Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018121.1 Corchorus olitorius cultivar O-4 contig18154, 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: 5135
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30


Found at i:116 original size:16 final size:15

Alignment explanation


    Indices: 78--119  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

         68 ACAGAGATTG

                   *       
         78 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
         93 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
        108 ACTAGAAAACAA
          1 AC-AGAAAACAA

        120 AGCAAAGCAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:3385 original size:21 final size:21

Alignment explanation


    Indices: 3361--3410  Score: 73
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       3351 GGAATGGCAA

                        **       
       3361 TGGCACGGGCATGGCCGGTGG
          1 TGGCACGGGCATAACCGGTGG

                      *          
       3382 TGGCACGGGCTTAACCGGTGG
          1 TGGCACGGGCATAACCGGTGG

                    
       3403 TGGCACGG
          1 TGGCACGG

       3411 TGAATGGGCG


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   26  1.00

ACGTcount: A:0.12, C:0.24, G:0.48, T:0.16


Consensus pattern (21 bp):   
TGGCACGGGCATAACCGGTGG

Found at i:3623 original size:21 final size:21

Alignment explanation


    Indices: 3578--3623  Score: 58
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       3568 CTGGCAGGCG

                                *
       3578 GCGCAGATGGCCGGTTACGGT
          1 GCGCAGATGGCCGGTTACGGC

                *                 
       3599 GCGCGGATGGCCGGTT-CTGGC
          1 GCGCAGATGGCCGGTTAC-GGC

                
       3620 GCGC
          1 GCGC

       3624 CGAGGAGTCC


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  20    1  0.05
  21   21  0.95

ACGTcount: A:0.09, C:0.28, G:0.46, T:0.17


Consensus pattern (21 bp):   
GCGCAGATGGCCGGTTACGGC
Done.