Origin IGS: tgtttctccattgttaaagggagcatttccatatcctcctacttcgtgataatcgcttattaaacgttggtttgcttcaatttgtggtttagcctttgccaccactcctgaaaggactggtgtattcatcatctgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acagatgatgaatacaccagtcctttcaggagtggtggcaaaggctaaaccacaaattgaagcaaaccaacgtttaataagcgattatcacgaagtaggaggatatggaaatgctccctttaacaatggagaaaca Mask Tandem Repeat Region ================================================ tgtttctccattgttaaagggagcatttccatatcctcctacttcgtgataatcgcttattaaacgttggtttgcttcaatttgtggtttagcctttgccaccactcctgaaaggactggtgtattcatcatctgt Find is-nt database================================================ Query_seq: PI1991:PI1992|PI1991:PI1992:conserved hypothetical protein:hypothetical protein:->->:1946431..1946566 136 tgtttctccattgttaaagggagcatttccatatcctcctacttcgtgataatcgcttattaaacgttggtttgcttcaatttgtggtttagcctttgccaccactcctgaaaggactggtgtattcatcatctgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1991:PI1992|PI1991:PI1992:conserved hypothetical protein:hypothetical protein:->->:1946431..1946566 136 tgtttctccattgttaaagggagcatttccatatcctcctacttcgtgataatcgcttattaaacgttggtttgcttcaatttgtggtttagcctttgccaccactcctgaaaggactggtgtattcatcatctgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1991:PI1992|PI1991:PI1992:conserved hypothetical protein:hypothetical protein:->->:1946431..1946566 136 tgtttctccattgttaaagggagcatttccatatcctcctacttcgtgataatcgcttattaaacgttggtttgcttcaatttgtggtttagcctttgccaccactcctgaaaggactggtgtattcatcatctgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtttctccattgttaaagggagcatttccatatcctcctacttcgtgataatcgcttattaaacgttggtttgcttcaatttgtggtttagcctttgccaccactcctgaaaggactggtgtattcatcatctgt Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: - Start: 1 End: 132 T E G N N F P A N G Y G G V E H Y D S I L R Q N A E I Q P K A K A V V G S L V P T N M M .... tgtttctccattgttaaagggagcatttccatatcctcctacttcgtgataatcgcttattaaacgttggtttgcttcaatttgtggtttagcctttgccaccactcctgaaaggactggtgtattcatcatctgt 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================================================ tgtttctccattgttaaagggagcatttccatatcctcctacttcgtgataatcgcttattaaacgttggtttgcttcaatttgtggtttagcctttgccaccactcctgaaaggactggtgtattcatcatctgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1991:PI1992|PI1991:PI1992:conserved hypothetical protein:hypothetical protein:->->:1946431..1946566 136 tgtttctccattgttaaagggagcatttccatatcctcctacttcgtgataatcgcttattaaacgttggtttgcttcaatttgtggtttagcctttgccaccactcctgaaaggactggtgtattcatcatctgt Intra-Species Hit: Count: 1 Min: 1 Max: 136 Len: 136 Subject: pint_PI1991_PI1992|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1946431,1946566]|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 tgtttctccattgttaaagggagcatttccatatcctcctacttcgtgataatcgcttattaaacgttggtttgcttcaatttgtggtttagcctttgccaccactcctgaaaggactggtgtattcatcatctgt tgtttctccattgttaaagggagcatttccatatcctcctacttcgtgataatcgcttattaaacgttggtttgcttcaatttgtggtttagcctttgccaccactcctgaaaggactggtgtattcatcatctgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUCUCCAUUGUUAAAGGGAGCAUUUCCAUAUCCUCCUACUUCGUGAUAAUCGCUUAUUAAACGUUGGUUUGCUUCAAUUUGUGGUUUAGCCUUUGCCACCACUCCUGAAAGGACUGGUGUAUUCAUCAUCUGU .(((...((((........((((((...(((..............(((.....)))...........)))..)))))).....))))...)))......(((((.(((.....))).))))).............. (-26.53) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAGAUGAUGAAUACACCAGUCCUUUCAGGAGUGGUGGCAAAGGCUAAACCACAAAUUGAAGCAAACCAACGUUUAAUAAGCGAUUAUCACGAAGUAGGAGGAUAUGGAAAUGCUCCCUUUAACAAUGGAGAAACA ...((((((.....(((((.(((.....))).)))))((...((.....))........((((........)))).....)).))))))..((((..((((.((......)).))))))))............... (-27.