Origin IGS: aagaaatattttatcataaaaaagtaaagaaggttacagaaaaatattgacaaacgtgatataatgggttggtaagtctttaagcattaagacccactgtaaaataaaaagagagaagttaattgagtaaactctaattacaagataaaatcaggctgttactagatttaataagttcgatttgttgctacagctgtttggttttgcttgtagaggagtaggaagtctaagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acttagacttcctactcctctacaagcaaaaccaaacagctgtagcaacaaatcgaacttattaaatctagtaacagcctgattttatcttgtaattagagtttactcaattaacttctctctttttattttacagtgggtcttaatgcttaaagacttaccaacccattatatcacgtttgtcaatatttttctgtaaccttctttacttttttatgataaaatatttctt Mask Tandem Repeat Region ================================================ aagaaatattttatcataaaaaagtaaagaaggttacagaaaaatattgacaaacgtgatataatgggttggtaagtctttaagcattaagacccactgtaaaataaaaagagagaagttaattgagtaaactctaattacaagataaaatcaggctgttactagatttaataagttcgatttgttgctacagctgtttggttttgcttgtagaggagtaggaagtctaagt Find is-nt database================================================ Query_seq: SSA_0801:SSA_0802|SSA_0801:SSA_0802:Mur ligase family protein, putative:hypothetical protein:<-->:784208..784439 232 aagaaatattttatcataaaaaagtaaagaaggttacagaaaaatattgacaaacgtgatataatgggttggtaagtctttaagcattaagacccactgtaaaataaaaagagagaagttaattgagtaaactctaattacaagataaaatcaggctgttactagatttaataagttcgatttgttgctacagctgtttggttttgcttgtagaggagtaggaagtctaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0801:SSA_0802|SSA_0801:SSA_0802:Mur ligase family protein, putative:hypothetical protein:<-->:784208..784439 232 aagaaatattttatcataaaaaagtaaagaaggttacagaaaaatattgacaaacgtgatataatgggttggtaagtctttaagcattaagacccactgtaaaataaaaagagagaagttaattgagtaaactctaattacaagataaaatcaggctgttactagatttaataagttcgatttgttgctacagctgtttggttttgcttgtagaggagtaggaagtctaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0801:SSA_0802|SSA_0801:SSA_0802:Mur ligase family protein, putative:hypothetical protein:<-->:784208..784439 232 aagaaatattttatcataaaaaagtaaagaaggttacagaaaaatattgacaaacgtgatataatgggttggtaagtctttaagcattaagacccactgtaaaataaaaagagagaagttaattgagtaaactctaattacaagataaaatcaggctgttactagatttaataagttcgatttgttgctacagctgtttggttttgcttgtagaggagtaggaagtctaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagaaatattttatcataaaaaagtaaagaaggttacagaaaaatattgacaaacgtgatataatgggttggtaagtctttaagcattaagacccactgtaaaataaaaagagagaagttaattgagtaaactctaattacaagataaaatcaggctgttactagatttaataagttcgatttgttgctacagctgtttggttttgcttgtagaggagtaggaagtctaagt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 37 End: 138 .................................... L F I N V F T I Y H T P L D K L M L V W Q L I F L S F N I S Y V R M .............................................................................................. aagaaatattttatcataaaaaagtaaagaaggttacagaaaaatattgacaaacgtgatataatgggttggtaagtctttaagcattaagacccactgtaaaataaaaagagagaagttaattgagtaaactctaattacaagataaaatcaggctgttactagatttaataagttcgatttgttgctacagctgtttggttttgcttgtagaggagtaggaagtctaagt 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: 83 Start: 122 End: 151 .........................................................................................................................ATTGAGTAAACTCTAATTACAAGATAAAAT................