Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold57
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: 4071704
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82236 characters in sequence are not A, C, G, or T
File 10 of 27
Found at i:1166885 original size:34 final size:34
Alignment explanation
Indices: 1166842--1166941 Score: 191
Period size: 34 Copynumber: 2.9 Consensus size: 34
1166832 CATTGTAAAA
1166842 TGTATCGATACAATGAGCAATGTATCGATACATT
1 TGTATCGATACAATGAGCAATGTATCGATACATT
1166876 TGTATCGATACAATGAGCAATGTATCGATACATT
1 TGTATCGATACAATGAGCAATGTATCGATACATT
*
1166910 TGCATCGATACAATGAGCAATGTATCGATACA
1 TGTATCGATACAATGAGCAATGTATCGATACA
1166942 ATGCAAAATG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 65 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (34 bp):
TGTATCGATACAATGAGCAATGTATCGATACATT
Found at i:1172274 original size:18 final size:21
Alignment explanation
Indices: 1172228--1172277 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 21
1172218 GATAAAATTT
*
1172228 ATTATTAAATATTAATTTAAG
1 ATTATTAAATATTAATTCAAG
1172249 ATTTATTAAA-A-TAATTCAA-
1 A-TTATTAAATATTAATTCAAG
1172268 ATTATTAAAT
1 ATTATTAAAT
1172278 TTTTTACCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 8 0.31
19 1 0.04
20 7 0.27
21 2 0.08
22 8 0.31
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
ATTATTAAATATTAATTCAAG
Found at i:1173544 original size:10 final size:10
Alignment explanation
Indices: 1173516--1173553 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1173506 CTTTTATATT
*
1173516 ATTATTTTAA
1 ATTATTTTTA
1173526 ATATATTTTTA
1 AT-TATTTTTA
1173537 ATTATTTTTA
1 ATTATTTTTA
1173547 A-TATTTT
1 ATTATTTT
1173554 GATATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 6 0.23
10 11 0.42
11 9 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
ATTATTTTTA
Found at i:1173583 original size:42 final size:44
Alignment explanation
Indices: 1173484--1173583 Score: 102
Period size: 44 Copynumber: 2.3 Consensus size: 44
1173474 TTTATAATAA
* *
1173484 ATAATTTAAATT-TATTTAAATACTTTTATATTATTATTTTAAAT
1 ATAATTTTAATTAT-TTTTAATACTTTTATATTATTATTTTAAAT
*
1173528 ATATTTTTAATTATTTTTAATA-TTTTGATA-TATT-TTTT-AAT
1 ATAATTTTAATTATTTTTAATACTTTT-ATATTATTATTTTAAAT
*
1173569 AATAATTTTCATTAT
1 -ATAATTTTAATTAT
1173584 AAAAATGTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
41 3 0.06
42 16 0.33
43 8 0.17
44 20 0.42
45 1 0.02
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (44 bp):
ATAATTTTAATTATTTTTAATACTTTTATATTATTATTTTAAAT
Found at i:1173744 original size:18 final size:20
Alignment explanation
Indices: 1173716--1173757 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1173706 TTCGTTATCA
1173716 AAAATCTGA-TTATTTTTTT
1 AAAATCTGATTTATTTTTTT
1173735 AAAA-CTGATTTTATTTTTTT
1 AAAATCTGA-TTTATTTTTTT
1173755 AAA
1 AAA
1173758 TTTATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.19
19 4 0.19
20 13 0.62
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (20 bp):
AAAATCTGATTTATTTTTTT
Found at i:1177544 original size:2 final size:2
Alignment explanation
Indices: 1177532--1177564 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1177522 TCTTTCTTGC
*
1177532 AG AG AG CG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1177565 AAAGAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1183260 original size:2 final size:2
Alignment explanation
Indices: 1183255--1183280 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1183245 TTTAAAAGTC
1183255 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1183281 AAGATTTGGT
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):
TA
Found at i:1183390 original size:22 final size:24
Alignment explanation
Indices: 1183356--1183409 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
1183346 TCAGTATTTA
* *
1183356 AAAAAAATCTTA-TATTTTAAA-T
1 AAAATAATCTTATTAATTTAAATT
*
1183378 AAAATAATGTTATTAATTTAAATTT
1 AAAATAATCTTATTAATTTAAA-TT
1183403 AAAATAA
1 AAAATAA
1183410 ATAATATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 10 0.38
23 8 0.31
25 8 0.31
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (24 bp):
AAAATAATCTTATTAATTTAAATT
Found at i:1183483 original size:20 final size:18
Alignment explanation
Indices: 1183445--1183483 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
1183435 AAATTAAAAT
*
1183445 AAAATATTAAATCAATTA
1 AAAATATTAAATAAATTA
1183463 AAAATATTTAATATAAATTA
1 AAAATA-TTAA-ATAAATTA
1183483 A
1 A
1183484 TTAATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATATTAAATAAATTA
Found at i:1187502 original size:31 final size:32
Alignment explanation
Indices: 1187465--1187533 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 32
1187455 TTTAAAGTAT
* *
1187465 TTTATAAATTTTAATATGTTAATA-ATTTATA
1 TTTATAAATTTTAAAATATTAATATATTTATA
*
1187496 TTTATAAATTTTAAAATATTTATATATTTATA
1 TTTATAAATTTTAAAATATTAATATATTTATA
1187528 TTTATA
1 TTTATA
1187534 TTATATTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 21 0.62
32 13 0.38
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (32 bp):
TTTATAAATTTTAAAATATTAATATATTTATA
Found at i:1187530 original size:14 final size:14
Alignment explanation
Indices: 1187511--1187579 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
1187501 AAATTTTAAA
1187511 ATATTTATATATTT
1 ATATTTATATATTT
1187525 ATATTTATATTATATT
1 ATATTTATA-TAT-TT
* * * *
1187541 TTATTT-TTTAATC
1 ATATTTATATATTT
*
1187554 ATATTTATATAATT
1 ATATTTATATATTT
1187568 ATATTTA-ATATT
1 ATATTTATATATT
1187580 ATCTCAGCTA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
13 10 0.23
14 23 0.52
15 4 0.09
16 7 0.16
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (14 bp):
ATATTTATATATTT
Found at i:1187539 original size:43 final size:44
Alignment explanation
Indices: 1187487--1187581 Score: 124
Period size: 43 Copynumber: 2.2 Consensus size: 44
1187477 AATATGTTAA
*
1187487 TAAT-TTATATTTATAAATTTTAA-AATATTTATATATTTATATT
1 TAATATTATATTT-TAAATTTTAATAATATTTATATAATTATATT
** *
1187530 T-ATATTATATTTTATTTTTTAATCATATTTATATAATTATATT
1 TAATATTATATTTTAAATTTTAATAATATTTATATAATTATATT
1187573 TAATATTAT
1 TAATATTAT
1187582 CTCAGCTATA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
42 10 0.22
43 28 0.62
44 7 0.16
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (44 bp):
TAATATTATATTTTAAATTTTAATAATATTTATATAATTATATT
Found at i:1188765 original size:17 final size:18
Alignment explanation
Indices: 1188739--1188776 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1188729 AAATTTTTAT
* *
1188739 TAAAAGAATTATAAA-TA
1 TAAAAAAATTAAAAATTA
1188756 TAAAAAAATTAAAAATTA
1 TAAAAAAATTAAAAATTA
1188774 TAA
1 TAA
1188777 TATTAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
TAAAAAAATTAAAAATTA
Found at i:1190555 original size:46 final size:46
Alignment explanation
Indices: 1190488--1190579 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
1190478 TTAGTTTTTA
1190488 GCAACAAAATTCAACAAACAAGATGGAACCCTGGAATATAATGAAG
1 GCAACAAAATTCAACAAACAAGATGGAACCCTGGAATATAATGAAG
*
1190534 GCAACAAAATTCAACAAACAAGGTGGAACCCTGGAATATAATGAAG
1 GCAACAAAATTCAACAAACAAGATGGAACCCTGGAATATAATGAAG
1190580 TGAATGGACT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.49, C:0.17, G:0.18, T:0.15
Consensus pattern (46 bp):
GCAACAAAATTCAACAAACAAGATGGAACCCTGGAATATAATGAAG
