Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022881.1 Corchorus olitorius cultivar O-4 contig22914, 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: 7234
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.30


Found at i:3247 original size:38 final size:38

Alignment explanation


    Indices: 3186--3634  Score: 207
    Period size: 39  Copynumber: 11.6  Consensus size: 38

       3176 TAGGTCCTGC

                    *         *                   
       3186 CATTTAAGTAAACCTGCTAAGGTCTATGTTTAGATTTT
          1 CATTTAAGCAAACCTGCTTAGGTCTATGTTTAGATTTT

                         *                    *   
       3224 CATTTAAGCAAACATGCTTAGGTCTATGTTTAGAATTT
          1 CATTTAAGCAAACCTGCTTAGGTCTATGTTTAGATTTT

                    *      **               * *    *
       3262 CATTTAAGTAAACCTAATTAGGTTCT-TGCTTAAAATTTC
          1 CATTTAAGCAAACCTGCTTAGG-TCTATG-TTTAGATTTT

             *                                  * * 
       3301 CGTTTAAGCAAACCTGCTTAGGTCCT-TGTTTAGAACTCT
          1 CATTTAAGCAAACCTGCTTAGGT-CTATGTTTAG-ATTTT

              *     *                 * *          
       3340 C-GTTAAGTAAACCTGCTTAGGTCTACGCTTAGAGTTTT
          1 CATTTAAGCAAACCTGCTTAGGTCTATGTTTAGA-TTTT

            **     *                   *             *
       3378 TGTTTAATCAAACCTGCTTAGGTCCCTCT-TTGTA-ATCTTG
          1 CATTTAAGCAAACCTGCTTAGGT--CTATGTT-TAGAT-TTT

              *      *       * * *    *  *          
       3418 C-CTT-AGAAAAACCTGATCACGTCTCTGCTTAGAATTTT
          1 CATTTAAG-CAAACCTGCTTAGGTCTATGTTTAG-ATTTT

                    *       *         *  *      *   
       3456 CATTTAAGAAAACCTGTTTAGGATCTCTGCTTAGAGCTTT
          1 CATTTAAGCAAACCTGCTTAGG-TCTATGTTTAGA-TTTT

            *   *   *  *            ** * *       **
       3496 GA-TCAAGTAAGCCTGCTTAGGTCCCTATATAGAGTTGC
          1 CATTTAAGCAAACCTGCTTAGGTCTATGTTTAGA-TTTT

                    *                     *   *   
       3534 CATTTAAGTAAACCTGCTTAGGTCTATGTTCAGAATTT
          1 CATTTAAGCAAACCTGCTTAGGTCTATGTTTAGATTTT

             *      *                  *             
       3572 CGTTTAAGAAAACCTGCTTAGGTTCT-CGTTTAGAATTCTT
          1 CATTTAAGCAAACCTGCTTAGG-TCTATGTTTAG-ATT-TT

             *     *                
       3612 -GTTTAATCAAACCTGCTTAGGTC
          1 CATTTAAGCAAACCTGCTTAGGTC

       3635 CCCCCTCTAC


Statistics
Matches: 309,  Mismatches: 79, Indels: 46
        0.71            0.18        0.11

Matches are distributed among these distances:
  37    9  0.03
  38  128  0.41
  39  145  0.47
  40   23  0.07
  41    4  0.01

ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38


Consensus pattern (38 bp):   
CATTTAAGCAAACCTGCTTAGGTCTATGTTTAGATTTT

Found at i:3624 original size:77 final size:74

Alignment explanation


    Indices: 3188--3634  Score: 258
    Period size: 77  Copynumber: 5.8  Consensus size: 74

       3178 GGTCCTGCCA

                            *       * *                       *              
       3188 TTTAAGTAAACCTGCTAAGGTCTATGTTTAG-ATTTTCATTTAAGCAAACATGCTTAGGTCTATG
          1 TTTAAGTAAACCTGCTTAGGTCT-CGCTTAGAATTTT-ATTTAAGCAAACCTGCTTAGGTCTATG

                       *
       3252 TTTAGAATTTCA
         64 -TTAGAATTTCG

                         **         *     *      **                          
       3264 TTTAAGTAAACCTAATTAGGTTCTTGCTTAAAATTTCCGTTTAAGCAAACCTGCTTAGGTCCT-T
          1 TTTAAGTAAACCTGCTTAGG-TCTCGCTTAGAATTT-TATTTAAGCAAACCTGCTTAGGT-CTAT

                      *   
       3328 GTTTAGAACTCTCG
         63 G-TTAGAA-TTTCG

                                             *    *     *                ** *
       3342 -TTAAGTAAACCTGCTTAGGTCTACGCTTAGAGTTTTTGTTTAATCAAACCTGCTTAGGTCCCTC
          1 TTTAAGTAAACCTGCTTAGGTCT-CGCTTAGA-ATTTTATTTAAGCAAACCTGCTTAGGTCTATG

              *          
       3406 TTTGTAATCTT-G
         64 TTAG-AAT-TTCG

             *      *       * * *                          *       *         
       3418 CCTT-AGAAAAACCTGATCACGTCTCTGCTTAGAATTTTCATTTAAGAAAACCTGTTTAGGATCT
          1 -TTTAAG-TAAACCTGCTTAGGTCTC-GCTTAGAATTTT-ATTTAAGCAAACCTGCTTAGG-TCT

            *         *     
       3482 CTGCTTAGAGCTTT-G
         61 ATG-TTAGA-ATTTCG

            * *      *            * **      *   **       *                   
       3497 ATCAAGTAAGCCTGCTTAGGTCCCTATATAGAGTTGCCATTTAAGTAAACCTGCTTAGGTCTATG
          1 TTTAAGTAAACCTGCTTAGGTCTCGCT-TAGAATT-TTATTTAAGCAAACCTGCTTAGGTCTATG

                        
       3562 TTCAGAATTTCG
         64 TT-AGAATTTCG

                  *                   *           *     *                
       3574 TTTAAGAAAACCTGCTTAGGTTCTCGTTTAGAATTCTTGTTTAATCAAACCTGCTTAGGTC
          1 TTTAAGTAAACCTGCTTAGG-TCTCGCTTAGAATT-TTATTTAAGCAAACCTGCTTAGGTC

       3635 CCCCCTCTAC


Statistics
Matches: 282,  Mismatches: 65, Indels: 47
        0.72            0.16        0.12

Matches are distributed among these distances:
  76   36  0.13
  77  143  0.51
  78   89  0.32
  79   10  0.04
  80    4  0.01

ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38


Consensus pattern (74 bp):   
TTTAAGTAAACCTGCTTAGGTCTCGCTTAGAATTTTATTTAAGCAAACCTGCTTAGGTCTATGTT
AGAATTTCG
Done.