Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1164

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: 144783
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32


File 2 of 2

Found at i:144373 original size:13 final size:13

Alignment explanation


    Indices: 144355--144393  Score: 78
    Period size: 13  Copynumber: 3.0  Consensus size: 13

     144345 ACATTTTTCT

                         
     144355 TTGTATCGATACA
          1 TTGTATCGATACA

                         
     144368 TTGTATCGATACA
          1 TTGTATCGATACA

                         
     144381 TTGTATCGATACA
          1 TTGTATCGATACA

     144394 GGGTGATTAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   26  1.00

ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38


Consensus pattern (13 bp):   
TTGTATCGATACA

Found at i:144538 original size:21 final size:21

Alignment explanation


    Indices: 144514--144560  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

     144504 AAATCTTTTG

                                   
     144514 CAAAAT-ACTT-GTTTTTCACTT
          1 CAAAATAACTTCGTTTTTCA--T

                                 
     144535 C-AAATAACTTCGTTTTTCAT
          1 CAAAATAACTTCGTTTTTCAT

                  
     144555 CAAAAT
          1 CAAAAT

     144561 TAGCATCAAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 6
        0.79            0.00        0.21

Matches are distributed among these distances:
  20    6  0.26
  21    9  0.39
  22    8  0.35

ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43


Consensus pattern (21 bp):   
CAAAATAACTTCGTTTTTCAT

Found at i:144557 original size:20 final size:19

Alignment explanation


    Indices: 144516--144558  Score: 52
    Period size: 20  Copynumber: 2.2  Consensus size: 19

     144506 ATCTTTTGCA

                                
     144516 AAATACTTGTTTTTCACTTC
          1 AAATACTTGTTTTTCAC-TC

                                 
     144536 AAATAACTTCGTTTTTCA-TC
          1 AAAT-ACTT-GTTTTTCACTC

               
     144556 AAA
          1 AAA

     144559 ATTAGCATCA


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  20    9  0.43
  21    4  0.19
  22    8  0.38

ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44


Consensus pattern (19 bp):   
AAATACTTGTTTTTCACTC

Done.