Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010636.1 Corchorus olitorius cultivar O-4 contig10668, 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: 3288
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:155 original size:39 final size:39

Alignment explanation


    Indices: 24--242  Score: 246
    Period size: 38  Copynumber: 5.7  Consensus size: 39

         14 GGCTGTGCAT

                     *               *             
         24 AGTGGACCCATACCTCAGGGGGTTAGACTGA-TGGTAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGATTGGTAAG

                              *       *     *      
         62 AGTGGACCCGTACCTCAGAGGGTTAATCTGA-CGGTAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGATTGGTAAG

               *   *   *      *                    
        100 AGTAGACTCGTGCCTCAGTGGGTTAAACTGATTGGTAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGATTGGTAAG

             *        *                            
        139 ACTGGACCCGCACCTCAGGGGGTTAAACTGATTGGTAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGATTGGTAAG

            *    *    **   *           *           
        178 GGTGGCCCCGCGCCTTAGGGGGTTAAATTG-TTGGTAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGATTGGTAAG

                       *               
        216 AGTGGACCCGTGCCTCAGGGGGGTTAA
          1 AGTGGACCCGTACCTCA-GGGGGTTAA

        243 TTATTGGCTA


Statistics
Matches: 152,  Mismatches: 27, Indels: 3
        0.84            0.15        0.02

Matches are distributed among these distances:
  38   80  0.53
  39   72  0.47

ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23


Consensus pattern (39 bp):   
AGTGGACCCGTACCTCAGGGGGTTAAACTGATTGGTAAG

Found at i:162 original size:77 final size:78

Alignment explanation


    Indices: 36--243  Score: 251
    Period size: 77  Copynumber: 2.7  Consensus size: 78

         26 TGGACCCATA

                         *                               *                   
         36 CCTCAGGGGGTTAGACTGA-TGGTAAGAGTGGACCCGTACCTCAGAGGGTTAATCTGA-CGGTAA
          1 CCTCAGGGGGTTAAACTGATTGGTAAGAGTGGACCCGTACCTCAGGGGGTTAATCTGATCGGTAA

                    *  * 
         99 GAGTAGACTCGTG
         66 GAGTAGACCCGCG

                  *                     *        *               *     *     
        112 CCTCAGTGGGTTAAACTGATTGGTAAGACTGGACCCGCACCTCAGGGGGTTAAACTGATTGGTAA
          1 CCTCAGGGGGTTAAACTGATTGGTAAGAGTGGACCCGTACCTCAGGGGGTTAATCTGATCGGTAA

             *  * *      
        177 GGGTGGCCCCGCG
         66 GAGTAGACCCGCG

               *           *                      *                
        190 CCTTAGGGGGTTAAATTG-TTGGTAAGAGTGGACCCGTGCCTCAGGGGGGTTAAT
          1 CCTCAGGGGGTTAAACTGATTGGTAAGAGTGGACCCGTACCTCA-GGGGGTTAAT

        244 TATTGGCTAG


Statistics
Matches: 110,  Mismatches: 19, Indels: 4
        0.83            0.14        0.03

Matches are distributed among these distances:
  76   17  0.15
  77   56  0.51
  78   37  0.34

ACGTcount: A:0.23, C:0.19, G:0.35, T:0.24


Consensus pattern (78 bp):   
CCTCAGGGGGTTAAACTGATTGGTAAGAGTGGACCCGTACCTCAGGGGGTTAATCTGATCGGTAA
GAGTAGACCCGCG

Found at i:2315 original size:39 final size:39

Alignment explanation


    Indices: 2195--2412  Score: 262
    Period size: 38  Copynumber: 5.7  Consensus size: 39

       2185 GGCTGTGCAT

                     * *   *                       
       2195 AGTGGACCCATACCTAAGGGGGTTAAACTGA-TGGTAAG
          1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGTAAG

                       *   *  *          *         
       2233 AGTGGACCCGTACCTTAGAGGGTTAAACTTA-TGGTAAG
          1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGTAAG

                   *       * *                     
       2271 AGTGGACTCGTGCCTGAAGGGGTTAAACTGATTGGTAAG
          1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGTAAG

                      * *                        * 
       2310 AGTGGACCCGCGTCTCAGGGGGTTAAACTGATTGGTAGG
          1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGTAAG

             *        *                            
       2349 AATGGACCCGCGCCTCAGGGGGTTAAACTG-TTGGTAAG
          1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGTAAG

                  *        *          
       2387 AGTGGAACCGTGCCTTAGGGGGTTAA
          1 AGTGGACCCGTGCCTCAGGGGGTTAA

       2413 CTGTTAGCTA


Statistics
Matches: 156,  Mismatches: 23, Indels: 2
        0.86            0.13        0.01

Matches are distributed among these distances:
  38   88  0.56
  39   68  0.44

ACGTcount: A:0.26, C:0.17, G:0.34, T:0.23


Consensus pattern (39 bp):   
AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGTAAG

Found at i:2333 original size:77 final size:78

Alignment explanation


    Indices: 2213--2412  Score: 262
    Period size: 77  Copynumber: 2.6  Consensus size: 78

       2203 CATACCTAAG

                                            *      *          *          *   
       2213 GGGGTTAAACTGA-TGGTAAGAGTGGACCCGTACCTTAGAGGGTTAAACTTA-TGGTAAGAGTGG
          1 GGGGTTAAACTGATTGGTAAGAGTGGACCCGTGCCTTAGGGGGTTAAACTGATTGGTAAGAATGG

              *  *    *  
       2276 ACTCGTGCCTGAA
         66 ACCCGCGCCTCAA

                                           * *  *                     *      
       2289 GGGGTTAAACTGATTGGTAAGAGTGGACCCGCGTCTCAGGGGGTTAAACTGATTGGTAGGAATGG
          1 GGGGTTAAACTGATTGGTAAGAGTGGACCCGTGCCTTAGGGGGTTAAACTGATTGGTAAGAATGG

                        *
       2354 ACCCGCGCCTCAG
         66 ACCCGCGCCTCAA

                                       *                   
       2367 GGGGTTAAACTG-TTGGTAAGAGTGGAACCGTGCCTTAGGGGGTTAA
          1 GGGGTTAAACTGATTGGTAAGAGTGGACCCGTGCCTTAGGGGGTTAA

       2413 CTGTTAGCTA


Statistics
Matches: 106,  Mismatches: 16, Indels: 3
        0.85            0.13        0.02

Matches are distributed among these distances:
  76   13  0.12
  77   62  0.58
  78   31  0.29

ACGTcount: A:0.25, C:0.15, G:0.35, T:0.24


Consensus pattern (78 bp):   
GGGGTTAAACTGATTGGTAAGAGTGGACCCGTGCCTTAGGGGGTTAAACTGATTGGTAAGAATGG
ACCCGCGCCTCAA

Found at i:3105 original size:24 final size:23

Alignment explanation


    Indices: 3070--3115  Score: 58
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       3060 TGATGATTGT

                                    
       3070 TGTTTGATATGTTTCATTGTTATG
          1 TGTTTGATATG-TTCATTGTTATG

                          *        
       3094 TGTTCTGA-ATGTTGATTGTTAT
          1 TGTT-TGATATGTTCATTGTTAT

       3116 CCTATTAAGT


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  23   10  0.50
  24    7  0.35
  25    3  0.15

ACGTcount: A:0.17, C:0.04, G:0.22, T:0.57


Consensus pattern (23 bp):   
TGTTTGATATGTTCATTGTTATG
Done.