Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017790.1 Corchorus olitorius cultivar O-4 contig17823, 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: 5144
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30


Found at i:619 original size:62 final size:62

Alignment explanation


    Indices: 535--864  Score: 590
    Period size: 62  Copynumber: 5.3  Consensus size: 62

        525 ATTTCCTCAG

                                             *                            
        535 CATGACAACTTCTGGTGTCAAGATAATAATTTGCTATGACAACTTCTGGTGTCAAAAATTTT
          1 CATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTT

                                                                   *      
        597 CATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAATAATTTT
          1 CATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTT

                                             *             *              
        659 CATGACAACTTCTGGTGTCAAGATAATAATTTGCTATGACAACTTCTAGTGTCAAAAATTTT
          1 CATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTT

                                                                          
        721 CATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTT
          1 CATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTT

                                                                   *      
        783 CATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAATAA-TTT
          1 CATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTT

              *                  
        844 CTGTGACAACTTCTGGTGTCA
          1 C-ATGACAACTTCTGGTGTCA

        865 TTTGTAAGAC


Statistics
Matches: 258,  Mismatches: 9, Indels: 2
        0.96            0.03        0.01

Matches are distributed among these distances:
  61    4  0.02
  62  254  0.98

ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Consensus pattern (62 bp):   
CATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTT

Found at i:883 original size:30 final size:30

Alignment explanation


    Indices: 847--911  Score: 121
    Period size: 30  Copynumber: 2.2  Consensus size: 30

        837 ATAATTTCTG

                              *           
        847 TGACAACTTCTGGTGTCATTTGTAAGACCA
          1 TGACAACTTCTGGTGTCAATTGTAAGACCA

                                          
        877 TGACAACTTCTGGTGTCAATTGTAAGACCA
          1 TGACAACTTCTGGTGTCAATTGTAAGACCA

                 
        907 TGACA
          1 TGACA

        912 GGTGTCATTT


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   34  1.00

ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31


Consensus pattern (30 bp):   
TGACAACTTCTGGTGTCAATTGTAAGACCA

Found at i:923 original size:24 final size:26

Alignment explanation


    Indices: 857--926  Score: 81
    Period size: 30  Copynumber: 2.6  Consensus size: 26

        847 TGACAACTTC

                                      
        857 TGGTGTCATTTGTAAGACCATGACAA
          1 TGGTGTCATTTGTAAGACCATGACAA

                        *                 
        883 CTTCTGGTGTCAATTGTAAGACCATGAC-A
          1 ----TGGTGTCATTTGTAAGACCATGACAA

                            
        912 -GGTGTCATTTGTAAG
          1 TGGTGTCATTTGTAAG

        927 TAGAATAAAT


Statistics
Matches: 38,  Mismatches: 2, Indels: 6
        0.83            0.04        0.13

Matches are distributed among these distances:
  24   14  0.37
  29    1  0.03
  30   23  0.61

ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33


Consensus pattern (26 bp):   
TGGTGTCATTTGTAAGACCATGACAA

Found at i:2110 original size:22 final size:24

Alignment explanation


    Indices: 2075--2133  Score: 61
    Period size: 22  Copynumber: 2.5  Consensus size: 24

       2065 ATAAATGTAG

                            *      *
       2075 CTGATAA-TCTTCT-CTTTTATCT
          1 CTGATAATTCTTCTCCATTTATCA

                                    
       2097 CTGATAATTC-TCTCCATTTATCA
          1 CTGATAATTCTTCTCCATTTATCA

                          
       2120 CTTGATAATATCTT
          1 C-TGATAAT-TCTT

       2134 GTCAGGTAAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 6
        0.79            0.05        0.16

Matches are distributed among these distances:
  22   10  0.33
  23   10  0.33
  24    7  0.23
  25    2  0.07
  26    1  0.03

ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49


Consensus pattern (24 bp):   
CTGATAATTCTTCTCCATTTATCA

Found at i:4299 original size:25 final size:27

Alignment explanation


    Indices: 4270--4337  Score: 74
    Period size: 25  Copynumber: 2.7  Consensus size: 27

       4260 CCGTTTAGTA

                                       
       4270 ATTAAATATATATTAT-TTATTTAT-T
          1 ATTAAATATATATTATATTATTTATAT

            *    *                      
       4295 TTTAACTCAT-TATT-TATTATTTATAT
          1 ATTAAAT-ATATATTATATTATTTATAT

                              
       4321 ATT-AATATATATTATAT
          1 ATTAAATATATATTATAT

       4338 CTAAGATTAG


Statistics
Matches: 34,  Mismatches: 4, Indels: 9
        0.72            0.09        0.19

Matches are distributed among these distances:
  24    3  0.09
  25   23  0.68
  26    8  0.24

ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59


Consensus pattern (27 bp):   
ATTAAATATATATTATATTATTTATAT
Done.