Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006074.1 Corchorus olitorius cultivar O-4 contig06099, 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, 803

Length: 1339
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36


Found at i:577 original size:33 final size:33

Alignment explanation


    Indices: 489--671  Score: 156
    Period size: 33  Copynumber: 5.5  Consensus size: 33

        479 AAGAGTAATT

                  *               **       * 
        489 CTAAATATGTTTTAGATGTTGTAAGTGATGATA
          1 CTAAATCTGTTTTAGATGTTGTTTGTGATGACA

            *    *  **        *               
        522 TTAAACCTAATTT-GAGTATTGTTTGTGATGACA
          1 CTAAATCTGTTTTAGA-TGTTGTTTGTGATGACA

                                     *     * 
        555 CTAAATCTGTTTTAGATGTTGTTTGCGATGATA
          1 CTAAATCTGTTTTAGATGTTGTTTGTGATGACA

                 *  **                        
        588 CTAAACCTAATTT-GAGTGTTGTTTGTGATGACA
          1 CTAAATCTGTTTTAGA-TGTTGTTTGTGATGACA

                           *      *        * 
        621 CTAAATCTGTTTTAGGTGTTGTCTGTGATGAAA
          1 CTAAATCTGTTTTAGATGTTGTTTGTGATGACA

                          *    
        654 C-AAATTCTGTTTTGGATG
          1 CTAAA-TCTGTTTTAGATG

        672 CTAATTGTGA


Statistics
Matches: 116,  Mismatches: 29, Indels: 10
        0.75            0.19        0.06

Matches are distributed among these distances:
  32    7  0.06
  33  106  0.91
  34    3  0.03

ACGTcount: A:0.27, C:0.09, G:0.21, T:0.43


Consensus pattern (33 bp):   
CTAAATCTGTTTTAGATGTTGTTTGTGATGACA

Found at i:595 original size:66 final size:66

Alignment explanation


    Indices: 489--651  Score: 254
    Period size: 66  Copynumber: 2.5  Consensus size: 66

        479 AAGAGTAATT

                  *                *         *                               
        489 CTAAATATGTTTTAGATGTTGTAAGTGATGATATTAAACCTAATTTGAGTATTGTTTGTGATGAC
          1 CTAAATCTGTTTTAGATGTTGTATGTGATGATACTAAACCTAATTTGAGTATTGTTTGTGATGAC

             
        554 A
         66 A

                                  *  *                        *              
        555 CTAAATCTGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGTGATGAC
          1 CTAAATCTGTTTTAGATGTTGTATGTGATGATACTAAACCTAATTTGAGTATTGTTTGTGATGAC

             
        620 A
         66 A

                           *      *        
        621 CTAAATCTGTTTTAGGTGTTGTCTGTGATGA
          1 CTAAATCTGTTTTAGATGTTGTATGTGATGA

        652 AACAAATTCT


Statistics
Matches: 88,  Mismatches: 9, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  66   88  1.00

ACGTcount: A:0.27, C:0.09, G:0.21, T:0.43


Consensus pattern (66 bp):   
CTAAATCTGTTTTAGATGTTGTATGTGATGATACTAAACCTAATTTGAGTATTGTTTGTGATGAC
A

Found at i:680 original size:66 final size:66

Alignment explanation


    Indices: 489--684  Score: 180
    Period size: 66  Copynumber: 3.0  Consensus size: 66

        479 AAGAGTAATT

                  *               ** *     * *                ** **          
        489 CTAAATATGTTTTAGATGTTGTAAGTGATGATATTAAACCTAATTTGAGTATTGTTTGTGATGAC
          1 CTAAATCTGTTTTAGATGTTGTCTGCGATGAAACTAAACCTAATTTGAGTGCTAATTGTGATGAC

             
        554 A
         66 A

                                  *        *                   * **          
        555 CTAAATCTGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGTGATGAC
          1 CTAAATCTGTTTTAGATGTTGTCTGCGATGAAACTAAACCTAATTTGAGTGCTAATTGTGATGAC

             
        620 A
         66 A

                           *         *             *  **                     
        621 CTAAATCTGTTTTAGGTGTTGTCTGTGATGAAAC-AAATTCTGTTTTG-GATGCTAATTGTGATG
          1 CTAAATCTGTTTTAGATGTTGTCTGCGATGAAACTAAA-CCTAATTTGAG-TGCTAATTGTGATG

             
        684 A
         64 A

        685 AAAAGATTCT


Statistics
Matches: 112,  Mismatches: 16, Indels: 4
        0.85            0.12        0.03

Matches are distributed among these distances:
  65    4  0.04
  66  108  0.96

ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42


Consensus pattern (66 bp):   
CTAAATCTGTTTTAGATGTTGTCTGCGATGAAACTAAACCTAATTTGAGTGCTAATTGTGATGAC
A
Done.