Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397260.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_51.0, 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: 10072460
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 70252 characters in sequence are not A, C, G, or T
File 10 of 20
Found at i:3629562 original size:13 final size:13
Alignment explanation
Indices: 3629533--3629572 Score: 71
Period size: 13 Copynumber: 3.0 Consensus size: 13
3629523 TAATTATATT
3629533 AATTATTTAATAAA
1 AATTATTTAA-AAA
3629547 AATTATTTAAAAA
1 AATTATTTAAAAA
3629560 AATTATTTAAAAA
1 AATTATTTAAAAA
3629573 TAAATAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTATTTAAAAA
Found at i:3629589 original size:19 final size:19
Alignment explanation
Indices: 3629554--3629591 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3629544 AAAAATTATT
*
3629554 TAAAAAAATTATTTAAAAA
1 TAAAAAAATTATATAAAAA
3629573 TAAATAAAA-TATATAAAAA
1 TAAA-AAAATTATATAAAAA
3629592 ATTTCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAAAAAATTATATAAAAA
Found at i:3640996 original size:129 final size:128
Alignment explanation
Indices: 3640767--3641024 Score: 385
Period size: 129 Copynumber: 2.0 Consensus size: 128
3640757 CGCTCAAGTG
3640767 AAACATTTAGATGGGTCGATTAAGCCATTCTAATGTTACAGACTACATTTGGGGCATTGAATTTA
1 AAACATTTAGATGGGTCGATTAAGCCATTCTAATGTTACAGACTACATTTGGGGCATTGAATTTA
* *
3640832 TCATCTCTTATTAATGGTGGAACAAACAAACTTATTTAATTGCACCATAACGACAATGATTTA
66 TCATCTCTTATTAACGGTGGAACAAACAAACTTATTTAATTGCACCATAACAACAATGATTTA
* * * *
3640895 AAACATTTAGATGGGTCGATT-AGATCATTCTACTGTTATAGACCT-CGTTTGGGGACATTGAAT
1 AAACATTTAGATGGGTCGATTAAG-CCATTCTAATGTTACAGA-CTACATTTGGGG-CATTGAAT
* * * *
3640958 TTATCATCTCTTATTAACGGTGGAACAAAGAAATTTATTTAATTGCACCGTAACAATAATGATTT
63 TTATCATCTCTTATTAACGGTGGAACAAACAAACTTATTTAATTGCACCATAACAACAATGATTT
3641023 A
128 A
3641024 A
1 A
3641025 TTCTTCACGA
Statistics
Matches: 117, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
127 2 0.02
128 44 0.38
129 71 0.61
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (128 bp):
AAACATTTAGATGGGTCGATTAAGCCATTCTAATGTTACAGACTACATTTGGGGCATTGAATTTA
TCATCTCTTATTAACGGTGGAACAAACAAACTTATTTAATTGCACCATAACAACAATGATTTA
Found at i:3649312 original size:2 final size:2
Alignment explanation
Indices: 3649301--3649347 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
3649291 AGAAATGTAC
3649301 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3649342 AT AT AT
1 AT AT AT
3649348 TTTCTTCTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3652910 original size:47 final size:44
Alignment explanation
Indices: 3652859--3653474 Score: 583
Period size: 47 Copynumber: 13.1 Consensus size: 44
3652849 TCACCCAAAA
*
3652859 GGACTCGTGGGAGCTGGATGGGGACGGGC-CGGCCGCAGGGGGAATCG
1 GGACTCGTGGGA-CTGGA-GGGG--GGGCAGGGCCGCAGGGGGAATCG
* *
3652906 GGACTCGTGGGACTGTGGGAGGGGGGCAGGGCCGCAGGGGGGAACCG
1 GGACTCGTGGGACTG-GAG-GGGGGGCAGGGCCGCA-GGGGGAATCG
*
3652953 GGAATCGTGGGACTGTGGGAGGGGGGGCAGGGCCGCAGGGGGGAATCG
1 GGACTCGTGGGAC--T-GGAGGGGGGGCAGGGCCGCA-GGGGGAATCG
* *
3653001 GGACTCGTGGGAGCCGGGAGGGGGCGGCAGGGCTGCAGGGGGAATCG
1 GGACTCGTGGGA--CTGGAGGGGG-GGCAGGGCCGCAGGGGGAATCG
*
3653048 GGACTCGTGGGACTGTGGGAGGGGGGGCAGGGCCGCAGGGGGAACCG
1 GGACTCGTGGGAC--T-GGAGGGGGGGCAGGGCCGCAGGGGGAATCG
* *
3653095 AGAATCGTGGGACTGTGGGAGGGGGGGCAGGGCCGCAGGGGGAAATCG
1 GGACTCGTGGGAC--T-GGAGGGGGGGCAGGGCCGCAGGGGG-AATCG
* *
3653143 GGACTCGTGGGAGCCGGAGGGGGGCGGGCAGGGCTGCAGGGGGGAATCG
1 GGACTCGTGGGA-CTGGA--GGGG-GGGCAGGGCCGCA-GGGGGAATCG
*
3653192 GGACTCGTGGGACTGTGGGAGGGGGGGCAGGGCCGCAGGGGGAACCG
1 GGACTCGTGGGAC--T-GGAGGGGGGGCAGGGCCGCAGGGGGAATCG
* *
3653239 AGAATCGTGGGACTGTGGAAGGGGGGGCAGGGCCGCAGGGGGGAATCG
1 GGACTCGTGGGAC--TGG-AGGGGGGGCAGGGCCGCA-GGGGGAATCG
*
3653287 GGACTCGTGGGAGCCGGAAGGGGGCAGGCAAGGGCCGCAAGGGGGAATCG
1 GGACTCGTGGGA-CTGG-AGGGGG--GGC-AGGGCCGC-AGGGGGAATCG
* * *
3653337 GGACTCGTGGGACTGTGGGGGGGGGCATGG-CGCAGGGGGAACCG
1 GGACTCGTGGGACTG-GAGGGGGGGCAGGGCCGCAGGGGGAATCG
* * *
3653381 GGAATCGTGGGACTGTG-GAGGGGGGCAGGGCCGCAGGGGGGACCG
1 GGACTCGTGGGACTG-GAG-GGGGGGCAGGGCCGCAGGGGGAATCG
* * *
3653426 GGAATCGTGGGACTGTGGGAGGGGGGTAGGG-CGCAAGGGGGAATCG
1 GGACTCGTGGGACTG-GAG-GGGGGGCAGGGCCGC-AGGGGGAATCG
3653472 GGA
1 GGA
3653475 GTCGAGACTA
Statistics
Matches: 497, Mismatches: 38, Indels: 69
0.82 0.06 0.11
Matches are distributed among these distances:
43 1 0.00
44 36 0.07
45 41 0.08
46 43 0.09
47 180 0.36
48 106 0.21
49 48 0.10
50 38 0.08
51 4 0.01
ACGTcount: A:0.17, C:0.17, G:0.56, T:0.09
Consensus pattern (44 bp):
GGACTCGTGGGACTGGAGGGGGGGCAGGGCCGCAGGGGGAATCG
Found at i:3653039 original size:142 final size:143
Alignment explanation
Indices: 3652859--3653474 Score: 902
Period size: 142 Copynumber: 4.4 Consensus size: 143
3652849 TCACCCAAAA
* * *
3652859 GGACTCGTGGGAG-CTGGATGGGGACGGGC-CGGCCGCAGGGGGAATCGGGACTCGTGGGACTGT
1 GGACTCGTGGGAGCCGGGA-GGGGGCGGGCAGGGCCGCAGGGGGAATCGGGACTCGTGGGACTGT
*
3652922 GGGA-GGGGGGCAGGGCCGCAGGGGGGAACCGGGAATCGTGGGACTGTGGGAGGGGGGGCAGGGC
65 GGGAGGGGGGGCAGGGCCGCA-GGGGGAACCGAGAATCGTGGGACTGTGGGAGGGGGGGCAGGGC
3652986 CGCAGGGGGGAATCG
129 CGCAGGGGGGAATCG
*
3653001 GGACTCGTGGGAGCCGGGAGGGGGC-GGCAGGGCTGCAGGGGGAATCGGGACTCGTGGGACTGTG
1 GGACTCGTGGGAGCCGGGAGGGGGCGGGCAGGGCCGCAGGGGGAATCGGGACTCGTGGGACTGTG
3653065 GGAGGGGGGGCAGGGCCGCAGGGGGAACCGAGAATCGTGGGACTGTGGGAGGGGGGGCAGGGCCG
66 GGAGGGGGGGCAGGGCCGCAGGGGGAACCGAGAATCGTGGGACTGTGGGAGGGGGGGCAGGGCCG
*
3653130 CAGGGGGAAATCG
131 CAGGGGGGAATCG
*
3653143 GGACTCGTGGGAGCC-GGAGGGGGGCGGGCAGGGCTGCAGGGGGGAATCGGGACTCGTGGGACTG
1 GGACTCGTGGGAGCCGGGA-GGGGGCGGGCAGGGCCGCA-GGGGGAATCGGGACTCGTGGGACTG
*
3653207 TGGGAGGGGGGGCAGGGCCGCAGGGGGAACCGAGAATCGTGGGACTGTGGAAGGGGGGGCAGGGC
64 TGGGAGGGGGGGCAGGGCCGCAGGGGGAACCGAGAATCGTGGGACTGTGGGAGGGGGGGCAGGGC
3653272 CGCAGGGGGGAATCG
129 CGCAGGGGGGAATCG
* *
3653287 GGACTCGTGGGAGCCGGAAGGGGGCAGGCAAGGGCCGCAAGGGGGAATCGGGACTCGTGGGACTG
1 GGACTCGTGGGAGCCGGGAGGGGGCGGGC-AGGGCCGC-AGGGGGAATCGGGACTCGTGGGACTG
* *
3653352 T-GG-GGGGGGGCATGG-CGCAGGGGGAACCGGGAATCGTGGGACTGT-GGA-GGGGGGCAGGGC
64 TGGGAGGGGGGGCAGGGCCGCAGGGGGAACCGAGAATCGTGGGACTGTGGGAGGGGGGGCAGGGC
*
3653412 CGCAGGGGGG-ACCG
129 CGCAGGGGGGAATCG
* * * *
3653426 GGAATCGTGGGA-CTGTGG-GAGGG-GGGTAGGG-CGCAAGGGGGAATCGGGA
1 GGACTCGTGGGAGCCG-GGAGGGGGCGGGCAGGGCCGC-AGGGGGAATCGGGA
3653475 GTCGAGACTA
Statistics
Matches: 443, Mismatches: 21, Indels: 27
0.90 0.04 0.05
Matches are distributed among these distances:
135 18 0.04
136 4 0.01
137 2 0.00
138 6 0.01
139 15 0.03
140 22 0.05
141 8 0.02
142 160 0.36
143 43 0.10
144 129 0.29
145 35 0.08
146 1 0.00
ACGTcount: A:0.17, C:0.17, G:0.56, T:0.09
Consensus pattern (143 bp):
GGACTCGTGGGAGCCGGGAGGGGGCGGGCAGGGCCGCAGGGGGAATCGGGACTCGTGGGACTGTG
GGAGGGGGGGCAGGGCCGCAGGGGGAACCGAGAATCGTGGGACTGTGGGAGGGGGGGCAGGGCCG
CAGGGGGGAATCG
Found at i:3653611 original size:21 final size:21
Alignment explanation
Indices: 3653582--3653628 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
3653572 ACATTTTGTA
*
3653582 GCCCATATAAAATATGGGCTG
1 GCCCGTATAAAATATGGGCTG
3653603 GCCCGTATAAAATATGGGCTG
1 GCCCGTATAAAATATGGGCTG
3653624 GCCCG
1 GCCCG
3653629 ACCCTGCCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (21 bp):
GCCCGTATAAAATATGGGCTG
Found at i:3654564 original size:25 final size:25
Alignment explanation
Indices: 3654531--3654599 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
3654521 AGATTTCAAC
* *
3654531 AAAAAAAAAACT-TAAAATATTAAAT
1 AAAAAAAAAA-TATAAAAAATAAAAT
*
3654556 AAAATAAAAATATAAAAAATAAAAT
1 AAAAAAAAAATATAAAAAATAAAAT
*
3654581 AAAAATTAAAAAAATAAAA
1 AAAAA--AAAAATATAAAA
3654600 CTGAAATTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 1 0.03
25 24 0.67
27 11 0.31
ACGTcount: A:0.78, C:0.01, G:0.00, T:0.20
Consensus pattern (25 bp):
AAAAAAAAAATATAAAAAATAAAAT
Found at i:3654574 original size:27 final size:27
Alignment explanation
Indices: 3654534--3654599 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
3654524 TTTCAACAAA
* *
3654534 AAAAAAACTTAAAATATTAAAT-AAAA-T
1 AAAAAAA--TAAAAAATAAAATAAAAATT
*
3654561 AAAAATATAAAAAATAAAATAAAAATT
1 AAAAAAATAAAAAATAAAATAAAAATT
3654588 AAAAAAATAAAA
1 AAAAAAATAAAA
3654600 CTGAAATTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 11 0.33
26 4 0.12
27 18 0.55
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (27 bp):
AAAAAAATAAAAAATAAAATAAAAATT
Found at i:3654607 original size:20 final size:20
Alignment explanation
Indices: 3654552--3654599 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
3654542 TTAAAATATT
3654552 AAATAAAATAAAAA-TATAAA
1 AAATAAAATAAAAATTA-AAA
3654572 AAATAAAATAAAAATTAAAA
1 AAATAAAATAAAAATTAAAA
3654592 AAATAAAA
1 AAATAAAA
3654600 CTGAAATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (20 bp):
AAATAAAATAAAAATTAAAA
Found at i:3655321 original size:20 final size:23
Alignment explanation
Indices: 3655284--3655328 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
3655274 CATTTAACTA
