Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 86 of 318
Found at i:29305380 original size:23 final size:22
Alignment explanation
Indices: 29305278--29305402 Score: 94
Period size: 23 Copynumber: 5.4 Consensus size: 22
29305268 CAACCCAACC
* *
29305278 TTTATTTTTTACT-TTTCTTAATT
1 TTTATTTTTTAGTATTTATT-A-T
* *
29305301 TTTATTATTTATTATTTATTAT
1 TTTATTTTTTAGTATTTATTAT
29305323 TTTATTTTATTAGTATTTATTATTTT
1 TTTATTTT-TTAGTATTTATTA---T
29305349 ATTTCATTTTATTAGTATTTATTAT
1 -TTT-ATTTT-TTAGTATTTATTAT
* *
29305374 TTTATTTTGT--TATTTATTAC
1 TTTATTTTTTAGTATTTATTAT
29305394 TTTATTTTT
1 TTTATTTTT
29305403 GGATATTGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 17
0.78 0.07 0.15
Matches are distributed among these distances:
20 17 0.20
22 9 0.10
23 29 0.33
24 8 0.09
25 1 0.01
26 1 0.01
27 3 0.03
28 19 0.22
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTATTTTTTAGTATTTATTAT
Found at i:29310571 original size:21 final size:21
Alignment explanation
Indices: 29310532--29310593 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 21
29310522 TTTTTAAGTA
29310532 AAAATAAATAAAAGAAAAAAATT
1 AAAA-AAA-AAAAGAAAAAAATT
*
29310555 AAAAGTAAAAAAGAAAAAAATT
1 AAAA-AAAAAAAGAAAAAAATT
29310577 AAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAGAAAAA
29310594 GAAAAAGAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 12 0.33
22 18 0.50
23 6 0.17
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.11
Consensus pattern (21 bp):
AAAAAAAAAAAGAAAAAAATT
Found at i:29310604 original size:15 final size:14
Alignment explanation
Indices: 29310531--29310605 Score: 55
Period size: 14 Copynumber: 5.1 Consensus size: 14
29310521 ATTTTTAAGT
*
29310531 AAAAATAAATAAAAG
1 AAAAAGAAA-AAAAG
*
29310546 AAAAA-AATTAAAAG
1 AAAAAGAA-AAAAAG
*
29310560 TAAAAAAGAAAAAAAT
1 --AAAAAGAAAAAAAG
*
29310576 TAAAA-AAAAAAAG
1 AAAAAGAAAAAAAG
29310589 AAAAAGAAAAAGAAG
1 AAAAAGAAAAA-AAG
29310604 AA
1 AA
29310606 TGAGGTATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
13 11 0.23
14 16 0.33
15 10 0.21
16 9 0.19
17 2 0.04
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:29311241 original size:10 final size:10
Alignment explanation
Indices: 29311226--29311275 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
29311216 TTAATTTAGG
29311226 ATTTAT-TTT
1 ATTTATCTTT
29311235 CATTTATCTTT
1 -ATTTATCTTT
*
29311246 AATTATCTTT
1 ATTTATCTTT
29311256 ATTTAT-TTGT
1 ATTTATCTT-T
29311266 ATTTATCTTT
1 ATTTATCTTT
29311276 TAGAATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:29315453 original size:26 final size:25
Alignment explanation
Indices: 29315399--29315466 Score: 59
Period size: 26 Copynumber: 2.6 Consensus size: 25
29315389 TAGTTAAAAT
* *
29315399 AATT-AATATAATTAATTTTTAGATTA
1 AATTAAATATAATT--TTTTTAAATAA
29315425 AATTAAATATAATTTTTTCTAAATAA
1 AATTAAATATAATTTTTT-TAAATAA
*
29315451 AATAAAAT-TATATTTT
1 AATTAAATATA-ATTTT
29315467 AATCTTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 6 0.17
26 21 0.58
27 9 0.25
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (25 bp):
AATTAAATATAATTTTTTTAAATAA
Found at i:29316662 original size:18 final size:17
Alignment explanation
Indices: 29316630--29316722 Score: 59
Period size: 18 Copynumber: 5.2 Consensus size: 17
29316620 AAGTTCTTTT
29316630 TTTTTTTTACTT-ATTTA
1 TTTTTTTT-CTTAATTTA
29316647 TTTTTTTTCTTATATTT-
1 TTTTTTTTCTTA-ATTTA
* *
29316664 TGTCTCTTTCTTAGATTT-
1 T-TTTTTTTCTTA-ATTTA
29316682 TTTTCTTTT-TTAAGTTTTA
1 TTTT-TTTTCTTAA--TTTA
*
29316701 TATTATTTTCTTAATTTA
1 T-TTTTTTTCTTAATTTA
29316719 TTTT
1 TTTT
29316723 GCTTATTTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
16 4 0.07
17 16 0.27
18 29 0.48
19 5 0.08
20 6 0.10
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.73
Consensus pattern (17 bp):
TTTTTTTTCTTAATTTA
Found at i:29316739 original size:36 final size:36
Alignment explanation
Indices: 29316670--29316743 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 36
29316660 ATTTTGTCTC
*
29316670 TTTCTTAGATTTTTTTCTTTTTTAAGTTTTATATTAT
1 TTTCTTAGATTTTTTTCTTATTTAAG-TTTATATTAT
29316707 TTTCTTA-ATTTATTTTGCTTATTTAA-TTTATATTAT
1 TTTCTTAGATTT-TTTT-CTTATTTAAGTTTATATTAT
29316743 T
1 T
29316744 AATTTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 15 0.44
37 11 0.32
38 8 0.24
ACGTcount: A:0.22, C:0.05, G:0.04, T:0.69
Consensus pattern (36 bp):
TTTCTTAGATTTTTTTCTTATTTAAGTTTATATTAT
Found at i:29316748 original size:18 final size:17
Alignment explanation
Indices: 29316697--29316744 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
29316687 TTTTTTAAGT
*
29316697 TTTATATTATTTTCTTAA
1 TTTATATTATTAT-TTAA
* *
29316715 TTTATTTTGCTTATTTAA
1 TTTATATT-ATTATTTAA
29316733 TTTATATTATTA
1 TTTATATTATTA
29316745 ATTTTAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 3 0.12
18 18 0.75
19 3 0.12
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTATATTATTATTTAA
Found at i:29317133 original size:11 final size:11
Alignment explanation
Indices: 29317117--29317159 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
29317107 AAATTTTAAA
29317117 AAATATATATT
1 AAATATATATT
29317128 AAATAT-TATT
1 AAATATATATT
** *
29317138 TTATAAATATT
1 AAATATATATT
29317149 AAATATATATT
1 AAATATATATT
29317160 TTTCTTTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
10 7 0.28
11 18 0.72
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
AAATATATATT
Found at i:29317333 original size:26 final size:26
Alignment explanation
Indices: 29317301--29317368 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
29317291 AAATTTTATA
*
29317301 TATAATTTTTAAATACATTTAA-AAAT
1 TATAATTTTTAAATA-ATATAAGAAAT
*
29317327 TATAATTTTTTAATAATATAAGAAAT
1 TATAATTTTTAAATAATATAAGAAAT
*
29317353 CATAATCTTTTAAATA
1 TATAAT-TTTTAAATA
29317369 TTTTTTTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 5 0.14
26 23 0.64
27 8 0.22
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (26 bp):
TATAATTTTTAAATAATATAAGAAAT
Found at i:29317534 original size:21 final size:21
Alignment explanation
Indices: 29317495--29317538 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
29317485 ATTTAAAATG
29317495 TTTTATAATATATTTTTTACAA
1 TTTTATAATATATTTTTTA-AA
29317517 TTTTA-AATAT-TATTTTTAAA
1 TTTTATAATATAT-TTTTTAAA
29317537 TT
1 TT
29317539 CTTTTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
21 11 0.52
22 5 0.24
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTATAATATATTTTTTAAA
Found at i:29317640 original size:12 final size:12
Alignment explanation
Indices: 29317623--29317652 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
29317613 GTGACTATTA
29317623 ATAAATTTAAAT
1 ATAAATTTAAAT
29317635 ATAAATTTAAAT
1 ATAAATTTAAAT
*
29317647 TTAAAT
1 ATAAAT
29317653 ATATATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATAAATTTAAAT
Found at i:29317647 original size:18 final size:19
Alignment explanation
Indices: 29317624--29317665 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
29317614 TGACTATTAA
29317624 TAAATTTAAATATAAAT-T
1 TAAATTTAAATATAAATAT
*
29317642 TAAATTTAAATATATATAT
1 TAAATTTAAATATAAATAT
29317661 TAAAT
1 TAAAT
29317666 ATATTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAATTTAAATATAAATAT
Found at i:29320692 original size:30 final size:30
Alignment explanation
Indices: 29320656--29320728 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
29320646 GTCCCAGAAT
*
29320656 AGTTCATATAACCCGGACATAGGTGGTTCG
1 AGTTCATATAACCCGGACATAGGCGGTTCG
* * *
29320686 AGTTCATATCACCCGGATATATGCGGTTCG
1 AGTTCATATAACCCGGACATAGGCGGTTCG
* *
29320716 AGTCCATTTAACC
1 AGTTCATATAACC
29320729 TAGAGCAACC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (30 bp):
AGTTCATATAACCCGGACATAGGCGGTTCG
Found at i:29322261 original size:25 final size:20
Alignment explanation
Indices: 29322213--29322254 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
29322203 AGACCCTTTG
29322213 ATCTGTCAGATATAATGCAA
1 ATCTGTCAGATATAATGCAA
29322233 ATCTGTCAGATATAATGCAA
1 ATCTGTCAGATATAATGCAA
29322253 AT
1 AT
29322255 GTTATCTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (20 bp):
ATCTGTCAGATATAATGCAA
Found at i:29324223 original size:14 final size:13
Alignment explanation
Indices: 29324189--29324230 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
29324179 ACTTGAAATG
29324189 TATTTTTTA-AAA
1 TATTTTTTATAAA
*
29324201 -ATGTTTTATAATA
1 TATTTTTTATAA-A
29324214 TATTTTTTATAAA
1 TATTTTTTATAAA
29324227 TATT
1 TATT
29324231 AAAAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 7 0.28
12 2 0.08
13 6 0.24
14 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
TATTTTTTATAAA
Found at i:29324329 original size:9 final size:10
Alignment explanation
Indices: 29324237--29324330 Score: 58
Period size: 10 Copynumber: 9.7 Consensus size: 10
29324227 TATTAAAAAT
*
29324237 ATATTTTCAA
1 ATATTTTTAA
29324247 ATTATTTTTTAA
1 A-TA-TTTTTAA
29324259 ATA---TTAA
1 ATATTTTTAA
*
29324266 ATATATTT-A
1 ATATTTTTAA
* *
29324275 ATATTATAAA
1 ATATTTTTAA
*
29324285 ACATTTTTAA
1 ATATTTTTAA
29324295 ATCA-TTTTAA
1 AT-ATTTTTAA
29324305 ATGA-TTTTAA
1 AT-ATTTTTAA
29324315 ATATTTTTAA
1 ATATTTTTAA
29324325 A-ATTTT
1 ATATTTT
29324331 ACATAGAATT
Statistics
Matches: 67, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
7 7 0.10
9 12 0.18
10 36 0.54
11 5 0.07
12 7 0.10
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (10 bp):
ATATTTTTAA
Found at i:29325066 original size:37 final size:36
Alignment explanation
Indices: 29324996--29325121 Score: 114
Period size: 37 Copynumber: 3.5 Consensus size: 36
29324986 AATAATTATT
*
29324996 TTTTTAAAATTTTAAAAAATTAATTTGAAAAATACA
1 TTTTTAAAATTTTAAAAAATTAATTTCAAAAATACA
* * *
29325032 TTTTTAAAATTTATAAATAATTAATTTCACAAATATA
1 TTTTTAAAATTT-TAAAAAATTAATTTCAAAAATACA
* * * * *
29325069 TATATATAAA-GTTAAAAAA-TATTTTTAAAAATA-A
1 TTTTTA-AAATTTTAAAAAATTAATTTCAAAAATACA
**
29325103 TAATTAAAATTTTAAAAAA
1 TTTTTAAAATTTTAAAAAA
29325122 ATATTATAAA
Statistics
Matches: 73, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
33 3 0.04
34 13 0.18
35 11 0.15
36 18 0.25
37 25 0.34
38 3 0.04
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (36 bp):
