Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1180

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: 2456
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.25

Warning! 423 characters in sequence are not A, C, G, or T


Found at i:1200 original size:22 final size:22

Alignment explanation


    Indices: 1172--1215  Score: 79
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1162 AAACAAATCT

                                  
       1172 CTTTACATAAAGCAGATATATA
          1 CTTTACATAAAGCAGATATATA

                         *        
       1194 CTTTACATAAAGCGGATATATA
          1 CTTTACATAAAGCAGATATATA

       1216 TACGGCTTTG


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32


Consensus pattern (22 bp):   
CTTTACATAAAGCAGATATATA

Found at i:1595 original size:16 final size:16

Alignment explanation


    Indices: 1574--1605  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       1564 GACAAGCTCT

                            
       1574 CTATTAACAACCGAAC
          1 CTATTAACAACCGAAC

                            
       1590 CTATTAACAACCGAAC
          1 CTATTAACAACCGAAC

       1606 GTGAATCAAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.44, C:0.31, G:0.06, T:0.19


Consensus pattern (16 bp):   
CTATTAACAACCGAAC

Found at i:2314 original size:58 final size:58

Alignment explanation


    Indices: 2224--2337  Score: 183
    Period size: 58  Copynumber: 2.0  Consensus size: 58

       2214 AAAAATTTTG

                  *     *     *                          *            
       2224 GTTGTCGACTTTTAAAAATAAAAACTGGAGTCGCCACCGATCCTTTATTAAGGTGTTA
          1 GTTGTCCACTTTAAAAAACAAAAACTGGAGTCGCCACCGATCCTTGATTAAGGTGTTA

                                    *                               
       2282 GTTGTCCACTTTAAAAAACAAAAATTGGAGTCGCCACCGATCCTTGATTAAGGTGT
          1 GTTGTCCACTTTAAAAAACAAAAACTGGAGTCGCCACCGATCCTTGATTAAGGTGT

       2338 GACCGGCCCA


Statistics
Matches: 51,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  58   51  1.00

ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Consensus pattern (58 bp):   
GTTGTCCACTTTAAAAAACAAAAACTGGAGTCGCCACCGATCCTTGATTAAGGTGTTA

Found at i:2354 original size:58 final size:58

Alignment explanation


    Indices: 2237--2357  Score: 161
    Period size: 58  Copynumber: 2.1  Consensus size: 58

       2227 GTCGACTTTT

                 *                          *          * *** *    *   
       2237 AAAAATAAAAACTGGAGTCGCCACCGATCCTTTATTAAGGTGTTAGTTGTCCACTTTA
          1 AAAAACAAAAACTGGAGTCGCCACCGATCCTTGATTAAGGTGTGACCGGCCCACCTTA

                       *                                              
       2295 AAAAACAAAAATTGGAGTCGCCACCGATCCTTGATTAAGGTGTGACCGGCCCACCTTA
          1 AAAAACAAAAACTGGAGTCGCCACCGATCCTTGATTAAGGTGTGACCGGCCCACCTTA

                 
       2353 AAAAA
          1 AAAAA

       2358 AATACTTTGG


Statistics
Matches: 54,  Mismatches: 9, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  58   54  1.00

ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25


Consensus pattern (58 bp):   
AAAAACAAAAACTGGAGTCGCCACCGATCCTTGATTAAGGTGTGACCGGCCCACCTTA
Done.