Origin IGS: agataaagaaattaatcccatttcgaatgagtttattaggattcttttatttgataggatgaatttgaggttttcaatgccaaaaatatattataattcctctattgctatcatattattgaaaaaatcactatctttgcaatca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgattgcaaagatagtgattttttcaataatatgatagcaatagaggaattataatatatttttggcattgaaaacctcaaattcatcctatcaaataaaagaatcctaataaactcattcgaaatgggattaatttctttatct Mask Tandem Repeat Region ================================================ agataaagaaattaatcccatttcgaatgagtttattaggattcttttatttgataggatgaatttgaggttttcaatgccaaaaatatattataattcctctattgctatcatattattgaaaaaatcactatctttgcaatca Find is-nt database================================================ Query_seq: PI0402:PI0403|PI0402:PI0403:conserved hypothetical protein:probable integrase:->->:370084..370228 145 agataaagaaattaatcccatttcgaatgagtttattaggattcttttatttgataggatgaatttgaggttttcaatgccaaaaatatattataattcctctattgctatcatattattgaaaaaatcactatctttgcaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0402:PI0403|PI0402:PI0403:conserved hypothetical protein:probable integrase:->->:370084..370228 145 agataaagaaattaatcccatttcgaatgagtttattaggattcttttatttgataggatgaatttgaggttttcaatgccaaaaatatattataattcctctattgctatcatattattgaaaaaatcactatctttgcaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0402:PI0403|PI0402:PI0403:conserved hypothetical protein:probable integrase:->->:370084..370228 145 agataaagaaattaatcccatttcgaatgagtttattaggattcttttatttgataggatgaatttgaggttttcaatgccaaaaatatattataattcctctattgctatcatattattgaaaaaatcactatctttgcaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agataaagaaattaatcccatttcgaatgagtttattaggattcttttatttgataggatgaatttgaggttttcaatgccaaaaatatattataattcctctattgctatcatattattgaaaaaatcactatctttgcaatca Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 11 End: 145 .......... M N P I S N E F I R I L L F D R M N L R F S M P K I Y Y N S S I A I I L L K K S L S L Q S agataaagaaattaatcccatttcgaatgagtttattaggattcttttatttgataggatgaatttgaggttttcaatgccaaaaatatattataattcctctattgctatcatattattgaaaaaatcactatctttgcaatca 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================================================ agataaagaaattaatcccatttcgaatgagtttattaggattcttttatttgataggatgaatttgaggttttcaatgccaaaaatatattataattcctctattgctatcatattattgaaaaaatcactatctttgcaatca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0402:PI0403|PI0402:PI0403:conserved hypothetical protein:probable integrase:->->:370084..370228 145 agataaagaaattaatcccatttcgaatgagtttattaggattcttttatttgataggatgaatttgaggttttcaatgccaaaaatatattataattcctctattgctatcatattattgaaaaaatcactatctttgcaatca Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: pint_PI0402_PI0403|conserved hypothetical protein:probable integrase|POSITIVE:POSITIVE|[370084,370228]|145 HSP 1 e-value: 5.0E-77 bit: 287.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 145 agataaagaaattaatcccatttcgaatgagtttattaggattcttttatttgataggatgaatttgaggttttcaatgccaaaaatatattataattcctctattgctatcatattattgaaaaaatcactatctttgcaatca agataaagaaattaatcccatttcgaatgagtttattaggattcttttatttgataggatgaatttgaggttttcaatgccaaaaatatattataattcctctattgctatcatattattgaaaaaatcactatctttgcaatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUAAAGAAAUUAAUCCCAUUUCGAAUGAGUUUAUUAGGAUUCUUUUAUUUGAUAGGAUGAAUUUGAGGUUUUCAAUGCCAAAAAUAUAUUAUAAUUCCUCUAUUGCUAUCAUAUUAUUGAAAAAAUCACUAUCUUUGCAAUCA .(.((((((.....((((....(((((((((..............)))))))))..)))).....(((..(((((((((......((((..((((((......)))).))..)))))))))))))..)))...)))))))..... (-20.74) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUGCAAAGAUAGUGAUUUUUUCAAUAAUAUGAUAGCAAUAGAGGAAUUAUAAUAUAUUUUUGGCAUUGAAAACCUCAAAUUCAUCCUAUCAAAUAAAAGAAUCCUAAUAAACUCAUUCGAAAUGGGAUUAAUUUCUUUAUCU ..((((.((((((....)))))).))))............((((((((((((.....(((((.(((...((((.........))))..)))..)))))................(((((.....)))))..)))))))))))).. (-17.