Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011548.1 Corchorus olitorius cultivar O-4 contig11581, 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: 3659
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37


Found at i:307 original size:154 final size:154

Alignment explanation


    Indices: 1--2650  Score: 3758
    Period size: 154  Copynumber: 17.2  Consensus size: 154

                     **                            *                       * 
          1 AAGTTTTTAAATCATTTGGAACACTT-TTATTTTGGGCCAATCGGGGCCCATTAGTGACGTTTCG
          1 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTG

                  *             *                                 *          
         65 AATCGTATTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTTACTATAATCA
         66 AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA

                *                   
        130 TTTTAGTGAGATTAGTCCACTGTG
        131 TTTTGGTGAGATTAGTCCACTGTG

               *        *                                    *   *           
        154 AAGATTTTAGCTAATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCAATTTGTGACGTTTTG
          1 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTG

                                *                           *                
        219 AATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTACGGCCTAACTATAATCA
         66 AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA

                     *              
        284 TTTTGGTGAAATTAGTCCACTGTG
        131 TTTTGGTGAGATTAGTCCACTGTG

              *         *            *                               **      
        308 AACTTTTTAGCTAATTTGGAACACTAGTTA-TTTGAGGCCTATCGGGGCCCATTAGTTCCGTTTT
          1 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG-GGCCTATCGGGGCCCATTAGTGACGTTTT

                     *               *                             *         
        372 GAATCGTCTCCGATTTGGC-AACTCCCAATGCTTTTCTTTCCATTGTTTATGGCCAAACTATAAT
         65 GAATCGTCTTCGATTTGGCAAAC-CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT

                                      
        436 CATTTTGGTGAGATTAGTCCACTGTG
        129 CATTTTGGTGAGATTAGTCCACTGTG

                *                      *                  *  *               
        462 AAGTCTTTAGCTCATTTGGAACACTTGCTATTTTGGGCCTATCGGGACCAATTAGTGACGTTTTG
          1 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTG

                                 *                             *             
        527 AATCGTCTTCGATTTGGCAAATCTCAATGCTTTTCTTTCCATTGTTTATGGTCTAACTATAATCA
         66 AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA

                   *                
        592 TTTTGGTCAGATTAGTCCACTGT-
        131 TTTTGGTGAGATTAGTCCACTGTG

                        *                       *         *                  
        615 AATGTTTTTAGCGCATTTGGAACACTTGTTATTTTGAGCCTATCGGTGCCCATTAGTGACGTTTT
          1 AA-GTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTT

                                                                             
        680 GAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
         65 GAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC

              *       *           *  
        745 ATATTGGTGACATTAGTCCACTATG
        130 ATTTTGGTGAGATTAGTCCACTGTG

                            *                          *    *       **       
        770 AAGTTTTT-GCTCATTCGGAACACTTGTTATTTTGGGCCTATCTGGGCTCATTAGTTCCGTTTTG
          1 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTG

                                     *   * *                   *             
        834 AATTC-TCTTCGATTTGGCAAACCTTAATACCTTTCTTTCCATTGTTTATGACCTAACTATAATC
         66 AA-TCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC

                         *          *
        898 ATTTTGGTGAGATCAGTCCACTGTA
        130 ATTTTGGTGAGATTAGTCCACTGTG

              *           *      *                            *     **      *
        923 AACTTTTTAGCTCAGTTGGAAAACTTGTTATTTTGGGCCTATCGGGGCCCTTTAGTTTCGTTTTC
          1 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTG

                                       * *                *                  
        988 AATCGTCTTCGATTTGGCAAACCTCAACGATTTTCTTTCCATTGTTAAT-GCCTAACTATAATCA
         66 AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA

                                 *  
       1052 TTTTGGTGAGATTAGTCCACTATG
        131 TTTTGGTGAGATTAGTCCACTGTG

                            *                              **       **       
       1076 AAGTTTTTAGCTCATTCGGAACACTTGTTATTTTGGGCCTATCGGGGTTCATTAGTTCCGTTTTG
          1 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTG

                                                              *              
       1141 AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGACCTAACTATAATCA
         66 AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA

                 *     *         *  
       1206 TTTTGATGAGAATAGTCCACTCTG
        131 TTTTGGTGAGATTAGTCCACTGTG

              *   *       *                                         **       
       1230 AACTTTATAGCTCAGTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTG
          1 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTG

                        *        *                                           
       1295 AATCGTCTTCGACTTGGCAAAGCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
         66 AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA

                                    
       1360 TTTTGGTGAGATTAGTCCACTGTG
        131 TTTTGGTGAGATTAGTCCACTGTG

              *                           *                              *   
       1384 AACTTTTTAGCTCATTTGGAACACTTGTTAATTTGGGCCTATCGGGGCCCATTAGTGACGTATTG
          1 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTG

                * *     *     *               *                              
       1449 AATCTTTTTCGAATTGGCTAACCTCAATGCTTTTGTTTCCATTGTTTATGGCCTAACTATAATCA
         66 AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA

