Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007983.1 Corchorus capsularis cultivar CVL-1 contig08004, 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: 5225
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32


Found at i:928 original size:48 final size:48

Alignment explanation


    Indices: 802--1220  Score: 385
    Period size: 49  Copynumber: 8.6  Consensus size: 48

        792 TCACTTGCTA

                                         *  * *             *
        802 TTTCCCAAAATGCCCTTCCCGGACGGAAGACATTTATTTTTACCTGCTA
          1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTGATTTTTACCTG-TT

              *       **                                   *
        851 TTACCCAAAACACCCTTCCCGGACGGAAGGCACTGATTTTTACCTGTA
          1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTGATTTTTACCTGTT

                 *    *                                       
        899 TTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACTTCT-TT
          1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTGATTTTTAC--CTGTT

                 *    *            *     *       *          
        948 TTTCCTAAAACGCCCTTCCCGGATGGAAGACACTGATCTTTACCTGTT
          1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTGATTTTTACCTGTT

                                              *        *      
        996 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA-TTTTACTTGCTAT
          1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTGATTTTTACCTG-T-T

                 *       *         *     * *  *         **  
       1045 TTTCCAAAAATGCTCTTCCCGGATGGAAGACGCTTATTTTTACCCATT
          1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTGATTTTTACCTGTT

                      *        *               *        *    
       1093 TTTCCCCAAAGTGCCCTTCTCGGACGGAAGGCACTAATTTTTACTTGTT
          1 TTT-CCCAAAATGCCCTTCCCGGACGGAAGGCACTGATTTTTACCTGTT

               * *    **           *            *        **  
       1142 TTTTCTAAAACACCCTTCCCGGATGGAAGGCACT-AGTTTTACTCACTT
          1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTGATTTTTAC-CTGTT

                **           *       *     
       1190 TTTCTTAAAATGCCCTTTCCGGACGAAAGGC
          1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGC

       1221 TGGTTCACTT


Statistics
Matches: 305,  Mismatches: 57, Indels: 17
        0.80            0.15        0.04

Matches are distributed among these distances:
  47   16  0.05
  48  130  0.43
  49  151  0.50
  50    8  0.03

ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32


Consensus pattern (48 bp):   
TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTGATTTTTACCTGTT

Found at i:958 original size:97 final size:97

Alignment explanation


    Indices: 802--1220  Score: 459
    Period size: 97  Copynumber: 4.3  Consensus size: 97

        792 TCACTTGCTA

                                         *  *            *   *  *  *         
        802 TTTCCCAAAATGCCCTTCCCGGACGGAAGACATTTATTTTTACCTGC-TATTACCCAAAACACCC
          1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTA-CTTCTTTTTTCCTAAAACACCC

                    *     *                 *
        866 TTCCCGGACGGAAGGCACTGATTTTTACCTGTA
         65 TTCCCGGATGGAAGACACTGATTTTTACCTGTT

                 *    *                       *                         *    
        899 TTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACTTCTTTTTTCCTAAAACGCCCT
          1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTCTTTTTTCCTAAAACACCCT

                                 *          
        964 TCCCGGATGGAAGACACTGATCTTTACCTGTT
         66 TCCCGGATGGAAGACACTGATTTTTACCTGTT

                                                            *      *    ** * 
        996 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA-TTTTACTTGCTATTTTCCAAAAATGCTC
          1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACTT-CTTTTTTCCTAAAACACCC

                            *  *         **  
       1060 TTCCCGGATGGAAGACGCTTATTTTTACCCATT
         65 TTCCCGGATGGAAGACACTGATTTTTACCTGTT

                      *        *               *          *                  
       1093 TTTCCCCAAAGTGCCCTTCTCGGACGGAAGGCACTAATTTTTACTTGTTTTTT-CTAAAACACCC
          1 TTT-CCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTCTTTTTTCCTAAAACACCC

                          *      *        **  
       1157 TTCCCGGATGGAAGGCACT-AGTTTTACTCACTT
         65 TTCCCGGATGGAAGACACTGATTTTTAC-CTGTT

                **           *       *     
       1190 TTTCTTAAAATGCCCTTTCCGGACGAAAGGC
          1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGC

       1221 TGGTTCACTT


Statistics
Matches: 271,  Mismatches: 46, Indels: 11
        0.83            0.14        0.03

Matches are distributed among these distances:
  96   40  0.15
  97  188  0.69
  98   35  0.13
  99    8  0.03

ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32


Consensus pattern (97 bp):   
TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTCTTTTTTCCTAAAACACCCT
TCCCGGATGGAAGACACTGATTTTTACCTGTT
Done.