Origin IGS: taaaaatatgtaagcaagtcttttcgcagccttgtagcatcgttcagttgtacaacttcgttactttacaacctattattctattcttcttgtctgatataaagttacttatacgtgtttgtagccttattcggcaatttacttacacgtaaagaaatatttatttacgtgtaagtaaattcttacttacgtgtagaaaaatatttatttacacgtaaataatttggctggctggctttttaaacgaatgcagggcatcggtagaagcaggagaatggggtagaaagcactctgaaaactgtatgtgggtgagacttaggggcgtgaaagttaggcatattgaagtatgttgaaaacgaaaagcgggtgtgccagaagttctattcggcacacccgcttaaattataatacttttaagagcaaacttctgcagaagtttctcgtttta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaacgagaaacttctgcagaagtttgctcttaaaagtattataatttaagcgggtgtgccgaatagaacttctggcacacccgcttttcgttttcaacatacttcaatatgcctaactttcacgcccctaagtctcacccacatacagttttcagagtgctttctaccccattctcctgcttctaccgatgccctgcattcgtttaaaaagccagccagccaaattatttacgtgtaaataaatatttttctacacgtaagtaagaatttacttacacgtaaataaatatttctttacgtgtaagtaaattgccgaataaggctacaaacacgtataagtaactttatatcagacaagaagaatagaataataggttgtaaagtaacgaagttgtacaactgaacgatgctacaaggctgcgaaaagacttgcttacatattttta Mask Tandem Repeat Region ================================================ taaaaatatgtaagcaagtcttttcgcagccttgtagcatcgttcagttgtacaacttcgttactttacaacctattattctattcttcttgtctgatataaagttacttatacgtgtttgtagccttattcggcannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntaatttggctggctggctttttaaacgaatgcagggcatcggtagaagcaggagaatggggtagaaagcactctgaaaactgtatgtgggtgagacttaggggcgtgaaagttaggcatattgaagtatgttgaaaacgaaaagcgggtgtgccagaagttctattcggcacacccgcttaaattataatacttttaagagcaaacttctgcagaagtttctcgtttta Find is-nt database================================================ Query_seq: PI0424:PI0426|PI0424:PI0426:methylated-DNA--[protein]-cysteine S-methyltransferase:conserved hypothetical protein:->->:389037..389484 448 taaaaatatgtaagcaagtcttttcgcagccttgtagcatcgttcagttgtacaacttcgttactttacaacctattattctattcttcttgtctgatataaagttacttatacgtgtttgtagccttattcggcaatttacttacacgtaaagaaatatttatttacgtgtaagtaaattcttacttacgtgtagaaaaatatttatttacacgtaaataatttggctggctggctttttaaacgaatgcagggcatcggtagaagcaggagaatggggtagaaagcactctgaaaactgtatgtgggtgagacttaggggcgtgaaagttaggcatattgaagtatgttgaaaacgaaaagcgggtgtgccagaagttctattcggcacacccgcttaaattataatacttttaagagcaaacttctgcagaagtttctcgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0424:PI0426|PI0424:PI0426:methylated-DNA--[protein]-cysteine S-methyltransferase:conserved hypothetical protein:->->:389037..389484 448 taaaaatatgtaagcaagtcttttcgcagccttgtagcatcgttcagttgtacaacttcgttactttacaacctattattctattcttcttgtctgatataaagttacttatacgtgtttgtagccttattcggcaatttacttacacgtaaagaaatatttatttacgtgtaagtaaattcttacttacgtgtagaaaaatatttatttacacgtaaataatttggctggctggctttttaaacgaatgcagggcatcggtagaagcaggagaatggggtagaaagcactctgaaaactgtatgtgggtgagacttaggggcgtgaaagttaggcatattgaagtatgttgaaaacgaaaagcgggtgtgccagaagttctattcggcacacccgcttaaattataatacttttaagagcaaacttctgcagaagtttctcgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0424:PI0426|PI0424:PI0426:methylated-DNA--[protein]-cysteine S-methyltransferase:conserved hypothetical protein:->->:389037..389484 448 taaaaatatgtaagcaagtcttttcgcagccttgtagcatcgttcagttgtacaacttcgttactttacaacctattattctattcttcttgtctgatataaagttacttatacgtgtttgtagccttattcggcaatttacttacacgtaaagaaatatttatttacgtgtaagtaaattcttacttacgtgtagaaaaatatttatttacacgtaaataatttggctggctggctttttaaacgaatgcagggcatcggtagaagcaggagaatggggtagaaagcactctgaaaactgtatgtgggtgagacttaggggcgtgaaagttaggcatattgaagtatgttgaaaacgaaaagcgggtgtgccagaagttctattcggcacacccgcttaaattataatacttttaagagcaaacttctgcagaagtttctcgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaatatgtaagcaagtcttttcgcagccttgtagcatcgttcagttgtacaacttcgttactttacaacctattattctattcttcttgtctgatataaagttacttatacgtgtttgtagccttattcggcaatttacttacacgtaaagaaatatttatttacgtgtaagtaaattcttacttacgtgtagaaaaatatttatttacacgtaaataatttggctggctggctttttaaacgaatgcagggcatcggtagaagcaggagaatggggtagaaagcactctgaaaactgtatgtgggtgagacttaggggcgtgaaagttaggcatattgaagtatgttgaaaacgaaaagcgggtgtgccagaagttctattcggcacacccgcttaaattataatacttttaagagcaaacttctgcagaagtttctcgtttta Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 