Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013672.1 Corchorus capsularis cultivar CVL-1 contig13693, 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: 47357
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:12459 original size:44 final size:44
Alignment explanation
Indices: 12394--12482 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
12384 CTTGAATCTT
*
12394 TCAACTAATGACAAGACCATGCTATATATTTACCAGCAGAAACC
1 TCAACTAATGACAAGAACATGCTATATATTTACCAGCAGAAACC
*
12438 TCAACTAATGACAAGAACATGCTATATATTTTCCAGCAGAAACC
1 TCAACTAATGACAAGAACATGCTATATATTTACCAGCAGAAACC
12482 T
1 T
12483 ATATGACTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.40, C:0.24, G:0.11, T:0.25
Consensus pattern (44 bp):
TCAACTAATGACAAGAACATGCTATATATTTACCAGCAGAAACC
Found at i:13618 original size:122 final size:121
Alignment explanation
Indices: 13484--13725 Score: 439
Period size: 122 Copynumber: 2.0 Consensus size: 121
13474 GCAATAGAAA
13484 AAAAACACCAAACACCAAAATCATTAATAACCCAACACAATTTTCCAAACAATTTACCCTAAAAC
1 AAAAACACCAAACACCAAAATCATTAATAACCCAACACAATTTTCCAAACAATTTACCCTAAAAC
*
13549 CCTAAAATTCAGAAATTTTAGTTGCTAAAAACTAGAATGGGGCAATAATTGCAATAG
66 CCTAAAATTCAGAAATTTTAGTTGCTAAAAACTAGAAT-GGGCAATAATTGAAATAG
* **
13606 AAAAACACCAAACACCGAAATCATTAATAACCCAACACAATTTTCCAAACAATTTACTTTAAAAC
1 AAAAACACCAAACACCAAAATCATTAATAACCCAACACAATTTTCCAAACAATTTACCCTAAAAC
13671 CCTAAAATTCAGAAATTTTAGTTGCTAAAAACTAGAATGGGCAATAATTGAAATA
66 CCTAAAATTCAGAAATTTTAGTTGCTAAAAACTAGAATGGGCAATAATTGAAATA
13726 AATTTGGGTA
Statistics
Matches: 116, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
121 16 0.14
122 100 0.86
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (121 bp):
AAAAACACCAAACACCAAAATCATTAATAACCCAACACAATTTTCCAAACAATTTACCCTAAAAC
CCTAAAATTCAGAAATTTTAGTTGCTAAAAACTAGAATGGGCAATAATTGAAATAG
Found at i:16863 original size:15 final size:15
Alignment explanation
Indices: 16843--16871 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16833 GAATGTGAGT
16843 TTGTTTGTTTATTTG
1 TTGTTTGTTTATTTG
16858 TTGTTTGTTTATTT
1 TTGTTTGTTTATTT
16872 ATTAGGTGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.17, T:0.76
Consensus pattern (15 bp):
TTGTTTGTTTATTTG
Found at i:22159 original size:30 final size:31
Alignment explanation
Indices: 22085--22160 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 31
22075 TACCGTACAT
*
22085 GTCTCTCTACTTACAAAAAGGGATCAATTTG
1 GTCTCTCTACTTACAAAAACGGATCAATTTG
* * *
22116 GTCCCCCTA-TTACAAAAACTG-TCAATTTG
1 GTCTCTCTACTTACAAAAACGGATCAATTTG
22145 GTCTCTCTACTTACAA
1 GTCTCTCTACTTACAA
22161 TTTGGTGTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 15 0.39
30 16 0.42
31 7 0.18
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (31 bp):
GTCTCTCTACTTACAAAAACGGATCAATTTG
Found at i:34235 original size:11 final size:11
Alignment explanation
Indices: 34192--34229 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
34182 TTCCTATATA
*
34192 AAATAAATTAT
1 AAATTAATTAT
34203 CAAA-TAATTAT
