Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018984.1 Corchorus olitorius cultivar O-4 contig19017, 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: 41787
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Found at i:6 original size:1 final size:1
Alignment explanation
Indices: 1--26 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
27 AAGCATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:10217 original size:16 final size:16
Alignment explanation
Indices: 10179--10217 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
10169 CCACAAAATG
10179 CAAAAAGAAGAAAACA
1 CAAAAAGAAGAAAACA
*
10195 -AAGAAAGAGGAAAACA
1 CAA-AAAGAAGAAAACA
10211 CAAAAAG
1 CAAAAAG
10218 CAAGTTAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 2 0.10
16 16 0.80
17 2 0.10
ACGTcount: A:0.72, C:0.10, G:0.18, T:0.00
Consensus pattern (16 bp):
CAAAAAGAAGAAAACA
Found at i:12308 original size:10 final size:10
Alignment explanation
Indices: 12293--12350 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
12283 GAAAAAAAAA
12293 CTAATTAAAT
1 CTAATTAAAT
*
12303 CTAATTAAGT
1 CTAATTAAAT
*
12313 CTAATTAAAC
1 CTAATTAAAT
*
12323 CTTAACT-AAT
1 C-TAATTAAAT
*
12333 CTAAATAAAT
1 CTAATTAAAT
12343 -T-ATTAAAT
1 CTAATTAAAT
12351 ACTAGCCCTA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
8 6 0.15
9 5 0.13
10 24 0.62
11 4 0.10
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (10 bp):
CTAATTAAAT
Found at i:13685 original size:49 final size:49
Alignment explanation
Indices: 13580--13729 Score: 216
Period size: 49 Copynumber: 3.1 Consensus size: 49
13570 AGACCATGGT
* * *
13580 CCAACGTGATGACCCAAGTGGAAACAAAAAGAAA-A-A-AGAAATGAAC
1 CCAACATGATGGCCCAAGTGGAAACAAAAAGAAATAGATGGAAATGAAC
**
13626 CCAACATGATGGCCCAAGTATAAACAAAAAGAAATAGATGGAAATGAAC
1 CCAACATGATGGCCCAAGTGGAAACAAAAAGAAATAGATGGAAATGAAC
* *
13675 CCAACATGATGGCCCAAGTGGAAACAAAAAGAAATAGTTGGAAATGAGC
1 CCAACATGATGGCCCAAGTGGAAACAAAAAGAAATAGATGGAAATGAAC
13724 CCAACA
1 CCAACA
13730 ACACAAGAAA
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
46 30 0.33
47 1 0.01
48 1 0.01
49 60 0.65
ACGTcount: A:0.50, C:0.18, G:0.20, T:0.12
Consensus pattern (49 bp):
CCAACATGATGGCCCAAGTGGAAACAAAAAGAAATAGATGGAAATGAAC
Found at i:14314 original size:28 final size:27
Alignment explanation
Indices: 14275--14395 Score: 145
Period size: 28 Copynumber: 4.3 Consensus size: 27
14265 TATTTCTTAA
*
14275 TTGGTCATTTGCACTCTCAGGGGCATT
1 TTGGTCATTTGCACTCTCAAGGGCATT
*
14302 TTGGGTCATTTGCACTCTCAGGGGCATT
1 TT-GGTCATTTGCACTCTCAAGGGCATT
*
14330 TTGGTCATTTGCA-TATTCAAGGGCATTT
1 TTGGTCATTTGCACT-CTCAAGGGCA-TT
* *
14358 TTTGTCATTTTTGCACTTTCAAGGGCATT
1 TTGGTCA--TTTGCACTCTCAAGGGCATT
14387 TTGGTCATT
1 TTGGTCATT
14396 CTGAATGCTT
Statistics
Matches: 84, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
26 1 0.01
27 23 0.27
28 35 0.42
29 8 0.10
30 16 0.19
31 1 0.01
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.42
Consensus pattern (27 bp):
TTGGTCATTTGCACTCTCAAGGGCATT
Found at i:14365 original size:55 final size:56
Alignment explanation
Indices: 14275--14395 Score: 156
Period size: 55 Copynumber: 2.2 Consensus size: 56
14265 TATTTCTTAA
* *
14275 TTGGTCATTTGCACTCTCAGGGGCATTTTGGGTCA-TTTGCACTCTCAGGGGCATT
1 TTGGTCATTTGCACTCTCAAGGGCATTTTGGGTCATTTTGCACTCTCAAGGGCATT
* ** *
14330 TTGGTCATTTGCA-TATTCAAGGGCATTTTTTGTCATTTTTGCACTTTCAAGGGCATT
1 TTGGTCATTTGCACT-CTCAAGGGCATTTTGGGTCA-TTTTGCACTCTCAAGGGCATT
14387 TTGGTCATT
1 TTGGTCATT
14396 CTGAATGCTT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 1 0.02
55 29 0.51
57 27 0.47
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.42
Consensus pattern (56 bp):
TTGGTCATTTGCACTCTCAAGGGCATTTTGGGTCATTTTGCACTCTCAAGGGCATT
Found at i:15091 original size:39 final size:39
Alignment explanation
Indices: 15037--15111 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
15027 CAGGTATGGT
15037 TGTCTAACTTTCTCTCTTCTCTCGTAATCTAGATCTGGC
1 TGTCTAACTTTCTCTCTTCTCTCGTAATCTAGATCTGGC
*
15076 TGTCTAACTTTCTCTCTTCTCTCTTAATCTAGATCT
1 TGTCTAACTTTCTCTCTTCTCTCGTAATCTAGATCT
15112 AGTATCTGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.16, C:0.28, G:0.09, T:0.47
Consensus pattern (39 bp):
TGTCTAACTTTCTCTCTTCTCTCGTAATCTAGATCTGGC
Found at i:23876 original size:13 final size:13
Alignment explanation
Indices: 23860--23885 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23850 ATGAGAAAAT
23860 CAAAAGTGTTTTC
1 CAAAAGTGTTTTC
23873 CAAAAGTGTTTTC
1 CAAAAGTGTTTTC
23886 AAGTATGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
CAAAAGTGTTTTC
Done.