Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010570.1 Corchorus olitorius cultivar O-4 contig10602, 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, 668

Length: 1114
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31


Found at i:803 original size:35 final size:35

Alignment explanation


    Indices: 757--1111  Score: 462
    Period size: 35  Copynumber: 10.0  Consensus size: 35

        747 ATCAATATGA

                              *                
        757 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
          1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

                               *               * 
        792 AGATCAACTCTGATCATAAAAAAAACTTCTTGAAAGG
          1 AGATCAACTCTGATCAT--CAAAAACTTCTTGAAATG

                         *                       
        829 AGATCAACTCTGACCATACAAAAAACTTCTTGAAATG
          1 AGATCAACTCTGATCAT-C-AAAAACTTCTTGAAATG

                         *          *           
        866 AGATCAACTCTGACCAT-AAAAACATCTTGAAAATG
          1 AGATCAACTCTGATCATCAAAAACTTCTTG-AAATG

                             *         *     * 
        901 AGATCAACTCTGATCATAAAAAACTTCCTGAAACG
          1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

                              *                
        936 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
          1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

                         *          *           
        971 AGATCAACTCTGACCAT-AAAAACATCTTGAAAATG
          1 AGATCAACTCTGATCATCAAAAACTTCTTG-AAATG

                             *         *     * 
       1006 AGATCAACTCTGATCATAAAAAACTTCCTGAAAGG
          1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

                            * *              * 
       1041 AGATCAACTCTGATCACCGAAAACTTCTTGAAACG
          1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

                              *           *    
       1076 AGATCAACTCTGATCATCGAAAACTTCTTGGAATG
          1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

             
       1111 A
          1 A

       1112 CCG


Statistics
Matches: 283,  Mismatches: 30, Indels: 14
        0.87            0.09        0.04

Matches are distributed among these distances:
  34   21  0.07
  35  177  0.63
  36   21  0.07
  37   64  0.23

ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25


Consensus pattern (35 bp):   
AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

Found at i:987 original size:105 final size:105

Alignment explanation


    Indices: 757--1088  Score: 531
    Period size: 105  Copynumber: 3.1  Consensus size: 105

        747 ATCAATATGA

                         *    *     *                                        
        757 AGATCAACTCTGATCATCGAAAACTTCTTG-AAATGAGATCAACTCTGATCATAAAAAAAACTTC
          1 AGATCAACTCTGACCAT-AAAAACATCTTGAAAATGAGATCAACTCTGATCAT--AAAAAACTTC

            *                    *      *                
        821 TTGAAAGGAGATCAACTCTGACCATACAAAAAACTTCTTGAAATG
         63 CTGAAAGGAGATCAACTCTGATCAT-C-GAAAACTTCTTGAAATG

                                                                             
        866 AGATCAACTCTGACCATAAAAACATCTTGAAAATGAGATCAACTCTGATCATAAAAAACTTCCTG
          1 AGATCAACTCTGACCATAAAAACATCTTGAAAATGAGATCAACTCTGATCATAAAAAACTTCCTG

               *                                    
        931 AAACGAGATCAACTCTGATCATCGAAAACTTCTTGAAATG
         66 AAAGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATG

                                                                             
        971 AGATCAACTCTGACCATAAAAACATCTTGAAAATGAGATCAACTCTGATCATAAAAAACTTCCTG
          1 AGATCAACTCTGACCATAAAAACATCTTGAAAATGAGATCAACTCTGATCATAAAAAACTTCCTG

                                 *                * 
       1036 AAAGGAGATCAACTCTGATCACCGAAAACTTCTTGAAACG
         66 AAAGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATG

                         
       1076 AGATCAACTCTGA
          1 AGATCAACTCTGA

       1089 TCATCGAAAA


Statistics
Matches: 212,  Mismatches: 10, Indels: 6
        0.93            0.04        0.03

Matches are distributed among these distances:
 105  131  0.62
 106    1  0.00
 107   32  0.15
 108   10  0.05
 109   38  0.18

ACGTcount: A:0.42, C:0.21, G:0.13, T:0.24


Consensus pattern (105 bp):   
AGATCAACTCTGACCATAAAAACATCTTGAAAATGAGATCAACTCTGATCATAAAAAACTTCCTG
AAAGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATG

Done.