Origin IGS: tagttatataaaaggttgaatcttttaattaaggattcaatcttttattatagaaatctgcaacctttacaaaagttgataaaaatagtataatttaaaaaagttttaattatagaaggagaaaaatttatgaataaaaaaattataattgtaggtggggttgcagcaggc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcctgctgcaaccccacctacaattataatttttttattcataaatttttctccttctataattaaaacttttttaaattatactatttttatcaacttttgtaaaggttgcagatttctataataaaagattgaatccttaattaaaagattcaaccttttatataacta Mask Tandem Repeat Region ================================================ tagttatataaaaggttgaatcttttaattaaggattcaatcttttattatagaaatctgcaacctttacaaaagttgataaaaatagtataatttaaaaaagttttaattatagaaggagaaaaatttatgaataaaaaaattataattgtaggtggggttgcagcaggc Find is-nt database================================================ Query_seq: FN1087:FN1088|FN1087:FN1088:hypothetical protein:NADH oxidase:->->:1731677..1731847 171 tagttatataaaaggttgaatcttttaattaaggattcaatcttttattatagaaatctgcaacctttacaaaagttgataaaaatagtataatttaaaaaagttttaattatagaaggagaaaaatttatgaataaaaaaattataattgtaggtggggttgcagcaggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1087:FN1088|FN1087:FN1088:hypothetical protein:NADH oxidase:->->:1731677..1731847 171 tagttatataaaaggttgaatcttttaattaaggattcaatcttttattatagaaatctgcaacctttacaaaagttgataaaaatagtataatttaaaaaagttttaattatagaaggagaaaaatttatgaataaaaaaattataattgtaggtggggttgcagcaggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1087:FN1088|FN1087:FN1088:hypothetical protein:NADH oxidase:->->:1731677..1731847 171 tagttatataaaaggttgaatcttttaattaaggattcaatcttttattatagaaatctgcaacctttacaaaagttgataaaaatagtataatttaaaaaagttttaattatagaaggagaaaaatttatgaataaaaaaattataattgtaggtggggttgcagcaggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagttatataaaaggttgaatcttttaattaaggattcaatcttttattatagaaatctgcaacctttacaaaagttgataaaaatagtataatttaaaaaagttttaattatagaaggagaaaaatttatgaataaaaaaattataattgtaggtggggttgcagcaggc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 51 End: 149 .................................................. L F R C G K C F N I F I T Y N L F T K I I S P S F N I F L F I I M ...................... tagttatataaaaggttgaatcttttaattaaggattcaatcttttattatagaaatctgcaacctttacaaaagttgataaaaatagtataatttaaaaaagttttaattatagaaggagaaaaatttatgaataaaaaaattataattgtaggtggggttgcagcaggc 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: 87 Start: 65 End: 94 ................................................................CTTTACAAAAGTTGATAAAAATAGTATAAT............................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagttatataaaaggttgaatcttttaattaaggattcaatcttttattatagaaatctgcaacctttacaaaagttgataaaaatagtataatttaaaaaagttttaattatagaaggagaaaaatttatgaataaaaaaattataattgtaggtggggttgcagcaggc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1087:FN1088|FN1087:FN1088:hypothetical protein:NADH oxidase:->->:1731677..1731847 171 tagttatataaaaggttgaatcttttaattaaggattcaatcttttattatagaaatctgcaacctttacaaaagttgataaaaatagtataatttaaaaaagttttaattatagaaggagaaaaatttatgaataaaaaaattataattgtaggtggggttgcagcaggc Intra-Species Hit: Count: 1 Min: 1 Max: 171 Len: 171 Subject: NC_003454_FN1087_FN1088|hypothetical protein:NADH oxidase|POSITIVE:POSITIVE|[1731677,1731847]|171 HSP 1 e-value: 6.0E-37 bit: 155.0 Len: 78 Query Start:1 Query End:78 Subject Strand: POSITIVE Subject Start: 1 Subject End: 78 tagttatataaaaggttgaatcttttaattaaggattcaatcttttattatagaaatctgcaacctttacaaaagttg............................................................................................. tagttatataaaaggttgaatcttttaattaaggattcaatcttttattatagaaatctgcaacctttacaaaagttg............................................................................................. HSP 2 e-value: 2.0E-6 bit: 54.0 Len: 27 Query Start:145 Query End:171 Subject Strand: POSITIVE Subject Start: 145 Subject End: 171 ................................................................................................................................................ataattgtaggtggggttgcagcaggc ................................................................................................................................................ataattgtaggtggggttgcagcaggc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUUAUAUAAAAGGUUGAAUCUUUUAAUUAAGGAUUCAAUCUUUUAUUAUAGAAAUCUGCAACCUUUACAAAAGUUGAUAAAAAUAGUAUAAUUUAAAAAAGUUUUAAUUAUAGAAGGAGAAAAAUUUAUGAAUAAAAAAAUUAUAAUUGUAGGUGGGGUUGCAGCAGGC ...((((((((((((((((((((((.....))))))))))))))))).)))))....((((((((((.((....(((......)))..(((((((........(((((.