Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014382.1 Corchorus olitorius cultivar O-4 contig14415, 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: 5076
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Found at i:1878 original size:7 final size:7
Alignment explanation
Indices: 1866--1915 Score: 59
Period size: 7 Copynumber: 7.1 Consensus size: 7
1856 CCCATCAGCG
1866 AAAGAAA
1 AAAGAAA
1873 AAAGAAA
1 AAAGAAA
*
1880 AGCAAG-CA
1 A--AAGAAA
1888 AAA-AAA
1 AAAGAAA
1894 AAAGAAA
1 AAAGAAA
1901 AAAGAAA
1 AAAGAAA
1908 AAAGAAA
1 AAAGAAA
1915 A
1 A
1916 TTTGAAAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 6 0.16
7 26 0.70
8 2 0.05
9 3 0.08
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:2410 original size:26 final size:26
Alignment explanation
Indices: 2381--2443 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
2371 AGAAGGAGAC
2381 AAGAAAAATGAAGAAAAGAA-TTGAAA
1 AAGAAAAATGAAGAAAA-AAGTTGAAA
*
2407 AAGAAAAGA-AAAGAAAAAAGTTGAAA
1 AAGAAAA-ATGAAGAAAAAAGTTGAAA
*
2433 ATGTAAAAATG
1 AAG-AAAAATG
2444 GAGTAAAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
25 2 0.07
26 23 0.77
27 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.19, T:0.13
Consensus pattern (26 bp):
AAGAAAAATGAAGAAAAAAGTTGAAA
Found at i:2422 original size:16 final size:16
Alignment explanation
Indices: 2391--2424 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2381 AAGAAAAATG
**
2391 AAGAAAAGAATTGAAA
1 AAGAAAAGAAAAGAAA
2407 AAGAAAAGAAAAGAAA
1 AAGAAAAGAAAAGAAA
2423 AA
1 AA
2425 AGTTGAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (16 bp):
AAGAAAAGAAAAGAAA
Found at i:4686 original size:35 final size:35
Alignment explanation
Indices: 3840--4685 Score: 1008
Period size: 35 Copynumber: 24.0 Consensus size: 35
3830 CCTAGTGCGG
*
3840 TCATTTCAAGAAGATTTT-TATGATCAGAGTTGATC
1 TCATTTCAAGAAG-TTTTCGATGATCAGAGTTGATC
*
3875 TCATTTCAAGAAGTTTT-TATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
3909 TCATTTCCAAGAAGTTTTCGATGATCAG-GTTGATC
1 TCATTT-CAAGAAGTTTTCGATGATCAGAGTTGATC
* **
3944 TCATTTCAATAAGTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* * * **
3979 TTATTTCCATAAGTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* * *
4014 TCCTTTCAAGAAGTTTTCGTTGATCAGAGTTAATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
*
4049 T-AGTTTCAAGAAGTTTTCGTTGATCAGAGTTGATC
1 TCA-TTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* *
4084 TCATTTCAAGAAGTTTTCGTTGATCAGAGTTAATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* ** *
4119 TCGTTTCAAGAAGTTTTTTATGATCAGAGTTAATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* * * *
4154 TCCTTTCAAGAAGTTTTCGTTGATTAGAGATGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
**
4189 TCATTTCAAGAAGTGTTTTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAA--G---TTTTCGATGATCAGAGTTGATC
* ** * *
4229 TCGTTTCAAGAAGTTTTTTATGATTAGAGTTTATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* *
4264 TCCTTTCAAGAAGTTTTCGTTGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
**
4299 TCATTTCAAGAAGTTTTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAG---TTTTCGATGATCAGAGTTGATC
* * *
4337 TTATTCCAAGAAGCTTTT-TATGATCAGAGTTGATC
1 TCATTTCAAGAAG-TTTTCGATGATCAGAGTTGATC
* * *
4372 TCCTTTCAAGAAGTTTTCGTTGATCAAAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* *
4407 TCATTTCAAGAAGTTTT-TATGATCTGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* *
4441 TCGTTTCAAGAAGTATT--ATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* * *
4474 TCCTTCCAAGAAGTTTTCGATGATCAGAGTTAAATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTT-GATC
*
4510 TCGTTTCAAGAAGTTTT-GATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
**
4544 TCATTTCAAGAAGTTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAG-TTTTCGATGATCAGAGTTGATC
* *
4580 TTATTTCAAGAAGTTTTCGGTGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
*
4615 TCGTTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
*
4650 TTATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
4685 T
1 T
4686 TCACATTGAT
Statistics
Matches: 710, Mismatches: 82, Indels: 38
0.86 0.10 0.05
Matches are distributed among these distances:
33 29 0.04
34 92 0.13
35 470 0.66
36 59 0.08
37 1 0.00
38 31 0.04
40 28 0.04
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.41
Consensus pattern (35 bp):
TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
Done.