Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018491.1 Corchorus olitorius cultivar O-4 contig18524, 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: 19206
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:15754 original size:44 final size:44

Alignment explanation


    Indices: 15713--15963  Score: 125
    Period size: 44  Copynumber: 5.7  Consensus size: 44

      15703 AGACATGTTG

                                      *                  
      15713 GAGATTTG-GGGATAAAGAAGACATGGTTTGGGGATAGCATGTAA
          1 GAGATTTGTGGGATAAAGAAGACAT-ATTTGGGGATAGCATGTAA

            ***         *                      *        
      15757 TTTATTTGTGGGTTAAAGAAGACATATTTGGGGATGGCATGTAA
          1 GAGATTTGTGGGATAAAGAAGACATATTTGGGGATAGCATGTAA

            ***            *                              
      15801 TTTATTTGTGGGATATAGAAGAC--ATTTGGGG-TATGACATGTAA
          1 GAGATTTGTGGGATAAAGAAGACATATTTGGGGATA-G-CATGTAA

            ***  *    *   *  *     * *      *         *  
      15844 TTTATATGTGAGATCAATAAGACTTTTTTGGGTAT-GACATGCAA
          1 GAGATTTGTGGGATAAAGAAGACATATTTGGGGATAG-CATGTAA

            ***                   *  *      *   *       
      15888 TTTATTTGTGGGATAAAGAAGATATTTTTGGGTATAACATGTAA
          1 GAGATTTGTGGGATAAAGAAGACATATTTGGGGATAGCATGTAA

            ***         *  *         *      
      15932 TTTATTTGTGGGCTAGAGAAGACATTTTTGGG
          1 GAGATTTGTGGGATAAAGAAGACATATTTGGG

      15964 CATGACATAT


Statistics
Matches: 172,  Mismatches: 28, Indels: 14
        0.80            0.13        0.07

Matches are distributed among these distances:
  41    1  0.01
  42    9  0.05
  43   25  0.15
  44  115  0.67
  45   21  0.12
  46    1  0.01

ACGTcount: A:0.31, C:0.05, G:0.28, T:0.36


Consensus pattern (44 bp):   
GAGATTTGTGGGATAAAGAAGACATATTTGGGGATAGCATGTAA

Found at i:15764 original size:22 final size:23

Alignment explanation


    Indices: 15739--15815  Score: 63
    Period size: 22  Copynumber: 3.5  Consensus size: 23

      15729 GAAGACATGG

                                   
      15739 TTTG-GGGATAGCATGTAATTTA
          1 TTTGTGGGATAGCATGTAATTTA

                    *     * *   **  
      15761 TTTGTGGGTTA--AAGAAGACATA
          1 TTTGTGGGATAGCATGTA-ATTTA

                      *            
      15783 TTTG-GGGATGGCATGTAATTTA
          1 TTTGTGGGATAGCATGTAATTTA

                       
      15805 TTTGTGGGATA
          1 TTTGTGGGATA

      15816 TAGAAGACAT


Statistics
Matches: 38,  Mismatches: 12, Indels: 9
        0.64            0.20        0.15

Matches are distributed among these distances:
  21    7  0.18
  22   18  0.47
  23   13  0.34

ACGTcount: A:0.27, C:0.04, G:0.30, T:0.39


Consensus pattern (23 bp):   
TTTGTGGGATAGCATGTAATTTA

Found at i:15866 original size:87 final size:87

Alignment explanation


    Indices: 15716--15971  Score: 275
    Period size: 87  Copynumber: 2.9  Consensus size: 87

      15706 CATGTTGGAG

                                                                 * *         
      15716 ATTTG-GGGATAAAGAAGACATGGTTTGGGG-ATAGCATGTAATTTATTTGTGGGTTAAAGAAGA
          1 ATTTGTGGGATAAAGAAGACA--GTTTGGGGTATA-CATGTAATTTATTTGTGAGATAAAGAAGA

                          *    *     
      15779 CATATTTGGGGATGGCATGTAATTT
         63 CATATTTGGGGATGACATGCAATTT

                        *                                 *        *  *     *
      15804 ATTTGTGGGATATAGAAGACA-TTTGGGGTATGACATGTAATTTATATGTGAGATCAATAAGACT
          1 ATTTGTGGGATAAAGAAGACAGTTTGGGGTAT-ACATGTAATTTATTTGTGAGATAAAGAAGACA

             *      *              
      15868 TTTTTGGGTATGACATGCAATTT
         65 TATTTGGGGATGACATGCAATTT

                               * *   *                         * *  *        
      15891 ATTTGTGGGATAAAGAAGATATTTTTGGGTATAACATGTAATTTATTTGTGGGCTAGAGAAGACA
          1 ATTTGTGGGATAAAGAAGACAGTTTGGGGTAT-ACATGTAATTTATTTGTGAGATAAAGAAGACA

             *      *       
      15956 TTTTTGGGCATGACAT
         65 TATTTGGGGATGACAT

      15972 ATAATAAATA


Statistics
Matches: 141,  Mismatches: 23, Indels: 8
        0.82            0.13        0.05

Matches are distributed among these distances:
  86    7  0.05
  87   65  0.46
  88   55  0.39
  89   14  0.10

ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36


Consensus pattern (87 bp):   
ATTTGTGGGATAAAGAAGACAGTTTGGGGTATACATGTAATTTATTTGTGAGATAAAGAAGACAT
ATTTGGGGATGACATGCAATTT

Found at i:15899 original size:24 final size:22

Alignment explanation


    Indices: 15872--15943  Score: 58
    Period size: 24  Copynumber: 3.2  Consensus size: 22

      15862 AAGACTTTTT

                                    
      15872 TGGGTATGACATGCAATTTATTTG
          1 TGGGTAT-ACATG-AATTTATTTG

                      *   **     *
      15896 TGGG-ATA-AAGAAGATATTTT
          1 TGGGTATACATGAATTTATTTG

                                    
      15916 TGGGTATAACATGTAATTTATTTG
          1 TGGGTAT-ACATG-AATTTATTTG

                
      15940 TGGG
          1 TGGG

      15944 CTAGAGAAGA


Statistics
Matches: 36,  Mismatches: 8, Indels: 8
        0.69            0.15        0.15

Matches are distributed among these distances:
  20   11  0.31
  21    4  0.11
  22    2  0.06
  23    4  0.11
  24   15  0.42

ACGTcount: A:0.29, C:0.04, G:0.26, T:0.40


Consensus pattern (22 bp):   
TGGGTATACATGAATTTATTTG

Found at i:16304 original size:2 final size:2

Alignment explanation


    Indices: 16297--16331  Score: 52
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      16287 TAAACTGAAT

                                           *                   
      16297 TA TA TA TA TA TA TA TA TA TA TC TA TA TA CTA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA

      16332 AGTCTAAACT


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
   2   28  0.93
   3    2  0.07

ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Done.