Origin IGS: taagtaaaaaagattataaaatacagacagaagtatgattaaaagcaagtttttactgttggcagcattagccattacagtgctttcaagttgtggaggaggcaaacgcgagttgcccaagaacaacgagtatccc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gggatactcgttgttcttgggcaactcgcgtttgcctcctccacaacttgaaagcactgtaatggctaatgctgccaacagtaaaaacttgcttttaatcatacttctgtctgtattttataatcttttttactta Mask Tandem Repeat Region ================================================ taagtaaaaaagattataaaatacagacagaagtatgattaaaagcaagtttttactgttggcagcattagccattacagtgctttcaagttgtggaggaggcaaacgcgagttgcccaagaacaacgagtatccc Find is-nt database================================================ Query_seq: PI1515:PI1516|PI1515:PI1516:hypothetical protein:multidrug resistance protein; HlyD family secretion protein:->->:1434385..1434520 136 taagtaaaaaagattataaaatacagacagaagtatgattaaaagcaagtttttactgttggcagcattagccattacagtgctttcaagttgtggaggaggcaaacgcgagttgcccaagaacaacgagtatccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1515:PI1516|PI1515:PI1516:hypothetical protein:multidrug resistance protein; HlyD family secretion protein:->->:1434385..1434520 136 taagtaaaaaagattataaaatacagacagaagtatgattaaaagcaagtttttactgttggcagcattagccattacagtgctttcaagttgtggaggaggcaaacgcgagttgcccaagaacaacgagtatccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1515:PI1516|PI1515:PI1516:hypothetical protein:multidrug resistance protein; HlyD family secretion protein:->->:1434385..1434520 136 taagtaaaaaagattataaaatacagacagaagtatgattaaaagcaagtttttactgttggcagcattagccattacagtgctttcaagttgtggaggaggcaaacgcgagttgcccaagaacaacgagtatccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagtaaaaaagattataaaatacagacagaagtatgattaaaagcaagtttttactgttggcagcattagccattacagtgctttcaagttgtggaggaggcaaacgcgagttgcccaagaacaacgagtatccc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 35 End: 136 .................................. M I K S K F L L L A A L A I T V L S S C G G G K R E L P K N N E Y P Protein_Len: 42 Strand: - Start: 1 End: 126 L Y F L N Y F V S L L I I L L L N K S N A A N A M V T S E L Q P P P L R S N G L F M .......... taagtaaaaaagattataaaatacagacagaagtatgattaaaagcaagtttttactgttggcagcattagccattacagtgctttcaagttgtggaggaggcaaacgcgagttgcccaagaacaacgagtatccc 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================================================ taagtaaaaaagattataaaatacagacagaagtatgattaaaagcaagtttttactgttggcagcattagccattacagtgctttcaagttgtggaggaggcaaacgcgagttgcccaagaacaacgagtatccc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1515:PI1516|PI1515:PI1516:hypothetical protein:multidrug resistance protein; HlyD family secretion protein:->->:1434385..1434520 136 taagtaaaaaagattataaaatacagacagaagtatgattaaaagcaagtttttactgttggcagcattagccattacagtgctttcaagttgtggaggaggcaaacgcgagttgcccaagaacaacgagtatccc Intra-Species Hit: Count: 1 Min: 1 Max: 136 Len: 136 Subject: pint_PI1515_PI1516|hypothetical protein:multidrug resistance protein; HlyD family secretion protein|POSITIVE:POSITIVE|[1434385,1434520]|136 HSP 1 e-value: 1.0E-71 bit: 270.0 Len: 136 Query Start:1 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 136 taagtaaaaaagattataaaatacagacagaagtatgattaaaagcaagtttttactgttggcagcattagccattacagtgctttcaagttgtggaggaggcaaacgcgagttgcccaagaacaacgagtatccc taagtaaaaaagattataaaatacagacagaagtatgattaaaagcaagtttttactgttggcagcattagccattacagtgctttcaagttgtggaggaggcaaacgcgagttgcccaagaacaacgagtatccc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUAAAAAAGAUUAUAAAAUACAGACAGAAGUAUGAUUAAAAGCAAGUUUUUACUGUUGGCAGCAUUAGCCAUUACAGUGCUUUCAAGUUGUGGAGGAGGCAAACGCGAGUUGCCCAAGAACAACGAGUAUCCC ..((((((((...((.(((.((((........))))..))).)).....))))))))..((((.......)))).....((((((....(((((....(.(((((.(....)))))))....)))))))))))... (-28.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGAUACUCGUUGUUCUUGGGCAACUCGCGUUUGCCUCCUCCACAACUUGAAAGCACUGUAAUGGCUAAUGCUGCCAACAGUAAAAACUUGCUUUUAAUCAUACUUCUGUCUGUAUUUUAUAAUCUUUUUUACUUA (((((((..(((((....((((((.......)))))).....))))).((((((((((((..((((.......)))))))))