Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014769.1 Corchorus capsularis cultivar CVL-1 contig14790, 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: 3850
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33


Found at i:463 original size:44 final size:44

Alignment explanation


    Indices: 350--493  Score: 198
    Period size: 45  Copynumber: 3.2  Consensus size: 44

        340 TGCAACTTTG

                   *               *           * *    *  
        350 GAAAACCCTTTTATCAAAACCCTCTTGAAAACCATAATTCTTCTT
          1 GAAAACCATTTTATCAAAA-CCTTTTGAAAACCATGACTCTTTTT

                  *                                      
        395 GAAAAAACATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTT
          1 G-AAAACCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTT

                                                   *     
        440 GAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTATTTTTT
          1 GAAAACCATTTTATCAAAACCTTTTGAAAACCATGACT-CTTTTT

                     
        485 GAAAACCAT
          1 GAAAACCAT

        494 CGTTGCTCTT


Statistics
Matches: 89,  Mismatches: 8, Indels: 4
        0.88            0.08        0.04

Matches are distributed among these distances:
  44   36  0.40
  45   37  0.42
  46   16  0.18

ACGTcount: A:0.39, C:0.21, G:0.06, T:0.34


Consensus pattern (44 bp):   
GAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTT

Found at i:484 original size:45 final size:45

Alignment explanation


    Indices: 350--493  Score: 188
    Period size: 44  Copynumber: 3.2  Consensus size: 45

        340 TGCAACTTTG

                   *               *                        
        350 GAAAACCCTTTTATCAAAACCCTCTTGAAAACCAT-A--ATTCTTCTT
          1 GAAAACCATTTTATCAAAA-CCTTTTGAAAACCATGACTATT-TT-TT

                  *                                 *     
        395 GAAAAAACATTTTATCAAAACCTTTTGAAAACCATGACT-CTTTTT
          1 G-AAAACCATTTTATCAAAACCTTTTGAAAACCATGACTATTTTTT

                                                         
        440 GAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTATTTTTT
          1 GAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTATTTTTT

                     
        485 GAAAACCAT
          1 GAAAACCAT

        494 CGTTGCTCTT


Statistics
Matches: 88,  Mismatches: 6, Indels: 10
        0.85            0.06        0.10

Matches are distributed among these distances:
  44   36  0.41
  45   32  0.36
  46   19  0.22
  47    1  0.01

ACGTcount: A:0.39, C:0.21, G:0.06, T:0.34


Consensus pattern (45 bp):   
GAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTATTTTTT

Found at i:1036 original size:19 final size:19

Alignment explanation


    Indices: 1012--1049  Score: 76
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       1002 CTCCTGAAGT

                               
       1012 GCACTTTATTTCATTACTC
          1 GCACTTTATTTCATTACTC

                               
       1031 GCACTTTATTTCATTACTC
          1 GCACTTTATTTCATTACTC

       1050 ATGATAAAAG


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.21, C:0.26, G:0.05, T:0.47


Consensus pattern (19 bp):   
GCACTTTATTTCATTACTC
Done.