Origin IGS: taaaacttctcttttccattctacctccatttgttgcaatcagaagttgtaacaggtggaggttttgtgcatttatcataagcacaaacaatttagcaatataaaaatcataatatgaaacaactgattgaaacagaaacctttgagttgctgctatcagacaatagcaaaactgcaacagacaatcttatcaaggaaattataaggttgggggaaaccgaagcaaaccttgcttcattgtatcgtactctccattacactcgattccatttagaaagtatgactgaaacatcaggcataccaactgaaatgggaaaaaaatgtatcagagctgctctttgtcattgacacggagctggaatta .........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 taattccagctccgtgtcaatgacaaagagcagctctgatacatttttttcccatttcagttggtatgcctgatgtttcagtcatactttctaaatggaatcgagtgtaatggagagtacgatacaatgaagcaaggtttgcttcggtttcccccaaccttataatttccttgataagattgtctgttgcagttttgctattgtctgatagcagcaactcaaaggtttctgtttcaatcagttgtttcatattatgatttttatattgctaaattgtttgtgcttatgataaatgcacaaaacctccacctgttacaacttctgattgcaacaaatggaggtagaatggaaaagagaagtttta Mask Tandem Repeat Region ================================================ taaaacttctcttttccattctacctccatttgttgcaatcagaagttgtaacaggtggaggttttgtgcatttatcataagcacaaacaatttagcaatataaaaatcataatatgaaacaactgattgaaacagaaacctttgagttgctgctatcagacaatagcaaaactgcaacagacaatcttatcaaggaaattataaggttgggggaaaccgaagcaaaccttgcttcattgtatcgtactctccattacactcgattccatttagaaagtatgactgaaacatcaggcataccaactgaaatgggaaaaaaatgtatcagagctgctctttgtcattgacacggagctggaatta Find is-nt database================================================ Query_seq: PI0240:PI0241|PI0240:PI0241:conserved hypothetical protein:possible tetracycline resistance element /mobilization regulatory protein:->->:239403..239766 364 taaaacttctcttttccattctacctccatttgttgcaatcagaagttgtaacaggtggaggttttgtgcatttatcataagcacaaacaatttagcaatataaaaatcataatatgaaacaactgattgaaacagaaacctttgagttgctgctatcagacaatagcaaaactgcaacagacaatcttatcaaggaaattataaggttgggggaaaccgaagcaaaccttgcttcattgtatcgtactctccattacactcgattccatttagaaagtatgactgaaacatcaggcataccaactgaaatgggaaaaaaatgtatcagagctgctctttgtcattgacacggagctggaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0240:PI0241|PI0240:PI0241:conserved hypothetical protein:possible tetracycline resistance element /mobilization regulatory protein:->->:239403..239766 364 taaaacttctcttttccattctacctccatttgttgcaatcagaagttgtaacaggtggaggttttgtgcatttatcataagcacaaacaatttagcaatataaaaatcataatatgaaacaactgattgaaacagaaacctttgagttgctgctatcagacaatagcaaaactgcaacagacaatcttatcaaggaaattataaggttgggggaaaccgaagcaaaccttgcttcattgtatcgtactctccattacactcgattccatttagaaagtatgactgaaacatcaggcataccaactgaaatgggaaaaaaatgtatcagagctgctctttgtcattgacacggagctggaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0240:PI0241|PI0240:PI0241:conserved hypothetical protein:possible tetracycline resistance element /mobilization regulatory protein:->->:239403..239766 364 taaaacttctcttttccattctacctccatttgttgcaatcagaagttgtaacaggtggaggttttgtgcatttatcataagcacaaacaatttagcaatataaaaatcataatatgaaacaactgattgaaacagaaacctttgagttgctgctatcagacaatagcaaaactgcaacagacaatcttatcaaggaaattataaggttgggggaaaccgaagcaaaccttgcttcattgtatcgtactctccattacactcgattccatttagaaagtatgactgaaacatcaggcataccaactgaaatgggaaaaaaatgtatcagagctgctctttgtcattgacacggagctggaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaacttctcttttccattctacctccatttgttgcaatcagaagttgtaacaggtggaggttttgtgcatttatcataagcacaaacaatttagcaatataaaaatcataatatgaaacaactgattgaaacagaaacctttgagttgctgctatcagacaatagcaaaactgcaacagacaatcttatcaaggaaattataaggttgggggaaaccgaagcaaaccttgcttcattgtatcgtactctccattacactcgattccatttagaaagtatgactgaaacatcaggcataccaactgaaatgggaaaaaaatgtatcagagctgctctttgtcattgacacggagctggaatta Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 115 End: 345 .................................................................................................................. M K Q L I E T E T F E L L L S D N S K T A T D N L I K E I I R L G E T E A N L A S L Y R T L H Y T R F H L E S M