Origin IGS: taatatgcttctacagataaacagaagcgagcctggctgtagcgatatatcggatcgctaacgtacgtagtgaatcattgcatgtgagggaggcggctaccattgaaaaactatgccgtttccccacaaaaaaaacaaaaaacacgcagggataaaaaaaacgttatctttgcgttaacaaacattcaaatgct .........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 agcatttgaatgtttgttaacgcaaagataacgttttttttatccctgcgtgttttttgttttttttgtggggaaacggcatagtttttcaatggtagccgcctccctcacatgcaatgattcactacgtacgttagcgatccgatatatcgctacagccaggctcgcttctgtttatctgtagaagcatatta Mask Tandem Repeat Region ================================================ taatatgcttctacagataaacagaagcgagcctggctgtagcgatatatcggatcgctaacgtacgtagtgaatcattgcatgtgagggaggcggctaccattgaaaaactatgccgtttccccacaaaaaaaacaaaaaacacgcagggataaaaaaaacgttatctttgcgttaacaaacattcaaatgct Find is-nt database================================================ Query_seq: TF0667:TF0668|TF0667:TF0668:conserved hypothetical protein:inorganic pyrophosphatase:->->:712439..712632 194 taatatgcttctacagataaacagaagcgagcctggctgtagcgatatatcggatcgctaacgtacgtagtgaatcattgcatgtgagggaggcggctaccattgaaaaactatgccgtttccccacaaaaaaaacaaaaaacacgcagggataaaaaaaacgttatctttgcgttaacaaacattcaaatgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0667:TF0668|TF0667:TF0668:conserved hypothetical protein:inorganic pyrophosphatase:->->:712439..712632 194 taatatgcttctacagataaacagaagcgagcctggctgtagcgatatatcggatcgctaacgtacgtagtgaatcattgcatgtgagggaggcggctaccattgaaaaactatgccgtttccccacaaaaaaaacaaaaaacacgcagggataaaaaaaacgttatctttgcgttaacaaacattcaaatgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0667:TF0668|TF0667:TF0668:conserved hypothetical protein:inorganic pyrophosphatase:->->:712439..712632 194 taatatgcttctacagataaacagaagcgagcctggctgtagcgatatatcggatcgctaacgtacgtagtgaatcattgcatgtgagggaggcggctaccattgaaaaactatgccgtttccccacaaaaaaaacaaaaaacacgcagggataaaaaaaacgttatctttgcgttaacaaacattcaaatgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatatgcttctacagataaacagaagcgagcctggctgtagcgatatatcggatcgctaacgtacgtagtgaatcattgcatgtgagggaggcggctaccattgaaaaactatgccgtttccccacaaaaaaaacaaaaaacacgcagggataaaaaaaacgttatctttgcgttaacaaacattcaaatgct Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 33 End: 152 ................................ M A V A I Y R I A N V R S E S L H V R E A A T I E K L C R F P T K K T K N T Q G .......................................... Protein_Len: 30 Strand: + Start: 103 End: 192 ...................................................................................................... M K N Y A V S P Q K K Q K T R R D K K N V I F A L T N I Q M .. Protein_Len: 44 Strand: - Start: 14 End: 145 ............. L Y V S A L R A T A I Y R I A L T R L S D N C T L S A A V M S F S H R K G V F F V F F M ................................................. taatatgcttctacagataaacagaagcgagcctggctgtagcgatatatcggatcgctaacgtacgtagtgaatcattgcatgtgagggaggcggctaccattgaaaaactatgccgtttccccacaaaaaaaacaaaaaacacgcagggataaaaaaaacgttatctttgcgttaacaaacattcaaatgct 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================================================ taatatgcttctacagataaacagaagcgagcctggctgtagcgatatatcggatcgctaacgtacgtagtgaatcattgcatgtgagggaggcggctaccattgaaaaactatgccgtttccccacaaaaaaaacaaaaaacacgcagggataaaaaaaacgttatctttgcgttaacaaacattcaaatgct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0667:TF0668|TF0667:TF0668:conserved