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagaaatattttatcataaaaaagtaaagaaggttacagaaaaatattgacaaacgtgatataatgggttggtaagtctttaagcattaagacccactgtaaaataaaaagagagaagttaattgagtaaactctaattacaagataaaatcaggctgttactagatttaataagttcgatttgttgctacagctgtttggttttgcttgtagaggagtaggaagtctaagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0801:SSA_0802|SSA_0801:SSA_0802:Mur ligase family protein, putative:hypothetical protein:<-->:784208..784439 232 aagaaatattttatcataaaaaagtaaagaaggttacagaaaaatattgacaaacgtgatataatgggttggtaagtctttaagcattaagacccactgtaaaataaaaagagagaagttaattgagtaaactctaattacaagataaaatcaggctgttactagatttaataagttcgatttgttgctacagctgtttggttttgcttgtagaggagtaggaagtctaagt Intra-Species Hit: Count: 1 Min: 1 Max: 232 Len: 232 Subject: NC_009009_SSA_0801_SSA_0802|Mur ligase family protein, putative:hypothetical protein|NEGATIVE:POSITIVE|[784208,784439]|232 HSP 1 e-value: 1.0E-128 bit: 460.0 Len: 232 Query Start:1 Query End:232 Subject Strand: POSITIVE Subject Start: 1 Subject End: 232 aagaaatattttatcataaaaaagtaaagaaggttacagaaaaatattgacaaacgtgatataatgggttggtaagtctttaagcattaagacccactgtaaaataaaaagagagaagttaattgagtaaactctaattacaagataaaatcaggctgttactagatttaataagttcgatttgttgctacagctgtttggttttgcttgtagaggagtaggaagtctaagt aagaaatattttatcataaaaaagtaaagaaggttacagaaaaatattgacaaacgtgatataatgggttggtaagtctttaagcattaagacccactgtaaaataaaaagagagaagttaattgagtaaactctaattacaagataaaatcaggctgttactagatttaataagttcgatttgttgctacagctgtttggttttgcttgtagaggagtaggaagtctaagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAAAUAUUUUAUCAUAAAAAAGUAAAGAAGGUUACAGAAAAAUAUUGACAAACGUGAUAUAAUGGGUUGGUAAGUCUUUAAGCAUUAAGACCCACUGUAAAAUAAAAAGAGAGAAGUUAAUUGAGUAAACUCUAAUUACAAGAUAAAAUCAGGCUGUUACUAGAUUUAAUAAGUUCGAUUUGUUGCUACAGCUGUUUGGUUUUGCUUGUAGAGGAGUAGGAAGUCUAAGU .......((((((((..................((((((.....(((..((...(((......))).))..))).(((((........)))))...))))))...............((.(((((((....))).))))))..)))))))).(((((.(((((...(((.((((((..((((....((....)).....))))..)))))).))).)))))..))))).... (-43.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUAGACUUCCUACUCCUCUACAAGCAAAACCAAACAGCUGUAGCAACAAAUCGAACUUAUUAAAUCUAGUAACAGCCUGAUUUUAUCUUGUAAUUAGAGUUUACUCAAUUAACUUCUCUCUUUUUAUUUUACAGUGGGUCUUAAUGCUUAAAGACUUACCAACCCAUUAUAUCACGUUUGUCAAUAUUUUUCUGUAACCUUCUUUACUUUUUUAUGAUAAAAUAUUUCUU .....................((((((.........(((((((.((........................)).)))).))).........((((((..(((....)))...........................(((((((((........)))))))))......))))))....)))))).((((((((..(((((..............)))))..)))))))).... (-27.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 848 100 51 191 142 NC_009009:SSA_0801|5end_Mur_ligase_family_protein,_putative_784117..784347_NEGATIVE 295 220 175 62 19 NC_009009:SSA_0251|5end_D-tyrosyl-tRNA(Tyr)_deacylase,_putative_244455..244685_POSITIVE 286 227 183 52 15 NC_009009:SSA_0898|5end_hypothetical_protein_889863..890093_NEGATIVE 285 96 51 223 177 NC_009009:SSA_0317|5end_Ribosomal_protein_alanine_acetyl_transferase,_putative_311259..311489_POSITIVE 275 220 171 192 138 NC_009009:SSA_0492|5end_NADH-dependent_flavin_oxidoreductase,_putative_491588..491818_POSITIVE 273 220 187 41 1 NC_009009:SSA_1876|5end_hypothetical_protein_1871120..1871350_POSITIVE 273 220 187 41 1 NC_009009:SSA_1875|5end_hypothetical_protein_1870558..1870788_POSITIVE 271 228 183 45 8 NC_009009:SSA_0438|5end_Single-strand_binding_protein,_putative_440615..440845_POSITIVE 270 226 185 185 141 NC_009009:SSA_1514|5end_Cell-wall_biogenesis_glycosyltransferase,_putative_1521780..1522010_NEGATIVE 