Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013674.1 Corchorus olitorius cultivar O-4 contig13707, 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: 15895
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26


Found at i:13048 original size:2 final size:2

Alignment explanation


    Indices: 13041--13083  Score: 63
    Period size: 2  Copynumber: 22.5  Consensus size: 2

      13031 CTGGTACTCC

                                                                   *      
      13041 TA TA TA TA TA TA TA TA T- TA TA TA TA -A TA TA TA TA TG TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                
      13081 TA T
          1 TA T

      13084 GTTAAATTCC


Statistics
Matches: 37,  Mismatches: 2, Indels: 4
        0.86            0.05        0.09

Matches are distributed among these distances:
   1    2  0.05
   2   35  0.95

ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:13822 original size:50 final size:51

Alignment explanation


    Indices: 13742--13861  Score: 206
    Period size: 50  Copynumber: 2.4  Consensus size: 51

      13732 ACCAGATATC

                *                                              
      13742 AAGAGTGAATTGGAAGACAGTTCGAAGGATAAGCAGAAGACGGTCCTTT-T
          1 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCAGAAGACGGTCCTTTCT

                                              *                
      13792 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTCT
          1 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCAGAAGACGGTCCTTTCT

               *               
      13843 AAGTTTGAATTGGAAGACA
          1 AAGATTGAATTGGAAGACA

      13862 ACTCGAAGAA


Statistics
Matches: 66,  Mismatches: 3, Indels: 1
        0.94            0.04        0.01

Matches are distributed among these distances:
  50   47  0.71
  51   19  0.29

ACGTcount: A:0.36, C:0.12, G:0.29, T:0.23


Consensus pattern (51 bp):   
AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCAGAAGACGGTCCTTTCT

Found at i:14124 original size:28 final size:28

Alignment explanation


    Indices: 14092--14180  Score: 106
    Period size: 28  Copynumber: 3.2  Consensus size: 28

      14082 TTATTTAGGC

                                     *  
      14092 CATTTTGCAAGTCCAGGGGCATTTTGGT
          1 CATTTTGCAAGTCCAGGGGCATTTTAGT

                         *     *        
      14120 CATTTTGCAAGTCTAGGGGTATTTTAGT
          1 CATTTTGCAAGTCCAGGGGCATTTTAGT

                   * *  *       *    *  
      14148 CATTTTGTACGTGCAGGGGCGTTTTCGT
          1 CATTTTGCAAGTCCAGGGGCATTTTAGT

                 
      14176 CATTT
          1 CATTT

      14181 AAAGTCTACT


Statistics
Matches: 51,  Mismatches: 10, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  28   51  1.00

ACGTcount: A:0.17, C:0.16, G:0.27, T:0.40


Consensus pattern (28 bp):   
CATTTTGCAAGTCCAGGGGCATTTTAGT
Done.