Origin IGS: taacaaatcaaaacaggaggtcattcaggattgcggttgttccacaacagtaacagccgcaattcaatattgaaagtatcataaacacaaacaattcatatcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagatatgaattgtttgtgtttatgatactttcaatattgaattgcggctgttactgttgtggaacaaccgcaatcctgaatgacctcctgttttgatttgtta Mask Tandem Repeat Region ================================================ taacaaatcaaaacaggaggtcattcaggattgcggttgttccacaacagtaacagccgcaattcaatattgaaagtatcataaacacaaacaattcatatcta Find is-nt database================================================ Query_seq: TF1152:TF1153|TF1152:TF1153:permease, major facilitator superfamily:pyruvate-formate lyase-activating enzyme:->->:1234679..1234782 104 taacaaatcaaaacaggaggtcattcaggattgcggttgttccacaacagtaacagccgcaattcaatattgaaagtatcataaacacaaacaattcatatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1152:TF1153|TF1152:TF1153:permease, major facilitator superfamily:pyruvate-formate lyase-activating enzyme:->->:1234679..1234782 104 taacaaatcaaaacaggaggtcattcaggattgcggttgttccacaacagtaacagccgcaattcaatattgaaagtatcataaacacaaacaattcatatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1152:TF1153|TF1152:TF1153:permease, major facilitator superfamily:pyruvate-formate lyase-activating enzyme:->->:1234679..1234782 104 taacaaatcaaaacaggaggtcattcaggattgcggttgttccacaacagtaacagccgcaattcaatattgaaagtatcataaacacaaacaattcatatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taacaaatcaaaacaggaggtcattcaggattgcggttgttccacaacagtaacagccgcaattcaatattgaaagtatcataaacacaaacaattcatatcta Predict ORF larger than 30AA ================================================ taacaaatcaaaacaggaggtcattcaggattgcggttgttccacaacagtaacagccgcaattcaatattgaaagtatcataaacacaaacaattcatatcta 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================================================ taacaaatcaaaacaggaggtcattcaggattgcggttgttccacaacagtaacagccgcaattcaatattgaaagtatcataaacacaaacaattcatatcta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -9.5 Tail_Score: -3.18728 Start: 31 End: 62 Full_Region: GGAGGTCATTCAGGA TTGCGGTTGTTCC ACAACA GTAACAGCCGCAA TTCAATATTGAAAGT ..............................TTGCGGTTGTTCCACAACAGTAACAGCCGCAA.......................................... Find igs database================================================ Query_seq: TF1152:TF1153|TF1152:TF1153:permease, major facilitator superfamily:pyruvate-formate lyase-activating enzyme:->->:1234679..1234782 104 taacaaatcaaaacaggaggtcattcaggattgcggttgttccacaacagtaacagccgcaattcaatattgaaagtatcataaacacaaacaattcatatcta Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: tfor_TF1152_TF1153|permease, major facilitator superfamily:pyruvate-formate lyase-activating enzyme|POSITIVE:POSITIVE|[1234679,1234782]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 taacaaatcaaaacaggaggtcattcaggattgcggttgttccacaacagtaacagccgcaattcaatattgaaagtatcataaacacaaacaattcatatcta taacaaatcaaaacaggaggtcattcaggattgcggttgttccacaacagtaacagccgcaattcaatattgaaagtatcataaacacaaacaattcatatcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAAAUCAAAACAGGAGGUCAUUCAGGAUUGCGGUUGUUCCACAACAGUAACAGCCGCAAUUCAAUAUUGAAAGUAUCAUAAACACAAACAAUUCAUAUCUA .......((((....(((.....))).((((((((((((((.(......).))))))))))))))....))))............................... (-23.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAUAUGAAUUGUUUGUGUUUAUGAUACUUUCAAUAUUGAAUUGCGGCUGUUACUGUUGUGGAACAACCGCAAUCCUGAAUGACCUCCUGUUUUGAUUUGUUA .(((((.((((((...(((((...)))))...))))...(.(((((((.((((.((.....)))))).))))))).).........)).))))).......... (-17.