Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011501.1 Corchorus olitorius cultivar O-4 contig11534, 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: 2525
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.36


Found at i:286 original size:154 final size:154

Alignment explanation


    Indices: 1--1678  Score: 2673
    Period size: 154  Copynumber: 10.9  Consensus size: 154

                                  *               *                    *     
          1 TGGTGAGATTAGTCCACTGTGATGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCTTATCG
          1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG

                        *    *       *                              *        
         66 GGGCCCATTAGTGACGTATTGAATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCGTTCCATTG
         66 GGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG

                   *                
        131 TTTATGGCCTAACTATAATCATTT
        131 TTTATGGACTAACTATAATCATTT

                                *                                       *    
        155 TGGTGAGATTAGTCCACTGTAAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCCATCG
          1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG

                         *          *      *                *   *       *    
        220 GGGCCCATTAGTTCCGTTTTGAATTGTCTTCAATTTGGCAAACCTCAAAGCTATTCTTT-AAGTT
         66 GGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCA-TT

                    *                
        284 GTTTATGGCCTAACTATAATCATTT
        130 GTTTATGGACTAACTATAATCATTT

              *               *       *        *  *                   *      
        309 TGATGAGATTAGTCCACTATGAAGTTCTTAGCTCAATTCGAACACTTGTTATTTTGGGACTATCG
          1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG

                         * *                                *               *
        374 GGGCCCATTAGTTCCATTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTT
         66 GGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG

                                    
        439 TTTATGGACTAACTATAATCATTT
        131 TTTATGGACTAACTATAATCATTT

                                                       *             *       
        463 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACTCTTGTTATTTTGGACCTATCG
          1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG

                 *      *                                                    
        528 GGGCCTATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
         66 GGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG

                                  *  
        593 TTTATGG-CGTAACTATAATCAATT
        131 TTTATGGAC-TAACTATAATCATTT

                                                                *            
        617 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATATTGGGCCTATCG
          1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG

                     **  *                       *             *   *         
        682 GGGCCCATTTCTTCCGTTTTGAATCGTCTTCGATTTGACAAACCTCAATGCATTTATTTCCATTG
         66 GGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG

                  *                 
        747 TTTATGAACTAACTATAATCATTT
        131 TTTATGGACTAACTATAATCATTT

            *     *      *         *                                         
        771 CGGTGAAATTAGTACACTGTGAAATTTTTAGCTCATTTGGAACACTTGTTATTTT-GGCCTATCG
          1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG

            * *                                      **                      
        835 AGCCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAATTCTCAATGCTTTTCTTTCCATTG
         66 GGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG

                               *    
        900 TTTATGGACTAACTATAATAATTT
        131 TTTATGGACTAACTATAATCATTT

                               *           *                                 
        924 TGGTGAGATTAGTCCACTGCGAAGTTTTTAGGTCATTTGGAACACTTGTTATTTTGGGCCTATCG
          1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG

            *           *         *                                          
        989 CGGCCCATTAGTGACGTTTTGAGTCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
         66 GGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG

               *   *           * *  
       1054 TTTGTGGCCTAACTATAATGAATT
        131 TTTATGGACTAACTATAATCATTT

                                      *         *           *  *             
       1078 TGGTGAGATTAGTCCACTGTGAAGTTCTTAGCTCATCTGGAACACTTGCTAATTTGGG-CTATC-
          1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG

                         *                                                   
       1141 GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
         66 GGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG

                                    
       1206 TTTATGGACTAACTATAATCATTT
        131 TTTATGGACTAACTATAATCATTT

                                                                             
       1230 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
          1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG

                        *                                                    
       1295 GGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
         66 GGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG

                                    
       1360 TTTATGGACTAACTATAATCATTT
        131 TTTATGGACTAACTATAATCATTT

                                                                             
       1384 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
          1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG

                     *  *  *                         *                       
       1449 GGGCCCATTCGTGACATTTTGAATCGTCTTCGATTTGGCAAGCCTCAATGCTTTTCTTTCCATTG
         66 GGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG

                                    
       1514 TTTATGGACTAACTATAATCATTT
        131 TTTATGGACTAACTATAATCATTT

                                                                             
       1538 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
          1 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG

                         *                      *                            
       1603 GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTCGCAAACCTCAATGCTTTTCTTTCCATTG
         66 GGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG

                       
       1668 TTTATGGACTA
        131 TTTATGGACTA

       1679 TGATACGAAT


Statistics
Matches: 1397,  Mismatches: 120, Indels: 14
        0.91            0.08        0.01

Matches are distributed among these distances:
 152  135  0.10
 153  147  0.11
 154  1113  0.80
 155    2  0.00

ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40


Consensus pattern (154 bp):   
TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
GGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
TTTATGGACTAACTATAATCATTT

Found at i:2502 original size:21 final size:21

Alignment explanation


    Indices: 2476--2517  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2466 GCATCTTAGG

                                 
       2476 CAACTCCGATGAGCTTGAAAC
          1 CAACTCCGATGAGCTTGAAAC

                  *              
       2497 CAACTCTGATGAGCTTGAAAC
          1 CAACTCCGATGAGCTTGAAAC

       2518 TTACTTCC


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21


Consensus pattern (21 bp):   
CAACTCCGATGAGCTTGAAAC
Done.