Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020594.1 Corchorus olitorius cultivar O-4 contig20627, 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: 2487
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25


Found at i:74 original size:15 final size:15

Alignment explanation


    Indices: 16--75  Score: 57
    Period size: 15  Copynumber: 4.0  Consensus size: 15

          6 GGGTTGGTAT

                       *   
         16 GGCATAGGTGGCAAC
          1 GGCATAGGTGGAAAC

                  * *   *  
         31 GGCATACGCGGATAC
          1 GGCATAGGTGGAAAC

                *    *     
         46 GGCAAAGGTTGAAAC
          1 GGCATAGGTGGAAAC

             *             
         61 GCCATAGGTGGAAAC
          1 GGCATAGGTGGAAAC

         76 ATCATTGGCG


Statistics
Matches: 33,  Mismatches: 12, Indels: 0
        0.73            0.27        0.00

Matches are distributed among these distances:
  15   33  1.00

ACGTcount: A:0.32, C:0.20, G:0.35, T:0.13


Consensus pattern (15 bp):   
GGCATAGGTGGAAAC

Found at i:1535 original size:11 final size:11

Alignment explanation


    Indices: 1505--1560  Score: 67
    Period size: 11  Copynumber: 4.8  Consensus size: 11

       1495 ACTTATGCCC

                        
       1505 AAAACATTTATT
          1 AAAACATTTA-T

                       
       1517 AAAACATTTAT
          1 AAAACATTTAT

               *       
       1528 AAAGCATTTAT
          1 AAAACATTTAT

                    *    
       1539 ATAAAGCAGTTAT
          1 A-AAA-CATTTAT

                     
       1552 AAAACATTT
          1 AAAACATTT

       1561 CCTCAACGGG


Statistics
Matches: 38,  Mismatches: 4, Indels: 5
        0.81            0.09        0.11

Matches are distributed among these distances:
  11   16  0.42
  12   15  0.39
  13    7  0.18

ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36


Consensus pattern (11 bp):   
AAAACATTTAT

Found at i:1543 original size:13 final size:13

Alignment explanation


    Indices: 1509--1560  Score: 51
    Period size: 13  Copynumber: 4.4  Consensus size: 13

       1499 ATGCCCAAAA

                        *
       1509 CATTTAT-TAAAA
          1 CATTTATATAAAG

                         
       1521 CA-TT-TATAAAG
          1 CATTTATATAAAG

                         
       1532 CATTTATATAAAG
          1 CATTTATATAAAG

              *          
       1545 CAGTTATA-AAA-
          1 CATTTATATAAAG

                 
       1556 CATTT
          1 CATTT

       1561 CCTCAACGGG


Statistics
Matches: 34,  Mismatches: 3, Indels: 7
        0.77            0.07        0.16

Matches are distributed among these distances:
  10    1  0.03
  11   12  0.35
  12    7  0.21
  13   14  0.41

ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38


Consensus pattern (13 bp):   
CATTTATATAAAG

Found at i:1551 original size:24 final size:23

Alignment explanation


    Indices: 1505--1560  Score: 76
    Period size: 24  Copynumber: 2.4  Consensus size: 23

       1495 ACTTATGCCC

                              *    
       1505 AAAACATTTATTAAAACATTTAT
          1 AAAACATTTATTAAAACAGTTAT

               *            *       
       1528 AAAGCATTTATATAAAGCAGTTAT
          1 AAAACATTTAT-TAAAACAGTTAT

                     
       1552 AAAACATTT
          1 AAAACATTT

       1561 CCTCAACGGG


Statistics
Matches: 28,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  23   10  0.36
  24   18  0.64

ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36


Consensus pattern (23 bp):   
AAAACATTTATTAAAACAGTTAT
Done.