Origin IGS: ttgggtataatcgtttttttaatgatgacgaaaggggtagggggcggttctcgaaatactgccgatccttcgggatataggcaaagcctcctgttgcggaggcaaaaataagaaaaattgtcggtgccggc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gccggcaccgacaatttttcttatttttgcctccgcaacaggaggctttgcctatatcccgaaggatcggcagtatttcgagaaccgccccctacccctttcgtcatcattaaaaaaacgattatacccaa Mask Tandem Repeat Region ================================================ ttgggtataatcgtttttttaatgatgacgaaaggggtagggggcggttctcgaaatactgccgatccttcgggatataggcaaagcctcctgttgcggaggcaaaaataagaaaaattgtcggtgccggc Find is-nt database================================================ Query_seq: PG0568:PG0569|PG0568:PG0569:elongation factor P:hypothetical protein:<-<-:624656..624786 131 ttgggtataatcgtttttttaatgatgacgaaaggggtagggggcggttctcgaaatactgccgatccttcgggatataggcaaagcctcctgttgcggaggcaaaaataagaaaaattgtcggtgccggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0568:PG0569|PG0568:PG0569:elongation factor P:hypothetical protein:<-<-:624656..624786 131 ttgggtataatcgtttttttaatgatgacgaaaggggtagggggcggttctcgaaatactgccgatccttcgggatataggcaaagcctcctgttgcggaggcaaaaataagaaaaattgtcggtgccggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0568:PG0569|PG0568:PG0569:elongation factor P:hypothetical protein:<-<-:624656..624786 131 ttgggtataatcgtttttttaatgatgacgaaaggggtagggggcggttctcgaaatactgccgatccttcgggatataggcaaagcctcctgttgcggaggcaaaaataagaaaaattgtcggtgccggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgggtataatcgtttttttaatgatgacgaaaggggtagggggcggttctcgaaatactgccgatccttcgggatataggcaaagcctcctgttgcggaggcaaaaataagaaaaattgtcggtgccggc Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 1 End: 108 M G I I V F L M M T K G V G G G S R N T A D P S G Y R Q S L L L R R Q K ....................... Protein_Len: 39 Strand: - Start: 2 End: 118 . P Y L R K K L S S S L P L P R N E F Y Q R D K P I Y A F G G T A S A F I L F M ............. ttgggtataatcgtttttttaatgatgacgaaaggggtagggggcggttctcgaaatactgccgatccttcgggatataggcaaagcctcctgttgcggaggcaaaaataagaaaaattgtcggtgccggc 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================================================ ttgggtataatcgtttttttaatgatgacgaaaggggtagggggcggttctcgaaatactgccgatccttcgggatataggcaaagcctcctgttgcggaggcaaaaataagaaaaattgtcggtgccggc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0568:PG0569|PG0568:PG0569:elongation factor P:hypothetical protein:<-<-:624656..624786 131 ttgggtataatcgtttttttaatgatgacgaaaggggtagggggcggttctcgaaatactgccgatccttcgggatataggcaaagcctcctgttgcggaggcaaaaataagaaaaattgtcggtgccggc Intra-Species Hit: Count: 1 Min: 21 Max: 131 Len: 111 Subject: NC_002950_PG0568_PG0569|elongation factor P:hypothetical protein|NEGATIVE:NEGATIVE|[624656,624786]|131 HSP 1 e-value: 9.0E-57 bit: 220.0 Len: 111 Query Start:21 Query End:131 Subject Strand: POSITIVE Subject Start: 21 Subject End: 131 ....................aatgatgacgaaaggggtagggggcggttctcgaaatactgccgatccttcgggatataggcaaagcctcctgttgcggaggcaaaaataagaaaaattgtcggtgccggc ....................aatgatgacgaaaggggtagggggcggttctcgaaatactgccgatccttcgggatataggcaaagcctcctgttgcggaggcaaaaataagaaaaattgtcggtgccggc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAUGACGAAAGGGGUAGGGGGCGGUUCUCGAAAUACUGCCGAUCCUUCGGGAUAUAGGCAAAGCCUCCUGUUGCGGAGGCAAAAAUAAGAAAAAUUGUCGGUGCCGGC ....((..(....)..))....(.((((.(.(((.....((((.((((....))))...))))..((((((......)))))).................)))).)))).) (-37.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCGGCACCGACAAUUUUUCUUAUUUUUGCCUCCGCAACAGGAGGCUUUGCCUAUAUCCCGAAGGAUCGGCAGUAUUUCGAGAACCGCCCCCUACCCCUUUCGUCAUCAUU ...(((......................((((((......)))))).(((((...((((....)))).))))).............)))