Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015682.1 Corchorus olitorius cultivar O-4 contig15715, 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: 23635
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:3170 original size:5 final size:5
Alignment explanation
Indices: 3162--3226 Score: 80
Period size: 5 Copynumber: 13.4 Consensus size: 5
3152 TAATATATTA
* *
3162 TATAT TATAT TATAT TATAT TATAT TATA- T-TAT TATAT AATAA TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
* *
3210 CATAT TATAT CATAT TA
1 TATAT TATAT TATAT TA
3227 ATTGTCATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
3 2 0.04
4 2 0.04
5 46 0.92
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (5 bp):
TATAT
Found at i:3224 original size:15 final size:14
Alignment explanation
Indices: 3146--3224 Score: 85
Period size: 15 Copynumber: 5.8 Consensus size: 14
3136 ATTTTCGACT
3146 TTATATTA-ATATA
1 TTATATTATATATA
3159 TTATA-TAT-TATA
1 TTATATTATATATA
3171 TTATATTATATTATA
1 TTATATTATA-TATA
3186 TTATATTAT-TATA
1 TTATATTATATATA
* *
3199 TAATAATATATCATA
1 TTATATTATAT-ATA
*
3214 TTATATCATAT
1 TTATATTATAT
3225 TAATTGTCAT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
12 11 0.20
13 19 0.35
14 1 0.02
15 24 0.44
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (14 bp):
TTATATTATATATA
Found at i:11382 original size:2 final size:2
Alignment explanation
Indices: 11375--11403 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11365 TACTATTTAG
11375 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11404 GTGTCAAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12937 original size:34 final size:34
Alignment explanation
Indices: 12899--12968 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
12889 ACCGATCTAA
*
12899 AGAATTAGCGTTGTTAATCTAAAAACAAATTGAT
1 AGAATCAGCGTTGTTAATCTAAAAACAAATTGAT
*
12933 AGAATCAGCGTTGTTAATCTAAGAACAAATTGAT
1 AGAATCAGCGTTGTTAATCTAAAAACAAATTGAT
12967 AG
1 AG
12969 GGGTATTTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (34 bp):
AGAATCAGCGTTGTTAATCTAAAAACAAATTGAT
Found at i:14273 original size:15 final size:15
Alignment explanation
Indices: 14255--14283 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
14245 AATCGTTCTC
14255 CTGGGAATCACTCTT
1 CTGGGAATCACTCTT
14270 CTGGGAATCACTCT
1 CTGGGAATCACTCT
14284 CCTATGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.31
Consensus pattern (15 bp):
CTGGGAATCACTCTT
Found at i:18109 original size:11 final size:11
Alignment explanation
Indices: 18093--18131 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
18083 TAGGATTTAT
18093 TTATTTATATA
1 TTATTTATATA
18104 TTATTTATATA
1 TTATTTATATA
*
18115 -TATTCTACATA
1 TTATT-TATATA
18126 TTATTT
1 TTATTT
18132 TTGTAACCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTATATA
Found at i:18339 original size:37 final size:37
Alignment explanation
Indices: 18298--18372 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
18288 TAATTTGAGG
18298 TTCCCTTTAATTATTGATATGTTAAGTGGGGTTTTAA
1 TTCCCTTTAATTATTGATATGTTAAGTGGGGTTTTAA
*
18335 TTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAA
1 TTCCCTTTAATTATTGATATGTTAAGTGGGGTTTTAA
18372 T
1 T
18373 ATGTTATAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.08, G:0.17, T:0.51
Consensus pattern (37 bp):
TTCCCTTTAATTATTGATATGTTAAGTGGGGTTTTAA
Found at i:20868 original size:27 final size:27
Alignment explanation
Indices: 20830--20887 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
20820 TTTGCTACTC
* * **
20830 AACTTTTCCTACTCCTTTACATTACCA
1 AACTGTTCCTACTCCTTAACAACACCA
*
20857 AACTGTTCCTACTTCTTAACAACACCA
1 AACTGTTCCTACTCCTTAACAACACCA
20884 AACT
1 AACT
20888 ACACCAAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.33, G:0.02, T:0.34
Consensus pattern (27 bp):
AACTGTTCCTACTCCTTAACAACACCA
Found at i:21168 original size:2 final size:2
Alignment explanation
Indices: 21161--21188 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21151 TCTCTTAGTA
21161 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
21189 CCCAAGCTTC
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
Done.