Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018697.1 Corchorus olitorius cultivar O-4 contig18730, 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, 961

Length: 1603
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32


Found at i:248 original size:48 final size:48

Alignment explanation


    Indices: 169--322  Score: 218
    Period size: 48  Copynumber: 3.1  Consensus size: 48

        159 GAACAAGAAG

                                      *                      
        169 TTTTACAATAAAATTGCTTTCCATTTATGAGTTCAAGATCAAAATTCGC
          1 TTTT-CAATAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGC

                                    *          *         *  
        218 TTTTCAATAAAATTGCTTTCCATTCGTGAGTTCAATATCAAAATTTGC
          1 TTTTCAATAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGC

                        *     *              *                
        266 TTTTCAAAGTAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGC
          1 TTTTC-AA-TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGC

                   
        316 TTTTCAA
          1 TTTTCAA

        323 AGGACATTGA


Statistics
Matches: 93,  Mismatches: 10, Indels: 4
        0.87            0.09        0.04

Matches are distributed among these distances:
  48   45  0.48
  49    8  0.09
  50   40  0.43

ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39


Consensus pattern (48 bp):   
TTTTCAATAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGC

Found at i:308 original size:50 final size:50

Alignment explanation


    Indices: 177--324  Score: 219
    Period size: 50  Copynumber: 3.0  Consensus size: 50

        167 AGTTTTACAA

                              *                               
        177 TAAAATTGCTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTC-AA-
          1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG

                             *          *         *           
        225 TAAAATTGCTTTCCATTCGTGAGTTCAATATCAAAATTTGCTTTTCAAAG
          1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG

               *     *              *                         
        275 TAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
          1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG

        325 GACATTGAAG


Statistics
Matches: 88,  Mismatches: 10, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
  48   42  0.48
  49    2  0.02
  50   44  0.50

ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38


Consensus pattern (50 bp):   
TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG

Found at i:1070 original size:50 final size:50

Alignment explanation


    Indices: 993--1261  Score: 448
    Period size: 50  Copynumber: 5.4  Consensus size: 50

        983 TCCGAATGCT

                                              *               
        993 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATATGAGTCAATTATCAAC
          1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAAC

             *                                                
       1043 ACAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAAC
          1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAAC

             **                *               *              
       1093 ACCGGCTTTTCCACAAGCCGAACTCGTTTCCATACAAGTCAATTATCAAC
          1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAAC

                               *                              
       1143 ATAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAAC
          1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAAC

                 *                                            
       1193 ATAGGATTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAAC
          1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAAC

              *          *     
       1243 ATGGGCTTTTCCATAAGCC
          1 ATAGGCTTTTCCACAAGCC

       1262 GAGTTTAATG


Statistics
Matches: 206,  Mismatches: 13, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  50  206  1.00

ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28


Consensus pattern (50 bp):   
ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAAC

Done.