Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023009.1 Corchorus olitorius cultivar O-4 contig23042, 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: 7510
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32


Found at i:276 original size:3 final size:3

Alignment explanation


    Indices: 270--302  Score: 66
    Period size: 3  Copynumber: 11.0  Consensus size: 3

        260 AATTCAGATT

                                                       
        270 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

        303 AAAAAATAAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   30  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTA

Found at i:1325 original size:17 final size:17

Alignment explanation


    Indices: 1278--1325  Score: 53
    Period size: 17  Copynumber: 2.8  Consensus size: 17

       1268 GTGGCATAAA

                             *
       1278 AAATTAATTTTTTTATTT
          1 AAATTAA-TTTTTTATTG

            *                 
       1296 TAATATAA-TTTTTATTG
          1 AAAT-TAATTTTTTATTG

                         
       1313 AAATTAATTTTTT
          1 AAATTAATTTTTT

       1326 TAATAATAAT


Statistics
Matches: 25,  Mismatches: 3, Indels: 5
        0.76            0.09        0.15

Matches are distributed among these distances:
  16    3  0.12
  17   16  0.64
  18    3  0.12
  19    3  0.12

ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62


Consensus pattern (17 bp):   
AAATTAATTTTTTATTG

Found at i:1741 original size:14 final size:14

Alignment explanation


    Indices: 1722--1750  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       1712 TTAATTCTAA

                          
       1722 GAAATGGGCTTTGG
          1 GAAATGGGCTTTGG

                          
       1736 GAAATGGGCTTTGG
          1 GAAATGGGCTTTGG

             
       1750 G
          1 G

       1751 TATTTTCTAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.21, C:0.07, G:0.45, T:0.28


Consensus pattern (14 bp):   
GAAATGGGCTTTGG
Done.