Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013687.1 Corchorus olitorius cultivar O-4 contig13720, 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: 4049
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:2039 original size:29 final size:30

Alignment explanation


    Indices: 1998--2070  Score: 94
    Period size: 30  Copynumber: 2.4  Consensus size: 30

       1988 AGTCTATTTT

                                     **    
       1998 CCTTCCCCTGGCAAAAACCAGAAAATGTT-C
          1 CCTTCCCC-GGCAAAAACCAGAAAAAATTAC

                         *   *            
       2028 CCTTCCCCGGCAAGAACTAGAAAAAATTAC
          1 CCTTCCCCGGCAAAAACCAGAAAAAATTAC

                         
       2058 CCTTCCCCGGCAA
          1 CCTTCCCCGGCAA

       2071 CGGCGCCAAA


Statistics
Matches: 38,  Mismatches: 4, Indels: 2
        0.86            0.09        0.05

Matches are distributed among these distances:
  29   16  0.42
  30   22  0.58

ACGTcount: A:0.33, C:0.36, G:0.14, T:0.18


Consensus pattern (30 bp):   
CCTTCCCCGGCAAAAACCAGAAAAAATTAC

Found at i:2263 original size:15 final size:15

Alignment explanation


    Indices: 2243--2283  Score: 55
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       2233 ACAGAGATTG

                   *       
       2243 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                     *     
       2258 ACAGAAAACGATTAA
          1 ACAGAAAACAATTAA

                       
       2273 ACTAGAAAACA
          1 AC-AGAAAACA

       2284 GAGCAGAGTA


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  15   15  0.68
  16    7  0.32

ACGTcount: A:0.61, C:0.15, G:0.12, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:3060 original size:11 final size:11

Alignment explanation


    Indices: 3044--3069  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       3034 CCTTTGCCTA

                       
       3044 AAAACTAGAAG
          1 AAAACTAGAAG

                       
       3055 AAAACTAGAAG
          1 AAAACTAGAAG

                
       3066 AAAA
          1 AAAA

       3070 GAAATTATCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08


Consensus pattern (11 bp):   
AAAACTAGAAG
Done.