Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023934.1 Corchorus olitorius cultivar O-4 contig23967, 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: 21632
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32


Found at i:7399 original size:36 final size:36

Alignment explanation


    Indices: 7359--7432  Score: 112
    Period size: 36  Copynumber: 2.1  Consensus size: 36

       7349 TTAGCAGGAG

                 *                              
       7359 TTGTGTATCAAATATACTTAATTGATGGTGTCTTGC
          1 TTGTGCATCAAATATACTTAATTGATGGTGTCTTGC

                         * *   *                
       7395 TTGTGCATCAAATCTGCTTGATTGATGGTGTCTTGC
          1 TTGTGCATCAAATATACTTAATTGATGGTGTCTTGC

              
       7431 TT
          1 TT

       7433 ATAGTCAATT


Statistics
Matches: 34,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  36   34  1.00

ACGTcount: A:0.20, C:0.14, G:0.22, T:0.45


Consensus pattern (36 bp):   
TTGTGCATCAAATATACTTAATTGATGGTGTCTTGC

Found at i:12746 original size:54 final size:54

Alignment explanation


    Indices: 12666--12778  Score: 226
    Period size: 54  Copynumber: 2.1  Consensus size: 54

      12656 CCCAATCAAC

                                                                  
      12666 TCAAGCAAGGCCTAAGCTTAAGTCCATGGTGATTGATCCCAAATCGGCACAAAA
          1 TCAAGCAAGGCCTAAGCTTAAGTCCATGGTGATTGATCCCAAATCGGCACAAAA

                                                                  
      12720 TCAAGCAAGGCCTAAGCTTAAGTCCATGGTGATTGATCCCAAATCGGCACAAAA
          1 TCAAGCAAGGCCTAAGCTTAAGTCCATGGTGATTGATCCCAAATCGGCACAAAA

                 
      12774 TCAAG
          1 TCAAG

      12779 GTAATTGTTC


Statistics
Matches: 59,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  54   59  1.00

ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20


Consensus pattern (54 bp):   
TCAAGCAAGGCCTAAGCTTAAGTCCATGGTGATTGATCCCAAATCGGCACAAAA

Found at i:14169 original size:13 final size:13

Alignment explanation


    Indices: 14151--14175  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      14141 TTTGCCAAAA

                         
      14151 AATAATTTTAAGC
          1 AATAATTTTAAGC

                        
      14164 AATAATTTTAAG
          1 AATAATTTTAAG

      14176 GTGGTAAAAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40


Consensus pattern (13 bp):   
AATAATTTTAAGC
Done.