Origin IGS: tcaatgaatagttgaaaaacatgggggtgcaaagatactgtttttttgcgtatgatatgtcagcccctatgtttttatcattttataacgctataacaatctcaccgaccgatgagttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaactcatcggtcggtgagattgttatagcgttataaaatgataaaaacataggggctgacatatcatacgcaaaaaaacagtatctttgcacccccatgtttttcaactattcattga Mask Tandem Repeat Region ================================================ tcaatgaatagttgaaaaacatgggggtgcaaagatactgtttttttgcgtatgatatgtcagcccctatgtttttatcattttataacgctataacaatctcaccgaccgatgagttta Find is-nt database================================================ Query_seq: TF1449:TF1450|TF1449:TF1450:RNA polymerase sigma factor, RpoD:periplasmic serine protease:->->:1534122..1534241 120 tcaatgaatagttgaaaaacatgggggtgcaaagatactgtttttttgcgtatgatatgtcagcccctatgtttttatcattttataacgctataacaatctcaccgaccgatgagttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1449:TF1450|TF1449:TF1450:RNA polymerase sigma factor, RpoD:periplasmic serine protease:->->:1534122..1534241 120 tcaatgaatagttgaaaaacatgggggtgcaaagatactgtttttttgcgtatgatatgtcagcccctatgtttttatcattttataacgctataacaatctcaccgaccgatgagttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1449:TF1450|TF1449:TF1450:RNA polymerase sigma factor, RpoD:periplasmic serine protease:->->:1534122..1534241 120 tcaatgaatagttgaaaaacatgggggtgcaaagatactgtttttttgcgtatgatatgtcagcccctatgtttttatcattttataacgctataacaatctcaccgaccgatgagttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcaatgaatagttgaaaaacatgggggtgcaaagatactgtttttttgcgtatgatatgtcagcccctatgtttttatcattttataacgctataacaatctcaccgaccgatgagttta Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 12 End: 119 ........... M K N M G V Q R Y C F F A Y D M S A P M F L S F Y N A I T I S P T D E F . tcaatgaatagttgaaaaacatgggggtgcaaagatactgtttttttgcgtatgatatgtcagcccctatgtttttatcattttataacgctataacaatctcaccgaccgatgagttta 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================================================ tcaatgaatagttgaaaaacatgggggtgcaaagatactgtttttttgcgtatgatatgtcagcccctatgtttttatcattttataacgctataacaatctcaccgaccgatgagttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1449:TF1450|TF1449:TF1450:RNA polymerase sigma factor, RpoD:periplasmic serine protease:->->:1534122..1534241 120 tcaatgaatagttgaaaaacatgggggtgcaaagatactgtttttttgcgtatgatatgtcagcccctatgtttttatcattttataacgctataacaatctcaccgaccgatgagttta Intra-Species Hit: Count: 1 Min: 1 Max: 120 Len: 120 Subject: tfor_TF1449_TF1450|RNA polymerase sigma factor, RpoD:periplasmic serine protease|POSITIVE:POSITIVE|[1534122,1534241]|120 HSP 1 e-value: 1.0E-49 bit: 196.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 1 Subject End: 120 tcaatgaatagttgaaaaacatgggggtgcaaagatactgnnnnnnngcgtatgatatgtcagcccctatgtttttatcattttataacgctataacaatctcaccgaccgatgagttta tcaatgaatagttgaaaaacatgggggtgcaaagatactgtttttttgcgtatgatatgtcagcccctatgtttttatcattttataacgctataacaatctcaccgaccgatgagttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAUGAAUAGUUGAAAAACAUGGGGGUGCAAAGAUACUGUUUUUUUGCGUAUGAUAUGUCAGCCCCUAUGUUUUUAUCAUUUUAUAACGCUAUAACAAUCUCACCGACCGAUGAGUUUA ...(((((......(((((((((((((((((((((.......)))))))...(((....))))))))))))))))).....)))))..............((((.(....).)))).... (-29.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACUCAUCGGUCGGUGAGAUUGUUAUAGCGUUAUAAAAUGAUAAAAACAUAGGGGCUGACAUAUCAUACGCAAAAAAACAGUAUCUUUGCACCCCCAUGUUUUUCAACUAUUCAUUGA ....((((((....))))))..................(((((.((((((((.((((.((.((....((((...........))))...)))))))).)))))))).......))))).. (-25.