Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000283.1 Corchorus capsularis cultivar CVL-1 contig00283, 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, 909

Length: 1515
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30


Found at i:63 original size:22 final size:20

Alignment explanation


    Indices: 16--392  Score: 162
    Period size: 21  Copynumber: 18.1  Consensus size: 20

          6 AAGAATGATA

                     *          
         16 AAGAGTAAAGGGTAATCAGT
          1 AAGAGTAAAAGGTAATCAGT

                                 
         36 AAGAGTAAGAAGGTAATCAGT
          1 AAGAGTAA-AAGGTAATCAGT

                        *         
         57 AAGGAGTAAAACAGTAATCAGT
          1 AA-GAGTAAAA-GGTAATCAGT

               *                **
         79 AAAAAGTAAGAAGGTAATCAAC
          1 -AAGAGTAA-AAGGTAATCAGT

                       *   *     
        101 AAGAGTAAAATAGTAGTCAGT
          1 AAGAGTAAAA-GGTAATCAGT

              *           *      
        122 AAAAGTAAATA-GTGATCAGT
          1 AAGAGTAAA-AGGTAATCAGT

                            *   
        142 -A-A--AAAA-GTAATAAGT
          1 AAGAGTAAAAGGTAATCAGT

                         *    *  
        157 AAGAAGTAAAAGGAAATCGGT
          1 AAG-AGTAAAAGGTAATCAGT

                          *   *  
        178 AAGAGTAAAAAGGTGATCCGT
          1 AAGAGT-AAAAGGTAATCAGT

                         *       *
        199 AAAGAGTAAAAAGCTAATCAGC
          1 -AAGAGT-AAAAGGTAATCAGT

                  *      *       
        221 AAGAAGCAAAAGGCAATCAGT
          1 AAG-AGTAAAAGGTAATCAGT

               *                  
        242 AAAAAGTAAAAGAGTAATCAGT
          1 -AAGAGTAAAAG-GTAATCAGT

                 **         *    *
        264 CAA-AAAAAAAGG-AAGCAGAA
          1 -AAGAGTAAAAGGTAATCAG-T

              *                  
        284 AATAGT-AAAGAGTAATCAGT
          1 AAGAGTAAAAG-GTAATCAGT

                          *    *   
        304 AAAAGAGTAAAATGATAATTAGT
          1 --AAGAGTAAAA-GGTAATCAGT

               *            *   **
        327 AAAAAGTAAGAAGGTAGTCAAC
          1 -AAGAGTAA-AAGGTAATCAGT

                       *         
        349 AAGAGTAAAATAGTAATCAGT
          1 AAGAGTAAAA-GGTAATCAGT

               *         *        
        370 ACAAAGT-AAAGAATAATCAGT
          1 A-AGAGTAAAAG-GTAATCAGT

              
        391 AA
          1 AA

        393 AATAGTGATG


Statistics
Matches: 268,  Mismatches: 59, Indels: 60
        0.69            0.15        0.16

Matches are distributed among these distances:
  15    8  0.03
  16    4  0.01
  18    2  0.01
  19   12  0.04
  20   30  0.11
  21  114  0.43
  22   81  0.30
  23   16  0.06
  24    1  0.00

ACGTcount: A:0.54, C:0.07, G:0.21, T:0.18


Consensus pattern (20 bp):   
AAGAGTAAAAGGTAATCAGT

Found at i:78 original size:43 final size:42

Alignment explanation


    Indices: 27--378  Score: 155
    Period size: 43  Copynumber: 8.4  Consensus size: 42

         17 AGAGTAAAGG

                       *                **             
         27 GTAATCAGTAAGAGTAAGAAGGTAATCAGTAAGGAGTAAAACA
          1 GTAATCAGTAAAAGTAAGAAGGTAATCAACAA-GAGTAAAACA

                                                     * 
         70 GTAATCAGTAAAAAGTAAGAAGGTAATCAACAAGAGTAAAATA
          1 GTAATCAGT-AAAAGTAAGAAGGTAATCAACAAGAGTAAAACA

               *                    *                * 
        113 GTAGTCAGTAAAAGTAA-ATA-GTGAT---C---AGTAAAAAA
          1 GTAATCAGTAAAAGTAAGA-AGGTAATCAACAAGAGTAAAACA

                 *                 *    ***            
        148 GTAATAAGTAAGAAGTAA-AAGGAAATCGGTAAGAGTAAAA-A
          1 GTAATCAGTAA-AAGTAAGAAGGTAATCAACAAGAGTAAAACA

               *   *           *   *      *       *     *
        189 GGTGATCCGTAAAGAGTAAAAAGCTAATCAGCAAGAAGCAAAA-G
          1 -GTAATCAGTAAA-AGTAAGAAGGTAATCAACAAG-AGTAAAACA

             *                             *           * 
        233 GCAATCAGTAAAAAGTAA-AAGAGTAATCAGTCAA-A--AAAAAA
          1 GTAATCAGT-AAAAGTAAGAAG-GTAATCA-ACAAGAGTAAAACA

             *  *   *                        *           *
        274 GGAAGCAGAAAATAGT-A-AAGAGTAATCAGTAAAAGAGTAAAA-T
          1 GTAATCAGTAAA-AGTAAGAAG-GTAATCA--ACAAGAGTAAAACA

                  *                   *               * 
        317 GATAATTAGTAAAAAGTAAGAAGGTAGTCAACAAGAGTAAAATA
          1 G-TAATCAGT-AAAAGTAAGAAGGTAATCAACAAGAGTAAAACA

                              
        361 GTAATCAGTACAAAGTAA
          1 GTAATCAGTA-AAAGTAA

        379 AGAATAATCA


Statistics
Matches: 238,  Mismatches: 42, Indels: 58
        0.70            0.12        0.17

Matches are distributed among these distances:
  35   18  0.08
  36   10  0.04
  38    1  0.00
  40   19  0.08
  41   18  0.08
  42   35  0.15
  43   80  0.34
  44   44  0.18
  45   10  0.04
  46    3  0.01

ACGTcount: A:0.54, C:0.07, G:0.21, T:0.18


Consensus pattern (42 bp):   
GTAATCAGTAAAAGTAAGAAGGTAATCAACAAGAGTAAAACA

Done.