Origin IGS: aacctaaacaatctccttataatcccctacatttcaagcatccagctagattcaatcccgcaaactcctactcggaaactgaataactgtcctttacgctgctttcttaaaaactgtttcaaatctagcttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagctagatttgaaacagtttttaagaaagcagcgtaaaggacagttattcagtttccgagtaggagtttgcgggattgaatctagctggatgcttgaaatgtaggggattataaggagattgtttaggtt Mask Tandem Repeat Region ================================================ aacctaaacaatctccttataatcccctacatttcaagcatccagctagattcaatcccgcaaactcctactcggaaactgaataactgtcctttacgctgctttcttaaaaactgtttcaaatctagcttt Find is-nt database================================================ Query_seq: SSA_2017:SSA_2018|SSA_2017:SSA_2018:Hypothetical protein (possibly membrane-associated):hypothetical protein:<-<-:2017422..2017553 132 aacctaaacaatctccttataatcccctacatttcaagcatccagctagattcaatcccgcaaactcctactcggaaactgaataactgtcctttacgctgctttcttaaaaactgtttcaaatctagcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2017:SSA_2018|SSA_2017:SSA_2018:Hypothetical protein (possibly membrane-associated):hypothetical protein:<-<-:2017422..2017553 132 aacctaaacaatctccttataatcccctacatttcaagcatccagctagattcaatcccgcaaactcctactcggaaactgaataactgtcctttacgctgctttcttaaaaactgtttcaaatctagcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2017:SSA_2018|SSA_2017:SSA_2018:Hypothetical protein (possibly membrane-associated):hypothetical protein:<-<-:2017422..2017553 132 aacctaaacaatctccttataatcccctacatttcaagcatccagctagattcaatcccgcaaactcctactcggaaactgaataactgtcctttacgctgctttcttaaaaactgtttcaaatctagcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacctaaacaatctccttataatcccctacatttcaagcatccagctagattcaatcccgcaaactcctactcggaaactgaataactgtcctttacgctgctttcttaaaaactgtttcaaatctagcttt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 19 End: 132 .................. M I P Y I S S I Q L D S I P Q T P T R K L N N C P L R C F L K N C F K S S F Protein_Len: 31 Strand: - Start: 30 End: 122 ............................. M E L M W S S E I G C V G V R F S F L Q G K R Q K R L F Q K M .......... aacctaaacaatctccttataatcccctacatttcaagcatccagctagattcaatcccgcaaactcctactcggaaactgaataactgtcctttacgctgctttcttaaaaactgtttcaaatctagcttt 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================================================ aacctaaacaatctccttataatcccctacatttcaagcatccagctagattcaatcccgcaaactcctactcggaaactgaataactgtcctttacgctgctttcttaaaaactgtttcaaatctagcttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2017:SSA_2018|SSA_2017:SSA_2018:Hypothetical protein (possibly membrane-associated):hypothetical protein:<-<-:2017422..2017553 132 aacctaaacaatctccttataatcccctacatttcaagcatccagctagattcaatcccgcaaactcctactcggaaactgaataactgtcctttacgctgctttcttaaaaactgtttcaaatctagcttt Intra-Species Hit: Count: 1 Min: 1 Max: 132 Len: 132 Subject: NC_009009_SSA_2017_SSA_2018|Hypothetical protein (possibly membrane-associated):hypothetical protein|NEGATIVE:NEGATIVE|[2017422,2017553]|132 HSP 1 e-value: 3.0E-69 bit: 262.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 aacctaaacaatctccttataatcccctacatttcaagcatccagctagattcaatcccgcaaactcctactcggaaactgaataactgtcctttacgctgctttcttaaaaactgtttcaaatctagcttt aacctaaacaatctccttataatcccctacatttcaagcatccagctagattcaatcccgcaaactcctactcggaaactgaataactgtcctttacgctgctttcttaaaaactgtttcaaatctagcttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACCUAAACAAUCUCCUUAUAAUCCCCUACAUUUCAAGCAUCCAGCUAGAUUCAAUCCCGCAAACUCCUACUCGGAAACUGAAUAACUGUCCUUUACGCUGCUUUCUUAAAAACUGUUUCAAAUCUAGCUUU ...........................................(((((((((.............(((.....)))....(((.....((.......))....)))...............))))))))).. (-11.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGCUAGAUUUGAAACAGUUUUUAAGAAAGCAGCGUAAAGGACAGUUAUUCAGUUUCCGAGUAGGAGUUUGCGGGAUUGAAUCUAGCUGGAUGCUUGAAAUGUAGGGGAUUAUAAGGAGAUUGUUUAGGUU ..(((((((((..(....(((((....)))))..((((...(((..((((((.......))))))..)))))))...)..)))))))))..........(((.((((.((((.......)))).)))).))) (-27.