Origin IGS: tctttactccctttcttactgttcttttacacttatattctgaagccaatagctgttcaaaatgaacttaataaaaaactaagttatcctgatatttggctctcctaatgcattaatttctggagttccaaaaaaataggccaagacgaagtcagagcccatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatgggctctgacttcgtcttggcctatttttttggaactccagaaattaatgcattaggagagccaaatatcaggataacttagttttttattaagttcattttgaacagctattggcttcagaatataagtgtaaaagaacagtaagaaagggagtaaaga Mask Tandem Repeat Region ================================================ tctttactccctttcttactgttcttttacacttatattctgaagccaatagctgttcaaaatgaacttaataaaaaactaagttatcctgatatttggctctcctaatgcattaatttctggagttccaaaaaaataggccaagacgaagtcagagcccatt Find is-nt database================================================ Query_seq: SSA_1603:SSA_1604|SSA_1603:SSA_1604:hypothetical protein:Protein-export membrane protein secG, putative:<-<-:1610125..1610287 163 tctttactccctttcttactgttcttttacacttatattctgaagccaatagctgttcaaaatgaacttaataaaaaactaagttatcctgatatttggctctcctaatgcattaatttctggagttccaaaaaaataggccaagacgaagtcagagcccatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1603:SSA_1604|SSA_1603:SSA_1604:hypothetical protein:Protein-export membrane protein secG, putative:<-<-:1610125..1610287 163 tctttactccctttcttactgttcttttacacttatattctgaagccaatagctgttcaaaatgaacttaataaaaaactaagttatcctgatatttggctctcctaatgcattaatttctggagttccaaaaaaataggccaagacgaagtcagagcccatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1603:SSA_1604|SSA_1603:SSA_1604:hypothetical protein:Protein-export membrane protein secG, putative:<-<-:1610125..1610287 163 tctttactccctttcttactgttcttttacacttatattctgaagccaatagctgttcaaaatgaacttaataaaaaactaagttatcctgatatttggctctcctaatgcattaatttctggagttccaaaaaaataggccaagacgaagtcagagcccatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctttactccctttcttactgttcttttacacttatattctgaagccaatagctgttcaaaatgaacttaataaaaaactaagttatcctgatatttggctctcctaatgcattaatttctggagttccaaaaaaataggccaagacgaagtcagagcccatt Predict ORF larger than 30AA ================================================ tctttactccctttcttactgttcttttacacttatattctgaagccaatagctgttcaaaatgaacttaataaaaaactaagttatcctgatatttggctctcctaatgcattaatttctggagttccaaaaaaataggccaagacgaagtcagagcccatt 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================================================ tctttactccctttcttactgttcttttacacttatattctgaagccaatagctgttcaaaatgaacttaataaaaaactaagttatcctgatatttggctctcctaatgcattaatttctggagttccaaaaaaataggccaagacgaagtcagagcccatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1603:SSA_1604|SSA_1603:SSA_1604:hypothetical protein:Protein-export membrane protein secG, putative:<-<-:1610125..1610287 163 tctttactccctttcttactgttcttttacacttatattctgaagccaatagctgttcaaaatgaacttaataaaaaactaagttatcctgatatttggctctcctaatgcattaatttctggagttccaaaaaaataggccaagacgaagtcagagcccatt Intra-Species Hit: Count: 1 Min: 1 Max: 163 Len: 163 Subject: NC_009009_SSA_1603_SSA_1604|hypothetical protein:Protein-export membrane protein secG, putative|NEGATIVE:NEGATIVE|[1610125,1610287]|163 HSP 1 e-value: 3.0E-75 bit: 281.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 tctttactccctttcttactgttcttttacacttatattctgaagccaatagctgttcaaaatgaacttaataaaaaactaagttatcctgatatttggctctcctaatgcattaatttctggagttccnnnnnnntaggccaagacgaagtcagagcccatt tctttactccctttcttactgttcttttacacttatattctgaagccaatagctgttcaaaatgaacttaataaaaaactaagttatcctgatatttggctctcctaatgcattaatttctggagttccaaaaaaataggccaagacgaagtcagagcccatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUACUCCCUUUCUUACUGUUCUUUUACACUUAUAUUCUGAAGCCAAUAGCUGUUCAAAAUGAACUUAAUAAAAAACUAAGUUAUCCUGAUAUUUGGCUCUCCUAAUGCAUUAAUUUCUGGAGUUCCAAAAAAAUAGGCCAAGACGAAGUCAGAGCCCAUU ....................(((((.....((((....(((...(((.((((((((((.....))))..............)))))).......(((((..((((.(((......)))...))))..)))))......)))..)))..)))).)))))..... (-25.93) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGGGCUCUGACUUCGUCUUGGCCUAUUUUUUUGGAACUCCAGAAAUUAAUGCAUUAGGAGAGCCAAAUAUCAGGAUAACUUAGUUUUUUAUUAAGUUCAUUUUGAACAGCUAUUGGCUUCAGAAUAUAAGUGUAAAAGAACAGUAAGAAAGGGAGUAAAGA ((((((((..(((...)))..))))))))........(((((............(((..((.((((((...(((((((((((((((.....)))))))).))))))).......))))))))..)))...(.(((......))).).......)))))..... (-37.