AlignACE version 2.2  July 7, 1998
alignACE -z/skink1/amcguire/genomes/ecoli.fna -a/home/amcguire/alignace/lib/ORF_ecoli.txt -b/home/amcguire/alignace/lib/bimes_ecoli.txt -k0 -l300 -jfnr.reg -g0.5 -x5 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	157

Input sequences:
#1	cydA 300 bp cydA 523 1-1572 CDS
#2	focA 300 bp focA 285 1-858 CDS
#3	ndh 271 bp ndh 434 1-1305 CDS
#4	narK 300 bp narK 463 1-1392 CDS
#5	narG 300 bp narG 1247 1-3744 CDS
#6	fdnG 231 bp fdnG 1015 1-3048 CDS
#7	ansB 175 bp ansB 348 1-1047 CDS
#8	nirB 261 bp nirB 847 1-2544 CDS
#9	nrfA 300 bp nrfA 478 1-1437 CDS

Motif number 1

TTCAGCCAATTTGATCGAGAACAATTTATCT   	1	8	0	TTGAGAACAA	    0.813491	-293
TTTGCATTTTTCGACGGTGATCAATTTATAGCTA	1	53	0	TCGAGTACAA	    0.884916	-248
AGATGAGAAATTGATATAGATCATATCTCGCCTG	2	227	0	TTGATAACAT	     0.63114	-74
CATACCAAAATTGATGTTAATCAAGTTTTGTTGC	3	122	0	TTGATTACAA	    0.618885	-150
TTATCTATCATTGATATTTATCATTACCCATAGT	4	190	0	TTGATTACAT	    0.916195	-111
ATCTTATCGTTTGATTTACATCAAATTGCCTTTA	4	228	1	TTGATAACAA	    0.499753	-73
CCCATCACTCTTGATCGTTATCAATTCCCACGCT	5	196	1	TTGAGTACAA	    0.919688	-105
GAGCGTTACCTTGCCCTTAAACATTAGCAATGTC	5	236	1	TTGCTTACAT	    0.842698	-65
CCTTCGCAAATTGACCTACCTCAATAGCGGTAGA	6	99	0	TTGATACCAA	    0.588912	-133
CTGAATCTTTTTGCGCGAAATCAAAAAGAACATC	6	154	0	TTGCGAACAA	    0.750179	-78
TATGGGAAATTTGACGTTAAACAATTTACAACGT	7	105	0	TTGATTACAA	    0.979187	-71
AAAGGTGAATTTGATTTACATCAATAAGCGGGGT	8	190	1	TTGATAACAA	    0.499753	-72
AGGGTAATTTTTGAAGGTCAGCAACAAAAGTTGA	9	44	1	TTGAGTACAA	    0.980868	-257
ACTGTGAATGTTGTCTTTAATCAATTGTAAGTGC	9	160	0	TTGTTTACAA	    0.842695	-141
          ****  ** * ***

Masking position 13
Map Score:   21.6283

Number of sites scoring better than the average of aligned sites = 59
Number in coding regions = 31
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 2

