Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004944.1 Corchorus capsularis cultivar CVL-1 contig04962, 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: 27207
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:6229 original size:14 final size:14
Alignment explanation
Indices: 6210--6247 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
6200 CATCTCCTCA
6210 CACCTTTTTCAGTT
1 CACCTTTTTCAGTT
6224 CACCTTTGCTTCAGTT
1 CACCTTT--TTCAGTT
6240 C-CCTTTTT
1 CACCTTTTT
6248 TTTTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.09
14 7 0.32
15 5 0.23
16 8 0.36
ACGTcount: A:0.11, C:0.32, G:0.08, T:0.50
Consensus pattern (14 bp):
CACCTTTTTCAGTT
Found at i:7758 original size:44 final size:46
Alignment explanation
Indices: 7695--7786 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
7685 CTAAAGTTGC
7695 TTCATCAAGCAATGTTAAAAC-A-ATATAGGTAATTTGCATATAGA
1 TTCATCAAGCAATGTTAAAACAATATATAGGTAATTTGCATATAGA
* *
7739 TTCATTAAGCAATGTTAAAACAATATATAGGTAATTTGCTTATAGA
1 TTCATCAAGCAATGTTAAAACAATATATAGGTAATTTGCATATAGA
7785 TT
1 TT
7787 TGGGTTTAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 20 0.45
45 1 0.02
46 23 0.52
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (46 bp):
TTCATCAAGCAATGTTAAAACAATATATAGGTAATTTGCATATAGA
Found at i:9184 original size:1 final size:1
Alignment explanation
Indices: 9173--9203 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
9163 ATCATTCCTC
*
9173 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
9204 AAATCCTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:12610 original size:1 final size:1
Alignment explanation
Indices: 12606--12631 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
12596 AAAAAGAATG
12606 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
12632 GAAAGGAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20079 original size:19 final size:19
Alignment explanation
Indices: 20052--20088 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20042 GTTGCTCTAA
* *
20052 TAATCTCATCTGTACAGTG
1 TAATATCATATGTACAGTG
20071 TAATATCATATGTACAGT
1 TAATATCATATGTACAGT
20089 TGCTAAACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATATCATATGTACAGTG
Found at i:26867 original size:21 final size:22
Alignment explanation
Indices: 26841--26886 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
26831 TTCAACTGGA
26841 TTGCTAAAT-ACCG-CCCCATTT
1 TTGCT-AATCACCGCCCCCATTT
*
26862 TTGCTATTCACCGCCCCCATTT
1 TTGCTAATCACCGCCCCCATTT
26884 TTG
1 TTG
26887 ACCTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 2 0.09
21 9 0.41
22 11 0.50
ACGTcount: A:0.17, C:0.35, G:0.11, T:0.37
Consensus pattern (22 bp):
TTGCTAATCACCGCCCCCATTT
Found at i:27138 original size:34 final size:33
Alignment explanation
Indices: 27072--27199 Score: 143
Period size: 33 Copynumber: 3.9 Consensus size: 33
27062 TGACCCGTGT
**
27072 CGCCCCAAGAGGGCGGCTT-ACCATGGGCAGGC
1 CGCCCCACTAGGGCGGCTTCACCATGGGCAGGC
*
27104 CGCCCTACTAGGGCGGCTTCACCATTGGGCAGGC
1 CGCCCCACTAGGGCGGCTTCACCA-TGGGCAGGC
** ***
27138 CGCCCCACTAGGGCGGCTTCATTATGAATAGGC
1 CGCCCCACTAGGGCGGCTTCACCATGGGCAGGC
* *
27171 CGCCCCACTGGGGCGGCTTCGCCA-GGGCA
1 CGCCCCACTAGGGCGGCTTCACCATGGGCA
27200 AGTAAATA
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
32 18 0.23
33 30 0.38
34 30 0.38
ACGTcount: A:0.16, C:0.35, G:0.34, T:0.15
Consensus pattern (33 bp):
CGCCCCACTAGGGCGGCTTCACCATGGGCAGGC
Found at i:27176 original size:33 final size:34
Alignment explanation
Indices: 27072--27190 Score: 118
Period size: 34 Copynumber: 3.6 Consensus size: 34
27062 TGACCCGTGT
** **
27072 CGCCCCAAGAGGGCGGCTT-ACCA-TGGGCAGGC
1 CGCCCCACTAGGGCGGCTTCACCATTGAACAGGC
* **
27104 CGCCCTACTAGGGCGGCTTCACCATTGGGCAGGC
1 CGCCCCACTAGGGCGGCTTCACCATTGAACAGGC
** *
27138 CGCCCCACTAGGGCGGCTTCATTA-TGAATAGGC
1 CGCCCCACTAGGGCGGCTTCACCATTGAACAGGC
*
27171 CGCCCCACTGGGGCGGCTTC
1 CGCCCCACTAGGGCGGCTTC
27191 GCCAGGGCAA
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
32 16 0.21
33 29 0.39
34 30 0.40
ACGTcount: A:0.16, C:0.35, G:0.33, T:0.16
Consensus pattern (34 bp):
CGCCCCACTAGGGCGGCTTCACCATTGAACAGGC
Done.