6 End: 149 ..... M C K Q V F S Q P C S I V Q L Y N F V T L Q P I I L F F L S D I K L L I R V C S L I R Q F T Y T ........................................................................................................................................................................................................................................................................................................... Protein_Len: 44 Strand: + Start: 219 End: 350 .......................................................................................................................................................................................................................... M I W L A G F L N E C R A S V E A G E W G R K H S E N C M W V R L R G V K V R H I E V C .................................................................................................. Protein_Len: 34 Strand: + Start: 347 End: 448 .......................................................................................................................................................................................................................................................................................................................................................... M L K T K S G C A R S S I R H T R L N Y N T F K S K L L Q K F L V L Protein_Len: 32 Strand: - Start: 243 End: 338 .................................................................................................................................................................................................................................................. V F A P C R Y F C S F P T S L V R F V T H P H S K P A H F N P M .............................................................................................................. Protein_Len: 60 Strand: - Start: 212 End: 391 ................................................................................................................................................................................................................... V Y I I Q S A P K K F S H L A D T S A P S H P L F C E S F Q I H T L S L P T F T L C I S T H Q F R F A P T G S T R N P M ......................................................... taaaaatatgtaagcaagtcttttcgcagccttgtagcatcgttcagttgtacaacttcgttactttacaacctattattctattcttcttgtctgatataaagttacttatacgtgtttgtagccttattcggcaatttacttacacgtaaagaaatatttatttacgtgtaagtaaattcttacttacgtgtagaaaaatatttatttacacgtaaataatttggctggctggctttttaaacgaatgcagggcatcggtagaagcaggagaatggggtagaaagcactctgaaaactgtatgtgggtgagacttaggggcgtgaaagttaggcatattgaagtatgttgaaaacgaaaagcgggtgtgccagaagttctattcggcacacccgcttaaattataatacttttaagagcaaacttctgcagaagtttctcgtttta 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================================================ taaaaatatgtaagcaagtcttttcgcagccttgtagcatcgttcagttgtacaacttcgttactttacaacctattattctattcttcttgtctgatataaagttacttatacgtgtttgtagccttattcggcaatttacttacacgtaaagaaatatttatttacgtgtaagtaaattcttacttacgtgtagaaaaatatttatttacacgtaaataatttggctggctggctttttaaacgaatgcagggcatcggtagaagcaggagaatggggtagaaagcactctgaaaactgtatgtgggtgagacttaggggcgtgaaagttaggcatattgaagtatgttgaaaacgaaaagcgggtgtgccagaagttctattcggcacacccgcttaaattataatacttttaagagcaaacttctgcagaagtttctcgtttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -16.3 Tail_Score: -3.83006 Start: 138 End: 179 Full_Region: AGCCTTATTCGGCAA TTTACTTACACGTAAAGAA ATAT TTATTTACGTGTAAGTAAA TTCTTACTTACGTGT .........................................................................................................................................TTTACTTACACGTAAAGAAATATTTATTTACGTGTAAGTAAA............................