Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014897.1 Corchorus capsularis cultivar CVL-1 contig14918, 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: 14117
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31


Found at i:1704 original size:20 final size:20

Alignment explanation


    Indices: 1679--1716  Score: 67
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       1669 TTTAACCCAT

                   *            
       1679 CATATATTTATATTTTCATC
          1 CATATATCTATATTTTCATC

                              
       1699 CATATATCTATATTTTCA
          1 CATATATCTATATTTTCA

       1717 CTTTTAACCC


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:0.32, C:0.16, G:0.00, T:0.53


Consensus pattern (20 bp):   
CATATATCTATATTTTCATC

Found at i:12034 original size:30 final size:29

Alignment explanation


    Indices: 11955--12034  Score: 99
    Period size: 29  Copynumber: 2.7  Consensus size: 29

      11945 GTAGCGTTTA

                                          
      11955 GACGTTTTGCCCCC-CGAACTTCAATCTTG
          1 GACGTTTTGCCCCCTC-AACTTCAATCTTG

               *    *      *         *    
      11984 GACATTTTACCCCCTGAACTTCAATTTTGG
          1 GACGTTTTGCCCCCTCAACTTCAATCTT-G

                                 
      12014 GACGTTTTGCCCCCTCAACTT
          1 GACGTTTTGCCCCCTCAACTT

      12035 AACGGTTCCG


Statistics
Matches: 42,  Mismatches: 7, Indels: 3
        0.81            0.13        0.06

Matches are distributed among these distances:
  29   23  0.55
  30   19  0.45

ACGTcount: A:0.19, C:0.33, G:0.15, T:0.34


Consensus pattern (29 bp):   
GACGTTTTGCCCCCTCAACTTCAATCTTG

Found at i:12243 original size:29 final size:30

Alignment explanation


    Indices: 12196--12269  Score: 98
    Period size: 29  Copynumber: 2.5  Consensus size: 30

      12186 CGTTAGGTTG

                                          
      12196 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
          1 AGGGGGCAAAACGTCCCAAAATTGAAGTTC

                  *    *       *          
      12226 AGGGGGTAAAATGT-CCAAGATTGAAGTTC
          1 AGGGGGCAAAACGTCCCAAAATTGAAGTTC

                            
      12255 -GGTGGGCAAAACGTC
          1 AGG-GGGCAAAACGTC

      12270 TAAACGCTAC


Statistics
Matches: 37,  Mismatches: 5, Indels: 4
        0.80            0.11        0.09

Matches are distributed among these distances:
  28    2  0.05
  29   23  0.62
  30   12  0.32

ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19


Consensus pattern (30 bp):   
AGGGGGCAAAACGTCCCAAAATTGAAGTTC
Done.