# prss -q -O prss.out sequence2.fasta sequence1.fasta
PRSS evaluates statistical signficance using Smith-Waterman version 34.26.5 April 26, 2007
Please cite:
 W.R. Pearson (1996) Meth. Enzymol. 266:227-258

 sequence2.fasta, 502 nt
 vs 126742336 Ochotona curzoniae hemoglobin alpha chain mRNA, complete cds. GBMAM:126742336, 429 bp shuffled sequence

       opt      E()
< 20     0     0:
  22     0     0:           one = represents 1 library sequences
  24     0     0:
  26     0     0:
  28     0     0:
  30     0     0:
  32     2     1:*=
  34     6     3:==*===
  36     4     6:==== *
  38     8    10:======== *
  40    16    14:=============*==
  42    22    17:================*=====
  44    18    18:=================*
  46    13    19:=============     *
  48    12    18:============     *
  50    24    16:===============*========
  52    17    14:=============*===
  54    14    12:===========*==
  56     5    10:=====    *
  58    11     8:=======*===
  60     6     7:======*
  62     3     5:=== *
  64     3     4:===*
  66     5     3:==*==
  68     3     3:==*
  70     1     2:=*
  72     1     2:=*
  74     4     1:*===
  76     0     1:*
  78     0     1:*
  80     1     1:*
  82     0     0:
  84     0     0:
  86     0     0:
  88     1     0:=
  90     0     0:
  92     0     0:
  94     0     0:
  96     0     0:
  98     0     0:
 100     0     0:
 102     0     0:
 104     0     0:
 106     0     0:
 108     0     0:
 110     0     0:
 112     0     0:
 114     0     0:
 116     0     0:
 118     0     0:
>120     0     0:
  85800 residues in   200 sequences
 (shuffled) MLE statistics: Lambda= 0.1363;  K=0.0335
 Kolmogorov-Smirnov  statistic: 0.0379 (N=24) at  42

 Smith-Waterman (3.5 Sept 2006) function [+5/-4 matrix (5:-4)], open/ext: -12/-4
The best scores are:                                      s-w bits E(200)
126742336 Ochotona curzoniae hemoglobin alpha  ( 429) [f] 1614 322.4 3.9e-90



502 residues in 1 query   sequences
85800 residues in 200 library sequences
 Scomplib [34.26]
 start: Mon Jan 21 19:16:15 2008 done: Mon Jan 21 19:16:16 2008
 Scan time:  0.930 Display time:  0.000

Function used was PRSS [version 34.26.5 April 26, 2007]