AlignACE 3.0 04/13/02
./AlignACE -expect 5 -gcback 0.61 -i 1256.in
Parameter values:
expect = 5
gcback = 0.61
minpass = 200
seed = 1078933791
numcols = 10
undersample = 1
oversample = 1

Input sequences:
#0 1256_Gsul, G.sulfurreducens sequence for operon 1256

#1 1256_Dvul, D.vulgaris sequence for operon 1256

#2 1256_Gmet, G.metallireducens sequence for operon 1256 from contig 9

Motif 1
CAGGACTGGCAGATGCT 0 74 0
CTGCAGTCGTGGATGTT 0 155 0
CCGCAAACGGCGATTTT 0 197 1
CGGTACACGGCGATGGT 0 233 1
CTGTAGATGGCGATGCT 1 253 0
TAAGAATTGATGATGGT 2 32 0
CCAGACAGGTGGTTGGT 2 176 0
* * * * * **** *
MAP Score: 6.01732

Motif 2
ATCGAATCCACGT 0 329 1
ATCGAACTCTCGG 1 130 1
ATGGAATCCACGT 1 161 0
AAGGAACGTTCCT 1 312 1
ATGGAACGTACCG 1 506 1
ATTGACTCGTTGT 2 92 1
ATAGAATTTTTGT 2 203 0
ATTGAATACATCT 2 230 1
** **** ****
MAP Score: 4.57595

Motif 3
GGGCTCCGGCGATTG 0 3 0
AGTTGCCGATCATGG 0 120 1
GGGCTGCGCACATGT 1 73 1
GGTTGACGGGGATGG 1 170 0
GGGTTCCCGGAATGG 1 194 0
GGTCTACGAGGATGT 1 290 0
GGGTTTCGACAATGG 2 159 0
GGGTGCCAGACATGG 2 275 0
GGGCGGCCACCATTT 2 329 1
***** * ****
MAP Score: 3.52428

Motif 4
AGATAGTTGCCGATCATGG 0 116 1
AGACGGTACACGGCGATGG 0 230 1
AGAGGCGTCCCTTCGATGG 0 290 1
AGGAAGTTGAGAGGGATCG 0 314 1
AGCAGGTTGACGGGGATGG 1 170 0
AGCGGGGTTCCCGGAATGG 1 194 0
AGTCTGTAGATGGCGATGC 1 254 0
AGGTCGGTACGTTCCATGC 1 504 0
** *** * ****
MAP Score: 3.17477

Motif 5
GTCCGGAAGGATG 0 217 1
GTACACGGCGATG 0 235 1
GTTGAGAGGGATC 0 319 1
GTTGACGGGGATG 1 171 0
GTAGATGGCGATG 1 255 0
GTCTACGAGGATG 1 291 0
GTGCGAGGCGATC 1 566 1
** * *******
MAP Score: 3.01511

Motif 6
CATCGAAGGGACG 0 295 0
CCACGAAGGAACG 1 307 1
CTTCGAAGGTGCG 1 358 1
CCACGAAGGCGCG 1 398 0
AAACGAAAGCCCG 1 456 0
* ******* **
MAP Score: 1.67244

Motif 7
GGTGGTGGTAAGATAGT 0 106 1
GATGGTCTTGAGGCATT 0 244 1
GATGGGATTCAGGAAGT 0 304 1
GGTCGTACTCACGAAGT 2 254 0
GGGGGTGGTCACGAAAT 2 340 0
* **** * * * * *
MAP Score: 0.405581

Motif 8
GTAGCGGCGGCA 1 86 1
GCATGGGCGAGA 1 104 1
GAATGGGCGACA 1 188 0
GCATGGGTGGCA 1 230 0
GGATGGGTGGCG 1 331 0
GAAGGGGTGCCA 2 282 0
* ******* **
MAP Score: 0.290459

Motif 9
GACCGGTGGT 0 102 1
GACTGCAGGT 0 164 1
GACAGCAGGT 1 182 0
GACAGGTGGT 2 180 0
GACAACAGGT 2 375 0
**********
MAP Score: 0.224046