Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold92
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: 2337674
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 10 of 19
Found at i:1269606 original size:20 final size:20
Alignment explanation
Indices: 1269568--1269612 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1269558 AATTTTTAAA
*
1269568 AATTT-ATTAAATTTTAATT
1 AATTTAATTAAATTTAAATT
*
1269587 AATTTAATTCAATTTAAATT
1 AATTTAATTAAATTTAAATT
1269607 AATTTA
1 AATTTA
1269613 TTTTAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
AATTTAATTAAATTTAAATT
Found at i:1269648 original size:18 final size:18
Alignment explanation
Indices: 1269607--1269653 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
1269597 AATTTAAATT
*
1269607 AATTTATTTTAAAAATAA
1 AATTTTTTTTAAAAATAA
*
1269625 AA-TTTTTTTAATAATAA
1 AATTTTTTTTAAAAATAA
1269642 AATTTTTATTTA
1 AATTTTT-TTTA
1269654 TAACATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 15 0.60
18 6 0.24
19 4 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTTTTTTTAAAAATAA
Found at i:1269656 original size:18 final size:17
Alignment explanation
Indices: 1269607--1269648 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
1269597 AATTTAAATT
*
1269607 AATTTATTTTAAAAATAA
1 AATTT-TTTTAATAATAA
1269625 AATTTTTTTAATAATAA
1 AATTTTTTTAATAATAA
1269642 AATTTTT
1 AATTTTT
1269649 ATTTATAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTTTTTTAATAATAA
Found at i:1270546 original size:25 final size:26
Alignment explanation
Indices: 1270492--1270547 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
1270482 TGATATTTAC
*
1270492 ATTTAAATAATTTGATTTATATATAT
1 ATTTAAATAATTTGATTTATATATAA
1270518 ATTTAAA-AATTAT-ATTTA-ATAATAA
1 ATTTAAATAATT-TGATTTATAT-ATAA
1270543 ATTTA
1 ATTTA
1270548 TATTAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 2 0.07
25 17 0.63
26 8 0.30
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
ATTTAAATAATTTGATTTATATATAA
Found at i:1270598 original size:20 final size:21
Alignment explanation
Indices: 1270573--1270611 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1270563 ATTTATAATT
*
1270573 ATTTTT-ATCATTAAATTATG
1 ATTTTTAATAATTAAATTATG
1270593 ATTTTTAATAATTAAATTA
1 ATTTTTAATAATTAAATTA
1270612 AATTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (21 bp):
ATTTTTAATAATTAAATTATG
Found at i:1270616 original size:20 final size:20
Alignment explanation
Indices: 1270573--1270617 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1270563 ATTTATAATT
* *
1270573 ATTTTTATCATTAAATTATG
1 ATTTTTATAATTAAATTATA
1270593 ATTTTTAATAATTAAATTA-A
1 ATTTTT-ATAATTAAATTATA
1270613 ATTTT
1 ATTTT
1270618 AAAAAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTTTTATAATTAAATTATA
Found at i:1270619 original size:19 final size:19
Alignment explanation
Indices: 1270595--1270655 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
1270585 AAATTATGAT
1270595 TTTTAATAATTAAATTAAA
1 TTTTAATAATTAAATTAAA
* * *
1270614 TTTTAAAAAATATAATAAAA
1 TTTTAATAATTA-AATTAAA
* *
1270634 TTTAAAT-ATAAAATTTAAA
1 TTTTAATAATTAAA-TTAAA
1270653 TTT
1 TTT
1270656 ATTAAATATT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
18 2 0.06
19 19 0.59
20 11 0.34
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTTAATAATTAAATTAAA
Found at i:1270646 original size:13 final size:13
Alignment explanation
Indices: 1270628--1270653 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1270618 AAAAAATATA
1270628 ATAAAATTTAAAT
1 ATAAAATTTAAAT
1270641 ATAAAATTTAAAT
1 ATAAAATTTAAAT
1270654 TTATTAAATA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAAAATTTAAAT
Found at i:1271585 original size:16 final size:16
Alignment explanation
Indices: 1271566--1271597 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1271556 AATTATTTTT
1271566 AATTACTATTAAATTA
1 AATTACTATTAAATTA
*
1271582 AATTATTATTAAATTA
1 AATTACTATTAAATTA
1271598 TATTCTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTACTATTAAATTA
Found at i:1272247 original size:18 final size:18
Alignment explanation
Indices: 1272179--1272249 Score: 58
Period size: 18 Copynumber: 4.0 Consensus size: 18
1272169 GATAGTAATA
* *
1272179 AAAAATAAATTTATAATT
1 AAAAATAAATTGATAAAT
**
1272197 AAAAATATTTTGAGTAAAAT
1 AAAAATAAATTGA-T-AAAT
*
1272217 AATAA-AAA-T-ATAAAT
1 AAAAATAAATTGATAAAT
1272232 AAAAATAAATTGATAAAT
1 AAAAATAAATTGATAAAT
1272250 GATATATTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
15 8 0.20
16 4 0.10
17 2 0.05
18 17 0.43
19 2 0.05
20 7 0.17
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.32
Consensus pattern (18 bp):
AAAAATAAATTGATAAAT
Found at i:1272523 original size:2 final size:2
Alignment explanation
Indices: 1272516--1272546 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1272506 TAACTTCTTT
1272516 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1272547 GTAGTCCCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1275649 original size:42 final size:42
Alignment explanation
Indices: 1275562--1275659 Score: 101
Period size: 42 Copynumber: 2.3 Consensus size: 42
1275552 TGATTTATTT
* *
1275562 ATAATAATAATATTATTATTTATAATTAAATAAAAAATTTAAA
1 ATAA-AATTATATTAATATTTATAATTAAATAAAAAATTTAAA
** * *
1275605 ATAATTTTATATTAATATTTATATATT-TATAATTAAATTT-AA
1 ATAAAATTATATTAATATTTATA-ATTAAATAA-AAAATTTAAA
1275647 ATAAAATTATATT
1 ATAAAATTATATT
1275660 TTAAATAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
42 32 0.71
43 13 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (42 bp):
ATAAAATTATATTAATATTTATAATTAAATAAAAAATTTAAA
Found at i:1275660 original size:16 final size:17
Alignment explanation
Indices: 1275635--1275667 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1275625 ATATATTTAT
1275635 AATTAAA-TTTAAATAA
1 AATTAAATTTTAAATAA
*
1275651 AATTATATTTTAAATAA
1 AATTAAATTTTAAATAA
1275668 TTAAATATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTAAATTTTAAATAA
Found at i:1276517 original size:20 final size:20
Alignment explanation
Indices: 1276494--1276533 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1276484 TATATTTAAA
1276494 TAAA-AATAATTTTTTATTAT
1 TAAATAATAA-TTTTTATTAT
1276514 TAAATAATAATTTTTATTAT
1 TAAATAATAATTTTTATTAT
1276534 ATTAAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAAATAATAATTTTTATTAT
Found at i:1276528 original size:22 final size:21
Alignment explanation
Indices: 1276494--1276540 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
1276484 TATATTTAAA
1276494 TAAA-AATAATTTT-TTATTAT
1 TAAATAATAATTTTATTA-TAT
1276514 TAAATAATAATTTTTATTATAT
1 TAAATAATAA-TTTTATTATAT
1276536 TAAAT
1 TAAAT
1276541 CAATTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.17
21 5 0.21
22 12 0.50
23 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAAATAATAATTTTATTATAT
Found at i:1276762 original size:11 final size:12
Alignment explanation
Indices: 1276746--1276790 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
1276736 TTATTTAAAA
1276746 ATATTAAT-TTT
1 ATATTAATATTT
*
1276757 ATATTAATCTTT
1 ATATTAATATTT
1276769 ATA-TAATATTT
1 ATATTAATATTT
1276780 A-ATTAA-ATTT
1 ATATTAATATTT
1276790 A
1 A
1276791 AATAAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
10 6 0.19
11 19 0.61
12 6 0.19
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATTAATATTT
Found at i:1277361 original size:23 final size:23
Alignment explanation
Indices: 1277338--1277382 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1277328 TTTTAACTAT
1277338 TTAAAAAAATTA-TTTATATTTA
1 TTAAAAAAATTATTTTATATTTA
* *
1277360 TTATACAAATTATTTTATATTTA
