Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016280.1 Corchorus capsularis cultivar CVL-1 contig16301, 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: 5862
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.32


Found at i:2083 original size:33 final size:33

Alignment explanation


    Indices: 1997--2084  Score: 95
    Period size: 33  Copynumber: 2.7  Consensus size: 33

       1987 GTGTTTCAGA

                                          *  
       1997 TGTTGTTTGCGATGATACTAAACCTAATTTGAG
          1 TGTTGTTTGCGATGATACTAAACCTAATTTAAG

             **       *    *      *  **      
       2030 TAATGTTTGCAATGACACTAAATCTTTTTTAAG
          1 TGTTGTTTGCGATGATACTAAACCTAATTTAAG

                     *            
       2063 TGTTGTTTGTGATGATACTAAA
          1 TGTTGTTTGCGATGATACTAAA

       2085 ATGCTAATTG


Statistics
Matches: 42,  Mismatches: 13, Indels: 0
        0.76            0.24        0.00

Matches are distributed among these distances:
  33   42  1.00

ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42


Consensus pattern (33 bp):   
TGTTGTTTGCGATGATACTAAACCTAATTTAAG

Found at i:2201 original size:30 final size:33

Alignment explanation


    Indices: 2110--2213  Score: 133
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       2100 AAAACAAATA

                                  *        **
       2110 TGTTTTGGTTGATCATAGCATTAAAAATAATTT
          1 TGTTTTGGTTGATCATAGCATTGAAAATAATCC

                                   *         
       2143 TGTTTTGGTTGATCATAGCATTGCAAATAATCC
          1 TGTTTTGGTTGATCATAGCATTGAAAATAATCC

                     *                    *  
       2176 TGTTTTGGTAGAT-A-A-CATTGAAAATAAACC
          1 TGTTTTGGTTGATCATAGCATTGAAAATAATCC

                    
       2206 TGTTTTGG
          1 TGTTTTGG

       2214 GTGACGAAAA


Statistics
Matches: 64,  Mismatches: 7, Indels: 3
        0.86            0.09        0.04

Matches are distributed among these distances:
  30   21  0.33
  31    1  0.02
  32    1  0.02
  33   41  0.64

ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41


Consensus pattern (33 bp):   
TGTTTTGGTTGATCATAGCATTGAAAATAATCC

Found at i:4048 original size:33 final size:33

Alignment explanation


    Indices: 3998--4121  Score: 144
    Period size: 33  Copynumber: 3.7  Consensus size: 33

       3988 CCGCGCAACA

                                              *
       3998 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
          1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGC

                                             *
       4033 CCGGCCATC-ACCGGCCACGCGACATGGACATGG
          1 CCGGCCA-CAACCGGCCACGCGACATGGACATGC

                 *           **         *     
       4066 CCGGCTACAACCGGCCAAACGAC-TCGGCCATGC
          1 CCGGCCACAACCGGCCACGCGACAT-GGACATGC

                                   
       4099 CCGGCCACAACCGGCCACGCGAC
          1 CCGGCCACAACCGGCCACGCGAC

       4122 CCTTTGTCTA


Statistics
Matches: 77,  Mismatches: 9, Indels: 8
        0.82            0.10        0.09

Matches are distributed among these distances:
  32    2  0.03
  33   67  0.87
  35    7  0.09
  36    1  0.01

ACGTcount: A:0.23, C:0.42, G:0.27, T:0.07


Consensus pattern (33 bp):   
CCGGCCACAACCGGCCACGCGACATGGACATGC
Done.