Origin IGS: tttacctcctattttattttatagggaaaggcagatttccccaaatttaagtatagtatgagccaacatatttgtcaatattataatttattgattatattaattatgtttttgtacaataaaagcagctcttatgaactgcttttatatatttagttagattctaaagtttgttttgatattagattttatattattaattatatatatccattttgttgttttttgtctaaaaaatactttagtataagat .........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 atcttatactaaagtattttttagacaaaaaacaacaaaatggatatatataattaataatataaaatctaatatcaaaacaaactttagaatctaactaaatatataaaagcagttcataagagctgcttttattgtacaaaaacataattaatataatcaataaattataatattgacaaatatgttggctcatactatacttaaatttggggaaatctgcctttccctataaaataaaataggaggtaaa Mask Tandem Repeat Region ================================================ tttacctcctattttattttatagggaaaggcagatttccccaaatttaagtatagtatgagccaacatatttgtcaatattataatttattgattatattaattatgtttttgtacaataaaagcagctcttatgaactgcttttatatatttagttagattctaaagtttgttttgatattagattttatattattaattatatatatccattttgttgttttttgtctaaaaaatactttagtataagat Find is-nt database================================================ Query_seq: SSA_2320:SSA_2321|SSA_2320:SSA_2321:hypothetical protein:Cation (Co/Zn/Cd) efflux protein, putative:<-<-:2325887..2326139 253 tttacctcctattttattttatagggaaaggcagatttccccaaatttaagtatagtatgagccaacatatttgtcaatattataatttattgattatattaattatgtttttgtacaataaaagcagctcttatgaactgcttttatatatttagttagattctaaagtttgttttgatattagattttatattattaattatatatatccattttgttgttttttgtctaaaaaatactttagtataagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2320:SSA_2321|SSA_2320:SSA_2321:hypothetical protein:Cation (Co/Zn/Cd) efflux protein, putative:<-<-:2325887..2326139 253 tttacctcctattttattttatagggaaaggcagatttccccaaatttaagtatagtatgagccaacatatttgtcaatattataatttattgattatattaattatgtttttgtacaataaaagcagctcttatgaactgcttttatatatttagttagattctaaagtttgttttgatattagattttatattattaattatatatatccattttgttgttttttgtctaaaaaatactttagtataagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2320:SSA_2321|SSA_2320:SSA_2321:hypothetical protein:Cation (Co/Zn/Cd) efflux protein, putative:<-<-:2325887..2326139 253 tttacctcctattttattttatagggaaaggcagatttccccaaatttaagtatagtatgagccaacatatttgtcaatattataatttattgattatattaattatgtttttgtacaataaaagcagctcttatgaactgcttttatatatttagttagattctaaagtttgttttgatattagattttatattattaattatatatatccattttgttgttttttgtctaaaaaatactttagtataagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttacctcctattttattttatagggaaaggcagatttccccaaatttaagtatagtatgagccaacatatttgtcaatattataatttattgattatattaattatgtttttgtacaataaaagcagctcttatgaactgcttttatatatttagttagattctaaagtttgttttgatattagattttatattattaattatatatatccattttgttgttttttgtctaaaaaatactttagtataagat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 58 End: 153 ......................................................... M S Q H I C Q Y Y N L L I I L I M F L Y N K S S S Y E L L L Y I .................................................................................................... tttacctcctattttattttatagggaaaggcagatttccccaaatttaagtatagtatgagccaacatatttgtcaatattataatttattgattatattaattatgtttttgtacaataaaagcagctcttatgaactgcttttatatatttagttagattctaaagtttgttttgatattagattttatattattaattatatatatccattttgttgttttttgtctaaaaaatactttagtataagat 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: 90 Start: 50 End: 79 .................................................ATTGACAAATATGTTGGCTCATACTATACT.............................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 16 End: 45 ...............TTTGGGGAAATCTGCCTTTCCCTATAAAAT................................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 175 End: 204 ..............................................................................................................................................................................TTTGATATTAGATTTTATATTATTAATTAT................