Found at i:1201160 original size:17 final size:17
Alignment explanation
Indices: 1201140--1201210 Score: 63
Period size: 17 Copynumber: 4.1 Consensus size: 17
1201130 AATTATACAA
1201140 ATAAAATATAAAAAATT
1 ATAAAATATAAAAAATT
*
1201157 ATAAATTATAAATAAATAT
1 ATAAAATATAAA-AAAT-T
* **
1201176 ATAAACATCT-AAATTTT
1 ATAAA-ATATAAAAAATT
*
1201193 ATAAAATATAAAATATT
1 ATAAAATATAAAAAATT
1201210 A
1 A
1201211 ATATATTAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
16 3 0.07
17 24 0.56
18 6 0.14
19 8 0.19
20 2 0.05
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAAAATATAAAAAATT
Found at i:1201242 original size:53 final size:53
Alignment explanation
Indices: 1201140--1201242 Score: 120
Period size: 53 Copynumber: 1.9 Consensus size: 53
1201130 AATTATACAA
* *
1201140 ATAAAATATAAAAAATTATAAATTATAAATAAATATATAAACATCTAAATTTT
1 ATAAAATATAAAAAATTATAAATTATAAATAAATATAAAAAAATCTAAATTTT
* * * *
1201193 ATAAAATATAAAATATTAATATATTA-AAATATATA-AAAAATAATTTAAAT
1 ATAAAATATAAAAAATT-ATAAATTATAAATAAATATAAAAA-AATCTAAAT
1201243 ATAATTATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
52 4 0.10
53 31 0.74
54 7 0.17
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (53 bp):
ATAAAATATAAAAAATTATAAATTATAAATAAATATAAAAAAATCTAAATTTT
Found at i:1201554 original size:6 final size:6
Alignment explanation
Indices: 1201543--1201623 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
1201533 TATTTTATTT
* *
1201543 ATTATA ATTATA AATATA ATTA-A A-TATT ATTATA A-T-TA ATTATA
1 ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA
* *
1201587 A-TA-A ATATATA ATTAAA ATTTTAA ATTATA A-TATA AT
1 ATTATA AT-TATA ATTATA ATTAT-A ATTATA ATTATA AT
1201624 AGTAAAATAA
Statistics
Matches: 58, Mismatches: 8, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
4 7 0.12
5 12 0.21
6 31 0.53
7 8 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
ATTATA
Found at i:1201568 original size:10 final size:11
Alignment explanation
Indices: 1201545--1201623 Score: 64
Period size: 10 Copynumber: 7.5 Consensus size: 11
1201535 TTTTATTTAT
1201545 TATAATTATAAA
1 TATAATTAT-AA
1201557 TATAATTA-AA
1 TATAATTATAA
*
1201567 TATTATTATAA
1 TATAATTATAA
1201578 T-TAATTATAA
1 TATAATTATAA
1201588 TA-AATATATAA
1 TATAAT-TATAA
*
1201599 TTAAAATT-T--
1 -TATAATTATAA
1201608 TA-AATTATAA
1 TATAATTATAA
1201618 TATAAT
1 TATAAT
1201624 AGTAAAATAA
Statistics
Matches: 56, Mismatches: 2, Indels: 19
0.73 0.03 0.25
Matches are distributed among these distances:
7 4 0.07
8 3 0.05
10 23 0.41
11 12 0.21
12 11 0.20
13 3 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TATAATTATAA
Found at i:1201570 original size:25 final size:24
Alignment explanation
Indices: 1201542--1201605 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 24
1201532 ATATTTTATT
1201542 TATTATAATTATAAATATAATTAAA
1 TATTATAATTATAAATATAA-TAAA
* * *
1201567 TATTATTATAATTAATTATAATAAA
1 TATTATAATTA-TAAATATAATAAA
1201592 TA-TATAATTA-AAAT
1 TATTATAATTATAAAT
1201606 TTTAAATTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
22 3 0.09
24 6 0.19
25 15 0.47
26 8 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TATTATAATTATAAATATAATAAA
Found at i:1201746 original size:47 final size:49
Alignment explanation
Indices: 1201686--1201779 Score: 111
Period size: 47 Copynumber: 2.0 Consensus size: 49
1201676 AATTAAATAA
** * *
1201686 AAATTATCTATATTTTATATTATTGAATT-TAACATCA-ATTTTTATAT
1 AAATTATAAATATTTAATATTATTAAATTATAACATCAGATTTTTATAT
* * *
1201733 AAATTATAAATATTTAATTTTATTAAATTATATCATTAGATTTTTAT
1 AAATTATAAATATTTAATATTATTAAATTATAACATCAGATTTTTAT
1201780 TATTAATAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
47 24 0.63
48 6 0.16
49 8 0.21
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (49 bp):
AAATTATAAATATTTAATATTATTAAATTATAACATCAGATTTTTATAT
Found at i:1206212 original size:2 final size:2
Alignment explanation
Indices: 1206205--1206238 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1206195 ATTGATGTCC
1206205 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
1206239 CTTGATCCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1206660 original size:15 final size:15
Alignment explanation
Indices: 1206640--1206670 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1206630 AAAGATTTCG
1206640 TGTAACAGATAAGGT
1 TGTAACAGATAAGGT
1206655 TGTAACAGATAAGGT
1 TGTAACAGATAAGGT
1206670 T
1 T
1206671 AATGGACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (15 bp):
TGTAACAGATAAGGT
Found at i:1207190 original size:18 final size:18
Alignment explanation
Indices: 1207164--1207208 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1207154 GTATAATTAA
*
1207164 TATACTTATTTTATATAT
1 TATATTTATTTTATATAT
1207182 TATATTTATTTTATATAT
1 TATATTTATTTTATATAT
1207200 TATATTTAT
1 TATATTTAT
1207209 ATTGAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TATATTTATTTTATATAT
Found at i:1207195 original size:11 final size:12
Alignment explanation
Indices: 1207164--1207211 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 12
1207154 GTATAATTAA
*
1207164 TATACTTAT-TT
1 TATATTTATATT
1207175 TATATATTATATT
1 TATAT-TTATATT
1207188 TAT-TTTATATAT
1 TATATTTATAT-T
1207200 TATATTTATATT
1 TATATTTATATT
1207212 GAAAATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
11 10 0.31
12 10 0.31
13 12 0.38
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (12 bp):
TATATTTATATT
Found at i:1209624 original size:96 final size:95
Alignment explanation
Indices: 1209506--1209693 Score: 322
Period size: 96 Copynumber: 2.0 Consensus size: 95
1209496 ATTTTGACAA
* *
1209506 TACAATAATTAGAAATGATTTTAAGAATTTAGCTTTGATGCATAAATATTTTAGAATTATAACTC
1 TACAATAATTAGAAATGATTTTAAAAACTTAGCTTTGATGCATAAATA-TTTAGAATTATAACTC
* *
1209571 TTTAAAGTTCATATGCAAAACTTTTATATTT
65 TTTAAAATTCATATGCAAAACCTTTATATTT
*
1209602 TACAATGATTAGAAATGATTTTAAAAACTTAGCTTTGATGCATAAATATTTAGAATTATAACTCT
1 TACAATAATTAGAAATGATTTTAAAAACTTAGCTTTGATGCATAAATATTTAGAATTATAACTCT
1209667 TTAAAATTCATATGCAAAACCTTTATA
66 TTAAAATTCATATGCAAAACCTTTATA
1209694 CTCTATTTTT
Statistics
Matches: 87, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
95 42 0.48
96 45 0.52
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (95 bp):
TACAATAATTAGAAATGATTTTAAAAACTTAGCTTTGATGCATAAATATTTAGAATTATAACTCT
TTAAAATTCATATGCAAAACCTTTATATTT
Found at i:1210756 original size:22 final size:20
Alignment explanation
Indices: 1210717--1210756 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
1210707 CCTATGTTAA
*
1210717 TAATTTAATTTTTTATAAAC
1 TAATTTAATTTTTAATAAAC
1210737 TAATTTATTATTTTTAATAA
1 TAATTTA--ATTTTTAATAA
1210757 TTAAAAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
22 10 0.59
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
TAATTTAATTTTTAATAAAC
Found at i:1210844 original size:31 final size:31
Alignment explanation
Indices: 1210806--1210865 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1210796 TAAATCATTT
1210806 AAAATTAAAATTAAAAGATAAAATTTAATCA
1 AAAATTAAAATTAAAAGATAAAATTTAATCA
* *
1210837 AAAATTAAAATTTAATGATAAAATTTAAT
1 AAAATTAAAATTAAAAGATAAAATTTAAT
1210866 TAAATTACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (31 bp):
AAAATTAAAATTAAAAGATAAAATTTAATCA
Found at i:1210882 original size:29 final size:30
Alignment explanation
Indices: 1210806--1210907 Score: 100
