Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016218.1 Corchorus olitorius cultivar O-4 contig16251, 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: 2322
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37


Found at i:1831 original size:22 final size:22

Alignment explanation


    Indices: 1805--2008  Score: 126
    Period size: 22  Copynumber: 9.2  Consensus size: 22

       1795 TTAAACCTAA

                     *        * * 
       1805 TATGAAATTCCGATAACCTCCC
          1 TATGAAATTTCGATAACCACAC

                   *              
       1827 TATGAAAATTCGATAACCACAC
          1 TATGAAATTTCGATAACCACAC

             *        * *         
       1849 TGTGAAATTTGGGTAACCACAC
          1 TATGAAATTTCGATAACCACAC

                            * *  *
       1871 TATGAAATTTCGATAATCTCAG
          1 TATGAAATTTCGATAACCACAC

             *        *       **   
       1893 TGTGAAATTTTGATAATCTGC-C
          1 TATGAAATTTCGATAA-CCACAC

               *      **    *     
       1915 TATAAAATTTTAATAATCACAC
          1 TATGAAATTTCGATAACCACAC

                     *    *     *   
       1937 TAAAT-AAAATT-GGTAACCGCAC
          1 T--ATGAAATTTCGATAACCACAC

                       *           
       1959 TATGAAAATTTTGATAACCACAC
          1 TATG-AAATTTCGATAACCACAC

            *                 * * 
       1982 CATGAAATTTCGATAACCTCCC
          1 TATGAAATTTCGATAACCACAC

                 
       2004 TATGA
          1 TATGA

       2009 GAATGAAAAT


Statistics
Matches: 136,  Mismatches: 39, Indels: 14
        0.72            0.21        0.07

Matches are distributed among these distances:
  20    2  0.01
  21    1  0.01
  22  113  0.83
  23   18  0.13
  24    2  0.01

ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30


Consensus pattern (22 bp):   
TATGAAATTTCGATAACCACAC

Found at i:1857 original size:44 final size:45

Alignment explanation


    Indices: 1805--2008  Score: 157
    Period size: 44  Copynumber: 4.6  Consensus size: 45

       1795 TTAAACCTAA

                     *                                   
       1805 TATGAAATTCCGATAACCTCCCTATGAAAA-TTCGATAACCACAC
          1 TATGAAATTTCGATAACCTCCCTATGAAAATTTCGATAACCACAC

             *        * *     * *                  * *  *
       1849 TGTGAAATTTGGGTAACCACACTATG-AAATTTCGATAATCTCAG
          1 TATGAAATTTCGATAACCTCCCTATGAAAATTTCGATAACCACAC

             *        *     *  *             **    *     
       1893 TGTGAAATTTTGATAATCTGCCTAT-AAAATTTTAATAATCACAC
          1 TATGAAATTTCGATAACCTCCCTATGAAAATTTCGATAACCACAC

                     *    *     * *            *           
       1937 TAAAT-AAAATT-GGTAACCGCACTATGAAAATTTTGATAACCACAC
          1 T--ATGAAATTTCGATAACCTCCCTATGAAAATTTCGATAACCACAC

            *                          
       1982 CATGAAATTTCGATAACCTCCCTATGA
          1 TATGAAATTTCGATAACCTCCCTATGA

       2009 GAATGAAAAT


Statistics
Matches: 120,  Mismatches: 33, Indels: 13
        0.72            0.20        0.08

Matches are distributed among these distances:
  43    5  0.04
  44   79  0.66
  45   35  0.29
  46    1  0.01

ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30


Consensus pattern (45 bp):   
TATGAAATTTCGATAACCTCCCTATGAAAATTTCGATAACCACAC

Found at i:2163 original size:22 final size:22

Alignment explanation


    Indices: 2138--2259  Score: 106
    Period size: 22  Copynumber: 5.5  Consensus size: 22

       2128 CCTCCCTCCC

                        *        *
       2138 TATGAAATTTTGGTAACCTCTG
          1 TATGAAATTTTGATAACCTCTA

                                   
       2160 TATGAAATTTTGATAA-CTAC-A
          1 TATGAAATTTTGATAACCT-CTA

                   *               
       2181 CTATGAAGTTTTGATAACCTCTA
          1 -TATGAAATTTTGATAACCTCTA

                        *     *   
       2204 TATGAAATTTTGGTAACCAC-A
          1 TATGAAATTTTGATAACCTCTA

               *             *  * *
       2225 CTACGAAATTTTGATAATCTTTC
          1 -TATGAAATTTTGATAACCTCTA

                *       
       2248 TATGTAATTTTG
          1 TATGAAATTTTG

       2260 GTTTGATTGT


Statistics
Matches: 80,  Mismatches: 14, Indels: 12
        0.75            0.13        0.11

Matches are distributed among these distances:
  21    3  0.04
  22   74  0.93
  23    3  0.04

ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41


Consensus pattern (22 bp):   
TATGAAATTTTGATAACCTCTA

Found at i:2193 original size:44 final size:44

Alignment explanation


    Indices: 2137--2259  Score: 156
    Period size: 44  Copynumber: 2.8  Consensus size: 44

       2127 ACCTCCCTCC

                         *        *                 *   
       2137 CTATGAAATTTTGGTAACCTCTGTATGAAATTTTGATAACTACA
          1 CTATGAAATTTTGATAACCTCTATATGAAATTTTGATAACCACA

                   *                           *        
       2181 CTATGAAGTTTTGATAACCTCTATATGAAATTTTGGTAACCACA
          1 CTATGAAATTTTGATAACCTCTATATGAAATTTTGATAACCACA

               *             *  * *    *       
       2225 CTACGAAATTTTGATAATCTTTCTATGTAATTTTG
          1 CTATGAAATTTTGATAACCTCTATATGAAATTTTG

       2260 GTTTGATTGT


Statistics
Matches: 68,  Mismatches: 11, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  44   68  1.00

ACGTcount: A:0.33, C:0.14, G:0.13, T:0.41


Consensus pattern (44 bp):   
CTATGAAATTTTGATAACCTCTATATGAAATTTTGATAACCACA

Done.