Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015634.1 Corchorus capsularis cultivar CVL-1 contig15655, 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, 1000

Length: 18890
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31


Found at i:16963 original size:30 final size:30

Alignment explanation


    Indices: 16927--17235  Score: 351
    Period size: 30  Copynumber: 10.4  Consensus size: 30

      16917 AATAGTGTAT

                              *       *   
      16927 ATGACAACTTCTTGTGTCGATTGCAAGATC
          1 ATGACAACTTCTTGTGTCAATTGCAAAATC

                                      *   
      16957 ATGACAA---CTTGTGTCAATTGCAAGATC
          1 ATGACAACTTCTTGTGTCAATTGCAAAATC

                                           
      16984 ATGACAACTTC-TGTTGTCAATTGCAAAATC
          1 ATGACAACTTCTTG-TGTCAATTGCAAAATC

                      * *                 
      17014 ATGACAACTTATGGTGTCAATTGCAAAATC
          1 ATGACAACTTCTTGTGTCAATTGCAAAATC

                      * *  *              
      17044 ATGACAACTTATGGTATCAATTGCAAAATC
          1 ATGACAACTTCTTGTGTCAATTGCAAAATC

                  *      *                 
      17074 ATGACATCTT-TAAGTGTCAATTGCAAAATC
          1 ATGACAACTTCT-TGTGTCAATTGCAAAATC

                        *                 
      17104 ATGACAACTTCTGGTGTCAATTGCAAAATC
          1 ATGACAACTTCTTGTGTCAATTGCAAAATC

                        *          *      
      17134 ATGACAACTTCTAGTGTCAATTGTAAAATC
          1 ATGACAACTTCTTGTGTCAATTGCAAAATC

                        *      *   *  * * 
      17164 ATGACAACTTCTAGTGTCATTTGTAAGACC
          1 ATGACAACTTCTTGTGTCAATTGCAAAATC

                                *   *  *  *
      17194 ATGACAACTTC-TGATGTCATTTGTAAGATT
          1 ATGACAACTTCTTG-TGTCAATTGCAAAATC

                        
      17224 ATGACAACTTCT
          1 ATGACAACTTCT

      17236 AATGTCATTT


Statistics
Matches: 252,  Mismatches: 18, Indels: 17
        0.88            0.06        0.06

Matches are distributed among these distances:
  27   26  0.10
  29    4  0.02
  30  220  0.87
  31    2  0.01

ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33


Consensus pattern (30 bp):   
ATGACAACTTCTTGTGTCAATTGCAAAATC

Found at i:17234 original size:90 final size:90

Alignment explanation


    Indices: 16927--17242  Score: 399
    Period size: 90  Copynumber: 3.5  Consensus size: 90

      16917 AATAGTGTAT

                        *     *       *                             *        
      16927 ATGACAACTTCTTGTGTCGATTGCAAGATCATGACAAC-T-T-GTGTCAATTGCAAGATCATGAC
          1 ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTAGTGTCAATTGCAAAATCATGAC

                                      
      16989 AACTTCT-GTTGTCAATTGCAAAATC
         66 AACTTCTAG-TGTCAATTGCAAAATC

                      *                             * *  *                   
      17014 ATGACAACTTATGGTGTCAATTGCAAAATCATGACAACTTATGGTATCAATTGCAAAATCATGAC
          1 ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTAGTGTCAATTGCAAAATCATGAC

             *                        
      17079 ATCTT-TAAGTGTCAATTGCAAAATC
         66 AACTTCT-AGTGTCAATTGCAAAATC

                                                                 *           
      17104 ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTAGTGTCAATTGTAAAATCATGAC
          1 ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTAGTGTCAATTGCAAAATCATGAC

                          *   *  * * 
      17169 AACTTCTAGTGTCATTTGTAAGACC
         66 AACTTCTAGTGTCAATTGCAAAATC

                         *     *   *  *  *             *     
      17194 ATGACAACTTCTGATGTCATTTGTAAGATTATGACAACTTCTAATGTCA
          1 ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTAGTGTCA

      17243 TTTGTTGCAG


Statistics
Matches: 200,  Mismatches: 23, Indels: 9
        0.86            0.10        0.04

Matches are distributed among these distances:
  87   34  0.17
  88    1  0.00
  89    2  0.01
  90  161  0.81
  91    2  0.01

ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33


Consensus pattern (90 bp):   
ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTAGTGTCAATTGCAAAATCATGAC
AACTTCTAGTGTCAATTGCAAAATC

Done.