Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020028.1 Corchorus olitorius cultivar O-4 contig20061, 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: 5984
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.35


Found at i:112 original size:27 final size:27

Alignment explanation


    Indices: 82--142  Score: 68
    Period size: 28  Copynumber: 2.2  Consensus size: 27

         72 ATGTTATCAA

                         **  *         
         82 AATAACTATATTGCTATCAATAAATTC
          1 AATAACTATATTGAGATAAATAAATTC

                    * *                 
        109 AATAACCTTTTTTGAGATAAATAAATTC
          1 AATAA-CTATATTGAGATAAATAAATTC

                  
        137 AATAAC
          1 AATAAC

        143 CTTATATCCT


Statistics
Matches: 28,  Mismatches: 5, Indels: 2
        0.80            0.14        0.06

Matches are distributed among these distances:
  27    6  0.21
  28   22  0.79

ACGTcount: A:0.46, C:0.13, G:0.05, T:0.36


Consensus pattern (27 bp):   
AATAACTATATTGAGATAAATAAATTC

Found at i:3075 original size:15 final size:15

Alignment explanation


    Indices: 3051--3081  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       3041 ATATAAATAA

                 *         
       3051 TATTGTAATTTTAAC
          1 TATTGGAATTTTAAC

                           
       3066 TATTGGAATTTTAAC
          1 TATTGGAATTTTAAC

             
       3081 T
          1 T

       3082 TGTTGATGTT


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52


Consensus pattern (15 bp):   
TATTGGAATTTTAAC

Found at i:3298 original size:6 final size:6

Alignment explanation


    Indices: 3289--3322  Score: 59
    Period size: 6  Copynumber: 5.7  Consensus size: 6

       3279 ATTTAGATTT

                *                                  
       3289 ATATTG ATATAG ATATAG ATATAG ATATAG ATAT
          1 ATATAG ATATAG ATATAG ATATAG ATATAG ATAT

       3323 TTTTGAAGAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   6   27  1.00

ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38


Consensus pattern (6 bp):   
ATATAG

Done.