Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017959.1 Corchorus olitorius cultivar O-4 contig17992, 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: 23364
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30


Found at i:455 original size:44 final size:45

Alignment explanation


    Indices: 405--512  Score: 137
    Period size: 45  Copynumber: 2.4  Consensus size: 45

        395 GAAAACGTGC

                      *            *                     
        405 AGGAGATCAAGGAAAG-TTAGAATCCATGACTGCCAAATGCTTTA
          1 AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTTA

                         *     * **       *              
        449 AGGAGATCAAAGAGAGCTTTGGCCCCATGATTGCCAAATGCTTTA
          1 AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTTA

                         *     
        494 AGGAGATCAAAGAGAGCTT
          1 AGGAGATCAAAGAAAGCTT

        513 TGGCTCCATG


Statistics
Matches: 56,  Mismatches: 7, Indels: 1
        0.88            0.11        0.02

Matches are distributed among these distances:
  44   14  0.25
  45   42  0.75

ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22


Consensus pattern (45 bp):   
AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTTA

Found at i:484 original size:45 final size:45

Alignment explanation


    Indices: 428--528  Score: 184
    Period size: 45  Copynumber: 2.2  Consensus size: 45

        418 AAGTTAGAAT

                  *                                      
        428 CCATGACTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
          1 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC

                                                        *
        473 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCT
          1 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC

                       
        518 CCATGATTGCC
          1 CCATGATTGCC

        529 GAGTGCACAA


Statistics
Matches: 54,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  45   54  1.00

ACGTcount: A:0.30, C:0.22, G:0.24, T:0.25


Consensus pattern (45 bp):   
CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC

Found at i:6200 original size:25 final size:25

Alignment explanation


    Indices: 6172--6221  Score: 66
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       6162 AAAAACAAAC

                        *             
       6172 AGAAGTAAGAAACGAAAT-CAAGAAA
          1 AGAAG-AAGAAAAGAAATACAAGAAA

                  *                  
       6197 AGAAGATGAAAAGAAATACAAGAAA
          1 AGAAGAAGAAAAGAAATACAAGAAA

       6222 TCAGATCTAG


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  24   10  0.45
  25   12  0.55

ACGTcount: A:0.66, C:0.06, G:0.20, T:0.08


Consensus pattern (25 bp):   
AGAAGAAGAAAAGAAATACAAGAAA

Found at i:7081 original size:17 final size:18

Alignment explanation


    Indices: 7059--7093  Score: 54
    Period size: 17  Copynumber: 2.0  Consensus size: 18

       7049 TTTTTTTAAT

                  *           
       7059 AATTATTTTAA-TAATTA
          1 AATTATATTAATTAATTA

                              
       7076 AATTATATTAATTAATTA
          1 AATTATATTAATTAATTA

       7094 CATAAATATA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17   10  0.62
  18    6  0.38

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (18 bp):   
AATTATATTAATTAATTA

Found at i:10816 original size:28 final size:28

Alignment explanation


    Indices: 10772--10825  Score: 72
    Period size: 28  Copynumber: 1.9  Consensus size: 28

      10762 GATGAACTTT

                                        
      10772 ATTCTAACATCTAGACTACCCAGTTGGG
          1 ATTCTAACATCTAGACTACCCAGTTGGG

                   *    *    *  *     
      10800 ATTCTAATATCTGGACTTCCTAGTTG
          1 ATTCTAACATCTAGACTACCCAGTTG

      10826 AAAGTGAACC


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  28   22  1.00

ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35


Consensus pattern (28 bp):   
ATTCTAACATCTAGACTACCCAGTTGGG

Found at i:17729 original size:57 final size:57

Alignment explanation


    Indices: 17641--17762  Score: 226
    Period size: 57  Copynumber: 2.1  Consensus size: 57

      17631 GAAACCAACT

                                            *                        
      17641 TCAGATGCAGAATCTTGTTCCAGAATAGGAGTCTGATGACACTCAGTTACCCGCTCA
          1 TCAGATGCAGAATCTTGTTCCAGAATAGGAGTATGATGACACTCAGTTACCCGCTCA

                                                    *                
      17698 TCAGATGCAGAATCTTGTTCCAGAATAGGAGTATGATGACTCTCAGTTACCCGCTCA
          1 TCAGATGCAGAATCTTGTTCCAGAATAGGAGTATGATGACACTCAGTTACCCGCTCA

                    
      17755 TCAGATGC
          1 TCAGATGC

      17763 TTCAGCAATC


Statistics
Matches: 63,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  57   63  1.00

ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27


Consensus pattern (57 bp):   
TCAGATGCAGAATCTTGTTCCAGAATAGGAGTATGATGACACTCAGTTACCCGCTCA
Done.