Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016349.1 Corchorus capsularis cultivar CVL-1 contig16370, 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, 609

Length: 1016
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.36


Found at i:618 original size:104 final size:105

Alignment explanation


    Indices: 510--742  Score: 280
    Period size: 102  Copynumber: 2.2  Consensus size: 105

        500 AAAGGTAACA

                      *                 *                                    
        510 TTTTATTTACTAATTACTTAAAAAAAGTTC-AATCTTTCATTAAAATG-CT-AATGCTTTATTTA
          1 TTTTATTTACCAATTACTTAAAAAAA-TCCAAATCTTTCATTAAAA-GACTAAAT-CTTTATTTA

                          *      *             *       
        572 CCAATCACTCTAAAGATTCAATCTTTTACCC-AAAGACGACAT
         63 CCAATCACTCTAAAAATTCAACCTTTTACCCAAAAAACGACAT

                                                 *   *                     * 
        614 TTTTATTTACCAATTACTT--AAAAATCCAAATCTTTTATTCAAAGACTAAATCTTTATTTACTA
          1 TTTTATTTACCAATTACTTAAAAAAATCCAAATCTTTCATTAAAAGACTAAATCTTTATTTACCA

              *                                *  *  
        677 ATTACTCTAAAAATTCAACCTTTTACCCAAAAAAATGATAT
         66 ATCACTCTAAAAATTCAACCTTTTACCC-AAAAAACGACAT

                                     
        718 TTTTATTTACCAATTTACTTAAAAA
          1 TTTTATTTACCAA-TTACTTAAAAA

        743 TTCAATCTTT


Statistics
Matches: 110,  Mismatches: 11, Indels: 13
        0.82            0.08        0.10

Matches are distributed among these distances:
 101    3  0.03
 102   56  0.51
 103    3  0.03
 104   39  0.35
 105    6  0.05
 107    3  0.03

ACGTcount: A:0.39, C:0.17, G:0.03, T:0.40


Consensus pattern (105 bp):   
TTTTATTTACCAATTACTTAAAAAAATCCAAATCTTTCATTAAAAGACTAAATCTTTATTTACCA
ATCACTCTAAAAATTCAACCTTTTACCCAAAAAACGACAT

Found at i:619 original size:51 final size:50

Alignment explanation


    Indices: 564--761  Score: 216
    Period size: 51  Copynumber: 3.8  Consensus size: 50

        554 ATGCTAATGC

                         *        *                        *   
        564 TTTATTTACCAATCACTCTAAAGATTCAATCTTTTACCCAAAGACGACATT
          1 TTTATTTACCAATTACT-TAAAAATTCAATCTTTTACCCAAAGACGAAATT

                                    *           **       *    *
        615 TTTATTTACCAATTACTTAAAAATCCAAATCTTTTATTCAAAGACTAAATC
          1 TTTATTTACCAATTACTTAAAAATTC-AATCTTTTACCCAAAGACGAAATT

                     *                   *              * *  *   
        666 TTTATTTACTAATTACTCTAAAAATTCAACCTTTTACCCAAAAAAATGATATT
          1 TTTATTTACCAATTACT-TAAAAATTCAATCTTTTACCC--AAAGACGAAATT

                                                *      
        719 TTTATTTACCAATTTACTTAAAAATTCAATCTTTTATCCAAAG
          1 TTTATTTACCAA-TTACTTAAAAATTCAATCTTTTACCCAAAG

        762 GTTGAATCTT


Statistics
Matches: 120,  Mismatches: 22, Indels: 10
        0.79            0.14        0.07

Matches are distributed among these distances:
  50    7  0.06
  51   63  0.52
  52    8  0.07
  53   37  0.31
  54    5  0.04

ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39


Consensus pattern (50 bp):   
TTTATTTACCAATTACTTAAAAATTCAATCTTTTACCCAAAGACGAAATT

Found at i:769 original size:20 final size:19

Alignment explanation


    Indices: 746--800  Score: 74
    Period size: 20  Copynumber: 2.8  Consensus size: 19

        736 TTAAAAATTC

                     *         
        746 AATCTTTTATCCAAAGGTT
          1 AATCTTTTAGCCAAAGGTT

                    *           
        765 GAATCTTTAAGCCAAAGGTT
          1 -AATCTTTTAGCCAAAGGTT

                            
        785 ATATCTTTTAGCCAAA
          1 A-ATCTTTTAGCCAAA

        801 TATCCTATTT


Statistics
Matches: 31,  Mismatches: 3, Indels: 2
        0.86            0.08        0.06

Matches are distributed among these distances:
  19    1  0.03
  20   30  0.97

ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36


Consensus pattern (19 bp):   
AATCTTTTAGCCAAAGGTT

Found at i:770 original size:104 final size:100

Alignment explanation


    Indices: 510--773  Score: 303
    Period size: 104  Copynumber: 2.5  Consensus size: 100

        500 AAAGGTAACA

                      *                          *   *   *                   
        510 TTTTATTTACTAATTACTTAAAAAAAGTTCAATCTTTCATTAAAATGCTAATGCTTTATTTACCA
          1 TTTTATTTACCAATTACTT--AAAAA-TTCAATCTTTTATTCAAAGGCTAAT-CTTTATTTACCA

                       *      *            *       
        575 ATCACTCTAAAGATTCAATCTTTTACCCAAAGACGACAT
         62 ATCACTCTAAAAATTCAACCTTTTACCCAAAAACGACAT

                                     *                  *                *   
        614 TTTTATTTACCAATTACTTAAAAATCCAAATCTTTTATTCAAAGACTAAATCTTTATTTACTAAT
          1 TTTTATTTACCAATTACTTAAAAATTC-AATCTTTTATTCAAAGGCT-AATCTTTATTTACCAAT

            *                                *  *  
        679 TACTCTAAAAATTCAACCTTTTACCCAAAAAAATGATAT
         64 CACTCTAAAAATTCAACCTTTTACCC--AAAAACGACAT

                                                  *      *          
        718 TTTTATTTACCAATTTACTTAAAAATTCAATCTTTTATCCAAAGGTTGAATCTTTA
          1 TTTTATTTACCAA-TTACTTAAAAATTCAATCTTTTATTCAAAGGCT-AATCTTTA

        774 AGCCAAAGGT


Statistics
Matches: 137,  Mismatches: 18, Indels: 10
        0.83            0.11        0.06

Matches are distributed among these distances:
 101    2  0.01
 102   56  0.41
 103    3  0.02
 104   63  0.46
 105   13  0.09

ACGTcount: A:0.38, C:0.17, G:0.04, T:0.41


Consensus pattern (100 bp):   
TTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGCTAATCTTTATTTACCAATCA
CTCTAAAAATTCAACCTTTTACCCAAAAACGACAT
Done.