Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006469.1 Corchorus capsularis cultivar CVL-1 contig06490, 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: 23964
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:2270 original size:2 final size:2
Alignment explanation
Indices: 2263--2292 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2253 CAATCAAACC
2263 AT AT 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 AT AT
2293 CAAAGGATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2883 original size:21 final size:22
Alignment explanation
Indices: 2844--2889 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
2834 GACGGTGTAT
2844 TATATATATAAATCCTATATAAA
1 TATATATATAAAT-CTATATAAA
* *
2867 TATATATATATAT-TATATTAA
1 TATATATATAAATCTATATAAA
2888 TA
1 TA
2890 CATAAGTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
23 12 0.57
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (22 bp):
TATATATATAAATCTATATAAA
Found at i:3485 original size:84 final size:84
Alignment explanation
Indices: 3385--3552 Score: 282
Period size: 84 Copynumber: 2.0 Consensus size: 84
3375 GACCAATTCG
* *
3385 TTATAGGAGGAAGTGCTATCAATGTTGTTGCCGGTTTGATTTGATATCGCTAATATATTACTACC
1 TTATAGAAGGAAGTGCTATCAATGTTGTTACCGGTTTGATTTGATATCGCTAATATATTACTACC
3450 TTGATTATAAAACCTAAAC
66 TTGATTATAAAACCTAAAC
* * *
3469 TTATAGAAGGAGGTGCTATCAATTTTGTTACTGGTTTGATTTGATATCGCTAATATATTACTACC
1 TTATAGAAGGAAGTGCTATCAATGTTGTTACCGGTTTGATTTGATATCGCTAATATATTACTACC
*
3534 TTGATTATAAAGCCTAAAC
66 TTGATTATAAAACCTAAAC
3553 AAAAGGCTTC
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (84 bp):
TTATAGAAGGAAGTGCTATCAATGTTGTTACCGGTTTGATTTGATATCGCTAATATATTACTACC
TTGATTATAAAACCTAAAC
Found at i:17601 original size:29 final size:30
Alignment explanation
Indices: 17563--17646 Score: 104
Period size: 28 Copynumber: 2.9 Consensus size: 30
17553 TTTACTATAA
17563 CAATTAAAACTGATTGATTAATTGATT-G-
1 CAATTAAAACTGATTGATTAATTGATTCGC
* **
17591 CAAGTTAAAACTGATTGATT-TTTTTTTCGC
1 CAA-TTAAAACTGATTGATTAATTGATTCGC
17621 CAA-TAAAACTGATTGATTAATTGATT
1 CAATTAAAACTGATTGATTAATTGATT
17647 TCAAATTGGA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
28 22 0.48
29 21 0.46
30 3 0.07
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.42
Consensus pattern (30 bp):
CAATTAAAACTGATTGATTAATTGATTCGC
Found at i:18864 original size:7 final size:7
Alignment explanation
Indices: 18852--18877 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18842 AAGCTAGTCT
18852 AATAAGA
1 AATAAGA
18859 AATAAGA
1 AATAAGA
18866 AATAAGA
1 AATAAGA
18873 AATAA
1 AATAA
18878 CAAAATACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (7 bp):
AATAAGA
Found at i:20835 original size:6 final size:6
Alignment explanation
Indices: 20828--20881 Score: 90
Period size: 6 Copynumber: 9.0 Consensus size: 6
20818 TCTCTGTCTC
* *
20828 TAAATC TAAATC TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA
20876 TAAATA
1 TAAATA
20882 AATATATGCC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (6 bp):
TAAATA
Found at i:22637 original size:27 final size:27
Alignment explanation
Indices: 22600--22656 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
22590 TAGGATCGAA
22600 ACACAAAAATTAGCTCCTAAGTTTTTC
1 ACACAAAAATTAGCTCCTAAGTTTTTC
22627 ACACAAAAATTAGCTCCTAAGTTTTTC
1 ACACAAAAATTAGCTCCTAAGTTTTTC
22654 ACA
1 ACA
22657 AAAGTTGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.39, C:0.23, G:0.07, T:0.32
Consensus pattern (27 bp):
ACACAAAAATTAGCTCCTAAGTTTTTC
Found at i:23357 original size:5 final size:5
Alignment explanation
Indices: 23347--23383 Score: 65
Period size: 5 Copynumber: 7.2 Consensus size: 5
23337 CATAAGTTTA
23347 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT A
23384 GTGTAGATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:23933 original size:2 final size:2
Alignment explanation
Indices: 23926--23964 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
23916 AAGCCATTGG
23926 AT AT AT 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 AT AT AT A
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.