Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016419.1 Corchorus capsularis cultivar CVL-1 contig16440, 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: 72005
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:11020 original size:15 final size:15
Alignment explanation
Indices: 11000--11029 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
10990 AAGGGATTTT
11000 AAGAAAGCAATTAAA
1 AAGAAAGCAATTAAA
11015 AAGAAAGCAATTAAA
1 AAGAAAGCAATTAAA
11030 CTAAAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (15 bp):
AAGAAAGCAATTAAA
Found at i:11050 original size:21 final size:20
Alignment explanation
Indices: 11011--11055 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
11001 AGAAAGCAAT
* *
11011 TAAAAAGAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
11031 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
11052 TAAA
1 TAAA
11056 TCTAGATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Found at i:27122 original size:24 final size:24
Alignment explanation
Indices: 27077--27125 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
27067 TTTATGCATG
*
27077 TATTGAGTTATTGATTTGATTTTT
1 TATTGAGTGATTGATTTGATTTTT
* *
27101 TATTGA-TGATTGCTTTGAATTTT
1 TATTGAGTGATTGATTTGATTTTT
27124 TA
1 TA
27126 AGAATGTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.22, C:0.02, G:0.16, T:0.59
Consensus pattern (24 bp):
TATTGAGTGATTGATTTGATTTTT
Found at i:34236 original size:12 final size:12
Alignment explanation
Indices: 34211--34259 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
34201 CGTATATATA
34211 TTGATTTATTGAT
1 TTGATTT-TTGAT
34224 TTGATTTTTGA-
1 TTGATTTTTGAT
**
34235 TTGATGATTGAT
1 TTGATTTTTGAT
34247 TTGATTTTTGAT
1 TTGATTTTTGAT
34259 T
1 T
34260 GATGATTGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
11 9 0.29
12 15 0.48
13 7 0.23
ACGTcount: A:0.20, C:0.00, G:0.18, T:0.61
Consensus pattern (12 bp):
TTGATTTTTGAT
Found at i:34239 original size:16 final size:16
Alignment explanation
Indices: 34211--34262 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 16
34201 CGTATATATA
34211 TTGATTTATTGATTTGATTT
1 TTGATTT-TTGA-TTGA--T
**
34231 TTGATTGATGATTGAT
1 TTGATTTTTGATTGAT
34247 TTGATTTTTGATTGAT
1 TTGATTTTTGATTGAT
34263 GATTGCTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 15 0.54
18 4 0.14
19 3 0.11
20 6 0.21
ACGTcount: A:0.21, C:0.00, G:0.19, T:0.60
Consensus pattern (16 bp):
TTGATTTTTGATTGAT
Found at i:34246 original size:23 final size:23
Alignment explanation
Indices: 34218--34279 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
34208 ATATTGATTT
34218 ATTGATTTGATTTTTGATTGATG
1 ATTGATTTGATTTTTGATTGATG
34241 ATTGATTTGATTTTTGATTGATG
1 ATTGATTTGATTTTTGATTGATG
*
34264 ATTGCTTTGAATTTTT
1 ATTGATTTG-ATTTTT