3655284 TTTATATTTTATGCATTAT-AGT
1 TTTATATTTTATGCATTATAAGT
*
3655306 TTTAT-TTTTA-GTATTATAAGT
1 TTTATATTTTATGCATTATAAGT
3655327 TT
1 TT
3655329 AAATAGAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 10 0.48
22 5 0.24
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.62
Consensus pattern (23 bp):
TTTATATTTTATGCATTATAAGT
Found at i:3661045 original size:19 final size:18
Alignment explanation
Indices: 3661023--3661089 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
3661013 TTCAACAAAA
*
3661023 AAATAAAACTTAAAATATT
1 AAATAAAA-TAAAAATATT
*
3661042 AAATAAAATAAAAATATA
1 AAATAAAATAAAAATATT
*
3661060 AAAAATAAATAAAAA-ATT
1 AAATA-AAATAAAAATATT
3661078 AAA-AAAATAAAA
1 AAATAAAATAAAA
3661090 CTGAAATTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
16 8 0.19
17 1 0.02
18 17 0.40
19 17 0.40
ACGTcount: A:0.76, C:0.01, G:0.00, T:0.22
Consensus pattern (18 bp):
AAATAAAATAAAAATATT
Found at i:3661054 original size:24 final size:24
Alignment explanation
Indices: 3661022--3661073 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
3661012 TTTCAACAAA
* *
3661022 AAAATAAAACT-TAAAATATTAAAT
1 AAAATAAAAATATAAAA-AATAAAT
3661046 AAAATAAAAATATAAAAAATAAAT
1 AAAATAAAAATATAAAAAATAAAT
3661070 AAAA
1 AAAA
3661074 AATTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (24 bp):
AAAATAAAAATATAAAAAATAAAT
Found at i:3661067 original size:20 final size:20
Alignment explanation
Indices: 3661020--3661089 Score: 67
Period size: 19 Copynumber: 3.5 Consensus size: 20
3661010 AATTTCAACA
*
3661020 AAAAAATAAAACTTAAAATAT
1 AAAAAATAAAA-TAAAAATAT
*
3661041 --TAAATAAAATAAAAATAT
1 AAAAAATAAAATAAAAATAT
3661059 AAAAAAT-AAATAAAAA-ATT
1 AAAAAATAAAATAAAAATA-T
3661078 AAAAAAATAAAA
1 -AAAAAATAAAA
3661090 CTGAAATTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
18 9 0.22
19 18 0.44
20 11 0.27
21 3 0.07
ACGTcount: A:0.77, C:0.01, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAAAATAAAATAAAAATAT
Found at i:3661970 original size:15 final size:16
Alignment explanation
Indices: 3661939--3661974 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
3661929 GTTTGGTATT
*
3661939 TTATAATGTAATGTGA
1 TTATAATGTAATATGA
3661955 TTATAA-GTAATATGA
1 TTATAATGTAATATGA
3661970 TTATA
1 TTATA
3661975 GATAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (16 bp):
TTATAATGTAATATGA
Found at i:3662788 original size:21 final size:21
Alignment explanation
Indices: 3662758--3662804 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3662748 GTGATTAGTT
* *
3662758 TTTAGGCATTGCGTGACTT-AC
1 TTTAGACATTGCATGA-TTGAC
3662779 TTTAGACATTGCATGATTGAC
1 TTTAGACATTGCATGATTGAC
3662800 TTTAG
1 TTTAG
3662805 GTATTACATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.40
Consensus pattern (21 bp):
TTTAGACATTGCATGATTGAC
Found at i:3662814 original size:21 final size:22
Alignment explanation
Indices: 3662790--3662831 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3662780 TTAGACATTG
*
3662790 CATGATTGA-CTTTAGGTATTA
1 CATGATTAATCTTTAGGTATTA
*
3662811 CATGATTAATTTTTAGGTATT
1 CATGATTAATCTTTAGGTATT
3662832 GCGTGAATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.48
Consensus pattern (22 bp):
CATGATTAATCTTTAGGTATTA
Found at i:3663933 original size:33 final size:33
Alignment explanation
Indices: 3663895--3663962 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
3663885 TTTAATTTCT
3663895 TATATTTTATTTT-AT-TTTTTAATTCTTATATTA
1 TATATTTTATTTTAATGTTTTTAATT-TTA-ATTA
*
3663928 TATATTTTATTTTAATGTTTTTTATTTTAATTA
1 TATATTTTATTTTAATGTTTTTAATTTTAATTA
3663961 TA
1 TA
3663963 GCATTACAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 19 0.59
34 5 0.16
35 8 0.25
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (33 bp):
TATATTTTATTTTAATGTTTTTAATTTTAATTA
Found at i:3665436 original size:57 final size:57
Alignment explanation
Indices: 3665330--3665438 Score: 155
Period size: 57 Copynumber: 1.9 Consensus size: 57
3665320 CTTATTAGTC
* *
3665330 ATCCAATTTATCACTAAATAAATTAAGATAATTTACAGATAAAATCCAAATTTGGTT
1 ATCCAATTTATCACTAAATAAATTAAGATAATTTACAAATAAAACCCAAATTTGGTT
*** * *
3665387 ATCCAATTTATGTTTAAATAAATTAAGATAATTTATAAATAATACCCAAATT
1 ATCCAATTTATCACTAAATAAATTAAGATAATTTACAAATAAAACCCAAATT
3665439 CAACCAATCA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.37
Consensus pattern (57 bp):
ATCCAATTTATCACTAAATAAATTAAGATAATTTACAAATAAAACCCAAATTTGGTT
Found at i:3666330 original size:44 final size:44
Alignment explanation
Indices: 3666265--3666352 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
3666255 AAAGAAAACA
**
3666265 ACTATTTGAAGAGTTACTTTATAAAAAGAA-ACAAGTCATTTCAT
1 ACTATTTGAAGAGACACTTTAT-AAAAGAATACAAGTCATTTCAT
* * *
3666309 ACTATTTGAAGAGACATTTTATGAAAGAATACAAGTCTTTTCAT
1 ACTATTTGAAGAGACACTTTATAAAAGAATACAAGTCATTTCAT
3666353 TAAAAGACTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
43 6 0.16
44 32 0.84
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.35
Consensus pattern (44 bp):
ACTATTTGAAGAGACACTTTATAAAAGAATACAAGTCATTTCAT
Found at i:3674218 original size:29 final size:29
Alignment explanation
Indices: 3674185--3674241 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
3674175 AAATATTTAA
3674185 AATATCCACAATAGATAAACAAGATATAC
1 AATATCCACAATAGATAAACAAGATATAC
* * * *
3674214 AATATCCATAGTAGCTAAGCAAGATATA
1 AATATCCACAATAGATAAACAAGATATA
3674242 TTGAATATCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.51, C:0.16, G:0.11, T:0.23
Consensus pattern (29 bp):
AATATCCACAATAGATAAACAAGATATAC
Found at i:3683325 original size:3 final size:3
Alignment explanation
Indices: 3683317--3683352 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3683307 CTCTATGTAT
3683317 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3683353 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3683958 original size:50 final size:51
Alignment explanation
Indices: 3683879--3684126 Score: 240
Period size: 51 Copynumber: 4.9 Consensus size: 51
3683869 GCTCCCACAT
* * * ** *
3683879 TTTGGGGTGCGATGTTAGCCCATATCAAACTCCACACTTTCAATTTGACAC
1 TTTGGGATGCCATGTTAGCCCATACCAAACTCCACACTTTCGCTTTAACAC
* * *
3683930 TTTGGGATGCCAT-TTAGCCCATACCAAACTCCACAATTTCGCTTTGATAC
1 TTTGGGATGCCATGTTAGCCCATACCAAACTCCACACTTTCGCTTTAACAC
* * *
3683980 TTTGAGATGCCATGTTA-CCTCATACCAAACTCCACACTTTCGGTTCAACAC
1 TTTGGGATGCCATGTTAGCC-CATACCAAACTCCACACTTTCGCTTTAACAC
* * * * *
3684031 CTT-GGAGGGCCATTTTAGCCGATACCTAACTCCACACTTTC-CTTTCAACAC
1 TTTGGGA-TGCCATGTTAGCCCATACCAAACTCCACACTTTCGCTTT-AACAC
*
3684082 TTTGAGG-TGTCATGTTAGCCCA-AGCCAAACTCCACACTTTC-CTTT
1 TTTG-GGATGCCATGTTAGCCCATA-CCAAACTCCACACTTTCGCTTT
3684127 TATTGGTTTC
Statistics
Matches: 162, Mismatches: 27, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
50 51 0.31
51 107 0.66
52 2 0.01
53 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (51 bp):
TTTGGGATGCCATGTTAGCCCATACCAAACTCCACACTTTCGCTTTAACAC
Found at i:3684087 original size:102 final size:101
Alignment explanation
Indices: 3683890--3684122 Score: 267
Period size: 102 Copynumber: 2.3 Consensus size: 101
3683880 TTGGGGTGCG
* ** * *
3683890 ATGTTAGCCCATATCAAACTCCACACTTTCAATTTGACACTTTGGGATGCCATTTAGCCCATACC
1 ATGTTAGCCCATACCAAACTCCACACTTTCAATTCAACACCTTGGGAGGCCATTTAGCCCATACC
* *
3683955 AAACTCCACAATTTCGCTTTGATACTTTGAGATGCC
66 AAACTCCACAATTTCGCTTTAACACTTTGAGATGCC
** *
3683991 ATGTTA-CCTCATACCAAACTCCACACTTTCGGTTCAACACCTT-GGAGGGCCATTTTAGCCGAT
1 ATGTTAGCC-CATACCAAACTCCACACTTTCAATTCAACACCTTGGGA-GGCCA-TTTAGCCCAT
* * * *
3684054 ACCTAACTCCACACTTTC-CTTTCAACACTTTGAGGTGTC
63 ACCAAACTCCACAATTTCGCTTT-AACACTTTGAGATGCC
3684093 ATGTTAGCCCA-AGCCAAACTCCACACTTTC
1 ATGTTAGCCCATA-CCAAACTCCACACTTTC
3684123 CTTTTATTGG
Statistics
Matches: 112, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
100 5 0.04
101 43 0.38
102 62 0.55
103 2 0.02
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.30
Consensus pattern (101 bp):
ATGTTAGCCCATACCAAACTCCACACTTTCAATTCAACACCTTGGGAGGCCATTTAGCCCATACC
AAACTCCACAATTTCGCTTTAACACTTTGAGATGCC
Found at i:3689601 original size:21 final size:18
Alignment explanation
Indices: 3689559--3689603 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 18
3689549 CATGTGTTTT
*
3689559 ATTTTTATTTTTATTATA
1 ATTTTTATTTTTAATATA
3689577 ATTTTATATATTTTAATATA
1 ATTTT-TAT-TTTTAATATA
3689597 CATTTTT
1 -ATTTTT
3689604 TACTATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 5 0.22
19 3 0.13
20 10 0.43
21 5 0.22
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTATTTTTAATATA
Found at i:3701759 original size:43 final size:43
Alignment explanation
Indices: 3701696--3701792 Score: 124
Period size: 43 Copynumber: 2.3 Consensus size: 43
3701686 ATCATGACAT
* * *
3701696 ATCAAGGATATCAAATATTATAATTGG-AACTATAGCACTTCAA
1 ATCAAGGATATCAAACATTATAATGGGAAAC-ATAGCACTACAA
* * *
3701739 ATCAAGGATATCAAGCATTATACTGGGAAACGTAGCACTACAA
1 ATCAAGGATATCAAACATTATAATGGGAAACATAGCACTACAA
3701782 ATCAAGGATAT
1 ATCAAGGATAT
