Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, whole genome shotgun sequence
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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 99 of 113
Found at i:19886406 original size:82 final size:84
Alignment explanation
Indices: 19886260--19886424 Score: 217
Period size: 82 Copynumber: 2.0 Consensus size: 84
19886250 CTAAAATAAG
* * * * * * ** *
19886260 ATCAAATTTTAAAAATCTCTAAATTGGGATTAAGTTCCAAGAATCCCTAAATTGGGATCAAATTT
1 ATCAAATTTCAAAAATCTCTAAATTAGGATAAAATTCCAAAAATCACTAAATTGAAACCAAATTT
19886325 CAAGAATCCCTAAATTGGA
66 CAAGAATCCCTAAATTGGA
*
19886344 ATCAAATTTCAAGAA-CT-TAAATTAGGATAAAATTCCAAAAATCACTAAATTGAAACCAAATTT
1 ATCAAATTTCAAAAATCTCTAAATTAGGATAAAATTCCAAAAATCACTAAATTGAAACCAAATTT
*
19886407 CAAGAATCCTTAAATTGG
66 CAAGAATCCCTAAATTGG
19886425 GGCTAAGTTC
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
82 55 0.79
83 2 0.03
84 13 0.19
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (84 bp):
ATCAAATTTCAAAAATCTCTAAATTAGGATAAAATTCCAAAAATCACTAAATTGAAACCAAATTT
CAAGAATCCCTAAATTGGA
Found at i:19890323 original size:113 final size:113
Alignment explanation
Indices: 19890197--19890460 Score: 264
Period size: 113 Copynumber: 2.3 Consensus size: 113
19890187 AAGATGAACA
*
19890197 ATCTAAAGAACAAAGTGTCTAAAATTCCAACAAACAAATTCAATAAGACAATTG-AGGAAAAGA-
1 ATCTAAAGAACAAAGTGTCTAAAATTCCAACAAAC-AATTCAAGAAGACAATTGAAGGAAAAGAT
* * * ** *
19890260 AGATTTGAAGATTCAAACTCTCCAAAACTGTCATAAGTTCAAGAAGGTAT
65 A-ATTTGAAAAATCAAAATCTCCAAAACTCACACAAGTTCAAGAAGGTAT
* * * * * * * *
19890310 ATCTGAAGAACAAAGTTTTTAGAGTTCCAACAAACAATTCAAGATGCCAATTGAAGGAAGAGATA
1 ATCTAAAGAACAAAGTGTCTAAAATTCCAACAAACAATTCAAGAAGACAATTGAAGGAAAAGATA
* *** *
19890375 ATTTGAAAAATCAAAATCTCCAAAGCTCACACAAGTTCAAGACAAAAAAA
66 ATTTGAAAAATCAAAATCTCCAAAACTCACACAAGTTCAAG--AAGGTAT
* * *
19890425 ATCTAAA-AACAAAGTTTTTAAAATTTCAACAAACAA
1 ATCTAAAGAACAAAGTGTCTAAAATTCCAACAAACAA
19890461 ATCTAAAACG
Statistics
Matches: 123, Mismatches: 24, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
112 15 0.12
113 72 0.59
114 27 0.22
115 9 0.07
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.23
Consensus pattern (113 bp):
ATCTAAAGAACAAAGTGTCTAAAATTCCAACAAACAATTCAAGAAGACAATTGAAGGAAAAGATA
ATTTGAAAAATCAAAATCTCCAAAACTCACACAAGTTCAAGAAGGTAT
Found at i:19890532 original size:28 final size:28
Alignment explanation
Indices: 19890500--19890625 Score: 132
Period size: 28 Copynumber: 4.6 Consensus size: 28
19890490 ACTGAATATC
19890500 CAAAAATCCCTAAATTGAGA-CTAAATTT
1 CAAAAATCCCTAAATTGAGATC-AAATTT
*
19890528 CAAAAATCCCTAAATTAAGATCAAATTT
1 CAAAAATCCCTAAATTGAGATCAAATTT
* * *
19890556 -AAAAATTCTTAAATTGACATCAAATTT
1 CAAAAATCCCTAAATTGAGATCAAATTT
* * * *
19890583 TAAGAATCCTTAAATTGGGATCAAATTT
1 CAAAAATCCCTAAATTGAGATCAAATTT
* *
19890611 TAAAAA-CTCTAAATT
1 CAAAAATCCCTAAATT
19890626 AAGGCCAAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
27 30 0.36
28 53 0.63
29 1 0.01
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (28 bp):
CAAAAATCCCTAAATTGAGATCAAATTT
Found at i:19890569 original size:55 final size:55
Alignment explanation
Indices: 19890509--19890625 Score: 139
Period size: 55 Copynumber: 2.1 Consensus size: 55
19890499 CCAAAAATCC
*
19890509 CTAAATTGAGA-CTAAATTTCAAAAATCCCTAAATTAAGATCAAA-TTTAAAAATT
1 CTAAATTGACATC-AAATTTCAAAAATCCCTAAATTAAGATCAAATTTTAAAAATT
* * * ** *
19890563 CTTAAATTGACATCAAATTTTAAGAATCCTTAAATTGGGATCAAATTTTAAAAACT
1 C-TAAATTGACATCAAATTTCAAAAATCCCTAAATTAAGATCAAATTTTAAAAATT
19890619 CTAAATT
1 CTAAATT
19890626 AAGGCCAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
54 1 0.02
55 41 0.77
56 11 0.21
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (55 bp):
CTAAATTGACATCAAATTTCAAAAATCCCTAAATTAAGATCAAATTTTAAAAATT
Found at i:19890635 original size:55 final size:55
Alignment explanation
Indices: 19890522--19890644 Score: 133
Period size: 55 Copynumber: 2.3 Consensus size: 55
19890512 AATTGAGACT
* * * *
19890522 AAATTTCAAAAATCCCTAAATTAAGATCAAATTTAAAAATTCTTAAATTGACATC
1 AAATTTCAAGAATCCCTAAATTAAGATCAAATTTAAAAACTCTTAAATTAACACC
* * ** **
19890577 AAATTTTAAGAATCCTTAAATTGGGATCAAATTTTAAAAACTC-TAAATTAAGGCC
1 AAATTTCAAGAATCCCTAAATTAAGATCAAA-TTTAAAAACTCTTAAATTAACACC
19890632 AAA-TTCAAGAATC
1 AAATTTCAAGAATC
19890645 TTTAGGGACC
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
54 9 0.16
55 37 0.66
56 10 0.18
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.32
Consensus pattern (55 bp):
AAATTTCAAGAATCCCTAAATTAAGATCAAATTTAAAAACTCTTAAATTAACACC
Found at i:19894948 original size:2 final size:2
Alignment explanation
Indices: 19894941--19894978 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
19894931 AAATTTCATC
19894941 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
19894979 GGGTAATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 32 0.94
3 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:19895185 original size:50 final size:50
Alignment explanation
Indices: 19895110--19895210 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
19895100 GAACCATTTC
*
19895110 TAGTGCCCTTATTAATTATTAGACTTGCTAACACGAAGCACTTTGTTGCT
1 TAGTGCCCTTATTAATTACTAGACTTGCTAACACGAAGCACTTTGTTGCT
19895160 TAGTGCCCTTATTAATTACTAGACTTGCTAACACGAAGCACTTTGTTGCT
1 TAGTGCCCTTATTAATTACTAGACTTGCTAACACGAAGCACTTTGTTGCT
19895210 T
1 T
19895211 CTGTTGAAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (50 bp):
TAGTGCCCTTATTAATTACTAGACTTGCTAACACGAAGCACTTTGTTGCT
Found at i:19897276 original size:2 final size:2
Alignment explanation
Indices: 19897269--19897294 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19897259 AAGCAGGCTG
19897269 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
19897295 AGGGAGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:19899960 original size:11 final size:11
Alignment explanation
Indices: 19899938--19899969 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
19899928 TATAATAAAT
19899938 AAAATTTA-AA
1 AAAATTTAGAA
19899948 AAAATTTAGAA
1 AAAATTTAGAA
19899959 AAAATTT-GAA
1 AAAATTTAGAA
19899969 A
1 A
19899970 TATTAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (11 bp):
AAAATTTAGAA
Found at i:19900652 original size:30 final size:29
Alignment explanation
Indices: 19900586--19900652 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
19900576 ATGATATTTT
*
19900586 TAAATTTAAAAATATTAAAAATTCAAAAAA
1 TAAA-TTAAAAATAATAAAAATTCAAAAAA
*
19900616 TGAAATTAAAAA-AATAAAATATTGAAAAAA
1 T-AAATTAAAAATAATAAAA-ATTCAAAAAA
19900646 GTAAATT
1 -TAAATT
19900653 TATTTTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 6 0.19
30 22 0.69
31 4 0.12
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.28
Consensus pattern (29 bp):
TAAATTAAAAATAATAAAAATTCAAAAAA
Found at i:19906079 original size:31 final size:31
Alignment explanation
Indices: 19906044--19906115 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
19906034 AATCATTAGA
* *
19906044 ACTTGATAGGGATCACCACAGCACTGATACC
1 ACTTGTTAGGGATAACCACAGCACTGATACC
* * * *
19906075 ACTTGTTAGAGATAACCATAGCTCTGATATC
1 ACTTGTTAGGGATAACCACAGCACTGATACC
19906106 ACTTGTTAGG
1 ACTTGTTAGG
19906116 CTAAAAGCCT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (31 bp):
ACTTGTTAGGGATAACCACAGCACTGATACC
Found at i:19908600 original size:64 final size:64
Alignment explanation
Indices: 19908532--19908778 Score: 191
Period size: 63 Copynumber: 3.9 Consensus size: 64
19908522 GAGTGACCGA
* * *
19908532 GAATGAACTACAAGTTTAAAAATAAAATGATCTAAACTGAGCCGAGATCAAAATAAGCAACTAG
1 GAATGAACTACAAGTTTAAAAATAAAATGATCTAGACTGAGCCAAGATCAAAATGAGCAACTAG
* * * * * * *
19908596 GAATGAGC--CAAATATTTAAAATGAAATGATCTAGACTGAACCAATATC-AAATGAGCGACTAG
1 GAATGAACTACAAGT-TTAAAAATAAAATGATCTAGACTGAGCCAAGATCAAAATGAGCAACTAG
* * * *
19908658 GAAT-AAATCACAGGTCTAAAAATAAAATGATCTAGA-TCGAGCCAAGATTAAAATGAGCAACT-
1 GAATGAACT-ACAAGTTTAAAAATAAAATGATCTAGACT-GAGCCAAGATCAAAATGAGCAACTA
19908720 G
64 G
* * * * * ** * * *
19908721 AGAATAAACAATATGTTTGAAAGCAAACATTATCTTGACTAAGCCAAGATCAAAATGA
1 -GAATGAACTACAAGTTTAAAAATAAA-ATGATCTAGACTGAGCCAAGATCAAAATGA
19908779 ATGATCGAGA
Statistics
Matches: 140, Mismatches: 33, Indels: 19
0.73 0.17 0.10
Matches are distributed among these distances:
61 1 0.01
62 21 0.15
63 55 0.39
64 36 0.26
65 26 0.19
66 1 0.01
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.22
Consensus pattern (64 bp):
GAATGAACTACAAGTTTAAAAATAAAATGATCTAGACTGAGCCAAGATCAAAATGAGCAACTAG
Found at i:19908808 original size:65 final size:65
Alignment explanation
Indices: 19908698--19908862 Score: 163
Period size: 65 Copynumber: 2.5 Consensus size: 65
19908688 TCTAGATCGA
* * * * * * * * *
19908698 GCCAAGATTAAAATGAGCA-ACTGAGAATAAACAATATGTTTGAAAGCAAACATTATCTTGACTA
1 GCCAAGATCAAAATGA-AAGACCGAGAATGAACCATAAGTTCGAAAGCAAACATGATCTGGAC-A
19908762 A-
64 AC
* *
19908763 GCCAAGATCAAAATGAATGATCGAGAATGAACCATAAGTTCGAAAGCAAACATGATCTGGACAAC
1 GCCAAGATCAAAATGAAAGACCGAGAATGAACCATAAGTTCGAAAGCAAACATGATCTGGACAAC
* * * *
19908828 GTCGAGATCAAAATGAAAGACCAAGATTGAACCAT
1 GCCAAGATCAAAATGAAAGACCGAGAATGAACCAT
19908863 GGGTAAAAAA
Statistics
Matches: 81, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
64 2 0.02
65 79 0.98
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.20
Consensus pattern (65 bp):
GCCAAGATCAAAATGAAAGACCGAGAATGAACCATAAGTTCGAAAGCAAACATGATCTGGACAAC
Found at i:19913717 original size:16 final size:17
Alignment explanation
Indices: 19913696--19913727 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
19913686 TCCTCTACCA
19913696 TTATCTCTCA-TCCTCT
1 TTATCTCTCATTCCTCT
19913712 TTATCTCTCATTCCTC
1 TTATCTCTCATTCCTC
19913728 AACTTCATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.12, C:0.38, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATCTCTCATTCCTCT
Found at i:19922816 original size:32 final size:32
Alignment explanation
Indices: 19922759--19922855 Score: 117
Period size: 32 Copynumber: 3.1 Consensus size: 32
19922749 ACAAACTTGC
* *
19922759 CTATCAAGAATC-ATTTTCTCCTAGAATTC-T
1 CTATCAAGAATCTCTTTTCTCTTAGAATTCTT
* *
19922789 CTTATCAAGAATTTTTTTTCTCTTAGAATTCTT
1 C-TATCAAGAATCTCTTTTCTCTTAGAATTCTT
* *
19922822 CTATCAAGAATCTCTTTCCTTTTAGAATTCTT
1 CTATCAAGAATCTCTTTTCTCTTAGAATTCTT
19922854 CT
1 CT
19922856 TTTACACATT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
30 1 0.02
31 10 0.18
32 44 0.77
33 2 0.04
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.47
Consensus pattern (32 bp):
CTATCAAGAATCTCTTTTCTCTTAGAATTCTT
