Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023640.1 Corchorus olitorius cultivar O-4 contig23673, 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: 17814
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32


Found at i:145 original size:33 final size:33

Alignment explanation


    Indices: 98--178  Score: 92
    Period size: 33  Copynumber: 2.5  Consensus size: 33

         88 GTGTTTTAGA

                     *     *                  
         98 TGTTGTTTGGGATGATACTAAACCTAATTTGA-G
          1 TGTTGTTTGTGATGACACTAAACCT-ATTTGAGG

                                  *  *   *   
        131 TGTTGTTTGTGATGACACTAAATCTGTTTTAGG
          1 TGTTGTTTGTGATGACACTAAACCTATTTGAGG

             *             
        164 TATTGTTTGTGATGA
          1 TGTTGTTTGTGATGA

        179 AACAAATTCT


Statistics
Matches: 41,  Mismatches: 6, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  32    4  0.10
  33   37  0.90

ACGTcount: A:0.23, C:0.07, G:0.25, T:0.44


Consensus pattern (33 bp):   
TGTTGTTTGTGATGACACTAAACCTATTTGAGG

Found at i:1995 original size:21 final size:21

Alignment explanation


    Indices: 1969--2058  Score: 112
    Period size: 21  Copynumber: 4.3  Consensus size: 21

       1959 TGCTAGGAGA

                                  
       1969 TCATTGGAGTAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                  
       1990 TCATTGGA-AGAGGTTCCAAGC
          1 TCATTGGAGA-AGGTTCCAAGC

             *                   
       2011 TTATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                       *   *  *  
       2032 TCATTGGAGAATGTTTCATGC
          1 TCATTGGAGAAGGTTCCAAGC

                  
       2053 TCATTG
          1 TCATTG

       2059 TAATTGCTTA


Statistics
Matches: 61,  Mismatches: 5, Indels: 6
        0.85            0.07        0.08

Matches are distributed among these distances:
  19    1  0.02
  20    1  0.02
  21   58  0.95
  22    1  0.02

ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:2953 original size:25 final size:24

Alignment explanation


    Indices: 2917--2963  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       2907 TCCTTCTATT

                                    
       2917 CATCTATCATC-AAGTTTTTCATC
          1 CATCTATCATCAAAGTTTTTCATC

                                    
       2940 CATCTCATCCATCAAAGTTTTTCA
          1 CATCT-AT-CATCAAAGTTTTTCA

       2964 AATTTTCTAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    2  0.10
  25    4  0.19
  26   10  0.48

ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40


Consensus pattern (24 bp):   
CATCTATCATCAAAGTTTTTCATC

Found at i:4555 original size:33 final size:33

Alignment explanation


    Indices: 4508--4588  Score: 92
    Period size: 33  Copynumber: 2.5  Consensus size: 33

       4498 GTGTTTTAGA

                     *     *                  
       4508 TGTTGTTTGGGATGATACTAAACCTAATTTGA-G
          1 TGTTGTTTGTGATGACACTAAACCT-ATTTGAGG

                                  *  *   *   
       4541 TGTTGTTTGTGATGACACTAAATCTGTTTTAGG
          1 TGTTGTTTGTGATGACACTAAACCTATTTGAGG

             *             
       4574 TATTGTTTGTGATGA
          1 TGTTGTTTGTGATGA

       4589 AACAAATTCT


Statistics
Matches: 41,  Mismatches: 6, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  32    4  0.10
  33   37  0.90

ACGTcount: A:0.23, C:0.07, G:0.25, T:0.44


Consensus pattern (33 bp):   
TGTTGTTTGTGATGACACTAAACCTATTTGAGG

Found at i:6407 original size:21 final size:21

Alignment explanation


    Indices: 6381--6472  Score: 141
    Period size: 21  Copynumber: 4.4  Consensus size: 21

       6371 TGCTAGGAGA

                                  
       6381 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                 
       6402 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                            *    
       6423 TCATTGGAGAAGGTTCTAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                   *       *     
       6444 TCATTGGTGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       6465 TCATTGGA
          1 TCATTGGA

       6473 ATTGCCTAAG


Statistics
Matches: 65,  Mismatches: 5, Indels: 2
        0.90            0.07        0.03

Matches are distributed among these distances:
  20    2  0.03
  21   63  0.97

ACGTcount: A:0.27, C:0.17, G:0.27, T:0.28


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Done.