Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021700.1 Corchorus olitorius cultivar O-4 contig21733, 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: 14978
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Found at i:1731 original size:45 final size:45
Alignment explanation
Indices: 1682--1978 Score: 515
Period size: 45 Copynumber: 6.6 Consensus size: 45
1672 TGGCTCAATC
* *
1682 AGAGGGCGATAAAAATCAACCCCGCCGAGAGTCTGATGCAGAGGT
1 AGAGGGCGATAAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGT
* *
1727 AGAGGGCGATAAACATCAACCCCGCCAAGAGTCCTATGCAGAGGT
1 AGAGGGCGATAAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGT
*
1772 AGAGGGCGATAAAAATCAACCCCGACAAGAGTCCGATGCAGAGGT
1 AGAGGGCGATAAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGT
**
1817 AGAGGGCGATAAGGATCAACCCCGCCAAGAGTCCGATGCAGAGGT
1 AGAGGGCGATAAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGT
*
1862 AGAGGGCGATAAAAATCAA-CCCGCCAAGAGTCCGATGAAGAGGT
1 AGAGGGCGATAAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGT
1906 AGAGGGCGATAAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGT
1 AGAGGGCGATAAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGT
1951 AGAGGGCGATAAAAATCAACCCCGCCAA
1 AGAGGGCGATAAAAATCAACCCCGCCAA
1979 AAAGCCGTAG
Statistics
Matches: 237, Mismatches: 14, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
44 43 0.18
45 194 0.82
ACGTcount: A:0.36, C:0.24, G:0.29, T:0.11
Consensus pattern (45 bp):
AGAGGGCGATAAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGT
Found at i:2206 original size:39 final size:40
Alignment explanation
Indices: 2140--2215 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 40
2130 ACCTCGTTGT
*
2140 CGCTGAAAAGTTTCTTCGGGACGCGATTGGGA-CCATTGG
1 CGCTGAAAAGTTTCTTCGGGACACGATTGGGAGCCATTGG
* * *
2179 CGCTTAAAGGTTTCTTCTGGACACGATTGGGAGCCAT
1 CGCTGAAAAGTTTCTTCGGGACACGATTGGGAGCCAT
2216 GATGGTGGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 28 0.88
40 4 0.12
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (40 bp):
CGCTGAAAAGTTTCTTCGGGACACGATTGGGAGCCATTGG
Found at i:3289 original size:11 final size:10
Alignment explanation
Indices: 3273--3299 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3263 TGTTGTTCTT
3273 AAAAAAAAAC
1 AAAAAAAAAC
3283 AAAAAAAAAC
1 AAAAAAAAAC
3293 AAAAAAA
1 AAAAAAA
3300 TAGAGAGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:4689 original size:36 final size:36
Alignment explanation
Indices: 4615--4692 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 36
4605 CATAAGAAAA
** *
4615 GCCCAAATACATAATTAAGTTGGCTTAATTCTATTG
1 GCCCAAATACATAATTAAGTTGGCCCAATTCTACTG
4651 GCCCAAATACATAATTAAGTTGGCCCAACTT-TACTG
1 GCCCAAATACATAATTAAGTTGGCCCAA-TTCTACTG
4687 GCCCAA
1 GCCCAA
4693 TACTACCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 36 0.95
37 2 0.05
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.29
Consensus pattern (36 bp):
GCCCAAATACATAATTAAGTTGGCCCAATTCTACTG
Found at i:4860 original size:12 final size:12
Alignment explanation
Indices: 4852--4943 Score: 64
Period size: 12 Copynumber: 7.7 Consensus size: 12
4842 ATCCAAGCTT
4852 TTCATCAAGTTA
1 TTCATCAAGTTA
*
4864 TTCATCAAAGTTC
1 TTCATC-AAGTTA
* *
4877 TTCAACAAG-TC
1 TTCATCAAGTTA
* *
4888 TTCACCAAGGTA
1 TTCATCAAGTTA
*
4900 TTCATCAAAGTTC
1 TTCATC-AAGTTA
*
4913 TTCAACAAGTT-
1 TTCATCAAGTTA
*
4924 TTCA-CACAGTTC
1 TTCATCA-AGTTA
4936 TTCATCAA
1 TTCATCAA
4944 ATTCTCCACC
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
10 2 0.03
11 18 0.27
12 25 0.38
13 21 0.32
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.35
Consensus pattern (12 bp):
TTCATCAAGTTA
Found at i:4940 original size:36 final size:36
Alignment explanation
Indices: 4845--4948 Score: 133
Period size: 36 Copynumber: 2.9 Consensus size: 36
4835 AGGAGAAATC
4845 CAAGCTTTTCATCA-AGTTATTCATCAAAGTTCTTCAA
1 CAAG-TTTTCA-CACAGTTATTCATCAAAGTTCTTCAA
* *
4882 CAAGTCTTCAC-CAAGGTATTCATCAAAGTTCTTCAA
1 CAAGTTTTCACAC-AGTTATTCATCAAAGTTCTTCAA
*
4918 CAAGTTTTCACACAGTTCTTCATCAAA-TTCT
1 CAAGTTTTCACACAGTTATTCATCAAAGTTCT
4949 CCACCAATCT
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
35 5 0.08
36 49 0.83
37 5 0.08
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.36
Consensus pattern (36 bp):
CAAGTTTTCACACAGTTATTCATCAAAGTTCTTCAA
Found at i:10714 original size:7 final size:7
Alignment explanation
Indices: 10702--10746 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
10692 TAGTCATGAT
10702 TATTATA
1 TATTATA
10709 TATTAT-
1 TATTATA
10715 T-TTATA
1 TATTATA
10721 TATTATA
1 TATTATA
10728 T-TATATA
1 TAT-TATA
10735 TATTAT-
1 TATTATA
10741 TATTAT
1 TATTAT
10747 TCTTTTAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
5 4 0.12
6 9 0.26
7 20 0.59
8 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TATTATA
Found at i:10719 original size:12 final size:12
Alignment explanation
Indices: 10704--10746 Score: 59
Period size: 12 Copynumber: 3.3 Consensus size: 12
10694 GTCATGATTA
10704 TTATATATTATT
1 TTATATATTATT
10716 TTATATATTATAT
1 TTATATATTAT-T
10729 TATATATATTATT
1 T-TATATATTATT
10742 ATTAT
1 -TTAT
10747 TCTTTTAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 11 0.39
13 6 0.21
14 11 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTATATATTATT
Done.