Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012520.1 Corchorus olitorius cultivar O-4 contig12553, 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: 10824
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:1430 original size:29 final size:31
Alignment explanation
Indices: 1388--1461 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 31
1378 GCTAAATAAT
*
1388 CAATTCAGGATATAACGTTA-CAAAA-CAAA
1 CAATTAAGGATATAACGTTATCAAAAGCAAA
* * *
1417 CAATTAAGGATATAACGTTATGAAAAGCGAG
1 CAATTAAGGATATAACGTTATCAAAAGCAAA
1448 CAATTAAGGATATA
1 CAATTAAGGATATA
1462 GTCCATTAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 19 0.49
30 4 0.10
31 16 0.41
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.23
Consensus pattern (31 bp):
CAATTAAGGATATAACGTTATCAAAAGCAAA
Found at i:1660 original size:31 final size:31
Alignment explanation
Indices: 1591--1732 Score: 135
Period size: 31 Copynumber: 4.6 Consensus size: 31
1581 CCCTAACTGA
* *
1591 TTATATCCTTAATTGCTTGAAATAAAAAAACA
1 TTATATCCTTAATTGCTTGAAA-CAAAAAACG
*
1623 TCATATCCTTAATTGCTTGAAACAAAAAACG
1 TTATATCCTTAATTGCTTGAAACAAAAAACG
******
1654 TTATATCCTTAATTGCTTG--TTTTGTAACG
1 TTATATCCTTAATTGCTTGAAACAAAAAACG
*** *
1683 TTATATCCTTAATTGCTTGCGGCAGAAAACG
1 TTATATCCTTAATTGCTTGAAACAAAAAACG
*
1714 TTATATCCTAAATTGCTTG
1 TTATATCCTTAATTGCTTG
1733 CTTATCATCT
Statistics
Matches: 91, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
29 23 0.25
31 47 0.52
32 21 0.23
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (31 bp):
TTATATCCTTAATTGCTTGAAACAAAAAACG
Found at i:1784 original size:16 final size:17
Alignment explanation
Indices: 1763--1795 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1753 TATTCAGAAG
1763 AAAATATTTT-TTTAAA
1 AAAATATTTTATTTAAA
1779 AAAATATTTTATTTAAA
1 AAAATATTTTATTTAAA
1796 TAACTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAAATATTTTATTTAAA
Found at i:1905 original size:16 final size:16
Alignment explanation
Indices: 1868--1898 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1858 GCATTGCTTG
1868 GTAGAAAAATGTATTA
1 GTAGAAAAATGTATTA
1884 GTAGAAAAATGTATT
1 GTAGAAAAATGTATT
1899 CTTAGAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.32
Consensus pattern (16 bp):
GTAGAAAAATGTATTA
Found at i:2775 original size:31 final size:31
Alignment explanation
Indices: 2736--2815 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 31
2726 TTGCTGCCAC
**
2736 AAGCAATTAAGGATATAACGTTTTTTATTTA
1 AAGCAATTAAGGATATAACGTTTTCGATTTA
* * * *
2767 AAGTAATTAAGGATATGAGGTTTTCGATTTC
1 AAGCAATTAAGGATATAACGTTTTCGATTTA
2798 AAGCAATTAAGGATATAA
1 AAGCAATTAAGGATATAA
2816 TCAGTTAGGG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.36
Consensus pattern (31 bp):
AAGCAATTAAGGATATAACGTTTTCGATTTA
Found at i:2997 original size:29 final size:31
Alignment explanation
Indices: 2923--2989 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
2913 TTTAACGGAC
2923 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
*
2954 TATATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
2983 TATATCC
1 TATATCC
2990 CAAATTGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGCTTTTCGTAACGT
Found at i:4516 original size:14 final size:14
Alignment explanation
Indices: 4494--4526 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
4484 TTGACGTTTG
*
4494 TTGAGTATATTGAA
1 TTGAATATATTGAA
4508 TTGAATATATTGAA
1 TTGAATATATTGAA
4522 TTGAA
1 TTGAA
4527 GGAGTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (14 bp):
TTGAATATATTGAA
Found at i:10255 original size:2 final size:2
Alignment explanation
Indices: 10248--10276 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10238 TCCATTGTTT
10248 TA TA 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 TA TA T
10277 TTAAACTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.