Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021768.1 Corchorus olitorius cultivar O-4 contig21801, 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: 7712
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:6967 original size:58 final size:58

Alignment explanation


    Indices: 6871--6985  Score: 169
    Period size: 58  Copynumber: 2.0  Consensus size: 58

       6861 ATTAATCAAA

                                                          * *         
       6871 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCAAGGCT
          1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGAACCAAGGCT

                *            *            *                           
       6929 TATCGAGTGACATGTTATTTTATTAGATGCCT-AAAAAAGACGTTTTAGAACCAAGGC
          1 TATCAAGTGACATGTT-CTTTATTAGATGCATAAAAAAAGACGTTTTAGAACCAAGGC

       6986 ATGATGCTAT


Statistics
Matches: 51,  Mismatches: 5, Indels: 2
        0.88            0.09        0.03

Matches are distributed among these distances:
  58   38  0.75
  59   13  0.25

ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31


Consensus pattern (58 bp):   
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGAACCAAGGCT

Found at i:7197 original size:19 final size:20

Alignment explanation


    Indices: 7173--7210  Score: 69
    Period size: 19  Copynumber: 1.9  Consensus size: 20

       7163 TAAGTAATAA

                                
       7173 GATATCTTACATCT-TAATT
          1 GATATCTTACATCTCTAATT

                               
       7192 GATATCTTACATCTCTAAT
          1 GATATCTTACATCTCTAAT

       7211 AAGTAATTAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19   14  0.78
  20    4  0.22

ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45


Consensus pattern (20 bp):   
GATATCTTACATCTCTAATT

Found at i:7199 original size:161 final size:162

Alignment explanation


    Indices: 7023--7338  Score: 616
    Period size: 161  Copynumber: 2.0  Consensus size: 162

       7013 TTAATTATAT

                                  *                                          
       7023 TCTTAATTGATATCTTACATCTTTAATAAGTAATTAATACCGATTTTCTTACATAAGTAACCCCA
          1 TCTTAATTGATATCTTACATCTCTAATAAGTAATTAATACCGATTTTCTTACATAAGTAACCCCA

                                                                             
       7088 AAAAAACCTTTAGAGGTTATTAAAAAGGCTACGATGCTATCAAT-AAAATTAAGTAACCTTAAAT
         66 AAAAAACCTTTAGAGGTTATTAAAAAGGCTACGATGCTATCAATAAAAATTAAGTAACCTTAAAT

                                            
       7152 CCTTAGTAGCTTAAGTAATAAGATATCTTACA
        131 CCTTAGTAGCTTAAGTAATAAGATATCTTACA

                                                                             
       7184 TCTTAATTGATATCTTACATCTCTAATAAGTAATTAATACCGATTTTCTTACATAAGTAACCCCA
          1 TCTTAATTGATATCTTACATCTCTAATAAGTAATTAATACCGATTTTCTTACATAAGTAACCCCA

                                                                             
       7249 AAAAAACCTTTAGAGGTTATTAAAAAGGCTACGATGCTATCAATAAAAATTAAGTAACCTTAAAT
         66 AAAAAACCTTTAGAGGTTATTAAAAAGGCTACGATGCTATCAATAAAAATTAAGTAACCTTAAAT

                                     
       7314 CCTTAGTAGCTTAAGTAATAAGATA
        131 CCTTAGTAGCTTAAGTAATAAGATA

       7339 GTTATCAATT


Statistics
Matches: 153,  Mismatches: 1, Indels: 1
        0.99            0.01        0.01

Matches are distributed among these distances:
 161  108  0.71
 162   45  0.29

ACGTcount: A:0.41, C:0.16, G:0.10, T:0.34


Consensus pattern (162 bp):   
TCTTAATTGATATCTTACATCTCTAATAAGTAATTAATACCGATTTTCTTACATAAGTAACCCCA
AAAAAACCTTTAGAGGTTATTAAAAAGGCTACGATGCTATCAATAAAAATTAAGTAACCTTAAAT
CCTTAGTAGCTTAAGTAATAAGATATCTTACA
Done.