Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005653.1 Corchorus olitorius cultivar O-4 contig05677, 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, 639

Length: 1066
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31


Found at i:43 original size:29 final size:29

Alignment explanation


    Indices: 1--124  Score: 176
    Period size: 29  Copynumber: 4.0  Consensus size: 29

                                         
          1 ATAATGAAATCAAAATGACATATAAAAAT
          1 ATAATGAAATCAAAATGACATATAAAAAT

                                                 
         30 ATAATGAAATCAAAATGACATATAAAAATATAAAAAT
          1 ATAATGAAATCAAAATGAC--------ATATAAAAAT

                                         
         67 ATAATGAAATCAAAATGACATATAAAAAT
          1 ATAATGAAATCAAAATGACATATAAAAAT

                                         
         96 ATAATGAAATCAAAATGACATATAAAAAT
          1 ATAATGAAATCAAAATGACATATAAAAAT

        125 GACATATAAT


Statistics
Matches: 87,  Mismatches: 0, Indels: 16
        0.84            0.00        0.16

Matches are distributed among these distances:
  29   58  0.67
  37   29  0.33

ACGTcount: A:0.63, C:0.06, G:0.06, T:0.24


Consensus pattern (29 bp):   
ATAATGAAATCAAAATGACATATAAAAAT

Found at i:61 original size:37 final size:37

Alignment explanation


    Indices: 20--99  Score: 160
    Period size: 37  Copynumber: 2.2  Consensus size: 37

         10 TCAAAATGAC

                                                 
         20 ATATAAAAATATAATGAAATCAAAATGACATATAAAA
          1 ATATAAAAATATAATGAAATCAAAATGACATATAAAA

                                                 
         57 ATATAAAAATATAATGAAATCAAAATGACATATAAAA
          1 ATATAAAAATATAATGAAATCAAAATGACATATAAAA

                  
         94 ATATAA
          1 ATATAA

        100 TGAAATCAAA


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  37   43  1.00

ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25


Consensus pattern (37 bp):   
ATATAAAAATATAATGAAATCAAAATGACATATAAAA

Found at i:107 original size:66 final size:66

Alignment explanation


    Indices: 1--124  Score: 248
    Period size: 66  Copynumber: 1.9  Consensus size: 66

                                                                             
          1 ATAATGAAATCAAAATGACATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAAAAA
          1 ATAATGAAATCAAAATGACATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAAAAA

             
         66 T
         66 T

                                                                      
         67 ATAATGAAATCAAAATGACATATAAAAATATAATGAAATCAAAATGACATATAAAAAT
          1 ATAATGAAATCAAAATGACATATAAAAATATAATGAAATCAAAATGACATATAAAAAT

        125 GACATATAAT


Statistics
Matches: 58,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  66   58  1.00

ACGTcount: A:0.63, C:0.06, G:0.06, T:0.24


Consensus pattern (66 bp):   
ATAATGAAATCAAAATGACATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAAAAA
T

Found at i:125 original size:13 final size:13

Alignment explanation


    Indices: 107--133  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

         97 TAATGAAATC

                         
        107 AAAATGACATATA
          1 AAAATGACATATA

                         
        120 AAAATGACATATA
          1 AAAATGACATATA

             
        133 A
          1 A

        134 TTAAATATAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.63, C:0.07, G:0.07, T:0.22


Consensus pattern (13 bp):   
AAAATGACATATA
Done.