Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012688.1 Corchorus capsularis cultivar CVL-1 contig12709, 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: 17734
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28


Found at i:3965 original size:13 final size:14

Alignment explanation


    Indices: 3947--3975  Score: 51
    Period size: 13  Copynumber: 2.1  Consensus size: 14

       3937 ATAATTGGAC

                          
       3947 TTTGCATTCAT-CA
          1 TTTGCATTCATGCA

                          
       3960 TTTGCATTCATGCA
          1 TTTGCATTCATGCA

              
       3974 TT
          1 TT

       3976 GAGTAGAAGT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   11  0.73
  14    4  0.27

ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48


Consensus pattern (14 bp):   
TTTGCATTCATGCA

Found at i:16658 original size:59 final size:58

Alignment explanation


    Indices: 16592--16936  Score: 443
    Period size: 59  Copynumber: 6.0  Consensus size: 58

      16582 AGTCATCGGA

                                 * *  *          *                     
      16592 TCTGAAGACAGTTCCTGGAAGGTTTTTAGAATGAGTACGAAGACTGCTCATAGATGGGT
          1 TCTGAAGACAGTTCCTGG-AGATATTAAGAATGAGTATGAAGACTGCTCATAGATGGGT

                                                            *         
      16651 TCTGAAGACAGTTCCT-G-GATATTAAGAATGAGTATGAAGACTGCTCGTAGATGGGT
          1 TCTGAAGACAGTTCCTGGAGATATTAAGAATGAGTATGAAGACTGCTCATAGATGGGT

                                                          *      *    
      16707 TCTGAAGACAGTTCC--GAGATATTAA-AATGAGTATGAAGACTGCCCATAGAGGGGT
          1 TCTGAAGACAGTTCCTGGAGATATTAAGAATGAGTATGAAGACTGCTCATAGATGGGT

                  * *                                       *         
      16762 TCTGAAAATAGTTCCT--AGATATTAAGAATGAGTATGAAGACTGCTCGTAGATGGGT
          1 TCTGAAGACAGTTCCTGGAGATATTAAGAATGAGTATGAAGACTGCTCATAGATGGGT

                        *    **   *         *                          
      16818 TCTGAAGACAGTCCCTAAAAGAAATTAAGAATCAGTATGAAGACTGCTCATAGATGGGT
          1 TCTGAAGACAGTTCCT-GGAGATATTAAGAATGAGTATGAAGACTGCTCATAGATGGGT

                              *    *                         * *       
      16877 TCTGAAGACAGTTCCTGAAAGATTTTAAGAATGAGTATGAAGACTGCTCGTCGATGGGT
          1 TCTGAAGACAGTTCCTG-GAGATATTAAGAATGAGTATGAAGACTGCTCATAGATGGGT

             
      16936 T
          1 T

      16937 ACTCAAGTTA


Statistics
Matches: 253,  Mismatches: 26, Indels: 14
        0.86            0.09        0.05

Matches are distributed among these distances:
  55   50  0.20
  56   97  0.38
  58    1  0.00
  59  105  0.42

ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28


Consensus pattern (58 bp):   
TCTGAAGACAGTTCCTGGAGATATTAAGAATGAGTATGAAGACTGCTCATAGATGGGT

Found at i:16749 original size:111 final size:113

Alignment explanation


    Indices: 16619--16936  Score: 469
    Period size: 111  Copynumber: 2.8  Consensus size: 113

      16609 GAAGGTTTTT

                      *                                                      
      16619 AGAATGAGTACGAAGACTGCTCATAGATGGGTTCTGAAGACAGTTCCTGGATATTAAGAATGAGT
          1 AGAATGAGTATGAAGACTGCTCATAGATGGGTTCTGAAGACAGTTCCTGGATATTAAGAATGAGT

                                               *   *   *    
      16684 ATGAAGACTGCTCGTAGATGGGTTCTGAAGACAGTTCC-GAGATATTA
         66 ATGAAGACTGCTCGTAGATGGGTTCTGAAGACAGTCCCAAAGAAATTA

                                *      *          * *       *                
      16731 A-AATGAGTATGAAGACTGCCCATAGAGGGGTTCTGAAAATAGTTCCTAGATATTAAGAATGAGT
          1 AGAATGAGTATGAAGACTGCTCATAGATGGGTTCTGAAGACAGTTCCTGGATATTAAGAATGAGT

                                                              
      16795 ATGAAGACTGCTCGTAGATGGGTTCTGAAGACAGTCCCTAAAAGAAATTA
         66 ATGAAGACTGCTCGTAGATGGGTTCTGAAGACAGTCCC--AAAGAAATTA

                 *                                                 *         
      16845 AGAATCAGTATGAAGACTGCTCATAGATGGGTTCTGAAGACAGTTCCTGAAAGATTTTAAGAATG
          1 AGAATGAGTATGAAGACTGCTCATAGATGGGTTCTGAAGACAGTTCCTG---GATATTAAGAATG

                              *        
      16910 AGTATGAAGACTGCTCGTCGATGGGTT
         63 AGTATGAAGACTGCTCGTAGATGGGTT

      16937 ACTCAAGTTA


Statistics
Matches: 182,  Mismatches: 17, Indels: 8
        0.88            0.08        0.04

Matches are distributed among these distances:
 111   94  0.52
 112    1  0.01
 114    8  0.04
 115   41  0.23
 118   38  0.21

ACGTcount: A:0.34, C:0.13, G:0.26, T:0.27


Consensus pattern (113 bp):   
AGAATGAGTATGAAGACTGCTCATAGATGGGTTCTGAAGACAGTTCCTGGATATTAAGAATGAGT
ATGAAGACTGCTCGTAGATGGGTTCTGAAGACAGTCCCAAAGAAATTA
Done.