Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold947

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: 10636
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37


Found at i:52 original size:2 final size:2

Alignment explanation


    Indices: 47--97  Score: 66
    Period size: 2  Copynumber: 25.5  Consensus size: 2

         37 ACTGTGTGTG

                                       *  *   *     *                     
         47 TA TA TA TA TA TA TA TA TA CA AA TT TA TG TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                         
         89 TA TA TA TA T
          1 TA TA TA TA T

         98 GAACAAAAAG


Statistics
Matches: 42,  Mismatches: 7, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
   2   42  1.00

ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:5201 original size:21 final size:20

Alignment explanation


    Indices: 5163--5210  Score: 53
    Period size: 20  Copynumber: 2.4  Consensus size: 20

       5153 TTAAATGCAA

                        **      
       5163 ATAATTATTTATTTTATAAT
          1 ATAATTATTTATAATATAAT

                                 
       5183 ATAATTGATTTATAATAT-AT
          1 ATAATT-ATTTATAATATAAT

             *      
       5203 AGAATTAT
          1 ATAATTAT

       5211 AAAATTATGT


Statistics
Matches: 24,  Mismatches: 3, Indels: 3
        0.80            0.10        0.10

Matches are distributed among these distances:
  19    2  0.08
  20   13  0.54
  21    9  0.38

ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52


Consensus pattern (20 bp):   
ATAATTATTTATAATATAAT

Found at i:5691 original size:20 final size:20

Alignment explanation


    Indices: 5654--5699  Score: 56
    Period size: 20  Copynumber: 2.3  Consensus size: 20

       5644 TTAAATGCAA

                      * **      
       5654 ATAATTATTTGTTTTATAAT
          1 ATAATTATTTATAATATAAT

                                
       5674 ATAATTATTTATAATATAAT
          1 ATAATTATTTATAATATAAT

             *    
       5694 AGAATT
          1 ATAATT

       5700 GTAAAATTGT


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   22  1.00

ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52


Consensus pattern (20 bp):   
ATAATTATTTATAATATAAT

Found at i:5868 original size:166 final size:167

Alignment explanation


    Indices: 5409--5905  Score: 900
    Period size: 165  Copynumber: 3.0  Consensus size: 167

       5399 CTTATGCGAG

                                 *           *                               
       5409 TTTTTTT-GGTTAGTTTTCATTGATTTTTAT-TCTATATGAAAGTATTTTACTTTTAGTCTTTTC
          1 TTTTTTTGGGTTAGTTTTCATCGATTTTTATCTTTATATGAAAGTATTTTACTTTTAGTCTTTTC

                           *                                                 
       5472 -TTTTTGTTTAAATGTAAATAATTATTTG-TTTATAATATAATTGATTTATAATATAATAGAATT
         66 TTTTTTGTTTAAATGCAAATAATTATTTGTTTTATAATATAATTGATTTATAATATAATAGAATT

                                                 
       5535 GTAAAATTGTGTAGTAATTCTATTATATTAT-AATAT
        131 GTAAAATTGTGTAGTAATTCTATTATATTATAAATAT

                                                   *                         
       5571 TTTTTTTGGGTTAGTTTTCATCGATTTTTATCTTTATATAAAAGTATTTTACTTTTAGTCTTTTC
          1 TTTTTTTGGGTTAGTTTTCATCGATTTTTATCTTTATATGAAAGTATTTTACTTTTAGTCTTTTC

                                                                             
       5636 TTTTTTGTTTAAATGCAAATAATTATTTGTTTTATAATATAATT-ATTTATAATATAATAGAATT
         66 TTTTTTGTTTAAATGCAAATAATTATTTGTTTTATAATATAATTGATTTATAATATAATAGAATT

                                                 
       5700 GTAAAATTGTGTAGTAATTCTATTATATTATAAATAT
        131 GTAAAATTGTGTAGTAATTCTATTATATTATAAATAT

                                                                             
       5737 TTTTTTTGGGTTAG-TTTCATCGATTTTTATCTTTATATGAAAGTATTTTACTTTTAGTCTTTTC
          1 TTTTTTTGGGTTAGTTTTCATCGATTTTTATCTTTATATGAAAGTATTTTACTTTTAGTCTTTTC

                                                                             
       5801 TTTTTTGTTTAAATGCAAATAATTATTTGTTTTATAATATAATTGATTTATAATATAATAGAATT
         66 TTTTTTGTTTAAATGCAAATAATTATTTGTTTTATAATATAATTGATTTATAATATAATAGAATT

                                               * 
       5866 GTAAAATTGTGTAGTAATTCTATTATATTATAAATGT
        131 GTAAAATTGTGTAGTAATTCTATTATATTATAAATAT

               
       5903 TTT
          1 TTT

       5906 GTATATTATA


Statistics
Matches: 323,  Mismatches: 6, Indels: 8
        0.96            0.02        0.02

Matches are distributed among these distances:
 162    7  0.02
 163   22  0.07
 164   31  0.10
 165  171  0.53
 166   92  0.28

ACGTcount: A:0.31, C:0.04, G:0.10, T:0.55


Consensus pattern (167 bp):   
TTTTTTTGGGTTAGTTTTCATCGATTTTTATCTTTATATGAAAGTATTTTACTTTTAGTCTTTTC
TTTTTTGTTTAAATGCAAATAATTATTTGTTTTATAATATAATTGATTTATAATATAATAGAATT
GTAAAATTGTGTAGTAATTCTATTATATTATAAATAT

Found at i:7584 original size:13 final size:13

Alignment explanation


    Indices: 7566--7590  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       7556 ATTTAAAATA

                         
       7566 TTTTTTAAATTTT
          1 TTTTTTAAATTTT

                        
       7579 TTTTTTAAATTT
          1 TTTTTTAAATTT

       7591 AAAATTTTAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76


Consensus pattern (13 bp):   
TTTTTTAAATTTT
Done.