Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008775.1 Corchorus capsularis cultivar CVL-1 contig08796, 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: 88874
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:395 original size:32 final size:32
Alignment explanation
Indices: 359--425 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 32
349 TTAGTAATAG
*
359 CAATTTAGAAATATGTTTTAAAGAA-AAGGGTA
1 CAATTTAGAAATATATTTTAAA-AATAAGGGTA
*
391 CAA-TTGGAAATATATTTTAAAAATAAGGGTA
1 CAATTTAGAAATATATTTTAAAAATAAGGGTA
422 CAAT
1 CAAT
426 CGGAAAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 2 0.06
31 26 0.84
32 3 0.10
ACGTcount: A:0.48, C:0.04, G:0.16, T:0.31
Consensus pattern (32 bp):
CAATTTAGAAATATATTTTAAAAATAAGGGTA
Found at i:401 original size:31 final size:31
Alignment explanation
Indices: 366--431 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
356 TAGCAATTTA
* *
366 GAAATATGTTTTAAAGAA-AAGGGTACAATTG
1 GAAATATATTTTAAA-AATAAGGGTACAATCG
397 GAAATATATTTTAAAAATAAGGGTACAATCG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
428 GAAA
1 GAAA
432 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATCG
Found at i:515 original size:2 final size:2
Alignment explanation
Indices: 460--503 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
450 TTCTTACTTT
* *
460 TA TA TA TA GTA TA GA TA TA TA GA TA TA TA 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 TA
503 T
1 T
504 GTGTGTATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2089 original size:29 final size:30
Alignment explanation
Indices: 2041--2099 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
2031 GGAGGCTGAC
* *
2041 ATTGATAGTTCAGGGTGCAATTTGTCCAAA
1 ATTGATAGTTCAGGGTGCAAATCGTCCAAA
2071 ATTGA-AGTTCATGGG-GCAAATCGTCCAAA
1 ATTGATAGTTCA-GGGTGCAAATCGTCCAAA
2100 TGATATAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (30 bp):
ATTGATAGTTCAGGGTGCAAATCGTCCAAA
Found at i:5591 original size:7 final size:7
Alignment explanation
Indices: 5579--5605 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5569 TTCACTGATC
5579 TTAGGGT
1 TTAGGGT
5586 TTAGGGT
1 TTAGGGT
5593 TTAGGGT
1 TTAGGGT
5600 TTAGGG
1 TTAGGG
5606 AAGGATTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.44, T:0.41
Consensus pattern (7 bp):
TTAGGGT
Found at i:11109 original size:100 final size:100
Alignment explanation
Indices: 10936--11133 Score: 396
Period size: 100 Copynumber: 2.0 Consensus size: 100
10926 ACACTTAAAA
10936 GAATTGATCATCACTTAAAACTTTGATTGGCAAGGAAATTCAGATGCTACATAATTACCTAGTTA
1 GAATTGATCATCACTTAAAACTTTGATTGGCAAGGAAATTCAGATGCTACATAATTACCTAGTTA
11001 TTTACATGGTCTTTGCATCTGATATAAGGTCAAGT
66 TTTACATGGTCTTTGCATCTGATATAAGGTCAAGT
11036 GAATTGATCATCACTTAAAACTTTGATTGGCAAGGAAATTCAGATGCTACATAATTACCTAGTTA
1 GAATTGATCATCACTTAAAACTTTGATTGGCAAGGAAATTCAGATGCTACATAATTACCTAGTTA
11101 TTTACATGGTCTTTGCATCTGATATAAGGTCAA