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 84 HP_score: -12.7 Tail_Score: -2.52896 Start: 142 End: 175 Full_Region: gtaagtaagaattta cttacacgtaaataa atat ttctttacgtgtaag taaattgccgaataa .............................................................................................................................................cttacacgtaaataaatatttctttacgtgtaag................................................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 91 HP_score: -10.1 Tail_Score: -4.42806 Start: 158 End: 203 Full_Region: TTACACGTAAAGAAA TATTTATTTACGTGTAAGTAA ATTC TTACTTACGTGTAGAAAAATA TTTATTTACACGTAA .............................................................................................................................................................TATTTATTTACGTGTAAGTAAATTCTTACTTACGTGTAGAAAAATA..................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 52 HP_score: -5.2 Tail_Score: -2.9462 Start: 164 End: 219 Full_Region: GTAAAGAAATATTTA TTTACGTGTAAGTAAATTCTTACT TACGTGT AGAAAAATATTTATTTACACGTAAA TAATTTGGCTGGCTG ...................................................................................................................................................................TTTACGTGTAAGTAAATTCTTACTTACGTGTAGAAAAATATTTATTTACACGTAAA..................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 69 HP_score: -7.9 Tail_Score: -3.52111 Start: 358 End: 402 Full_Region: AAGTATGTTGAAAAC GAAAAGCGGGTGTGCCAGAA GTTCTA TTCGGCACACCCGCTTAAA TTATAATACTTTTAA .....................................................................................................................................................................................................................................................................................................................................................................GAAAAGCGGGTGTGCCAGAAGTTCTATTCGGCACACCCGCTTAAA.............................................. TransTerm Strand: - Conf: 100 HP_score: -16.6 Tail_Score: -4.67038 Start: 363 End: 397 Full_Region: agtattataatttaa gcgggtgtgccgaa tagaac ttctggcacacccgc ttttcgttttcaaca ..........................................................................................................................................................................................................................................................................................................................................................................gcgggtgtgccgaatagaacttctggcacacccgc................................................... Find igs database================================================ Query_seq: PI0424:PI0426|PI0424:PI0426:methylated-DNA--[protein]-cysteine S-methyltransferase:conserved hypothetical protein:->->:389037..389484 448 taaaaatatgtaagcaagtcttttcgcagccttgtagcatcgttcagttgtacaacttcgttactttacaacctattattctattcttcttgtctgatataaagttacttatacgtgtttgtagccttattcggcaatttacttacacgtaaagaaatatttatttacgtgtaagtaaattcttacttacgtgtagaaaaatatttatttacacgtaaataatttggctggctggctttttaaacgaatgcagggcatcggtagaagcaggagaatggggtagaaagcactctgaaaactgtatgtgggtgagacttaggggcgtgaaagttaggcatattgaagtatgttgaaaacgaaaagcgggtgtgccagaagttctattcggcacacccgcttaaattataatacttttaagagcaaacttctgcagaagtttctcgtttta Intra-Species Hit: Count: 1 Min: 1 Max: 448 Len: 448 Subject: pint_PI0424_PI0426|methylated-DNA--[protein]-cysteine S-methyltransferase:conserved hypothetical protein|POSITIVE:POSITIVE|[389037,389484]|448 HSP 1 e-value: 0.0 bit: 888.0 Len: 448 Query