Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021420.1 Corchorus olitorius cultivar O-4 contig21453, 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: 8035
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31


Found at i:470 original size:217 final size:221

Alignment explanation


    Indices: 57--481  Score: 569
    Period size: 217  Copynumber: 1.9  Consensus size: 221

         47 AACAATCTAG

                      *        *   * *  *       *                            
         57 TATTAGATGGCACTAAAATGATATAGACGGGGTTTATTCAATTAATTAGGATGAAAAATATGGAT
          1 TATTAGATGGAACTAAAATCATACAAACAGGGTTTAATCAATTAATTAGGATGAAAAATATGGAT

                *   **                                                       
        122 TAAAGCACTTTTTAAAGCCAATTTTGGGTATATGAGAAAAAAAATGTCAATCTCTAAAGAATTTG
         66 TAAAACACGGTTTAAAGCCAATTTTGGGTATAT--GAAAAAAAATGTCAATCTCTAAAGAATTTG

                                                      *              * *     
        187 GGGATGATGCATATGATTATTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGG
        129 GGGATGATGCATATGATTATTGGGGATGATGAGAAATGATTTAGGTATAAAGTATATAACTTTGG

                   *                    
        252 GGATACTTAATTTTTCATTTTTTTTAAT
        194 GGATACTGAATTTTTCATTTTTTTTAAT

                        *                                                    
        280 TATTAGATGGAAGTAAAATCATACAAACAGGGTTTAATCAATTAATTAGGATG-AAAATAT-GAT
          1 TATTAGATGGAACTAAAATCATACAAACAGGGTTTAATCAATTAATTAGGATGAAAAATATGGAT

                 *                             *          *                  
        343 TAAAATA-GGTTTAAAGCCAATTTTGGGT-T-T-ATAAAAAATCGTTAATCTCTCAAA-AATTTG
         66 TAAAACACGGTTTAAAGCCAATTTTGGGTATATGAAAAAAAAT-GTCAATCTCT-AAAGAATTTG

                       *                           *                         
        403 GGGAT-AGTGCTTATGATTATTTGGGGATGATGAGAAATTATTTAGGTATAAAGTATATAACTTT
        129 GGGATGA-TGCATATGATTA-TTGGGGATGATGAGAAATGATTTAGGTATAAAGTATATAACTTT

                           
        467 GGGGATACTGAATTT
        192 GGGGATACTGAATTT

        482 ATAGCATGTC


Statistics
Matches: 179,  Mismatches: 19, Indels: 14
        0.84            0.09        0.07

Matches are distributed among these distances:
 215    9  0.05
 216   31  0.17
 217   57  0.32
 218    1  0.01
 219    1  0.01
 220   19  0.11
 221    8  0.04
 222    7  0.04
 223   46  0.26

ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36


Consensus pattern (221 bp):   
TATTAGATGGAACTAAAATCATACAAACAGGGTTTAATCAATTAATTAGGATGAAAAATATGGAT
TAAAACACGGTTTAAAGCCAATTTTGGGTATATGAAAAAAAATGTCAATCTCTAAAGAATTTGGG
GATGATGCATATGATTATTGGGGATGATGAGAAATGATTTAGGTATAAAGTATATAACTTTGGGG
ATACTGAATTTTTCATTTTTTTTAAT

Found at i:2636 original size:16 final size:15

Alignment explanation


    Indices: 2615--2688  Score: 85
    Period size: 16  Copynumber: 4.7  Consensus size: 15

       2605 GACAATTGGG

                      *     
       2615 CGGGTTCAGGCTTTTT
          1 CGGGTTC-GGGTTTTT

                            
       2631 CGGGTTCGGGTTTATT
          1 CGGGTTCGGGTTT-TT

                            
       2647 CGGGTTCGGGTGTTTT
          1 CGGGTTCGGGT-TTTT

                     *    * 
       2663 CGGGTTCGGATTATGT
          1 CGGGTTCGGGTT-TTT

                      
       2679 CGGGTTCGGG
          1 CGGGTTCGGG

       2689 GCGGATCGGG


Statistics
Matches: 51,  Mismatches: 4, Indels: 6
        0.84            0.07        0.10

Matches are distributed among these distances:
  15    6  0.12
  16   43  0.84
  17    2  0.04

ACGTcount: A:0.05, C:0.15, G:0.41, T:0.39


Consensus pattern (15 bp):   
CGGGTTCGGGTTTTT

Found at i:2663 original size:32 final size:32

Alignment explanation


    Indices: 2627--2688  Score: 99
    Period size: 32  Copynumber: 1.9  Consensus size: 32

       2617 GGTTCAGGCT

                          *                  
       2627 TTTTCGGGTTCGGGTTTAT-TCGGGTTCGGGTG
          1 TTTTCGGGTTC-GGATTATGTCGGGTTCGGGTG

                                          
       2659 TTTTCGGGTTCGGATTATGTCGGGTTCGGG
          1 TTTTCGGGTTCGGATTATGTCGGGTTCGGG

       2689 GCGGATCGGG


Statistics
Matches: 28,  Mismatches: 1, Indels: 2
        0.90            0.03        0.06

Matches are distributed among these distances:
  31    6  0.21
  32   22  0.79

ACGTcount: A:0.05, C:0.13, G:0.40, T:0.42


Consensus pattern (32 bp):   
TTTTCGGGTTCGGATTATGTCGGGTTCGGGTG

Found at i:6324 original size:69 final size:70

Alignment explanation


    Indices: 6242--6393  Score: 207
    Period size: 69  Copynumber: 2.2  Consensus size: 70

       6232 AATAACTCCT

                 *                                          *          *     
       6242 GGACAAGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATT-TGCGCTCCTCAACAGCACAA
          1 GGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTCTGCACTCCTCAACAACACAA

                 
       6306 GTCCG
         66 GTCCG

                             *        *        *     *       *           *   
       6311 GGACAGGACTTGGGTAATTCCTGCCCCGGTCTTGTTCTGTATTTCTGCATTCCTCAACAACCCAA
          1 GGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTCTGCACTCCTCAACAACACAA

                *
       6376 GTCCT
         66 GTCCG

                         
       6381 GGACAGGACTTGG
          1 GGACAGGACTTGG

       6394 CCAAGATCTG


Statistics
Matches: 72,  Mismatches: 10, Indels: 1
        0.87            0.12        0.01

Matches are distributed among these distances:
  69   39  0.54
  70   33  0.46

ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27


Consensus pattern (70 bp):   
GGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTCTGCACTCCTCAACAACACAA
GTCCG
Done.