Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010525.1 Corchorus olitorius cultivar O-4 contig10557, 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: 2371
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34


Found at i:235 original size:35 final size:35

Alignment explanation


    Indices: 1--475  Score: 417
    Period size: 35  Copynumber: 13.4  Consensus size: 35

                                               
          1 GGATCAACTGAAATAAATTGAAGAAAGACCACCCT
          1 GGATCAACTGAAATAAATTGAAGAAAGACCACCCT

                              * *         * *    
         36 AGG-TC-ACTGAAATAAACTAAAGAAAGGATCGCCCT
          1 -GGATCAACTGAAATAAATTGAAGAAA-GACCACCCT

                   * *        *           * *    
         71 GGATCAAATCAGAATAAACTGAAAGAAAGATCGCCCT
          1 GGATCAACTGA-AATAAATTG-AAGAAAGACCACCCT

                        *    *            *      
        108 GGATCAACTGAATTAAACT-AGAGAAAAGATCACCCT
          1 GGATCAACTGAAATAAATTGA-AG-AAAGACCACCCT

                        *    *                  
        144 GGATCAACTGAAGTAAAATGAAGAAAAGACCACCCT
          1 GGATCAACTGAAATAAATTGAAG-AAAGACCACCCT

               *                       *         
        180 GGAGCAAACTGAAATAAATTGAA-ATAGGACCACCCT
          1 GGATC-AACTGAAATAAATTGAAGA-AAGACCACCCT

                          *              * *    
        216 GGATCAACTGAAATGAATTG-AGTAAAGATCGCCCT
          1 GGATCAACTGAAATAAATTGAAG-AAAGACCACCCT

                        * *               *  * 
        251 GGATCAACTGAAGTGAATTGAAGAAAGACCGCCTT
          1 GGATCAACTGAAATAAATTGAAGAAAGACCACCCT

                             *                * 
        286 GGATCAACTGAAATAAACTGAAGAAAAGACCACCAT
          1 GGATCAACTGAAATAAATTGAAG-AAAGACCACCCT

                              *           * *    
        322 AGG-TC-ACTGAAATAAACTGAAGAAAGGATCGCCCT
          1 -GGATCAACTGAAATAAATTGAAGAAA-GACCACCCT

                      *                   *    
        357 GGATCAACTGGAATAAATTGAAGAAAGACCGCCCT
          1 GGATCAACTGAAATAAATTGAAGAAAGACCACCCT

              *  * *             *   *         
        392 GGGTCGATTGAAATAAATTGACGAAGGACCACCCT
          1 GGATCAACTGAAATAAATTGAAGAAAGACCACCCT

              *              *    *     *      
        427 GGGTCAACTGAAATAAACTGAATAAAGATCACCCT
          1 GGATCAACTGAAATAAATTGAAGAAAGACCACCCT

                           
        462 AGG-TCAACTGAAAT
          1 -GGATCAACTGAAAT

        476 GAACTAAAGC


Statistics
Matches: 369,  Mismatches: 51, Indels: 39
        0.80            0.11        0.08

Matches are distributed among these distances:
  34   27  0.07
  35  185  0.50
  36  107  0.29
  37   44  0.12
  38    6  0.02

ACGTcount: A:0.43, C:0.19, G:0.20, T:0.18


Consensus pattern (35 bp):   
GGATCAACTGAAATAAATTGAAGAAAGACCACCCT

Found at i:359 original size:106 final size:105

Alignment explanation


    Indices: 4--473  Score: 456
    Period size: 106  Copynumber: 4.4  Consensus size: 105

          1 GGA

                          *          *                   *    * *         *  
          4 TCAACTGAAATAAATTGAAGAAAGACCACCCTAGG-TC-ACTGAAATAAACTAAAGAAAGGATCG
          1 TCAACTGAAATAAACTGAAGAAAGATCACCCT-GGATCAACTGAAGTAAATTGAAGAAA-GACCG

                       * *        *            * *      
         67 CCCTGGATCAAATCAGAATAAACTGAAAGAAA-GATCGCCCTGG
         64 CCCTGGATCAACTGA-AATAAATTG-AAGAAAGGACCACCCTGG

                      *                                         *            
        110 ATCAACTGAATTAAACT-AGAGAAAAGATCACCCTGGATCAACTGAAGTAAAATGAAGAAAAGAC
          1 -TCAACTGAAATAAACTGA-AG-AAAGATCACCCTGGATCAACTGAAGTAAATTGAAG-AAAGAC

             *       *                     *             
        174 CACCCTGGAGCAAACTGAAATAAATTGAA-ATAGGACCACCCTGG
         62 CGCCCTGGATC-AACTGAAATAAATTGAAGAAAGGACCACCCTGG

                        *  *             *                  *                
        218 ATCAACTGAAATGAATTG-AGTAAAGATCGCCCTGGATCAACTGAAGTGAATTGAAGAAAGACCG
          1 -TCAACTGAAATAAACTGAAG-AAAGATCACCCTGGATCAACTGAAGTAAATTGAAGAAAGACCG

              *                  *        *       *    
        282 CCTTGGATCAACTGAAATAAACTGAAGAAAAGACCACCATAGG
         64 CCCTGGATCAACTGAAATAAATTGAAGAAAGGACCACCCT-GG

                                        *                                    
        325 TC-ACTGAAATAAACTGAAGAAAGGATCGCCCTGGATCAACTGGAA-TAAATTGAAGAAAGACCG
          1 TCAACTGAAATAAACTGAAGAAA-GATCACCCTGGATCAACT-GAAGTAAATTGAAGAAAGACCG

                  *  * *             *                 
        388 CCCTGGGTCGATTGAAATAAATTGACG-AAGGACCACCCTGGG
         64 CCCTGGATCAACTGAAATAAATTGAAGAAAGGACCACCCT-GG

                               *                         
        430 TCAACTGAAATAAACTGAATAAAGATCACCCTAGG-TCAACTGAA
          1 TCAACTGAAATAAACTGAAGAAAGATCACCCT-GGATCAACTGAA

        474 ATGAACTAAA


Statistics
Matches: 305,  Mismatches: 43, Indels: 33
        0.80            0.11        0.09

Matches are distributed among these distances:
 104    3  0.01
 105   59  0.19
 106  106  0.35
 107   59  0.19
 108   38  0.12
 109   33  0.11
 110    7  0.02

ACGTcount: A:0.43, C:0.19, G:0.20, T:0.18


Consensus pattern (105 bp):   
TCAACTGAAATAAACTGAAGAAAGATCACCCTGGATCAACTGAAGTAAATTGAAGAAAGACCGCC
CTGGATCAACTGAAATAAATTGAAGAAAGGACCACCCTGG

Found at i:2003 original size:14 final size:15

Alignment explanation


    Indices: 1978--2006  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       1968 ACAAACTTTG

                           
       1978 AAAACCATTTTTTTA
          1 AAAACCATTTTTTTA

                          
       1993 AAAACCATTTTTTT
          1 AAAACCATTTTTTT

       2007 TTGAAAAAAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48


Consensus pattern (15 bp):   
AAAACCATTTTTTTA
Done.