Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, 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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 28 of 105
Found at i:5606513 original size:3 final size:3
Alignment explanation
Indices: 5606507--5606616 Score: 57
Period size: 3 Copynumber: 34.7 Consensus size: 3
5606497 AGTCAAAAAA
* * *
5606507 AAT AAT AAT AAT AAAT AAAT AAA AAT ATT AAT AGAT AAAT GAT AA- AAT
1 AAT AAT AAT AAT -AAT -AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AAT
5606555 AA- ACATT AAT AGAT AAAT AAT AA- AAT AAAT AAT AAT AAT AA- AAT
1 AAT A-A-T AAT A-AT -AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
* *
5606599 AAAT AAT ATT ATT AAT AA
1 -AAT AAT AAT AAT AAT AA
5606617 ATAAACAAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 26
0.72 0.07 0.22
Matches are distributed among these distances:
2 7 0.08
3 54 0.63
4 22 0.26
5 3 0.03
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:5606538 original size:26 final size:26
Alignment explanation
Indices: 5606509--5606616 Score: 75
Period size: 26 Copynumber: 4.2 Consensus size: 26
5606499 TCAAAAAAAA
5606509 TAATAATAATAAATAAATAAAAATAT
1 TAATAATAATAAATAAATAAAAATAT
* * *
5606535 TAATAGATAA-ATGATAAA-ATAAACAT
1 TAATA-ATAATA-AATAAATAAAAATAT
* *
5606561 TAAT-A-GATAAAT-AAT-AAAATAAA
1 TAATAATAATAAATAAATAAAAAT-AT
* *
5606584 TAATAATAATAAAATAAATAATATTAT
1 TAATAATAAT-AAATAAATAAAAATAT
5606611 TAATAA
1 TAATAA
5606617 ATAAACAAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 19
0.66 0.13 0.21
Matches are distributed among these distances:
22 5 0.08
23 8 0.13
24 3 0.05
25 2 0.03
26 20 0.33
27 19 0.32
28 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.31
Consensus pattern (26 bp):
TAATAATAATAAATAAATAAAAATAT
Found at i:5606556 original size:12 final size:13
Alignment explanation
Indices: 5606506--5606606 Score: 95
Period size: 12 Copynumber: 7.8 Consensus size: 13
5606496 AAGTCAAAAA
5606506 AAATAATAATAAT
1 AAATAATAATAAT
5606519 AAAT-A-AATAA-
1 AAATAATAATAAT
*
5606529 AAATATTAATAGAT
1 AAATAATAATA-AT
*
5606543 AAATGATAA-AAT
1 AAATAATAATAAT
* *
5606555 AAACATTAATAGAT
1 AAATAATAATA-AT
5606569 AAATAATAA-AAT
1 AAATAATAATAAT
5606581 AAATAATAATAAT
1 AAATAATAATAAT
5606594 AAAATAAATAATA
1 -AAAT-AATAATA
5606607 TTATTAATAA
Statistics
Matches: 71, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
10 4 0.06
11 5 0.07
12 24 0.34
13 11 0.15
14 20 0.28
15 7 0.10
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:5606851 original size:16 final size:16
Alignment explanation
Indices: 5606830--5606863 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5606820 TTTGTGTTGG
*
5606830 TTTTTTCCACAACCAA
1 TTTTTTCCACAACAAA
5606846 TTTTTTCCACAACAAA
1 TTTTTTCCACAACAAA
5606862 TT
1 TT
5606864 GTCAAAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTTTTCCACAACAAA
Found at i:5608303 original size:17 final size:17
Alignment explanation
Indices: 5608266--5608303 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
5608256 CAAATAATTA
5608266 ATTATTTTTAAATCATTT
1 ATTATTTTTAAAT-ATTT
5608284 ATTATTTGTTAAAT-TTT
1 ATTATTT-TTAAATATTT
5608301 ATT
1 ATT
5608304 CCTAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 7 0.37
19 6 0.32
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (17 bp):
ATTATTTTTAAATATTT
Found at i:5608486 original size:3 final size:3
Alignment explanation
Indices: 5608478--5608520 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
5608468 TAAAAGAATG
5608478 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5608521 TCATAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5608567 original size:21 final size:21
Alignment explanation
Indices: 5608525--5608585 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
5608515 ATAATATCAT
* ** *
5608525 AAAAAACAAAAAAATGAGATG
1 AAAAAAAAAAAAAAAAAAATG
* * *
5608546 AAATAAAATAAAATAAAAATG
1 AAAAAAAAAAAAAAAAAAATG
5608567 AAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAA
5608586 ACAAAAATAA
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.82, C:0.02, G:0.07, T:0.10
Consensus pattern (21 bp):
AAAAAAAAAAAAAAAAAAATG
Found at i:5609031 original size:17 final size:16
Alignment explanation
Indices: 5608974--5609022 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
5608964 ACCATTTAGA
5608974 TTGAAATTTT-TTTATT
1 TTGAAATTTTCTTT-TT
* *
5608990 CTCAAA-TTTCTTTTT
1 TTGAAATTTTCTTTTT
5609005 TTGAAATTTTCTTTTT
1 TTGAAATTTTCTTTTT
5609021 TT
1 TT
5609023 TGAATTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.20, C:0.08, G:0.04, T:0.67
Consensus pattern (16 bp):
TTGAAATTTTCTTTTT
Found at i:5616368 original size:2 final size:2
Alignment explanation
Indices: 5616361--5616389 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5616351 ACAATTTTAC
5616361 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 A
5616390 GACCTATTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5619276 original size:16 final size:16
Alignment explanation
Indices: 5619250--5619282 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5619240 ATTTGATTAG
5619250 AAATATTTAAATATATT
1 AAATATTTAAATA-ATT
5619267 AAAT-TTTAAATAATT
1 AAATATTTAAATAATT
5619282 A
1 A
5619283 TTATAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATATTTAAATAATT
Found at i:5619300 original size:23 final size:22
Alignment explanation
Indices: 5619270--5619314 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
5619260 ATATATTAAA
*
5619270 TTTTAAATAATTATTATAATTT
1 TTTTAAATAATAATTATAATTT
5619292 TTTTAAAATAATAATTATAATTT
1 TTTT-AAATAATAATTATAATTT
5619315 CATATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTAAATAATAATTATAATTT
Found at i:5619754 original size:83 final size:81
Alignment explanation
Indices: 5619606--5619767 Score: 189
Period size: 83 Copynumber: 2.0 Consensus size: 81
5619596 AAACATATTT
* * *
5619606 AATAACCCCATTTAAAAATTTTTTTAAGACTATTCAAGCGTTTTTCACAAAAAATGCCTTAAGTA
1 AATAACCCCATTAAAAAATTTTTTTAAGACTATTCAAGCGTTTTTCACAAAAAATACATTAAGTA
5619671 ATCACCTCATAAAATC
66 ATCACCTCATAAAATC
* * * * ** * *
5619687 AATAACCGCATTAAAAAAATTTTTTTGAGATTATTCAAGATGTTTTTTGCTAAAAATACATTGAG
1 AATAACCCCATT-AAAAAATTTTTTTAAGACTATTCAAG-CGTTTTTCACAAAAAATACATTAAG
* *
5619752 TAATTACGTCATAAAA
64 TAATCACCTCATAAAA
5619768 ATTTATAAGG
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
81 11 0.17
82 23 0.35
83 32 0.48
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (81 bp):
AATAACCCCATTAAAAAATTTTTTTAAGACTATTCAAGCGTTTTTCACAAAAAATACATTAAGTA
ATCACCTCATAAAATC
Found at i:5619922 original size:126 final size:127
Alignment explanation
Indices: 5619696--5619928 Score: 305
Period size: 126 Copynumber: 1.8 Consensus size: 127
5619686 CAATAACCGC
* * * * * *
5619696 ATTAAAAAAATTTTTTTGAGATTATTCAAGATGTTTTTTGCTAAAAATACATTGAGTAATTACGT
1 ATTAAAAAAATTTTTTTGAAATTATTCAAGATGATTTATGATAAAAATACATTAAGTAATTACAT
* *
5619761 CATAAAAATTTATAAGGAGATTATTGAATATATTTTTAGTCAAAAATACCTTTAATAATCCT
66 CATAAAAATTTATAAGAAGATTATTGAATACATTTTTAGTCAAAAATACCTTTAATAATCCT
5619823 ATTAAAAAAA-TTTTTTGAAATTATTCAAGAT-ATTTATGATAAAAA-ACACCTTAAGTAATTAC
1 ATTAAAAAAATTTTTTTGAAATTATTCAAGATGATTTATGATAAAAATACA--TTAAGTAATTAC
* *
5619885 ATCATAAAATTTTATGAA-AAGATTATTGAA-AGCATTTTTTGTCA
64 ATCATAAAAATTTAT-AAGAAGATTATTGAATA-CATTTTTAGTCA
5619929 TTTCAAGCAT
Statistics
Matches: 92, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
124 3 0.03
125 12 0.13
126 65 0.71
127 12 0.13
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (127 bp):
ATTAAAAAAATTTTTTTGAAATTATTCAAGATGATTTATGATAAAAATACATTAAGTAATTACAT
CATAAAAATTTATAAGAAGATTATTGAATACATTTTTAGTCAAAAATACCTTTAATAATCCT
Found at i:5622229 original size:23 final size:24
Alignment explanation
Indices: 5622178--5622229 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
5622168 AAAAGAGGTT
*
5622178 AGTATAATTTTAAATTTAGATATG
1 AGTATAATTTTAAATTTAGATATA
*
5622202 TGTATAATTTT-AATTTGAGATA-A
1 AGTATAATTTTAAATTT-AGATATA
5622225 AGTAT
1 AGTAT
5622230 TTTTCTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.46
Consensus pattern (24 bp):
AGTATAATTTTAAATTTAGATATA
Found at i:5627010 original size:50 final size:50
Alignment explanation
Indices: 5626956--5627055 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
5626946 AAAAGTTTCA
5626956 ACAATAGCTTATATATAAGGAACTCTTTAATTGCACCCATAAACATTTAC
1 ACAATAGCTTATATATAAGGAACTCTTTAATTGCACCCATAAACATTTAC
5627006 ACAATAGCTTATATATAAGGAACTCTTTAATTGCACCCATAAACATTTAC
1 ACAATAGCTTATATATAAGGAACTCTTTAATTGCACCCATAAACATTTAC
5627056 GAGGATAGAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (50 bp):
ACAATAGCTTATATATAAGGAACTCTTTAATTGCACCCATAAACATTTAC
Found at i:5627159 original size:50 final size:49
Alignment explanation
Indices: 5627076--5627177 Score: 114
Period size: 50 Copynumber: 2.1 Consensus size: 49
5627066 TGATATTGTG
* ** * * *
5627076 ATTAACAAATCTATAACTATTTGTGTAAGTTAAAATTATTTCATGCATGC
1 ATTAACAAATCTATAACTATTAGCATAACTT-AAATTACTTCATGCATAC
* * *
5627126 ATTAACAAATTTATAACTGTTAGCATAACTTAAATTGCTTCATGCATAC
1 ATTAACAAATCTATAACTATTAGCATAACTTAAATTACTTCATGCATAC
5627175 ATT
1 ATT
5627178 TTTTTAATAT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
49 18 0.42
50 25 0.58
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (49 bp):
ATTAACAAATCTATAACTATTAGCATAACTTAAATTACTTCATGCATAC
Found at i:5627305 original size:10 final size:10
Alignment explanation
Indices: 5627290--5627331 Score: 57
Period size: 10 Copynumber: 3.9 Consensus size: 10
5627280 CCATTTATTA
5627290 TTTTTTTTTC
1 TTTTTTTTTC
5627300 TTTTTTTTTC
1 TTTTTTTTTC
5627310 TATTTTTTCTTTC
1 --TTTTTT-TTTC
5627323 TTTTTTTTT
1 TTTTTTTTT
5627332 TCTTCTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 13 0.45
11 6 0.21
12 6 0.21
13 4 0.14
