Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021259.1 Corchorus olitorius cultivar O-4 contig21292, 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: 9487
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--114 Score: 214
Period size: 2 Copynumber: 58.0 Consensus size: 2
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
43 CT CT CT CT CT C- CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
83 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
115 TGACCATTAA
Statistics
Matches: 110, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
1 2 0.02
2 108 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1115 original size:36 final size:36
Alignment explanation
Indices: 1068--1139 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
1058 TCTAGGGATT
*
1068 TGATACGCAGCGTTTTAATGGCACACGTGAGGAGCA
1 TGATACACAGCGTTTTAATGGCACACGTGAGGAGCA
*
1104 TGATACACAGCGTTTTGATGGCACACGTGAGGAGCA
1 TGATACACAGCGTTTTAATGGCACACGTGAGGAGCA
1140 CGGGGATGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.22
Consensus pattern (36 bp):
TGATACACAGCGTTTTAATGGCACACGTGAGGAGCA
Found at i:2094 original size:30 final size:32
Alignment explanation
Indices: 2058--2119 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
2048 ATAAAATGAG
* *
2058 TAGCCCA-TATATAA-GTGGGTTGTGCCGTGC
1 TAGCCCATTATATAATATGGGTCGTGCCGTGC
*
2088 TAGCCCATTTTATAATATGGGTCGTGCCGTGC
1 TAGCCCATTATATAATATGGGTCGTGCCGTGC
2120 CAATCCATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 7 0.26
31 6 0.22
32 14 0.52
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.32
Consensus pattern (32 bp):
TAGCCCATTATATAATATGGGTCGTGCCGTGC
Found at i:2413 original size:22 final size:22
Alignment explanation
Indices: 2385--2444 Score: 111
Period size: 22 Copynumber: 2.7 Consensus size: 22
2375 ACATTAAAAA
2385 TGGGTCGTGCTGTGCCGGCACG
1 TGGGTCGTGCTGTGCCGGCACG
*
2407 TGGGTCGTGCTATGCCGGCACG
1 TGGGTCGTGCTGTGCCGGCACG
2429 TGGGTCGTGCTGTGCC
1 TGGGTCGTGCTGTGCC
2445 ATGCTATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.05, C:0.27, G:0.43, T:0.25
Consensus pattern (22 bp):
TGGGTCGTGCTGTGCCGGCACG
Found at i:6727 original size:36 final size:36
Alignment explanation
Indices: 6680--6751 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
6670 GGGGAGGCAT
*
6680 TGATACGCAGCGTATTAATGGCACACATGAGGAGCA
1 TGATACACAGCGTATTAATGGCACACATGAGGAGCA
* * *
6716 TGATACACAGCGTTTTGATGGCACACGTGAGGAGCA
1 TGATACACAGCGTATTAATGGCACACATGAGGAGCA
6752 CGGGGATGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (36 bp):
TGATACACAGCGTATTAATGGCACACATGAGGAGCA
Found at i:8419 original size:119 final size:119
Alignment explanation
Indices: 8279--8516 Score: 449
Period size: 119 Copynumber: 2.0 Consensus size: 119
8269 GGGGGGGGGG
*
8279 GGGGGTCGATGCCTTTATATAGGCAAAGGATCGACCTAAACTATCCAAAAATAAGCCCTCTAGGC
1 GGGGGTCGATGCCTTTATATAGGCAAAGGATCGACATAAACTATCCAAAAATAAGCCCTCTAGGC
8344 GGTTTAAAATGCCTTGGGCGGCACACATAAGGAAAAGACAAGGAAATAGCCTAA
66 GGTTTAAAATGCCTTGGGCGGCACACATAAGGAAAAGACAAGGAAATAGCCTAA
8398 GGGGGTCGATGCCTTTATATAGGCAAAGGATCGACATAAACTATCCAAAAATAAGCCCTCTAGGC
1 GGGGGTCGATGCCTTTATATAGGCAAAGGATCGACATAAACTATCCAAAAATAAGCCCTCTAGGC
* *
8463 GGTTTACAATGCCTTGGGTGGCACACATAAGGAAAAGACAAGGAAATAGCCTAA
66 GGTTTAAAATGCCTTGGGCGGCACACATAAGGAAAAGACAAGGAAATAGCCTAA
8517 TTCCAAGTCC
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
119 116 1.00
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (119 bp):
GGGGGTCGATGCCTTTATATAGGCAAAGGATCGACATAAACTATCCAAAAATAAGCCCTCTAGGC
GGTTTAAAATGCCTTGGGCGGCACACATAAGGAAAAGACAAGGAAATAGCCTAA
Found at i:8574 original size:14 final size:15
Alignment explanation
Indices: 8537--8574 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
8527 AACTAGGAAA
8537 AATAAAT-AACAAGG
1 AATAAATAAACAAGG
8551 AATAAATAAACAAGG
1 AATAAATAAACAAGG
8566 AA-AAATAAA
1 AATAAATAAA
8575 TGATCTCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.71, C:0.05, G:0.11, T:0.13
Consensus pattern (15 bp):
AATAAATAAACAAGG
Done.