T E T S ................... Protein_Len: 40 Strand: - Start: 203 End: 322 .......................................................................................................................................................................................................... L T P P F R L L G Q K M T D Y E G N C E I G N L F Y S Q F M L C V L Q F P F F M .......................................... Protein_Len: 31 Strand: - Start: 111 End: 203 .............................................................................................................. L I F C S I S V S V K S N S S D S L L L V A V S L R I L S I M ................................................................................................................................................................. Protein_Len: 60 Strand: - Start: 2 End: 181 . F S R K E M R G G N T A I L L Q L L H L N Q A N I M L V F L K A I Y F D Y Y S V V S Q F L F R Q T A A I L C Y C F Q L M ....................................................................................................................................................................................... taaaacttctcttttccattctacctccatttgttgcaatcagaagttgtaacaggtggaggttttgtgcatttatcataagcacaaacaatttagcaatataaaaatcataatatgaaacaactgattgaaacagaaacctttgagttgctgctatcagacaatagcaaaactgcaacagacaatcttatcaaggaaattataaggttgggggaaaccgaagcaaaccttgcttcattgtatcgtactctccattacactcgattccatttagaaagtatgactgaaacatcaggcataccaactgaaatgggaaaaaaatgtatcagagctgctctttgtcattgacacggagctggaatta 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================================================ taaaacttctcttttccattctacctccatttgttgcaatcagaagttgtaacaggtggaggttttgtgcatttatcataagcacaaacaatttagcaatataaaaatcataatatgaaacaactgattgaaacagaaacctttgagttgctgctatcagacaatagcaaaactgcaacagacaatcttatcaaggaaattataaggttgggggaaaccgaagcaaaccttgcttcattgtatcgtactctccattacactcgattccatttagaaagtatgactgaaacatcaggcataccaactgaaatgggaaaaaaatgtatcagagctgctctttgtcattgacacggagctggaatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -11.9 Tail_Score: -4.52803 Start: 24 End: 62 Full_Region: CTCTTTTCCATTCTA CCTCCATTTGTTGCAAT CAGAA GTTGTAACAGGTGGAGG TTTTGTGCATTTATC .......................CCTCCATTTGTTGCAATCAGAAGTTGTAACAGGTGGAGG.............................................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 74 HP_score: -4.0 Tail_Score: -5.1244 Start: 108 End: 118 Full_Region: tttcaatcagttgtt tcat att atga tttttatattgctaa ...........................................................................................................tcatattatga...................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 72 HP_score: -9.5 Tail_Score: -2.7371 Start: 220 End: 236 Full_Region: AGGTTGGGGGAAACC GAAGCAA ACC TTGCTTC ATTGTATCGTACTCT ...........................................................................................................................................................................................................................GAAGCAAACCTTGCTTC................................................................................................................................ TransTerm Strand: - Conf: 77 HP_score: -8.2 Tail_Score: -3.92373 Start: 278 End: 301 Full_Region: ttcccatttcagttg gtatgcctga tgtt tcagtcatac tttctaaatggaatc .....................................................................................................................................................................................................................................................................................gtatgcctgatgtttcagtcatac............................................................... TransTerm Strand: + Conf: 40 HP_score: -2.1 Tail_Score: -2.70932 