Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019784.1 Corchorus olitorius cultivar O-4 contig19817, 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: 4252
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33


Found at i:51 original size:25 final size:24

Alignment explanation


    Indices: 1--52  Score: 61
    Period size: 25  Copynumber: 2.1  Consensus size: 24

                     *           *  
          1 AAAATCATTTAATAAAACCATTTA
          1 AAAATCATTAAATAAAACCATATA

                                      
         25 AAAATCATATAAATAAAA-CAGTATA
          1 AAAATCAT-TAAATAAAACCA-TATA

               
         50 AAA
          1 AAA

         53 CAGTTCCTCA


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  24   10  0.42
  25   14  0.58

ACGTcount: A:0.62, C:0.10, G:0.02, T:0.27


Consensus pattern (24 bp):   
AAAATCATTAAATAAAACCATATA

Found at i:3324 original size:89 final size:92

Alignment explanation


    Indices: 3208--3386  Score: 274
    Period size: 94  Copynumber: 2.0  Consensus size: 92

       3198 AGGGTAATTC

                 *                                                        ** 
       3208 TATTTTCAACTTT-A-ATA-TATGTTATGTTATAGATATGTTATAGATGTTACATCTAGCTAGCA
          1 TATTTCCAACTTTAATATATTATGTTATGTTATAGATATGTTATAGATGTTACATCTAGCTAAAA

                                       
       3270 TTGATCTTTCATTGAATATCTCTAGAA
         66 TTGATCTTTCATTGAATATCTCTAGAA

                                                        *         *          
       3297 TATTTCCAACTTTAATATATGTTATGTTATGTTATAGATATGTTTTAGATGTTATATCTAGCTAA
          1 TATTTCCAACTTTAATATA--TTATGTTATGTTATAGATATGTTATAGATGTTACATCTAGCTAA

                                     
       3362 AATTGATCTTTCATTGAATATCTCT
         64 AATTGATCTTTCATTGAATATCTCT

       3387 TCTAGAGAAG


Statistics
Matches: 80,  Mismatches: 5, Indels: 5
        0.89            0.06        0.06

Matches are distributed among these distances:
  89   12  0.15
  90    1  0.01
  91    3  0.04
  94   64  0.80

ACGTcount: A:0.31, C:0.11, G:0.12, T:0.47


Consensus pattern (92 bp):   
TATTTCCAACTTTAATATATTATGTTATGTTATAGATATGTTATAGATGTTACATCTAGCTAAAA
TTGATCTTTCATTGAATATCTCTAGAA
Done.