1 TTAAAAAAATTATTTTATATTTA
1277383 ATACAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TTAAAAAAATTATTTTATATTTA
Found at i:1277400 original size:23 final size:22
Alignment explanation
Indices: 1277344--1277408 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
1277334 CTATTTAAAA
1277344 AAATTAT-TTATATTTATTATAC
1 AAATTATATTATATTTA-TATAC
*
1277366 AAATTATTTTATATTTA-ATAC
1 AAATTATATTATATTTATATAC
1277387 AAATAATATATTATA-TTATATA
1 AAAT--TATATTATATTTATATA
1277409 ATTTTAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
21 8 0.21
22 10 0.26
23 20 0.53
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATTATATTATATTTATATAC
Found at i:1277438 original size:18 final size:18
Alignment explanation
Indices: 1277391--1277439 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1277381 TAATACAAAT
*
1277391 AATATATTATATTATATA
1 AATATATTTTATTATATA
* * **
1277409 ATTTTAAATTATTATATA
1 AATATATTTTATTATATA
1277427 AATATATTTTATT
1 AATATATTTTATT
1277440 TTTATTATAT
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AATATATTTTATTATATA
Found at i:1277595 original size:15 final size:16
Alignment explanation
Indices: 1277558--1277595 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1277548 TGAATCAATC
1277558 AATTAATTTTAAACTTA
1 AATTAA-TTTAAACTTA
1277575 AA-TAATTTAAA-TTA
1 AATTAATTTAAACTTA
1277589 AATTAAT
1 AATTAAT
1277596 CAAATATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.25
15 10 0.50
16 3 0.15
17 2 0.10
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTAATTTAAACTTA
Found at i:1278662 original size:16 final size:16
Alignment explanation
Indices: 1278624--1278664 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1278614 TTTAAATTCG
1278624 TTAAAAATT--TAAAT
1 TTAAAAATTAATAAAT
* *
1278638 TTAATAATTAATAATT
1 TTAAAAATTAATAAAT
1278654 TTAAAAATTAA
1 TTAAAAATTAA
1278665 GGTTCGATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 8 0.36
16 14 0.64
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAAATTAATAAAT
Found at i:1279611 original size:3 final size:3
Alignment explanation
Indices: 1279605--1279642 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1279595 TTAGTTGGAT
1279605 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1279643 GTTAGTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1279894 original size:8 final size:8
Alignment explanation
Indices: 1279881--1279918 Score: 58
Period size: 8 Copynumber: 4.5 Consensus size: 8
1279871 TACATAAATT
1279881 TTTATATA
1 TTTATATA
1279889 TTTATATA
1 TTTATATA
1279897 TTTATATA
1 TTTATATA
1279905 TTATATTATA
1 TT-TA-TATA
1279915 TTTA
1 TTTA
1279919 AAATTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 18 0.64
9 4 0.14
10 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTTATATA
Found at i:1280522 original size:27 final size:28
Alignment explanation
Indices: 1280475--1280527 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
1280465 TTAAAAATTA
* *
1280475 AAGATTTATTTAGATATAATAAAATATG
1 AAGATTTATTTAGAAAAAATAAAATATG
1280503 AAGATTTATTT-GAAAAAATAAAATA
1 AAGATTTATTTAGAAAAAATAAAATA
1280528 ATTTATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (28 bp):
AAGATTTATTTAGAAAAAATAAAATATG
Found at i:1281035 original size:20 final size:20
Alignment explanation
Indices: 1281007--1281051 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1280997 TACTAAACGA
*
1281007 TTTTAATTTATTTTTTAA-AG
1 TTTTAATTT-TTTTATAAGAG
*
1281027 TTTTTATTTTTTTATAAGAG
1 TTTTAATTTTTTTATAAGAG
1281047 TTTTA
1 TTTTA
1281052 TGATAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (20 bp):
TTTTAATTTTTTTATAAGAG
Found at i:1282155 original size:33 final size:34
Alignment explanation
Indices: 1282118--1282195 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 34
1282108 TATTTATTTA
1282118 ATAAAAAAATTATTTAA-ATTTAATTATAAA-AAT
1 ATAAAAAAATTATTTAATATTTAATT-TAAACAAT
* *
1282151 ATAAAAATATTTTTTTAATATTTAATTTAAACAAT
1 ATAAAAA-AATTATTTAATATTTAATTTAAACAAT
*
1282186 A-AAACAAATT
1 ATAAAAAAATT
1282196 TACATGTTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
33 10 0.26
34 16 0.42
35 12 0.32
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (34 bp):
ATAAAAAAATTATTTAATATTTAATTTAAACAAT
Found at i:1283220 original size:21 final size:21
Alignment explanation
Indices: 1283194--1283242 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 21
1283184 ATTTTTATAT
*
1283194 TTTTAA-TATATTTAAATAAAA
1 TTTTAATTATAATTAAAT-AAA
1283215 TTTTAATTTATAATTAAATAAA
1 TTTTAA-TTATAATTAAATAAA
1283237 TTTTAA
1 TTTTAA
1283243 CTTTGAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 6 0.24
22 9 0.36
23 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTAATTATAATTAAATAAA
Found at i:1283237 original size:22 final size:23
Alignment explanation
Indices: 1283200--1283242 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1283190 ATATTTTTAA
*
1283200 TATATTTAAATAAAATTTTAATT
1 TATAATTAAATAAAATTTTAATT
1283223 TATAATTAAAT-AAATTTTAA
1 TATAATTAAATAAAATTTTAA
1283243 CTTTGAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TATAATTAAATAAAATTTTAATT
Found at i:1283346 original size:14 final size:15
Alignment explanation
Indices: 1283329--1283362 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1283319 TCAAATGTTA
*
1283329 AAAATTT-TTTAAAT
1 AAAATTTATTAAAAT
1283343 AAAATTTATTAAAAT
1 AAAATTTATTAAAAT
1283358 AAAAT
1 AAAAT
1283363 AATAAAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATTTATTAAAAT
Found at i:1283351 original size:44 final size:44
Alignment explanation
Indices: 1283290--1283387 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
1283280 TCAACTTTCA
* * *
1283290 TTTTTATAA-AAAATTTATTTAAATATAAATCA-AATGTTAAAAAT
1 TTTTTA-AATAAAATTTATTAAAATA-AAATAATAAAGTTAAAAAT
* *
1283334 TTTTTAAATAAAATTTATTAAAATAAAATAATAAAGTTTAAATT
1 TTTTTAAATAAAATTTATTAAAATAAAATAATAAAGTTAAAAAT
1283378 TTTTTAAATA
1 TTTTTAAATA
1283388 TTTTAATTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 7 0.15
44 40 0.85
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (44 bp):
TTTTTAAATAAAATTTATTAAAATAAAATAATAAAGTTAAAAAT
Found at i:1283584 original size:24 final size:24
Alignment explanation
Indices: 1283552--1283597 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1283542 ATAAACTAAT
* *
1283552 AATAAAAATCAAAATATTTAATAA
1 AATAAAAATAAAAATATATAATAA
1283576 AATAAAAATAAAAATATATAAT
1 AATAAAAATAAAAATATATAAT
1283598 TTTAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (24 bp):
AATAAAAATAAAAATATATAATAA
Found at i:1283886 original size:23 final size:27
Alignment explanation
Indices: 1283855--1283933 Score: 98
Period size: 23 Copynumber: 3.1 Consensus size: 27
1283845 TTTACTTTTC
1283855 AATAT-AAATATAATATAAAA-A-AT-
1 AATATAAAATATAATATAAAATATATA
*
1283878 AAT-TAAAATATTATATAAAATATATAA
1 AATATAAAATATAATATAAAATATAT-A
1283905 AATATAAAATATAATAT-AAATATATA
1 AATATAAAATATAATATAAAATATATA
1283931 AAT
1 AAT
1283934 TATTATAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
22 1 0.02
23 17 0.35
24 1 0.02
25 2 0.04
26 4 0.08
27 11 0.23
28 12 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (27 bp):
AATATAAAATATAATATAAAATATATA
Found at i:1283897 original size:21 final size:21
Alignment explanation
Indices: 1283856--1283941 Score: 66
Period size: 21 Copynumber: 3.8 Consensus size: 21
1283846 TTACTTTTCA
*
1283856 ATATAAATATAATATAAAAAAT
1 ATATAAA-ATATTATAAAAAAT
*
1283878 A-ATTAAAATATTATATAAAAT
1 ATA-TAAAATATTATAAAAAAT
1283899 ATATAAAATATAAAATATAATATAAAT
1 ATATAAAATAT----TATAA-A-AAAT
*
1283926 ATATAAATTATTATAA
1 ATATAAAATATTATAA
