Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021552.1 Corchorus olitorius cultivar O-4 contig21585, 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: 8553
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32


Found at i:6258 original size:18 final size:19

Alignment explanation


    Indices: 6235--6273  Score: 62
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       6225 TCCTTGAAAT

                               
       6235 AAATCTTC-AATGATCTTC
          1 AAATCTTCAAATGATCTTC

                        *      
       6253 AAATCTTCAAATTATCTTC
          1 AAATCTTCAAATGATCTTC

              
       6272 AA
          1 AA

       6274 TGAGTCTTCA


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18    8  0.42
  19   11  0.58

ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38


Consensus pattern (19 bp):   
AAATCTTCAAATGATCTTC

Found at i:6281 original size:11 final size:10

Alignment explanation


    Indices: 6237--6284  Score: 55
    Period size: 11  Copynumber: 4.8  Consensus size: 10

       6227 CTTGAAATAA

                      
       6237 ATCTTCAATG
          1 ATCTTCAATG

                      
       6247 ATCTTCAA--
          1 ATCTTCAATG

                      *
       6255 ATCTTCAAATT
          1 ATCTTC-AATG

                      
       6266 ATCTTCAATG
          1 ATCTTCAATG

                     
       6276 AGTCTTCAA
          1 A-TCTTCAA

       6285 ACACGAACTT


Statistics
Matches: 33,  Mismatches: 1, Indels: 7
        0.80            0.02        0.17

Matches are distributed among these distances:
   8    6  0.18
   9    2  0.06
  10   12  0.36
  11   13  0.39

ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40


Consensus pattern (10 bp):   
ATCTTCAATG

Found at i:6615 original size:13 final size:13

Alignment explanation


    Indices: 6597--6639  Score: 61
    Period size: 13  Copynumber: 3.3  Consensus size: 13

       6587 GTATCATTAT

                  *      
       6597 CAAAGTCATAAAC
          1 CAAAGTAATAAAC

                         
       6610 CAAAGTAATAAAC
          1 CAAAGTAATAAAC

                          
       6623 CAGAA-TAATAAAC
          1 CA-AAGTAATAAAC

                
       6636 CAAA
          1 CAAA

       6640 ATAGTAAAAT


Statistics
Matches: 28,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  12    2  0.07
  13   24  0.86
  14    2  0.07

ACGTcount: A:0.60, C:0.19, G:0.07, T:0.14


Consensus pattern (13 bp):   
CAAAGTAATAAAC

Found at i:6642 original size:13 final size:13

Alignment explanation


    Indices: 6604--6647  Score: 61
    Period size: 13  Copynumber: 3.4  Consensus size: 13

       6594 TATCAAAGTC

                      *  
       6604 ATAAACCAAAGTA
          1 ATAAACCAAAATA

                    *    
       6617 ATAAACCAGAATA
          1 ATAAACCAAAATA

                         
       6630 ATAAACCAAAATA
          1 ATAAACCAAAATA

            *    
       6643 GTAAA
          1 ATAAA

       6648 ATAAAACATA


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  13   27  1.00

ACGTcount: A:0.64, C:0.14, G:0.07, T:0.16


Consensus pattern (13 bp):   
ATAAACCAAAATA
Done.