Origin IGS: agcacctcctcaaatcacactactttcattatatcatgattctcactaacatgaaagtgttttctttaccggacttaaatttcattccttccgtttgataatcgaaagccttgctcctccttgatttttgcgttacaattagattaattgattttaaaacacaaggaaaaatacagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actgtatttttccttgtgttttaaaatcaattaatctaattgtaacgcaaaaatcaaggaggagcaaggctttcgattatcaaacggaaggaatgaaatttaagtccggtaaagaaaacactttcatgttagtgagaatcatgatataatgaaagtagtgtgatttgaggaggtgct Mask Tandem Repeat Region ================================================ agcacctcctcaaatcacactactttcattatatcatgattctcactaacatgaaagtgttttctttaccggacttaaatttcattccttccgtttgataatcgaaagccttgctcctccttgatttttgcgttacaattagattaattgattttaaaacacaaggaaaaatacagt Find is-nt database================================================ Query_seq: SSA_1261:SSA_1262|SSA_1261:SSA_1262:Ribose-5-phosphate isomerase A, putative:tRNA modification GTPase, possibly iron-binding, putative:<-->:1287745..1287921 177 agcacctcctcaaatcacactactttcattatatcatgattctcactaacatgaaagtgttttctttaccggacttaaatttcattccttccgtttgataatcgaaagccttgctcctccttgatttttgcgttacaattagattaattgattttaaaacacaaggaaaaatacagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1261:SSA_1262|SSA_1261:SSA_1262:Ribose-5-phosphate isomerase A, putative:tRNA modification GTPase, possibly iron-binding, putative:<-->:1287745..1287921 177 agcacctcctcaaatcacactactttcattatatcatgattctcactaacatgaaagtgttttctttaccggacttaaatttcattccttccgtttgataatcgaaagccttgctcctccttgatttttgcgttacaattagattaattgattttaaaacacaaggaaaaatacagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1261:SSA_1262|SSA_1261:SSA_1262:Ribose-5-phosphate isomerase A, putative:tRNA modification GTPase, possibly iron-binding, putative:<-->:1287745..1287921 177 agcacctcctcaaatcacactactttcattatatcatgattctcactaacatgaaagtgttttctttaccggacttaaatttcattccttccgtttgataatcgaaagccttgctcctccttgatttttgcgttacaattagattaattgattttaaaacacaaggaaaaatacagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcacctcctcaaatcacactactttcattatatcatgattctcactaacatgaaagtgttttctttaccggacttaaatttcattccttccgtttgataatcgaaagccttgctcctccttgatttttgcgttacaattagattaattgattttaaaacacaaggaaaaatacagt Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: - Start: 32 End: 172 ............................... I M I R V L M F T N E K G S K F K M G E T Q Y D F A K S R R S K Q T V I L N I S K L V C P F M ..... agcacctcctcaaatcacactactttcattatatcatgattctcactaacatgaaagtgttttctttaccggacttaaatttcattccttccgtttgataatcgaaagccttgctcctccttgatttttgcgttacaattagattaattgattttaaaacacaaggaaaaatacagt 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: 83 Start: 110 End: 139 .............................................................................................................CTTGCTCCTCCTTGATTTTTGCGTTACAAT...................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 28 End: 57 ...........................CTTTCATGTTAGTGAGAATCATGATATAAT........................