Origin IGS: agttgtcaaagagcgtaagctctttttcttttgtctaattcagacctgccagaggtcaaattcttgcaatctcaagcattttcgggtatcatataagaaaatccagactgtaagaaaggagtctccc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gggagactcctttcttacagtctggattttcttatatgatacccgaaaatgcttgagattgcaagaatttgacctctggcaggtctgaattagacaaaagaaaaagagcttacgctctttgacaact Mask Tandem Repeat Region ================================================ agttgtcaaagagcgtaagctctttttcttttgtctaattcagacctgccagaggtcaaattcttgcaatctcaagcattttcgggtatcatataagaaaatccagactgtaagaaaggagtctccc Find is-nt database================================================ Query_seq: SSA_1832:SSA_1833|SSA_1832:SSA_1833:hypothetical protein:hypothetical protein:->->:1822675..1822801 127 agttgtcaaagagcgtaagctctttttcttttgtctaattcagacctgccagaggtcaaattcttgcaatctcaagcattttcgggtatcatataagaaaatccagactgtaagaaaggagtctccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1832:SSA_1833|SSA_1832:SSA_1833:hypothetical protein:hypothetical protein:->->:1822675..1822801 127 agttgtcaaagagcgtaagctctttttcttttgtctaattcagacctgccagaggtcaaattcttgcaatctcaagcattttcgggtatcatataagaaaatccagactgtaagaaaggagtctccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1832:SSA_1833|SSA_1832:SSA_1833:hypothetical protein:hypothetical protein:->->:1822675..1822801 127 agttgtcaaagagcgtaagctctttttcttttgtctaattcagacctgccagaggtcaaattcttgcaatctcaagcattttcgggtatcatataagaaaatccagactgtaagaaaggagtctccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agttgtcaaagagcgtaagctctttttcttttgtctaattcagacctgccagaggtcaaattcttgcaatctcaagcattttcgggtatcatataagaaaatccagactgtaagaaaggagtctccc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 38 End: 127 ..................................... M Q T C Q R S N S C N L K H F R V S Y K K I Q T V R K E S P agttgtcaaagagcgtaagctctttttcttttgtctaattcagacctgccagaggtcaaattcttgcaatctcaagcattttcgggtatcatataagaaaatccagactgtaagaaaggagtctccc 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: 88 Start: 63 End: 92 ..............................................................CTTGCAATCTCAAGCATTTTCGGGTATCAT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agttgtcaaagagcgtaagctctttttcttttgtctaattcagacctgccagaggtcaaattcttgcaatctcaagcattttcgggtatcatataagaaaatccagactgtaagaaaggagtctccc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1832:SSA_1833|SSA_1832:SSA_1833:hypothetical protein:hypothetical protein:->->:1822675..1822801 127 agttgtcaaagagcgtaagctctttttcttttgtctaattcagacctgccagaggtcaaattcttgcaatctcaagcattttcgggtatcatataagaaaatccagactgtaagaaaggagtctccc Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: NC_009009_SSA_1832_SSA_1833|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1822675,1822801]|127 HSP 1 e-value: 2.0E-66 bit: 252.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 agttgtcaaagagcgtaagctctttttcttttgtctaattcagacctgccagaggtcaaattcttgcaatctcaagcattttcgggtatcatataagaaaatccagactgtaagaaaggagtctccc agttgtcaaagagcgtaagctctttttcttttgtctaattcagacctgccagaggtcaaattcttgcaatctcaagcattttcgggtatcatataagaaaatccagactgtaagaaaggagtctccc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUGUCAAAGAGCGUAAGCUCUUUUUCUUUUGUCUAAUUCAGACCUGCCAGAGGUCAAAUUCUUGCAAUCUCAAGCAUUUUCGGGUAUCAUAUAAGAAAAUCCAGACUGUAAGAAAGGAGUCUCCC ....(..(((((((....)))))))..).........((((.(((((.....)))))...((((((((.(((...(.((((((..(((...)))..)))))).)))).))))))))..))))..... (-31.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGAGACUCCUUUCUUACAGUCUGGAUUUUCUUAUAUGAUACCCGAAAAUGCUUGAGAUUGCAAGAAUUUGACCUCUGGCAGGUCUGAAUUAGACAAAAGAAAAAGAGCUUACGCUCUUUGACAACU .((((......(((((.(((((((.((((((.............)))))).)...)))))).)))))......)))).....(((((...)))))....(..(((((((....)))))))