Origin IGS: tgaaagaaaagggattggtttacggctgtttcctcgccatacgtatccggcaggaagaaaaagccatgaagggaatgtggagctctaccaatccctgatattgttttcgtcgggaaaataattgtattgatctaaaagaggataaagcgttttgccgtagtgaagccgtagggatatggcgtatgttttataacatggcgtaacgttgcagcaggtcgttttttgggtagtagggggattatcggtttttttgtgaaaaaatcggattgtttgcagtaacattaaaaaaagaataccc .........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 gggtattctttttttaatgttactgcaaacaatccgattttttcacaaaaaaaccgataatccccctactacccaaaaaacgacctgctgcaacgttacgccatgttataaaacatacgccatatccctacggcttcactacggcaaaacgctttatcctcttttagatcaatacaattattttcccgacgaaaacaatatcagggattggtagagctccacattcccttcatggctttttcttcctgccggatacgtatggcgaggaaacagccgtaaaccaatcccttttctttca Mask Tandem Repeat Region ================================================ tgaaagaaaagggattggtttacggctgtttcctcgccatacgtatccggcaggaagaaaaagccatgaagggaatgtggagctctaccaatccctgatattgttttcgtcgggaaaataattgtattgatctaaaagaggataaagcgttttgccgtagtgaagccgtagggatatggcgtatgttttataacatggcgtaacgttgcagcaggtcgttttttgggtagtagggggattatcggtttttttgtgaaaaaatcggattgtttgcagtaacattaaaaaaagaataccc Find is-nt database================================================ Query_seq: TF2184:TF2185|TF2184:TF2185:conserved hypothetical protein:outer membrane protein, TonB dependent receptor:->->:2357104..2357401 298 tgaaagaaaagggattggtttacggctgtttcctcgccatacgtatccggcaggaagaaaaagccatgaagggaatgtggagctctaccaatccctgatattgttttcgtcgggaaaataattgtattgatctaaaagaggataaagcgttttgccgtagtgaagccgtagggatatggcgtatgttttataacatggcgtaacgttgcagcaggtcgttttttgggtagtagggggattatcggtttttttgtgaaaaaatcggattgtttgcagtaacattaaaaaaagaataccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2184:TF2185|TF2184:TF2185:conserved hypothetical protein:outer membrane protein, TonB dependent receptor:->->:2357104..2357401 298 tgaaagaaaagggattggtttacggctgtttcctcgccatacgtatccggcaggaagaaaaagccatgaagggaatgtggagctctaccaatccctgatattgttttcgtcgggaaaataattgtattgatctaaaagaggataaagcgttttgccgtagtgaagccgtagggatatggcgtatgttttataacatggcgtaacgttgcagcaggtcgttttttgggtagtagggggattatcggtttttttgtgaaaaaatcggattgtttgcagtaacattaaaaaaagaataccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2184:TF2185|TF2184:TF2185:conserved hypothetical protein:outer membrane protein, TonB dependent receptor:->->:2357104..2357401 298 tgaaagaaaagggattggtttacggctgtttcctcgccatacgtatccggcaggaagaaaaagccatgaagggaatgtggagctctaccaatccctgatattgttttcgtcgggaaaataattgtattgatctaaaagaggataaagcgttttgccgtagtgaagccgtagggatatggcgtatgttttataacatggcgtaacgttgcagcaggtcgttttttgggtagtagggggattatcggtttttttgtgaaaaaatcggattgtttgcagtaacattaaaaaaagaataccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaaagaaaagggattggtttacggctgtttcctcgccatacgtatccggcaggaagaaaaagccatgaagggaatgtggagctctaccaatccctgatattgttttcgtcgggaaaataattgtattgatctaaaagaggataaagcgttttgccgtagtgaagccgtagggatatggcgtatgttttataacatggcgtaacgttgcagcaggtcgttttttgggtagtagggggattatcggtttttttgtgaaaaaatcggattgtttgcagtaacattaaaaaaagaataccc Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 14 End: 118 ............. M G L R L F P R H T Y P A G R K S H E G N V E L Y Q S L I L F S S G K .................................................................................................................................................................................... Protein_Len: 36 Strand: - Start: 135 End: 242 ...................................................................................................................................... F L I F R K A T T F G Y P Y P T H K I V H R L T A A P R K K P L L P I M ........................................................ Protein_Len: 60 Strand: - Start: 88 End: 294 ....................................................................................... F Y N Y Q D L L P Y L T K G Y H L R L S I A Y T K Y C P T V N C C T T K Q T T P P N D T K K H F F R I T Q L L M L F L M .... Protein_Len: 54 Strand: - Start: 23 End: 184 ...................... P Q K R A M R I R C S S F A M F P I H L E V L G Q Y Q K R R S F L Q I S R F S S L A N Q R L S A T P I H R M .................................................................................................................. Protein_Len: 43 Strand: - Start: 3 End: 131 .. F F L S Q N V A T E E G Y T D P L F F F G H L S H P A R G I G S I T K T P F I I T N M ....................................................................................................................................................................... tgaaagaaaagggattggtttacggctgtttcctcgccatacgtatccggcaggaagaaaaagccatgaagggaatgtggagctctaccaatccctgatattgttttcgtcgggaaaataattgtattgatctaaaagaggataaagcgttttgccgtagtgaagccgtagggatatggcgtatgttttataacatggcgtaacgttgcagcaggtcgttttttgggtagtagggggattatcggtttttttgtgaaaaaatcggattgtttgcagtaacattaaaaaaagaataccc 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================================================ tgaaagaaaagggattggtttacggctgtttcctcgccatacgtatccggcaggaagaaaaagccatgaagggaatgtggagctctaccaatccctgatattgttttcgtcgggaaaataattgtattgatctaaaagaggataaagcgttttgccgtagtgaagccgtagggatatggcgtatgttttataacatggcgtaacgttgcagcaggtcgttttttgggtagtagggggattatcggtttttttgtgaaaaaatcggattgtttgcagtaacattaaaaaaagaataccc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2184:TF2185|TF2184:TF2185:conserved hypothetical protein:outer membrane protein, TonB dependent receptor:->->:2357104..2357401 298 tgaaagaaaagggattggtttacggctgtttcctcgccatacgtatccggcaggaagaaaaagccatgaagggaatgtggagctctaccaatccctgatattgttttcgtcgggaaaataattgtattgatctaaaagaggataaagcgttttgccgtagtgaagccgtagggatatggcgtatgttttataacatggcgtaacgttgcagcaggtcgttttttgggtagtagggggattatcggtttttttgtgaaaaaatcggattgtttgcagtaacattaaaaaaagaataccc Intra-Species Hit: Count: 1 Min: 1 Max: 283 Len: 283 Subject: tfor_TF2184_TF2185|conserved hypothetical protein:outer membrane protein, TonB dependent receptor|POSITIVE:POSITIVE|[2357104,2357401]|298 HSP 1 e-value: 1.0E-146 bit: 519.0 Len: 283 Query Start:1 Query End:283 Subject Strand: POSITIVE Subject Start: 1 Subject End: 283 tgaaagaaaagggattggtttacggctgtttcctcgccatacgtatccggcaggaagaaaaagccatgaagggaatgtggagctctaccaatccctgatattgttttcgtcgggaaaataattgtattgatctaaaagaggataaagcgttttgccgtagtgaagccgtagggatatggcgtatgttttataacatggcgtaacgttgcagcaggtcgttttttgggtagtagggggattatcggnnnnnnngtgaaaaaatcggattgtttgcagtaacatt............... tgaaagaaaagggattggtttacggctgtttcctcgccatacgtatccggcaggaagaaaaagccatgaagggaatgtggagctctaccaatccctgatattgttttcgtcgggaaaataattgtattgatctaaaagaggataaagcgttttgccgtagtgaagccgtagggatatggcgtatgttttataacatggcgtaacgttgcagcaggtcgttttttgggtagtagggggattatcggtttttttgtgaaaaaatcggattgtttgcagtaacatt............... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAGAAAAGGGAUUGGUUUACGGCUGUUUCCUCGCCAUACGUAUCCGGCAGGAAGAAAAAGCCAUGAAGGGAAUGUGGAGCUCUACCAAUCCCUGAUAUUGUUUUCGUCGGGAAAAUAAUUGUAUUGAUCUAAAAGAGGAUAAAGCGUUUUGCCGUAGUGAAGCCGUAGGGAUAUGGCGUAUGUUUUAUAACAUGGCGUAACGUUGCAGCAGGUCGUUUUUUGGGUAGUAGGGGGAUUAUCGGUUUUUUUGUGAAAAAAUCGGAUUGUUUGCAGUAACAUU .........((((((((((....((((.((((((.(((..........)))))))))....))))....((((.........))))))))))))))...(((((((((.....)))))))))..((((.((((((((((.(((..((((((.((((........((((((....))))))..(((((....))))))))).)))))).......))).)))))))))))))).(.((((..((((((((((....))))))))))...)))).)......... (-82.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGUUACUGCAAACAAUCCGAUUUUUUCACAAAAAAACCGAUAAUCCCCCUACUACCCAAAAAACGACCUGCUGCAACGUUACGCCAUGUUAUAAAACAUACGCCAUAUCCCUACGGCUUCACUACGGCAAAACGCUUUAUCCUCUUUUAGAUCAAUACAAUUAUUUUCCCGACGAAAACAAUAUCAGGGAUUGGUAGAGCUCCACAUUCCCUUCAUGGCUUUUUCUUCCUGCCGGAUACGUAUGGCGAGGAAACAGCCGUAAACCAAUCCCUUUUCUUUCA ..((((..((((.......((.((((((....)))))).)).................(.......)......)))).((((..(((.((((....))))...(((..........)))........))).....(.((((........)))).).................))))..)))).....((((((((((.(((.......))).....((((((.(((((((..((((........))))))))))).))))))..))))))))))