Origin IGS: accttgcccagcattgattgactgtgtactgtaagatgtaaatagtcgataacgctaacgcatggcacaagacaagaatggtctccatcttaatgaataaagatataataaaatagaatattcctgttctgataatttatatatcaggatatacgacgtatttccataccggatgacggtatgattcctgttgtccggcactcatgaggtcggacaggtgaaaaataagtttta .........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 taaaacttatttttcacctgtccgacctcatgagtgccggacaacaggaatcataccgtcatccggtatggaaatacgtcgtatatcctgatatataaattatcagaacaggaatattctattttattatatctttattcattaagatggagaccattcttgtcttgtgccatgcgttagcgttatcgactatttacatcttacagtacacagtcaatcaatgctgggcaaggt Mask Tandem Repeat Region ================================================ accttgcccagcattgattgactgtgtactgtaagatgtaaatagtcgataacgctaacgcatggcacaagacaagaatggtctccatcttaatgaataaagatataataaaatagaatattcctgttctgataatttatatatcaggatatacgacgtatttccataccggatgacggtatgattcctgttgtccggcactcatgaggtcggacaggtgaaaaataagtttta Find is-nt database================================================ Query_seq: TF0301:TF0303|TF0301:TF0303:outer membrane protein, TonB dependent receptor:conserved hypothetical protein:->->:328237..328470 234 accttgcccagcattgattgactgtgtactgtaagatgtaaatagtcgataacgctaacgcatggcacaagacaagaatggtctccatcttaatgaataaagatataataaaatagaatattcctgttctgataatttatatatcaggatatacgacgtatttccataccggatgacggtatgattcctgttgtccggcactcatgaggtcggacaggtgaaaaataagtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0301:TF0303|TF0301:TF0303:outer membrane protein, TonB dependent receptor:conserved hypothetical protein:->->:328237..328470 234 accttgcccagcattgattgactgtgtactgtaagatgtaaatagtcgataacgctaacgcatggcacaagacaagaatggtctccatcttaatgaataaagatataataaaatagaatattcctgttctgataatttatatatcaggatatacgacgtatttccataccggatgacggtatgattcctgttgtccggcactcatgaggtcggacaggtgaaaaataagtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0301:TF0303|TF0301:TF0303:outer membrane protein, TonB dependent receptor:conserved hypothetical protein:->->:328237..328470 234 accttgcccagcattgattgactgtgtactgtaagatgtaaatagtcgataacgctaacgcatggcacaagacaagaatggtctccatcttaatgaataaagatataataaaatagaatattcctgttctgataatttatatatcaggatatacgacgtatttccataccggatgacggtatgattcctgttgtccggcactcatgaggtcggacaggtgaaaaataagtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 accttgcccagcattgattgactgtgtactgtaagatgtaaatagtcgataacgctaacgcatggcacaagacaagaatggtctccatcttaatgaataaagatataataaaatagaatattcctgttctgataatttatatatcaggatatacgacgtatttccataccggatgacggtatgattcctgttgtccggcactcatgaggtcggacaggtgaaaaataagtttta Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: - Start: 58 End: 201 ......................................................... R M A C S L F P R W R L S Y L Y L L I S Y E Q E S L K Y I L I Y S T N G Y R I V T H N R N D P M ................................. Protein_Len: 45 Strand: - Start: 2 End: 136 . R A W C Q N V T Y Q L I Y I T S L A L A H C L V L I T E M K I F L S I I F Y F I G T R I M .................................................................................................. accttgcccagcattgattgactgtgtactgtaagatgtaaatagtcgataacgctaacgcatggcacaagacaagaatggtctccatcttaatgaataaagatataataaaatagaatattcctgttctgataatttatatatcaggatatacgacgtatttccataccggatgacggtatgattcctgttgtccggcactcatgaggtcggacaggtgaaaaataagtttta 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================================================ accttgcccagcattgattgactgtgtactgtaagatgtaaatagtcgataacgctaacgcatggcacaagacaagaatggtctccatcttaatgaataaagatataataaaatagaatattcctgttctgataatttatatatcaggatatacgacgtatttccataccggatgacggtatgattcctgttgtccggcactcatgaggtcggacaggtgaaaaataagtttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 