Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011982.1 Corchorus capsularis cultivar CVL-1 contig12003, 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: 24264
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:326 original size:1 final size:1
Alignment explanation
Indices: 320--344 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
310 AGCAATCCAG
320 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
345 ATATATTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:4091 original size:68 final size:68
Alignment explanation
Indices: 3982--4118 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
3972 TCCAACGAAA
3982 TCAAACTCTCAACAAATGCAAAAGCATTCCTAGATCTAATCTTGCTGTCGGCTGCTAGAAATTTA
1 TCAAACTCTCAACAAATGCAAAAGCATTCCTAGATCTAATCTTGCTGTCGGCTGCTAGAAATTTA
4047 AGT
66 AGT
4050 TCAAACTCTCAACAAATGCAAAAGCATTCCTAGATCTAATCTTGCTGTCGGCTGCTAGAAATTTA
1 TCAAACTCTCAACAAATGCAAAAGCATTCCTAGATCTAATCTTGCTGTCGGCTGCTAGAAATTTA
4115 AGT
66 AGT
4118 T
1 T
4119 GAGTTCCTCT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.30
Consensus pattern (68 bp):
TCAAACTCTCAACAAATGCAAAAGCATTCCTAGATCTAATCTTGCTGTCGGCTGCTAGAAATTTA
AGT
Found at i:6674 original size:12 final size:12
Alignment explanation
Indices: 6657--6685 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
6647 AAATCAATAC
6657 AAAGATTCAAAT
1 AAAGATTCAAAT
6669 AAAGATTCAAAT
1 AAAGATTCAAAT
6681 AAAGA
1 AAAGA
6686 AGGAATCAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (12 bp):
AAAGATTCAAAT
Found at i:7080 original size:28 final size:28
Alignment explanation
Indices: 7048--7104 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
7038 ATCTTATCTG
*
7048 TTTTTCAGCAAACTATATGGTTGTTCTT
1 TTTTTCAGCAAACTATACGGTTGTTCTT
** * *
7076 TTTTTTGGCCAGCTATACGGTTGTTCTT
1 TTTTTCAGCAAACTATACGGTTGTTCTT
7104 T
1 T
7105 AGGAACCTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.51
Consensus pattern (28 bp):
TTTTTCAGCAAACTATACGGTTGTTCTT
Found at i:9548 original size:3 final size:3
Alignment explanation
Indices: 9540--9597 Score: 55
Period size: 3 Copynumber: 18.3 Consensus size: 3
9530 TTTCTGGAAG
*
9540 TTA TTA TTA TATA TTA TTA TTA -TA TTA TATA TATA TAA TATA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA T-TA T-TA TTA T-TA TTA TTA
*
9588 TCA TTA TTA T
1 TTA TTA TTA T
9598 ATTTTAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
2 2 0.04
3 33 0.70
4 12 0.26
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:9558 original size:13 final size:13
Alignment explanation
Indices: 9540--9597 Score: 64
Period size: 13 Copynumber: 4.3 Consensus size: 13
9530 TTTCTGGAAG
9540 TTATTATTATATA
1 TTATTATTATATA
9553 TTATTATTATATTA
1 TTATTATTATA-TA
*
9567 TATATATATAATATA
1 T-TAT-TATTATATA
*
9582 TTATTATCAT-TA
1 TTATTATTATATA
9594 TTAT
1 TTAT
9598 ATTTTAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
12 6 0.15
13 16 0.40
14 6 0.15
15 6 0.15
16 6 0.15
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (13 bp):
TTATTATTATATA
Found at i:9567 original size:18 final size:18
Alignment explanation
Indices: 9544--9600 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
9534 TGGAAGTTAT
9544 TATTATATATTATTATTA
1 TATTATATATTATTATTA
*
9562 TATTATATA-TATATAATA
1 TATTATATATTAT-TATTA
*
9580 TATTAT-TATCATTATTA
1 TATTATATATTATTATTA
9597 TATT
1 TATT
9601 TTAATTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 13 0.38
18 21 0.62
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTATATATTATTATTA
Found at i:9583 original size:26 final size:24
Alignment explanation
Indices: 9540--9599 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 24
9530 TTTCTGGAAG
9540 TTATTATTATATATTATTATTAT-A
1 TTATTA-TATATATTATTATTATCA
9564 TTATATATATATAATATATTATTATCA
1 TTAT-TATATAT-AT-TATTATTATCA
9591 TTATTATAT
1 TTATTATAT
9600 TTTAATTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
24 9 0.28
25 4 0.12
26 14 0.44
27 5 0.16
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATTATATATATTATTATTATCA
Found at i:20055 original size:3 final size:3
Alignment explanation
Indices: 20049--20087 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
20039 TTGTTGTTAA
20049 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20088 ATTTCAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:20437 original size:57 final size:57
Alignment explanation
Indices: 20369--20483 Score: 194
Period size: 57 Copynumber: 2.0 Consensus size: 57
20359 TAGATAAGCT
* *
20369 TATTGAAGTTACCAACAAAGGTGATGTTGTTGTACCTGAGTCTGCGAAAAGTGAGCC
1 TATTGAAGTTACCAACAAAGGTGATGTTATTGTACCTGAGCCTGCGAAAAGTGAGCC
* *
20426 TATTGAAGTTACCAACAAGGGTGATGTTATTGTACCTGAGCCTGTGAAAAGTGAGCC
1 TATTGAAGTTACCAACAAAGGTGATGTTATTGTACCTGAGCCTGCGAAAAGTGAGCC
20483 T
1 T
20484 GAAATAAGTG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.29
Consensus pattern (57 bp):
TATTGAAGTTACCAACAAAGGTGATGTTATTGTACCTGAGCCTGCGAAAAGTGAGCC
Done.