Origin IGS: tttgtcccccttaacaatttaatgaaatattttatataacttataatatattacaaattataaaaaatgtctatctctttttttttaaaatattaaaaaataaatattttgtataggaaatatattgacttttaaagatgtttgatatatgatagaagagtaataaaactttataacaagctaaatattttaggggtgaaagaaatgaagaagtattttaaatct .........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 agatttaaaatacttcttcatttctttcacccctaaaatatttagcttgttataaagttttattactcttctatcatatatcaaacatctttaaaagtcaatatatttcctatacaaaatatttattttttaatattttaaaaaaaaagagatagacattttttataatttgtaatatattataagttatataaaatatttcattaaattgttaagggggacaaa Mask Tandem Repeat Region ================================================ tttgtcccccttaacaatttaatgaaatattttatataacttataatatattacaaattataaaaaatgtctatctctttttttttaaaatattaaaaaataaatattttgtataggaaatatattgacttttaaagatgtttgatatatgatagaagagtaataaaactttataacaagctaaatattttaggggtgaaagaaatgaagaagtattttaaatct Find is-nt database================================================ Query_seq: FN1250:FN1251|FN1250:FN1251:Guanine-hypoxanthine permease:High-affinity iron permease:<-->:1907923..1908147 225 tttgtcccccttaacaatttaatgaaatattttatataacttataatatattacaaattataaaaaatgtctatctctttttttttaaaatattaaaaaataaatattttgtataggaaatatattgacttttaaagatgtttgatatatgatagaagagtaataaaactttataacaagctaaatattttaggggtgaaagaaatgaagaagtattttaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1250:FN1251|FN1250:FN1251:Guanine-hypoxanthine permease:High-affinity iron permease:<-->:1907923..1908147 225 tttgtcccccttaacaatttaatgaaatattttatataacttataatatattacaaattataaaaaatgtctatctctttttttttaaaatattaaaaaataaatattttgtataggaaatatattgacttttaaagatgtttgatatatgatagaagagtaataaaactttataacaagctaaatattttaggggtgaaagaaatgaagaagtattttaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1250:FN1251|FN1250:FN1251:Guanine-hypoxanthine permease:High-affinity iron permease:<-->:1907923..1908147 225 tttgtcccccttaacaatttaatgaaatattttatataacttataatatattacaaattataaaaaatgtctatctctttttttttaaaatattaaaaaataaatattttgtataggaaatatattgacttttaaagatgtttgatatatgatagaagagtaataaaactttataacaagctaaatattttaggggtgaaagaaatgaagaagtattttaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttgtcccccttaacaatttaatgaaatattttatataacttataatatattacaaattataaaaaatgtctatctctttttttttaaaatattaaaaaataaatattttgtataggaaatatattgacttttaaagatgtttgatatatgatagaagagtaataaaactttataacaagctaaatattttaggggtgaaagaaatgaagaagtattttaaatct Predict ORF larger than 30AA ================================================ tttgtcccccttaacaatttaatgaaatattttatataacttataatatattacaaattataaaaaatgtctatctctttttttttaaaatattaaaaaataaatattttgtataggaaatatattgacttttaaagatgtttgatatatgatagaagagtaataaaactttataacaagctaaatattttaggggtgaaagaaatgaagaagtattttaaatct 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: 124 End: 153 ...........................................................................................................................ATTGACTTTTAAAGATGTTTGATATATGAT........................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 45 End: 74 ............................................ATAGACATTTTTTATAATTTGTAATATATT....................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 18 End: 47 .................TTTAATGAAATATTTTATATAACTTATAAT.................