Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017332.1 Corchorus olitorius cultivar O-4 contig17365, 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: 29109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1017 original size:26 final size:26
Alignment explanation
Indices: 986--1040 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
976 ACAAAATCTT
**
986 TTTACC-ATTTGATTTTTTTCTAAAAA
1 TTTACCAATTTGATTAATTTC-AAAAA
*
1012 TTTACCAATTTTATTAATTTCAAAAA
1 TTTACCAATTTGATTAATTTCAAAAA
1038 TTT
1 TTT
1041 TCTTTCGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.53
Consensus pattern (26 bp):
TTTACCAATTTGATTAATTTCAAAAA
Found at i:1729 original size:37 final size:37
Alignment explanation
Indices: 1687--1778 Score: 184
Period size: 37 Copynumber: 2.5 Consensus size: 37
1677 TTATGATTTT
1687 TTTATGATAATTATTATTAATTAGGGTCAATATAGGG
1 TTTATGATAATTATTATTAATTAGGGTCAATATAGGG
1724 TTTATGATAATTATTATTAATTAGGGTCAATATAGGG
1 TTTATGATAATTATTATTAATTAGGGTCAATATAGGG
1761 TTTATGATAATTATTATT
1 TTTATGATAATTATTATT
1779 GATGATTGAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (37 bp):
TTTATGATAATTATTATTAATTAGGGTCAATATAGGG
Found at i:2541 original size:12 final size:13
Alignment explanation
Indices: 2524--2558 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2514 GGTGGATTCT
2524 TCTCCTTCTT-CA
1 TCTCCTTCTTGCA
2536 TCTCCTTCTTGCA
1 TCTCCTTCTTGCA
*
2549 TCTTCTTCTT
1 TCTCCTTCTT
2559 TCAATTCCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.06, C:0.37, G:0.03, T:0.54
Consensus pattern (13 bp):
TCTCCTTCTTGCA
Found at i:8486 original size:32 final size:32
Alignment explanation
Indices: 8450--8516 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
8440 TTCCCAGTTG
*
8450 GTTCTTAACCATTACAAAGTTACAAAGGTATA
1 GTTCTTAACCATTACAAAGTTAAAAAGGTATA
8482 GTTCTTAACCATTACAAAGTTAAAAAGGTATA
1 GTTCTTAACCATTACAAAGTTAAAAAGGTATA
8514 GTT
1 GTT
8517 TGACTTATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (32 bp):
GTTCTTAACCATTACAAAGTTAAAAAGGTATA
Found at i:10024 original size:27 final size:27
Alignment explanation
Indices: 9986--10037 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
9976 AAGGTGATAT
9986 CTTATCTCAATTGGATTTTGTTGACAA
1 CTTATCTCAATTGGATTTTGTTGACAA
10013 CTTATCTCAATTGGATTTTGTTGAC
1 CTTATCTCAATTGGATTTTGTTGAC
10038 TAGGATGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (27 bp):
CTTATCTCAATTGGATTTTGTTGACAA
Found at i:14438 original size:16 final size:15
Alignment explanation
Indices: 14401--14439 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
14391 GGGTTTTTGG
*
14401 GAAAAAAAATAACAA
1 GAAAATAAATAACAA
*
14416 TAAAATAAATAAGCAA
1 GAAAATAAATAA-CAA
14432 GAAAATAA
1 GAAAATAA
14440 TAAAATCAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (15 bp):
GAAAATAAATAACAA
Found at i:14444 original size:24 final size:25
Alignment explanation
Indices: 14414--14464 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
14404 AAAAAATAAC
14414 AATAAAAT-AAATAAGCAAGA-AAAT
1 AATAAAATCAAATAA-CAAGATAAAT
*
14438 AATAAAATCAAGTAACAAGATAAAT
1 AATAAAATCAAATAACAAGATAAAT
14463 AA
1 AA
14465 ATACTCCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.69, C:0.06, G:0.08, T:0.18
Consensus pattern (25 bp):
AATAAAATCAAATAACAAGATAAAT
Found at i:15064 original size:16 final size:17
Alignment explanation
Indices: 15045--15081 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
15035 AATCAGGAAC
15045 AAGAAAAATAGAAGA-A
1 AAGAAAAATAGAAGAGA
*
15061 AAGAAGAATAGAAGAGA
1 AAGAAAAATAGAAGAGA
15078 AAGA
1 AAGA
15082 TTGTAGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.05
Consensus pattern (17 bp):
AAGAAAAATAGAAGAGA
Found at i:19967 original size:66 final size:66
Alignment explanation
Indices: 19896--20019 Score: 196
Period size: 66 Copynumber: 1.9 Consensus size: 66
19886 ACGAATTACA
* *
19896 AGTTTCTCCAAAGAATGAAGTCCATC-GGTTAAAGTTACAACCAATTTGGGACAATTCTGAATGA
1 AGTTTCTCCAAAGAATGAAGGCCATCAGG-CAAAGTTACAACCAATTTGGGACAATTCTGAATGA
19960 AG
65 AG
* *
19962 AGTTTCTCCAAAGAATGAAGGCCATCAGGCAGAGTTCCAACCAATTTGGGACAATTCT
1 AGTTTCTCCAAAGAATGAAGGCCATCAGGCAAAGTTACAACCAATTTGGGACAATTCT
20020 TGATAAAGAG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
66 51 0.96
67 2 0.04
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (66 bp):
AGTTTCTCCAAAGAATGAAGGCCATCAGGCAAAGTTACAACCAATTTGGGACAATTCTGAATGAA
G
Found at i:25732 original size:59 final size:59
Alignment explanation
Indices: 25640--25757 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
25630 AATCTCCCCT
25640 GATTCACTTGTGAGTCCTCATCTCTCCCCCATGCGGGCCAACACGTCAAGTTTTAAGCC
1 GATTCACTTGTGAGTCCTCATCTCTCCCCCATGCGGGCCAACACGTCAAGTTTTAAGCC
25699 GATTCACTTGTGAGTCCTCATCTCTCCCCCATGCGGGCCAACACGTCAAGTTTTAAGCC
1 GATTCACTTGTGAGTCCTCATCTCTCCCCCATGCGGGCCAACACGTCAAGTTTTAAGCC
25758 AATTACCGGT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.20, C:0.34, G:0.19, T:0.27
Consensus pattern (59 bp):
GATTCACTTGTGAGTCCTCATCTCTCCCCCATGCGGGCCAACACGTCAAGTTTTAAGCC
Found at i:26167 original size:2 final size:2
Alignment explanation
Indices: 26160--26196 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
26150 AGAACGACTA
26160 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26197 ATCATTGGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.