Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012269.1 Corchorus olitorius cultivar O-4 contig12302, 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: 28808
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:4374 original size:2 final size:2

Alignment explanation


    Indices: 4367--4393  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       4357 GAAAAACTTT

                                                    
       4367 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 T

       4394 GTTGCGCCAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:8382 original size:19 final size:19

Alignment explanation


    Indices: 8354--8390  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       8344 TTGGAGGTTT

                      *        
       8354 TTATTAATTGTTTTCTTGA
          1 TTATTAATTGCTTTCTTGA

                 *            
       8373 TTATTCATTGCTTTCTTG
          1 TTATTAATTGCTTTCTTG

       8391 TCAATTGTTT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   16  1.00

ACGTcount: A:0.16, C:0.11, G:0.11, T:0.62


Consensus pattern (19 bp):   
TTATTAATTGCTTTCTTGA

Found at i:17079 original size:11 final size:10

Alignment explanation


    Indices: 17063--17109  Score: 53
    Period size: 11  Copynumber: 4.7  Consensus size: 10

      17053 AAGTTCGTAT

                       
      17063 TTGAAGACTCA
          1 TTGAAGA-TCA

                    * 
      17074 TTGAAGATAA
          1 TTGAAGATCA

                       
      17084 TTTGAAGAT--
          1 -TTGAAGATCA

                      
      17093 TTGAAGATCA
          1 TTGAAGATCA

                   
      17103 TTGAAGA
          1 TTGAAGA

      17110 ATTATTTCAA


Statistics
Matches: 32,  Mismatches: 1, Indels: 7
        0.80            0.03        0.17

Matches are distributed among these distances:
   8    8  0.25
  10    9  0.28
  11   15  0.47

ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32


Consensus pattern (10 bp):   
TTGAAGATCA

Found at i:17098 original size:19 final size:18

Alignment explanation


    Indices: 17074--17109  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      17064 TGAAGACTCA

                               
      17074 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
      17093 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

      17110 ATTATTTCAA


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

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT

Found at i:19441 original size:13 final size:13

Alignment explanation


    Indices: 19423--19447  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      19413 GCTAATAGGG

                         
      19423 AGAATATAGCAAT
          1 AGAATATAGCAAT

                        
      19436 AGAATATAGCAA
          1 AGAATATAGCAA

      19448 AAGCAAATTT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.56, C:0.08, G:0.16, T:0.20


Consensus pattern (13 bp):   
AGAATATAGCAAT
Done.