Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 110 of 143
Found at i:33496571 original size:13 final size:13
Alignment explanation
Indices: 33496553--33496578 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33496543 ATTTGACTAT
33496553 TGATGAATTTTAA
1 TGATGAATTTTAA
33496566 TGATGAATTTTAA
1 TGATGAATTTTAA
33496579 CCTATTTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TGATGAATTTTAA
Found at i:33496795 original size:35 final size:35
Alignment explanation
Indices: 33496755--33496822 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
33496745 AATTAAATAC
*
33496755 AAATTAGAAA-TCCTTAACCTTAATT-TCAAAACCCT
1 AAATTA-AAATTCCTTAACCCTAATTCT-AAAACCCT
*
33496790 AAATTAAAATTTCTTAACCCTAATTCTAAAACC
1 AAATTAAAATTCCTTAACCCTAATTCTAAAACC
33496823 AATGTACAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 3 0.10
35 25 0.86
36 1 0.03
ACGTcount: A:0.44, C:0.22, G:0.01, T:0.32
Consensus pattern (35 bp):
AAATTAAAATTCCTTAACCCTAATTCTAAAACCCT
Found at i:33502746 original size:28 final size:28
Alignment explanation
Indices: 33502684--33502752 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
33502674 GGACATTAAT
* *
33502684 AATAATTAAATCATAAATAATAAAAATGA
1 AATAATTAATTTA-AAATAATAAAAATGA
33502713 AATAATTCAATTTAAAATAATAAAAA-GA
1 AATAATT-AATTTAAAATAATAAAAATGA
*
33502741 ACTAATTAATTT
1 AATAATTAATTT
33502753 TTAAGGAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 5 0.14
28 8 0.22
29 19 0.53
30 4 0.11
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (28 bp):
AATAATTAATTTAAAATAATAAAAATGA
Found at i:33502756 original size:29 final size:29
Alignment explanation
Indices: 33502698--33502752 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
33502688 ATTAAATCAT
33502698 AAATAATAAAAATGAAATAATTCAATTTA
1 AAATAATAAAAATGAAATAATTCAATTTA
*
33502727 AAATAATAAAAA-GAACTAATT-AATTT
1 AAATAATAAAAATGAAATAATTCAATTT
33502753 TTAAGGAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 5 0.20
28 8 0.32
29 12 0.48
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (29 bp):
AAATAATAAAAATGAAATAATTCAATTTA
Found at i:33513026 original size:19 final size:19
Alignment explanation
Indices: 33513002--33513039 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
33512992 AAAAGTTAAT
*
33513002 AACAAATTTGATTATGGTG
1 AACAAATTTGATTACGGTG
33513021 AACAAATTTGATTACGGTG
1 AACAAATTTGATTACGGTG
33513040 GGTGACAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (19 bp):
AACAAATTTGATTACGGTG
Found at i:33537348 original size:19 final size:18
Alignment explanation
Indices: 33537303--33537353 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
33537293 ATTACCACTG
33537303 ATCGA-TTAATTGAATTAA
1 ATCGATTTAATTG-ATTAA
*
33537321 ATCGATTTAGTTGATTAA
1 ATCGATTTAATTGATTAA
*
33537339 TTCGATTTTAATTGA
1 ATCGA-TTTAATTGA
33537354 AGTTTGAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (18 bp):
ATCGATTTAATTGATTAA
Found at i:33540967 original size:20 final size:19
Alignment explanation
Indices: 33540942--33541012 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 19
33540932 AAAATTGTAG
33540942 AAAAATAGTGAGAAAACAAA
1 AAAAATAGT-AGAAAACAAA
33540962 AAAAATAGTAGCAAAACAGCAAA
1 AAAAATAGTAG--AAA-A-CAAA
*
33540985 AAAAATAGCAAGAAAACAACA
1 AAAAATAG-TAGAAAACAA-A
33541006 AAAAATA
1 AAAAATA
33541013 AGAGTTTTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
19 2 0.05
20 12 0.27
21 12 0.27
22 4 0.09
23 12 0.27
24 2 0.05
ACGTcount: A:0.70, C:0.10, G:0.11, T:0.08
Consensus pattern (19 bp):
AAAAATAGTAGAAAACAAA
Found at i:33540988 original size:23 final size:23
Alignment explanation
Indices: 33540956--33541010 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
33540946 ATAGTGAGAA
*
33540956 AACAAAAAAAATAG-TAGCAAAAC
1 AACAAAAAAAATAGCAAG-AAAAC
*
33540979 AGCAAAAAAAATAGCAAGAAAAC
1 AACAAAAAAAATAGCAAGAAAAC
33541002 AACAAAAAA
1 AACAAAAAA
33541011 TAAGAGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 26 0.93
24 2 0.07
ACGTcount: A:0.73, C:0.13, G:0.09, T:0.05
Consensus pattern (23 bp):
AACAAAAAAAATAGCAAGAAAAC
Found at i:33549814 original size:23 final size:23
Alignment explanation
Indices: 33549762--33549814 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
33549752 TAGCCGTTTG
* * *
33549762 GAGTTAAATTTTAATTTTTATAA
1 GAGTAAAAGTTTAATTTTTAAAA
*
33549785 TAGTAAAAGTTTAATTTTTAAAA
1 GAGTAAAAGTTTAATTTTTAAAA
*
33549808 GATTAAA
1 GAGTAAA
33549815 TTAAAATTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (23 bp):
GAGTAAAAGTTTAATTTTTAAAA
Found at i:33549832 original size:30 final size:30
Alignment explanation
Indices: 33549786--33549865 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
33549776 TTTTTATAAT
* *
33549786 AGTAAAAGTTTA--ATTTTTAAAAGATTAA
1 AGTAAAATTTTATTATTTTTAAAAGATCAA
* *
33549814 ATTAAAATTTTATTATTTTTAAAATATCAA
1 AGTAAAATTTTATTATTTTTAAAAGATCAA
*
33549844 AGTATAATTTTATT-TTTATTAA
1 AGTAAAATTTTATTATTT-TTAA
33549866 TTTAAAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
28 10 0.23
29 3 0.07
30 30 0.70
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (30 bp):
AGTAAAATTTTATTATTTTTAAAAGATCAA
Found at i:33550059 original size:3 final size:3
Alignment explanation
Indices: 33550051--33550087 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
33550041 TAGTTGAGAC
33550051 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
33550088 GTGTTATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:33551045 original size:20 final size:21
Alignment explanation
Indices: 33550980--33551047 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 21
33550970 AACACATAAA
*
33550980 AAAATAACATCTAAATAACAACC
1 AAAACAACAT-TAAA-AACAACC
* *
33551003 AAAACAACA--ACAAAATAAGC
1 AAAACAACATTA-AAAACAACC
*
33551023 AAAACAACATTAAAAACAACA
1 AAAACAACATTAAAAACAACC
33551044 AAAA
1 AAAA
33551048 TAATAACAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
20 15 0.42
21 12 0.33
22 1 0.03
23 8 0.22
ACGTcount: A:0.69, C:0.19, G:0.01, T:0.10
Consensus pattern (21 bp):
AAAACAACATTAAAAACAACC
Found at i:33551055 original size:12 final size:12
Alignment explanation
Indices: 33551040--33551076 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
33551030 CATTAAAAAC
33551040 AACAAAAATAAT
1 AACAAAAATAAT
*
33551052 AACAAAAATAAC
1 AACAAAAATAAT
33551064 AACAAAAATAAT
1 AACAAAAATAAT
33551076 A
1 A
33551077 CGAAAACAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.76, C:0.11, G:0.00, T:0.14
Consensus pattern (12 bp):
AACAAAAATAAT
Found at i:33551951 original size:11 final size:12
Alignment explanation
Indices: 33551906--33551951 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
33551896 ATAATATCCA
*
33551906 AACAACAAAAAT
1 AACAGCAAAAAT
* *
33551918 AACAACTAAAAT
1 AACAGCAAAAAT
*
33551930 AGCAGCAAAAAT
1 AACAGCAAAAAT
33551942 AACAGCAAAA
1 AACAGCAAAA
33551952 CAACATTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.67, C:0.17, G:0.07, T:0.09
Consensus pattern (12 bp):
AACAGCAAAAAT
Found at i:33552030 original size:45 final size:43
Alignment explanation
Indices: 33551882--33552030 Score: 122
Period size: 44 Copynumber: 3.3 Consensus size: 43
33551872 AACAATAATA
* * *
33551882 AAAAC-GCATAAAAAATAATATCCAAACAACA-AAAATAACAACT
1 AAAACAGCA-AAAAAATAACAGCAAAACAACAGAAAA-AACAACT
* * ** *
33551925 AAAATAGCAGCAAAAATAACAGCAAAACAACATTAAAAACAACA
1 AAAACAGCA-AAAAAATAACAGCAAAACAACAGAAAAAACAACT
* *
33551969 AAAACGGGCAACAAAAATAACAGCAAAACGACACGAAAACAACAACT
1 AAAAC-AGCAA-AAAAATAACAGCAAAACAACA-GAAAA-AACAACT
*
33552016 AAAACAGTAAAAAAA
1 AAAACAGCAAAAAAA
33552031 GCACCGAAAT
Statistics
Matches: 83, Mismatches: 17, Indels: 10
0.75 0.15 0.09
Matches are distributed among these distances:
43 4 0.05
44 31 0.37
45 31 0.37
46 6 0.07
47 11 0.13
ACGTcount: A:0.65, C:0.19, G:0.07, T:0.09
Consensus pattern (43 bp):
AAAACAGCAAAAAAATAACAGCAAAACAACAGAAAAAACAACT
Found at i:33552528 original size:17 final size:16
Alignment explanation
Indices: 33552474--33552528 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
33552464 TTAATTTTTA
33552474 AAAATTATAAAAATAT
1 AAAATTATAAAAATAT
* *
33552490 -GAATTATTAAAATAAT
1 AAAATTATAAAAAT-AT
33552506 AAAATTAATAAAAATAT
1 AAAATT-ATAAAAATAT
*
33552523 ATAATT
1 AAAATT
33552529 TAATTTCCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 11 0.35
16 2 0.06
17 11 0.35
18 7 0.23
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
AAAATTATAAAAATAT
Found at i:33553554 original size:98 final size:99
Alignment explanation
Indices: 33553376--33553568 Score: 235
Period size: 98 Copynumber: 1.9 Consensus size: 99
33553366 TTTTGTTGGA
* * * * *
33553376 TAATTAAAATTAATACTTATTGATTTGGTTTGACTAATAAATATAGAGATGGATGCATGTAGGAT
1 TAATTAAAATTAATACTCATTGA--T--TTTGACTAATAAATATACAGATGCATGCATGGAGGAC
*
33553441 AAAAGTACAAAATTGAGTACATTAATTTAAAATCTCTT
62 AAAAGTACAAAATTGAATACATTAATTTAAAATCTCTT
* * * *
33553479 TAATTAAAATTAATACTCATTGA-TTTGATTAATACATATACAGCTGCATGCATGGAGGACAAAT
1 TAATTAAAATTAATACTCATTGATTTTGACTAATAAATATACAGATGCATGCATGGAGGACAAAA
* *
33553543 GTATAAGATTGAATACATTAATTTAA
66 GTACAAAATTGAATACATTAATTTAA
33553569 TTAAAAGGAT
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
98 56 0.72
103 22 0.28
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (99 bp):
TAATTAAAATTAATACTCATTGATTTTGACTAATAAATATACAGATGCATGCATGGAGGACAAAA
GTACAAAATTGAATACATTAATTTAAAATCTCTT
Found at i:33555246 original size:30 final size:31
Alignment explanation
Indices: 33555210--33555272 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
33555200 ATTTACATTT
33555210 CAGTCCCTCAAC-TTTAAAAATATGACAAAA
1 CAGTCCCTCAACTTTTAAAAATATGACAAAA
* *
33555240 CAGTCCCTCAACTTTTGAAAATGTGACAAAA
1 CAGTCCCTCAACTTTTAAAAATATGACAAAA
33555271 CA
1 CA
33555273 ATCCTTTTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 12 0.40
31 18 0.60
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.24
Consensus pattern (31 bp):
CAGTCCCTCAACTTTTAAAAATATGACAAAA
Found at i:33555402 original size:30 final size:31
Alignment explanation
Indices: 33555366--33555432 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
33555356 ATTACGTTTA
* *
33555366 ACAAAACTGTCACTCAACTT-T-GAAAATGTG
1 ACAAAACAGTCACTAAACTTATCGAAAA-GTG
*
33555396 ACAAAACAGTCACTAAAGTTATCGAAAAGTG
1 ACAAAACAGTCACTAAACTTATCGAAAAGTG
