Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015351.1 Corchorus capsularis cultivar CVL-1 contig15372, 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: 12156
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:1426 original size:19 final size:18

Alignment explanation


    Indices: 1402--1437  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       1392 TGAAGATTTG

                               
       1402 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       1421 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

       1438 ATTAATTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT

Found at i:5634 original size:16 final size:16

Alignment explanation


    Indices: 5609--5681  Score: 94
    Period size: 16  Copynumber: 4.6  Consensus size: 16

       5599 CGGGTTGATC

                            
       5609 GGGTTCGGGTCATTTT
          1 GGGTTCGGGTCATTTT

                 *         *
       5625 GGGTTTGGGTCATTTC
          1 GGGTTCGGGTCATTTT

                        *   
       5641 GGGTTCGGGTC-GTTT
          1 GGGTTCGGGTCATTTT

              *       *     
       5656 GGATTCGGGTAATTTT
          1 GGGTTCGGGTCATTTT

                      
       5672 GGGTTCGGGT
          1 GGGTTCGGGT

       5682 GCCCAAAAAT


Statistics
Matches: 47,  Mismatches: 9, Indels: 2
        0.81            0.16        0.03

Matches are distributed among these distances:
  15   11  0.23
  16   36  0.77

ACGTcount: A:0.07, C:0.11, G:0.41, T:0.41


Consensus pattern (16 bp):   
GGGTTCGGGTCATTTT

Found at i:5676 original size:31 final size:32

Alignment explanation


    Indices: 5607--5681  Score: 98
    Period size: 31  Copynumber: 2.4  Consensus size: 32

       5597 GTCGGGTTGA

                          *     *  *    *   
       5607 TCGGGTTCGGGTCATTTTGGGTTTGGGTCATT
          1 TCGGGTTCGGGTCAGTTTGGATTCGGGTAATT

                                            
       5639 TCGGGTTCGGGTC-GTTTGGATTCGGGTAATT
          1 TCGGGTTCGGGTCAGTTTGGATTCGGGTAATT

             *          
       5670 TTGGGTTCGGGT
          1 TCGGGTTCGGGT

       5682 GCCCAAAAAT


Statistics
Matches: 38,  Mismatches: 5, Indels: 1
        0.86            0.11        0.02

Matches are distributed among these distances:
  31   25  0.66
  32   13  0.34

ACGTcount: A:0.07, C:0.12, G:0.40, T:0.41


Consensus pattern (32 bp):   
TCGGGTTCGGGTCAGTTTGGATTCGGGTAATT

Found at i:12071 original size:19 final size:18

Alignment explanation


    Indices: 12047--12082  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      12037 TGAAGATTTC

                               
      12047 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
      12066 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

      12083 ATTATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT
Done.