Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017074.1 Corchorus olitorius cultivar O-4 contig17107, 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: 13348
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32


Found at i:2111 original size:13 final size:12

Alignment explanation


    Indices: 2089--2118  Score: 51
    Period size: 13  Copynumber: 2.4  Consensus size: 12

       2079 ATAAATGAAA

                        
       2089 TTTTTTTTCTTT
          1 TTTTTTTTCTTT

                         
       2101 TTTTTTCTTCTTT
          1 TTTTTT-TTCTTT

                 
       2114 TTTTT
          1 TTTTT

       2119 AAAAAAATTT


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

Matches are distributed among these distances:
  12    6  0.35
  13   11  0.65

ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90


Consensus pattern (12 bp):   
TTTTTTTTCTTT

Found at i:3430 original size:53 final size:53

Alignment explanation


    Indices: 3350--3454  Score: 183
    Period size: 53  Copynumber: 2.0  Consensus size: 53

       3340 AATAGTATAC

                             *                                   
       3350 TATTTTGTTAGTAAAAGTTCAATCTTTTTATTAAGATTCAAATATTTAGGATA
          1 TATTTTGTTAGTAAAAGCTCAATCTTTTTATTAAGATTCAAATATTTAGGATA

                     *  *                                       
       3403 TATTTTGTTGGTGAAAGCTCAATCTTTTTATTAAGATTCAAATATTTAGGAT
          1 TATTTTGTTAGTAAAAGCTCAATCTTTTTATTAAGATTCAAATATTTAGGAT

       3455 TTGCTTGGTT


Statistics
Matches: 49,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  53   49  1.00

ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47


Consensus pattern (53 bp):   
TATTTTGTTAGTAAAAGCTCAATCTTTTTATTAAGATTCAAATATTTAGGATA

Found at i:10491 original size:19 final size:17

Alignment explanation


    Indices: 10463--10503  Score: 57
    Period size: 18  Copynumber: 2.4  Consensus size: 17

      10453 GGTATACTGG

                              
      10463 CTTTTTTCTTTTGTTTTT
          1 CTTTTTTCTTTT-TTTTT

                              
      10481 CTTTCTTTCTTTTTTTTT
          1 CTTT-TTTCTTTTTTTTT

                  
      10499 -TTTTT
          1 CTTTTT

      10504 GTATTTCAGG


Statistics
Matches: 22,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  16    2  0.09
  17    3  0.14
  18    9  0.41
  19    8  0.36

ACGTcount: A:0.00, C:0.12, G:0.02, T:0.85


Consensus pattern (17 bp):   
CTTTTTTCTTTTTTTTT
Done.