Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018522.1 Corchorus olitorius cultivar O-4 contig18555, 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: 21165
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.28


Found at i:2931 original size:63 final size:63

Alignment explanation


    Indices: 2828--2953  Score: 155
    Period size: 63  Copynumber: 2.0  Consensus size: 63

       2818 CAGAGACAGT

                     *   *           *         *                           
       2828 GGAGGAGGAGCAATAACGTCACCCACTGCAGCAAGTAGAGGATCAACAAATACAACTAAGGCA
          1 GGAGGAGGACCAACAACGTCACCCAATGCAGCAAGCAGAGGATCAACAAATACAACTAAGGCA

                                  *                       *   * *  *        
       2891 GGAGGAGGACCAACAA-GTTCATCCAATGCAGCAAGCAGAGGATCAGCAATTGCACCTAAGGCA
          1 GGAGGAGGACCAACAACG-TCACCCAATGCAGCAAGCAGAGGATCAACAAATACAACTAAGGCA

       2954 ACAAAATGAT


Statistics
Matches: 53,  Mismatches: 9, Indels: 2
        0.83            0.14        0.03

Matches are distributed among these distances:
  62    1  0.02
  63   52  0.98

ACGTcount: A:0.39, C:0.23, G:0.26, T:0.12


Consensus pattern (63 bp):   
GGAGGAGGACCAACAACGTCACCCAATGCAGCAAGCAGAGGATCAACAAATACAACTAAGGCA

Found at i:14904 original size:35 final size:35

Alignment explanation


    Indices: 14864--14938  Score: 116
    Period size: 35  Copynumber: 2.1  Consensus size: 35

      14854 AGTTCGTTTA

                              *                 
      14864 TGTTCACGAACATG-CTCGTTTATTGTTCATTTAAG
          1 TGTTCACGAACA-GACTCATTTATTGTTCATTTAAG

                    *                          
      14899 TGTTCACGCACAGACTCATTTATTGTTCATTTAAG
          1 TGTTCACGAACAGACTCATTTATTGTTCATTTAAG

                 
      14934 TGTTC
          1 TGTTC

      14939 GTTTATATAA


Statistics
Matches: 37,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
  34    1  0.03
  35   36  0.97

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


Consensus pattern (35 bp):   
TGTTCACGAACAGACTCATTTATTGTTCATTTAAG

Found at i:15005 original size:22 final size:20

Alignment explanation


    Indices: 14971--15010  Score: 62
    Period size: 22  Copynumber: 1.9  Consensus size: 20

      14961 CATTTATTAT

                                
      14971 ATAATTATTTATTAATAATA
          1 ATAATTATTTATTAATAATA

                                
      14991 ATAATATATATTATTAATAA
          1 ATAAT-TAT-TTATTAATAA

      15011 AAATTATAAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20    5  0.28
  21    3  0.17
  22   10  0.56

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


Consensus pattern (20 bp):   
ATAATTATTTATTAATAATA

Found at i:15169 original size:18 final size:18

Alignment explanation


    Indices: 15142--15176  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      15132 AATTATTACA

                              
      15142 TTGTTCATGAACAATTTT
          1 TTGTTCATGAACAATTTT

                 *           
      15160 TTGTTTATGAACAATTT
          1 TTGTTCATGAACAATTT

      15177 CAATTTTTGT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51


Consensus pattern (18 bp):   
TTGTTCATGAACAATTTT

Found at i:20085 original size:22 final size:22

Alignment explanation


    Indices: 20028--20089  Score: 81
    Period size: 22  Copynumber: 2.8  Consensus size: 22

      20018 TATTGGGATT

                   * *            
      20028 ACCTTTTGTGAAGTAAATAGGC
          1 ACCTTTTTTCAAGTAAATAGGC

                                  
      20050 ACCTTTTTTCAAGTAAATAGGC
          1 ACCTTTTTTCAAGTAAATAGGC

                      *        
      20072 A-CTTTTCTTTAAGTAAAT
          1 ACCTTTT-TTCAAGTAAAT

      20090 TGGTAGGATA


Statistics
Matches: 36,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  21    5  0.14
  22   31  0.86

ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39


Consensus pattern (22 bp):   
ACCTTTTTTCAAGTAAATAGGC
Done.