Origin IGS: tataattgttacaacaacctttatcaaaatttaaaagtctaagaagtagtgaaaaaaggaatataaatgattatattaaattcttggcttcaacttttgaagtgttaattaatattgaagattcaaataaatttaaaataaaaaaggaatgatatttatgaaaaaattttttaaaatacttatagtatttacatttatatttaatact .........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 agtattaaatataaatgtaaatactataagtattttaaaaaattttttcataaatatcattccttttttattttaaatttatttgaatcttcaatattaattaacacttcaaaagttgaagccaagaatttaatataatcatttatattccttttttcactacttcttagacttttaaattttgataaaggttgttgtaacaattata Mask Tandem Repeat Region ================================================ tataattgttacaacaacctttatcaaaatttaaaagtctaagaagtagtgaaaaaaggaatataaatgattatattaaattcttggcttcaacttttgaagtgttaattaatattgaagattcaaataaatttaaaataaaaaaggaatgatatttatgaaaaaattttttaaaatacttatagtatttacatttatatttaatact Find is-nt database================================================ Query_seq: FN1233:FN1234|FN1233:FN1234:Putative NAD(P)H oxidoreductase:hypothetical protein:->->:1890072..1890279 208 tataattgttacaacaacctttatcaaaatttaaaagtctaagaagtagtgaaaaaaggaatataaatgattatattaaattcttggcttcaacttttgaagtgttaattaatattgaagattcaaataaatttaaaataaaaaaggaatgatatttatgaaaaaattttttaaaatacttatagtatttacatttatatttaatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1233:FN1234|FN1233:FN1234:Putative NAD(P)H oxidoreductase:hypothetical protein:->->:1890072..1890279 208 tataattgttacaacaacctttatcaaaatttaaaagtctaagaagtagtgaaaaaaggaatataaatgattatattaaattcttggcttcaacttttgaagtgttaattaatattgaagattcaaataaatttaaaataaaaaaggaatgatatttatgaaaaaattttttaaaatacttatagtatttacatttatatttaatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1233:FN1234|FN1233:FN1234:Putative NAD(P)H oxidoreductase:hypothetical protein:->->:1890072..1890279 208 tataattgttacaacaacctttatcaaaatttaaaagtctaagaagtagtgaaaaaaggaatataaatgattatattaaattcttggcttcaacttttgaagtgttaattaatattgaagattcaaataaatttaaaataaaaaaggaatgatatttatgaaaaaattttttaaaatacttatagtatttacatttatatttaatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tataattgttacaacaacctttatcaaaatttaaaagtctaagaagtagtgaaaaaaggaatataaatgattatattaaattcttggcttcaacttttgaagtgttaattaatattgaagattcaaataaatttaaaataaaaaaggaatgatatttatgaaaaaattttttaaaatacttatagtatttacatttatatttaatact Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 6 End: 149 ..... M L Q Q P L S K F K S L R S S E K R N I N D Y I K F L A S T F E V L I N I E D S N K F K I K K E ........................................................... Protein_Len: 44 Strand: - Start: 74 End: 205 ......................................................................... I L N K A E V K S T N I L I S S E F L N L I F F S H Y K H F F K K F Y K Y Y K C K Y K M ... tataattgttacaacaacctttatcaaaatttaaaagtctaagaagtagtgaaaaaaggaatataaatgattatattaaattcttggcttcaacttttgaagtgttaattaatattgaagattcaaataaatttaaaataaaaaaggaatgatatttatgaaaaaattttttaaaatacttatagtatttacatttatatttaatact 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: 81 Start: 148 End: 177 ...................................................................................................................................................AATGATATTTATGAAAAAATTTTTTAAAAT............................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tataattgttacaacaacctttatcaaaatttaaaagtctaagaagtagtgaaaaaaggaatataaatgattatattaaattcttggcttcaacttttgaagtgttaattaatattgaagattcaaataaatttaaaataaaaaaggaatgatatttatgaaaaaattttttaaaatacttatagtatttacatttatatttaatact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1233:FN1234|FN1233:FN1234:Putative NAD(P)H oxidoreductase:hypothetical protein:->->:1890072..1890279 208 tataattgttacaacaacctttatcaaaatttaaaagtctaagaagtagtgaaaaaaggaatataaatgattatattaaattcttggcttcaacttttgaagtgttaattaatattgaagattcaaataaatttaaaataaaaaaggaatgatatttatgaaaaaattttttaaaatacttatagtatttacatttatatttaatact Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: NC_003454_FN1233_FN1234|Putative NAD(P)H oxidoreductase:hypothetical protein|POSITIVE:POSITIVE|[1890072,1890279]|208 HSP 1 e-value: 2.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 tataattgttacaacaacctttatcaaaatttaaaagtctaagaagtagtgaaaaaaggaatataaatgattatattaaattcttggcttcaacttttgaagtg........................................................................................................ tataattgttacaacaacctttatcaaaatttaaaagtctaagaagtagtgaaaaaaggaatataaatgattatattaaattcttggcttcaacttttgaagtg........................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAUUGUUACAACAACCUUUAUCAAAAUUUAAAAGUCUAAGAAGUAGUGAAAAAAGGAAUAUAAAUGAUUAUAUUAAAUUCUUGGCUUCAACUUUUGAAGUG .....((((....))))............(((((((((....(((((...(((......(((((((....)))))))...)))...))))).)))))))))... (-14.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACUUCAAAAGUUGAAGCCAAGAAUUUAAUAUAAUCAUUUAUAUUCCUUUUUUCACUACUUCUUAGACUUUUAAAUUUUGAUAAAGGUUGUUGUAACAAUUAUA ......(((((((((((..(((((...(((((((....)))))))...))))).....))))...))))))).............((((((....))))))... (-11.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 196 100 62 229 179 NC_003454:FN1029|5end_Zinc_protease_1683611..1683841_NEGATIVE 190 60 17 116 81 NC_003454:FN0580|5end_Penicillin-binding_protein_1234930..1235160_POSITIVE 176 44 5 207 169 NC_003454:FN2102|5end_ABC_transporter_ATP-binding_protein_611177..611407_POSITIVE 172 59 17 168 122 NC_003454:FN1845|5end_Ceramide_glucosyltransferase_334387..334617_POSITIVE 171 89 42 149 95 NC_003454:FN1292|5end_hypothetical_protein_1950804..1951034_NEGATIVE 167 98 79 38 17 NC_003454:FN1107|5end_Acetyltransferase_1751961..1752191_POSITIVE 163 100 66 79 32 NC_003454:FN1312|5end_Biopolymer_transport_exbB_protein_1966948..1967178_NEGATIVE 157 42 3 104 65 NC_003454:FN0151|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_778771..779001_POSITIVE 157 100 81 58 34 NC_003454:FN2042|5end_Protein_translocase_subunit_SecE_549832..550062_NEGATIVE 157 100 81 231 207 NC_003454:FN2041|5end_Transcription_antitermination_protein_nusG_549659..549889_NEGATIVE 156 98 79 220 201 NC_003454:FN1380|5end_Citrate_lyase_beta_chain_2027248..2027478_POSITIVE 154 95 72 154 129 NC_003454:FN1917|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_413756..413986_NEGATIVE 153 82 45 53 15 NC_003454:FN1398|5end_Amino_acid_carrier_protein_alsT_2052808..2053038_POSITIVE 153 71 34 228 191 NC_003454:FN0829|5end_hypothetical_protein_1489873..1490103_NEGATIVE 150 41 9 220 186 NC_003454:FN0052|5end_Arsenate_reductase_688849..689079_POSITIVE 149 50 20 191 153 NC_003454:FN0343|5end_hypothetical_protein_976653..976883_NEGATIVE 149 59 19 52 13 NC_003454:FN1684|5end_N-acetylneuraminate_synthase_180138..180368_NEGATIVE 146 47 7 225 184 NC_003454:FN0214|5end_Crossover_junction_endodeoxyribonuclease_ruvC_839240..839470_NEGATIVE 145 96 71 118 88 NC_003454:FN0497|5end_Plasmid_addiction_system_poison_protein_1141133..1141363_POSITIVE 145 42 7 46 20 NC_003454:FN0173|5end_hypothetical_protein_797839..798069_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 173 86 43 149 104 NC_003454:FN1008|3end_hypothetical_protein_1662528..1662678_NEGATIVE 172 59 17 147 101 NC_003454:FN1844|3end_Ketoacyl_reductase_hetN_334446..334596_POSITIVE 152 100 68 126 83 NC_003454:FN1348|3end_ABC_transporter_ATP-binding_protein_2000470..2000620_NEGATIVE 150 41 9 90 56 NC_003454:FN0050|3end_Fumarate_reductase_flavoprotein_subunit_688799..688949_POSITIVE 149 100 57 134 87 NC_003454:FN0030|3end_5-nitroimidazole_antibiotic_resistance_protein_667676..667826_POSITIVE 149 59 19 55 16 NC_003454:FN1685|3end_dTDP-4-dehydrorhamnose_reductase_180135..180285_NEGATIVE 145 96 71 116 86 NC_003454:FN0496|3end_hypothetical_protein_1141211..1141361_POSITIVE 145 67 21 126 72 NC_003454:FN0023|3end_Short-chain_fatty_acids_transporter_662780..662930_POSITIVE 144 100 61 94 57 NC_003454:FN0810|3end_Low-specificity_threonine_aldolase_1470140..1470290_POSITIVE 144 62 33 48 11 NC_003454:FN0219|3end_Autolysin_response_regulator_842594..842744_NEGATIVE 142 53 20 41 10 NC_003454:FN0116|3end_Chaperone_protein_dnaK_750156..750306_POSITIVE 142 53 20 127 95 NC_003454:FN1754|3end_thiazole_synthase_250344..250494_NEGATIVE 142 58 36 49 21 NC_003454:FN1624|3end_preprotein_translocase_SecY_131080..131230_NEGATIVE 141 100 56 84 36 NC_003454:FN0118|3end_Chaperone_protein_dnaJ_752156..752306_POSITIVE 140 31 7 75 52 NC_003454:FN0358|3end_ATP_synthase_subunit_B_988286..988436_NEGATIVE 138 100 81 69 50 NC_003454:FN0073|3end_Dihydropteroate_synthase_713433..713583_POSITIVE 136 77 34 64 21 NC_003454:FN0699|3end_Protein_translocase_subunit_secD_1358366..1358516_POSITIVE 136 50 4 56 23 NC_003454:FN0698|3end_DNA_integration/recombination/invertion_protein_1357107..1357257_POSITIVE 135 61 31 47 16 NC_003454:FN0047|3end_Exodeoxyribonuclease_III_685268..685418_POSITIVE 135 99 68 51 22 NC_003454:FN0005|3end_Jag_protein_644579..644729_POSITIVE