Origin IGS: taatttcttcatcatacaaaaaagtcattctatcatataaaagagaagagccactctcgctgtagtacaaagagagtggctcttatatattaataaggtagtggaaatataacta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagttatatttccactaccttattaatatataagagccactctctttgtactacagcgagagtggctcttctcttttatatgatagaatgacttttttgtatgatgaagaaatta Mask Tandem Repeat Region ================================================ taatttcttcatcatacaaaaaagtcattctatcatataaaagagaagagccactctcgctgtagtacaaagagagtggctcttatatattaataaggtagtggaaatataacta Find is-nt database================================================ Query_seq: PI1404:PI1405|PI1404:PI1405:hypothetical protein:conserved hypothetical protein:->->:1326060..1326174 115 taatttcttcatcatacaaaaaagtcattctatcatataaaagagaagagccactctcgctgtagtacaaagagagtggctcttatatattaataaggtagtggaaatataacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1404:PI1405|PI1404:PI1405:hypothetical protein:conserved hypothetical protein:->->:1326060..1326174 115 taatttcttcatcatacaaaaaagtcattctatcatataaaagagaagagccactctcgctgtagtacaaagagagtggctcttatatattaataaggtagtggaaatataacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1404:PI1405|PI1404:PI1405:hypothetical protein:conserved hypothetical protein:->->:1326060..1326174 115 taatttcttcatcatacaaaaaagtcattctatcatataaaagagaagagccactctcgctgtagtacaaagagagtggctcttatatattaataaggtagtggaaatataacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatttcttcatcatacaaaaaagtcattctatcatataaaagagaagagccactctcgctgtagtacaaagagagtggctcttatatattaataaggtagtggaaatataacta Predict ORF larger than 30AA ================================================ taatttcttcatcatacaaaaaagtcattctatcatataaaagagaagagccactctcgctgtagtacaaagagagtggctcttatatattaataaggtagtggaaatataacta 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================================================ taatttcttcatcatacaaaaaagtcattctatcatataaaagagaagagccactctcgctgtagtacaaagagagtggctcttatatattaataaggtagtggaaatataacta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -13.7 Tail_Score: -4.57353 Start: 43 End: 87 Full_Region: actaccttattaata tataagagccactctctttgt act acagcgagagtggctcttctc ttttatatgatagaa ..........................................tataagagccactctctttgtactacagcgagagtggctcttctc............................ TransTerm Strand: - Conf: 100 HP_score: -18.0 Tail_Score: -4.05861 Start: 48 End: 82 Full_Region: cttattaatatataa gagccactctctttgt act acagcgagagtggctc ttctcttttatatga ...............................................gagccactctctttgtactacagcgagagtggctc................................. Find igs database================================================ Query_seq: PI1404:PI1405|PI1404:PI1405:hypothetical protein:conserved hypothetical protein:->->:1326060..1326174 115 taatttcttcatcatacaaaaaagtcattctatcatataaaagagaagagccactctcgctgtagtacaaagagagtggctcttatatattaataaggtagtggaaatataacta Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: pint_PI1404_PI1405|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1326060,1326174]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 taatttcttcatcatacaaaaaagtcattctatcatataaaagagaagagccactctcgctgtagtacaaagagagtggctcttatatattaataaggtagtggaaatataacta taatttcttcatcatacaaaaaagtcattctatcatataaaagagaagagccactctcgctgtagtacaaagagagtggctcttatatattaataaggtagtggaaatataacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUCUUCAUCAUACAAAAAAGUCAUUCUAUCAUAUAAAAGAGAAGAGCCACUCUCGCUGUAGUACAAAGAGAGUGGCUCUUAUAUAUUAAUAAGGUAGUGGAAAUAUAACUA ........................((...(((((.(((.......(((((((((((((..((.....))..)))))))))))))........))).)))))..)).......... (-31.26) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUUAUAUUUCCACUACCUUAUUAAUAUAUAAGAGCCACUCUCUUUGUACUACAGCGAGAGUGGCUCUUCUCUUUUAUAUGAUAGAAUGACUUUUUUGUAUGAUGAAGAAAUUA ...............................