Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013885.1 Corchorus capsularis cultivar CVL-1 contig13906, 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: 4555
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36


Found at i:130 original size:2 final size:2

Alignment explanation


    Indices: 123--175  Score: 81
    Period size: 2  Copynumber: 26.0  Consensus size: 2

        113 CCATTGACAG

                                                                            
        123 TA TA TA TA TA TA -A TCA TCA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA T-A T-A TA TA TA TA TA TA TA TA TA TA TA TA

                          
        166 TA TA TA TA TA
          1 TA TA TA TA TA

        176 GTAAATTTTA


Statistics
Matches: 49,  Mismatches: 0, Indels: 4
        0.92            0.00        0.08

Matches are distributed among these distances:
   1    1  0.02
   2   43  0.88
   3    5  0.10

ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:2853 original size:2 final size:2

Alignment explanation


    Indices: 2812--2841  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       2802 TTATTATTAG

                                                        
       2812 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       2842 CTTTCTATAT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:4328 original size:127 final size:127

Alignment explanation


    Indices: 4191--4423  Score: 342
    Period size: 127  Copynumber: 1.8  Consensus size: 127

       4181 ATAATTTAAT

                        *                  *   *           *     **  *       
       4191 TTTTTTAATAAATAATCTAAAACCCTAGTTCTATATATATAACAAAATAGGACTTACTCTATAAT
          1 TTTTTTAATAAAAAATCTAAAACCCTAGTTCGATAAATATAACAAAAAAGGACCAACCCTATAAT

                    *                                                      
       4256 TTATTTC-CTTATATTAATTTGGGGCTAAACCTTATGAAAAACAATATCCTATTTTTAAGGAG
         66 TTATTTCATTTA-ATTAATTTGGGGCTAAACCTTATGAAAAACAATATCCTATTTTTAAGGAG

                                                    **       *               
       4318 TTTTTTAATAAAAAATCTAAAACCCTAGTTCGATAAATATTTCAAAAAATGACCAACCCTATAAT
          1 TTTTTTAATAAAAAATCTAAAACCCTAGTTCGATAAATATAACAAAAAAGGACCAACCCTATAAT

              *                                      
       4383 TTCTTTCATTTAATTAATTTGGGGCTAAACCTTATGAAAAA
         66 TTATTTCATTTAATTAATTTGGGGCTAAACCTTATGAAAAA

       4424 GGCTAAAATC


Statistics
Matches: 93,  Mismatches: 12, Indels: 2
        0.87            0.11        0.02

Matches are distributed among these distances:
 127   90  0.97
 128    3  0.03

ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38


Consensus pattern (127 bp):   
TTTTTTAATAAAAAATCTAAAACCCTAGTTCGATAAATATAACAAAAAAGGACCAACCCTATAAT
TTATTTCATTTAATTAATTTGGGGCTAAACCTTATGAAAAACAATATCCTATTTTTAAGGAG
Done.