..).... (-28.02) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 56 15 203 157 NC_009009:SSA_1085|5end_Dihydrodipicolinate_reductase,_putative_1102564..1102794_POSITIVE 313 89 41 54 3 NC_009009:SSA_0593|5end_Rhodanese-like_sulfurtransferase,_putative_584485..584715_POSITIVE 303 69 33 210 167 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 295 88 46 63 29 NC_009009:SSA_0744|5end_S-adenosylmethio_nine:tRNA-ribosyltransferase-isomerase_(queuine_synthetase),_putative_726804..727034_NEGATIVE 295 90 45 214 160 NC_009009:SSA_0492|5end_NADH-dependent_flavin_oxidoreductase,_putative_491588..491818_POSITIVE 292 69 21 196 142 NC_009009:SSA_0611|5end_HtpX_protease,_putative_599539..599769_POSITIVE 292 50 2 134 78 NC_009009:SSA_0005|5end_GTP-binding_protein,_putative_3821..4051_POSITIVE 291 90 41 98 46 NC_009009:SSA_1610|5end_hypothetical_protein_1614909..1615139_NEGATIVE 289 60 17 134 97 NC_009009:SSA_1932|5end_Biotin_carboxylase,_putative_1920874..1921104_NEGATIVE 288 90 42 100 49 NC_009009:SSA_0910|5end_ABC-type_multidrug_transporter,_ATPase_component,_putative_921356..921586_POSITIVE 288 72 32 186 146 NC_009009:SSA_0077|5end_Oxidoreductase,_putative_80738..80968_POSITIVE 283 86 48 172 129 NC_009009:SSA_2339|5end_Microcin_C7_resistance_protein,_putative_2340456..2340686_POSITIVE 281 66 21 154 105 NC_009009:SSA_0883|5end_Glycerate_kinase,_putative_877560..877790_POSITIVE 278 83 41 101 49 NC_009009:SSA_0383|5end_Beta-glucosidase,_putative_374534..374764_POSITIVE 277 88 44 147 98 NC_009009:SSA_0368|5end_hypothetical_protein_359274..359504_POSITIVE 274 67 21 222 179 NC_009009:SSA_1113|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_domain_and_a_winged-helix_DNA-binding_domains),_putative_1139742..1139972_POSITIVE 272 51 12 132 87 NC_009009:SSA_0590|5end_hypothetical_protein_582144..582374_POSITIVE 271 53 12 225 178 NC_009009:SSA_1955|5end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1952602..1952832_NEGATIVE 271 97 54 210 172 NC_009009:SSA_1114|5end_Histidine_kinase,_putative_1140437..1140667_POSITIVE 271 59 13 135 88 NC_009009:SSA_0896|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_887705..887935_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 325 89 41 119 50 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 319 55 13 149 107 NC_009009:SSA_1686|3end_hypothetical_protein_1680470..1680620_POSITIVE 310 58 13 143 102 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 295 88 46 53 19 NC_009009:SSA_0745|3end_hypothetical_protein_726814..726964_NEGATIVE 289 60 17 115 78 NC_009009:SSA_1933|3end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase,_putative_1920893..1921043_NEGATIVE 288 72 32 128 88 NC_009009:SSA_0076|3end_ABC_sugar_transporter,_permease_protein,_putative_80760..80910_POSITIVE 284 49 1 105 64 NC_009009:SSA_0812|3end_hypothetical_protein_794434..794584_POSITIVE 281 66 21 144 95 NC_009009:SSA_0882|3end_Phosphoserine_phosphatase,_putative_877630..877780_POSITIVE 278 48 1 121 60 NC_009009:SSA_0141|3end_Copper_chaperone,_putative_137191..137341_POSITIVE 277 57 20 141 101 NC_009009:SSA_2388|3end_hypothetical_protein_2031667..2031817_NEGATIVE 277 88 44 84 35 NC_009009:SSA_0367|3end_hypothetical_protein_359291..359441_POSITIVE 274 67 21 138 95 NC_009009:SSA_1112|3end_Cell_wall_surface_anchor_family_protein,_putative_1139738..1139888_POSITIVE 272 51 12 115 70 NC_009009:SSA_0589|3end_Acetylornithine_deacetylase/succinyl-diaminopimelate_desuccinylase_(M20/M25/M40_family_peptidase),_putative_582207..582357_POSITIVE 271 59 13 113 66 NC_009009:SSA_0895|3end_ATP-binding_cassette_transporter-like_protein,_putative_887763..887913_POSITIVE 270 85 45 112 65 NC_009009:SSA_1680|3end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1673200..1673350_NEGATIVE 270 67 25 49 5 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 267 67 31 38 1 NC_009009:SSA_2007|3end_Chaperone_protein_dnaK/HSP70,_putative_2007443..2007593_NEGATIVE 265 50 2 100 50 NC_009009:SSA_1230|3end_Conserved_uncharacterized_protein_1252612..1252762_NEGATIVE 264 58 11 140 86 NC_009009:SSA_2343|3end_hypothetical_protein_2343703..2343853_NEGATIVE 264 50 3 118 74 NC_009009:SSA_1679|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1672183..1672333_NEGATIVE