Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024592.1 Corchorus olitorius cultivar O-4 contig24625, 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, 1000

Length: 12695
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.32


Found at i:10927 original size:38 final size:38

Alignment explanation


    Indices: 10885--10960  Score: 152
    Period size: 38  Copynumber: 2.0  Consensus size: 38

      10875 GTACTAAATG

                                                  
      10885 GAATTGCTAATCTAAACTAAAAGTATAACTAAGATGAC
          1 GAATTGCTAATCTAAACTAAAAGTATAACTAAGATGAC

                                                  
      10923 GAATTGCTAATCTAAACTAAAAGTATAACTAAGATGAC
          1 GAATTGCTAATCTAAACTAAAAGTATAACTAAGATGAC

      10961 CAAAGAGAAC


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  38   38  1.00

ACGTcount: A:0.47, C:0.13, G:0.13, T:0.26


Consensus pattern (38 bp):   
GAATTGCTAATCTAAACTAAAAGTATAACTAAGATGAC

Found at i:11332 original size:29 final size:29

Alignment explanation


    Indices: 10979--11333  Score: 349
    Period size: 29  Copynumber: 12.2  Consensus size: 29

      10969 ACCCAGAGTA

                                       * 
      10979 TGCAAAAATGACCAAAATGCCCCTGGACG
          1 TGCAAAAATGACCAAAATGCCCCTGGATG

                                *         
      11008 TGCAAAAAATGACCAAAATGTCCCTGGATG
          1 TGC-AAAAATGACCAAAATGCCCCTGGATG

              *   * *            *  *    
      11038 TGTAAATACGACCAAAATGCCTCTAGATG
          1 TGCAAAAATGACCAAAATGCCCCTGGATG

                    *  *             *    
      11067 TGCAAAAACGATCAAAATGCCCCTGAATTG
          1 TGCAAAAATGACCAAAATGCCCCTGGA-TG

                                  *  *   
      11097 TGCAAAAATGACCAAAATGCCCTTGAATG
          1 TGCAAAAATGACCAAAATGCCCCTGGATG

                                    *    
      11126 TGC-AAAATGACCAAAATGCCCCTAGATG
          1 TGCAAAAATGACCAAAATGCCCCTGGATG

                                  *     *
      11154 TGCAAAAATGACCAAAATGCCCTTGGATA
          1 TGCAAAAATGACCAAAATGCCCCTGGATG

               **               *    *   
      11183 TGCGTAAATGACCAAAATGCTCCTGAATG
          1 TGCAAAAATGACCAAAATGCCCCTGGATG

                       **         *      *
      11212 TGCAAAAATGATAAAAATG-CCATGGGATA
          1 TGCAAAAATGACCAAAATGCCCCT-GGATG

            *  *          *         **  *
      11241 CGCTAAAATGACCATAATG-CCCTTCATA
          1 TGCAAAAATGACCAAAATGCCCCTGGATG

                                *    *   
      11269 TGCAAAAATGACCAAAATGCTCCTGAATG
          1 TGCAAAAATGACCAAAATGCCCCTGGATG

             *            *              
      11298 TACAAAAATGACCATAATGCCCCTGGAT-
          1 TGCAAAAATGACCAAAATGCCCCTGGATG

                    
      11326 TCGCAAAA
          1 T-GCAAAA

      11334 GGTCAATTAA


Statistics
Matches: 263,  Mismatches: 57, Indels: 12
        0.79            0.17        0.04

Matches are distributed among these distances:
  28   47  0.18
  29  164  0.62
  30   52  0.20

ACGTcount: A:0.40, C:0.22, G:0.17, T:0.21


Consensus pattern (29 bp):   
TGCAAAAATGACCAAAATGCCCCTGGATG

Found at i:12196 original size:28 final size:28

Alignment explanation


    Indices: 12165--12273  Score: 94
    Period size: 28  Copynumber: 3.8  Consensus size: 28

      12155 CATTAACCAT

                                        
      12165 GTCCAGGGGCACTTTGATCATTTTGCAC
          1 GTCCAGGGGCACTTTGATCATTTTGCAC

                            *             *
      12193 GTCCAGGGG-ACATTTTAGTCACTTTTGCAT
          1 GTCCAGGGGCAC-TTTGA-TCA-TTTTGCAC

            *          *    *    *      
      12223 ATCCAGGGGCATTTTGGTCATCTTGCAC
          1 GTCCAGGGGCACTTTGATCATTTTGCAC

               *     * *    *      
      12251 GTCTAGGGGTATTTTGGTCATTT
          1 GTCCAGGGGCACTTTGATCATTT

      12274 CAAGTGCACT


Statistics
Matches: 65,  Mismatches: 12, Indels: 8
        0.76            0.14        0.09

Matches are distributed among these distances:
  27    2  0.03
  28   38  0.58
  29    6  0.09
  30   18  0.28
  31    1  0.02

ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37


Consensus pattern (28 bp):   
GTCCAGGGGCACTTTGATCATTTTGCAC
Done.