Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002133.1 Corchorus olitorius cultivar O-4 contig02133, 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, 643

Length: 1073
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41


Found at i:861 original size:35 final size:35

Alignment explanation


    Indices: 821--895  Score: 141
    Period size: 35  Copynumber: 2.1  Consensus size: 35

        811 AGTTCGTTTA

                         *                     
        821 TGTTCACGAACAGGCTCGTTTATTGTTCATTTAAG
          1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG

                                               
        856 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
          1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG

                 
        891 TGTTC
          1 TGTTC

        896 GTTTATATAA


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  35   39  1.00

ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41


Consensus pattern (35 bp):   
TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG

Found at i:958 original size:16 final size:16

Alignment explanation


    Indices: 937--968  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

        927 TATAATTATT

                            
        937 TATATATTAATAATAA
          1 TATATATTAATAATAA

                     *      
        953 TATATATTATTAATAA
          1 TATATATTAATAATAA

        969 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:963 original size:19 final size:19

Alignment explanation


    Indices: 921--973  Score: 63
    Period size: 19  Copynumber: 2.8  Consensus size: 19

        911 GAACGTTCGT

                        *  *    
        921 TTATTATATAATTATTTATA
          1 TTATTA-ATAATAATATATA

                               
        941 -TATTAATAATAATATATA
          1 TTATTAATAATAATATATA

                      *    
        959 TTATTAATAAAAATA
          1 TTATTAATAATAATA

        974 ATAATATCTA


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:975 original size:25 final size:26

Alignment explanation


    Indices: 945--993  Score: 82
    Period size: 25  Copynumber: 1.9  Consensus size: 26

        935 TTTATATATT

                                      
        945 AATAATAATATATATTAT-TAATAAA
          1 AATAATAATATATATTATCTAATAAA

                       *            
        970 AATAATAATATCTATTATCTAATA
          1 AATAATAATATATATTATCTAATA

        994 TATTTAAATT


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  25   17  0.77
  26    5  0.23

ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41


Consensus pattern (26 bp):   
AATAATAATATATATTATCTAATAAA
Done.