66 TTTACATGGTCTTTGCATCTGATATAAGGTCAA
11134 AGAAATCTGT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 98 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (100 bp):
GAATTGATCATCACTTAAAACTTTGATTGGCAAGGAAATTCAGATGCTACATAATTACCTAGTTA
TTTACATGGTCTTTGCATCTGATATAAGGTCAAGT
Found at i:14723 original size:15 final size:15
Alignment explanation
Indices: 14703--14736 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
14693 TTTTGGCCAA
14703 AATATTATAAAGAAC
1 AATATTATAAAGAAC
14718 AATATTATAAAGAAC
1 AATATTATAAAGAAC
14733 AATA
1 AATA
14737 ATTAGGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (15 bp):
AATATTATAAAGAAC
Found at i:14780 original size:42 final size:42
Alignment explanation
Indices: 14721--14805 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
14711 AAAGAACAAT
14721 ATTATAAAGAACAATAATTAGGAGAAGTGTAAATACTATAAA
1 ATTATAAAGAACAATAATTAGGAGAAGTGTAAATACTATAAA
14763 ATTATAAAGAACAATAATTAGGAGAAGTGTAAATACTATAAA
1 ATTATAAAGAACAATAATTAGGAGAAGTGTAAATACTATAAA
14805 A
1 A
14806 CCAATGTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.26
Consensus pattern (42 bp):
ATTATAAAGAACAATAATTAGGAGAAGTGTAAATACTATAAA
Found at i:15028 original size:28 final size:24
Alignment explanation
Indices: 14983--15036 Score: 56
Period size: 28 Copynumber: 2.1 Consensus size: 24
14973 AAGCTTTTTT
14983 CTCTTTCTTCTCCACTGT-TCCTTC
1 CTCTTTCTTCTCCACTGTCT-CTTC
15007 CTCTTTCTTCTCTCCATTCTGTCTCTTC
1 CTCTTTC-T-TCTCCA--CTGTCTCTTC
15035 CT
1 CT
15037 TCCCTCCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
24 7 0.28
25 1 0.04
26 6 0.24
28 10 0.40
29 1 0.04
ACGTcount: A:0.04, C:0.41, G:0.04, T:0.52
Consensus pattern (24 bp):
CTCTTTCTTCTCCACTGTCTCTTC
Found at i:15038 original size:22 final size:22
Alignment explanation
Indices: 15007--15048 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
14997 CTGTTCCTTC
* *
15007 CTCTTTCTTCTCTCCATTCTGT
1 CTCTTCCTTCCCTCCATTCTGT
15029 CTCTTCCTTCCCTCCATTCT
1 CTCTTCCTTCCCTCCATTCT
15049 CTTTCCTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.05, C:0.43, G:0.02, T:0.50
Consensus pattern (22 bp):
CTCTTCCTTCCCTCCATTCTGT
Found at i:15060 original size:22 final size:21
Alignment explanation
Indices: 15007--15061 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
14997 CTGTTCCTTC
*
15007 CTCT-TTCTTCTCTCCATTCT
1 CTCTCTTCTTCCCTCCATTCT
*
15027 GTCTCTTCCTTCCCTCCATTCT
1 CTCTCTT-CTTCCCTCCATTCT
*
15049 CTTTCCTTCTTCC
1 CTCT-CTTCTTCC
15062 TCTTCTATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.11
21 2 0.07
22 20 0.71
23 3 0.11
ACGTcount: A:0.04, C:0.44, G:0.02, T:0.51
Consensus pattern (21 bp):
CTCTCTTCTTCCCTCCATTCT
Found at i:28193 original size:2 final size:2
Alignment explanation
Indices: 28182--28219 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
28172 CTAATTTATT
* *