34280 AAGAATGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 31 0.84
24 6 0.16
ACGTcount: A:0.21, C:0.02, G:0.19, T:0.58
Consensus pattern (23 bp):
ATTGATTTGATTTTTGATTGATG
Found at i:37514 original size:27 final size:27
Alignment explanation
Indices: 37333--37528 Score: 150
Period size: 27 Copynumber: 7.2 Consensus size: 27
37323 TATTTCTTGA
* *
37333 TTACTAATTACCATTTTTTACTC-TTT
1 TTACTGATTACCACTTTTTACTCTTTT
* *
37359 GTACTGATTACCA-TATTTTACTATTTT
1 TTACTGATTACCACT-TTTTACTCTTTT
* *
37386 TTACTGATTACCCCTTTTCTTACTATTTT
1 TTACTGATTACCAC-TTT-TTACTCTTTT
* *
37415 TTACTGAATATCACTTTTTACTC-TTT
1 TTACTGATTACCACTTTTTACTCTTTT
* * *
37441 TTATTTAATTACCA-TTTCTTACTCTTTG
1 TTA-CTGATTACCACTTT-TTACTCTTTT
* *
37469 TTACTAATTA-CTCTCTTTTACTCTTTT
1 TTACTGATTACCACT-TTTTACTCTTTT
* * *
37496 TTACTGATCACAACTTTTTACTCATTTC
1 TTACTGATTACCACTTTTTACTC-TTTT
37524 TTACT
1 TTACT
37529 CTTTTTACTG
Statistics
Matches: 136, Mismatches: 22, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
25 1 0.01
26 28 0.21
27 63 0.46
28 22 0.16
29 22 0.16
ACGTcount: A:0.22, C:0.20, G:0.03, T:0.55
Consensus pattern (27 bp):
TTACTGATTACCACTTTTTACTCTTTT
Found at i:37517 original size:37 final size:36
Alignment explanation
Indices: 37476--37566 Score: 96
Period size: 37 Copynumber: 2.4 Consensus size: 36
37466 TTGTTACTAA
37476 TTACTCTCTTTTACTCTTTTTTACTGATCACAAC-TTT-
1 TTACTCT-TTTTACTC-TTTTTACTGATCAC-ACTTTTC
* *
37513 TTACTCATTTCTTACTCTTTTTACTGATTACTCTTTTC
1 TTACTC-TTT-TTACTCTTTTTACTGATCACACTTTTC
37551 TTACTCTTTTTTACTC
1 TTACTC-TTTTTACTC
37567 AATATCACTT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
36 1 0.02
37 30 0.64
38 16 0.34
ACGTcount: A:0.16, C:0.24, G:0.02, T:0.57
Consensus pattern (36 bp):
TTACTCTTTTTACTCTTTTTACTGATCACACTTTTC
Found at i:37577 original size:65 final size:64
Alignment explanation
Indices: 37449--37623 Score: 191
Period size: 65 Copynumber: 2.7 Consensus size: 64
37439 TTTTATTTAA
* *
37449 TTAC-CATTTCTTACTCTTTGTTACTAATTACTCTCTTTTACTCTTTTTTACTGATCACAACTTT
1 TTACTCATTTCTTACTCTTT-TTACTGATTACTCTCTTTTACTCTTTTTTACTAATCACAACTTT
*
37513 TTACTCATTTCTTACTCTTTTTACTGATTACTCTTTTCTTACTCTTTTTTACTCAAT-ATC-ACT
1 TTACTCATTTCTTACTCTTTTTACTGATTACTCTCTT-TTACTCTTTTTTACT-AATCA-CAACT
37576 TT
63 TT
* * *
37578 TTACTCTTCTTCTT-CTTCTCTTTTACTGACTAC-C-ATTTTACTCTTT
1 TTACTCAT-TTCTTAC-TCT-TTTTACTGATTACTCTCTTTTACTCTTT
37624 GAATTTAATT
Statistics
Matches: 98, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
64 28 0.29
65 46 0.47
66 12 0.12
67 12 0.12
ACGTcount: A:0.18, C:0.25, G:0.02, T:0.55
Consensus pattern (64 bp):
TTACTCATTTCTTACTCTTTTTACTGATTACTCTCTTTTACTCTTTTTTACTAATCACAACTTT
Found at i:37773 original size:166 final size:166
Alignment explanation
Indices: 37575--37881 Score: 530
Period size: 166 Copynumber: 1.8 Consensus size: 166
