Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 185 of 198
Found at i:57522356 original size:15 final size:15
Alignment explanation
Indices: 57522336--57522370 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
57522326 TTTCTATGCC
57522336 ATTGTTATATTTATT
1 ATTGTTATATTTATT
*
57522351 ATTGTTGTATTTATT
1 ATTGTTATATTTATT
57522366 ATTGT
1 ATTGT
57522371 GGCATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.66
Consensus pattern (15 bp):
ATTGTTATATTTATT
Found at i:57524729 original size:22 final size:20
Alignment explanation
Indices: 57524692--57524731 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
57524682 ATCTTATATC
57524692 ATAAAAAATTAAAATTAATT
1 ATAAAAAATTAAAATTAATT
57524712 ATAAAACAATTCAAAATTAA
1 ATAAAA-AATT-AAAATTAA
57524732 AAATTAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 4 0.22
22 8 0.44
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (20 bp):
ATAAAAAATTAAAATTAATT
Found at i:57529469 original size:20 final size:20
Alignment explanation
Indices: 57529441--57529479 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
57529431 CAGGTTAATA
57529441 TTCCATATGATCATATATTC
1 TTCCATATGATCATATATTC
* * *
57529461 TTCCGTATGTTCATGTATT
1 TTCCATATGATCATATATT
57529480 TTGGACGCAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (20 bp):
TTCCATATGATCATATATTC
Found at i:57539013 original size:16 final size:18
Alignment explanation
Indices: 57538980--57539015 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
57538970 TTTTTTTATC
57538980 ATAACTAATTTATAAATT
1 ATAACTAATTTATAAATT
57538998 ATAACT-ATTT-TAAATT
1 ATAACTAATTTATAAATT
57539014 AT
1 AT
57539016 CATAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 4 0.22
18 6 0.33
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAACTAATTTATAAATT
Found at i:57545136 original size:20 final size:20
Alignment explanation
Indices: 57545113--57545150 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
57545103 AGGAATTCAT
*
57545113 TCATTCATAATTGAATAGCA
1 TCATTCATAAGTGAATAGCA
57545133 TCATTCATAAGTGAATAG
1 TCATTCATAAGTGAATAG
57545151 TATTCAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (20 bp):
TCATTCATAAGTGAATAGCA
Found at i:57558123 original size:2 final size:2
Alignment explanation
Indices: 57558116--57558148 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
57558106 TGCAATTTGA
*
57558116 TG TG TG TG TG TG TG TG TG TG TT TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
57558149 TAGGTGTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.45, T:0.55
Consensus pattern (2 bp):
TG
Found at i:57561027 original size:19 final size:18
Alignment explanation
Indices: 57561003--57561053 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
57560993 ATATATTGGT
57561003 TTTATATTATTTTTGAATA
1 TTTATATTATTTTTGAA-A
*
57561022 TTTATA-TCTTTTTGAAA
1 TTTATATTATTTTTGAAA
*
57561039 TTTTTATGTATTTTT
1 TTTATAT-TATTTTT
57561054 TATTTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 6 0.22
18 9 0.33
19 12 0.44
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (18 bp):
TTTATATTATTTTTGAAA
Found at i:57564677 original size:23 final size:23
Alignment explanation
Indices: 57564651--57564772 Score: 190
Period size: 23 Copynumber: 5.3 Consensus size: 23
57564641 ATAAGTGCAA
*
57564651 CACTGATATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
57564674 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
57564697 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
57564720 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
57564743 CACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
57564766 CACTGAT
1 CACTGAT
57564773 CAATAACACT
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 89 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:57564718 original size:46 final size:46
Alignment explanation
Indices: 57564651--57564770 Score: 213
Period size: 46 Copynumber: 2.6 Consensus size: 46
57564641 ATAAGTGCAA
* *
57564651 CACTGATATGTAGCTGAAGCTACCACTGTTATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
57564697 CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
*
57564743 CACTGAAACGTAGCCGAAGCTACCACTG
1 CACTGAAATGTAGCCGAAGCTACCACTG
57564771 ATCAATAACA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.22
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
Found at i:57567902 original size:21 final size:23
Alignment explanation
Indices: 57567852--57567906 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 23
57567842 TTTTGCTTAT
*
57567852 TCAAATAAAATCATAATTTATACA
1 TCAAATAAAAT-ATAATCTATACA
57567876 TCAAATAAAAT-TAATCTA-ACA
1 TCAAATAAAATATAATCTATACA
*
57567897 TGAAATAAAA
1 TCAAATAAAA
57567907 CACGGTGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 12 0.41
22 6 0.21
24 11 0.38
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (23 bp):
TCAAATAAAATATAATCTATACA
Found at i:57568259 original size:8 final size:8
Alignment explanation
Indices: 57568210--57568261 Score: 63
Period size: 8 Copynumber: 6.6 Consensus size: 8
57568200 ATATGTATGT
57568210 ATATATAA
1 ATATATAA
57568218 AT-TATAA
1 ATATATAA
57568225 AGTATA-AA
1 A-TATATAA
57568233 ATATATAA
1 ATATATAA
* *
57568241 GTATGTAA
1 ATATATAA
57568249 ATATATAA
1 ATATATAA
57568257 ATATA
1 ATATA
57568262 CACTTATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
7 10 0.27
8 25 0.68
9 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.37
Consensus pattern (8 bp):
ATATATAA
Found at i:57568300 original size:16 final size:16
Alignment explanation
Indices: 57568281--57568314 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
57568271 AAATTAAAAT
57568281 ATATATGTAGACATAA
1 ATATATGTAGACATAA
*
57568297 ATATATGTATACATAA
1 ATATATGTAGACATAA
57568313 AT
1 AT
57568315 TATAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (16 bp):
ATATATGTAGACATAA
Found at i:57568615 original size:3 final size:3
Alignment explanation
Indices: 57568607--57568700 Score: 138
Period size: 3 Copynumber: 31.3 Consensus size: 3
57568597 GTAAATGATC
57568607 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
57568655 ATA ATA ATA ATA ATA AT- ATA GCTA ATTA AT- TTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA A-TA ATA ATA ATA ATA ATA ATA
57568700 A
1 A
57568701 CCAACGGGAC
Statistics
Matches: 83, Mismatches: 4, Indels: 8
0.87 0.04 0.08
Matches are distributed among these distances:
2 3 0.04
3 75 0.90
4 5 0.06
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:57569430 original size:4 final size:4
Alignment explanation
Indices: 57569421--57569447 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
57569411 ATATGAGAGA
57569421 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
57569448 AGCTGAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:57574567 original size:39 final size:36
Alignment explanation
Indices: 57574524--57574623 Score: 101
Period size: 38 Copynumber: 2.6 Consensus size: 36
57574514 CTATATATAT
*
57574524 TTTTTAGAATTTTTTAATTTTAAAAAATAAATTTTGAAA
1 TTTTTAAAATTTTTTAATTTT-AAAAAT-AATTTT-AAA
* *
57574563 TTTTTATAAATATTTTGAATTTTAAAAATTATTTTAAA
1 TTTTTA-AAAT-TTTTTAATTTTAAAAATAATTTTAAA
*
57574601 TTTTTGAAAATTATTTTTATTTT
1 TTTTT-AAAATT-TTTTAATTTT
57574624 TATTTTTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
37 1 0.02
38 20 0.38
39 12 0.23
40 9 0.17
41 10 0.19
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (36 bp):
TTTTTAAAATTTTTTAATTTTAAAAATAATTTTAAA
Found at i:57574585 original size:19 final size:20
Alignment explanation
Indices: 57574554--57574626 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
57574544 TAAAAAATAA
57574554 ATTTTGAAATTTTTATAAA-T
1 ATTTTG-AATTTTTATAAATT
*
57574574 ATTTTGAA-TTTTAAAAATT
1 ATTTTGAATTTTTATAAATT
*
57574593 ATTTTAAATTTTTGA-AAATT
1 ATTTTGAATTTTT-ATAAATT
*
57574613 ATTTT-TATTTTTAT
1 ATTTTGAATTTTTAT
57574627 TTTTATTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
18 9 0.20
19 16 0.35
20 20 0.43
21 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (20 bp):
ATTTTGAATTTTTATAAATT
Found at i:57574586 original size:41 final size:37
Alignment explanation
Indices: 57574522--57574605 Score: 98
Period size: 40 Copynumber: 2.2 Consensus size: 37
57574512 TTCTATATAT
*
57574522 ATTTTTTAGAATTTTTTAATTTTAAAAAATAAATTTTGAA
1 ATTTTTTAGAATTTTTGAATTTT-AAAAAT-AATTTT-AA
*
57574562 ATTTTTATA-AATATTTTGAATTTTAAAAATTATTTTAA
1 ATTTTT-TAGAAT-TTTTGAATTTTAAAAATAATTTTAA
57574600 ATTTTT
1 ATTTTT
57574606 GAAAATTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
38 8 0.20
39 5 0.12
40 15 0.38
41 12 0.30
