Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022153.1 Corchorus olitorius cultivar O-4 contig22186, 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: 7699
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Found at i:3385 original size:27 final size:28
Alignment explanation
Indices: 3355--3431 Score: 93
Period size: 29 Copynumber: 2.8 Consensus size: 28
3345 AAATGAACCT
* *
3355 AAAATGACCAAAATGCCCTTAG-ACGTA
1 AAAATGACCAAAATGCCCCTAGAACGCA
* *
3382 AAAATGACTAAAATGCCCCTAGATATGCA
1 AAAATGACCAAAATGCCCCTAGA-ACGCA
*
3411 AAAATGACCAAAATCCCCCTA
1 AAAATGACCAAAATGCCCCTA
3432 AATGACCTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 20 0.48
29 22 0.52
ACGTcount: A:0.45, C:0.25, G:0.12, T:0.18
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTAGAACGCA
Found at i:6267 original size:6 final size:6
Alignment explanation
Indices: 6256--6318 Score: 58
Period size: 6 Copynumber: 10.3 Consensus size: 6
6246 AAAAGAGAGG
* * *
6256 AAAGAA AAAGAA AAAGGAA AAGGAA AAAGGAA AAGGAA AAA-AA AAGGAA
1 AAAGAA AAAGAA AAA-GAA AAAGAA AAA-GAA AAAGAA AAAGAA AAAGAA
6305 AAGAGAA AAA-AA AA
1 AA-AGAA AAAGAA AA
6319 TATTAATAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
5 8 0.17
6 24 0.51
7 15 0.32
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:6281 original size:13 final size:13
Alignment explanation
Indices: 6259--6306 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
6249 AGAGAGGAAA
*
6259 GAAAAAGAAAAAG
1 GAAAAGGAAAAAG
6272 GAAAAGGAAAAAG
1 GAAAAGGAAAAAG
6285 GAAAAGGAAAAA-
1 GAAAAGGAAAAAG
6297 -AAAAGGAAAA
1 GAAAAGGAAAA
6307 GAGAAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
11 10 0.29
13 24 0.71
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (13 bp):
GAAAAGGAAAAAG
Found at i:6283 original size:19 final size:18
Alignment explanation
Indices: 6260--6318 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 18
6250 GAGAGGAAAG
* *
6260 AAAAAGAAAAAGGAAAAGG
1 AAAAAGGAAAAGGAAAA-A
6279 AAAAAGGAAAAGG-AAAA
1 AAAAAGGAAAAGGAAAAA
6296 AAAAAGGAAAAGAGAAAAA
1 AAAAAGGAAAAG-GAAAAA
6315 AAAA
1 AAAA
6319 TATTAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
17 12 0.33
18 4 0.11
19 20 0.56
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (18 bp):
AAAAAGGAAAAGGAAAAA
Found at i:6313 original size:13 final size:13
Alignment explanation
Indices: 6256--6313 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
6246 AAAAGAGAGG
*
6256 AAAGA-AAAAGAA
1 AAAGAGAAAAGGA
6268 AAAG-GAAAAGGA
1 AAAGAGAAAAGGA
6280 AAA-AGGAAAAGGA
1 AAAGA-GAAAAGGA
6293 AAA-A-AAAAGGA
1 AAAGAGAAAAGGA
6304 AAAGAGAAAA
1 AAAGAGAAAA
6314 AAAAATATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
11 10 0.25
12 14 0.35
13 16 0.40
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAGAGAAAAGGA
Found at i:7528 original size:13 final size:13
Alignment explanation
Indices: 7498--7550 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 13
7488 CCCGTTGAGG
7498 AAATG-TTT-TAT
1 AAATGCTTTATAT
*
7509 AACTGCTTTATAT
1 AAATGCTTTATAT
7522 AAATGCTTTATA-
1 AAATGCTTTATAT
*
7534 AAATGTTTTA-AT
1 AAATGCTTTATAT
7546 AAATG
1 AAATG
7551 TTTTGGGTGC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 5 0.14
12 17 0.47
13 14 0.39
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (13 bp):
AAATGCTTTATAT
Done.