28182 TA TA TA -A TA TA TA TA TA TA TA TA TT TA TT TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28220 TCAATTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:28764 original size:165 final size:166
Alignment explanation
Indices: 28476--28790 Score: 483
Period size: 165 Copynumber: 1.9 Consensus size: 166
28466 TGAATCATTT
* *
28476 GTCAATTGAGAAATGACCAAAAAGTTTAGATATTTAATCCCCTCAAGAATAAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGTCTAGATATTTAATCACCTCAAGAATAAAAAGTTAGGACAT
* * *
28541 TTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTACTTCTCCAGCTCATCATTAATCCGGG
66 TTAAGTAATCGGCCAAGTAGGAAAAGACGAAAAAAATTACTTCTCCAGCTCATCATTAATCCGGG
28606 GTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
131 GTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* *
28642 GTCAATTGAGAAATGACC-AAAAGTCTAGTTATTTAATCACCTCAAGAATCAAAAA-TTAGGGCA
1 GTCAATTGAGAAATGACCAAAAAGTCTAGATATTTAATCACCTCAAGAAT-AAAAAGTTAGGACA
* * ** *
28705 TTTAAGTAATCGGTCAAGT-GTGAAAAGACGAAAAAAATTAGTTCTCTTGCTCCTCATTAATCCG
65 TTTAAGTAATCGGCCAAGTAG-GAAAAGACGAAAAAAATTACTTCTCCAGCTCATCATTAATCCG
28769 GGGTAGGGATCTTTTAGTAATT
129 GGGTAGGGATCTTTTAGTAATT
28791 TCCATATGTT
Statistics
Matches: 135, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
164 1 0.01
165 111 0.82
166 23 0.17
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (166 bp):
GTCAATTGAGAAATGACCAAAAAGTCTAGATATTTAATCACCTCAAGAATAAAAAGTTAGGACAT
TTAAGTAATCGGCCAAGTAGGAAAAGACGAAAAAAATTACTTCTCCAGCTCATCATTAATCCGGG
GTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:42494 original size:49 final size:49
Alignment explanation
Indices: 42422--42520 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
42412 CTCTAGAGCC
*
42422 AATTCAAACCCAAAACGTATCGCATGGACATCAGCATATAAAGAATCAA
1 AATTCAAACCCAAAAAGTATCGCATGGACATCAGCATATAAAGAATCAA
* *
42471 AATTCAAACCCAAAAAGTATCGCATGGGCATCAGCATATAAAGGATCAA
1 AATTCAAACCCAAAAAGTATCGCATGGACATCAGCATATAAAGAATCAA
42520 A
1 A
42521 GCTCAACTGC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.46, C:0.21, G:0.14, T:0.18
Consensus pattern (49 bp):
AATTCAAACCCAAAAAGTATCGCATGGACATCAGCATATAAAGAATCAA
Found at i:43182 original size:23 final size:23
Alignment explanation
Indices: 43155--43202 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
43145 GTCTGTTGCC
43155 AATATGCATATTCTCTCGTCCCA
1 AATATGCATATTCTCTCGTCCCA
43178 AATATGCATATTCTCTCGTCCCA
1 AATATGCATATTCTCTCGTCCCA
43201 AA
1 AA
43203 ATTCCCCTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (23 bp):
AATATGCATATTCTCTCGTCCCA
Found at i:45775 original size:17 final size:14
Alignment explanation
Indices: 45741--45778 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
45731 AATATATCTA
45741 TATCTATCTATATT
1 TATCTATCTATATT
45755 TATCTATGCTATA--
1 TATCTAT-CTATATT
45768 TATCTATCTAT
1 TATCTATCTAT
45779 CATAATGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.17
13 7 0.30
14 7 0.30
15 5 0.22
ACGTcount: A:0.29, C:0.16, G:0.03, T:0.53
Consensus pattern (14 bp):
TATCTATCTATATT
