Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012396.1 Corchorus olitorius cultivar O-4 contig12429, 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: 5682
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27


Found at i:5145 original size:58 final size:58

Alignment explanation


    Indices: 5049--5261  Score: 390
    Period size: 58  Copynumber: 3.7  Consensus size: 58

       5039 TCGCTTATCC

                                                    *                 
       5049 TGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTTAATTCAAAATATCATCT
          1 TGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCATCT

             *                               *                        
       5107 TCTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAAAGTTTTCAATTCAAAATATCATCT
          1 TGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCATCT

                                                                      
       5165 TGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCATCT
          1 TGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCATCT

                           *                       
       5223 TGTTTTAAAATCCTGCTCGAGGTCTCTGTTAGAGAGTTT
          1 TGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTT

       5262 ATATTTCAGA


Statistics
Matches: 149,  Mismatches: 6, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  58  149  1.00

ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42


Consensus pattern (58 bp):   
TGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCATCT

Found at i:5539 original size:29 final size:29

Alignment explanation


    Indices: 5493--5679  Score: 257
    Period size: 29  Copynumber: 6.4  Consensus size: 29

       5483 TTAATTGACC

                       *            *  * 
       5493 TTTTTGCACATTCAGGGGCATTTTGGTTA
          1 TTTTTGCACATCCAGGGGCATTTTAGTCA

                    *    *          *    
       5522 TTTTTGCATATCCGGGGGCATTTTGGTCA
          1 TTTTTGCACATCCAGGGGCATTTTAGTCA

                 *      *                
       5551 TTTTTTCACATCTAGGGGCATTTTAGTCA
          1 TTTTTGCACATCCAGGGGCATTTTAGTCA

                        *                
       5580 TTTTTGCACATCTAGGGGCATTTTAGTCA
          1 TTTTTGCACATCCAGGGGCATTTTAGTCA

                        *                
       5609 TTTTTGCACATCTAGGGGCATTTTAGTCA
          1 TTTTTGCACATCCAGGGGCATTTTAGTCA

                       *            *    
       5638 TTTTTGCACATTCAGGGGCATTTTGGTCA
          1 TTTTTGCACATCCAGGGGCATTTTAGTCA

                         
       5667 TTTTTTGCACATC
          1 -TTTTTGCACATC

       5680 TAG


Statistics
Matches: 143,  Mismatches: 14, Indels: 1
        0.91            0.09        0.01

Matches are distributed among these distances:
  29  132  0.92
  30   11  0.08

ACGTcount: A:0.18, C:0.17, G:0.21, T:0.43


Consensus pattern (29 bp):   
TTTTTGCACATCCAGGGGCATTTTAGTCA

Found at i:5583 original size:58 final size:58

Alignment explanation


    Indices: 5493--5682  Score: 283
    Period size: 58  Copynumber: 3.3  Consensus size: 58

       5483 TTAATTGACC

                                     *  *         *    *               
       5493 TTTTTGCACAT-TCAGGGGCATTTTGGTTATTTTTGCATATCCGGGGGCATTTTGGTCA
          1 TTTTTGCACATCT-AGGGGCATTTTAGTCATTTTTGCACATCCAGGGGCATTTTGGTCA

                 *                                   *           *    
       5551 TTTTTTCACATCTAGGGGCATTTTAGTCATTTTTGCACATCTAGGGGCATTTTAGTCA
          1 TTTTTGCACATCTAGGGGCATTTTAGTCATTTTTGCACATCCAGGGGCATTTTGGTCA

                                                    *                 
       5609 TTTTTGCACATCTAGGGGCATTTTAGTCATTTTTGCACATTCAGGGGCATTTTGGTCA
          1 TTTTTGCACATCTAGGGGCATTTTAGTCATTTTTGCACATCCAGGGGCATTTTGGTCA

                            
       5667 TTTTTTGCACATCTAG
          1 -TTTTTGCACATCTAG


Statistics
Matches: 119,  Mismatches: 11, Indels: 3
        0.89            0.08        0.02

Matches are distributed among these distances:
  58  103  0.87
  59   16  0.13

ACGTcount: A:0.18, C:0.17, G:0.22, T:0.43


Consensus pattern (58 bp):   
TTTTTGCACATCTAGGGGCATTTTAGTCATTTTTGCACATCCAGGGGCATTTTGGTCA

Done.