Origin IGS: caacagatattccaataaaagtcagagatattatcattatttggtttgagagagtggtcatatctttaatattgatagtacccatagtaaagtttattttttaataaaaaaggaggttcttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagaacctccttttttattaaaaaataaactttactatgggtactatcaatattaaagatatgaccactctctcaaaccaaataatgataatatctctgacttttattggaatatctgttg Mask Tandem Repeat Region ================================================ caacagatattccaataaaagtcagagatattatcattatttggtttgagagagtggtcatatctttaatattgatagtacccatagtaaagtttattttttaataaaaaaggaggttcttt Find is-nt database================================================ Query_seq: FN1402:FN1403|FN1402:FN1403:Hypothetical membrane-spanning protein:Histidine permease:->->:2061761..2061882 122 caacagatattccaataaaagtcagagatattatcattatttggtttgagagagtggtcatatctttaatattgatagtacccatagtaaagtttattttttaataaaaaaggaggttcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1402:FN1403|FN1402:FN1403:Hypothetical membrane-spanning protein:Histidine permease:->->:2061761..2061882 122 caacagatattccaataaaagtcagagatattatcattatttggtttgagagagtggtcatatctttaatattgatagtacccatagtaaagtttattttttaataaaaaaggaggttcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1402:FN1403|FN1402:FN1403:Hypothetical membrane-spanning protein:Histidine permease:->->:2061761..2061882 122 caacagatattccaataaaagtcagagatattatcattatttggtttgagagagtggtcatatctttaatattgatagtacccatagtaaagtttattttttaataaaaaaggaggttcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caacagatattccaataaaagtcagagatattatcattatttggtttgagagagtggtcatatctttaatattgatagtacccatagtaaagtttattttttaataaaaaaggaggttcttt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 9 End: 101 ........ M P I K V R D I I I I W F E R V V I S L I L I V P I V K F I F ..................... Protein_Len: 32 Strand: - Start: 2 End: 97 . V S I G I F T L S I I M I Q N S L T T M D K I N I T G M T F N M ......................... caacagatattccaataaaagtcagagatattatcattatttggtttgagagagtggtcatatctttaatattgatagtacccatagtaaagtttattttttaataaaaaaggaggttcttt 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: 83 Start: 71 End: 100 ......................................................................ATTGATAGTACCCATAGTAAAGTTTATTTT...................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caacagatattccaataaaagtcagagatattatcattatttggtttgagagagtggtcatatctttaatattgatagtacccatagtaaagtttattttttaataaaaaaggaggttcttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1402:FN1403|FN1402:FN1403:Hypothetical membrane-spanning protein:Histidine permease:->->:2061761..2061882 122 caacagatattccaataaaagtcagagatattatcattatttggtttgagagagtggtcatatctttaatattgatagtacccatagtaaagtttattttttaataaaaaaggaggttcttt Intra-Species Hit: Count: 1 Min: 1 Max: 122 Len: 122 Subject: NC_003454_FN1402_FN1403|Hypothetical membrane-spanning protein:Histidine permease|POSITIVE:POSITIVE|[2061761,2061882]|122 HSP 1 e-value: 2.0E-63 bit: 242.0 Len: 122 Query Start:1 Query End:122 Subject Strand: POSITIVE Subject Start: 1 Subject End: 122 caacagatattccaataaaagtcagagatattatcattatttggtttgagagagtggtcatatctttaatattgatagtacccatagtaaagtttattttttaataaaaaaggaggttcttt caacagatattccaataaaagtcagagatattatcattatttggtttgagagagtggtcatatctttaatattgatagtacccatagtaaagtttattttttaataaaaaaggaggttcttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAACAGAUAUUCCAAUAAAAGUCAGAGAUAUUAUCAUUAUUUGGUUUGAGAGAGUGGUCAUAUCUUUAAUAUUGAUAGUACCCAUAGUAAAGUUUAUUUUUUAAUAAAAAAGGAGGUUCUUU ....(((..((((..........((((((((.((((((.(((......))).)))))).))))))))..((((((.((((..(........)..))))..)))))).....))))..))).. (-19.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGAACCUCCUUUUUUAUUAAAAAAUAAACUUUACUAUGGGUACUAUCAAUAUUAAAGAUAUGACCACUCUCUCAAACCAAAUAAUGAUAAUAUCUCUGACUUUUAUUGGAAUAUCUGUUG ..(((...(((...((((((....)))))).........(((((.(((((.((((........((......))........)))).))))).)))))............)))