(((((((((((((.(((.....))).))))))))))))).(((((......((((((......)))))).....)))))..... (-30.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 84 44 85 51 pint:PI1760|5end_hypothetical_protein_1684413..1684643_POSITIVE 302 84 42 206 165 pint:PI1178|5end_histidyl-tRNA_synthetase_1099249..1099479_POSITIVE 301 90 42 199 158 pint:PI0815|5end_hypothetical_protein_754475..754705_POSITIVE 299 89 44 212 173 pint:PI1870|5end_hypothetical_protein_1815302..1815532_POSITIVE 299 89 44 41 2 pint:PI1869|5end_hypothetical_protein_1815131..1815361_POSITIVE 297 85 42 70 17 pint:PI1043|5end_conserved_hypothetical_protein_960855..961085_POSITIVE 270 80 36 132 92 pint:PI0574|5end_hypothetical_protein_519260..519490_POSITIVE 267 110 61 74 31 pint:PI1428|5end_quinolinate_synthetase_A_1346626..1346856_POSITIVE 249 84 44 124 90 pint:PI1948|5end_hypothetical_protein_1903084..1903314_POSITIVE 249 82 50 150 122 pint:PI0732|5end_conserved_hypothetical_protein_663598..663828_POSITIVE 247 91 51 136 97 pint:PI0241|5end_possible_tetracycline_resistance_element_/mobilization_regulatory_protein_239627..239857_POSITIVE 246 80 41 167 125 pint:PI0786|5end_conserved_hypothetical_protein;_possible_glycosyltransferase_723240..723470_POSITIVE 246 80 41 71 29 pint:PI0783|5end_hypothetical_protein_723144..723374_POSITIVE 242 82 48 158 122 pint:PI2097|5end_conserved_hypothetical_protein_2050912..2051142_POSITIVE 242 81 51 163 132 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 241 80 33 73 24 pint:PI0253|5end_conjugative_transposon_protein,_TraD_248294..248524_POSITIVE 239 87 44 64 16 pint:PI2141|5end_hypothetical_protein_2087169..2087399_POSITIVE 234 80 39 119 73 pint:PI2089|5end_conserved_hypothetical_protein_2046200..2046430_POSITIVE 232 86 49 222 182 pint:PI0442|5end_50S_ribosomal_protein_L1_411644..411874_POSITIVE 229 80 57 170 150 pint:PI2115|5end_hypothetical_protein_2064966..2065196_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 491 84 46 45 7 pint:PI1404|3end_hypothetical_protein_1325999..1326149_POSITIVE 319 84 44 135 101 pint:PI1761|3end_hypothetical_protein_1684543..1684693_POSITIVE 301 90 42 70 29 pint:PI0814|3end_conserved_hypothetical_protein_754426..754576_POSITIVE 268 84 48 31 1 pint:PI1177|3end_hypothtical_protein_1099154..1099304_POSITIVE 262 80 45 123 94 pint:PI1577|3end_conserved_hypothetical_protein_1503879..1504029_POSITIVE 259 84 41 44 5 pint:PI0685|3end_elongation_factor_G_623048..623198_POSITIVE 255 89 49 47 14 pint:PI1706|3end_GTP-binding_protein_1623668..1623818_POSITIVE 249 82 50 145 117 pint:PI0731|3end_conserved_hypothetical_protein_663673..663823_POSITIVE 246 80 41 150 108 pint:PI0784|3end_possible_amidase_enhancer_precursor_723303..723453_POSITIVE 242 82 48 50 14 pint:PI2096|3end_conserved_hypothetical_protein;_possible_phosphoesterase_2050884..2051034_POSITIVE 241 80 33 82 33 pint:PI0252|3end_conserved_hypothetical_protein_248383..248533_POSITIVE 240 80 51 80 50 pint:PI0684|3end_coproporphyrinogen_III_oxidase_620507..620657_POSITIVE 238 80 43 133 82 pint:PI0304|3end_hypothetical_protein_289705..289855_POSITIVE 232 87 42 78 20 pint:PI0904|3end_conserved_hypothetical_protein_834295..834445_POSITIVE 229 100 55 73 18 pint:PI0717|3end_conserved_hypothetical_protein_653120..653270_POSITIVE 229 84 41 113 73 pint:PI0200|3end_hypothetical_protein_191735..191885_POSITIVE 229 79 45 56 17 pint:PI0159|3end_hypothetical_protein_152120..152270_POSITIVE 227 81 47 45 7 pint:PI0436|3end_integrase/recombinase_408221..408371_POSITIVE 227 107 62 97 46 pint:PI0188|3end_phosphomethylpyrimidine_kinase_179670..179820_POSITIVE 225 80 50 25 1 pint:PI1639|3end_conserved_hypothetical_protein_1558133..1558283_POSITIVE