Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013991.1 Corchorus olitorius cultivar O-4 contig14024, 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: 9303
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31


Found at i:2714 original size:21 final size:21

Alignment explanation


    Indices: 2689--2729  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2679 TTAGAAACCC

                                  
       2689 TAGTACCACTTAG-ATCCAATT
          1 TAGTACCACTT-GTATCCAATT

                                
       2710 TAGTACCACTTGTATCCAAT
          1 TAGTACCACTTGTATCCAAT

       2730 AGGGCTTCAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20    1  0.05
  21   18  0.95

ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34


Consensus pattern (21 bp):   
TAGTACCACTTGTATCCAATT

Found at i:8107 original size:39 final size:38

Alignment explanation


    Indices: 8014--8282  Score: 203
    Period size: 39  Copynumber: 6.8  Consensus size: 38

       8004 GAAATCTTTA

                                                   ** 
       8014 ATGGGATCTTTCCCCT-AATTGAAAACTTTGAAAAAGACCAG
          1 ATGGGATCTTT-CCCTAAATT-AAAACTTTG-AAAA-ACTTG

                  *                                
       8055 ATGGGACCTTTCCCTAAATTAAAACTTCTGAAAAACTTG
          1 ATGGGATCTTTCCCTAAATTAAAACTT-TGAAAAACTTG

                                           *        * 
       8094 ATGGGATCTTTCCCTAAATTAAAGACTTTAAAAAGAAACTGG
          1 ATGGGATCTTTCCCTAAATTAAA-ACTTT--GAA-AAACTTG

                                *         *          
       8136 ATGGGATCTTTCCCTAAATCGAAAGAC-TTAAACAAACTTG
          1 ATGGGATCTTTCCCTAAAT-TAAA-ACTTTGAA-AAACTTG

                  *                            *    
       8176 ATGGGACCTTTCCC--AATTAGAAA-TCTTG-AAAGCTTG
          1 ATGGGATCTTTCCCTAAATTA-AAACT-TTGAAAAACTTG

                            *                        
       8212 ATGGGATCTTTCCCTATATTAAAAAC-TTGAGAAATAC-TG
          1 ATGGGATCTTTCCCTAAATT-AAAACTTTGA-AAA-ACTTG

            *                *      *       
       8251 GTGGGATCTTTCCCTAATTTGAAATCTTTGAA
          1 ATGGGATCTTTCCCTAAATT-AAAACTTTGAA

       8283 TTGAAAACTT


Statistics
Matches: 189,  Mismatches: 21, Indels: 38
        0.76            0.08        0.15

Matches are distributed among these distances:
  36   19  0.10
  37    6  0.03
  38   13  0.07
  39   54  0.29
  40   46  0.24
  41   18  0.10
  42   27  0.14
  43    6  0.03

ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Consensus pattern (38 bp):   
ATGGGATCTTTCCCTAAATTAAAACTTTGAAAAACTTG

Found at i:8550 original size:15 final size:15

Alignment explanation


    Indices: 8520--8575  Score: 94
    Period size: 15  Copynumber: 3.6  Consensus size: 15

       8510 TCTAAACCTA

                             
       8520 GATGCATGAATGCATAT
          1 GATGCATG--TGCATAT

                           
       8537 GATGCATGTGCATAT
          1 GATGCATGTGCATAT

                           
       8552 GATGCATGTGCATAT
          1 GATGCATGTGCATAT

                     
       8567 GATGCATGT
          1 GATGCATGT

       8576 TTTCCGGTTA


Statistics
Matches: 39,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  15   31  0.79
  17    8  0.21

ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32


Consensus pattern (15 bp):   
GATGCATGTGCATAT
Done.