Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold78
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: 2238306
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 23262 characters in sequence are not A, C, G, or T
File 7 of 15
Found at i:992269 original size:27 final size:28
Alignment explanation
Indices: 992239--992326 Score: 65
Period size: 27 Copynumber: 3.1 Consensus size: 28
992229 AAATTAATAA
**
992239 TTAATAATTT-AAT-ATTTTTTATTATTT
1 TTAATAATTTAAATAATTTAATA-TATTT
*
992266 TTAA-AATATAAATAATTTAATATATTT
1 TTAATAATTTAAATAATTTAATATATTT
* *
992293 TTAATATTTATACAATAATATTATATTTATTT
1 TTAATAATT-TA-AATAAT-TTA-ATATATTT
992325 TT
1 TT
992327 TATATTATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
26 4 0.08
27 16 0.33
28 8 0.17
29 2 0.04
30 6 0.12
31 3 0.06
32 9 0.19
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (28 bp):
TTAATAATTTAAATAATTTAATATATTT
Found at i:992269 original size:42 final size:47
Alignment explanation
Indices: 992212--992301 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 47
992202 ACAACATTGC
*
992212 TTTATATATTTTTTAAAAAATTAATAA-TTAATA-A-TTTAATATTT
1 TTTATATATTTTTTAAAAAATAAATAATTTAATATATTTTAATATTT
*
992256 TTTAT-TA-TTTTTAAAATATAAATAATTTAATATATTTTTAATATTT
1 TTTATATATTTTTTAAAAAATAAATAATTTAATATA-TTTTAATATTT
992302 ATACAATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
42 16 0.40
43 8 0.20
44 6 0.15
46 10 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (47 bp):
TTTATATATTTTTTAAAAAATAAATAATTTAATATATTTTAATATTT
Found at i:992332 original size:32 final size:29
Alignment explanation
Indices: 992272--992343 Score: 81
Period size: 35 Copynumber: 2.3 Consensus size: 29
992262 ATTTTTAAAA
992272 TATAAATAATTTAATATATTTTTAATATT
1 TATAAATAATTTAATATATTTTTAATATT
*
992301 TATACAATAATATTATATTTATTTTTTATATTATT
1 TATA-AATAAT-TTA-ATATA-TTTTTA-A-TATT
992336 TATAAATA
1 TATAAATA
992344 TTGTTTTGGC
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
29 4 0.11
30 6 0.17
31 3 0.08
32 4 0.11
33 6 0.17
34 5 0.14
35 8 0.22
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (29 bp):
TATAAATAATTTAATATATTTTTAATATT
Found at i:992515 original size:15 final size:14
Alignment explanation
Indices: 992489--992519 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
992479 TTACGTGTAA
992489 AAAAATTATTTTTT
1 AAAAATTATTTTTT
992503 AAAAATTATTTTTT
1 AAAAATTATTTTTT
992517 AAA
1 AAA
992520 TTTAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AAAAATTATTTTTT
Found at i:992575 original size:2 final size:2
Alignment explanation
Indices: 992568--992595 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
992558 AATAATTAAC
992568 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
992596 CTAACCATAA
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:992897 original size:25 final size:24
Alignment explanation
Indices: 992862--992909 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
992852 TACTTTTAAT
992862 TTATTTTTAATTAT-TTTAAAAAA
1 TTATTTTTAATTATATTTAAAAAA
992885 TTATTCTTGTAATTATATTTAAAAA
1 TTATT-TT-TAATTATATTTAAAAA
992910 TATTTATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.23
24 2 0.09
25 7 0.32
26 8 0.36
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
TTATTTTTAATTATATTTAAAAAA
Found at i:993740 original size:28 final size:28
Alignment explanation
Indices: 993708--993770 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
993698 CAAATGCCAC
*
993708 TCTTTTTATTTGTCAAATATGGTGGTTT
1 TCTTTGTATTTGTCAAATATGGTGGTTT
*
993736 TCTTTGTATTTGTCAAATATTGTGGTTAT
1 TCTTTGTATTTGTCAAATATGGTGGTT-T
993765 T-TTTGT
1 TCTTTGT
993771 TTGTAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 30 0.94
29 2 0.06
ACGTcount: A:0.17, C:0.06, G:0.17, T:0.59
Consensus pattern (28 bp):
TCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:993795 original size:24 final size:24
Alignment explanation
Indices: 993767--993812 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
993757 GTGGTTATTT
993767 TTGTTTGTAAAAAATGATGGCTTG
1 TTGTTTGTAAAAAATGATGGCTTG
* * *
993791 TTGTTTGTCAAAATTGGTGGCT
1 TTGTTTGTAAAAAATGATGGCT
993813 AATTTTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.07, G:0.26, T:0.43
Consensus pattern (24 bp):
TTGTTTGTAAAAAATGATGGCTTG
Found at i:996368 original size:21 final size:22
Alignment explanation
Indices: 996339--996384 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
996329 TGTTCAGACA
** *
996339 AGTAGTACTCCGTAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
996361 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
996382 AGT
1 AGT
996385 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.22
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:998355 original size:24 final size:24
Alignment explanation
Indices: 998319--998383 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
998309 GTGGTTATTT
*
998319 TTGTTTGTAAAAAATGGTGGCTTG
1 TTGTTTATAAAAAATGGTGGCTTG
* * **
998343 TTGTTTATCAAAATTGGTGGCTAA
1 TTGTTTATAAAAAATGGTGGCTTG
998367 TT-TTTATTAAAAAATGG
1 TTGTTTA-TAAAAAATGG
998384 GGGAGGATGG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
23 4 0.12
24 29 0.88
ACGTcount: A:0.31, C:0.05, G:0.22, T:0.43
Consensus pattern (24 bp):
TTGTTTATAAAAAATGGTGGCTTG
Found at i:1000086 original size:2 final size:2
Alignment explanation
Indices: 1000079--1000108 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1000069 CATGTAAGCA
1000079 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1000109 CTAAAATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1001579 original size:14 final size:14
Alignment explanation
Indices: 1001555--1001591 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1001545 CATATAAAGA
1001555 ATAAATA-TATA-T
1 ATAAATATTATAGT
1001567 ATATAATATTATAGT
1 ATA-AATATTATAGT
1001582 ATAAATATTA
1 ATAAATATTA
1001592 AAAAAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.14
13 4 0.18
14 11 0.50
15 4 0.18
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (14 bp):
ATAAATATTATAGT
Found at i:1001662 original size:27 final size:27
Alignment explanation
Indices: 1001583--1001663 Score: 65
Period size: 27 Copynumber: 2.9 Consensus size: 27
1001573 TATTATAGTA
* * *
1001583 TAAATATTAAAAAAATATATTAAATTATC
1 TAAAT-TTTAAAAATTAAATTAAA-TATC
* * **
1001612 TATATTTTAAAACTTAAAAAAAATAT-
1 TAAATTTTAAAAATTAAATTAAATATC
1001638 TAAATTGTTAAAAATTAAATTAAATA
1 TAAATT-TTAAAAATTAAATTAAATA
1001664 AAACATATTT
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
26 5 0.12
27 19 0.47
28 12 0.30
29 4 0.10
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.38
Consensus pattern (27 bp):
TAAATTTTAAAAATTAAATTAAATATC
Found at i:1003629 original size:18 final size:17
Alignment explanation
Indices: 1003595--1003649 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 17
1003585 GTTTTAAAGT
1003595 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
1003612 ATTTTAATATGTTA-AT-A
1 ATTTT-ATAT-TTATATAA
1003629 A-TTTATA-TTATATAA
1 ATTTTATATTTATATAA
1003644 ATTTTA
1 ATTTTA
1003650 AGATATTCGT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.09
14 2 0.06
15 5 0.15
16 7 0.21
17 7 0.21
18 6 0.18
19 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:1006349 original size:15 final size:15
Alignment explanation
Indices: 1006331--1006362 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1006321 AAATTGATTT
*
1006331 AAAATTATTTTTTAA
1 AAAATAATTTTTTAA
1006346 AAAATAATTTTTTAA
1 AAAATAATTTTTTAA
1006361 AA
1 AA
1006363 TGAGATGCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAATAATTTTTTAA
Found at i:1009710 original size:34 final size:34
Alignment explanation
Indices: 1009672--1009754 Score: 166
Period size: 34 Copynumber: 2.4 Consensus size: 34
1009662 CTAACATATT
1009672 ACCTAACACACCTAACATTCTCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
1009706 ACCTAACACACCTAACATTCTCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
1009740 ACCTAACACACCTAA
1 ACCTAACACACCTAA
1009755 TATACTTCAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.42, C:0.39, G:0.00, T:0.19
Consensus pattern (34 bp):
ACCTAACACACCTAACATTCTCACCAAATACATC
Found at i:1014464 original size:34 final size:34
Alignment explanation
Indices: 1014419--1014535 Score: 207
Period size: 34 Copynumber: 3.4 Consensus size: 34
1014409 CTAACATATT
* *
1014419 ACCTAATACACCTAACATTCTCACCAAATGCATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
1014453 ACCTAACACACCTAACATTCTCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