TTTTTAAAATTTTAAAAAATTAATTTCAAAAATACA
Found at i:29325116 original size:21 final size:21
Alignment explanation
Indices: 29325091--29325177 Score: 63
Period size: 22 Copynumber: 4.0 Consensus size: 21
29325081 TAAAAAATAT
29325091 TTTTAAAAATAATAATTAAAA
1 TTTTAAAAATAATAATTAAAA
*
29325112 TTTTAAAAA-AATATTATAAAACA
1 TTTTAAAAATAATA--ATTAAA-A
*
29325135 TTTTAAATAT-AT-ATTACAAA
1 TTTTAAAAATAATAATTA-AAA
*
29325155 TTTTTTAAAATTAATAATATAAA
1 --TTTTAAAAATAATAAT-TAAA
29325178 TTAAATAAGT
Statistics
Matches: 51, Mismatches: 5, Indels: 17
0.70 0.07 0.23
Matches are distributed among these distances:
20 8 0.16
21 11 0.22
22 13 0.25
23 13 0.25
24 4 0.08
25 2 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTTAAAAATAATAATTAAAA
Found at i:29325178 original size:23 final size:22
Alignment explanation
Indices: 29325089--29325179 Score: 62
Period size: 23 Copynumber: 4.1 Consensus size: 22
29325079 GTTAAAAAAT
*
29325089 ATTTTTAAAAATAATAAT-TAA
1 ATTTTTTAAAATAATAATATAA
* * *
29325110 A-ATTTTAAAAAAATATTATAAA
1 ATTTTTTAAAATAATAATAT-AA
** * *
29325132 ACATTTT-AAATATATATTACAA
1 ATTTTTTAAAATA-ATAATATAA
29325154 ATTTTTTAAAATTAATAATATAA
1 ATTTTTTAAAA-TAATAATATAA
29325177 ATT
1 ATT
29325180 AAATAAGTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
20 12 0.22
21 2 0.04
22 14 0.26
23 24 0.44
24 2 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTTTTAAAATAATAATATAA
Found at i:29325212 original size:18 final size:18
Alignment explanation
Indices: 29325162--29325213 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
29325152 AAATTTTTTA
*
29325162 AAATTAATAATATAAATT
1 AAATAAATAATATAAATT
* *
29325180 AAATAAGTAAAATAAATT
1 AAATAAATAATATAAATT
29325198 AAGA-AAATAATATAAA
1 AA-ATAAATAATATAAA
29325214 ACTTAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (18 bp):
AAATAAATAATATAAATT
Found at i:29325264 original size:9 final size:9
Alignment explanation
Indices: 29325250--29325291 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
29325240 AAATATAAGA
29325250 AAAAAAAGT
1 AAAAAAAGT
29325259 -AAAAAAGT
1 AAAAAAAGT
*
29325267 TAAAAAAGT
1 AAAAAAAGT
29325276 AAAAAAAGT
1 AAAAAAAGT
29325285 AAAAAAA
1 AAAAAAA
29325292 AATATAAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 8 0.26
9 23 0.74
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.12
Consensus pattern (9 bp):
AAAAAAAGT
Found at i:29341735 original size:39 final size:39
Alignment explanation
Indices: 29341650--29341884 Score: 205
Period size: 39 Copynumber: 6.0 Consensus size: 39
29341640 CAAATCCAAT
* * *
29341650 CACCACCACAAAGCATGT-GGGACTTTAAGCCCGAATATAA
1 CACCAGCACAAAGCCT-TCGGGACTTT-AGCCCGGATATAA
** *
29341690 TGCCAGCATAAAGCCTGT-GGGACTTTAGCCCGGATATAA
1 CACCAGCACAAAGCCT-TCGGGACTTTAGCCCGGATATAA
** * *
29341729 CACCAGCACGATTGCCTTCGGGGC-TTAACCCGGATATAA
1 CACCAGCAC-AAAGCCTTCGGGACTTTAGCCCGGATATAA
29341768 CACCAGCACAAATGCCTTCGGGAC-TTAGCCCGGATATAA
1 CACCAGCACAAA-GCCTTCGGGACTTTAGCCCGGATATAA
* *
29341807 CACCAGTACGAATA-CCTTCAGGA-TTTAGCCCGGATATAA
1 CACCAGCAC-AA-AGCCTTCGGGACTTTAGCCCGGATATAA
* * * *
29341846 CACCAGCACGAATGCTTTCAGGAC-TTAGCCCGAATATAA
1 CACCAGCAC-AAAGCCTTCGGGACTTTAGCCCGGATATAA
29341885 TTCTCCATTA
Statistics
Matches: 164, Mismatches: 23, Indels: 17
0.80 0.11 0.08
Matches are distributed among these distances:
38 1 0.01
39 130 0.79
40 32 0.20
41 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.20
Consensus pattern (39 bp):
CACCAGCACAAAGCCTTCGGGACTTTAGCCCGGATATAA
Found at i:29341796 original size:78 final size:78
Alignment explanation
Indices: 29341669--29341884 Score: 247
Period size: 78 Copynumber: 2.7 Consensus size: 78
29341659 AAAGCATGTG
* ** *
29341669 GGACTTTAAGCCCGAATATAATGCCAGCATAAA-GCCTGT-GGGACTTTAGCCCGGATATAACAC
1 GGAC-TTAA-CCCGGATATAACACCAGCACAAATGCCT-TCGGGAC-TTAGCCCGGATATAACAC
* * *
29341732 CAGCACGATTGCCTTCG
62 CAGCACGAATACCTTCA
* *
29341749 GGGCTTAACCCGGATATAACACCAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACACCAGT
1 GGACTTAACCCGGATATAACACCAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACACCAGC
29341814 ACGAATACCTTCA
66 ACGAATACCTTCA
* * * * * *
29341827 GGATTTAGCCCGGATATAACACCAGCACGAATGCTTTCAGGACTTAGCCCGAATATAA
1 GGACTTAACCCGGATATAACACCAGCACAAATGCCTTCGGGACTTAGCCCGGATATAA
29341885 TTCTCCATTA
Statistics
Matches: 118, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
78 102 0.86
79 13 0.11
80 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (78 bp):
GGACTTAACCCGGATATAACACCAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACACCAGC
ACGAATACCTTCA
Found at i:29348342 original size:39 final size:39
Alignment explanation
Indices: 29348274--29348490 Score: 285
Period size: 39 Copynumber: 5.5 Consensus size: 39
29348264 ACAAAGCATG
* ** * *
29348274 CGGGACTTTAAGCCCGTATATAATGCCAGCAC-AAAGCCTG
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
29348314 CGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTT
*
29348354 CGGG-CTTAACCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
29348392 TGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* * *
29348431 CAGGACTTAGCCCAGATATAACACCAGCATGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
29348470 CAGGACTTAGCCCGAATATAA
1 CGGGACTTAGCCCGGATATAA
29348491 TTCTCCATTA
Statistics
Matches: 161, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
38 35 0.22
39 107 0.66
40 19 0.12
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:29350603 original size:22 final size:22
Alignment explanation
Indices: 29350575--29350737 Score: 91
Period size: 22 Copynumber: 7.5 Consensus size: 22
29350565 ATTTTAACCC
*
29350575 TAAACCCTAATTTAATTTATTT
1 TAAACCCTAACTTAATTTATTT
29350597 TAAACCCTAACTTAATTTATTT
1 TAAACCCTAACTTAATTTATTT
* *
29350619 AAAACCCTAGAACCTTAATTTA-AT
1 TAAACCCT--AA-CTTAATTTATTT
*** * * * *
29350643 TAATTTC-AACCT-A-TAAATA
1 TAAACCCTAACTTAATTTATTT
* ** ***
29350662 TAAACCCTAATTTAATAAACCC
1 TAAACCCTAACTTAATTTATTT
* *
29350684 AAAACCCTAATTTAATTTATTT
1 TAAACCCTAACTTAATTTATTT
*
29350706 TAAAACCTAACTTAATTTATTT
1 TAAACCCTAACTTAATTTATTT
*
29350728 AAAACCCTAA
1 TAAACCCTAA
29350738 AACCCTAATT
Statistics
Matches: 103, Mismatches: 31, Indels: 14
0.70 0.21 0.09
Matches are distributed among these distances:
18 2 0.02
19 5 0.05
20 5 0.05
21 3 0.03
22 73 0.71
24 6 0.06
25 9 0.09
ACGTcount: A:0.43, C:0.18, G:0.01, T:0.38
Consensus pattern (22 bp):
TAAACCCTAACTTAATTTATTT
Found at i:29350694 original size:109 final size:109
Alignment explanation
Indices: 29350570--29350820 Score: 360
Period size: 109 Copynumber: 2.3 Consensus size: 109
29350560 AATTTATTTT
* * *
29350570 AACCCTAAACCCTAATTTAATTTATTTTAAACCCTAACTTAATTTATTTAAAACCCTAGAACCTT
1 AACCCAAAACCCTAATTTAATTTATTTTAAACCCTAACTTAATTTATTTAAAACCCTAAAACCCT
* *
29350635 AATTTAATTAATTTCAACCTATAAATATAAAC-CCTAATTTAATA
66 AATTTAATTAATTTCAACCAAAAAATAT-AACTCCTAATTTAATA
*
29350679 AACCCAAAACCCTAATTTAATTTATTTTAAAACCTAACTTAATTTATTTAAAACCCTAAAACCCT
1 AACCCAAAACCCTAATTTAATTTATTTTAAACCCTAACTTAATTTATTTAAAACCCTAAAACCCT
* * *
29350744 AATTTAATTAATTTTAACCAAAAAATATAACTGCTAATTTAATT
66 AATTTAATTAATTTCAACCAAAAAATATAACTCCTAATTTAATA
* *** *
29350788 TATTTAAAACCCTAACTTAATTTATTTTAAACC
1 AACCCAAAACCCTAATTTAATTTATTTTAAACC
29350821 TTAAAACCCT
Statistics
Matches: 126, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
108 3 0.02
109 123 0.98
ACGTcount: A:0.43, C:0.18, G:0.01, T:0.38
Consensus pattern (109 bp):
AACCCAAAACCCTAATTTAATTTATTTTAAACCCTAACTTAATTTATTTAAAACCCTAAAACCCT
AATTTAATTAATTTCAACCAAAAAATATAACTCCTAATTTAATA
Found at i:29350807 original size:22 final size:22
Alignment explanation
Indices: 29350777--29350820 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
29350767 AATATAACTG
*
29350777 CTAATTTAATTTATTTAAAACC
1 CTAACTTAATTTATTTAAAACC
*
29350799 CTAACTTAATTTATTTTAAACC
1 CTAACTTAATTTATTTAAAACC
29350821 TTAAAACCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (22 bp):
CTAACTTAATTTATTTAAAACC
Found at i:29350827 original size:30 final size:29
Alignment explanation
Indices: 29350705--29350832 Score: 102
Period size: 30 Copynumber: 4.4 Consensus size: 29
29350695 TTAATTTATT
*
29350705 TTAAAA-CCTAACTTAATTTATTTAAAACC
1 TTAAAACCCTAACTTAATTTATTT-TAACC
* * *
29350734 CTAAAACCCTAATTTAATTAATTTTAACC
1 TTAAAACCCTAACTTAATTTATTTTAACC
* *** * *
29350763 -AAAAAATATAACTGCTAATTTAATTT-A-T
1 TTAAAACCCTAACT--TAATTTATTTTAACC
29350791 TTAAAACCCTAACTTAATTTATTTTAAACC
1 TTAAAACCCTAACTTAATTTATTTT-AACC
29350821 TTAAAACCCTAA
1 TTAAAACCCTAA
29350833 TTTACTTAAT
Statistics
Matches: 74, Mismatches: 18, Indels: 13
0.70 0.17 0.12
Matches are distributed among these distances:
27 10 0.14
28 8 0.11
29 20 0.27
30 36 0.49
ACGTcount: A:0.45, C:0.17, G:0.01, T:0.38
Consensus pattern (29 bp):
TTAAAACCCTAACTTAATTTATTTTAACC
Found at i:29350886 original size:22 final size:21
Alignment explanation
Indices: 29350845--29350893 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
29350835 TACTTAATCT
*
29350845 ATTTAA-AAACATAAATCCTA
1 ATTTAATAAACATAAACCCTA
29350865 ATTTAATAAACACTAAACCCTA
1 ATTTAATAAACA-TAAACCCTA
29350887 ATTTAAT
1 ATTTAAT
29350894 TTATTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 6 0.23
21 5 0.19
22 15 0.58
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTTAATAAACATAAACCCTA
Found at i:29350901 original size:85 final size:85
Alignment explanation
Indices: 29350706--29350909 Score: 225
Period size: 87 Copynumber: 2.4 Consensus size: 85
29350696 TAATTTATTT
* *
29350706 TAAAACCTAACTTAATTTATTTAAAACCCTAAAACCCTAATTTAATTAATTTTAACCAAAAAATA
1 TAAACCCTAACTTAATTTATTTTAAACCCTAAAACCCTAATTTAATTAATTTTAA-CAAAAAATA
* ** **
29350771 TAACTGCTAATTTAATTTATT
65 TAACTCCTAATTTAATAAAAC
* * * *
29350792 TAAAACCCTAACTTAATTTATTTTAAACCTTAAAACCCTAATTTACTTAATCTATTTA-AAAACA
1 T-AAACCCTAACTTAATTTATTTTAAACCCTAAAACCCTAATTTAATTAAT-T-TTAACAAAAAA
29350856 TA-AA-TCCTAATTTAATAAACAC
63 TATAACTCCTAATTTAATAAA-AC
* *
29350878 TAAACCCTAATTTAATTTATTTTAAACACTAA
1 TAAACCCTAACTTAATTTATTTTAAACCCTAA
29350910 CTTAATTTAT
Statistics
Matches: 100, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
85 40 0.40
86 4 0.04
87 52 0.52
88 1 0.01
89 3 0.03
