Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000232.1 Corchorus olitorius cultivar O-4 contig00232, 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, 612

Length: 1021
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29


Found at i:757 original size:35 final size:35

Alignment explanation


    Indices: 629--1021  Score: 535
    Period size: 35  Copynumber: 11.2  Consensus size: 35

        619 ATCAATGTGA

                              *               *
        629 AGATCAACTCTGATCATCGAAAACTTCTTGAAATA
          1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

                     *    *    *                 
        664 AGATCAACTTTGATTATAAAAAAAAC-TCTTGAAATG
          1 AGATCAACTCTGATCAT--CAAAAACTTCTTGAAATG

                         *    *                 
        700 AGATCAACTCTGACCATAAAAAAACTTCTTGAAATG
          1 AGATCAACTCTGATCAT-CAAAAACTTCTTGAAATG

                         *   *                 
        736 AGATCAACTCTGACCATAAAAAACTTCTTGAAATG
          1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

                                *         *   * 
        771 AGATCAACTCTGATCGA-CAGAAACTTCTTAAAAGG
          1 AGATCAACTCTGATC-ATCAAAAACTTCTTGAAATG

                                               
        806 AGATCAACTCTGATCAT-AAAAACTTCTTGAAATG
          1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

                              *              * 
        840 AGATCAACTCTGATCATCGAAAACTTCTTGAAACG
          1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

                              *                
        875 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
          1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

                                                
        910 AGATCAACTCTGATCAT-AGAAAACTTCTTGAAATG
          1 AGATCAACTCTGATCATCA-AAAACTTCTTGAAATG

                              *                
        945 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
          1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

            *                            *     
        980 CGATCAACTCTGATCATC-AAAACTTCTTAAAATG
          1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

            *       
       1014 TGATCAAC
          1 AGATCAAC


Statistics
Matches: 326,  Mismatches: 24, Indels: 17
        0.89            0.07        0.05

Matches are distributed among these distances:
  34   54  0.17
  35  216  0.66
  36   51  0.16
  37    5  0.02

ACGTcount: A:0.40, C:0.19, G:0.13, T:0.27


Consensus pattern (35 bp):   
AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

Found at i:881 original size:139 final size:139

Alignment explanation


    Indices: 629--1021  Score: 542
    Period size: 139  Copynumber: 2.8  Consensus size: 139

        619 ATCAATGTGA

                                               *         *    *              
        629 AGATCAACTCTGATCATC-GAAAACTTCTTGAAATAAGATCAACTTTGATTATAAAAAAAAC-TC
          1 AGATCAACTCTGATCA-CAGAAAACTTCTTGAAATGAGATCAACTCTGATCAT--AAAAAACTTC

                                 *     *                                     
        692 TTGAAATGAGATCAACTCTGACCATAAAAAAACTTCTTGAAATGAGATCAACTCTGACCATAAAA
         63 TTGAAATGAGATCAACTCTGATCAT--CAAAACTTCTTGAAATGAGATCAACTCTGACCATAAAA

                          
        757 AACTTCTTGAAATG
        126 AACTTCTTGAAATG

                                          *   *                              
        771 AGATCAACTCTGATCGACAG-AAACTTCTTAAAAGGAGATCAACTCTGATCAT-AAAAACTTCTT
          1 AGATCAACTCTGATC-ACAGAAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAAACTTCTT

                                                   *              *   **     
        834 GAAATGAGATCAACTCTGATCATCGAAAACTTCTTGAAACGAGATCAACTCTGATCATCGAAAAC
         65 GAAATGAGATCAACTCTGATCATC-AAAACTTCTTGAAATGAGATCAACTCTGACCATAAAAAAC

                       
        899 TTCTTGAAATG
        129 TTCTTGAAATG

                            *                                   **           
        910 AGATCAACTCTGATCATAGAAAACTTCTTGAAATGAGATCAACTCTGATCATCGAAAACTTCTTG
          1 AGATCAACTCTGATCACAGAAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAAACTTCTTG

                 *                           *     *       
        975 AAATGCGATCAACTCTGATCATCAAAACTTCTTAAAATGTGATCAAC
         66 AAATGAGATCAACTCTGATCATCAAAACTTCTTGAAATGAGATCAAC


Statistics
Matches: 226,  Mismatches: 19, Indels: 15
        0.87            0.07        0.06

Matches are distributed among these distances:
 138    3  0.01
 139  119  0.53
 140   59  0.26
 142   43  0.19
 143    2  0.01

ACGTcount: A:0.40, C:0.19, G:0.13, T:0.27


Consensus pattern (139 bp):   
AGATCAACTCTGATCACAGAAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAAACTTCTTG
AAATGAGATCAACTCTGATCATCAAAACTTCTTGAAATGAGATCAACTCTGACCATAAAAAACTT
CTTGAAATG
Done.