Period size: 31 Copynumber: 3.4 Consensus size: 30
1210796 TAAATCATTT
*
1210806 AAAATTAAAATTA-AAAGATAAAATTTAATCA
1 AAAATTAAAA-TAGAATGATAAAATTTAAT-A
**
1210837 AAAATTAAAATTTAATGATAAAATTTAAT-
1 AAAATTAAAATAGAATGATAAAATTTAATA
* * *
1210866 TAAATTACAATAGAATGATAAAATTCAATA
1 AAAATTAAAATAGAATGATAAAATTTAATA
**
1210896 TTAATTAAAATA
1 AAAATTAAAATA
1210908 TGTGACAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
29 24 0.40
30 11 0.18
31 25 0.42
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (30 bp):
AAAATTAAAATAGAATGATAAAATTTAATA
Found at i:1210948 original size:20 final size:20
Alignment explanation
Indices: 1210923--1210960 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1210913 CAAATTTCTT
1210923 TAATCTCGAAGGTTTATTGG
1 TAATCTCGAAGGTTTATTGG
1210943 TAATCTCGAAGGTTTATT
1 TAATCTCGAAGGTTTATT
1210961 CCTAACATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (20 bp):
TAATCTCGAAGGTTTATTGG
Found at i:1211419 original size:18 final size:17
Alignment explanation
Indices: 1211398--1211454 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 17
1211388 ATTTTATTAA
1211398 ATTATATTAATAAATTTT
1 ATTAT-TTAATAAATTTT
* *
1211416 ATTATTAAATAAA-TTA
1 ATTATTTAATAAATTTT
1211432 AGTTATTTATATAAATTTT
1 A-TTATTTA-ATAAATTTT
1211451 ATTA
1 ATTA
1211455 AGTAATTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
16 3 0.09
17 13 0.41
18 13 0.41
19 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTATTTAATAAATTTT
Found at i:1211428 original size:17 final size:17
Alignment explanation
Indices: 1211402--1211454 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
1211392 TATTAAATTA
1211402 TATT-AATAAATTTTAT
1 TATTAAATAAATTTTAT
*
1211418 TATTAAATAAA-TTAAGT
1 TATTAAATAAATTTTA-T
*
1211435 TATTTATATAAATTTTAT
1 TA-TTAAATAAATTTTAT
1211453 TA
1 TA
1211455 AGTAATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 7 0.23
17 9 0.30
18 11 0.37
19 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
TATTAAATAAATTTTAT
Found at i:1211621 original size:13 final size:14
Alignment explanation
Indices: 1211571--1211657 Score: 56
Period size: 13 Copynumber: 6.0 Consensus size: 14
1211561 ACTTAATTTA
1211571 TTAATAATTAAAAT
1 TTAATAATTAAAAT
* *
1211585 TTAATGA-TATAAT
1 TTAATAATTAAAAT
1211598 TTAATAAAATTAAAAT
1 TTAAT--AATTAAAAT
*
1211614 TT-ATAATTTTTATAAAA
1 TTAATAA---TTA-AAAT
1211631 TTAAT-ATT-AAAT
1 TTAATAATTAAAAT
1211643 TTAATAATTTAAAAT
1 TTAATAA-TTAAAAT
1211658 ATAAATGATC
Statistics
Matches: 56, Mismatches: 6, Indels: 21
0.67 0.07 0.25
Matches are distributed among these distances:
12 8 0.14
13 13 0.23
14 10 0.18
15 7 0.12
16 10 0.18
17 6 0.11
18 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (14 bp):
TTAATAATTAAAAT
Found at i:1212034 original size:23 final size:23
Alignment explanation
Indices: 1211987--1212034 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1211977 TAAAAAAGAC
* *
1211987 TTTTATTTATTTTATTATTATAA
1 TTTTATTTATTTTATTAATAAAA
1212010 TTTTATTT-TTTTATTAAATAAAA
1 TTTTATTTATTTTATT-AATAAAA
1212033 TT
1 TT
1212035 ATATAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTATTTATTTTATTAATAAAA
Found at i:1218437 original size:18 final size:18
Alignment explanation
Indices: 1218410--1218444 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1218400 GGTTGAAATA
1218410 CATGGCTGATCTTCCAAT
1 CATGGCTGATCTTCCAAT
*
1218428 CATGGTTGATCTTCCAA
1 CATGGCTGATCTTCCAA
1218445 CAACCCCCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (18 bp):
CATGGCTGATCTTCCAAT
Found at i:1219691 original size:2 final size:2
Alignment explanation
Indices: 1219684--1219723 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1219674 TGCACTGGAG
1219684 AT AT 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
1219724 CTTGGAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1231471 original size:110 final size:110
Alignment explanation
Indices: 1231272--1231595 Score: 486
Period size: 110 Copynumber: 2.9 Consensus size: 110
1231262 TTTTCCTGCT
* * ** *
1231272 AGGACATATGTATGCTATCCATCTTAAGTTTTAAGATGAACATCCAGCCAAAAACCAATTAACAA
1 AGGACGTATGTATGCTATCCATCTTAAATTTTAAGATGGGCATCCAGCCTAAAACCAATTAACAA
* *
1231337 TAGGTGGAGAGGCCCTTGTTTTATTTATGTGCCTAGGATATTACA
66 TAGGTGGAGAGGCCCTTGTTTTATTTATGTGCCTAAGATATAACA
* * * *
1231382 AGGATGTATGTATGCTATCCATCCTAAATTTTAAGATGGGCATCCAGGCTAAAACCTATTAACAA
1 AGGACGTATGTATGCTATCCATCTTAAATTTTAAGATGGGCATCCAGCCTAAAACCAATTAACAA
*
1231447 CAGGTGGAGAGGCCCTTGTTTTATTTATGTGCCTAAGATATAACA
66 TAGGTGGAGAGGCCCTTGTTTTATTTATGTGCCTAAGATATAACA
* * *
1231492 AGGACGTATGTATGCTATCCATCTTAAATTTAAAGAGGGGCATCCAACCTAAAACCAATTAACAA
1 AGGACGTATGTATGCTATCCATCTTAAATTTTAAGATGGGCATCCAGCCTAAAACCAATTAACAA
* * *
1231557 TAGGTGGAGACGCCTTTGTTATATTTATGTGCCTAAGAT
66 TAGGTGGAGAGGCCCTTGTTTTATTTATGTGCCTAAGAT
1231596 TGCCCACAAT
Statistics
Matches: 191, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
110 191 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (110 bp):
AGGACGTATGTATGCTATCCATCTTAAATTTTAAGATGGGCATCCAGCCTAAAACCAATTAACAA
TAGGTGGAGAGGCCCTTGTTTTATTTATGTGCCTAAGATATAACA
Found at i:1234186 original size:16 final size:16
Alignment explanation
Indices: 1234165--1234198 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1234155 GCTTGCTTCT
1234165 AGCTACCTCCATCTCA
1 AGCTACCTCCATCTCA
1234181 AGCTACCTCCATCTCA
1 AGCTACCTCCATCTCA
1234197 AG
1 AG
1234199 AAAGTACTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.41, G:0.09, T:0.24
Consensus pattern (16 bp):
AGCTACCTCCATCTCA
Found at i:1257462 original size:21 final size:24
Alignment explanation
Indices: 1257411--1257458 Score: 78
Period size: 26 Copynumber: 1.9 Consensus size: 24
1257401 ATATCATTTG
1257411 ATACTACCTTTCCTTTTCACTTCGCT
1 ATACTACCTTTCCTTTTCACTT--CT
1257437 ATACTACCTTTCCTTTTCACTT
1 ATACTACCTTTCCTTTTCACTT
1257459 TACTTGTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.17, C:0.33, G:0.02, T:0.48
Consensus pattern (24 bp):
ATACTACCTTTCCTTTTCACTTCT
Found at i:1258095 original size:32 final size:32
Alignment explanation
Indices: 1258054--1258118 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
1258044 AGCAGCAATG
* *
1258054 CGTTTAAGAAAACATAAGGTAGCGATTAACCA
1 CGTTTAAGAAAACATAACGTAGCAATTAACCA
*
1258086 CGTTTAAGAAAACATAACGTAGCAATTCACCA
1 CGTTTAAGAAAACATAACGTAGCAATTAACCA
1258118 C
1 C
1258119 ATGCATGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (32 bp):
CGTTTAAGAAAACATAACGTAGCAATTAACCA
Found at i:1272987 original size:27 final size:27
Alignment explanation
Indices: 1272948--1273009 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
1272938 GCTGATAGAT
*
1272948 AATGCCCTCAACTCAAGTTGGGATTTA
1 AATGCCCTCAACTCAAATTGGGATTTA
*
1272975 AATGCCCTTAACTCAAATTGGGATTTA
1 AATGCCCTCAACTCAAATTGGGATTTA
*
1273002 AAAGCCCT
1 AATGCCCT
1273010 GTTGACCCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (27 bp):
AATGCCCTCAACTCAAATTGGGATTTA
Found at i:1277875 original size:18 final size:17
Alignment explanation
Indices: 1277860--1277893 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1277850 TGTATTTAGA
1277860 ATTTCATTTATATTTAAC
1 ATTT-ATTTATATTTAAC
*
1277878 ATTTTTTTATATTTAA
1 ATTTATTTATATTTAA
1277894 TTTCAAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTATTTATATTTAAC
Found at i:1278160 original size:2 final size:2
Alignment explanation