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:5627306 original size:11 final size:11
Alignment explanation
Indices: 5627290--5627335 Score: 67
Period size: 12 Copynumber: 4.1 Consensus size: 11
5627280 CCATTTATTA
5627290 TTTTTTTTTC-
1 TTTTTTTTTCT
5627300 TTTTTTTTTCT
1 TTTTTTTTTCT
5627311 ATTTTTTCTTTCT
1 -TTTTTT-TTTCT
5627324 TTTTTTTTTCT
1 TTTTTTTTTCT
5627335 T
1 T
5627336 CTTCTTTCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.30
11 6 0.18
12 12 0.36
13 5 0.15
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:5627322 original size:23 final size:22
Alignment explanation
Indices: 5627288--5627331 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
5627278 CACCATTTAT
5627288 TATTTTTTTTTCTTTTTTTTTC
1 TATTTTTTTTTCTTTTTTTTTC
5627310 TATTTTTTCTTTCTTTTTTTTT
1 TATTTTTT-TTTCTTTTTTTTT
5627332 TCTTCTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.05, C:0.09, G:0.00, T:0.86
Consensus pattern (22 bp):
TATTTTTTTTTCTTTTTTTTTC
Found at i:5627591 original size:25 final size:24
Alignment explanation
Indices: 5627563--5627618 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
5627553 ATGATCGATT
5627563 AAAAAA-TCGAGAGGGGATCAATAAA
1 AAAAAACTCGAGA--GGATCAATAAA
* *
5627588 AAAAAACTTTGAGAGGATCGATAAA
1 AAAAAAC-TCGAGAGGATCAATAAA
5627613 AAAAAA
1 AAAAAA
5627619 AACCTTTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 22 0.81
27 5 0.19
ACGTcount: A:0.59, C:0.07, G:0.20, T:0.14
Consensus pattern (24 bp):
AAAAAACTCGAGAGGATCAATAAA
Found at i:5632780 original size:12 final size:10
Alignment explanation
Indices: 5632736--5632774 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
5632726 AAAATTTTTG
5632736 AAAAAAATTT
1 AAAAAAATTT
*
5632746 AAATATAAAATT
1 AAA-A-AAATTT
5632758 AAAAAAATTT
1 AAAAAAATTT
5632768 AAAAAAA
1 AAAAAAA
5632775 CTTTTATGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 15 0.60
11 2 0.08
12 8 0.32
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAAAAATTT
Found at i:5632780 original size:194 final size:190
Alignment explanation
Indices: 5632410--5632795 Score: 573
Period size: 194 Copynumber: 2.0 Consensus size: 190
5632400 ATAAATGTAG
*
5632410 ACATTTCTTTTTTAAAAATTTTGCATATACATATTTTTCTTTTTTCAATAAATAATAATTATTTA
1 ACATTTCTTTTTTAAAAATTTTACATATACATATTTTTCTTTTTTCAATAAATAATAATTATTTA
**
5632475 CTGTATTTTTAAAATATAAGTATATAGAAAATATTTATTATTTGATACCATTATCGAAAACAATT
66 CAATATTTTTAAAATATAAGTATATAGAAAATATTTATTATTTGATACC----TCGAAAACAATT
*
5632540 TTTGAAAAAAGTTTAAATATAAAATTAAAAAATAAAAAATACTTTTAT-CAGTTCCAATGTACAT
127 TTTGAAAAAAATTTAAATATAAAATTAAAAAATAAAAAATACTTTTATGCA-TTCCAATGTACAT
**
5632604 ACATTTCTTTTTTATTAATTTTACATATACATATTTTTCTTTTTTCAATAAATAATAATTATTTT
1 ACATTTCTTTTTTAAAAATTTTACATATACATATTTTTCTTTTTTCAATAAATAATAATTA---T
*
5632669 TTACAATATTTTTTAAATATAAGTATATAGAAAAATATTTATTATTTGATACC-CGAAAA-AATT
63 TTACAATATTTTTAAAATATAAGTATATAG-AAAATATTTATTATTTGATACCTCGAAAACAATT
5632732 TTTGAAAAAAATTTAAATATAAAATTAAAAAAATTTAAAAAA-ACTTTTATGCATTCCAATGTAC
127 TTTGAAAAAAATTTAAATATAAAATT-AAAAAA--TAAAAAATACTTTTATGCATTCCAATGTAC
5632796 TATGTTTTCA
Statistics
Matches: 177, Mismatches: 7, Indels: 16
0.88 0.04 0.08
Matches are distributed among these distances:
192 29 0.16
193 12 0.07
194 77 0.44
195 9 0.05
197 28 0.16
198 22 0.12
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (190 bp):
ACATTTCTTTTTTAAAAATTTTACATATACATATTTTTCTTTTTTCAATAAATAATAATTATTTA
CAATATTTTTAAAATATAAGTATATAGAAAATATTTATTATTTGATACCTCGAAAACAATTTTTG
AAAAAAATTTAAATATAAAATTAAAAAATAAAAAATACTTTTATGCATTCCAATGTACAT
Found at i:5634227 original size:28 final size:28
Alignment explanation
Indices: 5634172--5634227 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
5634162 AGCTCAGAGG
* * *
5634172 TATATTTGGTATTAAGCCTTCATGTTAT
1 TATACTTGGTATTAAGCCTTAATATTAT
5634200 TATACTTGGTATTAAGCCTTAATATTAT
1 TATACTTGGTATTAAGCCTTAATATTAT
5634228 ATGTTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.48
Consensus pattern (28 bp):
TATACTTGGTATTAAGCCTTAATATTAT
Found at i:5636623 original size:15 final size:15
Alignment explanation
Indices: 5636603--5636632 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5636593 CTATGATATT
5636603 TCTATAGAGTCCTCA
1 TCTATAGAGTCCTCA
5636618 TCTATAGAGTCCTCA
1 TCTATAGAGTCCTCA
5636633 CGCTTCCTAA
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:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (15 bp):
TCTATAGAGTCCTCA
Found at i:5636767 original size:2 final size:2
Alignment explanation
Indices: 5636760--5636786 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5636750 TTCTGTGTAG
5636760 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5636787 ATTTTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5638807 original size:13 final size:13
Alignment explanation
Indices: 5638767--5638805 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
5638757 TAAATAATTG
5638767 TAAATAATAAAAA
1 TAAATAATAAAAA
*
5638780 TGAATAATAAAAA
1 TAAATAATAAAAA
5638793 TAAATGAATAAAA
1 TAAAT-AATAAAA
5638806 TAGAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (13 bp):
TAAATAATAAAAA
Found at i:5642017 original size:18 final size:15
Alignment explanation
Indices: 5641981--5642009 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5641971 ACATCATTAT
5641981 TTAAAAATAAATATA
1 TTAAAAATAAATATA
5641996 TTAAAAATAAATAT
1 TTAAAAATAAATAT
5642010 CATATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAAAAATAAATATA
Found at i:5642832 original size:106 final size:106
Alignment explanation
Indices: 5642701--5642905 Score: 311
Period size: 106 Copynumber: 1.9 Consensus size: 106
5642691 TATCTATGAA
* *
5642701 TTGAATTATTAATCTAATTTGAAGTTTTCTCTTATTCAAGTCAAGTTTTAAGTAAAAATTTTTCA
1 TTGAATTATTAATCTAATTTGAAGTTTTATCTTATTCAAGTCAAGTTTTAAATAAAAATTTTTCA
* *
5642766 ATTCGATTCATTTTGATCTAAAATATTAAATTATACATAAG
66 ATTCGATTCATTTTGATCCAAAAAATTAAATTATACATAAG
* * *
5642807 TTGAATTATTCATTTAATTTGAAGTTTTATCTTATTCAAGTCGAGTTTTAAATAAAAATTTTTCA
1 TTGAATTATTAATCTAATTTGAAGTTTTATCTTATTCAAGTCAAGTTTTAAATAAAAATTTTTCA
* * **
5642872 GTTTGATTTGTTTTGATCCAAAAAATTAAATTAT
66 ATTCGATTCATTTTGATCCAAAAAATTAAATTAT
5642906 TAATAAAAGT
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
106 88 1.00
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (106 bp):
TTGAATTATTAATCTAATTTGAAGTTTTATCTTATTCAAGTCAAGTTTTAAATAAAAATTTTTCA
ATTCGATTCATTTTGATCCAAAAAATTAAATTATACATAAG
Found at i:5644274 original size:153 final size:153
Alignment explanation
Indices: 5643971--5644431 Score: 845
Period size: 153 Copynumber: 3.0 Consensus size: 153
5643961 TTTTAGGTTT
*
5643971 ACCGGAAATTGATTTTAAAAAATGTTTATTATTTTTAAAAAAGTAAAATTTTTTTATCATATGGA
1 ACCGGAAATTGATTTTAAAAAATGTTTATAATTTTTAAAAAAGTAAAATTTTTTTATCATATGGA
*
5644036 TATGTCAATTAAAAATATTTTTTTATTATTTGATTTTTTAAAAAAATTTATTTTTTTAAAATAAT
66 TATGTCAATTAAAAATATTTTTTTATTATTTGATTTTTTAAAAAAATTTA-ATTTTTAAAATAAT
5644101 ATTAACATAACTATTAAAATATTA
130 ATTAACATAACTATTAAAATATTA
5644125 ACCGGAAATTGATTTTAAAAAATGTTTATAATTTTTAAAAAAGTAAAATTTTTTTATCATATGGA
1 ACCGGAAATTGATTTTAAAAAATGTTTATAATTTTTAAAAAAGTAAAATTTTTTTATCATATGGA
*
5644190 TATGTCAATTAAAAATATTTTTTTATTATTTGATTTTTT-AAAAAATTTAACTTTTAAAAATAAT
66 TATGTCAATTAAAAATATTTTTTTATTATTTGATTTTTTAAAAAAATTTAA-TTTTTAAAATAAT
5644254 ATTAACATAACTATTAAAATATTA
130 ATTAACATAACTATTAAAATATTA
*
5644278 ACCGAAAATTGATTTTAAAAAATGTTTATAATTTTTAAAAAA-TAAAATTTTTTTATCATATGGA
1 ACCGGAAATTGATTTTAAAAAATGTTTATAATTTTTAAAAAAGTAAAATTTTTTTATCATATGGA
5644342 TATGTCAATTAAAAATATTTTTTTATTATTTGATTTTTTAAAAAAAATTTAATTTTTAAAATAAT
66 TATGTCAATTAAAAATATTTTTTTATTATTTGATTTTTT-AAAAAAATTTAATTTTTAAAATAAT
5644407 ATTAACATAACTATTAAAATATTA
130 ATTAACATAACTATTAAAATATTA
5644431 A
1 A
5644432 AAATTATTTA
Statistics
Matches: 299, Mismatches: 5, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
152 61 0.20
153 124 0.41
154 114 0.38
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.46
Consensus pattern (153 bp):
ACCGGAAATTGATTTTAAAAAATGTTTATAATTTTTAAAAAAGTAAAATTTTTTTATCATATGGA
TATGTCAATTAAAAATATTTTTTTATTATTTGATTTTTTAAAAAAATTTAATTTTTAAAATAATA
TTAACATAACTATTAAAATATTA
Found at i:5644847 original size:42 final size:42
Alignment explanation
Indices: 5644801--5644896 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
5644791 TTTAAATCAA
*
5644801 AAAATAATAATGATATTATTAAAT-TATTTAATATTCATTATT
1 AAAATAATAATAATATTATTAAATATA-TTAATATTCATTATT
* * *
5644843 AAAATAATCAA-AATATTATTTAATATATTATTATTTATTATT
1 AAAATAAT-AATAATATTATTAAATATATTAATATTCATTATT
*
5644885 CAAATAATAATA
1 AAAATAATAATA
5644897 TAATACTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
41 2 0.04
42 40 0.87
43 4 0.09
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (42 bp):
AAAATAATAATAATATTATTAAATATATTAATATTCATTATT
Found at i:5644895 original size:29 final size:29
Alignment explanation
Indices: 5644863--5644919 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
5644853 AAATATTATT
* *
5644863 TAATATATTATTATTTATTATTCAAATAA
1 TAATATAATACTATTTATTATTCAAATAA
*
5644892 TAATATAATACTATTTATTATTGAAATA
1 TAATATAATACTATTTATTATTCAAATA
5644920 TTAAAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (29 bp):
TAATATAATACTATTTATTATTCAAATAA
Found at i:5644929 original size:32 final size:29
Alignment explanation
Indices: 5644864--5644930 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
5644854 AATATTATTT
* * * *
5644864 AATATATTATTATTTATTATTCAAATAAT
1 AATATAATACTATTTATTATTAAAATAAA
5644893 AATATAATACTATTTATTATTGAAATATTAAA
1 AATATAATACTATTTATTATT-AAA-A-TAAA
5644925 AATATA
1 AATATA
5644931 TATGTTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 19 0.61
30 2 0.06
31 1 0.03
32 9 0.29
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (29 bp):
AATATAATACTATTTATTATTAAAATAAA
Found at i:5644962 original size:24 final size:25
Alignment explanation
