Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001037.1 Corchorus olitorius cultivar O-4 contig01037, 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, 770

Length: 1284
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41


Found at i:81 original size:22 final size:22

Alignment explanation


    Indices: 11--263  Score: 96
    Period size: 22  Copynumber: 11.7  Consensus size: 22

          1 TTACATATGA

                             *    
         11 TGGTTATCAAAATTT-ATATAG
          1 TGGTTATCAAAATTTCAAATAG

               ***                 
         32 -GGCCCTCAAAATTTC-AATCA-
          1 TGGTTATCAAAATTTCAAAT-AG

            *             *       
         52 AGGTTATCAAAATTACAAATAG
          1 TGGTTATCAAAATTTCAAATAG

                            *   * 
         74 TGGTTATCAAAATTTCGAATGG
          1 TGGTTATCAAAATTTCAAATAG

                         *       * *
         96 TGGAATT-TCAAATTTTCAAAAAA
          1 TGG--TTATCAAAATTTCAAATAG

             *                     
        119 TAGTTATCAAAATTTC--ATAGG
          1 TGGTTATCAAAATTTCAAATA-G

             *  * *              * 
        140 ACGGCTGTCAAAATTTC-AATCG
          1 -TGGTTATCAAAATTTCAAATAG

            **     *      *    * *
        162 AAGTTATTAAAATTACAAAGAA
          1 TGGTTATCAAAATTTCAAATAG

                 *   *       *      
        184 TGGTTCTCATAA-TT-ATATAGGG
          1 TGGTTATCAAAATTTCAAATA--G

            *    *                
        206 CGGTTGTCAAAATTTC-AATAG
          1 TGGTTATCAAAATTTCAAATAG

            *         *   *       
        227 AGGTTATCAAGATTACAAATAG
          1 TGGTTATCAAAATTTCAAATAG

                           
        249 TGGTTATCAAAATTT
          1 TGGTTATCAAAATTT

        264 TGAATGGTGA


Statistics
Matches: 160,  Mismatches: 55, Indels: 33
        0.65            0.22        0.13

Matches are distributed among these distances:
  20   18  0.11
  21   39  0.24
  22   81  0.51
  23   20  0.12
  24    2  0.01

ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34


Consensus pattern (22 bp):   
TGGTTATCAAAATTTCAAATAG

Found at i:253 original size:65 final size:65

Alignment explanation


    Indices: 103--262  Score: 178
    Period size: 65  Copynumber: 2.5  Consensus size: 65

         93 TGGTGGAATT

                 *  *    *   *                                        *      
        103 TCAAATTTTCAAAAAATAGTTATCAAAATT-TCATAGGACGGCTGTCAAAATTTCAATCGAAGTT
          1 TCAAAATTACAAAGAATGGTTATCAAAATTAT-ATAGGACGGCTGTCAAAATTTCAATAGAAGTT

             
        167 A
         65 A

             *                   *   *           *   *                  *    
        168 TTAAAATTACAAAGAATGGTTCTCATAATTATATAGGGCGGTTGTCAAAATTTCAATAGAGGTTA
          1 TCAAAATTACAAAGAATGGTTATCAAAATTATATAGGACGGCTGTCAAAATTTCAATAGAAGTTA

                *        * *              
        233 TCAAGATTACAAATAGTGGTTATCAAAATT
          1 TCAAAATTACAAAGAATGGTTATCAAAATT

        263 TTGAATGGTG


Statistics
Matches: 77,  Mismatches: 17, Indels: 2
        0.80            0.18        0.02

Matches are distributed among these distances:
  65   76  0.99
  66    1  0.01

ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33


Consensus pattern (65 bp):   
TCAAAATTACAAAGAATGGTTATCAAAATTATATAGGACGGCTGTCAAAATTTCAATAGAAGTTA
Done.