Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011001.1 Corchorus olitorius cultivar O-4 contig11033, 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: 5873
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Found at i:27 original size:21 final size:21
Alignment explanation
Indices: 1--50 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
1 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
22 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
43 TCCAATGA
1 TCCAATGA
51 ACTTCTAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACTTGC
Found at i:1096 original size:251 final size:252
Alignment explanation
Indices: 653--1153 Score: 810
Period size: 251 Copynumber: 2.0 Consensus size: 252
643 TTTCACATCG
653 CAATTGATACGAATCTAGTTGTATTAGATTCAAATCTATCATTGAGACCTGCCAAGAATCAACTT
1 CAATTGATACGAATCTAGTTGTATTAGATTCAAATCTATCATTGAGACCTGCCAAGAATCAACTT
* * * *
718 GAACAACTTCAACTTCTAGATGTGTTTGTTGATGATCTTCACTAAAGCAATCTTCTTCTTTCGTC
66 GAACAACCTCAACTTCTAGATGTGTATGTCGATGATCTTCACTAAAGCAATCTTCTTCGTTCGTC
** *
783 GGCCTTAGATGAACAATTAGACCTGCAATTGTCAACCTAAGATCACAAGATTCACAAACAATCAA
131 GGCCTTAGACCAACAATTAGACCTGCAATTGACAACCTAAGATCACAAGATTCACAAACAATCAA
848 GCAA-CACAACTTAATTGTTTGCTAGGACTCTACAAGATTGAAGAACCCTAAGTTAC
196 GCAATCACAACTTAATTGTTTGCTAGGACTCTACAAGATTGAAGAACCCTAAGTTAC
* * * *
904 CAATTGATACTAATCTAGTTGTATTAGATTCAAATCTATCCTTGAGAGCTGCCAATAATCAACTT
1 CAATTGATACGAATCTAGTTGTATTAGATTCAAATCTATCATTGAGACCTGCCAAGAATCAACTT
**
969 GAACTTCCTCAACTTCTAGATGTGTATGTCGATGATCTTCACCT-AAGCAATCTTCTTCGTTCGT
66 GAACAACCTCAACTTCTAGATGTGTATGTCGATGATCTTCA-CTAAAGCAATCTTCTTCGTTCGT
** *
1033 CGGCCTTAGACCTTCAATTTGACCTGCAATTGA-ACACCTAAGATCACAAGATTCACAAACAATC
130 CGGCCTTAGACCAACAATTAGACCTGCAATTGACA-ACCTAAGATCACAAGATTCACAAACAATC
*
1097 AAGCAATCACAACTTAATTGTTTGCTAGGACTCTACATGATTGAAGAACCCTAAGTT
194 AAGCAATCACAACTTAATTGTTTGCTAGGACTCTACAAGATTGAAGAACCCTAAGTT
1154 TGCTCAAACT
Statistics
Matches: 230, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
250 1 0.00
251 178 0.77
252 51 0.22
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (252 bp):
CAATTGATACGAATCTAGTTGTATTAGATTCAAATCTATCATTGAGACCTGCCAAGAATCAACTT
GAACAACCTCAACTTCTAGATGTGTATGTCGATGATCTTCACTAAAGCAATCTTCTTCGTTCGTC
GGCCTTAGACCAACAATTAGACCTGCAATTGACAACCTAAGATCACAAGATTCACAAACAATCAA
GCAATCACAACTTAATTGTTTGCTAGGACTCTACAAGATTGAAGAACCCTAAGTTAC
Found at i:5808 original size:40 final size:39
Alignment explanation
Indices: 5635--5860 Score: 164
Period size: 40 Copynumber: 5.7 Consensus size: 39
5625 GAAATCTTTA
* **
5635 ATGGGATCTTTCCCCT-AATTGAAA-ACTTTGAAAAAGACCAG
1 ATGGGACCTTT-CCCTAAATT-AAAGACTTT-AAAAA-ACTTG
*
5676 ATGGGACCTTTCCCTAAATTAAA-ACTTCTGAAAAACTTG
1 ATGGGACCTTTCCCTAAATTAAAGACTT-TAAAAAACTTG
* *
5715 ATGGGATCTTTCCCTAAATTAAAGACTTTAAAAAGAAACTGG
1 ATGGGACCTTTCCCTAAATTAAAGACTTT--AAA-AAACTTG
* *
5757 ATGGGATCTTTCCCTAAATCGAAAGAC-TTAAACAAACTTG
1 ATGGGACCTTTCCCTAAAT-TAAAGACTTTAAA-AAACTTG
* *
5797 ATGGGACCTTTCCC--AATTAGAA-A-TCTT-GAAAGCTTG
1 ATGGGACCTTTCCCTAAATTA-AAGACT-TTAAAAAACTTG
* * *
5833 ATGGGATCTTTCCCTATATTAAAAACTT
1 ATGGGACCTTTCCCTAAATTAAAGACTT
5861 GAGAAATACT
Statistics
Matches: 155, Mismatches: 16, Indels: 31
0.77 0.08 0.15
Matches are distributed among these distances:
36 19 0.12
37 5 0.03
38 13 0.08
39 27 0.17
40 41 0.26
41 17 0.11
42 27 0.17
43 6 0.04
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (39 bp):
ATGGGACCTTTCCCTAAATTAAAGACTTTAAAAAACTTG
Done.