Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014377.1 Corchorus capsularis cultivar CVL-1 contig14398, 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: 15037
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33


Found at i:129 original size:41 final size:42

Alignment explanation


    Indices: 18--152  Score: 206
    Period size: 42  Copynumber: 3.3  Consensus size: 42

          8 TTGAATTAGG

                                  *   *             * 
         18 ACTATGTTTG-CTTTTCTTAATTACCATGGATTACAACTTCA
          1 ACTATGTTTGACTTTTCTTAATCACCCTGGATTACAACTTTA

                                                      
         59 ACTATGTTTGACTTTTCTTAATCACCCTGGATTACAACTTTA
          1 ACTATGTTTGACTTTTCTTAATCACCCTGGATTACAACTTTA

                                   *                  
        101 ACTATGTTTGAC-TTTCTTAATCGCCCTGGATT--AACTTTA
          1 ACTATGTTTGACTTTTCTTAATCACCCTGGATTACAACTTTA

                         
        140 ACTATGTTTGACT
          1 ACTATGTTTGACT

        153 ATCCAAATTA


Statistics
Matches: 88,  Mismatches: 4, Indels: 5
        0.91            0.04        0.05

Matches are distributed among these distances:
  39   19  0.22
  41   29  0.33
  42   40  0.45

ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44


Consensus pattern (42 bp):   
ACTATGTTTGACTTTTCTTAATCACCCTGGATTACAACTTTA

Found at i:171 original size:41 final size:39

Alignment explanation


    Indices: 52--160  Score: 103
    Period size: 39  Copynumber: 2.7  Consensus size: 39

         42 CATGGATTAC

                 *               *  **               
         52 AACTTCAACTATGTTTGACTTTTCTTAATC-ACCCTGGATT
          1 AACTTTAACTATGTTTGAC-TATCCAAATCGA-CCTGGATT

                                  *  **     *        
         92 ACAACTTTAACTATGTTTGACTTTCTTAATCGCCCTGGATT
          1 --AACTTTAACTATGTTTGACTATCCAAATCGACCTGGATT

                                        
        133 AACTTTAACTATGTTTGACTATCCAAAT
          1 AACTTTAACTATGTTTGACTATCCAAAT

        161 TAGGACCTGG


Statistics
Matches: 61,  Mismatches: 5, Indels: 5
        0.86            0.07        0.07

Matches are distributed among these distances:
  39   25  0.41
  41   18  0.30
  42   18  0.30

ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41


Consensus pattern (39 bp):   
AACTTTAACTATGTTTGACTATCCAAATCGACCTGGATT

Found at i:302 original size:15 final size:14

Alignment explanation


    Indices: 282--311  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

        272 CCAACATGGG

                           
        282 ACCTTGACTTTGCTT
          1 ACCTTGACTTT-CTT

                          
        297 ACCTTGACTTTCTT
          1 ACCTTGACTTTCTT

             
        311 A
          1 A

        312 ATTATCTCTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    4  0.27
  15   11  0.73

ACGTcount: A:0.17, C:0.27, G:0.10, T:0.47


Consensus pattern (14 bp):   
ACCTTGACTTTCTT

Found at i:3611 original size:14 final size:15

Alignment explanation


    Indices: 3585--3613  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       3575 TTTTCTTTTA

                           
       3585 TTTTATTTATTATTT
          1 TTTTATTTATTATTT

                           
       3600 TTTTATTT-TTATTT
          1 TTTTATTTATTATTT

       3614 GGATAGGGAC


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14    6  0.43
  15    8  0.57

ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83


Consensus pattern (15 bp):   
TTTTATTTATTATTT
Done.