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (85 bp):
TAAACCCTAACTTAATTTATTTTAAACCCTAAAACCCTAATTTAATTAATTTTAACAAAAAATAT
AACTCCTAATTTAATAAAAC
Found at i:29350903 original size:22 final size:22
Alignment explanation
Indices: 29350878--29350930 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
29350868 TAATAAACAC
*
29350878 TAAACCCTAATTTAATTTATTT
1 TAAACCCTAACTTAATTTATTT
*
29350900 TAAACACTAACTTAATTTATTT
1 TAAACCCTAACTTAATTTATTT
* *
29350922 AAAATCCTA
1 TAAACCCTA
29350931 GAACCCTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAACCCTAACTTAATTTATTT
Found at i:29350990 original size:24 final size:24
Alignment explanation
Indices: 29350963--29351029 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
29350953 TTAAAACCAC
*
29350963 AAACCCTAAGCCCTAATTTGTTT-A
1 AAACCCTAA-CCCTAATTTATTTAA
*
29350987 AAACCCTAA-CTTAATTTATTTAA
1 AAACCCTAACCCTAATTTATTTAA
*
29351010 AAACCATTAACCCTAATTTA
1 AAACC-CTAACCCTAATTTA
29351030 AATAATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 10 0.28
23 6 0.17
24 12 0.33
25 8 0.22
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.34
Consensus pattern (24 bp):
AAACCCTAACCCTAATTTATTTAA
Found at i:29351010 original size:107 final size:106
Alignment explanation
Indices: 29350777--29350971 Score: 277
Period size: 107 Copynumber: 1.8 Consensus size: 106
29350767 AATATAACTG
* *
29350777 CTAATTTAATTTATTTAAAACCCTAACTTAATTTATTTTAAACCTTAAAACCCTAATTTACTTAA
1 CTAATTTAATTTATTT-AAACACTAACTTAATTTATTTAAAACCTTAAAACCCTAATTTACTTAA
* * **
29350842 TCTATTTAAAAACATAAATCCTAATTTAATAAACACTAAACC
65 TCTATTTAAAAACACAAACCCTAACCTAATAAACACTAAACC
*
29350884 CTAATTTAATTTATTTTAAACACTAACTTAATTTATTTAAAATCC-TAGAACCCTAATTTACTTA
1 CTAATTTAATTTA-TTTAAACACTAACTTAATTTATTTAAAA-CCTTAAAACCCTAATTTACTTA
*
29350948 A-CTATTTAAAACCACAAACCCTAA
64 ATCTATTTAAAAACACAAACCCTAA
29350972 GCCCTAATTT
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
106 20 0.25
107 55 0.69
108 5 0.06
ACGTcount: A:0.43, C:0.18, G:0.01, T:0.38
Consensus pattern (106 bp):
CTAATTTAATTTATTTAAACACTAACTTAATTTATTTAAAACCTTAAAACCCTAATTTACTTAAT
CTATTTAAAAACACAAACCCTAACCTAATAAACACTAAACC
Found at i:29359393 original size:21 final size:22
Alignment explanation
Indices: 29359359--29359410 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
29359349 CAATAACAAC
* *
29359359 AAAATAGTAAC-AAATA-ATAG
1 AAAATAATAACAAAATAGAGAG
*
29359379 TAAAATAATAGCAAAATAGAGAG
1 -AAAATAATAACAAAATAGAGAG
29359402 AAAATAATA
1 AAAATAATA
29359411 TTTAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 9 0.35
22 14 0.54
23 3 0.12
ACGTcount: A:0.65, C:0.04, G:0.12, T:0.19
Consensus pattern (22 bp):
AAAATAATAACAAAATAGAGAG
Found at i:29362667 original size:16 final size:16
Alignment explanation
Indices: 29362648--29362680 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29362638 TCTAGAAGAT
*
29362648 TTAGTATTTATTAGTA
1 TTAGCATTTATTAGTA
29362664 TTAGCATTTATTAGTA
1 TTAGCATTTATTAGTA
29362680 T
1 T
29362681 AGTTTATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.55
Consensus pattern (16 bp):
TTAGCATTTATTAGTA
Found at i:29362688 original size:13 final size:15
Alignment explanation
Indices: 29362648--29362688 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
29362638 TCTAGAAGAT
29362648 TTAGTATTTATTAGTA
1 TTAG-ATTTATTAGTA
29362664 TTAGCATTTATTAGTA
1 TTAG-ATTTATTAGTA
29362680 -TAG-TTTATT
1 TTAGATTTATT
29362689 TGACTTACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 6 0.25
15 3 0.12
16 15 0.62
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.56
Consensus pattern (15 bp):
TTAGATTTATTAGTA
Found at i:29365051 original size:41 final size:41
Alignment explanation
Indices: 29364994--29365074 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
29364984 TTTCTTAAAG
29364994 GTATTTAGAGGAGAAAATAGTAAGGGCATTTTTATGTTTAT
1 GTATTTAGAGGAGAAAATAGTAAGGGCATTTTTATGTTTAT
29365035 GTATTTAGAGGAGAAAATAGTAAGGGCATTTTTATGTTTA
1 GTATTTAGAGGAGAAAATAGTAAGGGCATTTTTATGTTTA
29365075 CTTTTAGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (41 bp):
GTATTTAGAGGAGAAAATAGTAAGGGCATTTTTATGTTTAT
Found at i:29365261 original size:17 final size:16
Alignment explanation
Indices: 29365226--29365275 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
29365216 TGAACTAAAA
*
29365226 AAAAATTTAAAAGTAGC
1 AAAAA-TTAAAAGTTGC
29365243 AAAAATTAAATAGTTGC
1 AAAAATTAAA-AGTTGC
*
29365260 AAGAAATCAAAAGTTG
1 AA-AAATTAAAAGTTG
29365276 TCATTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 5 0.17
17 17 0.59
18 7 0.24
ACGTcount: A:0.56, C:0.06, G:0.14, T:0.24
Consensus pattern (16 bp):
AAAAATTAAAAGTTGC
Found at i:29366075 original size:74 final size:74
Alignment explanation
Indices: 29365987--29366148 Score: 306
Period size: 74 Copynumber: 2.2 Consensus size: 74
29365977 ATTTTATATT
29365987 ATTTTTAAATATATATAATACATCAAAAATACTAAAAATATCAAAATAAATATTTCCCAACAAAT
1 ATTTTTAAATATATATAATACATCAAAAATACTAAAAATATCAAAATAAATATTTCCCAACAAAT
29366052 TGAAAATAA
66 TGAAAATAA
29366061 ATTTTTAAATATATATAATACATCAAAAATACTAAAAATATCAAAATAAATATTTCCCAACAAAT
1 ATTTTTAAATATATATAATACATCAAAAATACTAAAAATATCAAAATAAATATTTCCCAACAAAT
29366126 TGAAAATAA
66 TGAAAATAA
* *
29366135 ATTTTGAAAAATAT
1 ATTTTTAAATATAT
29366149 GTAGACTTAA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
74 86 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.32
Consensus pattern (74 bp):
ATTTTTAAATATATATAATACATCAAAAATACTAAAAATATCAAAATAAATATTTCCCAACAAAT
TGAAAATAA
Found at i:29371712 original size:2 final size:2
Alignment explanation
Indices: 29371705--29371744 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
29371695 TGTAAATTAG
29371705 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
29371745 TGGAAACAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:29380388 original size:32 final size:31
Alignment explanation
Indices: 29380327--29380390 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 31
29380317 AAAACGAAAT
*
29380327 TTTAAATTTGTTTATTTTCAACTAATTTAAA
1 TTTAAATTTGTTTATTTTCAAATAATTTAAA
* *
29380358 TTTAAAGTTT-TTTATTTTTTAAATATTTTAAA
1 TTTAAA-TTTGTTTA-TTTTCAAATAATTTAAA
29380390 T
1 T
29380391 GAATTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 10 0.36
32 18 0.64
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (31 bp):
TTTAAATTTGTTTATTTTCAAATAATTTAAA
Found at i:29382433 original size:24 final size:24
Alignment explanation
Indices: 29382380--29382433 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
29382370 CAAAGCTAAA
*
29382380 GATGGAGATGAAGATAAAGACGAC
1 GATGGAAATGAAGATAAAGACGAC
* *
29382404 -AGTGGAAATGAATATAAAGATGAC
1 GA-TGGAAATGAAGATAAAGACGAC
29382428 GATGGA
1 GATGGA
29382434 GGTAAAGACG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 1 0.04
24 23 0.92
25 1 0.04
ACGTcount: A:0.46, C:0.06, G:0.31, T:0.17
Consensus pattern (24 bp):
GATGGAAATGAAGATAAAGACGAC
Found at i:29388418 original size:19 final size:20
Alignment explanation
Indices: 29388365--29388418 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 20
29388355 TCTTTATTAA
*
29388365 CTAATTATTATTTTATTTTTT
1 CTAATTATTA-TTAATTTTTT
*
29388386 CTAATGAGTT-TTAATTTTTT
1 CTAATTA-TTATTAATTTTTT
29388406 -TAATTATTATTAA
1 CTAATTATTATTAA
29388419 ATTAAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 2 0.07
19 9 0.32
20 9 0.32
21 6 0.21
22 2 0.07
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (20 bp):
CTAATTATTATTAATTTTTT
Found at i:29394244 original size:21 final size:23
Alignment explanation
Indices: 29394206--29394259 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
29394196 TCAATTTGAC
29394206 CAATTTTAATAAAAAAAAT-T-A
1 CAATTTTAATAAAAAAAATCTAA
**
29394227 CAATTTTAATAATTAAAATCTAGA
1 CAATTTTAATAAAAAAAATCTA-A
29394251 CAATTTTAA
1 CAATTTTAA
29394260 GATTTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 17 0.61
22 1 0.04
24 10 0.36
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (23 bp):
CAATTTTAATAAAAAAAATCTAA
Found at i:29400670 original size:20 final size:20
Alignment explanation
Indices: 29400625--29400661 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29400615 ATAGTAAATG
29400625 TTAATTCTATTCTAAATTTT
1 TTAATTCTATTCTAAATTTT
29400645 TTAATTCT-TT-TAAATTT
1 TTAATTCTATTCTAAATTT
29400662 ATTTTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 2 0.12
20 8 0.47
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAATTCTATTCTAAATTTT
Found at i:29402168 original size:21 final size:21
Alignment explanation
Indices: 29402142--29402186 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
29402132 ATATTGAATG
29402142 TTAATGGGGCAATAAACCTAA
1 TTAATGGGGCAATAAACCTAA
29402163 TTAATGGGGCAATAAACCTAA
1 TTAATGGGGCAATAAACCTAA
29402184 TTA
1 TTA
29402187 GAAACCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (21 bp):
TTAATGGGGCAATAAACCTAA
Found at i:29407012 original size:779 final size:779
Alignment explanation
Indices: 29405515--29407074 Score: 3095
Period size: 779 Copynumber: 2.0 Consensus size: 779
29405505 TCAGTTACGC
29405515 GCGAGGAAGGTATTAGCAACCTCGCGACGCCCAAAATTGGTATCTCATAAACATTTGTTGACTTG
1 GCGAGGAAGGTATTAGCAACCTCGCGACGCCCAAAATTGGTATCTCATAAACATTTGTTGACTTG
29405580 ATTTTCAAAAATACGAGTTCAATATAATATTTAATCGTGATCCGATTGAAAAATGAGAATTTTTA
66 ATTTTCAAAAATACGAGTTCAATATAATATTTAATCGTGATCCGATTGAAAAATGAGAATTTTTA
29405645 GTTTTCGATTTTAGAAAGGGTGTCCCGTTTTTTAACACAAGCCGACGAATTTCACCCAACATAGC
131 GTTTTCGATTTTAGAAAGGGTGTCCCGTTTTTTAACACAAGCCGACGAATTTCACCCAACATAGC
29405710 GATGAAATCGATGGCTTAATATTAAATCGGTACATTGCCTTATTTTTGAAATTAATTAAAACATG
196 GATGAAATCGATGGCTTAATATTAAATCGGTACATTGCCTTATTTTTGAAATTAATTAAAACATG
29405775 AGAAAAATATTCCTAAAGTGAGAAATTAAAAATAGATAAAGGACGCAAAAAAATGATATCATTAA
261 AGAAAAATATTCCTAAAGTGAGAAATTAAAAATAGATAAAGGACGCAAAAAAATGATATCATTAA
29405840 TGAAAAATATTAACATGGAATACTAGAATATTAGAATAACAATAATAATGATATTTACAAAATAA
326 TGAAAAATATTAACATGGAATACTAGAATATTAGAATAACAATAATAATGATATTTACAAAATAA
29405905 AAACAAATCATGTACTAATAATAAAATAGGAAAAATGATATATTTGATAATAATAATATAAAATA
391 AAACAAATCATGTACTAATAATAAAATAGGAAAAATGATATATTTGATAATAATAATATAAAATA
29405970 ATAATATGTACATAAAAATACATATATATATATGCATATAATAAAAGTATGTAATAATAATATCT
456 ATAATATGTACATAAAAATACATATATATATATGCATATAATAAAAGTATGTAATAATAATATCT
