Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold541

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: 10464
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37


Found at i:1399 original size:50 final size:49

Alignment explanation


    Indices: 1316--1449  Score: 169
    Period size: 50  Copynumber: 2.7  Consensus size: 49

       1306 AAATGGTCCT

                           *        *   *       *           * 
       1316 GAATGTATCGATACATTGAGAAATATATTGATACATCTAGGTAAAACCTA
          1 GAATGTATCGATACAATGA-AAATGTATCGATACATATAGGTAAAACCCA

                                                  *           
       1366 GAATGTATCGATACAATGAATAATGTATCGATACATATGGGTAAAACCCA
          1 GAATGTATCGATACAATGAA-AATGTATCGATACATATAGGTAAAACCCA

            *                *                
       1416 AAATGTATCGATACAATTAAGAATGTATCGATAC
          1 GAATGTATCGATACAATGAA-AATGTATCGATAC

       1450 GAATTGTGAA


Statistics
Matches: 74,  Mismatches: 9, Indels: 2
        0.87            0.11        0.02

Matches are distributed among these distances:
  49    1  0.01
  50   73  0.99

ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28


Consensus pattern (49 bp):   
GAATGTATCGATACAATGAAAATGTATCGATACATATAGGTAAAACCCA

Found at i:4327 original size:2 final size:2

Alignment explanation


    Indices: 4320--4358  Score: 62
    Period size: 2  Copynumber: 20.0  Consensus size: 2

       4310 TTCTTTACAA

                                                            *          
       4320 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT TT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       4359 GAGAACAAGA


Statistics
Matches: 34,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   33  0.97

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (2 bp):   
AT

Found at i:5168 original size:23 final size:24

Alignment explanation


    Indices: 5142--5190  Score: 73
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       5132 TTATATGTAA

                                    
       5142 ATAT-AAATTTAAAAATTTTAAAT
          1 ATATAAAATTTAAAAATTTTAAAT

                       *   *        
       5165 ATATAAAATTTTAAATTTTTAAAT
          1 ATATAAAATTTAAAAATTTTAAAT

              
       5189 AT
          1 AT

       5191 CAAATAAAAT


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  23    4  0.17
  24   19  0.83

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (24 bp):   
ATATAAAATTTAAAAATTTTAAAT

Found at i:5410 original size:19 final size:20

Alignment explanation


    Indices: 5371--5425  Score: 58
    Period size: 20  Copynumber: 2.7  Consensus size: 20

       5361 TTTTTAAAAA

                            *    
       5371 AATATAAAATTTATAGTAATT
          1 AATAT-AAATTTATAGCAATT

            *                   
       5392 TATATAAATTTATA-CAATT
          1 AATATAAATTTATAGCAATT

                 *         
       5411 AATATGAATTATATA
          1 AATATAAATT-TATA

       5426 AAATCAAAAT


Statistics
Matches: 29,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  19   12  0.41
  20   13  0.45
  21    4  0.14

ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44


Consensus pattern (20 bp):   
AATATAAATTTATAGCAATT

Found at i:7482 original size:2 final size:2

Alignment explanation


    Indices: 7461--7509  Score: 71
    Period size: 2  Copynumber: 24.5  Consensus size: 2

       7451 CAGTTTTTCA

                     *      *     *                                       
       7461 TC TC TC CC TC TT TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                      
       7503 TC TC TC T
          1 TC TC TC T

       7510 TTAAGCAAAG


Statistics
Matches: 41,  Mismatches: 6, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
   2   41  1.00

ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53


Consensus pattern (2 bp):   
TC

Done.