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (37 bp):
ATTTTTTAGAATTTTTGAATTTTAAAAATAATTTTAA
Found at i:57574624 original size:20 final size:20
Alignment explanation
Indices: 57574531--57574617 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
57574521 TATTTTTTAG
*
57574531 AATT-TTTT-AATTTTAAAA
1 AATTATTTTAAATTTTTAAA
* *
57574549 AATAAATTTTGAAATTTTTATA
1 AAT-TATTTT-AAATTTTTAAA
*
57574571 AA-TATTTTGAA-TTTTAAA
1 AATTATTTTAAATTTTTAAA
*
57574589 AATTATTTTAAATTTTTGAA
1 AATTATTTTAAATTTTTAAA
57574609 AATTATTTT
1 AATTATTTT
57574618 TATTTTTATT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
18 11 0.20
19 10 0.18
20 24 0.44
22 10 0.18
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
AATTATTTTAAATTTTTAAA
Found at i:57574629 original size:5 final size:6
Alignment explanation
Indices: 57574611--57574636 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
57574601 TTTTTGAAAA
57574611 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
57574637 GTAATTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:57576703 original size:11 final size:10
Alignment explanation
Indices: 57576673--57576706 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
57576663 AATTTCTTCC
57576673 TTTTTCTCTT
1 TTTTTCTCTT
57576683 TTTTTC-CTT
1 TTTTTCTCTT
57576692 TGTTTTCTCTT
1 T-TTTTCTCTT
57576703 TTTT
1 TTTT
57576707 CTTCCTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.18
10 14 0.64
11 4 0.18
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (10 bp):
TTTTTCTCTT
Found at i:57578395 original size:43 final size:43
Alignment explanation
Indices: 57578329--57578457 Score: 156
Period size: 43 Copynumber: 3.0 Consensus size: 43
57578319 ATAGGATTTC
* *
57578329 CGATATGTGTTTTCATGTAAGACCACGTCTGGGACGTTGGCTT
1 CGATCTGTGTTTTCATGTAAGACCACGTCTGGGACGTTGGCAT
*
57578372 CGA-CTTGTGTTTTCGTGTAAGACC-CTGTCTGGGACAG-TGGCAT
1 CGATC-TGTGTTTTCATGTAAGACCAC-GTCTGGGAC-GTTGGCAT
* **
57578415 CGATCTGTGATCACATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATCTGTGTTTTCATGTAAGACCACGTCTGGGACGTTGGCAT
57578458 TGTACAAGCT
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.03
43 68 0.93
44 3 0.04
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (43 bp):
CGATCTGTGTTTTCATGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:57581480 original size:5 final size:5
Alignment explanation
Indices: 57581470--57581497 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
57581460 GGTGTGACAT
57581470 ATAAA ATAAA ATAAA ATAAA ATAAA ATA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATA
57581498 GGACTACCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:57595433 original size:17 final size:17
Alignment explanation
Indices: 57595410--57595453 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
57595400 AACCAATCTG
*
57595410 ATTAAAAAATATCAAAA
1 ATTAAAAAAAATCAAAA
* *
57595427 TTTAAAAAAAATTAAAA
1 ATTAAAAAAAATCAAAA
57595444 ATTAAAAAAA
1 ATTAAAAAAA
57595454 TCCGCTTCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
ATTAAAAAAAATCAAAA
Found at i:57599282 original size:14 final size:15
Alignment explanation
Indices: 57599254--57599287 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
57599244 GATTTTGATC
*
57599254 ATTAATTTAATATTA
1 ATTAATTTAAGATTA
57599269 ATTAA-TTAAGATTA
1 ATTAATTTAAGATTA
57599283 ATTAA
1 ATTAA
57599288 ATTGATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
ATTAATTTAAGATTA
Found at i:57602208 original size:9 final size:9
Alignment explanation
Indices: 57602191--57602227 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
57602181 TGAGTTTTCG
57602191 AATTCGAAT
1 AATTCGAAT
*
57602200 AACTCGAAT
1 AATTCGAAT
57602209 AATTCGAAT
1 AATTCGAAT
57602218 AATTCGAAT
1 AATTCGAAT
57602227 A
1 A
57602228 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:57602587 original size:19 final size:19
Alignment explanation
Indices: 57602555--57602591 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
57602545 TTTTTAATAT
57602555 TTTCCCTCCAAACTATTTAC
1 TTTCCCTCCAAACT-TTTAC
57602575 TTTCCCT-CAAACTTTTA
1 TTTCCCTCCAAACTTTTA
57602592 TTCTCCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTCCCTCCAAACTTTTAC
Found at i:57602639 original size:21 final size:20
Alignment explanation
Indices: 57602564--57602639 Score: 56
Period size: 20 Copynumber: 4.0 Consensus size: 20
57602554 TTTTCCCTCC
*
57602564 AAACTATTTACTT-T-CCCT
1 AAACTTTTTACTTCTCCCCT
*
57602582 CAAAC-TTTTA-TTCT--CCA
1 -AAACTTTTTACTTCTCCCCT
* *
57602599 AAACTTTTTATTTTTCCCCT
1 AAACTTTTTACTTCTCCCCT
57602619 AAACTTTTTACTTCTCACCCT
1 AAACTTTTTACTTCTC-CCCT
57602640 TTACTCTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
16 4 0.09
17 9 0.20
18 8 0.18
19 4 0.09
20 16 0.36
21 4 0.09
ACGTcount: A:0.25, C:0.29, G:0.00, T:0.46
Consensus pattern (20 bp):
AAACTTTTTACTTCTCCCCT
Found at i:57602771 original size:17 final size:17
Alignment explanation
Indices: 57602717--57602797 Score: 69
Period size: 17 Copynumber: 4.6 Consensus size: 17
57602707 TTATATCTAC
57602717 TATTTATATTATTAAAT
1 TATTTATATTATTAAAT
* *
57602734 TAAATTTCACATT-TTATAT
1 T--ATTT-ATATTATTAAAT
57602753 TATTTATATTATTAAAT
1 TATTTATATTATTAAAT
*
57602770 TATTTAGTCA-TATTGAA-
1 TATTTA-T-ATTATTAAAT
57602787 TATTTATATTA
1 TATTTATATTA
57602798 AAATTGAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
15 1 0.02
16 7 0.13
17 22 0.42
18 7 0.13
19 11 0.21
20 4 0.08
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (17 bp):
TATTTATATTATTAAAT
Found at i:57605691 original size:43 final size:41
Alignment explanation
Indices: 57605666--57605783 Score: 134
Period size: 41 Copynumber: 2.8 Consensus size: 41
57605656 TATCTCATAT
57605666 CGATGCCACTGTCCCAGACAGGGTCTTACACGAATCAAATA
1 CGATGCCACTGTCCCAGACAGGGTCTTACACGAATCAAATA
* * * *
57605707 CGATGCCAATGTCCTAGACATGGTCTTACACGTAAACACAAGT-
1 CGATGCCACTGTCCCAGACAGGGTCTTACACG-AATCA-AA-TA
57605750 CGATGCCGAC-GTCCCAGAC-GTGGTCTTACACGAA
1 CGATGCC-ACTGTCCCAGACAG-GGTCTTACACGAA
57605784 AACACATATC
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
41 29 0.45
42 6 0.09
43 28 0.43
44 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (41 bp):
CGATGCCACTGTCCCAGACAGGGTCTTACACGAATCAAATA
Found at i:57605787 original size:43 final size:41
Alignment explanation
Indices: 57605625--57605789 Score: 156
Period size: 43 Copynumber: 3.9 Consensus size: 41
57605615 ATATTGAACA
* * * *
57605625 ATGCCAACGTCCCAGACGTGGTCTTACATGCTATCTCATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG-AAACACA-ATCG
*
57605668 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAATCA-AATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGAAACACAAT-CG
* * *
57605709 ATGCCAATGTCCTAGACATGGTCTTACACGTAAACACAAGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG-AAACACAA-TCG
*
57605752 ATGCCGACGTCCCAGACGTGGTCTTACACGAAAACACA
1 ATGCCAACGTCCCAGACGTGGTCTTACACG-AAACACA
57605790 TATCAGAGTA
Statistics
Matches: 102, Mismatches: 12, Indels: 16
0.78 0.09 0.12
Matches are distributed among these distances:
40 2 0.02
41 27 0.26
42 10 0.10
43 61 0.60
44 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (41 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGAAACACAATCG
Found at i:57608111 original size:32 final size:32
Alignment explanation
Indices: 57608070--57608134 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
57608060 GTAACTACTC
57608070 TTCCCAATAATGTTGCTTTCAAGTTTCAAATT
1 TTCCCAATAATGTTGCTTTCAAGTTTCAAATT
57608102 TTCCCAATAATGTTGCTTTCAAGTTTCAAATT
1 TTCCCAATAATGTTGCTTTCAAGTTTCAAATT
57608134 T
1 T
57608135 GTGTTCACCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.45
Consensus pattern (32 bp):
TTCCCAATAATGTTGCTTTCAAGTTTCAAATT
Found at i:57610434 original size:14 final size:13
Alignment explanation
Indices: 57610386--57610439 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
57610376 ATATATTTAT
*
57610386 TTTCAAATTTAAA
1 TTTCAATTTTAAA
* *
57610399 TATT-AATATAAAA
1 T-TTCAATTTTAAA
57610412 TTTCAATTTTAAA
1 TTTCAATTTTAAA
57610425 TTTCATATTTTAAA
1 TTTCA-ATTTTAAA
57610439 T
1 T
57610440 AAATATAACA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
12 2 0.06
13 20 0.61
14 11 0.33
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTCAATTTTAAA
Found at i:57611214 original size:21 final size:23
Alignment explanation
Indices: 57611164--57611218 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 23
57611154 TTTTGCTTAT
*
57611164 TCAAATAAAATCATAATTTATACA
1 TCAAATAAAAT-ATAATCTATACA
57611188 TCAAATAAAAT-TAATCTA-ACA
1 TCAAATAAAATATAATCTATACA
*
57611209 TGAAATAAAA
1 TCAAATAAAA
57611219 CACGGTGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 12 0.41
