Origin IGS: gacttctgattttgaaactataaacgctgggaaaaatttctcagcgtttttaaatcttaaaaaatgtgttctgataggtaagtcgatttccttttagcttctaaggacctcatcaatgaaaaaatggaaaaagtcaaggcttatcaatctgtcgtggccattgcttgctattttatggtataatgaaaaaaataagtaggagaagtgataatt .........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 aattatcacttctcctacttatttttttcattataccataaaatagcaagcaatggccacgacagattgataagccttgactttttccattttttcattgatgaggtccttagaagctaaaaggaaatcgacttacctatcagaacacattttttaagatttaaaaacgctgagaaatttttcccagcgtttatagtttcaaaatcagaagtc Mask Tandem Repeat Region ================================================ gacttctgattttgaaactataaacgctgggaaaaatttctcagcgtttttaaatcttaaaaaatgtgttctgataggtaagtcgatttccttttagcttctaaggacctcatcaatgaaaaaatggaaaaagtcaaggcttatcaatctgtcgtggccattgcttgctattttatggtataatgaaaaaaataagtaggagaagtgataatt Find is-nt database================================================ Query_seq: SSA_0808:SSA_0809|SSA_0808:SSA_0809:hypothetical protein:Translation initiation inhibitor, yjgF family / endoribonuclease L-PSP, putative:->->:791073..791285 213 gacttctgattttgaaactataaacgctgggaaaaatttctcagcgtttttaaatcttaaaaaatgtgttctgataggtaagtcgatttccttttagcttctaaggacctcatcaatgaaaaaatggaaaaagtcaaggcttatcaatctgtcgtggccattgcttgctattttatggtataatgaaaaaaataagtaggagaagtgataatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0808:SSA_0809|SSA_0808:SSA_0809:hypothetical protein:Translation initiation inhibitor, yjgF family / endoribonuclease L-PSP, putative:->->:791073..791285 213 gacttctgattttgaaactataaacgctgggaaaaatttctcagcgtttttaaatcttaaaaaatgtgttctgataggtaagtcgatttccttttagcttctaaggacctcatcaatgaaaaaatggaaaaagtcaaggcttatcaatctgtcgtggccattgcttgctattttatggtataatgaaaaaaataagtaggagaagtgataatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0808:SSA_0809|SSA_0808:SSA_0809:hypothetical protein:Translation initiation inhibitor, yjgF family / endoribonuclease L-PSP, putative:->->:791073..791285 213 gacttctgattttgaaactataaacgctgggaaaaatttctcagcgtttttaaatcttaaaaaatgtgttctgataggtaagtcgatttccttttagcttctaaggacctcatcaatgaaaaaatggaaaaagtcaaggcttatcaatctgtcgtggccattgcttgctattttatggtataatgaaaaaaataagtaggagaagtgataatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacttctgattttgaaactataaacgctgggaaaaatttctcagcgtttttaaatcttaaaaaatgtgttctgataggtaagtcgatttccttttagcttctaaggacctcatcaatgaaaaaatggaaaaagtcaaggcttatcaatctgtcgtggccattgcttgctattttatggtataatgaaaaaaataagtaggagaagtgataatt Predict ORF larger than 30AA ================================================ gacttctgattttgaaactataaacgctgggaaaaatttctcagcgtttttaaatcttaaaaaatgtgttctgataggtaagtcgatttccttttagcttctaaggacctcatcaatgaaaaaatggaaaaagtcaaggcttatcaatctgtcgtggccattgcttgctattttatggtataatgaaaaaaataagtaggagaagtgataatt 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================================================ gacttctgattttgaaactataaacgctgggaaaaatttctcagcgtttttaaatcttaaaaaatgtgttctgataggtaagtcgatttccttttagcttctaaggacctcatcaatgaaaaaatggaaaaagtcaaggcttatcaatctgtcgtggccattgcttgctattttatggtataatgaaaaaaataagtaggagaagtgataatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 74 HP_score: -9.7 Tail_Score: -2.74144 Start: 19 End: 52 Full_Region: acattttttaagatt taaaaacgctgagaa attt ttcccagcgtttata gtttcaaaatcagaa ..................taaaaacgctgagaaatttttcccagcgtttata................................................................................................................................................................. TransTerm Strand: - Conf: 82 HP_score: -8.7 Tail_Score: -4.13654 Start: 25 End: 46 Full_Region: tttaagatttaaaaa cgctgagaa attt ttcccagcg tttatagtttcaaaa ........................cgctgagaaatttttcccagcg....................