Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006372.1 Corchorus capsularis cultivar CVL-1 contig06393, 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: 11933
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36


Found at i:1316 original size:45 final size:45

Alignment explanation


    Indices: 1241--1328  Score: 124
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       1231 TGATGATTGC

                     *                                    
       1241 ATGATTTCTTAATGTTTGTGCTGCTAAATGG-TTTACGGATTTTGG
          1 ATGATTTCTAAATGTTTGTGCTGCTAAATGGTTTTA-GGATTTTGG

                               *   * *                 
       1286 ATGATTTCTAAATGTTTGTTCTGTTTAATGGTTTTAGGATTTT
          1 ATGATTTCTAAATGTTTGTGCTGCTAAATGGTTTTAGGATTTT

       1329 AGTTCTTCCT


Statistics
Matches: 38,  Mismatches: 4, Indels: 2
        0.86            0.09        0.05

Matches are distributed among these distances:
  45   34  0.89
  46    4  0.11

ACGTcount: A:0.20, C:0.07, G:0.22, T:0.51


Consensus pattern (45 bp):   
ATGATTTCTAAATGTTTGTGCTGCTAAATGGTTTTAGGATTTTGG

Found at i:3672 original size:45 final size:45

Alignment explanation


    Indices: 3599--3684  Score: 129
    Period size: 45  Copynumber: 1.9  Consensus size: 45

       3589 ATGATTGCAC

                                                          
       3599 GATTTCTTAATGTTTGTGCTGCTCAATGG-TTTATGGATTTTGGAT
          1 GATTTCTTAATGTTTGTGCTGCTCAATGGTTTTA-GGATTTTGGAT

                             *   * *                 
       3644 GATTTCTTAATGTTTGTTCTGTTTAATGGTTTTAGGATTTT
          1 GATTTCTTAATGTTTGTGCTGCTCAATGGTTTTAGGATTTT

       3685 AGTTCTTCCT


Statistics
Matches: 37,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  45   33  0.89
  46    4  0.11

ACGTcount: A:0.17, C:0.07, G:0.22, T:0.53


Consensus pattern (45 bp):   
GATTTCTTAATGTTTGTGCTGCTCAATGGTTTTAGGATTTTGGAT

Found at i:10037 original size:33 final size:32

Alignment explanation


    Indices: 9983--10082  Score: 110
    Period size: 33  Copynumber: 3.1  Consensus size: 32

       9973 CATGTGGCTG

                           **             * 
       9983 GGTGTGGCCGGGCATGGCCATGTCGCGTGGGC
          1 GGTGTGGCCGGGCATCTCCATGTCGCGTGGCC

                                    *  *     
      10015 GGTGATGGCCGGGCATCTCCATGTTGCATGGCC
          1 GGTG-TGGCCGGGCATCTCCATGTCGCGTGGCC

                 *               *    *      
      10048 GGTGTTGCGCGGGCATCTCCAAGTCGTGTGGCC
          1 GGTGTGGC-CGGGCATCTCCATGTCGCGTGGCC

              
      10081 GG
          1 GG

      10083 ATCTCCAAGT


Statistics
Matches: 56,  Mismatches: 10, Indels: 3
        0.81            0.14        0.04

Matches are distributed among these distances:
  32    7  0.12
  33   49  0.88

ACGTcount: A:0.09, C:0.26, G:0.43, T:0.22


Consensus pattern (32 bp):   
GGTGTGGCCGGGCATCTCCATGTCGCGTGGCC

Found at i:10086 original size:21 final size:21

Alignment explanation


    Indices: 10062--10124  Score: 99
    Period size: 21  Copynumber: 3.0  Consensus size: 21

      10052 TTGCGCGGGC

                        **       
      10062 ATCTCCAAGTCGTGTGGCCGG
          1 ATCTCCAAGTCGCATGGCCGG

                               * 
      10083 ATCTCCAAGTCGCATGGCCAG
          1 ATCTCCAAGTCGCATGGCCGG

                                 
      10104 ATCTCCAAGTCGCATGGCCGG
          1 ATCTCCAAGTCGCATGGCCGG

      10125 TCACTTGTAC


Statistics
Matches: 38,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   38  1.00

ACGTcount: A:0.19, C:0.32, G:0.29, T:0.21


Consensus pattern (21 bp):   
ATCTCCAAGTCGCATGGCCGG
Done.