Origin IGS: tgctttatattcttttttatgttattatgcgattataaacattacgccgagacataatcccacgttatgggctgcaaaattactcattctttttcaattaaccaagaaaagaaagttttttagcaaaataatttatgtttttttctatattttgcttatctttgcaccgcaaagcgaattattccgtaacaaataaataacaaattatatataagcagatt .........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 aatctgcttatatataatttgttatttatttgttacggaataattcgctttgcggtgcaaagataagcaaaatatagaaaaaaacataaattattttgctaaaaaactttcttttcttggttaattgaaaaagaatgagtaattttgcagcccataacgtgggattatgtctcggcgtaatgtttataatcgcataataacataaaaaagaatataaagca Mask Tandem Repeat Region ================================================ tgctttatattcttttttatgttattatgcgattataaacattacgccgagacataatcccacgttatgggctgcaaaattactcattctttttcaattaaccaagaaaagaaagttttttagcaaaataatttatgtttttttctatattttgcttatctttgcaccgcaaagcgaattattccgtaacaaataaataacaaattatatataagcagatt Find is-nt database================================================ Query_seq: PI2018:PI2019|PI2018:PI2019:50S ribosomal protein L34:elongation factor P:->->:1976050..1976270 221 tgctttatattcttttttatgttattatgcgattataaacattacgccgagacataatcccacgttatgggctgcaaaattactcattctttttcaattaaccaagaaaagaaagttttttagcaaaataatttatgtttttttctatattttgcttatctttgcaccgcaaagcgaattattccgtaacaaataaataacaaattatatataagcagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2018:PI2019|PI2018:PI2019:50S ribosomal protein L34:elongation factor P:->->:1976050..1976270 221 tgctttatattcttttttatgttattatgcgattataaacattacgccgagacataatcccacgttatgggctgcaaaattactcattctttttcaattaaccaagaaaagaaagttttttagcaaaataatttatgtttttttctatattttgcttatctttgcaccgcaaagcgaattattccgtaacaaataaataacaaattatatataagcagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2018:PI2019|PI2018:PI2019:50S ribosomal protein L34:elongation factor P:->->:1976050..1976270 221 tgctttatattcttttttatgttattatgcgattataaacattacgccgagacataatcccacgttatgggctgcaaaattactcattctttttcaattaaccaagaaaagaaagttttttagcaaaataatttatgtttttttctatattttgcttatctttgcaccgcaaagcgaattattccgtaacaaataaataacaaattatatataagcagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgctttatattcttttttatgttattatgcgattataaacattacgccgagacataatcccacgttatgggctgcaaaattactcattctttttcaattaaccaagaaaagaaagttttttagcaaaataatttatgtttttttctatattttgcttatctttgcaccgcaaagcgaattattccgtaacaaataaataacaaattatatataagcagatt Predict ORF larger than 30AA ================================================ Protein_Len: 54 Strand: + Start: 32 End: 193 ............................... M I N I T P R H N P T L W A A K L L I L F Q L T K K R K F F S K I I Y V F F Y I L L I F A P Q S E L F R N K ............................ tgctttatattcttttttatgttattatgcgattataaacattacgccgagacataatcccacgttatgggctgcaaaattactcattctttttcaattaaccaagaaaagaaagttttttagcaaaataatttatgtttttttctatattttgcttatctttgcaccgcaaagcgaattattccgtaacaaataaataacaaattatatataagcagatt 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================================================ tgctttatattcttttttatgttattatgcgattataaacattacgccgagacataatcccacgttatgggctgcaaaattactcattctttttcaattaaccaagaaaagaaagttttttagcaaaataatttatgtttttttctatattttgcttatctttgcaccgcaaagcgaattattccgtaacaaataaataacaaattatatataagcagatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI2018:PI2019|PI2018:PI2019:50S ribosomal protein L34:elongation factor P:->->:1976050..1976270 221 tgctttatattcttttttatgttattatgcgattataaacattacgccgagacataatcccacgttatgggctgcaaaattactcattctttttcaattaaccaagaaaagaaagttttttagcaaaataatttatgtttttttctatattttgcttatctttgcaccgcaaagcgaattattccgtaacaaataaataacaaattatatataagcagatt Intra-Species Hit: Count: 1 Min: 1 Max: 221 Len: 221 Subject: pint_PI2018_PI2019|50S ribosomal protein L34:elongation factor P|POSITIVE:POSITIVE|[1976050,1976270]|221 HSP 1 e-value: 1.0E-109 bit: 396.0 Len: 221 Query Start:1 Query End:221 Subject Strand: POSITIVE Subject Start: 1 Subject End: 221 tgctttatattcttttttatgttattatgcgattataaacattacgccgagacataatcccacgttatgggctgcaaaattactcattctttttcaattaaccaagaaaagaaagttttttagcaaaataatttatgnnnnnnnctatattttgcttatctttgcaccgcaaagcgaattattccgtaacaaataaataacaaattatatataagcagatt tgctttatattcttttttatgttattatgcgattataaacattacgccgagacataatcccacgttatgggctgcaaaattactcattctttttcaattaaccaagaaaagaaagttttttagcaaaataatttatgtttttttctatattttgcttatctttgcaccgcaaagcgaattattccgtaacaaataaataacaaattatatataagcagatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUUUAUAUUCUUUUUUAUGUUAUUAUGCGAUUAUAAACAUUACGCCGAGACAUAAUCCCACGUUAUGGGCUGCAAAAUUACUCAUUCUUUUUCAAUUAACCAAGAAAAGAAAGUUUUUUAGCAAAAUAAUUUAUGUUUUUUUCUAUAUUUUGCUUAUCUUUGCACCGCAAAGCGAAUUAUUCCGUAACAAAUAAAUAACAAAUUAUAUAUAAGCAGAUU ((((((((((..(((.((((.(((((.((((.................(((((((((.((((.....)))).(((.(((..(((..((((((((...........)))))))))))..))).))).......))))))))).....(((.(((((((.....(((...)))))))))).)))..))))...))))))))).)))..))))).))))).... (-37.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCUGCUUAUAUAUAAUUUGUUAUUUAUUUGUUACGGAAUAAUUCGCUUUGCGGUGCAAAGAUAAGCAAAAUAUAGAAAAAAACAUAAAUUAUUUUGCUAAAAAACUUUCUUUUCUUGGUUAAUUGAAAAAGAAUGAGUAAUUUUGCAGCCCAUAACGUGGGAUUAUGUCUCGGCGUAAUGUUUAUAAUCGCAUAAUAACAUAAAAAAGAAUAUAAAGCA .....((((.(((((..(((.(((((((((.....((((....))))...((((((((((((...(((((((((.................))))))))).....((((....(((((..((....))..))))).))))..))))))..(((((...)))))(((((((....))))))).......)))))).))))).)))).)))..))))))))). (-41.53) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 187 144 152 114 pint:PI1779|5end_16S_rRNA_processing_protein_1711335..1711565_POSITIVE 283 90 45 68 22 pint:PI0812|5end_conserved_hypothetical_protein;_possible_ferredoxin_750185..750415_POSITIVE 271 88 46 110 63 pint:PI0259|5end_conserved_protein_found_in_conjugation,_TraI_252355..252585_POSITIVE 265 78 39 50 15 pint:PI0234|5end_integrase_234473..234703_POSITIVE 259 76 40 44 7 pint:PI0796|5end_competence_protein_733324..733554_POSITIVE 257 77 44 216 178 pint:PI0126|5end_conserved_hypothetical_protein_117925..118155_POSITIVE 256 50 2 71 20 pint:PI0725|5end_hypothetical_protein_658623..658853_POSITIVE 255 80 37 165 121 pint:PI0435|5end_30S_ribosomal_protein_S21_406997..407227_POSITIVE 254 86 