37565 TCAATATCAC
*
37575 TTTTTACTCTTCTTCTTCTTCTCTTTTACTGACTACCATTTTACTCTTTGAATTTAATTACTGAC
1 TTTTTACTCTTCTTCTTCTTCTCTTTTACTGACTACCATTTTACTCTTTGAACTTAATTACTGAC
*
37640 TATCATTTTACTCTTTACTGATTATTTTTTTACTTTTTTATT-GATTACTA-TTTCACTCTTACT
66 TATCATTTTACTCTTTACTGATTATTTCTTTACTTTTTTATTAG-TTACTACTTT-ACTCTTACT
37703 GATTACC-ATTACTTTTTGAACTTGAACACTGATTACCT
129 GATT-CCTATTACTTTTTGAACTTGAACACTGATTACCT
* *
37741 TTTTTACTTTTCTTCTTTTTCTCTTTTACTGACTACCATTTTACTCTTTGAACTTAATTACTGAC
1 TTTTTACTCTTCTTCTTCTTCTCTTTTACTGACTACCATTTTACTCTTTGAACTTAATTACTGAC
37806 TATCATTTTACTCTTTACTGATTATTTCTTTACTTTTTTATTAGTTACTACTTTACTCTTACTGA
66 TATCATTTTACTCTTTACTGATTATTTCTTTACTTTTTTATTAGTTACTACTTTACTCTTACTGA
37871 TTCCTATTACT
131 TTCCTATTACT
37882 CTTTACTGAT
Statistics
Matches: 134, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
165 2 0.01
166 128 0.96
167 4 0.03
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.54
Consensus pattern (166 bp):
TTTTTACTCTTCTTCTTCTTCTCTTTTACTGACTACCATTTTACTCTTTGAACTTAATTACTGAC
TATCATTTTACTCTTTACTGATTATTTCTTTACTTTTTTATTAGTTACTACTTTACTCTTACTGA
TTCCTATTACTTTTTGAACTTGAACACTGATTACCT
Found at i:37826 original size:22 final size:22
Alignment explanation
Indices: 37798--38041 Score: 136
Period size: 22 Copynumber: 11.3 Consensus size: 22
37788 TTGAACTTAA
*
37798 TTACTGACTATCATTTTACTCT
1 TTACTGATTATCATTTTACTCT
* *
37820 TTACTGATTAT-TTCTTTACTTTT
1 TTACTGATTATCAT-TTTAC-TCT
* *
37843 TTA-TTAGTTA-CTACTTTACTC-
1 TTACTGA-TTATC-ATTTTACTCT
* *
37864 TTACTGA-T-TCCTATTACTCT
1 TTACTGATTATCATTTTACTCT
*
37884 TTACTGATTATCACTTTACTCT
1 TTACTGATTATCATTTTACTCT
* *
37906 TTACTGATTACCATTGTAC-CT
1 TTACTGATTATCATTTTACTCT
* * * *
37927 ATTACTGACTACCTTTTTACTTTT
1 -TTACTGATTATCATTTTAC-TCT
*
37951 TTACTGATTAACA--TTACT-T
1 TTACTGATTATCATTTTACTCT
*
37970 CTTACTGATTA-C-TATTACTCT
1 -TTACTGATTATCATTTTACTCT
* * * *
37991 ATACTGATTACCATATTGCTCT
1 TTACTGATTATCATTTTACTCT
*
38013 TTACTAATTATCATTTTAC-CTT
1 TTACTGATTATCATTTTACTC-T
38035 TTACTGA
1 TTACTGA
38042 CAACCATTAT
Statistics
Matches: 170, Mismatches: 32, Indels: 40
0.70 0.13 0.17
Matches are distributed among these distances:
19 8 0.05
20 34 0.20
21 14 0.08
22 90 0.53
23 23 0.14
24 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.05, T:0.50
Consensus pattern (22 bp):
TTACTGATTATCATTTTACTCT
Found at i:37990 original size:107 final size:103
Alignment explanation
Indices: 37858--38118 Score: 304
Period size: 107 Copynumber: 2.5 Consensus size: 103
37848 AGTTACTACT
*
37858 TTAC-TCTTACTGATTCCTATTACTCTTTACTGATTATCACTTTACTCTTTACTGATTACCATTG
1 TTACTTCTTACTGATTACTATTACTCTTTACTGATTATCA-TTTACTCTTTACTGATTACCATTG
* *
37922 TACCTATTACTGACTACC-TTTTTACTTTTTTACTGATTAAC
65 TACCTATTACTGACAACCATTATT--TTTTTTACTGATT-AC
* * * * *
