Origin IGS: ttcgacggttagcgaaagacaataattaaatcgattatggaaagagggtgtgtcgaaatcgcaattaggcgatttttgcacaccttctttttatccctttgatacaccgctcgttcttttgtattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaatacaaaagaacgagcggtgtatcaaagggataaaaagaaggtgtgcaaaaatcgcctaattgcgatttcgacacaccctctttccataatcgatttaattattgtctttcgctaaccgtcgaa Mask Tandem Repeat Region ================================================ ttcgacggttagcgaaagacaataattaaatcgattatggaaagagggtgtgtcgaaatcgcaattaggcgatttttgcacaccttctttttatccctttgatacaccgctcgttcttttgtattt Find is-nt database================================================ Query_seq: PG1280:PG1281|PG1280:PG1281:hypothetical protein:hypothetical protein:->->:1358862..1358987 126 ttcgacggttagcgaaagacaataattaaatcgattatggaaagagggtgtgtcgaaatcgcaattaggcgatttttgcacaccttctttttatccctttgatacaccgctcgttcttttgtattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1280:PG1281|PG1280:PG1281:hypothetical protein:hypothetical protein:->->:1358862..1358987 126 ttcgacggttagcgaaagacaataattaaatcgattatggaaagagggtgtgtcgaaatcgcaattaggcgatttttgcacaccttctttttatccctttgatacaccgctcgttcttttgtattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1280:PG1281|PG1280:PG1281:hypothetical protein:hypothetical protein:->->:1358862..1358987 126 ttcgacggttagcgaaagacaataattaaatcgattatggaaagagggtgtgtcgaaatcgcaattaggcgatttttgcacaccttctttttatccctttgatacaccgctcgttcttttgtattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcgacggttagcgaaagacaataattaaatcgattatggaaagagggtgtgtcgaaatcgcaattaggcgatttttgcacaccttctttttatccctttgatacaccgctcgttcttttgtattt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 12 End: 107 ........... R F V I I L D I I S L P H T S I A I L R N K C V K K K D R Q Y M ................... ttcgacggttagcgaaagacaataattaaatcgattatggaaagagggtgtgtcgaaatcgcaattaggcgatttttgcacaccttctttttatccctttgatacaccgctcgttcttttgtattt 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================================================ ttcgacggttagcgaaagacaataattaaatcgattatggaaagagggtgtgtcgaaatcgcaattaggcgatttttgcacaccttctttttatccctttgatacaccgctcgttcttttgtattt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -14.3 Tail_Score: -2.67803 Start: 38 End: 93 Full_Region: TAATTAAATCGATTA TGGAAAGAGGGTGTGTCGAAATCGC AATTAG GCGATTTTTGCACACCTTCTTTTTA TCCCTTTGATACACC .....................................TGGAAAGAGGGTGTGTCGAAATCGCAATTAGGCGATTTTTGCACACCTTCTTTTTA................................. TransTerm Strand: + Conf: 100 HP_score: -13.3 Tail_Score: -4.94992 Start: 44 End: 87 Full_Region: AATCGATTATGGAAA GAGGGTGTGTCGAAATCGC AATTAG GCGATTTTTGCACACCTTC TTTTTATCCCTTTGA ...........................................GAGGGTGTGTCGAAATCGCAATTAGGCGATTTTTGCACACCTTC....................................... TransTerm Strand: - Conf: 65 HP_score: -6.7 Tail_Score: -3.69094 Start: 44 End: 87 Full_Region: tcaaagggataaaaa gaaggtgtgcaaaaatcgc ctaatt gcgatttcgacacaccctc tttccataatcgatt ...........................................gaaggtgtgcaaaaatcgcctaattgcgatttcgacacaccctc....................................... TransTerm Strand: - Conf: 59 HP_score: -7.0 Tail_Score: -2.65116 Start: 47 End: 84 Full_Region: aagggataaaaagaa ggtgtgcaaaaatcgc ctaatt gcgatttcgacacacc ctctttccataatcg ..............................................ggtgtgcaaaaatcgcctaattgcgatttcgacacacc.......................................... Find igs database================================================ Query_seq: PG1280:PG1281|PG1280:PG1281:hypothetical protein:hypothetical protein:->->:1358862..1358987 126 ttcgacggttagcgaaagacaataattaaatcgattatggaaagagggtgtgtcgaaatcgcaattaggcgatttttgcacaccttctttttatccctttgatacaccgctcgttcttttgtattt Intra-Species Hit: Count: 1 Min: 1 Max: 126 Len: 126 Subject: NC_002950_PG1280_PG1281|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1358862,1358987]|126 HSP 1 e-value: 9.0E-66 bit: 250.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 ttcgacggttagcgaaagacaataattaaatcgattatggaaagagggtgtgtcgaaatcgcaattaggcgatttttgcacaccttctttttatccctttgatacaccgctcgttcttttgtattt ttcgacggttagcgaaagacaataattaaatcgattatggaaagagggtgtgtcgaaatcgcaattaggcgatttttgcacaccttctttttatccctttgatacaccgctcgttcttttgtattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCGACGGUUAGCGAAAGACAAUAAUUAAAUCGAUUAUGGAAAGAGGGUGUGUCGAAAUCGCAAUUAGGCGAUUUUUGCACACCUUCUUUUUAUCCCUUUGAUACACCGCUCGUUCUUUUGUAUUU ..