Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015090.1 Corchorus olitorius cultivar O-4 contig15123, 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: 21139
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:602 original size:105 final size:106
Alignment explanation
Indices: 368--628 Score: 316
Period size: 106 Copynumber: 2.5 Consensus size: 106
358 TTATAGAGTC
*
368 TTTTAGAAATAAAATAAAAAACTAATTTCACTAAGTTTAGTCCCAAATT-AAACTTTATTTTTAT
1 TTTTAGAAATAAAATAAAAAACTAATTTCACTAAATTTAG-CCCAAATTAAAACTTTATTTTTAT
* * *
432 TTTAAGGGTAGATTTCAAAATTGATTATTTATTGTTAATGGG
65 TTTAAGGGTAAATTTCAAAATTGAATATATATTGTTAATGGG
* * * *
474 TTTTAGAAATTAAATACAAAACTAATTTCACAAAATTTAGCCCCAAATTAAAATTTTATTTTTAT
1 TTTTAGAAATAAAATAAAAAACTAATTTCACTAAATTTAG-CCCAAATTAAAACTTTATTTTTAT
* ** *
539 TTTAAGGGTAAATTT-GATGTTTAATA-ATATTGTT-ATAGGG
65 TTTAAGGGTAAATTTCAAAATTGAATATATATTGTTAAT-GGG
* * * *
579 TTTTAGAAATAAAATATATAACTAA-TTCACTAAACTTAGCTCAAATTAAA
1 TTTTAGAAATAAAATAAAAAACTAATTTCACTAAATTTAGCCCAAATTAAA
629 GTTAAAATTT
Statistics
Matches: 134, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
103 10 0.07
104 14 0.10
105 32 0.24
106 50 0.37
107 28 0.21
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (106 bp):
TTTTAGAAATAAAATAAAAAACTAATTTCACTAAATTTAGCCCAAATTAAAACTTTATTTTTATT
TTAAGGGTAAATTTCAAAATTGAATATATATTGTTAATGGG
Found at i:5630 original size:9 final size:9
Alignment explanation
Indices: 5616--5645 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
5606 TTTTTACTTC
5616 TTCTTTTAT
1 TTCTTTTAT
5625 TTCTTTTAAT
1 TTCTTTT-AT
5635 TTCTTTTAT
1 TTCTTTTAT
5644 TT
1 TT
5646 AAAAGAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (9 bp):
TTCTTTTAT
Found at i:7912 original size:31 final size:31
Alignment explanation
Indices: 7874--7937 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
7864 AACCAAACAC
7874 AACCTTAGTAAATGTTCGAGTTTTTTGAATT
1 AACCTTAGTAAATGTTCGAGTTTTTTGAATT
7905 AACCTTAGTAAATGTTCGAGTTTTTTGAATT
1 AACCTTAGTAAATGTTCGAGTTTTTTGAATT
7936 AA
1 AA
7938 GAAGATAGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (31 bp):
AACCTTAGTAAATGTTCGAGTTTTTTGAATT
Found at i:9136 original size:50 final size:50
Alignment explanation
Indices: 9061--9163 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
9051 AATCCAGGAG
9061 AAAGTTATTCGCAATTTATTCAATCCACCAGATTTAAGGATACATTGTGC
1 AAAGTTATTCGCAATTTATTCAATCCACCAGATTTAAGGATACATTGTGC
9111 AAAGTTATTCGCAATTTATTCAATCCACCAGATTTAAGGATACATTGTGC
1 AAAGTTATTCGCAATTTATTCAATCCACCAGATTTAAGGATACATTGTGC
9161 AAA
1 AAA
9164 CTACACAGGC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (50 bp):
AAAGTTATTCGCAATTTATTCAATCCACCAGATTTAAGGATACATTGTGC
Found at i:10472 original size:12 final size:12
Alignment explanation
Indices: 10457--10486 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
10447 AAACACACGC
10457 ACACACACACAA
1 ACACACACACAA
*
10469 ACACAAACACAA
1 ACACACACACAA
10481 ACACAC
1 ACACAC
10487 TCTCAAAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (12 bp):
ACACACACACAA
Found at i:14244 original size:438 final size:434
Alignment explanation
Indices: 13380--14263 Score: 1169
Period size: 438 Copynumber: 2.0 Consensus size: 434
13370 AAAAAAATTA
* * *
13380 AAGCGTTAAATCGAGTAAAATAGAATTTGTAAAGGATTAAGTAGTATAAAGTAGAAAATTATAAG
