Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015241.1 Corchorus olitorius cultivar O-4 contig15274, 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: 14125
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:1102 original size:27 final size:27
Alignment explanation
Indices: 1072--1127 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
1062 ACTTAGGTCA
*
1072 TTTAGGGGCATTTTGGTCATTTCCCTG
1 TTTAGGGCCATTTTGGTCATTTCCCTG
*
1099 TTTAGGGCCATTTTGGTCATTTCCTTG
1 TTTAGGGCCATTTTGGTCATTTCCCTG
1126 TT
1 TT
1128 CATTTTTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (27 bp):
TTTAGGGCCATTTTGGTCATTTCCCTG
Found at i:2135 original size:24 final size:24
Alignment explanation
Indices: 2081--2137 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
2071 ACCAGTTTTA
*
2081 AATCAAGATTAACAAAGAGAGGGG
1 AATCAATATTAACAAAGAGAGGGG
2105 AATCAATATTAACAAAGAGAGGGG
1 AATCAATATTAACAAAGAGAGGGG
*
2129 AGTCAATAT
1 AATCAATAT
2138 ACCTCAGAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.49, C:0.09, G:0.25, T:0.18
Consensus pattern (24 bp):
AATCAATATTAACAAAGAGAGGGG
Found at i:5788 original size:19 final size:18
Alignment explanation
Indices: 5764--5799 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5754 AAGTTCGTGT
5764 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
5783 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
5800 TCTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATATTTGAAGAC
Found at i:6464 original size:54 final size:54
Alignment explanation
Indices: 6356--6464 Score: 132
Period size: 54 Copynumber: 2.0 Consensus size: 54
6346 TTTCTCTTAG
* **
6356 TCTCTGCGTTTCTGTCCTAAAAAATAAAAATAAATTTCTTTGCGTTTTTCTTTT
1 TCTCTGCGTTTCTATCCTAAAAAATAAAAATAAATTTCTTTGCGTTTTAATTTT
* **
6410 TCTCTGCGTTT-TATTCTGAAAAAA-AAAAATATTTTTCTTTGCGTCTTTAATTTT
1 TCTCTGCGTTTCTATCCT-AAAAAATAAAAATAAATTTCTTTGCGT-TTTAATTTT
6464 T
1 T
6465 AAAAAAATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 22 0.47
54 25 0.53
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.50
Consensus pattern (54 bp):
TCTCTGCGTTTCTATCCTAAAAAATAAAAATAAATTTCTTTGCGTTTTAATTTT
Found at i:10726 original size:19 final size:18
Alignment explanation
Indices: 10702--10739 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
10692 GAAGACCATT
10702 TGAAGATAATTTGAAGATC
1 TGAAGAT-ATTTGAAGATC
*
10721 TGAAGATTTTTGAAGATC
1 TGAAGATATTTGAAGATC
10739 T
1 T
10740 ATTTCAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (18 bp):
TGAAGATATTTGAAGATC
Found at i:11351 original size:11 final size:12
Alignment explanation
Indices: 11325--11351 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
11315 AGATAATTTC
11325 TTTTCTTCTAGT
1 TTTTCTTCTAGT
11337 TTTTCTTCTAGT
1 TTTTCTTCTAGT
11349 TTT
1 TTT
11352 AGGGCTAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.15, G:0.07, T:0.70
Consensus pattern (12 bp):
TTTTCTTCTAGT
Done.