Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005055.1 Corchorus olitorius cultivar O-4 contig05076, 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, 727

Length: 1212
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:492 original size:11 final size:10

Alignment explanation


    Indices: 476--525  Score: 55
    Period size: 11  Copynumber: 4.6  Consensus size: 10

        466 TCGATTAATA

                       
        476 TTCGTTTAGTG
          1 TTCGTTTA-TG

                       
        487 TTCGTTTATTG
          1 TTCGTTTA-TG

                        
        498 TTCGTTTAATAG
          1 TTCGTTT-AT-G

            *         
        510 CTCGTTTATG
          1 TTCGTTTATG

                  
        520 TTCGTT
          1 TTCGTT

        526 AATTAAGATT


Statistics
Matches: 34,  Mismatches: 3, Indels: 5
        0.81            0.07        0.12

Matches are distributed among these distances:
  10    6  0.18
  11   20  0.59
  12    8  0.24

ACGTcount: A:0.12, C:0.12, G:0.20, T:0.56


Consensus pattern (10 bp):   
TTCGTTTATG

Found at i:649 original size:30 final size:30

Alignment explanation


    Indices: 590--654  Score: 87
    Period size: 30  Copynumber: 2.2  Consensus size: 30

        580 ATTTAAATTT

                                  ***     
        590 TATTAGAAATATTTATTAATATGTGATAAA
          1 TATTAGAAATATTTATTAATATACAATAAA

                                           
        620 TATTAG-AATATTTATTTAATATACAATAAA
          1 TATTAGAAATATTTA-TTAATATACAATAAA

                 
        650 TATTA
          1 TATTA

        655 TTAAAAATAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 2
        0.86            0.08        0.06

Matches are distributed among these distances:
  29    8  0.26
  30   23  0.74

ACGTcount: A:0.48, C:0.02, G:0.06, T:0.45


Consensus pattern (30 bp):   
TATTAGAAATATTTATTAATATACAATAAA

Found at i:657 original size:33 final size:33

Alignment explanation


    Indices: 583--663  Score: 80
    Period size: 30  Copynumber: 2.5  Consensus size: 33

        573 AAATAATATT

                 *                       *** 
        583 TAAATTTTATTAGAAATATTTATTAATATGTGA
          1 TAAATATTATTAGAAATATTTATTAATATACAA

                                              
        616 T-AA-A-TATTAG-AATATTTATTTAATATACAA
          1 TAAATATTATTAGAAATATTTA-TTAATATACAA

                        *     
        646 TAAATATTATTAAAAATA
          1 TAAATATTATTAGAAATA

        664 ATATGTAATT


Statistics
Matches: 38,  Mismatches: 5, Indels: 9
        0.73            0.10        0.17

Matches are distributed among these distances:
  29    8  0.21
  30   15  0.39
  31    2  0.05
  32    3  0.08
  33    6  0.16
  34    4  0.11

ACGTcount: A:0.49, C:0.01, G:0.05, T:0.44


Consensus pattern (33 bp):   
TAAATATTATTAGAAATATTTATTAATATACAA
Done.