Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold221
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: 2539808
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 13 of 19
Found at i:1536151 original size:54 final size:50
Alignment explanation
Indices: 1536087--1536192 Score: 119
Period size: 53 Copynumber: 2.0 Consensus size: 50
1536077 ATATGATTTA
1536087 ATTTAATA-TTTTATATAATT-ATTTAAAATATTAAAA-ATTTATTTTACATTAAT
1 ATTTAATATTTTTAT-TAATTAATTT-AAATA--AAAATA-TTATTTTA-ATTAAT
1536140 ATTTATATATTTTTATTAATTAAATTTAAATAAAAATATTATTTTAATTAAT
1 ATTTA-ATATTTTTATTAATT-AATTTAAATAAAAATATTATTTTAATTAAT
1536192 A
1 A
1536193 AAATAATAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
52 7 0.15
53 17 0.35
54 9 0.19
55 11 0.23
56 4 0.08
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (50 bp):
ATTTAATATTTTTATTAATTAATTTAAATAAAAATATTATTTTAATTAAT
Found at i:1536188 original size:23 final size:21
Alignment explanation
Indices: 1536153--1536208 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 21
1536143 TATATATTTT
1536153 TATTAATTAAATTTAAATAAAAA
1 TATTAATTAAA-TT-AATAAAAA
* *
1536176 TATTATTTTAATTAAT-AAAA
1 TATTAATTAAATTAATAAAAA
*
1536196 TAATAATCTAAAT
1 TATTAAT-TAAAT
1536209 CGAATTCATC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 9 0.33
21 7 0.26
22 2 0.07
23 9 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TATTAATTAAATTAATAAAAA
Found at i:1536582 original size:12 final size:13
Alignment explanation
Indices: 1536567--1536595 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1536557 ATTATTTTAT
1536567 TTTATTAT-AAAA
1 TTTATTATCAAAA
1536579 TTTATTATCAAAA
1 TTTATTATCAAAA
1536592 TTTA
1 TTTA
1536596 AGTAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTATTATCAAAA
Found at i:1536604 original size:10 final size:10
Alignment explanation
Indices: 1536589--1536635 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
1536579 TTTATTATCA
1536589 AAATTTAAGT
1 AAATTTAAGT
*
1536599 AAATTTAATAT
1 AAATTTAA-GT
*
1536610 AAAAATTAAGT
1 -AAATTTAAGT
1536621 AAATTTAAGT
1 AAATTTAAGT
1536631 AAATT
1 AAATT
1536636 AATTATTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
10 22 0.71
11 2 0.06
12 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (10 bp):
AAATTTAAGT
Found at i:1536618 original size:22 final size:23
Alignment explanation
Indices: 1536576--1536628 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
1536566 TTTTATTATA
* *
1536576 AAATTTATTATCAAAATTTAAGT
1 AAATTTAATATCAAAAATTAAGT
1536599 AAATTTAATAT-AAAAATTAAGT
1 AAATTTAATATCAAAAATTAAGT
1536621 AAATTTAA
1 AAATTTAA
1536629 GTAAATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (23 bp):
AAATTTAATATCAAAAATTAAGT
Found at i:1536692 original size:39 final size:35
Alignment explanation
Indices: 1536620--1536696 Score: 118
Period size: 39 Copynumber: 2.1 Consensus size: 35
1536610 AAAAATTAAG
1536620 TAAATTTAAGTAAATTAATTATTTATTAAATAATA
1 TAAATTTAAGTAAATTAATTATTTATTAAATAATA
1536655 TAAATTTAAGTGTAAAATTAATTATTTTATTAAATAATA
1 TAAATTTAA--GT-AAATTAATTA-TTTATTAAATAATA
1536694 TAA
1 TAA
1536697 TGATTCGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
35 9 0.24
37 2 0.05
38 10 0.26
39 17 0.45
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (35 bp):
TAAATTTAAGTAAATTAATTATTTATTAAATAATA
Found at i:1538227 original size:19 final size:19
Alignment explanation
Indices: 1538205--1538249 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1538195 ATATATATAA
1538205 AAATATAATAT-AAATTATT
1 AAATATAATATAAAATT-TT
*
1538224 AAATAT-ATTTAAAATTTT
1 AAATATAATATAAAATTTT
1538242 AAATATAA
1 AAATATAA
1538250 ACATTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATATAATATAAAATTTT
Found at i:1538471 original size:24 final size:23
Alignment explanation
Indices: 1538442--1538506 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 23
1538432 ACATTGATAG
1538442 TAATATGATGTTATTATTTTGTAA
1 TAATAT-ATGTTATTATTTTGTAA
* *
1538466 TAATAT-TGATATT-TTTTGTAT
1 TAATATATGTTATTATTTTGTAA
*
1538487 TAATATTATTGTTAATATTT
1 TAATA-TA-TGTTATTATTT
1538507 AATATAATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
21 12 0.36
22 7 0.21
24 11 0.33
25 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.58
Consensus pattern (23 bp):
TAATATATGTTATTATTTTGTAA
Found at i:1538482 original size:21 final size:22
Alignment explanation
Indices: 1538453--1538493 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1538443 AATATGATGT
1538453 TATTATTTTGTAATAATATTGA
1 TATTATTTTGTAATAATATTGA
*
1538475 TATT-TTTTGTATTAATATT
1 TATTATTTTGTAATAATATT
1538494 ATTGTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TATTATTTTGTAATAATATTGA
Found at i:1552627 original size:27 final size:28
Alignment explanation
Indices: 1552568--1552626 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
1552558 AATTCGATTT
*
1552568 TAAAATTTTAAAATTTAATTAAATTAAA
1 TAAAATTTTAAAATTCAATTAAATTAAA
* *
1552596 TAAAATTTTAAAA-TCGATTGAATT-AA
1 TAAAATTTTAAAATTCAATTAAATTAAA
1552622 TAAAA
1 TAAAA
1552627 AAAATCTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 7 0.25
27 8 0.29
28 13 0.46
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (28 bp):
TAAAATTTTAAAATTCAATTAAATTAAA
Found at i:1552885 original size:18 final size:19
Alignment explanation
Indices: 1552870--1552907 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1552860 TTAAAAATTG
1552870 ATTGAATT-AATTAAATAA
1 ATTGAATTAAATTAAATAA
*
1552888 ATTGAATTAAATTAATTAA
1 ATTGAATTAAATTAAATAA
1552907 A
1 A
1552908 ATTAATTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (19 bp):
ATTGAATTAAATTAAATAA
Found at i:1553229 original size:21 final size:20
Alignment explanation
Indices: 1553192--1553230 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1553182 TTAAAATTCT
* *
1553192 AAAATTAAATTAAATAATCA
1 AAAATAAAAATAAATAATCA
1553212 AAAATAAAAATAATATAAT
1 AAAATAAAAATAA-ATAAT
1553231 ATATTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATAAAAATAAATAATCA
Found at i:1553725 original size:30 final size:28
Alignment explanation
Indices: 1553665--1553725 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 28
1553655 CTGAAGTGAG
* * * *
1553665 TTTAAATTTATTTTTTTATTTAAATTAA
1 TTTAAATTTATTTATTAATTAAAATAAA
1553693 TTTAAATCATTATTTATTAATTAAAATAAA
1 TTTAAAT--TTATTTATTAATTAAAATAAA
1553723 TTT
1 TTT
1553726 TTATTTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 7 0.26
30 20 0.74
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTAAATTTATTTATTAATTAAAATAAA
Found at i:1554003 original size:13 final size:13
Alignment explanation
Indices: 1553970--1554011 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
1553960 TAAAAATATT
* *
1553970 ATAATATATATTA
1 ATAATATAAATAA
1553983 AT-ATATAAATAA
1 ATAATATAAATAA
1553995 ATAATATAAATAA
1 ATAATATAAATAA
1554008 ATAA
1 ATAA
1554012 ATTATAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAATATAAATAA
Found at i:1554240 original size:15 final size:16
Alignment explanation
Indices: 1554215--1554247 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1554205 AATTTGATTC
1554215 AAATAATTATTATATA
1 AAATAATTATTATATA
*
1554231 AAAT-ATTATTATTTA
1 AAATAATTATTATATA
1554246 AA
1 AA
1554248 TAAAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATAATTATTATATA
Found at i:1554292 original size:17 final size:15
Alignment explanation
Indices: 1554270--1554318 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 15
1554260 TATTAATATA
*
1554270 AAATTAACTTTATTATT
1 AAATTAA-TTTA-AATT
1554287 AAATTATAATTTAAATT
1 AAA-T-TAATTTAAATT
1554304 AAATTAATTTAAATT
1 AAATTAATTTAAATT
1554319 TATAGAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 11 0.38
16 1 0.03
17 9 0.31
18 5 0.17
19 3 0.10
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATTAATTTAAATT
Found at i:1556507 original size:21 final size:22
Alignment explanation
Indices: 1556468--1556509 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1556458 AAAAAAAAAG
