Origin IGS: aagacaagaacaaccgcaagatgggacatgtgactttgtttagtgataagccagatagtgtggttgagtttggggagtaagacaggaccccagttataaggtccgtcgtcttacccctgcaaggttgactaggcttgtcgtagctgataaagtcagcaagagaagccagtcaactactgctagaagggattgatttttaggacaagcct .........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 aggcttgtcctaaaaatcaatcccttctagcagtagttgactggcttctcttgctgactttatcagctacgacaagcctagtcaaccttgcaggggtaagacgacggaccttataactggggtcctgtcttactccccaaactcaaccacactatctggcttatcactaaacaaagtcacatgtcccatcttgcggttgttcttgtctt Mask Tandem Repeat Region ================================================ aagacaagaacaaccgcaagatgggacatgtgactttgtttagtgataagccagatagtgtggttgagtttggggagtaagacaggaccccagttataaggtccgtcgtcttacccctgcaaggttgactaggcttgtcgtagctgataaagtcagcaagagaagccagtcaactactgctagaagggattgatttttaggacaagcct Find is-nt database================================================ Query_seq: SSA_0042:SSA_0043|SSA_0042:SSA_0043:Amino acid recemase, putative:hypothetical protein:->->:48732..48940 209 aagacaagaacaaccgcaagatgggacatgtgactttgtttagtgataagccagatagtgtggttgagtttggggagtaagacaggaccccagttataaggtccgtcgtcttacccctgcaaggttgactaggcttgtcgtagctgataaagtcagcaagagaagccagtcaactactgctagaagggattgatttttaggacaagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0042:SSA_0043|SSA_0042:SSA_0043:Amino acid recemase, putative:hypothetical protein:->->:48732..48940 209 aagacaagaacaaccgcaagatgggacatgtgactttgtttagtgataagccagatagtgtggttgagtttggggagtaagacaggaccccagttataaggtccgtcgtcttacccctgcaaggttgactaggcttgtcgtagctgataaagtcagcaagagaagccagtcaactactgctagaagggattgatttttaggacaagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0042:SSA_0043|SSA_0042:SSA_0043:Amino acid recemase, putative:hypothetical protein:->->:48732..48940 209 aagacaagaacaaccgcaagatgggacatgtgactttgtttagtgataagccagatagtgtggttgagtttggggagtaagacaggaccccagttataaggtccgtcgtcttacccctgcaaggttgactaggcttgtcgtagctgataaagtcagcaagagaagccagtcaactactgctagaagggattgatttttaggacaagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagacaagaacaaccgcaagatgggacatgtgactttgtttagtgataagccagatagtgtggttgagtttggggagtaagacaggaccccagttataaggtccgtcgtcttacccctgcaaggttgactaggcttgtcgtagctgataaagtcagcaagagaagccagtcaactactgctagaagggattgatttttaggacaagcct Predict ORF larger than 30AA ================================================ Protein_Len: 56 Strand: - Start: 2 End: 169 . S L F L R L I P C T V K N L S L G S L T T S N P S Y S L V G T I L D T T K G R C P Q S P K D Y S I F D A L S A M ........................................ aagacaagaacaaccgcaagatgggacatgtgactttgtttagtgataagccagatagtgtggttgagtttggggagtaagacaggaccccagttataaggtccgtcgtcttacccctgcaaggttgactaggcttgtcgtagctgataaagtcagcaagagaagccagtcaactactgctagaagggattgatttttaggacaagcct 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================================================ aagacaagaacaaccgcaagatgggacatgtgactttgtttagtgataagccagatagtgtggttgagtttggggagtaagacaggaccccagttataaggtccgtcgtcttacccctgcaaggttgactaggcttgtcgtagctgataaagtcagcaagagaagccagtcaactactgctagaagggattgatttttaggacaagcct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0042:SSA_0043|SSA_0042:SSA_0043:Amino acid recemase, putative:hypothetical