Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023586.1 Corchorus olitorius cultivar O-4 contig23619, 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: 56391
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4735 original size:30 final size:30
Alignment explanation
Indices: 4699--4760 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
4689 GTTATTAAGA
*
4699 CATTAAAATTTGAGGGTGTAAGAGGAAAGT
1 CATTAAAATTTGAGGGTATAAGAGGAAAGT
4729 CATTAAAATTTGAGGGTATAAGAGGAAAGT
1 CATTAAAATTTGAGGGTATAAGAGGAAAGT
4759 CA
1 CA
4761 AGATAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.42, C:0.05, G:0.27, T:0.26
Consensus pattern (30 bp):
CATTAAAATTTGAGGGTATAAGAGGAAAGT
Found at i:10176 original size:23 final size:23
Alignment explanation
Indices: 10150--10193 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
10140 AATTCTATAA
10150 TCTTTTATTTCTCCTTCCAAGAT
1 TCTTTTATTTCTCCTTCCAAGAT
10173 TCTTTTATTTCTCCTTCCAAG
1 TCTTTTATTTCTCCTTCCAAG
10194 TTGAGCATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.16, C:0.27, G:0.05, T:0.52
Consensus pattern (23 bp):
TCTTTTATTTCTCCTTCCAAGAT
Found at i:13624 original size:22 final size:22
Alignment explanation
Indices: 13592--13651 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
13582 TGAATATTTT
* *
13592 TATGAAATTTTGGTAACTATCCA
1 TATGAAATTTTGATAACCA-CCA
*
13615 -ATTAAATTTTGATAACCACCA
1 TATGAAATTTTGATAACCACCA
13636 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
13652 TTACTTATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 3 0.09
22 29 0.91
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACCA
Found at i:16191 original size:18 final size:18
Alignment explanation
Indices: 16168--16205 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
16158 GTGCAAGGGC
16168 TGCAAGGAAG-CATGGAGA
1 TGCAA-GAAGTCATGGAGA
16186 TGCAAGAAGTTCATGGAGA
1 TGCAAGAAG-TCATGGAGA
16205 T
1 T
16206 ATCGATGAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 5 0.28
19 9 0.50
ACGTcount: A:0.37, C:0.11, G:0.34, T:0.18
Consensus pattern (18 bp):
TGCAAGAAGTCATGGAGA
Found at i:16259 original size:21 final size:21
Alignment explanation
Indices: 16233--16291 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
16223 AAGCACCAAG
16233 AAGATGACAT-TTGATCCATTA
1 AAGATG-CATATTGATCCATTA
*
16254 AAGATGCCTATTGATCCATTA
1 AAGATGCATATTGATCCATTA
*
16275 AAGATGCCTATTGATCC
1 AAGATGCATATTGATCC
16292 GATGACAAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.06
21 34 0.94
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (21 bp):
AAGATGCATATTGATCCATTA
Found at i:17859 original size:2 final size:2
Alignment explanation
Indices: 17852--17887 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
17842 GCAAGAAAAG
*
17852 TA TA TA TA TA TA CA TA 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
17888 GTTACAGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:24128 original size:13 final size:13
Alignment explanation
Indices: 24110--24150 Score: 82
Period size: 13 Copynumber: 3.2 Consensus size: 13
24100 ACATGCCAAG
24110 TGTTATAATCTTA
1 TGTTATAATCTTA
24123 TGTTATAATCTTA
1 TGTTATAATCTTA
24136 TGTTATAATCTTA
1 TGTTATAATCTTA
24149 TG
1 TG
24151 ACACCAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.54
Consensus pattern (13 bp):
TGTTATAATCTTA
Found at i:28025 original size:18 final size:18
Alignment explanation
Indices: 27993--28027 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27983 GAATTGATGG
*
27993 ATATGTTGGAGTCGATTT
1 ATATGTTGAAGTCGATTT
*
28011 ATATGTTGAATTCGATT
1 ATATGTTGAAGTCGATT
28028 ACTAATATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.46
Consensus pattern (18 bp):
ATATGTTGAAGTCGATTT
Found at i:35395 original size:14 final size:15
Alignment explanation
Indices: 35362--35399 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
35352 AAATTTTCTT
35362 AACCCGAAACTAACCC
1 AACCC-AAACTAACCC
*
35378 AACCCAAAC-AACCG
1 AACCCAAACTAACCC
35392 AACCCAAA
1 AACCCAAA
35400 TCCAACCCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.57
15 4 0.19
16 5 0.24
ACGTcount: A:0.50, C:0.42, G:0.05, T:0.03
Consensus pattern (15 bp):
AACCCAAACTAACCC
Found at i:37546 original size:79 final size:83
Alignment explanation
Indices: 37438--37604 Score: 202