29406035 ACAATAAAAGAAAATATTAGGAAACGTACATAAAAAATATATACATAAAAAATTTACAACAATAA
521 ACAATAAAAGAAAATATTAGGAAACGTACATAAAAAATATATACATAAAAAATTTACAACAATAA
29406100 TATAAAATAATGATATGTGCAAAAATATATATATATACATATGTACATAAAATATACACCAATAT
586 TATAAAATAATGATATGTGCAAAAATATATATATATACATATGTACATAAAATATACACCAATAT
29406165 AATAATAGTTATAATAATACTAGCAATAGTAATAATTTGTAATGATAATATATACACAATATGGT
651 AATAATAGTTATAATAATACTAGCAATAGTAATAATTTGTAATGATAATATATACACAATATGGT
29406230 ATTTAATATATATATGTATATAATAGTATTTAAGAATATATACATAAGAAATATATAACTAATG
716 ATTTAATATATATATGTATATAATAGTATTTAAGAATATATACATAAGAAATATATAACTAATG
*
29406294 GCGAGGAAGGTATTAGCAACCTCGCGACGCCCAAAATTGGTATCTCATAAACATTTGTTGATTTG
1 GCGAGGAAGGTATTAGCAACCTCGCGACGCCCAAAATTGGTATCTCATAAACATTTGTTGACTTG
29406359 ATTTTCAAAAATACGAGTTCAATATAATATTTAATCGTGATCCGATTGAAAAATGAGAATTTTTA
66 ATTTTCAAAAATACGAGTTCAATATAATATTTAATCGTGATCCGATTGAAAAATGAGAATTTTTA
29406424 GTTTTCGATTTTAGAAAGGGTGTCCCGTTTTTTAACACAAGCCGACGAATTTCACCCAACATAGC
131 GTTTTCGATTTTAGAAAGGGTGTCCCGTTTTTTAACACAAGCCGACGAATTTCACCCAACATAGC
29406489 GATGAAATCGATGGCTTAATATTAAATCGGTACATTGCCTTATTTTTGAAATTAATTAAAACATG
196 GATGAAATCGATGGCTTAATATTAAATCGGTACATTGCCTTATTTTTGAAATTAATTAAAACATG
29406554 AGAAAAAATATTCCTAAAGTGAGAAATTAAAAATAGATAAAGGACGCAAAAAAATGATATCATTA
261 AG-AAAAATATTCCTAAAGTGAGAAATTAAAAATAGATAAAGGACGCAAAAAAATGATATCATTA
29406619 ATGAAAAATATTAACATGGAATACTAGAATATTAGAATAACAATAATAATGATATTTACAAAATA
325 ATGAAAAATATTAACATGGAATACTAGAATATTAGAATAACAATAATAATGATATTTACAAAATA
29406684 AAAACAAATCATGTACTAATAATAAAATAGGAAAAATGATATATTTGATAATAATAATATAAAAT
390 AAAACAAATCATGTACTAATAATAAAATAGGAAAAATGATATATTTGATAATAATAATATAAAAT
29406749 AATAATATGTACATAAAAATACATATATATATATGCATATAATAAAAGTATGTAATAATAATATC
455 AATAATATGTACATAAAAATACATATATATATATGCATATAATAAAAGTATGTAATAATAATATC
29406814 TACAATAAAAGAAAATATTAGGAAACGTACATAAAAAATATATACAT-AAAAATTTACAACAATA
520 TACAATAAAAGAAAATATTAGGAAACGTACATAAAAAATATATACATAAAAAATTTACAACAATA
29406878 ATATAAAATAATGATATGTGCAAAAATATATATATATACATATGTACATAAAATATACACCAATA
585 ATATAAAATAATGATATGTGCAAAAATATATATATATACATATGTACATAAAATATACACCAATA
29406943 TAATAATAGTTATAATAATACTAGCAATAGTAATAATTTGTAATGATAATATATACACAATATGG
650 TAATAATAGTTATAATAATACTAGCAATAGTAATAATTTGTAATGATAATATATACACAATATGG
29407008 TATTTAATATATATATGTATATAATAGTATTTAAGAATATATACATAAGAAATATATAACTAATG
715 TATTTAATATATATATGTATATAATAGTATTTAAGAATATATACATAAGAAATATATAACTAATG
29407073 GC
1 GC
29407075 ATTAAAAAAT
Statistics
Matches: 779, Mismatches: 1, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
779 475 0.61
780 304 0.39
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.31
Consensus pattern (779 bp):
GCGAGGAAGGTATTAGCAACCTCGCGACGCCCAAAATTGGTATCTCATAAACATTTGTTGACTTG
ATTTTCAAAAATACGAGTTCAATATAATATTTAATCGTGATCCGATTGAAAAATGAGAATTTTTA
GTTTTCGATTTTAGAAAGGGTGTCCCGTTTTTTAACACAAGCCGACGAATTTCACCCAACATAGC
GATGAAATCGATGGCTTAATATTAAATCGGTACATTGCCTTATTTTTGAAATTAATTAAAACATG
AGAAAAATATTCCTAAAGTGAGAAATTAAAAATAGATAAAGGACGCAAAAAAATGATATCATTAA
TGAAAAATATTAACATGGAATACTAGAATATTAGAATAACAATAATAATGATATTTACAAAATAA
AAACAAATCATGTACTAATAATAAAATAGGAAAAATGATATATTTGATAATAATAATATAAAATA
ATAATATGTACATAAAAATACATATATATATATGCATATAATAAAAGTATGTAATAATAATATCT
ACAATAAAAGAAAATATTAGGAAACGTACATAAAAAATATATACATAAAAAATTTACAACAATAA
TATAAAATAATGATATGTGCAAAAATATATATATATACATATGTACATAAAATATACACCAATAT
AATAATAGTTATAATAATACTAGCAATAGTAATAATTTGTAATGATAATATATACACAATATGGT
ATTTAATATATATATGTATATAATAGTATTTAAGAATATATACATAAGAAATATATAACTAATG
Found at i:29408641 original size:72 final size:72
Alignment explanation
Indices: 29408414--29409328 Score: 963
Period size: 72 Copynumber: 12.6 Consensus size: 72
29408404 AGTGTGTGAT
* * * *
29408414 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTCAAAGACAGAAATTGAAAAT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----ATTTTGAAA-ACAGAAATTGAAATT
*
29408479 ACCTCAGCATGTGAAC
60 ACCTCAGC--GTG-TC
* * *
29408495 C-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAGAAATTGAAAATA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----ATTTTGAAAACAGAAATTGAAATTA
*
29408559 CCTCAACGTGTC
61 CCTCAGCGTGTC
* ** *
29408571 TTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
29408636 GCGTGTC
66 GCGTGTC
* * *
29408643 CCGAGGCTCAACTCACCTCTCGCAATATGAGTT-AATTTTTTTGAAAGACAAAAATTGAAAATAC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAA---TTTTGAAA-ACAGAAATTGAAATTAC
* *
29408707 CTTAGCATGTC
62 CTCAGCGTGTC
* **
29408718 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
29408783 GCGTGTC
66 GCGTGTC
** * * *
29408790 CTGAGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTTTAACAACAGAAATTGAAATTACCT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-ATTTTGAA-AACAGAAATTGAAATTACCT
29408855 CAGCGTGTC
64 CAGCGTGTC
* * * *
29408864 CTGAGGCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTTTGAAAGACAAAAATTGAAAATACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--ATTTTGAAA-ACAGAAATTGAAATTACC
*
29408929 TCAACGTGTC
63 TCAGCGTGTC
* ** *
29408939 TTGAGGCTCAACTCATTTCTTGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
29409004 GCGTGTC
66 GCGTGTC
* **
29409011 CCGAGGCTCAACTCACCTCTCTTAATATGAGTTG-ATTTTGAAAACAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
29409075 GCGTGTC
66 GCGTGTC
* * * * *
29409082 CCGAAGCTCAACTCATCTCTCGCAA-AGTGAGTTGATTTTTTTGACAACAGAAATTGAAATTACC
1 CTGAGGCTCAACTCACCTCTCGCAATA-TGAGTTGA--ATTTTGAAAACAGAAATTGAAATTACC
29409146 TCAGCGTGTC
63 TCAGCGTGTC
* *
29409156 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTT-----C-----TTAAAAATACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
*
29409210 GCGCGTC
66 GCGTGTC
* ** * *
29409217 CTGAGGCTCAGCTCACCTCTCGCAATATGAGTTGAA-CAT--ATAGA-AAATTGACAA-TACCTC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGA-AATTACCTC
29409277 AGCGTGTC
65 AGCGTGTC
* *
29409285 CCGAGGCTCAACTCACCTCTCGCAATATGAGCTG-ATTTTGAAAA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAA
29409329 AGTAGAAATT
Statistics
Matches: 726, Mismatches: 81, Indels: 65
0.83 0.09 0.07
Matches are distributed among these distances:
61 52 0.07
62 1 0.00
66 1 0.00
67 1 0.00
68 48 0.07
69 2 0.00
70 3 0.00
71 71 0.10
72 171 0.24
73 22 0.03
74 133 0.18
75 117 0.16
76 3 0.00
77 34 0.05
79 22 0.03
80 44 0.06
81 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.30
Consensus pattern (72 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
GCGTGTC
Found at i:29408735 original size:147 final size:146
Alignment explanation
Indices: 29408414--29409328 Score: 982
Period size: 147 Copynumber: 6.3 Consensus size: 146
29408404 AGTGTGTGAT
* * * *
29408414 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTCAAAGACAGAAATTGAAAAT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----ATTTTGAAA-ACAGAAATTGAAATT
** * * *
29408479 ACCTCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAA
60 ACCTCAGC--GTGTCCCGAGGCTCAACTCATCTCTCGCAATATGAGTT-A--ATTTTTTTGAAAA
* *
29408544 CAGAAATTGAAAATACCTCAACGTGTC
120 CAGAAATTGAAATTACCTCAGCGTGTC
* ** *
29408571 TTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
* *
29408636 GCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTGAAAGACAAAAATTGA
66 GCGTGTCCCGAGGCTCAACTCATCTCTCGCAATATGAGTTAATTTTTTTGAAA-ACAGAAATTGA
* * *
29408701 AAATACCTTAGCATGTC
130 AATTACCTCAGCGTGTC
* **
29408718 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
* * * *
29408783 GCGTGTCCTGAGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTTT-AACAACAGAAATTGA
66 GCGTGTCCCGAGGCTCAACTCATCTCTCGCAATATGAGTTAATTTTTTTGAA-AACAGAAATTGA
29408847 AATTACCTCAGCGTGTC
130 AATTACCTCAGCGTGTC
* * * *
29408864 CTGAGGCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTTTGAAAGACAAAAATTGAAAATACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--ATTTTGAAA-ACAGAAATTGAAATTACC
* ** * *
29408929 TCAACGTGTCTTGAGGCTCAACTCATTTCTTGCAATATGAGTTGAA---TTTTGAAAACAGAAAT
63 TCAGCGTGTCCCGAGGCTCAACTCATCTCTCGCAATATGAGTT-AATTTTTTTGAAAACAGAAAT
29408991 TGAAATTACCTCAGCGTGTC
127 TGAAATTACCTCAGCGTGTC
* **
29409011 CCGAGGCTCAACTCACCTCTCTTAATATGAGTTG-ATTTTGAAAACAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
* * *
29409075 GCGTGTCCCGAAGCTCAACTCATCTCTCGCAA-AGTGAGTTGATTTTTTTGACAACAGAAATTGA
66 GCGTGTCCCGAGGCTCAACTCATCTCTCGCAATA-TGAGTTAATTTTTTTGAAAACAGAAATTGA
29409139 AATTACCTCAGCGTGTC
130 AATTACCTCAGCGTGTC
* *
29409156 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTT-----C-----TTAAAAATACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
* * * * ** * *
29409210 GCGCGTCCTGAGGCTCAGCTCACCTCTCGCAATATGAGTTGAA----CAT--ATAGA-AAATTGA
66 GCGTGTCCCGAGGCTCAACTCATCTCTCGCAATATGAGTT-AATTTTTTTGAAAACAGAAATTGA
29409268 CAA-TACCTCAGCGTGTC
130 -AATTACCTCAGCGTGTC
* *
29409285 CCGAGGCTCAACTCACCTCTCGCAATATGAGCTG-ATTTTGAAAA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAA
29409329 AGTAGAAATT
Statistics
Matches: 668, Mismatches: 71, Indels: 61
0.83 0.09 0.08
Matches are distributed among these distances:
129 58 0.09
130 4 0.01
132 1 0.00
135 45 0.07
136 2 0.00
140 1 0.00
142 2 0.00
143 51 0.08
144 8 0.01
145 71 0.11
146 68 0.10
147 196 0.29
148 11 0.02
149 90 0.13
150 1 0.00
151 22 0.03
152 7 0.01
157 30 0.04
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.30
Consensus pattern (146 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
GCGTGTCCCGAGGCTCAACTCATCTCTCGCAATATGAGTTAATTTTTTTGAAAACAGAAATTGAA
ATTACCTCAGCGTGTC
Found at i:29408883 original size:221 final size:218
Alignment explanation
Indices: 29408419--29409315 Score: 1092
Period size: 221 Copynumber: 4.1 Consensus size: 218
29408409 GTGATCTGAA
* * *
29408419 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTCAAAGACAGAAATTGAAAATACCTC
1 GCTCAACTCACCTCTCGCAATATGAGTT-A--ATTTTTTTGAAAGACAAAAATTGAAAATACCTC
* * *
29408484 AGCATGTGAAC-CGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAGA
63 AGCATGT---CTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----ATTTTGAAAACAGA
* * ** *
29408548 AATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTGA
120 AATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTGA
29408613 AAACAGAAATTGAAATTACCTCAGCGTGTCCCGAG
