Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017599.1 Corchorus olitorius cultivar O-4 contig17632, 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: 1782
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38


Found at i:220 original size:22 final size:22

Alignment explanation


    Indices: 190--335  Score: 143
    Period size: 22  Copynumber: 6.6  Consensus size: 22

        180 TCCAACGTAG

                                *  
        190 AAATATTGATAACCACACTGCGA
          1 AAAT-TTGATAACCACACTGTGA

                         *  *     
        213 AAATTTGATAACCTCATTGTG-
          1 AAATTTGATAACCACACTGTGA

                          * *  *   
        234 AAATTTCGATAACCTCCCTATGA
          1 AAATTT-GATAACCACACTGTGA

                            *     
        257 AAATTTGATAACCACAATGTGA
          1 AAATTTGATAACCACACTGTGA

              *                   
        279 AATTTTGATAACCACACTGTG-
          1 AAATTTGATAACCACACTGTGA

                              **   
        300 AAATTCTGATAACCACACAATGA
          1 AAATT-TGATAACCACACTGTGA

             **          
        323 AGTTTTGATAACC
          1 AAATTTGATAACC

        336 TCATTGTCTA


Statistics
Matches: 102,  Mismatches: 17, Indels: 9
        0.80            0.13        0.07

Matches are distributed among these distances:
  21   10  0.10
  22   79  0.77
  23   13  0.13

ACGTcount: A:0.39, C:0.19, G:0.12, T:0.29


Consensus pattern (22 bp):   
AAATTTGATAACCACACTGTGA

Found at i:323 original size:66 final size:66

Alignment explanation


    Indices: 190--335  Score: 177
    Period size: 66  Copynumber: 2.2  Consensus size: 66

        180 TCCAACGTAG

                             *                  *  *                  * * *  
        190 AAATATTGATAACCACACTGCGAAAATTTGATAACCTCATTGTGAAATTTCGATAACCTCCCTAT
          1 AAAT-TTGATAACCACAATGCGAAAATTTGATAACCACACTGTGAAATTTCGATAACCACACAAT

              
        255 GA
         65 GA

                               *    *                                        
        257 AAATTTGATAACCACAATGTGAAATTTTGATAACCACACTGTGAAA-TTCTGATAACCACACAAT
          1 AAATTTGATAACCACAATGCGAAAATTTGATAACCACACTGTGAAATTTC-GATAACCACACAAT

              
        321 GA
         65 GA

             **          
        323 AGTTTTGATAACC
          1 AAATTTGATAACC

        336 TCATTGTCTA


Statistics
Matches: 68,  Mismatches: 10, Indels: 3
        0.84            0.12        0.04

Matches are distributed among these distances:
  65    3  0.04
  66   61  0.90
  67    4  0.06

ACGTcount: A:0.39, C:0.19, G:0.12, T:0.29


Consensus pattern (66 bp):   
AAATTTGATAACCACAATGCGAAAATTTGATAACCACACTGTGAAATTTCGATAACCACACAATG
A

Found at i:329 original size:44 final size:43

Alignment explanation


    Indices: 189--335  Score: 161
    Period size: 44  Copynumber: 3.3  Consensus size: 43

        179 CTCCAACGTA

                 *               *               *   *  
        189 GAAATATTGATAACCACACTGCGAAAATTTGATAACCTCATTGT
          1 GAAATTTTGATAACCACACTGTGAAAATTTGATAACCACA-AGT

                   *       * *  *                       
        233 GAAATTTCGATAACCTCCCTATGAAAATTTGATAACCACAATGT
          1 GAAATTTTGATAACCACACTGTGAAAATTTGATAACCACAA-GT

                                                       * 
        277 GAAATTTTGATAACCACACTGTG-AAATTCTGATAACCACACAAT
          1 GAAATTTTGATAACCACACTGTGAAAATT-TGATAACCACA-AGT

               *           
        321 GAAGTTTTGATAACC
          1 GAAATTTTGATAACC

        336 TCATTGTCTA


Statistics
Matches: 86,  Mismatches: 14, Indels: 6
        0.81            0.13        0.06

Matches are distributed among these distances:
  43    5  0.06
  44   80  0.93
  45    1  0.01

ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29


Consensus pattern (43 bp):   
GAAATTTTGATAACCACACTGTGAAAATTTGATAACCACAAGT

Found at i:621 original size:22 final size:22

Alignment explanation


    Indices: 545--729  Score: 101
    Period size: 22  Copynumber: 8.4  Consensus size: 22

        535 TGATAAGAAC

                         *         
        545 AAATTTTGATAACGTTC-TAAT-
          1 AAATTTTGATAACCTTCAT-ATG

            *           *  *      *
        566 TAATTTTGATAATC-ACACTATA
          1 AAATTTTGATAACCTTCA-TATG

                  **         *    
        588 AAATTTCAATAACCTTCGTATG
          1 AAATTTTGATAACCTTCATATG

                        *  *    * 
        610 AAATTTTGATAATCTCCATAAG
          1 AAATTTTGATAACCTTCATATG

             *                **    
        632 AGATTTTGATAACCTTTTTTTATG
          1 AAATTTTGATAACC--TTCATATG

                    *       **    
        656 AAATTTTGGTAACCTTTGTATG
          1 AAATTTTGATAACCTTCATATG

                                  * 
        678 AAATTTTGATAA--TTACACTACG
          1 AAATTTTGATAACCTT-CA-TATG

              *            *      
        700 AAGTTTTGATAACCTCCATATG
          1 AAATTTTGATAACCTTCATATG

                    
        722 AAATTTTG
          1 AAATTTTG

        730 GTTTGATTGT


Statistics
Matches: 120,  Mismatches: 34, Indels: 19
        0.69            0.20        0.11

Matches are distributed among these distances:
  20    3  0.03
  21   13  0.11
  22   84  0.70
  23    3  0.03
  24   17  0.14

ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42


Consensus pattern (22 bp):   
AAATTTTGATAACCTTCATATG

Done.