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3 Table 1 A list of the tandems A name of a bacterium(genus and species,(strain) Classification in the database a tandem:trna genes(, rrnas and CDS) and space length (bp) between them [Accesion Number] Acholeplasma laidlawii Bacteria; Firmicutes; Mollicutes; Acholeplasmatales; Acholeplasmataceae; Acholeplasma 16S 139 Igat 22 Atgc 70 23S [D13259] Frag. S??? 2 Ettc [X61065] Frag. Hgtg 23 Qttg 28 Ltag [X61067] Frag. 23S 63 5S 28 Vtac 8 Ttgt 6 Kttt 14 Ltaa 22 Atgc 4 5 Mcat 4 Mcat 22 Stga 40 Mcat 24 Dgtc 7 Fgaa [X61068] Agrobacterium tumefaciens str. C58 Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium 16S 321 Igat 55 Atgc 471 ~Atu S 235 Mcat 152 recq [AE ] Frag. ~Vtac 445 Dgtc 38 Dgtc [AE009088] Frag. ~Atu Ygta 22 Gtcc 266 Atu1990 [AE009151*] Frag. ~purc S 321 Igat 55 Atgc 15 ~Atu2544 [AE009201*] Frag. Igat 55 Atgc 471 ~Atu S 235 Mcat 46 Atu3945 [AE009325] Frag. ~Atu S 308 Igat 55 Atgc 403 ~Atu S 236 Mcat ~Atu4188 [AE009348] Bacillus amyloliquefaciens Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus 16S 98 Igat 18 Atgc 83 23S [AF478079] Bacillus anthracis str. Ames Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus; Bacillus cereus group pura 139 Kttt 13 Ettc 20 Dgtc 41 Fgaa 403 yycf BA S S 101 5S 4 Vtac 4 Ttgt 9 Hgtg 22 L t ag 29 Ggcc 16 Ltaa 3 Racg 10 Ptgg 15 Atgc 20 Mcat 4 Mcat 17 Stga 27 Mcat 1 Dgtc 12 Fgaa 14 Ttgt 10 K t tt 13 Gtcc 10 Igat 7 Ngtt 7 Sgct 6 Ettc 657 ldh BA Gtcc 1 Rtct 407 BA ~BA ~Ettc 1 ~ N gtt 8 ~Igat 10 ~Wcca 6 ~Ttgt 9 ~Fgaa 8 ~Dgtc 4 ~Mcat 2 0 ~Stga 54 ~Stga 20 ~Atgc 16 ~Ptgg 10 ~Racg 3 ~Ltaa 16 ~ G gcc 29 ~Ltag 14 ~Kttt 4 ~Qttg 11 ~Vtac 5 ~5S 101 ~23S 178 ~16S 722 BA BA ~Lcaa 10 ~Cgca 14 ~Ggcc 5 ~Qt

4 tg 63 ~Hgtg 19 ~Wcca 7 ~Ygta 10 ~Ttgt 18 ~Fgaa 9 ~Dgtc 3 ~Mcat 24 ~Vtac 5 ~Ettc 17 ~Sgga 2 ~Ngtt 8 ~5S 100 ~23 S 171 ~16S -5 ~BA ~pure 698 ~5S 50 ~23S 178 ~16S 504 BA baca ~5S 50 ~23S 178 ~16S -5 ~BA B A ~5S 49 ~23S 178 ~16S 322 ~BA ~BA ~Dgtc 3 ~Mcat 12 ~5S 49 ~23S 178 ~16S 103 ~Gtcc 1 ~Ptgg 4 ~Ra cg 95 ~Lgag 17 ~Kttt 5 ~Qttg 88 ~Dgtc 46 ~Vtac 4 ~Ettc 8 ~Sgct 3 ~Ngtt 114 ~BA ~rocf 1470 ~Atgc 10 ~Ggcc 5 ~Kt tt 5 ~Qttg 65 ~Ygta 17 ~Vtac 5 ~Ettc 24 ~Tggt 4 ~Ngtt 9 ~5S 86 ~23S 178 ~16S -5 ~BA ~ctsr 206 ~5S 49 ~23 S 178 ~16S 400 ~lyss ~spoiie 352 ~Ettc 13 ~Mcat 160 ~BA ~BA ~5S 48 ~23S 94 ~Atgc 8 ~Igat 150 ~16S 245 ~bo fa ~guab 1149 ~5S 48 ~23S 94 ~Atgc 8 ~Igat 150 ~16S 268 ~gyra [AE016879*] Comp. gyra S 150 Igat 8 Atgc 94 23S 48 5S 1149 guab bofa S 150 Igat 8 Atgc 94 23S 48 5S 190 B A BA Mcat 13 Ettc 352 spoiie lyss S S 49 5S 206 ctsr BA S S 86 5 S 9 Ngtt 4 Tggt 24 Ettc 5 Vtac 17 Ygta 65 Qttg 5 Kttt 5 Ggcc 10 Atgc 1470 rocf BA Ngtt 3 S g ct 8 Ettc 4 Vtac 46 Dgtc 88 Qttg 5 Kttt 17 Lgag 9 5 Racg 4 Ptgg 1 Gtcc S S 49 5S 12 M cat 3 Dgtc 174 BA BA S S 49 5S 137 ~BA BA S S 50 5S 450 ~baca ~ B A S S 50 5S 698 pure BA S S 100 5S 8 Ngtt 2 Sgga 17 Ettc 5 Vtac 24 M cat 3 Dgtc 9 Fgaa 18 Ttgt 10 Ygta 7 Wcca 19 Hgtg 6 3 Qttg 5 Ggcc 14 Cgca 10 Lcaa 207 ~BA ~BA S S 101 5S 5 Vtac 11 Qttg 4 Kttt 14 Ltag 2 9 Ggcc 16 Ltaa 3 Racg 10 Ptgg 16 Atgc 20 Stga 54 S t ga 20 Mcat 4 Dgtc 8 Fgaa 9 Ttgt 6 Wcca 10 Igat 8 Ngtt 1 Ettc 138 BA ~BA ~Rtct 1 ~Gtcc -15 ~ B A ~ldh ~Ettc 6 ~Sgct 7 ~Ngtt 7 ~Igat 10 ~Gtcc 1 3 ~Kttt 10 ~Ttgt 14 ~Fgaa 12 ~Dgtc 1 ~Mcat 27 ~Stga 17 ~ M cat 4 ~Mcat 20 ~Atgc 15 ~Ptgg 10 ~Racg 3 ~Ltaa 16 ~Ggcc 2 9 ~Ltag 22 ~Hgtg 9 ~Ttgt 4 ~Vtac 4 ~5S 101 ~23S 178 ~16 S 131 ~BA ~yycf 403 ~Fgaa 41 ~Dgtc 20 ~Ettc 13 ~Kttt 139 ~pura [AE016879] Comp. gyra S 150 Igat 8 Atgc 94 23S 48 5S 1149 guab bofa S 150 Igat 8 Atgc 94 23S 48 5S 190? C DS 29299?CDS 160 Mcat 13 Ettc 352 spoiie lyss S S 49 5S 206 ctsr 57544?CDS -5 16S S 86 5 S

5 9 Ngtt 4 Tggt 24 Ettc 5 Vtac 17 Ygta 65 Qttg 5 Kttt 5 Ggcc 10 Atgc 1470 rocf 90939?CDS 114 Ngtt 3 S g ct 8 Ettc 4 Vtac 46 Dgtc 88 Qttg 5 Kttt 17 Lgag 9 5 Racg 4 Ptgg 1 Gtcc S S 49 5S 12 M cat 3 Dgtc 174?CDS 13177?CDS S S 49 5S 137 ~?CDS 7355?CDS -5 16S S 50 5S 450 ~baca-1 [AE017024] Co mp. 16S S 50 5S 698 pure ?CDS -5 16S S 100 5S 8 Ngtt 2 Sgga 17 Ettc 5 Vtac 24 Mcat 3 Dg tc 9 Fgaa 18 Ttgt 10 Ygta 7 Wcca 19 Hgtg 63 Qttg 5 Ggcc 14 Cgca 10 Lcaa 207 ~?CDS [AE017025] Comp. ~?CDS S S 101 5S 5 Vtac 11 Qttg 4 Kttt 1 4 Ltag 29 Ggcc 16 Ltaa 3 Racg 10 Ptgg 16 Atgc 20 S t ga 54 Stga 20 Mcat 4 Dgtc 8 Fgaa 9 Ttgt 6 Wcca 1 0 Igat 8 Ngtt 1 Ettc 138?CDS [AE017026] Comp.?CDS -15 Gtcc 1 Rtct 407?CDS [AE017038*] Comp.?CDS S S 101 5S 4 Vtac 4 Ttgt 9 Hgtg 2 2 Ltag 29 Ggcc 16 Ltaa 3 Racg 10 Ptgg 15 Atgc 20 M cat 4 Mcat 17 Stga 27 Mcat 1 Dgtc 12 Fgaa 14 Ttgt 1 0 Kttt 13 Gtcc 10 Igat 7 Ngtt 7 Sgct 6 Ettc 657 l d h-2 [AE017039*] Comp. pura 139 Kttt 13 Ettc 20 Dgtc 41 Fgaa 403 yycf [AE017041*] Chlamydia muridarum Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae; Chlamydia TC Vtac 7 Dgtc 23 TC kdta 26 Mcat 16 Mcat 2 6 ~pfka TC Atgc 4 Igat 27 TC ~TC ~ Y gta 7 ~Ttgt 50 ~TC ~tkt 250 ~5S 114 ~23S 242 ~16S 507 TC TC ~23S 241 ~16S frr 101 Ettc 17 K t tt 79 TC0047 [AE002160*] Comp. ~TC ~Kttt 17 ~Ettc 101 ~frr S S -502 ~TC ~TC S S 114 5S 250 tkt TC T t gt 7 Ygta 164 TC ~TC ~Igat 4 ~Atgc 190 ~TC pfka-2 26 ~Mcat 16 ~Mcat 26 ~kdta ~TC ~Dgtc 7 ~Vt ac 199 ~TC0495 [AE002160] Comp. frr 101 Ettc 17 Kttt 79?CDS [AE002272*] Comp.?CDS 50 Ttgt 7 Ygta 164?CDS [AE002308] Comp.?CDS 190 Atgc 4 Igat 27?CDS [AE002314*] Comp. kdta 26 Mcat 16 Mcat 26 ~pfka-2 [AE002316*] Comp.?CDS 199 Vtac 7 Dgtc 23?CDS [AE002318*] Comp. rrf 101 Ettc 17 Kttt [U60196] Frag

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8 Hatg 23 ~gsea B Chlamydophila pneumoniae CWL029 [AE001602*] 34 taub CPj Hatg 23 ~gsea B Chlamydophila pneumoniae J138 [AP002545*] 34 taub CPn Hatg 23 ~gsea B Chlamydophila pneumoniae [AE001363*] 21 Ettc 39 Ltag S 65 Atgc S A Methanocaldococcus jannaschii [U67517] 106 Ptgg 31 Rtct 51 Ettc 233 phet B Chlorobium tepidum TLS [AE012843] 106 Ptgg 31 Rtct 51 Ettc 233 phet #### ~CT ~Lcaa 26 ~Ltag -> B Chlorobium tepidum TLS [AE006470] ~BB Ggcc 40 BB B Borrelia burgdorferi B31 [AE001162] 4 Dgtc 4 Fgaa 22 Gtcc 26 Igat 6 Ngtt 36 Sgct 5 Ettc -> B Listeria innocua [AL592022*] 4 Dgtc 4 Fgaa 22 Gtcc 26 Igat 6 Ngtt 36 Sgct 5 Ettc -> B Listeria innocua [AL596170*] 4 Dgtc 4 Fgaa 23 Gtcc 25 Igat 6 Ngtt 34 Sgct 5 Ettc -> B Listeria monocytogenes [AL591980*] 4 Dgtc 4 Fgaa 23 Gtcc 25 Igat 6 Ngtt 34 Sgct 5 Ettc -> B Listeria monocytogenes EGD-e [NC_003210*] 4 Dgtc 4 Fgaa 24 Gtcc 25 Igat 6 Ngtt 34 Sgct 5 Ettc -> B Listeria monocytogenes str. 4b F2365 [AE017327*] 11 Dgtc 12 Fgaa 10 Gtcc 15 Igat 10 Ngtt 3 Sgct 25 Ettc --- B Bacillus subtilis [K00637] 11 Dgtc 12 Fgaa 10 Gtcc 15 Igat 10 Ngtt 3 Sgct 25 Ettc -> B Bacillus subtilis [AL009126*] 11 Dgtc 12 Fgaa 10 Gtcc 15 Igat 10 Ngtt 3 Sgct 25 Ettc -> B Bacillus subtilis [AF008220] 11 Dgtc 12 Fgaa 10 Gtcc 15 Igat 10 Ngtt 3 Sgct 25 Ettc -> B Bacillus subtilis subsp. subtilis str. 168 [Z99119*] 13 Dgtc 12 Fgaa 10 Gtcc 15 Igat 10 Ngtt 3 Sgct 25 Ettc --- B Bacillus subtilis [K01390] 14 Dgtc 10 Fgaa 17 Gtcc 9 Ngtt 1 Ettc 53 Sgga 209 ~?CDS --- B Staphylococcus epidermidis ATCC [AE016749*] 21 