Origin IGS: atccttctcctttcactcctgtttgcaagccctgacacctaaattccaactactcccagcttttattttctgaacaaaaccttctcaattcgaccagaaaatatgaaagcgtttctatcatcttctatattattttactatcttattcaacccattgctagtacagtcaaaaataaattgaaaaggacgaactctgagttcatccttctctattgtttataaatctttgtaggctctctttagcaagcaatgtaggattgagagct .........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 agctctcaatcctacattgcttgctaaagagagcctacaaagatttataaacaatagagaaggatgaactcagagttcgtccttttcaatttatttttgactgtactagcaatgggttgaataagatagtaaaataatatagaagatgatagaaacgctttcatattttctggtcgaattgagaaggttttgttcagaaaataaaagctgggagtagttggaatttaggtgtcagggcttgcaaacaggagtgaaaggagaaggat Mask Tandem Repeat Region ================================================ atccttctcctttcactcctgtttgcaagccctgacacctaaattccaactactcccagcttttattttctgaacaaaaccttctcaattcgaccagaaaatatgaaagcgtttctatcatcttctatattattttactatcttattcaacccattgctagtacagtcaaaaataaattgaaaaggacgaactctgagttcatccttctctattgtttataaatctttgtaggctctctttagcaagcaatgtaggattgagagct Find is-nt database================================================ Query_seq: SSA_1382:SSA_1383|SSA_1382:SSA_1383:hypothetical protein:Aspartate aminotransferase, putative:<-<-:1400361..1400626 266 atccttctcctttcactcctgtttgcaagccctgacacctaaattccaactactcccagcttttattttctgaacaaaaccttctcaattcgaccagaaaatatgaaagcgtttctatcatcttctatattattttactatcttattcaacccattgctagtacagtcaaaaataaattgaaaaggacgaactctgagttcatccttctctattgtttataaatctttgtaggctctctttagcaagcaatgtaggattgagagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1382:SSA_1383|SSA_1382:SSA_1383:hypothetical protein:Aspartate aminotransferase, putative:<-<-:1400361..1400626 266 atccttctcctttcactcctgtttgcaagccctgacacctaaattccaactactcccagcttttattttctgaacaaaaccttctcaattcgaccagaaaatatgaaagcgtttctatcatcttctatattattttactatcttattcaacccattgctagtacagtcaaaaataaattgaaaaggacgaactctgagttcatccttctctattgtttataaatctttgtaggctctctttagcaagcaatgtaggattgagagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1382:SSA_1383|SSA_1382:SSA_1383:hypothetical protein:Aspartate aminotransferase, putative:<-<-:1400361..1400626 266 atccttctcctttcactcctgtttgcaagccctgacacctaaattccaactactcccagcttttattttctgaacaaaaccttctcaattcgaccagaaaatatgaaagcgtttctatcatcttctatattattttactatcttattcaacccattgctagtacagtcaaaaataaattgaaaaggacgaactctgagttcatccttctctattgtttataaatctttgtaggctctctttagcaagcaatgtaggattgagagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atccttctcctttcactcctgtttgcaagccctgacacctaaattccaactactcccagcttttattttctgaacaaaaccttctcaattcgaccagaaaatatgaaagcgtttctatcatcttctatattattttactatcttattcaacccattgctagtacagtcaaaaataaattgaaaaggacgaactctgagttcatccttctctattgtttataaatctttgtaggctctctttagcaagcaatgtaggattgagagct Predict ORF larger than 30AA ================================================ Protein_Len: 59 Strand: + Start: 43 End: 219 .......................................... M P T T P S F Y F L N K T F S I R P E N M K A F L S S S I L F Y Y L I Q P I A S T V K N K L K R T N S E F I L L Y C L ............................................... atccttctcctttcactcctgtttgcaagccctgacacctaaattccaactactcccagcttttattttctgaacaaaaccttctcaattcgaccagaaaatatgaaagcgtttctatcatcttctatattattttactatcttattcaacccattgctagtacagtcaaaaataaattgaaaaggacgaactctgagttcatccttctctattgtttataaatctttgtaggctctctttagcaagcaatgtaggattgagagct 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================================================ atccttctcctttcactcctgtttgcaagccctgacacctaaattccaactactcccagcttttattttctgaacaaaaccttctcaattcgaccagaaaatatgaaagcgtttctatcatcttctatattattttactatcttattcaacccattgctagtacagtcaaaaataaattgaaaaggacgaactctgagttcatccttctctattgtttataaatctttgtaggctctctttagcaagcaatgtaggattgagagct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -11.6 Tail_Score: -4.89966 Start: 178 End: 212 Full_Region: aagatttataaacaa tagagaaggatgaact