Origin IGS: gagtacggcgatagtaattgaggagtttttattgttgttaatcagtaaaagcatgctgaaaatctatttgctcaggctttctttgtgctataataaagaaaaacgatgaggagacatac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtatgtctcctcatcgtttttctttattatagcacaaagaaagcctgagcaaatagattttcagcatgcttttactgattaacaacaataaaaactcctcaattactatcgccgtactc Mask Tandem Repeat Region ================================================ gagtacggcgatagtaattgaggagtttttattgttgttaatcagtaaaagcatgctgaaaatctatttgctcaggctttctttgtgctataataaagaaaaacgatgaggagacatac Find is-nt database================================================ Query_seq: SSA_1020:SSA_1021|SSA_1020:SSA_1021:hypothetical protein:Conserved uncharacterized protein:->->:1036165..1036283 119 gagtacggcgatagtaattgaggagtttttattgttgttaatcagtaaaagcatgctgaaaatctatttgctcaggctttctttgtgctataataaagaaaaacgatgaggagacatac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1020:SSA_1021|SSA_1020:SSA_1021:hypothetical protein:Conserved uncharacterized protein:->->:1036165..1036283 119 gagtacggcgatagtaattgaggagtttttattgttgttaatcagtaaaagcatgctgaaaatctatttgctcaggctttctttgtgctataataaagaaaaacgatgaggagacatac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1020:SSA_1021|SSA_1020:SSA_1021:hypothetical protein:Conserved uncharacterized protein:->->:1036165..1036283 119 gagtacggcgatagtaattgaggagtttttattgttgttaatcagtaaaagcatgctgaaaatctatttgctcaggctttctttgtgctataataaagaaaaacgatgaggagacatac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagtacggcgatagtaattgaggagtttttattgttgttaatcagtaaaagcatgctgaaaatctatttgctcaggctttctttgtgctataataaagaaaaacgatgaggagacatac Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 11 End: 106 .......... M V I E E F L L L L I S K S M L K I Y L L R L S L C Y N K E K R ............. gagtacggcgatagtaattgaggagtttttattgttgttaatcagtaaaagcatgctgaaaatctatttgctcaggctttctttgtgctataataaagaaaaacgatgaggagacatac 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================================================ gagtacggcgatagtaattgaggagtttttattgttgttaatcagtaaaagcatgctgaaaatctatttgctcaggctttctttgtgctataataaagaaaaacgatgaggagacatac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1020:SSA_1021|SSA_1020:SSA_1021:hypothetical protein:Conserved uncharacterized protein:->->:1036165..1036283 119 gagtacggcgatagtaattgaggagtttttattgttgttaatcagtaaaagcatgctgaaaatctatttgctcaggctttctttgtgctataataaagaaaaacgatgaggagacatac Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: NC_009009_SSA_1020_SSA_1021|hypothetical protein:Conserved uncharacterized protein|POSITIVE:POSITIVE|[1036165,1036283]|119 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 gagtacggcgatagtaattgaggagtttttattgttgttaatcagtaaaagcatgctgaaaatctatttgctcaggctttctttgtgctataataaagaaaaacgatgaggagacatac gagtacggcgatagtaattgaggagtttttattgttgttaatcagtaaaagcatgctgaaaatctatttgctcaggctttctttgtgctataataaagaaaaacgatgaggagacatac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGUACGGCGAUAGUAAUUGAGGAGUUUUUAUUGUUGUUAAUCAGUAAAAGCAUGCUGAAAAUCUAUUUGCUCAGGCUUUCUUUGUGCUAUAAUAAAGAAAAACGAUGAGGAGACAUAC (((((....(((((...((.((.(((((((((((........)))))))))).).)).))...)))))))))).(..(((((((((......)))))))))..).....(....).... (-28.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAUGUCUCCUCAUCGUUUUUCUUUAUUAUAGCACAAAGAAAGCCUGAGCAAAUAGAUUUUCAGCAUGCUUUUACUGAUUAACAACAAUAAAAACUCCUCAAUUACUAUCGCCGUACUC (((((.(..((((..(((((.((((..........))))))))).))))...........((((..........))))................................).))))).. (-11.