Dgtc 16 Fgaa 15 Gtcc 14 Ngtt 1 Ettc 54 Sgga 1244 ~MW B Staphylococcus aureus subsp. aureus MW2 [AP004828*] 14 Dgtc 10 Fgaa 17 Gtcc 9 Ngtt 1 Ettc 53 Sgga 209 ~SE150-> B Staphylococcus epidermidis ATCC [AE015929*] 21 Dgtc 16 Fgaa 15 Gtcc 17 Ngtt 1 Ettc 54 Sgga 213 seo --- B Staphylococcus aureus subsp. aureus N315 [AP003135*] 21 Dgtc 16 Fgaa 15 Gtcc 17 Ngtt 1 Ettc 54 Sgga 213 seo -> B Staphylococcus aureus subsp. aureus N315 [BA000018*] 21 Dgtc 19 Fgaa 18 Gtcc 20 Ngtt 4 Ettc 54 Sgga 213 seo --- B Staphylococcus aureus subsp. aureus Mu50 [AP003363*] 21 Dgtc 19 Fgaa 18 Gtcc 20 Ngtt 4 Ettc 54 Sgga 213 seo -> B Staphylococcus aureus subsp. aureus Mu50 [BA000017*] 18 Rtct 27 Hgtg 26 Hgtg 31 ~?CDS B Chromobacterium violaceum ATCC [AE016916*] 18 Rtct 27 Hgtg 26 Hgtg 31 ~CV192 #### ~CV ~Sgga 53 ~Sgga -> B Chromobacterium violaceum ATCC [AE016825*] 225 Ptgg 18 Rtct 45 Hgtg 26 Hgtg 31 ~?CDS B Chromobacterium violaceum ATCC [AE016916*] 225 Ptgg 18 Rtct 45 Hgtg 26 Hgtg 31 ~CV192 #### ~CV ~Sgga -> B Chromobacterium violaceum ATCC [AE016825*] 176 Ptgg 63 Rtct 110 Kctt 494?CDS B Xylella fastidiosa Temecula1 [AE012561] 162 Ptgg 43 Rtct 83 Kctt 77 Ltag 202 tig 4962 hupb 11 Vtac -> B Xanthomonas campestris pv. campestris str. ATCC [AE012195] 162 Ptgg 43 Rtct 83 Kctt 77 Ltag 202 tig 4962 hupb 11 Vtac -> B Xanthomonas campestris pv. campestris str. ATCC [AE008922] 176 Ptgg 63 Rtct 110 Kctt 494 PD B Xylella fastidiosa Temecula1 [AE009442] 176 Ptgg 61 Rtct 110 Kctt 311 ~XF B Xylella fastidiosa 9a5c [AE004082] 176 Ptgg 61 Rtct 110 Kctt 311 ~XF B Xylella fastidiosa [AE003849] 107 Ptgg 7 Gtcc 3 Kttt 12 Ltag 40 Qttg 175 FN B Fusobacterium nucleatum subsp. nucleatum ATCC [AE010498*] 107 Ptgg 7 Gtcc 3 Kttt 12 Ltag 40 Qttg 175 FN FN194-> B Fusobacterium nucleatum subsp. nucleatum ATCC [AE009951*] ansp3 148 Rccg 16 Lcag -38 ~?CDS #### ~?CDS 51 ~5S -1 ~23S -> B Yersinia pestis biovar Mediaevails str [AE017042] ansp3 148 Rccg 16 Lcag -38 ~?CDS #### ~?CDS 51 ~5S -1 ~23S -> B Yersinia pestis biovar Mediaevails str [AE017139] Rccg 20 Lcag 71 Ptgg B Aeromonas hydrophila [X12977] Rccg 20 Lcag 42 Ptgg B Escherichia coli [K01994] ---?CDS 102 Rccg 20 Lcag 42 Ptgg B Salmonella typhimurium [M95047]

9 --- yifk 102 Rccg 20 Lcag 42 Ptgg B Escherichia coli K12 [AE000455] yifk 283 Rccg 15 Lcag 42 Ptgg 987 ISPlu #### orn 199 Ggcc -> B Photorhabdus luminescens subsp. laumondii TTO1 [BX470251*] yifk 283 Rccg 15 Lcag 42 Ptgg 987 ISPlu #### orn 199 Ggcc -> B Photorhabdus luminescens subsp. laumondii TTO1 [BX571874*] --- ECs Rccg 20 Lcag 43 Ptgg 22 Lcag 42 Ptgg 146 ECs47-> B Escherichia coli O157:H7 [AP002567] ECs Rccg 20 Lcag 43 Ptgg 22 Lcag 42 Ptgg 146 ECs47-> B Escherichia coli O157:H7 [BA000007] STY Rccg 20 Lcag 42 Ptgg 581 ~STY36 #### STY S -> B Salmonella enterica subsp. enterica serovar Typhi [AL513382*] YPO Rccg 16 Lcag 75 Ptgg 866 YPO B Yersinia pestis CO92 [AJ414159*] --- yifk 102 Rccg 20 Lcag 42 Ptgg 146 aslb B Escherichia coli O157:H7 EDL933 [AE005611] --- yifk 233 Rccg 20 Lcag 42 Ptgg 116 aslb B Shigella flexneri 2a str. 301 [AE015394] yifk 102 Rccg 20 Lcag 42 Ptgg 146 aslb B Escherichia coli CFT073 [AE016769] --- yifk 102 Rccg 20 Lcag 42 Ptgg 146 aslb #### hemg S -> B Shigella flexneri 2a str. 2457T [AE016990*] yifk 233 Rccg 20 Lcag 42 Ptgg 116 aslb #### hemg S -> B Shigella flexneri 2a str. 301 [AE005674] yifk 102 Rccg 20 Lcag 42 Ptgg 146 aslb #### hemg S -> B Shigella flexneri 2a str. 2457T [AE014073*] yifk 102 Rccg 20 Lcag 42 Ptgg 146 aslb #### hemg S -> B