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 842 130 81 221 172 NC_009009:SSA_1603|5end_hypothetical_protein_1610034..1610264_NEGATIVE 289 60 12 190 140 NC_009009:SSA_0012|5end_Beta-lactamase_class_A,_putative_9916..10146_POSITIVE 289 60 12 69 19 NC_009009:SSA_0011|5end_hypothetical_protein_9795..10025_POSITIVE 282 159 117 56 8 NC_009009:SSA_1667|5end_hypothetical_protein_1667704..1667934_NEGATIVE 280 159 120 65 25 NC_009009:SSA_1634|5end_Heme_utilization/adhesion_exoprotein,_putative_1637062..1637292_NEGATIVE 274 70 23 60 15 NC_009009:SSA_2281|5end_hypothetical_protein_2282370..2282600_NEGATIVE 269 159 120 61 18 NC_009009:SSA_0908|5end_ABC-type_uncharacterized_transport_system,_periplasmic_component,_putative_919700..919930_POSITIVE 264 130 85 90 52 NC_009009:SSA_2356|5end_Replicative_DNA_helicase,_putative_2357958..2358188_NEGATIVE 262 47 1 187 138 NC_009009:SSA_0034|5end_hypothetical_protein_39547..39777_POSITIVE 256 58 13 138 96 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 252 150 101 146 93 NC_009009:SSA_1695|5end_Transcriptional_antiterminator,_BglG/SacY_family_(induction_of_sugar_metabolism),_putative_1688010..1688240_NEGATIVE 249 160 124 58 29 NC_009009:SSA_1927|5end_Exfoliative_toxin,_putative_1915873..1916103_NEGATIVE 243 128 82 145 94 NC_009009:SSA_1697|5end_Tagatose-6-phosphate_kinase,_putative_1690120..1690350_NEGATIVE 241 158 138 37 13 NC_009009:SSA_0218|5end_Sugar-binding_periplasmic_protein,_putative_213863..214093_POSITIVE 239 127 88 68 25 NC_009009:SSA_1551|5end_Transcriptional_accessory_ribonuclease_(YqgFc,_S1),_putative_1554784..1555014_NEGATIVE 238 58 13 55 3 NC_009009:SSA_1509|5end_Polysaccharide_biosynthesis_protein/_rhamnosyltransferase,_putative_1514191..1514421_NEGATIVE 236 154 120 66 25 NC_009009:SSA_1632|5end_Surface_protein,_putative_1634045..1634275_NEGATIVE 234 142 102 71 34 NC_009009:SSA_2189|5end_hypothetical_protein_2191097..2191327_NEGATIVE 234 158 120 34 3 NC_009009:SSA_2093|5end_PTS_system,_membrane_component,_putative_2097462..2097692_NEGATIVE 234 55 12 131 83 NC_009009:SSA_0750|5end_hypothetical_protein_731789..732019_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 60 12 66 16 NC_009009:SSA_0010|3end_Cell_division_protein_DivIC,_putative_9872..10022_POSITIVE 274 70 23 53 8 NC_009009:SSA_2282|3end_Phage_infection_protein,_putative_2282377..2282527_NEGATIVE 264 130 85 63 25 NC_009009:SSA_2357|3end_50S_ribosomal_protein_L9,_putative_2357985..2358135_NEGATIVE 261 160 119 55 16 NC_009009:SSA_0287|3end_Glycerol_dehydrogenase,_NAD+_dependent,_putative_280702..280852_POSITIVE 247 148 108 148 112 NC_009009:SSA_1740|3end_hypothetical_protein_1727081..1727231_NEGATIVE 244 155 118 144 101 NC_009009:SSA_1314|3end_Fe-S-cluster_oxidoreductase,_putative_1330746..1330896_NEGATIVE 243 128 82 132 81 NC_009009:SSA_1698|3end_Galactose-6-phosphate_isomerase,_LacB_subunit,_putative_1690133..1690283_NEGATIVE 241 158 138 40 16 NC_009009:SSA_0217|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213946..214096_POSITIVE 238 58 13 58 6 NC_009009:SSA_1510|3end_Rhamnosyltransferase,_putative_1514188..1514338_NEGATIVE 234 160 140 146 123 NC_009009:SSA_0258|3end_hypothetical_protein_253022..253172_POSITIVE 233 158 116 69 17 NC_009009:SSA_1048|3end_ABC_transporter_ATP-binding_protein-spermidine/putrescine_transport,_putative_1064184..1064334_POSITIVE 231 128 83 138 84 NC_009009:SSA_0335|3end_Phosphomevalonate_kinase,_putative_329891..330041_POSITIVE 228 46 5 123 71 NC_009009:SSA_1721|3end_DNA_polymerase_III,_delta'_subunit,_putative_1707138..1707288_NEGATIVE 227 129 84 55 10 NC_009009:SSA_2030|3end_hypothetical_protein_2036514..2036664_NEGATIVE 221 58 12 122 82 NC_009009:SSA_1496|3end_hypothetical_protein_1502473..1502623_NEGATIVE 218 160 111 151 98 NC_009009:SSA_1657|3end_hypothetical_protein_1652962..1653112_NEGATIVE 218 159 117 147 105 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 217 129 87 117 71 NC_009009:SSA_0244|3end_hypothetical_protein_239170..239320_POSITIVE 216 159 118 61 13 NC_009009:SSA_1982|3end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975427..1975577_NEGATIVE 216 57 11 130 86 NC_009009:SSA_1900|3end_N_utilization_substance_protein_A,_putative_1894750..1894900_NEGATIVE