Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019850.1 Corchorus olitorius cultivar O-4 contig19883, 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: 9682
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:268 original size:17 final size:17

Alignment explanation


    Indices: 243--277  Score: 61
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        233 TAACCCTCGA

                *            
        243 CTCTTCTCTTCTTCTTC
          1 CTCTCCTCTTCTTCTTC

                             
        260 CTCTCCTCTTCTTCTTC
          1 CTCTCCTCTTCTTCTTC

             
        277 C
          1 C

        278 CTCGACGGCT


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

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54


Consensus pattern (17 bp):   
CTCTCCTCTTCTTCTTC

Found at i:3739 original size:10 final size:10

Alignment explanation


    Indices: 3726--3783  Score: 50
    Period size: 10  Copynumber: 6.0  Consensus size: 10

       3716 GAAAAAAAAA

                      
       3726 CTAATTAAAT
          1 CTAATTAAAT

                    * 
       3736 CTAATTAAGT
          1 CTAATTAAAT

                     *
       3746 CTAATTAAAC
          1 CTAATTAAAT

                 *     
       3756 CTTAAAT-AAT
          1 C-TAATTAAAT

                *     
       3766 CTAAATAAA-
          1 CTAATTAAAT

                      
       3775 -TAATTAAAT
          1 CTAATTAAAT

       3784 ACTAGCCCTA


Statistics
Matches: 39,  Mismatches: 6, Indels: 7
        0.75            0.12        0.13

Matches are distributed among these distances:
   8    7  0.18
   9    5  0.13
  10   23  0.59
  11    4  0.10

ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36


Consensus pattern (10 bp):   
CTAATTAAAT

Found at i:5412 original size:38 final size:37

Alignment explanation


    Indices: 5370--5442  Score: 103
    Period size: 38  Copynumber: 1.9  Consensus size: 37

       5360 CTCTAGAATT

                                                   
       5370 TTCTTTTAG-GTTTAGCGTTTTTAATTAAAAAAATTTTC
          1 TTCTTTT-GTGTTTAGCGTTTTTAA-TAAAAAAATTTTC

                         *        *            
       5408 TTCTTTTGTGTTTTGCGTTTTTGATAAAAAAATTT
          1 TTCTTTTGTGTTTAGCGTTTTTAATAAAAAAATTT

       5443 AATTTTTGCG


Statistics
Matches: 32,  Mismatches: 2, Indels: 3
        0.86            0.05        0.08

Matches are distributed among these distances:
  37   12  0.38
  38   20  0.62

ACGTcount: A:0.26, C:0.07, G:0.12, T:0.55


Consensus pattern (37 bp):   
TTCTTTTGTGTTTAGCGTTTTTAATAAAAAAATTTTC
Done.