Origin IGS: acgaaaactcatcgtaaatgctattgtggaaaaccaatttgcattgctgaagatcagatttagatttaatttttcaagcaaaaatggataagactttttaagtcctatccattttgctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagcaaaatggataggacttaaaaagtcttatccatttttgcttgaaaaattaaatctaaatctgatcttcagcaatgcaaattggttttccacaatagcatttacgatgagttttcgt Mask Tandem Repeat Region ================================================ acgaaaactcatcgtaaatgctattgtggaaaaccaatttgcattgctgaagatcagatttagatttaatttttcaagcaaaaatggataagactttttaagtcctatccattttgctt Find is-nt database================================================ Query_seq: SSA_2390:SSA_0004|SSA_2390:SSA_0004:hypothetical protein:Lipoprotein, putative:-><-:3184..3302 119 acgaaaactcatcgtaaatgctattgtggaaaaccaatttgcattgctgaagatcagatttagatttaatttttcaagcaaaaatggataagactttttaagtcctatccattttgctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2390:SSA_0004|SSA_2390:SSA_0004:hypothetical protein:Lipoprotein, putative:-><-:3184..3302 119 acgaaaactcatcgtaaatgctattgtggaaaaccaatttgcattgctgaagatcagatttagatttaatttttcaagcaaaaatggataagactttttaagtcctatccattttgctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2390:SSA_0004|SSA_2390:SSA_0004:hypothetical protein:Lipoprotein, putative:-><-:3184..3302 119 acgaaaactcatcgtaaatgctattgtggaaaaccaatttgcattgctgaagatcagatttagatttaatttttcaagcaaaaatggataagactttttaagtcctatccattttgctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acgaaaactcatcgtaaatgctattgtggaaaaccaatttgcattgctgaagatcagatttagatttaatttttcaagcaaaaatggataagactttttaagtcctatccattttgctt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 1 End: 108 R F S M T F A I T S F W N A N S F I L N L N L K E L L F P Y S K K L G M ........... acgaaaactcatcgtaaatgctattgtggaaaaccaatttgcattgctgaagatcagatttagatttaatttttcaagcaaaaatggataagactttttaagtcctatccattttgctt 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================================================ acgaaaactcatcgtaaatgctattgtggaaaaccaatttgcattgctgaagatcagatttagatttaatttttcaagcaaaaatggataagactttttaagtcctatccattttgctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2390:SSA_0004|SSA_2390:SSA_0004:hypothetical protein:Lipoprotein, putative:-><-:3184..3302 119 acgaaaactcatcgtaaatgctattgtggaaaaccaatttgcattgctgaagatcagatttagatttaatttttcaagcaaaaatggataagactttttaagtcctatccattttgctt Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: NC_009009_SSA_2390_SSA_0004|hypothetical protein:Lipoprotein, putative|POSITIVE:NEGATIVE|[3184,3302]|119 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 acgaaaactcatcgtaaatgctattgtggaaaaccaatttgcattgctgaagatcagatttagatttaatttttcaagcaaaaatggataagactttttaagtcctatccattttgctt acgaaaactcatcgtaaatgctattgtggaaaaccaatttgcattgctgaagatcagatttagatttaatttttcaagcaaaaatggataagactttttaagtcctatccattttgctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGAAAACUCAUCGUAAAUGCUAUUGUGGAAAACCAAUUUGCAUUGCUGAAGAUCAGAUUUAGAUUUAAUUUUUCAAGCAAAAAUGGAUAAGACUUUUUAAGUCCUAUCCAUUUUGCUU ..(((((...(((...(((((.....(((....)))....))))).(((.....))).....))).....))))).(((((((.((((((.((((.....)))).))))))))))))). (-29.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCAAAAUGGAUAGGACUUAAAAAGUCUUAUCCAUUUUUGCUUGAAAAAUUAAAUCUAAAUCUGAUCUUCAGCAAUGCAAAUUGGUUUUCCACAAUAGCAUUUACGAUGAGUUUUCGU (((((((((((((((((((.....))))))))))).))))))))(((((.....(((.....(((.....))).(((((..((((........)))).)))))...)))...))))).. (-33.