Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012569.1 Corchorus olitorius cultivar O-4 contig12602, 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: 20142
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:79 original size:28 final size:27
Alignment explanation
Indices: 31--85 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
21 TTTTTATTTG
*
31 AGTTTGTTTTTGAGTCGGTTT-GAGTC
1 AGTTTGTTTTTGAGTCAGTTTCGAGTC
57 AGTTTGTTTTTTCGAGTCAGTTTCGAGTC
1 AGTTTG-TTTTT-GAGTCAGTTTCGAGTC
86 TAGTCTCAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 6 0.24
27 5 0.20
28 9 0.36
29 5 0.20
ACGTcount: A:0.13, C:0.11, G:0.27, T:0.49
Consensus pattern (27 bp):
AGTTTGTTTTTGAGTCAGTTTCGAGTC
Found at i:2294 original size:58 final size:58
Alignment explanation
Indices: 2198--2307 Score: 168
Period size: 58 Copynumber: 1.9 Consensus size: 58
2188 ATTAATCAAA
*
2198 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCAAAACT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAAACT
* * *
2256 TATCGAGTGACATGTTTTTTTATTAGATGCCT-AAAAAAGACGTTTTAGGACC
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACC
2308 GAGGCATGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
58 32 0.68
59 15 0.32
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAAACT
Found at i:4524 original size:202 final size:203
Alignment explanation
Indices: 4126--4537 Score: 720
Period size: 203 Copynumber: 2.0 Consensus size: 203
4116 GCTTAATAAC
*
4126 TTTATGAATGATGAATGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAGTAAATAA
1 TTTATCAATGATGAATGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAGTAAATAA
* *
4191 GATACAACACATTATTATTATTATATATAACTATAACAAAAAAAAGTAGTTGAACATTAGTGGTT
66 GATACAACACATTACTATTATTATATAGAACTATAACAAAAAAAAGTAGTTGAACATTAGTGGTT
*
4256 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
131 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAAATATTAAAGAT
4321 CCGATTTA
196 CCGATTTA
* *
4329 TTTATCAATGGTGAATGTTATTAATTT-TTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGATGAATGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAGTAAATAA
* **
4393 GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAATTTAGTTGAACATTAGTGGT
66 GATACAACACATTACTATTAT-TATATAGAACTATAACAAAAAAAAGTAGTTGAACATTAGTGGT
4458 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAAATATT-AAGA
130 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAAATATTAAAGA
4522 TCCGATTTA
195 TCCGATTTA
4531 TTTATCA
1 TTTATCA
4538 TTAAGGAAAC
Statistics
Matches: 199, Mismatches: 9, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
202 76 0.38
203 123 0.62
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (203 bp):
TTTATCAATGATGAATGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAGTAAATAA
GATACAACACATTACTATTATTATATAGAACTATAACAAAAAAAAGTAGTTGAACATTAGTGGTT
GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAAATATTAAAGAT
CCGATTTA
Found at i:6886 original size:27 final size:29
Alignment explanation
Indices: 6838--6895 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 29
6828 ACACATATTT
6838 ATTTTTTAAAATAAAATAATAATAA-TTAA
1 ATTTTTTAAAATAAAATAATAA-AATTTAA
* *
6867 ATTTTTT-TAATAAAA-CATAAAATTTAA
1 ATTTTTTAAAATAAAATAATAAAATTTAA
6894 AT
1 AT
6896 ATTAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 2 0.08
27 10 0.38
28 7 0.27
29 7 0.27
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (29 bp):
ATTTTTTAAAATAAAATAATAAAATTTAA
Found at i:7046 original size:29 final size:30
Alignment explanation
Indices: 6988--7048 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
6978 ATTCTAATTA
* *
6988 ATGTATACATATAAATTATTCAATTTTATT
1 ATGTATAAATATAAATTATTCAATTATATT
*
7018 ATGTATAAATAT-AATTATTTAATTATATT
1 ATGTATAAATATAAATTATTCAATTATATT
7047 AT
1 AT
7049 ATTATATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (30 bp):
ATGTATAAATATAAATTATTCAATTATATT
Found at i:7894 original size:26 final size:26
Alignment explanation
Indices: 7837--7896 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
7827 AATTTGGAAG
* *
7837 ATTAAATTACTTTGCAATATCTTCTA
1 ATTAATTTACTTTGCAATATCTTCCA
7863 ATTAATTTACTTTGCAATATCTTCCA
1 ATTAATTTACTTTGCAATATCTTCCA
7889 ATTAATTT
1 ATTAATTT
7897 TGTGTAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.48
Consensus pattern (26 bp):
ATTAATTTACTTTGCAATATCTTCCA
Found at i:10970 original size:29 final size:30
Alignment explanation
Indices: 10938--10996 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
10928 ATTTAGGTTT
*
10938 AAACCTTTTAT-TTCGTCCAATTTGGTACC
1 AAACCTTTTATAATCGTCCAATTTGGTACC
*
10967 AAACCTTTTATAAATGGTCCAATTTGGTAC
1 AAACCTTTTAT-AATCGTCCAATTTGGTAC
10997 TTTTTTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 11 0.42
31 15 0.58
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (30 bp):
AAACCTTTTATAATCGTCCAATTTGGTACC
Found at i:11589 original size:15 final size:15
Alignment explanation
Indices: 11569--11598 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
11559 TTTTTTATGG
11569 GTTTTCTGGGTTTGT
1 GTTTTCTGGGTTTGT
11584 GTTTTCTGGGTTTGT
1 GTTTTCTGGGTTTGT
11599 TCTATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.33, T:0.60
Consensus pattern (15 bp):
GTTTTCTGGGTTTGT
Found at i:12360 original size:18 final size:18
Alignment explanation
Indices: 12339--12380 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
12329 GAGGTTGAAA
*
12339 ATGATGTTCAGAGT-GAGG
1 ATGAAGTTCAG-GTGGAGG
*
12357 ATGAAGTTGAGGTGGAGG
1 ATGAAGTTCAGGTGGAGG
12375 ATGAAG
1 ATGAAG
12381 CTGTCGATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.31, C:0.02, G:0.43, T:0.24
Consensus pattern (18 bp):
ATGAAGTTCAGGTGGAGG
Done.