265 217 174 97 44 NC_009009:SSA_1738|5end_Polysaccharide_biosynthesis_protein,_putative_1725503..1725733_NEGATIVE 260 212 190 26 3 NC_009009:SSA_1098|5end_Formate-nitrate_transporter,_putative_1114134..1114364_POSITIVE 260 223 187 66 18 NC_009009:SSA_0667|5end_Transcriptional_regulator,_putative_649778..650008_POSITIVE 259 86 50 45 6 NC_009009:SSA_2099|5end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2104313..2104543_NEGATIVE 259 217 183 51 15 NC_009009:SSA_1027|5end_hypothetical_protein_1043527..1043757_POSITIVE 256 225 183 184 129 NC_009009:SSA_0350|5end_Helicase,_putative_344218..344448_NEGATIVE 253 197 153 197 146 NC_009009:SSA_0831|5end_Nucleotide_sugar_synthetase-like_protein,_putative_815671..815901_POSITIVE 252 225 189 166 130 NC_009009:SSA_2349|5end_DTDP-4-dehydrorhamnose_3,5-epimerase,_putative_2351708..2351938_NEGATIVE 250 210 174 220 180 NC_009009:SSA_2082|5end_Carbohydrate_kinase,_FGGY_family,_putative_2086874..2087104_NEGATIVE 250 220 175 165 119 NC_009009:SSA_0621|5end_SOS_responce_UmuC_protein,_putative_613737..613967_NEGATIVE 249 226 187 101 54 NC_009009:SSA_2038|5end_hypothetical_protein_2041627..2041857_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 227 183 147 110 NC_009009:SSA_0898|3end_hypothetical_protein_889768..889918_NEGATIVE 279 219 174 51 12 NC_009009:SSA_0705|3end_hypothetical_protein_690552..690702_NEGATIVE 278 219 173 99 54 NC_009009:SSA_0819|3end_hypothetical_protein_801181..801331_POSITIVE 275 220 171 137 83 NC_009009:SSA_0491|3end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_491613..491763_POSITIVE 259 217 183 61 25 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 256 225 183 124 69 NC_009009:SSA_0351|3end_Signal_peptidase_I,_putative_344278..344428_NEGATIVE 251 227 187 114 57 NC_009009:SSA_1065|3end_Beta-hexosamidase_A,_putative_1084130..1084280_POSITIVE 250 210 174 144 104 NC_009009:SSA_2083|3end_hypothetical_protein_2086950..2087100_NEGATIVE 247 228 185 43 2 NC_009009:SSA_0292|3end_Transcriptional_regulator,_AraC_family_(arabinose_operon_control),_putative_287262..287412_POSITIVE 246 223 187 119 74 NC_009009:SSA_0813|3end_Thioredoxin_reductase,_putative_794438..794588_NEGATIVE 244 220 174 96 48 NC_009009:SSA_2257|3end_DNA_mismatch_repair_protein,_putative_2251241..2251391_NEGATIVE 243 227 183 142 82 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 240 216 174 140 102 NC_009009:SSA_2130|3end_hypothetical_protein_2134020..2134170_POSITIVE 239 217 174 151 113 NC_009009:SSA_2189|3end_hypothetical_protein_2190279..2190429_NEGATIVE 238 214 175 149 108 NC_009009:SSA_1630|3end_hypothetical_protein_1631508..1631658_POSITIVE 235 226 187 144 107 NC_009009:SSA_1569|3end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1572630..1572780_POSITIVE 235 215 175 76 32 NC_009009:SSA_0899|3end_Conserved_permease,_putative_891161..891311_POSITIVE 235 101 64 115 73 NC_009009:SSA_0831|3end_Nucleotide_sugar_synthetase-like_protein,_putative_816755..816905_POSITIVE 235 228 187 80 33 NC_009009:SSA_0589|3end_Acetylornithine_deacetylase/succinyl-diaminopimelate_desuccinylase_(M20/M25/M40_family_peptidase),_putative_582207..582357_POSITIVE 235 213 172 126 92 NC_009009:SSA_0047|3end_NAD(P)H_dehydrogenase_(Quinone),_putative_52284..52434_NEGATIVE