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 56 12 210 169 NC_009009:SSA_1183|5end_hypothetical_protein_1211453..1211683_NEGATIVE 258 109 70 174 130 NC_009009:SSA_0997|5end_DNA-directed_DNA_polymerase_III_chain,_putative_996779..997009_POSITIVE 247 53 11 194 153 NC_009009:SSA_1612|5end_Diacylglycerol_kinase,_putative_1616497..1616727_NEGATIVE 238 49 10 195 163 NC_009009:SSA_1794|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1777049..1777279_NEGATIVE 238 106 61 99 53 NC_009009:SSA_1395|5end_hypothetical_protein_1409773..1410003_NEGATIVE 238 50 2 181 136 NC_009009:SSA_0522|5end_Ethanolamine_utilization_protein,_putative_521067..521297_POSITIVE 228 58 12 80 31 NC_009009:SSA_0506|5end_Iron-sulfur_cluster-binding_protein,_putative_505629..505859_NEGATIVE 227 68 34 133 104 NC_009009:SSA_1867|5end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1863096..1863326_NEGATIVE 223 58 20 127 87 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 218 58 24 231 193 NC_009009:SSA_0496|5end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_495946..496176_POSITIVE 217 56 17 223 187 NC_009009:SSA_0812|5end_hypothetical_protein_793443..793673_POSITIVE 217 110 69 176 139 NC_009009:SSA_0245|5end_hypothetical_protein_239136..239366_POSITIVE 216 49 17 35 5 NC_009009:SSA_0873|5end_ATP-dependent_DNA_helicase;_DNA_polymerase_III,_epsilon_subunit,_putative_865391..865621_POSITIVE 208 53 12 60 11 NC_009009:SSA_0490|5end_Cobalamin_5'-phosphate_synthase,_putative_490236..490466_POSITIVE 205 57 19 57 22 NC_009009:SSA_1277|5end_D-alanyl-D-alanine_carboxypeptidase_1299216..1299446_NEGATIVE 204 107 69 60 23 NC_009009:SSA_0675|5end_Exodeoxyribonuclease_VII_small_subunit,_putative_658389..658619_POSITIVE 201 93 51 213 177 NC_009009:SSA_1613|5end_hypothetical_protein_1616975..1617205_NEGATIVE 200 110 77 169 142 NC_009009:SSA_2109|5end_Elongation_factor_G,_putative_2114868..2115098_NEGATIVE 200 80 41 81 29 NC_009009:SSA_1079|5end_hypothetical_protein_1096385..1096615_POSITIVE 199 59 11 120 75 NC_009009:SSA_1776|5end_Potassium_uptake_protein,_Trk_family,_putative_1762639..1762869_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 56 12 151 110 NC_009009:SSA_1184|3end_DNA_topoisomerase_I,_putative_1211512..1211662_NEGATIVE 239 78 33 147 109 NC_009009:SSA_0644|3end_DNA_Protection_System,_DNA-binding_ferritin-like_protein_(oxidative_damage_protectant),_putative_630765..630915_POSITIVE 238 106 61 82 36 NC_009009:SSA_1396|3end_hypothetical_protein_1409790..1409940_NEGATIVE 227 68 34 133 104 NC_009009:SSA_1868|3end_ABC-type_arginine/histidine_transport_system,_permease_component,_putative_1863096..1863246_NEGATIVE 220 59 17 140 106 NC_009009:SSA_1166|3end_hypothetical_protein_1192350..1192500_POSITIVE 217 110 69 130 93 NC_009009:SSA_0244|3end_hypothetical_protein_239170..239320_POSITIVE 216 60 19 62 33 NC_009009:SSA_0184|3end_Competence_protein_ComYA,_putative_189177..189327_POSITIVE 211 66 25 150 112 NC_009009:SSA_0406|3end_hypothetical_protein_402196..402346_NEGATIVE 209 87 45 115 64 NC_009009:SSA_2010|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_2011296..2011446_NEGATIVE 208 96 65 128 97 NC_009009:SSA_2158|3end_Methyltransferase,_putative_2158421..2158571_NEGATIVE 208 53 12 63 14 NC_009009:SSA_0489|3end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_490319..490469_POSITIVE 206 50 1 121 72 NC_009009:SSA_2373|3end_DNA_replication_and_repair_protein_recF,_putative_2375382..2375532_POSITIVE 204 87 41 119 58 NC_009009:SSA_0741|3end_Acetylornithine_deacetylase/Succinyl-diaminopimelate_desuccinylase,_putative_725190..725340_POSITIVE 204 107 69 82 45 NC_009009:SSA_0674|3end_Exodeoxyribonuclease_VII_large_subunit,_putative_658491..658641_POSITIVE 200 80 41 67 15 NC_009009:SSA_1078|3end_hypothetical_protein_1096451..1096601_POSITIVE 199 59 11 114 69 NC_009009:SSA_1775|3end_Potassium_uptake_protein,_Trk_family,_putative_1762713..1762863_POSITIVE 199 46 3 90 44 NC_009009:SSA_1624|3end_hypothetical_protein_1626497..1626647_POSITIVE 199 80 37 86 49 NC_009009:SSA_0493|3end_ABC-type_dipeptide/nickel_transport_system,_periplasmic_component,_putative_494483..494633_POSITIVE 198 67 28 62 6 NC_009009:SSA_0910|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_922161..922311_POSITIVE 196 50 8 114 76 NC_009009:SSA_1808|3end_hypothetical_protein_1791394..1791544_NEGATIVE