Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017943.1 Corchorus olitorius cultivar O-4 contig17976, 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: 20760
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31


Found at i:6458 original size:19 final size:18

Alignment explanation


    Indices: 6425--6466  Score: 57
    Period size: 19  Copynumber: 2.3  Consensus size: 18

       6415 TGGAAATAAT

                              
       6425 TCTTCAATGGTCTTCAAA
          1 TCTTCAATGGTCTTCAAA

                     *        *
       6443 TCTTCAAATTGTCTTCAAT
          1 TCTTC-AATGGTCTTCAAA

                 
       6462 TCTTC
          1 TCTTC

       6467 GAATCTCCAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  18    5  0.24
  19   16  0.76

ACGTcount: A:0.24, C:0.24, G:0.07, T:0.45


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAA

Found at i:6465 original size:27 final size:28

Alignment explanation


    Indices: 6425--6478  Score: 74
    Period size: 27  Copynumber: 1.9  Consensus size: 28

       6415 TGGAAATAAT

                                 *       
       6425 TCTTCAATGGTCTTCAAATCTTCAAATTG
          1 TCTTCAAT-GTCTTCAAATCTCCAAATTG

                          *           
       6454 TCTTCAAT-TCTTCGAATCTCCAAAT
          1 TCTTCAATGTCTTCAAATCTCCAAAT

       6479 CTATACTCAA


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  27   15  0.65
  29    8  0.35

ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41


Consensus pattern (28 bp):   
TCTTCAATGTCTTCAAATCTCCAAATTG

Found at i:13351 original size:19 final size:18

Alignment explanation


    Indices: 13318--13353  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      13308 TGGAAATAAT

                              
      13318 TCTTCAATGGTCTTCAAA
          1 TCTTCAATGGTCTTCAAA

                     *        
      13336 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATGGTCTTCAA

      13354 TAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAA

Found at i:19444 original size:21 final size:21

Alignment explanation


    Indices: 19406--19446  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      19396 CCTTTGCTTA

                         *       
      19406 TGATCTTCAATACTCTTCAAT
          1 TGATCTTCAATACACTTCAAT

                       **       
      19427 TGATCTTCAATGGACTTCAA
          1 TGATCTTCAATACACTTCAA

      19447 GCCTTCAAGA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39


Consensus pattern (21 bp):   
TGATCTTCAATACACTTCAAT
Done.