Origin IGS: acttcttatattttagttgaacgtttaaatttaacactttcatacaacaaaagaaactcaaaaatgatgcaattattccttttgaaggtgattttttaacacttttaacggctacattcggcacttaaccgcgtttaacgataaaaagagggatttcgcttcattttaacacttcgcatcggccattttgacagtcagaaaaacaaagagactacgcccctccaaccaatggcgcagtctcttgaaatataggctttccggtgtttta .........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 taaaacaccggaaagcctatatttcaagagactgcgccattggttggaggggcgtagtctctttgtttttctgactgtcaaaatggccgatgcgaagtgttaaaatgaagcgaaatccctctttttatcgttaaacgcggttaagtgccgaatgtagccgttaaaagtgttaaaaaatcaccttcaaaaggaataattgcatcatttttgagtttcttttgttgtatgaaagtgttaaatttaaacgttcaactaaaatataagaagt Mask Tandem Repeat Region ================================================ acttcttatattttagttgaacgtttaaatttaacactttcatacaacaaaagaaactcaaaaatgatgcaattattccttttgaaggtgattttttaacacttttaacggctacattcggcacttaaccgcgtttaacgataaaaagagggatttcgcttcattttaacacttcgcatcggccattttgacagtcagaaaaacaaagagactacgcccctccaaccaatggcgcagtctcttgaaatataggctttccggtgtttta Find is-nt database================================================ Query_seq: TF1450:TF1451|TF1450:TF1451:periplasmic serine protease:conserved hypothetical protein:->->:1535748..1536015 268 acttcttatattttagttgaacgtttaaatttaacactttcatacaacaaaagaaactcaaaaatgatgcaattattccttttgaaggtgattttttaacacttttaacggctacattcggcacttaaccgcgtttaacgataaaaagagggatttcgcttcattttaacacttcgcatcggccattttgacagtcagaaaaacaaagagactacgcccctccaaccaatggcgcagtctcttgaaatataggctttccggtgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1450:TF1451|TF1450:TF1451:periplasmic serine protease:conserved hypothetical protein:->->:1535748..1536015 268 acttcttatattttagttgaacgtttaaatttaacactttcatacaacaaaagaaactcaaaaatgatgcaattattccttttgaaggtgattttttaacacttttaacggctacattcggcacttaaccgcgtttaacgataaaaagagggatttcgcttcattttaacacttcgcatcggccattttgacagtcagaaaaacaaagagactacgcccctccaaccaatggcgcagtctcttgaaatataggctttccggtgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1450:TF1451|TF1450:TF1451:periplasmic serine protease:conserved hypothetical protein:->->:1535748..1536015 268 acttcttatattttagttgaacgtttaaatttaacactttcatacaacaaaagaaactcaaaaatgatgcaattattccttttgaaggtgattttttaacacttttaacggctacattcggcacttaaccgcgtttaacgataaaaagagggatttcgcttcattttaacacttcgcatcggccattttgacagtcagaaaaacaaagagactacgcccctccaaccaatggcgcagtctcttgaaatataggctttccggtgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acttcttatattttagttgaacgtttaaatttaacactttcatacaacaaaagaaactcaaaaatgatgcaattattccttttgaaggtgattttttaacacttttaacggctacattcggcacttaaccgcgtttaacgataaaaagagggatttcgcttcattttaacacttcgcatcggccattttgacagtcagaaaaacaaagagactacgcccctccaaccaatggcgcagtctcttgaaatataggctttccggtgtttta Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: - Start: 2 End: 124 . K K Y K L Q V N L N L V K M C C F F S L F S A I I G K S P S K K V S K V A V N P M ................................................................................................................................................ acttcttatattttagttgaacgtttaaatttaacactttcatacaacaaaagaaactcaaaaatgatgcaattattccttttgaaggtgattttttaacacttttaacggctacattcggcacttaaccgcgtttaacgataaaaagagggatttcgcttcattttaacacttcgcatcggccattttgacagtcagaaaaacaaagagactacgcccctccaaccaatggcgcagtctcttgaaatataggctttccggtgtttta 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================================================ acttcttatattttagttgaacgtttaaatttaacactttcatacaacaaaagaaactcaaaaatgatgcaattattccttttgaaggtgattttttaacacttttaacggctacattcggcacttaaccgcgtttaacgataaaaagagggatttcgcttcattttaacacttcgcatcggccattttgacagtcagaaaaacaaagagactacgcccctccaaccaatggcgcagtctcttgaaatataggctttccggtgtttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -9.6 