Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009394.1 Corchorus olitorius cultivar O-4 contig09425, 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, 665

Length: 1109
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Found at i:601 original size:321 final size:322

Alignment explanation


    Indices: 1--691  Score: 980
    Period size: 321  Copynumber: 2.1  Consensus size: 322

                                                                             
          1 AGAAAATTGAGGAAAAATTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTT
          1 AGAAAATTGA-GAAAAATTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTT

                                             *             *       *    *    
         66 TTTGGCTAAAAACGCGTTCCAGAGCCCAAGTCATTTTTACATGATTTTGCGCGCATAGACTCCTT
         65 TTTGGCTAAAAACGCGTTCCAGAGCCCAAGTCAGTTTTACATGATTTAGCGCGCAAAGACACCTT

                                            *   *                           *
        131 GAAATACCTATATTCATCAAACCAAATCTCAGCCACGTTGGATTTAAAGATTTGTTTTTACGAGC
        130 GAAATACCTATATTCATCAAACCAAATCTCAGACACATTGGATTTAAAGATTTGTTTTTACGAGA

                                         *                  **               
        196 ATCTGAATCTTGTTTCTATTTAATTAGAATTTAATTAGGAAAATAGTTGGAAAATGATATTAGAA
        195 ATCTGAATCTTGTTTCTATTTAATTAGAAATTAATTAGGAAAATAGTTCAAAAATGATATTAGAA

                      **              *           *                *        
        261 GCGTGAAAAATTCTTTAATCTTTTTGGCGTTGAATTATTTATTTTTT-ATAAGTATTGTGGC-A
        260 GCGTGAAAAAACCTTTAATCTTTTTGCCGTTGAATTATATATTTTTTCA-AAGTAGTGTGGCAA

                            *                   *                       *    
        323 AGAAAATTGAGAAAAACTTTTCGGGTCAGTTTTTAGTCGAAATCGTGTACTAACCATCACGGTTT
          1 AGAAAATTGAGAAAAATTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTT

                               *       *   *                 * *             
        388 TTGGCTAAAAACGCGTTCCGGAGCCC-GGCTTAGTTTTACATGATTTAGGGTGCAAAGACACCTT
         66 TTGGCTAAAAACGCGTTCCAGAGCCCAAG-TCAGTTTTACATGATTTAGCGCGCAAAGACACCTT

                  *           **                           *             *   
        452 GAAATATCTATATTCATCTTACCAAATCTCAGACACATTGGATTTAAGGATTTGTTTTTACTAGA
        130 GAAATACCTATATTCATCAAACCAAATCTCAGACACATTGGATTTAAAGATTTGTTTTTACGAGA

                                                 *                           
        517 ATCTGAATCTTGTTT-TGATTTAATTAGAAATTAATTCGGAAAA-AGGTTCAAAAATGATATTAG
        195 ATCTGAATCTTGTTTCT-ATTTAATTAGAAATTAATTAGGAAAATA-GTTCAAAAATGATATTAG

               *                                               *             
        580 AAGTGTGAAAAAACCTTTAATCTTTTTGCCGTTGAATTATATATTTTTTCAGAGTAGTGTGGCAA
        258 AAGCGTGAAAAAACCTTTAATCTTTTTGCCGTTGAATTATATATTTTTTCAAAGTAGTGTGGCAA

             *         *                 *        *         
        645 AAAAAATTGAGGAAAATTTTTCGGGTCA-ATTTTAGCCAAAATCGTGT
          1 AGAAAATTGAGAAAAATTTTTCGGGTCAGTTTTTAGCCGAAATCGTGT

        692 CACATTTTTT


Statistics
Matches: 327,  Mismatches: 37, Indels: 11
        0.87            0.10        0.03

Matches are distributed among these distances:
 320    3  0.01
 321  287  0.88
 322   37  0.11

ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36


Consensus pattern (322 bp):   
AGAAAATTGAGAAAAATTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTT
TTGGCTAAAAACGCGTTCCAGAGCCCAAGTCAGTTTTACATGATTTAGCGCGCAAAGACACCTTG
AAATACCTATATTCATCAAACCAAATCTCAGACACATTGGATTTAAAGATTTGTTTTTACGAGAA
TCTGAATCTTGTTTCTATTTAATTAGAAATTAATTAGGAAAATAGTTCAAAAATGATATTAGAAG
CGTGAAAAAACCTTTAATCTTTTTGCCGTTGAATTATATATTTTTTCAAAGTAGTGTGGCAA
Done.