1556468 AGCAAATATAACAAATTTTTGA
1 AGCAAATATAACAAATTTTTGA
*
1556490 AGCAAA-AGTAACAATTTTTT
1 AGCAAATA-TAACAAATTTTT
1556510 TTAATCAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (22 bp):
AGCAAATATAACAAATTTTTGA
Found at i:1558472 original size:31 final size:32
Alignment explanation
Indices: 1558413--1558474 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
1558403 TTTAATTTAA
*
1558413 ATAAATATTTTTATTATAATTTTATTAAATAT
1 ATAAATATTTTTATTATAATTATATTAAATAT
*
1558445 ATAAATATTTTATATT-T-ATTATGTTAAATA
1 ATAAATATTTT-TATTATAATTATATTAAATA
1558475 AATATTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 11 0.41
32 12 0.44
33 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (32 bp):
ATAAATATTTTTATTATAATTATATTAAATAT
Found at i:1558610 original size:31 final size:31
Alignment explanation
Indices: 1558575--1558657 Score: 77
Period size: 31 Copynumber: 2.8 Consensus size: 31
1558565 TTATATATTA
**
1558575 AATATTATATTAATATTTATTTAATAATTTT
1 AATATTATATTAATATTTATTTAATAAAATT
*
1558606 AATATTAAATATTCATA--TATTTAATAAAATT
1 AATATT--ATATTAATATTTATTTAATAAAATT
*
1558637 -ATA--ATATAAATATTTATTTAA
1 AATATTATATTAATATTTATTTAA
1558658 ATCAAATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
26 7 0.16
28 7 0.16
30 3 0.07
31 18 0.42
33 8 0.19
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (31 bp):
AATATTATATTAATATTTATTTAATAAAATT
Found at i:1558618 original size:33 final size:31
Alignment explanation
Indices: 1558581--1558650 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 31
1558571 ATTAAATATT
*
1558581 ATATTAATATTTATTTAAT-AATTTTAATATTAA
1 ATATTAATA--TATTTAATAAATTATAATA-TAA
*
1558614 ATATTCATATATTTAATAAAATTATAATATAA
1 ATATTAATATATTTAAT-AAATTATAATATAA
1558646 ATATT
1 ATATT
1558651 TATTTAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
31 8 0.24
32 8 0.24
33 17 0.52
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (31 bp):
ATATTAATATATTTAATAAATTATAATATAA
Found at i:1562260 original size:28 final size:31
Alignment explanation
Indices: 1562222--1562295 Score: 78
Period size: 33 Copynumber: 2.3 Consensus size: 31
1562212 ATTTAAATTT
* *
1562222 AAATTAGTATTTATAAATT-AATAAAAATAAA
1 AAATTATTATATAT-AATTAAATAAAAATAAA
**
1562253 AAATTATTTTATATATAATTAAATGTAAATAAA
1 AAATTA--TTATATATAATTAAATAAAAATAAA
1562286 AAATTATTAT
1 AAATTATTAT
1562296 TTAATAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
31 10 0.28
32 4 0.11
33 22 0.61
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (31 bp):
AAATTATTATATATAATTAAATAAAAATAAA
Found at i:1565369 original size:10 final size:10
Alignment explanation
Indices: 1565350--1565397 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
1565340 AAGCAGCACA
*
1565350 ATATATATAT
1 ATATAAATAT
1565360 ATATAAATAT
1 ATATAAATAT
*
1565370 ATATAAATAA
1 ATATAAATAT
1565380 ATAATAAATA-
1 AT-ATAAATAT
1565390 A-ATAAATA
1 ATATAAATA
1565398 AATAATAGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 7 0.20
10 21 0.60
11 7 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
ATATAAATAT
Found at i:1565369 original size:12 final size:12
Alignment explanation
Indices: 1565358--1565416 Score: 63
Period size: 11 Copynumber: 5.1 Consensus size: 12
1565348 CAATATATAT
1565358 ATATATAAAT--
1 ATATATAAATAA
1565368 ATATATAAATAA
1 ATATATAAATAA
1565380 ATA-ATAAATAA
1 ATATATAAATAA
*
1565391 ATAAATAAAT-A
1 ATATATAAATAA
1565402 ATAGTCATAAATAA
1 ATA-T-ATAAATAA
1565416 A
1 A
1565417 ATGCCCAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
10 10 0.24
11 15 0.36
12 9 0.21
13 6 0.14
14 2 0.05
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (12 bp):
ATATATAAATAA
Found at i:1565390 original size:25 final size:25
Alignment explanation
Indices: 1565363--1565416 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1565353 TATATATATA
1565363 TAAATATATATAAATAA-A-TAATAAA
1 TAAATA-A-ATAAATAATAGTAATAAA
*
1565388 TAAATAAATAAATAATAGTCATAAA
1 TAAATAAATAAATAATAGTAATAAA
1565413 TAAA
1 TAAA
1565417 ATGCCCAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 8 0.31
24 2 0.08
25 16 0.62
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (25 bp):
TAAATAAATAAATAATAGTAATAAA
Found at i:1565404 original size:15 final size:15
Alignment explanation
Indices: 1565362--1565398 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1565352 ATATATATAT
*
1565362 ATAAAT-ATATATAA
1 ATAAATAATAAATAA
1565376 ATAAATAATAAATAA
1 ATAAATAATAAATAA
1565391 ATAAATAA
1 ATAAATAA
1565399 ATAATAGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATAAATAATAAATAA
Found at i:1565416 original size:4 final size:4
Alignment explanation
Indices: 1565362--1565402 Score: 57
Period size: 4 Copynumber: 10.0 Consensus size: 4
1565352 ATATATATAT
1565362 ATAA ATATA TATAA ATAA AT-A ATAA ATAA ATAA ATAA ATAA
1 ATAA ATA-A -ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1565403 TAGTCATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 3 0.09
4 26 0.76
5 2 0.06
6 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAA
Found at i:1567455 original size:6 final size:6
Alignment explanation
Indices: 1567444--1567470 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1567434 TTTAATATTA
1567444 TTATAT TTATAT TTATAT TTATAT TTA
1 TTATAT TTATAT TTATAT TTATAT TTA
1567471 AATAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTATAT
Found at i:1567761 original size:2 final size:2
Alignment explanation
Indices: 1567754--1567810 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
1567744 GAATTGATCC
* *
1567754 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1567796 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1567811 GGGATAATCC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1570529 original size:11 final size:12
Alignment explanation
Indices: 1570510--1570547 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
1570500 TATTTATTAA
1570510 ATATGTTATATTT
1 ATAT-TTATATTT
1570523 ATATTATATATTT
1 ATATT-TATATTT
1570536 ATA-TTATATTT
1 ATATTTATATTT
1570547 A
1 A
1570548 AAATTATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.33
12 2 0.08
13 14 0.58
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (12 bp):
ATATTTATATTT
Found at i:1570532 original size:13 final size:13
Alignment explanation
Indices: 1570516--1570544 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1570506 TTAAATATGT
1570516 TATATTTATATTA
1 TATATTTATATTA
1570529 TATATTTATATTA
1 TATATTTATATTA
1570542 TAT
1 TAT
1570545 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATATTTATATTA
Found at i:1571218 original size:34 final size:34
Alignment explanation
Indices: 1571162--1571345 Score: 237
Period size: 34 Copynumber: 5.4 Consensus size: 34
1571152 AGTGTGGAAT
*
1571162 TTGTTGATTAAAT-GGTGATTTGGTAGTTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* * *
1571195 TTGTTGATTAAATGGGTGATTTGGTGGTTTGCCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* *
1571229 TTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
*
1571263 TTGTTGATTAAATGGGTGATTTGGTGGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* * * * *
1571297 TTATTGACTAAAT-GGTATATTTGGTAGGTTGCCA
1 TTGTTGATTAAATGGGT-GATTTGGTAGCTTACCA
1571331 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
1571346 TGGTTTTTAC
Statistics
Matches: 130, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
33 16 0.12
34 113 0.87
35 1 0.01
ACGTcount: A:0.23, C:0.08, G:0.27, T:0.42
Consensus pattern (34 bp):
TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
Found at i:1571270 original size:68 final size:68
Alignment explanation
Indices: 1571162--1571345 Score: 271
Period size: 68 Copynumber: 2.7 Consensus size: 68
1571152 AGTGTGGAAT
* * * * *
1571162 TTGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 TTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
1571226 CCA
66 CCA
1571229 TTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
1 TTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
1571294 CCA
