Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024681.1 Corchorus olitorius cultivar O-4 contig24714, 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: 9513
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28


Found at i:2622 original size:35 final size:35

Alignment explanation


    Indices: 2577--2709  Score: 110
    Period size: 35  Copynumber: 3.6  Consensus size: 35

       2567 GGTCATAGTT

                *                              
       2577 TTTTTAAATTGGGAAAGTTCCCACCAGTTTTTAAG
          1 TTTTCAAATTGGGAAAGTTCCCACCAGTTTTTAAG

                        *           **               *
       2612 TTTTCAAATTGGAAAAGTTCCCATTTAGTTTTTTTTCAAACA
          1 TTTTCAAATTGGGAAAGTTCCCA-CCAG---TTTTT--AA-G

                                                
       2654 TTTT-AAATTGGGAAAGTTCCCACCAAG-TTTT-AG
          1 TTTTCAAATTGGGAAAGTTCCCACC-AGTTTTTAAG

                   *               
       2687 TTTTCAATTTAGGGAAAGTTCCC
          1 TTTTCAAATT-GGGAAAGTTCCC

       2710 GTCATATTCA


Statistics
Matches: 78,  Mismatches: 10, Indels: 20
        0.72            0.09        0.19

Matches are distributed among these distances:
  33    4  0.05
  34    5  0.06
  35   33  0.42
  36    2  0.03
  37    4  0.05
  39    5  0.06
  41   21  0.27
  42    4  0.05

ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41


Consensus pattern (35 bp):   
TTTTCAAATTGGGAAAGTTCCCACCAGTTTTTAAG

Found at i:2683 original size:41 final size:39

Alignment explanation


    Indices: 2578--2693  Score: 107
    Period size: 41  Copynumber: 2.9  Consensus size: 39

       2568 GTCATAGTTT

                                                  *
       2578 TTTTAAATTGGGAAAGTTCCCACCAG---TTTTT--AAG
          1 TTTTAAATTGGGAAAGTTCCCACCAGTTTTTTTTCAAAA

                        *           **                
       2612 TTTTCAAATTGGAAAAGTTCCCATTTAGTTTTTTTTCAAACA
          1 TTTT-AAATTGGGAAAGTTCCCA-CCAGTTTTTTTTCAAA-A

                                                    
       2654 TTTTAAATTGGGAAAGTTCCCACCAAGTTTTAGTTTTCAA
          1 TTTTAAATTGGGAAAGTTCCCACC-AGTTTT--TTTTCAA

       2694 TTTAGGGAAA


Statistics
Matches: 64,  Mismatches: 7, Indels: 13
        0.76            0.08        0.15

Matches are distributed among these distances:
  34    4  0.06
  35   17  0.27
  36    2  0.03
  39    5  0.08
  41   25  0.39
  42    4  0.06
  43    7  0.11

ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41


Consensus pattern (39 bp):   
TTTTAAATTGGGAAAGTTCCCACCAGTTTTTTTTCAAAA
Done.