1283942 TATTAAAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
21 22 0.42
22 6 0.12
23 5 0.10
25 4 0.08
26 1 0.02
27 14 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATATAAAATATTATAAAAAAT
Found at i:1283940 original size:12 final size:12
Alignment explanation
Indices: 1283856--1283979 Score: 57
Period size: 13 Copynumber: 10.6 Consensus size: 12
1283846 TTACTTTTCA
1283856 ATATAAATATAAT
1 ATATAAAT-TAAT
* *
1283869 ATAAAAAATAAT
1 ATATAAATTAAT
*
1283881 -TA-AAA-TATT
1 ATATAAATTAAT
*
1283890 ATATAAAAT-AT
1 ATATAAATTAAT
*
1283901 ATA-AAATATAAA
1 ATATAAAT-TAAT
*
1283913 ATATAATATAAAT
1 ATATAA-ATTAAT
1283926 ATATAAATT-AT
1 ATATAAATTAAT
*
1283937 -TATAATATTAAA
1 ATATAA-ATTAAT
* *
1283949 ATTTATATTTAAT
1 ATATA-AATTAAT
*
1283962 ATAT-TATTAAT
1 ATATAAATTAAT
1283973 ATATAAA
1 ATATAAA
1283980 ATTATATCTC
Statistics
Matches: 82, Mismatches: 17, Indels: 25
0.66 0.14 0.20
Matches are distributed among these distances:
9 3 0.04
10 13 0.16
11 24 0.29
12 13 0.16
13 26 0.32
14 3 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATAAATTAAT
Found at i:1283940 original size:18 final size:17
Alignment explanation
Indices: 1283889--1283986 Score: 57
Period size: 16 Copynumber: 5.8 Consensus size: 17
1283879 ATTAAAATAT
*
1283889 TATATAAAATATATAAA
1 TATATAAATTATATAAA
1283906 -ATATAAAATATAATATAAA
1 TATAT-AAAT-T-ATATAAA
1283925 TATATAAATTAT-TATAA
1 TATATAAATTATATA-AA
**
1283942 TAT-TAAAATT-TATATT
1 TATAT-AAATTATATAAA
*
1283958 TA-ATATATTAT-T-AA
1 TATATAAATTATATAAA
1283972 TATATAAAATTATAT
1 TATAT-AAATTATAT
1283987 CTCATCAATA
Statistics
Matches: 62, Mismatches: 7, Indels: 24
0.67 0.08 0.26
Matches are distributed among these distances:
14 2 0.03
15 7 0.11
16 18 0.29
17 18 0.29
18 2 0.03
19 11 0.18
20 4 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATATAAATTATATAAA
Found at i:1283963 original size:36 final size:36
Alignment explanation
Indices: 1283866--1283981 Score: 92
Period size: 36 Copynumber: 3.1 Consensus size: 36
1283856 ATATAAATAT
* *
1283866 AATATAAAAAATAATTAAAATATTATATAAAATATATAA
1 AATATAAAATATAA-TATAA-A-TATATAAAATATATAA
* *
1283905 AATATAAAATATAATATAAATATATAAATTAT-TAT
1 AATATAAAATATAATATAAATATATAAAATATATAA
* * *
1283940 AATATTAAAAT-TTATATTTAATATATTATTAATATATAA
1 AATA-TAAAATATAATA-TAAATATA-TA-AAATATATAA
1283979 AAT
1 AAT
1283982 TATATCTCAT
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
35 10 0.16
36 24 0.38
37 3 0.05
38 8 0.13
39 18 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (36 bp):
AATATAAAATATAATATAAATATATAAAATATATAA
Found at i:1284266 original size:5 final size:5
Alignment explanation
Indices: 1284256--1284285 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
1284246 TAGTTTCCGT
1284256 CTTTC CTTTC CTTTC CTTTC CTTTTC CTTT
1 CTTTC CTTTC CTTTC CTTTC C-TTTC CTTT
1284286 GACGGTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (5 bp):
CTTTC
Found at i:1284276 original size:15 final size:16
Alignment explanation
Indices: 1284256--1284285 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1284246 TAGTTTCCGT
1284256 CTTTCC-TTTCCTTTC
1 CTTTCCTTTTCCTTTC
1284271 CTTTCCTTTTCCTTT
1 CTTTCCTTTTCCTTT
1284286 GACGGTTCCT
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:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (16 bp):
CTTTCCTTTTCCTTTC
Found at i:1288556 original size:6 final size:6
Alignment explanation
Indices: 1288545--1288575 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1288535 TTTTTTATAA
*
1288545 TAAATT TAAATT TAAATT TAAATG TAAATT T
1 TAAATT TAAATT TAAATT TAAATT TAAATT T
1288576 TTAAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (6 bp):
TAAATT
Found at i:1289755 original size:15 final size:15
Alignment explanation
Indices: 1289735--1289764 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1289725 ATATGTAATG
1289735 TATTATTATTATTGT
1 TATTATTATTATTGT
1289750 TATTATTATTATTGT
1 TATTATTATTATTGT
1289765 AAAATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
TATTATTATTATTGT
Found at i:1290485 original size:13 final size:13
Alignment explanation
Indices: 1290457--1290499 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
1290447 ATTTTTTAAA
*
1290457 TAAATAATATTTT
1 TAAAAAATATTTT
1290470 TAAAAAAT-TTTAT
1 TAAAAAATATTT-T
1290483 TAAAAAATATTTT
1 TAAAAAATATTTT
1290496 TAAA
1 TAAA
1290500 TATTTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 3 0.11
13 21 0.78
14 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAAAAAATATTTT
Found at i:1290503 original size:36 final size:38
Alignment explanation
Indices: 1290462--1290534 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 38
1290452 TTAAATAAAT
* * *
1290462 AATATTTTTAAAA-AATTTTATTAAAAA-ATATTTTTA
1 AATATTTTAAAAATAATTATATAAAAAATATATTTTTA
1290498 AATATTTTAAAAATAATTATATAAAAAATATATTTTT
1 AATATTTTAAAAATAATTATATAAAAAATATATTTTT
1290535 TTATTTCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 12 0.38
37 12 0.38
38 8 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (38 bp):
AATATTTTAAAAATAATTATATAAAAAATATATTTTTA
Found at i:1291621 original size:27 final size:27
Alignment explanation
Indices: 1291577--1291644 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 27
1291567 AATATAAAAA
*
1291577 ATATAAATATTATTAATAAATTAA-AATTT
1 ATATAAATA-TA-AAATAAATTAAGAA-TT
*
1291606 ATATAAATATAAAATAATTTAAGAATT
1 ATATAAATATAAAATAAATTAAGAATT
*
1291633 ATAAAAATATAA
1 ATATAAATATAA
1291645 GTCCTAGATG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 22 0.63
28 4 0.11
29 9 0.26
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (27 bp):
ATATAAATATAAAATAAATTAAGAATT
Found at i:1292451 original size:12 final size:12
Alignment explanation
Indices: 1292436--1292477 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1292426 GATAGATTAA
*
1292436 AAAAATGTATTT
1 AAAAATGTAATT
*
1292448 AAAAA-GTAAGAT
1 AAAAATGTAA-TT
1292460 AAAAATGTAATT
1 AAAAATGTAATT
1292472 AAAAAT
1 AAAAAT
1292478 TTTTAAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 3 0.12
12 18 0.72
13 4 0.16
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.29
Consensus pattern (12 bp):
AAAAATGTAATT
Found at i:1293636 original size:19 final size:19
Alignment explanation
Indices: 1293604--1293691 Score: 108
Period size: 19 Copynumber: 4.5 Consensus size: 19
1293594 AATATCTTCG
*
1293604 TTATTA-ATTCATATATTT
1 TTATTATATTTATATATTT
1293622 TTATTATATTTATATTATTT
1 TTATTATATTTATA-TATTT
1293642 TTATTTATTAATTTATATATTT
1 TTA-TTA-T-ATTTATATATTT
*
1293664 TTATTATATTTATATTTTT
1 TTATTATATTTATATATTT
1293683 TTATT-TATT
1 TTATTATATT
1293692 ATAATCATAA
Statistics
Matches: 63, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
18 10 0.16
19 22 0.35
20 9 0.14
21 6 0.10
22 9 0.14
23 7 0.11
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATTATATTTATATATTT
Found at i:1293660 original size:42 final size:41
Alignment explanation
Indices: 1293604--1293692 Score: 160
Period size: 42 Copynumber: 2.1 Consensus size: 41
1293594 AATATCTTCG
1293604 TTATTAATTCATATATTTTTATTATATTTATATTATTTTTAT
1 TTATTAATTCATATATTTTTATTATATTTATATT-TTTTTAT
*
1293646 TTATTAATTTATATATTTTTATTATATTTATATTTTTTTAT
1 TTATTAATTCATATATTTTTATTATATTTATATTTTTTTAT
1293687 TTATTA
1 TTATTA
1293693 TAATCATAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 13 0.28
42 33 0.72
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (41 bp):
TTATTAATTCATATATTTTTATTATATTTATATTTTTTTAT
Found at i:1293669 original size:31 final size:33
Alignment explanation
Indices: 1293621--1293690 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 33
1293611 TTCATATATT
