Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021242.1 Corchorus olitorius cultivar O-4 contig21275, 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: 17578
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:6765 original size:19 final size:18

Alignment explanation


    Indices: 6741--6776  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       6731 TGAAGACTTA

                               
       6741 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       6760 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       6777 ATAATTTCAA


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

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

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


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:6783 original size:30 final size:30

Alignment explanation


    Indices: 6729--6788  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       6719 GAAGTTCGTG

                      *              *    
       6729 TTTGAAGACTTATTGAAGACAATTTGAAGA
          1 TTTGAAGACTCATTGAAGACAATTTCAAGA

                                *          
       6759 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
          1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA

       6789 GCAAGAATTG


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  29    7  0.27
  30   19  0.73

ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32


Consensus pattern (30 bp):   
TTTGAAGACTCATTGAAGACAATTTCAAGA

Found at i:12349 original size:18 final size:18

Alignment explanation


    Indices: 12314--12348  Score: 54
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      12304 CACCTCTATC

                     *        
      12314 ATGAAAACACTTCTTTTT
          1 ATGAAAACAATTCTTTTT

                              
      12332 ATGAAAACAATT-TTTTT
          1 ATGAAAACAATTCTTTTT

      12349 TTTAATTACC


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

Matches are distributed among these distances:
  17    5  0.31
  18   11  0.69

ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46


Consensus pattern (18 bp):   
ATGAAAACAATTCTTTTT

Found at i:13028 original size:30 final size:29

Alignment explanation


    Indices: 12989--13045  Score: 89
    Period size: 30  Copynumber: 1.9  Consensus size: 29

      12979 GTTTATTAAT

                                           
      12989 GAAACTTGAAAATTAAAGACATAAGATAAAG
          1 GAAACTTGAAAATTAAAG-CATAA-ATAAAG

                                       
      13020 GAAA-TTGAAAATTAAAGCATAAATAA
          1 GAAACTTGAAAATTAAAGCATAAATAA

      13046 CTAATCCTAA


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

Matches are distributed among these distances:
  28    4  0.15
  29    5  0.19
  30   13  0.50
  31    4  0.15

ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21


Consensus pattern (29 bp):   
GAAACTTGAAAATTAAAGCATAAATAAAG
Done.