Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011932.1 Corchorus capsularis cultivar CVL-1 contig11953, 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: 19141
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Found at i:3926 original size:33 final size:34
Alignment explanation
Indices: 3861--3930 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
3851 TATGTGACTG
3861 AAATGCAAGAATATTGAGATGCAAAAAAATGCCA
1 AAATGCAAGAATATTGAGATGCAAAAAAATGCCA
*
3895 AAATGCAAGATTATTGAGATGC-AAAAAATGCCA
1 AAATGCAAGAATATTGAGATGCAAAAAAATGCCA
3928 AAA
1 AAA
3931 GTACACATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 14 0.40
34 21 0.60
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (34 bp):
AAATGCAAGAATATTGAGATGCAAAAAAATGCCA
Found at i:8104 original size:18 final size:18
Alignment explanation
Indices: 8062--8097 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
8052 ATGCGGGTTA
*
8062 GAATGATAATGCAATGTC
1 GAATGCTAATGCAATGTC
*
8080 GAATGCTAATGTAATGTC
1 GAATGCTAATGCAATGTC
8098 ATATGCTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (18 bp):
GAATGCTAATGCAATGTC
Found at i:15004 original size:16 final size:16
Alignment explanation
Indices: 14983--15014 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
14973 GTCAAAAATC
*
14983 GTTATTATTTTTTATT
1 GTTATTATTTATTATT
14999 GTTATTATTTATTATT
1 GTTATTATTTATTATT
15015 ATCATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (16 bp):
GTTATTATTTATTATT
Found at i:15009 original size:13 final size:13
Alignment explanation
Indices: 14984--15027 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
14974 TCAAAAATCG
*
14984 TTATTATTTTTTA
1 TTATTATTATTTA
*
14997 TTGTTATTATTTA
1 TTATTATTATTTA
* *
15010 TTATTATCATTTT
1 TTATTATTATTTA
15023 TTATT
1 TTATT
15028 TTTTTTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (13 bp):
TTATTATTATTTA
Found at i:17619 original size:17 final size:19
Alignment explanation
Indices: 17587--17624 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
17577 TGCAAAATGC
*
17587 AAAGCGAAAGAAC-AAAGA
1 AAAGCGAAACAACAAAAGA
17605 AAAGC-AAACAACAAAAGA
1 AAAGCGAAACAACAAAAGA
17623 AA
1 AA
17625 TTAGTTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.71, C:0.13, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAGCGAAACAACAAAAGA
Found at i:18920 original size:13 final size:13
Alignment explanation
Indices: 18874--18920 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
18864 TATCATTTTT
18874 TCTCTTTTCTTAC
1 TCTCTTTTCTTAC
* *
18887 TCT-TTTTACTAAT
1 TCTCTTTT-CTTAC
18900 TACTCTTTTCTTAC
1 T-CTCTTTTCTTAC
18914 TCTCTTT
1 TCTCTTT
18921 ATTTATTACC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.62
Consensus pattern (13 bp):
TCTCTTTTCTTAC
Found at i:19090 original size:21 final size:20
Alignment explanation
Indices: 18981--19083 Score: 107
Period size: 21 Copynumber: 5.0 Consensus size: 20
18971 ACTCTTTGAA
*
18981 TTACTGATCACCTTTTACTC
1 TTACTGATTACCTTTTACTC
**
19001 TTTACTGATTATTATTTTACTC
1 -TTACTGATTA-CCTTTTACTC
* * *
19023 TTACTAATTACCACTTTGCTC
1 TTACTGATTACC-TTTTACTC
*
19044 TTACTGATTACTGTTTTACTC
1 TTACTGATTAC-CTTTTACTC
19065 TTACTGATTACCTTTTACT
1 TTACTGATTACCTTTTACT
19084 GATTACTATT
Statistics
Matches: 66, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
20 7 0.11
21 51 0.77
22 8 0.12
ACGTcount: A:0.21, C:0.22, G:0.06, T:0.50
Consensus pattern (20 bp):
TTACTGATTACCTTTTACTC
Found at i:19090 original size:42 final size:41
Alignment explanation
Indices: 18981--19090 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 41
18971 ACTCTTTGAA
* * *
18981 TTACTGATCACCTTTTACTCTTTACTGATTATTATTTTACTC
1 TTACTGATTACCTTTTACT-ATTACTGATTACTATTTTACTC
* * * * *
19023 TTACTAATTACCACTTTGCTCTTACTGATTACTGTTTTACTC
1 TTACTGATTACC-TTTTACTATTACTGATTACTATTTTACTC
19065 TTACTGATTACCTTTTACTGATTACT
1 TTACTGATTACCTTTTACT-ATTACT
19091 ATTTTACTCT
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
41 5 0.09
42 45 0.82
43 5 0.09
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (41 bp):
TTACTGATTACCTTTTACTATTACTGATTACTATTTTACTC
Found at i:19122 original size:38 final size:37
Alignment explanation
Indices: 19045--19140 Score: 142
Period size: 38 Copynumber: 2.6 Consensus size: 37
19035 ACTTTGCTCT
* *
19045 TACTGATTACTGTTTTACTC--TTACTGATTACCTTT
1 TACTGATTACTATTTTACTCTTTTACTGATTACCTTC
*
19080 TACTGATTACTATTTTACTCTTTTGCTTGATTACCTTC
1 TACTGATTACTATTTTACTCTTTTAC-TGATTACCTTC
19118 TACTGATTACTATTTTACTCTTT
1 TACTGATTACTATTTTACTCTTT
19141 A
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
35 19 0.35
37 3 0.05
38 33 0.60
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (37 bp):
TACTGATTACTATTTTACTCTTTTACTGATTACCTTC
Done.