GGGATCAATTTGAGTTTTTATTAACATGTTTGCAA	1	142	1	TGTTATTAAC	    0.846653	-159
TAAATACAAATTACCGATATTTAACCTTATAATTA	2	12	0	TCATTTTAAC	    0.845444	-289
CGCCTGATGCTCCCTTTTAATTAACTGTTTTAGCG	2	76	1	TCTTATTAAC	    0.983922	-225
    ACTAACTCTCTCTTTATTAAGTCGGCGACGA	2	280	0	TCTTATTAAG	    0.916627	-21
TAAAGTCGCCTATCTTTTCAGCAACAAAACTTGAT	3	102	1	TCTTAGCAAC	    0.874153	-170
GTTATTAACATAGCTCTTAATTAACAACAGGTTAC	3	207	0	TCTTATTAAC	    0.983922	-65
GCTATGTTAATAACCATTAATTAACAATTGGTTAA	3	228	1	TCTTATTAAC	    0.983922	-44
AAAGTTATCTTATCGTTTGATTTACATCAAATTGC	4	222	1	TCTTATTTAC	    0.848536	-79
TGTTATGTGGTGGCTGTTAATTATCCTAAAGGGGT	5	133	1	TCTTATTATC	    0.848536	-168
TAAATCGACATTGCTAATGTTTAAGGGCAAGGTAA	5	241	0	TCATTTTAAG	    0.495647	-60
CTGAATTTTATAGCATTTTTTTAACTGGCCTGTCA	6	48	1	TCTTTTTAAC	    0.969248	-184
ATATTCACGTTGTAAATTGTTTAACGTCAAATTTC	7	99	1	TATTTTTAAC	    0.657369	-77
CCGCCTACCTTAACGATTCAGCAACCCCGCTTATT	8	212	0	TCTTAGCAAC	    0.874153	-50
AGTCAGTATCTTCCTCTTTTTCAACAGCATGCATA	9	102	0	TCTTTTCAAC	    0.930198	-199
TTACATGCACTTACAATTGATTAAAGACAACATTC	9	154	1	TCTTATTAAA	    0.801223	-147
          *  *  ** ******

Masking position 8
Map Score:   13.6498

Number of sites scoring better than the average of aligned sites = 248
Number in coding regions = 184
Number in noncoding regions = 64
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 3

ATATATTACGCCGCAAAATCCTTACAATAAACAG	1	104	0	CGCAATCCTA	     0.92912	-197
TGAATTTTTTCCGCATCCTCCGCTAAAACAGTTA	2	97	0	CGCATTCCCT	    0.993425	-204
  CGAACGCCCTGCATACACCCCTCACTCTATAT	3	9	1	CGCATACCCT	    0.945943	-263
TGATCTCACCCGGTAAAGTCGCCTATCTTTTCAG	3	89	1	CGTAATCGCT	     0.84452	-183
TCTGGAATGGCAGTATTCTCGGCTATTGGCTGAA	4	32	1	CGTATTCGCT	    0.912837	-269
TTTCACGGTGCTGTAAAATCCCTACCCTTACCGA	4	124	0	CGTAATCCTA	    0.808721	-177
TATTTTAAGACGGCATAATACTTTTTTATGCCGT	7	16	1	CGCATTACTT	    0.871309	-160
CGTGAACGCTACGCATTATCCCTTAGCTCTGTAT	7	136	0	AGCATTCCTT	    0.777602	-40
TATCGTCGTCCGGCCTTTTCCTCTCTTCCCCCGC	8	31	1	CGCCTTCCCT	    0.962875	-231
TTATACAAATCAGCAATATACCCATTAAGGAGTA	8	153	1	CGCAATACCA	    0.849548	-109
GCATGCATAACTGCATGTTCCTCAAAGAATTAAT	9	77	0	CGCATTCCCA	    0.987399	-224
TAGAGTTAGTCAGTATCTTCCTCTTTTTCAACAG	9	110	0	CGTATTCCCT	    0.979891	-191
          * ****  *** **

Masking position 3
Map Score:   10.5524

Number of sites scoring better than the average of aligned sites = 647
Number in coding regions = 599
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 4

