Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015314.1 Corchorus olitorius cultivar O-4 contig15347, 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: 2039
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29


Found at i:1607 original size:54 final size:54

Alignment explanation


    Indices: 1438--1606  Score: 266
    Period size: 54  Copynumber: 3.1  Consensus size: 54

       1428 GTGCGGTCTT

                      *                                *  *        
       1438 TTGATCCTCAAATGATCCAGTGCGGTCATTCCAAGAAGTTTTTTAAGGATCAGAG
          1 TTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGAAG-TTTTCAATGATCAGAG

                    *                                      *      
       1493 TTGATCCTAAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAG
          1 TTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAG

                  *                                    *          
       1547 TTGATCTTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCGATGATCAGAG
          1 TTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAG

                  
       1601 TTGATC
          1 TTGATC

       1607 TCGTTTCAAG


Statistics
Matches: 105,  Mismatches: 9, Indels: 1
        0.91            0.08        0.01

Matches are distributed among these distances:
  54   69  0.66
  55   36  0.34

ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31


Consensus pattern (54 bp):   
TTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAG

Found at i:1619 original size:35 final size:35

Alignment explanation


    Indices: 1572--1924  Score: 442
    Period size: 35  Copynumber: 10.0  Consensus size: 35

       1562 TCCAGTGCGG

                 *                             
       1572 TCATTCCAAGAAGTTTTCGATGATCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC

              *             *               * *
       1607 TCGTTTCAAGAAGTTTCCGATGATCAGAGTTGGTT
          1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC

              *                 *               
       1642 TCGTTTCAA-AGAGTTTTCGTTGATCAGAGTTGATC
          1 TCATTTCAAGA-AGTTTTCGATGATCAGAGTTGATC

              *     *        **                
       1677 TCCTTTCAGGAAGTTTTTTATGATCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC

                        *      *   *            
       1712 TCATTTTCAAGATGTTTT-TATGGTCAGAGTTGATC
          1 TCA-TTTCAAGAAGTTTTCGATGATCAGAGTTGATC

                                               
       1747 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC

              *                 *               
       1782 TCGTTTCAA-AGAGTTTTCGTTGATCAGAGTTGATC
          1 TCATTTCAAGA-AGTTTTCGATGATCAGAGTTGATC

                               **   *            
       1817 TCATTTCAAGAAGTTTTTTATATGGTCAGAGTTGATC
          1 TCATTTCAAGAAG--TTTTCGATGATCAGAGTTGATC

              *              **                
       1854 TCCTTTCAAGAAGTTTTTTATGATCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC

                                               
       1889 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC

             
       1924 T
          1 T

       1925 TCACATTGAT


Statistics
Matches: 276,  Mismatches: 34, Indels: 16
        0.85            0.10        0.05

Matches are distributed among these distances:
  34   15  0.05
  35  217  0.79
  36   14  0.05
  37   30  0.11

ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40


Consensus pattern (35 bp):   
TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC

Found at i:1742 original size:140 final size:142

Alignment explanation


    Indices: 1578--1924  Score: 556
    Period size: 140  Copynumber: 2.5  Consensus size: 142

       1568 GCGGTCATTC

                       **                  *             *               * * 
       1578 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTCCGATGATCAGAGTTGGTTT
          1 CAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCT

                                                *     *                      
       1643 CGTTTCAAAGAGTTTTCGTTGATCAGAGTTGATCTCCTTTCAGGAAG-TTTTT-TATGATCAGAG
         66 CGTTTCAAAGAGTTTTCGTTGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATATGATCAGAG

                     *   
       1706 TTGATCTCATTTT
        131 TTGATCTC-CTTT

                 *          *                                                
       1719 CAAGATG-TTTTTATGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
          1 CAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCT

                                                                      *      
       1783 CGTTTCAAAGAGTTTTCGTTGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATATGGTCAGAG
         66 CGTTTCAAAGAGTTTTCGTTGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATATGATCAGAG

                        
       1848 TTGATCTCCTTT
        131 TTGATCTCCTTT

                                                                             
       1860 CAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
          1 CAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCT

       1925 TCACATTGAT


Statistics
Matches: 189,  Mismatches: 14, Indels: 5
        0.91            0.07        0.02

Matches are distributed among these distances:
 140   95  0.50
 141   20  0.11
 142   74  0.39

ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40


Consensus pattern (142 bp):   
CAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
CGTTTCAAAGAGTTTTCGTTGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATATGATCAGAG
TTGATCTCCTTT
Done.