37963 ATTACTTCTTACTGATTACTATTACTCTATACTGATTACCATATTGCTCTTTACTAATTATCATT
1 -TTACTTCTTACTGATTACTATTACTCTTTACTGATTATCAT-TTACTCTTTACTGATTACCATT
* *
38028 TTACCTTTTACTGACAACCATTATTTTTTTTACTGATTAC
64 GTACCTATTACTGACAACCATTATTTTTTTTACTGATTAC
*
38068 -TA-TT-TTACTGATTATCTTTTA--CTTTACTGATTATCATTTACTC-TTACTGAT
1 TTACTTCTTACTGATTA-CTATTACTCTTTACTGATTATCATTTACTCTTTACTGAT
38119 CACCTTTCAC
Statistics
Matches: 136, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
98 7 0.05
99 5 0.04
100 14 0.10
101 10 0.07
102 7 0.05
103 2 0.01
105 2 0.01
106 18 0.13
107 67 0.49
108 4 0.03
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.50
Consensus pattern (103 bp):
TTACTTCTTACTGATTACTATTACTCTTTACTGATTATCATTTACTCTTTACTGATTACCATTGT
ACCTATTACTGACAACCATTATTTTTTTTACTGATTAC
Found at i:38089 original size:14 final size:15
Alignment explanation
Indices: 38055--38090 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
38045 CCATTATTTT
38055 TTTTACTGATTACTA
1 TTTTACTGATTACTA
*
38070 TTTTACTGATTA-TC
1 TTTTACTGATTACTA
38084 TTTTACT
1 TTTTACT
38091 TTACTGATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.22, C:0.14, G:0.06, T:0.58
Consensus pattern (15 bp):
TTTTACTGATTACTA
Found at i:38095 original size:19 final size:20
Alignment explanation
Indices: 38072--38331 Score: 111
Period size: 20 Copynumber: 14.1 Consensus size: 20
38062 GATTACTATT
38072 TTACTGATTATCTTTTACT-
1 TTACTGATTATCTTTTACTC
*
38091 TTACTGATTATCATTTACTC
1 TTACTGATTATCTTTTACTC
* * *
38111 TTACTGATCACCTTTCACTC
1 TTACTGATTATCTTTTACTC
*
38131 TTACTGATTAT-TTTT--GC
1 TTACTGATTATCTTTTACTC
* *
38148 -TA---ATTACCCTTTTGCTC
1 TTACTGATTA-TCTTTTACTC
* *
38165 TTAATGATTA-C----CCTC
1 TTACTGATTATCTTTTACTC
*
38180 TTACTGATTACCTTTTACTC
1 TTACTGATTATCTTTTACTC
* * *
38200 TTATTGATTA-C----CCAC
1 TTACTGATTATCTTTTACTC
* *
38215 -TAGCTGATTACCTTTTACTT
1 TTA-CTGATTATCTTTTACTC
* *
38235 TTACTGATTA-CTTTTTGCTA
1 TTACTGATTATC-TTTTACTC
38255 TTACTGATTATC---T--TC
1 TTACTGATTATCTTTTACTC
* * *
38270 TTACCGATTACCTCTTACTC
1 TTACTGATTATCTTTTACTC
*
38290 TTACTGATTACCTTTTACTC
1 TTACTGATTATCTTTTACTC
* *
38310 TTACTAATCATCTTTTACTC
1 TTACTGATTATCTTTTACTC
38330 TT
1 TT
38332 TATGTTTATT
Statistics
Matches: 182, Mismatches: 31, Indels: 55
0.68 0.12 0.21
Matches are distributed among these distances:
13 4 0.02
14 2 0.01
15 35 0.19
16 4 0.02
17 3 0.02
18 3 0.02
19 24 0.13
20 100 0.55
21 7 0.04
ACGTcount: A:0.21, C:0.23, G:0.06, T:0.49
Consensus pattern (20 bp):
TTACTGATTATCTTTTACTC
Found at i:38180 original size:15 final size:15
Alignment explanation
Indices: 38162--38191 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38152 TACCCTTTTG
38162 CTCTTAATGATTACC
1 CTCTTAATGATTACC
*
38177 CTCTTACTGATTACC
1 CTCTTAATGATTACC
38192 TTTTACTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (15 bp):