Found at i:19923620 original size:17 final size:17
Alignment explanation
Indices: 19923600--19923655 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
19923590 TTAAGAATCT
19923600 TTTTTCTCTTAGAATTC
1 TTTTTCTCTTAGAATTC
* *
19923617 -TTTTATC-AAGAA-TC
1 TTTTTCTCTTAGAATTC
19923631 TATTTTCTCTTAGAATTC
1 T-TTTTCTCTTAGAATTC
*
19923649 TTCTTCT
1 TTTTTCT
19923656 GTAAGTTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 2 0.07
15 4 0.13
16 12 0.40
17 9 0.30
18 3 0.10
ACGTcount: A:0.21, C:0.18, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTTTCTCTTAGAATTC
Found at i:19923650 original size:32 final size:32
Alignment explanation
Indices: 19923555--19923650 Score: 138
Period size: 32 Copynumber: 3.0 Consensus size: 32
19923545 ACAAACTTAC
* * *
19923555 TTATCAAGAATTTTTTTTCTCTTAAAATTCTC
1 TTATCAAGAATCTTTTTTCTCTTAGAATTCTT
* *
19923587 CTATTAAGAATCTTTTTTCTCTTAGAATTCTT
1 TTATCAAGAATCTTTTTTCTCTTAGAATTCTT
*
19923619 TTATCAAGAATCTATTTTCTCTTAGAATTCTT
1 TTATCAAGAATCTTTTTTCTCTTAGAATTCTT
19923651 CTTCTGTAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.27, C:0.16, G:0.05, T:0.52
Consensus pattern (32 bp):
TTATCAAGAATCTTTTTTCTCTTAGAATTCTT
Found at i:19925000 original size:19 final size:18
Alignment explanation
Indices: 19924973--19925008 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19924963 TTGTCTTTTT
*
19924973 TTTTATCTTTTTTTTATG
1 TTTTATCTTTTATTTATG
19924991 TTTTAGTCTTTTATTTAT
1 TTTTA-TCTTTTATTTAT
19925009 CTAGTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.75
Consensus pattern (18 bp):
TTTTATCTTTTATTTATG
Found at i:19926094 original size:21 final size:21
Alignment explanation
Indices: 19926068--19926109 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
19926058 ATTTCTATGG
19926068 ATCTATGGATGTAATGGAGCT
1 ATCTATGGATGTAATGGAGCT
19926089 ATCTATGGATGTAATGGAGCT
1 ATCTATGGATGTAATGGAGCT
19926110 TTGCTGGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.33
Consensus pattern (21 bp):
ATCTATGGATGTAATGGAGCT
Found at i:19929041 original size:37 final size:37
Alignment explanation
Indices: 19928991--19929065 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 37
19928981 ATTAGTAAAG
* *
19928991 TCTCCTAATAGTTTGGTAAGAC-TTATTTTGAAAAAAA
1 TCTCCTAATAGTTTGATAAGACTTTATTGT-AAAAAAA
*
19929028 TCTCCTAATAGTTTGATGAGACTTTATTGTAAAAAAA
1 TCTCCTAATAGTTTGATAAGACTTTATTGTAAAAAAA
19929065 T
1 T
19929066 TAGGTAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 28 0.82
38 6 0.18
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (37 bp):
TCTCCTAATAGTTTGATAAGACTTTATTGTAAAAAAA
Found at i:19929181 original size:18 final size:19
Alignment explanation
Indices: 19929158--19929195 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
19929148 GAGGATAAAA
19929158 ATTATTTTT-TTATTTTTT
1 ATTATTTTTGTTATTTTTT
*
19929176 ATTATTTTTGTTTTTTTTT
1 ATTATTTTTGTTATTTTTT
19929195 A
1 A
19929196 CTTTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.82
Consensus pattern (19 bp):
ATTATTTTTGTTATTTTTT
Found at i:19929206 original size:17 final size:16
Alignment explanation
Indices: 19929159--19929209 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
19929149 AGGATAAAAA
19929159 TTATT-TTTTTATTTT
1 TTATTATTTTTATTTT
*
19929174 TTATTATTTTTGTTTT
1 TTATTATTTTTATTTT
* *
19929190 TTTTTACTTTTAATTTT
1 TTATTA-TTTTTATTTT
19929207 TTA
1 TTA
19929210 AAACTAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
15 5 0.17
16 14 0.48
17 10 0.34
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (16 bp):
TTATTATTTTTATTTT
Found at i:19929487 original size:21 final size:20
Alignment explanation
Indices: 19929451--19929501 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
19929441 AATACAAATG
*
19929451 AATAAAT-AAACCAATAAAA
1 AATAAATAAAACAAATAAAA
19929470 AATAAATGAAAACAAATAAAA
1 AATAAAT-AAAACAAATAAAA
19929491 AATAAATAAAA
1 AATAAATAAAA
19929502 TAAAATAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 7 0.24
20 4 0.14
21 18 0.62
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.16
Consensus pattern (20 bp):
AATAAATAAAACAAATAAAA
Found at i:19929492 original size:11 final size:11
Alignment explanation
Indices: 19929451--19929501 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
19929441 AATACAAATG
*
19929451 AATAAATAAACC
1 AATAAA-AAACA
*
19929463 AATAAAAAATA
1 AATAAAAAACA
*
19929474 AAT-GAAAACA
1 AATAAAAAACA
*
19929484 AATAAAAAATA
1 AATAAAAAACA
19929495 AATAAAA
1 AATAAAA
19929502 TAAAATAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
10 8 0.25
11 18 0.56
12 6 0.19
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.16
Consensus pattern (11 bp):
AATAAAAAACA
Found at i:19929507 original size:21 final size:21
Alignment explanation
Indices: 19929463--19929509 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
19929453 TAAATAAACC
*
19929463 AATAAAAAATAAATGAAAACA
1 AATAAAAAATAAATGAAAAAA
19929484 AATAAAAAATAAAT-AAAATAA
1 AATAAAAAATAAATGAAAA-AA
19929505 AATAA
1 AATAA
19929510 TTAAATGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (21 bp):
AATAAAAAATAAATGAAAAAA
Found at i:19929940 original size:21 final size:21
Alignment explanation
Indices: 19929914--19929960 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
19929904 AAAAACCTAG
19929914 ATTTCCTAAAAAAACACAAAA
1 ATTTCCTAAAAAAACACAAAA
19929935 ATTTCCTAAAAAAACACAAAA
1 ATTTCCTAAAAAAACACAAAA
19929956 ATTTC
1 ATTTC
19929961 TCAGATTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.57, C:0.19, G:0.00, T:0.23
Consensus pattern (21 bp):
ATTTCCTAAAAAAACACAAAA
Found at i:19930425 original size:15 final size:16
Alignment explanation
Indices: 19930396--19930459 Score: 60
Period size: 15 Copynumber: 4.1 Consensus size: 16
19930386 AAGAGAAAGA
19930396 AAAAAATAAAAATAAT
1 AAAAAATAAAAATAAT
*
19930412 AAAAAA-AAATATAAT
1 AAAAAATAAAAATAAT
** *
19930427 ACCAAATAATAATAAT
1 AAAAAATAAAAATAAT
* *
19930443 -AATAATAACAATAAT
1 AAAAAATAAAAATAAT
19930458 AA
1 AA
19930460 TAATAGTATA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
15 23 0.62
16 14 0.38
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAAATAAAAATAAT
Found at i:19930437 original size:3 final size:3
Alignment explanation
Indices: 19930431--19930565 Score: 94
Period size: 3 Copynumber: 48.0 Consensus size: 3
19930421 TATAATACCA
* *
19930431 AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AGT -AT AA- AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
19930476 AAT -AC AAT -AT TAT CCAT AGT ACT AAT AAT AAT AAT AAT -AT AA-
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
19930518 AAT -AT AAAT AAT AAT AAT -AT AAT -AT AAT -AT AAA AAT AAT ACT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19930560 AAT AAT
1 AAT AAT
19930566 TAAAATCGAT
Statistics
Matches: 104, Mismatches: 15, Indels: 26
0.72 0.10 0.18
Matches are distributed among these distances:
2 20 0.19
3 80 0.77
4 4 0.04
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19930527 original size:16 final size:16
Alignment explanation
Indices: 19930508--19930555 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
19930498 TAATAATAAT
19930508 AATAATATAAAATATA
1 AATAATATAAAATATA
*
19930524 AATAATA-ATAATATA
1 AATAATATAAAATATA
19930539 ATATAATATAAAA-ATA
1 A-ATAATATAAAATATA
19930555 A
1 A
19930556 TACTAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 8 0.29
16 17 0.61
17 3 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAATATAAAATATA
Found at i:19930770 original size:37 final size:37
Alignment explanation
Indices: 19930729--19930827 Score: 108
Period size: 37 Copynumber: 2.7 Consensus size: 37
19930719 CACAAGTCAA
* *
19930729 GAAAATGATCTGGACTGAGTTGAGACCAAATAGTTAG
1 GAAAATGATCTGGACTGAGCTGAGACCAAAGAGTTAG
* * ** * **
19930766 GAAAATTATCTGGATTGAGCCAAAATGAAAGAGTTAG
1 GAAAATGATCTGGACTGAGCTGAGACCAAAGAGTTAG
*
19930803 GAAAATGATTTGGACTGAGCTGAGA
1 GAAAATGATCTGGACTGAGCTGAGA
19930828 TCGAATGACT
Statistics
Matches: 47, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.39, C:0.09, G:0.27, T:0.24
Consensus pattern (37 bp):
GAAAATGATCTGGACTGAGCTGAGACCAAAGAGTTAG
Found at i:19931355 original size:121 final size:121
Alignment explanation
Indices: 19931212--19931469 Score: 270
Period size: 121 Copynumber: 2.1 Consensus size: 121
19931202 TGAAACTGCA
* * * * *
19931212 AGTCTAAAAGGAGAAA-CGACCAATACCAAGTTAAAGTC-GAAGATGAATGATCGGGAAAAAATC
1 AGTCTAAAA-GATAAAGCAACCAAGACCAAG-TAAAGGCTGAAAATGAATGATCGGGAAAAAATC
* * * ** * *
19931275 GTAAGTTAAAAAAATTATCTAGATTAAGTTGAGATCGAATAATCAAGACAAAA-TCGTG
64 GTAAGTTAAAAAAATAATCTAGACTAAATCAAGATCGAATAACCAAGACAAAACT-ATG
* * * * * ** *
19931333 AGTCTAAAAGATAAAGCAACCAAGATCGAGTCAAGGCTGAAAATGAATTATTGGGATGAAATCTT
1 AGTCTAAAAGATAAAGCAACCAAGACCAAGTAAAGGCTGAAAATGAATGATCGGGAAAAAATCGT
* *
19931398 AAGTTAAAAAAATAATCTAGACTAAATCAAGATTGAATGACCAAGACAAAACTATG
66 AAGTTAAAAAAATAATCTAGACTAAATCAAGATCGAATAACCAAGACAAAACTATG
19931454 AGTCTAAAAGATAAAG
1 AGTCTAAAAGATAAAG
19931470 TGACCATGAT
Statistics
Matches: 112, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
120 10 0.09
121 101 0.90
122 1 0.01
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.22
Consensus pattern (121 bp):
AGTCTAAAAGATAAAGCAACCAAGACCAAGTAAAGGCTGAAAATGAATGATCGGGAAAAAATCGT
AAGTTAAAAAAATAATCTAGACTAAATCAAGATCGAATAACCAAGACAAAACTATG
Found at i:19931481 original size:121 final size:122
Alignment explanation
Indices: 19931255--19931544 Score: 332
Period size: 121 Copynumber: 2.4 Consensus size: 122
19931245 AAGTCGAAGA
* * * * * * ** *
19931255 TGAATGATCGGGAAAAAATCGTAAGTTAAAAAAATTATCTAGATTAAGTTGAGATCGAATAATCA
1 TGAATGATTGGGATAAAATCATAAGTTAAAAAAATAATCTAGACTAAATCAAGATCGAATAACCA
* *
19931320 AGACAAAATCGTGAGTCTAAAAGATAAAGCAACCAAGATCGAGTCAAGGCTGAAAA-
66 AGACAAAATCATGAGTCTAAAAGATAAAGCAACCAAGATCGAGTCAAGGCTAAAAAG
* * * * *
19931376 TGAATTATTGGGATGAAATCTTAAGTTAAAAAAATAATCTAGACTAAATCAAGATTGAATGACCA
1 TGAATGATTGGGATAAAATCATAAGTTAAAAAAATAATCTAGACTAAATCAAGATCGAATAACCA
** * *
19931441 AGACAAAA-CTATGAGTCTAAAAGATAAAGTGACCATGATCGAGTCAAGGTTAAAAAG
66 AGACAAAATC-ATGAGTCTAAAAGATAAAGCAACCAAGATCGAGTCAAGGCTAAAAAG
* * * * *
19931498 TGAATGATTGGGATAAAATAATGAGTCAAAAAAACAATCTGGACTAA
1 TGAATGATTGGGATAAAATCATAAGTTAAAAAAATAATCTAGACTAA
19931545 GCCAAGATAA
Statistics
Matches: 140, Mismatches: 27, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
120 1 0.01
121 100 0.71
122 39 0.28
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (122 bp):
TGAATGATTGGGATAAAATCATAAGTTAAAAAAATAATCTAGACTAAATCAAGATCGAATAACCA
