442707 ATGTGAAAAT
5442717 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5442749 TATCTTTCAT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5451012 original size:12 final size:12
Alignment explanation
Indices: 5450995--5451019 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5450985 GTGGTAAAGA
5450995 TTGGGTGGAATC
1 TTGGGTGGAATC
5451007 TTGGGTGGAATC
1 TTGGGTGGAATC
5451019 T
1 T
5451020 GATTTTTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.40, T:0.36
Consensus pattern (12 bp):
TTGGGTGGAATC
Found at i:5451209 original size:3 final size:3
Alignment explanation
Indices: 5451201--5451231 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5451191 TTCTTTGGAA
5451201 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
5451232 CATGAAGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:5451990 original size:12 final size:12
Alignment explanation
Indices: 5451975--5452011 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
5451965 CACAAAAACC
*
5451975 AGATTCCACCCA
1 AGATTTCACCCA
*
5451987 AGATTTCACCTA
1 AGATTTCACCCA
5451999 AGATTTCACCCA
1 AGATTTCACCCA
5452011 A
1 A
5452012 CCTTTACCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.35, C:0.32, G:0.08, T:0.24
Consensus pattern (12 bp):
AGATTTCACCCA
Found at i:5457664 original size:13 final size:13
Alignment explanation
Indices: 5457646--5457671 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5457636 TTATGGTACG
5457646 ATGACTCATCACT
1 ATGACTCATCACT
5457659 ATGACTCATCACT
1 ATGACTCATCACT
5457672 TATTTGACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (13 bp):
ATGACTCATCACT
Found at i:5457702 original size:18 final size:18
Alignment explanation
Indices: 5457679--5457714 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5457669 ACTTATTTGA
*
5457679 CATAAAGTAAATGTGACT
1 CATAAAGTAAATATGACT
5457697 CATAAAGTAAATATGACT
1 CATAAAGTAAATATGACT
5457715 TGACTTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (18 bp):
CATAAAGTAAATATGACT
Found at i:5466536 original size:2 final size:2
Alignment explanation
Indices: 5466529--5466574 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
5466519 TCCCCCTTGC
* * * *
5466529 AT AT AT AT AA AT AT AA AT AT AT AT AT AT AT TT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5466571 AT AT
1 AT AT
5466575 CTTTCGGTTC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5468105 original size:2 final size:2
Alignment explanation
Indices: 5468098--5468128 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5468088 TCATGTGTAT
5468098 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5468129 TGTGCTAGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5469509 original size:3 final size:3
Alignment explanation
Indices: 5469501--5469529 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5469491 TCATGCACAA
5469501 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5469530 AGGCAAACTT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5471461 original size:22 final size:20
Alignment explanation
Indices: 5471436--5471475 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
5471426 TATTTGGTTT
5471436 AATAAAATAATAAAGTGCATGA
1 AATAAAAT-ATAAAG-GCATGA
*
5471458 AATAGAATATAAAGGCAT
1 AATAAAATATAAAGGCAT
5471476 ACATTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 6 0.35
22 7 0.41
ACGTcount: A:0.57, C:0.05, G:0.15, T:0.23
Consensus pattern (20 bp):
AATAAAATATAAAGGCATGA
Found at i:5475406 original size:16 final size:17
Alignment explanation
Indices: 5475374--5475411 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
5475364 AATGAGATTA
5475374 AATTAATATAATTTTTT
1 AATTAATATAATTTTTT
* *
5475391 TATTAA-ATATTTTTTT
1 AATTAATATAATTTTTT
5475407 AATTA
1 AATTA
5475412 CAATTATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTAATATAATTTTTT
Found at i:5475426 original size:24 final size:24
Alignment explanation
Indices: 5475392--5475452 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
5475382 TAATTTTTTT
5475392 ATTA-AAT-ATTTTTTTAATTACA
1 ATTATAATAATTTTTTTAATTACA
**
5475414 ATTATAATAATTTTTTTAATTGTA
1 ATTATAATAATTTTTTTAATTACA
*
5475438 ATTATAATAAATTTT
1 ATTATAATAATTTTT
5475453 ATTATTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 4 0.12
23 3 0.09
24 27 0.79
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTATAATAATTTTTTTAATTACA
Found at i:5487791 original size:15 final size:15
Alignment explanation
Indices: 5487771--5487809 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
5487761 AACATTAAAA
**
5487771 AAAATTTTAATTCAC
1 AAAATTTTAAAACAC
*
5487786 AAAATTTTAAAACAT
1 AAAATTTTAAAACAC
5487801 AAAATTTTA
1 AAAATTTTA
5487810 CAAAAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATTTTAAAACAC
Found at i:5487820 original size:16 final size:15
Alignment explanation
Indices: 5487786--5487820 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5487776 TTTAATTCAC
*
5487786 AAAATTTTAAAACAT
1 AAAATTTTAAAAAAT
5487801 AAAATTTTACAAAAAT
1 AAAATTTTA-AAAAAT
5487817 AAAA
1 AAAA
5487821 ATAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATTTTAAAAAAT
Found at i:5487821 original size:24 final size:24
Alignment explanation
Indices: 5487794--5487840 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5487784 ACAAAATTTT
* *
5487794 AAAACATAAAATTTTACAAAAATA
1 AAAACAAAAAATTTTAAAAAAATA
*
5487818 AAAATAAAAAATTTTAAAAAAAT
1 AAAACAAAAAATTTTAAAAAAAT
5487841 TGAAAAAATT
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:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (24 bp):
AAAACAAAAAATTTTAAAAAAATA
Found at i:5487986 original size:25 final size:24
Alignment explanation
Indices: 5487958--5488014 Score: 53
Period size: 25 Copynumber: 2.3 Consensus size: 24
5487948 AAAATTAAAT
**
5487958 TTTTAAAATTCAAAAA-ACTAAAAAA
1 TTTTAAAATAAAAAAATAC-AAAA-A
*
5487983 TTTTGAAATAAAAAAATACAAAAA
1 TTTTAAAATAAAAAAATACAAAAA
*
5488007 TCTTAAAA
1 TTTTAAAA
5488015 ATTTAAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 7 0.27
25 17 0.65
26 2 0.08
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (24 bp):
TTTTAAAATAAAAAAATACAAAAA
Found at i:5488197 original size:38 final size:38
Alignment explanation
Indices: 5488155--5488232 Score: 86
Period size: 38 Copynumber: 2.1 Consensus size: 38
5488145 TCTTTTAAAC
* *
5488155 TTTTTATAAATTTTCAAAATTTT-TTAAAAAAAATTAGA
1 TTTTTATAAA-TTTAAAAATTTTATCAAAAAAAATTAGA
* * **
5488193 TTTTTTTTAATTTAAAAATTTTATCAAAAAATTTTAGA
1 TTTTTATAAATTTAAAAATTTTATCAAAAAAAATTAGA
5488231 TT
1 TT
5488233 ATTAATTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
37 11 0.33
38 22 0.67
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (38 bp):
TTTTTATAAATTTAAAAATTTTATCAAAAAAAATTAGA
Found at i:5488391 original size:20 final size:19
Alignment explanation
Indices: 5488362--5488408 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
5488352 TCAAATGTTT
5488362 AAAT-TTTTATAATTTCTAA
1 AAATATTTTAT-ATTTCTAA
*
5488381 AAATATTTTATATTTTTAA
1 AAATATTTTATATTTCTAA
5488400 AAA-ATTTTA
1 AAATATTTTA
5488409 AAACATTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 6 0.23
19 14 0.54
20 6 0.23
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATATTTTATATTTCTAA
Found at i:5488762 original size:21 final size:21
Alignment explanation
Indices: 5488708--5488763 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
5488698 ACAAACATTC
*
5488708 AAAAATTTTTAAAAT-TTTTTT
1 AAAAA-TTATAAAATATTTTTT
*
5488729 AAAAAATAT-AAATATTTTTT
1 AAAAATTATAAAATATTTTTT
5488749 AAAAATTATAAAATA
