Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold840

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: 5475
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.32

Warning! 167 characters in sequence are not A, C, G, or T


Found at i:703 original size:10 final size:10

Alignment explanation


    Indices: 688--712  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

        678 GTGCCTGGTT

                      
        688 TTTTTTTTTG
          1 TTTTTTTTTG

                      
        698 TTTTTTTTTG
          1 TTTTTTTTTG

                 
        708 TTTTT
          1 TTTTT

        713 GGTAATTAGT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92


Consensus pattern (10 bp):   
TTTTTTTTTG

Found at i:3018 original size:126 final size:126

Alignment explanation


    Indices: 2774--3026  Score: 283
    Period size: 126  Copynumber: 2.0  Consensus size: 126

       2764 AAACAGTTTG

                                    *                                  *     
       2774 ATAACATTTCATTTTCAGGAGCCTTTATCTGCCAATGCTGGTCATACAGAGTCAACAGCGATTGA
          1 ATAACATTTCATTTTCAGGAGCCTGTATCTGCCAATGCTGGTCATACAGAGTCAACAGCAATTGA

               *  **  **   *      *            *                  *      
       2839 GTTTCAGTGCGTTATCAGGGTACAACAGAGAATACCACTTTAATTTTTGGTTTTCCTTTCA
         66 GTTGCAACGCACTATAAGGGTAAAACAGAGAATACAACTTTAATTTTTGGTTTTACTTTCA

                           * *   *              *        *       ** *        
       2900 ATAACATTTCATTTTTATGAGTCTGTATCTGCCAATTCTGGTCATGCAGAGTCGGCTGCAATTGA
          1 ATAACATTTCATTTTCAGGAGCCTGTATCTGCCAATGCTGGTCATACAGAGTCAACAGCAATTGA

                                      *    *     *   *                    
       2965 GTTGCAACGCACTATAAGGGTAAAACGGAGAGTACAATTTTGATTCTTT-GTTTTACTTTCA
         66 GTTGCAACGCACTATAAGGGTAAAACAGAGAATACAACTTTAATT-TTTGGTTTTACTTTCA

             
       3026 A
          1 A

       3027 GGATGGAAAA


Statistics
Matches: 103,  Mismatches: 23, Indels: 2
        0.80            0.18        0.02

Matches are distributed among these distances:
 126  100  0.97
 127    3  0.03

ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36


Consensus pattern (126 bp):   
ATAACATTTCATTTTCAGGAGCCTGTATCTGCCAATGCTGGTCATACAGAGTCAACAGCAATTGA
GTTGCAACGCACTATAAGGGTAAAACAGAGAATACAACTTTAATTTTTGGTTTTACTTTCA

Found at i:4657 original size:28 final size:28

Alignment explanation


    Indices: 4617--4670  Score: 90
    Period size: 28  Copynumber: 1.9  Consensus size: 28

       4607 GAAACACGCA

                                *       
       4617 TCAATTAATCTATCTTCATCTTATTATT
          1 TCAATTAATCTATCTTCATCGTATTATT

                             *        
       4645 TCAATTAATCTATCTTCTTCGTATTA
          1 TCAATTAATCTATCTTCATCGTATTA

       4671 ATTAAATATT


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  28   24  1.00

ACGTcount: A:0.28, C:0.19, G:0.02, T:0.52


Consensus pattern (28 bp):   
TCAATTAATCTATCTTCATCGTATTATT

Found at i:5452 original size:1 final size:1

Alignment explanation


    Indices: 5446--5475  Score: 60
    Period size: 1  Copynumber: 30.0  Consensus size: 1

       5436 GCCACCCGTC

                                          
       5446 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   29  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Done.