Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2432

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: 4328
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36


Found at i:265 original size:16 final size:16

Alignment explanation


    Indices: 236--297  Score: 58
    Period size: 16  Copynumber: 3.9  Consensus size: 16

        226 GTAAAAATCG

                               
        236 ATAAATATCAAAAATAATA
          1 ATAAATAT--AAAATAA-A

                            
        255 A-AAATATAAAATAAA
          1 ATAAATATAAAATAAA

                      *     
        270 ATAAATATAATA-AAA
          1 ATAAATATAAAATAAA

              *           
        285 ATTAATA-AAAATA
          1 ATAAATATAAAATA

        298 GAAAAATAGA


Statistics
Matches: 38,  Mismatches: 3, Indels: 8
        0.78            0.06        0.16

Matches are distributed among these distances:
  14    3  0.08
  15   12  0.32
  16   16  0.42
  18    6  0.16
  19    1  0.03

ACGTcount: A:0.73, C:0.02, G:0.00, T:0.26


Consensus pattern (16 bp):   
ATAAATATAAAATAAA

Found at i:296 original size:10 final size:9

Alignment explanation


    Indices: 245--297  Score: 63
    Period size: 9  Copynumber: 5.8  Consensus size: 9

        235 GATAAATATC

                     
        245 AAAAATAAT
          1 AAAAATAAT

                     
        254 AAAAAT-AT
          1 AAAAATAAT

                  *   
        262 AAAATAAAAT
          1 AAAA-ATAAT

               *     
        272 AAATATAAT
          1 AAAAATAAT

                      
        281 AAAAATTAAT
          1 AAAAA-TAAT

                   
        291 AAAAATA
          1 AAAAATA

        298 GAAAAATAGA


Statistics
Matches: 37,  Mismatches: 4, Indels: 6
        0.79            0.09        0.13

Matches are distributed among these distances:
   8    6  0.16
   9   17  0.46
  10   14  0.38

ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25


Consensus pattern (9 bp):   
AAAAATAAT

Found at i:1989 original size:22 final size:23

Alignment explanation


    Indices: 1964--2007  Score: 54
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       1954 GTCATTCTGA

                                   
       1964 ATTCAAGTT-AATCAGGTTTAAC
          1 ATTCAAGTTAAATCAGGTTTAAC

                **        *       
       1986 ATTCGGGTTAAATCGGGTTTAA
          1 ATTCAAGTTAAATCAGGTTTAA

       2008 GTCATTTTAT


Statistics
Matches: 18,  Mismatches: 3, Indels: 1
        0.82            0.14        0.05

Matches are distributed among these distances:
  22    7  0.39
  23   11  0.61

ACGTcount: A:0.32, C:0.11, G:0.20, T:0.36


Consensus pattern (23 bp):   
ATTCAAGTTAAATCAGGTTTAAC

Found at i:2316 original size:20 final size:21

Alignment explanation


    Indices: 2291--2338  Score: 57
    Period size: 20  Copynumber: 2.4  Consensus size: 21

       2281 TCGATTTTTG

                      *           
       2291 AATTTTACATGATTTGA-T-TT
          1 AATTTTACA-AATTTGAGTATT

                                 
       2311 AATTTT-CAAATTTGAGTATT
          1 AATTTTACAAATTTGAGTATT

                    
       2331 AATTTTAC
          1 AATTTTAC

       2339 TTAAATAAGT


Statistics
Matches: 24,  Mismatches: 1, Indels: 5
        0.80            0.03        0.17

Matches are distributed among these distances:
  18    6  0.25
  19    3  0.12
  20   14  0.58
  21    1  0.04

ACGTcount: A:0.33, C:0.06, G:0.08, T:0.52


Consensus pattern (21 bp):   
AATTTTACAAATTTGAGTATT
Done.