Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006553.1 Corchorus olitorius cultivar O-4 contig06578, 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: 2148
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Found at i:43 original size:30 final size:30
Alignment explanation
Indices: 5--973 Score: 1079
Period size: 30 Copynumber: 32.5 Consensus size: 30
1 CCTG
* * *
5 GTTT-AGGATCATTACTTCATTTTAATCAT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
* *
34 GTTTGAGGATCATCGCTCTATTTTAATCCT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
*
64 GTTTGAGGATCATTGCTTTATTTTTATCCT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
* * **
94 GGTCGAGGATCATTGCTTCCTTTTAATCCT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
* * *
124 GTTCGAGGATCATTACTTTATTTTAATCAT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
** *
154 GTTTGAGGATCATTGCTTTATTTTTTTCAT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
* *
184 GTTTGAGGATCGTTGATTTATTTTAATCCT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
* *
214 GATTAAGG---A-T-CTTTATTTTAATCCT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
* * *
239 -TTCTAAGGATCATTACTTTATTATAATCCT
1 GTT-TGAGGATCATTGCTTTATTTTAATCCT
**
269 GTTTGAGGATCATTGCTTTATTTTTGTCCT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
*
299 GTTTGAGGATCGTTGCTTTA-TTTAATCCT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
* * *
328 GGTTGAGGATCATTACTTCACTTCATTTTAATCTT
1 GTTTGAGGATCATTGC-T---TT-ATTTTAATCCT
* *
363 GTTTGAGGATCATTGCTTTATTTTTATCTT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
*
393 GTTTGAGGATCGTTGCTTTATTTTAATCCT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
*
423 GTTTGAGGATCATTGCTTTATTTTTATCCT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
* * **
453 GGTCGAGGATCATTGCTTCCTTTTAATCCT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
* *
483 GTTTGAGGATCATTACTTTATTTTAATCCA
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
** *
513 GTTTGAGGATCATTGCTTTATTTTTGTCAT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
*
543 GTTTGAGGATCGTTGCTTTATTTTAATCCT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
* * *
573 GATTAAGG---A-T-CTTTATTTTAATCAT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
* *
598 GTTTGAGGATCATTTCTTTCTTTTAATCCT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
* **
628 GTTTGAAGATCATTGCTTTATTTTTGTCCT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
**
658 GTTTGAGGATCATTGCTTTATTTTTGTCCT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
*
688 GTTTGAGGATCATTGCTTTATTTTTATCCT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
* ** * *
718 GGTTGATAAT-ATTTGCTCTATGTTAATCCT
1 GTTTGAGGATCA-TTGCTTTATTTTAATCCT
* * *
748 GGTTT-AGGATCATTACTTCATTTTAATCAT
1 -GTTTGAGGATCATTGCTTTATTTTAATCCT
* *
778 GTTTGAGGATCATCGCTCTATTTTAATCCT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
* *
808 GTTTGAGGATCATCGCTCTATTTTAATCCT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
* *
838 GTTTGAGGATCATTGCTTCAGTTTTAATCAT
1 GTTTGAGGATCATTGCTTTA-TTTTAATCCT
*
869 GTTTGAGGATCATTGCTTCATTTTAATCCT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
* * *
899 GTTTTAGGATCATTGCTTCATTTTAATCCG
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
*
929 GGTTGAGGATCATTGCTTTATTTTAATCCT
1 GTTTGAGGATCATTGCTTTATTTTAATCCT
959 GGTTT-AGGATCATTG
1 -GTTTGAGGATCATTG
974 TTTCATCAGT
Statistics
Matches: 796, Mismatches: 119, Indels: 49
0.83 0.12 0.05
Matches are distributed among these distances:
24 1 0.00
25 39 0.05
26 2 0.00
28 2 0.00
29 31 0.04
30 655 0.82
31 40 0.05
33 2 0.00
34 2 0.00
35 22 0.03
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (30 bp):
GTTTGAGGATCATTGCTTTATTTTAATCCT
Found at i:606 original size:25 final size:25
Alignment explanation
Indices: 558--608 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
548 AGGATCGTTG
*
558 CTTTATTTTAATCCTGATTAAGGAT
1 CTTTATTTTAATCATGATTAAGGAT
* *
583 CTTTATTTTAATCATGTTTGAGGAT
1 CTTTATTTTAATCATGATTAAGGAT
608 C
1 C
609 ATTTCTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (25 bp):
CTTTATTTTAATCATGATTAAGGAT
Found at i:1529 original size:27 final size:27
Alignment explanation
Indices: 1492--1618 Score: 121
Period size: 27 Copynumber: 4.7 Consensus size: 27
1482 AGGTTTAACT
*
1492 AGGGGCATTTTGGTCATTTTCAAAATCC
1 AGGGGCATTTTGGTCATTTAC-AAATCC
* *
1520 AGGGGCTTTTTGGTCATTTACACATCC
1 AGGGGCATTTTGGTCATTTACAAATCC
** * *
1547 AGGATCATTTTGGTCATTTGCAGATCC
1 AGGGGCATTTTGGTCATTTACAAATCC
* * *
1574 AGGGGCATTCTGGTCATTTCCACAGT-C
1 AGGGGCATTTTGGTCATTTACA-AATCC
* *
1601 AAGGGCATTGTGGTCATT
1 AGGGGCATTTTGGTCATT
1619 CGAACCCTTA
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
27 62 0.76
28 20 0.24
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTACAAATCC
Found at i:1615 original size:54 final size:54
Alignment explanation
Indices: 1494--1618 Score: 153
Period size: 54 Copynumber: 2.3 Consensus size: 54
1484 GTTTAACTAG
* * * *
1494 GGGCATTTTGGTCATTTTCAAAATCCAGGGGCTTTTTGGTCATTTACACATCCA
1 GGGCATTTTGGTCATTTGCAAAATCCAGGGGCATTCTGGTCATTTACACATCAA
* * *
1548 GGATCATTTTGGTCATTTGC-AGATCCAGGGGCATTCTGGTCATTTCCACAGTCAA
1 GG-GCATTTTGGTCATTTGCAAAATCCAGGGGCATTCTGGTCATTTACACA-TCAA
*
1603 GGGCATTGTGGTCATT
1 GGGCATTTTGGTCATT
1619 CGAACCCTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
54 40 0.67
55 20 0.33
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (54 bp):
GGGCATTTTGGTCATTTGCAAAATCCAGGGGCATTCTGGTCATTTACACATCAA
Done.