Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011335.1 Corchorus capsularis cultivar CVL-1 contig11356, 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: 25854
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:6026 original size:13 final size:13
Alignment explanation
Indices: 6008--6043 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
5998 ATTAACAAAG
6008 CAAATCATAATCA
1 CAAATCATAATCA
*
6021 CAAATCATGATCA
1 CAAATCATAATCA
6034 CAAAT-ATAAT
1 CAAATCATAAT
6044 ATGAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.53, C:0.19, G:0.03, T:0.25
Consensus pattern (13 bp):
CAAATCATAATCA
Found at i:7636 original size:17 final size:19
Alignment explanation
Indices: 7603--7642 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
7593 TGCTGGCATT
7603 TTTTGTATTTTTCTTTT-A
1 TTTTGTATTTTTCTTTTAA
7621 TTTT-TATTTATT-TTTTAA
1 TTTTGTATTT-TTCTTTTAA
7639 TTTT
1 TTTT
7643 CATGGTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.80
Consensus pattern (19 bp):
TTTTGTATTTTTCTTTTAA
Found at i:13130 original size:3 final size:3
Alignment explanation
Indices: 13122--13154 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
13112 GTTCCTTGTA
13122 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
13155 TGGCATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:23879 original size:32 final size:32
Alignment explanation
Indices: 23818--23956 Score: 178
Period size: 32 Copynumber: 4.4 Consensus size: 32
23808 ACAGTGTCCG
23818 ACGTGGCACGCCACGTGTAT-AAAAAAGTGAC
1 ACGTGGCACGCCACGTGTATCAAAAAAGTGAC
*
23849 ATGTGGCACGCCACGTGTATCAAAAAAGTGAC
1 ACGTGGCACGCCACGTGTATCAAAAAAGTGAC
*
23881 ACGTGTCACGCCACGTGTA-CAAAAAAAGTGAC
1 ACGTGGCACGCCACGTGTATC-AAAAAAGTGAC
* * *
23913 ACGTGGCATGCCATGTGTA-CCAAAAA-TGAC
1 ACGTGGCACGCCACGTGTATCAAAAAAGTGAC
* *
23943 ACGTGACATGCCAC
1 ACGTGGCACGCCAC
23957 ATGCACAAAA
Statistics
Matches: 97, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
30 16 0.16
31 25 0.26
32 56 0.58
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (32 bp):
ACGTGGCACGCCACGTGTATCAAAAAAGTGAC
Found at i:24556 original size:14 final size:14
Alignment explanation
Indices: 24539--24568 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
24529 TGACTTTACG
24539 AACAATTATTCATA
1 AACAATTATTCATA
24553 AACAATTATTCATA
1 AACAATTATTCATA
24567 AA
1 AA
24569 GTTACCTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (14 bp):
AACAATTATTCATA
Found at i:25435 original size:2 final size:2
Alignment explanation
Indices: 25282--25419 Score: 64
Period size: 2 Copynumber: 74.5 Consensus size: 2
25272 TAGAAATTTT
* * * *
25282 TA TA TA -A TA TA TA TA TT TA -A AA TA TA T- TA TA TA TA TG TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
25321 TT TA T- TA TA TA TA AA TA TA TA TA AA TT TA -A AA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
25360 TA TA TA T- TA TA AA TA TA T- TT TC TA TA AA TA TA TT TA -A AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25399 TA TA T- TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
25420 GTTTTTATTA
Statistics
Matches: 103, Mismatches: 22, Indels: 22
0.70 0.15 0.15
Matches are distributed among these distances:
1 11 0.11
2 92 0.89
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Done.