Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold845

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: 129140
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


File 2 of 2

Found at i:117387 original size:21 final size:20

Alignment explanation


    Indices: 117359--117397  Score: 60
    Period size: 21  Copynumber: 1.9  Consensus size: 20

     117349 ATATTATTTT

                      *         
     117359 AATTAATAAACTTATTAAAA
          1 AATTAATAAAATTATTAAAA

                               
     117379 AATTAAATAAAATTATTAA
          1 AATT-AATAAAATTATTAA

     117398 TAATAGATAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20    4  0.24
  21   13  0.76

ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36


Consensus pattern (20 bp):   
AATTAATAAAATTATTAAAA

Found at i:117399 original size:12 final size:12

Alignment explanation


    Indices: 117360--117400  Score: 52
    Period size: 12  Copynumber: 3.7  Consensus size: 12

     117350 TATTATTTTA

                     *  
     117360 ATTAATAAACTT
          1 ATTAATAAAATT

                        
     117372 ATTAA-AAAATT
          1 ATTAATAAAATT

                        
     117383 A--AATAAAATT
          1 ATTAATAAAATT

                    
     117393 ATTAATAA
          1 ATTAATAA

     117401 TAGATATAAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 6
        0.78            0.03        0.19

Matches are distributed among these distances:
   9    2  0.08
  10    7  0.28
  11    6  0.24
  12   10  0.40

ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37


Consensus pattern (12 bp):   
ATTAATAAAATT

Found at i:117976 original size:18 final size:18

Alignment explanation


    Indices: 117940--117975  Score: 65
    Period size: 17  Copynumber: 2.1  Consensus size: 18

     117930 TTTGTTAGAG

                              
     117940 ATAATTATAAAAAATAAA
          1 ATAATTATAAAAAATAAA

                              
     117958 ATAATTAT-AAAAATAAA
          1 ATAATTATAAAAAATAAA

             
     117975 A
          1 A

     117976 AAATAAAAAC


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  17   10  0.56
  18    8  0.44

ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28


Consensus pattern (18 bp):   
ATAATTATAAAAAATAAA

Found at i:118149 original size:3 final size:3

Alignment explanation


    Indices: 118141--118173  Score: 57
    Period size: 3  Copynumber: 11.0  Consensus size: 3

     118131 TTAAAGGGTG

                                *                      
     118141 TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

     118174 CTAAATTTGG


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   28  1.00

ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64


Consensus pattern (3 bp):   
TTA

Found at i:126287 original size:15 final size:16

Alignment explanation


    Indices: 126255--126295  Score: 57
    Period size: 15  Copynumber: 2.6  Consensus size: 16

     126245 TTGTTTGGTA

                   *        
     126255 TATTGGAATTTTTAAT
          1 TATTGGATTTTTTAAT

                         *  
     126271 TATT-GATTTTTTTAT
          1 TATTGGATTTTTTAAT

                      
     126286 TATTGGATTT
          1 TATTGGATTT

     126296 AATAAATGAT


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.24, C:0.00, G:0.12, T:0.63


Consensus pattern (16 bp):   
TATTGGATTTTTTAAT

Done.