AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i250_fts_cell_wall_synecho_reg_100.orf -o250_synecho_100.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -x5 -e 
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 =  	0.48
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RCY09804	120	Synechocystis
#2	RCY06805	249	Synechocystis
#3	RCY33828	162	Synechocystis
#4	RCY50530	178	Synechocystis
#5	RCY34375	180	Synechocystis
#6	RCY29867	300	Synechocystis
#7	RCY07516	147	Synechocystis
#8	RCY07197	190	Synechocystis
#9	RCY14422	284	Synechocystis
#10	RCY11010	269	Synechocystis
#11	RCY50049	71	Synechocystis
#12	RCY41993	184	Synechocystis

Motif number 1

GAGCCATGGACTCCTCCCACCCAAAACTAAATT	1	18	1	CTCCCCACCA	    0.945902	-103
AATTCATCTCCCTTTACCAAGCATATTTCCCGT	1	62	1	CCTACCAGCA	    0.942819	-59
TATTTTTACCCTCCACTCCAGCCATTCTCCCGT	2	11	1	CTCCTCCGCC	    0.961473	-239
ACAGAGATCCCCTCGCCCAAGCACAAATCCCAG	2	115	0	CCTCCCAGCA	    0.987999	-135
TCCCCTAATACTTCCCCCCTGCA          	2	237	1	CTTCCCCGCA	    0.991472	-13
CTCCACGGAACTTATCCCCGGCAAAGTAATTCA	3	101	0	CTTCCCCGCA	    0.991472	-62
CCATGTCCCCCTTGCCCCCTGCCGTTGGCCTGA	4	22	0	CTTCCCCGCC	    0.993407	-157
CCACTGTTATCTATGCCCATGTCCCCCTTGCCC	4	38	0	CTACCCAGTC	    0.727611	-141
CGCCAACTAACCAAAACCCCCCCAGGGATAAAG	5	59	0	CCAACCCCCC	    0.925309	-122
TGAGCAGTTGCCCATTCCCACCATTGGCATTGG	9	32	1	CCCTCCCCCA	    0.795866	-253
TCCGCCGTCACCAAAACCTGGCCGTCACACTGG	9	74	0	CCAACCTGCC	    0.767754	-211
AACAACCGCCCTTTGCTCCGGCCTATCTGAATT	9	127	1	CTTCTCCGCC	    0.955641	-158
TTAGTTTGTTCCCTAACCCCGCCGGGGAAATTG	9	216	0	CCCACCCGCC	    0.982549	-69
AACAGGCTGCCCAGGCTCCAGCAATGACCATAA	9	258	1	CCACTCCGCA	     0.95852	-27
AGCAAAAACTCTACCCCCAGGCATAGACAAAAC	10	166	0	CTACCCAGCA	     0.97784	-104
   AGCAACGCTCCTCACAAGCCATAAATGTTA	10	250	0	CTCCACAGCC	    0.812825	-20
ACGGAGGAATCCTGACCCACCCAAAGATGGTTA	12	55	0	CCTCCCACCA	     0.96049	-130
ATCAAAATGTCCAATCCCCCGCATAACGGAGGA	12	80	0	CCACCCCGCA	    0.993851	-105
          ***  **** ***

Masking position 8
Map Score:   30.5029

Number of sites scoring better than the average of aligned sites = 2257
Number in coding regions = 2103
Number in noncoding regions = 154
Number of orfs with sites within 600 bp upstream = 169
Fraction of orfs with sites within 600 bp upstream = 0.0271442


