Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022480.1 Corchorus olitorius cultivar O-4 contig22513, 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: 17526
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:3165 original size:15 final size:14

Alignment explanation


    Indices: 3147--3176  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       3137 CTATAGAAAG

                           
       3147 ACTTTCTACCTTTCT
          1 ACTTTCTA-CTTTCT

                          
       3162 ACTTTCTACTTTCT
          1 ACTTTCTACTTTCT

             
       3176 A
          1 A

       3177 TGGAAACTTC


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    7  0.47
  15    8  0.53

ACGTcount: A:0.17, C:0.30, G:0.00, T:0.53


Consensus pattern (14 bp):   
ACTTTCTACTTTCT

Found at i:3168 original size:7 final size:7

Alignment explanation


    Indices: 3147--3176  Score: 51
    Period size: 7  Copynumber: 4.1  Consensus size: 7

       3137 CTATAGAAAG

                   
       3147 ACTTTCT
          1 ACTTTCT

                    
       3154 ACCTTTCT
          1 A-CTTTCT

                   
       3162 ACTTTCT
          1 ACTTTCT

                   
       3169 ACTTTCT
          1 ACTTTCT

             
       3176 A
          1 A

       3177 TGGAAACTTC


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
   7   15  0.68
   8    7  0.32

ACGTcount: A:0.17, C:0.30, G:0.00, T:0.53


Consensus pattern (7 bp):   
ACTTTCT

Found at i:4754 original size:2 final size:2

Alignment explanation


    Indices: 4747--4776  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       4737 TATGATTTAC

                                                        
       4747 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       4777 CCATCCTAGT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:17153 original size:2 final size:2

Alignment explanation


    Indices: 17146--17185  Score: 57
    Period size: 2  Copynumber: 21.0  Consensus size: 2

      17136 CTCGATACGA

                                                 *                        
      17146 AT AT AT AT AT AT AT AT AT AT AT AT AC AT A- AT AT -T AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      17186 TTAATTAAAA


Statistics
Matches: 34,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
   1    2  0.06
   2   32  0.94

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Done.