Origin IGS: atctaaagtaatttttgcatctggattttctgttacagaaaggtcaggcatttcaggcgctgtaatagctggtatttctcctaaggcataaccaggtactaacatttcattttcatttgaaacttctttttctgttgagacttgagtattattagtagtttttttatcataataagtcttaacaccaaaaactaaaagaatagctactattattgatattaaaaattctttcttcataaaacctccattataat .........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 attataatggaggttttatgaagaaagaatttttaatatcaataatagtagctattcttttagtttttggtgttaagacttattatgataaaaaaactactaataatactcaagtctcaacagaaaaagaagtttcaaatgaaaatgaaatgttagtacctggttatgccttaggagaaataccagctattacagcgcctgaaatgcctgacctttctgtaacagaaaatccagatgcaaaaattactttagat Mask Tandem Repeat Region ================================================ atctaaagtaatttttgcatctggattttctgttacagaaaggtcaggcatttcaggcgctgtaatagctggtatttctcctaaggcataaccaggtactaacatttcattttcatttgaaacttctttttctgttgagacttgagtattattagtagtttttttatcataataagtcttaacaccaaaaactaaaagaatagctactattattgatattaaaaattctttcttcataaaacctccattataat Find is-nt database================================================ Query_seq: FN1124:FN1125|FN1124:FN1125:Outer membrane porin F:LemA protein:<-<-:1769096..1769349 254 atctaaagtaatttttgcatctggattttctgttacagaaaggtcaggcatttcaggcgctgtaatagctggtatttctcctaaggcataaccaggtactaacatttcattttcatttgaaacttctttttctgttgagacttgagtattattagtagtttttttatcataataagtcttaacaccaaaaactaaaagaatagctactattattgatattaaaaattctttcttcataaaacctccattataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1124:FN1125|FN1124:FN1125:Outer membrane porin F:LemA protein:<-<-:1769096..1769349 254 atctaaagtaatttttgcatctggattttctgttacagaaaggtcaggcatttcaggcgctgtaatagctggtatttctcctaaggcataaccaggtactaacatttcattttcatttgaaacttctttttctgttgagacttgagtattattagtagtttttttatcataataagtcttaacaccaaaaactaaaagaatagctactattattgatattaaaaattctttcttcataaaacctccattataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1124:FN1125|FN1124:FN1125:Outer membrane porin F:LemA protein:<-<-:1769096..1769349 254 atctaaagtaatttttgcatctggattttctgttacagaaaggtcaggcatttcaggcgctgtaatagctggtatttctcctaaggcataaccaggtactaacatttcattttcatttgaaacttctttttctgttgagacttgagtattattagtagtttttttatcataataagtcttaacaccaaaaactaaaagaatagctactattattgatattaaaaattctttcttcataaaacctccattataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atctaaagtaatttttgcatctggattttctgttacagaaaggtcaggcatttcaggcgctgtaatagctggtatttctcctaaggcataaccaggtactaacatttcattttcatttgaaacttctttttctgttgagacttgagtattattagtagtttttttatcataataagtcttaacaccaaaaactaaaagaatagctactattattgatattaaaaattctttcttcataaaacctccattataat Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: - Start: 1 End: 237 A T I A P I E G L A Y G P V L M E N E N S V E K E T S V Q T N N T T K K D Y Y T K V G F V L L I A V I I S I L F E K K M ................. atctaaagtaatttttgcatctggattttctgttacagaaaggtcaggcatttcaggcgctgtaatagctggtatttctcctaaggcataaccaggtactaacatttcattttcatttgaaacttctttttctgttgagacttgagtattattagtagtttttttatcataataagtcttaacaccaaaaactaaaagaatagctactattattgatattaaaaattctttcttcataaaacctccattataat 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: 85 Start: 141 End: 170 ............................................................................................................................................CTTGAGTATTATTAGTAGTTTTTTTATCAT.................