Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015620.1 Corchorus olitorius cultivar O-4 contig15653, 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: 4625
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33


Found at i:4194 original size:6 final size:6

Alignment explanation


    Indices: 4179--4236  Score: 62
    Period size: 6  Copynumber: 8.8  Consensus size: 6

       4169 TAGCTTTCGT

                 *                                                      
       4179 AAAAAA AAAAAC AAAAGAC AAAAAAC AAAAAAAC AAAAAAC AAAAAC AAAAAC
          1 AAAAAC AAAAAC AAAA-AC -AAAAAC --AAAAAC -AAAAAC AAAAAC AAAAAC

                 
       4232 AAAAA
          1 AAAAA

       4237 ACTGGTAGCT


Statistics
Matches: 48,  Mismatches: 1, Indels: 6
        0.87            0.02        0.11

Matches are distributed among these distances:
   6   26  0.54
   7   11  0.23
   8   11  0.23

ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00


Consensus pattern (6 bp):   
AAAAAC

Found at i:4202 original size:8 final size:7

Alignment explanation


    Indices: 4179--4238  Score: 81
    Period size: 7  Copynumber: 8.9  Consensus size: 7

       4169 TAGCTTTCGT

                   
       4179 AAAAA-A
          1 AAAAACA

                   
       4185 AAAAACA
          1 AAAAACA

               *   
       4192 AAAGACA
          1 AAAAACA

                    
       4199 AAAAACAA
          1 AAAAAC-A

                   
       4207 AAAAACA
          1 AAAAACA

                   
       4214 AAAAAC-
          1 AAAAACA

                   
       4220 AAAAAC-
          1 AAAAACA

                   
       4226 AAAAACA
          1 AAAAACA

                  
       4233 AAAAAC
          1 AAAAAC

       4239 TGGTAGCTGA


Statistics
Matches: 49,  Mismatches: 2, Indels: 5
        0.88            0.04        0.09

Matches are distributed among these distances:
   6   17  0.35
   7   25  0.51
   8    7  0.14

ACGTcount: A:0.85, C:0.13, G:0.02, T:0.00


Consensus pattern (7 bp):   
AAAAACA

Found at i:4211 original size:22 final size:21

Alignment explanation


    Indices: 4179--4238  Score: 81
    Period size: 22  Copynumber: 3.0  Consensus size: 21

       4169 TAGCTTTCGT

                             *    
       4179 AAAA-AAAAAAACAAAAGACAA
          1 AAAACAAAAAAACAAAAAAC-A

                                 
       4200 AAAACAAAAAAACAAAAAACA
          1 AAAACAAAAAAACAAAAAACA

                                
       4221 AAAAC--AAAAACAAAAAAC
          1 AAAACAAAAAAACAAAAAAC

       4239 TGGTAGCTGA


Statistics
Matches: 37,  Mismatches: 1, Indels: 4
        0.88            0.02        0.10

Matches are distributed among these distances:
  19   13  0.35
  21   10  0.27
  22   14  0.38

ACGTcount: A:0.85, C:0.13, G:0.02, T:0.00


Consensus pattern (21 bp):   
AAAACAAAAAAACAAAAAACA
Done.