Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010022.1 Corchorus olitorius cultivar O-4 contig10054, 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: 6939
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--29 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1 ATA
4 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
30 TTGTATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3404 original size:2 final size:2
Alignment explanation
Indices: 3392--3538 Score: 103
Period size: 2 Copynumber: 73.0 Consensus size: 2
3382 ATTTAATTAC
3392 TA TA GTA TA TA TA TA TA TA T- TA TA TA TA GTA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * *
3435 T- TA TA TA TA TA TA TA TA AA CT- TCA -A TCC CA CA GTA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA -TA T-A TA T-A TA TA -TA TA TA TA
* *
3475 TA TA TA TA GTA TA TA TA TA TA TA -A AA TT TA -A T- TA CTA TA GTA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA
3517 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
3539 CTAGTATTTT
Statistics
Matches: 119, Mismatches: 9, Indels: 34
0.73 0.06 0.21
Matches are distributed among these distances:
1 8 0.07
2 100 0.84
3 11 0.09
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:4000 original size:21 final size:21
Alignment explanation
Indices: 3974--4027 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
3964 AAAAAATAAG
*
3974 GCTTATAAAATTACTAAAAAT
1 GCTTATAAAATTACTAAAAAA
* * **
3995 GCTTATGAAGTTTGTAAAAAA
1 GCTTATAAAATTACTAAAAAA
*
4016 GCTTATATAATT
1 GCTTATAAAATT
4028 TACTTAAACC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.37
Consensus pattern (21 bp):
GCTTATAAAATTACTAAAAAA
Found at i:4210 original size:31 final size:30
Alignment explanation
Indices: 4167--4234 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
4157 GCACAAAATC
* * *
4167 CCCCCTGAAGTATTACAAAAATGACACTTTG
1 CCCCATGAAGTATGA-AAAAAGGACACTTTG
* *
4198 CCCCATGAAGTATGAAATAAGGACAGTTTG
1 CCCCATGAAGTATGAAAAAAGGACACTTTG
4228 CCCCATG
1 CCCCATG
4235 TCGTAACGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 19 0.59
31 13 0.41
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (30 bp):
CCCCATGAAGTATGAAAAAAGGACACTTTG
Found at i:5312 original size:25 final size:24
Alignment explanation
Indices: 5284--5331 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
5274 GTTTAGGTAG
5284 GATGGATATATCGAACGGAAATATT
1 GATGGATATATCG-ACGGAAATATT
*
5309 GATGGATATATCGACGGATATAT
1 GATGGATATATCGACGGAAATAT
5332 CAAGATATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (24 bp):
GATGGATATATCGACGGAAATATT
Found at i:5327 original size:12 final size:12
Alignment explanation
Indices: 5287--5332 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
5277 TAGGTAGGAT
5287 GGATATATCGAAC
1 GGATATATCG-AC
* * *
5300 GGAAATATTGAT
1 GGATATATCGAC
5312 GGATATATCGAC
1 GGATATATCGAC
5324 GGATATATC
1 GGATATATC
5333 AAGATATCGA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 19 0.70
13 8 0.30
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (12 bp):
GGATATATCGAC
Found at i:6336 original size:10 final size:10
Alignment explanation
Indices: 6321--6356 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
6311 AATTTAATAT
6321 GGATATTTAC
1 GGATATTTAC
*
6331 GGATATTTCC
1 GGATATTTAC
*
6341 GGATACTTAC
1 GGATATTTAC
6351 GGATAT
1 GGATAT
6357 ATCGAGAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (10 bp):
GGATATTTAC
Found at i:6692 original size:2 final size:2
Alignment explanation
Indices: 6685--6722 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6675 CAAAAGCTTT
6685 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6723 CTTACTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.