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 225 End: 254 ................................................................................................................................................................................................................................ATTCTTTCTTCATAAAACCTCCATTATAAT Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atctaaagtaatttttgcatctggattttctgttacagaaaggtcaggcatttcaggcgctgtaatagctggtatttctcctaaggcataaccaggtactaacatttcattttcatttgaaacttctttttctgttgagacttgagtattattagtagtttttttatcataataagtcttaacaccaaaaactaaaagaatagctactattattgatattaaaaattctttcttcataaaacctccattataat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1124:FN1125|FN1124:FN1125:Outer membrane porin F:LemA protein:<-<-:1769096..1769349 254 atctaaagtaatttttgcatctggattttctgttacagaaaggtcaggcatttcaggcgctgtaatagctggtatttctcctaaggcataaccaggtactaacatttcattttcatttgaaacttctttttctgttgagacttgagtattattagtagtttttttatcataataagtcttaacaccaaaaactaaaagaatagctactattattgatattaaaaattctttcttcataaaacctccattataat Intra-Species Hit: Count: 1 Min: 1 Max: 254 Len: 254 Subject: NC_003454_FN1124_FN1125|Outer membrane porin F:LemA protein|NEGATIVE:NEGATIVE|[1769096,1769349]|254 HSP 1 e-value: 1.0E-129 bit: 462.0 Len: 254 Query Start:1 Query End:254 Subject Strand: POSITIVE Subject Start: 1 Subject End: 254 atctaaagtaatttttgcatctggattttctgttacagaaaggtcaggcatttcaggcgctgtaatagctggtatttctcctaaggcataaccaggtactaacatttcattttcatttgaaacttctttttctgttgagacttgagtattattagtagnnnnnnnatcataataagtcttaacaccaaaaactaaaagaatagctactattattgatattaaaaattctttcttcataaaacctccattataat atctaaagtaatttttgcatctggattttctgttacagaaaggtcaggcatttcaggcgctgtaatagctggtatttctcctaaggcataaccaggtactaacatttcattttcatttgaaacttctttttctgttgagacttgagtattattagtagtttttttatcataataagtcttaacaccaaaaactaaaagaatagctactattattgatattaaaaattctttcttcataaaacctccattataat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUAAAGUAAUUUUUGCAUCUGGAUUUUCUGUUACAGAAAGGUCAGGCAUUUCAGGCGCUGUAAUAGCUGGUAUUUCUCCUAAGGCAUAACCAGGUACUAACAUUUCAUUUUCAUUUGAAACUUCUUUUUCUGUUGAGACUUGAGUAUUAUUAGUAGUUUUUUUAUCAUAAUAAGUCUUAACACCAAAAACUAAAAGAAUAGCUACUAUUAUUGAUAUUAAAAAUUCUUUCUUCAUAAAACCUCCAUUAUAAU ....((((.((((((((..((((..(((((((...)))))))..))))......((..(((((..((.(((((((.(((....))).)).))))).))......(((((........)))))....((((..((((((((((....((((((..((((.....)))).))))))))))))))))..)))).........)))))..))...........))))))))))))....................... (-41.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUAAUGGAGGUUUUAUGAAGAAAGAAUUUUUAAUAUCAAUAAUAGUAGCUAUUCUUUUAGUUUUUGGUGUUAAGACUUAUUAUGAUAAAAAAACUACUAAUAAUACUCAAGUCUCAACAGAAAAAGAAGUUUCAAAUGAAAAUGAAAUGUUAGUACCUGGUUAUGCCUUAGGAGAAAUACCAGCUAUUACAGCGCCUGAAAUGCCUGACCUUUCUGUAACAGAAAAUCCAGAUGCAAAAAUUACUUUAGAU .......((((..((((.(..((((((..................((((((((.((((((((.(((((..((((.(((((((((((................))))))....))))).))))..)))))..((((((........))))))..........((.....)).)))))))).....))))))))(((.((.......)))))..))))))...).))))..))))