Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011584.1 Corchorus capsularis cultivar CVL-1 contig11605, 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: 10341
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32


Found at i:1930 original size:20 final size:20

Alignment explanation


    Indices: 1902--1983  Score: 83
    Period size: 20  Copynumber: 3.8  Consensus size: 20

       1892 TAGAAATTTT

                *       *       
       1902 ATATAATATATAAATTTAAA
          1 ATATTATATATATATTTAAA

                                 
       1922 ATATTATATATATATTATAAA
          1 ATATTATATATATATT-TAAA

                         *           
       1943 TATATTTTCTATAAATATATTTAAA
          1 -ATA---T-TATATATATATTTAAA

                            
       1968 ATATTATATATATATT
          1 ATATTATATATATATT

       1984 ATATATGTTT


Statistics
Matches: 52,  Mismatches: 4, Indels: 12
        0.76            0.06        0.18

Matches are distributed among these distances:
  20   25  0.48
  21    5  0.10
  22    3  0.06
  24    3  0.06
  25    5  0.10
  26   11  0.21

ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49


Consensus pattern (20 bp):   
ATATTATATATATATTTAAA

Found at i:1938 original size:11 final size:11

Alignment explanation


    Indices: 1901--1989  Score: 65
    Period size: 11  Copynumber: 8.1  Consensus size: 11

       1891 ATAGAAATTT

                 *     
       1901 TATATAATATA
          1 TATATTATATA

              *        
       1912 TAAATT-TA-A
          1 TATATTATATA

            *          
       1921 AATATTATATA
          1 TATATTATATA

                     * 
       1932 TATATTATAAA
          1 TATATTATATA

                  * *  
       1943 TATATTTTCTA
          1 TATATTATATA

              *      *   
       1954 TAAATATATTTAA
          1 TATAT-TATAT-A

            *          
       1967 AATATTATATA
          1 TATATTATATA

                       
       1978 TATATTATATA
          1 TATATTATATA

             
       1989 T
          1 T

       1990 GTTTTTATTA


Statistics
Matches: 58,  Mismatches: 16, Indels: 8
        0.71            0.20        0.10

Matches are distributed among these distances:
   9    5  0.09
  10    4  0.07
  11   38  0.66
  12    7  0.12
  13    4  0.07

ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49


Consensus pattern (11 bp):   
TATATTATATA

Found at i:6130 original size:2 final size:2

Alignment explanation


    Indices: 6123--6160  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

       6113 TGTGCACGTC

                                                                    
       6123 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       6161 CACACGAGTG


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.