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_0808:SSA_0809|SSA_0808:SSA_0809:hypothetical protein:Translation initiation inhibitor, yjgF family / endoribonuclease L-PSP, putative:->->:791073..791285 213 gacttctgattttgaaactataaacgctgggaaaaatttctcagcgtttttaaatcttaaaaaatgtgttctgataggtaagtcgatttccttttagcttctaaggacctcatcaatgaaaaaatggaaaaagtcaaggcttatcaatctgtcgtggccattgcttgctattttatggtataatgaaaaaaataagtaggagaagtgataatt Intra-Species Hit: Count: 1 Min: 1 Max: 213 Len: 213 Subject: NC_009009_SSA_0808_SSA_0809|hypothetical protein:Translation initiation inhibitor, yjgF family / endoribonuclease L-PSP, putative|POSITIVE:POSITIVE|[791073,791285]|213 HSP 1 e-value: 1.0E-105 bit: 381.0 Len: 213 Query Start:1 Query End:213 Subject Strand: POSITIVE Subject Start: 1 Subject End: 213 gacttctgattttgaaactataaacgctgggaaaaatttctcagcgtttttaaatcttaaaaaatgtgttctgataggtaagtcgatttccttttagcttctaaggacctcatcaatgaaaaaatggaaaaagtcaaggcttatcaatctgtcgtggccattgcttgctattttatggtataatgnnnnnnntaagtaggagaagtgataatt gacttctgattttgaaactataaacgctgggaaaaatttctcagcgtttttaaatcttaaaaaatgtgttctgataggtaagtcgatttccttttagcttctaaggacctcatcaatgaaaaaatggaaaaagtcaaggcttatcaatctgtcgtggccattgcttgctattttatggtataatgaaaaaaataagtaggagaagtgataatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACUUCUGAUUUUGAAACUAUAAACGCUGGGAAAAAUUUCUCAGCGUUUUUAAAUCUUAAAAAAUGUGUUCUGAUAGGUAAGUCGAUUUCCUUUUAGCUUCUAAGGACCUCAUCAAUGAAAAAAUGGAAAAAGUCAAGGCUUAUCAAUCUGUCGUGGCCAUUGCUUGCUAUUUUAUGGUAUAAUGAAAAAAAUAAGUAGGAGAAGUGAUAAUU .((((((..((((((......((((((((((((....)))))))))))).......)))))).(((.((..((((((((.....((..(((((.........)))))..))...................((((....))))....))))))))..)))))((((((...((((((......))))))....))))))..))))))....... (-46.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAUCACUUCUCCUACUUAUUUUUUUCAUUAUACCAUAAAAUAGCAAGCAAUGGCCACGACAGAUUGAUAAGCCUUGACUUUUUCCAUUUUUUCAUUGAUGAGGUCCUUAGAAGCUAAAAGGAAAUCGACUUACCUAUCAGAACACAUUUUUUAAGAUUUAAAAACGCUGAGAAAUUUUUCCCAGCGUUUAUAGUUUCAAAAUCAGAAGUC .......((((((............((((((((......(((((.(.((((((.(((..(((....)))....)))))).)))...).))))).....))))))))......(((((((..(((((......)).)))..........................((((((((.(((....))).)))))))).)))))))......)))))). (-35.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 165 125 75 34 NC_009009:SSA_1634|5end_Heme_utilization/adhesion_exoprotein,_putative_1637062..1637292_NEGATIVE 342 178 131 44 4 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 339 46 2 40 2 NC_009009:SSA_1791|5end_Acylphosphatase,_putative_1773676..1773906_POSITIVE 298 180 132 211 156 NC_009009:SSA_0421|5end_Phosphoglycerate_mutase_family_protein,_putative_419564..419794_POSITIVE 296 180 137 201 147 NC_009009:SSA_1088|5end_hypothetical_protein_1107048..1107278_POSITIVE 290 172 133 55 6 NC_009009:SSA_0263|5end_Zinc_metalloproteinase_in_scaA_5'region,_putative_256274..256504_POSITIVE 288 180 137 43 5 NC_009009:SSA_0166|5end_hypothetical_protein_164641..164871_POSITIVE 287 167 137 230 190 