Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008752.1 Corchorus capsularis cultivar CVL-1 contig08773, 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: 8942
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Found at i:435 original size:10 final size:10
Alignment explanation
Indices: 415--448 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
405 GATGTAAGGT
415 TTTTGTTTTTG
1 TTTT-TTTTTG
426 TTTTTTTTTG
1 TTTTTTTTTG
436 TTTTTTTTT-
1 TTTTTTTTTG
445 TTTT
1 TTTT
449 GCACCAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 4 0.17
10 15 0.65
11 4 0.17
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:435 original size:16 final size:15
Alignment explanation
Indices: 414--448 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
404 GGATGTAAGG
414 TTTTTGTTTTTGTTTT
1 TTTTTGTTTTT-TTTT
430 TTTTTGTTTTTTTTT
1 TTTTTGTTTTTTTTT
445 TTTT
1 TTTT
449 GCACCAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (15 bp):
TTTTTGTTTTTTTTT
Found at i:5682 original size:273 final size:273
Alignment explanation
Indices: 5195--5742 Score: 1087
Period size: 273 Copynumber: 2.0 Consensus size: 273
5185 ATTAACGTAA
5195 GTACAATTCTTATAGCTGATAACATTACCACCCAATTGCTCACCTCAACAGCCCATGATACTGGA
1 GTACAATTCTTATAGCTGATAACATTACCACCCAATTGCTCACCTCAACAGCCCATGATACTGGA
5260 TTAAGGTTATCACCTTGTATGGTCCTAAAGAAAGTGAAGTTTGGGGGGGAATGAAACAGAAAGCG
66 TTAAGGTTATCACCTTGTATGGTCCTAAAGAAAGTGAAGTTTGGGGGGGAATGAAACAGAAAGCG
*
5325 GTCTTTACATGTTATATTGATAAACCCCTCCTAAGAGTTAATACTTAAGCATACACTCTTTTAAT
131 GTCTTCACATGTTATATTGATAAACCCCTCCTAAGAGTTAATACTTAAGCATACACTCTTTTAAT
5390 CATTTCAGTTCCTTGATGTTGCAGCAAAAGACCCAACAAGAGTGTTTGATCACCTACATACATCT
196 CATTTCAGTTCCTTGATGTTGCAGCAAAAGACCCAACAAGAGTGTTTGATCACCTACATACATCT
5455 ATCTTGCGTGTGT
261 ATCTTGCGTGTGT
5468 GTACAATTCTTATAGCTGATAACATTACCACCCAATTGCTCACCTCAACAGCCCATGATACTGGA
1 GTACAATTCTTATAGCTGATAACATTACCACCCAATTGCTCACCTCAACAGCCCATGATACTGGA
5533 TTAAGGTTATCACCTTGTATGGTCCTAAAGAAAGTGAAGTTTGGGGGGGAATGAAACAGAAAGCG
66 TTAAGGTTATCACCTTGTATGGTCCTAAAGAAAGTGAAGTTTGGGGGGGAATGAAACAGAAAGCG
5598 GTCTTCACATGTTATATTGATAAACCCCTCCTAAGAGTTAATACTTAAGCATACACTCTTTTAAT
131 GTCTTCACATGTTATATTGATAAACCCCTCCTAAGAGTTAATACTTAAGCATACACTCTTTTAAT
5663 CATTTCAGTTCCTTGATGTTGCAGCAAAAGACCCAACAAGAGTGTTTGATCACCTACATACATCT
196 CATTTCAGTTCCTTGATGTTGCAGCAAAAGACCCAACAAGAGTGTTTGATCACCTACATACATCT
5728 ATCTTGCGTGTGT
261 ATCTTGCGTGTGT
5741 GT
1 GT
5743 GTGTGAACAT
Statistics
Matches: 274, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
273 274 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (273 bp):
GTACAATTCTTATAGCTGATAACATTACCACCCAATTGCTCACCTCAACAGCCCATGATACTGGA
TTAAGGTTATCACCTTGTATGGTCCTAAAGAAAGTGAAGTTTGGGGGGGAATGAAACAGAAAGCG
GTCTTCACATGTTATATTGATAAACCCCTCCTAAGAGTTAATACTTAAGCATACACTCTTTTAAT
CATTTCAGTTCCTTGATGTTGCAGCAAAAGACCCAACAAGAGTGTTTGATCACCTACATACATCT
ATCTTGCGTGTGT
Found at i:6815 original size:75 final size:75
Alignment explanation
Indices: 6689--6838 Score: 241
Period size: 75 Copynumber: 2.0 Consensus size: 75
6679 TCACATCAAG
* *
6689 ATTATATCATTATTTGGTGAAAATCCAGATTAATGCTTCAAAGATTCAAAACGAA-ATGACTTAA
1 ATTATATCATTATTTGGTGAAAATCCAGATAAATGCTTCAAAGATTCAAAAC-AAGATGACTAAA
6753 AATGCAATAAA
65 AATGCAATAAA
*
6764 ATTATATCATTA-TTGGTGAAAAATCCAGATAAATGCTTCAAAGATTTAAAACAAGATGACTAAA
1 ATTATATCATTATTTGGTG-AAAATCCAGATAAATGCTTCAAAGATTCAAAACAAGATGACTAAA
6828 AATGCAATAAA
65 AATGCAATAAA
6839 GAAACTGGCA
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
74 8 0.11
75 62 0.89
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.29
Consensus pattern (75 bp):
ATTATATCATTATTTGGTGAAAATCCAGATAAATGCTTCAAAGATTCAAAACAAGATGACTAAAA
ATGCAATAAA
Done.