Found at i:54949 original size:20 final size:20
Alignment explanation
Indices: 54924--54964 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
54914 GGATAAGCTG
*
54924 CTGTTAAATATATCTCCTTT
1 CTGTTAAATAAATCTCCTTT
54944 CTGTTAAATAAATCTCCTTT
1 CTGTTAAATAAATCTCCTTT
54964 C
1 C
54965 AGATCTGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.46
Consensus pattern (20 bp):
CTGTTAAATAAATCTCCTTT
Found at i:54996 original size:31 final size:31
Alignment explanation
Indices: 54958--55019 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
54948 TAAATAAATC
54958 TCCTTTCAGATCTGTATTTGTTCTTATTTGT
1 TCCTTTCAGATCTGTATTTGTTCTTATTTGT
* *
54989 TCCTTTCAGATCTGTATTTGTTGTTCTTTGT
1 TCCTTTCAGATCTGTATTTGTTCTTATTTGT
55020 CAAGCTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.11, C:0.16, G:0.15, T:0.58
Consensus pattern (31 bp):
TCCTTTCAGATCTGTATTTGTTCTTATTTGT
Found at i:57194 original size:21 final size:21
Alignment explanation
Indices: 57181--57459 Score: 137
Period size: 21 Copynumber: 13.0 Consensus size: 21
57171 TACTATTTTT
57181 TCTTTACTGATTACTTTTTAC
1 TCTTTACTGATTACTTTTTAC
** **
57202 TCTTTACTCTTTACTGATTAC
1 TCTTTACTGATTACTTTTTAC
**
57223 TCTTTACT-ATTTTTTCTTTTAC
1 TCTTTACTGA-TTACT-TTTTAC
* * *
57245 TTTTTACTAATTACCATTTTAC
1 TCTTTACTGATTA-CTTTTTAC
*
57267 TTTTTACTGATTACCCTTTTT-C
1 TCTTTACTGATTA--CTTTTTAC
* * *
57289 TCTTTTCTAATTACCCTTTTAC
1 TCTTTACTGATTA-CTTTTTAC
*
57311 T-TTTCACTGATTACCTTTT-C
1 TCTTT-ACTGATTACTTTTTAC
**
57331 -CTTATCACTGATTACCACTTTACC
1 TCTT-T-ACTGATTA-CTTTTTA-C
* * *
57355 TTTTTATTGATTACCCTTTTAC
1 TCTTTACTGATTA-CTTTTTAC
* **
57377 TTTTTACTGATTAC-CATTAC
1 TCTTTACTGATTACTTTTTAC
* *
57397 T-TCTTACTAATTAC-TATTAC
1 TCT-TTACTGATTACTTTTTAC
57417 TCTTTACTGATTATCATTTTT--
1 TCTTTACTGATTA-C-TTTTTAC
57438 TCTTTACTGATTACTTTTTAC
1 TCTTTACTGATTACTTTTTAC
57459 T
1 T
57460 TTACTCTTTA
Statistics
Matches: 204, Mismatches: 34, Indels: 40
0.73 0.12 0.14
Matches are distributed among these distances:
19 6 0.03
20 34 0.17
21 70 0.34
22 67 0.33
23 23 0.11
24 2 0.01
25 2 0.01
ACGTcount: A:0.20, C:0.22, G:0.03, T:0.55
Consensus pattern (21 bp):
TCTTTACTGATTACTTTTTAC
Found at i:57200 original size:14 final size:14
Alignment explanation
Indices: 57181--57230 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 14
57171 TACTATTTTT
57181 TCTTTACTGATTAC
1 TCTTTACTGATTAC
* **
57195 TTTTTACTCTTTAC
1 TCTTTACTGATTAC
57209 TCTTTACTGATTAC
1 TCTTTACTGATTAC
57223 TCTTTACT
1 TCTTTACT
57231 ATTTTTTCTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.18, C:0.22, G:0.04, T:0.56
Consensus pattern (14 bp):
TCTTTACTGATTAC
Found at i:57201 original size:7 final size:7
Alignment explanation
Indices: 57191--57274 Score: 53
Period size: 7 Copynumber: 11.7 Consensus size: 7
57181 TCTTTACTGA
57191 TTACTTT
1 TTACTTT
*
57198 TTACTCT
1 TTACTTT
*
57205 TTACTCT
1 TTACTTT
**
57212 TTACTGA
1 TTACTTT
*
