Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014056.1 Corchorus olitorius cultivar O-4 contig14089, 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: 2722
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31


Found at i:905 original size:14 final size:14

Alignment explanation


    Indices: 881--928  Score: 73
    Period size: 14  Copynumber: 3.5  Consensus size: 14

        871 TAAAGGACGT

                          
        881 TTTTCAA-AAATGA
          1 TTTTCAAGAAATGA

                           
        894 TTTTCAAGAAATTG-
          1 TTTTCAAGAAA-TGA

                          
        908 TTTTCAAGAAATGA
          1 TTTTCAAGAAATGA

                   
        922 TTTTCAA
          1 TTTTCAA

        929 AAAGGTTTTG


Statistics
Matches: 32,  Mismatches: 0, Indels: 5
        0.86            0.00        0.14

Matches are distributed among these distances:
  13    9  0.28
  14   21  0.66
  15    2  0.06

ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42


Consensus pattern (14 bp):   
TTTTCAAGAAATGA

Found at i:2216 original size:26 final size:26

Alignment explanation


    Indices: 2187--2241  Score: 110
    Period size: 26  Copynumber: 2.1  Consensus size: 26

       2177 ATGTTGGAAA

                                      
       2187 GATGACAAATGTTGTCAATTTGGATT
          1 GATGACAAATGTTGTCAATTTGGATT

                                      
       2213 GATGACAAATGTTGTCAATTTGGATT
          1 GATGACAAATGTTGTCAATTTGGATT

               
       2239 GAT
          1 GAT

       2242 AAGGGGGGCA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   29  1.00

ACGTcount: A:0.31, C:0.07, G:0.24, T:0.38


Consensus pattern (26 bp):   
GATGACAAATGTTGTCAATTTGGATT

Found at i:2659 original size:37 final size:37

Alignment explanation


    Indices: 2618--2722  Score: 133
    Period size: 37  Copynumber: 2.8  Consensus size: 37

       2608 ATATTTCTGT

                                                 
       2618 TTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGC
          1 TTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGC

                                       *   * *    *
       2655 TTAGGTGT-TTCATCAAAAT-CTTATTCAAGATTCCTGT
          1 TTAGGTGTCTT-ATC-AAATCCTTATTTAAGGTCCCTGC

                                  *        
       2692 TTAGGTGTCTTATCAAATCCTTGTTTAAGGT
          1 TTAGGTGTCTTATCAAATCCTTATTTAAGGT


Statistics
Matches: 57,  Mismatches: 7, Indels: 8
        0.79            0.10        0.11

Matches are distributed among these distances:
  36    6  0.11
  37   45  0.79
  38    6  0.11

ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43


Consensus pattern (37 bp):   
TTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGC
Done.