Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009605.1 Corchorus olitorius cultivar O-4 contig09637, 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: 3737
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31


Found at i:1858 original size:39 final size:40

Alignment explanation


    Indices: 1804--1986  Score: 243
    Period size: 39  Copynumber: 4.7  Consensus size: 40

       1794 GCTTAATGAA

                                                *     
       1804 TTTTATTAATTTCCAAAATCTTCTTTTGGGATAT-CTTAAAC
          1 TTTTATT--TTTCCAAAATCTTCTTTTGGGATATACCTAAAC

                                *      *            
       1845 TTTTATTTTTCCAAAATCTTATTTTGGAAT-TACCTAAAC
          1 TTTTATTTTTCCAAAATCTTCTTTTGGGATATACCTAAAC

                                       *      *     
       1884 TTTTA-TTTTCCAAAATCTTCTTTTGGTATAT-CTTAAAC
          1 TTTTATTTTTCCAAAATCTTCTTTTGGGATATACCTAAAC

                                *         *         
       1922 TTTTATTTTTCCAAAATCTTATTTT-GGATTTACCTAAAC
          1 TTTTATTTTTCCAAAATCTTCTTTTGGGATATACCTAAAC

                                       
       1961 TTTTA-TTTTCCAAAATCTTCTTTTGG
          1 TTTTATTTTTCCAAAATCTTCTTTTGG

       1987 AGTTGCTTAA


Statistics
Matches: 126,  Mismatches: 11, Indels: 12
        0.85            0.07        0.08

Matches are distributed among these distances:
  38   56  0.44
  39   63  0.50
  41    7  0.06

ACGTcount: A:0.27, C:0.15, G:0.06, T:0.51


Consensus pattern (40 bp):   
TTTTATTTTTCCAAAATCTTCTTTTGGGATATACCTAAAC

Found at i:1896 original size:77 final size:77

Alignment explanation


    Indices: 1813--1986  Score: 330
    Period size: 77  Copynumber: 2.3  Consensus size: 77

       1803 ATTTTATTAA

                                                                             
       1813 TTTCCAAAATCTTCTTTTGGGATATCTTAAACTTTTATTTTTCCAAAATCTTATTTTGGAATTAC
          1 TTTCCAAAATCTTCTTTTGGGATATCTTAAACTTTTATTTTTCCAAAATCTTATTTTGGAATTAC

                        
       1878 CTAAACTTTTAT
         66 CTAAACTTTTAT

                                *                                       *    
       1890 TTTCCAAAATCTTCTTTTGGTATATCTTAAACTTTTATTTTTCCAAAATCTTATTTTGGATTTAC
          1 TTTCCAAAATCTTCTTTTGGGATATCTTAAACTTTTATTTTTCCAAAATCTTATTTTGGAATTAC

                        
       1955 CTAAACTTTTAT
         66 CTAAACTTTTAT

                                
       1967 TTTCCAAAATCTTCTTTTGG
          1 TTTCCAAAATCTTCTTTTGG

       1987 AGTTGCTTAA


Statistics
Matches: 95,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  77   95  1.00

ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51


Consensus pattern (77 bp):   
TTTCCAAAATCTTCTTTTGGGATATCTTAAACTTTTATTTTTCCAAAATCTTATTTTGGAATTAC
CTAAACTTTTAT

Found at i:2136 original size:22 final size:23

Alignment explanation


    Indices: 2104--2146  Score: 61
    Period size: 22  Copynumber: 1.9  Consensus size: 23

       2094 TTTATTGCGC

                                   
       2104 CTTTTTATTTTCTGAT-TTTTCT
          1 CTTTTTATTTTCTGATATTTTCT

                  *    *         
       2126 CTTTTTTTTTTTTGATATTTT
          1 CTTTTTATTTTCTGATATTTT

       2147 TCTATCTCTA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  22   14  0.78
  23    4  0.22

ACGTcount: A:0.09, C:0.09, G:0.05, T:0.77


Consensus pattern (23 bp):   
CTTTTTATTTTCTGATATTTTCT
Done.