Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019806.1 Corchorus olitorius cultivar O-4 contig19839, 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: 8258
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:755 original size:50 final size:50
Alignment explanation
Indices: 689--874 Score: 275
Period size: 50 Copynumber: 3.7 Consensus size: 50
679 AAAATCGACC
* * *
689 TTTGGTCTTGGTCTCACAAATGGAGTGCAATCTTATTTTGAAAAGCGAAT
1 TTTGATCTTGGACTCACAAATGGAATGCAATCTTATTTTGAAAAGCGAAT
**
739 TTTGATCTTGGACTCACAAATGGAATGCAAT-TCGTTTTGAAAAGCGAAT
1 TTTGATCTTGGACTCACAAATGGAATGCAATCTTATTTTGAAAAGCGAAT
* * * *
788 TTTGATCTTGAACTCACAAATGGAAAGCAATTTTACTTTGAAAAGCGAAT
1 TTTGATCTTGGACTCACAAATGGAATGCAATCTTATTTTGAAAAGCGAAT
*
838 TTTGATCTTGGGCTCACAAATGGAATGCAATCTTATT
1 TTTGATCTTGGACTCACAAATGGAATGCAATCTTATT
875 GTAAATCTTC
Statistics
Matches: 120, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
49 45 0.38
50 75 0.62
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (50 bp):
TTTGATCTTGGACTCACAAATGGAATGCAATCTTATTTTGAAAAGCGAAT
Found at i:1462 original size:6 final size:6
Alignment explanation
Indices: 1451--1494 Score: 58
Period size: 5 Copynumber: 7.7 Consensus size: 6
1441 ATCAATTATC
1451 TTTTGA TTTTGA -TTTGA -TTTGA TTTTTGA TTTTGA -TTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA -TTTTGA TTTTGA TTTTGA TTTT
1495 TTTTATTAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 15 0.43
6 15 0.43
7 5 0.14
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (6 bp):
TTTTGA
Found at i:1468 original size:5 final size:5
Alignment explanation
Indices: 1452--1537 Score: 51
Period size: 5 Copynumber: 17.6 Consensus size: 5
1442 TCAATTATCT
* *
1452 TTTGA TTTTGA TTTGA TTTGA TTTTTGA TTTTGA TTTGA TTT-T TTTTA
1 TTTGA -TTTGA TTTGA TTTGA --TTTGA -TTTGA TTTGA TTTGA TTTGA
*
1500 -TTAA CTTTGA TTTGA TTT-- TTTGA TTT-- TTTGA -TTGA TTT
1 TTTGA -TTTGA TTTGA TTTGA TTTGA TTTGA TTTGA TTTGA TTT
1538 TTTTTTATGG
Statistics
Matches: 66, Mismatches: 4, Indels: 21
0.73 0.04 0.23
Matches are distributed among these distances:
3 6 0.09
4 10 0.15
5 31 0.47
6 14 0.21
7 5 0.08
ACGTcount: A:0.17, C:0.01, G:0.14, T:0.67
Consensus pattern (5 bp):
TTTGA
Found at i:1477 original size:23 final size:23
Alignment explanation
Indices: 1451--1526 Score: 90
Period size: 23 Copynumber: 3.4 Consensus size: 23
1441 ATCAATTATC
1451 TTTTGATTTTGATTTGATTTGAT
1 TTTTGATTTTGATTTGATTTGAT
1474 TTTTGATTTTGATTTGATTT--T
1 TTTTGATTTTGATTTGATTTGAT
*
1495 TTTT-A--TTAACTTTGATTTGATT
1 TTTTGATTTTGA-TTTGATTTGA-T
1517 TTTTGATTTT
1 TTTTGATTTT
1527 TTGATTGATT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
18 3 0.07
19 8 0.18
20 1 0.02
21 5 0.11
22 5 0.11
23 21 0.47
25 2 0.04
ACGTcount: A:0.17, C:0.01, G:0.13, T:0.68
Consensus pattern (23 bp):
TTTTGATTTTGATTTGATTTGAT
Found at i:1513 original size:24 final size:23
Alignment explanation
Indices: 1458--1543 Score: 81
Period size: 24 Copynumber: 3.8 Consensus size: 23
1448 ATCTTTTGAT
** * *
1458 TTTGATTTGATTTGATTTTTGAT
1 TTTGATTTGATTTTTTTTTTAAC
1481 TTTGATTTGATTTTTTTTATTAAC
1 TTTGATTTGATTTTTTTT-TTAAC
*
1505 TTTGATTTGATTTTTTGATTT---
1 TTTGATTTGATTTTTT-TTTTAAC
1526 TTTGA-TTGATTTTTTTTT
1 TTTGATTTGATTTTTTTTT
1544 ATGGAGTGGA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
19 2 0.04
20 10 0.18
21 5 0.09
23 16 0.29
24 21 0.38
25 1 0.02
ACGTcount: A:0.16, C:0.01, G:0.13, T:0.70
Consensus pattern (23 bp):
TTTGATTTGATTTTTTTTTTAAC
Done.