Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016321.1 Corchorus capsularis cultivar CVL-1 contig16342, 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: 8488
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Found at i:729 original size:33 final size:33
Alignment explanation
Indices: 691--757 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
681 AGGCATGAGG
691 ATAGTAATCAAAGTACATATCCAATTTCGGGAT
1 ATAGTAATCAAAGTACATATCCAATTTCGGGAT
724 ATAGTAATCAAAGTACATATCCAATTTCGGGAT
1 ATAGTAATCAAAGTACATATCCAATTTCGGGAT
757 A
1 A
758 GTGAACCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (33 bp):
ATAGTAATCAAAGTACATATCCAATTTCGGGAT
Found at i:1399 original size:212 final size:212
Alignment explanation
Indices: 1032--1456 Score: 850
Period size: 212 Copynumber: 2.0 Consensus size: 212
1022 CAAGTTGTTG
1032 CATGATTTGTTGCAACATGGTATTCGTATTTAATTCTTGATTTTGCTCATCTTGCCTATCTCCCA
1 CATGATTTGTTGCAACATGGTATTCGTATTTAATTCTTGATTTTGCTCATCTTGCCTATCTCCCA
1097 TTGTACCTACAAAAAGAACAAAGATTAGTAATAAAAATTCTCACAAGTGTGTGTGTGCTTATTCC
66 TTGTACCTACAAAAAGAACAAAGATTAGTAATAAAAATTCTCACAAGTGTGTGTGTGCTTATTCC
1162 TTTGACTTGTGCTCTCGTATTTGCACTCAAATCCTATGGATTGGCGGTCCACTACTCTCTTGATG
131 TTTGACTTGTGCTCTCGTATTTGCACTCAAATCCTATGGATTGGCGGTCCACTACTCTCTTGATG
1227 ATCTCACAAGATTATGC
196 ATCTCACAAGATTATGC
1244 CATGATTTGTTGCAACATGGTATTCGTATTTAATTCTTGATTTTGCTCATCTTGCCTATCTCCCA
1 CATGATTTGTTGCAACATGGTATTCGTATTTAATTCTTGATTTTGCTCATCTTGCCTATCTCCCA
1309 TTGTACCTACAAAAAGAACAAAGATTAGTAATAAAAATTCTCACAAGTGTGTGTGTGCTTATTCC
66 TTGTACCTACAAAAAGAACAAAGATTAGTAATAAAAATTCTCACAAGTGTGTGTGTGCTTATTCC
1374 TTTGACTTGTGCTCTCGTATTTGCACTCAAATCCTATGGATTGGCGGTCCACTACTCTCTTGATG
131 TTTGACTTGTGCTCTCGTATTTGCACTCAAATCCTATGGATTGGCGGTCCACTACTCTCTTGATG
1439 ATCTCACAAGATTATGC
196 ATCTCACAAGATTATGC
1456 C
1 C
1457 TTTTTCTAGC
Statistics
Matches: 213, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
212 213 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (212 bp):
CATGATTTGTTGCAACATGGTATTCGTATTTAATTCTTGATTTTGCTCATCTTGCCTATCTCCCA
TTGTACCTACAAAAAGAACAAAGATTAGTAATAAAAATTCTCACAAGTGTGTGTGTGCTTATTCC
TTTGACTTGTGCTCTCGTATTTGCACTCAAATCCTATGGATTGGCGGTCCACTACTCTCTTGATG
ATCTCACAAGATTATGC
Found at i:2049 original size:12 final size:12
Alignment explanation
Indices: 2032--2062 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
2022 TTTTTGTCGA
2032 ATTTTTTTTTATT
1 ATTTTTTTTTA-T
2045 ATTTTTTTTTAT
1 ATTTTTTTTTAT
2057 ATTTTT
1 ATTTTT
2063 CGATATAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
ATTTTTTTTTAT
Found at i:6865 original size:33 final size:32
Alignment explanation
Indices: 6828--6934 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 32
6818 CGCCTAGCGA
*
6828 TGGCCGGT-TGTGGCCGGACATGTCCATGTCGCG
1 TGGCCGGTGT-TGGCCGGACATCTCCA-GTCGCG
* *
6861 TGGCCGGTGTTGGCCGGGCATCTCCGAGTCACG
1 TGGCCGGTGTTGGCCGGACATCTCC-AGTCGCG
* *
6894 TGGCCGGTGTTGGCCGGACTTCTCCAAGTCGCA
1 TGGCCGGTGTTGGCCGGACATCTCC-AGTCGCG
6927 TGGCCGGT
1 TGGCCGGT
6935 CACTAGTGCT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
33 62 0.97
34 2 0.03
ACGTcount: A:0.09, C:0.29, G:0.38, T:0.23
Consensus pattern (32 bp):
TGGCCGGTGTTGGCCGGACATCTCCAGTCGCG
Done.