Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 187 of 198
Found at i:58177229 original size:21 final size:21
Alignment explanation
Indices: 58177205--58177245 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
58177195 TCCACGACCA
*
58177205 CCTCCTCTACCACCACCTCTG
1 CCTCCTCCACCACCACCTCTG
*
58177226 CCTCCTCCACGACCACCTCT
1 CCTCCTCCACCACCACCTCT
58177246 TCCACCACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.59, G:0.05, T:0.22
Consensus pattern (21 bp):
CCTCCTCCACCACCACCTCTG
Found at i:58177248 original size:69 final size:69
Alignment explanation
Indices: 58177121--58177250 Score: 161
Period size: 69 Copynumber: 1.9 Consensus size: 69
58177111 ACCTCTAAAT
** *** *
58177121 CCACCGCCACGACCACCACCCCTAGGACCACCTCTGCCACCTCTTGGAGCACCCCTTCCACGAAA
1 CCACCGCCACGACCACCACCCCTACCACCACCTCTGCCACCTCCACGACCACCCCTTCCACGAAA
58177186 TCCA
66 TCCA
* * * * *
58177190 CCACCTCCACGACCACCTCCTCTACCACCACCTCTGCCTCCTCCACGACCACCTCTTCCAC
1 CCACCGCCACGACCACCACCCCTACCACCACCTCTGCCACCTCCACGACCACCCCTTCCAC
58177251 CACCTTGTGC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
69 50 1.00
ACGTcount: A:0.21, C:0.55, G:0.09, T:0.15
Consensus pattern (69 bp):
CCACCGCCACGACCACCACCCCTACCACCACCTCTGCCACCTCCACGACCACCCCTTCCACGAAA
TCCA
Found at i:58185112 original size:13 final size:14
Alignment explanation
Indices: 58185094--58185122 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
58185084 GTACTACAAG
58185094 ATTATTTT-TTTAA
1 ATTATTTTATTTAA
58185107 ATTATTTTATTTAA
1 ATTATTTTATTTAA
58185121 AT
1 AT
58185123 GTCTATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTATTTTATTTAA
Found at i:58185538 original size:25 final size:25
Alignment explanation
Indices: 58185468--58185527 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
58185458 ACTTTAGCGC
58185468 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
58185493 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
*
58185518 GCTCTTTGAT
1 GCTCTCTGAT
58185528 ATTTAGTACG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.15, C:0.20, G:0.23, T:0.42
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTTGGT
Found at i:58185588 original size:22 final size:21
Alignment explanation
Indices: 58185540--58185595 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
58185530 TTAGTACGTC
* *
58185540 AGTGCTATCTGTTTAGCACAT
1 AGTGCTCTCTGTATAGCACAT
*
58185561 ATGTGCTCTCTGTATAGCACTTT
1 A-GTGCTCTCTGTATAGCAC-AT
58185584 AGTGCTCTCTGT
1 AGTGCTCTCTGT
58185596 TCATTAGTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 27 0.90
23 2 0.07
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (21 bp):
AGTGCTCTCTGTATAGCACAT
Found at i:58190349 original size:67 final size:67
Alignment explanation
Indices: 58190241--58190372 Score: 255
Period size: 67 Copynumber: 2.0 Consensus size: 67
58190231 TTTTCAATTC
*
58190241 AGAGAGCACACTCCCGTGAACCTCATTTCTTACAGCGAGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGAGATTACCAGTCCAGGCTAAATCCCCTG
58190306 CA
66 CA
58190308 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGAGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGAGATTACCAGTCCAGGCTAAATCCCCTG
58190373 TAATATAAAC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.20
Consensus pattern (67 bp):
AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGAGATTACCAGTCCAGGCTAAATCCCCTG
CA
Found at i:58192686 original size:19 final size:17
Alignment explanation
Indices: 58192641--58192689 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
58192631 TGATGAACTC
*
58192641 TTTTATAATTTTCTTGAA
1 TTTTGTAATTTT-TTGAA
58192659 TTTTG-AATTTTTTGAA
1 TTTTGTAATTTTTTGAA
58192675 TATCTTGTAATTTTT
1 T-T-TTGTAATTTTT
58192690 AAACTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 6 0.22
17 7 0.26
18 7 0.26
19 7 0.26
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.63
Consensus pattern (17 bp):
TTTTGTAATTTTTTGAA
Found at i:58202272 original size:25 final size:25
Alignment explanation
Indices: 58202225--58202272 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
58202215 TAGTCATACC
* * * *
58202225 AGTTTTTAATAATAGAAATAGATGA
1 AGTTTTTAACAAAAAAAAAAGATGA
58202250 AGTTTTTAACAAAAAAAAAAGAT
1 AGTTTTTAACAAAAAAAAAAGAT
58202273 TAATTTCCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.31
Consensus pattern (25 bp):
AGTTTTTAACAAAAAAAAAAGATGA
Found at i:58204080 original size:124 final size:124
Alignment explanation
Indices: 58203897--58204133 Score: 370
Period size: 124 Copynumber: 1.9 Consensus size: 124
58203887 CATGTACAAT
* * * * *
58203897 GTATTAATTATGTCATTTTAAGTTTTAGTTTAATGTATTGTAATAACGAGGATAACATAAGTTTA
1 GTATTAATTATGTCATTTTAAGTTTCAGTTTAATCTATTGTAATAACCAGGAGAACATAAGTTCA
* *
58203962 AACGTGCTTAATCGTGTATTTCTCTTT-GATTTAAGAGTTTGAGAGGATTATAAGTAAAAC
66 AACGTGCTTAATCATGTATTT-T-TTTCAATTTAAGAGTTTGAGAGGATTATAAGTAAAAC
*
58204022 GTATTAATTATGTCA-TTTGAGTTTCAGTTTAATCTATTGTAATAACCAGGAGAACATAAGTTCA
1 GTATTAATTATGTCATTTTAAGTTTCAGTTTAATCTATTGTAATAACCAGGAGAACATAAGTTCA
58204086 AACGTGCTTAATCATGTATTTTTTTCAATTTAAGAGTTTGAGAGGATT
66 AACGTGCTTAATCATGTATTTTTTTCAATTTAAGAGTTTGAGAGGATT
58204134 TTAAACAAAA
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
122 3 0.03
123 22 0.21
124 63 0.61
125 15 0.15
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.41
Consensus pattern (124 bp):
GTATTAATTATGTCATTTTAAGTTTCAGTTTAATCTATTGTAATAACCAGGAGAACATAAGTTCA
AACGTGCTTAATCATGTATTTTTTTCAATTTAAGAGTTTGAGAGGATTATAAGTAAAAC
Found at i:58215974 original size:22 final size:22
Alignment explanation
Indices: 58215912--58215976 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
58215902 CTCTGATTAT
* *
58215912 TAGCACATTAAG-GCTCTCCGTT
1 TAGCACATT-AGTGCTCTCTGTA
*
58215934 TAGCACATTCGTGCTCTCTGTA
1 TAGCACATTAGTGCTCTCTGTA
*
58215956 TAGCACTTTAGTGCTCTCTGT
1 TAGCACATTAGTGCTCTCTGT
58215977 TCAATAATGC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 1 0.03
22 36 0.97
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.37
Consensus pattern (22 bp):
TAGCACATTAGTGCTCTCTGTA
Found at i:58220999 original size:11 final size:11
Alignment explanation
Indices: 58220977--58221028 Score: 77
Period size: 11 Copynumber: 4.6 Consensus size: 11
58220967 AACTAATACT
58220977 CTCTCAAATTTC
1 CTCTC-AATTTC
58220989 CTCTCAATTTC
1 CTCTCAATTTC
*
58221000 CTCTAAATTTC
1 CTCTCAATTTC
*
58221011 CTCTCAATTTG
1 CTCTCAATTTC
58221022 CTCTCAA
1 CTCTCAA
58221029 ATTACTTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
11 32 0.86
12 5 0.14
ACGTcount: A:0.23, C:0.33, G:0.02, T:0.42
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:58221010 original size:22 final size:23
Alignment explanation
Indices: 58220977--58221031 Score: 94
Period size: 22 Copynumber: 2.4 Consensus size: 23
58220967 AACTAATACT
58220977 CTCTCAAATTTCCTCTCAATTTC
1 CTCTCAAATTTCCTCTCAATTTC
*
58221000 CTCT-AAATTTCCTCTCAATTTG
1 CTCTCAAATTTCCTCTCAATTTC
58221022 CTCTCAAATT
1 CTCTCAAATT
58221032 ACTTCCAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 21 0.70
23 9 0.30
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.44
Consensus pattern (23 bp):
CTCTCAAATTTCCTCTCAATTTC
Found at i:58221042 original size:34 final size:34
Alignment explanation
Indices: 58220977--58221052 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 34
58220967 AACTAATACT
* *
58220977 CTCTCAAATTTCCTCTCAATTTCCTCTAAATTTC
1 CTCTCAAATTTCCTCTCAATTACCTCCAAATTTC
* *
58221011 CTCTC-AATTTGCTCTCAAATTACTTCCAAATTT-
1 CTCTCAAATTTCCTCTC-AATTACCTCCAAATTTC
*
58221044 CTCTAAAAT
1 CTCTCAAAT
58221053 CCATATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
33 14 0.40
34 21 0.60
ACGTcount: A:0.28, C:0.29, G:0.01, T:0.42
Consensus pattern (34 bp):
CTCTCAAATTTCCTCTCAATTACCTCCAAATTTC
Found at i:58221070 original size:51 final size:51
Alignment explanation
Indices: 58221012--58221111 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
58221002 CTAAATTTCC
*
58221012 TCTCAATTTGCTCTCAAATTACTTC-CAAATTTCTCTAAAATCCATATTTAA
1 TCTCAATTTGCTCTC-AATTACCTCTCAAATTTCTCTAAAATCCATATTTAA
* * * * *
58221063 TCTCAATTTTCTCTCAATTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAATTACCTCTCAAATTTCTCTAAAATCCATATTT
58221112 TTAAATAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 7 0.17
51 35 0.83
ACGTcount: A:0.28, C:0.25, G:0.01, T:0.46
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAATTACCTCTCAAATTTCTCTAAAATCCATATTTAA
Found at i:58221767 original size:30 final size:30
Alignment explanation
Indices: 58221733--58221793 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
58221723 TCAACCGAAG
58221733 TAGAAAGAATCTGATATGCTCGGGCATACA
1 TAGAAAGAATCTGATATGCTCGGGCATACA
58221763 TAGAAAGAATCTGATATGCTCGGGCATACA
1 TAGAAAGAATCTGATATGCTCGGGCATACA
58221793 T
1 T
58221794 TCTTCAGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (30 bp):
TAGAAAGAATCTGATATGCTCGGGCATACA
Found at i:58226040 original size:125 final size:126
Alignment explanation
Indices: 58225604--58226047 Score: 660
Period size: 125 Copynumber: 3.5 Consensus size: 126
58225594 CCCAAACATG
*
58225604 CTACTGTAGCAAAAGCGCGTCCACGAGAGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTG
*
58225668 CTAGAAGCG-TTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
65 CTTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
* *
58225729 ATACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTTTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
*
58225794 TTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
66 TTGAAGCG-TTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
* ** * * *
58225856 TTACTGTAGCAAAAGCGCGTCCGTGAGGGCGTGATTTCACAAATTCTTTTCATATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* *
