Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010037.1 Corchorus olitorius cultivar O-4 contig10069, 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: 6102
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34


Found at i:2121 original size:21 final size:21

Alignment explanation


    Indices: 2083--2127  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       2073 ACTGCTCTAA

                       * *     * 
       2083 TAATTTCATCTGTTCAGTATC
          1 TAATTTCATCTATACAGTACC

                  *              
       2104 TAATTTGATCTATACAGTACC
          1 TAATTTCATCTATACAGTACC

               
       2125 TAA
          1 TAA

       2128 ACAATGTCAA


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42


Consensus pattern (21 bp):   
TAATTTCATCTATACAGTACC

Found at i:2640 original size:20 final size:20

Alignment explanation


    Indices: 2615--2653  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       2605 AAATTCTAAA

                  *      *      
       2615 AAAAATTATTTATTTTTATC
          1 AAAAATGATTTATATTTATC

                               
       2635 AAAAATGATTTATATTTAT
          1 AAAAATGATTTATATTTAT

       2654 TTTATGGATA


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

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51


Consensus pattern (20 bp):   
AAAAATGATTTATATTTATC

Found at i:5034 original size:11 final size:13

Alignment explanation


    Indices: 5006--5037  Score: 50
    Period size: 11  Copynumber: 2.6  Consensus size: 13

       4996 TATGTGAATA

                         
       5006 TATTTATATAAGT
          1 TATTTATATAAGT

                         
       5019 TATTTA-ATAA-T
          1 TATTTATATAAGT

                    
       5030 TATTTATA
          1 TATTTATA

       5038 GTCGTAAATA


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  11    7  0.39
  12    5  0.28
  13    6  0.33

ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56


Consensus pattern (13 bp):   
TATTTATATAAGT

Found at i:5440 original size:4 final size:4

Alignment explanation


    Indices: 5433--5467  Score: 61
    Period size: 4  Copynumber: 8.8  Consensus size: 4

       5423 AGAAGAAAAA

                                                 *     
       5433 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAGG AAA
          1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA

       5468 ATGGTAGGAA


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   4   29  1.00

ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00


Consensus pattern (4 bp):   
AAAG

Done.