57 HP_score: -5.4 Tail_Score: -3.41745 Start: 164 End: 184 Full_Region: ATATACGACGTATTT CCATACCG GATGA CGGTATGA TTCCTGTTGTCCGGC ...................................................................................................................................................................CCATACCGGATGACGGTATGA.................................................. TransTerm Strand: + Conf: 67 HP_score: -8.9 Tail_Score: -2.64726 Start: 165 End: 183 Full_Region: TATACGACGTATTTC CATACCG GATGA CGGTATG ATTCCTGTTGTCCGG ....................................................................................................................................................................CATACCGGATGACGGTATG................................................... Find igs database================================================ Query_seq: TF0301:TF0303|TF0301:TF0303:outer membrane protein, TonB dependent receptor:conserved hypothetical protein:->->:328237..328470 234 accttgcccagcattgattgactgtgtactgtaagatgtaaatagtcgataacgctaacgcatggcacaagacaagaatggtctccatcttaatgaataaagatataataaaatagaatattcctgttctgataatttatatatcaggatatacgacgtatttccataccggatgacggtatgattcctgttgtccggcactcatgaggtcggacaggtgaaaaataagtttta Intra-Species Hit: Count: 1 Min: 1 Max: 234 Len: 234 Subject: tfor_TF0301_TF0303|outer membrane protein, TonB dependent receptor:conserved hypothetical protein|POSITIVE:POSITIVE|[328237,328470]|234 HSP 1 e-value: 1.0E-130 bit: 464.0 Len: 234 Query Start:1 Query End:234 Subject Strand: POSITIVE Subject Start: 1 Subject End: 234 accttgcccagcattgattgactgtgtactgtaagatgtaaatagtcgataacgctaacgcatggcacaagacaagaatggtctccatcttaatgaataaagatataataaaatagaatattcctgttctgataatttatatatcaggatatacgacgtatttccataccggatgacggtatgattcctgttgtccggcactcatgaggtcggacaggtgaaaaataagtttta accttgcccagcattgattgactgtgtactgtaagatgtaaatagtcgataacgctaacgcatggcacaagacaagaatggtctccatcttaatgaataaagatataataaaatagaatattcctgttctgataatttatatatcaggatatacgacgtatttccataccggatgacggtatgattcctgttgtccggcactcatgaggtcggacaggtgaaaaataagtttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUUGCCCAGCAUUGAUUGACUGUGUACUGUAAGAUGUAAAUAGUCGAUAACGCUAACGCAUGGCACAAGACAAGAAUGGUCUCCAUCUUAAUGAAUAAAGAUAUAAUAAAAUAGAAUAUUCCUGUUCUGAUAAUUUAUAUAUCAGGAUAUACGACGUAUUUCCAUACCGGAUGACGGUAUGAUUCCUGUUGUCCGGCACUCAUGAGGUCGGACAGGUGAAAAAUAAGUUUUA .((.(((..(((....(((((((((.(((........))).)))))))))...)))...))).))(((..((((.((((.(((...(((((........)))))....................((((((((((.......))))))))))...))).......(((((((.....))))))))))).))))(((((((.((....)))))))))..))).............. (-62.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAACUUAUUUUUCACCUGUCCGACCUCAUGAGUGCCGGACAACAGGAAUCAUACCGUCAUCCGGUAUGGAAAUACGUCGUAUAUCCUGAUAUAUAAAUUAUCAGAACAGGAAUAUUCUAUUUUAUUAUAUCUUUAUUCAUUAAGAUGGAGACCAUUCUUGUCUUGUGCCAUGCGUUAGCGUUAUCGACUAUUUACAUCUUACAGUACACAGUCAAUCAAUGCUGGGCAAGGU ..................((((((.(((....)).).)))))).(((((.((((((((.....))))))))..((((...)))).))))).............((..((((((((.((((((((((..(((....)))....))))))))))...))))))))..)).(((.(((.((((((((((.((((.(.(((........))).).)))).)).))))))))))).))) (-59.