GGTTAAATATCGGTAATTTGTATTTAATAAATA	2	21	1	CGATTTGTAT	    0.635856	-280
TTGATTAACATCAATTTTGGTATGACCAATGCA	3	132	1	TCTTTGGTAT	    0.641627	-140
TAACTCTTTCCGGGTATGGGTATACTTCAGCCA	4	58	0	CGATGGGTAT	    0.968267	-243
GTCACTGTACTCACTATGGGTAATGATAAATAT	4	178	1	TCATGGGTAA	    0.964408	-123
TAAGGAGTATTCCCCATGGGTAACATATTAATG	5	32	0	TCATGGGTAA	    0.964408	-269
AAGATTTTTATGCAGATGGGTATTAAGGAGTAT	5	55	0	TGATGGGTAT	    0.967684	-246
TGTTAATTATCCTAAAGGGGTATCTTAGGAATT	5	147	1	CCAGGGGTAT	    0.967855	-154
CTTTCCTCTTTTTTCAGGGGTATTACTGCGCGA	6	207	0	TTAGGGGTAT	    0.743371	-25
ATCCCTTAGCTCTGTATGGGAAATTTGACGTTA	7	120	0	TCATGGGAAA	    0.742501	-56
ATGGGTATATTGCTGATTTGTATAAATTTTCTT	8	145	0	TGATTTGTAT	    0.631487	-117
TTTATATACTCCTTAATGGGTATATTGCTGATT	8	160	0	CCATGGGTAT	     0.98351	-102
ACTGACTAACTCTAAAGTGGTATTTTACATGCA	9	130	1	TCAGTGGTAT	    0.894662	-171
ACATTGCTCGCCCCTATGTGTAACAAATAACCA	9	195	0	CCATGTGTAA	    0.846084	-106
          **   ********

Masking position 12
Map Score:   7.65628

Number of sites scoring better than the average of aligned sites = 505
Number in coding regions = 462
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 5

TTCAGCCAATTTGATCGAGAACAATTTATCT 	1	10	0	TTGATGAAAC	    0.770501	-291
TTTGCATTTTTCGACGGTGATCAATTTATAGC	1	55	0	TCGACGTATC	    0.795923	-246
AGATGAGAAATTGATATAGATCATATCTCGCC	2	229	0	TTGATTAATC	    0.953949	-72
CATACCAAAATTGATGTTAATCAAGTTTTGTT	3	124	0	TTGATTTATC	    0.959997	-148
GTGTGGTTAGTCGCTTTACATCGGTAAGGGTA	4	104	1	TCGCTTAATC	    0.694015	-197
TTATCTATCATTGATATTTATCATTACCCATA	4	192	0	TTGATTTATC	    0.959997	-109
TAAAGGCAATTTGATGTAAATCAAACGATAAG	4	230	0	TTGATTAATC	    0.953949	-71
CCCATCACTCTTGATCGTTATCAATTCCCACG	5	196	1	TTGATGTATC	     0.92375	-105
GAGCGTTACCTTGCCCTTAAACATTAGCAATG	5	236	1	TTGCCTTAAC	    0.731247	-65
CCTTCGCAAATTGACCTACCTCAATAGCGGTA	6	101	0	TTGACTACTC	    0.769018	-131
TATGGGAAATTTGACGTTAAACAATTTACAAC	7	107	0	TTGACTTAAC	    0.887017	-69
ACCCCGCTTATTGATGTAAATCAAATTCACCT	8	192	0	TTGATTAATC	    0.953949	-70
ACTGTGAATGTTGTCTTTAATCAATTGTAAGT	9	162	0	TTGTCTTATC	    0.756522	-139
          ***** ** ***

Masking position 1
Map Score:   10.6139

Number of sites scoring better than the average of aligned sites = 208
Number in coding regions = 157
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 58
Fraction of orfs with sites within 600 bp upstream = 0.00931577


Motif number 6

AACAGGTTTTTGTTGAAGCAAATTTGCATTTT	1	77	0	TGTTGGCAAA	    0.936818	-224
ATTGTAAGGATTTTGCGGCGTAATATATACGT	1	110	1	TTTTGGCGTA	    0.847703	-191
TTTAATTAACTGTTTTAGCGGAGGATGCGGAA	2	91	1	TGTTTGCGGA	    0.939066	-210
ACTCGCATGGTTTTTATGCAAATACGGAGTAA	2	180	0	TTTTTGCAAA	    0.939454	-121
TATTGTTTATTATTTGAGCGAATTTGTGAGAG	3	45	0	TATTTGCGAA	    0.781673	-227
GTTAATCAAGTTTTGTTGCTGAAAAGATAGGC	3	109	0	TTTTGGCTGA	    0.907536	-163
ACTATTAAGATTTTTATGCAGATGGGTATTAA	5	62	0	TTTTTGCAGA	    0.943859	-239
AGGCGGATTATTTTGTGGCAAACAGATGTTCT	6	130	1	TTTTGGCAAA	    0.954175	-102
ATTCTGAATCTTTTTGCGCGAAATCAAAAAGA	6	159	0	TTTTTGCGAA	    0.952332	-73
TGATATTTCATGTTTGTGCAAAAAATAGACAA	8	97	0	TGTTTGCAAA	    0.917004	-165
ATTAATCAACTTTTGTTGCTGACCTTCAAAAA	9	51	0	TTTTGGCTGA	    0.907536	-250
          *****  *****