1293621 TTTATTATATTTATATTAT-TTT-TATTTATTAA
1 TTTA-TATATTTATATTATATTTATATTTATTAA
* * *
1293653 TTTATATATTTTTATTATATTTATATTTTTTTA
1 TTTATATATTTATATTATATTTATATTTATTAA
1293686 TTTAT
1 TTTAT
1293691 TATAATCATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 13 0.39
32 7 0.21
33 13 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (33 bp):
TTTATATATTTATATTATATTTATATTTATTAA
Found at i:1293674 original size:33 final size:32
Alignment explanation
Indices: 1293621--1293694 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 32
1293611 TTCATATATT
*
1293621 TTTATTATATTTATATTATTTTTATTTATTAA
1 TTTATTATATTTATATTATTTATATTTATTAA
* * *
1293653 TTTA-TATATTTTTATTATATTTATATTTTTTTA
1 TTTATTATATTTATA-T-TATTTATATTTATTAA
1293686 TTTATTATA
1 TTTATTATA
1293695 ATCATAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
31 9 0.26
32 5 0.14
33 17 0.49
34 4 0.11
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (32 bp):
TTTATTATATTTATATTATTTATATTTATTAA
Found at i:1293693 original size:23 final size:23
Alignment explanation
Indices: 1293621--1293694 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
1293611 TTCATATATT
1293621 TTTATTATATTTATATTATTTTTA
1 TTTATTATATTTATATT-TTTTTA
*
1293645 TTTATTA-ATTTATA---TATT-
1 TTTATTATATTTATATTTTTTTA
1293663 TTTATTATATTTATATTTTTTTA
1 TTTATTATATTTATATTTTTTTA
1293686 TTTATTATA
1 TTTATTATA
1293695 ATCATAATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
18 7 0.16
19 10 0.23
22 3 0.07
23 16 0.37
24 7 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTATTATATTTATATTTTTTTA
Found at i:1295599 original size:18 final size:18
Alignment explanation
Indices: 1295578--1295612 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1295568 GGGGGGTTGC
*
1295578 AGGGGCCGAGGGTGATAG
1 AGGGACCGAGGGTGATAG
1295596 AGGGACCGAGGGTGATA
1 AGGGACCGAGGGTGATA
1295613 AGAGAGAGAT
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:0.26, C:0.11, G:0.51, T:0.11
Consensus pattern (18 bp):
AGGGACCGAGGGTGATAG
Found at i:1297222 original size:2 final size:2
Alignment explanation
Indices: 1297215--1297239 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1297205 TGCGCACGTG
1297215 CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA C
1297240 GGACGATAAC
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:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1298612 original size:40 final size:40
Alignment explanation
Indices: 1298561--1298680 Score: 231
Period size: 40 Copynumber: 3.0 Consensus size: 40
1298551 TCCAAAGGAT
1298561 TTTACTTAACTTATGGAAACAGTGGGATATGGGATTAACC
1 TTTACTTAACTTATGGAAACAGTGGGATATGGGATTAACC
*
1298601 TTTACTCAACTTATGGAAACAGTGGGATATGGGATTAACC
1 TTTACTTAACTTATGGAAACAGTGGGATATGGGATTAACC
1298641 TTTACTTAACTTATGGAAACAGTGGGATATGGGATTAACC
1 TTTACTTAACTTATGGAAACAGTGGGATATGGGATTAACC
1298681 AAGCACATAT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.32
Consensus pattern (40 bp):
TTTACTTAACTTATGGAAACAGTGGGATATGGGATTAACC
Found at i:1302803 original size:16 final size:16
Alignment explanation
Indices: 1302782--1302812 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1302772 CAATTTTTCA
*
1302782 TTTTATCTTTTATTAT
1 TTTTATATTTTATTAT
1302798 TTTTATATTTTATTA
1 TTTTATATTTTATTA
1302813 ATTTAAATAT
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:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTATATTTTATTAT
Found at i:1302842 original size:288 final size:287
Alignment explanation
Indices: 1302323--1302848 Score: 844
Period size: 288 Copynumber: 1.8 Consensus size: 287
1302313 ATTATTATTA
* * *
1302323 TTTTAATTTATATATTGTTCAATAATCAAATCATGATATTTAATTAAAAATAAAATTATTTATAT
1 TTTTAATTTATATAATGTTCAATAAACAAATCATAATATTTAATTAAAAATAAAATTATTTATAT
* *
1302388 TTATTTTTAAAAAATTTTAATAACCTCTTTGTTGAGATATTTTATATATAAATGAAGTAAAAATT
66 TTATTTTTAAAAAA-TATAATAACCTCTTTGTTGAGATATTTTATATATAAATAAAGTAAAAATT
* *
1302453 AATCCAAAATAAAAAAATCTAAACACTTAAACAATTTGTGATTTTATTTTTTAATTTTTTTATAT
130 AATCCAAAATAAAAAAATCTAAACACTTAAACAATTTGTCATTTTATCTTTTAATTTTTTTATAT
*
1302518 TTTACTAATTTAAATATTAAAATATATTTAAAAATATAATTATCAAATTAATTTTACTGTATGTT
195 TTTACTAATTTAAATATTAAAATATATTCAAAAATATAATTATCAAATTAATTTTACTGTATGTT
1302583 TTATATAAATTAAAACTTTTTTGTTAAC
260 TTATATAAATTAAAACTTTTTTGTTAAC
*
1302611 TTTTAATTTATATAATGTT-AATTAAACAAA-CGGTAATATTTAATTAAAAATAAAATTATTTAT
1 TTTTAATTTATATAATGTTCAA-TAAACAAATC-ATAATATTTAATTAAAAATAAAATTATTTAT
*
1302674 ATTTATTTTTAAAAAA-ATAATAATCTCTTTGTTGAGATATTTTATATATAAATAAAGTAAAAAT
64 ATTTATTTTTAAAAAATATAATAACCTCTTTGTTGAGATATTTTATATATAAATAAAGTAAAAAT
*
1302738 TAATCCAAAATAATAAAAAATCTAAACACTTAAACAATTTTTCATTTTATCTTTT-ATTATTTTT
129 TAATCCAAAAT-A-AAAAAATCTAAACACTTAAACAATTTGTCATTTTATCTTTTAATT-TTTTT
* * *
1302802 ATATTTTATTAATTTAAATATTAAAATATATTCGAAAATATTATTAT
191 ATATTTTACTAATTTAAATATTAAAATATATTCAAAAATATAATTAT
1302849 TGCAATGTAA
Statistics
Matches: 219, Mismatches: 14, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
286 56 0.26
287 7 0.03
288 156 0.71
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (287 bp):
TTTTAATTTATATAATGTTCAATAAACAAATCATAATATTTAATTAAAAATAAAATTATTTATAT
TTATTTTTAAAAAATATAATAACCTCTTTGTTGAGATATTTTATATATAAATAAAGTAAAAATTA
ATCCAAAATAAAAAAATCTAAACACTTAAACAATTTGTCATTTTATCTTTTAATTTTTTTATATT
TTACTAATTTAAATATTAAAATATATTCAAAAATATAATTATCAAATTAATTTTACTGTATGTTT
TATATAAATTAAAACTTTTTTGTTAAC
Found at i:1303029 original size:15 final size:15
Alignment explanation
Indices: 1303009--1303038 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1302999 TTTTTCTCTT
1303009 TTATGCTTCTAAGAC
1 TTATGCTTCTAAGAC
1303024 TTATGCTTCTAAGAC
1 TTATGCTTCTAAGAC
1303039 ATCCTCTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (15 bp):
TTATGCTTCTAAGAC
Found at i:1304320 original size:19 final size:21
Alignment explanation
Indices: 1304279--1304323 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1304269 AATTACTAAC
1304279 ATATCAGAATTGATATAATAT
1 ATATCAGAATTGATATAATAT
1304300 ATATCAGAATTGATATAATAT
1 ATATCAGAATTGATATAATAT
1304321 ATA
1 ATA
1304324 ATGATTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (21 bp):
ATATCAGAATTGATATAATAT
Found at i:1304755 original size:41 final size:41
Alignment explanation
Indices: 1304674--1304766 Score: 109
Period size: 41 Copynumber: 2.2 Consensus size: 41
1304664 TTAATATTTT
*
1304674 AAATATAAAAAATTTTAAAAAATCAAAAATACGTACTTTAAAA
1 AAATA-AAAAAATTTAAAAAAATCAAAAATAC-TACTTTAAAA
*
1304717 AAATAAAAAAATTTAAAAATATATCAAATATA-TA-TTTAAAA
1 AAATAAAAAAATTTAAAAA-A-ATCAAAAATACTACTTTAAAA
*
1304758 AAGTAAAAA
1 AAATAAAAA
1304767 TAAAAACTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
41 15 0.33
42 15 0.33
43 6 0.13
44 9 0.20
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (41 bp):
AAATAAAAAAATTTAAAAAAATCAAAAATACTACTTTAAAA
Found at i:1306684 original size:34 final size:35
Alignment explanation
Indices: 1306618--1306694 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 35
1306608 ATTTAAAATA
*
1306618 TAAATAATTAAAAAATTATTATTAAAAAATAAACT
1 TAAATAATTAAAAAATTAGTATTAAAAAATAAACT
**
1306653 TAAA-AATTAATAAAATT-GTATTAAACTATAAA-T
1 TAAATAATTAA-AAAATTAGTATTAAAAAATAAACT
*
1306686 GAAATAATT
1 TAAATAATT
1306695 TTTTTATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 4 0.11
34 22 0.61
35 10 0.28
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (35 bp):
TAAATAATTAAAAAATTAGTATTAAAAAATAAACT
Found at i:1307381 original size:23 final size:24
Alignment explanation
Indices: 1307354--1307420 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 24
1307344 AATAAAGATA
*
1307354 ATTAAAATATTATATTATA-ATAT
1 ATTAAAATATTATATTATATAAAT