66 CCA
* * * * *
1571297 TTATTGACTAAATGGTATATTTGGTAGGTTGCCATTGTTGATTAAATGG
1 TTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGG
1571346 TGGTTTTTAC
Statistics
Matches: 106, Mismatches: 10, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
67 12 0.11
68 94 0.89
ACGTcount: A:0.23, C:0.08, G:0.27, T:0.42
Consensus pattern (68 bp):
TTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
CCA
Found at i:1571337 original size:102 final size:101
Alignment explanation
Indices: 1571162--1571345 Score: 273
Period size: 102 Copynumber: 1.8 Consensus size: 101
1571152 AGTGTGGAAT
* * *
1571162 TTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGC
1 TTGTTGATTAAATGGTGATTTGGTAGCTTACCATTATTGACTAAATGGGTGATTTGGTGGTTTGC
1571227 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
66 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
* *
1571263 TTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTATTGACTAAAT-GGTATATTTGGTAGG-T
1 TTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTATTGACTAAATGGGT-GATTTGGT-GGTT
*
1571326 TGCCATTGTTGATTAAATGG
63 TGCCATTGTTGACTAAATGG
1571346 TGGTTTTTAC
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
101 16 0.22
102 56 0.76
103 2 0.03
ACGTcount: A:0.23, C:0.08, G:0.27, T:0.42
Consensus pattern (101 bp):
TTGTTGATTAAATGGTGATTTGGTAGCTTACCATTATTGACTAAATGGGTGATTTGGTGGTTTGC
CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
Found at i:1575811 original size:34 final size:34
Alignment explanation
Indices: 1575754--1575938 Score: 239
Period size: 34 Copynumber: 5.5 Consensus size: 34
1575744 AAGTGGGAGA
*
1575754 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1575787 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1575821 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
*
1575855 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * * *
1575889 ATTATTGACTAAAT-GGTATATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
1575923 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1575939 TGGTTTTTAC
Statistics
Matches: 131, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
33 17 0.13
34 113 0.86
35 1 0.01
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.42
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:1575854 original size:68 final size:68
Alignment explanation
Indices: 1575754--1575938 Score: 273
Period size: 68 Copynumber: 2.7 Consensus size: 68
1575744 AAGTGGGAGA
* * * *
1575754 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTT
1 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
*
1575818 GCC
66 ACC
1575821 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
1575886 ACC
66 ACC
* * * * *
1575889 ATTATTGACTAAATGGTATATTTGGTAGGTTGCCATTGTTGATTAAATGG
1 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGG
1575939 TGGTTTTTAC
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
67 13 0.12
68 94 0.88
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.42
Consensus pattern (68 bp):
ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
ACC
Found at i:1575902 original size:102 final size:101
Alignment explanation
Indices: 1575754--1575938 Score: 275
Period size: 102 Copynumber: 1.8 Consensus size: 101
1575744 AAGTGGGAGA
* * *
1575754 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGT-GATTTGGT-GGTT
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTATTGACTAAAT-GGTAGATTTGGTAGG-T
1575817 TGCCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
64 TGCCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
* *
1575855 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTATTGACTAAATGGTATATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTATTGACTAAATGGTAGATTTGGTAGGTT
*
1575920 GCCATTGTTGATTAAATGG
65 GCCATTGTTGACTAAATGG
1575939 TGGTTTTTAC
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
101 17 0.23
102 56 0.75
103 2 0.03
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.42
Consensus pattern (101 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTATTGACTAAATGGTAGATTTGGTAGGTTG
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:1578298 original size:13 final size:14
Alignment explanation
Indices: 1578280--1578308 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1578270 TGATTTATTT
1578280 TGGAAAAATT-GTA
1 TGGAAAAATTCGTA
1578293 TGGAAAAATTCGTA
1 TGGAAAAATTCGTA
1578307 TG
1 TG
1578309 AACTTCAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (14 bp):
TGGAAAAATTCGTA
Found at i:1578904 original size:33 final size:32
Alignment explanation
Indices: 1578831--1578906 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 32
1578821 GTTTAAATTT
1578831 AAATTATTATTTATA-AATTAATAAAAATAAAA
1 AAATTATT-TTTATATAATTAATAAAAATAAAA
* *
1578863 AAAATATTTTATATATAATTAAATATAAAT-AAA
1 AAATTATTTT-TATATAATT-AATAAAAATAAAA
1578896 AAATTATTTTT
1 AAATTATTTTT
1578907 TAATAATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
31 2 0.05
32 12 0.32
33 16 0.42
34 8 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
AAATTATTTTTATATAATTAATAAAAATAAAA
Found at i:1580315 original size:28 final size:27
Alignment explanation
Indices: 1580275--1580329 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
1580265 TCAAATTGTT
1580275 ATTTAATAATAAAAATATTA-TTATTTAA
1 ATTTAATAAT--AAATATTATTTATTTAA
*
1580303 ATTTAATTATAAATATTATTTATTTAA
1 ATTTAATAATAAATATTATTTATTTAA
1580330 TTATTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 8 0.32
27 8 0.32
28 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTTAATAATAAATATTATTTATTTAA
Found at i:1581802 original size:2 final size:2
Alignment explanation
Indices: 1581795--1581839 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
1581785 TCCGGGGCTA
* *
1581795 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1581837 AT A
1 AT A
1581840 CACACACAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1582179 original size:35 final size:34
Alignment explanation
Indices: 1582124--1582189 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
1582114 TATGTATATA
*
1582124 TATATATTTAAATTTAATTT-AATTTAGTTTAAAG
1 TATAAATTTAAATTTAATTTAAATTTA-TTTAAAG
*
1582158 TATAAATTTAAAATTTTATTTAAATTTATTTA
1 TATAAATTT-AAATTTAATTTAAATTTATTTA
1582190 TATTTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 8 0.29
35 14 0.50
36 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (34 bp):
TATAAATTTAAATTTAATTTAAATTTATTTAAAG
Found at i:1582187 original size:10 final size:10
Alignment explanation
Indices: 1582128--1582229 Score: 64
Period size: 10 Copynumber: 9.6 Consensus size: 10
1582118 TATATATATA
1582128 TATTTAAATT
1 TATTTAAATT
1582138 TAATTT-AATT
1 T-ATTTAAATT
1582148 TAGTTTAAAGTAT
1 TA-TTTAAA-T-T
*
1582161 AAATTTAAAATTT
1 -TATTT-AAA-TT
1582174 TATTTAAATT
1 TATTTAAATT
*
1582184 TATTTATATT
1 TATTTAAATT
** *
1582194 TATAAAAAAT
1 TATTTAAATT
*
1582204 AATTT-AATT
1 TATTTAAATT
1582213 TCATTTAAATT
1 T-ATTTAAATT
1582224 TATTTA
1 TATTTA
1582230 TATTAATTTT
Statistics
Matches: 70, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
9 4 0.06
10 37 0.53
11 14 0.20
12 5 0.07
13 5 0.07
14 5 0.07
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (10 bp):
TATTTAAATT
Found at i:1582258 original size:23 final size:22
Alignment explanation
Indices: 1582205--1582281 Score: 65
Period size: 25 Copynumber: 3.5 Consensus size: 22
1582195 ATAAAAAATA
1582205 ATTTAATTTCATTTAAATTTATTT
1 ATTTAATTT--TTTAAATTTATTT
1582229 ATATTAATTTTTTAAATATATATTT
1 AT-TTAATTTTTTAAAT-T-TATTT
1582254 -TTTAA--TTTT-AATATT-TTT
1 ATTTAATTTTTTAAAT-TTATTT
1582272 ATTTAATTTT
1 ATTTAATTTT
1582282 AAAATATAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 15
0.76 0.00 0.24
Matches are distributed among these distances:
18 3 0.06
19 6 0.13
20 5 0.11
21 6 0.13
23 11 0.23
24 4 0.09
25 12 0.26
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTTAATTTTTTAAATTTATTT
Found at i:1582579 original size:98 final size:99
Alignment explanation
