Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007655.1 Corchorus olitorius cultivar O-4 contig07681, 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: 2833
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:2330 original size:84 final size:82

Alignment explanation


    Indices: 2171--2334  Score: 285
    Period size: 84  Copynumber: 2.0  Consensus size: 82

       2161 CTCGTAGCAC

                                                                             
       2171 CAATCCGTTACCCACCATAAAATAGAAAGTCTTTTTTTTTCTGCTAACCCATAAAATAGAAAGTC
          1 CAATCCGTTACCCACCATAAAATAGAAAGTCTTTTTTTTTCTGCTAACCCATAAAATAGAAAGTC

                             
       2236 TAAAGGCATTGTTTTAT
         66 TAAAGGCATTGTTTTAT

                 *                                                           
       2253 CAATCTGTTACCCACCATAAAATAGAAAGTCTTTTTTTTTTACTGGC-AACCCATAAAATAGAAA
          1 CAATCCGTTACCCACCATAAAATAGAAAGTC-TTTTTTTTT-CT-GCTAACCCATAAAATAGAAA

                              
       2317 GTCTAAAGGCATTGTTTT
         63 GTCTAAAGGCATTGTTTT

       2335 CTACAAAAAA


Statistics
Matches: 78,  Mismatches: 1, Indels: 4
        0.94            0.01        0.05

Matches are distributed among these distances:
  82   30  0.38
  83    9  0.12
  84   37  0.47
  85    2  0.03

ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34


Consensus pattern (82 bp):   
CAATCCGTTACCCACCATAAAATAGAAAGTCTTTTTTTTTCTGCTAACCCATAAAATAGAAAGTC
TAAAGGCATTGTTTTAT

Found at i:2761 original size:2 final size:2

Alignment explanation


    Indices: 2754--2820  Score: 98
    Period size: 2  Copynumber: 33.5  Consensus size: 2

       2744 TAGGCATTGT

                         *        *             *                         
       2754 TA TA TA TA TC TA TA TC TA TA TA TA GA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

             *                                   
       2796 TC TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

       2821 GTGTATGTAT


Statistics
Matches: 57,  Mismatches: 8, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   2   57  1.00

ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49


Consensus pattern (2 bp):   
TA

Done.