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 235 81 57 219 193 pint:PI2100|5end_conserved_hypothetical_protein_2053351..2053581_POSITIVE 215 47 2 153 104 pint:PI0847|5end_thiamine_biosynthesis_lipoprotein,_ApbE_781130..781360_POSITIVE 208 71 35 150 109 pint:PI0229|5end_hypothetical_protein_228146..228376_POSITIVE 198 80 51 157 128 pint:PI1708|5end_hypothetical_protein_1625087..1625317_POSITIVE 197 140 117 45 22 pint:PI0770|5end_hypothetical_protein_706170..706400_POSITIVE 195 140 118 187 163 pint:PI1912|5end_possible_DNA_repair_protein_1856364..1856594_POSITIVE 192 83 42 124 76 pint:PI1488|5end_hypothetical_protein_1406994..1407224_POSITIVE 190 81 56 46 21 pint:PI1703|5end_conserved_hypothetical_protein_1620876..1621106_POSITIVE 189 73 35 212 167 pint:PI1073|5end_hemogluttinin_A-related_protein_(HagA)_990593..990823_POSITIVE 188 49 17 80 39 pint:PI1532|5end_uridylate_kinase_1451644..1451874_POSITIVE 185 63 39 27 4 pint:PI2060|5end_conserved_hypothetical_protein;_possible_metalloprotease_2017595..2017825_POSITIVE 183 81 54 107 79 pint:PI1036|5end_ATP-dependent__Lon_protease_954446..954676_POSITIVE 183 110 67 162 127 pint:PI0441|5end_50S_ribosomal_protein_L11_411182..411412_POSITIVE 182 83 51 36 1 pint:PI0002|5end_conserved_hypothetical_protein_2972..3202_POSITIVE 181 62 24 146 107 pint:PI1332|5end_aminotransferase,_possible_pyridoxal-phosphate-dependent_aminotransferase_1249374..1249604_POSITIVE 181 70 21 124 86 pint:PI0799|5end_alpha-amylase_family_protein_737083..737313_POSITIVE 180 100 53 137 90 pint:PI1976|5end_hypothetical_protein_1932993..1933223_POSITIVE 180 83 43 206 171 pint:PI0870|5end_branched-chain_amino_acid_aminotransferase_805933..806163_POSITIVE 179 80 32 176 134 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 179 76 35 74 29 pint:PI0230|5end_hypothetical_protein_228590..228820_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 235 81 57 65 39 pint:PI2099|3end_D-alanyl-D-alanine_dipeptidase_2053277..2053427_POSITIVE 211 69 21 108 48 pint:PI0590|3end_ribosomal_large_subunit_pseudouridine_synthase_B_538545..538695_POSITIVE 208 71 35 128 87 pint:PI0228|3end_outer_membrane_cobalamin_receptor_protein_228204..228354_POSITIVE 207 46 1 77 30 pint:PI1345|3end_conserved_hypothetical_protein;_possible_TPR-repeat-containing_protein_1260680..1260830_POSITIVE 198 80 51 139 110 pint:PI1707|3end_GTP-binding_protein_1625149..1625299_POSITIVE 197 140 117 149 126 pint:PI0770|3end_hypothetical_protein_706354..706504_POSITIVE 194 83 45 144 106 pint:PI1082|3end_polypeptide_deformylase_1001922..1002072_POSITIVE 194 140 98 42 2 pint:PI0508|3end_possible_cell_filamentation_protein_467436..467586_POSITIVE 193 63 24 79 33 pint:PI0003|3end_pseudouridylate_synthase_6044..6194_POSITIVE 192 83 42 112 64 pint:PI1486|3end_alginate_O-acetylation_protein_1407062..1407212_POSITIVE 190 96 54 126 96 pint:PI0576|3end_helicase,_UvrD/Rep_521724..521874_POSITIVE 188 49 17 90 49 pint:PI1531|3end_biotin--acetyl-CoA-carboxylase_ligase_1451734..1451884_POSITIVE 183 81 54 114 86 pint:PI1035|3end_queuine_tRNA-ribosyltransferase_(tRNA-guanine_transglycosylase)_954533..954683_POSITIVE 183 110 67 104 69 pint:PI0440|3end_transcription_antiterminator_411204..411354_POSITIVE 182 80 38 48 3 pint:PI0864|3end_dihydrodipicolinate_synthase_801458..801608_POSITIVE 181 113 71 85 46 pint:PI0866|3end_hypothetical_protein_803993..804143_POSITIVE 178 60 17 49 3 pint:PI0525|3end_transcriptional_regulator,_Arac_family_482275..482425_POSITIVE 178 140 103 119 89 pint:PI0423|3end_hypothetical_protein_388432..388582_POSITIVE 177 69 24 66 17 pint:PI1796|3end_2-hydroxyhepta-2,4-diene-1,7-dioate_isomerase,_fumarylacetoacetate_hydrolase_family_protein_1731086..1731236_POSITIVE 176 140 105 60 25 pint:PI0021|3end_orotate_phosphoribosyltransferase_25648..25798_POSITIVE