Escherichia coli CFT073 [AE014075] yifk 102 Rccg 20 Lcag 42 Ptgg 146 aslb #### hemg S -> B Escherichia coli O157:H7 [AE005174] yifk 102 Rccg 20 Lcag 42 Ptgg 146 aslb #### hemg S -> B Escherichia coli [U00096] 7202 rho 296 Rccg 30 Lcag 12 Ptgg 101 ~hemd #### ~purh S -> B Candidatus Blochmannia floridanus [BX248583*] 7202 rho 296 Rccg 30 Lcag 12 Ptgg 101 ~hemd #### ~purh S -> B Candidatus Blochmannia floridanus [BX248586*] --- yifk 102 Rccg 23 Lcag 45 Ptgg 584 ~hemy B Salmonella typhimurium LT2 [AE008883] yifk 102 Rccg 20 Lcag 42 Ptgg 581 ~hemy B Salmonella enterica subsp. enterica serovar Typhi [AL627279*] yifk 102 Rccg 20 Lcag 42 Ptgg 581 ~hemy #### hemg S -> B Salmonella enterica subsp. enterica serovar Typhi Ty2 [AE016845*] yifk 102 Rccg 20 Lcag 42 Ptgg 581 ~hemy #### hemg S -> B Salmonella enterica subsp. enterica serovar Typhi Ty2 [AE014613*] yifk 102 Rccg 23 Lcag 45 Ptgg 584 ~hemy #### hemg S -> B Salmonella typhimurium LT2 [AE006468] YPO Rccg 16 Lcag 75 Ptgg 866 tnp #### hemg S -> B Yersinia pestis [AL590842*] --- y Rccg 19 Lcag -35 ~y B Yersinia pestis KIM [AE013638] y Rccg 19 Lcag -35 ~y0376 #### hemg S 59 Igat -> B Yersinia pestis KIM [AE009952] ~fold- 293 Rtct 56 Ltag 571?CDS B Pseudomonas syringae pv. tomato str. DC3000 [AE016869*] 39?CDS 1E+05?CDS 50 Ltag 37?CDS #### ~?CDS 52 ~Rtct 35 ~Gtcc -> B Thermus thermophilus HB27 [AE017221] 39?CDS 1E+05?CDS 50 Ltag 37?CDS #### ~?CDS 52 ~Rtct 35 ~Gtcc -> B Thermus thermophilus HB27 [AE017301] ~DR Ltag 141 DR B Deinococcus radiodurans R1 [AE001945*] -398 DR126 3E+05 ~DR Ltag 141 DR092 #### ~DR Ptgg 20 Gtcc -> B Deinococcus radiodurans [AE000513*] 361 Vtac 4 Ttgt 22 Ltag 29 Ggcc 16 Ltaa 3 Racg 10 Ptgg -> B Bacillus cereus ATCC [AE017013*] 361 Vtac 4 Ttgt 22 Ltag 29 Ggcc 16 Ltaa 3 Racg 10 Ptgg -> B Bacillus cereus ATCC [AE016877*] 4 Vtac 4 Ttgt 22 Ltag 29 Ggcc 16 Ltaa 3 Racg 10 Ptgg -> B Bacillus cereus [AY224388] 4 Vtac 4 Ttgt 22 Ltag 29 Ggcc 16 Ltaa 3 Racg 10 Ptgg -> B Bacillus anthracis str. Ames [AE016879*] 4 Vtac 4 Ttgt 22 Ltag 29 Ggcc 16 Ltaa 3 Racg 10 Ptgg -> B Bacillus anthracis str. Ames [AE017039*] 4 Vtac 4 Ttgt 22 Ltag 29 Ggcc 16 Ltaa 3 Racg 10 Ptgg -> B Bacillus anthracis str. Ames 0581 [AE017334*] --- ~fold 278 Rtct 54 Ltag 66 Hgtg 697 ~?CDS B Pseudomonas aeruginosa PAO1 [AE004605] 1E+06 ~fold 278 Rtct 54 Ltag 66 Hgtg 697 ~PA179 #### PA ~Ggcc -> B Pseudomonas aeruginosa [AE004091] ~fold- 293 Rtct 56 Ltag 571 PSPTO #### ~PSPTO S 103 Igat -> B Pseudomonas syringae pv. tomato str. DC3000 [AE016853*] 47 Ptgg 5 Rtct 62 Ltag 115 tig 1885 lon Dgtc 11 Vtac -> B Geobacter sulfurreducens PCA [AE017180*] 47 Ptgg 5 Rtct 62 Ltag 115 tig 1885 lon Dgtc 11 Vtac -> B Geobacter sulfurreducens PCA [AE017213*] 719 Ngtt 1 Mcat 26 Mcat 13 Stga 152 Fgaa 169 OB B Oceanobacillus iheyensis HTE831 [AP004599*]

10 719 Ngtt 1 Mcat 26 Mcat 13 Stga 152 Fgaa 169 OB193#### ~OB090-> B Oceanobacillus iheyensis [BA000028*] Ptgg 53 Ptgg B Photobacterium phosphoreum [X12975] 34 Hgtg 76 Ptgg 64 Ptgg B Vibrio harveyi [M29762] 53 Ptgg 174 Ptgg 149 Ptgg B Photobacterium phosphoreum [X12976] --- Mcat 2418 Rccg 24 Ptgg S 131 Ettc S 247 5S -> B Haemophilus influenzae Rd KW20 [U32697*] 1283 Mcat 2418 Rccg 24 Ptgg S 131 Ettc S 247 5S -> B Haemophilus influenzae Rd [L42023*] wecg 157 Rccg 29 Ptgg S 80 Ettc S 242 5S -> B Haemophilus ducreyi 35000HP [AE017156*] wecg 157 Rccg 29 Ptgg S 80 Ettc S 242 5S -> B Haemophilus ducreyi 35000HP [AE017143*] 41 Hgtg 29 Ptgg 27 Ptgg 1282?CDS ####?CDS 167 Ettc 4 Kttt -> B Vibrio vulnificus CMCP6 [AE016800] 34 Hgtg 66 Ptgg 51 Ptgg 723 AGAD B Photobacterium profundum [CR378663] Rccg 76 Ptgg 49 Hgtg 64 Ptgg B Vibrio harveyi [M29762] ~?CDS 254 Rccg 29 Ptgg 77 Hgtg 27 Ptgg 1282?CDS ####?CDS -> B Vibrio vulnificus CMCP6 [AE016800] ~NMB Rccg 66 Ptgg 9 Hgtg 51 Ptgg 723 AGAD B Photobacterium profundum [CR378663] --- ~VC Rccg 61 Ptgg 70 Hgtg 61 Ptgg 435 ~VC B Vibrio cholerae O1 biovar eltor str. N16961 [AE004107] 9186 ~VC Rccg 61 Ptgg 70 Hgtg 61 Ptgg 435 ~VC016#### VC031-> B Vibrio cholerae [AE003852] 9312 ~VP Rccg 72 Ptgg 49 Hgtg 24 Ptgg 66 ~VP B Vibrio parahaemolyticus [AP005073] 9312 ~VP Rccg 72 Ptgg 49 Hgtg 24 Ptgg 66 ~VP004#### VP056-> B Vibrio parahaemolyticus RIMD [BA000031] 9269 ~VV Rccg 26 Ptgg 74 Hgtg 24 Ptgg 942 ~VV004#### ~VV016-> B Vibrio vulnificus YJ016 [AP005330] 9269 ~VV Rccg 26 Ptgg 74 Hgtg 24 Ptgg 942 ~VV004#### ~VV016-> B Vibrio vulnificus YJ016 [BA000037] ~VV Rccg 29 Ptgg 77 Hgtg 27 Ptgg 1282 VV110#### VV111-> B Vibrio vulnificus CMCP6 [AE016795] --- ~?CDS 206 Rccg 15 Ptgg 53 Ptgg 184 ~?CDS B Shewanella oneidensis MR-1 [AE015865*] 176 Ptgg 176 Ptgg 53 Ptgg 174 Ptgg 8 Hgtg 149 Ptgg B Photobacterium phosphoreum [X12976] 2E+05 ~SO Rccg 15 Ptgg 53 Ptgg 184 ~SO432 #### seca S -> B Shewanella oneidensis MR-1 [AE014299*] 35 Hgtg 61 Ptgg 61 Ptgg 435 ~VC B Vibrio cholerae O1 biovar eltor str. N16961 [AE004107] 35 Hgtg 61 Ptgg 61 Ptgg 435 ~VC016 #### VC S 63 Igat -> B Vibrio cholerae [AE003852] 32 Hgtg 72 Ptgg 24 Ptgg 66 ~VP B Vibrio parahaemolyticus [AP005073] 32 Hgtg 72 Ptgg 24 Ptgg 66 ~VP004 #### VP S 177 Aggc -> B Vibrio parahaemolyticus RIMD [BA000031] 38 Hgtg 26 Ptgg 24 Ptgg 942 ~VV004 #### ~VV S 68 Ettc -> B Vibrio vulnificus YJ016 [AP005330] 38 Hgtg 26 Ptgg 24 Ptgg 942 ~VV004 #### ~VV S 68 Ettc -> B Vibrio vulnificus YJ016 [BA000037] 41 Hgtg 29 Ptgg 27 Ptgg 1282 VV110 #### VV Ettc 4 Kttt -> B Vibrio vulnificus CMCP6 [AE016795] --- rho 100 Rccg 33 Ptgg 1773 ~cyay B Buchnera aphidicola str. Sg (Schizaphis graminum) [AE014131*] --- rho 282 Rccg 35 Ptgg 91 ~cyay #### aroe 204 Ettc S -> B Buchnera aphidicola str. Bp (Baizongia pistaciae) [AE014017*] --- rho 100 Rccg 33 Ptgg 1773 ~cyay #### dut 734 ~Mcat 133 Ngtt -> B Buchnera aphidicola str. Sg (Schizaphis graminum) [AE013218*] --- rho 282 Rccg 35 Ptgg 91 ~cyay #### ~pyre 118 ~Mcat 193 Ngtt -> B Buchnera aphidicola (Baizongia pistaciae) [AE016826*] --- rho 188 Rccg 36 Ptgg 757 ~hemc #### aroe 152 Ettc S -> B Buchnera aphidicola str. APS (Acyrthosiphon pisum) [AP001119*] --- rho 188 Rccg 36 Ptgg 757 ~hemc #### ~pyre 95 ~Mcat 134 Ngtt -> B Buchnera sp. APS [AP000398*] 4 Ygta 8 Wcca 11 Qttg 5 Cgca 9 Gtcc 14 Gtcc 11 Gtcc -> B Staphylococcus epidermidis ATCC [AE015929*] 4 Ygta 8 Wcca 11 Qttg 5 Cgca 9 Gtcc 14 Gtcc 11 Gtcc -> B Staphylococcus epidermidis ATCC [AE016749*] 5 Ygta 15 Wcca 11 Qttg 5 Cgca 7 Gtcc 103 Gtcc 38 Lcaa -> B Staphylococcus aureus subsp. aureus N315 [AP003135*] 5 Ygta 15 Wcca 11 Qttg 5 Cgca 7 Gtcc 103 Gtcc 38 Lcaa -> B Staphylococcus aureus subsp. aureus MW2 [AP004828*] 5 Ygta 15 Wcca 11 Qttg 5 Cgca 7 Gtcc 103 Gtcc 38 Lcaa -> B Staphylococcus aureus subsp. aureus N315 [BA000018*] 8 Ygta 15 Wcca 11 Qttg 5 Cgca 10 Gtcc 106 Gtcc 41 Lcaa -> B Staphylococcus aureus subsp. aureus Mu50 [AP003363*] 8 Ygta 15 Wcca 11 Qttg 5 Cgca 10 Gtcc 106 Gtcc 41 Lcaa -> B Staphylococcus aureus subsp. aureus Mu50 [BA000017*]