22 6 0.21
24 11 0.38
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (23 bp):
TCAAATAAAATATAATCTATACA
Found at i:57612886 original size:17 final size:18
Alignment explanation
Indices: 57612855--57612889 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
57612845 CTCTTCCCGA
57612855 AAAGGAAAAAGAAAAATC
1 AAAGGAAAAAGAAAAATC
57612873 AAAGGAAAAA-AAAAATC
1 AAAGGAAAAAGAAAAATC
57612890 CCCCCTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.74, C:0.06, G:0.14, T:0.06
Consensus pattern (18 bp):
AAAGGAAAAAGAAAAATC
Found at i:57615514 original size:5 final size:5
Alignment explanation
Indices: 57615504--57615535 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
57615494 GCGTTTCTTG
57615504 TTATT TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TT
57615536 TACTTTACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:57616325 original size:3 final size:3
Alignment explanation
Indices: 57616319--57616355 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
57616309 AACTAATAAG
* *
57616319 TTA TTA TTA TTA TGA TTA TTA TTA TTA TTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
57616356 CTATGTCTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:57616473 original size:17 final size:18
Alignment explanation
Indices: 57616444--57616480 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
57616434 CTTTTTTATT
57616444 TTATATAGATATAAATAC
1 TTATATAGATATAAATAC
*
57616462 TTATAT-GATATATATAC
1 TTATATAGATATAAATAC
57616479 TT
1 TT
57616481 TACACTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (18 bp):
TTATATAGATATAAATAC
Found at i:57618182 original size:18 final size:18
Alignment explanation
Indices: 57618161--57618195 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
57618151 GTTATTGCAC
57618161 TAATTTATAA-TATTTTTG
1 TAATTT-TAAGTATTTTTG
57618179 TAATTTTAAGTATTTTT
1 TAATTTTAAGTATTTTT
57618196 ATCATTTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
TAATTTTAAGTATTTTTG
Found at i:57622803 original size:21 final size:20
Alignment explanation
Indices: 57622779--57622822 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
57622769 GATCTGTTGA
*
57622779 TTAGTAATTTCATCTTAAATT
1 TTAGGAATTTCAT-TTAAATT
* *
57622800 TTAGGATTTTCATTTAGATT
1 TTAGGAATTTCATTTAAATT
57622820 TTA
1 TTA
57622823 ATTTTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.55
Consensus pattern (20 bp):
TTAGGAATTTCATTTAAATT
Found at i:57643628 original size:27 final size:30
Alignment explanation
Indices: 57643566--57643633 Score: 75
Period size: 33 Copynumber: 2.1 Consensus size: 30
57643556 AAATAACATG
57643566 ATATATAAATTTTGATTTAATTTAATTATAT
1 ATATATAAATTTTGATTT-ATTTAATTATAT
*
57643597 ATATATGAAATTTT-ATTTTTTATTTAATTATAC
1 ATATAT-AAATTTTGA---TTTATTTAATTATAT
57643630 ATAT
1 ATAT
57643634 TTTAAAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
31 7 0.22
32 7 0.22
33 15 0.47
34 3 0.09
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (30 bp):
ATATATAAATTTTGATTTATTTAATTATAT
Found at i:57654519 original size:108 final size:108
Alignment explanation
Indices: 57654324--57654628 Score: 488
Period size: 108 Copynumber: 2.8 Consensus size: 108
57654314 AAAAATCAAG
* * * *
57654324 AGGATATTTGGCAATTTGGTTAAACGAG-AAATCGAAACCCAGCACCTTAGGGCACG-TTCCTCG
1 AGGATATTTAGCAATTTGGTTGAACGAGAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCG
* * *
57654387 AATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGAA
66 AATTTCCAAACGCAAAACATTGCCTTATTGTAAAATTTTTAAA
*
57654430 AGGATATTTAGCAATTTGGTTGAACGAGAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCG
1 AGGATATTTAGCAATTTGGTTGAACGAGAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCG
57654495 AATTTCCAAACGCAAAACATTGCCTTATTGTAAAATTTTTAAA
66 AATTTCCAAACGCAAAACATTGCCTTATTGTAAAATTTTTAAA
*
57654538 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCAATTTGGTTGAACGAG-AAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
* *
57654603 GAATTTCCAAACGCTAAATATTGCCT
65 GAATTTCCAAACGCAAAACATTGCCT
57654629 CAATTAGAAA
Statistics
Matches: 184, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
106 26 0.14
107 26 0.14
108 73 0.40
109 59 0.32
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (108 bp):
AGGATATTTAGCAATTTGGTTGAACGAGAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCG
AATTTCCAAACGCAAAACATTGCCTTATTGTAAAATTTTTAAA
Found at i:57654933 original size:13 final size:13
Alignment explanation
Indices: 57654915--57654971 Score: 64
Period size: 13 Copynumber: 4.4 Consensus size: 13
57654905 AATTATAAAA
57654915 ATATAAAATATAT
1 ATATAAAATATAT
*
57654928 ATAT-AAGTATAT
1 ATATAAAATATAT
*
57654940 ATTTTAAAAT-TACT
1 A-TATAAAATATA-T
57654954 ATATAAAATATAT
1 ATATAAAATATAT
57654967 ATATA
1 ATATA
57654972 TAAGTAAGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
12 8 0.22
13 21 0.58
14 7 0.19
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (13 bp):
ATATAAAATATAT
Found at i:57655076 original size:13 final size:13
Alignment explanation
Indices: 57655058--57655085 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
57655048 GAATCATAAA
57655058 ATATAAAATACAT
1 ATATAAAATACAT
57655071 ATATAAAATACAT
1 ATATAAAATACAT
57655084 AT
1 AT
57655086 TTTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (13 bp):
ATATAAAATACAT
Found at i:57655258 original size:3 final size:3
Alignment explanation
Indices: 57655250--57655315 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
57655240 ACTCCTATAT
57655250 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
57655298 ATA ATA ATA ATA ACA ATA
1 ATA ATA ATA ATA ATA ATA
57655316 GGACTAAATC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:57657810 original size:37 final size:37
Alignment explanation
Indices: 57657768--57657953 Score: 300
Period size: 37 Copynumber: 5.0 Consensus size: 37
57657758 GGTAGTTTTA
**
57657768 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
57657805 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
* *
57657842 GTTACACTTATCTGATCAAGAAACAAAGTGATGAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
57657879 GTTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
** *
57657916 GCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
57657953 G
1 G
57657954 TAGCCTTAGC
Statistics
Matches: 140, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 140 1.00
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.26
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:57658024 original size:45 final size:46
Alignment explanation
Indices: 57657916--57658041 Score: 213
Period size: 46 Copynumber: 2.8 Consensus size: 46
57657906 GTGATAAGTG
*
57657916 GCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
57657962 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCC-TA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
*
57658007 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
57658042 ATTATACGTA
Statistics
Matches: 78, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
43 12 0.15
44 5 0.06
45 19 0.24
46 42 0.54
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
Found at i:57659506 original size:20 final size:21
Alignment explanation
Indices: 57659465--57659502 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 21
57659455 TCTTTTGTGA
57659465 TTTGGGCTATTAGGGTTTGTT
1 TTTGGGCTATTAGGGTTTGTT
57659486 TTTGGG-TATT-GGGTTTG
1 TTTGGGCTATTAGGGTTTG
57659503 GTTTAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 4 0.24
21 6 0.35
ACGTcount: A:0.08, C:0.03, G:0.37, T:0.53
Consensus pattern (21 bp):
TTTGGGCTATTAGGGTTTGTT
Found at i:57662321 original size:44 final size:44
Alignment explanation
Indices: 57662262--57662416 Score: 152
Period size: 44 Copynumber: 3.4 Consensus size: 44
57662252 TATTATTAAG
* *
57662262 AATTTTATGAAATTATATATCATTATTAAATTATATTTAATATT
1 AATTATATTAAATTATATATCATTATTAAATTATATTTAATATT
* ** * *
57662306 AATTATGTTAAATTATATAAATTCATATAAGAAAATT-TATTATCA-AGT
1 AATTATATTAAATTATAT--A-TCAT-T-ATTAAATTATATT-TAATATT
* *
57662354 AATTTTATGAAATTATATATCATTATTAAATTATATTTAATATT
1 AATTATATTAAATTATATATCATTATTAAATTATATTTAATATT
*
57662398 AATTATTTTAAATTATATA
1 AATTATATTAAATTATATA
57662417 AATTCATATA
Statistics
Matches: 86, Mismatches: 17, Indels: 16
0.72 0.14 0.13
Matches are distributed among these distances:
43 8 0.09
44 38 0.44
45 4 0.05
46 2 0.02
47 4 0.05
48 22 0.26
49 8 0.09
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (44 bp):
AATTATATTAAATTATATATCATTATTAAATTATATTTAATATT
Found at i:57662374 original size:92 final size:91
Alignment explanation
