Origin IGS: tgaacataaaagatatgattatgctaagacttactcaaactgaagactttaagacaataatctctttatgctctacaaaaggacagatacaaaaagcgtcagacaactttattctgaagattattgccctatgtgatgcagaaagagatttagtctcattgtttcggaccctccgttatacacgcttttgcctgcaaccgttgcaaaggggagattcaatggacggagaggggaaaaaatgtatcagaactgctctttgtcattgacacggagcttgaattactgaaa .........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 tttcagtaattcaagctccgtgtcaatgacaaagagcagttctgatacattttttcccctctccgtccattgaatctcccctttgcaacggttgcaggcaaaagcgtgtataacggagggtccgaaacaatgagactaaatctctttctgcatcacatagggcaataatcttcagaataaagttgtctgacgctttttgtatctgtccttttgtagagcataaagagattattgtcttaaagtcttcagtttgagtaagtcttagcataatcatatcttttatgttca Mask Tandem Repeat Region ================================================ tgaacataaaagatatgattatgctaagacttactcaaactgaagactttaagacaataatctctttatgctctacaaaaggacagatacaaaaagcgtcagacaactttattctgaagattattgccctatgtgatgcagaaagagatttagtctcattgtttcggaccctccgttatacacgcttttgcctgcaaccgttgcaaaggggagattcaatggacggagaggggaaaaaatgtatcagaactgctctttgtcattgacacggagcttgaattactgaaa Find is-nt database================================================ Query_seq: PI0395:PI0396|PI0395:PI0396:Na+-driven multidrug efflux pump:possible tetracycline resistance element mobilization regulatory protein, C-terminal fragment:->->:361845..362132 288 tgaacataaaagatatgattatgctaagacttactcaaactgaagactttaagacaataatctctttatgctctacaaaaggacagatacaaaaagcgtcagacaactttattctgaagattattgccctatgtgatgcagaaagagatttagtctcattgtttcggaccctccgttatacacgcttttgcctgcaaccgttgcaaaggggagattcaatggacggagaggggaaaaaatgtatcagaactgctctttgtcattgacacggagcttgaattactgaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0395:PI0396|PI0395:PI0396:Na+-driven multidrug efflux pump:possible tetracycline resistance element mobilization regulatory protein, C-terminal fragment:->->:361845..362132 288 tgaacataaaagatatgattatgctaagacttactcaaactgaagactttaagacaataatctctttatgctctacaaaaggacagatacaaaaagcgtcagacaactttattctgaagattattgccctatgtgatgcagaaagagatttagtctcattgtttcggaccctccgttatacacgcttttgcctgcaaccgttgcaaaggggagattcaatggacggagaggggaaaaaatgtatcagaactgctctttgtcattgacacggagcttgaattactgaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0395:PI0396|PI0395:PI0396:Na+-driven multidrug efflux pump:possible tetracycline resistance element mobilization regulatory protein, C-terminal fragment:->->:361845..362132 288 tgaacataaaagatatgattatgctaagacttactcaaactgaagactttaagacaataatctctttatgctctacaaaaggacagatacaaaaagcgtcagacaactttattctgaagattattgccctatgtgatgcagaaagagatttagtctcattgtttcggaccctccgttatacacgcttttgcctgcaaccgttgcaaaggggagattcaatggacggagaggggaaaaaatgtatcagaactgctctttgtcattgacacggagcttgaattactgaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaacataaaagatatgattatgctaagacttactcaaactgaagactttaagacaataatctctttatgctctacaaaaggacagatacaaaaagcgtcagacaactttattctgaagattattgccctatgtgatgcagaaagagatttagtctcattgtttcggaccctccgttatacacgcttttgcctgcaaccgttgcaaaggggagattcaatggacggagaggggaaaaaatgtatcagaactgctctttgtcattgacacggagcttgaattactgaaa Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 6 End: 263 ..... M K D M I M L R L T Q T E D F K T I I S L C S T K G Q I Q K A S D N F I L K I I A L C D A E R D L V S L F R T L R Y T R ......................... Protein_Len: 43 Strand: + Start: 158 End: 283 ............................................................................................................................................................. M V S D P P L Y T L L P A T V A K G R F N G R R G E K M Y Q N C S L S L T R S L N Y * ..... Protein_Len: 37 Strand: + Start: 178 End: 288 ................................................................................................................................................................................. M H A F A C N R C K G E I Q W T E R G K N V S E L L F V I D T E L E L L K Protein_Len: 39 Strand: - Start: 124 End: 240 ........................................................................................................................... Q G I H H L F L N L R M T E S G G N Y V S K G A V T A F P L N L P R L P S F M ................................................ tgaacataaaagatatgattatgctaagacttactcaaactgaagactttaagacaataatctctttatgctctacaaaaggacagatacaaaaagcgtcagacaactttattctgaagattattgccctatgtgatgcagaaagagatttagtctcattgtttcggaccctccgttatacacgcttttgcctgcaaccgttgcaaaggggagattcaatggacggagaggggaaaaaatgtatcagaactgctctttgtcattgacacggagcttgaattactgaaa 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================================================ tgaacataaaagatatgattatgctaagacttactcaaactgaagactttaagacaataatctctttatgctctacaaaaggacagatacaaaaagcgtcagacaactttattctgaagattattgccctatgtgatgcagaaagagatttagtctcattgtttcggaccctccgttatacacgcttttgcctgcaaccgttgcaaaggggagattcaatggacggagaggggaaaaaatgtatcagaactgctctttgtcattgacacggagcttgaattactgaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 55 HP_score: -3.4 Tail_Score: -3.92373 Start: 145 End: 157 Full_Region: agggtccgaaacaat gaga ctaaa tctc tttctgcatcacata ................................................................................................................................................gagactaaatctc................................................................................................................................... Find igs database================================================ Query_seq: PI0395:PI0396|PI0395:PI0396:Na+-driven multidrug efflux pump:possible tetracycline resistance element mobilization regulatory protein, C-terminal fragment:->->:361845..362132 288 tgaacataaaagatatgattatgctaagacttactcaaactgaagactttaagacaataatctctttatgctctacaaaaggacagatacaaaaagcgtcagacaactttattctgaagattattgccctatgtgatgcagaaagagatttagtctcattgtttcggaccctccgttatacacgcttttgcctgcaaccgttgcaaaggggagattcaatggacggagaggggaaaaaatgtatcagaactgctctttgtcattgacacggagcttgaattactgaaa Intra-Species Hit: Count: 1 Min: 1 Max: 288 Len: 288 Subject: pint_PI0395_PI0396|Na+-driven multidrug efflux pump:possible tetracycline resistance element mobilization regulatory protein, C-terminal fragment|POSITIVE:POSITIVE|[361845,362132]|288 HSP 1 e-value: 1.0E-162 bit: 571.0 Len: 288 Query Start:1 Query End:288 Subject Strand: POSITIVE Subject Start: 1 Subject End: 288 tgaacataaaagatatgattatgctaagacttactcaaactgaagactttaagacaataatctctttatgctctacaaaaggacagatacaaaaagcgtcagacaactttattctgaagattattgccctatgtgatgcagaaagagatttagtctcattgtttcggaccctccgttatacacgcttttgcctgcaaccgttgcaaaggggagattcaatggacggagaggggaaaaaatgtatcagaactgctctttgtcattgacacggagcttgaattactgaaa tgaacataaaagatatgattatgctaagacttactcaaactgaagactttaagacaataatctctttatgctctacaaaaggacagatacaaaaagcgtcagacaactttattctgaagattattgccctatgtgatgcagaaagagatttagtctcattgtttcggaccctccgttatacacgcttttgcctgcaaccgttgcaaaggggagattcaatggacggagaggggaaaaaatgtatcagaactgctctttgtcattgacacggagcttgaattactgaaa Inter-species Hit: Count: 3 Min: 1 Max: 288 Len: 288 Subject: NC_002950_PG1444_PG1446|hypothetical protein:MATE efflux family protein|POSITIVE:NEGATIVE|[1529303,1529997]|695 HSP 1 e-value: 1.0E-158 bit: 557.0 Len: 285 Query Start:4 Query End:288 Subject Strand: NEGATIVE Subject Start: 411 Subject End: 695 ...acataaaagatatgattatgctaagacttactcaaactgaagactttaagacaataatctctttatgctctacaaaaggacagatacaaaaagcgtcagacaactttattctgaagattattgccctatgtgatgcagaaagagatttagtctcattgtttcggaccctccgttatacacgcttttgcctgcaaccgttgcaaaggggagattcaatggacggagaggggaaaaaatgtatcagaactgctctttgtcattgacacggagcttgaattactgaaa ...acataaaagatatgattatgctaagacttactcaaactgaagactttaagacaataatctctttatgctctacaaaaggacagatacaaaaagcgtcagacaactttattctgaagattattgccctatgtgatgcagaaagagatttagtctcattgtttcggaccctccgttatacacgcttttgcctgcaacctttgcaaaggggagattcaatggacggagaggggaaaaaatgtatcagaactgctctttgtcattgacacggagcttgaattactgaaa Subject: NC_002950_PG0827_PG0829|MATE efflux family protein:hypothetical protein|POSITIVE:NEGATIVE|[885665,886359]|695 HSP 1 e-value: 1.0E-158 bit: 557.0 Len: 285 Query Start:4 Query End:288 Subject Strand: POSITIVE Subject Start: 1 Subject End: 285 ...acataaaagatatgattatgctaagacttactcaaactgaagactttaagacaataatctctttatgctctacaaaaggacagatacaaaaagcgtcagacaactttattctgaagattattgccctatgtgatgcagaaagagatttagtctcattgtttcggaccctccgttatacacgcttttgcctgcaaccgttgcaaaggggagattcaatggacggagaggggaaaaaatgtatcagaactgctctttgtcattgacacggagcttgaattactgaaa ...acataaaagatatgattatgctaagacttactcaaactgaagactttaagacaataatctctttatgctctacaaaaggacagatacaaaaagcgtcagacaactttattctgaagattattgccctatgtgatgcagaaagagatttagtctcattgtttcggaccctccgttatacacgcttttgcctgcaacctttgcaaaggggagattcaatggacggagaggggaaaaaatgtatcagaactgctctttgtcattgacacggagcttgaattactgaaa Subject: tfor_TF0922_TF0923|MATE efflux family protein:tetracycline resistance element mobilization regulatory protein|POSITIVE:POSITIVE|[961147,961395]|249 HSP 1 e-value: 2.0E-38 bit: 161.0 Len: 181 Query Start:1 Query End:181 Subject Strand: POSITIVE Subject Start: 7 Subject End: 187 tgaacataaaagatatgattatgctaagacttactcaaactgaagactttaagacaataatctctttatgctctacaaaaggacagatacaaaaagcgtcagacaactttattctgaagattattgccctatgtgatgcagaaagagatttagtctcattgtttcggaccctccgttatac........................................................................................................... tgaacttaaaagatatgattatgctaagacttactcaaacagaaaactttaagataatgctctctttttgttctacaaaagaacagatacaaaaggcgtcagacaactttatattgaaggttgttgctctatgtgatacagaagaagatactgtctcgttgtttcgtatcctccgctatac........................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAACAUAAAAGAUAUGAUUAUGCUAAGACUUACUCAAACUGAAGACUUUAAGACAAUAAUCUCUUUAUGCUCUACAAAAGGACAGAUACAAAAAGCGUCAGACAACUUUAUUCUGAAGAUUAUUGCCCUAUGUGAUGCAGAAAGAGAUUUAGUCUCAUUGUUUCGGACCCUCCGUUAUACACGCUUUUGCCUGCAACCGUUGCAAAGGGGAGAUUCAAUGGACGGAGAGGGGAAAAAAUGUAUCAGAACUGCUCUUUGUCAUUGACACGGAGCUUGAAUUACUGAAA ....((((.....)))).................((((.((((.(((..(.((((...(((((((((.(((..((((..(((...((((.........(((((.........)))))....))))..))).))))..))).)))))))))..)))).)..)))))))...((((((......(.(((((((..((....)).))))))).)....((((((.((((((((.((................)).)))))))))))))).)))))).)))).......... (-67.91) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCAGUAAUUCAAGCUCCGUGUCAAUGACAAAGAGCAGUUCUGAUACAUUUUUUCCCCUCUCCGUCCAUUGAAUCUCCCCUUUGCAACGGUUGCAGGCAAAAGCGUGUAUAACGGAGGGUCCGAAACAAUGAGACUAAAUCUCUUUCUGCAUCACAUAGGGCAAUAAUCUUCAGAAUAAAGUUGUCUGACGCUUUUUGUAUCUGUCCUUUUGUAGAGCAUAAAGAGAUUAUUGUCUUAAAGUCUUCAGUUUGAGUAAGUCUUAGCAUAAUCAUAUCUUUUAUGUUCA ........(((((.((((..((((...))))..))))....((((.((....((((..((((((((((.(((((........)).))).)).((((.((....)).))))..))))))))...))))...((((((..(((((((((.(((.(((((.((((((.......(((((.........))))).((.....))...))))))..))).))))).)))))))))...))))))..))..))))..))))).......(((((((.........))))))).. (-73.