Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015707.1 Corchorus olitorius cultivar O-4 contig15740, 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: 6401
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33


Found at i:1764 original size:32 final size:32

Alignment explanation


    Indices: 1728--1905  Score: 241
    Period size: 32  Copynumber: 5.5  Consensus size: 32

       1718 GTGTGGAAAG

                                            
       1728 AAAACGCCCTTATTTAGCGGCGTTTAAAGAAC
          1 AAAACGCCCTTATTTAGCGGCGTTTAAAGAAC

                 *                 *        
       1760 AAAACACCCTTATTTAGCGGCGTCTAAAGAAC
          1 AAAACGCCCTTATTTAGCGGCGTTTAAAGAAC

                            *         *     
       1792 AAAACGCCCTTATTTAACGGCGTTTAGAGAAC
          1 AAAACGCCCTTATTTAGCGGCGTTTAAAGAAC

                                   *  * *   
       1824 AAAACGCCCTTATTTAGCGGCGTCTAGACAAC
          1 AAAACGCCCTTATTTAGCGGCGTTTAAAGAAC

                              *        *     
       1856 AAAACGCCCTTATTTAGCAGCGTCTT-TAGAAC
          1 AAAACGCCCTTATTTAGCGGCGT-TTAAAGAAC

                              
       1888 AAAACGCCGCTATATTTA
          1 AAAACGCC-CT-TATTTA

       1906 ACTGCTTTTA


Statistics
Matches: 130,  Mismatches: 13, Indels: 4
        0.88            0.09        0.03

Matches are distributed among these distances:
  32  121  0.93
  33    3  0.02
  34    6  0.05

ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25


Consensus pattern (32 bp):   
AAAACGCCCTTATTTAGCGGCGTTTAAAGAAC

Found at i:1866 original size:96 final size:98

Alignment explanation


    Indices: 1728--1907  Score: 283
    Period size: 96  Copynumber: 1.9  Consensus size: 98

       1718 GTGTGGAAAG

                                   *    *                     *              
       1728 AAAACGCCCTTATTTAGCGGCGTTTAAAGAACAAAACACCCTTATTTAGCGGCGTCTAAAGAACA
          1 AAAACGCCCTTATTTAGCGGCGTCTAAACAACAAAACACCCTTATTTAGCAGCGTCTAAAGAACA

                                             
       1793 AAACGCC-CT-TATTTAACGGCGTTTAGAGAAC
         66 AAACGCCGCTATATTTAACGGCGTTTAGAGAAC

                                      *          *                   **      
       1824 AAAACGCCCTTATTTAGCGGCGTCTAGACAACAAAACGCCCTTATTTAGCAGCGTCTTTAGAACA
          1 AAAACGCCCTTATTTAGCGGCGTCTAAACAACAAAACACCCTTATTTAGCAGCGTCTAAAGAACA

                               
       1889 AAACGCCGCTATATTTAAC
         66 AAACGCCGCTATATTTAAC

       1908 TGCTTTTAAA


Statistics
Matches: 75,  Mismatches: 7, Indels: 2
        0.89            0.08        0.02

Matches are distributed among these distances:
  96   65  0.87
  97    2  0.03
  98    8  0.11

ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24


Consensus pattern (98 bp):   
AAAACGCCCTTATTTAGCGGCGTCTAAACAACAAAACACCCTTATTTAGCAGCGTCTAAAGAACA
AAACGCCGCTATATTTAACGGCGTTTAGAGAAC

Found at i:3518 original size:9 final size:9

Alignment explanation


    Indices: 3504--3534  Score: 53
    Period size: 9  Copynumber: 3.4  Consensus size: 9

       3494 AAAAGGTTAT

                     
       3504 ATATACTAA
          1 ATATACTAA

                     
       3513 ATATACTAA
          1 ATATACTAA

                   * 
       3522 ATATACTGA
          1 ATATACTAA

                
       3531 ATAT
          1 ATAT

       3535 TATTTGAAAC


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   9   21  1.00

ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35


Consensus pattern (9 bp):   
ATATACTAA

Found at i:4558 original size:20 final size:19

Alignment explanation


    Indices: 4524--4561  Score: 58
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       4514 ATGATTACTA

                      *        
       4524 AAAACAATTAGAGGTTATC
          1 AAAACAATTAAAGGTTATC

                               
       4543 AAAACAATTATAAGGTTAT
          1 AAAACAATTA-AAGGTTAT

       4562 TAATAAGCAC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19   10  0.59
  20    7  0.41

ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29


Consensus pattern (19 bp):   
AAAACAATTAAAGGTTATC

Found at i:5324 original size:42 final size:45

Alignment explanation


    Indices: 5273--5366  Score: 142
    Period size: 45  Copynumber: 2.2  Consensus size: 45

       5263 AGTGCATTAC

                                      *                  
       5273 CTAA-ATTCTACT-C-C-ATCTCTAGGTAATTCATCAAAATAAAG
          1 CTAATATTCTACTCCTCTATCTCTAGATAATTCATCAAAATAAAG

                                    *                    
       5314 CTAATATTCTACTCCTCTATCTCTTGATAATTCATCAAAATAAAG
          1 CTAATATTCTACTCCTCTATCTCTAGATAATTCATCAAAATAAAG

                    
       5359 CTAATATT
          1 CTAATATT

       5367 ATTTGTTGCT


Statistics
Matches: 47,  Mismatches: 2, Indels: 4
        0.89            0.04        0.08

Matches are distributed among these distances:
  41    4  0.09
  42    8  0.17
  43    1  0.02
  44    1  0.02
  45   33  0.70

ACGTcount: A:0.37, C:0.21, G:0.05, T:0.36


Consensus pattern (45 bp):   
CTAATATTCTACTCCTCTATCTCTAGATAATTCATCAAAATAAAG

Done.