Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1608

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: 7739
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33


Found at i:4424 original size:21 final size:21

Alignment explanation


    Indices: 4398--4455  Score: 107
    Period size: 21  Copynumber: 2.8  Consensus size: 21

       4388 AAAAAAACCC

                                 
       4398 AGAATGTATCGATACAATCCT
          1 AGAATGTATCGATACAATCCT

                      *          
       4419 AGAATGTATCAATACAATCCT
          1 AGAATGTATCGATACAATCCT

                            
       4440 AGAATGTATCGATACA
          1 AGAATGTATCGATACA

       4456 GTTACTTGAG


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   35  1.00

ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28


Consensus pattern (21 bp):   
AGAATGTATCGATACAATCCT

Found at i:4599 original size:111 final size:113

Alignment explanation


    Indices: 4465--4700  Score: 377
    Period size: 113  Copynumber: 2.1  Consensus size: 113

       4455 AGTTACTTGA

                                               *                    *   *    
       4465 GTATCGATACTTACTGTCCAAAAATCGAATTTTAGTTA-CTGCCAAGGCTTGTATCGATATAATC
          1 GTATCGATACTTACTGTCCAAAAATCGAATTTTAGCTACCTGCCAAGGCTTGTATCAATACAATC

                                     * *                    
       4529 ACACTAAGTATCAATACCACACCCTGGGTATCAATACCAAGCCTTCAT
         66 ACACTAAGTATCAATACCACACCCTAGATATCAATACCAAGCCTTCAT

                *                    *                                       
       4577 GTATTGAT-CTTACTGTCCAAAAATTGAATTTTAGCTACTCTGCCAAGGCTTGTATCAATACAAT
          1 GTATCGATACTTACTGTCCAAAAATCGAATTTTAGCTAC-CTGCCAAGGCTTGTATCAATACAAT

                                                          *  
       4641 CACACTAAGTATCAATACCACACCCTAGATATCAATACCAAGCCTTTAT
         65 CACACTAAGTATCAATACCACACCCTAGATATCAATACCAAGCCTTCAT

                       
       4690 GTATCGATACT
          1 GTATCGATACT

       4701 ACCATGGAAA


Statistics
Matches: 112,  Mismatches: 9, Indels: 4
        0.90            0.07        0.03

Matches are distributed among these distances:
 111   27  0.24
 112    7  0.06
 113   76  0.68
 114    2  0.02

ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31


Consensus pattern (113 bp):   
GTATCGATACTTACTGTCCAAAAATCGAATTTTAGCTACCTGCCAAGGCTTGTATCAATACAATC
ACACTAAGTATCAATACCACACCCTAGATATCAATACCAAGCCTTCAT

Found at i:6323 original size:31 final size:30

Alignment explanation


    Indices: 6285--6347  Score: 117
    Period size: 31  Copynumber: 2.1  Consensus size: 30

       6275 AAAGGACACA

                                           
       6285 TTGAAGGCATTAGAACCATTAGTAACAATTC
          1 TTGAAGGCATTAGAACCATTAGT-ACAATTC

                                          
       6316 TTGAAGGCATTAGAACCATTAGTACAATTC
          1 TTGAAGGCATTAGAACCATTAGTACAATTC

              
       6346 TT
          1 TT

       6348 TATCTAATAT


Statistics
Matches: 32,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  30    9  0.28
  31   23  0.72

ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32


Consensus pattern (30 bp):   
TTGAAGGCATTAGAACCATTAGTACAATTC
Done.