*
1014487 ACCTAACACACTTAACATTCTCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
1014521 ACCTAACACACCTAA
1 ACCTAACACACCTAA
1014536 TATGTTTCAC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 79 1.00
ACGTcount: A:0.41, C:0.37, G:0.01, T:0.21
Consensus pattern (34 bp):
ACCTAACACACCTAACATTCTCACCAAATACATC
Found at i:1014528 original size:25 final size:25
Alignment explanation
Indices: 1014427--1014528 Score: 62
Period size: 25 Copynumber: 4.4 Consensus size: 25
1014417 TTACCTAATA
*
1014427 CACCTAACATTCTCACCAAATGCAT
1 CACCTAACATTCTCACCAAATACAT
*
1014452 CACCTAACA----CACCTAACATTC-T
1 CACCTAACATTCTCACC-AA-ATACAT
* *
1014474 CACC-AA-ATACATCACC-TA-ACA-
1 CACCTAACATTC-TCACCAAATACAT
*
1014495 CACTTAACATTCTCACCAAATACAT
1 CACCTAACATTCTCACCAAATACAT
1014520 CACCTAACA
1 CACCTAACA
1014529 CACCTAATAT
Statistics
Matches: 57, Mismatches: 7, Indels: 26
0.63 0.08 0.29
Matches are distributed among these distances:
20 1 0.02
21 10 0.18
22 15 0.26
23 7 0.12
24 3 0.05
25 21 0.37
ACGTcount: A:0.40, C:0.37, G:0.01, T:0.22
Consensus pattern (25 bp):
CACCTAACATTCTCACCAAATACAT
Found at i:1014725 original size:15 final size:14
Alignment explanation
Indices: 1014702--1014734 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1014692 ATCTAGTAAC
1014702 TTTTTTTCTTTTCT
1 TTTTTTTCTTTTCT
1014716 TTTCTTTTCTTTT-T
1 TTT-TTTTCTTTTCT
1014730 TTTTT
1 TTTTT
1014735 ATTTTCCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 7 0.39
15 9 0.50
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTCTTTTCT
Found at i:1017294 original size:10 final size:9
Alignment explanation
Indices: 1017279--1017321 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
1017269 ATTCGAGTTG
1017279 TTATATATAT
1 TTATATA-AT
1017289 TTATATAAAT
1 TTATAT-AAT
*
1017299 TTTTATAAT
1 TTATATAAT
1017308 TTA-ATAAT
1 TTATATAAT
1017316 TTATAT
1 TTATAT
1017322 TATATAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 8 0.28
9 7 0.24
10 13 0.45
11 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TTATATAAT
Found at i:1019321 original size:2 final size:2
Alignment explanation
Indices: 1019314--1019354 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1019304 TTGAGTATTT
1019314 TA TA TA TA TA 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 TA TA TA TA TA T
1019355 GTGTGTGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1019475 original size:20 final size:18
Alignment explanation
Indices: 1019433--1019478 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
1019423 ATAAATATTT
1019433 TAAATAAA-AATATATGA
1 TAAATAAATAATATATGA
*
1019450 -ATATAAATAATATCATGTA
1 TAAATAAATAATAT-ATG-A
1019469 TAAATAAATA
1 TAAATAAATA
1019479 TATTTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 6 0.26
17 5 0.22
18 3 0.13
19 1 0.04
20 8 0.35
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (18 bp):
TAAATAAATAATATATGA
Found at i:1021121 original size:2 final size:2
Alignment explanation
Indices: 1021114--1021151 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1021104 CAAGTAATTG
1021114 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1021152 GACAAGATGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1021419 original size:10 final size:11
Alignment explanation
Indices: 1021393--1021422 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1021383 ATATAAATAT
1021393 ATTTATTTTTA
1 ATTTATTTTTA
1021404 ATTTATTTTTA
1 ATTTATTTTTA
1021415 A-TTATTTT
1 ATTTATTTT
1021423 AAAAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTATTTTTA
Found at i:1021815 original size:27 final size:27
Alignment explanation
Indices: 1021783--1021839 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
1021773 TTACAATTTT
1021783 TTTAAAAT-TAAAATTTATTTA-ATATAA
1 TTTAAAATCTAAAA-TTATTTATAT-TAA
*
1021810 TTTAAAATCTGAAATTATTTATATTAA
1 TTTAAAATCTAAAATTATTTATATTAA
1021837 TTT
1 TTT
1021840 TTTATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
TTTAAAATCTAAAATTATTTATATTAA
Found at i:1021947 original size:16 final size:16
Alignment explanation
Indices: 1021928--1021958 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1021918 AATTTTTAAA
1021928 AAATAAAAATTAAATT
1 AAATAAAAATTAAATT
1021944 AAATAAAAATTAAAT
1 AAATAAAAATTAAAT
1021959 ATGTAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAAAAATTAAATT
Found at i:1022098 original size:43 final size:42
Alignment explanation
Indices: 1022051--1022134 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 42
1022041 ATTATTTGAA
*
1022051 TAAAAATTAAAATAAAT-TTAAATTTAAATATTTAAAATTTATT
1 TAAAAATTAAAATAAATAATAAATTT-AATATTT-AAATTTATT
* * *
1022094 TAAAATTTAATATAAATAATAAATTTGATATTTAAATTTAT
1 TAAAAATTAAAATAAATAATAAATTTAATATTTAAATTTAT
1022135 AAATTATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 8 0.22
43 21 0.58
44 7 0.19
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (42 bp):
TAAAAATTAAAATAAATAATAAATTTAATATTTAAATTTATT
Found at i:1022105 original size:25 final size:25
Alignment explanation
Indices: 1022057--1022130 Score: 71
Period size: 25 Copynumber: 2.9 Consensus size: 25
1022047 TGAATAAAAA
1022057 TTAAAATAAATTTAAATTTAAATAT
1 TTAAAATAAATTTAAATTTAAATAT
**
1022082 TTAAAATTTATTTAAAATTT-AATA-
1 TTAAAATAAATTT-AAATTTAAATAT
* *
1022106 TAAATAATAAATTTGATATTTAAAT
1 TTAA-AATAAATTT-AAATTTAAAT
1022131 TTATAAATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
24 3 0.08
25 27 0.69
26 9 0.23
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (25 bp):
TTAAAATAAATTTAAATTTAAATAT
Found at i:1022663 original size:18 final size:18
Alignment explanation
Indices: 1022642--1022701 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
1022632 TAAATTATTA
1022642 TTTATTAAATAAAAATAT
1 TTTATTAAATAAAAATAT
** *
1022660 TTTATTTAAATTTAATTAT
1 TTTA-TTAAATAAAAATAT
*
1022679 ATATATTAATATAAAAATAT
1 -TTTATTAA-ATAAAAATAT
1022699 TTT
1 TTT
1022702 TAAAATAATA
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
18 4 0.13
19 17 0.55
20 10 0.32
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTATTAAATAAAAATAT
Found at i:1022693 original size:39 final size:37
Alignment explanation
Indices: 1022606--1022701 Score: 117
Period size: 39 Copynumber: 2.6 Consensus size: 37
1022596 CGTAATAAAA
* *
1022606 ATATTTATATCAAAATTATTTTAATTTAAATTATTATT
1 ATATTAATAT-AAAAATATTTTAATTTAAATTATTATT
1022644 -TATTAA-ATAAAAATATTTT-ATTTAAATTTAATTATAT
1 ATATTAATATAAAAATATTTTAATTTAAA-TT-ATTAT-T
1022681 ATATTAATATAAAAATATTTT
1 ATATTAATATAAAAATATTTT
1022702 TAAAATAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
34 7 0.14
35 12 0.24
36 7 0.14
37 6 0.12
38 6 0.12
39 13 0.25
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (37 bp):
ATATTAATATAAAAATATTTTAATTTAAATTATTATT
Found at i:1023489 original size:12 final size:12
Alignment explanation
Indices: 1023472--1023510 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1023462 ATCGTATTAA
*
1023472 TATATTAAAATT
1 TATATTAAATTT
*
1023484 TATATTAATTTT
1 TATATTAAATTT
1023496 TATATGTAAATTT
1 TATAT-TAAATTT
1023509 TA
1 TA
1023511 ATAAATTCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 15 0.65
13 8 0.35
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (12 bp):
TATATTAAATTT
Found at i:1023517 original size:24 final size:24
Alignment explanation
Indices: 1023472--1023554 Score: 60
Period size: 24 Copynumber: 3.3 Consensus size: 24
1023462 ATCGTATTAA
*
1023472 TATATTAAAATTTATATTAATTTT
1 TATATTAAAATTTATATAAATTTT
* **
1023496 TATATGTAAATTTTA-ATAAATTCG
1 TATAT-TAAAATTTATATAAATTTT
* *
1023520 TATATTTATATTATATATAACTTATTTT
1 TATATTAAAATT-TATATAA---ATTTT
1023548 TATATTA
1 TATATTA
1023555 TTTTTTAATT
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
23 4 0.09
24 18 0.42
25 12 0.28
28 9 0.21
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TATATTAAAATTTATATAAATTTT
Found at i:1023569 original size:20 final size:19
Alignment explanation
Indices: 1023524--1023588 Score: 76
Period size: 19 Copynumber: 3.2 Consensus size: 19
1023514 AATTCGTATA
1023524 TTTATATTATATATAACTTATT
1 TTTATATTATATATAA--T-TT
* *
1023546 TTTATATTATTTTTTAATTT
1 TTTATATTA-TATATAATTT
1023566 TTTATATTATATATAATTT
1 TTTATATTATATATAATTT
1023585 TTTA
1 TTTA
1023589 ATTTATCTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
19 12 0.32
20 11 0.29
21 1 0.03
22 9 0.24
23 5 0.13
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTATATTATATATAATTT
Found at i:1023603 original size:27 final size:27