AGACAAAATCATGAGTCTAAAAGATAAAGCAACCAAGATCGAGTCAAGGCTAAAAAG
Found at i:19932548 original size:58 final size:58
Alignment explanation
Indices: 19932411--19932751 Score: 348
Period size: 58 Copynumber: 5.7 Consensus size: 58
19932401 TTCTGTATAG
* * ** *
19932411 GGAAAATTGATACTTTCAACTTTT-CTCCAAAGTATTTTTTAGAAATTTTAATTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTATTTTCAA
* * *
19932468 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCA-CTTTT-GAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAT--ATTTTTTAGAAAACTTATTTTCAA
* * * *
19932526 GGAAAATTGATACTTTCAACTTTTTCTCACAAATCTATTTTT-GAAAACTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATAT-TTTTTAGAAAACTTATTTTCAA
* *
19932584 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTAGAAAGCTTATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTATTTTCAA
* * *
19932642 GGAAAATTGATACTTTCATCTTTTCCTCAAAAATATATATATATATTTTTGAAAAAAACTTGTTT
1 GGAAAATTGATACTTTCAACTTTTCCTC----A-A-A-A-ATAT-TTTTT--AGAAAACTTATTT
19932707 TCAA
55 TCAA
* * *
19932711 GGAAAATTGAAACTTTCAACTTTTTCTTAAAAATATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
19932752 TGAATTTTAT
Statistics
Matches: 241, Mismatches: 26, Indels: 31
0.81 0.09 0.10
Matches are distributed among these distances:
57 29 0.12
58 143 0.59
59 4 0.02
60 6 0.02
61 4 0.02
62 2 0.01
63 2 0.01
64 2 0.01
65 2 0.01
66 4 0.02
67 5 0.02
69 38 0.16
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTATTTTCAA
Found at i:19933684 original size:44 final size:41
Alignment explanation
Indices: 19933636--19933793 Score: 126
Period size: 44 Copynumber: 3.7 Consensus size: 41
19933626 TAAAAAAGAT
19933636 AAATATATTAATAGATAACAAAAAAAATAATTATATAAATAAAA
1 AAATATATTAATAGATAACAAAAAAAA-AA-TA-ATAAATAAAA
* * * * *
19933680 AAATAGATAAATA-ATAATAAAAAAATAAAAGCAGATAAATAATA
1 AAATATATTAATAGATAA-CAAAAAA-AAAA-TA-ATAAATAAAA
*
19933724 AAA-ATATTAATAGATAA-AAAAATAAAATAA-AAATAAAA
1 AAATATATTAATAGATAACAAAAAAAAAATAATAAATAAAA
* *
19933762 ATATATATTAATAAATAGACAAATAATAAAAA
1 AAATATATTAATAGATA-ACAAA-AA-AAAAA
19933794 AAATGAAAAT
Statistics
Matches: 91, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
38 9 0.10
39 13 0.14
40 2 0.02
41 7 0.08
42 7 0.08
43 15 0.16
44 36 0.40
45 2 0.02
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (41 bp):
AAATATATTAATAGATAACAAAAAAAAAATAATAAATAAAA
Found at i:19933698 original size:22 final size:22
Alignment explanation
Indices: 19933624--19933708 Score: 91
Period size: 24 Copynumber: 3.6 Consensus size: 22
19933614 AATTAATCAA
19933624 AATAAAAAAGATAAATATATTAAT
1 AATAAAAAA-ATAAATA-ATTAAT
19933648 AGATAACAAAAA-AAATAATTATAT
1 A-ATAA-AAAAATAAATAATTA-AT
* *
19933672 AAATAAAAAAATAGATAAATAAT
1 -AATAAAAAAATAAATAATTAAT
19933695 AATAAAAAAATAAA
1 AATAAAAAAATAAA
19933709 AGCAGATAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
22 13 0.25
23 11 0.21
24 19 0.36
25 6 0.11
26 4 0.08
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.24
Consensus pattern (22 bp):
AATAAAAAAATAAATAATTAAT
Found at i:19933758 original size:23 final size:23
Alignment explanation
Indices: 19933678--19933758 Score: 56
Period size: 26 Copynumber: 3.3 Consensus size: 23
19933668 ATATAAATAA
19933678 AAAAATAGATAAATAATAATAAAA-
1 AAAAATAGATAAA-AA-AATAAAAT
* * *
19933702 AAATAAAAGCAGATAAATAATAAAAAT
1 AAA-AATAG-ATA-AAAAAAT-AAAAT
**
19933729 ATTAATAGATAAAAAAATAAAAT
1 AAAAATAGATAAAAAAATAAAAT
19933752 AAAAATA
1 AAAAATA
19933759 AAAATATATA
Statistics
Matches: 42, Mismatches: 10, Indels: 11
0.67 0.16 0.17
Matches are distributed among these distances:
23 10 0.24
24 9 0.21
25 9 0.21
26 11 0.26
27 3 0.07
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (23 bp):
AAAAATAGATAAAAAAATAAAAT
Found at i:19933762 original size:12 final size:12
Alignment explanation
Indices: 19933714--19933813 Score: 53
Period size: 12 Copynumber: 8.0 Consensus size: 12
19933704 ATAAAAGCAG
19933714 ATAAATAATAAAA
1 ATAAA-AATAAAA
** *
19933727 ATATTAATAGATA
1 ATAAAAATA-AAA
19933740 A-AAAAAT-AAA
1 ATAAAAATAAAA
19933750 ATAAAAATAAAA
1 ATAAAAATAAAA
* *
19933762 ATATATATTAATAA
1 ATA-AAAATAA-AA
19933776 ATAGACAAATAATAA
1 ATA-A-AAATAA-AA
*
19933791 A-AAAAATGAAA
1 ATAAAAATAAAA
*
19933802 ATAAACATAAAA
1 ATAAAAATAAAA
19933814 GCCTATTGGG
Statistics
Matches: 66, Mismatches: 14, Indels: 15
0.69 0.15 0.16
Matches are distributed among these distances:
10 3 0.05
11 9 0.14
12 27 0.41
13 12 0.18
14 7 0.11
15 8 0.12
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (12 bp):
ATAAAAATAAAA
Found at i:19934227 original size:10 final size:10
Alignment explanation
Indices: 19934212--19934247 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
19934202 CTAAGTCTCC
19934212 CTTTTTTTTT
1 CTTTTTTTTT
19934222 C-TTTTTTTT
1 CTTTTTTTTT
*
19934231 CTCTTTTTTT
1 CTTTTTTTTT
19934241 CTTTTTT
1 CTTTTTT
19934248 CACTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:19934228 original size:9 final size:9
Alignment explanation
Indices: 19934214--19934267 Score: 65
Period size: 9 Copynumber: 5.9 Consensus size: 9
19934204 AAGTCTCCCT
19934214 TTTTTTTTC
1 TTTTTTTTC
19934223 TTTTTTTTC
1 TTTTTTTTC
19934232 TCTTTTTTTC
1 T-TTTTTTTC
**
19934242 TTTTTTCAC
1 TTTTTTTTC
19934251 TTTTTTTT-
1 TTTTTTTTC
19934259 TTATTTTTT
1 TT-TTTTTT
19934268 AAAACTTTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
8 2 0.05
9 28 0.72
10 9 0.23
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:19934256 original size:19 final size:19
Alignment explanation
Indices: 19934212--19934259 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
19934202 CTAAGTCTCC
**
19934212 CTTTTTTTTTCTTTTTTTT
1 CTTTTTTTTTCTTTTTTCA
*
19934231 CTCTTTTTTTCTTTTTTCA
1 CTTTTTTTTTCTTTTTTCA
19934250 CTTTTTTTTT
1 CTTTTTTTTT
19934260 TATTTTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (19 bp):
CTTTTTTTTTCTTTTTTCA
Found at i:19934605 original size:22 final size:19
Alignment explanation
Indices: 19934575--19934625 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 19
19934565 ATTCTTTTCA
19934575 TTTTCTTTGTTTTCTCTTCTT
1 TTTTCTTTGTTTTC-CTT-TT
19934596 TTTTCTTTTGTTTTCCTTTT
1 TTTTC-TTTGTTTTCCTTTT
*
19934616 TTTTGTTTGT
1 TTTTCTTTGT
19934626 CCATCATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 5 0.18
20 6 0.21
21 8 0.29
22 9 0.32
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (19 bp):
TTTTCTTTGTTTTCCTTTT
Found at i:19938867 original size:7 final size:7
Alignment explanation
Indices: 19938857--19938910 Score: 65
Period size: 7 Copynumber: 7.7 Consensus size: 7
19938847 AAAATTAGTG
19938857 TTTTATT
1 TTTTATT
19938864 TTTTATT
1 TTTTATT
*
19938871 ATTTATT
1 TTTTATT
*
19938878 ATTTATT
1 TTTTATT
19938885 TCTTTA-T
1 T-TTTATT
19938892 TTTTATT
1 TTTTATT
*
19938899 TTTAATT
1 TTTTATT
19938906 TTTTA
1 TTTTA
19938911 AAAAACTGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 4 0.10
7 33 0.80
8 4 0.10
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTATT
Found at i:19939205 original size:14 final size:15
Alignment explanation
Indices: 19939171--19939204 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
19939161 AAACCAACAA
19939171 AAAAATCAAAAAAAT
1 AAAAATCAAAAAAAT
19939186 AAAAAT-AAAGAAAAT
1 AAAAATCAAA-AAAAT
19939201 AAAA
1 AAAA
19939205 TGAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (15 bp):
AAAAATCAAAAAAAT
Found at i:19939219 original size:20 final size:20
Alignment explanation
Indices: 19939181--19939219 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19939171 AAAAATCAAA
*
19939181 AAAATAAAAATAAAGAAAAT
1 AAAATAAAAATAAAAAAAAT
*
19939201 AAAATGAAAATAAAAAAAA
1 AAAATAAAAATAAAAAAAA
19939220 AAGTTTACGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (20 bp):
AAAATAAAAATAAAAAAAAT
Found at i:19940092 original size:3 final size:3
Alignment explanation
Indices: 19940084--19940110 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
19940074 TATAATACCA
19940084 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
19940111 GATGATGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19940212 original size:16 final size:16
Alignment explanation
Indices: 19940176--19940222 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
19940166 ACTATAGTAC
19940176 TAATA-AAAATAACATAA
1 TAATATAAAAT-A-ATAA
19940193 -AATATAAAATAATAA
1 TAATATAAAATAATAA
*
19940208 TAATATAATATAATA
1 TAATATAAAATAATA
19940223 TAAAAATAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 4 0.15
16 18 0.67
17 5 0.19
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAAAATAATAA
Found at i:19940212 original size:26 final size:26
Alignment explanation
Indices: 19940176--19940227 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
19940166 ACTATAGTAC
19940176 TAATAAAAATA-ACATAAAATATAAAA
1 TAATAAAAATATA-ATAAAATATAAAA
* *
19940202 TAATAATAATATAATATAATATAAAA
1 TAATAAAAATATAATAAAATATAAAA
19940228 ATAACATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (26 bp):
TAATAAAAATATAATAAAATATAAAA
Found at i:19941454 original size:21 final size:21
Alignment explanation
Indices: 19941428--19941495 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
19941418 CGAAACTTTG
19941428 AATGTGAATCTCTAATTTTCA
1 AATGTGAATCTCTAATTTTCA
* * *
19941449 AATGTGAATCTTCAAAACTTT-G
1 AATGTGAATC-TC-TAATTTTCA
*
19941471 AATATGAATCTCTAATTTTTCA
1 AATGTGAATCTCTAA-TTTTCA
19941493 AAT
1 AAT
19941496 TTGAGTCTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
20 2 0.06
21 15 0.42
22 14 0.39
23 5 0.14
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (21 bp):
AATGTGAATCTCTAATTTTCA
Found at i:19941471 original size:43 final size:44
Alignment explanation
Indices: 19941415--19941525 Score: 161
Period size: 44 Copynumber: 2.5 Consensus size: 44
19941405 GAAAAAAAAC
19941415 CTTCGAAACTTTGAATGTGAATCTCTAA-TTTTCAAATGTGAAT
1 CTTCGAAACTTTGAATGTGAATCTCTAATTTTTCAAATGTGAAT
* * * *
19941458 CTTCAAAACTTTGAATATGAATCTCTAATTTTTCAAATTTGAGT
1 CTTCGAAACTTTGAATGTGAATCTCTAATTTTTCAAATGTGAAT
* *
19941502 CTTTGAAACTTTGGATGTGAATCT
1 CTTCGAAACTTTGAATGTGAATCT
19941526 TTAAAATTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
43 26 0.44
44 33 0.56
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (44 bp):
CTTCGAAACTTTGAATGTGAATCTCTAATTTTTCAAATGTGAAT
Found at i:19941536 original size:22 final size:22
Alignment explanation
Indices: 19941501--19941545 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
19941491 CAAATTTGAG
* *
19941501 TCTTTGAAACTTTGGATGTGAA
1 TCTTTAAAACTTTGGATGGGAA