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agcacctcctcaaatcacactactttcattatatcatgattctcactaacatgaaagtgttttctttaccggacttaaatttcattccttccgtttgataatcgaaagccttgctcctccttgatttttgcgttacaattagattaattgattttaaaacacaaggaaaaatacagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1261:SSA_1262|SSA_1261:SSA_1262:Ribose-5-phosphate isomerase A, putative:tRNA modification GTPase, possibly iron-binding, putative:<-->:1287745..1287921 177 agcacctcctcaaatcacactactttcattatatcatgattctcactaacatgaaagtgttttctttaccggacttaaatttcattccttccgtttgataatcgaaagccttgctcctccttgatttttgcgttacaattagattaattgattttaaaacacaaggaaaaatacagt Intra-Species Hit: Count: 1 Min: 1 Max: 177 Len: 177 Subject: NC_009009_SSA_1261_SSA_1262|Ribose-5-phosphate isomerase A, putative:tRNA modification GTPase, possibly iron-binding, putative|NEGATIVE:POSITIVE|[1287745,1287921]|177 HSP 1 e-value: 5.0E-96 bit: 351.0 Len: 177 Query Start:1 Query End:177 Subject Strand: POSITIVE Subject Start: 1 Subject End: 177 agcacctcctcaaatcacactactttcattatatcatgattctcactaacatgaaagtgttttctttaccggacttaaatttcattccttccgtttgataatcgaaagccttgctcctccttgatttttgcgttacaattagattaattgattttaaaacacaaggaaaaatacagt agcacctcctcaaatcacactactttcattatatcatgattctcactaacatgaaagtgttttctttaccggacttaaatttcattccttccgtttgataatcgaaagccttgctcctccttgatttttgcgttacaattagattaattgattttaaaacacaaggaaaaatacagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCACCUCCUCAAAUCACACUACUUUCAUUAUAUCAUGAUUCUCACUAACAUGAAAGUGUUUUCUUUACCGGACUUAAAUUUCAUUCCUUCCGUUUGAUAAUCGAAAGCCUUGCUCCUCCUUGAUUUUUGCGUUACAAUUAGAUUAAUUGAUUUUAAAACACAAGGAAAAAUACAGU ((((.................((((((((.......((.....)).....))))))))((((((.(((.(((((..................))))).)))..))))))..))))..((((((..(((((.....((((((...))))))....)))))..)))))).......... (-23.07) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUGUAUUUUUCCUUGUGUUUUAAAAUCAAUUAAUCUAAUUGUAACGCAAAAAUCAAGGAGGAGCAAGGCUUUCGAUUAUCAAACGGAAGGAAUGAAAUUUAAGUCCGGUAAAGAAAACACUUUCAUGUUAGUGAGAAUCAUGAUAUAAUGAAAGUAGUGUGAUUUGAGGAGGUGCU ..(((..(((((((((.(((((.....((((((...)))))).......)))))))))))))))))..((((((....((((..((((..((((...))))...)))).........((((((((((....(((.....)))......)))))))).)).))))....))))))... (-36.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 884 120 71 211 162 NC_009009:SSA_1261|5end_Ribose-5-phosphate_isomerase_A,_putative_1287654..1287884_NEGATIVE 298 120 74 190 150 NC_009009:SSA_1119|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_AraC-type_DNA-binding_domains),_putative_1144491..1144721_POSITIVE 294 120 79 77 45 NC_009009:SSA_1254|5end_hypothetical_protein_1281484..1281714_NEGATIVE 294 133 91 113 66 NC_009009:SSA_0603|5end_Cobalt_transporter,_putative_591596..591826_POSITIVE 287 126 82 133 88 NC_009009:SSA_0676|5end_Farnesyl_diphosphate_synthase,_putative_658598..658828_POSITIVE 282 117 87 200 172 NC_009009:SSA_0025|5end_DNA_repair_protein_recO,_putative_29694..29924_POSITIVE 278 114 73 146 103 NC_009009:SSA_1649|5end_hypothetical_protein_1648886..1649116_NEGATIVE 276 133 104 174 131 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 276 136 91 49 6 NC_009009:SSA_0095|5end_Threonine_synthase,_putative_96555..96785_POSITIVE 271 122 81 226 180 NC_009009:SSA_1871|5end_Penicillin-binding_protein_2X,_putative_1868873..1869103_NEGATIVE 271 142 106 153 126 NC_009009:SSA_0490|5end_Cobalamin_5'-phosphate_synthase,_putative_490236..490466_POSITIVE 270 136 101 145 111 NC_009009:SSA_1209|5end_Inorganic_polyphosphate/ATP-NAD_kinase,_putative_1234030..1234260_NEGATIVE 