Masking position 12
Map Score:   10.5968

Number of sites scoring better than the average of aligned sites = 372
Number in coding regions = 307
Number in noncoding regions = 65
Number of orfs with sites within 600 bp upstream = 85
Fraction of orfs with sites within 600 bp upstream = 0.0136524


Motif number 7

ACAAAACTTGATTAACATCAATTTTGGTAT	3	125	1	ATTAACATCA	    0.759816	-147
ATAGCTCTTAATTAACAACAGGTTACAGCA	3	203	0	ATTAACAACA	    0.759816	-69
AGGGTAGGGATTTTACAGCACCGTGAAAAA	4	130	1	TTTTACAGCA	    0.793132	-171
CTTTAGGATAATTAACAGCCACCACATAAC	5	134	0	ATTAACAGCC	    0.751579	-167
ATTGCTAATGTTTAAGGGCAAGGTAACGCT	5	237	0	TTTAAGGGCA	    0.858198	-64
CAGCTTAATTTTTAACGGCAAGAGAGACAA	6	21	0	TTTAACGGCA	    0.981069	-211
AAACGAAGAATTAAACGGCATAAAAAAGTA	7	34	0	TTAAACGGCA	     0.93509	-142
TTGTAAATTGTTTAACGTCAAATTTCCCAT	7	108	1	TTTAACGTCA	    0.910753	-68
AATTGTGCAAATAAACGGCAGGGTAATTTT	9	25	1	ATAAACGGCA	    0.894669	-276
CTTCCTCTTTTTCAACAGCATGCATAACTG	9	98	0	TTCAACAGCA	    0.864246	-203
TTTTATTGTTTTTCACGACAGTAACCGCAC	9	241	0	TTTCACGACA	    0.680328	-60
          **********

Masking position 5
Map Score:   5.32169

Number of sites scoring better than the average of aligned sites = 838
Number in coding regions = 768
Number in noncoding regions = 70
Number of orfs with sites within 600 bp upstream = 78
Fraction of orfs with sites within 600 bp upstream = 0.0125281


Motif number 8

CTAAATTACCGCCTTTCAGCCAATTTGATCG	1	25	0	GCCTTCAGCC	    0.915398	-276
CGAGTTACGGGCCTATAAGCCAGGCGAGATA	2	207	1	GCCTTAAGCC	    0.965876	-94
TCCTGTGGGAGCCTGTCGGCCCTCTGATAAA	5	272	0	GCCTTCGGCC	    0.968379	-29
TTTTTAACTGGCCTGTCAGGCAGTGGTGCGT	6	65	1	GCCTTCAGGC	    0.525041	-167
          **** ******

Masking position 6
Map Score:   2.5992

Number of sites scoring better than the average of aligned sites = 29
Number in coding regions = 24
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 9

ACAATAAACTCTGTTTTTTGATCTCACCCGGTAAAGTCG	3	71	1	CTTTTTCCCC	     0.87785	-201
TAGCGAAGAACATTTTCATTGCTGTAACCTGTTGTTAAT	3	184	1	CTTTTCTTCC	     0.98866	-88
CTCTGATACTCGTTTCGATGTCTGCCACCTTAGTGTCTG	4	266	0	CTTCTCTCCC	    0.982271	-35
     GCTCGCTGTTTTGTCTCTCTTGCCGTTAAAAATT	6	6	1	CTTTTCTTCC	     0.98866	-226
TTTAATTCTTCGTTTTGTTACCTGCCTCTAACTTTGTAG	7	49	1	CTTTTCTCCT	    0.958943	-127
CGTCGTCCGGCCTTTTCCTCTCTTCCCCCGCTACGTGCA	8	34	1	CTTTTCTCCC	    0.994477	-228
  TTTTGCCTCGATTTCTTTTCTATTACCGCCTACCTTA	8	235	0	CTTTTCTTCC	     0.98866	-27
          *  ***  *  ** *  **

