Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000045.1 Corchorus olitorius cultivar O-4 contig00045, 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, 636

Length: 1060
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36


Found at i:269 original size:25 final size:24

Alignment explanation


    Indices: 235--281  Score: 76
    Period size: 25  Copynumber: 1.9  Consensus size: 24

        225 ACGTTTGCAC

                                     
        235 AAATACCTAAGAATTTGAATTAAAA
          1 AAATACCTAAGAATTT-AATTAAAA

                 *                
        260 AAATATCTAAGAATTTAATTAA
          1 AAATACCTAAGAATTTAATTAA

        282 TGTAAGCATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  24    6  0.29
  25   15  0.71

ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32


Consensus pattern (24 bp):   
AAATACCTAAGAATTTAATTAAAA

Found at i:326 original size:39 final size:40

Alignment explanation


    Indices: 272--352  Score: 128
    Period size: 39  Copynumber: 2.0  Consensus size: 40

        262 ATATCTAAGA

                                             *      
        272 ATTTAATTAATGTAAGCATTTCAGTTATTATA-GTATTAC
          1 ATTTAATTAATGTAAGCATTTCAGTTATTATATATATTAC

                            *    *                  
        311 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
          1 ATTTAATTAATGTAAGCATTTCAGTTATTATATATATTAC

              
        351 AT
          1 AT

        353 AGGAATTAAA


Statistics
Matches: 38,  Mismatches: 3, Indels: 1
        0.90            0.07        0.02

Matches are distributed among these distances:
  39   30  0.79
  40    8  0.21

ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49


Consensus pattern (40 bp):   
ATTTAATTAATGTAAGCATTTCAGTTATTATATATATTAC

Found at i:328 original size:22 final size:22

Alignment explanation


    Indices: 272--330  Score: 56
    Period size: 17  Copynumber: 2.9  Consensus size: 22

        262 ATATCTAAGA

                            *   * 
        272 ATTTAATTAATGTAAGCATTTC
          1 ATTTAATTAATGTAAGTATTAC

             *                    
        294 AGTT-ATT-A--T-AGTATTAC
          1 ATTTAATTAATGTAAGTATTAC

                                
        311 ATTTAATTAATGTAAGTATT
          1 ATTTAATTAATGTAAGTATT

        331 TTAGTTATTA


Statistics
Matches: 28,  Mismatches: 4, Indels: 10
        0.67            0.10        0.24

Matches are distributed among these distances:
  17    9  0.32
  18    4  0.14
  19    1  0.04
  20    1  0.04
  21    4  0.14
  22    9  0.32

ACGTcount: A:0.37, C:0.05, G:0.10, T:0.47


Consensus pattern (22 bp):   
ATTTAATTAATGTAAGTATTAC
Done.