Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019928.1 Corchorus olitorius cultivar O-4 contig19961, 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: 2678
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:1741 original size:12 final size:13

Alignment explanation


    Indices: 1726--1808  Score: 59
    Period size: 13  Copynumber: 6.3  Consensus size: 13

       1716 TCCATCAAAA

                         
       1726 AAAAAATC-AATC
          1 AAAAAATCAAATC

                         
       1738 AAAAAATCAAATC
          1 AAAAAATCAAATC

                 *         
       1751 AAAGTTAAT-AAA--
          1 AAA--AAATCAAATC

                         
       1763 AAAAAATCAAATC
          1 AAAAAATCAAATC

                    *     
       1776 AAAATAA-AAAATC
          1 AAAA-AATCAAATC

                            
       1789 AAATCAAATCAAAATC
          1 AAA--AAATC-AAATC

                
       1805 AAAA
          1 AAAA

       1809 GAGAATTGAT


Statistics
Matches: 56,  Mismatches: 4, Indels: 20
        0.70            0.05        0.25

Matches are distributed among these distances:
  10    3  0.05
  11    3  0.05
  12   11  0.20
  13   19  0.34
  14    8  0.14
  15    4  0.07
  16    8  0.14

ACGTcount: A:0.70, C:0.12, G:0.01, T:0.17


Consensus pattern (13 bp):   
AAAAAATCAAATC

Found at i:1769 original size:20 final size:18

Alignment explanation


    Indices: 1722--1796  Score: 89
    Period size: 18  Copynumber: 4.1  Consensus size: 18

       1712 CCACTCCATC

                              
       1722 AAAAAAAAAATC-AATCA
          1 AAAAAAAAAATCAAATCA

                 **          * 
       1739 AAAAATCAAATCAAAGTTA
          1 AAAAAAAAAATCAAA-TCA

                               
       1758 ATAAAAAAAAATCAAATCA
          1 A-AAAAAAAAATCAAATCA

               *              
       1777 AAATAAAAAATCAAATCA
          1 AAAAAAAAAATCAAATCA

              
       1795 AA
          1 AA

       1797 TCAAAATCAA


Statistics
Matches: 48,  Mismatches: 7, Indels: 5
        0.80            0.12        0.08

Matches are distributed among these distances:
  17   10  0.21
  18   20  0.42
  19    6  0.12
  20   12  0.25

ACGTcount: A:0.72, C:0.11, G:0.01, T:0.16


Consensus pattern (18 bp):   
AAAAAAAAAATCAAATCA

Found at i:1786 original size:23 final size:23

Alignment explanation


    Indices: 1738--1808  Score: 88
    Period size: 23  Copynumber: 3.0  Consensus size: 23

       1728 AAAATCAATC

                             *       
       1738 AAAAAATCAAATCAAAGTTAATAAA
          1 AAAAAATCAAATCAAA-ATAA-AAA

                                   
       1763 AAAAAATCAAATCAAAATAAAAA
          1 AAAAAATCAAATCAAAATAAAAA

             **               *    
       1786 ATCAAATCAAATCAAAATCAAAA
          1 AAAAAATCAAATCAAAATAAAAA

       1809 GAGAATTGAT


Statistics
Matches: 42,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  23   23  0.55
  24    3  0.07
  25   16  0.38

ACGTcount: A:0.70, C:0.11, G:0.01, T:0.17


Consensus pattern (23 bp):   
AAAAAATCAAATCAAAATAAAAA

Found at i:2599 original size:50 final size:50

Alignment explanation


    Indices: 2402--2588  Score: 259
    Period size: 50  Copynumber: 3.7  Consensus size: 50

       2392 GAAGATTTAC

                                     *                        
       2402 AATAAGATTGCATTCCATTTGTGAGCCCAAGATCAAAATTCGCTTTTCAA
          1 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA

             *   *     *  * *         *                       
       2452 AGTAAAATTGCTTTTCGTTTGTGAGTTCAAGATCAAAATTCGCTTTTCAA
          1 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA

               *                                               
       2502 AACGAA-ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
          1 AA-TAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA

                        *            *      *    
       2552 AATAAGATTGCACTCCATTTGTGAGACCAAGACCAAA
          1 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAA

       2589 GGTCGATTTT


Statistics
Matches: 118,  Mismatches: 17, Indels: 4
        0.85            0.12        0.03

Matches are distributed among these distances:
  49    2  0.02
  50  114  0.97
  51    2  0.02

ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32


Consensus pattern (50 bp):   
AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA

Done.