Indices: 57662231--57662491 Score: 432
Period size: 92 Copynumber: 2.8 Consensus size: 91
57662221 ATGATTTTAG
* *
57662231 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
57662296 ATTTAATATTAATTATGTTAAATTATA
65 ATTTAATATTAATTATGTTAAATTATA
57662323 TAAATTCATATAAGAAAATTTATTATCAAGTAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAAAATTTATTATCAAG-AATTTTATGAAATTATATATCATTATTAAATTAT
*
57662388 ATTTAATATTAATTATTTTAAATTATA
65 ATTTAATATTAATTATGTTAAATTATA
* *
57662415 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTTATATATTATTATTAAATTTT
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAA-TTATATATCATTATTAAATTAT
*
57662480 ATTAAATCATTA
65 ATTTAAT-ATTA
57662492 TATTTTTAAT
Statistics
Matches: 160, Mismatches: 6, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
91 24 0.15
92 132 0.82
93 4 0.03
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATATTAATTATGTTAAATTATA
Found at i:57662436 original size:44 final size:44
Alignment explanation
Indices: 57662296--57662436 Score: 144
Period size: 44 Copynumber: 3.1 Consensus size: 44
57662286 ATTAAATTAT
*
57662296 ATTTAATATTAATTATGTTAAATTATATAAATTCATATAAGAAA
1 ATTTAATATTAATTATTTTAAATTATATAAATTCATATAAGAAA
* * * * *
57662340 ATTTATTATCAAGTAATTTTATGAAATTATATATCATT-AT-TAA-ATTAT
1 ATTTAATATTAA-TTA-TTT-T-AAATTATATA-AATTCATATAAGA--AA
57662388 ATTTAATATTAATTATTTTAAATTATATAAATTCATATAAGAAA
1 ATTTAATATTAATTATTTTAAATTATATAAATTCATATAAGAAA
57662432 ATTTA
1 ATTTA
57662437 TTATCAAGAA
Statistics
Matches: 76, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
43 3 0.04
44 28 0.37
45 6 0.08
46 7 0.09
47 6 0.08
48 23 0.30
49 3 0.04
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (44 bp):
ATTTAATATTAATTATTTTAAATTATATAAATTCATATAAGAAA
Found at i:57662482 original size:44 final size:43
Alignment explanation
Indices: 57662248--57662483 Score: 140
Period size: 44 Copynumber: 5.2 Consensus size: 43
57662238 ATATAAGAAC
*
57662248 ATTTTATTATTAAGAATTTTATGAAA-TTATATATCATTATTAA
1 ATTTTATTA-TAAGAATTTTATGAAATTTATATATTATTATTAA
* * * **
57662291 ATTATATT-TAA-TATTAATTATGTTAAATTATATAAATTCATATAAGAA
1 ATTTTATTATAAGAATT--TTATG--AAATT-TATATATT-AT-TATTAA
* *
57662339 AATTTATTATCAAGTAATTTTATGAAA-TTATATATCATTATTAA
1 ATTTTATTAT-AAG-AATTTTATGAAATTTATATATTATTATTAA
* ** * * **
57662383 ATTATATTTAATATTAATTATT-TTAAATTATATAAATTCATATAAGAA
1 ATTTTA-TT-ATAAGAATT-TTATGAAATT-TATATATT-AT-TATTAA
*
57662431 AATTTATTATCAAGAATTTTATGAAATTTATATATTATTATTAA
1 ATTTTATTAT-AAGAATTTTATGAAATTTATATATTATTATTAA
57662475 ATTTTATTA
1 ATTTTATTA
57662484 AATCATTATA
Statistics
Matches: 141, Mismatches: 31, Indels: 41
0.66 0.15 0.19
Matches are distributed among these distances:
40 3 0.02
41 3 0.02
42 5 0.04
43 7 0.05
44 31 0.22
45 11 0.08
46 31 0.22
47 18 0.13
48 21 0.15
49 1 0.01
50 7 0.05
52 3 0.02
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (43 bp):
ATTTTATTATAAGAATTTTATGAAATTTATATATTATTATTAA
Found at i:57662653 original size:121 final size:120
Alignment explanation
Indices: 57662462--57662773 Score: 479
Period size: 121 Copynumber: 2.6 Consensus size: 120
57662452 TGAAATTTAT
*
57662462 ATATT-ATTATT-A-AATTTTATTAAATCATTATA-TTTTTAATTAAAAATATATTTAATATTAA
1 ATATTGATTATTAAGAATTTTATT-AAT--TTATATTTTTTAATT-AAAATATATTTAATAATAA
* * *
57662523 TTATTTTAAATTATATTTTATAGTATCATATATCATGATTTTAGTAAATTCATATATGA
62 TTATGTTAAATTATATTTTATAGTATCATATATCATGATTTGAGTAAATTCATATAAGA
57662582 ATATTGATTATTAAGAATTTTATTAATTTATATTTTTTAAATTAAAATATATTTAATAATAATTA
1 ATATTGATTATTAAGAATTTTATTAATTTATATTTTTT-AATTAAAATATATTTAATAATAATTA
*
57662647 TGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGA
65 TGTTAAATTATATTTTATAGTATCATATATCATGATTTGAGTAAATTCATATAAGA
* * *
57662703 ATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTAT
1 ATATTGATTATTAAGAATTTTATTAATTTATATTTTTTAATTAAAATATATTTAATAATAATTAT
57662768 GTTAAA
66 GTTAAA
57662774 ATATGATTAA
Statistics
Matches: 179, Mismatches: 8, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
120 42 0.23
121 120 0.67
122 8 0.04
123 9 0.05
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (120 bp):
ATATTGATTATTAAGAATTTTATTAATTTATATTTTTTAATTAAAATATATTTAATAATAATTAT
GTTAAATTATATTTTATAGTATCATATATCATGATTTGAGTAAATTCATATAAGA
Found at i:57662758 original size:15 final size:15
Alignment explanation
Indices: 57662723--57662764 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
57662713 TTAAGAATTT
*
57662723 TATTAAATTAT-ATA
1 TATTTAATTATAATA
57662737 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
57662751 TATTTAATAATAAT
1 TATTTAATTATAAT
57662765 TATGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:57669807 original size:15 final size:15
Alignment explanation
Indices: 57669789--57669819 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
57669779 AAATAAACTT
57669789 CAAATAAATTCGGCC
1 CAAATAAATTCGGCC
57669804 CAAATAAATTCGGCC
1 CAAATAAATTCGGCC
57669819 C
1 C
57669820 TATATACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.19
Consensus pattern (15 bp):
CAAATAAATTCGGCC
Found at i:57670967 original size:10 final size:9
Alignment explanation
Indices: 57670942--57670974 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
57670932 AATCAATTCA
57670942 ATTAAAAAT
1 ATTAAAAAT
57670951 ATTAAAAAT
1 ATTAAAAAT
57670960 ATTAAAAA-
1 ATTAAAAAT
57670968 ATTAAAA
1 ATTAAAA
57670975 TAATTTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
ATTAAAAAT
Found at i:57670979 original size:9 final size:8
Alignment explanation
Indices: 57670941--57670979 Score: 51
Period size: 9 Copynumber: 4.5 Consensus size: 8
57670931 TAATCAATTC
57670941 AATTAAAA
1 AATTAAAA
57670949 ATATTAAAA
1 A-ATTAAAA
57670958 ATATTAAAA
1 A-ATTAAAA
57670967 AATTAAAA
1 AATTAAAA
57670975 TAATT
1 -AATT
57670980 TGATTCAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.28
9 21 0.72
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AATTAAAA
Found at i:57683224 original size:29 final size:27
Alignment explanation
Indices: 57683184--57683256 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 27
57683174 TTTTTTACAA
57683184 AAAATAATATATAAATTTTAAAAATATAT
1 AAAATAA-ATATAAATTTTAAAAA-ATAT
*
57683213 ACAAATAAATAT---TTTCAAAAAATAT
1 A-AAATAAATATAAATTTTAAAAAATAT
*
57683238 AACAATAAATTTAAATTTT
1 AA-AATAAATATAAATTTT
57683257 CTATTAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
24 1 0.03
25 13 0.36
26 8 0.22
28 3 0.08
29 5 0.14
30 6 0.17
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (27 bp):
AAAATAAATATAAATTTTAAAAAATAT
Found at i:57683296 original size:25 final size:26
Alignment explanation
Indices: 57683268--57683317 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
57683258 TATTAATATT
57683268 TATATTAATATTAAATA-AATAAAAC
1 TATATTAATATTAAATAGAATAAAAC
*
57683293 TATATTCATATTAAATAGAATAAAA
1 TATATTAATATTAAATAGAATAAAA
57683318 ATTCCCACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (26 bp):
TATATTAATATTAAATAGAATAAAAC
Found at i:57690090 original size:27 final size:25
Alignment explanation
Indices: 57690060--57690110 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
57690050 TTTTTTTAGG
57690060 AGCCGAAATTAAATTATAATTTTTAAT
1 AGCCGAAA-T-AATTATAATTTTTAAT
* *
57690087 AGCCTAAATATTTATAATTTTTAA
1 AGCCGAAATAATTATAATTTTTAA
57690111 AGAATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 14 0.64
26 1 0.05
27 7 0.32
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (25 bp):
AGCCGAAATAATTATAATTTTTAAT
Found at i:57699584 original size:29 final size:29
Alignment explanation
Indices: 57699542--57699597 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
57699532 AAAAGCTCCT
57699542 TTTTTTCAATATTTACCGAAATGGGCCGG
1 TTTTTTCAATATTTACCGAAATGGGCCGG
* *
57699571 TTTTTT-AATTATTTACCGGAATTGGCC
1 TTTTTTCAA-TATTTACCGAAATGGGCC
57699598 ATTTTCCGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (29 bp):
TTTTTTCAATATTTACCGAAATGGGCCGG
Found at i:57703458 original size:27 final size:30
Alignment explanation
Indices: 57703408--57703477 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
57703398 TGTTATCTGG
* *
57703408 AAAGTATATATATTAAATTCTTAAAAAT-AA
1 AAAGTATAGAGATT-AATTCTTAAAAATAAA
**
57703438 AAA-TATAGAGATTAATT-TTAAATTTAAA
1 AAAGTATAGAGATTAATTCTTAAAAATAAA
57703466 AAAGTATAGAGA
1 AAAGTATAGAGA
57703478 CTTATGATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
27 6 0.18
28 9 0.26
29 16 0.47
30 3 0.09
ACGTcount: A:0.56, C:0.01, G:0.09, T:0.34
Consensus pattern (30 bp):
AAAGTATAGAGATTAATTCTTAAAAATAAA
Found at i:57704390 original size:4 final size:4
Alignment explanation
