Origin IGS: catctgtttaggaagttactcagacgactgctaaataagaaagaccctctattgtctgcaatagagggaatttttataagcagattttgtatgtaaaggttttaatttctgaaagcaccttgatatttttctgaaaaggagtaaactggatatacaagtgatggaggtttggt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 accaaacctccatcacttgtatatccagtttactccttttcagaaaaatatcaaggtgctttcagaaattaaaacctttacatacaaaatctgcttataaaaattccctctattgcagacaatagagggtctttcttatttagcagtcgtctgagtaacttcctaaacagatg Mask Tandem Repeat Region ================================================ catctgtttaggaagttactcagacgactgctaaataagaaagaccctctattgtctgcaatagagggaatttttataagcagattttgtatgtaaaggttttaatttctgaaagcaccttgatatttttctgaaaaggagtaaactggatatacaagtgatggaggtttggt Find is-nt database================================================ Query_seq: SSA_0841:SSA_0842|SSA_0841:SSA_0842:hypothetical protein:Effector of murein hydrolase LrgA/holin-like protein, putative:->->:827297..827469 173 catctgtttaggaagttactcagacgactgctaaataagaaagaccctctattgtctgcaatagagggaatttttataagcagattttgtatgtaaaggttttaatttctgaaagcaccttgatatttttctgaaaaggagtaaactggatatacaagtgatggaggtttggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0841:SSA_0842|SSA_0841:SSA_0842:hypothetical protein:Effector of murein hydrolase LrgA/holin-like protein, putative:->->:827297..827469 173 catctgtttaggaagttactcagacgactgctaaataagaaagaccctctattgtctgcaatagagggaatttttataagcagattttgtatgtaaaggttttaatttctgaaagcaccttgatatttttctgaaaaggagtaaactggatatacaagtgatggaggtttggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0841:SSA_0842|SSA_0841:SSA_0842:hypothetical protein:Effector of murein hydrolase LrgA/holin-like protein, putative:->->:827297..827469 173 catctgtttaggaagttactcagacgactgctaaataagaaagaccctctattgtctgcaatagagggaatttttataagcagattttgtatgtaaaggttttaatttctgaaagcaccttgatatttttctgaaaaggagtaaactggatatacaagtgatggaggtttggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 catctgtttaggaagttactcagacgactgctaaataagaaagaccctctattgtctgcaatagagggaatttttataagcagattttgtatgtaaaggttttaatttctgaaagcaccttgatatttttctgaaaaggagtaaactggatatacaagtgatggaggtttggt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 4 End: 93 ... M F R K L L R R L L N K K D P L L S A I E G I F I S R F C M ................................................................................ Protein_Len: 37 Strand: - Start: 52 End: 162 ................................................... Q R C Y L S N K Y A S K T H L P K L K Q F C R S I K R F L L L S S I C T M ........... Protein_Len: 30 Strand: - Start: 3 End: 92 .. R N L F N S L R S S F L F S G R N D A I S P I K I L L N Q M ................................................................................. catctgtttaggaagttactcagacgactgctaaataagaaagaccctctattgtctgcaatagagggaatttttataagcagattttgtatgtaaaggttttaatttctgaaagcaccttgatatttttctgaaaaggagtaaactggatatacaagtgatggaggtttggt 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================================================ catctgtttaggaagttactcagacgactgctaaataagaaagaccctctattgtctgcaatagagggaatttttataagcagattttgtatgtaaaggttttaatttctgaaagcaccttgatatttttctgaaaaggagtaaactggatatacaagtgatggaggtttggt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 83 HP_score: -7.0 Tail_Score: -4.83169 Start: 43 End: 70 Full_Region: CTGCTAAATAAGAAA GACCCTCTATTG TCTG CAATAGAGGGAA TTTTTATAAGCAGAT ..........................................GACCCTCTATTGTCTGCAATAGAGGGAA....................................................................................................... TransTerm Strand: - Conf: 80 HP_score: -7.0 Tail_Score: -4.56978 Start: 43 End: 70 Full_Region: atctgcttataaaaa ttccctctattg caga caatagagggtc