Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020491.1 Corchorus olitorius cultivar O-4 contig20524, 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: 6521
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.36


Found at i:608 original size:29 final size:29

Alignment explanation


    Indices: 571--629  Score: 118
    Period size: 29  Copynumber: 2.0  Consensus size: 29

        561 AAGAAACAAT

                                         
        571 TGGGTTTGGTAATTATTGTGAAGTATTGC
          1 TGGGTTTGGTAATTATTGTGAAGTATTGC

                                         
        600 TGGGTTTGGTAATTATTGTGAAGTATTGC
          1 TGGGTTTGGTAATTATTGTGAAGTATTGC

             
        629 T
          1 T

        630 ATGTTATTTA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   30  1.00

ACGTcount: A:0.20, C:0.03, G:0.31, T:0.46


Consensus pattern (29 bp):   
TGGGTTTGGTAATTATTGTGAAGTATTGC

Found at i:1188 original size:19 final size:18

Alignment explanation


    Indices: 1155--1190  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       1145 TTGAAATTAT

                              
       1155 TCTTCAATGGTCTTCAAA
          1 TCTTCAATGGTCTTCAAA

                     *        
       1173 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATGGTCTTCAA

       1191 TAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAA

Found at i:6335 original size:16 final size:17

Alignment explanation


    Indices: 6314--6345  Score: 57
    Period size: 16  Copynumber: 1.9  Consensus size: 17

       6304 GAAATTGTGT

                             
       6314 TTTATTTTTCT-TTTTC
          1 TTTATTTTTCTATTTTC

                            
       6330 TTTATTTTTCTATTTT
          1 TTTATTTTTCTATTTT

       6346 AATTTGCACT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16   11  0.73
  17    4  0.27

ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81


Consensus pattern (17 bp):   
TTTATTTTTCTATTTTC
Done.