Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012816.1 Corchorus olitorius cultivar O-4 contig12849, 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: 12893
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23


Found at i:4003 original size:205 final size:205

Alignment explanation


    Indices: 3651--4062  Score: 797
    Period size: 205  Copynumber: 2.0  Consensus size: 205

       3641 AATAAGATGC

                                                     *                       
       3651 TGCGTGGACTTCAGAGACCTGAACAAAGCGTGTCCCAAAGATGATTTTCCACCGCCAAACATGGA
          1 TGCGTGGACTTCAGAGACCTGAACAAAGCGTGTCCCAAAGACGATTTTCCACCGCCAAACATGGA

                                                                             
       3716 TGTCCTCATTGATTCCACGGCAGGACATGCCATGTTCTCCTTCATGGACGGCTTTAGTGGTTATA
         66 TGTCCTCATTGATTCCACGGCAGGACATGCCATGTTCTCCTTCATGGACGGCTTTAGTGGTTATA

                                                  *                          
       3781 ATCAGATCAAGATGACCCAAAAGGATGCTGAGAAGACAGCATTCAGGACACCCATCAGCAACTTC
        131 ATCAGATCAAGATGACCCAAAAGGATGCTGAGAAGACAACATTCAGGACACCCATCAGCAACTTC

                      
       3846 TATTACACGG
        196 TATTACACGG

                                                                             
       3856 TGCGTGGACTTCAGAGACCTGAACAAAGCGTGTCCCAAAGACGATTTTCCACCGCCAAACATGGA
          1 TGCGTGGACTTCAGAGACCTGAACAAAGCGTGTCCCAAAGACGATTTTCCACCGCCAAACATGGA

                                                                             
       3921 TGTCCTCATTGATTCCACGGCAGGACATGCCATGTTCTCCTTCATGGACGGCTTTAGTGGTTATA
         66 TGTCCTCATTGATTCCACGGCAGGACATGCCATGTTCTCCTTCATGGACGGCTTTAGTGGTTATA

                                                                    *        
       3986 ATCAGATCAAGATGACCCAAAAGGATGCTGAGAAGACAACATTCAGGACACCCATCGGCAACTTC
        131 ATCAGATCAAGATGACCCAAAAGGATGCTGAGAAGACAACATTCAGGACACCCATCAGCAACTTC

                      
       4051 TATTACACGG
        196 TATTACACGG

              
       4061 TG
          1 TG

       4063 ATGCCCTTTG


Statistics
Matches: 204,  Mismatches: 3, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 205  204  1.00

ACGTcount: A:0.29, C:0.25, G:0.22, T:0.23


Consensus pattern (205 bp):   
TGCGTGGACTTCAGAGACCTGAACAAAGCGTGTCCCAAAGACGATTTTCCACCGCCAAACATGGA
TGTCCTCATTGATTCCACGGCAGGACATGCCATGTTCTCCTTCATGGACGGCTTTAGTGGTTATA
ATCAGATCAAGATGACCCAAAAGGATGCTGAGAAGACAACATTCAGGACACCCATCAGCAACTTC
TATTACACGG

Found at i:12236 original size:43 final size:41

Alignment explanation


    Indices: 12175--12503  Score: 403
    Period size: 41  Copynumber: 7.8  Consensus size: 41

      12165 CAATAGCCAA

                                        *              
      12175 AAAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCA-CTTTA-TAC

                   *                           *      
      12218 AAAGTCCTCAAACACATATATAACACAGAGGCA-TCTATATC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCACTTTATA-C

                                        *       *      
      12259 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTACTAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGC-ACTTTA-TAC

                   *                      *     *     
      12302 AAAGTCCTCAAACACATATATAACACAGAGACATCTGTAT-C
          1 AAAGTCCCCAAACACATATATAACACAGAGGCA-CTTTATAC

                                        *       *      
      12343 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGC-ACTTTA-TAC

                   *                                  
      12386 AAAGTCCTCAAACACATATATAACACAGAGGCA-TTTATATC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCACTTTATA-C

                                        *    *         
      12427 AAAGTCCCCAAACACATATATAACACAGGGGCATTTCTATTAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCACTT-TA-TAC

                    *                         
      12470 AAAAGTCCTCAAACACATATATAACACAGAGGCA
          1 -AAAGTCCCCAAACACATATATAACACAGAGGCA

      12504 TTTCTCCTTA


Statistics
Matches: 253,  Mismatches: 20, Indels: 25
        0.85            0.07        0.08

Matches are distributed among these distances:
  40    4  0.02
  41  103  0.41
  42    8  0.03
  43  103  0.41
  44   35  0.14

ACGTcount: A:0.43, C:0.26, G:0.11, T:0.20


Consensus pattern (41 bp):   
AAAGTCCCCAAACACATATATAACACAGAGGCACTTTATAC

Found at i:12272 original size:84 final size:84

Alignment explanation


    Indices: 12175--12504  Score: 579
    Period size: 84  Copynumber: 3.9  Consensus size: 84

      12165 CAATAGCCAA

                                             *  *                            
      12175 AAAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTACAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA

                               
      12240 ACACAGAGGCATCTATATC
         66 ACACAGAGGCATCTATATC

                                                   *                         
      12259 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTACTACAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA

                    *     *    
      12324 ACACAGAGACATCTGTATC
         66 ACACAGAGGCATCTATATC

                                                                             
      12343 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA

                        *      
      12408 ACACAGAGGCATTTATATC
         66 ACACAGAGGCATCTATATC

                                             **                              
      12427 AAAGTCCCCAAACACATATATAACACAGGGGCATTTCTATTACAAAAGTCCTCAAACACATATAT
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT

                         
      12492 AACACAGAGGCAT
         65 AACACAGAGGCAT

      12505 TTCTCCTTAT


Statistics
Matches: 234,  Mismatches: 11, Indels: 1
        0.95            0.04        0.00

Matches are distributed among these distances:
  84  200  0.85
  85   34  0.15

ACGTcount: A:0.43, C:0.26, G:0.11, T:0.21


Consensus pattern (84 bp):   
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC

Found at i:12624 original size:2 final size:2

Alignment explanation


    Indices: 12617--12653  Score: 65
    Period size: 2  Copynumber: 18.5  Consensus size: 2

      12607 AATCTACTAT

                                                         *         
      12617 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      12654 GTGACAAAAG


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Done.