Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006643.1 Corchorus olitorius cultivar O-4 contig06668, 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, 680

Length: 1134
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31


Found at i:705 original size:13 final size:13

Alignment explanation


    Indices: 687--733  Score: 67
    Period size: 13  Copynumber: 3.5  Consensus size: 13

        677 CCAAAAAGGG

                         
        687 AGAAAAATAGAAA
          1 AGAAAAATAGAAA

                         
        700 AGAAAAATAGAAA
          1 AGAAAAATAGAAA

            *       *     
        713 GGAAAAGAAAGAAA
          1 AGAAAA-ATAGAAA

                   
        727 AGAAAAA
          1 AGAAAAA

        734 GGAAGGAAAA


Statistics
Matches: 30,  Mismatches: 3, Indels: 2
        0.86            0.09        0.06

Matches are distributed among these distances:
  13   19  0.63
  14   11  0.37

ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04


Consensus pattern (13 bp):   
AGAAAAATAGAAA

Found at i:739 original size:25 final size:25

Alignment explanation


    Indices: 679--746  Score: 77
    Period size: 25  Copynumber: 2.7  Consensus size: 25

        669 GGCCTAGCCC

                   *        *        
        679 AAAAAGGGA-GAAAAATAGAAAAGA
          1 AAAAAGGAAGGAAAAAAAGAAAAGA

                   *                   
        703 AAAATAGAAAGGAAAAGAAAGAAAAG-
          1 AAAA-AGGAAGGAAAA-AAAGAAAAGA

                              
        729 AAAAAGGAAGGAAAAAAA
          1 AAAAAGGAAGGAAAAAAA

        747 AGGGAAAATA


Statistics
Matches: 37,  Mismatches: 4, Indels: 6
        0.79            0.09        0.13

Matches are distributed among these distances:
  24    7  0.19
  25   13  0.35
  26    9  0.24
  27    8  0.22

ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03


Consensus pattern (25 bp):   
AAAAAGGAAGGAAAAAAAGAAAAGA

Found at i:754 original size:27 final size:27

Alignment explanation


    Indices: 689--748  Score: 79
    Period size: 25  Copynumber: 2.3  Consensus size: 27

        679 AAAAAGGGAG

                 *                     
        689 AAAAATAGAAAAGAAAAATAGAAAGGA
          1 AAAAAAAGAAAAGAAAAATAGAAAGGA

               *                 *     
        716 AAAGAAAGAAAAG-AAAA-AGGAAGGA
          1 AAAAAAAGAAAAGAAAAATAGAAAGGA

                    
        741 AAAAAAAG
          1 AAAAAAAG

        749 GGAAAATAAG


Statistics
Matches: 29,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  25   14  0.48
  26    4  0.14
  27   11  0.38

ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03


Consensus pattern (27 bp):   
AAAAAAAGAAAAGAAAAATAGAAAGGA

Found at i:894 original size:27 final size:27

Alignment explanation


    Indices: 826--895  Score: 70
    Period size: 27  Copynumber: 2.6  Consensus size: 27

        816 TTACTATTTT

                       **        *     
        826 ACCCTTTGATGGGTAAAGTACTAAATC
          1 ACCCTTTGATGATTAAAGTACGAAATC

                   *   *      *         
        853 ACCC-TTAAGTTATTAAATTACGAAATC
          1 ACCCTTTGA-TGATTAAAGTACGAAATC

                            
        880 ACCCTTTGATGATTAA
          1 ACCCTTTGATGATTAA

        896 TTTTAAGAAT


Statistics
Matches: 33,  Mismatches: 8, Indels: 4
        0.73            0.18        0.09

Matches are distributed among these distances:
  26    3  0.09
  27   27  0.82
  28    3  0.09

ACGTcount: A:0.36, C:0.19, G:0.13, T:0.33


Consensus pattern (27 bp):   
ACCCTTTGATGATTAAAGTACGAAATC
Done.