Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009798.1 Corchorus olitorius cultivar O-4 contig09830, 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: 3439
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:1321 original size:16 final size:16
Alignment explanation
Indices: 1300--1333 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1290 AGGCCTGCCT
1300 TTTATTAT-TATTAATA
1 TTTATTATATATT-ATA
1316 TTTATTATATATTATA
1 TTTATTATATATTATA
1332 TT
1 TT
1334 CCTTTGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATTATATATTATA
Found at i:2164 original size:77 final size:77
Alignment explanation
Indices: 1952--2212 Score: 260
Period size: 77 Copynumber: 3.4 Consensus size: 77
1942 TCCCATTCAG
* * * *** * *
1952 AAATGTCATTTAAGTAAACCTGCTTAGGCCTCCATTCAGAAATGT-CATTTAAGTAAACCTGCTT
1 AAATTTCATTTAAGCAAACCTGCTTAGGTCTATGTTTAG-AAT-TCCATTTAAATAAACCTGCTT
*
2016 AGGTT-TATGTTTA
64 AGGTTCTATGCTTA
* * *
2029 GAATTTCATTTAAGCAAACCTGCTTAGGTCTATGTTTAGAATTTCATTTAAGTAAACCTGCTTAG
1 AAATTTCATTTAAGCAAACCTGCTTAGGTCTATGTTTAGAATTCCATTTAAATAAACCTGCTTAG
2094 GTTCT-TGCTTA
66 GTTCTATGCTTA
* *
2105 AAATTTCCGTTTAAGCAAACCTGCTTAGGTCT-TGTTTAGAATTCCCTTTAAAATAAACCTGCTT
1 AAATTT-CATTTAAGCAAACCTGCTTAGGTCTATGTTTAGAATTCCATTT-AAATAAACCTGCTT
* *
2169 AGGATCTCTGCTTA
64 AGGTTCTATGCTTA
* * * ** *
2183 GAGTTTTATTTAAGTGAACCTACTTAGGTC
1 AAATTTCATTTAAGCAAACCTGCTTAGGTC
2213 CTCATTTAGA
Statistics
Matches: 157, Mismatches: 22, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
75 1 0.01
76 52 0.33
77 94 0.60
78 10 0.06
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (77 bp):
AAATTTCATTTAAGCAAACCTGCTTAGGTCTATGTTTAGAATTCCATTTAAATAAACCTGCTTAG
GTTCTATGCTTA
Found at i:2275 original size:72 final size:72
Alignment explanation
Indices: 2157--2291 Score: 191
Period size: 72 Copynumber: 1.9 Consensus size: 72
2147 TCCCTTTAAA
* * * * * *
2157 ATAAACCTGCTTAGGATCTCTGCTTAGAGTTTTATTTAAGTGAACCTACTTAGGTCCTCATTTAG
1 ATAAACCTGCTTAGGATCTCTGCTTAGACTTTGATTCAAGTAAACCTACTTAGGCCCCCATTTAG
2222 AATTTCC
66 AATTTCC
*
2229 ATAAACCTGCTTAGGATCTCTGCTTAGACCTTTGA-TCAAGTAAACCTGCTTAGGCCCCCATTT
1 ATAAACCTGCTTAGGATCTCTGCTTAGA-CTTTGATTCAAGTAAACCTACTTAGGCCCCCATTT
2292 TGAGTTACCA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 51 0.93
73 4 0.07
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.36
Consensus pattern (72 bp):
ATAAACCTGCTTAGGATCTCTGCTTAGACTTTGATTCAAGTAAACCTACTTAGGCCCCCATTTAG
AATTTCC
Found at i:2361 original size:41 final size:38
