Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016813.1 Corchorus olitorius cultivar O-4 contig16846, 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, 942

Length: 1571
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34


Found at i:939 original size:29 final size:27

Alignment explanation


    Indices: 876--1067  Score: 114
    Period size: 29  Copynumber: 6.7  Consensus size: 27

        866 CCACATCTAG

                *          *   *    *   
        876 GGGCGTTTTGGTCATCTTGTACATCCAA
          1 GGGCATTTTGGTCATTTTGCACATTC-A

                                        
        904 GGGCATTTTGGTCAATTTTGCACATTCA
          1 GGGCATTTTGGTC-ATTTTGCACATTCA

                      *                * *
        932 GGAGCATTTTAGTCATTTCTGCACAATCCG
          1 GG-GCATTTTGGTCATTT-TGCAC-ATTCA

                      *       *      **  *
        962 GGGCATTTTGATCATTTTTCACCCACCCGT
          1 GGGCATTTTGGTCATTTTGCA--CATTC-A

                               *     *  
        992 GGGCATTTTGGTCATTTTCACACATCCA
          1 GGGCATTTTGGTCATTTT-GCACATTCA

                      *              *    
       1020 GGGGCATTTTAGTCATTTCTGCACAATCTA
          1 -GGGCATTTTGGTCATTT-TGCACATTC-A

               **             
       1050 GGGTGTTTTGGTCATTTT
          1 GGGCATTTTGGTCATTTT

       1068 TGTTTTATTT


Statistics
Matches: 130,  Mismatches: 23, Indels: 22
        0.74            0.13        0.13

Matches are distributed among these distances:
  28   23  0.18
  29   80  0.62
  30   25  0.19
  31    2  0.02

ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38


Consensus pattern (27 bp):   
GGGCATTTTGGTCATTTTGCACATTCA

Found at i:1059 original size:88 final size:88

Alignment explanation


    Indices: 904--1068  Score: 242
    Period size: 88  Copynumber: 1.9  Consensus size: 88

        894 GTACATCCAA

                               *     *                               *       
        904 GGGCATTTTGGTCAATTTTGCACATTCAGGAGCATTTTAGTCATTTCTGCACAATCCGGGGCATT
          1 GGGCATTTTGGTCAATTTTACACATCCAGGAGCATTTTAGTCATTTCTGCACAATCCAGGGCATT

                                   
        969 TTGATCATTTTTCACCCACCCGT
         66 TTGATCATTTTTCACCCACCCGT

                                           *                         *    ** 
        992 GGGCATTTTGGTC-ATTTTCACACATCCAGGGGCATTTTAGTCATTTCTGCACAATCTAGGGTGT
          1 GGGCATTTTGGTCAATTTT-ACACATCCAGGAGCATTTTAGTCATTTCTGCACAATCCAGGGCAT

                *        
       1056 TTTGGTCATTTTT
         65 TTTGATCATTTTT

       1069 GTTTTATTTT


Statistics
Matches: 68,  Mismatches: 8, Indels: 2
        0.87            0.10        0.03

Matches are distributed among these distances:
  87    5  0.07
  88   63  0.93

ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39


Consensus pattern (88 bp):   
GGGCATTTTGGTCAATTTTACACATCCAGGAGCATTTTAGTCATTTCTGCACAATCCAGGGCATT
TTGATCATTTTTCACCCACCCGT
Done.