Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020150.1 Corchorus olitorius cultivar O-4 contig20183, 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: 24285
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:3179 original size:24 final size:24

Alignment explanation


    Indices: 3128--3179  Score: 70
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       3118 TTATAGTTTC

                                 * *
       3128 TTGAATCTGAATTTTTTTGTTGAC
          1 TTGAATCTGAATTTTTTTGTTCAA

                                     
       3152 TTGAATCTGAATTTTTTT-TCTCAA
          1 TTGAATCTGAATTTTTTTGT-TCAA

                
       3176 TTGA
          1 TTGA

       3180 TTCTCCTTTC


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  23    1  0.04
  24   24  0.96

ACGTcount: A:0.23, C:0.10, G:0.13, T:0.54


Consensus pattern (24 bp):   
TTGAATCTGAATTTTTTTGTTCAA

Found at i:3412 original size:28 final size:28

Alignment explanation


    Indices: 3372--3427  Score: 94
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       3362 TGTTGTGGTT

                                        
       3372 TAATTGGTATGGAATTGATTATCATTTG
          1 TAATTGGTATGGAATTGATTATCATTTG

                    *    *              
       3400 TAATTGGTTTGGACTTGATTATCATTTG
          1 TAATTGGTATGGAATTGATTATCATTTG

       3428 GTGTAATTGT


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  28   26  1.00

ACGTcount: A:0.25, C:0.05, G:0.21, T:0.48


Consensus pattern (28 bp):   
TAATTGGTATGGAATTGATTATCATTTG

Found at i:7155 original size:19 final size:19

Alignment explanation


    Indices: 7133--7177  Score: 63
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       7123 CCGAATCCAA

                 *         *   
       7133 GAACCTGCTCAATCCTCTC
          1 GAACCCGCTCAATCCGCTC

                         *     
       7152 GAACCCGCTCAATTCGCTC
          1 GAACCCGCTCAATCCGCTC

                   
       7171 GAACCCG
          1 GAACCCG

       7178 AAACCCGTCT


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  19   23  1.00

ACGTcount: A:0.22, C:0.42, G:0.16, T:0.20


Consensus pattern (19 bp):   
GAACCCGCTCAATCCGCTC
Done.