Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009534.1 Corchorus capsularis cultivar CVL-1 contig09555, 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: 28223
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:14751 original size:30 final size:29

Alignment explanation


    Indices: 14678--14755  Score: 111
    Period size: 29  Copynumber: 2.7  Consensus size: 29

      14668 ACTTGTAGCG

                       *       *         
      14678 TTTGGACGTTTCGCCCCCTTAACTTCAAT
          1 TTTGGACGTTTTGCCCCCTGAACTTCAAT

                   *       *             
      14707 TTTGGACATTTTGCCTCCTGAACTTCAAT
          1 TTTGGACGTTTTGCCCCCTGAACTTCAAT

                                
      14736 TTTCGGACGTTTTGCCCCCT
          1 TTT-GGACGTTTTGCCCCCT

      14756 CAACCTAATG


Statistics
Matches: 42,  Mismatches: 6, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  29   28  0.67
  30   14  0.33

ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40


Consensus pattern (29 bp):   
TTTGGACGTTTTGCCCCCTGAACTTCAAT

Found at i:20074 original size:8 final size:8

Alignment explanation


    Indices: 20061--20090  Score: 51
    Period size: 8  Copynumber: 3.8  Consensus size: 8

      20051 TTTGGTTAGG

                  * 
      20061 TTAAATAC
          1 TTAAATGC

                    
      20069 TTAAATGC
          1 TTAAATGC

                    
      20077 TTAAATGC
          1 TTAAATGC

                  
      20085 TTAAAT
          1 TTAAAT

      20091 CAAACTATGG


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   8   21  1.00

ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40


Consensus pattern (8 bp):   
TTAAATGC

Found at i:22933 original size:109 final size:112

Alignment explanation


    Indices: 22737--22952  Score: 321
    Period size: 109  Copynumber: 1.9  Consensus size: 112

      22727 AAGAAAGAAT

                                                        *                    
      22737 ACTAGAACTACAAAATGTCTTTGTCAGAAGCATGCATGCTTCATTCAGAGTTCTTTAAAATATAG
          1 ACTAGAACTACAAAATGTCTTTGTCAGAA-CATGCATGCTTCATGCAGAGTTCTTTAAAATATAG

                     ***               *                    
      22802 TTTATTTCACTTTCACAATTTAGTTTTCAAACAGGACAAGCTAGAAAA
         65 TTTATTTCAAAATCACAATTTAGTTTTAAAACAGGACAAGCTAGAAAA

                       *            *                               *        
      22850 ACTAGAACTACGAAATGTCTTTGTGAGAA-A-GCATGCTTCATGCAGAGTTCTTTACAA-ATAGT
          1 ACTAGAACTACAAAATGTCTTTGTCAGAACATGCATGCTTCATGCAGAGTTCTTTAAAATATAGT

                            *                        
      22912 TTATTTCAAAATCACAGTTTAGTTTTAAAACAGGACAAGCT
         66 TTATTTCAAAATCACAATTTAGTTTTAAAACAGGACAAGCT

      22953 TAAAAGCAGA


Statistics
Matches: 94,  Mismatches: 9, Indels: 4
        0.88            0.08        0.04

Matches are distributed among these distances:
 109   41  0.44
 110   25  0.27
 111    1  0.01
 113   27  0.29

ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33


Consensus pattern (112 bp):   
ACTAGAACTACAAAATGTCTTTGTCAGAACATGCATGCTTCATGCAGAGTTCTTTAAAATATAGT
TTATTTCAAAATCACAATTTAGTTTTAAAACAGGACAAGCTAGAAAA

Found at i:24858 original size:16 final size:16

Alignment explanation


    Indices: 24833--24866  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      24823 TTGGCCCAAA

                 *          
      24833 TCTTCTTATATCATTT
          1 TCTTCATATATCATTT

                       *    
      24849 TCTTCATATATTATTT
          1 TCTTCATATATCATTT

              
      24865 TC
          1 TC

      24867 AATTTTAAGT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.21, C:0.18, G:0.00, T:0.62


Consensus pattern (16 bp):   
TCTTCATATATCATTT
Done.