3701793 AATTAACTAG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 44 0.94
44 3 0.06
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.26
Consensus pattern (43 bp):
ATCAAGGATATCAAACATTATAATGGGAAACATAGCACTACAA
Found at i:3701893 original size:43 final size:42
Alignment explanation
Indices: 3701846--3702034 Score: 171
Period size: 43 Copynumber: 4.4 Consensus size: 42
3701836 TAGTACCTCG
* * *
3701846 GATCAAGGATATCAAGCATTAGGTTTAGAAGTGTAGCATTACA
1 GATCAAGGATATCAAGCATAAGATTT-GAAGTGTAGCACTACA
* * * * *
3701889 GATCAAGGATATTAAGTATAAGGATTTGAATTGTATCACTATA
1 GATCAAGGATATCAAGCATAA-GATTTGAAGTGTAGCACTACA
* * *
3701932 GATTAAGGATATCAAGCATCAGACTTGGAAGTGTAGCACTACA
1 GATCAAGGATATCAAGCATAAGA-TTTGAAGTGTAGCACTACA
* * * * ** * *
3701975 GATCAAGTATATTAAGCATAATGATTTCAACTGTATTATTATA
1 GATCAAGGATATCAAGCATAA-GATTTGAAGTGTAGCACTACA
3702018 GATCAAGGATATCAAGC
1 GATCAAGGATATCAAGC
3702035 GTTATGCTTG
Statistics
Matches: 114, Mismatches: 29, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
42 2 0.02
43 106 0.93
44 6 0.05
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.30
Consensus pattern (42 bp):
GATCAAGGATATCAAGCATAAGATTTGAAGTGTAGCACTACA
Found at i:3701963 original size:86 final size:86
Alignment explanation
Indices: 3701846--3702034 Score: 261
Period size: 86 Copynumber: 2.2 Consensus size: 86
3701836 TAGTACCTCG
* ** * *
3701846 GATCAAGGATATCAAGCATTAGGTTTAGAAGTGTAGCATTACAGATCAAGGATATTAAGTATAAG
1 GATCAAGGATATCAAGCATCAGACTTAGAAGTGTAGCACTACAGATCAAGGATATTAAGCATAAG
* *
3701911 GATTTGAATTGTATCACTATA
66 GATTTCAACTGTATCACTATA
* * * *
3701932 GATTAAGGATATCAAGCATCAGACTTGGAAGTGTAGCACTACAGATCAAGTATATTAAGCATAAT
1 GATCAAGGATATCAAGCATCAGACTTAGAAGTGTAGCACTACAGATCAAGGATATTAAGCATAAG
* *
3701997 GATTTCAACTGTATTATTATA
66 GATTTCAACTGTATCACTATA
3702018 GATCAAGGATATCAAGC
1 GATCAAGGATATCAAGC
3702035 GTTATGCTTG
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
86 89 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.30
Consensus pattern (86 bp):
GATCAAGGATATCAAGCATCAGACTTAGAAGTGTAGCACTACAGATCAAGGATATTAAGCATAAG
GATTTCAACTGTATCACTATA
Found at i:3705142 original size:42 final size:42
Alignment explanation
Indices: 3705083--3705325 Score: 227
Period size: 42 Copynumber: 5.5 Consensus size: 42
3705073 TCAACATACC
*
3705083 TGAATTAATGCTATGGTAAAGTGATGTATGCTGAGTTAACCT
1 TGAATTAATGCTATGGTAAAGTGATGTATGCTGAGTTAAACT
* *
3705125 TGAATTAATGCTATGGTAGAGTAATTTATGCTGGTATGCTGAGTTAAACT
1 TGAATTAATGCTATGGT--A--AA---GTGAT-GTATGCTGAGTTAAACT
* * * * *
3705175 TGAATTAATGCTATGGTAGAGTAACGTATGCTGGGTCAAACT
1 TGAATTAATGCTATGGTAAAGTGATGTATGCTGAGTTAAACT
** * *
3705217 TGAATTGCTGGTATGGTGAAGTGATGTATGCTGAGTTAAAACT
1 TGAATTAATGCTATGGTAAAGTGATGTATGCTGAGTT-AAACT
* * *
3705260 TGAATAAAATGGC-ATGGTAGAGTGATGTATGCTGAGTTAAAGT
1 TGAAT-TAAT-GCTATGGTAAAGTGATGTATGCTGAGTTAAACT
* *
3705303 TGAATTAATGGTATGGTATAGTG
1 TGAATTAATGCTATGGTAAAGTG
3705326 TATGCTGGTT
Statistics
Matches: 160, Mismatches: 29, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
41 1 0.01
42 73 0.46
43 20 0.12
44 25 0.16
45 1 0.01
46 3 0.02
48 1 0.01
49 3 0.02
50 33 0.21
ACGTcount: A:0.31, C:0.07, G:0.27, T:0.35
Consensus pattern (42 bp):
TGAATTAATGCTATGGTAAAGTGATGTATGCTGAGTTAAACT
Found at i:3705183 original size:50 final size:50
Alignment explanation
Indices: 3705108--3705208 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 50
3705098 GTAAAGTGAT
* **
3705108 GTATGCTGAGTTAACCTTGAATTAATGCTATGGTAGAGTAATTTATGCTG
1 GTATGCTGAGTTAAACTTGAATTAATGCTATGGTAGAGTAACGTATGCTG
3705158 GTATGCTGAGTTAAACTTGAATTAATGCTATGGTAGAGTAACGTATGCTG
1 GTATGCTGAGTTAAACTTGAATTAATGCTATGGTAGAGTAACGTATGCTG
3705208 G
1 G
3705209 GTCAAACTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.36
Consensus pattern (50 bp):
GTATGCTGAGTTAAACTTGAATTAATGCTATGGTAGAGTAACGTATGCTG
Found at i:3705306 original size:86 final size:84
Alignment explanation
Indices: 3705158--3705319 Score: 218
Period size: 86 Copynumber: 1.9 Consensus size: 84
3705148 ATTTATGCTG
* *
3705158 GTATGCTGAGTTAAACTTGAATTAATGCTATGGTAGAGTAACGTATGCTGGGTCAAACTTGAATT
1 GTATGCTGAGTTAAACTTGAATAAATGCTATGGTAGAGTAACGTATGCTGAGTCAAACTTGAATT
**
3705223 GCTGGTATGGTGAAGTGAT
66 AATGGTATGGTGAAGTGAT
* * * *
3705242 GTATGCTGAGTTAAAACTTGAATAAAATGGC-ATGGTAGAGTGATGTATGCTGAGTTAAAGTTGA
1 GTATGCTGAGTT-AAACTTGAAT-AAAT-GCTATGGTAGAGTAACGTATGCTGAGTCAAACTTGA
3705306 ATTAATGGTATGGT
63 ATTAATGGTATGGT
3705320 ATAGTGTATG
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
84 12 0.18
85 10 0.15
86 43 0.64
87 2 0.03
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.33
Consensus pattern (84 bp):
GTATGCTGAGTTAAACTTGAATAAATGCTATGGTAGAGTAACGTATGCTGAGTCAAACTTGAATT
AATGGTATGGTGAAGTGAT
Found at i:3707453 original size:36 final size:37
Alignment explanation
Indices: 3707372--3707477 Score: 144
Period size: 36 Copynumber: 2.9 Consensus size: 37
3707362 AGCCTTAAAA
* *
3707372 ATCAAGACGCTCTACAAATACTAATATTCAGATATCCC
1 ATCAAGATGCTCTACAAATACTAA-ATTCAAATATCCC
* *
3707410 -TCGAGATGCTCTACAAATAATAAATTCAAATA-CCC
1 ATCAAGATGCTCTACAAATACTAAATTCAAATATCCC
*
3707445 ATCAAGATGCTCTACAAATACTATATTCAAATA
1 ATCAAGATGCTCTACAAATACTAAATTCAAATA
3707478 GCAAAGCAGG
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
35 3 0.05
36 37 0.62
37 20 0.33
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (37 bp):
ATCAAGATGCTCTACAAATACTAAATTCAAATATCCC
Found at i:3717142 original size:40 final size:39
Alignment explanation
Indices: 3717098--3717231 Score: 101
Period size: 40 Copynumber: 3.4 Consensus size: 39
3717088 TATAAATCTT
*
3717098 GAAAAATATAAAAATAATTTTTTATTTTTTAGAAATTTTA
1 GAAAAATA-AAAAATAATTTTTTATTTTTTAGAAATTATA
** * ** * *
3717138 GAAAAACCCAAAAATAATTTTTAATTATTAAAAAAAGTATA
1 GAAAAA-TAAAAAATAATTTTTTATT-TTTTAGAAATTATA
* **
3717179 GAACAATAAAAAATAA-AATTTATTTTTTAGAAATTA-A
1 GAAAAATAAAAAATAATTTTTTATTTTTTAGAAATTATA
*
3717216 AAAAAGATAAGAAAAT
1 GAAAA-ATAA-AAAAT
3717232 CCAGAAAATA
Statistics
Matches: 70, Mismatches: 20, Indels: 9
0.71 0.20 0.09
Matches are distributed among these distances:
37 4 0.06
38 12 0.17
39 10 0.14
40 30 0.43
41 14 0.20
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (39 bp):
GAAAAATAAAAAATAATTTTTTATTTTTTAGAAATTATA
Found at i:3717948 original size:26 final size:28
Alignment explanation
Indices: 3717889--3717959 Score: 87
Period size: 26 Copynumber: 2.6 Consensus size: 28
3717879 CTAAGTTTGT
*
3717889 ATTATAATAAATAAAAATAAAATATAAG
1 ATTATAATAAATAAAAATAAAATATAAA
3717917 ATTATAAT-AA-AAAAATAAAA-ATAAA
1 ATTATAATAAATAAAAATAAAATATAAA
*
3717942 ATATATAA-AATTAAAAAT
1 AT-TATAATAAATAAAAAT
3717960 TTATTTAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 6 0.16
26 16 0.42
27 8 0.21
28 8 0.21
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.28
Consensus pattern (28 bp):
ATTATAATAAATAAAAATAAAATATAAA
Found at i:3723589 original size:14 final size:14
Alignment explanation
Indices: 3723570--3723600 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3723560 TTCACCATTA
*
3723570 CTCTTCTTCCTCTC
1 CTCTTCCTCCTCTC
3723584 CTCTTCCTCCTCTC
1 CTCTTCCTCCTCTC
3723598 CTC
1 CTC
3723601 CTTCGTCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (14 bp):
CTCTTCCTCCTCTC
Found at i:3724687 original size:28 final size:28
Alignment explanation
Indices: 3724622--3724687 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 28
3724612 TTACTATCTA
3724622 AATTAGAT-TATAAATAATAATTTTTAGTT
1 AATTA-ATATATAAATAATAATTTTTAG-T
* *
3724651 AATT-TTATATAAATATATATTTTTTA-T
1 AATTAATATATAAATA-ATAATTTTTAGT
3724678 AATTAATATA
1 AATTAATATA
3724688 ATACTTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
27 6 0.19
28 12 0.39
29 13 0.42
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (28 bp):
AATTAATATATAAATAATAATTTTTAGT
Found at i:3724697 original size:21 final size:21
Alignment explanation
Indices: 3724653--3724713 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
3724643 TTTTAGTTAA
* *
3724653 TTTTAT-ATAAATAT-ATATT
1 TTTTATAATTAATATAATACT
3724672 TTTTATAATTAATATAATACT
1 TTTTATAATTAATATAATACT
*
3724693 TTTTAAAATTAAT-TAAT-CT
1 TTTTATAATTAATATAATACT
3724712 TT
1 TT
3724714 CTAAGTATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 10 0.27
20 11 0.30
21 16 0.43
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTATAATTAATATAATACT
Found at i:3725996 original size:17 final size:18
Alignment explanation
Indices: 3725970--3726008 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
3725960 TAAGATTTAT
3725970 TTTCTCTCCC-TAAATAC
1 TTTCTCTCCCTTAAATAC
*
3725987 TTTCTTTCCCTTTAAATAC
1 TTTCTCTCCC-TTAAATAC
3726006 TTT
1 TTT
3726009 TTCTTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
19 10 0.53
ACGTcount: A:0.21, C:0.28, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTCTCTCCCTTAAATAC
Found at i:3726143 original size:25 final size:25
Alignment explanation
Indices: 3726114--3726162 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
3726104 TTTCATTATC
3726114 TTCAAGCTTAAAAAAGATTTCAATT
