Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014028.1 Corchorus capsularis cultivar CVL-1 contig14049, 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: 17702
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1422 original size:31 final size:32
Alignment explanation
Indices: 1337--1449 Score: 147
Period size: 32 Copynumber: 3.5 Consensus size: 32
1327 CGCTATATAT
1337 TAAATATAGCGGCGTTTTGTTCTTTAGACGCCGC
1 TAAATA-AG-GGCGTTTTGTTCTTTAGACGCCGC
* * *
1371 TATATAAGGCCGTTTAGTTCTTTAGACGCCGC
1 TAAATAAGGGCGTTTTGTTCTTTAGACGCCGC
* * *
1403 TAAAT-AGGGCGTTTTGTTCTATAGACACCAC
1 TAAATAAGGGCGTTTTGTTCTTTAGACGCCGC
1434 TAAATAAGGGCGTTTT
1 TAAATAAGGGCGTTTT
1450 CTTTTCATAC
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
31 26 0.38
32 36 0.52
33 2 0.03
34 5 0.07
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.35
Consensus pattern (32 bp):
TAAATAAGGGCGTTTTGTTCTTTAGACGCCGC
Found at i:2210 original size:34 final size:34
Alignment explanation
Indices: 2167--2243 Score: 136
Period size: 34 Copynumber: 2.3 Consensus size: 34
2157 TAATTGGATA
* *
2167 AATACATGGATGTCATTGAACAAAATCATATATC
1 AATACATGGATGGCATTGAACAAAATCATAAATC
2201 AATACATGGATGGCATTGAACAAAATCATAAATC
1 AATACATGGATGGCATTGAACAAAATCATAAATC
2235 AATACATGG
1 AATACATGG
2244 CATTGAAAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.26
Consensus pattern (34 bp):
AATACATGGATGGCATTGAACAAAATCATAAATC
Found at i:4567 original size:124 final size:123
Alignment explanation
Indices: 4376--4980 Score: 763
Period size: 124 Copynumber: 4.9 Consensus size: 123
4366 GTCAAAAGGT
** * * * *
4376 TTCGTCACAAAAACAAGTACATTATTTGTGTCGAAATTGTTGTAACTA-TCGTTTCATTTGTCGT
1 TTCGTCACAAAAA-AAGTACATTATGAGTGTCCAAATTGTTGTCACTACT-GTTTTA-TTATCGT
4440 CACAAATAAATATGCAAAAATGACAAAAGAAAAATGATTTAGTGACCATGTCCTAACATAA
63 CACAAATAAATATGCAAAAATGACAAAAGAAAAATGATTTAGTGACCATGTCCTAACATAA
* * *
4501 TTCGTCACAAAAAAAGTACATTATGTGTGTCCAAATTGTTGTCACTACTGTTTTAGTTCTCATCA
1 TTCGTCACAAAAAAAGTACATTATGAGTGTCCAAATTGTTGTCACTACTGTTTTA-TTATCGTCA
* * *
4566 CAAATAAATATGCAAAGATGACAAAAGAAAAATGATTTAGTGACCATGACCTAGCATAA
65 CAAATAAATATGCAAAAATGACAAAAGAAAAATGATTTAGTGACCATGTCCTAACATAA
** * * * *
4625 TTCGTCACAGTAAATGTACATCATGAGTGTCCAAATTGTTGTCACTATTGTGTTATGTATCGTCA
1 TTCGTCACAAAAAAAGTACATTATGAGTGTCCAAATTGTTGTCACTACTGTTTTAT-TATCGTCA
* *
4690 CAAATAAATATGCAAAGATGACAACAA-AAAAATTGATTTAGTGA-CATGTCCTAGCATAA
65 CAAATAAATATGCAAAAATGACAA-AAGAAAAA-TGATTTAGTGACCATGTCCTAACATAA
* * * *
4749 TTCGTCACAATAAATGTACATTATGAGTGTCCAAATTGTTGTCACTATTGTTTTATTAATTGTCA
1 TTCGTCACAAAAAAAGTACATTATGAGTGTCCAAATTGTTGTCACTACTGTTTTATT-ATCGTCA
* * *
4814 CAAATAAATATGCAAAAATGACAAAAGAAAAATGATTCAGTGACTATGTTCTAACATAA
65 CAAATAAATATGCAAAAATGACAAAAGAAAAATGATTTAGTGACCATGTCCTAACATAA
* * *
4873 TTTGTCACAATAAATA-TACATTATGAGTGT-CAAACATGTTGTCACTACTGTTTTATTTATCGT
1 TTCGTCACAA-AAAAAGTACATTATGAGTGTCCAAA-TTGTTGTCACTACTGTTTTA-TTATCGT
