Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007291.1 Corchorus olitorius cultivar O-4 contig07316, 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, 977

Length: 1629
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39


Found at i:481 original size:180 final size:180

Alignment explanation


    Indices: 174--510  Score: 575
    Period size: 180  Copynumber: 1.9  Consensus size: 180

        164 ATGGATACAT

                                                                             
        174 TAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTTTAGTAACTTTTTATGATCAATA
          1 TAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTTTAGTAACTTTTTATGATCAATA

                     *                   *  *     *                          
        239 ATGAAAGTTGCCAATTTAATTACTTAAGTGATCTACTATAAAAGCTAAAAAAGTTATTAAAATTG
         66 ATGAAAGTTACCAATTTAATTACTTAAGTAATATACTAAAAAAGCTAAAAAAGTTATTAAAATTG

                  *                                           
        304 TATTTATCAATCCTTACATTCTTAATATTTTTTTTTGCCGAAAAACATTA
        131 TATTTACCAATCCTTACATTCTTAATATTTTTTTTTGCCGAAAAACATTA

                               *           *                                 
        354 TAGTACTATCTAGATTCAAGTAATCTTACATTCTTATTAATTTTAGTAACTTTTTATGATCAATA
          1 TAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTTTAGTAACTTTTTATGATCAATA

                                     *                     *       *         
        419 ATGAAAGTTACCAATTTAATTACTTGAGTAATATACTAAAAAAGCTATAAAAGTTTTTAAAATTG
         66 ATGAAAGTTACCAATTTAATTACTTAAGTAATATACTAAAAAAGCTAAAAAAGTTATTAAAATTG

                            *          
        484 TATTTACCAATCCTTAGATTCTTAATA
        131 TATTTACCAATCCTTACATTCTTAATA

        511 ACATTAGTAA


Statistics
Matches: 146,  Mismatches: 11, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
 180  146  1.00

ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42


Consensus pattern (180 bp):   
TAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTTTAGTAACTTTTTATGATCAATA
ATGAAAGTTACCAATTTAATTACTTAAGTAATATACTAAAAAAGCTAAAAAAGTTATTAAAATTG
TATTTACCAATCCTTACATTCTTAATATTTTTTTTTGCCGAAAAACATTA

Found at i:1007 original size:36 final size:36

Alignment explanation


    Indices: 966--1035  Score: 122
    Period size: 36  Copynumber: 1.9  Consensus size: 36

        956 TTCAATAACG

                                *               
        966 TTACATTTTTTGTAATTTTGGTTATCATAATTCTTA
          1 TTACATTTTTTGTAATTTTGATTATCATAATTCTTA

                                         *    
       1002 TTACATTTTTTGTAATTTTGATTATCATATTTCT
          1 TTACATTTTTTGTAATTTTGATTATCATAATTCT

       1036 CCAAAATCTC


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  36   32  1.00

ACGTcount: A:0.24, C:0.09, G:0.07, T:0.60


Consensus pattern (36 bp):   
TTACATTTTTTGTAATTTTGATTATCATAATTCTTA
Done.