33555427 ACAAAA
1 ACAAAA
33555433 TAGTACTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 17 0.53
31 10 0.31
32 5 0.16
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.21
Consensus pattern (31 bp):
ACAAAACAGTCACTAAACTTATCGAAAAGTG
Found at i:33557360 original size:19 final size:18
Alignment explanation
Indices: 33557333--33557380 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
33557323 TTATATATTC
*
33557333 TTTAGAATTTTTTTTAAAA
1 TTTA-AATTTTTTTAAAAA
33557352 TTTATAATTTTTTTAAAAA
1 TTTA-AATTTTTTTAAAAA
*
33557371 TATAAATTTT
1 TTTAAATTTT
33557381 GAAATTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 6 0.23
19 20 0.77
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTAAATTTTTTTAAAAA
Found at i:33557374 original size:17 final size:19
Alignment explanation
Indices: 33557341--33557380 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
33557331 TCTTTAGAAT
*
33557341 TTTTTTTAAAATTTAT-AA
1 TTTTTTTAAAATATATAAA
33557359 TTTTTTTAAAA-ATATAAA
1 TTTTTTTAAAATATATAAA
33557377 TTTT
1 TTTT
33557381 GAAATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTTTTAAAATATATAAA
Found at i:33557378 original size:18 final size:19
Alignment explanation
Indices: 33557338--33557380 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
33557328 TATTCTTTAG
* *
33557338 AATTTTTTTTAAAATTTAT
1 AATTTTTTTAAAAATATAT
33557357 AATTTTTTTAAAAATATA-
1 AATTTTTTTAAAAATATAT
33557375 AATTTT
1 AATTTT
33557381 GAAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
AATTTTTTTAAAAATATAT
Found at i:33557392 original size:18 final size:19
Alignment explanation
Indices: 33557371--33557407 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
33557361 TTTTTAAAAA
33557371 TATAAAT-TTTGAAATTTT
1 TATAAATATTTGAAATTTT
*
33557389 TATAAATATTTTAAATTTT
1 TATAAATATTTGAAATTTT
33557408 AAGAATCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TATAAATATTTGAAATTTT
Found at i:33557408 original size:18 final size:17
Alignment explanation
Indices: 33557343--33557408 Score: 53
Period size: 18 Copynumber: 3.8 Consensus size: 17
33557333 TTTAGAATTT
* *
33557343 TTTTTAAAATTTATAATT
1 TTTTTAAATTTTATAA-A
**
33557361 TTTTTAAA-AATATAAA
1 TTTTTAAATTTTATAAA
*
33557377 TTTTGAAATTTTTATAAA
1 TTTTTAAA-TTTTATAAA
33557395 TATTTTAAATTTTA
1 T-TTTTAAATTTTA
33557409 AGAATCATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
16 7 0.18
17 5 0.13
18 20 0.53
19 6 0.16
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTTTAAATTTTATAAA
Found at i:33567729 original size:19 final size:18
Alignment explanation
Indices: 33567690--33567731 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
33567680 TTTCTGCAAT
*
33567690 GAAAAATATGAGAAGAGA
1 GAAAAATATGAGAAAAGA
33567708 GAAAAATA-GAGGAAAAGAA
1 GAAAAATATGA-GAAAAG-A
33567727 GAAAA
1 GAAAA
33567732 GGAAAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 2 0.10
18 13 0.62
19 6 0.29
ACGTcount: A:0.67, C:0.00, G:0.26, T:0.07
Consensus pattern (18 bp):
GAAAAATATGAGAAAAGA
Found at i:33567736 original size:14 final size:13
Alignment explanation
Indices: 33567717--33567749 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
33567707 AGAAAAATAG
33567717 AGGAAAAGAAGAAA
1 AGGAAAAGAA-AAA
33567731 AGGAAAAGAAAAA
1 AGGAAAAGAAAAA
33567744 A-GAAAA
1 AGGAAAA
33567750 AAATTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 4 0.21
14 10 0.53
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AGGAAAAGAAAAA
Found at i:33573021 original size:30 final size:30
Alignment explanation
Indices: 33572969--33573033 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
33572959 TGGGTTGCTG
*
33572969 ATTTTTTGAAAGTTAGTATGACTGATTTGTT
1 ATTTTTTGAAAGTTAG-ATGACTGATTTGTC
*
33573000 ATTTTTTGAAAGTT-GAGTGACTGTTTTGTC
1 ATTTTTTGAAAGTTAGA-TGACTGATTTGTC
33573030 ATTT
1 ATTT
33573034 ACCTTTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 1 0.03
30 16 0.52
31 14 0.45
ACGTcount: A:0.23, C:0.05, G:0.20, T:0.52
Consensus pattern (30 bp):
ATTTTTTGAAAGTTAGATGACTGATTTGTC
Found at i:33576063 original size:23 final size:23
Alignment explanation
Indices: 33576036--33576089 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
33576026 GTTGAATTAT
* *
33576036 AAAGTACTGGGTTAAAAGTATAG
1 AAAGTACTGGGCTAAAAGTATAA
*
33576059 GAAGTACTGGGCTAAAAGTATAA
1 AAAGTACTGGGCTAAAAGTATAA
33576082 AAAGTACT
1 AAAGTACT
33576090 TGTAATTGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.24, T:0.24
Consensus pattern (23 bp):
AAAGTACTGGGCTAAAAGTATAA
Found at i:33578410 original size:29 final size:28
Alignment explanation
Indices: 33578378--33578522 Score: 91
Period size: 29 Copynumber: 5.0 Consensus size: 28
33578368 TTTTCAGAGG
*
33578378 TTCGAGGTCAAAAATAAAATTTTTGGATA
1 TTCGAGGTCAAAAATGAAATTTTTGGA-A
* *
33578407 TTCGGGGGT--AAAATGGTAATTTTTGGAA
1 TTC-GAGGTCAAAAAT-GAAATTTTTGGAA
*
33578435 CTTCGAGGTCAAAAATGGAATTTTTGGAAA
1 -TTCGAGGTCAAAAATGAAATTTTTGG-AA
* * *
33578465 TTCGGGAGT--AAAATGGTAATTATTGGAAA
1 TTCGAG-GTCAAAAAT-GAAATTTTTGG-AA
* * *
33578494 GTTTGGGGTCAAAAATGGAATTTTTGGAA
1 -TTCGAGGTCAAAAATGAAATTTTTGGAA
33578523 ATTTAGGGGT
Statistics
Matches: 94, Mismatches: 11, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
28 15 0.16
29 47 0.50
30 27 0.29
31 5 0.05
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33
Consensus pattern (28 bp):
TTCGAGGTCAAAAATGAAATTTTTGGAA
Found at i:33578535 original size:59 final size:60
Alignment explanation
Indices: 33578383--33578648 Score: 289
Period size: 59 Copynumber: 4.5 Consensus size: 60
33578373 AGAGGTTCGA
** * ** * * *
33578383 GGTCAAAAATAAAATTTTTGGATATTCGGGGGTAAAATGGTAATTTTTGG-AA-CTTCGA
1 GGTCAAAAATGGAATTTTTGGAAATTTAGGGGTAAAATGGTAATTTTTGGAAAGTTTGGG
* *
33578441 GGTCAAAAATGGAATTTTTGGAAA-TTCGGGAGTAAAATGGTAATTATTGGAAAGTTT-GG
1 GGTCAAAAATGGAATTTTTGGAAATTTAGGG-GTAAAATGGTAATTTTTGGAAAGTTTGGG
*
33578500 GGTCAAAAATGGAATTTTTGGAAATTTAGGGGT-AAATGGTAATTTTTTGAAAAGTTTGGG
1 GGTCAAAAATGGAATTTTTGGAAATTTAGGGGTAAAATGGTAA-TTTTTGGAAAGTTTGGG
* * *
33578560 GGT-AAAAATGAAATTTTTGGAAATTT-GAAGGTAAAATGGTAATTTTTAGAAAGTTTGGG
1 GGTCAAAAATGGAATTTTTGGAAATTTAG-GGGTAAAATGGTAATTTTTGGAAAGTTTGGG
*
33578619 GGTCAAAATAT-G-ATTTTTGGATAGTTTAGG
1 GGTCAAAA-ATGGAATTTTTGGA-AATTTAGG
33578649 CACCTTTTAG
Statistics
Matches: 178, Mismatches: 18, Indels: 22
0.82 0.08 0.10
Matches are distributed among these distances:
57 4 0.02
58 49 0.28
59 93 0.52
60 29 0.16
61 3 0.02
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (60 bp):
GGTCAAAAATGGAATTTTTGGAAATTTAGGGGTAAAATGGTAATTTTTGGAAAGTTTGGG
Found at i:33578560 original size:29 final size:29
Alignment explanation
Indices: 33578411--33578645 Score: 191
Period size: 30 Copynumber: 8.0 Consensus size: 29
33578401 TGGATATTCG
* *
33578411 GGGGTAAAATGGTAATTTTTGG-AACTTC
1 GGGGTAAAATGGTAATTTTTGGAAAGTTT
* *
33578439 GAGGTCAAAAATGG-AATTTTTGGAAA-TTC
1 GGGGT--AAAATGGTAATTTTTGGAAAGTTT
*
33578468 GGGAGTAAAATGGTAATTATTGGAAAGTTT
1 GGG-GTAAAATGGTAATTTTTGGAAAGTTT
33578498 GGGGTCAAAAATGG-AATTTTTGGAAA-TTT
1 GGGGT--AAAATGGTAATTTTTGGAAAGTTT
*
33578527 AGGGGT-AAATGGTAATTTTTTGAAAAGTTT
1 -GGGGTAAAATGGTAA-TTTTTGGAAAGTTT
*
33578557 GGGGGTAAAAAT-GAAATTTTTGGAAA-TTT
1 -GGGGT-AAAATGGTAATTTTTGGAAAGTTT
* *
33578586 GAAGGTAAAATGGTAATTTTTAGAAAGTTT
1 G-GGGTAAAATGGTAATTTTTGGAAAGTTT
* * *
33578616 GGGGGTCAAAAT-ATGATTTTTGGATAGTTT
1 -GGGGT-AAAATGGTAATTTTTGGAAAGTTT
33578646 AGGCACCTTT
Statistics
Matches: 171, Mismatches: 17, Indels: 36
0.76 0.08 0.16
Matches are distributed among these distances:
27 6 0.04
28 19 0.11
29 57 0.33
30 69 0.40
31 16 0.09
32 4 0.02
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTTGGAAAGTTT
Found at i:33579729 original size:3 final size:3
Alignment explanation
Indices: 33579718--33579776 Score: 52
Period size: 3 Copynumber: 20.0 Consensus size: 3
33579708 TCCTTTTTTT
* * *
33579718 TTA TT- TTA TTA -TA ATA TTA TTA ATG TTA TGT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
33579761 TTAA TTA TTA TTA TTA
1 TT-A TTA TTA TTA TTA
33579777 ATACTATTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
2 5 0.11
3 37 0.80
4 4 0.09
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:33579769 original size:13 final size:13
Alignment explanation
Indices: 33579751--33579778 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
33579741 TGTTATGTTT
33579751 ATTATTATTATTA
1 ATTATTATTATTA
33579764 ATTATTATTATTA
1 ATTATTATTATTA
33579777 AT
1 AT
33579779 ACTATTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTATTATTATTA
Found at i:33580557 original size:6 final size:6
Alignment explanation
Indices: 33580530--33580626 Score: 58
Period size: 6 Copynumber: 16.2 Consensus size: 6
33580520 GGCTTTCATC
* ** *
33580530 ATTTAA ATTTAGA A--TAA TTTTAA ATTTAA AAATAA ATTTACTT ATATTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTA--A AT-TTAA
* ** *
33580580 ATTTAA ACTTAA A-ACAA ATTTAA ATTT-A ATATAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
33580626 A
1 A
33580627 GTAAACTTAA
Statistics
Matches: 68, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
4 1 0.01
5 9 0.13
6 49 0.72
7 4 0.06
8 2 0.03
9 3 0.04
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:33580598 original size:17 final size:17
Alignment explanation
Indices: 33580530--33580654 Score: 110
Period size: 17 Copynumber: 7.4 Consensus size: 17
33580520 GGCTTTCATC
* *
33580530 ATTTAAATTTAGAATAA
1 ATTTAAACTTAAAATAA
* *
33580547 TTTTAAATTTAAAAATAA
1 ATTTAAACTT-AAAATAA
* *
33580565 ATTT--ACTTATATTAA
1 ATTTAAACTTAAAATAA
*
33580580 ATTTAAACTTAAAACAA
1 ATTTAAACTTAAAATAA
* *
33580597 ATTTAAATTTAATATAA
1 ATTTAAACTTAAAATAA
* *
33580614 ATTTAAATTTAAAGTAA
1 ATTTAAACTTAAAATAA
* *
33580631 ACTTAATCTTAAAATAA
1 ATTTAAACTTAAAATAA
33580648 ATTTAAA
1 ATTTAAA
33580655 AAATGATTTT
Statistics
Matches: 85, Mismatches: 20, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
15 9 0.11
16 3 0.04
17 64 0.75
18 9 0.11
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (17 bp):
ATTTAAACTTAAAATAA
Found at i:33589869 original size:13 final size:15
Alignment explanation
Indices: 33589840--33589871 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
33589830 CCTTACACAG
33589840 TTTTAAATTGCTTTA
1 TTTTAAATTGCTTTA
33589855 TTTT-AATTG-TTTA