Alignment explanation
Indices: 1023548--1023603 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1023538 AACTTATTTT
* * *
1023548 TATATTATTTTTTAATTTTTTATATTA
1 TATATAATTTTTTAATTTTCTATAATA
1023575 TATATAATTTTTTAATTTATCTA-AATA
1 TATATAATTTTTTAATTT-TCTATAATA
1023602 TA
1 TA
1023604 ATTTATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 22 0.88
28 3 0.12
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
TATATAATTTTTTAATTTTCTATAATA
Found at i:1023625 original size:18 final size:18
Alignment explanation
Indices: 1023596--1023639 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1023586 TTAATTTATC
*
1023596 TAAATATAATTTATAATAT
1 TAAATTTAATTT-TAATAT
*
1023615 T-AATTTAATTTTAATCT
1 TAAATTTAATTTTAATAT
1023632 TAAATTTA
1 TAAATTTA
1023640 TTAATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 6 0.27
18 15 0.68
19 1 0.05
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAAATTTAATTTTAATAT
Found at i:1028625 original size:48 final size:48
Alignment explanation
Indices: 1028572--1028671 Score: 200
Period size: 48 Copynumber: 2.1 Consensus size: 48
1028562 TTGGGACTTG
1028572 CAGAGGCATATAAATAGTGAAATTGTACCTGTATCTTGAGTCCCATTT
1 CAGAGGCATATAAATAGTGAAATTGTACCTGTATCTTGAGTCCCATTT
1028620 CAGAGGCATATAAATAGTGAAATTGTACCTGTATCTTGAGTCCCATTT
1 CAGAGGCATATAAATAGTGAAATTGTACCTGTATCTTGAGTCCCATTT
1028668 CAGA
1 CAGA
1028672 AACACAGGAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (48 bp):
CAGAGGCATATAAATAGTGAAATTGTACCTGTATCTTGAGTCCCATTT
Found at i:1029672 original size:16 final size:16
Alignment explanation
Indices: 1029651--1029702 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
1029641 GAACTCGAAC
1029651 TAATTTTAATTCAAAA
1 TAATTTTAATTCAAAA
* *
1029667 TAATTTGAATT--AAC
1 TAATTTTAATTCAAAA
1029681 TAATTTTAATTCAAAA
1 TAATTTTAATTCAAAA
1029697 TAATTT
1 TAATTT
1029703 GAACTTGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 12 0.40
16 18 0.60
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (16 bp):
TAATTTTAATTCAAAA
Found at i:1029684 original size:30 final size:30
Alignment explanation
Indices: 1029648--1029705 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
1029638 CCTGAACTCG
1029648 AACTAATTTTAATTCAAAATAATTTGAATT
1 AACTAATTTTAATTCAAAATAATTTGAATT
1029678 AACTAATTTTAATTCAAAATAATTTGAA
1 AACTAATTTTAATTCAAAATAATTTGAA
1029706 CTTGAAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTAATTTTAATTCAAAATAATTTGAATT
Found at i:1029792 original size:16 final size:16
Alignment explanation
Indices: 1029751--1029792 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1029741 AGATAACTCG
*
1029751 AACTTAAAATTATTTG
1 AACTTAAAATTATTTA
*
1029767 AATTTAAAATTATTTA
1 AACTTAAAATTATTTA
*
1029783 AACTTGAAAT
1 AACTTAAAAT
1029793 ACTCAAATCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (16 bp):
AACTTAAAATTATTTA
Found at i:1030130 original size:24 final size:25
Alignment explanation
Indices: 1030089--1030137 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1030079 GTATATTTTT
*
1030089 AAAATATAAAAAATTAATTTTTTAA
1 AAAATATAAAAAATTAATTTATTAA
* *
1030114 AAAATATATATAA-TAATTTATTAA
1 AAAATATAAAAAATTAATTTATTAA
1030138 TTTTACTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AAAATATAAAAAATTAATTTATTAA
Found at i:1035357 original size:2 final size:2
Alignment explanation
Indices: 1035350--1035376 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1035340 TGTAAGTGTT
1035350 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1035377 TTCCAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1037561 original size:2 final size:2
Alignment explanation
Indices: 1037554--1037592 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1037544 AAATTAAGTT
1037554 TA TA TA TA 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 TA TA TA TA T
1037593 TATGTTGGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1039335 original size:6 final size:6
Alignment explanation
Indices: 1039324--1039350 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1039314 ATTTTTAAAA
1039324 TAATTT TAATTT TAATTT TAATTT TAA
1 TAATTT TAATTT TAATTT TAATTT TAA
1039351 AAATAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TAATTT
Found at i:1039946 original size:15 final size:16
Alignment explanation
Indices: 1039893--1039946 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
1039883 TTTATAATTA
1039893 AATTTAAA-TAAAAAT
1 AATTTAAATTAAAAAT
* *
1039908 ATTTTATTATTAAATAAT
1 AATTTA-AATTAAA-AAT
1039926 AATTTAAATTAAAAA-
1 AATTTAAATTAAAAAT
1039941 AATTTA
1 AATTTA
1039947 TGTTTCAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 11 0.34
16 3 0.09
17 10 0.31
18 8 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTTAAATTAAAAAT
Found at i:1040772 original size:11 final size:11
Alignment explanation
Indices: 1040756--1040780 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1040746 GTAGAAAACT
1040756 AGAGACAAAGA
1 AGAGACAAAGA
1040767 AGAGACAAAGA
1 AGAGACAAAGA
1040778 AGA
1 AGA
1040781 ATAGAGAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.08, G:0.28, T:0.00
Consensus pattern (11 bp):
AGAGACAAAGA
Found at i:1042171 original size:600 final size:600
Alignment explanation
Indices: 1041031--1042227 Score: 2295
Period size: 600 Copynumber: 2.0 Consensus size: 600
1041021 TTAGAAACTT
*
1041031 TAAGTAAATTGGGTTTTCTAGAATCCTCTAAGTATTGGACTTATTTTGGTGAGCCAAATACTTCA
1 TAAGTAAACTGGGTTTTCTAGAATCCTCTAAGTATTGGACTTATTTTGGTGAGCCAAATACTTCA
1041096 TGTAATTTGGGTCATTGGGCCTAGGTTAATTTGTGGCTCGTGACATTCTCCCCCACCTATTTCAG
66 TGTAATTTGGGTCATTGGGCCTAGGTTAATTTGTGGCTCGTGACATTCTCCCCCACCTATTTCAG
* **
1041161 CGACGCCCTCATCGCATCCTCTAAATGGAACTGCTTGATCTTATCTTGGAACTGTCATAATGCCT
131 CGACGCCCTCATCGCATCCTCTAAATGGAACTACTTGATCTTATCTTGGAACTACCATAATGCCT
1041226 CAGCTGGCTCCCAACTCGTCTCACTGTTGGGTAGTCCTTTCCATCGGACAAAGTACTCAAGCCTT
196 CAGCTGGCTCCCAACTCGTCTCACTGTTGGGTAGTCCTTTCCATCGGACAAAGTACTCAAGCCTT
1041291 GGCCTATGACCTCTTTGTCGTACCACTCAATCTACAAGAATACATTATACCTCTTTGTCGTAAGA
261 GGCCTATGACCTCTTTGTCGTACCACTCAATCTACAAGAATACATTATACCTCTTTGTCGTAAGA
1041356 GGCCTTCACTCCTACCGGTGCACGTTGTGACTTGCCTCGGTCTAGATCCTCTTGATCCTCATGGA
326 GGCCTTCACTCCTACCGGTGCACGTTGTGACTTGCCTCGGTCTAGATCCTCTTGATCCTCATGGA
1041421 ATGGCTTAAGCATAGTGACATGAAAAACGGGATGTATCTTGAGCTTTAGGGCCTTCATATTTTCG
391 ATGGCTTAAGCATAGTGACATGAAAAACGGGATGTATCTTGAGCTTTAGGGCCTTCATATTTTCG
* *
1041486 CACAAGCCCTTTGTGCATGCATAGGTTGCATAACACCAAGTTCAATTTAATAAGGACTAAGTTTC
456 CACAAGCCCTTTGTGCATGCATAGGTTGCATAACACCAAGTACAATTTAATAAAGACTAAGTTTC
*
1041551 CAACCTGAAACTATACATCCCTATGTTTCTGAACTGCTCACTTCTTCATGTGCTTTCCTACCTTG
521 CAACCTGAAACTATACATCCCTATGTTTCTGAACTGCTCACTTCTTCATGCGCTTTCCTACCTTG
1041616 TGTAAATAAACCTTA
586 TGTAAATAAACCTTA
1041631 TAAGTAAACTGGGTTTTCTAGAATCCTCTAAGTATTGGACTTATTTTGGTGAGCCAAATACTTCA
1 TAAGTAAACTGGGTTTTCTAGAATCCTCTAAGTATTGGACTTATTTTGGTGAGCCAAATACTTCA
1041696 TGTAATTTGGGTCATTGGGCCTAGGTTAATTTGTGGCTCGTGACATTCTCCCCCACCTATTTCAG
66 TGTAATTTGGGTCATTGGGCCTAGGTTAATTTGTGGCTCGTGACATTCTCCCCCACCTATTTCAG
*
1041761 CGATGCCCTCATCGCATCCTCTAAATGGAACTACTTGATCTTATCTTGGAACTACCATAATGCCT
131 CGACGCCCTCATCGCATCCTCTAAATGGAACTACTTGATCTTATCTTGGAACTACCATAATGCCT
*
1041826 CAGCTGGCTCCCAACTCGTCTCACTGTTGGGTAGTCCTTTCCATCGGACAAAGTATTCAAGCCTT
196 CAGCTGGCTCCCAACTCGTCTCACTGTTGGGTAGTCCTTTCCATCGGACAAAGTACTCAAGCCTT
*
1041891 GGCCTATGACCTCTTTGTCGTACCACTCAATCTACAAGAATACATTATACCTCTTTGTCGTAGGA
261 GGCCTATGACCTCTTTGTCGTACCACTCAATCTACAAGAATACATTATACCTCTTTGTCGTAAGA
1041956 GGCCTTCACTCCTACCGGTGCACGTTGTGACTTGCCTCGGTCTAGATCCTCTTGATCCTCATGGA
326 GGCCTTCACTCCTACCGGTGCACGTTGTGACTTGCCTCGGTCTAGATCCTCTTGATCCTCATGGA
1042021 ATGGCTTAAGCATAGTGACATGAAAAACGGGATGTATCTTGAGCTTTAGGGCCTTCATATTTTCG
391 ATGGCTTAAGCATAGTGACATGAAAAACGGGATGTATCTTGAGCTTTAGGGCCTTCATATTTTCG
1042086 CACAAGCCCTTTGTGCATGCATAGGTTGCATAACACCAAGTACAATTTAATAAAGACTAAGTTTC
456 CACAAGCCCTTTGTGCATGCATAGGTTGCATAACACCAAGTACAATTTAATAAAGACTAAGTTTC
*
1042151 CAACCTGAAACTATACATCCCTATGTTTCTGAACTGCTCACTTCTTCGTGCGCTTTCCTACCTTG
521 CAACCTGAAACTATACATCCCTATGTTTCTGAACTGCTCACTTCTTCATGCGCTTTCCTACCTTG
1042216 TGTAAATAAACC
586 TGTAAATAAACC
1042228 CTAGCTAAGT
Statistics
Matches: 586, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
600 586 1.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (600 bp):
TAAGTAAACTGGGTTTTCTAGAATCCTCTAAGTATTGGACTTATTTTGGTGAGCCAAATACTTCA
TGTAATTTGGGTCATTGGGCCTAGGTTAATTTGTGGCTCGTGACATTCTCCCCCACCTATTTCAG
CGACGCCCTCATCGCATCCTCTAAATGGAACTACTTGATCTTATCTTGGAACTACCATAATGCCT
