Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021755.1 Corchorus olitorius cultivar O-4 contig21788, 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: 4447
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Found at i:2955 original size:204 final size:200
Alignment explanation
Indices: 2617--3025 Score: 737
Period size: 204 Copynumber: 2.0 Consensus size: 200
2607 GCTTAATAAC
*
2617 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTGAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
2682 GATACAACACATTATTATTATATATAAAACTATACAAAAAAAAGTAGTTGAACATTAGTGGTTGA
66 GATACAACACATTACTATTATATATAAAACTATACAAAAAAAAGTAGTTGAACATTAGTGGTAGA
2747 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
131 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCC
2812 GATTTA
195 GATTTA
2818 TTTATCAATGGTGAATGTTATTAATTTTTTAAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
1 TTTATCAATGGTGAATGTTATTAATTTTTT-AAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
* *
2883 AGATACAACACATTACTATTATATATATATAACTATACCAAAAAAATTAGTTGAACATTAGTGGT
65 AGATACAACACATTACTATTATATATA-A-AACTATACAAAAAAAAGTAGTTGAACATTAGTGGT
2948 AGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
128 AGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
3013 CCGATTTA
193 CCGATTTA
3021 TTTAT
1 TTTAT
3026 TATTAAGGAA
Statistics
Matches: 200, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
201 30 0.15
202 59 0.29
203 19 0.09
204 92 0.46
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (200 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATAAAACTATACAAAAAAAAGTAGTTGAACATTAGTGGTAGA
TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCG
ATTTA
Found at i:3128 original size:24 final size:23
Alignment explanation
Indices: 3096--3141 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
3086 ACGTTTGCAC
3096 AAATACCTAAGAATTTGAATTAAA
1 AAATACCTAAGAATTT-AATTAAA
3120 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
3142 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (23 bp):
AAATACCTAAGAATTTAATTAAA
Found at i:3186 original size:39 final size:40
Alignment explanation
Indices: 3132--3212 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
3122 ATACCTAAGA
*
3132 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
3171 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
3211 AT
1 AT
3213 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:3460 original size:15 final size:15
Alignment explanation
Indices: 3428--3466 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
3418 AGTTTAGACT
3428 TATATAG-TATATAG
1 TATATAGATATATAG
3442 -ATATAGATATATAG
1 TATATAGATATATAG
3456 TATATAGATAT
1 TATATAGATAT
3467 TGATGAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 7 0.30
15 10 0.43
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (15 bp):
TATATAGATATATAG
Found at i:4408 original size:19 final size:20
Alignment explanation
Indices: 4384--4422 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4374 AATGAGACAC
4384 CAATAAG-CAACAACTATGA
1 CAATAAGTCAACAACTATGA
*
4403 CAATAAGTCAATAACTATGA
1 CAATAAGTCAACAACTATGA
4423 AAAGAAGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.51, C:0.18, G:0.10, T:0.21
Consensus pattern (20 bp):
CAATAAGTCAACAACTATGA
Done.