Origin IGS: attaaaacctccaacaaagaaaaaacccttgcatcggacgtatccgtgtcatattgacaagcaagggtattgatctcttatttatgtacttgtattttaaactattttatttgctttgtcaattagaatcttcttttacaaattttaaaaatttaattttatattagtataactttcattttatatcctttagaaatagttttattttaaataaagctaaccatgtattttatattatcataatttctcttttttttcaagcctatatattaattataagaagtaaggaaatttacccttaaataaaatatatgacttagatttcttaaatttttcacttcactatataaaatagtaacactcaaattatttttatttgattttttattttaatcataataaaatatactatatgtattctctaaattagaatttaaatttagacatagtctatt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatagactatgtctaaatttaaattctaatttagagaatacatatagtatattttattatgattaaaataaaaaatcaaataaaaataatttgagtgttactattttatatagtgaagtgaaaaatttaagaaatctaagtcatatattttatttaagggtaaatttccttacttcttataattaatatataggcttgaaaaaaaagagaaattatgataatataaaatacatggttagctttatttaaaataaaactatttctaaaggatataaaatgaaagttatactaatataaaattaaatttttaaaatttgtaaaagaagattctaattgacaaagcaaataaaatagtttaaaatacaagtacataaataagagatcaatacccttgcttgtcaatatgacacggatacgtccgatgcaagggttttttctttgttggaggttttaat Mask Tandem Repeat Region ================================================ attaaaacctccaacaaagaaaaaacccttgcatcggacgtatccgtgtcatattgacaagcaagggtattgatctcttatttatgtacttgtattttaaactattttatttgctttgtcaattagaatcttcttttacaaattttaaaaatttaattttatattagtataactttcattttatatcctttagaaatagttttattttaaataaagctaaccatgtattttatattatcataatttctcttttttttcaagcctatatattaattataagaagtaaggaaatttacccttaaataaaatatatgacttagatttcttaaatttttcacttcactatataaaatagtaacactcaaattatttttatttgattttttattttaatcataataaaatatactatatgtattctctaaattagaatttaaatttagacatagtctatt Find is-nt database================================================ Query_seq: FN1184:FN1185|FN1184:FN1185:hypothetical protein:SIR2 family protein:<-<-:1847198..1847652 455 attaaaacctccaacaaagaaaaaacccttgcatcggacgtatccgtgtcatattgacaagcaagggtattgatctcttatttatgtacttgtattttaaactattttatttgctttgtcaattagaatcttcttttacaaattttaaaaatttaattttatattagtataactttcattttatatcctttagaaatagttttattttaaataaagctaaccatgtattttatattatcataatttctcttttttttcaagcctatatattaattataagaagtaaggaaatttacccttaaataaaatatatgacttagatttcttaaatttttcacttcactatataaaatagtaacactcaaattatttttatttgattttttattttaatcataataaaatatactatatgtattctctaaattagaatttaaatttagacatagtctatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1184:FN1185|FN1184:FN1185:hypothetical protein:SIR2 family protein:<-<-:1847198..1847652 455 attaaaacctccaacaaagaaaaaacccttgcatcggacgtatccgtgtcatattgacaagcaagggtattgatctcttatttatgtacttgtattttaaactattttatttgctttgtcaattagaatcttcttttacaaattttaaaaatttaattttatattagtataactttcattttatatcctttagaaatagttttattttaaataaagctaaccatgtattttatattatcataatttctcttttttttcaagcctatatattaattataagaagtaaggaaatttacccttaaataaaatatatgacttagatttcttaaatttttcacttcactatataaaatagtaacactcaaattatttttatttgattttttattttaatcataataaaatatactatatgtattctctaaattagaatttaaatttagacatagtctatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1184:FN1185|FN1184:FN1185:hypothetical protein:SIR2 family protein:<-<-:1847198..1847652 455 attaaaacctccaacaaagaaaaaacccttgcatcggacgtatccgtgtcatattgacaagcaagggtattgatctcttatttatgtacttgtattttaaactattttatttgctttgtcaattagaatcttcttttacaaattttaaaaatttaattttatattagtataactttcattttatatcctttagaaatagttttattttaaataaagctaaccatgtattttatattatcataatttctcttttttttcaagcctatatattaattataagaagtaaggaaatttacccttaaataaaatatatgacttagatttcttaaatttttcacttcactatataaaatagtaacactcaaattatttttatttgattttttattttaatcataataaaatatactatatgtattctctaaattagaatttaaatttagacatagtctatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attaaaacctccaacaaagaaaaaacccttgcatcggacgtatccgtgtcatattgacaagcaagggtattgatctcttatttatgtacttgtattttaaactattttatttgctttgtcaattagaatcttcttttacaaattttaaaaatttaattttatattagtataactttcattttatatcctttagaaatagttttattttaaataaagctaaccatgtattttatattatcataatttctcttttttttcaagcctatatattaattataagaagtaaggaaatttacccttaaataaaatatatgacttagatttcttaaatttttcacttcactatataaaatagtaacactcaaattatttttatttgattttttattttaatcataataaaatatactatatgtattctctaaattagaatttaaatttagacatagtctatt Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 33 End: 164 ................................ M G R I R V I L T S K G I D L L F M Y L Y F K L F Y L L C Q L E S S F T N F K N L I L Y ................................................................................................................................................................................................................................................................................................... Protein_Len: 39 Strand: + Start: 183 End: 299 ...................................................................................................................................................................................... M S F R N S F I L N K A N H V F Y I I I I S L F F Q A Y I L I I R S K E I Y P ............................................................................................................................................................ Protein_Len: 31 Strand: - Start: 273 End: 365 ................................................................................................................................................................................................................................................................................ N Y S T L F N V R L Y F I H S L N R L N K V E S Y L I T V S M .......................................................................................... attaaaacctccaacaaagaaaaaacccttgcatcggacgtatccgtgtcatattgacaagcaagggtattgatctcttatttatgtacttgtattttaaactattttatttgctttgtcaattagaatcttcttttacaaattttaaaaatttaattttatattagtataactttcattttatatcctttagaaatagttttattttaaataaagctaaccatgtattttatattatcataatttctcttttttttcaagcctatatattaattataagaagtaaggaaatttacccttaaataaaatatatgacttagatttcttaaatttttcacttcactatataaaatagtaacactcaaattatttttatttgattttttattttaatcataataaaatatactatatgtattctctaaattagaatttaaatttagacatagtctatt 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: 90 Start: 94 End: 123 .............................................................................................ATTGACAAAGCAAATAAAATAGTTTAAAAT............................................................................................................................................................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 232 End: 261 .......................................................................................................................................................................................................................................CTTGAAAAAAAAGAGAAATTATGATAATAT.................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 376 End: 405 .......................................................................................................................................................................................................................................................................................................................................................................................TTTGATTTTTTATTTTAATCATAATAAAAT.................................