CAGCTGGCTCCCAACTCGTCTCACTGTTGGGTAGTCCTTTCCATCGGACAAAGTACTCAAGCCTT
GGCCTATGACCTCTTTGTCGTACCACTCAATCTACAAGAATACATTATACCTCTTTGTCGTAAGA
GGCCTTCACTCCTACCGGTGCACGTTGTGACTTGCCTCGGTCTAGATCCTCTTGATCCTCATGGA
ATGGCTTAAGCATAGTGACATGAAAAACGGGATGTATCTTGAGCTTTAGGGCCTTCATATTTTCG
CACAAGCCCTTTGTGCATGCATAGGTTGCATAACACCAAGTACAATTTAATAAAGACTAAGTTTC
CAACCTGAAACTATACATCCCTATGTTTCTGAACTGCTCACTTCTTCATGCGCTTTCCTACCTTG
TGTAAATAAACCTTA
Found at i:1047249 original size:22 final size:23
Alignment explanation
Indices: 1047215--1047263 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1047205 TTAATTTCAC
*
1047215 TTTT-AAAACTAA-CTATCTATT
1 TTTTAAAAACTAACCTATATATT
* *
1047236 TTTTAAAAATTAACCTATATTTT
1 TTTTAAAAACTAACCTATATATT
1047259 TTTTA
1 TTTTA
1047264 TTTTTTTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 4 0.17
22 7 0.30
23 12 0.52
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTAAAAACTAACCTATATATT
Found at i:1047521 original size:2 final size:2
Alignment explanation
Indices: 1047514--1047548 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1047504 TCGCCATTCC
*
1047514 CT CT CT CT CT CT CT CT CG CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1047549 CCCCGCCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.51, G:0.03, T:0.46
Consensus pattern (2 bp):
CT
Found at i:1048039 original size:21 final size:19
Alignment explanation
Indices: 1048015--1048057 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
1048005 ACTTTATTTA
1048015 TTTTCTAGAAGATTCTGTTTT
1 TTTTCTAGAA-ATTCT-TTTT
* *
1048036 TTTTCTTGAATTTCTTTTT
1 TTTTCTAGAAATTCTTTTT
1048055 TTT
1 TTT
1048058 GAACTGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 4 0.20
21 9 0.45
ACGTcount: A:0.14, C:0.09, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTTCTAGAAATTCTTTTT
Found at i:1051075 original size:17 final size:16
Alignment explanation
Indices: 1051049--1051099 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
1051039 AATTTTAAAA
*
1051049 TATTTATATATGTATAT
1 TATTTTTATAT-TATAT
1051066 TATTTTTATATTATAT
1 TATTTTTATATTATAT
* *
1051082 CATATTTTGTATTATAT
1 TAT-TTTTATATTATAT
1051099 T
1 T
1051100 TAATTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (16 bp):
TATTTTTATATTATAT
Found at i:1051455 original size:11 final size:12
Alignment explanation
Indices: 1051425--1051466 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
1051415 CACTTATAAG
1051425 TTTTTAAATCACA
1 TTTTTAAAT-ACA
* *
1051438 TTTTTTATTACA
1 TTTTTAAATACA
1051450 TTTTTAAATACA
1 TTTTTAAATACA
1051462 TTTTT
1 TTTTT
1051467 TCAATTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
12 18 0.72
13 7 0.28
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTTAAATACA
Found at i:1051598 original size:12 final size:13
Alignment explanation
Indices: 1051581--1051609 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1051571 AATAGTTATC
1051581 ATTTAAA-AAGAT
1 ATTTAAACAAGAT
1051593 ATTTAAACAAGAT
1 ATTTAAACAAGAT
1051606 ATTT
1 ATTT
1051610 CTGTTTACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (13 bp):
ATTTAAACAAGAT
Found at i:1053093 original size:20 final size:20
Alignment explanation
Indices: 1053068--1053111 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1053058 CATAAAACGA
*
1053068 ATAAAATATATT-TAATAGAT
1 ATAAAA-ATATTATAATAAAT
1053088 ATAAAAATATTATAATAAAT
1 ATAAAAATATTATAATAAAT
1053108 ATAA
1 ATAA
1053112 TAAAATATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
ATAAAAATATTATAATAAAT
Found at i:1054232 original size:2 final size:2
Alignment explanation
Indices: 1054225--1054257 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1054215 ATGTCCGAGA
1054225 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1054258 ATAAATCTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1059212 original size:2 final size:2
Alignment explanation
Indices: 1059205--1059230 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1059195 GTACTAATGA
1059205 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
1059231 CTGATTTTGG
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:1072768 original size:12 final size:14
Alignment explanation
Indices: 1072733--1072768 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1072723 AAAAAAATAT
1072733 TAAATTTAAA-AAA
1 TAAATTTAAATAAA
1072746 TAAATTTAAATAAA
1 TAAATTTAAATAAA
1072760 -AAA-TTAAAT
1 TAAATTTAAAT
1072769 TCATTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.27
13 13 0.59
14 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAATTTAAATAAA
Found at i:1072777 original size:18 final size:17
Alignment explanation
Indices: 1072736--1072779 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1072726 AAAATATTAA
*
1072736 ATTTAAAAAATAAATTT
1 ATTTAAAAAATAAATTC
**
1072753 AAATAAAAAATTAAATTC
1 ATTTAAAAAA-TAAATTC
1072771 ATTTAAAAA
1 ATTTAAAAA
1072780 TAGATTAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTTAAAAAATAAATTC
Found at i:1072791 original size:17 final size:17
Alignment explanation
Indices: 1072722--1072791 Score: 56
Period size: 17 Copynumber: 4.1 Consensus size: 17
1072712 TAAATAAAAA
1072722 TAAAAA-AATATTAAATT
1 TAAAAATAA-ATTAAATT
1072739 TAAAAAATAAATTTAAA-T
1 T-AAAAATAAA-TTAAATT
* *
1072757 AAAAAATTAAATT-CATT
1 TAAAAA-TAAATTAAATT
*
1072774 TAAAAATAGATTAAATT
1 TAAAAATAAATTAAATT
1072791 T
1 T
1072792 TGATTTTCAC
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
16 6 0.14
17 18 0.43
18 11 0.26
19 7 0.17
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (17 bp):
TAAAAATAAATTAAATT
Found at i:1073003 original size:16 final size:15
Alignment explanation
Indices: 1072983--1073026 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 15
1072973 ATTAAATTAC
*
1072983 TAAAAATTAAATTTT
1 TAAAAAATAAATTTT
*
1072998 TAAAAAATATATTTTT
1 TAAAAAATA-AATTTT
1073014 TAAAAAATAAATT
1 TAAAAAATAAATT
1073027 AAAAAAATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAAAAATAAATTTT
Found at i:1073283 original size:23 final size:23
Alignment explanation
Indices: 1073228--1073286 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 23
1073218 CTTAATTTTA
*
1073228 ATTAATCATATAATAATAAATAT
1 ATTAATTATATAATAATAAATAT
*
1073251 ATGTTTATTATATAATAATAAATAT
1 A--TTAATTATATAATAATAAATAT
1073276 ATTAATTATAT
1 ATTAATTATAT
1073287 TAAATTATAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 10 0.32
25 21 0.68
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTAATTATATAATAATAAATAT
Found at i:1073720 original size:24 final size:24
Alignment explanation
Indices: 1073693--1073740 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1073683 ATTATTTCTT
*
1073693 TTTTATTTAA-TTTATATTTTTTTA
1 TTTTAATTAAGTTT-TATTTTTTTA
1073717 TTTTAATTAAGTTTTATTTTTTTA
1 TTTTAATTAAGTTTTATTTTTTTA
1073741 ATTAGACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTTAATTAAGTTTTATTTTTTTA
Found at i:1073731 original size:19 final size:19
Alignment explanation
Indices: 1073691--1073744 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
1073681 ATATTATTTC
1073691 TTTTTTA-TTTAATTTATAT
1 TTTTTTATTTTAA-TTATAT
1073710 TTTTTTATTTTAATTA-AGT
1 TTTTTTATTTTAATTATA-T
1073729 TTTATTT-TTTTAATTA
1 TTT-TTTATTTTAATTA
1073745 GACTTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 1 0.03
19 23 0.72
20 8 0.25
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTTTTATTTTAATTATAT
Found at i:1073764 original size:23 final size:23
Alignment explanation
Indices: 1073737--1073789 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1073727 GTTTTATTTT
*
1073737 TTTAATTAGACTTTTAATTTAGA
1 TTTAAATAGACTTTTAATTTAGA
** *
1073760 TTTAAATAGGTTTTTAGTTTAGA
1 TTTAAATAGACTTTTAATTTAGA
1073783 TTTAAAT
1 TTTAAAT
1073790 GGGTTTAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.53
Consensus pattern (23 bp):
TTTAAATAGACTTTTAATTTAGA
Found at i:1073794 original size:23 final size:23
Alignment explanation
Indices: 1073748--1073795 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1073738 TTAATTAGAC
1073748 TTTTAATTTAGATTTAAATAGGT
1 TTTTAATTTAGATTTAAATAGGT
* *
1073771 TTTTAGTTTAGATTTAAATGGGT
1 TTTTAATTTAGATTTAAATAGGT
1073794 TT
1 TT
1073796 AAGTTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (23 bp):
TTTTAATTTAGATTTAAATAGGT
Found at i:1074153 original size:25 final size:25
Alignment explanation
Indices: 1074115--1074199 Score: 77
Period size: 25 Copynumber: 3.4 Consensus size: 25
1074105 AATTTAATAA
*
1074115 TTTT-AATTATTATTTAAAAATATT
1 TTTTAAATTAATATTTAAAAATATT
*
1074139 TTTTAAATTAATATTTATAAATA--