57219 TTACTCT
1 TTACTTT
57226 TTACTATT
1 TTACT-TT
*
57234 TT-TTCTT
1 TTACT-TT
57241 TTACTTT
1 TTACTTT
**
57248 TTACTAA
1 TTACTTT
*
57255 TTACCATT
1 TTA-CTTT
57263 TTACTTT
1 TTACTTT
57270 TTACT
1 TTACT
57275 GATTACCCTT
Statistics
Matches: 59, Mismatches: 15, Indels: 6
0.74 0.19 0.08
Matches are distributed among these distances:
7 51 0.86
8 8 0.14
ACGTcount: A:0.19, C:0.19, G:0.01, T:0.61
Consensus pattern (7 bp):
TTACTTT
Found at i:57202 original size:28 final size:28
Alignment explanation
Indices: 57165--57241 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 28
57155 ATTTCTTCTC
*
57165 ACTTCTTACTATTTTTTCTTTACTGATT
1 ACTTTTTACTATTTTTTCTTTACTGATT
* **
57193 ACTTTTTACTCTTTACTCTTTACTGATT
1 ACTTTTTACTATTTTTTCTTTACTGATT
*
57221 ACTCTTTACTATTTTTTCTTT
1 ACTTTTTACTATTTTTTCTTT
57242 TACTTTTTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.17, C:0.19, G:0.03, T:0.61
Consensus pattern (28 bp):
ACTTTTTACTATTTTTTCTTTACTGATT
Found at i:57240 original size:14 final size:14
Alignment explanation
Indices: 57170--57241 Score: 51
Period size: 14 Copynumber: 5.1 Consensus size: 14
57160 TTCTCACTTC
*
57170 TTACTATTTTTTCT
1 TTACTATTTATTCT
57184 TTACTGA-TTACTT-T
1 TTACT-ATTTA-TTCT
* *
57198 TTACTCTTTACTCT
1 TTACTATTTATTCT
*
57212 TTACTGA-TTACTCT
1 TTACT-ATTTATTCT
*
57226 TTACTATTTTTTCT
1 TTACTATTTATTCT
57240 TT
1 TT
57242 TACTTTTTAC
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
13 2 0.04
14 41 0.89
15 3 0.07
ACGTcount: A:0.17, C:0.18, G:0.03, T:0.62
Consensus pattern (14 bp):
TTACTATTTATTCT
Found at i:57258 original size:14 final size:13
Alignment explanation
Indices: 57183--57258 Score: 52
Period size: 14 Copynumber: 5.8 Consensus size: 13
57173 CTATTTTTTC
57183 TTTACTGATTACTT
1 TTTACT-ATTACTT
* *
57197 TTTACTCTTTACTC
1 TTTACT-ATTACTT
*
57211 TTTACTGATTACTC
1 TTTACT-ATTACTT
57225 TTTACTA-T--TT
1 TTTACTATTACTT
*
57235 TTT-CTTTTACTT
1 TTTACTATTACTT
57247 TTTACTAATTAC
1 TTTACT-ATTAC
57259 CATTTTACTT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
9 2 0.04
10 5 0.10
12 6 0.12
13 3 0.06
14 33 0.67
ACGTcount: A:0.20, C:0.18, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTACTATTACTT
Found at i:57264 original size:22 final size:22
Alignment explanation
Indices: 57239--57489 Score: 202
Period size: 22 Copynumber: 11.8 Consensus size: 22
57229 CTATTTTTTC
*
57239 TTTTACTTTTTACTAATTACCA
1 TTTTACTTTTTACTGATTACCA
*
57261 TTTTACTTTTTACTGATTACCC
1 TTTTACTTTTTACTGATTACCA
* * *
57283 TTTTTCTCTTTT-CTAATTACCC
1 TTTTACT-TTTTACTGATTACCA
*
57305 TTTTACTTTTCACTGATTACC-
1 TTTTACTTTTTACTGATTACCA
* * *
57326 TTTTCCTTATCACTGATTACCA
1 TTTTACTTTTTACTGATTACCA
* * *
57348 CTTTACCTTTTTATTGATTACCC
1 TTTTA-CTTTTTACTGATTACCA
57371 TTTTACTTTTTACTGATTACCA
1 TTTTACTTTTTACTGATTACCA
* *
57393 --TTACTTCTTACTAATTA-C-
1 TTTTACTTTTTACTGATTACCA
* * *
57411 TATTACTCTTTACTGATTATCA
1 TTTTACTTTTTACTGATTACCA
