Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014267.1 Corchorus capsularis cultivar CVL-1 contig14288, 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: 4909
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:33 original size:14 final size:16

Alignment explanation


    Indices: 3--41  Score: 55
    Period size: 15  Copynumber: 2.5  Consensus size: 16

          1 AA

                             
          3 AATTAAATAAAAGTAAT
          1 AATTAAA-AAAAGTAAT

                            
         20 AA-TAAAAAAA-TAAT
          1 AATTAAAAAAAGTAAT

                    
         34 AATTAAAA
          1 AATTAAAA

         42 GANAATTTTA


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  14    6  0.29
  15    9  0.43
  16    4  0.19
  17    2  0.10

ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26


Consensus pattern (16 bp):   
AATTAAAAAAAGTAAT

Found at i:4409 original size:9 final size:8

Alignment explanation


    Indices: 4371--4425  Score: 58
    Period size: 8  Copynumber: 6.5  Consensus size: 8

       4361 TCCCATCAGC

                    
       4371 AAAAG-AA
          1 AAAAGAAA

                    
       4378 AAAAGAAA
          1 AAAAGAAA

                  *    
       4386 ATCAAGTGAAA
          1 A--AA-AGAAA

                     
       4397 AAAAGAGAA
          1 AAAAGA-AA

                    
       4406 AAAAGAAA
          1 AAAAGAAA

                    
       4414 AAAAGAAA
          1 AAAAGAAA

                
       4422 AAAA
          1 AAAA

       4426 TGTGAAAGAA


Statistics
Matches: 41,  Mismatches: 2, Indels: 9
        0.79            0.04        0.17

Matches are distributed among these distances:
   7    5  0.12
   8   19  0.46
   9   10  0.24
  10    2  0.05
  11    5  0.12

ACGTcount: A:0.80, C:0.02, G:0.15, T:0.04


Consensus pattern (8 bp):   
AAAAGAAA

Found at i:4413 original size:17 final size:16

Alignment explanation


    Indices: 4371--4425  Score: 58
    Period size: 17  Copynumber: 3.2  Consensus size: 16

       4361 TCCCATCAGC

                            
       4371 AAAAG-AAAAAAGAAA
          1 AAAAGAAAAAAAGAAA

                  *             
       4386 ATCAAGTGAAAAAAAGAGAA
          1 A--AA-AGAAAAAAAGA-AA

                            
       4406 AAAAGAAAAAAAGAAA
          1 AAAAGAAAAAAAGAAA

                
       4422 AAAA
          1 AAAA

       4426 TGTGAAAGAA


Statistics
Matches: 33,  Mismatches: 2, Indels: 9
        0.75            0.05        0.20

Matches are distributed among these distances:
  15    1  0.03
  16    6  0.18
  17   12  0.36
  18    3  0.09
  19    8  0.24
  20    3  0.09

ACGTcount: A:0.80, C:0.02, G:0.15, T:0.04


Consensus pattern (16 bp):   
AAAAGAAAAAAAGAAA
Done.