NC_009009:SSA_0530|5end_Ethanolamine_utilization_protein_(transporter),_putative_526243..526473_POSITIVE 282 160 111 203 146 NC_009009:SSA_2071|5end_hypothetical_protein_2074766..2074996_NEGATIVE 281 110 64 166 125 NC_009009:SSA_1074|5end_Pyrroline-5-carboxylate_reductase,_putative_1092151..1092381_POSITIVE 281 180 138 197 150 NC_009009:SSA_0710|5end_Exopolysaccharide_biosynthesis_protein,_acetyltransferase,_putative_695639..695869_NEGATIVE 280 161 125 182 138 NC_009009:SSA_2045|5end_Reductase,_putative_2048948..2049178_NEGATIVE 279 177 134 52 1 NC_009009:SSA_1029|5end_hypothetical_protein_1047009..1047239_NEGATIVE 277 180 131 186 139 NC_009009:SSA_1896|5end_Translation_initiation_factor_IF-2,_putative_1894134..1894364_NEGATIVE 276 180 133 191 144 NC_009009:SSA_2193|5end_ADP-ribose_pyrophosphatase,_putative_2194793..2195023_NEGATIVE 275 155 119 175 144 NC_009009:SSA_1311|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_1328393..1328623_NEGATIVE 274 179 133 224 181 NC_009009:SSA_0854|5end_hypothetical_protein_841335..841565_POSITIVE 274 180 137 198 153 NC_009009:SSA_0538|5end_PduH_protein,_putative_533794..534024_POSITIVE 272 180 132 79 27 NC_009009:SSA_1014|5end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1017846..1018076_POSITIVE 268 119 73 210 151 NC_009009:SSA_0878|5end_DNA_gyrase,_putative_871596..871826_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 49 22 69 42 NC_009009:SSA_0808|3end_hypothetical_protein_791012..791162_POSITIVE 277 169 124 149 95 NC_009009:SSA_2137|3end_hypothetical_protein_2137780..2137930_NEGATIVE 276 180 133 136 89 NC_009009:SSA_2194|3end_Nicotinamide_mononucleotide_transporter,_putative_2194848..2194998_NEGATIVE 272 180 132 86 34 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE 261 130 88 44 7 NC_009009:SSA_2251|3end_hypothetical_protein_2247997..2248147_POSITIVE 260 58 16 88 44 NC_009009:SSA_2323|3end_Transporter,_putative_2328850..2329000_POSITIVE 260 169 133 58 22 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 259 121 82 128 90 NC_009009:SSA_0750|3end_hypothetical_protein_732255..732405_POSITIVE 257 46 7 84 45 NC_009009:SSA_0505|3end_Conserved_protein/domain_typically_associated_with_flavoprotein_oxygenases,_DIM6/NTAB_family,_putative_504427..504577_POSITIVE 253 109 84 87 60 NC_009009:SSA_0963|3end_Peptidoglycan_N-acetylglucosamine_deacetylase_A,_putative_972890..973040_POSITIVE 253 106 70 64 20 NC_009009:SSA_0885|3end_hypothetical_protein_879065..879215_NEGATIVE 250 169 133 74 36 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 249 168 125 149 101 NC_009009:SSA_1746|3end_hypothetical_protein_1732292..1732442_NEGATIVE 247 159 112 117 63 NC_009009:SSA_1958|3end_Adapter_protein_mecA,_putative_1954661..1954811_NEGATIVE 247 53 26 55 26 NC_009009:SSA_1659|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1654831..1654981_NEGATIVE 247 62 26 79 39 NC_009009:SSA_0234|3end_hypothetical_protein_228423..228573_NEGATIVE 246 169 123 72 33 NC_009009:SSA_1043|3end_Homoserine_dehydrogenase,_putative_1059931..1060081_POSITIVE 246 178 131 81 31 NC_009009:SSA_0136|3end_ABC_transporter,_Zn_porter,_putative_131804..131954_POSITIVE 245 140 97 48 1 NC_009009:SSA_1024|3end_Alpha-amylase,_putative_1041182..1041332_NEGATIVE 244 176 133 60 9 NC_009009:SSA_1846|3end_Phosphoprotein_phosphatase,_putative_1840178..1840328_NEGATIVE