Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005379.1 Corchorus capsularis cultivar CVL-1 contig05397, 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: 10182
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--49 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
43 TC TC TC T
1 TC TC TC T
50 TTTTTTAAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:680 original size:11 final size:11
Alignment explanation
Indices: 666--701 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
656 TTTGTTTTTT
666 GTTTTTGTTTC
1 GTTTTTGTTTC
*
677 GTTTTCGTTTC
1 GTTTTTGTTTC
*
688 GTTTTTGTTAC
1 GTTTTTGTTTC
699 GTT
1 GTT
702 GTCAATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.03, C:0.11, G:0.19, T:0.67
Consensus pattern (11 bp):
GTTTTTGTTTC
Found at i:4610 original size:15 final size:14
Alignment explanation
Indices: 4562--4613 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
4552 ATAATTTTCA
*
4562 ATTATTTATTAAATT
1 ATTATTT-TTAATTT
* *
4577 ATTAATTATACATTT
1 ATTATTTTTA-ATTT
4592 ATTATTTTTAATTT
1 ATTATTTTTAATTT
4606 AATTATTT
1 -ATTATTT
4614 ATTTTTATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 6 0.20
15 24 0.80
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATTTTTAATTT
Found at i:4834 original size:74 final size:73
Alignment explanation
Indices: 4756--4903 Score: 253
Period size: 74 Copynumber: 2.0 Consensus size: 73
4746 TGGTCTTTTC
*
4756 ACACTTTTCAGG-TGACTAAAAAGCCCCTCTATGAGTTTCCCCTATTCCTTTTCCTTCTACCCTT
1 ACACTTTTC-GGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTA-CCTT
*
4820 TTTTGTAATT
64 TTTCGTAATT
4830 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCTTTT
1 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCTTTT
4895 TCGTAATT
66 TCGTAATT
4903 A
1 A
4904 ACATTCCTTA
Statistics
Matches: 71, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
73 16 0.23
74 55 0.77
ACGTcount: A:0.21, C:0.29, G:0.09, T:0.41
Consensus pattern (73 bp):
ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCTTTT
TCGTAATT
Found at i:7036 original size:32 final size:32
Alignment explanation
Indices: 6995--7060 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
6985 TATCATGCAA
6995 TGTATCCTTCCTCCAAAAACGTACCGGTCCCT
1 TGTATCCTTCCTCCAAAAACGTACCGGTCCCT
7027 TGTATCCTTCCTCCAAAAACGTACCGGTCCCT
1 TGTATCCTTCCTCCAAAAACGTACCGGTCCCT
7059 TG
1 TG
7061 ACAATTGCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (32 bp):
TGTATCCTTCCTCCAAAAACGTACCGGTCCCT
Found at i:9428 original size:12 final size:12
Alignment explanation
Indices: 9411--9462 Score: 86
Period size: 12 Copynumber: 4.2 Consensus size: 12
9401 CATCGATACC
9411 TCGATATATCCG
1 TCGATATATCCG
*
9423 TCGATATATCCA
1 TCGATATATCCG
9435 TCGATATATCCG
1 TCGATATATCCG
9447 TTCGATATATCCG
1 -TCGATATATCCG
9460 TCG
1 TCG
9463 GTACCTGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
12 25 0.68
13 12 0.32
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:9613 original size:6 final size:6
Alignment explanation
Indices: 9604--9640 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
9594 TGGGGATAGG
9604 GATGAA GATGAA GATGAA GATGAA GATGAA GAT-AA GA
1 GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA GA
9641 AAAAAGATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.51, C:0.00, G:0.32, T:0.16
Consensus pattern (6 bp):
GATGAA
Found at i:10001 original size:137 final size:137
Alignment explanation
Indices: 9763--10177 Score: 719
Period size: 137 Copynumber: 3.0 Consensus size: 137
9753 GGATCTAATA
* *
9763 TTATCTCAATCCAACCTTTGGATTAAAAGTGAGATTCAAATGTGACCGTTAATTTGAATCCTTAT
1 TTATCTCAATCTAACCGTTGGATTAAAAGTGAGATTCAAATGTGACCGTTAATTTGAATCCTTAT
* *
9828 CTCTTCCAACACAATATCTAAGATATGTCAGAAAATCTAACACAATAGTCAATAATTTCAGAGAA
66 CTCTTCCAACACAATATCCAAGATATGTCAAAAAATCTAACACAATAGTCAATAATTTCAGAGAA
9893 TCTAACC
131 TCTAACC
9900 TTATCTCAATCTAACCGTTGGATTAAAAGTGAGATTCAAATGTGACCGTTAATTTGAATCCTTAT
1 TTATCTCAATCTAACCGTTGGATTAAAAGTGAGATTCAAATGTGACCGTTAATTTGAATCCTTAT
* *
9965 CTCTTCCAACACAATATCCAACATGTGTCAAAAAATCTAACACAATAGTCAATAATTTCAGAGAA
66 CTCTTCCAACACAATATCCAAGATATGTCAAAAAATCTAACACAATAGTCAATAATTTCAGAGAA
*
10030 TCTAGCC
131 TCTAACC
*
10037 TTATCTCAATCTAACCGTTGAATTAAAAGTGAGATTCAAATGTG--CGTTAATTTGAATCCTTAT
1 TTATCTCAATCTAACCGTTGGATTAAAAGTGAGATTCAAATGTGACCGTTAATTTGAATCCTTAT
*
10100 CTCTTCCAACACAATATCCAAGATATGT-AAGAAAATCTAACACAATAGTCAATAATTTCAAAGA
66 CTCTTCCAACACAATATCCAAGATATGTCAA-AAAATCTAACACAATAGTCAATAATTTCAGAGA
10164 ATCTAACC
130 ATCTAACC
10172 TTATCT
1 TTATCT
10178 TAATA
Statistics
Matches: 265, Mismatches: 12, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
134 2 0.01
135 90 0.34
137 173 0.65
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.32
Consensus pattern (137 bp):
TTATCTCAATCTAACCGTTGGATTAAAAGTGAGATTCAAATGTGACCGTTAATTTGAATCCTTAT
CTCTTCCAACACAATATCCAAGATATGTCAAAAAATCTAACACAATAGTCAATAATTTCAGAGAA
TCTAACC
Done.