Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2728

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: 30133
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:6894 original size:22 final size:22

Alignment explanation


    Indices: 6868--6927  Score: 59
    Period size: 21  Copynumber: 2.8  Consensus size: 22

       6858 ACACATTGTC

                            * *  *
       6868 GATAAACCACCACATATTTGCT
          1 GATAAACCACCACATAATCGCA

                   **             
       6890 GAT-AACGGCCACATAATCGCA
          1 GATAAACCACCACATAATCGCA

                   *         
       6911 GATAAACTACCACATAA
          1 GATAAACCACCACATAA

       6928 CTTCCACCTT


Statistics
Matches: 30,  Mismatches: 7, Indels: 2
        0.77            0.18        0.05

Matches are distributed among these distances:
  21   16  0.53
  22   14  0.47

ACGTcount: A:0.42, C:0.27, G:0.12, T:0.20


Consensus pattern (22 bp):   
GATAAACCACCACATAATCGCA

Found at i:9758 original size:19 final size:19

Alignment explanation


    Indices: 9731--9770  Score: 53
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       9721 CCTAGTCGGA

                               
       9731 AAGTAGTTTCGGGACCACT
          1 AAGTAGTTTCGGGACCACT

                *    *      *  
       9750 AAGTGGTTTTGGGACCGCT
          1 AAGTAGTTTCGGGACCACT

              
       9769 AA
          1 AA

       9771 AGAGTCACCG


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28


Consensus pattern (19 bp):   
AAGTAGTTTCGGGACCACT

Found at i:11469 original size:40 final size:40

Alignment explanation


    Indices: 11414--11555  Score: 234
    Period size: 40  Copynumber: 3.6  Consensus size: 40

      11404 TATTCGAATG

                                                    
      11414 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT

                                                    
      11454 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT

                          *                 *        
      11494 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT

                         *         
      11534 ATATCC-GGCTAAATCCCGAAGG
          1 ATATCCGGGCTAAGTCCCGAAGG

      11556 TACTTGGGTT


Statistics
Matches: 97,  Mismatches: 4, Indels: 3
        0.93            0.04        0.03

Matches are distributed among these distances:
  39   14  0.14
  40   81  0.84
  41    2  0.02

ACGTcount: A:0.24, C:0.23, G:0.27, T:0.25


Consensus pattern (40 bp):   
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT

Found at i:19430 original size:40 final size:40

Alignment explanation


    Indices: 19375--19516  Score: 207
    Period size: 40  Copynumber: 3.6  Consensus size: 40

      19365 TATTCGAATG

                                                    
      19375 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT

                                        *           
      19415 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT

                          *  *            * *        
      19455 ATATCCGGGCTAAGACCTGAAGGCATTTGTACGAGTTG-CT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT

                         *         
      19495 ATATCC-GGCTAAATCCCGAAGG
          1 ATATCCGGGCTAAGTCCCGAAGG

      19517 TACTTGGGTT


Statistics
Matches: 92,  Mismatches: 9, Indels: 3
        0.88            0.09        0.03

Matches are distributed among these distances:
  39   13  0.14
  40   77  0.84
  41    2  0.02

ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26


Consensus pattern (40 bp):   
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT

Found at i:22515 original size:10 final size:10

Alignment explanation


    Indices: 22491--22524  Score: 50
    Period size: 10  Copynumber: 3.3  Consensus size: 10

      22481 TCCTTGTGTG

                      
      22491 TTTTTATTTT
          1 TTTTTATTTT

                       
      22501 CTTTTTATTTT
          1 -TTTTTATTTT

                *     
      22512 TTTTGATTTT
          1 TTTTTATTTT

               
      22522 TTT
          1 TTT

      22525 CATCATATCT


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  10   12  0.55
  11   10  0.45

ACGTcount: A:0.09, C:0.03, G:0.03, T:0.85


Consensus pattern (10 bp):   
TTTTTATTTT

Found at i:29971 original size:15 final size:15

Alignment explanation


    Indices: 29951--29984  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

      29941 CATATTGGGC

                  *  *     
      29951 AAAAAATAACAATTA
          1 AAAAAAAAAAAATTA

                           
      29966 AAAAAAAAAAAATTA
          1 AAAAAAAAAAAATTA

                
      29981 AAAA
          1 AAAA

      29985 CCGAAAGCAT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15


Consensus pattern (15 bp):   
AAAAAAAAAAAATTA
Done.