Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012130.1 Corchorus olitorius cultivar O-4 contig12163, 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: 23036
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33


Found at i:3349 original size:19 final size:18

Alignment explanation


    Indices: 3327--3362  Score: 54
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       3317 AAGGTAATTA

                    *         
       3327 AAAAAAAATTGTTTTCAT
          1 AAAAAAAAGTGTTTTCAT

                 *            
       3345 AAAAAGAAGTGTTTTCAT
          1 AAAAAAAAGTGTTTTCAT

       3363 GATAGAGGAG


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36


Consensus pattern (18 bp):   
AAAAAAAAGTGTTTTCAT

Found at i:4233 original size:19 final size:18

Alignment explanation


    Indices: 4209--4244  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       4199 TGAAGATTTA

                               
       4209 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       4228 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       4245 ATTATTTCCA


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

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

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


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:9457 original size:6 final size:6

Alignment explanation


    Indices: 9446--9472  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

       9436 CAATATTTGC

                                           
       9446 TTTAGT TTTAGT TTTAGT TTTAGT TTT
          1 TTTAGT TTTAGT TTTAGT TTTAGT TTT

       9473 TGTATTTTAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70


Consensus pattern (6 bp):   
TTTAGT

Done.