Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007555.1 Corchorus olitorius cultivar O-4 contig07580, 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, 826

Length: 1378
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:754 original size:33 final size:33

Alignment explanation


    Indices: 717--782  Score: 96
    Period size: 33  Copynumber: 2.0  Consensus size: 33

        707 TCCTTCCTCT

                    *     *  *               
        717 ACACATCCGTCACCCACTATCACACCTCCATCC
          1 ACACATCCCTCACCAACCATCACACCTCCATCC

                                       *     
        750 ACACATCCCTCACCAACCATCACACCTTCATCC
          1 ACACATCCCTCACCAACCATCACACCTCCATCC

        783 GCTCCTCCTT


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  33   29  1.00

ACGTcount: A:0.29, C:0.52, G:0.02, T:0.18


Consensus pattern (33 bp):   
ACACATCCCTCACCAACCATCACACCTCCATCC

Found at i:836 original size:33 final size:33

Alignment explanation


    Indices: 798--885  Score: 95
    Period size: 33  Copynumber: 2.6  Consensus size: 33

        788 TCCTTCCCCA

                             *            *  
        798 ACACATCCTTCACCCACTATCACACCTCCATCC
          1 ACACATCCTTCACCCACCATCACACCTCCACCC

                    *     *            *     
        831 ACACATCCCTCACCAACCATCACACCTTCACCC
          1 ACACATCCTTCACCCACCATCACACCTCCACCC

              * *      *          
        864 ACTCCTCCTTCCCCCACACATC
          1 ACACATCCTTCACCCAC-CATC

        886 CTACACCAAC


Statistics
Matches: 44,  Mismatches: 10, Indels: 1
        0.80            0.18        0.02

Matches are distributed among these distances:
  33   40  0.91
  34    4  0.09

ACGTcount: A:0.26, C:0.55, G:0.00, T:0.19


Consensus pattern (33 bp):   
ACACATCCTTCACCCACCATCACACCTCCACCC

Found at i:842 original size:81 final size:81

Alignment explanation


    Indices: 707--892  Score: 309
    Period size: 81  Copynumber: 2.3  Consensus size: 81

        697 GGTACTTGAA

                   * *        *                                              
        707 TCCTTCCTCTACACATCCGTCACCCACTATCACACCTCCATCCACACATCCCTCACCAACCATCA
          1 TCCTTCCCCAACACATCCTTCACCCACTATCACACCTCCATCCACACATCCCTCACCAACCATCA

                    *  *    
        772 CACCTTCATCCGCTCC
         66 CACCTTCACCCACTCC

                                                                             
        788 TCCTTCCCCAACACATCCTTCACCCACTATCACACCTCCATCCACACATCCCTCACCAACCATCA
          1 TCCTTCCCCAACACATCCTTCACCCACTATCACACCTCCATCCACACATCCCTCACCAACCATCA

                            
        853 CACCTTCACCCACTCC
         66 CACCTTCACCCACTCC

                     *         *    
        869 TCCTTCCCCCACACATCCTACACC
          1 TCCTTCCCCAACACATCCTTCACC

        893 AACCAACATA


Statistics
Matches: 98,  Mismatches: 7, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  81   98  1.00

ACGTcount: A:0.24, C:0.54, G:0.01, T:0.21


Consensus pattern (81 bp):   
TCCTTCCCCAACACATCCTTCACCCACTATCACACCTCCATCCACACATCCCTCACCAACCATCA
CACCTTCACCCACTCC

Found at i:847 original size:48 final size:48

Alignment explanation


    Indices: 750--866  Score: 117
    Period size: 48  Copynumber: 2.4  Consensus size: 48

        740 ACCTCCATCC

                    *     *  *         *     * * *   *  *   
        750 ACACATCCCTCACCAACCATCACACCTTCATCCGCTCCTCCTTCCCCA
          1 ACACATCCTTCACCCACTATCACACCTCCATCCACACATCCCTCACCA

                                                            
        798 ACACATCCTTCACCCACTATCACACCTCCATCCACACATCCCTCACCA
          1 ACACATCCTTCACCCACTATCACACCTCCATCCACACATCCCTCACCA

                    *            
        846 ACCATCACACCTTCACCCACT
          1 A-CA-CA-TCCTTCACCCACT

        867 CCTCCTTCCC


Statistics
Matches: 56,  Mismatches: 10, Indels: 3
        0.81            0.14        0.04

Matches are distributed among these distances:
  48   40  0.71
  49    2  0.04
  50    2  0.04
  51   12  0.21

ACGTcount: A:0.26, C:0.53, G:0.01, T:0.20


Consensus pattern (48 bp):   
ACACATCCTTCACCCACTATCACACCTCCATCCACACATCCCTCACCA
Done.