Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold287

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: 11710
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33


Found at i:1305 original size:41 final size:41

Alignment explanation


    Indices: 1217--1443  Score: 266
    Period size: 41  Copynumber: 5.5  Consensus size: 41

       1207 TTTAAACAGA

                 *                    *     *           
       1217 TTCACTGGCACTT-AGCCTGCTAGACTTAAAGCCTG-ATTCAG-
          1 TTCACCGGCA-TTAAGCCTGCTAGACGTAAAGTCTGAATT--GT

             *                        *  *        *   
       1258 TACACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGT
          1 TTCACCGGCA-TTAAGCCTGCTAGACGTAAAGTCTGAATTGT

                                                      
       1299 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
          1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGA-ATTGT

                 *                                  * 
       1341 TTCACTGG-ATTAAGCCTGCTAGACGTAAAGTCTGAAATTAT
          1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTG-AATTGT

                                                      
       1382 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
          1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGA-ATTGT

                                
       1424 TTCACCGGCATTAAGTCCTG
          1 TTCACCGGCATTAAG-CCTG

       1444 ATAGGCACTG


Statistics
Matches: 164,  Mismatches: 14, Indels: 14
        0.85            0.07        0.07

Matches are distributed among these distances:
  40    3  0.02
  41   98  0.60
  42   59  0.36
  43    4  0.02

ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30


Consensus pattern (41 bp):   
TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTGT

Found at i:1411 original size:83 final size:83

Alignment explanation


    Indices: 1217--1443  Score: 293
    Period size: 83  Copynumber: 2.7  Consensus size: 83

       1207 TTTAAACAGA

                 *                    *     *        *   *                   
       1217 TTCACTGGCACTT-AGCCTGCTAGACTTAAAGCCTGAT-TCAG-TACACCGGCACTT-AGCCTGC
          1 TTCACCGGCA-TTAAGCCTGCTAGACGTAAAGTCTGATAT-TGTTTCACCGGCA-TTAAGCCTGC

                    *          * 
       1278 TAGACATATAGTCTGAAATGT
         63 TAGACATAAAGTCTGAAATAT

                                                           *                 
       1299 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGTTTCACTGG-ATTAAGCCTGCTAG
          1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTAAGCCTGCTAG

              *                
       1363 ACGTAAAGTCTGAAATTAT
         66 ACATAAAGTCTGAAA-TAT

                                                                          
       1382 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTAAGTCCTG
          1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTAAG-CCTG

       1444 ATAGGCACTG


Statistics
Matches: 128,  Mismatches: 10, Indels: 11
        0.86            0.07        0.07

Matches are distributed among these distances:
  81    4  0.03
  82   56  0.44
  83   58  0.45
  84    6  0.05
  85    4  0.03

ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30


Consensus pattern (83 bp):   
TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTAAGCCTGCTAG
ACATAAAGTCTGAAATAT

Found at i:8788 original size:42 final size:42

Alignment explanation


    Indices: 8650--8875  Score: 291
    Period size: 42  Copynumber: 5.5  Consensus size: 42

       8640 TTTAAACAGA

                 *                    *     *        *  
       8650 TTCACTGGCACTT-AGCCTGCTAGACTTAAAGCCTGAT-TCAG-
          1 TTCACCGGCA-TTAAGCCTGCTAGACGTAAAGTCTGATAT-TGT

             *   *      *            *  *         *   
       8691 TACACTGGCATTTAGCCTGCTAGACATATAGTCTGA-AATGT
          1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT

                                                      
       8732 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
          1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT

                                                *   * 
       8774 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATTAT
          1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT

                                                      
       8816 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
          1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT

                               
       8858 TTCACCGGCATTAA-CCTG
          1 TTCACCGGCATTAAGCCTG

       8876 ATAGGCACTG


Statistics
Matches: 165,  Mismatches: 16, Indels: 8
        0.87            0.08        0.04

Matches are distributed among these distances:
  40    3  0.02
  41   64  0.39
  42   98  0.59

ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30


Consensus pattern (42 bp):   
TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT

Found at i:11134 original size:4 final size:4

Alignment explanation


    Indices: 11127--11164  Score: 67
    Period size: 4  Copynumber: 9.5  Consensus size: 4

      11117 CACACACAAC

                                *                          
      11127 CATA CATA CATA CATA TATA CATA CATA CATA CATA CA
          1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CA

      11165 ACAACTTCTC


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   4   32  1.00

ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26


Consensus pattern (4 bp):   
CATA

Done.