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttgtcccccttaacaatttaatgaaatattttatataacttataatatattacaaattataaaaaatgtctatctctttttttttaaaatattaaaaaataaatattttgtataggaaatatattgacttttaaagatgtttgatatatgatagaagagtaataaaactttataacaagctaaatattttaggggtgaaagaaatgaagaagtattttaaatct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 39 HP_score: -2.2 Tail_Score: -3.28745 Start: 23 End: 55 Full_Region: acattttttataatt tgtaatatattata agtta tataaaatatttca ttaaattgttaaggg ......................tgtaatatattataagttatataaaatatttca.......................................................................................................................................................................... Find igs database================================================ Query_seq: FN1250:FN1251|FN1250:FN1251:Guanine-hypoxanthine permease:High-affinity iron permease:<-->:1907923..1908147 225 tttgtcccccttaacaatttaatgaaatattttatataacttataatatattacaaattataaaaaatgtctatctctttttttttaaaatattaaaaaataaatattttgtataggaaatatattgacttttaaagatgtttgatatatgatagaagagtaataaaactttataacaagctaaatattttaggggtgaaagaaatgaagaagtattttaaatct Intra-Species Hit: Count: 1 Min: 1 Max: 225 Len: 225 Subject: NC_003454_FN1250_FN1251|Guanine-hypoxanthine permease:High-affinity iron permease|NEGATIVE:POSITIVE|[1907923,1908147]|225 HSP 1 e-value: 2.0E-43 bit: 176.0 Len: 89 Query Start:137 Query End:225 Subject Strand: POSITIVE Subject Start: 137 Subject End: 225 ........................................................................................................................................gatgtttgatatatgatagaagagtaataaaactttataacaagctaaatattttaggggtgaaagaaatgaagaagtattttaaatct ........................................................................................................................................gatgtttgatatatgatagaagagtaataaaactttataacaagctaaatattttaggggtgaaagaaatgaagaagtattttaaatct HSP 2 e-value: 3.0E-36 bit: 153.0 Len: 77 Query Start:1 Query End:77 Subject Strand: POSITIVE Subject Start: 1 Subject End: 77 tttgtcccccttaacaatttaatgaaatattttatataacttataatatattacaaattataaaaaatgtctatctc.................................................................................................................................................... tttgtcccccttaacaatttaatgaaatattttatataacttataatatattacaaattataaaaaatgtctatctc.................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGUCCCCCUUAACAAUUUAAUGAAAUAUUUUAUAUAACUUAUAAUAUAUUACAAAUUAUAAAAAAUGUCUAUCUCUUUUUUUUUAAAAUAUUAAAAAAUAAAUAUUUUGUAUAGGAAAUAUAUUGACUUUUAAAGAUGUUUGAUAUAUGAUAGAAGAGUAAUAAAACUUUAUAACAAGCUAAAUAUUUUAGGGGUGAAAGAAAUGAAGAAGUAUUUUAAAUCU ....(((((((.....(((((.((.(((((.(((((.....))))).))))).))..(((((((..........((((((((((((((....))))))).((((((((((....((..((....))..))....)))))))))).........))))))).........))))))).....))))).....))))).))..((((((......))))))...... (-30.51) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUUUAAAAUACUUCUUCAUUUCUUUCACCCCUAAAAUAUUUAGCUUGUUAUAAAGUUUUAUUACUCUUCUAUCAUAUAUCAAACAUCUUUAAAAGUCAAUAUAUUUCCUAUACAAAAUAUUUAUUUUUUAAUAUUUUAAAAAAAAAGAGAUAGACAUUUUUUAUAAUUUGUAAUAUAUUAUAAGUUAUAUAAAAUAUUUCAUUAAAUUGUUAAGGGGGACAAA ..........................((.(((((..((((...(((((......))))).)))).....((((((...........................((((((........))))))...((((((((....)))))))).....)))))).(((((.((((((((((((....)))))))))))).))))).................))))))).... (-31.