Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016814.1 Corchorus olitorius cultivar O-4 contig16847, 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: 14626
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32


Found at i:2616 original size:35 final size:35

Alignment explanation


    Indices: 2566--2887  Score: 398
    Period size: 35  Copynumber: 9.2  Consensus size: 35

       2556 AGTTATTTAT

                      *                         
       2566 TTAATTACCCAGAATTAAGTTACTTACT-ATCTTAC
          1 TTAATTACCCTGAATTAAGTTACTTACTGA-CTTAC

                      *                 *       
       2601 TTAATTACCCCGAATTAAGTTGA-TTACCGACTTAC
          1 TTAATTACCCTGAATTAAGTT-ACTTACTGACTTAC

                                       *   *    
       2636 TTAATTACCCTGAATTAAGTTGA-TTATTGAATTAC
          1 TTAATTACCCTGAATTAAGTT-ACTTACTGACTTAC

                 *               *        *    
       2671 TTAATAACCCTGAATTAAGTTGCTTACTGAATTAC
          1 TTAATTACCCTGAATTAAGTTACTTACTGACTTAC

              *    *              *     *      
       2706 TTGATTATCCTGAATTAAGTTATTTACTAACTTAC
          1 TTAATTACCCTGAATTAAGTTACTTACTGACTTAC

                       *          *         *  
       2741 TTAATTACCCTAAATTAAGTTAATTACTGACTGAC
          1 TTAATTACCCTGAATTAAGTTACTTACTGACTTAC

                                  *          * 
       2776 TTAATTACCCTGAATTAAGTTAATTACTGACTTTC
          1 TTAATTACCCTGAATTAAGTTACTTACTGACTTAC

                                      *        
       2811 TTAATTACCCTGAATTAAGTTACTTATTGACTTAC
          1 TTAATTACCCTGAATTAAGTTACTTACTGACTTAC

                      *          *     *  *    
       2846 TTAATTACCCAGAATTAAGTTGCTTACAGAATTAC
          1 TTAATTACCCTGAATTAAGTTACTTACTGACTTAC

                   
       2881 TTAATTA
          1 TTAATTA

       2888 AGTTATTAAC


Statistics
Matches: 251,  Mismatches: 33, Indels: 6
        0.87            0.11        0.02

Matches are distributed among these distances:
  35  249  0.99
  36    2  0.01

ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40


Consensus pattern (35 bp):   
TTAATTACCCTGAATTAAGTTACTTACTGACTTAC

Found at i:2765 original size:19 final size:18

Alignment explanation


    Indices: 2741--2802  Score: 56
    Period size: 19  Copynumber: 3.4  Consensus size: 18

       2731 ACTAACTTAC

                               
       2741 TTAATTACCCTAAATTAAG
          1 TTAATTACCCT-AATTAAG

                       * * * *
       2760 TTAATTA--CTGACTGAC
          1 TTAATTACCCTAATTAAG

                               
       2776 TTAATTACCCTGAATTAAG
          1 TTAATTACCCT-AATTAAG

                    
       2795 TTAATTAC
          1 TTAATTAC

       2803 TGACTTTCTT


Statistics
Matches: 32,  Mismatches: 8, Indels: 6
        0.70            0.17        0.13

Matches are distributed among these distances:
  16   10  0.31
  17    2  0.06
  18    2  0.06
  19   18  0.56

ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39


Consensus pattern (18 bp):   
TTAATTACCCTAATTAAG

Found at i:5843 original size:21 final size:21

Alignment explanation


    Indices: 5813--5866  Score: 72
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       5803 GCATGGAATG

                                 
       5813 GTGATGGCACGGGCATGGCCA
          1 GTGATGGCACGGGCATGGCCA

               *      *   *     *
       5834 GTGGTGGCACAGGCTTGGCCG
          1 GTGATGGCACGGGCATGGCCA

                        
       5855 GTGATGGCACGG
          1 GTGATGGCACGG

       5867 TGTTGGGTGT


Statistics
Matches: 27,  Mismatches: 6, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  21   27  1.00

ACGTcount: A:0.15, C:0.22, G:0.46, T:0.17


Consensus pattern (21 bp):   
GTGATGGCACGGGCATGGCCA

Found at i:5872 original size:21 final size:20

Alignment explanation


    Indices: 5812--5872  Score: 59
    Period size: 21  Copynumber: 2.9  Consensus size: 20

       5802 AGCATGGAAT

                           *     
       5812 GGTGATGGCACGGGCATGGCC
          1 GGTGATGGCACGGG-TTGGCC

            *   *         *      
       5833 AGTGGTGGCACAGGCTTGGCC
          1 GGTGATGGCAC-GGGTTGGCC

                               
       5854 GGTGATGGCACGGTGTTGG
          1 GGTGATGGCACGG-GTTGG

       5873 GTGTATGAGT


Statistics
Matches: 31,  Mismatches: 7, Indels: 4
        0.74            0.17        0.10

Matches are distributed among these distances:
  20    2  0.06
  21   27  0.87
  22    2  0.06

ACGTcount: A:0.13, C:0.20, G:0.48, T:0.20


Consensus pattern (20 bp):   
GGTGATGGCACGGGTTGGCC
Done.