1 TTTTAAATTAATATTTAAAAATATT
* *
1074162 TTTAAAATTAATATTAAATAAAATATT
1 TTTTAAATTAATATT-TA-AAAATATT
1074189 ATATTTAAATT
1 -T-TTTAAATT
1074200 TAATTCAACT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
23 14 0.29
24 5 0.10
25 21 0.44
28 1 0.02
29 7 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTTAAATTAATATTTAAAAATATT
Found at i:1074953 original size:18 final size:17
Alignment explanation
Indices: 1074920--1075022 Score: 52
Period size: 16 Copynumber: 5.8 Consensus size: 17
1074910 TATTTCAAAT
1074920 ATTTATATTTATATAAA
1 ATTTATATTTATATAAA
*
1074937 ATTTA-ATATAT-TAATA
1 ATTTATATTTATATAA-A
*
1074953 ATTTATTATAATTATTTTAAA
1 ATTTA-TAT--TTA-TATAAA
* * *
1074974 A-ATATATTTATATTAT
1 ATTTATATTTATATAAA
*
1074990 ATTT-TATTTATTTTAAA
1 ATTTATATTTA-TATAAA
1075007 TATATTATATTTATAT
1 -AT-TTATATTTATAT
1075023 CATCATATAT
Statistics
Matches: 63, Mismatches: 11, Indels: 22
0.66 0.11 0.23
Matches are distributed among these distances:
15 3 0.05
16 21 0.33
17 12 0.19
18 4 0.06
19 7 0.11
20 10 0.16
21 3 0.05
22 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTATATTTATATAAA
Found at i:1074965 original size:26 final size:25
Alignment explanation
Indices: 1074906--1074965 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
1074896 TTAAATTAAA
*
1074906 ATTAT-ATTTCAAATATTTATATTT
1 ATTATAATTTCAAATATTAATATTT
*
1074930 ATATAAAATTT-AATATATTAATAATTT
1 AT-TATAATTTCAA-ATATTAAT-ATTT
1074957 ATTATAATT
1 ATTATAATT
1074966 ATTTTAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 2 0.07
25 4 0.14
26 17 0.59
27 6 0.21
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTATAATTTCAAATATTAATATTT
Found at i:1074978 original size:33 final size:33
Alignment explanation
Indices: 1074941--1075022 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 33
1074931 TATAAAATTT
1074941 AATATATTAATAATT-TATTATAATTATTTTAAA
1 AATATATTAAT-ATTATATTATAATTATTTTAAA
* * *
1074974 AATATATTTATATTATATTTTATTTATTTT--A
1 AATATATTAATATTATATTATAATTATTTTAAA
1075005 AATATATT-ATATTTATAT
1 AATATATTAATA-TTATAT
1075023 CATCATATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
30 3 0.07
31 15 0.34
32 3 0.07
33 23 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
AATATATTAATATTATATTATAATTATTTTAAA
Found at i:1080574 original size:2 final size:2
Alignment explanation
Indices: 1080567--1080605 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1080557 ACATAAAGAA
1080567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1080606 AACTGAGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1081706 original size:19 final size:18
Alignment explanation
Indices: 1081672--1081745 Score: 71
Period size: 18 Copynumber: 4.1 Consensus size: 18
1081662 TGATCGAATT
1081672 ATTTATTTAAATTTAAAA
1 ATTTATTTAAATTTAAAA
1081690 ATTTATTTAATATTTAAAAAA
1 ATTTATTTAA-ATTT--AAAA
** **
1081711 ATTTAAATAAAAATAAAA
1 ATTTATTTAAATTTAAAA
1081729 A-TTA-TTAAATTTAAAA
1 ATTTATTTAAATTTAAAA
1081745 A
1 A
1081746 ATAAATTTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
16 10 0.22
17 3 0.07
18 15 0.33
19 4 0.09
20 2 0.04
21 12 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTATTTAAATTTAAAA
Found at i:1081716 original size:17 final size:17
Alignment explanation
Indices: 1081676--1081726 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 17
1081666 CGAATTATTT
*
1081676 ATTTAAATTTAAAAATTT
1 ATTTAAATTTAAAAA-TA
1081694 ATTTAATATTTAAAAA-A
1 ATTTAA-ATTTAAAAATA
1081711 ATTTAAA--TAAAAATA
1 ATTTAAATTTAAAAATA
1081726 A
1 A
1081727 AAATTATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.20
15 2 0.07
16 1 0.03
17 6 0.20
18 6 0.20
19 9 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTAAATTTAAAAATA
Found at i:1081745 original size:17 final size:17
Alignment explanation
Indices: 1081678--1081747 Score: 52
Period size: 19 Copynumber: 3.9 Consensus size: 17
1081668 AATTATTTAT
*
1081678 TTAAATTTAAAAATTTA
1 TTAAATTTAAAAAATTA
*
1081695 TTTAATATTTAAAAAAAT-
1 -TTAA-ATTTAAAAAATTA
**
1081713 TTAAATAAAAATAAAAATTA
1 TTAAAT--TTA-AAAAATTA
1081733 TTAAATTTAAAAAAT
1 TTAAATTTAAAAAAT
1081748 AAATTTAAGT
Statistics
Matches: 40, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
16 2 0.05
17 10 0.25
18 6 0.15
19 16 0.40
20 6 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAATTTAAAAAATTA
Found at i:1081957 original size:26 final size:24
Alignment explanation
Indices: 1081890--1081939 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1081880 ATTTTAATCA
*
1081890 TATAATAATACATA-TAAAAAATAT
1 TATAAT-ATAAATATTAAAAAATAT
1081914 TATAATATAAATATTAAAAAATAT
1 TATAATATAAATATTAAAAAATAT
1081938 TA
1 TA
1081940 AATTATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
TATAATATAAATATTAAAAAATAT
Found at i:1081977 original size:38 final size:34
Alignment explanation
Indices: 1081929--1082038 Score: 113
Period size: 30 Copynumber: 3.3 Consensus size: 34
1081919 TATAAATATT
*
1081929 AAAAAATATTAAATTATTTAAATTTTAAATTTTAATA
1 AAAAAATATTAAATTA-TTAAATATTAAATTTT--TA
1081966 AAAAAATTATTAAATTATTAAATATTAAATTTTT-
1 AAAAAA-TATTAAATTATTAAATATTAAATTTTTA
* * *
1082000 AAAAAATA-T--ATTTTTAAAAAATAAA-TTTTA
1 AAAAAATATTAAATTATTAAATATTAAATTTTTA
1082030 AAAAAATAT
1 AAAAAATAT
1082039 GGATATATCT
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
29 4 0.06
30 21 0.32
32 1 0.02
33 2 0.03
34 6 0.09
35 1 0.02
37 21 0.32
38 10 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (34 bp):
AAAAAATATTAAATTATTAAATATTAAATTTTTA
Found at i:1081982 original size:8 final size:8
Alignment explanation
Indices: 1081935--1082002 Score: 63
Period size: 8 Copynumber: 8.9 Consensus size: 8
1081925 TATTAAAAAA
1081935 TATTAAAT
1 TATTAAAT
1081943 TATTTAAAT
1 TA-TTAAAT
1081952 T-TTAAAT
1 TATTAAAT
1081959 T-TT-AAT
1 TATTAAAT
* **
1081965 AAAAAAAT
1 TATTAAAT
1081973 TATTAAAT
1 TATTAAAT
1081981 TATTAAA-
1 TATTAAAT
1081988 TATTAAAT
1 TATTAAAT
*
1081996 TTTTAAA
1 TATTAAA
1082003 AAATATATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
6 3 0.06
7 16 0.33
8 23 0.47
9 7 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (8 bp):
TATTAAAT
Found at i:1082001 original size:15 final size:15
Alignment explanation
Indices: 1081932--1082028 Score: 59
Period size: 15 Copynumber: 5.9 Consensus size: 15
1081922 AAATATTAAA
1081932 AAATATTAAATTATTT
1 AAATATTAAATT-TTT
*
1081948 AAATTTTAAATTTTAAT
1 AAATATTAAATTTT--T
*
1081965 AAAAAAATTATTAAATTATT
1 ----AAA-TATTAAATTTTT
1081985 AAATATTAAATTTTT
1 AAATATTAAATTTTT
* * *
1082000 AAAAAATATATTTTT
1 AAATATTAAATTTTT
* *
1082015 AAAAAATAAATTTT
1 AAATATTAAATTTT
1082029 AAAAAAATAT
Statistics
Matches: 66, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
15 38 0.58
16 14 0.21
17 1 0.02
20 1 0.02
21 3 0.05
22 9 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AAATATTAAATTTTT
Found at i:1082033 original size:15 final size:15
Alignment explanation
Indices: 1081976--1082037 Score: 79
Period size: 15 Copynumber: 4.1 Consensus size: 15
1081966 AAAAAATTAT
* * *
1081976 TAAATTATTAAATAT
1 TAAATTTTTAAAAAA
1081991 TAAATTTTTAAAAAA
1 TAAATTTTTAAAAAA
*
1082006 TATATTTTTAAAAAA
1 TAAATTTTTAAAAAA
*
1082021 TAAATTTTAAAAAAA
1 TAAATTTTTAAAAAA
1082036 TA
1 TA
1082038 TGGATATATC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAATTTTTAAAAAA
Found at i:1082554 original size:23 final size:23
Alignment explanation
Indices: 1082499--1082557 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 23
1082489 CTTAATTTTA
* * *
1082499 ATTAATCATATTATAATAAATAT
1 ATTAATTATATAACAATAAATAT
*
1082522 ATGTTTATTATATAACAATAAATAT
1 A--TTAATTATATAACAATAAATAT
1082547 ATTAATTATAT
1 ATTAATTATAT
1082558 TAAATTATAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
23 10 0.34
25 19 0.66
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTAATTATATAACAATAAATAT
Found at i:1082859 original size:20 final size:20
Alignment explanation
Indices: 1082831--1082868 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1082821 ATAATTTTTT
1082831 ATTTAAATTATAATTTAATA
1 ATTTAAATTATAATTTAATA
* *
1082851 ATTTTAATTATTATTTAA
1 ATTTAAATTATAATTTAA
1082869 AATATTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTAAATTATAATTTAATA
Found at i:1082912 original size:21 final size:22
Alignment explanation
Indices: 1082886--1082927 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1082876 TTATATTTTT
1082886 ATAA-TTAATATTAAAT-AAATA
1 ATAATTTAA-ATTAAATCAAATA
1082907 ATAATTTAAATTAAATCAAAT
1 ATAATTTAAATTAAATCAAAT
