Origin IGS: caggctgactcttgagttaaaacatatttgttcggcacaaacttacagaaaaaaaaatgagaaatccgcactttgacagaaatatacatcctgtaaatatgcccaaaagcatactttacgcagctaaaaatactacctcggagggtaaaaaaaacactccgatgacgggcttcccctcccccccatccgaacacaaaatcaaacggaaaaaggactgccattcgatactcgggcagtccttatgtagaggtgtattttatcaggtctaaacggctctctgaagcaaaccggagcttctcagccgaaaagccggagagata .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatctctccggcttttcggctgagaagctccggtttgcttcagagagccgtttagacctgataaaatacacctctacataaggactgcccgagtatcgaatggcagtcctttttccgtttgattttgtgttcggatgggggggaggggaagcccgtcatcggagtgttttttttaccctccgaggtagtatttttagctgcgtaaagtatgcttttgggcatatttacaggatgtatatttctgtcaaagtgcggatttctcatttttttttctgtaagtttgtgccgaacaaatatgttttaactcaagagtcagcctg Mask Tandem Repeat Region ================================================ caggctgactcttgagttaaaacatatttgttcggcacaaacttacagaaaaaaaaatgagaaatccgcactttgacagaaatatacatcctgtaaatatgcccaaaagcatactttacgcagctaaaaatactacctcggagggtaaaaaaaacactccgatgacgggcttcccctcccccccatccgaacacaaaatcaaacggaaaaaggactgccattcgatactcgggcagtccttatgtagaggtgtattttatcaggtctaaacggctctctgaagcaaaccggagcttctcagccgaaaagccggagagata Find is-nt database================================================ Query_seq: PG0243:PG0245|PG0243:PG0245:hypothetical protein:universal stress protein family:<-<-:279543..279862 320 caggctgactcttgagttaaaacatatttgttcggcacaaacttacagaaaaaaaaatgagaaatccgcactttgacagaaatatacatcctgtaaatatgcccaaaagcatactttacgcagctaaaaatactacctcggagggtaaaaaaaacactccgatgacgggcttcccctcccccccatccgaacacaaaatcaaacggaaaaaggactgccattcgatactcgggcagtccttatgtagaggtgtattttatcaggtctaaacggctctctgaagcaaaccggagcttctcagccgaaaagccggagagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0243:PG0245|PG0243:PG0245:hypothetical protein:universal stress protein family:<-<-:279543..279862 320 caggctgactcttgagttaaaacatatttgttcggcacaaacttacagaaaaaaaaatgagaaatccgcactttgacagaaatatacatcctgtaaatatgcccaaaagcatactttacgcagctaaaaatactacctcggagggtaaaaaaaacactccgatgacgggcttcccctcccccccatccgaacacaaaatcaaacggaaaaaggactgccattcgatactcgggcagtccttatgtagaggtgtattttatcaggtctaaacggctctctgaagcaaaccggagcttctcagccgaaaagccggagagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0243:PG0245|PG0243:PG0245:hypothetical protein:universal stress protein family:<-<-:279543..279862 320 caggctgactcttgagttaaaacatatttgttcggcacaaacttacagaaaaaaaaatgagaaatccgcactttgacagaaatatacatcctgtaaatatgcccaaaagcatactttacgcagctaaaaatactacctcggagggtaaaaaaaacactccgatgacgggcttcccctcccccccatccgaacacaaaatcaaacggaaaaaggactgccattcgatactcgggcagtccttatgtagaggtgtattttatcaggtctaaacggctctctgaagcaaaccggagcttctcagccgaaaagccggagagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caggctgactcttgagttaaaacatatttgttcggcacaaacttacagaaaaaaaaatgagaaatccgcactttgacagaaatatacatcctgtaaatatgcccaaaagcatactttacgcagctaaaaatactacctcggagggtaaaaaaaacactccgatgacgggcttcccctcccccccatccgaacacaaaatcaaacggaaaaaggactgccattcgatactcgggcagtccttatgtagaggtgtattttatcaggtctaaacggctctctgaagcaaaccggagcttctcagccgaaaagccggagagata Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 24 End: 266 ....................... M F V R H K L T E K K M R N P H F D R N I H P V N M P K S I L Y A A K N T T S E G K K N T P M T G F P S P P S E H K I K ...................................................... Protein_Len: 