1 TTCAAGCTTAAAAAAGATTTCAATT
*
3726139 TTCAAGCTTCAAAAAGATTTCAAT
1 TTCAAGCTTAAAAAAGATTTCAAT
3726163 GATGGGGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (25 bp):
TTCAAGCTTAAAAAAGATTTCAATT
Found at i:3726400 original size:53 final size:54
Alignment explanation
Indices: 3726325--3726484 Score: 160
Period size: 53 Copynumber: 2.9 Consensus size: 54
3726315 GCTATTATAT
* * ** * *
3726325 AGCTATTGATGAAAAACCATGAATGTCCATTCCCGGAAGTGAATGTGACAAATA
1 AGCTATTAATAAAAAATTATGAATGTCCATTCCCTGAAGTGAATGTGACAAACA
* * * *
3726379 AGCTATTAAT-AAAAATTATGAATGTTCATTCCCTGTAGTGAATGTGATAAACG
1 AGCTATTAATAAAAAATTATGAATGTCCATTCCCTGAAGTGAATGTGACAAACA
* * * *
3726432 AGATACTAATAAAAATATTATAAATTCGTCCATTCCCTGAAGTGAATGCGACA
1 AGCTATTAATAAAAA-ATTATGAA-T-GTCCATTCCCTGAAGTGAATGTGACA
3726485 TCATTTAATA
Statistics
Matches: 86, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
53 43 0.50
54 13 0.15
55 7 0.08
56 1 0.01
57 22 0.26
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (54 bp):
AGCTATTAATAAAAAATTATGAATGTCCATTCCCTGAAGTGAATGTGACAAACA
Found at i:3731397 original size:64 final size:64
Alignment explanation
Indices: 3731325--3731446 Score: 208
Period size: 64 Copynumber: 1.9 Consensus size: 64
3731315 TTCATAACAC
* *
3731325 CTATCTCTTTTTATCTCTTTTTCTCCCTATCCTAAAGAGTAGTAATGACATCACGATAATTCCT
1 CTATCTCTTTTTATCTCTTTTTCTCCATATCCCAAAGAGTAGTAATGACATCACGATAATTCCT
* *
3731389 CTATCTCTTTTTATCTCTTTTTCTTCATATCCCAAAGAGTAGTAATGGCATCACGATA
1 CTATCTCTTTTTATCTCTTTTTCTCCATATCCCAAAGAGTAGTAATGACATCACGATA
3731447 TGTGTTTTAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.25, C:0.24, G:0.09, T:0.42
Consensus pattern (64 bp):
CTATCTCTTTTTATCTCTTTTTCTCCATATCCCAAAGAGTAGTAATGACATCACGATAATTCCT
Found at i:3731742 original size:22 final size:22
Alignment explanation
Indices: 3731717--3731766 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
3731707 GTATTATTTG
**
3731717 TTTTTA-GACATTGTGTCACTGA
1 TTTTTACG-CATTGTGAAACTGA
*
3731739 TTTTTACGTATTGTGAAACTGA
1 TTTTTACGCATTGTGAAACTGA
3731761 TTTTTA
1 TTTTTA
3731767 AGTATTGCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.50
Consensus pattern (22 bp):
TTTTTACGCATTGTGAAACTGA
Found at i:3731873 original size:23 final size:22
Alignment explanation
Indices: 3731798--3731875 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
3731788 TGTATCTTTG
* *
3731798 ATTTTTAAACATTACGTAACTA
1 ATTTTTAAGCATTACGTGACTA
*
3731820 ATTTTTAGGCATTACGTGACTA
1 ATTTTTAAGCATTACGTGACTA
** * *
3731842 GGTTCTAAGCATTTACATGACTA
1 ATTTTTAAGCA-TTACGTGACTA
3731865 ATTTTTAAGCA
1 ATTTTTAAGCA
3731876 ATGCCTAAGT
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
22 26 0.59
23 18 0.41
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (22 bp):
ATTTTTAAGCATTACGTGACTA
Found at i:3732204 original size:60 final size:60
Alignment explanation
Indices: 3732116--3732237 Score: 190
Period size: 60 Copynumber: 2.0 Consensus size: 60
3732106 CTCGGAGAAG
* * * *
3732116 AATGCTTAAAATGCTCAAAAGTTTTTCTTCATGTATCAAAAATCATTCCAAAATGTTTAA
1 AATGCTCAAAACGCTCAAAAATTTTTCTTCATGTATCAAAAACCATTCCAAAATGTTTAA
* *
3732176 AATGCTCAAAACGCTGAAAAATTTTTCTTCGTGTATCAAAAACCATTCCAAAATGTTTAA
1 AATGCTCAAAACGCTCAAAAATTTTTCTTCATGTATCAAAAACCATTCCAAAATGTTTAA
3732236 AA
1 AA
3732238 GTTTTTCTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (60 bp):
AATGCTCAAAACGCTCAAAAATTTTTCTTCATGTATCAAAAACCATTCCAAAATGTTTAA
Found at i:3732366 original size:16 final size:16
Alignment explanation
Indices: 3732334--3732376 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
3732324 ATAAACATAT
*
3732334 AGATAACTTTCATTCAA
1 AGATAA-TTTTATTCAA
3732351 AGATAATTTTATTCAA
1 AGATAATTTTATTCAA
3732367 A-ATTAATTTT
1 AGA-TAATTTT
3732377 TCTTAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (16 bp):
AGATAATTTTATTCAA
Found at i:3733231 original size:2 final size:2
Alignment explanation
Indices: 3733224--3733248 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3733214 GGTATGTCTC
3733224 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3733249 GATACATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3746871 original size:31 final size:29
Alignment explanation
Indices: 3746804--3746874 Score: 79
Period size: 31 Copynumber: 2.4 Consensus size: 29
3746794 TATATATTTT
*
3746804 ATTTAATTTAATTTTTATATTTAAAATTA
1 ATTTAATTTAACTTTTATATTTAAAATTA
** *
3746833 AAATAATTTAACCTTTTATTTTTTAAAATTA
1 ATTTAATTTAA-CTTTTA-TATTTAAAATTA
*
3746864 TTTTAATTTAA
1 ATTTAATTTAA
3746875 TTTATCTCCT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
29 9 0.27
30 5 0.15
31 19 0.58
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (29 bp):
ATTTAATTTAACTTTTATATTTAAAATTA
Found at i:3750180 original size:10 final size:10
Alignment explanation
Indices: 3750161--3750196 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
3750151 CACAGCATTG
3750161 AAAT-TTATT
1 AAATGTTATT
3750170 AAATGTTATT
1 AAATGTTATT
3750180 AAATGTTATT
1 AAATGTTATT
3750190 AAATGTT
1 AAATGTT
3750197 TTTGGGATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.15
10 22 0.85
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (10 bp):
AAATGTTATT
Found at i:3755412 original size:66 final size:66
Alignment explanation
Indices: 3755301--3755426 Score: 173
Period size: 66 Copynumber: 1.9 Consensus size: 66
3755291 GCAATTCAAA
* * ** *
3755301 AAGGGTAAAGGCTGAGGTTCCAGACTATTTGGATGGGTTTTCAAGGAAAGCAAAGACTGATTTGA
1 AAGGATAAAGGCTAAGGTTCCAGAAAATTAGGATGGGTTTTCAAGGAAAGCAAAGACTGATTTGA
3755366 G
66 G
* *
3755367 AAGGATAAAGGCTAAGGTTCCAGAAAATTCAGG-TGGTTTTTCAAGGAAAGCAAAGGCTGA
1 AAGGATAAAGGCTAAGGTTCCAGAAAATT-AGGATGGGTTTTCAAGGAAAGCAAAGACTGA
3755427 GATGTCGAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
66 50 0.96
67 2 0.04
ACGTcount: A:0.35, C:0.11, G:0.30, T:0.24
Consensus pattern (66 bp):
AAGGATAAAGGCTAAGGTTCCAGAAAATTAGGATGGGTTTTCAAGGAAAGCAAAGACTGATTTGA
G
Found at i:3762020 original size:43 final size:37
Alignment explanation
Indices: 3761936--3762009 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
3761926 CAAAACTTTA
3761936 AGAAAAAGGACATCAACATCAGCTTCGACTTTAGGTT
1 AGAAAAAGGACATCAACATCAGCTTCGACTTTAGGTT
3761973 AGAAAAAGGACATCAACATCAGCTTCGACTTTAGGTT
1 AGAAAAAGGACATCAACATCAGCTTCGACTTTAGGTT
3762010 CTGATCAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (37 bp):
AGAAAAAGGACATCAACATCAGCTTCGACTTTAGGTT
Found at i:3769991 original size:3 final size:3
Alignment explanation
Indices: 3769983--3770015 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
3769973 TTGTTTTGTC
*
3769983 GGT GGT GGT GGT GGT GGT GGT GGT GAT GGT GGT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
3770016 TGACGTAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.64, T:0.33
Consensus pattern (3 bp):
GGT
Found at i:3770514 original size:22 final size:22
Alignment explanation
Indices: 3770443--3770516 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 22
3770433 TAGTTTTATT
* * *
3770443 TTATTTTTTAAATATTAATATT
1 TTATTTATAAAATATTAATATA
* ***
3770465 TTATTTATAATATAACCAT-TA
1 TTATTTATAAAATATTAATATA
*
3770486 ATA-TTATAAAATATTAATATA
1 TTATTTATAAAATATTAATATA
3770507 TTATTTATAA
1 TTATTTATAA
3770517 TTTAAATGTT
Statistics
Matches: 37, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
20 11 0.30
21 7 0.19
22 19 0.51
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (22 bp):
TTATTTATAAAATATTAATATA
Found at i:3770604 original size:27 final size:25
Alignment explanation
Indices: 3770548--3770605 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
3770538 TTATTTTATT
3770548 TTATTT-TTAAATATTAATAATTTA
1 TTATTTATTAAATATTAATAATTTA
*
3770572 TAATTTATTAAAAGTATTAAT-ATTTAA
1 TTATTTATT-AAA-TATTAATAATTT-A
3770599 TTATTTA
1 TTATTTA
3770606 CATATTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 5 0.18
25 2 0.07
26 7 0.25
27 14 0.50
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
TTATTTATTAAATATTAATAATTTA
Found at i:3778874 original size:71 final size:71
Alignment explanation
Indices: 3778790--3778931 Score: 257
Period size: 71 Copynumber: 2.0 Consensus size: 71
3778780 GCAATGTAAG
* *
3778790 ACTCCCATGCATAGTGAGATTATAGTAATTTTGATAATTTCTTTGAAGTGCAATCAGTATCTTTA
1 ACTCCCATGCATAGTGAGATTATAGTAATTTTGATAATTTCTTCGAAGTGCAATCAGTATCATTA
3778855 TCTGCT
66 TCTGCT
*
3778861 ACTCCCATGCATAGTGAGATTATAGTAATTTTGATCATTTCTTCGAAGTGCAATCAGTATCATTA
1 ACTCCCATGCATAGTGAGATTATAGTAATTTTGATAATTTCTTCGAAGTGCAATCAGTATCATTA
3778926 TCTGCT
66 TCTGCT
3778932 TAAATTTGGG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (71 bp):
ACTCCCATGCATAGTGAGATTATAGTAATTTTGATAATTTCTTCGAAGTGCAATCAGTATCATTA
TCTGCT
Found at i:3784700 original size:29 final size:29
Alignment explanation
Indices: 3784668--3784734 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
3784658 ATTTCTCTTA
3784668 ATTTTTTTAAAAAATTAAA-ATAAATTTTC
1 ATTTTTTTAAAAAATTAAATA-AAATTTTC
* * * * *
3784697 ATTTTTATATAATATTCAATAAAATTTTT
1 ATTTTTTTAAAAAATTAAATAAAATTTTC