......... (-51.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 181 146 146 111 tfor:TF3108|5end_glutamine-hydrolyzing_carbamoyl-phosphate_synthase,_large_subunit_3338732..3338962_POSITIVE 396 70 23 222 172 tfor:TF0439|5end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_1_462284..462514_POSITIVE 395 70 22 79 20 tfor:TF2267|5end_lysozyme-related_protein_2434869..2435099_POSITIVE 381 70 23 76 31 tfor:TF1292|5end_sensor_histidine_protein_kinase_1372567..1372797_POSITIVE 379 247 204 194 156 tfor:TF2051|5end_hypothetical_protein_2215183..2215413_POSITIVE 372 237 196 57 5 tfor:TF0746|5end_possible_DNA_polymerase_III_792261..792491_POSITIVE 369 220 171 158 98 tfor:TF2160|5end_magnesium_chelatase,_subunit_I_2335974..2336204_POSITIVE 364 60 14 228 182 tfor:TF2524|5end_conserved_hypothetical_protein;_possible_endonuclease/exonuclease/phosphatase_family_protein_2702910..2703140_POSITIVE 364 246 206 104 56 tfor:TF0584|5end_phosphopantetheinyl_transferase_613755..613985_POSITIVE 357 56 13 209 176 tfor:TF2381|5end_muramidase/hemagglutinin_2545757..2545987_POSITIVE 350 85 42 208 158 tfor:TF1725|5end_hypothetical_protein_1851808..1852038_POSITIVE 350 245 204 43 4 tfor:TF0888|5end_transfer_region-related_protein,_TraN_938392..938622_POSITIVE 347 49 11 40 1 tfor:TF3026|5end_conserved_hypothetical_protein_3249137..3249367_POSITIVE 345 66 23 63 17 tfor:TF0299|5end_hypothetical_protein_324821..325051_POSITIVE 345 240 192 79 13 tfor:TF0148|5end_conserved_hypothetical_protein_159448..159678_POSITIVE 343 56 11 107 51 tfor:TF2986|5end_conserved_hypothetical_protein;_possible_glycosyltransferase_3201818..3202048_POSITIVE 339 56 11 177 131 tfor:TF2886|5end_RNA_methylase_SpoU_family_3075651..3075881_POSITIVE 339 53 11 51 8 tfor:TF1775|5end_oxidoreductase,_Gfo/Idh/MocA_family_1913135..1913365_POSITIVE 339 236 198 37 1 tfor:TF0433|5end_60_kDa_inner_membrane_protein_453357..453587_POSITIVE 338 217 177 55 9 tfor:TF2796|5end_cytochrome_D_ubiquinol_oxidase,_subunit_II_2981269..2981499_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 181 146 70 35 tfor:TF3107|3end_hypothetical_protein_3338736..3338886_POSITIVE 395 70 22 79 20 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 381 70 23 76 31 tfor:TF1291|3end_response_regulator_(fimR__protein)_1372647..1372797_POSITIVE 364 246 206 98 50 tfor:TF0583|3end_possible_gliding_motility-related_protein_613829..613979_POSITIVE 358 57 11 115 78 tfor:TF0759|3end_heat_shock_protein_15,_RNA-binding_domain_S4_806366..806516_POSITIVE 353 80 32 58 8 tfor:TF0368|3end_hypothetical_protein_385834..385984_POSITIVE 348 57 11 80 18 tfor:TF0247|3end_conserved_hypothetical_protein_278348..278498_POSITIVE 339 60 12 70 13 tfor:TF3009|3end_RNA_polymerase_ECF-type_sigma_factor_3229709..3229859_POSITIVE 336 83 46 112 67 tfor:TF1623|3end_5-formyltetrahydrofolate_cyclo-ligase_1737332..1737482_POSITIVE 335 237 195 71 17 tfor:TF1432|3end_possible_hemolysin_A_1516990..1517140_POSITIVE 335 80 31 118 66 tfor:TF0811|3end_conserved_hypothetical_protein;_posible_sugar_phosphate_isomerase_870724..870874_POSITIVE 330 57 14 151 108 tfor:TF2523|3end_NAD(P)H-flavin_oxidoreductase_2702916..2703066_POSITIVE 330 66 23 46 5 tfor:TF1818|3end_conserved_hypothetical_protein_1958754..1958904_POSITIVE 330 172 132 123 73 tfor:TF1183|3end_hypothetical_protein_1268728..1268878_POSITIVE 328 245 204 68 29 tfor:TF1914|3end_conserved_hypothetical_protein_2067656..2067806_POSITIVE 328 80 32 58 8 tfor:TF0348|3end_hypothetical_protein_370447..370597_POSITIVE 327 246 204 105 65 tfor:TF0545|3end_glucose-inhibited_division_protein_B_576453..576603_POSITIVE 325 58 12 59 5 tfor:TF2846|3end_cobyric_acid_synthase_3036469..3036619_POSITIVE 325 181 147 38 4 tfor:TF1834|3end_3-isopropylmalate_dehydrogenase_1984311..1984461_POSITIVE 323 80 32 57 7 tfor:TF2170|3end_hypothetical_protein_2345070..2345220_POSITIVE