184 AAACAGAAATTGAAATTACCTCAGCGTGTCCCGAG
*
29408648 GCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTGAAAGACAAAAATTGAAAATACCTTAGC
1 GCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTGAAAGACAAAAATTGAAAATACCTCAGC
** *
29408713 ATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTA
66 ATGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATA
** * *
29408778 CCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTTTAACAACAGAAA
131 CCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTGAA-AACAGAAA
*
29408843 TTGAAATTACCTCAGCGTGTCCTGAG
193 TTGAAATTACCTCAGCGTGTCCCGAG
* * *
29408869 GCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTTTGAAAGACAAAAATTGAAAATACCTCAAC
1 GCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTGAAAGACAAAAATTGAAAATACCTCAGC
* ** * *
29408934 GTGTCTTGAGGCTCAACTCATTTCTTGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTA
66 ATGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATA
* **
29408999 CCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCTTAATATGAGTTGATTTTGAAAACAGAAATTG
131 CCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTG
*
29409064 AAATTACCTCAGCGTGTCCCGAA
196 AAATTACCTCAGCGTGTCCCGAG
* * * * *
29409087 GCTCAACTCATCTCTCGCAA-AGTGAGTTGATTTTTTTGACA-ACAGAAATTGAAATTACCTCAG
1 GCTCAACTCACCTCTCGCAATA-TGAGTTAATTTTTTTGAAAGACAAAAATTGAAAATACCTCAG
* * *
29409150 CGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTT-----C-----TTAAAAAT
65 CATGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAAT
* * *** * *
29409204 ACCTCAGCGCGTCCTGAGGCTCAGCTCACCTCTCGCAATATGAGTTGAACAT--ATAGA-AAATT
130 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATT
29409266 GACAA-TACCTCAGCGTGTCCCGAG
195 GA-AATTACCTCAGCGTGTCCCGAG
29409290 GCTCAACTCACCTCTCGCAATATGAG
1 GCTCAACTCACCTCTCGCAATATGAG
29409316 CTGATTTTGA
Statistics
Matches: 607, Mismatches: 54, Indels: 40
0.87 0.08 0.06
Matches are distributed among these distances:
203 48 0.08
204 6 0.01
206 50 0.08
211 1 0.00
216 5 0.01
217 56 0.09
218 69 0.11
219 71 0.12
220 6 0.01
221 199 0.33
223 1 0.00
224 30 0.05
226 36 0.06
228 1 0.00
229 28 0.05
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (218 bp):
GCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTGAAAGACAAAAATTGAAAATACCTCAGC
ATGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATA
CCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTG
AAATTACCTCAGCGTGTCCCGAG
Found at i:29409237 original size:61 final size:61
Alignment explanation
Indices: 29409142--29409323 Score: 220
Period size: 68 Copynumber: 2.9 Consensus size: 61
29409132 AAATTGAAAT
*
29409142 TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTAAAAA
1 TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTATTAAAAA
* * ** *
29409203 TACCTCAGCGCGTCCTGAGGCTCAGCTCACCTCTCGCAATATGAGTTGAACATATAGAAAATTGA
1 TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG---AT-T---TTATTAA
*
29409268 CAA
59 AAA
* *
29409271 TACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
1 TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
29409324 GAAAAAGTAG
Statistics
Matches: 101, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
61 46 0.46
64 3 0.03
65 3 0.03
68 49 0.49
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.27
Consensus pattern (61 bp):
TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTATTAAAAA
Found at i:29409392 original size:54 final size:54
Alignment explanation
Indices: 29409292--29409397 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 54
29409282 GTCCCGAGGC
*
29409292 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* *
29409346 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
29409398 CAGAAATTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
54 33 0.72
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:29409513 original size:140 final size:140
Alignment explanation
Indices: 29409261--29409732 Score: 881
Period size: 140 Copynumber: 3.4 Consensus size: 140
29409251 AACATATAGA
* * *
29409261 AAATTGACAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGA
1 AAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGA
29409326 AAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGTAAA
66 AAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGTAAA
29409391 TTGAAAACAG
131 TTGAAAACAG
29409401 AAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGA
1 AAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGA
29409466 AAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGTAAA
66 AAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGTAAA
*
29409531 TTGAAAACAA
131 TTGAAAACAG
*
29409541 AAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCAACTCTCGCAATATGAGCTGATTTTGA
1 AAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGA
*
29409606 AAAAGTAGAAATTAAAAGGTTCAACCCATCTCTCGCAATATGAGTTGATTCTTGAACAACGTAAA
66 AAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGTAAA
29409671 TTGAAAACAG
131 TTGAAAACAG
*
29409681 AAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGGAATAT
1 AAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
29409733 ATGTTGAAAT
Statistics
Matches: 323, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 323 1.00
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (140 bp):
AAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGA
AAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGTAAA
TTGAAAACAG
Found at i:29409532 original size:54 final size:54
Alignment explanation
Indices: 29409432--29409537 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 54
29409422 GACCTGAGGC
*
29409432 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* *
29409486 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
29409538 CAAAAATTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
54 33 0.72
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:29409672 original size:54 final size:54
Alignment explanation
Indices: 29409572--29409677 Score: 135
Period size: 54 Copynumber: 1.9 Consensus size: 54
29409562 GACCTGAGGC
*
29409572 TCAACTCAACTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCAACTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* * *
29409626 TCAACCCATCTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCAACTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
29409678 CAGAAATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
54 32 0.71
55 9 0.20
56 4 0.09
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (54 bp):
TCAACCCAACTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:29409804 original size:72 final size:71
Alignment explanation
Indices: 29409668--29409833 Score: 212
Period size: 72 Copynumber: 2.3 Consensus size: 71
29409658 TGAACAACGT
* * * * *
29409668 AAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGGAATAT
1 AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
29409733 -ATGTTG
66 GA-GTTG
29409739 AAATTAAAACACAAAAATTGAAAATACCTCAGCGT-ACCCCGAGGCTCAACTCACCTCTAGCAAT
1 AAATTAAAA-ACAAAAATTGAAAATACCTCAGCGTGA-CCCGAGGCTCAACTCACCTCTAGCAAT
29409803 ATGAGTTG
64 ATGAGTTG
**
29409811 ATTTTGAAAAACAAAAATT-AAAA
1 AAATT-AAAAACAAAAATTGAAAA
29409834 GGCTTAACTC
Statistics
Matches: 84, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
71 13 0.15
72 66 0.79
73 5 0.06
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.23
Consensus pattern (71 bp):
AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
GAGTTG
Found at i:29409979 original size:71 final size:70
Alignment explanation
Indices: 29409832--29410007 Score: 194
Period size: 71 Copynumber: 2.5 Consensus size: 70
29409822 CAAAAATTAA
* * * * * *
29409832 AAGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCAGCGT
1 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGT
29409896 GCCCC
66 GCCCC
* * * *
29409901 GATGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTTAACG
1 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAACAAAAACTAAAAATACCTCAACG
** **
29409966 TTTCTT
65 TGCCCC
29409972 AAGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTT
1 AAGGCTCAACTCACT-TCTCGCAATATGAGTTGATTT
29410008 CCCTTGAAAA
Statistics
Matches: 88, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
69 25 0.28
70 6 0.07
71 57 0.65
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (70 bp):
AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGT
GCCCC
Found at i:29417000 original size:39 final size:37
Alignment explanation
Indices: 29416933--29417025 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
29416923 ACCAGAATGG
* *
29416933 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
29416972 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
29417009 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
29417026 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:29417388 original size:3 final size:3
Alignment explanation
Indices: 29417380--29417418 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
29417370 ATTCCCACTC
29417380 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
29417419 CTTACCTCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29418144 original size:16 final size:16
Alignment explanation
Indices: 29418125--29418159 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
29418115 TTCTTTGTTC
29418125 TTTCTATTCTGTTTCT
1 TTTCTATTCTGTTTCT
* *
29418141 TTTCTGTTTTGTTTCT
1 TTTCTATTCTGTTTCT
29418157 TTT
1 TTT
29418160 ATATATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.14, G:0.09, T:0.74
Consensus pattern (16 bp):
TTTCTATTCTGTTTCT
Found at i:29418185 original size:17 final size:17
Alignment explanation
Indices: 29418163--29418240 Score: 53
Period size: 15 Copynumber: 4.9 Consensus size: 17
29418153 TTCTTTTATA
29418163 TATAATAATATAATATT
1 TATAATAATATAATATT
* *
29418180 TATAAT-ATA-ATTAAT
1 TATAATAATATAATATT
*
29418195 T-TAATAATAT-A-CTT
1 TATAATAATATAATATT
*
29418209 TATAATTAATTTATATATT
1 TATAA-TAATATA-ATATT
29418228 TAT-ATAA-ATAATA
1 TATAATAATATAATA
29418241 ATATAAAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
14 6 0.13
15 14 0.30
16 10 0.22
17 9 0.20
18 2 0.04
19 5 0.11
