Origin IGS: atttataaaattgttttggtttagctatttaaaatctttagtgctgcaaaggtaagaaagatattgcatattaaaaaacttttactccttaaatattaatttattagtatgtggttgtgctgttttaaacttgatgttgcttaaaagtaatggcggaattaaggtcgaatggggaggcgaactgtctgttggattagattttttaatatactcttctgccttttctcttttttattgattatct .........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 agataatcaataaaaaagagaaaaggcagaagagtatattaaaaaatctaatccaacagacagttcgcctccccattcgaccttaattccgccattacttttaagcaacatcaagtttaaaacagcacaaccacatactaataaattaatatttaaggagtaaaagttttttaatatgcaatatctttcttacctttgcagcactaaagattttaaatagctaaaccaaaacaattttataaat Mask Tandem Repeat Region ================================================ atttataaaattgttttggtttagctatttaaaatctttagtgctgcaaaggtaagaaagatattgcatattaaaaaacttttactccttaaatattaatttattagtatgtggttgtgctgttttaaacttgatgttgcttaaaagtaatggcggaattaaggtcgaatggggaggcgaactgtctgttggattagattttttaatatactcttctgccttttctcttttttattgattatct Find is-nt database================================================ Query_seq: PI0934:PI0935|PI0934:PI0935:hypothetical protein:collagenase, protease:->->:866193..866436 244 atttataaaattgttttggtttagctatttaaaatctttagtgctgcaaaggtaagaaagatattgcatattaaaaaacttttactccttaaatattaatttattagtatgtggttgtgctgttttaaacttgatgttgcttaaaagtaatggcggaattaaggtcgaatggggaggcgaactgtctgttggattagattttttaatatactcttctgccttttctcttttttattgattatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0934:PI0935|PI0934:PI0935:hypothetical protein:collagenase, protease:->->:866193..866436 244 atttataaaattgttttggtttagctatttaaaatctttagtgctgcaaaggtaagaaagatattgcatattaaaaaacttttactccttaaatattaatttattagtatgtggttgtgctgttttaaacttgatgttgcttaaaagtaatggcggaattaaggtcgaatggggaggcgaactgtctgttggattagattttttaatatactcttctgccttttctcttttttattgattatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0934:PI0935|PI0934:PI0935:hypothetical protein:collagenase, protease:->->:866193..866436 244 atttataaaattgttttggtttagctatttaaaatctttagtgctgcaaaggtaagaaagatattgcatattaaaaaacttttactccttaaatattaatttattagtatgtggttgtgctgttttaaacttgatgttgcttaaaagtaatggcggaattaaggtcgaatggggaggcgaactgtctgttggattagattttttaatatactcttctgccttttctcttttttattgattatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttataaaattgttttggtttagctatttaaaatctttagtgctgcaaaggtaagaaagatattgcatattaaaaaacttttactccttaaatattaatttattagtatgtggttgtgctgttttaaacttgatgttgcttaaaagtaatggcggaattaaggtcgaatggggaggcgaactgtctgttggattagattttttaatatactcttctgccttttctcttttttattgattatct Predict ORF larger than 30AA ================================================ Protein_Len: 56 Strand: + Start: 68 End: 235 ................................................................... M L K N F Y S L N I N L L V C G C A V L N L M L L K S N G G I K V E W G G E L S V G L D F L I Y S S A F S L F Y ......... Protein_Len: 41 Strand: - Start: 85 End: 207 .................................................................................... E K F I L K N T H P Q A T K F K I N S L L L P P I L T S H P P S S D T P N S K K M ..................................... atttataaaattgttttggtttagctatttaaaatctttagtgctgcaaaggtaagaaagatattgcatattaaaaaacttttactccttaaatattaatttattagtatgtggttgtgctgttttaaacttgatgttgcttaaaagtaatggcggaattaaggtcgaatggggaggcgaactgtctgttggattagattttttaatatactcttctgccttttctcttttttattgattatct 