1082928 TAAATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAATTTAAATTAAATCAAATA
Found at i:1083102 original size:18 final size:17
Alignment explanation
Indices: 1083082--1083159 Score: 78
Period size: 17 Copynumber: 4.9 Consensus size: 17
1083072 AATAATTTTA
1083082 AAAATAATATATTAATT
1 AAAATAATATATTAATT
1083099 AAAATAA-ATA-T-A-T
1 AAAATAATATATTAATT
* *
1083112 AATATAATATATTTAAAT
1 AAAATAATATA-TTAATT
*
1083130 AAAATTA-ATA-TAATT
1 AAAATAATATATTAATT
1083145 AAAATAATATATTAA
1 AAAATAATATATTAA
1083160 AATATATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
13 7 0.14
14 4 0.08
15 11 0.22
16 7 0.14
17 14 0.29
18 6 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATAATATATTAATT
Found at i:1083104 original size:14 final size:14
Alignment explanation
Indices: 1083087--1083167 Score: 53
Period size: 15 Copynumber: 5.6 Consensus size: 14
1083077 TTTTAAAAAT
1083087 AATATATTAATTAA
1 AATATATTAATTAA
*
1083101 AATAAATATATAA-TAT
1 AAT--ATAT-TAATTAA
*
1083117 AATATATTTAAATAA
1 AATATA-TTAATTAA
1083132 AAT-TAATATAATTAA
1 AATAT-AT-TAATTAA
1083147 AATA-A-TATATTAA
1 AATATATTA-ATTAA
1083160 AATATATT
1 AATATATT
1083168 TAAAAAATAA
Statistics
Matches: 53, Mismatches: 3, Indels: 21
0.69 0.04 0.27
Matches are distributed among these distances:
12 2 0.04
13 9 0.17
14 13 0.25
15 17 0.32
16 9 0.17
17 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATATATTAATTAA
Found at i:1083131 original size:43 final size:43
Alignment explanation
Indices: 1083083--1083176 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 43
1083073 ATAATTTTAA
*
1083083 AAATAATA-T-AT-TAATTAAAATAAATATATAATATAATATATTT
1 AAATAATATTAATATAATTAAAAT-AATATAT--TAAAATATATTT
*
1083126 AAATAAAATTAATATAATTAAAATAATATATTAAAATATATTT
1 AAATAATATTAATATAATTAAAATAATATATTAAAATATATTT
*
1083169 AAAAAATA
1 AAATAATA
1083177 AATACTGCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
43 24 0.55
44 1 0.02
45 9 0.20
46 10 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (43 bp):
AAATAATATTAATATAATTAAAATAATATATTAAAATATATTT
Found at i:1083140 original size:19 final size:21
Alignment explanation
Indices: 1083083--1083176 Score: 70
Period size: 20 Copynumber: 4.4 Consensus size: 21
1083073 ATAATTTTAA
**
1083083 AAATAATATATTAAT-TAAAAT
1 AAATAATATATTAATAT-ATTT
1083104 AAAT-ATATAATATAATATATTT
1 AAATAATAT-AT-TAATATATTT
*
1083126 AAATAA-A-ATTAATATAATTA
1 AAATAATATATTAATAT-ATTT
1083146 AAATAATATATTAAAATATATTT
1 AAATAATATATT--AATATATTT
*
1083169 AAAAAATA
1 AAATAATA
1083177 AATACTGCAA
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
19 6 0.10
20 15 0.25
21 7 0.12
22 14 0.24
23 12 0.20
24 5 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATAATATATTAATATATTT
Found at i:1083157 original size:33 final size:31
Alignment explanation
Indices: 1083082--1083163 Score: 103
Period size: 33 Copynumber: 2.6 Consensus size: 31
1083072 AATAATTTTA
*
1083082 AAAATAATATA-TTAATTAAAATAAATATAT
1 AAAATAATATATTTAAATAAAATAAATATAT
* *
1083112 AATATAATATATTTAAATAAAATTAATATAATT
1 AAAATAATATATTTAAATAAAATAAATAT-A-T
*
1083145 AAAATAATATATTAAAATA
1 AAAATAATATATTTAAATA
1083164 TATTTAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
30 10 0.23
31 15 0.34
32 1 0.02
33 18 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (31 bp):
AAAATAATATATTTAAATAAAATAAATATAT
Found at i:1083612 original size:30 final size:31
Alignment explanation
Indices: 1083578--1083664 Score: 92
Period size: 30 Copynumber: 2.8 Consensus size: 31
1083568 TTTTAAAATT
1083578 TTTATATAATATAAATTATTAAAAT-AAAAA
1 TTTATATAATATAAATTATTAAAATAAAAAA
1083608 TTTATATAA-ATATAATTA-TAATATATAAAAAA
1 TTTATATAATATA-AATTATTAA-A-ATAAAAAA
*
1083640 TATAAATATAATATAAA-TATTAAAA
1 T-T-TATATAATATAAATTATTAAAA
1083665 GTATCAAAAC
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
29 6 0.12
30 15 0.31
31 2 0.04
32 7 0.15
33 4 0.08
34 11 0.23
35 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (31 bp):
TTTATATAATATAAATTATTAAAATAAAAAA
Found at i:1083620 original size:6 final size:6
Alignment explanation
Indices: 1083580--1083659 Score: 53
Period size: 6 Copynumber: 13.5 Consensus size: 6
1083570 TTAAAATTTT
* ** *
1083580 TATATAA TATAAA TTATTAAA -ATAAA AATTTA TATAAA TATAAT TAT-AA
1 TATA-AA TATAAA -TA-TAAA TATAAA TATAAA TATAAA TATAAA TATAAA
1083629 TATATAA -A-AAA TATAAA TAT-AA TATAAA TAT
1 TATA-AA TATAAA TATAAA TATAAA TATAAA TAT
1083660 TAAAAGTATC
Statistics
Matches: 58, Mismatches: 7, Indels: 17
0.71 0.09 0.21
Matches are distributed among these distances:
4 2 0.03
5 15 0.26
6 29 0.50
7 8 0.14
8 4 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
TATAAA
Found at i:1083651 original size:28 final size:26
Alignment explanation
Indices: 1083611--1083664 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
1083601 ATAAAAATTT
1083611 ATATAAATATAATTATAATATATAAAAA
1 ATATAAATATAA-TATAA-ATATAAAAA
*
1083639 ATATAAATATAATATAAATATTAAAA
1 ATATAAATATAATATAAATATAAAAA
1083665 GTATCAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 8 0.32
27 5 0.20
28 12 0.48
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
ATATAAATATAATATAAATATAAAAA
Found at i:1083837 original size:15 final size:15
Alignment explanation
Indices: 1083819--1083873 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 15
1083809 ATTATATTTA
1083819 TATATTTTATTAAAT
1 TATATTTTATTAAAT
*
1083834 TATAATTATATTAAA-
1 TAT-ATTTTATTAAAT
*
1083849 TATATTTATATTATAT
1 TATATTT-TATTAAAT
1083865 TATATTTTA
1 TATATTTTA
1083874 ATTATTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 3 0.09
15 14 0.41
16 17 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATATTTTATTAAAT
Found at i:1083863 original size:20 final size:20
Alignment explanation
Indices: 1083833--1083918 Score: 67
Period size: 18 Copynumber: 4.5 Consensus size: 20
1083823 TTTTATTAAA
1083833 TTATAATTATATTAAATATAT
1 TTAT-ATTATATTAAATATAT
1083854 TTATATTATATT--ATAT-T
1 TTATATTATATTAAATATAT
* *
1083871 TTA-ATTATTTTAAAAATA-
1 TTATATTATATTAAATATAT
*
1083889 TTATATT-TATTTAATTATAT
1 TTATATTATA-TTAAATATAT
*
1083909 ATATAATTAT
1 TTAT-ATTAT
1083919 TCAATTTAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
16 7 0.14
17 4 0.08
18 11 0.22
19 10 0.20
20 11 0.22
21 7 0.14
22 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATATTATATTAAATATAT
Found at i:1083866 original size:36 final size:34
Alignment explanation
Indices: 1083819--1083907 Score: 106
Period size: 36 Copynumber: 2.5 Consensus size: 34
1083809 ATTATATTTA
*
1083819 TATATTTTATTAAATTATAATTATATTAAATATATT
1 TATA-TTTATTAAATTATAATTATATTAAAAATA-T
* * *
1083855 TATATTATATTATATTTTAATTATTTTAAAAATAT
1 TATATT-TATTAAATTATAATTATATTAAAAATAT
*
1083890 TATATTTATTTAATTATA
1 TATATTTATTAAATTATA
1083908 TATATAATTA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
34 9 0.20
35 9 0.20
36 27 0.60
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (34 bp):
TATATTTATTAAATTATAATTATATTAAAAATAT
Found at i:1083870 original size:16 final size:16
Alignment explanation
Indices: 1083810--1083918 Score: 74
Period size: 15 Copynumber: 7.2 Consensus size: 16
1083800 AACTTCTGTA
1083810 TTATATT-TA-TATAT
1 TTATATTATATTATAT
* *
1083824 TT-TATTAAATTATAA
1 TTATATTATATTATAT
*
1083839 TTATATTA-AATATAT
1 TTATATTATATTATAT
1083854 TTATATTATATTATAT
1 TTATATTATATTATAT
*
1083870 TT-TAATTAT-TT-TAA
1 TTAT-ATTATATTATAT
**
1083884 AAATATTATATT-TAT
1 TTATATTATATTATAT
*
1083899 TTA-ATTATATATATAA
1 TTATATTATAT-TATAT
1083915 TTAT
1 TTAT
1083919 TCAATTTAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 17
0.72 0.12 0.17
Matches are distributed among these distances:
13 4 0.05
14 17 0.23
15 29 0.40
16 23 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATATTATATTATAT
Found at i:1083919 original size:20 final size:19
Alignment explanation
Indices: 1083809--1083924 Score: 73
Period size: 20 Copynumber: 6.2 Consensus size: 19
1083799 CAACTTCTGT
*
1083809 ATTATATT-T-ATATATTTT
1 ATTATATTATAAT-TATTTA
*
1083827 ATTAAATTATAATTATATTA
1 ATTATATTATAATTAT-TTA
*
1083847 AATATATT-T-A-TA-TTA
1 ATTATATTATAATTATTTA
*
1083862 TATTATATTTTAATTATTTTA
1 -ATTATATTATAATTA-TTTA
** *
1083883 AAAATATTATATTTATTTA
1 ATTATATTATAATTATTTA
*
1083902 ATTATATATATAATTATTCA
1 ATTATAT-TATAATTATTTA
1083922 ATT
1 ATT
1083925 TAAATATATT
Statistics
Matches: 75, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
15 3 0.04
16 7 0.09
17 3 0.04
18 9 0.12
19 16 0.21
20 34 0.45
21 3 0.04
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTATATTATAATTATTTA
Found at i:1083933 original size:21 final size:20
Alignment explanation
Indices: 1083884--1083933 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
1083874 ATTATTTTAA
* *
1083884 AAATATTATATTTATTTAATT
1 AAATA-TATAATTATTCAATT
*
1083905 ATATATATAATTATTCAATTT
1 AAATATATAATTATTCAA-TT
1083926 AAATATAT
1 AAATATAT
1083934 TCATTGCCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
AAATATATAATTATTCAATT
Found at i:1087942 original size:2 final size:2
Alignment explanation
Indices: 1087935--1087965 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1087925 TTCTTTTCTT
1087935 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
1087966 TTTTTTTTTT
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:1089875 original size:19 final size:18
Alignment explanation
Indices: 1089854--1089889 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1089844 ATCATATAAA
1089854 AAAATTTAAATTTTTTAT
1 AAAATTTAAATTTTTTAT
1089872 AAAATTTAAATTTTTTAT
1 AAAATTTAAATTTTTTAT
1089890 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAAATTTAAATTTTTTAT
Found at i:1090423 original size:19 final size:19
Alignment explanation
Indices: 1090395--1090439 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1090385 GAAATGATAA
*
1090395 AAAAAT-TAAATTAAAATT
1 AAAAATATAAAATAAAATT
*
1090413 AAAAATATAAAATAAGATT
1 AAAAATATAAAATAAAATT
1090432 AAAAATAT
1 AAAAATAT
1090440 TTAAGTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAATATAAAATAAAATT
Found at i:1093497 original size:15 final size:15
Alignment explanation
Indices: 1093477--1093506 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1093467 ATCATACTTC
1093477 TGCTTTTTATTTACA
1 TGCTTTTTATTTACA
1093492 TGCTTTTTATTTACA
1 TGCTTTTTATTTACA
1093507 GAAAAGCCAC
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:0.20, C:0.13, G:0.07, T:0.60
Consensus pattern (15 bp):
TGCTTTTTATTTACA
Found at i:1102856 original size:13 final size:13
Alignment explanation
Indices: 1102840--1102866 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1102830 AGATTATTTT
1102840 TTTAAATCTAATC
1 TTTAAATCTAATC
1102853 TTTAAATCTAATC
1 TTTAAATCTAATC
1102866 T
1 T
1102867 GACTTATAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTAAATCTAATC
Found at i:1103137 original size:2 final size:2
Alignment explanation
Indices: 1103125--1103154 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1103115 ATTGAAGCAC
*
1103125 TA TA TA CA 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
1103155 GACACACACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1104032 original size:12 final size:12
Alignment explanation
Indices: 1104007--1104041 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1103997 AGGCTTTTGC
* *
1104007 AACAACAAGGAG
1 AACAAGAAGAAG
1104019 AACAAGAAGAAG
1 AACAAGAAGAAG
1104031 AACAAGAAGAA
1 AACAAGAAGAA
1104042 CGAGGAGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.66, C:0.11, G:0.23, T:0.00
Consensus pattern (12 bp):
AACAAGAAGAAG
Found at i:1104588 original size:3 final size:3
Alignment explanation
Indices: 1104580--1104613 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1104570 GAAGCTAGCA
* *
1104580 AAG AAG AAG AAG AAG AAG AGG TAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1104614 CGGGATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:1106636 original size:12 final size:12
Alignment explanation
Indices: 1106590--1106640 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
1106580 TAACCAAATC
1106590 AATATTTTTATTT
1 AATA-TTTTATTT
1106603 --TATTTTATTT
1 AATATTTTATTT
* **
1106613 CATATTGCATTT
1 AATATTTTATTT
1106625 AATATTTTATTT
1 AATATTTTATTT
1106637 AATA
1 AATA
1106641 CAAAAATCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
10 8 0.26
11 2 0.06
12 21 0.68
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (12 bp):
AATATTTTATTT
Found at i:1108015 original size:20 final size:22
Alignment explanation
Indices: 1107974--1108016 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1107964 GGAAGGATTT
1107974 CAACCAATTCAAAATGTAATAAA
1 CAACCAATT-AAAATGTAATAAA
1107997 CAACCAATT-AAAT-TAATAAA
1 CAACCAATTAAAATGTAATAAA
1108017 TGATCAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 4 0.20
23 9 0.45
ACGTcount: A:0.58, C:0.16, G:0.02, T:0.23
Consensus pattern (22 bp):
CAACCAATTAAAATGTAATAAA
Found at i:1114824 original size:436 final size:436
Alignment explanation
Indices: 1114012--1115754 Score: 3396
Period size: 436 Copynumber: 4.0 Consensus size: 436
1114002 CCTTAAGTTT
1114012 ATTGTAATTATGGTAGTTCCTATATTTATTTTTTGACTAGGTCATAACCTAATATAGCACTAGCT
1 ATTGTAATTATGGTAGTTCCTATATTTATTTTTTGACTAGGTCATAACCTAATATAGCACTAGCT
*
1114077 GTGTATAAATATACACTGTAATTTTGGAGATTATGTTTATGAGAGAAGTATTATTCCTCACTTGA
66 GTGTATAAATATACACTGTAATTTTGGAGATTATGATTATGAGAGAAGTATTATTCCTCACTTGA
*
1114142 TTTGTTTCATGGTATCATAGCCATGCGACTCCTGCCGACATTAGTCTTTGGTTAAACCCTAATTT
131 TTTGTTTCATGGTATCATAGCCATGCGACTCCTGCCGGCATTAGTCTTTGGTTAAACCCTAATTT
1114207 TTCATTCTAGAATGTCTACCGAAGAGATGTCCTCAACACAAACCTCTCAAATCCCACCAAACCCA
196 TTCATTCTAGAATGTCTACCGAAGAGATGTCCTCAACACAAACCTCTCAAATCCCACCAAACCCA
*
1114272 AATCTCAATTTATCCCAAACCTCTGAAATTCCCCACTCGCTTCAGATCACCCAACACAAGCTCAA
261 AATCTCAATTTATCCCAAACCTCTGAAATTCCCCACTCACTTCAGATCACCCAACACAAGCTCAA
1114337 TGGAGCGAATTTCCGTGATTGGTTTCAGTCTGTGGTGCTTGTGATTAGAGGGAAAGGAAAGATGG
326 TGGAGCGAATTTCCGTGATTGGTTTCAGTCTGTGGTGCTTGTGATTAGAGGGAAAGGAAAGATGG
1114402 GTTATCTTACCGACGAGACTGCTCCACCTGATAGCTAGGATATCGA
391 GTTATCTTACCGACGAGACTGCTCCACCTGATAGCTAGGATATCGA
1114448 ATTGTAATTATGGTAGTTCCTATATTTATTTTTTGACTAGGTCATAACCTAATATAGCACTAGCT
1 ATTGTAATTATGGTAGTTCCTATATTTATTTTTTGACTAGGTCATAACCTAATATAGCACTAGCT
1114513 GTGTATAAATATACACTGTAATTTTGGAGATTATGATTATGAGAGAAGTATTATTCCTCACTTGA
66 GTGTATAAATATACACTGTAATTTTGGAGATTATGATTATGAGAGAAGTATTATTCCTCACTTGA
* *
1114578 TTTGTTTCATGATATCATAGCCATGCGACTCCTGCCAGCATTAGTCTTTGGTTAAACCCTAATTT
131 TTTGTTTCATGGTATCATAGCCATGCGACTCCTGCCGGCATTAGTCTTTGGTTAAACCCTAATTT
1114643 TTCATTCTAGAATGTCTACCGAAGAGATGTCCTCAACACAAACCTCTCAAATCCCACCAAACCCA
196 TTCATTCTAGAATGTCTACCGAAGAGATGTCCTCAACACAAACCTCTCAAATCCCACCAAACCCA
* *
1114708 AATCTCAATTTATCCTAAACCTCTGAAATTCCCCACTCACTACAGATCACCCAACACAAGCTCAA
261 AATCTCAATTTATCCCAAACCTCTGAAATTCCCCACTCACTTCAGATCACCCAACACAAGCTCAA
1114773 TGGAGCGAATTTCCGTGATTGGTTTCAGTCTGTGGTGCTTGTGATTAGAGGGAAAGGAAAGATGG
326 TGGAGCGAATTTCCGTGATTGGTTTCAGTCTGTGGTGCTTGTGATTAGAGGGAAAGGAAAGATGG
1114838 GTTATCTTACCGACGAGACTGCTCCACCTGATAGCTAGGATATCGA
391 GTTATCTTACCGACGAGACTGCTCCACCTGATAGCTAGGATATCGA
1114884 ATTGTAATTATGGTAGTTCCTATATTTATTTTTTGACTAGGTCATAACCTAATATAGCACTAGCT
1 ATTGTAATTATGGTAGTTCCTATATTTATTTTTTGACTAGGTCATAACCTAATATAGCACTAGCT
1114949 GTGTATAAATATACACTGTAATTTTGGAGATTATGATTATGAGAGAAGTATTATTCCTCACTTGA
66 GTGTATAAATATACACTGTAATTTTGGAGATTATGATTATGAGAGAAGTATTATTCCTCACTTGA
1115014 TTTGTTTCATGGTATCATAGCCATGCGACTCCTGCCGGCATTAGTCTTTGGTTAAACCCTAATTT
131 TTTGTTTCATGGTATCATAGCCATGCGACTCCTGCCGGCATTAGTCTTTGGTTAAACCCTAATTT
1115079 TTCATTCTAGAATGTCTACCGAAGAGATGTCCTCAACACAAACCTCTCAAATCCCACCAAACCCA
196 TTCATTCTAGAATGTCTACCGAAGAGATGTCCTCAACACAAACCTCTCAAATCCCACCAAACCCA
1115144 AATCTCAATTTATCCCAAACCTCTGAAATTCCCCACTCACTTCAGATCACCCAACACAAGCTCAA
261 AATCTCAATTTATCCCAAACCTCTGAAATTCCCCACTCACTTCAGATCACCCAACACAAGCTCAA
1115209 TGGAGCGAATTTCCGTGATTGGTTTCAGTCTGTGGTGCTTGTGATTAGAGGGAAAGGAAAGATGG
326 TGGAGCGAATTTCCGTGATTGGTTTCAGTCTGTGGTGCTTGTGATTAGAGGGAAAGGAAAGATGG
1115274 GTTATCTTACCGACGAGACTGCTCCACCTGATAGCTAGGATATCGA
391 GTTATCTTACCGACGAGACTGCTCCACCTGATAGCTAGGATATCGA
1115320 ATTGTAATTATGGTAGTTCCTATATTTATTTTTTGACTAGGTCATAACCTAATATAGCACTAGCT
1 ATTGTAATTATGGTAGTTCCTATATTTATTTTTTGACTAGGTCATAACCTAATATAGCACTAGCT
1115385 GTGTATAAATATACACTGTAATTTTGGAGATTATGATTATGAGAGAAGTATTATTCCTCACTTGA
66 GTGTATAAATATACACTGTAATTTTGGAGATTATGATTATGAGAGAAGTATTATTCCTCACTTGA
*
1115450 TTTGTTTCATGGTATCATAGCCATGCGACTCCTGCCGGCATTAGTCTTTGGTTAAACCCTCATTT
131 TTTGTTTCATGGTATCATAGCCATGCGACTCCTGCCGGCATTAGTCTTTGGTTAAACCCTAATTT
1115515 TTCATTCTAGAATGTCTACCGAAGAGATGTCCTCAACACAAACCTCTCAAATCCCACCAAACCCA
196 TTCATTCTAGAATGTCTACCGAAGAGATGTCCTCAACACAAACCTCTCAAATCCCACCAAACCCA
1115580 AATCTCAATTTATCCCAAACCTCTGAAATTCCCCACTCACTTCAGATCACCCAACACAAGCTCAA
261 AATCTCAATTTATCCCAAACCTCTGAAATTCCCCACTCACTTCAGATCACCCAACACAAGCTCAA
1115645 TGGAGCGAATTTCCGTGATTGGTTTCAGTCTGTGGTGCTTGTGATTAGAGGGAAAGGAAAGATGG
326 TGGAGCGAATTTCCGTGATTGGTTTCAGTCTGTGGTGCTTGTGATTAGAGGGAAAGGAAAGATGG
* *
1115710 ATTATCTTACCGGCGAGACTGCTCCACCTGATAGCTAGGATATCG