1 TTTTAAATTGCTTTA
33589868 TTTT
1 TTTT
33589872 TTTTATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 5 0.29
15 4 0.24
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69
Consensus pattern (15 bp):
TTTTAAATTGCTTTA
Found at i:33602134 original size:45 final size:45
Alignment explanation
Indices: 33602068--33602170 Score: 134
Period size: 45 Copynumber: 2.2 Consensus size: 45
33602058 ATGGGTCTTC
**
33602068 AAAATAAGGAAAATTAGTTACTAGTCTCGTTTCAACAGAAACCTTAA
1 AAAATAA--AAAATTAGTTACTAAACTCGTTTCAACAGAAACCTTAA
* * **
33602115 AAAATAAAAAATTAGTTACTAAACTCGTTTCAGCAGATATTTTAA
1 AAAATAAAAAATTAGTTACTAAACTCGTTTCAACAGAAACCTTAA
33602160 AAAATAAAAAA
1 AAAATAAAAAA
33602171 ATTGGCCTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
45 43 0.86
47 7 0.14
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (45 bp):
AAAATAAAAAATTAGTTACTAAACTCGTTTCAACAGAAACCTTAA
Found at i:33602359 original size:27 final size:28
Alignment explanation
Indices: 33602308--33602371 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
33602298 TATGAAAAAA
*
33602308 TATGTTTTTTTTTACAAAAATAAGAGTAT
1 TATG-TTTTTTTTACAAAAATAAGAATAT
* *
33602337 TATGTTTTTTTTATATAAA-AAGAATAT
1 TATGTTTTTTTTACAAAAATAAGAATAT
*
33602364 TATATTTT
1 TATGTTTT
33602372 AGACATAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 14 0.45
28 13 0.42
29 4 0.13
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.53
Consensus pattern (28 bp):
TATGTTTTTTTTACAAAAATAAGAATAT
Found at i:33604535 original size:29 final size:29
Alignment explanation
Indices: 33604496--33604575 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 29
33604486 TTTGACTCCC
*
33604496 GAGGGCAAAAATGTAATTTTAGAAAAATTT
1 GAGGGTAAAAATGTAATTTT-GAAAAATTT
** **
33604526 G-GGGTTAAAAATGGGATTTTGAAAGGTTT
1 GAGGG-TAAAAATGTAATTTTGAAAAATTT
33604555 GAGGGT-AAAATGGTAATTTTG
1 GAGGGTAAAAAT-GTAATTTTG
33604576 GTGAAACCGG
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
28 5 0.12
29 19 0.47
30 16 0.40
ACGTcount: A:0.38, C:0.01, G:0.29, T:0.33
Consensus pattern (29 bp):
GAGGGTAAAAATGTAATTTTGAAAAATTT
Found at i:33604633 original size:29 final size:29
Alignment explanation
Indices: 33604592--33604780 Score: 103
Period size: 30 Copynumber: 6.5 Consensus size: 29
33604582 CCGGGGTCAA
33604592 AAAATGG-AATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTGGAAAGTTTAGGGGT
* *
33604620 AAAATGGTAATTTTTAGTGAAA--TCAGGGTT
1 AAAATGGTAA-TTTT-G-GAAAGTTTAGGGGT
*
33604650 AAAAATGCG--ATTTTGGAAAG-TTCGGAGGT
1 -AAAATG-GTAATTTTGGAAAGTTTAGG-GGT
** ***
33604679 AAAATGGTAATTTTTGATGAAA-TCAAGGTCA
1 AAAATGGTAA-TTTTG--GAAAGTTTAGGGGT
33604710 AAAATGG-AATTTTGGAAAGTTT-GGGGAT
1 AAAATGGTAATTTTGGAAAGTTTAGGGG-T
* *
33604738 AAAATGGTAATTTTTGG-AAGTTTCGAGGT
1 AAAATGGTAA-TTTTGGAAAGTTTAGGGGT
33604767 CAAAAT-GTAATTTT
1 -AAAATGGTAATTTT
33604781 TAGAAGTTTT
Statistics
Matches: 124, Mismatches: 17, Indels: 40
0.69 0.09 0.22
Matches are distributed among these distances:
27 11 0.09
28 29 0.23
29 27 0.22
30 32 0.26
31 14 0.11
32 11 0.09
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTGGAAAGTTTAGGGGT
Found at i:33604752 original size:59 final size:58
Alignment explanation
Indices: 33604527--33604753 Score: 282
Period size: 59 Copynumber: 3.8 Consensus size: 58
33604517 GAAAAATTTG
* * * * *
33604527 GGGTTAAAAATGGGATTTT-GAAAGGTTTGAGGGTAAAATGGTAA-TTTTGGTGAAACCG
1 GGGTCAAAAATGGAATTTTGGAAA-GTTTG-GGGTAAAATGGTAATTTTTGATGAAATCA
33604585 GGGTCAAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTT-AGTGAAATCA
1 GGGTC-AAAAATGGAATTTTGGAAAGTTT-GGGGTAAAATGGTAATTTTTGA-TGAAATCA
* *
33604645 GGGTTAAAAATGCG-ATTTTGGAAAGTTCGGAGGTAAAATGGTAATTTTTGATGAAATCA
1 GGGTCAAAAATG-GAATTTTGGAAAGTTTGG-GGTAAAATGGTAATTTTTGATGAAATCA
*
33604704 AGGTCAAAAATGGAATTTTGGAAAGTTTGGGGATAAAATGGTAATTTTTG
1 GGGTCAAAAATGGAATTTTGGAAAGTTTGGGG-TAAAATGGTAATTTTTG
33604754 GAAGTTTCGA
Statistics
Matches: 149, Mismatches: 10, Indels: 19
0.84 0.06 0.11
Matches are distributed among these distances:
58 9 0.06
59 119 0.80
60 21 0.14
ACGTcount: A:0.36, C:0.04, G:0.29, T:0.32
Consensus pattern (58 bp):
GGGTCAAAAATGGAATTTTGGAAAGTTTGGGGTAAAATGGTAATTTTTGATGAAATCA
Found at i:33604752 original size:118 final size:118
Alignment explanation
Indices: 33604527--33604752 Score: 334
Period size: 118 Copynumber: 1.9 Consensus size: 118
33604517 GAAAAATTTG
* * * **
33604527 GGGTTAAAAATGGGATTTTGAAAGGTTTGAGGGTAAAATGGTAATTTTGGTGAAACCGGGGTCAA
1 GGGTTAAAAATGCGATTTTGAAAGGTTGGAGGGTAAAATGGTAATTTTGATGAAACCAAGGTCAA
33604592 AAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTAGTGAAATCA
66 AAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTAGTGAAATCA
*
33604645 GGGTTAAAAATGCGATTTTGGAAA-GTTCGGA-GGTAAAATGGTAATTTTTGATGAAATCAAGGT
1 GGGTTAAAAATGCGATTTT-GAAAGGTT-GGAGGGTAAAATGGTAA-TTTTGATGAAACCAAGGT
33604708 C-AAAAATGGAATTTTGGAAAGTTT-GGGGATAAAATGGTAATTTTT
63 CAAAAAATGGAATTTTGGAAAGTTTAGGGG-TAAAATGGTAATTTTT
33604753 GGAAGTTTCG
Statistics
Matches: 98, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
117 4 0.04
118 73 0.74
119 21 0.21
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (118 bp):
GGGTTAAAAATGCGATTTTGAAAGGTTGGAGGGTAAAATGGTAATTTTGATGAAACCAAGGTCAA
AAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTAGTGAAATCA
Found at i:33604767 original size:59 final size:57
Alignment explanation
Indices: 33604532--33604780 Score: 274
Period size: 59 Copynumber: 4.2 Consensus size: 57
33604522 ATTTGGGGTT
* * * *
33604532 AAAAATGGGATTTT-GAAAGGTTTGAGGGTAAAATGGTAATTTTGGTGAAACCGGGGTC
1 AAAAATGGAATTTTGGAAA-GTTTG-GGGTAAAATGGTAATTTTTGTGAAATCGAGGTC
*
33604590 AAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTAGTGAAATC-AGGGTT
1 -AAAAATGGAATTTTGGAAAGTTT-GGGGTAAAATGGTAATTTTT-GTGAAATCGA-GGTC
* *
33604650 AAAAATGCG-ATTTTGGAAAGTTCGGAGGTAAAATGGTAATTTTTGATGAAATCAAGGTC
1 AAAAATG-GAATTTTGGAAAGTTTGG-GGTAAAATGGTAATTTTTG-TGAAATCGAGGTC
*
33604709 AAAAATGGAATTTTGGAAAGTTTGGGGATAAAATGGTAATTTTTG-GAAGTTTCGAGGTC
1 AAAAATGGAATTTTGGAAAGTTTGGGG-TAAAATGGTAATTTTTGTGAA--ATCGAGGTC
*
33604768 -AAAATGTAATTTT
1 AAAAATGGAATTTT
33604781 TAGAAGTTTT
Statistics
Matches: 167, Mismatches: 11, Indels: 25
0.82 0.05 0.12
Matches are distributed among these distances:
57 3 0.02
58 18 0.11
59 129 0.77
60 17 0.10
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (57 bp):
AAAAATGGAATTTTGGAAAGTTTGGGGTAAAATGGTAATTTTTGTGAAATCGAGGTC
Found at i:33604781 original size:29 final size:28
Alignment explanation
Indices: 33604704--33604789 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 28
33604694 GATGAAATCA
*
33604704 AGGTCAAAAATGGAA-TTTTGGAAAGTTTG
1 AGGTC-AAAATGTAATTTTTGG-AAGTTTG
*
33604733 GGGAT-AAAATGGTAATTTTTGGAAGTTTCG
1 AGG-TCAAAAT-GTAATTTTTGGAAGTTT-G
*
33604763 AGGTCAAAATGTAATTTTTAGAAGTTT
1 AGGTCAAAATGTAATTTTTGGAAGTTT
33604790 TGGGTTTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
28 5 0.10
29 28 0.58
30 15 0.31
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (28 bp):
AGGTCAAAATGTAATTTTTGGAAGTTTG
Found at i:33604800 original size:29 final size:28
Alignment explanation
Indices: 33604726--33604880 Score: 96
Period size: 30 Copynumber: 5.2 Consensus size: 28
33604716 GAATTTTGGA
* * *
33604726 AAGTTTGGGGATAAAATGGTAATTTTTGG
1 AAGTTTTGGGTTAAAAT-GTAATTTTTAG
* *
33604755 AAGTTTCGAGGTCAAAATGTAATTTTTAG
1 AAGTTTTG-GGTTAAAATGTAATTTTTAG
* *
33604784 AAGTTTTGGGTTTAAAAATATAA-TTTCAG
1 AAGTTTTGGG-TT-AAAATGTAATTTTTAG
** * * *
33604813 AGGAGTTCGGGGGTCAAAATGTAATTTTCAA
1 A--AGTT-TTGGGTTAAAATGTAATTTTTAG
*
33604844 AAGGTTTTAGGGTTAAAATATAATTTTTAG
1 AA-GTTTT-GGGTTAAAATGTAATTTTTAG
33604874 ACAGTTT
1 A-AGTTT
33604881 AGGGACCTAT
Statistics
Matches: 97, Mismatches: 19, Indels: 19
0.72 0.14 0.14
Matches are distributed among these distances:
28 2 0.02
29 32 0.33
30 48 0.49
31 12 0.12
32 3 0.03
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (28 bp):
AAGTTTTGGGTTAAAATGTAATTTTTAG
Found at i:33609311 original size:18 final size:18
Alignment explanation
Indices: 33609288--33609322 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
33609278 GAGTTAAACG
*
33609288 AATCGAGTTATTTGAGTT
1 AATCGAATTATTTGAGTT
33609306 AATCGAATTATTTGAGT
1 AATCGAATTATTTGAGT
33609323 CAACTCGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (18 bp):
AATCGAATTATTTGAGTT
Found at i:33609436 original size:22 final size:22
Alignment explanation
Indices: 33609404--33609450 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
33609394 AATTATAATA
*
33609404 TTTTACATTTTTACCTCAAACTT
1 TTTTACA-TTTTACCTCAAAATT
*
33609427 TTTTAC-TTTTCCCTCAAAATT
1 TTTTACATTTTACCTCAAAATT
33609448 TTT
1 TTT
33609451 ATTCCTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.73
23 6 0.27
ACGTcount: A:0.23, C:0.21, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTACATTTTACCTCAAAATT
Found at i:33610113 original size:19 final size:19
Alignment explanation
Indices: 33610078--33610115 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
33610068 AAAATCACAA
*
33610078 TTTTACATTTAATATATAT
1 TTTTACATTTAAAATATAT
33610097 TTTTA-ATTTCAAAATATAT
1 TTTTACATTT-AAAATATAT
33610116 AGTGACAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTACATTTAAAATATAT
Found at i:33613542 original size:24 final size:24
Alignment explanation
Indices: 33613503--33613560 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
33613493 TTTTTTACTG
* *
33613503 TTTTGTTGCTGCTTTTGCTATTAT
1 TTTTGTTGTTGCTTTTACTATTAT
* *
33613527 TTTTGTTGTTGTTTTTACTGTTAT
1 TTTTGTTGTTGCTTTTACTATTAT
*
33613551 TTTTATTGTT
1 TTTTGTTGTT
33613561 TTTGTTGTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.09, C:0.07, G:0.16, T:0.69
Consensus pattern (24 bp):
TTTTGTTGTTGCTTTTACTATTAT
Found at i:33614218 original size:29 final size:29
Alignment explanation
Indices: 33614181--33614241 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
33614171 ATAATAAAGC
* *
33614181 AATATAGTTTAAATACT-AAGATGAGATAA
1 AATAAAGTTTAAATACTGAAG-TGAGAAAA
*
33614210 AATAAAGTTTAAATATTGAAGTGAGAAAA
1 AATAAAGTTTAAATACTGAAGTGAGAAAA
33614239 AAT
1 AAT
33614242 TATAATAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 25 0.89
30 3 0.11
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.30
Consensus pattern (29 bp):
AATAAAGTTTAAATACTGAAGTGAGAAAA