*
57433 TTTT--TTCTTTACTGATTA-CT
1 TTTTACTT-TTTACTGATTACCA
**
57453 TTTTAC--TTTACTCTTTACCA
1 TTTTACTTTTTACTGATTACCA
*
57473 TTTT-CTTTTTATTGATT
1 TTTTACTTTTTACTGATT
57490 TCTCTTTACT
Statistics
Matches: 183, Mismatches: 32, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
19 11 0.06
20 40 0.22
21 41 0.22
22 70 0.38
23 21 0.11
ACGTcount: A:0.20, C:0.21, G:0.03, T:0.55
Consensus pattern (22 bp):
TTTTACTTTTTACTGATTACCA
Found at i:57461 original size:19 final size:21
Alignment explanation
Indices: 57418--57464 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
57408 TACTATTACT
*
57418 CTTTACTGATTATCATTTTTT
1 CTTTACTGATTATCATTTTTA
57439 CTTTACTGATTA-C-TTTTTA
1 CTTTACTGATTATCATTTTTA
57458 CTTTACT
1 CTTTACT
57465 CTTTACCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 12 0.48
20 1 0.04
21 12 0.48
ACGTcount: A:0.19, C:0.17, G:0.04, T:0.60
Consensus pattern (21 bp):
CTTTACTGATTATCATTTTTA
Found at i:57462 original size:40 final size:40
Alignment explanation
Indices: 57170--57502 Score: 124
Period size: 40 Copynumber: 7.9 Consensus size: 40
57160 TTCTCACTTC
* **
57170 TTACTATTTTTTCTTTACTGATTACTTTTTACTCTTTACTCT
1 TTACCATTTTTTCTTTACTGATTACTTTTTA--CTTTACTGA
* ** ** *
57212 TTACTGA-TTACTCTTTACT-ATTTTTTCTTTTACTTTTTACTAA
1 TTAC-CATTTTTTCTTTACTGA-TTACT-TTTTAC--TTTACTGA
* * *
57255 TTACCATTTTACTT-TTTACTGATTACCCTTTTTCTCTTTTCTAA
1 TTACCATTTT--TTCTTTACTGATTA--CTTTTT-ACTTTACTGA
* * * *
57299 TTACCCTTTTACTT-TTCACTGATTACCTTTTCCTTATCACTGA
1 TTACCATTTT--TTCTTTACTGATTACTTTTTACTT-T-ACTGA
* * *
57342 TTACCACTTTACCTT-TTTATTGATTACCCTTTTACTTTTTACTGA
1 TTACCA-TTT--TTTCTTTACTGATTA-CTTTTTAC--TTTACTGA
** * *
57387 TTACCATTACTTC-TTACTAATTAC-TATTACTCTTTACTGA
1 TTACCATTTTTTCTTTACTGATTACTTTTTA--CTTTACTGA
* **
57427 TTATCATTTTTTCTTTACTGATTACTTTTTACTTTACTCT
1 TTACCATTTTTTCTTTACTGATTACTTTTTACTTTACTGA
* * *
57467 TTACCATTTTCTT-TTTATTGATTTCTCTTTACTTTA
1 TTACCATTTT-TTCTTTACTGATTACTTTTTACTTTA
57503 TTCTTTACTC
Statistics
Matches: 225, Mismatches: 40, Indels: 54
0.71 0.13 0.17
Matches are distributed among these distances:
40 58 0.26
41 18 0.08
42 40 0.18
43 26 0.12
44 54 0.24
45 24 0.11
46 3 0.01
47 2 0.01
ACGTcount: A:0.20, C:0.21, G:0.03, T:0.57
Consensus pattern (40 bp):
TTACCATTTTTTCTTTACTGATTACTTTTTACTTTACTGA
Found at i:57470 original size:19 final size:19
Alignment explanation
Indices: 57373--57470 Score: 57
Period size: 20 Copynumber: 5.2 Consensus size: 19
57363 GATTACCCTT
57373 TTACTTTTTACTGATTAC-CA
1 TTACTTTTTACT--TTACTCA
*
57393 TTACTTCTTACTAATTACT-A
1 TTACTTTTTACT--TTACTCA
*
57413 TTACTCTTTACTGATTA-TCA
1 TTACTTTTTACT--TTACTCA
*
57433 -T--TTTTT-CTTTACTGA
1 TTACTTTTTACTTTACTCA
*
57448 TTACTTTTTACTTTACTCT
1 TTACTTTTTACTTTACTCA
57467 TTAC
1 TTAC
57471 CATTTTCTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
14 3 0.05
15 2 0.03
16 3 0.05
17 4 0.06
18 5 0.08
19 13 0.21
20 32 0.52
