Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015073.1 Corchorus capsularis cultivar CVL-1 contig15094, 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: 6657
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33


Found at i:1082 original size:13 final size:14

Alignment explanation


    Indices: 1051--1087  Score: 65
    Period size: 14  Copynumber: 2.6  Consensus size: 14

       1041 CCTATATATG

                          
       1051 AATTTAATTTGTAA
          1 AATTTAATTTGTAA

                          
       1065 AATTTAATTTGTAA
          1 AATTTAATTTGTAA

             *       
       1079 ATTTTAATT
          1 AATTTAATT

       1088 CTCCTCTCAG


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  14   22  1.00

ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54


Consensus pattern (14 bp):   
AATTTAATTTGTAA

Found at i:2018 original size:18 final size:18

Alignment explanation


    Indices: 1991--2026  Score: 63
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       1981 TCTACCCTTC

                 *            
       1991 GAATATCCACCAAAGTCG
          1 GAATAGCCACCAAAGTCG

                              
       2009 GAATAGCCACCAAAGTCG
          1 GAATAGCCACCAAAGTCG

       2027 ACTTGAAGTT


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

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.39, C:0.28, G:0.19, T:0.14


Consensus pattern (18 bp):   
GAATAGCCACCAAAGTCG

Found at i:2367 original size:21 final size:21

Alignment explanation


    Indices: 2341--2382  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2331 AGCATAAGTG

                    *            
       2341 ACCGGCCATGCGACTTGGAGA
          1 ACCGGCCACGCGACTTGGAGA

                                 
       2362 ACCGGCCACGCGACTTGGAGA
          1 ACCGGCCACGCGACTTGGAGA

       2383 TGTCCGCGCA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.24, C:0.31, G:0.33, T:0.12


Consensus pattern (21 bp):   
ACCGGCCACGCGACTTGGAGA

Found at i:2408 original size:33 final size:33

Alignment explanation


    Indices: 2362--2445  Score: 116
    Period size: 33  Copynumber: 2.5  Consensus size: 33

       2352 GACTTGGAGA

                          *        *          
       2362 ACCGGCCACGCGACTTGGAGATGTCCGCG-CAAC
          1 ACCGGCCACGCGACATGGAGATGCCCG-GTCAAC

                    *                      * 
       2395 ACCGGCCATGCGACATGGAGATGCCCGGTCATC
          1 ACCGGCCACGCGACATGGAGATGCCCGGTCAAC

                              
       2428 ACCGGCCACGCGACATGG
          1 ACCGGCCACGCGACATGG

       2446 CATGCCTGGC


Statistics
Matches: 45,  Mismatches: 5, Indels: 2
        0.87            0.10        0.04

Matches are distributed among these distances:
  32    1  0.02
  33   44  0.98

ACGTcount: A:0.21, C:0.36, G:0.31, T:0.12


Consensus pattern (33 bp):   
ACCGGCCACGCGACATGGAGATGCCCGGTCAAC
Done.