Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004965.1 Corchorus capsularis cultivar CVL-1 contig04983, 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: 8043
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:205 original size:9 final size:9
Alignment explanation
Indices: 191--240 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
181 TTAAAAATAC
191 AAATGTTAT
1 AAATGTTAT
*
200 AAATGTTCT
1 AAATGTTAT
209 AAATGTTAT
1 AAATGTTAT
*
218 ACATGTTAT
1 AAATGTTAT
*
227 AAGTGTTAT
1 AAATGTTAT
236 AAATG
1 AAATG
241 ATAGAACAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.42
Consensus pattern (9 bp):
AAATGTTAT
Found at i:481 original size:17 final size:17
Alignment explanation
Indices: 459--491 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
449 TCATGTAAAG
459 CCTAAACAAGTTTTAAT
1 CCTAAACAAGTTTTAAT
476 CCTAAACAAGTTTTAA
1 CCTAAACAAGTTTTAA
492 AGCAACTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.33
Consensus pattern (17 bp):
CCTAAACAAGTTTTAAT
Found at i:2263 original size:36 final size:36
Alignment explanation
Indices: 2203--2277 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
2193 TGATCAAGAC
* * * *
2203 GAATCTGAGCCTCTCTCTGAAGCTCTCTCTCCCTTT
1 GAATATGAACCTCCCTCTGAAGCTCTCTCTCCCTCT
2239 GAATATGAACCTCCCTCTGAAGCTCTCTCTCCCTCT
1 GAATATGAACCTCCCTCTGAAGCTCTCTCTCCCTCT
2275 GAA
1 GAA
2278 GCTCAGCCTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.19, C:0.36, G:0.13, T:0.32
Consensus pattern (36 bp):
GAATATGAACCTCCCTCTGAAGCTCTCTCTCCCTCT
Found at i:2270 original size:18 final size:18
Alignment explanation
Indices: 2217--2281 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
2207 CTGAGCCTCT
2217 CTCTGAAGCTCTCTCTCC
1 CTCTGAAGCTCTCTCTCC
* ** **
2235 CTTTGAATATGAAC-CTCC
1 CTCTGAAGCT-CTCTCTCC
2253 CTCTGAAGCTCTCTCTCC
1 CTCTGAAGCTCTCTCTCC
2271 CTCTGAAGCTC
1 CTCTGAAGCTC
2282 AGCCTCTCTC
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
17 1 0.03
18 33 0.94
19 1 0.03
ACGTcount: A:0.17, C:0.38, G:0.12, T:0.32
Consensus pattern (18 bp):
CTCTGAAGCTCTCTCTCC
Found at i:2292 original size:18 final size:17
Alignment explanation
Indices: 2248--2292 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
2238 TGAATATGAA
*
2248 CCTCCCTCTGAAGCTCT
1 CCTCCCTCTGAAGCTCG
2265 CTCTCCCTCTGAAGCTCAG
1 C-CTCCCTCTGAAGCTC-G
*
2284 CCTCTCTCT
1 CCTCCCTCT
2293 CCCTGTGGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.11, C:0.47, G:0.11, T:0.31
Consensus pattern (17 bp):
CCTCCCTCTGAAGCTCG
Found at i:2440 original size:18 final size:18
Alignment explanation
Indices: 2417--2460 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2407 ATTAATCGTA
2417 AATAAACTAATTAAAACT
1 AATAAACTAATTAAAACT
* **
2435 AATAAAATAATTAACCCT
1 AATAAACTAATTAAAACT
2453 AATAAACT
1 AATAAACT
2461 TCCCTAAATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (18 bp):
AATAAACTAATTAAAACT
Found at i:2499 original size:7 final size:7
Alignment explanation
Indices: 2487--2524 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
2477 AATGTTACTT
2487 AATTCAA
1 AATTCAA
2494 AATTCAA
1 AATTCAA
*
2501 AATTTAA
1 AATTCAA
*
2508 ATTTCAA
1 AATTCAA
2515 AATTCAA
1 AATTCAA
2522 AAT
1 AAT
2525 AAATTAATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (7 bp):
AATTCAA
Found at i:8010 original size:2 final size:2
Alignment explanation
Indices: 8003--8043 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
7993 TCGTTATAGA
8003 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.