Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold969

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: 3734
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.29

Warning! 479 characters in sequence are not A, C, G, or T


Found at i:1073 original size:48 final size:47

Alignment explanation


    Indices: 1002--1093  Score: 141
    Period size: 48  Copynumber: 1.9  Consensus size: 47

        992 NNNNNNNNNN

                           *              *                
       1002 TTTTTTTTTACTCAAGGCTCCCTTTGTAGGGTTTCACCTTGGTCTCC
          1 TTTTTTTTTACTCAAAGCTCCCTTTGTAGGCTTTCACCTTGGTCTCC

                                                          
       1049 TTTTTTTTTGACTCAAAG-TGCCCTTTGTAGGCTTTCACCTTGGTC
          1 TTTTTTTTT-ACTCAAAGCT-CCCTTTGTAGGCTTTCACCTTGGTC

       1094 CCACCCTTTT


Statistics
Matches: 41,  Mismatches: 2, Indels: 3
        0.89            0.04        0.07

Matches are distributed among these distances:
  47   10  0.24
  48   31  0.76

ACGTcount: A:0.12, C:0.24, G:0.17, T:0.47


Consensus pattern (47 bp):   
TTTTTTTTTACTCAAAGCTCCCTTTGTAGGCTTTCACCTTGGTCTCC

Found at i:1104 original size:48 final size:48

Alignment explanation


    Indices: 1004--1105  Score: 118
    Period size: 48  Copynumber: 2.1  Consensus size: 48

        994 NNNNNNNNTT

                  *      *              *                ***
       1004 TTTTTTTACTCAAGGCTCCCTTTGTAGGGTTTCACCTTGGTCTCCTTT
          1 TTTTTTGACTCAAAGCTCCCTTTGTAGGCTTTCACCTTGGTCTCCCCC

                                                              
       1052 TTTTTTGACTCAAAG-TGCCCTTTGTAGGCTTTCACCTTGGTC-CCACCC
          1 TTTTTTGACTCAAAGCT-CCCTTTGTAGGCTTTCACCTTGGTCTCC-CCC

                  
       1100 TTTTTT
          1 TTTTTT

       1106 AAGCAGAGTA


Statistics
Matches: 46,  Mismatches: 6, Indels: 4
        0.82            0.11        0.07

Matches are distributed among these distances:
  47    3  0.07
  48   43  0.93

ACGTcount: A:0.12, C:0.26, G:0.16, T:0.46


Consensus pattern (48 bp):   
TTTTTTGACTCAAAGCTCCCTTTGTAGGCTTTCACCTTGGTCTCCCCC

Found at i:3072 original size:234 final size:234

Alignment explanation


    Indices: 2646--3113  Score: 731
    Period size: 234  Copynumber: 2.0  Consensus size: 234

       2636 GTGCTTTCAG

                                                                             
       2646 GGTGTTAATGAATAGCATGGTCATTTCCTTTTCCAAGAGTGGTGGCTGAACTTGGACTGCGACCT
          1 GGTGTTAATGAATAGCATGGTCATTTCCTTTTCCAAGAGTGGTGGCTGAACTTGGACTGCGACCT

                                              *     *                        
       2711 CCCTCCATCTCTGTGCATACTGCCTAAAGCTTTCGCTCGGGTTCTTCTCCATATTCTGAAGGGTG
         66 CCCTCCATCTCTGTGCATACTGCCTAAAGCTTTCACTCGGCTTCTTCTCCATATTCTGAAGGGTG

                                *              *                   *         
       2776 ATTCTATCAGGAGCCATGTCTGTCACATGACTATATTGTTTCATGAATGCTTGCGTCAAGTCCCT
        131 ATTCTATCAGGAGCCATGTCAGTCACATGACTATACTGTTTCATGAATGCTTGCGCCAAGTCCCT

                                       *           
       2841 CCATGAACCAATCGTGGCACGACTCAATTGATTGTACCA
        196 CCATGAACCAATCGTGGCACGACTCAACTGATTGTACCA

                              *                          *                 * 
       2880 GGTGTTAATGAATAGCATTGTCATTTCCTTTTCCAAGAGTGGTGGTTGAACTTGGACTGCGACTT
          1 GGTGTTAATGAATAGCATGGTCATTTCCTTTTCCAAGAGTGGTGGCTGAACTTGGACTGCGACCT

                      *        *     *                           *  *        
       2945 CCCTCCATCTTTGTGCATATTGCCTGAAGCTTTCAAC-CGGCTTCTTCTCCATGTTTTGAAGGGT
         66 CCCTCCATCTCTGTGCATACTGCCTAAAGCTTTC-ACTCGGCTTCTTCTCCATATTCTGAAGGGT

                                                       *      *   *          
       3009 GATTCTATCAGGAGCCATGTCAGTCACATGACTATACTGTTTCTTGAATGTTTGTGCCAAGTCCC
        130 GATTCTATCAGGAGCCATGTCAGTCACATGACTATACTGTTTCATGAATGCTTGCGCCAAGTCCC

             *                *   *    *            
       3074 TTCATGAACCAATCGTGGTACGGCTCAGCTGATTGTACCA
        195 TCCATGAACCAATCGTGGCACGACTCAACTGATTGTACCA

       3114 CTTGGATGCT


Statistics
Matches: 212,  Mismatches: 21, Indels: 2
        0.90            0.09        0.01

Matches are distributed among these distances:
 234  211  1.00
 235    1  0.00

ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33


Consensus pattern (234 bp):   
GGTGTTAATGAATAGCATGGTCATTTCCTTTTCCAAGAGTGGTGGCTGAACTTGGACTGCGACCT
CCCTCCATCTCTGTGCATACTGCCTAAAGCTTTCACTCGGCTTCTTCTCCATATTCTGAAGGGTG
ATTCTATCAGGAGCCATGTCAGTCACATGACTATACTGTTTCATGAATGCTTGCGCCAAGTCCCT
CCATGAACCAATCGTGGCACGACTCAACTGATTGTACCA
Done.