Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000409.1 Corchorus olitorius cultivar O-4 contig00409, 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, 855

Length: 1426
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.36


Found at i:785 original size:22 final size:22

Alignment explanation


    Indices: 760--952  Score: 151
    Period size: 22  Copynumber: 8.8  Consensus size: 22

        750 TAATAGTGTT

                *         *       
        760 GTTACCAAAATTTCGTATGAAG
          1 GTTATCAAAATTTCATATGAAG

                      *             
        782 GTTATCAAAACTTCATAGTGTAA-
          1 GTTATCAAAATTTCATA-TG-AAG

               *           *       
        805 -TTTTCAAAATTTCACAT-AGAG
          1 GTTATCAAAATTTCATATGA-AG

                *   *        **   
        826 GTTACCAAGATTTCATAAAAAG
          1 GTTATCAAAATTTCATATGAAG

                          *  * *  
        848 GTTATCAAAATTTCTTAGGGAG
          1 GTTATCAAAATTTCATATGAAG

                *            *   *
        870 GTTAACAAAATTTCATACGAAA
          1 GTTATCAAAATTTCATATGAAG

                         *       * 
        892 GTTATCAAAATTTTATAGTG-TG
          1 GTTATCAAAATTTCATA-TGAAG

                             *    
        914 GTTATCAAAATTTCATAAGAAG
          1 GTTATCAAAATTTCATATGAAG

                *            
        936 GTTAACAAAATTTCATA
          1 GTTATCAAAATTTCATA

        953 GGGAGGAAAT


Statistics
Matches: 132,  Mismatches: 31, Indels: 16
        0.74            0.17        0.09

Matches are distributed among these distances:
  19    1  0.01
  20    1  0.01
  21    2  0.02
  22  122  0.92
  23    4  0.03
  24    2  0.02

ACGTcount: A:0.40, C:0.11, G:0.14, T:0.34


Consensus pattern (22 bp):   
GTTATCAAAATTTCATATGAAG

Found at i:1275 original size:22 final size:22

Alignment explanation


    Indices: 1141--1307  Score: 79
    Period size: 22  Copynumber: 7.6  Consensus size: 22

       1131 ATCATAGGGA

                             *   * 
       1141 GGTTATCGAAA-TTTCAAAGTAT
          1 GGTTATC-AAATTTTCACAGTGT

                             *    *
       1163 GGTTATCAAAATTTTCATAGTGC
          1 GGTTATC-AAATTTTCACAGTGT

            * *       *     *     
       1186 AGCTATC-AACTTT-ATAGTGT
          1 GGTTATCAAATTTTCACAGTGT

             *        *  *  *  * *
       1206 GATTATCAAAATTCCATAGGGA
          1 GGTTATCAAATTTTCACAGTGT

             *        *       * **
       1228 GATTATCAAAATTTCACACTAA
          1 GGTTATCAAATTTTCACAGTGT

                           ***    
       1250 GGTTATCAAATTTTCTTTGTGT
          1 GGTTATCAAATTTTCACAGTGT

                      *           
       1272 GGTTATCAAAATTTCACAGTGT
          1 GGTTATCAAATTTTCACAGTGT

                          
       1294 GGTTATCCAAATTT
          1 GGTTAT-CAAATTT

       1308 CTATGTTGGA


Statistics
Matches: 108,  Mismatches: 33, Indels: 7
        0.73            0.22        0.05

Matches are distributed among these distances:
  20   10  0.09
  21    9  0.08
  22   70  0.65
  23   19  0.18

ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38


Consensus pattern (22 bp):   
GGTTATCAAATTTTCACAGTGT
Done.