Indices: 5644916--5644963 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
5644906 TTATTATTGA
* * *
5644916 AATATTAAAAATATATATGTTTAAT
1 AATATTAAAAATAAAAATATTTAAT
5644941 AATA-TAAAAATAAAAATATTTAA
1 AATATTAAAAATAAAAATATTTAA
5644964 AACTAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
AATATTAAAAATAAAAATATTTAAT
Found at i:5655877 original size:4 final size:4
Alignment explanation
Indices: 5655868--5655893 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5655858 TATAGTGGTC
5655868 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
5655894 TTTCAAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:5658502 original size:3 final size:3
Alignment explanation
Indices: 5658494--5658524 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5658484 TTGATAAAAA
5658494 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5658525 CTAAAGAATA
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:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5658612 original size:2 final size:2
Alignment explanation
Indices: 5658607--5658633 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5658597 ACACACATAA
5658607 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5658634 AGTATCAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5662801 original size:21 final size:22
Alignment explanation
Indices: 5662768--5662811 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
5662758 CTTGCTACTA
*
5662768 CACTCTTTATCTCACAAACTCT
1 CACTCTTTATCTCACAAAATCT
* *
5662790 CACT-TTTCTCTCTCAAAATCT
1 CACTCTTTATCTCACAAAATCT
5662811 C
1 C
5662812 TAATTTGGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.25, C:0.36, G:0.00, T:0.39
Consensus pattern (22 bp):
CACTCTTTATCTCACAAAATCT
Found at i:5666228 original size:24 final size:23
Alignment explanation
Indices: 5666178--5666233 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
5666168 TGACACTCAT
* * **
5666178 ATAATTATTTATTTAATATTTTC
1 ATAATTATTTATTTAACATATGA
5666201 ATAATATATTTATTTAACATATGA
1 ATAAT-TATTTATTTAACATATGA
5666225 ATAACTTAT
1 ATAA-TTAT
5666234 AGAAATAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 5 0.19
24 21 0.78
25 1 0.04
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (23 bp):
ATAATTATTTATTTAACATATGA
Found at i:5669778 original size:2 final size:2
Alignment explanation
Indices: 5669771--5669799 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5669761 CATTGATACT
5669771 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
5669800 TTATGTGTGT
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:5669890 original size:3 final size:3
Alignment explanation
Indices: 5669882--5669909 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5669872 TATTCTTTAG
5669882 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5669910 TTTTTATCAA
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):
AAT
Found at i:5673555 original size:29 final size:29
Alignment explanation
Indices: 5673522--5673577 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
5673512 TCATTTGGAA
5673522 ATATAAATTACTCTAGTATTCTTGCACAT
1 ATATAAATTACTCTAGTATTCTTGCACAT
5673551 ATATAAATTACTCTAGTATTCTTGCAC
1 ATATAAATTACTCTAGTATTCTTGCAC
5673578 CTATGTTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (29 bp):
ATATAAATTACTCTAGTATTCTTGCACAT
Found at i:5683467 original size:29 final size:29
Alignment explanation
Indices: 5683435--5683510 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
5683425 TTTATATTAT
*
5683435 TAAACA-TATATATTTTAATATTTCAATAA
1 TAAACAGTAT-TATATTAATATTTCAATAA
* * *
5683464 TAAATAGTATTATATTATTATTTGAATAA
1 TAAACAGTATTATATTAATATTTCAATAA
* * *
5683493 TAAATAATAATATATTAA
1 TAAACAGTATTATATTAA
5683511 ATAATATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 36 0.92
30 3 0.08
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (29 bp):
TAAACAGTATTATATTAATATTTCAATAA
Found at i:5683522 original size:34 final size:34
Alignment explanation
Indices: 5683444--5683549 Score: 81
Period size: 34 Copynumber: 3.1 Consensus size: 34
5683434 TTAAACATAT
* * * *
5683444 ATATTTT-AATATTTCAATAATAAATAGTATTATA
1 ATATTTTGAATATATAAATAATAAATATTA-AATA
*
5683478 TTATTATTTGAATA-ATAAATAATAATATATTAAATA
1 ATA-T-TTTGAATATATAAATAATAA-ATATTAAATA
* * * *
5683514 ATATTTTGATTATTTTAATAATGAATATTAAATA
1 ATATTTTGAATATATAAATAATAAATATTAAATA
5683548 AT
1 AT
5683550 TTAATAATAT
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
34 21 0.37
35 10 0.18
36 17 0.30
37 9 0.16
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (34 bp):
ATATTTTGAATATATAAATAATAAATATTAAATA
Found at i:5683568 original size:42 final size:41
Alignment explanation
Indices: 5683474--5683571 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 41
5683464 TAAATAGTAT
*
5683474 TATATTATTATTTGAATAATAAATAATAATATATTAAATAA
1 TATATTATTATTTTAATAATAAATAATAATATATTAAATAA
* * * *
5683515 TATTTTGATTATTTTAATAATGAATATTAA-ATAATTTAATAA
1 TATATT-ATTATTTTAATAATAAATAATAATAT-ATTAAATAA
5683557 TATCATTATTATTTT
1 TAT-ATTATTATTTT
5683572 TTGATTTAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
41 7 0.15
42 39 0.81
43 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (41 bp):
TATATTATTATTTTAATAATAAATAATAATATATTAAATAA
Found at i:5683993 original size:17 final size:17
Alignment explanation
Indices: 5683971--5684003 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5683961 GTTAATATTA
*
5683971 TTTTAAAAAATTAAATT
1 TTTTAAAAAATCAAATT
5683988 TTTTAAAAAATCAAAT
1 TTTTAAAAAATCAAAT
5684004 AATAAAAAAA
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:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTTAAAAAATCAAATT
Found at i:5684208 original size:150 final size:153
Alignment explanation
Indices: 5683942--5684398 Score: 827
Period size: 150 Copynumber: 3.0 Consensus size: 153
5683932 ATAAATAATT
5683942 TTAATATTTTAATAGTTATGTTAATATTATTTTAAAAAATTAAATTTTTTAAAAAATCAAATAAT
1 TTAATATTTTAATAGTTATGTTAATATTATTTTAAAAAATTAAATTTTTTAAAAAATCAAATAAT
5684007 AAAAAAATATTTTTAATTGACATATCCATATGATAAAAAAATTTTA--TTTTTAAAAATTATAAA
66 AAAAAAATATTTTTAATTGACATATCCATATGATAAAAAAATTTTACTTTTTTAAAAATTATAAA
*
5684070 CATTTTTTAAAATCAATTTTCGG
131 CATTTTTTAAAATCAATTTCCGG
5684093 TTAATATTTTAATAGTTATGTTAATATTATTTT-AAAAATTAAATTTTTTAAAAAATCAAATAAT
1 TTAATATTTTAATAGTTATGTTAATATTATTTTAAAAAATTAAATTTTTTAAAAAATCAAATAAT
5684157 -AAAAAATATTTTTAATTGACATATCCATATGAT-AAAAAATTTTACTTTTTTAAAAATTATAAA
66 AAAAAAATATTTTTAATTGACATATCCATATGATAAAAAAATTTTACTTTTTTAAAAATTATAAA
5684220 CATTTTTTAAAATCAATTTCCGG
131 CATTTTTTAAAATCAATTTCCGG
5684243 TTAATATTTTAATAGTTATGTTAATATTATTTTAAAAAATTAAATTTTTTTAAAAAATCAAATAA
1 TTAATATTTTAATAGTTATGTTAATATTATTTTAAAAAATTAAA-TTTTTTAAAAAATCAAATAA
*
5684308 TAAAAAAATATTTTTAATTGAC-TCATCCATATGATAAAAATAATTTTACTTTTTTAAAAATTAA
65 TAAAAAAATATTTTTAATTGACAT-ATCCATATGATAAAAA-AATTTTACTTTTTTAAAAATTAT
5684372 AAACATTTTTTAAAATCAATTTCCGG
128 AAACATTTTTTAAAATCAATTTCCGG
5684398 T
1 T
5684399 AAACCTAAAA
Statistics
Matches: 296, Mismatches: 2, Indels: 12
0.95 0.01 0.04
Matches are distributed among these distances:
148 11 0.04
149 33 0.11
150 103 0.35
151 43 0.15
152 22 0.07
153 31 0.10
154 4 0.01
155 49 0.17
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (153 bp):
TTAATATTTTAATAGTTATGTTAATATTATTTTAAAAAATTAAATTTTTTAAAAAATCAAATAAT
AAAAAAATATTTTTAATTGACATATCCATATGATAAAAAAATTTTACTTTTTTAAAAATTATAAA
CATTTTTTAAAATCAATTTCCGG
Found at i:5685559 original size:106 final size:106
Alignment explanation
Indices: 5685433--5685637 Score: 257
Period size: 106 Copynumber: 1.9 Consensus size: 106
5685423 ATTTTTATTA
* * *
5685433 ATAATTTAATTTTTTAGATCAAAACAAATCAAACCGAAAAAATTTTATTTAACACTCAACTTGAA
1 ATAATTTAATATTTTAGATCAAAACAAATCAAACCGAAAAAATTTTACTTAAAACTCAACTTGAA
* *
5685498 AAAGATAAAATTTCAAATTAGATGAATAATTCAACTTATGG
66 AAAGAGAAAACTTCAAATTAGATGAATAATTCAACTTATGG
* ** * ** * **
5685539 ATAATTTAATATTTTGGATCAAAATGAATCGAATTGAAAAATTTTTACTTAAAACTTGACTTGAA
1 ATAATTTAATATTTTAGATCAAAACAAATCAAACCGAAAAAATTTTACTTAAAACTCAACTTGAA
** *
5685604 TCAGAGAAAACTTCAAATTAGATTAATAATTCAA
66 AAAGAGAAAACTTCAAATTAGATGAATAATTCAA
5685638 TTCATAGATA
Statistics
Matches: 82, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
106 82 1.00
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.34
Consensus pattern (106 bp):
ATAATTTAATATTTTAGATCAAAACAAATCAAACCGAAAAAATTTTACTTAAAACTCAACTTGAA
AAAGAGAAAACTTCAAATTAGATGAATAATTCAACTTATGG
Found at i:5686360 original size:16 final size:15
Alignment explanation
Indices: 5686329--5686357 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5686319 AATTAATATG
5686329 ATATTTATTTTTAAT
1 ATATTTATTTTTAAT
5686344 ATATTTATTTTTAA
1 ATATTTATTTTTAA
5686358 ATAATGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATATTTATTTTTAAT
Found at i:5693319 original size:12 final size:12
Alignment explanation
Indices: 5693289--5693327 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5693279 CAAACAATGT
*
5693289 CATATACATATA
1 CATATGCATATA
* *
5693301 CACATGCATATG
1 CATATGCATATA
5693313 CATATGCATATA
1 CATATGCATATA
5693325 CAT
1 CAT
5693328 TTATATGTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (12 bp):
CATATGCATATA
Found at i:5699080 original size:57 final size:57
Alignment explanation
Indices: 5699016--5699170 Score: 247
Period size: 57 Copynumber: 2.7 Consensus size: 57
5699006 TCTCTTATGT
* *
5699016 ATCATTAAATTATTATATGTCAAACATTAATATATGCATTCTTTCATTCATTCATGC
1 ATCATTAAATTATTATATGTCAAACATTAATACATGCATTCCTTCATTCATTCATGC
*
5699073 ATTATTAAATTATTATATGTCAAACATTAATACATGCATTCCTTCATTCATTCATGC
1 ATCATTAAATTATTATATGTCAAACATTAATACATGCATTCCTTCATTCATTCATGC
* * * *
5699130 ATCATTAAATTGTTATAGGTCAAACATTAATGCGTGCATTC
1 ATCATTAAATTATTATATGTCAAACATTAATACATGCATTC
5699171 ATCATTAATT