Start: 327 End: 341 Full_Region: GGGAAAAAAATGTAT CAGAG CTGCT CTTTG TCATTGACACGGAGC ......................................................................................................................................................................................................................................................................................................................................CAGAGCTGCTCTTTG....................... Find igs database================================================ Query_seq: PI0240:PI0241|PI0240:PI0241:conserved hypothetical protein:possible tetracycline resistance element /mobilization regulatory protein:->->:239403..239766 364 taaaacttctcttttccattctacctccatttgttgcaatcagaagttgtaacaggtggaggttttgtgcatttatcataagcacaaacaatttagcaatataaaaatcataatatgaaacaactgattgaaacagaaacctttgagttgctgctatcagacaatagcaaaactgcaacagacaatcttatcaaggaaattataaggttgggggaaaccgaagcaaaccttgcttcattgtatcgtactctccattacactcgattccatttagaaagtatgactgaaacatcaggcataccaactgaaatgggaaaaaaatgtatcagagctgctctttgtcattgacacggagctggaatta Intra-Species Hit: Count: 1 Min: 1 Max: 364 Len: 364 Subject: pint_PI0240_PI0241|conserved hypothetical protein:possible tetracycline resistance element /mobilization regulatory protein|POSITIVE:POSITIVE|[239403,239766]|364 HSP 1 e-value: 0.0 bit: 680.0 Len: 364 Query Start:1 Query End:364 Subject Strand: POSITIVE Subject Start: 1 Subject End: 364 taaaacttctcttttccattctacctccatttgttgcaatcagaagttgtaacaggtggaggttttgtgcatttatcataagcacaaacaatttagcaatataaaaatcataatatgaaacaactgattgaaacagaaacctttgagttgctgctatcagacaatagcaaaactgcaacagacaatcttatcaaggaaattataaggttgggggaaaccgaagcaaaccttgcttcattgtatcgtactctccattacactcgattccatttagaaagtatgactgaaacatcaggcataccaactgaaatgggnnnnnnntgtatcagagctgctctttgtcattgacacggagctggaatta taaaacttctcttttccattctacctccatttgttgcaatcagaagttgtaacaggtggaggttttgtgcatttatcataagcacaaacaatttagcaatataaaaatcataatatgaaacaactgattgaaacagaaacctttgagttgctgctatcagacaatagcaaaactgcaacagacaatcttatcaaggaaattataaggttgggggaaaccgaagcaaaccttgcttcattgtatcgtactctccattacactcgattccatttagaaagtatgactgaaacatcaggcataccaactgaaatgggaaaaaaatgtatcagagctgctctttgtcattgacacggagctggaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAACUUCUCUUUUCCAUUCUACCUCCAUUUGUUGCAAUCAGAAGUUGUAACAGGUGGAGGUUUUGUGCAUUUAUCAUAAGCACAAACAAUUUAGCAAUAUAAAAAUCAUAAUAUGAAACAACUGAUUGAAACAGAAACCUUUGAGUUGCUGCUAUCAGACAAUAGCAAAACUGCAACAGACAAUCUUAUCAAGGAAAUUAUAAGGUUGGGGGAAACCGAAGCAAACCUUGCUUCAUUGUAUCGUACUCUCCAUUACACUCGAUUCCAUUUAGAAAGUAUGACUGAAACAUCAGGCAUACCAACUGAAAUGGGAAAAAAAUGUAUCAGAGCUGCUCUUUGUCAUUGACACGGAGCUGGAAUUA .............((((.....((((((((((((((((((.....))))))))))))))))))(((((((...........)))))))......(((..........((((...)))).....(((((.((.((((..........(((((((((((......)))))).....)))))...(((((((((.((.....))))))))))).((....))((((((.....)))))).)))).))....................((((((((((...(((((.((((....)))).)))))...))).))))))).........))))).)))(((((.((((...)))).))))).))))... (-99.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUCCAGCUCCGUGUCAAUGACAAAGAGCAGCUCUGAUACAUUUUUUUCCCAUUUCAGUUGGUAUGCCUGAUGUUUCAGUCAUACUUUCUAAAUGGAAUCGAGUGUAAUGGAGAGUACGAUACAAUGAAGCAAGGUUUGCUUCGGUUUCCCCCAACCUUAUAAUUUCCUUGAUAAGAUUGUCUGUUGCAGUUUUGCUAUUGUCUGAUAGCAGCAACUCAAAGGUUUCUGUUUCAAUCAGUUGUUUCAUAUUAUGAUUUUUAUAUUGCUAAAUUGUUUGUGCUUAUGAUAAAUGCACAAAACCUCCACCUGUUACAACUUCUGAUUGCAACAAAUGGAGGUAGAAUGGAAAAGAGAAGUUUUA ...(((((((((..((((...))))..))))..(((((.(((((((..((((.((((.((..((((((.((((....)))).))))))..))))))))))..))))))).))))).((((((.(((((..(((((((...((....))..)).......(((((((.....(((...(((((..((..((((...(((((((....)))))))..((((....)))).))))..))..)))))...))).)))))))........)))))..)))))))))))..................(((((((..((((.((((....).))).))))..)))))))....)))))............. (-100.