Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024593.1 Corchorus olitorius cultivar O-4 contig24626, 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: 4347
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:467 original size:30 final size:31

Alignment explanation


    Indices: 431--508  Score: 88
    Period size: 30  Copynumber: 2.5  Consensus size: 31

        421 ACATTTTCGT

                                         *  
        431 AACGTTATATCCTGAATTGTCA-TATCA-TCA
          1 AACGTTATATCCTGAATTG-CATTATCAGGCA

                         * *   *   *       
        461 AACGTTATATCCTTATTTGGATTTTCAGGCA
          1 AACGTTATATCCTGAATTGCATTATCAGGCA

                             
        492 AACGTTATATCCTGAAT
          1 AACGTTATATCCTGAAT

        509 CGATCATTTA


Statistics
Matches: 39,  Mismatches: 7, Indels: 3
        0.80            0.14        0.06

Matches are distributed among these distances:
  29    1  0.03
  30   21  0.54
  31   17  0.44

ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38


Consensus pattern (31 bp):   
AACGTTATATCCTGAATTGCATTATCAGGCA

Found at i:608 original size:55 final size:55

Alignment explanation


    Indices: 526--634  Score: 218
    Period size: 55  Copynumber: 2.0  Consensus size: 55

        516 TTAGCCCTTA

                                                                   
        526 TATATATATATATATATTAGACTTTGTCTTAAATTAAATCAACCCAAAATTGACT
          1 TATATATATATATATATTAGACTTTGTCTTAAATTAAATCAACCCAAAATTGACT

                                                                  
        581 TATATATATATATATATTAGACTTTGTCTTAAATTAAATCAACCCAAAATTGAC
          1 TATATATATATATATATTAGACTTTGTCTTAAATTAAATCAACCCAAAATTGAC

        635 CCATTGGATA


Statistics
Matches: 54,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  55   54  1.00

ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39


Consensus pattern (55 bp):   
TATATATATATATATATTAGACTTTGTCTTAAATTAAATCAACCCAAAATTGACT

Found at i:730 original size:25 final size:25

Alignment explanation


    Indices: 684--747  Score: 112
    Period size: 25  Copynumber: 2.6  Consensus size: 25

        674 CTCTTGATTT

                                     
        684 AAACAAACAATTATTTTAACCAAAA
          1 AAACAAACAATTATTTTAACCAAAA

                                      
        709 AAA-AAACAATTACTTTTAACCAAAA
          1 AAACAAACAATTA-TTTTAACCAAAA

                          
        734 AAACAAACAATTAT
          1 AAACAAACAATTAT

        748 CAAATCCCAT


Statistics
Matches: 37,  Mismatches: 0, Indels: 4
        0.90            0.00        0.10

Matches are distributed among these distances:
  24    9  0.24
  25   19  0.51
  26    9  0.24

ACGTcount: A:0.61, C:0.16, G:0.00, T:0.23


Consensus pattern (25 bp):   
AAACAAACAATTATTTTAACCAAAA

Found at i:3990 original size:31 final size:32

Alignment explanation


    Indices: 3952--4020  Score: 104
    Period size: 32  Copynumber: 2.2  Consensus size: 32

       3942 AATTTTGGGT

                            *               
       3952 ACCCGAACCCG-AAATTACCCGAATCCAAACA
          1 ACCCGAACCCGAAAATGACCCGAATCCAAACA

                                       * *  
       3983 ACCCGAACCCGAAAATGACCCGAATCCGATCA
          1 ACCCGAACCCGAAAATGACCCGAATCCAAACA

                  
       4015 ACCCGA
          1 ACCCGA

       4021 CATATTAACC


Statistics
Matches: 34,  Mismatches: 3, Indels: 1
        0.89            0.08        0.03

Matches are distributed among these distances:
  31   11  0.32
  32   23  0.68

ACGTcount: A:0.39, C:0.39, G:0.13, T:0.09


Consensus pattern (32 bp):   
ACCCGAACCCGAAAATGACCCGAATCCAAACA

Done.