AlignACE 3.0 04/13/02
./AlignACE -expect 5 -gcback 0.61 -i 188.in
Parameter values:
expect = 5
gcback = 0.61
minpass = 200
seed = 1078854421
numcols = 10
undersample = 1
oversample = 1

Input sequences:
#0 188_Gsul, G.sulfurreducens sequence for operon 188

#1 188_Dvul, D.vulgaris sequence for operon 188

#2 188_Gmet, G.metallireducens sequence for operon 188 from contig 39

Motif 1
CCTGCCCAAGGATGTGACCCTGGCC 0 72 1
GAGGGGAAAGTCGGCAAGACCATCC 0 112 1
CAGCAGAAAGGCGAGAAATGCCCCG 0 234 0
CAGGGCCAAGAGCGCGATCCAGACC 2 0 1
GCCGCACAAGGGAGCGACGAGGACG 2 216 1
CAGGACCAGGTAATAGAGGGGGCCG 2 279 1
CACGACGAAGACGCCGAACACCGCC 2 350 1
GAGGTAGAAGGTCCAGCCGGTGTCG 2 410 1
GAGGTTCAGGCGGGGAAAGGCCACG 2 506 1
CATGATGAGGTTGCCGAAGGAGCCC 2 554 1
GATGATGAAGAGAAAGACCATCACC 2 590 1
** * *** ** **
MAP Score: 5.78459

Motif 2
GCGGATGATGGTGCCGTCCCCGGCGAT 0 25 0
CCTGCCCAAGGATGTGACCCTGGCCTT 0 72 1
GGAGTCATGGGTAGCGGTCACGACGAT 1 72 0
GCTGACAACGGTCTGGATCGCGCTCTT 2 7 0
GCCGCACAAGGGAGCGACGAGGACGGC 2 216 1
GCCGAGCTTGGCGCCGGCTGGGTCTTT 2 300 1
GGAGACGTTGGTCCCGGTCCGGCCGCT 2 377 1
GCCGGTGTCGGGGGGGCCGCCGCCGGT 2 425 1
GCGGGGAAAGGCCACGTCCCGGGCGCC 2 515 1
ACCGTCCACGGGGTGGTGATGGTCTTT 2 602 0
** * * ** * * * *
MAP Score: 4.90647

Motif 3
AAAGCAGTATCCC 0 147 0
GAAGCAGAAAACC 0 171 1
GAAGCAACAGACA 1 17 1
GAAGCGGCACACA 1 134 0
AAATCCGCAGCCC 2 150 0
AAAGCCGCAGCCC 2 257 1
GACTCAGAACCCC 2 338 1
GACGCCGAACACC 2 359 1
GAAGAGAAAGACC 2 596 1
***** * * ***
MAP Score: 4.60496

Motif 4
CGAAGCAGAAAA 0 170 1
GCAGGTTGAAGA 0 188 0
CCACGACGAAGA 2 349 1
GGCCGCTGAAGG 2 397 1
GGAGGTAGAAGG 2 409 1
CGCCGGTGAAGA 2 445 1
GGATGATGAAGA 2 589 1
GGACGGTGAAGA 2 622 1
*** * ******
MAP Score: 4.42863

Motif 5
CCCGTAGAGATAGCGGATGATGGT 0 40 0
GGAGGGGAAAGTCGGCAAGACCAT 0 111 1
GGCCAAGAGCGCGATCCAGACCGT 2 3 1
GCTGCGGATTTTGCACCAGATCGT 2 152 1
GCCGAACACCGCCAGGGAGACGTT 2 362 1
GCCGCTGAAGGGGAGGTAGAAGGT 2 398 1
GCCGGTGAAGAGCGACGTGAGGAT 2 446 1
GATCTGGATCGGCATGATGAGGTT 2 542 1
GGGGATGATGAAGAGAAAGACCAT 2 587 1
* * ** * *** * *
MAP Score: 3.52012