1 AAAAATTATAAAATA
5488764 ATTTAAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 4 0.13
20 16 0.53
21 10 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAAATTATAAAATATTTTTT
Found at i:5488768 original size:19 final size:20
Alignment explanation
Indices: 5488726--5488780 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
5488716 TTAAAATTTT
* **
5488726 TTTAAAAAATATAAATATTT
1 TTTAAAAATTATAAATATAA
5488746 TTTAAAAATTATAAA-ATAA
1 TTTAAAAATTATAAATATAA
5488765 TTTAAATAATT-TAAAT
1 TTTAAA-AATTATAAAT
5488781 TTTATGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTAAAAATTATAAATATAA
Found at i:5488892 original size:17 final size:18
Alignment explanation
Indices: 5488854--5488896 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
5488844 AAAAATTATG
5488854 AAAATTTTAAACAAAATA
1 AAAATTTTAAACAAAATA
5488872 AAAATTTTAATAC-AAAT-
1 AAAATTTTAA-ACAAAATA
5488889 AAAATTTT
1 AAAATTTT
5488897 CATCAAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.33
18 14 0.58
19 2 0.08
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATTTTAAACAAAATA
Found at i:5488983 original size:20 final size:19
Alignment explanation
Indices: 5488843--5488996 Score: 77
Period size: 20 Copynumber: 7.9 Consensus size: 19
5488833 TCGAAAACTT
*
5488843 AAAAAATTATGAAAATTTTA
1 AAAAAATTA-AAAAATTTTA
5488863 AACAAAA-T-AAAAATTTTA
1 AA-AAAATTAAAAAATTTTA
* *
5488881 ATACAAA-T--AAAATTTTC
1 A-AAAAATTAAAAAATTTTA
** * *
5488898 ATCAAATTCAAAAAAATTCA
1 AAAAAATT-AAAAAATTTTA
** *
5488918 CAAAAACGTAAAAAATTTGA
1 -AAAAAATTAAAAAATTTTA
* *
5488938 AAATAAA-AAAAAAATTTCA
1 AAA-AAATTAAAAAATTTTA
5488957 AAAAAATCTAAAAAATTTTA
1 AAAAAAT-TAAAAAATTTTA
5488977 AAAAAATTAGAAAAACTTTT
1 AAAAAATTA-AAAAA-TTTT
5488997 TTTTTAATTA
Statistics
Matches: 104, Mismatches: 18, Indels: 23
0.72 0.12 0.16
Matches are distributed among these distances:
16 4 0.04
17 10 0.10
18 17 0.16
19 19 0.18
20 42 0.40
21 12 0.12
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (19 bp):
AAAAAATTAAAAAATTTTA
Found at i:5489364 original size:19 final size:18
Alignment explanation
Indices: 5489342--5489392 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
5489332 TTTTAATCCT
5489342 TTTTTTAATTTTTAAGACA
1 TTTTTTAATTTTTAAGA-A
*
5489361 TTTTTT-TTATTTTAAGAA
1 TTTTTTAAT-TTTTAAGAA
5489379 TTTTTTGAATTTTT
1 TTTTTT-AATTTTT
5489393 TCTCAAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 8 0.30
19 18 0.67
20 1 0.04
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (18 bp):
TTTTTTAATTTTTAAGAA
Found at i:5489528 original size:27 final size:27
Alignment explanation
Indices: 5489476--5489528 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
5489466 TATTTCATAT
* * *
5489476 ATTTAAAATTTTTTTAATTTTTAAAAC
1 ATTTAAAATTTTTTAAAATTTAAAAAC
*
5489503 ATTTCAAATTTTTTAAAATTTAAAAA
1 ATTTAAAATTTTTTAAAATTTAAAAA
5489529 AAATTTTCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTTAAAATTTTTTAAAATTTAAAAAC
Found at i:5489828 original size:31 final size:29
Alignment explanation
Indices: 5489776--5489856 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 29
5489766 TTATTTTTTC
*
5489776 ATATTTCATATTTTTAGAAAAAATTTTAAA
1 ATATTTCATATTTTTA-AAAAAAATTTAAA
5489806 ATATTTCATACTTTTTAAAAAAAATTTAAA
1 ATATTTCATA-TTTTTAAAAAAAATTTAAA
* * *
5489836 ATTTTTAAAATTTTATAAAAA
1 ATATTTCATATTTT-TAAAAA
5489857 TATTTCATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
29 4 0.09
30 35 0.78
31 6 0.13
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (29 bp):
ATATTTCATATTTTTAAAAAAAATTTAAA
Found at i:5490325 original size:18 final size:17
Alignment explanation
Indices: 5490291--5490333 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
5490281 AAAAATTACG
5490291 AAAATTTTAAACAAAAT
1 AAAATTTTAAACAAAAT
*
5490308 AAAAATTTTAGTAC-AAAT
1 -AAAATTTTA-AACAAAAT
5490326 AAAATTTT
1 AAAATTTT
5490334 CATCAAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 8 0.35
18 13 0.57
19 2 0.09
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (17 bp):
AAAATTTTAAACAAAAT
Found at i:5490498 original size:19 final size:20
Alignment explanation
Indices: 5490474--5490549 Score: 61
Period size: 20 Copynumber: 3.8 Consensus size: 20
5490464 TTAATCTTAC
5490474 TATTTT-AATTTTTTATATA
1 TATTTTGAATTTTTTATATA
*
5490493 TATTTTATGAATTTTTT-TAGA
1 TA-TTT-TGAATTTTTTATATA
*
5490514 TTTTTTGAAATTTTTTAT-TAA
1 TATTTTG-AATTTTTTATAT-A
*
5490535 AATTTT-AATTTTTTA
1 TATTTTGAATTTTTTA
5490550 ATTTTTTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
19 13 0.28
20 14 0.30
21 11 0.24
22 8 0.17
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (20 bp):
TATTTTGAATTTTTTATATA
Found at i:5490559 original size:31 final size:34
Alignment explanation
Indices: 5490524--5490592 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 34
5490514 TTTTTTGAAA
*
5490524 TTTTTTATTAAAATTT-T-AATTTTTTA-ATTTT
1 TTTTTTACTAAAATTTATAAATTTTTTATATTTT
5490555 TTTTTTACTAAAATTTATAAAATTTTTTATATTTT
1 TTTTTTACTAAAATTTAT-AAATTTTTTATATTTT
5490590 TTT
1 TTT
5490593 GTAATATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
31 15 0.45
32 1 0.03
34 9 0.27
35 8 0.24
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.68
Consensus pattern (34 bp):
TTTTTTACTAAAATTTATAAATTTTTTATATTTT
Found at i:5490606 original size:37 final size:34
Alignment explanation
Indices: 5490541--5490626 Score: 91
Period size: 37 Copynumber: 2.4 Consensus size: 34
5490531 TTAAAATTTT
*
5490541 AATTTTTTAATTTTTTTTTTACTAAAATTTATAA
1 AATTTTTTAATTTTTTTTATACTAAAATTTATAA
* * *
5490575 AATTTTTTATATTTTTTTGTAATATTTAAATTTTTAA
1 AATTTTTTA-ATTTTTTT-T-ATACTAAAATTTATAA
* *
5490612 AAATTTTTACTTTTT
1 AATTTTTTAATTTTT
5490627 CAAAATTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
34 9 0.21
35 8 0.19
36 6 0.14
37 20 0.47
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (34 bp):
AATTTTTTAATTTTTTTTATACTAAAATTTATAA
Found at i:5490618 original size:27 final size:27
Alignment explanation
Indices: 5490588--5490645 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
5490578 TTTTTATATT
5490588 TTTTTGTAATATTT-AAATTTTTAAAAA
1 TTTTT-TAATATTTAAAATTTTTAAAAA
* *
5490615 -TTTTTACTTTTTCAAAATTTTTAAAAA
1 TTTTTTAATATTT-AAAATTTTTAAAAA
5490642 TTTT
1 TTTT
5490646 AGACAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 6 0.23
26 4 0.15
27 13 0.50
28 3 0.12
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTTTTAATATTTAAAATTTTTAAAAA
Found at i:5490625 original size:17 final size:17
Alignment explanation
Indices: 5490605--5490637 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5490595 AATATTTAAA
5490605 TTTTTAAAAATTTTTAC
1 TTTTTAAAAATTTTTAC
*
5490622 TTTTTCAAAATTTTTA
1 TTTTTAAAAATTTTTA
5490638 AAAATTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTTAAAAATTTTTAC
Found at i:5490814 original size:19 final size:18
Alignment explanation
Indices: 5490759--5490825 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
5490749 TTTTTAATCC
5490759 TTTTTTTAATTTTAAGAA
1 TTTTTTTAATTTTAAGAA
* * * **
5490777 -ATATTTATTTTTATTAA
1 TTTTTTTAATTTTAAGAA
5490794 TTTGTTTTAATTTTAAGAA
1 TTT-TTTTAATTTTAAGAA
*
5490813 TTTTTTGAATTTT
1 TTTTTTTAATTTT
5490826 TTATTAAGAT
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
17 12 0.33
18 10 0.28
19 14 0.39
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (18 bp):
TTTTTTTAATTTTAAGAA
Found at i:5490871 original size:27 final size:29
Alignment explanation
Indices: 5490815--5490882 Score: 88
Period size: 27 Copynumber: 2.4 Consensus size: 29
5490805 TTTAAGAATT
*