ACGTcount: A:0.22, C:0.19, G:0.03, T:0.55
Consensus pattern (19 bp):
TTACTTTTTACTTTACTCA
Found at i:57504 original size:19 final size:19
Alignment explanation
Indices: 57480--57517 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
57470 CCATTTTCTT
57480 TTTATTGATTT-CTCTTTAC
1 TTTATT-ATTTACTCTTTAC
*
57499 TTTATTCTTTACTCTTTAC
1 TTTATTATTTACTCTTTAC
57518 CATTTTACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.16, C:0.18, G:0.03, T:0.63
Consensus pattern (19 bp):
TTTATTATTTACTCTTTAC
Found at i:57508 original size:40 final size:40
Alignment explanation
Indices: 57431--57610 Score: 125
Period size: 35 Copynumber: 4.7 Consensus size: 40
57421 TACTGATTAT
*
57431 CATTTTTTCTTTACTGATTACTTTTTACTTTACTCTTTAC
1 CATTTTTTCTTTACTGATTACTCTTTACTTTACTCTTTAC
* * *
57471 CATTTTCTT-TTTATTGATTTCTCTTTACTTTATTCTTTA-
1 CATTTT-TTCTTTACTGATTACTCTTTACTTTACTCTTTAC
** * *
57510 C-TCTTTACCATTTTACTAATTACTC-TT-C---ATTCTTTAC
1 CAT-TTTTTC--TTTACTGATTACTCTTTACTTTACTCTTTAC
* * *
57547 CATTTTTCCTTTACTAATTACTC-TT-C---ATTCTTTAC
1 CATTTTTTCTTTACTGATTACTCTTTACTTTACTCTTTAC
*
57582 CATTTTTCCTTTACTGATTACTCTTTACT
1 CATTTTTTCTTTACTGATTACTCTTTACT
57611 CTTTACCATT
Statistics
Matches: 119, Mismatches: 11, Indels: 22
0.78 0.07 0.14
Matches are distributed among these distances:
35 48 0.40
36 10 0.08
37 7 0.06
38 2 0.02
39 5 0.04
40 34 0.29
41 13 0.11
ACGTcount: A:0.18, C:0.22, G:0.02, T:0.58
Consensus pattern (40 bp):
CATTTTTTCTTTACTGATTACTCTTTACTTTACTCTTTAC
Found at i:57564 original size:35 final size:35
Alignment explanation
Indices: 57521--57620 Score: 173
Period size: 35 Copynumber: 2.9 Consensus size: 35
57511 TCTTTACCAT
57521 TTTACTAATTACTCTTCATTCTTTACCATTTTTCC
1 TTTACTAATTACTCTTCATTCTTTACCATTTTTCC
57556 TTTACTAATTACTCTTCATTCTTTACCATTTTTCC
1 TTTACTAATTACTCTTCATTCTTTACCATTTTTCC
* * *
57591 TTTACTGATTACTCTTTACTCTTTACCATT
1 TTTACTAATTACTCTTCATTCTTTACCATT
57621 ATTCTTCACT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 62 1.00
ACGTcount: A:0.20, C:0.25, G:0.01, T:0.54
Consensus pattern (35 bp):
TTTACTAATTACTCTTCATTCTTTACCATTTTTCC
Found at i:57664 original size:6 final size:6
Alignment explanation
Indices: 57653--57683 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
57643 CTGATCACTG
57653 ATTACT ATTACT ATTACT AATTACT ATTACT
1 ATTACT ATTACT ATTACT -ATTACT ATTACT
57684 TTTTACTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTACT
Found at i:57677 original size:13 final size:12
Alignment explanation
Indices: 57653--57683 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
57643 CTGATCACTG
57653 ATTACTATTACT
1 ATTACTATTACT
57665 ATTACTAATTACT
1 ATTACT-ATTACT
57678 ATTACT
1 ATTACT
57684 TTTTACTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTACTATTACT
Found at i:57677 original size:19 final size:20
Alignment explanation
Indices: 57653--57696 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
