Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015043.1 Corchorus olitorius cultivar O-4 contig15076, 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: 5385
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35


Found at i:3336 original size:14 final size:15

Alignment explanation


    Indices: 3317--3350  Score: 52
    Period size: 14  Copynumber: 2.3  Consensus size: 15

       3307 AACTACAACT

                        *  
       3317 AAAAATTGA-GGGAA
          1 AAAAATTGACGGCAA

                           
       3331 AAAAATTGACGGCAA
          1 AAAAATTGACGGCAA

                 
       3346 AAAAA
          1 AAAAA

       3351 AAAAACTACA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  14    9  0.50
  15    9  0.50

ACGTcount: A:0.62, C:0.06, G:0.21, T:0.12


Consensus pattern (15 bp):   
AAAAATTGACGGCAA

Found at i:5194 original size:20 final size:22

Alignment explanation


    Indices: 5158--5197  Score: 66
    Period size: 20  Copynumber: 1.9  Consensus size: 22

       5148 GGAGTTCGTG

                                  
       5158 TTTGAAGACCATTTGAAGATAA
          1 TTTGAAGACCATTTGAAGATAA

                                
       5180 TTTGAAGA-C-TTTGAAGAT
          1 TTTGAAGACCATTTGAAGAT

       5198 TTATTTCAAG


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20    9  0.50
  21    1  0.06
  22    8  0.44

ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35


Consensus pattern (22 bp):   
TTTGAAGACCATTTGAAGATAA

Found at i:5208 original size:21 final size:20

Alignment explanation


    Indices: 5169--5208  Score: 53
    Period size: 21  Copynumber: 1.9  Consensus size: 20

       5159 TTGAAGACCA

                          *     
       5169 TTTGAAGATAATTTGAAGAC
          1 TTTGAAGATAATTTCAAGAC

                      *         
       5189 TTTGAAGATTTATTTCAAGA
          1 TTTGAAGA-TAATTTCAAGA

       5209 GCAAGAATTG


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  20    8  0.47
  21    9  0.53

ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40


Consensus pattern (20 bp):   
TTTGAAGATAATTTCAAGAC
Done.