Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018890.1 Corchorus olitorius cultivar O-4 contig18923, 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: 4077
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29


Found at i:399 original size:15 final size:16

Alignment explanation


    Indices: 375--414  Score: 64
    Period size: 15  Copynumber: 2.6  Consensus size: 16

        365 AGAGATTGAC

                 *          
        375 AGAAAGCAATTAAA-T
          1 AGAAAACAATTAAACT

                            
        390 AGAAAACAATTAAACT
          1 AGAAAACAATTAAACT

                     
        406 AGAAAACAA
          1 AGAAAACAA

        415 AGCAAAGTGA


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  15   13  0.57
  16   10  0.43

ACGTcount: A:0.65, C:0.10, G:0.10, T:0.15


Consensus pattern (16 bp):   
AGAAAACAATTAAACT

Found at i:1191 original size:11 final size:11

Alignment explanation


    Indices: 1175--1200  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       1165 CCTTTGCCTA

                       
       1175 AAAACTAGAAG
          1 AAAACTAGAAG

                       
       1186 AAAACTAGAAG
          1 AAAACTAGAAG

                
       1197 AAAA
          1 AAAA

       1201 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

Found at i:3669 original size:21 final size:21

Alignment explanation


    Indices: 3644--3694  Score: 84
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       3634 TGAATGGTGA

                                 
       3644 TGGCACGGGCATAGCCAGTGG
          1 TGGCACGGGCATAGCCAGTGG

                            *    
       3665 TGGCACGGGCATAGCCGGTGG
          1 TGGCACGGGCATAGCCAGTGG

              *      
       3686 TGACACGGG
          1 TGGCACGGG

       3695 AATGGGCGGA


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  21   28  1.00

ACGTcount: A:0.18, C:0.24, G:0.45, T:0.14


Consensus pattern (21 bp):   
TGGCACGGGCATAGCCAGTGG
Done.