Origin IGS: tttttcctcccatttataaaattatatgaatattttatcaaatttttataaaatagcaagattctaagtataaaatgttataatttatatggaggagatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatctcctccatataaattataacattttatacttagaatcttgctattttataaaaatttgataaaatattcatataattttataaatgggaggaaaaa Mask Tandem Repeat Region ================================================ tttttcctcccatttataaaattatatgaatattttatcaaatttttataaaatagcaagattctaagtataaaatgttataatttatatggaggagatttt Find is-nt database================================================ Query_seq: FN0896:FN0897|FN0896:FN0897:hypothetical protein:Hypothetical cytosolic protein:<-->:1555871..1555972 102 tttttcctcccatttataaaattatatgaatattttatcaaatttttataaaatagcaagattctaagtataaaatgttataatttatatggaggagatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0896:FN0897|FN0896:FN0897:hypothetical protein:Hypothetical cytosolic protein:<-->:1555871..1555972 102 tttttcctcccatttataaaattatatgaatattttatcaaatttttataaaatagcaagattctaagtataaaatgttataatttatatggaggagatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0896:FN0897|FN0896:FN0897:hypothetical protein:Hypothetical cytosolic protein:<-->:1555871..1555972 102 tttttcctcccatttataaaattatatgaatattttatcaaatttttataaaatagcaagattctaagtataaaatgttataatttatatggaggagatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttcctcccatttataaaattatatgaatattttatcaaatttttataaaatagcaagattctaagtataaaatgttataatttatatggaggagatttt Predict ORF larger than 30AA ================================================ tttttcctcccatttataaaattatatgaatattttatcaaatttttataaaatagcaagattctaagtataaaatgttataatttatatggaggagatttt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 13 End: 42 ............TTTGATAAAATATTCATATAATTTTATAAA............................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttttcctcccatttataaaattatatgaatattttatcaaatttttataaaatagcaagattctaagtataaaatgttataatttatatggaggagatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0896:FN0897|FN0896:FN0897:hypothetical protein:Hypothetical cytosolic protein:<-->:1555871..1555972 102 tttttcctcccatttataaaattatatgaatattttatcaaatttttataaaatagcaagattctaagtataaaatgttataatttatatggaggagatttt Intra-Species Hit: Count: 1 Min: 1 Max: 102 Len: 102 Subject: NC_003454_FN0896_FN0897|hypothetical protein:Hypothetical cytosolic protein|NEGATIVE:POSITIVE|[1555871,1555972]|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 tttttcctcccatttataaaattatatgaatattttatcaaatttttataaaatagcaagattctaagtataaaatgttataatttatatggaggagatttt tttttcctcccatttataaaattatatgaatattttatcaaatttttataaaatagcaagattctaagtataaaatgttataatttatatggaggagatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCCUCCCAUUUAUAAAAUUAUAUGAAUAUUUUAUCAAAUUUUUAUAAAAUAGCAAGAUUCUAAGUAUAAAAUGUUAUAAUUUAUAUGGAGGAGAUUUU ..((((((((....((((((....((((((.((((....)))).))))))..((((((.................))))))..)))))).)))))))).... (-17.33) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUCUCCUCCAUAUAAAUUAUAACAUUUUAUACUUAGAAUCUUGCUAUUUUAUAAAAAUUUGAUAAAAUAUUCAUAUAAUUUUAUAAAUGGGAGGAAAAA ......((((((.(((((((((((..((((((....)))))).....((((((((.........))))))))....))))).))))))....)))))).... (-16.