Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016534.1 Corchorus olitorius cultivar O-4 contig16567, 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: 7647
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34


Found at i:1105 original size:18 final size:19

Alignment explanation


    Indices: 1084--1122  Score: 71
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       1074 TTAAAAAATC

                               
       1084 AAAAT-ATAATGGACTGAA
          1 AAAATGATAATGGACTGAA

                               
       1102 AAAATGATAATGGACTGAA
          1 AAAATGATAATGGACTGAA

              
       1121 AA
          1 AA

       1123 TTTCAAAATA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  18    5  0.25
  19   15  0.75

ACGTcount: A:0.56, C:0.05, G:0.18, T:0.21


Consensus pattern (19 bp):   
AAAATGATAATGGACTGAA

Found at i:2474 original size:2 final size:2

Alignment explanation


    Indices: 2467--2500  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       2457 ATTATAGGGT

                                                              
       2467 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       2501 GGTCCGTGCC


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:2774 original size:16 final size:16

Alignment explanation


    Indices: 2753--2801  Score: 57
    Period size: 16  Copynumber: 3.1  Consensus size: 16

       2743 TTGCCACAAT

                            
       2753 TTTTTTAATAATTGAA
          1 TTTTTTAATAATTGAA

                    *  *    
       2769 TTTTTTAAAAAAT--A
          1 TTTTTTAATAATTGAA

                             
       2783 TATTTTTAATAATTGAA
          1 T-TTTTTAATAATTGAA

              
       2800 TT
          1 TT

       2802 GTATTTGTAA


Statistics
Matches: 26,  Mismatches: 4, Indels: 6
        0.72            0.11        0.17

Matches are distributed among these distances:
  14    2  0.08
  15   10  0.38
  16   12  0.46
  17    2  0.08

ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55


Consensus pattern (16 bp):   
TTTTTTAATAATTGAA

Found at i:5269 original size:33 final size:33

Alignment explanation


    Indices: 5227--5292  Score: 132
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       5217 TTGTAAAAGT

                                             
       5227 CACCAATCCCAAACACACATTTTACATTGTAAA
          1 CACCAATCCCAAACACACATTTTACATTGTAAA

                                             
       5260 CACCAATCCCAAACACACATTTTACATTGTAAA
          1 CACCAATCCCAAACACACATTTTACATTGTAAA

       5293 AGTAATACCA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   33  1.00

ACGTcount: A:0.42, C:0.30, G:0.03, T:0.24


Consensus pattern (33 bp):   
CACCAATCCCAAACACACATTTTACATTGTAAA
Done.