Origin IGS: taaaagctttcgggtttcttttcctctgatataaggggaaagaaacttcgcaaggtaaagtcttttagtttaacagtcggtgatggttggtaaataaaagactcaaaagaaaaagaaaataaaagttttgctggagatttgttaataacaggttgagtaaatgttcaagagtggacgttgaagaacgaaaagacgacagcctccgcagaattactaaatttttaaataaaa .........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 ttttatttaaaaatttagtaattctgcggaggctgtcgtcttttcgttcttcaacgtccactcttgaacatttactcaacctgttattaacaaatctccagcaaaacttttattttctttttcttttgagtcttttatttaccaaccatcaccgactgttaaactaaaagactttaccttgcgaagtttctttccccttatatcagaggaaaagaaacccgaaagctttta Mask Tandem Repeat Region ================================================ taaaagctttcgggtttcttttcctctgatataaggggaaagaaacttcgcaaggtaaagtcttttagtttaacagtcggtgatggttggtaaataaaagactcaaaagaaaaagaaaataaaagttttgctggagatttgttaataacaggttgagtaaatgttcaagagtggacgttgaagaacgaaaagacgacagcctccgcagaattactaaatttttaaataaaa Find is-nt database================================================ Query_seq: PI0456:PI0457|PI0456:PI0457:30S ribosomal protein S12:30S ribosomal protein S7:->->:429280..429510 231 taaaagctttcgggtttcttttcctctgatataaggggaaagaaacttcgcaaggtaaagtcttttagtttaacagtcggtgatggttggtaaataaaagactcaaaagaaaaagaaaataaaagttttgctggagatttgttaataacaggttgagtaaatgttcaagagtggacgttgaagaacgaaaagacgacagcctccgcagaattactaaatttttaaataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0456:PI0457|PI0456:PI0457:30S ribosomal protein S12:30S ribosomal protein S7:->->:429280..429510 231 taaaagctttcgggtttcttttcctctgatataaggggaaagaaacttcgcaaggtaaagtcttttagtttaacagtcggtgatggttggtaaataaaagactcaaaagaaaaagaaaataaaagttttgctggagatttgttaataacaggttgagtaaatgttcaagagtggacgttgaagaacgaaaagacgacagcctccgcagaattactaaatttttaaataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0456:PI0457|PI0456:PI0457:30S ribosomal protein S12:30S ribosomal protein S7:->->:429280..429510 231 taaaagctttcgggtttcttttcctctgatataaggggaaagaaacttcgcaaggtaaagtcttttagtttaacagtcggtgatggttggtaaataaaagactcaaaagaaaaagaaaataaaagttttgctggagatttgttaataacaggttgagtaaatgttcaagagtggacgttgaagaacgaaaagacgacagcctccgcagaattactaaatttttaaataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaagctttcgggtttcttttcctctgatataaggggaaagaaacttcgcaaggtaaagtcttttagtttaacagtcggtgatggttggtaaataaaagactcaaaagaaaaagaaaataaaagttttgctggagatttgttaataacaggttgagtaaatgttcaagagtggacgttgaagaacgaaaagacgacagcctccgcagaattactaaatttttaaataaaa Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: - Start: 68 End: 211 ................................................................... N L L R H H N T F L L S L L F L F Y F N Q Q L N T L L L N L L H E L T S T S S R F S S L R R L M .................... Protein_Len: 48 Strand: - Start: 3 End: 146 .. F S E P K K E E S I L P F F S R L T F D K L K V T P S P Q Y I F S E F S F S F L L K A P S K N M ..................................................................................... taaaagctttcgggtttcttttcctctgatataaggggaaagaaacttcgcaaggtaaagtcttttagtttaacagtcggtgatggttggtaaataaaagactcaaaagaaaaagaaaataaaagttttgctggagatttgttaataacaggttgagtaaatgttcaagagtggacgttgaagaacgaaaagacgacagcctccgcagaattactaaatttttaaataaaa 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================================================ taaaagctttcgggtttcttttcctctgatataaggggaaagaaacttcgcaaggtaaagtcttttagtttaacagtcggtgatggttggtaaataaaagactcaaaagaaaaagaaaataaaagttttgctggagatttgttaataacaggttgagtaaatgttcaagagtggacgttgaagaacgaaaagacgacagcctccgcagaattactaaatttttaaataaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0456:PI0457|PI0456:PI0457:30S ribosomal protein S12:30S ribosomal protein S7:->->:429280..429510 231 taaaagctttcgggtttcttttcctctgatataaggggaaagaaacttcgcaaggtaaagtcttttagtttaacagtcggtgatggttggtaaataaaagactcaaaagaaaaagaaaataaaagttttgctggagatttgttaataacaggttgagtaaatgttcaagagtggacgttgaagaacgaaaagacgacagcctccgcagaattactaaatttttaaataaaa Intra-Species Hit: Count: 1 Min: 1 Max: 231 Len: 231 Subject: pint_PI0456_PI0457|30S ribosomal protein S12:30S ribosomal protein S7|POSITIVE:POSITIVE|[429280,429510]|231 HSP 1 e-value: 2.0E-53 bit: 210.0 Len: 106 Query Start:126 Query End:231 Subject Strand: POSITIVE Subject Start: 126 Subject End: 231 .............................................................................................................................ttttgctggagatttgttaataacaggttgagtaaatgttcaagagtggacgttgaagaacgaaaagacgacagcctccgcagaattactaaatttttaaataaaa .............................................................................................................................ttttgctggagatttgttaataacaggttgagtaaatgttcaagagtggacgttgaagaacgaaaagacgacagcctccgcagaattactaaatttttaaataaaa HSP 2 e-value: 1.0E-44 bit: 180.0 Len: 91 Query Start:1 Query End:91 Subject Strand: POSITIVE Subject Start: 1 Subject End: 91 taaaagctttcgggtttcttttcctctgatataaggggaaagaaacttcgcaaggtaaagtcttttagtttaacagtcggtgatggttggt............................................................................................................................................ taaaagctttcgggtttcttttcctctgatataaggggaaagaaacttcgcaaggtaaagtcttttagtttaacagtcggtgatggttggt............................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGCUUUCGGGUUUCUUUUCCUCUGAUAUAAGGGGAAAGAAACUUCGCAAGGUAAAGUCUUUUAGUUUAACAGUCGGUGAUGGUUGGUAAAUAAAAGACUCAAAAGAAAAAGAAAAUAAAAGUUUUGCUGGAGAUUUGUUAAUAACAGGUUGAGUAAAUGUUCAAGAGUGGACGUUGAAGAACGAAAAGACGACAGCCUCCGCAGAAUUACUAAAUUUUUAAAUAAAA .....(((((((((((((((((((.((......))))))))))))).))).)))))..(((((((((.((((.((..((....))..)).)))))))))))))...........((((((...((((((((.((((..(((((........(((.....((((((((....))))))))....)))........))))).)))))))))))).....))))))........ (-56.79) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAUUUAAAAAUUUAGUAAUUCUGCGGAGGCUGUCGUCUUUUCGUUCUUCAACGUCCACUCUUGAACAUUUACUCAACCUGUUAUUAACAAAUCUCCAGCAAAACUUUUAUUUUCUUUUUCUUUUGAGUCUUUUAUUUACCAACCAUCACCGACUGUUAAACUAAAAGACUUUACCUUGCGAAGUUUCUUUCCCCUUAUAUCAGAGGAAAAGAAACCCGAAAGCUUUUA ........................((((((((.............((((................))))............(((.....)))..))))).)))...(((((..(((((((((((((.((((((((((((((.((..(......)..)).)))).))))))))))........((((....))))..........)))))))))))))...)))))...... (-34.19) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 207 163 51 1 pint:PI0486|5end_DNA-directed_RNA_polymerase,_alpha_subunit_445073..445303_POSITIVE 303 57 15 58 11 pint:PI0253|5end_conjugative_transposon_protein,_TraD_248294..248524_POSITIVE 289 208 166 63 10 pint:PI1898|5end_S-adenosyl-methyltransferase_1841288..1841518_POSITIVE 283 208 168 82 35 pint:PI1284|5end_ATP_synthase,_delta_subunit_1199800..1200030_POSITIVE 280 210 168 91 39 