Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1094

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: 4473
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32


Found at i:843 original size:13 final size:13

Alignment explanation


    Indices: 803--854  Score: 53
    Period size: 13  Copynumber: 4.5  Consensus size: 13

        793 CCGTTTGAAG

                         
        803 CAATGTATCGATA
          1 CAATGTATCGATA

                         
        816 CAA--T-TC-AT-
          1 CAATGTATCGATA

                         
        824 C-ATGTATCGATA
          1 CAATGTATCGATA

                         
        836 CAATGTATCGATA
          1 CAATGTATCGATA

            *     
        849 TAATGT
          1 CAATGT

        855 GCCAAGTATC


Statistics
Matches: 32,  Mismatches: 1, Indels: 12
        0.71            0.02        0.27

Matches are distributed among these distances:
   7    1  0.03
   8    1  0.03
   9    3  0.09
  10    4  0.12
  11    3  0.09
  12    1  0.03
  13   19  0.59

ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35


Consensus pattern (13 bp):   
CAATGTATCGATA

Found at i:925 original size:20 final size:19

Alignment explanation


    Indices: 900--953  Score: 63
    Period size: 19  Copynumber: 2.8  Consensus size: 19

        890 CTGCCAGTTT

                   *          **
        900 CATGTATAGATACAATTGTC
          1 CATGTATCGATACAA-TGAA

                        *      
        920 CATGTATCGATATAATGAA
          1 CATGTATCGATACAATGAA

                           
        939 CATGTATCGATACAA
          1 CATGTATCGATACAA

        954 AGCATAATGT


Statistics
Matches: 29,  Mismatches: 5, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  19   16  0.55
  20   13  0.45

ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31


Consensus pattern (19 bp):   
CATGTATCGATACAATGAA

Found at i:3389 original size:74 final size:74

Alignment explanation


    Indices: 3268--3415  Score: 296
    Period size: 74  Copynumber: 2.0  Consensus size: 74

       3258 TTGGAAGAGC

                                                                             
       3268 TTGAAAAGTTTAAAAAAGGTAAAAATTTAAGTTTTAGGTGAAGATCAAGGTTGGAGTATCGCCTC
          1 TTGAAAAGTTTAAAAAAGGTAAAAATTTAAGTTTTAGGTGAAGATCAAGGTTGGAGTATCGCCTC

                     
       3333 AGAGATGTT
         66 AGAGATGTT

                                                                             
       3342 TTGAAAAGTTTAAAAAAGGTAAAAATTTAAGTTTTAGGTGAAGATCAAGGTTGGAGTATCGCCTC
          1 TTGAAAAGTTTAAAAAAGGTAAAAATTTAAGTTTTAGGTGAAGATCAAGGTTGGAGTATCGCCTC

                     
       3407 AGAGATGTT
         66 AGAGATGTT

       3416 GGGGTTGGAG


Statistics
Matches: 74,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  74   74  1.00

ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31


Consensus pattern (74 bp):   
TTGAAAAGTTTAAAAAAGGTAAAAATTTAAGTTTTAGGTGAAGATCAAGGTTGGAGTATCGCCTC
AGAGATGTT

Found at i:3652 original size:80 final size:78

Alignment explanation


    Indices: 3405--3670  Score: 266
    Period size: 80  Copynumber: 3.3  Consensus size: 78

       3395 GAGTATCGCC

                              *        *         *    * * *                  
       3405 TCAGAGATGTTGGGGTTGGAGTATCCCTAAAGATGAAGAATTTGGTATTTTAGAAGTAAAAATGG
          1 TCAGAGATG-TGGGGTTGAAGTATCCCCAAAGATGAAAAATTCGATGTTTTAGAAGTAAAAATGG

                            
       3470 GGTTGAAGTATCCCCT
         65 GGTTGAA-TAT-CCCT

              *  *     *              *                         *            
       3486 T-GGAAATGGTAGGGTT-AGAGTATCTCCAAAGATGAAAAATTCGATGTTTTGGAAGTAAAAATG
          1 TCAGAGAT-GTGGGGTTGA-AGTATCCCCAAAGATGAAAAATTCGATGTTTTAGAAGTAAAAATG

                    * *  *  
       3549 GGGTTCGAGTCTCACT
         64 GGGTT-GAATATCCCT

             **                                            *   *             
       3565 TTGGAGATAGTGGGGTTGAAGTATCCCCAAAGATGAAAAATTCGATGCTTTCGAAGTAAAAATGG
          1 TCAGAGAT-GTGGGGTTGAAGTATCCCCAAAGATGAAAAATTCGATGTTTTAGAAGTAAAAATGG

                     *     
       3630 GGTTAGAATGTCCCT
         65 GGTT-GAATATCCCT

                                      
       3645 TCAGAGATTGTGGGGTTGAAGTATCC
          1 TCAGAGA-TGTGGGGTTGAAGTATCC

       3671 TAGATATCAA


Statistics
Matches: 153,  Mismatches: 26, Indels: 13
        0.80            0.14        0.07

Matches are distributed among these distances:
  79    4  0.03
  80  143  0.93
  81    6  0.04

ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29


Consensus pattern (78 bp):   
TCAGAGATGTGGGGTTGAAGTATCCCCAAAGATGAAAAATTCGATGTTTTAGAAGTAAAAATGGG
GTTGAATATCCCT
Done.