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 396 End: 425 ...........................................................................................................................................................................................................................................................................................................................................................................................................TTAGAGAATACATATAGTATATTTTATTAT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attaaaacctccaacaaagaaaaaacccttgcatcggacgtatccgtgtcatattgacaagcaagggtattgatctcttatttatgtacttgtattttaaactattttatttgctttgtcaattagaatcttcttttacaaattttaaaaatttaattttatattagtataactttcattttatatcctttagaaatagttttattttaaataaagctaaccatgtattttatattatcataatttctcttttttttcaagcctatatattaattataagaagtaaggaaatttacccttaaataaaatatatgacttagatttcttaaatttttcacttcactatataaaatagtaacactcaaattatttttatttgattttttattttaatcataataaaatatactatatgtattctctaaattagaatttaaatttagacatagtctatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 75 HP_score: -3.2 Tail_Score: -5.83211 Start: 362 End: 380 Full_Region: ATAAAATAGTAACAC TCAAATTA TTT TTATTTGA TTTTTTATTTTAATC .........................................................................................................................................................................................................................................................................................................................................................................TCAAATTATTTTTATTTGA........................................................................... Find igs database================================================ Query_seq: FN1184:FN1185|FN1184:FN1185:hypothetical protein:SIR2 family protein:<-<-:1847198..1847652 455 attaaaacctccaacaaagaaaaaacccttgcatcggacgtatccgtgtcatattgacaagcaagggtattgatctcttatttatgtacttgtattttaaactattttatttgctttgtcaattagaatcttcttttacaaattttaaaaatttaattttatattagtataactttcattttatatcctttagaaatagttttattttaaataaagctaaccatgtattttatattatcataatttctcttttttttcaagcctatatattaattataagaagtaaggaaatttacccttaaataaaatatatgacttagatttcttaaatttttcacttcactatataaaatagtaacactcaaattatttttatttgattttttattttaatcataataaaatatactatatgtattctctaaattagaatttaaatttagacatagtctatt Intra-Species Hit: Count: 1 Min: 1 Max: 455 Len: 455 Subject: NC_003454_FN1184_FN1185|hypothetical protein:SIR2 family protein|NEGATIVE:NEGATIVE|[1847198,1847652]|455 HSP 1 e-value: 9.0E-66 bit: 252.0 Len: 151 Query Start:215 Query End:365 Subject Strand: POSITIVE Subject Start: 215 Subject End: 365 ......................................................................................................................................................................................................................agctaaccatgtattttatattatcataatttctcnnnnnnnncaagcctatatattaattataagaagtaaggaaatttacccttaaataaaatatatgacttagatttcttaaatttttcacttcactatataaaatagtaacactcaa.......................................................................................... ......................................................................................................................................................................................................................agctaaccatgtattttatattatcataatttctcttttttttcaagcctatatattaattataagaagtaaggaaatttacccttaaataaaatatatgacttagatttcttaaatttttcacttcactatataaaatagtaacactcaa.......................................................................................... HSP 2 e-value: 8.0E-51 bit: 202.0 Len: 102 Query Start:1 Query End:102 Subject Strand: POSITIVE Subject Start: 1 Subject End: 102 