Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006654.1 Corchorus capsularis cultivar CVL-1 contig06675, 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, 767

Length: 1279
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23


Found at i:355 original size:155 final size:155

Alignment explanation


    Indices: 8--1279  Score: 1787
    Period size: 154  Copynumber: 8.2  Consensus size: 155

          1 ATGAGTT

                   *   *         *   *      *          *                     
          8 AAAACTTGACAGTGGACTAATATCACCAAAATGATTATAGTTATGCCATAAACAATGGAAAGAAA
          1 AAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAA

                                          *                 *        *       
         73 AG-TATTGTGGTTTGCCAAATCGAATACGAGTCAAAATAGCACTAATGGGCCCCGAATGGCCCGA
         66 AGCTATTGTGGTTTGCCAAATCGAATACGATTCAAAATAGCACTAATGCGCCCCGAAAGGCCCGA

                           *         
        137 AATAACAAGTGTTCTAAATGAGCTA
        131 AATAACAAGTGTTCTGAATGAGCTA

              *                    *               *                         
        162 AAGACTTCACAATGGACTAATCTTATCAAAATAAATTATTGTTAGGCCATAAACAATGGAAAGAA
          1 AAAACTTCACAATGGACTAATCTCATCAAAAT-AATTATAGTTAGGCCATAAACAATGGAAAGAA

                     *      *  *      *     *     *                          
        227 AAGCT-TTGCGGTTTGTCATATCGAAGACGATACAAAACAGCACTAATGCGCCCCGAAAGGCCCG
         65 AAGCTATTGTGGTTTGCCAAATCGAATACGATTCAAAATAGCACTAATGCGCCCCGAAAGGCCCG

                                       
        291 AAATAACAAGTGTTCTGAATGAGCTAA
        130 AAATAACAAGTGTTCTGAATGAGCT-A

                       *             *      *        * *                     
        318 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTAATGCCATAAACAATGGAAAGAAA
          1 AAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAA

                    *      *  *      *     *      *               *        * 
        383 AGCT-TTGCGGTTTGTCATATCGAAGACGATACAAAACAAGCACTAATGCGCCCTGAAAGGCCTG
         66 AGCTATTGTGGTTTGCCAAATCGAATACGATTCAAAA-TAGCACTAATGCGCCCCGAAAGGCCCG

                                   *  
        447 AAATAACAAGTGTTCTGAATGAGGTA
        130 AAATAACAAGTGTTCTGAATGAGCTA

                                     *                   *                   
        473 AAAACTTCACAATGGACTAATCTCAACAAAATAATTATAGTTAGGACATAAACAATGGAAAG-AA
          1 AAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAA

                                                            *                
        537 AG-TATTGTGGTTTGCCAAATCGAATACGATTCAAAATAGCACTAATGGGCCCCCGAAAGGCCCG
         66 AGCTATTGTGGTTTGCCAAATCGAATACGATTCAAAATAGCACTAATGCG-CCCCGAAAGGCCCG

                                       
        601 AAATAACAAGTGTTCTGAATGAGCTAA
        130 AAATAACAAGTGTTCTGAATGAGCT-A

                       *         **  *      *          *                     
        628 AAAAC-TCACAGTGGACTAATAACACCAAAATGATTATAGTTATGCCATAAACAATGGAAAGAAA
          1 AAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAA

                                                            *        *       
        692 AG-TATTGTGGTTTGCCAAATCGAATACGATTCAAAATAGCACTAATGGGCCCCGAATGGCCCGA
         66 AGCTATTGTGGTTTGCCAAATCGAATACGATTCAAAATAGCACTAATGCGCCCCGAAAGGCCCGA

                           *         
        756 AATAACAAGTGTTCTAAATGAGCTA
        131 AATAACAAGTGTTCTGAATGAGCTA

              *                                                              
        781 AAGACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAA
          1 AAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAA

                    **     *  *      *     *                                 
        846 AGCT-TTGCCGTTTGTCATATCGAAGACGATACAAAA-ATGCACTAATGCGCCCCGAAAGGCCCG
         66 AGCTATTGTGGTTTGCCAAATCGAATACGATTCAAAATA-GCACTAATGCGCCCCGAAAGGCCCG

                                     *
        909 AAATAACAAGTGTTCTGAATGAG-TT
        130 AAATAACAAGTGTTCTGAATGAGCTA

                                                                  *          
        934 AAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACATTGGAAAGAAA
          1 AAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAA

                                  *                         *                
        999 AGC-ATTGTGGTTTGCCAAATCAAATACGATTCAAAATAGCACTAATGGGCCCCGAAAGGCCCGA
         66 AGCTATTGTGGTTTGCCAAATCGAATACGATTCAAAATAGCACTAATGCGCCCCGAAAGGCCCGA

                                      
       1063 AATAACAAGT-TCTCTGAATGAGCTA
        131 AATAACAAGTGT-TCTGAATGAGCTA

                                          *   *          *          *        
       1088 AAAACTTCACAATGGACTAATCTCATCAAATTAACTATAGTTAGGACATAAACAATAGAAAGAAA
          1 AAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAA

              *                                  *                        *  
       1153 A-TTATTGTGGTTTGCCAAATCGAATACGATTCAAAACAGCACTAATGCGCCCCGAAAGGCCTGA
         66 AGCTATTGTGGTTTGCCAAATCGAATACGATTCAAAATAGCACTAATGCGCCCCGAAAGGCCCGA

                                     
       1217 AATAACAAGTGTTCTGAATGAGCTA
        131 AATAACAAGTGTTCTGAATGAGCTA

                       *      *      *      *     
       1242 AAAACTTCACAGTGGACTGATCTCAACAAAATGATTAT
          1 AAAACTTCACAATGGACTAATCTCATCAAAATAATTAT


Statistics
Matches: 1001,  Mismatches: 100, Indels: 34
        0.88            0.09        0.03

Matches are distributed among these distances:
 152    1  0.00
 153  155  0.15
 154  480  0.48
 155  287  0.29
 156   78  0.08

ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23


Consensus pattern (155 bp):   
AAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAA
AGCTATTGTGGTTTGCCAAATCGAATACGATTCAAAATAGCACTAATGCGCCCCGAAAGGCCCGA
AATAACAAGTGTTCTGAATGAGCTA

Found at i:1085 original size:307 final size:309

Alignment explanation


    Indices: 8--1279  Score: 1905
    Period size: 307  Copynumber: 4.1  Consensus size: 309

          1 ATGAGTT

                   *             *                                           
          8 AAAACTTGACAGTGGACTAATATCACCAAAATGATTATAGTTATGCCATAAACAATGGAAAGAAA
          1 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTATGCCATAAACAATGGAAAGAAA

              *                          *                          *        
         73 AGTATTGTGGTTTGCCAAATCGAATACGAGTCAAAATAGCACTAATGGGCCCCGAATGGCCCGAA
         66 AGCATTGTGGTTTGCCAAATCGAATACGATTCAAAATAGCACTAATGGGCCCCGAAAGGCCCGAA

                                      *                    *               * 
        138 ATAACAAGTGTTCTAAATGAGCTAAAGACTTCACAATGGACTAATCTTATCAAAATAAATTATTG
        131 ATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAAT-AATTATAG

                 *                                  *  *                     
        203 TTAGGCCATAAACAATGGAAAGAAAAGCT-TTGCGGTTTGTCATATCGAAGACGATACAAAACAG
        195 TTAGGACATAAACAATGGAAAGAAAAGCTATTGCGGTTTGCCAAATCGAAGACGATACAAAACAG

                                                               
        267 CACTAATGCGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAA
        260 CACTAATGCGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCT-A

                                                     *                       
        318 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTAATGCCATAAACAATGGAAAGAAA
          1 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTATGCCATAAACAATGGAAAGAAA

               *   *      *  *      *     *      *          *    *        *  
        383 AGCTTTGCGGTTTGTCATATCGAAGACGATACAAAACAAGCACTAATGCGCCCTGAAAGGCCTGA
         66 AGCATTGTGGTTTGCCAAATCGAATACGATTCAAAA-TAGCACTAATGGGCCCCGAAAGGCCCGA

                           *      *                           *              
        448 AATAACAAGTGTTCTGAATGAGGTAAAAACTTCACAATGGACTAATCTCAACAAAATAATTATAG
        130 AATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAG

                                             *                *     *     *  
        513 TTAGGACATAAACAATGGAAAG-AAAG-TATTGTGGTTTGCCAAATCGAATACGATTCAAAATAG
        195 TTAGGACATAAACAATGGAAAGAAAAGCTATTGCGGTTTGCCAAATCGAAGACGATACAAAACAG

                    *                                           
        576 CACTAATGGGCCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAA
        260 CACTAATGCG-CCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCT-A

                                 **                                          
        628 AAAAC-TCACAGTGGACTAATAACACCAAAATGATTATAGTTATGCCATAAACAATGGAAAGAAA
          1 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTATGCCATAAACAATGGAAAGAAA

              *                                                     *        
        692 AGTATTGTGGTTTGCCAAATCGAATACGATTCAAAATAGCACTAATGGGCCCCGAATGGCCCGAA
         66 AGCATTGTGGTTTGCCAAATCGAATACGATTCAAAATAGCACTAATGGGCCCCGAAAGGCCCGAA

                                      *                                      
        757 ATAACAAGTGTTCTAAATGAGCTAAAGACTTCACAATGGACTAATCTCATCAAAATAATTATAGT
        131 ATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGT

                *                            *     *  *                      
        822 TAGGCCATAAACAATGGAAAGAAAAGCT-TTGCCGTTTGTCATATCGAAGACGATACAAAA-ATG
        196 TAGGACATAAACAATGGAAAGAAAAGCTATTGCGGTTTGCCAAATCGAAGACGATACAAAACA-G

                                                             *
        885 CACTAATGCGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAG-TT
        260 CACTAATGCGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTA

                       *             *      *          *          *          
        934 AAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACATTGGAAAGAAA
          1 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTATGCCATAAACAATGGAAAGAAA

                                 *                                           
        999 AGCATTGTGGTTTGCCAAATCAAATACGATTCAAAATAGCACTAATGGGCCCCGAAAGGCCCGAA
         66 AGCATTGTGGTTTGCCAAATCGAATACGATTCAAAATAGCACTAATGGGCCCCGAAAGGCCCGAA

                           *                                       *   *     
       1064 ATAACAAGT-TCTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAATTAACTATAG
        131 ATAACAAGTGT-TCTAAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAG

                            *          *     *                *     *        
       1128 TTAGGACATAAACAATAGAAAGAAAA-TTATTGTGGTTTGCCAAATCGAATACGATTCAAAACAG
        195 TTAGGACATAAACAATGGAAAGAAAAGCTATTGCGGTTTGCCAAATCGAAGACGATACAAAACAG

                                  *                           
       1192 CACTAATGCGCCCCGAAAGGCCTGAAATAACAAGTGTTCTGAATGAGCTA
        260 CACTAATGCGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTA

                              *      *            
       1242 AAAACTTCACAGTGGACTGATCTCAACAAAATGATTAT
          1 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT


Statistics
Matches: 864,  Mismatches: 87, Indels: 24
        0.89            0.09        0.02

Matches are distributed among these distances:
 306    7  0.01
 307  270  0.31
 308  180  0.21
 309  167  0.19
 310  165  0.19
 311   75  0.09

ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23


Consensus pattern (309 bp):   
AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTATGCCATAAACAATGGAAAGAAA
AGCATTGTGGTTTGCCAAATCGAATACGATTCAAAATAGCACTAATGGGCCCCGAAAGGCCCGAA
ATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGT
TAGGACATAAACAATGGAAAGAAAAGCTATTGCGGTTTGCCAAATCGAAGACGATACAAAACAGC
ACTAATGCGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTA
Done.