Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005415.1 Corchorus capsularis cultivar CVL-1 contig05433, 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: 11974
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:619 original size:13 final size:13
Alignment explanation
Indices: 601--625 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
591 GTTAAGTAAT
601 AGTTAGTTATATG
1 AGTTAGTTATATG
614 AGTTAGTTATAT
1 AGTTAGTTATAT
626 TAGACTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (13 bp):
AGTTAGTTATATG
Found at i:4398 original size:29 final size:30
Alignment explanation
Indices: 4338--4401 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 30
4328 ACCTAAAAAA
4338 GTACTAAATTGAACCATTAATAAAACGGTTG
1 GTACTAAATTGAACCA-TAATAAAACGGTTG
* *
4369 GTACTAAATTGGACGA-AATAAAA-GGTTTG
1 GTACTAAATTGAACCATAATAAAACGG-TTG
4398 GTAC
1 GTAC
4402 CAAGTTACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.07
29 14 0.47
31 14 0.47
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (30 bp):
GTACTAAATTGAACCATAATAAAACGGTTG
Found at i:5278 original size:7 final size:7
Alignment explanation
Indices: 5268--5296 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
5258 CAAAAGAGAA
5268 AAAAGAG
1 AAAAGAG
5275 AAAAGAG
1 AAAAGAG
5282 AAAAGAG
1 AAAAGAG
5289 AAAAGAG
1 AAAAGAG
5296 A
1 A
5297 GAAAAGGGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (7 bp):
AAAAGAG
Found at i:5280 original size:16 final size:15
Alignment explanation
Indices: 5259--5302 Score: 63
Period size: 14 Copynumber: 2.9 Consensus size: 15
5249 AAAAGATAAC
5259 AAAAGAGAAAAAAGAG
1 AAAAGAG-AAAAAGAG
5275 AAAAGAG-AAAAGAG
1 AAAAGAGAAAAAGAG
5289 AAAAGAGAGAAAAG
1 AAAAGAGA-AAAAG
5303 GGGCCTGACG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 14 0.54
16 12 0.46
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AAAAGAGAAAAAGAG
Found at i:5294 original size:21 final size:20
Alignment explanation
Indices: 5233--5296 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
5223 GTTTTGAAGA
* *
5233 AGAAAA-AAGAAGAGAAAAA
1 AGAAAACAAAAAGAGAAAAG
* *
5252 AGATAACAAAAGAGAAAAAAG
1 AGAAAACAAAA-AGAGAAAAG
*
5273 AGAAAAGAGAAAAGAGAAAAG
1 AGAAAACA-AAAAGAGAAAAG
5294 AGA
1 AGA
5297 GAAAAGGGGC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
19 5 0.14
20 3 0.09
21 24 0.69
22 3 0.09
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.02
Consensus pattern (20 bp):
AGAAAACAAAAAGAGAAAAG
Found at i:5302 original size:9 final size:9
Alignment explanation
Indices: 5232--5301 Score: 67
Period size: 9 Copynumber: 8.0 Consensus size: 9
5222 GGTTTTGAAG
*
5232 AAGAAAAAA
1 AAGAGAAAA
5241 GAAGAGAAAA
1 -AAGAGAAAA
*
5251 AAGATAACAA
1 AAGAGAA-AA
5261 AAGAGAAAA
1 AAGAGAAAA
5270 AAGAG--AA
1 AAGAGAAAA
5277 AAGAG--AA
1 AAGAGAAAA
5284 AAGAGAAAA
1 AAGAGAAAA
*
5293 GAGAGAAAA
1 AAGAGAAAA
5302 GGGGCCTGAC
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
7 14 0.26
9 23 0.43
10 16 0.30
