Origin IGS: ccccttaatctttcctatttagtcttgctccaaagggggtttaccaagcttttttagtttcctaaaaaactggtggtctcttacaccaccttttcacccttaccttaatggcggtctattttctgtggcactttccttaaaattgcttttagtagccgttagctacccttttgctctgtggagctcggactttcctctgccataaagacagcgattaacttgaatacctaaaattttt .........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 aaaaattttaggtattcaagttaatcgctgtctttatggcagaggaaagtccgagctccacagagcaaaagggtagctaacggctactaaaagcaattttaaggaaagtgccacagaaaatagaccgccattaaggtaagggtgaaaaggtggtgtaagagaccaccagttttttaggaaactaaaaaagcttggtaaaccccctttggagcaagactaaataggaaagattaagggg Mask Tandem Repeat Region ================================================ ccccttaatctttcctatttagtcttgctccaaagggggtttaccaagcttttttagtttcctaaaaaactggtggtctcttacaccaccttttcacccttaccttaatggcggtctattttctgtggcactttccttaaaattgcttttagtagccgttagctacccttttgctctgtggagctcggactttcctctgccataaagacagcgattaacttgaatacctaaaattttt Find is-nt database================================================ Query_seq: FN1314:FN1315|FN1314:FN1315:hypothetical protein:hypothetical protein:<-<-:1968773..1969010 238 ccccttaatctttcctatttagtcttgctccaaagggggtttaccaagcttttttagtttcctaaaaaactggtggtctcttacaccaccttttcacccttaccttaatggcggtctattttctgtggcactttccttaaaattgcttttagtagccgttagctacccttttgctctgtggagctcggactttcctctgccataaagacagcgattaacttgaatacctaaaattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1314:FN1315|FN1314:FN1315:hypothetical protein:hypothetical protein:<-<-:1968773..1969010 238 ccccttaatctttcctatttagtcttgctccaaagggggtttaccaagcttttttagtttcctaaaaaactggtggtctcttacaccaccttttcacccttaccttaatggcggtctattttctgtggcactttccttaaaattgcttttagtagccgttagctacccttttgctctgtggagctcggactttcctctgccataaagacagcgattaacttgaatacctaaaattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1314:FN1315|FN1314:FN1315:hypothetical protein:hypothetical protein:<-<-:1968773..1969010 238 ccccttaatctttcctatttagtcttgctccaaagggggtttaccaagcttttttagtttcctaaaaaactggtggtctcttacaccaccttttcacccttaccttaatggcggtctattttctgtggcactttccttaaaattgcttttagtagccgttagctacccttttgctctgtggagctcggactttcctctgccataaagacagcgattaacttgaatacctaaaattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccccttaatctttcctatttagtcttgctccaaagggggtttaccaagcttttttagtttcctaaaaaactggtggtctcttacaccaccttttcacccttaccttaatggcggtctattttctgtggcactttccttaaaattgcttttagtagccgttagctacccttttgctctgtggagctcggactttcctctgccataaagacagcgattaacttgaatacctaaaattttt Predict ORF larger than 30AA ================================================ ccccttaatctttcctatttagtcttgctccaaagggggtttaccaagcttttttagtttcctaaaaaactggtggtctcttacaccaccttttcacccttaccttaatggcggtctattttctgtggcactttccttaaaattgcttttagtagccgttagctacccttttgctctgtggagctcggactttcctctgccataaagacagcgattaacttgaatacctaaaattttt 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================================================ ccccttaatctttcctatttagtcttgctccaaagggggtttaccaagcttttttagtttcctaaaaaactggtggtctcttacaccaccttttcacccttaccttaatggcggtctattttctgtggcactttccttaaaattgcttttagtagccgttagctacccttttgctctgtggagctcggactttcctctgccataaagacagcgattaacttgaatacctaaaattttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 72 HP_score: -7.4 Tail_Score: -4.1466 Start: 72 End: 90 Full_Region: GTTTCCTAAAAAACT GGTGGTCT CTT ACACCACC TTTTCACCCTTACCT .......................................................................GGTGGTCTCTTACACCACC.................................................................................................................................................... Find igs database================================================ Query_seq: FN1314:FN1315|FN1314:FN1315:hypothetical protein:hypothetical protein:<-<-:1968773..1969010 238 ccccttaatctttcctatttagtcttgctccaaagggggtttaccaagcttttttagtttcctaaaaaactggtggtctcttacaccaccttttcacccttaccttaatggcggtctattttctgtggcactttccttaaaattgcttttagtagccgttagctacccttttgctctgtggagctcggactttcctctgccataaagacagcgattaacttgaatacctaaaattttt Intra-Species Hit: Count: 1 Min: 1 Max: 238 Len: 238 Subject: NC_003454_FN1314_FN1315|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1968773,1969010]|238 HSP 1 e-value: 1.0E-132 bit: 472.0 Len: 238 Query Start:1 Query End:238 Subject Strand: POSITIVE Subject Start: 1 Subject End: 238 ccccttaatctttcctatttagtcttgctccaaagggggtttaccaagcttttttagtttcctaaaaaactggtggtctcttacaccaccttttcacccttaccttaatggcggtctattttctgtggcactttccttaaaattgcttttagtagccgttagctacccttttgctctgtggagctcggactttcctctgccataaagacagcgattaacttgaatacctaaaattttt ccccttaatctttcctatttagtcttgctccaaagggggtttaccaagcttttttagtttcctaaaaaactggtggtctcttacaccaccttttcacccttaccttaatggcggtctattttctgtggcactttccttaaaattgcttttagtagccgttagctacccttttgctctgtggagctcggactttcctctgccataaagacagcgattaacttgaatacctaaaattttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCCUUAAUCUUUCCUAUUUAGUCUUGCUCCAAAGGGGGUUUACCAAGCUUUUUUAGUUUCCUAAAAAACUGGUGGUCUCUUACACCACCUUUUCACCCUUACCUUAAUGGCGGUCUAUUUUCUGUGGCACUUUCCUUAAAAUUGCUUUUAGUAGCCGUUAGCUACCCUUUUGCUCUGUGGAGCUCGGACUUUCCUCUGCCAUAAAGACAGCGAUUAACUUGAAUACCUAAAAUUUUU ...............((((((((.(((((...(((((.........((.((((((((....))))))))))((((((.......))))))......)))))..(((.(((((((.......((((.((((.(((.....))).))))....(((((.....)))))......((((....)))).)))).......))))))).)))..)))))...)).))))))............ (-52.34) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUUUUAGGUAUUCAAGUUAAUCGCUGUCUUUAUGGCAGAGGAAAGUCCGAGCUCCACAGAGCAAAAGGGUAGCUAACGGCUACUAAAAGCAAUUUUAAGGAAAGUGCCACAGAAAAUAGACCGCCAUUAAGGUAAGGGUGAAAAGGUGGUGUAAGAGACCACCAGUUUUUUAGGAAACUAAAAAAGCUUGGUAAACCCCCUUUGGAGCAAGACUAAAUAGGAAAGAUUAAGGGG ....................((((((.(((((.....))))).....((((...((((((....((.....((((((.....))))))....))......((((....(((((.((.......((((((.....)))...))).....((((((.......))))))..((((((((....)))))))).))))))).....))))))))))..))))..........)))))).... (-63.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 943 120 71 211 162 NC_003454:FN1314|5end_hypothetical_protein_1968682..1968912_NEGATIVE 316 209 168 76 34 NC_003454:FN0508|5end_Serine_protease_1158652..1158882_NEGATIVE 282 220 174 212 173 NC_003454:FN1226|5end_uracil-DNA_glycosylase_1885503..1885733_NEGATIVE 262 217 178 212 166 NC_003454:FN1904|5end_Transcriptional_regulator,_MarR_family_393107..393337_POSITIVE 261 177 131 229 181 NC_003454:FN1787|5end_Tetratricopeptide_repeat_family_protein_267762..267992_POSITIVE 260 128 89 66 24 NC_003454:FN1092|5end_hypothetical_protein_1737267..1737497_POSITIVE 257 175 131 135 95 NC_003454:FN1367|5end_Methyl-accepting_chemotaxis_protein_2018143..2018373_NEGATIVE 256 200 151 85 17 NC_003454:FN1253|5end_hypothetical_protein_1910405..1910635_NEGATIVE 256 156 111 37 3 NC_003454:FN0325|5end_50S_ribosomal_protein_L20_961274..961504_NEGATIVE 254 185 143 117 73 NC_003454:FN1733|5end_ATP_synthase_subunit_D_232871..233101_NEGATIVE 252 186 144 168 124 NC_003454:FN0764|5end_Transporter,_LysE_family_1420327..1420557_POSITIVE 250 47 2 54 12 NC_003454:FN0934|5end_chorismate_synthase_1586440..1586670_POSITIVE 249 200 157 45 3 NC_003454:FN1490|5end_4-hydroxybenzoate_octaprenyltransferase_2172283..2172513_NEGATIVE 246 100 51 106 61 NC_003454:FN1713|5end_tRNA_(Uracil-5-)_-methyltransferase_207494..207724_POSITIVE 243 91 69 187 164 NC_003454:FN1487|5end_hypothetical_protein_2170020..2170250_NEGATIVE 243 198 156 227 178 NC_003454:FN1126|5end_Acetyltransferase_1770287..1770517_NEGATIVE 243 164 125 65 22 NC_003454:FN2003|5end_bioY_protein_503745..503975_POSITIVE 242 200 151 216 165 NC_003454:FN1051|5end_hypothetical_protein_1699781..1700011_POSITIVE 242 200 151 185 135 NC_003454:FN1506|5end_5-amino-6-(5-phosphoribosylamino)uracil_reductase_10871..11101_POSITIVE 241 41 10 192 165 NC_003454:FN0237|5end_ABC_transporter_permease_protein_862128..862358_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 171 131 128 85 NC_003454:FN2059|3end_Outer_membrane_protein_572877..573027_NEGATIVE 296 171 131 128 85 NC_003454:FN2048|3end_Outer_membrane_protein_558801..558951_NEGATIVE 260 128 89 57 15 NC_003454:FN1091|3end_Sigma_factor_sigB_regulation_protein_rsbU_1737338..1737488_POSITIVE 257 175 131 121 81 NC_003454:FN1368|3end_COMF_operon_protein_3_2018157..2018307_NEGATIVE 254 185 143 106 62 NC_003454:FN1734|3end_V-type_ATP_synthase_subunit_B_232882..233032_NEGATIVE 251 71 32 145 105 NC_003454:FN0069|3end_glycyl-tRNA_synthetase_alpha_subunit_708761..708911_POSITIVE 250 47 2 70 28 NC_003454:FN0933|3end_3-phosphoshikimate_1-carboxyvinyltransferase_1586536..1586686_POSITIVE 246 100 51 140 95 NC_003454:FN1712|3end_hypothetical_protein_207608..207758_POSITIVE 237 209 163 58 9 NC_003454:FN0183|3end_Glycerol-3-phosphate_dehydrogenase_807078..807228_NEGATIVE 237 137 94 136 91 NC_003454:FN1833|3end_Biopolymer_transport_exbD_protein_322222..322372_NEGATIVE 236 105 63 112 54 NC_003454:FN1429|3end_Branched-chain_amino_acid_transport_ATP-binding_protein_livG_2097573..2097723_NEGATIVE 236 129 86 138 98 NC_003454:FN0540|3end_Glutamate-1-semialdehyde_2,1-aminomutase_1192641..1192791_NEGATIVE 236 190 146 140 75 NC_003454:FN0272|3end_Acetoacetate:butyrate/acetate_coenzyme_A_transferase_899503..899653_POSITIVE 235 77 32 70 30 NC_003454:FN1994|3end_hypothetical_protein_498091..498241_POSITIVE 231 46 1 133 99 NC_003454:FN1639|3end_SSU_ribosomal_protein_S3P_137504..137654_NEGATIVE 228 203 163 53 10 NC_003454:FN0041|3end_hypothetical_protein_680619..680769_NEGATIVE 228 179 142 81 40 NC_003454:FN1641|3end_SSU_ribosomal_protein_S19P_138552..138702_NEGATIVE 227 173 145 137 98 NC_003454:FN1780|3end_hypothetical_protein_260921..261071_NEGATIVE 226 186 143 134 91 NC_003454:FN0136|3end_Transposase_770813..770963_POSITIVE 226 186 143 134 91 NC_003454:FN1887|3end_Transposase_372260..372410_POSITIVE