Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012576.1 Corchorus olitorius cultivar O-4 contig12609, 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: 17279
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:1654 original size:44 final size:45

Alignment explanation


    Indices: 1591--1684  Score: 154
    Period size: 44  Copynumber: 2.1  Consensus size: 45

       1581 AAAAGAGAAT

                                                        *
       1591 GTTTTCTATTTAAGTAATTCCAAAAGAAAATTTTGGAAAACAAAG
          1 GTTTTCTATTTAAGTAATTCCAAAAGAAAATTTTGGAAAACAAAA

                                        *           *    
       1636 GTTTTCT-TTTAAGTAATTCCAAAAGAAGATTTTGGAAAATAAAA
          1 GTTTTCTATTTAAGTAATTCCAAAAGAAAATTTTGGAAAACAAAA

                 
       1680 GTTTT
          1 GTTTT

       1685 TAAGAGACCA


Statistics
Matches: 46,  Mismatches: 3, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  44   39  0.85
  45    7  0.15

ACGTcount: A:0.41, C:0.07, G:0.14, T:0.37


Consensus pattern (45 bp):   
GTTTTCTATTTAAGTAATTCCAAAAGAAAATTTTGGAAAACAAAA

Found at i:5064 original size:27 final size:27

Alignment explanation


    Indices: 5026--5080  Score: 110
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       5016 AGTTATAACA

                                       
       5026 TTCACAATTGCTAGATTTTTTTTTGTT
          1 TTCACAATTGCTAGATTTTTTTTTGTT

                                       
       5053 TTCACAATTGCTAGATTTTTTTTTGTT
          1 TTCACAATTGCTAGATTTTTTTTTGTT

             
       5080 T
          1 T

       5081 GCTCATGAAC


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.18, C:0.11, G:0.11, T:0.60


Consensus pattern (27 bp):   
TTCACAATTGCTAGATTTTTTTTTGTT

Found at i:9800 original size:14 final size:13

Alignment explanation


    Indices: 9779--9827  Score: 80
    Period size: 13  Copynumber: 3.7  Consensus size: 13

       9769 TTAACCCCAA

                *        
       9779 TTTTAAAAAGCAC
          1 TTTTCAAAAGCAC

                         
       9792 TTTTCAAAAGCAC
          1 TTTTCAAAAGCAC

                         
       9805 TTTTCAAAAGCAC
          1 TTTTCAAAAGCAC

                      
       9818 TTCTTCAAAA
          1 TT-TTCAAAA

       9828 CCAAGCTTTT


Statistics
Matches: 34,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  13   27  0.79
  14    7  0.21

ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33


Consensus pattern (13 bp):   
TTTTCAAAAGCAC

Found at i:13400 original size:12 final size:12

Alignment explanation


    Indices: 13383--13407  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      13373 AAACCGAAAC

                        
      13383 TTTTCCCCAAAA
          1 TTTTCCCCAAAA

                        
      13395 TTTTCCCCAAAA
          1 TTTTCCCCAAAA

             
      13407 T
          1 T

      13408 CTAAACTGCC


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

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36


Consensus pattern (12 bp):   
TTTTCCCCAAAA

Found at i:15996 original size:2 final size:2

Alignment explanation


    Indices: 15989--16019  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      15979 TAATATTTAG

                                                          
      15989 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      16020 GTTGCACGCC


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

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:16224 original size:13 final size:12

Alignment explanation


    Indices: 16188--16234  Score: 51
    Period size: 13  Copynumber: 3.8  Consensus size: 12

      16178 TCAATCTTTA

                        *
      16188 TATATATTGATAA
          1 TATATATT-ATAT

                 *      
      16201 TA-ATGTTATAT
          1 TATATATTATAT

                         
      16212 TATATTATTATAT
          1 TATA-TATTATAT

                      
      16225 TATATATTAT
          1 TATATATTAT

      16235 CAATAAACTT


Statistics
Matches: 29,  Mismatches: 3, Indels: 5
        0.78            0.08        0.14

Matches are distributed among these distances:
  11    5  0.17
  12   11  0.38
  13   13  0.45

ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55


Consensus pattern (12 bp):   
TATATATTATAT
Done.