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 109 65 163 122 pint:PI0261|5end_conjugative_transposon_protein,_TraK_254065..254295_POSITIVE 328 110 65 69 19 pint:PI0932|5end_conserved_hypothetical_protein;_possible_hemin_receptor_863854..864084_POSITIVE 317 129 83 91 31 pint:PI1848|5end_hypothetical_protein_1793799..1794029_POSITIVE 315 122 81 49 15 pint:PI1438|5end_penicillin_tolerance_protein/steroid_biosynthesis_1356263..1356493_POSITIVE 313 58 11 168 123 pint:PI0380|5end_conserved_hypothetical_protein_350162..350392_POSITIVE 310 127 81 169 108 pint:PI0265|5end_conjugative_transposon_protein,_TraO_257296..257526_POSITIVE 307 80 31 217 170 pint:PI2022|5end_hypothetical_protein_1978631..1978861_POSITIVE 307 80 31 171 124 pint:PI2023|5end_hypothetical_protein_1978585..1978815_POSITIVE 305 110 69 116 73 pint:PI1475|5end_possible_short_chain_dehydrogenase_1397142..1397372_POSITIVE 303 115 71 204 150 pint:PI0460|5end_50S_ribosomal_protein_L3_432471..432701_POSITIVE 302 110 68 61 19 pint:PI0262|5end_conserved_hypothetical_protein_254685..254915_POSITIVE 290 47 7 146 107 pint:PI1083|5end_TPR-repeat-containing_protein_1001975..1002205_POSITIVE 290 102 65 199 165 pint:PI0562|5end_conserved_hypothetical_protein_509096..509326_POSITIVE 290 102 65 55 21 pint:PI0561|5end_hypothetical_protein_508952..509182_POSITIVE 289 123 83 154 112 pint:PI0122|5end_outer_membrane_protein,_ompH_family_113319..113549_POSITIVE 287 57 12 222 165 pint:PI0506|5end_conserved_hypothetical_protein_465501..465731_POSITIVE 285 119 72 150 102 pint:PI1516|5end_multidrug_resistance_protein;_HlyD_family_secretion_protein_1434381..1434611_POSITIVE 285 124 82 158 123 pint:PI0691|5end_hypothetical_protein_627885..628115_POSITIVE 283 110 64 69 6 pint:PI0700|5end_UDP-glucose_4-epimerase_637299..637529_POSITIVE 282 110 68 218 177 pint:PI1163|5end_single-strand_DNA_binding_protein_1087757..1087987_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 109 65 140 99 pint:PI0260|3end_conjugative_transposon_protein,_TraJ_254122..254272_POSITIVE 317 129 83 61 1 pint:PI1847|3end_conserved_hypothetical_protein;_possible_integral_membrane_protein_1793849..1793999_POSITIVE 315 122 81 113 79 pint:PI1437|3end_hypothetical_protein_1356407..1356557_POSITIVE 307 80 31 137 90 pint:PI2021|3end_DNA_repair_protein_1978631..1978781_POSITIVE 303 115 71 120 66 pint:PI0459|3end_30S_ribosomal_protein_S10_432467..432617_POSITIVE 302 110 68 61 19 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 284 109 65 122 72 pint:PI1706|3end_GTP-binding_protein_1623668..1623818_POSITIVE 282 109 66 132 87 pint:PI1726|3end_ATP-dependent_DNA_helicase_1645542..1645692_POSITIVE 282 110 68 133 92 pint:PI1162|3end_hemolysin-related_protein,_with_CBS_domain_1087752..1087902_POSITIVE 273 129 81 66 10 pint:PI1825|3end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_1765705..1765855_POSITIVE 269 98 56 118 74 pint:PI0959|3end_uridine_kinase_891204..891354_POSITIVE 268 110 67 120 88 pint:PI0639|3end_small_heat_shock_protein_583165..583315_POSITIVE 268 99 55 117 61 pint:PI0109|3end_hypothetical_protein_107183..107333_POSITIVE 265 109 72 151 112 pint:PI1073|3end_hemogluttinin_A-related_protein_(HagA)_993693..993843_POSITIVE 263 70 21 81 25 pint:PI1807|3end_hypothetical_protein_1742481..1742631_POSITIVE 263 100 51 90 38 pint:PI1187|3end_conserved_hypothetical_protein_1107245..1107395_POSITIVE 261 100 53 61 8 pint:PI1380|3end_conserved_hypothetical_protein_1303242..1303392_POSITIVE 259 97 55 120 70 pint:PI1713|3end_ABC_transporter,_ATP-binding_protein_1630192..1630342_POSITIVE 259 121 85 40 2 pint:PI0858|3end_carbamyl_phosphate_synthase,_large_subunit_793394..793544_POSITIVE 257 122 91 44 15 pint:PI0267|3end_conjugative_transposon_protein,_TraQ_259291..259441_POSITIVE