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (17 bp):
TATAATAATATAATATT
Found at i:29418186 original size:14 final size:17
Alignment explanation
Indices: 29418165--29418205 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 17
29418155 CTTTTATATA
29418165 TAATAATATAA-T-ATT
1 TAATAATATAATTAATT
29418180 T-ATAATATAATTAATT
1 TAATAATATAATTAATT
29418196 TAATAATATA
1 TAATAATATA
29418206 CTTTATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.39
15 2 0.09
16 4 0.17
17 8 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAATAATATAATTAATT
Found at i:29418223 original size:11 final size:11
Alignment explanation
Indices: 29418185--29418223 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
29418175 ATATTTATAA
29418185 TATAATTAATT
1 TATAATTAATT
*
29418196 TAATAATATACTT
1 T-ATAAT-TAATT
29418209 TATAATTAATT
1 TATAATTAATT
29418220 TATA
1 TATA
29418224 TATTTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 10 0.42
13 5 0.21
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
TATAATTAATT
Found at i:29418242 original size:24 final size:24
Alignment explanation
Indices: 29418159--29418239 Score: 87
Period size: 24 Copynumber: 3.4 Consensus size: 24
29418149 TTGTTTCTTT
*
29418159 TATATATAA-TAATATAATATTTA
1 TATATATAATTAATTTAATATTTA
*
29418182 TA-ATATAATTAATTTAATA-ATA
1 TATATATAATTAATTTAATATTTA
*
29418204 TACTTTATAATTAATTTATATATTTA
1 TA-TATATAATTAATTTA-ATATTTA
*
29418230 TATAAATAAT
1 TATATATAAT
29418240 AATATAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
22 10 0.21
23 11 0.23
24 13 0.28
25 9 0.19
26 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (24 bp):
TATATATAATTAATTTAATATTTA
Found at i:29424295 original size:39 final size:37
Alignment explanation
Indices: 29424228--29424320 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
29424218 ACCAGAATGG
* *
29424228 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
29424267 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
29424304 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
29424321 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:29424683 original size:3 final size:3
Alignment explanation
Indices: 29424675--29424710 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
29424665 ATTCCCACTC
29424675 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
29424711 CTTACCTCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29425436 original size:16 final size:16
Alignment explanation
Indices: 29425417--29425451 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
29425407 TTCTTTGTTC
29425417 TTTCTATTCTGTTTCT
1 TTTCTATTCTGTTTCT
* *
29425433 TTTCTGTTTTGTTTCT
1 TTTCTATTCTGTTTCT
29425449 TTT
1 TTT
29425452 ATATATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.14, G:0.09, T:0.74
Consensus pattern (16 bp):
TTTCTATTCTGTTTCT
Found at i:29425477 original size:17 final size:17
Alignment explanation
Indices: 29425455--29425532 Score: 53
Period size: 15 Copynumber: 4.9 Consensus size: 17
29425445 TTCTTTTATA
29425455 TATAATAATATAATATT
1 TATAATAATATAATATT
* *
29425472 TATAAT-ATA-ATTAAT
1 TATAATAATATAATATT
*
29425487 T-TAATAATAT-A-CTT
1 TATAATAATATAATATT
*
29425501 TATAATTAATTTATATATT
1 TATAA-TAATATA-ATATT
29425520 TAT-ATAA-ATAATA
1 TATAATAATATAATA
29425533 ATATAAAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
14 6 0.13
15 14 0.30
16 10 0.22
17 9 0.20
18 2 0.04
19 5 0.11
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (17 bp):
TATAATAATATAATATT
Found at i:29425478 original size:14 final size:17
Alignment explanation
Indices: 29425457--29425497 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 17
29425447 CTTTTATATA
29425457 TAATAATATAA-T-ATT
1 TAATAATATAATTAATT
29425472 T-ATAATATAATTAATT
1 TAATAATATAATTAATT
29425488 TAATAATATA
1 TAATAATATA
29425498 CTTTATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.39
15 2 0.09
16 4 0.17
17 8 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAATAATATAATTAATT
Found at i:29425515 original size:11 final size:11
Alignment explanation
Indices: 29425477--29425515 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
29425467 ATATTTATAA
29425477 TATAATTAATT
1 TATAATTAATT
*
29425488 TAATAATATACTT
1 T-ATAAT-TAATT
29425501 TATAATTAATT
1 TATAATTAATT
29425512 TATA
1 TATA
29425516 TATTTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 10 0.42
13 5 0.21
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
TATAATTAATT
Found at i:29425534 original size:24 final size:24
Alignment explanation
Indices: 29425451--29425531 Score: 87
Period size: 24 Copynumber: 3.4 Consensus size: 24
29425441 TTGTTTCTTT
*
29425451 TATATATAA-TAATATAATATTTA
1 TATATATAATTAATTTAATATTTA
*
29425474 TA-ATATAATTAATTTAATA-ATA
1 TATATATAATTAATTTAATATTTA
*
29425496 TACTTTATAATTAATTTATATATTTA
1 TA-TATATAATTAATTTA-ATATTTA
*
29425522 TATAAATAAT
1 TATATATAAT
29425532 AATATAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
22 10 0.21
23 11 0.23
24 13 0.28
25 9 0.19
26 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (24 bp):
TATATATAATTAATTTAATATTTA
Found at i:29430660 original size:24 final size:22
Alignment explanation
Indices: 29430628--29430677 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 22
29430618 GGTTTCTTAG
*
29430628 TTTTTTTTTTGGGTTAGGTTTT
1 TTTTTTTTTTTGGTTAGGTTTT
29430650 TCTTTTTTTTTTGGTTAGGTTTT
1 T-TTTTTTTTTTGGTTAGGTTTT
29430673 TTTTT
1 TTTTT
29430678 GGGGGCTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.04, C:0.02, G:0.18, T:0.76
Consensus pattern (22 bp):
TTTTTTTTTTTGGTTAGGTTTT
Found at i:29435510 original size:11 final size:11
Alignment explanation
Indices: 29435494--29435522 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
29435484 TCGTTTTTAC
29435494 TGCAAGAAGCT
1 TGCAAGAAGCT
29435505 TGCAAGAAGCT
1 TGCAAGAAGCT
29435516 TGCAAGA
1 TGCAAGA
29435523 GACTTTCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.17
Consensus pattern (11 bp):
TGCAAGAAGCT
Found at i:29436102 original size:13 final size:13
Alignment explanation
Indices: 29436068--29436105 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
29436058 TAAGTATATA
29436068 AAAATTTAAAAA-
1 AAAATTTAAAAAT
*
29436080 ATAATTTAAAAAT
1 AAAATTTAAAAAT
*
29436093 AAAATATAAAAAT
1 AAAATTTAAAAAT
29436106 TTATTTACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAATTTAAAAAT
Found at i:29438982 original size:31 final size:31
Alignment explanation
Indices: 29438947--29439007 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
29438937 ACTCGGTGAT
* *
29438947 TTAAATAAAAACTTTTGAATAGTTCAATGAC
1 TTAAATAAAAACTTTCGAATAATTCAATGAC
29438978 TTAAATAAAAACTTTCGAATAATTCAATGA
1 TTAAATAAAAACTTTCGAATAATTCAATGA
29439008 TCAAATTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (31 bp):
TTAAATAAAAACTTTCGAATAATTCAATGAC
Found at i:29440827 original size:30 final size:30
Alignment explanation
Indices: 29440786--29440872 Score: 122
Period size: 30 Copynumber: 2.9 Consensus size: 30
29440776 CCTAAACTTT
* *
29440786 TCCACCACCAACTCCACTAGCCATACTTGC
1 TCCAACACCAACTCCACTAGCCACACTTGC
*
29440816 TCCAACACCAACTCTACTAGCCACACTTGC
1 TCCAACACCAACTCCACTAGCCACACTTGC
*
29440846 TCC-ACTACCTACTCCACTAGCCACACT
1 TCCAAC-ACCAACTCCACTAGCCACACT
29440873 CCACCACCAC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
29 2 0.04
30 49 0.96
ACGTcount: A:0.28, C:0.46, G:0.06, T:0.21
Consensus pattern (30 bp):
TCCAACACCAACTCCACTAGCCACACTTGC
Found at i:29441406 original size:24 final size:23
Alignment explanation
Indices: 29441358--29441409 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
29441348 CTTTTTTTGT
*
29441358 TATTATTATATTTCTTAATATTA
1 TATTATTATATTTCTTAATAATA
*
29441381 TATTATATATATATTCTT-TTAATA
1 TATTAT-TATAT-TTCTTAATAATA
29441405 TATTA
1 TATTA
29441410 GGTATATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 14 0.56
25 5 0.20
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTATTATATTTCTTAATAATA
Found at i:29441465 original size:27 final size:26
Alignment explanation
Indices: 29441434--29441496 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 26
29441424 TTTATATTAC
29441434 GTATATATATATT-ATACTAT-TTTAT
1 GTATATATATATTAATACTATATTT-T
*
29441459 GTATATATCT-TTAATACTATATTTT
1 GTATATATATATTAATACTATATTTT
*
29441484 TTATATATATATT
1 GTATATATATATT
29441497 TTTTTCTACA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 2 0.06
25 25 0.78
26 5 0.16
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (26 bp):
GTATATATATATTAATACTATATTTT
Found at i:29441534 original size:22 final size:22
Alignment explanation
Indices: 29441509--29441575 Score: 71
Period size: 25 Copynumber: 2.9 Consensus size: 22
29441499 TTTCTACATG
*
29441509 TTATCTTATGTATATATTTTAA
1 TTATATTATGTATATATTTTAA
*
29441531 TTATATTATGTATGTATTTTTTACA
1 TTATATTATGTA--TATATTTTA-A
* *
29441556 CTATATTATGTACATATTTT
1 TTATATTATGTATATATTTT
29441576 TAATATTATC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
22 11 0.30
23 6 0.16
24 8 0.22
25 12 0.32
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (22 bp):
TTATATTATGTATATATTTTAA
Found at i:29441565 original size:25 final size:24
Alignment explanation
Indices: 29441515--29441601 Score: 70
Period size: 24 Copynumber: 3.5 Consensus size: 24
29441505 CATGTTATCT
*
29441515 TATGTATATATTTTAATTATATTATG
1 TATGTAT-T-TTTTAACTATATTATG
29441541 TATGTATTTTTTACACTATATTATG
1 TATGTATTTTTTA-ACTATATTATG
** * *
29441566 TACATA-TTTTTAA-TATTATCACG
1 TATGTATTTTTTAACTA-TATTATG
*
29441589 TATTTATTTTTTA
1 TATGTATTTTTTA
29441602 TATATGCACA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
22 2 0.04
23 10 0.20
24 17 0.33
25 15 0.29
26 7 0.14
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (24 bp):
TATGTATTTTTTAACTATATTATG
Found at i:29441596 original size:23 final size:23
Alignment explanation
Indices: 29441570--29441618 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
29441560 ATTATGTACA
*
29441570 TATTTTTAATATTAT-CACGTATT
1 TATTTTTAATA-TATGCACATATT
*
29441593 TATTTTTTATATATGCACATATT
1 TATTTTTAATATATGCACATATT
29441616 TAT
1 TAT
29441619 GTAGTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (23 bp):