58225921 TTGAAGCGTTTTTTATACTATTTGCTCAGAAATGTTAACTCGAAATTATTT-TTCCAGGAC
66 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
* * * * * * * *
58225981 CTACTGTAGCAAAAGCGCGTACAAGTGGGCGCGACTTCAGAAATCCTTCTGATAAAGCATTCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
58226046 TT
66 TT
58226048 TGATTTTATC
Statistics
Matches: 288, Mismatches: 28, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
125 129 0.45
126 42 0.15
127 117 0.41
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
Found at i:58226209 original size:15 final size:15
Alignment explanation
Indices: 58226172--58226219 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
58226162 TAAAACTCTA
*
58226172 AAAATCCTAAAAACAT
1 AAAATCC-AAAAACCT
* * *
58226188 TAAATCCTAAACCCT
1 AAAATCCAAAAACCT
58226203 AAAATCCAAAAACCT
1 AAAATCCAAAAACCT
58226218 AA
1 AA
58226220 CGTGGGAAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAATCCAAAAACCT
Found at i:58232426 original size:23 final size:23
Alignment explanation
Indices: 58232400--58232445 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
58232390 TTACGATAGC
58232400 AAAAG-TTAAATTTAATTATTTTT
1 AAAAGATTAAA-TTAATTATTTTT
*
58232423 AAAAGATTAAATTAATTTTTTTT
1 AAAAGATTAAATTAATTATTTTT
58232446 CTTTTTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
AAAAGATTAAATTAATTATTTTT
Found at i:58241981 original size:11 final size:12
Alignment explanation
Indices: 58241965--58241994 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
58241955 ATTTTTTATA
58241965 TTTAAAATA-TT
1 TTTAAAATACTT
58241976 TTTAAAATACTT
1 TTTAAAATACTT
58241988 TTTAAAA
1 TTTAAAA
58241995 AAAATTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (12 bp):
TTTAAAATACTT
Found at i:58242005 original size:16 final size:16
Alignment explanation
Indices: 58241986--58242016 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58241976 TTTAAAATAC
58241986 TTTTTAAAAAAAATTA
1 TTTTTAAAAAAAATTA
*
58242002 TTTTTAAAATAAATT
1 TTTTTAAAAAAAATT
58242017 TGAAGTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTTAAAAAAAATTA
Found at i:58256489 original size:9 final size:9
Alignment explanation
Indices: 58256477--58256580 Score: 57
Period size: 9 Copynumber: 10.7 Consensus size: 9
58256467 ATAAAAATAA
58256477 ATAAAATTT
1 ATAAAATTT
58256486 ATAAAATTT
1 ATAAAATTT
*
58256495 ATTAAATTTT
1 A-TAAAATTT
58256505 AGTAAAAAATATT
1 A-T--AAAAT-TT
*
58256518 A-AAAATTAG
1 ATAAAATT-T
*
58256527 AAAAAATTT
1 ATAAAATTT
*
58256536 ATAAAAATT
1 ATAAAATTT
*
58256545 ATAAAAAATT
1 AT-AAAATTT
*
58256555 GTAAAATTTTT
1 ATAAAA--TTT
*
58256566 ATAAAAATT
1 ATAAAATTT
58256575 ATAAAA
1 ATAAAA
58256581 AATTCGAGTG
Statistics
Matches: 75, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
8 1 0.01
9 37 0.49
10 23 0.31
11 7 0.09
12 4 0.05
13 3 0.04
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (9 bp):
ATAAAATTT
Found at i:58256541 original size:30 final size:30
Alignment explanation
Indices: 58256502--58256584 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 30
58256492 TTTATTAAAT
* *
58256502 TTTAGTAAAAAATATTAAAAATTAG-AAAAAA
1 TTTA-TAAAAATTATAAAAAATT-GTAAAAAA
**
58256533 TTTATAAAAATTATAAAAAATTGTAAAATT
1 TTTATAAAAATTATAAAAAATTGTAAAAAA
58256563 TTTATAAAAATTATAAAAAATT
1 TTTATAAAAATTATAAAAAATT
58256585 CGAGTGTCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
29 1 0.02
30 42 0.89
31 4 0.09
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (30 bp):
TTTATAAAAATTATAAAAAATTGTAAAAAA
Found at i:58256551 original size:10 final size:10
Alignment explanation
Indices: 58256507--58256584 Score: 72
Period size: 10 Copynumber: 7.9 Consensus size: 10
58256497 TAAATTTTAG
58256507 TAAAAAA-TA
1 TAAAAAATTA
*
58256516 TTAAAAATTA
1 TAAAAAATTA
*
58256526 GAAAAAATT-
1 TAAAAAATTA
58256535 TATAAAAATTA
1 TA-AAAAATTA
*
58256546 TAAAAAATTG
1 TAAAAAATTA
* *
58256556 T-AAAATTTT
1 TAAAAAATTA
58256565 TATAAAAATTA
1 TA-AAAAATTA
58256576 TAAAAAATT
1 TAAAAAATT
58256585 CGAGTGTCTT
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
9 14 0.25
10 31 0.56
11 10 0.18
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:58256554 original size:20 final size:20
Alignment explanation
Indices: 58256479--58256581 Score: 79
Period size: 20 Copynumber: 5.2 Consensus size: 20
58256469 AAAAATAAAT
*
58256479 AAAATT-TATAAAATTTATTA
1 AAAATTATAAAAAATTTA-TA
** *
58256499 AATTTTAGTAAAAAATAT-TA
1 AAAATTA-TAAAAAATTTATA
*
58256519 AAAATTAGAAAAAATTTATA
1 AAAATTATAAAAAATTTATA
*
58256539 AAAATTATAAAAAA-TTGTA
1 AAAATTATAAAAAATTTATA
* *
58256558 AAATTTTTATAAAAA-TTATA
1 AAAATTATA-AAAAATTTATA
58256578 AAAA
1 AAAA
58256582 ATTCGAGTGT
Statistics
Matches: 65, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
19 19 0.29
20 38 0.58
22 8 0.12
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
AAAATTATAAAAAATTTATA
Found at i:58256581 original size:9 final size:9
Alignment explanation
Indices: 58256467--58256581 Score: 68
Period size: 10 Copynumber: 11.8 Consensus size: 9
58256457 AATAATGAAA
*
58256467 ATAAAAATAA
1 ATAAAAAT-T
*
58256477 ATAAAATTT
1 ATAAAAATT
*
58256486 ATAAAATTT
1 ATAAAAATT
**
58256495 ATTAAATTTT
1 A-TAAAAATT
*
58256505 AGTAAAAAAT
1 A-TAAAAATT
58256515 ATTAAAAATT
1 A-TAAAAATT
*
58256525 AGAAAAAATTT
1 A-TAAAAA-TT
58256536 ATAAAAATT
1 ATAAAAATT
58256545 ATAAAAAATT
1 AT-AAAAATT
* *
58256555 GTAAAATTTTT
1 ATAAAA--ATT
58256566 ATAAAAATT
1 ATAAAAATT
58256575 ATAAAAA
1 ATAAAAA
58256582 ATTCGAGTGT
Statistics
Matches: 84, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
9 27 0.32
10 47 0.56
11 10 0.12
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (9 bp):
ATAAAAATT
Found at i:58257286 original size:32 final size:33
Alignment explanation
Indices: 58257227--58257293 Score: 109
Period size: 32 Copynumber: 2.0 Consensus size: 33
58257217 AAAAATTGCA
*
58257227 ACATAAGCCCCTCTACTTTTTTTTATATAAATTT
1 ACATAAACCCCTCTAC-TTTTTTTATATAAATTT
58257261 ACATAAACCCCTCTAC-TTTTTTATATAAATTT
1 ACATAAACCCCTCTACTTTTTTTATATAAATTT
58257293 A
1 A
58257294 ATTGGTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 17 0.53
34 15 0.47
ACGTcount: A:0.33, C:0.21, G:0.01, T:0.45
Consensus pattern (33 bp):
ACATAAACCCCTCTACTTTTTTTATATAAATTT
Found at i:58258657 original size:24 final size:24
Alignment explanation
Indices: 58258630--58258678 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
58258620 AAATGTTCAT
* *
58258630 GGATTGATCAATCCTAGAATGAAG
1 GGATTGAGCAATCCTAGAACGAAG
58258654 GGATTGAGCAATCCTAGAACGAAG
1 GGATTGAGCAATCCTAGAACGAAG
58258678 G
1 G
58258679 AGGAAGATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.14, G:0.29, T:0.20
Consensus pattern (24 bp):
GGATTGAGCAATCCTAGAACGAAG
Found at i:58261438 original size:87 final size:87
Alignment explanation
Indices: 58261308--58261483 Score: 271
Period size: 87 Copynumber: 2.0 Consensus size: 87
58261298 CCAACTGATT
* * *
58261308 AGGGGTCACTCTATTAGATAATCCAGAGGAACTAACACCAGAATCAGCACTTGGACCTGATAATG
1 AGGGATCACTCTATTAGATAATCCAGAAGAACTAACACCAGAATCACCACTTGGACCTGATAATG
*
58261373 AAGGTAACACTTCTGCAGTTCC
66 AAGGCAACACTTCTGCAGTTCC
* * ** *
58261395 AGGGATCACTCTATTAGATGATCCGGAAGAACTAACAGTAGAATCACCAGTTGGACCTGATAATG
1 AGGGATCACTCTATTAGATAATCCAGAAGAACTAACACCAGAATCACCACTTGGACCTGATAATG
58261460 AAGGCAACACTTCTGCAGTTCC
66 AAGGCAACACTTCTGCAGTTCC
58261482 AG
1 AG
58261484 TACTTGACCC
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 80 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (87 bp):
AGGGATCACTCTATTAGATAATCCAGAAGAACTAACACCAGAATCACCACTTGGACCTGATAATG
AAGGCAACACTTCTGCAGTTCC
Found at i:58269321 original size:31 final size:31
Alignment explanation
Indices: 58269285--58269343 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
58269275 AAATGGTCAT
*
58269285 TGAACTATTT-GAAAGTTTTTATTTAAATCAC
1 TGAACTATTTGGAAA-TTTTCATTTAAATCAC
58269316 TGAACTATTTGGAAATTTTCATTTAAAT
1 TGAACTATTTGGAAATTTTCATTTAAAT
58269344 TAATGAGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (31 bp):
TGAACTATTTGGAAATTTTCATTTAAATCAC
Found at i:58269355 original size:31 final size:31
Alignment explanation
Indices: 58269285--58269355 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
58269275 AAATGGTCAT
* *
58269285 TGAACTATTTGAAAGTTTTTATTTAAATCAC
1 TGAACTATTTGAAAGTTTTCATTTAAATCAA
*
58269316 TGAACTATTTGGAAA-TTTTCATTTAAATTAA
1 TGAACTATTT-GAAAGTTTTCATTTAAATCAA
*
58269347 TGAGCTATT
1 TGAACTATT
58269356 AATTTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 31 0.89
32 4 0.11
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.45
Consensus pattern (31 bp):
TGAACTATTTGAAAGTTTTCATTTAAATCAA
Found at i:58276029 original size:18 final size:18
Alignment explanation
Indices: 58276003--58276045 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
58275993 TATTAAATAA
*
58276003 ATATTTTTTTAAT-TTTT
1 ATATTTTTTGAATGTTTT
58276020 ATACTTTTTTGAATGTTTT
1 ATA-TTTTTTGAATGTTTT
58276039 ATATTTT
1 ATATTTT
58276046 AAAAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 13 0.57
19 7 0.30
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (18 bp):
ATATTTTTTGAATGTTTT
Found at i:58276171 original size:3 final size:3
Alignment explanation
Indices: 58276163--58276208 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
58276153 TCATTATGCC
58276163 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
58276209 CCAAAGAGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:58284596 original size:22 final size:21
Alignment explanation
Indices: 58284544--58284607 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
58284534 TAAATATCCC
58284544 ATAAAAATATTTTAAAATATAT