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 90 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (57 bp):
ATCATTAAATTATTATATGTCAAACATTAATACATGCATTCCTTCATTCATTCATGC
Found at i:5699906 original size:142 final size:143
Alignment explanation
Indices: 5699679--5699962 Score: 394
Period size: 142 Copynumber: 2.0 Consensus size: 143
5699669 GCATAAGGTC
* * *
5699679 ATTTTTAGAGTTATATTAATATTGTCTTTAAAGAAAAGTCATCAGATCCAGTTTTCATTCCTAAC
1 ATTTCTAGAGTTATATTAATATTGTCTTTAAAGAAAAGACATCAGATCCAATTTTCATTCCTAAC
* *
5699744 CTAGATAACCTTAAGGAAAAAGAGAAATTAAAGATAAATGCATCTAAAG-TAATCAAAGATTCAA
66 CTAGATAACCTTAAGGAAAAAGAGAAATTAAAGATAAAAGCAT-TAAAGCCAATCAAAGATTCAA
*
5699808 GCTTTTAGCAAAAG
130 GCTCTTAGCAAAAG
* ** * * * *
5699822 ATTTCTAGAGTTATATTAATCTTGTCTTTGGAG-AAAGACGTCATATCCAA-TTTCTATTCTTGA
1 ATTTCTAGAGTTATATTAATATTGTCTTTAAAGAAAAGACATCAGATCCAATTTTC-ATTCCTAA
**
5699885 CCTAGATAACCTTAAGGAAAAAGAGAAATTAAAGATAAAAGCATTTGAGCCAATCAAAGATTCAA
65 CCTAGATAACCTTAAGGAAAAAGAGAAATTAAAGATAAAAGCATTAAAGCCAATCAAAGATTCAA
5699950 GCTCTTAGCAAAA
130 GCTCTTAGCAAAA
5699963 TATGAATTTG
Statistics
Matches: 124, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
141 7 0.06
142 88 0.71
143 29 0.23
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (143 bp):
ATTTCTAGAGTTATATTAATATTGTCTTTAAAGAAAAGACATCAGATCCAATTTTCATTCCTAAC
CTAGATAACCTTAAGGAAAAAGAGAAATTAAAGATAAAAGCATTAAAGCCAATCAAAGATTCAAG
CTCTTAGCAAAAG
Found at i:5700489 original size:67 final size:67
Alignment explanation
Indices: 5700361--5700513 Score: 166
Period size: 67 Copynumber: 2.3 Consensus size: 67
5700351 TTTTTATCTT
* * ** * *
5700361 GAGTCGAGCTTAAACTTAAAAATTAAAACTTAATCAAGCTTGATATGAGTTTCAAGTAGTGAATT
1 GAGTCGAGCTCAAACTTAAAAATTAAAACTCAATCAAGCTCAATATAAGTTTCAAGCAGTGAATT
5700426 TC
66 TC
* * * *
5700428 GAGTCGAGCTCGAACTTGAAAATTAAAACTCGATCAAGCTCAATCTAAGTTGT-AAGCAGTGAAT
1 GAGTCGAGCTCAAACTTAAAAATTAAAACTCAATCAAGCTCAATATAAGTT-TCAAGCAGTGAAT
5700492 TT-
65 TTC
* *
5700494 GAAGTTGAGCTCAAGCTTAA
1 G-AGTCGAGCTCAAACTTAA
5700514 GTTTCTTACT
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
66 1 0.01
67 68 0.97
68 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (67 bp):
GAGTCGAGCTCAAACTTAAAAATTAAAACTCAATCAAGCTCAATATAAGTTTCAAGCAGTGAATT
TC
Found at i:5702849 original size:20 final size:19
Alignment explanation
Indices: 5702814--5702870 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 19
5702804 AAATAAGGAC
5702814 AAAAAAGATG-AAAAAATG
1 AAAAAAGATGAAAAAAATG
5702832 AAAAATAGATGAAAAAAATG
1 AAAAA-AGATGAAAAAAATG
*
5702852 AAAAAAGAGGAGAAAAAAT
1 AAAAAAGATGA-AAAAAAT
5702871 AATTAAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
18 5 0.14
19 10 0.29
20 20 0.57
ACGTcount: A:0.72, C:0.00, G:0.18, T:0.11
Consensus pattern (19 bp):
AAAAAAGATGAAAAAAATG
Found at i:5702957 original size:20 final size:21
Alignment explanation
Indices: 5702922--5702960 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5702912 GATATTTGGG
*
5702922 CTAAAAACACGAAAAGACAGC
1 CTAAAAACAAGAAAAGACAGC
5702943 CTAAAAACAAG-AAAGACA
1 CTAAAAACAAGAAAAGACA
5702961 ATATCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.62, C:0.21, G:0.13, T:0.05
Consensus pattern (21 bp):
CTAAAAACAAGAAAAGACAGC
Found at i:5703665 original size:14 final size:14
Alignment explanation
Indices: 5703646--5703689 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5703636 TTTTTACCAC
5703646 TTGTATTCATGGCA
1 TTGTATTCATGGCA
*
5703660 TTGTATTCATAGCA
1 TTGTATTCATGGCA
** *
5703674 TTACAATCATGGCA
1 TTGTATTCATGGCA
5703688 TT
1 TT
5703690 CATTGCAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (14 bp):
TTGTATTCATGGCA
Found at i:5704137 original size:33 final size:33
Alignment explanation
Indices: 5704095--5704276 Score: 172
Period size: 33 Copynumber: 5.5 Consensus size: 33
5704085 AATATCTTTG
* **
5704095 ATTTTATTTTTAGACTTCGGTTTAATTCAAGTC
1 ATTTCATTTTTAGACTTCGGTTTAAGCCAAGTC
* * *
5704128 ATTTCATTTTTAAACTTCAGCTT-AGTCCAA-TC
1 ATTTCATTTTTAGACTTCGGTTTAAG-CCAAGTC
* * ** * * *
5704160 AATTCAATTTTAGACTTTAG-CTCAGTCTAAGTC
1 ATTTCATTTTTAGACTTCGGTTTAAG-CCAAGTC
* *
5704193 ATTTCATTTTCAGACTTCGGTTCAAGCCAAGTC
1 ATTTCATTTTTAGACTTCGGTTTAAGCCAAGTC
5704226 ATTTCATTTTTAGACTTCGGTTTAAGCCAAGTC
1 ATTTCATTTTTAGACTTCGGTTTAAGCCAAGTC
* *
5704259 ATTTTATTTTCAGACTTC
1 ATTTCATTTTTAGACTTC
5704277 TACTCAACTC
Statistics
Matches: 120, Mismatches: 25, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
31 1 0.01
32 25 0.21
33 92 0.77
34 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.44
Consensus pattern (33 bp):
ATTTCATTTTTAGACTTCGGTTTAAGCCAAGTC
Found at i:5704202 original size:32 final size:33
Alignment explanation
Indices: 5704095--5704473 Score: 155
Period size: 33 Copynumber: 11.5 Consensus size: 33
5704085 AATATCTTTG
* * * * * *
5704095 ATTTTATTTTTAGACTTCGGTTTAATTCAAGTC
1 ATTTCATTTTTAGACTTCAGCTCAGTCCAAGTC
* *
5704128 ATTTCATTTTTAAACTTCAGCTTAGTCCAA-TC
1 ATTTCATTTTTAGACTTCAGCTCAGTCCAAGTC
* * * *
5704160 AATTCAATTTTAGACTTTAGCTCAGTCTAAGTC
1 ATTTCATTTTTAGACTTCAGCTCAGTCCAAGTC
* * *
5704193 ATTTCATTTTCAGACTTCGGTTCAAG-CCAAGTC
1 ATTTCATTTTTAGACTTCAGCTC-AGTCCAAGTC
* * *
5704226 ATTTCATTTTTAGACTTCGGTTTAAG-CCAAGTC
1 ATTTCATTTTTAGACTTCAG-CTCAGTCCAAGTC
* * *
5704259 ATTTTATTTTCAGACTTCTA-CTCAACTCC-AGT-
1 ATTTCATTTTTAGACTTC-AGCTC-AGTCCAAGTC
* ** * * *
5704291 AGTTTCATTTTTAGAGTTTGGCTCTGTCTAGGTC
1 A-TTTCATTTTTAGACTTCAGCTCAGTCCAAGTC
* * ** * * * *
5704325 ATTT-TTTTTTCAAACTTTGGTTTAATTCAAGTC
1 ATTTCATTTTT-AGACTTCAGCTCAGTCCAAGTC
* * * * * *
5704358 ATTTTA-TTTTGGGCTTTAACTCAGTTCAAGTC
1 ATTTCATTTTTAGACTTCAGCTCAGTCCAAGTC
* ** * ** * *
5704390 TTTTTTTTTTTACA-TTTTGACTCAATTCAAGTC
1 ATTTCATTTTTAGACTTCAG-CTCAGTCCAAGTC
* * * *
5704423 ATTTCATTTTTAGACTTAAACTCAGTCCTACTC
1 ATTTCATTTTTAGACTTCAGCTCAGTCCAAGTC
5704456 ATTTCATTTTTAGACTTC
1 ATTTCATTTTTAGACTTC
5704474 GATTTAGTTC
Statistics
Matches: 256, Mismatches: 75, Indels: 30
0.71 0.21 0.08
Matches are distributed among these distances:
32 56 0.22
33 191 0.75
34 9 0.04
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.46
Consensus pattern (33 bp):
ATTTCATTTTTAGACTTCAGCTCAGTCCAAGTC
Found at i:5704924 original size:22 final size:20
Alignment explanation
Indices: 5704894--5704949 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 20
5704884 TTTTCTTTTC
5704894 TTTTTTATTTACTTTATTCAT
1 TTTTTTATTTA-TTTATTCAT
*
5704915 TTTTTGTATTTATTTATTTAT
1 TTTTT-TATTTATTTATTCAT
5704936 TTTTATT-TTTATTT
1 TTTT-TTATTTATTT
5704950 TTGAAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 7 0.22
21 18 0.56
22 7 0.22
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTTTATTTATTTATTCAT
Found at i:5705253 original size:31 final size:32
Alignment explanation
Indices: 5705215--5705276 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
5705205 ATAATAATAT
* *
5705215 GACAAGGCCCACTTGCTTTATT-TTTATAATG
1 GACAAGGCCAACTTGCTTTATTACTTATAATG
*
5705246 GACAAGGCCAATTTGCTTTATTACTTATAAT
1 GACAAGGCCAACTTGCTTTATTACTTATAAT
5705277 AAGATAAAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (32 bp):
GACAAGGCCAACTTGCTTTATTACTTATAATG
Found at i:5712374 original size:9 final size:10
Alignment explanation
Indices: 5712348--5712378 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
5712338 GACCTCACAC
5712348 TTAAACAAAAA
1 TTAAA-AAAAA
5712359 TTAAAAAAAA
1 TTAAAAAAAA
5712369 TTAAAAAAAA
1 TTAAAAAAAA
5712379 ACCTAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.75
11 5 0.25
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (10 bp):
TTAAAAAAAA
Found at i:5717447 original size:17 final size:17
Alignment explanation
Indices: 5717412--5717445 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5717402 ATATCTTTTT
5717412 ATAAAAATATATTTAAA
1 ATAAAAATATATTTAAA
*
5717429 ATAAAATTAT-TTTAAA
1 ATAAAAATATATTTAAA
5717445 A
1 A
5717446 ATGTTGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAAAATATATTTAAA
Found at i:5721973 original size:2 final size:2
Alignment explanation
Indices: 5721966--5721991 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5721956 TCACTCTTTC
5721966 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
5721992 TCTTGACAAT
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:5724533 original size:9 final size:9
Alignment explanation
Indices: 5724494--5724535 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
5724484 AACAATATCT
*
5724494 TATTATTTA
1 TATTTTTTA
**
5724503 TATTTTGAA
1 TATTTTTTA
5724512 TATTTTTTA
1 TATTTTTTA
5724521 -ATTTTTTA
1 TATTTTTTA
5724529 TATTTTT
1 TATTTTT
5724536 GACAATAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (9 bp):
TATTTTTTA
Found at i:5724558 original size:13 final size:13
Alignment explanation
Indices: 5724540--5724573 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5724530 ATTTTTGACA
*
5724540 ATAAAAATATTGT
1 ATAAAAATATTAT
5724553 ATAAAAATATTAT
1 ATAAAAATATTAT
*
5724566 AAAAAAAT
1 ATAAAAAT
5724574 TAAATTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (13 bp):
ATAAAAATATTAT
Found at i:5726795 original size:2 final size:2
Alignment explanation
Indices: 5726790--5726815 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5726780 TCCCATACAA
5726790 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
5726816 TTATGAATGT
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:5727326 original size:30 final size:31
Alignment explanation
Indices: 5727292--5727367 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
5727282 TTATTCGTAT
5727292 TAAATAAACCTCTAAATTTT-AACTTATATA
1 TAAATAAACCTCTAAATTTTCAACTTATATA
* * * *
5727322 TAAATAAATACT-TAAATTTTCAATTTGTATC
1 TAAATAAA-CCTCTAAATTTTCAACTTATATA
5727353 TAAATAAACCTCTAA
1 TAAATAAACCTCTAA
5727368 CATAAATTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
30 18 0.47
31 20 0.53
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.39