3784726 ATTTTTTTA
1 ATTTTTTTA
3784735 TTTTTAATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 30 0.97
30 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (29 bp):
ATTTTTTTAAAAAATTAAATAAAATTTTC
Found at i:3785651 original size:22 final size:21
Alignment explanation
Indices: 3785604--3785651 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
3785594 TGGTCTAATA
**
3785604 TTTTAAAAAAAATTTTAAACT
1 TTTTAAAAAAAATTAAAAACT
* *
3785625 ATTTAAAAAAAATTAAATAAGT
1 TTTTAAAAAAAATTAAA-AACT
3785647 TTTTA
1 TTTTA
3785652 TATTTTTATT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
TTTTAAAAAAAATTAAAAACT
Found at i:3785824 original size:23 final size:23
Alignment explanation
Indices: 3785771--3785830 Score: 63
Period size: 25 Copynumber: 2.7 Consensus size: 23
3785761 GAAGTTAACG
3785771 TGACAT-ATTAATATATTATAAT
1 TGACATAATTAATATATTATAAT
* *
3785793 TGATGATAATGTAATATATTA-ATT
1 TGA-CATAAT-TAATATATTATAAT
3785817 TGACATAA-TAATAT
1 TGACATAATTAATAT
3785831 GATCATGTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 6 0.19
22 3 0.09
23 6 0.19
24 7 0.22
25 10 0.31
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.43
Consensus pattern (23 bp):
TGACATAATTAATATATTATAAT
Found at i:3785967 original size:30 final size:30
Alignment explanation
Indices: 3785933--3786006 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
3785923 ATTAATCATT
3785933 AAATATAAAGATTTATTTGATAAAAAATAA
1 AAATATAAAGATTTATTTGATAAAAAATAA
3785963 AAATATAAAGATTTATTTGATAAAAAATAA
1 AAATATAAAGATTTATTTGATAAAAAATAA
*
3785993 AAATATAAAAATTT
1 AAATATAAAGATTT
3786007 TATTGAACAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (30 bp):
AAATATAAAGATTTATTTGATAAAAAATAA
Found at i:3797850 original size:84 final size:84
Alignment explanation
Indices: 3797662--3798077 Score: 218
Period size: 84 Copynumber: 5.0 Consensus size: 84
3797652 CCTGTGCTAT
* * * * * *
3797662 CACC-ATCACCAATCAATTCCTCTGGACCAGAACCATCTACATTTTCACCCTGATTATCATTCAA
1 CACCTATCACTAATCAATTCCTTTGAACCAGAACCATCCACATTCTCACACTGATTATCATTCAA
3797726 ACAAACCACACCATCACCA
66 ACAAACCACACCATCACCA
* * * * * *
3797745 CACCTACCA-TCCATCATTTCCTTTGAACCAGAACTATCCACATTCTCAGACTGATTTTCATTCA
1 CACCTATCACT-AATCAATTCCTTTGAACCAGAACCATCCACATTCTCACACTGATTATCATTCA
* * * *
3797809 AGCATACCACACTATGACCA
65 AACAAACCACACCATCACCA
* * * * * ** * * **
3797829 TC-CTTATCACTAATCAATTCCTTGGAGCCAGCACAATGTACATTCTCACCCTGATTCTCATTGG
1 -CACCTATCACTAATCAATTCCTTTGAACCAGAACCATCCACATTCTCACACTGATTATCATTCA
* *** *
3797893 AGCAAACTGTACTATCACCA
65 AACAAACCACACCATCACCA
* ** * * ** * * * *
3797913 CACCTATCACCT-GTCAAGACATCTGAAAAAGAACCATCCACATTCTCACCCAGATTTTCATTTG
1 CACCTATCA-CTAATCAATTCCTTTGAACCAGAACCATCCACATTCTCACACTGATTATCA-TTC
* ** * *
3797977 AGA-AAACTGCACTATC-CCTG
64 AAACAAACCACACCATCACC-A
** * * * *
3797997 CACCTATCACCCATCAATTCCTTTGAACTAGAACCATCCACACTT-TCACCCCGATTTTC-TTCC
1 CACCTATCACTAATCAATTCCTTTGAACCAGAACCATCCACA-TTCTCACACTGATTATCATT-C
*
3798060 AAACAAACCACACAATCA
64 AAACAAACCACACCATCA
3798078 TTGCACCTAT
Statistics
Matches: 249, Mismatches: 71, Indels: 24
0.72 0.21 0.07
Matches are distributed among these distances:
82 2 0.01
83 10 0.04
84 228 0.92
85 9 0.04
ACGTcount: A:0.32, C:0.34, G:0.08, T:0.26
Consensus pattern (84 bp):
CACCTATCACTAATCAATTCCTTTGAACCAGAACCATCCACATTCTCACACTGATTATCATTCAA
ACAAACCACACCATCACCA
Found at i:3799501 original size:29 final size:28
Alignment explanation
Indices: 3799473--3799556 Score: 73
Period size: 31 Copynumber: 2.8 Consensus size: 28
3799463 TTTAAATTAT
3799473 TTAAATAATTTTATTTTATTTTATTTTA
1 TTAAATAATTTTATTTTATTTTATTTTA
*
3799501 TTCAATCACACTTTTA-TTT-TTTTATTTTAAA
1 TTAAAT-A-A-TTTTATTTTATTTTATTTT--A
*
3799532 TTAAATAATTTCACTTTCTATTTTA
1 TTAAATAATTTTA-TTT-TATTTTA
3799557 ATACCACGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
28 9 0.20
29 11 0.25
30 7 0.16
31 12 0.27
32 5 0.11
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.61
Consensus pattern (28 bp):
TTAAATAATTTTATTTTATTTTATTTTA
Found at i:3800159 original size:2 final size:2
Alignment explanation
Indices: 3800152--3800179 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3800142 GACATGAAAC
3800152 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
3800180 CTTGTTGCAT
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:3800668 original size:18 final size:17
Alignment explanation
Indices: 3800641--3800674 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3800631 TTTTTATTTA
3800641 ATATTAAAATAATAATT
1 ATATTAAAATAATAATT
*
3800658 ATATGTAAAATACTAAT
1 ATAT-TAAAATAATAAT
3800675 ATTTCTTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
ATATTAAAATAATAATT
Found at i:3804846 original size:31 final size:31
Alignment explanation
Indices: 3804811--3804869 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
3804801 AGGCAACGCC
3804811 CATTTGGTTTTGTACATTATGCAATACTATG
1 CATTTGGTTTTGTACATTATGCAATACTATG
*
3804842 CATTTTGTTTTGTACATTATGCAATACT
1 CATTTGGTTTTGTACATTATGCAATACT
3804870 TGTTGATTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (31 bp):
CATTTGGTTTTGTACATTATGCAATACTATG
Found at i:3805655 original size:20 final size:22
Alignment explanation
Indices: 3805630--3805670 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3805620 TATTTACACT
3805630 TATAATAC-T-AAATATAAATC
1 TATAATACATAAAATATAAATC
3805650 TATAATACATAAAATATAAAT
1 TATAATACATAAAATATAAAT
3805671 AGTTAAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 1 0.05
22 10 0.53
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (22 bp):
TATAATACATAAAATATAAATC
Found at i:3806102 original size:19 final size:18
Alignment explanation
Indices: 3806074--3806109 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3806064 AAAAGAACAT
*
3806074 ATGAACAAATAGAACAAAA
1 ATGAAAAAATA-AACAAAA
3806093 ATGAAAAAATAAACAAA
1 ATGAAAAAATAAACAAA
3806110 TATAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.72, C:0.08, G:0.08, T:0.11
Consensus pattern (18 bp):
ATGAAAAAATAAACAAAA
Found at i:3806423 original size:2 final size:2
Alignment explanation
Indices: 3806416--3806440 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3806406 CTCCACCAAC
3806416 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3806441 GAGAGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3810408 original size:18 final size:18
Alignment explanation
Indices: 3810385--3810420 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3810375 GTTACGTCCC
3810385 TTAATGAAAACAAATCAA
1 TTAATGAAAACAAATCAA
3810403 TTAATGAAAACAAATCAA
1 TTAATGAAAACAAATCAA
3810421 AAGACCAACT
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:0.61, C:0.11, G:0.06, T:0.22
Consensus pattern (18 bp):
TTAATGAAAACAAATCAA
Found at i:3811964 original size:18 final size:18
Alignment explanation
Indices: 3811934--3811974 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
3811924 ATTTTTATTT
3811934 AAAATAAAAAAATTAATTA
1 AAAATAAAAAAA-TAATTA
*
3811953 AAAAT-AAAAAATAATTT
1 AAAATAAAAAAATAATTA
3811970 AAAAT
1 AAAAT
3811975 TTTTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 6 0.29
19 5 0.24
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAATAAAAAAATAATTA
Found at i:3814676 original size:27 final size:27
Alignment explanation
Indices: 3814613--3814664 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
3814603 TATGGTTGGA
3814613 ATGTCATCTGCATTCTGCGTTGAGCTC
1 ATGTCATCTGCATTCTGCGTTGAGCTC
* **
3814640 ATTTCATCTGCATTCTTTGTTGAGC
1 ATGTCATCTGCATTCTGCGTTGAGC
3814665 GTGAGTCATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.42
Consensus pattern (27 bp):
ATGTCATCTGCATTCTGCGTTGAGCTC
Found at i:3816594 original size:20 final size:21
Alignment explanation
Indices: 3816569--3816607 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3816559 AAGGAGCGTG
*
3816569 TAATG-TGTTTTATTGCTTTA
1 TAATGTTGTTTCATTGCTTTA
3816589 TAATGTTGTTTCATTGCTT
1 TAATGTTGTTTCATTGCTT
3816608 GTTATGCAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.18, C:0.08, G:0.15, T:0.59
Consensus pattern (21 bp):
TAATGTTGTTTCATTGCTTTA
Found at i:3823195 original size:11 final size:11
Alignment explanation
Indices: 3823179--3823212 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3823169 TTTCACTTGG
3823179 TTTTTTCTTTT
1 TTTTTTCTTTT
3823190 TTTTTTCTTCTT
1 TTTTTTCTT-TT
*
3823202 TGTTTTCTTTT
1 TTTTTTCTTTT
3823213 ATTTCAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:3836511 original size:2 final size:2
Alignment explanation
Indices: 3836504--3836530 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3836494 TACCATTATC
3836504 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3836531 TACTTCATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3837353 original size:2 final size:2
Alignment explanation
Indices: 3837346--3837376 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3837336 GCAAGGGCTA
3837346 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
3837377 AAGGTTGTTC
