Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020731.1 Corchorus olitorius cultivar O-4 contig20764, 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: 36897
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:4438 original size:14 final size:14

Alignment explanation


    Indices: 4405--4440  Score: 54
    Period size: 14  Copynumber: 2.6  Consensus size: 14

       4395 AAGTTTTTTT

                 *       *
       4405 TTTTCCTTTTCCTT
          1 TTTTCTTTTTCCTA

                          
       4419 TTTTCTTTTTCCTA
          1 TTTTCTTTTTCCTA

                    
       4433 TTTTCTTT
          1 TTTTCTTT

       4441 AAACAAAGAG


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  14   20  1.00

ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75


Consensus pattern (14 bp):   
TTTTCTTTTTCCTA

Found at i:29757 original size:23 final size:23

Alignment explanation


    Indices: 29725--29775  Score: 86
    Period size: 23  Copynumber: 2.3  Consensus size: 23

      29715 ATTGTTCAAG

                 *                 
      29725 TTCAAATGAGAAAGAAAATCTAC
          1 TTCAAGTGAGAAAGAAAATCTAC

                                   
      29748 TTCAAGTGAGAAAGAAAATCTAC
          1 TTCAAGTGAGAAAGAAAATCTAC

                  
      29771 -TCAAG
          1 TTCAAG

      29776 CAAGAGAAAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  22    5  0.19
  23   22  0.81

ACGTcount: A:0.49, C:0.14, G:0.16, T:0.22


Consensus pattern (23 bp):   
TTCAAGTGAGAAAGAAAATCTAC

Found at i:32602 original size:351 final size:350

Alignment explanation


    Indices: 31907--32604  Score: 986
    Period size: 351  Copynumber: 2.0  Consensus size: 350

      31897 TCTAAAACAG

                             *              *                            **  
      31907 TCTCCAAGTCGGTTTAGGAGAAGATCAATTCTGTCCAGAAATTCAAGGGCAAAATCGTCCATGGG
          1 TCTCCAAGTCGGTTTAGAAGAAGATCAATTCTATCCAGAAATTCAAGGGCAAAATCGTCCACAGG

                               *                                             
      31972 AACTGCAGAATTAGGTCTCGAGGTAAACATAAAAGTTGTAAATCTTGGAATCCTCTTTCCAACGA
         66 AACTGCAGAATTAGGTCTCAAGGTAAACATAAAAGTTGTAAATCTTGGAATCCTCTTTCCAACGA

            *                         *         *               *            
      32037 TACCTCATTTAAATTTTTCTGAGCTCTAGACCAAAAGTTATGAATTTTCTTCCAAAACTGCTCTT
        131 CACCTCATTTAAATTTTTCTGAGCTCCAGACCAAAAATTATGAATTTTCTTCAAAAACTGCTCTT

                       * **   *         *          *  * *                    
      32102 GTGAAATCCTCTTTTGAATAGGATTTAATAATGCTGCATTAGGGGTGAATCAATACTACATCATA
        196 GTGAAATCCTCCTCCGAACAGGATTTAACAATGCTGCATCAGAGCTGAATCAATACTACATCATA

                * *      *               *        *          *    *          
      32167 ATTATTTATTGGATTTGGACTCCTTCTTTTGACTTCCATATTAACGAATTGGGTTTAAAAATATC
        261 ATTACTGATTGGACTTGGACTCCTTCTTTGGACTTCCACATTAACGAATCGGGTCTAAAAATATC

                  *     *            
      32232 AGATTTGGACTTTAAGACATCAGGC
        326 AGATTTAGACTTCAAGACATCAGGC

                                                                             
      32257 TCTCCAAGTCGGTTTAGAAGAAGATCAATTCTATCCAGAAATTTCAAGGGCAAAATCGTCCACAG
          1 TCTCCAAGTCGGTTTAGAAGAAGATCAATTCTATCCAGAAA-TTCAAGGGCAAAATCGTCCACAG

               *                                     *                       
      32322 GAATTGCAGAATTAGGTCTCAAGGTAAACATAAAAGTTGTAGATCTTGGAATCCTCTTTCCAACG
         65 GAACTGCAGAATTAGGTCTCAAGGTAAACATAAAAGTTGTAAATCTTGGAATCCTCTTTCCAACG

                  *     *            *   *  *                                
      32387 ACACCTGATTTTGAA-TTTTCTGAGTTCCGGATCAAAAATTATGAATTTTCTTCAAAAACTGCTC
        130 ACACCTCA-TTTAAATTTTTCTGAGCTCCAGACCAAAAATTATGAATTTTCTTCAAAAACTGCTC

              *    *                           *                  *    *     
      32451 TTTTGAAGTCCTCCTCCGAACAGGATTTAACAATGTTGCATCAGAGCTGAATCATTACTGCATCA
        194 TTGTGAAATCCTCCTCCGAACAGGATTTAACAATGCTGCATCAGAGCTGAATCAATACTACATCA

                                             *                           *   
      32516 TAATTACTGATTGGACTTGGACTCCTTCTTTGGGCTTCCACAGTT-ACGAATCGGGTCTAAGAAT
        259 TAATTACTGATTGGACTTGGACTCCTTCTTTGGACTTCCACA-TTAACGAATCGGGTCTAAAAAT

              *                      
      32580 ATTAGATTTAGACTTCAAGACATCA
        323 ATCAGATTTAGACTTCAAGACATCA

      32605 TCTGGCTTTG


Statistics
Matches: 304,  Mismatches: 41, Indels: 5
        0.87            0.12        0.01

Matches are distributed among these distances:
 350   39  0.13
 351  258  0.85
 352    7  0.02

ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33


Consensus pattern (350 bp):   
TCTCCAAGTCGGTTTAGAAGAAGATCAATTCTATCCAGAAATTCAAGGGCAAAATCGTCCACAGG
AACTGCAGAATTAGGTCTCAAGGTAAACATAAAAGTTGTAAATCTTGGAATCCTCTTTCCAACGA
CACCTCATTTAAATTTTTCTGAGCTCCAGACCAAAAATTATGAATTTTCTTCAAAAACTGCTCTT
GTGAAATCCTCCTCCGAACAGGATTTAACAATGCTGCATCAGAGCTGAATCAATACTACATCATA
ATTACTGATTGGACTTGGACTCCTTCTTTGGACTTCCACATTAACGAATCGGGTCTAAAAATATC
AGATTTAGACTTCAAGACATCAGGC

Found at i:36208 original size:30 final size:32

Alignment explanation


    Indices: 36174--36238  Score: 89
    Period size: 35  Copynumber: 2.0  Consensus size: 32

      36164 CATATGGCCT

                                            
      36174 TTATAT-A-CTATTTTGTAATGGTATGCTATG
          1 TTATATAAGCTATTTTGTAATGGTATGCTATG

                                               
      36204 TTATATACAAAGCTATTTTGTAATGGTATGCTATG
          1 TTATAT---AAGCTATTTTGTAATGGTATGCTATG

      36239 GAGTAGCATA


Statistics
Matches: 30,  Mismatches: 0, Indels: 5
        0.86            0.00        0.14

Matches are distributed among these distances:
  30    6  0.20
  34    1  0.03
  35   23  0.77

ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46


Consensus pattern (32 bp):   
TTATATAAGCTATTTTGTAATGGTATGCTATG
Done.