Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018573.1 Corchorus olitorius cultivar O-4 contig18606, 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: 15888
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Found at i:1540 original size:22 final size:22
Alignment explanation
Indices: 1510--1561 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1500 AATGCTTTCC
*
1510 TCTTGAAATAATTCTTC-AATAG
1 TCTTCAAATAA-TCTTCAAATAG
*
1532 TCTTCAAATTATCTTCAAATAG
1 TCTTCAAATAATCTTCAAATAG
1554 TCTTCAAA
1 TCTTCAAA
1562 CACGAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAAATAG
Found at i:1546 original size:11 final size:11
Alignment explanation
Indices: 1522--1561 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
1512 TTGAAATAAT
1522 TCTTC-AATAG
1 TCTTCAAATAG
1532 TCTTCAAATTA-
1 TCTTCAAA-TAG
1543 TCTTCAAATAG
1 TCTTCAAATAG
1554 TCTTCAAA
1 TCTTCAAA
1562 CACGAACTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 7 0.26
11 18 0.67
12 2 0.07
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAG
Found at i:4984 original size:11 final size:11
Alignment explanation
Indices: 4970--5001 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
4960 GAAGACTCAA
4970 AGAAGAAAAAG
1 AGAAGAAAAAG
4981 AGAAGAAAAAG
1 AGAAGAAAAAG
*
4992 AAAAGAAAAA
1 AGAAGAAAAA
5002 AAGGAAGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AGAAGAAAAAG
Found at i:4986 original size:14 final size:14
Alignment explanation
Indices: 4969--5016 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 14
4959 GGAAGACTCA
4969 AAGAAG-AAAA-AG
1 AAGAAGAAAAAGAG
*
4981 -AGAAGAAAAAGAA
1 AAGAAGAAAAAGAG
4994 AAGAA-AAAAAG-G
1 AAGAAGAAAAAGAG
5006 AAGAAGAAAAA
1 AAGAAGAAAAA
5017 TGTTTCAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
11 5 0.17
12 9 0.30
13 12 0.40
14 4 0.13
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AAGAAGAAAAAGAG
Found at i:6219 original size:35 final size:34
Alignment explanation
Indices: 6190--6403 Score: 189
Period size: 35 Copynumber: 6.1 Consensus size: 34
6180 TTAAGTAGAC
*
6190 CAGTAGTTAACTTAATTCAGGGTAATTAAGTAAAT
1 CAGTAG-TAACTTAATTCAGGGTAATTAAGTAAGT
* * * *
6225 CAGTAGTCAATTTAGTTTAGGGTAATTAAGTAAAGG
1 CAGTAGT-AACTTAATTCAGGGTAATTAAGT-AAGT
* *
6261 CAGTTAGTAACTTAGTTCCGGGTAATTAAGTAAGT
1 CAG-TAGTAACTTAATTCAGGGTAATTAAGTAAGT
* * *
6296 TAGTGAGTAACTTAATTCAGAGTAATTAAGCAAGT
1 CAGT-AGTAACTTAATTCAGGGTAATTAAGTAAGT
* * *
6331 CGGTAAATAACTTAATTCAGGGTAATTAAGTGAGT
1 CAGT-AGTAACTTAATTCAGGGTAATTAAGTAAGT
** * * *
6366 CA-TAACCAATTTAATTCAGTGTAA-TAAATAAGT
1 CAGT-AGTAACTTAATTCAGGGTAATTAAGTAAGT
6399 CAGTA
1 CAGTA
6404 ATTGGCTTAT
Statistics
Matches: 146, Mismatches: 28, Indels: 12
0.78 0.15 0.06
Matches are distributed among these distances:
33 10 0.07
34 21 0.14
35 86 0.59
36 25 0.17
37 4 0.03
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (34 bp):
CAGTAGTAACTTAATTCAGGGTAATTAAGTAAGT
Found at i:6321 original size:71 final size:70
Alignment explanation
Indices: 6197--6361 Score: 188
Period size: 71 Copynumber: 2.3 Consensus size: 70
6187 GACCAGTAGT
* * * *
6197 TAACTTAATTCAGGGTAATTAAGTAAATCAGTAGTCAATTTAGTTTAGGGTAATTAAGTAAAGGC
1 TAACTTAATTCAGGGTAATTAAGTAAATCAGTAGTCAACTTAATTCAGAGTAATTAAG-AAAGGC
* *
6262 AGTTAG
65 AGTAAA
* * * * * *
6268 TAACTTAGTTCCGGGTAATTAAGTAAGTTAGTGAGT-AACTTAATTCAGAGTAATTAAGCAAGTC
1 TAACTTAATTCAGGGTAATTAAGTAAATCAGT-AGTCAACTTAATTCAGAGTAATTAAGAAAGGC
*
6332 GGTAAA
65 AGTAAA
6338 TAACTTAATTCAGGGTAATTAAGT
1 TAACTTAATTCAGGGTAATTAAGT
6362 GAGTCATAAC
Statistics
Matches: 78, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
70 29 0.37
71 46 0.59
72 3 0.04
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (70 bp):
TAACTTAATTCAGGGTAATTAAGTAAATCAGTAGTCAACTTAATTCAGAGTAATTAAGAAAGGCA
GTAAA
Done.