Origin IGS: cagaggcaaagtatttgcagatttcatctatctatcgtattttggtgcccgaaatacggaaaatcaaacaaaatgtttcactaacaaaaaagataaacgaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gttcgtttatcttttttgttagtgaaacattttgtttgattttccgtatttcgggcaccaaaatacgatagatagatgaaatctgcaaatactttgcctctg Mask Tandem Repeat Region ================================================ cagaggcaaagtatttgcagatttcatctatctatcgtattttggtgcccgaaatacggaaaatcaaacaaaatgtttcactaacaaaaaagataaacgaac Find is-nt database================================================ Query_seq: PG0615:PG0616|PG0615:PG0616:GTP-binding protein TypA:thioredoxin, putative:->->:668973..669074 102 cagaggcaaagtatttgcagatttcatctatctatcgtattttggtgcccgaaatacggaaaatcaaacaaaatgtttcactaacaaaaaagataaacgaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0615:PG0616|PG0615:PG0616:GTP-binding protein TypA:thioredoxin, putative:->->:668973..669074 102 cagaggcaaagtatttgcagatttcatctatctatcgtattttggtgcccgaaatacggaaaatcaaacaaaatgtttcactaacaaaaaagataaacgaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0615:PG0616|PG0615:PG0616:GTP-binding protein TypA:thioredoxin, putative:->->:668973..669074 102 cagaggcaaagtatttgcagatttcatctatctatcgtattttggtgcccgaaatacggaaaatcaaacaaaatgtttcactaacaaaaaagataaacgaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cagaggcaaagtatttgcagatttcatctatctatcgtattttggtgcccgaaatacggaaaatcaaacaaaatgtttcactaacaaaaaagataaacgaac Predict ORF larger than 30AA ================================================ cagaggcaaagtatttgcagatttcatctatctatcgtattttggtgcccgaaatacggaaaatcaaacaaaatgtttcactaacaaaaaagataaacgaac 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================================================ cagaggcaaagtatttgcagatttcatctatctatcgtattttggtgcccgaaatacggaaaatcaaacaaaatgtttcactaacaaaaaagataaacgaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0615:PG0616|PG0615:PG0616:GTP-binding protein TypA:thioredoxin, putative:->->:668973..669074 102 cagaggcaaagtatttgcagatttcatctatctatcgtattttggtgcccgaaatacggaaaatcaaacaaaatgtttcactaacaaaaaagataaacgaac Intra-Species Hit: Count: 1 Min: 1 Max: 102 Len: 102 Subject: NC_002950_PG0615_PG0616|GTP-binding protein TypA:thioredoxin, putative|POSITIVE:POSITIVE|[668973,669074]|102 HSP 1 e-value: 2.0E-51 bit: 202.0 Len: 102 Query Start:1 Query End:102 Subject Strand: POSITIVE Subject Start: 1 Subject End: 102 cagaggcaaagtatttgcagatttcatctatctatcgtattttggtgcccgaaatacggaaaatcaaacaaaatgtttcactaacaaaaaagataaacgaac cagaggcaaagtatttgcagatttcatctatctatcgtattttggtgcccgaaatacggaaaatcaaacaaaatgtttcactaacaaaaaagataaacgaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGAGGCAAAGUAUUUGCAGAUUUCAUCUAUCUAUCGUAUUUUGGUGCCCGAAAUACGGAAAAUCAAACAAAAUGUUUCACUAACAAAAAAGAUAAACGAAC .....((((.....))))....(((...(((((.(((((((((((...)))))))))))..............((((.....))))....)))))...))). (-18.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUCGUUUAUCUUUUUUGUUAGUGAAACAUUUUGUUUGAUUUUCCGUAUUUCGGGCACCAAAAUACGAUAGAUAGAUGAAAUCUGCAAAUACUUUGCCUCUG .(((((((((((........(((.((((.....)))).)))...(((((((.((...)).)))))))..)))))))))))....((((.....))))..... (-21.