Indices: 1278153--1278194 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1278143 TCAACATACA
1278153 AT AT AT 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
1278195 CTACACAGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1280358 original size:22 final size:21
Alignment explanation
Indices: 1280333--1280374 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1280323 TTTTAAAAAA
1280333 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
1280353 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
1280374 A
1 A
1280375 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:1288970 original size:39 final size:38
Alignment explanation
Indices: 1288914--1289004 Score: 123
Period size: 39 Copynumber: 2.4 Consensus size: 38
1288904 CTTAATCAAT
* *
1288914 AATTTAAA-TTAAAATAATTAATAAT-TTTAGTTTTAAAA
1 AATTTAAATTTAAAATAATTAA-AATATTAAATTTT-AAA
1288952 AATTTAAATTTAAAATAATTAAAATAATTAAATTTTAAA
1 AATTTAAATTTAAAATAATTAAAAT-ATTAAATTTTAAA
1288991 AATTTAAATTTAAA
1 AATTTAAATTTAAA
1289005 TTTAAATTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
38 11 0.23
39 30 0.62
40 7 0.15
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (38 bp):
AATTTAAATTTAAAATAATTAAAATATTAAATTTTAAA
Found at i:1289124 original size:16 final size:16
Alignment explanation
Indices: 1289099--1289154 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
1289089 TATAACAATA
*
1289099 AAAATTATTTAAATTT
1 AAAATAATTTAAATTT
* *
1289115 AAAATGATTTTAATTT
1 AAAATAATTTAAATTT
*
1289131 AAAATAATTAAAATTT
1 AAAATAATTTAAATTT
1289147 AAAATAAT
1 AAAATAAT
1289155 ATGAATAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
AAAATAATTTAAATTT
Found at i:1289178 original size:12 final size:11
Alignment explanation
Indices: 1289142--1289203 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
1289132 AAATAATTAA
1289142 AATTTAAAA-T
1 AATTTAAAATT
*
1289152 AATATGAATAATT
1 AAT-TTAA-AATT
1289165 AATTTTAAAATT
1 AA-TTTAAAATT
*
1289177 AATTTAAATTT
1 AATTTAAAATT
* *
1289188 AAATTAAAAAT
1 AATTTAAAATT
1289199 AATTT
1 AATTT
1289204 TATACTCTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
10 3 0.07
11 23 0.56
12 8 0.20
13 6 0.15
14 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:1298765 original size:94 final size:92
Alignment explanation
Indices: 1298621--1298794 Score: 253
Period size: 94 Copynumber: 1.9 Consensus size: 92
1298611 TTATTTGAAC
* *
1298621 TTTTAGTAATTTTACTAAAAGTTGGTGTCACTTAACTTGTGATACCAAACTCAGTT-GGAAACAT
1 TTTTAGTAATTTTACTAAAAGTTGGTGTCACTTAACTTGTGACACCAAACTCAATTAGG-AACAT
1298685 TATAATAGTATAGATAGTTTATCTATTT
65 TATAATAGTATAGATAGTTTATCTATTT
**
1298713 TTTTAGTAATTTTAC-AAACTGAGTTGGTGTCACTTAACTTGTGACACCAAACTCAATTAGGGGC
1 TTTTAGTAATTTTACTAAA---AGTTGGTGTCACTTAACTTGTGACACCAAACTCAATTAGGAAC
*
1298777 ATTATATTAGTATAGATA
63 ATTATAATAGTATAGATA
1298795 ATGGCTTTAC
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
91 3 0.04
92 15 0.21
94 53 0.73
95 2 0.03
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (92 bp):
TTTTAGTAATTTTACTAAAAGTTGGTGTCACTTAACTTGTGACACCAAACTCAATTAGGAACATT
ATAATAGTATAGATAGTTTATCTATTT
Found at i:1303742 original size:2 final size:2
Alignment explanation
Indices: 1303730--1303778 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
1303720 TACAAGAGTG
*
1303730 AT AT AT GT 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
1303772 AT AT AT A
1 AT AT AT A
1303779 ATTGAGAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1303967 original size:2 final size:2
Alignment explanation
Indices: 1303962--1303993 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1303952 ACACACACAC
1303962 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
1303994 TCTAACAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1304747 original size:2 final size:2
Alignment explanation
Indices: 1304740--1304770 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1304730 ACTGGAATCG
1304740 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
1304771 AAGATGATGG
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:1307083 original size:2 final size:2
Alignment explanation
Indices: 1307078--1307120 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1307068 TTTTTGCTTT
1307078 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1307120 T
1 T
1307121 CATTCAATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1310071 original size:3 final size:3
Alignment explanation
Indices: 1310063--1310096 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1310053 ATTTGAAGCA
1310063 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1310097 GTGAGCTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1310887 original size:13 final size:13
Alignment explanation
Indices: 1310869--1310894 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1310859 CAATTTTTTG
1310869 TGTATCGATACAT
1 TGTATCGATACAT
1310882 TGTATCGATACAT
1 TGTATCGATACAT
1310895 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1310906 original size:32 final size:33
Alignment explanation
Indices: 1310849--1310912 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1310839 TACAAGCCAA
**
1310849 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1310882 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1310913 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1311629 original size:21 final size:21
Alignment explanation
Indices: 1311586--1311631 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1311576 TAATTCACGC
* *
1311586 ATTCTCCCCCGTTTATTAATA
1 ATTCTCCCCCGTTAATCAATA
1311607 ATTCTCCCCC-TTAATCAAGTA
1 ATTCTCCCCCGTTAATCAA-TA
1311628 ATTC
1 ATTC
1311632 ATATCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.26, C:0.30, G:0.04, T:0.39
Consensus pattern (21 bp):
ATTCTCCCCCGTTAATCAATA
Found at i:1312059 original size:30 final size:31
Alignment explanation
Indices: 1312003--1312070 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 31
1311993 TTCATGCAAC
* *
1312003 TAATACCAAAAGTTTATGCAAGCTCTCCCCCT
1 TAATA-CAAAAGTTTATACAAACTCTCCCCCT
1312035 TAATACAAAA-TTTATACAAACTCTCCCCCT
1 TAATACAAAAGTTTATACAAACTCTCCCCCT
1312065 TAATAC
1 TAATAC
1312071 GTTGTCACCC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 24 0.71
31 5 0.15
32 5 0.15
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.29
Consensus pattern (31 bp):
TAATACAAAAGTTTATACAAACTCTCCCCCT
Found at i:1312903 original size:13 final size:13
Alignment explanation
Indices: 1312885--1312909 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1312875 ACTGAAGTAA
1312885 TGTATCGATACAT
1 TGTATCGATACAT
1312898 TGTATCGATACA
1 TGTATCGATACA
1312910 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1314587 original size:84 final size:84
Alignment explanation
Indices: 1314432--1314596 Score: 201
Period size: 84 Copynumber: 2.0 Consensus size: 84
1314422 CATTTTCCAC
* * * *
1314432 TTGCAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTCTTTTTAAAAGAATTATTTTCTAAAC
1 TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
1314497 TCATTGATTTACTTTCATT
66 TCATTGATTTACTTTCATT
* *
1314516 TTGCAACTC-TTTCATATTCTTCTCTAATTCACTTAATTTC-TTTT-CAAGAATATCATTCTCTA
1 TTGCAACTCATTTC-TATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAAT-T-ATTCTCTA
* * *
1314578 CACTTATTGATTTATTTTC
63 AACTCATTGATTTACTTTC
