Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022064.1 Corchorus olitorius cultivar O-4 contig22097, 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: 7636
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31


Found at i:152 original size:29 final size:30

Alignment explanation


    Indices: 118--339  Score: 175
    Period size: 29  Copynumber: 6.9  Consensus size: 30

        108 GGTTTTTTCA

                                          
        118 AAGTTTTCAAATTTAGGGAAAGATCCCATC
          1 AAGTTTTCAAATTTAGGGAAAGATCCCATC

                                                    
        148 -AGTTTCTTCAAGGTTTTCAATTTAGGGAAAGATCCCATC
          1 AAG-TT-TTCAA--------ATTTAGGGAAAGATCCCATC

                    *                     
        187 AAG-TTTCCAATTTAGGGAAAGATCCCATC
          1 AAGTTTTCAAATTTAGGGAAAGATCCCATC

                    *                     
        216 AAG-TTTCCAATTTAGGGAAAGATCCCATC
          1 AAGTTTTCAAATTTAGGGAAAGATCCCATC

                           * *            
        245 AAGTTTTCAAATTTATGTAAAGATCCCATC
          1 AAGTTTTCAAATTTAGGGAAAGATCCCATC

                                           *        
        275 -AGTTTCTTCAAGATTTTTAATTTAGGGAAATATCCCATC
          1 AAG-TT-TTC---A-----AATTTAGGGAAAGATCCCATC

                                  *    
        314 AAGTTTTC-AATTTAGGGAAAGTTCCC
          1 AAGTTTTCAAATTTAGGGAAAGATCCC

        340 GTCATTTTAA


Statistics
Matches: 160,  Mismatches: 9, Indels: 47
        0.74            0.04        0.22

Matches are distributed among these distances:
  29   72  0.45
  30   27  0.17
  31    8  0.05
  34    1  0.01
  37    4  0.03
  38    4  0.03
  39   40  0.25
  40    4  0.03

ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34


Consensus pattern (30 bp):   
AAGTTTTCAAATTTAGGGAAAGATCCCATC

Found at i:180 original size:39 final size:41

Alignment explanation


    Indices: 109--193  Score: 138
    Period size: 39  Copynumber: 2.1  Consensus size: 41

         99 GAAAAAAAAG

                *                                    
        109 GTTTTTTCAAAGTTTTCAAATTTAGGGAAAGATCCCATC-A
          1 GTTTCTTCAAAGTTTTCAAATTTAGGGAAAGATCCCATCAA

                      *                              
        149 GTTTCTTCAAGGTTTTC-AATTTAGGGAAAGATCCCATCAA
          1 GTTTCTTCAAAGTTTTCAAATTTAGGGAAAGATCCCATCAA

                 
        189 GTTTC
          1 GTTTC

        194 CAATTTAGGG


Statistics
Matches: 42,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
  39   21  0.50
  40   21  0.50

ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38


Consensus pattern (41 bp):   
GTTTCTTCAAAGTTTTCAAATTTAGGGAAAGATCCCATCAA

Found at i:267 original size:30 final size:30

Alignment explanation


    Indices: 155--279  Score: 186
    Period size: 29  Copynumber: 4.3  Consensus size: 30

        145 ATCAGTTTCT

                                           
        155 TCAAGGTTTT-CAATTTAGGGAAAGATCCCA
          1 TCAA-GTTTTCCAATTTAGGGAAAGATCCCA

                                          
        185 TCAAG-TTTCCAATTTAGGGAAAGATCCCA
          1 TCAAGTTTTCCAATTTAGGGAAAGATCCCA

                                          
        214 TCAAG-TTTCCAATTTAGGGAAAGATCCCA
          1 TCAAGTTTTCCAATTTAGGGAAAGATCCCA

                      *      * *          
        243 TCAAGTTTTCAAATTTATGTAAAGATCCCA
          1 TCAAGTTTTCCAATTTAGGGAAAGATCCCA

                    
        273 TC-AGTTT
          1 TCAAGTTT

        280 CTTCAAGATT


Statistics
Matches: 90,  Mismatches: 3, Indels: 5
        0.92            0.03        0.05

Matches are distributed among these distances:
  28    3  0.03
  29   60  0.67
  30   27  0.30

ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Consensus pattern (30 bp):   
TCAAGTTTTCCAATTTAGGGAAAGATCCCA

Done.