Motif number 2

CAAAAGCAACCACAGGGAGAGCAACGCTTCCGAAG	2	177	0	CACAGGGAAC	    0.904817	-73
AGCGACTAGGCGCATGGTTATTAGCTCACGTCCCT	3	19	0	CGCATGGAAC	    0.640627	-144
GAATTACTTTGCCGGGGATAAGTTCCGTGGAGGCT	3	102	1	GCCGGGGATC	     0.87227	-61
ATCCCGCCTTCCCAGGGTAACAGCCTCCACGGAAC	3	123	0	CCCAGGGAGC	    0.995556	-40
CCAAAACCCCCCCAGGGATAAAGCCGGGATATTTC	5	47	0	CCCAGGGAGC	    0.995561	-134
TACGGGGCGACCCATTGACAGCGACACCAACATTC	7	33	0	CCCATTGAGC	     0.93249	-115
TTCGTCCCTTCCCAGTTGGAAAAACCCCAGTGGCA	8	140	1	CCCAGTTAAC	    0.882864	-51
TTGGAAAAACCCCAGTGGCAAAACCTTACTAATCC	8	155	1	CCCAGTGAAC	     0.98482	-36
TGGGCAACTGCTCAGTGATACTAGCCGCTAGTTCG	9	11	0	CTCAGTGAAC	    0.900039	-274
GGGGCAGGGCCCCAGTGTGACGGCCAGGTTTTGGT	9	63	1	CCCAGTGAGC	    0.991743	-222
GGCGGATTTACTCGGTTTGACAGTCAAACAACCGC	9	101	1	CTCGGTTAGC	    0.563484	-184
ATTCAGATAGGCCGGAGCAAAGGGCGGTTGTTTGA	9	124	0	GCCGGAGAGC	    0.871856	-161
CCCTAACCCCGCCGGGGAAATTGTCTTTGTCGCAC	9	204	0	GCCGGGGAGC	    0.983747	-81
AAACCCAGAGGCCACGGTAAACAGCGACGGAGAGA	10	135	0	GCCACGGAAC	    0.840534	-135
          *******  *  * *

Masking position 10
Map Score:   17.0772

Number of sites scoring better than the average of aligned sites = 1548
Number in coding regions = 1432
Number in noncoding regions = 116
Number of orfs with sites within 600 bp upstream = 139
Fraction of orfs with sites within 600 bp upstream = 0.0223257


Motif number 3

          CCCCTGTTGTTGGGTTTTTT	1	111	0	CCCCTGTTGT	    0.850917	-10
CAAGCACAAATCCCAGCGGTCTATCGTCCC	2	101	0	TCCCAGCGGT	    0.982388	-149
AGCGTTGCTCTCCCTGTGGTTGCTTTTGCG	2	184	1	TCCCTGTGGT	      0.9784	-66
TCCCCCTTGCCCCCTGCCGTTGGCCTGATC	4	20	0	CCCCTGCCGT	    0.817734	-159
CCCGGCTTTATCCCTGGGGGGGTTTTGGTT	5	54	1	TCCCTGGGGG	     0.97708	-127
GCGACATCGATGCCAGGGGCGTTCCCTTTT	5	118	1	TGCCAGGGGC	    0.910805	-63
CTAGATCACCTCCCATGGGTGCTTGCATCA	6	73	0	TCCCATGGGT	     0.85854	-228
ACACCAACATTCCCTTTGGTCAGGATAGTT	7	15	0	TCCCTTTGGT	     0.84024	-133
CTTCGTCCCTTCCCAGTTGGAAAAACCCCA	8	139	1	TCCCAGTTGG	    0.905421	-52
GTTGGAAAAACCCCAGTGGCAAAACCTTAC	8	154	1	CCCCAGTGGC	    0.969223	-37
CCTGCCCCAATGCCAATGGTGGGAATGGGC	9	41	0	TGCCAATGGT	    0.595368	-244
TGGGGCAGGGCCCCAGTGTGACGGCCAGGT	9	62	1	CCCCAGTGTG	    0.834901	-223
AAGACAATTTCCCCGGCGGGGTTAGGGAAC	9	212	1	CCCCGGCGGG	    0.950731	-73
GTTTTGTCTATGCCTGGGGGTAGAGTTTTT	10	166	1	TGCCTGGGGG	    0.956284	-104
TTTGTTACTCCGCCAGCGGGTGGGGTATTT	12	112	1	CGCCAGCGGG	    0.968992	-73
          **********

