Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021752.1 Corchorus olitorius cultivar O-4 contig21785, 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: 21106
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:5671 original size:116 final size:116
Alignment explanation
Indices: 5467--5699 Score: 466
Period size: 116 Copynumber: 2.0 Consensus size: 116
5457 AACGGTCCCG
5467 TCTGATTTTCTTCTGAATTTACACAATCCGATAACGTTATATCCTGAAATAACACAAATGGTAAC
1 TCTGATTTTCTTCTGAATTTACACAATCCGATAACGTTATATCCTGAAATAACACAAATGGTAAC
5532 GGTGCATCCTGAATTGAATATCAGGCGAAACATTATATCCTGAATTGAGTA
66 GGTGCATCCTGAATTGAATATCAGGCGAAACATTATATCCTGAATTGAGTA
5583 TCTGATTTTCTTCTGAATTTACACAATCCGATAACGTTATATCCTGAAATAACACAAATGGTAAC
1 TCTGATTTTCTTCTGAATTTACACAATCCGATAACGTTATATCCTGAAATAACACAAATGGTAAC
5648 GGTGCATCCTGAATTGAATATCAGGCGAAACATTATATCCTGAATTGAGTA
66 GGTGCATCCTGAATTGAATATCAGGCGAAACATTATATCCTGAATTGAGTA
5699 T
1 T
5700 TTAGCCATTT
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 117 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (116 bp):
TCTGATTTTCTTCTGAATTTACACAATCCGATAACGTTATATCCTGAAATAACACAAATGGTAAC
GGTGCATCCTGAATTGAATATCAGGCGAAACATTATATCCTGAATTGAGTA
Found at i:9417 original size:22 final size:22
Alignment explanation
Indices: 9391--9432 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
9381 AACAAACCCG
*
9391 TAACCCAAATGACCCCAGAAGT
1 TAACCCAAATGACCCAAGAAGT
9413 TAACCCAAATGACCCAAGAA
1 TAACCCAAATGACCCAAGAA
9433 TATTATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.31, G:0.12, T:0.12
Consensus pattern (22 bp):
TAACCCAAATGACCCAAGAAGT
Found at i:12213 original size:18 final size:17
Alignment explanation
Indices: 12188--12223 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
12178 TTTTTCTTCA
12188 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
12205 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
12223 T
1 T
12224 TTTCCTAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Found at i:18667 original size:11 final size:11
Alignment explanation
Indices: 18651--18681 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
18641 AGTATAATAG
18651 TATTATTATTA
1 TATTATTATTA
18662 TATTATTATTA
1 TATTATTATTA
18673 TATTATTAT
1 TATTATTAT
18682 ATTACTAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTATTATTA
Found at i:18801 original size:27 final size:27
Alignment explanation
Indices: 18771--18829 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
18761 TGTGCATATC
18771 TGTAAAAATTCGTAATCATTATCAAGG
1 TGTAAAAATTCGTAATCATTATCAAGG
* *
18798 TGTAAAAATTCGTAATCATTATTAAGT
1 TGTAAAAATTCGTAATCATTATCAAGG
18825 TGTAA
1 TGTAA
18830 GGTGAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (27 bp):
TGTAAAAATTCGTAATCATTATCAAGG
Found at i:18914 original size:19 final size:19
Alignment explanation
Indices: 18878--18915 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
18868 TAGAAAAGCC
18878 AAACACAATATAAGCCAAA
1 AAACACAATATAAGCCAAA
18897 AAACAACAATATAA-CCAAA
1 AAAC-ACAATATAAGCCAAA
18916 TAGCAGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.66, C:0.21, G:0.03, T:0.11
Consensus pattern (19 bp):
AAACACAATATAAGCCAAA
Done.