CTCTTAATGATTACC
Found at i:38201 original size:35 final size:35
Alignment explanation
Indices: 38057--38314 Score: 143
Period size: 35 Copynumber: 7.1 Consensus size: 35
38047 ATTATTTTTT
** * *
38057 TTACTGATTACTATTTTACTGATTATCTTTTACT-
1 TTACTGATTACCCTCTTACTGATTACCTTTTACTC
* * *
38091 TTACTGATTATCATTTACTCTTACTGATCACCTTTCACTC
1 TTACTGATTA-C----CCTCTTACTGATTACCTTTTACTC
* * * * *
38131 TTACTGATTA--TTTTTGCTAATTACCCTTTTGCTC
1 TTACTGATTACCCTCTTACTGATTA-CCTTTTACTC
*
38165 TTAATGATTACCCTCTTACTGATTACCTTTTACTC
1 TTACTGATTACCCTCTTACTGATTACCTTTTACTC
* * *
38200 TTATTGATTACCCAC-TAGCTGATTACCTTTTACTT
1 TTACTGATTACCCTCTTA-CTGATTACCTTTTACTC
* * * *
38235 TTACTGATTA-CTTTTTGCT-ATTA-CTGATTATCTTC
1 TTACTGATTACCCTCTTACTGATTACCT-TTTA-C-TC
*
38270 TTACCGATTACCTCTTACTCTTACTGATTACCTTTTACTC
1 TTACTGATTA-C-C---CTCTTACTGATTACCTTTTACTC
38310 TTACT
1 TTACT
38315 AATCATCTTT
Statistics
Matches: 167, Mismatches: 35, Indels: 38
0.70 0.15 0.16
Matches are distributed among these distances:
32 2 0.01
33 15 0.09
34 33 0.20
35 59 0.35
36 9 0.05
38 1 0.01
39 17 0.10
40 16 0.10
41 6 0.04
42 7 0.04
43 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.07, T:0.49
Consensus pattern (35 bp):
TTACTGATTACCCTCTTACTGATTACCTTTTACTC
Found at i:38202 original size:20 final size:20
Alignment explanation
Indices: 38177--38331 Score: 116
Period size: 20 Copynumber: 8.2 Consensus size: 20
38167 AATGATTACC
38177 CTCTTACTGATTACCTTTTA
1 CTCTTACTGATTACCTTTTA
*
38197 CTCTTATTGATTACC-----
1 CTCTTACTGATTACCTTTTA
*
38212 CAC-TAGCTGATTACCTTTTA
1 CTCTTA-CTGATTACCTTTTA
* * *
38232 CTTTTACTGATTACTTTTTG
1 CTCTTACTGATTACCTTTTA
* *
38252 CTATTACTGATTA---TCT-
1 CTCTTACTGATTACCTTTTA
* *
38268 -TCTTACCGATTACCTCTTA
1 CTCTTACTGATTACCTTTTA
38287 CTCTTACTGATTACCTTTTA
1 CTCTTACTGATTACCTTTTA
* * *
38307 CTCTTACTAATCATCTTTTA
1 CTCTTACTGATTACCTTTTA
38327 CTCTT
1 CTCTT
38332 TATGTTTATT
Statistics
Matches: 105, Mismatches: 18, Indels: 24
0.71 0.12 0.16
Matches are distributed among these distances:
14 2 0.02
15 20 0.19
17 2 0.02
18 1 0.01
20 78 0.74
21 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.06, T:0.49
Consensus pattern (20 bp):
CTCTTACTGATTACCTTTTA
Found at i:38323 original size:55 final size:55
Alignment explanation
Indices: 38177--38327 Score: 171
Period size: 55 Copynumber: 2.8 Consensus size: 55
38167 AATGATTACC
* * ** * *
38177 CTCTTACTGATTACCTTTTACTCTTATTGATTACCCAC-TAGCTGATTACCTTTTA
1 CTCTTACTGATTACCTTTTACTCTTACTGATTATCTTCTTA-CCGATTACCTCTTA
* * * *
38232 CTTTTACTGATTACTTTTTGCTATTACTGATTATCTTCTTACCGATTACCTCTTA
1 CTCTTACTGATTACCTTTTACTCTTACTGATTATCTTCTTACCGATTACCTCTTA
* *
38287 CTCTTACTGATTACCTTTTACTCTTACTAATCATCTT-TTAC
1 CTCTTACTGATTACCTTTTACTCTTACTGATTATCTTCTTAC
38328 TCTTTATGTT
Statistics
