Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016415.1 Corchorus olitorius cultivar O-4 contig16448, 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: 11678
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35


Found at i:494 original size:34 final size:34

Alignment explanation


    Indices: 454--525  Score: 144
    Period size: 34  Copynumber: 2.1  Consensus size: 34

        444 TTGAAATTTA

                                              
        454 TTAGGGCTATATTTTTTGTAGTTGTTTAAGTCGG
          1 TTAGGGCTATATTTTTTGTAGTTGTTTAAGTCGG

                                              
        488 TTAGGGCTATATTTTTTGTAGTTGTTTAAGTCGG
          1 TTAGGGCTATATTTTTTGTAGTTGTTTAAGTCGG

                
        522 TTAG
          1 TTAG

        526 TAAGAAGATA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  34   38  1.00

ACGTcount: A:0.18, C:0.06, G:0.26, T:0.50


Consensus pattern (34 bp):   
TTAGGGCTATATTTTTTGTAGTTGTTTAAGTCGG

Found at i:1714 original size:16 final size:15

Alignment explanation


    Indices: 1693--1731  Score: 60
    Period size: 16  Copynumber: 2.5  Consensus size: 15

       1683 GTCACTAAAA

                            
       1693 ATAATATATAGTATAT
          1 ATAATATATA-TATAT

                           
       1709 ATAATATATATATAT
          1 ATAATATATATATAT

                    
       1724 ATTAATAT
          1 A-TAATAT

       1732 CTTTATTCAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  15    6  0.27
  16   16  0.73

ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46


Consensus pattern (15 bp):   
ATAATATATATATAT

Found at i:11027 original size:148 final size:149

Alignment explanation


    Indices: 10847--11132  Score: 461
    Period size: 148  Copynumber: 1.9  Consensus size: 149

      10837 ACCTCCCCGA

                                   *   *          *  * *             *       
      10847 TGTTAAAGCACTTTCTCACTTTGGAGAGAAAGTATTTGTGTTAGTTAAACTTTCTTATCCTAAAC
          1 TGTTAAAGCACTTTCTCACTTTGAAGAAAAAGTATTTGGGTCAATTAAACTTTCTTACCCTAAAC

                                                                             
      10912 TTTCTCTTAAA-AAAAAACCAAACATGCTGAAATTGTTTCCTATCC-TATACTTTCCATAGAAAG
         66 TTTCTCTTAAAGAAAAAA-CAAACATGCTGAAATTGTTTCCTA-CCATATACTTTCCATAGAAAG

                                 
      10975 TGATTAAATTTCTTACTTTGG
        129 TGATTAAATTTCTTACTTTGG

                                                                             
      10996 TGTT-AAGCACTTTCTCACTTTGAAGAAAAAGTATTTGGGTCAATTAAACTTTCTTACCCTAAAC
          1 TGTTAAAGCACTTTCTCACTTTGAAGAAAAAGTATTTGGGTCAATTAAACTTTCTTACCCTAAAC

                                  *                               *          
      11060 TTTCTCTTAAAGAAAAAACAAATATGCTGAAATTGTTTCCTACCATATACTTTCTATAGAAAGTG
         66 TTTCTCTTAAAGAAAAAACAAACATGCTGAAATTGTTTCCTACCATATACTTTCCATAGAAAGTG

                    
      11125 ATTAAATT
        131 ATTAAATT

      11133 ATATCAAAAC


Statistics
Matches: 127,  Mismatches: 8, Indels: 5
        0.91            0.06        0.04

Matches are distributed among these distances:
 147    2  0.02
 148  115  0.91
 149   10  0.08

ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38


Consensus pattern (149 bp):   
TGTTAAAGCACTTTCTCACTTTGAAGAAAAAGTATTTGGGTCAATTAAACTTTCTTACCCTAAAC
TTTCTCTTAAAGAAAAAACAAACATGCTGAAATTGTTTCCTACCATATACTTTCCATAGAAAGTG
ATTAAATTTCTTACTTTGG
Done.