Masking position 9
Map Score:   2.63459

Number of sites scoring better than the average of aligned sites = 104
Number in coding regions = 93
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 10

TTTATGCAAATACGGAGTAAATATTTGATT	2	170	0	TACGGAGTAA	     0.87317	-131
ACACGGCAAATAAGGAGTAACTCTTTCCGG	4	78	0	TAAGGAGTAA	    0.962853	-223
GCAGACATCGAAACGAGTATCAGAGGTGTC	4	280	1	AAACGAGTAT	     0.71586	-21
AGATGGGTATTAAGGAGTATTCCCCATGGG	5	45	0	TAAGGAGTAT	    0.976516	-256
TAATTATCCTAAAGGGGTATCTTAGGAATT	5	150	1	AAAGGGGTAT	    0.937189	-151
TCCTCTTTTTTCAGGGGTATTACTGCGCGA	6	207	0	TCAGGGGTAT	    0.915437	-25
CATACAGAGCTAAGGGATAATGCGTAGCGT	7	135	1	TAAGGGATAA	    0.739387	-41
ATATACCCATTAAGGAGTATATAAAGGTGA	8	168	1	TAAGGAGTAT	    0.976516	-94
          **********

Masking position 9
Map Score:   4.64327

Number of sites scoring better than the average of aligned sites = 95
Number in coding regions = 64
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 11

TTACGCCGTTTTTGTGTGCATTCACATGGT	1	184	1	TTTGTGTGCA	    0.924028	-117
ACTCGCATGGTTTTTATGCAAATACGGAGT	2	182	0	TTTTTATGCA	    0.975673	-119
AATCTCATAATTTTTATGAAGTCACTGTAC	4	158	1	TTTTTATGAA	    0.861226	-143
ACTATTAAGATTTTTATGCAGATGGGTATT	5	64	0	TTTTTATGCA	    0.975673	-237
GCATAATACTTTTTTATGCCGTTTAATTCT	7	28	1	TTTTTATGCC	    0.936187	-148
TGATATTTCATGTTTGTGCAAAAAATAGAC	8	99	0	TGTTTGTGCA	    0.924025	-163
          **********

Masking position 5
Map Score:   2.33362

Number of sites scoring better than the average of aligned sites = 51
Number in coding regions = 25
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 12

TCACACGCATGCCCCAATAGAAATTTGTTTG	1	228	0	GCCCCATAGA	    0.954728	-73
CCGAGAGTGAACCCCGTTAGAAAGGGTCACA	1	254	0	ACCCCTTAGA	    0.990395	-47
      CGTGACCCCCTTAAATTTATTAACC	3	257	0	ACCCCTTAAA	    0.941007	-15
TTCGATGTCTGCCACCTTAGTGTCTGTAGCT	4	261	0	GCCACTTAGT	    0.897737	-40
TTCCTAAGATACCCCTTTAGGATAATTAACA	5	147	0	ACCCCTTAGG	    0.978925	-154
CATGTAAAATACCACTTTAGAGTTAGTCAGT	9	130	0	ACCACTTAGA	    0.972097	-171
          ***** *****

Masking position 8
Map Score:   2.0393

Number of sites scoring better than the average of aligned sites = 15
Number in coding regions = 8
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 13

