Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006243.1 Corchorus capsularis cultivar CVL-1 contig06262, 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, 871

Length: 1452
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40


Found at i:1375 original size:155 final size:154

Alignment explanation


    Indices: 1--1452  Score: 1933
    Period size: 154  Copynumber: 9.3  Consensus size: 154

                  *     *     *  *   *  *          *       *                *
          1 AGTGCTATTTTGAATCGTATTTGATTTGGCAAACCACAATGCTTTTCCTTCCATTGTTTATGGCC
          1 AGTGCTGTTTTGTATCGTCTTCGATATGACAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCA

               *      *      *             *                                 
         66 TAAATATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTT
         66 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCAGAACACTTGTT

                           *         
        131 ATTTCAGGCCGTTTCAGGGCGCATT
        131 ATTTCAGGCC-TTTCGGGGCGCATT

             *                                 *                             
        156 ACTGCTGTTTTGTATCGTCTTCGATATGACAAACCGCAAAGCTTTTCTTTCCATTGTTTATGGCA
          1 AGTGCTGTTTTGTATCGTCTTCGATATGACAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCA

                                                                             
        221 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACGTTTTTAGCTCATTCAGAACACTTGT
         66 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA-GTTTTTAGCTCATTCAGAACACTTGT

                                       
        286 TATTTTCAGGCCTTTCGGGGTCGCATT
        130 TA-TTTCAGGCCTTTCGGGG-CGCATT

                                                *                            
        313 AGTGCTGTTTTGTATCGTCTTCGTATATGACAAACCGCAAAGCTTTTCTTTCCTATTGTTTATGG
          1 AGTGCTGTTTTGTATCGTCTTCG-ATATGACAAACCACAAAGCTTTTCTTTCC-ATTGTTTATGG

                                                                             
        378 CATAACTATAATCATTTTGGTTGAGATTAGTCCACTGTGAAGTTTTTAGTCTCATTCTAGAACAC
         64 CATAACTATAATCATTTTGG-TGAGATTAGTCCACTGTGAAGTTTTTAG-CTCATTC-AGAACAC

                        *                   
        443 TTGTTATTTCTAAGCCTTTCGGGGTCGGCATT
        126 TTGTTATTTC-AGGCCTTTCGGGG-C-GCATT

                                                                             
        475 AGTGCTGTTTTGTTATCGTCTTCGTATATGACAAACCGACAAAGACTTTTCTTTCCATTGTTTAT
          1 AGTGCTGTTTTG-TATCGTCTTCG-ATATGACAAACC-ACAAAG-CTTTTCTTTCCATTGTTTAT

                                                                             
        540 GGCATAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCAGAACACT
         62 GGCATAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCAGAACACT

                              *       * 
        605 TGTTATTTCAGGCCTTTCAGGGCGCAGT
        127 TGTTATTTCAGGCCTTTCGGGGCGCATT

                                             *                               
        633 AGTGCTGTTTTGTATCGTCTTCGATATGACAAATCACAAAGCTTTTCTTTCCATTGTTTATGGCA
          1 AGTGCTGTTTTGTATCGTCTTCGATATGACAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCA

                                                                       *     
        698 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCAGAACATTTGTT
         66 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCAGAACACTTGTT

                *   *               
        763 ATTTTAGGTCTTTCGGGGCGCATT
        131 ATTTCAGGCCTTTCGGGGCGCATT

                                               *                            *
        787 AGTGCTGTTTTGTATCGTCTTCGATATGACAAACCGCAAAGCTTTTCTTTCCATTGTTTATGGCT
          1 AGTGCTGTTTTGTATCGTCTTCGATATGACAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCA

                      *      *             *                 *               
        852 TAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCTTTCAGAACACTTGTT
         66 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCAGAACACTTGTT

                                * *  
        917 ATTTCAGGTCCTTTCGGGGCCCTTT
        131 ATTTCAGG-CCTTTCGGGGCGCATT

                     *   *    *          *             *          *        * 
        942 AGTGTCTGTATTGAATCGGCTTTCGAT-TTAGCAAACCACAAATCTTTTCTTTCAATTGTTTACG
          1 AGTG-CTGTTTTGTATCGTC-TTCGATATGA-CAAACCACAAAGCTTTTCTTTCCATTGTTTATG

              *                          * *                            *    
       1006 GCCTAACTATAATCATTTTGGTGAGATTATTACACTGTGAAGTTTTTAGCTCATTCAGAATACTT
         63 GCATAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCAGAACACTT

                    *             *     
       1071 GTTATTTCGGGCCTTTCGGGGCCCACTT
        128 GTTATTTCAGGCCTTTCGGGGCGCA-TT

                *       *            *  *                       *        * * 
       1099 AGTGTTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCTAATTGTTTACGAC
          1 AGTGCTGTTTTGTATCGTCTTCGATATGACAAACCACAAAGCTTTTCTTTC-CATTGTTTATGGC

            *                            *                                   
       1164 CTAACTATAATCATTTTGGTGAGATTAGTACACTGTGAAGTTTTTAGCTCATTCAGAACACTTGT
         65 ATAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCAGAACACTTGT

                  *         *   *  * 
       1229 TATTTCGGGCCTTTCGAGGCCCAAT
        130 TATTTCAGGCCTTTCGGGGCGCATT

                       **          *  *  *                       *        *  
       1254 AGTGCTGTTTTAAATCAG-CTTCAATTTGGC-AACCAACAAAGCTTTTCTTTCAATTGTTTACGA
          1 AGTGCTGTTTTGTATC-GTCTTCGATATGACAAACC-ACAAAGCTTTTCTTTCCATTGTTTATG-

                 *                *           *              *               
       1317 GC-TACCTATAATCATTTTGGTAAGATTAGTCCATTCGTGAAGTTTTTAACTCATTCAGAACACT
         63 GCATAACTATAATCATTTTGGTGAGATTAGTCCACT-GTGAAGTTTTTAGCTCATTCAGAACACT

            *                       * *  
       1381 AGTTTATTTCAGGCCTTTCGGGGCCCTTT
        127 TG-TTATTTCAGGCCTTTCGGGGCGCATT

                    *         *       *  *              
       1410 AGTGCTGTATTG-AGTCGGCTTCGATTTGGCAAACCACAAAGCT
          1 AGTGCTGTTTTGTA-TCGTCTTCGATATGACAAACCACAAAGCT


Statistics
Matches: 1183,  Mismatches: 86, Indels: 55
        0.89            0.06        0.04

Matches are distributed among these distances:
 154  281  0.24
 155  211  0.18
 156  237  0.20
 157  160  0.14
 158   45  0.04
 159   40  0.03
 160   42  0.04
 161   44  0.04
 162   24  0.02
 163   52  0.04
 164   36  0.03
 165   11  0.01

ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40


Consensus pattern (154 bp):   
AGTGCTGTTTTGTATCGTCTTCGATATGACAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCA
TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCAGAACACTTGTT
ATTTCAGGCCTTTCGGGGCGCATT
Done.