Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020988.1 Corchorus olitorius cultivar O-4 contig21021, 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: 3714
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21


Found at i:2449 original size:43 final size:42

Alignment explanation


    Indices: 2401--2730  Score: 454
    Period size: 43  Copynumber: 7.8  Consensus size: 42

       2391 CAATAGCCAA

                                        *    *  *      
       2401 AAAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTA-TAC

                   *                            *     
       2444 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATAT-C
          1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATAC

                                        *    *         
       2485 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTACTAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTA-TAC

                     *                            *     
       2528 AAAGTCCTCAAACACACATATATAACACAGAGGCATCTATAT-C
          1 AAAGTCC-CCAA-ACACATATATAACACAGAGGCATCTCTATAC

                                             *         
       2571 AAAGTCCCCAAACACATATATAACACAGAGGCAACTCTATTAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTA-TAC

                   *                                   
       2614 AAAGTCCTCAAACACATATATAACACAGAGGCAT-T-TATATC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATA-C

                                                       
       2655 AAAGT-CCCAAACACATATATAACACAGAGGCATCTCTATTAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTA-TAC

                   *                          
       2697 AAAGTCCTCAAACACATATATAACACAGAGGCAT
          1 AAAGTCCCCAAACACATATATAACACAGAGGCAT

       2731 TTCTCCTTAT


Statistics
Matches: 257,  Mismatches: 19, Indels: 22
        0.86            0.06        0.07

Matches are distributed among these distances:
  40   29  0.11
  41   71  0.28
  42   15  0.06
  43  113  0.44
  44    4  0.02
  45   25  0.10

ACGTcount: A:0.43, C:0.26, G:0.10, T:0.20


Consensus pattern (42 bp):   
AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATAC

Found at i:2567 original size:86 final size:84

Alignment explanation


    Indices: 2401--2730  Score: 572
    Period size: 84  Copynumber: 3.9  Consensus size: 84

       2391 CAATAGCCAA

                                        *    *  *                            
       2401 AAAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTACAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGAGGCAACTCTATTACAAAGTCCTCAAACACATATATA

                               
       2466 ACACAGAGGCATCTATATC
         66 ACACAGAGGCATCTATATC

                                        *          *                         
       2485 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTACTACAAAGTCCTCAAACACACATATA
          1 AAAGTCCCCAAACACATATATAACACAGAGGCAACTCTATTACAAAGTCCTC-AA-ACACATATA

                                 
       2550 TAACACAGAGGCATCTATATC
         64 TAACACAGAGGCATCTATATC

                                                                             
       2571 AAAGTCCCCAAACACATATATAACACAGAGGCAACTCTATTACAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGAGGCAACTCTATTACAAAGTCCTCAAACACATATATA

                        *      
       2636 ACACAGAGGCATTTATATC
         66 ACACAGAGGCATCTATATC

                                             *                               
       2655 AAAGT-CCCAAACACATATATAACACAGAGGCATCTCTATTACAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGAGGCAACTCTATTACAAAGTCCTCAAACACATATATA

                        
       2719 ACACAGAGGCAT
         66 ACACAGAGGCAT

       2731 TTCTCCTTAT


Statistics
Matches: 237,  Mismatches: 7, Indels: 5
        0.95            0.03        0.02

Matches are distributed among these distances:
  83   70  0.30
  84   83  0.35
  85    4  0.02
  86   80  0.34

ACGTcount: A:0.43, C:0.26, G:0.10, T:0.20


Consensus pattern (84 bp):   
AAAGTCCCCAAACACATATATAACACAGAGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Done.