Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018768.1 Corchorus olitorius cultivar O-4 contig18801, 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: 1742
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30


Found at i:872 original size:27 final size:27

Alignment explanation


    Indices: 833--891  Score: 82
    Period size: 27  Copynumber: 2.2  Consensus size: 27

        823 AACAAGAAAA

                   **         *   *    
        833 TTTTTTATTTATGACGCAGAAATTTTT
          1 TTTTTTAAATATGACGCAAAAACTTTT

                                       
        860 TTTTTTAAATATGACGCAAAAACTTTT
          1 TTTTTTAAATATGACGCAAAAACTTTT

                 
        887 TTTTT
          1 TTTTT

        892 CCGATGCAAA


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.29, C:0.08, G:0.08, T:0.54


Consensus pattern (27 bp):   
TTTTTTAAATATGACGCAAAAACTTTT

Found at i:982 original size:36 final size:36

Alignment explanation


    Indices: 900--975  Score: 134
    Period size: 36  Copynumber: 2.1  Consensus size: 36

        890 TTCCGATGCA

                                          *     
        900 AAACACAAAACAAACTTTTTTTTTTCAAAACGACGC
          1 AAACACAAAACAAACTTTTTTTTTTCAAAAAGACGC

                          *                     
        936 AAACACAAAACAAATTTTTTTTTTTCAAAAAGACGC
          1 AAACACAAAACAAACTTTTTTTTTTCAAAAAGACGC

                
        972 AAAC
          1 AAAC

        976 TAAAAACGCA


Statistics
Matches: 38,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  36   38  1.00

ACGTcount: A:0.47, C:0.20, G:0.05, T:0.28


Consensus pattern (36 bp):   
AAACACAAAACAAACTTTTTTTTTTCAAAAAGACGC

Found at i:1379 original size:16 final size:15

Alignment explanation


    Indices: 1341--1382  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       1331 ACAGAGGTTG

                           
       1341 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
       1356 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       1371 ACTAGAAAACAA
          1 AC-AGAAAACAA

       1383 AAAAAATAAA


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

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.