Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021851.1 Corchorus olitorius cultivar O-4 contig21884, 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: 10617
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:3190 original size:29 final size:28

Alignment explanation


    Indices: 3157--3220  Score: 74
    Period size: 29  Copynumber: 2.2  Consensus size: 28

       3147 AAAATTAAGT

                     *                   
       3157 GTAAAACATTCAAAATTAAAGTACAAAGG
          1 GTAAAACATCCAAAATTAAAGTAC-AAGG

                  **      *             
       3186 GTAAAATGTCCAAACTTAAAGTACAAGG
          1 GTAAAACATCCAAAATTAAAGTACAAGG

             *     
       3214 GCAAAAC
          1 GTAAAAC

       3221 GTCTAAACTG


Statistics
Matches: 29,  Mismatches: 6, Indels: 1
        0.81            0.17        0.03

Matches are distributed among these distances:
  28    9  0.31
  29   20  0.69

ACGTcount: A:0.52, C:0.14, G:0.16, T:0.19


Consensus pattern (28 bp):   
GTAAAACATCCAAAATTAAAGTACAAGG

Found at i:3228 original size:28 final size:29

Alignment explanation


    Indices: 3167--3229  Score: 83
    Period size: 28  Copynumber: 2.2  Consensus size: 29

       3157 GTAAAACATT

                *               *    *   
       3167 CAAAATTAAAGTACAAAGGGTAAAATGTC
          1 CAAACTTAAAGTACAAAGGGCAAAACGTC

                                         
       3196 CAAACTTAAAGTAC-AAGGGCAAAACGTC
          1 CAAACTTAAAGTACAAAGGGCAAAACGTC

            *     
       3224 TAAACT
          1 CAAACT

       3230 GTACAAGTTC


Statistics
Matches: 30,  Mismatches: 4, Indels: 1
        0.86            0.11        0.03

Matches are distributed among these distances:
  28   17  0.57
  29   13  0.43

ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19


Consensus pattern (29 bp):   
CAAACTTAAAGTACAAAGGGCAAAACGTC

Found at i:5845 original size:39 final size:38

Alignment explanation


    Indices: 5794--5882  Score: 115
    Period size: 39  Copynumber: 2.3  Consensus size: 38

       5784 TGTTGACCAA

                             *         **           
       5794 TTCCTTTTGATTTTGCTTGCTGCAATCTGTCTTTGATCCT
          1 TTCC-TTTGATTTTGCTAGCTGCAATCAAT-TTTGATCCT

                                            *   * 
       5834 TTCCTTTGATTTTGCTAGCTGCAATCAATTTTTATCTT
          1 TTCCTTTGATTTTGCTAGCTGCAATCAATTTTGATCCT

                       
       5872 TTCCTTTGATT
          1 TTCCTTTGATT

       5883 CTTCTATGAT


Statistics
Matches: 44,  Mismatches: 5, Indels: 2
        0.86            0.10        0.04

Matches are distributed among these distances:
  38   18  0.41
  39   22  0.50
  40    4  0.09

ACGTcount: A:0.13, C:0.20, G:0.12, T:0.54


Consensus pattern (38 bp):   
TTCCTTTGATTTTGCTAGCTGCAATCAATTTTGATCCT

Found at i:10111 original size:22 final size:23

Alignment explanation


    Indices: 10085--10131  Score: 60
    Period size: 24  Copynumber: 2.0  Consensus size: 23

      10075 AATAATGTGC

                          *  *     
      10085 AGAGAA-ATCATTATAATCAAAG
          1 AGAGAAGATCATTACAAGCAAAG

                                    
      10107 AGAGAATGATCATTACAAGCAAAG
          1 AGAGAA-GATCATTACAAGCAAAG

             
      10131 A
          1 A

      10132 CATTATCAGA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  22    6  0.29
  24   15  0.71

ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19


Consensus pattern (23 bp):   
AGAGAAGATCATTACAAGCAAAG
Done.