Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014754.1 Corchorus olitorius cultivar O-4 contig14787, 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: 18400
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30


Found at i:6292 original size:15 final size:15

Alignment explanation


    Indices: 6262--6303  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       6252 TTACTTTGTT

                            
       6262 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
       6278 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
       6293 TTGCTTTCTGT
          1 TTGTTTTCTGT

       6304 CAACCTCTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:15436 original size:21 final size:22

Alignment explanation


    Indices: 15412--15453  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 22

      15402 TTTGCCTCAT

                                  
      15412 GCATTCATTCAT-CATACCATG
          1 GCATTCATTCATGCATACCATG

                            *    
      15433 GCATTCATTCATGCATCCCAT
          1 GCATTCATTCATGCATACCAT

      15454 TAAACCTTAG


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21   12  0.63
  22    7  0.37

ACGTcount: A:0.26, C:0.31, G:0.10, T:0.33


Consensus pattern (22 bp):   
GCATTCATTCATGCATACCATG

Found at i:17545 original size:20 final size:19

Alignment explanation


    Indices: 17517--17569  Score: 56
    Period size: 19  Copynumber: 2.7  Consensus size: 19

      17507 CCAATAATAA

                            *   
      17517 AAAAT-AAAAAAAAACGAAG
          1 AAAATGAAAAAAAAA-AAAG

                                 
      17536 AAAA-GAAAAAAATGAAAAAG
          1 AAAATGAAAAAAA--AAAAAG

                          
      17556 AAAATGAAAAAAAA
          1 AAAATGAAAAAAAA

      17570 GCACTTGGAA


Statistics
Matches: 29,  Mismatches: 1, Indels: 8
        0.76            0.03        0.21

Matches are distributed among these distances:
  19   12  0.41
  20    7  0.24
  21   10  0.34

ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06


Consensus pattern (19 bp):   
AAAATGAAAAAAAAAAAAG

Found at i:17566 original size:27 final size:27

Alignment explanation


    Indices: 17515--17568  Score: 72
    Period size: 29  Copynumber: 1.9  Consensus size: 27

      17505 TCCCAATAAT

                                       
      17515 AAAAAATAAAAAAAAACGAAGAAAAGA
          1 AAAAAATAAAAAAAAACGAAGAAAAGA

                              *   *    
      17542 AAAAAATGAAAAAGAAAATGAAAAAAA
          1 AAAAAAT-AAAAA-AAAACGAAGAAAA

      17569 AGCACTTGGA


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  27    7  0.30
  28    5  0.22
  29   11  0.48

ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06


Consensus pattern (27 bp):   
AAAAAATAAAAAAAAACGAAGAAAAGA
Done.