Origin IGS: cctttcttccattttcataaacctcatggacaggtactacatctgtctttttgtttacatttattctgcaacgaaatcttttaaatatgatacaataataacagattataaacggacaagggcggcagagtaatcttgccatgttgttcgctagatgaggagaagctg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cagcttctcctcatctagcgaacaacatggcaagattactctgccgcccttgtccgtttataatctgttattattgtatcatatttaaaagatttcgttgcagaataaatgtaaacaaaaagacagatgtagtacctgtccatgaggtttatgaaaatggaagaaagg Mask Tandem Repeat Region ================================================ cctttcttccattttcataaacctcatggacaggtactacatctgtctttttgtttacatttattctgcaacgaaatcttttaaatatgatacaataataacagattataaacggacaagggcggcagagtaatcttgccatgttgttcgctagatgaggagaagctg Find is-nt database================================================ Query_seq: SSA_0954:SSA_0955|SSA_0954:SSA_0955:hypothetical protein:Aminopeptidase N, putative:->->:958491..958658 168 cctttcttccattttcataaacctcatggacaggtactacatctgtctttttgtttacatttattctgcaacgaaatcttttaaatatgatacaataataacagattataaacggacaagggcggcagagtaatcttgccatgttgttcgctagatgaggagaagctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0954:SSA_0955|SSA_0954:SSA_0955:hypothetical protein:Aminopeptidase N, putative:->->:958491..958658 168 cctttcttccattttcataaacctcatggacaggtactacatctgtctttttgtttacatttattctgcaacgaaatcttttaaatatgatacaataataacagattataaacggacaagggcggcagagtaatcttgccatgttgttcgctagatgaggagaagctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0954:SSA_0955|SSA_0954:SSA_0955:hypothetical protein:Aminopeptidase N, putative:->->:958491..958658 168 cctttcttccattttcataaacctcatggacaggtactacatctgtctttttgtttacatttattctgcaacgaaatcttttaaatatgatacaataataacagattataaacggacaagggcggcagagtaatcttgccatgttgttcgctagatgaggagaagctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cctttcttccattttcataaacctcatggacaggtactacatctgtctttttgtttacatttattctgcaacgaaatcttttaaatatgatacaataataacagattataaacggacaagggcggcagagtaatcttgccatgttgttcgctagatgaggagaagctg Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 11 End: 130 .......... M F I N L M D R Y Y I C L F V Y I Y S A T K S F K Y D T I I T D Y K R T R A A E ...................................... Protein_Len: 47 Strand: - Start: 2 End: 142 . K R G N E Y V E H V P V V D T K K N V N I R C R F R K F I I C Y Y C I I F P C P R C L L R A M .......................... cctttcttccattttcataaacctcatggacaggtactacatctgtctttttgtttacatttattctgcaacgaaatcttttaaatatgatacaataataacagattataaacggacaagggcggcagagtaatcttgccatgttgttcgctagatgaggagaagctg 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================================================ cctttcttccattttcataaacctcatggacaggtactacatctgtctttttgtttacatttattctgcaacgaaatcttttaaatatgatacaataataacagattataaacggacaagggcggcagagtaatcttgccatgttgttcgctagatgaggagaagctg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0954:SSA_0955|SSA_0954:SSA_0955:hypothetical protein:Aminopeptidase N, putative:->->:958491..958658 168 cctttcttccattttcataaacctcatggacaggtactacatctgtctttttgtttacatttattctgcaacgaaatcttttaaatatgatacaataataacagattataaacggacaagggcggcagagtaatcttgccatgttgttcgctagatgaggagaagctg Intra-Species Hit: Count: 1 Min: 1 Max: 168 Len: 168 Subject: NC_009009_SSA_0954_SSA_0955|hypothetical protein:Aminopeptidase N, putative|POSITIVE:POSITIVE|[958491,958658]|168 HSP 1 e-value: 1.0E-90 bit: 333.0 Len: 168 Query Start:1 Query End:168 Subject Strand: POSITIVE Subject Start: 1 Subject End: 168 cctttcttccattttcataaacctcatggacaggtactacatctgtctttttgtttacatttattctgcaacgaaatcttttaaatatgatacaataataacagattataaacggacaagggcggcagagtaatcttgccatgttgttcgctagatgaggagaagctg cctttcttccattttcataaacctcatggacaggtactacatctgtctttttgtttacatttattctgcaacgaaatcttttaaatatgatacaataataacagattataaacggacaagggcggcagagtaatcttgccatgttgttcgctagatgaggagaagctg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUUUCUUCCAUUUUCAUAAACCUCAUGGACAGGUACUACAUCUGUCUUUUUGUUUACAUUUAUUCUGCAACGAAAUCUUUUAAAUAUGAUACAAUAAUAACAGAUUAUAAACGGACAAGGGCGGCAGAGUAAUCUUGCCAUGUUGUUCGCUAGAUGAGGAGAAGCUG ..((((((((((((.....(((..(((((.((((...(((.(((((((((((((((.....((.((((.......(((..........)))..........)))).)).....))))))))).)))))))))..)))))))))..)))....))))).)))))))... (-40.03) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGCUUCUCCUCAUCUAGCGAACAACAUGGCAAGAUUACUCUGCCGCCCUUGUCCGUUUAUAAUCUGUUAUUAUUGUAUCAUAUUUAAAAGAUUUCGUUGCAGAAUAAAUGUAAACAAAAAGACAGAUGUAGUACCUGUCCAUGAGGUUUAUGAAAAUGGAAGAAAGG ...