Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004311.1 Corchorus capsularis cultivar CVL-1 contig04319, 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, 903

Length: 1506
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38


Found at i:942 original size:19 final size:18

Alignment explanation


    Indices: 918--953  Score: 63
    Period size: 19  Copynumber: 1.9  Consensus size: 18

        908 ATCATTATTG

                               
        918 ATTATTATATGATTAATTA
          1 ATTATTATATGA-TAATTA

                             
        937 ATTATTATATGATAATT
          1 ATTATTATATGATAATT

        954 CATTTTTGAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  18    5  0.29
  19   12  0.71

ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53


Consensus pattern (18 bp):   
ATTATTATATGATAATTA

Found at i:996 original size:50 final size:50

Alignment explanation


    Indices: 937--1062  Score: 245
    Period size: 49  Copynumber: 2.5  Consensus size: 50

        927 TGATTAATTA

                                                              
        937 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATTCATTATTG
          1 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATTCATTATTG

                                                              
        987 ATTATTATATGATAATTCA-TTTTGAAATTTAGAATTTCATTCATTATTG
          1 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATTCATTATTG

                                       
       1036 ATTATTATATGATAATTCATTTTTGAA
          1 ATTATTATATGATAATTCATTTTTGAA

       1063 TGATGATTTT


Statistics
Matches: 75,  Mismatches: 0, Indels: 2
        0.97            0.00        0.03

Matches are distributed among these distances:
  49   49  0.65
  50   26  0.35

ACGTcount: A:0.35, C:0.06, G:0.08, T:0.52


Consensus pattern (50 bp):   
ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATTCATTATTG

Found at i:1053 original size:25 final size:25

Alignment explanation


    Indices: 937--1061  Score: 93
    Period size: 25  Copynumber: 5.0  Consensus size: 25

        927 TGATTAATTA

                                 *   
        937 ATTATTATATGATAATTCATTTTTG
          1 ATTATTATATGATAATTCATTATTG

              *             *           
        962 A-AATT-TA-GAATTTCATTCATTATTG
          1 ATTATTATATG-A--TAATTCATTATTG

                                     
        987 ATTATTATATGATAATTCATT-TTG
          1 ATTATTATATGATAATTCATTATTG

              *             *           
       1011 A-AATT-TA-GAATTTCATTCATTATTG
          1 ATTATTATATG-A--TAATTCATTATTG

                                 *   
       1036 ATTATTATATGATAATTCATTTTTG
          1 ATTATTATATGATAATTCATTATTG

             
       1061 A
          1 A

       1062 ATGATGATTT


Statistics
Matches: 77,  Mismatches: 10, Indels: 26
        0.68            0.09        0.23

Matches are distributed among these distances:
  21    1  0.01
  22    4  0.05
  23    6  0.08
  24   15  0.19
  25   37  0.48
  26    6  0.08
  27    6  0.08
  28    2  0.03

ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52


Consensus pattern (25 bp):   
ATTATTATATGATAATTCATTATTG
Done.