Origin IGS: aaagttatatgtccgaccgccatttgccaaaatctctttgacgaatcacagctttacttttgacgaataataatatattttcatttaatccgttaactttgcagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actgcaaagttaacggattaaatgaaaatatattattattcgtcaaaagtaaagctgtgattcgtcaaagagattttggcaaatggcggtcggacatataacttt Mask Tandem Repeat Region ================================================ aaagttatatgtccgaccgccatttgccaaaatctctttgacgaatcacagctttacttttgacgaataataatatattttcatttaatccgttaactttgcagt Find is-nt database================================================ Query_seq: PI0235:PI0237|PI0235:PI0237:hypothetical protein:predicted two-component system sensor histidine kinase:->->:236014..236118 105 aaagttatatgtccgaccgccatttgccaaaatctctttgacgaatcacagctttacttttgacgaataataatatattttcatttaatccgttaactttgcagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0235:PI0237|PI0235:PI0237:hypothetical protein:predicted two-component system sensor histidine kinase:->->:236014..236118 105 aaagttatatgtccgaccgccatttgccaaaatctctttgacgaatcacagctttacttttgacgaataataatatattttcatttaatccgttaactttgcagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0235:PI0237|PI0235:PI0237:hypothetical protein:predicted two-component system sensor histidine kinase:->->:236014..236118 105 aaagttatatgtccgaccgccatttgccaaaatctctttgacgaatcacagctttacttttgacgaataataatatattttcatttaatccgttaactttgcagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagttatatgtccgaccgccatttgccaaaatctctttgacgaatcacagctttacttttgacgaataataatatattttcatttaatccgttaactttgcagt Predict ORF larger than 30AA ================================================ aaagttatatgtccgaccgccatttgccaaaatctctttgacgaatcacagctttacttttgacgaataataatatattttcatttaatccgttaactttgcagt 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================================================ aaagttatatgtccgaccgccatttgccaaaatctctttgacgaatcacagctttacttttgacgaataataatatattttcatttaatccgttaactttgcagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0235:PI0237|PI0235:PI0237:hypothetical protein:predicted two-component system sensor histidine kinase:->->:236014..236118 105 aaagttatatgtccgaccgccatttgccaaaatctctttgacgaatcacagctttacttttgacgaataataatatattttcatttaatccgttaactttgcagt Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: pint_PI0235_PI0237|hypothetical protein:predicted two-component system sensor histidine kinase|POSITIVE:POSITIVE|[236014,236118]|105 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 aaagttatatgtccgaccgccatttgccaaaatctctttgacgaatcacagctttacttttgacgaataataatatattttcatttaatccgttaactttgcagt aaagttatatgtccgaccgccatttgccaaaatctctttgacgaatcacagctttacttttgacgaataataatatattttcatttaatccgttaactttgcagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUUAUAUGUCCGACCGCCAUUUGCCAAAAUCUCUUUGACGAAUCACAGCUUUACUUUUGACGAAUAAUAAUAUAUUUUCAUUUAAUCCGUUAACUUUGCAGU (((((((.(((.......((.(((((.((((.....)))).)))))....))........(((.(((((......)))))))).......))))))))))..... ( -9.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUGCAAAGUUAACGGAUUAAAUGAAAAUAUAUUAUUAUUCGUCAAAAGUAAAGCUGUGAUUCGUCAAAGAGAUUUUGGCAAAUGGCGGUCGGACAUAUAACUUU .....(((((((((((((..(((((.......))))))))))).....((...(((((.(((.(((((((...))))))).))).)))))...))...))))))) (-20.