1 ATAAAAA-ATTTTAAAATATAT
** *
58284566 ATGTCAAAATTTTAAAATTATTT
1 AT-AAAAAATTTTAAAA-TATAT
*
58284589 ATAAAAAATTAGTAAAATA
1 ATAAAAAATT-TTAAAATA
58284608 GTTAATTTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
22 19 0.58
23 14 0.42
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (21 bp):
ATAAAAAATTTTAAAATATAT
Found at i:58284977 original size:24 final size:25
Alignment explanation
Indices: 58284941--58284997 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
58284931 AAAAGAGAAT
58284941 GAAAAAAAGTTAAAAGAA-CATAAAA
1 GAAAAAAAGTTAAAAGAATCA-AAAA
* *
58284966 GAAAAAAA-TTAAAATAATCAAAAT
1 GAAAAAAAGTTAAAAGAATCAAAAA
58284990 GAAAAAAA
1 GAAAAAAA
58284998 ATATAATAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 19 0.66
25 10 0.34
ACGTcount: A:0.74, C:0.04, G:0.09, T:0.14
Consensus pattern (25 bp):
GAAAAAAAGTTAAAAGAATCAAAAA
Found at i:58285005 original size:24 final size:23
Alignment explanation
Indices: 58284962--58285006 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
58284952 AAAAGAACAT
*
58284962 AAAAGAAAAAAATTAAAATAATC
1 AAAAGAAAAAAAATAAAATAATC
*
58284985 AAAATGAAAAAAAATATAATAA
1 AAAA-GAAAAAAAATAAAATAA
58285007 CTAATTTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (23 bp):
AAAAGAAAAAAAATAAAATAATC
Found at i:58285230 original size:16 final size:16
Alignment explanation
Indices: 58285209--58285278 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
58285199 TTTGGTTCGC
* *
58285209 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
58285225 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
58285241 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
58285257 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
58285273 TGTAAT
1 TGTAAT
58285279 AGCAAATCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:58285311 original size:45 final size:44
Alignment explanation
Indices: 58285257--58285351 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 44
58285247 GGAATAGAGG
*
58285257 TGTAATGGAATAGAGGTGTAATAGCAAATCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGC-AATC-ATGTGTTTGGTTGAA
*
58285302 TGTAATGGAATAGAGGCGTAATAGCAATCCTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAATCATGTGTTTGGTTGAA
58285346 TGTAAT
1 TGTAAT
58285352 AGAGGTGTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.47
45 24 0.51
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAATCATGTGTTTGGTTGAA
Found at i:58285532 original size:18 final size:17
Alignment explanation
Indices: 58285511--58285545 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
58285501 TTATTATTAA
*
58285511 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
58285529 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
58285546 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:58288147 original size:2 final size:2
Alignment explanation
Indices: 58288140--58288170 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
58288130 GACAACATTA
58288140 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58288171 AACACAGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58289764 original size:51 final size:51
Alignment explanation
Indices: 58289688--58289789 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
58289678 TATTCAACAC
*
58289688 TAGTTCGAGTCTGGATAATGATTCAAGATAGAAGAAGAAACCTACAAAGGG
1 TAGTTCGAGTCTGGATAATAATTCAAGATAGAAGAAGAAACCTACAAAGGG
*
58289739 TAGTTCGAGTCTGGATAATAATTCAAGATAGAAGAAGAAACCTGCAAAGGG
1 TAGTTCGAGTCTGGATAATAATTCAAGATAGAAGAAGAAACCTACAAAGGG
58289790 GAACTACTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (51 bp):
TAGTTCGAGTCTGGATAATAATTCAAGATAGAAGAAGAAACCTACAAAGGG
Found at i:58292227 original size:150 final size:147
Alignment explanation
Indices: 58292048--58292449 Score: 436
Period size: 149 Copynumber: 2.7 Consensus size: 147
58292038 GGACTCAGTC
* * * *
58292048 TGAAAATGTTATGTTATATGCAATTTGGTTCATATGGCTGCCTTCTGAGTTCAACGTTTCATTAC
1 TGAAAATGTT-TGTTATATGCTATATGGTTCATATGGCTGCTTTC-AAGTTCAACGTTTCATTAC
* * * *
58292113 TTGTATTTCAGTTCTAGAAT-CTCAATGACTAATGGAAAAGCAGGC-CAAACGAAGAAATCTCAA
64 TTCTATTTCAGTTCTACAATGCTCAATGACTAATGGAAAAGCAGGCAC-AACCAACAAATCTCAA
*
58292176 GCATGATGCTAACAGATTAACTT
128 GC-T--TGATAACAGATTAACTT
* * * *
58292199 T-AAAATGTATTGTTATATGCTATATGGTTCATGTAGCTGCTTTCAAGTTC-ACTCTTTCATTTC
1 TGAAAATGT-TTGTTATATGCTATATGGTTCATATGGCTGCTTTCAAGTTCAAC-GTTTCATTAC
* * * *
58292262 TTCTATTTCAGTTCTACAATGCTCAATGGCTAATGGAAAGGCAGGCACTACCAACAAATCTCAGG
64 TTCTATTTCAGTTCTACAATGCTCAATGACTAATGGAAAAGCAGGCACAACCAACAAATCTCAAG
*
58292327 CTTGATAACAGATTCACTT
129 CTTGATAACAGATTAACTT
* * * * *
58292346 TGAAAATGTCTTGTTATAATGCTA-ATGGCTTCATATGGATGCTTTCAAGCTCAATGCTTCATTG
1 TGAAAATGT-TTGTTAT-ATGCTATATGG-TTCATATGGCTGCTTTCAAGTTCAACGTTTCATTA
* * *
58292410 CTTCTATTTCAGCTCTACAATGTTCGATGACTAATGGAAA
63 CTTCTATTTCAGTTCTACAATGCTCAATGACTAATGGAAA
58292450 CCAAAAAGCA
Statistics
Matches: 212, Mismatches: 31, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
147 16 0.08
148 20 0.09
149 99 0.47
150 74 0.35
151 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (147 bp):
TGAAAATGTTTGTTATATGCTATATGGTTCATATGGCTGCTTTCAAGTTCAACGTTTCATTACTT
CTATTTCAGTTCTACAATGCTCAATGACTAATGGAAAAGCAGGCACAACCAACAAATCTCAAGCT
TGATAACAGATTAACTT
Found at i:58301026 original size:2 final size:2
Alignment explanation
Indices: 58301019--58301043 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58301009 TTTAAAATGC
58301019 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
58301044 TTAAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58301128 original size:44 final size:43
Alignment explanation
Indices: 58301072--58301207 Score: 150
Period size: 44 Copynumber: 3.1 Consensus size: 43
58301062 ATTTAGGTCC
* * *
58301072 TAGGATTTAAATAGGTTAACGTTTTATTTTTCTCATTTATATTT
1 TAGGATTCAAATAGGTTAACGTTTT-TTTTTCTAATTTAAATTT
* *
58301116 TAGGATTCAAATAGGTT-ACATTTTTTTTTCTAATTTAGATCTT
1 TAGGATTCAAATAGGTTAACGTTTTTTTTTCTAATTTAAAT-TT
* * * *
58301159 AAGG-TTCAAATAGGTTAGAAGTTTGTTTTTCTAATTTAAATCT
1 TAGGATTCAAATAGGTTA-ACGTTTTTTTTTCTAATTTAAATTT
58301202 TAGGAT
1 TAGGAT
58301208 AAAATTTTAT
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
42 26 0.34
43 15 0.19
44 36 0.47
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.49
Consensus pattern (43 bp):
TAGGATTCAAATAGGTTAACGTTTTTTTTTCTAATTTAAATTT
Found at i:58303043 original size:14 final size:14
Alignment explanation
Indices: 58303024--58303063 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
58303014 TTGTTTACCA
*
58303024 GTAAAATGTTTTCC
1 GTAAAATGATTTCC
*
58303038 GTAAAATGATTTCT
1 GTAAAATGATTTCC
*
58303052 GAAAAATGATTT
1 GTAAAATGATTT
58303064 ATTTTTATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (14 bp):
GTAAAATGATTTCC
Found at i:58303162 original size:32 final size:32
Alignment explanation
Indices: 58303077--58303162 Score: 93
Period size: 33 Copynumber: 2.7 Consensus size: 32
58303067 TTTATGGAAA
*
58303077 ATGATTTACTGAAAATATTTTCTGGTGTTTGG
1 ATGATTTACTGAAAATATTTTCTGCTGTTTGG
* ** *
58303109 ATGAATCTGTTTAAAATATTTTCTGCTGTTTGG
1 ATG-ATTTACTGAAAATATTTTCTGCTGTTTGG
*
58303142 -TAGATTTCCTGAAAATATTTT
1 AT-GATTTACTGAAAATATTTT
58303163 TCGGAAAAGT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
32 18 0.42
33 25 0.58
ACGTcount: A:0.27, C:0.08, G:0.17, T:0.48
Consensus pattern (32 bp):
ATGATTTACTGAAAATATTTTCTGCTGTTTGG
Found at i:58305887 original size:3 final size:3
Alignment explanation
Indices: 58305879--58305929 Score: 50
Period size: 3 Copynumber: 16.3 Consensus size: 3
58305869 GTTAAATATG
* *
58305879 ATT ATT ATT ATTT ATT AATT ATT ATT ATT ATT CTT ACT A-T AGTT ATT
1 ATT ATT ATT A-TT ATT -ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT
58305926 ATT A
1 ATT A
58305930 CCCATTACTA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
2 2 0.05
3 31 0.76
4 8 0.20
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:58308049 original size:19 final size:20
Alignment explanation
Indices: 58308005--58308049 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
58307995 NNNNNNNNTT
*
58308005 TATGCA-TTCATTTCATGCA
1 TATGCATTTCATTACATGCA
58308024 T-TCGCATTTCATTACAT-CA
1 TAT-GCATTTCATTACATGCA
58308043 TATGCAT
1 TATGCAT
58308050 CAAAGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
18 1 0.05
19 11 0.50
20 10 0.45
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (20 bp):
TATGCATTTCATTACATGCA
Found at i:58312184 original size:45 final size:45
Alignment explanation
Indices: 58312057--58312404 Score: 330
Period size: 45 Copynumber: 7.8 Consensus size: 45
58312047 GATCGAATAT
*
58312057 ACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAA
1 ACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAA
* * * *** * * *
58312102 ACGGATCATATCTTCATGTACTGG-CGTGAAGTAGATCAAAGATA
1 ACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAA
*
58312146 CCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAA
1 ACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAA
*** * *
58312191 ACAGATCTTGTCTTCATGTAC-GG-GCGTGAAGTAGATCAAAGATA
1 ACAGATCTTGTCTTCCCATACTGGTG-GCGAAGTAGATCAAAGAAA
* *
58312235 CCAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAAA-AAA
1 ACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC-AAAGAAA
*** * * * *
58312280 ACAGATCTTGTCTTCATGTA-TCGG-CGTGAAGTAGATCAAACACA
1 ACAGATCTTGTCTTCCCATACT-GGTGGCGAAGTAGATCAAAGAAA
* * * * * **
58312324 ATAGATATTGTCTCCCCATACTGGTGGTGGAGTAGATTGAAGAAA
1 ACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAA
*
58312369 GCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGA
1 ACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGA
58312405 NNNNNNNNNN
Statistics
Matches: 235, Mismatches: 59, Indels: 18
0.75 0.19 0.06
Matches are distributed among these distances:
43 4 0.02
44 98 0.42
45 129 0.55
46 4 0.02
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (45 bp):
ACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAA
Found at i:58312209 original size:89 final size:89
Alignment explanation
Indices: 58312041--58312383 Score: 467
Period size: 89 Copynumber: 3.9 Consensus size: 89
58312031 TATTGGTAGC
* * * * *
58312041 GAAGTGGATCGAATATA-CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACG
1 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAACA
* *
58312105 GATCATATCTTCATGTACTGGCGT
66 GATCTTGTCTTCATGTACTGGCGT
58312129 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAACA
1 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAACA
*
58312194 GATCTTGTCTTCATGTACGGGCGT
66 GATCTTGTCTTCATGTACTGGCGT
*
58312218 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAAA-AAAAC
1 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC-AAAGAAAAC
58312282 AGATCTTGTCTTCATGTA-TCGGCGT
65 AGATCTTGTCTTCATGTACT-GGCGT
* * ** * * * * ** *
58312307 GAAGTAGATCAAACACAATAGATATTGTCTCCCCATACTGGTGGTGGAGTAGATTGAAGAAAGCA
1 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAACA
58312372 GATCTTGTCTTC
66 GATCTTGTCTTC
58312384 CCATACTGGT
Statistics
Matches: 229, Mismatches: 22, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
88 16 0.07
89 210 0.92
90 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (89 bp):
GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAACA
GATCTTGTCTTCATGTACTGGCGT
Found at i:58312288 original size:134 final size:134
Alignment explanation
Indices: 58312057--58312400 Score: 304
Period size: 134 Copynumber: 2.6 Consensus size: 134
58312047 GATCGAATAT
* * * * * * * ***
58312057 ACAGATCTTGTCTTCC-CATACTGGTGGCGAAGTAGATCGAAGAAAACGGATCATATCTTCATGT
1 ACAGATATTGTC-TCCACATACTGGTGGTGAAGTAGATCAAAGAAACCAGATCTTGTCTTCCCAT
* * * * * * *
58312121 ACTGG-CGTGAAGTAGATC-AAAGATACCAGATCTTGTCTTCCCATA-CTGGTGGCGAAGTAGAT
65 ACTGGTGGCGAAGCAGATCGAAA-AAAACAGATCTTGTCTTCACATATC-GG-CGCGAAGTAGAT
*
58312183 CAAAGAAA
127 CAAACAAA
* * ** *
58312191 ACAGATCTTGTCTTCATGTAC-GG-GCGTGAAGTAGATCAAAGATACCAGATCTTGTCTTCCCAT
1 ACAGATATTGTCTCCACATACTGGTG-GTGAAGTAGATCAAAGAAACCAGATCTTGTCTTCCCAT
** *
58312254 ACTGGTGGCGAAGCAGATCGAAAAAAACAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCAA
65 ACTGGTGGCGAAGCAGATCGAAAAAAACAGATCTTGTCTTCACATATCGGCGCGAAGTAGATCAA
*
58312319 ACACA
130 ACAAA
* * * ** *
58312324 ATAGATATTGTCTCCCCATACTGGTGGTGGAGTAGATTGAAGAAAGCAGATCTTGTCTTCCCATA
1 ACAGATATTGTCTCCACATACTGGTGGTGAAGTAGATCAAAGAAACCAGATCTTGTCTTCCCATA
58312389 CTGGTGGCGAAG
66 CTGGTGGCGAAG
58312401 TAGANNNNNN
Statistics
Matches: 167, Mismatches: 36, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
132 1 0.01
133 68 0.41
134 93 0.56
135 5 0.03
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (134 bp):
ACAGATATTGTCTCCACATACTGGTGGTGAAGTAGATCAAAGAAACCAGATCTTGTCTTCCCATA
CTGGTGGCGAAGCAGATCGAAAAAAACAGATCTTGTCTTCACATATCGGCGCGAAGTAGATCAAA
CAAA
Found at i:58314515 original size:3 final size:3
Alignment explanation
Indices: 58314504--58314576 Score: 103
Period size: 3 Copynumber: 24.0 Consensus size: 3
58314494 TTTAATTATG
58314504 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
58314550 TTA TTA TTC TTA CTA -TA GTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA
58314577 CCATTACTTT
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.03
3 57 0.89
4 5 0.08
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:58315808 original size:18 final size:17
Alignment explanation
Indices: 58315785--58315819 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
58315775 TTTGCAACCC
58315785 AAGGGGAAGGAGAAAAGG
1 AAGGGGAAGG-GAAAAGG
58315803 AAGGGGAAGGGAAAAGG
1 AAGGGGAAGGGAAAAGG
58315820 GGAGAAGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (17 bp):
AAGGGGAAGGGAAAAGG
Found at i:58315987 original size:14 final size:14
Alignment explanation
Indices: 58315968--58315995 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
58315958 AGAAAAGCCT
58315968 GAAAAGCTTTTACA
1 GAAAAGCTTTTACA
58315982 GAAAAGCTTTTACA
1 GAAAAGCTTTTACA
58315996 AGTTATCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
GAAAAGCTTTTACA
Found at i:58318506 original size:3 final size:3
Alignment explanation
Indices: 58318498--58318523 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
58318488 TGTTTCCTTT
58318498 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
58318524 TGTGTACTAT
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:58320329 original size:22 final size:20
Alignment explanation
Indices: 58320287--58320330 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
58320277 CAACAAATAT
*
58320287 ATTTATTAAAATATAACTTA
1 ATTTATTAAAATAAAACTTA
*
58320307 ATTTATATATAAATAAAATTTA
1 ATTTAT-TA-AAATAAAACTTA
58320329 AT
1 AT
58320331 AATTTTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 2 0.10
22 12 0.60
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTATTAAAATAAAACTTA
Found at i:58323337 original size:24 final size:24
Alignment explanation
Indices: 58323309--58323354 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
58323299 TATATGAAAT
* *
58323309 ATAAATTTTAAATATTTTTAAACA
1 ATAAATATTAAATATTTATAAACA
*
58323333 ATAAATATTAATTATTTATAAA
1 ATAAATATTAAATATTTATAAA
58323355 ATTTAATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAATATTAAATATTTATAAACA
Found at i:58326574 original size:17 final size:16
Alignment explanation
Indices: 58326534--58326584 Score: 68
Period size: 17 Copynumber: 3.2 Consensus size: 16
58326524 AAAAATATAT
58326534 AAAAAAA-AGAAAGAA
1 AAAAAAAGAGAAAGAA
*
58326549 AAATAAAGAGAAAGAA
1 AAAAAAAGAGAAAGAA
*
58326565 AAAAAGAAGAAAAAGAA
1 AAAAA-AAGAGAAAGAA
58326582 AAA
1 AAA
58326585 GGAGAGGCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
15 6 0.19
16 12 0.39
17 13 0.42
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (16 bp):
AAAAAAAGAGAAAGAA
Found at i:58327088 original size:107 final size:106
Alignment explanation
Indices: 58326903--58327213 Score: 450
Period size: 107 Copynumber: 2.9 Consensus size: 106
58326893 TAATTTATTC
58326903 TCATTTCGTATCTTAGC-AAATTTGCTATCTTG--A-TTATTTATTTCGAGCTTTGTTCTCAATA
1 TCATTTCGTATCTTAGCAAAATTTGCTATCTTGTTATTTATTTATTTCGAGCTTTGTTCTCAATA
* *
58326964 AAATTCCATATTGTCCATTGTGATAATCCTTTTCATTTTAT
66 AAATTCCATCTTGTCCATTGTGATAATCCTTTTCATCTTAT
*
58327005 TCATTTCGTATCTTAGCAAAATTTGCTATCTTGATTATTTATTTATTTCGAGCATTGTTCTCAAT
1 TCATTTCGTATCTTAGCAAAATTTGCTATCTTG-TTATTTATTTATTTCGAGCTTTGTTCTCAAT
* *
58327070 AAAATCCCATCTTATCCATTGTGATAATCCTTTTCATCTTAT
65 AAAATTCCATCTTGTCCATTGTGATAATCCTTTTCATCTTAT
* * * *
58327112 TCAGTTCGTATCTTAGCAAAAGTTGCTATCTTGGTTAATTTATTCATCTCGAGCTTTGTTCTCAA
1 TCATTTCGTATCTTAGCAAAATTTGCTATCTT-GTT-ATTTATTTATTTCGAGCTTTGTTCTCAA
* * * *
58327177 TAAAATTTCATCTTGTCCATTGTAAGAATCTTTTTCA
64 TAAAATTCCATCTTGTCCATTGTGATAATCCTTTTCA
58327214 AGCATTTTTC
Statistics
Matches: 186, Mismatches: 16, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
102 17 0.09
103 15 0.08
106 1 0.01
107 96 0.52
108 57 0.31
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.47
Consensus pattern (106 bp):
TCATTTCGTATCTTAGCAAAATTTGCTATCTTGTTATTTATTTATTTCGAGCTTTGTTCTCAATA
AAATTCCATCTTGTCCATTGTGATAATCCTTTTCATCTTAT
Found at i:58327917 original size:2 final size:2
Alignment explanation
Indices: 58327910--58327949 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
58327900 GAAAACAGTT
* * *
58327910 TA TA TA TA CA TA TA TA CA TA TA TA CA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58327950 AGAAAACAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Found at i:58327924 original size:8 final size:8
Alignment explanation
Indices: 58327911--58327949 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
58327901 AAAACAGTTT
58327911 ATATATAC
1 ATATATAC
58327919 ATATATAC
1 ATATATAC
58327927 ATATATAC
1 ATATATAC
*
58327935 ATATATAT
1 ATATATAC
58327943 ATATATA
1 ATATATA
58327950 AGAAAACAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATATAC
Found at i:58328618 original size:15 final size:15
Alignment explanation
Indices: 58328598--58328630 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
58328588 TGTTATTATG
58328598 TTTCCAATTTGTTTA
1 TTTCCAATTTGTTTA
58328613 TTTCCAATTTGTTTA
1 TTTCCAATTTGTTTA
58328628 TTT
1 TTT
58328631 ACTTAGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (15 bp):
TTTCCAATTTGTTTA
Found at i:58334273 original size:13 final size:14
Alignment explanation
Indices: 58334254--58334311 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 14
58334244 TAAAGTTAAA
58334254 ATATATATTATAAT
1 ATATATATTATAAT
58334268 ATTATAATATTAT-AT
1 A-TAT-ATATTATAAT
*
58334283 CT-TA-ATTATTAAGT
1 ATATATATTA-TAA-T
58334297 ATATATATTATAAT
1 ATATATATTATAAT
58334311 A
1 A
58334312 AGTAAATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
11 4 0.11
12 2 0.06
13 2 0.06
14 6 0.17
15 10 0.29
16 11 0.31
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (14 bp):
ATATATATTATAAT
Found at i:58334321 original size:22 final size:21
Alignment explanation
Indices: 58334249--58334321 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 21
58334239 AAACTTAAAG
58334249 TTAAA-ATATATATTATAATA
1 TTAAATATATATATTATAATA
58334269 TTATAATAT-TATATCT-TAATTA
1 TTA-AATATATATAT-TATAA-TA
*
58334291 TTAAGTATATATATTATAATAA
1 TTAAATATATATATTATAAT-A
*
58334313 GTAAATATA
1 TTAAATATA
58334322 AATAAAAGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
