Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017362.1 Corchorus olitorius cultivar O-4 contig17395, 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: 3099
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36


Found at i:1657 original size:2 final size:2

Alignment explanation


    Indices: 1650--1683  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       1640 TGGTGGAATC

                                                              
       1650 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       1684 CACATTATTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:2541 original size:2 final size:2

Alignment explanation


    Indices: 2536--2563  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       2526 TCTCTCTTAG

                                                     
       2536 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT

       2564 ATAAAGAAAC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
CT

Found at i:2900 original size:12 final size:11

Alignment explanation


    Indices: 2885--2980  Score: 63
    Period size: 12  Copynumber: 8.5  Consensus size: 11

       2875 CAGCCTGCTA

                        
       2885 GCCAGCACGCGG
          1 GCCAGC-CGCGG

                       
       2897 GCCAG-CGCGG
          1 GCCAGCCGCGG

            *         **
       2907 CCCAGCCTGCTA
          1 GCCAGCC-GCGG

                        
       2919 GCCAGCACGCGG
          1 GCCAGC-CGCGG

                       
       2931 GCCAG-CGCGG
          1 GCCAGCCGCGG

            *         **
       2941 CCCAGCCTGCTA
          1 GCCAGCC-GCGG

                        
       2953 GCCAGCACGCGG
          1 GCCAGC-CGCGG

                       
       2965 GCCAG-CGCGG
          1 GCCAGCCGCGG

            *     
       2975 CCCAGC
          1 GCCAGC

       2981 GTGCTGGGCT


Statistics
Matches: 64,  Mismatches: 13, Indels: 15
        0.70            0.14        0.16

Matches are distributed among these distances:
  10   27  0.42
  11    2  0.03
  12   33  0.52
  13    2  0.03

ACGTcount: A:0.15, C:0.45, G:0.36, T:0.04


Consensus pattern (11 bp):   
GCCAGCCGCGG

Found at i:2910 original size:34 final size:34

Alignment explanation


    Indices: 2860--2985  Score: 225
    Period size: 34  Copynumber: 3.6  Consensus size: 34

       2850 TAAATGGGCT

                                                
       2860 GGCCAGGCGCAGGCCCAGCCTGCTAGCCAGCACGCG
          1 GGCCA-GCGC-GGCCCAGCCTGCTAGCCAGCACGCG

                                              
       2896 GGCCAGCGCGGCCCAGCCTGCTAGCCAGCACGCG
          1 GGCCAGCGCGGCCCAGCCTGCTAGCCAGCACGCG

                                              
       2930 GGCCAGCGCGGCCCAGCCTGCTAGCCAGCACGCG
          1 GGCCAGCGCGGCCCAGCCTGCTAGCCAGCACGCG

                             *    
       2964 GGCCAGCGCGGCCCAGCGTGCT
          1 GGCCAGCGCGGCCCAGCCTGCT

       2986 GGGCTTGGTG


Statistics
Matches: 89,  Mismatches: 1, Indels: 2
        0.97            0.01        0.02

Matches are distributed among these distances:
  34   80  0.90
  35    4  0.04
  36    5  0.06

ACGTcount: A:0.14, C:0.43, G:0.37, T:0.06


Consensus pattern (34 bp):   
GGCCAGCGCGGCCCAGCCTGCTAGCCAGCACGCG

Found at i:2979 original size:22 final size:21

Alignment explanation


    Indices: 2886--2980  Score: 59
    Period size: 22  Copynumber: 4.2  Consensus size: 21

       2876 AGCCTGCTAG

                                  
       2886 CCAGCACGCGGGCCAGCGCGGC
          1 CCAGC-CGCGGGCCAGCGCGGC

                     **            *
       2908 CCAGCCTGCTAGCCAGCACGCGGG
          1 CCAGCC-GCGGGCCAG--CGCGGC

                      *       *  
       2932 CCAG-CGCGGCCCAGC-CTGC
          1 CCAGCCGCGGGCCAGCGCGGC

                                     
       2951 TAGCCAGCACGCGGGCCAGCGCGGC
          1 ---CCAGC-CGCGGGCCAGCGCGGC

                 
       2976 CCAGC
          1 CCAGC

       2981 GTGCTGGGCT


Statistics
Matches: 54,  Mismatches: 10, Indels: 18
        0.66            0.12        0.22

Matches are distributed among these distances:
  19    2  0.04
  20    1  0.02
  21    1  0.02
  22   27  0.50
  23    1  0.02
  24   19  0.35
  25    3  0.06

ACGTcount: A:0.15, C:0.45, G:0.36, T:0.04


Consensus pattern (21 bp):   
CCAGCCGCGGGCCAGCGCGGC
Done.