Origin IGS: gcgttctttatttttgagcgcgttgcgcagctcctctctccatggttcagagcgacgcagtcggataagttcttctgtagtcatgtcaataaggcagaaaataagg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccttattttctgccttattgacatgactacagaagaacttatccgactgcgtcgctctgaaccatggagagaggagctgcgcaacgcgctcaaaaataaagaacgc Mask Tandem Repeat Region ================================================ gcgttctttatttttgagcgcgttgcgcagctcctctctccatggttcagagcgacgcagtcggataagttcttctgtagtcatgtcaataaggcagaaaataagg Find is-nt database================================================ Query_seq: PG2033:PG2034|PG2033:PG2034:glutamate synthase, small subunit:oxidoreductase, FAD-binding, putative:<-<-:2134894..2134999 106 gcgttctttatttttgagcgcgttgcgcagctcctctctccatggttcagagcgacgcagtcggataagttcttctgtagtcatgtcaataaggcagaaaataagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2033:PG2034|PG2033:PG2034:glutamate synthase, small subunit:oxidoreductase, FAD-binding, putative:<-<-:2134894..2134999 106 gcgttctttatttttgagcgcgttgcgcagctcctctctccatggttcagagcgacgcagtcggataagttcttctgtagtcatgtcaataaggcagaaaataagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2033:PG2034|PG2033:PG2034:glutamate synthase, small subunit:oxidoreductase, FAD-binding, putative:<-<-:2134894..2134999 106 gcgttctttatttttgagcgcgttgcgcagctcctctctccatggttcagagcgacgcagtcggataagttcttctgtagtcatgtcaataaggcagaaaataagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcgttctttatttttgagcgcgttgcgcagctcctctctccatggttcagagcgacgcagtcggataagttcttctgtagtcatgtcaataaggcagaaaataagg Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 10 End: 105 ......... M F E R V A Q L L S P W F R A T Q S D K F F C S H V N K A E N K . Protein_Len: 31 Strand: + Start: 14 End: 106 ............. M S A L R S S S L H G S E R R S R I S S S V V M S I R Q K I R Protein_Len: 34 Strand: - Start: 1 End: 102 R E K N K L A N R L E E R W P E S R R L R I L E E T T M D I L C F M .... gcgttctttatttttgagcgcgttgcgcagctcctctctccatggttcagagcgacgcagtcggataagttcttctgtagtcatgtcaataaggcagaaaataagg 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================================================ gcgttctttatttttgagcgcgttgcgcagctcctctctccatggttcagagcgacgcagtcggataagttcttctgtagtcatgtcaataaggcagaaaataagg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG2033:PG2034|PG2033:PG2034:glutamate synthase, small subunit:oxidoreductase, FAD-binding, putative:<-<-:2134894..2134999 106 gcgttctttatttttgagcgcgttgcgcagctcctctctccatggttcagagcgacgcagtcggataagttcttctgtagtcatgtcaataaggcagaaaataagg Intra-Species Hit: Count: 1 Min: 1 Max: 106 Len: 106 Subject: NC_002950_PG2033_PG2034|glutamate synthase, small subunit:oxidoreductase, FAD-binding, putative|NEGATIVE:NEGATIVE|[2134894,2134999]|106 HSP 1 e-value: 6.0E-54 bit: 210.0 Len: 106 Query Start:1 Query End:106 Subject Strand: POSITIVE Subject Start: 1 Subject End: 106 gcgttctttatttttgagcgcgttgcgcagctcctctctccatggttcagagcgacgcagtcggataagttcttctgtagtcatgtcaataaggcagaaaataagg gcgttctttatttttgagcgcgttgcgcagctcctctctccatggttcagagcgacgcagtcggataagttcttctgtagtcatgtcaataaggcagaaaataagg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGUUCUUUAUUUUUGAGCGCGUUGCGCAGCUCCUCUCUCCAUGGUUCAGAGCGACGCAGUCGGAUAAGUUCUUCUGUAGUCAUGUCAAUAAGGCAGAAAAUAAGG ((((((.........)))))).(((((..((((....((....))....))))..))))).((((........))))...((.((((.....))))))........ (-25.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUUAUUUUCUGCCUUAUUGACAUGACUACAGAAGAACUUAUCCGACUGCGUCGCUCUGAACCAUGGAGAGAGGAGCUGCGCAACGCGCUCAAAAAUAAAGAACGC .....(((((((..((((....))))...)))))))...........(((((.(((((...(....).....))))).)))))..(((.((.........)).))) (-21.