........)))))))...............)))))))................. (-28.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 410 108 62 77 33 pint:PI1045|5end_cytidine/deoxycytidylate_deaminase_family_protein_965104..965334_POSITIVE 357 117 71 53 16 pint:PI1781|5end_membrane-associated_zinc_metalloprotease_1713074..1713304_POSITIVE 349 116 71 131 82 pint:PI0705|5end_conserved_hypothetical_protein;_possible_lipoprotein_641274..641504_POSITIVE 342 108 61 65 11 pint:PI0765|5end_conserved_hypothetical_protein;_possible_surface_protein_699753..699983_POSITIVE 333 130 81 82 37 pint:PI1816|5end_acid_phosphatase_1754646..1754876_POSITIVE 332 128 88 56 12 pint:PI0106|5end_ABC_transport_system,_ATP-binding/permease_101381..101611_POSITIVE 329 110 69 111 73 pint:PI1440|5end_conserved_hypothetical_protein_1357185..1357415_POSITIVE 326 130 81 88 35 pint:PI0668|5end_peptidyl-prolyl_cis-trans_isomerase_SlyD,_FKBP-type_(peptidylprolyl_isomerase)_610216..610446_POSITIVE 323 93 56 196 148 pint:PI1332|5end_aminotransferase,_possible_pyridoxal-phosphate-dependent_aminotransferase_1249374..1249604_POSITIVE 321 130 81 64 22 pint:PI2159|5end_immunoreactive_84_kDa_antigen_PG93_2105267..2105497_POSITIVE 318 108 62 94 41 pint:PI2162|5end_conserved_hypothetical_protein_2108796..2109026_POSITIVE 317 119 80 70 20 pint:PI0009|5end_NAD-dependent_epimerase/dehydratase_family_protein_9653..9883_POSITIVE 315 130 95 34 1 pint:PI0175|5end_succinyl-CoA_synthetase_beta_subunit_167023..167253_POSITIVE 313 98 55 220 186 pint:PI1728|5end_ATP-dependent_Clp_protease,_proteolytic_subunit_1646916..1647146_POSITIVE 311 100 57 199 155 pint:PI1263|5end_probable_integrase_1184502..1184732_POSITIVE 311 127 92 200 163 pint:PI0198|5end_hypothetical_protein_190719..190949_POSITIVE 309 117 73 230 182 pint:PI1231|5end_hypothetical_protein_1153175..1153405_POSITIVE 308 117 75 77 31 pint:PI1145|5end_50S_ribosomal_protein_L35_1072520..1072750_POSITIVE 308 117 80 52 14 pint:PI0244|5end_possible_mobilization_protein_C_240752..240982_POSITIVE 307 117 72 165 119 pint:PI0578|5end_methyltransferase_522646..522876_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 116 71 141 92 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 332 128 88 48 4 pint:PI0105|3end_possible_sulfatase_101453..101603_POSITIVE 330 90 43 149 77 pint:PI1380|3end_conserved_hypothetical_protein_1303242..1303392_POSITIVE 329 110 69 121 83 pint:PI1438|3end_penicillin_tolerance_protein/steroid_biosynthesis_1357275..1357425_POSITIVE 321 130 81 64 22 pint:PI2158|3end_glycosyl_transferase,_group_2_family_protein_2105347..2105497_POSITIVE 307 110 61 70 14 pint:PI0906|3end_hypothetical_protein_836008..836158_POSITIVE 307 117 72 139 93 pint:PI0577|3end_conserved_hypothetical_protein_522700..522850_POSITIVE 306 110 61 56 3 pint:PI0750|3end_zinc_protease_680633..680783_POSITIVE 303 103 61 62 14 pint:PI1541|3end_hypothetical_protein_1461884..1462034_POSITIVE 301 120 71 78 32 pint:PI0411|3end_conserved_hypothetial_protein;_possible_hydrolase_379828..379978_POSITIVE 294 119 71 59 19 pint:PI1402|3end_3-deoxy-7-phosphoheptulonate_synthase_1323980..1324130_POSITIVE 291 119 71 144 100 pint:PI1490|3end_GTP_cyclohydrolase_I_1409127..1409277_POSITIVE 289 124 82 71 20 pint:PI1761|3end_hypothetical_protein_1684543..1684693_POSITIVE 288 117 74 141 98 pint:PI0584|3end_hypothetical_protein_527656..527806_POSITIVE 287 117 71 118 56 pint:PI0768|3end_conserved_hypothetical_protein;_possible_acetyltransferase_704661..704811_POSITIVE 286 129 87 83 28 pint:PI1270|3end_probable_dipeptidyl_peptidase_1190829..1190979_POSITIVE 285 87 43 133 90 pint:PI0748|3end_possible_mobilization_protein_677214..677364_POSITIVE 284 118 71 139 61 pint:PI1676|3end_phosphatidate_cytidylyltransferase_1591773..1591923_POSITIVE 281 96 51 150 104 pint:PI1893|3end_phospho-N-acetylmuramoyl-pentapeptide-transferase__1836972..1837122_POSITIVE 281 106 61 68 25 pint:PI0891|3end_transketolase_822905..823055_POSITIVE