Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005907.1 Corchorus capsularis cultivar CVL-1 contig05925, 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: 2653
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34


Found at i:136 original size:76 final size:76

Alignment explanation


    Indices: 4--332  Score: 534
    Period size: 76  Copynumber: 4.3  Consensus size: 76

          1 TTT

                                                                *      *     
          4 ATGTTAATCCTGATCTAGGATCATTGC-TTATAAGTTAATTTTAATCCTGATTTAGGATAATTGA
          1 ATGTTAATCCTGATCTAGGATCATTGCTTTATAAGTTAATTTTAATCCTGATCTAGGATCATTGA

                       
         68 TTTATCAATTC
         66 TTTATCAATTC

                             *                                              *
         79 ATGTTAATCCTGATCTAAGATCATTGCTTTATAAGTTAATTTTAATCCTGATCTAGGATCATTGC
          1 ATGTTAATCCTGATCTAGGATCATTGCTTTATAAGTTAATTTTAATCCTGATCTAGGATCATTGA

                       
        144 TTTATCAATTC
         66 TTTATCAATTC

                            *                                               *
        155 ATGTTAATCCTGATCTCGGATCATTGCTTTATAAGTTAATTTTAATCCTGATCTAGGATCATTGC
          1 ATGTTAATCCTGATCTAGGATCATTGCTTTATAAGTTAATTTTAATCCTGATCTAGGATCATTGA

                       
        220 TTTATCAATTC
         66 TTTATCAATTC

                                                 *            * *            
        231 ATGTTAATCCTGATCTAGGATCATTGCTTTATAAGTTCATTTTAATCCTGGTTTAGGATCATTGA
          1 ATGTTAATCCTGATCTAGGATCATTGCTTTATAAGTTAATTTTAATCCTGATCTAGGATCATTGA

                 *   * 
        296 TTTATTAATGC
         66 TTTATCAATTC

              *           *           
        307 ATTTTAATCCTGATTTAGGATCATTG
          1 ATGTTAATCCTGATCTAGGATCATTG

        333 ATTAATCAGT


Statistics
Matches: 238,  Mismatches: 15, Indels: 1
        0.94            0.06        0.00

Matches are distributed among these distances:
  75   26  0.11
  76  212  0.89

ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44


Consensus pattern (76 bp):   
ATGTTAATCCTGATCTAGGATCATTGCTTTATAAGTTAATTTTAATCCTGATCTAGGATCATTGA
TTTATCAATTC

Found at i:335 original size:38 final size:38

Alignment explanation


    Indices: 7--332  Score: 437
    Period size: 38  Copynumber: 8.6  Consensus size: 38

          1 TTTATG

                                              *   
          7 TTAATCCTGATCTAGGATCATTGC-TTATAAGTTAATT
          1 TTAATCCTGATCTAGGATCATTGCTTTATAAGTTCATT

                       *      *    *              *
         44 TTAATCCTGATTTAGGATAATTGATTTATCAA-TTCATG
          1 TTAATCCTGATCTAGGATCATTGCTTTAT-AAGTTCATT

                          *                   *   
         82 TTAATCCTGATCTAAGATCATTGCTTTATAAGTTAATT
          1 TTAATCCTGATCTAGGATCATTGCTTTATAAGTTCATT

                                                  *
        120 TTAATCCTGATCTAGGATCATTGCTTTATCAA-TTCATG
          1 TTAATCCTGATCTAGGATCATTGCTTTAT-AAGTTCATT

                         *                    *   
        158 TTAATCCTGATCTCGGATCATTGCTTTATAAGTTAATT
          1 TTAATCCTGATCTAGGATCATTGCTTTATAAGTTCATT

                                                  *
        196 TTAATCCTGATCTAGGATCATTGCTTTATCAA-TTCATG
          1 TTAATCCTGATCTAGGATCATTGCTTTAT-AAGTTCATT

                                                  
        234 TTAATCCTGATCTAGGATCATTGCTTTATAAGTTCATT
          1 TTAATCCTGATCTAGGATCATTGCTTTATAAGTTCATT

                     * *           *          *    
        272 TTAATCCTGGTTTAGGATCATTGATTTATTAA-TGCATT
          1 TTAATCCTGATCTAGGATCATTGCTTTA-TAAGTTCATT

                       *           
        310 TTAATCCTGATTTAGGATCATTG
          1 TTAATCCTGATCTAGGATCATTG

        333 ATTAATCAGT


Statistics
Matches: 255,  Mismatches: 26, Indels: 15
        0.86            0.09        0.05

Matches are distributed among these distances:
  37   27  0.11
  38  219  0.86
  39    9  0.04

ACGTcount: A:0.28, C:0.14, G:0.13, T:0.44


Consensus pattern (38 bp):   
TTAATCCTGATCTAGGATCATTGCTTTATAAGTTCATT

Found at i:740 original size:63 final size:61

Alignment explanation


    Indices: 663--783  Score: 197
    Period size: 63  Copynumber: 2.0  Consensus size: 61

        653 GTTTGAGAGT

                                          *   *                            
        663 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCATG
          1 TTCATTTCAAATCCTGCTTGAGGTCTCTAGCCGAAAGTTTC-TGTTTCAA-TCCAAAATCATG

                                                               *      
        726 TTCATTTCAAATCCTGCTTGAGGTCTCTAGCCGAAAGTTTCTGTTTCAATCTAAAATC
          1 TTCATTTCAAATCCTGCTTGAGGTCTCTAGCCGAAAGTTTCTGTTTCAATCCAAAATC

        784 TTGCTCGAGA


Statistics
Matches: 55,  Mismatches: 3, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
  61    8  0.15
  62    8  0.15
  63   39  0.71

ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39


Consensus pattern (61 bp):   
TTCATTTCAAATCCTGCTTGAGGTCTCTAGCCGAAAGTTTCTGTTTCAATCCAAAATCATG
Done.