Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014724.1 Corchorus capsularis cultivar CVL-1 contig14745, 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: 23369
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:1619 original size:2 final size:2
Alignment explanation
Indices: 1612--1654 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
1602 CATTAGCTAG
1612 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TCA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
1654 T
1 T
1655 GTAATGATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6024 original size:21 final size:19
Alignment explanation
Indices: 5999--6061 Score: 74
Period size: 19 Copynumber: 3.2 Consensus size: 19
5989 GAGTGATTTT
5999 TCATTACACTCAAA-ATTGA
1 TCATTACAC-CAAACATTGA
* *
6018 TACCATTACACCAAATAATGA
1 T--CATTACACCAAACATTGA
6039 TCATTACACCAAACATTGA
1 TCATTACACCAAACATTGA
6058 TCAT
1 TCAT
6062 ATTTTCCTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
19 21 0.55
20 4 0.11
21 13 0.34
ACGTcount: A:0.43, C:0.24, G:0.05, T:0.29
Consensus pattern (19 bp):
TCATTACACCAAACATTGA
Found at i:8224 original size:11 final size:11
Alignment explanation
Indices: 8207--8237 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
8197 CTTGAAATGA
8207 CATATATATAT
1 CATATATATAT
*
8218 TATATATATAT
1 CATATATATAT
8229 CATATATAT
1 CATATATAT
8238 GTATAATGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (11 bp):
CATATATATAT
Found at i:11858 original size:17 final size:18
Alignment explanation
Indices: 11833--11875 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
11823 CTTTAAGCTC
11833 GGTAAAGTGTTCAG-TTT
1 GGTAAAGTGTTCAGCTTT
* *
11850 GGTATAGTGTTTAGCTTT
1 GGTAAAGTGTTCAGCTTT
11868 GGTAAAGT
1 GGTAAAGT
11876 ATTTGCTAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.23, C:0.05, G:0.30, T:0.42
Consensus pattern (18 bp):
GGTAAAGTGTTCAGCTTT
Found at i:12569 original size:18 final size:18
Alignment explanation
Indices: 12546--12598 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
12536 CATCGCATGA
12546 GCCATCCGGCCACAACCG
1 GCCATCCGGCCACAACCG
*
12564 GCCAT-C-G---C-ACGG
1 GCCATCCGGCCACAACCG
12576 GCCATCCGGCCACAACCG
1 GCCATCCGGCCACAACCG
12594 GCCAT
1 GCCAT
12599 TTGATCCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
12 8 0.30
13 2 0.07
14 1 0.04
16 1 0.04
17 2 0.07
18 13 0.48
ACGTcount: A:0.21, C:0.47, G:0.25, T:0.08
Consensus pattern (18 bp):
GCCATCCGGCCACAACCG
Found at i:12570 original size:30 final size:30
Alignment explanation
Indices: 12536--12598 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
12526 TCGCACAGGA
*
12536 CATCGCATGAGCCATCCGGCCACAACCGGC
1 CATCGCACGAGCCATCCGGCCACAACCGGC
*
12566 CATCGCACGGGCCATCCGGCCACAACCGGC
1 CATCGCACGAGCCATCCGGCCACAACCGGC
12596 CAT
1 CAT
12599 TTGATCCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.22, C:0.44, G:0.24, T:0.10
Consensus pattern (30 bp):
CATCGCACGAGCCATCCGGCCACAACCGGC
Found at i:19094 original size:30 final size:30
Alignment explanation
Indices: 19058--19120 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
19048 TCGCACGGGA
* *
19058 CATCGCATGAGCCATCCGGCCACAACCGGC
1 CATCGCACGAGCCATCCAGCCACAACCGGC
*
19088 CATCGCACGGGCCATCCAGCCACAACCGGC
1 CATCGCACGAGCCATCCAGCCACAACCGGC
19118 CAT
1 CAT
19121 TCGATCCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.24, C:0.44, G:0.22, T:0.10
Consensus pattern (30 bp):
CATCGCACGAGCCATCCAGCCACAACCGGC
Found at i:19937 original size:15 final size:15
Alignment explanation
Indices: 19898--19939 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
19888 AACCGATTTA
*
19898 CAACTAGATTCGTAT
1 CAACTAGATTTGTAT
19913 CAATCTAGATTTGTAT
1 CAA-CTAGATTTGTAT
19929 CAACTAGATTT
1 CAACTAGATTT
19940 ATTGTTGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (15 bp):
CAACTAGATTTGTAT
Done.