Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002170.1 Corchorus capsularis cultivar CVL-1 contig02175, 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, 631

Length: 1052
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36


Found at i:828 original size:336 final size:330

Alignment explanation


    Indices: 1--912  Score: 949
    Period size: 334  Copynumber: 2.7  Consensus size: 330

                          *  *      *          *                             
          1 ATATATATAATTTATCGTCAAAAATATTGAAGGGATTTTCACGCTTTTAATATCGTTTTTCATAT
          1 ATATATATAATTTAACGCCAAAAACATT-AAGGGACTTTCACGCTTTTAATATCGTTTTTCATAT

                      *              *                                     * 
         66 TTTTTCTGAAATAATTTCTAATTAATTCAAAACAAGATTTAGGTGCTCGTAAAAACAAATCCTCA
         65 TTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTTAGGTGCTCGTAAAAACAAATCCTTA

                                                *                  *      *  
        131 AATGCAATGTGCCTAAGATTTTATTAGATGAATATAGATATTTCAAGGAGTCTCGACGCCAACAA
        130 AATGCAATGTG-CTAAGATTTTATTAGATGAATATAAATATTTCAAGGAGTCTCGGCGCCAAAAA

                   *                                 *       * *        *    
        196 TCATGCAGAA-TAGAGTCGGGGCGCCGAAAGACGTTTTTAGGC-AAAAACTGTAATTAATGTACA
        194 TCATGCAAAACT-GAGTCGGGGCGCCGAAAG-CGTTTTTAGCCAAAAAAATATAATTAATATACA

                           *** *            *                *        **     
        259 CGATTTTTGCTAAAATTTTGCGAAAAAAATGTCCCGAAAAATTTTTCATCAATCTTTGGGTAAAG
        257 C-ATTTTTGCTAAAACACTCCGAAAAAAATGTACCGAAAAATTTTTCATAAATCTTTGCATAAAG

                      
        324 TACTCCTAAA
        321 TACTCCTAAA

                    *    *  * *     *    *        *              **      *   
        334 ATATATATGATTTCACTCTAAAAAGATTAGGGGACTTTTACTG-TTTTAATATAATTTCTTTATA
          1 ATATATATAATTTAACGCCAAAAACATTAAGGGACTTTCAC-GCTTTTAATATCGTTT-TTCATA

                     *     *   *          *          *  *            *  *  * 
        398 TTTTTTTCTAAATTAGTTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAATTCTT
         64 -TTTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTTAGGTGCTCGTAAAAACAAATCCT

                *                                 *                          
        463 TAAAGGCAATGTGGCTAAGATTTTATTAGATGAATATATATATTTCAAGGAGTCTCGGCGCCAAA
        128 TAAATGCAATGT-GCTAAGATTTTATTAGATGAATATAAATATTTCAAGGAGTCTCGGCGCCAAA

                             *      *         *                   **        *
        528 AATCATGCAAAACTGAGCCGGGGCTCCGAAATGCATTTTTA-CCAAAAAAATATTTTTAATATAT
        192 AATCATGCAAAACTGAGTCGGGGCGCCGAAA-GCGTTTTTAGCCAAAAAAATATAATTAATATAC

              *           *        *      ** *                         *   * 
        592 A-TTTTTTGC-ACAGACACTCCTTAAAATATTTTTACC-AAAAATATTTT-ACTAAATTTTTTTC
        256 ACATTTTTGCTA-AAACACTCC-GAAAA-AAATGTACCGAAAAAT-TTTTCA-TAAA-TCTTTGC

               * *           
        653 ATAGATTACTCCTAAAA
        315 ATAAAGTACTCCT-AAA

                                               *                             
        670 TATATATATAATTTAACGCCAAAAACATTAAAGGGCCTTTCACGCTTTTAATATCGTTTTTCATA
          1 -ATATATATAATTTAACGCCAAAAACATT-AAGGGACTTTCACGCTTTTAATATCGTTTTTCATA

                                                             *      *        
        735 TTTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTTAGGTGCTCATAAAAATAAATCCTT
         64 TTTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTTAGGTGCTCGTAAAAACAAATCCTT

                               *                        *   *               *
        800 AAATGCAATGTAGCTAAGACTTTATTAGATGAATATAAATATTTTAAGAAGTCTCGGCGCCAAAT
        129 AAATGCAATGT-GCTAAGATTTTATTAGATGAATATAAATATTTCAAGGAGTCTCGGCGCCAAAA

                      *  *                 *                
        865 ATCATGCAAATCTAAGTCGGGGCGCCGAAACACGTTTTTAGCCAAAAA
        193 ATCATGCAAAACTGAGTCGGGGCGCCGAAA-GCGTTTTTAGCCAAAAA

        913 CTGTGATGGT


Statistics
Matches: 468,  Mismatches: 93, Indels: 32
        0.79            0.16        0.05

Matches are distributed among these distances:
 331    1  0.00
 332   33  0.07
 333   39  0.08
 334  171  0.37
 335   17  0.04
 336  149  0.32
 337   36  0.08
 338   22  0.05

ACGTcount: A:0.37, C:0.14, G:0.13, T:0.35


Consensus pattern (330 bp):   
ATATATATAATTTAACGCCAAAAACATTAAGGGACTTTCACGCTTTTAATATCGTTTTTCATATT
TTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTTAGGTGCTCGTAAAAACAAATCCTTAA
ATGCAATGTGCTAAGATTTTATTAGATGAATATAAATATTTCAAGGAGTCTCGGCGCCAAAAATC
ATGCAAAACTGAGTCGGGGCGCCGAAAGCGTTTTTAGCCAAAAAAATATAATTAATATACACATT
TTTGCTAAAACACTCCGAAAAAAATGTACCGAAAAATTTTTCATAAATCTTTGCATAAAGTACTC
CTAAA
Done.