Origin IGS: aatttttccttatccagagaataattctcaattataaaagtgaaagtttttgtaagctcataacatttataatgatattattctttctgttattttcttagtttttaagtattttttaaataatatttatcatttttagtataccatatttctaagaaatttcaataagaaaaagtgattttaacttaaaatttcttaaagaaaaatttttataaaattatattaaatttattatttcaatttcacaatattttttgtagtttttttcaattttattttttataatattgtccttagtctaaagtagatat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 atatctactttagactaaggacaatattataaaaaataaaattgaaaaaaactacaaaaaatattgtgaaattgaaataataaatttaatataattttataaaaatttttctttaagaaattttaagttaaaatcactttttcttattgaaatttcttagaaatatggtatactaaaaatgataaatattatttaaaaaatacttaaaaactaagaaaataacagaaagaataatatcattataaatgttatgagcttacaaaaactttcacttttataattgagaattattctctggataaggaaaaatt Mask Tandem Repeat Region ================================================ aatttttccttatccagagaataattctcaattataaaagtgaaagtttttgtaagctcataacatttataatgatattattctttctgttattttcttagtttttaagtattttttaaataatatttatcatttttagtataccatatttctaagaaatttcaataagaaaaagtgattttaacttaaaatttcttaaagaaaaatttttataaaattatattaaatttattatttcaatttcacaatattttttgtagtttttttcaattttattttttataatattgtccttagtctaaagtagatat Find is-nt database================================================ Query_seq: FN0954:FN0955|FN0954:FN0955:Hypothetical cytosolic protein:hypothetical protein:<-<-:1611707..1612017 311 aatttttccttatccagagaataattctcaattataaaagtgaaagtttttgtaagctcataacatttataatgatattattctttctgttattttcttagtttttaagtattttttaaataatatttatcatttttagtataccatatttctaagaaatttcaataagaaaaagtgattttaacttaaaatttcttaaagaaaaatttttataaaattatattaaatttattatttcaatttcacaatattttttgtagtttttttcaattttattttttataatattgtccttagtctaaagtagatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0954:FN0955|FN0954:FN0955:Hypothetical cytosolic protein:hypothetical protein:<-<-:1611707..1612017 311 aatttttccttatccagagaataattctcaattataaaagtgaaagtttttgtaagctcataacatttataatgatattattctttctgttattttcttagtttttaagtattttttaaataatatttatcatttttagtataccatatttctaagaaatttcaataagaaaaagtgattttaacttaaaatttcttaaagaaaaatttttataaaattatattaaatttattatttcaatttcacaatattttttgtagtttttttcaattttattttttataatattgtccttagtctaaagtagatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0954:FN0955|FN0954:FN0955:Hypothetical cytosolic protein:hypothetical protein:<-<-:1611707..1612017 311 aatttttccttatccagagaataattctcaattataaaagtgaaagtttttgtaagctcataacatttataatgatattattctttctgttattttcttagtttttaagtattttttaaataatatttatcatttttagtataccatatttctaagaaatttcaataagaaaaagtgattttaacttaaaatttcttaaagaaaaatttttataaaattatattaaatttattatttcaatttcacaatattttttgtagtttttttcaattttattttttataatattgtccttagtctaaagtagatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatttttccttatccagagaataattctcaattataaaagtgaaagtttttgtaagctcataacatttataatgatattattctttctgttattttcttagtttttaagtattttttaaataatatttatcatttttagtataccatatttctaagaaatttcaataagaaaaagtgattttaacttaaaatttcttaaagaaaaatttttataaaattatattaaatttattatttcaatttcacaatattttttgtagtttttttcaattttattttttataatattgtccttagtctaaagtagatat Predict ORF larger than 30AA ================================================ aatttttccttatccagagaataattctcaattataaaagtgaaagtttttgtaagctcataacatttataatgatattattctttctgttattttcttagtttttaagtattttttaaataatatttatcatttttagtataccatatttctaagaaatttcaataagaaaaagtgattttaacttaaaatttcttaaagaaaaatttttataaaattatattaaatttattatttcaatttcacaatattttttgtagtttttttcaattttattttttataatattgtccttagtctaaagtagatat 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================================================ aatttttccttatccagagaataattctcaattataaaagtgaaagtttttgtaagctcataacatttataatgatattattctttctgttattttcttagtttttaagtattttttaaataatatttatcatttttagtataccatatttctaagaaatttcaataagaaaaagtgattttaacttaaaatttcttaaagaaaaatttttataaaattatattaaatttattatttcaatttcacaatattttttgtagtttttttcaattttattttttataatattgtccttagtctaaagtagatat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 36 HP_score: -2.1 Tail_Score: -2.81725 Start: 268 End: 290 Full_Region: TTTTGTAGTTTTTTT CAATTTTAT TTTTT