Indices: 1582413--1582601 Score: 272
Period size: 98 Copynumber: 1.9 Consensus size: 99
1582403 ATATGATGAT
* * * *
1582413 ATATGTATTTTAAAATATAATAAAAAATTAATTAAAATTAAAACAAAATACGTGATAAATCTTAA
1 ATATATATTTTAAAATATAATAAAAAATTAATTAAAAATAAAACAAAACACGTAATAAATCTTAA
** *
1582478 TTTACTTGTAAAATTAAAAAATATTAACACGATA
66 TTTACTCATAAAATTAAAAAAAATTAACACGATA
* * *
1582512 ATATATATTTTAAAATATAAT-AAAAATTAATTAAAAATAAAATAAAACATGTAATAACTCTTAA
1 ATATATATTTTAAAATATAATAAAAAATTAATTAAAAATAAAACAAAACACGTAATAAATCTTAA
*
1582576 TTTACTCATAAATTTAAAAAAAATTA
66 TTTACTCATAAAATTAAAAAAAATTA
1582602 CTGTAACTAT
Statistics
Matches: 79, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
98 59 0.75
99 20 0.25
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (99 bp):
ATATATATTTTAAAATATAATAAAAAATTAATTAAAAATAAAACAAAACACGTAATAAATCTTAA
TTTACTCATAAAATTAAAAAAAATTAACACGATA
Found at i:1582718 original size:16 final size:17
Alignment explanation
Indices: 1582697--1582734 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1582687 TTAATAACAA
1582697 AAATTAA-CTCATTTTT
1 AAATTAACCTCATTTTT
*
1582713 AAATTAACCTTATTTTT
1 AAATTAACCTCATTTTT
*
1582730 TAATT
1 AAATT
1582735 TATTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATTAACCTCATTTTT
Found at i:1583749 original size:19 final size:19
Alignment explanation
Indices: 1583704--1583750 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1583694 TAATTATTTT
1583704 TATATAAATATTTAAATATA
1 TATATAAATA-TTAAATATA
*
1583724 TAT-TAAATA-TAAATTTA
1 TATATAAATATTAAATATA
1583741 CTATATAAAT
1 -TATATAAAT
1583751 TTATTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 7 0.29
18 3 0.12
19 11 0.46
20 3 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
TATATAAATATTAAATATA
Found at i:1585668 original size:20 final size:19
Alignment explanation
Indices: 1585636--1585674 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1585626 TAAATTATAA
*
1585636 TCAAAATTTAAAAATTTAT
1 TCAAAATTTAAAAAGTTAT
*
1585655 TCAATATTTAAAAAAGTTAT
1 TCAAAATTT-AAAAAGTTAT
1585675 GAAATGAGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (19 bp):
TCAAAATTTAAAAAGTTAT
Found at i:1585845 original size:18 final size:18
Alignment explanation
Indices: 1585805--1585837 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1585795 AATATTATAA
1585805 TATAAGCATTATTAAAAT
1 TATAAGCATTATTAAAAT
1585823 TATAA-CATT-TTAAAA
1 TATAAGCATTATTAAAA
1585838 CTTAATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (18 bp):
TATAAGCATTATTAAAAT
Found at i:1587093 original size:39 final size:37
Alignment explanation
Indices: 1587050--1587168 Score: 100
Period size: 39 Copynumber: 3.1 Consensus size: 37
1587040 ATATATCATA
1587050 TTAATTATATTTAATTATATTATTTTATATTTAATTTTT
1 TTAA-TATATTTAATTATATTATTTTATA-TTAATTTTT
* ** *
1587089 TTAATATTTATTAAACATATTATATTATATT-ATGTTTT
1 TTAATATAT-TTAATTATATTATTTTATATTAAT-TTTT
* *
1587127 TTAACATATTTAAAATTTTA-TATATTTATA-TAATTTTT
1 TTAATATATTT--AATTATATTAT-TTTATATTAATTTTT
1587165 TTAA
1 TTAA
1587169 GAAAATGACG
Statistics
Matches: 64, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
37 4 0.06
38 29 0.45
39 31 0.48
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.61
Consensus pattern (37 bp):
TTAATATATTTAATTATATTATTTTATATTAATTTTT
Found at i:1587382 original size:16 final size:16
Alignment explanation
Indices: 1587361--1587391 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1587351 AAAATTTAAG
1587361 TTATCTTTAAATAAAT
1 TTATCTTTAAATAAAT
*
1587377 TTATCTTTACATAAA
1 TTATCTTTAAATAAA
1587392 AATTTTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATCTTTAAATAAAT
Found at i:1587827 original size:21 final size:21
Alignment explanation
Indices: 1587765--1587828 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 21
1587755 ATTGAAGTGG
* *
1587765 TTGAGTTTAAATGAGAATTT-T
1 TTGA-TTTAAATTAGTATTTAT
1587786 TTGATTTAAATTAGT-TTTAT
1 TTGATTTAAATTAGTATTTAT
*
1587806 TTGATTTAAATTATTATTTAT
1 TTGATTTAAATTAGTATTTAT
1587827 TT
1 TT
1587829 TAAAAAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 3 0.08
20 24 0.63
21 11 0.29
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (21 bp):
TTGATTTAAATTAGTATTTAT
Found at i:1589798 original size:2 final size:2
Alignment explanation
Indices: 1589787--1589817 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1589777 AAAAAACTGA
*
1589787 AT AT AC 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
1589818 CCAGTGTCGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1592325 original size:29 final size:29
Alignment explanation
Indices: 1592275--1592353 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 29
1592265 CGATAATTCG
* * *
1592275 TTTTAATATTTTATTT-ATATATTTTA-A
1 TTTTTATAATTTATTTAAAATATTTTATA
1592302 TCTTTTATAATTTATTTAAAATATTTTATA
1 T-TTTTATAATTTATTTAAAATATTTTATA
* *
1592332 TTTATATAAATTA--TAAAATATT
1 TTTTTATAATTTATTTAAAATATT
1592354 AATTTATTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
27 10 0.23
28 13 0.30
29 19 0.43
30 2 0.05
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTTTATAATTTATTTAAAATATTTTATA
Found at i:1592366 original size:14 final size:14
Alignment explanation
Indices: 1592326--1592381 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
1592316 TTTAAAATAT
*
1592326 TTTATATTTATATAA
1 TTTATA-TTATATTA
* **
1592341 ATTATAAAATATTAA
1 TTTATATTATATT-A
1592356 TTTAT-TTATATTA
1 TTTATATTATATTA
1592369 TTTATATTATATT
1 TTTATATTATATT
1592382 TTAATTATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
13 6 0.19
14 16 0.50
15 10 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTATATTATATTA
Found at i:1592404 original size:11 final size:11
Alignment explanation
Indices: 1592358--1592406 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
1592348 AATATTAATT
1592358 TATTTATA-T-
1 TATTTATATTA
1592367 TATTTATATTA
1 TATTTATATTA
1592378 TATTT-TAATTA
1 TATTTAT-ATTA
*
1592389 T-TTTATATCA
1 TATTTATATTA
1592399 TATTTATA
1 TATTTATA
1592407 ACTAATGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
9 8 0.24
10 9 0.26
11 17 0.50
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTTATATTA
Found at i:1593082 original size:27 final size:26
Alignment explanation
Indices: 1593044--1593095 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
1593034 TTATAATCGT
*
1593044 ATTTAAATTATT-TTATATTTATATAA
1 ATTTAAATTATTAATA-ATTTATATAA
*
1593070 ATTTTAATATATTAATAATTTATATA
1 ATTTAAAT-TATTAATAATTTATATA
1593096 TTCATGTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 7 0.32
27 13 0.59
28 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTTAAATTATTAATAATTTATATAA
Found at i:1593512 original size:30 final size:28
Alignment explanation
Indices: 1593471--1593605 Score: 81
Period size: 27 Copynumber: 4.9 Consensus size: 28
1593461 AAAATCATAA
*
1593471 ATATTATATTTATATATTTTTATAATATT
1 ATATAATATTTATATATTTTTATAAT-TT
* *
1593500 ATAATAATATTTA-AAATAATTTAT-ATTT
1 AT-ATAATATTTATATAT-TTTTATAATTT
* *
1593528 ATATAA-ATATTA-ATATGTTAATAATTT
1 ATATAATAT-TTATATATTTTTATAATTT
1593555 ATTATAAT-TTTATAT-TATTTT-TAATATT
1 A-TATAATATTTATATAT-TTTTATAAT-TT
*
1593583 ATATTATATTT-TA-ATTATTTATA
1 ATATAATATTTATATATT-TTTATA
1593606 CGTAATTATA
Statistics
Matches: 84, Mismatches: 9, Indels: 27
0.70 0.08 0.22
Matches are distributed among these distances:
26 7 0.08
27 34 0.40
28 22 0.26
29 7 0.08
30 14 0.17
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (28 bp):
ATATAATATTTATATATTTTTATAATTT
Found at i:1593601 original size:19 final size:19
Alignment explanation
Indices: 1593554--1593601 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 19
1593544 GTTAATAATT
*
1593554 TATTATAATT-TTATATTA
1 TATTTTAATTATTATATTA
1593572 T-TTTTAA-TATTATATTA
1 TATTTTAATTATTATATTA
1593589 TATTTTAATTATT
1 TATTTTAATTATT
1593602 TATACGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.04
17 14 0.54
18 7 0.27
19 4 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTTAATTATTATATTA
Found at i:1593614 original size:30 final size:31
Alignment explanation
Indices: 1593546--1593644 Score: 88
Period size: 30 Copynumber: 3.3 Consensus size: 31
1593536 ATTAATATGT
*
1593546 TAATAATT-TATTATAATTTTATATTATTTT
1 TAATAATTATATTATAATTTTATATTATTTA
1593576 TAAT-ATTATATTAT-ATTTTA-ATTATTTA
1 TAATAATTATATTATAATTTTATATTATTTA
*
1593604 TACGTAATTATATCGTATAA--TTATATTATATT-
1 TA-ATAATTATAT--TATAATTTTATATTAT-TTA
1593636 TAAT-ATTAT
1 TAATAATTAT
1593645 TTAATTTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
28 9 0.16
29 10 0.17
30 22 0.38
31 4 0.07
32 10 0.17
33 3 0.05
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (31 bp):
TAATAATTATATTATAATTTTATATTATTTA
Found at i:1593766 original size:8 final size:8
Alignment explanation
Indices: 1593753--1593842 Score: 82
Period size: 8 Copynumber: 11.5 Consensus size: 8
1593743 ATATTCATAC
1593753 ATATATTT
1 ATATATTT
1593761 ATATATTT
1 ATATATTT
1593769 -TAT-TTT
1 ATATATTT
*
1593775 ATTATAATT
1 A-TATATTT
*
1593784 ATAT-TTA
1 ATATATTT
*
1593791 AAATATTT
1 ATATATTT
1593799 -TATATTT
1 ATATATTT
1593806 ATATATTTT
1 ATATA-TTT
*
1593815 AATATATTA
1 -ATATATTT
1593824 ATA-ATTT
1 ATATATTT
1593831 ATATATTT
1 ATATATTT
1593839 ATAT
1 ATAT
1593843 TATATTTATA
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
6 3 0.05
7 19 0.29
8 31 0.47
9 8 0.12
10 5 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATATATTT
Found at i:1593771 original size:29 final size:29
Alignment explanation
Indices: 1593738--1593867 Score: 90
Period size: 29 Copynumber: 4.4 Consensus size: 29
1593728 AAATTTAAAA
*
1593738 TTTATATATTCATACA-TATATTT-ATATAT
1 TTTATATATT-ATA-ATTATATTTAAAATAT
*
1593767 TTTATTTTATTATAATTATATTTAAAATAT
1 TTTA-TATATTATAATTATATTTAAAATAT
* * * *
1593797 TTTATAT-TTATATATTTTAATATATTAATAA
1 TTTATATATTATA-ATTAT-ATTTA-AAATAT
*
1593828 TTTATATATT-TATATTATATTTATAATAT
1 TTTATATATTATA-ATTATATTTAAAATAT
*
1593857 TTTTTAT-TTAT
1 TTTATATATTAT
1593868 TACTATGTTA
Statistics
Matches: 82, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
28 8 0.10
29 32 0.39
30 22 0.27
31 18 0.22
32 2 0.02
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTATATATTATAATTATATTTAAAATAT
Found at i:1593801 original size:16 final size:16
Alignment explanation
Indices: 1593782--1593866 Score: 58
Period size: 16 Copynumber: 5.6 Consensus size: 16
1593772 TTTATTATAA
1593782 TTATATTTAAAATATT
1 TTATATTTAAAATATT
*
1593798 TTATATTT-ATATATT
1 TTATATTTAAAATATT
1593813 TTAATATATTAATAAT-TT
1 TT-ATAT-TTAA-AATATT
*
1593831 ATATATTT---ATA--
1 TTATATTTAAAATATT
*
1593842 TTATATTTATAATATT
1 TTATATTTAAAATATT
*
1593858 TTTTATTTA
1 TTATATTTA
1593867 TTACTATGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 20
0.68 0.06 0.25
Matches are distributed among these distances:
11 7 0.13
12 2 0.04
14 3 0.06
15 8 0.15
16 22 0.41
17 6 0.11
18 4 0.07
19 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATATTTAAAATATT
Found at i:1593804 original size:45 final size:43
Alignment explanation
Indices: 1593754--1593882 Score: 125
Period size: 45 Copynumber: 2.9 Consensus size: 43
1593744 TATTCATACA
* *
1593754 TATATTTATATATTTTATTTTATTATAATTATATTTAAAATATTT
1 TATATTTATATATTTTATTTTATTATAATT-TATAT-AAATATAT
* * **
1593799 TATATTTATATATTTTAATATATTAATAATTTATATATTTATAT
1 TATATTTATATATTTTATTTTATT-ATAATTTATATAAATATAT
*
1593843 TATATTTATAATATTTTTTATTTATTACT-ATGTTATATAA
1 TATATTTAT-ATATTTTAT-TTTATTA-TAAT-TTATATAA
1593883 TGTACTGAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
44 14 0.20
45 36 0.52
46 19 0.28
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (43 bp):
TATATTTATATATTTTATTTTATTATAATTTATATAAATATAT
Found at i:1593815 original size:25 final size:25
Alignment explanation
Indices: 1593783--1593838 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
1593773 TTATTATAAT
*
1593783 TATA-TTTAAAATATT-TTATATTTA
1 TATATTTTAAAATATTAATA-ATTTA
*
1593807 TATATTTTAATATATTAATAATTTA
1 TATATTTTAAAATATTAATAATTTA
1593832 TATATTT
1 TATATTT
1593839 ATATTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 4 0.14
25 22 0.79
26 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TATATTTTAAAATATTAATAATTTA
Found at i:1594064 original size:5 final size:5
Alignment explanation
Indices: 1594047--1594099 Score: 56
Period size: 5 Copynumber: 10.6 Consensus size: 5
1594037 AATTTTAAAA
* *
1594047 TATAT TCATAT TATAT TATAT TATAT TATAAT TAT-T TATTT TTTA- TATAT
1 TATAT T-ATAT TATAT TATAT TATAT TAT-AT TATAT TATAT TATAT TATAT
1594097 TAT
1 TAT
1594100 CGAATAATGA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
4 7 0.17
5 24 0.59
6 10 0.24
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:1594282 original size:9 final size:9
Alignment explanation
Indices: 1594270--1594367 Score: 53
Period size: 9 Copynumber: 10.9 Consensus size: 9
1594260 TATTATAATT
1594270 ATATTTTAA
1 ATATTTTAA
*
1594279 ATATTTTAT
1 ATATTTTAA
1594288 AT-TTTTATA
1 ATATTTTA-A
1594297 A-ATTTT-A
1 ATATTTTAA
*
1594304 ATATATTAA
1 ATATTTTAA
*
1594313 ATA--ATAA
1 ATATTTTAA
* *
1594320 TTATATTAA
1 ATATTTTAA
*
1594329 TATTTTTTAAA
1 -ATATTTT-AA
*
1594340 ATATTTTATT
1 ATATTTTA-A
1594350 ATATTTTAA
1 ATATTTTAA
1594359 ATATATTTA
1 ATAT-TTTA
1594368 TATAATATTA
Statistics
Matches: 67, Mismatches: 12, Indels: 19
0.68 0.12 0.19
Matches are distributed among these distances:
7 7 0.10
8 9 0.13
9 27 0.40
10 22 0.33
11 2 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
ATATTTTAA
Found at i:1594353 original size:44 final size:42
Alignment explanation
Indices: 1594289--1594376 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 42
1594279 ATATTTTATA
*
1594289 TTTTTATAAATTTTAATATA-TTAAATAATAATTATATTAATAT
1 TTTTTAAAAATTTTAATATATTTAAAT-ATAATTATA-TAATAT
* *
1594332 TTTTTAAAATATTTTATTATATTTTAAATATATTTATATAATAT
1 TTTTTAAAA-ATTTTAATATA-TTTAAATATAATTATATAATAT
1594376 T
1 T
1594377 ATACGTATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
43 8 0.21
44 17 0.44
45 8 0.21
46 6 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (42 bp):
TTTTTAAAAATTTTAATATATTTAAATATAATTATATAATAT
Found at i:1594982 original size:6 final size:6
Alignment explanation
Indices: 1594973--1595007 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1594963 GATTAAAGTT
*
1594973 AAAAAG AAAAGG AAAAA- AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
1595008 TTTGATTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1594995 original size:17 final size:17
Alignment explanation
Indices: 1594973--1595006 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1594963 GATTAAAGTT
*
1594973 AAAAAGAAAAGGAAAAA
1 AAAAAGAAAAAGAAAAA
1594990 AAAAAGAAAAAGAAAAA
1 AAAAAGAAAAAGAAAAA
1595007 GTTTGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAGAAAAA
Found at i:1599471 original size:15 final size:17
Alignment explanation
Indices: 1599438--1599474 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1599428 TTGGATTCAG
1599438 ATGTTAGATATATGTAT
1 ATGTTAGATATATGTAT
*
1599455 ATGTTCGATATA-G-AT
1 ATGTTAGATATATGTAT
1599470 ATGTT
1 ATGTT
1599475 TAATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 1 0.05
17 11 0.58
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (17 bp):
ATGTTAGATATATGTAT
Found at i:1605305 original size:24 final size:23
Alignment explanation
Indices: 1605278--1605323 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
1605268 GTAAATATAA
1605278 AATACAAATGATATATAGTAATTT
1 AATACAAATGATATATA-TAATTT
* * *
1605302 AATATATATTATATATATAATT
1 AATACAAATGATATATATAATT
1605324 AAAAATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.43
Consensus pattern (23 bp):
AATACAAATGATATATATAATTT
Found at i:1609153 original size:17 final size:17
Alignment explanation
Indices: 1609117--1609162 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
1609107 AAATGATCTG
*
1609117 AACTCGAAAATAA-CTCA
1 AACTCG-AAATAACCTAA
1609134 AACTCGAAATAACCTAA
1 AACTCGAAATAACCTAA
*
1609151 AAC-CCAAATAAC
1 AACTCGAAATAAC
