AlignACE 3.0 04/13/02
./AlignACE -expect 5 -gcback 0.61 -i 1410.in
Parameter values:
expect = 5
gcback = 0.61
minpass = 200
seed = 1078802125
numcols = 10
undersample = 1
oversample = 1

Input sequences:
#0 1410_Gsul, G.sulfurreducens sequence for operon 1410

#1 1410_Dvul, D.vulgaris sequence for operon 1410

#2 1410_Gmet, G.metallireducens sequence for operon 1410 from contig 78

Motif 1
AGAGAGGTTGAACG 0 41 0
AGAGAGGGGAGTCG 0 163 1
AGAAACATTCGACT 1 21 0
ATAGATATCCTCTT 2 35 1
AGAAAGATCAGACG 2 87 1
AGAAATGGACTTCT 2 128 1
AGAGATATTGTTGT 2 180 0
AAAGAGGGAATCTT 2 202 1
AGAGAGGGGATCTG 2 218 0
ATAGAGGTGAATAT 2 416 1
AGAAAAATGATCCG 2 510 1
ATAGATGTCGTAAG 2 542 1
AGAAAAGGTTTTTG 2 712 0
AGAAACACGCTCCG 2 734 1
AAAGAAATCTTTTT 2 759 1
AAAGAAAGGATAAG 2 811 0
ATAGATATTCAATT 2 882 0
***** ** ** *
MAP Score: 6.84915

Motif 2
GAATGAAGAGGA 2 42 0
GAAGGGAGAAGT 2 136 0
GAAAGAACAGGT 2 321 1
GAAGGGAAAGGT 2 663 0
GATAGAAAAGGT 2 717 0
GAAAGGATAAGT 2 810 0
*** *** ****
MAP Score: 6.78224

Motif 3
ATTAATAATCATATTAA 0 69 0
AATGAAGAGGATATCTA 2 36 0
ATTCACCTCTATATCAA 2 411 0
GTTTTTGGTCAGATTCA 2 702 0
ACTCTGTCTGATATTCA 2 836 0
AATGAAAGGCAGATTGA 2 861 1
ATTGAATTGAATATCTA 2 878 1
*** * ***** *
MAP Score: 6.5545

Motif 4
GATTATTTGAATATC 2 829 1
GAACACAACAATATC 2 176 1
AATGAAGAGGATATC 2 38 0
ATTGAATTGAATATC 2 878 1
ATAGAGGTGAATATC 2 416 1
GATCAGACGGTTATC 2 92 1
GAAAACAACAATCTC 0 105 1
AATAATCATATTAAC 0 68 0
GAAAAAAAAGATTTC 2 762 0
AAAAAGCGGAACAAC 2 152 1
*** * ******
MAP Score: 6.27775

Motif 5
TATTAACACTACCCCAATGGAGAGAGG 0 48 0
TGTGACAGTTATGCGCAAGTCGAGACA 1 42 0
TGTCAGCCCTGTAGCTGGTGCGAGAGG 1 208 0
TCTGATCTTTCTCGCTACCCAGAAAAA 2 72 0
GTTCCGCTTTTTGTCGGAAGGGAGAAG 2 137 0
GATTCCCTCTTTTACCATTAAGAGATA 2 187 0
TGTCGTGACTGCCGGTATGGCGATATA 2 372 0
GAGCGTGTTTCTGCCGAGATAGAAAAG 2 719 0
TGTCGAGTCTCTCAGCAGCGTGAAAAA 2 771 0
* * ** * * ** * *
MAP Score: 6.05116

Motif 6
ACCCAGAAACATTCGA 1 23 0
AGGACGAAAAAGGGGA 1 346 0
ACCCAGAAAAACGCCA 2 67 0
AGCGAGAAAGATCAGA 2 83 1
TCCGACAAAAAGCGGA 2 146 1
AGCAGCGAAAATCTGA 2 332 0
AGCGTGAAAAAAAAGA 2 766 0
TCCAGAAAAGAAAGGA 2 815 0
*** ***** **
MAP Score: 5.72041

Motif 7
GCGAGAGAGGGG 0 160 1
GCGAGAGTGGCG 0 227 0
GCGAGAGTGGCG 1 135 1
GCGAGAGGGGAG 1 204 0
******* ** *
MAP Score: 4.91563

