Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007492.1 Corchorus olitorius cultivar O-4 contig07517, 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: 4528
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:185 original size:7 final size:7
Alignment explanation
Indices: 173--205 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
163 TTTAATCTCT
173 ATTATAC
1 ATTATAC
180 ATTATAC
1 ATTATAC
187 ATTATAC
1 ATTATAC
194 ATTATAC
1 ATTATAC
201 ATTAT
1 ATTAT
206 TATACATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (7 bp):
ATTATAC
Found at i:236 original size:14 final size:16
Alignment explanation
Indices: 176--240 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 16
166 AATCTCTATT
*
176 ATACAT-TATACAT-T
1 ATACATATATACATAC
*
190 ATACAT-TATACATTATT
1 ATACATATATACA-TA-C
207 ATACATATATACATAC
1 ATACATATATACATAC
223 ATACATA-A-ACATAC
1 ATACATATATACATAC
237 ATAC
1 ATAC
241 TTATGAGTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
14 22 0.48
15 2 0.04
16 7 0.15
17 9 0.20
18 6 0.13
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (16 bp):
ATACATATATACATAC
Found at i:1314 original size:11 final size:11
Alignment explanation
Indices: 1298--1323 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1288 TTAACTTCAG
1298 AAAAAAAAATA
1 AAAAAAAAATA
1309 AAAAAAAAATA
1 AAAAAAAAATA
1320 AAAA
1 AAAA
1324 CTTGAAGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAAAAATA
Found at i:1378 original size:22 final size:23
Alignment explanation
Indices: 1337--1382 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1327 GAAGCATAAA
1337 ATTTCATAAAAAAGTAATAATTT
1 ATTTCATAAAAAAGTAATAATTT
* *
1360 ATTTCATTAAAAA-TTATAATTT
1 ATTTCATAAAAAAGTAATAATTT
1382 A
1 A
1383 CAAATTACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (23 bp):
ATTTCATAAAAAAGTAATAATTT
Found at i:1430 original size:17 final size:19
Alignment explanation
Indices: 1384--1430 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1374 TATAATTTAC
1384 AAATTACA-AATGAAAAAT
1 AAATTACATAATGAAAAAT
*
1402 AATTTAACATAAT-AAAAA-
1 AAATT-ACATAATGAAAAAT
1420 AAATTACATAA
1 AAATTACATAA
1431 AACTACAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 6 0.24
18 8 0.32
19 8 0.32
20 3 0.12
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (19 bp):
AAATTACATAATGAAAAAT
Found at i:3426 original size:21 final size:21
Alignment explanation
Indices: 3400--3439 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3390 ACGTTGGCAT
*
3400 CCATGTTAGCATGTCAGAGTG
1 CCATGTCAGCATGTCAGAGTG
3421 CCATGTCAGCATGTCAGAG
1 CCATGTCAGCATGTCAGAG
3440 CGCGTGTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (21 bp):
CCATGTCAGCATGTCAGAGTG
Done.