33 Strand: + Start: 220 End: 318 ........................................................................................................................................................................................................................... M R Y S G S P Y V E V Y F I R S K R L S E A N R S F S A E K P E R .. Protein_Len: 36 Strand: - Start: 119 End: 226 ...................................................................................................................... A A L F V V E S P L F F V G I V P K G E G G D S C L I L R F F S Q W E M .............................................................................................. Protein_Len: 31 Strand: - Start: 20 End: 112 ................... F M N T R C L S V S F F I L F G C K S L F I C G T F I G L L M ................................................................................................................................................................................................................ Protein_Len: 60 Strand: - Start: 3 End: 236 .. H S I R V K V S I Y M R Y I H G F A Y K V C S F I S G R L T F F V S R H R A E G G G W G F V F D F P F L V A M R Y E P M .................................................................................... caggctgactcttgagttaaaacatatttgttcggcacaaacttacagaaaaaaaaatgagaaatccgcactttgacagaaatatacatcctgtaaatatgcccaaaagcatactttacgcagctaaaaatactacctcggagggtaaaaaaaacactccgatgacgggcttcccctcccccccatccgaacacaaaatcaaacggaaaaaggactgccattcgatactcgggcagtccttatgtagaggtgtattttatcaggtctaaacggctctctgaagcaaaccggagcttctcagccgaaaagccggagagata 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================================================ caggctgactcttgagttaaaacatatttgttcggcacaaacttacagaaaaaaaaatgagaaatccgcactttgacagaaatatacatcctgtaaatatgcccaaaagcatactttacgcagctaaaaatactacctcggagggtaaaaaaaacactccgatgacgggcttcccctcccccccatccgaacacaaaatcaaacggaaaaaggactgccattcgatactcgggcagtccttatgtagaggtgtattttatcaggtctaaacggctctctgaagcaaaccggagcttctcagccgaaaagccggagagata Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 50 HP_score: -4.5 Tail_Score: -3.02902 Start: 136 End: 164 Full_Region: ggaggggaagcccgt catcggagtgt ttttttt accctccgagg tagtatttttagctg .......................................................................................................................................catcggagtgttttttttaccctccgagg............................................................................................................................................................ TransTerm Strand: - Conf: 78 HP_score: -5.6 Tail_Score: -4.83759 Start: 212 End: 239 Full_Region: tacacctctacataa ggactgcc cgagtatcgaat ggcagtcc tttttccgtttgatt ...................................................................................................................................................................................................................ggactgcccgagtatcgaatggcagtcc................................................................................. Find igs database================================================ Query_seq: PG0243:PG0245|PG0243:PG0245:hypothetical protein:universal stress protein family:<-<-:279543..279862 320 