Found at i:33625116 original size:16 final size:16
Alignment explanation
Indices: 33625073--33625108 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
33625063 TAGTTCACTC
*
33625073 TAATGAAATAGAATTG
1 TAATGAAATAAAATTG
33625089 TAATGAAATAAAATTG
1 TAATGAAATAAAATTG
33625105 TAAT
1 TAAT
33625109 AGAATAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (16 bp):
TAATGAAATAAAATTG
Found at i:33625302 original size:25 final size:26
Alignment explanation
Indices: 33625274--33625325 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
33625264 GTAAATGATT
*
33625274 ATTATTATT-ATTA-AATGTTAATAAA
1 ATTATTATTAAATATAAT-TTAATAAA
33625299 ATTATTATTAAATATAATTTAATAAA
1 ATTATTATTAAATATAATTTAATAAA
33625325 A
1 A
33625326 ATAATAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 9 0.38
26 12 0.50
27 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
ATTATTATTAAATATAATTTAATAAA
Found at i:33625360 original size:58 final size:58
Alignment explanation
Indices: 33625298--33625424 Score: 202
Period size: 58 Copynumber: 2.2 Consensus size: 58
33625288 ATGTTAATAA
* *
33625298 AATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATTATA-TTTTAACAT
1 AATTATTATTAAATATAATGTAAT-AAAATAATAAATAATTTAATAATATTTTTAACAT
* *
33625356 AATTATTATTAAATATAATGTAATAAAATAATATATAATTTAATAATATTTTTAATAT
1 AATTATTATTAAATATAATGTAATAAAATAATAAATAATTTAATAATATTTTTAACAT
33625414 AATTATTATTA
1 AATTATTATTA
33625425 TTGTTATTAA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
57 22 0.34
58 42 0.66
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (58 bp):
AATTATTATTAAATATAATGTAATAAAATAATAAATAATTTAATAATATTTTTAACAT
Found at i:33626556 original size:71 final size:70
Alignment explanation
Indices: 33626463--33626599 Score: 156
Period size: 71 Copynumber: 1.9 Consensus size: 70
33626453 ATATATTATG
* * * *
33626463 TAATTTAAAACACATT-AAAAAAA-TA-AAATTATATTAAATATATATTAATACTCTAATATAAA
1 TAATTTAAAACACATTAAAAAAAATTAGAAATT-TACTAAATAT-TA-AAATAATATAATATAAA
33626525 TATTAAAA
63 TATTAAAA
*
33626533 TAATGTTAAAATA-ATTATAAAAAAATTAGAAATTTACTAAATATTAAAATAATATAATATAAAT
1 TAAT-TTAAAACACATTA-AAAAAAATTAGAAATTTACTAAATATTAAAATAATATAATATAAAT
33626597 ATT
64 ATT
33626600 TTTAAAAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
70 7 0.12
71 25 0.44
72 9 0.16
73 11 0.19
74 5 0.09
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (70 bp):
TAATTTAAAACACATTAAAAAAAATTAGAAATTTACTAAATATTAAAATAATATAATATAAATAT
TAAAA
Found at i:33630840 original size:29 final size:31
Alignment explanation
Indices: 33630797--33630854 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
33630787 TAAAAGTTGG
* * *
33630797 TAAAAACAATAAATT-TGGGTCTTTAAAAAC
1 TAAAAACAAAAAATTGAGGGTCCTTAAAAAC
33630827 TAAAAA-AAAAAATTGAGGGTCCTTAAAA
1 TAAAAACAAAAAATTGAGGGTCCTTAAAA
33630855 GTTGGTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (31 bp):
TAAAAACAAAAAATTGAGGGTCCTTAAAAAC
Found at i:33631215 original size:49 final size:49
Alignment explanation
Indices: 33631158--33631264 Score: 169
Period size: 49 Copynumber: 2.2 Consensus size: 49
33631148 CTATCATAGA
*
33631158 ACTTAAACCTATGACCGCATAACCATCGTCAACTAGGAGCCCGAGTTAT
1 ACTTAAACCTATGACCGCATAACCATCATCAACTAGGAGCCCGAGTTAT
* * *
33631207 ACTTAAACCTATGATCGCTTAACCATCATCAACTAGGAGCCCTAGTTAT
1 ACTTAAACCTATGACCGCATAACCATCATCAACTAGGAGCCCGAGTTAT
*
33631256 ACTTCAACC
1 ACTTAAACC
33631265 CGTGACCATA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.25
Consensus pattern (49 bp):
ACTTAAACCTATGACCGCATAACCATCATCAACTAGGAGCCCGAGTTAT
Found at i:33631279 original size:49 final size:50
Alignment explanation
Indices: 33631158--33631281 Score: 148
Period size: 49 Copynumber: 2.5 Consensus size: 50
33631148 CTATCATAGA
* * *
33631158 ACTTAAACCTATGACCGC-ATAACCATCGTCAACTAGGAGCCCGAGTTAT
1 ACTTAAACCCATGATCGCTATAACCATCATCAACTAGGAGCCCGAGTTAT
* *
33631207 ACTTAAACCTATGATCGCT-TAACCATCATCAACTAGGAGCCCTAGTTAT
1 ACTTAAACCCATGATCGCTATAACCATCATCAACTAGGAGCCCGAGTTAT
* *
33631256 ACTTCAACCCGTGA-C-CATATAACCAT
1 ACTTAAACCCATGATCGC-TATAACCAT
33631282 TGTGAATTGG
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
47 1 0.02
48 2 0.03
49 63 0.95
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.25
Consensus pattern (50 bp):
ACTTAAACCCATGATCGCTATAACCATCATCAACTAGGAGCCCGAGTTAT
Found at i:33632356 original size:17 final size:18
Alignment explanation
Indices: 33632317--33632356 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
33632307 TATGAATTAA
33632317 TTTTTTAAAGTTATGTTC
1 TTTTTTAAAGTTATGTTC
*
33632335 TTTTTTAGAGTTACT-TTC
1 TTTTTTAAAGTTA-TGTTC
33632353 TTTT
1 TTTT
33632357 GGTTCAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.65
Consensus pattern (18 bp):
TTTTTTAAAGTTATGTTC
Found at i:33649467 original size:304 final size:296
Alignment explanation
Indices: 33648993--33649630 Score: 767
Period size: 304 Copynumber: 2.1 Consensus size: 296
33648983 CTTTAATTGT
*
33648993 TAATAAAGTATGCATAATACAATTAAAATGTAAATATTATATTAAATTAAAGTCGTGGTTTAGTG
1 TAATAAAATATGCATAATACAATTAAAATGTAAATATTATATTAAATTAAAGTCGTGGTTTAGTG
* * * *
33649058 GTAAAATTGTTTAATTATTGTCAATAACTTGAGTTAAAATCCAATCACATATAATTTTTTATTGG
66 GTAAAATTGTTTAATTAATGTAAATAACATAAGTTAAAATCCAATCACATATAATTTTTTATTGG
*
33649123 TTTTTTAGAAATAAAAAGACTAAATACTCTAAAAAATATAACTTATTTTAATTATGAAAGGATAT
131 TTTTTTAGAAATAAAAAGACTAAATACTCTAAAAAATATAACTTATTTTAATTACGAAAGGATAT
* * * *
33649188 TTTTGAAAATTT-TCTAATTGAGTTGGTGTTCGGTTGACTCATGATACCAACTTAATCAGGAGTT
196 TTTTG-AAATTTCTCTAATTGAGTTGATATTCGGTTAACTCATGACACCAACTTAATCAGGAGTT
33649252 TAAATAATAGAATAAATAAATATATAATTGATGGAGA
260 TAAATAATAGAATAAATAAATATATAATTGATGGAGA
* *
33649289 TAATAAAAATATGCATAATACAAATTAAAATGTAGATATTATATTAAAATAAATCTAAA-TCTTT
1 TAAT-AAAATATGCATAATAC-AATTAAAATGTAAATATTATA-T----TAAAT-TAAAGTC-GT
* * * * *
33649353 GGTTTAGTGGTAGAATTGTTTTATTAATGTAAATAGCATAAGTTCAAATCTAATCACATATAATT
57 GGTTTAGTGGTAAAATTGTTTAATTAATGTAAATAACATAAGTTAAAATCCAATCACATATAATT
33649418 TTTTATT-G-TTTTTAGAAATAAAAA-AGCTAAAATAGC-C-ACAAATAATATAACTTATTTTAA
122 TTTTATTGGTTTTTTAGAAATAAAAAGA-CT-AAATA-CTCTA-AAA-AATATAACTTATTTTAA
*
33649478 TTACGAAATGATATTTTTGAAATTTCTCTAATTGAGTTGATATTCGGTTAACTCATGACACCAAC
182 TTACGAAAGGATATTTTTGAAATTTCTCTAATTGAGTTGATATTCGGTTAACTCATGACACCAAC
* * * * * * *
33649543 TCAAT---G-GTTCAAGTAATAGTATAGAGTATATATATACAATTGATAGAGA
247 TTAATCAGGAGTTTAAATAATAGAATA-A--ATAAATATATAATTGATGGAGA
* * * * *
33649592 TAATAAAGTAGGTATAATATAATTAAAATATAAATATTA
1 TAATAAAATATGCATAATACAATTAAAATGTAAATATTA
33649631 AAATAAAGCT
Statistics
Matches: 293, Mismatches: 31, Indels: 31
0.83 0.09 0.09
Matches are distributed among these distances:
296 4 0.01
297 15 0.05
298 20 0.07
299 1 0.00
300 14 0.05
301 20 0.07
302 31 0.11
303 46 0.16
304 142 0.48
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.38
Consensus pattern (296 bp):
TAATAAAATATGCATAATACAATTAAAATGTAAATATTATATTAAATTAAAGTCGTGGTTTAGTG
GTAAAATTGTTTAATTAATGTAAATAACATAAGTTAAAATCCAATCACATATAATTTTTTATTGG
TTTTTTAGAAATAAAAAGACTAAATACTCTAAAAAATATAACTTATTTTAATTACGAAAGGATAT
TTTTGAAATTTCTCTAATTGAGTTGATATTCGGTTAACTCATGACACCAACTTAATCAGGAGTTT
AAATAATAGAATAAATAAATATATAATTGATGGAGA
Found at i:33650943 original size:25 final size:25
Alignment explanation
Indices: 33650899--33650948 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
33650889 TTTGATCTTA
* *
33650899 AAAAAAAAAACCTATTTGACCAATT
1 AAAAAAAAAACATATGTGACCAATT
* *
33650924 AAAAAAAGAACATATGTGACTAATT
1 AAAAAAAAAACATATGTGACCAATT
33650949 TAATCTAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (25 bp):
AAAAAAAAAACATATGTGACCAATT
Found at i:33659941 original size:27 final size:27
Alignment explanation
Indices: 33659908--33659962 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
33659898 TTCAGTTTCG
33659908 AAGACAATTTATGGAGGTCGAATCGAA
1 AAGACAATTTATGGAGGTCGAATCGAA
33659935 AAGACAATTTATGGAGGTCGAATCGAA
1 AAGACAATTTATGGAGGTCGAATCGAA
33659962 A
1 A
33659963 TAAGTTGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.22
Consensus pattern (27 bp):
AAGACAATTTATGGAGGTCGAATCGAA
Found at i:33662068 original size:19 final size:18
Alignment explanation
Indices: 33662036--33662074 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
33662026 TGTCCCTTTT
33662036 TTATTGATTGATTAATATA
1 TTATTGATTGATTAAT-TA
* *
33662055 TTATTTATTTATTAATTA
1 TTATTGATTGATTAATTA
33662073 TT
1 TT
33662075 TCCCTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TTATTGATTGATTAATTA
Found at i:33665003 original size:21 final size:22
Alignment explanation
Indices: 33664947--33665010 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
33664937 TAGGCTCTTT
33664947 ATAATTTATAAAATTTTAAATTA
1 ATAATTT-TAAAATTTTAAATTA
** * *
33664970 ATAATGATAAAATTTTGATTTA
1 ATAATTTTAAAATTTTAAATTA
33664992 AT-ATTTTAAAATTTATAAA
1 ATAATTTTAAAATTT-TAAA
33665011 AATAAATAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
21 10 0.31
22 17 0.53
23 5 0.16
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (22 bp):
ATAATTTTAAAATTTTAAATTA
Found at i:33676000 original size:26 final size:28
Alignment explanation
Indices: 33675970--33676033 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
33675960 AATTTTTTTA
33675970 AAATTTTTTATCAA-CTTTAAGGGTCTC
1 AAATTTTTTATCAATCTTTAAGGGTCTC
* * *
33675997 -AATTCTTTTTTTAATTTTTAAGGGTCTC
1 AAATT-TTTTATCAATCTTTAAGGGTCTC
33676025 AAATTTTTT
1 AAATTTTTT
33676034 TTTACTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 4 0.13
27 7 0.23
28 16 0.52
29 4 0.13
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.53
Consensus pattern (28 bp):
AAATTTTTTATCAATCTTTAAGGGTCTC
Found at i:33676005 original size:29 final size:30
Alignment explanation
Indices: 33675973--33676049 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
33675963 TTTTTTAAAA
33675973 TTTTTTATCAA-CTTTAAGGGTCTC-AATTC
1 TTTTTTAT-AATCTTTAAGGGTCTCAAATTC
* *
33676002 TTTTTT-TAATTTTTAAGGGTCTCAAATTT
1 TTTTTTATAATCTTTAAGGGTCTCAAATTC
*
33676031 TTTTTTACTAATTTTTAAG
1 TTTTTTA-TAATCTTTAAG
33676050 AGATTCAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 2 0.05
28 13 0.31
29 16 0.38
31 11 0.26
ACGTcount: A:0.25, C:0.10, G:0.09, T:0.56
Consensus pattern (30 bp):
TTTTTTATAATCTTTAAGGGTCTCAAATTC
Found at i:33676046 original size:31 final size:28
