Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1171

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: 6344
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30


Found at i:1988 original size:52 final size:52

Alignment explanation


    Indices: 1909--2029  Score: 206
    Period size: 52  Copynumber: 2.3  Consensus size: 52

       1899 GAAAATATGT

                                                                
       1909 CTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTAC
          1 CTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTAC

               *                *                             * 
       1961 CTGTATGTATCGATACATTTTATAGTGTATCGATACATCTGGGCAAATTTGC
          1 CTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTAC

                       *     
       2013 CTGCATGTATCAATACA
          1 CTGCATGTATCGATACA

       2030 AAGATCAGTG


Statistics
Matches: 64,  Mismatches: 5, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  52   64  1.00

ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36


Consensus pattern (52 bp):   
CTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTAC

Found at i:2040 original size:52 final size:52

Alignment explanation


    Indices: 1909--2049  Score: 176
    Period size: 52  Copynumber: 2.7  Consensus size: 52

       1899 GAAAATATGT

                       *      ***                               
       1909 CTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTAC
          1 CTGCATGTATCAATACATAAGATAGTGTATCGATACATCTGGGCAAATTTAC

               *       *      ***                             * 
       1961 CTGTATGTATCGATACATTTTATAGTGTATCGATACATCTGGGCAAATTTGC
          1 CTGCATGTATCAATACATAAGATAGTGTATCGATACATCTGGGCAAATTTAC

                                                  
       2013 CTGCATGTATCAATACA-AAGATCAGTGTATCGATACA
          1 CTGCATGTATCAATACATAAGAT-AGTGTATCGATACA

       2050 ATGTATCGAT


Statistics
Matches: 80,  Mismatches: 8, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
  51    2  0.03
  52   78  0.98

ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34


Consensus pattern (52 bp):   
CTGCATGTATCAATACATAAGATAGTGTATCGATACATCTGGGCAAATTTAC

Found at i:2056 original size:13 final size:13

Alignment explanation


    Indices: 2038--2062  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       2028 CAAAGATCAG

                         
       2038 TGTATCGATACAA
          1 TGTATCGATACAA

                        
       2051 TGTATCGATACA
          1 TGTATCGATACA

       2063 TTTGAGTAAT


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:0.36, C:0.16, G:0.16, T:0.32


Consensus pattern (13 bp):   
TGTATCGATACAA

Found at i:2141 original size:32 final size:33

Alignment explanation


    Indices: 2100--2168  Score: 113
    Period size: 32  Copynumber: 2.1  Consensus size: 33

       2090 GGCAGTAGCT

                                             
       2100 TACATTGTATCGATACAAAAC-TTATGTATCGA
          1 TACATTGTATCGATACAAAACTTTATGTATCGA

                              *            * 
       2132 TACATTGTATCGATACAACACTTTATGTATCTA
          1 TACATTGTATCGATACAAAACTTTATGTATCGA

                
       2165 TACA
          1 TACA

       2169 AATCGTTGAA


Statistics
Matches: 34,  Mismatches: 2, Indels: 1
        0.92            0.05        0.03

Matches are distributed among these distances:
  32   20  0.59
  33   14  0.41

ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36


Consensus pattern (33 bp):   
TACATTGTATCGATACAAAACTTTATGTATCGA

Found at i:2142 original size:13 final size:13

Alignment explanation


    Indices: 2124--2148  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       2114 ACAAAACTTA

                         
       2124 TGTATCGATACAT
          1 TGTATCGATACAT

                        
       2137 TGTATCGATACA
          1 TGTATCGATACA

       2149 ACACTTTATG


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:0.32, C:0.16, G:0.16, T:0.36


Consensus pattern (13 bp):   
TGTATCGATACAT

Found at i:3185 original size:174 final size:173

Alignment explanation


    Indices: 2884--3233  Score: 637
    Period size: 174  Copynumber: 2.0  Consensus size: 173

       2874 ATAAGAAAAT

                                         *                                   
       2884 CATCTCTAAACTAAATGAAGAAAATAAATCAATAAGTTTAGAGAATGTTGAGCTTAAAAAAAATT
          1 CATCTCTAAACTAAATGAAGAAAATAAATAAATAAGTTTAGAGAATGTTGAGCTTAAAAAAAATT

                      *                                                      
       2949 AATCAAATTAGAGAAACAATTGAATGAGGTACAAGATAATAATAAAGTCTTAACAAATGAAAACA
         66 AATCAAATTAAAGAAACAATTGAATGAGGTACAAGATAATAATAAAGTCTTAACAAATGAAAACA

                                                       
       3014 ATGAATTAGTTAAGAAAAACAAAAATTTGCATGAGTCATTCAC
        131 ATGAATTAGTTAAGAAAAACAAAAATTTGCATGAGTCATTCAC

                                                                             
       3057 CATCTCTAAACTAAATGAAGAAAATAAATAAATAAGTTTAGAGAATGTTGAGCTTAAAAAGAAAT
          1 CATCTCTAAACTAAATGAAGAAAATAAATAAATAAGTTTAGAGAATGTTGAGCTTAAAAA-AAAT

                **                                    *                      
       3122 TAATTGAATTAAAGAAACAATTGAATGAGGTACAAGATAATACTAAAGTCTTAACAAATGAAAAC
         65 TAATCAAATTAAAGAAACAATTGAATGAGGTACAAGATAATAATAAAGTCTTAACAAATGAAAAC

                                     *                  
       3187 AATGAATTAGTTAAGAAAAACAAAATTTTGCATGAGTCATTCAC
        130 AATGAATTAGTTAAGAAAAACAAAAATTTGCATGAGTCATTCAC

               
       3231 CAT
          1 CAT

       3234 GTTTTACAAA


Statistics
Matches: 170,  Mismatches: 6, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
 173   59  0.35
 174  111  0.65

ACGTcount: A:0.51, C:0.10, G:0.13, T:0.26


Consensus pattern (173 bp):   
CATCTCTAAACTAAATGAAGAAAATAAATAAATAAGTTTAGAGAATGTTGAGCTTAAAAAAAATT
AATCAAATTAAAGAAACAATTGAATGAGGTACAAGATAATAATAAAGTCTTAACAAATGAAAACA
ATGAATTAGTTAAGAAAAACAAAAATTTGCATGAGTCATTCAC

Done.