ACGTcount: A:0.74, C:0.01, G:0.23, T:0.01
Consensus pattern (9 bp):
AAGAGAAAA
Found at i:5513 original size:26 final size:23
Alignment explanation
Indices: 5454--5505 Score: 70
Period size: 22 Copynumber: 2.2 Consensus size: 23
5444 AAGGGTTAAA
*
5454 TAAATAATAAA-TAATTATTTTT
1 TAAATTATAAATTAATTATTTTT
5476 TAAATTATAAATTAATTATAGTTTT
1 TAAATTATAAATTAATTAT--TTTT
5501 TAAAT
1 TAAAT
5506 CTTAAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 10 0.38
23 7 0.27
25 9 0.35
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TAAATTATAAATTAATTATTTTT
Found at i:5818 original size:24 final size:26
Alignment explanation
Indices: 5768--5828 Score: 90
Period size: 27 Copynumber: 2.4 Consensus size: 26
5758 CGATTTCCGG
5768 TTTATTTTTTTGCTTACCTTTCCTTGT
1 TTTATTTTTTTGCTTACCTTT-CTTGT
*
5795 TTTATTTTTTTGCTTAGC-TT-TTGT
1 TTTATTTTTTTGCTTACCTTTCTTGT
5819 TTTATTTTTT
1 TTTATTTTTT
5829 GTTCAATTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 14 0.42
26 2 0.06
27 17 0.52
ACGTcount: A:0.08, C:0.11, G:0.08, T:0.72
Consensus pattern (26 bp):
TTTATTTTTTTGCTTACCTTTCTTGT
Found at i:8153 original size:16 final size:16
Alignment explanation
Indices: 8132--8312 Score: 144
Period size: 16 Copynumber: 11.6 Consensus size: 16
8122 CAGTCAGTTT
8132 TTTCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
*
8148 TTTCGGGTCATTTGGG
1 TTTCGGGTCATTCGGG
* *
8164 -TTCGGGTTAATCGGG
1 TTTCGGGTCATTCGGG
8179 TTTCGGGTCAATT-GGG
1 TTTCGGGTC-ATTCGGG
* * *
8195 TCTCAGGTTATTCGGG
1 TTTCGGGTCATTCGGG
* * *
8211 TCTCGAGTTATTCGGG
1 TTTCGGGTCATTCGGG
*
8227 TCTCGGGTTCATT-GGG
1 TTTCGGG-TCATTCGGG
8243 TTTCGGGTCATTC-GG
1 TTTCGGGTCATTCGGG
*
8258 TTCTCGGGTTATTCGGG
1 TT-TCGGGTCATTCGGG
* *
8275 -TTCGGGT--TT-AGA
1 TTTCGGGTCATTCGGG
*
8287 CTTCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
*
8303 TCTCGGGTCA
1 TTTCGGGTCA
8313 AATGAGTCAG
Statistics
Matches: 133, Mismatches: 21, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
12 1 0.01
13 9 0.07
15 32 0.24
16 83 0.62
17 8 0.06
ACGTcount: A:0.09, C:0.18, G:0.35, T:0.38
Consensus pattern (16 bp):
TTTCGGGTCATTCGGG
Found at i:8210 original size:32 final size:33
Alignment explanation
Indices: 8134--8281 Score: 166
Period size: 32 Copynumber: 4.7 Consensus size: 33
8124 GTCAGTTTTT
* *
8134 TCGGGTCATTCGGGTTTCGGGTC-ATTTGGGT-
1 TCGGGTTATTCGGGTTTCGGGTCAATTCGGGTC
*
8165 TCGGGTTAATCGGGTTTCGGGTCAATT-GGGTC
1 TCGGGTTATTCGGGTTTCGGGTCAATTCGGGTC
* * * *
8197 TCAGGTTATTCGGGTCTCGAGT-TATTCGGGTC
1 TCGGGTTATTCGGGTTTCGGGTCAATTCGGGTC
*
8229 TCGGGTTCATT-GGGTTTCGGGTC-ATTCGGTTC
1 TCGGGTT-ATTCGGGTTTCGGGTCAATTCGGGTC
8261 TCGGGTTATTCGGG-TTCGGGT
1 TCGGGTTATTCGGGTTTCGGGT
8282 TTAGACTTCG
Statistics
Matches: 100, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
31 38 0.38
32 59 0.59
33 3 0.03
ACGTcount: A:0.09, C:0.17, G:0.36, T:0.38
Consensus pattern (33 bp):
TCGGGTTATTCGGGTTTCGGGTCAATTCGGGTC
Found at i:8233 original size:48 final size:46
Alignment explanation