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 325 88 41 159 108 NC_009009:SSA_1307|5end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1326270..1326500_NEGATIVE 285 89 56 215 180 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 277 89 42 151 103 NC_009009:SSA_0185|5end_Competence_protein_ComYB,_putative_189057..189287_POSITIVE 261 48 2 169 127 NC_009009:SSA_1197|5end_DNA_alkylation_repair_enzyme,_putative_1222699..1222929_NEGATIVE 261 87 41 228 181 NC_009009:SSA_0498|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_systems,_permease_components,_putative_497910..498140_POSITIVE 261 77 33 165 123 NC_009009:SSA_0476|5end_Precorrin-2_C20-methyltransferase,_putative_478500..478730_POSITIVE 258 89 53 205 171 NC_009009:SSA_0634|5end_Anthranilate_phosphoribosyltransferase,_putative_623387..623617_POSITIVE 257 88 49 73 26 NC_009009:SSA_2064|5end_hypothetical_protein_2065031..2065261_NEGATIVE 250 89 43 179 130 NC_009009:SSA_2028|5end_Conserved_uncharacterized_protein_2035452..2035682_NEGATIVE 248 58 21 211 178 NC_009009:SSA_0944|5end_Phosphate_import_ATP-binding_protein_pstB_2,_putative_951741..951971_POSITIVE 247 89 51 48 4 NC_009009:SSA_2231|5end_Heme/copper-type_cytochrome/quinol_oxidases,_subunit_1,_putative_2232928..2233158_NEGATIVE 247 99 54 155 107 NC_009009:SSA_2161|5end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160600..2160830_NEGATIVE 247 93 52 132 89 NC_009009:SSA_1787|5end_Diaminopimelate_decarboxylase,_putative_1771551..1771781_NEGATIVE 245 77 59 175 157 NC_009009:SSA_1096|5end_Methyltransferase,_putative_1113072..1113302_POSITIVE 243 99 52 126 70 NC_009009:SSA_1367|5end_hypothetical_protein_1383593..1383823_POSITIVE 242 89 44 49 3 NC_009009:SSA_0927|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_936049..936279_POSITIVE 238 77 31 176 130 NC_009009:SSA_2029|5end_Transposase_and_inactivated_derivatives,_putative_2036028..2036258_NEGATIVE 236 84 54 109 74 NC_009009:SSA_1992|5end_Fructose-bisphosphate_aldolase,_putative_1989972..1990202_NEGATIVE 236 89 55 161 120 NC_009009:SSA_1395|5end_hypothetical_protein_1409773..1410003_NEGATIVE 234 89 50 166 123 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 86 41 74 25 NC_009009:SSA_0358|3end_hypothetical_protein_351288..351438_NEGATIVE 285 89 56 130 95 NC_009009:SSA_1460|3end_Transcriptional_attenuator_LytR,_putative_1467566..1467716_NEGATIVE 262 84 41 150 111 NC_009009:SSA_1308|3end_hypothetical_protein_1326267..1326417_NEGATIVE 257 88 49 53 6 NC_009009:SSA_2065|3end_hypothetical_protein_2065051..2065201_NEGATIVE 255 79 44 145 106 NC_009009:SSA_1179|3end_Carbamoylphosphate_synthase_large_subunit_/_biotin_carboxylase,_putative_1206640..1206790_NEGATIVE 249 66 21 68 14 NC_009009:SSA_0964|3end_DEAD_RNA_helicase,_putative_972954..973104_NEGATIVE 245 77 59 111 93 NC_009009:SSA_1095|3end_Peptidoglycan_hydrolase,_putative_1113088..1113238_POSITIVE 236 89 55 144 103 NC_009009:SSA_1396|3end_hypothetical_protein_1409790..1409940_NEGATIVE 235 50 3 67 13 NC_009009:SSA_0663|3end_Acetyltransferase,_putative_648788..648938_POSITIVE 233 84 48 80 51 NC_009009:SSA_1591|3end_Dipeptidase,_putative_1593403..1593553_NEGATIVE 233 77 31 96 43 NC_009009:SSA_1077|3end_N-acetyl-glucosamine_matabolism,_putative_1095829..1095979_POSITIVE 231 82 47 33 2 NC_009009:SSA_2371|3end_Zn-dependent_peptidase,_putative_2372422..2372572_NEGATIVE 230 100 51 116 77 NC_009009:SSA_0141|3end_Copper_chaperone,_putative_137191..137341_POSITIVE 228 77 40 40 3 NC_009009:SSA_1912|3end_hypothetical_protein_1903113..1903263_NEGATIVE 226 93 64 27 1 NC_009009:SSA_1788|3end_Integral_membrane_protein,_possible_receptor,_putative_1771656..1771806_NEGATIVE 226 89 63 62 35 NC_009009:SSA_0528|3end_Conserved_uncharacterized_protein_526010..526160_POSITIVE 224 89 49 110 67 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 223 106 64 79 36 NC_009009:SSA_0281|3end_hypothetical_protein_273963..274113_POSITIVE 221 77 31 147 90 NC_009009:SSA_1740|3end_hypothetical_protein_1727081..1727231_NEGATIVE 218 91 51 119 86 NC_009009:SSA_0508|3end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_508064..508214_POSITIVE