Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013557.1 Corchorus olitorius cultivar O-4 contig13590, 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: 2470
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30


Found at i:202 original size:11 final size:11

Alignment explanation


    Indices: 174--209  Score: 54
    Period size: 11  Copynumber: 3.2  Consensus size: 11

        164 TTTGATTCAC

                   *   
        174 TTTGATTAGAA
          1 TTTGATTTGAA

                        
        185 CTTTGATTTGAA
          1 -TTTGATTTGAA

                       
        197 TTTGATTTGAA
          1 TTTGATTTGAA

              
        208 TT
          1 TT

        210 ACTTAACGAA


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

Matches are distributed among these distances:
  11   13  0.57
  12   10  0.43

ACGTcount: A:0.28, C:0.03, G:0.17, T:0.53


Consensus pattern (11 bp):   
TTTGATTTGAA

Found at i:521 original size:14 final size:12

Alignment explanation


    Indices: 494--529  Score: 54
    Period size: 14  Copynumber: 2.8  Consensus size: 12

        484 TAAAAGACTC

                        
        494 AAAACCTTTTTG
          1 AAAACCTTTTTG

                          
        506 AAAACCTATCTTTG
          1 AAAACCT-T-TTTG

                      
        520 AAAACCTTTT
          1 AAAACCTTTT

        530 CTTGAAAGCA


Statistics
Matches: 22,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  12    9  0.41
  13    2  0.09
  14   11  0.50

ACGTcount: A:0.36, C:0.19, G:0.06, T:0.39


Consensus pattern (12 bp):   
AAAACCTTTTTG

Found at i:534 original size:14 final size:13

Alignment explanation


    Indices: 494--536  Score: 52
    Period size: 14  Copynumber: 3.2  Consensus size: 13

        484 TAAAAGACTC

                         
        494 AAAACCTTT-TTG
          1 AAAACCTTTCTTG

                   *      
        506 AAAACCTATCTTTG
          1 AAAACCTTTC-TTG

                          
        520 AAAACCTTTTCTTG
          1 AAAACC-TTTCTTG

               
        534 AAA
          1 AAA

        537 GCAATTTTCT


Statistics
Matches: 26,  Mismatches: 2, Indels: 4
        0.81            0.06        0.12

Matches are distributed among these distances:
  12    8  0.31
  14   15  0.58
  15    3  0.12

ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37


Consensus pattern (13 bp):   
AAAACCTTTCTTG
Done.