caggctgactcttgagttaaaacatatttgttcggcacaaacttacagaaaaaaaaatgagaaatccgcactttgacagaaatatacatcctgtaaatatgcccaaaagcatactttacgcagctaaaaatactacctcggagggtaaaaaaaacactccgatgacgggcttcccctcccccccatccgaacacaaaatcaaacggaaaaaggactgccattcgatactcgggcagtccttatgtagaggtgtattttatcaggtctaaacggctctctgaagcaaaccggagcttctcagccgaaaagccggagagata Intra-Species Hit: Count: 1 Min: 1 Max: 320 Len: 320 Subject: NC_002950_PG0243_PG0245|hypothetical protein:universal stress protein family|NEGATIVE:NEGATIVE|[279543,279862]|320 HSP 1 e-value: 1.0E-138 bit: 492.0 Len: 320 Query Start:1 Query End:320 Subject Strand: POSITIVE Subject Start: 1 Subject End: 320 caggctgactcttgagttaaaacatatttgttcggcacaaacttacagnnnnnnnnntgagaaatccgcactttgacagaaatatacatcctgtaaatatgcccaaaagcatactttacgcagctaaaaatactacctcggagggtnnnnnnnncactccgatgacgggcttcccctnnnnnnnatccgaacacaaaatcaaacggaaaaaggactgccattcgatactcgggcagtccttatgtagaggtgtattttatcaggtctaaacggctctctgaagcaaaccggagcttctcagccgaaaagccggagagata caggctgactcttgagttaaaacatatttgttcggcacaaacttacagaaaaaaaaatgagaaatccgcactttgacagaaatatacatcctgtaaatatgcccaaaagcatactttacgcagctaaaaatactacctcggagggtaaaaaaaacactccgatgacgggcttcccctcccccccatccgaacacaaaatcaaacggaaaaaggactgccattcgatactcgggcagtccttatgtagaggtgtattttatcaggtctaaacggctctctgaagcaaaccggagcttctcagccgaaaagccggagagata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGGCUGACUCUUGAGUUAAAACAUAUUUGUUCGGCACAAACUUACAGAAAAAAAAAUGAGAAAUCCGCACUUUGACAGAAAUAUACAUCCUGUAAAUAUGCCCAAAAGCAUACUUUACGCAGCUAAAAAUACUACCUCGGAGGGUAAAAAAAACACUCCGAUGACGGGCUUCCCCUCCCCCCCAUCCGAACACAAAAUCAAACGGAAAAAGGACUGCCAUUCGAUACUCGGGCAGUCCUUAUGUAGAGGUGUAUUUUAUCAGGUCUAAACGGCUCUCUGAAGCAAACCGGAGCUUCUCAGCCGAAAAGCCGGAGAGAUA .....(((((....))))).....(((((.((((((.....................((((((((..(((((((.(((..........(((.((((((((((......))))).)))))..................((((((((............((((....))))............))).)))))..............)))..((((((((((...((.....)))))))))))).))).)))))))))))).)))........(((((....(((((........)))))..)))))....)))))).))))) (-85.55) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCUCUCCGGCUUUUCGGCUGAGAAGCUCCGGUUUGCUUCAGAGAGCCGUUUAGACCUGAUAAAAUACACCUCUACAUAAGGACUGCCCGAGUAUCGAAUGGCAGUCCUUUUUCCGUUUGAUUUUGUGUUCGGAUGGGGGGGAGGGGAAGCCCGUCAUCGGAGUGUUUUUUUUACCCUCCGAGGUAGUAUUUUUAGCUGCGUAAAGUAUGCUUUUGGGCAUAUUUACAGGAUGUAUAUUUCUGUCAAAGUGCGGAUUUCUCAUUUUUUUUUCUGUAAGUUUGUGCCGAACAAAUAUGUUUUAACUCAAGAGUCAGCCUG ......((.((((...(((((..(((((........)))))....)))))...)).)).)).((((((((((((.....((((((((((((.....))...))))))))))(..((((((((........))))))))..)((((((...(((((....))).))..........))))))))))).)))))))..((((..........((((((((((((((((((((((((......(((((......))))).....)))).......))))))))..))))).((((....))))......)))))))))))... (-97.53) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 853 140 91 231 182 NC_002950:PG0243|5end_hypothetical_protein_279452..279682_NEGATIVE 438 317 271 58 5 NC_002950:PG0451|5end_CBS_domain_protein_491519..491749_POSITIVE 391 188 141 165 120 NC_002950:PG0446|5end_thiF_protein_486599..486829_POSITIVE 385 320 272 190 141 NC_002950:PG0809|5end_hypothetical_protein_872014..872244_NEGATIVE 380 299 251 218 171 NC_002950:PG1640|5end_DNA-damage-inducible_protein_F_1721245..1721475_NEGATIVE 379 319 271 127 60 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 