tttcttatttagcag ..........................................ttccctctattgcagacaatagagggtc....................................................................................................... TransTerm Strand: + Conf: 85 HP_score: -10.5 Tail_Score: -3.49419 Start: 44 End: 69 Full_Region: TGCTAAATAAGAAAG ACCCTCTATTG TCTG CAATAGAGGGA ATTTTTATAAGCAGA ...........................................ACCCTCTATTGTCTGCAATAGAGGGA........................................................................................................ TransTerm Strand: + Conf: 93 HP_score: -14.0 Tail_Score: -2.6933 Start: 45 End: 68 Full_Region: GCTAAATAAGAAAGA CCCTCTATTG TCTG CAATAGAGGG AATTTTTATAAGCAG ............................................CCCTCTATTGTCTGCAATAGAGGG......................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -14.0 Tail_Score: -3.89033 Start: 45 End: 68 Full_Region: ctgcttataaaaatt ccctctattg caga caatagaggg tctttcttatttagc ............................................ccctctattgcagacaatagaggg......................................................................................................... Find igs database================================================ Query_seq: SSA_0841:SSA_0842|SSA_0841:SSA_0842:hypothetical protein:Effector of murein hydrolase LrgA/holin-like protein, putative:->->:827297..827469 173 catctgtttaggaagttactcagacgactgctaaataagaaagaccctctattgtctgcaatagagggaatttttataagcagattttgtatgtaaaggttttaatttctgaaagcaccttgatatttttctgaaaaggagtaaactggatatacaagtgatggaggtttggt Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: NC_009009_SSA_0841_SSA_0842|hypothetical protein:Effector of murein hydrolase LrgA/holin-like protein, putative|POSITIVE:POSITIVE|[827297,827469]|173 HSP 1 e-value: 1.0E-93 bit: 343.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 catctgtttaggaagttactcagacgactgctaaataagaaagaccctctattgtctgcaatagagggaatttttataagcagattttgtatgtaaaggttttaatttctgaaagcaccttgatatttttctgaaaaggagtaaactggatatacaagtgatggaggtttggt catctgtttaggaagttactcagacgactgctaaataagaaagaccctctattgtctgcaatagagggaatttttataagcagattttgtatgtaaaggttttaatttctgaaagcaccttgatatttttctgaaaaggagtaaactggatatacaagtgatggaggtttggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUCUGUUUAGGAAGUUACUCAGACGACUGCUAAAUAAGAAAGACCCUCUAUUGUCUGCAAUAGAGGGAAUUUUUAUAAGCAGAUUUUGUAUGUAAAGGUUUUAAUUUCUGAAAGCACCUUGAUAUUUUUCUGAAAAGGAGUAAACUGGAUAUACAAGUGAUGGAGGUUUGGU ((((.((((..(......)..))))..(((((..(((((((...((((((((((....))))))))))..))))))).)))))..(((((((((...(((((...((((.(((((...........))))).))))......)))))..))))))))).)))).......... (-44.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCAAACCUCCAUCACUUGUAUAUCCAGUUUACUCCUUUUCAGAAAAAUAUCAAGGUGCUUUCAGAAAUUAAAACCUUUACAUACAAAAUCUGCUUAUAAAAAUUCCCUCUAUUGCAGACAAUAGAGGGUCUUUCUUAUUUAGCAGUCGUCUGAGUAACUUCCUAAACAGAUG .....................((((..(((((......((((((........(((((................)))))............(((((.(((((((..((((((((((....))))))))))..))).))))..)))))...))))))........))))).)))) (-34.43) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 81 42 188 148 NC_009009:SSA_1800|5end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1782371..1782601_NEGATIVE 271 29 1 149 118 NC_009009:SSA_1605|5end_Major_facilitator_superfamily_multi-drug_resistance_efflux_pump_pmrA,_putative_1611732..1611962_NEGATIVE 267 89 56 55 28 NC_009009:SSA_0838|5end_GtfB,_putative_825406..825636_POSITIVE 260 60 14 94 36 NC_009009:SSA_1210|5end_GTP_pyrophosphokinase,_putative_1234655..1234885_NEGATIVE 257 70 21 205 164 NC_009009:SSA_2300|5end_hypothetical_protein_2302508..2302738_NEGATIVE 256 67 25 96 47 