5490815 TTTTGAATTTTTTATTAAGATTTTTAAAA
1 TTTTGAATTTTTTATTAAGATTTTGAAAA
5490844 TTTTGAATTTTTT-TT-AG-TTTTGATAAA
1 TTTTGAATTTTTTATTAAGATTTTGA-AAA
*
5490871 TTTTTAATTTTT
1 TTTTGAATTTTT
5490883 ATAATTTCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
26 5 0.14
27 16 0.44
28 2 0.06
29 13 0.36
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (29 bp):
TTTTGAATTTTTTATTAAGATTTTGAAAA
Found at i:5490932 original size:17 final size:18
Alignment explanation
Indices: 5490876--5490955 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 18
5490866 ATAAATTTTT
5490876 AATTTTTATA-ATTTCTAAA
1 AATTTTT-TAGATTT-TAAA
*
5490895 AATATATTTTATATTTT-AA
1 AAT-T-TTTTAGATTTTAAA
5490914 AATTTTTTA-ATTTTAAA
1 AATTTTTTAGATTTTAAA
* *
5490931 AATATTTTAGATTTTTTAA
1 AATTTTTTAGA-TTTTAAA
5490950 AATTTT
1 AATTTT
5490956 AAAAAAAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
16 5 0.10
17 15 0.29
18 2 0.04
19 19 0.37
20 4 0.08
21 7 0.13
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (18 bp):
AATTTTTTAGATTTTAAA
Found at i:5490946 original size:27 final size:28
Alignment explanation
Indices: 5490905--5490960 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
5490895 AATATATTTT
*
5490905 ATATTTTAAAATTTTT-TAATTTTAAAA
1 ATATTTTAAAATTTTTAAAATTTTAAAA
* *
5490932 ATATTTTAGATTTTTTAAAATTTTAAAA
1 ATATTTTAAAATTTTTAAAATTTTAAAA
5490960 A
1 A
5490961 AAATTTCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
ATATTTTAAAATTTTTAAAATTTTAAAA
Found at i:5490948 original size:36 final size:38
Alignment explanation
Indices: 5490876--5490955 Score: 112
Period size: 36 Copynumber: 2.2 Consensus size: 38
5490866 ATAAATTTTT
*
5490876 AATTTTTATAATTTCTAAAAATATATTTTATATTTTAA
1 AATTTTTATAATTTCTAAAAATATATTTGATATTTTAA
*
5490914 AATTTTT-TAATTT-TAAAAATAT-TTTAGATTTTTTAA
1 AATTTTTATAATTTCTAAAAATATATTT-GATATTTTAA
5490950 AATTTT
1 AATTTT
5490956 AAAAAAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
35 3 0.08
36 23 0.59
37 6 0.15
38 7 0.18
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (38 bp):
AATTTTTATAATTTCTAAAAATATATTTGATATTTTAA
Found at i:5490971 original size:27 final size:26
Alignment explanation
Indices: 5490915--5490971 Score: 62
Period size: 28 Copynumber: 2.2 Consensus size: 26
5490905 ATATTTTAAA
* * *
5490915 ATTTTTTAATTTTAAAAATATTTTAG
1 ATTTTTTAATTTTAAAAAAAATTTAC
5490941 ATTTTTTAAAATTTTAAAAAAAATTT-C
1 ATTTTTT--AATTTTAAAAAAAATTTAC
5490968 ATTT
1 ATTT
5490972 AATGCTAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 7 0.27
27 4 0.15
28 15 0.58
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
ATTTTTTAATTTTAAAAAAAATTTAC
Found at i:5500284 original size:137 final size:138
Alignment explanation
Indices: 5500036--5500310 Score: 471
Period size: 137 Copynumber: 2.0 Consensus size: 138
5500026 GATTTCAAGA
*
5500036 TATGATGCATATTTATGACAATAAAACCCAGGAATGGATTTTGACATCCCTGTGCAAATTCTTTT
1 TATGATGCAAATTTATGACAATAAAACCCA-GAATGGATTTTGACATCCCTGTGCAAATTCTTTT
5500101 TGAACATAAAACCAGCCCAATGTAGGCACCTGTAACTTTTGAGATTGATTTATGTTCTATCAAGC
65 TGAACATAAAACCAGCCCAATGTAGGCACCTGTAACTTTTGAGATTGATTTATGTTCTATCAAGC
5500166 CCACAAATT
130 CCACAAATT
*
5500175 TATGATGCAAATTTATGACAATAAAGCCC-GAATGGATTTTGACATCCCTGTGCAAATTCTTTTT
1 TATGATGCAAATTTATGACAATAAAACCCAGAATGGATTTTGACATCCCTGTGCAAATTCTTTTT
* * * * *
5500239 GAACATAAAACCAGCCTAATGTGGGCACCTGTAATTTTTTAGATTGATTTATGTTCTATCAAGCG
66 GAACATAAAACCAGCCCAATGTAGGCACCTGTAACTTTTGAGATTGATTTATGTTCTATCAAGCC
5500304 CACAAAT
131 CACAAAT
5500311 CCCAAATGTT
Statistics
Matches: 129, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
137 102 0.79
139 27 0.21
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (138 bp):
TATGATGCAAATTTATGACAATAAAACCCAGAATGGATTTTGACATCCCTGTGCAAATTCTTTTT
GAACATAAAACCAGCCCAATGTAGGCACCTGTAACTTTTGAGATTGATTTATGTTCTATCAAGCC
CACAAATT
Found at i:5505212 original size:3 final size:3
Alignment explanation
Indices: 5505204--5505234 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5505194 AATATTTGCA
5505204 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
5505235 GGGTGATGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5506072 original size:11 final size:11
Alignment explanation
Indices: 5506056--5506123 Score: 63
Period size: 11 Copynumber: 6.5 Consensus size: 11
5506046 GATGTCAATG
5506056 ATATTTTAATA
1 ATATTTTAATA
*
5506067 ATATTTTAGTA
1 ATATTTTAATA
5506078 ATATTTT-A-A
1 ATATTTTAATA
**
5506087 AT-TGATAATA
1 ATATTTTAATA
*
5506097 TTATTTTAATA
1 ATATTTTAATA
*
5506108 ATA-TTTAGTA
1 ATATTTTAATA
5506118 ATATTT
1 ATATTT
5506124 AAGATTAATT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
8 2 0.05
9 4 0.09
10 11 0.25
11 27 0.61
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (11 bp):
ATATTTTAATA
Found at i:5506171 original size:12 final size:12
Alignment explanation
Indices: 5506154--5506178 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5506144 TTAGAGAATA
5506154 TTAAATATTGAT
1 TTAAATATTGAT
5506166 TTAAATATTGAT
1 TTAAATATTGAT
5506178 T
1 T
5506179 AAGTAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TTAAATATTGAT
Found at i:5510611 original size:11 final size:12
Alignment explanation
Indices: 5510597--5510627 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
5510587 AATATTCTTA
5510597 ATTGATTTA-AT
1 ATTGATTTAGAT
5510608 ATTGATTTAGAT
1 ATTGATTTAGAT
5510620 ATTGATTT
1 ATTGATTT
5510628 GAAGATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (12 bp):
ATTGATTTAGAT
Found at i:5510935 original size:57 final size:56
Alignment explanation
Indices: 5510871--5510985 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 56
5510861 AATTACTTTA
5510871 AGTATGTATTTGATATATAAAATTATGATAAAATAAAATAAAATTATAAATATAATT
1 AGTATGTATTTGATATATAAAATTATGATAAAATAAAA-AAAATTATAAATATAATT
*
5510928 AGTATGTATTTGATATATAAAATTATGATAAAATAAAAAATATTATAAATATAATT
1 AGTATGTATTTGATATATAAAATTATGATAAAATAAAAAAAATTATAAATATAATT
5510984 AG
1 AG
5510986 ATTTAATAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 19 0.33
57 38 0.67
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (56 bp):
AGTATGTATTTGATATATAAAATTATGATAAAATAAAAAAAATTATAAATATAATT
Found at i:5510981 original size:18 final size:18
Alignment explanation
Indices: 5510940--5510981 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
5510930 TATGTATTTG
*
5510940 ATATATAAAATTATGATAA
1 ATATA-AAAAATATGATAA
*
5510959 A-ATAAAAAATATTATAA
1 ATATAAAAAATATGATAA
5510976 ATATAA
1 ATATAA
5510982 TTAGATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 12 0.60
18 7 0.35
19 1 0.05
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
ATATAAAAAATATGATAA
Found at i:5511663 original size:12 final size:11
Alignment explanation
Indices: 5511648--5511688 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
5511638 TTGTAAATTT
5511648 TTTAAAAAATAA
1 TTTAAAAAA-AA
*
5511660 TTTAATAAAAA
1 TTTAAAAAAAA
5511671 TTTAATAAAAAA
1 TTTAA-AAAAAA
5511683 TTTAAA
1 TTTAAA
5511689 TTGATAGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 8 0.31
12 18 0.69
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TTTAAAAAAAA
Found at i:5513569 original size:3 final size:3
Alignment explanation
Indices: 5513555--5513590 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
5513545 TATTCTAAAT
5513555 TTA TTCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5513591 TTGTAAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5514474 original size:58 final size:56
Alignment explanation
Indices: 5514351--5514479 Score: 141
Period size: 58 Copynumber: 2.2 Consensus size: 56
