Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007622.1 Corchorus capsularis cultivar CVL-1 contig07643, 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: 2515
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.25


Found at i:1099 original size:52 final size:54

Alignment explanation


    Indices: 1011--1112  Score: 145
    Period size: 52  Copynumber: 1.9  Consensus size: 54

       1001 CTATGCCTAA

                       *  *                                       
       1011 AAAAAAAACTGGGCTTAAAACAGAAAGAGGTCGCAAAAAGAAAAAAGAAAAACG
          1 AAAAAAAACTGAGCCTAAAACAGAAAGAGGTCGCAAAAAGAAAAAAGAAAAACG

                                           *         *   *    
       1065 AAAAAAAACTGAGCCTAAAA-A-AAAGAGGTTGCAAAAAGAGAAATGAAA
          1 AAAAAAAACTGAGCCTAAAACAGAAAGAGGTCGCAAAAAGAAAAAAGAAA

       1113 TATAAGGAGA


Statistics
Matches: 43,  Mismatches: 5, Indels: 2
        0.86            0.10        0.04

Matches are distributed among these distances:
  52   24  0.56
  53    1  0.02
  54   18  0.42

ACGTcount: A:0.62, C:0.10, G:0.20, T:0.09


Consensus pattern (54 bp):   
AAAAAAAACTGAGCCTAAAACAGAAAGAGGTCGCAAAAAGAAAAAAGAAAAACG

Found at i:2145 original size:50 final size:50

Alignment explanation


    Indices: 2039--2229  Score: 283
    Period size: 50  Copynumber: 3.8  Consensus size: 50

       2029 CGCATCAGAA

                   *                                *          
       2039 ACAGTTCGAAGGATAAGCGGAAGACGATCCTTTTTAAGATTGAATTGGAAG
          1 ACAGTTCAAAGGATAAGCGGAAGACGATCC-TTTTAAGATGGAATTGGAAG

                              *                               
       2090 ACAGTTCAAAGGATAAGCAGAAGACGATCCTTTTAAGATGGAATTGGAAG
          1 ACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTAAGATGGAATTGGAAG

                           *                    *  **         
       2140 ACAGTTCAAAGGATAGGCGGAAGACGATCCTTTTAATATTAAATTGGAAG
          1 ACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTAAGATGGAATTGGAAG

               *                    * *             
       2190 ACAATTCAAAGGATAAGCGGAAGATGGTCCTTTTAAGATG
          1 ACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTAAGATG

       2230 TGGAAGACAG


Statistics
Matches: 126,  Mismatches: 14, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
  50   98  0.78
  51   28  0.22

ACGTcount: A:0.38, C:0.12, G:0.26, T:0.25


Consensus pattern (50 bp):   
ACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTAAGATGGAATTGGAAG

Done.