*
19941523 TCTTTAAAATTTTGGATGGGAA
1 TCTTTAAAACTTTGGATGGGAA
19941545 T
1 T
19941546 TCCTAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (22 bp):
TCTTTAAAACTTTGGATGGGAA
Found at i:19941648 original size:22 final size:23
Alignment explanation
Indices: 19941597--19941648 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
19941587 TGAAATGTTA
* *
19941597 AAGTTTTTCAATGTGAATTTTTG
1 AAGTTTTTCAATGTGAATCTCTG
* *
19941620 AA-ATTTTCGATGTGAATCTCT-
1 AAGTTTTTCAATGTGAATCTCTG
19941641 AAGTTTTT
1 AAGTTTTT
19941649 AGAATAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
21 2 0.09
22 19 0.83
23 2 0.09
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (23 bp):
AAGTTTTTCAATGTGAATCTCTG
Found at i:19941760 original size:81 final size:81
Alignment explanation
Indices: 19941620--19941775 Score: 210
Period size: 81 Copynumber: 1.9 Consensus size: 81
19941610 TGAATTTTTG
*
19941620 AAATTTTCGATGTGAATCTCTAAGTTTTTAGAATAAAAATCTTTAACTTTTGAAAGTGAAT-TTC
1 AAATTTTCGATGTGAATCTCTAAATTTTTAGAATAAAAATCTTTAACTTTTGAAAGTGAATCTT-
19941684 AAAAATTTTTTGAATAT
65 AAAAATTTTTTGAATAT
* ***
19941701 AAATTTTGGATGTGAAT-TCTTAAATTTTTCA-AATAAAAATCTTTAACTTTTGGGTGTGAATCT
1 AAATTTTCGATGTGAATCTC-TAAATTTTT-AGAATAAAAATCTTTAACTTTTGAAAGTGAATCT
*
19941764 TTAAAATTTTTT
64 TAAAAATTTTTT
19941776 AATGAGAATC
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
80 2 0.03
81 61 0.92
82 3 0.05
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.46
Consensus pattern (81 bp):
AAATTTTCGATGTGAATCTCTAAATTTTTAGAATAAAAATCTTTAACTTTTGAAAGTGAATCTTA
AAAATTTTTTGAATAT
Found at i:19941875 original size:23 final size:21
Alignment explanation
Indices: 19941738--19941875 Score: 55
Period size: 21 Copynumber: 6.3 Consensus size: 21
19941728 TTCAAATAAA
* **
19941738 AATCTTTAACTTTTGGGTGTG
1 AATCTTTAAATTTTGAATGTG
* *
19941759 AATCTTTAAAATTTTTTAATGAG
1 AATCTTT-AAA-TTTTGAATGTG
* * *
19941782 AATCTTTGAATTCTAAATGTG
1 AATCTTTAAATTTTGAATGTG
*
19941803 -AGCTTTGAAATTTTTG-ATGTG
1 AATCTTT-AAA-TTTTGAATGTG
** ** * *
19941824 AATCCATAAACTTTTTTATATA
1 AATCTTTAAA-TTTTGAATGTG
*
19941846 AAACTTTAAATCTTTTGAATGTG
1 AATCTTTAAA--TTTTGAATGTG
19941869 AATCTTT
1 AATCTTT
19941876 GAATATTGTC
Statistics
Matches: 82, Mismatches: 28, Indels: 12
0.67 0.23 0.10
Matches are distributed among these distances:
20 5 0.06
21 29 0.35
22 20 0.24
23 28 0.34
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (21 bp):
AATCTTTAAATTTTGAATGTG
Found at i:19942007 original size:17 final size:17
Alignment explanation
Indices: 19941950--19942007 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
19941940 ACTCTTAGAT
*
19941950 TTCTTGCAAACCTTAAA-
1 TTCTTGCAAATC-TAAAG
* * *
19941967 TTCTTGCAATTTTAAGG
1 TTCTTGCAAATCTAAAG
*
19941984 TTATTGCAAATCTAAAG
1 TTCTTGCAAATCTAAAG
19942001 TTCTTGC
1 TTCTTGC
19942008 CTGAAATTCT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 3 0.10
17 28 0.90
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (17 bp):
TTCTTGCAAATCTAAAG
Found at i:19942127 original size:21 final size:20
Alignment explanation
Indices: 19942103--19942141 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
19942093 TGAAAATCTA
*
19942103 ACAAATATTTGAAGTTTTCTG
1 ACAAACATTTGAA-TTTTCTG
*
19942124 ACAAACCTTTGAATTTTC
1 ACAAACATTTGAATTTTC
19942142 AAATAGTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (20 bp):
ACAAACATTTGAATTTTCTG
Found at i:19942402 original size:84 final size:84
Alignment explanation
Indices: 19942314--19942629 Score: 320
Period size: 84 Copynumber: 3.8 Consensus size: 84
19942304 GTAAGATTCA
* * * *
19942314 TAAGT-TTTCTAAGTTGAATCTATTTTAGAATTAAGATTTGTAAGACCTTCGAGTGTAATCTCTA
1 TAAGTCTTT-TAAGCTGAATCTATTTTAGAATCAAGATTTGTAAAACCTTCGAGCGTAATCTCTA
* *
19942378 TGTCATTTGGGAAAGATTTG
65 AGTCTTTTGGGAAAGATTTG
* * * * *
19942398 TAAGTCTTTTAAGTTGAATCTGTTTTAGAGTCAAGATTTGTAAAACC-TCTTAGCATAATCTCTA
1 TAAGTCTTTTAAGCTGAATCTATTTTAGAATCAAGATTTGTAAAACCTTC-GAGCGTAATCTCTA
19942462 AGTCTTTTGGGCAAA-ATTTG
65 AGTCTTTTGGG-AAAGATTTG
** * * * * *
19942482 TATA-TCTTACAAGCTGAATATATTTTAGAGTCAAGATTTGTAAAACCTCCAAGTGTAATCTCTA
1 TA-AGTCTTTTAAGCTGAATCTATTTTAGAATCAAGATTTGTAAAACCTTCGAGCGTAATCTCTA
* *
19942546 AGT-TTTTTGGATAAGATTCG
65 AGTCTTTTGGGA-AAGATTTG
* * * * *
19942566 TAAGTCTTTTGAGCTAAATCTA-TTTAGAATCAAGATTTGTAAGACCTTTGGGCGTAATCTCTAA
1 TAAGTCTTTTAAGCTGAATCTATTTTAGAATCAAGATTTGTAAAACCTTCGAGCGTAATCTCTAA
19942630 TACCTTCAGG
Statistics
Matches: 192, Mismatches: 32, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
82 1 0.01
83 46 0.24
84 137 0.71
85 8 0.04
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (84 bp):
TAAGTCTTTTAAGCTGAATCTATTTTAGAATCAAGATTTGTAAAACCTTCGAGCGTAATCTCTAA
GTCTTTTGGGAAAGATTTG
Found at i:19942571 original size:168 final size:167
Alignment explanation
Indices: 19942328--19942629 Score: 401
Period size: 168 Copynumber: 1.8 Consensus size: 167
19942318 TTTTCTAAGT
* * * * * *
19942328 TGAATCTATTTTAGAATTAAGATTTGTAAGACCTTCGAGTGTAATCTCTATGTCATTTGGGAAAG
1 TGAATATATTTTAGAATCAAGATTTGTAAAACCTCCAAGTGTAATCTCTAAGTCATTTGGGAAAG
* * * * *
19942393 ATTTGTAAGTCTTTTAAGTTGAATCTGTTTTAGAGTCAAGATTTGTAAAACCTCTT-AGCATAAT
66 ATTCGTAAGTCTTTTAAGCTAAATCT-ATTTAGAATCAAGATTTGTAAAACCT-TTGAGCATAAT
19942457 CTCTAAGTCTTTTGGGCAAAATTTGTATATCTTACAAGC
129 CTCTAAGTCTTTTGGGCAAAATTTGTATATCTTACAAGC
* * *
19942496 TGAATATATTTTAGAGTCAAGATTTGTAAAACCTCCAAGTGTAATCTCTAAGT-TTTTTGGATAA
1 TGAATATATTTTAGAATCAAGATTTGTAAAACCTCCAAGTGTAATCTCTAAGTCATTTGGGA-AA
* * * *
19942560 GATTCGTAAGTCTTTTGAGCTAAATCTATTTAGAATCAAGATTTGTAAGACCTTTGGGCGTAATC
65 GATTCGTAAGTCTTTTAAGCTAAATCTATTTAGAATCAAGATTTGTAAAACCTTTGAGCATAATC
19942625 TCTAA
130 TCTAA
19942630 TACCTTCAGG
Statistics
Matches: 114, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
166 2 0.02
167 41 0.36
168 71 0.62
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (167 bp):
TGAATATATTTTAGAATCAAGATTTGTAAAACCTCCAAGTGTAATCTCTAAGTCATTTGGGAAAG
ATTCGTAAGTCTTTTAAGCTAAATCTATTTAGAATCAAGATTTGTAAAACCTTTGAGCATAATCT
CTAAGTCTTTTGGGCAAAATTTGTATATCTTACAAGC
Found at i:19944064 original size:102 final size:100
Alignment explanation
Indices: 19943815--19944125 Score: 349
Period size: 102 Copynumber: 3.1 Consensus size: 100
19943805 TGAAAATTCA
* * *
19943815 TAATGAA-TTTTGAAAAAAA-AATAATAAAATTTTCAATCCTACCAGACTACTAAAAGATTTAAA
1 TAATGAATTTTTGAAAAAAATAATAATAAAATTTTCAATCCTACCAAACTATTAAAGGATTTAAA
* * * * *
19943878 TCTTAAATTAAGTTTTAGCAAACTA-TGGAAGACT
66 TCTTGAATTAAATCTTATCAAAATATTGGAAGACT
* * * * * *
19943912 TAATGAATTTTTAAAAAACAATAATAATAAAGTTTTTAATCTTACTAAACTATTATAGGATTTAA
1 TAATGAATTTTTGAAAAA-AATAATAATAAAATTTTCAATCCTACCAAACTATTAAAGGATTTAA
*
19943977 ATCTTGAATTAAATCTTATCAAAATATTGAAAGACT
65 ATCTTGAATTAAATCTTATCAAAATATTGGAAGACT
* * **
19944013 TAATGAATTTTTTGTAAAAAAATAATAATAAAATTTTCAATCGTACCAAACTTTTGGAGGATTTA
1 TAATGAA-TTTTTG-AAAAAAATAATAATAAAATTTTCAATCCTACCAAACTATTAAAGGATTTA
* * ** **
19944078 AATATTGAATTAGATCTTATCAACTTATTGGAAGGTT
64 AATCTTGAATTAAATCTTATCAAAATATTGGAAGACT
19944115 TAATGAATTTT
1 TAATGAATTTT
19944126 CTTAAAATAA
Statistics
Matches: 178, Mismatches: 30, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
97 7 0.04
98 9 0.05
99 2 0.01
100 56 0.31
101 19 0.11
102 80 0.45
103 5 0.03
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (100 bp):
TAATGAATTTTTGAAAAAAATAATAATAAAATTTTCAATCCTACCAAACTATTAAAGGATTTAAA
TCTTGAATTAAATCTTATCAAAATATTGGAAGACT
Found at i:19949007 original size:21 final size:20
Alignment explanation
Indices: 19948975--19949021 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
19948965 TGGAAATATG
19948975 AAGAAAAAAGAAAAAAAGAA
1 AAGAAAAAAGAAAAAAAGAA
*
19948995 AAGAAAAAGAGAACAAAAGAA
1 AAGAAAAA-AGAAAAAAAGAA
*
19949016 ATGAAA
1 AAGAAA
19949022 GAAAAAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (20 bp):
AAGAAAAAAGAAAAAAAGAA
Found at i:19950807 original size:46 final size:46
Alignment explanation
Indices: 19950703--19950860 Score: 176
Period size: 46 Copynumber: 3.5 Consensus size: 46
19950693 GAAAAATAAC
* * * *
19950703 CTTTGAAACTTTGAATGTGAATCTCT-AATTTTTTTAAATGTGAGT
1 CTTTGAAACTTTGGATGTGAATCTCTAAAATTTTTCAAATGTGAAT
* * * *
19950748 CTTTGAAACTTTGGATGTGAATCTCTAAAAATTTTCGAAGGTAAAT
1 CTTTGAAACTTTGGATGTGAATCTCTAAAATTTTTCAAATGTGAAT
* **
19950794 CTTTGAAATTTTGGATGAAAAT-TCCTAAAATTTTTCAAATGTGAAT
1 CTTTGAAACTTTGGATGTGAATCT-CTAAAATTTTTCAAATGTGAAT
* *
19950840 CTTTGAAATTTTGGTTGTGAA
1 CTTTGAAACTTTGGATGTGAA
19950861 ATGTTAAAGT
Statistics
Matches: 93, Mismatches: 18, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
45 26 0.28
46 67 0.72
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.42
Consensus pattern (46 bp):
CTTTGAAACTTTGGATGTGAATCTCTAAAATTTTTCAAATGTGAAT
Found at i:19950874 original size:46 final size:46
Alignment explanation
Indices: 19950703--19950884 Score: 160
Period size: 46 Copynumber: 4.0 Consensus size: 46
19950693 GAAAAATAAC
* * * * *
19950703 CTTTGAAACTTTGAATGTG-AATCTCT-AATTTTTTTAAATGTGAGT
1 CTTTGAAATTTTGGATGTGAAAT-TCTAAAATTTTTCAAATGTGAAT
* * * * *
19950748 CTTTGAAACTTTGGATGTG-AATCTCTAAAAATTTTCGAAGGTAAAT
1 CTTTGAAATTTTGGATGTGAAAT-TCTAAAATTTTTCAAATGTGAAT
*
19950794 CTTTGAAATTTTGGATG-AAAATTCCTAAAATTTTTCAAATGTGAAT
1 CTTTGAAATTTTGGATGTGAAATT-CTAAAATTTTTCAAATGTGAAT
* * *
19950840 CTTTGAAATTTTGGTTGTGAAATGT-TAAAGTTTTT-TAATGTGAAT
1 CTTTGAAATTTTGGATGTGAAAT-TCTAAAATTTTTCAAATGTGAAT
19950885 TTTTTAAAAT
Statistics
Matches: 114, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
45 35 0.31
46 74 0.65
47 4 0.04
48 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.43
Consensus pattern (46 bp):
CTTTGAAATTTTGGATGTGAAATTCTAAAATTTTTCAAATGTGAAT
Found at i:19951094 original size:21 final size:21
Alignment explanation
Indices: 19951073--19951130 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
19951063 TCTTAAAGTG
19951073 ATCCTTAAAATTTTTTATGTGA
1 ATCCTT-AAATTTTTTATGTGA
* *
19951095 ATCCTTGAATTTTTTATATGA
1 ATCCTTAAATTTTTTATGTGA
* * *
19951116 AACTTTAAATCTTTT
1 ATCCTTAAATTTTTT
19951131 GAATGCTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 24 0.80
22 6 0.20
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (21 bp):
ATCCTTAAATTTTTTATGTGA
Found at i:19951241 original size:17 final size:17
Alignment explanation
Indices: 19951221--19951426 Score: 88
Period size: 17 Copynumber: 12.3 Consensus size: 17
19951211 TTTACAAACA
*
19951221 TGAAGTTCTTGCAAATC
1 TGAAATTCTTGCAAATC
* * * *
19951238 TGAAGTTTTTACAAACC
1 TGAAATTCTTGCAAATC
*
19951255 TTAAATTCTTGCAAA-C
