Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012805.1 Corchorus olitorius cultivar O-4 contig12838, 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: 33941
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:105 original size:22 final size:22

Alignment explanation


    Indices: 80--129  Score: 91
    Period size: 22  Copynumber: 2.3  Consensus size: 22

         70 AAAAGGATGG

                                  
         80 ATGCAAAAGATACCATGCAAAA
          1 ATGCAAAAGATACCATGCAAAA

                       *          
        102 ATGCAAAAGATGCCATGCAAAA
          1 ATGCAAAAGATACCATGCAAAA

                  
        124 ATGCAA
          1 ATGCAA

        130 CTATTAAACT


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   27  1.00

ACGTcount: A:0.52, C:0.18, G:0.16, T:0.14


Consensus pattern (22 bp):   
ATGCAAAAGATACCATGCAAAA

Found at i:1003 original size:28 final size:28

Alignment explanation


    Indices: 963--1021  Score: 118
    Period size: 28  Copynumber: 2.1  Consensus size: 28

        953 TTAAAGTTAT

                                        
        963 TCATATATATTTAGGCATGAATTTAGCA
          1 TCATATATATTTAGGCATGAATTTAGCA

                                        
        991 TCATATATATTTAGGCATGAATTTAGCA
          1 TCATATATATTTAGGCATGAATTTAGCA

               
       1019 TCA
          1 TCA

       1022 AGTTTAATCC


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   31  1.00

ACGTcount: A:0.36, C:0.12, G:0.14, T:0.39


Consensus pattern (28 bp):   
TCATATATATTTAGGCATGAATTTAGCA

Found at i:10250 original size:18 final size:22

Alignment explanation


    Indices: 10207--10246  Score: 66
    Period size: 20  Copynumber: 1.9  Consensus size: 22

      10197 ATGAGGATTC

                                  
      10207 AAGAGAGAAACGATGAAAAACA
          1 AAGAGAGAAACGATGAAAAACA

                                
      10229 AAGA-AGAAAC-ATGAAAAA
          1 AAGAGAGAAACGATGAAAAA

      10247 AAGACTCAGA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20    8  0.44
  21    6  0.33
  22    4  0.22

ACGTcount: A:0.68, C:0.07, G:0.20, T:0.05


Consensus pattern (22 bp):   
AAGAGAGAAACGATGAAAAACA

Found at i:19906 original size:22 final size:21

Alignment explanation


    Indices: 19838--19908  Score: 54
    Period size: 22  Copynumber: 3.2  Consensus size: 21

      19828 ACTAATAAGT

                      *           
      19838 AATGACCCTTCAACTATTTTCA
          1 AATGA-CCTTAAACTATTTTCA

                           *  ** * 
      19860 AATGACCTTTAATA-AATAATAA
          1 AATGACC-TTAA-ACTATTTTCA

                                  
      19882 AATGATCCTTAAACTATTTTCA
          1 AATGA-CCTTAAACTATTTTCA

                 
      19904 AATGA
          1 AATGA

      19909 ACAAATTAAC


Statistics
Matches: 36,  Mismatches: 9, Indels: 8
        0.68            0.17        0.15

Matches are distributed among these distances:
  21    3  0.08
  22   30  0.83
  23    3  0.08

ACGTcount: A:0.42, C:0.17, G:0.06, T:0.35


Consensus pattern (21 bp):   
AATGACCTTAAACTATTTTCA

Found at i:33905 original size:2 final size:2

Alignment explanation


    Indices: 33898--33940  Score: 86
    Period size: 2  Copynumber: 21.5  Consensus size: 2

      33888 AGTTTTATGT

                                                                          
      33898 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

             
      33940 T
          1 T

      33941 G


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   41  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Done.