Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021770.1 Corchorus olitorius cultivar O-4 contig21803, 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: 25873
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:201 original size:14 final size:14

Alignment explanation


    Indices: 182--214  Score: 50
    Period size: 14  Copynumber: 2.4  Consensus size: 14

        172 AATCCACACA

                     *    
        182 TCTGGGTTTTGATT
          1 TCTGGGTTTCGATT

                          
        196 TCTGGGTTTCGATT
          1 TCTGGGTTTCGATT

                  
        210 T-TGGG
          1 TCTGGG

        215 GAGCCGTTTA


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

Matches are distributed among these distances:
  13    4  0.22
  14   14  0.78

ACGTcount: A:0.06, C:0.09, G:0.33, T:0.52


Consensus pattern (14 bp):   
TCTGGGTTTCGATT

Found at i:1500 original size:108 final size:107

Alignment explanation


    Indices: 1311--1526  Score: 414
    Period size: 108  Copynumber: 2.0  Consensus size: 107

       1301 CATGAAGATG

                                                                     *       
       1311 TGCCTGCCAACAGCGAGGCAACATTGCTCAAGGCAGTAGCCAATCAACATGTTTCTGTTGCTATT
          1 TGCCTGCCAACAGCGAGGCAACATTGCTCAAGGCAGTAGCCAATCAACATGTTTCTGCTGCTATT

                                                       
       1376 GATGCCAGTGGTTCCGAGTTCCAATCTTACTCGGGCGGTATAT
         66 GATGCCAGTGGTTCCGAGTTCCAATCTTACT-GGGCGGTATAT

                                                                             
       1419 TGCCTGCCAACAGCGAGGCAACATTGCTCAAGGCAGTAGCCAATCAACATGTTTCTGCTGCTATT
          1 TGCCTGCCAACAGCGAGGCAACATTGCTCAAGGCAGTAGCCAATCAACATGTTTCTGCTGCTATT

                                                      
       1484 GATGCCAGTGGTTCCGAGTTCCAATCTTACTGGGCGGTATAT
         66 GATGCCAGTGGTTCCGAGTTCCAATCTTACTGGGCGGTATAT

             
       1526 T
          1 T

       1527 TATAGGACCT


Statistics
Matches: 107,  Mismatches: 1, Indels: 1
        0.98            0.01        0.01

Matches are distributed among these distances:
 107   12  0.11
 108   95  0.89

ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28


Consensus pattern (107 bp):   
TGCCTGCCAACAGCGAGGCAACATTGCTCAAGGCAGTAGCCAATCAACATGTTTCTGCTGCTATT
GATGCCAGTGGTTCCGAGTTCCAATCTTACTGGGCGGTATAT

Found at i:1931 original size:34 final size:34

Alignment explanation


    Indices: 1888--1956  Score: 138
    Period size: 34  Copynumber: 2.0  Consensus size: 34

       1878 TTTACTGCCT

                                              
       1888 ACTGCAACAATGGCTTCCTTTTTAATTTAACTCA
          1 ACTGCAACAATGGCTTCCTTTTTAATTTAACTCA

                                              
       1922 ACTGCAACAATGGCTTCCTTTTTAATTTAACTCA
          1 ACTGCAACAATGGCTTCCTTTTTAATTTAACTCA

             
       1956 A
          1 A

       1957 AACTGCAGAG


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  34   35  1.00

ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38


Consensus pattern (34 bp):   
ACTGCAACAATGGCTTCCTTTTTAATTTAACTCA

Found at i:8528 original size:59 final size:59

Alignment explanation


    Indices: 8428--8545  Score: 182
    Period size: 59  Copynumber: 2.0  Consensus size: 59

       8418 AAGAGGGGAA

                                        *  *                  *        
       8428 GTCGAACTGGGATTTCATTTGTCTCTTGTTGTTTAAAAAATTTGGGTTCATATTTTTTT
          1 GTCGAACTGGGATTTCATTTGTCTCTTGATGCTTAAAAAATTTGGGTTCAAATTTTTTT

                       *                      * *                      
       8487 GTCGAACTGGGTTTTCATTTGTCTCTTGATGCTTGATAAATTTGGGTTCAAATTTTTTT
          1 GTCGAACTGGGATTTCATTTGTCTCTTGATGCTTAAAAAATTTGGGTTCAAATTTTTTT

       8546 TTGACATTTT


Statistics
Matches: 53,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  59   53  1.00

ACGTcount: A:0.19, C:0.11, G:0.19, T:0.50


Consensus pattern (59 bp):   
GTCGAACTGGGATTTCATTTGTCTCTTGATGCTTAAAAAATTTGGGTTCAAATTTTTTT

Found at i:11618 original size:11 final size:11

Alignment explanation


    Indices: 11598--11629  Score: 55
    Period size: 11  Copynumber: 2.9  Consensus size: 11

      11588 TTGACAATGT

                       
      11598 AACAAAAACAA
          1 AACAAAAACAA

               *       
      11609 AACGAAAACAA
          1 AACAAAAACAA

                      
      11620 AACAAAAACA
          1 AACAAAAACA

      11630 GAAAAACGAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.78, C:0.19, G:0.03, T:0.00


Consensus pattern (11 bp):   
AACAAAAACAA

Found at i:24548 original size:33 final size:33

Alignment explanation


    Indices: 24503--24601  Score: 180
    Period size: 33  Copynumber: 3.0  Consensus size: 33

      24493 TCTTCCTGCA

                   *         *               
      24503 TGAAGATGCAGCTGGGGTTGGAGTAGCAGTTGC
          1 TGAAGATACAGCTGGGGCTGGAGTAGCAGTTGC

                                             
      24536 TGAAGATACAGCTGGGGCTGGAGTAGCAGTTGC
          1 TGAAGATACAGCTGGGGCTGGAGTAGCAGTTGC

                                             
      24569 TGAAGATACAGCTGGGGCTGGAGTAGCAGTTGC
          1 TGAAGATACAGCTGGGGCTGGAGTAGCAGTTGC

      24602 CGGTTGCATT


Statistics
Matches: 64,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  33   64  1.00

ACGTcount: A:0.23, C:0.14, G:0.40, T:0.22


Consensus pattern (33 bp):   
TGAAGATACAGCTGGGGCTGGAGTAGCAGTTGC
Done.