57643 CTGATCACTG
57653 ATTACTATTAC-TATTACTA
1 ATTACTATTACTTATTACTA
*
57672 ATTACTATTACTTTTTACTA
1 ATTACTATTACTTATTACTA
57692 ATTAC
1 ATTAC
57697 CATTTTTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTACTATTACTTATTACTA
Found at i:57712 original size:42 final size:44
Alignment explanation
Indices: 57666--57762 Score: 121
Period size: 42 Copynumber: 2.3 Consensus size: 44
57656 ACTATTACTA
*
57666 TTACTAATTACT-ATTACTTTTTACTAATTACCATTTTTC-CTT
1 TTACTAATTACTCATTACTTTTTACTAATTACCATTTTACTCTT
* * * *
57708 TTACTGATCA-TCATTACTTTTTACTGATTACTATTTTACTCTT
1 TTACTAATTACTCATTACTTTTTACTAATTACCATTTTACTCTT
57751 TT-CTAATTACTC
1 TTACTAATTACTC
57763 TCATTATCAC
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
41 1 0.02
42 37 0.82
43 7 0.16
ACGTcount: A:0.25, C:0.20, G:0.02, T:0.54
Consensus pattern (44 bp):
TTACTAATTACTCATTACTTTTTACTAATTACCATTTTACTCTT
Found at i:57819 original size:30 final size:30
Alignment explanation
Indices: 57783--57851 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
57773 ATTACTCTTT
* * * *
57783 ACTGATTGCTTTTTCTTATTGAACTTAGTC
1 ACTGATTGCTTTTCCTTACTAAACTTAATC
* *
57813 ACTGATTACTTTTCCTTACTAAACTTAATT
1 ACTGATTGCTTTTCCTTACTAAACTTAATC
57843 ACTGATTGC
1 ACTGATTGC
57852 CCTTTTTACT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.46
Consensus pattern (30 bp):
ACTGATTGCTTTTCCTTACTAAACTTAATC
Found at i:57899 original size:36 final size:34
Alignment explanation
Indices: 57834--57900 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 34
57824 TTCCTTACTA
*
57834 AACTTAATTACTGATTGCCCTTTTTACTTTTTGG
1 AACTTAATTACTGATTGACCTTTTTACTTTTTGG
57868 AACTTAATTACTCTGATT-ACCTTTTTCACTTTT
1 AACTTAATTA--CTGATTGACCTTTTT-ACTTTT
57901 CTGACTGATC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 10 0.34
35 7 0.24
36 12 0.41
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.51
Consensus pattern (34 bp):
AACTTAATTACTGATTGACCTTTTTACTTTTTGG
Found at i:61295 original size:27 final size:27
Alignment explanation
Indices: 61237--61330 Score: 116
Period size: 27 Copynumber: 3.4 Consensus size: 27
61227 AAACGCAAAG
* * *
61237 AATGACCAAAATGCCCCCTGAGTGTCAA
1 AATGACCAAAAT-ACCCCTGAATGCCAA
*
61265 AATGACCAAAATACCCCTGAATGCCAG
1 AATGACCAAAATACCCCTGAATGCCAA
* *
61292 AATGACCAAAATACCCCTAAATGCAAA
1 AATGACCAAAATACCCCTGAATGCCAA
*
61319 AAAGACCAAAAT
1 AATGACCAAAAT
61331 GCTAATCCGA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
27 46 0.79
28 12 0.21
ACGTcount: A:0.46, C:0.27, G:0.13, T:0.15
Consensus pattern (27 bp):
AATGACCAAAATACCCCTGAATGCCAA
Found at i:69588 original size:15 final size:14
Alignment explanation
Indices: 69563--69592 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
69553 TTCCCGGGCT
69563 GCTGGTCAGCTTGA
1 GCTGGTCAGCTTGA
69577 GCTGGCTCAGCTTGA
1 GCTGG-TCAGCTTGA
69592 G
1 G
69593 ACTTGCTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (14 bp):
GCTGGTCAGCTTGA
Done.