Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013259.1 Corchorus olitorius cultivar O-4 contig13292, 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: 1983
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33


Found at i:1320 original size:30 final size:29

Alignment explanation


    Indices: 1286--1342  Score: 96
    Period size: 30  Copynumber: 1.9  Consensus size: 29

       1276 AGTGGAGCAA

                                          
       1286 AATTTAACCTTTAATCCTTAATAAAATTTC
          1 AATTTAACCTTTAATCCTTAA-AAAATTTC

                 *                     
       1316 AATTTCACCTTTAATCCTTAAAAAATT
          1 AATTTAACCTTTAATCCTTAAAAAATT

       1343 AATTCAACCA


Statistics
Matches: 26,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  29    6  0.23
  30   20  0.77

ACGTcount: A:0.40, C:0.18, G:0.00, T:0.42


Consensus pattern (29 bp):   
AATTTAACCTTTAATCCTTAAAAAATTTC

Found at i:1728 original size:43 final size:42

Alignment explanation


    Indices: 1604--1933  Score: 375
    Period size: 43  Copynumber: 7.8  Consensus size: 42

       1594 CAATAACCAA

                                              *      * 
       1604 AAAGTCCCCAAACACATATATAACACAGGGGCATTTCTATTCC
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATATCTA-TAC

                    *                     *   *         
       1647 AAAAGTCCTCAAACACATATATAACACA-GAG-ACATCTATACC
          1 -AAAGTCCCCAAACACATATATAACACAGGGGCATATCTATA-C

            *                                *         
       1689 CAAGTCCCCAAACACATATATAACACAGGGGCAAATCTATTAC
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATATCTA-TAC

                   **                   *              
       1732 AAAGTCCTGAAACACATATATAACACAGAGGCAT-T-TATATC
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATATCTATA-C

                                              *       *
       1773 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAT
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATATCTA-TAC

                   *                    *              
       1816 AAAGTCCTCAAACACATATATAACACAGAGGCAT-T-TATATC
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATATCTATA-C

                                       *      *       *
       1857 AAAGTCCCCAAACACATATATAACACATGGGCATCTCTATTAT
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATATCTA-TAC

                   *                    *     
       1900 AAAGTCCTCAAACACATATATAACACAGAGGCAT
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAT

       1934 TTCTCCTTAT


Statistics
Matches: 246,  Mismatches: 28, Indels: 25
        0.82            0.09        0.08

Matches are distributed among these distances:
  40    4  0.02
  41   93  0.38
  42   12  0.05
  43  105  0.43
  44   32  0.13

ACGTcount: A:0.42, C:0.25, G:0.11, T:0.22


Consensus pattern (42 bp):   
AAAGTCCCCAAACACATATATAACACAGGGGCATATCTATAC

Found at i:1782 original size:84 final size:84

Alignment explanation


    Indices: 1604--1935  Score: 547
    Period size: 84  Copynumber: 3.9  Consensus size: 84

       1594 CAATAACCAA

                                              *      *                       
       1604 AAAGTCCCCAAACACATATATAACACAGGGGCATTTCTATTCCAAAAGTCCTCAAACACATATAT
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC-AAAGTCCTCAAACACATATAT

                     *   *    * 
       1669 AACACAGAGACATCTATACC
         65 AACACAGAGGCATTTATATC

            *                                **                *             
       1689 CAAGTCCCCAAACACATATATAACACAGGGGCAAATCTATTACAAAGTCCTGAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA

                               
       1754 ACACAGAGGCATTTATATC
         66 ACACAGAGGCATTTATATC

                                                      *                      
       1773 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTATAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA

                               
       1838 ACACAGAGGCATTTATATC
         66 ACACAGAGGCATTTATATC

                                       *              *                      
       1857 AAAGTCCCCAAACACATATATAACACATGGGCATCTCTATTATAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA

                          
       1922 ACACAGAGGCATTT
         66 ACACAGAGGCATTT

       1936 CTCCTTATGG


Statistics
Matches: 233,  Mismatches: 14, Indels: 1
        0.94            0.06        0.00

Matches are distributed among these distances:
  84  194  0.83
  85   39  0.17

ACGTcount: A:0.42, C:0.25, G:0.11, T:0.23


Consensus pattern (84 bp):   
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATTTATATC

Done.