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================================================ atttataaaattgttttggtttagctatttaaaatctttagtgctgcaaaggtaagaaagatattgcatattaaaaaacttttactccttaaatattaatttattagtatgtggttgtgctgttttaaacttgatgttgcttaaaagtaatggcggaattaaggtcgaatggggaggcgaactgtctgttggattagattttttaatatactcttctgccttttctcttttttattgattatct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0934:PI0935|PI0934:PI0935:hypothetical protein:collagenase, protease:->->:866193..866436 244 atttataaaattgttttggtttagctatttaaaatctttagtgctgcaaaggtaagaaagatattgcatattaaaaaacttttactccttaaatattaatttattagtatgtggttgtgctgttttaaacttgatgttgcttaaaagtaatggcggaattaaggtcgaatggggaggcgaactgtctgttggattagattttttaatatactcttctgccttttctcttttttattgattatct Intra-Species Hit: Count: 1 Min: 1 Max: 244 Len: 244 Subject: pint_PI0934_PI0935|hypothetical protein:collagenase, protease|POSITIVE:POSITIVE|[866193,866436]|244 HSP 1 e-value: 1.0E-136 bit: 484.0 Len: 244 Query Start:1 Query End:244 Subject Strand: POSITIVE Subject Start: 1 Subject End: 244 atttataaaattgttttggtttagctatttaaaatctttagtgctgcaaaggtaagaaagatattgcatattaaaaaacttttactccttaaatattaatttattagtatgtggttgtgctgttttaaacttgatgttgcttaaaagtaatggcggaattaaggtcgaatggggaggcgaactgtctgttggattagattttttaatatactcttctgccttttctcttttttattgattatct atttataaaattgttttggtttagctatttaaaatctttagtgctgcaaaggtaagaaagatattgcatattaaaaaacttttactccttaaatattaatttattagtatgtggttgtgctgttttaaacttgatgttgcttaaaagtaatggcggaattaaggtcgaatggggaggcgaactgtctgttggattagattttttaatatactcttctgccttttctcttttttattgattatct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUAUAAAAUUGUUUUGGUUUAGCUAUUUAAAAUCUUUAGUGCUGCAAAGGUAAGAAAGAUAUUGCAUAUUAAAAAACUUUUACUCCUUAAAUAUUAAUUUAUUAGUAUGUGGUUGUGCUGUUUUAAACUUGAUGUUGCUUAAAAGUAAUGGCGGAAUUAAGGUCGAAUGGGGAGGCGAACUGUCUGUUGGAUUAGAUUUUUUAAUAUACUCUUCUGCCUUUUCUCUUUUUUAUUGAUUAUCU (((.((((((((((((((((((.((((((....((((((..((((.....))))..))))))...((((((((((((((...(((.((....(((((((....)))))))..))..)))..)))))....)))))).)))........)))))).))))))))).)))..(..((((((((..((.(((((((........))))))).))..))).)))))..)....)))))).)))..... (-50.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUAAUCAAUAAAAAAGAGAAAAGGCAGAAGAGUAUAUUAAAAAAUCUAAUCCAACAGACAGUUCGCCUCCCCAUUCGACCUUAAUUCCGCCAUUACUUUUAAGCAACAUCAAGUUUAAAACAGCACAACCACAUACUAAUAAAUUAAUAUUUAAGGAGUAAAAGUUUUUUAAUAUGCAAUAUCUUUCUUACCUUUGCAGCACUAAAGAUUUUAAAUAGCUAAACCAAAACAAUUUUAUAAAU .........((((((......(((((..(((((((((((((((((((..............((.(((..........))).))..(((((........((((((((........))))))))...................(((((....))))).)))))....))))))))))))))....)))))....)))))..(((.................)))............)))))).... (-28.03) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 375 192 151 228 178 pint:PI0318|5end_conserved_hypothetical_protein_300679..300909_POSITIVE 367 188 151 49 7 pint:PI0734|5end_ABC_transporter,_ATP-binding_/_permease_667052..667282_POSITIVE 336 188 144 205 161 pint:PI0846|5end_transcription_regulator,_CRP_family_780435..780665_POSITIVE 336 188 146 53 8 pint:PI0261|5end_conjugative_transposon_protein,_TraK_254065..254295_POSITIVE 329 192 154 217 174 pint:PI1207|5end_hypothtical_protein_1126977..1127207_POSITIVE 