Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015472.1 Corchorus olitorius cultivar O-4 contig15505, 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: 11727
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35


Found at i:896 original size:32 final size:32

Alignment explanation


    Indices: 855--928  Score: 139
    Period size: 32  Copynumber: 2.3  Consensus size: 32

        845 ATGTTGTATT

                                        *   
        855 GTCACGTCAGACCAAAAATGCCACGTAGTAAG
          1 GTCACGTCAGACCAAAAATGCCACGTAGCAAG

                                            
        887 GTCACGTCAGACCAAAAATGCCACGTAGCAAG
          1 GTCACGTCAGACCAAAAATGCCACGTAGCAAG

                      
        919 GTCACGTCAG
          1 GTCACGTCAG

        929 CAATATTGTT


Statistics
Matches: 41,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  32   41  1.00

ACGTcount: A:0.35, C:0.27, G:0.23, T:0.15


Consensus pattern (32 bp):   
GTCACGTCAGACCAAAAATGCCACGTAGCAAG

Found at i:7067 original size:137 final size:136

Alignment explanation


    Indices: 6821--7081  Score: 486
    Period size: 137  Copynumber: 1.9  Consensus size: 136

       6811 AATTATCAGA

                                                                             
       6821 TTTTTAGGTAAATGTTGAAGAATTATTATCATGATAATTTGGAATTTTCAGAAATTGTTTTGATG
          1 TTTTTAGGTAAATGTTGAAGAATTATTATCATGATAATTTGGAATTTTCAGAAATTGTTTTGATG

                                                                             
       6886 TGCTAATTTGACAAATTTCAGCTCAGATTCTGTTTATTGCTTATGATTTTATAATTAATTAATCA
         66 TGCTAATTTGACAAATTTCAGCTCAGATTCTGTTTATTGCTTATGATTTTATAATTAATTAATCA

                  
       6951 TTCCTT
        131 TTCCTT

                                                                  *          
       6957 TTTTTAGGTAAATGTTGAAGAATTATTATCATGATAATTTTGGAATTTTCAGAACTTGTTTTGAT
          1 TTTTTAGGTAAATGTTGAAGAATTATTATCATGATAA-TTTGGAATTTTCAGAAATTGTTTTGAT

                                                    *             *     
       7022 GTGCTAATTTGACAAATTTCAGCTCAGATTCTGTTTATTGTTTATGATTTTATAGTTAAT
         65 GTGCTAATTTGACAAATTTCAGCTCAGATTCTGTTTATTGCTTATGATTTTATAATTAAT

       7082 CATTCCTCTT


Statistics
Matches: 121,  Mismatches: 3, Indels: 1
        0.97            0.02        0.01

Matches are distributed among these distances:
 136   37  0.31
 137   84  0.69

ACGTcount: A:0.30, C:0.08, G:0.15, T:0.48


Consensus pattern (136 bp):   
TTTTTAGGTAAATGTTGAAGAATTATTATCATGATAATTTGGAATTTTCAGAAATTGTTTTGATG
TGCTAATTTGACAAATTTCAGCTCAGATTCTGTTTATTGCTTATGATTTTATAATTAATTAATCA
TTCCTT

Found at i:10482 original size:31 final size:31

Alignment explanation


    Indices: 10447--10552  Score: 92
    Period size: 31  Copynumber: 3.5  Consensus size: 31

      10437 ATACCGTACA

                                           
      10447 GGTCCCTCTACTTAAAAAAAGGGATCAATTT
          1 GGTCCCTCTACTTAAAAAAAGGGATCAATTT

                  *       *     **         
      10478 GGTCCCCCTA-TTACAAAAACTG-TCAATTT
          1 GGTCCCTCTACTTAAAAAAAGGGATCAATTT

                   *      *  ***  *        
      10507 GGTCCCTTTACTTACAATTTGGTATCAA-TT
          1 GGTCCCTCTACTTAAAAAAAGGGATCAATTT

                            
      10537 GAGTCCCTCTACTTAA
          1 G-GTCCCTCTACTTAA

      10553 TAGAATCTGT


Statistics
Matches: 58,  Mismatches: 14, Indels: 6
        0.74            0.18        0.08

Matches are distributed among these distances:
  29   15  0.26
  30   18  0.31
  31   25  0.43

ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34


Consensus pattern (31 bp):   
GGTCCCTCTACTTAAAAAAAGGGATCAATTT
Done.