Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019658.1 Corchorus olitorius cultivar O-4 contig19691, 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: 5807
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34


Found at i:1252 original size:9 final size:9

Alignment explanation


    Indices: 1238--1274  Score: 56
    Period size: 9  Copynumber: 4.0  Consensus size: 9

       1228 ACGTGAGAAA

                     
       1238 AAAGAAAAG
          1 AAAGAAAAG

                      
       1247 AAAGAAAAAG
          1 AAAG-AAAAG

                     
       1257 AAAGAAAAG
          1 AAAGAAAAG

               *     
       1266 AAAAAAAAG
          1 AAAGAAAAG

       1275 GCTAGTGGCT


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
   9   17  0.65
  10    9  0.35

ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00


Consensus pattern (9 bp):   
AAAGAAAAG

Found at i:1256 original size:15 final size:15

Alignment explanation


    Indices: 1236--1274  Score: 55
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       1226 GAACGTGAGA

                            
       1236 AAAAAGAAA-AGAAAG
          1 AAAAAGAAAGA-AAAG

                           
       1251 AAAAAGAAAGAAAAG
          1 AAAAAGAAAGAAAAG

                      
       1266 AAAAA-AAAG
          1 AAAAAGAAAG

       1275 GCTAGTGGCT


Statistics
Matches: 23,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  14    4  0.17
  15   18  0.78
  16    1  0.04

ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00


Consensus pattern (15 bp):   
AAAAAGAAAGAAAAG

Found at i:1262 original size:19 final size:18

Alignment explanation


    Indices: 1238--1274  Score: 65
    Period size: 19  Copynumber: 2.0  Consensus size: 18

       1228 ACGTGAGAAA

                               
       1238 AAAGAAAAGAAAGAAAAAG
          1 AAAGAAAAGAAA-AAAAAG

                              
       1257 AAAGAAAAGAAAAAAAAG
          1 AAAGAAAAGAAAAAAAAG

       1275 GCTAGTGGCT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  18    6  0.33
  19   12  0.67

ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00


Consensus pattern (18 bp):   
AAAGAAAAGAAAAAAAAG

Found at i:1542 original size:38 final size:39

Alignment explanation


    Indices: 1476--1563  Score: 142
    Period size: 38  Copynumber: 2.3  Consensus size: 39

       1466 TTTGGGTATA

                *         *   *                    
       1476 TATTGAAATATATAGTATTTAATATTTTTTGTTTTTTGG
          1 TATTTAAATATATACTATCTAATATTTTTTGTTTTTTGG

                                                   
       1515 TATTTAAATATATACTATCTAAT-TTTTTTGTTTTTTGG
          1 TATTTAAATATATACTATCTAATATTTTTTGTTTTTTGG

                       
       1553 TATTTAAATAT
          1 TATTTAAATAT

       1564 TTAAATATAT


Statistics
Matches: 46,  Mismatches: 3, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  38   26  0.57
  39   20  0.43

ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59


Consensus pattern (39 bp):   
TATTTAAATATATACTATCTAATATTTTTTGTTTTTTGG

Found at i:4143 original size:56 final size:56

Alignment explanation


    Indices: 3999--4220  Score: 354
    Period size: 57  Copynumber: 3.9  Consensus size: 56

       3989 AACATTACGA

                   *                           *          *          
       3999 AAAAAAAAGCTTATTAGATGCCCTCAAACTTGCAAGAAAAGGACAACTTGGTAGGGG
          1 AAAAAAAGGCTTATTAGATGCCCTCAAACTTGCAATAAAAGGACAATTTGGTA-GGG

                                                                     
       4056 AAAAAAGAGGCTTATTAGATGCCCTCAAACTTGCAATAAAAGGACAATTTGGTAGGG
          1 AAAAAA-AGGCTTATTAGATGCCCTCAAACTTGCAATAAAAGGACAATTTGGTAGGG

                                  *  *                              
       4113 AAAAAAAGGCTTATTAGATGCCTTCCAACTTGCAATAAAAGGACAATTTGGTAGGG
          1 AAAAAAAGGCTTATTAGATGCCCTCAAACTTGCAATAAAAGGACAATTTGGTAGGG

                                      *              *          
       4169 AAAAAAAAGGCTTATTAGATGCCCTCCAACTTGCAATAAAAAGACAATTTGG
          1 -AAAAAAAGGCTTATTAGATGCCCTCAAACTTGCAATAAAAGGACAATTTGG

       4221 CCCTTGAGAG


Statistics
Matches: 156,  Mismatches: 7, Indels: 4
        0.93            0.04        0.02

Matches are distributed among these distances:
  56   48  0.31
  57   64  0.41
  58   44  0.28

ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23


Consensus pattern (56 bp):   
AAAAAAAGGCTTATTAGATGCCCTCAAACTTGCAATAAAAGGACAATTTGGTAGGG

Found at i:4201 original size:57 final size:57

Alignment explanation


    Indices: 3997--4220  Score: 360
    Period size: 56  Copynumber: 3.9  Consensus size: 57

       3987 AGAACATTAC

                     *                           *          *         
       3997 GAAAAAAAAAGCTTATTAGATGCCCTCAAACTTGCAAGAAAAGGACAACTTGGTAGGG
          1 GAAAAAAAAGGCTTATTAGATGCCCTCAAACTTGCAATAAAAGGACAATTTGGTA-GG

                   *                                                 
       4055 GAAAAAAGAGGCTTATTAGATGCCCTCAAACTTGCAATAAAAGGACAATTTGGTAGG
          1 GAAAAAAAAGGCTTATTAGATGCCCTCAAACTTGCAATAAAAGGACAATTTGGTAGG

                                    *  *                             
       4112 G-AAAAAAAGGCTTATTAGATGCCTTCCAACTTGCAATAAAAGGACAATTTGGTAGG
          1 GAAAAAAAAGGCTTATTAGATGCCCTCAAACTTGCAATAAAAGGACAATTTGGTAGG

                                       *              *          
       4168 GAAAAAAAAGGCTTATTAGATGCCCTCCAACTTGCAATAAAAAGACAATTTGG
          1 GAAAAAAAAGGCTTATTAGATGCCCTCAAACTTGCAATAAAAGGACAATTTGG

       4221 CCCTTGAGAG


Statistics
Matches: 156,  Mismatches: 9, Indels: 3
        0.93            0.05        0.02

Matches are distributed among these distances:
  56   53  0.34
  57   52  0.33
  58   51  0.33

ACGTcount: A:0.42, C:0.15, G:0.21, T:0.22


Consensus pattern (57 bp):   
GAAAAAAAAGGCTTATTAGATGCCCTCAAACTTGCAATAAAAGGACAATTTGGTAGG
Done.