Start:1 Query End:448 Subject Strand: POSITIVE Subject Start: 1 Subject End: 448 taaaaatatgtaagcaagtcttttcgcagccttgtagcatcgttcagttgtacaacttcgttactttacaacctattattctattcttcttgtctgatataaagttacttatacgtgtttgtagccttattcggcaatttacttacacgtaaagaaatatttatttacgtgtaagtaaattcttacttacgtgtagaaaaatatttatttacacgtaaataatttggctggctggctttttaaacgaatgcagggcatcggtagaagcaggagaatggggtagaaagcactctgaaaactgtatgtgggtgagacttaggggcgtgaaagttaggcatattgaagtatgttgaaaacgaaaagcgggtgtgccagaagttctattcggcacacccgcttaaattataatacttttaagagcaaacttctgcagaagtttctcgtttta taaaaatatgtaagcaagtcttttcgcagccttgtagcatcgttcagttgtacaacttcgttactttacaacctattattctattcttcttgtctgatataaagttacttatacgtgtttgtagccttattcggcaatttacttacacgtaaagaaatatttatttacgtgtaagtaaattcttacttacgtgtagaaaaatatttatttacacgtaaataatttggctggctggctttttaaacgaatgcagggcatcggtagaagcaggagaatggggtagaaagcactctgaaaactgtatgtgggtgagacttaggggcgtgaaagttaggcatattgaagtatgttgaaaacgaaaagcgggtgtgccagaagttctattcggcacacccgcttaaattataatacttttaagagcaaacttctgcagaagtttctcgtttta HSP 2 e-value: 1.0E-12 bit: 75.8 Len: 46 Query Start:136 Query End:181 Subject Strand: NEGATIVE Subject Start: 136 Subject End: 181 .......................................................................................................................................aatttacttacacgtaaagaaatatttatttacgtgtaagtaaatt........................................................................................................................................................................................................................................................................... .......................................................................................................................................aatttacttacacgtaaataaatatttctttacgtgtaagtaaatt........................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAUAUGUAAGCAAGUCUUUUCGCAGCCUUGUAGCAUCGUUCAGUUGUACAACUUCGUUACUUUACAACCUAUUAUUCUAUUCUUCUUGUCUGAUAUAAAGUUACUUAUACGUGUUUGUAGCCUUAUUCGGCAAUUUACUUACACGUAAAGAAAUAUUUAUUUACGUGUAAGUAAAUUCUUACUUACGUGUAGAAAAAUAUUUAUUUACACGUAAAUAAUUUGGCUGGCUGGCUUUUUAAACGAAUGCAGGGCAUCGGUAGAAGCAGGAGAAUGGGGUAGAAAGCACUCUGAAAACUGUAUGUGGGUGAGACUUAGGGGCGUGAAAGUUAGGCAUAUUGAAGUAUGUUGAAAACGAAAAGCGGGUGUGCCAGAAGUUCUAUUCGGCACACCCGCUUAAAUUAUAAUACUUUUAAGAGCAAACUUCUGCAGAAGUUUCUCGUUUUA .................((((((((((.(((((..((..(((..((..((((((..((((...((((....((((((.((((.((((.(((((((..(((((......))))).((((((((((((....(((((.(((((((((((((((((..........)))))))))))))))))..(((.(((((((((((.((....)).))))))))))).)))....)))))..))))......)))))))).)))))..)).))))..)))).))))))....)))).....))))...))))))))..)))..))..)))))))))))...)))).....(((((((.(((....))).(((((((((((((.(((......))))))))))))))))........)))))))...(((.(((((((....))))))))))...... (-135.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAACGAGAAACUUCUGCAGAAGUUUGCUCUUAAAAGUAUUAUAAUUUAAGCGGGUGUGCCGAAUAGAACUUCUGGCACACCCGCUUUUCGUUUUCAACAUACUUCAAUAUGCCUAACUUUCACGCCCCUAAGUCUCACCCACAUACAGUUUUCAGAGUGCUUUCUACCCCAUUCUCCUGCUUCUACCGAUGCCCUGCAUUCGUUUAAAAAGCCAGCCAGCCAAAUUAUUUACGUGUAAAUAAAUAUUUUUCUACACGUAAGUAAGAAUUUACUUACACGUAAAUAAAUAUUUCUUUACGUGUAAGUAAAUUGCCGAAUAAGGCUACAAACACGUAUAAGUAACUUUAUAUCAGACAAGAAGAAUAGAAUAAUAGGUUGUAAAGUAACGAAGUUGUACAACUGAACGAUGCUACAAGGCUGCGAAAAGACUUGCUUACAUAUUUUUA ......((((((((((....))))))).))).(((((((((........((((((((((((((((......))).)))))))))))))...(((.....((((......))))...)))...........(((((((..........(((((..(((.((((((((.(((..(((((....(((((...(((((...))))).((((............((((...(((((((((((((..............))))))))))))).((((((((((((((((((.((....)).)))))))))))))))))).........))))........(((((((....))))))).)))).)))))...)))))....))).).))))).))....)))...)))))..((..(((....)))..))