Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009928.1 Corchorus olitorius cultivar O-4 contig09960, 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: 6803
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27


Found at i:1661 original size:43 final size:40

Alignment explanation


    Indices: 1613--1942  Score: 351
    Period size: 41  Copynumber: 7.8  Consensus size: 40

       1603 TAATAGCCAA

                                             *         
       1613 AAAGTCCCCAAACACATATATAACACATGGGCACCTTCATTAC
          1 AAAGTCCCCAAACACATATATAACACA-GGGCATC-TCA-TAC

                   *               *                  
       1656 AAAGTCCTCAAACACATATATAAGACAGAGGCATCT-ATATC
          1 AAAGTCCCCAAACACATATATAACACAG-GGCATCTCATA-C

                                             *         
       1697 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTACTAC
          1 AAAGTCCCCAAACACATATATAACACA-GGGCATCTC-A-TAC

                   *                     *            
       1740 AAAGTCCTCAAACACATATATAACACAGATGCATCT-ATATC
          1 AAAGTCCCCAAACACATATATAACACAG-GGCATCTCATA-C

                            *                *         
       1781 AAAGTCCCCAAACACACATATAACACAGGGGCAACTCTACTAC
          1 AAAGTCCCCAAACACATATATAACACA-GGGCATCTC-A-TAC

                   *                      *     *     
       1824 AAAGTCCTCAAACACATATATAACACAGAGACAT-TTATATC
          1 AAAGTCCCCAAACACATATATAACACAG-GGCATCTCATA-C

                                                       
       1865 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
          1 AAAGTCCCCAAACACATATATAACACA-GGGCATCTC-A-TAC

                    *                          
       1908 AAAAGTCCTCAAACACATATATAACACAGAGGCAT
          1 -AAAGTCCCCAAACACATATATAACACAG-GGCAT

       1943 TTCTCCTTAT


Statistics
Matches: 245,  Mismatches: 22, Indels: 39
        0.80            0.07        0.13

Matches are distributed among these distances:
  40    6  0.02
  41   97  0.40
  42    9  0.04
  43   96  0.39
  44   37  0.15

ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20


Consensus pattern (40 bp):   
AAAGTCCCCAAACACATATATAACACAGGGCATCTCATAC

Found at i:1708 original size:84 final size:84

Alignment explanation


    Indices: 1613--1942  Score: 545
    Period size: 84  Copynumber: 3.9  Consensus size: 84

       1603 TAATAGCCAA

                                       *     *      *                        
       1613 AAAGTCCCCAAACACATATATAACACATGGGCACCT-TCATTACAAAGTCCTCAAACACATATAT
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCT-ACTACAAAGTCCTCAAACACATATAT

              *                 
       1677 AAGACAGAGGCATCTATATC
         65 AACACAGAGGCATCTATATC

                                                                             
       1697 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTACTACAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTACTACAAAGTCCTCAAACACATATATA

                   *           
       1762 ACACAGATGCATCTATATC
         66 ACACAGAGGCATCTATATC

                            *                                                
       1781 AAAGTCCCCAAACACACATATAACACAGGGGCAACTCTACTACAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTACTACAAAGTCCTCAAACACATATATA

                    *   *      
       1846 ACACAGAGACATTTATATC
         66 ACACAGAGGCATCTATATC

                                             *     *                         
       1865 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTACTAC-AAAGTCCTCAAACACATATAT

                         
       1930 AACACAGAGGCAT
         65 AACACAGAGGCAT

       1943 TTCTCCTTAT


Statistics
Matches: 231,  Mismatches: 13, Indels: 3
        0.94            0.05        0.01

Matches are distributed among these distances:
  84  197  0.85
  85   34  0.15

ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20


Consensus pattern (84 bp):   
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTACTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC

Found at i:2063 original size:2 final size:2

Alignment explanation


    Indices: 2051--2086  Score: 56
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       2041 ACCAAATTCC

                                                         *         
       2051 TA TA T- 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

       2087 GTGACAAAGG


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

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

ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:6383 original size:28 final size:26

Alignment explanation


    Indices: 6322--6394  Score: 78
    Period size: 24  Copynumber: 2.8  Consensus size: 26

       6312 AAGGAGTGTA

                                      
       6322 GTAAATTTAATCAAATCCAAAGTCTT
          1 GTAAATTTAATCAAATCCAAAGTCTT

               **                      
       6348 -T-TTTTTAATCAAATCCAAAGTCTCT
          1 GTAAATTTAATCAAATCCAAAGTCT-T

                 *      *         
       6373 GGTAAGTTTAATTAAATCCAAA
          1 -GTAAATTTAATCAAATCCAAA

       6395 TTAATTGAAT


Statistics
Matches: 38,  Mismatches: 5, Indels: 6
        0.78            0.10        0.12

Matches are distributed among these distances:
  24   20  0.53
  25    2  0.05
  27    1  0.03
  28   15  0.39

ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37


Consensus pattern (26 bp):   
GTAAATTTAATCAAATCCAAAGTCTT
Done.