TATTTTTAATATATGCACATATT
Found at i:29441755 original size:16 final size:15
Alignment explanation
Indices: 29441731--29441778 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
29441721 TAATTATTAT
*
29441731 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
29441747 TATTTTAATATTTTA
1 TATTTTAATATTTTA
*
29441762 TATTTTATATACTTTA
1 TATTTTA-ATATTTTA
29441778 T
1 T
29441779 TATTCACATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:29441766 original size:7 final size:8
Alignment explanation
Indices: 29441731--29441782 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
29441721 TAATTATTAT
*
29441731 TATTCTAA
1 TATTTTAA
*
29441739 TATTTTGA
1 TATTTTAA
29441747 TATTTTAA
1 TATTTTAA
29441755 TATTTT-A
1 TATTTTAA
29441762 TATTTTATA
1 TATTTTA-A
* *
29441771 TACTTTAT
1 TATTTTAA
29441779 TATT
1 TATT
29441783 CACATCACTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 7 0.19
8 22 0.61
9 7 0.19
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (8 bp):
TATTTTAA
Found at i:29442914 original size:32 final size:32
Alignment explanation
Indices: 29442877--29442941 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
29442867 GATGAGAACT
29442877 TATTAAAGAAAACCTTTTCAAATTTTCATAGA
1 TATTAAAGAAAACCTTTTCAAATTTTCATAGA
29442909 TATTAAAGAAAACCTTTTCAAATTTTCATAGA
1 TATTAAAGAAAACCTTTTCAAATTTTCATAGA
29442941 T
1 T
29442942 CTAATGTGGT
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:0.43, C:0.12, G:0.06, T:0.38
Consensus pattern (32 bp):
TATTAAAGAAAACCTTTTCAAATTTTCATAGA
Found at i:29445478 original size:22 final size:22
Alignment explanation
Indices: 29445435--29445480 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
29445425 AAAATTTATC
*
29445435 TTAATTTAGAACAAATATTCAA
1 TTAATTTAAAACAAATATTCAA
*
29445457 TTAATTTATAAACATATA-TCAA
1 TTAATTTA-AAACAAATATTCAA
29445479 TT
1 TT
29445481 CATAGAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (22 bp):
TTAATTTAAAACAAATATTCAA
Found at i:29446407 original size:23 final size:23
Alignment explanation
Indices: 29446381--29446429 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
29446371 CAGAGTGTAA
29446381 AATCTACTTAACTTGCTTTAAGT
1 AATCTACTTAACTTGCTTTAAGT
*
29446404 AATCTACTTGACTTGCTTTAAGT
1 AATCTACTTAACTTGCTTTAAGT
29446427 AAT
1 AAT
29446430 GTAGTCACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (23 bp):
AATCTACTTAACTTGCTTTAAGT
Found at i:29447940 original size:20 final size:20
Alignment explanation
Indices: 29447885--29447952 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
29447875 GATGCAAAAC
* * *
29447885 AGGGGCACCAAAGTGTAATC
1 AGGGGCACCAGAGTGCAATT
* * * *
29447905 AAGAGCACGAGTGTGCAATT
1 AGGGGCACCAGAGTGCAATT
*
29447925 AGGGGCACCAGAGTGCATTT
1 AGGGGCACCAGAGTGCAATT
29447945 AGGGGCAC
1 AGGGGCAC
29447953 GAATGTGCTG
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.31, C:0.19, G:0.34, T:0.16
Consensus pattern (20 bp):
AGGGGCACCAGAGTGCAATT
Found at i:29447960 original size:20 final size:20
Alignment explanation
Indices: 29447909--29447969 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
29447899 GTAATCAAGA
* *
29447909 GCACGAGTGTGCAATTAGGG
1 GCACGAATGTGCATTTAGGG
*
29447929 GCACCAGA-GTGCATTTAGGG
1 GCACGA-ATGTGCATTTAGGG
29447949 GCACGAATGTGC-TGTTAGGG
1 GCACGAATGTGCAT-TTAGGG
29447969 G
1 G
29447970 AAAAATTGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 2 0.06
20 32 0.94
ACGTcount: A:0.23, C:0.16, G:0.39, T:0.21
Consensus pattern (20 bp):
GCACGAATGTGCATTTAGGG
Found at i:29448041 original size:40 final size:40
Alignment explanation
Indices: 29447964--29448079 Score: 142
Period size: 40 Copynumber: 2.9 Consensus size: 40
29447954 AATGTGCTGT
* *
29447964 TAGGGGAAAAATTGTGCAAATAGGGACACCAAAGTGTTTA
1 TAGGGGCAAAATTGTGCAAATAGGAACACCAAAGTGTTTA
* *
29448004 TAGGGGCACAATTGTGCAAATAGGAACACCGAAGTGTTTA
1 TAGGGGCAAAATTGTGCAAATAGGAACACCAAAGTGTTTA
* * * * * *
29448044 CAGTGGCATAGTTGTGCAAACAGGAACATCAAAGTG
1 TAGGGGCAAAATTGTGCAAATAGGAACACCAAAGTG
29448080 CAATCAAGGA
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.37, C:0.14, G:0.28, T:0.22
Consensus pattern (40 bp):
TAGGGGCAAAATTGTGCAAATAGGAACACCAAAGTGTTTA
Found at i:29453628 original size:11 final size:12
Alignment explanation
Indices: 29453612--29453642 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
29453602 CGAGATAGAA
29453612 ATAATTATTTT-
1 ATAATTATTTTG
29453623 ATAATTATTTTG
1 ATAATTATTTTG
29453635 ATAATTAT
1 ATAATTAT
29453643 GATATGATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (12 bp):
ATAATTATTTTG
Found at i:29454429 original size:46 final size:46
Alignment explanation
Indices: 29454375--29454550 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
29454365 TGGTTGAGCA
29454375 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
29454421 TCCAAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
29454466 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
29454514 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29454551 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:29454531 original size:93 final size:93
Alignment explanation
Indices: 29454372--29454543 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
29454362 GGATGGTTGA
* *
29454372 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCAAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAACTCGTTGAGT
29454437 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
29454465 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAACTCGTTGAGT
29454530 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
29454544 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:29455547 original size:24 final size:23
Alignment explanation
Indices: 29455511--29455556 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
29455501 TATATTAGTG
*
29455511 AAAGATTTATTGATCAGAAGCAT
1 AAAGATTTATTGAGCAGAAGCAT
* *
29455534 AAAGAATTTCTTGAGCTGAAGCA
1 AAAG-ATTTATTGAGCAGAAGCA
29455557 AGGTAATATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (23 bp):
AAAGATTTATTGAGCAGAAGCAT
Found at i:29462521 original size:12 final size:12
Alignment explanation
Indices: 29462504--29462534 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
29462494 TCTTTTGGAT
*
29462504 TTATTTATTTAA
1 TTATTTATGTAA
29462516 TTATTTATGTAA
1 TTATTTATGTAA
29462528 TTATTTA
1 TTATTTA
29462535 CTTTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (12 bp):
TTATTTATGTAA
Found at i:29462585 original size:12 final size:13
Alignment explanation
Indices: 29462550--29462586 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
29462540 TTTAAAAATA
29462550 TATTATTTT-AACC
1 TATTATTTTGAA-C
29462563 TATTATTTTGAAC
1 TATTATTTTGAAC
29462576 TATT-TTTTGAA
1 TATTATTTTGAA
29462587 TTCCATTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 14 0.61
14 2 0.09
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.57
Consensus pattern (13 bp):
TATTATTTTGAAC
Found at i:29467129 original size:7 final size:7
Alignment explanation
Indices: 29467117--29467157 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
29467107 GGAGTTAAAA
29467117 ATAAATT
1 ATAAATT
29467124 ATAAATT
1 ATAAATT
29467131 ATAAATT
1 ATAAATT
*
29467138 AAAAACTT
1 ATAAA-TT
29467146 A-AAA-T
1 ATAAATT
29467151 ATAAATT
1 ATAAATT
29467158 TACCAATGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
5 2 0.07
6 3 0.10
7 22 0.73
8 3 0.10
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (7 bp):
ATAAATT
Found at i:29473504 original size:3 final size:3
Alignment explanation
Indices: 29473496--29473520 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29473486 TTTAAAGCAT
29473496 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
29473521 TGATTTATGG
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:29481017 original size:115 final size:115
Alignment explanation
Indices: 29480815--29481044 Score: 451
Period size: 115 Copynumber: 2.0 Consensus size: 115
29480805 GAAAATCTGG
29480815 TTGCACAAGAATAAAGTAAATTTACGAAGGAATAAAACCAAACTCTGTCGCAGAAATCAAGGAAG
1 TTGCACAAGAATAAAGTAAATTTACGAAGGAATAAAACCAAACTCTGTCGCAGAAATCAAGGAAG
29480880 CAAAGGATTACTTTCAAAAGATCAAGAAAGCAACAAGGGATGGGATTACA
66 CAAAGGATTACTTTCAAAAGATCAAGAAAGCAACAAGGGATGGGATTACA
29480930 TTGCACAAGAATAAAGTAAATTTACGAAGGAATAAAACCAAACTCTGTCGCAGAAATCAAGGAAG
1 TTGCACAAGAATAAAGTAAATTTACGAAGGAATAAAACCAAACTCTGTCGCAGAAATCAAGGAAG
*
29480995 CAAAGGATTGCTTTCAAAAGATCAAGAAAGCAACAAGGGATGGGATTACA
66 CAAAGGATTACTTTCAAAAGATCAAGAAAGCAACAAGGGATGGGATTACA
29481045 GTGAACAAAA
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 114 1.00
ACGTcount: A:0.47, C:0.15, G:0.20, T:0.18
Consensus pattern (115 bp):
TTGCACAAGAATAAAGTAAATTTACGAAGGAATAAAACCAAACTCTGTCGCAGAAATCAAGGAAG
CAAAGGATTACTTTCAAAAGATCAAGAAAGCAACAAGGGATGGGATTACA
Found at i:29484135 original size:29 final size:30
Alignment explanation
Indices: 29484072--29484138 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 30
29484062 ATCTCAAAAC
29484072 TATACATGAACTATGATTTAATGTGCAATTG
1 TATACATGAACTATGATTT-ATGTGCAATTG
* *
29484103 TATACATGAACTTTGATTT-TGTGCAATTT
1 TATACATGAACTATGATTTATGTGCAATTG
29484132 TATACAT
1 TATACAT
29484139 AAAATTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 16 0.47
31 18 0.53
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (30 bp):
TATACATGAACTATGATTTATGTGCAATTG
Found at i:29484152 original size:29 final size:29
Alignment explanation
Indices: 29484072--29484151 Score: 88
Period size: 31 Copynumber: 2.7 Consensus size: 29
29484062 ATCTCAAAAC
* *
29484072 TATACATGAACTATGATTTAATGTGCAATTG
1 TATACATAAACTTTGATTT--TGTGCAATTG
* *
29484103 TATACATGAACTTTGATTTTGTGCAATTT
1 TATACATAAACTTTGATTTTGTGCAATTG
*
29484132 TATACATAAAATTTTGATTT
1 TATACAT-AAACTTTGATTT
29484152 GATCTAATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 16 0.36
30 10 0.23
31 18 0.41
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (29 bp):
TATACATAAACTTTGATTTTGTGCAATTG
Found at i:29484397 original size:31 final size:29
Alignment explanation
Indices: 29484310--29484403 Score: 89
Period size: 31 Copynumber: 3.1 Consensus size: 29
29484300 AGTTTCAACC
* * *
29484310 ATACATTTGAACCACAATCAGAGTTTCATGT