1609163 ACGAACACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.54, C:0.26, G:0.04, T:0.15
Consensus pattern (17 bp):
AACTCGAAATAACCTAA
Found at i:1610370 original size:2 final size:2
Alignment explanation
Indices: 1610359--1610392 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1610349 TAAATTAGAA
1610359 AT AT -T 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 AT A
1610393 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1610397 original size:2 final size:2
Alignment explanation
Indices: 1610392--1610416 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1610382 ATATATATAT
1610392 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 A
1610417 AATTATTGTG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1610976 original size:19 final size:20
Alignment explanation
Indices: 1610955--1610992 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
1610945 TAAAAAATAT
1610955 TTTTTAAA-TAAATA-ATTA
1 TTTTTAAATTAAATATATTA
1610973 TTTTTAAATTAAATATATTA
1 TTTTTAAATTAAATATATTA
1610993 AAATAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 6 0.33
20 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTTTAAATTAAATATATTA
Found at i:1611825 original size:12 final size:14
Alignment explanation
Indices: 1611815--1611933 Score: 57
Period size: 15 Copynumber: 8.0 Consensus size: 14
1611805 ATGATAATTT
1611815 TAAATATAATTATA
1 TAAATATAATTATA
1611829 TAAATATAAAATATATCA
1 TAAATAT--AAT-TAT-A
* *
1611847 TAAA-ATAAATATC
1 TAAATATAATTATA
*
1611860 TCAAAATATAAATAATA
1 T--AAATAT-AATTATA
*
1611877 TAAATTATAAATATA
1 TAAA-TATAATTATA
1611892 TTAAA-AT--TTATA
1 -TAAATATAATTATA
* *
1611904 TAAATATTAAATATTT
1 TAAATA-TAATTA-TA
1611920 TAAATATAATTATA
1 TAAATATAATTATA
1611934 ATATAATAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 30
0.65 0.10 0.25
Matches are distributed among these distances:
11 4 0.05
12 5 0.06
13 2 0.03
14 13 0.17
15 20 0.26
16 19 0.24
17 10 0.13
18 5 0.06
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAATATAATTATA
Found at i:1611831 original size:8 final size:8
Alignment explanation
Indices: 1611818--1611927 Score: 70
Period size: 7 Copynumber: 13.4 Consensus size: 8
1611808 ATAATTTTAA
*
1611818 ATATAATT
1 ATATAAAT
1611826 ATATAAAT
1 ATATAAAT
1611834 ATA-AAAT
1 ATATAAAT
1611841 ATATCATAA-
1 ATAT-A-AAT
1611850 A-ATAAAT
1 ATATAAAT
*
1611857 ATCTCAAA-
1 ATAT-AAAT
1611865 ATATAAAT
1 ATATAAAT
1611873 AATATAAAT
1 -ATATAAAT
1611882 -TATAAAT
1 ATATAAAT
1611889 ATATTAAAATTT
1 ATA-T-AAA--T
1611901 ATATAAAT
1 ATATAAAT
1611909 AT-TAAAT
1 ATATAAAT
*
1611916 ATTTTAAAT
1 A-TATAAAT
1611925 ATA
1 ATA
1611928 ATTATAATAT
Statistics
Matches: 83, Mismatches: 4, Indels: 30
0.71 0.03 0.26
Matches are distributed among these distances:
6 2 0.02
7 25 0.30
8 23 0.28
9 20 0.24
10 8 0.10
11 1 0.01
12 4 0.05
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAAAT
Found at i:1611858 original size:16 final size:16
Alignment explanation
Indices: 1611815--1611949 Score: 91
Period size: 16 Copynumber: 8.9 Consensus size: 16
1611805 ATGATAATTT
1611815 TAAATAT-AAT-TATA
1 TAAATATAAATATATA
1611829 TAAATATAAAATATATCA
1 TAAATAT-AAATATAT-A
*
1611847 TAAA-ATAAATATCTCA
1 TAAATATAAATATAT-A
1611863 -AAATATAAATA-ATA
1 TAAATATAAATATATA
1611877 TAAATTATAAATATAT-
1 TAAA-TATAAATATATA
1611893 TAAA-AT---T-TATA
1 TAAATATAAATATATA
*
1611904 TAAATATTAAATAT-TT
1 TAAATA-TAAATATATA
*
1611920 TAAATATAATTATA-A
1 TAAATATAAATATATA
1611935 TATAATA-AAATATAT
1 TA-AATATAAATATAT
1611950 GAATTATCAA
Statistics
Matches: 97, Mismatches: 6, Indels: 34
0.71 0.04 0.25
Matches are distributed among these distances:
10 3 0.03
11 5 0.05
12 1 0.01
13 1 0.01
14 10 0.10
15 21 0.22
16 43 0.44
17 8 0.08
18 5 0.05
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATATAAATATATA
Found at i:1611910 original size:18 final size:18
Alignment explanation
Indices: 1611865--1611919 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
1611855 ATATCTCAAA
*
1611865 ATATAAATAATATAAA-TT
1 ATATAAATATTA-AAATTT
1611883 ATA-AATATATTAAAATTT
1 ATATAA-ATATTAAAATTT
1611901 ATATAAATATTAAATATTT
1 ATATAAATATTAAA-ATTT
1611920 TAAATATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
17 5 0.16
18 21 0.66
19 6 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATAAATATTAAAATTT
Found at i:1612032 original size:17 final size:16
Alignment explanation
Indices: 1611997--1612032 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1611987 TAAAATGAGT
*
1611997 ATTTTAAAAAAAATTA
1 ATTTTAAAAAAAATAA
1612013 ATTTTAAAAAAATATAA
1 ATTTTAAAAAAA-ATAA
1612030 ATT
1 ATT
1612033 ATTTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTTTAAAAAAAATAA
Found at i:1618927 original size:4 final size:4
Alignment explanation
Indices: 1618909--1618956 Score: 78
Period size: 4 Copynumber: 11.8 Consensus size: 4
1618899 GTATAAAATG
*
1618909 TGTA TGAA TGATA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TG-TA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
1618957 TTTTCTGGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
4 38 0.93
5 3 0.07
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (4 bp):
TGTA
Found at i:1620285 original size:21 final size:22
Alignment explanation
Indices: 1620245--1620285 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1620235 TAACACGTAA
*
1620245 TAAAAATATTATATGATTATTT
1 TAAAAATATTACATGATTATTT
1620267 TAAAAATATTACATG-TTAT
1 TAAAAATATTACATGATTAT
1620286 AATTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (22 bp):
TAAAAATATTACATGATTATTT
Found at i:1620291 original size:22 final size:22
Alignment explanation
Indices: 1620245--1620292 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1620235 TAACACGTAA
* *
1620245 TAAAAATATTATATGATTATTT
1 TAAAAATATTACATGATTATAT
1620267 TAAAAATATTACATG-TTATAAT
1 TAAAAATATTACATGATTAT-AT
1620289 TAAA
1 TAAA
1620293 TTAAATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (22 bp):
TAAAAATATTACATGATTATAT
Found at i:1629918 original size:18 final size:17
Alignment explanation
Indices: 1629887--1629920 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1629877 AATAAAAATT
*
1629887 TAATAAATTTATTTAAA
1 TAATAAATTAATTTAAA
1629904 TAATCAAATTAATTTAA
1 TAAT-AAATTAATTTAA
1629921 TTTAAAAAAT
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:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATAAATTAATTTAAA
Found at i:1630048 original size:20 final size:20
Alignment explanation
Indices: 1630004--1630042 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1629994 ACGTAAAAAT
*
1630004 AATTTTAATTAAATTATTTA
1 AATTTTAAATAAATTATTTA
*
1630024 AATTTTAAATAATTTATTT
1 AATTTTAAATAAATTATTT
1630043 TTATTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AATTTTAAATAAATTATTTA
Found at i:1634771 original size:17 final size:17
Alignment explanation
Indices: 1634735--1634783 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
1634725 AGTTAATTTG
*
1634735 ATTTATATTAGATTATT
1 ATTTATATTAAATTATT
1634752 ATTTATATTATAATTA-T
1 ATTTATATTA-AATTATT
*
1634769 ATTTTTATTTAAATT
1 ATTTATA-TTAAATT
1634784 TAATTGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 21 0.75
18 7 0.25
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
ATTTATATTAAATTATT
Found at i:1634776 original size:23 final size:23
Alignment explanation
Indices: 1634737--1634788 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1634727 TTAATTTGAT
*
1634737 TTAT-ATTAGATTATTATTTATA
1 TTATAATTAGATTATTATTTAAA
* *
1634759 TTATAATTATATTTTTATTTAAA
1 TTATAATTAGATTATTATTTAAA
1634782 TT-TAATT
1 TTATAATT
1634789 GTAAAATAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
TTATAATTAGATTATTATTTAAA
Found at i:1639099 original size:29 final size:31
Alignment explanation
Indices: 1639057--1639117 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
1639047 TGGTACGGTT
1639057 ACATGATACAAAAAAATAAT-TAAA-ATATG
1 ACATGATACAAAAAAATAATATAAATATATG
** *
1639086 ACATGATATTAAAAAATTATATAAATATATG
