Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007080.1 Corchorus capsularis cultivar CVL-1 contig07101, 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: 3598
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36


Found at i:976 original size:27 final size:27

Alignment explanation


    Indices: 911--1004  Score: 152
    Period size: 27  Copynumber: 3.4  Consensus size: 27

        901 TGCTTCTTAC

                                          
        911 TGATTCTGCTTTGTTTTCATGCTGGACACT
          1 TGATT-TGC-TTGTTTTCATGCTGGA-ACT

                            *          
        941 TGATTTGCTTGTTTTCGTGCTGGAACT
          1 TGATTTGCTTGTTTTCATGCTGGAACT

                                       
        968 TGATTTGCTTGTTTTCATGCTGGAACT
          1 TGATTTGCTTGTTTTCATGCTGGAACT

                      
        995 TGATTTGCTT
          1 TGATTTGCTT

       1005 CGATTCCATG


Statistics
Matches: 62,  Mismatches: 2, Indels: 3
        0.93            0.03        0.04

Matches are distributed among these distances:
  27   39  0.63
  28   15  0.24
  29    3  0.05
  30    5  0.08

ACGTcount: A:0.13, C:0.16, G:0.22, T:0.49


Consensus pattern (27 bp):   
TGATTTGCTTGTTTTCATGCTGGAACT

Found at i:1017 original size:55 final size:57

Alignment explanation


    Indices: 911--1017  Score: 157
    Period size: 55  Copynumber: 1.9  Consensus size: 57

        901 TGCTTCTTAC

                                                     *  * *          
        911 TGATTCTGCTTTGTTTTCATGCTGGACACTTGATTTGCTTGTTTTCGTGCTGGAACT
          1 TGATTCTGCTTTGTTTTCATGCTGGACACTTGATTTGCTTGATTCCATGCTGGAACT

                                                                 
        968 TGATT-TGC-TTGTTTTCATGCTGGA-ACTTGATTTGCTTCGATTCCATGCTG
          1 TGATTCTGCTTTGTTTTCATGCTGGACACTTGATTTGCTT-GATTCCATGCTG

       1018 AATTGACCTC


Statistics
Matches: 46,  Mismatches: 3, Indels: 4
        0.87            0.06        0.08

Matches are distributed among these distances:
  54   13  0.28
  55   25  0.54
  56    3  0.07
  57    5  0.11

ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47


Consensus pattern (57 bp):   
TGATTCTGCTTTGTTTTCATGCTGGACACTTGATTTGCTTGATTCCATGCTGGAACT

Found at i:3271 original size:204 final size:205

Alignment explanation


    Indices: 2891--3296  Score: 672
    Period size: 204  Copynumber: 2.0  Consensus size: 205

       2881 GCCCTAGTTA

                 *            *                                            * 
       2891 TCTAATGATCCTTCTTCTTTTAATTTGGCTATCCATCCATAAAGAATGGGGATGCCCTACTAGTC
          1 TCTAACGATCCTTCTTCTCTTAATTTGGCTATCCATCCATAAAGAATGGGGATGCCCTACTAGCC

                   *                    *                                    
       2956 CAAAAGCTCAAGGGCAAGTAACTTGTTGTGGTAAGCTGGGTCACCATTATCAATATGTTTAAACC
         66 CAAAAGCCCAAGGGCAAGTAACTTGTTGGGGTAAGCTGGGTCACCATTATCAATATGTTTAAACC

                         *                                        *          
       3021 ATACAATACATGTTATTTTTTTGCACTCTATAGACGACAAGATGATTTTATTAGCTACTAAAAGT
        131 ATACAATACATGTAATTTTTTTGCACTCTATAGACGACAAGATGATTTTATTAGATACTAAAAGT

                      
       3086 AAAAGTATTC
        196 AAAAGTATTC

                                                     *                       
       3096 TCTAACGA-CCTTCTTCTCTTAATTTGGCTATCCATCCATAGAGAATGGGGATGCCCTACTAGCC
          1 TCTAACGATCCTTCTTCTCTTAATTTGGCTATCCATCCATAAAGAATGGGGATGCCCTACTAGCC

               **                                                         *  
       3160 CAACTGCCCAAGGGCAAGTAACTTGTTGGGGTAAGCTGGGTCACCATTATCAATATGTTTAAGCC
         66 CAAAAGCCCAAGGGCAAGTAACTTGTTGGGGTAAGCTGGGTCACCATTATCAATATGTTTAAACC

                                               *    *                        
       3225 ATACAATACATGTCAATTTTTTTGCACTCTA-AGATGACATGATGATTTTATTAGATACTAAAAG
        131 ATACAATACATGT-AATTTTTTTGCACTCTATAGACGACAAGATGATTTTATTAGATACTAAAAG

                    
       3289 TAAAAGTA
        195 TAAAAGTA

       3297 CAAGAAGAGT


Statistics
Matches: 187,  Mismatches: 13, Indels: 3
        0.92            0.06        0.01

Matches are distributed among these distances:
 204  164  0.88
 205   23  0.12

ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33


Consensus pattern (205 bp):   
TCTAACGATCCTTCTTCTCTTAATTTGGCTATCCATCCATAAAGAATGGGGATGCCCTACTAGCC
CAAAAGCCCAAGGGCAAGTAACTTGTTGGGGTAAGCTGGGTCACCATTATCAATATGTTTAAACC
ATACAATACATGTAATTTTTTTGCACTCTATAGACGACAAGATGATTTTATTAGATACTAAAAGT
AAAAGTATTC
Done.