Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010537.1 Corchorus olitorius cultivar O-4 contig10569, 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: 4367
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34


Found at i:894 original size:45 final size:45

Alignment explanation


    Indices: 830--952  Score: 198
    Period size: 42  Copynumber: 2.8  Consensus size: 45

        820 AGCAACAATT

                 *  *                                    
        830 AATATCAGGTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
          1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG

                                                        *
        875 AATATTAGCTTTATTTTGATGAATTACCT--AGA-GGAGGAGTAT
          1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG

                                                
        917 AATATTAGCTTTATTTTGATGAATTACCTAGAGATG
          1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATG

        953 AAGTAGAATT


Statistics
Matches: 72,  Mismatches: 3, Indels: 6
        0.89            0.04        0.07

Matches are distributed among these distances:
  42   38  0.53
  43    3  0.04
  44    3  0.04
  45   28  0.39

ACGTcount: A:0.33, C:0.07, G:0.22, T:0.37


Consensus pattern (45 bp):   
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG

Found at i:2002 original size:18 final size:18

Alignment explanation


    Indices: 1958--2010  Score: 52
    Period size: 18  Copynumber: 2.8  Consensus size: 18

       1948 TATGTAATTA

                             *  
       1958 TATTTCTTAATAATATTTAT
          1 TATTT-TTAATAAT-TTAAT

            *                  
       1978 AATTTTTTAATAATTTAAT
          1 TA-TTTTTAATAATTTAAT

                  *       
       1997 TATTTTCAATAATT
          1 TATTTTTAATAATT

       2011 AAAACCTAAA


Statistics
Matches: 28,  Mismatches: 4, Indels: 4
        0.78            0.11        0.11

Matches are distributed among these distances:
  18   11  0.39
  19    5  0.18
  20    9  0.32
  21    3  0.11

ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58


Consensus pattern (18 bp):   
TATTTTTAATAATTTAAT

Found at i:2323 original size:45 final size:45

Alignment explanation


    Indices: 2250--2387  Score: 213
    Period size: 45  Copynumber: 3.0  Consensus size: 45

       2240 GCCTTGGCCT

                                  *                        
       2250 AGTTTTCTTTAATTTTTTTCCCTAAAGTATTGGACTTCTTTTAAGTG
          1 AGTTTTC-TT-ATTTTTTTCCCCAAAGTATTGGACTTCTTTTAAGTG

                                 *       *               
       2297 AGTTTTCTTATTTTTTTCCCCCAAGTATTAGACTTCTTTTAAGTG
          1 AGTTTTCTTATTTTTTTCCCCAAAGTATTGGACTTCTTTTAAGTG

                    *            *                       
       2342 AGTTTTCTAATTTTTTTCCCCTAAGTATTGGACTTCTTTTAAGTG
          1 AGTTTTCTTATTTTTTTCCCCAAAGTATTGGACTTCTTTTAAGTG

             
       2387 A
          1 A

       2388 TTTAATTTAA


Statistics
Matches: 85,  Mismatches: 6, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  45   76  0.89
  46    2  0.02
  47    7  0.08

ACGTcount: A:0.21, C:0.15, G:0.12, T:0.51


Consensus pattern (45 bp):   
AGTTTTCTTATTTTTTTCCCCAAAGTATTGGACTTCTTTTAAGTG

Found at i:3407 original size:15 final size:15

Alignment explanation


    Indices: 3387--3428  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       3377 ACAGAGATTG

                   *       
       3387 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       3402 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                *       
       3417 ACTAAAAAACAA
          1 AC-AGAAAACAA

       3429 ACCAGAGTAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  15   16  0.67
  16    8  0.33

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Done.