Matches: 79, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
54 4 0.05
55 73 0.92
56 2 0.03
ACGTcount: A:0.21, C:0.25, G:0.06, T:0.48
Consensus pattern (55 bp):
CTCTTACTGATTACCTTTTACTCTTACTGATTATCTTCTTACCGATTACCTCTTA
Found at i:39701 original size:19 final size:19
Alignment explanation
Indices: 39677--39715 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
39667 ATCAAAGGGA
39677 AATCGACGGAAAGAGAGCC
1 AATCGACGGAAAGAGAGCC
39696 AATCGACGGAAAGAGAGCC
1 AATCGACGGAAAGAGAGCC
39715 A
1 A
39716 CTCAAGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.21, G:0.31, T:0.05
Consensus pattern (19 bp):
AATCGACGGAAAGAGAGCC
Found at i:43239 original size:28 final size:29
Alignment explanation
Indices: 43163--43242 Score: 119
Period size: 28 Copynumber: 2.8 Consensus size: 29
43153 TGCTTCTTAC
43163 TGATTCTGCTTTGTTTTCATGCTGGACACT
1 TGATT-TGCTTTGTTTTCATGCTGGACACT
43193 TGATTTGC-TTGTTTTCATGCTGGA-ACT
1 TGATTTGCTTTGTTTTCATGCTGGACACT
* *
43220 TGATTTGCTTTGATTCCATGCTG
1 TGATTTGCTTTGTTTTCATGCTG
43243 AATTGACCTC
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
27 11 0.23
28 28 0.60
29 3 0.06
30 5 0.11
ACGTcount: A:0.14, C:0.17, G:0.21, T:0.47
Consensus pattern (29 bp):
TGATTTGCTTTGTTTTCATGCTGGACACT
Found at i:47800 original size:2 final size:2
Alignment explanation
Indices: 47793--47818 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47783 TGAATTTTTC
47793 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
47819 TGAGAGATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49024 original size:36 final size:36
Alignment explanation
Indices: 48979--49050 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
48969 TTTTCCTATG
48979 CTTTTTGGTATTTTTATGTGGAATTTAACTCTATTT
1 CTTTTTGGTATTTTTATGTGGAATTTAACTCTATTT
49015 CTTTTTGGTATTTTTATGTGGAATTTAACTCTATTT
1 CTTTTTGGTATTTTTATGTGGAATTTAACTCTATTT
49051 TGCAAGTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.19, C:0.08, G:0.14, T:0.58
Consensus pattern (36 bp):
CTTTTTGGTATTTTTATGTGGAATTTAACTCTATTT
Found at i:49929 original size:123 final size:123
Alignment explanation
Indices: 49710--50079 Score: 713
Period size: 123 Copynumber: 3.0 Consensus size: 123
49700 TAGAGTCTTA
*
49710 TCCTAAGTATAATATGAGTCTTTAGGTTATTTTTCCACTATAAATACCCACCTTATGTAGCCTTA
1 TCCTAAGTATAATAGGAGTCTTTAGGTTATTTTTCCACTATAAATACCCACCTTATGTAGCCTTA
*
49775 GAAAACAATCTCTCATAATTCTCTTCGTCTACTTTTCTTTAGTTTTGTTTCTCTCTAG
66 GAAAACAATCTCTCATAATTCTCTTCTTCTACTTTTCTTTAGTTTTGTTTCTCTCTAG
*
49833 TCCTAAGTATAATAGGAGTCTTTAGGTTATTTTTCCACTATAAATACCCACCTTATGTAGTCTTA
1 TCCTAAGTATAATAGGAGTCTTTAGGTTATTTTTCCACTATAAATACCCACCTTATGTAGCCTTA
49898 GAAAACAATCTCTCATAATTCTCTTCTTCTACTTTTCTTTAGTTTTGTTTCTCTCTAG
66 GAAAACAATCTCTCATAATTCTCTTCTTCTACTTTTCTTTAGTTTTGTTTCTCTCTAG
49956 TCCTAAGTATAATAGGAGTCTTTAGGTTATTTTTCCACTATAAATACCCACCTTATGTAGCCTTA
