Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016251.1 Corchorus olitorius cultivar O-4 contig16284, 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: 19780
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Found at i:9294 original size:186 final size:186
Alignment explanation
Indices: 8974--9495 Score: 972
Period size: 186 Copynumber: 2.8 Consensus size: 186
8964 TTATTAGTGT
*
8974 AACAACAAATCATTGTTGTCCAAGCAACAATATCTTTCTCTTCCATAGCATCAAAAACACTTTGT
1 AACAACAAATCATTGCTGTCCAAGCAACAATATCTTTCTCTTCCATAGCATCAAAAACACTTTGT
*
9039 GCACCAATCAGATTACATAAAGAGATAACAGTCTTGATTACATCTGATCTAATTCAAAGATTGTA
66 GCACCAATCAGATTACATAAAGAGATAACAGTCTTGATTACATCTGACCTAATTCAAAGATTGTA
*
9104 ACTAATCTAAAAAAAATCTTTCATAAAGAGATAACCTTTCATATAGACTAGGATAA
131 ACTAATCTAAAAAAAACCTTTCATAAAGAGATAACCTTTCATATAGACTAGGATAA
9160 AACAACAAATCATTGCTGTCCAAGCAACAATATCTTTCTCTTCCATAGCATCAAAAACACTTTGT
1 AACAACAAATCATTGCTGTCCAAGCAACAATATCTTTCTCTTCCATAGCATCAAAAACACTTTGT
* *
9225 GCACCAATCAGATTACATAAAGAGATAACAGTCTTGATTACATTTGACCTAATTCAAAGATTTTA
66 GCACCAATCAGATTACATAAAGAGATAACAGTCTTGATTACATCTGACCTAATTCAAAGATTGTA
*
9290 ACTAATCTAGAAAAAACCTTTCATAAAGAGATAACCTTTCATATAGACTAGGATAA
131 ACTAATCTAAAAAAAACCTTTCATAAAGAGATAACCTTTCATATAGACTAGGATAA
* *
9346 AACAACAAATCATTGCTGTCCAAGCAACAATATCTTTCTCTTCCATAGCATCAAAAACTCTTTGC
1 AACAACAAATCATTGCTGTCCAAGCAACAATATCTTTCTCTTCCATAGCATCAAAAACACTTTGT
9411 GCACCAATCAGATTACATAAAGAGATAACAGTCTTGATTACATCTGACCTAATTCAAAGATTGTA
66 GCACCAATCAGATTACATAAAGAGATAACAGTCTTGATTACATCTGACCTAATTCAAAGATTGTA
9476 ACTAATCTAAAAAAAACCTT
131 ACTAATCTAAAAAAAACCTT
9496 ACAAGGTGTA
Statistics
Matches: 325, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
186 325 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (186 bp):
AACAACAAATCATTGCTGTCCAAGCAACAATATCTTTCTCTTCCATAGCATCAAAAACACTTTGT
GCACCAATCAGATTACATAAAGAGATAACAGTCTTGATTACATCTGACCTAATTCAAAGATTGTA
ACTAATCTAAAAAAAACCTTTCATAAAGAGATAACCTTTCATATAGACTAGGATAA
Found at i:10282 original size:12 final size:12
Alignment explanation
Indices: 10265--10289 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10255 GGAGTTGAAA
10265 TCTTTCTGTTTC
1 TCTTTCTGTTTC
10277 TCTTTCTGTTTC
1 TCTTTCTGTTTC
10289 T
1 T
10290 GCGCCTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.24, G:0.08, T:0.68
Consensus pattern (12 bp):
TCTTTCTGTTTC
Found at i:13874 original size:2 final size:2
Alignment explanation
Indices: 13867--13894 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13857 GGCCTAGGGC
13867 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
13895 GCAATGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17576 original size:3 final size:3
Alignment explanation
Indices: 17568--17597 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
17558 TCTAAGGGTA
17568 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
17598 GTGTGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TGT
Done.