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:3837898 original size:20 final size:20
Alignment explanation
Indices: 3837861--3837911 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
3837851 ATATTATTAA
*
3837861 TAAAAATTAAATTAATAAAT
1 TAAAAATTAAAATAATAAAT
* *
3837881 TAAAAGTTAAAATCAT-AAT
1 TAAAAATTAAAATAATAAAT
3837900 TAGAATAATTAA
1 TA-AA-AATTAA
3837912 TAAATTTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 5 0.20
20 15 0.60
21 5 0.20
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (20 bp):
TAAAAATTAAAATAATAAAT
Found at i:3843432 original size:16 final size:16
Alignment explanation
Indices: 3843375--3843431 Score: 64
Period size: 15 Copynumber: 3.6 Consensus size: 16
3843365 CTTTCCTCAC
3843375 TAAATTAAAATGAATT
1 TAAATTAAAATGAATT
**
3843391 TAAAATTAAAA-GAAAA
1 T-AAATTAAAATGAATT
*
3843407 AAAATTAAAATGAATT
1 TAAATTAAAATGAATT
3843423 TAAA-TAAAA
1 TAAATTAAAA
3843432 AGGTTTAAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
15 14 0.42
16 10 0.30
17 9 0.27
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (16 bp):
TAAATTAAAATGAATT
Found at i:3843599 original size:27 final size:29
Alignment explanation
Indices: 3843567--3843635 Score: 97
Period size: 27 Copynumber: 2.4 Consensus size: 29
3843557 TTAATGTTTT
3843567 AATATAAATTATTAAT-ATTT-TAAATGA
1 AATATAAATTATTAATAATTTGTAAATGA
*
3843594 AATATAAATTATTAATAATTTGTAAATTA
1 AATATAAATTATTAATAATTTGTAAATGA
*
3843623 AATAAATAATTAT
1 AATATA-AATTAT
3843636 ATTAACATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 16 0.43
28 4 0.11
29 11 0.30
30 6 0.16
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (29 bp):
AATATAAATTATTAATAATTTGTAAATGA
Found at i:3843721 original size:21 final size:22
Alignment explanation
Indices: 3843679--3843721 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
3843669 AATAAATTTA
**
3843679 TTAAAACAATAAATATTTTAAT
1 TTAAAACAATAAATATCATAAT
*
3843701 TTAAAA-ATTAAATATCATAAT
1 TTAAAACAATAAATATCATAAT
3843722 AAATGATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAAACAATAAATATCATAAT
Found at i:3867824 original size:2 final size:2
Alignment explanation
Indices: 3867817--3867847 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3867807 GAAAAATGTA
3867817 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
3867848 AGAAATAAAA
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:3868957 original size:20 final size:22
Alignment explanation
Indices: 3868932--3868973 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
3868922 TTATTTAAGG
3868932 ATAATGGAAT-ACTG-TGAATA
1 ATAATGGAATAACTGTTGAATA
3868952 ATAATGGAATAACTGTTGAATA
1 ATAATGGAATAACTGTTGAATA
3868974 GGCCATTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.50
21 4 0.20
22 6 0.30
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.31
Consensus pattern (22 bp):
ATAATGGAATAACTGTTGAATA
Found at i:3880259 original size:81 final size:82
Alignment explanation
Indices: 3880121--3880276 Score: 242
Period size: 81 Copynumber: 1.9 Consensus size: 82
3880111 GGGAGTTATA
* * * **
3880121 AGGTTCTCTGCCCTGGGTATGGCCTTTTATTTTTCCTGTTTTAATATGTTTATTATATACCCGCA
1 AGGTTCTCTGCCCTGGGTATGGCCTTCTATTTTTACTGTTTTAATAGGTTTATTATATACAAGCA
*
3880186 TATGTGTCAAGCCCCCG
66 TACGTGTCAAGCCCCCG
*
3880203 AGGTTCTCTGCCCTGGGTATGGCCTTCT-TTTTTACTGTTTTAATGGGTTTATTATATACAAGCA
1 AGGTTCTCTGCCCTGGGTATGGCCTTCTATTTTTACTGTTTTAATAGGTTTATTATATACAAGCA
3880267 TACGTGTCAA
66 TACGTGTCAA
3880277 CTCCAAGTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
81 40 0.60
82 27 0.40
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (82 bp):
AGGTTCTCTGCCCTGGGTATGGCCTTCTATTTTTACTGTTTTAATAGGTTTATTATATACAAGCA
TACGTGTCAAGCCCCCG
Found at i:3881190 original size:21 final size:23
Alignment explanation
Indices: 3881156--3881203 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
3881146 TTTTGATATA
3881156 ATTTT-TTATTTTTT-A-TCTCT
1 ATTTTCTTATTTTTTCATTCTCT
*
3881176 ATTTTCTTTTTTTTTCATTCTCT
1 ATTTTCTTATTTTTTCATTCTCT
3881199 -TTTTC
1 ATTTTC
3881204 CTCTTTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 5 0.21
21 8 0.33
22 6 0.25
23 5 0.21
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (23 bp):
ATTTTCTTATTTTTTCATTCTCT
Found at i:3881210 original size:23 final size:22
Alignment explanation
Indices: 3881164--3881215 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
3881154 TAATTTTTTA
*
3881164 TTTTTT-ATCTCTATTTTCTTT
1 TTTTTTCATCTCTATTTTCTCT
3881185 TTTTTTCATTCTCT-TTTTCCTCT
1 TTTTTTCA-TCTCTATTTT-CTCT
3881208 TTTCTTTC
1 TTT-TTTC
3881216 CTTTCTTGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 6 0.23
22 5 0.19
23 11 0.42
24 4 0.15
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTTTCATCTCTATTTTCTCT
Found at i:3884606 original size:17 final size:17
Alignment explanation
Indices: 3884584--3884633 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
3884574 TAAAAAAATC
3884584 TTAAAATATTTAATTTT
1 TTAAAATATTTAATTTT
* *
3884601 TTAAAATTTTTTTATTTT
1 TTAAAA-TATTTAATTTT
**
3884619 TTATTATATTTAATT
1 TTAAAATATTTAATT
3884634 AAATTTTTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTAAAATATTTAATTTT
Found at i:3884657 original size:20 final size:21
Alignment explanation
Indices: 3884616--3884655 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
3884606 ATTTTTTTAT
3884616 TTTTTATTATATTTAATTAAA
1 TTTTTATTATATTTAATTAAA
*
3884637 TTTTTA-TAT-TTTTATTAAA
1 TTTTTATTATATTTAATTAAA
3884656 ATCAAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 3 0.17
21 6 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTATTATATTTAATTAAA
Found at i:3889367 original size:2 final size:2
Alignment explanation
Indices: 3889360--3889388 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3889350 CGTATAGCGA
3889360 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3889389 TTTTGTGTTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3898947 original size:16 final size:17
Alignment explanation
Indices: 3898926--3898974 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
3898916 ATTATCAGGT
3898926 AAAAATTAATAAA-TAA
1 AAAAATTAATAAATTAA
*
3898942 AAAAATT-TTAAATTAA
1 AAAAATTAATAAATTAA
*
3898958 AAATATT-A-AAATTAA
1 AAAAATTAATAAATTAA
3898973 AA
1 AA
3898975 TATGTAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.45
16 16 0.55
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAATTAATAAATTAA
Found at i:3898975 original size:14 final size:16
Alignment explanation
Indices: 3898951--3898982 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3898941 AAAAAATTTT
3898951 AAATTAAAAATAT-TA
1 AAATTAAAAATATGTA
3898966 AAATT-AAAATATGTA
1 AAATTAAAAATATGTA
3898981 AA
1 AA
3898983 TAAACTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AAATTAAAAATATGTA
Found at i:3898982 original size:15 final size:15
Alignment explanation
Indices: 3898942--3898974 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3898932 TAATAAATAA
*
3898942 AAAAAT-TTTAAATT
1 AAAAATATTAAAATT
3898956 AAAAATATTAAAATT
1 AAAAATATTAAAATT
3898971 AAAA
1 AAAA
3898975 TATGTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAAATATTAAAATT
Found at i:3898983 original size:14 final size:14
Alignment explanation
Indices: 3898942--3898983 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
3898932 TAATAAATAA
*
3898942 AAAAATTTTAAATT
1 AAAAATATTAAATT
3898956 AAAAATATTAAAATT
1 AAAAATATT-AAATT
3898971 -AAAATATGTAAAT
1 AAAAATAT-TAAAT
3898984 AAACTAATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
AAAAATATTAAATT
Found at i:3899371 original size:64 final size:63
Alignment explanation
Indices: 3899291--3899469 Score: 168
Period size: 64 Copynumber: 2.9 Consensus size: 63
3899281 CATAAGAGTA
* ** * * * *
3899291 AAATAATAAAATTTTTAAAAATTAAAAATATGTTAGAAAAATTTTAAAATTTTTTATAATGGCG
1 AAATTATAAAATTTTTAAAAATTAAAAATAAATTAGAAAAA-TTTAAAAATTATTAAAAAGGCG
* * * * *
3899355 ATATTAT-AAATGTTTTAAAAAGTAAAGATAAATTATAAAAATTTAAAAATTATTAAAAAGGTG
1 AAATTATAAAAT-TTTTAAAAATTAAAAATAAATTAGAAAAATTTAAAAATTATTAAAAAGGCG
* * *
3899418 AAATTATAAAATTTTTTAAAAA-TACAAA-AAATT-TAAAAATTTAAAAGTTATT
1 AAATTATAAAA-TTTTTAAAAATTAAAAATAAATTAGAAAAATTTAAAAATTATT
3899470 GAGGGACCCA
Statistics
Matches: 96, Mismatches: 16, Indels: 9
0.79 0.13 0.07
Matches are distributed among these distances:
61 18 0.19
62 5 0.05
63 31 0.32
64 41 0.43
65 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.37
Consensus pattern (63 bp):
AAATTATAAAATTTTTAAAAATTAAAAATAAATTAGAAAAATTTAAAAATTATTAAAAAGGCG
Found at i:3899406 original size:17 final size:17
Alignment explanation
Indices: 3899384--3899463 Score: 58
Period size: 17 Copynumber: 4.6 Consensus size: 17
3899374 AAGTAAAGAT
3899384 AAATTATAAAAATTTAA
1 AAATTATAAAAATTTAA
** *
3899401 AAATTATTAAAAAGGT-G
1 AAATTA-TAAAAATTTAA
*
3899418 AAATTATAAAATTTTTTAA
1 AAATTATAAAA--ATTTAA
*
3899437 AAA-TACAAAAAATTTAA
1 AAATTA-TAAAAATTTAA
3899454 AAATT-TAAAA
1 AAATTATAAAA
3899464 GTTATTGAGG
Statistics
