Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012157.1 Corchorus olitorius cultivar O-4 contig12190, 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: 20966
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Found at i:3837 original size:22 final size:23
Alignment explanation
Indices: 3812--3860 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
3802 CGCCTGTCCC
3812 AGCG-ACAAGG-TGCCTCCAGCGG
1 AGCGAACAAGGTTGCCTCC-GCGG
*
3834 AGCGCAACAAGGTTGCTTCCGCGG
1 AGCG-AACAAGGTTGCCTCCGCGG
3858 AGC
1 AGC
3861 ATCTTGCTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 4 0.17
24 13 0.57
25 6 0.26
ACGTcount: A:0.22, C:0.31, G:0.35, T:0.12
Consensus pattern (23 bp):
AGCGAACAAGGTTGCCTCCGCGG
Found at i:4895 original size:11 final size:11
Alignment explanation
Indices: 4879--4903 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4869 AGAAAATTGT
4879 TTGTTTTTGGA
1 TTGTTTTTGGA
4890 TTGTTTTTGGA
1 TTGTTTTTGGA
4901 TTG
1 TTG
4904 ATTATTCCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.28, T:0.64
Consensus pattern (11 bp):
TTGTTTTTGGA
Found at i:4952 original size:37 final size:37
Alignment explanation
Indices: 4911--4981 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
4901 TTGATTATTC
4911 CCCAATTTTTAAAAATTGATTTTCGAATTAAAAAAAA
1 CCCAATTTTTAAAAATTGATTTTCGAATTAAAAAAAA
4948 CCCAATTTTTAAAAATTGATTTTCGAATTAAAAA
1 CCCAATTTTTAAAAATTGATTTTCGAATTAAAAA
4982 TTTTTTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (37 bp):
CCCAATTTTTAAAAATTGATTTTCGAATTAAAAAAAA
Found at i:7853 original size:28 final size:28
Alignment explanation
Indices: 7815--7890 Score: 107
Period size: 28 Copynumber: 2.7 Consensus size: 28
7805 AGTGCATTTG
**
7815 AAATGACCCAAAATGCCCCTGGATGTGCA
1 AAATGA-CCAAAATGCCCCTGGACATGCA
*
7844 AAATGACCAAAATGCCCCTGGACATGTA
1 AAATGACCAAAATGCCCCTGGACATGCA
*
7872 AAATGACCAGAATGCCCCT
1 AAATGACCAAAATGCCCCT
7891 TAAGTGATCC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 37 0.86
29 6 0.14
ACGTcount: A:0.37, C:0.28, G:0.18, T:0.17
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGACATGCA
Found at i:8191 original size:35 final size:35
Alignment explanation
Indices: 8152--8385 Score: 362
Period size: 35 Copynumber: 6.7 Consensus size: 35
8142 AGTTCATATC
* *
8152 GAAGATGCTACATCGAGTCATCTGAATTCATCTTT
1 GAAGATGCTACACCGAGTCATCTGAATTTATCTTT
* *
8187 GAAGATGCTACACCGAGTCATCTAAATTCATCTTT
1 GAAGATGCTACACCGAGTCATCTGAATTTATCTTT
*
8222 GAAGATGCTACACCGAGTCATCTAAATTTATCTTT
1 GAAGATGCTACACCGAGTCATCTGAATTTATCTTT
*
8257 GAAGATGCTACACCGAGTCATCTAAATTTATCTTT
1 GAAGATGCTACACCGAGTCATCTGAATTTATCTTT
* *
8292 GAAGATGCTTCACCGAGTCATCTGGATTTATCTTT
1 GAAGATGCTACACCGAGTCATCTGAATTTATCTTT
* *
8327 GAAGATGCTTCACCGAGTCATCTGGATTTATCTTT
1 GAAGATGCTACACCGAGTCATCTGAATTTATCTTT
8362 GAAGATGCTACACCG-GCTCATCTG
1 GAAGATGCTACACCGAG-TCATCTG
8386 TATTCCTGAG
Statistics
Matches: 191, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
34 1 0.01
35 190 0.99
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (35 bp):
GAAGATGCTACACCGAGTCATCTGAATTTATCTTT
Found at i:9290 original size:1 final size:1
Alignment explanation
Indices: 9286--9317 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
9276 GCTTGTTTAG
*
9286 TTTTTTTTTTTTTTTTTTTTTTTTTATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
9318 ATTTGAAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:9318 original size:7 final size:7
Alignment explanation
Indices: 9281--9321 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
9271 TTTAGGCTTG
9281 TTTAGTTT
1 TTTA-TTT
9289 TTT-TTT
1 TTTATTT
9295 TTT-TTT
1 TTTATTT
*
9301 TTTTTTT
1 TTTATTT
9308 TTTATTT
1 TTTATTT
9315 TTTATTT
1 TTTATTT
9322 GAAAGCATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
6 12 0.39
7 16 0.52
8 3 0.10
ACGTcount: A:0.07, C:0.00, G:0.02, T:0.90
Consensus pattern (7 bp):
TTTATTT
Found at i:20269 original size:5 final size:5
Alignment explanation
Indices: 20254--20294 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
20244 GTAAAACATT
* *
20254 AAAAC -AAAC AAAAC AAAAC AAACC AAAAC GAAAC AAAAC AA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AA
20295 CCATTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.76, C:0.22, G:0.02, T:0.00
Consensus pattern (5 bp):
AAAAC
Done.