Masking position 4
Map Score:   17.8008

Number of sites scoring better than the average of aligned sites = 2535
Number in coding regions = 2353
Number in noncoding regions = 182
Number of orfs with sites within 600 bp upstream = 188
Fraction of orfs with sites within 600 bp upstream = 0.030196


Motif number 4

TTGTTGGGTTTTTTGTCTGTGCCTTTCCTGA	1	94	0	TTTTTCTGTG	    0.981417	-27
ATGGTTTGCATTTTCTGTTTGAATTACTTTG	3	82	1	TTTTTGTTTG	    0.721679	-81
TGCGTCCCACTGTTATCTATGCCCATGTCCC	4	46	0	TGTTTCTATG	    0.874118	-133
AAAAGGGGAATTTTTTCTGTAACTGACAGCT	4	95	1	TTTTTCTGTA	    0.821879	-84
TGTCGCACCATTTTAGCTTTGAGGGGGATCA	5	93	0	TTTTGCTTTG	    0.897152	-88
CATTTGCAATTTTTATCTGTGATCTAGATCA	6	95	0	TTTTTCTGTG	    0.981417	-206
TGAACTAATTTTTTGACTATGGCCAACGCAA	8	105	1	TTTTACTATG	    0.856466	-86
GGCCTCTGGGTTTTGTCTATGCCTGGGGGTA	10	157	1	TTTTTCTATG	    0.970843	-113
GGGGGTAGAGTTTTTGCTATGATGTCGCTCA	10	181	1	TTTTGCTATG	    0.942115	-89
GGGTGGGGTATTTTTTTTGTGGGCTTATCAA	12	129	1	TTTTTTTGTG	    0.838124	-56
          **** ******

Masking position 4
Map Score:   8.64105

Number of sites scoring better than the average of aligned sites = 184
Number in coding regions = 144
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 48
Fraction of orfs with sites within 600 bp upstream = 0.0077096


Motif number 5

GGCTGGAGTGGAGGGTAAAAATA       	2	4	0	GAGGGTAAAA	    0.912412	-246
TCCCGTGATAGAGGGAAAAAGCTCAGATTC	2	38	1	GAGGGAAAAA	    0.963398	-212
CAAATTCTTAGGGCGCAAAAGCAACCACAG	2	197	0	GGGCGCAAAA	    0.962658	-53
GAAGTATTAGGGGAGCAAAATGAGCAAATT	2	221	0	GGGAGCAAAA	    0.945634	-29
GCCAACGGCAGGGGGCAAGGGGGACATGGG	4	26	1	GGGGGCAAGG	    0.927661	-153
TGCCCAATCAAGCGGCAAAAAATCTTAAAT	5	11	1	AGCGGCAAAA	    0.850544	-170
ATTGAAAGTTGGGGGCAAAAAGGGAACGCC	5	135	0	GGGGGCAAAA	    0.994395	-46
GAAAGAATAGGAGTGAAAAATATGGCGGAG	6	162	0	GAGTGAAAAA	    0.720699	-139
GAAAAACCCCAGTGGCAAAACCTTACTAAT	8	158	1	AGTGGCAAAA	    0.793376	-33
CTAAAACAGAGAGGGCAAGACGAAC     	10	6	0	GAGGGCAAGA	    0.972828	-264
GACGGAGAGAAAGGGAAAAAGATTCCCACC	10	115	0	AAGGGAAAAA	    0.867019	-155
          **********

Masking position 7
Map Score:   10.1347

Number of sites scoring better than the average of aligned sites = 1382
Number in coding regions = 1202
Number in noncoding regions = 180
Number of orfs with sites within 600 bp upstream = 192
Fraction of orfs with sites within 600 bp upstream = 0.0308384