                 * **            *  
       1514 TTTTGTTTTGATTAGTCCACTTTG
        131 TTTTGGTGAGATTAGTCCACTGTG

                                   *      *   *     *                    *   
       1538 AAGTTTTTAGCTCATTTGGAACAATTGTTACTTTAGGCCTTTCGGGGCCCATTAGTGACGTATTG
          1 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTG

                                                           *   *            *
       1603 AATCGTCTTCGATTTGGCAAACCTTC-ATGCTTTTCTTTCCATTGTTCATGCCCTAACTATAATT
         66 AATCGTCTTCGATTTGGCAAACC-TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC

                  *        *         
       1667 ATTTTGCTGAGATTACTCCACTGTG
        130 ATTTTGGTGAGATTAGTCCACTGTG

             *          *                         *  *              ** *     
       1692 ATGTTTTTAGCTTATTTGGAACACTTGTTATTTTGGGCTTACCGGGGCCCATTAGTTCCATTTTG
          1 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTG

                                                                *    *       
       1757 AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCGTAACCATAATCA
         66 AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA

            *                       
       1822 ATTTGGTGAGATTAGTCCACTGTG
        131 TTTTGGTGAGATTAGTCCACTGTG

              *               *                                          *   
       1846 AAATTTTTAGCTCATTTGCAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTG
          1 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTG

                *  *              *                  *                       
       1911 AATCTTCATCGATTTGGCAAACGTCAATGCTTTTCTTTCCACTGTTTATGGCCTAACTATAATCA
         66 AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA

                 * *             *  
       1976 TTTTGTTTAGATTAGTCCACTTTG
        131 TTTTGGTGAGATTAGTCCACTGTG

                  *    *                              *            *     * * 
       2000 AAGTTTATAGCACATTTGGAACACTTGTTATTTTGGGCCTATTGGGGCCCATTAGAGACGTATAG
          1 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTG

                           *       *                                 *     * 
       2065 AATCGTCTTCGATTTAGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACCATAATAA
         66 AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA

                                    
       2130 TTTTGGTGAGATTAGTCCACTGTG
        131 TTTTGGTGAGATTAGTCCACTGTG

                                      *           *   *   **             *   
       2154 AAGTTTTTAGCTCATTTGGAACACTTCTTATTTTGGGCTTATTGGGTTCCATTAGTGACGTATTG
          1 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTG

                           **  *               *    *  *                     
       2219 AATCGTCTTCGATTTATCAGACCTCAATGCTTTTCATTCCTTTTTTTATGGCCTAACTATAATCA
         66 AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA

                                   *
       2284 TTTTGGTGAGATTAGTCCACTGTA
        131 TTTTGGTGAGATTAGTCCACTGTG

                                            *           *           **       
       2308 AAGTTTTTAGCTCATTTGGAACACTTGTTATTCTGGGCCTATCGAGGCCCATTAGTTCCGTTTTG
          1 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTG

                           *                                   *             
       2373 AATCGTCTTCGATTTCGCAAACCTCAATGC-TTTCTTTCCATTGTTTATGGACTAACTATAATCA
         66 AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA

                                    
       2437 TTTTGGTGAGATTAGTCCACTGTG
        131 TTTTGGTGAGATTAGTCCACTGTG

                         *           *                    *           **     
       2461 ACA-TTTTTAGCTGATTTGGAACACATGTTATTTT-GGCCTATC-GAGCCCTATTAGTTCCGTTT
          1 A-AGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCC-ATTAGTGACGTTT

                             **    *                             **          
       2523 TGAATCGTCTTCGATTTACCAAATCTCAATGCTTTTCTTTCCATTGTTTATGGAATAACTATAAT
         64 TGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT

                                      
       2588 CATTTTGGTGAGATTAGTCCACTGTG
        129 CATTTTGGTGAGATTAGTCCACTGTG

                                                 
       2614 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
          1 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG

       2651 ACTGATACGA


Statistics
Matches: 2223,  Mismatches: 256, Indels: 35
        0.88            0.10        0.01

Matches are distributed among these distances:
 151    4  0.00
 152   51  0.02
 153  472  0.21
 154  1686  0.76
 155   10  0.00

ACGTcount: A:0.22, C:0.19, G:0.18, T:0.40


Consensus pattern (154 bp):   
AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTG
AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
TTTTGGTGAGATTAGTCCACTGTG

Found at i:3478 original size:21 final size:21

Alignment explanation


    Indices: 3454--3566  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

       3444 CTTAGGCATT

                         *       
       3454 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
       3475 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *          * 
       3496 TCCAATGAACTTGGAACCTGC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       3517 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                                  
       3538 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       3559 TCCAATGA
          1 TCCAATGA

       3567 ACTTCTAGCA


Statistics
Matches: 85,  Mismatches: 6, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  20    2  0.02
  21   83  0.98

ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Done.