Indices: 57704381--57704411 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
57704371 TTTCTTAAAA
57704381 TATC TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TAT
57704412 ATATTATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:57709020 original size:31 final size:33
Alignment explanation
Indices: 57708960--57709022 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
57708950 TACTTTTAAT
*
57708960 TTAATATATTTTAATTTATTAAATATATATAAA
1 TTAATATATTTTAATATATTAAATATATATAAA
* *
57708993 TTAATATTTTTTAATAT-TTACAT-TATATAA
1 TTAATATATTTTAATATATTAAATATATATAA
57709023 TCATATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 7 0.26
32 5 0.19
33 15 0.56
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (33 bp):
TTAATATATTTTAATATATTAAATATATATAAA
Found at i:57710477 original size:117 final size:117
Alignment explanation
Indices: 57710269--57710492 Score: 274
Period size: 117 Copynumber: 1.9 Consensus size: 117
57710259 GCACATTCTT
* * * *
57710269 CTGAGAATGTTGGAACTCCGGAGAAGAATTTTGATCAACAGACAATGAAGGATAATGTCTCTGCT
1 CTGAGAATGTTGGAACTCAGGAGAAGAATTTGGATCAACAGACAATGAAGGAGAATGTCTCCGCT
** *
57710334 ACATATGCTTCGACTTTCCAGAATTTTTTTCGTCCTTTAGGTGAACAATCTA
66 ACATATGCTTCGACTTTCCAGAATTTTACTCGTCCTTCAGGTGAACAATCTA
* * *
57710386 CTGAGAATGTTGG-ACATCTAGG-GAGGAATTTGGATCAACAGGCAGTGAAAGG-GAATGTCTCC
1 CTGAGAATGTTGGAAC-TC-AGGAGAAGAATTTGGATCAACAGACAATG-AAGGAGAATGTCTCC
* * * *
57710448 GCTAGATATGCTTCGGCTTTCCGGGATTTTACTCGTCCTTCAGGT
63 GCTACATATGCTTCGACTTTCCAGAATTTTACTCGTCCTTCAGGT
57710493 CAAACAGAAT
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
116 2 0.02
117 82 0.91
118 6 0.07
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (117 bp):
CTGAGAATGTTGGAACTCAGGAGAAGAATTTGGATCAACAGACAATGAAGGAGAATGTCTCCGCT
ACATATGCTTCGACTTTCCAGAATTTTACTCGTCCTTCAGGTGAACAATCTA
Found at i:57714329 original size:19 final size:19
Alignment explanation
Indices: 57714305--57714366 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 19
57714295 CAAATTCTGG
57714305 AAAAATTAAAAATATTTTA
1 AAAAATTAAAAATATTTTA
* *
57714324 AAAAATATATAATAGTTTTTTA
1 AAAAAT-TA-AA-AATATTTTA
*
57714346 AAAAAAT-AAAA-ATTTTA
1 AAAAATTAAAAATATTTTA
57714363 AAAA
1 AAAA
57714367 TTTTGGTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
17 9 0.26
18 1 0.03
19 8 0.23
20 2 0.06
21 3 0.09
22 12 0.34
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAAATTAAAAATATTTTA
Found at i:57714674 original size:22 final size:21
Alignment explanation
Indices: 57714633--57714681 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
57714623 TAATTTTATG
*
57714633 TATAAAATAAACATTTAATTA
1 TATAAAATAAACATTAAATTA
*
57714654 TATAAACATAAAC-TTAAAATTT
1 TATAAA-ATAAACATT-AAATTA
57714676 TATAAA
1 TATAAA
57714682 TATTTAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (21 bp):
TATAAAATAAACATTAAATTA
Found at i:57715433 original size:25 final size:26
Alignment explanation
Indices: 57715366--57715437 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 26
57715356 AAAATTTTCT
* *
57715366 TTAAAAATGTTAAATTTTATACAAAATA
1 TTAAAAA-G-TAAATTATATTCAAAATA
*
57715394 TTAAAAAGTAAATTATATTCATAATA
1 TTAAAAAGTAAATTATATTCAAAATA
*
57715420 TTATAAA-TAAATTATATT
1 TTAAAAAGTAAATTATATT
57715438 TTAAAAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
25 11 0.28
26 21 0.52
27 1 0.03
28 7 0.17
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (26 bp):
TTAAAAAGTAAATTATATTCAAAATA
Found at i:57716014 original size:2 final size:2
Alignment explanation
Indices: 57716007--57716038 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
57715997 TAACAATGAC
57716007 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57716039 TTCACTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57722540 original size:18 final size:19
Alignment explanation
Indices: 57722501--57722540 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
57722491 TATATAAATT
**
57722501 AATGTATAATAAATATTTA
1 AATGTATAATAAATATCAA
57722520 AATGTATAA-AAATATCAA
1 AATGTATAATAAATATCAA
57722538 AAT
1 AAT
57722541 AAATGTTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (19 bp):
AATGTATAATAAATATCAA
Found at i:57724830 original size:90 final size:90
Alignment explanation
Indices: 57724451--57724818 Score: 574
Period size: 90 Copynumber: 4.1 Consensus size: 90
57724441 ACTGTTTGAA
* * *
57724451 CGTCGCCGTCTTCTCCAAGATGAAGATCAACTTCCGGTTGTCGGCCATTCTGATTGGACTTCTTT
1 CGTCGCCGTCTTCTCCAAGACGAAGATCAACTTCCGGTTGTCGGCCATTCCGATTGGACATCTTT
57724516 TTTAGAACGAAACAAGGAATGGAAT
66 TTTAGAACGAAACAAGGAATGGAAT
* *
57724541 CGTCGCCGTCTTCTCCAAGACGAAGATCAACTTCCGGTTGTCGGCCATTCTGATTGGACTTCTTT
1 CGTCGCCGTCTTCTCCAAGACGAAGATCAACTTCCGGTTGTCGGCCATTCCGATTGGACATCTTT
57724606 TTTAGAACGAAACAAGGAATGGAAT
66 TTTAGAACGAAACAAGGAATGGAAT
** * * * *
57724631 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGACTGGACATCCTT
1 CGTCGCCGTCTTCTCCAAGACGAAGATCAACTTCCGGTTGTCGGCCATTCCGATTGGACATCTTT
57724696 TTTAGAACGAAACAAGGAATGGAAT
66 TTTAGAACGAAACAAGGAATGGAAT
** *
57724721 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTGTCGGCCATTCCGATTGGACATCATT
1 CGTCGCCGTCTTCTCCAAGACGAAGATCAACTTCCGGTTGTCGGCCATTCCGATTGGACATCTTT
* * *
57724786 TTTAGAACGGAACAAGGATTGGAAC
66 TTTAGAACGAAACAAGGAATGGAAT
*
57724811 CGCCGCCG
1 CGTCGCCG
57724819 GATGCTCCAA
Statistics
Matches: 261, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 261 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (90 bp):
CGTCGCCGTCTTCTCCAAGACGAAGATCAACTTCCGGTTGTCGGCCATTCCGATTGGACATCTTT
TTTAGAACGAAACAAGGAATGGAAT
Found at i:57726020 original size:51 final size:51
Alignment explanation
Indices: 57725948--57726326 Score: 499
Period size: 51 Copynumber: 7.4 Consensus size: 51
57725938 TCCCTTACAT
** * * * * * *
57725948 CCCAGATCTTTCCATTGGTAAAGCTGAAGACAAAGGGTTGATCCCTA-CGTC
1 CCCAGATCTTTCCGCTAGTAAACCTGAAAATAATGGGGTGATCCCTATC-TC
* * * * * * *
57725999 CCCAGATGTTCCCGCTAGTAAACCCGAAAACAATGGGTTCATCCCTACCTC
1 CCCAGATCTTTCCGCTAGTAAACCTGAAAATAATGGGGTGATCCCTATCTC
* * * * * *
57726050 CCCAGATGTTCCCGCTAGTAAACCCGAAAACAGTGGGTTGATCCCTATCTC
1 CCCAGATCTTTCCGCTAGTAAACCTGAAAATAATGGGGTGATCCCTATCTC
*
57726101 CCCAGATCTTTCCGCTAGTAAACCTGAAAATAATGGGGTGATGCCTATCTC
1 CCCAGATCTTTCCGCTAGTAAACCTGAAAATAATGGGGTGATCCCTATCTC
* * *
57726152 TCCAGATCTTTCCGCTAGTAAACCTGAAAATAATGGGGTGATGCCTGTCTC
1 CCCAGATCTTTCCGCTAGTAAACCTGAAAATAATGGGGTGATCCCTATCTC
57726203 CCCAGATCTTTCCGCTAGTAAACCTGAAAATAATGGGGTGATCCCTATCTC
1 CCCAGATCTTTCCGCTAGTAAACCTGAAAATAATGGGGTGATCCCTATCTC
*
57726254 CCCAGATCTTTCCGCTAGTAAACCTGAATATAATGGGGTGATCCCTATCTC
1 CCCAGATCTTTCCGCTAGTAAACCTGAAAATAATGGGGTGATCCCTATCTC
*
57726305 CCCAAATCTTTCCGCTAGTAAA
1 CCCAGATCTTTCCGCTAGTAAA
57726327 GCCGCACACA
Statistics
Matches: 300, Mismatches: 27, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
51 299 1.00
52 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.26
Consensus pattern (51 bp):
CCCAGATCTTTCCGCTAGTAAACCTGAAAATAATGGGGTGATCCCTATCTC
Found at i:57726399 original size:21 final size:21
Alignment explanation
Indices: 57726375--57726443 Score: 120
Period size: 21 Copynumber: 3.3 Consensus size: 21
57726365 ACACAAGAAA
57726375 AAGAAGCACCATGGAAAAGGG
1 AAGAAGCACCATGGAAAAGGG
57726396 AAGAAGCACCATGGAAAAGGG
1 AAGAAGCACCATGGAAAAGGG
* *
57726417 AAGAAGCACCGTGGGAAAGGG
1 AAGAAGCACCATGGAAAAGGG
57726438 AAGAAG
1 AAGAAG
57726444 AAAGGGAAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.46, C:0.13, G:0.36, T:0.04
Consensus pattern (21 bp):
AAGAAGCACCATGGAAAAGGG
Found at i:57728938 original size:6 final size:6
Alignment explanation
Indices: 57728927--57728954 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
57728917 ATTTGTAAGT
57728927 TAAAAA TAAAAA TAAAAA TAAAAA TAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAA
57728955 TCTAAAGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:57742364 original size:14 final size:14
Alignment explanation
Indices: 57742345--57742372 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
57742335 AAAATATGAC
57742345 CAATATGGTCATTA
1 CAATATGGTCATTA
57742359 CAATATGGTCATTA
1 CAATATGGTCATTA
57742373 TTAGTTATTT
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:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
CAATATGGTCATTA
Found at i:57750190 original size:41 final size:41
Alignment explanation
Indices: 57750140--57750219 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
57750130 AATCACAATC
* *
57750140 ACAATTCAATTCAAATTCACTTTCCAC-TTTCTAATCAATAT
1 ACAATTCAATACAAATACACTTTCCACTTTTC-AATCAATAT
* *
57750181 ACAATTCAATACTAATACATTTTCCACTTTTCAATCAAT
1 ACAATTCAATACAAATACACTTTCCACTTTTCAATCAAT
