Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1392

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: 15429
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36


Found at i:2841 original size:21 final size:21

Alignment explanation


    Indices: 2803--2843  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2793 GAAAAAAATT

                     *  **       
       2803 ATTAAAATTTAATTTTTAATC
          1 ATTAAAATTAAAAATTTAATC

                                
       2824 ATTAAAATTAAAAATTTAAT
          1 ATTAAAATTAAAAATTTAAT

       2844 ACTTTACTAA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46


Consensus pattern (21 bp):   
ATTAAAATTAAAAATTTAATC

Found at i:3304 original size:21 final size:17

Alignment explanation


    Indices: 3253--3300  Score: 62
    Period size: 17  Copynumber: 2.8  Consensus size: 17

       3243 ATATATCATC

                               
       3253 AAAAATAATAATATTTAAT
          1 AAAAAT-AT-ATATTTAAT

                             
       3272 AAAAATATATATTTAAT
          1 AAAAATATATATTTAAT

            *            
       3289 TAAAATAT-TATT
          1 AAAAATATATATT

       3301 ATATCTGATA


Statistics
Matches: 28,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  16    4  0.14
  17   16  0.57
  18    2  0.07
  19    6  0.21

ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42


Consensus pattern (17 bp):   
AAAAATATATATTTAAT

Found at i:4624 original size:15 final size:16

Alignment explanation


    Indices: 4592--4627  Score: 65
    Period size: 16  Copynumber: 2.3  Consensus size: 16

       4582 ACCCTTACTC

                            
       4592 TTTTATGTTTTAGCTT
          1 TTTTATGTTTTAGCTT

                            
       4608 TTTTATGTTTTAG-TT
          1 TTTTATGTTTTAGCTT

                 
       4623 TTTTA
          1 TTTTA

       4628 GAGATAAAGT


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  15    7  0.35
  16   13  0.65

ACGTcount: A:0.14, C:0.03, G:0.11, T:0.72


Consensus pattern (16 bp):   
TTTTATGTTTTAGCTT

Found at i:4866 original size:3 final size:3

Alignment explanation


    Indices: 4858--4884  Score: 54
    Period size: 3  Copynumber: 9.0  Consensus size: 3

       4848 AAATATAGTA

                                               
       4858 AAT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT

       4885 CATTTTTATC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   24  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
AAT

Found at i:6180 original size:2 final size:2

Alignment explanation


    Indices: 6173--6209  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       6163 TGATGGAGGC

                                                                   
       6173 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       6210 ACTAAAATAC


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:7107 original size:2 final size:2

Alignment explanation


    Indices: 7100--7158  Score: 66
    Period size: 2  Copynumber: 30.0  Consensus size: 2

       7090 AGCACATACT

                                    *  *                        *     *   
       7100 TA TA TA TA TA TA TA TA AA AA TA TA TA TA TA TA TA TT TA TT TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

               *                      
       7142 TA AA TA TA TA TA T- TA TA
          1 TA TA TA TA TA TA TA TA TA

       7159 AATTTTTTTT


Statistics
Matches: 48,  Mismatches: 8, Indels: 2
        0.83            0.14        0.03

Matches are distributed among these distances:
   1    1  0.02
   2   47  0.98

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Done.