Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014149.1 Corchorus olitorius cultivar O-4 contig14182, 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: 5348
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Found at i:3020 original size:9 final size:9
Alignment explanation
Indices: 3006--3058 Score: 81
Period size: 9 Copynumber: 6.0 Consensus size: 9
2996 AATTACTTAT
3006 GGAAATTAA
1 GGAAATTAA
*
3015 GGAAATTAT
1 GGAAATTAA
3024 GGAAATTAA
1 GGAAATTAA
*
3033 GGAAATTAT
1 GGAAATTAA
3042 GGAAATT-A
1 GGAAATTAA
3050 GGAAATTAA
1 GGAAATTAA
3059 ATGAATTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
8 7 0.18
9 32 0.82
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (9 bp):
GGAAATTAA
Found at i:3025 original size:18 final size:18
Alignment explanation
Indices: 3002--3057 Score: 105
Period size: 18 Copynumber: 3.2 Consensus size: 18
2992 CCCAAATTAC
3002 TTATGGAAATTAAGGAAA
1 TTATGGAAATTAAGGAAA
3020 TTATGGAAATTAAGGAAA
1 TTATGGAAATTAAGGAAA
3038 TTATGGAAATT-AGGAAA
1 TTATGGAAATTAAGGAAA
3055 TTA
1 TTA
3058 AATGAATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 9 0.24
18 29 0.76
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.30
Consensus pattern (18 bp):
TTATGGAAATTAAGGAAA
Found at i:4452 original size:49 final size:48
Alignment explanation
Indices: 4334--4462 Score: 145
Period size: 49 Copynumber: 2.7 Consensus size: 48
4324 CAAGCAATCC
* **
4334 TTTACTTTTCA-CTGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
1 TTTAATTTTCATC-GCACTTTTTCTCAATTTTTAAGACAAAATTGAACT
* * * *
4382 TTT-ATTTTTACTTGCATTTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTAATTTTCA-TCGCA-CTTTTTCTCAATTTTTAAGACAAAATTGAACT
*
4431 TTTAATTTTCATCGCACTTTTTATCAATTTTT
1 TTTAATTTTCATCGCACTTTTTCTCAATTTTT
4463 TGAAAAAAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
47 5 0.08
48 20 0.30
49 35 0.53
50 6 0.09
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (48 bp):
TTTAATTTTCATCGCACTTTTTCTCAATTTTTAAGACAAAATTGAACT
Found at i:5303 original size:17 final size:18
Alignment explanation
Indices: 5263--5298 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5253 ACCTTAAAAA
*
5263 GAAAATTTGTGCTTTTTT
1 GAAAGTTTGTGCTTTTTT
5281 GAAAGTTTGTGCTTTTTT
1 GAAAGTTTGTGCTTTTTT
5299 CAAGTGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.56
Consensus pattern (18 bp):
GAAAGTTTGTGCTTTTTT
Done.