Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007518.1 Corchorus olitorius cultivar O-4 contig07543, 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, 766

Length: 1277
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39


Found at i:628 original size:180 final size:180

Alignment explanation


    Indices: 318--654  Score: 575
    Period size: 180  Copynumber: 1.9  Consensus size: 180

        308 ATGAATACAT

                        *                                               *    
        318 TAGTACTATCTATATTCAAATAATCTTACATCCTTATTAATTTTAGAAACTTTTTATGATTAATA
          1 TAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTTTAGAAACTTTTTATGATCAATA

                     *                            *                          
        383 ATGAAAGTTGCCAATTTAATTACTTAAGTAATCTACTATAAAAGCTAAAAAAGTTATTAAAATTG
         66 ATGAAAGTTACCAATTTAATTACTTAAGTAATCTACTAAAAAAGCTAAAAAAGTTATTAAAATTG

                                                              
        448 TATTTATCAATCCTTACATTCTTAATATTTTTTTTTGCCGAAAAACATTA
        131 TATTTATCAATCCTTACATTCTTAATATTTTTTTTTGCCGAAAAACATTA

                               *                          *                  
        498 TAGTACTATCTAGATTCAAGTAATCTTACATCCTTATTAATTTTAGTAACTTTTTATGATCAATA
          1 TAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTTTAGAAACTTTTTATGATCAATA

                                     *                 *   *       *  *      
        563 ATGAAAGTTACCAATTTAATTACTTGAGTAATCTACTAAAAAATCTATAAAAGTTTTTTAAATTG
         66 ATGAAAGTTACCAATTTAATTACTTAAGTAATCTACTAAAAAAGCTAAAAAAGTTATTAAAATTG

                                       
        628 TATTTATCAATCCTTACATTCTTAATA
        131 TATTTATCAATCCTTACATTCTTAATA

        655 ACATTAGTTA


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:0.07, T:0.42


Consensus pattern (180 bp):   
TAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTTTAGAAACTTTTTATGATCAATA
ATGAAAGTTACCAATTTAATTACTTAAGTAATCTACTAAAAAAGCTAAAAAAGTTATTAAAATTG
TATTTATCAATCCTTACATTCTTAATATTTTTTTTTGCCGAAAAACATTA

Found at i:1172 original size:36 final size:36

Alignment explanation


    Indices: 1111--1180  Score: 104
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       1101 TTCAATAACG

                               **               
       1111 TTACATTTTTTGTAATTATGGTTATCATAATTCTTA
          1 TTACATTTTTTGTAATTATAATTATCATAATTCTTA

                             *           *    
       1147 TTACATTTTTTGTAATTTTAATTATCATATTTCT
          1 TTACATTTTTTGTAATTATAATTATCATAATTCT

       1181 CCAAAATCTC


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  36   30  1.00

ACGTcount: A:0.27, C:0.09, G:0.06, T:0.59


Consensus pattern (36 bp):   
TTACATTTTTTGTAATTATAATTATCATAATTCTTA
Done.