Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018921.1 Corchorus olitorius cultivar O-4 contig18954, 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: 10322
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.30


Found at i:4165 original size:41 final size:43

Alignment explanation


    Indices: 4069--4313  Score: 347
    Period size: 43  Copynumber: 5.8  Consensus size: 43

       4059 CCAATAACCA

                                                 *    * 
       4069 AAAGTCCCCAAACACATATATAACACATG-GGCATCTCTATTCC
          1 AAAGTCCCCAAACACATATATAACACA-GAGGCATCTATATTAC

                   *       *                           
       4112 AAAGTCCTCAAACACTTATATAACACAGAGGCATCTATA-T-C
          1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTAC

                                          *  *  *      
       4153 AAAGTCCCCAAACACATATATAACACAGAGACACCTTTATTAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTAC

                   *                                   
       4196 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATA-T-C
          1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTAC

                                        *       *      
       4237 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTAC

                   *                          
       4280 AAAGTCCTCAAACACATATATAACACAGAGGCAT
          1 AAAGTCCCCAAACACATATATAACACAGAGGCAT

       4314 TTCTCCTTAT


Statistics
Matches: 180,  Mismatches: 17, Indels: 10
        0.87            0.08        0.05

Matches are distributed among these distances:
  41   72  0.40
  42    5  0.03
  43  103  0.57

ACGTcount: A:0.42, C:0.27, G:0.10, T:0.22


Consensus pattern (43 bp):   
AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTAC

Found at i:4342 original size:84 final size:84

Alignment explanation


    Indices: 4069--4313  Score: 427
    Period size: 84  Copynumber: 2.9  Consensus size: 84

       4059 CCAATAACCA

                                       *             *                *      
       4069 AAAGTCCCCAAACACATATATAACACATGGGCATCTCTATTCCAAAGTCCTCAAACACTTATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA

                               
       4134 ACACAGAGGCATCTATATC
         66 ACACAGAGGCATCTATATC

                                        * *  *  *                            
       4153 AAAGTCCCCAAACACATATATAACACAGAGACACCTTTATTACAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA

                               
       4218 ACACAGAGGCATCTATATC
         66 ACACAGAGGCATCTATATC

                                                                             
       4237 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA

                        
       4302 ACACAGAGGCAT
         66 ACACAGAGGCAT

       4314 TTCTCCTTAT


Statistics
Matches: 150,  Mismatches: 11, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  84  150  1.00

ACGTcount: A:0.42, C:0.27, G:0.10, T:0.22


Consensus pattern (84 bp):   
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC

Found at i:4435 original size:2 final size:2

Alignment explanation


    Indices: 4423--4456  Score: 61
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       4413 ACCAAATTCC

                                                                
       4423 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       4457 CCCCAAGCCA


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   30  0.97

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Done.