Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011345.1 Corchorus olitorius cultivar O-4 contig11378, 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: 8423
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30


Found at i:877 original size:21 final size:22

Alignment explanation


    Indices: 851--891  Score: 66
    Period size: 21  Copynumber: 1.9  Consensus size: 22

        841 CGGCCTGCTA

                                  
        851 CCCGCGCCTGGGCA-CTCCTTG
          1 CCCGCGCCTGGGCATCTCCTTG

                  *             
        872 CCCGCGTCTGGGCATCTCCT
          1 CCCGCGCCTGGGCATCTCCT

        892 GGGTGTTCAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21   13  0.72
  22    5  0.28

ACGTcount: A:0.05, C:0.46, G:0.27, T:0.22


Consensus pattern (22 bp):   
CCCGCGCCTGGGCATCTCCTTG

Found at i:4237 original size:36 final size:36

Alignment explanation


    Indices: 4133--4220  Score: 140
    Period size: 36  Copynumber: 2.4  Consensus size: 36

       4123 CCTTACCTTT

                    *               *           
       4133 CTTGTAGCGCACCACATATGGAAAGGATTCAATGAA
          1 CTTGTAGCACACCACATATGGAAATGATTCAATGAA

                                                
       4169 CTTGTAGCACACCACATATGGAAATGATTCAATGAA
          1 CTTGTAGCACACCACATATGGAAATGATTCAATGAA

                            
       4205 CTTGTATCGCACACCA
          1 CTTGTA--GCACACCA

       4221 TATGGATTGA


Statistics
Matches: 48,  Mismatches: 2, Indels: 2
        0.92            0.04        0.04

Matches are distributed among these distances:
  36   40  0.83
  38    8  0.17

ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24


Consensus pattern (36 bp):   
CTTGTAGCACACCACATATGGAAATGATTCAATGAA

Found at i:6252 original size:21 final size:21

Alignment explanation


    Indices: 6228--6319  Score: 141
    Period size: 21  Copynumber: 4.4  Consensus size: 21

       6218 CTTAGGCATT

                         *        
       6228 TCCAATGAGCTTGAAACCTT-C
          1 TCCAATGAGCTTGGAA-CTTGC

                    *        *   
       6249 TCCAATGATCTTGGAACCTGC
          1 TCCAATGAGCTTGGAACTTGC

                                 
       6270 TCCAATGAGCTTGGAACTTGC
          1 TCCAATGAGCTTGGAACTTGC

                                 
       6291 TCCAATGAGCTTGGAACTTGC
          1 TCCAATGAGCTTGGAACTTGC

                    
       6312 TCCAATGA
          1 TCCAATGA

       6320 ACTTCTAGCA


Statistics
Matches: 65,  Mismatches: 5, Indels: 2
        0.90            0.07        0.03

Matches are distributed among these distances:
  20    2  0.03
  21   63  0.97

ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACTTGC

Found at i:8202 original size:33 final size:31

Alignment explanation


    Indices: 8129--8274  Score: 123
    Period size: 33  Copynumber: 4.5  Consensus size: 31

       8119 GCTATGATCA

                                       ** * 
       8129 ACCAAAACAGATTTGTTTTCATCACAATTAGC
          1 ACCAAAACAGATTTG-TTTCATCACAAACAAC

                                             
       8161 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
          1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC

                              *              
       8194 ACCTAAAACAGATTTAGTGTCATCACAAACAAC
          1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC

                   **  *             *        
       8227 ACTCAAATTAGGTTTAGTATT-ATCGCAAACAAC
          1 AC-CAAAACAGATTT-GT-TTCATCACAAACAAC

               *           
       8260 ATCTAAAACAGATTT
          1 A-CCAAAACAGATTT

       8275 AGAATTACTC


Statistics
Matches: 94,  Mismatches: 13, Indels: 13
        0.78            0.11        0.11

Matches are distributed among these distances:
  32    7  0.07
  33   79  0.84
  34    8  0.09

ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27


Consensus pattern (31 bp):   
ACCAAAACAGATTTGTTTCATCACAAACAAC

Done.