Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019126.1 Corchorus olitorius cultivar O-4 contig19159, 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: 10134
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:1954 original size:12 final size:12

Alignment explanation


    Indices: 1937--1963  Score: 54
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       1927 GCATTCTATC

                        
       1937 ACAAGTTTAATT
          1 ACAAGTTTAATT

                        
       1949 ACAAGTTTAATT
          1 ACAAGTTTAATT

               
       1961 ACA
          1 ACA

       1964 CCGACCGCAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   15  1.00

ACGTcount: A:0.44, C:0.11, G:0.07, T:0.37


Consensus pattern (12 bp):   
ACAAGTTTAATT

Found at i:4733 original size:61 final size:61

Alignment explanation


    Indices: 4635--4758  Score: 221
    Period size: 61  Copynumber: 2.0  Consensus size: 61

       4625 GGAAGTTTCC

                                            *                            
       4635 TAAAGATTTTCTGAGAGATCAGATTCGAGAAGCAATTAAAGCAGGACAAGTCAGATTGAAG
          1 TAAAGATTTTCTGAGAGATCAGATTCGAGAAGAAATTAAAGCAGGACAAGTCAGATTGAAG

                             *                       *                   
       4696 TAAAGATTTTCTGAGAGGTCAGATTCGAGAAGAAATTAAAGTAGGACAAGTCAGATTGAAG
          1 TAAAGATTTTCTGAGAGATCAGATTCGAGAAGAAATTAAAGCAGGACAAGTCAGATTGAAG

              
       4757 TA
          1 TA

       4759 GACAATTAAT


Statistics
Matches: 60,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  61   60  1.00

ACGTcount: A:0.41, C:0.10, G:0.25, T:0.24


Consensus pattern (61 bp):   
TAAAGATTTTCTGAGAGATCAGATTCGAGAAGAAATTAAAGCAGGACAAGTCAGATTGAAG

Found at i:8059 original size:13 final size:13

Alignment explanation


    Indices: 8041--8066  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       8031 TTCATAGACT

                         
       8041 TATAATCAAAAGG
          1 TATAATCAAAAGG

                         
       8054 TATAATCAAAAGG
          1 TATAATCAAAAGG

       8067 ATGATAGTAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23


Consensus pattern (13 bp):   
TATAATCAAAAGG

Found at i:9444 original size:2 final size:2

Alignment explanation


    Indices: 9432--9463  Score: 55
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       9422 AATACAAATG

                                                           
       9432 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A

       9464 AACAAACAAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2   27  0.93
   3    2  0.07

ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47


Consensus pattern (2 bp):   
AT

Done.