pint:PI0381|5end_probable_transcriptional_regulator,_AraC_family_350572..350802_POSITIVE 279 50 5 227 186 pint:PI0495|5end_conserved_hypothetical_protein_454872..455102_POSITIVE 279 50 5 218 177 pint:PI0494|5end_hypothetical_protein_454863..455093_POSITIVE 276 55 12 160 108 pint:PI0641|5end_conserved_hypothetical_protein_583791..584021_POSITIVE 275 200 151 107 51 pint:PI0949|5end_endonuclease_882264..882494_POSITIVE 274 89 48 100 64 pint:PI1321|5end_conserved_hypothetical_protein_1239764..1239994_POSITIVE 270 196 160 87 47 pint:PI1045|5end_cytidine/deoxycytidylate_deaminase_family_protein_965104..965334_POSITIVE 266 61 21 99 58 pint:PI1313|5end_possible_POT_family_(proton-dependent_oligopeptide_transport_family)_1229710..1229940_POSITIVE 262 89 41 192 139 pint:PI1512|5end_hypothetical_protein_1429529..1429759_POSITIVE 262 210 167 102 48 pint:PI0341|5end_conserved_hypothetical_protein_317038..317268_POSITIVE 261 207 166 221 174 pint:PI0630|5end_peptidyl-tRNA_hydrolase_(aminoacyl-tRNA_hydrolase)_577045..577275_POSITIVE 261 210 168 82 46 pint:PI0171|5end_hypothetical_protein_163850..164080_POSITIVE 256 209 168 48 13 pint:PI0780|5end_DNA_gyrase,_subunit_A_(DNA_topoisomerase_(ATP-hydrolyzing))_715902..716132_POSITIVE 255 117 76 72 23 pint:PI0374|5end_MbpB_protein_344571..344801_POSITIVE 254 55 11 65 13 pint:PI1708|5end_hypothetical_protein_1625087..1625317_POSITIVE 254 213 172 51 8 pint:PI1263|5end_probable_integrase_1184502..1184732_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 50 1 80 24 pint:PI0456|3end_30S_ribosomal_protein_S12_429219..429369_POSITIVE 303 57 15 67 20 pint:PI0252|3end_conserved_hypothetical_protein_248383..248533_POSITIVE 283 208 168 66 19 pint:PI1283|3end_ATP_synthase,_alpha_subunit_1199864..1200014_POSITIVE 279 209 162 87 36 pint:PI1940|3end_conserved_hypothetical_protein;_possible_outer_membrane_protein_1897267..1897417_POSITIVE 276 55 12 110 58 pint:PI0640|3end_conserved_hypothetical_protein_583821..583971_POSITIVE 272 59 11 144 93 pint:PI0394|3end_transcriptional_regulator,_AraC_family_360329..360479_POSITIVE 261 210 168 43 7 pint:PI0170|3end_hypothetical_protein_163891..164041_POSITIVE 250 209 161 73 8 pint:PI0007|3end_hypothetical_protein_7300..7450_POSITIVE 248 189 145 119 77 pint:PI2027|3end_arginine_decarboxylase_1982130..1982280_POSITIVE 248 200 155 67 20 pint:PI0830|3end_conserved_hypothetical_protein_768206..768356_POSITIVE 247 207 162 76 31 pint:PI0837|3end_conserved_hypothetical_protein_772681..772831_POSITIVE 245 89 41 99 58 pint:PI0345|3end_conserved_hypothetical_protein_320809..320959_POSITIVE 242 89 41 85 43 pint:PI2159|3end_immunoreactive_84_kDa_antigen_PG93_2107371..2107521_POSITIVE 241 65 24 47 13 pint:PI0547|3end_fructose-bisphosphate_aldolase_499466..499616_POSITIVE 239 209 163 104 53 pint:PI1437|3end_hypothetical_protein_1356407..1356557_POSITIVE 237 208 168 80 40 pint:PI1206|3end_ATP-dependent_DNA_helicase,_UvrD/PcrA/Rep_family_1127132..1127282_POSITIVE 234 188 146 108 60 pint:PI1249|3end_conserved_hypothetical_protein_1174147..1174297_POSITIVE 234 29 4 49 21 pint:PI0746|3end_hypothetical_protein_676419..676569_POSITIVE 234 60 11 77 21 pint:PI0719|3end_conserved_hypothetical_protein_654010..654160_POSITIVE 234 212 173 48 2 pint:PI0300|3end_transposase_285761..285911_POSITIVE