Origin IGS: gtgtctccttattatattttattaataatttataaaagtctttttctatgaaaatgtaaactccccaactatcatatttcttttcaccatcaaactcaaaatatacattttatattctactttacttgctacataacaaggctctaaaaatatccaaagatagataaattttaaatttttgtctatttcttacttattttcattctaaatgtttttattaatttgtcaataaaaaaagattaaaattagtatattttccaatataatactttaatcttttcaatt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattgaaaagattaaagtattatattggaaaatatactaattttaatctttttttattgacaaattaataaaaacatttagaatgaaaataagtaagaaatagacaaaaatttaaaatttatctatctttggatatttttagagccttgttatgtagcaagtaaagtagaatataaaatgtatattttgagtttgatggtgaaaagaaatatgatagttggggagtttacattttcatagaaaaagacttttataaattattaataaaatataataaggagacac Mask Tandem Repeat Region ================================================ gtgtctccttattatattttattaataatttataaaagtctttttctatgaaaatgtaaactccccaactatcatatttcttttcaccatcaaactcaaaatatacattttatattctactttacttgctacataacaaggctctaaaaatatccaaagatagataaattttaaatttttgtctatttcttacttattttcattctaaatgtttttattaatttgtcaataaaaaaagattaaaattagtatattttccaatataatactttaatcttttcaatt Find is-nt database================================================ Query_seq: FN1599:FN1600|FN1599:FN1600:hypothetical protein:tRNA pseudouridine synthase A:<-<-:108874..109158 285 gtgtctccttattatattttattaataatttataaaagtctttttctatgaaaatgtaaactccccaactatcatatttcttttcaccatcaaactcaaaatatacattttatattctactttacttgctacataacaaggctctaaaaatatccaaagatagataaattttaaatttttgtctatttcttacttattttcattctaaatgtttttattaatttgtcaataaaaaaagattaaaattagtatattttccaatataatactttaatcttttcaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1599:FN1600|FN1599:FN1600:hypothetical protein:tRNA pseudouridine synthase A:<-<-:108874..109158 285 gtgtctccttattatattttattaataatttataaaagtctttttctatgaaaatgtaaactccccaactatcatatttcttttcaccatcaaactcaaaatatacattttatattctactttacttgctacataacaaggctctaaaaatatccaaagatagataaattttaaatttttgtctatttcttacttattttcattctaaatgtttttattaatttgtcaataaaaaaagattaaaattagtatattttccaatataatactttaatcttttcaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1599:FN1600|FN1599:FN1600:hypothetical protein:tRNA pseudouridine synthase A:<-<-:108874..109158 285 gtgtctccttattatattttattaataatttataaaagtctttttctatgaaaatgtaaactccccaactatcatatttcttttcaccatcaaactcaaaatatacattttatattctactttacttgctacataacaaggctctaaaaatatccaaagatagataaattttaaatttttgtctatttcttacttattttcattctaaatgtttttattaatttgtcaataaaaaaagattaaaattagtatattttccaatataatactttaatcttttcaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtgtctccttattatattttattaataatttataaaagtctttttctatgaaaatgtaaactccccaactatcatatttcttttcaccatcaaactcaaaatatacattttatattctactttacttgctacataacaaggctctaaaaatatccaaagatagataaattttaaatttttgtctatttcttacttattttcattctaaatgtttttattaatttgtcaataaaaaaagattaaaattagtatattttccaatataatactttaatcttttcaatt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 32 End: 133 ............................... M K V F F Y E N V N S P T I I F L F T I K L K I Y I L Y S T L L A T ........................................................................................................................................................ Protein_Len: 46 Strand: - Start: 49 End: 186 ................................................ S F T F E G V I M N R K V M L S L I Y M K Y E V K S A V Y C P E L F I W L Y I F K L N K D M ................................................................................................... gtgtctccttattatattttattaataatttataaaagtctttttctatgaaaatgtaaactccccaactatcatatttcttttcaccatcaaactcaaaatatacattttatattctactttacttgctacataacaaggctctaaaaatatccaaagatagataaattttaaatttttgtctatttcttacttattttcattctaaatgtttttattaatttgtcaataaaaaaagattaaaattagtatattttccaatataatactttaatcttttcaatt 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================================================ gtgtctccttattatattttattaataatttataaaagtctttttctatgaaaatgtaaactccccaactatcatatttcttttcaccatcaaactcaaaatatacattttatattctactttacttgctacataacaaggctctaaaaatatccaaagatagataaattttaaatttttgtctatttcttacttattttcattctaaatgtttttattaatttgtcaataaaaaaagattaaaattagtatattttccaatataatactttaatcttttcaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1599:FN1600|FN1599:FN1600:hypothetical protein:tRNA pseudouridine synthase A:<-<-:108874..109158 285 gtgtctccttattatattttattaataatttataaaagtctttttctatgaaaatgtaaactccccaactatcatatttcttttcaccatcaaactcaaaatatacattttatattctactttacttgctacataacaaggctctaaaaatatccaaagatagataaattttaaatttttgtctatttcttacttattttcattctaaatgtttttattaatttgtcaataaaaaaagattaaaattagtatattttccaatataatactttaatcttttcaatt Intra-Species Hit: Count: 1 Min: 1 Max: 285 Len: 285 Subject: NC_003454_FN1599_FN1600|hypothetical protein:tRNA pseudouridine synthase A|NEGATIVE:NEGATIVE|[108874,109158]|285 HSP 1 e-value: 5.0E-88 bit: 325.0 Len: 164 Query Start:1 Query End:164 Subject Strand: POSITIVE Subject Start: 1 Subject End: 164 gtgtctccttattatattttattaataatttataaaagtctttttctatgaaaatgtaaactccccaactatcatatttcttttcaccatcaaactcaaaatatacattttatattctactttacttgctacataacaaggctctaaaaatatccaaagataga......................................................................................................................... gtgtctccttattatattttattaataatttataaaagtctttttctatgaaaatgtaaactccccaactatcatatttcttttcaccatcaaactcaaaatatacattttatattctactttacttgctacataacaaggctctaaaaatatccaaagataga......................................................................................................................... HSP 2 e-value: 8.0E-19 bit: 95.6 Len: 48 Query Start:238 Query End:285 Subject Strand: POSITIVE Subject Start: 238 Subject End: 285 .............................................................................................................................................................................................................................................gattaaaattagtatattttccaatataatactttaatcttttcaatt .............................................................................................................................................................................................................................................gattaaaattagtatattttccaatataatactttaatcttttcaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGUCUCCUUAUUAUAUUUUAUUAAUAAUUUAUAAAAGUCUUUUUCUAUGAAAAUGUAAACUCCCCAACUAUCAUAUUUCUUUUCACCAUCAAACUCAAAAUAUACAUUUUAUAUUCUACUUUACUUGCUACAUAACAAGGCUCUAAAAAUAUCCAAAGAUAGAUAAAUUUUAAAUUUUUGUCUAUUUCUUACUUAUUUUCAUUCUAAAUGUUUUUAUUAAUUUGUCAAUAAAAAAAGAUUAAAAUUAGUAUAUUUUCCAAUAUAAUACUUUAAUCUUUUCAAUU ................(((((((.((((...(((((((..(((....((((((((((((..............((((((....................((((((.....))))))........((((........)))).......))))))....(((((((((((.........))))))))))).))))..))))))))...)))..)))))))....)))).)))))))((((((((((.....((((((....))))))....))))))))))...... (-33.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUGAAAAGAUUAAAGUAUUAUAUUGGAAAAUAUACUAAUUUUAAUCUUUUUUUAUUGACAAAUUAAUAAAAACAUUUAGAAUGAAAAUAAGUAAGAAAUAGACAAAAAUUUAAAAUUUAUCUAUCUUUGGAUAUUUUUAGAGCCUUGUUAUGUAGCAAGUAAAGUAGAAUAUAAAAUGUAUAUUUUGAGUUUGAUGGUGAAAAGAAAUAUGAUAGUUGGGGAGUUUACAUUUUCAUAGAAAAAGACUUUUAUAAAUUAUUAAUAAAAUAUAAUAAGGAGACAC ....((((((((((((((..((((((....))))))...))))))))))))))(((((((....))))))).....................((................(((((((..((((((....)))))).))))))).(((((((((((.((...((((.(((((((((.....)))))))))..))))...))...........((((((((.((((((((...(((((...)))))))))))))...)))))))).....)))))))))))..)).. (-50.