Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_5509

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: 10666
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36


Found at i:506 original size:11 final size:11

Alignment explanation


    Indices: 474--510  Score: 58
    Period size: 11  Copynumber: 3.5  Consensus size: 11

        464 ATGTATATAT

                       
        474 AAAGAAAGAAA
          1 AAAGAAAGAAA

                   *   
        485 AAA-AAACAAA
          1 AAAGAAAGAAA

                       
        495 AAAGAAAGAAA
          1 AAAGAAAGAAA

                 
        506 AAAGA
          1 AAAGA

        511 TTCGAAAGAA


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  10    9  0.39
  11   14  0.61

ACGTcount: A:0.84, C:0.03, G:0.14, T:0.00


Consensus pattern (11 bp):   
AAAGAAAGAAA

Found at i:808 original size:18 final size:18

Alignment explanation


    Indices: 785--833  Score: 71
    Period size: 18  Copynumber: 2.7  Consensus size: 18

        775 GGTTTCTTGT

                              
        785 TTTTTTTGGGGGGGTTAG
          1 TTTTTTTGGGGGGGTTAG

                   **         
        803 TTTTTTTTTGGGGGTTAG
          1 TTTTTTTGGGGGGGTTAG

            *            
        821 GTTTTTTGGGGGG
          1 TTTTTTTGGGGGG

        834 CTTAATGGCT


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  18   26  1.00

ACGTcount: A:0.04, C:0.00, G:0.43, T:0.53


Consensus pattern (18 bp):   
TTTTTTTGGGGGGGTTAG

Found at i:6802 original size:3 final size:3

Alignment explanation


    Indices: 6794--6845  Score: 54
    Period size: 3  Copynumber: 18.0  Consensus size: 3

       6784 AATATTGCTA

                         *               *          *                    * 
       6794 ATT ATT ATT -GT ATT ATT ATT ACT ATT A-T GTT ATT ATT ATT ATT ACT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT

                   
       6840 ATT ATT
          1 ATT ATT

       6846 TGCTCAATTT


Statistics
Matches: 39,  Mismatches: 8, Indels: 4
        0.76            0.16        0.08

Matches are distributed among these distances:
   2    2  0.05
   3   37  0.95

ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62


Consensus pattern (3 bp):   
ATT

Found at i:6819 original size:17 final size:17

Alignment explanation


    Indices: 6794--6845  Score: 68
    Period size: 17  Copynumber: 3.0  Consensus size: 17

       6784 AATATTGCTA

                     *       
       6794 ATTATTATTGTATTATT
          1 ATTATTATTATATTATT

                *      *     
       6811 ATTACTATTATGTTATT
          1 ATTATTATTATATTATT

                              
       6828 ATTATTATTACTATTATT
          1 ATTATTATTA-TATTATT

       6846 TGCTCAATTT


Statistics
Matches: 29,  Mismatches: 5, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  17   23  0.79
  18    6  0.21

ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62


Consensus pattern (17 bp):   
ATTATTATTATATTATT

Found at i:6821 original size:20 final size:21

Alignment explanation


    Indices: 6796--6845  Score: 66
    Period size: 23  Copynumber: 2.3  Consensus size: 21

       6786 TATTGCTAAT

                                 
       6796 TATTATT-GTATTATTATTAC
          1 TATTATTAGTATTATTATTAC

                      *            
       6816 TATTATGTTATTATTATTATTAC
          1 TATTA--TTAGTATTATTATTAC

                   
       6839 TATTATT
          1 TATTATT

       6846 TGCTCAATTT


Statistics
Matches: 26,  Mismatches: 1, Indels: 5
        0.81            0.03        0.16

Matches are distributed among these distances:
  20    5  0.19
  21    2  0.08
  22    2  0.08
  23   17  0.65

ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62


Consensus pattern (21 bp):   
TATTATTAGTATTATTATTAC

Found at i:7851 original size:107 final size:107

Alignment explanation


    Indices: 7690--7970  Score: 374
    Period size: 107  Copynumber: 2.6  Consensus size: 107

       7680 TTAGCGTTTG

                         *                              *   *              * 
       7690 AATTCGA-GAAACTTGCCCTAATGTGCT-GGTTTTGATTTTTCTTGTTCAACCAAATAGCTAAGT
          1 AATTCGATGAAACGTGCCCTAATGTGCTGGGTTTTGA--TTTCTCGTTTAACCAAATAGCTAAAT

                                   *                    
       7753 ATCCTTTTAAAAATTTCAAAATAGGGCAATGTTTTGCATTTGGA
         64 ATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCATTTGGA

                                                               *             
       7797 AA-TCTGA-GAAAACGTGCCCTAATGTGCTGGGTTTTGATTTCTCGTTTAATCAAATAGCTAAAT
          1 AATTC-GATG-AAACGTGCCCTAATGTGCTGGGTTTTGATTTCTCGTTTAACCAAATAGCTAAAT

                                                 *      
       7860 ATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGA
         64 ATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCATTTGGA

                       *  *                   *                   *   *   *  
       7904 AATTCGATG-AGCGCGCCCTAATGTGCTGGGTTTCGATTTCTCGTTTAACCAAACAGCCAAACAT
          1 AATTCGATGAAACGTGCCCTAATGTGCTGGGTTTTGATTTCTCGTTTAACCAAATAGCTAAATAT

               
       7968 CCT
         66 CCT

       7971 CTTGAATTTT


Statistics
Matches: 155,  Mismatches: 14, Indels: 11
        0.86            0.08        0.06

Matches are distributed among these distances:
 106   53  0.34
 107   73  0.47
 108   21  0.14
 109    8  0.05

ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35


Consensus pattern (107 bp):   
AATTCGATGAAACGTGCCCTAATGTGCTGGGTTTTGATTTCTCGTTTAACCAAATAGCTAAATAT
CCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCATTTGGA
Done.