11 5 Ygta 4 Wcca 14 Qttg 25 Cgca 13 Lcaa 576 ~?CDS B Enterococcus faecalis V583 [AE016950] 4 Ygta 7 Wcca 4 Qttg 20 Cgca 31 Lcaa 115?CDS 2136?CDS -> B Lactobacillus johnsonii NCC 533 [AE017198*] 4 Ygta 7 Wcca 4 Qttg 20 Cgca 31 Lcaa 115?CDS 2136?CDS -> B Lactobacillus johnsonii NCC 533 [AE017205*] 5 Ygta 4 Wcca 14 Qttg 25 Cgca 13 Lcaa 576 ~EF105#### EF132-> B Enterococcus faecalis V583 [AE016830] 5 Ygta 7 Wcca 9 Qttg 27 Cgca 37 Lcaa 89 labj B Lactobacillus sakei [AF401668] 5 Ygta 8 Wcca 7 Qttg 22 Cgca 55 Lcaa 150 ~lp_12#### lp_13-> B Lactobacillus plantarum WCFS1 [AL935263] 5 Ygta 8 Wcca 7 Qttg 22 Cgca 55 Lcaa 150 ~lp_12#### uvra2-> B Lactobacillus plantarum WCFS1 [AL935255] 10 Ygta 7 Wcca 63 Qttg 5 Ggcc 14 Cgca 10 Lcaa B Bacillus cereus [AY224386] 20 Ygta 7 Wcca 29 Qttg 5 Ggcc 19 Cgca 45 Lcaa 348?CDS --- B Listeria monocytogenes str. 4b F2365 [AE017330*] 10 Ygta 7 Wcca 63 Qttg 5 Ggcc 14 Cgca 10 Lcaa 206 ~?CDS --- B Bacillus cereus ATCC [AE016999] 10 Ygta 7 Wcca 63 Qttg 5 Ggcc 14 Cgca 10 Lcaa 207 ~?CDS --- B Bacillus anthracis str. Ames [AE017025] 10 Ygta 7 Wcca 63 Qttg 5 Ggcc 14 Cgca 10 Lcaa 207 ~?CDS -> B Bacillus anthracis str. Ames 0581 [AE017334] 10 Ygta 7 Wcca 63 Qttg 5 Ggcc 14 Cgca 10 Lcaa 487?CDS -> B Bacillus cereus ATCC [AE017266] 10 Ygta 7 Wcca 63 Qttg 5 Ggcc 14 Cgca 10 Lcaa 207 ~BA054-> B Bacillus anthracis str. Ames [AE016879] 10 Ygta 7 Wcca 63 Qttg 5 Ggcc 14 Cgca 10 Lcaa 206 ~BC053-> B Bacillus cereus ATCC [AE016877] 15 Ygta 15 Wcca 24 Qttg 2 Ggcc 8 Cgca 4 Lcaa 186 OB B Oceanobacillus iheyensis HTE831 [AP004596] 15 Ygta 15 Wcca 24 Qttg 2 Ggcc 8 Cgca 4 Lcaa 186 OB090-> B Oceanobacillus iheyensis [BA000028] 22 Ygta 7 Wcca 31 Qttg 5 Ggcc 19 Cgca 45 Lcaa 187 lin24--- B Listeria innocua [AL596172*] 22 Ygta 7 Wcca 31 Qttg 5 Ggcc 19 Cgca 45 Lcaa 187 lin24-> B Listeria innocua [AL592022*] 20 Ygta 7 Wcca 29 Qttg 5 Ggcc 19 Cgca 45 Lcaa 351 lmo23--- B Listeria monocytogenes [AL591983*] 20 Ygta 7 Wcca 29 Qttg 5 Ggcc 19 Cgca 45 Lcaa 351 lmo23-> B Listeria monocytogenes EGD-e [NC_003210*] 19 Ygta 5 Wcca 9 Qttg 46 Ggcc 5 Cgca 4 Ltaa 265 Lcaa -> B Bacillus subtilis subsp. subtilis str. 168 [Z99108] 22 Ygta 5 Wcca 9 Qttg 49 Ggcc 5 Cgca 7 Ltaa 265 Lcaa --- B Bacillus subtilis [K01389] 22 Ygta 5 Wcca 9 Qttg 49 Ggcc 5 Cgca 7 Ltaa 265 Lcaa -> B Bacillus subtilis [AL009126] 22 Ygta 5 Wcca 9 Qttg 49 Ggcc 5 Cgca 7 Ltaa 265 Lcaa -> B Bacillus subtilis [Z82044] 54 Ygta 11 Wcca 13 Qttg 4 Ggcc 7 Cgca 26 Ltaa 15 Racg -> B Bacillus halodurans C-125 [AP001510] 154 Atgc 363 Ygta 15 Qttg 4 Ggcc 1 Racg B Bacillus halodurans [AB013377] 171 Mcat 5 Ygta 15 Qttg 4 Ggcc 1 Racg 185 Gtcc 41 ~BH B Bacillus halodurans C-125 [AP001516*] 54 Ygta 11 Wcca 13 Qttg 4 Ggcc 464 ~TnpA B Bacillus halodurans [AB031215] 7 Gtcc 82 Rtct 6 Qttg 9 Kttt 22 Kttt 13 Ltag 29 Ggcc -> B Clostridium perfringens str. 13 [AP003193*] 7 Gtcc 82 Rtct 6 Qttg 9 Kttt 22 Kttt 13 Ltag 29 Ggcc -> B Clostridium perfringens [BA000016*] --- Gtcc 4 Rtct 3 Qttg 4 Kttt 38 Lcag 5 Ggcc 25 Kctt -> B Thermoanaerobacter tengcongensis [AE013030*] 198 Gtcc 4 Rtct 3 Qttg 4 Kttt 38 Lcag 5 Ggcc 25 Kctt -> B Thermoanaerobacter tengcongensis [AE008691*] 10 Gtcc 9 Kctt 7 Qttg 25 Kttt 6 Ltag 18 Ggcc 8 Gtcc -> B Clostridium acetobutylicum [AE001437*] 10 Gtcc 9 Kctt 7 Qttg 25 Kttt 6 Ltag 18 Ggcc 8 Gtcc -> B Clostridium acetobutylicum [AE007764*] 4 Rtct 4 Kctt 9 Qttg 3 Kttt 23 Ltag 19 Ggcc 11 Gtcc -> B Clostridium tetani E88 [AE015944*] 4 Rtct 4 Kctt 9 Qttg 3 Kttt 23 Ltag 19 Ggcc 11 Gtcc -> B Clostridium tetani E88 [AE015927*] 6 Gtcc 38 Rtct 8 Qttg 10 Kttt 13 Ltag 26 Ggcc 6 Gtcc -> B Clostridium perfringens str. 13 [AP003193*] 6 Gtcc 38 Rtct 8 Qttg 10 Kttt 13 Ltag 26 Ggcc 6 Gtcc -> B Clostridium perfringens [BA000016*] 9 Gtcc 9 Rtct 7 Qttg 25 Kttt 6 Ltag 18 Ggcc 8 Gtcc -> B Clostridium acetobutylicum [AE007764*] 9 Gtcc 9 Rtct 7 Qttg 25 Kttt 6 Ltag 18 Ggcc 8 Gtcc -> B Clostridium acetobutylicum [AE001437*] 2 Fgaa 98 Wcca 6 Qttg -1 Lcaa B Streptococcus agalactiae [AF302130] 11 Ygta 34 Wcca 6 Qttg 0 Lcaa B Streptococcus agalactiae [AF302131]