Motif 6
CTTGCCACCGGATGCA 0 2 0
CCCACCACCGTCCGGA 0 134 0
CTGACAACGGGCAGAA 0 256 1
CTGACAACGGTCTGGA 2 17 0
CAACAAACGGGCCGGA 2 98 0
CGTCGCACCCGCAGGA 2 173 1
CCCTTCAGCGGCCGGA 2 394 0
CCCGACACCGGCTGGA 2 421 0
CTCTTCACCGGCGGCG 2 442 0
CATGGCAGGCGCGGCA 2 473 0
* ******* * *
MAP Score: 3.33035

Motif 7
AGGCGCGGGAGGGGAAAG 0 104 1
ACGCGCAGCAGGTTGAAG 0 189 0
ATGCGTAGTAGTGTCATG 2 51 1
AGGCGTAGCAGCGCTACG 2 199 1
AGGCGGGGAAAGGCCACG 2 513 1
* *** * ** * * *
MAP Score: 2.95417

Motif 8
CGGTCACGACGA 1 73 0
AGGTTGCGATGA 1 149 0
CGGGTGCGACGA 2 172 0
AGGGAGCGACGA 2 224 1
CGGGTCTGATGA 2 328 1
CGGGGATGATGA 2 586 1
**** ******
MAP Score: 2.57955

Motif 9
GCTTCGGATCAAAGGAAAAG 0 156 0
GTGGCGCTCACGCGCAGCAG 0 196 0
GCAGCGCAAGGGAGGATCTG 0 282 1
GCCGTGAGAAGAAGCAACAG 1 7 1
GGCACGAACACCCTGATATG 1 31 0
GATGCGCATCACATCATAAG 1 55 0
GTTTTGTAGCCGATGACATG 2 34 1
GGGCCGGATTCGAGGAGAAG 2 86 0
GCAGCGCTACGCCGCACAAG 2 206 1
GCGGCGAGATGGCGTAAAAG 2 241 1
* ** * ** * ***
MAP Score: 2.11248

Motif 10
ACGAGGACGGCGGCGA 2 232 1
ACGACGAAGACGCCGA 2 351 1
CCGGTCCGGCCGCTGA 2 390 1
CCGCCGCCGGTGAAGA 2 441 1
ACGTCCCGGGCGCCGA 2 528 1
ATGATGAGGTTGCCGA 2 555 1
CCGGGGATGATGAAGA 2 585 1
CCGTGGACGGTGAAGA 2 618 1
*** ** * ** **
MAP Score: 1.92433

Motif 11
GGTGGCAAGCGT 0 9 1
GAAGACATAGGT 0 181 0
GATGACTACCGT 0 214 0
GCTGACAACGGG 0 255 1
GGAGTCATGGGT 1 87 0
GCTGACAACGGT 2 22 0
GATGACATGCGT 2 45 1
AGTGTCATGGGT 2 60 1
GGAGACGTTGGT 2 377 1
* ****** ***
MAP Score: 1.74884

Motif 12
AAAAGCAGTA 0 151 0
AGAAGAAGCA 1 13 1
AGGAGAAGCA 2 84 0
AAAATCCGCA 2 154 0
AAAAGCCGCA 2 256 1
AAAAGACCCA 2 318 0
**********
MAP Score: 1.3714

Motif 13
TGGCAAGCGTGGTGAT 0 11 1
TGACTACCGTGGCGCT 0 208 0
TGACAGCCGGGGCATT 0 227 1
TGACATGCGTAGTAGT 2 47 1
TGGCAGGCGCGGCAAT 2 471 0
** ** ** ** * *
MAP Score: 0.457148

Motif 14
GGCGCGGGAGGGGAAAGTCGGCA 0 105 1
GCTGACAACGGGCAGAACGGGCT 0 255 1
GACGATCTGGTGCAAAATCCGCA 2 154 0
GGAGAGACCGCGGAGGCGTAGCA 2 186 1
GGCGAGATGGCGTAAAAGCCGCA 2 243 1
GACGAAGACGCCGAACACCGCCA 2 353 1
GATGAGGTTGCCGAAGGAGCCCT 2 557 1
GGGGATGATGAAGAGAAAGACCA 2 587 1
* ** * *** ***
MAP Score: 0.0292947