Motif 8
AAGAAAACAA 0 103 1
AGAGAGGGGA 0 163 1
AAAAAGGGGA 1 346 0
AAAAAGCGGA 2 152 1
AAAGAGGGAA 2 202 1
AGAGAGGGGA 2 222 0
ACAGAAAGAA 2 318 1
AAGAAGAGAA 2 453 1
AGGAAGGGAA 2 667 0
AAAAAAAGAT 2 765 0
AAAGAAAGGA 2 815 0
**********
MAP Score: 4.32022

Motif 9
AGGATATCTATTCG 2 32 0
AAGAGATATTGTTG 2 181 0
AGGTCAGATTTTCG 2 329 1
ACGACATCTATTCG 2 539 0
ATAACATATGGTTT 2 613 0
AGAAAAGGTTTTTG 2 712 0
AAGAAATCTTTTTT 2 760 1
* ** ** * ****
MAP Score: 3.38615

Motif 10
TCTCCATTGGGGTAGTGTTAATA 0 52 1
TCTCCGGGCGGGTAATTAAGAAA 0 116 1
TTTCTGGGTAGCGAGAAAGATCA 2 74 1
TCTCCCTTCCGACAAAAAGCGGA 2 139 1
TCTCTTAATGGTAAAAGAGGGAA 2 189 1
TCGCCATACCGGCAGTCACGACA 2 376 1
TTTCTGCCGAGATAGAAAAGGTT 2 716 0
TCTCAGCAGCGTGAAAAAAAAGA 2 766 0
**** * *** * *
MAP Score: 3.31461

Motif 11
ATTCAAACATGTGT 0 142 0
AGTCGAATGTTTCT 1 21 1
AATCGAATAGATAT 2 29 1
ACAACAATATCTCT 2 180 1
AGGTGAATATCCTT 2 420 1
AAAGAAATCTTTTT 2 759 1
AATTCAATCTGCCT 2 867 0
AATTGAATATCTAT 2 882 1
* * ****** * *
MAP Score: 3.28878

Motif 12
CAATGGAGAGA 0 50 0
TAATTAAGAAA 0 128 1
CATTTAAGAAA 0 292 0
CATTTGTGACA 1 62 0
CAGTTATGACA 1 242 0
CCTTTGTGAGA 1 478 0
CCATTAAGAGA 2 189 0
********* *
MAP Score: 3.18393

Motif 13
AGACGCACTGGACTT 0 204 0
AGAAACATTCGACTT 1 20 0
AGACGCACTGGACTT 1 155 1
ATATCTATTCGATTG 2 28 0
AGATAGAAAAGGTTT 2 715 0
TGAAAAAAAAGATTT 2 763 0
AGATTGAATTGAATT 2 871 1
*** * * *****
MAP Score: 3.07614

Motif 14
TCCGATTAATAATCATATTAACACT 0 65 0
TTTCTTAATTACCCGCCCGGAGATT 0 114 0
TGACAGTTATGCGCAAGTCGAGACA 1 42 0
TGGCGTTTTTCTGGGTAGCGAGAAA 2 67 1
TCCGCTTTTTGTCGGAAGGGAGAAG 2 137 0
TTCCCTCTTTTACCATTAAGAGATA 2 187 0
GATCGTCAATGGGGCCGCCAAGAAA 2 490 1
AAAGGTTTTTGGTCAGATTCAGAAG 2 698 0
GAGCGTGTTTCTGCCGAGATAGAAA 2 721 0
TCTTTTTTTTCACGCTGCTGAGAGA 2 766 1
TTCTGGATTATTTGAATATCAGACA 2 824 1
GCAGAGGATTCCCCCCCGATAGATA 2 889 0
* * *** * *** *
MAP Score: 3.0582

Motif 15
GACAGTTATGC 1 55 0
GACAGTTATGA 1 244 0
GATATCTATTC 2 33 0
GACATCTATTC 2 540 0
GATAGATATTC 2 886 0
***** *****
MAP Score: 2.94288

Motif 16
GCACTGGACTT 0 204 0
GAACGGGGCTT 0 269 0
GCACTGGACTT 1 159 1
GGACGGGGCGT 1 519 1
GAACGGGGCGT 1 542 0
GAAATGGACTT 2 129 1
* *********
MAP Score: 2.90232

Motif 17
CAGATTGTCGCAACCAA 0 238 1
CCCTGATTGATAACAGA 1 398 0
CAGCATATCGCCATCGA 1 457 1
CTCTTAATGGTAAAAGA 2 190 1
CTGGCTCTTGCCACAGA 2 306 1
CGGAGAGTTGATATAGA 2 404 1
CGGCCTCTAAGAAGAGA 2 445 1
CTGAATCTGACCAAAAA 2 701 1
CGGAATTTCGAAAGAAA 2 749 1
CAGCGTGAAAAAAAAGA 2 766 0
* * * * * ** ***
MAP Score: 2.62602

