Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018303.1 Corchorus olitorius cultivar O-4 contig18336, 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: 18769
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.30


Found at i:10514 original size:65 final size:63

Alignment explanation


    Indices: 10405--10532  Score: 159
    Period size: 65  Copynumber: 2.0  Consensus size: 63

      10395 GGAAAAACTG

                *                                **               *  *     
      10405 GTCCTACCCATGCATGGGTACCCTGACCACCCCACGCCTGGGCTAGTGCAGAAAGTTTGAATC
          1 GTCCAACCCATGCATGGGTACCCTGACCACCCCACGCAAGGGCTAGTGCAGAAAATTGGAATC

                                    *            *                           
      10468 GTCCAACCCATGCATGAGGTATCCTTGACCTA-CCCATGCAAGGGCTAGTGCAGAAAATTGGAAT
          1 GTCCAACCCATGCATG-GGTA-CCCTGACC-ACCCCACGCAAGGGCTAGTGCAGAAAATTGGAAT

             
      10532 C
         63 C

      10533 AATAGCAAGC


Statistics
Matches: 55,  Mismatches: 7, Indels: 4
        0.83            0.11        0.06

Matches are distributed among these distances:
  63   15  0.27
  64    4  0.07
  65   35  0.64
  66    1  0.02

ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21


Consensus pattern (63 bp):   
GTCCAACCCATGCATGGGTACCCTGACCACCCCACGCAAGGGCTAGTGCAGAAAATTGGAATC

Found at i:18603 original size:35 final size:35

Alignment explanation


    Indices: 18563--18637  Score: 132
    Period size: 35  Copynumber: 2.1  Consensus size: 35

      18553 AGTTCGTTTA

                      *  *                     
      18563 TGTTCACGAATAGGCTCGTTTATTGTTCATTTAAG
          1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG

                                               
      18598 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
          1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG

                 
      18633 TGTTC
          1 TGTTC

      18638 GTTTATATAA


Statistics
Matches: 38,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  35   38  1.00

ACGTcount: A:0.23, C:0.16, G:0.19, T:0.43


Consensus pattern (35 bp):   
TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG

Found at i:18700 original size:16 final size:16

Alignment explanation


    Indices: 18679--18710  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

      18669 TATAATTATT

                            
      18679 TATATATTAATAATAA
          1 TATATATTAATAATAA

                     *      
      18695 TATATATTATTAATAA
          1 TATATATTAATAATAA

      18711 AAATAATAAT


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (16 bp):   
TATATATTAATAATAA

Found at i:18705 original size:19 final size:19

Alignment explanation


    Indices: 18663--18715  Score: 63
    Period size: 19  Copynumber: 2.8  Consensus size: 19

      18653 GAACGTTCGT

                        *  *    
      18663 TTATTATATAATTATTTATA
          1 TTATTA-ATAATAATATATA

                               
      18683 -TATTAATAATAATATATA
          1 TTATTAATAATAATATATA

                      *    
      18701 TTATTAATAAAAATA
          1 TTATTAATAATAATA

      18716 ATAATATTCT


Statistics
Matches: 29,  Mismatches: 3, Indels: 3
        0.83            0.09        0.09

Matches are distributed among these distances:
  18   11  0.38
  19   18  0.62

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (19 bp):   
TTATTAATAATAATATATA

Found at i:18717 original size:25 final size:27

Alignment explanation


    Indices: 18687--18736  Score: 77
    Period size: 25  Copynumber: 1.9  Consensus size: 27

      18677 TTTATATATT

                                       
      18687 AATAATAATA-TATATTAT-TAATAAA
          1 AATAATAATATTATATTATCTAATAAA

                        *            
      18712 AATAATAATATTCTATTATCTAATA
          1 AATAATAATATTATATTATCTAATA

      18737 TATTTAAATT


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  25   10  0.45
  26    7  0.32
  27    5  0.23

ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42


Consensus pattern (27 bp):   
AATAATAATATTATATTATCTAATAAA
Done.