Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008151.1 Corchorus olitorius cultivar O-4 contig08178, 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, 645

Length: 1076
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28


Found at i:837 original size:35 final size:35

Alignment explanation


    Indices: 792--1072  Score: 343
    Period size: 35  Copynumber: 7.9  Consensus size: 35

        782 ATCAATGTGA

                             **               *
        792 AGATCAACTCTGATCATCGAAAACTTCTTGAAATA
          1 AGATCAACTCTGATCATAAAAAACTTCTTGAAATG

                                                * 
        827 AGATCAACTCTGATCATAAAAAAAAACTTCTTGAAAGG
          1 AGATCAACTCTGATCAT---AAAAAACTTCTTGAAATG

                         *                    * 
        865 AGATCAACTCTGACCATAAAAAAACTTCTTGAAACG
          1 AGATCAACTCTGATCAT-AAAAAACTTCTTGAAATG

                              *           *   * 
        901 AGATCAACTCTGATCGA-CAAAAACTTCTTAAAAGG
          1 AGATCAACTCTGATC-ATAAAAAACTTCTTGAAATG

                                               
        936 AGATCAACTCTGATCAT-AAAAACTTCTTGAAATG
          1 AGATCAACTCTGATCATAAAAAACTTCTTGAAATG

               *             **              * 
        970 AGACCAACTCTGATCATTGAAAACTTCTTGAAACG
          1 AGATCAACTCTGATCATAAAAAACTTCTTGAAATG

                             **                 
       1005 AGATCAACTCTGATCATCGAAAACTTCTT-ACAATG
          1 AGATCAACTCTGATCATAAAAAACTTCTTGA-AATG

                              *              
       1040 AGATCAACTCTGATCATAGAAAACTTCTTGAAA
          1 AGATCAACTCTGATCATAAAAAACTTCTTGAAA

       1073 CGAG


Statistics
Matches: 219,  Mismatches: 19, Indels: 16
        0.86            0.07        0.06

Matches are distributed among these distances:
  34   33  0.15
  35  122  0.56
  36   33  0.15
  37    1  0.00
  38   30  0.14

ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26


Consensus pattern (35 bp):   
AGATCAACTCTGATCATAAAAAACTTCTTGAAATG

Found at i:1028 original size:104 final size:105

Alignment explanation


    Indices: 792--1072  Score: 404
    Period size: 104  Copynumber: 2.6  Consensus size: 105

        782 ATCAATGTGA

                                         *    *                              
        792 AGATCAACTCTGATCATCGAAAACTTCTTGAAATAAGATCAACTCTGATCATAAAAAAAAACTTC
          1 AGATCAACTCTGATCATCGAAAACTTCTTAAAATGAGATCAACTCTGATCAT----AAAAACTTC

                       *                                
        857 TTGAAAGGAGATCAACTCTGACCATAAAAAAACTTCTTGAAACG
         62 TTGAAAGGAGACCAACTCTGACCATAAAAAAACTTCTTGAAACG

                               *              *                              
        901 AGATCAACTCTGATCGA-CAAAAACTTCTTAAAAGGAGATCAACTCTGATCATAAAAACTTCTTG
          1 AGATCAACTCTGATC-ATCGAAAACTTCTTAAAATGAGATCAACTCTGATCATAAAAACTTCTTG

               *              *    **                
        965 AAATGAGACCAACTCTGATCAT-TGAAAACTTCTTGAAACG
         65 AAAGGAGACCAACTCTGACCATAAAAAAACTTCTTGAAACG

                                          *                                  
       1005 AGATCAACTCTGATCATCGAAAACTTCTTACAATGAGATCAACTCTGATCATAGAAAACTTCTTG
          1 AGATCAACTCTGATCATCGAAAACTTCTTAAAATGAGATCAACTCTGATCATA-AAAACTTCTTG

               
       1070 AAA
         65 AAA

       1073 CGAG


Statistics
Matches: 157,  Mismatches: 12, Indels: 10
        0.88            0.07        0.06

Matches are distributed among these distances:
 103    1  0.01
 104   64  0.41
 105   45  0.29
 109   46  0.29
 110    1  0.01

ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26


Consensus pattern (105 bp):   
AGATCAACTCTGATCATCGAAAACTTCTTAAAATGAGATCAACTCTGATCATAAAAACTTCTTGA
AAGGAGACCAACTCTGACCATAAAAAAACTTCTTGAAACG
Done.