Origin IGS: cgcttactcttttctaaacattcttctattcagtatatcatttttaagggcataaaaaaagcagcggaggaaaaatcagcttgttgataaactgattttgtctcgccacttgatgatggggtgtttgttcctacccgacacttat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataagtgtcgggtaggaacaaacaccccatcatcaagtggcgagacaaaatcagtttatcaacaagctgatttttcctccgctgctttttttatgcccttaaaaatgatatactgaatagaagaatgtttagaaaagagtaagcg Mask Tandem Repeat Region ================================================ cgcttactcttttctaaacattcttctattcagtatatcatttttaagggcataaaaaaagcagcggaggaaaaatcagcttgttgataaactgattttgtctcgccacttgatgatggggtgtttgttcctacccgacacttat Find is-nt database================================================ Query_seq: SSA_1417:SSA_1418|SSA_1417:SSA_1418:SAM-dependent methyltransferase, putative:Conserved uncharacterized protein:<-<-:1428084..1428228 145 cgcttactcttttctaaacattcttctattcagtatatcatttttaagggcataaaaaaagcagcggaggaaaaatcagcttgttgataaactgattttgtctcgccacttgatgatggggtgtttgttcctacccgacacttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1417:SSA_1418|SSA_1417:SSA_1418:SAM-dependent methyltransferase, putative:Conserved uncharacterized protein:<-<-:1428084..1428228 145 cgcttactcttttctaaacattcttctattcagtatatcatttttaagggcataaaaaaagcagcggaggaaaaatcagcttgttgataaactgattttgtctcgccacttgatgatggggtgtttgttcctacccgacacttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1417:SSA_1418|SSA_1417:SSA_1418:SAM-dependent methyltransferase, putative:Conserved uncharacterized protein:<-<-:1428084..1428228 145 cgcttactcttttctaaacattcttctattcagtatatcatttttaagggcataaaaaaagcagcggaggaaaaatcagcttgttgataaactgattttgtctcgccacttgatgatggggtgtttgttcctacccgacacttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgcttactcttttctaaacattcttctattcagtatatcatttttaagggcataaaaaaagcagcggaggaaaaatcagcttgttgataaactgattttgtctcgccacttgatgatggggtgtttgttcctacccgacacttat Predict ORF larger than 30AA ================================================ cgcttactcttttctaaacattcttctattcagtatatcatttttaagggcataaaaaaagcagcggaggaaaaatcagcttgttgataaactgattttgtctcgccacttgatgatggggtgtttgttcctacccgacacttat 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================================================ cgcttactcttttctaaacattcttctattcagtatatcatttttaagggcataaaaaaagcagcggaggaaaaatcagcttgttgataaactgattttgtctcgccacttgatgatggggtgtttgttcctacccgacacttat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 84 HP_score: -3.3 Tail_Score: -5.63504 Start: 61 End: 109 Full_Region: acaccccatcatcaa gtggcgagacaaaatcagttt atcaac aagctgatttttcctccgctgc tttttttatgccctt ............................................................gtggcgagacaaaatcagtttatcaacaagctgatttttcctccgctgc.................................... TransTerm Strand: - Conf: 52 HP_score: -3.6 Tail_Score: -3.56036 Start: 64 End: 106 Full_Region: ccccatcatcaagtg gcgagacaaaatcagttt atcaac aagctgatttttcctccgc tgctttttttatgcc ...............................................................gcgagacaaaatcagtttatcaacaagctgatttttcctccgc....................................... Find igs database================================================ Query_seq: SSA_1417:SSA_1418|SSA_1417:SSA_1418:SAM-dependent methyltransferase, putative:Conserved uncharacterized protein:<-<-:1428084..1428228 145 cgcttactcttttctaaacattcttctattcagtatatcatttttaagggcataaaaaaagcagcggaggaaaaatcagcttgttgataaactgattttgtctcgccacttgatgatggggtgtttgttcctacccgacacttat Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: NC_009009_SSA_1417_SSA_1418|SAM-dependent methyltransferase, putative:Conserved uncharacterized protein|NEGATIVE:NEGATIVE|[1428084,1428228]|145 HSP 1 e-value: 2.0E-64 bit: 246.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 145 cgcttactcttttctaaacattcttctattcagtatatcatttttaagggcatnnnnnnngcagcggaggaaaaatcagcttgttgataaactgattttgtctcgccacttgatgatggggtgtttgttcctacccgacacttat cgcttactcttttctaaacattcttctattcagtatatcatttttaagggcataaaaaaagcagcggaggaaaaatcagcttgttgataaactgattttgtctcgccacttgatgatggggtgtttgttcctacccgacacttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCUUACUCUUUUCUAAACAUUCUUCUAUUCAGUAUAUCAUUUUUAAGGGCAUAAAAAAAGCAGCGGAGGAAAAAUCAGCUUGUUGAUAAACUGAUUUUGUCUCGCCACUUGAUGAUGGGGUGUUUGUUCCUACCCGACACUUAU ..............((((((((((..((((.(((......((((((......)))))).....(((.((..((((((((.(((....))).))))))))..))))).))).))))..)))))))))).................. (-26.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAGUGUCGGGUAGGAACAAACACCCCAUCAUCAAGUGGCGAGACAAAAUCAGUUUAUCAACAAGCUGAUUUUUCCUCCGCUGCUUUUUUUAUGCCCUUAAAAAUGAUAUACUGAAUAGAAGAAUGUUUAGAAAAGAGUAAGCG ....