1307377 ATTAATAAT-TTATATTATATAAAT
1 ATTAA-AATATTATATTATATAAAT
*
1307401 TTTAAAATATT-TAGTTATAT
1 ATTAAAATATTATA-TTATAT
1307421 TATTTTTGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (24 bp):
ATTAAAATATTATATTATATAAAT
Found at i:1310974 original size:21 final size:21
Alignment explanation
Indices: 1310950--1311007 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
1310940 TGCGGATATG
1310950 ATATATTTAATAAATATAAAA
1 ATATATTTAATAAATATAAAA
1310971 ATATATTTAATAAATATAAAA
1 ATATATTTAATAAATATAAAA
*
1310992 ATAT-TATAATAAATAT
1 ATATATTTAATAAATAT
1311008 GATATGATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 11 0.31
21 25 0.69
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATATTTAATAAATATAAAA
Found at i:1311296 original size:17 final size:17
Alignment explanation
Indices: 1311274--1311317 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1311264 TATATAAATA
1311274 TTAATATAAATAATTTT
1 TTAATATAAATAATTTT
* *
1311291 TTAATATATTATTATTTT
1 TTAATATA-AATAATTTT
*
1311309 TTAAAATAA
1 TTAATATAA
1311318 TAAAATAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAATATAAATAATTTT
Found at i:1315147 original size:31 final size:34
Alignment explanation
Indices: 1315097--1315168 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
1315087 ACATAAATTT
* *
1315097 TTAATAATATTATGACCTTT-T-TATATATAAAAA
1 TTAAT-ATATTATAACCTTTCTCTAAATATAAAAA
1315130 TTAATATATT-TAACCTTTCTCTAAATATAAAAA
1 TTAATATATTATAACCTTTCTCTAAATATAAAAA
*
1315163 ATAATA
1 TTAATA
1315169 CATAAGTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 7 0.21
32 6 0.18
33 21 0.62
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.43
Consensus pattern (34 bp):
TTAATATATTATAACCTTTCTCTAAATATAAAAA
Found at i:1315241 original size:21 final size:21
Alignment explanation
Indices: 1315215--1315255 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1315205 TTTTTTTGAA
1315215 TATATAATT-TTAAAATTTTTT
1 TATAT-ATTATTAAAATTTTTT
*
1315236 TATATATTATTAAGATTTTT
1 TATATATTATTAAAATTTTT
1315256 ATTTACATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TATATATTATTAAAATTTTTT
Found at i:1315499 original size:2 final size:2
Alignment explanation
Indices: 1315492--1315517 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1315482 AGGAAGAATT
1315492 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
1315518 AATCGGAGAA
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:1315740 original size:7 final size:7
Alignment explanation
Indices: 1315728--1315779 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
1315718 ATATATAATT
1315728 TTATTAA
1 TTATTAA
1315735 TTATTAA
1 TTATTAA
*
1315742 TTA-TAT
1 TTATTAA
*
1315748 TTATTAT
1 TTATTAA
1315755 TTATTTAA
1 TTA-TTAA
*
1315763 TTTTTAA
1 TTATTAA
*
1315770 TTTTTAA
1 TTATTAA
1315777 TTA
1 TTA
1315780 AACAGATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
6 5 0.13
7 29 0.74
8 5 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (7 bp):
TTATTAA
Found at i:1316196 original size:18 final size:18
Alignment explanation
Indices: 1316128--1316196 Score: 50
Period size: 18 Copynumber: 3.8 Consensus size: 18
1316118 AAATTTTATT
*
1316128 TAATTTAAATTTTAAAAAA
1 TAATTT-AATTTTAATAAA
* * * *
1316147 TTATTTAGTTTAAAT-TA
1 TAATTTAATTTTAATAAA
* **
1316164 TTATTTAATAATAATAAA
1 TAATTTAATTTTAATAAA
1316182 TAATTTAATTTTAAT
1 TAATTTAATTTTAAT
1316197 TATAAAATAT
Statistics
Matches: 36, Mismatches: 13, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
17 12 0.33
18 19 0.53
19 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (18 bp):
TAATTTAATTTTAATAAA
Found at i:1316478 original size:16 final size:15
Alignment explanation
Indices: 1316444--1316474 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1316434 ATCATGTGAG
1316444 TAAAAATTAATATTT
1 TAAAAATTAATATTT
1316459 TAAAAATTAATATTT
1 TAAAAATTAATATTT
1316474 T
1 T
1316475 TAAAGGAGAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAAATTAATATTT
Found at i:1318029 original size:14 final size:14
Alignment explanation
Indices: 1318012--1318039 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1318002 AAAATACAAT
1318012 TTTCAATTATTGGA
1 TTTCAATTATTGGA
1318026 TTTCAATTATTGGA
1 TTTCAATTATTGGA
1318040 AGCTCTTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (14 bp):
TTTCAATTATTGGA
Found at i:1318460 original size:34 final size:34
Alignment explanation
Indices: 1318424--1318566 Score: 131
Period size: 34 Copynumber: 4.3 Consensus size: 34
1318414 AAATATGGTT
* *
1318424 ATATAAATATAATATATATAAAGTATATAATATT
1 ATATAAATATAATATATATAAAATATATAATATA
1318458 ATAT-AATATAAATATATATTAAAAT-T-T-ATATA
1 ATATAAATAT-AATATATA-TAAAATATATAATATA
* *
1318490 ATATGAATTATTAATATAT-TAAAATTTA-AATA-A
1 ATAT-AAATA-TAATATATATAAAATATATAATATA
* *
1318523 ATATAATTATAATATA-ATAAAATATATAAAATA
1 ATATAAATATAATATATATAAAATATATAATATA
*
1318556 ATATGAATATA
1 ATATAAATATA
1318567 TAAATTATTA
Statistics
Matches: 91, Mismatches: 7, Indels: 23
0.75 0.06 0.19
Matches are distributed among these distances:
31 15 0.16
32 22 0.24
33 22 0.24
34 26 0.29
35 6 0.07
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (34 bp):
ATATAAATATAATATATATAAAATATATAATATA
Found at i:1318510 original size:32 final size:32
Alignment explanation
Indices: 1318471--1318578 Score: 123
Period size: 32 Copynumber: 3.3 Consensus size: 32
1318461 TAATATAAAT
*
1318471 ATATATTAAAATTTATATAATATGAATTATTA
1 ATATATTAAAATTTAAATAATATGAATTATTA
1318503 ATATATTAAAATTTAAATAAATAT-AATTA-TA
1 ATATATTAAAATTTAAAT-AATATGAATTATTA
* *
1318534 ATATAATAAAATATATAAAATAATATGAATATATAA
1 ATATATTAAAAT-T-T-AAATAATATGAAT-TATTA
1318570 AT-TATTAAA
1 ATATATTAAA
1318579 TTTCGATACT
Statistics
Matches: 65, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
31 13 0.20
32 23 0.35
33 11 0.17
34 7 0.11
35 8 0.12
36 3 0.05
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (32 bp):
ATATATTAAAATTTAAATAATATGAATTATTA
Found at i:1318559 original size:10 final size:9
Alignment explanation
Indices: 1318430--1318570 Score: 55
Period size: 9 Copynumber: 15.8 Consensus size: 9
1318420 GGTTATATAA
*
1318430 ATATAATAT
1 ATATAAAAT
*
1318439 ATATAAAGT
1 ATATAAAAT
*
1318448 ATATAATAT
1 ATATAAAAT
*
1318457 -TATATAAT
1 ATATAAAAT
*
1318465 ATA-AATAT
1 ATATAAAAT
1318473 ATATTAAAAT
1 ATA-TAAAAT
* *
1318483 TTATATAAT
1 ATATAAAAT
*
1318492 ATGAATTATTAAT
1 AT--A-TA-AAAT
1318505 ATATTAAAAT
1 ATA-TAAAAT
1318515 -T-T-AAAT
1 ATATAAAAT
* *
1318521 AAATATAAT
1 ATATAAAAT
*
1318530 -TATAATAT
1 ATATAAAAT
1318538 A-ATAAAAT
1 ATATAAAAT
1318546 ATATAAAAT
1 ATATAAAAT
*
1318555 A-ATATGAAT
1 ATATA-AAAT
1318564 ATATAAA
1 ATATAAA
1318571 TTATTAAATT
Statistics
Matches: 97, Mismatches: 21, Indels: 28
0.66 0.14 0.19
Matches are distributed among these distances:
6 4 0.04
7 1 0.01
8 28 0.29
9 39 0.40
10 12 0.12
11 5 0.05
12 2 0.02
13 6 0.06
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (9 bp):
ATATAAAAT
Found at i:1319694 original size:16 final size:17
Alignment explanation
Indices: 1319665--1319697 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1319655 AAAATTTTGA
*
1319665 TATATTTTATTTAAATT
1 TATATTTTAATTAAATT
1319682 TATA-TTTAATTAAATT
1 TATATTTTAATTAAATT
1319698 AATTATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATATTTTAATTAAATT
Found at i:1319728 original size:26 final size:27
Alignment explanation
Indices: 1319668--1319744 Score: 72
Period size: 26 Copynumber: 2.9 Consensus size: 27
1319658 ATTTTGATAT
1319668 ATTTTATT-TAAATTTATATTTAATTA
1 ATTTTATTATAAATTTATATTTAATTA
* *
1319694 AATTAATTATAAAATTTAT-TTT-ATTA
1 ATTTTATTAT-AAATTTATATTTAATTA
