Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019214.1 Corchorus olitorius cultivar O-4 contig19247, 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: 41984
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4536 original size:39 final size:39
Alignment explanation
Indices: 4482--4556 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
4472 TATTGAGAAG
*
4482 ATGGATGTCAGCAATCTTTAATTGAAGATTTCCTTTTCT
1 ATGGATGTCAGCAATCTTTAATGGAAGATTTCCTTTTCT
*
4521 ATGGATGTCAGCAATCTTTAATGGAAGATTTTCTTT
1 ATGGATGTCAGCAATCTTTAATGGAAGATTTCCTTT
4557 CTTCTTGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (39 bp):
ATGGATGTCAGCAATCTTTAATGGAAGATTTCCTTTTCT
Found at i:4977 original size:79 final size:79
Alignment explanation
Indices: 4846--5004 Score: 300
Period size: 79 Copynumber: 2.0 Consensus size: 79
4836 GTGCTTTGGG
4846 GTTGGAAGAAGTAATTAGCTAATAGCTAGGGTATAGTATATAGGAGTATGTCATCAAGGGGACAA
1 GTTGGAAGAAGTAATTAGCTAATAGCTAGGGTATAGTATATAGGAGTATGTCATCAAGGGGACAA
4911 TCCAGTGATTAAGA
66 TCCAGTGATTAAGA
* *
4925 GTTGGAAGAAGTAATTAGCTAATAGTTAGGGTATAGTATATAGGAGTATGTCATCGAGGGGACAA
1 GTTGGAAGAAGTAATTAGCTAATAGCTAGGGTATAGTATATAGGAGTATGTCATCAAGGGGACAA
4990 TCCAGTGATTAAGA
66 TCCAGTGATTAAGA
5004 G
1 G
5005 GTTTCAGGTT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.36, C:0.08, G:0.29, T:0.27
Consensus pattern (79 bp):
GTTGGAAGAAGTAATTAGCTAATAGCTAGGGTATAGTATATAGGAGTATGTCATCAAGGGGACAA
TCCAGTGATTAAGA
Found at i:8205 original size:41 final size:41
Alignment explanation
Indices: 8158--8237 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
8148 ATTATAACTA
*
8158 GGGGCTAAACATGGATTTAATTT-TTTACTTTAATTATTAGG
1 GGGGCTAAACATGGATTTAATTTATTT-CCTTAATTATTAGG
*
8199 GGGGCTAAACCTGGATTTAATTTATTTCCTTAATTATTA
1 GGGGCTAAACATGGATTTAATTTATTTCCTTAATTATTA
8238 TGAGGGTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 33 0.92
42 3 0.08
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (41 bp):
GGGGCTAAACATGGATTTAATTTATTTCCTTAATTATTAGG
Found at i:8359 original size:66 final size:67
Alignment explanation
Indices: 8252--8399 Score: 201
Period size: 67 Copynumber: 2.2 Consensus size: 67
8242 GGTCAAGCTG
* *
8252 GGGACAAGTTGGAGGGTAAAAAAGAATTATCCTTGTGGTAATTAAG-TTTTCT-AGTGACACGTA
1 GGGACAAG-TGGAGGGTAAAAAAGAATTATCCTTATGGTAATTAAGATTTT-TAAGTGAAACGTA
8315 AGGA
64 AGGA
* * * * *
8319 GGGACAAGTGGATGGTCAAGAAGAATTATTCTTATGGTAATTAAGATTTTTAAGTGAAACGTCAG
1 GGGACAAGTGGAGGGTAAAAAAGAATTATCCTTATGGTAATTAAGATTTTTAAGTGAAACGTAAG
8384 GA
66 GA
8386 GGGACAAGTGGAGG
1 GGGACAAGTGGAGG
8400 ATCATGTAGC
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
66 33 0.46
67 38 0.54
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.27
Consensus pattern (67 bp):
GGGACAAGTGGAGGGTAAAAAAGAATTATCCTTATGGTAATTAAGATTTTTAAGTGAAACGTAAG
GA
Found at i:10015 original size:36 final size:36
Alignment explanation
Indices: 9968--10045 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 36
9958 TACCAATCTC
*
9968 ATTAATCAAAAAGTTTATTTCTCAAAAAAAAATATA
1 ATTAATCAAAAAATTTATTTCTCAAAAAAAAATATA
* **
10004 ATTAATCAAAAAATTTATTTCTTAAAAAACTATATA
1 ATTAATCAAAAAATTTATTTCTCAAAAAAAAATATA
10040 ATTAAT
1 ATTAAT
10046 ACTAGCTGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.54, C:0.08, G:0.01, T:0.37
Consensus pattern (36 bp):
ATTAATCAAAAAATTTATTTCTCAAAAAAAAATATA
Found at i:16930 original size:19 final size:19
Alignment explanation
Indices: 16906--16942 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16896 CCACCATGAA
16906 GAGCACATTTCCTTGCCAG
1 GAGCACATTTCCTTGCCAG
* *
16925 GAGCACGTTTTCTTGCCA
1 GAGCACATTTCCTTGCCA
16943 AAATAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.30, G:0.22, T:0.30
Consensus pattern (19 bp):
GAGCACATTTCCTTGCCAG
Found at i:29120 original size:13 final size:13
Alignment explanation
Indices: 29102--29126 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29092 GCTTTGCCCT
29102 TTTTTAAAAAATA
1 TTTTTAAAAAATA
29115 TTTTTAAAAAAT
1 TTTTTAAAAAAT
29127 TGGCCCAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTTAAAAAATA
Done.