Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016317.1 Corchorus olitorius cultivar O-4 contig16350, 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: 3574
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30


Found at i:3069 original size:19 final size:19

Alignment explanation


    Indices: 3035--3087  Score: 63
    Period size: 19  Copynumber: 2.7  Consensus size: 19

       3025 CCCATCAGCG

                               **
       3035 AAAGAAAAAAGAAAAGCAAGC
          1 AAAGAAAAAAG-AAAG-AAAA

                               
       3056 AAA-AAAAAAGAAAGAAAA
          1 AAAGAAAAAAGAAAGAAAA

                          
       3074 AAAGAAAAAAGAAA
          1 AAAGAAAAAAGAAA

       3088 ATATGAAAGA


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  18    5  0.17
  19   14  0.48
  20    7  0.24
  21    3  0.10

ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00


Consensus pattern (19 bp):   
AAAGAAAAAAGAAAGAAAA

Found at i:3095 original size:15 final size:15

Alignment explanation


    Indices: 3035--3088  Score: 58
    Period size: 15  Copynumber: 3.5  Consensus size: 15

       3025 CCCATCAGCG

                           
       3035 AAAG-AAAAAAGAAA
          1 AAAGAAAAAAAGAAA

                             *
       3049 AGCAAGCAAAAAAA-AAG
          1 A--AAG-AAAAAAAGAAA

                           
       3066 AAAGAAAAAAAGAAA
          1 AAAGAAAAAAAGAAA

                    
       3081 AAAGAAAA
          1 AAAGAAAA

       3089 TATGAAAGAA


Statistics
Matches: 33,  Mismatches: 2, Indels: 9
        0.75            0.05        0.20

Matches are distributed among these distances:
  14    8  0.24
  15   13  0.39
  16    3  0.09
  17    3  0.09
  18    6  0.18

ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00


Consensus pattern (15 bp):   
AAAGAAAAAAAGAAA

Found at i:3096 original size:19 final size:18

Alignment explanation


    Indices: 3034--3099  Score: 62
    Period size: 19  Copynumber: 3.4  Consensus size: 18

       3024 TCCCATCAGC

                                
       3034 GAAAGAAAAAAGAAAAGCAA
          1 GAAAGAAAAAAGAAAA--AA

                                
       3054 GCAAA-AAAAAAGAAAGAAA
          1 G-AAAGAAAAAAGAAA-AAA

            *                 *
       3073 AAAAGAAAAAAGAAAATAT
          1 GAAAGAAAAAAGAAAA-AA

                    
       3092 GAAAGAAA
          1 GAAAGAAA

       3100 TGGACTGATT


Statistics
Matches: 39,  Mismatches: 3, Indels: 9
        0.76            0.06        0.18

Matches are distributed among these distances:
  18    4  0.10
  19   20  0.51
  20   11  0.28
  21    4  0.10

ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03


Consensus pattern (18 bp):   
GAAAGAAAAAAGAAAAAA
Done.