Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014561.1 Corchorus capsularis cultivar CVL-1 contig14582, 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: 17615
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34


Found at i:11972 original size:21 final size:21

Alignment explanation


    Indices: 11946--11989  Score: 63
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      11936 GGGTTAGGGG

                                  
      11946 TTTTTTT-AAAGTTCCAAAGTT
          1 TTTTTTTGAAAGTTCC-AAGTT

                          *      
      11967 TTTTTTTGAAAGTTTCAAGTT
          1 TTTTTTTGAAAGTTCCAAGTT

              
      11988 TT
          1 TT

      11990 AATTACGATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21   14  0.67
  22    7  0.33

ACGTcount: A:0.25, C:0.07, G:0.11, T:0.57


Consensus pattern (21 bp):   
TTTTTTTGAAAGTTCCAAGTT

Found at i:12901 original size:51 final size:51

Alignment explanation


    Indices: 12812--12922  Score: 159
    Period size: 51  Copynumber: 2.2  Consensus size: 51

      12802 CATCAGCAAC

                        *         *        *                   
      12812 GATCCTGAAATGTTAAGGCAAATTGCAAAAAGTCTTAGAGCTGATGCAAGG
          1 GATCCTGAAATGCTAAGGCAAACTGCAAAAACTCTTAGAGCTGATGCAAGG

                              *        *     *                 
      12863 GATCCTGAAATGCTAAGGGAAACTGCAGAAACTTTTAGAGCTGATGCAAGG
          1 GATCCTGAAATGCTAAGGCAAACTGCAAAAACTCTTAGAGCTGATGCAAGG

                *    
      12914 GATCTTGAA
          1 GATCCTGAA

      12923 GCACTAGCCA


Statistics
Matches: 53,  Mismatches: 7, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  51   53  1.00

ACGTcount: A:0.36, C:0.14, G:0.26, T:0.23


Consensus pattern (51 bp):   
GATCCTGAAATGCTAAGGCAAACTGCAAAAACTCTTAGAGCTGATGCAAGG

Found at i:13429 original size:17 final size:17

Alignment explanation


    Indices: 13407--13439  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

      13397 GTCTGTGTCG

                             
      13407 AAGCGTAAGCGCCGTCT
          1 AAGCGTAAGCGCCGTCT

                            
      13424 AAGCGTAAGCGCCGTC
          1 AAGCGTAAGCGCCGTC

      13440 GACCATTGGT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.24, C:0.30, G:0.30, T:0.15


Consensus pattern (17 bp):   
AAGCGTAAGCGCCGTCT

Found at i:14048 original size:1 final size:1

Alignment explanation


    Indices: 14044--14075  Score: 64
    Period size: 1  Copynumber: 32.0  Consensus size: 1

      14034 TCTCTCTCTC

                                            
      14044 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

      14076 AATTTGGCTT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   31  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:15087 original size:33 final size:33

Alignment explanation


    Indices: 15045--15180  Score: 110
    Period size: 33  Copynumber: 4.4  Consensus size: 33

      15035 AAAAAGTCTC

                                     *       
      15045 GGAAATTGAAGCAAGTCTTAGAGCTCATGCAAG
          1 GGAAATTGAAGCAAGTCTTAGAGCTTATGCAAG

                *                    * *     
      15078 GGAACTTGAAGC-A--C---GA-CTGAAG-AA-
          1 GGAAATTGAAGCAAGTCTTAGAGCTTATGCAAG

                  **        *           *    
      15102 GGAAATAAAAGCAAGTTTTAGAGCTTATACAAG
          1 GGAAATTGAAGCAAGTCTTAGAGCTTATGCAAG

                *           *                
      15135 GGAAGTTGAAGCAAGTATTAGAGCTTATGCAAG
          1 GGAAATTGAAGCAAGTCTTAGAGCTTATGCAAG

                *        
      15168 GGAACTTGAAGCA
          1 GGAAATTGAAGCA

      15181 CAACAGAAGA


Statistics
Matches: 78,  Mismatches: 16, Indels: 18
        0.70            0.14        0.16

Matches are distributed among these distances:
  24    9  0.12
  25    3  0.04
  26    4  0.05
  27    2  0.03
  30    3  0.04
  31    3  0.04
  32    3  0.04
  33   51  0.65

ACGTcount: A:0.40, C:0.12, G:0.27, T:0.21


Consensus pattern (33 bp):   
GGAAATTGAAGCAAGTCTTAGAGCTTATGCAAG
Done.