Origin IGS: caaatgctacaggaagtccttatgcttatggcagtggtttttcattgccaaaggaatattaaaaaaaataaaatataaaaaataaagaaaataataaaaggaggaggctatatggaaaatatttattttccattatagataaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttatctataatggaaaataaatattttccatatagcctcctccttttattattttctttattttttatattttattttttttaatattcctttggcaatgaaaaaccactgccataagcataaggacttcctgtagcatttg Mask Tandem Repeat Region ================================================ caaatgctacaggaagtccttatgcttatggcagtggtttttcattgccaaaggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggaggaggctatatggaaaatatttattttccattatagataaaaa Find is-nt database================================================ Query_seq: FN0696:FN0697|FN0696:FN0697:hypothetical protein:Alanyl-tRNA synthetase:->->:1353987..1354131 145 caaatgctacaggaagtccttatgcttatggcagtggtttttcattgccaaaggaatattaaaaaaaataaaatataaaaaataaagaaaataataaaaggaggaggctatatggaaaatatttattttccattatagataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0696:FN0697|FN0696:FN0697:hypothetical protein:Alanyl-tRNA synthetase:->->:1353987..1354131 145 caaatgctacaggaagtccttatgcttatggcagtggtttttcattgccaaaggaatattaaaaaaaataaaatataaaaaataaagaaaataataaaaggaggaggctatatggaaaatatttattttccattatagataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0696:FN0697|FN0696:FN0697:hypothetical protein:Alanyl-tRNA synthetase:->->:1353987..1354131 145 caaatgctacaggaagtccttatgcttatggcagtggtttttcattgccaaaggaatattaaaaaaaataaaatataaaaaataaagaaaataataaaaggaggaggctatatggaaaatatttattttccattatagataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caaatgctacaggaagtccttatgcttatggcagtggtttttcattgccaaaggaatattaaaaaaaataaaatataaaaaataaagaaaataataaaaggaggaggctatatggaaaatatttattttccattatagataaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: - Start: 10 End: 126 ......... L F D K H K H C H N K M A L P I N F F I F Y L F Y L F Y Y F S S A I H F I N M ................... caaatgctacaggaagtccttatgcttatggcagtggtttttcattgccaaaggaatattaaaaaaaataaaatataaaaaataaagaaaataataaaaggaggaggctatatggaaaatatttattttccattatagataaaaa 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: 82 Start: 91 End: 120 ..........................................................................................ATTTTCCATATAGCCTCCTCCTTTTATTAT......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caaatgctacaggaagtccttatgcttatggcagtggtttttcattgccaaaggaatattaaaaaaaataaaatataaaaaataaagaaaataataaaaggaggaggctatatggaaaatatttattttccattatagataaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0696:FN0697|FN0696:FN0697:hypothetical protein:Alanyl-tRNA synthetase:->->:1353987..1354131 145 caaatgctacaggaagtccttatgcttatggcagtggtttttcattgccaaaggaatattaaaaaaaataaaatataaaaaataaagaaaataataaaaggaggaggctatatggaaaatatttattttccattatagataaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: NC_003454_FN0696_FN0697|hypothetical protein:Alanyl-tRNA synthetase|POSITIVE:POSITIVE|[1353987,1354131]|145 HSP 1 e-value: 1.0E-25 bit: 117.0 Len: 59 Query Start:1 Query End:59 Subject Strand: POSITIVE Subject Start: 1 Subject End: 59 caaatgctacaggaagtccttatgcttatggcagtggtttttcattgccaaaggaatat...................................................................................... caaatgctacaggaagtccttatgcttatggcagtggtttttcattgccaaaggaatat...................................................................................... HSP 2 e-value: 6.0E-18 bit: 91.7 Len: 46 Query Start:100 Query End:145 Subject Strand: POSITIVE Subject Start: 100 Subject End: 145 ...................................................................................................ggaggaggctatatggaaaatatttattttccattatagataaaaa ...................................................................................................ggaggaggctatatggaaaatatttattttccattatagataaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAUGCUACAGGAAGUCCUUAUGCUUAUGGCAGUGGUUUUUCAUUGCCAAAGGAAUAUUAAAAAAAAUAAAAUAUAAAAAAUAAAGAAAAUAAUAAAAGGAGGAGGCUAUAUGGAAAAUAUUUAUUUUCCAUUAUAGAUAAAAA ................(((((...(((.(((((((((....))))))))).)))..((((......))))..............................)))))..(((((((((((((....)))))))).)))))....... (-29.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUAUCUAUAAUGGAAAAUAAAUAUUUUCCAUAUAGCCUCCUCCUUUUAUUAUUUUCUUUAUUUUUUAUAUUUUAUUUUUUUUAAUAUUCCUUUGGCAAUGAAAAACCACUGCCAUAAGCAUAAGGACUUCCUGUAGCAUUUG .......