Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005432.1 Corchorus capsularis cultivar CVL-1 contig05450, 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: 8140
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Found at i:2031 original size:103 final size:103
Alignment explanation
Indices: 1677--1987 Score: 613
Period size: 103 Copynumber: 3.0 Consensus size: 103
1667 ATTCTTTTAA
1677 CTTGGATATTTGTAATTGCGCTTAAAGTTTATTCCTTTAGATTGTTCTAGGCCTGATTGTGTGTA
1 CTTGGATATTTGTAATTGCGCTTAAAGTTTATTCCTTTAGATTGTTCTAGGCCTGATTGTGTGTA
1742 TCTCGATCTTGTAGGATCAATTTTTACACCTTGATACT
66 TCTCGATCTTGTAGGATCAATTTTTACACCTTGATACT
1780 CTTGGATATTTGTAATTGCGCTTAAAGTTTATTCCTTTAGATTGTTCTAGGCCTGATTGTGTGTA
1 CTTGGATATTTGTAATTGCGCTTAAAGTTTATTCCTTTAGATTGTTCTAGGCCTGATTGTGTGTA
1845 TCTCGATCTTGTAGGATCAATTTTTACACCTTGATACT
66 TCTCGATCTTGTAGGATCAATTTTTACACCTTGATACT
*
1883 CTTGGATATTTGTAATTGCGCTTAAAGTTTATTCCTTTAGATTGTTCTAGGCCTAATTGTGTGTA
1 CTTGGATATTTGTAATTGCGCTTAAAGTTTATTCCTTTAGATTGTTCTAGGCCTGATTGTGTGTA
1948 TCTCGATCTTGTAGGATCAATTTTTACACCTTGATACT
66 TCTCGATCTTGTAGGATCAATTTTTACACCTTGATACT
1986 CT
1 CT
1988 GTTATTTGTA
Statistics
Matches: 207, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 207 1.00
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.45
Consensus pattern (103 bp):
CTTGGATATTTGTAATTGCGCTTAAAGTTTATTCCTTTAGATTGTTCTAGGCCTGATTGTGTGTA
TCTCGATCTTGTAGGATCAATTTTTACACCTTGATACT
Found at i:4524 original size:21 final size:21
Alignment explanation
Indices: 4500--4539 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4490 AAATTGCATT
4500 TTTTCCTTTTT-ATGTTTGCTC
1 TTTT-CTTTTTAATGTTTGCTC
*
4521 TTTTTTTTTTAATGTTTGC
1 TTTTCTTTTTAATGTTTGC
4540 ATGCATTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.07, C:0.12, G:0.10, T:0.70
Consensus pattern (21 bp):
TTTTCTTTTTAATGTTTGCTC
Found at i:6840 original size:292 final size:292
Alignment explanation
Indices: 6316--6899 Score: 1168
Period size: 292 Copynumber: 2.0 Consensus size: 292
6306 TGCGCTATTC
6316 CAGATTCGATTTCACAGCTCTTCTTTGTTCTCTGTTTCTTCCCCAAATCTCTTCGACTCTTCGTT
1 CAGATTCGATTTCACAGCTCTTCTTTGTTCTCTGTTTCTTCCCCAAATCTCTTCGACTCTTCGTT
6381 CTAATCGCCATTGAAGATCAAACTTTGATTTGTTATTCGATTATGTTACCTGTTGCTTCTTTTCA
66 CTAATCGCCATTGAAGATCAAACTTTGATTTGTTATTCGATTATGTTACCTGTTGCTTCTTTTCA
6446 TGCTTCAATTTGATTACTTCAACAATCGCTTCCTTTCTCCATTTGTCTTTCCCCCTTTCTCTCAT
131 TGCTTCAATTTGATTACTTCAACAATCGCTTCCTTTCTCCATTTGTCTTTCCCCCTTTCTCTCAT
6511 GATCCTAATCCTAACCCTAGCTCATTAACCAGGTATATTCCAGTGATTTCTCTTAGTTTTCCTTG
196 GATCCTAATCCTAACCCTAGCTCATTAACCAGGTATATTCCAGTGATTTCTCTTAGTTTTCCTTG
6576 AAATTTCACATTAATCTGTTGATTTCATCTTT
261 AAATTTCACATTAATCTGTTGATTTCATCTTT
6608 CAGATTCGATTTCACAGCTCTTCTTTGTTCTCTGTTTCTTCCCCAAATCTCTTCGACTCTTCGTT
1 CAGATTCGATTTCACAGCTCTTCTTTGTTCTCTGTTTCTTCCCCAAATCTCTTCGACTCTTCGTT
6673 CTAATCGCCATTGAAGATCAAACTTTGATTTGTTATTCGATTATGTTACCTGTTGCTTCTTTTCA
66 CTAATCGCCATTGAAGATCAAACTTTGATTTGTTATTCGATTATGTTACCTGTTGCTTCTTTTCA
6738 TGCTTCAATTTGATTACTTCAACAATCGCTTCCTTTCTCCATTTGTCTTTCCCCCTTTCTCTCAT
131 TGCTTCAATTTGATTACTTCAACAATCGCTTCCTTTCTCCATTTGTCTTTCCCCCTTTCTCTCAT
6803 GATCCTAATCCTAACCCTAGCTCATTAACCAGGTATATTCCAGTGATTTCTCTTAGTTTTCCTTG
196 GATCCTAATCCTAACCCTAGCTCATTAACCAGGTATATTCCAGTGATTTCTCTTAGTTTTCCTTG
6868 AAATTTCACATTAATCTGTTGATTTCATCTTT
261 AAATTTCACATTAATCTGTTGATTTCATCTTT
6900 AATTGAGCTC
Statistics
Matches: 292, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
292 292 1.00
ACGTcount: A:0.20, C:0.26, G:0.10, T:0.44
Consensus pattern (292 bp):
CAGATTCGATTTCACAGCTCTTCTTTGTTCTCTGTTTCTTCCCCAAATCTCTTCGACTCTTCGTT
CTAATCGCCATTGAAGATCAAACTTTGATTTGTTATTCGATTATGTTACCTGTTGCTTCTTTTCA
TGCTTCAATTTGATTACTTCAACAATCGCTTCCTTTCTCCATTTGTCTTTCCCCCTTTCTCTCAT
GATCCTAATCCTAACCCTAGCTCATTAACCAGGTATATTCCAGTGATTTCTCTTAGTTTTCCTTG
AAATTTCACATTAATCTGTTGATTTCATCTTT
Done.