hypothetical protein:inorganic pyrophosphatase:->->:712439..712632 194 taatatgcttctacagataaacagaagcgagcctggctgtagcgatatatcggatcgctaacgtacgtagtgaatcattgcatgtgagggaggcggctaccattgaaaaactatgccgtttccccacaaaaaaaacaaaaaacacgcagggataaaaaaaacgttatctttgcgttaacaaacattcaaatgct Intra-Species Hit: Count: 1 Min: 1 Max: 194 Len: 194 Subject: tfor_TF0667_TF0668|conserved hypothetical protein:inorganic pyrophosphatase|POSITIVE:POSITIVE|[712439,712632]|194 HSP 1 e-value: 4.0E-66 bit: 252.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 taatatgcttctacagataaacagaagcgagcctggctgtagcgatatatcggatcgctaacgtacgtagtgaatcattgcatgtgagggaggcggctaccattgaaaaactatgccgtttccccac................................................................... taatatgcttctacagataaacagaagcgagcctggctgtagcgatatatcggatcgctaacgtacgtagtgaatcattgcatgtgagggaggcggctaccattgaaaaactatgccgtttccccac................................................................... HSP 2 e-value: 5.0E-10 bit: 65.9 Len: 33 Query Start:162 Query End:194 Subject Strand: POSITIVE Subject Start: 162 Subject End: 194 .................................................................................................................................................................cgttatctttgcgttaacaaacattcaaatgct .................................................................................................................................................................cgttatctttgcgttaacaaacattcaaatgct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUGCUUCUACAGAUAAACAGAAGCGAGCCUGGCUGUAGCGAUAUAUCGGAUCGCUAACGUACGUAGUGAAUCAUUGCAUGUGAGGGAGGCGGCUACCAUUGAAAAACUAUGCCGUUUCCCCACAAAAAAAACAAAAAACACGCAGGGAUAAAAAAAACGUUAUCUUUGCGUUAACAAACAUUCAAAUGCU .....(((((((..........))))))).....(((..(((((((.......)))))))..((..((((((...)))))).((((.((((((((((.....((....))....))))))))))))))......)).......((((((((((((........))))))))))))................))) (-56.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCAUUUGAAUGUUUGUUAACGCAAAGAUAACGUUUUUUUUAUCCCUGCGUGUUUUUUGUUUUUUUUGUGGGGAAACGGCAUAGUUUUUCAAUGGUAGCCGCCUCCCUCACAUGCAAUGAUUCACUACGUACGUUAGCGAUCCGAUAUAUCGCUACAGCCAGGCUCGCUUCUGUUUAUCUGUAGAAGCAUAUUA (((...(((((..((((..(((((..(((((........)))))..)))))...............((((((((..((((.((.(........).))))))..)))).)))).))))..)))))........((.((((((.......))))))))......))).(((((((........)))))))...... (-50.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 378 80 35 97 52 tfor:TF1891|5end_hypothetical_protein_2043389..2043619_POSITIVE 377 88 41 226 174 tfor:TF2906|5end_phosphatidylserine_decarboxylase_3102182..3102412_POSITIVE 375 105 62 42 3 tfor:TF3087|5end_conserved_hypothetical_protein_3319878..3320108_POSITIVE 372 96 51 229 182 tfor:TF0328|5end_conserved_hypothetical_protein_354182..354412_POSITIVE 360 88 41 231 182 tfor:TF0971|5end_conserved_hypothetical_protein_1021355..1021585_POSITIVE 359 106 63 155 100 tfor:TF1292|5end_sensor_histidine_protein_kinase_1372567..1372797_POSITIVE 357 61 27 181 131 tfor:TF1253|5end_hypothetical_protein_1335982..1336212_POSITIVE 356 98 51 72 15 