Origin IGS: taggaaaaattatcctattactctaaggtgtttgctactttcctcactaggtttgaaaatggaggcagcaaactgtatagataaaagaagatttgagacaaaagtttcaaatctttttcttgactctgaccttagaggagggtgtatactggtggaaattagaaaaggagattacc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggtaatctccttttctaatttccaccagtatacaccctcctctaaggtcagagtcaagaaaaagatttgaaacttttgtctcaaatcttcttttatctatacagtttgctgcctccattttcaaacctagtgaggaaagtagcaaacaccttagagtaataggataatttttccta Mask Tandem Repeat Region ================================================ taggaaaaattatcctattactctaaggtgtttgctactttcctcactaggtttgaaaatggaggcagcaaactgtatagataaaagaagatttgagacaaaagtttcaaatctttttcttgactctgaccttagaggagggtgtatactggtggaaattagaaaaggagattacc Find is-nt database================================================ Query_seq: SSA_0366:SSA_0367|SSA_0366:SSA_0367:hypothetical protein:hypothetical protein:->->:358273..358448 176 taggaaaaattatcctattactctaaggtgtttgctactttcctcactaggtttgaaaatggaggcagcaaactgtatagataaaagaagatttgagacaaaagtttcaaatctttttcttgactctgaccttagaggagggtgtatactggtggaaattagaaaaggagattacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0366:SSA_0367|SSA_0366:SSA_0367:hypothetical protein:hypothetical protein:->->:358273..358448 176 taggaaaaattatcctattactctaaggtgtttgctactttcctcactaggtttgaaaatggaggcagcaaactgtatagataaaagaagatttgagacaaaagtttcaaatctttttcttgactctgaccttagaggagggtgtatactggtggaaattagaaaaggagattacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0366:SSA_0367|SSA_0366:SSA_0367:hypothetical protein:hypothetical protein:->->:358273..358448 176 taggaaaaattatcctattactctaaggtgtttgctactttcctcactaggtttgaaaatggaggcagcaaactgtatagataaaagaagatttgagacaaaagtttcaaatctttttcttgactctgaccttagaggagggtgtatactggtggaaattagaaaaggagattacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taggaaaaattatcctattactctaaggtgtttgctactttcctcactaggtttgaaaatggaggcagcaaactgtatagataaaagaagatttgagacaaaagtttcaaatctttttcttgactctgaccttagaggagggtgtatactggtggaaattagaaaaggagattacc Predict ORF larger than 30AA ================================================ Protein_Len: 53 Strand: + Start: 17 End: 175 ................ M T L R C L L L S S L G L K M E A A N C I D K R R F E T K V S N L F L D S D L R G G C I L V E I R K G D Y . Protein_Len: 32 Strand: + Start: 81 End: 176 ................................................................................ M K E D L R Q K F Q I F F L T L T L E E G V Y W W K L E K E I T Protein_Len: 30 Strand: - Start: 21 End: 110 .................... E L T N A V K R V L N S F P P L L S Y L Y F F I Q S L L K M .................................................................. Protein_Len: 49 Strand: - Start: 13 End: 159 ............ G I V R L H K S S E E S P K F I S A A F Q I S L L L N S V F T E F R K R S E S R L P P H I S T S M ................. taggaaaaattatcctattactctaaggtgtttgctactttcctcactaggtttgaaaatggaggcagcaaactgtatagataaaagaagatttgagacaaaagtttcaaatctttttcttgactctgaccttagaggagggtgtatactggtggaaattagaaaaggagattacc 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: 81 Start: 31 End: 60 ..............................TTTGCTACTTTCCTCACTAGGTTTGAAAAT.................