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 59 15 171 129 tfor:TF0366|5end_hypothetical_protein_383564..383794_POSITIVE 342 59 15 171 129 tfor:TF0362|5end_hypothetical_protein_379952..380182_POSITIVE 323 60 15 172 129 tfor:TF2171|5end_hypothetical_protein_2345485..2345715_POSITIVE 323 60 15 172 129 tfor:TF2166|5end_hypothetical_protein_2342115..2342345_POSITIVE 308 40 14 61 33 tfor:TF1416|5end_outer_membrane_protein_1497576..1497806_POSITIVE 300 60 16 65 11 tfor:TF0001|5end_hypothetical_protein_-116..114_POSITIVE 293 60 14 124 61 tfor:TF1299|5end_conserved_hypothetical_protein_1380937..1381167_POSITIVE 287 59 14 163 121 tfor:TF2992|5end_hexapeptide_transferase_family_protein_3209042..3209272_POSITIVE 287 54 12 71 30 tfor:TF2447|5end_lipoprotein_2623549..2623779_POSITIVE 285 60 14 201 157 tfor:TF3022|5end_chorismate_synthase_3246136..3246366_POSITIVE 284 80 34 80 31 tfor:TF2021|5end_hypothetical_protein_2177702..2177932_POSITIVE 282 60 14 79 31 tfor:TF1945|5end_glycerate_dehydrogenase_2093229..2093459_POSITIVE 280 59 15 225 177 tfor:TF1308|5end_50S_ribosomal_protein_L28_1387224..1387454_POSITIVE 280 60 14 197 140 tfor:TF0804|5end_possible_phosphatidylglycerophosphate_synthase_861875..862105_POSITIVE 278 59 12 72 26 tfor:TF2114|5end_1-hydroxy-2-methyl-2-(E)-butenyl_4-diphosphate_synthase,_GcpE_2283006..2283236_POSITIVE 276 60 19 54 2 tfor:TF1323|5end_metallo-beta-lactamase_superfamily_protein_1402650..1402880_POSITIVE 275 60 12 76 37 tfor:TF1885|5end_conserved_hypothetical_protein_2037307..2037537_POSITIVE 274 59 15 230 191 tfor:TF0997|5end_conserved_hypothetical_protein_1051475..1051705_POSITIVE 272 57 12 77 39 tfor:TF2250|5end_transfer_region-related_protein,_TraD_2423380..2423610_POSITIVE 270 60 13 64 26 tfor:TF0304|5end_peptidyl-prolyl_cis-trans_isomerase_329567..329797_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 372 65 24 63 17 tfor:TF1152|3end_permease,_major_facilitator_superfamily_1234618..1234768_POSITIVE 287 59 14 148 106 tfor:TF2991|3end_conserved_hypothetical_protein_3209107..3209257_POSITIVE 284 59 15 132 76 tfor:TF0610|3end_conserved_hypothetical_protein;_possible_phosphatidylglycerophosphate_synthase_644043..644193_POSITIVE 282 60 14 79 31 tfor:TF1944|3end_conserved_hypothetical_protein_2093309..2093459_POSITIVE 281 40 18 25 1 tfor:TF1415|3end_outer_membrane_protein,_TonB_dependent_receptor_1497620..1497770_POSITIVE 278 59 12 72 26 tfor:TF2113|3end_phosphoribosylaminoimidazole_carboxylase_2283086..2283236_POSITIVE 272 60 16 61 10 tfor:TF0419|3end_conserved_hypothetical_protein_435794..435944_POSITIVE 268 60 20 74 30 tfor:TF2160|3end_magnesium_chelatase,_subunit_I_2337049..2337199_POSITIVE 268 57 16 50 6 tfor:TF0328|3end_conserved_hypothetical_protein_355266..355416_POSITIVE 265 60 17 57 5 tfor:TF0881|3end_conserved_hypothetical_protein_935993..936143_POSITIVE 261 69 26 118 78 tfor:TF0528|3end_two-component_system_sensor_histidine_kinase_554779..554929_POSITIVE 258 60 18 141 103 tfor:TF2723|3end_30S_ribosomal_protein_S20_2898020..2898170_POSITIVE 257 60 14 62 26 tfor:TF1755|3end_periplasmic_protease_1892867..1893017_POSITIVE 253 57 14 68 35 tfor:TF1061|3end_glycosyltransferase_1131807..1131957_POSITIVE 252 60 16 110 58 tfor:TF3021|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_3246194..3246344_POSITIVE 252 58 16 147 102 tfor:TF1801|3end_conserved_hypothetical_protein;_possible_TPR-repeat-containing_protein_1945669..1945819_POSITIVE 251 60 15 68 25 tfor:TF2171|3end_hypothetical_protein_2345792..2345942_POSITIVE 251 63 24 132 95 tfor:TF0490|3end_conserved_hypothetical_protein_513904..514054_POSITIVE 251 60 36 31 8 tfor:TF0478|3end_conserved_hypothetical_protein_498627..498777_POSITIVE 251 44 14 64 38 tfor:TF0413|3end_succinyl-diaminopimelate_desuccinylase_431869..432019_POSITIVE