Tail_Score: -4.97405 Start: 208 End: 241 Full_Region: aagcctatatttcaa gagactgcgccatt ggttgg aggggcgtagtctc tttgtttttctgact ...............................................................................................................................................................................................................gagactgcgccattggttggaggggcgtagtctc........................... Find igs database================================================ Query_seq: TF1450:TF1451|TF1450:TF1451:periplasmic serine protease:conserved hypothetical protein:->->:1535748..1536015 268 acttcttatattttagttgaacgtttaaatttaacactttcatacaacaaaagaaactcaaaaatgatgcaattattccttttgaaggtgattttttaacacttttaacggctacattcggcacttaaccgcgtttaacgataaaaagagggatttcgcttcattttaacacttcgcatcggccattttgacagtcagaaaaacaaagagactacgcccctccaaccaatggcgcagtctcttgaaatataggctttccggtgtttta Intra-Species Hit: Count: 1 Min: 1 Max: 268 Len: 268 Subject: tfor_TF1450_TF1451|periplasmic serine protease:conserved hypothetical protein|POSITIVE:POSITIVE|[1535748,1536015]|268 HSP 1 e-value: 1.0E-150 bit: 531.0 Len: 268 Query Start:1 Query End:268 Subject Strand: POSITIVE Subject Start: 1 Subject End: 268 acttcttatattttagttgaacgtttaaatttaacactttcatacaacaaaagaaactcaaaaatgatgcaattattccttttgaaggtgattttttaacacttttaacggctacattcggcacttaaccgcgtttaacgataaaaagagggatttcgcttcattttaacacttcgcatcggccattttgacagtcagaaaaacaaagagactacgcccctccaaccaatggcgcagtctcttgaaatataggctttccggtgtttta acttcttatattttagttgaacgtttaaatttaacactttcatacaacaaaagaaactcaaaaatgatgcaattattccttttgaaggtgattttttaacacttttaacggctacattcggcacttaaccgcgtttaacgataaaaagagggatttcgcttcattttaacacttcgcatcggccattttgacagtcagaaaaacaaagagactacgcccctccaaccaatggcgcagtctcttgaaatataggctttccggtgtttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUCUUAUAUUUUAGUUGAACGUUUAAAUUUAACACUUUCAUACAACAAAAGAAACUCAAAAAUGAUGCAAUUAUUCCUUUUGAAGGUGAUUUUUUAACACUUUUAACGGCUACAUUCGGCACUUAACCGCGUUUAACGAUAAAAAGAGGGAUUUCGCUUCAUUUUAACACUUCGCAUCGGCCAUUUUGACAGUCAGAAAAACAAAGAGACUACGCCCCUCCAACCAAUGGCGCAGUCUCUUGAAAUAUAGGCUUUCCGGUGUUUUA ...............(((((((((..........((((((((...............(((....)))...............))))))))....................(((......)))........)))))))))..(((((.(((((....).)))).))))).......(((((((((.(((((.....))))).....((((((((.((((............)))).))))))))........)))....)))))).... (-54.81) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAACACCGGAAAGCCUAUAUUUCAAGAGACUGCGCCAUUGGUUGGAGGGGCGUAGUCUCUUUGUUUUUCUGACUGUCAAAAUGGCCGAUGCGAAGUGUUAAAAUGAAGCGAAAUCCCUCUUUUUAUCGUUAAACGCGGUUAAGUGCCGAAUGUAGCCGUUAAAAGUGUUAAAAAAUCACCUUCAAAAGGAAUAAUUGCAUCAUUUUUGAGUUUCUUUUGUUGUAUGAAAGUGUUAAAUUUAAACGUUCAACUAAAAUAUAAGAAGU ...(((((((.(..(((........(((((((((((((.((......)).))))))))))))).(((.....))).........)))...).))..)))))(((((((.((((.....(.(((((.((.((((....((((.....))))....)))).)).))))).)...........(((.....))).....)))).)))))))....((((((.((((...((((.((...........)).)))).....)))).)))))). (-58.