Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015355.1 Corchorus capsularis cultivar CVL-1 contig15376, 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: 3982
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33


Found at i:1368 original size:25 final size:25

Alignment explanation


    Indices: 1340--1411  Score: 63
    Period size: 25  Copynumber: 3.2  Consensus size: 25

       1330 CAAGCATAGC

                                     
       1340 ACATGGGCGCCCAGCGCTAGTCCAG
          1 ACATGGGCGCCCAGCGCTAGTCCAG

                              *       
       1365 ACAT--GC-CACCA--GCAAG--C--
          1 ACATGGGCGC-CCAGCGCTAGTCCAG

                                     
       1382 ACATGGGCGCCCAGCGCTAGTCCAG
          1 ACATGGGCGCCCAGCGCTAGTCCAG

                 
       1407 ACATG
          1 ACATG

       1412 CCACCAGCAA


Statistics
Matches: 35,  Mismatches: 2, Indels: 20
        0.61            0.04        0.35

Matches are distributed among these distances:
  17    4  0.11
  19    6  0.17
  20    1  0.03
  21    8  0.23
  22    1  0.03
  23    6  0.17
  25    9  0.26

ACGTcount: A:0.25, C:0.36, G:0.28, T:0.11


Consensus pattern (25 bp):   
ACATGGGCGCCCAGCGCTAGTCCAG

Found at i:1383 original size:42 final size:42

Alignment explanation


    Indices: 1332--1433  Score: 195
    Period size: 42  Copynumber: 2.4  Consensus size: 42

       1322 TGGGGCGCCA

                                                       
       1332 AGCATAGCACATGGGCGCCCAGCGCTAGTCCAGACATGCCACC
          1 AGCA-AGCACATGGGCGCCCAGCGCTAGTCCAGACATGCCACC

                                                      
       1375 AGCAAGCACATGGGCGCCCAGCGCTAGTCCAGACATGCCACC
          1 AGCAAGCACATGGGCGCCCAGCGCTAGTCCAGACATGCCACC

                             
       1417 AGCAAGCACATGGGCGC
          1 AGCAAGCACATGGGCGC

       1434 TAGCGACATG


Statistics
Matches: 59,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  42   55  0.93
  43    4  0.07

ACGTcount: A:0.26, C:0.36, G:0.27, T:0.10


Consensus pattern (42 bp):   
AGCAAGCACATGGGCGCCCAGCGCTAGTCCAGACATGCCACC
Done.