Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006204.1 Corchorus olitorius cultivar O-4 contig06229, 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, 689

Length: 1149
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35


Found at i:76 original size:50 final size:50

Alignment explanation


    Indices: 1--220  Score: 388
    Period size: 50  Copynumber: 4.4  Consensus size: 50

                                                              
          1 ATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGA
          1 ATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGA

                                             **               
         51 ATTGGAAGACAGTTCGAAGGATAAGCGGAAGACAATCCTTTTAAGATTGA
          1 ATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGA

                                                              
        101 ATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGA
          1 ATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGA

                                                                
        151 ATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTCTAAG-TTGGA
          1 ATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTT-TAAGATT-GA

                       *       
        202 ATTGGAAGACAATTCGAAG
          1 ATTGGAAGACAGTTCGAAG

        221 AAGTTGATCG


Statistics
Matches: 163,  Mismatches: 5, Indels: 3
        0.95            0.03        0.02

Matches are distributed among these distances:
  50  139  0.85
  51   24  0.15

ACGTcount: A:0.35, C:0.12, G:0.29, T:0.24


Consensus pattern (50 bp):   
ATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGA

Found at i:500 original size:28 final size:28

Alignment explanation


    Indices: 440--535  Score: 176
    Period size: 28  Copynumber: 3.5  Consensus size: 28

        430 ATTTACTTCT

                                        
        440 CATTTTGGTCATTTTTCATCTCCAGGGG
          1 CATTTTGGTCATTTTTCATCTCCAGGGG

                                        
        468 -ATTTTGGTCATTTTTCATCTCCAGGGG
          1 CATTTTGGTCATTTTTCATCTCCAGGGG

                                        
        495 CATTTTGGTCATTTTTCATCTCCAGGGG
          1 CATTTTGGTCATTTTTCATCTCCAGGGG

                  *      
        523 CATTTTTGTCATT
          1 CATTTTGGTCATT

        536 ACGAGTGCAC


Statistics
Matches: 66,  Mismatches: 1, Indels: 2
        0.96            0.01        0.03

Matches are distributed among these distances:
  27   27  0.41
  28   39  0.59

ACGTcount: A:0.15, C:0.20, G:0.20, T:0.46


Consensus pattern (28 bp):   
CATTTTGGTCATTTTTCATCTCCAGGGG
Done.