Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014606.1 Corchorus olitorius cultivar O-4 contig14639, 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: 4332
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32


Found at i:187 original size:32 final size:31

Alignment explanation


    Indices: 146--275  Score: 125
    Period size: 32  Copynumber: 4.1  Consensus size: 31

        136 CATATACTTA

                *        *     * *          
        146 AATGAATTGCAAAATTGTCTCTATTCGAAATT
          1 AATGCATTGCAAATTTGTCCCCATT-GAAATT

                                     *      
        178 AATGCATTGCAAATTTGTCCCCATTTACAATT
          1 AATGCATTGCAAATTTGTCCCCATTGA-AATT

                     *      *          *    
        210 AATGCATTGTAAATTTATCCCCATTTGTAATT
          1 AATGCATTGCAAATTTGTCCCCA-TTGAAATT

                     *          *    *  *  
        242 AATGCATTGGAAATTTGTCCTCATTCAATTT
          1 AATGCATTGCAAATTTGTCCCCATTGAAATT

               
        273 AAT
          1 AAT

        276 AAAGCCTATT


Statistics
Matches: 81,  Mismatches: 15, Indels: 5
        0.80            0.15        0.05

Matches are distributed among these distances:
  31    9  0.11
  32   70  0.86
  33    2  0.02

ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40


Consensus pattern (31 bp):   
AATGCATTGCAAATTTGTCCCCATTGAAATT

Found at i:1113 original size:26 final size:26

Alignment explanation


    Indices: 1082--1133  Score: 72
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       1072 AAATTTTAAT

                                        
       1082 ATTTAAATT-TTATTTT-TTATTAAAAA
          1 ATTT-AATTATTATTTTATT-TTAAAAA

                                      
       1108 ATTTAATTATTATTTTATTTTAAAAA
          1 ATTTAATTATTATTTTATTTTAAAAA

       1134 TAAACAAGCT


Statistics
Matches: 24,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  25    4  0.17
  26   18  0.75
  27    2  0.08

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (26 bp):   
ATTTAATTATTATTTTATTTTAAAAA
Done.