Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010638.1 Corchorus olitorius cultivar O-4 contig10670, 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: 2258
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29


Found at i:526 original size:63 final size:63

Alignment explanation


    Indices: 450--623  Score: 249
    Period size: 72  Copynumber: 2.6  Consensus size: 63

        440 TACACAAACA

                                      *                                    
        450 AACATATTCAAGTTTGAAAGCAAGTACTTGGAAATTGAATACGTTGGGAACATTTATTATTTG
          1 AACATATTCAAGTTTGAAAGCAAGTATTTGGAAATTGAATACGTTGGGAACATTTATTATTTG

                                                                             
        513 AACATATTCAAGTTTGAAAGCAAGTATTTGGAAATTGAAAACTAAAGATACGTTGGGAACATTTA
          1 AACATATTCAAGTTTGAAAGCAAGTATTTGGAAATTG--------A-ATACGTTGGGAACATTTA

                   
        578 TTATTTG
         57 TTATTTG

                                             *     
        585 AACATATTCAAGTTTGAAAGCAAGTATTTGGAAGTTGAA
          1 AACATATTCAAGTTTGAAAGCAAGTATTTGGAAATTGAA

        624 AACTAAAGAT


Statistics
Matches: 100,  Mismatches: 2, Indels: 18
        0.83            0.02        0.15

Matches are distributed among these distances:
  63   37  0.37
  64    1  0.01
  71    1  0.01
  72   61  0.61

ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33


Consensus pattern (63 bp):   
AACATATTCAAGTTTGAAAGCAAGTATTTGGAAATTGAATACGTTGGGAACATTTATTATTTG

Found at i:573 original size:72 final size:72

Alignment explanation


    Indices: 488--641  Score: 299
    Period size: 72  Copynumber: 2.1  Consensus size: 72

        478 TGGAAATTGA

                                                                             
        488 ATACGTTGGGAACATTTATTATTTGAACATATTCAAGTTTGAAAGCAAGTATTTGGAAATTGAAA
          1 ATACGTTGGGAACATTTATTATTTGAACATATTCAAGTTTGAAAGCAAGTATTTGGAAATTGAAA

                   
        553 ACTAAAG
         66 ACTAAAG

                                                                      *      
        560 ATACGTTGGGAACATTTATTATTTGAACATATTCAAGTTTGAAAGCAAGTATTTGGAAGTTGAAA
          1 ATACGTTGGGAACATTTATTATTTGAACATATTCAAGTTTGAAAGCAAGTATTTGGAAATTGAAA

                   
        625 ACTAAAG
         66 ACTAAAG

                      
        632 ATACGTTGGG
          1 ATACGTTGGG

        642 CTCAAAATGT


Statistics
Matches: 81,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  72   81  1.00

ACGTcount: A:0.38, C:0.08, G:0.20, T:0.33


Consensus pattern (72 bp):   
ATACGTTGGGAACATTTATTATTTGAACATATTCAAGTTTGAAAGCAAGTATTTGGAAATTGAAA
ACTAAAG

Found at i:1774 original size:26 final size:26

Alignment explanation


    Indices: 1742--1799  Score: 116
    Period size: 26  Copynumber: 2.2  Consensus size: 26

       1732 GTGTTTGAGT

                                      
       1742 GTGAGCGGCGGTGAGGGTAAGGAAGA
          1 GTGAGCGGCGGTGAGGGTAAGGAAGA

                                      
       1768 GTGAGCGGCGGTGAGGGTAAGGAAGA
          1 GTGAGCGGCGGTGAGGGTAAGGAAGA

                  
       1794 GTGAGC
          1 GTGAGC

       1800 TAGCGGCTGT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   32  1.00

ACGTcount: A:0.26, C:0.09, G:0.53, T:0.12


Consensus pattern (26 bp):   
GTGAGCGGCGGTGAGGGTAAGGAAGA
Done.