Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010005.1 Corchorus olitorius cultivar O-4 contig10037, 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: 6619
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36


Found at i:668 original size:24 final size:24

Alignment explanation


    Indices: 636--686  Score: 84
    Period size: 24  Copynumber: 2.1  Consensus size: 24

        626 TATTTAGTTC

                       *            
        636 TTTTTTTTTCTGCTATAGTTTGCT
          1 TTTTTTTTTCTACTATAGTTTGCT

                     *              
        660 TTTTTTTTTTTACTATAGTTTGCT
          1 TTTTTTTTTCTACTATAGTTTGCT

               
        684 TTT
          1 TTT

        687 CCACGCCAAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71


Consensus pattern (24 bp):   
TTTTTTTTTCTACTATAGTTTGCT

Found at i:5785 original size:13 final size:13

Alignment explanation


    Indices: 5767--5791  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       5757 TTCAATTTTC

                         
       5767 TAAATATTATTTA
          1 TAAATATTATTTA

                        
       5780 TAAATATTATTT
          1 TAAATATTATTT

       5792 GGAATTCCAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (13 bp):   
TAAATATTATTTA

Found at i:6360 original size:30 final size:27

Alignment explanation


    Indices: 6275--6357  Score: 121
    Period size: 30  Copynumber: 3.0  Consensus size: 27

       6265 GTTAATTTAG

                                       
       6275 ACTTATTATTATTATAATAATTATTAA
          1 ACTTATTATTATTATAATAATTATTAA

                              *           
       6302 ACTTATTATTAGTGGTATTATAATTATTAA
          1 ACTTATTATTA-T--TATAATAATTATTAA

                        *             
       6332 ACTTATTATTATAATAATAATTATTA
          1 ACTTATTATTATTATAATAATTATTA

       6358 TTAGTGGTAT


Statistics
Matches: 50,  Mismatches: 3, Indels: 6
        0.85            0.05        0.10

Matches are distributed among these distances:
  27   23  0.46
  28    1  0.02
  29    1  0.02
  30   25  0.50

ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51


Consensus pattern (27 bp):   
ACTTATTATTATTATAATAATTATTAA
Done.