Origin IGS: atatactttaaaatattttttttaaggataatttgatttaaaaaataattgacttatagatatatttattataaaataaacacagaatatttgtttaggaggtattttatgaaaaaatttttatttgcatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatgcaaataaaaattttttcataaaatacctcctaaacaaatattctgtgtttattttataataaatatatctataagtcaattattttttaaatcaaattatccttaaaaaaaatattttaaagtatat Mask Tandem Repeat Region ================================================ atatactttaaaatattttttttaaggataatttgatttaaaaaataattgacttatagatatatttattataaaataaacacagaatatttgtttaggaggtattttatgaaaaaatttttatttgcatta Find is-nt database================================================ Query_seq: FN1851:FN1852|FN1851:FN1852:Ribonuclease PH:hypothetical protein:->->:341624..341755 132 atatactttaaaatattttttttaaggataatttgatttaaaaaataattgacttatagatatatttattataaaataaacacagaatatttgtttaggaggtattttatgaaaaaatttttatttgcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1851:FN1852|FN1851:FN1852:Ribonuclease PH:hypothetical protein:->->:341624..341755 132 atatactttaaaatattttttttaaggataatttgatttaaaaaataattgacttatagatatatttattataaaataaacacagaatatttgtttaggaggtattttatgaaaaaatttttatttgcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1851:FN1852|FN1851:FN1852:Ribonuclease PH:hypothetical protein:->->:341624..341755 132 atatactttaaaatattttttttaaggataatttgatttaaaaaataattgacttatagatatatttattataaaataaacacagaatatttgtttaggaggtattttatgaaaaaatttttatttgcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atatactttaaaatattttttttaaggataatttgatttaaaaaataattgacttatagatatatttattataaaataaacacagaatatttgtttaggaggtattttatgaaaaaatttttatttgcatta Predict ORF larger than 30AA ================================================ atatactttaaaatattttttttaaggataatttgatttaaaaaataattgacttatagatatatttattataaaataaacacagaatatttgtttaggaggtattttatgaaaaaatttttatttgcatta 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: 88 Start: 48 End: 77 ...............................................ATTGACTTATAGATATATTTATTATAAAAT....................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 37 End: 66 ....................................TTTAAAAAATAATTGACTTATAGATATATT.................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atatactttaaaatattttttttaaggataatttgatttaaaaaataattgacttatagatatatttattataaaataaacacagaatatttgtttaggaggtattttatgaaaaaatttttatttgcatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1851:FN1852|FN1851:FN1852:Ribonuclease PH:hypothetical protein:->->:341624..341755 132 atatactttaaaatattttttttaaggataatttgatttaaaaaataattgacttatagatatatttattataaaataaacacagaatatttgtttaggaggtattttatgaaaaaatttttatttgcatta Intra-Species Hit: Count: 1 Min: 24 Max: 132 Len: 109 Subject: NC_003454_FN1851_FN1852|Ribonuclease PH:hypothetical protein|POSITIVE:POSITIVE|[341624,341755]|132 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:24 Query End:132 Subject Strand: POSITIVE Subject Start: 24 Subject End: 132 .......................aaggataatttgatttaaaaaataattgacttatagatatatttattataaaataaacacagaatatttgtttaggaggtattttatgaaaaaatttttatttgcatta .......................aaggataatttgatttaaaaaataattgacttatagatatatttattataaaataaacacagaatatttgtttaggaggtattttatgaaaaaatttttatttgcatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGAUAAUUUGAUUUAAAAAAUAAUUGACUUAUAGAUAUAUUUAUUAUAAAAUAAACACAGAAUAUUUGUUUAGGAGGUAUUUUAUGAAAAAAUUUUUAUUUGCAUUA ....((((.(..(((........)))..).)))).......(((.((((((((((....(.((((....)))).)....)))))))))).)))................ ( -9.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGCAAAUAAAAAUUUUUUCAUAAAAUACCUCCUAAACAAAUAUUCUGUGUUUAUUUUAUAAUAAAUAUAUCUAUAAGUCAAUUAUUUUUUAAAUCAAAUUAUCCUU ......((((((..(((((.....)))))...................((((((((((....))))))))))............))))))................... ( -5.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 97 51 211 155 NC_003454:FN0122|5end_hypothetical_protein_753401..753631_POSITIVE 184 90 41 216 175 NC_003454:FN1802|5end_hypothetical_protein_283948..284178_POSITIVE 180 94 61 152 110 NC_003454:FN1904|5end_Transcriptional_regulator,_MarR_family_393107..393337_POSITIVE 170 94 61 180 149 NC_003454:FN0588|5end_hypothetical_protein_1242402..1242632_NEGATIVE 166 97 66 88 54 NC_003454:FN0037|5end_hypothetical_protein_678061..678291_NEGATIVE 165 80 38 199 156 NC_003454:FN0278|5end_Xaa-His_dipeptidase_905664..905894_NEGATIVE 162 85 62 55 30 NC_003454:FN1514|5end_Phophatidylinositol-4-phosphate_5-kinase_17376..17606_POSITIVE 160 87 56 55 23 NC_003454:FN0955|5end_hypothetical_protein_1612455..1612685_NEGATIVE 158 83 49 189 151 NC_003454:FN0331|5end_hypothetical_protein_965099..965329_POSITIVE 157 90 71 67 47 NC_003454:FN1640|5end_LSU_ribosomal_protein_L22P_138517..138747_NEGATIVE 153 66 28 208 174 NC_003454:FN1348|5end_ABC_transporter_ATP-binding_protein_2001141..2001371_NEGATIVE 153 89 46 201 152 NC_003454:FN0190|5end_Two-component_sensor_kinase_yesM_813975..814205_POSITIVE 152 93 65 130 99 NC_003454:FN0686|5end_Integral_membrane_protein_1342498..1342728_NEGATIVE 150 93 53 225 190 NC_003454:FN0602|5end_hypothetical_protein_1256649..1256879_POSITIVE 148 92 68 207 186 NC_003454:FN1232|5end_Transcriptional_regulator,_MarR_family_1889341..1889571_NEGATIVE 147 64 29 230 187 NC_003454:FN0710|5end_hypothetical_protein_1368875..1369105_POSITIVE 145 88 44 208 165 NC_003454:FN1418|5end_AMINOTRANSFERASE_CLASS-I_2080500..2080730_NEGATIVE 145 83 43 202 160 NC_003454:FN1679|5end_LPS_biosynthesis_protein_WbpG_175711..175941_NEGATIVE 144 53 17 214 177 NC_003454:FN1313|5end_Oligopeptide-binding_protein_oppA_1967053..1967283_POSITIVE 143 95 66 231 198 NC_003454:FN0917|5end_hypothetical_protein_1572595..1572825_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 160 87 56 52 20 NC_003454:FN0956|3end_hypothetical_protein_1612458..1612608_NEGATIVE 159 93 67 30 7 NC_003454:FN1007|3end_hypothetical_protein_1662482..1662632_POSITIVE 158 83 49 74 36 NC_003454:FN0330|3end_SSU_ribosomal_protein_S9P_965064..965214_POSITIVE 157 90 71 32 12 NC_003454:FN1641|3end_SSU_ribosomal_protein_S19P_138552..138702_NEGATIVE 149 86 42 127 87 NC_003454:FN0575|3end_hypothetical_protein_1225584..1225734_POSITIVE 145 100 58 107 68 NC_003454:FN0935|3end_hypothetical_protein_1587558..1587708_NEGATIVE 143 85 43 48 1 NC_003454:FN1714|3end_hypothetical_protein_211036..211186_POSITIVE 138 90 41 117 56 NC_003454:FN0299|3end_Aspartyl-tRNA_synthetase_934251..934401_POSITIVE 137 98 51 60 19 NC_003454:FN0418|3end_pyrimidine_regulatory_protein_PyrR_1059731..1059881_POSITIVE 136 93 72 64 43 NC_003454:FN0819|3end_Tetratricopeptide_repeat_family_protein_1479325..1479475_POSITIVE 136 85 58 134 108 NC_003454:FN0751|3end_L-asparaginase_I_1409721..1409871_NEGATIVE 135 83 52 82 40 NC_003454:FN0054|3end_tyrosyl-tRNA_synthetase_692136..692286_POSITIVE 133 85 66 146 126 NC_003454:FN0287|3end_Dimethyladenosine_transferase_914434..914584_NEGATIVE 132 100 61 151 114 NC_003454:FN0582|3end_Lipoprotein_releasing_system_ATP-binding_protein_lolD_1239027..1239177_POSITIVE 129 85 60 110 86 NC_003454:FN1283|3end_DNA-directed_RNA_polymerase_alpha_subunit_1941647..1941797_NEGATIVE 129 51 25 43 15 NC_003454:FN0884|3end_Hemin_transport_system_permease_protein_hmuU_1543704..1543854_NEGATIVE 122 89 72 62 42 NC_003454:FN1999|3end_HIPA_protein_500869..501019_POSITIVE 121 90 65 120 92 NC_003454:FN0701|3end_Methyltransferase_1360894..1361044_POSITIVE 120 87 67 134 109 NC_003454:FN0214|3end_Crossover_junction_endodeoxyribonuclease_ruvC_838668..838818_NEGATIVE 119 86 53 113 76 NC_003454:FN0152|3end_Ribonuclease_III_780812..780962_POSITIVE