Consensus pattern (31 bp):
TAAATAAACCTCTAAATTTTCAACTTATATA
Found at i:5728911 original size:20 final size:19
Alignment explanation
Indices: 5728870--5728913 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
5728860 AATTTGTAGG
*
5728870 TTTAATTGAGTTTTAATGT
1 TTTAATTGAGTTTTAATAT
* *
5728889 TTTAATTTATGTTTTATTAT
1 TTTAATTGA-GTTTTAATAT
5728909 TTTAA
1 TTTAA
5728914 ACAAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (19 bp):
TTTAATTGAGTTTTAATAT
Found at i:5734171 original size:2 final size:2
Alignment explanation
Indices: 5734164--5734194 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5734154 CCTGGATGAA
5734164 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
5734195 AAGAAAAACA
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:5736884 original size:17 final size:17
Alignment explanation
Indices: 5736847--5736881 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5736837 ATAAGATAAT
*
5736847 AATAATTTTATCTTATC
1 AATAATTTTATCATATC
5736864 AATAATTTTAT-ATATC
1 AATAATTTTATCATATC
5736880 AA
1 AA
5736882 ATATGATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (17 bp):
AATAATTTTATCATATC
Found at i:5736945 original size:9 final size:9
Alignment explanation
Indices: 5736931--5736975 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
5736921 ATTAGTGTAT
5736931 TAAAATATA
1 TAAAATATA
5736940 TAAAATATA
1 TAAAATATA
*
5736949 AAAAATA-A
1 TAAAATATA
*
5736957 TAAAA-ATT
1 TAAAATATA
5736965 TAAAAT-TA
1 TAAAATATA
5736973 TAA
1 TAA
5736976 GACAAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
7 1 0.03
8 14 0.47
9 15 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
TAAAATATA
Found at i:5740355 original size:27 final size:28
Alignment explanation
Indices: 5740324--5740380 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
5740314 AGGTTATAGC
*
5740324 TTATTTTATATAAAAAAAT-TAATATTT
1 TTATTTTATATAAAAAAATAAAATATTT
* * *
5740351 TTATTTTTTTTAGAAAAATAAAATATTT
1 TTATTTTATATAAAAAAATAAAATATTT
5740379 TT
1 TT
5740381 TTATACAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
TTATTTTATATAAAAAAATAAAATATTT
Found at i:5741076 original size:32 final size:29
Alignment explanation
Indices: 5741040--5741098 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 29
5741030 TGTAATGAAA
*
5741040 AATATAAAAATATTTGAATCAAAATTTAAAGT
1 AATATAAAAATA-AT-AA-CAAAATTTAAAGT
5741072 AATATAAAAATAATAACAAAATTTAAA
1 AATATAAAAATAATAACAAAATTTAAA
5741099 AATTAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 2 0.08
31 1 0.04
32 12 0.46
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (29 bp):
AATATAAAAATAATAACAAAATTTAAAGT
Found at i:5744443 original size:12 final size:12
Alignment explanation
Indices: 5744426--5744457 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
5744416 TCTCTCTCTC
5744426 TCTATATATATA
1 TCTATATATATA
5744438 TCTATATATATA
1 TCTATATATATA
*
5744450 TGTATATA
1 TCTATATA
5744458 GCACCTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (12 bp):
TCTATATATATA
Found at i:5749531 original size:29 final size:29
Alignment explanation
Indices: 5749470--5749547 Score: 140
Period size: 29 Copynumber: 2.7 Consensus size: 29
5749460 AAACATATTT
5749470 TTATGCAATGAGGTTAAGT-AGGATTTCA
1 TTATGCAATGAGGTTAAGTGAGGATTTCA
5749498 TTATGCAATGAGGTTAAGTGAGGATTTCA
1 TTATGCAATGAGGTTAAGTGAGGATTTCA
*
5749527 TTATGCAATGAGCTTAAGTGA
1 TTATGCAATGAGGTTAAGTGA
5749548 AGATATTCTT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 19 0.40
29 29 0.60
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.35
Consensus pattern (29 bp):
TTATGCAATGAGGTTAAGTGAGGATTTCA
Found at i:5752583 original size:18 final size:17
Alignment explanation
Indices: 5752562--5752599 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
5752552 AAAATATTAT
5752562 TTTTTAAAATATAAAATA
1 TTTTTAAAATAT-AAATA
*
5752580 TTTTTTAAATATAAATA
1 TTTTTAAAATATAAATA
5752597 TTT
1 TTT
5752600 AAATATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTTAAAATATAAATA
Found at i:5752595 original size:17 final size:19
Alignment explanation
Indices: 5752559--5752599 Score: 68
Period size: 17 Copynumber: 2.3 Consensus size: 19
5752549 AATAAAATAT
5752559 TATTTTTTAAAATATAAAA
1 TATTTTTTAAAATATAAAA
5752578 TATTTTTT-AAATAT-AAA
1 TATTTTTTAAAATATAAAA
5752595 TATTT
1 TATTT
5752600 AAATATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.36
18 6 0.27
19 8 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTTTTAAAATATAAAA
Found at i:5752615 original size:24 final size:25
Alignment explanation
Indices: 5752588--5752648 Score: 83
Period size: 24 Copynumber: 2.5 Consensus size: 25
5752578 TATTTTTTAA
5752588 ATATAAATATT-TAAATATATT-ATT
1 ATATAAATATTATAAATA-ATTAATT
5752612 ATATAAATATTATAAATAATTAATT
1 ATATAAATATTATAAATAATTAATT
*
5752637 AAATAAA-ATTAT
1 ATATAAATATTAT
5752649 TTTTATATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
24 19 0.56
25 15 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
ATATAAATATTATAAATAATTAATT
Found at i:5752760 original size:15 final size:16
Alignment explanation
Indices: 5752742--5752776 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
5752732 TAAAAAAAAT
*
5752742 AATTGGATCTTAT-AA
1 AATTGGATCTGATCAA
5752757 AATTGGATCTGATCAA
1 AATTGGATCTGATCAA
5752773 AATT
1 AATT
5752777 CGATGGGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (16 bp):
AATTGGATCTGATCAA
Found at i:5753198 original size:196 final size:197
Alignment explanation
Indices: 5752857--5753258 Score: 671
Period size: 196 Copynumber: 2.0 Consensus size: 197
5752847 CTTGGACTGT
* * *
5752857 TTAATGTTTGGAAACCAAACTAATGGTGCGATTGCACCAAAATTTTCTCAAAGCAGCCGAAATTA
1 TTAATATTTGGAAACCAAACAAATGGTGCGATTACACCAAAATTTTCTCAAAGCAGCCGAAATTA
* *
5752922 CGATTGGAGGGGGAATGAGTGCGGTGGTTCATCGTACCCTAAATTGGACAATTATGTTCCTATAA
66 CGATTGGAGGGGGAATGAGTGCGGTGGTTCACCGCACCCTAAATTGGACAATTATGTTCCTATAA
*
5752987 ATTGATTTTTGTTCAATTTTATTCTTATATTTATTAACTTTTGTCCCACAAATACCTTAAAAAAT
131 ATTGATTTTTGTTCAATTTTATTCTTATATTTATGAACTTTTGTCCCACAAATACCTTAAAAAAT
5753052 TA
196 TA
* * * *
5753054 TTAATATTTGGAAACCAAACAAATGGTGCGATTACACTAAAATTTTCTTAAAGCAGCTGCAATTA
1 TTAATATTTGGAAACCAAACAAATGGTGCGATTACACCAAAATTTTCTCAAAGCAGCCGAAATTA
* * *
5753119 TGATTGGA-GGGGAATGAGTGCGGTGGTTCGCCGCACCCTAAATTGGACAATTATGTTCCTATAT
66 CGATTGGAGGGGGAATGAGTGCGGTGGTTCACCGCACCCTAAATTGGACAATTATGTTCCTATAA
*
5753183 ATTGATTTTTGTTCAATTTTATTCTTATATTTATGAACTTTTGTCCCACAAATACCTTAAAAACT
131 ATTGATTTTTGTTCAATTTTATTCTTATATTTATGAACTTTTGTCCCACAAATACCTTAAAAAAT
5753248 TA
196 TA
5753250 TTAATATTT
1 TTAATATTT
5753259 CCTATTGAAT
Statistics
Matches: 191, Mismatches: 14, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
196 126 0.66
197 65 0.34
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (197 bp):
TTAATATTTGGAAACCAAACAAATGGTGCGATTACACCAAAATTTTCTCAAAGCAGCCGAAATTA
CGATTGGAGGGGGAATGAGTGCGGTGGTTCACCGCACCCTAAATTGGACAATTATGTTCCTATAA
ATTGATTTTTGTTCAATTTTATTCTTATATTTATGAACTTTTGTCCCACAAATACCTTAAAAAAT
TA
Found at i:5759633 original size:16 final size:15
Alignment explanation
Indices: 5759597--5759625 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5759587 AATTATATAA
5759597 AATTTAAATCATTTC
1 AATTTAAATCATTTC
5759612 AATTTAAATCATTT
1 AATTTAAATCATTT
5759626 AGAATTTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTTAAATCATTTC
Found at i:5759999 original size:2 final size:2
Alignment explanation
Indices: 5759994--5760028 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5759984 TTTTGTTGAT
*
5759994 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5760029 TTAATTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5761379 original size:20 final size:19
Alignment explanation
Indices: 5761356--5761400 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
5761346 TAAATTCAAC
*
5761356 AAATTTCACATAAT-TCACA
1 AAATTACACA-AATGTCACA
5761375 TAAATTACACAAATGTCACA
1 -AAATTACACAAATGTCACA
5761395 AAATTA
1 AAATTA
5761401 TCTAAAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.29
Consensus pattern (19 bp):
AAATTACACAAATGTCACA
Found at i:5763027 original size:40 final size:41
Alignment explanation
Indices: 5762946--5763029 Score: 134
Period size: 40 Copynumber: 2.1 Consensus size: 41
5762936 ACAAAATTAA
* *
5762946 AAGTCAAATATGAGAAATAAACAATTCAGGTAATTGGAAGC
1 AAGTCAAATATGAGAAATAAACAATTCAAGTAATTGAAAGC
*
5762987 AAGTCAAATATGAGGAATAAA-AATTCAAGTAATTGAAAGC
1 AAGTCAAATATGAGAAATAAACAATTCAAGTAATTGAAAGC
5763027 AAG
1 AAG
5763030 GATAAGCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 20 0.50
41 20 0.50
ACGTcount: A:0.51, C:0.08, G:0.19, T:0.21
Consensus pattern (41 bp):
AAGTCAAATATGAGAAATAAACAATTCAAGTAATTGAAAGC
Found at i:5765902 original size:132 final size:132
Alignment explanation
Indices: 5765662--5765920 Score: 421
Period size: 132 Copynumber: 2.0 Consensus size: 132
5765652 TGACGGCCAA
* * * * * *
5765662 AAGGAATCTCTTTTTTGACATATGGTCAGATTGTCAAGAATTTGATATTTTGTCGGCTACCCTTT
1 AAGGAATCTCTTTTTCGACATATCGTCAAACTGTCAAGAATTTGATATTTTGTCAGCTACCCTTC
*
5765727 TTGAATATTATCTAAATTAATTACCTTTTCATCTTCTGGATTAAAAGAATGTCGAGAGGTTGTTT
66 TTGAATATTATCTAAATTAATTACCTTTTCATCTTCTGAATTAAAAGAATGTCGAGAGGTTGTTT
5765792 CT
131 CT
5765794 AAGGAATCTCTTTTTCGACATATCGTCAAACTGTCATA-AATTTGATATTTTGTCAGCTACCCTT
1 AAGGAATCTCTTTTTCGACATATCGTCAAACTGTCA-AGAATTTGATATTTTGTCAGCTACCCTT
* *
5765858 CTTGAATATTATCTAAATTAATTGCCTTTTCATCTTCTGAATTAAAAGAATGTGGAGAGGTTG
65 CTTGAATATTATCTAAATTAATTACCTTTTCATCTTCTGAATTAAAAGAATGTCGAGAGGTTG
5765921 AGTTAGAATC
Statistics
Matches: 117, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
132 116 0.99
133 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.41
Consensus pattern (132 bp):
AAGGAATCTCTTTTTCGACATATCGTCAAACTGTCAAGAATTTGATATTTTGTCAGCTACCCTTC
