Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005074.1 Corchorus capsularis cultivar CVL-1 contig05092, 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: 7957
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:3384 original size:17 final size:18

Alignment explanation


    Indices: 3362--3420  Score: 63
    Period size: 17  Copynumber: 3.5  Consensus size: 18

       3352 CTTACCATGG

                           * *
       3362 TGATCTAATCACT-ATGT
          1 TGATCTAATCACTCAAGA

                              
       3379 TGATCTAATCA-TCAAGA
          1 TGATCTAATCACTCAAGA

                              
       3396 TGATCTAATCAC-CAAG-
          1 TGATCTAATCACTCAAGA

            *        
       3412 GGATCTAAT
          1 TGATCTAAT

       3421 TGGTGGTCAT


Statistics
Matches: 37,  Mismatches: 3, Indels: 5
        0.82            0.07        0.11

Matches are distributed among these distances:
  16    9  0.24
  17   28  0.76

ACGTcount: A:0.36, C:0.19, G:0.14, T:0.32


Consensus pattern (18 bp):   
TGATCTAATCACTCAAGA

Found at i:5953 original size:168 final size:165

Alignment explanation


    Indices: 5705--6149  Score: 606
    Period size: 168  Copynumber: 2.7  Consensus size: 165

       5695 ATGAGGAGCG

                    *                   *      *               *             
       5705 AGAGAACTAATTTTTTTTCGTCTTTTCCCACTTGATC-GATTACTTAAATGCCCTAACTTTTGAT
          1 AGAGAACTTATTTTTTTTCGTCTTTTCCTACTTG-GCAGATTACTTAAATGTCCTAACTTTTGAT

                     *                                        *              
       5769 TCTTGAGGTCATTAAATAACTAGACTTTTTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGA
         65 TCTTGAGGTGATTAAATAACTA-ACTTTTTGGTCATTTCTCAATTGACTTGAATAGAGTAGTGGA

                *                  **   * **       
       5834 ATTACTAAAAGATCCCCACCAAGGCTTGCTTTTGGAGTT
        129 ATTAATAAAAGAT-CCCACCAAGAATTGATGAT-GAGTT

                                                                *            
       5873 AGAGAACTTATTTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCATAACTTTTGATT
          1 AGAGAACTTATTTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATT

                              *                    *   *                     
       5938 CTTGAGGTGATTAAATAAGTAATCTTTTTGGTCATTTCTTAATGGACTTGAATAGAGTAGTGGAA
         66 CTTGAGGTGATTAAATAACTAA-CTTTTTGGTCATTTCTCAATTGACTTGAATAGAGTAGTGGAA

                            *                   
       6003 TTAATAAAAGATCCCATCAAGAATTGATGATGAGTT
        130 TTAATAAAAGATCCCACCAAGAATTGATGATGAGTT

               *      * *  *         *                                       
       6039 AGAAAAC-TAATCTTATTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATT
          1 AGAGAACTTATTTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATT

               *   *                                       
       6103 CTTTAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATTGAC
         66 CTTGAGGTGATTAAATAACT-AACTTTTTGGTCATTTCTCAATTGAC

       6150 AAATGACTCA


Statistics
Matches: 246,  Mismatches: 28, Indels: 9
        0.87            0.10        0.03

Matches are distributed among these distances:
 165   91  0.37
 166   13  0.05
 167   15  0.06
 168  127  0.52

ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40


Consensus pattern (165 bp):   
AGAGAACTTATTTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATT
CTTGAGGTGATTAAATAACTAACTTTTTGGTCATTTCTCAATTGACTTGAATAGAGTAGTGGAAT
TAATAAAAGATCCCACCAAGAATTGATGATGAGTT

Done.