Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014433.1 Corchorus olitorius cultivar O-4 contig14466, 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: 4682
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:853 original size:44 final size:43

Alignment explanation


    Indices: 777--862  Score: 102
    Period size: 44  Copynumber: 2.0  Consensus size: 43

        767 ATCTCCGTTG

                *            *         *                
        777 ATATTTGTTATACATCCTTCATGCATGGTCCATGT-CTTTGTAT
          1 ATATATGTTATACATCCATCATGCATGATCCAT-TCCTTTGTAT

                            *          *               
        820 ATATATGTTCATACATTCATCATGCATTATCCATTCCTTTGTA
          1 ATATATGTT-ATACATCCATCATGCATGATCCATTCCTTTGTA

        863 CATAGGTTCA


Statistics
Matches: 36,  Mismatches: 5, Indels: 3
        0.82            0.11        0.07

Matches are distributed among these distances:
  43    9  0.25
  44   27  0.75

ACGTcount: A:0.24, C:0.20, G:0.10, T:0.45


Consensus pattern (43 bp):   
ATATATGTTATACATCCATCATGCATGATCCATTCCTTTGTAT

Found at i:3098 original size:33 final size:33

Alignment explanation


    Indices: 3056--3122  Score: 125
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       3046 TTTGTGAGTT

                                         *   
       3056 CAAGATCAAAATTCGCTTTTCAAAACAAGTTTG
          1 CAAGATCAAAATTCGCTTTTCAAAACAAGATTG

                                             
       3089 CAAGATCAAAATTCGCTTTTCAAAACAAGATTG
          1 CAAGATCAAAATTCGCTTTTCAAAACAAGATTG

             
       3122 C
          1 C

       3123 TTTCCATTTG


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  33   33  1.00

ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28


Consensus pattern (33 bp):   
CAAGATCAAAATTCGCTTTTCAAAACAAGATTG

Found at i:3149 original size:48 final size:48

Alignment explanation


    Indices: 3091--3184  Score: 136
    Period size: 48  Copynumber: 2.0  Consensus size: 48

       3081 CAAGTTTGCA

                                                     *       
       3091 AGATCAAAATTCGCTTTTCAAAACAAGATTGC-TTTCCATTTGTGAGCC
          1 AGATCAAAATTCGCTTTTCAAAACAAGATTGCATTT-CATTCGTGAGCC

                *                 **                      
       3139 AGATTAAAATTCGCTTTTCAAAGTAAGATTGCATTTCATTCGTGAG
          1 AGATCAAAATTCGCTTTTCAAAACAAGATTGCATTTCATTCGTGAG

       3185 TCTAAGATCA


Statistics
Matches: 41,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  48   38  0.93
  49    3  0.07

ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35


Consensus pattern (48 bp):   
AGATCAAAATTCGCTTTTCAAAACAAGATTGCATTTCATTCGTGAGCC

Found at i:3770 original size:35 final size:34

Alignment explanation


    Indices: 3724--3958  Score: 346
    Period size: 35  Copynumber: 6.7  Consensus size: 34

       3714 CATTTACCAA

                                               
       3724 AGATGACTCGGTGTAGCATCTTCAAAGTTATACTC
          1 AGATGACTCGGTGTAGCATCTTCAAAGTTA-ACTC

                                               
       3759 AGATGACTCGGTGTAGCATCTTCAAAGTTATACTC
          1 AGATGACTCGGTGTAGCATCTTCAAAGTTA-ACTC

                                         *   * 
       3794 AGATGACTCGGTGTAGCATCTTCAAAGATGAACCC
          1 AGATGACTCGGTGTAGCATCTTCAAAG-TTAACTC

                                      *         
       3829 AGATGACTCGGTGTAGCATCTTCAAAATTGAA-TCC
          1 AGATGACTCGGTGTAGCATCTTCAAAGTT-AACT-C

                                      *        
       3864 AGATGACTCGGTGTAGCATCTTCAAAATTGAACTC
          1 AGATGACTCGGTGTAGCATCTTCAAAGTT-AACTC

                                         *  *  
       3899 AGATGACTCGGTGTAGCATCTTCAAAGATGAATTC
          1 AGATGACTCGGTGTAGCATCTTCAAAG-TTAACTC

                                     
       3934 AGATGACTCGGTGTAGCATCTTCAA
          1 AGATGACTCGGTGTAGCATCTTCAA

       3959 TATGGACTCA


Statistics
Matches: 187,  Mismatches: 8, Indels: 10
        0.91            0.04        0.05

Matches are distributed among these distances:
  34    1  0.01
  35  182  0.97
  36    4  0.02

ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29


Consensus pattern (34 bp):   
AGATGACTCGGTGTAGCATCTTCAAAGTTAACTC

Found at i:3906 original size:105 final size:105

Alignment explanation


    Indices: 3724--3958  Score: 386
    Period size: 105  Copynumber: 2.2  Consensus size: 105

       3714 CATTTACCAA

                                      *                                  *   
       3724 AGATGACTCGGTGTAGCATCTTCAAAGTTATACTCAGATGACTCGGTGTAGCATCTTCAAAGTTA
          1 AGATGACTCGGTGTAGCATCTTCAAAATTATACTCAGATGACTCGGTGTAGCATCTTCAAAATTA

                                                    
       3789 TACTCAGATGACTCGGTGTAGCATCTTCAAAGATGAACCC
         66 TACTCAGATGACTCGGTGTAGCATCTTCAAAGATGAACCC

                                                                             
       3829 AGATGACTCGGTGTAGCATCTTCAAAATTGA-A-TCCAGATGACTCGGTGTAGCATCTTCAAAAT
          1 AGATGACTCGGTGTAGCATCTTCAAAATT-ATACT-CAGATGACTCGGTGTAGCATCTTCAAAAT

                                                    ** 
       3892 TGA-ACTCAGATGACTCGGTGTAGCATCTTCAAAGATGAATTC
         64 T-ATACTCAGATGACTCGGTGTAGCATCTTCAAAGATGAACCC

                                     
       3934 AGATGACTCGGTGTAGCATCTTCAA
          1 AGATGACTCGGTGTAGCATCTTCAA

       3959 TATGGACTCA


Statistics
Matches: 123,  Mismatches: 4, Indels: 6
        0.92            0.03        0.05

Matches are distributed among these distances:
 104    1  0.01
 105  120  0.98
 106    2  0.02

ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29


Consensus pattern (105 bp):   
AGATGACTCGGTGTAGCATCTTCAAAATTATACTCAGATGACTCGGTGTAGCATCTTCAAAATTA
TACTCAGATGACTCGGTGTAGCATCTTCAAAGATGAACCC
Done.