cag agttcgtccttttcaa tttatttttgactgt .................................................................................................................................................................................tagagaaggatgaactcagagttcgtccttttcaa...................................................... TransTerm Strand: - Conf: 93 HP_score: -14.2 Tail_Score: -2.70327 Start: 180 End: 210 Full_Region: gatttataaacaata gagaaggatgaact cag agttcgtccttttc aatttatttttgact ...................................................................................................................................................................................gagaaggatgaactcagagttcgtccttttc........................................................ Find igs database================================================ Query_seq: SSA_1382:SSA_1383|SSA_1382:SSA_1383:hypothetical protein:Aspartate aminotransferase, putative:<-<-:1400361..1400626 266 atccttctcctttcactcctgtttgcaagccctgacacctaaattccaactactcccagcttttattttctgaacaaaaccttctcaattcgaccagaaaatatgaaagcgtttctatcatcttctatattattttactatcttattcaacccattgctagtacagtcaaaaataaattgaaaaggacgaactctgagttcatccttctctattgtttataaatctttgtaggctctctttagcaagcaatgtaggattgagagct Intra-Species Hit: Count: 1 Min: 1 Max: 266 Len: 266 Subject: NC_009009_SSA_1382_SSA_1383|hypothetical protein:Aspartate aminotransferase, putative|NEGATIVE:NEGATIVE|[1400361,1400626]|266 HSP 1 e-value: 1.0E-149 bit: 527.0 Len: 266 Query Start:1 Query End:266 Subject Strand: POSITIVE Subject Start: 1 Subject End: 266 atccttctcctttcactcctgtttgcaagccctgacacctaaattccaactactcccagcttttattttctgaacaaaaccttctcaattcgaccagaaaatatgaaagcgtttctatcatcttctatattattttactatcttattcaacccattgctagtacagtcaaaaataaattgaaaaggacgaactctgagttcatccttctctattgtttataaatctttgtaggctctctttagcaagcaatgtaggattgagagct atccttctcctttcactcctgtttgcaagccctgacacctaaattccaactactcccagcttttattttctgaacaaaaccttctcaattcgaccagaaaatatgaaagcgtttctatcatcttctatattattttactatcttattcaacccattgctagtacagtcaaaaataaattgaaaaggacgaactctgagttcatccttctctattgtttataaatctttgtaggctctctttagcaagcaatgtaggattgagagct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCCUUCUCCUUUCACUCCUGUUUGCAAGCCCUGACACCUAAAUUCCAACUACUCCCAGCUUUUAUUUUCUGAACAAAACCUUCUCAAUUCGACCAGAAAAUAUGAAAGCGUUUCUAUCAUCUUCUAUAUUAUUUUACUAUCUUAUUCAACCCAUUGCUAGUACAGUCAAAAAUAAAUUGAAAAGGACGAACUCUGAGUUCAUCCUUCUCUAUUGUUUAUAAAUCUUUGUAGGCUCUCUUUAGCAAGCAAUGUAGGAUUGAGAGCU .........((((((.((((((((((.((((.((((......................((((((((((((((......................))))))..)))))))).........................(((((.(..............).)))))..))))...((((((.((.(((((.((((.....)))).))))).))....))))))...........)))).......)))))).....)))).)))))).. (-49.69) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUCUCAAUCCUACAUUGCUUGCUAAAGAGAGCCUACAAAGAUUUAUAAACAAUAGAGAAGGAUGAACUCAGAGUUCGUCCUUUUCAAUUUAUUUUUGACUGUACUAGCAAUGGGUUGAAUAAGAUAGUAAAAUAAUAUAGAAGAUGAUAGAAACGCUUUCAUAUUUUCUGGUCGAAUUGAGAAGGUUUUGUUCAGAAAAUAAAAGCUGGGAGUAGUUGGAAUUUAGGUGUCAGGGCUUGCAAACAGGAGUGAAAGGAGAAGGAU ..((((((.((((...((((..(((...((..(((((...................(((((((((((((.....))))))))))))).......(((..((((..(((((......(((((((((((..(..(((....((((((((((.((.....)).)))..))))))).....)))...)..))))))))))).........)))))...))))..)))..))))).))..)))..))))..)))).)))...)))