Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023954.1 Corchorus olitorius cultivar O-4 contig23987, 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: 11828
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:315 original size:16 final size:17
Alignment explanation
Indices: 289--320 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
279 AGTGCAAATT
289 AAAATAGAAAAATAAAG
1 AAAATAGAAAAATAAAG
306 AAAA-AGAAAAATAAA
1 AAAATAGAAAAATAAA
321 ACGCAATCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAATAGAAAAATAAAG
Found at i:2923 original size:30 final size:31
Alignment explanation
Indices: 2851--2936 Score: 129
Period size: 32 Copynumber: 2.8 Consensus size: 31
2841 TTTCTTAAGC
* *
2851 AAATCCAAAAGAAGACTTTGGAAAATAAGGT
1 AAATCCAAAAGAAGATTTTGGAAAATAAAGT
*
2882 AATTCCCAAAAGAAGATTTTGGAAAATAAAG-
1 AAAT-CCAAAAGAAGATTTTGGAAAATAAAGT
2913 AAATCCAAAAGAAGATTTTGGAAA
1 AAATCCAAAAGAAGATTTTGGAAA
2937 TTAATAAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
30 20 0.40
31 6 0.12
32 24 0.48
ACGTcount: A:0.52, C:0.09, G:0.17, T:0.21
Consensus pattern (31 bp):
AAATCCAAAAGAAGATTTTGGAAAATAAAGT
Found at i:5772 original size:37 final size:35
Alignment explanation
Indices: 5731--5824 Score: 134
Period size: 37 Copynumber: 2.6 Consensus size: 35
5721 ATTTAAGTTC
5731 TTTTCAAATTGGGAAAGTTCCCATCCAGTTTTCAGAG
1 TTTTCAAATTGGGAAAGTTCCCAT-CAGTTTTCA-AG
*
5768 TTTTCGAATTGGGAAAGTTCCCATCAGTTTTCAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAG
* *
5803 TTTTCAATTTAGGAAAAGTTCC
1 TTTTCAAATT-GGGAAAGTTCC
5825 TATTGTCGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
35 10 0.19
36 19 0.37
37 23 0.44
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (35 bp):
TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAG
Found at i:10057 original size:27 final size:27
Alignment explanation
Indices: 10018--10144 Score: 155
Period size: 27 Copynumber: 4.7 Consensus size: 27
10008 TAAGGGTTCG
* * * *
10018 AATGACCACAATGCACTTGACTGTGCA
1 AATGACCAAAATGCCCCTGAATGTGCA
*
10045 AATGACCAGAATGCCCCTGAATGTGCA
1 AATGACCAAAATGCCCCTGAATGTGCA
*
10072 AATGACCAAAATGCCCCTGAATGTGTA
1 AATGACCAAAATGCCCCTGAATGTGCA
* * *
10099 AATGACCAAAATGCCCCTGGATTTTGAA
1 AATGACCAAAATGCCCCT-GAATGTGCA
*
10127 AATTACCAAAATGCCCCT
1 AATGACCAAAATGCCCCT
10145 AGTTGATCCT
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
27 66 0.74
28 23 0.26
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22
Consensus pattern (27 bp):
AATGACCAAAATGCCCCTGAATGTGCA
Found at i:10527 original size:39 final size:39
Alignment explanation
Indices: 10484--10572 Score: 97
Period size: 39 Copynumber: 2.3 Consensus size: 39
10474 ATTAATTGGC
* * *
10484 AAGCAATGATCCTGAACCAAGACCGAAATAAAACTGACG
1 AAGCAATGATCCTAAACCAAGACCGAAACAAAACTGACA
* * * * * *
10523 AAGCAATAATACTAAATCAAGACTGAAACATAACTGATA
1 AAGCAATGATCCTAAACCAAGACCGAAACAAAACTGACA
10562 AAGCAATGATC
1 AAGCAATGATC
10573 AAAATTCAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.49, C:0.19, G:0.15, T:0.17
Consensus pattern (39 bp):
AAGCAATGATCCTAAACCAAGACCGAAACAAAACTGACA
Found at i:10699 original size:30 final size:30
Alignment explanation
Indices: 10663--11242 Score: 719
Period size: 30 Copynumber: 19.3 Consensus size: 30
10653 ACTGATGAAA
10663 CAATGATCCT-AAACCAGGATTAAAATAAAG
1 CAATGATCCTCAAA-CAGGATTAAAATAAAG
* * *
10693 CAATGATCCTCAACCCGGATTAAAATGAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* *
10723 CAATGATCCTAAAACAGGATTAAAATGAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
*
10753 CAATGATCCTCAAACAGGATTAAAAATGAAG
1 CAATGATCCTCAAACAGGATT-AAAATAAAG
*
10784 CAATGATCCTCAAACAGGATTAAAATAGAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* *
10814 CGATGATCCTCAAACAGGATTAAAATAGAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* * *
10844 CGATGATCCT-AAACCAGGATTAACATAGAG
1 CAATGATCCTCAAA-CAGGATTAAAATAAAG
* *
10874 CAAAT-ATCCTCAACCAGGATAAAAATAAAG
1 C-AATGATCCTCAAACAGGATTAAAATAAAG
**
10904 CAATGATCCTCAAACAGGACAAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
*
10934 CAATGATCCTCAAACAGGATTAAAA-AACG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
*
10963 TAATGATCCTCAAACAGGATTAAAAT--A-
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* *
10990 -AA-GATCCTTAATCAGGATTAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* * *
11018 CAACGATCCTCAAACATGATAAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
*
11048 CAATGATCCTCAAACAGGATTAAAATAAAA
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* *
11078 TAATGATCCTCAAACAGGATAAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* *
11108 CAACGATCCTCAAACAGGATAAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
11138 CAATGATCCTCAAACAGGATTAAAATGAAGTGAAG
1 CAATGATCCTCAAACAGGATTAAAAT--A---AAG
* *
11173 TAATGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* **
11203 CAACGATCCTCAAACAGGACAAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
11233 CAATGATCCT
1 CAATGATCCT
11243 GTCGTAACGT
Statistics
Matches: 485, Mismatches: 48, Indels: 34
0.86 0.08 0.06
Matches are distributed among these distances:
25 20 0.04
26 2 0.00
27 1 0.00
29 35 0.07
30 362 0.75
31 36 0.07
32 1 0.00
33 1 0.00
35 27 0.06
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (30 bp):
CAATGATCCTCAAACAGGATTAAAATAAAG
Done.