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 630 50 1 141 92 NC_003454:FN1250|5end_Guanine-hypoxanthine_permease_1907832..1908062_NEGATIVE 213 219 183 79 39 NC_003454:FN0051|5end_hypothetical_protein_688929..689159_NEGATIVE 204 71 35 165 131 NC_003454:FN0308|5end_Iron(III)-binding_protein_943022..943252_POSITIVE 201 214 186 231 201 NC_003454:FN0917|5end_hypothetical_protein_1572595..1572825_POSITIVE 197 215 178 224 193 NC_003454:FN0115|5end_hypothetical_protein_748511..748741_NEGATIVE 189 50 3 143 94 NC_003454:FN2053|5end_Serine/threonine_sodium_symporter_562415..562645_NEGATIVE 186 76 31 162 112 NC_003454:FN1162|5end_Hydroxyacylglutathione_hydrolase_1820161..1820391_POSITIVE 186 23 1 162 140 NC_003454:FN1147|5end_hypothetical_protein_1797829..1798059_NEGATIVE 184 24 1 116 94 NC_003454:FN1862|5end_L-beta-lysine_5,6-aminomutase_beta_subunit_353122..353352_NEGATIVE 183 185 156 137 110 NC_003454:FN0774|5end_Hypothetical_cytosolic_protein_1429692..1429922_POSITIVE 181 220 187 221 187 NC_003454:FN1134|5end_Hypothetical_cytosolic_protein_1781495..1781725_POSITIVE 178 35 5 129 95 NC_003454:FN1942|5end_Hypothetical_cytosolic_protein_444689..444919_NEGATIVE 173 200 154 180 125 NC_003454:FN0882|5end_Hemin_transport_system_ATP-binding_protein_hmuV_1543717..1543947_NEGATIVE 172 44 5 98 55 NC_003454:FN0735|5end_Cell_surface_protein_1392666..1392896_POSITIVE 170 136 107 183 148 NC_003454:FN0731|5end_hypothetical_protein_1387720..1387950_POSITIVE 169 157 112 230 189 NC_003454:FN1218|5end_hypothetical_protein_1878414..1878644_NEGATIVE 167 92 68 120 96 NC_003454:FN0455|5end_Rubrerythrin_1101194..1101424_POSITIVE 164 139 97 226 184 NC_003454:FN0015|5end_hypothetical_protein_653500..653730_NEGATIVE 163 208 170 231 191 NC_003454:FN1420|5end_NA+/H+_antiporter_NHAC_2081899..2082129_POSITIVE 163 120 74 195 142 NC_003454:FN1650|5end_Oligopeptide_transport_system_permease_protein_oppC_144834..145064_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 205 157 112 45 1 NC_003454:FN1913|3end_hydrolase_(HD_superfamily)_410054..410204_NEGATIVE 193 217 177 75 32 NC_003454:FN1964|3end_O-linked_GLCNAC_transferase_461646..461796_NEGATIVE 184 24 1 116 94 NC_003454:FN1863|3end_L-beta-lysine_5,6-aminomutase_alpha_subunit_353122..353272_NEGATIVE 182 160 113 151 111 NC_003454:FN0246|3end_hypothetical_protein_870633..870783_NEGATIVE 169 175 132 95 39 NC_003454:FN1445|3end_DNA_helicase_2115953..2116103_POSITIVE 169 71 38 32 1 NC_003454:FN0307|3end_Iron(III)_dicitrate_transport_ATP-binding_protein_fecE_942969..943119_POSITIVE 168 220 178 118 88 NC_003454:FN1467|3end_hypothetical_protein_2149841..2149991_POSITIVE 168 208 168 50 6 NC_003454:FN0625|3end_Aspartate_aminotransferase_1284319..1284469_NEGATIVE 168 220 173 60 8 NC_003454:FN1743|3end_Multidrug-efflux_transporter_2_regulator_241032..241182_NEGATIVE 166 145 105 130 87 NC_003454:FN0793|3end_Sodium/glutamate_symport_carrier_protein_1451791..1451941_POSITIVE 165 219 171 99 45 NC_003454:FN1419|3end_methionine_gamma-lyase_2081832..2081982_POSITIVE 162 159 114 62 20 NC_003454:FN1478|3end_hypothetical_protein_2160328..2160478_NEGATIVE 161 26 5 97 78 NC_003454:FN1051|3end_hypothetical_protein_1700580..1700730_POSITIVE 158 205 169 74 30 NC_003454:FN0265|3end_Cell_division_protein_ftsX_892410..892560_POSITIVE 157 16 5 86 75 NC_003454:FN1342|3end_Holo-[acyl-carrier_protein]_synthase_1996091..1996241_NEGATIVE 157 197 154 100 48 NC_003454:FN1517|3end_Leucyl-tRNA_synthetase_20876..21026_NEGATIVE 156 214 183 34 1 NC_003454:FN0538|3end_Protein_translocase_subunit_secG_1192151..1192301_POSITIVE 155 37 1 130 95 NC_003454:FN1521|3end_Dipeptide_transport_system_permease_protein_dppB_27406..27556_POSITIVE 154 20 5 97 81 NC_003454:FN1830|3end_DNA_polymerase_III_subunits_gamma_and_tau_318571..318721_NEGATIVE 153 161 124 80 41 NC_003454:FN1174|3end_hypothetical_protein_1835732..1835882_POSITIVE