Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold496

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: 11086
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.29


Found at i:1288 original size:25 final size:26

Alignment explanation


    Indices: 1251--1302  Score: 70
    Period size: 25  Copynumber: 2.0  Consensus size: 26

       1241 TCAAACATGC

                                      
       1251 ATTTAGGTCAATTTAACCCTAGGGGT
          1 ATTTAGGTCAATTTAACCCTAGGGGT

                *          * *        
       1277 ATTTCGGT-AATTTATCTCTAGGGGT
          1 ATTTAGGTCAATTTAACCCTAGGGGT

             
       1302 A
          1 A

       1303 AAACTGTAAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  25   16  0.70
  26    7  0.30

ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38


Consensus pattern (26 bp):   
ATTTAGGTCAATTTAACCCTAGGGGT

Found at i:2842 original size:26 final size:26

Alignment explanation


    Indices: 2786--2866  Score: 155
    Period size: 26  Copynumber: 3.2  Consensus size: 26

       2776 TGAAATGCCC

                                      
       2786 ATCATGGAACATTTACCTAA-CCATT
          1 ATCATGGAACATTTACCTAACCCATT

                                      
       2811 ATCATGGAACATTTACCTAACCCATT
          1 ATCATGGAACATTTACCTAACCCATT

                                      
       2837 ATCATGGAACATTTACCTAACCCATT
          1 ATCATGGAACATTTACCTAACCCATT

                
       2863 ATCA
          1 ATCA

       2867 ATTTGTACCA


Statistics
Matches: 55,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  25   20  0.36
  26   35  0.64

ACGTcount: A:0.36, C:0.26, G:0.07, T:0.31


Consensus pattern (26 bp):   
ATCATGGAACATTTACCTAACCCATT

Found at i:5776 original size:13 final size:13

Alignment explanation


    Indices: 5753--5785  Score: 57
    Period size: 13  Copynumber: 2.5  Consensus size: 13

       5743 GTCAGTTTGT

                          
       5753 TCAACTGGCGATAA
          1 TCAA-TGGCGATAA

                         
       5767 TCAATGGCGATAA
          1 TCAATGGCGATAA

                  
       5780 TCAATG
          1 TCAATG

       5786 CACATCGCAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  13   15  0.79
  14    4  0.21

ACGTcount: A:0.36, C:0.18, G:0.21, T:0.24


Consensus pattern (13 bp):   
TCAATGGCGATAA

Found at i:9792 original size:26 final size:27

Alignment explanation


    Indices: 9749--9799  Score: 86
    Period size: 26  Copynumber: 1.9  Consensus size: 27

       9739 CATGAAATTC

                                       
       9749 TTATCATGAAAACATTTACCTAACCCA
          1 TTATCATGAAAACATTTACCTAACCCA

                     *               
       9776 TTATCATG-GAACATTTACCTAACC
          1 TTATCATGAAAACATTTACCTAACC

       9800 TTTATCAATT


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  26   15  0.65
  27    8  0.35

ACGTcount: A:0.37, C:0.25, G:0.06, T:0.31


Consensus pattern (27 bp):   
TTATCATGAAAACATTTACCTAACCCA
Done.