Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007680.1 Corchorus olitorius cultivar O-4 contig07706, 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, 976

Length: 1628
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.35


Found at i:481 original size:21 final size:21

Alignment explanation


    Indices: 455--567  Score: 149
    Period size: 21  Copynumber: 5.4  Consensus size: 21

        445 TGCTAGAAGT

                                 
        455 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                                 
        476 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                       *   *    *
        497 TCATTGGAGCAGGTTACAAGT
          1 TCATTGGAGCAAGTTCCAAGC

                                 *
        518 TCATTGGAG-AAGGTTCCAAGA
          1 TCATTGGAGCAA-GTTCCAAGC

                            *     
        539 TCATTGGAG-AAGGTTTCAAGC
          1 TCATTGGAGCAA-GTTCCAAGC

                    
        560 TCATTGGA
          1 TCATTGGA

        568 AATGCCTAAG


Statistics
Matches: 83,  Mismatches: 8, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
  20    1  0.01
  21   82  0.99

ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGCAAGTTCCAAGC

Found at i:1494 original size:42 final size:42

Alignment explanation


    Indices: 1448--1532  Score: 134
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       1438 TTTGTATTAA

                                              *       
       1448 TTTTGAATATTAAATACATAAATAATTATCAGGTGGGGTATG
          1 TTTTGAATATTAAATACATAAATAATTATCAGGTAGGGTATG

                                 * *     *            
       1490 TTTTGAATATTAAATACATAATTTATTATTAGGTAGGGTATG
          1 TTTTGAATATTAAATACATAAATAATTATCAGGTAGGGTATG

             
       1532 T
          1 T

       1533 GTCAACATTT


Statistics
Matches: 39,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  42   39  1.00

ACGTcount: A:0.36, C:0.04, G:0.18, T:0.42


Consensus pattern (42 bp):   
TTTTGAATATTAAATACATAAATAATTATCAGGTAGGGTATG
Done.