Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009744.1 Corchorus olitorius cultivar O-4 contig09776, 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: 3100
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.34


Found at i:120 original size:20 final size:20

Alignment explanation


    Indices: 95--132  Score: 67
    Period size: 20  Copynumber: 1.9  Consensus size: 20

         85 CCAAACATAA

                     *          
         95 TTAGCACCATTACCAAATAG
          1 TTAGCACCACTACCAAATAG

                              
        115 TTAGCACCACTACCAAAT
          1 TTAGCACCACTACCAAAT

        133 TGTAATTGTG


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.39, C:0.29, G:0.08, T:0.24


Consensus pattern (20 bp):   
TTAGCACCACTACCAAATAG

Found at i:670 original size:16 final size:17

Alignment explanation


    Indices: 646--678  Score: 50
    Period size: 16  Copynumber: 2.0  Consensus size: 17

        636 ACGGTGTACG

                             
        646 TATAAATTATAT-TTAA
          1 TATAAATTATATATTAA

                *            
        662 TATATATTATATATTAA
          1 TATAAATTATATATTAA

        679 CAAATAAAAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  16   11  0.73
  17    4  0.27

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (17 bp):   
TATAAATTATATATTAA

Found at i:2018 original size:41 final size:41

Alignment explanation


    Indices: 1972--2053  Score: 137
    Period size: 41  Copynumber: 2.0  Consensus size: 41

       1962 ATTTATAACA

                                   *                 
       1972 GGGGCTAAACCTAGATTTAATTTCTTACCTTAATTATTAGG
          1 GGGGCTAAACCTAGATTTAATTTATTACCTTAATTATTAGG

                        *             *              
       2013 GGGGCTAAACCTGGATTTAATTTATTTCCTTAATTATTAGG
          1 GGGGCTAAACCTAGATTTAATTTATTACCTTAATTATTAGG

       2054 AGGGTCAAGT


Statistics
Matches: 38,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  41   38  1.00

ACGTcount: A:0.28, C:0.13, G:0.18, T:0.40


Consensus pattern (41 bp):   
GGGGCTAAACCTAGATTTAATTTATTACCTTAATTATTAGG

Found at i:2070 original size:13 final size:13

Alignment explanation


    Indices: 2052--2088  Score: 56
    Period size: 13  Copynumber: 2.8  Consensus size: 13

       2042 TTAATTATTA

                      *  
       2052 GGAGGGTCAAGTT
          1 GGAGGGTCAAATT

                  *      
       2065 GGAGGGACAAATT
          1 GGAGGGTCAAATT

                       
       2078 GGAGGGTCAAA
          1 GGAGGGTCAAA

       2089 AAGAGTTATC


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  13   21  1.00

ACGTcount: A:0.32, C:0.08, G:0.43, T:0.16


Consensus pattern (13 bp):   
GGAGGGTCAAATT
Done.