Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022779.1 Corchorus olitorius cultivar O-4 contig22812, 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: 8672
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:191 original size:21 final size:21

Alignment explanation


    Indices: 167--213  Score: 85
    Period size: 21  Copynumber: 2.2  Consensus size: 21

        157 ATTATATATA

                                 
        167 TGATTTATAATCTCTATCAAT
          1 TGATTTATAATCTCTATCAAT

                                 
        188 TGATTTATAATCTCTATCAAT
          1 TGATTTATAATCTCTATCAAT

            *    
        209 AGATT
          1 TGATT

        214 AAATAGTATT


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   25  1.00

ACGTcount: A:0.34, C:0.13, G:0.06, T:0.47


Consensus pattern (21 bp):   
TGATTTATAATCTCTATCAAT

Found at i:1944 original size:10 final size:10

Alignment explanation


    Indices: 1929--1953  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       1919 GACAATGTGC

                      
       1929 ATAAAAATTA
          1 ATAAAAATTA

                      
       1939 ATAAAAATTA
          1 ATAAAAATTA

                 
       1949 ATAAA
          1 ATAAA

       1954 GTATGTTTTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28


Consensus pattern (10 bp):   
ATAAAAATTA

Found at i:2382 original size:21 final size:21

Alignment explanation


    Indices: 2358--2397  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       2348 GAAAAAAAAG

                *                
       2358 AAAAGAAAAAGATGAAAGTAA
          1 AAAAAAAAAAGATGAAAGTAA

                         *     
       2379 AAAAAAAAAAGATTAAAGT
          1 AAAAAAAAAAGATGAAAGT

       2398 GGTGGGCAGC


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.72, C:0.00, G:0.15, T:0.12


Consensus pattern (21 bp):   
AAAAAAAAAAGATGAAAGTAA

Found at i:4341 original size:62 final size:62

Alignment explanation


    Indices: 4270--4388  Score: 229
    Period size: 62  Copynumber: 1.9  Consensus size: 62

       4260 GTGGAATCGA

                                                                          
       4270 ACAAACGCTGAAGTCAAAACGCCGGAGTCAAGAGGCTGCGAAGAGGTTGAGGTTAGGGCTTG
          1 ACAAACGCTGAAGTCAAAACGCCGGAGTCAAGAGGCTGCGAAGAGGTTGAGGTTAGGGCTTG

                      *                                              
       4332 ACAAACGCTGCAGTCAAAACGCCGGAGTCAAGAGGCTGCGAAGAGGTTGAGGTTAGG
          1 ACAAACGCTGAAGTCAAAACGCCGGAGTCAAGAGGCTGCGAAGAGGTTGAGGTTAGG

       4389 CCTTTAGAGT


Statistics
Matches: 56,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  62   56  1.00

ACGTcount: A:0.31, C:0.18, G:0.35, T:0.15


Consensus pattern (62 bp):   
ACAAACGCTGAAGTCAAAACGCCGGAGTCAAGAGGCTGCGAAGAGGTTGAGGTTAGGGCTTG
Done.