TTGAATATTATCTAAATTAATTACCTTTTCATCTTCTGAATTAAAAGAATGTCGAGAGGTTGTTT
CT
Found at i:5766623 original size:165 final size:163
Alignment explanation
Indices: 5766337--5766663 Score: 469
Period size: 165 Copynumber: 2.0 Consensus size: 163
5766327 ACTTCTTGGA
5766337 TAGGGATCTGAAGGTTGAAGGATTCCATCTAACAGTCCCTTAGCTTTTACAATCATGAATAGTCT
1 TAGGGATCTGAAGGTTGAAGGATTCCATCTAACAGTCCCTTAGCTTTTACAATCATGAATAGTCT
* *
5766402 TACTAGGTAACTATATAGACTTGCTTTGTTGAATGGTTTAAGAACTAATTTTAAATTTTCTTGAT
66 TACTAGGAAACTATATAGACTTGCTTTGTTGAATGGTTTAAGAACTAATCTTAAATTTT-TTGAT
* *
5766467 CTTCATTTAGAGGTGACAAATCTGGTCCATAAAG
130 CTTCATTTACAAGTGACAAATCTGGTCCATAAAG
* ** * * *
5766501 TAGGGATTTTGAAGGTTGAAGGATTTTATCTAATAGTCCCTTAGCTTTTACAATCTTGGATAGTC
1 TAGGGA-TCTGAAGGTTGAAGGATTCCATCTAACAGTCCCTTAGCTTTTACAATCATGAATAGTC
* * * *
5766566 TTGCTTGGAAACTATATAGACTTG-TTCTGTTGAATTGTTTAAGAA-TAAATCTTAAATTTTTTT
65 TTACTAGGAAACTATATAGACTTGCTT-TGTTGAATGGTTTAAGAACT-AATCTTAAATTTTTTG
*
5766629 ATCTTCATTTACAAGTGACAAATCTTGTCCATAAA
128 ATCTTCATTTACAAGTGACAAATCTGGTCCATAAA
5766664 ATACACTTTT
Statistics
Matches: 145, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
164 43 0.30
165 102 0.70
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (163 bp):
TAGGGATCTGAAGGTTGAAGGATTCCATCTAACAGTCCCTTAGCTTTTACAATCATGAATAGTCT
TACTAGGAAACTATATAGACTTGCTTTGTTGAATGGTTTAAGAACTAATCTTAAATTTTTTGATC
TTCATTTACAAGTGACAAATCTGGTCCATAAAG
Found at i:5769067 original size:39 final size:39
Alignment explanation
Indices: 5769012--5769087 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
5769002 TATGAAAATG
*
5769012 CTATACTTACATTTAATGATAAT-AATCCATCATCATCAT
1 CTATACTTACACTTAATGATAATAAAT-CATCATCATCAT
*
5769051 CTATACTTACACTTAATGATGATAAATCATCATCATC
1 CTATACTTACACTTAATGATAATAAATCATCATCATC
5769088 TTAAAAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 31 0.91
40 3 0.09
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.37
Consensus pattern (39 bp):
CTATACTTACACTTAATGATAATAAATCATCATCATCAT
Found at i:5769927 original size:22 final size:21
Alignment explanation
Indices: 5769886--5769928 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5769876 AAATTACTAC
*
5769886 TATATCAAATTTGTTAAAAAA
1 TATAACAAATTTGTTAAAAAA
* *
5769907 TATAACAAATTTATTTAAAAA
1 TATAACAAATTTGTTAAAAAA
5769928 T
1 T
5769929 GAATTTTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (21 bp):
TATAACAAATTTGTTAAAAAA
Found at i:5770439 original size:18 final size:17
Alignment explanation
Indices: 5770418--5770451 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5770408 AAAGTGTTAG
5770418 TTTGACAAAAAGAAAAAA
1 TTTGAC-AAAAGAAAAAA
*
5770436 TTTGTCAAAAGAAAAA
1 TTTGACAAAAGAAAAA
5770452 CTCTAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.21
Consensus pattern (17 bp):
TTTGACAAAAGAAAAAA
Found at i:5786248 original size:29 final size:29
Alignment explanation
Indices: 5786179--5786249 Score: 117
Period size: 29 Copynumber: 2.4 Consensus size: 29
5786169 CAGACTAAAG
5786179 TAGTAAAGGTCATACATAAACACAAGATC
1 TAGTAAAGGTCATACATAAACACAAGATC
*
5786208 TCGTAAAGGTCATACATAAACACAAGATC
1 TAGTAAAGGTCATACATAAACACAAGATC
5786237 TAGTTAAA-GTCAT
1 TAG-TAAAGGTCAT
5786250 CCGGAAATAC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 35 0.90
30 4 0.10
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (29 bp):
TAGTAAAGGTCATACATAAACACAAGATC
Found at i:5792508 original size:45 final size:44
Alignment explanation
Indices: 5792415--5792518 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 44
5792405 AAAGTTTTAA
* ****
5792415 AAAATTATAATTTTAATGTATTTAATATTAAAATTAATTTTTTAT
1 AAAATTATAATTTT-ATGTATTTAATATTAAAAATAAAAAATTAT
* *
5792460 AAAATTATAATTTTATGATTTTTAATATTAAAAATAAAAAATTGT
1 AAAATTATAATTTTATG-TATTTAATATTAAAAATAAAAAATTAT
5792505 AAAA-TATAATTTTA
1 AAAATTATAATTTTA
5792519 AAATATAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 13 0.25
45 38 0.75
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (44 bp):
AAAATTATAATTTTATGTATTTAATATTAAAAATAAAAAATTAT
Found at i:5792521 original size:23 final size:21
Alignment explanation
Indices: 5792494--5792565 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 21
5792484 ATATTAAAAA
5792494 TAAAAAATTGTAAAATATAATTT
1 TAAAAAA-T-TAAAATATAATTT
** *
5792517 TAAAATATAAAAAAATAAACATTT
1 TAAAA-A-ATTAAAATATA-ATTT
5792541 TAAAAAA-TAAAATATAATTT
1 TAAAAAATTAAAATATAATTT
5792561 TAAAA
1 TAAAA
5792566 CATCTCAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
20 9 0.22
21 7 0.17
22 1 0.02
23 13 0.32
24 10 0.24
25 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (21 bp):
TAAAAAATTAAAATATAATTT
Found at i:5792522 original size:21 final size:21
Alignment explanation
Indices: 5792497--5792565 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
5792487 TTAAAAATAA
*
5792497 AAAATTGTAAAATATAATTTT
1 AAAATTATAAAATATAATTTT
* *
5792518 AAAATATAAAAAAATAAACATTTT
1 AAAAT-T-ATAAAATATA-ATTTT
*
5792542 AAAA-AATAAAATATAATTTT
1 AAAATTATAAAATATAATTTT
5792562 AAAA
1 AAAA
5792566 CATCTCAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
20 9 0.23
21 13 0.33
22 1 0.03
23 7 0.18
24 9 0.23
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (21 bp):
AAAATTATAAAATATAATTTT
Found at i:5792544 original size:24 final size:23
Alignment explanation
Indices: 5792505--5792552 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
5792495 AAAAAATTGT
* *
5792505 AAAATATAATTTTAAAATATAAA
1 AAAATAAAATTTTAAAAAATAAA
5792528 AAAATAAACATTTTAAAAAATAAA
1 AAAATAAA-ATTTTAAAAAATAAA
5792552 A
1 A
5792553 TATAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAATAAAATTTTAAAAAATAAA
Found at i:5803103 original size:4 final size:4
Alignment explanation
Indices: 5803094--5803235 Score: 82
Period size: 4 Copynumber: 35.8 Consensus size: 4
5803084 GGTATTTTAG
* * * * * *
5803094 TATT TATT TA-T TA-T TA-T TATG TATT AATA TATG TATA TCTT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
* * *
5803139 TATT TATT TATT TA-T T-TT TATT TATAT GTATTT TATT TATA TAGT TATA
1 TATT TATT TATT TATT TATT TATT TAT-T -TA-TT TATT TATT TATT TATT
* *
5803188 TATT TA-T TATT ATATT ATAATT TATT TATT TA-T TATT TTTT TTTT TAT
1 TATT TATT TATT -TATT -T-ATT TATT TATT TATT TATT TATT TATT TAT
5803236 CTTGTAATAT
Statistics
Matches: 110, Mismatches: 18, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
3 19 0.17
4 74 0.67
5 10 0.09
6 6 0.05
7 1 0.01
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.68
Consensus pattern (4 bp):
TATT
Found at i:5803174 original size:15 final size:15
Alignment explanation
Indices: 5803141--5803271 Score: 62
Period size: 15 Copynumber: 8.5 Consensus size: 15
5803131 TCTTTATTTA
5803141 TTTATTTAT-TTATT
1 TTTATTTATATTATT
5803155 TTTATTTATATGTA-T
1 TTTATTTATAT-TATT
5803170 TTTATTTATA-TAGTT
1 TTTATTTATATTA-TT
*
5803185 ATATATTTATTATTATAT
1 -TTTATTTA-TATTAT-T
*
5803203 TATAATTTAT-TTATT
1 T-TTATTTATATTATT
5803218 TATTATTT-T-TT-TT
1 T-TTATTTATATTATT
*
5803231 TTTATCTTGTAATATTTTT
1 TTTA--TT-T-ATATTATT
*
5803250 TTTGATTTATCTTA-T
1 TTT-ATTTATATTATT
5803265 TTTATTT
1 TTTATTT
5803272 TTAATTATCT
Statistics
Matches: 94, Mismatches: 6, Indels: 34
0.70 0.04 0.25
Matches are distributed among these distances:
12 3 0.03
13 5 0.05
14 18 0.19
15 26 0.28
16 17 0.18
17 7 0.07
18 12 0.13
19 5 0.05
20 1 0.01
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTATTTATATTATT
Found at i:5803180 original size:49 final size:48
Alignment explanation
Indices: 5803094--5803212 Score: 123
Period size: 49 Copynumber: 2.4 Consensus size: 48
5803084 GGTATTTTAG
* ** *
5803094 TATTTATTTATTATTATTATGTATTAATATATGTATATCTTTATTTATT
1 TATTTATTTATTATTATT-TATATTAATATATGTATATAGTTATATATT
* * * *
5803143 TATTTATTTATTTTTATTTATATGTATTTTATTTATATAGTTATATATT
1 TATTTATTTATTATTATTTATAT-TAATATATGTATATAGTTATATATT
*
5803192 TA-TTATTATATTATAATTTAT
1 TATTTATT-TATTATTATTTAT
5803213 TTATTTATTA
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
48 9 0.16
49 49 0.84
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (48 bp):
TATTTATTTATTATTATTTATATTAATATATGTATATAGTTATATATT
Found at i:5803181 original size:57 final size:56
Alignment explanation
Indices: 5803096--5803279 Score: 155
Period size: 57 Copynumber: 3.2 Consensus size: 56
5803086 TATTTTAGTA
*
5803096 TTTATTTATTATTATTATGTATTAATATATGTATATCTTTATTTATTTATTTATTTATT
1 TTTATTTATTATTATT-T-TATTTATATATGTATAT-TTTATTTATTTATTTATTTATT
5803155 TTTATTTA-TATGTATTTTATTTATATA-GTTATATATTTA-TTATTATATTATAATTTA--
1 TTTATTTATTAT-TATTTTATTTATATATG-TATAT-TTTATTTATT-TATT-T-ATTTATT
* * * *
5803212 TTTATTTATTATTTTTTTTTTTATCT-TGTAATATTTTTTTTGATTTATCTTATTTTATT
1 TTTATTTATTATTATTTTATTTATATATGT-ATATTTTATTT-ATTTAT-TTA-TTTATT
*
5803271 TTTAATTAT
1 TTTATTTAT
5803280 CTGTTTTTTT
Statistics
Matches: 104, Mismatches: 7, Indels: 28
0.75 0.05 0.20
Matches are distributed among these distances:
56 11 0.11
57 56 0.54
58 12 0.12
59 25 0.24
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (56 bp):
TTTATTTATTATTATTTTATTTATATATGTATATTTTATTTATTTATTTATTTATT
Found at i:5803212 original size:26 final size:26
Alignment explanation
Indices: 5803161--5803224 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
5803151 TATTTTTATT
*
5803161 TATATGTATT-TTATTTATATAGTTA
1 TATATTTATTATTATTTATATAGTTA
*
5803186 TATATTTATTATTATATTATA-ATTTA
1 TATATTTATTATTAT-TTATATAGTTA
*
5803212 TTTATTTATTATT
1 TATATTTATTATT
5803225 TTTTTTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 9 0.26
26 20 0.59
27 5 0.15
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (26 bp):
TATATTTATTATTATTTATATAGTTA
Found at i:5803234 original size:19 final size:19
Alignment explanation
Indices: 5803133--5803292 Score: 58
Period size: 20 Copynumber: 8.1 Consensus size: 19
5803123 TATGTATATC
5803133 TTTATTTATTTATTTATTTATT
