Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013117.1 Corchorus capsularis cultivar CVL-1 contig13138, 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: 19630
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:2888 original size:3 final size:3
Alignment explanation
Indices: 2882--2930 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
2872 AATCATCATC
*
2882 ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2930 A
1 A
2931 AGTCAACAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:5453 original size:30 final size:29
Alignment explanation
Indices: 5417--5517 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 29
5407 CATCAGAATA
5417 GGGCTTATTTGGCCTTTTTTAAGAGTTCAG
1 GGGCTTATTTGGCCTTTTTT-AGAGTTCAG
***
5447 GGGCTTATTTGG-CTGCAATTAGAGTTCAG
1 GGGCTTATTTGGCCT-TTTTTAGAGTTCAG
*
5476 GGGCTTATTTGACCGTTTTGTGTA-AGTTCAG
1 GGGCTTATTTGGCC-TTTT-T-TAGAGTTCAG
*
5507 GGGCTTTTTTG
1 GGGCTTATTTG
5518 AGAAATAAGC
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
29 22 0.38
30 15 0.26
31 19 0.33
32 2 0.03
ACGTcount: A:0.16, C:0.13, G:0.30, T:0.42
Consensus pattern (29 bp):
GGGCTTATTTGGCCTTTTTTAGAGTTCAG
Found at i:10794 original size:20 final size:19
Alignment explanation
Indices: 10754--10791 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
10744 TTCTGACCAA
* *
10754 AAAATAGCCATGTGGCATT
1 AAAATAGCCACGTGGAATT
10773 AAAATAGCCACGTGGAATT
1 AAAATAGCCACGTGGAATT
10792 TAATTAATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (19 bp):
AAAATAGCCACGTGGAATT
Found at i:11978 original size:11 final size:12
Alignment explanation
Indices: 11962--12000 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
11952 AGCAATAATA
11962 ATAATAATTA-T
1 ATAATAATTACT
11973 ATAATAATTACT
1 ATAATAATTACT
*
11985 ATAATTAATTAGT
1 ATAA-TAATTACT
11998 ATA
1 ATA
12001 TATCATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 10 0.40
12 5 0.20
13 10 0.40
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (12 bp):
ATAATAATTACT
Found at i:12870 original size:11 final size:11
Alignment explanation
Indices: 12854--12879 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12844 TAATTCCCCC
12854 TATATATATAG
1 TATATATATAG
12865 TATATATATAG
1 TATATATATAG
12876 TATA
1 TATA
12880 AATCAGAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (11 bp):
TATATATATAG
Found at i:13277 original size:15 final size:15
Alignment explanation
Indices: 13223--13279 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
13213 TCCGAACCGT
*
13223 ATGACCCGAAACCGAAA
1 ATGACCCG-AACC-CAA
*
13240 ATGA-CCAAACCCAGA
1 ATGACCCGAACCCA-A
13255 ATTGACCCGAACCCAA
1 A-TGACCCGAACCCAA
13271 ATGACCCGA
1 ATGACCCGA
13280 CATTTCATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 1 0.03
15 14 0.41
16 7 0.21
17 12 0.35
ACGTcount: A:0.42, C:0.33, G:0.16, T:0.09
Consensus pattern (15 bp):
ATGACCCGAACCCAA
Found at i:16016 original size:1 final size:1
Alignment explanation
Indices: 16012--16038 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
16002 TTTTTTAAGG
16012 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
16039 AACTTTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:16304 original size:17 final size:17
Alignment explanation
Indices: 16282--16316 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
16272 CGAGAGTCAC
16282 AAATTTGTCCCCAATCA
1 AAATTTGTCCCCAATCA
16299 AAATTTGTCCCCAATCA
1 AAATTTGTCCCCAATCA
16316 A
1 A
16317 TTTGTAGGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.29
Consensus pattern (17 bp):
AAATTTGTCCCCAATCA
Found at i:16320 original size:15 final size:16
Alignment explanation
Indices: 16281--16321 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
16271 TCGAGAGTCA
16281 CAAATTTGTCCCCAAT
1 CAAATTTGTCCCCAAT
16297 CAAAATTTGTCCCCAAT
1 C-AAATTTGTCCCCAAT
16314 C-AATTTGT
1 CAAATTTGT
16322 AGGCTTCCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.29
