Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012178.1 Corchorus olitorius cultivar O-4 contig12211, 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: 24750
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32


Found at i:1013 original size:19 final size:19

Alignment explanation


    Indices: 963--1013  Score: 61
    Period size: 19  Copynumber: 2.7  Consensus size: 19

        953 TGTGGAATTT

                               
        963 TTAATAA-TAATTATTCAA
          1 TTAATAATTAATTATTCAA

              *              *  
        981 TAAAATAATT-ATTATTTAA
          1 T-TAATAATTAATTATTCAA

                          
       1000 TTAATAATTAATTA
          1 TTAATAATTAATTA

       1014 ATTTCAGCCA


Statistics
Matches: 27,  Mismatches: 3, Indels: 5
        0.77            0.09        0.14

Matches are distributed among these distances:
  18    8  0.30
  19   18  0.67
  20    1  0.04

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47


Consensus pattern (19 bp):   
TTAATAATTAATTATTCAA

Found at i:16654 original size:43 final size:43

Alignment explanation


    Indices: 16597--16751  Score: 192
    Period size: 43  Copynumber: 3.7  Consensus size: 43

      16587 AACGTTTTTA

                                                       
      16597 AAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGTTTTATTT
          1 AAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGTTTTATTT

                     *                                  *
      16640 AAGTAATTCGAAAAGAAGATTTTGGAAAATAAAAGTTTTCAGTTC
          1 AAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGTTTT-A-TTT

                 **                     * *        *   
      16685 AAGTACCTCCAAAAGAAGATTTTGGAAAGTTAAAG---TCTTT
          1 AAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGTTTTATTT

                  *                     
      16725 AAG-AAATCCAAAAGAAGATTTTGGAAA
          1 AAGTAATTCCAAAAGAAGATTTTGGAAA

      16752 TTAATAAAAT


Statistics
Matches: 99,  Mismatches: 11, Indels: 8
        0.84            0.09        0.07

Matches are distributed among these distances:
  39   22  0.22
  40    5  0.05
  42    1  0.01
  43   38  0.38
  44    1  0.01
  45   32  0.32

ACGTcount: A:0.46, C:0.08, G:0.17, T:0.30


Consensus pattern (43 bp):   
AAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGTTTTATTT

Found at i:23361 original size:18 final size:18

Alignment explanation


    Indices: 23320--23364  Score: 54
    Period size: 18  Copynumber: 2.5  Consensus size: 18

      23310 TATAAGGGAA

                            * 
      23320 ATAATAATTATTATTTCG
          1 ATAATAATTATTATTTAG

             *               *
      23338 AAAATAATTATTATTTAT
          1 ATAATAATTATTATTTAG

            *        
      23356 TTAATAATT
          1 ATAATAATT

      23365 TTCAGCACTA


Statistics
Matches: 22,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  18   22  1.00

ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51


Consensus pattern (18 bp):   
ATAATAATTATTATTTAG

Found at i:24216 original size:31 final size:31

Alignment explanation


    Indices: 24167--24229  Score: 74
    Period size: 31  Copynumber: 2.0  Consensus size: 31

      24157 AAAACTTAGT

                                            
      24167 AAACCTACAAACGCTTAA-CAAAACAATGAGC
          1 AAACCTACAAACGCTTAACCAAAA-AATGAGC

                   *   * *      *          
      24198 AAACCTATAAATGTTTAACCCAAAAATGAGC
          1 AAACCTACAAACGCTTAACCAAAAAATGAGC

             
      24229 A
          1 A

      24230 TTTAGCCTAT


Statistics
Matches: 27,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  31   23  0.85
  32    4  0.15

ACGTcount: A:0.51, C:0.22, G:0.10, T:0.17


Consensus pattern (31 bp):   
AAACCTACAAACGCTTAACCAAAAAATGAGC
Done.