Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012691.1 Corchorus olitorius cultivar O-4 contig12724, 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: 27022
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:871 original size:15 final size:15
Alignment explanation
Indices: 840--881 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
830 TTACTTTGCT
*
840 TTGTTTTCTACTTTAA
1 TTGTTTTCT-GTTTAA
856 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
871 TTGCTTTCTGT
1 TTGTTTTCTGT
882 CAATCTCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:2610 original size:17 final size:17
Alignment explanation
Indices: 2590--2623 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2580 ATCTTTTTGG
2590 TTTTTTGTG-TTTTTGAA
1 TTTTTTG-GATTTTTGAA
2607 TTTTTTGGATTTTTGAA
1 TTTTTTGGATTTTTGAA
2624 ACCTTCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 15 0.94
ACGTcount: A:0.15, C:0.00, G:0.18, T:0.68
Consensus pattern (17 bp):
TTTTTTGGATTTTTGAA
Found at i:8406 original size:2 final size:2
Alignment explanation
Indices: 8399--8425 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8389 ATTAAACAAT
8399 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
8426 TAAGCATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10295 original size:13 final size:14
Alignment explanation
Indices: 10277--10326 Score: 52
Period size: 13 Copynumber: 3.7 Consensus size: 14
10267 AGTTAGTAAC
10277 AAAAATTCAAAA-T
1 AAAAATTCAAAATT
*
10290 AAAAA-TGAAAATT
1 AAAAATTCAAAATT
10303 AAAAATT-AAGAATT
1 AAAAATTCAA-AATT
*
10317 AGAAATTCAA
1 AAAAATTCAA
10327 TTGGGTTGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 5 0.16
13 13 0.42
14 11 0.35
15 2 0.06
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.24
Consensus pattern (14 bp):
AAAAATTCAAAATT
Found at i:11535 original size:15 final size:16
Alignment explanation
Indices: 11515--11549 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
11505 TTTAAAAATC
11515 ACAATTAAA-AAGAAA
1 ACAATTAAACAAGAAA
*
11530 ACAATTAAACTAGAAA
1 ACAATTAAACAAGAAA
11546 ACAA
1 ACAA
11550 AACAAAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.69, C:0.11, G:0.06, T:0.14
Consensus pattern (16 bp):
ACAATTAAACAAGAAA
Found at i:12953 original size:29 final size:30
Alignment explanation
Indices: 12916--12975 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
12906 CAATTCTTGC
*
12916 TCTTAAAATAATTCTTCAAT-GTCTTCAAA
1 TCTTAAAATAAGTCTTCAATAGTCTTCAAA
*
12945 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA
1 TCTTAAAATAAGTCTTCAAT-AGTCTTCAAA
12976 CACGAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 18 0.67
31 9 0.33
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (30 bp):
TCTTAAAATAAGTCTTCAATAGTCTTCAAA
Found at i:14819 original size:21 final size:21
Alignment explanation
Indices: 14793--14845 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
14783 AAATTTCAAA
14793 GGTGATGGCACGGGCTTAACC
1 GGTGATGGCACGGGCTTAACC
14814 GGTGATGGCACGGGCTTAACC
1 GGTGATGGCACGGGCTTAACC
*
14835 GGTGGTGGCAC
1 GGTGATGGCAC
14846 TGTGAATGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.17, C:0.23, G:0.42, T:0.19
Consensus pattern (21 bp):
GGTGATGGCACGGGCTTAACC
Found at i:18332 original size:15 final size:16
Alignment explanation
Indices: 18312--18346 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
18302 TTTAAAAATC
18312 ACAATTAAA-AAGAAA
1 ACAATTAAACAAGAAA
*
18327 ACAATTAAACTAGAAA
1 ACAATTAAACAAGAAA
18343 ACAA
1 ACAA
18347 AGCAAAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.69, C:0.11, G:0.06, T:0.14
Consensus pattern (16 bp):
ACAATTAAACAAGAAA
Found at i:19752 original size:29 final size:30
Alignment explanation
Indices: 19715--19774 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
19705 CAATTCTTGC
*
19715 TCTTAAAATAATTCTTCAAT-GTCTTCAAA
1 TCTTAAAATAAGTCTTCAATAGTCTTCAAA
*
19744 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA
1 TCTTAAAATAAGTCTTCAAT-AGTCTTCAAA
19775 CACGAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 18 0.67
31 9 0.33
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (30 bp):
TCTTAAAATAAGTCTTCAATAGTCTTCAAA
Done.