* * *
4936 CACAAATAAATACGCACAATTGACAAAAGACAAAA-GATTTAGTGA
63 CACAAATAAATATGCAAAAATGACAAAAGA-AAAATGATTTAGTGA
4981 TCGAGCTAAA
Statistics
Matches: 429, Mismatches: 40, Indels: 23
0.87 0.08 0.05
Matches are distributed among these distances:
123 18 0.04
124 376 0.88
125 35 0.08
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (123 bp):
TTCGTCACAAAAAAAGTACATTATGAGTGTCCAAATTGTTGTCACTACTGTTTTATTATCGTCAC
AAATAAATATGCAAAAATGACAAAAGAAAAATGATTTAGTGACCATGTCCTAACATAA
Found at i:7527 original size:16 final size:15
Alignment explanation
Indices: 7506--7535 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
7496 CACTCCCTCT
7506 TAAAACAAGAGAAAAC
1 TAAAACAAGA-AAAAC
7522 TAAAACAAGAAAAA
1 TAAAACAAGAAAAA
7536 GATGAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.73, C:0.10, G:0.10, T:0.07
Consensus pattern (15 bp):
TAAAACAAGAAAAAC
Found at i:8109 original size:30 final size:30
Alignment explanation
Indices: 8075--8135 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
8065 TAATTCTTGC
*
8075 TTCTTGAAATAATTCTTCAAT-GATCTTCAA
1 TTCTTGAAATAA-TCTTCAATAAATCTTCAA
*
8105 TTCTTGAAATTATCTTCAATAAATCTTCAA
1 TTCTTGAAATAATCTTCAATAAATCTTCAA
8135 T
1 T
8136 CACGAATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.44
Consensus pattern (30 bp):
TTCTTGAAATAATCTTCAATAAATCTTCAA
Found at i:13209 original size:25 final size:25
Alignment explanation
Indices: 13181--13234 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
13171 TTTGATTTTT
13181 TAAAAGCCTATAGGAATTTATTTAA
1 TAAAAGCCTATAGGAATTTATTTAA
** * * *
13206 TAAATTCGTTTTGGAATTTATTTAA
1 TAAAAGCCTATAGGAATTTATTTAA
13231 TAAA
1 TAAA
13235 TTCGTTTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.43
Consensus pattern (25 bp):
TAAAAGCCTATAGGAATTTATTTAA
Found at i:13235 original size:25 final size:25
Alignment explanation
Indices: 13193--13242 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
13183 AAAGCCTATA
13193 GGAATTTATTTAATAAATTCGTTTT
1 GGAATTTATTTAATAAATTCGTTTT
13218 GGAATTTATTTAATAAATTCGTTTT
1 GGAATTTATTTAATAAATTCGTTTT
13243 TACCATGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.52
Consensus pattern (25 bp):
GGAATTTATTTAATAAATTCGTTTT
Found at i:13854 original size:21 final size:21
Alignment explanation
Indices: 13816--13855 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13806 GATGCCCACA
* *
13816 TGGTTTGTCTGAAGACCCATG
1 TGGTTTGCCTGAACACCCATG
*
13837 TGGTTTGCCTGATCACCCA
1 TGGTTTGCCTGAACACCCA
13856 GGTAGGCAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (21 bp):
TGGTTTGCCTGAACACCCATG
Found at i:15304 original size:2 final size:2
Alignment explanation
Indices: 15297--15324 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15287 TTGTCCTCAA
15297 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
15325 CTAGTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Done.