tfor:TF1481|5end_ABC_transporter,_ATP-binding_protein_1574783..1575013_POSITIVE 356 80 31 93 36 tfor:TF0146|5end_glutamine-dependent_NAD(+)_synthetase_154855..155085_POSITIVE 352 70 27 191 138 tfor:TF2402|5end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2574582..2574812_POSITIVE 350 96 51 56 7 tfor:TF2457|5end_ABC_transporter,_permease_component,_zinc-binding_protein_2633147..2633377_POSITIVE 345 97 51 184 142 tfor:TF2256|5end_transfer_region-related_protein,_TraI_2427908..2428138_POSITIVE 344 67 22 172 129 tfor:TF0005|5end_possible_beta-lactamase_600..830_POSITIVE 341 67 27 44 2 tfor:TF1002|5end_replicative_DNA_helicase_1056620..1056850_POSITIVE 340 98 51 68 19 tfor:TF1472|5end_acyl-ACP_thioesterase_1565475..1565705_POSITIVE 335 127 84 70 18 tfor:TF2439|5end_conserved_hypothetical_protein_2616380..2616610_POSITIVE 329 58 21 166 119 tfor:TF2775|5end_conserved_hypothetical_protein;_possible_mucoidy_inhibitor-related_protein_2959668..2959898_POSITIVE 324 68 21 212 165 tfor:TF1068|5end_conserved_hypothetical_protein;_possible_N-acetylglucosamine_kinase_1138036..1138266_POSITIVE 324 70 23 57 1 tfor:TF0792|5end_pyruvate_ferredoxin;_flavodoxin_oxidoreductase_846454..846684_POSITIVE 324 96 51 192 154 tfor:TF0352|5end_transposase_element_371223..371453_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 399 68 21 151 116 tfor:TF0100|3end_conserved_hypothetical_protein_111703..111853_POSITIVE 367 130 83 143 90 tfor:TF0012|3end_conserved_hypothetical_protein_6641..6791_POSITIVE 360 118 73 48 2 tfor:TF3086|3end_conserved_hypothetical_protein_3319949..3320099_POSITIVE 356 98 51 75 18 tfor:TF1480|3end_ABC_transporter,_permease_component_1574866..1575016_POSITIVE 344 67 22 139 96 tfor:TF0002|3end_hypothetical_protein_647..797_POSITIVE 330 99 54 151 106 tfor:TF1291|3end_response_regulator_(fimR__protein)_1372647..1372797_POSITIVE 329 58 21 137 90 tfor:TF2774|3end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_2959719..2959869_POSITIVE 324 96 51 115 77 tfor:TF0351|3end_hypothetical_protein_371226..371376_POSITIVE 322 68 23 59 11 tfor:TF2049|3end_glycosyltransferase_2213992..2214142_POSITIVE 322 58 14 45 6 tfor:TF0889|3end_conjugative_transposon_protein,_TraO_940078..940228_POSITIVE 319 70 21 150 99 tfor:TF1954|3end_long-chain-fatty-acid--CoA_ligase_2106940..2107090_POSITIVE 315 90 42 97 47 tfor:TF3139|3end_Na+-translocating_NADH-quinone_reductase,_subunit_C_3373389..3373539_POSITIVE 314 60 13 143 106 tfor:TF3031|3end_conserved_hypothetical_protein_3255086..3255236_POSITIVE 313 98 51 68 18 tfor:TF1382|3end_hypothetical_protein_1457777..1457927_POSITIVE 313 98 51 64 14 tfor:TF1383|3end_hypothetical_protein_1457773..1457923_POSITIVE 312 58 26 137 103 tfor:TF0644|3end_pyruvate_phosphate_dikinase_688581..688731_POSITIVE 312 63 27 123 93 tfor:TF0041|3end_outer_membrane_protein,_TonB_dependent_receptor_45942..46092_POSITIVE 307 96 51 83 26 tfor:TF1213|3end_D-3-phosphoglycerate_dehydrogenase_1301196..1301346_POSITIVE 306 63 24 82 43 tfor:TF2527|3end_RNA_polymerase_ECF-type_sigma_factor_2710749..2710899_POSITIVE 305 56 13 47 7 tfor:TF3070|3end_conserved_hypothetical_protein_3294783..3294933_POSITIVE