(((((.((((((((....))))))))))))).........................................................(((((.((......)).)))))...((...(((....)))...))..... (-23.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 269 48 5 94 56 NC_003454:FN1003|5end_Outer_membrane_protein_P1_precursor_1658822..1659052_POSITIVE 257 48 7 64 15 NC_003454:FN0483|5end_Uracil_phosphoribosyltransferase_1128577..1128807_POSITIVE 250 51 16 91 43 NC_003454:FN0855|5end_glucose-1-phosphate_adenylyltransferase_1514662..1514892_NEGATIVE 238 47 2 175 130 NC_003454:FN1919|5end_Methyltransferase_415882..416112_NEGATIVE 234 57 17 161 98 NC_003454:FN0357|5end_ATP_synthase_epsilon_chain,_sodium_ion_specific_988276..988506_NEGATIVE 216 63 22 138 96 NC_003454:FN2041|5end_Transcription_antitermination_protein_nusG_549659..549889_NEGATIVE 215 45 7 77 39 NC_003454:FN0032|5end_hypothetical_protein_669778..670008_NEGATIVE 212 59 12 75 27 NC_003454:FN0534|5end_hypothetical_protein_1188858..1189088_POSITIVE 212 48 3 189 137 NC_003454:FN2073|5end_adenine_phosphoribosyltransferase_583585..583815_POSITIVE 212 50 5 90 44 NC_003454:FN1544|5end_Probable_electron_transfer_flavoprotein-quinone_oxidoreductase_ydiS_57835..58065_POSITIVE 211 33 5 228 203 NC_003454:FN2004|5end_Cobalt_transport_ATP-binding_protein_cbiO_504303..504533_POSITIVE 209 55 18 110 76 NC_003454:FN0825|5end_Hypothetical_cytosolic_protein_1485124..1485354_POSITIVE 207 50 1 50 4 NC_003454:FN1326|5end_Undecaprenyl_pyrophosphate_synthetase_1981890..1982120_NEGATIVE 207 50 1 56 7 NC_003454:FN1790|5end_Cob(I)alamin_adenosyltransferase_271511..271741_POSITIVE 206 138 113 96 72 NC_003454:FN0870|5end_Rhodanese-related_sulfurtransferase_1529635..1529865_NEGATIVE 205 47 6 66 27 NC_003454:FN1421|5end_Pyruvate-flavodoxin_oxidoreductase_2083305..2083535_POSITIVE 204 48 1 109 69 NC_003454:FN1792|5end_hypothetical_protein_273264..273494_NEGATIVE 203 44 10 81 49 NC_003454:FN1917|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_413756..413986_NEGATIVE 202 129 91 216 173 NC_003454:FN0807|5end_3-deoxy-manno-octulosonate_cytidylyltransferase_1467894..1468124_NEGATIVE 201 43 6 55 9 NC_003454:FN1253|5end_hypothetical_protein_1910405..1910635_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 250 51 16 64 16 NC_003454:FN0856|3end_glycogen_branching_enzyme_1514689..1514839_NEGATIVE 234 57 17 151 88 NC_003454:FN0358|3end_ATP_synthase_subunit_B_988286..988436_NEGATIVE 225 50 5 116 76 NC_003454:FN0029|3end_Flavodoxin_666596..666746_NEGATIVE 216 63 22 141 99 NC_003454:FN2042|3end_Protein_translocase_subunit_SecE_549656..549806_NEGATIVE 212 57 14 56 24 NC_003454:FN0246|3end_hypothetical_protein_870633..870783_NEGATIVE 212 50 5 64 18 NC_003454:FN1543|3end_Ubiquinone/menaquinone_biosynthesis_methyltransferase_UBIE_57889..58039_POSITIVE 203 44 10 97 65 NC_003454:FN1918|3end_SPO0B-associated_GTP-binding_protein_413740..413890_NEGATIVE 200 53 25 66 38 NC_003454:FN0696|3end_hypothetical_protein_1353926..1354076_POSITIVE 199 49 17 54 10 NC_003454:FN0241|3end_Dihydrofolate_reductase_865295..865445_POSITIVE 195 55 17 145 97 NC_003454:FN1353|3end_ABC_transporter_permease_protein_2004184..2004334_NEGATIVE 195 50 14 44 11 NC_003454:FN1789|3end_Na+_driven_multidrug_efflux_pump_271579..271729_POSITIVE 194 50 4 149 101 NC_003454:FN1280|3end_Endonuclease_1940261..1940411_POSITIVE 186 40 7 151 114 NC_003454:FN1398|3end_Amino_acid_carrier_protein_alsT_2054300..2054450_POSITIVE 185 59 16 133 85 NC_003454:FN0397|3end_Dipeptide_transport_system_permease_protein_dppB_1036828..1036978_POSITIVE 185 45 4 74 26 NC_003454:FN0251|3end_Hypothetical_membrane-spanning_Protein_874256..874406_POSITIVE 185 45 4 74 26 NC_003454:FN2061|3end_Hypothetical_membrane-spanning_protein_573666..573816_NEGATIVE 185 45 4 74 26 NC_003454:FN2050|3end_Hypothetical_membrane-spanning_protein_559590..559740_NEGATIVE 184 49 18 123 90 NC_003454:FN2124|3end_Hypothetical_protein_with_Metallo-phosphoesterase_motif_633251..633401_NEGATIVE 184 45 5 57 20 NC_003454:FN1668|3end_Cholinephosphate_cytidylyltransferase_164691..164841_NEGATIVE 183 111 72 67 20 NC_003454:FN1986|3end_hypothetical_protein_490007..490157_POSITIVE