5514341 TCTATTTAGA
* * *
5514351 CTTTTTATTGTTGGATTTCTAAATTTTTCACTATTTAAGTCAATTTAGAAAAATTTT
1 CTTTTTTTTTTTGGATTTCTAAATTTTTCACCATTTAAGTCAATTTAG-AAAATTTT
* ** * *
5514408 CTTCTTTTTTTTGGAATTTCTAAATTTTTCACCATTTGTGTCTATTTAGAAATTCTTT
1 CTTTTTTTTTTTGG-ATTTCTAAATTTTTCACCATTTAAGTCAATTTAGAAAAT-TTT
*
5514466 TTATTTTTTTTTTG
1 CT-TTTTTTTTTTG
5514480 TTTTCGAAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
57 15 0.25
58 34 0.58
59 10 0.17
ACGTcount: A:0.23, C:0.10, G:0.09, T:0.58
Consensus pattern (56 bp):
CTTTTTTTTTTTGGATTTCTAAATTTTTCACCATTTAAGTCAATTTAGAAAATTTT
Found at i:5515089 original size:19 final size:17
Alignment explanation
Indices: 5515061--5515099 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
5515051 AAAAATACTT
*
5515061 AAAAAAAAAACACATAAA
1 AAAAAAAAAAAACA-AAA
5515079 AAAATAAAAAAAACAAAA
1 AAAA-AAAAAAAACAAAA
5515097 AAA
1 AAA
5515100 TGAAACGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.87, C:0.08, G:0.00, T:0.05
Consensus pattern (17 bp):
AAAAAAAAAAAACAAAA
Found at i:5515890 original size:20 final size:21
Alignment explanation
Indices: 5515865--5515916 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
5515855 AACAAAAATT
5515865 AATAAATAAAAAAGA-TA-AAC
1 AATAAATAAAAAA-ATTAGAAC
*
5515885 AATAAAGAAAAAAATTAGAAC
1 AATAAATAAAAAAATTAGAAC
5515906 AATAAAATAAA
1 AAT-AAATAAA
5515917 TAATGAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 14 0.52
21 6 0.22
22 6 0.22
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (21 bp):
AATAAATAAAAAAATTAGAAC
Found at i:5516217 original size:44 final size:43
Alignment explanation
Indices: 5516141--5516271 Score: 142
Period size: 43 Copynumber: 3.0 Consensus size: 43
5516131 ACTGAATGAC
* * *
5516141 ATAAGGCTCTCCTAAGTAGAGGCT-TACAACTTTGAAAAAATAA
1 ATAAAGCTCT-CTAAATAGAGGCTCAACAACTTTGAAAAAATAA
* * *
5516184 ATACAGCTCCTTTAAATAGAGGCTCAACAACTTTTAAAAAATAA
1 ATAAAGCT-CTCTAAATAGAGGCTCAACAACTTTGAAAAAATAA
* *
5516228 ATAAAGCTCTCTAAATAAAGG-TACAACGACTTTG-AAAAATAA
1 ATAAAGCTCTCTAAATAGAGGCT-CAACAACTTTGAAAAAATAA
5516270 AT
1 AT
5516272 GCTCCTCTAA
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
42 11 0.15
43 37 0.50
44 26 0.35
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (43 bp):
ATAAAGCTCTCTAAATAGAGGCTCAACAACTTTGAAAAAATAA
Found at i:5517358 original size:18 final size:17
Alignment explanation
Indices: 5517328--5517384 Score: 80
Period size: 18 Copynumber: 3.3 Consensus size: 17
5517318 TGAGTCTTCA
5517328 TTTTTCATTTTTTAATT
1 TTTTTCATTTTTTAATT
*
5517345 TTTTCTCTTTTTTTAAATT
1 TTTT-TCATTTTTT-AATT
5517364 TTTTTCATTTTTT-ATT
1 TTTTTCATTTTTTAATT
5517380 TTTTT
1 TTTTT
5517385 AAGTATAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
16 8 0.22
17 4 0.11
18 16 0.44
19 8 0.22
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCATTTTTTAATT
Found at i:5526795 original size:50 final size:50
Alignment explanation
Indices: 5526730--5526834 Score: 165
Period size: 50 Copynumber: 2.1 Consensus size: 50
5526720 AGAATGATGC
**
5526730 AAATGTTAAAACATGAGCATGAAAATGATGCATAGAATGAAATGATATGA
1 AAATGTTAAAACATGAGCATGAAAATGACACATAGAATGAAATGATATGA
* * *
5526780 TAATGTTAAGACATGAGCATGAAAATGACACATAGGATGAAATGATATGA
1 AAATGTTAAAACATGAGCATGAAAATGACACATAGAATGAAATGATATGA
5526830 AAATG
1 AAATG
5526835 ATGCAAATGC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.49, C:0.07, G:0.21, T:0.24
Consensus pattern (50 bp):
AAATGTTAAAACATGAGCATGAAAATGACACATAGAATGAAATGATATGA
Found at i:5527982 original size:61 final size:61
Alignment explanation
Indices: 5527887--5528077 Score: 180
Period size: 61 Copynumber: 3.2 Consensus size: 61
5527877 AAATTAAAAA
* * * *
5527887 TATTTTTTTTTAATTTCTAAATTTTTTACCATTTGGGCTTATTTAGAAATTCTTTTTTTTT
1 TATTTTTGTTTGATTTCTAAATTTTTCATCATTTGGGCTTATTTAGAAATTCTTTTTTTTT
* * * *
5527948 TATTTTTGTTTGATTTCTAAATTTTTCATTATTTGGG-TCAATTTAGAAA---TATTTTCTT
1 TATTTTTGTTTGATTTCTAAATTTTTCATCATTTGGGCT-TATTTAGAAATTCTTTTTTTTT
* * * * *
5528006 TCTTTTTGGTGGAAATTTCTAAA-TTTTCATCATTTGGGCCTA-TTAGAAATTCTTTTACTTTT
1 TATTTTTGTTTG--ATTTCTAAATTTTTCATCATTTGGGCTTATTTAGAAATTCTTTT-TTTTT
5528068 T-TTTTTGTTT
1 TATTTTTGTTT
5528078 CGAAAAGAAC
Statistics
Matches: 103, Mismatches: 19, Indels: 16
0.75 0.14 0.12
Matches are distributed among these distances:
58 23 0.22
59 15 0.15
60 10 0.10
61 51 0.50
62 4 0.04
ACGTcount: A:0.21, C:0.09, G:0.10, T:0.60
Consensus pattern (61 bp):
TATTTTTGTTTGATTTCTAAATTTTTCATCATTTGGGCTTATTTAGAAATTCTTTTTTTTT
Found at i:5528455 original size:19 final size:19
Alignment explanation
Indices: 5528414--5528455 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
5528404 ATTCTAAAAT
*
5528414 TTTTATTATATTTTTTATT
1 TTTTATTATATTTTTTATG
5528433 TTTTATTATATATTTTT-TG
1 TTTTATTATAT-TTTTTATG
5528452 TTTT
1 TTTT
5528456 GAAAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTATTATATTTTTTATG
Found at i:5531200 original size:18 final size:17
Alignment explanation
Indices: 5531170--5531226 Score: 80
Period size: 18 Copynumber: 3.3 Consensus size: 17
5531160 TGAGTCTTCA
5531170 TTTTTCATTTTTTAATT
1 TTTTTCATTTTTTAATT
*
5531187 TTTTCTCTTTTTTTAAATT
1 TTTT-TCATTTTTT-AATT
5531206 TTTTTCATTTTTT-ATT
1 TTTTTCATTTTTTAATT
5531222 TTTTT
1 TTTTT
5531227 AAGTATAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
16 8 0.22
17 4 0.11
18 16 0.44
19 8 0.22
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCATTTTTTAATT
Found at i:5540600 original size:50 final size:50
Alignment explanation
Indices: 5540535--5540639 Score: 165
Period size: 50 Copynumber: 2.1 Consensus size: 50
5540525 AGAATGATAC
**
5540535 AAATGTTAAAACATGAGCATGAAAATGATGCATAGAATGAAATGATATGA
1 AAATGTTAAAACATGAGCATGAAAATGACACATAGAATGAAATGATATGA
* * *
5540585 TAATGTTAAGACATGAGCATGAAAATGACACATAGGATGAAATGATATGA
1 AAATGTTAAAACATGAGCATGAAAATGACACATAGAATGAAATGATATGA
5540635 AAATG
1 AAATG
5540640 ATGCAAATGC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.49, C:0.07, G:0.21, T:0.24
Consensus pattern (50 bp):
AAATGTTAAAACATGAGCATGAAAATGACACATAGAATGAAATGATATGA
Found at i:5541831 original size:60 final size:57
Alignment explanation
Indices: 5541709--5541899 Score: 193
Period size: 60 Copynumber: 3.2 Consensus size: 57
5541699 ATTAAAAATA
* * * * * * * *
5541709 TTTTTTTTAATTTCTAAATTTTTTACCGTTTGGGCCTATTTAGAATTTTTTTTTTAATT
1 TTTTTTTTGATTTCTAAATTTTTCATCATTTGGGCCAATTTAGAA-ATTCTTTTT-ACT
* * * *
5541768 TTTTTGTTTGATTTCTAAATTTTTCATTATTTGGGTCAATTTAGAAATATTTTCTTTTCT
1 TTTTT-TTTGATTTCTAAATTTTTCATCATTTGGGCCAATTTAGAAAT-TCTT-TTTACT
* *
5541828 TTTTTTTGGAATTTCTAAATTTTTCATCATTTGGGCCTATTTAGAAATTCTTTTTACT
1 TTTTTTTTG-ATTTCTAAATTTTTCATCATTTGGGCCAATTTAGAAATTCTTTTTACT
*
5541886 TTTTTTTTGTTTTC
1 TTTTTTTTGATTTC
5541900 GAAAAGAAAA
Statistics
Matches: 110, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
57 4 0.04
58 13 0.12
59 12 0.11
60 78 0.71
61 3 0.03
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.61
Consensus pattern (57 bp):
TTTTTTTTGATTTCTAAATTTTTCATCATTTGGGCCAATTTAGAAATTCTTTTTACT
Found at i:5542455 original size:202 final size:200
Alignment explanation
Indices: 5542074--5542456 Score: 497
Period size: 202 Copynumber: 1.9 Consensus size: 200
5542064 CAAAATTTTA
* * *
5542074 TTTGGAAAAAATATAATTACTTTTATTAAAATTTTATCTAAATTATTTCACAATTTGAAACAAAT
1 TTTGAAAAAAATATAATTACTTTTATTAAAACTTTATCTAAATTATTCCACAATTTGAAACAAAT
* * * *
5542139 TTAGAGAAAATTTTTCACCTAGAGATTTATTAGAAATTTACCATTTGAAATTTTTAAAATCTCAT
66 TTAGAGAAAAATTTTCACCTAGAGATTTATTAAAAATTTACCATTAGAAATTTCTAAAATCTCAT
* * **** *