NC_009009:SSA_1172|5end_hypothetical_protein_1199926..1200156_NEGATIVE 252 60 19 113 55 NC_009009:SSA_0374|5end_Peptide_methionine_sulfoxide_reductase_msrA/msrB,_putative_363163..363393_POSITIVE 249 83 48 51 15 NC_009009:SSA_1861|5end_Aminopeptidase_C,_putative_1857902..1858132_NEGATIVE 242 60 11 84 28 NC_009009:SSA_0657|5end_PyridoxaL_5'-phosphate_Dependent_Enzymes_class_III,_putative_641445..641675_POSITIVE 241 60 11 71 13 NC_009009:SSA_0652|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase,_putative_635036..635266_POSITIVE 239 48 7 229 187 NC_009009:SSA_1234|5end_5'-nucleotidase,_putative_1259795..1260025_NEGATIVE 237 60 13 90 37 NC_009009:SSA_0508|5end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_506668..506898_POSITIVE 236 81 41 44 4 NC_009009:SSA_1372|5end_hypothetical_protein_1389137..1389367_NEGATIVE 236 58 15 54 9 NC_009009:SSA_1055|5end_Conserved_uncharacterized_protein_1070899..1071129_POSITIVE 235 32 1 42 7 NC_009009:SSA_1614|5end_Acetyltransferase,_GNAT_family,_putative_1618045..1618275_NEGATIVE 234 68 29 230 189 NC_009009:SSA_2288|5end_Cadmium_resistance_transporter,_putative_2290461..2290691_POSITIVE 231 69 26 71 33 NC_009009:SSA_0465|5end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_469185..469415_POSITIVE 231 86 45 159 123 NC_009009:SSA_0129|5end_Translation_initiation_factor_IF-1,_putative_119957..120187_POSITIVE 228 60 19 39 3 NC_009009:SSA_1374|5end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393095..1393325_NEGATIVE 226 64 21 213 165 NC_009009:SSA_0990|5end_hypothetical_protein_991733..991963_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 376 68 24 46 1 NC_009009:SSA_0841|3end_hypothetical_protein_827236..827386_POSITIVE 297 68 21 76 17 NC_009009:SSA_1432|3end_HflX_GTPase,_putative_1438663..1438813_NEGATIVE 271 29 1 52 21 NC_009009:SSA_1606|3end_Dephospho-CoA_kinase,_putative_1611829..1611979_NEGATIVE 268 69 21 133 69 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 267 89 56 71 44 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE 257 70 21 44 3 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 254 47 3 151 97 NC_009009:SSA_1065|3end_Beta-hexosamidase_A,_putative_1084130..1084280_POSITIVE 248 60 14 49 3 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 247 69 28 58 21 NC_009009:SSA_2096|3end_ATP-dependent_protease,_ATP-binding_subunit,_putative_2099557..2099707_NEGATIVE 242 60 11 75 19 NC_009009:SSA_0656|3end_Cell_division_protein_FtsZ,_putative_641516..641666_POSITIVE 240 70 25 84 45 NC_009009:SSA_0177|3end_DNA-directed_RNA_polymerase_I,_beta_chain_(160_kDa_subunit),_putative_182132..182282_POSITIVE 239 48 7 65 23 NC_009009:SSA_1235|3end_Dihydroorotase,_putative_1259959..1260109_NEGATIVE 236 58 15 48 3 NC_009009:SSA_1054|3end_CBS_domain_protein,_putative_1070973..1071123_POSITIVE 235 97 58 58 17 NC_009009:SSA_0909|3end_Transcriptional_regulator,_AbrB_family_(stationary/sporulation_gene_expression),_putative_921158..921308_POSITIVE 231 69 26 61 23 NC_009009:SSA_0464|3end_Cobalamin_biosynthesis_protein_cobD,_putative_469255..469405_POSITIVE 231 86 45 41 5 NC_009009:SSA_0128|3end_Adenylate_kinase,_putative_119919..120069_POSITIVE 229 87 41 92 48 NC_009009:SSA_2056|3end_Cinnamoyl_ester_hydrolase,_putative_2059593..2059743_POSITIVE 226 60 19 115 67 NC_009009:SSA_0831|3end_Nucleotide_sugar_synthetase-like_protein,_putative_816755..816905_POSITIVE 225 84 48 114 79 NC_009009:SSA_1191|3end_hypothetical_protein_1218222..1218372_NEGATIVE 224 60 19 41 8 NC_009009:SSA_0211|3end_hypothetical_protein_208456..208606_POSITIVE