Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016520.1 Corchorus capsularis cultivar CVL-1 contig16541, 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: 12145
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34


Found at i:4050 original size:13 final size:13

Alignment explanation


    Indices: 4019--4061  Score: 52
    Period size: 13  Copynumber: 3.3  Consensus size: 13

       4009 GTCTGACTGT

                   *     
       4019 TTTGGTTGATTA-
          1 TTTGGTTTATTAC

                          
       4031 TTCTGGTTTATTAC
          1 TT-TGGTTTATTAC

                      *  
       4045 TTTGGTTTATAAC
          1 TTTGGTTTATTAC

                
       4058 TTTG
          1 TTTG

       4062 ATTATGATAC


Statistics
Matches: 27,  Mismatches: 2, Indels: 3
        0.84            0.06        0.09

Matches are distributed among these distances:
  12    2  0.07
  13   23  0.85
  14    2  0.07

ACGTcount: A:0.16, C:0.07, G:0.19, T:0.58


Consensus pattern (13 bp):   
TTTGGTTTATTAC

Found at i:6166 original size:20 final size:22

Alignment explanation


    Indices: 6131--6172  Score: 70
    Period size: 20  Copynumber: 2.0  Consensus size: 22

       6121 AAAGGTTTTC

                                  
       6131 CAAAATTCCAAAAAAATCAAAT
          1 CAAAATTCCAAAAAAATCAAAT

                                  
       6153 CAAAATT-C-AAAAAATCAAAT
          1 CAAAATTCCAAAAAAATCAAAT

       6173 TTTTCTTCAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  20   12  0.60
  21    1  0.05
  22    7  0.35

ACGTcount: A:0.64, C:0.17, G:0.00, T:0.19


Consensus pattern (22 bp):   
CAAAATTCCAAAAAAATCAAAT

Found at i:8173 original size:27 final size:28

Alignment explanation


    Indices: 8121--8182  Score: 74
    Period size: 27  Copynumber: 2.2  Consensus size: 28

       8111 AAAGTGTAAT

                                 *      
       8121 AAAAATGACAAAAATGCCCCTGAATG-C
          1 AAAAATGACAAAAATGCCCCTAAATGTC

                     *                   
       8148 AAAAATGACCAAAATG-CCCTCAAATGTC
          1 AAAAATGACAAAAATGCCCCT-AAATGTC

            *      
       8176 CAAAATG
          1 AAAAATG

       8183 TCCTTGGGCG


Statistics
Matches: 30,  Mismatches: 3, Indels: 3
        0.83            0.08        0.08

Matches are distributed among these distances:
  26    4  0.13
  27   19  0.63
  28    7  0.23

ACGTcount: A:0.48, C:0.23, G:0.13, T:0.16


Consensus pattern (28 bp):   
AAAAATGACAAAAATGCCCCTAAATGTC

Found at i:8547 original size:35 final size:35

Alignment explanation


    Indices: 8494--8563  Score: 88
    Period size: 35  Copynumber: 2.0  Consensus size: 35

       8484 TGTGCTGCAT

                         *         *           
       8494 TGAGCTCATCGAATCCAATCTTGGAGATGCCACAC
          1 TGAGCTCATCGAAGCCAATCTTGAAGATGCCACAC

                                *          *    
       8529 TGAG-TCATCTGAAGCCAATTTTGAAGATGCTACAC
          1 TGAGCTCATC-GAAGCCAATCTTGAAGATGCCACAC

       8564 CAAGTCGTCT


Statistics
Matches: 30,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  34    5  0.17
  35   25  0.83

ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26


Consensus pattern (35 bp):   
TGAGCTCATCGAAGCCAATCTTGAAGATGCCACAC

Found at i:8575 original size:35 final size:35

Alignment explanation


    Indices: 8499--8576  Score: 86
    Period size: 35  Copynumber: 2.3  Consensus size: 35

       8489 TGCATTGAGC

                     *         *           **  
       8499 TCATC-GAATCCAATCTTGGAGATGCCACACTGAG
          1 TCATCTGAAGCCAATCTTGAAGATGCCACACCAAG

                           *          *        
       8533 TCATCTGAAGCCAATTTTGAAGATGCTACACCAAG
          1 TCATCTGAAGCCAATCTTGAAGATGCCACACCAAG

              *      
       8568 TCGTCTGAA
          1 TCATCTGAA

       8577 TTCCTGAAAA


Statistics
Matches: 36,  Mismatches: 7, Indels: 1
        0.82            0.16        0.02

Matches are distributed among these distances:
  34    5  0.14
  35   31  0.86

ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26


Consensus pattern (35 bp):   
TCATCTGAAGCCAATCTTGAAGATGCCACACCAAG
Done.