1 TCCTAAGTATAATAGGAGTCTTTAGGTTATTTTTCCACTATAAATACCCACCTTATGTAGCCTTA
50021 GAAAACAATCTCTCATAATTCTCTTCTTCTACTTTTCTTTAGTTTTGTTTCTCTCTAG
66 GAAAACAATCTCTCATAATTCTCTTCTTCTACTTTTCTTTAGTTTTGTTTCTCTCTAG
50079 T
1 T
50080 TTTAGGCTAA
Statistics
Matches: 243, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 243 1.00
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.44
Consensus pattern (123 bp):
TCCTAAGTATAATAGGAGTCTTTAGGTTATTTTTCCACTATAAATACCCACCTTATGTAGCCTTA
GAAAACAATCTCTCATAATTCTCTTCTTCTACTTTTCTTTAGTTTTGTTTCTCTCTAG
Found at i:56096 original size:11 final size:12
Alignment explanation
Indices: 56080--56109 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
56070 CTCAAAATTT
56080 AAACCGAC-AAA
1 AAACCGACTAAA
56091 AAACCGACTAAA
1 AAACCGACTAAA
56103 AAACCGA
1 AAACCGA
56110 AAATCGACCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.60, C:0.27, G:0.10, T:0.03
Consensus pattern (12 bp):
AAACCGACTAAA
Found at i:63126 original size:31 final size:33
Alignment explanation
Indices: 63052--63128 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
63042 AAACGTTTTT
* *
63052 TAAAATACTTTCTCACGTTTTTTAGGGAGGTGT
1 TAAAATACTTTCTCACGTTTTTTAGGGAAGTGA
*
63085 TAAAATACTTTCTCACGTTTTTTA-TGAAG-GA
1 TAAAATACTTTCTCACGTTTTTTAGGGAAGTGA
*
63116 TAAAACACTTTCT
1 TAAAATACTTTCT
63129 TAAGAATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 13 0.32
32 3 0.08
33 24 0.60
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (33 bp):
TAAAATACTTTCTCACGTTTTTTAGGGAAGTGA
Found at i:67481 original size:109 final size:109
Alignment explanation
Indices: 67285--67580 Score: 450
Period size: 109 Copynumber: 2.7 Consensus size: 109
67275 ACTATTATAG
* *
67285 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
67350 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
*
67399 TTTTATTCTATTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
67464 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* **
67508 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAATTTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTT-TATAA-TTACTTTA
67572 TTTTTACCA
63 TTTTTACCA
67581 TTTTAATTTA
Statistics
Matches: 171, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
108 1 0.01
109 125 0.73
110 8 0.05
111 17 0.10
114 20 0.12
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:69859 original size:16 final size:16
Alignment explanation
Indices: 69838--69871 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
69828 ACAATTCAGA
69838 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
69854 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
69870 AA
1 AA
69872 TTATTTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.12
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Done.