((...(((((((..........))......(((..(((((..(((((((((((......)))))))))))..)).)))..)))......)))))..............(((((((......)))))))..........)). (-33.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 963 140 91 231 182 NC_009009:SSA_1417|5end_SAM-dependent_methyltransferase,_putative_1427993..1428223_NEGATIVE 313 135 101 183 149 NC_009009:SSA_0838|5end_GtfB,_putative_825406..825636_POSITIVE 296 109 62 188 134 NC_009009:SSA_0018|5end_Cell-shape_determining_protein_MreD,_putative_23628..23858_POSITIVE 286 80 38 157 117 NC_009009:SSA_2089|5end_L-xylulose-5-phosphate_3-epimerase,_putative_2094339..2094569_NEGATIVE 280 109 62 72 28 NC_009009:SSA_1775|5end_Potassium_uptake_protein,_Trk_family,_putative_1761284..1761514_POSITIVE 280 140 101 193 155 NC_009009:SSA_0535|5end_Propanediol_utilization:_dehydratase,_medium_subunit,_putative_530643..530873_POSITIVE 278 136 93 65 25 NC_009009:SSA_0026|5end_Fatty_acid/phospholipid_synthesis_protein_plsX,_putative_30473..30703_POSITIVE 277 109 62 50 2 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 276 132 91 221 166 NC_009009:SSA_2070|5end_Zinc_metalloprotease,_putative_2074574..2074804_NEGATIVE 275 110 66 169 127 NC_009009:SSA_1728|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1714293..1714523_NEGATIVE 270 140 92 57 7 NC_009009:SSA_0395|5end_6-phospho-beta-glucosidase,_putative_391061..391291_POSITIVE 264 138 92 200 154 NC_009009:SSA_0143|5end_Conserved_uncharacterized_protein_137465..137695_POSITIVE 263 108 62 138 86 NC_009009:SSA_0977|5end_3-isopropylmalate_dehydrogenase,_putative_982771..983001_POSITIVE 263 138 94 59 3 NC_009009:SSA_0615|5end_RggD,_putative_609195..609425_NEGATIVE 263 107 63 55 2 NC_009009:SSA_0603|5end_Cobalt_transporter,_putative_591596..591826_POSITIVE 261 138 91 201 140 NC_009009:SSA_2302|5end_Type_IV_fimbrial_biogenesis_protein,_prepilin_cysteine_protease_(C20)_PilD,_putative_2304044..2304274_NEGATIVE 260 130 81 229 186 NC_009009:SSA_2120|5end_GTPase,_putative_2121751..2121981_NEGATIVE 260 108 61 179 129 NC_009009:SSA_1544|5end_Conserved_uncharacterized_protein_1548796..1549026_NEGATIVE 259 108 64 169 130 NC_009009:SSA_2277|5end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2280407..2280637_NEGATIVE 258 106 63 189 148 NC_009009:SSA_1687|5end_NADH-binding_ferric-oxidoreductase,_putative_1680547..1680777_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 136 93 59 19 NC_009009:SSA_0025|3end_DNA_repair_protein_recO,_putative_30547..30697_POSITIVE 276 132 92 91 60 NC_009009:SSA_0965|3end_Oxidoreductase,_putative_974035..974185_NEGATIVE 272 135 92 43 1 NC_009009:SSA_0799|3end_hypothetical_protein_781713..781863_NEGATIVE 269 107 62 62 6 NC_009009:SSA_0602|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_591683..591833_POSITIVE 266 138 97 151 105 NC_009009:SSA_1297|3end_Nuclease_subunit_of_the_excinuclease_complex,_subunit_C,_putative_1313141..1313291_NEGATIVE 264 138 92 144 98 NC_009009:SSA_0142|3end_hypothetical_protein_137489..137639_POSITIVE 263 108 62 56 4 NC_009009:SSA_0975|3end_2-isopropylmalate_synthase,_putative_982769..982919_POSITIVE 261 138 91 132 71 NC_009009:SSA_2303|3end_hypothetical_protein_2304113..2304263_NEGATIVE 258 70 31 75 38 NC_009009:SSA_0410|3end_hypothetical_protein_405750..405900_NEGATIVE 257 49 1 57 17 NC_009009:SSA_0568|3end_Aspartyl-tRNA_synthetase_1,_putative_563490..563640_POSITIVE 256 121 92 36 4 NC_009009:SSA_1974|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_1969512..1969662_NEGATIVE 251 130 83 52 8 NC_009009:SSA_1011|3end_hypothetical_protein_1014804..1014954_POSITIVE 250 109 63 48 1 NC_009009:SSA_1403|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1416222..1416372_NEGATIVE 249 129 106 42 17 NC_009009:SSA_0532|3end_Propanediol_utilization_protein_PduB,_putative_529028..529178_POSITIVE 248 139 97 65 7 NC_009009:SSA_2254|3end_Holliday_junction_DNA_helicase_ruvA,_putative_2249434..2249584_NEGATIVE 247 104 61 74 26 NC_009009:SSA_0572|3end_Dehydrogenase,_putative_568552..568702_POSITIVE 247 67 49 35 15 NC_009009:SSA_0281|3end_hypothetical_protein_273963..274113_POSITIVE 245 126 81 138 81 NC_009009:SSA_0446|3end_hypothetical_protein_444764..444914_NEGATIVE 244 83 49 76 38 NC_009009:SSA_2144|3end_Glutamyl-tRNA_synthetase,_putative_2144315..2144465_NEGATIVE 243 136 91 80 3 NC_009009:SSA_2275|3end_hypothetical_protein_2275225..2275375_NEGATIVE