Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018207.1 Corchorus olitorius cultivar O-4 contig18240, 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: 8207
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31


Found at i:1444 original size:21 final size:21

Alignment explanation


    Indices: 1418--1530  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

       1408 TGCTAGAAGT

                                 
       1418 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                                 
       1439 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                       *        *
       1460 TCATTGGAGCAGGTTCCAAGT
          1 TCATTGGAGCAAGTTCCAAGC

                                 *
       1481 TCATTGGAG-AAGGTTCCAAGA
          1 TCATTGGAGCAA-GTTCCAAGC

                            *     
       1502 TCATTGGAG-AAGGTTTCAAGC
          1 TCATTGGAGCAA-GTTCCAAGC

                    
       1523 TCATTGGA
          1 TCATTGGA

       1531 AATGCCTAAG


Statistics
Matches: 85,  Mismatches: 6, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  20    1  0.01
  21   84  0.99

ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGCAAGTTCCAAGC

Found at i:5864 original size:13 final size:14

Alignment explanation


    Indices: 5846--5876  Score: 55
    Period size: 13  Copynumber: 2.3  Consensus size: 14

       5836 AGCTTCCTAG

                          
       5846 AAAAACTCAAAA-A
          1 AAAAACTCAAAAGA

                          
       5859 AAAAACTCAAAAGA
          1 AAAAACTCAAAAGA

                
       5873 AAAA
          1 AAAA

       5877 TTGTTAGTAG


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

Matches are distributed among these distances:
  13   12  0.71
  14    5  0.29

ACGTcount: A:0.77, C:0.13, G:0.03, T:0.06


Consensus pattern (14 bp):   
AAAAACTCAAAAGA

Found at i:6396 original size:16 final size:15

Alignment explanation


    Indices: 6358--6399  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       6348 ACAGAGATTG

                   *       
       6358 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       6373 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       6388 ACTAGAAAACAA
          1 AC-AGAAAACAA

       6400 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.