Motif 18
TGAATGAAAGGCAGATTGAATTGAAT 2 859 1
TTATTCGTATGTGTAGTTGGTTGCGA 0 245 0
TTATTACGACCGGTAATTCTGTTCCA 2 623 1
TAAATGGGGTGGCTAGTGGGATTTGA 0 297 1
TTAATATGATTATTAATCGGACGGGA 0 69 1
TGAAGAGGATATCTATTCGATTGGTA 2 25 0
TGGTTTCCGGAGGGAATATGCTCGTA 2 593 0
TGAATCTGACCAAAAACCTTTTCTAT 2 702 1
TAATTAAGAAAGCCACACATGTTTGA 0 128 1
TGATTGATAACAGAAGAGGCGTAGCC 1 386 0
TTGATATAGAGGTGAATATCCTTGTC 2 411 1
TGGATCCTAAGTCCAGTGCGTCTGCC 0 196 1
TGGATTCTAAGTCCAGTGCGTCTACC 1 152 0
GGAATTTCGAAAGAAATCTTTTTTTT 2 750 1
TTATGCGCAAGTCGAGACATTTACCC 1 35 0
***** * * * * *
MAP Score: 2.60188

Motif 19
TGGGCAAGAAAACAACAATCTC 0 98 1
TCGACTTGCGCATAACTGTCAC 1 46 1
TCTATTCGATTGGTACGGTTTC 2 18 0
TGTGCGGGAACACAACAATATC 2 169 1
TTGAGCGGTTGACTACCTTGAT 2 231 1
TATAGAGGTGAATATCCTTGTC 2 415 1
TGGGGCCGCCAAGAAAAATGAT 2 499 1
TCAGAAGGCGCGAATAGATGTC 2 529 1
TGAATCTGACCAAAAACCTTTT 2 702 1
GCAGCGTGAAAAAAAAGATTTC 2 762 0
TTCATTCAGTAACAACTCTGTC 2 845 0
TGAATTGAATTGAATATCTATC 2 875 1
* * * * *** * **
MAP Score: 2.34276

Motif 20
AACAACAATCTCCGGG 0 108 1
AACAACCCCGTGTGCG 1 120 1
AACAACCATGTGCGGG 2 161 1
CACAACAATATCTCTT 2 179 1
AAGAAAAATGATCCGG 2 509 1
AAGAGCGCTCTCCCCT 2 553 1
CAAAAACCTTTTCTAT 2 712 1
AAGAAATCTTTTTTTT 2 760 1
AACAACTCTGTCTGAT 2 841 0
** *** ** * * *
MAP Score: 2.22193

Motif 21
CACAGGTTACGTT 0 32 1
AACGGGGCTTATT 0 266 0
CACGGGGCTCTTT 0 282 1
AATAGATATCCTC 2 34 1
AAGAGATATTGTT 2 182 0
AAGAGGGAATCTT 2 203 1
AACAGGTCAGATT 2 326 1
AATAGATGTCGTA 2 541 1
AACGGGGTACCTT 2 655 1
AAAAGATTTCTTT 2 759 0
** **** ** **
MAP Score: 1.81593

Motif 22
GCAAGAAAAC 0 101 1
AAACGATATC 1 258 1
GATTGATAAC 1 401 0
AATAGATATC 2 34 1
GAACGATAAC 2 101 0
AAGAGATATT 2 185 0
GCACGATAAT 2 251 0
AATAGATGTC 2 541 1
GATAGAAAAG 2 719 0
GAAAGAAATC 2 758 1
GATAGATATT 2 887 0
**********
MAP Score: 1.61596

Motif 23
AATAATCATATTA 0 70 0
AGATATCCTCTTC 2 37 1
AGAAATGGACTTC 2 128 1
GGTAATTCTGTTC 2 634 1
AGAAAAGGTTTTT 2 713 0
AGAAATCTTTTTT 2 761 1
AGATATTCAATTC 2 881 0
****** * ***
MAP Score: 0.41862

Motif 24
GGGGAGTCGAA 0 168 1
GGGAAGTCGAA 1 17 1
GGAGACTCGAA 1 197 0
GGGATCTGGAA 2 215 0
GGAATTTCGAA 2 750 1
***** *****
MAP Score: 0.39566