Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1206

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: 53865
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31


Found at i:1043 original size:38 final size:39

Alignment explanation


    Indices: 991--1075  Score: 154
    Period size: 38  Copynumber: 2.2  Consensus size: 39

        981 TGAGACATTA

                                                   
        991 GTAATTAGTAAGACTTTACCTGTTGAGTCTATTGAGTTT
          1 GTAATTAGTAAGACTTTACCTGTTGAGTCTATTGAGTTT

                                                   
       1030 GTAA-TAGTAAGACTTTACCTGTTGAGTCTATTGAGTTT
          1 GTAATTAGTAAGACTTTACCTGTTGAGTCTATTGAGTTT

              *     
       1068 GTGATTAG
          1 GTAATTAG

       1076 AGTTTCAAAC


Statistics
Matches: 44,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  38   37  0.84
  39    7  0.16

ACGTcount: A:0.26, C:0.09, G:0.22, T:0.42


Consensus pattern (39 bp):   
GTAATTAGTAAGACTTTACCTGTTGAGTCTATTGAGTTT

Found at i:20204 original size:38 final size:39

Alignment explanation


    Indices: 20152--20236  Score: 154
    Period size: 38  Copynumber: 2.2  Consensus size: 39

      20142 TGAGACATTA

                                                   
      20152 GTAATTAGTAAGACTTTACCTGTTGAGTCTATTGAGTTT
          1 GTAATTAGTAAGACTTTACCTGTTGAGTCTATTGAGTTT

                                                   
      20191 GTAA-TAGTAAGACTTTACCTGTTGAGTCTATTGAGTTT
          1 GTAATTAGTAAGACTTTACCTGTTGAGTCTATTGAGTTT

              *     
      20229 GTGATTAG
          1 GTAATTAG

      20237 AGTTTCAAAC


Statistics
Matches: 44,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  38   37  0.84
  39    7  0.16

ACGTcount: A:0.26, C:0.09, G:0.22, T:0.42


Consensus pattern (39 bp):   
GTAATTAGTAAGACTTTACCTGTTGAGTCTATTGAGTTT

Found at i:20880 original size:33 final size:33

Alignment explanation


    Indices: 20843--20910  Score: 127
    Period size: 33  Copynumber: 2.1  Consensus size: 33

      20833 AAGATGGAAC

                                             
      20843 TATGAGAATGTGCATTGATTATAGACAGCTCAA
          1 TATGAGAATGTGCATTGATTATAGACAGCTCAA

                        *                    
      20876 TATGAGAATGTGTATTGATTATAGACAGCTCAA
          1 TATGAGAATGTGCATTGATTATAGACAGCTCAA

              
      20909 TA
          1 TA

      20911 AGGTGACTAT


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  33   34  1.00

ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32


Consensus pattern (33 bp):   
TATGAGAATGTGCATTGATTATAGACAGCTCAA

Found at i:37389 original size:27 final size:26

Alignment explanation


    Indices: 37340--37451  Score: 125
    Period size: 27  Copynumber: 4.2  Consensus size: 26

      37330 AGGAAGCGTC

                     *   *             
      37340 CTGGTGGCTATGCTACAATTATCTGAT
          1 CTGGTGGCTCTGCCAC-ATTATCTGAT

                       *             * 
      37367 CTGGTGGCTCTACCACATATATCTGTT
          1 CTGGTGGCTCTGCCACAT-TATCTGAT

                                        
      37394 CTGGTGGCTCTGCCACGATTATCTGTAT
          1 CTGGTGGCTCTGCCAC-ATTATCTG-AT

                  *     *           * 
      37422 CTGGTGACTCTGTCACATTATCTGTT
          1 CTGGTGGCTCTGCCACATTATCTGAT

                
      37448 CTGG
          1 CTGG

      37452 CAGCCATGCT


Statistics
Matches: 73,  Mismatches: 9, Indels: 7
        0.82            0.10        0.08

Matches are distributed among these distances:
  26    7  0.10
  27   49  0.67
  28   17  0.23

ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38


Consensus pattern (26 bp):   
CTGGTGGCTCTGCCACATTATCTGAT

Found at i:37444 original size:54 final size:54

Alignment explanation


    Indices: 37340--37451  Score: 154
    Period size: 54  Copynumber: 2.1  Consensus size: 54

      37330 AGGAAGCGTC

                         *                   *                    
      37340 CTGGTGGCTATGCTACAATTATCTGATCTGGTGGCTCTACCACATATATCTGTT
          1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTACCACATATATCTGTT

                     *      *                      **              
      37394 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
          1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTACCACATATATCTGTT

                
      37448 CTGG
          1 CTGG

      37452 CAGCCATGCT


Statistics
Matches: 51,  Mismatches: 6, Indels: 2
        0.86            0.10        0.03

Matches are distributed among these distances:
  54   34  0.67
  55   17  0.33

ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38


Consensus pattern (54 bp):   
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTACCACATATATCTGTT

Found at i:48359 original size:38 final size:38

Alignment explanation


    Indices: 48317--48392  Score: 152
    Period size: 38  Copynumber: 2.0  Consensus size: 38

      48307 CAAGAACTCC

                                                  
      48317 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
          1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA

                                                  
      48355 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
          1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA

      48393 AAAGGATGAA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  38   38  1.00

ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32


Consensus pattern (38 bp):   
TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Done.