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttacctcctattttattttatagggaaaggcagatttccccaaatttaagtatagtatgagccaacatatttgtcaatattataatttattgattatattaattatgtttttgtacaataaaagcagctcttatgaactgcttttatatatttagttagattctaaagtttgttttgatattagattttatattattaattatatatatccattttgttgttttttgtctaaaaaatactttagtataagat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -7.4 Tail_Score: -3.56675 Start: 118 End: 149 Full_Region: ATTATGTTTTTGTAC AATAAAAGCAGCTC TTAT GAACTGCTTTTATA TATTTAGTTAGATTC .....................................................................................................................AATAAAAGCAGCTCTTATGAACTGCTTTTATA........................................................................................................ TransTerm Strand: + Conf: 81 HP_score: -10.0 Tail_Score: -3.3487 Start: 120 End: 147 Full_Region: TATGTTTTTGTACAA TAAAAGCAGCTC TTAT GAACTGCTTTTA TATATTTAGTTAGAT .......................................................................................................................TAAAAGCAGCTCTTATGAACTGCTTTTA.......................................................................................................... TransTerm Strand: - Conf: 90 HP_score: -12.2 Tail_Score: -3.28924 Start: 120 End: 147 Full_Region: atctaactaaatata taaaagcagttc ataa gagctgctttta ttgtacaaaaacata .......................................................................................................................taaaagcagttcataagagctgctttta.......................................................................................................... TransTerm Strand: + Conf: 74 HP_score: -5.5 Tail_Score: -4.74917 Start: 125 End: 142 Full_Region: TTTTGTACAATAAAA GCAGCTC TTAT GAACTGC TTTTATATATTTAGT ............................................................................................................................GCAGCTCTTATGAACTGC............................................................................................................... TransTerm Strand: - Conf: 84 HP_score: -7.7 Tail_Score: -4.77165 Start: 125 End: 142 Full_Region: actaaatatataaaa gcagttc ataa gagctgc ttttattgtacaaaa ............................................................................................................................gcagttcataagagctgc............................................................................................................... Find igs database================================================ Query_seq: SSA_2320:SSA_2321|SSA_2320:SSA_2321:hypothetical protein:Cation (Co/Zn/Cd) efflux protein, putative:<-<-:2325887..2326139 253 tttacctcctattttattttatagggaaaggcagatttccccaaatttaagtatagtatgagccaacatatttgtcaatattataatttattgattatattaattatgtttttgtacaataaaagcagctcttatgaactgcttttatatatttagttagattctaaagtttgttttgatattagattttatattattaattatatatatccattttgttgttttttgtctaaaaaatactttagtataagat Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: NC_009009_SSA_2320_SSA_2321|hypothetical protein:Cation (Co/Zn/Cd) efflux protein, putative|NEGATIVE:NEGATIVE|[2325887,2326139]|253 HSP 1 e-value: 6.0E-75 bit: 281.0 Len: 142 Query Start:1 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 142 tttacctcctattttattttatagggaaaggcagatttccccaaatttaagtatagtatgagccaacatatttgtcaatattataatttattgattatattaattatgtttttgtacaataaaagcagctcttatgaactgc............................................................................................................... tttacctcctattttattttatagggaaaggcagatttccccaaatttaagtatagtatgagccaacatatttgtcaatattataatttattgattatattaattatgtttttgtacaataaaagcagctcttatgaactgc............................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUACCUCCUAUUUUAUUUUAUAGGGAAAGGCAGAUUUCCCCAAAUUUAAGUAUAGUAUGAGCCAACAUAUUUGUCAAUAUUAUAAUUUAUUGAUUAUAUUAAUUAUGUUUUUGUACAAUAAAAGCAGCUCUUAUGAACUGC .......................((((((......))))))........(((...(((.((((....((((..(((((((........))))))).))))......(((((((((...))))))))))))).)))..))).. (-24.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAGUUCAUAAGAGCUGCUUUUAUUGUACAAAAACAUAAUUAAUAUAAUCAAUAAAUUAUAAUAUUGACAAAUAUGUUGGCUCAUACUAUACUUAAAUUUGGGGAAAUCUGCCUUUCCCUAUAAAAUAAAAUAGGAGGUAAA (((((((....)))))))........(((..........((((((((.((((((........))))))....))))))))......((((.........((((((((......)))))))).........))))