Origin IGS: taacgtaaagataacgtagcgttaacacaaggctcgaaaaagcggttttacctttgctgtcggaatataagaaaacaaaggatcattagatgtgataataatagttagtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taactaactattattatcacatctaatgatcctttgttttcttatattccgacagcaaaggtaaaaccgctttttcgagccttgtgttaacgctacgttatctttacgtta Mask Tandem Repeat Region ================================================ taacgtaaagataacgtagcgttaacacaaggctcgaaaaagcggttttacctttgctgtcggaatataagaaaacaaaggatcattagatgtgataataatagttagtta Find is-nt database================================================ Query_seq: TF2283:TF2284|TF2283:TF2284:hypothetical protein:hypothetical protein:->->:2440586..2440696 111 taacgtaaagataacgtagcgttaacacaaggctcgaaaaagcggttttacctttgctgtcggaatataagaaaacaaaggatcattagatgtgataataatagttagtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2283:TF2284|TF2283:TF2284:hypothetical protein:hypothetical protein:->->:2440586..2440696 111 taacgtaaagataacgtagcgttaacacaaggctcgaaaaagcggttttacctttgctgtcggaatataagaaaacaaaggatcattagatgtgataataatagttagtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2283:TF2284|TF2283:TF2284:hypothetical protein:hypothetical protein:->->:2440586..2440696 111 taacgtaaagataacgtagcgttaacacaaggctcgaaaaagcggttttacctttgctgtcggaatataagaaaacaaaggatcattagatgtgataataatagttagtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taacgtaaagataacgtagcgttaacacaaggctcgaaaaagcggttttacctttgctgtcggaatataagaaaacaaaggatcattagatgtgataataatagttagtta Predict ORF larger than 30AA ================================================ taacgtaaagataacgtagcgttaacacaaggctcgaaaaagcggttttacctttgctgtcggaatataagaaaacaaaggatcattagatgtgataataatagttagtta 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================================================ taacgtaaagataacgtagcgttaacacaaggctcgaaaaagcggttttacctttgctgtcggaatataagaaaacaaaggatcattagatgtgataataatagttagtta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2283:TF2284|TF2283:TF2284:hypothetical protein:hypothetical protein:->->:2440586..2440696 111 taacgtaaagataacgtagcgttaacacaaggctcgaaaaagcggttttacctttgctgtcggaatataagaaaacaaaggatcattagatgtgataataatagttagtta Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: tfor_TF2283_TF2284|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2440586,2440696]|111 HSP 1 e-value: 7.0E-57 bit: 220.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 taacgtaaagataacgtagcgttaacacaaggctcgaaaaagcggttttacctttgctgtcggaatataagaaaacaaaggatcattagatgtgataataatagttagtta taacgtaaagataacgtagcgttaacacaaggctcgaaaaagcggttttacctttgctgtcggaatataagaaaacaaaggatcattagatgtgataataatagttagtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACGUAAAGAUAACGUAGCGUUAACACAAGGCUCGAAAAAGCGGUUUUACCUUUGCUGUCGGAAUAUAAGAAAACAAAGGAUCAUUAGAUGUGAUAAUAAUAGUUAGUUA ...........((((.((..((((.((((..(((......))).......((((((...((.........))...)))))).........)))).))))..)))))).... (-17.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACUAACUAUUAUUAUCACAUCUAAUGAUCCUUUGUUUUCUUAUAUUCCGACAGCAAAGGUAAAACCGCUUUUUCGAGCCUUGUGUUAACGCUACGUUAUCUUUACGUUA .............(((.((((.........((((((((.((.........)).)))))))).......((((....))))..)))).)))....((((.......)))).. (-16.