Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011372.1 Corchorus capsularis cultivar CVL-1 contig11393, 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: 14115
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Found at i:31 original size:20 final size:20
Alignment explanation
Indices: 3--70 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
1 TA
*
3 AAAGTAAAAGAGTAATCAGT
1 AAAGAAAAAGAGTAATCAGT
* **
23 AAAGAAAAAGGGTAAAGAGT
1 AAAGAAAAAGAGTAATCAGT
*
43 AAAG-AGAAGAGTAATCAGT
1 AAAGAAAAAGAGTAATCAGT
62 AAAGAAAAA
1 AAAGAAAAA
71 TGGTAAAGGG
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
19 15 0.39
20 23 0.61
ACGTcount: A:0.60, C:0.03, G:0.24, T:0.13
Consensus pattern (20 bp):
AAAGAAAAAGAGTAATCAGT
Found at i:79 original size:46 final size:47
Alignment explanation
Indices: 29--121 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 47
19 CAGTAAAGAA
*
29 AAAGGGTAAAGAGTAAAG-AGAAGAGTAATCAGTAAAG-AAAAATGGT
1 AAAGGGTAAAGAGTAAAGTA-AAGAGTAATCAATAAAGAAAAAATGGT
* *
75 AAAGGGTAAATAGTAGAGTAAAGAGTAATCAATAAAGAAAAAATGGT
1 AAAGGGTAAAGAGTAAAGTAAAGAGTAATCAATAAAGAAAAAATGGT
122 GAAGAGTGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
46 32 0.76
47 10 0.24
ACGTcount: A:0.55, C:0.02, G:0.26, T:0.17
Consensus pattern (47 bp):
AAAGGGTAAAGAGTAAAGTAAAGAGTAATCAATAAAGAAAAAATGGT
Found at i:83 original size:20 final size:19
Alignment explanation
Indices: 20--84 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
10 AAGAGTAATC
20 AGTAAAGAAAAAGGGTAAAG
1 AGTAAAGAAAAA-GGTAAAG
* **
40 AGTAAAG-AGAAGAGTAATC
1 AGTAAAGAAAAAG-GTAAAG
59 AGTAAAGAAAAATGGTAAAG
1 AGTAAAGAAAAA-GGTAAAG
*
79 GGTAAA
1 AGTAAA
85 TAGTAGAGTA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
18 1 0.03
19 14 0.40
20 19 0.54
21 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.28, T:0.14
Consensus pattern (19 bp):
AGTAAAGAAAAAGGTAAAG
Found at i:102 original size:39 final size:39
Alignment explanation
Indices: 10--95 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 39
1 TAAAAGTAA
10 AAGAGTAATCAGTAAAGAAAAAGGGTAAAGAGTAAAGAG
1 AAGAGTAATCAGTAAAGAAAAAGGGTAAAGAGTAAAGAG
* * *
49 AAGAGTAATCAGTAAAGAAAAATGGTAAAGGGTAAATAG
1 AAGAGTAATCAGTAAAGAAAAAGGGTAAAGAGTAAAGAG
*
88 TAGAGTAA
1 AAGAGTAA
96 AGAGTAATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.55, C:0.02, G:0.27, T:0.16
Consensus pattern (39 bp):
AAGAGTAATCAGTAAAGAAAAAGGGTAAAGAGTAAAGAG
Found at i:159 original size:34 final size:35
Alignment explanation
Indices: 89--200 Score: 122
Period size: 35 Copynumber: 3.2 Consensus size: 35
79 GGTAAATAGT
* *
89 AGAGTAAAGAGTAAT-CAATAAAGAAAAAATGGTGA
1 AGAGTAAAGAGGAATCCAGTAAAG-AAAAATGGTGA
* *
124 AGAGTGAAG-GGAAGT-CAGTAAAGAAGAATGGTGA
1 AGAGTAAAGAGGAA-TCCAGTAAAGAAAAATGGTGA
* *
158 AGAGTAAAGAGTAATCCAGTAAAGAAAAATGGTAA
1 AGAGTAAAGAGGAATCCAGTAAAGAAAAATGGTGA
*
193 AAAGTAAA
1 AGAGTAAA
201 ATATTAATCA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
34 22 0.34
35 43 0.66
ACGTcount: A:0.54, C:0.04, G:0.27, T:0.16
Consensus pattern (35 bp):
AGAGTAAAGAGGAATCCAGTAAAGAAAAATGGTGA
Found at i:213 original size:35 final size:34
Alignment explanation
Indices: 91--215 Score: 117
Period size: 35 Copynumber: 3.6 Consensus size: 34
81 TAAATAGTAG
* * *
91 AGTAAAGAGTAATCAATAAAGAAAAAATGGTGAAG
1 AGTAAAGAGTAATCAGTAAAG-AAAAATGGTAAAA
* * * * *
126 AGTGAAG-GGAAGTCAGTAAAGAAGAATGGTGAAG
1 AGTAAAGAGTAA-TCAGTAAAGAAAAATGGTAAAA
160 AGTAAAGAGTAATCCAGTAAAGAAAAATGGTAAAA
1 AGTAAAGAGTAAT-CAGTAAAGAAAAATGGTAAAA
* *
195 AGTAAAATATTAATCAGTAAA
1 AGT-AAAGAGTAATCAGTAAA
216 AAGTAATGGC
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
34 22 0.29
35 45 0.60
36 8 0.11
ACGTcount: A:0.54, C:0.04, G:0.24, T:0.18
Consensus pattern (34 bp):
AGTAAAGAGTAATCAGTAAAGAAAAATGGTAAAA
Found at i:278 original size:21 final size:20
Alignment explanation
Indices: 254--305 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
244 TGGTAACTAG
254 TAATCAGTACAA-AGTAAAGAA
1 TAATCAGTA-AATAGTAAAG-A
*
275 TAATCAGTGAAATAGTAATGA
1 TAATCAGT-AAATAGTAAAGA
296 TAATCAGTAA
1 TAATCAGTAA
306 TTCAGTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.07
21 19 0.68
22 7 0.25
ACGTcount: A:0.52, C:0.08, G:0.15, T:0.25
Consensus pattern (20 bp):
TAATCAGTAAATAGTAAAGA
Found at i:8438 original size:11 final size:11
Alignment explanation
Indices: 8422--8450 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
8412 TATTAAGAAG
8422 TCCGTAGTTAT
1 TCCGTAGTTAT
8433 TCCGTAGTTAT
1 TCCGTAGTTAT
8444 TCCGTAG
1 TCCGTAG
8451 CTAAGTCCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (11 bp):
TCCGTAGTTAT
Done.