...))).. (-27.87) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 842 70 21 161 112 NC_009009:SSA_2320|5end_hypothetical_protein_2325796..2326026_NEGATIVE 286 42 1 143 95 NC_009009:SSA_1611|5end_Era-like_GTP-binding_protein,_putative_1616032..1616262_NEGATIVE 266 62 22 96 56 NC_009009:SSA_2358|5end_hypothetical_protein_2360497..2360727_NEGATIVE 256 42 1 135 96 NC_009009:SSA_2391|5end_30S_ribosomal_protein_S14,_putative_114252..114482_POSITIVE 242 36 1 43 11 NC_009009:SSA_1760|5end_hypothetical_protein_1747284..1747514_NEGATIVE 242 50 5 70 28 NC_009009:SSA_0427|5end_DNA-binding_transcriptional_activator,_SARP_family,_putative_424497..424727_POSITIVE 237 63 21 75 32 NC_009009:SSA_1126|5end_Thiamine_biosynthesis_lipoprotein,_putative_1151522..1151752_NEGATIVE 230 48 4 202 156 NC_009009:SSA_2064|5end_hypothetical_protein_2065031..2065261_NEGATIVE 230 60 18 231 192 NC_009009:SSA_1971|5end_hypothetical_protein_1967167..1967397_POSITIVE 225 35 5 126 96 NC_009009:SSA_1695|5end_Transcriptional_antiterminator,_BglG/SacY_family_(induction_of_sugar_metabolism),_putative_1688010..1688240_NEGATIVE 223 64 21 196 155 NC_009009:SSA_1643|5end_hypothetical_protein_1645269..1645499_NEGATIVE 221 38 1 129 87 NC_009009:SSA_1500|5end_Translation_initiation_factor_IF-3,_putative_1504921..1505151_NEGATIVE 221 43 7 51 12 NC_009009:SSA_0238|5end_hypothetical_protein_232481..232711_POSITIVE 215 35 1 59 23 NC_009009:SSA_1757|5end_hypothetical_protein_1745890..1746120_NEGATIVE 215 49 4 157 97 NC_009009:SSA_1179|5end_Carbamoylphosphate_synthase_large_subunit_/_biotin_carboxylase,_putative_1207806..1208036_NEGATIVE 214 67 21 161 104 NC_009009:SSA_1085|5end_Dihydrodipicolinate_reductase,_putative_1102564..1102794_POSITIVE 213 42 5 197 146 NC_009009:SSA_1453|5end_hypothetical_protein_1460208..1460438_NEGATIVE 213 70 23 197 137 NC_009009:SSA_0796|5end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_777085..777315_POSITIVE 212 76 50 102 75 NC_009009:SSA_0401|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_398462..398692_POSITIVE 211 65 21 90 55 NC_009009:SSA_2215|5end_Oligosaccharide_repeat_unit_polymerase_Wzy,_putative_2217157..2217387_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 42 1 76 28 NC_009009:SSA_1612|3end_Diacylglycerol_kinase,_putative_1616099..1616249_NEGATIVE 256 42 1 117 78 NC_009009:SSA_0119|3end_50S_ribosomal_protein_L5,_putative_114314..114464_POSITIVE 224 46 6 127 77 NC_009009:SSA_0599|3end_hypothetical_protein_589007..589157_POSITIVE 217 78 33 144 88 NC_009009:SSA_1740|3end_hypothetical_protein_1727081..1727231_NEGATIVE 215 49 4 144 84 NC_009009:SSA_1180|3end_hypothetical_protein_1207819..1207969_NEGATIVE 214 67 21 120 63 NC_009009:SSA_1084|3end_Conserved_uncharacterized_protein_1102603..1102753_POSITIVE 213 42 5 150 99 NC_009009:SSA_1454|3end_hypothetical_protein_1460255..1460405_NEGATIVE 213 70 23 97 37 NC_009009:SSA_0795|3end_hypothetical_protein_777065..777215_POSITIVE 211 65 21 90 55 NC_009009:SSA_2216|3end_LPS_biosynthesis_protein,_putative_2217157..2217307_NEGATIVE 210 41 6 62 26 NC_009009:SSA_2146|3end_Metallo-beta-lactamase,_putative_2146732..2146882_NEGATIVE 210 63 25 135 99 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE 207 65 30 73 40 NC_009009:SSA_0495|3end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_496036..496186_POSITIVE 206 53 15 52 16 NC_009009:SSA_0927|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_936740..936890_POSITIVE 205 37 1 148 97 NC_009009:SSA_0075|3end_ABC_sugar_transporter,_permease_protein,_putative_79927..80077_POSITIVE 204 60 17 123 80 NC_009009:SSA_2257|3end_DNA_mismatch_repair_protein,_putative_2251241..2251391_NEGATIVE 202 62 21 58 18 NC_009009:SSA_2292|3end_DNA_segregation_ATPase_FtsK/SpoIIIE-like_protein,_putative_2295353..2295503_POSITIVE 201 41 6 68 41 NC_009009:SSA_1634|3end_Heme_utilization/adhesion_exoprotein,_putative_1635602..1635752_NEGATIVE 199 44 5 149 87 NC_009009:SSA_1684|3end_Histidine_kinase,_putative_1677426..1677576_NEGATIVE 197 66 23 67 26 NC_009009:SSA_0210|3end_hypothetical_protein_208124..208274_POSITIVE 196 66 28 67 17 NC_009009:SSA_0625|3end_Phosphopantetheine_adenylyltransferase_616182..616332_POSITIVE