...................... (-26.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1057 70 21 181 132 NC_002950:PG0568|5end_elongation_factor_P_624565..624795_NEGATIVE 1018 90 41 201 152 NC_002950:PG1274|5end_elongation_factor_P_1351843..1352073_POSITIVE 406 70 22 220 176 NC_002950:PG0143|5end_hydrolase,_carbon-nitrogen_family_166625..166855_NEGATIVE 393 47 10 89 50 NC_002950:PG0320|5end_hypothetical_protein_353409..353639_POSITIVE 392 53 13 212 151 NC_002950:PG0166|5end_peptidyl-tRNA_hydrolase_188370..188600_NEGATIVE 388 56 15 223 178 NC_002950:PG0923|5end_ribosome-binding_factor_A_982814..983044_NEGATIVE 378 110 61 67 12 NC_002950:PG1230|5end_hypothetical_protein_1308068..1308298_NEGATIVE 372 82 41 62 12 NC_002950:PG2227|5end_hypothetical_protein_2342008..2342238_POSITIVE 368 70 21 193 141 NC_002950:PG0538|5end_outer_membrane_efflux_protein_589142..589372_POSITIVE 367 82 43 53 1 NC_002950:PG0630|5end_pyridoxal_phosphate_biosynthetic_protein_683392..683622_POSITIVE 366 80 32 147 105 NC_002950:PG0544|5end_type_I_restriction-modification_system,_M_subunit,_putative_596052..596282_POSITIVE 358 57 16 83 51 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 354 110 61 114 66 NC_002950:PG0711|5end_hypothetical_protein_766070..766300_POSITIVE 351 80 32 132 89 NC_002950:PG1029|5end_hypothetical_protein_1091080..1091310_POSITIVE 349 53 13 186 145 NC_002950:PG2029|5end_hypothetical_protein_2126543..2126773_POSITIVE 349 79 31 173 106 NC_002950:PG0216|5end_hypothetical_protein_251956..252186_POSITIVE 346 84 43 44 1 NC_002950:PG0463|5end_folylpolyglutamate_synthase_507606..507836_NEGATIVE 341 79 31 225 160 NC_002950:PG2082|5end_POT_family_protein_2183384..2183614_NEGATIVE 341 87 41 59 7 NC_002950:PG0960|5end_tRNA_(guanine-N(7)-)-methyltransferase_1021895..1022125_NEGATIVE 340 83 42 78 28 NC_002950:PG1632|5end_aldose_1-epimerase_1712268..1712498_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 510 60 14 127 72 NC_002950:PG2036|3end_ion_transporter_2137552..2137702_POSITIVE 413 82 41 50 15 NC_002950:PG1118|3end_clpB_protein_1192083..1192233_NEGATIVE 400 55 12 150 115 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 393 82 41 138 98 NC_002950:PG0515|3end_hypothetical_protein_556363..556513_NEGATIVE 393 47 10 57 18 NC_002950:PG0319|3end_hypothetical_protein_353457..353607_POSITIVE 392 53 13 70 9 NC_002950:PG0167|3end_ribosomal_protein_L25_188512..188662_NEGATIVE 377 48 2 89 40 NC_002950:PG0199|3end_TatD_family_protein_237424..237574_NEGATIVE 375 55 15 68 8 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 372 82 41 65 15 NC_002950:PG2226|3end_hypothetical_protein_2342091..2342241_POSITIVE 352 83 48 109 64 NC_002950:PG1559|3end_aminomethyltransferase_1637904..1638054_NEGATIVE 351 80 32 68 25 NC_002950:PG1028|3end_TPR_domain_protein_1091096..1091246_POSITIVE 351 54 13 106 36 NC_002950:PG1012|3end_tRNA-i(6)A37_modification_enzyme_MiaB_1070089..1070239_NEGATIVE 346 44 3 141 96 NC_002950:PG1351|3end_hypothetical_protein_1432238..1432388_NEGATIVE 345 56 16 115 66 NC_002950:PG0021|3end_TIM-barrel_protein,_putative,_NifR3_family_24122..24272_NEGATIVE 344 79 41 149 106 NC_002950:PG1750|3end_alpha-1,3/4-fucosidase,_putative_1837223..1837373_POSITIVE 341 83 41 75 38 NC_002950:PG2082|3end_POT_family_protein_2181843..2181993_NEGATIVE 337 56 13 43 4 NC_002950:PG1772|3end_endonuclease_III_1859833..1859983_POSITIVE 337 108 63 150 104 NC_002950:PG1305|3end_glycine_dehydrogenase_1383671..1383821_NEGATIVE 336 84 41 101 43 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 331 52 15 58 17 NC_002950:PG0733|3end_riboflavin_synthase_subunit_alpha_783856..784006_POSITIVE