Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020260.1 Corchorus olitorius cultivar O-4 contig20293, 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: 12396
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:303 original size:12 final size:12

Alignment explanation


    Indices: 286--310  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

        276 TGGAGTGGGC

                        
        286 TAAAAGATCCAT
          1 TAAAAGATCCAT

                        
        298 TAAAAGATCCAT
          1 TAAAAGATCCAT

             
        310 T
          1 T

        311 TTTAATAGGA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28


Consensus pattern (12 bp):   
TAAAAGATCCAT

Found at i:490 original size:108 final size:111

Alignment explanation


    Indices: 297--499  Score: 315
    Period size: 108  Copynumber: 1.8  Consensus size: 111

        287 AAAAGATCCA

                            *        *                                       
        297 TTAAAAGATCCATTTTTAATAGGACTCACTCAACTCAACCCAACTCCACCAAATCATCAATAAGG
          1 TTAAAAGATCCATTTTAAATAGGA-GCACTCAACTCAACCCAACTCCACCAAATCATCAATAAGG

                                                           
        362 AACTAATTTAGAAGACTCAATATGCAAAACCTTAATTTTGGAGTGGG
         65 AACTAATTTAGAAGACTCAATATGCAAAACCTTAATTTTGGAGTGGG

                                                                         *   
        409 TTAAAAGATCCATTTTAAATAGG-GC-C-C-ACTCAACCCAACTCCACCAAATTCATCAATCAGG
          1 TTAAAAGATCCATTTTAAATAGGAGCACTCAACTCAACCCAACTCCACCAAA-TCATCAATAAGG

              *                  *        
        470 AATTAATTTAGAAGACTCAATCTGCAAAAC
         65 AACTAATTTAGAAGACTCAATATGCAAAAC

        500 AGGGTCAATT


Statistics
Matches: 85,  Mismatches: 5, Indels: 6
        0.89            0.05        0.06

Matches are distributed among these distances:
 107   21  0.25
 108   40  0.47
 109    1  0.01
 110    1  0.01
 112   22  0.26

ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26


Consensus pattern (111 bp):   
TTAAAAGATCCATTTTAAATAGGAGCACTCAACTCAACCCAACTCCACCAAATCATCAATAAGGA
ACTAATTTAGAAGACTCAATATGCAAAACCTTAATTTTGGAGTGGG

Found at i:6453 original size:12 final size:12

Alignment explanation


    Indices: 6436--6467  Score: 55
    Period size: 12  Copynumber: 2.7  Consensus size: 12

       6426 TACTCTATGT

                        
       6436 AAACACGACACG
          1 AAACACGACACG

                  *     
       6448 AAACACAACACG
          1 AAACACGACACG

                    
       6460 AAACACGA
          1 AAACACGA

       6468 ATTGCCAGGT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  12   18  1.00

ACGTcount: A:0.56, C:0.31, G:0.12, T:0.00


Consensus pattern (12 bp):   
AAACACGACACG

Found at i:10216 original size:21 final size:20

Alignment explanation


    Indices: 10160--10222  Score: 65
    Period size: 21  Copynumber: 3.0  Consensus size: 20

      10150 ATTCTACTTC

                  *              
      10160 AAAAAAACTTATAAAGTTATT
          1 AAAAAATCTTAT-AAGTTATT

                                  
      10181 AAAAAATC-TACTAAGCTTATT
          1 AAAAAATCTTA-TAAG-TTATT

                *                
      10202 AAAAGATCTTATAAGATTATT
          1 AAAAAATCTTATAAG-TTATT

      10223 TTTAAAAAGA


Statistics
Matches: 36,  Mismatches: 3, Indels: 6
        0.80            0.07        0.13

Matches are distributed among these distances:
  20    5  0.14
  21   29  0.81
  22    2  0.06

ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35


Consensus pattern (20 bp):   
AAAAAATCTTATAAGTTATT
Done.