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 309 67 28 70 24 NC_002950:PG0271|5end_single-stranded_binding_protein_303842..304072_POSITIVE 302 49 5 221 165 NC_002950:PG0356|5end_hypothetical_protein_390611..390841_POSITIVE 279 80 35 86 40 NC_002950:PG1051|5end_hypothetical_protein_1118210..1118440_POSITIVE 271 49 5 113 77 NC_002950:PG0489|5end_polysaccharide_biosynthesis-related_protein_529247..529477_POSITIVE 261 60 13 177 130 NC_002950:PG0648|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_701285..701515_NEGATIVE 249 53 17 38 1 NC_002950:PG0710|5end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_766034..766264_NEGATIVE 248 50 3 211 167 NC_002950:PG2209|5end_hypothetical_protein_2320928..2321158_NEGATIVE 247 48 2 166 110 NC_002950:PG0422|5end_hypothetical_protein_462302..462532_NEGATIVE 245 59 14 211 159 NC_002950:PG1392|5end_rod_shape-determining_protein_RodA,_putative_1474416..1474646_NEGATIVE 243 50 5 75 32 NC_002950:PG0493|5end_hypothetical_protein_534900..535130_NEGATIVE 240 49 5 55 8 NC_002950:PG2067|5end_pyridoxal_phosphate_biosynthetic_protein_PdxA_2163215..2163445_POSITIVE 239 49 1 110 58 NC_002950:PG1546|5end_hypothetical_protein_1624087..1624317_POSITIVE 238 50 2 65 32 NC_002950:PG2116|5end_hypothetical_protein_2224635..2224865_POSITIVE 238 45 4 230 189 NC_002950:PG0319|5end_hypothetical_protein_352949..353179_POSITIVE 237 60 15 131 78 NC_002950:PG1534|5end_hypothetical_protein_1614147..1614377_NEGATIVE 237 59 16 45 9 NC_002950:PG0063|5end_outer_membrane_efflux_protein_77056..77286_NEGATIVE 235 42 1 180 143 NC_002950:PG1763|5end_ribonuclease_III_1851712..1851942_NEGATIVE 233 49 9 80 30 NC_002950:PG0123|5end_hypothetical_protein_144987..145217_POSITIVE 232 60 14 69 13 NC_002950:PG1213|5end_ribonuclease_H_1292433..1292663_POSITIVE 232 47 1 219 176 NC_002950:PG0722|5end_hypothetical_protein_774891..775121_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 271 49 5 66 30 NC_002950:PG0488|3end_Holliday_junction_DNA_helicase_RuvB_529280..529430_POSITIVE 269 49 2 54 14 NC_002950:PG1866|3end_hypothetical_protein_1964736..1964886_POSITIVE 256 79 31 88 31 NC_002950:PG0615|3end_GTP-binding_protein_TypA_668912..669062_POSITIVE 253 50 1 143 95 NC_002950:PG1854|3end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1953325..1953475_NEGATIVE 249 60 11 122 78 NC_002950:PG0282|3end_ABC_transporter,_ATP-binding_protein_316244..316394_NEGATIVE 239 49 1 98 46 NC_002950:PG1545|3end_superoxide_dismutase,_Fe-Mn_1624155..1624305_POSITIVE 237 60 15 128 75 NC_002950:PG1535|3end_transcriptional_regulator,_putative_1614150..1614300_NEGATIVE 237 49 2 52 5 NC_002950:PG1274|3end_elongation_factor_P_1352489..1352639_POSITIVE 235 42 1 96 59 NC_002950:PG1764|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_II_1851796..1851946_NEGATIVE 235 49 1 141 92 NC_002950:PG1441|3end_lysozyme-related_protein_1527358..1527508_NEGATIVE 234 57 12 75 23 NC_002950:PG1701|3end_glutamine_amidotransferase,_class_II/dipeptidase_1786145..1786295_NEGATIVE 229 44 1 111 71 NC_002950:PG0113|3end_hypothetical_protein_136862..137012_POSITIVE 225 46 3 91 52 NC_002950:PG0258|3end_ABC_transporter,_ATP-binding_protein_292351..292501_POSITIVE 224 47 1 150 92 NC_002950:PG0226|3end_transglutaminase-related_protein_259838..259988_NEGATIVE 223 80 38 44 1 NC_002950:PG1050|3end_hypothetical_protein_1118248..1118398_POSITIVE 223 60 19 83 43 NC_002950:PG0687|3end_succinate-semialdehyde_dehydrogenase_743168..743318_NEGATIVE 223 54 22 133 96 NC_002950:PG0391|3end_50S_ribosomal_protein_L1_424058..424208_POSITIVE 222 46 1 95 62 NC_002950:PG0012|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_15661..15811_POSITIVE 221 49 1 111 60 NC_002950:PG2099|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2206649..2206799_NEGATIVE 220 61 22 41 7 NC_002950:PG1900|3end_ribosome-associated_GTPase_1999799..1999949_NEGATIVE