324 192 152 119 80 pint:PI0670|5end_hypothetical_protein_611000..611230_POSITIVE 324 192 152 43 4 pint:PI0669|5end_hypothetical_protein_610924..611154_POSITIVE 316 199 153 72 21 pint:PI0029|5end_glutamine_amidotransferase_(GMP_synthase_(glutamine-hydrolyzing))_32593..32823_POSITIVE 314 196 151 190 133 pint:PI0749|5end_hypothetical_protein_677234..677464_POSITIVE 310 179 147 74 32 pint:PI0084|5end_conserved_hypothetical_protein_84195..84425_POSITIVE 306 195 152 141 98 pint:PI1200|5end_carbon-nitrogen_hydrolase/beta-alanine_synthase_1115662..1115892_POSITIVE 303 180 134 83 48 pint:PI0736|5end_transcriptional_regulator,_TetR_family_670580..670810_POSITIVE 298 179 135 149 105 pint:PI2029|5end_DNA_topoisomerase_I_1982775..1983005_POSITIVE 296 180 134 72 23 pint:PI0159|5end_hypothetical_protein_151273..151503_POSITIVE 294 200 153 227 175 pint:PI0304|5end_hypothetical_protein_288582..288812_POSITIVE 294 193 151 65 16 pint:PI0127|5end_conserved_hypothetical_protein_118683..118913_POSITIVE 292 178 135 61 12 pint:PI0301|5end_probable_transposase_285672..285902_POSITIVE 290 199 163 70 40 pint:PI1755|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1681930..1682160_POSITIVE 289 196 151 229 173 pint:PI0030|5end_transcriptional_regulator,_AsnC_family_34509..34739_POSITIVE 287 185 146 181 136 pint:PI1789|5end_hypothetical_protein_1718727..1718957_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 188 144 129 85 pint:PI0845|3end_peptidyl-dipeptidase_780439..780589_POSITIVE 316 199 153 126 75 pint:PI0028|3end_aminopeptidase_32727..32877_POSITIVE 314 196 151 90 33 pint:PI0748|3end_possible_mobilization_protein_677214..677364_POSITIVE 308 193 151 57 10 pint:PI0043|3end_thiamine_phosphate_pyrophosphorylase_43156..43306_POSITIVE 306 195 152 145 102 pint:PI1199|3end_possible_acetyltransferase_1115746..1115896_POSITIVE 298 179 135 96 52 pint:PI2028|3end_shikimate_kinase_1982802..1982952_POSITIVE 296 180 134 106 57 pint:PI0157|3end_hypothetical_protein_151387..151537_POSITIVE 292 178 135 70 21 pint:PI0300|3end_transposase_285761..285911_POSITIVE 290 199 163 70 40 pint:PI1754|3end_conserved_hypothetical_protein_1682010..1682160_POSITIVE 290 193 151 143 92 pint:PI0724|3end_DNA_polymerase_III,_delta_subunit_658601..658751_POSITIVE 287 185 146 81 36 pint:PI1788|3end_hypothetical_protein_1718707..1718857_POSITIVE 285 193 153 139 95 pint:PI1225|3end_hypothetical_protein_1147933..1148083_POSITIVE 284 54 23 49 18 pint:PI1038|3end_hypothetical_protein_958920..959070_POSITIVE 284 177 132 105 60 pint:PI0128|3end_dipeptidase,_pathogenicity_island-encoded_protein_D_121826..121976_POSITIVE 282 207 163 54 3 pint:PI0260|3end_conjugative_transposon_protein,_TraJ_254122..254272_POSITIVE 278 191 151 102 59 pint:PI0053|3end_hypothetical_protein_55124..55274_POSITIVE 275 155 111 109 62 pint:PI1185|3end_hypothetical_protein_1106557..1106707_POSITIVE 268 188 159 69 28 pint:PI0584|3end_hypothetical_protein_527656..527806_POSITIVE 267 193 151 114 63 pint:PI0779|3end_predicted_TPR-repeat-containing_protein_715800..715950_POSITIVE 262 193 151 134 92 pint:PI1571|3end_surface_antigen_BspA_1495780..1495930_POSITIVE