attaaaacctccaacaaagaaaaaacccttgcatcggacgtatccgtgtcatattgacaagcaagggtattgatctcttatttatgtacttgtattttaaac................................................................................................................................................................................................................................................................................................................................................................. attaaaacctccaacaaagaaaaaacccttgcatcggacgtatccgtgtcatattgacaagcaagggtattgatctcttatttatgtacttgtattttaaac................................................................................................................................................................................................................................................................................................................................................................. HSP 3 e-value: 1.0E-27 bit: 125.0 Len: 63 Query Start:393 Query End:455 Subject Strand: POSITIVE Subject Start: 393 Subject End: 455 ........................................................................................................................................................................................................................................................................................................................................................................................................atcataataaaatatactatatgtattctctaaattagaatttaaatttagacatagtctatt ........................................................................................................................................................................................................................................................................................................................................................................................................atcataataaaatatactatatgtattctctaaattagaatttaaatttagacatagtctatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAAAACCUCCAACAAAGAAAAAACCCUUGCAUCGGACGUAUCCGUGUCAUAUUGACAAGCAAGGGUAUUGAUCUCUUAUUUAUGUACUUGUAUUUUAAACUAUUUUAUUUGCUUUGUCAAUUAGAAUCUUCUUUUACAAAUUUUAAAAAUUUAAUUUUAUAUUAGUAUAACUUUCAUUUUAUAUCCUUUAGAAAUAGUUUUAUUUUAAAUAAAGCUAACCAUGUAUUUUAUAUUAUCAUAAUUUCUCUUUUUUUUCAAGCCUAUAUAUUAAUUAUAAGAAGUAAGGAAAUUUACCCUUAAAUAAAAUAUAUGACUUAGAUUUCUUAAAUUUUUCACUUCACUAUAUAAAAUAGUAACACUCAAAUUAUUUUUAUUUGAUUUUUUAUUUUAAUCAUAAUAAAAUAUACUAUAUGUAUUCUCUAAAUUAGAAUUUAAAUUUAGACAUAGUCUAUU ................((((.((.((((((((..((((....)))).(((.....)))..)))))))).))....))))...((((((..(((((((((.((((((((((....(((((.....(((....)))...)))))....(((((((((...........((((((........)))))).....((((((((((((((.....)))))))))..((((((((((((.(((....((((((.(((...((((.....................)))).)))))))))......))))))))))))))).......))))))))))))))...........)))))))))).....((((((.......))))))...................))))))))).)))))).....((((((((........))))))))........... (-70.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAGACUAUGUCUAAAUUUAAAUUCUAAUUUAGAGAAUACAUAUAGUAUAUUUUAUUAUGAUUAAAAUAAAAAAUCAAAUAAAAAUAAUUUGAGUGUUACUAUUUUAUAUAGUGAAGUGAAAAAUUUAAGAAAUCUAAGUCAUAUAUUUUAUUUAAGGGUAAAUUUCCUUACUUCUUAUAAUUAAUAUAUAGGCUUGAAAAAAAAGAGAAAUUAUGAUAAUAUAAAAUACAUGGUUAGCUUUAUUUAAAAUAAAACUAUUUCUAAAGGAUAUAAAAUGAAAGUUAUACUAAUAUAAAAUUAAAUUUUUAAAAUUUGUAAAAGAAGAUUCUAAUUGACAAAGCAAAUAAAAUAGUUUAAAAUACAAGUACAUAAAUAAGAGAUCAAUACCCUUGCUUGUCAAUAUGACACGGAUACGUCCGAUGCAAGGGUUUUUUCUUUGUUGGAGGUUUUAAU ..(((((...)))))........(((((((..((((((........((((.(((((((.(((((.........)))))))))))).........(((((((((((((((...........((((((((((......(((((((((((((.....(((((((((......)))).))))).....))))))).))))))..............(((((.((.(((((....(((..(((...((.(((((((((....))))).)))).))..))).)))....))))).)).)))))..))))))))))....(((((...(((....))).....)))))....))))))))))....)))))..)))).................((((((((..(((.....))).((((....))))..)))))))).))))))..)))))))........ (-79.