Matches: 47, Mismatches: 10, Indels: 13
0.67 0.14 0.19
Matches are distributed among these distances:
16 9 0.19
17 20 0.43
18 11 0.23
19 7 0.15
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (17 bp):
AAATTATAAAAATTTAA
Found at i:3901439 original size:6 final size:6
Alignment explanation
Indices: 3901428--3901457 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
3901418 CATAAAGTCG
3901428 TGGCTA TGGCTA TGGCTA TGGCTA TGGCTA
1 TGGCTA TGGCTA TGGCTA TGGCTA TGGCTA
3901458 CCCACTCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (6 bp):
TGGCTA
Found at i:3909557 original size:21 final size:22
Alignment explanation
Indices: 3909497--3909557 Score: 52
Period size: 24 Copynumber: 2.7 Consensus size: 22
3909487 AAAATATCAA
* *
3909497 TTATTATAATTTAAAATTTATT
1 TTATTATAATTTAATACTTATT
* **
3909519 TTATAAAATAATAAAATACTT-TT
1 TTAT--TATAATTTAATACTTATT
3909542 TTATTATAATTTAATA
1 TTATTATAATTTAATA
3909558 ATATTTATGT
Statistics
Matches: 29, Mismatches: 8, Indels: 5
0.69 0.19 0.12
Matches are distributed among these distances:
21 9 0.31
22 4 0.14
23 6 0.21
24 10 0.34
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATTATAATTTAATACTTATT
Found at i:3909578 original size:45 final size:44
Alignment explanation
Indices: 3909497--3909890 Score: 281
Period size: 45 Copynumber: 8.9 Consensus size: 44
3909487 AAAATATCAA
**
3909497 TTATTATAATTTAA-AATTTATTTT-AT-AAAATAATAAAATACTTTT
1 TTATTATAATTTAATAA--TATTTTCATCAAAA-AATAAAATAC-CCT
* *
3909542 TTATTATAATTTAATAATATTTAT-GTCAAAAGATAAAATTACCCT
1 TTATTATAATTTAATAATATTT-TCATCAAAAAATAAAA-TACCCT
* * **
3909587 TTATTATAATTTAATAATA--TTCATCAAAATACAATCTACCCT
1 TTATTATAATTTAATAATATTTTCATCAAAAAATAAAATACCCT
* * ** *
3909629 TTATTATAGTTAAATAATATTTTTGTC-AAAAATAAAATA-TCT
1 TTATTATAATTTAATAATATTTTCATCAAAAAATAAAATACCCT
** * * *
3909671 TGTGCTATAATTTAATATTATTTTCATCAGAAGACA-AAAATA-TCT
1 T-TATTATAATTTAATAATATTTTCATCA-AA-AAATAAAATACCCT
* * * **
3909716 TTATTATAATTTAATCATATTTTCACCGAAATACA-AAAATATGCT
1 TTATTATAATTTAATAATATTTTCATC-AAA-AAATAAAATACCCT
*
3909761 TTATTATAATTTAAAAATATTTTTCATCAAAAAATAAAAATACCCT
1 TTATTATAATTTAATAATA-TTTTCATCAAAAAAT-AAAATACCCT
* * * * *
3909807 CTATTATAA-TTAATAACATTTTCACCAAAACATAAAAATACCTT
1 TTATTATAATTTAATAATATTTTCATCAAAAAAT-AAAATACCCT
* ** *
3909851 TTATTACAATTTAATAATATTTTTGTCAAAAAACAAAATA
1 TTATTATAATTTAATAATATTTTCATCAAAAAATAAAATA
3909891 ACCTAAAATG
Statistics
Matches: 279, Mismatches: 53, Indels: 35
0.76 0.14 0.10
Matches are distributed among these distances:
42 27 0.10
43 37 0.13
44 79 0.28
45 102 0.37
46 34 0.12
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.41
Consensus pattern (44 bp):
TTATTATAATTTAATAATATTTTCATCAAAAAATAAAATACCCT
Found at i:3909628 original size:42 final size:44
Alignment explanation
Indices: 3909541--3909871 Score: 173
Period size: 44 Copynumber: 7.5 Consensus size: 44
3909531 AAAATACTTT
*
3909541 TTTATTATAATTTAATAATATTTATGTCAAAAGATAAAATTACCC
1 TTTATTATAATTTAATAATATTCA-GTCAAAAGATAAAATTACCC
*
3909586 TTTATTATAATTTAATAATATTCA-TC-AAA-ATACAATCTACCC
1 TTTATTATAATTTAATAATATTCAGTCAAAAGATAAAAT-TACCC
* * ** *
3909628 TTTATTATAGTTAAATAATATTTTTGTCAAAA-ATAAAA-TA-TC
1 TTTATTATAATTTAATAATA-TTCAGTCAAAAGATAAAATTACCC
** * * * * *
3909670 TTGTGCTATAATTTAATATTATTTTCA-TCAGAAGACAAAAATA-TC
1 TT-TATTATAATTTAATA--ATATTCAGTCAAAAGATAAAATTACCC
* * * * * * **
3909715 TTTATTATAATTTAATCATATTTTCA-CCGAAATACAAAAATATGC
1 TTTATTATAATTTAAT-A-ATATTCAGTCAAAAGATAAAATTACCC
* * *
3909760 TTTATTATAATTTAAAAATATTTTTCA-TCAAAAAATAAAAATACCC
1 TTTATTATAATTTAATAATA---TTCAGTCAAAAGATAAAATTACCC
* * * * * *
3909806 TCTATTATAA-TTAATAACATTTTCA-CCAAAACATAAAAATACCT
1 TTTATTATAATTTAAT-A-ATATTCAGTCAAAAGATAAAATTACCC
*
3909850 TTTATTACAATTTAATAATATT
1 TTTATTATAATTTAATAATATT
3909872 TTTGTCAAAA
Statistics
Matches: 228, Mismatches: 41, Indels: 36
0.75 0.13 0.12
Matches are distributed among these distances:
41 6 0.03
42 29 0.13
43 28 0.12
44 71 0.31
45 65 0.29
46 27 0.12
47 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.41
Consensus pattern (44 bp):
TTTATTATAATTTAATAATATTCAGTCAAAAGATAAAATTACCC
Found at i:3917799 original size:14 final size:14
Alignment explanation
Indices: 3917780--3917809 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3917770 CAAGCAAAAC
3917780 AAAAACAAAAACAA
1 AAAAACAAAAACAA
*
3917794 AAAAACAAAAGCAA
1 AAAAACAAAAACAA
3917808 AA
1 AA
3917810 GAAATGTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.13, G:0.03, T:0.00
Consensus pattern (14 bp):
AAAAACAAAAACAA
Found at i:3925022 original size:219 final size:221
Alignment explanation
Indices: 3924639--3925078 Score: 632
Period size: 219 Copynumber: 2.0 Consensus size: 221
3924629 ACCGCTCCAT
* *
3924639 CACTTCTCTATTTTGCCGGATTGTTTCTTGTTTTTAATTTTTTTCACCATTCCTAGTATCTTTGA
1 CACTTCTCTATTTTGCCGGATTGTTTCTTGTTTTTAATTCTTTTCACCATTCCTAGTATCCTTGA
* * * *
3924704 TGGTTTGTACAAACTAATGAAAAAGAGTCTGCTGTATCTTGGGGGATGACTACTACAATCATTTC
66 TAGTTTGTACAAACTAATAAAAAAGAG-CTGCTGAATCTTGGGGGATGACCACTACAATCATTTC
* * *
3924769 ACACCAAGTTTCATACTCCAAAAGGACAAAAATTATCGTTAAGGACAATGTATCTCACTTCAGAC
130 ACACCAAGTTTCATACTCCAAAAGGACAAAAATTATCATTAAGGACAATGTATCGCACTTCAAAC
*
3924834 TAGTTGATAACCACTATAATCTTTTTA
195 TAGTGGATAACCACTATAATCTTTTTA
* * **
3924861 CACTTCTTTATTTTGCCGGATTGTTTCTTGTTTTTAATTCTTTT-ATCATTTTTAGTATCCTTGA
1 CACTTCTCTATTTTGCCGGATTGTTTCTTGTTTTTAATTCTTTTCACCATTCCTAGTATCCTTGA
* * *
3924925 TAGTTTGTGCAAACTAATAAAAAAGAG-TGTTGAATCTTGGGGGATGACCACTACAATCATTTTA
66 TAGTTTGTACAAACTAATAAAAAAGAGCTGCTGAATCTTGGGGGATGACCACTACAATCATTTCA
*** ** * *
3924989 CACCAAGTTTCATACTTTGAAAGGATGAAAATTATCATTAAGGACAATGTATCGCATTTCAAATT
131 CACCAAGTTTCATACTCCAAAAGGACAAAAATTATCATTAAGGACAATGTATCGCACTTCAAACT
*
3925054 AGTGGATAACTACTATAATCTTTTT
196 AGTGGATAACCACTATAATCTTTTT
3925079 GCATTGAGTT
Statistics
Matches: 193, Mismatches: 25, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
219 111 0.58
221 40 0.21
222 42 0.22
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (221 bp):
CACTTCTCTATTTTGCCGGATTGTTTCTTGTTTTTAATTCTTTTCACCATTCCTAGTATCCTTGA
TAGTTTGTACAAACTAATAAAAAAGAGCTGCTGAATCTTGGGGGATGACCACTACAATCATTTCA
CACCAAGTTTCATACTCCAAAAGGACAAAAATTATCATTAAGGACAATGTATCGCACTTCAAACT
AGTGGATAACCACTATAATCTTTTTA
Found at i:3927017 original size:21 final size:21
Alignment explanation
Indices: 3926992--3927047 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
3926982 AAGTTGGAGC
*
3926992 CGGAGTTATCATCTTGGACTA
1 CGGAGTTATCATCTTGGACGA
3927013 CGGAGTTATCATCTTGGACGA
1 CGGAGTTATCATCTTGGACGA
*
3927034 CGGGAATTATCATC
1 C-GGAGTTATCATC
3927048 GTTTCATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (21 bp):
CGGAGTTATCATCTTGGACGA
Found at i:3934853 original size:21 final size:20
Alignment explanation
Indices: 3934828--3934866 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3934818 ATAAGCATAA
3934828 TATTTGAACAAAATTTAAAAT
1 TATTT-AACAAAATTTAAAAT
*
3934849 TATTTAAGAAAATTTAAA
1 TATTTAACAAAATTTAAA
3934867 TAAAATCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (20 bp):
TATTTAACAAAATTTAAAAT
Found at i:3965893 original size:12 final size:12
Alignment explanation
Indices: 3965876--3965911 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
3965866 GAGCAAGCCC
3965876 CTTCAGCTTGAG
1 CTTCAGCTTGAG
3965888 CTTCAGCTTGAG
1 CTTCAGCTTGAG
3965900 CTTCAGCTTGAG
1 CTTCAGCTTGAG
3965912 TTCGGTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (12 bp):
CTTCAGCTTGAG
Found at i:3970715 original size:2 final size:2
Alignment explanation
Indices: 3970708--3970740 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3970698 TTAATTATGA
3970708 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3970741 AGTGGATTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3979810 original size:3 final size:3
Alignment explanation
Indices: 3979804--3979833 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3979794 CGAGGTCGTC
3979804 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
3979834 TTCTTCTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
GTT
Found at i:3982123 original size:24 final size:24
Alignment explanation
Indices: 3982096--3982142 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
3982086 CCTGTACAAG
*
3982096 CTAATGTTGTTCCCTCTTAACCTA
1 CTAATGTTGTTCCCTCTCAACCTA
*
3982120 CTAATGTTGTTTCCTCTCAACCT
1 CTAATGTTGTTCCCTCTCAACCT
3982143 CATATCACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.19, C:0.30, G:0.09, T:0.43
Consensus pattern (24 bp):
CTAATGTTGTTCCCTCTCAACCTA
Found at i:3984212 original size:20 final size:20
Alignment explanation
Indices: 3984173--3984220 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
3984163 AATACCTAAG
*
3984173 AAGGAGGATGTGGCTTGAAA
1 AAGGAGGATGTGGCTAGAAA
3984193 AAGGAGGATGTGG-TCAGAAA
1 AAGGAGGATGTGGCT-AGAAA
*
3984213 TAGGAGGA
1 AAGGAGGA
3984221 GACAACTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.38, C:0.04, G:0.42, T:0.17
Consensus pattern (20 bp):