1 TGAAATTCTTGCAAATC
* *
19951271 TTGAAACTCTTGCGAATC
1 -TGAAATTCTTGCAAATC
* *
19951289 TAAAACTCTTGCAAATC
1 TGAAATTCTTGCAAATC
19951306 T-AAAGTTCTTGC----C
1 TGAAA-TTCTTGCAAATC
*
19951319 TTAAATTCTTGCAAATC
1 TGAAATTCTTGCAAATC
*** **
19951336 TTCCATTCTTGTGAATC
1 TGAAATTCTTGCAAATC
*
19951353 TGAAAGTCTTGCAAATC
1 TGAAATTCTTGCAAATC
* *
19951370 TTTG-AACTCTTATGC-ACT-
1 --TGAAATTC-T-TGCAAATC
* **
19951388 TGAAGTTCTTGTGAATC
1 TGAAATTCTTGCAAATC
*
19951405 TGAAAATCTTGCAAATC
1 TGAAATTCTTGCAAATC
19951422 TGAAA
1 TGAAA
19951427 GTTTTACGAA
Statistics
Matches: 141, Mismatches: 33, Indels: 30
0.69 0.16 0.15
Matches are distributed among these distances:
13 9 0.06
14 3 0.02
15 2 0.01
16 9 0.06
17 105 0.74
18 5 0.04
19 5 0.04
20 3 0.02
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (17 bp):
TGAAATTCTTGCAAATC
Found at i:19951860 original size:84 final size:80
Alignment explanation
Indices: 19951709--19951969 Score: 231
Period size: 82 Copynumber: 3.1 Consensus size: 80
19951699 GATTTTCGAG
* * ** * * *
19951709 CATAATCTCTAAACTCCTTAGGTAAAATTTGTAA-TCTTTCAAGCTAAATCTGTTTTAAAGTTAA
1 CATAATCTCT-AAGTCCTTAGG-CAAATTCATAAGTC-TTCAAGCTAAATCTATTTTTAAGTTGA
19951773 GA-TTGATAAGACCTCCGAA
63 GATTTG-TAAGACCTCC-AA
19951792 CATAATCTCTAAGTCCTTCAGGCAAGATTCATAAGTCTTACAAGCTAAATCTATTTTTAAGTTGA
1 CATAATCTCTAAGTCCTT-AGGCAA-ATTCATAAGTCTT-CAAGCTAAATCTATTTTTAAGTTGA
*
19951857 GATTTGTAAGACCTCCAGG
63 GATTTGTAAGACCTCCA-A
** ** * * * *
19951876 TGTAATCTCTAAGTTTTTGGGCAAATTCATAAGTCTTCTGAGCTGAATCTA-TTTTAGAGTCGAG
1 CATAATCTCTAAGTCCTTAGGCAAATTCATAAGTCTTC-AAGCTAAATCTATTTTTA-AGTTGAG
* *
19951940 ATTTGTAAAACCTCTAA
64 ATTTGTAAGACCTCCAA
19951957 GCATAATCTCTAA
1 -CATAATCTCTAA
19951970 TACTTTCAAA
Statistics
Matches: 148, Mismatches: 21, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
81 6 0.04
82 62 0.42
83 27 0.18
84 50 0.34
85 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (80 bp):
CATAATCTCTAAGTCCTTAGGCAAATTCATAAGTCTTCAAGCTAAATCTATTTTTAAGTTGAGAT
TTGTAAGACCTCCAA
Found at i:19953122 original size:100 final size:95
Alignment explanation
Indices: 19952974--19953281 Score: 373
Period size: 100 Copynumber: 3.1 Consensus size: 95
19952964 GAGAATTTCA
* * *
19952974 TAATGAAGTTTTTGAAAAAAAATAACAAAATTTTTAATTTTATCAAACTATTAGAGGATTTAAAT
1 TAATGAA-TTTTTGAAAAAAAATAATAAAA-TTTTAATTCTATCAAACTATTGGAGGATTTAAAT
* *
19953039 ATTGAATTAGGTTTTACCAAACTATTAGAGAGTT
64 ATTGAATTAGGTCTTATCAAACTATT-GA-AGTT
* * *
19953073 TAATGAATTTTTTAAAATAATAATAATAAAATGTTTAATTCTACCAAACTATTGGAAGATTTAAA
1 TAATGAATTTTTGAAAA-AA-AATAATAAAAT-TTTAATTCTATCAAACTATTGGAGGATTTAAA
* * * *
19953138 TCTTGAATTAAGTCTTATCAAAATATTGAAGGACT
63 TATTGAATTAGGTCTTATCAAACTATTGAA-G-TT
* *
19953173 TAATGAATTTTTGAAAAAAAATAATAAAATTTTAAATCTTATCAAACTTTTGGAGGATTTAAATA
1 TAATGAATTTTTGAAAAAAAATAATAAAATTTTAATTC-TATCAAACTATTGGAGGATTTAAATA
*
19953238 TTGAATTAGATCTTATCAAACTATTGGAAAGTT
65 TTGAATTAGGTCTTATCAAACTATT-G-AAGTT
19953271 TAATGAATTTT
1 TAATGAATTTT
19953282 CTTAAAATAA
Statistics
Matches: 179, Mismatches: 22, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
97 7 0.04
98 77 0.43
99 17 0.09
100 78 0.44
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (95 bp):
TAATGAATTTTTGAAAAAAAATAATAAAATTTTAATTCTATCAAACTATTGGAGGATTTAAATAT
TGAATTAGGTCTTATCAAACTATTGAAGTT
Found at i:19953235 original size:98 final size:98
Alignment explanation
Indices: 19952974--19953281 Score: 365
Period size: 98 Copynumber: 3.1 Consensus size: 98
19952964 GAGAATTTCA
* * * *
19952974 TAATGAAGTTTTTGAAAAAAAATAACAAAATTTTTAATTTTATCAAACTATTAGAGGATTTAAAT
1 TAATGAA-TTTTTGAAAAAAAATAATAAAATTTTAAATCTTATCAAACTATTGGAGGATTTAAAT
* * *
19953039 ATTGAATTAGGTTTTACCAAACTATT--AGAGAGTT
65 ATTGAATTAAGTCTTATCAAACTATTGAAG-GA-TT
* * * *
19953073 TAATGAATTTTTTAAAATAATAATAATAAAATGTTTAATTC-TACCAAACTATTGGAAGATTTAA
1 TAATGAATTTTTGAAAA-AA-AATAATAAAAT-TTTAAATCTTATCAAACTATTGGAGGATTTAA
* * *
19953137 ATCTTGAATTAAGTCTTATCAAAATATTGAAGGACT
63 ATATTGAATTAAGTCTTATCAAACTATTGAAGGATT
*
19953173 TAATGAATTTTTGAAAAAAAATAATAAAATTTTAAATCTTATCAAACTTTTGGAGGATTTAAATA
1 TAATGAATTTTTGAAAAAAAATAATAAAATTTTAAATCTTATCAAACTATTGGAGGATTTAAATA
*
19953238 TTGAATT-AGATCTTATCAAACTATTGGAAAG-TT
66 TTGAATTAAG-TCTTATCAAACTATT-GAAGGATT
19953271 TAATGAATTTT
1 TAATGAATTTT
19953282 CTTAAAATAA
Statistics
Matches: 178, Mismatches: 23, Indels: 17
0.82 0.11 0.08
Matches are distributed among these distances:
97 9 0.05
98 75 0.42
99 15 0.08
100 70 0.39
101 7 0.04
102 2 0.01
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (98 bp):
TAATGAATTTTTGAAAAAAAATAATAAAATTTTAAATCTTATCAAACTATTGGAGGATTTAAATA
TTGAATTAAGTCTTATCAAACTATTGAAGGATT
Found at i:19955666 original size:101 final size:101
Alignment explanation
Indices: 19955607--19955794 Score: 245
Period size: 101 Copynumber: 1.9 Consensus size: 101
19955597 CTGAATTCTC
* * *
19955607 ACAAGTTTAAGAATAAAGATTAAGAACACAA-TTAAGAAAAATAAAACATGAAGACAAATGGGAA
1 ACAAGTTTAAGAATAAAGATTAAGAACACAACTAAAG-AAAAGAAAACATAAAGACAAATGGGAA
*
19955671 AGATAAGATATGAACAATCAAAATCTCTAGAAGTCCT
65 AGATAAGATATGAAAAATCAAAATCTCTAGAAGTCCT
* * * *
19955708 ACAAGTTTAAGAATGAAGATTAAGAACATAACTAAAGAAAAGAAAACCTAAAGACAAATGGTG-T
1 ACAAGTTTAAGAATAAAGATTAAGAACACAACTAAAGAAAAGAAAACATAAAGACAAATGG-GAA
* * *
19955772 AGAAAATATTTGAAAAATCAAAA
65 AGATAAGATATGAAAAATCAAAA
19955795 CCTCCAAAGT
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
101 69 0.93
102 5 0.07
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (101 bp):
ACAAGTTTAAGAATAAAGATTAAGAACACAACTAAAGAAAAGAAAACATAAAGACAAATGGGAAA
GATAAGATATGAAAAATCAAAATCTCTAGAAGTCCT
Found at i:19956189 original size:28 final size:28
Alignment explanation
Indices: 19956154--19956207 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
19956144 GAAGATCTAA
* *
19956154 AAAAATCCGTAAATTGATATCAAATTCT
1 AAAAATCCCTAAATTGAGATCAAATTCT
*
19956182 AAAAATCCCTAAATTGGGATCAAATT
1 AAAAATCCCTAAATTGAGATCAAATT
19956208 TCAAGAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (28 bp):
AAAAATCCCTAAATTGAGATCAAATTCT
Found at i:19961285 original size:14 final size:14
Alignment explanation
Indices: 19961266--19961296 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
19961256 TGAGAAAATG
19961266 TTTTTTATTTTCAT
1 TTTTTTATTTTCAT
*
19961280 TTTTTTATTTTGAT
1 TTTTTTATTTTCAT
19961294 TTT
1 TTT
19961297 CTAGAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.81
Consensus pattern (14 bp):
TTTTTTATTTTCAT
Found at i:19962441 original size:111 final size:112
Alignment explanation
Indices: 19962320--19962601 Score: 279
Period size: 113 Copynumber: 2.5 Consensus size: 112
19962310 AAAATCTTCT
*
19962320 CATAAGTTTAAGATGAAAAATCTAAAAAACAAAGTTTCTAAAGTTCCAACAAACAAATTCA-AAG
1 CATAAGTTTAAGAAGAAAAATCTAAAAAACAAAGTTT-TAAAGTTCCAACAAACAAATTCAGAAG
* * * * *
19962384 AC-AATTAAGGAAAAGA-AGATTTGAAG-ATTCAAAGTTTCCAAAGCTGC-
65 ACAAATAAAGGAAAAGATA-ATCTGAAGAATT-AAAATCTCCAAAACT-CA
* ** * * * * * *
19962431 CATAAGTTTAAAAAGGTATATATGAAGAACAAAGTTTTTAGAGTTCCAATAAAC-AATTCAGGAA
1 CATAAGTTTAAGAAGAAAAATCTAAAAAACAAAG-TTTTAAAGTTCCAACAAACAAATTCA-GAA
*
19962495 GACAAATAAAGGAAGAGATAATCTGAAGAATTAAAATCTCCAAAACTCA
64 GACAAATAAAGGAAAAGATAATCTGAAGAATTAAAATCTCCAAAACTCA
* * * *
19962544 CACAAGTTCAAGAAGAAAAATCTAAAAAACAAAGTCTTTAAAATTTCAACAAACAAAT
1 CATAAGTTTAAGAAGAAAAATCTAAAAAACAAAGT-TTTAAAGTTCCAACAAACAAAT
19962602 CTAAAATGAA
Statistics
Matches: 133, Mismatches: 29, Indels: 15
0.75 0.16 0.08
Matches are distributed among these distances:
110 6 0.05
111 40 0.30
112 10 0.08
113 70 0.53
114 7 0.05
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23
Consensus pattern (112 bp):
CATAAGTTTAAGAAGAAAAATCTAAAAAACAAAGTTTTAAAGTTCCAACAAACAAATTCAGAAGA
CAAATAAAGGAAAAGATAATCTGAAGAATTAAAATCTCCAAAACTCA
Found at i:19962707 original size:56 final size:55
Alignment explanation
Indices: 19962640--19962776 Score: 152
Period size: 56 Copynumber: 2.5 Consensus size: 55
19962630 TTGAATATCC
* *
19962640 AAAAATCCCTAAATTGAGACTAAATTTAAAAAAT-CTCTAAATTAAGATCAAATTTT
1 AAAAATTCCTAAATTGAGACAAAATTT-AAAAATCCT-TAAATTAAGATCAAATTTT
* * **
19962696 AAAAATTCCTAAATTGACATCAAAATTTAAGAATCCTTAAATTGGGATCAAATTTT
1 AAAAATTCCTAAATTGAGA-CAAAATTTAAAAATCCTTAAATTAAGATCAAATTTT
* * *
19962752 AAAAACT-CTAGATTGAGACCAAATT
1 AAAAATTCCTAAATTGAGACAAAATT
19962777 CAAGAATCTT
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
54 6 0.09
55 9 0.13
56 45 0.65
57 9 0.13
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.31
Consensus pattern (55 bp):
AAAAATTCCTAAATTGAGACAAAATTTAAAAATCCTTAAATTAAGATCAAATTTT
Found at i:19962748 original size:27 final size:27
Alignment explanation
Indices: 19962640--19962776 Score: 118
Period size: 28 Copynumber: 5.0 Consensus size: 27
19962630 TTGAATATCC
*
19962640 AAAAATCCCTAAATTGAGA-CTAAATTT
1 AAAAATTCCTAAATTGAGATC-AAATTT
* *
19962667 AAAAAATCTCTAAATTAAGATCAAATTTT
1 AAAAATTC-CTAAATTGAGATCAAA-TTT
*
19962696 AAAAATTCCTAAATTGACATCAAAATTT
1 AAAAATTCCTAAATTGAGATC-AAATTT
* *
19962724 AAGAA-TCCTTAAATTGGGATCAAATTTT
1 AAAAATTCC-TAAATTGAGATCAAA-TTT
* * *
19962752 AAAAACT-CTAGATTGAGACCAAATT
1 AAAAATTCCTAAATTGAGATCAAATT
19962777 CAAGAATCTT
Statistics
Matches: 90, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.02
27 24 0.27
28 49 0.54
29 15 0.17
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.31
Consensus pattern (27 bp):
AAAAATTCCTAAATTGAGATCAAATTT
Found at i:19963791 original size:17 final size:16
Alignment explanation
Indices: 19963765--19963803 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 16
19963755 CCTGTATCAA
19963765 TTTAAAATTTTTTAAT
1 TTTAAAATTTTTTAAT
19963781 TTTATAAATTTTTTAAT
1 TTTA-AAATTTTTTAAT
19963798 TATTAA
1 T-TTAA
19963804 TTTTAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.19
17 14 0.67
18 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTAAAATTTTTTAAT
Found at i:19963800 original size:15 final size:16
Alignment explanation
Indices: 19963763--19963807 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
19963753 AGCCTGTATC
19963763 AATTTA-AAATTTTTT
1 AATTTATAAATTTTTT
19963778 AATTTTATAAATTTTTT
1 AA-TTTATAAATTTTTT
*
19963795 AA-TTATTAATTTT
1 AATTTATAAATTTT
19963808 AATAAATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 12 0.44
16 4 0.15
17 11 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
AATTTATAAATTTTTT
Found at i:19968813 original size:12 final size:12
Alignment explanation
Indices: 19968796--19968822 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
19968786 CGTTTGCTAG
