Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022657.1 Corchorus olitorius cultivar O-4 contig22690, 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: 20978
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:10355 original size:19 final size:18

Alignment explanation


    Indices: 10318--10357  Score: 53
    Period size: 19  Copynumber: 2.2  Consensus size: 18

      10308 TTCTTGAAAT

                       **     
      10318 AATTCTTCAATGGTCTTC
          1 AATTCTTCAATCATCTTC

                               
      10336 AATTCTTCAAATCATCTTC
          1 AATTCTTC-AATCATCTTC

               
      10355 AAT
          1 AAT

      10358 AAATCTTCAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  18    8  0.42
  19   11  0.58

ACGTcount: A:0.30, C:0.23, G:0.05, T:0.42


Consensus pattern (18 bp):   
AATTCTTCAATCATCTTC

Found at i:15084 original size:117 final size:117

Alignment explanation


    Indices: 14878--15095  Score: 330
    Period size: 117  Copynumber: 1.9  Consensus size: 117

      14868 TGGAATTATT

                            *              **             *                  
      14878 AATAGAAGCATTTGCTGACAATGAGATTAGAGGAAACTAAACATATTAGAAGAAAATCTAATAAG
          1 AATAGAAGCATTTGCTAACAATGAGATTAGAACAAACTAAACATATGAGAAGAAAATCTAATAAG

            *                                                   
      14943 GTTGCCATCCTCACAATTCATTTAATTCTCCACTCTGTTTTTCCTAAGTAAG
         66 ATTGCCATCCTCACAATTCATTTAATTCTCCACTCTGTTTTTCCTAAGTAAG

                          *                                       *     *    
      14995 AATAGAAGCATTTGTTAACAATGAGATTAGAACAAACTAAACATAGTGA-AAGACAATCTGATAA
          1 AATAGAAGCATTTGCTAACAATGAGATTAGAACAAACTAAACATA-TGAGAAGAAAATCTAATAA

                      * *                        
      15059 GATTGCCATCTTGACAATTCATTTAATTCTCCACTCT
         65 GATTGCCATCCTCACAATTCATTTAATTCTCCACTCT

      15096 AATTTTTGAA


Statistics
Matches: 90,  Mismatches: 10, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
 117   88  0.98
 118    2  0.02

ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30


Consensus pattern (117 bp):   
AATAGAAGCATTTGCTAACAATGAGATTAGAACAAACTAAACATATGAGAAGAAAATCTAATAAG
ATTGCCATCCTCACAATTCATTTAATTCTCCACTCTGTTTTTCCTAAGTAAG

Found at i:17748 original size:18 final size:19

Alignment explanation


    Indices: 17714--17751  Score: 60
    Period size: 18  Copynumber: 2.1  Consensus size: 19

      17704 GTCCATCGTT

                      *        
      17714 ATCTCCATGGTCTCCATGC
          1 ATCTCCATGGCCTCCATGC

                               
      17733 ATCTCCAT-GCCTCCATGC
          1 ATCTCCATGGCCTCCATGC

             
      17751 A
          1 A

      17752 ACCCCTGCAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18   10  0.56
  19    8  0.44

ACGTcount: A:0.18, C:0.39, G:0.13, T:0.29


Consensus pattern (19 bp):   
ATCTCCATGGCCTCCATGC

Found at i:17831 original size:30 final size:30

Alignment explanation


    Indices: 17795--17857  Score: 101
    Period size: 30  Copynumber: 2.1  Consensus size: 30

      17785 CATCTTCAAG

                       *                   
      17795 TCCATGATAAGTCCTT-GGCGCATCATTCCC
          1 TCCATGATAA-ACCTTGGGCGCATCATTCCC

                                          
      17825 TCCATGATAAACCTTGGGCGCATCATTCCC
          1 TCCATGATAAACCTTGGGCGCATCATTCCC

               
      17855 TCC
          1 TCC

      17858 CCTTGAAGAA


Statistics
Matches: 31,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  29    4  0.13
  30   27  0.87

ACGTcount: A:0.21, C:0.35, G:0.16, T:0.29


Consensus pattern (30 bp):   
TCCATGATAAACCTTGGGCGCATCATTCCC
Done.