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 757 110 61 201 152 NC_003454:FN1599|5end_hypothetical_protein_108783..109013_NEGATIVE 234 196 153 227 186 NC_003454:FN1715|5end_ATPase_211040..211270_POSITIVE 233 76 39 154 108 NC_003454:FN1227|5end_hypothetical_protein_1885707..1885937_NEGATIVE 223 87 41 190 141 NC_003454:FN0751|5end_L-asparaginase_I_1410731..1410961_NEGATIVE 223 110 61 159 104 NC_003454:FN1797|5end_Spermidine/putrescine_transport_ATP-binding_protein_potA_278821..279051_POSITIVE 222 113 83 127 98 NC_003454:FN1755|5end_thiamine_biosynthesis_protein_ThiF_251737..251967_NEGATIVE 217 130 86 41 1 NC_003454:FN0093|5end_Thioredoxin_729169..729399_POSITIVE 215 261 225 225 182 NC_003454:FN1362|5end_Dipeptide_transport_ATP-binding_protein_dppD_2013818..2014048_POSITIVE 213 41 2 140 98 NC_003454:FN1522|5end_Dipeptide_transport_system_permease_protein_dppC_27327..27557_POSITIVE 207 107 66 221 184 NC_003454:FN1793|5end_Phosphoenolpyruvate-protein_phosphotransferase_275273..275503_NEGATIVE 206 99 61 231 193 NC_003454:FN1426|5end_Serine_protease_2095462..2095692_NEGATIVE 206 138 96 148 112 NC_003454:FN0724|5end_flavodoxin_1384167..1384397_NEGATIVE 204 119 71 134 87 NC_003454:FN1030|5end_Hypothetical_membrane-spanning_protein_1684721..1684951_NEGATIVE 203 85 41 105 63 NC_003454:FN0915|5end_PTS_system,_N-acetylglucosamine-specific_IIA_component_1572037..1572267_NEGATIVE 197 148 116 47 14 NC_003454:FN1209|5end_Hypothetical_RNA_binding_protein_1868914..1869144_NEGATIVE 196 207 170 102 54 NC_003454:FN0424|5end_Dihydroorotate_dehydrogenase_1067119..1067349_POSITIVE 194 98 56 208 161 NC_003454:FN1862|5end_L-beta-lysine_5,6-aminomutase_beta_subunit_353122..353352_NEGATIVE 193 228 182 59 9 NC_003454:FN0678|5end_Ser/Thr_protein_kinase_1333969..1334199_POSITIVE 191 150 106 130 89 NC_003454:FN1919|5end_Methyltransferase_415882..416112_NEGATIVE 190 106 62 82 32 NC_003454:FN0796|5end_pyruvate_phosphate_dikinase_1453008..1453238_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 234 196 153 143 102 NC_003454:FN1714|3end_hypothetical_protein_211036..211186_POSITIVE 222 113 83 123 94 NC_003454:FN1756|3end_ThiS_protein_251741..251891_NEGATIVE 213 41 2 139 97 NC_003454:FN1521|3end_Dipeptide_transport_system_permease_protein_dppB_27406..27556_POSITIVE 206 138 96 134 98 NC_003454:FN0725|3end_Molybdopterin_biosynthesis_MoeB_protein_1384181..1384331_NEGATIVE 204 119 71 134 87 NC_003454:FN1031|3end_Hypothetical_membrane-spanning_protein_1684721..1684871_NEGATIVE 203 85 41 77 35 NC_003454:FN0916|3end_hypothetical_protein_1572065..1572215_NEGATIVE 196 207 170 90 42 NC_003454:FN0423|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit_1067187..1067337_POSITIVE 192 92 62 145 104 NC_003454:FN1106|3end_L-serine_dehydratase_1751873..1752023_POSITIVE 191 150 106 133 92 NC_003454:FN1920|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)_-methyltransferase_415879..416029_NEGATIVE 190 106 62 70 20 NC_003454:FN0795|3end_CBS_domain_containing_protein_1453076..1453226_POSITIVE 190 220 179 127 81 NC_003454:FN1618|3end_hypothetical_protein_126666..126816_NEGATIVE 189 96 51 125 82 NC_003454:FN0064|3end_Hypothetical_cytosolic_protein_699922..700072_POSITIVE 189 218 185 150 116 NC_003454:FN1712|3end_hypothetical_protein_207608..207758_POSITIVE 188 159 111 131 87 NC_003454:FN1088|3end_NADH_oxidase_1733095..1733245_POSITIVE 187 49 2 117 60 NC_003454:FN1052|3end_hypothetical_protein_1701067..1701217_POSITIVE 187 207 167 90 50 NC_003454:FN1857|3end_Acetoacetate:butyrate/acetate_coenzyme_A_transferase_346164..346314_NEGATIVE 185 189 157 138 108 NC_003454:FN0729|3end_Phosphoglycerate_mutase_1387120..1387270_POSITIVE 183 130 86 92 45 NC_003454:FN0951|3end_Precorrin-3B_C17-methyltransferase_1607747..1607897_NEGATIVE 183 47 2 109 61 NC_003454:FN2062|3end_hypothetical_protein_574107..574257_NEGATIVE 183 47 2 109 61 NC_003454:FN2051|3end_hypothetical_protein_560031..560181_NEGATIVE