*
1319720 TTTTTATTATTAAA-TTATAATTTAA
1 ATTTTATTA-TAAATTTAT-ATTTAA
1319745 ATCGATTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
25 4 0.10
26 19 0.47
27 8 0.20
28 9 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
ATTTTATTATAAATTTATATTTAATTA
Found at i:1320219 original size:23 final size:19
Alignment explanation
Indices: 1320176--1320223 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 19
1320166 ATAAAAATAT
*
1320176 TTTTATTTTATTTTTGATA
1 TTTTATTTTATATTTGATA
1320195 TTATTATTATTATATTTGACTTA
1 TT-TTATT-TTATATTTGA--TA
1320218 TTTTAT
1 TTTTAT
1320224 AATTTTATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 2 0.08
20 5 0.21
21 9 0.38
22 4 0.17
23 4 0.17
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (19 bp):
TTTTATTTTATATTTGATA
Found at i:1320590 original size:3 final size:3
Alignment explanation
Indices: 1320582--1320608 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1320572 TTAAAAATTT
1320582 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1320609 GAGATCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1321127 original size:35 final size:35
Alignment explanation
Indices: 1321035--1321127 Score: 150
Period size: 35 Copynumber: 2.6 Consensus size: 35
1321025 TTAAATCATG
*
1321035 AATATAAAATTTTAAAATATTCATATTTAATATTTA
1 AATAT-AAATTTTAAAATATTTATATTTAATATTTA
1321071 AATATAAATTTTAAAATATTTATATTTAATATTTA
1 AATATAAATTTTAAAATATTTATATTTAATATTTA
* *
1321106 AATATAAATTTAAAAAAATTTA
1 AATATAAATTTTAAAATATTTA
1321128 AATATGGTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 49 0.91
36 5 0.09
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (35 bp):
AATATAAATTTTAAAATATTTATATTTAATATTTA
Found at i:1321346 original size:15 final size:15
Alignment explanation
Indices: 1321322--1321354 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1321312 TTGTATTTTT
*
1321322 TATCATATTTAAATA
1 TATCAAATTTAAATA
1321337 TATCAAATTTAAATA
1 TATCAAATTTAAATA
1321352 TAT
1 TAT
1321355 TAATATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
TATCAAATTTAAATA
Found at i:1321382 original size:15 final size:15
Alignment explanation
Indices: 1321347--1321375 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1321337 TATCAAATTT
1321347 AAATATATTAATATC
1 AAATATATTAATATC
1321362 AAATATATTAATAT
1 AAATATATTAATAT
1321376 TTTATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATATATTAATATC
Found at i:1321500 original size:2 final size:2
Alignment explanation
Indices: 1321493--1321539 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1321483 GTTGTTTAAG
1321493 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
1321535 TA TA T
1 TA TA T
1321540 TGTCCCTTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1323492 original size:25 final size:25
Alignment explanation
Indices: 1323440--1323508 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 25
1323430 AAATCATATA
* **
1323440 AAAAATTAATTTAATTTTACCTTATT
1 AAAAA-TAATTTTATTTTAAATTATT
*
1323466 AAAAATAATTTTATTTTAAATTTTT
1 AAAAATAATTTTATTTTAAATTATT
* *
1323491 AATAA-AATATTATTTTAA
1 AAAAATAATTTTATTTTAA
1323509 TCCGTGTTGG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
24 12 0.32
25 20 0.54
26 5 0.14
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (25 bp):
AAAAATAATTTTATTTTAAATTATT
Found at i:1324746 original size:14 final size:14
Alignment explanation
Indices: 1324727--1324761 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1324717 ACAATATTGA
*
1324727 TCTCTCTGACTCTC
1 TCTCTCTCACTCTC
*
1324741 TCTCTCTCCCTCTC
1 TCTCTCTCACTCTC
1324755 TCTCTCT
1 TCTCTCT
1324762 TTGACAGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.03, C:0.49, G:0.03, T:0.46
Consensus pattern (14 bp):
TCTCTCTCACTCTC
Found at i:1325172 original size:17 final size:18
Alignment explanation
Indices: 1325136--1325174 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
1325126 CCCTAAAAGG
1325136 CTAAAGTCTTGCATATTGT
1 CTAAAGTCTTGCA-ATTGT
1325155 CTAAAGTCTTGC-ATTGT
1 CTAAAGTCTTGCAATTGT
1325172 CTA
1 CTA
1325175 TCTCATATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.40
19 12 0.60
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (18 bp):
CTAAAGTCTTGCAATTGT
Found at i:1331380 original size:3 final size:3
Alignment explanation
Indices: 1331372--1331397 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1331362 TTTGCTTCAC
1331372 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
1331398 TTTATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1333572 original size:22 final size:22
Alignment explanation
Indices: 1333540--1333589 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1333530 ATTTGAGCTT
*
1333540 AAATATTTAAAT-TTAATTATAA
1 AAATATATAAATATTAA-TATAA
1333562 AAATATATAAATATTAATATAA
1 AAATATATAAATATTAATATAA
1333584 AAATAT
1 AAATAT
1333590 TTTTTAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATATATAAATATTAATATAA
Found at i:1334229 original size:22 final size:22
Alignment explanation
Indices: 1334201--1334242 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1334191 TTTATTTTAT
1334201 GAATTAAAAATTAAATTAAACC
1 GAATTAAAAATTAAATTAAACC
1334223 GAATTAAAAATTAAATTAAA
1 GAATTAAAAATTAAATTAAA
1334243 TATTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (22 bp):
GAATTAAAAATTAAATTAAACC
Found at i:1334280 original size:18 final size:18
Alignment explanation
Indices: 1334237--1334277 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1334227 TAAAAATTAA
1334237 ATTAAA-TATTTATTTTAT
1 ATTAAATTA-TTATTTTAT
*
1334255 ATTTAATTATTATTTTA-
1 ATTAAATTATTATTTTAT
1334272 ATTAAA
1 ATTAAA
1334278 ATTGAATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 5 0.25
18 13 0.65
19 2 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTAAATTATTATTTTAT
Found at i:1336008 original size:26 final size:25
Alignment explanation
Indices: 1335946--1335997 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
1335936 ATTCATAATT
*
1335946 TTAAATATAATATAATAAAATAAATAA
1 TTAAATATTA-AT-ATAAAATAAATAA
1335973 TTAAATATTAATATAAAATATAATA
1 TTAAATATTAATATAAAATA-AATA
1335998 TGTATATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
26 6 0.26
27 9 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
TTAAATATTAATATAAAATAAATAA
Found at i:1336173 original size:14 final size:14
Alignment explanation
Indices: 1336150--1336196 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
1336140 AAATTTAATT
1336150 ATAA-AATATATAA
1 ATAATAATATATAA
* *
1336163 ATATTAATATAAAA
1 ATAATAATATATAA
*
1336177 ATAATATTA-ATAA
1 ATAATAATATATAA
1336190 ATAATAA
1 ATAATAA
1336197 AATTTGCCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
13 12 0.44
14 15 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATAATATATAA
Found at i:1336351 original size:31 final size:29
Alignment explanation
Indices: 1336315--1336372 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 29
1336305 ACACATGATA
1336315 AAAATTCATAT-AATAAAAATTATTAATATAT
1 AAAATT-ATATAAATAAAAA-TA-TAATATAT
*
1336346 AAAATTTTATAAATAAAAATATAATAT
1 AAAATTATATAAATAAAAATATAATAT
1336373 TTTACATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 6 0.24
30 5 0.20
31 14 0.56
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
AAAATTATATAAATAAAAATATAATATAT
Found at i:1336404 original size:23 final size:25
Alignment explanation
Indices: 1336353--1336422 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 25
1336343 TATAAAATTT
* * *
1336353 TATAAATAAAAATATAATATTTTACA
1 TATAAAT-AAAATACAAAAATTTACA
* *
1336379 TATAATTATAATA-AAAAATTTA-A
1 TATAAATAAAATACAAAAATTTACA