...))))))).....))))))))) (-114.34) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 618 228 183 170 125 pint:PI0648|5end_hypothetical_protein_589448..589678_POSITIVE 532 399 355 158 112 pint:PI0313|5end_conserved_hypothetical_protein_294833..295063_POSITIVE 523 399 356 46 1 pint:PI0311|5end_hypothetical_protein_294721..294951_POSITIVE 473 200 151 164 115 pint:PI0579|5end_hypothetical_protein_523419..523649_POSITIVE 456 399 353 148 105 pint:PI2040|5end_conserved_hypothetical_protein;_possible_transporter_1993068..1993298_POSITIVE 446 190 143 223 176 pint:PI0702|5end_conserved_hypothetical_protein;_possible_tetracenomycin_C_synthesis_protein_homolog_638640..638870_POSITIVE 443 178 137 164 123 pint:PI1673|5end_hypothetical_protein_1587718..1587948_POSITIVE 443 173 136 130 93 pint:PI0983|5end_hypothetical_protein_909750..909980_POSITIVE 425 178 137 138 97 pint:PI0312|5end_hypothetical_protein_294591..294821_POSITIVE 423 178 137 142 101 pint:PI1450|5end_hypothetical_protein_1372683..1372913_POSITIVE 420 190 143 110 63 pint:PI1462|5end_hypothetical_protein_1385094..1385324_POSITIVE 417 288 241 229 176 pint:PI2075|5end_conserved_hypothetical_protein_2034421..2034651_POSITIVE 399 399 351 99 49 pint:PI1314|5end_hypothetical_protein_1231188..1231418_POSITIVE 397 174 137 172 135 pint:PI0619|5end_hypothetical_protein_569364..569594_POSITIVE 374 174 131 116 72 pint:PI0535|5end_hypothetical_protein_489508..489738_POSITIVE 359 286 244 48 6 pint:PI2084|5end_hypothetical_protein_2040387..2040617_POSITIVE 341 178 131 165 117 pint:PI0115|5end_hypothetical_protein_108062..108292_POSITIVE 341 178 131 151 103 pint:PI0111|5end_hypothetical_protein_108048..108278_POSITIVE 341 178 131 116 68 pint:PI0112|5end_hypothetical_protein_108013..108243_POSITIVE 340 395 357 81 39 pint:PI1431|5end_conserved_hypothetical_protein_1352079..1352309_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 569 399 355 56 11 pint:PI0128|3end_dipeptidase,_pathogenicity_island-encoded_protein_D_121826..121976_POSITIVE 561 229 183 78 33 pint:PI0533|3end_ABC_transporter,_permease_protein_488421..488571_POSITIVE 436 296 251 113 69 pint:PI2074|3end_conserved_hypothetical_protein_2034375..2034525_POSITIVE 435 226 187 54 15 pint:PI0797|3end_tRNA_pseudouridine_synthase_A_(pseudouridylate_synthase)_735752..735902_POSITIVE 432 186 143 62 19 pint:PI1314|3end_hypothetical_protein_1231423..1231573_POSITIVE 415 197 151 47 1 pint:PI0701|3end_hypothetical_protein_638537..638687_POSITIVE 399 399 351 72 22 pint:PI1313|3end_possible_POT_family_(proton-dependent_oligopeptide_transport_family)_1231241..1231391_POSITIVE 382 230 183 52 5 pint:PI0808|3end_ISPg3-related_transposase_746457..746607_POSITIVE 375 226 183 45 2 pint:PI1461|3end_conserved_hypothetical_protein_1385073..1385223_POSITIVE 372 230 183 134 88 pint:PI0725|3end_hypothetical_protein_658933..659083_POSITIVE 360 227 181 52 9 pint:PI2160|3end_hypothetical_protein_2108357..2108507_POSITIVE 360 219 171 142 94 pint:PI2105|3end_hypothetical_protein_2059586..2059736_POSITIVE 360 219 171 54 6 pint:PI2106|3end_hypothetical_protein_2059498..2059648_POSITIVE 328 290 244 82 31 pint:PI0644|3end_dnaJ_protein_586569..586719_POSITIVE 325 182 144 57 20 pint:PI0598|3end_hypothetical_protein_547233..547383_POSITIVE 323 335 292 109 67 pint:PI0431|3end_Xaa-Pro_aminopeptidase_404673..404823_POSITIVE 323 377 345 148 118 pint:PI0129|3end_hypothetical_protein_121941..122091_POSITIVE 321 270 225 88 39 pint:PI0345|3end_conserved_hypothetical_protein_320809..320959_POSITIVE 317 396 352 47 4 pint:PI2038|3end_conserved_hypothetical_protein;_possible_internalin-related_protein_1992591..1992741_POSITIVE 312 378 332 130 75 pint:PI0054|3end_hypothetical_protein_54829..54979_POSITIVE