1 -AAATTAATTAT
34214 AAATTAATTAT
1 AAATTAATTAT
34225 AAATT
1 AAATT
34230 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:40462 original size:65 final size:65
Alignment explanation
Indices: 40383--40519 Score: 159
Period size: 65 Copynumber: 2.1 Consensus size: 65
40373 AATCCCGGCG
* * * *
40383 GTCGCGACCCACCGCCGGCTAGG-TCGCGTGTGACCCAGGGTCGGACGCGACCCAGCCGACGGTA
1 GTCGCGACCCACCGCCGGC-AGGCTCGCGCGCGACCCACGGTCGGACGCGACACAGCCGACGGTA
40447 A
65 A
* * * * * **
40448 GTCGCGACCGACCGCCGGCCGGCTCGCGCGCGACCCACGGTCGGTCTCGATATTGCCGACGGTAA
1 GTCGCGACCCACCGCCGGCAGGCTCGCGCGCGACCCACGGTCGGACGCGACACAGCCGACGGTAA
40513 GTCGCGA
1 GTCGCGA
40520 TCAAGTCGCG
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
64 2 0.03
65 58 0.97
ACGTcount: A:0.15, C:0.37, G:0.35, T:0.12
Consensus pattern (65 bp):
GTCGCGACCCACCGCCGGCAGGCTCGCGCGCGACCCACGGTCGGACGCGACACAGCCGACGGTAA
Found at i:40664 original size:11 final size:11
Alignment explanation
Indices: 40648--40682 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
40638 ACGGCCCTTT
*
40648 TTTAATTTTTA
1 TTTAATTATTA
40659 TTTAATTATTA
1 TTTAATTATTA
*
40670 ATTAATTATTA
1 TTTAATTATTA
40681 TT
1 TT
40683 ATTTTTAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTAATTATTA
Found at i:42223 original size:15 final size:16
Alignment explanation
Indices: 42197--42232 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
42187 AAACGGCCGA
42197 ATTAACAAATAAAATC
1 ATTAACAAATAAAATC
*
42213 ATTAA-AAATAATATC
1 ATTAACAAATAAAATC
42228 ATTAA
1 ATTAA
42233 TTATTAATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTAACAAATAAAATC
Found at i:42941 original size:79 final size:79
Alignment explanation
Indices: 42810--42967 Score: 316
Period size: 79 Copynumber: 2.0 Consensus size: 79
42800 TTGTAGGTCG
42810 AATCCATGCCAATGAACCAATGGTAGTTTCGGACTAATTTCGCTGATTCTGGATGTACCATAAAA
1 AATCCATGCCAATGAACCAATGGTAGTTTCGGACTAATTTCGCTGATTCTGGATGTACCATAAAA
42875 AGATGAGTCAACAC
66 AGATGAGTCAACAC
42889 AATCCATGCCAATGAACCAATGGTAGTTTCGGACTAATTTCGCTGATTCTGGATGTACCATAAAA
1 AATCCATGCCAATGAACCAATGGTAGTTTCGGACTAATTTCGCTGATTCTGGATGTACCATAAAA
42954 AGATGAGTCAACAC
66 AGATGAGTCAACAC
42968 GTTTGTTTCC
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (79 bp):
AATCCATGCCAATGAACCAATGGTAGTTTCGGACTAATTTCGCTGATTCTGGATGTACCATAAAA
AGATGAGTCAACAC
Found at i:43639 original size:14 final size:15
Alignment explanation
Indices: 43606--43641 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
43596 AATAAAACCT
43606 ACAAAAT-TTAACTA
1 ACAAAATATTAACTA
43620 AC-AAATATT-ACTA
1 ACAAAATATTAACTA
43633 ACAAAATAT
1 ACAAAATAT
43642 AATTAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (15 bp):
ACAAAATATTAACTA
Found at i:45253 original size:6 final size:6
Alignment explanation
Indices: 45242--45282 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
45232 TATCTATTTC
45242 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
45283 TTCTCTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
GAAAAA
Done.