Alignment explanation
Indices: 33675985--33676049 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 28
33675975 TTTTATCAAC
33675985 TTTAAGGGTCTCAATTCTTTTTTTAATT
1 TTTAAGGGTCTCAATTCTTTTTTTAATT
*
33676013 TTTAAGGGTCTCAAATTTTTTTTTACTAATT
1 TTTAAGGGTCTC-AATTCTTTTTT--TAATT
33676044 TTTAAG
1 TTTAAG
33676050 AGATTCAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 12 0.36
29 10 0.30
31 11 0.33
ACGTcount: A:0.25, C:0.09, G:0.11, T:0.55
Consensus pattern (28 bp):
TTTAAGGGTCTCAATTCTTTTTTTAATT
Found at i:33676653 original size:24 final size:23
Alignment explanation
Indices: 33676577--33676662 Score: 95
Period size: 22 Copynumber: 3.7 Consensus size: 23
33676567 TAATATTTAC
*
33676577 GAACATGTTCATTTAAC-TTAATT
1 GAACATGTTCA-TGAACATTAATT
* * *
33676600 GAGCATGTTCACGAACATTAA-C
1 GAACATGTTCATGAACATTAATT
*
33676622 GAACATGTTCGTGAACATATAATT
1 GAACATGTTCATGAACAT-TAATT
33676646 GAACATGTTCATGAACA
1 GAACATGTTCATGAACA
33676663 ATGTTAATGA
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
22 18 0.35
23 17 0.33
24 16 0.31
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.31
Consensus pattern (23 bp):
GAACATGTTCATGAACATTAATT
Found at i:33678727 original size:12 final size:12
Alignment explanation
Indices: 33678710--33678749 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 12
33678700 GTTGGATACG
33678710 CTAATTTGTTTT
1 CTAATTTGTTTT
33678722 CTAATTTGTAGCTTT
1 CTAATTTGT---TTT
33678737 CTAATTTGTTTT
1 CTAATTTGTTTT
33678749 C
1 C
33678750 ACCAAATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 13 0.52
15 12 0.48
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.60
Consensus pattern (12 bp):
CTAATTTGTTTT
Found at i:33684058 original size:24 final size:24
Alignment explanation
Indices: 33684031--33684105 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
33684021 AATTTGACTC
* *
33684031 AAACAAATAAAAAGAATTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
33684055 AAACAAATAAGCAGAGTTT-ATATG
1 AAACAAATAAACAGAGTTTAAT-TG
*
33684079 AAACAATTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
33684103 AAA
1 AAA
33684106 ATTTATTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
23 2 0.05
24 40 0.91
25 2 0.05
ACGTcount: A:0.56, C:0.07, G:0.12, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:33687216 original size:17 final size:17
Alignment explanation
Indices: 33687187--33687298 Score: 95
Period size: 17 Copynumber: 6.5 Consensus size: 17
33687177 CAAATTCATT
*
33687187 TTAAATTTTTTTTAAGA
1 TTAAATTTATTTTAAGA
* * *
33687204 TTAAGTTTGTTTTAAAGT
1 TTAAATTTATTTT-AAGA
33687222 TTAAATTTATTTTAA-A
1 TTAAATTTATTTTAAGA
*
33687238 TTTAAATTTATTTTAAGT
1 -TTAAATTTATTTTAAGA
33687256 TTAAATTTATTTTCAA-A
1 TTAAATTTATTTT-AAGA
* *
33687273 TTTAAAATTATTATAA-A
1 -TTAAATTTATTTTAAGA
33687290 TTTAAATTT
1 -TTAAATTT
33687299 CAATGTTCAA
Statistics
Matches: 79, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
17 52 0.66
18 27 0.34
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (17 bp):
TTAAATTTATTTTAAGA
Found at i:33687226 original size:35 final size:34
Alignment explanation
Indices: 33687186--33687298 Score: 138
Period size: 35 Copynumber: 3.3 Consensus size: 34
33687176 CCAAATTCAT
* * *
33687186 TTTAAATTTTTTTTAAGA-TTAAGTTTGTTTTAAAG
1 TTTAAATTTATTTTAA-ATTTAAATTTATTTT-AAG
33687221 TTTAAATTTATTTTAAATTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAATTTAAATTTATTTTAAG
* * *
33687255 TTTAAATTTATTTTCAAATTTAAAATTATTATAAA
1 TTTAAATTTATTTT-AAATTTAAATTTATTTTAAG
33687290 TTTAAATTT
1 TTTAAATTT
33687299 CAATGTTCAA
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
34 18 0.26
35 52 0.74
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTTAAG
Found at i:33687235 original size:11 final size:11
Alignment explanation
Indices: 33687221--33687276 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
33687211 TGTTTTAAAG
33687221 TTTAAATTTAT
1 TTTAAATTTAT
*
33687232 TTTAAATTTAAA
1 TTTAAATTT-AT
* *
33687244 TTT-ATTTTAAG
1 TTTAAATTT-AT
33687255 TTTAAATTTAT
1 TTTAAATTTAT
33687266 TTTCAAATTTA
1 TTT-AAATTTA
33687277 AAATTATTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
11 22 0.59
12 15 0.41
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:33687241 original size:6 final size:6
Alignment explanation
Indices: 33687214--33687298 Score: 63
Period size: 6 Copynumber: 14.5 Consensus size: 6
33687204 TTAAGTTTGT
* * *
33687214 TTTAAA GTTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTAAG TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
33687261 TTT-AT TTTCAAA TTTAAA ATT--A TTATAAA TTTAAA TTT
1 TTTAAA TTT-AAA TTTAAA TTTAAA TT-TAAA TTTAAA TTT
33687299 CAATGTTCAA
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
4 2 0.03
5 13 0.21
6 34 0.55
7 13 0.21
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:33687277 original size:52 final size:52
Alignment explanation
Indices: 33687186--33687298 Score: 156
Period size: 52 Copynumber: 2.2 Consensus size: 52
33687176 CCAAATTCAT
* * * * *
33687186 TTTAAATTTTTTTTAAGATTAAGTTTGTTTTAAAGTTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAGATTAAATTTATTTTAAAGTTTAAAATTATTATAAA
*
33687238 TTTAAATTTATTTTAAGTTTAAATTTATTTTCAAA-TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAGATTAAATTTATTTT-AAAGTTTAAAATTATTATAAA
33687290 TTTAAATTT
1 TTTAAATTT
33687299 CAATGTTCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
52 51 0.94
53 3 0.06
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (52 bp):
TTTAAATTTATTTTAAGATTAAATTTATTTTAAAGTTTAAAATTATTATAAA
Found at i:33689055 original size:35 final size:34
Alignment explanation
Indices: 33689016--33689145 Score: 147
Period size: 35 Copynumber: 3.8 Consensus size: 34
33689006 TCAAATTCAT
* *
33689016 TTTAAATTTATTTTAAGATTAAGTTTGTTTTAAA
1 TTTAAATTTATTTTAAGATTAAATTTATTTTAAA
*
33689050 GTTTAAACTTATTTTAA-ATTTAAATTTATTTTAAA
1 -TTTAAATTTATTTTAAGA-TTAAATTTATTTTAAA
* *
33689085 TTTAAATTTAATTTAAGTTTAAATTTATTTTCAAA
1 TTTAAATTTATTTTAAGATTAAATTTATTTT-AAA
* *
33689120 TTTAAAATTATTATAA-ATTTAAATTT
1 TTTAAATTTATTTTAAGA-TTAAATTT
33689146 CAATGTTCAA
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
34 28 0.35
35 53 0.65
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (34 bp):
TTTAAATTTATTTTAAGATTAAATTTATTTTAAA
Found at i:33689073 original size:6 final size:6
Alignment explanation
Indices: 33689044--33689145 Score: 81
Period size: 6 Copynumber: 17.5 Consensus size: 6
33689034 TTAAGTTTGT
* * *
33689044 TTTAAA GTTTAAA CTT-AT TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
33689091 TTT-AA TTTAAG TTTAAA TTT-AT TTTCAAA TTTAAA ATT--A TTATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TT-TAAA
33689137 TTTAAA TTT
1 TTTAAA TTT
33689146 CAATGTTCAA
Statistics
Matches: 75, Mismatches: 12, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
4 2 0.03
5 17 0.23
6 43 0.57
7 13 0.17
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:33689073 original size:17 final size:17
Alignment explanation
Indices: 33689016--33689145 Score: 163
Period size: 17 Copynumber: 7.5 Consensus size: 17
33689006 TCAAATTCAT
33689016 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
* *
33689034 -TTAAGTTTGTTTTAAA
1 TTTAAATTTATTTTAAA
*
33689050 GTTTAAACTTATTTTAAA
1 -TTTAAATTTATTTTAAA
33689068 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
33689085 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
33689102 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
33689120 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
33689137 TTTAAATTT
1 TTTAAATTT
33689146 CAATGTTCAA
Statistics
Matches: 96, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
16 1 0.01
17 68 0.71
18 27 0.28
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:33689082 original size:11 final size:11
Alignment explanation
Indices: 33689068--33689123 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
33689058 TTATTTTAAA
33689068 TTTAAATTTAT
1 TTTAAATTTAT
*
33689079 TTTAAATTTAAA
1 TTTAAATTT-AT
*
33689091 TTT-AATTTAAG
1 TTTAAATTT-AT
33689102 TTTAAATTTAT
1 TTTAAATTTAT
33689113 TTTCAAATTTA
1 TTT-AAATTTA
33689124 AAATTATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
11 23 0.59
12 16 0.41
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:33689088 original size:23 final size:23
Alignment explanation
Indices: 33689063--33689111 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
33689053 TAAACTTATT
*
33689063 TTAAATTTAAATTT-ATTTTAAAT
1 TTAAATTT-AATTTAAGTTTAAAT
33689086 TTAAATTTAATTTAAGTTTAAAT
1 TTAAATTTAATTTAAGTTTAAAT
33689109 TTA
1 TTA
33689112 TTTTCAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TTAAATTTAATTTAAGTTTAAAT
Found at i:33689100 original size:52 final size:52
Alignment explanation
Indices: 33689016--33689145 Score: 174
Period size: 52 Copynumber: 2.5 Consensus size: 52
33689006 TCAAATTCAT
* **
33689016 TTTAAATTTATTTTAAGA-TTAAGTTTGTTTTAAAGTTTAAACTTATTTT-AAA
1 TTTAAATTTATTTTAA-ATTTAAATTTAATTT-AAGTTTAAACTTATTTTCAAA
*
33689068 TTTAAATTTATTTTAAATTTAAATTTAATTTAAGTTTAAATTTATTTTCAAA
1 TTTAAATTTATTTTAAATTTAAATTTAATTTAAGTTTAAACTTATTTTCAAA
* *
33689120 TTTAAAATTATTATAAATTTAAATTT
1 TTTAAATTTATTTTAAATTTAAATTT
33689146 CAATGTTCAA
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
51 17 0.24
52 53 0.76
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (52 bp):
TTTAAATTTATTTTAAATTTAAATTTAATTTAAGTTTAAACTTATTTTCAAA
Found at i:33692707 original size:35 final size:34
Alignment explanation
Indices: 33692668--33692760 Score: 107
Period size: 35 Copynumber: 2.7 Consensus size: 34
33692658 CCAAATTCAT
* *
33692668 TTTAAATTTAGTTTAAGA-TTAAGTTTGTTTTAAAG
1 TTTAAATTTAGTTTAA-ATTTAAATTTATTTT-AAG
* *
33692703 TTTAAACTTATTTTAAATTTAAATTTATTTTAAG
1 TTTAAATTTAGTTTAAATTTAAATTTATTTTAAG
*
33692737 TTTAAATTTATTTTCAAATTTAAA
1 TTTAAATTTAGTTT-AAATTTAAA
33692761 ATTCAATGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
34 17 0.33
35 34 0.67
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (34 bp):
TTTAAATTTAGTTTAAATTTAAATTTATTTTAAG
Found at i:33692725 original size:17 final size:17
Alignment explanation
Indices: 33692668--33692760 Score: 107
Period size: 17 Copynumber: 5.4 Consensus size: 17
