Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022409.1 Corchorus olitorius cultivar O-4 contig22442, 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: 48117
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Found at i:7541 original size:35 final size:35
Alignment explanation
Indices: 7495--7579 Score: 116
Period size: 35 Copynumber: 2.4 Consensus size: 35
7485 ACCAATGGCC
*
7495 CAAACATAAAAATTACTCCTACTACCCAACAGCAA
1 CAAACATAAAAATTACTCCTACTACCCAACAACAA
* **
7530 CAAACATAAAAAGTACTCCTGGTACCCAACAACAA
1 CAAACATAAAAATTACTCCTACTACCCAACAACAA
7565 CAAAGCATAAGAAAT
1 CAAA-CATAA-AAAT
7580 ATTGGACCCA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
35 35 0.81
36 5 0.12
37 3 0.07
ACGTcount: A:0.51, C:0.27, G:0.07, T:0.15
Consensus pattern (35 bp):
CAAACATAAAAATTACTCCTACTACCCAACAACAA
Found at i:7619 original size:41 final size:41
Alignment explanation
Indices: 7573--7654 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
7563 AACAAAGCAT
*
7573 AAGAAATATTGGACCCAACCCAAACAATAAAGGAGAGGCAG
1 AAGAAATATTGGACCCAACCCAAACAATAAAGGAAAGGCAG
* *
7614 AAGAAATGTTGGACCCAACCCAAACGATAAAGGAAAGGCAG
1 AAGAAATATTGGACCCAACCCAAACAATAAAGGAAAGGCAG
7655 TTTCTCAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.48, C:0.20, G:0.23, T:0.10
Consensus pattern (41 bp):
AAGAAATATTGGACCCAACCCAAACAATAAAGGAAAGGCAG
Found at i:13292 original size:7 final size:7
Alignment explanation
Indices: 13280--13325 Score: 92
Period size: 7 Copynumber: 6.6 Consensus size: 7
13270 ATCTAATCTA
13280 AGTGGTG
1 AGTGGTG
13287 AGTGGTG
1 AGTGGTG
13294 AGTGGTG
1 AGTGGTG
13301 AGTGGTG
1 AGTGGTG
13308 AGTGGTG
1 AGTGGTG
13315 AGTGGTG
1 AGTGGTG
13322 AGTG
1 AGTG
13326 AAACTGAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.15, C:0.00, G:0.57, T:0.28
Consensus pattern (7 bp):
AGTGGTG
Found at i:14315 original size:14 final size:14
Alignment explanation
Indices: 14296--14326 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
14286 AACCACCAAC
14296 AAGATGAATCACAA
1 AAGATGAATCACAA
14310 AAGATGAATCACAA
1 AAGATGAATCACAA
14324 AAG
1 AAG
14327 TCTTCTGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.13, G:0.16, T:0.13
Consensus pattern (14 bp):
AAGATGAATCACAA
Found at i:14796 original size:30 final size:30
Alignment explanation
Indices: 14760--14824 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
14750 ATCTGTCATA
14760 GCTATGGCTACGGCTTCGACTGCGTCCACG
1 GCTATGGCTACGGCTTCGACTGCGTCCACG
* *
14790 GCTATGGCTACGGCTTCGACTGTGTCTACG
1 GCTATGGCTACGGCTTCGACTGCGTCCACG
14820 GCTAT
1 GCTAT
14825 AGCTTCGACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.28
Consensus pattern (30 bp):
GCTATGGCTACGGCTTCGACTGCGTCCACG
Found at i:14840 original size:30 final size:30
Alignment explanation
Indices: 14760--14840 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 30
14750 ATCTGTCATA
* * *
14760 GCTATGGCTACGGCTTCGACTGCGTCCACG
1 GCTATAGCTACGACTACGACTGCGTCCACG
* * * * *
14790 GCTATGGCTACGGCTTCGACTGTGTCTACG
1 GCTATAGCTACGACTACGACTGCGTCCACG
*
14820 GCTATAGCTTCGACTACGACT
1 GCTATAGCTACGACTACGACT
14841 ACGGCCCGGA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.16, C:0.30, G:0.27, T:0.27
Consensus pattern (30 bp):
GCTATAGCTACGACTACGACTGCGTCCACG
Found at i:15251 original size:33 final size:33
Alignment explanation
Indices: 15212--15338 Score: 121
Period size: 33 Copynumber: 3.8 Consensus size: 33
15202 CTCCCTCCAG
*
15212 GACCATCGAAGCCACCATCCCTCATACCGCCAC
1 GACCATCAAAGCCACCATCCCTCATACCGCCAC
* * * *
15245 GCCCATCAAAACCACCATCTCTCTTACCGCCAC
1 GACCATCAAAGCCACCATCCCTCATACCGCCAC
*** * * *
15278 GGTTACCAAAGCCACCATCCCTCATTCCACCAC
1 GACCATCAAAGCCACCATCCCTCATACCGCCAC
* *
15311 GACCAGT-GAAGCTACCATCCCTCATACC
1 GACCA-TCAAAGCCACCATCCCTCATACC
15339 ACCCCGGCCG
Statistics
Matches: 72, Mismatches: 21, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
33 72 1.00
ACGTcount: A:0.28, C:0.46, G:0.10, T:0.17
Consensus pattern (33 bp):
GACCATCAAAGCCACCATCCCTCATACCGCCAC
Found at i:21955 original size:2 final size:2
Alignment explanation
Indices: 21948--21980 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
21938 AGTCCTAACC
21948 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21981 TTATGACCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.