Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01003925.1 Corchorus olitorius cultivar O-4 contig03935, 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: 2008
ACGTcount: A:0.18, C:0.30, G:0.34, T:0.18


Found at i:485 original size:4 final size:4

Alignment explanation


    Indices: 476--509  Score: 50
    Period size: 4  Copynumber: 8.5  Consensus size: 4

        466 CAAGTATAGC

                        *               *             
        476 AACA AACA AAGA AACA AACA AACT AACA AACA AA
          1 AACA AACA AACA AACA AACA AACA AACA AACA AA

        510 TAAAAGGCGG


Statistics
Matches: 26,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
   4   26  1.00

ACGTcount: A:0.74, C:0.21, G:0.03, T:0.03


Consensus pattern (4 bp):   
AACA

Found at i:1702 original size:23 final size:23

Alignment explanation


    Indices: 1672--1752  Score: 87
    Period size: 23  Copynumber: 3.6  Consensus size: 23

       1662 CGCTCCGCAT

                            ** *    
       1672 CGGCGATAGACGAGTTGGGGAC-A
          1 CGGCGATAGACGAG-TCAGAACTA

                                   
       1695 CGGCGATAGACGAGTCAGAACTA
          1 CGGCGATAGACGAGTCAGAACTA

                             *      
       1718 CGGCGATAGACGAG--AAAACTGA
          1 CGGCGATAGACGAGTCAGAACT-A

                         
       1740 CGGCGATAGACGA
          1 CGGCGATAGACGA

       1753 TGACACGCGA


Statistics
Matches: 52,  Mismatches: 4, Indels: 5
        0.85            0.07        0.08

Matches are distributed among these distances:
  21    5  0.10
  22   18  0.35
  23   29  0.56

ACGTcount: A:0.33, C:0.20, G:0.36, T:0.11


Consensus pattern (23 bp):   
CGGCGATAGACGAGTCAGAACTA

Found at i:1990 original size:17 final size:17

Alignment explanation


    Indices: 1968--2001  Score: 68
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       1958 AGTCCTTTTC

                             
       1968 GACGGCGATAGACGAGT
          1 GACGGCGATAGACGAGT

                             
       1985 GACGGCGATAGACGAGT
          1 GACGGCGATAGACGAGT

       2002 CATCAGG


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.29, C:0.18, G:0.41, T:0.12


Consensus pattern (17 bp):   
GACGGCGATAGACGAGT
Done.