1336402 TATAAATAAAATACAAAAATT
1 TATAAATAAAATACAAAAATT
1336423 GGTGTTGACA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
23 12 0.32
24 14 0.38
25 5 0.14
26 6 0.16
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (25 bp):
TATAAATAAAATACAAAAATTTACA
Found at i:1336981 original size:23 final size:23
Alignment explanation
Indices: 1336936--1336981 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1336926 AATAATCGAA
*
1336936 TAGATTTAATTAATTGATTTTTT
1 TAGATTTAATTAATTGATATTTT
1336959 TAGATTTATATTAATT-ATATTTT
1 TAGATTTA-ATTAATTGATATTTT
1336982 AAATATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.61
Consensus pattern (23 bp):
TAGATTTAATTAATTGATATTTT
Found at i:1337880 original size:16 final size:16
Alignment explanation
Indices: 1337844--1337892 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1337834 TTAATTAGTT
*
1337844 AATATAAATATTTTTAAA
1 AATAT-AATA-TTTAAAA
1337862 AATATAATATTTAAAA
1 AATATAATATTTAAAA
* *
1337878 AATTTAAAATTTAAA
1 AATATAATATTTAAA
1337893 TTAATTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 19 0.68
17 4 0.14
18 5 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATAATATTTAAAA
Found at i:1341510 original size:23 final size:23
Alignment explanation
Indices: 1341484--1341542 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
1341474 TTATATATAT
1341484 AAATATTATATAAAAATAATTAA
1 AAATATTATATAAAAATAATTAA
* * * *
1341507 AAATAATATAATATAAATATTTTA
1 AAATATTAT-ATAAAAATAATTAA
1341531 AAAT-TTATATAA
1 AAATATTATATAA
1341543 TATAAATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 3 0.10
23 11 0.38
24 15 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATATTATATAAAAATAATTAA
Found at i:1341522 original size:10 final size:11
Alignment explanation
Indices: 1341462--1341522 Score: 54
Period size: 10 Copynumber: 5.6 Consensus size: 11
1341452 AATAATTTTG
1341462 AATATAATATA
1 AATATAATATA
**
1341473 TTTATATATATA
1 AATATA-ATATA
*
1341485 AATATTATATA
1 AATATAATATA
*
1341496 AAAATAAT-TA
1 AATATAATATA
*
1341506 AAAATAATAT-
1 AATATAATATA
1341516 AATATAA
1 AATATAA
1341523 ATATTTTAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
10 16 0.40
11 16 0.40
12 8 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AATATAATATA
Found at i:1341564 original size:32 final size:30
Alignment explanation
Indices: 1341509--1341567 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
1341499 ATAATTAAAA
*
1341509 ATAATATAATATAAATATTTTAAAATTTAT
1 ATAATATAATATAAATATATTAAAATTTAT
*
1341539 ATAATATAAATTATTAATATATTAAAATT
1 ATAATAT-AA-TATAAATATATTAAAATT
1341568 AATTTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 7 0.28
31 2 0.08
32 16 0.64
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
ATAATATAATATAAATATATTAAAATTTAT
Found at i:1341820 original size:43 final size:45
Alignment explanation
Indices: 1341755--1341838 Score: 104
Period size: 43 Copynumber: 1.9 Consensus size: 45
1341745 TTAAAAATAA
1341755 TTATATTTAATTTTAAAAATATA-T-ATATTTACAAA-ATTATATT
1 TTATATTTAATTTTAAAAATATATTAATA-TTACAAATATTATATT
**
1341798 TTATATTT-ATATTTAAGCATATATTAATATTACAAATATTA
1 TTATATTTAAT-TTTAAAAATATATTAATATTACAAATATTA
1341839 AAAAAAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
42 2 0.06
43 18 0.51
44 8 0.23
45 7 0.20
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (45 bp):
TTATATTTAATTTTAAAAATATATTAATATTACAAATATTATATT
Found at i:1342810 original size:32 final size:33
Alignment explanation
Indices: 1342768--1342841 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 33
1342758 CAATCATAAT
* * *
1342768 TAAATATAAAAAATCATTCAAT-AATGAAACATA
1 TAAAT-TAAAAAATAATTAAATAAATCAAACATA
* *
1342801 TAAATTAAAATATAATTAAATAAATCTAACATA
1 TAAATTAAAAAATAATTAAATAAATCAAACATA
1342834 -AAATTAAA
1 TAAATTAAA
1342842 TCAAATTTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
32 21 0.60
33 14 0.40
ACGTcount: A:0.62, C:0.07, G:0.01, T:0.30
Consensus pattern (33 bp):
TAAATTAAAAAATAATTAAATAAATCAAACATA
Found at i:1342840 original size:21 final size:20
Alignment explanation
Indices: 1342800--1342848 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
1342790 AATGAAACAT
*
1342800 ATAAATTAAAATATAATTAA
1 ATAAATTAAAATAAAATTAA
*
1342820 ATAAATCTAACATAAAATTAA
1 ATAAAT-TAAAATAAAATTAA
1342841 ATCAAATT
1 AT-AAATT
1342849 TACCCATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.24
21 15 0.60
22 4 0.16
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAATTAAAATAAAATTAA
Found at i:1348575 original size:34 final size:34
Alignment explanation
Indices: 1348504--1348575 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 34
1348494 AAAATTTTTA
*
1348504 TTTTTTAATTTTTTAATTTAAATCATCACAAATTT
1 TTTTTTAATTTTTTAATTT-AATCATAACAAATTT
*
1348539 TTTTTTAATTTTTTATATTT-TTCATAACATAATTT
1 TTTTTTAATTTTTTA-ATTTAATCATAACA-AATTT
1348574 TT
1 TT
1348576 ATTATATATC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 7 0.21
35 22 0.67
36 4 0.12
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (34 bp):
TTTTTTAATTTTTTAATTTAATCATAACAAATTT
Found at i:1349007 original size:21 final size:20
Alignment explanation
Indices: 1348979--1349018 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1348969 TTTATAATTA
* *
1348979 AATTTAAATAAATTATTTAT
1 AATTTAAAAAAATAATTTAT
1348999 AATTATAAAAAAATAATTTA
1 AATT-TAAAAAAATAATTTA
1349019 AGCCGATTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTTAAAAAAATAATTTAT
Found at i:1351182 original size:19 final size:20
Alignment explanation
Indices: 1351151--1351189 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1351141 CTATCATATA
1351151 TATTTTTTAAAAT-TATTTT
1 TATTTTTTAAAATATATTTT
1351170 TATTTATTT-AAATATATTTT
1 TATTT-TTTAAAATATATTTT
1351190 AAAAAATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTTTTAAAATATATTTT
Found at i:1351908 original size:13 final size:13
Alignment explanation
Indices: 1351873--1351917 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
1351863 ATTAATAATT
1351873 TTTAAATACTAAA-
1 TTTAAATA-TAAAG
*
1351886 -TTAAAAATAAAG
1 TTTAAATATAAAG
1351898 TTTAAATAT-AAG
1 TTTAAATATAAAG
1351910 TTTAAATA
1 TTTAAATA
1351918 AATATTTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 4 0.14
12 17 0.61
13 7 0.25
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (13 bp):
TTTAAATATAAAG
Found at i:1352639 original size:3 final size:3
Alignment explanation
Indices: 1352631--1352663 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1352621 TTAATGTGAC
1352631 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1352664 AGATTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1352995 original size:2 final size:2
Alignment explanation
Indices: 1352988--1353015 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1352978 ATAACATTAA
1352988 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
1353016 TTGTTCAACA
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:1353375 original size:19 final size:20
Alignment explanation
Indices: 1353335--1353376 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1353325 ATAATTAATC
* *
1353335 ATAATAATATTTTTTTATAG
1 ATAATAATATTTTTTAAAAG
1353355 ATAA-AATATTTTTTAAAAG
1 ATAATAATATTTTTTAAAAG
1353374 ATA
1 ATA
1353377 CATATTTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (20 bp):
ATAATAATATTTTTTAAAAG
Found at i:1353496 original size:32 final size:32
Alignment explanation
Indices: 1353460--1353525 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
1353450 TAAAAAATTT
*
1353460 ATATCGAATATATATTTAAATATTAGTACGAG
1 ATATCAAATATATATTTAAATATTAGTACGAG
*
1353492 ATATCAAATATATATTTAGATATTAGTACGAG