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 366 213 171 57 4 pint:PI1845|5end_hypothetical_protein_1791457..1791687_POSITIVE 363 230 183 61 6 pint:PI1736|5end_topoisomerase_IV,_subunit_A_1654254..1654484_POSITIVE 355 230 189 52 7 pint:PI0256|5end_conjugative_transposon_protein,_TraE_249044..249274_POSITIVE 354 235 191 117 71 pint:PI0828|5end_GMP_synthase_(glutamine_amidotransferase)_764077..764307_POSITIVE 351 235 192 133 96 pint:PI0073|5end_dihydropteroate_synthase_70956..71186_POSITIVE 348 230 182 174 125 pint:PI1309|5end_excinuclease_ABC,_A_subunit_1223751..1223981_POSITIVE 343 233 194 87 52 pint:PI1560|5end_integrase_1476962..1477192_POSITIVE 343 209 174 100 65 pint:PI0206|5end_TPR-repeat-containing_protein_198112..198342_POSITIVE 339 230 188 231 185 pint:PI1767|5end_fructokinase,_pfkB_family_1694285..1694515_POSITIVE 332 228 181 164 115 pint:PI0273|5end_hypothetical_protein_262956..263186_POSITIVE 332 228 181 64 15 pint:PI0274|5end_conserved_hypothetical_protein_262856..263086_POSITIVE 328 270 221 195 148 pint:PI1498|5end_probable_membrane_associated_lipoprotein_1418427..1418657_POSITIVE 327 213 171 118 54 pint:PI1604|5end_hypothetical_protein_1534017..1534247_POSITIVE 325 229 184 209 147 pint:PI0029|5end_glutamine_amidotransferase_(GMP_synthase_(glutamine-hydrolyzing))_32593..32823_POSITIVE 322 233 195 54 13 pint:PI0493|5end_surface_antigen_BspA_452844..453074_POSITIVE 321 235 192 52 4 pint:PI0101|5end_lauroyl/myristoyl_acyltransferase_96729..96959_POSITIVE 320 210 165 68 8 pint:PI0221|5end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_212356..212586_POSITIVE 319 229 181 109 57 pint:PI0189|5end_integrase_179623..179853_POSITIVE 318 229 182 74 20 pint:PI0265|5end_conjugative_transposon_protein,_TraO_257296..257526_POSITIVE 314 236 193 183 143 pint:PI0222|5end_conserved_hypothetical_protein_217808..218038_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 235 191 123 77 pint:PI0827|3end_hypothetical_protein_764163..764313_POSITIVE 351 235 192 89 52 pint:PI0072|3end_conserved_hypothetical_protein_70992..71142_POSITIVE 348 230 182 60 11 pint:PI1308|3end_hypothetical_protein_1223717..1223867_POSITIVE 342 230 191 50 6 pint:PI1735|3end_conserved_hypothetical_protein_1654323..1654473_POSITIVE 332 228 181 71 22 pint:PI0272|3end_conserved_hypothetical_protein_262943..263093_POSITIVE 319 229 181 76 24 pint:PI0188|3end_phosphomethylpyrimidine_kinase_179670..179820_POSITIVE 318 229 182 69 15 pint:PI0264|3end_transfer_region-related_protein,_TraN_257371..257521_POSITIVE 318 269 222 50 9 pint:PI0128|3end_dipeptidase,_pathogenicity_island-encoded_protein_D_121826..121976_POSITIVE 314 236 193 91 51 pint:PI0221|3end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_217796..217946_POSITIVE 309 230 191 151 110 pint:PI0825|3end_hypothetical_protein_764196..764346_POSITIVE 306 211 174 50 16 pint:PI0717|3end_conserved_hypothetical_protein_653120..653270_POSITIVE 306 210 164 112 59 pint:PI0377|3end_DNA_primase/mobilizable_transposon,_excision_protein_347823..347973_POSITIVE 304 200 153 129 85 pint:PI0998|3end_possible_flavin_reductase_domain_protein_923336..923486_POSITIVE 303 230 181 66 16 pint:PI1741|3end_lipid-A-disaccharide_synthase_1663856..1664006_POSITIVE 302 234 191 137 85 pint:PI1178|3end_histidyl-tRNA_synthetase_1100564..1100714_POSITIVE 302 210 168 109 55 pint:PI1143|3end_hypothetical_protein_1070504..1070654_POSITIVE 301 210 165 56 3 pint:PI1943|3end_hypothetical_protein_1902206..1902356_POSITIVE 300 237 192 83 30 pint:PI1490|3end_GTP_cyclohydrolase_I_1409127..1409277_POSITIVE 299 233 192 79 35 pint:PI0084|3end_conserved_hypothetical_protein_84520..84670_POSITIVE 299 236 193 105 69 pint:PI0059|3end_peptide_chain_release_factor_RF-2_58171..58321_POSITIVE