Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012275.1 Corchorus olitorius cultivar O-4 contig12308, 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: 37925
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:1591 original size:44 final size:44
Alignment explanation
Indices: 1528--1616 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
1518 TACAATTTTC
* *
1528 TTTCATATTAATGAAGTGTCACTTTTTGGTGAACTGACAGTGTA
1 TTTCATATTAATGAAGTGTCACTTTTTGGTGAACTAACAATGTA
1572 TTTCATATTAATGAAGTGTCACTTTTTGGTGAACTAACAATGTA
1 TTTCATATTAATGAAGTGTCACTTTTTGGTGAACTAACAATGTA
1616 T
1 T
1617 GACTTGTATA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (44 bp):
TTTCATATTAATGAAGTGTCACTTTTTGGTGAACTAACAATGTA
Found at i:18612 original size:39 final size:39
Alignment explanation
Indices: 18558--18674 Score: 234
Period size: 39 Copynumber: 3.0 Consensus size: 39
18548 ATCGGTACCA
18558 CAAACAACCTGATGGCCTAGATTTGGGGAGTTAGAGAGG
1 CAAACAACCTGATGGCCTAGATTTGGGGAGTTAGAGAGG
18597 CAAACAACCTGATGGCCTAGATTTGGGGAGTTAGAGAGG
1 CAAACAACCTGATGGCCTAGATTTGGGGAGTTAGAGAGG
18636 CAAACAACCTGATGGCCTAGATTTGGGGAGTTAGAGAGG
1 CAAACAACCTGATGGCCTAGATTTGGGGAGTTAGAGAGG
18675 AGCTACTACT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.31, C:0.15, G:0.33, T:0.21
Consensus pattern (39 bp):
CAAACAACCTGATGGCCTAGATTTGGGGAGTTAGAGAGG
Found at i:19108 original size:38 final size:38
Alignment explanation
Indices: 19045--19118 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
19035 TTTTATATGG
* *
19045 TCATAGTTAAAAGTGAAAAAGTAATGAGTTTGTAATGA
1 TCATAGTTAAAAGTGAAAAAATAATGAATTTGTAATGA
*
19083 TCATAGTTAGAAGT-AAATAAATAATGAATTTGTAAT
1 TCATAGTTAAAAGTGAAA-AAATAATGAATTTGTAAT
19119 TTGAATGATC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 3 0.09
38 29 0.91
ACGTcount: A:0.46, C:0.03, G:0.18, T:0.34
Consensus pattern (38 bp):
TCATAGTTAAAAGTGAAAAAATAATGAATTTGTAATGA
Found at i:22620 original size:21 final size:21
Alignment explanation
Indices: 22595--22647 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
22585 AGGGAACTGC
* *
22595 AAAAACAAACGGAATTAAATA
1 AAAAACAAACGGAATAAAAGA
*
22616 AAAAATCAAAAGGAATAAAAGA
1 AAAAA-CAAACGGAATAAAAGA
*
22638 CAAAACAAAC
1 AAAAACAAAC
22648 ATTCAAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.70, C:0.11, G:0.09, T:0.09
Consensus pattern (21 bp):
AAAAACAAACGGAATAAAAGA
Found at i:25616 original size:28 final size:30
Alignment explanation
Indices: 25561--25616 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
25551 CCTATTGTCC
25561 TGAATTTGAGAAATTCAGGAGGACAAGTCT
1 TGAATTTGAGAAATTCAGGAGGACAAGTCT
* *
25591 TGAATTT-TGAAATTCATG-GGACAAGT
1 TGAATTTGAGAAATTCAGGAGGACAAGT
25617 TGTCATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.33
29 9 0.38
30 7 0.29
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.30
Consensus pattern (30 bp):
TGAATTTGAGAAATTCAGGAGGACAAGTCT
Found at i:26597 original size:2 final size:2
Alignment explanation
Indices: 26590--26619 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
26580 TAGTATTTAG
