Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022161.1 Corchorus olitorius cultivar O-4 contig22194, 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: 22937
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35


Found at i:2430 original size:12 final size:12

Alignment explanation


    Indices: 2413--2462  Score: 55
    Period size: 12  Copynumber: 3.8  Consensus size: 12

       2403 TGTAGAAAAA

                        
       2413 ATATTTTTGTTG
          1 ATATTTTTGTTG

                         
       2425 ATATTTTTGTATG
          1 ATATTTTTGT-TG

                       *   
       2438 AAAATATTTTTATTG
          1 ---ATATTTTTGTTG

                      
       2453 ATATTTTTGT
          1 ATATTTTTGT

       2463 ATGAAAATAT


Statistics
Matches: 32,  Mismatches: 2, Indels: 8
        0.76            0.05        0.19

Matches are distributed among these distances:
  12   19  0.59
  13    2  0.06
  15    2  0.06
  16    9  0.28

ACGTcount: A:0.26, C:0.00, G:0.12, T:0.62


Consensus pattern (12 bp):   
ATATTTTTGTTG

Found at i:2476 original size:27 final size:28

Alignment explanation


    Indices: 2410--2475  Score: 123
    Period size: 28  Copynumber: 2.4  Consensus size: 28

       2400 AAATGTAGAA

                       *                
       2410 AAAATATTTTTGTTGATATTTTTGTATG
          1 AAAATATTTTTATTGATATTTTTGTATG

                                        
       2438 AAAATATTTTTATTGATATTTTTGTATG
          1 AAAATATTTTTATTGATATTTTTGTATG

                      
       2466 AAAATATTTT
          1 AAAATATTTT

       2476 AAAAAAATAC


Statistics
Matches: 37,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  28   37  1.00

ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56


Consensus pattern (28 bp):   
AAAATATTTTTATTGATATTTTTGTATG

Found at i:5601 original size:27 final size:27

Alignment explanation


    Indices: 5563--5617  Score: 110
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       5553 GGTGTATTGA

                                       
       5563 ATAATTTTCCTAATGATAATAGGCTTT
          1 ATAATTTTCCTAATGATAATAGGCTTT

                                       
       5590 ATAATTTTCCTAATGATAATAGGCTTT
          1 ATAATTTTCCTAATGATAATAGGCTTT

             
       5617 A
          1 A

       5618 GCTAACGGGT


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:0.35, C:0.11, G:0.11, T:0.44


Consensus pattern (27 bp):   
ATAATTTTCCTAATGATAATAGGCTTT

Found at i:21221 original size:25 final size:25

Alignment explanation


    Indices: 21170--21222  Score: 61
    Period size: 25  Copynumber: 2.1  Consensus size: 25

      21160 ATATGGGTGC

                   *        * *   *  
      21170 TCGGCAATGTATTAATGTTGGAGGA
          1 TCGGCAAGGTATTAATATCGGACGA

                         *           
      21195 TCGGCAAGGTATTGATATCGGACGA
          1 TCGGCAAGGTATTAATATCGGACGA

               
      21220 TCG
          1 TCG

      21223 ACAATGTCTT


Statistics
Matches: 23,  Mismatches: 5, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  25   23  1.00

ACGTcount: A:0.26, C:0.13, G:0.32, T:0.28


Consensus pattern (25 bp):   
TCGGCAAGGTATTAATATCGGACGA
Done.