ATAATATTG TCCTTAGTCTAAAGT ...........................................................................................................................................................................................................................................................................CAATTTTATTTTTTATAATATTG..................... Find igs database================================================ Query_seq: FN0954:FN0955|FN0954:FN0955:Hypothetical cytosolic protein:hypothetical protein:<-<-:1611707..1612017 311 aatttttccttatccagagaataattctcaattataaaagtgaaagtttttgtaagctcataacatttataatgatattattctttctgttattttcttagtttttaagtattttttaaataatatttatcatttttagtataccatatttctaagaaatttcaataagaaaaagtgattttaacttaaaatttcttaaagaaaaatttttataaaattatattaaatttattatttcaatttcacaatattttttgtagtttttttcaattttattttttataatattgtccttagtctaaagtagatat Intra-Species Hit: Count: 1 Min: 1 Max: 311 Len: 311 Subject: NC_003454_FN0954_FN0955|Hypothetical cytosolic protein:hypothetical protein|NEGATIVE:NEGATIVE|[1611707,1612017]|311 HSP 1 e-value: 2.0E-28 bit: 127.0 Len: 64 Query Start:1 Query End:64 Subject Strand: POSITIVE Subject Start: 1 Subject End: 64 aatttttccttatccagagaataattctcaattataaaagtgaaagtttttgtaagctcataac....................................................................................................................................................................................................................................................... aatttttccttatccagagaataattctcaattataaaagtgaaagtttttgtaagctcataac....................................................................................................................................................................................................................................................... HSP 2 e-value: 5.0E-8 bit: 60.0 Len: 30 Query Start:282 Query End:311 Subject Strand: POSITIVE Subject Start: 282 Subject End: 311 .........................................................................................................................................................................................................................................................................................ataatattgtccttagtctaaagtagatat .........................................................................................................................................................................................................................................................................................ataatattgtccttagtctaaagtagatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUUCCUUAUCCAGAGAAUAAUUCUCAAUUAUAAAAGUGAAAGUUUUUGUAAGCUCAUAACAUUUAUAAUGAUAUUAUUCUUUCUGUUAUUUUCUUAGUUUUUAAGUAUUUUUUAAAUAAUAUUUAUCAUUUUUAGUAUACCAUAUUUCUAAGAAAUUUCAAUAAGAAAAAGUGAUUUUAACUUAAAAUUUCUUAAAGAAAAAUUUUUAUAAAAUUAUAUUAAAUUUAUUAUUUCAAUUUCACAAUAUUUUUUGUAGUUUUUUUCAAUUUUAUUUUUUAUAAUAUUGUCCUUAGUCUAAAGUAGAUAU ((((((((......(((((((((((..(((.(((((((.((...(((((....)))))....)).)))))))))).)))))))..))))....((((((((.......((((...(((((..............))))).)))).......))))))))......(((((((((((.......))))....)))))))..)))))))).....(((((((((..((((.....................))))..)))))))))...((((.((((.....)))).))))......(((((...))))).. (-40.78) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUCUACUUUAGACUAAGGACAAUAUUAUAAAAAAUAAAAUUGAAAAAAACUACAAAAAAUAUUGUGAAAUUGAAAUAAUAAAUUUAAUAUAAUUUUAUAAAAAUUUUUCUUUAAGAAAUUUUAAGUUAAAAUCACUUUUUCUUAUUGAAAUUUCUUAGAAAUAUGGUAUACUAAAAAUGAUAAAUAUUAUUUAAAAAAUACUUAAAAACUAAGAAAAUAACAGAAAGAAUAAUAUCAUUAUAAAUGUUAUGAGCUUACAAAAACUUUCACUUUUAUAAUUGAGAAUUAUUCUCUGGAUAAGGAAAAAUU ............((.....(((.............(((((((((........(((((......)))))..((((((........)))))).))))))))).(((((((((.....)))))))))..)))....))..(((((((((((....((((((((......(((((.....(((((((....))))))).....)))))......))))))))....((((..(((((((.((((((((((.((...(((.((....)).)))..)).))))))).)))..))))))))))))))))))))))... (-44.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 718 60 11 151 102 NC_003454:FN0954|5end_Hypothetical_cytosolic_protein_1611616..1611846_NEGATIVE 238 156 112 199 161 NC_003454:FN1433|5end_Short_chain_dehydrogenase_2102520..2102750_NEGATIVE 231 118 75 133 90 NC_003454:FN0658|5end_ABC_transporter_substrate-binding_protein_1315675..1315905_NEGATIVE 231 308 272 121 87 NC_003454:FN1498|5end_Integral_membrane_protein_2563..2793_POSITIVE 224 98 51 118 77 NC_003454:FN2080|5end_ABC_transporter_integral_membrane_protein_591957..592187_NEGATIVE 218 118 71 189 136 NC_003454:FN0949|5end_DNA_helicase_1606759..1606989_NEGATIVE 214 270 240 183 153 NC_003454:FN0231|5end_hypothetical_protein_857351..857581_NEGATIVE 212 94 54 114 84 NC_003454:FN1214|5end_Fe-S_oxidoreductase_1875473..1875703_NEGATIVE 212 117 71 210 162 NC_003454:FN1170|5end_Pyruvate-flavodoxin_oxidoreductase_1832273..1832503_NEGATIVE 210 130 81 128 87 NC_003454:FN0988|5end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_1640968..1641198_NEGATIVE 209 305 261 141 99 NC_003454:FN1068|5end_Smf_protein_1713811..1714041_POSITIVE 209 294 253 102 62 NC_003454:FN1745|5end_Cystathionine_gamma-synthase_244143..244373_NEGATIVE 208 87 48 177 120 NC_003454:FN0177|5end_Cell_division_inhibitor_MinE_801957..802187_POSITIVE 205 41 4 102 64 NC_003454:FN1261|5end_Two-component_response_regulator_1917871..1918101_NEGATIVE 204 107 67 72 36 NC_003454:FN0316|5end_hypothetical_protein_953689..953919_NEGATIVE 203 269 228 126 87 NC_003454:FN1369|5end_Zinc_finger_protein_2019006..2019236_NEGATIVE 199 309 261 202 154 NC_003454:FN1669|5end_Choline_transport_protein_166486..166716_NEGATIVE 197 239 192 209 156 NC_003454:FN0299|5end_Aspartyl-tRNA_synthetase_932393..932623_POSITIVE 196 29 3 119 92 NC_003454:FN0167|5end_hypothetical_protein_794106..794336_POSITIVE 195 310 261 65 18 NC_003454:FN0745|5end_metal_dependent_phosphohydrolase_1403275..1403505_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 231 118 75 118 75 NC_003454:FN0659|3end_ABC_transporter_permease_protein_1315690..1315840_NEGATIVE 223 299 251 125 75 NC_003454:FN0713|3end_Chromate_transport_protein_1371943..1372093_POSITIVE 212 94 54 127 97 NC_003454:FN1215|3end_Hypothetical_cytosolic_protein_1875460..1875610_NEGATIVE 212 117 71 118 70 NC_003454:FN1171|3end_Acetate_kinase_1832365..1832515_NEGATIVE 209 305 261 129 87 NC_003454:FN1067|3end_Tetratricopeptide_repeat_family_protein_1713879..1714029_POSITIVE 203 269 228 142 103 NC_003454:FN1370|3end_Endonuclease_2018990..2019140_NEGATIVE 198 287 249 127 85 NC_003454:FN0682|3end_Fibronectin-binding_protein-like_protein_A_1338499..1338649_POSITIVE 196 29 3 110 83 NC_003454:FN0166|3end_hypothetical_protein_794177..794327_POSITIVE 195 310 261 68 21 NC_003454:FN0744|3end_metal_dependent_phosphohydrolase_1403358..1403508_POSITIVE 193 115 79 129 96 NC_003454:FN1996|3end_Transporter_499742..499892_POSITIVE 192 106 75 115 88 NC_003454:FN1839|3end_glycerol_kinase_329845..329995_POSITIVE 191 114 78 120 83 NC_003454:FN0444|3end_Phosphoadenosine_phosphosulfate_reductase_1084878..1085028_POSITIVE 190 300 256 107 63 NC_003454:FN0697|3end_Alanyl-tRNA_synthetase_1356675..1356825_POSITIVE 185 272 245 61 32 NC_003454:FN0277|3end_hypothetical_protein_903421..903571_NEGATIVE 184 300 258 111 57 NC_003454:FN1915|3end_Anti-sigma_B_factor_411991..412141_NEGATIVE 180 185 142 62 15 NC_003454:FN0093|3end_Thioredoxin_729560..729710_POSITIVE 179 116 81 83 51 NC_003454:FN1539|3end_Iron-sulfur_cluster-binding_protein_53092..53242_POSITIVE 178 53 13 85 44 NC_003454:FN1335|3end_Protein_translocase_subunit_YajC_1988727..1988877_NEGATIVE 177 100 51 89 41 NC_003454:FN1270|3end_Hypothetical_cytosolic_protein_1926326..1926476_NEGATIVE 174 276 232 66 8 NC_003454:FN0890|3end_Thiamin_pyrophosphokinase_1551458..1551608_NEGATIVE