Origin IGS: aaaatgaagcaggagaatgggagagagtgccgcgatttggagattgtagcatgcttctccccgctcctgttttttgcttttcttttcttttggcggtaaaaatagtacaatatagtaaatattgatgcactattatcaagtaagaaaaagcggagagatgtg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cacatctctccgctttttcttacttgataatagtgcatcaatatttactatattgtactatttttaccgccaaaagaaaagaaaagcaaaaaacaggagcggggagaagcatgctacaatctccaaatcgcggcactctctcccattctcctgcttcatttt Mask Tandem Repeat Region ================================================ aaaatgaagcaggagaatgggagagagtgccgcgatttggagattgtagcatgcttctccccgctcctgttttttgcttttcttttcttttggcggtaaaaatagtacaatatagtaaatattgatgcactattatcaagtaagaaaaagcggagagatgtg Find is-nt database================================================ Query_seq: SSA_0379:SSA_0380|SSA_0379:SSA_0380:PTS system, beta-glucoside-specific EII component, putative:Enzyme of poly-gamma-glutamate biosynthesis (capsule formation), putative:->->:370894..371055 162 aaaatgaagcaggagaatgggagagagtgccgcgatttggagattgtagcatgcttctccccgctcctgttttttgcttttcttttcttttggcggtaaaaatagtacaatatagtaaatattgatgcactattatcaagtaagaaaaagcggagagatgtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0379:SSA_0380|SSA_0379:SSA_0380:PTS system, beta-glucoside-specific EII component, putative:Enzyme of poly-gamma-glutamate biosynthesis (capsule formation), putative:->->:370894..371055 162 aaaatgaagcaggagaatgggagagagtgccgcgatttggagattgtagcatgcttctccccgctcctgttttttgcttttcttttcttttggcggtaaaaatagtacaatatagtaaatattgatgcactattatcaagtaagaaaaagcggagagatgtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0379:SSA_0380|SSA_0379:SSA_0380:PTS system, beta-glucoside-specific EII component, putative:Enzyme of poly-gamma-glutamate biosynthesis (capsule formation), putative:->->:370894..371055 162 aaaatgaagcaggagaatgggagagagtgccgcgatttggagattgtagcatgcttctccccgctcctgttttttgcttttcttttcttttggcggtaaaaatagtacaatatagtaaatattgatgcactattatcaagtaagaaaaagcggagagatgtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaatgaagcaggagaatgggagagagtgccgcgatttggagattgtagcatgcttctccccgctcctgttttttgcttttcttttcttttggcggtaaaaatagtacaatatagtaaatattgatgcactattatcaagtaagaaaaagcggagagatgtg Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 4 End: 96 ... M K Q E N G R E C R D L E I V A C F S P L L F F A F L F F W R .................................................................. Protein_Len: 32 Strand: + Start: 27 End: 122 .......................... M P R F G D C S M L L P A P V F C F S F L L A V K I V Q Y S K Y ........................................ Protein_Len: 40 Strand: - Start: 3 End: 122 .. I F C S F P L S H R S K S I T A H K E G S R N K A K R K K Q R Y F Y Y L I T F M ........................................ Protein_Len: 46 Strand: - Start: 2 End: 139 . F S A P S H S L T G R N P S Q L M S R G A G T K Q K E K R K A T F I T C Y L L Y Q H V I I M ....................... Protein_Len: 42 Strand: - Start: 1 End: 126 F H L L L I P S L A A I Q L N Y C A E G R E Q K K S K K E K P P L F L V I Y Y I N M .................................... aaaatgaagcaggagaatgggagagagtgccgcgatttggagattgtagcatgcttctccccgctcctgttttttgcttttcttttcttttggcggtaaaaatagtacaatatagtaaatattgatgcactattatcaagtaagaaaaagcggagagatgtg 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================================================ aaaatgaagcaggagaatgggagagagtgccgcgatttggagattgtagcatgcttctccccgctcctgttttttgcttttcttttcttttggcggtaaaaatagtacaatatagtaaatattgatgcactattatcaagtaagaaaaagcggagagatgtg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0379:SSA_0380|SSA_0379:SSA_0380:PTS system, beta-glucoside-specific EII component, putative:Enzyme of poly-gamma-glutamate biosynthesis (capsule formation), putative:->->:370894..371055 162 aaaatgaagcaggagaatgggagagagtgccgcgatttggagattgtagcatgcttctccccgctcctgttttttgcttttcttttcttttggcggtaaaaatagtacaatatagtaaatattgatgcactattatcaagtaagaaaaagcggagagatgtg Intra-Species Hit: Count: 1 Min: 1 Max: 162 Len: 162 Subject: NC_009009_SSA_0379_SSA_0380|PTS system, beta-glucoside-specific EII component, putative:Enzyme of poly-gamma-glutamate biosynthesis (capsule formation), putative|POSITIVE:POSITIVE|[370894,371055]|162 HSP 1 e-value: 8.0E-33 bit: 141.0 Len: 71 Query Start:92 Query End:162 Subject Strand: POSITIVE Subject Start: 92 Subject End: 162 ...........................................................................................ggcggtaaaaatagtacaatatagtaaatattgatgcactattatcaagtaagaaaaagcggagagatgtg ...........................................................................................ggcggtaaaaatagtacaatatagtaaatattgatgcactattatcaagtaagaaaaagcggagagatgtg HSP 2 e-value: 1.0E-31 bit: 137.0 Len: 69 Query Start:1 Query End:69 Subject Strand: POSITIVE Subject Start: 1 Subject End: 69 aaaatgaagcaggagaatgggagagagtgccgcgatttggagattgtagcatgcttctccccgctcctg............................................................................................. aaaatgaagcaggagaatgggagagagtgccgcgatttggagattgtagcatgcttctccccgctcctg............................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUGAAGCAGGAGAAUGGGAGAGAGUGCCGCGAUUUGGAGAUUGUAGCAUGCUUCUCCCCGCUCCUGUUUUUUGCUUUUCUUUUCUUUUGGCGGUAAAAAUAGUACAAUAUAGUAAAUAUUGAUGCACUAUUAUCAAGUAAGAAAAAGCGGAGAGAUGUG .....((((((((((...(((((((.((((..(((((....)))))..))))..)))))))..))))))))))..((.((((((..(((((.((......((((((.((((((.....))))))....)))))).....))....)))))..)))))).)). (-53.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACAUCUCUCCGCUUUUUCUUACUUGAUAAUAGUGCAUCAAUAUUUACUAUAUUGUACUAUUUUUACCGCCAAAAGAAAAGAAAAGCAAAAAACAGGAGCGGGGAGAAGCAUGCUACAAUCUCCAAAUCGCGGCACUCUCUCCCAUUCUCCUGCUUCAUUUU ...........((((((..((.(((...(((((((((...((((.....)))))))))))))...........))).))..))))))......((((((..((((((.(..(((..(............)..)))..)))))))...))))))......... (-39.14) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 369 69 23 158 101 NC_009009:SSA_2275|5end_hypothetical_protein_2275590..2275820_NEGATIVE 358 59 12 228 165 NC_009009:SSA_0017|5end_Cell_shape_determining_protein_MreC,_putative_22811..23041_POSITIVE 343 68 22 163 114 NC_009009:SSA_1209|5end_Inorganic_polyphosphate/ATP-NAD_kinase,_putative_1234030..1234260_NEGATIVE 338 90 43 134 82 NC_009009:SSA_1056|5end_Firmicute_fructose-1,6-bisphosphatase,_putative_1071760..1071990_POSITIVE 335 60 13 104 42 NC_009009:SSA_2206|5end_hypothetical_protein_2206839..2207069_POSITIVE 327 69 24 230 175 NC_009009:SSA_0913|5end_Acetyltransferase,_putative_924195..924425_POSITIVE 325 50 5 61 7 NC_009009:SSA_0639|5end_hypothetical_protein_627906..628136_NEGATIVE 321 97 53 67 13 NC_009009:SSA_1896|5end_Translation_initiation_factor_IF-2,_putative_1894134..1894364_NEGATIVE 321 79 31 194 134 