1 AAGCGTTAAATCGAGTAAAATAGAATTAGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATAAG
* *
13445 GGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTGATAGAGATCTTCAAACATAAAAAAT
66 GGTCATTTCATAAATAATCCAAATAAAAAAATGTTTGTTGATAGAGATCTTCAAACATAAAAAAT
* * * * * *
13510 CCCTTTTTAACCCTTCATGAAACTTGTAAATCAAATTTAGTTTTCGGGTACTTCATGAAAGTGGT
131 CCCTTTTGAACACTTAATGAAACTCGTAAATCAAATTTAGCTTTCGGGTACTTCATGAAAGTCGT
* * * * *
13575 AGATCACGCAATAACCTTTTAATCGATACTTAAATTACTTTAATCGGACATGTGGATCTAAAATT
196 AGATCACACAATAACCTTTTAACCAACACTTAAA-TACATTAATCGGACATGTGGATCTAAAATT
* * * * *
13640 ATATGGTATTAAATAGATTGATAATCAAAACCAGCAAATTTGGGAAGCATTTTTCTTTGAATTGA
260 ATATGATATTAAATAGATCGACAATCAAAACCACCAAATTTCGGAAGCATTTTTCTTTGAATTGA
** * ** *
13705 AATGTAAAAATTGGCTTTTGAGTTTTTCATGAAAGTTAGAGATCATGAAATTACCTTTTAATCGA
325 AACATAAAAATTGGCTTTTAAGTCCTTCATGAAAGTTAGAAATCATGAAATTA-CTTTTAATCGA
* *
13770 CACCCGAATCACCTTAATCGGACAAATAGAAAAAAAAATAAAGCTT
389 CACCCGAATCACCTTAATCAGACAAATAAAAAAAAAAATAAAGCTT
* * *
13816 AAGCGTTAAATCGATTAAGATAGAATTAGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAG
1 AAGCGTTAAATCGAGTAAAATAGAATTAGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATAAG
*
13881 GGTCATTTCATAAATAATCCAAATAAAAAAAAATGTTTGTTGAT-GAAGATCTTGAAACATAAAA
66 GGTCATTTCATAAATAATCCAAAT--AAAAAAATGTTTGTTGATAG-AGATCTTCAAACATAAAA
* * * *
13945 ATTTCCTTTTGAACACTTAATGAAACTCGTAGATCAAATTTAGCTTTCGGGTCCTTCATGAAAGT
128 AATCCCTTTTGAACACTTAATGAAACTCGTAAATCAAATTTAGCTTTCGGGTACTTCATGAAAGT
* *
14010 CGTAGATCATACAATAACCTTTTAACCAACACTTGAGAA-ACATTAATCGGACATGTTGAT-TGA
193 CGTAGATCACACAATAACCTTTTAACCAACACTT-A-AATACATTAATCGGACATGTGGATCT-A
* *
14073 AAATTATATGATATTAAATAGATCGGCAATCAAAATCACCAAATTTCGGAAGCA-TTTT-TTTGA
255 AAATTATATGATATTAAATAGATCGACAATCAAAACCACCAAATTTCGGAAGCATTTTTCTTTGA
14136 ATTGAAACATAAAAATTGGCTTTTAAGTCCTTCATGAAAGTT-GTAAATCATGAAA-T-CTTTTA
320 ATTGAAACATAAAAATTGGCTTTTAAGTCCTTCATGAAAGTTAG-AAATCATGAAATTACTTTTA
** **
14198 A-CAGACACTTGAATCACCTTAATCAGACAAATACAAAATTAAAAAA-AAA-CAA
384 ATC-GACACCCGAATCACCTTAATCAGACAAATA-AAAA--AAAAAATAAAGCTT
14250 AAGCGTTAAATCGA
1 AAGCGTTAAATCGA
14264 TTTGTAAAGG
Statistics
Matches: 392, Mismatches: 45, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
432 1 0.00
433 34 0.09
434 18 0.05
435 5 0.01
436 140 0.36
437 6 0.02
438 185 0.47
439 1 0.00
440 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (434 bp):
AAGCGTTAAATCGAGTAAAATAGAATTAGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATAAG
GGTCATTTCATAAATAATCCAAATAAAAAAATGTTTGTTGATAGAGATCTTCAAACATAAAAAAT
CCCTTTTGAACACTTAATGAAACTCGTAAATCAAATTTAGCTTTCGGGTACTTCATGAAAGTCGT
AGATCACACAATAACCTTTTAACCAACACTTAAATACATTAATCGGACATGTGGATCTAAAATTA
TATGATATTAAATAGATCGACAATCAAAACCACCAAATTTCGGAAGCATTTTTCTTTGAATTGAA
ACATAAAAATTGGCTTTTAAGTCCTTCATGAAAGTTAGAAATCATGAAATTACTTTTAATCGACA
CCCGAATCACCTTAATCAGACAAATAAAAAAAAAAATAAAGCTT
Found at i:20909 original size:19 final size:19
Alignment explanation
Indices: 20885--20925 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
20875 GGTTTATCAG
*
20885 TGTTTTTCTTTTTAATTT-T
1 TGTTTTT-TTCTTAATTTCT
20904 TGTTTTTTTCTTAATTTCT
1 TGTTTTTTTCTTAATTTCT
20923 TGT
1 TGT
20926 ATGGTATCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.10, C:0.07, G:0.07, T:0.76
Consensus pattern (19 bp):
TGTTTTTTTCTTAATTTCT
Done.