Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007541.1 Corchorus olitorius cultivar O-4 contig07566, 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, 991

Length: 1652
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32


Found at i:808 original size:35 final size:35

Alignment explanation


    Indices: 707--811  Score: 122
    Period size: 35  Copynumber: 3.0  Consensus size: 35

        697 TCCAGTGCGG

                 *            * *   *      *   
        707 TCATTCCAAGAAGTTTTTAATGATTAGAGTTAATC
          1 TCATTTCAAGAAGTTTTTGAGGATCAGAGTTGATC

              *                                 
        742 TCGTTTCAAGAAGTTTTTGATGG-TCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTTGA-GGATCAGAGTTGATC

                  *          *                 
        777 TCATTTTAAGAAGTTTTCGAGGATCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTTGAGGATCAGAGTTGATC

        812 CCAGATGATC


Statistics
Matches: 59,  Mismatches: 9, Indels: 4
        0.82            0.12        0.06

Matches are distributed among these distances:
  34    2  0.03
  35   56  0.95
  36    1  0.02

ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39


Consensus pattern (35 bp):   
TCATTTCAAGAAGTTTTTGAGGATCAGAGTTGATC

Found at i:889 original size:87 final size:88

Alignment explanation


    Indices: 739--898  Score: 250
    Period size: 87  Copynumber: 1.8  Consensus size: 88

        729 ATTAGAGTTA

                 *              *    *                  *                    
        739 ATCTCGTTTCAAGAAGTTTTTGATGGTCAGAGTTGATCTCATTTTAAGAAGTTTTCGAGGATCAG
          1 ATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGAGGATCAG

                                   
        804 AGTTGATCCCAGATGATCTAGTG
         66 AGTTGATCCCAGATGATCTAGTG

                                                                   ** *      
        827 ATCTCATTTCAAGAAG-TTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAG
          1 ATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGAGGATCAG

                    
        891 AGTTGATC
         66 AGTTGATC

        899 TCATTTCAAG


Statistics
Matches: 65,  Mismatches: 7, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
  87   50  0.77
  88   15  0.23

ACGTcount: A:0.28, C:0.14, G:0.21, T:0.38


Consensus pattern (88 bp):   
ATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGAGGATCAG
AGTTGATCCCAGATGATCTAGTG

Found at i:894 original size:35 final size:35

Alignment explanation


    Indices: 825--1123  Score: 462
    Period size: 35  Copynumber: 8.6  Consensus size: 35

        815 GATGATCTAG

                                  *            
        825 TGATCTCATTTCAAGAAG-TTTCGATGATCAGAGT
          1 TGATCTCATTTCAAGAAGTTTTTGATGATCAGAGT

                                   *           
        859 TGATCTCATTTCAAGAAGTTTTTTATGATCAGAGT
          1 TGATCTCATTTCAAGAAGTTTTTGATGATCAGAGT

                                               
        894 TGATCTCATTTCAAGAAGTTTTT-ATGATCAGAGT
          1 TGATCTCATTTCAAGAAGTTTTTGATGATCAGAGT

                                               
        928 TGATCTCATTTCAAGAAGTTTTT-ATGATCAGAGT
          1 TGATCTCATTTCAAGAAGTTTTTGATGATCAGAGT

                   *               *            
        962 TGATCTCCTTTCAAGAAAG-TTTCGATGATCAGAGT
          1 TGATCTCATTTCAAG-AAGTTTTTGATGATCAGAGT

                   *              * *          
        997 TGATCTCGTTTCAAGAAGTTTTCGGTGATCAGAGT
          1 TGATCTCATTTCAAGAAGTTTTTGATGATCAGAGT

                   *                           
       1032 TGATCTCCTTTCAAGAAGTTTTTGATGATCAGAGT
          1 TGATCTCATTTCAAGAAGTTTTTGATGATCAGAGT

                 *     *                       
       1067 TGATCACATTTTAAGAAGTTTTTGATGATCAGAGT
          1 TGATCTCATTTCAAGAAGTTTTTGATGATCAGAGT

                 *                
       1102 TGATCGCATTTCAAGAAGTTTT
          1 TGATCTCATTTCAAGAAGTTTT

       1124 AATGAGTTGA


Statistics
Matches: 247,  Mismatches: 14, Indels: 7
        0.92            0.05        0.03

Matches are distributed among these distances:
  34   83  0.34
  35  164  0.66

ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39


Consensus pattern (35 bp):   
TGATCTCATTTCAAGAAGTTTTTGATGATCAGAGT

Found at i:936 original size:69 final size:69

Alignment explanation


    Indices: 825--1128  Score: 466
    Period size: 69  Copynumber: 4.4  Consensus size: 69

        815 GATGATCTAG

                                 *                                   *       
        825 TGATCTCATTTCAAGAAGTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCA
          1 TGATCTCATTTCAAGAAGTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTGATGATCA

                
        890 GAGT
         66 GAGT

                                  *                                          
        894 TGATCTCATTTCAAGAAGTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTT-ATGATCA
          1 TGATCTCATTTCAAGAAGTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTGATGATCA

                
        958 GAGT
         66 GAGT

                   *              *                   *              * *     
        962 TGATCTCCTTTCAAGAAAGTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGGTGATC
          1 TGATCTCATTTCAAG-AAGTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTGATGATC

                 
       1027 AGAGT
         65 AGAGT

                   *                                *     *                  
       1032 TGATCTCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATCACATTTTAAGAAGTTTTTGATGATC
          1 TGATCTCATTTCAAGAAG-TTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTGATGATC

                 
       1097 AGAGT
         65 AGAGT

                 *                *    
       1102 TGATCGCATTTCAAGAAGTTTTAATGA
          1 TGATCTCATTTCAAGAAGTTTTGATGA

       1129 GTTGATCTTC


Statistics
Matches: 215,  Mismatches: 17, Indels: 6
        0.90            0.07        0.03

Matches are distributed among these distances:
  68   25  0.12
  69  104  0.48
  70   86  0.40

ACGTcount: A:0.29, C:0.13, G:0.20, T:0.39


Consensus pattern (69 bp):   
TGATCTCATTTCAAGAAGTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTGATGATCA
GAGT
Done.