Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023331.1 Corchorus olitorius cultivar O-4 contig23364, 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: 10030
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31


Found at i:180 original size:10 final size:10

Alignment explanation


    Indices: 165--200  Score: 54
    Period size: 10  Copynumber: 3.6  Consensus size: 10

        155 AATTATGAAA

                      
        165 AAATCTAATT
          1 AAATCTAATT

                      
        175 AAATCTAATT
          1 AAATCTAATT

              * *     
        185 AAGTATAATT
          1 AAATCTAATT

                  
        195 AAATCT
          1 AAATCT

        201 TAAATAACCT


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  10   22  1.00

ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39


Consensus pattern (10 bp):   
AAATCTAATT

Found at i:3510 original size:19 final size:18

Alignment explanation


    Indices: 3477--3512  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       3467 TTGAAATTAT

                    *         
       3477 TCTTCAATGGTCTTCAAA
          1 TCTTCAATAGTCTTCAAA

                              
       3495 TCTTCAAATAGTCTTCAA
          1 TCTTC-AATAGTCTTCAA

       3513 TAAGTCTTCA


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:0.31, C:0.22, G:0.08, T:0.39


Consensus pattern (18 bp):   
TCTTCAATAGTCTTCAAA

Found at i:5576 original size:36 final size:36

Alignment explanation


    Indices: 5529--5598  Score: 122
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       5519 ATTTTCTCCA

                                                
       5529 ATTTATTTCATCAATATCTAAAGACATTGGCTAATC
          1 ATTTATTTCATCAATATCTAAAGACATTGGCTAATC

                           *   *              
       5565 ATTTATTTCATCAATGTCTCAAGACATTGGCTAA
          1 ATTTATTTCATCAATATCTAAAGACATTGGCTAA

       5599 ATCTCCATCT


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  36   32  1.00

ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39


Consensus pattern (36 bp):   
ATTTATTTCATCAATATCTAAAGACATTGGCTAATC

Found at i:6980 original size:2 final size:2

Alignment explanation


    Indices: 6973--6997  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       6963 TTTATGTCTA

                                                 
       6973 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

       6998 GGAGTAGAGT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.