Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022683.1 Corchorus olitorius cultivar O-4 contig22716, 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: 19036
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Found at i:2869 original size:12 final size:12
Alignment explanation
Indices: 2852--2910 Score: 100
Period size: 12 Copynumber: 4.8 Consensus size: 12
2842 AAGACGGTCA
2852 AAAGCAACAATG
1 AAAGCAACAATG
2864 AAAGCAACAATG
1 AAAGCAACAATG
2876 AAAGCAACAATG
1 AAAGCAACAATG
*
2888 AAAGCAACAATA
1 AAAGCAACAATG
2900 AAAGCTAACAA
1 AAAGC-AACAA
2911 AGAATTAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
12 40 0.89
13 5 0.11
ACGTcount: A:0.61, C:0.17, G:0.14, T:0.08
Consensus pattern (12 bp):
AAAGCAACAATG
Found at i:3090 original size:2 final size:2
Alignment explanation
Indices: 3083--3115 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3073 AGTATAACCA
3083 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 A
3116 AACTAGAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3328 original size:12 final size:12
Alignment explanation
Indices: 3311--3338 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3301 TAGTAATTAA
3311 TATATTATACAT
1 TATATTATACAT
3323 TATATTATACAT
1 TATATTATACAT
3335 TATA
1 TATA
3339 CATACTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (12 bp):
TATATTATACAT
Found at i:3591 original size:53 final size:53
Alignment explanation
Indices: 3527--3635 Score: 191
Period size: 53 Copynumber: 2.1 Consensus size: 53
3517 TGTTTATTCA
3527 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
* * *
3580 ATTGAATCTATTAAATAAGCACACATACTAAATAATACAAAATGCATTGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
3633 ATT
1 ATT
3636 AGATTTAAAG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.27
Consensus pattern (53 bp):
ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
Found at i:4225 original size:13 final size:13
Alignment explanation
Indices: 4187--4226 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
4177 TCTTCAAATA
* *
4187 ATCTTCAGTTGAA
1 ATCTTCTGTTGAT
*
4200 ATCTTCTGATGAT
1 ATCTTCTGTTGAT
4213 ATCTTCTGTTGAT
1 ATCTTCTGTTGAT
4226 A
1 A
4227 ATATTCTCCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (13 bp):
ATCTTCTGTTGAT
Found at i:9967 original size:29 final size:30
Alignment explanation
Indices: 9907--9986 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
9897 GCTAAATACC
* *
9907 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT-CTTTCGGGA
9938 CAAAATAATCCCTTATGTTTT-TTTCGGGA
1 CAAAATAATCCCTTATGTTTTCTTTCGGGA
* * *
9967 CAAATTAATCTCTTACGTTT
1 CAAAATAATCCCTTATGTTT
9987 CAAAAATGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 24 0.55
31 20 0.45
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTCGGGA
Found at i:10341 original size:31 final size:31
Alignment explanation
Indices: 10306--10388 Score: 157
Period size: 31 Copynumber: 2.7 Consensus size: 31
10296 ACTAAATACT
10306 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
10337 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
*
10368 GAAAAAATCCCTTATGTTTTT
1 AAAAAAATCCCTTATGTTTTT
10389 TTGGTACAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (31 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
Found at i:10596 original size:31 final size:29
Alignment explanation
Indices: 10530--10609 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
10520 CTCATTTTTG
* * *
10530 AAACGTAAGGGATTAATTTGTCCCGAAAA
1 AAACATAAGGGATTATTTTGTCCCAAAAA
10559 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTATTTTGTCCCAAAA--A
*
10590 AAACATAAGGGATTGTTTTG
1 AAACATAAGGGATTATTTTG
10610 GGTATTTAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 25 0.56
31 20 0.44
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (29 bp):
AAACATAAGGGATTATTTTGTCCCAAAAA
Found at i:15318 original size:29 final size:29
Alignment explanation
Indices: 15282--15355 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
15272 TTTGACACCG
15282 AGTGCAAACCCACACTCAAAACAACCCCA
1 AGTGCAAACCCACACTCAAAACAACCCCA
*
15311 AGTGCAAACCCACATTCAAAACAACCCCA
1 AGTGCAAACCCACACTCAAAACAACCCCA
15340 AGTGCAAACCCACACT
1 AGTGCAAACCCACACT
15356 TGAACAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.43, C:0.39, G:0.08, T:0.09
Consensus pattern (29 bp):
AGTGCAAACCCACACTCAAAACAACCCCA
Found at i:18308 original size:15 final size:16
Alignment explanation
Indices: 18288--18325 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
18278 AGATTGACAG
18288 AAAACAATTAAAC-AA
1 AAAACAATTAAACTAA
*
18303 AAAACAATTAAACTAG
1 AAAACAATTAAACTAA
18319 AAAACAA
1 AAAACAA
18326 ACCAGAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.71, C:0.13, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAACAATTAAACTAA
Done.