Indices: 8133--8310 Score: 200
Period size: 48 Copynumber: 3.8 Consensus size: 46
8123 AGTCAGTTTT
* *
8133 TTCGGGTCATTCGGGTTTCGGGTCATTTGGGT-TCGGGTTAATCGGG
1 TTCGGGTCATT-GGGTTTCGGGTCATTCGGGTCTCGGGTTATTCGGG
* * * *
8179 TTTCGGGTCAATTGGGTCTCAGGTTATTCGGGTCTCGAGTTATTCGGG
1 -TTCGGGTC-ATTGGGTTTCGGGTCATTCGGGTCTCGGGTTATTCGGG
*
8227 TCTCGGGTTCATTGGGTTTCGGGTCATTCGGTTCTCGGGTTATTCGGG
1 T-TCGGG-TCATTGGGTTTCGGGTCATTCGGGTCTCGGGTTATTCGGG
* **
8275 TTCGGGT--TTAGACTTCGGGTCATTCGGGTCTCGGGT
1 TTCGGGTCATTGGGTTTCGGGTCATTCGGGTCTCGGGT
8311 CAAATGAGTC
Statistics
Matches: 112, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
44 25 0.22
46 1 0.01
47 30 0.27
48 54 0.48
49 2 0.02
ACGTcount: A:0.09, C:0.17, G:0.36, T:0.38
Consensus pattern (46 bp):
TTCGGGTCATTGGGTTTCGGGTCATTCGGGTCTCGGGTTATTCGGG
Found at i:8699 original size:13 final size:13
Alignment explanation
Indices: 8667--8703 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
8657 ACAAAACAAG
8667 TTTATTCTATTTTC
1 TTTATTCTA-TTTC
*
8681 TATATTCTATTTC
1 TTTATTCTATTTC
8694 TTTATTCTAT
1 TTTATTCTAT
8704 AATTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTATTCTATTTC
Found at i:8807 original size:19 final size:21
Alignment explanation
Indices: 8783--8821 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
8773 TATCTAAATA
8783 ATAAAT-GAT-AACTTATAAT
1 ATAAATAGATAAACTTATAAT
*
8802 ATAAATAGGTAAACTTATAA
1 ATAAATAGATAAACTTATAA
8822 ATTCTCGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (21 bp):
ATAAATAGATAAACTTATAAT
Found at i:8869 original size:16 final size:16
Alignment explanation
Indices: 8846--8981 Score: 80
Period size: 16 Copynumber: 8.5 Consensus size: 16
8836 CGGGTCAACT
8846 TTTCGGGTTATTCGGG
1 TTTCGGGTTATTCGGG
*
8862 TCTCGGGTCTCA--CGGG
1 TTTCGGGT-T-ATTCGGG
* *
8878 TTTTGGGTT-TCACGGG
1 TTTCGGGTTAT-TCGGG
* *
8894 TTTCGGGTCATACGGG
1 TTTCGGGTTATTCGGG
* *
8910 TTTTGGGTTATACGGG
1 TTTCGGGTTATTCGGG
*
8926 TTTCGGGTTATTTGGG
1 TTTCGGGTTATTCGGG
** * *
8942 TCACGGGTCAATCGGG
1 TTTCGGGTTATTCGGG
** * *
8958 TCACGTGTTAGTCGGG
1 TTTCGGGTTATTCGGG
8974 TTTCGGGT
1 TTTCGGGT
8982 CGGGCGGGTT
Statistics
Matches: 93, Mismatches: 21, Indels: 12
0.74 0.17 0.10
Matches are distributed among these distances:
15 1 0.01
16 89 0.96
17 2 0.02
18 1 0.01
ACGTcount: A:0.10, C:0.16, G:0.38, T:0.37
Consensus pattern (16 bp):
TTTCGGGTTATTCGGG
Found at i:8894 original size:32 final size:32
Alignment explanation
Indices: 8845--8933 Score: 119
Period size: 32 Copynumber: 2.8 Consensus size: 32
8835 ACGGGTCAAC
* *
8845 TTTTCGGGTTATTCGGGTCTCGGGTC-TCACGGG
1 TTTT-GGGTTATACGGGTTTCGGGTCAT-ACGGG
8878 TTTTGGGTT-TCACGGGTTTCGGGTCATACGGG
1 TTTTGGGTTAT-ACGGGTTTCGGGTCATACGGG
8910 TTTTGGGTTATACGGGTTTCGGGT
1 TTTTGGGTTATACGGGTTTCGGGT
8934 TATTTGGGTC
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
31 1 0.02
32 44 0.86
33 6 0.12
ACGTcount: A:0.08, C:0.16, G:0.37, T:0.39
Consensus pattern (32 bp):
TTTTGGGTTATACGGGTTTCGGGTCATACGGG
Done.