Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1627

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: 17462
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34


Found at i:4101 original size:2 final size:2

Alignment explanation


    Indices: 4094--4125  Score: 55
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       4084 CAATAAATCA

                                                    *      
       4094 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       4126 CGATGTTTCG


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:5034 original size:29 final size:28

Alignment explanation


    Indices: 4992--5049  Score: 73
    Period size: 29  Copynumber: 2.0  Consensus size: 28

       4982 TGTATTCGAT

                            *            
       4992 TTTAATTGAATTAATTTATTGAAATAAAA
          1 TTTAATTGAATTAATTAATT-AAATAAAA

                                   *     
       5021 TTTAATTTG-ATTAATTAATTAATTAAAA
          1 TTTAA-TTGAATTAATTAATTAAATAAAA

             
       5049 T
          1 T

       5050 ATTTAGTTAT


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  28    8  0.31
  29   15  0.58
  30    3  0.12

ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48


Consensus pattern (28 bp):   
TTTAATTGAATTAATTAATTAAATAAAA

Found at i:5290 original size:23 final size:22

Alignment explanation


    Indices: 5253--5295  Score: 68
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       5243 GATGATTATA

                *                 
       5253 TAAATTATAAAAATTAAAATTT
          1 TAAAATATAAAAATTAAAATTT

                                 
       5275 TAAAATATAAATAATTAAAAT
          1 TAAAATATAAA-AATTAAAAT

       5296 CCGATTAATT


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  22   10  0.53
  23    9  0.47

ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37


Consensus pattern (22 bp):   
TAAAATATAAAAATTAAAATTT

Found at i:5776 original size:24 final size:24

Alignment explanation


    Indices: 5740--5785  Score: 74
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       5730 GTAGTTATTT

                                    
       5740 TTGTTTGTAAAAAATGGTGGCTTG
          1 TTGTTTGTAAAAAATGGTGGCTTG

                    *    *        
       5764 TTGTTTGTCAAAATTGGTGGCT
          1 TTGTTTGTAAAAAATGGTGGCT

       5786 AATTTTTATT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  24   20  1.00

ACGTcount: A:0.22, C:0.07, G:0.28, T:0.43


Consensus pattern (24 bp):   
TTGTTTGTAAAAAATGGTGGCTTG

Found at i:10141 original size:28 final size:28

Alignment explanation


    Indices: 10081--10158  Score: 90
    Period size: 28  Copynumber: 2.9  Consensus size: 28

      10071 AAATGCCACA

                                   *    
      10081 TTTTGTATTTGTCAAATATGGTGATTTC
          1 TTTTGTATTTGTCAAATATGGTGGTTTC

            *                            
      10109 CTTTGTATTTGTCAAATATGGTGGTTAT-
          1 TTTTGTATTTGTCAAATATGGTGGTT-TC

                        *   *       
      10137 TTTTG--TTTGTAAAAAATGGTGG
          1 TTTTGTATTTGTCAAATATGGTGG

      10159 CTTGTTGTTT


Statistics
Matches: 44,  Mismatches: 5, Indels: 4
        0.83            0.09        0.08

Matches are distributed among these distances:
  26   15  0.34
  28   28  0.64
  29    1  0.02

ACGTcount: A:0.23, C:0.05, G:0.22, T:0.50


Consensus pattern (28 bp):   
TTTTGTATTTGTCAAATATGGTGGTTTC

Found at i:10175 original size:24 final size:24

Alignment explanation


    Indices: 10116--10184  Score: 75
    Period size: 24  Copynumber: 2.8  Consensus size: 24

      10106 TTCCTTTGTA

                     *         *  *   
      10116 TTTGTCAAATATGGTGGTTATTTTTG
          1 TTTGTCAAAAATGGTGG--CTTGTTG

                 *                  
      10142 TTTGTAAAAAATGGTGGCTTGTTG
          1 TTTGTCAAAAATGGTGGCTTGTTG

                      *        
      10166 TTTGTCAAAATTGGTGGCT
          1 TTTGTCAAAAATGGTGGCT

      10185 AATTTTTATT


Statistics
Matches: 37,  Mismatches: 6, Indels: 2
        0.82            0.13        0.04

Matches are distributed among these distances:
  24   22  0.59
  26   15  0.41

ACGTcount: A:0.22, C:0.06, G:0.26, T:0.46


Consensus pattern (24 bp):   
TTTGTCAAAAATGGTGGCTTGTTG
Done.