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 366 257 214 225 189 tfor:TF1678|5end_periplasmic_protease_1791097..1791327_POSITIVE 365 190 143 115 69 tfor:TF0296|5end_hypothetical_protein_321941..322171_POSITIVE 360 240 191 178 136 tfor:TF2252|5end_transfer_region-related_protein,_TraF_2424621..2424851_POSITIVE 357 246 207 148 96 tfor:TF2443|5end_amidophosphoribosyl-transferase_2620287..2620517_POSITIVE 355 260 215 227 177 tfor:TF2224|5end_CTn_excision_protein_2394592..2394822_POSITIVE 334 237 191 204 153 tfor:TF1068|5end_conserved_hypothetical_protein;_possible_N-acetylglucosamine_kinase_1138036..1138266_POSITIVE 331 258 216 230 189 tfor:TF3118|5end_conserved_hypothetical_protein_3352373..3352603_POSITIVE 325 241 204 76 26 tfor:TF1710|5end_possible_cell_filamentation_protein_1829679..1829909_POSITIVE 322 220 172 88 19 tfor:TF2681|5end_conserved_hypothetical_protein_2855796..2856026_POSITIVE 321 249 204 125 64 tfor:TF1257|5end_hypothetical_protein_1338118..1338348_POSITIVE 321 249 204 90 29 tfor:TF1256|5end_hypothetical_protein_1338083..1338313_POSITIVE 318 180 131 158 104 tfor:TF1921|5end_hypothetical_protein_2070322..2070552_POSITIVE 316 159 112 108 61 tfor:TF0315|5end_hypothetical_protein_341198..341428_POSITIVE 314 160 114 92 30 tfor:TF1684|5end_zinc_protease_1797396..1797626_POSITIVE 307 159 111 76 6 tfor:TF3008|5end_zinc_protease_3228041..3228271_POSITIVE 307 227 181 179 123 tfor:TF1329|5end_glucose-1-phosphate_thymidyltransferase_1408578..1408808_POSITIVE 306 260 215 69 28 tfor:TF2833|5end_lipid_A_disaccharide_synthase_3023973..3024203_POSITIVE 305 241 212 207 176 tfor:TF2259|5end_transfer_region-related_protein,_TraK_2429577..2429807_POSITIVE 303 254 214 222 181 tfor:TF3007|5end_conserved_hypothetical_protein_3227256..3227486_POSITIVE 303 196 157 133 87 tfor:TF2931|5end_3-deoxy-D-manno-2-octulosonic_acid_(Kdo_transferase)_3134275..3134505_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 351 257 211 58 5 tfor:TF2442|3end_heat_shock_protein_60_2620271..2620421_POSITIVE 321 249 204 78 17 tfor:TF1255|3end_conserved_hypothetical_protein_1338151..1338301_POSITIVE 318 180 131 139 85 tfor:TF1919|3end_hypothetical_protein_2070383..2070533_POSITIVE 316 159 112 85 38 tfor:TF0313|3end_outer_membrane_protein,_TonB_dependent_receptor_341255..341405_POSITIVE 303 254 214 48 7 tfor:TF3006|3end_response_regulator,_transcriptional_regulator_RprY_3227162..3227312_POSITIVE 303 196 157 130 84 tfor:TF2930|3end_glutamyl-tRNA_synthetase_3134352..3134502_POSITIVE 303 164 121 55 13 tfor:TF2264|3end_transfer_region-related_protein,_TraO_2433542..2433692_POSITIVE 303 243 205 60 30 tfor:TF0709|3end_preprotein_translocase,_subunit_SecA_757241..757391_POSITIVE 299 260 212 95 42 tfor:TF1930|3end_two-component_response_regulator_2078203..2078353_POSITIVE 293 244 209 42 5 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 293 260 212 75 13 tfor:TF1946|3end_membrane_protein;_spore_maturation-like_protein_2095601..2095751_POSITIVE 292 219 179 139 95 tfor:TF0813|3end_glycosyl_hydrolase,_secreted_872181..872331_POSITIVE 290 186 148 129 93 tfor:TF2653|3end_hypothetical_protein_2822460..2822610_POSITIVE 288 260 216 117 67 tfor:TF2950|3end_chloromuconate_cycloisomerase_3158549..3158699_POSITIVE 282 183 150 138 104 tfor:TF1494|3end_cobinamide_kinase/cobinamide_phosphate_guanylyltransferase_1594602..1594752_POSITIVE 281 160 125 43 2 tfor:TF3146|3end_GTP-binding_protein_Obg_3383080..3383230_POSITIVE 281 140 97 119 73 tfor:TF3094|3end_translation_elongation_factor_Ts_3327023..3327173_POSITIVE 279 137 109 140 102 tfor:TF2133|3end_aspartate-semialdehyde_dehydrogenase_2311362..2311512_POSITIVE 278 256 212 77 32 tfor:TF3069|3end_hypothetical_protein_3294413..3294563_POSITIVE 278 260 214 54 9 tfor:TF2646|3end_conserved_hypothetical_protein_2816697..2816847_POSITIVE