12 12 Ygta 6 Wcca 16 Qttg 14 Lcaa 82 ~?CDS B Streptococcus mutans UA159 [AE014870] 11 Ygta 6 Wcca 6 Qttg 10 Lcaa 309 SAG B Streptococcus agalactiae 2603V/R [AE014202] 11 Ygta 6 Wcca 6 Qttg 10 Lcaa 410 SAG B Streptococcus agalactiae 2603V/R [AE014195] 11 Ygta 6 Wcca 6 Qttg 10 Lcaa 410 SAG00 #### SAG S -> B Streptococcus agalactiae [AE009948] 11 Ygta 6 Wcca 6 Qttg 10 Lcaa 309 SAG02 #### yfia S -> B Streptococcus agalactiae [AE009948] 12 Ygta 6 Wcca 16 Qttg 14 Lcaa 82 ~SMU.1 #### SMU ~Scga -> B Streptococcus mutans UA159 [AE014133] 12 Ygta 4 Wcca 10 Qttg 9 Lcaa 106 SP B Streptococcus pneumoniae TIGR4 [AE007495*] 12 Ygta 4 Wcca 10 Qttg 9 Lcaa 106 SP206 #### SP Ettc -> B Streptococcus pneumoniae [AE005672*] 19 Ygta 6 Wcca 8 Qttg 19 Lcaa 1767 SPs00 #### SPs S -> B Streptococcus pyogenes SSI-1 [AP005141] 19 Ygta 6 Wcca 8 Qttg 19 Lcaa 1767 SPs00 #### SPs S -> B Streptococcus pyogenes SSI-1 [BA000034] 19 Ygta 6 Wcca 9 Qttg 19 Lcaa 259 SPy B Streptococcus pyogenes M1 GAS [AE006479] 19 Ygta 6 Wcca 9 Qttg 19 Lcaa 259 SPy00 #### oppf S -> B Streptococcus pyogenes [AE004092] 19 Ygta 6 Wcca 8 Qttg 19 Lcaa 259 SpyM B Streptococcus pyogenes MGAS315 [AE014137] 19 Ygta 6 Wcca 8 Qttg 19 Lcaa 259 SpyM3 #### oppf S -> B Streptococcus pyogenes MGAS315 [AE014074] 11 Ygta 6 Wcca 6 Qttg 10 Lcaa 413 gbs B Streptococcus agalactiae NEM316 [AL766843] 11 Ygta 6 Wcca 6 Qttg 10 Lcaa 141 gbs02 #### gbs S -> B Streptococcus agalactiae NEM316 [AL732656] 11 Ygta 6 Wcca 6 Qttg 10 Lcaa 141 gbs02 #### gbs S -> B Streptococcus agalactiae NEM316 [AL766844] 11 Ygta 6 Wcca 6 Qttg 10 Lcaa 413 gbs00 #### gbs S -> B Streptococcus agalactiae NEM316 [AL732656] 12 Ygta 4 Wcca 10 Qttg 9 Lcaa 106 spr B Streptococcus pneumoniae R6 [AE008551*] 12 Ygta 4 Wcca 10 Qttg 9 Lcaa 106 spr18 #### comx2 93 Ettc -> B Streptococcus pneumoniae [AE007317*] Qttg 28 Ltag B Acholeplasma laidlawii [X61067] --- acka 46 Sgga 88 Qttg 53 Ltag 23 Wcca 431?CDS #### pepp -> B Onion yellows phytoplasma OY-M [AP006628] --- acka 46 Sgga 88 Qttg 53 Ltag 23 Wcca 431 PAM16#### pepp -> B Onion yellows phytoplasma [AP006628] ---?CDS 146 Ptgg 20 Rtcg 44 ~?CDS #### ~?CDS 25 Qttg 85 Mcat -> B Helicobacter hepaticus ATCC [AE017144] --- HH Ptgg 20 Rtcg 44 ~HH003 #### ~HH Qttg 85 Mcat -> B Helicobacter hepaticus ATCC [AE017125] --- HP Ptgg 60 Rtcg 25 Rtct 29 HP B Helicobacter pylori [AE000557] HP Ptgg 60 Rtcg 25 Rtct 29 HP041 #### ~HP S -> B Helicobacter pylori [AE000511] Cj Ptgg 3 Rtcg 14 Rtct 4 Ltag 174 Cj166#### ~ribd -> B Campylobacter jejuni [AL111168*] Cj Ptgg 3 Rtcg 14 Rtct 4 Ltag 174 Cj166#### ~ribd -> B Campylobacter jejuni subsp. jejuni NCTC [AL139079*] 88 Gtcc 14 Rtct 8 Rtcg 73 TM B Thermotoga maritima [AE001704*] 88 Gtcc 14 Rtct 8 Rtcg 73 TM019 #### ~TM ~5S 37 ~23S -> B Thermotoga maritima [AE000512*] ~Fgaa 14 Rtcg 80 TP B Treponema pallidum subsp. pallidum str. Nichols [AE001239*] 1E+05 ~TP ~Fgaa 14 Rtcg 80 TP063 #### ~TP Mcat 69 Dgtc -> B Treponema pallidum [AE000520*] ~?CDS 32 Rtcg 106 rpsd B Treponema denticola ATCC [AE017252*]

13 @Hatg Hatg B Chlamydophila 16S Atgc 23S A Methanocaldococcus Ettc B Chlorobium Ggcc B Borrelia Gtcc B6-1-1 Bacillus, Gtcc Igat B6-1-1 Bacillus, Gtcc Igat Ngtt B6-1-1 Bacillus, Gtcc Igat Ngtt Sgct B6-1-1 Bacillus, Gtcc Igat Ngtt Sgct Ettc B6-1-1 Bacillus, Gtcc Ngtt B Gtcc Ngtt Ettc B Gtcc Ngtt Ettc Sgga B Hgtg B Chromobacterium Hgtg Hgtg B Chromobacterium Kctt B7, B12 Fusobacterium, Xanthomonas, Kctt Ltag B7, B12 Fusobacterium, Kttt Ltag Qttg B Fusobacterium Lcag B12-3 Aeromonas, Blochmannia, Escherichia, Photorhabdus,Pseudomonas, Salmonella,Shigella, Lcag Ptgg B12-3 Aeromonas, Blochmannia, Escherichia, Photorhabdus, Salmonella,Shigella, Lcag Ptgg Lcag B Escherichia Lcag Ptgg Lcag Ptgg B Escherichia Ltag B4, B6,B12 Deinococcus, Thermus;Bacillus ; Geobacter, Ltag Ggcc B Ltag Ggcc Ltaa B Ltag Ggcc Ltaa Racg B Ltag Ggcc Ltaa Racg Ptgg B Ltag Hgtg B Pseudomonas Mcat B Oceanobacillus Mcat Stga B Oceanobacillus Mcat Stga Fgaa B Oceanobacillus Ptgg B11, B12 Buchnera, Ptgg 16S B Haemophilus Ptgg 16S Ettc B Haemophilus Ptgg 16S Ettc 23S B Haemophilus Ptgg 16S Ettc 23S 5S B Haemophilus Ptgg Hgtg B Ptgg Hgtg Ptgg B Ptgg Ptgg B11, B12 Photobacterium, Ptgg Ptgg Hgtg B Photobacterium Ptgg Ptgg Hgtg Ptgg B Photobacterium Qttg B6-1 Enterococcus, Lactobacillu, Staphylococcus

14 @Hgtg Qttg Cgca B6-1 Enterococcus, Lactobacillu, Qttg Cgca Gtcc B Qttg Cgca Gtcc Gtcc B Qttg Cgca Gtcc Gtcc Gtcc B Staphylococcus Qttg Cgca Gtcc Gtcc Gtcc B Staphylococcus Qttg Cgca Gtcc Gtcc Lcaa B Staphylococcus Qttg Cgca Lcaa B6-1-2 Enterococcus, Qttg Ggcc B6-1-1 Bacillus, Listeria, Qttg Ggcc Cgca B6-1-1 Bacillus, Listeria, Qttg Ggcc Cgca Lcaa B6-1-1 Bacillus, Listeria, Qttg Ggcc Cgca Ltaa Lcaa B Bacillus Qttg Ggcc Cgca Ltaa Racg B Bacillus Qttg Ggcc Racg B Bacillus Qttg Ggcc Racg Gtcc B Bacillus Qttg Kttt B Clostridium, Qttg Kttt Kttt B Clostridium, Qttg Kttt Kttt Ltag B Clostridium, Qttg Kttt Kttt Ltag Ggcc B Clostridium, Qttg Kttt Ltag B Qttg Kttt Ltag Ggcc B Qttg Kttt Ltag Ggcc Gtcc B Qttg Lcaa B Qttg Ltag B Qttg Ltag Wcca B Onion yellows Rtcg B3,B10,B12 Tehrmotoga, Treponema, Campylobacter, Rtcg Rtct B Campylobacter, Rtcg Rtct Ltag B Campylobacter jejuni

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19

20 Accesion Number index Accession No(s). [AB013377]to [AB031215] [AB071783] [AE000052] [AE000129] to[ae000453] [AE001652] [AE006473] to [AE006615] [AE007319] [AE008706] [AE014136] to [AE014168] [AE014192]to [AE014210] [AE015714] [AE016998] to [AE017013] [AE017205] [AE017280] to[ae017281] [AF074828] [AF074829] [AF074830] [AF074831] [AF074832] [AF074833] [AF074834] [AF074835] [AF074836] [AF074837] [AF074838] [AF074839] [AF074840] [AF074841] [AF130462] [AF223396] [AF223397] [AF223398] [AF223399] [AF268429] [AF302130] [AF302131] [AF312492] [AF312493] [AF312494] uncultured bacterium NAZ4

21 [AF312495] [AF338860] [AF338862] [AF338864] [AF375994] [AF397709] [AF397714] [AF440225] [AF510361] [AJ012700] [AJ012701] [AJ012702] [AJ012703] [AJ012704] [AJ012705] [AJ012706] [AJ012707] [AJ248283] [AJ248285] [AJ293101] [AP002547] [AP003363] [AP003604] [AP005141] to [AP005146] [AP005274]to [AP005279] [AY190662] [AY224382] [AY277896] [AY531069] [AY591324] to [AY591328] [BX248585]to [EX148586] [CR378668]to [CR378674] [D88802] [J01713] [K01983] [L00194] [L08236] [L26364] [L28154] [L28148]to [L28149] [L28156] to [L28158] [L28159] to [L18162] [L35100]

22 [L35101] [L35102] [L35103] [L36472] [L42976] [M13687] [M23210] [M65195] [M91385] [U15182] [U60278] [U60279] [U60280] [U60281] [X04108] [X06727]

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