Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008170.1 Corchorus capsularis cultivar CVL-1 contig08191, 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: 25899
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:2655 original size:81 final size:81
Alignment explanation
Indices: 2520--2670 Score: 275
Period size: 81 Copynumber: 1.9 Consensus size: 81
2510 TTCTATTGGA
* **
2520 GGGGCGAACTTGAACTTCAATTTATTTATAATATTAAAATTACGTAGGGTACTTAAGGCTTTTAG
1 GGGGCGAACTTGAACTTCAATTTATTTATAATAGTAAAATTACGTAGGACACTTAAGGCTTTTAG
2585 GAACCTTTGGGGGGGG
66 GAACCTTTGGGGGGGG
2601 GGGGCGAACTTGAACTTCAATTTATTTATAATAGTAAAATTACGTAGGACACTTAAGGCTTTTAG
1 GGGGCGAACTTGAACTTCAATTTATTTATAATAGTAAAATTACGTAGGACACTTAAGGCTTTTAG
2666 GAACC
66 GAACC
2671 CACCCCGCAC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 67 1.00
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (81 bp):
GGGGCGAACTTGAACTTCAATTTATTTATAATAGTAAAATTACGTAGGACACTTAAGGCTTTTAG
GAACCTTTGGGGGGGG
Found at i:6150 original size:130 final size:128
Alignment explanation
Indices: 5912--6160 Score: 365
Period size: 130 Copynumber: 1.9 Consensus size: 128
5902 TTGTTTAAAC
* * * *
5912 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTACTTAATAAAATCTAATATCCTTATAACTA
* *
5977 TTTTATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATTAGAATTTTTTTAATATAT
66 TTTTATTCTTACCATTTTACTAATTTAATTAAAAAAAC--ATATATTAGAATTTTTTTAATATAT
* *
6042 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTACTTAATAAAATCTAATATCTTTATACCTA
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTACTTAATAAAATCTAATATCCTTATAACTA
** *
6107 TTTTATTCTTACCATTTTACTAATTTAA-TAAAACTTAGATATATTAGAATTTTT
66 TTTTATTCTTACCATTTTACTAATTTAATTAAAA-AAACATATATTAGAATTTTT
6161 AAAATATGAA
Statistics
Matches: 107, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
128 16 0.15
129 5 0.05
130 86 0.80
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.50
Consensus pattern (128 bp):
TTTTATAATTTTACTCAACTAAAAACTCTATTTCTACTTAATAAAATCTAATATCCTTATAACTA
TTTTATTCTTACCATTTTACTAATTTAATTAAAAAAACATATATTAGAATTTTTTTAATATAT
Found at i:8232 original size:16 final size:17
Alignment explanation
Indices: 8199--8243 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
8189 TAATCAGTTC
8199 TAATT-AATATTTATTT
1 TAATTAAATATTTATTT
*
8215 TATTTAAATATTTA-TT
1 TAATTAAATATTTATTT
*
8231 TAATTGAATATTT
1 TAATTAAATATTT
8244 GTGATCTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 17 0.68
17 8 0.32
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TAATTAAATATTTATTT
Found at i:12062 original size:13 final size:13
Alignment explanation
Indices: 12044--12068 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12034 TTGACCAAAA
12044 CTTAAATTTTAAT
1 CTTAAATTTTAAT
12057 CTTAAATTTTAA
1 CTTAAATTTTAA
12069 ACTATGACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTAAATTTTAAT
Found at i:15545 original size:33 final size:33
Alignment explanation
Indices: 15503--15579 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 33
15493 CTTTTACACT
15503 GAGCCTCCCCACTAAGACGGCTCAGTCACGGCG
1 GAGCCTCCCCACTAAGACGGCTCAGTCACGGCG
*
15536 GAGCCTCCCCACTAGGACGGCTCAGTCACGGCG
1 GAGCCTCCCCACTAAGACGGCTCAGTCACGGCG
15569 GAGCCTCCCCA
1 GAGCCTCCCCA
15580 GTGGGGTGGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.19, C:0.42, G:0.27, T:0.12
Consensus pattern (33 bp):
GAGCCTCCCCACTAAGACGGCTCAGTCACGGCG
Found at i:19765 original size:14 final size:14
Alignment explanation
Indices: 19748--19774 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19738 AATTATCTAA
19748 AGTATATGGGTGTT
1 AGTATATGGGTGTT
19762 AGTATATGGGTGT
1 AGTATATGGGTGT
19775 ATGATTTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (14 bp):
AGTATATGGGTGTT
Found at i:25580 original size:31 final size:31
Alignment explanation
Indices: 25488--25587 Score: 105
Period size: 31 Copynumber: 3.3 Consensus size: 31
25478 AGTACCTAAA
* * *
25488 TAGTCCTTGTACTATTGAAAAAAGATCATTT
1 TAGTCCCTCTACTATTGAAAAAAGATCAATT
* * ***
25519 TAGTCCCTCCATTA-TGAAATCTG-TCAATT
1 TAGTCCCTCTACTATTGAAAAAAGATCAATT
*
25548 TAGTCCCTCTACTATTGAAAAGAGATCAATT
1 TAGTCCCTCTACTATTGAAAAAAGATCAATT
25579 TAGTCCCTC
1 TAGTCCCTC
25588 CATGAAACGG
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
29 17 0.31
30 12 0.22
31 25 0.46
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (31 bp):
TAGTCCCTCTACTATTGAAAAAAGATCAATT
Done.