Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013564.1 Corchorus capsularis cultivar CVL-1 contig13585, 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: 26590
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:1566 original size:19 final size:18

Alignment explanation


    Indices: 1542--1577  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       1532 TGAAGATTTC

                               
       1542 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       1561 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

       1578 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

Found at i:11741 original size:24 final size:24

Alignment explanation


    Indices: 11714--11760  Score: 60
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      11704 GTTATTTAAG

                                     
      11714 TTTATGCTT-TATCTTTAATTTTCC
          1 TTTAT-CTTATATCTTTAATTTTCC

                      *      *     
      11738 TTTATCTTATGTCTTTATTTTTC
          1 TTTATCTTATATCTTTAATTTTC

      11761 AAGTTTCATT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  23    3  0.15
  24   17  0.85

ACGTcount: A:0.15, C:0.15, G:0.04, T:0.66


Consensus pattern (24 bp):   
TTTATCTTATATCTTTAATTTTCC

Found at i:13330 original size:19 final size:18

Alignment explanation


    Indices: 13306--13341  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      13296 TGAAGATTTC

                               
      13306 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
      13325 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

      13342 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

Found at i:15642 original size:30 final size:31

Alignment explanation


    Indices: 15584--15753  Score: 213
    Period size: 30  Copynumber: 5.6  Consensus size: 31

      15574 ACGCCGTCCG

                *       * *                 
      15584 ACGTTGCATGCCCCATGTACCAAAAAAATGAC
          1 ACGTGGCATGCCACGTGTACC-AAAAAATGAC

                                           
      15616 ACGTGGCATGCC-CGTGTACCAAAAAATGAC
          1 ACGTGGCATGCCACGTGTACCAAAAAATGAC

                         *                 
      15646 ACGTGGCATGCCAAGTGTACCAAAAAATGAC
          1 ACGTGGCATGCCACGTGTACCAAAAAATGAC

              *          *              *  
      15677 ACATGGCATGCCATGTGTACC-AAAAATAAC
          1 ACGTGGCATGCCACGTGTACCAAAAAATGAC

             *      *                      
      15707 ATGTGGCACGCCACGTGTA-C-AAAAATGAC
          1 ACGTGGCATGCCACGTGTACCAAAAAATGAC

              *               
      15736 ACATGGCATGCCACGTGT
          1 ACGTGGCATGCCACGTGT

      15754 TAAAAATGGT


Statistics
Matches: 123,  Mismatches: 14, Indels: 5
        0.87            0.10        0.04

Matches are distributed among these distances:
  29   24  0.20
  30   45  0.37
  31   43  0.35
  32   11  0.09

ACGTcount: A:0.35, C:0.25, G:0.21, T:0.18


Consensus pattern (31 bp):   
ACGTGGCATGCCACGTGTACCAAAAAATGAC

Found at i:15686 original size:61 final size:61

Alignment explanation


    Indices: 15599--15753  Score: 217
    Period size: 61  Copynumber: 2.6  Consensus size: 61

      15589 GCATGCCCCA

                               *                         *          *      
      15599 TGTACCAAAAAAATGACACGTGGCATGCC-CGTGTACCAAAAAATGACACGTGGCATGCCAAG
          1 TGTACC-AAAAAATGACACATGGCATGCCACGTGTACC-AAAAATAACACGTGGCACGCCAAG

                                         *                 *           * 
      15661 TGTACCAAAAAATGACACATGGCATGCCATGTGTACCAAAAATAACATGTGGCACGCCACG
          1 TGTACCAAAAAATGACACATGGCATGCCACGTGTACCAAAAATAACACGTGGCACGCCAAG

                                              
      15722 TGTA-C-AAAAATGACACATGGCATGCCACGTGT
          1 TGTACCAAAAAATGACACATGGCATGCCACGTGT

      15754 TAAAAATGGT


Statistics
Matches: 85,  Mismatches: 7, Indels: 5
        0.88            0.07        0.05

Matches are distributed among these distances:
  59   26  0.31
  60    1  0.01
  61   45  0.53
  62   13  0.15

ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18


Consensus pattern (61 bp):   
TGTACCAAAAAATGACACATGGCATGCCACGTGTACCAAAAATAACACGTGGCACGCCAAG
Done.