5542204 CTTTGGATAATTTGTATTTAATTCTAAAATTTTTATTATATTTTTTATTTTTTATTATATATTTT
131 CATTAGATAACCAATATTTAATTCTAAAATTTTAATTATATTTTTTATTTTTTATTATATATTTT
5542269 TTTGT
196 TTTGT
*
5542274 TTTGAAAATAAATATGAATTA-TTGTTATTAAAACTTTATCTAAATTATTCCACAATTTGGAACA
1 TTTGAAAA-AAATAT-AATTACTT-TTATTAAAACTTTATCTAAATTATTCCACAATTTGAAACA
*
5542338 AATTTAGATAAAAATTTTCACCTATGA-ATTT-TATAAAAATTTACCATTAGAAATTTCTATAAA
63 AATTTAGAGAAAAATTTTCACCTA-GAGATTTAT-TAAAAATTTACCATTAGAAATTTCTA-AAA
* * *
5542401 TTTCATCATTAGATAACCAATATTT-ATTCTCAAA-TTTAATTTTATTTATTTATTTT
125 TCTCATCATTAGATAACCAATATTTAATTCTAAAATTTTAATTATATTT-TTTATTTT
5542457 ATTAATTTTT
Statistics
Matches: 157, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
200 7 0.04
201 20 0.13
202 107 0.68
203 23 0.15
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (200 bp):
TTTGAAAAAAATATAATTACTTTTATTAAAACTTTATCTAAATTATTCCACAATTTGAAACAAAT
TTAGAGAAAAATTTTCACCTAGAGATTTATTAAAAATTTACCATTAGAAATTTCTAAAATCTCAT
CATTAGATAACCAATATTTAATTCTAAAATTTTAATTATATTTTTTATTTTTTATTATATATTTT
TTTGT
Found at i:5542515 original size:25 final size:26
Alignment explanation
Indices: 5542481--5542532 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
5542471 TAAATTAGAT
*
5542481 CACAC-AAAAATACTTAAAAAAT-AAA
1 CACACAAAAAATAC-AAAAAAATGAAA
*
5542506 CACATAAAAAATACAAAAAAATGAAA
1 CACACAAAAAATACAAAAAAATGAAA
5542532 C
1 C
5542533 GGCTTGGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.69, C:0.15, G:0.02, T:0.13
Consensus pattern (26 bp):
CACACAAAAAATACAAAAAAATGAAA
Found at i:5542822 original size:15 final size:13
Alignment explanation
Indices: 5542785--5542823 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
5542775 CAGATCTCGC
*
5542785 TTCTTCCCTCTTT
1 TTCTTCCCTTTTT
5542798 TTCTTCCCTTTTT
1 TTCTTCCCTTTTT
5542811 TTCCTCTCCCTTT
1 TT-CT-TCCCTTT
5542824 CTCTCTGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 14 0.61
14 2 0.09
15 7 0.30
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (13 bp):
TTCTTCCCTTTTT
Found at i:5544426 original size:56 final size:56
Alignment explanation
Indices: 5544359--5544474 Score: 214
Period size: 56 Copynumber: 2.1 Consensus size: 56
5544349 AAAGATTTTT
5544359 TTTTTAGATTAAAAACATGATATTAGTTGAAAATATAATATGAAAAAAATTTATAC
1 TTTTTAGATTAAAAACATGATATTAGTTGAAAATATAATATGAAAAAAATTTATAC
* *
5544415 TTTTTAGATTAAAAACGTTATATTAGTTGAAAATATAATATGAAAAAAATTTATAC
1 TTTTTAGATTAAAAACATGATATTAGTTGAAAATATAATATGAAAAAAATTTATAC
5544471 TTTT
1 TTTT
5544475 CTTTTTATAG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (56 bp):
TTTTTAGATTAAAAACATGATATTAGTTGAAAATATAATATGAAAAAAATTTATAC
Found at i:5544524 original size:18 final size:18
Alignment explanation
Indices: 5544493--5544538 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
5544483 AGTTTCAATA
*
5544493 AAAATCATATTTTTTCTTG
1 AAAA-CATAATTTTTCTTG
*
5544512 AAAACATAATTTTTGTTG
1 AAAACATAATTTTTCTTG
*
5544530 AAAATATAA
1 AAAACATAA
5544539 AAAAACAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (18 bp):
AAAACATAATTTTTCTTG
Found at i:5547654 original size:16 final size:14
Alignment explanation
Indices: 5547622--5547671 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
5547612 ATGAATTTAA
*
5547622 AATATG-ATAGAAT
1 AATATGAATAAAAT
5547635 AATATGATATAAATAT
1 AATATGA-ATAAA-AT
*
5547651 AATACGAATAAAA-
1 AATATGAATAAAAT
5547664 AATATGAA
1 AATATGAA
5547672 AATAACATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 13 0.42
14 1 0.03
15 9 0.29
16 8 0.26
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.28
Consensus pattern (14 bp):
AATATGAATAAAAT
Found at i:5549132 original size:7 final size:7
Alignment explanation
Indices: 5549122--5549148 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5549112 TTTAAATTCT
5549122 AAAATTA
1 AAAATTA
5549129 AAAATTA
1 AAAATTA
5549136 AAAATTA
1 AAAATTA
5549143 AAAATT
1 AAAATT
5549149 TTATCAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AAAATTA
Found at i:5557200 original size:12 final size:12
Alignment explanation
Indices: 5557183--5557207 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5557173 ATAATGCGTA
5557183 AAAAAATTATTT
1 AAAAAATTATTT
5557195 AAAAAATTATTT
1 AAAAAATTATTT
5557207 A
1 A
5557208 TAATTTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAAAATTATTT
Found at i:5557602 original size:21 final size:21
Alignment explanation
Indices: 5557578--5557617 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5557568 TAACAGTGAG
5557578 ATTAAATATT-ATAATAATAAA
1 ATTAAA-ATTAATAATAATAAA
5557599 ATTAAAATTAATAATAATA
1 ATTAAAATTAATAATAATA
5557618 TTTATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATTAAAATTAATAATAATAAA
Found at i:5557730 original size:16 final size:16
Alignment explanation
Indices: 5557697--5557727 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5557687 AATATTAGAT
5557697 TAAAATTTATATATAA
1 TAAAATTTATATATAA
5557713 TAAAATTTATA-ATAA
1 TAAAATTTATATATAA
5557728 ATATTTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAATTTATATATAA
Found at i:5557733 original size:29 final size:30
Alignment explanation
Indices: 5557681--5557738 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
5557671 AAAAAATTAT
*
5557681 TAATAAAATATTAGATTAAAATTT-ATATA
1 TAATAAAATATTAGAATAAAATTTGATATA
*
5557710 TAATAAAAT-TTATAATAAATATTTGATAT
1 TAATAAAATATTAGAATAAA-ATTTGATAT
5557739 TTTTTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.32
29 13 0.52
30 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (30 bp):
TAATAAAATATTAGAATAAAATTTGATATA
Found at i:5558488 original size:13 final size:13
Alignment explanation
Indices: 5558470--5558504 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
5558460 TAAATTTAAT
5558470 ATAATAATATAAC
1 ATAATAATATAAC
*
5558483 ATAATAATATAAT
1 ATAATAATATAAC
*
5558496 ATAAAAATA
1 ATAATAATA
5558505 AATTAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAATAATATAAC
Found at i:5558504 original size:16 final size:16
Alignment explanation
Indices: 5558473--5558534 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 16
5558463 ATTTAATATA
5558473 ATAATATAACATAATAAT
1 ATAATATAA-A-AATAAT
5558491 ATAATAT--AAA-AAT
1 ATAATATAAAAATAAT
5558504 A-AAT-TAAAAATAAT
1 ATAATATAAAAATAAT
* *
5558518 ATAATTTAAAATTAAT
1 ATAATATAAAAATAAT
5558534 A
1 A
5558535 AAAATTGTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
11 1 0.03
12 3 0.08
13 7 0.18
14 6 0.16
15 4 0.11
16 10 0.26
18 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAATATAAAAATAAT
Found at i:5563269 original size:12 final size:12
Alignment explanation
Indices: 5563252--5563284 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
5563242 GCATAAAACA
5563252 CACACACACACG
1 CACACACACACG
5563264 CACACACACACG
1 CACACACACACG
*
5563276 CTCACACAC
1 CACACACAC
5563285 CTACTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.39, C:0.52, G:0.06, T:0.03
Consensus pattern (12 bp):
CACACACACACG
Found at i:5563269 original size:14 final size:14
Alignment explanation
Indices: 5563250--5563284 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5563240 CCGCATAAAA
5563250 CACACACACACACG
1 CACACACACACACG
* *
5563264 CACACACACACGCT
1 CACACACACACACG
5563278 CACACAC
1 CACACAC
5563285 CTACTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.51, G:0.06, T:0.03
Consensus pattern (14 bp):
CACACACACACACG
Found at i:5564563 original size:15 final size:15
Alignment explanation
Indices: 5564543--5564572 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5564533 CTAGCATTAT
5564543 GCAATTTTAAATTTA
1 GCAATTTTAAATTTA