20 3 0.07
21 16 0.37
22 24 0.56
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (21 bp):
TTAAATATATATATTATAATA
Found at i:58335377 original size:37 final size:40
Alignment explanation
Indices: 58335287--58335394 Score: 114
Period size: 37 Copynumber: 2.7 Consensus size: 40
58335277 CTTCGAGTCA
* *
58335287 ATGAGACACTGGGTGTCAATTTACTACTTTGGATTAATTCG
1 ATGAGACACTGGGTGTCAATTTA-TACTTCGGATTAACTCG
* * *
58335328 ATGAGGCACTGGGTGTCAA-TT-TACTTCGGTTTAGCT-G
1 ATGAGACACTGGGTGTCAATTTATACTTCGGATTAACTCG
* *
58335365 ATGAGACACTGGGTGTTAAATTATTACTTC
1 ATGAGACACTGGGTGTCAATTTA-TACTTC
58335395 AAATTATCTG
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
37 18 0.32
38 13 0.23
40 8 0.14
41 18 0.32
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (40 bp):
ATGAGACACTGGGTGTCAATTTATACTTCGGATTAACTCG
Found at i:58340428 original size:24 final size:25
Alignment explanation
Indices: 58340401--58340447 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
58340391 CTGTTAATTT
58340401 CTCTTCG-GAGCTACCCGTTATAGG
1 CTCTTCGTGAGCTACCCGTTATAGG
* *
58340425 CTCTTTGTGAGCTTCCCGTTATA
1 CTCTTCGTGAGCTACCCGTTATA
58340448 TTGCCCGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.15, C:0.28, G:0.21, T:0.36
Consensus pattern (25 bp):
CTCTTCGTGAGCTACCCGTTATAGG
Found at i:58345197 original size:45 final size:41
Alignment explanation
Indices: 58345143--58345320 Score: 146
Period size: 37 Copynumber: 4.5 Consensus size: 41
58345133 ATCACTTGTC
58345143 CTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTACCA
1 CTTGATCAGATAAGTGTAGCTA-G---CCACTTATCACTTTACCA
*
58345188 CTTGATCAGATAA--GT-G-TAGCCACTTATCACTTTATCA
1 CTTGATCAGATAAGTGTAGCTAGCCACTTATCACTTTACCA
****
58345225 CTTGATCAGATAA--GT-G-TAGCCACTTATCACTTTGTTT
1 CTTGATCAGATAAGTGTAGCTAGCCACTTATCACTTTACCA
****
58345262 CTTGATCAGATAAGTGTA---A-CCACTTATCACTTTGTTT
1 CTTGATCAGATAAGTGTAGCTAGCCACTTATCACTTTACCA
*
58345299 CTTGATTAGATAAGTGTAGCTA
1 CTTGATCAGATAAGTGTAGCTA
58345321 AAACTACCAC
Statistics
Matches: 122, Mismatches: 5, Indels: 17
0.85 0.03 0.12
Matches are distributed among these distances:
37 99 0.81
38 1 0.01
39 2 0.02
40 2 0.02
41 2 0.02
42 1 0.01
43 2 0.02
45 13 0.11
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.37
Consensus pattern (41 bp):
CTTGATCAGATAAGTGTAGCTAGCCACTTATCACTTTACCA
Found at i:58345220 original size:37 final size:37
Alignment explanation
Indices: 58345170--58345318 Score: 217
Period size: 37 Copynumber: 4.0 Consensus size: 37
58345160 AGCTAGGCTA
*
58345170 CCACTTATCACTTTACCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
58345207 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
* ** *
58345244 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
* ** *
58345281 CCACTTATCACTTTGTTTCTTGATTAGATAAGTGTAG
1 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
58345318 C
1 C
58345319 TAAAACTACC
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 105 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (37 bp):
CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
Found at i:58347448 original size:242 final size:242
Alignment explanation
Indices: 58346987--58347471 Score: 891
Period size: 242 Copynumber: 2.0 Consensus size: 242
58346977 AACAATCAGA
* *
58346987 CCATAACATTCCATATTTGACCCGTAAGCATTCGATTCTAATTTTTAGCTACTTCGATTTAATTA
1 CCATAACATTCCATATTTGACCCGTAAGCATTCCATTCTAATTTTCAGCTACTTCGATTTAATTA
*
58347052 AATCAACTTTGAACCAATTTTTCAACACGAACGAAAATCAGGTCATTACACCAAATGTAGCAAGG
66 AATCAACTTTGAACCAATTTTTCAACACGAACGAAAATCAGGTCAATACACCAAATGTAGCAAGG
*
58347117 CAAAGAGAGCTAGAAACATTGCTCTTCCGATAAATGAGAAATTGCCAACTCCCCAGAATGTTACC
131 CAAAGAGAGC-AGAAACATTGCTCTTCCGATAAATGAGAAATTCCCAACTCCCCAGAATGTTACC
*
58347182 ATTGAAGATCTTTAGGAGTAAATTGCCTTGCTTACTCAGAATTTTAGT
195 ATTGAAGATCTTCAGGAGTAAATTGCCTTGCTTACTCAGAATTTTAGT
58347230 CCATAACATTCCATATTTGACCCGTAAGCATTCCATTCTAATTTTCAGCTACTTCGATTTAATTT
1 CCATAACATTCCATATTTGACCCGTAAGCATTCCATTCTAATTTTCAGCTACTTCGATTTAA-TT
58347295 AAATCAACTTTGAACCAATTTTTCAACACGAACGAAAATCAGGTCAATACACCAAATGTAGCAAG
65 AAATCAACTTTGAACCAATTTTTCAACACGAACGAAAATCAGGTCAATACACCAAATGTAGCAAG
*
58347360 GCAAAGAGAG-AGAAACATTGCTCTTCCGATAAATGAGAAATTCCCAACTCCCCAGAATGTTACT
130 GCAAAGAGAGCAGAAACATTGCTCTTCCGATAAATGAGAAATTCCCAACTCCCCAGAATGTTACC
58347424 ATTGAAGATCTTCAGGAGTAAATTGCCTTGCTTACTCAGAATTTTAGT
195 ATTGAAGATCTTCAGGAGTAAATTGCCTTGCTTACTCAGAATTTTAGT
58347472 AAGACTTTTA
Statistics
Matches: 235, Mismatches: 6, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
242 99 0.42
243 60 0.26
244 76 0.32
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (242 bp):
CCATAACATTCCATATTTGACCCGTAAGCATTCCATTCTAATTTTCAGCTACTTCGATTTAATTA
AATCAACTTTGAACCAATTTTTCAACACGAACGAAAATCAGGTCAATACACCAAATGTAGCAAGG
CAAAGAGAGCAGAAACATTGCTCTTCCGATAAATGAGAAATTCCCAACTCCCCAGAATGTTACCA
TTGAAGATCTTCAGGAGTAAATTGCCTTGCTTACTCAGAATTTTAGT
Found at i:58353509 original size:18 final size:18
Alignment explanation
Indices: 58353459--58353510 Score: 50
Period size: 21 Copynumber: 2.7 Consensus size: 18
58353449 TTTATATATG
*
58353459 ATTTAGAATTTTTTTAAAA
1 ATTT-GAATTTTTTAAAAA
*
58353478 ATTATTATACTTTTTTAAAAA
1 ATT-TGA-A-TTTTTTAAAAA
58353499 ATTTGAATTTTT
1 ATTTGAATTTTT
58353511 AGAAATTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
18 5 0.19
19 5 0.19
20 4 0.15
21 13 0.48
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (18 bp):
ATTTGAATTTTTTAAAAA
Found at i:58354457 original size:23 final size:23
Alignment explanation
Indices: 58354424--58354473 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
58354414 CAATTATTTT
58354424 TTTAATAATTTTAAATAAATAAAA
1 TTTAATAATTTTAAATAAA-AAAA
* *
58354448 TTTAA-AATTTTAAGTATAAAAA
1 TTTAATAATTTTAAATAAAAAAA
58354470 TTTA
1 TTTA
58354474 CCATCAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.33
23 11 0.46
24 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TTTAATAATTTTAAATAAAAAAA
Found at i:58354508 original size:21 final size:21
Alignment explanation
Indices: 58354458--58354514 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
58354448 TTTAAAATTT
58354458 TAAGTATAAA-AAT-TTACCA
1 TAAGTATAAATAATATTACCA
58354477 TCAA--AGTAAATAATATTACCA
1 T-AAGTA-TAAATAATATTACCA
*
58354498 TAAGTATAAATATTATT
1 TAAGTATAAATAATATT
58354515 TATCTTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
18 1 0.03
19 5 0.16
20 7 0.23
21 17 0.55
22 1 0.03
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (21 bp):
TAAGTATAAATAATATTACCA
Found at i:58355979 original size:3 final size:3
Alignment explanation
Indices: 58355971--58356007 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
58355961 TGAAATATTG
58355971 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
58356008 TACTTATTTT
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):
AAT
Found at i:58380096 original size:19 final size:18
Alignment explanation
Indices: 58380038--58380102 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 18
58380028 TTCAAATATC
58380038 AATATTTTAATAA-TAAAAT
1 AATA-TTTAA-AATTAAAAT
* *
58380057 ATTATATTAATATTAAGAAT
1 AATAT-TTAAAATTAA-AAT
58380077 AATATTTAAAATTTAAAAT
1 AATATTTAAAA-TTAAAAT
58380096 AAATATT
1 -AATATT
58380103 ATTTTTAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
18 2 0.05
19 18 0.49
20 17 0.46
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
AATATTTAAAATTAAAAT
Found at i:58389605 original size:7 final size:7
Alignment explanation
Indices: 58389593--58389628 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
58389583 TTAAAAGTAT
58389593 TTTAAAA
1 TTTAAAA
58389600 TTTAAAA
1 TTTAAAA
58389607 TTTAAAA
1 TTTAAAA
58389614 TTTAAAA
1 TTTAAAA
58389621 TTTAAAA
1 TTTAAAA
58389628 T
1 T
58389629 ATATATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TTTAAAA
Found at i:58394030 original size:23 final size:23
Alignment explanation
Indices: 58393979--58394047 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 23
58393969 CGTATGTAAG
*
58393979 TTTTTATTTAATTTCTAATTAATATA
1 TTTTTAATT-ATTT-TAATT-ATATA
58394005 TTTTTAATTATTTTAATTATATA
1 TTTTTAATTATTTTAATTATATA
*
58394028 TTTTT-ATTTTTTTGAATTAT
1 TTTTTAATTATTTT-AATTAT
58394048 TGAACCTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.17
23 16 0.40
24 5 0.12
25 4 0.10
26 8 0.20
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (23 bp):
TTTTTAATTATTTTAATTATATA
Found at i:58404896 original size:20 final size:19
Alignment explanation
Indices: 58404873--58404911 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
58404863 AAAAAATAAA
58404873 ATAATAAAATTTAAAAATTT
1 ATAATAAAA-TTAAAAATTT
* *
58404893 ATAATTATATTAAAAATTT
1 ATAATAAAATTAAAAATTT
58404912 TATCACATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATAAAATTAAAAATTT
Found at i:58405673 original size:21 final size:21
Alignment explanation
Indices: 58405647--58405689 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
58405637 CAACTTCAAA
58405647 GTGGTTAATGCACTCATTGAT
1 GTGGTTAATGCACTCATTGAT
58405668 GTGGTTAATGCACTCATTGAT
1 GTGGTTAATGCACTCATTGAT
58405689 G
1 G
58405690 ACAATGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (21 bp):
GTGGTTAATGCACTCATTGAT
Found at i:58406892 original size:39 final size:40
Alignment explanation
Indices: 58406849--58407024 Score: 196
Period size: 40 Copynumber: 4.4 Consensus size: 40
58406839 CGTTTGGATA
58406849 AAAAACGCCGCTAAAAATCAAGTATTAGCGGCG-CTTTAG
1 AAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTCTTTAG
* * *
58406888 AAAAAACGCCGCTAAAGATCTAGTATTAGCGGCGTTTTTAG
1 -AAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTCTTTAG
* * * *
