Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021389.1 Corchorus olitorius cultivar O-4 contig21422, 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: 1869
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34


Found at i:161 original size:31 final size:32

Alignment explanation


    Indices: 90--161  Score: 87
    Period size: 31  Copynumber: 2.3  Consensus size: 32

         80 GTCTATCAGC

                                      *     
         90 TTTTAATTTGTTTAATTTAAGACTTTCATTTT
          1 TTTTAATTTGTTTAATTTAAGACTTTAATTTT

            **                               
        122 AATT-ATTTGTTTAATTTAATG-C-TTAATTTT
          1 TTTTAATTTGTTTAATTTAA-GACTTTAATTTT

                      
        152 TTTTAATTTG
          1 TTTTAATTTG

        162 CAATAATTTA


Statistics
Matches: 33,  Mismatches: 5, Indels: 5
        0.77            0.12        0.12

Matches are distributed among these distances:
  30    9  0.27
  31   21  0.64
  32    3  0.09

ACGTcount: A:0.26, C:0.04, G:0.07, T:0.62


Consensus pattern (32 bp):   
TTTTAATTTGTTTAATTTAAGACTTTAATTTT

Found at i:527 original size:15 final size:15

Alignment explanation


    Indices: 477--533  Score: 78
    Period size: 16  Copynumber: 3.7  Consensus size: 15

        467 CCTACCCGAG

                      *     
        477 CCCGAACCCAAAAATA
          1 CCCGAACCC-GAAATA

                            
        493 CCCGAACCCGAAAATA
          1 CCCGAACCCG-AAATA

                        *  
        509 CCCGAACCCGAAGTA
          1 CCCGAACCCGAAATA

                      
        524 CCCGAACCCG
          1 CCCGAACCCG

        534 CCCAAGCCCG


Statistics
Matches: 38,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  15   14  0.37
  16   24  0.63

ACGTcount: A:0.39, C:0.42, G:0.14, T:0.05


Consensus pattern (15 bp):   
CCCGAACCCGAAATA

Found at i:758 original size:22 final size:22

Alignment explanation


    Indices: 688--859  Score: 156
    Period size: 22  Copynumber: 7.9  Consensus size: 22

        678 TGAATATTCT

                                   
        688 TATGAAATTTTGATAA-CTACCC
          1 TATGAAATTTTGATAACCTA-CC

               *                **
        710 TATTAAATTTTGATAACC-ATG
          1 TATGAAATTTTGATAACCTACC

                             **    
        731 TAATGAAATTTTGATAATTTACC
          1 T-ATGAAATTTTGATAACCTACC

                     *      *     
        754 TATGAAATTGTGATAAACT-CC
          1 TATGAAATTTTGATAACCTACC

                    *            * 
        775 ATATGAAACTTTGATAACCTAAC
          1 -TATGAAATTTTGATAACCTACC

                       *        *  
        798 TATGAAATTTTAATAAACCTTCC
          1 TATGAAATTTTGAT-AACCTACC

                               *  
        821 TATGAAATTTTG-TAACCTTCC
          1 TATGAAATTTTGATAACCTACC

                  *            
        842 TATG-ATTTTTGATAACCT
          1 TATGAAATTTTGATAACCT

        860 CTCTGTGAGA


Statistics
Matches: 122,  Mismatches: 21, Indels: 15
        0.77            0.13        0.09

Matches are distributed among these distances:
  20    6  0.05
  21   21  0.17
  22   74  0.61
  23   21  0.17

ACGTcount: A:0.37, C:0.15, G:0.09, T:0.40


Consensus pattern (22 bp):   
TATGAAATTTTGATAACCTACC

Done.