1314597 TTCTTTGAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
82 6 0.09
83 9 0.13
84 54 0.78
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.52
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:1316144 original size:34 final size:35
Alignment explanation
Indices: 1316106--1316172 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1316096 CCTTACAACA
1316106 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
1316140 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1316173 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:1316649 original size:13 final size:13
Alignment explanation
Indices: 1316631--1316656 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1316621 CAATTTTTTG
1316631 TGTATCGATACAT
1 TGTATCGATACAT
1316644 TGTATCGATACAT
1 TGTATCGATACAT
1316657 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1316668 original size:32 final size:33
Alignment explanation
Indices: 1316611--1316674 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1316601 TATAAGCCAA
**
1316611 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1316644 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1316675 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1317037 original size:3 final size:3
Alignment explanation
Indices: 1317029--1317069 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1317019 GATCCTAACA
1317029 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1317070 CAATAAAATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1318578 original size:28 final size:28
Alignment explanation
Indices: 1318547--1318605 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
1318537 CATTTTTTAC
*
1318547 ATACAAAA-ATAACCATCATATTTGACAA
1 ATACAAAAGA-AACCACCATATTTGACAA
*
1318575 ATACAAAAGAAACTACCATATTTGACAA
1 ATACAAAAGAAACCACCATATTTGACAA
1318603 ATA
1 ATA
1318606 TAAAGGGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.54, C:0.17, G:0.05, T:0.24
Consensus pattern (28 bp):
ATACAAAAGAAACCACCATATTTGACAA
Found at i:1321559 original size:13 final size:13
Alignment explanation
Indices: 1321541--1321571 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1321531 TATTTTTTAA
1321541 AATATTTATATTT
1 AATATTTATATTT
1321554 AATATTTATATTT
1 AATATTTATATTT
*
1321567 TATAT
1 AATAT
1321572 ATTTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:1324140 original size:23 final size:22
Alignment explanation
Indices: 1324125--1324168 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
1324115 TTTTCATTTT
1324125 TATTCAGCTTTATTTTTCTTTAA
1 TATTCA-CTTTATTTTTCTTTAA
*
1324148 TATTTACTTTATTTTTTCTTT
1 TATTCACTTTA-TTTTTCTTT
1324169 CTATCTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.18, C:0.11, G:0.02, T:0.68
Consensus pattern (22 bp):
TATTCACTTTATTTTTCTTTAA
Found at i:1324355 original size:16 final size:19
Alignment explanation
Indices: 1324318--1324361 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
1324308 ATAATAAATT
1324318 TTATATTTATATATTTATA
1 TTATATTTATATATTTATA
1324337 TTATA-TTATA-ATTTA-A
1 TTATATTTATATATTTATA
*
1324353 TTATTTTTA
1 TTATATTTA
1324362 AAGTTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 5 0.22
17 8 0.35
18 5 0.22
19 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATATTTATATATTTATA
Found at i:1324357 original size:19 final size:21
Alignment explanation
Indices: 1324256--1324357 Score: 58
Period size: 19 Copynumber: 5.1 Consensus size: 21
1324246 TTGTATTTTA
* **
1324256 ATTATATTTTTATATTTTTTT
1 ATTATATTTATATATTTAATT
*
1324277 ATTATTAATTATAT-TATT-ATT
1 ATTA-TATTTATATAT-TTAATT
* * * *
1324298 AATATTTTTA-ATAATAAATT
1 ATTATATTTATATATTTAATT
1324318 -TTATATTTATATATTT-A-T
1 ATTATATTTATATATTTAATT
1324336 ATTATA-TTATA-ATTTAATT
1 ATTATATTTATATATTTAATT
1324355 ATT
1 ATT
1324358 TTTAAAGTTA
Statistics
Matches: 61, Mismatches: 12, Indels: 18
0.67 0.13 0.20
Matches are distributed among these distances:
17 4 0.07
18 7 0.11
19 20 0.33
20 11 0.18
21 10 0.16
22 9 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTATATTTATATATTTAATT
Found at i:1325046 original size:32 final size:32
Alignment explanation
Indices: 1324963--1325025 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1324953 ATAATTAAAA
* *
1324963 TATAATATAAATATTTAAATATATCAAAATTTT
1 TATAAAATAAAT-TTTTAATATATCAAAATTTT
* *
1324996 TATAAAATCAATTATTAATATATCAAAATT
1 TATAAAATAAATTTTTAATATATCAAAATT
1325026 CTTTTTACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 16 0.62
33 10 0.38
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (32 bp):
TATAAAATAAATTTTTAATATATCAAAATTTT
Found at i:1326942 original size:2 final size:2
Alignment explanation
Indices: 1326935--1326963 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1326925 GACATATGTG
1326935 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
1326964 TTACATTATA
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:1327990 original size:1 final size:1
Alignment explanation
Indices: 1327984--1328010 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1327974 GAAGGCTTTG
1327984 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1328011 AAGAAAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1328105 original size:4 final size:4
Alignment explanation
Indices: 1328082--1328132 Score: 66
Period size: 4 Copynumber: 12.0 Consensus size: 4
1328072 GCCCCTACAA
*
1328082 AAAT AAAAT AAAATT AAAT AAAT AAAT AAAC AAAT AAAT AAAT AAAT AAAT
1 AAAT -AAAT -AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1328133 GTGATCTTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
4 31 0.72
5 11 0.26
6 1 0.02
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1328501 original size:32 final size:29
Alignment explanation
Indices: 1328430--1328502 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 29
1328420 TATTATTTAA
*
1328430 AATAAT-ATTAAATAAATATTTTTATATT
1 AATAATAATTAAATAAATATTTTTATATC
1328458 AATATTTATAATTAAATTTAAATATTTTTATTATC
1 AATA---ATAATTAAA--TAAATATTTTTA-TATC
1328493 AATAATAATT
1 AATAATAATT
1328503 CGAAAAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
28 4 0.11
31 2 0.05
32 12 0.32
34 12 0.32
35 7 0.19
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (29 bp):
AATAATAATTAAATAAATATTTTTATATC
Found at i:1329207 original size:21 final size:21
Alignment explanation
Indices: 1329160--1329214 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
1329150 ATACCAAAAA
*
1329160 ATATTATAAATTTTTAAATTT
1 ATATTTTAAATTTTTAAATTT
* *
1329181 AAATTTTAAATTTTTTAATTACT
1 ATATTTTAAATTTTTAAATT--T
*
1329204 ATTTTTTAAAT
1 ATATTTTAAAT
1329215 ATAACCATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 17 0.63
23 10 0.37
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATTTTAAATTTTTAAATTT
Found at i:1329661 original size:20 final size:20
Alignment explanation
Indices: 1329616--1329675 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
1329606 AATTGTTTCG
*
1329616 ATAAAAATAATA-AA-AATAT
1 ATAAAATTAATATAATAA-AT
*
1329635 ATAAAA-TAATTATTATAAAT
1 ATAAAATTAA-TATAATAAAT
*
1329655 ATTAAATTAATATAATAAAT
1 ATAAAATTAATATAATAAAT
1329675 A
1 A
1329676 AATAAGGGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
18 3 0.09
19 8 0.24
20 18 0.53
21 5 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAAAATTAATATAATAAAT
Found at i:1338053 original size:14 final size:14
Alignment explanation
Indices: 1338034--1338060 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1338024 AAAATTTTTA
1338034 AAAAATTTAAAATT
1 AAAAATTTAAAATT
1338048 AAAAATTTAAAAT
1 AAAAATTTAAAAT
1338061 ATCTAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAATTTAAAATT
Found at i:1338850 original size:90 final size:89
Alignment explanation
Indices: 1338697--1338877 Score: 335
Period size: 90 Copynumber: 2.0 Consensus size: 89
1338687 GAAACTGCAG
1338697 ATTCTCTGTTCAAAACTGTATGATAGACCCAAACAACTCTCGAAAGGTACTAATCTTTCGCTTCT
1 ATTCTCTGTTCAAAACTGTATGATAGACCCAAACAACTCTCGAAAGGTACTAATCTTTCGCTTC-
*
1338762 TTTTTTTCTTAATGTGTCCCATTGC
65 ATTTTTTCTTAATGTGTCCCATTGC
*
1338787 ATTCTCTGTTCAAAACTGTCTGATAGACCCAAACAACTCTCGAAAGGTACTAATCTTTCGCTTCA
1 ATTCTCTGTTCAAAACTGTATGATAGACCCAAACAACTCTCGAAAGGTACTAATCTTTCGCTTCA
1338852 TTTTTTCTTAATGTGTCCCATTGC
66 TTTTTTCTTAATGTGTCCCATTGC
1338876 AT
1 AT
1338878 CTGGGATTTT
Statistics
Matches: 89, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
89 26 0.29
90 63 0.71
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (89 bp):
ATTCTCTGTTCAAAACTGTATGATAGACCCAAACAACTCTCGAAAGGTACTAATCTTTCGCTTCA
TTTTTTCTTAATGTGTCCCATTGC
Found at i:1343969 original size:21 final size:21
Alignment explanation
Indices: 1343943--1343983 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1343933 ACAATGAAAA
*
1343943 TTTAATTAATTTTAAAATTAT
1 TTTAATTAATTTCAAAATTAT
*
1343964 TTTAATTACTTTCAAAATTA
1 TTTAATTAATTTCAAAATTA
1343984 AATTACATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTAATTAATTTCAAAATTAT
Found at i:1344376 original size:15 final size:15
Alignment explanation
Indices: 1344338--1344377 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
1344328 TATTATTTTC
1344338 TCAATAATCATATTT
1 TCAATAATCATATTT
*
1344353 TTAATAATCATATTT
1 TCAATAATCATATTT
*
1344368 TCAAAAATCA
1 TCAATAATCA
1344378 CGTCCCATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (15 bp):
TCAATAATCATATTT
Found at i:1344500 original size:2 final size:2
Alignment explanation
Indices: 1344493--1344522 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1344483 TCAGTAGATA
1344493 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
1344523 TGATGTTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1355835 original size:28 final size:29
Alignment explanation
Indices: 1355799--1355872 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 29
1355789 ATTAAGTAAT
1355799 AAATAAATA-AATATAAATTTTA-TTTTAA
1 AAATAAATATAAT-TAAATTTTATTTTTAA
*
1355827 AAATAAATATAATTATATTTTATTTTTAAA
1 AAATAAATATAATTAAATTTTATTTTT-AA
* *
1355857 AAATAATTATATTTAA
1 AAATAAATATAATTAA
1355873 TATATAGATA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 17 0.44
29 7 0.18
30 15 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
AAATAAATATAATTAAATTTTATTTTTAA
Found at i:1355845 original size:23 final size:24
Alignment explanation
Indices: 1355803--1355848 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
1355793 AGTAATAAAT
*
1355803 AAATAAATATAAATTTTATTTTAA
1 AAATAAATATAAATTATATTTTAA
1355827 AAATAAATAT-AATTATATTTTA
1 AAATAAATATAAATTATATTTTA
1355849 TTTTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AAATAAATATAAATTATATTTTAA
Found at i:1357274 original size:6 final size:6
Alignment explanation
Indices: 1357265--1357301 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
1357255 TGAATCGCTT
*
1357265 ATAGCC ATAGCC ATAGCC ATAGCC GTAGCC ATTAGCC
1 ATAGCC ATAGCC ATAGCC ATAGCC ATAGCC A-TAGCC
1357302 TCTCTGCTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (6 bp):
ATAGCC
Found at i:1362653 original size:16 final size:15
Alignment explanation
Indices: 1362632--1362662 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
1362622 AAGTATAATT
1362632 TTTTTAAAAATAATAA
1 TTTTT-AAAATAATAA
1362648 TTTTTAAAATAATAA
1 TTTTTAAAATAATAA
1362663 ATATACAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTTTAAAATAATAA
Found at i:1362704 original size:26 final size:28
Alignment explanation
Indices: 1362652--1362706 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
1362642 TAATAATTTT
*
1362652 TAAAATAATAAATATACAAGATCATTAA
1 TAAAATAATAAATAGACAAGATCATTAA
*
1362680 TAAAATAA-AAAT-GACAAGATTATTAA
1 TAAAATAATAAATAGACAAGATCATTAA
1362706 T
1 T
1362707 TTTAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 13 0.52
27 4 0.16
28 8 0.32
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.29
Consensus pattern (28 bp):
TAAAATAATAAATAGACAAGATCATTAA
Found at i:1364893 original size:43 final size:43
Alignment explanation
Indices: 1364838--1364962 Score: 232
Period size: 43 Copynumber: 2.9 Consensus size: 43
1364828 ATAGAGATCT
* *
1364838 TTTTTTGATAAATTTAGATAAATTTGCTACTTAGAACTTTTTG
1 TTTTTGGATAAATTTAGATGAATTTGCTACTTAGAACTTTTTG
1364881 TTTTTGGATAAATTTAGATGAATTTGCTACTTAGAACTTTTTG
1 TTTTTGGATAAATTTAGATGAATTTGCTACTTAGAACTTTTTG
1364924 TTTTTGGATAAATTTAGATGAATTTGCTACTTAGAACTT
1 TTTTTGGATAAATTTAGATGAATTTGCTACTTAGAACTT
1364963 GTTCTTTGAT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 80 1.00
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.49
Consensus pattern (43 bp):
TTTTTGGATAAATTTAGATGAATTTGCTACTTAGAACTTTTTG
Found at i:1366436 original size:15 final size:15
Alignment explanation
Indices: 1366400--1366436 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1366390 AATTATGATG
* *
1366400 TTATTTGTTTTATTT
1 TTATTTTTTTTACTT
1366415 TTATTTTTTTTACTT
1 TTATTTTTTTTACTT
1366430 TTATTTT
1 TTATTTT
1366437 CTCTAGAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.81
Consensus pattern (15 bp):
TTATTTTTTTTACTT
Found at i:1372686 original size:9 final size:9
Alignment explanation
Indices: 1372674--1372699 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1372664 TATATATACT
1372674 GCAAAGCAG
1 GCAAAGCAG
1372683 GCAAAGCAG
1 GCAAAGCAG
1372692 GCAAAGCA
1 GCAAAGCA
1372700 AGCAGCCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.31, T:0.00
Consensus pattern (9 bp):
GCAAAGCAG
Found at i:1374695 original size:49 final size:48
Alignment explanation
Indices: 1374594--1374686 Score: 123
Period size: 49 Copynumber: 1.9 Consensus size: 48
1374584 ATAGGTTATG
* ** * *
1374594 AAATTTTATAATTTTAAATATAAATATAATATTATAATATTATAATAT
1 AAATTTTAAAATTTTAAATATAAATATAATAAAATAAAAATATAATAT
*
1374642 AAATTTATAAAATTTTAAATATAATTATAATAAAATAAAAATATA
1 AAATTT-TAAAATTTTAAATATAAATATAATAAAATAAAAATATA
1374687 TGTAAAATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
48 6 0.16
49 32 0.84
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (48 bp):
AAATTTTAAAATTTTAAATATAAATATAATAAAATAAAAATATAATAT
Found at i:1374718 original size:12 final size:12
Alignment explanation
Indices: 1374701--1374725 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1374691 AAATTAAATA
1374701 CATAAATTAGCG
1 CATAAATTAGCG
1374713 CATAAATTAGCG
1 CATAAATTAGCG
1374725 C
1 C
1374726 GCAGCTCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (12 bp):
CATAAATTAGCG
Found at i:1376619 original size:14 final size:14
Alignment explanation
Indices: 1376583--1376623 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1376573 AAAAATTTAT
1376583 AATT-TAAAAGAAA
1 AATTATAAAAGAAA
* *
1376596 AAGTAAAAAAGAAA
1 AATTATAAAAGAAA
1376610 AATTATAAAA-AAA
1 AATTATAAAAGAAA
