Origin IGS: ttgagcaaatcttccgtaaaaaagctggaaaaaatctttacagagtgtctcacctgattagataggagcagaaagaaatcagataaatatacccaaacagctgtctcaatccactgaaatttttttagttggaaatagctctattggttcattgagaatattaaaaaagaagccgggaaaccgacttctgaacaaatacaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttgtatttgttcagaagtcggtttcccggcttcttttttaatattctcaatgaaccaatagagctatttccaactaaaaaaatttcagtggattgagacagctgtttgggtatatttatctgatttctttctgctcctatctaatcaggtgagacactctgtaaagattttttccagcttttttacggaagatttgctcaa Mask Tandem Repeat Region ================================================ ttgagcaaatcttccgtaaaaaagctggaaaaaatctttacagagtgtctcacctgattagataggagcagaaagaaatcagataaatatacccaaacagctgtctcaatccactgaaatttttttagttggaaatagctctattggttcattgagaatattaaaaaagaagccgggaaaccgacttctgaacaaatacaaa Find is-nt database================================================ Query_seq: SSA_2349:SSA_2350|SSA_2349:SSA_2350:DTDP-4-dehydrorhamnose 3,5-epimerase, putative:30S ribosomal protein S4, putative:<-<-:2351799..2352000 202 ttgagcaaatcttccgtaaaaaagctggaaaaaatctttacagagtgtctcacctgattagataggagcagaaagaaatcagataaatatacccaaacagctgtctcaatccactgaaatttttttagttggaaatagctctattggttcattgagaatattaaaaaagaagccgggaaaccgacttctgaacaaatacaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2349:SSA_2350|SSA_2349:SSA_2350:DTDP-4-dehydrorhamnose 3,5-epimerase, putative:30S ribosomal protein S4, putative:<-<-:2351799..2352000 202 ttgagcaaatcttccgtaaaaaagctggaaaaaatctttacagagtgtctcacctgattagataggagcagaaagaaatcagataaatatacccaaacagctgtctcaatccactgaaatttttttagttggaaatagctctattggttcattgagaatattaaaaaagaagccgggaaaccgacttctgaacaaatacaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2349:SSA_2350|SSA_2349:SSA_2350:DTDP-4-dehydrorhamnose 3,5-epimerase, putative:30S ribosomal protein S4, putative:<-<-:2351799..2352000 202 ttgagcaaatcttccgtaaaaaagctggaaaaaatctttacagagtgtctcacctgattagataggagcagaaagaaatcagataaatatacccaaacagctgtctcaatccactgaaatttttttagttggaaatagctctattggttcattgagaatattaaaaaagaagccgggaaaccgacttctgaacaaatacaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgagcaaatcttccgtaaaaaagctggaaaaaatctttacagagtgtctcacctgattagataggagcagaaagaaatcagataaatatacccaaacagctgtctcaatccactgaaatttttttagttggaaatagctctattggttcattgagaatattaaaaaagaagccgggaaaccgacttctgaacaaatacaaa Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 62 End: 202 ............................................................. M G A E R N Q I N I P K Q L S Q S T E I F L V G N S S I G S L R I L K K K P G N R L L N K Y K Protein_Len: 31 Strand: - Start: 109 End: 201 ............................................................................................................ D V S I K K T P F L E I P E N L I N F F F G P F R S R F L Y M . Protein_Len: 36 Strand: - Start: 3 End: 110 .. L L D E T F F S S F I K V S H R V Q N S L L L F F D S L Y V W V A T E M ............................................................................................ ttgagcaaatcttccgtaaaaaagctggaaaaaatctttacagagtgtctcacctgattagataggagcagaaagaaatcagataaatatacccaaacagctgtctcaatccactgaaatttttttagttggaaatagctctattggttcattgagaatattaaaaaagaagccgggaaaccgacttctgaacaaatacaaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgagcaaatcttccgtaaaaaagctggaaaaaatctttacagagtgtctcacctgattagataggagcagaaagaaatcagataaatatacccaaacagctgtctcaatccactgaaatttttttagttggaaatagctctattggttcattgagaatattaaaaaagaagccgggaaaccgacttctgaacaaatacaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2349:SSA_2350|SSA_2349:SSA_2350:DTDP-4-dehydrorhamnose 3,5-epimerase, putative:30S ribosomal protein S4, putative:<-<-:2351799..2352000 202 ttgagcaaatcttccgtaaaaaagctggaaaaaatctttacagagtgtctcacctgattagataggagcagaaagaaatcagataaatatacccaaacagctgtctcaatccactgaaatttttttagttggaaatagctctattggttcattgagaatattaaaaaagaagccgggaaaccgacttctgaacaaatacaaa Intra-Species Hit: Count: 1 Min: 1 Max: 202 Len: 202 Subject: NC_009009_SSA_2349_SSA_2350|DTDP-4-dehydrorhamnose 3,5-epimerase, putative:30S ribosomal protein S4, putative|NEGATIVE:NEGATIVE|[2351799,2352000]|202 HSP 1 e-value: 2.0E-98 bit: 359.0 Len: 202 Query Start:1 Query End:202 Subject Strand: POSITIVE Subject Start: 1 Subject End: 202 ttgagcaaatcttccgtaaaaaagctggaaaaaatctttacagagtgtctcacctgattagataggagcagaaagaaatcagataaatatacccaaacagctgtctcaatccactgaaannnnnnnagttggaaatagctctattggttcattgagaatattaaaaaagaagccgggaaaccgacttctgaacaaatacaaa ttgagcaaatcttccgtaaaaaagctggaaaaaatctttacagagtgtctcacctgattagataggagcagaaagaaatcagataaatatacccaaacagctgtctcaatccactgaaatttttttagttggaaatagctctattggttcattgagaatattaaaaaagaagccgggaaaccgacttctgaacaaatacaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAGCAAAUCUUCCGUAAAAAAGCUGGAAAAAAUCUUUACAGAGUGUCUCACCUGAUUAGAUAGGAGCAGAAAGAAAUCAGAUAAAUAUACCCAAACAGCUGUCUCAAUCCACUGAAAUUUUUUUAGUUGGAAAUAGCUCUAUUGGUUCAUUGAGAAUAUUAAAAAAGAAGCCGGGAAACCGACUUCUGAACAAAUACAAA .(((((.....((((((......)).))))...((((...(((.(((...))))))...)))).(((((.....((...(((..................)))..))..(((((((((.....))))).))))....)))))....))))).......((((.....(((((.(((....))).))))).....)))).... (-42.27) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGUAUUUGUUCAGAAGUCGGUUUCCCGGCUUCUUUUUUAAUAUUCUCAAUGAACCAAUAGAGCUAUUUCCAACUAAAAAAAUUUCAGUGGAUUGAGACAGCUGUUUGGGUAUAUUUAUCUGAUUUCUUUCUGCUCCUAUCUAAUCAGGUGAGACACUCUGUAAAGAUUUUUUCCAGCUUUUUUACGGAAGAUUUGCUCAA ...(((((.....(((((((((....))))))))).....)))))................((((..(((((...(((((((.....((..((..(((((((.((..((....))..)).))).))))..))..))...((((...((((((...))).)))...))))..........))))))).)))))....)))).. (-43.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 861 70 21 161 112 NC_009009:SSA_2349|5end_DTDP-4-dehydrorhamnose_3,5-epimerase,_putative_2351708..2351938_NEGATIVE 306 97 53 178 137 NC_009009:SSA_0379|5end_PTS_system,_beta-glucoside-specific_EII_component,_putative_368822..369052_POSITIVE 292 134 91 44 9 NC_009009:SSA_1212|5end_Ribose-phosphate_pyrophosphokinase_2,_putative_1235401..1235631_POSITIVE 288 75 40 52 21 NC_009009:SSA_0209|5end_Glutamyl_aminopeptidase,_putative_207636..207866_NEGATIVE 281 184 146 226 194 NC_009009:SSA_1800|5end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1782371..1782601_NEGATIVE 278 69 25 198 151 NC_009009:SSA_1157|5end_PvaA-like_protein,_putative_1185536..1185766_POSITIVE 267 189 149 225 180 NC_009009:SSA_0139|5end_Copper_transport_operon_or_penicillinase_transcriptional_repressor,_putative_134183..134413_POSITIVE 259 150 101 210 163 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 257 108 61 69 23 NC_009009:SSA_2293|5end_hypothetical_protein_2295270..2295500_POSITIVE 256 125 92 58 18 NC_009009:SSA_1602|5end_Exoribonuclease,_VacB/Rnb_family,_putative_1609370..1609600_NEGATIVE 255 27 1 225 193 NC_009009:SSA_0496|5end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_495946..496176_POSITIVE 