19968796 AAACTAGTACAT
1 AAACTAGTACAT
19968808 AAACTAGTACAT
1 AAACTAGTACAT
19968820 AAA
1 AAA
19968823 ATAACAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (12 bp):
AAACTAGTACAT
Found at i:19974068 original size:22 final size:22
Alignment explanation
Indices: 19974042--19974084 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
19974032 AATAATAATC
*
19974042 TATAAGATAATAATCATTTTTA
1 TATAAAATAATAATCATTTTTA
*
19974064 TATAAAATAATAATTATTTTT
1 TATAAAATAATAATCATTTTT
19974085 TCTTCAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TATAAAATAATAATCATTTTTA
Found at i:19974624 original size:20 final size:19
Alignment explanation
Indices: 19974582--19974627 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
19974572 TTATTAGATA
*
19974582 AATTCAATGTGTAATCTACT
1 AATTC-ATGTGTAATCAACT
*
19974602 AATTCATGTGTAAGTCAATT
1 AATTCATGTGTAA-TCAACT
19974622 AATTCA
1 AATTCA
19974628 CAAATGAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (19 bp):
AATTCATGTGTAATCAACT
Found at i:19974989 original size:24 final size:25
Alignment explanation
Indices: 19974938--19974986 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
19974928 AATTTTTAGA
19974938 TTTTTTTATAAATATATATTAATAT
1 TTTTTTTATAAATATATATTAATAT
19974963 TTTTTTTCAATAAA-ATATATTAAT
1 TTTTTTT--ATAAATATATATTAAT
19974987 TTTAATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 7 0.32
26 10 0.45
27 5 0.23
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
TTTTTTTATAAATATATATTAATAT
Found at i:19975724 original size:35 final size:35
Alignment explanation
Indices: 19975680--19975757 Score: 122
Period size: 34 Copynumber: 2.3 Consensus size: 35
19975670 CATCTCTTAG
* *
19975680 ATTTATTAAAATTAGTAGTTATAAAAAAGTATAAA
1 ATTTTTTAAAATTAATAGTTATAAAAAAGTATAAA
*
19975715 ATTTTTT-AAATTAATAGTTATAAAAAAGTATAGA
1 ATTTTTTAAAATTAATAGTTATAAAAAAGTATAAA
19975749 ATTTTTTAA
1 ATTTTTTAA
19975758 TATAAGTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
34 32 0.82
35 7 0.18
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (35 bp):
ATTTTTTAAAATTAATAGTTATAAAAAAGTATAAA
Found at i:19979655 original size:194 final size:190
Alignment explanation
Indices: 19979407--19979756 Score: 479
Period size: 194 Copynumber: 1.8 Consensus size: 190
19979397 AACAAATTTT
* **
19979407 TTTAATAAATAATTTAAATTTAATATTTTAGATACTTATTTAAATTCAAATCAAAATCTATT-TG
1 TTTAATAAATAATTTAAATTTAATATTTTAGATAATTATTTAAATTCAAATCAAAATCT-TTCAA
* * ** * * *
19979471 AAATCGAAACTTTTTCATAAATTTTGAATTCAAATATA-TAAAGTCATAATATATCTTTTCTTTT
65 AAATCAAAAATTTAACATAAATTTTAAATTCAAATATATTAAA-TCATAATATATCATAT-TTTT
19979535 GAAATTTAATTATAGTTCCAAATATATATATTTAATAAAATTTTATTTTATGCCAACTAATTCTA
128 --AATTTAATTATAGTTCCAAATATATATATTTAATAAAATTTTATTTTATGCCAACTAATTCTA
* *
19979600 TTTAATAAATTATTTAAATTTAATATTTTTAGATAATTATTTAAATTCTAATCAAAATCTTTCAA
1 TTTAATAAATAATTTAAATTTAATA-TTTTAGATAATTATTTAAATTCAAATCAAAATCTTTCAA
* * * *
19979665 AAATTAAAAATTTAACATAAATTTTAAATTCAAATGTATTAAATCTTAATTTATCATATTTTTAA
65 AAATCAAAAATTTAACATAAATTTTAAATTCAAATATATTAAATCATAATATATCATATTTTTAA
*
19979730 TTTAATTATGGTTCCAAATATATATAT
130 TTTAATTATAGTTCCAAATATATATAT
19979757 GTGCTTAAAA
Statistics
Matches: 137, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
191 28 0.20
193 30 0.22
194 75 0.55
195 4 0.03
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (190 bp):
TTTAATAAATAATTTAAATTTAATATTTTAGATAATTATTTAAATTCAAATCAAAATCTTTCAAA
AATCAAAAATTTAACATAAATTTTAAATTCAAATATATTAAATCATAATATATCATATTTTTAAT
TTAATTATAGTTCCAAATATATATATTTAATAAAATTTTATTTTATGCCAACTAATTCTA
Found at i:19981420 original size:33 final size:36
Alignment explanation
Indices: 19981383--19981458 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 36
19981373 TATATTTATT
*
19981383 TTTATTTATTAACATAT-TAT-TTTT-TTTGTATCA
1 TTTATTTATTAACATATATATGTTTTCTTTATATCA
* *
19981416 TTTATTTATTAATATATATATGTTTTCTTTATATTA
1 TTTATTTATTAACATATATATGTTTTCTTTATATCA
19981452 TTTATTT
1 TTTATTT
19981459 TTTTTCTCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 16 0.43
34 3 0.08
35 4 0.11
36 14 0.38
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.66
Consensus pattern (36 bp):
TTTATTTATTAACATATATATGTTTTCTTTATATCA
Found at i:19981420 original size:55 final size:54
Alignment explanation
Indices: 19981360--19981463 Score: 120
Period size: 55 Copynumber: 1.9 Consensus size: 54
19981350 TATATTTATT
* *
19981360 ATTTATCTACTAGTATATTTAT-TTTTATTTATTAACATATTATTTTTTTTGTATC
1 ATTTATCTACTAATATATATATGTTTTATTTA-TAACAT-TTATTTTTTTTGTATC
* * * **
19981415 ATTTATTTATTAATATATATATGTTTTCTTTATATTATTTATTTTTTTT
1 ATTTATCTACTAATATATATATGTTTTATTTATAACATTTATTTTTTTT
19981464 CTCTTTAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
54 11 0.27
55 22 0.54
56 8 0.20
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (54 bp):
ATTTATCTACTAATATATATATGTTTTATTTATAACATTTATTTTTTTTGTATC
Found at i:19982209 original size:3 final size:3
Alignment explanation
Indices: 19982201--19982226 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19982191 GTTTATTTAT
19982201 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
19982227 TATTGATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19982458 original size:61 final size:59
Alignment explanation
Indices: 19982292--19982513 Score: 231
Period size: 59 Copynumber: 3.7 Consensus size: 59
19982282 AAAATTCTAA
*
19982292 AAAAATATATTTTTAAGGAAAAATTGAAAGTATCAATTTTCTTTGAAAATAAGTTTTTCT
1 AAAAA-ATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGTTTTTCT
* *
19982352 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAAT-A-TTTTTTT
1 AAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGTTTTTCT
* * * * * * *
19982409 AAAAAAGGGTTTTTTTTTAGGAGAAGTTGAAAGTATTAATTTTCCTTGAAATTAAAG--TTTCA
1 AAAAAA----TATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAAT-AAGTTTTTCT
* *
19982471 AAAAAATA-TATT-AGGAAAAAGTTGAAAGTATTAATTTTCTTTG
1 AAAAAATATTTTTAAGG-AAAAGTTGAAAGTATCAATTTTCTTTG
19982514 TACAAAAACA
Statistics
Matches: 139, Mismatches: 15, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
56 3 0.02
57 40 0.29
58 2 0.01
59 42 0.30
60 5 0.04
61 37 0.27
62 9 0.06
63 1 0.01
ACGTcount: A:0.41, C:0.04, G:0.14, T:0.41
Consensus pattern (59 bp):
AAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGTTTTTCT
Found at i:19992979 original size:12 final size:12
Alignment explanation
Indices: 19992964--19993000 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
19992954 TAAAAAAATG
19992964 AAATGAAAAAAA
1 AAATGAAAAAAA
19992976 AAATG---AAAA
1 AAATGAAAAAAA
19992985 AAATGAAAAAAA
1 AAATGAAAAAAA
19992997 AAAT
1 AAAT
19993001 AAAGAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 9 0.41
12 13 0.59
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (12 bp):
AAATGAAAAAAA
Found at i:19992986 original size:9 final size:9
Alignment explanation
Indices: 19992955--19992996 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
19992945 TACTATGCTT
19992955 AAAAAAATG
1 AAAAAAATG
*
19992964 AAATGAAA--
1 AAA-AAAATG
19992972 AAAAAAATG
1 AAAAAAATG
19992981 AAAAAAATG
1 AAAAAAATG
19992990 AAAAAAA
1 AAAAAAA
19992997 AAATAAAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
7 3 0.11
8 3 0.11
9 19 0.68
10 3 0.11
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (9 bp):
AAAAAAATG
Found at i:19992991 original size:26 final size:28
Alignment explanation
Indices: 19992955--19993025 Score: 89
Period size: 26 Copynumber: 2.7 Consensus size: 28
19992945 TACTATGCTT
*
19992955 AAAAAAATGAAATGAAAAAAA-AAA-TG
1 AAAAAAATGAAATGAAAAAAATAAAGAG
19992981 AAAAAAATGAAA--AAAAAAATAAAGAG
1 AAAAAAATGAAATGAAAAAAATAAAGAG
19993007 AAAAAAAGTG-AATGAAAAA
1 AAAAAAA-TGAAATGAAAAA
19993026 GGAGGACTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
24 7 0.18
25 3 0.08
26 22 0.56
27 2 0.05
28 5 0.13
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (28 bp):
AAAAAAATGAAATGAAAAAAATAAAGAG
Found at i:19994134 original size:83 final size:81
Alignment explanation
Indices: 19994022--19994207 Score: 241
Period size: 83 Copynumber: 2.3 Consensus size: 81
19994012 CTTAATCGTC
*
19994022 AAGGAGC-ATTTACTTTTCCAAAGTTGTGATGCTTCTATTTAGAGGAGCAATTTATTTTTCAAAA
1 AAGGAGCAATTTACTTTT-CAAAGTTGTGATGCCTCTATTTAGAGGAGCAATTTA-TTTTC-AAA
19994086 GTCCTAGTCGCCTCTGTTTA
63 GTCCTAGT-GCCTCTGTTTA
* *
19994106 GAGGAGCAATTTA-TTTTCAAAGTTGTGATGCCTCTGTTTAGAGGAGCAATTTATTTTCAAAGTC
1 AAGGAGCAATTTACTTTTCAAAGTTGTGATGCCTCTATTTAGAGGAGCAATTTATTTTCAAAGTC
* * *
19994170 GTGGTGCCTTTGTTTA
66 CTAGTGCCTCTGTTTA
* * *
19994186 AATGAGCAATTAATTTTTCAAA
1 AAGGAGCAATTTACTTTTCAAA
19994208 AGTCATGGTT
Statistics
Matches: 91, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
80 20 0.22
81 17 0.19
82 5 0.05
83 34 0.37
84 10 0.11
85 5 0.05
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.39
Consensus pattern (81 bp):
AAGGAGCAATTTACTTTTCAAAGTTGTGATGCCTCTATTTAGAGGAGCAATTTATTTTCAAAGTC
CTAGTGCCTCTGTTTA
Found at i:19994150 original size:40 final size:40
Alignment explanation
Indices: 19994023--19994295 Score: 230
Period size: 40 Copynumber: 6.5 Consensus size: 40
19994013 TTAATCGTCA
* *
19994023 AGGAGC-ATTTACTTTTCCAAAGTTGTGATGCTTCTATTTAG
1 AGGAGCAATTTA-TTTT-CAAAGTTGTGATGCCTCTGTTTAG
**
19994064 AGGAGCAATTTATTTTTCAAAAGTCCT-AGTCGCCTCTGTTTAG
1 AGGAGCAATTTA-TTTTC-AAAGTTGTGA-T-GCCTCTGTTTAG
19994107 AGGAGCAATTTATTTTCAAAGTTGTGATGCCTCTGTTTAG
1 AGGAGCAATTTATTTTCAAAGTTGTGATGCCTCTGTTTAG
* * * *
19994147 AGGAGCAATTTATTTTCAAAGTCGTGGTGCCTTTGTTTAA
1 AGGAGCAATTTATTTTCAAAGTTGTGATGCCTCTGTTTAG
* * * * *
19994187 ATGAGCAATTAATTTTTCAAAAGTCATG-GTTGCATCCGTTTAG
1 AGGAGCAATTTA-TTTTC-AAAGT--TGTGATGCCTCTGTTTAG
* * *
19994230 AAGAGCAATTCATTTTGCCCAAAG-TGTGATGCCTCTGATTAG
1 AGGAGCAATTTATTTT---CAAAGTTGTGATGCCTCTGTTTAG
*
19994272 AGGAGCTTTATTTATTTTCAAAGT
1 AGGAGC--AATTTATTTTCAAAGT
19994296 CGTTGAGCTT
Statistics
Matches: 188, Mismatches: 28, Indels: 31
0.76 0.11 0.13
Matches are distributed among these distances:
40 58 0.31
41 27 0.14
42 47 0.25
43 42 0.22
44 13 0.07
45 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (40 bp):
AGGAGCAATTTATTTTCAAAGTTGTGATGCCTCTGTTTAG
Found at i:19994228 original size:83 final size:82
Alignment explanation
Indices: 19994022--19994245 Score: 229
Period size: 83 Copynumber: 2.7 Consensus size: 82
19994012 CTTAATCGTC
* * * **
19994022 AAGGAGCATTTACTTTTCCAAAGTTGTGATGCTTCTATTTAGAGGAGCAATTTATTTTTCAAAAG
1 AAGGAGCAATTAATTTT-CAAAGTTGTGATGCATCCGTTTAGAGGAGCAATTTA-TTTTCAAAAG
19994087 TCCTAGTCGCCTCTGTTTA
64 TCCTAGTCGCCTCTGTTTA