26590 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26620 GTACTTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31875 original size:23 final size:23
Alignment explanation
Indices: 31839--31890 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
31829 GGTGTGACTT
* *
31839 TGATCCAGTCCCCATAATCGCTC
1 TGATCTAGTCCCCACAATCGCTC
*
31862 TTATCTAGTCCCCACAATCGCTC
1 TGATCTAGTCCCCACAATCGCTC
31885 TGATCT
1 TGATCT
31891 TTTAATCTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.37, G:0.12, T:0.31
Consensus pattern (23 bp):
TGATCTAGTCCCCACAATCGCTC
Found at i:32304 original size:2 final size:2
Alignment explanation
Indices: 32297--32328 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
32287 TTGTATTGCT
32297 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32329 CTACATACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32614 original size:56 final size:56
Alignment explanation
Indices: 32526--32636 Score: 177
Period size: 56 Copynumber: 2.0 Consensus size: 56
32516 TCTGTTTTCT
* *
32526 TTCACACAATAAATGTTATAATAAATCCTATCCCCCTATTTCTACTTAATTATTCC
1 TTCACACAATAAATGTTATAATAAATCCTATCCCCATATCTCTACTTAATTATTCC
* **
32582 TTCACACAATAAATGTTATAATAAGTTTTATCCCCATATCTCTACTTAATTATTC
1 TTCACACAATAAATGTTATAATAAATCCTATCCCCATATCTCTACTTAATTATTC
32637 TACAAAATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.41
Consensus pattern (56 bp):
TTCACACAATAAATGTTATAATAAATCCTATCCCCATATCTCTACTTAATTATTCC
Found at i:32760 original size:42 final size:42
Alignment explanation
Indices: 32701--32783 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
32691 GCTAAGGATC
*
32701 ATGATTTGAGTTGAGTATTTCGTAATTTACAAAGAATTTTCT
1 ATGATTTGAGTTGAGTATTCCGTAATTTACAAAGAATTTTCT
* *
32743 ATGATTTGAGTTGAGTATTCCTTAATTTACAGAGAATTTTC
1 ATGATTTGAGTTGAGTATTCCGTAATTTACAAAGAATTTTC
32784 AAGACTTAGC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (42 bp):
ATGATTTGAGTTGAGTATTCCGTAATTTACAAAGAATTTTCT
Found at i:36114 original size:151 final size:151
Alignment explanation
Indices: 35840--36131 Score: 521
Period size: 151 Copynumber: 1.9 Consensus size: 151
35830 GAAAGTTGAG
* * *
35840 TCAAATTTGACCTCATGTATATCTCTTACCTGTTGAAGTTCTTATATAATTCATTATCATTTTTA
1 TCAAATTCGACCTCATGTATATCTCTTACCTATTGAAGTTCTTATATAATTCATTATCAATTTTA
35905 TATCTATGTATGCTTAAAGTACTCAGCCATATGTCGTCCATGCTGAATACTTTCCATAGCTATGT
66 TATCTATGTATGCTTAAAGTACTCAGCCATATGTCGTCCATGCTGAATACTTTCCATAGCTATGT
35970 ATATTTGGGATGCTTTCCATA
131 ATATTTGGGATGCTTTCCATA
35991 TCAAATTCGACCTCATGTATATCTCTTACCTATTGAAGTTCTTATATAATTCATTATCAATTTTA
1 TCAAATTCGACCTCATGTATATCTCTTACCTATTGAAGTTCTTATATAATTCATTATCAATTTTA
* * * *
36056 TATCTATGTATGTTTAACGTACTCAGCCATATGTCGTCCATGCTTAATGCTTTCCATAGCTATGT
66 TATCTATGTATGCTTAAAGTACTCAGCCATATGTCGTCCATGCTGAATACTTTCCATAGCTATGT
36121 ATATTTGGGAT
131 ATATTTGGGAT
36132 ACTCGGTCAT
Statistics
Matches: 134, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
151 134 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (151 bp):
TCAAATTCGACCTCATGTATATCTCTTACCTATTGAAGTTCTTATATAATTCATTATCAATTTTA
TATCTATGTATGCTTAAAGTACTCAGCCATATGTCGTCCATGCTGAATACTTTCCATAGCTATGT
ATATTTGGGATGCTTTCCATA
Done.