Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019730.1 Corchorus olitorius cultivar O-4 contig19763, 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: 42788
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33


Found at i:23452 original size:14 final size:15

Alignment explanation


    Indices: 23428--23460  Score: 50
    Period size: 14  Copynumber: 2.3  Consensus size: 15

      23418 TTTAATTTTA

                         * 
      23428 AAAAAATTGAAAAGG
          1 AAAAAATTGAAAAAG

                           
      23443 AAAAAA-TGAAAAAG
          1 AAAAAATTGAAAAAG

                
      23457 AAAA
          1 AAAA

      23461 GATAAATAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  14   11  0.65
  15    6  0.35

ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09


Consensus pattern (15 bp):   
AAAAAATTGAAAAAG

Found at i:28731 original size:6 final size:6

Alignment explanation


    Indices: 28720--28745  Score: 52
    Period size: 6  Copynumber: 4.3  Consensus size: 6

      28710 AAATCTCACC

                                          
      28720 TATCTA TATCTA TATCTA TATCTA TA
          1 TATCTA TATCTA TATCTA TATCTA TA

      28746 CTGTATTAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   20  1.00

ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50


Consensus pattern (6 bp):   
TATCTA

Found at i:29046 original size:14 final size:14

Alignment explanation


    Indices: 29027--29058  Score: 55
    Period size: 14  Copynumber: 2.3  Consensus size: 14

      29017 TTCTATAATT

                          
      29027 ATTTTATTTTTACC
          1 ATTTTATTTTTACC

                         *
      29041 ATTTTATTTTTACT
          1 ATTTTATTTTTACC

                
      29055 ATTT
          1 ATTT

      29059 CAATTTAAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69


Consensus pattern (14 bp):   
ATTTTATTTTTACC

Found at i:30905 original size:15 final size:16

Alignment explanation


    Indices: 30885--30917  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      30875 CTTCAATGTC

                            
      30885 GGGTC-ATTTGGGTTT
          1 GGGTCAATTTGGGTTT

                      *     
      30900 GGGTCAATTTTGGTTT
          1 GGGTCAATTTGGGTTT

              
      30916 GG
          1 GG

      30918 TTCTTTTTTT


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

Matches are distributed among these distances:
  15    5  0.31
  16   11  0.69

ACGTcount: A:0.09, C:0.06, G:0.39, T:0.45


Consensus pattern (16 bp):   
GGGTCAATTTGGGTTT

Found at i:42193 original size:2 final size:2

Alignment explanation


    Indices: 42186--42224  Score: 55
    Period size: 2  Copynumber: 20.0  Consensus size: 2

      42176 TAATATTTAT

                                                                        
      42186 TA TA TA TA TA T- TA GTA TA TA TA TA TA TA TA TA TA T- TA TA
          1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA

      42225 GAATCTCTAA


Statistics
Matches: 34,  Mismatches: 0, Indels: 6
        0.85            0.00        0.15

Matches are distributed among these distances:
   1    2  0.06
   2   30  0.88
   3    2  0.06

ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51


Consensus pattern (2 bp):   
TA

Done.