Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022900.1 Corchorus olitorius cultivar O-4 contig22933, 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: 5181
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29


Found at i:352 original size:27 final size:26

Alignment explanation


    Indices: 306--453  Score: 197
    Period size: 27  Copynumber: 5.5  Consensus size: 26

        296 AGGCGAATTG

                                *     
        306 GGAGGATCCACTGCTGGGGTTGAAGT
          1 GGAGGATCCACTGCTGGGGTCGAAGT

                 *          *          
        332 GTGAGCATCCACTGCTAGGGTCGAAGT
          1 G-GAGGATCCACTGCTGGGGTCGAAGT

                               *       
        359 GGGAGGATCCACTGCTGGGCTCGAAGT
          1 -GGAGGATCCACTGCTGGGGTCGAAGT

                         *             
        386 GGGAGGATCCACTACTGGGGTCGAAGT
          1 -GGAGGATCCACTGCTGGGGTCGAAGT

                         *             
        413 GGAAGGATCCACTACTGGGGTCGAAGT
          1 GG-AGGATCCACTGCTGGGGTCGAAGT

                          
        440 GGAAGGATCCACTG
          1 GG-AGGATCCACTG

        454 TGGCAACAGT


Statistics
Matches: 110,  Mismatches: 9, Indels: 5
        0.89            0.07        0.04

Matches are distributed among these distances:
  26    3  0.03
  27  106  0.96
  28    1  0.01

ACGTcount: A:0.22, C:0.20, G:0.39, T:0.20


Consensus pattern (26 bp):   
GGAGGATCCACTGCTGGGGTCGAAGT

Found at i:439 original size:81 final size:81

Alignment explanation


    Indices: 299--453  Score: 231
    Period size: 81  Copynumber: 1.9  Consensus size: 81

        289 CGACCCGAGG

                *              *       *                  *               *  
        299 CGAATTGGGAGGATCCACTGCTGGGGTTGAAGTGTGAGCATCCACTGCTAGGGTCGAAGTGGGAG
          1 CGAAGTGGGAGGATCCACTACTGGGGTCGAAGTGTGAGCATCCACTACTAGGGTCGAAGTGGAAG

                            
        364 GATCCACTGCTGGGCT
         66 GATCCACTGCTGGGCT

                                                   *          *              
        380 CGAAGTGGGAGGATCCACTACTGGGGTCGAAGTG-GAAGGATCCACTACTGGGGTCGAAGTGGAA
          1 CGAAGTGGGAGGATCCACTACTGGGGTCGAAGTGTG-AGCATCCACTACTAGGGTCGAAGTGGAA

                      
        444 GGATCCACTG
         65 GGATCCACTG

        454 TGGCAACAGT


Statistics
Matches: 66,  Mismatches: 7, Indels: 2
        0.88            0.09        0.03

Matches are distributed among these distances:
  80    1  0.02
  81   65  0.98

ACGTcount: A:0.23, C:0.19, G:0.38, T:0.20


Consensus pattern (81 bp):   
CGAAGTGGGAGGATCCACTACTGGGGTCGAAGTGTGAGCATCCACTACTAGGGTCGAAGTGGAAG
GATCCACTGCTGGGCT

Found at i:3589 original size:151 final size:151

Alignment explanation


    Indices: 3297--3590  Score: 414
    Period size: 151  Copynumber: 1.9  Consensus size: 151

       3287 AGATGGTTAG

                                                                             
       3297 AAAACGCCACTATATATTATAGGCGTAGAGTTGCAAAAATTTCTTTGTTTTAGGAGGAGGGAATT
          1 AAAACGCCACTATATATTATAGGCGTAGAGTTGCAAAAATTTCTTTGTTTTAGGAGGAGGGAATT

                                                *                           *
       3362 TTTCCCTCCAAAAAAAGGGAAAAAAAATCTCTCCCTTCATATATTAAAATAGCGGCGTTTCCTTT
         66 TTTCCCTCCAAAAAAAGGGAAAAAAAATCTCTCCCTCCATATATTAAAATAGCGGCGTTTCCTTA

                * *              
       3427 TCAAGATGCCACTCTGATGTC
        131 TCAAAACGCCACTCTGATGTC

                    *              *          *   *                *         
       3448 AAAACGCCGCTATATATTATAGGTGTAGAGTTG-GAAACTTT-TTTGTTTTAGTGGGGAGGGAAT
          1 AAAACGCCACTATATATTATAGGCGTAGAGTTGCAAAAATTTCTTTGTTTTAG-GAGGAGGGAAT

                                               *             *  * *        * 
       3511 TTTTCCCTCCAAAAAAAGGAGAAAAAAAATCTCTCTCTCCATATATTAATATGGTGGCGTCTTTC
         65 TTTTCCCTCCAAAAAAAGG-GAAAAAAAATCTCTCCCTCCATATATTAAAATAGCGGCGT-TTCC

                            
       3576 -TATCAAAACGCCACT
        128 TTATCAAAACGCCACT

       3591 AAATGGCGGA


Statistics
Matches: 126,  Mismatches: 14, Indels: 6
        0.86            0.10        0.04

Matches are distributed among these distances:
 149   10  0.08
 150   35  0.28
 151   78  0.62
 152    3  0.02

ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32


Consensus pattern (151 bp):   
AAAACGCCACTATATATTATAGGCGTAGAGTTGCAAAAATTTCTTTGTTTTAGGAGGAGGGAATT
TTTCCCTCCAAAAAAAGGGAAAAAAAATCTCTCCCTCCATATATTAAAATAGCGGCGTTTCCTTA
TCAAAACGCCACTCTGATGTC
Done.