Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011298.1 Corchorus olitorius cultivar O-4 contig11331, 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, 837

Length: 1396
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33


Found at i:73 original size:17 final size:16

Alignment explanation


    Indices: 50--98  Score: 75
    Period size: 14  Copynumber: 3.1  Consensus size: 16

         40 AAAAAAAAGG

                            
         50 AATAAAAAAATAAAAT
          1 AATAAAAAAATAAAAT

                            
         66 AAT--AAAAATAAAAT
          1 AATAAAAAAATAAAAT

                             
         80 AATAAAAACAATAAAAT
          1 AATAAAAA-AATAAAAT

              
         97 AA
          1 AA

         99 CGATAGAACA


Statistics
Matches: 30,  Mismatches: 0, Indels: 5
        0.86            0.00        0.14

Matches are distributed among these distances:
  14   14  0.47
  16    6  0.20
  17   10  0.33

ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18


Consensus pattern (16 bp):   
AATAAAAAAATAAAAT

Found at i:76 original size:22 final size:23

Alignment explanation


    Indices: 50--95  Score: 67
    Period size: 23  Copynumber: 2.0  Consensus size: 23

         40 AAAAAAAAGG

                            *      
         50 AATAAAAAAAT-AAAATAATAAA
          1 AATAAAAAAATAAAAACAATAAA

                   *               
         72 AATAAAATAATAAAAACAATAAA
          1 AATAAAAAAATAAAAACAATAAA

             
         95 A
          1 A

         96 TAACGATAGA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  22   10  0.48
  23   11  0.52

ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17


Consensus pattern (23 bp):   
AATAAAAAAATAAAAACAATAAA

Found at i:94 original size:9 final size:8

Alignment explanation


    Indices: 50--95  Score: 51
    Period size: 8  Copynumber: 5.9  Consensus size: 8

         40 AAAAAAAAGG

                    
         50 AATAAAAA
          1 AATAAAAA

                   *
         58 AATAAAAT
          1 AATAAAAA

                    
         66 AAT--AAA
          1 AATAAAAA

                   *
         72 AATAAAAT
          1 AATAAAAA

                    
         80 AATAAAAA
          1 AATAAAAA

                    
         88 CAATAAAA
          1 -AATAAAA

         96 TAACGATAGA


Statistics
Matches: 31,  Mismatches: 4, Indels: 5
        0.77            0.10        0.12

Matches are distributed among these distances:
   6    5  0.16
   8   19  0.61
   9    7  0.23

ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17


Consensus pattern (8 bp):   
AATAAAAA

Done.