Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024138.1 Corchorus olitorius cultivar O-4 contig24171, 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: 5795
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33


Found at i:622 original size:15 final size:16

Alignment explanation


    Indices: 592--632  Score: 75
    Period size: 15  Copynumber: 2.6  Consensus size: 16

        582 TTACTTTGCT

                            
        592 TTGTTTTCTAGTTTAA
          1 TTGTTTTCTAGTTTAA

                            
        608 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTTTAA

                      
        623 TTGTTTTCTA
          1 TTGTTTTCTA

        633 TCAACCTCTG


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  15   15  0.62
  16    9  0.38

ACGTcount: A:0.15, C:0.07, G:0.12, T:0.66


Consensus pattern (16 bp):   
TTGTTTTCTAGTTTAA

Found at i:1121 original size:27 final size:28

Alignment explanation


    Indices: 1083--1137  Score: 94
    Period size: 27  Copynumber: 2.0  Consensus size: 28

       1073 TTTGTTTTGT

                                        
       1083 GTTTTTTGCGTTTTT-CTAAAAAAAAAA
          1 GTTTTTTGCGTTTTTACTAAAAAAAAAA

                            *           
       1110 GTTTTTTGCGTTTTTATTAAAAAAAAAA
          1 GTTTTTTGCGTTTTTACTAAAAAAAAAA

       1138 AATCTTTTCT


Statistics
Matches: 26,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  27   15  0.58
  28   11  0.42

ACGTcount: A:0.38, C:0.05, G:0.11, T:0.45


Consensus pattern (28 bp):   
GTTTTTTGCGTTTTTACTAAAAAAAAAA

Found at i:5058 original size:11 final size:11

Alignment explanation


    Indices: 5042--5089  Score: 50
    Period size: 11  Copynumber: 4.7  Consensus size: 11

       5032 GAAGTTCGTG

                       
       5042 TTTGAAGACCA
          1 TTTGAAGACCA

                    ** 
       5053 TTTGAAGATAA
          1 TTTGAAGACCA

                       
       5064 TTTGAAGA-C-
          1 TTTGAAGACCA

                       
       5073 -TTGAAGACCA
          1 TTTGAAGACCA

                    
       5083 -TTGAAGA
          1 TTTGAAGA

       5090 TTTATTTCAA


Statistics
Matches: 32,  Mismatches: 3, Indels: 5
        0.80            0.08        0.12

Matches are distributed among these distances:
   8    7  0.22
   9    1  0.03
  10    7  0.22
  11   17  0.53

ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29


Consensus pattern (11 bp):   
TTTGAAGACCA
Done.