Alignment explanation
Indices: 1929--2521 Score: 302
Period size: 38 Copynumber: 15.5 Consensus size: 38
1919 TTATCTTAGC
* * * *
1929 AAACCTGCTTAGGTC-CCATTCAGAAATGTCATTTAAGT
1 AAACCTGCTTAGGTCTCTATTTAG-AATTTCATTAAAGT
* * * * *
1967 AAACCTGCTTAGGCCTCCATTCAGAAATGTCATTTAAGT
1 AAACCTGCTTAGGTCTCTATTTAG-AATTTCATTAAAGT
* * * * *
2006 AAACCTGCTTAGGTTTATGTTTAGAATTTCATTTAAGC
1 AAACCTGCTTAGGTCTCTATTTAGAATTTCATTAAAGT
* * *
2044 AAACCTGCTTAGGTCTATGTTTAGAATTTCATTTAAGT
1 AAACCTGCTTAGGTCTCTATTTAGAATTTCATTAAAGT
* * * *
2082 AAACCTGCTTAGGT-TCT-TGCTTAAAATTTCCGTTTAAGC
1 AAACCTGCTTAGGTCTCTAT--TTAGAATTT-CATTAAAGT
* * * *
2121 AAACCTGCTTAGGTCT-TGTTTAGAATTCCCTTTAAAAT
1 AAACCTGCTTAGGTCTCTATTTAGAATT-TCATTAAAGT
** * * *
2159 AAACCTGCTTAGGATCTCTGCTTAGAGTTTTATTTAAGT
1 AAACCTGCTTAGG-TCTCTATTTAGAATTTCATTAAAGT
* * *
2198 GAACCTACTTAGGTC-CTCATTTAGAATTTC----CA-T
1 AAACCTGCTTAGGTCTCT-ATTTAGAATTTCATTAAAGT
** * * *
2231 AAACCTGCTTAGGATCTCTGCTTAGACCTTTGA-TCAAGT
1 AAACCTGCTTAGG-TCTCTATTTAGA-ATTTCATTAAAGT
* * * * * * *
2270 AAACCTGCTTAGGCCCCCATTTTGAGTTACCATTCAAGT
1 AAACCTGCTTAGGTCTCTATTTAGAATT-TCATTAAAGT
2309 AAACCTGCTTAGGTCTCTATTTAGAATGTTCATGTAAAGT
1 AAACCTGCTTAGGTCTCTATTTAGAAT-TTCAT-TAAAGT
* ** * *
2349 AAAACCTACTTAGGTCTCTGCTTAGAGTTTCATTTAA-T
1 -AAACCTGCTTAGGTCTCTATTTAGAATTTCATTAAAGT
* * *
2387 CAAGCCTGCTTAGGTCTCTATTTGGAATTTCCGTTTAAA-T
1 -AAACCTGCTTAGGTCTCTATTTAGAATTT-C-ATTAAAGT
* * ** * *
2427 GAACCTGCTTAAGG-CGCTGCTTA-AAGTTTCGTCT-AGGT
1 AAACCTGCTT-AGGTCTCTATTTAGAA-TTTCAT-TAAAGT
* * * *
2465 AAACATGCTTAGGTCTCTGTTTAGAATTTTCGTTTAAG-
1 AAACCTGCTTAGGTCTCTATTTAGAA-TTTCATTAAAGT
2503 AAACCCTGCTTAGGTCTCT
1 AAA-CCTGCTTAGGTCTCT
2522 GTTTCAGTAA
Statistics
Matches: 436, Mismatches: 87, Indels: 63
0.74 0.15 0.11
Matches are distributed among these distances:
33 12 0.03
34 8 0.02
35 5 0.01
36 1 0.00
37 11 0.03
38 175 0.40
39 171 0.39
40 30 0.07
41 23 0.05
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (38 bp):
AAACCTGCTTAGGTCTCTATTTAGAATTTCATTAAAGT
Found at i:2513 original size:39 final size:39
Alignment explanation
Indices: 1929--2525 Score: 388
Period size: 39 Copynumber: 15.6 Consensus size: 39
1919 TTATCTTAGC
** * * *
1929 AAACCTGCTTAGGTC-CCATTCAGAAATGTCATTTAAGT
1 AAACCTGCTTAGGTCTCTGTTTAGAATTTTCATTTAAGT
* ** * * *
1967 AAACCTGCTTAGGCCTCCATTCAGAAATGTCATTTAAGT
1 AAACCTGCTTAGGTCTCTGTTTAGAATTTTCATTTAAGT
* * *
2006 AAACCTGCTTAGGTTTATGTTTAGAA-TTTCATTTAAGC
1 AAACCTGCTTAGGTCTCTGTTTAGAATTTTCATTTAAGT
*
2044 AAACCTGCTTAGGTCTATGTTTAGAA-TTTCATTTAAGT
