Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001124.1 Corchorus capsularis cultivar CVL-1 contig01124, 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: 15135
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6829 original size:30 final size:30
Alignment explanation
Indices: 6795--6852 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
6785 CTAAGTTTCC
6795 AAGAAATTATAAGGTTACTAGGGAACTAAT
1 AAGAAATTATAAGGTTACTAGGGAACTAAT
6825 AAGAAATTATAAGGTTACTAGGGAACTA
1 AAGAAATTATAAGGTTACTAGGGAACTA
6853 CGTATACGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.26
Consensus pattern (30 bp):
AAGAAATTATAAGGTTACTAGGGAACTAAT
Found at i:11282 original size:18 final size:17
Alignment explanation
Indices: 11259--11301 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
11249 CTTGGACGAC
11259 GATCCTGACGAAGATTGG
1 GATCCTGA-GAAGATTGG
*
11277 GATCCTCGAGGAGATTGG
1 GATCCT-GAGAAGATTGG
*
11295 AATCCTG
1 GATCCTG
11302 TTAGCTGGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 19 0.86
19 2 0.09
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.23
Consensus pattern (17 bp):
GATCCTGAGAAGATTGG
Found at i:11464 original size:24 final size:24
Alignment explanation
Indices: 11432--11481 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
11422 CTGAAAAAAG
11432 TTCTAAAGAAAGTTCTTCTGCATC
1 TTCTAAAGAAAGTTCTTCTGCATC
* * *
11456 TTCTGAAGAAAGTTGTTGTGCATC
1 TTCTAAAGAAAGTTCTTCTGCATC
11480 TT
1 TT
11482 ATGGCCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (24 bp):
TTCTAAAGAAAGTTCTTCTGCATC
Found at i:13290 original size:6 final size:6
Alignment explanation
Indices: 13279--13312 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
13269 CATGAAATTT
13279 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAA
13313 ACCAATCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:14624 original size:253 final size:253
Alignment explanation
Indices: 14176--14682 Score: 1005
Period size: 253 Copynumber: 2.0 Consensus size: 253
14166 GGAATTAAAC
14176 ATGAGCATTTCCTTATAAAAACTCTAATGACCCATTTCCTTATTGGCCTTCCTCTGTACTGTTAT
1 ATGAGCATTTCCTTATAAAAACTCTAATGACCCATTTCCTTATTGGCCTTCCTCTGTACTGTTAT
14241 CCAATTGAAGAACAGAAACTGAAGTGGGTTTCTTCGAATGGACCAGCTGTTGAAGCTTTTGAGTA
66 CCAATTGAAGAACAGAAACTGAAGTGGGTTTCTTCGAATGGACCAGCTGTTGAAGCTTTTGAGTA
14306 GAATCTGAAGACAATTTGACACTGGGACTTAATTAACAAAATTAAATGTGTTAGATCCTTATTTG
131 GAATCTGAAGACAATTTGACACTGGGACTTAATTAACAAAATTAAATGTGTTAGATCCTTATTTG
14371 AGTATTTTTGCAAAGGTTGAGAACCAATTTGAATATTTATCCAAAAACCATGAAAAAT
196 AGTATTTTTGCAAAGGTTGAGAACCAATTTGAATATTTATCCAAAAACCATGAAAAAT
*
14429 ATGAGCATTTCCTTATGAAAACTCTAATGACCCATTTCCTTATTGGCCTTCCTCTGTACTGTTAT
1 ATGAGCATTTCCTTATAAAAACTCTAATGACCCATTTCCTTATTGGCCTTCCTCTGTACTGTTAT
14494 CCAATTGAAGAACAGAAACTGAAGTGGGTTTCTTCGAATGGACCAGCTGTTGAAGCTTTTGAGTA
66 CCAATTGAAGAACAGAAACTGAAGTGGGTTTCTTCGAATGGACCAGCTGTTGAAGCTTTTGAGTA
14559 GAATCTGAAGACAATTTGACACTGGGACTTAATTAACAAAATTAAATGTGTTAGATCCTTATTTG
131 GAATCTGAAGACAATTTGACACTGGGACTTAATTAACAAAATTAAATGTGTTAGATCCTTATTTG
14624 AGTATTTTTGCAAAGGTTGAGAACCAATTTGAATATTTATCCAAAAACCATGAAAAAT
196 AGTATTTTTGCAAAGGTTGAGAACCAATTTGAATATTTATCCAAAAACCATGAAAAAT
14682 A
1 A
14683 AATAAAAAGA
Statistics
Matches: 253, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
253 253 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (253 bp):
ATGAGCATTTCCTTATAAAAACTCTAATGACCCATTTCCTTATTGGCCTTCCTCTGTACTGTTAT
CCAATTGAAGAACAGAAACTGAAGTGGGTTTCTTCGAATGGACCAGCTGTTGAAGCTTTTGAGTA
GAATCTGAAGACAATTTGACACTGGGACTTAATTAACAAAATTAAATGTGTTAGATCCTTATTTG
AGTATTTTTGCAAAGGTTGAGAACCAATTTGAATATTTATCCAAAAACCATGAAAAAT
Found at i:14794 original size:101 final size:101
Alignment explanation
Indices: 14659--14865 Score: 396
Period size: 101 Copynumber: 2.0 Consensus size: 101
14649 AATTTGAATA
*
14659 TTTATCCAAAAACCATGAAAAATAAATAAAAAGAAAAAGAAAAGACCAACCAAGAAGGGTCATTT
1 TTTATCCAAAAACCATGAAAAATAAATAAAAAGAAAAAGAAAAGACCAACCAAGAAGGGCCATTT
14724 GTCATCCCTCATAAAAAGTAATCATGAGGGATTACT
66 GTCATCCCTCATAAAAAGTAATCATGAGGGATTACT
14760 TTTATCCAAAAACCATGAAAAATAAATAAAAAGAAAAAGAAAAGACCAACCAAGAAGGGCCATTT
1 TTTATCCAAAAACCATGAAAAATAAATAAAAAGAAAAAGAAAAGACCAACCAAGAAGGGCCATTT
*
14825 GTCATCCCTCATAAAAGGTAATCATGAGGGATTACT
66 GTCATCCCTCATAAAAAGTAATCATGAGGGATTACT
14861 TTTAT
1 TTTAT
14866 TATAGTAGAT
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 104 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (101 bp):
TTTATCCAAAAACCATGAAAAATAAATAAAAAGAAAAAGAAAAGACCAACCAAGAAGGGCCATTT
GTCATCCCTCATAAAAAGTAATCATGAGGGATTACT
Done.