...... (-71.66) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 961 60 11 151 102 NC_009009:SSA_1382|5end_hypothetical_protein_1400270..1400500_NEGATIVE 330 248 202 112 62 NC_009009:SSA_0248|5end_hypothetical_protein_241360..241590_POSITIVE 326 48 3 180 136 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 296 70 23 217 178 NC_009009:SSA_1928|5end_Acyl-CoA_dehydrogenase,_putative_1917010..1917240_NEGATIVE 295 33 3 133 98 NC_009009:SSA_0205|5end_NisK_(sensor-receptor_histidine_kinase_domain),_putative_202722..202952_POSITIVE 288 234 192 133 82 NC_009009:SSA_1967|5end_Threonine_desaminase,_putative_1963559..1963789_NEGATIVE 282 60 18 50 16 NC_009009:SSA_2049|5end_Polyribonucleotide_nucleotidyltransferase,_putative_2052894..2053124_NEGATIVE 282 98 56 140 99 NC_009009:SSA_0977|5end_3-isopropylmalate_dehydrogenase,_putative_982771..983001_POSITIVE 278 58 19 84 37 NC_009009:SSA_1408|5end_hypothetical_protein_1421005..1421235_NEGATIVE 276 39 3 43 1 NC_009009:SSA_1592|5end_hypothetical_protein_1596397..1596627_NEGATIVE 273 237 191 217 160 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 272 54 12 77 35 NC_009009:SSA_2243|5end_Conserved_uncharacterized_protein_2239341..2239571_NEGATIVE 270 60 15 195 149 NC_009009:SSA_0744|5end_S-adenosylmethio_nine:tRNA-ribosyltransferase-isomerase_(queuine_synthetase),_putative_726804..727034_NEGATIVE 269 250 203 142 98 NC_009009:SSA_0928|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_936679..936909_POSITIVE 268 40 1 71 20 NC_009009:SSA_0513|5end_ATP:cob(I)alamin_adenosyltransferase,_putative_511558..511788_POSITIVE 267 49 2 70 9 NC_009009:SSA_1074|5end_Pyrroline-5-carboxylate_reductase,_putative_1092151..1092381_POSITIVE 265 30 2 121 97 NC_009009:SSA_1867|5end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1863096..1863326_NEGATIVE 265 50 3 170 116 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 264 126 81 174 125 NC_009009:SSA_2023|5end_Fructan_beta-fructosidase_precursor,_putative_2028826..2029056_NEGATIVE 264 39 2 151 101 NC_009009:SSA_0218|5end_Sugar-binding_periplasmic_protein,_putative_213863..214093_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 248 202 127 77 NC_009009:SSA_0247|3end_hypothetical_protein_241455..241605_POSITIVE 322 41 8 120 85 NC_009009:SSA_0323|3end_Flavoprotein,_putative_315624..315774_NEGATIVE 319 209 163 148 104 NC_009009:SSA_1222|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_1245038..1245188_NEGATIVE 319 216 177 79 39 NC_009009:SSA_0427|3end_DNA-binding_transcriptional_activator,_SARP_family,_putative_427615..427765_POSITIVE 311 60 14 142 97 NC_009009:SSA_1495|3end_S-adenosylmethionine_synthetase,_putative_1501019..1501169_NEGATIVE 305 39 1 50 6 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 282 98 56 58 17 NC_009009:SSA_0975|3end_2-isopropylmalate_synthase,_putative_982769..982919_POSITIVE 269 250 203 123 79 NC_009009:SSA_0927|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_936740..936890_POSITIVE 268 40 1 58 7 NC_009009:SSA_0512|3end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_511625..511775_POSITIVE 267 48 7 137 83 NC_009009:SSA_1374|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1391359..1391509_NEGATIVE 267 49 2 67 6 NC_009009:SSA_1073|3end_Gamma-glutamyl_phosphate_reductase,_putative_1092228..1092378_POSITIVE 265 30 2 121 97 NC_009009:SSA_1868|3end_ABC-type_arginine/histidine_transport_system,_permease_component,_putative_1863096..1863246_NEGATIVE 263 47 2 143 101 NC_009009:SSA_2261|3end_Transcriptional_repressor_(arginine_synthesis),_putative_2258229..2258379_NEGATIVE 263 60 17 67 18 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 262 35 2 149 104 NC_009009:SSA_0217|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213946..214096_POSITIVE 261 235 195 146 105 NC_009009:SSA_1322|3end_Glycosyl_transferase,_putative_1338536..1338686_NEGATIVE 261 250 204 51 12 NC_009009:SSA_0246|3end_Conserved_uncharacterized_protein_240106..240256_POSITIVE 260 48 5 139 94 NC_009009:SSA_0750|3end_hypothetical_protein_732255..732405_POSITIVE 258 58 16 104 52 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 257 97 52 119 82 NC_009009:SSA_2154|3end_Conserved_uncharacterized_protein_2154762..2154912_NEGATIVE