Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021621.1 Corchorus olitorius cultivar O-4 contig21654, 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: 23334
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31


Found at i:9428 original size:15 final size:15

Alignment explanation


    Indices: 9408--9444  Score: 56
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       9398 TTATTGTTCA

                           
       9408 CACCATTGTTATTCG
          1 CACCATTGTTATTCG

                      *  * 
       9423 CACCATTGTTGTTTG
          1 CACCATTGTTATTCG

                   
       9438 CACCATT
          1 CACCATT

       9445 CACCCTAGCA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  15   20  1.00

ACGTcount: A:0.19, C:0.27, G:0.14, T:0.41


Consensus pattern (15 bp):   
CACCATTGTTATTCG

Found at i:10373 original size:48 final size:46

Alignment explanation


    Indices: 10295--10402  Score: 135
    Period size: 48  Copynumber: 2.3  Consensus size: 46

      10285 AAGGAACAAT

                                    **              *        
      10295 AAAAAGTAAAAGATCAATTTTATCTTAAAAATTGAGAAAATGTGCAAGG
          1 AAAAA-TAAAAGATCAATTTTATCGCAAAAATTGAGAAAAAGTGC-A-G

                                * *                       
      10344 AAAAATAAAAGATCAATTTTGTGGCAAAAATTGAGAAAAAGTGCAG
          1 AAAAATAAAAGATCAATTTTATCGCAAAAATTGAGAAAAAGTGCAG

                *        
      10390 AAAAGTAAAAGAT
          1 AAAAATAAAAGAT

      10403 TGCTTTGAGT


Statistics
Matches: 53,  Mismatches: 6, Indels: 3
        0.85            0.10        0.05

Matches are distributed among these distances:
  46   13  0.25
  47    1  0.02
  48   34  0.64
  49    5  0.09

ACGTcount: A:0.54, C:0.06, G:0.18, T:0.23


Consensus pattern (46 bp):   
AAAAATAAAAGATCAATTTTATCGCAAAAATTGAGAAAAAGTGCAG

Found at i:12315 original size:9 final size:10

Alignment explanation


    Indices: 12295--12319  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

      12285 CGTGAATGAC

                      
      12295 AAAATACAAA
          1 AAAATACAAA

                      
      12305 AAAATACAAA
          1 AAAATACAAA

                 
      12315 AAAAT
          1 AAAAT

      12320 TTAATGAAGC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12


Consensus pattern (10 bp):   
AAAATACAAA

Found at i:14324 original size:21 final size:21

Alignment explanation


    Indices: 14300--14339  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      14290 GATGCCAAAG

                    *            
      14300 ATGCCATTTGATCCAATGAAT
          1 ATGCCATTAGATCCAATGAAT

                      *        
      14321 ATGCCATTAGGTCCAATGA
          1 ATGCCATTAGATCCAATGA

      14340 CAAGAGCAAG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30


Consensus pattern (21 bp):   
ATGCCATTAGATCCAATGAAT

Found at i:15673 original size:21 final size:21

Alignment explanation


    Indices: 15647--15687  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      15637 TTGAAGCCCT

                                  
      15647 ATTGGAGAC-AAGTGGTACTAA
          1 ATTGGA-ACTAAGTGGTACTAA

                  *             
      15668 ATTGGATCTAAGTGGTACTA
          1 ATTGGAACTAAGTGGTACTA

      15688 GGGTTTCTAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  20    1  0.06
  21   17  0.94

ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29


Consensus pattern (21 bp):   
ATTGGAACTAAGTGGTACTAA
Done.