Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019927.1 Corchorus olitorius cultivar O-4 contig19960, 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: 7480
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34


Found at i:721 original size:19 final size:18

Alignment explanation


    Indices: 697--732  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

        687 TGAAGACTTA

                               
        697 TTGAAGACAATTGGAAGAT
          1 TTGAAGACAATT-GAAGAT

                    *        
        716 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

        733 ATTATTTTCA


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

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.42, C:0.08, G:0.25, T:0.25


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:2009 original size:22 final size:22

Alignment explanation


    Indices: 1967--2009  Score: 52
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1957 TTTCTAATTA

                           **     
       1967 ATTGTTTTCTTTAATTTTCTTG
          1 ATTGTTTTCTTTAATAGTCTTG

                                  
       1989 ATTGTTTTC-TTAGATAGTCTT
          1 ATTGTTTTCTTTA-ATAGTCTT

       2010 AATTACTAGT


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  21    3  0.17
  22   15  0.83

ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63


Consensus pattern (22 bp):   
ATTGTTTTCTTTAATAGTCTTG

Found at i:2714 original size:21 final size:22

Alignment explanation


    Indices: 2690--2731  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       2680 TTTGCCTCAT

                                  
       2690 GCATTCATTCAT-CATGCCATG
          1 GCATTCATTCATGCATGCCATG

                            *    
       2711 GCATTCATTCATGCATTCCAT
          1 GCATTCATTCATGCATGCCAT

       2732 TAAAGCCTAC


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21   12  0.63
  22    7  0.37

ACGTcount: A:0.24, C:0.29, G:0.12, T:0.36


Consensus pattern (22 bp):   
GCATTCATTCATGCATGCCATG

Found at i:4806 original size:14 final size:15

Alignment explanation


    Indices: 4776--4813  Score: 51
    Period size: 14  Copynumber: 2.5  Consensus size: 15

       4766 AAATCAAAAT

                            
       4776 AAATGAAAAATTGAAA
          1 AAATG-AAAATTGAAA

                           
       4792 AAATGAAAA-TGAAA
          1 AAATGAAAATTGAAA

               *    
       4806 AAAGGAAA
          1 AAATGAAA

       4814 GGCACTTGGA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  14   12  0.57
  15    4  0.19
  16    5  0.24

ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13


Consensus pattern (15 bp):   
AAATGAAAATTGAAA
Done.