...))).... (-11.19) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 236 98 53 70 17 NC_003454:FN1053|5end_hypothetical_protein_1701023..1701253_POSITIVE 226 80 37 226 176 NC_003454:FN1524|5end_Dipeptide_transport_ATP-binding_protein_dppD_29799..30029_POSITIVE 210 77 32 150 93 NC_003454:FN1070|5end_glucose-inhibited_division_protein_A_1717121..1717351_POSITIVE 209 51 16 191 154 NC_003454:FN1643|5end_LSU_ribosomal_protein_L23P_140017..140247_NEGATIVE 208 80 37 110 70 NC_003454:FN0381|5end_hypothetical_protein_1012348..1012578_POSITIVE 200 74 31 81 39 NC_003454:FN1898|5end_Sugar_transport_ATP-binding_protein_386569..386799_NEGATIVE 197 98 52 46 1 NC_003454:FN1975|5end_ATP-dependent_RNA_helicase_475599..475829_POSITIVE 196 69 38 84 55 NC_003454:FN1145|5end_Oligoendopeptidase_F_1795931..1796161_NEGATIVE 192 67 22 175 120 NC_003454:FN1666|5end_hypothetical_protein_162824..163054_POSITIVE 190 115 73 190 135 NC_003454:FN1182|5end_hypothetical_protein_1845438..1845668_NEGATIVE 189 71 47 228 205 NC_003454:FN1811|5end_Manganese_transport_system_ATP-binding_protein_mntA_292850..293080_NEGATIVE 187 117 76 128 92 NC_003454:FN0319|5end_Citrate_(pro-3S)-lyase_ligase_956855..957085_NEGATIVE 186 77 36 54 18 NC_003454:FN0345|5end_Permease_978756..978986_NEGATIVE 182 77 41 207 174 NC_003454:FN0904|5end_NAD(FAD)-utilizing_dehydrogenase_1562097..1562327_POSITIVE 179 58 20 53 14 NC_003454:FN1334|5end_N-acetylmuramoyl-L-alanine_amidase_1988619..1988849_NEGATIVE 179 77 32 90 37 NC_003454:FN0077|5end_Ethanolamine_two-component_sensor_kinase_714704..714934_POSITIVE 177 97 55 104 60 NC_003454:FN0911|5end_Alpha-ribazole-5'-phosphate_phosphatase_1569318..1569548_NEGATIVE 175 98 51 223 173 NC_003454:FN1032|5end_hypothetical_protein_1686348..1686578_NEGATIVE 175 46 4 81 43 NC_003454:FN1729|5end_4-amino-4-deoxychorismate_lyase_229087..229317_NEGATIVE 174 118 89 208 173 NC_003454:FN1200|5end_hypothetical_protein_1861006..1861236_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 217 47 13 82 45 NC_003454:FN1383|3end_DNA_polymerase_III_alpha_subunit_2034455..2034605_NEGATIVE 208 80 37 43 3 NC_003454:FN0380|3end_hypothetical_protein_1012361..1012511_POSITIVE 202 120 93 52 24 NC_003454:FN1423|3end_Flavoprotein_2088853..2089003_NEGATIVE 190 68 24 85 43 NC_003454:FN1987|3end_Transcriptional_regulator,_GntR_family_490018..490168_NEGATIVE 186 58 20 84 50 NC_003454:FN1824|3end_putative_manganese-dependent_inorganic_pyrophosphatase_312280..312430_NEGATIVE 185 56 20 47 8 NC_003454:FN0115|3end_hypothetical_protein_748215..748365_NEGATIVE 184 55 12 42 3 NC_003454:FN2078|3end_Transcriptional_regulator,_DeoR_family_589424..589574_NEGATIVE 179 77 32 90 37 NC_003454:FN0076|3end_Ethanolamine_two-component_response_regulator_714784..714934_POSITIVE 177 97 55 99 55 NC_003454:FN0912|3end_Cobalamin_[5'-phosphate]_synthase_1569323..1569473_NEGATIVE 175 46 4 87 49 NC_003454:FN1730|3end_Anthranilate_synthase_component_I_229081..229231_NEGATIVE 174 118 89 67 32 NC_003454:FN1201|3end_hypothetical_protein_1861147..1861297_NEGATIVE 174 67 36 38 6 NC_003454:FN0847|3end_TPR-repeat-containing_proteins_1507132..1507282_POSITIVE 172 88 50 58 22 NC_003454:FN1435|3end_Export_ABC_transporter_2105347..2105497_POSITIVE 170 80 35 144 105 NC_003454:FN1715|3end_ATPase_212412..212562_POSITIVE 169 114 73 50 7 NC_003454:FN1052|3end_hypothetical_protein_1701067..1701217_POSITIVE 169 83 41 87 36 NC_003454:FN0782|3end_Methyltransferase_1438281..1438431_NEGATIVE 168 46 5 141 103 NC_003454:FN1927|3end_DEGV_protein_425415..425565_NEGATIVE 166 59 13 43 1 NC_003454:FN0067|3end_Isoleucyl-tRNA_synthetase_707418..707568_POSITIVE 166 49 22 147 110 NC_003454:FN1665|3end_Virulence-associated_protein_I_162894..163044_POSITIVE 163 55 21 100 64 NC_003454:FN1452|3end_Cell_division_protein_ftsA_2132733..2132883_NEGATIVE