33692658 CCAAATTCAT
*
33692668 TTTAAATTTAGTTTAAGA
1 TTTAAATTTATTTTAA-A
* *
33692686 -TTAAGTTTGTTTTAAA
1 TTTAAATTTATTTTAAA
*
33692702 GTTTAAACTTATTTTAAA
1 -TTTAAATTTATTTTAAA
*
33692720 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAA
33692737 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
33692755 TTTAAA
1 TTTAAA
33692761 ATTCAATGTT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
16 1 0.02
17 41 0.65
18 21 0.33
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:33694543 original size:6 final size:6
Alignment explanation
Indices: 33694514--33694615 Score: 72
Period size: 6 Copynumber: 17.5 Consensus size: 6
33694504 TTAAGTTTGT
* * *
33694514 TTTAAA GTTTAAA CTT-AT TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
33694561 TTTAAA -ATAAG TTTAAA TTT-AT TTTCAAA TTTAAA ATT--A TTATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TT-TAAA
33694607 TTTAAA TTT
1 TTTAAA TTT
33694616 CAATGTTCAA
Statistics
Matches: 73, Mismatches: 14, Indels: 17
0.70 0.13 0.16
Matches are distributed among these distances:
4 2 0.03
5 15 0.21
6 43 0.59
7 13 0.18
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:33694543 original size:17 final size:17
Alignment explanation
Indices: 33694486--33694615 Score: 136
Period size: 17 Copynumber: 7.5 Consensus size: 17
33694476 CCAATTTCAT
*
33694486 TTTAAATTTAGTTTAAGA
1 TTTAAATTTATTTTAA-A
* *
33694504 -TTAAGTTTGTTTTAAA
1 TTTAAATTTATTTTAAA
*
33694520 GTTTAAACTTATTTTAAA
1 -TTTAAATTTATTTTAAA
33694538 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*** *
33694555 TTTAAATTTAAAATAAG
1 TTTAAATTTATTTTAAA
33694572 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
33694590 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
33694607 TTTAAATTT
1 TTTAAATTT
33694616 CAATGTTCAA
Statistics
Matches: 91, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
16 1 0.01
17 63 0.69
18 27 0.30
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:33694552 original size:11 final size:11
Alignment explanation
Indices: 33694538--33694593 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
33694528 TTATTTTAAA
33694538 TTTAAATTTAT
1 TTTAAATTTAT
*
33694549 TTTAAATTTAAA
1 TTTAAATTT-AT
* * *
33694561 TTTAAAATAAG
1 TTTAAATTTAT
33694572 TTTAAATTTAT
1 TTTAAATTTAT
33694583 TTTCAAATTTA
1 TTT-AAATTTA
33694594 AAATTATTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
11 21 0.58
12 15 0.42
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:33694558 original size:23 final size:23
Alignment explanation
Indices: 33694532--33694581 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
33694522 TTAAACTTAT
* * *
33694532 TTTAAATTTAAATTTATTTTAAA
1 TTTAAATTTAAAATAAGTTTAAA
33694555 TTTAAATTTAAAATAAGTTTAAA
1 TTTAAATTTAAAATAAGTTTAAA
33694578 TTTA
1 TTTA
33694582 TTTTCAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTAAATTTAAAATAAGTTTAAA
Found at i:33694591 original size:52 final size:51
Alignment explanation
Indices: 33694518--33694615 Score: 160
Period size: 52 Copynumber: 1.9 Consensus size: 51
33694508 GTTTGTTTTA
* *
33694518 AAGTTTAAACTTATTTTAAATTTAAATTTATTTTAAATTTAAATTTAAAAT
1 AAGTTTAAACTTATTTTAAATTTAAAATTATTATAAATTTAAATTTAAAAT
*
33694569 AAGTTTAAATTTATTTTCAAATTTAAAATTATTATAAATTTAAATTT
1 AAGTTTAAACTTATTTT-AAATTTAAAATTATTATAAATTTAAATTT
33694616 CAATGTTCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
51 16 0.37
52 27 0.63
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (51 bp):
AAGTTTAAACTTATTTTAAATTTAAAATTATTATAAATTTAAATTTAAAAT
Found at i:33694611 original size:35 final size:34
Alignment explanation
Indices: 33694504--33694615 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 34
33694494 TAGTTTAAGA
* * * *
33694504 TTAAGTTTGTTTTAAAGTTTAAACTTATTTTAAAT
1 TTAAATTTATTTTAAA-TTTAAAATTATTATAAAT
* ** *
33694539 TTAAATTTATTTTAAATTTAAATTTAAAATAAGT
1 TTAAATTTATTTTAAATTTAAAATTATTATAAAT
33694573 TTAAATTTATTTTCAAATTTAAAATTATTATAAAT
1 TTAAATTTATTTT-AAATTTAAAATTATTATAAAT
33694608 TTAAATTT
1 TTAAATTT
33694616 CAATGTTCAA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
34 26 0.40
35 39 0.60
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (34 bp):
TTAAATTTATTTTAAATTTAAAATTATTATAAAT
Found at i:33697644 original size:25 final size:26
Alignment explanation
Indices: 33697616--33697665 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
33697606 GTTTTTTATA
33697616 TTTTTAAATT-TT-TTAAATAATATTT
1 TTTTTAAATTATTGTTAAA-AATATTT
33697641 TTTTTAAATTATTGTTAAAAATATT
1 TTTTTAAATTATTGTTAAAAATATT
33697666 GTAAAAGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 10 0.43
26 8 0.35
27 5 0.22
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTTTAAATTATTGTTAAAAATATTT
Found at i:33709228 original size:3 final size:3
Alignment explanation
Indices: 33709220--33709251 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
33709210 AGAGAGGGAT
33709220 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
33709252 CTGAACTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:33711916 original size:108 final size:109
Alignment explanation
Indices: 33711786--33712178 Score: 358
Period size: 108 Copynumber: 3.6 Consensus size: 109
33711776 CGACACCCAA
* *
33711786 AAAAATATTTTGTTGGATGTTTGCCACCTACTGGCCTACACCACTTTTTTCAAATTTAAAT-TTT
1 AAAAATATTTTTTTGG-TGTTTGCCACCTAATGGCCTACACCACTTTTTTCAAATTTAAATATTT
* *
33711850 TTT-TTGTTTATCACCCAATGGGCTACACCATATTTTCCAAATTT
65 TTTGATGTTTACCACCCAATGGGCTACACCATATTTTCCAAATTT
* * *
33711894 AAAAATATTTTTTTGAGTGTTTGTCACCTAATGGCCTACACCAATTTTTTCAGATTTAAAAATAT
1 AAAAATATTTTTTTG-GTGTTTGCCACCTAATGGCCTACACCACTTTTTTCAAATTT--AAATAT
* * * *
33711959 TTTTTGGGTATTTACCACCCAATGGCCTACACCACATTTTCCAAA-TT
63 TTTTT-GATGTTTACCACCCAATGGGCTACACCATATTTTCCAAATTT
* * * *
33712006 ---AAT-TTTTTTTGAATGTTTGTCATCC-AATGGCCTACACCA-TCTTTTTCAGAGTTAAAAAT
1 AAAAATATTTTTTTG-GTGTTTGCCA-CCTAATGGCCTACACCACT-TTTTTCA-AATT-TAAAT
* * * * * *
33712065 ATTTTTTGGATGTTTGCCATCTAAT-AGCTTACATCATATTTTTCAAATTT
61 ATTTTTT-GATGTTTACCACCCAATGGGC-TACACCATATTTTCCAAATTT
* * * * * *
33712115 AAAAATATTTTTTAGGTGTTTACCACCCAATGGCTTACACCACCTTTATCAAATTTAAA-ATTTT
1 AAAAATATTTTTTTGGTGTTTGCCACCTAATGGCCTACACCACTTTTTTCAAATTTAAATATTTT
33712179 AAAATTATTT
Statistics
Matches: 234, Mismatches: 33, Indels: 35
0.77 0.11 0.12
Matches are distributed among these distances:
107 2 0.01
108 128 0.55
109 15 0.06
110 7 0.03
111 11 0.05
112 31 0.13
113 40 0.17
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (109 bp):
AAAAATATTTTTTTGGTGTTTGCCACCTAATGGCCTACACCACTTTTTTCAAATTTAAATATTTT
TTGATGTTTACCACCCAATGGGCTACACCATATTTTCCAAATTT
Found at i:33711983 original size:56 final size:56
Alignment explanation
Indices: 33711786--33712174 Score: 329
Period size: 56 Copynumber: 7.1 Consensus size: 56
33711776 CGACACCCAA
* * *
33711786 AAAAATATTTTGTTGGATGTTTGCCACCTACTGGCCTACACCACTTTTTTCAAATTT
1 AAAAATATTTT-TTGGATGTTTGCCACCCAATGGCCTACACCAATTTTTTCAAATTT
* ** * *
33711843 --AAAT-TTTTTT--TTGTTTATCACCCAATGGGCTACACC-ATATTTTCCAAATTT
1 AAAAATATTTTTTGGATGTTTGCCACCCAATGGCCTACACCAAT-TTTTTCAAATTT
* * * *
33711894 AAAAATATTTTTTTGAGTGTTTGTCACCTAATGGCCTACACCAATTTTTTCAGATTT
1 AAAAATATTTTTTGGA-TGTTTGCCACCCAATGGCCTACACCAATTTTTTCAAATTT
* * * *
33711951 AAAAATATTTTTTGGGTATTTACCACCCAATGGCCTACACCACA-TTTTCCAAA-TT
1 AAAAATATTTTTTGGATGTTTGCCACCCAATGGCCTACACCA-ATTTTTTCAAATTT
* * * * * *
33712006 ---AATTTTTTTTGAATGTTTGTCATCCAATGGCCTACACC-ATCTTTTTCAGAGTT
1 AAAAATATTTTTTGGATGTTTGCCACCCAATGGCCTACACCAAT-TTTTTCAAATTT
* * * * *
33712059 AAAAATATTTTTTGGATGTTTGCCATCTAATAGCTTACATC-ATATTTTTCAAATTT
1 AAAAATATTTTTTGGATGTTTGCCACCCAATGGCCTACACCAAT-TTTTTCAAATTT
* * ** *
33712115 AAAAATATTTTTTAGG-TGTTTACCACCCAATGGCTTACACCACCTTTATCAAATTT
1 AAAAATATTTTTT-GGATGTTTGCCACCCAATGGCCTACACCAATTTTTTCAAATTT
33712171 AAAA
1 AAAA
33712175 TTTTAAAATT
Statistics
Matches: 266, Mismatches: 49, Indels: 35
0.76 0.14 0.10
Matches are distributed among these distances:
50 2 0.01
51 31 0.12
52 38 0.14
53 8 0.03
54 10 0.04
55 6 0.02
56 120 0.45
57 49 0.18
58 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (56 bp):
AAAAATATTTTTTGGATGTTTGCCACCCAATGGCCTACACCAATTTTTTCAAATTT
Found at i:33712125 original size:164 final size:164
Alignment explanation
Indices: 33711786--33712178 Score: 472
Period size: 164 Copynumber: 2.4 Consensus size: 164
33711776 CGACACCCAA
* * * * * *
33711786 AAAAATATTTTGTTGGATGTTTGCCACCTACTGGCCTACACCACTTTTTTCAAATTTAAATTTTT
1 AAAAATATTTT-TTGGGTGTTTACCACCCAATGGCCTACACCACATTTTCCAAATTTAAATTTTT
* * *
33711851 TTTTGTTTATCACCCAATGGGCTACACCATATTTTCCAAATTTAAAAATATTTTTTTGAGTGTTT
65 TTTTGTTTATCACCCAATGGCCTACACCATATTTTCCAAAGTTAAAAATATTTTTTGGAGTGTTT
* * *
33711916 GTCACCTAATGGCCTACACCAATTTTTTCAGATTT
130 GCCACCTAATAGCCTACACCAATTTTTTCAAATTT
*
33711951 AAAAATATTTTTTGGGTATTTACCACCCAATGGCCTACACCACATTTTCCAAA-TT-AATTTTTT
1 AAAAATATTTTTTGGGTGTTTACCACCCAATGGCCTACACCACATTTTCCAAATTTAAATTTTTT
* * * * *
33712014 TTGAATGTTTGTCATCCAATGGCCTACACCATCTTTTTCAGAGTTAAAAATATTTTTTGGA-TGT
66 TT---TGTTTATCACCCAATGGCCTACACCATATTTTCCAAAGTTAAAAATATTTTTTGGAGTGT
* * *
33712078 TTGCCATCTAATAGCTTACATC-ATATTTTTCAAATTT
128 TTGCCACCTAATAGCCTACACCAAT-TTTTTCAAATTT
* * * *
33712115 AAAAATATTTTTTAGGTGTTTACCACCCAATGGCTTACACCACCTTTAT-CAAATTTAAAATTTT
1 AAAAATATTTTTTGGGTGTTTACCACCCAATGGCCTACACCACATTT-TCCAAATTTAAATTTTT
33712179 AAAATTATTT
Statistics
Matches: 195, Mismatches: 26, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
162 10 0.05
163 4 0.02
164 113 0.58
165 62 0.32
166 6 0.03
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (164 bp):
AAAAATATTTTTTGGGTGTTTACCACCCAATGGCCTACACCACATTTTCCAAATTTAAATTTTTT
TTTGTTTATCACCCAATGGCCTACACCATATTTTCCAAAGTTAAAAATATTTTTTGGAGTGTTTG
CCACCTAATAGCCTACACCAATTTTTTCAAATTT
Found at i:33712458 original size:17 final size:17
Alignment explanation
Indices: 33712431--33712472 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
33712421 GGATAAAGTA
*
33712431 GTTACAAGAATATGAAAT
1 GTTA-AAGAATATGAAAG
*
33712449 GTTAAAGAATATGGAAG
1 GTTAAAGAATATGAAAG
33712466 GTTAAAG
1 GTTAAAG
33712473 GTTAAGGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.24, T:0.26
Consensus pattern (17 bp):
GTTAAAGAATATGAAAG
Found at i:33712627 original size:43 final size:41