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 309 65 28 61 17 tfor:TF1730|5end_diaminopimelate_decarboxylase_1854670..1854900_POSITIVE 293 60 15 46 4 tfor:TF1402|5end_cation_efflux_system_protein_1477922..1478152_POSITIVE 284 69 30 139 100 tfor:TF1287|5end_hypothetical_protein_1369545..1369775_POSITIVE 282 60 18 211 167 tfor:TF2119|5end_conserved_hypothetical_protein_2291776..2292006_POSITIVE 280 58 13 41 9 tfor:TF2724|5end_anti-sigma_factor_2898193..2898423_POSITIVE 279 58 19 228 185 tfor:TF0007|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III_2557..2787_POSITIVE 278 59 15 77 26 tfor:TF2979|5end_possible_outer_membrane__protein_3190778..3191008_POSITIVE 275 57 13 228 197 tfor:TF2224|5end_CTn_excision_protein_2394592..2394822_POSITIVE 272 63 23 188 148 tfor:TF0779|5end_possible_outer_membrane_protein_830346..830576_POSITIVE 271 90 43 65 5 tfor:TF0652|5end_conserved_hypothetical_protein_694292..694522_POSITIVE 270 58 15 147 106 tfor:TF0062|5end_conserved_hypothetical_protein_64916..65146_POSITIVE 269 59 11 126 77 tfor:TF0215|5end_tRNA/rRNA_methyltransferase,_TrmH_family_241463..241693_POSITIVE 268 57 16 52 11 tfor:TF1638|5end_conserved_hypothetical_protein_1747359..1747589_POSITIVE 268 84 41 224 182 tfor:TF1308|5end_50S_ribosomal_protein_L28_1387224..1387454_POSITIVE 267 48 3 54 6 tfor:TF0582|5end_hemolysin-related_protein,_with_CBS_domains;_possible_gliding-motility_related_protein_611885..612115_POSITIVE 267 65 30 182 151 tfor:TF0431|5end_hypothetical_protein_452178..452408_POSITIVE 267 65 30 167 136 tfor:TF0430|5end_hypothetical_protein_452163..452393_POSITIVE 267 60 16 76 24 tfor:TF0175|5end_hypothetical_protein_185585..185815_POSITIVE 266 51 16 45 7 tfor:TF2830|5end_ABC_transporter,_ATP-binding_protein_3020581..3020811_POSITIVE 265 65 29 50 15 tfor:TF1423|5end_cell_division_protein_(ftsW)_1505942..1506172_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 60 15 69 27 tfor:TF1403|3end_hypothetical_protein_1478025..1478175_POSITIVE 292 59 13 130 74 tfor:TF2342|3end_glutathione_peroxidase_2506639..2506789_POSITIVE 290 68 32 96 59 tfor:TF0038|3end_conserved_hypothetical_protein_41213..41363_POSITIVE 282 60 18 48 4 tfor:TF2118|3end_conserved_hypothetical_protein_2291693..2291843_POSITIVE 280 47 4 44 11 tfor:TF0825|3end_hypothetical_protein_883850..884000_POSITIVE 278 59 15 81 30 tfor:TF2978|3end_conserved_hypothetical_protein_3190862..3191012_POSITIVE 272 59 15 139 95 tfor:TF0766|3end_hypothetical_protein_812256..812406_POSITIVE 267 65 30 151 120 tfor:TF0429|3end_ABC_transporter,_ATP-binding_protein_452227..452377_POSITIVE 266 51 16 45 7 tfor:TF2829|3end_conserved_hypothetical_protein_3020661..3020811_POSITIVE 265 51 15 148 116 tfor:TF0061|3end_hypothetical_protein_65006..65156_POSITIVE 264 79 31 77 21 tfor:TF1460|3end_6-phosphogluconate_dehydrogenase_1550790..1550940_POSITIVE 262 64 31 76 43 tfor:TF1479|3end_ABC_transporter,_permease_component_1573592..1573742_POSITIVE 260 72 31 137 92 tfor:TF0118|3end_5-keto-D-gluconate_5-reductase_130636..130786_POSITIVE 259 63 29 121 80 tfor:TF0408|3end_possible_gliding_motility-related_lipoprotein_426324..426474_POSITIVE 257 86 41 59 7 tfor:TF1729|3end_aspartokinase_1854718..1854868_POSITIVE 256 65 31 61 13 tfor:TF1011|3end_cell_division_protein;_rod_shape-determining_protein_1068169..1068319_POSITIVE 255 65 28 119 72 tfor:TF0538|3end_hypothetical_protein_567135..567285_POSITIVE 255 45 5 63 13 tfor:TF0035|3end_sialidase_35901..36051_POSITIVE 254 57 15 128 73 tfor:TF0701|3end_Fe-S-cluster_redox_enzyme_744922..745072_POSITIVE 252 70 28 145 105 tfor:TF2931|3end_3-deoxy-D-manno-2-octulosonic_acid_(Kdo_transferase)_3135584..3135734_POSITIVE