1 ACATGATACAAAAAAATAATATAAATATATG
1639117 A
1 A
1639118 ATTTTTCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 17 0.63
30 4 0.15
31 6 0.22
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.30
Consensus pattern (31 bp):
ACATGATACAAAAAAATAATATAAATATATG
Found at i:1639471 original size:13 final size:13
Alignment explanation
Indices: 1639437--1639486 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
1639427 ATTTATATAT
1639437 TATAATT-AAAT-
1 TATAATTAAAATA
*
1639448 T-TAAATAAAATA
1 TATAATTAAAATA
1639460 TATAATTAAAATA
1 TATAATTAAAATA
1639473 TATTAATATAAAAT
1 TA-TAAT-TAAAAT
1639487 TAATATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 4 0.12
11 5 0.16
12 1 0.03
13 12 0.38
14 4 0.12
15 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TATAATTAAAATA
Found at i:1639484 original size:15 final size:15
Alignment explanation
Indices: 1639448--1639486 Score: 57
Period size: 13 Copynumber: 2.8 Consensus size: 15
1639438 ATAATTAAAT
1639448 TTAA-ATAAAATATA
1 TTAATATAAAATATA
1639462 -TAAT-TAAAATATA
1 TTAATATAAAATATA
1639475 TTAATATAAAAT
1 TTAATATAAAAT
1639487 TAATATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 12 0.55
14 4 0.18
15 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAATATAAAATATA
Found at i:1639754 original size:20 final size:19
Alignment explanation
Indices: 1639715--1639758 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1639705 AAATATTTTT
1639715 ATATAAATTTATATTAAAA
1 ATATAAATTTATATTAAAA
1639734 ATATAAATATTA-ATATAAAA
1 ATATAAAT-TTATAT-TAAAA
1639754 ATATA
1 ATATA
1639759 TTTAAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATAAATTTATATTAAAA
Found at i:1641628 original size:23 final size:24
Alignment explanation
Indices: 1641573--1641633 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 24
1641563 ATTTAATAGA
* *
1641573 ATTATATTTTATATTATATTCGTAT
1 ATTATATATTATATTATAATC-TAT
1641598 ATT-T-TATTATATTATAAT-TAT
1 ATTATATATTATATTATAATCTAT
1641619 ATTATATATTATATT
1 ATTATATATTATATT
1641634 TTATATTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 6 0.19
22 1 0.03
23 21 0.66
24 1 0.03
25 3 0.09
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
ATTATATATTATATTATAATCTAT
Found at i:1641676 original size:18 final size:18
Alignment explanation
Indices: 1641580--1641677 Score: 52
Period size: 18 Copynumber: 5.7 Consensus size: 18
1641570 AGAATTATAT
*
1641580 TTTATATTATATTC-GTATA
1 TTTATATTATA-TCAATA-A
*
1641599 TTT-TATTATAT-TATAA
1 TTTATATTATATCAATAA
*
1641615 -TTATATTATAT-ATTATAT
1 TTTATATTATATCA--ATAA
1641633 TTTATATTTATATCAAT--
1 TTTATA-TTATATCAATAA
*
1641650 TTT-GA-TATATCAATAA
1 TTTATATTATATCAATAA
1641666 TTTATATTATAT
1 TTTATATTATAT
1641678 AGTTTTGAGA
Statistics
Matches: 63, Mismatches: 5, Indels: 23
0.69 0.05 0.25
Matches are distributed among these distances:
14 9 0.14
15 2 0.03
16 13 0.21
17 7 0.11
18 15 0.24
19 10 0.16
20 6 0.10
21 1 0.02
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTATATTATATCAATAA
Found at i:1641863 original size:25 final size:25
Alignment explanation
Indices: 1641835--1641886 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1641825 ATTAGACACC
* *
1641835 AATTCAATTATAAA-AATTATTTTAA
1 AATTAAATTA-AAATAATAATTTTAA
1641860 AATTAAATTAAAATAATAATTTTAA
1 AATTAAATTAAAATAATAATTTTAA
1641885 AA
1 AA
1641887 ATATTTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
AATTAAATTAAAATAATAATTTTAA
Found at i:1653003 original size:21 final size:20
Alignment explanation
Indices: 1652960--1653024 Score: 71
Period size: 19 Copynumber: 3.2 Consensus size: 20
1652950 TTTTTTATTA
**
1652960 TTAATTAAAAATTAAAA-AT
1 TTAATTAAATGTTAAAATAT
1652979 TTAATTAAAT-TTATAAATTAT
1 TTAATTAAATGTTA-AAA-TAT
1653000 TTAAATTAAATGTTAAAATAT
1 TT-AATTAAATGTTAAAATAT
1653021 TTAA
1 TTAA
1653025 AATTAACTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
18 3 0.08
19 12 0.30
20 2 0.05
21 9 0.22
22 11 0.28
23 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
TTAATTAAATGTTAAAATAT
Found at i:1654019 original size:6 final size:6
Alignment explanation
Indices: 1653992--1654084 Score: 54
Period size: 6 Copynumber: 16.0 Consensus size: 6
1653982 ATAAAAATAT
* * * *
1653992 TATAAA TATATAA -AT-AA T-TAAA TATAAA TATAAT TATTAT TTTAAA
1 TATAAA TATA-AA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA
* * *
1654038 TTTAAC T-TAAA AATACAA TATAAA TA-AAA TATAATA TATAAA -ATAAA
1 TATAAA TATAAA TATA-AA TATAAA TATAAA TATAA-A TATAAA TATAAA
1654085 ATTAAAATTA
Statistics
Matches: 70, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
4 3 0.04
5 16 0.23
6 38 0.54
7 13 0.19
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (6 bp):
TATAAA
Found at i:1654129 original size:18 final size:19
Alignment explanation
Indices: 1654085--1654131 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
1654075 ATAAAATAAA
1654085 ATTAAAATTATCTATTTAAT
1 ATTAAAATTA-CTATTTAAT
*
1654105 ATAAAAATTA-TATTT-AT
1 ATTAAAATTACTATTTAAT
1654122 ATTTAAAATT
1 A-TTAAAATT
1654132 TTAATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 3 0.12
18 12 0.50
20 9 0.38
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTAAAATTACTATTTAAT
Found at i:1654395 original size:22 final size:22
Alignment explanation
Indices: 1654370--1654412 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1654360 ACAGTATACA
*
1654370 TTAATATTATTTT-TATATCAAC
1 TTAATATCATTTTCTAT-TCAAC
1654392 TTAATATCATTTTCTATTCAA
1 TTAATATCATTTTCTATTCAA
1654413 ATAAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATATCATTTTCTATTCAAC
Found at i:1654499 original size:18 final size:18
Alignment explanation
Indices: 1654473--1654507 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1654463 AAAATATATT
* *
1654473 ATAATATAATCAAAATTA
1 ATAAAATAATAAAAATTA
1654491 ATAAAATAATAAAAATT
1 ATAAAATAATAAAAATT
1654508 TATATGCTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAAATAATAAAAATTA
Found at i:1654615 original size:19 final size:20
Alignment explanation
Indices: 1654593--1654645 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
1654583 TATTTTAAAA
1654593 TTATTATTATAAATATTT-T
1 TTATTATTATAAATATTTAT
1654612 TTATTATTAATAAAT-TTTAT
1 TTATTATT-ATAAATATTTAT
*
1654632 TTAAT-TTATAAATA
1 TTATTATTATAAATA
1654646 AAAATTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 6 0.20
19 13 0.43
20 11 0.37
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATTATTATAAATATTTAT
Found at i:1654629 original size:16 final size:16
Alignment explanation
Indices: 1654590--1654632 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1654580 TTATATTTTA
1654590 AAATTATTATTATAAAT
1 AAATT-TTATTATAAAT
** *
1654607 ATTTTTTATTATTAAT
1 AAATTTTATTATAAAT
1654623 AAATTTTATT
1 AAATTTTATT
1654633 TAATTTATAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AAATTTTATTATAAAT
Found at i:1654640 original size:22 final size:20
Alignment explanation
Indices: 1654593--1654653 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
1654583 TATTTTAAAA
1654593 TTATTATT-ATAAATATTTT
1 TTATTATTAATAAATATTTT
1654612 TTATTATTAATAAAT-TTTAT
1 TTATTATTAATAAATATTT-T
* *
1654632 TTAATTTATAAATAAAAATTTT
1 TT-A-TTATTAATAAATATTTT
1654654 AATTTTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
19 11 0.31
20 9 0.26
21 1 0.03
22 11 0.31
23 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATTATTAATAAATATTTT
Found at i:1654642 original size:18 final size:19
Alignment explanation
Indices: 1654599--1654645 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1654589 AAAATTATTA
1654599 TTATAAATATTTTTTATTAT
1 TTATAAATATTTTTTA-TAT
*
1654619 TAATAAAT-TTTATTTA-AT
1 TTATAAATATTT-TTTATAT
1654637 TTATAAATA
1 TTATAAATA
1654646 AAAATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 9 0.39
19 3 0.13
20 11 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATAAATATTTTTTATAT
Found at i:1654715 original size:57 final size:61
Alignment explanation
Indices: 1654588--1654723 Score: 145