Motif number 6

  CTACGTCCCCAAACGATCCCGCCTTCCCA	3	144	0	CCAACGATCC	    0.955914	-19
TTAAATTGAGCCGAAATATCCCGGCTTTATC	5	35	1	CCAAATATCC	    0.955008	-146
GGGGATCACCGCCAACTAACCAAAACCCCCC	5	70	0	GCAACTAACC	    0.937938	-111
CCTTTTTGCCCCCAACTTTCAATAGTTTTTA	5	142	1	CCAACTTTCA	    0.880733	-39
CCCATGAACTCCAAACTTTCCCTATTTGACA	6	191	1	CCAACTTTCC	    0.986887	-110
TTGTCTGTTACCAATCTTTCCGAGGATATAC	6	248	1	CCATCTTTCC	    0.922326	-53
     GCTGGGCAAACTAACCTAGGGTTATC	11	6	1	GCAACTAACC	    0.937923	-66
TTCCTGTCCCGCTAATTTTCCGGACCAACCG	11	49	1	GCAATTTTCC	    0.833307	-23
      CTTGCCCAAATATCCGTTAAAAACT	12	170	0	CCAAATATCC	    0.955008	-15
          ** ********

Masking position 4
Map Score:   7.85403

Number of sites scoring better than the average of aligned sites = 330
Number in coding regions = 282
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 7

GGTTTTTTGTCTGTGCCTTTCCTGACGGGAAATAT	1	84	0	CTTGTCCTGA	    0.881813	-37
CTTTTGCGCCCTAAGAATTTGCTCATTTTGCTCCC	2	206	1	CTAGTGCTCA	    0.986329	-44
ACCATTTTAGCTTTGAGGGGGATCACCGCCAACTA	5	83	0	CTTGGGATCA	    0.871967	-98
CAATTTTTATCTGTGATCTAGATCACCTCCCATGG	6	85	0	CTTGTGATCA	    0.970288	-216
 GTTAAAATTCTTCGACATAGCTGATAAATCCCGG	7	124	0	CTCGTGCTGA	    0.971874	-24
AAAAAATTAGTTCAGGGGTTGATCAATGACGTTTT	8	84	0	TTAGTGATCA	    0.640094	-107
GCTAGTATCACTGAGCAGTTGCCCATTCCCACCAT	9	21	1	CTAGTGCCCA	    0.937679	-264
CCGCCCTTTGCTCCGGCCTATCTGAATTTACGACA	9	132	1	CTCGTTCTGA	    0.772081	-153
GTCTTGCCCTCTCTGTTTTAGCTCAGTACATTTAA	10	15	1	CTTGTGCTCA	    0.991434	-255
AGAGTTTTTGCTATGATGTCGCTCAATTACAGGTG	10	187	1	CTTGTGCTCA	    0.991434	-83
          ** **   * *****

Masking position 2
Map Score:   5.38064

Number of sites scoring better than the average of aligned sites = 196
Number in coding regions = 164
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 8

GTGAGCTAATAACCATGCGCCTAGTCGCTTT	3	25	1	AACCTGCGCC	    0.954642	-138
     TGCCCAATCAAGCGGCAAAAAATCTT	5	6	1	AATCAGCGGC	    0.960617	-175
TTGGGAACTAGACCGATCGCCAATCCGTTTA	7	80	1	GACCATCGCC	    0.956618	-68
CTGTCAGCAAAATCGACAGCCAAAGGCCAGC	8	29	1	AATCACAGCC	    0.873587	-162
         CGAACTAGCGGCTAGTATCACT	9	2	1	GAACAGCGGC	    0.959853	-283
TTTGACAGTCAAACAACCGCCCTTTGCTCCG	9	116	1	AAACACCGCC	    0.967962	-169
GCATAGACAAAACCCAGAGGCCACGGTAAAC	10	148	0	AACCAGAGGC	    0.942892	-122
TAATTTTCCGGACCAACCGCC          	11	61	1	GACCACCGCC	    0.988715	-11
          **** ******

Masking position 2
Map Score:   4.59262

Number of sites scoring better than the average of aligned sites = 355
Number in coding regions = 329
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 9