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taggaaaaattatcctattactctaaggtgtttgctactttcctcactaggtttgaaaatggaggcagcaaactgtatagataaaagaagatttgagacaaaagtttcaaatctttttcttgactctgaccttagaggagggtgtatactggtggaaattagaaaaggagattacc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -9.0 Tail_Score: -5.12068 Start: 90 End: 113 Full_Region: GTATAGATAAAAGAA GATTTGAGAC AAAA GTTTCAAATC TTTTTCTTGACTCTG .........................................................................................GATTTGAGACAAAAGTTTCAAATC............................................................... TransTerm Strand: - Conf: 76 HP_score: -6.8 Tail_Score: -4.41422 Start: 90 End: 113 Full_Region: cagagtcaagaaaaa gatttgaaac tttt gtctcaaatc ttcttttatctatac .........................................................................................gatttgaaacttttgtctcaaatc............................................................... Find igs database================================================ Query_seq: SSA_0366:SSA_0367|SSA_0366:SSA_0367:hypothetical protein:hypothetical protein:->->:358273..358448 176 taggaaaaattatcctattactctaaggtgtttgctactttcctcactaggtttgaaaatggaggcagcaaactgtatagataaaagaagatttgagacaaaagtttcaaatctttttcttgactctgaccttagaggagggtgtatactggtggaaattagaaaaggagattacc Intra-Species Hit: Count: 1 Min: 1 Max: 176 Len: 176 Subject: NC_009009_SSA_0366_SSA_0367|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[358273,358448]|176 HSP 1 e-value: 2.0E-95 bit: 349.0 Len: 176 Query Start:1 Query End:176 Subject Strand: POSITIVE Subject Start: 1 Subject End: 176 taggaaaaattatcctattactctaaggtgtttgctactttcctcactaggtttgaaaatggaggcagcaaactgtatagataaaagaagatttgagacaaaagtttcaaatctttttcttgactctgaccttagaggagggtgtatactggtggaaattagaaaaggagattacc taggaaaaattatcctattactctaaggtgtttgctactttcctcactaggtttgaaaatggaggcagcaaactgtatagataaaagaagatttgagacaaaagtttcaaatctttttcttgactctgaccttagaggagggtgtatactggtggaaattagaaaaggagattacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGAAAAAUUAUCCUAUUACUCUAAGGUGUUUGCUACUUUCCUCACUAGGUUUGAAAAUGGAGGCAGCAAACUGUAUAGAUAAAAGAAGAUUUGAGACAAAAGUUUCAAAUCUUUUUCUUGACUCUGACCUUAGAGGAGGGUGUAUACUGGUGGAAAUUAGAAAAGGAGAUUACC ..((......((((((....((((((((((((((((.(((((.(((.......)))....))))).)))))))....((((((((((((((((((((((....))))))))))))))).)))..))))))))))))).))))))....(((((....)))))............)) (-51.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUAAUCUCCUUUUCUAAUUUCCACCAGUAUACACCCUCCUCUAAGGUCAGAGUCAAGAAAAAGAUUUGAAACUUUUGUCUCAAAUCUUCUUUUAUCUAUACAGUUUGCUGCCUCCAUUUUCAAACCUAGUGAGGAAAGUAGCAAACACCUUAGAGUAAUAGGAUAAUUUUUCCUA ((......)).............................((((((((..(((...((((...((((((((.((....)).))))))))))))...))).....(((((((((.(((....(((.......))))))..))))))))).))))))))...(((((.......))))) (-42.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 77 38 50 11 NC_009009:SSA_1544|5end_Conserved_uncharacterized_protein_1548796..1549026_NEGATIVE 279 69 21 224 179 NC_009009:SSA_1850|5end_DNA-directed_RNA_polymerase,_subunit_K/omega,_putative_1846024..1846254_NEGATIVE 279 77 32 194 147 NC_009009:SSA_1462|5end_Prephenate_dehydratase,_putative_1469767..1469997_NEGATIVE 265 155 111 231 185 NC_009009:SSA_0079|5end_ROK_family_protein,_putative_82855..83085_POSITIVE 264 68 27 67 26 NC_009009:SSA_0535|5end_Propanediol_utilization:_dehydratase,_medium_subunit,_putative_530643..530873_POSITIVE 264 70 21 50 2 NC_009009:SSA_0521|5end_Ethanolamine_utilization_protein_EutL,_putative_520392..520622_POSITIVE 264 66 25 216 164 NC_009009:SSA_0214|5end_Single-strand_DNA-binding_protein_(conjugal_DNA-protein_transfer_system),_putative_210215..210445_POSITIVE 262 70 26 60 7 