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1091 70 21 161 112 NC_002950:PG2033|5end_glutamate_synthase,_small_subunit_2134803..2135033_NEGATIVE 404 60 11 198 125 NC_002950:PG0684|5end_ABC_transporter,_permease_protein,_putative_737648..737878_POSITIVE 400 60 11 97 36 NC_002950:PG0091|5end_transporter,_putative_107400..107630_NEGATIVE 397 43 1 143 96 NC_002950:PG1929|5end_ribosomal_protein_S17_2020201..2020431_NEGATIVE 396 70 21 78 25 NC_002950:PG1479|5end_conjugative_transposon_protein_TraJ_1555234..1555464_NEGATIVE 391 57 16 227 187 NC_002950:PG2098|5end_hypothetical_protein_2206635..2206865_NEGATIVE 388 63 21 60 23 NC_002950:PG0143|5end_hydrolase,_carbon-nitrogen_family_166625..166855_NEGATIVE 380 60 18 168 113 NC_002950:PG1173|5end_YkgG_family_protein_1252435..1252665_POSITIVE 375 64 21 172 123 NC_002950:PG0715|5end_transporter_769596..769826_NEGATIVE 374 80 34 223 175 NC_002950:PG1640|5end_DNA-damage-inducible_protein_F_1721245..1721475_NEGATIVE 373 67 31 222 176 NC_002950:PG1671|5end_hypothetical_protein_1757658..1757888_NEGATIVE 373 67 31 222 176 NC_002950:PG1266|5end_hypothetical_protein_1346987..1347217_NEGATIVE 373 67 31 222 176 NC_002950:PG0101|5end_hypothetical_protein_119198..119428_POSITIVE 368 65 22 68 19 NC_002950:PG2024|5end_hemagglutinin_protein_HagE_2124203..2124433_NEGATIVE 365 66 21 120 67 NC_002950:PG1091|5end_DHH_subfamily_1_protein_1157017..1157247_POSITIVE 359 58 11 185 138 NC_002950:PG0259|5end_hypothetical_protein_292278..292508_POSITIVE 358 78 32 197 152 NC_002950:PG0021|5end_TIM-barrel_protein,_putative,_NifR3_family_25123..25353_NEGATIVE 355 60 14 192 149 NC_002950:PG0151|5end_signal_recognition_particle-docking_protein_FtsY_174494..174724_NEGATIVE 354 65 21 48 2 NC_002950:PG0429|5end_pyruvate_synthase_466100..466330_POSITIVE 352 57 15 82 34 NC_002950:PG0295|5end_DNA_processing_protein_DprA,_putative_331300..331530_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 458 54 15 55 1 NC_002950:PG2062|3end_histidyl-tRNA_synthetase_2160415..2160565_POSITIVE 405 65 21 123 61 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 397 43 1 129 82 NC_002950:PG1930|3end_50S_ribosomal_protein_L29_2020215..2020365_NEGATIVE 388 63 21 42 5 NC_002950:PG0144|3end_hypothetical_protein_166643..166793_NEGATIVE 383 60 19 46 6 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE 375 64 23 108 68 NC_002950:PG1600|3end_hypothetical_protein_1679959..1680109_NEGATIVE 352 57 15 89 41 NC_002950:PG0296|3end_phosphoribosylformylglycinamidine_synthase_331293..331443_NEGATIVE 349 68 25 71 25 NC_002950:PG1977|3end_hypothetical_protein_2064687..2064837_NEGATIVE 342 64 21 143 96 NC_002950:PG0280|3end_ABC_transporter,_permease_protein,_putative_313297..313447_NEGATIVE 339 60 14 82 28 NC_002950:PG0061|3end_yngK_protein_73763..73913_POSITIVE 335 60 12 82 35 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 334 80 31 48 5 NC_002950:PG1702|3end_DNA_gyrase,_B_subunit_1787946..1788096_NEGATIVE 330 60 15 141 96 NC_002950:PG0758|3end_peptidyl-dipeptidase_Dcp_806467..806617_NEGATIVE 325 59 11 55 6 NC_002950:PG1352|3end_hypothetical_protein_1432737..1432887_NEGATIVE 325 99 51 82 32 NC_002950:PG1308|3end_hypothetical_protein_1387883..1388033_NEGATIVE 325 61 24 41 5 NC_002950:PG0791|3end_adenylate_kinase_842593..842743_NEGATIVE 319 57 14 151 113 NC_002950:PG2167|3end_immunoreactive_53_kDa_antigen_PG123_2272104..2272254_NEGATIVE 318 57 19 150 102 NC_002950:PG0850|3end_DNA_binding_protein,_excisionase_family,_putative_911270..911420_NEGATIVE 318 51 17 69 27 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE 317 69 21 68 15 NC_002950:PG1760|3end_ABC_transporter,_ATP-binding_protein_1847216..1847366_POSITIVE