Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017559.1 Corchorus olitorius cultivar O-4 contig17592, 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: 41555
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:6294 original size:133 final size:130
Alignment explanation
Indices: 6039--6305 Score: 439
Period size: 133 Copynumber: 2.0 Consensus size: 130
6029 GCCTACATAA
**
6039 GAAATTGCCGGTAAATAGGTATTGCTAGTTCAAACAGCAACCCTATATTTGTGCAATAAAGCACC
1 GAAATTGCCGGTAAATAGGTATTGAAAGTTCAAACAGCAACCCTATATTTGTGCAATAAAGCACC
6104 AACAACATGGAGAACATTGACATAGGCATTAAGAGTGAACCCACAAGCTTGAAAGT-CCAAGGGT
66 AACAACATGGAGAACATTGACATAGGCATTAAGAGTGAACCCACAAGCTTGAAAGTCCCAAGGGT
*
6168 GAAATTGCCGGTAAATAGGTA-TGAAAGTTCAAACAGCAACCCTGTATTTGTGCAATAAAGCACC
1 GAAATTGCCGGTAAATAGGTATTGAAAGTTCAAACAGCAACCCTATATTTGTGCAATAAAGCACC
*
6232 AAGAACATGGAGAGGAGAACATTGACATAGGCATTAAGAGTGAACCCACAAGCTTGAAAGTCCCA
66 AACAACAT-----GGAGAACATTGACATAGGCATTAAGAGTGAACCCACAAGCTTGAAAGTCCCA
6297 AGGGT
126 AGGGT
6302 GAAA
1 GAAA
6306 ACACATCAAT
Statistics
Matches: 128, Mismatches: 4, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
128 47 0.37
129 21 0.16
133 48 0.38
134 12 0.09
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.20
Consensus pattern (130 bp):
GAAATTGCCGGTAAATAGGTATTGAAAGTTCAAACAGCAACCCTATATTTGTGCAATAAAGCACC
AACAACATGGAGAACATTGACATAGGCATTAAGAGTGAACCCACAAGCTTGAAAGTCCCAAGGGT
Found at i:8911 original size:21 final size:21
Alignment explanation
Indices: 8869--8924 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
8859 GTTTAGCAAT
* *
8869 TGTATAGATGAAATTA--TAC
1 TGTACAGATGAGATTAGGTAC
*
8888 TGTACAGATTAGATTAGGTAC
1 TGTACAGATGAGATTAGGTAC
8909 TGTACAGATGAGATTA
1 TGTACAGATGAGATTA
8925 TTAGAGCAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 13 0.42
21 18 0.58
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (21 bp):
TGTACAGATGAGATTAGGTAC
Found at i:18553 original size:162 final size:159
Alignment explanation
Indices: 18286--18603 Score: 503
Period size: 162 Copynumber: 2.0 Consensus size: 159
18276 TGTGTTGATT
*
18286 AGGAACCATGTCTGGTTCTCTGAAGGAAGTCGTCCTTGACATCGATCTGAAACTCATGGTTTTCG
1 AGGAACCATGTCTGGTTCTCTGAAGGAAGTCGTCCTTGACATCGATCTGAAACTCATGGTCTTCG
* * *
18351 GATTGATTCCTTTAACTAAACTTCCCTCCCCATTTTGGATTACAGAATTGGCATCAATATTCGTT
66 GATGGATTCCTTTAACTAAACTTCCATCCCCATTTTGGATTACAGAATTGCCATC-A-A-TCGTT
18416 TTCCCCAAACTCGAGTCTTGATCAACTTTCGA
128 TTCCCCAAACTCGAGTCTTGATCAACTTTCGA
* **
18448 AGGAACCATGTCTGGTTCTCTGAAGGAAGTTGTCCTTGACATCGATCTGGTACTCATGGTCTTCG
1 AGGAACCATGTCTGGTTCTCTGAAGGAAGTCGTCCTTGACATCGATCTGAAACTCATGGTCTTCG
* * *
18513 GATGG-TATCCTTTAAGTAAATTTCCATCCCCATTTTGGATTCCAGAATTGCCATCAATCGTTTT
66 GATGGAT-TCCTTTAACTAAACTTCCATCCCCATTTTGGATTACAGAATTGCCATCAATCGTTTT
18577 CCCCAAACTCGAGTCTTGATCAACTTT
130 CCCCAAACTCGAGTCTTGATCAACTTT
18604 TGGCTTCATG
Statistics
Matches: 145, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
159 34 0.23
160 1 0.01
161 2 0.01
162 108 0.74
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (159 bp):
AGGAACCATGTCTGGTTCTCTGAAGGAAGTCGTCCTTGACATCGATCTGAAACTCATGGTCTTCG
GATGGATTCCTTTAACTAAACTTCCATCCCCATTTTGGATTACAGAATTGCCATCAATCGTTTTC
CCCAAACTCGAGTCTTGATCAACTTTCGA
Found at i:18780 original size:21 final size:21
Alignment explanation
Indices: 18756--18795 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
18746 GTTACGTCAT
*
18756 CTGTTTTTTCCTCTGTTTCCC
1 CTGTTTTCTCCTCTGTTTCCC
18777 CTGTTTTCTCCTCTGTTTC
1 CTGTTTTCTCCTCTGTTTC
18796 TAATGGTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.33, G:0.10, T:0.57
Consensus pattern (21 bp):
CTGTTTTCTCCTCTGTTTCCC
Found at i:20511 original size:25 final size:26
Alignment explanation
Indices: 20471--20519 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
20461 TACAATATTA
*
20471 TTACTAAAAAACACAAGTATAGTAGT
1 TTACCAAAAAACACAAGTATAGTAGT
20497 TTACCAAAAAA-ACAAGTATAGTA
1 TTACCAAAAAACACAAGTATAGTA
20520 TATCAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.53, C:0.12, G:0.10, T:0.24
Consensus pattern (26 bp):
TTACCAAAAAACACAAGTATAGTAGT
Found at i:33125 original size:2 final size:2
Alignment explanation
Indices: 33118--33142 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33108 CTTTCTGCAT
33118 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
33143 TTTTTTTGGT
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.