Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018322.1 Corchorus olitorius cultivar O-4 contig18355, 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: 24890
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Found at i:4635 original size:24 final size:24
Alignment explanation
Indices: 4532--4629 Score: 144
Period size: 24 Copynumber: 4.1 Consensus size: 24
4522 TTGGAGCAAG
*
4532 GATGAT-ACTATTGAAGATAATTCA
1 GATGATGA-TATTGGAGATAATTCA
*
4556 GATGATGATATTGGAGACAATTCA
1 GATGATGATATTGGAGATAATTCA
*
4580 GATGATGGTATTGGAGATAATTCA
1 GATGATGATATTGGAGATAATTCA
*
4604 GATGATGATATTGGAGATGATTCA
1 GATGATGATATTGGAGATAATTCA
4628 GA
1 GA
4630 GCATGAAAGA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
24 66 0.99
25 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.32
Consensus pattern (24 bp):
GATGATGATATTGGAGATAATTCA
Found at i:9547 original size:39 final size:39
Alignment explanation
Indices: 9493--9594 Score: 195
Period size: 39 Copynumber: 2.6 Consensus size: 39
9483 TCTTAATTAG
*
9493 CTTCACGAATTGAATTGAGATTGACAAGAATGCCAATTC
1 CTTCATGAATTGAATTGAGATTGACAAGAATGCCAATTC
9532 CTTCATGAATTGAATTGAGATTGACAAGAATGCCAATTC
1 CTTCATGAATTGAATTGAGATTGACAAGAATGCCAATTC
9571 CTTCATGAATTGAATTGAGATTGA
1 CTTCATGAATTGAATTGAGATTGA
9595 GATTTGATTC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 62 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (39 bp):
CTTCATGAATTGAATTGAGATTGACAAGAATGCCAATTC
Found at i:10237 original size:22 final size:22
Alignment explanation
Indices: 10212--10585 Score: 166
Period size: 22 Copynumber: 16.8 Consensus size: 22
10202 GTTATATATG
*
10212 TATGAAATTTCGATAACCTCCC
1 TATGAAATTTTGATAACCTCCC
* * *
10234 TATGGAAA-TTTGATAATCACAC
1 TAT-GAAATTTTGATAACCTCCC
* * * **
10256 TGTGAAATTTTGATAAGCACAT
1 TATGAAATTTTGATAACCTCCC
* * **
10278 TATAAAATTTTGATAATCTCAG
1 TATGAAATTTTGATAACCTCCC
* * *
10300 TGTGAAATTTTGATAATCTCTC
1 TATGAAATTTTGATAACCTCCC
* * * *
10322 TATAAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCTCCC
* * *
10344 TAT-AAA-ATTGGTAACCGCACC
1 TATGAAATTTTGATAACCTC-CC
* *
10365 -ATGAAGTTTCGATAACCTCCC
1 TATGAAATTTTGATAACCTCCC
* * * *
10386 TATGAGAATGAAACTGTGATATCTTCTC
1 TATGA-AAT-----TTTGATAACCTCCC
*
10414 TATGTAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCC
* * *
10436 CATAAAATTTTCATAACCTCCC
1 TATGAAATTTTGATAACCTCCC
* * ***
10458 T-GGTAAATTTTGATAACATTTTT
1 TATG-AAATTTTGATAAC-CTCCC
* * **
10481 TATAAAATTTTGGTAACCTCTT
1 TATGAAATTTTGATAACCTCCC
*
10503 TATGAAATTTTGATAA-CTACAC
1 TATGAAATTTTGATAACCT-CCC
* * *
10525 TATGAAGTTTTGATAACTTCCA
1 TATGAAATTTTGATAACCTCCC
* * *
10547 TATGAAATTTTGGTAACCACGC
1 TATGAAATTTTGATAACCTCCC
10569 TATGAAATTTTGATAAC
1 TATGAAATTTTGATAAC
10586 TTTCTTATGT
Statistics
Matches: 262, Mismatches: 73, Indels: 34
0.71 0.20 0.09
Matches are distributed among these distances:
20 10 0.04
21 14 0.05
22 201 0.77
23 21 0.08
27 3 0.01
28 13 0.05
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:10894 original size:60 final size:60
Alignment explanation
Indices: 10773--10929 Score: 158
Period size: 60 Copynumber: 2.6 Consensus size: 60
10763 TATTGGTCAA
* * *
10773 TTGTTCAAAT-AGGTCCCTAATGTATGCAAAAATGCTCAATTTAGGGCTTATACTTTTAATT
1 TTGTT-AAATAAGG-CCCTAATGTATGCGAAAATGCTCAATTCAGGGCTCATACTTTTAATT
* * *
10834 TTGTTAAATAAGGCCCTAACGTATGCGAAAATGCTCAGTTCAGGG-TCCAT-GTTTTGAATT
1 TTGTTAAATAAGGCCCTAATGTATGCGAAAATGCTCAATTCAGGGCT-CATACTTTT-AATT
* ** * *
10894 TGGTTAAATAAGATCCTAATGTATGTGAAAAAGCTC
1 TTGTTAAATAAGGCCCTAATGTATGCGAAAATGCTC
10930 TAATAAGGGT
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
59 5 0.06
60 68 0.84
61 8 0.10
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (60 bp):
TTGTTAAATAAGGCCCTAATGTATGCGAAAATGCTCAATTCAGGGCTCATACTTTTAATT
Found at i:22322 original size:12 final size:11
Alignment explanation
Indices: 22305--22350 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 11
22295 TTCTCTCTAT
22305 TTATTATTATCA
1 TTATTATTAT-A
22317 TTATTATTATA
1 TTATTATTATA
*
22328 TATATTAAT-TA
1 T-TATTATTATA
22339 TTA-TATTATA
1 TTATTATTATA
22349 TT
1 TT
22351 TATCTCTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 3 0.10
10 6 0.20
11 5 0.17
12 16 0.53
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
TTATTATTATA
Found at i:22338 original size:19 final size:17
Alignment explanation
Indices: 22309--22350 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
22299 CTCTATTTAT
22309 TATTATCATT-ATTATTA
1 TATTAT-ATTAATTATTA
22326 TA-TATATTAATTATTA
1 TATTATATTAATTATTA
22342 TATTATATT
1 TATTATATT
22351 TATCTCTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 3 0.13
16 12 0.52
17 8 0.35
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTATATTAATTATTA
Found at i:24375 original size:2 final size:2
Alignment explanation
Indices: 24368--24392 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24358 TTTAGAATAC
24368 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 T
24393 CAAACACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.