1376623 A
1 A
1376624 TATTTTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (14 bp):
AATTATAAAAGAAA
Found at i:1383604 original size:2 final size:2
Alignment explanation
Indices: 1383597--1383648 Score: 79
Period size: 2 Copynumber: 26.0 Consensus size: 2
1383587 AGATCCTCCC
*
1383597 AT AT AT AT AT AT AT AT -T GAA 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
1383639 AT AT AT AT AT
1 AT AT AT AT AT
1383649 TGGTTTACAA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1385978 original size:29 final size:32
Alignment explanation
Indices: 1385938--1386013 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 32
1385928 AAATCTTTAA
* *
1385938 TATACAATATAAATAAAT-ATTT-T-AAATTT
1 TATATAATATAAATAAATAATTTATCAAAATT
* *
1385967 TATATAATATAAATTATTAATTTATCAAAATT
1 TATATAATATAAATAAATAATTTATCAAAATT
1385999 TATATAAATATAAAT
1 TATAT-AATATAAAT
1386014 TATTTTTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 15 0.38
30 4 0.10
31 1 0.03
32 10 0.26
33 9 0.23
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (32 bp):
TATATAATATAAATAAATAATTTATCAAAATT
Found at i:1385981 original size:16 final size:17
Alignment explanation
Indices: 1385960--1386027 Score: 56
Period size: 16 Copynumber: 4.2 Consensus size: 17
1385950 ATAAATATTT
1385960 TAAATT-TTATATAATA
1 TAAATTATTATATAATA
*
1385976 TAAATTATTA-AT-TTA
1 TAAATTATTATATAATA
*
1385991 TCAAAAT-TTATATAAATA
1 T-AAATTATTATAT-AATA
*
1386009 TAAATTATT-TTTAATA
1 TAAATTATTATATAATA
1386025 TAA
1 TAA
1386028 TAAAATATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
15 6 0.15
16 21 0.51
17 9 0.22
18 5 0.12
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAATTATTATATAATA
Found at i:1386281 original size:20 final size:21
Alignment explanation
Indices: 1386247--1386286 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1386237 AATAGATAAT
*
1386247 TTTTTAATATTTATTTATATA
1 TTTTTAATATATATTTATATA
1386268 TTTTTAA-ATATATTTATAT
1 TTTTTAATATATATTTATAT
1386287 CTGTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTAATATATATTTATATA
Found at i:1386301 original size:20 final size:20
Alignment explanation
Indices: 1386253--1386301 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1386243 TAATTTTTTA
*
1386253 ATATTTATTTATATATTTTT
1 ATATTTATTTATATATGTTT
* * *
1386273 AAATATATTTATATCTGTTT
1 ATATTTATTTATATATGTTT
1386293 ATATTTATT
1 ATATTTATT
1386302 AAAATTTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
ATATTTATTTATATATGTTT
Found at i:1386357 original size:33 final size:33
Alignment explanation
Indices: 1386319--1386395 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 33
1386309 TTTAAAATTG
1386319 TATTTAAAATTTCAGTTTATTT-ATTAAA-AAAAT
1 TATTTAAAATTT-A-TTTATTTAATTAAATAAAAT
*
1386352 TATTT-AAATTTATTTATTTAAATTAAATAAATT
1 TATTTAAAATTTATTTATTT-AATTAAATAAAAT
1386385 TATTTACAAAT
1 TATTTA-AAAT
1386396 ATTGAGTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
30 7 0.18
31 1 0.03
32 12 0.32
33 14 0.37
35 4 0.11
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (33 bp):
TATTTAAAATTTATTTATTTAATTAAATAAAAT
Found at i:1386366 original size:10 final size:10
Alignment explanation
Indices: 1386244--1386367 Score: 51
Period size: 10 Copynumber: 12.0 Consensus size: 10
1386234 TTAAATAGAT
1386244 AATTT-TTTA
1 AATTTATTTA
1386253 ATATTTATTTA
1 A-ATTTATTTA
*
1386264 TATATT-TTTA
1 AAT-TTATTTA
*
1386274 AATATATTTA
1 AATTTATTTA
* * *
1386284 TATCTGTTTA
1 AATTTATTTA
* *
1386294 TATTTATTAA
1 AATTTATTTA
1386304 AATTT-TTTAA
1 AATTTATTT-A
1386314 AATTGTATTTAA
1 AATT-TATTT-A
1386326 AATTTCAGTTT-
1 AATTT-A-TTTA
*
1386337 -ATTTATTAAAA
1 AATTTATT--TA
*
1386348 AAATTATTTA
1 AATTTATTTA
1386358 AATTTATTTA
1 AATTTATTTA
1386368 TTTAAATTAA
Statistics
Matches: 87, Mismatches: 15, Indels: 25
0.69 0.12 0.20
Matches are distributed among these distances:
8 2 0.02
9 5 0.06
10 53 0.61
11 8 0.09
12 16 0.18
13 3 0.03
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (10 bp):
AATTTATTTA
Found at i:1386626 original size:23 final size:24
Alignment explanation
Indices: 1386600--1386651 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
1386590 TTATTATTAT
*
1386600 AATAAAATTATAATTAAA-TAATA
1 AATAAAATTATAAATAAATTAATA
*
1386623 AAT-AAATTTTAAATAAATTAATA
1 AATAAAATTATAAATAAATTAATA
1386646 AATAAA
1 AATAAA
1386652 TAAATTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 12 0.48
23 11 0.44
24 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
AATAAAATTATAAATAAATTAATA
Found at i:1386629 original size:11 final size:11
Alignment explanation
Indices: 1386604--1386654 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
1386594 TATTATAATA
* *
1386604 AAATTATAATT
1 AAATAATAAAT
1386615 AAATAATAAAT
1 AAATAATAAAT
**
1386626 AAATTTTAAAT
1 AAATAATAAAT
1386637 AAATTAATAAAT
1 AAA-TAATAAAT
1386649 AAATAA
1 AAATAA
1386655 ATTTATTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
11 24 0.73
12 9 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:1386647 original size:19 final size:18
Alignment explanation
Indices: 1386613--1386648 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1386603 AAAATTATAA
1386613 TTAAATAATAAATAAATT
1 TTAAATAATAAATAAATT
*
1386631 TTAAATAAATTAATAAAT
1 TTAAAT-AATAAATAAAT
1386649 AAATAAATTT
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAATAATAAATAAATT
Found at i:1389301 original size:6 final size:6
Alignment explanation
Indices: 1389292--1389331 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
1389282 TTTAAAAAAT
*
1389292 TTTAAA TTTATA TTTAAA TTTAAA TTTAACGA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA--A TTTAAA TT
1389332 ATTATTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 24 0.80
8 6 0.20
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:1389404 original size:20 final size:22
Alignment explanation
Indices: 1389364--1389407 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
1389354 AATAAAATAT
*
1389364 TATTTTTATATTATTATTTAAA
1 TATTTTTATATTATAATTTAAA
1389386 TATTTTTA-ATTA-AATTTAAA
1 TATTTTTATATTATAATTTAAA
1389406 TA
1 TA
1389408 AAAATATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTTTTATATTATAATTTAAA
Found at i:1394323 original size:20 final size:18
Alignment explanation
Indices: 1394298--1394354 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 18
1394288 ATATATTTAT
1394298 ATTTAATTAAAAAATAAAA
1 ATTTAA-TAAAAAATAAAA
*
1394317 ATATTAATATAAAAATAATA
1 AT-TTAATA-AAAAATAAAA
*
1394337 ATTTAATAAATAATAAAA
1 ATTTAATAAAAAATAAAA
1394355 TAGATTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 8 0.24
19 10 0.30
20 15 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATTTAATAAAAAATAAAA
Found at i:1394347 original size:15 final size:14
Alignment explanation
Indices: 1394311--1394352 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1394301 TAATTAAAAA
*
1394311 ATAAAAATATTAAT
1 ATAAAAATAATAAT
1394325 ATAAAAATAATAAT
1 ATAAAAATAATAAT
*
1394339 TTAATAAATAATAA
1 ATAA-AAATAATAA
1394353 AATAGATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAAAATAATAAT
Found at i:1395334 original size:2 final size:2
Alignment explanation
Indices: 1395327--1395356 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1395317 TAACCTAAAG