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 934 70 21 161 112 NC_009009:SSA_2017|5end_Hypothetical_protein_(possibly_membrane-associated)_2017331..2017561_NEGATIVE 373 100 56 210 167 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 328 76 32 184 123 NC_009009:SSA_1617|5end_hypothetical_protein_1620651..1620881_NEGATIVE 301 70 23 185 131 NC_009009:SSA_2315|5end_Conserved_uncharacterized_protein_2316945..2317175_NEGATIVE 300 63 26 141 94 NC_009009:SSA_2090|5end_Hexulose-6-phosphate_synthase,_putative_2095038..2095268_NEGATIVE 300 130 84 77 37 NC_009009:SSA_0164|5end_hypothetical_protein_162478..162708_POSITIVE 299 74 32 58 10 NC_009009:SSA_1417|5end_SAM-dependent_methyltransferase,_putative_1427993..1428223_NEGATIVE 299 75 36 60 16 NC_009009:SSA_0723|5end_hypothetical_protein_708246..708476_POSITIVE 292 60 14 133 88 NC_009009:SSA_2218|5end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219941..2220171_NEGATIVE 282 130 87 62 11 NC_009009:SSA_0199|5end_GTP_cyclohydrolase_I,_putative_198276..198506_POSITIVE 282 68 22 214 172 NC_009009:SSA_0033|5end_Phosphoribosylglycinamide_(GAR)_formyltransferase,_putative_38957..39187_POSITIVE 279 108 61 51 4 NC_009009:SSA_1893|5end_N-acetylglucosamine-6-phosphate_deacetylase,_putative_1890572..1890802_NEGATIVE 275 50 3 50 1 NC_009009:SSA_1592|5end_hypothetical_protein_1596397..1596627_NEGATIVE 272 61 21 224 190 NC_009009:SSA_1074|5end_Pyrroline-5-carboxylate_reductase,_putative_1092151..1092381_POSITIVE 272 81 44 213 173 NC_009009:SSA_0336|5end_Isopentenyl-diphosphate_delta-isomerase,_putative_329792..330022_POSITIVE 270 100 52 146 88 NC_009009:SSA_0239|5end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_232961..233191_POSITIVE 270 63 22 210 161 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 269 99 57 205 162 NC_009009:SSA_1850|5end_DNA-directed_RNA_polymerase,_subunit_K/omega,_putative_1846024..1846254_NEGATIVE 268 69 31 39 6 NC_009009:SSA_2184|5end_hypothetical_protein_2183754..2183984_NEGATIVE 265 59 12 185 121 NC_009009:SSA_1691|5end_Transcriptional_regulator,_XRE_family,_putative_1683281..1683511_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 76 32 115 54 NC_009009:SSA_1618|3end_hypothetical_protein_1620720..1620870_NEGATIVE 300 63 26 117 70 NC_009009:SSA_2091|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095062..2095212_NEGATIVE 300 130 84 61 21 NC_009009:SSA_0163|3end_hypothetical_protein_162542..162692_POSITIVE 292 60 14 107 62 NC_009009:SSA_2219|3end_UDP-glucose_4-epimerase,_putative_2219967..2220117_NEGATIVE 282 130 87 81 30 NC_009009:SSA_0198|3end_Dihydrofolate_synthetase,_putative_198375..198525_POSITIVE 277 70 22 72 21 NC_009009:SSA_1047|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase,_putative_1062845..1062995_POSITIVE 275 50 3 57 8 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 275 130 87 110 67 NC_009009:SSA_0405|3end_Transcriptional_regulator,_XRE_family,_putative_402115..402265_POSITIVE 270 100 52 136 78 NC_009009:SSA_0238|3end_hypothetical_protein_233031..233181_POSITIVE 267 89 42 46 7 NC_009009:SSA_0502|3end_Peptide_ABC_transporter,_permease_protein,_putative_502323..502473_POSITIVE 261 120 87 125 91 NC_009009:SSA_0894|3end_ATP-binding_cassette_protein,_putative_886533..886683_POSITIVE 259 130 87 67 30 NC_009009:SSA_0971|3end_Conserved_uncharacterized_protein_980069..980219_POSITIVE 258 69 26 140 89 NC_009009:SSA_1484|3end_DNA_ligase,_putative_1490230..1490380_NEGATIVE 258 68 22 151 107 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE 255 68 27 148 108 NC_009009:SSA_1784|3end_Glutamate_racemase,_putative_1769103..1769253_NEGATIVE 254 99 53 44 2 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 251 100 55 142 97 NC_009009:SSA_2062|3end_hypothetical_protein_2063291..2063441_NEGATIVE 246 78 32 87 42 NC_009009:SSA_2296|3end_Transcriptional_regulator,_XRE_family,_putative_2298549..2298699_NEGATIVE 244 69 21 116 83 NC_009009:SSA_1232|3end_Topoisomerase_IV_subunit_B,_putative_1254806..1254956_NEGATIVE 243 98 55 63 26 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE