Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014360.1 Corchorus olitorius cultivar O-4 contig14393, 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: 6673
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Found at i:3861 original size:28 final size:28
Alignment explanation
Indices: 3828--3930 Score: 80
Period size: 28 Copynumber: 3.5 Consensus size: 28
3818 AAGTTTACTA
*
3828 AAAAAAATCGTAAATATAATTTTTATTT
1 AAAAAAATCATAAATATAATTTTTATTT
* * *** **
3856 AAAAAATTCATAAATGGAAAAGAAATTAGCAT
1 AAAAAAATCATAAAT--ATAA-TTTTTA-TTT
*
3888 AAAAAAATCGTAAATATAATTTTTATTT
1 AAAAAAATCATAAATATAATTTTTATTT
*
3916 AAAAAATTCATAAAT
1 AAAAAAATCATAAAT
3931 GGAAAAGAAA
Statistics
Matches: 53, Mismatches: 18, Indels: 8
0.67 0.23 0.10
Matches are distributed among these distances:
28 27 0.51
29 3 0.06
30 6 0.11
31 3 0.06
32 14 0.26
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (28 bp):
AAAAAAATCATAAATATAATTTTTATTT
Found at i:3900 original size:60 final size:60
Alignment explanation
Indices: 3828--3947 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
3818 AAGTTTACTA
3828 AAAAAAATCGTAAATATAATTTTTATTTAAAAAATTCATAAATGGAAAAGAAATTAGCAT
1 AAAAAAATCGTAAATATAATTTTTATTTAAAAAATTCATAAATGGAAAAGAAATTAGCAT
3888 AAAAAAATCGTAAATATAATTTTTATTTAAAAAATTCATAAATGGAAAAGAAATTAGCAT
1 AAAAAAATCGTAAATATAATTTTTATTTAAAAAATTCATAAATGGAAAAGAAATTAGCAT
3948 GACTAGGGTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (60 bp):
AAAAAAATCGTAAATATAATTTTTATTTAAAAAATTCATAAATGGAAAAGAAATTAGCAT
Found at i:4255 original size:49 final size:49
Alignment explanation
Indices: 4183--4280 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
4173 ATAAGGAAAT
4183 GAGATAAAAATAGACTAATGAGAGACCTGAAACTGAAAGTGATAATCCA
1 GAGATAAAAATAGACTAATGAGAGACCTGAAACTGAAAGTGATAATCCA
4232 GAGATAAAAATAGACTAATGAGAGACCTGAAACTGAAAGTGATAATCCA
1 GAGATAAAAATAGACTAATGAGAGACCTGAAACTGAAAGTGATAATCCA
4281 TATGTGCCGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.18
Consensus pattern (49 bp):
GAGATAAAAATAGACTAATGAGAGACCTGAAACTGAAAGTGATAATCCA
Found at i:5335 original size:79 final size:79
Alignment explanation
Indices: 5204--5365 Score: 324
Period size: 79 Copynumber: 2.1 Consensus size: 79
5194 TGCTGCATTG
5204 AAGAAAACAAATATATTGAGAGTATGACAACACACCTAAGGGCTAAAAATATAAAGTCAGATGTG
1 AAGAAAACAAATATATTGAGAGTATGACAACACACCTAAGGGCTAAAAATATAAAGTCAGATGTG
5269 TTGTGGGAAAAAAT
66 TTGTGGGAAAAAAT
5283 AAGAAAACAAATATATTGAGAGTATGACAACACACCTAAGGGCTAAAAATATAAAGTCAGATGTG
1 AAGAAAACAAATATATTGAGAGTATGACAACACACCTAAGGGCTAAAAATATAAAGTCAGATGTG
5348 TTGTGGGAAAAAAT
66 TTGTGGGAAAAAAT
5362 AAGA
1 AAGA
5366 TGTTTGATTG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 83 1.00
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.21
Consensus pattern (79 bp):
AAGAAAACAAATATATTGAGAGTATGACAACACACCTAAGGGCTAAAAATATAAAGTCAGATGTG
TTGTGGGAAAAAAT
Found at i:5867 original size:22 final size:22
Alignment explanation
Indices: 5842--5883 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5832 GACAAATCCG
* *
5842 TAACCTGAATGACCCGAGAAGT
1 TAACCCGAATGACCCAAGAAGT
5864 TAACCCGAATGACCCAAGAA
1 TAACCCGAATGACCCAAGAA
5884 TATTATAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.26, G:0.19, T:0.14
Consensus pattern (22 bp):
TAACCCGAATGACCCAAGAAGT
Done.