5564558 GCAATTTTAAATTTA
1 GCAATTTTAAATTTA
5564573 CTTTGTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (15 bp):
GCAATTTTAAATTTA
Found at i:5566844 original size:4 final size:4
Alignment explanation
Indices: 5566835--5566868 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
5566825 TCTCCTTCAT
* *
5566835 TTTA TTTA TTTG TTTA TTTA TTTA TTCA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
5566869 GTTATTATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:5574168 original size:72 final size:70
Alignment explanation
Indices: 5574013--5574493 Score: 338
Period size: 72 Copynumber: 6.7 Consensus size: 70
5574003 GTAGTAAAAT
* * ** *
5574013 TTGAAACTATATTGTTGAAATTCTAGAATTTTAATAAAGATCGCGTTTTTAAAATGAAAAACT-T
1 TTGAAACTTTATT-TTGAAATTCTAGAATTTTAACAAAGATCATGTTTTTAAAAT-AAAAAATGT
* * *
5574077 AGCGGATA
64 A-TGAATG
* * *
5574085 TTGAAATTTTATTCTTGAAATTCTGGAATTTTAACAAAGATTATGTTTTTAAAATAAAAAATGTG
1 TTGAAACTTTATT-TTGAAATTCTAGAATTTTAACAAAGATCATGTTTTTAAAATAAAAAATGT-
5574150 ATGAATG
64 ATGAATG
* * * * * *
5574157 TTAAAACTTTATTTTCGAAATTATGGAATTTTAACAAA-AACTATGTTTTTAAGATAAAAAAAAG
1 TTGAAACTTTATTTT-GAAATTCTAGAATTTTAACAAAGATC-ATGTTTTTAAAAT-AAAAAATG
*
5574221 TAGTGAATA
63 TA-TGAATG
* * *
5574230 TTGAAAC-TTATTTTCGAAATTTTAGAATTTTAACAAAGA--ATGTTTTTAAGATAGAAAATCAA
1 TTGAAACTTTATTTT-GAAATTCTAGAATTTTAACAAAGATCATGTTTTTAAAATA-AAAA--AT
5574292 GTA-G-ATG
62 GTATGAATG
* * * *
5574299 TTGAAA-TTGTATTTTTGAAATTCTAGAATTTTAACAAAGACCGTGATTTTAAGATAAAAAAACA
1 TTGAAACTT-TA-TTTTGAAATTCTAGAATTTTAACAAAGATCATGTTTTTAA-A-ATAAAAA-A
5574363 TAGTAT--ATG
61 T-GTATGAATG
* * * * * * *
5574372 ACT-AAAATTTCATTTTCAAATTTTCAAAATTTTAACAACGATCATGTTTTTAAGATAAAAAATG
1 -TTGAAACTTT-ATTTTGAAATTCT-AGAATTTTAACAAAGATCATGTTTTTAAAATAAAAAATG
5574436 TAATGAATG
63 T-ATGAATG
* * *
5574445 TTGAAACTTCATTTTCGAAATTCT-GAAAATTTAACAAAGATCGTGTTTT
1 TTGAAACTTTATTTT-GAAATTCTAG-AATTTTAACAAAGATCATGTTTT
5574494 AGGGTAAAAA
Statistics
Matches: 331, Mismatches: 49, Indels: 58
0.76 0.11 0.13
Matches are distributed among these distances:
69 10 0.03
70 45 0.14
71 17 0.05
72 171 0.52
73 59 0.18
74 29 0.09
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (70 bp):
TTGAAACTTTATTTTGAAATTCTAGAATTTTAACAAAGATCATGTTTTTAAAATAAAAAATGTAT
GAATG
Found at i:5574334 original size:142 final size:144
Alignment explanation
Indices: 5574082--5574466 Score: 396
Period size: 142 Copynumber: 2.7 Consensus size: 144
5574072 AACTTAGCGG
* * *
5574082 ATATTGAAATTTTATTCTT-GAAATTCTGGAATTTTAACAAAGATTATGTTTTTAAAATAAAAA-
1 ATATTGAAA-TTTATT-TTCGAAATTTTAGAATTTTAACAAAGA-TATGTTTTTAAGATAAAAAT
* * * *
5574145 ATGTGATGAATGTTAAAACTTTATTTTCGAAATTATGGAATTTTAACAAAAACTATGTTTTTAAG
63 AAGTGATGAATGTTAAAACTTTATTTTCGAAATTATAGAATTTTAACAAAAACCATGATTTTAAG
5574210 ATAAAAAAA-AGTAGTGA-
128 ATAAAAAAACA-TAGT-AT
*
5574227 ATATTGAAACTTATTTTCGAAATTTTAGAATTTTAACAAAGA-ATGTTTTTAAGATAGAAAATCA
1 ATATTGAAATTTATTTTCGAAATTTTAGAATTTTAACAAAGATATGTTTTTAAGATA-AAAAT-A
* * * * *
5574291 AGT-A-G-ATGTTGAAA-TTGTATTTTTGAAATTCTAGAATTTTAACAAAGACCGTGATTTTAAG
64 AGTGATGAATGTTAAAACTT-TATTTTCGAAATTATAGAATTTTAACAAAAACCATGATTTTAAG
5574352 ATAAAAAAACATAGTAT
128 ATAAAAAAACATAGTAT
* * * *
5574369 ATGACTAAAATTTCATTTTC-AAATTTTCAAAATTTTAACAACGATCATGTTTTTAAGATAAAAA
1 AT-ATTGAAATTT-ATTTTCGAAATTTT-AGAATTTTAACAAAGAT-ATGTTTTTAAGATAAAAA
* * * *
5574433 -ATGTAATGAATGTTGAAACTTCATTTTCGAAATT
62 TAAGTGATGAATGTTAAAACTTTATTTTCGAAATT
5574467 CTGAAAATTT
Statistics
Matches: 203, Mismatches: 21, Indels: 31
0.80 0.08 0.12
Matches are distributed among these distances:
141 3 0.01
142 73 0.36
143 25 0.12
144 49 0.24
145 17 0.08
146 34 0.17
147 2 0.01
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.39
Consensus pattern (144 bp):
ATATTGAAATTTATTTTCGAAATTTTAGAATTTTAACAAAGATATGTTTTTAAGATAAAAATAAG
TGATGAATGTTAAAACTTTATTTTCGAAATTATAGAATTTTAACAAAAACCATGATTTTAAGATA
AAAAAACATAGTAT
Found at i:5586410 original size:12 final size:12
Alignment explanation
Indices: 5586393--5586417 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5586383 TATGTTATGG
5586393 ATTATATTTTAA
1 ATTATATTTTAA
5586405 ATTATATTTTAA
1 ATTATATTTTAA
5586417 A
1 A
5586418 AATCTGATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTATATTTTAA
Found at i:5587275 original size:3 final size:3
Alignment explanation
Indices: 5587267--5587300 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5587257 CTTTTAACTA
5587267 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5587301 AAAGTAAGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5587854 original size:12 final size:12
Alignment explanation
Indices: 5587825--5587891 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
5587815 TCTAACCATA
*
5587825 TATATATAATTAT
1 TATATTTAATT-T
5587838 T-TATTTAATTT
1 TATATTTAATTT
5587849 TATATTT-ATTT
1 TATATTTAATTT
5587860 ATATATTT-A-TT
1 -TATATTTAATTT
*
5587871 TA-ATTTTATATT
1 TATATTTAAT-TT
5587883 TATATTTAA
1 TATATTTAA
5587892 AAAATAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
9 4 0.09
10 3 0.07
11 8 0.17
12 25 0.54
13 6 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TATATTTAATTT
Found at i:5587856 original size:16 final size:16
Alignment explanation
Indices: 5587835--5587885 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
5587825 TATATATAAT
5587835 TATTTATTTAATTTTA
1 TATTTATTTAATTTTA
5587851 TATTTATTT-A---TA
1 TATTTATTTAATTTTA
5587863 TATTTATTTAATTTTA
1 TATTTATTTAATTTTA
5587879 TATTTAT
1 TATTTAT
5587886 ATTTAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 11 0.35
13 1 0.03
15 1 0.03
16 18 0.58
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTTATTTAATTTTA
Found at i:5587872 original size:22 final size:22
Alignment explanation
Indices: 5587839--5587890 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
5587829 TATAATTATT
*
5587839 TATTTAATTTTATATTTAT-TTATA
1 TATTT-ATTTAAT-TTTATATT-TA
5587863 TATTTATTTAATTTTATATTTA
1 TATTTATTTAATTTTATATTTA
5587885 TATTTA
1 TATTTA
5587891 AAAAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 13 0.50
23 8 0.31
24 5 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTTATTTAATTTTATATTTA
Found at i:5587878 original size:18 final size:18
Alignment explanation
Indices: 5587835--5587891 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
5587825 TATATATAAT
*
5587835 TATTT-ATTTAAT-TTTA
1 TATTTAATTTTATATTTA
5587851 TATTT-A-TTTATATATT-
1 TATTTAATTTTATAT-TTA
5587867 TATTTAATTTTATATTTA
1 TATTTAATTTTATATTTA
5587885 TATTTAA
1 TATTTAA
5587892 AAAATAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
15 4 0.11
16 12 0.34
17 5 0.14
18 14 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTTAATTTTATATTTA
Found at i:5587903 original size:20 final size:20
Alignment explanation
Indices: 5587878--5587928 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
5587868 ATTTAATTTT
5587878 ATATTTATATTTAAAA-AATA
1 ATATTT-TATTTAAAATAATA
5587898 ATATTTTATATTAAAATAATA
1 ATATTTTAT-TTAAAATAATA
5587919 ATATTTTATT
1 ATATTTTATT
5587929 AATTTCGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.10
20 13 0.45
21 13 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATTTTATTTAAAATAATA
Found at i:5587907 original size:21 final size:21
Alignment explanation
Indices: 5587881--5587927 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
5587871 TAATTTTATA
5587881 TTTATATTTAAAA-AATAATAT
1 TTTATA-TTAAAATAATAATAT
5587902 TTTATATTAAAATAATAATAT
1 TTTATATTAAAATAATAATAT
5587923 TTTAT
1 TTTAT
5587928 TAATTTCGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTATATTAAAATAATAATAT
Found at i:5587928 original size:19 final size:19
Alignment explanation
Indices: 5587878--5587930 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 19
5587868 ATTTAATTTT
5587878 ATATTTATATTTAAAAAATA
1 ATATTTATA-TTAAAAAATA
5587898 ATATTTTATATTAAAATAATA
1 ATA-TTTATATTAAAA-AATA
5587919 ATATTT-TATTAA
1 ATATTTATATTAA
5587931 TTTCGAGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.19
20 12 0.39
21 13 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATATTAAAAAATA
Found at i:5592416 original size:21 final size:20
Alignment explanation
Indices: 5592393--5592437 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 20
5592383 TTAATTTTTT
*
5592393 AAAAAGAAAAAGTAAAAAAGTA
1 AAAAAG-AAAAG-AAAAAAATA
5592415 AAAAAGAAAAGAAAAAAATA
1 AAAAAGAAAAGAAAAAAATA
5592435 AAA
1 AAA
5592438 TTTAGTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
21 5 0.23
22 6 0.27
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (20 bp):
AAAAAGAAAAGAAAAAAATA
Found at i:5594367 original size:3 final size:3
Alignment explanation
Indices: 5594359--5594391 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5594349 GAAAATATAC
5594359 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5594392 GCATGAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5594536 original size:2 final size:2
Alignment explanation
Indices: 5594523--5594554 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5594513 AAAGCCCACA
*
5594523 AT AT AT AA 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
5594555 TAACAAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5594775 original size:13 final size:14
Alignment explanation
Indices: 5594753--5594797 Score: 56
Period size: 13 Copynumber: 3.1 Consensus size: 14
5594743 TAATAAATAT
5594753 AATATTAAATTTAA
1 AATATTAAATTTAA
5594767 AAT-TTAAATTTATA
1 AATATTAAATTTA-A
*
5594781 AATATTATATTTTAA
1 AATATTA-AATTTAA
5594796 AA
1 AA
5594798 ATAATTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 9 0.33
14 7 0.26
15 6 0.22
16 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATATTAAATTTAA
Found at i:5594799 original size:16 final size:17
Alignment explanation
Indices: 5594775--5594807 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5594765 AAAATTTAAA
*
5594775 TTTATAAAT-ATTATAT
1 TTTAAAAATAATTATAT
5594791 TTTAAAAATAATTATAT
1 TTTAAAAATAATTATAT
5594808 AAATCAATCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAAAAATAATTATAT
Found at i:5605396 original size:3 final size:3
Alignment explanation
Indices: 5605388--5605415 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5605378 ATTTATCAAC
5605388 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5605416 AAAAAATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5605677 original size:52 final size:51
Alignment explanation
Indices: 5605599--5605702 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 51
5605589 TATAACCAAA
* * *
5605599 CAAACTTGCCTATTAACAATCCTTTTTCTCTTAGAATTTTTCTTCTACAAGT
1 CAAACTTGCCTATTAAAAATCCTTTTTCTCTTAG-ATTCTTATTCTACAAGT
* * * *
5605651 CAAACTTGCTTATTAAAAATCTTTTTTCTTTTAGATTCTTATTTTACAAGT
1 CAAACTTGCCTATTAAAAATCCTTTTTCTCTTAGATTCTTATTCTACAAGT
5605702 C
1 C
5605703 TTCTTATCCA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 15 0.33
52 30 0.67
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (51 bp):
CAAACTTGCCTATTAAAAATCCTTTTTCTCTTAGATTCTTATTCTACAAGT
Found at i:5608492 original size:87 final size:87
Alignment explanation
Indices: 5608400--5608572 Score: 206
Period size: 87 Copynumber: 2.0 Consensus size: 87
5608390 TTTATAAAAA
* ** * *
5608400 TATAAAAGGATTATTTAAGGTGTTTTTGTACATA-AAAAGTCTTAAATAATT-TTTTATATTTTA
1 TATAAAAAGATTATTTAAGAAGTTTTTGT--ATAGAAAAGACTTAAATAATTCATTTATATTTTA
* *
5608463 CAAAGGGATTATTTAATGAGTTTT
64 CAAAAGAATTATTTAATGAGTTTT
* * * *
5608487 TATAAAAATATTATTTAAGAAGTTTTTGTATAGAAACGACTTAAATAATTCATTTATGTTTTATA
1 TATAAAAAGATTATTTAAGAAGTTTTTGTATAGAAAAGACTTAAATAATTCATTTATATTTTACA
*
5608552 AAAGAATTATTTAATGTGTTT
66 AAAGAATTATTTAATGAGTTT
5608573 CTGTACAGAA
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
85 3 0.04
86 15 0.21
87 54 0.75
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.46
Consensus pattern (87 bp):
TATAAAAAGATTATTTAAGAAGTTTTTGTATAGAAAAGACTTAAATAATTCATTTATATTTTACA
AAAGAATTATTTAATGAGTTTT
Found at i:5608605 original size:62 final size:61
Alignment explanation
Indices: 5608484--5608611 Score: 145
Period size: 61 Copynumber: 2.1 Consensus size: 61
5608474 TTTAATGAGT
* * *
5608484 TTTTATAAAAATATTATTTAAGAAGTTTTTGTATAGAAACGACTTAAATAATTCATTTATG
1 TTTTATAAAAATATTATTTAAGAAGTTTCTGTACAGAAACGACTTAAATAATTCATTTATA
* **
5608545 TTTTATAAAAGA-ATTATTTAATG-TGTTTCTGTACAGAAAAC-ATCTTAAATAATTTTTTTATA
1 TTTTATAAAA-ATATTATTTAA-GAAGTTTCTGTACAG-AAACGA-CTTAAATAATTCATTTATA
5608607 TTTTA
1 TTTTA
5608612 AAGTTTAGGG
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
61 30 0.53
62 27 0.47
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (61 bp):
TTTTATAAAAATATTATTTAAGAAGTTTCTGTACAGAAACGACTTAAATAATTCATTTATA
Found at i:5608699 original size:63 final size:63
Alignment explanation
Indices: 5608632--5608758 Score: 170
Period size: 63 Copynumber: 2.0 Consensus size: 63
5608622 TTTAGAGTTA
*
5608632 ATATTTTTATAAAA-AGACTATTTAAGACT-TTTTTGTAT-AGAAAATGCCTTAAATAATCTTTT
1 ATATTTTTATAAAAGA-ACTATTTAAG-CTGTTTTTGT-TGAGAAAATGCCTTAAATAATATTTT
5608694 T
63 T
* * *
5608695 ATATTTTTATAAATGAATTATTTAAGGTGTTTTTGTTGAGAAAATGCCTTAAATAATATTTTT
1 ATATTTTTATAAAAGAACTATTTAAGCTGTTTTTGTTGAGAAAATGCCTTAAATAATATTTTT
5608758 A
1 A
5608759 ATAAATGAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
62 2 0.04
63 54 0.95
64 1 0.02
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (63 bp):
ATATTTTTATAAAAGAACTATTTAAGCTGTTTTTGTTGAGAAAATGCCTTAAATAATATTTTT
Found at i:5608784 original size:56 final size:57
Alignment explanation
Indices: 5608695--5608815 Score: 167
Period size: 56 Copynumber: 2.2 Consensus size: 57
5608685 TAATCTTTTT
* * *
5608695 ATATTTTT-ATAAATGAATTATTTAAGGTGTTTTTGT-T-GAGAAAATGCCTTAAATA
1 ATATTTTTAATAAATGAATTATTTAAGGTCTTTTT-TATACAAAAAATGCCTTAAATA
*
5608750 ATATTTTTAATAAATGAATTATTTAAGGTCTTTTTTATACAAAAAATGTCTTAAATA
1 ATATTTTTAATAAATGAATTATTTAAGGTCTTTTTTATACAAAAAATGCCTTAAATA
*
5608807 ATCTTTTTA
1 ATATTTTTA
5608816 TATTTTATGA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
55 9 0.16
56 26 0.45
57 23 0.40
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (57 bp):
ATATTTTTAATAAATGAATTATTTAAGGTCTTTTTTATACAAAAAATGCCTTAAATA
Found at i:5613639 original size:22 final size:22
Alignment explanation
Indices: 5613609--5613658 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
5613599 GTTCAATTCG
* * *
5613609 ATTTGATTTTTTTATTTTTAAA
1 ATTTAATTTCTTTATTTATAAA
*
5613631 ATTTAATTTCTTTATTTATATA
1 ATTTAATTTCTTTATTTATAAA
5613653 ATTTAA
1 ATTTAA
5613659 AAATATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTTAATTTCTTTATTTATAAA
Found at i:5613744 original size:2 final size:2
Alignment explanation
Indices: 5613737--5613762 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5613727 TCTGAACTTA
5613737 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
5613763 TAACATCCAA
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:5628008 original size:2 final size:2
Alignment explanation
Indices: 5628003--5628033 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5627993 AAAAAACATC
5628003 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 A
