Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010411.1 Corchorus olitorius cultivar O-4 contig10443, 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, 837

Length: 1396
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30


Found at i:372 original size:154 final size:155

Alignment explanation


    Indices: 7--541  Score: 826
    Period size: 154  Copynumber: 3.4  Consensus size: 155

          1 AAACTA

                                                                             
          7 AACAAGTGTTCAAAATAGAGCTAAGAAACTTCACAATGGACTAATCTTACCAAAATGATTATAGT
          1 AACAAGTGTTCAAAATAGAGCTAA-AAACTTCACAATGGACTAATCTTACCAAAATGATTATAGT

                                                                     *       
         72 TAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGATATTTAAAACCG
         65 TAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACG--ATTCAAAACCG

             *                  *       
        137 AGCTAATGGGCCCCGAATGGTCCAAAAT
        128 AACTAATGGGCCCCGAATGGACCAAAAT

                                                      *                      
        165 AACAAGTGTT-AAAATAGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGTT
          1 AACAAGTGTTCAAAATAGAGCTAAAAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTT

                                        **                               *   
        229 AGGCCATAAACAATGGAAAGAAAAGCATGGTGGTTTGCCAAATCGAAGACGATTCAAAACCCAAC
         66 AGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGATTCAAAACCGAAC

                 **          *       
        294 TAATGCACCCCGAATGGCCCAAAAT
        131 TAATGGGCCCCGAATGGACCAAAAT

            *                                                *               
        319 TACAAGTGTTCAAAAT-GAGCTAAAAACTTCACAATGGACTAATCTTACGAAAATGATTATAGTT
          1 AACAAGTGTTCAAAATAGAGCTAAAAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTT

                          *                                                  
        383 AGGCCATAAACAATTGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGATTTTTC-AAACCG
         66 AGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGA---TTCAAAACCG

                                         
        447 AACTAATGGGCCCCGAATGGTACCAAAAT
        128 AACTAATGGGCCCCGAATGG-ACCAAAAT

              *                                  * *  *                      
        476 AAAAAGTGTTCAAAAT-GAGCTAAAAACTTCACAATGTAGTAGTCTTACCAAAATGATTATAGTT
          1 AACAAGTGTTCAAAATAGAGCTAAAAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTT

              
        540 AG
         66 AG

        542 TGATGCGCCA


Statistics
Matches: 347,  Mismatches: 25, Indels: 11
        0.91            0.07        0.03

Matches are distributed among these distances:
 154  137  0.39
 155    5  0.01
 156  112  0.32
 157   83  0.24
 158   10  0.03

ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24


Consensus pattern (155 bp):   
AACAAGTGTTCAAAATAGAGCTAAAAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTT
AGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGATTCAAAACCGAAC
TAATGGGCCCCGAATGGACCAAAAT
Done.