Alignment explanation
Indices: 33712580--33712670 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 41
33712570 TACTAGGAAA
*
33712580 AATCCTGTGAGACAAAAATCTAGTGAAGAAAAAAAAAGTACAT
1 AATCCT-T-AGACAAAAACCTAGTGAAGAAAAAAAAAGTACAT
* * * *
33712623 AATCCTTTGATAAAAACCTAGTGAAGGAAAAAAGAGTACAT
1 AATCCTTAGACAAAAACCTAGTGAAGAAAAAAAAAGTACAT
33712664 AATCCTT
1 AATCCTT
33712671 TGATACATAG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 36 0.84
42 1 0.02
43 6 0.14
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.22
Consensus pattern (41 bp):
AATCCTTAGACAAAAACCTAGTGAAGAAAAAAAAAGTACAT
Found at i:33712644 original size:41 final size:41
Alignment explanation
Indices: 33712593--33712675 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
33712583 CCTGTGAGAC
*
33712593 AAAAATCTAGTGAAGAAAAAAAAAGTACATAATCCTTTGAT
1 AAAAACCTAGTGAAGAAAAAAAAAGTACATAATCCTTTGAT
* *
33712634 AAAAACCTAGTGAAGGAAAAAAGAGTACATAATCCTTTGAT
1 AAAAACCTAGTGAAGAAAAAAAAAGTACATAATCCTTTGAT
33712675 A
1 A
33712676 CATAGTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.52, C:0.11, G:0.14, T:0.23
Consensus pattern (41 bp):
AAAAACCTAGTGAAGAAAAAAAAAGTACATAATCCTTTGAT
Found at i:33717944 original size:20 final size:21
Alignment explanation
Indices: 33717921--33717970 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
33717911 TAACAATTTT
*
33717921 TAATTATTTTAATTTA-ATTA
1 TAATTATTTTAAATTATATTA
* *
33717941 TAATT-TTTTAAATTATGTTT
1 TAATTATTTTAAATTATATTA
33717961 TAATTATTTT
1 TAATTATTTT
33717971 TTAAAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 9 0.36
20 12 0.48
21 4 0.16
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TAATTATTTTAAATTATATTA
Found at i:33718059 original size:57 final size:57
Alignment explanation
Indices: 33717998--33718201 Score: 209
Period size: 57 Copynumber: 3.6 Consensus size: 57
33717988 TGGTGTAGCT
* * **
33717998 ATTGGATGGCAAACATCT-AAAAAAATATTTTTATATCTGAAAAAGATGATGTAAACC
1 ATTGGATGACAAACATCTAAAAAAAATATTTTTAAAT-TGAAAAAGATGATGTAGGCC
* * * * *
33718055 ATTGGGTGGCAAACATC-AAAAAAAATATTTTTAAATTCAAAAA-AGTTAGTGTAGGCT
1 ATTGGATGACAAACATCTAAAAAAAATATTTTTAAATTGAAAAAGA-TGA-TGTAGGCC
* * * *
33718112 ATTGGATGACAAATA-CTCAAAAAAATATTTTTAAATTTGAGAAAGGTGATGTAGGCC
1 ATTGGATGACAAACATCTAAAAAAAATATTTTTAAA-TTGAAAAAGATGATGTAGGCC
* *
33718169 ATTAGATGACAAACACCTAAAAAAAATATTTTT
1 ATTGGATGACAAACATCTAAAAAAAATATTTTT
33718202 TTATTAGTAT
Statistics
Matches: 121, Mismatches: 19, Indels: 13
0.79 0.12 0.08
Matches are distributed among these distances:
55 1 0.01
56 9 0.07
57 87 0.72
58 24 0.20
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (57 bp):
ATTGGATGACAAACATCTAAAAAAAATATTTTTAAATTGAAAAAGATGATGTAGGCC
Found at i:33718116 original size:114 final size:114
Alignment explanation
Indices: 33717990--33718201 Score: 284
Period size: 114 Copynumber: 1.9 Consensus size: 114
33717980 TGGAGATATG
* *
33717990 GTGTAGCTATTGGATGGCAAACA-TCTAAAAAAATATTTTTATATCTGAAAAAGATGATGTAAAC
1 GTGTAGCTATTGGATGACAAACACTC-AAAAAAATATTTTTAAATCTGAAAAAGATGATGTAAAC
* * * *
33718054 CATTGGGTGGCAAACATC-AAAAAAAATATTTTTAAATTCAAAAAAGTTA
65 CATTAGATGACAAACACCTAAAAAAAATATTTTTAAATTCAAAAAAGTTA
* * * * **
33718103 GTGTAGGCTATTGGATGACAAATACTCAAAAAAATATTTTTAAATTTGAGAAAGGTGATGTAGGC
1 GTGTA-GCTATTGGATGACAAACACTCAAAAAAATATTTTTAAATCTGAAAAAGATGATGTAAAC
33718168 CATTAGATGACAAACACCTAAAAAAAATATTTTT
65 CATTAGATGACAAACACCTAAAAAAAATATTTTT
33718202 TTATTAGTAT
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
113 5 0.06
114 62 0.74
115 17 0.20
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (114 bp):
GTGTAGCTATTGGATGACAAACACTCAAAAAAATATTTTTAAATCTGAAAAAGATGATGTAAACC
ATTAGATGACAAACACCTAAAAAAAATATTTTTAAATTCAAAAAAGTTA
Found at i:33719206 original size:91 final size:89
Alignment explanation
Indices: 33719096--33719275 Score: 247
Period size: 90 Copynumber: 2.0 Consensus size: 89
33719086 AGTCTTTAAA
* * *
33719096 CTTTCTCAAAAAAGCAATTAAGTCCAT-CTTATTTTTTTGCACTCATTTGGGTACTTGAACTTTC
1 CTTTCTCAAAAAAGCAATTAAGCCCATAC-T-TTTTTTTGCACTCAATTGAGTACTTGAACTTTC
33719160 AAAATGCATCAAAAAAAGCCCTCAAAC
64 AAAATGCATCAAAAAAA-CCCTCAAAC
* * *
33719187 CTTT-TCAGAAAAAGTAATTAAGCCCCTACTTTTTTTTGCACTCAATTGAGTACTTGAACTTTTA
1 CTTTCTCA-AAAAAGCAATTAAGCCCATACTTTTTTTTGCACTCAATTGAGTACTTGAACTTTCA
*
33719251 AAATGCATCAAAAAGACCCTCAAAC
65 AAATGCATCAAAAAAACCCTCAAAC
33719276 TTAAAAAAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
89 9 0.11
90 49 0.61
91 21 0.26
92 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.33
Consensus pattern (89 bp):
CTTTCTCAAAAAAGCAATTAAGCCCATACTTTTTTTTGCACTCAATTGAGTACTTGAACTTTCAA
AATGCATCAAAAAAACCCTCAAAC
Found at i:33719300 original size:89 final size:90
Alignment explanation
Indices: 33719127--33719308 Score: 251
Period size: 90 Copynumber: 2.0 Consensus size: 90
33719117 GTCCATCTTA
* * **
33719127 TTTTTTTGCACTCATTTGGGTACTTGAACTTTCAAAATGCATCAAAAAAAGCCCTCAAACCTTTT
1 TTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAAAGCCCTCAAACCTTAA
* *
33719192 CAGAAAAAGTAATTAAGCCCCTACT
66 AAAAAAAAGTAATTAAGCCCCTACT
* *
33719217 TTTTTTTGCACTCAATTGAGTACTTGAACTTTTAAAATGCATCAAAAAGA-CCCTCAAA-CTTAA
1 TTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAAAGCCCTCAAACCTT-A
* *
33719280 AAAAAAAAAGTAATTTAGCCCCTGCT
65 AAAAAAAAAGTAATTAAGCCCCTACT
33719306 TTT
1 TTT
33719309 ACTAAAAAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
88 3 0.04
89 32 0.40
90 46 0.57
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.33
Consensus pattern (90 bp):
TTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAAAGCCCTCAAACCTTAA
AAAAAAAAGTAATTAAGCCCCTACT
Found at i:33719391 original size:9 final size:10
Alignment explanation
Indices: 33719366--33719538 Score: 113
Period size: 10 Copynumber: 18.2 Consensus size: 10
33719356 TTAAATTTTA
33719366 ATAAAAAATT
1 ATAAAAAATT
*
33719376 ATTAAAAATT
1 ATAAAAAATT
33719386 A-AAAAAA-T
1 ATAAAAAATT
*
33719394 AT-AAAAATC
1 ATAAAAAATT
33719403 ATAAAAAA-T
1 ATAAAAAATT
33719412 ATAAAAAATT
1 ATAAAAAATT
*
33719422 GTAAAAAATT
1 ATAAAAAATT
*
33719432 ATAAAATA-T
1 ATAAAAAATT
33719441 ATAGAAAAATT
1 ATA-AAAAATT
33719452 AT--AAAATT
1 ATAAAAAATT
33719460 AT--AAAATT
1 ATAAAAAATT
* * * *
33719468 CTATAAAGTC
1 ATAAAAAATT
33719478 ATAAGAAAATT
1 ATAA-AAAATT
*
33719489 ATACAAAA-T
1 ATAAAAAATT
33719498 ATAAAGAAA-T
1 ATAAA-AAATT
33719508 AT--AAAATT
1 ATAAAAAATT
*
33719516 CGTAAAAAATT
1 -ATAAAAAATT
33719527 -TATAAAAATT
1 ATA-AAAAATT
33719537 AT
1 AT
33719539 TGTACCAAAA
Statistics
Matches: 129, Mismatches: 18, Indels: 31
0.72 0.10 0.17
Matches are distributed among these distances:
7 3 0.02
8 24 0.19
9 27 0.21
10 58 0.45
11 17 0.13
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:33719397 original size:28 final size:28
Alignment explanation
Indices: 33719366--33719513 Score: 124
Period size: 28 Copynumber: 5.2 Consensus size: 28
33719356 TTAAATTTTA
33719366 ATAAAAAATTATTAAAAAT-TAAAAAAAT
1 ATAAAAAATTA-TAAAAATATAAAAAAAT
* *
33719394 AT-AAAAATCATAAAAAATATAAAAAATT
1 ATAAAAAATTAT-AAAAATATAAAAAAAT
* *
33719422 GTAAAAAATTATAAAATATATAGAAAAAT
1 ATAAAAAATTATAAAA-ATATAAAAAAAT
* * * * *
33719451 -TATAAAATTATAAAATTCT-ATAAAGT
1 ATAAAAAATTATAAAAATATAAAAAAAT
*
33719477 CATAAGAAAATTATACAAAATATAAAGAAAT
1 -ATAA-AAAATTATA-AAAATATAAAAAAAT
33719508 ATAAAA
1 ATAAAA
33719514 TTCGTAAAAA
Statistics
Matches: 93, Mismatches: 18, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
26 5 0.05
27 15 0.16
28 31 0.33
29 29 0.31
30 9 0.10
31 4 0.04
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (28 bp):
ATAAAAAATTATAAAAATATAAAAAAAT
Found at i:33719427 original size:38 final size:38
Alignment explanation
Indices: 33719366--33719538 Score: 133
Period size: 38 Copynumber: 4.6 Consensus size: 38
33719356 TTAAATTTTA
*
33719366 ATAAAAAATTATTAAAAA-T-TAAAAAAATATAAAAATC
1 ATAAAAAA-TATAAAAAATTATAAAAAAATATAAAAATC
* *
33719403 ATAAAAAATATAAAAAATTGTAAAAAATTATAAAATAT-
1 ATAAAAAATATAAAAAATTATAAAAAAATATAAAA-ATC
* *** *
33719441 ATAGAAAAAT-TATAAAATTATAAAATTCTAT-AAAGTC
1 ATA-AAAAATATAAAAAATTATAAAAAAATATAAAAATC
* * *
33719478 ATAAGAAAATTATACAAAA-TATAAAGAAATATAAAATTC
1 ATAA-AAAA-TATAAAAAATTATAAAAAAATATAAAAATC
* *
33719517 GTAAAAAATTTATAAAAATTAT
1 ATAAAAAATATA-AAAAATTAT
33719539 TGTACCAAAA
Statistics
Matches: 108, Mismatches: 17, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
36 10 0.09
37 22 0.20
38 51 0.47
39 25 0.23
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (38 bp):
ATAAAAAATATAAAAAATTATAAAAAAATATAAAAATC
Found at i:33719840 original size:21 final size:20
Alignment explanation
Indices: 33719808--33719859 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
33719798 TTTTAATAAA
* *
33719808 TTTTAAATTTTAAATATTTT
1 TTTTAAAATTTAAATAATTT
33719828 TTATTAAAATTT-AATAATTT
1 TT-TTAAAATTTAAATAATTT
*
33719848 TTCTAAAATTTA
1 TTTTAAAATTTA
33719860 TTTTTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 8 0.30
20 11 0.41
21 8 0.30
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTAAAATTTAAATAATTT
Found at i:33724179 original size:21 final size:21
Alignment explanation
Indices: 33724155--33724205 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
33724145 GAGATAATAT
*
33724155 TACCGATACAAGT-GTGACTTC
1 TACCGATACAAGTCATG-CTTC
* *
33724176 TACCGAAACATGTCATGCTTC
1 TACCGATACAAGTCATGCTTC
33724197 TACCGATAC
1 TACCGATAC
33724206 TAAAAACTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (21 bp):
TACCGATACAAGTCATGCTTC
Found at i:33725227 original size:24 final size:24
Alignment explanation
Indices: 33725200--33725251 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
33725190 CGTAAAAGAT
33725200 TCATATACTCACAATGACACATAG
1 TCATATACTCACAATGACACATAG
33725224 TCATATACTCACAATGACACATAG
1 TCATATACTCACAATGACACATAG
33725248 TCAT
1 TCAT
33725252 CGAATCTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.27
Consensus pattern (24 bp):
TCATATACTCACAATGACACATAG
Found at i:33725277 original size:76 final size:76
Alignment explanation
Indices: 33725148--33725303 Score: 249
Period size: 76 Copynumber: 2.1 Consensus size: 76
33725138 GTAAAAGGAT
* * * *
33725148 TCATATGCTCACGATAACACATAGTCATTGGACCTCATAATCCGTAAAAGATTCATATACTCACA
1 TCATATACTCACAATAACACATAGTCATCGAACCTCATAATCCGTAAAAGATTCATATACTCACA
