Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020063.1 Corchorus olitorius cultivar O-4 contig20096, 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: 7956
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Found at i:7441 original size:6 final size:6
Alignment explanation
Indices: 7430--7496 Score: 63
Period size: 6 Copynumber: 11.7 Consensus size: 6
7420 ATCAATTCTC
*
7430 TTTTGA TTTTGA -TTTGA -TTTGA TTTTTA TTTTGA -TTTGA TTTT--
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA
*
7473 TTGATTGA CTTTGA TTTTGA TTTT
1 TT--TTGA TTTTGA TTTTGA TTTT
7497 TTAATTCTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
4 2 0.04
5 15 0.29
6 33 0.65
8 1 0.02
ACGTcount: A:0.16, C:0.01, G:0.15, T:0.67
Consensus pattern (6 bp):
TTTTGA
Found at i:7455 original size:22 final size:22
Alignment explanation
Indices: 7430--7471 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
7420 ATCAATTCTC
7430 TTTTGATTTTGATTTGATTTGA
1 TTTTGATTTTGATTTGATTTGA
*
7452 TTTTTATTTTGATTTGATTT
1 TTTTGATTTTGATTTGATTT
7472 TTTGATTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (22 bp):
TTTTGATTTTGATTTGATTTGA
Found at i:7462 original size:17 final size:17
Alignment explanation
Indices: 7431--7496 Score: 75
Period size: 17 Copynumber: 3.9 Consensus size: 17
7421 TCAATTCTCT
7431 TTTGATTTTGA-TTTGA
1 TTTGATTTTGATTTTGA
*
7447 TTTGATTTTTATTTTGA
1 TTTGATTTTGATTTTGA
7464 TTTGATTTT--TTGATTGA
1 TTTGATTTTGATT--TTGA
7481 CTTTGATTTTGATTTT
1 -TTTGATTTTGATTTT
7497 TTAATTCTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
15 2 0.05
16 10 0.23
17 18 0.42
18 11 0.26
20 2 0.05
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.67
Consensus pattern (17 bp):
TTTGATTTTGATTTTGA
Found at i:7516 original size:20 final size:20
Alignment explanation
Indices: 7487--7542 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
7477 TTGACTTTGA
*
7487 TTTTGATTTTTTAATTCTTT
1 TTTTGTTTTTTTAATTCTTT
** *
7507 TTTTGTTTTTTTGTTTGTTT
1 TTTTGTTTTTTTAATTCTTT
7527 TTTT-TTTTTTTGAATT
1 TTTTGTTTTTTT-AATT
7543 TCTTGATGGA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 7 0.24
20 22 0.76
ACGTcount: A:0.09, C:0.02, G:0.09, T:0.80
Consensus pattern (20 bp):
TTTTGTTTTTTTAATTCTTT
Found at i:7523 original size:12 final size:11
Alignment explanation
Indices: 7504--7537 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
7494 TTTTTAATTC
7504 TTTTTTTGTTT
1 TTTTTTTGTTT
7515 TTTTGTTTGTTT
1 TTTT-TTTGTTT
7527 TTTTTTT-TTT
1 TTTTTTTGTTT
7537 T
1 T
7538 GAATTTCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.18
11 7 0.32
12 11 0.50
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (11 bp):
TTTTTTTGTTT
Done.