Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01003763.1 Corchorus olitorius cultivar O-4 contig03773, 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, 640

Length: 1067
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30


Found at i:820 original size:72 final size:73

Alignment explanation


    Indices: 643--1021  Score: 489
    Period size: 72  Copynumber: 5.1  Consensus size: 73

        633 CATTGTGAGT

                                      *             *                        
        643 GAACAGGGGCAAAGGCACAGAG-GGAATTTAGGGGATAGGATTTAGGCAAGGAGGCAGTAGTTTT
          1 GAACAGGGGCAAAGGCACAGAGTGG-GTTTAGGGGATAGGGTTTAGGCAAGGAGGCAGTAGTTTT

                 *   
        707 TTATTGAGG
         65 TTATTTAGG

                  *                                                          
        716 GAACAGCGGCAAAGGCACAGAGTGGGTTTAGGGGATAGGGTTTAGGCAAGGAGGCAGTAG-TTTT
          1 GAACAGGGGCAAAGGCACAGAGTGGGTTTAGGGGATAGGGTTTAGGCAAGGAGGCAGTAGTTTTT

                    
        780 TATTTAGG
         66 TATTTAGG

                       *                                      *      *       
        788 GAACAGGGGCATAGGCACAGAGTGGGTTTAGGGGATAGGCG-TTAGGCAAAGAGGCAATAG-TTT
          1 GAACAGGGGCAAAGGCACAGAGTGGGTTTAGGGGATAGG-GTTTAGGCAAGGAGGCAGTAGTTTT

                     
        851 TTATTTAGG
         65 TTATTTAGG

                       *                                      *      *       
        860 GAACAGGGGCATAGGCACAGAGTGGGTTTAGGGGATAGGCG-TTAGGCAAAGAGGCAATAGTTTT
          1 GAACAGGGGCAAAGGCACAGAGTGGGTTTAGGGGATAGG-GTTTAGGCAAGGAGGCAGTAGTTTT

               *     
        924 TTAATTAGG
         65 TTATTTAGG

                                          *         *                      * 
        933 GAACAGGGGCAAAGGCACAAAGGCACAAAGGGGGTTTAGGAGATAGGGTTTAGGCAAGGAGGCTG
          1 GAACAGGGGCAAAGGCAC--A-G-----AGTGGGTTTAGGGGATAGGGTTTAGGCAAGGAGGCAG

                        *   
        998 TAGTTTTTTATTGAGG
         58 TAGTTTTTTATTTAGG

                    
       1014 GAACAGGG
          1 GAACAGGG

       1022 ATAAGGCGTT


Statistics
Matches: 277,  Mismatches: 17, Indels: 16
        0.89            0.05        0.05

Matches are distributed among these distances:
  72  137  0.49
  73   83  0.30
  74    2  0.01
  75    1  0.00
  76    1  0.00
  80    1  0.00
  81   52  0.19

ACGTcount: A:0.30, C:0.09, G:0.38, T:0.22


Consensus pattern (73 bp):   
GAACAGGGGCAAAGGCACAGAGTGGGTTTAGGGGATAGGGTTTAGGCAAGGAGGCAGTAGTTTTT
TATTTAGG

Found at i:925 original size:145 final size:145

Alignment explanation


    Indices: 643--951  Score: 462
    Period size: 145  Copynumber: 2.1  Consensus size: 145

        633 CATTGTGAGT

                                                    *        *      *        
        643 GAACAGGGGCAAAGGCACAGAGGGAATTTAGGGGATAGGATTTAGGCAAGGAGGCAGTAGTTTTT
          1 GAACAGGGGCAAAGGCACAGAGGGAATTTAGGGGATAGGAGTTAGGCAAAGAGGCAATAGTTTTT

                                                                     *      *
        708 TATTGAGGGAACAGCGGCAAAGGCACAGAGTGGGTTTAGGGGATAGGGTTTAGGCAAGGAGGCAG
         66 TATTGAGGGAACAGCGGCAAAGGCACAGAGTGGGTTTAGGGGATAGGGTTTAGGCAAAGAGGCAA

                     *     
        773 TAGTTTTTATTTAGG
        131 TAGTTTTTAATTAGG

                       *              *             *                        
        788 GAACAGGGGCATAGGCACAGAGTGG-GTTTAGGGGATAGGCGTTAGGCAAAGAGGCAATAG-TTT
          1 GAACAGGGGCAAAGGCACAGAG-GGAATTTAGGGGATAGGAGTTAGGCAAAGAGGCAATAGTTTT

                 *         *    *                                            
        851 TTATTTAGGGAACAGGGGCATAGGCACAGAGTGGGTTTAGGGGATAGGCG-TTAGGCAAAGAGGC
         65 TTATTGAGGGAACAGCGGCAAAGGCACAGAGTGGGTTTAGGGGATAGG-GTTTAGGCAAAGAGGC

                              
        915 AATAGTTTTTTAATTAGG
        129 AATAG-TTTTTAATTAGG

                               
        933 GAACAGGGGCAAAGGCACA
          1 GAACAGGGGCAAAGGCACA

        952 AAGGCACAAA


Statistics
Matches: 148,  Mismatches: 13, Indels: 6
        0.89            0.08        0.04

Matches are distributed among these distances:
 144   65  0.44
 145   81  0.55
 146    2  0.01

ACGTcount: A:0.30, C:0.10, G:0.38, T:0.22


Consensus pattern (145 bp):   
GAACAGGGGCAAAGGCACAGAGGGAATTTAGGGGATAGGAGTTAGGCAAAGAGGCAATAGTTTTT
TATTGAGGGAACAGCGGCAAAGGCACAGAGTGGGTTTAGGGGATAGGGTTTAGGCAAAGAGGCAA
TAGTTTTTAATTAGG

Found at i:1059 original size:81 final size:81

Alignment explanation


    Indices: 872--1021  Score: 214
    Period size: 81  Copynumber: 1.9  Consensus size: 81

        862 ACAGGGGCAT

                   *                                                         
        872 AGGCACAGAGTGGGTTTAGGGGATAGGCGTTAGGCAAAGAGGCAATAGTTTTTTAATTAGGGAAC
          1 AGGCACAAAGTGGGTTTAGGGGATAGGCGTTAGGCAAAGAGGCAATAGTTTTTTAATTAGGGAAC

                            
        937 AGGGGCAAAGGCACAA
         66 AGGGGCAAAGGCACAA

                      *         *                 *     **                   
        953 AGGCACAAAGGGGGTTTAGGAGATAGG-GTTTAGGCAAGGAGGCTGTAGTTTTTT-ATTGAGGGA
          1 AGGCACAAAGTGGGTTTAGGGGATAGGCG-TTAGGCAAAGAGGCAATAGTTTTTTAATT-AGGGA

                  
       1016 ACAGGG
         64 ACAGGG

       1022 ATAAGGCGTT


Statistics
Matches: 61,  Mismatches: 6, Indels: 4
        0.86            0.08        0.06

Matches are distributed among these distances:
  80    4  0.07
  81   57  0.93

ACGTcount: A:0.31, C:0.09, G:0.38, T:0.22


Consensus pattern (81 bp):   
AGGCACAAAGTGGGTTTAGGGGATAGGCGTTAGGCAAAGAGGCAATAGTTTTTTAATTAGGGAAC
AGGGGCAAAGGCACAA
Done.