Origin IGS: tttgaatagatctcctattttttcataatttttactatttccgcccacaggggcattcgttttgttcctagctgggagaccccacaaactcccagcatccgaacggttttcctaactttttgtgcagagcaagtcctctgcgaattctaactttttctgtaaataatctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagattatttacagaaaaagttagaattcgcagaggacttgctctgcacaaaaagttaggaaaaccgttcggatgctgggagtttgtggggtctcccagctaggaacaaaacgaatgcccctgtgggcggaaatagtaaaaattatgaaaaaataggagatctattcaaa Mask Tandem Repeat Region ================================================ tttgaatagatctcctattttttcataatttttactatttccgcccacaggggcattcgttttgttcctagctgggagaccccacaaactcccagcatccgaacggttttcctaactttttgtgcagagcaagtcctctgcgaattctaactttttctgtaaataatctt Find is-nt database================================================ Query_seq: SSA_2315:SSA_2316|SSA_2315:SSA_2316:Conserved uncharacterized protein:General secretory pathway protein F, putative:<-<-:2317036..2317205 170 tttgaatagatctcctattttttcataatttttactatttccgcccacaggggcattcgttttgttcctagctgggagaccccacaaactcccagcatccgaacggttttcctaactttttgtgcagagcaagtcctctgcgaattctaactttttctgtaaataatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2315:SSA_2316|SSA_2315:SSA_2316:Conserved uncharacterized protein:General secretory pathway protein F, putative:<-<-:2317036..2317205 170 tttgaatagatctcctattttttcataatttttactatttccgcccacaggggcattcgttttgttcctagctgggagaccccacaaactcccagcatccgaacggttttcctaactttttgtgcagagcaagtcctctgcgaattctaactttttctgtaaataatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2315:SSA_2316|SSA_2315:SSA_2316:Conserved uncharacterized protein:General secretory pathway protein F, putative:<-<-:2317036..2317205 170 tttgaatagatctcctattttttcataatttttactatttccgcccacaggggcattcgttttgttcctagctgggagaccccacaaactcccagcatccgaacggttttcctaactttttgtgcagagcaagtcctctgcgaattctaactttttctgtaaataatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttgaatagatctcctattttttcataatttttactatttccgcccacaggggcattcgttttgttcctagctgggagaccccacaaactcccagcatccgaacggttttcctaactttttgtgcagagcaagtcctctgcgaattctaactttttctgtaaataatctt Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 10 End: 147 ......... M S Y F F I I F T I S A H R G I R F V P S W E T P Q T P S I R T V F L T F C A E Q V L C E F ....................... Protein_Len: 33 Strand: + Start: 72 End: 170 ....................................................................... M G D P T N S Q H P N G F P N F L C R A S P L R I L T F S V N N L tttgaatagatctcctattttttcataatttttactatttccgcccacaggggcattcgttttgttcctagctgggagaccccacaaactcccagcatccgaacggttttcctaactttttgtgcagagcaagtcctctgcgaattctaactttttctgtaaataatctt 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================================================ tttgaatagatctcctattttttcataatttttactatttccgcccacaggggcattcgttttgttcctagctgggagaccccacaaactcccagcatccgaacggttttcctaactttttgtgcagagcaagtcctctgcgaattctaactttttctgtaaataatctt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 51 HP_score: -3.1 Tail_Score: -3.57767 Start: 121 End: 144 Full_Region: GTTTTCCTAACTTTT TGTGCAGAG CAAGTC CTCTGCGAA TTCTAACTTTTTCTG ........................................................................................................................TGTGCAGAGCAAGTCCTCTGCGAA.......................... Find igs database================================================ Query_seq: SSA_2315:SSA_2316|SSA_2315:SSA_2316:Conserved uncharacterized protein:General secretory pathway protein F, putative:<-<-:2317036..2317205 170 tttgaatagatctcctattttttcataatttttactatttccgcccacaggggcattcgttttgttcctagctgggagaccccacaaactcccagcatccgaacggttttcctaactttttgtgcagagcaagtcctctgcgaattctaactttttctgtaaataatctt Intra-Species Hit: Count: 1 Min: 1 Max: 170 Len: 170 Subject: NC_009009_SSA_2315_SSA_2316|Conserved uncharacterized protein:General secretory pathway protein F, putative|NEGATIVE:NEGATIVE|[2317036,2317205]|170 HSP 1 e-value: 7.0E-92 bit: 337.0 Len: 170 Query Start:1 Query End:170 Subject Strand: POSITIVE Subject Start: 1 Subject End: 170 tttgaatagatctcctattttttcataatttttactatttccgcccacaggggcattcgttttgttcctagctgggagaccccacaaactcccagcatccgaacggttttcctaactttttgtgcagagcaagtcctctgcgaattctaactttttctgtaaataatctt tttgaatagatctcctattttttcataatttttactatttccgcccacaggggcattcgttttgttcctagctgggagaccccacaaactcccagcatccgaacggttttcctaactttttgtgcagagcaagtcctctgcgaattctaactttttctgtaaataatctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGAAUAGAUCUCCUAUUUUUUCAUAAUUUUUACUAUUUCCGCCCACAGGGGCAUUCGUUUUGUUCCUAGCUGGGAGACCCCACAAACUCCCAGCAUCCGAACGGUUUUCCUAACUUUUUGUGCAGAGCAAGUCCUCUGCGAAUUCUAACUUUUUCUGUAAAUAAUCUU ...((((((.....))))))..........(((((.......((((....))))....(((..((((...((((((((..........))))))))...((((.((((.....)))).)))).