16 1 0.04
17 16 0.67
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.34
Consensus pattern (16 bp):
CAAATTTGTCCCCAAT
Found at i:16560 original size:39 final size:39
Alignment explanation
Indices: 16506--16622 Score: 234
Period size: 39 Copynumber: 3.0 Consensus size: 39
16496 TCCCTCTGTC
16506 TCATAATATAAGTCCATTTTAACCGTATCACAAAGTTTA
1 TCATAATATAAGTCCATTTTAACCGTATCACAAAGTTTA
16545 TCATAATATAAGTCCATTTTAACCGTATCACAAAGTTTA
1 TCATAATATAAGTCCATTTTAACCGTATCACAAAGTTTA
16584 TCATAATATAAGTCCATTTTAACCGTATCACAAAGTTTA
1 TCATAATATAAGTCCATTTTAACCGTATCACAAAGTTTA
16623 AGAAAGTAGT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (39 bp):
TCATAATATAAGTCCATTTTAACCGTATCACAAAGTTTA
Found at i:16697 original size:91 final size:91
Alignment explanation
Indices: 16594--16775 Score: 337
Period size: 91 Copynumber: 2.0 Consensus size: 91
16584 TCATAATATA
* *
16594 AGTCCATTTTAACCGTATCACAAAGTTTAAGAAAGTAGTTACAATTCTAACTTTTATAAACTTTT
1 AGTCCATTTTAACCGTATCACAAAGTTTAAGAAAGTAGTTACAACTCTAACTTCTATAAACTTTT
16659 ATCTTCTCTTTCCAATTTTATCCATC
66 ATCTTCTCTTTCCAATTTTATCCATC
16685 AGTCCATTTTAACCGTATCACAAAGTTTAAGAAAGTAGTTACAACTCTAACTTCTATAAACTTTT
1 AGTCCATTTTAACCGTATCACAAAGTTTAAGAAAGTAGTTACAACTCTAACTTCTATAAACTTTT
*
16750 ATCTTTTCTTTCCAATTTTATCCATC
66 ATCTTCTCTTTCCAATTTTATCCATC
16776 TTCTCTCTCC
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (91 bp):
AGTCCATTTTAACCGTATCACAAAGTTTAAGAAAGTAGTTACAACTCTAACTTCTATAAACTTTT
ATCTTCTCTTTCCAATTTTATCCATC
Found at i:17125 original size:34 final size:34
Alignment explanation
Indices: 17087--17155 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
17077 GGTAATTTAG
17087 ATAACTTAGGTAAAAGTTGCATTGGGATTTAAAA
1 ATAACTTAGGTAAAAGTTGCATTGGGATTTAAAA
17121 ATAACTTAGGTAAAAGTTGCATTGGGATTTAAAA
1 ATAACTTAGGTAAAAGTTGCATTGGGATTTAAAA
17155 A
1 A
17156 GGGACTTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (34 bp):
ATAACTTAGGTAAAAGTTGCATTGGGATTTAAAA
Found at i:18478 original size:28 final size:28
Alignment explanation
Indices: 18443--18499 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
18433 TAATTATCCA
18443 TTTTGGGACAAATTGGCCCATTAACTTT
1 TTTTGGGACAAATTGGCCCATTAACTTT
18471 TTTTGGGACAAATTGGCCCATTAACTTT
1 TTTTGGGACAAATTGGCCCATTAACTTT
18499 T
1 T
18500 AAAAACGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.40
Consensus pattern (28 bp):
TTTTGGGACAAATTGGCCCATTAACTTT
Found at i:19232 original size:29 final size:30
Alignment explanation
Indices: 19195--19276 Score: 103
Period size: 29 Copynumber: 2.7 Consensus size: 30
19185 GTCTCGTTTT
19195 TAAAAGTTAAGGGGCCAATTTGTCCCAAAA
1 TAAAAGTTAAGGGGCCAATTTGTCCCAAAA
* * *
19225 -AAAAGTTAAGGGGTCAATCTATCCCAAAA
1 TAAAAGTTAAGGGGCCAATTTGTCCCAAAA
* *
19254 TAGATAGTTAAGGGGCTAATTTG
1 TA-AAAGTTAAGGGGCCAATTTG
19277 GGTATTAAGC
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 26 0.62
30 1 0.02
31 15 0.36
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (30 bp):
TAAAAGTTAAGGGGCCAATTTGTCCCAAAA
Found at i:19332 original size:2 final size:2
Alignment explanation
Indices: 19325--19365 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
19315 GTTCATGGTG
19325 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA T
19366 TCTTTAATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19599 original size:36 final size:37
Alignment explanation
Indices: 19526--19606 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
19516 TCGTTTAATT
*
19526 ATTAATAAAATTTGCCTTTAAAAAGAATTATTCCTAA
1 ATTAATAGAATTTGCCTTTAAAAAGAATTATTCCTAA
* *
19563 ATTAATAGCATTTGCCTTTAAAAA-AATTATTGCTAA
1 ATTAATAGAATTTGCCTTTAAAAAGAATTATTCCTAA
19599 ATTAATAG
1 ATTAATAG
19607 TATTGTTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 19 0.46
37 22 0.54
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.38
Consensus pattern (37 bp):
ATTAATAGAATTTGCCTTTAAAAAGAATTATTCCTAA
Done.