Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008693.1 Corchorus olitorius cultivar O-4 contig08720, 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, 769

Length: 1282
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32


Found at i:1031 original size:22 final size:22

Alignment explanation


    Indices: 1006--1152  Score: 111
    Period size: 22  Copynumber: 6.7  Consensus size: 22

        996 ACCAAAGTTA

                                  
       1006 CATAGGAAGGTTATCAAAATTT
          1 CATAGGAAGGTTATCAAAATTT

                 *  *     *        
       1028 CATAATG-TGGTTACCAAAATTT
          1 CAT-AGGAAGGTTATCAAAATTT

                    *           *  
       1050 CATATGG-TGGTTATCAAAACTT
          1 CATA-GGAAGGTTATCAAAATTT

                 *        *        
       1072 CATA-CAGAGGTTACCAAAATTT
          1 CATAGGA-AGGTTATCAAAATTT

                **         *      
       1094 CATAAAAAGGTTATCGAAATTT
          1 CATAGGAAGGTTATCAAAATTT

             *    *      * *      
       1116 CTTAGGGAGGTTAACCAAATTT
          1 CATAGGAAGGTTATCAAAATTT

                *          
       1138 CATATGAAGGTTATC
          1 CATAGGAAGGTTATC

       1153 GGAATTTTAT


Statistics
Matches: 97,  Mismatches: 23, Indels: 10
        0.75            0.18        0.08

Matches are distributed among these distances:
  21    1  0.01
  22   93  0.96
  23    3  0.03

ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33


Consensus pattern (22 bp):   
CATAGGAAGGTTATCAAAATTT

Found at i:1149 original size:66 final size:65

Alignment explanation


    Indices: 995--1150  Score: 150
    Period size: 66  Copynumber: 2.3  Consensus size: 65

        985 TTGACAATCA

                      *             *             ***                  *  *  
        995 AACCAAAGTTACATAGGAAGGTTATCAAAATTTCATAATGTGGTTACCAAAATTTCATATGGTGG
          1 AACCAAA-TTTCATA-GAAGGTTACCAAAATTTCATAAAAAGGTTACCAAAATTTCATAGGGAGG

              
       1060 TT
         64 TT

             * *   *      *                              * *       *         
       1062 ATCAAAACTTCATACAGAGGTTACCAAAATTTCATAAAAAGGTTATCGAAATTTCTTAGGGAGGT
          1 AACCAAATTTCATAGA-AGGTTACCAAAATTTCATAAAAAGGTTACCAAAATTTCATAGGGAGGT

             
       1127 T
         65 T

                                   
       1128 AACCAAATTTCATATGAAGGTTA
          1 AACCAAATTTCATA-GAAGGTTA

       1151 TCGGAATTTT


Statistics
Matches: 69,  Mismatches: 18, Indels: 5
        0.75            0.20        0.05

Matches are distributed among these distances:
  65    1  0.01
  66   62  0.90
  67    6  0.09

ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31


Consensus pattern (65 bp):   
AACCAAATTTCATAGAAGGTTACCAAAATTTCATAAAAAGGTTACCAAAATTTCATAGGGAGGTT

Found at i:1153 original size:44 final size:44

Alignment explanation


    Indices: 996--1152  Score: 163
    Period size: 44  Copynumber: 3.6  Consensus size: 44

        986 TGACAATCAA

                  *  *    *                      * *    
        996 ACCAAAGTTACATAGGAAGGTTATCAAAATTTCATAATGTGGTT
          1 ACCAAAATTTCATATGAAGGTTATCAAAATTTCATAAAGAGGTT

                            **           *      *       
       1040 ACCAAAATTTCATATGGTGGTTATCAAAACTTCATACAGAGGTT
          1 ACCAAAATTTCATATGAAGGTTATCAAAATTTCATAAAGAGGTT

                          **         *       *  **      
       1084 ACCAAAATTTCATAAAAAGGTTATCGAAATTTCTTAGGGAGGTT
          1 ACCAAAATTTCATATGAAGGTTATCAAAATTTCATAAAGAGGTT

                                      
       1128 AACC-AAATTTCATATGAAGGTTATC
          1 -ACCAAAATTTCATATGAAGGTTATC

       1153 GGAATTTTAT


Statistics
Matches: 92,  Mismatches: 20, Indels: 2
        0.81            0.18        0.02

Matches are distributed among these distances:
  44   89  0.97
  45    3  0.03

ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32


Consensus pattern (44 bp):   
ACCAAAATTTCATATGAAGGTTATCAAAATTTCATAAAGAGGTT

Done.