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 70 25 122 74 pint:PI1632|5end_hypothetical_protein_1552819..1553049_POSITIVE 309 73 33 68 21 pint:PI1738|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_1659343..1659573_POSITIVE 304 359 321 78 38 pint:PI0331|5end_hypothetical_protein_311656..311886_POSITIVE 293 66 32 227 192 pint:PI0427|5end_conserved_hypothetical_protein_391140..391370_POSITIVE 285 80 34 90 42 pint:PI0770|5end_hypothetical_protein_706170..706400_POSITIVE 282 255 211 231 186 pint:PI2097|5end_conserved_hypothetical_protein_2050912..2051142_POSITIVE 282 249 205 95 47 pint:PI1590|5end_transcriptional_regulator_1518053..1518283_POSITIVE 281 180 133 177 125 pint:PI0664|5end_dihydroorotate_dehydrogenase,_electron_transfer_subunit_606891..607121_POSITIVE 280 180 134 229 180 pint:PI0956|5end_conserved_hypothetical_protein_886077..886307_POSITIVE 280 245 204 171 132 pint:PI0354|5end_hypothetical_protein_325886..326116_POSITIVE 280 67 21 153 108 pint:PI0124|5end_outer_membrane_protein/protective_antigen_OMA87_114487..114717_POSITIVE 279 215 173 78 32 pint:PI0914|5end_ATPase,_AAA_family_843662..843892_POSITIVE 267 358 311 222 179 pint:PI0408|5end_hypothetical_protein_374154..374384_POSITIVE 266 237 204 104 60 pint:PI0760|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_694086..694316_POSITIVE 266 357 311 221 185 pint:PI0739|5end_conserved_hypothetical_protein_671794..672024_POSITIVE 265 245 205 97 49 pint:PI0250|5end_hypothetical_protein_246946..247176_POSITIVE 263 234 194 190 150 pint:PI0736|5end_transcriptional_regulator,_TetR_family_670580..670810_POSITIVE 263 69 21 49 2 pint:PI0687|5end_hypothetical_protein_624256..624486_POSITIVE 262 307 261 86 50 pint:PI0751|5end_conserved_hypothetical_protein_680623..680853_POSITIVE 262 59 14 217 171 pint:PI0146|5end_transcription_elongation_factor_140338..140568_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 455 63 23 68 28 pint:PI0240|3end_conserved_hypothetical_protein_239342..239492_POSITIVE 303 196 151 62 17 pint:PI0764|3end_permease_699145..699295_POSITIVE 291 229 181 65 11 pint:PI2167|3end_hypothetical_protein_2111891..2112041_POSITIVE 282 255 211 123 78 pint:PI2096|3end_conserved_hypothetical_protein;_possible_phosphoesterase_2050884..2051034_POSITIVE 280 245 204 139 100 pint:PI0352|3end_hypothetical_protein_325934..326084_POSITIVE 280 67 21 87 42 pint:PI0123|3end_outer_membrane_protein,_ompH_family_114501..114651_POSITIVE 279 215 173 69 23 pint:PI0913|3end_glycerate_dehydrogenase_843733..843883_POSITIVE 276 359 311 136 97 pint:PI2092|3end_hypothetical_protein_2049406..2049556_POSITIVE 267 358 311 135 92 pint:PI0407|3end_tryptophanyl-tRNA_synthetase_(tryptophan--tRNA_ligase)_374147..374297_POSITIVE 265 245 205 97 49 pint:PI0249|3end_conserved_hypothetical_protein_247026..247176_POSITIVE 263 234 194 121 81 pint:PI0735|3end_ABC_transporter,_ATP-binding_/_permease_670591..670741_POSITIVE 261 337 293 110 55 pint:PI1058|3end_possible_FHA_domain_protein_978184..978334_POSITIVE 259 249 204 145 100 pint:PI1646|3end_hypothetical_protein_1563128..1563278_POSITIVE 259 232 191 88 50 pint:PI1180|3end_ferric_uptake_regulation_protein_1102409..1102559_POSITIVE 257 237 195 73 32 pint:PI1918|3end_uracil-DNA_glycosylase_1862224..1862374_POSITIVE 257 236 205 52 14 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 256 350 305 108 55 pint:PI0428|3end_hypothetical_protein_396321..396471_POSITIVE 255 250 219 136 103 pint:PI1484|3end_conserved_hypothetical_protein_1405223..1405373_POSITIVE 254 357 326 32 1 pint:PI0472|3end_50S_ribosomal_protein_L5_438705..438855_POSITIVE 252 360 324 149 89 pint:PI0473|3end_30S_ribosomal_protein_S14_439013..439163_POSITIVE