Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005790.1 Corchorus capsularis cultivar CVL-1 contig05808, 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: 3206
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33


Found at i:2828 original size:27 final size:29

Alignment explanation


    Indices: 2798--2870  Score: 98
    Period size: 27  Copynumber: 2.6  Consensus size: 29

       2788 GGTCATCTAG

                               *         
       2798 GGGCATTTTGGTCATTTTTTACACT-A-A
          1 GGGCATTTTGGTCATTTTTCACACTCAGA

                                   *     
       2825 GGGCATTTTGGTCA-TTTTCACATTCAGA
          1 GGGCATTTTGGTCATTTTTCACACTCAGA

                    *         
       2853 GGGCATTTAGGTCATTTT
          1 GGGCATTTTGGTCATTTT

       2871 GAGTCCACTT


Statistics
Matches: 40,  Mismatches: 3, Indels: 4
        0.85            0.06        0.09

Matches are distributed among these distances:
  26    8  0.20
  27   15  0.38
  28   14  0.35
  29    3  0.08

ACGTcount: A:0.21, C:0.15, G:0.22, T:0.42


Consensus pattern (29 bp):   
GGGCATTTTGGTCATTTTTCACACTCAGA

Found at i:2865 original size:28 final size:26

Alignment explanation


    Indices: 2798--2870  Score: 92
    Period size: 28  Copynumber: 2.7  Consensus size: 26

       2788 GGTCATCTAG

                               *       
       2798 GGGCATTTTGGTCATTTTTTACACTAA
          1 GGGCATTTTGGTCA-TTTTCACACTAA

                                  *     
       2825 GGGCATTTTGGTCATTTTCACATTCAGA
          1 GGGCATTTTGGTCATTTTCACACT-A-A

                    *         
       2853 GGGCATTTAGGTCATTTT
          1 GGGCATTTTGGTCATTTT

       2871 GAGTCCACTT


Statistics
Matches: 41,  Mismatches: 3, Indels: 3
        0.87            0.06        0.06

Matches are distributed among these distances:
  26    8  0.20
  27   15  0.37
  28   18  0.44

ACGTcount: A:0.21, C:0.15, G:0.22, T:0.42


Consensus pattern (26 bp):   
GGGCATTTTGGTCATTTTCACACTAA

Found at i:3004 original size:24 final size:24

Alignment explanation


    Indices: 2977--3024  Score: 96
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       2967 ATTGTTGCAT

                                    
       2977 ATTCCATGGCATTTTCATTTAGTA
          1 ATTCCATGGCATTTTCATTTAGTA

                                    
       3001 ATTCCATGGCATTTTCATTTAGTA
          1 ATTCCATGGCATTTTCATTTAGTA

       3025 TTGTTGCATT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46


Consensus pattern (24 bp):   
ATTCCATGGCATTTTCATTTAGTA
Done.