ATTTGATCGAGAACAATTTATCT       	1	4	0	GAACAATTTA	     0.60869	-297
CGCAAAATCCTTACAATAAACAGGTTTTTG	1	97	0	TTACAATAAA	    0.414774	-204
TCCTCCGCTAAAACAGTTAATTAAAAGGGA	2	86	0	AAACAGTTAA	    0.744707	-215
AAATAAATTTTAAAAATTAACAAATGAGTT	2	130	0	TAAAAATTAA	     0.77812	-171
ATTATCCAAATAAAAATAAATTTTAAAAAT	2	143	0	TAAAAATAAA	    0.682263	-158
CTCAAATAATAAACAATAAACTCTGTTTTT	3	59	1	AAACAATAAA	      0.8773	-213
GCTATGTTAATAACCATTAATTAACAATTG	3	228	1	TAACCATTAA	     0.64741	-44
GTAGTTATTTAAACTATTAAGATTTTTATG	5	76	0	AAACTATTAA	    0.516782	-225
TGATGGGGATGAAAAATAAAGTAAATTCCT	5	173	0	GAAAAATAAA	    0.604565	-128
CTCTTGCCGTTAAAAATTAAGCTGAATTTT	6	27	1	TAAAAATTAA	     0.77812	-205
GCGAGGAAACTAACAGTAAAATTCTGAATC	6	181	0	TAACAGTAAA	    0.674082	-51
GTAACAAAACGAAGAATTAAACGGCATAAA	7	40	0	GAAGAATTAA	     0.67437	-136
ATTTGACGTTAAACAATTTACAACGTGAAT	7	101	0	AAACAATTTA	    0.653481	-75
CATGTTCCTCAAAGAATTAATCAACTTTTG	9	68	0	AAAGAATTAA	    0.715161	-233
CCCCTATGTGTAACAAATAACCACACTGTG	9	188	0	TAACAAATAA	    0.536613	-113
CTGTCGTGAAAAACAATAAAAACCGCCATT	9	250	1	AAACAATAAA	      0.8773	-51
          **********

Masking position 3
Map Score:   3.57107

Number of sites scoring better than the average of aligned sites = 332
Number in coding regions = 205
Number in noncoding regions = 127
Number of orfs with sites within 600 bp upstream = 161
Fraction of orfs with sites within 600 bp upstream = 0.0258593


Motif number 14

TTAGAAAGGGTCACACGCATGCCCCAATAGA	1	238	0	TACACGCATG	    0.945291	-63
TATTGTTACTTTATTCGCCTGATGCTCCCTT	2	61	1	TATTCGCCTG	     0.97557	-240
TATAGGCCCGTAACTCGCATGGTTTTTATGC	2	193	0	TACTCGCATG	    0.957444	-108
CTCGCCTGGCTTATAGGCCCGTAACTCGCAT	2	204	0	TATAGGCCCG	     0.79927	-97
ATATAGATCATATCTCGCCTGGCTTATAGGC	2	217	0	TTCTCGCCTG	     0.94482	-84
AGCATTTTTTTAACTGGCCTGTCAGGCAGTG	6	59	1	TACTGGCCTG	    0.972068	-173
CCTCGCGCAGTAATACCCCTGAAAAAAGAGG	6	205	1	TATACCCCTG	    0.854982	-27
          * *********

Masking position 1
Map Score:   1.13853

Number of sites scoring better than the average of aligned sites = 544
Number in coding regions = 501
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 15

ATGAGAAATTGATATAGATCATATCTCGCC	2	229	0	GATATAGATC	    0.639813	-72
AACAAAACTTGATTAACATCAATTTTGGTA	3	124	1	GATTAACATC	    0.954043	-148
GTGGTTAGTCGCTTTACATCGGTAAGGGTA	4	106	1	GCTTTACATC	    0.937032	-195
TATGGGTAATGATAAATATCAATGATAGAT	4	192	1	GATAAATATC	    0.609943	-109
CTTATCGTTTGATTTACATCAAATTGCCTT	4	230	1	GATTTACATC	    0.866055	-71
AGGTGAATTTGATTTACATCAATAAGCGGG	8	192	1	GATTTACATC	    0.866055	-70
          **********

Masking position 6
Map Score:   2.70688

Number of sites scoring better than the average of aligned sites = 53
Number in coding regions = 40
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


