Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006641.1 Corchorus capsularis cultivar CVL-1 contig06662, 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, 726

Length: 1210
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23


Found at i:280 original size:154 final size:153

Alignment explanation


    Indices: 1--1210  Score: 1694
    Period size: 154  Copynumber: 7.8  Consensus size: 153

                          *      *            * *       **                   
          1 ATGGACTAATCTCACCAAAATGATTATAGCTAGGTCGTAAACAATTGAAAGAAAAGCTTTGTTGG
          1 ATGGACTAATCTCATCAAAATAATTATAGCTAGGCCATAAACAAAGGAAAGAAAAGCTTTGTTGG

                    *    *     *  *                *                         
         66 TTGCAAATTGAAGCCGATTTAACACAGCACTAATGGGCCTCGAAAGGCCCGAAATAACAAGTGTT
         66 TTGCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTT

              *    *               
        131 CTAAATGTGCTAAAAACTTCACA
        131 CTGAATGAGCTAAAAACTTCACA

                                         *                     **            
        154 ATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGGTAAGCTTTG-TGG
          1 ATGGACTAATCTCATCAAAATAATTATAGCTAGGCCATAAACAAAGGAAAGAAAAGCTTTGTTGG

                                                                             
        218 TTTGGCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTG
         66 -TT-GCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTG

                                     
        283 TTCTGAATGAGCTAAAAACTTCACA
        129 TTCTGAATGAGCTAAAAACTTCACA

                          *       *            * *       **                  
        308 ATGGACTAATCTCACCAAAATCGATTATAGCTAGGTCGTAAACAATTGAAAGAAAAGCTTTGTTG
          1 ATGGACTAATCTCATCAAAAT-AATTATAGCTAGGCCATAAACAAAGGAAAGAAAAGCTTTGTTG

                     *    *     *  *                *                        
        373 GTTGCAAATTGAAGCCGATTTAACACAGCACTAATGGGCCTCGAAAGGCCCGAAATAACAAGTGT
         65 GTTGCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGT

                                    
        438 TCTGAATGAGCTAAAAACTTCACA
        130 TCTGAATGAGCTAAAAACTTCACA

                                         * **                                
        462 ATGGACTAATCTCATCAAAATAATTATAGTTCTGCCAATAAACAAAGGAAAGAATAAGTCTTTGT
          1 ATGGACTAATCTCATCAAAATAATTATAGCTAGGCC-ATAAACAAAGGAAAGAA-AAG-CTTTGT

                                                                             
        527 TGGTTTGACCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACA
         63 TGG-TTG--CAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACA

                         *               
        592 AGTGTTCTGAATGTGCTAAAAACTTCACA
        125 AGTGTTCTGAATGAGCTAAAAACTTCACA

                                         *       *                           
        621 ATGGACTAATCTCATCAAAATAATTATAGTTAGGCCAGAAACAATAGG-AAGAAAAGCTTTG-TG
          1 ATGGACTAATCTCATCAAAATAATTATAGCTAGGCCATAAACAA-AGGAAAGAAAAGCTTTGTTG

                                                                             
        684 GTTTGGCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGT
         65 G-TT-GCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGT

                 *                      
        749 GTTCTAAATGTAGCTAAAAAACTTCACA
        128 GTTCTGAATG-AGCT-AAAAACTTCACA

                                         *       *                           
        777 ATGGACTAATCTCATCAAAATAATTATAGTTAGGCCAGAAACAATAGG-AAGAAAAGCTTTG-TG
          1 ATGGACTAATCTCATCAAAATAATTATAGCTAGGCCATAAACAA-AGGAAAGAAAAGCTTTGTTG

                                                                             
        840 GTTTGGCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGT
         65 G-TT-GCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGT

                                      
        905 GTTCTGAATGAGCTAAAAACTTCACA
        128 GTTCTGAATGAGCTAAAAACTTCACA

                          *      *            * *       **          *        
        931 ATGGACTAATCTCACCAAAATGATTATAGCTAGGTCGTAAACAATTGAAAGAAAAGTTTTGTTGG
          1 ATGGACTAATCTCATCAAAATAATTATAGCTAGGCCATAAACAAAGGAAAGAAAAGCTTTGTTGG

                    *    *     *  *                *                         
        996 TTGCAAATTGAAGCCGATTTAACACAGCACTAATGGGCCTCGAAAGGCCCGAAATAACAAGTGTT
         66 TTGCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTT

                                   
       1061 CTGAATGAGCTAAAAACTTCACA
        131 CTGAATGAGCTAAAAACTTCACA

                            *    *              *       **          *        
       1084 ATGGACTAATCTCA-CCAAATGATTATAGCTAGGCCGTAAACAATTGAAAGAAAAGTTTTGTTGG
          1 ATGGACTAATCTCATCAAAATAATTATAGCTAGGCCATAAACAAAGGAAAGAAAAGCTTTGTTGG

                    *    *     *  *                *                       
       1148 TTGCAAATTGAAGCCGATTTAACACAGCACTAATGGGCCTCGAAAGGCCCGAAATAACAAGTG
         66 TTGCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTG


Statistics
Matches: 974,  Mismatches: 67, Indels: 33
        0.91            0.06        0.03

Matches are distributed among these distances:
 152  114  0.12
 153  160  0.16
 154  346  0.36
 155   53  0.05
 156  167  0.17
 157    6  0.01
 158   12  0.01
 159  116  0.12

ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23


Consensus pattern (153 bp):   
ATGGACTAATCTCATCAAAATAATTATAGCTAGGCCATAAACAAAGGAAAGAAAAGCTTTGTTGG
TTGCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTT
CTGAATGAGCTAAAAACTTCACA
Done.