(((((((..((....).).........(((((..(((((((((((((((((.((((((((......)))))))).)))))))))))))))))....)))))..)))).)))............. (-45.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUACAAAAGAACGAGCGGUGUAUCAAAGGGAUAAAAAGAAGGUGUGCAAAAAUCGCCUAAUUGCGAUUUCGACACACCCUCUUUCCAUAAUCGAUUUAAUUAUUGUCUUUCGCUAACCGUCGAA .............(((.((((.......(((((((((((((.((((((...(((((((......)))))))...)))))).)))))..................)))))))).....))))))).. (-31.96) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 380 90 46 43 8 NC_002950:PG1968|5end_hypothetical_protein_2058564..2058794_NEGATIVE 324 87 41 231 186 NC_002950:PG0768|5end_hypothetical_protein_822381..822611_NEGATIVE 318 90 42 224 179 NC_002950:PG0323|5end_hypothetical_protein_357388..357618_NEGATIVE 316 50 6 50 10 NC_002950:PG0926|5end_hypothetical_protein_984634..984864_NEGATIVE 314 78 31 229 178 NC_002950:PG0619|5end_alkyl_hydroperoxide_reductase,_F_subunit_671104..671334_POSITIVE 313 70 30 218 179 NC_002950:PG0749|5end_hypothetical_protein_795654..795884_NEGATIVE 307 89 42 77 38 NC_002950:PG1268|5end_hypothetical_protein_1347371..1347601_POSITIVE 297 50 4 65 11 NC_002950:PG2180|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_C_2288546..2288776_NEGATIVE 293 72 35 224 180 NC_002950:PG1605|5end_aminopeptidase_C_1685179..1685409_POSITIVE 291 80 31 86 41 NC_002950:PG1981|5end_CRISPR-associated_protein_Cas2_2069505..2069735_NEGATIVE 291 90 44 178 134 NC_002950:PG0043|5end_beta-hexosaminidase_51066..51296_POSITIVE 289 48 3 204 161 NC_002950:PG2216|5end_hypothetical_protein_2327720..2327950_POSITIVE 289 113 75 171 123 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 283 87 43 211 162 NC_002950:PG0782|5end_MotA/TolQ/ExbB_proton_channel_family_protein_834530..834760_NEGATIVE 280 74 31 107 45 NC_002950:PG1751|5end_aminotransferase,_class_V_1837280..1837510_POSITIVE 278 55 11 66 16 NC_002950:PG0092|5end_transporter,_putative_108598..108828_NEGATIVE 277 119 78 231 181 NC_002950:PG0336|5end_hypothetical_protein_371292..371522_NEGATIVE 272 70 30 220 165 NC_002950:PG0139|5end_membrane-bound_lytic_murein_transglycosylase_D,_putative_163141..163371_NEGATIVE 271 72 31 137 84 NC_002950:PG1365|5end_16S_rRNA-processing_protein_1446069..1446299_NEGATIVE 270 87 42 49 9 NC_002950:PG1779|5end_hypothetical_protein_1867924..1868154_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 507 90 41 50 1 NC_002950:PG1280|3end_hypothetical_protein_1358801..1358951_POSITIVE 488 90 41 76 25 NC_002950:PG0618|3end_alkyl_hydroperoxide_reductase,_C_subunit_671018..671168_POSITIVE 487 90 41 70 17 NC_002950:PG0138|3end_malonyl_CoA-acyl_carrier_protein_transacylase_161634..161784_POSITIVE 439 86 42 53 6 NC_002950:PG0537|3end_aminoacyl-histidine_dipeptidase_588394..588544_POSITIVE 399 88 41 68 24 NC_002950:PG0193|3end_cationic_outer_membrane_protein_OmpH_230720..230870_POSITIVE 388 89 43 58 5 NC_002950:PG2207|3end_hypothetical_protein_2319142..2319292_NEGATIVE 380 90 46 147 112 NC_002950:PG1968|3end_hypothetical_protein_2058460..2058610_NEGATIVE 373 90 42 49 10 NC_002950:PG0241|3end_lipoprotein,_putative_277360..277510_NEGATIVE 357 90 43 69 22 NC_002950:PG0474|3end_low-specificity_L-threonine_aldolase_515011..515161_NEGATIVE 334 87 44 52 20 NC_002950:PG0553|3end_extracellular_protease,_putative_608367..608517_NEGATIVE 329 89 42 64 24 NC_002950:PG1004|3end_prolyl_oligopeptidase_family_protein_1060433..1060583_NEGATIVE 324 87 41 57 12 NC_002950:PG0769|3end_fibronectin_type_III_domain_protein_822555..822705_NEGATIVE 316 50 6 50 10 NC_002950:PG0927|3end_conserved_hypothetical_protein_TIGR00150_984634..984784_NEGATIVE 309 89 43 58 20 NC_002950:PG1414|3end_hypothetical_protein_1499704..1499854_POSITIVE 305 90 42 42 3 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 295 89 42 45 8 NC_002950:PG0712|3end_hypothetical_protein_766784..766934_NEGATIVE 293 72 35 112 68 NC_002950:PG1604|3end_immunoreactive_84_kDa_antigen_PG93_1685147..1685297_POSITIVE 291 80 31 66 21 NC_002950:PG1982|3end_CRISPR-associated_protein_Cas1_2069525..2069675_NEGATIVE 286 120 78 147 96 NC_002950:PG0337|3end_hypothetical_protein_371377..371527_NEGATIVE 280 90 41 48 10 NC_002950:PG0989|3end_50S_ribosomal_protein_L20_1050699..1050849_NEGATIVE