(((((((..........))))))).))))).......))))))).))))))))))))..... (-40.96) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCUGCUGCAACCCCACCUACAAUUAUAAUUUUUUUAUUCAUAAAUUUUUCUCCUUCUAUAAUUAAAACUUUUUUAAAUUAUACUAUUUUUAUCAACUUUUGUAAAGGUUGCAGAUUUCUAUAAUAAAAGAUUGAAUCCUUAAUUAAAAGAUUCAACCUUUUAUAUAACUA .....((((((((.....(((((..((((.....))))...................(((((((.(((....))).)))))))................)))))..)))))))).........(((((((.(((((((.((.....)).))))))).)))))))....... (-26.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 170 126 181 140 NC_003454:FN1904|5end_Transcriptional_regulator,_MarR_family_393107..393337_POSITIVE 214 50 7 218 177 NC_003454:FN1361|5end_Dipeptide_transport_system_permease_protein_dppC_2013051..2013281_POSITIVE 204 168 126 218 183 NC_003454:FN0205|5end_Sodium/glutamate_symport_carrier_protein_831469..831699_POSITIVE 201 169 154 36 18 NC_003454:FN1735|5end_V-type_ATP_synthase_subunit_A_235399..235629_NEGATIVE 196 68 27 46 4 NC_003454:FN0178|5end_UNC-44_ankyrins_803370..803600_NEGATIVE 195 68 21 151 107 NC_003454:FN1994|5end_hypothetical_protein_497577..497807_POSITIVE 192 169 153 135 117 NC_003454:FN1711|5end_Methyltransferase_206325..206555_POSITIVE 190 164 141 70 44 NC_003454:FN2002|5end_Permease_503563..503793_NEGATIVE 185 155 114 228 180 NC_003454:FN0691|5end_hypothetical_protein_1346372..1346602_NEGATIVE 185 72 32 164 121 NC_003454:FN1576|5end_ATPase_and_helicase_subunits_involved_in_DNA_replication_87374..87604_NEGATIVE 184 68 21 155 108 NC_003454:FN2124|5end_Hypothetical_protein_with_Metallo-phosphoesterase_motif_633712..633942_NEGATIVE 182 69 27 147 110 NC_003454:FN1258|5end_C4-dicarboxylate-binding_protein_1914793..1915023_NEGATIVE 182 170 128 49 3 NC_003454:FN1732|5end_hypothetical_protein_232078..232308_NEGATIVE 178 85 52 185 149 NC_003454:FN0115|5end_hypothetical_protein_748511..748741_NEGATIVE 175 169 154 185 171 NC_003454:FN0422|5end_carbamoyl-phosphate_synthase_large_subunit_1063012..1063242_POSITIVE 173 79 52 180 153 NC_003454:FN1995|5end_hypothetical_protein_498245..498475_POSITIVE 172 76 56 211 194 NC_003454:FN1532|5end_murein_hydrolase_exporter_45319..45549_NEGATIVE 171 170 127 180 130 NC_003454:FN1362|5end_Dipeptide_transport_ATP-binding_protein_dppD_2013818..2014048_POSITIVE 171 77 31 204 161 NC_003454:FN1080|5end_Export_ABC_transporter_1725534..1725764_POSITIVE 171 68 24 107 65 NC_003454:FN0717|5end_Ribosomal_small_subunit_pseudouridine_synthase_A_1374913..1375143_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 361 48 8 83 43 NC_003454:FN1087|3end_hypothetical_protein_1731616..1731766_POSITIVE 217 130 102 63 36 NC_003454:FN1679|3end_LPS_biosynthesis_protein_WbpG_174590..174740_NEGATIVE 210 166 127 48 4 NC_003454:FN0794|3end_hypothetical_protein_1451840..1451990_NEGATIVE 204 168 126 75 40 NC_003454:FN0204|3end_Glutaconyl-CoA_decarboxylase_A_subunit_831406..831556_POSITIVE 201 169 154 22 4 NC_003454:FN1736|3end_V-type_sodium_ATP_synthase_subunit_A_235413..235563_NEGATIVE 195 68 21 144 100 NC_003454:FN1993|3end_SUA5_protein_497650..497800_POSITIVE 192 169 153 77 59 NC_003454:FN1710|3end_Integral_membrane_protein,_YGGT_family_206347..206497_POSITIVE 190 170 149 70 48 NC_003454:FN0033|3end_hypothetical_protein_670146..670296_NEGATIVE 184 68 21 142 95 NC_003454:FN2125|3end_DNA_gyrase_subunit_A_633725..633875_NEGATIVE 180 156 112 53 18 NC_003454:FN2054|3end_glucose-6-phosphate_isomerase_563962..564112_POSITIVE 177 50 1 44 3 NC_003454:FN1983|3end_Alkyl_hydroperoxide_reductase_C22_protein_485265..485415_POSITIVE 171 49 12 73 40 NC_003454:FN1421|3end_Pyruvate-flavodoxin_oxidoreductase_2086957..2087107_POSITIVE 171 77 31 67 24 NC_003454:FN1079|3end_Neutrophil-activating_protein_A_1725477..1725627_POSITIVE 171 68 24 107 65 NC_003454:FN0716|3end_Phophatidylinositol-4-phosphate_5-kinase_1374993..1375143_POSITIVE 168 169 142 134 107 NC_003454:FN1850|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_III_340214..340364_POSITIVE 164 127 93 54 14 NC_003454:FN1733|3end_ATP_synthase_subunit_D_232236..232386_NEGATIVE 164 165 147 45 27 NC_003454:FN1499|3end_Cell_surface_protein_5166..5316_POSITIVE 163 69 21 103 44 NC_003454:FN0287|3end_Dimethyladenosine_transferase_914434..914584_NEGATIVE 162 168 140 26 1 NC_003454:FN1755|3end_thiamine_biosynthesis_protein_ThiF_251240..251390_NEGATIVE 159 89 41 147 87 NC_003454:FN0704|3end_hypothetical_protein_1361661..1361811_NEGATIVE