..................... (-41.39) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 966 90 41 181 132 NC_003454:FN1124|5end_Outer_membrane_porin_F_1769005..1769235_NEGATIVE 268 87 41 76 17 NC_003454:FN0508|5end_Serine_protease_1158652..1158882_NEGATIVE 268 82 44 103 51 NC_003454:FN1823|5end_Transcriptional_regulator,_TetR_family_311720..311950_POSITIVE 265 120 80 229 176 NC_003454:FN1392|5end_SSU_ribosomal_protein_S16P_2049459..2049689_NEGATIVE 263 96 60 200 150 NC_003454:FN1413|5end_translation_initiation_factor_IF-2B_subunit_alpha_2074270..2074500_NEGATIVE 261 132 91 111 62 NC_003454:FN0985|5end_Phosphoribosylglycinamide_formyltransferase_1637857..1638087_NEGATIVE 260 121 83 179 133 NC_003454:FN1842|5end_Dihydroxyacetone_kinase_phosphotransfer_protein_331491..331721_POSITIVE 248 52 15 61 25 NC_003454:FN1610|5end_33_kDa_chaperonin_120597..120827_NEGATIVE 247 246 202 122 83 NC_003454:FN0063|5end_hypothetical_protein_698982..699212_POSITIVE 243 143 108 66 25 NC_003454:FN0896|5end_hypothetical_protein_1555780..1556010_NEGATIVE 242 90 46 74 25 NC_003454:FN1421|5end_Pyruvate-flavodoxin_oxidoreductase_2083305..2083535_POSITIVE 238 89 42 193 139 NC_003454:FN1868|5end_Hypothetical_cytosolic_protein_360433..360663_NEGATIVE 235 221 192 57 28 NC_003454:FN0345|5end_Permease_978756..978986_NEGATIVE 235 84 41 58 11 NC_003454:FN1859|5end_Major_outer_membrane_protein_349655..349885_NEGATIVE 234 61 22 230 188 NC_003454:FN1449|5end_Fusobacterium_outer_membrane_protein_family_2128109..2128339_NEGATIVE 230 97 51 46 7 NC_003454:FN1930|5end_Phosphatidylglycerophosphatase_A_430259..430489_NEGATIVE 228 81 41 43 1 NC_003454:FN0365|5end_ATP_synthase_protein_I,_sodium_ion_specific_994859..995089_NEGATIVE 224 48 2 81 39 NC_003454:FN2097|5end_hypothetical_protein_606853..607083_NEGATIVE 223 99 56 89 48 NC_003454:FN0815|5end_Propionate_permease_1474390..1474620_POSITIVE 223 80 33 84 34 NC_003454:FN1629|5end_50S_ribosomal_protein_L6_134508..134738_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 261 132 91 123 74 NC_003454:FN0986|3end_phosphoribosylaminoimidazole_synthetase_1637845..1637995_NEGATIVE 248 52 15 61 25 NC_003454:FN1611|3end_Competence_protein_120597..120747_NEGATIVE 235 97 51 82 23 NC_003454:FN1749|3end_Pyruvate-flavodoxin_oxidoreductase_247705..247855_POSITIVE 230 97 51 46 7 NC_003454:FN1931|3end_Protease_430259..430409_NEGATIVE 223 80 33 59 9 NC_003454:FN1630|3end_SSU_ribosomal_protein_S8P_134533..134683_NEGATIVE 219 191 152 46 6 NC_003454:FN1192|3end_hypothetical_protein_1855031..1855181_POSITIVE 218 120 73 120 72 NC_003454:FN0232|3end_hypothetical_protein_857821..857971_NEGATIVE 218 97 54 136 85 NC_003454:FN1674|3end_hypothetical_protein_172225..172375_POSITIVE 217 98 56 54 3 NC_003454:FN1267|3end_hypothetical_protein_1923054..1923204_NEGATIVE 217 114 78 49 13 NC_003454:FN0420|3end_dihydroorotase_1061998..1062148_POSITIVE 215 83 41 149 102 NC_003454:FN1375|3end_Citrate-sodium_symport_2023860..2024010_POSITIVE 214 82 55 40 10 NC_003454:FN1822|3end_Flavodoxin_311737..311887_POSITIVE 213 86 50 45 11 NC_003454:FN0227|3end_hypothetical_protein_854114..854264_NEGATIVE 212 68 21 149 99 NC_003454:FN1647|3end_hypothetical_protein_142482..142632_POSITIVE 211 246 214 36 7 NC_003454:FN0247|3end_Hypothetical_cytosolic_protein_871578..871728_POSITIVE 210 98 59 140 101 NC_003454:FN0606|3end_Translation_initiation_inhibitor_1261519..1261669_POSITIVE 210 62 31 57 24 NC_003454:FN1972|3end_hypothetical_protein_471703..471853_NEGATIVE 210 97 59 138 98 NC_003454:FN1792|3end_hypothetical_protein_272899..273049_NEGATIVE 208 55 11 71 35 NC_003454:FN1491|3end_PTS_system,_IIA_component_2172302..2172452_NEGATIVE 208 115 74 139 84 NC_003454:FN0755|3end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_C_1414663..1414813_NEGATIVE