NC_009009:SSA_0217|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213183..213413_POSITIVE 319 70 25 114 62 NC_009009:SSA_0883|5end_Glycerate_kinase,_putative_877560..877790_POSITIVE 314 70 27 222 163 NC_009009:SSA_0661|5end_Isoleucyl-tRNA_synthetase,_putative_644876..645106_POSITIVE 314 63 22 201 147 NC_009009:SSA_0607|5end_ABC_transporter,_permease_component,_putative_596926..597156_NEGATIVE 313 88 42 163 115 NC_009009:SSA_2322|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_2327044..2327274_POSITIVE 311 87 53 89 49 NC_009009:SSA_2175|5end_hypothetical_protein_2174042..2174272_NEGATIVE 309 78 32 175 128 NC_009009:SSA_1571|5end_Threonyl-tRNA_synthetase,_putative_1575154..1575384_NEGATIVE 307 90 47 47 1 NC_009009:SSA_0972|5end_hypothetical_protein_979973..980203_POSITIVE 305 43 7 83 37 NC_009009:SSA_2038|5end_hypothetical_protein_2041627..2041857_POSITIVE 304 50 4 190 139 NC_009009:SSA_1164|5end_hypothetical_protein_1191138..1191368_NEGATIVE 303 88 41 165 117 NC_009009:SSA_2228|5end_Acetyltransferase_(GNAT)_family,_putative_2228768..2228998_NEGATIVE 303 64 27 228 202 NC_009009:SSA_1501|5end_Cytidylate_kinase,_putative_1505772..1506002_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 69 21 68 4 NC_009009:SSA_0897|3end_Two_component_system_histidine_kinase,_putative_889811..889961_POSITIVE 338 90 43 91 39 NC_009009:SSA_1055|3end_Conserved_uncharacterized_protein_1071797..1071947_POSITIVE 330 79 32 84 27 NC_009009:SSA_0379|3end_PTS_system,_beta-glucoside-specific_EII_component,_putative_370833..370983_POSITIVE 319 70 25 104 52 NC_009009:SSA_0882|3end_Phosphoserine_phosphatase,_putative_877630..877780_POSITIVE 317 97 52 143 92 NC_009009:SSA_2206|3end_hypothetical_protein_2207275..2207425_POSITIVE 317 90 44 63 13 NC_009009:SSA_0971|3end_Conserved_uncharacterized_protein_980069..980219_POSITIVE 310 64 23 150 104 NC_009009:SSA_2276|3end_hypothetical_protein_2275587..2275737_NEGATIVE 307 50 8 37 1 NC_009009:SSA_1777|3end_Ribosomal_large_subunit_pseudouridine_synthase_B,_putative_1764427..1764577_NEGATIVE 303 88 41 112 64 NC_009009:SSA_2229|3end_hypothetical_protein_2228821..2228971_NEGATIVE 303 59 21 147 105 NC_009009:SSA_0482|3end_ATP:cobalamin_adenosyl_transferase,_putative_484113..484263_POSITIVE 300 64 24 150 100 NC_009009:SSA_0035|3end_Bifunctional_purine_biosynthesis_protein_purH,_putative_41957..42107_POSITIVE 299 61 21 54 8 NC_009009:SSA_2044|3end_Cysteinyl-tRNA_synthetase,_putative_2047066..2047216_NEGATIVE 297 70 24 81 21 NC_009009:SSA_1181|3end_Hydrolase,_alpha/beta_superfamily,_putative_1208592..1208742_NEGATIVE 296 80 31 65 9 NC_009009:SSA_0634|3end_Anthranilate_phosphoribosyltransferase,_putative_624471..624621_POSITIVE 292 98 52 151 106 NC_009009:SSA_1938|3end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1924764..1924914_NEGATIVE 291 49 8 50 3 NC_009009:SSA_1115|3end_Cytochrome_C-type_biogenesis_protein,_putative_1142404..1142554_POSITIVE 289 50 5 150 99 NC_009009:SSA_2018|3end_hypothetical_protein_2017464..2017614_NEGATIVE 288 54 24 143 107 NC_009009:SSA_1831|3end_hypothetical_protein_1821994..1822144_POSITIVE 287 60 12 106 47 NC_009009:SSA_0023|3end_Aspartate_aminotransferase,_putative_29781..29931_POSITIVE 285 68 24 85 44 NC_009009:SSA_1467|3end_Chorismate_synthase,_putative_1473127..1473277_NEGATIVE