Origin IGS: tacaatagcaatgcaaacttacacaaaaaataatgaaaacagaaaagttaaactgcttttttgtgaaagactaacaattcgagcggttgcttctgaatattgataaaatggagtgtaggattggttcaacagaatatcatcggagcgaactatttccacctcgttacttatggcaggaactaaaacacacgaaaaagagcgtattgtagatgaatcatacccctacgaaatagaagcagtttttagataaaaccgcctccattttgtaaatataattcgttagaaaaatgataatttcgat .........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 atcgaaattatcatttttctaacgaattatatttacaaaatggaggcggttttatctaaaaactgcttctatttcgtaggggtatgattcatctacaatacgctctttttcgtgtgttttagttcctgccataagtaacgaggtggaaatagttcgctccgatgatattctgttgaaccaatcctacactccattttatcaatattcagaagcaaccgctcgaattgttagtctttcacaaaaaagcagtttaacttttctgttttcattattttttgtgtaagtttgcattgctattgta Mask Tandem Repeat Region ================================================ tacaatagcaatgcaaacttacacaaaaaataatgaaaacagaaaagttaaactgcttttttgtgaaagactaacaattcgagcggttgcttctgaatattgataaaatggagtgtaggattggttcaacagaatatcatcggagcgaactatttccacctcgttacttatggcaggaactaaaacacacgaaaaagagcgtattgtagatgaatcatacccctacgaaatagaagcagtttttagataaaaccgcctccattttgtaaatataattcgttagaaaaatgataatttcgat Find is-nt database================================================ Query_seq: PI0321:PI0322|PI0321:PI0322:conserved hypothetical protein:hypothetical protein:->->:303347..303647 301 tacaatagcaatgcaaacttacacaaaaaataatgaaaacagaaaagttaaactgcttttttgtgaaagactaacaattcgagcggttgcttctgaatattgataaaatggagtgtaggattggttcaacagaatatcatcggagcgaactatttccacctcgttacttatggcaggaactaaaacacacgaaaaagagcgtattgtagatgaatcatacccctacgaaatagaagcagtttttagataaaaccgcctccattttgtaaatataattcgttagaaaaatgataatttcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0321:PI0322|PI0321:PI0322:conserved hypothetical protein:hypothetical protein:->->:303347..303647 301 tacaatagcaatgcaaacttacacaaaaaataatgaaaacagaaaagttaaactgcttttttgtgaaagactaacaattcgagcggttgcttctgaatattgataaaatggagtgtaggattggttcaacagaatatcatcggagcgaactatttccacctcgttacttatggcaggaactaaaacacacgaaaaagagcgtattgtagatgaatcatacccctacgaaatagaagcagtttttagataaaaccgcctccattttgtaaatataattcgttagaaaaatgataatttcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0321:PI0322|PI0321:PI0322:conserved hypothetical protein:hypothetical protein:->->:303347..303647 301 tacaatagcaatgcaaacttacacaaaaaataatgaaaacagaaaagttaaactgcttttttgtgaaagactaacaattcgagcggttgcttctgaatattgataaaatggagtgtaggattggttcaacagaatatcatcggagcgaactatttccacctcgttacttatggcaggaactaaaacacacgaaaaagagcgtattgtagatgaatcatacccctacgaaatagaagcagtttttagataaaaccgcctccattttgtaaatataattcgttagaaaaatgataatttcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tacaatagcaatgcaaacttacacaaaaaataatgaaaacagaaaagttaaactgcttttttgtgaaagactaacaattcgagcggttgcttctgaatattgataaaatggagtgtaggattggttcaacagaatatcatcggagcgaactatttccacctcgttacttatggcaggaactaaaacacacgaaaaagagcgtattgtagatgaatcatacccctacgaaatagaagcagtttttagataaaaccgcctccattttgtaaatataattcgttagaaaaatgataatttcgat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 5 End: 100 .... M A M Q T Y T K N N E N R K V K L L F C E R L T I R A V A S E Y ......................................................................................................................................................................................................... Protein_Len: 40 Strand: + Start: 87 End: 206 ...................................................................................... M L L N I D K M E C R I G S T E Y H R S E L F P P R Y L W Q E L K H T K K S V L ............................................................................................... Protein_Len: 38 Strand: + Start: 134 End: 247 ..................................................................................................................................... M S S E R T I S T S L L M A G T K T H E K E R I V D E S Y P Y E I E A V F R ...................................................... Protein_Len: 60 Strand: - Start: 22 End: 204 ..................... F F L S F L F T L S S K Q S L S V I R A T A E S Y Q Y F P T Y S Q N L L I D D S R V I E V E N S I A P V L V C S F S R M ................................................................................................. tacaatagcaatgcaaacttacacaaaaaataatgaaaacagaaaagttaaactgcttttttgtgaaagactaacaattcgagcggttgcttctgaatattgataaaatggagtgtaggattggttcaacagaatatcatcggagcgaactatttccacctcgttacttatggcaggaactaaaacacacgaaaaagagcgtattgtagatgaatcatacccctacgaaatagaagcagtttttagataaaaccgcctccattttgtaaatataattcgttagaaaaatgataatttcgat 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================================================ tacaatagcaatgcaaacttacacaaaaaataatgaaaacagaaaagttaaactgcttttttgtgaaagactaacaattcgagcggttgcttctgaatattgataaaatggagtgtaggattggttcaacagaatatcatcggagcgaactatttccacctcgttacttatggcaggaactaaaacacacgaaaaagagcgtattgtagatgaatcatacccctacgaaatagaagcagtttttagataaaaccgcctccattttgtaaatataattcgttagaaaaatgataatttcgat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -7.7 Tail_Score: -3.74251 Start: 231 End: 261 Full_Region: attatatttacaaaa tggaggcggtttt atcta aaaactgcttcta tttcgtaggggtatg ......................................................................................................................................................................................................................................tggaggcggttttatctaaaaactgcttcta........................................ TransTerm Strand: - Conf: 72 HP_score: -8.1 Tail_Score: -3.45324 Start: 233 End: 259 Full_Region: tatatttacaaaatg gaggcggtttt atcta aaaactgcttc tatttcgtaggggta ........................................................................................................................................................................................................................................gaggcggttttatctaaaaactgcttc.......................................... Find igs database================================================ Query_seq: PI0321:PI0322|PI0321:PI0322:conserved hypothetical protein:hypothetical protein:->->:303347..303647 301 tacaatagcaatgcaaacttacacaaaaaataatgaaaacagaaaagttaaactgcttttttgtgaaagactaacaattcgagcggttgcttctgaatattgataaaatggagtgtaggattggttcaacagaatatcatcggagcgaactatttccacctcgttacttatggcaggaactaaaacacacgaaaaagagcgtattgtagatgaatcatacccctacgaaatagaagcagtttttagataaaaccgcctccattttgtaaatataattcgttagaaaaatgataatttcgat Intra-Species Hit: Count: 1 Min: 1 Max: 301 Len: 301 Subject: pint_PI0321_PI0322|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[303347,303647]|301 HSP 1 e-value: 1.0E-170 bit: 597.0 Len: 301 Query Start:1 Query End:301 Subject Strand: POSITIVE Subject Start: 1 Subject End: 301 tacaatagcaatgcaaacttacacaaaaaataatgaaaacagaaaagttaaactgcttttttgtgaaagactaacaattcgagcggttgcttctgaatattgataaaatggagtgtaggattggttcaacagaatatcatcggagcgaactatttccacctcgttacttatggcaggaactaaaacacacgaaaaagagcgtattgtagatgaatcatacccctacgaaatagaagcagtttttagataaaaccgcctccattttgtaaatataattcgttagaaaaatgataatttcgat tacaatagcaatgcaaacttacacaaaaaataatgaaaacagaaaagttaaactgcttttttgtgaaagactaacaattcgagcggttgcttctgaatattgataaaatggagtgtaggattggttcaacagaatatcatcggagcgaactatttccacctcgttacttatggcaggaactaaaacacacgaaaaagagcgtattgtagatgaatcatacccctacgaaatagaagcagtttttagataaaaccgcctccattttgtaaatataattcgttagaaaaatgataatttcgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACAAUAGCAAUGCAAACUUACACAAAAAAUAAUGAAAACAGAAAAGUUAAACUGCUUUUUUGUGAAAGACUAACAAUUCGAGCGGUUGCUUCUGAAUAUUGAUAAAAUGGAGUGUAGGAUUGGUUCAACAGAAUAUCAUCGGAGCGAACUAUUUCCACCUCGUUACUUAUGGCAGGAACUAAAACACACGAAAAAGAGCGUAUUGUAGAUGAAUCAUACCCCUACGAAAUAGAAGCAGUUUUUAGAUAAAACCGCCUCCAUUUUGUAAAUAUAAUUCGUUAGAAAAAUGAUAAUUUCGAU ..............................(((((((..((((..(((..((((((((..((((.........))))...))))))))))))))).(((((.(((((((((((.(((((..(((((((((((.((.((...((((........)))).(((.((((....)))))))...................))..)).))))...)))))))....))))).........((.(((((.....))))).))))))))))))).)))))..)))))))................... (-61.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGAAAUUAUCAUUUUUCUAACGAAUUAUAUUUACAAAAUGGAGGCGGUUUUAUCUAAAAACUGCUUCUAUUUCGUAGGGGUAUGAUUCAUCUACAAUACGCUCUUUUUCGUGUGUUUUAGUUCCUGCCAUAAGUAACGAGGUGGAAAUAGUUCGCUCCGAUGAUAUUCUGUUGAACCAAUCCUACACUCCAUUUUAUCAAUAUUCAGAAGCAACCGCUCGAAUUGUUAGUCUUUCACAAAAAAGCAGUUUAACUUUUCUGUUUUCAUUAUUUUUUGUGUAAGUUUGCAUUGCUAUUGUA ...((((........))))....(((((((((((((.((((((((((((((((.....)))))))))))))))).))))..)))))))))...(((((((.((.....((((.(((.....(((.(((......((((.(((((((.....(((((..(.((......)).).))))).....)))).)))....)))).......))).)))...))).)))).(((....(((.(((((((((.......(((......))).......))))))))).)))...)))..))))))))) (-68.26) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 387 300 254 196 150 pint:PI0407|5end_tryptophanyl-tRNA_synthetase_(tryptophan--tRNA_ligase)_372973..373203_POSITIVE 345 298 254 231 187 pint:PI0183|5end_hypothetical_protein_174347..174577_POSITIVE 328 179 137 201 166 pint:PI0331|5end_hypothetical_protein_311656..311886_POSITIVE 309 129 81 104 52 pint:PI1206|5end_ATP-dependent_DNA_helicase,_UvrD/PcrA/Rep_family_1124698..1124928_POSITIVE 306 160 111 113 66 pint:PI2104|5end_carboxyl-terminal_protease_2057910..2058140_POSITIVE 302 119 71 170 112 pint:PI0831|5end_hypothetical_protein_768129..768359_POSITIVE 299 147 101 224 172 pint:PI0382|5end_conserved_hypothetical_protein_351510..351740_POSITIVE 288 264 226 120 67 pint:PI1954|5end_translation_initiation_factor_IF-2_1908784..1909014_POSITIVE 288 181 141 202 158 pint:PI1263|5end_probable_integrase_1184502..1184732_POSITIVE 286 300 252 228 182 pint:PI1734|5end_possible_carboxyl-terminal_protease-related_protein_1652409..1652639_POSITIVE 275 148 110 71 30 pint:PI0388|5end_integrase_354927..355157_POSITIVE 273 300 251 191 142 pint:PI1830|5end_conserved_hypothetical_protein_1769439..1769669_POSITIVE 272 299 251 195 147 pint:PI1143|5end_hypothetical_protein_1069780..1070010_POSITIVE 271 174 138 218 179 pint:PI1257|5end_dTDP-4-dehydrorhamnose_reductase_1177971..1178201_POSITIVE 269 86 41 149 103 pint:PI1805|5end_TPR_repeat_containing_protein_1738369..1738599_POSITIVE 269 229 184 153 106 pint:PI0134|5end_ISPg3-related_transposase_(IS5_family)_124721..124951_POSITIVE 268 111 74 154 112 pint:PI0221|5end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_212356..212586_POSITIVE 267 96 53 196 148 pint:PI1421|5end_hypothetical_protein_1341801..1342031_POSITIVE 264 260 222 153 111 pint:PI2171|5end_conserved_hypothetical_protein_2112735..2112965_POSITIVE 263 220 171 191 139 pint:PI1891|5end_hypothetical_protein_1835196..1835426_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 395 300 254 83 37 pint:PI0182|3end_hypothetical_protein_174277..174427_POSITIVE 393 299 254 140 95 pint:PI1129|3end_hypothetical_protein_1055603..1055753_POSITIVE 362 285 249 151 114 pint:PI2153|3end_hypothetical_protein_2099630..2099780_POSITIVE 344 300 253 89 33 pint:PI0670|3end_hypothetical_protein_611280..611430_POSITIVE 312 300 262 110 72 pint:PI1905|3end_hypothetical_protein_1847854..1848004_POSITIVE 306 160 111 57 10 pint:PI2103|3end_hypothetical_protein_2057934..2058084_POSITIVE 304 300 251 89 40 pint:PI2011|3end_hypothetical_protein_1970730..1970880_POSITIVE 287 300 254 89 43 pint:PI0689|3end_hypothetical_protein_625877..626027_POSITIVE 282 95 51 140 91 pint:PI1554|3end_hypothetical_protein_1470483..1470633_POSITIVE 282 300 264 129 93 pint:PI1167|3end_hypothetical_protein_1089890..1090040_POSITIVE 281 228 190 75 43 pint:PI1440|3end_conserved_hypothetical_protein_1363009..1363159_POSITIVE 274 300 254 89 43 pint:PI2131|3end_hypothetical_protein_2080868..2081018_POSITIVE 273 300 251 111 62 pint:PI1829|3end_hypothetical_protein_1769439..1769589_POSITIVE 270 300 254 89 42 pint:PI1814|3end_hypothetical_protein_1753233..1753383_POSITIVE 268 111 74 59 17 pint:PI0220|3end_conserved_hypothetical_protein_212341..212491_POSITIVE 264 260 222 126 84 pint:PI2170|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2112788..2112938_POSITIVE 264 240 191 80 13 pint:PI0647|3end_potassium_uptake_protein_589276..589426_POSITIVE 263 299 252 48 1 pint:PI1141|3end_hypothetical_protein_1069713..1069863_POSITIVE 259 189 142 79 29 pint:PI2027|3end_arginine_decarboxylase_1982130..1982280_POSITIVE 258 126 82 89 44 pint:PI0324|3end_conserved_hypothetical_protein_305680..305830_POSITIVE