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 68 22 203 151 tfor:TF2278|5end_conserved_hypothetical_protein_2438662..2438892_POSITIVE 308 65 21 205 146 tfor:TF3019|5end_tRNA_and_rRNA_cytosine-C5-methylase_3242164..3242394_POSITIVE 305 59 21 52 3 tfor:TF0087|5end_ABC_transporter,_permease_component_93185..93415_POSITIVE 293 62 22 224 189 tfor:TF1840|5end_transposase_1990221..1990451_POSITIVE 287 66 23 209 171 tfor:TF2818|5end_acetylornithine_aminotransferase_3007739..3007969_POSITIVE 279 67 25 157 106 tfor:TF0802|5end_glucose-1-phosphate_cytidylyltransferase_860310..860540_POSITIVE 277 67 44 225 203 tfor:TF3006|5end_response_regulator,_transcriptional_regulator_RprY_3226360..3226590_POSITIVE 277 67 24 172 128 tfor:TF0810|5end_possible_outer_membrane_efflux_protein_868438..868668_POSITIVE 275 66 21 157 108 tfor:TF1689|5end_conserved_hypothetical_protein_1805068..1805298_POSITIVE 267 65 21 215 156 tfor:TF1662|5end_possible_transcriptional_regulator,_PadR_family_1777214..1777444_POSITIVE 266 67 22 59 9 tfor:TF1816|5end_hypothetical_protein_1957643..1957873_POSITIVE 265 70 22 166 107 tfor:TF0764|5end_conserved_hypothetical_protein;_possible_exopolyphosphatase-related_protein_810251..810481_POSITIVE 262 64 23 181 137 tfor:TF2024|5end_conserved_hypothetical_protein_2181486..2181716_POSITIVE 262 76 38 180 120 tfor:TF1775|5end_oxidoreductase,_Gfo/Idh/MocA_family_1913135..1913365_POSITIVE 262 65 26 42 4 tfor:TF1503|5end_conserved_hypothetical_protein_1604298..1604528_POSITIVE 257 65 23 67 29 tfor:TF2489|5end_hypothetical_protein_2664418..2664648_POSITIVE 256 51 18 66 32 tfor:TF3042|5end_ferrous_iron_transport_protein_B_3269362..3269592_POSITIVE 254 55 11 94 45 tfor:TF3062|5end_conserved_hypothetical_protein_3286140..3286370_POSITIVE 251 66 26 201 153 tfor:TF0234|5end_5,10-methylenetetrahydrofolate_reductase_260482..260712_POSITIVE 248 66 21 182 134 tfor:TF2282|5end_hypothetical_protein_2439401..2439631_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 68 22 115 76 tfor:TF2173|3end_hypothetical_protein_2346063..2346213_POSITIVE 301 68 22 115 76 tfor:TF0346|3end_hypothetical_protein_367316..367466_POSITIVE 282 68 22 146 105 tfor:TF0178|3end_ferritin_188223..188373_POSITIVE 279 67 25 94 43 tfor:TF0801|3end_transport_permease_860327..860477_POSITIVE 268 52 15 110 62 tfor:TF0001|3end_hypothetical_protein_158..308_POSITIVE 265 70 22 120 61 tfor:TF0763|3end_chromate_transport_protein_810285..810435_POSITIVE 262 64 23 138 94 tfor:TF2023|3end_possible_Fe-S_oxidoreductase_2181523..2181673_POSITIVE 257 65 23 47 9 tfor:TF2488|3end_hypothetical_protein_2664478..2664628_POSITIVE 255 65 21 117 62 tfor:TF3013|3end_conserved_hypothetical_protein_3237539..3237689_POSITIVE 254 55 11 94 45 tfor:TF3061|3end_conserved_hypothetical_protein_3286220..3286370_POSITIVE 249 49 2 77 42 tfor:TF0896|3end_hypothetical_protein_945213..945363_POSITIVE 244 72 38 53 20 tfor:TF2440|3end_conserved_hypothetical_protein;_possible_DNA_mismatch_repair_protein_2618137..2618287_POSITIVE 244 66 23 120 69 tfor:TF2338|3end_conserved_hypothetical_protein_2500006..2500156_POSITIVE 244 50 10 50 9 tfor:TF0364|3end_ysyl_endopeptidase_382730..382880_POSITIVE 241 60 26 66 28 tfor:TF0681|3end_sugar_kinase,_PfkB_family_724209..724359_POSITIVE 237 50 9 76 31 tfor:TF3134|3end_HD_superfamily_hydrolase_3368618..3368768_POSITIVE 237 60 23 132 87 tfor:TF1357|3end_hypothetical_protein_1437708..1437858_POSITIVE 237 66 38 142 112 tfor:TF0537|3end_conserved_hypothetical_protein_566836..566986_POSITIVE 235 68 25 151 101 tfor:TF2280|3end_hypothetical_protein_2439474..2439624_POSITIVE 235 50 8 142 106 tfor:TF1918|3end_hypothetical_protein_2070105..2070255_POSITIVE