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 60 14 158 121 pint:PI0604|5end_O-succinylbenzoic_acid--CoA_ligase_550825..551055_POSITIVE 254 60 14 37 1 pint:PI1043|5end_conserved_hypothetical_protein_960855..961085_POSITIVE 253 57 13 85 37 pint:PI0028|5end_aminopeptidase_31559..31789_POSITIVE 249 57 12 127 73 pint:PI1613|5end_hypothetical_protein_1539978..1540208_POSITIVE 240 56 11 201 160 pint:PI1980|5end_conserved_hypothetical_protein_1937470..1937700_POSITIVE 240 46 2 47 4 pint:PI0945|5end_sodium:solute_symporter_family_protein_876249..876479_POSITIVE 237 60 18 181 133 pint:PI1033|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_950297..950527_POSITIVE 237 60 13 115 55 pint:PI0592|5end_DNA_mismatch_repair_protein_540795..541025_POSITIVE 234 49 7 229 191 pint:PI0951|5end_hypothetical_protein_884526..884756_POSITIVE 233 52 11 193 146 pint:PI2028|5end_shikimate_kinase_1982162..1982392_POSITIVE 232 57 14 143 101 pint:PI0756|5end_50S_ribosomal_protein_L7/L12_687146..687376_POSITIVE 232 45 14 49 13 pint:PI0202|5end_DNA_helicase_191753..191983_POSITIVE 231 48 9 69 38 pint:PI1671|5end_hypothetical_protein_1586397..1586627_POSITIVE 231 39 10 39 14 pint:PI0547|5end_fructose-bisphosphate_aldolase_498376..498606_POSITIVE 230 54 13 53 3 pint:PI1711|5end_ABC_transporter,_ATP-binding_protein_1627597..1627827_POSITIVE 229 53 14 116 76 pint:PI1115|5end_conserved_hypothetical_protein_1039244..1039474_POSITIVE 229 50 2 114 69 pint:PI0011|5end_conserved_hypothetical_protein_12142..12372_POSITIVE 228 59 11 160 103 pint:PI0088|5end_S-adenosylmethionine_synthetase_86663..86893_POSITIVE 227 56 14 208 171 pint:PI1928|5end_conserved_hypothetical_protein_1871996..1872226_POSITIVE 227 45 12 159 136 pint:PI1575|5end_LemA_protein_1501143..1501373_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 34 3 93 66 pint:PI1065|3end_hypothetical_protein_983650..983800_POSITIVE 267 51 15 114 72 pint:PI0225|3end_conserved_hypothetical_protein_222759..222909_POSITIVE 260 60 14 94 57 pint:PI0603|3end_3-dehydroquinate_synthase_550841..550991_POSITIVE 242 52 17 70 43 pint:PI0028|3end_aminopeptidase_32727..32877_POSITIVE 233 52 11 81 34 pint:PI2027|3end_arginine_decarboxylase_1982130..1982280_POSITIVE 232 54 11 150 93 pint:PI1712|3end_hypothetical_protein_1627774..1627924_POSITIVE 228 59 11 150 93 pint:PI0087|3end_conserved_hypothetical_protein_86733..86883_POSITIVE 222 66 33 145 101 pint:PI0468|3end_50S_ribosomal_protein_L29_437176..437326_POSITIVE 219 47 9 151 91 pint:PI0140|3end_conserved_hypothetical_protein_132106..132256_POSITIVE 218 44 3 45 3 pint:PI1807|3end_hypothetical_protein_1742481..1742631_POSITIVE 218 68 23 74 23 pint:PI0972|3end_glycine_cleavage_system_H_protein_2_899399..899549_POSITIVE 218 52 13 52 9 pint:PI0681|3end_hypothetical_protein_619256..619406_POSITIVE 215 70 23 133 73 pint:PI0759|3end_hypothetical_protein_693998..694148_POSITIVE 212 57 11 79 30 pint:PI1143|3end_hypothetical_protein_1070504..1070654_POSITIVE 209 55 11 82 35 pint:PI1766|3end_sugar_transporter,_possible_glucose/galactose_transporter_1694350..1694500_POSITIVE 207 60 14 83 45 pint:PI0838|3end_DNA_replication_and_repair_protein_773927..774077_POSITIVE 207 54 13 73 38 pint:PI0115|3end_hypothetical_protein_108669..108819_POSITIVE 206 54 13 41 10 pint:PI2060|3end_conserved_hypothetical_protein;_possible_metalloprotease_2018358..2018508_POSITIVE 204 60 11 127 69 pint:PI1732|3end_hypothetical_protein_1652098..1652248_POSITIVE 204 37 12 62 35 pint:PI0958|3end_G:T/U_mismatch-specific_DNA_glycosylase_890569..890719_POSITIVE