protein:->->:48732..48940 209 aagacaagaacaaccgcaagatgggacatgtgactttgtttagtgataagccagatagtgtggttgagtttggggagtaagacaggaccccagttataaggtccgtcgtcttacccctgcaaggttgactaggcttgtcgtagctgataaagtcagcaagagaagccagtcaactactgctagaagggattgatttttaggacaagcct Intra-Species Hit: Count: 1 Min: 1 Max: 209 Len: 209 Subject: NC_009009_SSA_0042_SSA_0043|Amino acid recemase, putative:hypothetical protein|POSITIVE:POSITIVE|[48732,48940]|209 HSP 1 e-value: 1.0E-115 bit: 414.0 Len: 209 Query Start:1 Query End:209 Subject Strand: POSITIVE Subject Start: 1 Subject End: 209 aagacaagaacaaccgcaagatgggacatgtgactttgtttagtgataagccagatagtgtggttgagtttggggagtaagacaggaccccagttataaggtccgtcgtcttacccctgcaaggttgactaggcttgtcgtagctgataaagtcagcaagagaagccagtcaactactgctagaagggattgatttttaggacaagcct aagacaagaacaaccgcaagatgggacatgtgactttgtttagtgataagccagatagtgtggttgagtttggggagtaagacaggaccccagttataaggtccgtcgtcttacccctgcaaggttgactaggcttgtcgtagctgataaagtcagcaagagaagccagtcaactactgctagaagggattgatttttaggacaagcct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGACAAGAACAACCGCAAGAUGGGACAUGUGACUUUGUUUAGUGAUAAGCCAGAUAGUGUGGUUGAGUUUGGGGAGUAAGACAGGACCCCAGUUAUAAGGUCCGUCGUCUUACCCCUGCAAGGUUGACUAGGCUUGUCGUAGCUGAUAAAGUCAGCAAGAGAAGCCAGUCAACUACUGCUAGAAGGGAUUGAUUUUUAGGACAAGCCU ....((((..((((((((..((.((.(.(((.(((......))).))).)))..))..))))))))..))))(((.(((((((.(((((..........)))))...)))))))))).((..((((((((.(((((.((...((((((...))))))..)).)))))))))))))....(((((((.......))))))).....)).. (-77.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGCUUGUCCUAAAAAUCAAUCCCUUCUAGCAGUAGUUGACUGGCUUCUCUUGCUGACUUUAUCAGCUACGACAAGCCUAGUCAACCUUGCAGGGGUAAGACGACGGACCUUAUAACUGGGGUCCUGUCUUACUCCCCAAACUCAACCACACUAUCUGGCUUAUCACUAAACAAAGUCACAUGUCCCAUCUUGCGGUUGUUCUUGUCUU .((.(((..........))).))......((((..((((((((((((.((..(((((.....)))))...)).))))).))))))).)))).(((((((((((..((((((((....))))))))))))))))))).(((...(((((.((..((..(((.....(((......))).....)))..))..)).)))))...))).... (-66.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 482 120 72 172 115 NC_009009:SSA_0060|5end_Tagatose-6-phosphate_ketose/aldose_isomerase,_putative_61477..61707_POSITIVE 438 148 104 203 159 NC_009009:SSA_1009|5end_Galactose-1-phosphate-uridylyltransferase,_putative_1011254..1011484_POSITIVE 403 154 116 61 18 NC_009009:SSA_2050|5end_Arabinose_efflux_permease,_putative_2053255..2053485_POSITIVE 395 140 92 214 158 NC_009009:SSA_1720|5end_Initiation-control_protein,_putative_1707113..1707343_NEGATIVE 377 180 131 229 166 NC_009009:SSA_1133|5end_TatA,_sec-independent_protein_secretion_pathway_component,_putative_1159397..1159627_POSITIVE 366 179 132 62 5 NC_009009:SSA_1792|5end_Preprotein_translocase_subunit_YidC,_putative_1774036..1774266_POSITIVE 363 189 142 75 26 NC_009009:SSA_1948|5end_Oligopeptide-binding_lipoprotein_precursor,_putative_1942170..1942400_NEGATIVE 363 157 117 55 18 NC_009009:SSA_0142|5end_hypothetical_protein_137230..137460_POSITIVE 349 119 71 72 24 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 339 143 101 145 100 NC_009009:SSA_0433|5end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435654..435884_NEGATIVE 337 145 102 137 95 