(((((..((((.....((((..(((((((.((((((((((.(....((((.(((((((..(((((.........(((..........)))......))))))))))))...))))...).)))).))))).).)).)))))..))))))))....)))))..... (-33.06) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 373 160 111 171 125 NC_009009:SSA_2063|5end_Aminopeptidase_PepS,_putative_2064857..2065087_NEGATIVE 305 160 113 192 141 NC_009009:SSA_2035|5end_Conserved_uncharacterized_protein_2040288..2040518_NEGATIVE 297 160 114 153 110 NC_009009:SSA_0339|5end_hypothetical_protein_333950..334180_NEGATIVE 288 152 112 159 111 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 287 160 113 54 14 NC_009009:SSA_0389|5end_hypothetical_protein_384172..384402_POSITIVE 285 160 123 60 18 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 283 48 1 188 132 NC_009009:SSA_0034|5end_hypothetical_protein_39547..39777_POSITIVE 279 154 113 49 6 NC_009009:SSA_1957|5end_Glycosyl_transferase_N-acetylglucosaminyltransferase,_putative_1954670..1954900_NEGATIVE 279 158 113 201 150 NC_009009:SSA_0546|5end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_540852..541082_POSITIVE 278 160 114 62 10 NC_009009:SSA_0794|5end_Zn-dependent_protease,_putative_775896..776126_POSITIVE 276 79 31 135 80 NC_009009:SSA_2363|5end_Phosphoglycolate_phosphatase,_putative_2365632..2365862_POSITIVE 276 153 123 36 2 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 276 140 99 128 86 NC_009009:SSA_0557|5end_hypothetical_protein_551900..552130_POSITIVE 275 157 111 215 168 NC_009009:SSA_1203|5end_hypothetical_protein_1226985..1227215_POSITIVE 273 158 114 200 129 NC_009009:SSA_1367|5end_hypothetical_protein_1383593..1383823_POSITIVE 270 159 120 206 161 NC_009009:SSA_1155|5end_Serine_hydroxymethyltransferase,_putative_1183298..1183528_POSITIVE 269 153 114 231 179 NC_009009:SSA_2245|5end_RecA_protein,_putative_2241109..2241339_NEGATIVE 265 152 112 68 35 NC_009009:SSA_0921|5end_Zn-dependeant_threonine_dehydrogenase,_putative_931047..931277_POSITIVE 265 158 122 193 142 NC_009009:SSA_0469|5end_Precorrin-6B_methylase_2,putative_472310..472540_POSITIVE 265 140 100 80 44 NC_009009:SSA_0233|5end_Permease,_putative_227203..227433_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 373 160 111 149 103 NC_009009:SSA_2064|3end_hypothetical_protein_2064879..2065029_NEGATIVE 297 160 114 148 105 NC_009009:SSA_0341|3end_hypothetical_protein_333955..334105_NEGATIVE 288 160 120 54 5 NC_009009:SSA_2122|3end_hypothetical_protein_2127200..2127350_NEGATIVE 287 160 113 50 10 NC_009009:SSA_0388|3end_Mismatch_repair_ATPase_(MutS_family),_putative_384248..384398_POSITIVE 285 160 123 75 33 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 279 154 113 58 15 NC_009009:SSA_1958|3end_Adapter_protein_mecA,_putative_1954661..1954811_NEGATIVE 276 79 31 83 28 NC_009009:SSA_2362|3end_L-serine_dehydratase_alpha_subunit_2365660..2365810_POSITIVE 276 140 99 70 28 NC_009009:SSA_0556|3end_hypothetical_protein_551922..552072_POSITIVE 273 160 117 79 31 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 273 140 104 71 35 NC_009009:SSA_0562|3end_hypothetical_protein_554859..555009_POSITIVE 272 155 113 136 88 NC_009009:SSA_0022|3end_Surface_protein_cell_wall_anchor,_sortase_B_family,_putative_28428..28578_POSITIVE 271 156 111 83 25 NC_009009:SSA_0062|3end_Aldose_1-epimerase,_putative_64858..65008_POSITIVE 270 158 115 144 98 NC_009009:SSA_2103|3end_hypothetical_protein_2106500..2106650_NEGATIVE 265 140 100 74 38 NC_009009:SSA_0232|3end_hypothetical_protein_227277..227427_POSITIVE 264 155 119 151 110 NC_009009:SSA_1839|3end_Cysteine_synthase,_putative_1833985..1834135_POSITIVE 261 142 105 55 14 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 258 156 112 49 3 NC_009009:SSA_1856|3end_hypothetical_protein_1852077..1852227_NEGATIVE 255 49 2 133 90 NC_009009:SSA_2394|3end_Competence_stimulating_peptide_2385261..2385411_NEGATIVE 255 155 119 51 14 NC_009009:SSA_0601|3end_Phosphorylase,_Pnp/Udp_family,_putative_589988..590138_POSITIVE 255 159 112 101 52 NC_009009:SSA_0407|3end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_402911..403061_NEGATIVE