254 70 22 121 69 NC_009009:SSA_1307|5end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1326270..1326500_NEGATIVE 253 90 41 191 129 NC_009009:SSA_0071|5end_N-acetylmannosamine-6-p_hosphate_2-epimerase_1,_putative_75210..75440_POSITIVE 250 70 21 205 162 NC_009009:SSA_1953|5end_NifU_family_protein,_putative_1950079..1950309_NEGATIVE 248 147 103 188 150 NC_009009:SSA_2001|5end_Hydroxymethylpyrimidine/phosphomethylpyrimidine_kinase,_putative_1998220..1998450_NEGATIVE 247 69 23 178 123 NC_009009:SSA_0770|5end_Ribonucleoside-diphosphate_reductase,_putative_751411..751641_NEGATIVE 246 85 46 206 164 NC_009009:SSA_0721|5end_Mn/Fe-dependent_superoxide_dismutase,_putative_706215..706445_POSITIVE 245 85 41 180 142 NC_009009:SSA_1946|5end_Oligopeptide_transport_system_permease_protein,_putative_1938624..1938854_NEGATIVE 243 86 41 78 14 NC_009009:SSA_0458|5end_Formylmethionine_deformylase,_putative_461609..461839_POSITIVE 242 117 75 231 185 NC_009009:SSA_1727|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1713420..1713650_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 189 149 77 32 NC_009009:SSA_0138|3end_Metal-binding_(Zn)_permease,_putative_134115..134265_POSITIVE 257 108 61 72 26 NC_009009:SSA_2292|3end_DNA_segregation_ATPase_FtsK/SpoIIIE-like_protein,_putative_2295353..2295503_POSITIVE 256 134 91 127 69 NC_009009:SSA_0172|3end_Transcriptional_regulator,_XRE_family,_putative_169672..169822_POSITIVE 254 70 22 124 72 NC_009009:SSA_1308|3end_hypothetical_protein_1326267..1326417_NEGATIVE 246 85 46 143 101 NC_009009:SSA_0720|3end_hypothetical_protein_706232..706382_POSITIVE 238 189 166 87 61 NC_009009:SSA_2014|3end_D-alanyl-D-alanine_carboxypeptidase,_putative_2014019..2014169_NEGATIVE 238 189 146 84 30 NC_009009:SSA_0908|3end_ABC-type_uncharacterized_transport_system,_periplasmic_component,_putative_920787..920937_POSITIVE 234 82 41 56 8 NC_009009:SSA_1780|3end_Tyrosine_recombinase_xerD,_putative_1766416..1766566_NEGATIVE 231 189 143 118 78 NC_009009:SSA_1226|3end_ParC,_putative_1248783..1248933_NEGATIVE 230 178 137 67 34 NC_009009:SSA_1521|3end_Phosphoenolpyruvate_carboxylase,_putative_1527837..1527987_NEGATIVE 225 57 11 147 96 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 225 189 142 99 40 NC_009009:SSA_0736|3end_Catabolite_gene_activator_and_regulatory_subunit_of_cAMP-dependent_protein_kinases,_putative_718414..718564_POSITIVE 225 70 22 61 5 NC_009009:SSA_0047|3end_NAD(P)H_dehydrogenase_(Quinone),_putative_52284..52434_NEGATIVE 221 190 141 73 18 NC_009009:SSA_0669|3end_ATP_dependent_protease,_putative_651450..651600_NEGATIVE 221 85 59 151 123 NC_009009:SSA_0614|3end_Transporter,_putative_606733..606883_NEGATIVE 218 76 41 110 69 NC_009009:SSA_2234|3end_Phosphatidylserine/phosphatidylglycerophosphate/_cardiolipin_synthase,_phospholipase_D_family,_putative_2233241..2233391_NEGATIVE 218 139 91 111 60 NC_009009:SSA_0672|3end_hypothetical_protein_656044..656194_POSITIVE 216 190 144 66 15 NC_009009:SSA_1984|3end_Cell_surface_SD_repeat_antigen_precursor,_putative_1976048..1976198_NEGATIVE 216 72 41 133 100 NC_009009:SSA_1628|3end_MutT/nudix_family_protein,_putative_1630363..1630513_POSITIVE 215 88 55 54 13 NC_009009:SSA_1650|3end_3-Ketoacyl-ACP_reductase,_putative_1648896..1649046_NEGATIVE