Period size: 87 Copynumber: 2.0 Consensus size: 83
37428 AATCTTGGTT
* * * *
37438 AAAAAAAATTATTTATAGAGAAAC-TTAA-A-ATAT-ATA-CGTGTAATCGAAGGTTAAATATTA
1 AAAAAAAATTATTTATAAAGAAACGTAAATATATATAATATCGTGTAATCAAAGGTCAAATATTA
*
37498 TTTTTATCGTTTCATTAC
66 TTTTTATCATTTCATTAC
37516 AAAACAAAATTATTTATAAAGATAA-GTAAAATATATATAATATTTCGTGTAATCAAAGGTCAAA
1 AAAA-AAAATTATTTATAAAGA-AACGT-AAATATATATAATA--TCGTGTAATCAAAGGTCAAA
37580 TATTATTTTTATCATTTCATTAC
61 TATTATTTTTATCATTTCATTAC
37603 AA
1 AA
37605 TAATTTATAC
Statistics
Matches: 74, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
78 4 0.05
79 16 0.22
80 3 0.04
81 2 0.03
82 1 0.01
83 4 0.05
84 3 0.04
87 41 0.55
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (83 bp):
AAAAAAAATTATTTATAAAGAAACGTAAATATATATAATATCGTGTAATCAAAGGTCAAATATTA
TTTTTATCATTTCATTAC
Found at i:39798 original size:16 final size:17
Alignment explanation
Indices: 39759--39802 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
39749 TTCGGGTTGA
39759 TCAGGTTCGGGTAAATT
1 TCAGGTTCGGGTAAATT
* *
39776 TGA-GTTCGGGT-TATT
1 TCAGGTTCGGGTAAATT
39791 TCAGGTTCGGGT
1 TCAGGTTCGGGT
39803 CATTGAGGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 5 0.22
16 16 0.70
17 2 0.09
ACGTcount: A:0.16, C:0.11, G:0.34, T:0.39
Consensus pattern (17 bp):
TCAGGTTCGGGTAAATT
Found at i:47131 original size:18 final size:18
Alignment explanation
Indices: 47108--47143 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
47098 TATCTATGTG
47108 AAAGGAGTCACACTGCTT
1 AAAGGAGTCACACTGCTT
*
47126 AAAGGAGTCAGACTGCTT
1 AAAGGAGTCACACTGCTT
47144 TAGCTTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.22
Consensus pattern (18 bp):
AAAGGAGTCACACTGCTT
Found at i:48555 original size:42 final size:42
Alignment explanation
Indices: 48496--48583 Score: 176
Period size: 42 Copynumber: 2.1 Consensus size: 42
48486 TGACAATGTC
48496 CATATTGTTGCTATTTCTCTGATTCGTCAAGTTGCTTTCTGA
1 CATATTGTTGCTATTTCTCTGATTCGTCAAGTTGCTTTCTGA
48538 CATATTGTTGCTATTTCTCTGATTCGTCAAGTTGCTTTCTGA
1 CATATTGTTGCTATTTCTCTGATTCGTCAAGTTGCTTTCTGA
48580 CATA
1 CATA
48584 ACATTCAAGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.18, C:0.19, G:0.16, T:0.47
Consensus pattern (42 bp):
CATATTGTTGCTATTTCTCTGATTCGTCAAGTTGCTTTCTGA
Found at i:48572 original size:24 final size:24
Alignment explanation
Indices: 48502--48573 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
48492 TGTCCATATT
48502 GTTGCTATTTCTCTGATTCGTCAA
1 GTTGCTATTTCTCTGATTCGTCAA
* *
48526 GTTGC---TT-TCTGA--CAT-ATT
1 GTTGCTATTTCTCTGATTCGTCA-A
48544 GTTGCTATTTCTCTGATTCGTCAA
1 GTTGCTATTTCTCTGATTCGTCAA
48568 GTTGCT
1 GTTGCT
48574 TTCTGACATA
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
17 1 0.03
18 7 0.19
20 5 0.14
21 4 0.11
22 5 0.14
24 13 0.36
25 1 0.03
ACGTcount: A:0.15, C:0.19, G:0.18, T:0.47
Consensus pattern (24 bp):
GTTGCTATTTCTCTGATTCGTCAA
Found at i:48576 original size:22 final size:22
Alignment explanation
Indices: 48509--48577 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
48499 ATTGTTGCTA
48509 TTTCTCTGATTCGTCAAGTTGC
1 TTTCTCTGATTCGTCAAGTTGC
* *
48531 -TT-TCTGA--CAT-ATTGTTGC
1 TTTCTCTGATTCGTCA-AGTTGC
48549 TATTTCTCTGATTCGTCAAGTTGC
1 --TTTCTCTGATTCGTCAAGTTGC
48573 TTTCT
1 TTTCT
48578 GACATAACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
17 1 0.03
18 7 0.20
20 5 0.14
21 4 0.11
22 10 0.29
24 7 0.20
25 1 0.03
ACGTcount: A:0.14, C:0.20, G:0.16, T:0.49
Consensus pattern (22 bp):
TTTCTCTGATTCGTCAAGTTGC
Found at i:52752 original size:15 final size:15
Alignment explanation
Indices: 52732--52761 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
52722 AAGATAACAT
52732 GCCACCATCAAGATC
1 GCCACCATCAAGATC
52747 GCCACCATCAAGATC
1 GCCACCATCAAGATC
52762 CAATTTTATT
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:0.33, C:0.40, G:0.13, T:0.13
Consensus pattern (15 bp):
GCCACCATCAAGATC
Found at i:53291 original size:12 final size:12
Alignment explanation
Indices: 53258--53284 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
53248 GTGTATTTAT
53258 TAAGAAACTAGG
1 TAAGAAACTAGG
53270 TAAGAAACTAGG
1 TAAGAAACTAGG
53282 TAA
1 TAA
53285 TGAACTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.22, T:0.19
Consensus pattern (12 bp):
TAAGAAACTAGG
Done.