NC_009009:SSA_2264|5end_hypothetical_protein_2261757..2261987_NEGATIVE 262 67 24 203 162 NC_009009:SSA_0883|5end_Glycerate_kinase,_putative_877560..877790_POSITIVE 261 140 96 115 71 NC_009009:SSA_1208|5end_23S_rRNA_pseudouridine_synthase,_putative_1233185..1233415_NEGATIVE 261 76 39 146 98 NC_009009:SSA_0056|5end_Phosphotransferase_system_sugar-specific_EIID_component,_putative_59926..60156_POSITIVE 259 169 134 203 151 NC_009009:SSA_1979|5end_Alkaline-shock_protein,_putative_1974301..1974531_NEGATIVE 259 156 111 150 101 NC_009009:SSA_1888|5end_hypothetical_protein_1886025..1886255_NEGATIVE 255 157 111 135 69 NC_009009:SSA_1264|5end_hypothetical_protein_1290042..1290272_NEGATIVE 249 159 115 192 144 NC_009009:SSA_1790|5end_SpoU_rRNA_Methylase_family_protein,_putative_1773641..1773871_NEGATIVE 247 69 21 85 42 NC_009009:SSA_1428|5end_hypothetical_protein_1436348..1436578_NEGATIVE 246 90 50 217 161 NC_009009:SSA_1613|5end_hypothetical_protein_1616975..1617205_NEGATIVE 246 70 21 151 98 NC_009009:SSA_0497|5end_Nickel_ABC_transporter,_putative_496922..497152_POSITIVE 245 55 13 116 77 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 245 66 21 225 174 NC_009009:SSA_1165|5end_Transcriptional_regulator,_GntR_family,_putative_1191087..1191317_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 69 22 149 96 NC_009009:SSA_0085|3end_V-type_sodium_ATPase,_subunit_I,_putative_87785..87935_POSITIVE 276 70 26 125 81 NC_009009:SSA_1776|3end_Potassium_uptake_protein,_Trk_family,_putative_1764158..1764308_POSITIVE 264 68 27 55 14 NC_009009:SSA_0533|3end_Glycerol_dehydratase_large_subunit_pduC,_putative_530711..530861_POSITIVE 261 140 96 118 74 NC_009009:SSA_1209|3end_Inorganic_polyphosphate/ATP-NAD_kinase,_putative_1233182..1233332_NEGATIVE 259 169 134 60 8 NC_009009:SSA_1980|3end_50S_ribosomal_protein_L28,_putative_1974444..1974594_NEGATIVE 257 155 111 68 25 NC_009009:SSA_0293|3end_hypothetical_protein_287356..287506_NEGATIVE 256 45 1 81 29 NC_009009:SSA_0539|3end_PduO_protein,_putative_534867..535017_POSITIVE 255 109 68 84 36 NC_009009:SSA_1206|3end_A/G-specific_adenine_glycosylase,_putative_1230071..1230221_NEGATIVE 252 148 104 141 99 NC_009009:SSA_0611|3end_HtpX_protease,_putative_600515..600665_POSITIVE 247 69 21 78 35 NC_009009:SSA_1429|3end_hypothetical_protein_1436355..1436505_NEGATIVE 245 55 13 115 76 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 243 69 33 141 106 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 241 80 44 74 40 NC_009009:SSA_0425|3end_Glycosyltransferase,_putative_422230..422380_NEGATIVE 240 160 118 69 31 NC_009009:SSA_0818|3end_SPX_domain-like_protein,_putative_800486..800636_POSITIVE 238 77 34 49 4 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 238 66 31 41 1 NC_009009:SSA_0292|3end_Transcriptional_regulator,_AraC_family_(arabinose_operon_control),_putative_287262..287412_POSITIVE 237 141 101 138 80 NC_009009:SSA_2142|3end_Argininosuccinate_synthase,_putative_2142216..2142366_NEGATIVE 237 162 123 133 97 NC_009009:SSA_0454|3end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_456050..456200_NEGATIVE 236 135 95 42 10 NC_009009:SSA_0912|3end_Phenylalanyl-tRNA_synthetase_alpha_chain,_putative_924229..924379_POSITIVE 236 70 26 143 95 NC_009009:SSA_0578|3end_Nicotinate-nucleotide_adenylyltransferase,_putative_572303..572453_POSITIVE