Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017304.1 Corchorus olitorius cultivar O-4 contig17337, 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: 8814
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29


Found at i:2408 original size:15 final size:16

Alignment explanation


    Indices: 2378--2416  Score: 62
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       2368 TTACTCTGCT

                            
       2378 TTGTTTTCTAGTTTAA
          1 TTGTTTTCTAGTTTAA

                            
       2394 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTTTAA

                    
       2409 TTGCTTTT
          1 TTG-TTTT

       2417 TGTCAATCTC


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  15    9  0.41
  16   13  0.59

ACGTcount: A:0.13, C:0.08, G:0.13, T:0.67


Consensus pattern (16 bp):   
TTGTTTTCTAGTTTAA

Found at i:4290 original size:50 final size:50

Alignment explanation


    Indices: 4231--4331  Score: 175
    Period size: 50  Copynumber: 2.0  Consensus size: 50

       4221 GAGGTGTATG

                            *       *    *                    
       4231 TAGATGACATGATTGCTAAGGCCATGTAGCCAAAAGAGCACAAAGATAAT
          1 TAGATGACATGATTGCCAAGGCCAGGTAGACAAAAGAGCACAAAGATAAT

                                                              
       4281 TAGATGACATGATTGCCAAGGCCAGGTAGACAAAAGAGCACAAAGATAAT
          1 TAGATGACATGATTGCCAAGGCCAGGTAGACAAAAGAGCACAAAGATAAT

             
       4331 T
          1 T

       4332 TGAGGAAGTT


Statistics
Matches: 48,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  50   48  1.00

ACGTcount: A:0.43, C:0.16, G:0.23, T:0.19


Consensus pattern (50 bp):   
TAGATGACATGATTGCCAAGGCCAGGTAGACAAAAGAGCACAAAGATAAT

Found at i:6864 original size:17 final size:18

Alignment explanation


    Indices: 6842--6879  Score: 51
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       6832 AGAGAAGGAG

                          *   
       6842 AATAAA-CTTATCCCAAA
          1 AATAAATCTTATCCAAAA

                      *       
       6859 AATAAATCTTTTCCAAAA
          1 AATAAATCTTATCCAAAA

               
       6877 AAT
          1 AAT

       6880 TTCTTTTAAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  17    6  0.33
  18   12  0.67

ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29


Consensus pattern (18 bp):   
AATAAATCTTATCCAAAA
Done.