33725213 ATGACACATAG
66 ATGACACATAG
* * *
33725224 TCATATACTCACAATGACACATAGTCATCGAATCTCATAATCCGTAAAGGATTCATATACTCACA
1 TCATATACTCACAATAACACATAGTCATCGAACCTCATAATCCGTAAAAGATTCATATACTCACA
33725289 ATGACACATAG
66 ATGACACATAG
33725300 TCAT
1 TCAT
33725304 TGAACCTCAT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (76 bp):
TCATATACTCACAATAACACATAGTCATCGAACCTCATAATCCGTAAAAGATTCATATACTCACA
ATGACACATAG
Found at i:33725302 original size:52 final size:51
Alignment explanation
Indices: 33725224--33725413 Score: 274
Period size: 52 Copynumber: 3.7 Consensus size: 51
33725214 TGACACATAG
*
33725224 TCATATACTCACAATGACACATAGTCATCGAATCTCATAATCCGTAAAGGAT
1 TCATATACTCACAATGACACATAGTCATCGAACCTCATAATCC-TAAAGGAT
*
33725276 TCATATACTCACAATGACACATAGTCATTGAACCTCATAATCCATAAAGGAT
1 TCATATACTCACAATGACACATAGTCATCGAACCTCATAATCC-TAAAGGAT
** * *
33725328 TCATATACTCATGATGACACATAGTCAT-TAGACCTCATAATCCTAAAAGAT
1 TCATATACTCACAATGACACATAGTCATCGA-ACCTCATAATCCTAAAGGAT
* *
33725379 TCATATACTCACGATGACACATAGTCATCGGACCT
1 TCATATACTCACAATGACACATAGTCATCGAACCT
33725414 TTTTGCATTT
Statistics
Matches: 126, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
51 39 0.31
52 87 0.69
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (51 bp):
TCATATACTCACAATGACACATAGTCATCGAACCTCATAATCCTAAAGGAT
Found at i:33725329 original size:128 final size:128
Alignment explanation
Indices: 33725100--33725355 Score: 372
Period size: 128 Copynumber: 2.0 Consensus size: 128
33725090 TTCCCATTTA
* * * *
33725100 ATACTCACAATGACACAAAGTTATCAGACCTTAAATCCGTAAAAGGATTCATATGCTCACGATAA
1 ATACTCACAATGACACAAAGTCATCAGACCTCAAATCCGTAAAAGGATTCATATACTCACAATAA
* *
33725165 CACATAGTCATTGGACCTCATAATCCGTAAAAGATTCATATACTCACAATGACACATAGTCAT
66 CACATAGTCATTGAACCTCATAATCCATAAAAGATTCATATACTCACAATGACACATAGTCAT
* *
33725228 ATACTCACAATGACACATAGTCATC-GAATCTCATAATCCGT-AAAGGATTCATATACTCACAAT
1 ATACTCACAATGACACAAAGTCATCAG-ACCTCA-AATCCGTAAAAGGATTCATATACTCACAAT
* * **
33725291 GACACATAGTCATTGAACCTCATAATCCATAAAGGATTCATATACTCATGATGACACATAGTCAT
64 AACACATAGTCATTGAACCTCATAATCCATAAAAGATTCATATACTCACAATGACACATAGTCAT
33725356 TAGACCTCAT
Statistics
Matches: 114, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
127 1 0.01
128 106 0.93
129 7 0.06
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (128 bp):
ATACTCACAATGACACAAAGTCATCAGACCTCAAATCCGTAAAAGGATTCATATACTCACAATAA
CACATAGTCATTGAACCTCATAATCCATAAAAGATTCATATACTCACAATGACACATAGTCAT
Found at i:33725338 original size:26 final size:26
Alignment explanation
Indices: 33725257--33725339 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
33725247 GTCATCGAAT
*
33725257 CTCATAATCCGTAAAGGATTCATATA
1 CTCATAATCCATAAAGGATTCATATA
* * * * * * *
33725283 CTCACAATGACACATAGTCATTGA-A-C
1 CTCATAAT-CCATAAAG-GATTCATATA
33725309 CTCATAATCCATAAAGGATTCATATA
1 CTCATAATCCATAAAGGATTCATATA
33725335 CTCAT
1 CTCAT
33725340 GATGACACAT
Statistics
Matches: 38, Mismatches: 15, Indels: 8
0.62 0.25 0.13
Matches are distributed among these distances:
24 4 0.11
25 6 0.16
26 19 0.50
27 5 0.13
28 4 0.11
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (26 bp):
CTCATAATCCATAAAGGATTCATATA
Found at i:33733986 original size:38 final size:37
Alignment explanation
Indices: 33733943--33734016 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 37
33733933 AAATAATAAT
33733943 AATTTCATATATATATATA-TATATATATTAT-TAAATTA
1 AATTTCATAT-T-T-TATACTATATATATTATATAAATTA
*
33733981 AATTTCATATTTTATACTATTTATATTATATAAATT
1 AATTTCATATTTTATACTATATATATTATATAAATT
33734017 TATGATAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
35 4 0.12
36 12 0.36
37 7 0.21
38 10 0.30
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (37 bp):
AATTTCATATTTTATACTATATATATTATATAAATTA
Found at i:33734612 original size:23 final size:23
Alignment explanation
Indices: 33734586--33734696 Score: 80
Period size: 23 Copynumber: 4.8 Consensus size: 23
33734576 TTAATGTTCA
**
33734586 CGAACATGCTCATTTAAC-TTAAT
1 CGAACATGCTCA-CGAACATTAAT
*
33734609 CGAACATGTTCACGAACATTAAT
1 CGAACATGCTCACGAACATTAAT
* ** *
33734632 CGAACATGTTCACGAATTTTAAA
1 CGAACATGCTCACGAACATTAAT
* *
33734655 CGAACATGTTCATGAACATATAAT
1 CGAACATGCTCACGAACAT-TAAT
* * * *
33734679 TGAAAACGTTCACGAACA
1 CGAACATGCTCACGAACA
33734697 ATATTAATGA
Statistics
Matches: 72, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
22 3 0.04
23 52 0.72
24 17 0.24
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.28
Consensus pattern (23 bp):
CGAACATGCTCACGAACATTAAT
Found at i:33734659 original size:46 final size:47
Alignment explanation
Indices: 33734604--33734694 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 47
33734594 CTCATTTAAC
* * *
33734604 TTAATCGAACATGTTCACGAACAT-TAATCGAACATGTTCACGAATT
1 TTAAACGAACATGTTCACGAACATATAATCGAAAACGTTCACGAATT
* *
33734650 TTAAACGAACATGTTCATGAACATATAATTGAAAACGTTCACGAA
1 TTAAACGAACATGTTCACGAACATATAATCGAAAACGTTCACGAA
33734695 CAATATTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
46 22 0.56
47 17 0.44
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.29
Consensus pattern (47 bp):
TTAAACGAACATGTTCACGAACATATAATCGAAAACGTTCACGAATT
Found at i:33734847 original size:24 final size:24
Alignment explanation
Indices: 33734794--33734862 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 24
33734784 ATCATTAATA
***
33734794 AATAAACGAAC-TATAAA-GAGTT
1 AATAAACGAACTTATAAACGAACC
* *
33734816 AATAAACGAGCTTATAAATGAACC
1 AATAAACGAACTTATAAACGAACC
*
33734840 AATAAACGAACTTTTAAACGAAC
1 AATAAACGAACTTATAAACGAAC
33734863 TTATTCGTGA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 10 0.26
23 6 0.16
24 22 0.58
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.22
Consensus pattern (24 bp):
AATAAACGAACTTATAAACGAACC
Found at i:33740564 original size:131 final size:131
Alignment explanation
Indices: 33740327--33740583 Score: 372
Period size: 131 Copynumber: 2.0 Consensus size: 131
33740317 ATTTAGGTTG
*
33740327 CGATCTTAAATAAGCGAGTCTTAATGACATCAATTACGATATTAAATCAATAAATTATTTCAAGC
1 CGATCTTAAATAAGCGAGTCTTAATGACATCAATTACGATATTAAATCAACAAATTATTTCAAGC
* * * *
33740392 AGCGACATTAAATCAATTAATTCAGATAAAATTGTTTATGATATTAAATCGAATGAACTTAGATC
66 AGCGACATTAAATCAACTAACTCAAATAAAATTGTTCATGATATTAAATCGAATGAACTTAGATC
33740457 A
131 A
* * * * * **
33740458 CGATCTTAAATCAA-CGAGTCTTAATGATATCAATTACGATTTTAAATCAACGAGTTGTTTGGAG
1 CGATCTTAAAT-AAGCGAGTCTTAATGACATCAATTACGATATTAAATCAACAAATTATTTCAAG
* *
33740522 CAGCGATATTAAATCACCTAACTCAAATAAAATTGTTCATGATATTAAATCGAATGAACTTA
65 CAGCGACATTAAATCAACTAACTCAAATAAAATTGTTCATGATATTAAATCGAATGAACTTA
33740584 AGCTGCGATA
Statistics
Matches: 111, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
131 109 0.98
132 2 0.02
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (131 bp):
CGATCTTAAATAAGCGAGTCTTAATGACATCAATTACGATATTAAATCAACAAATTATTTCAAGC
AGCGACATTAAATCAACTAACTCAAATAAAATTGTTCATGATATTAAATCGAATGAACTTAGATC
A
Found at i:33740625 original size:95 final size:95
Alignment explanation
Indices: 33740494--33740666 Score: 276
Period size: 95 Copynumber: 1.8 Consensus size: 95
33740484 ATATCAATTA
* *
33740494 CGATTTTAAATCAACGAGTTGTTTGGAGCAGCGATATTAAATCACCTAACTCAAATAAAATTGTT
1 CGATATTAAATCAACGAGTTGTTTGAAGCAGCGATATTAAATCACCTAACTCAAATAAAATTGTT
33740559 CATGATATTAAATCGAATGAACTTAAGCTG
66 CATGATATTAAATCGAATGAACTTAAGCTG
* * * *
33740589 CGATATTAAATCAGA-GAGTTGTTTGAAGTAGTGATATTAAATCAGCTAACTCAAGTAAAATTGT
1 CGATATTAAATCA-ACGAGTTGTTTGAAGCAGCGATATTAAATCACCTAACTCAAATAAAATTGT
33740653 TCATGATATTAAAT
65 TCATGATATTAAAT
33740667 ATCTTAAATG
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
95 70 0.99
96 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (95 bp):
CGATATTAAATCAACGAGTTGTTTGAAGCAGCGATATTAAATCACCTAACTCAAATAAAATTGTT
CATGATATTAAATCGAATGAACTTAAGCTG
Found at i:33740966 original size:131 final size:129
Alignment explanation
Indices: 33740686--33741071 Score: 434
Period size: 131 Copynumber: 3.0 Consensus size: 129
33740676 GAGTGAGCTA
* * * * *
33740686 TTTGGAGCAGGAACATTAAATTAACTAATTCAAATAAAATTGTTAATGATACTAAATCGAATGAA
1 TTTGGAGCA-GAACATTAAATCAACTAACTCAGATAAAATTGTTCATGATATTAAATC-AATGAA
* * * * * * * * * * *
33740751 CTT-GATTGCGATCTTAAAACACCGAACTTTAATGATATCGGTTGTGATCTTAAATTAGCGAGTT
64 CTTAGACTGCGATATTAAATCAACGAACTTTAATGATATCAGCTGCGATATTAAATCAACAAGTT
33740815 C
129 C
* *
33740816 TTTGAAGCAGAGACATTAAATCAACTAACTCAGGTAAAATTGTTCATGATATTAAATCAACTGAA
1 TTTGGAGCAGA-ACATTAAATCAACTAACTCAGATAAAATTGTTCATGATATTAAATCAA-TGAA
* * * *
33740881 CTTAGACTACGATATTAAATCAACGAACTTTAATGATATCAACTGCAATTTTAAATCAACAAGTT
64 CTTAGACTGCGATATTAAATCAACGAACTTTAATGATATCAGCTGCGATATTAAATCAACAAGTT
*
33740946 G
129 C
* *
33740947 TTTGGAGCAGCAATATTAAATCAACTAACTCAGATAAAATTGTTCATGATATTAAATTGAATGAA
1 TTTGGAGCAG-AACATTAAATCAACTAACTCAGATAAAATTGTTCATGATATTAAA-TCAATGAA
* * **
33741012 CTTA-AGCTGTGATATTAAATCAGCGAGTTTTAATGATATCAGCTGCGATATTAAATCAAC
64 CTTAGA-CTGCGATATTAAATCAACGAACTTTAATGATATCAGCTGCGATATTAAATCAAC
33741072 GAGCTTTAAA
Statistics
Matches: 216, Mismatches: 34, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
129 4 0.02
130 56 0.26
131 152 0.70
132 4 0.02
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.32
Consensus pattern (129 bp):
TTTGGAGCAGAACATTAAATCAACTAACTCAGATAAAATTGTTCATGATATTAAATCAATGAACT
TAGACTGCGATATTAAATCAACGAACTTTAATGATATCAGCTGCGATATTAAATCAACAAGTTC
Found at i:33746635 original size:25 final size:25
Alignment explanation
Indices: 33746607--33746656 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
33746597 TTTGTACTAA
33746607 AAAAATAAGTTAATTTCGAAATGAC
1 AAAAATAAGTTAATTTCGAAATGAC
33746632 AAAAATAAGTTAATTTCGAAATGAC
1 AAAAATAAGTTAATTTCGAAATGAC
33746657 CTGATTATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (25 bp):
AAAAATAAGTTAATTTCGAAATGAC
Found at i:33756015 original size:25 final size:23
Alignment explanation
Indices: 33755974--33756019 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
33755964 CTAATTAGGG
33755974 AATTATTGTTTAGATTTAATTAT
1 AATTATTGTTTAGATTTAATTAT
*
33755997 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
33756020 TGGATTCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.57
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTAT
Done.