TTCGAGCCATGGACTCCTCCCACCCAAAAC	1	15	1	GGACTCCTCC	    0.939382	-106
CGTCCCCAAACGATCCCGCCTTCCCAGGGT	3	140	0	CGATCCCGCC	    0.922277	-23
TTTTCTGTATCTATTTCTCCTCCAATGTAA	6	42	1	CTATTTCTCC	    0.868659	-259
TTCTAACTCAGTTTTCCTCCGCCATATTTT	6	146	1	GTTTTCCTCC	    0.927602	-155
TGATCAATGACGTTTTCTCCATCAGACTAG	8	70	0	CGTTTTCTCC	    0.961333	-121
GCAAAATCTTCGTCCCTTCCCAGTTGGAAA	8	132	1	CGTCCCTTCC	    0.857604	-59
ATCTTTTTCCCTTTCTCTCCGTCGCTGTTT	10	122	1	CTTTCTCTCC	    0.870484	-148
TATCTTTGACCGTTTCTTCCTGTCCCGCTA	11	33	1	CGTTTCTTCC	    0.937256	-39
GGGTGGGTCAGGATTCCTCCGTTATGCGGG	12	66	1	GGATTCCTCC	    0.969396	-119
          **********

Masking position 9
Map Score:   4.51523

Number of sites scoring better than the average of aligned sites = 655
Number in coding regions = 596
Number in noncoding regions = 59
Number of orfs with sites within 600 bp upstream = 71
Fraction of orfs with sites within 600 bp upstream = 0.0114038


Motif number 10

TGCTTGGGCGAGGGGATCTCTGTCGTCGTAAAAA	2	125	1	AGGGGATCGC	    0.985172	-125
CCGAAGCAGCAGGGTATTGAAGCCTTTTTACGAC	2	149	0	AGGGTATTGC	    0.917239	-101
TTAGCTTTGAGGGGGATCACCGCCAACTAACCAA	5	78	0	GGGGGATCGC	    0.992378	-103
CACCCATGGGAGGTGATCTAGATCACAGATAAAA	6	82	1	AGGTGATCAC	    0.887596	-219
TTAGTTCAGGGGTTGATCAATGACGTTTTCTCCA	8	79	0	GGTTGATCGC	    0.953547	-112
GTACATTTAAGGATTATTAATGACACCAATCATA	10	40	1	GGATTATTGC	     0.77397	-230
GTGAACCGGCAGGTGATTGTAGACGTTAACATTT	10	224	1	AGGTGATTGC	    0.963502	-46
AACTAACCTAGGGTTATCTTTGACCGTTTCTTCC	11	19	1	GGGTTATCGC	    0.987737	-53
TTTTTTTGTGGGCTTATCAAAGGCTTGTGTAGTT	12	140	1	GGCTTATCGC	    0.939329	-45
          ********   * *

Masking position 7
Map Score:   5.12787

Number of sites scoring better than the average of aligned sites = 633
Number in coding regions = 578
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 68
Fraction of orfs with sites within 600 bp upstream = 0.0109219


Motif number 11

CACAGGGAGAGCAACGCTTCCGAAGCAGCA	2	172	0	GCAACGCTTC	    0.922133	-78
AGATAACAGTGGGACGCACCAAGGCAATTA	4	59	1	GGGACGCACC	    0.846962	-120
GGGCAAAAAGGGAACGCCCCTGGCATCGAT	5	123	0	GGAACGCCCC	    0.674719	-58
CGCTGTCAATGGGTCGCCCCGTATAATAAC	7	45	1	GGGTCGCCCC	    0.588884	-103
TGGCATTGGGGCAGGGCCCCAGTGTGACGG	9	56	1	GCAGGGCCCC	    0.918964	-229
         AGCAACGCTCCTCACAAGCCA	10	259	0	GCAACGCTCC	    0.950965	-11
          **********

Masking position 6
Map Score:   2.95902

Number of sites scoring better than the average of aligned sites = 220
Number in coding regions = 204
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 12