378 195 166 37 1 NC_002950:PG1426|5end_hypothetical_protein_1511310..1511540_NEGATIVE 375 317 271 183 125 NC_002950:PG0779|5end_hypothetical_protein_832573..832803_NEGATIVE 372 190 142 201 139 NC_002950:PG0975|5end_PhoH_family_protein_1037284..1037514_POSITIVE 372 260 211 220 168 NC_002950:PG0677|5end_saccharopine_dehydrogenase_727653..727883_POSITIVE 371 319 274 205 159 NC_002950:PG1285|5end_glucosamine-6-phosphate_deaminase_1362894..1363124_POSITIVE 356 190 141 101 36 NC_002950:PG1850|5end_hypothetical_protein_1949957..1950187_NEGATIVE 354 319 272 70 6 NC_002950:PG1967|5end_TPR_domain_protein_2057168..2057398_POSITIVE 349 257 216 76 32 NC_002950:PG0553|5end_extracellular_protease,_putative_611189..611419_NEGATIVE 347 315 272 53 2 NC_002950:PG0146|5end_hypothetical_protein_169115..169345_NEGATIVE 345 320 271 52 6 NC_002950:PG1859|5end_glycerate_kinase_family_protein_1958334..1958564_NEGATIVE 342 255 215 227 186 NC_002950:PG0737|5end_hypothetical_protein_786188..786418_POSITIVE 341 191 154 67 14 NC_002950:PG1017|5end_pyruvate_phosphate_dikinase_1076138..1076368_POSITIVE 340 243 210 171 135 NC_002950:PG1279|5end_D-isomer_specific_2-hydroxyacid_dehydrogenase_family_protein_1356535..1356765_POSITIVE 340 312 271 183 147 NC_002950:PG0148|5end_sigma-54-dependent_transcriptional_regulator_170907..171137_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 438 317 271 61 8 NC_002950:PG0450|3end_hypothetical_protein_491602..491752_POSITIVE 391 250 203 69 4 NC_002950:PG0541|3end_hypothetical_protein_595136..595286_POSITIVE 379 319 271 146 79 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 373 192 165 128 95 NC_002950:PG1980|3end_hypothetical_protein_2067760..2067910_NEGATIVE 372 317 273 143 100 NC_002950:PG2117|3end_30S_ribosomal_protein_S16_2225235..2225385_NEGATIVE 361 317 274 66 24 NC_002950:PG0656|3end_50S_ribosomal_protein_L34_706945..707095_NEGATIVE 356 190 141 104 39 NC_002950:PG1851|3end_phosphopantothenoylcysteine_decarboxylase/phosphopantothenate--cysteine_ligase_1949954..1950104_NEGATIVE 354 319 271 98 34 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 354 303 269 151 107 NC_002950:PG0780|3end_hypothetical_protein_832589..832739_NEGATIVE 340 243 210 70 34 NC_002950:PG1278|3end_phosphoserine_aminotransferase_1356514..1356664_POSITIVE 339 176 131 150 89 NC_002950:PG2094|3end_hypothetical_protein_2193321..2193471_NEGATIVE 339 318 271 126 81 NC_002950:PG1392|3end_rod_shape-determining_protein_RodA,_putative_1472959..1473109_NEGATIVE 339 319 272 137 79 NC_002950:PG0897|3end_alpha-amylase_family_protein_960868..961018_NEGATIVE 338 249 207 76 30 NC_002950:PG0506|3end_arginine-specific_cysteine_proteinase_547625..547775_POSITIVE 337 310 261 55 6 NC_002950:PG2158|3end_hypothetical_protein_2264473..2264623_POSITIVE 333 240 203 56 17 NC_002950:PG1055|3end_thiol_protease_1121202..1121352_NEGATIVE 333 179 138 57 16 NC_002950:PG0524|3end_hypothetical_protein_568963..569113_POSITIVE 329 319 282 150 112 NC_002950:PG1826|3end_hypothetical_protein_1919646..1919796_NEGATIVE 329 249 204 69 17 NC_002950:PG1028|3end_TPR_domain_protein_1091096..1091246_POSITIVE 324 317 271 112 64 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE