Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020743.1 Corchorus olitorius cultivar O-4 contig20776, 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: 56069
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:11843 original size:125 final size:125
Alignment explanation
Indices: 11573--11891 Score: 613
Period size: 125 Copynumber: 2.6 Consensus size: 125
11563 TTCTTAATTT
11573 GAGTTGATAGCTTATTGGTGGATATATGGGCTTTTAAAAGGTCTTACGGCTTGCTCATGAGAGAA
1 GAGTTGATAGCTTATTGGTGGATATATGGGCTTTTAAAAGGTCTTACGGCTTGCTCATGAGAGAA
11638 GCGA-GGGGGGTGCTTAATTTGAGATTGTTGGGTCAAGGGTTTTCTAGCCAGTAGTGGTA
66 GCGAGGGGGGGTGCTTAATTTGAGATTGTTGGGTCAAGGGTTTTCTAGCCAGTAGTGGTA
11697 GAGTTGATAGCTTATTGGTGGATATATGGGCTTTTAAAAGGTCTTACGGCTTGCTCATGAGAGAA
1 GAGTTGATAGCTTATTGGTGGATATATGGGCTTTTAAAAGGTCTTACGGCTTGCTCATGAGAGAA
* *
11762 GCGAGGGGGGGTGCTTAATTTGAGATTGTTGGGTCAAGGGTTTTTTAGCCGGTAGTGGTA
66 GCGAGGGGGGGTGCTTAATTTGAGATTGTTGGGTCAAGGGTTTTCTAGCCAGTAGTGGTA
11822 GAGTTGATAGCTTATTGGTGGATATATGGGCTTTTAAAAGGTCTTACGGCTTGCTCATGAGAGAA
1 GAGTTGATAGCTTATTGGTGGATATATGGGCTTTTAAAAGGTCTTACGGCTTGCTCATGAGAGAA
11887 GCGAG
66 GCGAG
11892 TAATCCACCT
Statistics
Matches: 192, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
124 69 0.36
125 123 0.64
ACGTcount: A:0.23, C:0.10, G:0.34, T:0.33
Consensus pattern (125 bp):
GAGTTGATAGCTTATTGGTGGATATATGGGCTTTTAAAAGGTCTTACGGCTTGCTCATGAGAGAA
GCGAGGGGGGGTGCTTAATTTGAGATTGTTGGGTCAAGGGTTTTCTAGCCAGTAGTGGTA
Found at i:20383 original size:62 final size:62
Alignment explanation
Indices: 20286--20409 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
20276 AAAACTCCAC
20286 TTAAATAGTGGTGGGACCAATCTGCTGGACTAACCGTGTAAAAACATATCATGAGAGACCAA
1 TTAAATAGTGGTGGGACCAATCTGCTGGACTAACCGTGTAAAAACATATCATGAGAGACCAA
20348 TTAAATAGTGGTGGGACCAATCTGCTGGACTAACCGTGTAAAAACATATCATGAGAGACCAA
1 TTAAATAGTGGTGGGACCAATCTGCTGGACTAACCGTGTAAAAACATATCATGAGAGACCAA
20410 ATTACGGGTC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (62 bp):
TTAAATAGTGGTGGGACCAATCTGCTGGACTAACCGTGTAAAAACATATCATGAGAGACCAA
Found at i:26940 original size:18 final size:18
Alignment explanation
Indices: 26917--26951 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
26907 ACAAAAATTG
26917 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
26935 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
26952 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:28363 original size:23 final size:24
Alignment explanation
Indices: 28331--28380 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
28321 TATTTATTCG
*
28331 AAACTTCTAATTATACCTT-AAAA
1 AAACTCCTAATTATACCTTGAAAA
* *
28354 AAACTCCTAATTTTATCTTGAAAA
1 AAACTCCTAATTATACCTTGAAAA
28378 AAA
1 AAA
28381 ATATAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.48, C:0.16, G:0.02, T:0.34
Consensus pattern (24 bp):
AAACTCCTAATTATACCTTGAAAA
Found at i:29334 original size:3 final size:3
Alignment explanation
Indices: 29326--29360 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
29316 TCTTCCACCT
*
29326 CAA CAA CAA CAA CAA CAA CAA CAG CAA CAA CAA CA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA
29361 TTATGGTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.34, G:0.03, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:35377 original size:1 final size:1
Alignment explanation
Indices: 35371--35395 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
35361 GATATATTCC
35371 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
35396 CTCCTCCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:52570 original size:30 final size:29
Alignment explanation
Indices: 52530--52587 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
52520 GTTTGGTCAG
52530 AGGGGCTAAAACATCCAAAATTGAGAGTTT
1 AGGGGCTAAAACATCCAAAATTGA-AGTTT
* ** *
52560 AGGGGGTAAAATGTCCAAATTTGAAGTT
1 AGGGGCTAAAACATCCAAAATTGAAGTT
52588 CAGGACAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (29 bp):
AGGGGCTAAAACATCCAAAATTGAAGTTT
Found at i:56047 original size:2 final size:2
Alignment explanation
Indices: 56040--56069 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
56030 ATGTCATTTC
56040 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.