391 GTTATCTTACCGACGAGACTGCTCCACCTGATAGCTAGGATATCG
1115755 CATTCAAGAT
Statistics
Matches: 1293, Mismatches: 14, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
436 1293 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (436 bp):
ATTGTAATTATGGTAGTTCCTATATTTATTTTTTGACTAGGTCATAACCTAATATAGCACTAGCT
GTGTATAAATATACACTGTAATTTTGGAGATTATGATTATGAGAGAAGTATTATTCCTCACTTGA
TTTGTTTCATGGTATCATAGCCATGCGACTCCTGCCGGCATTAGTCTTTGGTTAAACCCTAATTT
TTCATTCTAGAATGTCTACCGAAGAGATGTCCTCAACACAAACCTCTCAAATCCCACCAAACCCA
AATCTCAATTTATCCCAAACCTCTGAAATTCCCCACTCACTTCAGATCACCCAACACAAGCTCAA
TGGAGCGAATTTCCGTGATTGGTTTCAGTCTGTGGTGCTTGTGATTAGAGGGAAAGGAAAGATGG
GTTATCTTACCGACGAGACTGCTCCACCTGATAGCTAGGATATCGA
Found at i:1115995 original size:32 final size:32
Alignment explanation
Indices: 1115954--1116017 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1115944 CACAACAGGG
1115954 GAGCAAGACAGTCACCGAATATTTCCATATTC
1 GAGCAAGACAGTCACCGAATATTTCCATATTC
1115986 GAGCAAGACAGTCACCGAATATTTCCATATTC
1 GAGCAAGACAGTCACCGAATATTTCCATATTC
1116018 TGCAGGAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (32 bp):
GAGCAAGACAGTCACCGAATATTTCCATATTC
Found at i:1120613 original size:18 final size:18
Alignment explanation
Indices: 1120592--1120637 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1120582 TTCTCTCTCT
1120592 CCTTTTCTCTTTCCTTCA
1 CCTTTTCTCTTTCCTTCA
* *
1120610 CCTTGTCTCTTTCCTTCT
1 CCTTTTCTCTTTCCTTCA
1120628 CCTTTTCTCT
1 CCTTTTCTCT
1120638 GTCCCTATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.02, C:0.39, G:0.02, T:0.57
Consensus pattern (18 bp):
CCTTTTCTCTTTCCTTCA
Found at i:1122309 original size:16 final size:16
Alignment explanation
Indices: 1122288--1122318 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1122278 TAATTATTTT
*
1122288 TATTTATTATTTATTA
1 TATTTAGTATTTATTA
1122304 TATTTAGTATTTATT
1 TATTTAGTATTTATT
1122319 TAATATTAAA
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:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TATTTAGTATTTATTA
Found at i:1122359 original size:20 final size:20
Alignment explanation
Indices: 1122303--1122363 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
1122293 ATTATTTATT
*
1122303 ATATTTAGTA-TTTATTT-A
1 ATATTTAATATTTTATTTAA
* *
1122321 ATA-TTAAAATTATTTTTTAA
1 ATATTTAATATT-TTATTTAA
1122341 ATATTTAATATTTTATTTAA
1 ATATTTAATATTTTATTTAA
1122361 ATA
1 ATA
1122364 AATCAATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 4 0.12
18 4 0.12
19 5 0.15
20 14 0.41
21 7 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
ATATTTAATATTTTATTTAA
Found at i:1129019 original size:10 final size:10
Alignment explanation
Indices: 1129004--1129028 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1128994 AGGGTTTTCA
1129004 TAATTTAAAT
1 TAATTTAAAT
1129014 TAATTTAAAT
1 TAATTTAAAT
1129024 TAATT
1 TAATT
1129029 ATTATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TAATTTAAAT
Found at i:1129061 original size:26 final size:27
Alignment explanation
Indices: 1129023--1129076 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
1129013 TTAATTTAAA
* *
1129023 TTAATTATTATTTAATTAATAA-AATTT
1 TTAATTATAATTT-ATTAAAAATAATTT
1129050 TTAATTA-AATTTATTAAAAATAATTT
1 TTAATTATAATTTATTAAAAATAATTT
1129076 T
1 T
1129077 ATTTTTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.29
26 10 0.42
27 7 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTAATTATAATTTATTAAAAATAATTT
Found at i:1130876 original size:21 final size:20
Alignment explanation
Indices: 1130852--1130923 Score: 57
Period size: 21 Copynumber: 3.9 Consensus size: 20
1130842 TATTCAATTT
1130852 TAATTTTAAAATATTAATATA
1 TAATTTTAAAATATTAATA-A
* * *
1130873 TAATTTTGATATTTTAATAA
1 TAATTTTAAAATATTAATAA
*
1130893 TAA---T--AATAATAATAA
1 TAATTTTAAAATATTAATAA
1130908 TAATTTT-AAATATTAA
1 TAATTTTAAAATATTAA
1130924 ACATGTTTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
15 11 0.28
17 1 0.03
18 1 0.03
19 7 0.17
20 4 0.10
21 16 0.40
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (20 bp):
TAATTTTAAAATATTAATAA
Found at i:1130877 original size:27 final size:26
Alignment explanation
Indices: 1130847--1130923 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 26
1130837 ATTTTTATTC
1130847 AATTTTAATTTTAAAATATTAATATAT
1 AATTTTAATTTTAAAATATTAATA-AT
*
1130874 AATTTTGATATTTTAATAATAATAATAAT
1 AATTTT-A-ATTTTAA-AATATTAATAAT
**
1130903 AATAATAATTTT-AAATATTAA
1 AATTTTAATTTTAAAATATTAA
1130924 ACATGTTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
25 7 0.16
26 1 0.02
27 11 0.26
28 2 0.05
29 13 0.30
30 9 0.21
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (26 bp):
AATTTTAATTTTAAAATATTAATAAT
Found at i:1130887 original size:35 final size:35
Alignment explanation
Indices: 1130848--1130914 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
1130838 TTTTTATTCA
** *
1130848 ATTTTAATTTTAA-AATATTAATATATAATTTTGAT
1 ATTTTAATAATAATAATAATAATA-ATAATTTTGAT
1130883 ATTTTAATAATAATAATAATAATAATAATTTT
1 ATTTTAATAATAATAATAATAATAATAATTTT
1130915 AAATATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 19 0.68
36 9 0.32
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (35 bp):
ATTTTAATAATAATAATAATAATAATAATTTTGAT
Found at i:1130895 original size:3 final size:3
Alignment explanation
Indices: 1130887--1130911 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1130877 TTTGATATTT
1130887 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
1130912 TTTAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1131353 original size:29 final size:29
Alignment explanation
Indices: 1131276--1131345 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
1131266 ATAAAAACAA
**
1131276 AAATA-AATTAAAAATATACGAATTTATTT
1 AAATATAA-TAAAAATATAAAAATTTATTT
1131305 AAATATAATAAAAATATAAAAATTTATTT
1 AAATATAATAAAAATATAAAAATTTATTT
*
1131334 AAAAAT-ATAAAA
1 AAATATAATAAAA
1131346 TAATTAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.16
29 29 0.78
30 2 0.05
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (29 bp):
AAATATAATAAAAATATAAAAATTTATTT
Found at i:1131759 original size:30 final size:30
Alignment explanation
Indices: 1131724--1131784 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1131714 AAATTGATTT
*
1131724 ATATTAAAGGCTTATTCAAATATAAATAAA
1 ATATTAAAGACTTATTCAAATATAAATAAA
* *
1131754 ATATTAAAGATTTATTTAAATATAAATAAA
1 ATATTAAAGACTTATTCAAATATAAATAAA
1131784 A
1 A
1131785 AAATTAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (30 bp):
ATATTAAAGACTTATTCAAATATAAATAAA
Found at i:1131800 original size:31 final size:31
Alignment explanation
Indices: 1131726--1131816 Score: 87
Period size: 31 Copynumber: 3.0 Consensus size: 31
1131716 ATTGATTTAT
** * *
1131726 ATTAAAGGCTTATTCAAATATAAAT-AAAAT
1 ATTAAAGAATTATTTAAATATAAATAAAAAA
*
1131756 ATTAAAGATTTATTTAAATATAAATAAAAAA
1 ATTAAAGAATTATTTAAATATAAATAAAAAA
* * *
1131787 ATTAATA-AATTATTTAGATACAATTAAAAA
1 ATTAA-AGAATTATTTAAATATAAATAAAAA
1131817 TTAAAATATT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
30 22 0.43
31 28 0.55
32 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.35
Consensus pattern (31 bp):
ATTAAAGAATTATTTAAATATAAATAAAAAA
Found at i:1131827 original size:29 final size:28
Alignment explanation
Indices: 1131783--1131878 Score: 92
Period size: 29 Copynumber: 3.4 Consensus size: 28
1131773 ATATAAATAA
1131783 AAAAATTAATAA-ATTATTT-AGATACAATT
1 AAAAATTAA-AATATTATTTGAG-TACAA-T
1131812 AAAAATTAAAATATTATTTGAGTACAAT
1 AAAAATTAAAATATTATTTGAGTACAAT
* * *
1131840 AAAAA-TAAAAT-TTATCTAAGTAAAAT
1 AAAAATTAAAATATTATTTGAGTACAAT
*
1131866 AATAAATTTAAAT
1 AA-AAATTAAAAT
1131879 GATTTTTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
26 14 0.24
27 9 0.15
28 13 0.22
29 21 0.36
30 2 0.03
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.35
Consensus pattern (28 bp):
AAAAATTAAAATATTATTTGAGTACAAT
Found at i:1131861 original size:26 final size:27
Alignment explanation
Indices: 1131805--1131872 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 27
1131795 ATTATTTAGA
* *
1131805 TACAATTAAAAATTAAAATATTATTTGAG
1 TACAA-TAAAAA-TAAAATATTATCTAAG
1131834 TACAATAAAAATAAAAT-TTATCTAAG
1 TACAATAAAAATAAAATATTATCTAAG
*
1131860 TAAAATAATAAAT
1 TACAATAA-AAAT
1131873 TTAAATGATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 14 0.40
27 10 0.29
28 6 0.17
29 5 0.14
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.34
Consensus pattern (27 bp):
TACAATAAAAATAAAATATTATCTAAG
Done.