Origin IGS: ggctttgtttttaccagcctcacaccggataactcccgcccgtttaaggcgggtttttatatggactgtcttctaggttttcatatcgggttaaaagtgataaaatagtaggcaggaattggagagacgag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctcgtctctccaattcctgcctactattttatcacttttaacccgatatgaaaacctagaagacagtccatataaaaacccgccttaaacgggcgggagttatccggtgtgaggctggtaaaaacaaagcc Mask Tandem Repeat Region ================================================ ggctttgtttttaccagcctcacaccggataactcccgcccgtttaaggcgggtttttatatggactgtcttctaggttttcatatcgggttaaaagtgataaaatagtaggcaggaattggagagacgag Find is-nt database================================================ Query_seq: SSA_0249:SSA_0250|SSA_0249:SSA_0250:hypothetical protein:GTP pyrophosphokinase, putative:->->:242176..242306 131 ggctttgtttttaccagcctcacaccggataactcccgcccgtttaaggcgggtttttatatggactgtcttctaggttttcatatcgggttaaaagtgataaaatagtaggcaggaattggagagacgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0249:SSA_0250|SSA_0249:SSA_0250:hypothetical protein:GTP pyrophosphokinase, putative:->->:242176..242306 131 ggctttgtttttaccagcctcacaccggataactcccgcccgtttaaggcgggtttttatatggactgtcttctaggttttcatatcgggttaaaagtgataaaatagtaggcaggaattggagagacgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0249:SSA_0250|SSA_0249:SSA_0250:hypothetical protein:GTP pyrophosphokinase, putative:->->:242176..242306 131 ggctttgtttttaccagcctcacaccggataactcccgcccgtttaaggcgggtttttatatggactgtcttctaggttttcatatcgggttaaaagtgataaaatagtaggcaggaattggagagacgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggctttgtttttaccagcctcacaccggataactcccgcccgtttaaggcgggtttttatatggactgtcttctaggttttcatatcgggttaaaagtgataaaatagtaggcaggaattggagagacgag Predict ORF larger than 30AA ================================================ ggctttgtttttaccagcctcacaccggataactcccgcccgtttaaggcgggtttttatatggactgtcttctaggttttcatatcgggttaaaagtgataaaatagtaggcaggaattggagagacgag Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 77 End: 106 ............................................................................GTTTTCATATCGGGTTAAAAGTGATAAAAT......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggctttgtttttaccagcctcacaccggataactcccgcccgtttaaggcgggtttttatatggactgtcttctaggttttcatatcgggttaaaagtgataaaatagtaggcaggaattggagagacgag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 46 HP_score: -2.5 Tail_Score: -3.34962 Start: 33 End: 55 Full_Region: gacagtccatataaa aacccgcct taaac gggcgggag ttatccggtgtgagg ................................aacccgccttaaacgggcgggag............................................................................ Find igs database================================================ Query_seq: SSA_0249:SSA_0250|SSA_0249:SSA_0250:hypothetical protein:GTP pyrophosphokinase, putative:->->:242176..242306 131 ggctttgtttttaccagcctcacaccggataactcccgcccgtttaaggcgggtttttatatggactgtcttctaggttttcatatcgggttaaaagtgataaaatagtaggcaggaattggagagacgag Intra-Species Hit: Count: 1 Min: 1 Max: 131 Len: 131 Subject: NC_009009_SSA_0249_SSA_0250|hypothetical protein:GTP pyrophosphokinase, putative|POSITIVE:POSITIVE|[242176,242306]|131 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 131 Query Start:1 Query End:131 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 ggctttgtttttaccagcctcacaccggataactcccgcccgtttaaggcgggtttttatatggactgtcttctaggttttcatatcgggttaaaagtgataaaatagtaggcaggaattggagagacgag ggctttgtttttaccagcctcacaccggataactcccgcccgtttaaggcgggtttttatatggactgtcttctaggttttcatatcgggttaaaagtgataaaatagtaggcaggaattggagagacgag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCUUUGUUUUUACCAGCCUCACACCGGAUAACUCCCGCCCGUUUAAGGCGGGUUUUUAUAUGGACUGUCUUCUAGGUUUUCAUAUCGGGUUAAAAGUGAUAAAAUAGUAGGCAGGAAUUGGAGAGACGAG ....((((((((.((((.......(((.((((..((((((.......))))))...)))).))).((((((.(((..((.((((............)))).))..))).))))))...)))))))))))). (-38.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCGUCUCUCCAAUUCCUGCCUACUAUUUUAUCACUUUUAACCCGAUAUGAAAACCUAGAAGACAGUCCAUAUAAAAACCCGCCUUAAACGGGCGGGAGUUAUCCGGUGUGAGGCUGGUAAAAACAAAGCC ((.(((((.((.....(((.((.(((..((.(((..((......))..))).))