Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020595.1 Corchorus olitorius cultivar O-4 contig20628, 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: 18202
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:306 original size:37 final size:37
Alignment explanation
Indices: 265--380 Score: 196
Period size: 37 Copynumber: 3.1 Consensus size: 37
255 GGGCCATACG
* * *
265 CTGGCCCGCGCACCAGGCCTGGGCGCTTGGGCTGTGC
1 CTGGCCCGCGCGCCAGGCCTGGGCGCTTGGGCCGCGC
*
302 CTGGCCCGTGCGCCAGGCCTGGGCGCTTGGGCCGCGC
1 CTGGCCCGCGCGCCAGGCCTGGGCGCTTGGGCCGCGC
339 CTGGCCCGCGCGCCAGGCCTGGGCGCTTGGGCCGCGC
1 CTGGCCCGCGCGCCAGGCCTGGGCGCTTGGGCCGCGC
376 CTGGC
1 CTGGC
381 TGGCCCAAGT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 74 1.00
ACGTcount: A:0.03, C:0.41, G:0.42, T:0.14
Consensus pattern (37 bp):
CTGGCCCGCGCGCCAGGCCTGGGCGCTTGGGCCGCGC
Found at i:323 original size:18 final size:18
Alignment explanation
Indices: 300--360 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
290 CTTGGGCTGT
300 GCCTGGCCCGTGCGCCAG
1 GCCTGGCCCGTGCGCCAG
* * *
318 GCCTGGGCGCTTGGGCC-G
1 GCCT-GGCCCGTGCGCCAG
*
336 CGCCTGGCCCGCGCGCCAG
1 -GCCTGGCCCGTGCGCCAG
355 GCCTGG
1 GCCTGG
361 GCGCTTGGGC
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 19 0.58
19 14 0.42
ACGTcount: A:0.03, C:0.43, G:0.43, T:0.11
Consensus pattern (18 bp):
GCCTGGCCCGTGCGCCAG
Found at i:4641 original size:17 final size:18
Alignment explanation
Indices: 4606--4641 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
4596 TTTCTAAAAC
4606 TTTATCTTTTAATAATTT
1 TTTATCTTTTAATAATTT
4624 TTTATC-TTTAA-AATTT
1 TTTATCTTTTAATAATTT
4640 TT
1 TT
4642 CATGTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 5 0.28
18 6 0.33
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATCTTTTAATAATTT
Found at i:14599 original size:22 final size:22
Alignment explanation
Indices: 14571--14614 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
14561 GATTTCCTAT
14571 TATTGTATGATTTATTGTATTA
1 TATTGTATGATTTATTGTATTA
*
14593 TATTGTATTATTTATTGTATTA
1 TATTGTATGATTTATTGTATTA
14615 AGCTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.61
Consensus pattern (22 bp):
TATTGTATGATTTATTGTATTA
Found at i:14613 original size:12 final size:12
Alignment explanation
Indices: 14570--14614 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
14560 AGATTTCCTA
*
14570 TTATTGTATGAT
1 TTATTGTATTAT
14582 TTATTGTATTA-
1 TTATTGTATTAT
14593 -TATTGTATTAT
1 TTATTGTATTAT
14604 TTATTGTATTA
1 TTATTGTATTA
14615 AGCTAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 10 0.33
12 20 0.67
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.62
Consensus pattern (12 bp):
TTATTGTATTAT
Found at i:16089 original size:25 final size:22
Alignment explanation
Indices: 16055--16108 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 22
16045 GTCCTATCTA
16055 GACCCAATAAACCTGTAACCCGAAT
1 GACCCAAT-AA-CT-TAACCCGAAT
* *
16080 GACCCGATAAGTTAACCCGAAT
1 GACCCAATAACTTAACCCGAAT
16102 GACCCAA
1 GACCCAA
16109 GAATATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 16 0.62
23 1 0.04
24 2 0.08
25 7 0.27
ACGTcount: A:0.39, C:0.31, G:0.15, T:0.15
Consensus pattern (22 bp):
GACCCAATAACTTAACCCGAAT
Found at i:18032 original size:131 final size:132
Alignment explanation
Indices: 17897--18152 Score: 460
Period size: 132 Copynumber: 1.9 Consensus size: 132
17887 AATATATTTT
* *
17897 AAAAATTCTAATATATCTAA-TTTTTTTAATTAAATTAGTAAAATGGTAAAAATAAAATAGGTAT
1 AAAAATTCTAATATATATAACTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTAT
* *
17961 AAGGATATTATATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATAAT
66 AAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGAAAAACTATAAAAGTATAAT
18026 TA
131 TA
*
18028 AAAAATTCTAATATATATAACTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTAT
1 AAAAATTCTAATATATATAACTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTAT
18093 AAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGAAAAACTATAAAAGT
66 AAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGAAAAACTATAAAAGT
18153 TTAAACCATG
Statistics
Matches: 119, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
131 19 0.16
132 100 0.84
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.37
Consensus pattern (132 bp):
AAAAATTCTAATATATATAACTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTAT
AAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGAAAAACTATAAAAGTATAAT
TA
Done.