Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013850.1 Corchorus olitorius cultivar O-4 contig13883, 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: 3070
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37


Found at i:525 original size:17 final size:17

Alignment explanation


    Indices: 500--533  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

        490 TTTAGGCCTT

                *            
        500 TCATTTCCATATGAAGA
          1 TCATGTCCATATGAAGA

                             
        517 TCATGTCCATATGAAGA
          1 TCATGTCCATATGAAGA

        534 AGAGAGTAAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32


Consensus pattern (17 bp):   
TCATGTCCATATGAAGA

Found at i:1100 original size:109 final size:109

Alignment explanation


    Indices: 909--1125  Score: 380
    Period size: 109  Copynumber: 2.0  Consensus size: 109

        899 AGTCATTTTT

                                                                     *       
        909 GTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGCTATGTGTGCTTA
          1 GTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGCTATGGGTGCTTA

                       *                                
        974 TTTAATAGGTTTAATTGAATAAACAACACAATTAATAATAATAG
         66 TTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATAG

                                                  *             *            
       1018 GTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCATTTTGTATTGTTTGGTATGGGTGCTTA
          1 GTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGCTATGGGTGCTTA

                                    * *                
       1083 TTTAATAGGTTCAATTGAATAAACCATACAATTAATAATAATA
         66 TTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA

       1126 TATATAATAG


Statistics
Matches: 102,  Mismatches: 6, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 109  102  1.00

ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44


Consensus pattern (109 bp):   
GTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGCTATGGGTGCTTA
TTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATAG

Found at i:2182 original size:27 final size:27

Alignment explanation


    Indices: 2147--2207  Score: 74
    Period size: 27  Copynumber: 2.3  Consensus size: 27

       2137 CCTTTTTTTC

                                         
       2147 AAAT-ATATTTCTAA-ATTGCCATTATT-
          1 AAATAATATTT-TAATATT-CCATTATTA

                                        
       2173 AAATAATATTTTAATTATTCCATTATTA
          1 AAATAATATTTTAA-TATTCCATTATTA

                   
       2201 AAATAAT
          1 AAATAAT

       2208 GAAAATTTAG


Statistics
Matches: 31,  Mismatches: 0, Indels: 6
        0.84            0.00        0.16

Matches are distributed among these distances:
  26    7  0.23
  27   14  0.45
  28   10  0.32

ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46


Consensus pattern (27 bp):   
AAATAATATTTTAATATTCCATTATTA
Done.