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 687 100 51 191 142 NC_003454:FN0896|5end_hypothetical_protein_1555780..1556010_NEGATIVE 217 98 52 180 138 NC_003454:FN1015|5end_5'-methylthioadenosine_nucleosidase_1670314..1670544_NEGATIVE 209 45 4 137 97 NC_003454:FN1863|5end_L-beta-lysine_5,6-aminomutase_alpha_subunit_354678..354908_NEGATIVE 196 31 3 120 94 NC_003454:FN1060|5end_Molybdate_metabolism_regulator_1707796..1708026_NEGATIVE 191 49 18 193 163 NC_003454:FN0224|5end_excinuclease_ABC_subunit_B_849602..849832_POSITIVE 190 60 21 202 161 NC_003454:FN1363|5end_Dipeptide_transport_ATP-binding_protein_dppF_2014501..2014731_POSITIVE 180 36 2 136 94 NC_003454:FN0212|5end_hypothetical_protein_838125..838355_NEGATIVE 179 63 28 149 113 NC_003454:FN0622|5end_N-glycosylase/DNA_lyase_1281278..1281508_POSITIVE 177 89 48 92 58 NC_003454:FN0554|5end_D-serine_permease_1207443..1207673_NEGATIVE 175 40 1 103 64 NC_003454:FN1287|5end_Bacterial_Protein_Translation_Initiation_Factor_1_(IF-1)_1944663..1944893_NEGATIVE 175 50 3 136 85 NC_003454:FN0449|5end_hypothetical_protein_1092683..1092913_POSITIVE 170 54 22 207 178 NC_003454:FN1513|5end_Phophatidylinositol-4-phosphate_5-kinase_17007..17237_POSITIVE 169 50 6 143 99 NC_003454:FN1185|5end_SIR2_family_protein_1848321..1848551_NEGATIVE 166 46 5 144 100 NC_003454:FN1547|5end_PTS_permease_for_N-acetylglucosamine_and_glucose_63270..63500_NEGATIVE 163 98 52 65 26 NC_003454:FN0716|5end_Phophatidylinositol-4-phosphate_5-kinase_1373969..1374199_POSITIVE 163 40 1 131 91 NC_003454:FN1942|5end_Hypothetical_cytosolic_protein_444689..444919_NEGATIVE 162 29 5 135 111 NC_003454:FN0018|5end_hypothetical_protein_656448..656678_NEGATIVE 161 46 1 217 175 NC_003454:FN1913|5end_hydrolase_(HD_superfamily)_411580..411810_NEGATIVE 159 23 3 113 95 NC_003454:FN1817|5end_Hemolysin_305273..305503_NEGATIVE 158 48 1 133 91 NC_003454:FN1188|5end_hypothetical_protein_1850780..1851010_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 209 45 4 137 97 NC_003454:FN1864|3end_DNA_mismatch_repair_protein_mutS_354678..354828_NEGATIVE 196 31 3 100 74 NC_003454:FN1061|3end_hypothetical_protein_1707816..1707966_NEGATIVE 180 36 2 109 67 NC_003454:FN0213|3end_N-acylneuraminate-9-phosphatase_838152..838302_NEGATIVE 176 67 22 128 86 NC_003454:FN0053|3end_Branched-chain_amino_acid_transport_system_carrier_protein_690694..690844_POSITIVE 175 50 3 120 69 NC_003454:FN0448|3end_DNA-repair_protein_1092747..1092897_POSITIVE 168 94 51 65 16 NC_003454:FN1900|3end_pfoS/R_389316..389466_POSITIVE 163 98 52 72 33 NC_003454:FN0715|3end_hypothetical_protein_1374056..1374206_POSITIVE 159 23 3 98 80 NC_003454:FN1818|3end_Hemolysin_activator_protein_precursor_305288..305438_NEGATIVE 158 41 6 94 53 NC_003454:FN1917|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_412845..412995_NEGATIVE 156 47 1 151 101 NC_003454:FN1232|3end_Transcriptional_regulator,_MarR_family_1889000..1889150_NEGATIVE 154 25 3 129 102 NC_003454:FN0066|3end_Two_component_system_histidine_kinase_704620..704770_POSITIVE 154 63 21 100 44 NC_003454:FN1955|3end_hypothetical_protein_460210..460360_POSITIVE 153 14 1 92 79 NC_003454:FN0913|3end_Cobinamide_kinase_1570172..1570322_NEGATIVE 153 48 1 151 106 NC_003454:FN0418|3end_pyrimidine_regulatory_protein_PyrR_1059731..1059881_POSITIVE 151 18 1 95 76 NC_003454:FN2104|3end_hypothetical_protein_614760..614910_POSITIVE 150 18 2 95 78 NC_003454:FN0309|3end_Iron(III)-transport_system_permease_protein_sfuB_945861..946011_POSITIVE 149 36 6 149 111 NC_003454:FN0280|3end_hypothetical_protein_906469..906619_NEGATIVE 147 77 41 146 109 NC_003454:FN1027|3end_Rod_shape-determining_protein_rodA_1680823..1680973_NEGATIVE 146 19 1 49 27 NC_003454:FN0709|3end_Virulence_factor_mviN_1368888..1369038_POSITIVE 145 31 3 100 67 NC_003454:FN1999|3end_HIPA_protein_500869..501019_POSITIVE