Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009418.1 Corchorus capsularis cultivar CVL-1 contig09439, 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: 3047
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30


Found at i:1893 original size:64 final size:63

Alignment explanation


    Indices: 1750--1906  Score: 206
    Period size: 64  Copynumber: 2.5  Consensus size: 63

       1740 GATAAAACTG

                                                 *        *         *    **
       1750 ACCCTTTGTCCGAAAGGGTATTTTGGGAAAACTAAACTTAAATGCAGGAATGTGACGAAACTG
          1 ACCCTTTGTCCGAAAGGGTATTTTGGGAAAACTAAACCTAAATGCAAGAATGTGACAAAACCA

            *        * *      **                                            
       1813 GCCCTTTGTTCAAAAGGGCGTTTTGGGAAAACTACAACCTAAATGCAAGAATGTGACAAAACCA
          1 ACCCTTTGTCCGAAAGGGTATTTTGGGAAAACTA-AACCTAAATGCAAGAATGTGACAAAACCA

                  *                       
       1877 ACCCTTGGTCCGAAAGGGTATTTTGGGAAA
          1 ACCCTTTGTCCGAAAGGGTATTTTGGGAAA

       1907 TAGCAAGTAA


Statistics
Matches: 77,  Mismatches: 16, Indels: 1
        0.82            0.17        0.01

Matches are distributed among these distances:
  63   29  0.38
  64   48  0.62

ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24


Consensus pattern (63 bp):   
ACCCTTTGTCCGAAAGGGTATTTTGGGAAAACTAAACCTAAATGCAAGAATGTGACAAAACCA

Found at i:2018 original size:49 final size:49

Alignment explanation


    Indices: 1890--2444  Score: 775
    Period size: 49  Copynumber: 11.4  Consensus size: 49

       1880 CTTGGTCCGA

                 *                         *          *        
       1890 AAGGGTATTTTGGGAAATAGCA-AGT-AAAATAAGT-ATCTTTCGTCCGGG
          1 AAGGGCATTTTGGGAAATAGCAGA-TAAAAACAAGTGA-CTTCCGTCCGGG

                                                             
       1938 AAGGGCATTTT-GGAAATAGCAGATAAAAACAAGTGACTTCCGTCCGGG
          1 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGACTTCCGTCCGGG

                                                     **      
       1986 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGACTTCTATCCGGG
          1 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGACTTCCGTCCGGG

                                                *         *  
       2035 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCAGG
          1 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGACTTCCGTCCGGG

              *            *                             *    
       2084 AAAGGCATTTTGGGACATAGCAGATAAAAACAAGTG-CTTTCCGTTCGGG
          1 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGAC-TTCCGTCCGGG

                               *                              
       2133 AAGGGCATTTTGGGAAATAACAGATAAAAACAAGT-ACCTTCCGTCCGGG
          1 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGA-CTTCCGTCCGGG

                               *  *                           
       2182 AAGGGCATTTTGGGAAATAACAAATAAAAACAAGT-ACCTTCCGTCCGGG
          1 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGA-CTTCCGTCCGGG

                                            *   *          * 
       2231 AAGGGCATTTTGGGAAATAGCAGATAAAAACAGGTGCCTTCCGTCCGAG
          1 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGACTTCCGTCCGGG

                                     *       *  *            
       2280 AAGGGCATTTTGGGAAATAGCAGATGAAAACAAATGCCTTCCGTCCGGG
          1 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGACTTCCGTCCGGG

                                 * *             *            
       2329 AAGGGCATTTTGGGAAAT-GTAAAATAAAAACAAGTGTCTTCCGTCCGGG
          1 AAGGGCATTTTGGGAAATAG-CAGATAAAAACAAGTGACTTCCGTCCGGG

                                     *       *  *            
       2378 AAGGGCATTTTGGGAAATAGCAGATGAAAACAAATGCCTTCCGTCCGGG
          1 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGACTTCCGTCCGGG

                              
       2427 AAGGGCATTTTGGGAAAT
          1 AAGGGCATTTTGGGAAAT

       2445 GTAAAATTTG


Statistics
Matches: 460,  Mismatches: 37, Indels: 19
        0.89            0.07        0.04

Matches are distributed among these distances:
  47   11  0.02
  48   43  0.09
  49  404  0.88
  50    2  0.00

ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22


Consensus pattern (49 bp):   
AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGACTTCCGTCCGGG

Found at i:2922 original size:25 final size:26

Alignment explanation


    Indices: 2888--2936  Score: 66
    Period size: 25  Copynumber: 1.9  Consensus size: 26

       2878 TTAAAATTAA

                 *                     
       2888 GTTTTTTTATT-TTTTATTA-TTTTAG
          1 GTTTTATTATTATTTT-TTACTTTTAG

                                    
       2913 GTTTTATTATTATTTTTTACTTTT
          1 GTTTTATTATTATTTTTTACTTTT

       2937 TCCCTTGTTC


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  25   13  0.62
  26    8  0.38

ACGTcount: A:0.16, C:0.02, G:0.06, T:0.76


Consensus pattern (26 bp):   
GTTTTATTATTATTTTTTACTTTTAG
Done.