Origin IGS: ttcattctgtaacatttttgaattatctgtaatatttactttatctatattgaagtaatctaatctgaaaaaattttgtggtaacatgtagattaaataaattattccacttaaaaacaacaatcttatccccattacttctcccaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgggagaagtaatggggataagattgttgtttttaagtggaataatttatttaatctacatgttaccacaaaattttttcagattagattacttcaatatagataaagtaaatattacagataattcaaaaatgttacagaatgaa Mask Tandem Repeat Region ================================================ ttcattctgtaacatttttgaattatctgtaatatttactttatctatattgaagtaatctaatctgaaaaaattttgtggtaacatgtagattaaataaattattccacttaaaaacaacaatcttatccccattacttctcccaa Find is-nt database================================================ Query_seq: FN1453:FN1454|FN1453:FN1454:hypothetical protein:D-alanine--D-alanine ligase:<-<-:2134739..2134885 147 ttcattctgtaacatttttgaattatctgtaatatttactttatctatattgaagtaatctaatctgaaaaaattttgtggtaacatgtagattaaataaattattccacttaaaaacaacaatcttatccccattacttctcccaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1453:FN1454|FN1453:FN1454:hypothetical protein:D-alanine--D-alanine ligase:<-<-:2134739..2134885 147 ttcattctgtaacatttttgaattatctgtaatatttactttatctatattgaagtaatctaatctgaaaaaattttgtggtaacatgtagattaaataaattattccacttaaaaacaacaatcttatccccattacttctcccaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1453:FN1454|FN1453:FN1454:hypothetical protein:D-alanine--D-alanine ligase:<-<-:2134739..2134885 147 ttcattctgtaacatttttgaattatctgtaatatttactttatctatattgaagtaatctaatctgaaaaaattttgtggtaacatgtagattaaataaattattccacttaaaaacaacaatcttatccccattacttctcccaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcattctgtaacatttttgaattatctgtaatatttactttatctatattgaagtaatctaatctgaaaaaattttgtggtaacatgtagattaaataaattattccacttaaaaacaacaatcttatccccattacttctcccaa Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: - Start: 1 End: 147 E N Q L M K S N D T I N V K D I N F Y D L R F F N Q P L M Y I L Y I I G S L F L L R I G M V E G M ttcattctgtaacatttttgaattatctgtaatatttactttatctatattgaagtaatctaatctgaaaaaattttgtggtaacatgtagattaaataaattattccacttaaaaacaacaatcttatccccattacttctcccaa 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================================================ ttcattctgtaacatttttgaattatctgtaatatttactttatctatattgaagtaatctaatctgaaaaaattttgtggtaacatgtagattaaataaattattccacttaaaaacaacaatcttatccccattacttctcccaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1453:FN1454|FN1453:FN1454:hypothetical protein:D-alanine--D-alanine ligase:<-<-:2134739..2134885 147 ttcattctgtaacatttttgaattatctgtaatatttactttatctatattgaagtaatctaatctgaaaaaattttgtggtaacatgtagattaaataaattattccacttaaaaacaacaatcttatccccattacttctcccaa Intra-Species Hit: Count: 1 Min: 1 Max: 147 Len: 147 Subject: NC_003454_FN1453_FN1454|hypothetical protein:D-alanine--D-alanine ligase|NEGATIVE:NEGATIVE|[2134739,2134885]|147 HSP 1 e-value: 3.0E-78 bit: 291.0 Len: 147 Query Start:1 Query End:147 Subject Strand: POSITIVE Subject Start: 1 Subject End: 147 ttcattctgtaacatttttgaattatctgtaatatttactttatctatattgaagtaatctaatctgaaaaaattttgtggtaacatgtagattaaataaattattccacttaaaaacaacaatcttatccccattacttctcccaa ttcattctgtaacatttttgaattatctgtaatatttactttatctatattgaagtaatctaatctgaaaaaattttgtggtaacatgtagattaaataaattattccacttaaaaacaacaatcttatccccattacttctcccaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAUUCUGUAACAUUUUUGAAUUAUCUGUAAUAUUUACUUUAUCUAUAUUGAAGUAAUCUAAUCUGAAAAAAUUUUGUGGUAACAUGUAGAUUAAAUAAAUUAUUCCACUUAAAAACAACAAUCUUAUCCCCAUUACUUCUCCCAA ........((((.(((.(((..(((..((.((((.((((((((.......))))))))..(((((((.........(((....)))..))))))).......)))).))..)))...))).))).)))).................. (-11.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGGGAGAAGUAAUGGGGAUAAGAUUGUUGUUUUUAAGUGGAAUAAUUUAUUUAAUCUACAUGUUACCACAAAAUUUUUUCAGAUUAGAUUACUUCAAUAUAGAUAAAGUAAAUAUUACAGAUAAUUCAAAAAUGUUACAGAAUGAA ......(((((((((..((.((..((((.((...((.(((((.(((.....))).))))).))..)).))))..))))..)).......)))))))............((((.((((...((....))...))))))))........ (-19.21) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 683 140 91 231 182 NC_003454:FN1453|5end_hypothetical_protein_2134648..2134878_NEGATIVE 202 48 5 103 68 NC_003454:FN0429|5end_hypothetical_protein_1070949..1071179_POSITIVE 188 67 33 105 76 NC_003454:FN0774|5end_Hypothetical_cytosolic_protein_1429692..1429922_POSITIVE 188 46 1 71 27 NC_003454:FN0223|5end_COME_operon_protein_3_848440..848670_POSITIVE 187 133 104 82 45 NC_003454:FN1747|5end_Cysteine_permease_245647..245877_POSITIVE 186 58 15 114 66 NC_003454:FN0697|5end_Alanyl-tRNA_synthetase_1353992..1354222_POSITIVE 180 101 74 154 127 NC_003454:FN1746|5end_Cystathionine_beta-lyase_244341..244571_POSITIVE 176 137 104 63 20 NC_003454:FN2093|5end_General_secretion_pathway_protein_G_603551..603781_NEGATIVE 171 51 14 141 107 NC_003454:FN1966|5end_hypothetical_protein_465377..465607_NEGATIVE 170 41 7 106 70 NC_003454:FN0535|5end_hypothetical_protein_1189351..1189581_POSITIVE 170 106 66 85 37 NC_003454:FN0016|5end_hypothetical_protein_653630..653860_POSITIVE 170 67 26 84 48 NC_003454:FN2058|5end_Fusobacterium_outer_membrane_protein_family_571095..571325_NEGATIVE 170 92 58 49 20 NC_003454:FN1903|5end_Coenzyme_A_disulfide_reductase/_disulfide_bond_regulator_domain_393104..393334_NEGATIVE 168 32 7 27 1 NC_003454:FN0548|5end_Regulatory_protein_recX_1200937..1201167_POSITIVE 166 61 39 146 126 NC_003454:FN0421|5end_carbamoyl-phosphate_synthase_small_subunit_1061936..1062166_POSITIVE 165 58 14 123 78 NC_003454:FN1750|5end_Pyruvate-flavodoxin_oxidoreductase_247811..248041_POSITIVE 164 47 4 66 15 NC_003454:FN0030|5end_5-nitroimidazole_antibiotic_resistance_protein_667120..667350_POSITIVE 163 40 6 200 162 NC_003454:FN0417|5end_Type_III_restriction-modification_system_restriction_subunit_1055887..1056117_POSITIVE 163 66 31 121 87 NC_003454:FN0109|5end_hypothetical_protein_744809..745039_NEGATIVE 162 48 3 139 70 NC_003454:FN1893|5end_Fusobacterium_outer_membrane_protein_family_378497..378727_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 185 49 1 109 53 NC_003454:FN1476|3end_N-acetylmannosamine-6-phosphate_2-epimerase_2159426..2159576_POSITIVE 171 51 14 65 31 NC_003454:FN1967|3end_hypothetical_protein_465453..465603_NEGATIVE 170 41 7 41 5 NC_003454:FN0534|3end_hypothetical_protein_1189366..1189516_POSITIVE 166 61 39 128 108 NC_003454:FN0420|3end_dihydroorotase_1061998..1062148_POSITIVE 163 66 31 137 103 NC_003454:FN0110|3end_seryl-tRNA_synthetase_744793..744943_NEGATIVE 158 58 15 99 62 NC_003454:FN1394|3end_Signal_recognition_particle_associated_protein_2050855..2051005_NEGATIVE 158 120 74 108 58 NC_003454:FN1160|3end_SWF/SNF_family_helicase_1819185..1819335_POSITIVE 156 69 35 133 104 NC_003454:FN1413|3end_translation_initiation_factor_IF-2B_subunit_alpha_2073221..2073371_NEGATIVE 155 68 39 123 84 NC_003454:FN0923|3end_Cardiolipin_synthetase_1577538..1577688_NEGATIVE 155 53 11 143 98 NC_003454:FN0782|3end_Methyltransferase_1438281..1438431_NEGATIVE 153 137 100 79 39 NC_003454:FN0979|3end_hypothetical_protein_1632544..1632694_POSITIVE 153 43 8 112 76 NC_003454:FN0948|3end_Cobalt-zinc-cadmium_resistance_protein_czcD_1601377..1601527_NEGATIVE 153 79 33 53 1 NC_003454:FN0537|3end_Hypothetical_membrane-spanning_protein_1191169..1191319_NEGATIVE 152 109 75 64 27 NC_003454:FN0223|3end_COME_operon_protein_3_849656..849806_POSITIVE 152 136 109 88 60 NC_003454:FN1832|3end_TonB_protein_321440..321590_NEGATIVE 150 51 14 128 93 NC_003454:FN1352|3end_ABC_transporter_ATP-binding_protein_2003506..2003656_NEGATIVE 150 46 7 145 107 NC_003454:FN1263|3end_Cobalt_chelatase_1919725..1919875_NEGATIVE 150 101 63 60 17 NC_003454:FN0422|3end_carbamoyl-phosphate_synthase_large_subunit_1066283..1066433_POSITIVE 149 60 13 132 92 NC_003454:FN0937|3end_Gamma-polyglutamic_acid_synthetase_1589097..1589247_NEGATIVE 149 46 6 71 39 NC_003454:FN0546|3end_Lipopolysaccharide_core_biosynthesis_protein_rfaQ_1199726..1199876_POSITIVE