1 AAACCTGCTTAGGTCTCTGTTTAGAATTTTCATTTAAGT
* * * * *
2082 AAACCTGCTTAGGT-TCTTGCTTAAAATTTCCGTTTAAGC
1 AAACCTGCTTAGGTCTC-TGTTTAGAATTTTCATTTAAGT
* * *
2121 AAACCTGCTTAGGTCT-TGTTTAGAA-TTCCCTTTAAAAT
1 AAACCTGCTTAGGTCTCTGTTTAGAATTTTCATTT-AAGT
* *
2159 AAACCTGCTTAGGATCTCTGCTTAGAGTTTT-ATTTAAGT
1 AAACCTGCTTAGG-TCTCTGTTTAGAATTTTCATTTAAGT
* * * *
2198 GAACCTACTTAGGTC-CTCATTTAGAA-TTTC----CA-T
1 AAACCTGCTTAGGTCTCT-GTTTAGAATTTTCATTTAAGT
* ** * *
2231 AAACCTGCTTAGGATCTCTGCTTAGACCTTTGA-TCAAGT
1 AAACCTGCTTAGG-TCTCTGTTTAGAATTTTCATTTAAGT
* * ** * * ** *
2270 AAACCTGCTTAGGCCCCCATTTTGAGTTACCATTCAAGT
1 AAACCTGCTTAGGTCTCTGTTTAGAATTTTCATTTAAGT
* * *
2309 AAACCTGCTTAGGTCTCTATTTAGAATGTTCATGTAAAGT
1 AAACCTGCTTAGGTCTCTGTTTAGAATTTTCAT-TTAAGT
* * *
2349 AAAACCTACTTAGGTCTCTGCTTAG-AGTTTCATTTAA-T
1 -AAACCTGCTTAGGTCTCTGTTTAGAATTTTCATTTAAGT
* * * * * *
2387 CAAGCCTGCTTAGGTCTCTATTTGGAATTTCCGTTTAAAT
1 -AAACCTGCTTAGGTCTCTGTTTAGAATTTTCATTTAAGT
* * * * * * *
2427 GAACCTGCTTAAGG-CGCTGCTTA-AAGTTTCGTCTAGGT
1 AAACCTGCTT-AGGTCTCTGTTTAGAATTTTCATTTAAGT
* *
2465 AAACATGCTTAGGTCTCTGTTTAGAATTTTCGTTTAAG-
1 AAACCTGCTTAGGTCTCTGTTTAGAATTTTCATTTAAGT
2503 AAACCCTGCTTAGGTCTCTGTTT
1 AAA-CCTGCTTAGGTCTCTGTTT
2526 CAGTAAGCCT
Statistics
Matches: 439, Mismatches: 94, Indels: 51
0.75 0.16 0.09
Matches are distributed among these distances:
33 12 0.03
34 8 0.02
35 5 0.01
37 16 0.04
38 167 0.38
39 182 0.41
40 26 0.06
41 23 0.05
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (39 bp):
AAACCTGCTTAGGTCTCTGTTTAGAATTTTCATTTAAGT
Found at i:2853 original size:37 final size:37
Alignment explanation
Indices: 2812--2886 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
2802 TCTCATGAAT
2812 AACTCCCGTTCTTTAAAATTGAGATTAATTTTGTTTC
1 AACTCCCGTTCTTTAAAATTGAGATTAATTTTGTTTC
2849 AACTCCCGTTCTTTAAAATTGAGATTAATTTTGTTTC
1 AACTCCCGTTCTTTAAAATTGAGATTAATTTTGTTTC
2886 A
1 A
2887 TTTCCTTACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.28, C:0.16, G:0.11, T:0.45
Consensus pattern (37 bp):
AACTCCCGTTCTTTAAAATTGAGATTAATTTTGTTTC
Found at i:3310 original size:19 final size:19
Alignment explanation
Indices: 3286--3325 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
3276 TTGAATTGAA
3286 AAAAAGAAGAAGAAAAGTC
1 AAAAAGAAGAAGAAAAGTC
3305 AAAAAGAAGAAGAAAAGTC
1 AAAAAGAAGAAGAAAAGTC
3324 AA
1 AA
3326 GTTCCATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.70, C:0.05, G:0.20, T:0.05
Consensus pattern (19 bp):
AAAAAGAAGAAGAAAAGTC
Done.