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 926 80 31 171 122 NC_003454:FN1184|5end_hypothetical_protein_1847107..1847337_NEGATIVE 291 260 217 115 67 NC_003454:FN0936|5end_CapC_protein_1589107..1589337_NEGATIVE 280 194 155 110 68 NC_003454:FN0574|5end_Hypothetical_cytosolic_protein_1223521..1223751_POSITIVE 262 367 325 59 6 NC_003454:FN1724|5end_Potassium_uptake_protein_KtrA_223310..223540_NEGATIVE 257 204 163 171 129 NC_003454:FN1264|5end_hypothetical_protein_1920766..1920996_POSITIVE 243 50 16 155 119 NC_003454:FN1182|5end_hypothetical_protein_1845438..1845668_NEGATIVE 243 269 223 217 161 NC_003454:FN0581|5end_Lipoprotein_releasing_system_transmembrane_protein_lolE_1237108..1237338_POSITIVE 241 91 56 203 178 NC_003454:FN0909|5end_DNA_repair_protein_radC_1567654..1567884_NEGATIVE 235 218 174 128 86 NC_003454:FN0147|5end_fatty_acid/phospholipid_synthesis_protein_775462..775692_POSITIVE 225 208 166 169 125 NC_003454:FN2101|5end_Transporter_610246..610476_POSITIVE 223 104 62 117 65 NC_003454:FN1952|5end_Na(+)-linked_D-alanine_glycine_permease_459050..459280_NEGATIVE 214 77 61 40 24 NC_003454:FN0675|5end_60_kDa_chaperonin_GROEL_1332090..1332320_NEGATIVE 214 79 37 214 177 NC_003454:FN1740|5end_ATP_synthase_subunit_K_238400..238630_NEGATIVE 208 96 51 216 168 NC_003454:FN1474|5end_N-acetylmannosamine_kinase_2156888..2157118_POSITIVE 208 148 105 57 13 NC_003454:FN1639|5end_SSU_ribosomal_protein_S3P_138163..138393_NEGATIVE 208 48 6 113 63 NC_003454:FN1586|5end_O-succinylbenzoate-CoA_synthase_98542..98772_NEGATIVE 207 295 252 169 131 NC_003454:FN1102|5end_tRNA_2'phosphotransferase_1745952..1746182_POSITIVE 206 279 231 93 50 NC_003454:FN1120|5end_phosphoenolpyruvate_carboxykinase_1761438..1761668_POSITIVE 204 268 223 60 11 NC_003454:FN1488|5end_Methenyltetrahydrofolate_cyclohydrolase_2170886..2171116_NEGATIVE 204 64 29 91 50 NC_003454:FN0276|5end_Sodium-dependent_phosphate_transporter_903323..903553_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 260 217 125 77 NC_003454:FN0937|3end_Gamma-polyglutamic_acid_synthetase_1589097..1589247_NEGATIVE 280 194 155 108 66 NC_003454:FN0573|3end_hypothetical_protein_1223599..1223749_POSITIVE 259 375 333 51 1 NC_003454:FN1725|3end_Potassium_uptake_protein_KtrB_223325..223475_NEGATIVE 214 77 61 22 6 NC_003454:FN0676|3end_10_kDa_chaperonin_GROES_1332108..1332258_NEGATIVE 214 79 37 53 16 NC_003454:FN1741|3end_ATP_synthase_subunit_I_238561..238711_NEGATIVE 212 137 105 91 62 NC_003454:FN1009|3end_hypothetical_protein_1663606..1663756_NEGATIVE 208 80 31 82 35 NC_003454:FN1315|3end_hypothetical_protein_1968921..1969071_NEGATIVE 204 268 223 66 17 NC_003454:FN1489|3end_Methionyl-tRNA_formyltransferase_2170880..2171030_NEGATIVE 203 270 225 121 72 NC_003454:FN0005|3end_Jag_protein_644579..644729_POSITIVE 201 207 161 90 50 NC_003454:FN0649|3end_Exoenzyme_regulatory_protein_aepA_precursor_1306089..1306239_NEGATIVE 201 127 92 100 64 NC_003454:FN0429|3end_hypothetical_protein_1071352..1071502_POSITIVE 199 108 63 70 20 NC_003454:FN1983|3end_Alkyl_hydroperoxide_reductase_C22_protein_485265..485415_POSITIVE 197 69 25 59 20 NC_003454:FN0704|3end_hypothetical_protein_1361661..1361811_NEGATIVE 192 101 61 50 4 NC_003454:FN0223|3end_COME_operon_protein_3_849656..849806_POSITIVE 192 210 161 113 64 NC_003454:FN0002|3end_Ribonuclease_P_protein_component_642963..643113_POSITIVE 190 447 409 110 73 NC_003454:FN1304|3end_Single-strand_DNA_binding_protein_1960299..1960449_NEGATIVE 190 271 234 135 87 NC_003454:FN1045|3end_hypothetical_protein_1695178..1695328_NEGATIVE 189 124 88 143 101 NC_003454:FN1125|3end_LemA_protein_1769260..1769410_NEGATIVE 188 264 224 91 49 NC_003454:FN2059|3end_Outer_membrane_protein_572877..573027_NEGATIVE 188 264 224 91 49 NC_003454:FN2048|3end_Outer_membrane_protein_558801..558951_NEGATIVE