Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018480.1 Corchorus olitorius cultivar O-4 contig18513, 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: 7598
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30


Found at i:3135 original size:30 final size:30

Alignment explanation


    Indices: 3073--3243  Score: 129
    Period size: 30  Copynumber: 5.9  Consensus size: 30

       3063 CCCCTGGATA

                    *             *   **  
       3073 TGCAAA-ATGACCAAAATGCCCTTG-GGTG
          1 TGCAAACACGACCAAAATGCCCCTGAATTG

                       *         *        
       3101 TGCAAACACGATCAAAATGCCTCTGAATTG
          1 TGCAAACACGACCAAAATGCCCCTGAATTG

                    *             *   *    
       3131 TGCAAACATGACCAAAATG-CCATCGGA-TG
          1 TGCAAACACGACCAAAATGCCCCT-GAATTG

                    *                 **  
       3160 TGCAAA-ATGACCAAAATGCCCCT-AGGTG
          1 TGCAAACACGACCAAAATGCCCCTGAATTG

                     * *              *   
       3188 TGCAAACACTATCAAAATGCCCCTGAGTTG
          1 TGCAAACACGACCAAAATGCCCCTGAATTG

                  * *   *             
       3218 TGCAAAAATGACAAAAATGCCCCTGA
          1 TGCAAACACGACCAAAATGCCCCTGA

       3244 GTGTGCGAAT


Statistics
Matches: 113,  Mismatches: 23, Indels: 12
        0.76            0.16        0.08

Matches are distributed among these distances:
  28   26  0.23
  29   41  0.36
  30   46  0.41

ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20


Consensus pattern (30 bp):   
TGCAAACACGACCAAAATGCCCCTGAATTG

Found at i:3164 original size:87 final size:87

Alignment explanation


    Indices: 3044--3238  Score: 284
    Period size: 87  Copynumber: 2.2  Consensus size: 87

       3034 CCCCCGGATA

                              *   *                            * *           
       3044 TGCAAAAATGACAAAAATACC-CCTGGATATGCAAAATGACCAAAATGCCCTTGGGTGTGCAAAC
          1 TGCAAAAATGACAAAAATGCCATC-GGATATGCAAAATGACCAAAATGCCCCTAGGTGTGCAAAC

                          *        
       3108 ACGATCAAAATGCCTCTGAATTG
         65 ACGATCAAAATGCCCCTGAATTG

                  *     *               *                                    
       3131 TGCAAACATGACCAAAATGCCATCGGATGTGCAAAATGACCAAAATGCCCCTAGGTGTGCAAACA
          1 TGCAAAAATGACAAAAATGCCATCGGATATGCAAAATGACCAAAATGCCCCTAGGTGTGCAAACA

             *                *   
       3196 CTATCAAAATGCCCCTGAGTTG
         66 CGATCAAAATGCCCCTGAATTG

                                 
       3218 TGCAAAAATGACAAAAATGCC
          1 TGCAAAAATGACAAAAATGCC

       3239 CCTGAGTGTG


Statistics
Matches: 95,  Mismatches: 12, Indels: 2
        0.87            0.11        0.02

Matches are distributed among these distances:
  87   94  0.99
  88    1  0.01

ACGTcount: A:0.39, C:0.23, G:0.18, T:0.19


Consensus pattern (87 bp):   
TGCAAAAATGACAAAAATGCCATCGGATATGCAAAATGACCAAAATGCCCCTAGGTGTGCAAACA
CGATCAAAATGCCCCTGAATTG

Found at i:3244 original size:30 final size:30

Alignment explanation


    Indices: 3013--3249  Score: 172
    Period size: 29  Copynumber: 8.1  Consensus size: 30

       3003 TAAATTAAAA

                            * * *    *     
       3013 GTGCAAAAACTGACCATACTACCCCCG-GAT
          1 GTGCAAAAA-TGACCAAAATGCCCCTGAGAT

            *            *     *          
       3043 ATGCAAAAATGACAAAAATACCCCTG-GAT
          1 GTGCAAAAATGACCAAAATGCCCCTGAGAT

            *                      *    * 
       3072 ATGC-AAAATGACCAAAATGCCCTTG-GGT
          1 GTGCAAAAATGACCAAAATGCCCCTGAGAT

                   * *  *         *        
       3100 GTGCAAACACGATCAAAATGCCTCTGA-ATT
          1 GTGCAAAAATGACCAAAATGCCCCTGAGA-T

                   *               *       
       3130 GTGCAAACATGACCAAAATG-CCATCG-GAT
          1 GTGCAAAAATGACCAAAATGCCCCT-GAGAT

                                        * 
       3159 GTGC-AAAATGACCAAAATGCCCCT-AGGT
          1 GTGCAAAAATGACCAAAATGCCCCTGAGAT

                     *   *               * 
       3187 GTGCAAACACT-ATCAAAATGCCCCTGAGTT
          1 GTGCAAA-AATGACCAAAATGCCCCTGAGAT

                         *                
       3217 GTGCAAAAATGACAAAAATGCCCCTGAG-T
          1 GTGCAAAAATGACCAAAATGCCCCTGAGAT

                
       3246 GTGC
          1 GTGC

       3250 GAATGGTCGG


Statistics
Matches: 167,  Mismatches: 29, Indels: 23
        0.76            0.13        0.11

Matches are distributed among these distances:
  28   43  0.26
  29   68  0.41
  30   56  0.34

ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19


Consensus pattern (30 bp):   
GTGCAAAAATGACCAAAATGCCCCTGAGAT

Done.