Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008177.1 Corchorus capsularis cultivar CVL-1 contig08198, 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: 33100
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Found at i:3629 original size:8 final size:8
Alignment explanation
Indices: 3601--3634 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
3591 GAATCGGCTA
3601 TGAATTTT
1 TGAATTTT
*
3609 TGAAGTTTC
1 TGAA-TTTT
3618 TGAATTTT
1 TGAATTTT
3626 TGAATTTT
1 TGAATTTT
3634 T
1 T
3635 CAAGAAGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:3794 original size:33 final size:34
Alignment explanation
Indices: 3757--3863 Score: 96
Period size: 33 Copynumber: 3.2 Consensus size: 34
3747 CGCCAAGCGA
*
3757 TGGCCGGTTG-TGGCAGGACATGTCC-ATGTCGCG
1 TGGCCGGTTGATGGCAGGACATCTCCGA-GTCGCG
* *
3790 TGGCCGG-TGATGGCCGGGCATCTCCGAGTCGCG
1 TGGCCGGTTGATGGCAGGACATCTCCGAGTCGCG
* * * * * *
3823 TGGCCGG-TGTTGGCCGGGCTTCTCCAAGTCGCA
1 TGGCCGGTTGATGGCAGGACATCTCCGAGTCGCG
3856 TGGCCGGT
1 TGGCCGGT
3864 CACTCGCGCC
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
32 2 0.03
33 61 0.95
34 1 0.02
ACGTcount: A:0.09, C:0.28, G:0.40, T:0.22
Consensus pattern (34 bp):
TGGCCGGTTGATGGCAGGACATCTCCGAGTCGCG
Found at i:4995 original size:8 final size:8
Alignment explanation
Indices: 4967--5000 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
4957 GAATTGGATA
4967 TGAATTTT
1 TGAATTTT
*
4975 TGAAGTTTC
1 TGAA-TTTT
4984 TGAATTTT
1 TGAATTTT
4992 TGAATTTT
1 TGAATTTT
5000 T
1 T
5001 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:10686 original size:19 final size:19
Alignment explanation
Indices: 10659--10696 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
10649 GGAGGCAACC
*
10659 CAATTTTAATTTTAATTTT
1 CAATCTTAATTTTAATTTT
*
10678 CAATCTTAATTTTTATTTT
1 CAATCTTAATTTTAATTTT
10697 GGTTTTATGA
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:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (19 bp):
CAATCTTAATTTTAATTTT
Found at i:13037 original size:33 final size:32
Alignment explanation
Indices: 13000--13106 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 32
12990 CGCCAAGCGA
* *
13000 TGGCCGGT-TGTGGCCGGACATGTCCATGTCGCG
1 TGGCCGGTGT-TGGCCGGGCATCTCCA-GTCGCG
*
13033 TGGCCGGTGTTGGCCGGGCATCTCCGAGTCACG
1 TGGCCGGTGTTGGCCGGGCATCTCC-AGTCGCG
* *
13066 TGGCCGGTGTTGGCCGGGCTTCTCCAAGTCGCA
1 TGGCCGGTGTTGGCCGGGCATCTCC-AGTCGCG
13099 TGGCCGGT
1 TGGCCGGT
13107 CACTAGTGCT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
33 63 0.97
34 2 0.03
ACGTcount: A:0.08, C:0.29, G:0.39, T:0.23
Consensus pattern (32 bp):
TGGCCGGTGTTGGCCGGGCATCTCCAGTCGCG
Found at i:13490 original size:24 final size:24
Alignment explanation
Indices: 13463--13509 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
13453 GTTATTTAAG
13463 TTTATGCTT-TATCTTTAATTTTCC
1 TTTAT-CTTATATCTTTAATTTTCC
* *
13487 TTTATCTTATGTCTTTATTTTTC
1 TTTATCTTATATCTTTAATTTTC
13510 AAGTTTCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.15, C:0.15, G:0.04, T:0.66
Consensus pattern (24 bp):
TTTATCTTATATCTTTAATTTTCC
Found at i:13805 original size:11 final size:11
Alignment explanation
Indices: 13789--13815 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
13779 GAAAAAAATT
13789 GATTGTTTTTG
1 GATTGTTTTTG
13800 GATTGTTTTTG
1 GATTGTTTTTG
13811 GATTG
1 GATTG
13816 ATATGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.11, C:0.00, G:0.30, T:0.59
Consensus pattern (11 bp):
GATTGTTTTTG
Found at i:20082 original size:33 final size:34
Alignment explanation
Indices: 20045--20118 Score: 107
Period size: 33 Copynumber: 2.2 Consensus size: 34
20035 CCGAGTCGTT
20045 TGGCCGGTTG-TAGCCGGACATGTCCATGTCGCA
1 TGGCCGGTTGATAGCCGGACATGTCCATGTCGCA
* * *
20078 TGGCC-GATGATGGCCGGACATGTCCATGTCGCG
1 TGGCCGGTTGATAGCCGGACATGTCCATGTCGCA
20111 TGGCCGGT
1 TGGCCGGT
20119 CTTGTGGCCG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 3 0.09
33 31 0.89
34 1 0.03
ACGTcount: A:0.14, C:0.27, G:0.36, T:0.23
Consensus pattern (34 bp):
TGGCCGGTTGATAGCCGGACATGTCCATGTCGCA
Found at i:27491 original size:30 final size:31
Alignment explanation
Indices: 27426--27497 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
27416 ACAGCTCATT
*
27426 TATCCTGAATTGACACAACCCGATAACGTTA
1 TATCCTGAATTGACACAACCCGATAACGATA
** *
27457 TATCCTGAATTGACACAAGTCG-TAACGATG
1 TATCCTGAATTGACACAACCCGATAACGATA
27487 TATCCTGAATT
1 TATCCTGAATT
27498 ACATTTTCGC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 17 0.46
31 20 0.54
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (31 bp):
TATCCTGAATTGACACAACCCGATAACGATA
Found at i:30259 original size:6 final size:6
Alignment explanation
Indices: 30248--30276 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
30238 TCCCTTTATT
30248 CTCTCC CTCTCC CTCTCC CTCTCC CTCTC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTC
30277 TTGCCAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CTCTCC
Done.