((((((......))))))))))...))).......)))))....... (-41.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAUUAUUUACAGAAAAAGUUAGAAUUCGCAGAGGACUUGCUCUGCACAAAAAGUUAGGAAAACCGUUCGGAUGCUGGGAGUUUGUGGGGUCUCCCAGCUAGGAACAAAACGAAUGCCCCUGUGGGCGGAAAUAGUAAAAAUUAUGAAAAAAUAGGAGAUCUAUUCAAA .(((((.(((((.......(((.......((((((......))))))...................((((....((((((((..........))))))))...))))..)))...(((((....)))))......)))))..((((......))))..)))))....... (-43.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1074 90 41 181 132 NC_009009:SSA_2315|5end_Conserved_uncharacterized_protein_2316945..2317175_NEGATIVE 441 100 52 50 5 NC_009009:SSA_1676|5end_Transcriptional_regulator,_LytTr_family,_putative_1671313..1671543_NEGATIVE 369 106 68 57 18 NC_009009:SSA_0175|5end_Penicillin-binding_protein_1B,_putative_172152..172382_POSITIVE 348 100 52 59 1 NC_009009:SSA_0090|5end_Acetyltransferase,_GNAT_family,_putative_90258..90488_POSITIVE 345 79 40 75 36 NC_009009:SSA_1417|5end_SAM-dependent_methyltransferase,_putative_1427993..1428223_NEGATIVE 340 109 62 211 145 NC_009009:SSA_0462|5end_ABC-type_multidrug_transport_system_(phospholipid,_LPS,_lipid_A_and_drug_exporter),_ATPase_and_permease_components,_putative_464815..465045_POSITIVE 330 110 64 67 13 NC_009009:SSA_1325|5end_Ketoacyl_reductase_hetN,_putative_1342343..1342573_NEGATIVE 330 107 68 225 169 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 326 112 71 55 8 NC_009009:SSA_0086|5end_V-type_sodium_ATPase,_subunit_K,_putative_87839..88069_POSITIVE 325 98 51 59 16 NC_009009:SSA_0709|5end_hypothetical_protein_695895..696125_NEGATIVE 325 80 39 211 174 NC_009009:SSA_0492|5end_NADH-dependent_flavin_oxidoreductase,_putative_491588..491818_POSITIVE 320 74 31 164 119 NC_009009:SSA_0479|5end_CbiQ_protein,_putative_480425..480655_POSITIVE 317 85 43 205 158 NC_009009:SSA_2351|5end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_ATPase_component,_putative_2353507..2353737_NEGATIVE 314 103 63 43 2 NC_009009:SSA_1111|5end_Branched-chain_amino_acid_transport_system_II_carrier_protein,_putative_1136532..1136762_POSITIVE 313 89 43 215 144 NC_009009:SSA_0789|5end_Proton-translocating_ATPase,_F1_sector,_epsilon_subunit,_putative_772451..772681_POSITIVE 312 66 33 74 42 NC_009009:SSA_0374|5end_Peptide_methionine_sulfoxide_reductase_msrA/msrB,_putative_363163..363393_POSITIVE 310 158 123 56 21 NC_009009:SSA_1313|5end_hypothetical_protein_1330548..1330778_NEGATIVE 310 139 91 176 115 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 309 108 61 62 1 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 308 85 42 113 56 NC_009009:SSA_1266|5end_crcB-like_protein_1,_putative_1291000..1291230_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 379 80 35 55 8 NC_009009:SSA_0728|3end_Protease,_putative_714523..714673_POSITIVE 379 148 106 81 30 NC_009009:SSA_0567|3end_Isochorismitase_family_protein,_putative_561442..561592_POSITIVE 333 80 35 117 62 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 325 98 51 69 26 NC_009009:SSA_0711|3end_hypothetical_protein_695885..696035_NEGATIVE 324 108 61 126 84 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 320 74 31 46 1 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 311 90 41 147 104 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 308 95 60 135 98 NC_009009:SSA_2023|3end_Fructan_beta-fructosidase_precursor,_putative_2024609..2024759_NEGATIVE 308 85 42 140 83 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 307 113 72 84 32 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 301 110 63 70 11 NC_009009:SSA_1970|3end_Acetolactate_synthase,_large_subunit,_biosynthetic_type,_putative_1965215..1965365_NEGATIVE 298 97 51 52 2 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 292 83 41 98 45 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE 292 85 41 73 17 NC_009009:SSA_0039|3end_Phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit,_putative_46401..46551_POSITIVE 291 130 85 141 97 NC_009009:SSA_1650|3end_3-Ketoacyl-ACP_reductase,_putative_1648896..1649046_NEGATIVE 287 136 96 136 96 NC_009009:SSA_0065|3end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67677..67827_POSITIVE 285 136 92 144 98 NC_009009:SSA_1016|3end_Phosphoenolpyruvate_synthase,_putative_1022165..1022315_POSITIVE 283 95 57 65 25 NC_009009:SSA_0834|3end_Accessory_secretory_protein_Asp2,_putative_821119..821269_POSITIVE 282 100 51 70 5 NC_009009:SSA_1132|3end_TatC,_sec-independent_protein_translocase,_putative_1159477..1159627_POSITIVE 282 110 69 138 94 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE