Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000910.1 Corchorus olitorius cultivar O-4 contig00910, 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, 804

Length: 1341
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30


Found at i:705 original size:35 final size:35

Alignment explanation


    Indices: 659--1155  Score: 599
    Period size: 35  Copynumber: 14.0  Consensus size: 35

        649 ATCAATGTGA

                              *                
        659 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
          1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

                               *               * 
        694 AGATCAACTCTGATCATAAAAAAAACTTCTTGAAAGG
          1 AGATCAACTCTGATCAT--CAAAAACTTCTTGAAATG

                         *     *                 
        731 AGATCAACTCTGACCATATAAAAAACTTCTTGAAATG
          1 AGATCAACTCTGATC--ATCAAAAACTTCTTGAAATG

                 *       *     *                 
        768 AGATCGACTCTGACCATATAAAAAACTTCTTGAAATG
          1 AGATCAACTCTGATC--ATCAAAAACTTCTTGAAATG

                            *                   
        805 AGATCAACTCTGATCAACAAAAAC-TCTTTGAAATG
          1 AGATCAACTCTGATCATCAAAAACTTC-TTGAAATG

                            *                 * 
        840 AGATCAACTCTGATCAACAAAAAC-TCTTTGAAACG
          1 AGATCAACTCTGATCATCAAAAACTTC-TTGAAATG

                              *                
        875 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
          1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

                         *          *           
        910 AGATCAACTCTGACCAT-AAAAACATCTTGAAAATG
          1 AGATCAACTCTGATCATCAAAAACTTCTTG-AAATG

                             *         *     * 
        945 AGATCAACTCTGATCATAAAAAACTTCCTGAAAGG
          1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

                            * *                
        980 AGATCAACTCTGATCACCGAAAACTTCTTGAAATG
          1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

                     *   *                       
       1015 AGATCAACTTTGACCAT-AAAAACATT-TTGAAAATG
          1 AGATCAACTCTGATCATCAAAAAC-TTCTTG-AAATG

                *            *               * 
       1050 AGATTAACTCTGATCATAAAAAACTTCTTGAAAGG
          1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

                            * *              * 
       1085 AGATCAACTCTGATCACCGAAAACTTCTTGAAACG
          1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

                              *           *    
       1120 AGATCAACTCTGATCATCGAAAACTTCTTGGAATG
          1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

             
       1155 A
          1 A

       1156 CCGCACTGGA


Statistics
Matches: 408,  Mismatches: 42, Indels: 24
        0.86            0.09        0.05

Matches are distributed among these distances:
  34   20  0.05
  35  270  0.66
  36   21  0.05
  37   95  0.23
  39    2  0.00

ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26


Consensus pattern (35 bp):   
AGATCAACTCTGATCATCAAAAACTTCTTGAAATG

Found at i:1202 original size:54 final size:54

Alignment explanation


    Indices: 1120--1228  Score: 182
    Period size: 54  Copynumber: 2.0  Consensus size: 54

       1110 TCTTGAAACG

                         *                           *     *      
       1120 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATTATCTGA
          1 AGATCAACTCTGACCATCGAAAACTTCTTGGAATGACCGCAATGGATCATCTGA

                             *                                    
       1174 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCAATGGATCATCTGA
          1 AGATCAACTCTGACCATCGAAAACTTCTTGGAATGACCGCAATGGATCATCTGA

             
       1228 A
          1 A

       1229 CACCTGTTCT


Statistics
Matches: 51,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  54   51  1.00

ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27


Consensus pattern (54 bp):   
AGATCAACTCTGACCATCGAAAACTTCTTGGAATGACCGCAATGGATCATCTGA
Done.