269 137 91 162 100 NC_009009:SSA_0636|5end_N-(5'-phosphoribosyl)anthranilate_isomerase,_putative_625184..625414_POSITIVE 268 144 101 134 92 NC_009009:SSA_1579|5end_ABC-type_Fe3+-siderophore_transport_system,_ATPase_component,_putative_1582851..1583081_POSITIVE 268 120 93 143 114 NC_009009:SSA_1311|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_1328393..1328623_NEGATIVE 268 126 81 144 94 NC_009009:SSA_1302|5end_tRNA_(Guanine-N(1)-)-methyltransferase,_putative_1322484..1322714_NEGATIVE 268 132 91 50 12 NC_009009:SSA_1227|5end_Aminoglycoside_adenylyltransferase,_putative_1252297..1252527_NEGATIVE 267 133 104 38 4 NC_009009:SSA_0475|5end_CbiK_protein,_putative_477723..477953_POSITIVE 264 109 70 217 176 NC_009009:SSA_0113|5end_30S_ribosomal_protein_S3,_putative_111322..111552_POSITIVE 264 119 85 193 155 NC_009009:SSA_0065|5end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67175..67405_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 120 74 130 90 NC_009009:SSA_1118|3end_Peptide_methionine_sulfoxide_reductase,_putative_1144511..1144661_POSITIVE 294 120 79 105 73 NC_009009:SSA_1255|3end_hypothetical_protein_1281456..1281606_NEGATIVE 294 133 91 120 73 NC_009009:SSA_0602|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_591683..591833_POSITIVE 288 100 60 141 98 NC_009009:SSA_0403|3end_CAAX_amino_terminal_protease_family,_putative_401388..401538_POSITIVE 287 126 82 136 91 NC_009009:SSA_0675|3end_Exodeoxyribonuclease_VII_small_subunit,_putative_658681..658831_POSITIVE 278 114 73 136 93 NC_009009:SSA_1650|3end_3-Ketoacyl-ACP_reductase,_putative_1648896..1649046_NEGATIVE 270 131 91 150 113 NC_009009:SSA_0489|3end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_490319..490469_POSITIVE 269 137 91 133 71 NC_009009:SSA_0635|3end_Indole-3-glycerol_phosphate_synthase,_putative_625235..625385_POSITIVE 268 144 101 132 90 NC_009009:SSA_1578|3end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1582929..1583079_POSITIVE 264 96 55 151 104 NC_009009:SSA_0613|3end_Glucosyltransferase,_putative_606633..606783_POSITIVE 262 121 88 72 45 NC_009009:SSA_1408|3end_hypothetical_protein_1420406..1420556_NEGATIVE 260 132 91 117 81 NC_009009:SSA_1846|3end_Phosphoprotein_phosphatase,_putative_1840178..1840328_NEGATIVE 257 139 91 150 99 NC_009009:SSA_0690|3end_Recombinational_DNA_repair_protein_(RecF_pathway),_putative_675108..675258_POSITIVE 252 138 98 59 5 NC_009009:SSA_1530|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1537510..1537660_NEGATIVE 251 74 36 111 73 NC_009009:SSA_0401|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_399222..399372_POSITIVE 248 120 71 111 54 NC_009009:SSA_0927|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_936740..936890_POSITIVE 247 149 102 60 10 NC_009009:SSA_0656|3end_Cell_division_protein_FtsZ,_putative_641516..641666_POSITIVE 246 124 93 140 105 NC_009009:SSA_1276|3end_Conserved_uncharacterized_protein_1298156..1298306_NEGATIVE 244 120 71 62 13 NC_009009:SSA_0918|3end_Conserved_uncharacterized_protein_930945..931095_POSITIVE 243 120 80 148 102 NC_009009:SSA_1822|3end_hypothetical_protein_1810871..1811021_NEGATIVE