1 TTTATTTA-TTATTT-TTT-TT
* *
5803155 TTTATTTA-TATGTATTTTA
1 TTTATTTATTAT-TTTTTTT
* * *
5803174 TTTATATAGTTA-TATATTT
1 TTTATTTA-TTATTTTTTTT
* ** *
5803193 ATTATTATATTA-TAATTTA
1 TTTATT-TATTATTTTTTTT
5803212 TTTATTTATTATTTTTTTT
1 TTTATTTATTATTTTTTTT
* * *
5803231 TTTATCTTGTAATATTTTTT
1 TTTAT-TTATTATTTTTTTT
* *
5803251 TTGATTTATCT-TATTTTATT
1 TTTATTTAT-TAT-TTTTTTT
* *
5803271 TTTAATTATCTGTTTTTTTT
1 TTTATTTAT-TATTTTTTTT
5803291 TT
1 TT
5803293 CTTTCTTTTT
Statistics
Matches: 104, Mismatches: 25, Indels: 20
0.70 0.17 0.13
Matches are distributed among these distances:
18 5 0.05
19 42 0.40
20 45 0.43
21 4 0.04
22 8 0.08
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (19 bp):
TTTATTTATTATTTTTTTT
Found at i:5803270 original size:24 final size:23
Alignment explanation
Indices: 5803133--5803273 Score: 80
Period size: 22 Copynumber: 6.0 Consensus size: 23
5803123 TATGTATATC
5803133 TTTATTTAT-TTA-TTTATTTATT
1 TTTATTTATCTTATTTTATTT-TT
*
5803155 TTTATTTATATGTATTTTATTTATAT
1 TTTATTTATCT-TATTTTATTT-T-T
* * *
5803181 AGTTATATAT-TTATTATTATATTATAA
1 -TTTATTTATCTTATT-TTAT-TT-T-T
5803208 TTTATTTAT-TTA--TTATTTTT
1 TTTATTTATCTTATTTTATTTTT
* **
5803228 TTT-TTTATCTTGTAATATTTTT
1 TTTATTTATCTTATTTTATTTTT
5803250 TTTGATTTATCTTATTTTATTTTT
1 TTT-ATTTATCTTATTTTATTTTT
5803274 AATTATCTGT
Statistics
Matches: 96, Mismatches: 11, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
19 5 0.05
20 5 0.05
21 1 0.01
22 21 0.22
23 5 0.05
24 18 0.19
25 13 0.14
26 16 0.17
27 12 0.12
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (23 bp):
TTTATTTATCTTATTTTATTTTT
Found at i:5803689 original size:19 final size:19
Alignment explanation
Indices: 5803661--5803699 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5803651 TCTAGATTTC
*
5803661 AGTTGAATTTTTTGACGAA
1 AGTTGAATTTTCTGACGAA
*
5803680 AGTTGCATTTTCTGACGAA
1 AGTTGAATTTTCTGACGAA
5803699 A
1 A
5803700 ATTTCGGTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (19 bp):
AGTTGAATTTTCTGACGAA
Found at i:5804153 original size:4 final size:4
Alignment explanation
Indices: 5804144--5804198 Score: 55
Period size: 4 Copynumber: 14.5 Consensus size: 4
5804134 TCCAGGTTTT
* *
5804144 TTTA TTTA TTTA TTTG TTTA TTTG TTT- TTT- TTTA -TTA TTTA TTT-
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
5804188 TATTA TTTA TT
1 T-TTA TTTA TT
5804199 AGATTATGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
3 10 0.23
4 33 0.75
5 1 0.02
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:5804205 original size:15 final size:12
Alignment explanation
Indices: 5804140--5804280 Score: 63
Period size: 11 Copynumber: 12.2 Consensus size: 12
5804130 CCGCTCCAGG
*
5804140 TTTTTTTATTTA
1 TTTTATTATTTA
*
5804152 -TTTATTTGTTTA
1 TTTTA-TTATTTA
*
5804164 -TTTGTT-TTT-
1 TTTTATTATTTA
5804173 TTTTATTATTTA
1 TTTTATTATTTA
5804185 TTTTATTATTTA
1 TTTTATTATTTA
**
5804197 TTAGATTATGTTTA
1 TTTTATTA--TTTA
*
5804211 TTTGA-TATTCT-
1 TTTTATTATT-TA
*
5804222 TTTTA-TCTTTA
1 TTTTATTATTTA
5804233 TTTTATT-TTTA
1 TTTTATTATTTA
5804244 TTTT-TGT-TTTA
1 TTTTAT-TATTTA
* *
5804255 CTTTTCTT-TATA
1 -TTTTATTATTTA
5804267 TTTTATT-TTTA
1 TTTTATTATTTA
5804278 TTT
1 TTT
5804281 ATTTTCACTT
Statistics
Matches: 105, Mismatches: 12, Indels: 25
0.74 0.08 0.18
Matches are distributed among these distances:
10 10 0.10
11 47 0.45
12 37 0.35
13 3 0.03
14 8 0.08
ACGTcount: A:0.18, C:0.03, G:0.04, T:0.75
Consensus pattern (12 bp):
TTTTATTATTTA
Found at i:5804242 original size:6 final size:6
Alignment explanation
Indices: 5804221--5804297 Score: 56
Period size: 6 Copynumber: 13.7 Consensus size: 6
5804211 TTTGATATTC
* * * * *
5804221 TTTTTA TCTTTA -TTTTA TTTTTA TTTTT- GTTTTA CTTTTC TTTATA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* *
5804267 -TTTTA TTTTTA --TTTA TTTTCA CTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
5804298 GTTTCATTAT
Statistics
Matches: 53, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
4 4 0.08
5 12 0.23
6 37 0.70
ACGTcount: A:0.16, C:0.06, G:0.01, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:5804243 original size:17 final size:16
Alignment explanation
Indices: 5804142--5804297 Score: 83
Period size: 17 Copynumber: 9.6 Consensus size: 16
5804132 GCTCCAGGTT
5804142 TTTTTA-TTTA-TTTA
1 TTTTTATTTTATTTTA
*
5804156 TTTGTT-TATTTGTTTT-
1 TTT-TTAT-TTTATTTTA
5804172 TTTTTATTATTTATTTTA
1 TTTTTA-T-TTTATTTTA
**
5804190 TTATTTA--TTAGATTA
1 TT-TTTATTTTATTTTA
* * * *
5804205 TGTTTATTTGATATTC
1 TTTTTATTTTATTTTA
5804221 TTTTTATCTTTATTTTA
1 TTTTTAT-TTTATTTTA
*
5804238 TTTTTATTTTTGTTTTA
1 TTTTTA-TTTTATTTTA
* *
5804255 CTTTTCTTTATATTTTA
1 TTTTTATTT-TATTTTA
5804272 TTTTTA-TTTATTTTCA
1 TTTTTATTTTATTTT-A
*
5804288 CTTTTATTTT
1 TTTTTATTTT
5804298 GTTTCATTAT
Statistics
Matches: 108, Mismatches: 19, Indels: 27
0.70 0.12 0.18
Matches are distributed among these distances:
14 7 0.06
15 17 0.16
16 28 0.26
17 49 0.45
18 3 0.03
19 4 0.04
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.74
Consensus pattern (16 bp):
TTTTTATTTTATTTTA
Found at i:5804253 original size:11 final size:11
Alignment explanation
Indices: 5804168--5804297 Score: 88
Period size: 11 Copynumber: 11.4 Consensus size: 11
5804158 TGTTTATTTG
5804168 TTTTT-TTTTA
1 TTTTTATTTTA
5804178 TTATTTATTTTA
1 TT-TTTATTTTA
5804190 TTATTTATTAGATTA
1 TT-TTTATT---TTA
* *
5804205 TGTTTATTTGA
1 TTTTTATTTTA
*
5804216 TATTCT-TTTTA
1 T-TTTTATTTTA
*
5804227 TCTTTATTTTA
1 TTTTTATTTTA
5804238 TTTTTATTTT-
1 TTTTTATTTTA
*
5804248 TGTTTTACTTTTC
1 T-TTTTA-TTTTA
*
5804261 TTTATATTTTA
1 TTTTTATTTTA
5804272 TTTTTA-TTTA
1 TTTTTATTTTA
*
5804282 TTTTCACTTTTA
1 TTTTTA-TTTTA
5804294 TTTT
1 TTTT
5804298 GTTTCATTAT
Statistics
Matches: 96, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
10 14 0.15
11 39 0.41
12 32 0.33
13 1 0.01
14 6 0.06
15 4 0.04
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:5804486 original size:59 final size:58
Alignment explanation
Indices: 5804331--5804895 Score: 570
Period size: 59 Copynumber: 9.4 Consensus size: 58
5804321 AATAAAAATA
* *
5804331 AAAAAAATATTTTTGAGGAAAAGTT-AAGAGTATCAATTTTTCTTAAAAATAAATTTTC
1 AAAAAAAGATTTTTGAGGAAAAGTTGAA-AGTATCAATTTTTCTTAAAAATAAAGTTTC
* * *
5804389 AAAAAAAGGTTTTTTAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTC
1 AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAAGTTTC
* * * * *
5804448 CAAAGAACATTTTTG-GAGAAAAGTTGAAAATATCAATTTTTCTTAAAAATAAATTTTC
1 AAAAAAAGATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAGTTTC
* *
5804506 AAAAAAAAAAGGAGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTTC
1 ---AAAAAAA-GA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAAG-TTTC
* * *
5804571 -AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTC
1 AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAAGTTTC
* * * *
5804629 CAAAAAATATTTTTG-GAGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTTGAAA
1 AAAAAAAGATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAA-GTTT---C
* * ** *
5804691 AAAAAAAGATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTC
1 AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAGTTTC
* * * *
5804749 AAGAAAAAAATAAATTTTTGAGGAAAAGTTGAAAATATCATTTTTTCTT-AAAATAAAATTTC
1 ----AAAAAA-AGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAGTTTC
*
5804811 AAAAAAAAAAGGAGTTTTTGA-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTC
1 ---AAAAAAA-GA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAGTTTC
*
5804872 -AAAAAAGGTTTTTGAGGAAAAGTT
1 AAAAAAAGATTTTTGAGGAAAAGTT
5804896 ATCAAAGTTT
Statistics
Matches: 433, Mismatches: 47, Indels: 56
0.81 0.09 0.10
Matches are distributed among these distances:
55 7 0.02
56 9 0.02
57 6 0.01
58 59 0.14
59 144 0.33
60 2 0.00
61 51 0.12
62 78 0.18
63 69 0.16
64 4 0.01
65 4 0.01
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (58 bp):
AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAGTTTC
Found at i:5804643 original size:181 final size:178
Alignment explanation
Indices: 5804330--5804877 Score: 716
Period size: 181 Copynumber: 3.0 Consensus size: 178
5804320 AAATAAAAAT
* * *
5804330 AAAAAAAATATTTTTGAGGAAAAGTT-AAGAGTATCAATTTTTCTTAAAAATAAA-TTTTCAAAA
1 AAAAAAAAGATTTTTGAGGAAAAGTTGAA-AGTATCAATTTTCCTTGAAAATAAAGTTTTCAAAA
* *
5804393 AA-AGGTTTTTTAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTCCAAAGAACA
65 AATA--TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTCCAAAAAACA
*
5804457 TTTTTGGAGAAAAGTTGAAAATATCAATTTTTCTTAAAAATAAATTTTCAA
128 TTTTTGGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAA
5804508 AAAAAAAAGGAGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTTCAA
1 AAAAAAAA-GA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAAGTTTTCAA
* *
5804573 AAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCAAAAAATA
63 AAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTCCAAAAAACA
*
5804638 TTTTTGGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTTGAA
128 TTTTTGGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAA-TTTTCAA
* * *
5804690 AAAAAAAAGATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAG-TTTCAAGAA
1 AAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAGTTTTC----A
* * * *
5804754 AAAAATAAATTTTTGAGGAAAAGTTGAAAATATCATTTTTTCTT-AAAAT-AAAATTTCAAAAAA
62 AAAAAT--ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTC---CAA
* *
5804817 AAAAGGAGTTTTT-GAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTCAA
122 AAAA-CA-TTTTTGGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAA
5804874 AAAA
1 AAAA
5804878 GGTTTTTGAG
Statistics
Matches: 332, Mismatches: 20, Indels: 30
0.87 0.05 0.08
Matches are distributed among these distances:
178 12 0.04
179 5 0.02
180 74 0.22
181 105 0.32
182 39 0.12