* * * *
19994106 GAGGAGCAATTTATTTTCAAAGTTGTGATGCCTCTGTTTAGAGGAGCAATTTATTTTC-AAAGTC
1 AAGGAGCAATTAATTTTCAAAGTTGTGATGCATCCGTTTAGAGGAGCAATTTATTTTCAAAAGTC
* * *
19994170 GTGGT-GCCTTTGTTTA
66 CTAGTCGCCTCTGTTTA
* * * *
19994186 AATGAGCAATTAATTTTTCAAAAGTCATG-GTTGCATCCGTTTAGAAGAGCAATTCATTTT
1 AAGGAGCAATTAA-TTTTC-AAAGT--TGTGATGCATCCGTTTAGAGGAGCAATTTATTTT
19994246 GCCCAAAGTG
Statistics
Matches: 119, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
80 20 0.17
81 14 0.12
82 10 0.08
83 60 0.50
84 15 0.13
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (82 bp):
AAGGAGCAATTAATTTTCAAAGTTGTGATGCATCCGTTTAGAGGAGCAATTTATTTTCAAAAGTC
CTAGTCGCCTCTGTTTA
Found at i:19994228 original size:123 final size:122
Alignment explanation
Indices: 19994023--19994308 Score: 326
Period size: 123 Copynumber: 2.3 Consensus size: 122
19994013 TTAATCGTCA
* * *
19994023 AGGAGCATTTACTTTTCCAAAGTTGTGATGCTTCTATTTAGAGGAGCAATTTATTTTTCAAAAGT
1 AGGAGCATTTA-TTTT-CAAAGTCGTGATGCTTCTATTTAAAGGAGCAATTAATTTTTCAAAAGT
* * * * * *
19994088 CCTAGTCGCCTCTGTTTAGAGGAGCAATTTATTTT-CAAAGTTGTGATGCCTCTGTTTAG
64 CATAGTCGCATCCGTTTAGAAGAGCAATTCATTTTCCAAAG-TGTGATGCCTCTGATTAG
* * *
19994147 AGGAGCAATTTATTTTCAAAGTCGTGGTGCCTT-TGTTTAAATGAGCAATTAATTTTTCAAAAGT
1 AGGAGC-ATTTATTTTCAAAGTCGTGATG-CTTCTATTTAAAGGAGCAATTAATTTTTCAAAAGT
* *
19994211 CATGGTTGCATCCGTTTAGAAGAGCAATTCATTTTGCCCAAAGTGTGATGCCTCTGATTAG
64 CATAGTCGCATCCGTTTAGAAGAGCAATTCATTTT--CCAAAGTGTGATGCCTCTGATTAG
19994272 AGGAGCTTTATTTATTTTCAAAGTCGTTGA-GCTTCTA
1 AGGAGC---ATTTATTTTCAAAGTCG-TGATGCTTCTA
19994309 ATTATAAGAG
Statistics
Matches: 136, Mismatches: 17, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
123 66 0.49
124 13 0.10
125 28 0.21
126 8 0.06
127 19 0.14
128 2 0.01
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.38
Consensus pattern (122 bp):
AGGAGCATTTATTTTCAAAGTCGTGATGCTTCTATTTAAAGGAGCAATTAATTTTTCAAAAGTCA
TAGTCGCATCCGTTTAGAAGAGCAATTCATTTTCCAAAGTGTGATGCCTCTGATTAG
Found at i:19994365 original size:45 final size:42
Alignment explanation
Indices: 19994260--19994368 Score: 128
Period size: 45 Copynumber: 2.5 Consensus size: 42
19994250 AAAGTGTGAT
* *
19994260 GCCTCTGATTAGAGGAGCTTTATTTATTTTCAAAGTCGTTGA
1 GCCTCTGATTAGAGGAGCTTTGTTTATTTTCAAAGTCATTGA
* * * *
19994302 GCTTCTAATTATAAGAGCTTTGTTTATGTTTTTCAAAGTCATTGA
1 GCCTCTGATTAGAGGAGCTTTGTTTA---TTTTCAAAGTCATTGA
*
19994347 GCCTCTGCTTAGAGGAGCTTTG
1 GCCTCTGATTAGAGGAGCTTTG
19994369 ATCAAAATTT
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
42 21 0.40
45 32 0.60
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (42 bp):
GCCTCTGATTAGAGGAGCTTTGTTTATTTTCAAAGTCATTGA
Found at i:19994642 original size:22 final size:22
Alignment explanation
Indices: 19994594--19994649 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
19994584 TTTTTTAAAT
**
19994594 ATATTTATTATTTATCTACTAGT
1 ATATTTATT-TTTATCTACTAAC
*
19994617 ATATTTATTTTTATCTATTAAC
1 ATATTTATTTTTATCTACTAAC
19994639 ATA-TTATTTTT
1 ATATTTATTTTT
19994650 TTTTGTATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 8 0.27
22 13 0.43
23 9 0.30
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (22 bp):
ATATTTATTTTTATCTACTAAC
Found at i:19994664 original size:34 final size:35
Alignment explanation
Indices: 19994626--19994699 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
19994616 TATATTTATT
* * *
19994626 TTTATCTATTAACATAT-TATTTTTTTTTGTATCA
1 TTTATCTATTAACATATATATATATTTTTATATCA
* *
19994660 TTTATCTATTAATATATATATATATTTTTATATTA
1 TTTATCTATTAACATATATATATATTTTTATATCA
19994695 TTTAT
1 TTTAT
19994700 TTTTTTTCTC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.47
35 18 0.53
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.62
Consensus pattern (35 bp):
TTTATCTATTAACATATATATATATTTTTATATCA
Found at i:19995517 original size:19 final size:19
Alignment explanation
Indices: 19995480--19995517 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
19995470 TTTTATTTAT
*
19995480 TTATTTATTATTATTATTA
1 TTATTTATTATTATGATTA
19995499 TTATTTATTGATTA-GATTA
1 TTATTTATT-ATTATGATTA
19995518 GAATTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TTATTTATTATTATGATTA
Found at i:19995634 original size:60 final size:58
Alignment explanation
Indices: 19995571--19995903 Score: 399
Period size: 60 Copynumber: 5.7 Consensus size: 58
19995561 AAATTTCAAA
*
19995571 AAAAAATATTTTTGAGGAAAAGTTGAAAGAATCAATTTTCCTTGAAAATAAGTTTTTCT
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTT-T
19995630 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATCTTT-CTTGAAAATAAGTTTTTTCT
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT-TTTCCTTGAAAATAAG-TTTTT-T
* *
19995690 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTTTTT
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTTT
* * *
19995748 AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAAT-ATTTTTTT
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTTT
* * * * * *
19995805 AAAAAAGATTTTTTTTGAGGAGAAG-TAAAATGTATCAATTTTTCTCGAAATTAAAG--TTTT
1 -AAAAA-A-TATTTTTGAGGAAAAGTTGAAA-GTATCAATTTTCCTTGAAAAT-AAGTTTTTT
* * *
19995865 AGAAAAATA-TTTTGCGAAAAAATTGAAAGTATCAATTTT
1 A-AAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
19995904 TTTTTGTACG
Statistics
Matches: 241, Mismatches: 22, Indels: 24
0.84 0.08 0.08
Matches are distributed among these distances:
57 27 0.11
58 56 0.23
59 62 0.26
60 95 0.39
62 1 0.00
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.40
Consensus pattern (58 bp):
AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTTT
Found at i:19995795 original size:118 final size:115
Alignment explanation
Indices: 19995570--19995903 Score: 435
Period size: 118 Copynumber: 2.9 Consensus size: 115
19995560 AAAATTTCAA
* *
19995570 AAAAAAATATTTTTGAGGAAAAGTTGAAAGAATCAATTTTCCTTGAAAATAAGTTTTTCTAAAAA
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTT-TAAAAA
*
19995635 ATATTTTTGAGGAAAAGTTGAAAGTATCAATCTTTCTTGAAAATAAGTTTTTTCT
65 ATATTTTTGAGAAAAAGTTGAAAGTATCAAT-TTTCTTGAAAAT-A-TTTTTT-T
*
19995690 -AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTTTTTAAAAAA
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTTTAAAAAA
19995754 TATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATATTTTTTT
66 TATTTTTGAGAAAAAGTTGAAAGTATCAATTTTC-TTGAAAATATTTTTTT
* * * * *
19995805 AAAAAAGATTTTTTTTGAGGAGAAG-TAAAATGTATCAATTTTTCTCGAAATTAAAG--TTTTAG
1 AAAAAA-A-TATTTTTGAGGAAAAGTTGAAA-GTATCAATTTTTCTTGAAAAT-AAGTTTTTTA-
* *
19995867 AAAAATA-TTTTGCGAAAAAATTGAAAGTATCAATTTT
61 AAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTT
19995904 TTTTTGTACG
Statistics
Matches: 195, Mismatches: 12, Indels: 17
0.87 0.05 0.08
Matches are distributed among these distances:
115 1 0.01
116 11 0.06
117 43 0.22
118 83 0.43
119 57 0.29
ACGTcount: A:0.43, C:0.05, G:0.13, T:0.40
Consensus pattern (115 bp):
AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTTTAAAAAA
TATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTGAAAATATTTTTTT
Found at i:19996011 original size:21 final size:21
Alignment explanation
Indices: 19995959--19996011 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
19995949 TACCTAAAGC
19995959 TGAATTTT-TTTTTGTTTTAT
1 TGAATTTTCTTTTTGTTTTAT
** *
19995979 T-TTTTTTCCTTTTTGTTTTCT
1 TGAATTTT-CTTTTTGTTTTAT
19996000 TGAATTTTCTTT
1 TGAATTTTCTTT
19996012 AATAATAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 5
0.71 0.14 0.14
Matches are distributed among these distances:
19 4 0.16
20 1 0.04
21 16 0.64
22 4 0.16
ACGTcount: A:0.09, C:0.08, G:0.08, T:0.75
Consensus pattern (21 bp):
TGAATTTTCTTTTTGTTTTAT
Found at i:19996695 original size:17 final size:17
Alignment explanation
Indices: 19996669--19996701 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19996659 TTAAATAATT
*
19996669 TTAAATTTATTCAAATA
1 TTAAAATTATTCAAATA
19996686 TTAAAATTATTCAAAT
1 TTAAAATTATTCAAAT
19996702 TATAGTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAAAATTATTCAAATA
Found at i:19996788 original size:21 final size:22
Alignment explanation
Indices: 19996763--19996813 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
19996753 TAAAATATGG
19996763 ATTTTATCTTC-TTAAT-AAATA
1 ATTTTAT-TTCATTAATCAAATA
*
19996784 ATTTTA-TTCATTTATCAAATA
1 ATTTTATTTCATTAATCAAATA
19996805 ATTTTATTT
1 ATTTTATTT
19996814 AAGAAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 3 0.12
20 4 0.15
21 17 0.65
22 2 0.08
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTATTTCATTAATCAAATA
Found at i:20004197 original size:15 final size:15
Alignment explanation
Indices: 20004177--20004210 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
20004167 CAAACAAAAG
*
20004177 CAAAAAAACATTTGA
1 CAAAAAAACATTCGA
*
20004192 CAAAAAAGCATTCGA
1 CAAAAAAACATTCGA
20004207 CAAA
1 CAAA
20004211 TAGCTGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.18, G:0.09, T:0.15
Consensus pattern (15 bp):
CAAAAAAACATTCGA
Found at i:20005250 original size:62 final size:63
Alignment explanation
Indices: 20005184--20005328 Score: 179
Period size: 63 Copynumber: 2.3 Consensus size: 63
20005174 GTTTCTAGCC
* * * * *
20005184 AAAAACACATTGAATAATCCCTTTCAATTTTTTAT-TG-GGATTTATTTAAGGTATTTTTGACAA
1 AAAAACACCTTGAATAATCCCCTTCAA-TTTTTATGAGAGGA-TTATTCAAGGTATTTTTAACAA
* * *
20005247 AAAAAAACCTTTAATAATCCCCTTCAATTTTTATGAGAGGATTATTCAAGGTATTTTTAAC-T
1 AAAAACACCTTGAATAATCCCCTTCAATTTTTATGAGAGGATTATTCAAGGTATTTTTAACAA
20005309 AAAAACACCTTGAATAATCC
1 AAAAACACCTTGAATAATCC
20005329 TTTACAAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
62 25 0.36
63 42 0.60
64 3 0.04
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (63 bp):
AAAAACACCTTGAATAATCCCCTTCAATTTTTATGAGAGGATTATTCAAGGTATTTTTAACAA
Found at i:20005267 original size:63 final size:62
Alignment explanation
Indices: 20005165--20005328 Score: 170
Period size: 63 Copynumber: 2.6 Consensus size: 62
20005155 GAATGAGGTA
* * * * * * * *
20005165 ATTCAAGGTGTTTCTAGCCAAAAACACATTGAATAATCCCTTTCAATTTTTTAT-TG-GGATTT
1 ATTCAAGGTATTTTTAACAAAAAAAACCTTGAATAATCCCCTTCAA-TTTTTATGAGAGGA-TT
* * *
20005227 ATTTAAGGTATTTTTGACAAAAAAAAACCTTTAATAATCCCCTTCAATTTTTATGAGAGGATT
1 ATTCAAGGTATTTTTAAC-AAAAAAAACCTTGAATAATCCCCTTCAATTTTTATGAGAGGATT
* *
20005290 ATTCAAGGTATTTTTAACTAAAAACACCTTGAATAATCC
1 ATTCAAGGTATTTTTAACAAAAAAAACCTTGAATAATCC
20005329 TTTACAAAAA
Statistics
Matches: 83, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
62 38 0.46
63 42 0.51
64 3 0.04
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (62 bp):
