Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008163.1 Corchorus olitorius cultivar O-4 contig08190, 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, 650

Length: 1084
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41


Found at i:724 original size:21 final size:21

Alignment explanation


    Indices: 700--763  Score: 64
    Period size: 17  Copynumber: 3.2  Consensus size: 21

        690 GTAATATATA

                    *            
        700 TAATAACTAAAATACTTACAT
          1 TAATAACTGAAATACTTACAT

                   *  *           
        721 TAATTAAATGTAATA-TT--A-
          1 TAA-TAACTGAAATACTTACAT

                                 
        739 TAATAACTGAAATACTTACAT
          1 TAATAACTGAAATACTTACAT

                
        760 TAAT
          1 TAAT

        764 TAAATTCTTA


Statistics
Matches: 33,  Mismatches: 5, Indels: 10
        0.69            0.10        0.21

Matches are distributed among these distances:
  17    9  0.27
  18    5  0.15
  19    1  0.03
  20    1  0.03
  21    9  0.27
  22    8  0.24

ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38


Consensus pattern (21 bp):   
TAATAACTGAAATACTTACAT

Found at i:745 original size:39 final size:40

Alignment explanation


    Indices: 688--768  Score: 146
    Period size: 39  Copynumber: 2.0  Consensus size: 40

        678 TTTAATTCCT

                                                    
        688 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

                                *                   
        728 ATGTAATAT-TATAATAACTGAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

              
        767 AT
          1 AT

        769 TCTTAGGTAT


Statistics
Matches: 40,  Mismatches: 1, Indels: 1
        0.95            0.02        0.02

Matches are distributed among these distances:
  39   31  0.77
  40    9  0.22

ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

Found at i:786 original size:24 final size:25

Alignment explanation


    Indices: 759--805  Score: 87
    Period size: 25  Copynumber: 1.9  Consensus size: 25

        749 AATACTTACA

                                     
        759 TTAATT-AAATTCTTAGGTATTTTT
          1 TTAATTCAAATTCTTAGGTATTTTT

                                   
        783 TTAATTCAAATTCTTAGGTATTT
          1 TTAATTCAAATTCTTAGGTATTT

        806 GTGCAAACGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24    6  0.27
  25   16  0.73

ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55


Consensus pattern (25 bp):   
TTAATTCAAATTCTTAGGTATTTTT

Done.