Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009430.1 Corchorus capsularis cultivar CVL-1 contig09451, 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: 12491
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33


Found at i:568 original size:99 final size:96

Alignment explanation


    Indices: 397--751  Score: 317
    Period size: 95  Copynumber: 3.7  Consensus size: 96

        387 TCAACTTTTT

                  *          *                     *                *    *   
        397 CCCAAAGCGCCCTTCCCAGACGGAAGCCATTTAT-TTTCGCTTGCTATTTCCCAAAGCGCCATTC
          1 CCCAAAACGCCCTTCCCGGACGGAAGCCATTTATCTTT-ACTTGCTATTTCCCAAAACGCCCTTC

                          * *   *  * *         
        461 CCAGACGGAAGCCATTTATTTTTGCTTGCTATCTC
         65 CC-GACGGAAGCCACTGATTATTACCTG-T-TCTC

                    *                   *                                   *
        496 CCCAAAACACCCTTCCCGGACGGAAGCCGTTTATCTTTACTTGCTATTTCCCAAAACGCCCTTCT
          1 CCCAAAACGCCCTTCCCGGACGGAAGCCATTTATCTTTACTTGCTATTTCCCAAAACGCCCTTCC

                      *                  * *
        561 CGTACGGAAGGCACTGATTATTACCTGTTTTT
         66 CG-ACGGAAGCCACTGATTATTACCTGTTCTC

                                      *  * *                                 
        593 CCCAAAACGCCCTTCCCGGACGGAAGACACTAATCTTTAC---CTATTTTCCCAAAACGCCCTTC
          1 CCCAAAACGCCCTTCCCGGACGGAAGCCATTTATCTTTACTTGCTA-TTTCCCAAAACGCCCTTC

                       *    *              * *
        655 CCGGACGGAAGGCACTAATCT-TTACCTGTTTTT
         65 CC-GACGGAAGCCACTGAT-TATTACCTGTTCTC

            *      *                  *  *         *            *    *       
        688 TCCAAAATGCCCTTCCCGGACGGAAGGCACTTAT-TTTATTTGCTATTTTCCAAAAATGCCCTTC
          1 CCCAAAACGCCCTTCCCGGACGGAAGCCATTTATCTTTACTTGCTA-TTTCCCAAAACGCCCTTC

        752 TTGGATGGAA


Statistics
Matches: 218,  Mismatches: 30, Indels: 18
        0.82            0.11        0.07

Matches are distributed among these distances:
  94    7  0.03
  95   75  0.34
  96    2  0.01
  97   57  0.26
  98    2  0.01
  99   72  0.33
 100    3  0.01

ACGTcount: A:0.23, C:0.32, G:0.15, T:0.30


Consensus pattern (96 bp):   
CCCAAAACGCCCTTCCCGGACGGAAGCCATTTATCTTTACTTGCTATTTCCCAAAACGCCCTTCC
CGACGGAAGCCACTGATTATTACCTGTTCTC

Found at i:858 original size:49 final size:48

Alignment explanation


    Indices: 391--863  Score: 297
    Period size: 49  Copynumber: 9.7  Consensus size: 48

        381 TTTTTATCAA

                        *          *        *  * *     ** *  
        391 CTTTTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTCGCTTG
          1 CTTTTT-CCAAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCTG

                  *     *    *     *        *  * *      * *  
        440 CTATTTCCCAAAGCGCCATTCCCAGACGGAAGCCATTTATTTTTGCTTG
          1 CT-TTTTCCAAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCTG

                  **       *                 * ** *  *     *  
        489 CTATCTCCCCAAAACACCCTTCCCGGACGGAAGCCGTTTATCTTTACTTG
          1 CT-T-TTTCCAAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCTG

                  *              *  *            *   *       
        539 CTATTTCCCAAAACGCCCTTCTCGTACGGAAGGCACTGATTATTACCTG
          1 CT-TTTTCCAAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCTG

                                            *       *        
        588 -TTTTTCCCAAAACGCCCTTCCCGGACGGAAGACACTAATCTTTACCT-
          1 CTTTTT-CCAAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCTG

            *    *                                 *        
        635 ATTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTAATCTTTACCTG
          1 CTTTTTCCAAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCTG

            *           *                       *       **  
        683 TTTTTTCCAAAATGCCCTTCCCGGACGGAAGGCACTTA-TTTTATTTG
          1 CTTTTTCCAAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCTG

                          *       **   *          *  *        **
        730 CTATTTTCCAAAAATGCCCTTCTTGGATGGAAGATGC-TTATTTTTTACCCA
          1 CT-TTTTCC-AAAACGCCCTTCCCGGACGGAAG--GCACTAATTTTTACCTG

                  *     **         *                      *  
        781 CTTTTCCCCAAAGTGCCCTTCCCCGACGGAAGGCACTAATTTTTACTTG
          1 CTTTT-TCCAAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCTG

                    *     *     *             
        830 CCTTTTTCTAAAACACCCTTTCCGGACGGAAGGC
          1 -CTTTTTCCAAAACGCCCTTCCCGGACGGAAGGC

        864 GTTACTCACT


Statistics
Matches: 344,  Mismatches: 67, Indels: 26
        0.79            0.15        0.06

Matches are distributed among these distances:
  47   50  0.15
  48   82  0.24
  49  130  0.38
  50   71  0.21
  51   11  0.03

ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31


Consensus pattern (48 bp):   
CTTTTTCCAAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCTG
Done.