Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010644.1 Corchorus olitorius cultivar O-4 contig10676, 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: 11573
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:5085 original size:38 final size:39

Alignment explanation


    Indices: 5036--5133  Score: 137
    Period size: 39  Copynumber: 2.5  Consensus size: 39

       5026 TTTTAATTAA

                                                   
       5036 GTAATTCCAAAAGAAGATTTTGGA-AAATAAAAGTTTAG
          1 GTAATTCCAAAAGAAGATTTTGGAGAAATAAAAGTTTAG

                  *                               *
       5074 GTAATTTCAAAAGAAGATTTTGGAGAAATAAAAGTTTAA
          1 GTAATTCCAAAAGAAGATTTTGGAGAAATAAAAGTTTAG

                  *     *         
       5113 G-ATATCCCAAAGGAAGATTTT
          1 GTA-ATTCCAAAAGAAGATTTT

       5134 TGAAATTAAT


Statistics
Matches: 53,  Mismatches: 5, Indels: 3
        0.87            0.08        0.05

Matches are distributed among these distances:
  38   24  0.45
  39   29  0.55

ACGTcount: A:0.46, C:0.06, G:0.18, T:0.30


Consensus pattern (39 bp):   
GTAATTCCAAAAGAAGATTTTGGAGAAATAAAAGTTTAG

Found at i:6686 original size:18 final size:19

Alignment explanation


    Indices: 6650--6686  Score: 51
    Period size: 18  Copynumber: 2.0  Consensus size: 19

       6640 AACGAAAGTC

                               
       6650 CTCTCTTCAACACACACAA
          1 CTCTCTTCAACACACACAA

                                
       6669 CTCTC-TC-ACACAACACAA
          1 CTCTCTTCAACAC-ACACAA

       6687 AATCTTGCCT


Statistics
Matches: 17,  Mismatches: 0, Indels: 3
        0.85            0.00        0.15

Matches are distributed among these distances:
  17    4  0.24
  18    8  0.47
  19    5  0.29

ACGTcount: A:0.38, C:0.43, G:0.00, T:0.19


Consensus pattern (19 bp):   
CTCTCTTCAACACACACAA
Done.