Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold708

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: 8672
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28


Found at i:6251 original size:28 final size:28

Alignment explanation


    Indices: 6170--6251  Score: 96
    Period size: 28  Copynumber: 2.9  Consensus size: 28

       6160 TTTTGGAGAT

                              *           
       6170 AATAACGAGGTTGGAGTGTTCCCTCG--GA
          1 AATAACGAGGTTGGAGT-AT-CCTCGATGA

             *     *             *      
       6198 AGTAACGGGGTTGGAGTATCCCCGATGA
          1 AATAACGAGGTTGGAGTATCCTCGATGA

                                      
       6226 AATAACGAGGTTGGAGTATCCTCGAT
          1 AATAACGAGGTTGGAGTATCCTCGAT

       6252 TGTGAAAAAA


Statistics
Matches: 45,  Mismatches: 7, Indels: 4
        0.80            0.12        0.07

Matches are distributed among these distances:
  26    4  0.09
  27    1  0.02
  28   40  0.89

ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24


Consensus pattern (28 bp):   
AATAACGAGGTTGGAGTATCCTCGATGA

Found at i:6354 original size:53 final size:50

Alignment explanation


    Indices: 6291--6405  Score: 140
    Period size: 50  Copynumber: 2.2  Consensus size: 50

       6281 AAAATCGGAA

                                  *    * * *                     
       6291 TGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGGGGT
          1 TGGAGTATCCCCGATT--AGGAAAAATCGATATT-TGAAAATAAAACCGGGGT

                             *                        **      
       6344 TGGAGTATCCCCGATTATGAAAAATCGATATTTGAAAATAAAGTCGGGGT
          1 TGGAGTATCCCCGATTAGGAAAAATCGATATTTGAAAATAAAACCGGGGT

                        
       6394 TGGAGTATCCCC
          1 TGGAGTATCCCC

       6406 TCAGAGAAGT


Statistics
Matches: 55,  Mismatches: 7, Indels: 3
        0.85            0.11        0.05

Matches are distributed among these distances:
  50   28  0.51
  51   11  0.20
  53   16  0.29

ACGTcount: A:0.33, C:0.14, G:0.27, T:0.26


Consensus pattern (50 bp):   
TGGAGTATCCCCGATTAGGAAAAATCGATATTTGAAAATAAAACCGGGGT

Found at i:6514 original size:214 final size:211

Alignment explanation


    Indices: 6178--6571  Score: 551
    Period size: 214  Copynumber: 1.9  Consensus size: 211

       6168 ATAATAACGA

                     * *                                                     
       6178 GGTTGGAGTGTTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
          1 GGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT

                *                    *         *                             
       6243 ATCCTCGATTGTGAAAAAATTGGTATTTTTTTGGACATAAAATCGGAATGGAGTATCCCCGATTA
         66 ATCCCCGATTGTGAAAAAATTGGTAGTTTTTTGGAAATAAAATCGGAATGGAGTATCCCCGATTA

                       **                    *      *                        
       6308 AAGGAGAAATTGGTGTTGTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCGAT
        131 AA-GA-AAATTAATGTTGTGAAAATAAAACCGGAGTTGGAATATCCCCGATTATGAAAAATCGAT

                              
       6373 ATTTGAAAATAAAGTCGG
        194 ATTTGAAAATAAAGTCGG

                                                               *             
       6391 GGTTGGAGTATCCCCTCAGAGAAGTAACGGGGTTGGAGTATCCCCGATG-ATTAACCG-GGTTGG
          1 GGTTGGAGTATCCCCTC-G-GAAGTAACGGGGTTGGAGTATCCCCGATGAAATAA-CGAGGTTGG

               *              *                                *             
       6454 AGTGTCCCCGATTGTGAAGAAATTGGT-GTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCG
         63 AGTATCCCCGATTGTGAAAAAATTGGTAGTTTTTTGGAAATAAAATCGGA-ATGGAGTATCCCCG

                *              *     *     *                *     
       6518 ATTATAGAAAATTAATGTTTTGAAAGTAAAATCGGAGTTGGAATATCCTCGATT
        127 ATTAAAGAAAATTAATGTTGTGAAAATAAAACCGGAGTTGGAATATCCCCGATT

       6572 GTGAGAATTG


Statistics
Matches: 159,  Mismatches: 18, Indels: 9
        0.85            0.10        0.05

Matches are distributed among these distances:
 212   38  0.24
 213   37  0.23
 214   53  0.33
 215   31  0.19

ACGTcount: A:0.30, C:0.13, G:0.28, T:0.29


Consensus pattern (211 bp):   
GGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
ATCCCCGATTGTGAAAAAATTGGTAGTTTTTTGGAAATAAAATCGGAATGGAGTATCCCCGATTA
AAGAAAATTAATGTTGTGAAAATAAAACCGGAGTTGGAATATCCCCGATTATGAAAAATCGATAT
TTGAAAATAAAGTCGG

Found at i:6516 original size:54 final size:53

Alignment explanation


    Indices: 6449--6575  Score: 145
    Period size: 51  Copynumber: 2.4  Consensus size: 53

       6439 GATTAACCGG

                    *                     **                        
       6449 GTTGGAGTGTCCCCGATTGTGAAG-AAATTGGTGTTTTTTGGAAA-TAAAATCGGA
          1 GTTGGAGTATCCCCGATTGTGAAGAAAATTAATG--TTTT-GAAAGTAAAATCGGA

                              *                                  
       6503 GTTGGAGTATCCCCGATTAT--AGAAAATTAATGTTTTGAAAGTAAAATCGGA
          1 GTTGGAGTATCCCCGATTGTGAAGAAAATTAATGTTTTGAAAGTAAAATCGGA

                  *     *         
       6554 GTTGGAATATCCTCGATTGTGA
          1 GTTGGAGTATCCCCGATTGTGA

       6576 GAATTGAGCA


Statistics
Matches: 62,  Mismatches: 7, Indels: 9
        0.79            0.09        0.12

Matches are distributed among these distances:
  50    4  0.06
  51   31  0.50
  52    2  0.03
  53    7  0.11
  54   18  0.29

ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33


Consensus pattern (53 bp):   
GTTGGAGTATCCCCGATTGTGAAGAAAATTAATGTTTTGAAAGTAAAATCGGA
Done.