..))).)).)))............(((((((.....)))))))........))...))))).))............. (-28.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 50 1 149 92 NC_009009:SSA_1793|5end_Histidine_kinase_(sensor_protein),_putative_1776361..1776591_NEGATIVE 356 80 32 145 90 NC_009009:SSA_1643|5end_hypothetical_protein_1645269..1645499_NEGATIVE 340 57 13 77 23 NC_009009:SSA_1669|5end_hypothetical_protein_1668442..1668672_NEGATIVE 339 49 1 230 161 NC_009009:SSA_1822|5end_hypothetical_protein_1811125..1811355_NEGATIVE 330 57 13 61 9 NC_009009:SSA_0695|5end_hypothetical_protein_678449..678679_POSITIVE 328 53 18 227 191 NC_009009:SSA_1251|5end_Hydrolase,_HD_superfamily,_putative_1276790..1277020_NEGATIVE 322 130 81 178 133 NC_009009:SSA_2191|5end_Conserved_uncharacterized_protein_2192049..2192279_POSITIVE 320 59 14 59 3 NC_009009:SSA_0793|5end_DNA-entry_nuclease,_putative_774859..775089_POSITIVE 317 40 1 231 200 NC_009009:SSA_2060|5end_Arabinose_efflux_permease,_putative_2062403..2062633_NEGATIVE 317 50 1 162 111 NC_009009:SSA_0479|5end_CbiQ_protein,_putative_480425..480655_POSITIVE 313 47 1 81 41 NC_009009:SSA_0240|5end_Acetyltransferase,_GNAT_family,_putative_233410..233640_POSITIVE 311 58 16 61 14 NC_009009:SSA_0956|5end_surface_protein_D_961223..961453_POSITIVE 307 73 31 228 184 NC_009009:SSA_0808|5end_hypothetical_protein_790771..791001_POSITIVE 306 57 18 188 158 NC_009009:SSA_1617|5end_hypothetical_protein_1620651..1620881_NEGATIVE 305 59 16 45 6 NC_009009:SSA_0093|5end_V-type_sodium_ATPase,_subunit_D,_putative_94286..94516_POSITIVE 298 57 11 121 65 NC_009009:SSA_0636|5end_N-(5'-phosphoribosyl)anthranilate_isomerase,_putative_625184..625414_POSITIVE 296 55 12 65 13 NC_009009:SSA_2312|5end_hypothetical_protein_2315281..2315511_NEGATIVE 296 91 61 76 38 NC_009009:SSA_1834|5end_30S_ribosomal_interface_protein_S30EA,_putative_1830194..1830424_NEGATIVE 294 77 33 220 165 NC_009009:SSA_1016|5end_Phosphoenolpyruvate_synthase,_putative_1019602..1019832_POSITIVE 294 59 11 176 133 NC_009009:SSA_0207|5end_hypothetical_protein_204430..204660_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 54 16 125 95 NC_009009:SSA_2077|3end_hypothetical_protein_2081352..2081502_NEGATIVE 334 79 35 77 32 NC_009009:SSA_1990|3end_Zn-porter_lipoprotein,_putative_1985402..1985552_NEGATIVE 327 67 25 46 2 NC_009009:SSA_2117|3end_DNA_recombination_protein_RmuC,_putative_2118556..2118706_NEGATIVE 318 70 21 135 89 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 313 47 1 84 44 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 306 57 18 119 89 NC_009009:SSA_1618|3end_hypothetical_protein_1620720..1620870_NEGATIVE 305 59 16 48 9 NC_009009:SSA_0092|3end_V-type_sodium_ATPase,_subunit_B,_putative_94369..94519_POSITIVE 302 40 1 147 108 NC_009009:SSA_1794|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1776345..1776495_NEGATIVE 301 80 31 125 62 NC_009009:SSA_1504|3end_hypothetical_protein_1506459..1506609_NEGATIVE 298 57 11 92 36 NC_009009:SSA_0635|3end_Indole-3-glycerol_phosphate_synthase,_putative_625235..625385_POSITIVE 291 70 26 147 104 NC_009009:SSA_1396|3end_hypothetical_protein_1409790..1409940_NEGATIVE 290 78 32 135 93 NC_009009:SSA_1345|3end_Bifunctional_pyrimidine_operon_transcriptional_attenuation_protein/uracil_phosphoribosyltransferase,_putative_1363361..1363511_NEGATIVE 290 60 19 79 36 NC_009009:SSA_0257|3end_N-acetylmuramidase/lysin,_putative_251840..251990_POSITIVE 289 53 14 64 27 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 288 57 16 138 93 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 288 67 24 57 6 NC_009009:SSA_0502|3end_Peptide_ABC_transporter,_permease_protein,_putative_502323..502473_POSITIVE 287 40 1 126 81 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 284 78 38 64 25 NC_009009:SSA_0624|3end_hypothetical_protein_615698..615848_POSITIVE 280 53 14 74 21 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 279 41 1 60 19 NC_009009:SSA_0475|3end_CbiK_protein,_putative_478570..478720_POSITIVE