183 6 0.02
184 42 0.13
185 6 0.02
186 38 0.11
187 5 0.02
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.34
Consensus pattern (178 bp):
AAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAGTTTTCAAAAA
ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTCCAAAAAACATTT
TTGGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAA
Found at i:5815381 original size:8 final size:8
Alignment explanation
Indices: 5815368--5815485 Score: 107
Period size: 8 Copynumber: 14.2 Consensus size: 8
5815358 TATGCTTAAA
5815368 AAAAAATG
1 AAAAAATG
5815376 AAAAAATG
1 AAAAAATG
* *
5815384 AAAACACG
1 AAAAAATG
5815392 AAAAAAATG
1 -AAAAAATG
5815401 -AAAAATG
1 AAAAAATG
5815408 AAAAAAATG
1 -AAAAAATG
5815417 AAAAATTATG
1 AAAAA--ATG
5815427 AAAAATTATG
1 AAAAA--ATG
5815437 AAAAAATG
1 AAAAAATG
5815445 AAAAAAATG
1 -AAAAAATG
*
5815454 AAAAAA-A
1 AAAAAATG
*
5815461 AAAAAAAG
1 AAAAAATG
5815469 AAAAAA-G
1 AAAAAATG
*
5815476 AAAAAGTG
1 AAAAAATG
5815484 AA
1 AA
5815486 TGAAAAAAGA
Statistics
Matches: 95, Mismatches: 7, Indels: 16
0.81 0.06 0.14
Matches are distributed among these distances:
7 19 0.20
8 37 0.39
9 21 0.22
10 18 0.19
ACGTcount: A:0.75, C:0.02, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:5815381 original size:10 final size:9
Alignment explanation
Indices: 5815367--5815474 Score: 106
Period size: 9 Copynumber: 12.7 Consensus size: 9
5815357 CTATGCTTAA
5815367 AAAAAAATG
1 AAAAAAATG
5815376 -AAAAAATG
1 AAAAAAATG
* *
5815384 -AAAACACG
1 AAAAAAATG
5815392 AAAAAAATG
1 AAAAAAATG
5815401 --AAAAATG
1 AAAAAAATG
5815408 AAAAAAATG
1 AAAAAAATG
*
5815417 AAAAATTATG
1 AAAAA-AATG
*
5815427 AAAAATTATG
1 AAAAA-AATG
5815437 -AAAAAATG
1 AAAAAAATG
5815445 AAAAAAATG
1 AAAAAAATG
5815454 AAAAAAA--
1 AAAAAAATG
5815461 AAAAAAA-G
1 AAAAAAATG
5815469 AAAAAA
1 AAAAAA
5815475 GAAAAAGTGA
Statistics
Matches: 87, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
7 14 0.16
8 23 0.26
9 37 0.43
10 13 0.15
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (9 bp):
AAAAAAATG
Found at i:5815489 original size:61 final size:61
Alignment explanation
Indices: 5815373--5815492 Score: 147
Period size: 61 Copynumber: 2.0 Consensus size: 61
5815363 TTAAAAAAAA
* * * *
5815373 ATGAAAAAATGAAAACACGAAAAAAATGAAAAATGAAAAAAATGAAAAATTATGAAAAATT
1 ATGAAAAAATGAAAAAACGAAAAAAATAAAAAAAGAAAAAAATGAAAAATAATGAAAAATT
*
5815434 ATGAAAAAATGAAAAAAATGAAAAAAA-AAAAAAAG-AAAAAA-GAAAAAGTGAATGAAAAA
1 ATGAAAAAATG-AAAAAACGAAAAAAATAAAAAAAGAAAAAAATGAAAAA-T-AATGAAAAA
5815493 AGAGGACTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
59 6 0.12
60 7 0.14
61 25 0.49
62 13 0.25
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.12
Consensus pattern (61 bp):
ATGAAAAAATGAAAAAACGAAAAAAATAAAAAAAGAAAAAAATGAAAAATAATGAAAAATT
Found at i:5816563 original size:42 final size:41
Alignment explanation
Indices: 5816493--5817004 Score: 510
Period size: 42 Copynumber: 12.1 Consensus size: 41
5816483 ATGATTGTCA
* *
5816493 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTATTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
5816534 AGGAGCAATTTATTTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTA-CTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * *
5816576 AGGAGTAATTTACTTTTCAAAAGTCATGGTGCCTCTGTTTGG
1 AGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
*
5816618 AGGAGCAATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAG
* *
5816660 AGGAGCAATTTGCTTTCCAAAGGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAA-GTCGTGGTGCCTCTGTTTAG
*
5816702 AAGAGCAATTTACTTTTCTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTAC-TTT-TCAAAGTCGTGGTGCCTCTGTTTAG
*
5816745 AGGAGCAAATTACTTTTCAAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
* * * ** * * * * * **** *
5816787 ACGTGGTGC-CTTT-GTTTAGAGGAG-CAAT-TTACTTTCCAAAAGTCG
1 A---GGAGCAATTTACTTTTCA-AAGTC-GTGGTGC-CT-C-TGTTTAG
* * *
5816832 TGGTGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
* *
5816874 GGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
5816915 AGGAGCAATTTACTTTTCCAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * * *
5816956 AGGAGCAATTTATGTTTCTCAAAGTCGTTGAGCCTCTATTTAG
1 AGGAGCAATTTA-CTTT-TCAAAGTCGTGGTGCCTCTGTTTAG
5816999 AGGAGC
1 AGGAGC
5817005 TTTGGTCAAA
Statistics
Matches: 391, Mismatches: 58, Indels: 42
0.80 0.12 0.09
Matches are distributed among these distances:
41 96 0.25
42 198 0.51
43 73 0.19
44 14 0.04
45 10 0.03
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:5816793 original size:19 final size:19
Alignment explanation
Indices: 5816769--5816806 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5816759 TTTCAAAAGT
5816769 CGTGGTGCCTCTGTTTAGA
1 CGTGGTGCCTCTGTTTAGA
*
5816788 CGTGGTGCCTTTGTTTAGA
1 CGTGGTGCCTCTGTTTAGA
5816807 GGAGCAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.18, G:0.32, T:0.39
Consensus pattern (19 bp):
CGTGGTGCCTCTGTTTAGA
Found at i:5816827 original size:61 final size:61
Alignment explanation
Indices: 5816727--5816915 Score: 236
Period size: 61 Copynumber: 3.0 Consensus size: 61
5816717 TTCTCAAAGT
* *
5816727 CGTGGTGCCTCTGTTTAGAGGAGCAAATTACTTTTCAAAAGTCGTGGTGCCTCTGTTTAGA
1 CGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGA
* * * *
5816788 CGTGGTGCCTTTGTTTAGAGGAGCAATTTACTTTCCAAAAGTCGTGGTGCAATTTACTTTCCAAA
1 CGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAGTCGTGGTGC-CTCT-GTTT-----
*
5816853 AGT
59 AGA
*
5816856 CGTGGTGCCTCTGTTTAGGGGAGCAATTTACTTTCC-AAAGTCGTGGTGCCTCTGTTTAGA
1 CGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGA
5816916 GGAGCAATTT
Statistics
Matches: 108, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
60 2 0.02
61 47 0.44
62 2 0.02
63 3 0.03
65 3 0.03
66 2 0.02
67 13 0.12
68 36 0.33
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (61 bp):
CGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGA
Found at i:5816846 original size:26 final size:26
Alignment explanation
Indices: 5816810--5816863 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
5816800 GTTTAGAGGA
5816810 GCAATTTACTTTCCAAAAGTCGTGGT
1 GCAATTTACTTTCCAAAAGTCGTGGT
5816836 GCAATTTACTTTCCAAAAGTCGTGGT
1 GCAATTTACTTTCCAAAAGTCGTGGT
5816862 GC
1 GC
5816864 CTCTGTTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (26 bp):
GCAATTTACTTTCCAAAAGTCGTGGT
Found at i:5817040 original size:19 final size:20
Alignment explanation
Indices: 5817011--5817061 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
5817001 GAGCTTTGGT
5817011 CAAAAACAAAAAAAT-AAAAA
1 CAAAAA-AAAAAAATAAAAAA
*
5817031 CAAAAAAAAAACATAAAAAA
1 CAAAAAAAAAAAATAAAAAA
5817051 CAAAAAAAAAA
1 CAAAAAAAAAA
5817062 TGAAAATGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 7 0.24
20 22 0.76
ACGTcount: A:0.86, C:0.10, G:0.00, T:0.04
Consensus pattern (20 bp):
CAAAAAAAAAAAATAAAAAA
Found at i:5817049 original size:14 final size:14
Alignment explanation
Indices: 5817011--5817061 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
5817001 GAGCTTTGGT
5817011 CAAAAACAAAAAAA
1 CAAAAACAAAAAAA
*
5817025 TAAAAAC--AAAAA
1 CAAAAACAAAAAAA
5817037 -AAAAACATAAAAAA
1 CAAAAACA-AAAAAA
5817051 CAAAAA-AAAAA
1 CAAAAACAAAAA
5817062 TGAAAATGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
11 6 0.19
12 5 0.16
13 4 0.12
14 12 0.38
15 5 0.16
ACGTcount: A:0.86, C:0.10, G:0.00, T:0.04
Consensus pattern (14 bp):
CAAAAACAAAAAAA
Found at i:5817319 original size:4 final size:4
Alignment explanation
Indices: 5817310--5817402 Score: 86
Period size: 4 Copynumber: 22.8 Consensus size: 4
5817300 TATGTATATC
*
5817310 TTTA TTTA TTTA TTTA TTTA -TT- TTTA TTTA TATGTA TTTTA TTTA TATA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-T-TA -TTTA TTTA TTTA
*
5817359 GTTA TTTA TTTA -TTA TTATA TTATAA TTTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TT-TA TT-T-A TTTA TTTA TTTA TTTA TTT
5817403 CTTTTTTTTA
Statistics
Matches: 76, Mismatches: 4, Indels: 18
0.78 0.04 0.18
Matches are distributed among these distances:
3 10 0.13
4 49 0.64
5 10 0.13
6 6 0.08
7 1 0.01
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:5817351 original size:37 final size:38
Alignment explanation
Indices: 5817298--5817465 Score: 150
Period size: 37 Copynumber: 4.3 Consensus size: 38
5817288 TATGTATTAA
5817298 TATATGTATATCTTTATTTATTTATTTATTTATTTTTATT
1 TATATGTATA--TTTATTTATTTATTTATTTATTTTTATT
* *
5817338 TATATGTAT-TTTATTTATATAGTTATTTATTTATTA-T
1 TATATGTATATTTATTTATTTATTTATTTATTT-TTATT
*
5817375 TATAT-TATAATTTATTTATTTA-TTATTTCTTTTT-TT
1 TATATGTAT-ATTTATTTATTTATTTATTTATTTTTATT
* * *
5817411 TATCTTGTAATATTTTTTTGATTTATCTTATTTTATTTTTAAT
1 TAT-ATGT-ATATTTATTT-ATTTAT-TTA-TTTATTTTTATT
*
5817454 TATCTGT-TATTT
1 TATATGTATATTT
5817466 TTTTTCTTTT
Statistics
Matches: 107, Mismatches: 9, Indels: 24
0.76 0.06 0.17
Matches are distributed among these distances:
36 9 0.08
37 37 0.35
38 22 0.21
39 7 0.07
40 14 0.13
41 3 0.03
42 11 0.10
43 4 0.04
ACGTcount: A:0.25, C:0.03, G:0.04, T:0.68
Consensus pattern (38 bp):
TATATGTATATTTATTTATTTATTTATTTATTTTTATT
Found at i:5817357 original size:49 final size:50
Alignment explanation
Indices: 5817266--5817389 Score: 128
Period size: 49 Copynumber: 2.4 Consensus size: 50
5817256 TTTTAGGTAT
* **
5817266 TTTAGTATTTATTTATTA-TTACTATGTATTAATATATGTATATCTTTATTTA
1 TTTATTATTTATTT-TTATTTA-TATGTATT-ATATATGTATATAGTTATTTA
*
5817318 TTTATTTATTTATTTTTATTTATATGTATT-T-TATTTATATAGTTATTTA
1 TTTA-TTATTTATTTTTATTTATATGTATTATATATGTATATAGTTATTTA
* *
5817367 TTTATTATTATATTATAATTTAT
1 TTTATTATT-TATTTTTATTTAT
5817390 TTATTTATTA
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
48 5 0.08
49 30 0.48
50 1 0.02
52 15 0.24
53 12 0.19
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (50 bp):
TTTATTATTTATTTTTATTTATATGTATTATATATGTATATAGTTATTTA
Done.