NC_009009:SSA_1451|5end_Exonuclease_RexA,_putative_1456418..1456648_NEGATIVE 337 167 123 130 92 NC_009009:SSA_1366|5end_Alkaline_D-stereospecific_endopeptidase_precursor,_putative_1383663..1383893_NEGATIVE 336 146 101 214 163 NC_009009:SSA_1600|5end_hypothetical_protein_1606595..1606825_NEGATIVE 331 160 117 68 18 NC_009009:SSA_2352|5end_ABC-type_nitrate/sulfonate/bicarbonate_transporter,_periplasmic_component,_putative_2354508..2354738_NEGATIVE 331 139 91 176 122 NC_009009:SSA_1017|5end_hypothetical_protein_1022072..1022302_POSITIVE 331 118 72 104 46 NC_009009:SSA_0993|5end_hypothetical_protein_994064..994294_POSITIVE 328 147 105 189 150 NC_009009:SSA_0618|5end_hypothetical_protein_611973..612203_NEGATIVE 325 144 104 66 29 NC_009009:SSA_1058|5end_Thiamine_biosynthesis_protein,_putative_1074917..1075147_POSITIVE 325 125 83 185 135 NC_009009:SSA_0568|5end_Aspartyl-tRNA_synthetase_1,_putative_561674..561904_POSITIVE 324 150 101 219 157 NC_009009:SSA_0179|5end_hypothetical_protein_183966..184196_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 363 179 131 80 35 NC_009009:SSA_2014|3end_D-alanyl-D-alanine_carboxypeptidase,_putative_2014019..2014169_NEGATIVE 349 119 71 75 27 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 339 169 123 141 96 NC_009009:SSA_1680|3end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1673200..1673350_NEGATIVE 339 185 141 43 2 NC_009009:SSA_1131|3end_High-affinity_Fe_2+/Pb2+_permease,_putative_1158768..1158918_POSITIVE 339 143 101 130 85 NC_009009:SSA_0434|3end_Glutamate_formiminotransferase,_putative_435669..435819_NEGATIVE 337 146 101 150 98 NC_009009:SSA_2137|3end_hypothetical_protein_2137780..2137930_NEGATIVE 337 145 102 140 98 NC_009009:SSA_1452|3end_Second_subunit_of_major_exonuclease,_putative_1456415..1456565_NEGATIVE 337 167 123 45 7 NC_009009:SSA_1368|3end_hypothetical_protein_1383748..1383898_NEGATIVE 331 118 72 107 49 NC_009009:SSA_0992|3end_hypothetical_protein_994147..994297_POSITIVE 325 144 104 62 25 NC_009009:SSA_1057|3end_Aminotransferase,_class-V,_putative_1074993..1075143_POSITIVE 321 103 61 71 21 NC_009009:SSA_1691|3end_Transcriptional_regulator,_XRE_family,_putative_1683570..1683720_POSITIVE 320 119 76 97 50 NC_009009:SSA_0354|3end_Uncharacterized_membrane_protein_346872..347022_POSITIVE 320 175 131 57 8 NC_009009:SSA_0160|3end_hypothetical_protein_159519..159669_POSITIVE 317 168 124 61 14 NC_009009:SSA_2118|3end_Thiamine_pyrophosphokinase,_putative_2119814..2119964_NEGATIVE 313 149 103 90 32 NC_009009:SSA_1444|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1446644..1446794_NEGATIVE 311 144 105 135 83 NC_009009:SSA_2090|3end_Hexulose-6-phosphate_synthase,_putative_2094343..2094493_NEGATIVE 311 166 122 51 13 NC_009009:SSA_1926|3end_hypothetical_protein_1915034..1915184_POSITIVE 310 138 105 78 42 NC_009009:SSA_0288|3end_hypothetical_protein_280740..280890_NEGATIVE 304 144 102 140 98 NC_009009:SSA_1402|3end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1414481..1414631_NEGATIVE 302 169 123 77 24 NC_009009:SSA_2140|3end_Ribonuclease_P_protein_component,_putative_2140308..2140458_NEGATIVE