Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001143.1 Corchorus capsularis cultivar CVL-1 contig01143, 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: 12528
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31


Found at i:9 original size:2 final size:2

Alignment explanation


    Indices: 3--37  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

          1 TC

                                                                
          3 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         38 CTGCATTGGC


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:635 original size:29 final size:29

Alignment explanation


    Indices: 560--635  Score: 82
    Period size: 29  Copynumber: 2.6  Consensus size: 29

        550 TTAGATTGAG

                *     *             *     
        560 GGGATAAAACGTCTCAAAATTGAAGTTCAA
          1 GGGACAAAACTTC-CAAAATTGAAATTCAA

                         *               *
        590 GGGACAAAA-TGTTCAAAATTGAAATTCAT
          1 GGGACAAAACT-TCCAAAATTGAAATTCAA

                             
        619 GGGACAAAACTTCCAAA
          1 GGGACAAAACTTCCAAA

        636 CACTACAAGT


Statistics
Matches: 38,  Mismatches: 6, Indels: 5
        0.78            0.12        0.10

Matches are distributed among these distances:
  29   28  0.74
  30   10  0.26

ACGTcount: A:0.45, C:0.14, G:0.18, T:0.22


Consensus pattern (29 bp):   
GGGACAAAACTTCCAAAATTGAAATTCAA

Found at i:1964 original size:2 final size:2

Alignment explanation


    Indices: 1957--1994  Score: 67
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       1947 TATTTGATTT

                                                                    
       1957 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T

       1995 GTAATAGCAA


Statistics
Matches: 35,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2   33  0.94
   3    2  0.06

ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:4307 original size:31 final size:31

Alignment explanation


    Indices: 4269--4335  Score: 107
    Period size: 31  Copynumber: 2.2  Consensus size: 31

       4259 ATAGACCCAT

                      *                    
       4269 TGGACATTGGTTCAATGGGTTAACTTCATAA
          1 TGGACATTGGCTCAATGGGTTAACTTCATAA

                                  **       
       4300 TGGACATTGGCTCAATGGGTTAGGTTCATAA
          1 TGGACATTGGCTCAATGGGTTAACTTCATAA

                 
       4331 TGGAC
          1 TGGAC

       4336 CCATGTCGAA


Statistics
Matches: 33,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  31   33  1.00

ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33


Consensus pattern (31 bp):   
TGGACATTGGCTCAATGGGTTAACTTCATAA

Found at i:12240 original size:14 final size:14

Alignment explanation


    Indices: 12221--12255  Score: 70
    Period size: 14  Copynumber: 2.5  Consensus size: 14

      12211 GGATATTCCG

                          
      12221 GCCGGTAGTCCAAA
          1 GCCGGTAGTCCAAA

                          
      12235 GCCGGTAGTCCAAA
          1 GCCGGTAGTCCAAA

                   
      12249 GCCGGTA
          1 GCCGGTA

      12256 CTGATAAACT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   21  1.00

ACGTcount: A:0.26, C:0.29, G:0.31, T:0.14


Consensus pattern (14 bp):   
GCCGGTAGTCCAAA
Done.