Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015357.1 Corchorus olitorius cultivar O-4 contig15390, 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: 4491
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28


Found at i:49 original size:23 final size:25

Alignment explanation


    Indices: 5--55  Score: 63
    Period size: 23  Copynumber: 2.1  Consensus size: 25

          1 AAGT

                                     
          5 TTTGTGTTTTGCGTCAAGAAAAA-A
          1 TTTGTGTTTTGCGTCAAGAAAAATA

                          *           
         29 TTTGT-TTTTGCGTTATA-AAAAATA
          1 TTTGTGTTTTGCGTCA-AGAAAAATA

               
         53 TTT
          1 TTT

         56 TCTTTATTTC


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  23   14  0.58
  24   10  0.42

ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47


Consensus pattern (25 bp):   
TTTGTGTTTTGCGTCAAGAAAAATA

Found at i:50 original size:24 final size:24

Alignment explanation


    Indices: 5--55  Score: 59
    Period size: 24  Copynumber: 2.1  Consensus size: 24

          1 AAGT

                             *      
          5 TTTGTGTTTTGCGTCAAGAAAAAA
          1 TTTGTGTTTTGCGTCAAAAAAAAA

                          *        * 
         29 TTTGT-TTTTGCGTTATAAAAAATA
          1 TTTGTGTTTTGCGTCA-AAAAAAAA

               
         53 TTT
          1 TTT

         56 TCTTTATTTC


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  23    9  0.39
  24   14  0.61

ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47


Consensus pattern (24 bp):   
TTTGTGTTTTGCGTCAAAAAAAAA

Found at i:130 original size:16 final size:16

Alignment explanation


    Indices: 111--144  Score: 59
    Period size: 16  Copynumber: 2.1  Consensus size: 16

        101 CTACTAACAA

                            
        111 TTTTTCTTTTGAGTTT
          1 TTTTTCTTTTGAGTTT

                 *          
        127 TTTTTTTTTTGAGTTT
          1 TTTTTCTTTTGAGTTT

              
        143 TT
          1 TT

        145 CTAGGAAGCT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   17  1.00

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


Consensus pattern (16 bp):   
TTTTTCTTTTGAGTTT
Done.