AAATATGCTTGGTAAAGGGAGATGAATTGG	1	60	0	GGTAAAGGGA	    0.929794	-61
ATTCTCCCGTGATAGAGGGAAAAAGCTCAG	2	34	1	GATAGAGGGA	    0.972739	-216
GTGTAGGGACGATAGACCGCTGGGATTTGT	2	96	1	GATAGACCGC	    0.858864	-154
GGCTATGCGAGATAAACCGATCTAAGCTTA	4	141	1	GATAAACCGA	    0.959767	-38
TCTTTCCGAGGATATACGGATAAATAATAT	6	262	1	GATATACGGA	    0.945004	-39
TTCTATGAAAGATAAACGGATTGGCGATCG	7	93	0	GATAAACGGA	    0.982619	-55
CAGCGACGGAGAGAAAGGGAAAAAGATTCC	10	119	0	GAGAAAGGGA	    0.929794	-151
          **********

Masking position 6
Map Score:   3.3844

Number of sites scoring better than the average of aligned sites = 45
Number in coding regions = 38
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 13

ACTGACAGCTTAAACTTTTGTGATAGGCTATG	4	116	1	TAACTTTGTG	    0.788276	-63
     ATGGTTTGACTTTACTGTTAAAAACTA	5	164	0	TGACTTTCTG	    0.977874	-17
ATGTTTTTACTGGTCATTACTGGCTTCCGATT	6	11	1	TGTCATTCTG	    0.945075	-290
TGCAAATGACTTAACATTCCTGAGTCAATTCT	6	118	1	TAACATTCTG	    0.965174	-183
        GTTAAACTATCCTGACCAAAGGGA	7	3	1	TAACTATCTG	    0.780035	-145
TTAAAATTCTTCGACATAGCTGATAAATCCCG	7	125	0	TGACATACTG	    0.895656	-23
CCTTTGGCTGTCGATTTTGCTGACAGATTTAA	8	23	0	TGATTTTCTG	    0.812481	-168
   TCGGTTATGGTCATTGCTGGAGCCTGGGC	9	266	0	TGTCATTCTG	    0.945075	-19
ATTGTAGACGTTAACATTTATGGCTTGTGAGG	10	239	1	TAACATTATG	    0.755791	-31
          * ****** ***

Masking position 11
Map Score:   2.93851

Number of sites scoring better than the average of aligned sites = 264
Number in coding regions = 229
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 14

ATAATAACTTGGGTTGGGAACTAGACCGATC	7	67	1	GGGTTGGGAC	    0.977045	-81
AAAGATAAACGGATTGGCGATCGGTCTAGTT	7	85	0	GGATTGGCAT	     0.96429	-63
CGAAGATTTTGCGTTGGCCATAGTCAAAAAA	8	113	0	GCGTTGGCAT	     0.94825	-78
TTTCAAAGGGGGGGTGGGAATCTTTTTCCCT	10	103	1	GGGGTGGGAT	    0.977045	-167
GTTATGCGGGGGATTGGACATTTTGATTTGT	12	86	1	GGATTGGAAT	    0.908258	-99
CTCCGCCAGCGGGTGGGGTATTTTTTTTGTG	12	119	1	GGGTGGGGAT	    0.977045	-66
          ******** **

Masking position 10
Map Score:   0.646123

Number of sites scoring better than the average of aligned sites = 357
Number in coding regions = 325
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 15

CAAAGCTAAAATGGTGCGACATCGATGCCAGG	5	103	1	ATGGTGACAT	    0.985743	-78
          ATGGTTTGACTTTACTGTTAAA	5	169	0	ATGGTGACTT	    0.947755	-12
TGACTCAGGAATGTTAAGTCATTTGCAATTTT	6	113	0	ATGTTGTCAT	    0.829107	-188
    GTTAAAATTCTTCGACATAGCTGATAAA	7	130	0	ATTCTGACAT	    0.821491	-18
TGTTTCCGTAATGGTATGTCGTAAATTCAGAT	9	151	0	ATGGTGTCGT	    0.921281	-134
CGCACCTGTAATTGAGCGACATCATAGCAAAA	10	192	0	ATTGAGACAT	    0.806459	-78
CCACCCAAAGATGGTTAGACATTTTCAATTAA	12	40	0	ATGGTGACAT	    0.985743	-145
          *****  *****

Masking position 1
Map Score:   0.485754

Number of sites scoring better than the average of aligned sites = 65
Number in coding regions = 56
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


