Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1131

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: 13522
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32


Found at i:7792 original size:13 final size:13

Alignment explanation


    Indices: 7774--7834  Score: 71
    Period size: 13  Copynumber: 5.2  Consensus size: 13

       7764 ATACAAAGAT

                         
       7774 CAATGTATCGATA
          1 CAATGTATCGATA

                         
       7787 CAATGTATCGATA
          1 CAATGTATCGATA

              *          
       7800 CATTG-A--G-T-
          1 CAATGTATCGATA

                         
       7808 -AATGTATCGATA
          1 CAATGTATCGATA

                         
       7820 CAATGTATCGATA
          1 CAATGTATCGATA

              
       7833 CA
          1 CA

       7835 TTGAGTAATG


Statistics
Matches: 40,  Mismatches: 2, Indels: 12
        0.74            0.04        0.22

Matches are distributed among these distances:
   7    3  0.08
   8    1  0.03
   9    1  0.03
  10    2  0.05
  11    1  0.03
  12    1  0.03
  13   31  0.77

ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31


Consensus pattern (13 bp):   
CAATGTATCGATA

Found at i:7797 original size:33 final size:33

Alignment explanation


    Indices: 7755--7854  Score: 166
    Period size: 33  Copynumber: 3.0  Consensus size: 33

       7745 AAATTTCCCA

                          **                  
       7755 AATGTATCGATACAAAGA-TCAATGTATCGATAC
          1 AATGTATCGATACATTGAGT-AATGTATCGATAC

                                             
       7788 AATGTATCGATACATTGAGTAATGTATCGATAC
          1 AATGTATCGATACATTGAGTAATGTATCGATAC

                                             
       7821 AATGTATCGATACATTGAGTAATGTATCGATAC
          1 AATGTATCGATACATTGAGTAATGTATCGATAC

             
       7854 A
          1 A

       7855 TTTCCTTGGC


Statistics
Matches: 64,  Mismatches: 2, Indels: 2
        0.94            0.03        0.03

Matches are distributed among these distances:
  33   63  0.98
  34    1  0.02

ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31


Consensus pattern (33 bp):   
AATGTATCGATACATTGAGTAATGTATCGATAC

Found at i:7813 original size:20 final size:20

Alignment explanation


    Indices: 7788--7856  Score: 89
    Period size: 20  Copynumber: 3.8  Consensus size: 20

       7778 GTATCGATAC

                                
       7788 AATGTATCGATACATTGAGT
          1 AATGTATCGATACATTGAGT

                                
       7808 AATGTATCGATAC-------
          1 AATGTATCGATACATTGAGT

                                
       7821 AATGTATCGATACATTGAGT
          1 AATGTATCGATACATTGAGT

                            
       7841 AATGTATCGATACATT
          1 AATGTATCGATACATT

       7857 TCCTTGGCAG


Statistics
Matches: 42,  Mismatches: 0, Indels: 14
        0.75            0.00        0.25

Matches are distributed among these distances:
  13   13  0.31
  20   29  0.69

ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35


Consensus pattern (20 bp):   
AATGTATCGATACATTGAGT

Found at i:7896 original size:13 final size:13

Alignment explanation


    Indices: 7878--7929  Score: 50
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       7868 AGCTTCGTAG

                         
       7878 CGATACATTGTAT
          1 CGATACATTGTAT

                               
       7891 CGATACAAAACTTATGTAT
          1 CGATAC---A-TT--GTAT

                         
       7910 CGATACATTGTAT
          1 CGATACATTGTAT

                   
       7923 CGATACA
          1 CGATACA

       7930 ACACTTGTAC


Statistics
Matches: 33,  Mismatches: 0, Indels: 12
        0.73            0.00        0.27

Matches are distributed among these distances:
  13   17  0.52
  15    2  0.06
  16    2  0.06
  17    2  0.06
  19   10  0.30

ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33


Consensus pattern (13 bp):   
CGATACATTGTAT

Found at i:7919 original size:32 final size:29

Alignment explanation


    Indices: 7878--7947  Score: 104
    Period size: 32  Copynumber: 2.3  Consensus size: 29

       7868 AGCTTCGTAG

                                           
       7878 CGATACATTGTATCGATACAAAACTTATGTA
          1 CGATACATTGTATCGATACAAAAC-T-TGTA

                                  *       
       7909 TCGATACATTGTATCGATACAACACTTGTA
          1 -CGATACATTGTATCGATACAAAACTTGTA

                     
       7939 CGATACATT
          1 CGATACATT

       7948 TACTGTTTGT


Statistics
Matches: 37,  Mismatches: 1, Indels: 3
        0.90            0.02        0.07

Matches are distributed among these distances:
  29    9  0.24
  30    4  0.11
  31    1  0.03
  32   23  0.62

ACGTcount: A:0.36, C:0.19, G:0.13, T:0.33


Consensus pattern (29 bp):   
CGATACATTGTATCGATACAAAACTTGTA
Done.