1395327 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1395357 AAGTATGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1397275 original size:21 final size:21
Alignment explanation
Indices: 1397251--1397291 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1397241 CTTAGGTGTA
1397251 GTTTTGTATA-ATGTTTTTTTG
1 GTTTTGTATATAT-TTTTTTTG
*
1397272 GTTTTTTATATATTTTTTTT
1 GTTTTGTATATATTTTTTTT
1397292 AAATATGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (21 bp):
GTTTTGTATATATTTTTTTTG
Found at i:1397367 original size:17 final size:18
Alignment explanation
Indices: 1397337--1397370 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1397327 TATAATTTTT
*
1397337 AAAAATTTTAAATATATA
1 AAAAAATTTAAATATATA
1397355 AAAAAATTT-AATATAT
1 AAAAAATTTAAATATAT
1397371 TATATTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAAATTTAAATATATA
Found at i:1399805 original size:15 final size:16
Alignment explanation
Indices: 1399785--1399814 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1399775 TTTATTCTAG
1399785 CATTTG-TTAAATTAA
1 CATTTGATTAAATTAA
1399800 CATTTGATTAAATTA
1 CATTTGATTAAATTA
1399815 CTAAACGCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (16 bp):
CATTTGATTAAATTAA
Found at i:1399990 original size:20 final size:19
Alignment explanation
Indices: 1399962--1400024 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
1399952 TTAGTATTAA
1399962 ATTTATATTATCATGTGTTT
1 ATTTATATTATCA-GTGTTT
* * * *
1399982 ATTTTTATTTTCAGTATTAA
1 ATTTATATTATCAGTGTT-T
1400002 ATTTATATTATCACGTGTTT
1 ATTTATATTATCA-GTGTTT
1400022 ATT
1 ATT
1400025 CTTACTTTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 4 0.12
20 25 0.76
21 4 0.12
ACGTcount: A:0.27, C:0.06, G:0.08, T:0.59
Consensus pattern (19 bp):
ATTTATATTATCAGTGTTT
Found at i:1400004 original size:40 final size:40
Alignment explanation
Indices: 1399950--1400048 Score: 155
Period size: 40 Copynumber: 2.5 Consensus size: 40
1399940 ATTGGTCTTT
* *
1399950 TTTTAGTATTAAATTTATATTATCATGTGTTTATTTTTA-
1 TTTTAGTATTAAATTTATATTATCACGTGTTTATTCTTAC
1399989 TTTTCAGTATTAAATTTATATTATCACGTGTTTATTCTTAC
1 TTTT-AGTATTAAATTTATATTATCACGTGTTTATTCTTAC
*
1400030 TTTTAATATTAAATTTATA
1 TTTTAGTATTAAATTTATA
1400049 CTATGACATG
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
39 4 0.07
40 47 0.85
41 4 0.07
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (40 bp):
TTTTAGTATTAAATTTATATTATCACGTGTTTATTCTTAC
Found at i:1400096 original size:16 final size:16
Alignment explanation
Indices: 1400070--1400153 Score: 105
Period size: 16 Copynumber: 5.2 Consensus size: 16
1400060 TTATGATTGG
1400070 ATTAGTTTTAAATTTAA
1 ATTA-TTTTAAATTTAA
*
1400087 ATTATTTTAAATTTTA
1 ATTATTTTAAATTTAA
* *
1400103 ATAATTCTAAATTTAA
1 ATTATTTTAAATTTAA
* * *
1400119 TTTATTTTGAACTTAA
1 ATTATTTTAAATTTAA
1400135 ATTATTTTAAATTTAA
1 ATTATTTTAAATTTAA
1400151 ATT
1 ATT
1400154 TAATTTTTAT
Statistics
Matches: 55, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
16 51 0.93
17 4 0.07
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTATTTTAAATTTAA
Found at i:1400520 original size:32 final size:33
Alignment explanation
Indices: 1400461--1400544 Score: 84
Period size: 32 Copynumber: 2.6 Consensus size: 33
1400451 TCAGTAAATT
* * *
1400461 TTTATTATAATATATTATTTTTAATAT-ATTTA
1 TTTATTAAAATATATTATTTATAATATAATTAA
*
1400493 TTTATTAAAATCTA-TATTTATATATATAATTAA
1 TTTATTAAAATATATTATTTATA-ATATAATTAA
*
1400526 TTT-TTAAATATTTATTATT
1 TTTATTAAA-ATATATTATT
1400545 ACAATATTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
31 7 0.16
32 21 0.49
33 11 0.26
34 4 0.09
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (33 bp):
TTTATTAAAATATATTATTTATAATATAATTAA
Found at i:1400680 original size:18 final size:18
Alignment explanation
Indices: 1400646--1400679 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1400636 TTAGTTGTGT
*
1400646 TTGTGTTATATAATTTTG
1 TTGTGTTATAAAATTTTG
1400664 TTGTGTT-TAAAATTTT
1 TTGTGTTATAAAATTTT
1400680 TAATTTTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.62
Consensus pattern (18 bp):
TTGTGTTATAAAATTTTG
Found at i:1401454 original size:22 final size:22
Alignment explanation
Indices: 1401418--1401461 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1401408 TAAAATTTAT
* *
1401418 GATATAATTTACTTTTTGATAA
1 GATATAATTCACTTTTTAATAA
*
1401440 GATATAATTCGCTTTTTAATAA
1 GATATAATTCACTTTTTAATAA
1401462 ATTAATATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (22 bp):
GATATAATTCACTTTTTAATAA
Found at i:1401667 original size:15 final size:16
Alignment explanation
Indices: 1401640--1401700 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
1401630 CAATCTCGAA
1401640 TTTAAATTTTTTTAAG
1 TTTAAATTTTTTTAAG
* *
1401656 TTTAAATTTTTTAAAA
1 TTTAAATTTTTTTAAG
** *
1401672 TTCGAATTCTTTT-AG
1 TTTAAATTTTTTTAAG
1401687 ATTTAAATTTTTTT
1 -TTTAAATTTTTTT
1401701 GAATTCAATT
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
15 1 0.03
16 33 0.97
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (16 bp):
TTTAAATTTTTTTAAG
Found at i:1401692 original size:32 final size:32
Alignment explanation
Indices: 1401644--1401725 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
1401634 CTCGAATTTA
*
1401644 AATTT-TTTTAAGTTTAAATTTTTTAAAATTC
1 AATTTATTTTAAATTTAAATTTTTTAAAATTC
* * **
1401675 GAA-TTCTTTTAGATTTAAATTTTTTTGAATTC
1 -AATTTATTTTAAATTTAAATTTTTTAAAATTC
1401707 AATTTATTTTAAATTTAAA
1 AATTTATTTTAAATTTAAA
1401726 CTATTTCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
31 4 0.10
32 38 0.90
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (32 bp):
AATTTATTTTAAATTTAAATTTTTTAAAATTC
Found at i:1401716 original size:16 final size:15
Alignment explanation
Indices: 1401644--1401721 Score: 57
Period size: 16 Copynumber: 4.9 Consensus size: 15
1401634 CTCGAATTTA
* *
1401644 AATTTTTTTAAGTTTA
1 AATTTTTTTAA-ATTC
*
1401660 AATTTTTTAAAATTC
1 AATTTTTTTAAATTC
* * *
1401675 GAATTCTTTTAGATTTA
1 -AATTTTTTTA-AATTC
*
1401692 AATTTTTTTGAATTC
1 AATTTTTTTAAATTC
1401707 AATTTATTTTAAATT
1 AATTT-TTTTAAATT
1401722 TAAACTATTT
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
15 10 0.21
16 34 0.72
17 3 0.06
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (15 bp):
AATTTTTTTAAATTC
Found at i:1409934 original size:2 final size:2
Alignment explanation
Indices: 1409929--1409953 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1409919 ATATACAAAT
1409929 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
1409954 ACGGGATTTT
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1410195 original size:10 final size:11
Alignment explanation
Indices: 1410179--1410204 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1410169 TTAATTGACT
1410179 TTTTTTTATAA
1 TTTTTTTATAA
1410190 TTTTTTTATAA
1 TTTTTTTATAA
1410201 TTTT
1 TTTT
1410205 CTATTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTTATAA
Found at i:1411159 original size:17 final size:18
Alignment explanation
Indices: 1411137--1411178 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1411127 AATCAATTTA
1411137 ATTAATTTGATTTA-AAT
1 ATTAATTTGATTTAGAAT
*
1411154 ATTAA-TCGATTTAGAAT
1 ATTAATTTGATTTAGAAT
*
1411171 ATTGATTT
1 ATTAATTT
1411179 AATTGATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 7 0.35
17 12 0.60
18 1 0.05
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (18 bp):
ATTAATTTGATTTAGAAT
Done.