58406929 GAAAACGCCGCTAAAGATCCAGTATTAGCGGCGTTTTTAG
1 AAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTCTTTAG
* * * **
58406969 GAAAACGCCGCTAAAAAT-GAGCATTAGCGGCG-CTTTCC
1 AAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTCTTTAG
*
58407007 AAAAAGCGCCGCAAAAAA
1 AAAAA-CGCCGCTAAAAA
58407025 CCTAAGCACA
Statistics
Matches: 121, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
38 7 0.06
39 23 0.19
40 86 0.71
41 5 0.04
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.20
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTCTTTAG
Found at i:58407126 original size:41 final size:41
Alignment explanation
Indices: 58407064--58407336 Score: 388
Period size: 41 Copynumber: 6.7 Consensus size: 41
58407054 TTTCGGGGCG
58407064 TTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTGGTCT
1 TTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTGGTCT
* * *
58407105 TTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCCGGGCT
1 TTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTGGTCT
* * * *
58407146 TTAGTGGCGTTTTTGAAGAAACGCTGCTAATGCTCTGGTCT
1 TTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTGGTCT
*
58407187 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
1 TTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTGGTCT
*
58407228 TTAGCGGCGTTTTTTGAA-AAGCGCCGCTAATGCTCAGGTCT
1 TTAGCGGCGTTTTTT-AAGAAGCGCCGCTAATGCTCTGGTCT
* *
58407269 TTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCT-TAGGGCT
1 TTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCT-GGTCT
* * *
58407310 TTAGCGACGTTTTTGAAAAAGCGCCGC
1 TTAGCGGCGTTTTTTAAGAAGCGCCGC
58407337 AAAATTTTTT
Statistics
Matches: 210, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
40 2 0.01
41 206 0.98
42 2 0.01
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.32
Consensus pattern (41 bp):
TTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTGGTCT
Found at i:58407385 original size:15 final size:14
Alignment explanation
Indices: 58407361--58407400 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
58407351 AGTTTTTTGG
58407361 ATACATTATTTAAA
1 ATACATTATTTAAA
58407375 ATACTATTATTTAAA
1 ATAC-ATTATTTAAA
58407390 ATA-ATT-TTTAA
1 ATACATTATTTAA
58407401 GTTTTTTGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.20
13 3 0.12
14 4 0.16
15 13 0.52
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (14 bp):
ATACATTATTTAAA
Found at i:58407811 original size:29 final size:27
Alignment explanation
Indices: 58407744--58407811 Score: 64
Period size: 29 Copynumber: 2.4 Consensus size: 27
58407734 AGGGATTATT
58407744 GTTTATGATTTGCGGTTTAAGAGTTGGG
1 GTTTATG-TTTGCGGTTTAAGAGTTGGG
* * * *
58407772 GTTTAAAGTTTAGGGGTTTATGATTTAGGG
1 GTTT-ATGTTT-GCGGTTTAAGAGTT-GGG
58407802 GTTTATGTTT
1 GTTTATGTTT
58407812 TATGATTTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 7 0.22
29 18 0.56
30 7 0.22
ACGTcount: A:0.19, C:0.01, G:0.32, T:0.47
Consensus pattern (27 bp):
GTTTATGTTTGCGGTTTAAGAGTTGGG
Found at i:58407827 original size:14 final size:15
Alignment explanation
Indices: 58407744--58407813 Score: 65
Period size: 15 Copynumber: 4.8 Consensus size: 15
58407734 AGGGATTATT
*
58407744 GTTTATGATTT-GCG
1 GTTTATGATTTAGGG
* *
58407758 GTTTAAGAGTT-GGG
1 GTTTATGATTTAGGG
*
58407772 GTTTA-AAGTTTAGGG
1 GTTTATGA-TTTAGGG
58407787 GTTTATGATTTAGGG
1 GTTTATGATTTAGGG
*
58407802 GTTTATGTTTTA
1 GTTTATGATTTA
58407814 TGATTTAGGG
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
13 1 0.02
14 18 0.39
15 26 0.57
16 1 0.02
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.47
Consensus pattern (15 bp):
GTTTATGATTTAGGG
Found at i:58412125 original size:43 final size:43
Alignment explanation
Indices: 58412072--58412237 Score: 235
Period size: 43 Copynumber: 3.9 Consensus size: 43
58412062 TTTGTGGAAG
* *
58412072 AAGCGTCGCTAAAGGTCATGGTCTTTAGCGGCGTTTATGAGAA
1 AAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTATGAGAA
* * *
58412115 AAGTGCCGCTAAAGATCATGGTTTTTAGCGGCGTTTATGGGAA
1 AAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTATGAGAA
* *
58412158 AAGCGCCGCTAAAGATAATGGTCTTTAGCGGCGTTTGTGA-AA
1 AAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTATGAGAA
* **
58412200 AAGCGCCGCTAAAGGTCATGACCTTTAGCGGCGTTTAT
1 AAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTAT
58412238 TTCTAAAAAT
Statistics
Matches: 108, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 35 0.32
43 73 0.68
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (43 bp):
AAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTATGAGAA
Found at i:58412226 original size:42 final size:43
Alignment explanation
Indices: 58412026--58412237 Score: 232
Period size: 43 Copynumber: 5.0 Consensus size: 43
58412016 CGTTCTTCAA
* * * ** *
58412026 AAAAAGCGCTGCTAAAAGTCATGATCTATT-GCGGTATTTGTGG
1 AAAAAGCGCCGCTAAAGGTCATGGTCT-TTAGCGGCGTTTATGG
* *
58412069 AAGAAGCGTCGCTAAAGGTCATGGTCTTTAGCGGCGTTTAT-G
1 AAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTATGG
* * *
58412111 AGAAAAGTGCCGCTAAAGATCATGGTTTTTAGCGGCGTTTATGG
1 A-AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTATGG
* * * *
58412155 GAAAAGCGCCGCTAAAGATAATGGTCTTTAGCGGCGTTTGT-G
1 AAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTATGG
**
58412197 AAAAAGCGCCGCTAAAGGTCATGACCTTTAGCGGCGTTTAT
1 AAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTAT
58412238 TTCTAAAAAT
Statistics
Matches: 142, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
42 40 0.28
43 101 0.71
44 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (43 bp):
AAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTATGG
Found at i:58424882 original size:13 final size:13
Alignment explanation
Indices: 58424866--58424899 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
58424856 ATTTTTTATG
58424866 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
58424879 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
*
58424892 CTTGGGTT
1 ATTGGGTT
58424900 TATATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.12, C:0.03, G:0.44, T:0.41
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:58428597 original size:19 final size:19
Alignment explanation
Indices: 58428571--58428623 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
58428561 TTTTAAAATA
58428571 ATTTTAACTTGATTGAAA-
1 ATTTTAACTTGATTGAAAC
**
58428589 ATGTTTAACTCAATTGAAACC
1 AT-TTTAACTTGATTGAAA-C
58428610 ATTTTAACTTGATT
1 ATTTTAACTTGATT
58428624 TTATCATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 2 0.07
19 14 0.50
20 10 0.36
21 2 0.07
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.43
Consensus pattern (19 bp):
ATTTTAACTTGATTGAAAC
Found at i:58428691 original size:23 final size:22
Alignment explanation
Indices: 58428650--58428697 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 22
58428640 TTTGTTGAAC
58428650 TTTAACTTTTATTCAAAAATAT
1 TTTAACTTTTATTCAAAAATAT
58428672 TTTAACTTGTTATATCAAAATATAT
1 TTTAACTT-TTAT-TCAAAA-ATAT
58428697 T
1 T
58428698 ATCAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.35
23 4 0.17
24 6 0.26
25 5 0.22
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTAACTTTTATTCAAAAATAT
Found at i:58429927 original size:30 final size:30
Alignment explanation
Indices: 58429893--58429955 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
58429883 ACTTATTTTA
58429893 TTGTTAATTTTGTTAATATTTTAAAGGCAT
1 TTGTTAATTTTGTTAATATTTTAAAGGCAT
* * *
58429923 TTGTTAATTTTTTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTAATATTTTAAAGGCAT
58429953 TTG
1 TTG
58429956 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTAATATTTTAAAGGCAT
Found at i:58430382 original size:27 final size:29
Alignment explanation
Indices: 58430327--58430386 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
58430317 TGAATCTCAA
58430327 AATTATATATAAATTTTAATTTAATGTGT
1 AATTATATATAAATTTTAATTTAATGTGT
58430356 AATTATATATAAATTTTAATTT-A-GTGT
1 AATTATATATAAATTTTAATTTAATGTGT
58430383 AATT
1 AATT
58430387 GGACACGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 8 0.26
28 1 0.03
29 22 0.71
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.52
Consensus pattern (29 bp):
AATTATATATAAATTTTAATTTAATGTGT
Found at i:58439930 original size:18 final size:16
Alignment explanation
Indices: 58439897--58439930 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
58439887 TAATTATAAT
58439897 TTAATATTTTTTATTA
1 TTAATATTTTTTATTA
*
58439913 TTAATA-TGTTTATTA
1 TTAATATTTTTTATTA
58439928 TTA
1 TTA
58439931 CAAAGAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTAATATTTTTTATTA
Found at i:58442738 original size:6 final size:6
Alignment explanation
Indices: 58442727--58442751 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
58442717 AATCCATCAG
58442727 ATTTAA ATTTAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA A
58442752 AAATTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:58446940 original size:50 final size:50
Alignment explanation
Indices: 58446865--58446964 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
58446855 TCTATCAGAG
* * * * *
58446865 AGTTTACTTTTAAATTGAGTTTTCCAATTGCTCTTTAGAGACTCAAATTT
1 AGTTTACCTTTAAATCGAGTCTTCCAACTGCTCTTTAGAGACCCAAATTT
58446915 AGTTTACCTTTAAATCGAGTCTTCCAACTGCTCTTTAGAGACCCAAATTT
1 AGTTTACCTTTAAATCGAGTCTTCCAACTGCTCTTTAGAGACCCAAATTT
58446965 GGGTGGATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (50 bp):
AGTTTACCTTTAAATCGAGTCTTCCAACTGCTCTTTAGAGACCCAAATTT
Found at i:58447878 original size:18 final size:18
Alignment explanation
Indices: 58447841--58447896 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
58447831 AATTTGAAAG
