Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022324.1 Corchorus olitorius cultivar O-4 contig22357, 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: 9145
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31


Found at i:4365 original size:14 final size:15

Alignment explanation


    Indices: 4346--4379  Score: 61
    Period size: 14  Copynumber: 2.3  Consensus size: 15

       4336 AAAGGTAGAG

                           
       4346 TTTTTGAGTTTT-TT
          1 TTTTTGAGTTTTCTT

                           
       4360 TTTTTGAGTTTTCTT
          1 TTTTTGAGTTTTCTT

                 
       4375 TTTTT
          1 TTTTT

       4380 TTGGTTTGAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  14   12  0.63
  15    7  0.37

ACGTcount: A:0.06, C:0.03, G:0.12, T:0.79


Consensus pattern (15 bp):   
TTTTTGAGTTTTCTT

Found at i:5141 original size:6 final size:6

Alignment explanation


    Indices: 5132--5183  Score: 52
    Period size: 6  Copynumber: 8.7  Consensus size: 6

       5122 AAGCTAAAAT

                              **      *       *                     
       5132 TCGAGC TCGAGC TCGAAT TCGATAC -CGAGT TCGAGC TCGAGC TCGAGC
          1 TCGAGC TCGAGC TCGAGC TCGA-GC TCGAGC TCGAGC TCGAGC TCGAGC

                
       5180 TCGA
          1 TCGA

       5184 CAGGTATATA


Statistics
Matches: 38,  Mismatches: 6, Indels: 4
        0.79            0.12        0.08

Matches are distributed among these distances:
   6   37  0.97
   7    1  0.03

ACGTcount: A:0.21, C:0.29, G:0.29, T:0.21


Consensus pattern (6 bp):   
TCGAGC

Found at i:5150 original size:18 final size:18

Alignment explanation


    Indices: 5129--5183  Score: 58
    Period size: 18  Copynumber: 3.1  Consensus size: 18

       5119 TTAAAGCTAA

                              
       5129 AATTCGAGCTCGAGCTCG
          1 AATTCGAGCTCGAGCTCG

                    *      *   
       5147 AATTCGATAC-CGAGTTCG
          1 AATTCGA-GCTCGAGCTCG

             **               
       5165 AGCTCGAGCTCGAGCTCG
          1 AATTCGAGCTCGAGCTCG

             
       5183 A
          1 A

       5184 CAGGTATATA


Statistics
Matches: 29,  Mismatches: 6, Indels: 4
        0.74            0.15        0.10

Matches are distributed among these distances:
  17    1  0.03
  18   27  0.93
  19    1  0.03

ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22


Consensus pattern (18 bp):   
AATTCGAGCTCGAGCTCG
Done.