Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014637.1 Corchorus olitorius cultivar O-4 contig14670, 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: 32089
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35


Found at i:25631 original size:4 final size:4

Alignment explanation


    Indices: 25622--25664  Score: 63
    Period size: 4  Copynumber: 11.0  Consensus size: 4

      25612 AATTTTTCCC

                                                                   
      25622 CTTT CTTT CTTT CTTT CTTT CTTT CTCTT -TTT C-TT CTTT CTTT
          1 CTTT CTTT CTTT CTTT CTTT CTTT CT-TT CTTT CTTT CTTT CTTT

      25665 TCTTATTTGA


Statistics
Matches: 36,  Mismatches: 0, Indels: 6
        0.86            0.00        0.14

Matches are distributed among these distances:
   3    5  0.14
   4   29  0.81
   5    2  0.06

ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74


Consensus pattern (4 bp):   
CTTT

Found at i:25696 original size:44 final size:44

Alignment explanation


    Indices: 25642--25730  Score: 160
    Period size: 44  Copynumber: 2.0  Consensus size: 44

      25632 TTCTTTCTTT

                       *                                
      25642 CTTTCTCTTTTTCTTCTTTCTTTTCTTATTTGAGCTTATTTATG
          1 CTTTCTCTTTTCCTTCTTTCTTTTCTTATTTGAGCTTATTTATG

                *                                       
      25686 CTTTTTCTTTTCCTTCTTTCTTTTCTTATTTGAGCTTATTTATG
          1 CTTTCTCTTTTCCTTCTTTCTTTTCTTATTTGAGCTTATTTATG

             
      25730 C
          1 C

      25731 AGCAACTCAG


Statistics
Matches: 43,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  44   43  1.00

ACGTcount: A:0.09, C:0.19, G:0.07, T:0.65


Consensus pattern (44 bp):   
CTTTCTCTTTTCCTTCTTTCTTTTCTTATTTGAGCTTATTTATG

Found at i:30830 original size:12 final size:12

Alignment explanation


    Indices: 30813--30873  Score: 65
    Period size: 12  Copynumber: 5.3  Consensus size: 12

      30803 GCTCCACGGT

                        
      30813 TGCTTGTGGTGG
          1 TGCTTGTGGTGG

                        
      30825 TGCTTGTGGT--
          1 TGCTTGTGGTGG

                *       
      30835 TG-TGGTGGTGG
          1 TGCTTGTGGTGG

               *  *     
      30846 TGCCTGCGGTGG
          1 TGCTTGTGGTGG

                  *     
      30858 TGCTTGCGGTGG
          1 TGCTTGTGGTGG

                
      30870 TGCT
          1 TGCT

      30874 GGTGAAAGTT


Statistics
Matches: 41,  Mismatches: 5, Indels: 6
        0.79            0.10        0.12

Matches are distributed among these distances:
   9    6  0.15
  10    2  0.05
  11    2  0.05
  12   31  0.76

ACGTcount: A:0.00, C:0.13, G:0.49, T:0.38


Consensus pattern (12 bp):   
TGCTTGTGGTGG
Done.