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 441 220 177 107 61 tfor:TF2017|5end_conserved_hypothetical_protein_2173504..2173734_POSITIVE 400 208 167 96 49 tfor:TF2036|5end_possible_pyruvate_formate-lyase_activating_enzyme_2196302..2196532_POSITIVE 380 220 171 57 8 tfor:TF0789|5end_preprotein_translocase,_secDF_family_841293..841523_POSITIVE 375 199 157 177 122 tfor:TF1069|5end_glucokinase_regulatory_protein,_sugar_phosphate_isomerase_domain_1138884..1139114_POSITIVE 373 220 171 144 98 tfor:TF1909|5end_cobalamin_(5`-phosphate)_synthase_2063207..2063437_POSITIVE 368 205 167 149 104 tfor:TF1623|5end_5-formyltetrahydrofolate_cyclo-ligase_1736698..1736928_POSITIVE 362 199 154 228 170 tfor:TF2307|5end_two-component_system_sensor_histidine_kinase/response_2462618..2462848_POSITIVE 347 220 171 62 5 tfor:TF1197|5end_transcriptional_regulator_1280780..1281010_POSITIVE 347 218 171 210 166 tfor:TF1067|5end_conserved_hypothetical_protein_1136867..1137097_POSITIVE 344 200 157 187 135 tfor:TF0285|5end_conserved_hypothetical_protein_314465..314695_POSITIVE 341 220 171 61 8 tfor:TF2457|5end_ABC_transporter,_permease_component,_zinc-binding_protein_2633147..2633377_POSITIVE 341 219 177 158 123 tfor:TF2087|5end_conserved_hypothetical_protein_2256856..2257086_POSITIVE 341 188 141 107 64 tfor:TF1560|5end_glycosyltransferase_1666989..1667219_POSITIVE 340 220 171 58 5 tfor:TF0710|5end_two_component_system_histidine_kinase_757250..757480_POSITIVE 340 199 154 51 1 tfor:TF0434|5end_CTP_synthetase_(UTP_ammonia_ligase)_455346..455576_POSITIVE 339 198 154 193 134 tfor:TF1609|5end_hypothetical_protein_1728340..1728570_POSITIVE 338 220 177 226 192 tfor:TF1910|5end_nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase_2064001..2064231_POSITIVE 338 220 171 208 151 tfor:TF0063|5end_conserved_hypothetical_protein_66110..66340_POSITIVE 337 220 171 217 158 tfor:TF3020|5end_possible_sulfatase_3243559..3243789_POSITIVE 336 226 190 49 8 tfor:TF2043|5end_fructokinase_2202267..2202497_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 380 220 171 54 5 tfor:TF0788|3end_protein-export_membrane_protein_841370..841520_POSITIVE 376 205 163 147 113 tfor:TF2535|3end_histidyl-tRNA_synthetase_2719178..2719328_POSITIVE 370 218 172 52 4 tfor:TF0326|3end_hypothetical_protein_354317..354467_POSITIVE 368 205 167 134 89 tfor:TF1622|3end_conserved_hypothetical_protein_1736763..1736913_POSITIVE 347 218 171 121 77 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 341 188 141 112 69 tfor:TF1559|3end_glycosyltransferase_1667074..1667224_POSITIVE 336 226 190 58 17 tfor:TF2042|3end_sugar_phosphate_isomerase,_polysialic_acid_capsule_expression_protein_2202356..2202506_POSITIVE 329 219 171 144 105 tfor:TF3087|3end_conserved_hypothetical_protein_3322582..3322732_POSITIVE 324 200 157 151 100 tfor:TF2483|3end_hypothetical_protein_2660022..2660172_POSITIVE 322 202 162 55 12 tfor:TF2496|3end_butyryl-CoA_dehydrogenase,_short_chain_acyl-CoA_dehydrogenase_2672065..2672215_POSITIVE 322 209 161 85 37 tfor:TF1479|3end_ABC_transporter,_permease_component_1573592..1573742_POSITIVE 319 221 185 139 97 tfor:TF1184|3end_hypothetical_protein_1269311..1269461_POSITIVE 319 221 185 139 97 tfor:TF1183|3end_hypothetical_protein_1268728..1268878_POSITIVE 319 220 171 48 1 tfor:TF0456|3end_conserved_hypothetical_protein_474172..474322_POSITIVE 318 200 153 144 96 tfor:TF2974|3end_conserved_hypothetical_protein;_possible_hydrolase_3182439..3182589_POSITIVE 315 200 155 66 13 tfor:TF0822|3end_hypothetical_protein_880764..880914_POSITIVE 313 216 171 65 13 tfor:TF2464|3end_RNA_polymerase_ECF-type_sigma_factor_2643746..2643896_POSITIVE 312 207 167 128 89 tfor:TF1273|3end_hypothetical_protein_1357462..1357612_POSITIVE 312 217 174 63 1 tfor:TF0120|3end_hexouronate_transporter_132811..132961_POSITIVE 311 215 171 151 110 tfor:TF1908|3end_possible_phosphoglycerate_mutase_2063299..2063449_POSITIVE