**
58447841 AAATA-TTAAAATTATAA
1 AAATAGTTAAAAAAATAA
*
58447858 AAATA-TTAAATAAATTAA
1 AAATAGTTAAA-AAAATAA
58447876 AAA-AGTTAAAAAAATAA
1 AAATAGTTAAAAAAATAA
58447893 AAAT
1 AAAT
58447897 CATTTAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
17 20 0.62
18 12 0.38
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (18 bp):
AAATAGTTAAAAAAATAA
Found at i:58448538 original size:19 final size:19
Alignment explanation
Indices: 58448514--58448552 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
58448504 TTTGAATTTT
*
58448514 ATTTATTTAT-TTTTATAAA
1 ATTTATTAATGTTTT-TAAA
58448533 ATTTATTAATGTTTTTAAA
1 ATTTATTAATGTTTTTAAA
58448552 A
1 A
58448553 AATTATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
ATTTATTAATGTTTTTAAA
Found at i:58448592 original size:16 final size:15
Alignment explanation
Indices: 58448520--58448594 Score: 53
Period size: 16 Copynumber: 4.5 Consensus size: 15
58448510 TTTTATTTAT
58448520 TTATTTTTATAAAATTTA
1 TTATTTTT-TAAAA--TA
*
58448538 TTAATGTTTTTAAAAAA
1 TT-AT-TTTTTAAAATA
58448555 TTATATTTTATAAAAT-
1 TTAT-TTTT-TAAAATA
*
58448571 TAATTTTTTAAAATA
1 TTATTTTTTAAAATA
58448586 TGTATTTTT
1 T-TATTTTT
58448595 AATTAATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
14 6 0.13
15 5 0.11
16 15 0.32
17 8 0.17
18 2 0.04
19 7 0.15
20 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
TTATTTTTTAAAATA
Found at i:58453153 original size:21 final size:21
Alignment explanation
Indices: 58453124--58453163 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
58453114 TAATGTTACC
58453124 GCTCACAAATTAAATCATACT
1 GCTCACAAATTAAATCATACT
*
58453145 GCTCTCAAATTAAATCATA
1 GCTCACAAATTAAATCATA
58453164 ACGTTGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.30
Consensus pattern (21 bp):
GCTCACAAATTAAATCATACT
Found at i:58456953 original size:20 final size:19
Alignment explanation
Indices: 58456930--58456968 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
58456920 AAAAAATAAA
58456930 ATAATAAAATTTAAAAATTT
1 ATAATAAAA-TTAAAAATTT
* *
58456950 ATAATTATATTAAAAATTT
1 ATAATAAAATTAAAAATTT
58456969 TATCACATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATAAAATTAAAAATTT
Found at i:58476759 original size:31 final size:29
Alignment explanation
Indices: 58476721--58476782 Score: 97
Period size: 31 Copynumber: 2.1 Consensus size: 29
58476711 ATCTCAAAAT
58476721 TATATATGAACTTTAACTTAATGTGTAATTA
1 TATATATGAACTTTAA-TTAA-GTGTAATTA
*
58476752 TATATATGAACTTTAATTTAGTGTAATTA
1 TATATATGAACTTTAATTAAGTGTAATTA
58476781 TA
1 TA
58476783 CACGTGAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 11 0.37
30 3 0.10
31 16 0.53
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.47
Consensus pattern (29 bp):
TATATATGAACTTTAATTAAGTGTAATTA
Found at i:58476790 original size:29 final size:31
Alignment explanation
Indices: 58476726--58476790 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 31
58476716 AAAATTATAT
* *
58476726 ATGAACTTTAACTTAATGTGTAATTATATAT
1 ATGAACTTTAACTTAATGTGTAATTATACAC
*
58476757 ATGAACTTTAA-TTTA-GTGTAATTATACAC
1 ATGAACTTTAACTTAATGTGTAATTATACAC
*
58476786 GTGAA
1 ATGAA
58476791 ATTCTGTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 16 0.53
30 3 0.10
31 11 0.37
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (31 bp):
ATGAACTTTAACTTAATGTGTAATTATACAC
Found at i:58479688 original size:18 final size:16
Alignment explanation
Indices: 58479672--58479719 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
58479662 AAAACAATAA
58479672 ATTTTATTATAAGAAT
1 ATTTTATTATAAGAAT
58479688 ATTTTATTAT---AA-
1 ATTTTATTATAAGAAT
*
58479700 ATTTTATTATAAAAAT
1 ATTTTATTATAAGAAT
58479716 ATTT
1 ATTT
58479720 ACGAGAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 10 0.36
13 2 0.07
15 2 0.07
16 14 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
ATTTTATTATAAGAAT
Found at i:58479705 original size:12 final size:12
Alignment explanation
Indices: 58479668--58479712 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 12
58479658 TTTAAAAACA
58479668 ATAAATTTTATT
1 ATAAATTTTATT
58479680 ATAAGAATATTTTATT
1 AT---AA-ATTTTATT
58479696 ATAAATTTTATT
1 ATAAATTTTATT
58479708 ATAAA
1 ATAAA
58479713 AATATTTACG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 15 0.52
13 2 0.07
15 2 0.07
16 10 0.34
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
ATAAATTTTATT
Found at i:58482750 original size:29 final size:30
Alignment explanation
Indices: 58482706--58482802 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
58482696 ATACAAAAAA
* *
58482706 AAAATTTATATTTTGATTCC-TTAACTTTTTT
1 AAAA-TTATATTTTGA-CCCTTTAACTTTTTC
*
58482737 AAAATTAT-TTTTGACCCTTTACCTTTTTC
1 AAAATTATATTTTGACCCTTTAACTTTTTC
* * * *
58482766 AAAATTATATTTTGACCCCTAAAGTTTCTC
1 AAAATTATATTTTGACCCTTTAACTTTTTC
58482796 AAAATTA
1 AAAATTA
58482803 CACTTGGCCT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 2 0.04
29 23 0.41
30 27 0.48
31 4 0.07
ACGTcount: A:0.32, C:0.15, G:0.04, T:0.48
Consensus pattern (30 bp):
AAAATTATATTTTGACCCTTTAACTTTTTC
Found at i:58483371 original size:11 final size:11
Alignment explanation
Indices: 58483347--58483419 Score: 53
Period size: 11 Copynumber: 6.6 Consensus size: 11
58483337 AAGAGGGAAG
58483347 GAAG-AAGAAGA
1 GAAGAAAGAA-A
58483358 GAAGAAAGAAA
1 GAAGAAAGAAA
*
58483369 GAA-AAAAAAA
1 GAAGAAAGAAA
*
58483379 GAAAAAAAGAAA
1 G-AAGAAAGAAA
58483391 GGAA-AAAGAAA
1 -GAAGAAAGAAA
* *
58483402 AAAAAAAGAAA
1 GAAGAAAGAAA
*
58483413 AAAGAAA
1 GAAGAAA
58483420 AAAATTAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
10 9 0.17
11 30 0.57
12 13 0.25
13 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
GAAGAAAGAAA
Found at i:58483388 original size:22 final size:21
Alignment explanation
Indices: 58483362--58483423 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
58483352 AGAAGAGAAG
58483362 AAAGAAAGAAAAAAAAAGAAAA
1 AAAGAAAGAAAAAAAAA-AAAA
*
58483384 AAAGAAAGGAAAAAGAAAAAAA
1 AAAGAAA-GAAAAAAAAAAAAA
*
58483406 AAAGAAA-AAAGAAAAAAA
1 AAAGAAAGAAAAAAAAAAA
58483424 TTAAAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 9 0.25
22 18 0.50
23 9 0.25
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAGAAAGAAAAAAAAAAAAA
Found at i:58483421 original size:8 final size:8
Alignment explanation
Indices: 58483372--58483442 Score: 58
Period size: 8 Copynumber: 9.0 Consensus size: 8
58483362 AAAGAAAGAA
58483372 AAAAAAAG
1 AAAAAAAG
58483380 AAAAAAAG
1 AAAAAAAG
**
58483388 AAAGGAA-
1 AAAAAAAG
*
58483395 AAAGAAA-
1 AAAAAAAG
58483402 AAAAAAAG
1 AAAAAAAG
58483410 -AAAAAAG
1 AAAAAAAG
*
58483417 AAAAAAATT
1 AAAAAAA-G
*
58483426 AAAAAAAT
1 AAAAAAAG
58483434 AATAAAAAG
1 AA-AAAAAG
58483443 TCGGGTCGAC
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
7 19 0.36
8 22 0.42
9 12 0.23
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (8 bp):
AAAAAAAG
Found at i:58483423 original size:18 final size:18
Alignment explanation
Indices: 58483359--58483423 Score: 87
Period size: 18 Copynumber: 3.6 Consensus size: 18
58483349 AGAAGAAGAG
*
58483359 AAGAAAGAAAGAAA-AAAA
1 AAGAAA-AAAAAAAGAAAA
*
58483377 AAGAAAAAAAGAAAGGAAA
1 AAGAAAAAAA-AAAGAAAA
58483396 AAGAAAAAAAAAAGAAAA
1 AAGAAAAAAAAAAGAAAA
58483414 AAGAAAAAAA
1 AAGAAAAAAA
58483424 TTAAAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
17 3 0.07
18 26 0.62
19 13 0.31
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
AAGAAAAAAAAAAGAAAA
Found at i:58483786 original size:15 final size:16
Alignment explanation
Indices: 58483766--58483808 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
58483756 CAGGCCAGCC
58483766 AAAAAAGGAAAAAAG-
1 AAAAAAGGAAAAAAGA
*
58483781 AAAAAA-GAGAAGAAGA
1 AAAAAAGGA-AAAAAGA
58483797 AAAAAAGGAAAA
1 AAAAAAGGAAAA
58483809 GACCCAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 8 0.35
17 2 0.09
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAAAGGAAAAAAGA
Found at i:58484311 original size:18 final size:18
Alignment explanation
Indices: 58484261--58484311 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
58484251 AAAAAGAAAG
*
58484261 ATCGTGTTTTCAAAAGTTT
1 ATCGTG-TTTCAAAAATTT
* *
58484280 -TCATGTTTCCAAAATTT
1 ATCGTGTTTCAAAAATTT
58484297 ATCGTGTTTCAAAAA
1 ATCGTGTTTCAAAAA
58484312 ATAATAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (18 bp):
ATCGTGTTTCAAAAATTT
Found at i:58484459 original size:18 final size:18
Alignment explanation
Indices: 58484438--58484570 Score: 68
Period size: 17 Copynumber: 7.6 Consensus size: 18
58484428 ACTTTTCGCT
58484438 TTTTCAAAAATTTTCCTG
1 TTTTCAAAAATTTTCCTG
*
58484456 TTTTC-AAAATTTCTCGTG
1 TTTTCAAAAATTT-TCCTG
* *
58484474 TTTTTC--GACTTTT-CTCG
1 -TTTTCAAAAATTTTCCT-G
*
58484491 TTTTCAAAAATTTTCGTG
1 TTTTCAAAAATTTTCCTG
*
58484509 TTTT-AGAAATTTT-CT-
1 TTTTCAAAAATTTTCCTG
* *
58484524 TATTTCTAAAATTCT-C-G
1 T-TTTCAAAAATTTTCCTG
*
58484541 TATTTCAAAAAATTTCCGTG
1 T-TTTCAAAAATTTTCC-TG
*
58484561 TTCTCAAAAA
1 TTTTCAAAAA
58484571 AATTATTATC
Statistics
Matches: 87, Mismatches: 16, Indels: 23
0.69 0.13 0.18
Matches are distributed among these distances:
15 1 0.01
16 10 0.11
17 36 0.41
18 24 0.28
19 14 0.16
20 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (18 bp):
TTTTCAAAAATTTTCCTG
Found at i:58484522 original size:35 final size:37
Alignment explanation
Indices: 58484445--58484523 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 37
58484435 GCTTTTTCAA
*
58484445 AAATTTTC-CTGTTTTCAAAATTTCTCGTGTTTTTCG
1 AAATTTTCTCTGTTTTCAAAATTTCTCGTGTTTTTAG
*
58484481 -ACTTTTCTC-GTTTTCAAAAATTT-TCGTG-TTTTAG
1 AAATTTTCTCTGTTTTC-AAAATTTCTCGTGTTTTTAG
58484515 AAATTTTCT
1 AAATTTTCT
