Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001171.1 Corchorus olitorius cultivar O-4 contig01171, 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, 853

Length: 1422
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32


Found at i:1270 original size:41 final size:41

Alignment explanation


    Indices: 1168--1422  Score: 275
    Period size: 41  Copynumber: 6.1  Consensus size: 41

       1158 CAATAACCAA

                                        *      *        
       1168 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTAT-TCC
          1 AAAGTCCCCAAACACATATATAACACAGAGGC-A-CCTATAT-C

                    *                                 
       1211 AAAAGTCCTCAAACACATATATAACACAGAGGCACCTATATC
          1 -AAAGTCCCCAAACACATATATAACACAGAGGCACCTATATC

            *                           *   *   *      
       1253 CAAGTCCCCAAACAC--ATATAACACAGGGGCGCCTTTATTAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCACCTATA-T-C

                   *                         *       
       1294 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATATC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCACCTATATC

                                        *               
       1335 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTAT-TAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGC-AC-CTATAT-C

                   *                 *       **      
       1378 AAAGTCCTCAAACACATATATAACATAGAGGCATTTATATC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCACCTATATC

                
       1419 AAAG
          1 AAAG


Statistics
Matches: 180,  Mismatches: 22, Indels: 21
        0.81            0.10        0.09

Matches are distributed among these distances:
  39   19  0.11
  40    1  0.01
  41   66  0.37
  42   10  0.06
  43   54  0.30
  44   30  0.17

ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21


Consensus pattern (41 bp):   
AAAGTCCCCAAACACATATATAACACAGAGGCACCTATATC

Found at i:1382 original size:84 final size:84

Alignment explanation


    Indices: 1168--1422  Score: 406
    Period size: 84  Copynumber: 3.0  Consensus size: 84

       1158 CAATAACCAA

                                              *      *                       
       1168 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTCCAAAAGTCCTCAAACACATATAT
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT

                        *       
       1233 AACACAGAGGCACCTATATC
         65 AACACAGAGGCATCTATATC

            *                               **  *                            
       1253 CAAGTCCCCAAACAC--ATATAACACAGGGGCGCCTTTATTACAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA

                               
       1316 ACACAGAGGCATCTATATC
         66 ACACAGAGGCATCTATATC

                                                                             
       1335 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA

               *        *      
       1400 ACATAGAGGCATTTATATC
         66 ACACAGAGGCATCTATATC

                
       1419 AAAG
          1 AAAG


Statistics
Matches: 155,  Mismatches: 13, Indels: 5
        0.90            0.08        0.03

Matches are distributed among these distances:
  82   54  0.35
  83   21  0.14
  84   66  0.43
  85   14  0.09

ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21


Consensus pattern (84 bp):   
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Done.