Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2547

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: 26517
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:1531 original size:11 final size:11

Alignment explanation


    Indices: 1515--1540  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       1505 TCCAGGTCAC

                       
       1515 TAAACTATTAG
          1 TAAACTATTAG

                       
       1526 TAAACTATTAG
          1 TAAACTATTAG

                
       1537 TAAA
          1 TAAA

       1541 TTTACATTTC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.50, C:0.08, G:0.08, T:0.35


Consensus pattern (11 bp):   
TAAACTATTAG

Found at i:14181 original size:7 final size:7

Alignment explanation


    Indices: 14171--14206  Score: 72
    Period size: 7  Copynumber: 5.1  Consensus size: 7

      14161 ATTTTAGTTA

                   
      14171 AGAATAT
          1 AGAATAT

                   
      14178 AGAATAT
          1 AGAATAT

                   
      14185 AGAATAT
          1 AGAATAT

                   
      14192 AGAATAT
          1 AGAATAT

                   
      14199 AGAATAT
          1 AGAATAT

             
      14206 A
          1 A

      14207 TGATCGAATG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   29  1.00

ACGTcount: A:0.58, C:0.00, G:0.14, T:0.28


Consensus pattern (7 bp):   
AGAATAT

Found at i:14479 original size:14 final size:14

Alignment explanation


    Indices: 14462--14490  Score: 51
    Period size: 13  Copynumber: 2.1  Consensus size: 14

      14452 AAATAATAAC

                          
      14462 AAAAAATTT-AAAT
          1 AAAAAATTTCAAAT

                          
      14475 AAAAAATTTCAAAT
          1 AAAAAATTTCAAAT

              
      14489 AA
          1 AA

      14491 TATACTAATT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    9  0.60
  14    6  0.40

ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28


Consensus pattern (14 bp):   
AAAAAATTTCAAAT

Found at i:20581 original size:39 final size:39

Alignment explanation


    Indices: 20526--20604  Score: 149
    Period size: 39  Copynumber: 2.0  Consensus size: 39

      20516 AAGCCTTTCC

                       *                           
      20526 TGGCAAGATTGGTAGTTTTTTATATGGATTCTTGTTTGA
          1 TGGCAAGATTGATAGTTTTTTATATGGATTCTTGTTTGA

                                                   
      20565 TGGCAAGATTGATAGTTTTTTATATGGATTCTTGTTTGA
          1 TGGCAAGATTGATAGTTTTTTATATGGATTCTTGTTTGA

             
      20604 T
          1 T

      20605 AGCAGTGGTG


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  39   39  1.00

ACGTcount: A:0.22, C:0.05, G:0.24, T:0.49


Consensus pattern (39 bp):   
TGGCAAGATTGATAGTTTTTTATATGGATTCTTGTTTGA

Found at i:21230 original size:25 final size:25

Alignment explanation


    Indices: 21179--21228  Score: 66
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      21169 TCGAACTATT

                               *     
      21179 TTTTTTTATTTGTAATATATATAAA
          1 TTTTTTTATTTGTAATATACATAAA

                                      
      21204 TTTTTTTATTT-TATACTATACATAA
          1 TTTTTTTATTTGTA-A-TATACATAA

      21229 TTAAATCAAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  24    2  0.09
  25   12  0.55
  26    8  0.36

ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60


Consensus pattern (25 bp):   
TTTTTTTATTTGTAATATACATAAA
Done.