Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015935.1 Corchorus olitorius cultivar O-4 contig15968, 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: 33241
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:12207 original size:51 final size:51
Alignment explanation
Indices: 12152--12305 Score: 290
Period size: 51 Copynumber: 3.0 Consensus size: 51
12142 ATTTCCCTTA
* *
12152 GATGTTTTTCTTCAATAATAAGTGTGAGAGATATAAATAGGGATAATGTTG
1 GATGTTTCTCTTCAATAATAAGTGTGAGAGATATAAATAGGGGTAATGTTG
12203 GATGTTTCTCTTCAATAATAAGTGTGAGAGATATAAATAGGGGTAATGTTG
1 GATGTTTCTCTTCAATAATAAGTGTGAGAGATATAAATAGGGGTAATGTTG
12254 GATGTTTCTCTTCAATAATAAGTGTGAGAGATATAAATAGGGGTAATGTTG
1 GATGTTTCTCTTCAATAATAAGTGTGAGAGATATAAATAGGGGTAATGTTG
12305 G
1 G
12306 GAGAGATCCG
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 101 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (51 bp):
GATGTTTCTCTTCAATAATAAGTGTGAGAGATATAAATAGGGGTAATGTTG
Found at i:14253 original size:39 final size:39
Alignment explanation
Indices: 14208--14288 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
14198 AATAATTTAT
14208 GGAAGGAAAAAAAATAAAGTTATTGAAATTTATAAAGAA
1 GGAAGGAAAAAAAATAAAGTTATTGAAATTTATAAAGAA
14247 GGAAGGAAAAAAAATAAAGTTATTGAAATTTATAAAGAA
1 GGAAGGAAAAAAAATAAAGTTATTGAAATTTATAAAGAA
14286 GGA
1 GGA
14289 CCTATTGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.58, C:0.00, G:0.20, T:0.22
Consensus pattern (39 bp):
GGAAGGAAAAAAAATAAAGTTATTGAAATTTATAAAGAA
Found at i:17504 original size:1 final size:1
Alignment explanation
Indices: 17498--17524 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
17488 TATGTTTTAG
17498 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
17525 GTTGTTGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:20389 original size:17 final size:17
Alignment explanation
Indices: 20369--20402 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
20359 GTGATTTTAC
20369 AAATCAATAAAGTAAAG
1 AAATCAATAAAGTAAAG
20386 AAATCAATAAAGTAAAG
1 AAATCAATAAAGTAAAG
20403 CCTTTGGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (17 bp):
AAATCAATAAAGTAAAG
Found at i:30385 original size:84 final size:84
Alignment explanation
Indices: 30234--30396 Score: 229
Period size: 84 Copynumber: 1.9 Consensus size: 84
30224 CTAAGAGTTA
* ** * * *
30234 TAACATGCCTATATATTATTAGTAAGCCCATATTTAACGAGTCTATTCACGAGTACACCTAGTTC
1 TAACAGGCCTATATATTATTAGTAAAACCATATTTAACGAGTATATTCACGAGTAAACCTAGGTC
30299 CAAATTTTAAAAAATTGCG
66 CAAATTTTAAAAAATTGCG
* * *
30318 TAACAGGCCTATATATTATTAGTAAAACCATATTTAATGGGTATATTCACGTGTAAACGC-AGGT
1 TAACAGGCCTATATATTATTAGTAAAACCATATTTAACGAGTATATTCACGAGTAAAC-CTAGGT
30382 CCAAATTTTAAAAAA
65 CCAAATTTTAAAAAA
30397 ATTTCCTGCA
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
84 68 0.99
85 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.33
Consensus pattern (84 bp):
TAACAGGCCTATATATTATTAGTAAAACCATATTTAACGAGTATATTCACGAGTAAACCTAGGTC
CAAATTTTAAAAAATTGCG
Found at i:31792 original size:45 final size:45
Alignment explanation
Indices: 31728--31848 Score: 178
Period size: 42 Copynumber: 2.8 Consensus size: 45
31718 CAGTTAGTAT
* *
31728 TAGCTATATTTTGATGAATTACCTAGAGATGGAGGAGTAGAATAC
1 TAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAGAAAAC
*
31773 TAGCTTTATTTT-AGTGAATTACCTAGAGA---AGGAGTAGAAAAT
1 TAGCTTTATTTTGA-TGAATTACCTAGAGATGGAGGAGTAGAAAAC
31815 TAGCTTTATTTTGATGAATTACCTAGAGATGGAG
1 TAGCTTTATTTTGATGAATTACCTAGAGATGGAG
31849 TAAAATTTAG
Statistics
Matches: 68, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
42 38 0.56
43 1 0.01
44 1 0.01
45 28 0.41
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.34
Consensus pattern (45 bp):
TAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAGAAAAC
Found at i:33171 original size:2 final size:2
Alignment explanation
Indices: 33164--33241 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
33154 GAATAATAGG
33164 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
33206 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Done.