45 162 121 pint:PI0088|5end_S-adenosylmethionine_synthetase_86663..86893_POSITIVE 250 190 153 201 148 pint:PI0960|5end_hypothetical_protein_891137..891367_POSITIVE 245 74 39 134 96 pint:PI1971|5end_possible_IS1249-related_transposase_1928027..1928257_POSITIVE 245 74 39 134 96 pint:PI1533|5end_conserved_hypothetical_protein;_possible_transposase_1452667..1452897_POSITIVE 245 74 39 134 96 pint:PI0534|5end_conserved_hypothetical_protein;_possible_transposase_488568..488798_POSITIVE 243 196 153 94 49 pint:PI0773|5end_D-3-phosphoglycerate_dehydrogenase_708498..708728_POSITIVE 241 184 142 231 192 pint:PI1874|5end_hypothetical_protein_1818437..1818667_POSITIVE 239 84 48 188 155 pint:PI0641|5end_conserved_hypothetical_protein_583791..584021_POSITIVE 238 200 152 152 104 pint:PI0190|5end_3-dehydroquinate_dehydratase_II_180618..180848_POSITIVE 238 89 41 162 109 pint:PI0047|5end_phosphomethylpyrimidine_kinase_45964..46194_POSITIVE 236 83 46 43 5 pint:PI2006|5end_potassium_uptake_system_protein_1964480..1964710_POSITIVE 236 77 45 185 154 pint:PI0753|5end_hypothetical_protein_683391..683621_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 187 144 136 98 pint:PI1778|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1711399..1711549_POSITIVE 275 180 144 137 95 pint:PI1575|3end_LemA_protein_1501852..1502002_POSITIVE 259 66 22 111 69 pint:PI0797|3end_tRNA_pseudouridine_synthase_A_(pseudouridylate_synthase)_735752..735902_POSITIVE 257 77 44 101 63 pint:PI0125|3end_undecaprenyl_pyrophosphate_synthase_117890..118040_POSITIVE 254 188 156 51 19 pint:PI1379|3end_hypothetical_protein_1302292..1302442_POSITIVE 252 78 40 142 108 pint:PI0087|3end_conserved_hypothetical_protein_86733..86883_POSITIVE 245 193 155 76 38 pint:PI1426|3end_flavodoxin_1345446..1345596_POSITIVE 241 184 142 133 94 pint:PI1873|3end_hypothetical_protein_1818419..1818569_POSITIVE 239 84 48 138 105 pint:PI0640|3end_conserved_hypothetical_protein_583821..583971_POSITIVE 234 82 43 84 47 pint:PI0983|3end_hypothetical_protein_909991..910141_POSITIVE 232 109 63 55 11 pint:PI1188|3end_hypothetical_protein_1108895..1109045_POSITIVE 232 168 122 66 25 pint:PI0523|3end_hypothetical_protein_479844..479994_POSITIVE 226 86 48 41 6 pint:PI1940|3end_conserved_hypothetical_protein;_possible_outer_membrane_protein_1897267..1897417_POSITIVE 226 77 39 134 90 pint:PI1781|3end_membrane-associated_zinc_metalloprotease_1714551..1714701_POSITIVE 224 184 145 56 26 pint:PI0272|3end_conserved_hypothetical_protein_262943..263093_POSITIVE 223 179 137 114 71 pint:PI0036|3end_glutathione_peroxidase_39289..39439_POSITIVE 221 88 44 83 38 pint:PI1806|3end_integral_membrane_transport_protein;_possible_sugar_transport_proteins_1742191..1742341_POSITIVE 221 189 164 145 119 pint:PI0929|3end_copper_homeostasis_protein_861048..861198_POSITIVE 220 187 152 138 96 pint:PI0560|3end_hypothetical_protein_508910..509060_POSITIVE 218 54 20 79 49 pint:PI1174|3end_hypothetical_protein_1097042..1097192_POSITIVE