Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021350.1 Corchorus olitorius cultivar O-4 contig21383, 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: 13715
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31


Found at i:4007 original size:2 final size:2

Alignment explanation


    Indices: 4002--4032  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       3992 CCCCTGAAAC

                                                          
       4002 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       4033 ATTGTTGAAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:9955 original size:6 final size:6

Alignment explanation


    Indices: 9946--9984  Score: 69
    Period size: 6  Copynumber: 6.5  Consensus size: 6

       9936 GACGACGCAT

                                 *                       
       9946 CTGCGG CTGCGG CTGCGG ATGCGG CTGCGG CTGCGG CTG
          1 CTGCGG CTGCGG CTGCGG CTGCGG CTGCGG CTGCGG CTG

       9985 ATCCATTATT


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   6   31  1.00

ACGTcount: A:0.03, C:0.31, G:0.49, T:0.18


Consensus pattern (6 bp):   
CTGCGG

Found at i:10519 original size:5 final size:5

Alignment explanation


    Indices: 10511--10537  Score: 54
    Period size: 5  Copynumber: 5.4  Consensus size: 5

      10501 AATCAGAGGG

                                            
      10511 GAAAA GAAAA GAAAA GAAAA GAAAA GA
          1 GAAAA GAAAA GAAAA GAAAA GAAAA GA

      10538 GGAAAGTTGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   22  1.00

ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00


Consensus pattern (5 bp):   
GAAAA

Found at i:12847 original size:17 final size:17

Alignment explanation


    Indices: 12819--12869  Score: 61
    Period size: 17  Copynumber: 3.0  Consensus size: 17

      12809 AAAGATTTGG

                  *          
      12819 AAAACATTACTAGTCAT
          1 AAAACAGTACTAGTCAT

                               
      12836 AAAAC-GTGACTAGTTC-T
          1 AAAACAGT-ACTAG-TCAT

                             
      12853 AAAACAGTACTAGTCAT
          1 AAAACAGTACTAGTCAT

      12870 GTGGTATGAG


Statistics
Matches: 29,  Mismatches: 1, Indels: 8
        0.76            0.03        0.21

Matches are distributed among these distances:
  16    3  0.10
  17   22  0.76
  18    4  0.14

ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27


Consensus pattern (17 bp):   
AAAACAGTACTAGTCAT
Done.