1 ATACAATTGCACCA-AATCAAAG-TTCATGT
* *
29484341 ATATAATTGCACCAAATTAAAGTTCATGT
1 ATACAATTGCACCAAATCAAAGTTCATGT
* *
29484370 ATACAATTGCACATTAAATCAAAGTTCATAT
1 ATACAATTGCAC--CAAATCAAAGTTCATGT
29484401 ATA
1 ATA
29484404 ATTTTGAGAT
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
29 18 0.35
30 6 0.12
31 28 0.54
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (29 bp):
ATACAATTGCACCAAATCAAAGTTCATGT
Found at i:29485334 original size:23 final size:23
Alignment explanation
Indices: 29485308--29485377 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
29485298 TTTGTTTCTT
*
29485308 AAAACCCAAGCTATTATGTTATA
1 AAAACCCATGCTATTATGTTATA
* * *
29485331 AAAA---ATGATATT-TGTTTCTT
1 AAAACCCATGCTATTATG-TTATA
29485351 AAAACCCATGCTATTATGTTATA
1 AAAACCCATGCTATTATGTTATA
29485374 AAAA
1 AAAA
29485378 ATTACCATGT
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
19 2 0.06
20 13 0.37
23 18 0.51
24 2 0.06
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.36
Consensus pattern (23 bp):
AAAACCCATGCTATTATGTTATA
Found at i:29485354 original size:43 final size:43
Alignment explanation
Indices: 29485288--29485379 Score: 166
Period size: 43 Copynumber: 2.1 Consensus size: 43
29485278 AAATGAAAAC
*
29485288 AAAACTGATATTTGTTTCTTAAAACCCAAGCTATTATGTTATA
1 AAAAATGATATTTGTTTCTTAAAACCCAAGCTATTATGTTATA
*
29485331 AAAAATGATATTTGTTTCTTAAAACCCATGCTATTATGTTATA
1 AAAAATGATATTTGTTTCTTAAAACCCAAGCTATTATGTTATA
29485374 AAAAAT
1 AAAAAT
29485380 TACCATGTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (43 bp):
AAAAATGATATTTGTTTCTTAAAACCCAAGCTATTATGTTATA
Found at i:29489465 original size:18 final size:18
Alignment explanation
Indices: 29489442--29489530 Score: 124
Period size: 18 Copynumber: 4.9 Consensus size: 18
29489432 CGTTTATGGT
29489442 ACTATTCACGTATACAGC
1 ACTATTCACGTATACAGC
* *
29489460 ACTATTCACGTATATAGT
1 ACTATTCACGTATACAGC
*
29489478 ACTATTCACGTATACGGC
1 ACTATTCACGTATACAGC
* *
29489496 ACTATTCACGTATACGGT
1 ACTATTCACGTATACAGC
*
29489514 ACTGTTCACGTATACAG
1 ACTATTCACGTATACAG
29489531 TAGTTGGGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (18 bp):
ACTATTCACGTATACAGC
Found at i:29489487 original size:36 final size:36
Alignment explanation
Indices: 29489440--29489530 Score: 146
Period size: 36 Copynumber: 2.5 Consensus size: 36
29489430 ACCGTTTATG
*
29489440 GTACTATTCACGTATACAGCACTATTCACGTATATA
1 GTACTATTCACGTATACAGCACTATTCACGTATACA
* *
29489476 GTACTATTCACGTATACGGCACTATTCACGTATACG
1 GTACTATTCACGTATACAGCACTATTCACGTATACA
*
29489512 GTACTGTTCACGTATACAG
1 GTACTATTCACGTATACAG
29489531 TAGTTGGGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (36 bp):
GTACTATTCACGTATACAGCACTATTCACGTATACA
Found at i:29499471 original size:46 final size:46
Alignment explanation
Indices: 29499404--29499762 Score: 504
Period size: 46 Copynumber: 7.8 Consensus size: 46
29499394 GTGTGCTCTC
* *
29499404 TGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACG
*
29499450 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACG
* * *
29499496 TGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACG
*
29499542 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACG
* *
29499588 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACG
* *
29499634 TGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACG
*** * * *
29499680 TGACGGGAAAATGAATAAGATCATGGTTGAAAGATACCATGGCAACA
1 TGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACG
* * * *
29499727 TGACA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 TGATATG-AAATGAGTAAGACCATGGTTGAAAGATAC
29499763 TATGACATCA
Statistics
Matches: 291, Mismatches: 21, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
46 250 0.86
47 41 0.14
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.22
Consensus pattern (46 bp):
TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACG
Found at i:29500981 original size:13 final size:13
Alignment explanation
Indices: 29500963--29500991 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
29500953 TAAAAGTCTC
29500963 AGTATAATCAATT
1 AGTATAATCAATT
29500976 AGTATAATCAATT
1 AGTATAATCAATT
29500989 AGT
1 AGT
29500992 CTAACTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (13 bp):
AGTATAATCAATT
Found at i:29513310 original size:57 final size:57
Alignment explanation
Indices: 29513196--29513310 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 57
29513186 GATAAGAATG
***
29513196 CATTAGTTATAGATACGAACAAAATATGTTTAACATGCATTAAAAGGCATCGTGGTT
1 CATTAGTTATAGATACGAACAAAATATGTTTAACATGCATTAAAAGGCATAACGGTT
* * * *
29513253 CATTGGTTCTAGATGCGAACAAATTATGTTTAACATGCATTAAAAGGCATAACGGTT
1 CATTAGTTATAGATACGAACAAAATATGTTTAACATGCATTAAAAGGCATAACGGTT
29513310 C
1 C
29513311 TTAAGGATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (57 bp):
CATTAGTTATAGATACGAACAAAATATGTTTAACATGCATTAAAAGGCATAACGGTT
Found at i:29514789 original size:31 final size:31
Alignment explanation
Indices: 29514753--29514812 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
29514743 TTAAACAACA
29514753 TATTTAGACAACAAATACATTATGTTCTTTG
1 TATTTAGACAACAAATACATTATGTTCTTTG
* *
29514784 TATTTAGACAGCAGATACATTATGTTCTT
1 TATTTAGACAACAAATACATTATGTTCTT
29514813 CAATTGGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (31 bp):
TATTTAGACAACAAATACATTATGTTCTTTG
Found at i:29514836 original size:16 final size:16
Alignment explanation
Indices: 29514815--29514846 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29514805 ATGTTCTTCA
29514815 ATTGGAATCCTTCTTT
1 ATTGGAATCCTTCTTT
*
29514831 ATTGGAATCTTTCTTT
1 ATTGGAATCCTTCTTT
29514847 TGACACCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (16 bp):
ATTGGAATCCTTCTTT
Found at i:29515799 original size:35 final size:35
Alignment explanation
Indices: 29515753--29515836 Score: 141
Period size: 35 Copynumber: 2.4 Consensus size: 35
29515743 TCTTTGTGTT
*
29515753 TAAATTTTAATGCAACTTCAAGATAATCAAAGTAC
1 TAAATTTTAATGCAACTTCAAAATAATCAAAGTAC
* *
29515788 TAAATTTTAATGCAACTTCAAAATAATTAATGTAC
1 TAAATTTTAATGCAACTTCAAAATAATCAAAGTAC
29515823 TAAATTTTAATGCA
1 TAAATTTTAATGCA
29515837 GATCGTTTAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (35 bp):
TAAATTTTAATGCAACTTCAAAATAATCAAAGTAC
Found at i:29517068 original size:11 final size:11
Alignment explanation
Indices: 29517028--29517067 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
29517018 ATAATAACAA
29517028 CAAAATAATAG
1 CAAAATAATAG
*
29517039 CAACATAATAG
1 CAAAATAATAG
* *
29517050 TAAAATAGTAG
1 CAAAATAATAG
29517061 CAAAATA
1 CAAAATA
29517068 GGAAGAAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.20
Consensus pattern (11 bp):
CAAAATAATAG
Found at i:29526314 original size:17 final size:17
Alignment explanation
Indices: 29526277--29526315 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
29526267 GTTTTTACTT
29526277 GAATAATATAAAAAATA
1 GAATAATATAAAAAATA
29526294 -AATAA-ATACAAAAATA
1 GAATAATATA-AAAAATA
29526310 GAATAA
1 GAATAA
29526316 CAATAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.15
16 12 0.60
17 5 0.25
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.21
Consensus pattern (17 bp):
GAATAATATAAAAAATA
Found at i:29529700 original size:34 final size:34
Alignment explanation
Indices: 29529656--29529732 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
29529646 GTTTGCATTT
* * *
29529656 CTGATACTGTTACT-ATAATGGGTTAAGGCCCACA
1 CTGATACTGTTACTCA-AATGAGCTAAAGCCCACA
*
29529690 TTGATACTGTTACTCAAATGAGCTAAAGCCCACA
1 CTGATACTGTTACTCAAATGAGCTAAAGCCCACA
29529724 CTGATACTG
1 CTGATACTG
29529733 GACTGTCACT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 36 0.97
35 1 0.03
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (34 bp):
CTGATACTGTTACTCAAATGAGCTAAAGCCCACA
Found at i:29536128 original size:34 final size:34
Alignment explanation
Indices: 29536081--29536146 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
29536071 TTTCTGATAC
* *
29536081 TGTTACTATAATGGGTTAAGACCCACATTGATGT
1 TGTTACTATAATGGGCTAAGACCCACACTGATGT
*
29536115 TGTTACTGA-AATGGGCTAAGGCCCACACTGAT
1 TGTTACT-ATAATGGGCTAAGACCCACACTGAT
29536147 ACTAGATTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 27 0.96
35 1 0.04
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (34 bp):
TGTTACTATAATGGGCTAAGACCCACACTGATGT
Found at i:29543201 original size:26 final size:27
Alignment explanation
Indices: 29543156--29543210 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
29543146 CAAGTGAAAG
29543156 AATAATTTAGTGCTTTAAAAA-AAAAC
1 AATAATTTAGTGCTTTAAAAACAAAAC
*
29543182 AATAATTTAG-GTTTTCAAAAACAAAAC
1 AATAATTTAGTGCTTT-AAAAACAAAAC
29543209 AA
1 AA
29543211 AACAATTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 4 0.15
26 15 0.58
27 7 0.27
ACGTcount: A:0.55, C:0.09, G:0.07, T:0.29
Consensus pattern (27 bp):
AATAATTTAGTGCTTTAAAAACAAAAC
Found at i:29544921 original size:4 final size:4
Alignment explanation
Indices: 29544912--29544957 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
29544902 AAGTAAATAC
29544912 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
29544958 ATAATAAGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:29547038 original size:17 final size:18
Alignment explanation
Indices: 29547013--29547050 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
29547003 TTTAAATTTA
29547013 ATTACATAAAT-ATAAAT
1 ATTACATAAATAATAAAT
*
29547030 ATTAGATAAATAATAAAT
1 ATTACATAAATAATAAAT
29547048 ATT
1 ATT
29547051 TACTATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (18 bp):
ATTACATAAATAATAAAT
Found at i:29549029 original size:10 final size:9
Alignment explanation
Indices: 29549005--29549072 Score: 61
Period size: 9 Copynumber: 7.7 Consensus size: 9
29548995 TGATTTTAGT
29549005 TATTTTATA
1 TATTTTATA
29549014 TA-TTTATA
1 TATTTTATA
29549022 TATTTT-TA
1 TATTTTATA
*
29549030 TAACTTTATA
1 T-ATTTTATA
*
29549040 AATTTTAGT-
1 TATTTTA-TA
* *
29549049 TAGTTTACA
1 TATTTTATA
29549058 TATTTTATA
1 TATTTTATA
29549067 TATTTT
1 TATTTT
29549073 TAAAATAATA
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
8 11 0.24
9 32 0.70
10 3 0.07
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTTATA
Done.