Period size: 57 Copynumber: 2.2 Consensus size: 61
1654578 CATTATATTT
* * ** *
1654588 TAAAATTATTATTATAAATATTTTTTATTATTAATAAATTTTATTTAATTTATAAATAAAAAT
1 TAAAATT-TTATTA-AAATATTATTTATTATTAATAAATCTTATTTAATCGATAAATAAAAAG
** *
1654651 TTTAATTTTATTAAAATA-TATTTA-TATTAATATA-CTTATTTAA-CGATAAATAAAAAG
1 TAAAATTTTATTAAAATATTATTTATTATTAATAAATCTTATTTAATCGATAAATAAAAAG
1654708 TAAAATTTTAATTAAA
1 TAAAATTTT-ATTAAA
1654724 TTACTTATAT
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
57 18 0.29
58 14 0.23
59 9 0.15
60 5 0.08
61 5 0.08
62 6 0.10
63 5 0.08
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (61 bp):
TAAAATTTTATTAAAATATTATTTATTATTAATAAATCTTATTTAATCGATAAATAAAAAG
Found at i:1661202 original size:21 final size:21
Alignment explanation
Indices: 1661176--1661217 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1661166 TTTAAATAAA
1661176 TAATT-ATTATTTAATAAAATT
1 TAATTAATTATTTAA-AAAATT
*
1661197 TAATTAATTTTTTAAAAAATT
1 TAATTAATTATTTAAAAAATT
1661218 AATAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TAATTAATTATTTAAAAAATT
Found at i:1666888 original size:40 final size:40
Alignment explanation
Indices: 1666838--1666919 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 40
1666828 TTAAATTTAT
1666838 TTTTAATTATACTTTATACATTATATAA-TATAATATAAA
1 TTTTAATTATACTTTATACATTATATAATTATAATATAAA
* **
1666877 TTTTACATTATATTTTATATGTTATATAATTATAATATAAA
1 TTTTA-ATTATACTTTATACATTATATAATTATAATATAAA
1666918 TT
1 TT
1666920 ATTTTTATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 5 0.13
40 20 0.53
41 13 0.34
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (40 bp):
TTTTAATTATACTTTATACATTATATAATTATAATATAAA
Found at i:1668498 original size:2 final size:2
Alignment explanation
Indices: 1668491--1668541 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
1668481 TGTAAATTTT
1668491 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1668531 TA TT TA TA TA T
1 TA TA TA TA TA T
1668542 TGCTTCCTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1669826 original size:2 final size:2
Alignment explanation
Indices: 1669813--1669880 Score: 73
Period size: 2 Copynumber: 34.0 Consensus size: 2
1669803 GCATGTTTGC
* * * * * * *
1669813 AT AT AC AT AT AT AT AT AT AT AT AT AT GT AT GT GT GT GT AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1669855 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
1669881 GCATCAACAT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1670121 original size:2 final size:2
Alignment explanation
Indices: 1670116--1670154 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1670106 AATATATACT
*
1670116 AC AC AC AC AC AC AC AT 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 AC AC AC AC AC AC AC A
1670155 TATATATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:1670159 original size:2 final size:2
Alignment explanation
Indices: 1670154--1670181 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1670144 ACACACACAC
1670154 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
1670182 GAACTTGCTC
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:1672738 original size:15 final size:14
Alignment explanation
Indices: 1672699--1672740 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1672689 TATTTATATA
*
1672699 TTTTATAATTAAAT
1 TTTTATAAATAAAT
*
1672713 TTATATAAATAAAT
1 TTTTATAAATAAAT
1672727 TTTTATTAAATAAA
1 TTTTA-TAAATAAA
1672741 GAATAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTATAAATAAAT
Found at i:1672915 original size:33 final size:33
Alignment explanation
Indices: 1672862--1672948 Score: 97
Period size: 33 Copynumber: 2.6 Consensus size: 33
1672852 ATATTATAAT
* *
1672862 TATATTTAAATTATTATATATTTATATAATTTTTAA
1 TATAATTAAA-TATT-TATATTT-TATAAATTTTAA
1672898 T-TAATT-AATAATTTATATTTTATAAATTTTAA
1 TATAATTAAAT-ATTTATATTTTATAAATTTTAA
*
1672930 TATATTTAAATATTTATAT
1 TATAATTAAATATTTATAT
1672949 CATGATTATA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
32 12 0.27
33 20 0.44
34 8 0.18
35 4 0.09
36 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
TATAATTAAATATTTATATTTTATAAATTTTAA
Found at i:1673238 original size:20 final size:22
Alignment explanation
Indices: 1673200--1673239 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1673190 TTTCTTCATA
*
1673200 TTTTTATAATATTATAAATAAT
1 TTTTTATAAAATTATAAATAAT
1673222 TTTTTA-AAAATTA-AAATA
1 TTTTTATAAAATTATAAATA
1673240 GATTATGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 6 0.35
22 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTTATAAAATTATAAATAAT
Found at i:1673265 original size:12 final size:12
Alignment explanation
Indices: 1673244--1673277 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1673234 AAAATAGATT
1673244 ATGA-GATGATA
1 ATGATGATGATA
1673255 ATGATGATGATA
1 ATGATGATGATA
*
1673267 ATGATAATGAT
1 ATGATGATGAT
1673278 TAAATATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (12 bp):
ATGATGATGATA
Found at i:1677025 original size:13 final size:14
Alignment explanation
Indices: 1677001--1677030 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1676991 TATTATTATA
1677001 ATTAATTTATAAAT
1 ATTAATTTATAAAT
1677015 ATTAA-TTATAAAT
1 ATTAATTTATAAAT
1677028 ATT
1 ATT
1677031 GATGATGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTAATTTATAAAT
Found at i:1677586 original size:14 final size:14
Alignment explanation
Indices: 1677567--1677593 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1677557 CTGATATTTA
1677567 AATATAAAATATAC
1 AATATAAAATATAC
1677581 AATATAAAATATA
1 AATATAAAATATA
1677594 TGAAGGGTAA
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:0.04, G:0.00, T:0.30
Consensus pattern (14 bp):
AATATAAAATATAC
Found at i:1677750 original size:16 final size:16
Alignment explanation
Indices: 1677731--1677784 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
1677721 AAAAAAATAA
*
1677731 TATATATTTTAAATTT
1 TATATATATTAAATTT
* *
1677747 TATATAATATAAAATAT
1 TATAT-ATATTAAATTT
*
1677764 TA-ATATATTAAAATT
1 TATATATATTAAATTT
1677779 TATATA
1 TATATA
1677785 AATATAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 10 0.33
16 10 0.33
17 10 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATATATATTAAATTT
Found at i:1677751 original size:32 final size:32
Alignment explanation
Indices: 1677724--1677791 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
1677714 ATATATGAAA
* *
1677724 AAAATAATATATATTTTAAATTTTATATAATAT
1 AAAATAATA-ATATATTAAAATTTATATAATAT
*
1677757 AAAATATTAATATATTAAAATTTATATAAATAT
1 AAAATAATAATATATTAAAATTTATAT-AATAT
1677790 AA
1 AA
1677792 TTTATTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
AAAATAATAATATATTAAAATTTATATAATAT
Found at i:1677769 original size:18 final size:18
Alignment explanation
Indices: 1677698--1677791 Score: 65
Period size: 18 Copynumber: 5.3 Consensus size: 18
1677688 TATACGATGG
1677698 ATATAAAATATTTAATAT-
1 ATATAAAATA-TTAATATA
* *
1677716 ATATGAAAAAAATAATATA
1 ATAT-AAAATATTAATATA
* * *
1677735 TATTTTAAAT-TTTATATA
1 -ATATAAAATATTAATATA
1677753 ATATAAAATATTAATAT-
1 ATATAAAATATTAATATA
1677770 AT-TAAAAT-TT-ATATAA
1 ATATAAAATATTAATAT-A
1677786 ATATAA
1 ATATAA
1677792 TTTATTTTAA
Statistics
Matches: 59, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
14 4 0.07
15 2 0.03
16 8 0.14
17 12 0.20
18 22 0.37
19 8 0.14
20 3 0.05
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (18 bp):
ATATAAAATATTAATATA
Found at i:1677778 original size:33 final size:33
Alignment explanation
Indices: 1677724--1677791 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
1677714 ATATATGAAA
*
1677724 AAAATAATATATATTTTAAATTT-TATATAATAT
1 AAAATAATATATATTTAAAATTTATATA-AATAT
*
1677757 AAAATATTA-ATATATTAAAATTTATATAAATAT
1 AAAATAATATATAT-TTAAAATTTATATAAATAT
1677790 AA
1 AA
1677792 TTTATTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 4 0.13
33 23 0.74
34 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
AAAATAATATATATTTAAAATTTATATAAATAT
Done.