Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005003.1 Corchorus capsularis cultivar CVL-1 contig05021, 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: 17115
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:125 original size:51 final size:51
Alignment explanation
Indices: 56--201 Score: 149
Period size: 48 Copynumber: 2.9 Consensus size: 51
46 AACAATTATT
56 TAAGAGACAAATAGAGGAAGTTCTTTTGTTAAATTCAAAATCGATACTTTACA
1 TAAGAGAC--ATAGAGGAAGTTCTTTTGTTAAATTCAAAATCGATACTTTACA
* * **
109 TAAGAGACATAGAGGAAGTTCTTTTGTT-AAGT----ATAGATACTTTATT
1 TAAGAGACATAGAGGAAGTTCTTTTGTTAAATTCAAAATCGATACTTTACA
* * * *
155 TAAGAGGGATAGAGAGGAAGTTCTTTTGTTAAGTTCAAAATCAATAC
1 TAAGA--GACATAGAGGAAGTTCTTTTGTTAAATTCAAAATCGATAC
202 CTTATTTAAG
Statistics
Matches: 76, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
46 16 0.21
48 21 0.28
49 2 0.03
50 3 0.04
51 20 0.26
53 14 0.18
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (51 bp):
TAAGAGACATAGAGGAAGTTCTTTTGTTAAATTCAAAATCGATACTTTACA
Found at i:680 original size:19 final size:20
Alignment explanation
Indices: 634--681 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
624 TGTGGCACGC
*
634 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
656 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
675 CACATGT
1 CACATGT
682 CACGCCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:686 original size:53 final size:53
Alignment explanation
Indices: 601--703 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
591 GACGTGGCAC
* **
601 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
* *
654 GCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGT
704 GACACCTGAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
Found at i:748 original size:31 final size:31
Alignment explanation
Indices: 653--750 Score: 115
Period size: 31 Copynumber: 3.2 Consensus size: 31
643 CAAAAAGTCG
*
653 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACATGACA
* * *
684 CGCCACGTGTACCAAAAAGTGACACCTGACA
1 TGCCACATGTACCAAAAAGTGACACATGACA
** * * *
715 TGCCACATGTTTCAAAAAGTGGCACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACATGACA
746 TGCCA
1 TGCCA
751 TGTGCACAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.18
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACATGACA
Found at i:1624 original size:27 final size:26
Alignment explanation
Indices: 1566--1627 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
1556 TCCGCTCTGA
* *
1566 AGCCTCCTATTTCCGGGCAAATTTCT
1 AGCCTCCTATTTCCCGGCAAATTTCG
*
1592 ATGCCTCCTATTTCCCGGCCAATTTCCG
1 A-GCCTCCTATTTCCCGGCAAATTT-CG
1620 AGCCTCCT
1 AGCCTCCT
1628 CAACATTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 28 0.90
28 2 0.06
ACGTcount: A:0.16, C:0.37, G:0.15, T:0.32
Consensus pattern (26 bp):
AGCCTCCTATTTCCCGGCAAATTTCG
Found at i:2378 original size:2 final size:2
Alignment explanation
Indices: 2371--2401 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2361 ATTTGCTATT
2371 TA 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 TA T
2402 GTAATATTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17075 original size:2 final size:2
Alignment explanation
Indices: 17068--17104 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
17058 ATGTGTATGC
17068 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
17105 GTACTGCTAC
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.