Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022825.1 Corchorus olitorius cultivar O-4 contig22858, 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: 13575
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30


Found at i:9686 original size:19 final size:19

Alignment explanation


    Indices: 9662--9707  Score: 83
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       9652 AGAAGCAAGG

                       *       
       9662 ATTGAAGATTGTAGCTTTA
          1 ATTGAAGATTGGAGCTTTA

                               
       9681 ATTGAAGATTGGAGCTTTA
          1 ATTGAAGATTGGAGCTTTA

                    
       9700 ATTGAAGA
          1 ATTGAAGA

       9708 CAAGCCATTG


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  19   26  1.00

ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37


Consensus pattern (19 bp):   
ATTGAAGATTGGAGCTTTA

Found at i:10978 original size:12 final size:13

Alignment explanation


    Indices: 10960--10989  Score: 53
    Period size: 12  Copynumber: 2.4  Consensus size: 13

      10950 GTTTTCTTTA

                         
      10960 ATTTTCTTGATTG
          1 ATTTTCTTGATTG

                         
      10973 -TTTTCTTGATTG
          1 ATTTTCTTGATTG

                 
      10985 ATTTT
          1 ATTTT

      10990 AATTGCTAGT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  12   12  0.75
  13    4  0.25

ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67


Consensus pattern (13 bp):   
ATTTTCTTGATTG

Found at i:11664 original size:15 final size:16

Alignment explanation


    Indices: 11637--11667  Score: 55
    Period size: 15  Copynumber: 2.0  Consensus size: 16

      11627 CCAGTACTTA

                            
      11637 CTTGAGAAACGTGGAG
          1 CTTGAGAAACGTGGAG

                            
      11653 CTTGAG-AACGTGGAG
          1 CTTGAGAAACGTGGAG

      11668 GCAGATACGC


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    9  0.60
  16    6  0.40

ACGTcount: A:0.29, C:0.13, G:0.39, T:0.19


Consensus pattern (16 bp):   
CTTGAGAAACGTGGAG

Found at i:12417 original size:15 final size:15

Alignment explanation


    Indices: 12397--12434  Score: 67
    Period size: 15  Copynumber: 2.5  Consensus size: 15

      12387 ACAGAGGTTG

                           
      12397 ACAGAAAGCAATTAA
          1 ACAGAAAGCAATTAA

                           
      12412 ACAGAAAGCAATTAA
          1 ACAGAAAGCAATTAA

                    
      12427 ACTAGAAA
          1 AC-AGAAA

      12435 ACAAAACAAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.77
  16    5  0.23

ACGTcount: A:0.61, C:0.13, G:0.13, T:0.13


Consensus pattern (15 bp):   
ACAGAAAGCAATTAA
Done.