1 ATATCAAATATATATTTAAATATTAGTACGAG
1353524 AT
1 AT
1353526 TATGATTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (32 bp):
ATATCAAATATATATTTAAATATTAGTACGAG
Found at i:1353761 original size:15 final size:16
Alignment explanation
Indices: 1353741--1353771 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1353731 TTTAAAAATT
1353741 AAATATATTT-ATATA
1 AAATATATTTCATATA
1353756 AAATATATTTCATATA
1 AAATATATTTCATATA
1353772 TGATATTTAC
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATATATTTCATATA
Found at i:1353937 original size:20 final size:20
Alignment explanation
Indices: 1353914--1353957 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1353904 ATTGATTTTA
*
1353914 TATAATAATAAT-TAAATAAT
1 TATAA-AATAATATAAAAAAT
*
1353934 TATAAAATTATATAAAAAAT
1 TATAAAATAATATAAAAAAT
1353954 TATA
1 TATA
1353958 TAAACCAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TATAAAATAATATAAAAAAT
Found at i:1353954 original size:12 final size:12
Alignment explanation
Indices: 1353937--1353961 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1353927 AAATAATTAT
1353937 AAAATTATATAA
1 AAAATTATATAA
1353949 AAAATTATATAA
1 AAAATTATATAA
1353961 A
1 A
1353962 CCAATTGAAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATTATATAA
Found at i:1354512 original size:22 final size:21
Alignment explanation
Indices: 1354468--1354513 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1354458 TAATTAAATT
*
1354468 TTTAATTTTTAATTTAATCAA
1 TTTAATTTTTAATTCAATCAA
* *
1354489 TTTAATTTATTAATTCGATTAA
1 TTTAATTT-TTAATTCAATCAA
1354511 TTT
1 TTT
1354514 CAATAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTAATTTTTAATTCAATCAA
Found at i:1356031 original size:18 final size:18
Alignment explanation
Indices: 1355977--1356037 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
1355967 TATATCATTT
* *
1355977 ATATAAATAAAATATAAA
1 ATATAAATAATATAAAAA
1355995 ATAT-AATAAT-TAAATAA
1 ATATAAATAATATAAA-AA
*
1356012 ATATAAATTATATAAAAA
1 ATATAAATAATATAAAAA
1356030 ATTATAAA
1 A-TATAAA
1356038 ATTAATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
16 3 0.08
17 11 0.31
18 12 0.33
19 10 0.28
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATATAAATAATATAAAAA
Found at i:1356082 original size:2 final size:2
Alignment explanation
Indices: 1356075--1356108 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1356065 CGAAGCCTCC
* *
1356075 TA TA TA TA CA TA CA 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
1356109 AAATTAAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1356376 original size:13 final size:13
Alignment explanation
Indices: 1356360--1356385 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1356350 ATTAAATAAA
1356360 TTAATTATAATTT
1 TTAATTATAATTT
1356373 TTAATTATAATTT
1 TTAATTATAATTT
1356386 ATTTTATTTA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTAATTATAATTT
Found at i:1356482 original size:31 final size:35
Alignment explanation
Indices: 1356417--1356484 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 35
1356407 TTTTATTATG
*
1356417 TTTGATTGATTATATTAATTTTTAAATGTGTTAAA
1 TTTGATTGATTATATTAATTTTAAAATGTGTTAAA
1356452 TTTGATTGATT-TA-TAATTTTAAAAT-T-TTAAA
1 TTTGATTGATTATATTAATTTTAAAATGTGTTAAA
1356483 TT
1 TT
1356485 AAATTGGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 7 0.22
32 1 0.03
33 11 0.34
34 2 0.06
35 11 0.34
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (35 bp):
TTTGATTGATTATATTAATTTTAAAATGTGTTAAA
Found at i:1358335 original size:25 final size:25
Alignment explanation
Indices: 1358287--1358337 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
1358277 ATTAATATAA
* *
1358287 ATATATTTAATTTTTTTTATTTTTT
1 ATATATTTAATTTTTTTAAATTTTT
*
1358312 ATATATTT-ATTTTTTTAAAATTTT
1 ATATATTTAATTTTTTTAAATTTTT
1358336 AT
1 AT
1358338 GTTTAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (25 bp):
ATATATTTAATTTTTTTAAATTTTT
Found at i:1360274 original size:110 final size:110
Alignment explanation
Indices: 1360079--1360420 Score: 382
Period size: 110 Copynumber: 3.1 Consensus size: 110
1360069 TTATTCGACA
* * * * * * * * *
1360079 TAAAATTGAATTACCTGAGCTCGTTAGATTAAACTCATTTACATAGTAAAAAAAATAGATAAATT
1 TAAATTTGAATTGCTTGAGTTCGTTCGATTAAGCTCGTTTACATAAT-AAAAAATTAGATAAATT
1360144 CTCGTACTTGACTTTAAACTCAAGTATTTATATTTAAGTTTAAGCT
65 CTCGTACTTGACTTTAAACTCAAGTATTTATATTTAAGTTTAAGCT
*
1360190 TAAATTTGAATTGCTTGAGTTCGTTCGATTAAGCTCGTTTACACAATAAAAAATTAGATAAATTC
1 TAAATTTGAATTGCTTGAGTTCGTTCGATTAAGCTCGTTTACATAATAAAAAATTAGATAAATTC
*** *
1360255 TCGTACTTGACTTTAAACTCAAGTATTTATATTTAAGAGCAAACT
66 TCGTACTTGACTTTAAACTCAAGTATTTATATTTAAGTTTAAGCT
* * ** * * * * *
1360300 TGAATTTAAACAGCTTGAGCTT-ATTCAATTAAGCTCGTTTACATATTAAAAAATTATATCAATT
1 TAAATTTGAATTGCTTGAG-TTCGTTCGATTAAGCTCGTTTACATAATAAAAAATTAGATAAATT
* * * * * * *
1360364 CTCATATTTAATTTTAGACTCAATTATTTATATTTAAGTTTGAGCT
65 CTCGTACTTGACTTTAAACTCAAGTATTTATATTTAAGTTTAAGCT
1360410 TAAATTT-AATT
1 TAAATTTGAATT
1360421 TAAATTTTTT
Statistics
Matches: 192, Mismatches: 38, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
109 2 0.01
110 150 0.78
111 40 0.21
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (110 bp):
TAAATTTGAATTGCTTGAGTTCGTTCGATTAAGCTCGTTTACATAATAAAAAATTAGATAAATTC
TCGTACTTGACTTTAAACTCAAGTATTTATATTTAAGTTTAAGCT
Found at i:1361643 original size:33 final size:35
Alignment explanation
Indices: 1361586--1361651 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 35
1361576 TAATATACTT
*
1361586 ACTTGAATAATAATATAATTTAA-TTTATAATTTA
1 ACTTGAATAATAATATAATATAATTTTATAATTTA
1361620 ACTTG-ATAATAAT-TAAATATAATTTTATAATT
1 ACTTGAATAATAATAT-AATATAATTTTATAATT
1361652 AAAAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 1 0.03
33 14 0.48
34 14 0.48
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (35 bp):
ACTTGAATAATAATATAATATAATTTTATAATTTA
Found at i:1361651 original size:18 final size:18
Alignment explanation
Indices: 1361628--1361677 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
1361618 TAACTTGATA
*
1361628 ATAATTAAATATAATTTT
1 ATAATTAAAAATAATTTT
*
1361646 ATAATTAAAAATTATTTT
1 ATAATTAAAAATAATTTT
1361664 A-AA-TAAAAATAATT
1 ATAATTAAAAATAATT
1361678 AATTAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 10 0.34
17 2 0.07
18 17 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAATTAAAAATAATTTT
Found at i:1362859 original size:13 final size:12
Alignment explanation
Indices: 1362843--1362930 Score: 54
Period size: 12 Copynumber: 7.2 Consensus size: 12
1362833 GATAAAAAAT
1362843 ATTTATAAATTAA
1 ATTTA-AAATTAA
*
1362856 ATTTAAATTTAA
1 ATTTAAAATTAA
**
1362868 ATTTAAAATTTTT
1 ATTTAAAA-TTAA
* *
1362881 ATTTAAATTTTA
1 ATTTAAAATTAA
* *
1362893 A--TATAATTTA
1 ATTTAAAATTAA
1362903 ATTTAAAATTAAA
1 ATTTAAAATT-AA
*
1362916 ATTTTAAAAATAA
1 A-TTTAAAATTAA
1362929 AT
1 AT
1362931 ATTATATTAT
Statistics
Matches: 59, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
10 8 0.14
12 24 0.41
13 19 0.32
14 8 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATTTAAAATTAA
Found at i:1362863 original size:6 final size:6
Alignment explanation
Indices: 1362848--1362915 Score: 61
Period size: 6 Copynumber: 11.7 Consensus size: 6
1362838 AAAATATTTA
** * *
1362848 TAAA-T TAAATT TAAATT TAAATT TAAAATT TTTATT TAAATT TTAATA
1 TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT TAAATT TAAATT
*
1362896 T-AATT T-AATT TAAAAT TAAA
1 TAAATT TAAATT TAAATT TAAA
1362916 ATTTTAAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
5 13 0.25
6 33 0.63
7 6 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAAATT
Done.