5628034 AAACTTGTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5637725 original size:22 final size:21
Alignment explanation
Indices: 5637695--5637735 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5637685 GGATTTGGGC
*
5637695 GTGGATTTGGCGGAGTTGGAAG
1 GTGGATTTGGAGGA-TTGGAAG
*
5637717 GTGGTTTTGGAGGATTGGA
1 GTGGATTTGGAGGATTGGA
5637736 TGAGAGAGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.17, C:0.02, G:0.49, T:0.32
Consensus pattern (21 bp):
GTGGATTTGGAGGATTGGAAG
Found at i:5641285 original size:2 final size:2
Alignment explanation
Indices: 5641278--5641303 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5641268 AATGCTACGA
5641278 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
5641304 GCAGATGTAC
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:5643562 original size:2 final size:2
Alignment explanation
Indices: 5643555--5643582 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5643545 AGTCATAATG
5643555 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
5643583 GAGCAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5648485 original size:18 final size:18
Alignment explanation
Indices: 5648462--5648497 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5648452 TCTGATACCA
5648462 TGTGGAAAAAATGAGAGT
1 TGTGGAAAAAATGAGAGT
5648480 TGTGGAAAAAATGAGAGT
1 TGTGGAAAAAATGAGAGT
5648498 ATATTGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (18 bp):
TGTGGAAAAAATGAGAGT
Found at i:5648507 original size:18 final size:18
Alignment explanation
Indices: 5648464--5648507 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5648454 TGATACCATG
*
5648464 TGGAAAAAATGAGAGTTG
1 TGGAAAAAATGAGAGTTA
5648482 TGGAAAAAATGAGAGTATA
1 TGGAAAAAATGAGAGT-TA
*
5648501 TTGAAAA
1 TGGAAAA
5648508 CTTTTGTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.27, T:0.23
Consensus pattern (18 bp):
TGGAAAAAATGAGAGTTA
Found at i:5649904 original size:36 final size:35
Alignment explanation
Indices: 5649864--5650043 Score: 146
Period size: 36 Copynumber: 5.0 Consensus size: 35
5649854 AATCTAGCAC
* *
5649864 AAAAGCACGACTTTCAAGTTAAACCCACTTCAACTA
1 AAAAGCAAGACTTTCAAGTTAAACCCAATTCAA-TA
* * *
5649900 AAAAGTAAAACTTTCAAGTTAAACCCAATTCAATGC
1 AAAAGCAAGACTTTCAAGTTAAACCCAATTCAAT-A
* * * *
5649936 AAAAGCAATACTTTCAATTTCAACTCAATTCAATA
1 AAAAGCAAGACTTTCAAGTTAAACCCAATTCAATA
* ** * *
5649971 GAAAAGCAACAGATTCAAATTAAACCCAATTCAACAA
1 -AAAAGCAAGACTTTCAAGTTAAACCCAATTCAA-TA
* * *
5650008 AAAAGTAAAATCTTTCAAAG-CAAACCCAATTCAATA
1 AAAAGCAAGA-CTTTC-AAGTTAAACCCAATTCAATA
5650044 CAATATCAAC
Statistics
Matches: 114, Mismatches: 25, Indels: 10
0.77 0.17 0.07
Matches are distributed among these distances:
35 1 0.01
36 94 0.82
37 17 0.15
38 2 0.02
ACGTcount: A:0.48, C:0.22, G:0.07, T:0.23
Consensus pattern (35 bp):
AAAAGCAAGACTTTCAAGTTAAACCCAATTCAATA
Found at i:5649939 original size:72 final size:72
Alignment explanation
Indices: 5649863--5650004 Score: 169
Period size: 72 Copynumber: 2.0 Consensus size: 72
5649853 CAATCTAGCA
* * * * *
5649863 CAAAAGCACGACTTTCAAGTTAAACCCACTTCAACTA-AAAAGTAAAACTTTCAAGTTAAACCCA
1 CAAAAGCAAGACTTTCAAGTTAAACCCAATTCAA-TAGAAAAGCAAAACATTCAAATTAAACCCA
5649927 ATTCAATG
65 ATTCAATG
* * * * * *
5649935 CAAAAGCAATACTTTCAATTTCAACTCAATTCAATAGAAAAGCAACAGATTCAAATTAAACCCAA
1 CAAAAGCAAGACTTTCAAGTTAAACCCAATTCAATAGAAAAGCAAAACATTCAAATTAAACCCAA
5650000 TTCAA
66 TTCAA
5650005 CAAAAAAGTA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
71 2 0.03
72 56 0.97
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.24
Consensus pattern (72 bp):
CAAAAGCAAGACTTTCAAGTTAAACCCAATTCAATAGAAAAGCAAAACATTCAAATTAAACCCAA
TTCAATG
Found at i:5651530 original size:29 final size:29
Alignment explanation
Indices: 5651497--5651565 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
5651487 ATAAAACAAA
* *
5651497 TAATACAAATATACACAAATAAACATGAC
1 TAATATAAATATACACAAATAAAAATGAC
** * *
5651526 TAATATGGATATATACAAATAAAAATGAT
1 TAATATAAATATACACAAATAAAAATGAC
5651555 TAATATAAATA
1 TAATATAAATA
5651566 ATACGAAAAC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.58, C:0.09, G:0.06, T:0.28
Consensus pattern (29 bp):
TAATATAAATATACACAAATAAAAATGAC
Found at i:5658658 original size:3 final size:3
Alignment explanation
Indices: 5658650--5658690 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
5658640 TAAAATTTGG
*
5658650 TTA TTA TTA TTC TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5658691 TAAAGTATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5663847 original size:135 final size:137
Alignment explanation
Indices: 5663603--5663877 Score: 536
Period size: 135 Copynumber: 2.0 Consensus size: 137
5663593 AGCTAAAAAT
5663603 CTAACACTCTACTATCTGATCATATGACTGTTGGATTTGATTTTTTTTTTTTTAAAAAGATATCT
1 CTAACACTCTACTATCTGATCATATGACTGTTGGATTTGATTTTTTTTTTTTTAAAAAGATATCT
5663668 TCCCTGTGTTTTCAGGATTTAGAGCAACTTTTGAATTTCATTGGTGTCAAGAGTTTAGGACCTCG
66 TCCCTGTGTTTTCAGGATTTAGAGCAACTTTTGAATTTCATTGGTGTCAAGAGTTTAGGACCTCG
5663733 CCATGTA
131 CCATGTA
5663740 CTAACACTCTACTATCTGATCATATGACTGTTGGATTTGA-TTTTTTTTTTTT-AAAAGATATCT
1 CTAACACTCTACTATCTGATCATATGACTGTTGGATTTGATTTTTTTTTTTTTAAAAAGATATCT
5663803 TCCCTGTGTTTTCAGGATTTAGAGCAACTTTTGAATTTCATTGGTGTCAAGAGTTTAGGACCTCG
66 TCCCTGTGTTTTCAGGATTTAGAGCAACTTTTGAATTTCATTGGTGTCAAGAGTTTAGGACCTCG
5663868 CCATGTA
131 CCATGTA
5663875 CTA
1 CTA
5663878 GCCAATTTGA
Statistics
Matches: 138, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
135 86 0.62
136 12 0.09
137 40 0.29
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (137 bp):
CTAACACTCTACTATCTGATCATATGACTGTTGGATTTGATTTTTTTTTTTTTAAAAAGATATCT
TCCCTGTGTTTTCAGGATTTAGAGCAACTTTTGAATTTCATTGGTGTCAAGAGTTTAGGACCTCG
CCATGTA
Found at i:5665315 original size:32 final size:29
Alignment explanation
Indices: 5665279--5665361 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
5665269 ACGTTAAAAA
* *
5665279 TAAATATCATATTAGTTAAATTATTCATAATT
1 TAAATATCATATTA--AAAATT-TTCAAAATT
* *
5665311 TAAATATCACATTAAAAATTTTTAAAATT
1 TAAATATCATATTAAAAATTTTCAAAATT
* *
5665340 TAAGTATCATATTAAATATTTT
1 TAAATATCATATTAAAAATTTT
5665362 ATTTTAATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 26 0.59
30 5 0.11
32 13 0.30
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (29 bp):
TAAATATCATATTAAAAATTTTCAAAATT
Found at i:5666111 original size:38 final size:38
Alignment explanation
Indices: 5666060--5666137 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 38
5666050 TTCAAATCCC
* *
5666060 TACCATTGAACATGTCCCAGAGTGATGAAGAAATAATA
1 TACCATCGAACATGTCCAAGAGTGATGAAGAAATAATA
* * *
5666098 TACCATCGAACATGTGCAAGCGTGATGAAGATATAATA
1 TACCATCGAACATGTCCAAGAGTGATGAAGAAATAATA
5666136 TA
1 TA
5666138 GTTAGTGATG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.24
Consensus pattern (38 bp):
TACCATCGAACATGTCCAAGAGTGATGAAGAAATAATA
Found at i:5667002 original size:58 final size:57
Alignment explanation
Indices: 5666919--5667034 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 57
5666909 AATTGGATAT
* * * *
5666919 AATAATTAATGTAGGTGATGTAGTCTTTATTTCCAAATAGAATAATATCATATATAAA
1 AATAAGTAATGTAGGTGATCTAGTCTTTATTTCCAAATAGAAT-ATAGCATACATAAA
*
5666977 AATAAGTAATGTTGGTGATCTAGTCTTTATTTCCAAATAGAATATAGCATACATAAA
1 AATAAGTAATGTAGGTGATCTAGTCTTTATTTCCAAATAGAATATAGCATACATAAA
5667034 A
1 A
5667035 CTCCAGTCAG
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 13 0.25
58 40 0.75
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (57 bp):
AATAAGTAATGTAGGTGATCTAGTCTTTATTTCCAAATAGAATATAGCATACATAAA
Done.