Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021337.1 Corchorus olitorius cultivar O-4 contig21370, 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: 23796
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:6558 original size:45 final size:45

Alignment explanation


    Indices: 6494--6580  Score: 165
    Period size: 45  Copynumber: 1.9  Consensus size: 45

       6484 TGTCATGCAT

                  *                                      
       6494 TAATAATAAAATCATGACAATATGTAATTTCGTCACCCAAATGGG
          1 TAATAAAAAAATCATGACAATATGTAATTTCGTCACCCAAATGGG

                                                      
       6539 TAATAAAAAAATCATGACAATATGTAATTTCGTCACCCAAAT
          1 TAATAAAAAAATCATGACAATATGTAATTTCGTCACCCAAAT

       6581 TATGAACACT


Statistics
Matches: 41,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  45   41  1.00

ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29


Consensus pattern (45 bp):   
TAATAAAAAAATCATGACAATATGTAATTTCGTCACCCAAATGGG

Found at i:10179 original size:21 final size:21

Alignment explanation


    Indices: 10140--10181  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      10130 TCACAAAGAA

                          *      
      10140 GTTTCAAGCTCATCGGAGTTG
          1 GTTTCAAGCTCATCAGAGTTG

                         *       
      10161 GTTTCAAGCTCATTAGAGTTG
          1 GTTTCAAGCTCATCAGAGTTG

      10182 TCTAAGGTGC


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36


Consensus pattern (21 bp):   
GTTTCAAGCTCATCAGAGTTG

Found at i:17037 original size:19 final size:18

Alignment explanation


    Indices: 17013--17048  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      17003 TGAAGACTTA

                               
      17013 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
      17032 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

      17049 ATAATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:17055 original size:30 final size:30

Alignment explanation


    Indices: 17001--17060  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      16991 GAAGTTCGTG

                      *              *    
      17001 TTTGAAGACTTATTGAAGACAATTTGAAGA
          1 TTTGAAGACTCATTGAAGACAATTTCAAGA

                                *          
      17031 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
          1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA

      17061 GCAAGAATTG


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  29    7  0.27
  30   19  0.73

ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32


Consensus pattern (30 bp):   
TTTGAAGACTCATTGAAGACAATTTCAAGA
Done.