########################################
# Program:  needle
# Rundate:  Thu Mar 27 06:24:01 2008
# Align_format: srspair
# Report_file: /ebi/extserv/old-work/needle-20080327-06235995386532.output
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: s.cerevisiae
# 2: s.paradoxus
# Matrix: EDNAFULL
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 311
# Identity:     171/311 (55.0%)
# Similarity:   171/311 (55.0%)
# Gaps:         100/311 (32.2%)
# Score: 442.5
# 
#
#=======================================

s.cerevisiae       1              aacgatccccgtccaagt-tatgagcttaatc--ttc     34
                                  ||            |||| |.|.|||  ||||  ||.
s.paradoxus        1 atttttgtttgcaaa------------aagtctcttagc--aatcaattg     36

s.cerevisiae      35 cataaaaatatttgaaagcaatagatcatgtactaaactaaaatcaggga     84
                     |     ||||.|.| |||.|||..|.||..|||||||  ||||       
s.paradoxus       37 c-----aatagtcg-aagtaatgaaccagatactaaa--aaaa-------     71

s.cerevisiae      85 aattaagactccttttgaagtaat-----acctat---tac------tta    120
                                 ||||| ||.|||     |.||||   |||      |||
s.paradoxus       72 ------------ttttg-aggaatgaggaagctatctataccagaaatta    108

s.cerevisiae     121 ctaata----cgtttgagaataagcgcaggt----actcct---ggtttt    159
                       .|||    |.|||.||||.||      ||    |..|||   ||||||
s.paradoxus      109 --tatagcaccatttaagaagaa------gtttaaaagccttggggtttt    150

s.cerevisiae     160 tgttaaaactacaaatttatacttagcattacgaagattctcgattcc-g    208
                     .|||||.|..|.||||||||.|||||.||||||.|||.|||.| |||| |
s.paradoxus      151 cgttaatataaaaaatttatgcttagtattacggagaatcttg-ttcctg    199

s.cerevisiae     209 aaaaacaaaaa-----ttttatcgtcatatacaaatct-agaaattacca    252
                     |||||.|||||     .||||..|||||||.|||||.| |.||||||..|
s.paradoxus      200 aaaaaaaaaaaggaatatttagtgtcatatgcaaatataaaaaattatta    249

s.cerevisiae     253 g-agctatcca    262
                     | |||.|.|||
s.paradoxus      250 gaagccagcca    260


#---------------------------------------
#---------------------------------------

Figure S2.  S. cerevisiae and S. paradoxus lack of sequence conservation between HMR-E Abf1 
binding site and HMR.

Pairwise global alignment (Needleman–Wunsch) of DNA sequence between the HMR-E Abf1 binding 
site and the HMR edge, comparing S. cerevisiae to S. paradoxus. Length of the intervening sequence 
between HMR-E and HMR was identical in both species, but sequence conservation itself was poor.