57750220 GTACCATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 30 0.88
42 4 0.12
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.39
Consensus pattern (41 bp):
ACAATTCAATACAAATACACTTTCCACTTTTCAATCAATAT
Found at i:57751273 original size:13 final size:13
Alignment explanation
Indices: 57751245--57751282 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
57751235 TAAGTTATAC
57751245 ATATATATATAA-A
1 ATATA-ATATAATA
57751258 ATATAATATAATA
1 ATATAATATAATA
57751271 ATATAAT-TAATA
1 ATATAATATAATA
57751283 TAATACTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATAATATAATA
Found at i:57757559 original size:16 final size:16
Alignment explanation
Indices: 57757538--57757573 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
57757528 TTTGGTTCGC
57757538 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
57757554 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
57757570 TGTA
1 TGTA
57757574 ATAGCTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:57757661 original size:39 final size:40
Alignment explanation
Indices: 57757559--57757667 Score: 112
Period size: 44 Copynumber: 2.6 Consensus size: 40
57757549 AGAGGTGTAT
*
57757559 TGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGGAATAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
* ***
57757599 TGTAATGAAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TG----G-AATAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
57757643 TGGAATAGAGGTGTAATAGCATAAT
1 TGGAATAGAGGTGTAATAGC-TAAT
57757668 GGAAAAAACT
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
39 15 0.27
40 3 0.05
41 4 0.07
44 20 0.36
45 14 0.25
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.34
Consensus pattern (40 bp):
TGGAATAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:57764337 original size:13 final size:13
Alignment explanation
Indices: 57764319--57764344 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57764309 CAGCTAAACT
57764319 GAAACAGAAGGAA
1 GAAACAGAAGGAA
57764332 GAAACAGAAGGAA
1 GAAACAGAAGGAA
57764345 CGGCAGCTAA
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:0.08, G:0.31, T:0.00
Consensus pattern (13 bp):
GAAACAGAAGGAA
Found at i:57764352 original size:39 final size:39
Alignment explanation
Indices: 57764308--57764383 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
57764298 AGGTTGTGAA
57764308 GCAGCTAAACTGAAACAGAAGGAAGAAACAGAAGGAACG
1 GCAGCTAAACTGAAACAGAAGGAAGAAACAGAAGGAACG
*
57764347 GCAGCTAAACTGAAACAGAAGGAAGAAACATAAGGAA
1 GCAGCTAAACTGAAACAGAAGGAAGAAACAGAAGGAA
57764384 AGGGGAAGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.53, C:0.14, G:0.26, T:0.07
Consensus pattern (39 bp):
GCAGCTAAACTGAAACAGAAGGAAGAAACAGAAGGAACG
Found at i:57767045 original size:27 final size:27
Alignment explanation
Indices: 57767015--57767066 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
57767005 GCTTAATAGC
57767015 CACTATTTCGCAGTAGCAGCGGCGTAT
1 CACTATTTCGCAGTAGCAGCGGCGTAT
57767042 CACTATTTCGCAGTAGCAGCGGCGT
1 CACTATTTCGCAGTAGCAGCGGCGT
57767067 GCGCCACCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (27 bp):
CACTATTTCGCAGTAGCAGCGGCGTAT
Found at i:57773631 original size:8 final size:9
Alignment explanation
Indices: 57773610--57773640 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
57773600 CCTAACTCTA
57773610 AAAAAATTT
1 AAAAAATTT
57773619 AAAAAATTT
1 AAAAAATTT
57773628 AAAAAATTAT
1 AAAAAATT-T
57773638 AAA
1 AAA
57773641 TATATAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 17 0.81
10 4 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AAAAAATTT
Found at i:57791855 original size:14 final size:14
Alignment explanation
Indices: 57791836--57791865 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
57791826 CACCTCACTC
57791836 TCCATCTAAACAGA
1 TCCATCTAAACAGA
57791850 TCCATCTAAACAGA
1 TCCATCTAAACAGA
57791864 TC
1 TC
57791866 GCAGAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.30, G:0.07, T:0.23
Consensus pattern (14 bp):
TCCATCTAAACAGA
Found at i:57792141 original size:2 final size:2
Alignment explanation
Indices: 57792134--57792159 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57792124 TGTATTCAAC
57792134 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
57792160 TGAATTCCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57797893 original size:10 final size:11
Alignment explanation
Indices: 57797862--57797894 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
57797852 TATGTAAAAA
57797862 TATAATAATTGT
1 TATAATAA-TGT
57797874 TATAATAATGT
1 TATAATAATGT
57797885 TAT-ATAATGT
1 TATAATAATGT
57797895 GTTGGAGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 6 0.29
12 8 0.38
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (11 bp):
TATAATAATGT
Found at i:57800844 original size:42 final size:43
Alignment explanation
Indices: 57800742--57800900 Score: 194
Period size: 43 Copynumber: 3.7 Consensus size: 43
57800732 AATGTGATAT
** * *
57800742 CGTGTAAGACCATGTCTGGGATGTTGGCATCGATTTAAGATCTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGATATATGAT-TA
*
57800786 CGTGTAAGACCATGTCTGGGACATTGGCGTCG-TATATGATTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGATATATGATTA
* * * *
57800828 CGTGTAAGACCTTGTCTGGGACAGTGGCATCGTTATTTGATTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGATATATGATTA
* * *
57800871 CATGTAATACCACGTCTGGGACATTGGCAT
1 CGTGTAAGACCATGTCTGGGACATTGGCAT
57800901 TGTACGAGCC
Statistics
Matches: 100, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
42 31 0.31
43 40 0.40
44 29 0.29
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTGGGACATTGGCATCGATATATGATTA
Found at i:57800928 original size:18 final size:18
Alignment explanation
Indices: 57800902--57800939 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
57800892 CATTGGCATT
*
57800902 GTACGAGCCTTTTGAGCC
1 GTACAAGCCTTTTGAGCC
57800920 GTACAAGCCTTTTGAGCC
1 GTACAAGCCTTTTGAGCC
57800938 GT
1 GT
57800940 CCGAGCATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (18 bp):
GTACAAGCCTTTTGAGCC
Found at i:57806235 original size:14 final size:14
Alignment explanation
Indices: 57806216--57806249 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
57806206 TAAATTTGAC
57806216 ATTTGAATTACAAT
1 ATTTGAATTACAAT
**
57806230 ATTTGAATTTTAAT
1 ATTTGAATTACAAT
57806244 ATTTGA
1 ATTTGA
57806250 TTCAAACAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (14 bp):
ATTTGAATTACAAT
Found at i:57808953 original size:45 final size:44
Alignment explanation
Indices: 57808890--57808978 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 44
57808880 AGCTTGTGTG
* *
57808890 CATCAATAACCTATCACATTTTTGCTCATGCTTATGAACTTAGT
1 CATCAATAACCTATCACATTTTTGCTCATGCTCATGAACATAGT
*
57808934 CATCAATTAACCTATCACATTTTTGCTCATGGTCATGAACATAGT
1 CATCAA-TAACCTATCACATTTTTGCTCATGCTCATGAACATAGT
57808979 GATTTCTTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 6 0.15
45 35 0.85
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.37
Consensus pattern (44 bp):
CATCAATAACCTATCACATTTTTGCTCATGCTCATGAACATAGT
Found at i:57820561 original size:6 final size:6
Alignment explanation
Indices: 57820550--57820585 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
57820540 TTTTTACCTT
57820550 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA
57820586 GAAATAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:57829858 original size:38 final size:38
Alignment explanation
Indices: 57829778--57829861 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 38
57829768 GGTGTAGTAG
* * * *
57829778 TTTGTTTGTTGAATTCAACCCATTCTTCTTTTTTCATT
1 TTTGTTTTTTGAATTCAACCCATTATTCTTTATTCATC
57829816 TTTGTTTTTGTGAGATTCAACCCATTATTC-TTATTCA-C
1 TTTGTTTTT-TGA-ATTCAACCCATTATTCTTTATTCATC
57829854 TTTGTTTT
1 TTTGTTTT
57829862 CCTTCACTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
38 16 0.40
39 9 0.22
40 15 0.38
ACGTcount: A:0.17, C:0.17, G:0.10, T:0.57
Consensus pattern (38 bp):
TTTGTTTTTTGAATTCAACCCATTATTCTTTATTCATC
Found at i:57831038 original size:18 final size:18
Alignment explanation
Indices: 57830983--57831038 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 18
57830973 TTCATAACAC
*
57830983 TTTTTTATAAATAATATAA
1 TTTTTTATAAATAAT-TTA
*
57831002 TTTTTTTGTCAAA-AA-TTA
1 -TTTTTTAT-AAATAATTTA
57831020 TTTTTTATAAATAATTTA
1 TTTTTTATAAATAATTTA
57831038 T
1 T
57831039 GATAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
16 3 0.10
17 9 0.30
18 6 0.20
20 9 0.30
21 3 0.10
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTTTTATAAATAATTTA
Found at i:57832657 original size:26 final size:24
Alignment explanation
Indices: 57832623--57832673 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
57832613 ATGTCACGTT
57832623 AATAAATAATTTAAAAATTATAAAAA
1 AATAAATAA-TTAAAAATT-TAAAAA
* *
57832649 AATATATAATTATAAATTTAAAAA
1 AATAAATAATTAAAAATTTAAAAA
57832673 A
1 A
57832674 TCATAAACGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
25 8 0.35
26 8 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
AATAAATAATTAAAAATTTAAAAA
Found at i:57839757 original size:15 final size:16
Alignment explanation
Indices: 57839730--57839760 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
57839720 TTATTCTTCA
57839730 AATTTTATATTTTTTT
1 AATTTTATATTTTTTT
57839746 AATTTT-TATTTTTTT
1 AATTTTATATTTTTTT
57839761 TAGAACTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
AATTTTATATTTTTTT
Found at i:57841962 original size:40 final size:39
Alignment explanation
Indices: 57841918--57842052 Score: 123
Period size: 37 Copynumber: 3.4 Consensus size: 39
57841908 ACCAGTTTGG
*
57841918 CACCCAGTGCCTCATCGGATAATTCAAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGGATAA-TCGAAGTAATAAATTGA
* * * * *
57841958 CACCCAGTGTCTCATCGGTTAAACCGAAG---TGAATTGG
1 CACCCAGTGCCTCATCGGAT-AATCGAAGTAATAAATTGA
* *
57841995 CGCCCAGTGCCTCATCGAATTAATCTGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGGA-TAATC-GAAGTAATAAATTGA
* *
57842036 CACCCAATGTCTCATCG
1 CACCCAGTGCCTCATCG
57842053 ACTCGAAGTC
Statistics
Matches: 73, Mismatches: 16, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
37 24 0.33
38 5 0.07
40 22 0.30
41 22 0.30
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAATCGAAGTAATAAATTGA
Found at i:57842050 original size:41 final size:41
Alignment explanation
Indices: 57841918--57842053 Score: 120
Period size: 40 Copynumber: 3.4 Consensus size: 41
57841908 ACCAGTTTGG
* * ** *
57841918 CACCCAGTGCCTCATCGGA-TAATTCAAAGTAATAAATTGA
1 CACCCAGTGTCTCATCGAATTAAACCGAAGTAATAAATTGA
* * *
57841958 CACCCAGTGTCTCATCG-GTTAAACCGAAG---TGAATTGG
1 CACCCAGTGTCTCATCGAATTAAACCGAAGTAATAAATTGA
* * * *
57841995 CGCCCAGTGCCTCATCGAATTAATCTGAAGTAATAAATTGA
1 CACCCAGTGTCTCATCGAATTAAACCGAAGTAATAAATTGA
*
57842036 CACCCAATGTCTCATCGA
1 CACCCAGTGTCTCATCGA
57842054 CTCGAAGTCA
Statistics
Matches: 74, Mismatches: 17, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
37 21 0.28
38 9 0.12
40 23 0.31
41 21 0.28
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (41 bp):
CACCCAGTGTCTCATCGAATTAAACCGAAGTAATAAATTGA
Found at i:57842938 original size:4 final size:4
Alignment explanation
Indices: 57842929--57842959 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
57842919 CTTCGTCTCC
*
57842929 TTCT TTCT TTCT TTCT TTTT TTCT TTCT TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
57842960 CCTTTCTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:57843014 original size:8 final size:8
Alignment explanation
Indices: 57843001--57843026 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
57842991 TCTAATTCTT
57843001 TTTCTTTA
1 TTTCTTTA
57843009 TTTCTTTA
1 TTTCTTTA
57843017 TTTCTTTA
1 TTTCTTTA
57843025 TT
1 TT
57843027 ATAATATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTCTTTA
Found at i:57843042 original size:7 final size:7
Alignment explanation
Indices: 57843030--57843055 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
57843020 CTTTATTATA
57843030 ATATAAT
1 ATATAAT
57843037 ATATAAT
1 ATATAAT
57843044 ATATAAT
1 ATATAAT
57843051 ATATA
1 ATATA
57843056 TACTTAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATATAAT
Found at i:57846890 original size:9 final size:9
Alignment explanation
Indices: 57846876--57846958 Score: 103
Period size: 9 Copynumber: 9.2 Consensus size: 9
57846866 TGGTTAAAAT
*
57846876 TTAACCAAA
1 TTAACCGAA
57846885 TTAACCGAA
1 TTAACCGAA
57846894 TTAACCGAA
1 TTAACCGAA
*
57846903 TTACCCGAA
1 TTAACCGAA
*
57846912 TTACCCGAA
1 TTAACCGAA
*
57846921 TTAATCGAA
1 TTAACCGAA
*
57846930 TTACCCGAA
1 TTAACCGAA
*
57846939 TTAACCAAA
1 TTAACCGAA
*
57846948 TTAACCAAA
1 TTAACCGAA
57846957 TT
1 TT
57846959 GAATCACTAC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 66 1.00
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.25
Consensus pattern (9 bp):
TTAACCGAA
Found at i:57846913 original size:27 final size:27
Alignment explanation
Indices: 57846883--57846958 Score: 116
Period size: 27 Copynumber: 2.8 Consensus size: 27
57846873 AATTTAACCA
57846883 AATTAACCGAATTAACCGAATTACCCG
1 AATTAACCGAATTAACCGAATTACCCG
* *
57846910 AATTACCCGAATTAATCGAATTACCCG
1 AATTAACCGAATTAACCGAATTACCCG
* *
57846937 AATTAACCAAATTAACCAAATT
1 AATTAACCGAATTAACCGAATT
57846959 GAATCACTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.25
Consensus pattern (27 bp):
AATTAACCGAATTAACCGAATTACCCG
Found at i:57847752 original size:37 final size:37
Alignment explanation
Indices: 57847702--57847776 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
57847692 CTTTGTAACA
57847702 TGCATCGATACATATATTGTACGTGATAACATTAGGC
1 TGCATCGATACATATATTGTACGTGATAACATTAGGC
57847739 TGCATCGATACATATATTGTACGTGATAACATTAGGC
1 TGCATCGATACATATATTGTACGTGATAACATTAGGC
57847776 T
1 T
57847777 CCATGCCATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (37 bp):
TGCATCGATACATATATTGTACGTGATAACATTAGGC
Found at i:57847766 original size:18 final size:18
Alignment explanation
Indices: 57847708--57847766 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
57847698 AACATGCATC
57847708 GATACATATATTGTACGT
1 GATACATATATTGTACGT
* * *
57847726 GATAACAT-TA-GGCTGCAT
1 GAT-ACATATATTG-TACGT
57847744 CGATACATATATTGTACGT
1 -GATACATATATTGTACGT
57847763 GATA
1 GATA
57847767 ACATTAGGCT
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
17 1 0.03
18 16 0.53
19 12 0.40
20 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34
Consensus pattern (18 bp):
GATACATATATTGTACGT
Found at i:57849874 original size:14 final size:14
Alignment explanation
Indices: 57849840--57849875 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
57849830 AACTTGAAAT
*
57849840 TAAACCTTAGACCT
1 TAAACCTTAGACCC
*
57849854 TAGACCTTAGACCC
1 TAAACCTTAGACCC
57849868 TAAACCTT
1 TAAACCTT
57849876 TGATTCTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.33, C:0.31, G:0.08, T:0.28
Consensus pattern (14 bp):
TAAACCTTAGACCC
Found at i:57850573 original size:25 final size:27
Alignment explanation
Indices: 57850523--57850573 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
57850513 TAATAAATTT
*
57850523 TAAAAAATATGTATACTTAAATAATAC
1 TAAAAAATATGTATACTTAAACAATAC
57850550 TAAAATAA-ATGTA-ACTT-AACAATA
1 TAAAA-AATATGTATACTTAAACAATA
57850574 AAATGTCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 6 0.27
26 4 0.18
27 10 0.45
28 2 0.09
ACGTcount: A:0.57, C:0.08, G:0.04, T:0.31
Consensus pattern (27 bp):
TAAAAAATATGTATACTTAAACAATAC
Found at i:57853177 original size:16 final size:16
Alignment explanation
Indices: 57853138--57853171 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
57853128 TTTCAAATTC
57853138 TAAAAAT-ATTAGAAT
1 TAAAAATAATTAGAAT
57853153 TAAAAATAATTA-AAT
1 TAAAAATAATTAGAAT
57853168 TAAA
1 TAAA
57853172 GTATAAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
TAAAAATAATTAGAAT
Found at i:57863856 original size:105 final size:105
Alignment explanation
Indices: 57863669--57863860 Score: 251
Period size: 105 Copynumber: 1.8 Consensus size: 105
57863659 TATAGGTAAC
* ** *
57863669 AACATCAGGCTCAATGCCTTGCTTTATCATTGTGTCAACAATATCTTTAGCTTTAGAAAGCATCC
1 AACATCAGGCTCAATGCCATGCTTTATCATTGTGTCAACAATATCTACAGCTTCAGAAAGCATCC
* *
57863734 CTTCTTTGTAACATGCATCGATACATATATTGTATGTGAT
66 CTTCCTTGCAACATGCATCGATACATATATTGTATGTGAT
* * * * *
57863774 AACATTAGGCTCAATGCCATGCTTTCTCATTGTGTCAACAATTTCTACAGCTTCCGAAATCATAC
1 AACATCAGGCTCAATGCCATGCTTTATCATTGTGTCAACAATATCTACAGCTTCAGAAAGCAT-C
**
57863839 CC-TCCTTGCAATGTGCATCGAT
65 CCTTCCTTGCAACATGCATCGAT
57863861 CAATGTATTA
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
105 70 0.96
106 3 0.04
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (105 bp):
AACATCAGGCTCAATGCCATGCTTTATCATTGTGTCAACAATATCTACAGCTTCAGAAAGCATCC
CTTCCTTGCAACATGCATCGATACATATATTGTATGTGAT
Found at i:57884264 original size:2 final size:2
Alignment explanation
Indices: 57884253--57884289 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
57884243 AAGTAAAGTT
57884253 CA CA -A CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
57884290 GAGCAATAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:57886858 original size:12 final size:13
Alignment explanation
Indices: 57886841--57886874 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
57886831 ATATGTCACC
*
57886841 TCAAAAGATA-AT
1 TCAAAAAATATAT
57886853 TCAAAAAATATAT
1 TCAAAAAATATAT
57886866 TCAAAAAAT
1 TCAAAAAAT
57886875 TAGTATGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.62, C:0.09, G:0.03, T:0.26
Consensus pattern (13 bp):
TCAAAAAATATAT
Found at i:57895395 original size:2 final size:2
Alignment explanation
Indices: 57895388--57895418 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
57895378 CTAGAAAACA
57895388 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
57895419 CAATTACTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57896520 original size:20 final size:20
Alignment explanation
Indices: 57896484--57896522 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
57896474 AAATAAACAC
**
57896484 ATAATTATTCATTTAATATA
1 ATAATTATTCAAATAATATA
57896504 ATAATTATTCAAATAATAT
1 ATAATTATTCAAATAATAT
57896523 TATTTAAATA
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:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAATTATTCAAATAATATA
Found at i:57899459 original size:25 final size:24
Alignment explanation
Indices: 57899428--57899517 Score: 78
Period size: 25 Copynumber: 3.7 Consensus size: 24
57899418 TTAAAGTTAA
57899428 AATATATATATTATAATATTATAAT
1 AATATATATATTA-AATATTATAAT
* * *
57899453 -AT-TATATCTTAATTATTA-AGT
1 AATATATATATTAAATATTATAAT
57899474 ATATATATTATATTAAATATTATAAT
1 A-ATATA-TATATTAAATATTATAAT
* *
57899500 AAGTAAATATAATAAATA
1 AA-TATATATATTAAATA
57899518 AAATAAACAA
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
21 2 0.04
22 6 0.12
23 10 0.20
24 4 0.08
25 23 0.45
26 6 0.12
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (24 bp):
AATATATATATTAAATATTATAAT
Found at i:57900597 original size:2 final size:2
Alignment explanation
Indices: 57900590--57900618 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
57900580 ATTGGTTGGT
57900590 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57900619 GAGTATATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57901285 original size:36 final size:36
Alignment explanation
Indices: 57901245--57901316 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
57901235 TTTGACTTGA
*
57901245 ATATTATATGATATGAAATGTTCTGAAATTATGTCT
1 ATATTATATGATATGAAATGTTCTAAAATTATGTCT
*
57901281 ATATTATATGATATGAAATGTTTTAAAATTATGTCT
1 ATATTATATGATATGAAATGTTCTAAAATTATGTCT
57901317 GTTTGATCGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (36 bp):
ATATTATATGATATGAAATGTTCTAAAATTATGTCT
Found at i:57902678 original size:12 final size:12
Alignment explanation
Indices: 57902661--57902693 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
57902651 TCTAATATGC
57902661 TTCAATTTTAAA
1 TTCAATTTTAAA
57902673 TTCAATTTTAAA
1 TTCAATTTTAAA
57902685 TTCAATTTT
1 TTCAATTTT
57902694 TATACTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (12 bp):
TTCAATTTTAAA
Found at i:57903704 original size:105 final size:105
Alignment explanation
Indices: 57903560--57904183 Score: 749
Period size: 105 Copynumber: 5.9 Consensus size: 105
57903550 GGAAAAAAAG
* * * * * * **
57903560 AAAAAAAAA-ATTGGTGCTGGTCTGTCAATGGTCGGCACCACATTTATGTAAAAAAAGGTACATT
1 AAAAAAAAATTTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAAAAAAATTACATT
*
57903624 TTGAGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
66 TTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
* * *
57903664 AAAAAAAAATTTTGGTGGTGGCCTGCTAATGGCCGACACCACCTTTATATAAAAAAAATTACATT
1 AAAAAAAAATTTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAAAAAAATTACATT
*
57903729 TTGGGTTGTCATTGGCCGGCACCAGTATACGAAAAAATT-
66 TTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
* *
57903768 AAAAAAAAA-TTT-GTGATGGCCTGCCAATGGCTGGCACCACCTTTATGTAAAAAAAAATTACAT
1 AAAAAAAAATTTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTATGT-AAAAAAAATTACAT
**
57903831 TTTGGGCTGTCATTGGTTGGCACCAGTATACGAAAAAATTC
65 TTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
* *****
57903872 AAAAAAAAATTTT-GTGGTGGCCTGCCAATGGCTGGCACCACCTTTATGTAAATTTTTTTTTTTA
1 AAAAAAAAATTTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAA----AAAAATTA
* *
57903936 CATTTTAGGCTGTCATTGGCCGGCACCAATATACGAAAAAATTC
62 CATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
** * * * *****
57903980 AAAAAAAAAAAATTGGTCGTGGCCTGCCAATGGCCGACAACACCTTTATGTAAATTTTTTTTTTA
1 -AAAAAAAAATTTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAA---AAAAATTA
*
57904045 CATTTTGGGCTGTCATTGGCCGGTACCAGTATACGAAAAAATTC
62 CATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
* *
57904089 AAAAAAAATAATTTTGGTGGTGGCCTGCCAATGGTCGGCATCACCTTTATGT-AAAAAAA-TACA
1 -AAAAAAA-AATTTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAAAAAAATTACA
*
57904152 TTTGGGGCTGTCATTGGCCGGCACCAGTATAC
64 TTTTGGGCTGTCATTGGCCGGCACCAGTATAC
57904184 CGTGAAGGAT
Statistics
Matches: 456, Mismatches: 53, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
102 31 0.07
103 54 0.12
104 30 0.07
105 153 0.34
108 43 0.09
109 73 0.16
110 72 0.16
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (105 bp):
AAAAAAAAATTTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTATGTAAAAAAAATTACATT
TTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
Found at i:57905332 original size:20 final size:20
Alignment explanation
Indices: 57905307--57905346 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
57905297 TTAATACTTC
57905307 TGACACACTTTTTTTTCATT
1 TGACACACTTTTTTTTCATT
**
57905327 TGACACTTTTTTTTTTCATT
1 TGACACACTTTTTTTTCATT
57905347 CAATCTCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.05, T:0.60
Consensus pattern (20 bp):
TGACACACTTTTTTTTCATT
Found at i:57905401 original size:56 final size:56
Alignment explanation
Indices: 57905332--57905726 Score: 568
Period size: 56 Copynumber: 7.1 Consensus size: 56
57905322 TCATTTGACA
*
57905332 CTTTTTTTTTTCATTCAATCTCATTTATTACAACTTTATTTTTCTACATCTAACAC
1 CTTTTTTTTTTCATTCAATCTCATTTATTTCAACTTTATTTTTCTACATCTAACAC
* * * *
57905388 CTTTTTTTTTTCATTCAATCCCATTCATTTCAAATTTATTTTTTTACATCTAACAC
1 CTTTTTTTTTTCATTCAATCTCATTTATTTCAACTTTATTTTTCTACATCTAACAC
* * *
57905444 C--CTTTTTTTCATTCAATCTCATTTATTTCAATTTTATTTTTCT--ATCTAATAC
1 CTTTTTTTTTTCATTCAATCTCATTTATTTCAACTTTATTTTTCTACATCTAACAC
*
57905496 CTTTTTTTTTTCATTCAATCTCATTTATTTCAATTTTATTTTTCTACATCTAACAC
1 CTTTTTTTTTTCATTCAATCTCATTTATTTCAACTTTATTTTTCTACATCTAACAC
** * *
57905552 C-CATTTTTTTCATTAAATCTCATTTATTACAACTTTATTTTTCTACATCTAACAC
1 CTTTTTTTTTTCATTCAATCTCATTTATTTCAACTTTATTTTTCTACATCTAACAC
** *
57905607 CCATTTTTTTTCATTCAATCTCATTTATTACAACTTTATTTTTCTACATCTAACA-
1 CTTTTTTTTTTCATTCAATCTCATTTATTTCAACTTTATTTTTCTACATCTAACAC
* * *
57905662 CTGATTTCTTTTCATTCAATCTCATTTATTTCAATTTTATTTTTCTACATCTAACAC
1 CT-TTTTTTTTTCATTCAATCTCATTTATTTCAACTTTATTTTTCTACATCTAACAC
57905719 CTTTTTTT
1 CTTTTTTT
57905727 GGTTTTTTTA
Statistics
Matches: 305, Mismatches: 27, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
52 9 0.03
54 78 0.26
55 51 0.17
56 165 0.54
57 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.00, T:0.54
Consensus pattern (56 bp):
CTTTTTTTTTTCATTCAATCTCATTTATTTCAACTTTATTTTTCTACATCTAACAC
Found at i:57905478 original size:26 final size:26
Alignment explanation
Indices: 57905449--57905532 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
57905439 AACACCCTTT
57905449 TTTTCATTCAATCTCATTTATTTCAA
1 TTTTCATTCAATCTCATTTATTTCAA
* * *** ***
57905475 TTTT-ATTTTTCTATCTAATACCTTTTTT
1 TTTTCA---TTCAATCTCATTTATTTCAA
57905503 TTTTCATTCAATCTCATTTATTTCAA
1 TTTTCATTCAATCTCATTTATTTCAA
57905529 TTTT
1 TTTT
57905533 ATTTTTCTAC
Statistics
Matches: 38, Mismatches: 16, Indels: 8
0.61 0.26 0.13
Matches are distributed among these distances:
25 1 0.03
26 20 0.53
28 16 0.42
29 1 0.03
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTTCATTCAATCTCATTTATTTCAA
Found at i:57905490 original size:28 final size:28
Alignment explanation
Indices: 57905459--57905541 Score: 75
Period size: 28 Copynumber: 3.0 Consensus size: 28
57905449 TTTTCATTCA
57905459 ATCTCATTTATTTCAATTTTATTTTTCT
1 ATCTCATTTATTTCAATTTTATTTTTCT
* *** *
57905487 ATCTAATACCTTT---TTTT-TTTCATTCA
1 ATCTCATTTATTTCAATTTTATTT--TTCT
57905513 ATCTCATTTATTTCAATTTTATTTTTCT
1 ATCTCATTTATTTCAATTTTATTTTTCT
57905541 A
1 A
57905542 CATCTAACAC
Statistics
Matches: 39, Mismatches: 10, Indels: 12
0.64 0.16 0.20
Matches are distributed among these distances:
24 3 0.08
25 4 0.10
26 12 0.31
28 13 0.33
29 4 0.10
30 3 0.08
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (28 bp):
ATCTCATTTATTTCAATTTTATTTTTCT
Done.