Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014684.1 Corchorus capsularis cultivar CVL-1 contig14705, 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: 20403
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5025 original size:14 final size:15
Alignment explanation
Indices: 5006--5039 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
4996 TGGTCCACTC
5006 GATGTTTACTTTTG-
1 GATGTTTACTTTTGT
5020 GATGTTTACTTTTGT
1 GATGTTTACTTTTGT
5035 GATGT
1 GATGT
5040 GGCAAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.15, C:0.06, G:0.24, T:0.56
Consensus pattern (15 bp):
GATGTTTACTTTTGT
Found at i:9994 original size:10 final size:10
Alignment explanation
Indices: 9979--10003 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9969 ATTTGATAGC
9979 AATATATGAA
1 AATATATGAA
9989 AATATATGAA
1 AATATATGAA
9999 AATAT
1 AATAT
10004 GAAATTGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (10 bp):
AATATATGAA
Found at i:10938 original size:21 final size:20
Alignment explanation
Indices: 10914--10956 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
10904 TAAAAACTCA
*
10914 ATAATTGTAATTAATCACAAT
1 ATAATTATAATTAATCA-AAT
*
10935 ATAATTATAATTATTCAAAT
1 ATAATTATAATTAATCAAAT
10955 AT
1 AT
10957 CAAAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (20 bp):
ATAATTATAATTAATCAAAT
Found at i:11472 original size:26 final size:26
Alignment explanation
Indices: 11443--11515 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
11433 TAAGCAAAAT
*
11443 TATATATATTATTTTTATTTAAATTA
1 TATATATATTATTTTTATTTAAAGTA
* *
11469 TATATATATTATATTATATATAAAGTA
1 TATATATATTAT-TTTTATTTAAAGTA
* *
11496 T-TTTAAATTATTTTCTATTT
1 TATATATATTATTTT-TATTT
11516 TCTAATAATC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 2 0.05
26 24 0.63
27 12 0.32
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (26 bp):
TATATATATTATTTTTATTTAAAGTA
Found at i:12391 original size:21 final size:20
Alignment explanation
Indices: 12354--12392 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12344 GAAGCAATTA
*
12354 ATTAATTAAAAGCATTAAAC
1 ATTAATTAAAAACATTAAAC
12374 ATTAATTAAAAACAATTAA
1 ATTAATTAAAAAC-ATTAA
12393 GGAAGAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (20 bp):
ATTAATTAAAAACATTAAAC
Found at i:12574 original size:2 final size:2
Alignment explanation
Indices: 12567--12595 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12557 GTTAAAAATA
12567 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 A
12596 AGACTCGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14043 original size:19 final size:18
Alignment explanation
Indices: 14009--14050 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
13999 AATTAATTAT
14009 TTTAATATTAACTTTTTA
1 TTTAATATTAACTTTTTA
14027 TTTATATATTATA-TTTTTA
1 TTTA-ATATTA-ACTTTTTA
*
14046 CTTAA
1 TTTAA
14051 AAATTACTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.24
19 15 0.71
20 1 0.05
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAATATTAACTTTTTA
Done.