Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020548.1 Corchorus olitorius cultivar O-4 contig20581, 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: 6958
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:1093 original size:21 final size:21

Alignment explanation


    Indices: 1067--1121  Score: 74
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       1057 CGGCCATTCA

                           **    
       1067 CCGTGCCACCACCGGTTAAGC
          1 CCGTGCCACCACCGGCCAAGC

                              *  
       1088 CCGTGCCACCACCGGCCATGC
          1 CCGTGCCACCACCGGCCAAGC

                    *    
       1109 CCGTGCCATCACC
          1 CCGTGCCACCACC

       1122 ATTCCAAGTC


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   30  1.00

ACGTcount: A:0.16, C:0.49, G:0.22, T:0.13


Consensus pattern (21 bp):   
CCGTGCCACCACCGGCCAAGC

Found at i:5510 original size:24 final size:24

Alignment explanation


    Indices: 5471--5574  Score: 127
    Period size: 24  Copynumber: 4.1  Consensus size: 24

       5461 TTAAAAATAA

                  *                 
       5471 TATTTAGCGGCGTCTAGACGCCAC
          1 TATTTAACGGCGTCTAGACGCCAC

               *                         
       5495 TATGTAACGGCGTCTAGACGCCACGCCAC
          1 TATTTAACGGCGTCT--A-G--ACGCCAC

                       *            
       5524 TATTTAACGGCATCTAGACGCCAC
          1 TATTTAACGGCGTCTAGACGCCAC

                                  * 
       5548 TATTTAACGGCGTCTAGACGCCGC
          1 TATTTAACGGCGTCTAGACGCCAC

               
       5572 TAT
          1 TAT

       5575 CTGGACACGT


Statistics
Matches: 69,  Mismatches: 6, Indels: 10
        0.81            0.07        0.12

Matches are distributed among these distances:
  24   45  0.65
  26    2  0.03
  27    2  0.03
  29   20  0.29

ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24


Consensus pattern (24 bp):   
TATTTAACGGCGTCTAGACGCCAC

Done.