58484524 TATTTCTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
34 5 0.14
35 24 0.65
36 8 0.22
ACGTcount: A:0.22, C:0.15, G:0.10, T:0.53
Consensus pattern (37 bp):
AAATTTTCTCTGTTTTCAAAATTTCTCGTGTTTTTAG
Found at i:58484535 original size:17 final size:17
Alignment explanation
Indices: 58484488--58484570 Score: 69
Period size: 17 Copynumber: 4.8 Consensus size: 17
58484478 TCGACTTTTC
58484488 TCGT-TTTCAAAAATTT
1 TCGTATTTCAAAAATTT
* * *
58484504 TCGTGTTTTAGAAATTT
1 TCGTATTTCAAAAATTT
* * *
58484521 TCTTATTTCTAAAATTC
1 TCGTATTTCAAAAATTT
58484538 TCGTATTTCAAAAAATTT
1 TCGTATTTC-AAAAATTT
* *
58484556 CCGTGTTCTCAAAAA
1 TCGTATT-TCAAAAA
58484571 AATTATTATC
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
16 4 0.08
17 29 0.57
18 16 0.31
19 2 0.04
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.46
Consensus pattern (17 bp):
TCGTATTTCAAAAATTT
Found at i:58490926 original size:77 final size:78
Alignment explanation
Indices: 58490801--58492216 Score: 1615
Period size: 78 Copynumber: 18.3 Consensus size: 78
58490791 AGAATTATAG
* * ** * *
58490801 TTTTCAATTTCTATTTTTC--AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTAGGCCG
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
58490864 CACGCCGAGGTA-
66 CACGCTGAGGTAT
** * * **
58490876 TTTTCAATTTCAATTTTTCAAAAAAATCAACTCAGAATGCGAGAAATGAGTTGAGCCTCGGGT--
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
58490939 CACGCTGAGATAT
66 CACGCTGAGGTAT
* * * * * *
58490952 TTTT-AGTTTCTATTTTTCAAAAAAATCAGCTCATAATGCGAGAAGTGGGTTGAGCCTCGGGT--
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
58491014 CACGCTGATGTAT
66 CACGCTGAGGTAT
* * *
58491027 TTTT-AATTTCTATTTTTC-AAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGT--
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
58491088 CACGCTGAGGTA-
66 CACGCTGAGGTAT
*** *
58491100 TTTTCAATTTCTGTTTTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
1 TTTTCAATTTCTG---TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
58491165 T--CACGCTGAGGTA-
63 TCACACGCTGAGGTAT
* *** * *
58491178 TTTTCAATTTCTTTTTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC-GGAC
1 TTTTCAATTTC-TGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
* *
58491242 ACACGCCGATGTAT
65 ACACGCTGAGGTAT
** * *
58491256 TTTTCAATTTAAGTTTTTC-GAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
58491320 CATC-CTGAGGTAT
66 CA-CGCTGAGGTAT
* *
58491333 TTTTCAATTTATGTTTTTC-AAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
* *
58491397 CATC-TTTAGGTAT
66 CA-CGCTGAGGTAT
58491410 TTTTCAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTCAATTTCTGTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
*
58491475 ACATC-TTGAGGTAT
65 ACA-CGCTGAGGTAT
* * * *
58491489 TTTTCAATTTTTTGCTTTTCAAAAAAATGAATTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTCAA-TTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
58491554 ACATC-CTGAGGTAT
65 ACA-CGCTGAGGTAT
* *
58491568 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTTA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
58491633 CATC-ATGAGGTAT
66 CA-CGCTGAGGTAT
* *
58491646 TTTTCAATTTCTGTTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
**
58491711 CACAG-TAAAAGAGAG-GG
66 CAC-GCT----GAG-GTAT
* * *
58491728 TTTTCAATTTTTGCTTTTCGAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
58491793 CACCCTGAGGTAT
66 CACGCTGAGGTAT
* * * *
58491806 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCAAGATGTGGGTTGAGCCTTGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
58491871 CACGCTGAGGTAT
66 CACGCTGAGGTAT
* *
58491884 TTTTCAATTTTTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
58491949 CACGCTGAGGTAT
66 CACGCTGAGGTAT
* * *
58491962 TTTTCAATTTCTGTTTTT--AAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCAGGTCG
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
58492025 CATGCTGAGGTAT
66 CACGCTGAGGTAT
* *
58492038 TTTTCAATTTCTGTTGTTCAAAAAAAATCAACTCATATTGCGATG-GGTGAGTTGAGCCTCAGG-
1 TTTTCAATTTCTGTTTTTC-AAAAAAATCAACTCATATTGCGA-GAGGTGAGTTGAGCCTCGGGT
* **
58492101 CACATGCCAAGGTA-
64 CACACGCTGAGGTAT
* * * * * * * *
58492115 TTTTCGATTTTTGTTTTTC--GAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCTTCGGGTCG
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
* *
58492178 CATGCTCG-GCTAT
66 CACGCT-GAGGTAT
* *
58492191 TTTT-GATTTCTGTTTTTTAATAAAAA
1 TTTTCAATTTCTGTTTTTCAA-AAAAA
58492217 ATAAAAAAAT
Statistics
Matches: 1185, Mismatches: 119, Indels: 71
0.86 0.09 0.05
Matches are distributed among these distances:
73 5 0.00
74 92 0.08
75 131 0.11
76 160 0.14
77 176 0.15
78 376 0.32
79 166 0.14
80 11 0.01
82 67 0.06
83 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (78 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
CACGCTGAGGTAT
Found at i:58492424 original size:59 final size:59
Alignment explanation
Indices: 58492353--58492469 Score: 155
Period size: 59 Copynumber: 2.0 Consensus size: 59
58492343 AATAAAAAAA
* * * * * * *
58492353 TTATATTTTGACCCCTTAATTTTTTCAAATTTTGTTTTGACCCCTTAGATTTT-TTCAAT
1 TTATATTTTGACCCCTCAACTTCTTAAAATTATATTTTGACCCC-TAAATTTTCTTCAAT
58492412 TTATATTTTGACCCCTCAACTTCTTAAAATTATATTTTGACCCCTAAATTTTCTTCAA
1 TTATATTTTGACCCCTCAACTTCTTAAAATTATATTTTGACCCCTAAATTTTCTTCAA
58492470 ATTACACTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
58 7 0.14
59 43 0.86
ACGTcount: A:0.26, C:0.20, G:0.05, T:0.50
Consensus pattern (59 bp):
TTATATTTTGACCCCTCAACTTCTTAAAATTATATTTTGACCCCTAAATTTTCTTCAAT
Found at i:58492473 original size:30 final size:29
Alignment explanation
Indices: 58492350--58492473 Score: 149
Period size: 29 Copynumber: 4.2 Consensus size: 29
58492340 AAAAATAAAA
*
58492350 AAATTATATTTTGACCCCTTAATTTTTTC
1 AAATTATATTTTGACCCCTAAATTTTTTC
* * *
58492379 AAATTTTGTTTTGACCCCTTAGATTTTTTC
1 AAATTATATTTTGACCCC-TAAATTTTTTC
* * * * *
58492409 AATTTATATTTTGACCCCTCAACTTCTTA
1 AAATTATATTTTGACCCCTAAATTTTTTC
58492438 AAATTATATTTTGACCCCTAAATTTTCTTC
1 AAATTATATTTTGACCCCTAAATTTT-TTC
58492468 AAATTA
1 AAATTA
58492474 CACTTGGCCC
Statistics
Matches: 76, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
29 44 0.58
30 32 0.42
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.48
Consensus pattern (29 bp):
AAATTATATTTTGACCCCTAAATTTTTTC
Found at i:58493947 original size:21 final size:21
Alignment explanation
Indices: 58493922--58493963 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
58493912 TAAAATTTCC
58493922 CGTG-TTTCAAAAAAATATATT
1 CGTGTTTTCAAAAAAAT-TATT
*
58493943 CGTGTTTTTAAAAAAATTATT
1 CGTGTTTTCAAAAAAATTATT
58493964 TCCGTATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (21 bp):
CGTGTTTTCAAAAAAATTATT
Found at i:58494078 original size:18 final size:18
Alignment explanation
Indices: 58494031--58494070 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
58494021 ACTTTTCGCT
*
58494031 TTTTCAAAAATGT-TCGTG
1 TTTTC-AAAATTTCTCGTG
58494049 TTTTCAAAATTTCTCGTG
1 TTTTCAAAATTTCTCGTG
58494067 TTTT
1 TTTT
58494071 AAATATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (18 bp):
TTTTCAAAATTTCTCGTG
Found at i:58494079 original size:27 final size:26
Alignment explanation
Indices: 58494049--58494106 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
58494039 AATGTTCGTG
* *
58494049 TTTTCAAAATTTCTCGTGTTTTAAATA
1 TTTTCAAAATTTCTCGT-TTTCAAAAA
* **
58494076 TTTTCGACTTTTCTCGTTTTCAAAAA
1 TTTTCAAAATTTCTCGTTTTCAAAAA
58494102 TTTTC
1 TTTTC
58494107 GTGTTTTAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.24, C:0.16, G:0.07, T:0.53
Consensus pattern (26 bp):
TTTTCAAAATTTCTCGTTTTCAAAAA
Found at i:58494096 original size:61 final size:62
Alignment explanation
Indices: 58493974--58494135 Score: 195
Period size: 61 Copynumber: 2.6 Consensus size: 62
58493964 TCCGTATTTC
* * * *
58493974 AAATTTTCATGTTTTCAAAAATTTCTCTTGTTTAAAAAAAAATTTCGACTTTTCGCTTTTTCAA
1 AAATTTTCGTGTTTTC-AAAATTTCTCGTGTTT-ATAAAAAATTTCGACTTTTCGCGTTTTCAA
* * * *
58494038 AAATGTTCGTGTTTTCAAAATTTCTCGTGTTT-TAAATATTTTCGACTTTTCTCGTTTTCAA
1 AAATTTTCGTGTTTTCAAAATTTCTCGTGTTTATAAAAAATTTCGACTTTTCGCGTTTTCAA
*
58494099 AAATTTTCGTGTTTT-AGAAATTT-TCGTGTTTCTAAAA
1 AAATTTTCGTGTTTTCA-AAATTTCTCGTGTTTATAAAA
58494136 TTCTTGTATT
Statistics
Matches: 86, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
60 9 0.10
61 48 0.56
63 15 0.17
64 14 0.16
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (62 bp):
AAATTTTCGTGTTTTCAAAATTTCTCGTGTTTATAAAAAATTTCGACTTTTCGCGTTTTCAA
Found at i:58494112 original size:18 final size:18
Alignment explanation
Indices: 58494091--58494171 Score: 71
Period size: 17 Copynumber: 4.6 Consensus size: 18
58494081 GACTTTTCTC
58494091 GTTTTCAAAAATTTTCGT
1 GTTTTCAAAAATTTTCGT
*
58494109 GTTTT-AGAAATTTTCGT
1 GTTTTCAAAAATTTTCGT
*
58494126 G-TTTCTAAAATTCTT-GT
1 GTTTTCAAAAATT-TTCGT
* *
58494143 -ATTTCAAAAAATTTCCGT
1 GTTTTC-AAAAATTTTCGT
*
58494161 GTTCTCAAAAA
1 GTTTTCAAAAA
58494172 AATTATTATC
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
16 3 0.06
17 24 0.48
18 20 0.40
19 3 0.06
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (18 bp):
GTTTTCAAAAATTTTCGT
Found at i:58494626 original size:29 final size:28
Alignment explanation
Indices: 58494593--58494657 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 28
58494583 TGAATCTCAA
58494593 AATTATAT-ATGAACTTTAATTTAATGTGT
1 AATTATATAATGAACTTTAATTT-A-GTGT
58494622 AATTATATACATGAACTTTAATTTAGTGT
1 AATTATATA-ATGAACTTTAATTTAGTGT
58494651 AATTATA
1 AATTATA
58494658 CACGTGAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 19 0.56
30 1 0.03
31 14 0.41
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (28 bp):
AATTATATAATGAACTTTAATTTAGTGT
Done.