Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009904.1 Corchorus olitorius cultivar O-4 contig09936, 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, 922

Length: 1537
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31


Found at i:348 original size:4 final size:4

Alignment explanation


    Indices: 341--366  Score: 52
    Period size: 4  Copynumber: 6.5  Consensus size: 4

        331 TTTCATCCAC

                                            
        341 TTAT TTAT TTAT TTAT TTAT TTAT TT
          1 TTAT TTAT TTAT TTAT TTAT TTAT TT

        367 TCCTTTGGTA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   22  1.00

ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77


Consensus pattern (4 bp):   
TTAT

Found at i:867 original size:17 final size:16

Alignment explanation


    Indices: 847--890  Score: 70
    Period size: 17  Copynumber: 2.6  Consensus size: 16

        837 TGTATGGAAT

                             
        847 CTTTCTCTGTACATCAG
          1 CTTTCT-TGTACATCAG

                             
        864 CTTTCTTTGTACATCAG
          1 CTTTC-TTGTACATCAG

                      
        881 CTTTCTTGTA
          1 CTTTCTTGTA

        891 TATGTATTTC


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  16    5  0.19
  17   20  0.77
  18    1  0.04

ACGTcount: A:0.16, C:0.25, G:0.11, T:0.48


Consensus pattern (16 bp):   
CTTTCTTGTACATCAG

Found at i:1497 original size:55 final size:54

Alignment explanation


    Indices: 1427--1537  Score: 186
    Period size: 55  Copynumber: 2.0  Consensus size: 54

       1417 GTGCGGTCTT

                                                                   
       1427 TTGATCCTCAAATGATCCAGTGCGGTCATTCCAAGAAGTTTTTTAAGGATCAGAG
          1 TTGATCCTCAAATGATCCAGTGCGGTCATTCCAAGAAG-TTTTTAAGGATCAGAG

                      *                                  *   *    
       1482 TTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAATGATTAGAG
          1 TTGATCCTCAAATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAAGGATCAGAG

              
       1536 TT
          1 TT


Statistics
Matches: 53,  Mismatches: 3, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  54   16  0.30
  55   37  0.70

ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33


Consensus pattern (54 bp):   
TTGATCCTCAAATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAAGGATCAGAG
Done.