Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008550.1 Corchorus olitorius cultivar O-4 contig08577, 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, 687

Length: 1146
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29


Found at i:914 original size:55 final size:54

Alignment explanation


    Indices: 812--1142  Score: 268
    Period size: 54  Copynumber: 6.0  Consensus size: 54

        802 CTTAATCAAC

                           *                          *               
        812 CGCACTGGATC-ATTTAAGATTCAAC-CTTGATCA-CGAAAACCTTTCTTGGAATGAT
          1 CGCACTGGATCAATTGAAGA-TCAACTC-TGATCATC-AAAAAC-TTCTTGGAATGAT

                               *                      *            
        867 CGCACTGGATCCAATTGAAAATCAACTCTGATCATCAAAAACGTCTTGGAATGA-
          1 CGCACTGGAT-CAATTGAAGATCAACTCTGATCATCAAAAACTTCTTGGAATGAT

                    *                          **    *         *  *
        921 CTGCACTGTATCAATTGAAGATCAACTCTGATCATTGAAAATTTCTTGGAACGAC
          1 C-GCACTGGATCAATTGAAGATCAACTCTGATCATCAAAAACTTCTTGGAATGAT

                  *           *                                    *
        976 CGCACTAGATC-ATCTG-GGATCAACTCTGAT--TCTAAAAACTTCTTGGAATGAC
          1 CGCACTGGATCAAT-TGAAGATCAACTCTGATCATC-AAAAACTTCTTGGAATGAT

                       *      *                    *              *    
       1028 CGCACTGGAT-TATCATGGAGATCAACTCTAGATCATTGGAAAAACTTCTTGGATTGAT
          1 CGCACTGGATCAAT--TGAAGATCAACTCT-GATCA-T-CAAAAACTTCTTGGAATGAT

                 *                        *                  *       
       1086 CGCACAGGATCAATT-AGAGATCAACTACTAATCATACAAAAACTTCTTAGAATGAT
          1 CGCACTGGATCAATTGA-AGATCAACT-CTGATCAT-CAAAAACTTCTTGGAATGAT

             
       1142 C
          1 C

       1143 ACAC


Statistics
Matches: 225,  Mismatches: 32, Indels: 37
        0.77            0.11        0.13

Matches are distributed among these distances:
  51    1  0.00
  52   27  0.12
  53   17  0.08
  54   58  0.26
  55   33  0.15
  56   36  0.16
  57   22  0.10
  58   29  0.13
  59    2  0.01

ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28


Consensus pattern (54 bp):   
CGCACTGGATCAATTGAAGATCAACTCTGATCATCAAAAACTTCTTGGAATGAT

Done.