AAGGAGGATGTGGCTAGAAA
Found at i:3984518 original size:80 final size:80
Alignment explanation
Indices: 3984384--3984582 Score: 319
Period size: 80 Copynumber: 2.5 Consensus size: 80
3984374 ATTTATCTCC
3984384 CAAAATAATTTAGAGATAATATTTATATTTTGACCAATCAAATATTAGCTATTGGTCATCCAATT
1 CAAAATAATTTAGAGATAATATTTATATTTTGACCAATCAAATATTAGCTATTGGTCATCCAATT
3984449 TATCTCTAAACAAA-
66 TATCTCTAAACAAAT
*
3984463 CTAAAATTATTTAGAGATAATATTTATATTTTGACCAATCAAATATTAGCTATTGGTCATCCAAT
1 C-AAAATAATTTAGAGATAATATTTATATTTTGACCAATCAAATATTAGCTATTGGTCATCCAAT
*
3984528 TTATCTCTAAATAAAT
65 TTATCTCTAAACAAAT
* * * *
3984544 CCAAATAATTTGGAGATAATCTTCATATTTTTGACCAAT
1 CAAAATAATTTAGAGATAATATTTATA-TTTTGACCAAT
3984583 TAAAATTTAA
Statistics
Matches: 110, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
79 1 0.01
80 97 0.88
81 12 0.11
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.39
Consensus pattern (80 bp):
CAAAATAATTTAGAGATAATATTTATATTTTGACCAATCAAATATTAGCTATTGGTCATCCAATT
TATCTCTAAACAAAT
Found at i:3984922 original size:17 final size:18
Alignment explanation
Indices: 3984889--3984922 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3984879 AAAAGCTTTT
3984889 GAAGATTGAGAAGCATTC
1 GAAGATTGAGAAGCATTC
3984907 GAAGATTGAG-AGCATT
1 GAAGATTGAGAAGCATT
3984923 TCNNNNNNNN
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.09, G:0.29, T:0.24
Consensus pattern (18 bp):
GAAGATTGAGAAGCATTC
Found at i:3996788 original size:2 final size:2
Alignment explanation
Indices: 3996736--3996768 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3996726 ACCAGAGTCA
3996736 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3996769 NNNNNNNNNN
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4004071 original size:16 final size:16
Alignment explanation
Indices: 4004039--4004072 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4004029 CATTAATAAA
*
4004039 TATTATATTATATTTT
1 TATTATATTATACTTT
*
4004055 TATTATATTTTACTTT
1 TATTATATTATACTTT
4004071 TA
1 TA
4004073 AAATAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTATATTATACTTT
Found at i:4011949 original size:2 final size:2
Alignment explanation
Indices: 4011942--4011969 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4011932 TCAAGACATA
4011942 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
4011970 GGAAACTTAT
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:4013103 original size:22 final size:20
Alignment explanation
Indices: 4013078--4013129 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
4013068 AATTTCGTAC
4013078 TATTTTAAATTATAAAAAATTA
1 TATTTTAAATT-TAAAAAA-TA
* *
4013100 TATTTTTAATTTATAAAATA
1 TATTTTAAATTTAAAAAATA
*
4013120 TATTTAAAAT
1 TATTTTAAAT
4013130 ATATTTTATG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 10 0.38
21 6 0.23
22 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TATTTTAAATTTAAAAAATA
Found at i:4031688 original size:52 final size:52
Alignment explanation
Indices: 4031609--4031720 Score: 188
Period size: 52 Copynumber: 2.1 Consensus size: 52
4031599 TCTCTCTCTC
4031609 TCTCTTTAGTGAATGGTGGAACAACCTCGACGTTTGCCCCACTGTATTACTT
1 TCTCTTTAGTGAATGGTGGAACAACCTCGACGTTTGCCCCACTGTATTACTT
* * *
4031661 TCTCTTTAGTGAATGGTGGAACGACCTCTACTTTTGCCCCACTGTATTACTT
1 TCTCTTTAGTGAATGGTGGAACAACCTCGACGTTTGCCCCACTGTATTACTT
4031713 TACTCTTT
1 T-CTCTTT
4031721 CTCTCTCTCT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
52 50 0.89
53 6 0.11
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (52 bp):
TCTCTTTAGTGAATGGTGGAACAACCTCGACGTTTGCCCCACTGTATTACTT
Found at i:4045251 original size:2 final size:2
Alignment explanation
Indices: 4045240--4045277 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
4045230 GTTTTGGAGG
*
4045240 GA GA GA -A GA GA GA GA GA GA GG GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4045278 CAGCTTAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4070280 original size:14 final size:14
Alignment explanation
Indices: 4070263--4070361 Score: 63
Period size: 14 Copynumber: 6.9 Consensus size: 14
4070253 CCCCACCCAC
4070263 TTTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
*** *
4070277 TTTTTAATTCAAAG
1 TTTTCCCTCCAAAG
* *
4070291 TATTCCCCCCAAAAG
1 TTTTCCCTCC-AAAG
*
4070306 ATTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
** *
4070320 TTTTCAATTCAAAG
1 TTTTCCCTCCAAAG
* *
4070334 TATTCCCCCCAAAAG
1 TTTTCCCTCC-AAAG
*
4070349 ATTTCCCTCCAAA
1 TTTTCCCTCCAAA
4070362 ACATTTGGGA
Statistics
Matches: 58, Mismatches: 25, Indels: 4
0.67 0.29 0.05
Matches are distributed among these distances:
14 36 0.62
15 22 0.38
ACGTcount: A:0.31, C:0.30, G:0.06, T:0.32
Consensus pattern (14 bp):
TTTTCCCTCCAAAG
Found at i:4070311 original size:15 final size:15
Alignment explanation
Indices: 4070293--4070367 Score: 57
Period size: 15 Copynumber: 5.1 Consensus size: 15
4070283 ATTCAAAGTA
*
4070293 TTCCCCCCAAAAGAT
1 TTCCCTCCAAAAGAT
*
4070308 TTCCCTCC-AAAGTT
1 TTCCCTCCAAAAGAT
** *
4070322 TTCAATTC-AAAG-T
1 TTCCCTCCAAAAGAT
*
4070335 ATTCCCCCCAAAAGAT
1 -TTCCCTCCAAAAGAT
*
4070351 TTCCCTCCAAAACAT
1 TTCCCTCCAAAAGAT
4070366 TT
1 TT
4070368 GGGAGGTTCT
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
13 1 0.02
14 18 0.39
15 26 0.57
16 1 0.02
ACGTcount: A:0.32, C:0.33, G:0.05, T:0.29
Consensus pattern (15 bp):
TTCCCTCCAAAAGAT
Found at i:4070312 original size:43 final size:43
Alignment explanation
Indices: 4070264--4070361 Score: 187
Period size: 43 Copynumber: 2.3 Consensus size: 43
4070254 CCCACCCACT
*
4070264 TTTCCCTCCAAAGTTTTTAATTCAAAGTATTCCCCCCAAAAGA
1 TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCAAAAGA
4070307 TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCAAAAGA
1 TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCAAAAGA
4070350 TTTCCCTCCAAA
1 TTTCCCTCCAAA
4070362 ACATTTGGGA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.32, C:0.31, G:0.06, T:0.32
Consensus pattern (43 bp):
TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCAAAAGA
Found at i:4070488 original size:35 final size:35
Alignment explanation
Indices: 4070449--4070515 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
4070439 GGGCTGGCAC
4070449 CCTCTTGGGCCTCCTGGCGGGTCCGGACTGTGTCA
1 CCTCTTGGGCCTCCTGGCGGGTCCGGACTGTGTCA
* *
4070484 CCTCTTGGGCCTCCTGGTGGGTCTGGACTGTG
1 CCTCTTGGGCCTCCTGGCGGGTCCGGACTGTG
4070516 GCCCGTGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.04, C:0.31, G:0.36, T:0.28
Consensus pattern (35 bp):
CCTCTTGGGCCTCCTGGCGGGTCCGGACTGTGTCA
Found at i:4077021 original size:79 final size:80
Alignment explanation
Indices: 4076931--4077087 Score: 228
Period size: 79 Copynumber: 2.0 Consensus size: 80
4076921 CCATTTATCA
* * * *
4076931 ACATAAATCCTAGAGAGTAAAAATGATTTCCAGGAGAATCTACA-CACAGTATTTATAAGACA-A
1 ACATAAATCCTAGAGAGAAAAAAAGATTGCCAGGAGAATCTACATCA-AGTATTAATAAGACAGA
*
4076994 CTATTAAACAAATACT
65 CTATTAAAAAAATACT
* *
4077010 ACATAAATCCTAGAGAGAAAAAAAGATTGCCAGGAGAATCTACATGAAGTATTAATAAGACAGGC
1 ACATAAATCCTAGAGAGAAAAAAAGATTGCCAGGAGAATCTACATCAAGTATTAATAAGACAGAC
4077075 TATTAAAAAAATA
66 TATTAAAAAAATA
4077088 TTGAGTTATG
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
79 55 0.80
80 14 0.20
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (80 bp):
ACATAAATCCTAGAGAGAAAAAAAGATTGCCAGGAGAATCTACATCAAGTATTAATAAGACAGAC
TATTAAAAAAATACT
Found at i:4078953 original size:2 final size:2
Alignment explanation
Indices: 4078946--4078993 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
4078936 TAGCAAGACA
4078946 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4078988 TC TC TC
1 TC TC TC
4078994 CAACTTCTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4081120 original size:93 final size:93
Alignment explanation
Indices: 4081019--4081205 Score: 374
Period size: 93 Copynumber: 2.0 Consensus size: 93
4081009 ATCATTAATT
4081019 AATTTTATTAAGATCTTAAATATGTATTTAAATATGTAATAAATATATAATAGATTTATTTACAT
1 AATTTTATTAAGATCTTAAATATGTATTTAAATATGTAATAAATATATAATAGATTTATTTACAT
4081084 AATTAAAATTTATACAACTTATAATCTC
66 AATTAAAATTTATACAACTTATAATCTC
4081112 AATTTTATTAAGATCTTAAATATGTATTTAAATATGTAATAAATATATAATAGATTTATTTACAT
1 AATTTTATTAAGATCTTAAATATGTATTTAAATATGTAATAAATATATAATAGATTTATTTACAT
4081177 AATTAAAATTTATACAACTTATAATCTC
66 AATTAAAATTTATACAACTTATAATCTC
4081205 A
1 A
4081206 TTAGATGATT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (93 bp):
AATTTTATTAAGATCTTAAATATGTATTTAAATATGTAATAAATATATAATAGATTTATTTACAT
AATTAAAATTTATACAACTTATAATCTC
Found at i:4083567 original size:12 final size:10
Alignment explanation
Indices: 4083534--4083566 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
4083524 AATCAAGCTA
4083534 ATATTT-TAT
1 ATATTTATAT
4083543 ATATTTATAT
1 ATATTTATAT
*
4083553 ATATTAATAT
1 ATATTTATAT
4083563 ATAT
1 ATAT
4083567 AATATTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 6 0.27
10 16 0.73
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
ATATTTATAT
Done.