ATTCAAGGTATTTTTAACAAAAAAAACCTTGAATAATCCCCTTCAATTTTTATGAGAGGATT
Found at i:20005375 original size:61 final size:61
Alignment explanation
Indices: 20005288--20005524 Score: 201
Period size: 61 Copynumber: 3.9 Consensus size: 61
20005278 TATGAGAGGA
* * *
20005288 TTATTCAAGGTATTTTTAACTAAAAACACCTTGAATAATCCTTTACAAAAAATTGTATAGG
1 TTATTCAAGGTATTTTTAGCCAAAAACACCTTGAATAATCCTTTACAAAAAATTATATAGG
* * * * * **** *
20005349 TTATTCAAGGTGTTTCTAGCCAAAAACATCTTGAATAATCCCTTATAATTTTTTAT-TAAGAA
1 TTATTCAAGGTATTTTTAGCCAAAAACACCTTGAATAATCCTTTACAAAAAATTATAT-AG-G
* * * * * *
20005411 TTATTGAAGGTGTTTTTAGCCAGAAATACCTTGAATAATCCTTTACAAAAAA-TAAATGGG
1 TTATTCAAGGTATTTTTAGCCAAAAACACCTTGAATAATCCTTTACAAAAAATTATATAGG
* * * **
20005471 ATTATTTAAGGCATTTTTGGCCAAAAATGCCTTGAATAAT-CTCTTACAAAAAAT
1 -TTATTCAAGGTATTTTTAGCCAAAAACACCTTGAATAATCCT-TTACAAAAAAT
20005525 GCATTAAATA
Statistics
Matches: 137, Mismatches: 33, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
60 3 0.02
61 92 0.67
62 42 0.31
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (61 bp):
TTATTCAAGGTATTTTTAGCCAAAAACACCTTGAATAATCCTTTACAAAAAATTATATAGG
Found at i:20005431 original size:62 final size:61
Alignment explanation
Indices: 20005165--20005455 Score: 218
Period size: 62 Copynumber: 4.7 Consensus size: 61
20005155 GAATGAGGTA
* * ** *
20005165 ATTCAAGGTGTTTCTAGCCAAAAACACATTGAATAATCCCTTTCAATTTTTTATTGGGATTT
1 ATTCAAGGTGTTTTTAGCCAAAAACACCTTGAATAATCCCTTT-AATTTTTTATTAAGAATT
* * * * * * * *
20005227 ATTTAAGGTATTTTT-GACAAAAAAAAACCTTTAATAATCCCCTTCAA-TTTTTATGAGAGGATT
1 ATTCAAGGTGTTTTTAG-C-CAAAAACACCTTGAATAAT-CCCTTTAATTTTTTATTA-AGAATT
* * * ** * *
20005290 ATTCAAGGTATTTTTAACTAAAAACACCTTGAATAAT-CCTTTACAAAAAATTGTA-T-AG-GTT
1 ATTCAAGGTGTTTTTAGCCAAAAACACCTTGAATAATCCCTTT----AATTTTTTATTAAGAATT
* *
20005351 ATTCAAGGTGTTTCTAGCCAAAAACATCTTGAATAATCCCTTATAATTTTTTATTAAGAATT
1 ATTCAAGGTGTTTTTAGCCAAAAACACCTTGAATAATCCCTT-TAATTTTTTATTAAGAATT
* * *
20005413 ATTGAAGGTGTTTTTAGCCAGAAATACCTTGAATAAT-CCTTTA
1 ATTCAAGGTGTTTTTAGCCAAAAACACCTTGAATAATCCCTTTA
20005456 CAAAAAATAA
Statistics
Matches: 177, Mismatches: 37, Indels: 32
0.72 0.15 0.13
Matches are distributed among these distances:
59 6 0.03
60 7 0.04
61 41 0.23
62 76 0.43
63 36 0.20
64 7 0.04
65 4 0.02
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (61 bp):
ATTCAAGGTGTTTTTAGCCAAAAACACCTTGAATAATCCCTTTAATTTTTTATTAAGAATT
Found at i:20005494 original size:123 final size:124
Alignment explanation
Indices: 20005165--20005519 Score: 317
Period size: 123 Copynumber: 2.9 Consensus size: 124
20005155 GAATGAGGTA
* * * * *** * *
20005165 ATTCAAGGTGTTTCTAGCCAAAAACACATTGAATAATCCCTTT-C-AATTTTTTATTGGGATTTA
1 ATTCAAGGTATTTTTAACCAAAAACACCTTGAATAAT-CCTTTACAAAAAATTAAATGGGA-TTA
* * * *
20005228 TTTAAGGTATTTTTGACAAAAAAAAACCTTTAATAATCCCCTT-CAATTTTTATGAGAGGATT
64 TTTAAGGTATTTTTGGC-CAAAAAAACCTTGAATAAT-CCCTTACAATTTTTATGAGAGAATT
* ** *
20005290 ATTCAAGGTATTTTTAACTAAAAACACCTTGAATAATCCTTTACAAAAAATTGTATAGG-TTATT
1 ATTCAAGGTATTTTTAACCAAAAACACCTTGAATAATCCTTTACAAAAAATTAAATGGGATTATT
* * * * * * * *
20005354 CAAGGTGTTTCTAGCCAAAAACATCTTGAATAATCCCTTATAATTTTTTATTA-AGAATT
66 TAAGGTATTTTTGGCCAAAAAAACCTTGAATAATCCCTTACAA-TTTTTATGAGAGAATT
* * * * *
20005413 ATTGAAGGTGTTTTTAGCCAGAAATACCTTGAATAATCCTTTACAAAAAA-TAAATGGGATTATT
1 ATTCAAGGTATTTTTAACCAAAAACACCTTGAATAATCCTTTACAAAAAATTAAATGGGATTATT
* ** *
20005477 TAAGGCATTTTTGGCCAAAAATGCCTTGAATAATCTCTTACAA
66 TAAGGTATTTTTGGCCAAAAAAACCTTGAATAATCCCTTACAA
20005520 AAAATGCATT
Statistics
Matches: 182, Mismatches: 43, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
122 10 0.05
123 104 0.57
124 28 0.15
125 33 0.18
126 7 0.04
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (124 bp):
ATTCAAGGTATTTTTAACCAAAAACACCTTGAATAATCCTTTACAAAAAATTAAATGGGATTATT
TAAGGTATTTTTGGCCAAAAAAACCTTGAATAATCCCTTACAATTTTTATGAGAGAATT
Found at i:20007883 original size:17 final size:18
Alignment explanation
Indices: 20007852--20007885 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20007842 ATTAATATTA
*
20007852 GAAATGTGAATAGAAAGT
1 GAAATGTGAAAAGAAAGT
20007870 GAAA-GTGAAAAGAAAG
1 GAAATGTGAAAAGAAAG
20007886 ATAGTAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.00, G:0.29, T:0.15
Consensus pattern (18 bp):
GAAATGTGAAAAGAAAGT
Found at i:20009926 original size:20 final size:21
Alignment explanation
Indices: 20009901--20009940 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
20009891 TTTAAGGTTT
20009901 GTTTATATTCATTT-GGATTG
1 GTTTATATTCATTTAGGATTG
* *
20009921 GTTTATCTTCGTTTAGGATT
1 GTTTATATTCATTTAGGATT
20009941 TATTTGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.17, C:0.07, G:0.20, T:0.55
Consensus pattern (21 bp):
GTTTATATTCATTTAGGATTG
Found at i:20009957 original size:14 final size:15
Alignment explanation
Indices: 20009938--20009968 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20009928 TTCGTTTAGG
20009938 ATTTA-TTTGTTTAA
1 ATTTATTTTGTTTAA
20009952 ATTTATTTTGTTTAA
1 ATTTATTTTGTTTAA
20009967 AT
1 AT
20009969 AGTTATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (15 bp):
ATTTATTTTGTTTAA
Found at i:20013213 original size:17 final size:17
Alignment explanation
Indices: 20013191--20013224 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
20013181 TGTCACCACC
20013191 TTCCCTGAACCACTGGA
1 TTCCCTGAACCACTGGA
20013208 TTCCCTGAACCACTGGA
1 TTCCCTGAACCACTGGA
20013225 AATAACTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.24
Consensus pattern (17 bp):
TTCCCTGAACCACTGGA
Found at i:20014014 original size:51 final size:49
Alignment explanation
Indices: 20013944--20014093 Score: 183
Period size: 51 Copynumber: 3.0 Consensus size: 49
20013934 ATTAAAACTG
* *
20013944 ATTTTAGGATTATTCTGACTTTTTGGTGAAATCCCAAAACTTATTAAACAA
1 ATTTTAAGATTATT-TGACTTTTTGGTGAAATCCTAAAA-TTATTAAACAA
* * *
20013995 ATTTTACGATTATCTTGACTTTATGGTGAAATCCTAAAAATTATTAAACAT
1 ATTTTAAGATTAT-TTGACTTTTTGGTGAAATCCT-AAAATTATTAAACAA
* * *
20014046 ATTTTAAGATTATTTTGATTTTTTTGTGAAATCCTAAAATTTTTAAAC
1 ATTTTAAGATTA-TTTGACTTTTTGGTGAAATCCTAAAATTATTAAAC
20014094 TGATTTTAGA
Statistics
Matches: 87, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
50 12 0.14
51 69 0.79
52 6 0.07
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (49 bp):
ATTTTAAGATTATTTGACTTTTTGGTGAAATCCTAAAATTATTAAACAA
Found at i:20014443 original size:16 final size:15
Alignment explanation
Indices: 20014419--20014452 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
20014409 TTTGTTTTTA
20014419 AAATATTATTTAAAT
1 AAATATTATTTAAAT
*
20014434 AAATATTTATTTTAAT
1 AAATA-TTATTTAAAT
20014450 AAA
1 AAA
20014453 AATAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATATTATTTAAAT
Found at i:20014836 original size:3 final size:3
Alignment explanation
Indices: 20014830--20014874 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
20014820 GTAGTAGTAG
20014830 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20014875 AATCAAAATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20016555 original size:19 final size:19
Alignment explanation
Indices: 20016528--20016568 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
20016518 ATTTCTTTCT
* *
20016528 TTTTCTTTATTTCTAAATG
1 TTTTATTTATTTATAAATG
*
20016547 TTTTATTTATTTATTAATG
1 TTTTATTTATTTATAAATG
20016566 TTT
1 TTT
20016569 GCTTGTGTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTATTTATTTATAAATG
Found at i:20016816 original size:44 final size:43
Alignment explanation
Indices: 20016731--20016816 Score: 109
Period size: 44 Copynumber: 2.0 Consensus size: 43
20016721 AATTTTGCAT
* **
20016731 AAATAAACTTTACCAACATATTGGAAGGTTTATAAATTTTTTA
1 AAATAAACTTTACCAACATATTGAAAAATTTATAAATTTTTTA
* *
20016774 AAATAAGATTTTACCAACATATTGAAAAATATTATTAATTTTT
1 AAATAA-ACTTTACCAACATATTGAAAAAT-TTATAAATTTTT
20016817 GATAAAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
43 6 0.17
44 19 0.53
45 11 0.31
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (43 bp):
AAATAAACTTTACCAACATATTGAAAAATTTATAAATTTTTTA
Found at i:20018531 original size:17 final size:17
Alignment explanation
Indices: 20018501--20018545 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
20018491 CTGGACTTGA
20018501 AAAATTCTTATGAATCTT
1 AAAA-TCTTATGAATCTT
* *
20018519 CAAATCTTGTGAATCTT
1 AAAATCTTATGAATCTT
20018536 AAAATTCTTA
1 AAAA-TCTTA
20018546 CAAATTTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (17 bp):
AAAATCTTATGAATCTT
Found at i:20018673 original size:18 final size:18
Alignment explanation
Indices: 20018617--20018673 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 18
20018607 TGTGAATTTG
* *
20018617 AAAATTCTTACAAATCTA
1 AAAATTCTTGCCAATCTA
* *
20018635 AAAATTCTTGCCAAACAA
1 AAAATTCTTGCCAATCTA
* **
20018653 AAAATTTTTGTGAATCTA
1 AAAATTCTTGCCAATCTA
20018671 AAA
1 AAA
20018674 GCTTTGCGAA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (18 bp):
AAAATTCTTGCCAATCTA
Found at i:20024023 original size:27 final size:26
Alignment explanation
Indices: 20023945--20024024 Score: 92
Period size: 27 Copynumber: 3.1 Consensus size: 26
20023935 AATTTCATGG
* *
20023945 ACAACCCTCA-CATTCTTGCTTGGGT
1 ACAACCCTCACCATTCTTGCTAGGCT
*
20023970 -CAACCCTCACCATTCTTGCTAACGCT
1 ACAACCCTCACCATTCTTGCT-AGGCT
*
20023996 ACTACCCTCACCATTCTTGCTAGTGCT
1 ACAACCCTCACCATTCTTGCTAG-GCT
20024023 AC
1 AC
20024025 CAACACTTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
24 9 0.20
25 10 0.22
26 3 0.07
27 24 0.52
ACGTcount: A:0.21, C:0.38, G:0.11, T:0.30
Consensus pattern (26 bp):
ACAACCCTCACCATTCTTGCTAGGCT
Found at i:20024586 original size:31 final size:31
Alignment explanation
Indices: 20024551--20024609 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
20024541 ACTAAAAGAG
20024551 CCCATCAGACAAAATTTTAAAAGTTTTCCAT
1 CCCATCAGACAAAATTTTAAAAGTTTTCCAT
20024582 CCCATCAGACAAAATTTTAAAAGTTTTC
1 CCCATCAGACAAAATTTTAAAAGTTTTC
20024610 TTTGTGGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.32
Consensus pattern (31 bp):
CCCATCAGACAAAATTTTAAAAGTTTTCCAT
Found at i:20028262 original size:21 final size:21
Alignment explanation
Indices: 20028238--20028280 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
20028228 GGTTTCCTAT
20028238 TACTCAAGTTGGTGATATTGA
1 TACTCAAGTTGGTGATATTGA
*
20028259 TACTCAAGTTGGTGATCTTGA
1 TACTCAAGTTGGTGATATTGA
20028280 T
1 T
20028281 GTTTAAAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.40
Consensus pattern (21 bp):
TACTCAAGTTGGTGATATTGA
Done.