Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011407.1 Corchorus capsularis cultivar CVL-1 contig11428, 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, 618

Length: 1030
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32


Found at i:991 original size:325 final size:324

Alignment explanation


    Indices: 1--999  Score: 1235
    Period size: 326  Copynumber: 3.0  Consensus size: 324

                                               *                             
          1 AAAAATCATGCAAAACTTAGTCGAACCCCGGAACGTGGTTTTTGCCGAAAACCGTGATGGTTAGT
          1 AAAAATCATGCAAAACTTAGTCGAACCCCGGAACGCGGTTTTTGCCGAAAACCGTGA---TT-GT

                                                            *    *      *    
         66 ACATGATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAAGATTTTTCTTCGAGTTCTAGCGAAA
         62 ACATGATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAAGATTTTTCCTCGATTTCTAGTGAAA

                    *                            *                           
        131 ATACTCATGAAAAATATATAATTAAACACCAAAAAAAATGAAAGCCTTTTTCACGCTTTTAATAT
        127 ATACTCATAAAAAATATATAATTAAACACC-AAAAAATTGAAAGCCTTTTTCACGCTTTTAATAT

                                                                     *  *    
        196 CGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGTG-ACAAGATTCAGATACACATAA
        191 CGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAAT--TGAACAAGATTCAGATGCATATAA

                  *                                                   *      
        260 AAACAACTCCTTAAATCCAATGTGCCTGAGATTTGATTAGATGAATAAAGATATTTCATGGAGTC
        253 AAACAAATCCTTAAATCCAATGTGCCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTC

                 *  
        325 TCGGTTCC
        318 TC-GTGCC

                  *         **        *   *     *          * *          ***  
        333 AAAAATAATGCAAAACAGAGTC-ATGGCCCTGGAACAC-GTTTTTAGTCAAAAACCGT-AACATA
          1 AAAAATCATGCAAAACTTAGTCGA--ACCCCGGAACGCGGTTTTT-GCCGAAAACCGTGATTGTA

                    **            *                    *       *    * *      
        395 CATGATTTTTGCTAAAATTTTGTAAAAATTGA-TCCGAAAGATATTTCCTCAATTTTTGGCT-AA
         63 CATGATTTCGGCTAAAATTTTGCAAAAATTGACT-CGAAAGATTTTTCCTCGATTTCTAG-TGAA

                        *   *       **   **            * *      *      *     
        458 AATACTCATAAACAATTTATAATTTGACATAAAAAAGATTGAAGGGC-TTTTAACGCTTCTAATA
        126 AATACTCATAAAAAATATATAATTAAACACCAAAAA-ATTGAAAGCCTTTTTCACGCTTTTAATA

             *       *       * *              *    *                     *   
        522 TTGTTTTTCCTATTTTTTTAAATTAATTTCTAATAAAATCGAAACAAGATTCAGATGC-TCGTAA
        190 TCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATTG-AACAAGATTCAGATGCAT-ATAA

                             *      **         *           *               * 
        586 AAACAAATCCTTAAATCTAATGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGAC
        253 AAACAAATCCTTAAATCCAATGTGCCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTC

             *       
        651 TTG-GCAAC
        318 TCGTGC--C

                                *         *                                  
        659 AAAAATCATGCAAAACTTAGCCGAACCCCGAAACGCGGTTTTTGCCGAAAACCGTGATTGTACAT
          1 AAAAATCATGCAAAACTTAGTCGAACCCCGGAACGCGGTTTTTGCCGAAAACCGTGATTGTACAT

                                                                             
        724 GATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAAGATTTTTCCTCGATTTCTAGTGAAAATAC
         66 GATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAAGATTTTTCCTCGATTTCTAGTGAAAATAC

                                                                             
        789 TCATAAAAAATATATAATTAAACACCAAAAAATTGAAAGCCTTTTTCACGCTTTTAATATCGTTT
        131 TCATAAAAAATATATAATTAAACACCAAAAAATTGAAAGCCTTTTTCACGCTTTTAATATCGTTT

                                                         *                   
        854 TTCATATTTTTCTGAA-TAATTTCTAATTAAATTGAAGCAAGATTTAGATGCATATAAAAACAAA
        196 TTCATATTTTTCTGAATTAATTTCTAATTAAATTGAA-CAAGATTCAGATGCATATAAAAACAAA

                                                                             
        918 TCCTTAAATCCAATGTGCCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTCGCTGC
        260 TCCTTAAATCCAATGTGCCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTCG-TGC

             
        983 C
        324 C

                            
        984 AAAAATCATGCAAAAC
          1 AAAAATCATGCAAAAC

       1000 AGAGCTATGG


Statistics
Matches: 548,  Mismatches: 98, Indels: 49
        0.79            0.14        0.07

Matches are distributed among these distances:
 324    4  0.01
 325  138  0.25
 326  243  0.44
 327   35  0.06
 328   83  0.15
 331    1  0.00
 332   26  0.05
 333   18  0.03

ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33


Consensus pattern (324 bp):   
AAAAATCATGCAAAACTTAGTCGAACCCCGGAACGCGGTTTTTGCCGAAAACCGTGATTGTACAT
GATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAAGATTTTTCCTCGATTTCTAGTGAAAATAC
TCATAAAAAATATATAATTAAACACCAAAAAATTGAAAGCCTTTTTCACGCTTTTAATATCGTTT
TTCATATTTTTCTGAATTAATTTCTAATTAAATTGAACAAGATTCAGATGCATATAAAAACAAAT
CCTTAAATCCAATGTGCCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTCGTGCC
Done.