Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012637.1 Corchorus capsularis cultivar CVL-1 contig12658, 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: 10225
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:2313 original size:13 final size:14
Alignment explanation
Indices: 2296--2348 Score: 63
Period size: 13 Copynumber: 3.6 Consensus size: 14
2286 CAAGATTTGA
2296 AAAAAAAAAAGAA-
1 AAAAAAAAAAGAAG
*
2309 AAAAAAAAGAGAAG
1 AAAAAAAAAAGAAG
2323 AAGAAAAAAGAAGAAG
1 AA-AAAAAA-AAGAAG
2339 AAAAGAAAAA
1 AAAA-AAAAA
2349 TCTAGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 12 0.35
14 2 0.06
15 9 0.26
16 11 0.32
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGAAG
Found at i:2316 original size:16 final size:16
Alignment explanation
Indices: 2295--2348 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 16
2285 TCAAGATTTG
2295 AAAAAAAAAAAGAAAA
1 AAAAAAAAAAAGAAAA
2311 AAAAAAGAGAAGAAGAAAA
1 AAAAAA-A-AA-AAGAAAA
*
2330 AAGAAGAAGAAAAGAAAA
1 AA-AA-AAAAAAAGAAAA
2348 A
1 A
2349 TCTAGAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
16 6 0.19
17 1 0.03
18 10 0.31
19 11 0.34
20 2 0.06
21 2 0.06
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAGAAAA
Found at i:2329 original size:18 final size:18
Alignment explanation
Indices: 2302--2348 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
2292 TTGAAAAAAA
2302 AAAAGAAAAAAAAA-AGAG
1 AAAAGAAAAAAAAAGA-AG
*
2320 AAGAAGAAAAAAGAAGAAG
1 AA-AAGAAAAAAAAAGAAG
2339 AAAAGAAAAA
1 AAAAGAAAAA
2349 TCTAGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 10 0.38
19 15 0.58
20 1 0.04
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAAAAAGAAG
Found at i:2357 original size:26 final size:26
Alignment explanation
Indices: 2324--2383 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 26
2314 AAAGAGAAGA
*
2324 AGAAAAAAGAAGAAGAAAAG-AAAAATCT
1 AGAAAAAAGAA-AA-AAAGGAAAAAAT-T
*
2352 AGAAAAATGAAAAAAAGGAAAAAATT
1 AGAAAAAAGAAAAAAAGGAAAAAATT
2378 AGAAAA
1 AGAAAA
2384 TTAAAAGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 11 0.38
27 8 0.28
28 10 0.34
ACGTcount: A:0.73, C:0.02, G:0.17, T:0.08
Consensus pattern (26 bp):
AGAAAAAAGAAAAAAAGGAAAAAATT
Found at i:7959 original size:14 final size:14
Alignment explanation
Indices: 7922--7960 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
7912 TTAAATTAAA
*
7922 AAAAAAGGTTTTTC
1 AAAAATGGTTTTTC
*
7936 AAAAGT-GTTTTTC
1 AAAAATGGTTTTTC
7949 AAAAATGGTTTT
1 AAAAATGGTTTT
7961 CGAAATTCGT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.41
Consensus pattern (14 bp):
AAAAATGGTTTTTC
Found at i:8267 original size:19 final size:20
Alignment explanation
Indices: 8235--8280 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
8225 AGAATTTTAA
8235 AAAAAAAATCAAAATCAATT
1 AAAAAAAATCAAAATCAATT
*
8255 AAAAATAAT-AAAATCAATT
1 AAAAAAAATCAAAATCAATT
8274 AAAAAAA
1 AAAAAAA
8281 GAAGAAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAAAAAATCAAAATCAATT
Found at i:8566 original size:12 final size:13
Alignment explanation
Indices: 8538--8566 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
8528 TGGTCAAAAC
8538 TTTTGAAAAGAGT
1 TTTTGAAAAGAGT
8551 TTTTGAAAAGAGT
1 TTTTGAAAAGAGT
8564 TTT
1 TTT
8567 CGGGTTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (13 bp):
TTTTGAAAAGAGT
Found at i:9979 original size:22 final size:22
Alignment explanation
Indices: 9954--10027 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 22
9944 TCCAGGCACA
*
9954 AATTCAGAAACCTCCGGGTGTT
1 AATTCAGAAACCTCCGGGTATT
* * **
9976 AATTCTGATAAGTCCTCCGGGCACA
1 AATTCAGA-AA--CCTCCGGGTATT
10001 AATTCAGAAACCTCCGGGTATT
1 AATTCAGAAACCTCCGGGTATT
10023 AATTC
1 AATTC
10028 TGATAAGTCT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
22 21 0.52
23 2 0.05
24 2 0.05
25 15 0.38
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (22 bp):
AATTCAGAAACCTCCGGGTATT
Found at i:9993 original size:25 final size:25
Alignment explanation
Indices: 9964--10043 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
9954 AATTCAGAAA
*
9964 CCTCCGGGTGTTAATTCTGATAAGT
1 CCTCCGGGTATTAATTCTGATAAGT
* ** *
9989 CCTCCGGGCACAAATTCAGA-AA--
1 CCTCCGGGTATTAATTCTGATAAGT
10011 CCTCCGGGTATTAATTCTGATAAGT
1 CCTCCGGGTATTAATTCTGATAAGT
*
10036 CTTCCGGG
1 CCTCCGGG
10044 CAATTGGTAA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
22 16 0.38
23 2 0.05
24 2 0.05
25 22 0.52
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.29
Consensus pattern (25 bp):
CCTCCGGGTATTAATTCTGATAAGT
Found at i:10006 original size:47 final size:47
Alignment explanation
Indices: 9937--10045 Score: 191
Period size: 47 Copynumber: 2.3 Consensus size: 47
9927 TTTGCATTGG
* *
9937 TAAGTCCTCCAGGCACAAATTCAGAAACCTCCGGGTGTTAATTCTGA
1 TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
9984 TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
1 TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
*
10031 TAAGTCTTCCGGGCA
1 TAAGTCCTCCGGGCA
10046 ATTGGTAAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (47 bp):
TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
Found at i:10203 original size:25 final size:25
Alignment explanation
Indices: 10145--10204 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 25
10135 TTTGCATTGG
10145 TAAGTCCTCCGGGTACAAATTCAGA
1 TAAGTCCTCCGGGTACAAATTCAGA
** *
10170 -AA--CCTCCGGGTATTAATTCTGA
1 TAAGTCCTCCGGGTACAAATTCAGA
10192 TAAGTCCTCCGGG
1 TAAGTCCTCCGGG
10205 CAATGGTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 17 0.59
23 2 0.07
24 2 0.07
25 8 0.28
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (25 bp):
TAAGTCCTCCGGGTACAAATTCAGA
Done.