Origin IGS: agttgtttctcctttagcaaatttatacaacaaaaacattatatcaacaatcactttaggtttcaagcttttaaagatatttttttagaaaacatattgacaagttgtcaaccaaattcattcaaacatctgatactataacgttttctcctgttagaattaagcct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aggcttaattctaacaggagaaaacgttatagtatcagatgtttgaatgaatttggttgacaacttgtcaatatgttttctaaaaaaatatctttaaaagcttgaaacctaaagtgattgttgatataatgtttttgttgtataaatttgctaaaggagaaacaact Mask Tandem Repeat Region ================================================ agttgtttctcctttagcaaatttatacaacaaaaacattatatcaacaatcactttaggtttcaagcttttaaagatatttttttagaaaacatattgacaagttgtcaaccaaattcattcaaacatctgatactataacgttttctcctgttagaattaagcct Find is-nt database================================================ Query_seq: SSA_2283:SSA_2284|SSA_2283:SSA_2284:Conserved uncharacterized protein:Histidyl-tRNA synthetase, putative:<-<-:2285915..2286081 167 agttgtttctcctttagcaaatttatacaacaaaaacattatatcaacaatcactttaggtttcaagcttttaaagatatttttttagaaaacatattgacaagttgtcaaccaaattcattcaaacatctgatactataacgttttctcctgttagaattaagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2283:SSA_2284|SSA_2283:SSA_2284:Conserved uncharacterized protein:Histidyl-tRNA synthetase, putative:<-<-:2285915..2286081 167 agttgtttctcctttagcaaatttatacaacaaaaacattatatcaacaatcactttaggtttcaagcttttaaagatatttttttagaaaacatattgacaagttgtcaaccaaattcattcaaacatctgatactataacgttttctcctgttagaattaagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2283:SSA_2284|SSA_2283:SSA_2284:Conserved uncharacterized protein:Histidyl-tRNA synthetase, putative:<-<-:2285915..2286081 167 agttgtttctcctttagcaaatttatacaacaaaaacattatatcaacaatcactttaggtttcaagcttttaaagatatttttttagaaaacatattgacaagttgtcaaccaaattcattcaaacatctgatactataacgttttctcctgttagaattaagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agttgtttctcctttagcaaatttatacaacaaaaacattatatcaacaatcactttaggtttcaagcttttaaagatatttttttagaaaacatattgacaagttgtcaaccaaattcattcaaacatctgatactataacgttttctcctgttagaattaagcct Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 25 End: 138 ........................ M Q Q K H Y I N N H F R F Q A F K D I F L E N I L T S C Q P N S F K H L I L ............................. agttgtttctcctttagcaaatttatacaacaaaaacattatatcaacaatcactttaggtttcaagcttttaaagatatttttttagaaaacatattgacaagttgtcaaccaaattcattcaaacatctgatactataacgttttctcctgttagaattaagcct 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: 90 Start: 38 End: 67 .....................................CTTGAAACCTAAAGTGATTGTTGATATAAT.................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agttgtttctcctttagcaaatttatacaacaaaaacattatatcaacaatcactttaggtttcaagcttttaaagatatttttttagaaaacatattgacaagttgtcaaccaaattcattcaaacatctgatactataacgttttctcctgttagaattaagcct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -7.2 Tail_Score: -3.48115 Start: 97 End: 111 Full_Region: tttgaatgaatttgg ttgaca act tgtcaa tatgttttctaaaaa ................................................................................................ttgacaacttgtcaa........................................................ Find igs database================================================ Query_seq: SSA_2283:SSA_2284|SSA_2283:SSA_2284:Conserved uncharacterized protein:Histidyl-tRNA synthetase, putative:<-<-:2285915..2286081 167 agttgtttctcctttagcaaatttatacaacaaaaacattatatcaacaatcactttaggtttcaagcttttaaagatatttttttagaaaacatattgacaagttgtcaaccaaattcattcaaacatctgatactataacgttttctcctgttagaattaagcct Intra-Species Hit: Count: 1 Min: 1 Max: 167 Len: 167 Subject: NC_009009_SSA_2283_SSA_2284|Conserved uncharacterized protein:Histidyl-tRNA synthetase, putative|NEGATIVE:NEGATIVE|[2285915,2286081]|167 HSP 1 e-value: 1.0E-77 bit: 289.0 Len: 167 Query Start:1 Query End:167 Subject Strand: POSITIVE Subject Start: 1 Subject End: 167 agttgtttctcctttagcaaatttatacaacaaaaacattatatcaacaatcactttaggtttcaagcttttaaagatannnnnnnagaaaacatattgacaagttgtcaaccaaattcattcaaacatctgatactataacgttttctcctgttagaattaagcct agttgtttctcctttagcaaatttatacaacaaaaacattatatcaacaatcactttaggtttcaagcttttaaagatatttttttagaaaacatattgacaagttgtcaaccaaattcattcaaacatctgatactataacgttttctcctgttagaattaagcct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUGUUUCUCCUUUAGCAAAUUUAUACAACAAAAACAUUAUAUCAACAAUCACUUUAGGUUUCAAGCUUUUAAAGAUAUUUUUUUAGAAAACAUAUUGACAAGUUGUCAACCAAAUUCAUUCAAACAUCUGAUACUAUAACGUUUUCUCCUGUUAGAAUUAAGCCU .(((((....................)))))..........................((((((.....(((((((((....)))))))))......(((((.....)))))........((((.((((...((.((......))..))...)))).)))).)))))) (-18.75) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGCUUAAUUCUAACAGGAGAAAACGUUAUAGUAUCAGAUGUUUGAAUGAAUUUGGUUGACAACUUGUCAAUAUGUUUUCUAAAAAAAUAUCUUUAAAAGCUUGAAACCUAAAGUGAUUGUUGAUAUAAUGUUUUUGUUGUAUAAAUUUGCUAAAGGAGAAACAACU .(((..((((...((((..((((((((((((.....((((((((....(((....((((((.....)))))).....))).....))))))))......((((........)))).........)))))))))))).))))...)))).)))............... (-31.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 740 140 91 231 182 NC_009009:SSA_2283|5end_Conserved_uncharacterized_protein_2285824..2286054_NEGATIVE 250 156 121 90 45 NC_009009:SSA_2047|5end_hypothetical_protein_2049953..2050183_NEGATIVE 241 158 113 107 61 NC_009009:SSA_1707|5end_Conserved_uncharacterized_protein_1697782..1698012_POSITIVE 222 157 111 108 51 NC_009009:SSA_1762|5end_Permease,_putative_1750052..1750282_NEGATIVE 221 155 111 113 66 NC_009009:SSA_0523|5end_Aldehyde_dehydrogenase,_putative_521637..521867_POSITIVE 219 99 51 78 24 NC_009009:SSA_0342|5end_Pyruvate_formate-lyase,_putative_337206..337436_NEGATIVE 210 158 115 111 75 NC_009009:SSA_2317|5end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2319410..2319640_NEGATIVE 209 109 62 229 191 NC_009009:SSA_1066|5end_ABC-type_oligopeptide_transport_system,_putative_1084335..1084565_POSITIVE 206 158 114 71 24 NC_009009:SSA_0281|5end_hypothetical_protein_273404..273634_POSITIVE 201 150 105 97 48 NC_009009:SSA_1379|5end_hypothetical_protein_1398528..1398758_NEGATIVE 198 135 92 225 191 NC_009009:SSA_1011|5end_hypothetical_protein_1014134..1014364_POSITIVE 194 158 125 113 76 NC_009009:SSA_1980|5end_50S_ribosomal_protein_L28,_putative_1974632..1974862_NEGATIVE 194 159 112 109 66 NC_009009:SSA_0315|5end_Transcriptional_regulator,_MarR_family,_putative_310102..310332_POSITIVE 193 133 97 122 74 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 193 158 128 160 126 NC_009009:SSA_0088|5end_V-type_sodium_ATPase,_subunit_C,_putative_88930..89160_POSITIVE 190 155 116 220 179 NC_009009:SSA_0748|5end_Sugar:H+_symporter,_permease_of_the_major_facilitator_superfamily,_putative_729386..729616_POSITIVE 187 160 112 195 147 NC_009009:SSA_0034|5end_hypothetical_protein_39547..39777_POSITIVE 186 89 57 196 159 NC_009009:SSA_1832|5end_hypothetical_protein_1822001..1822231_POSITIVE 185 148 105 231 191 NC_009009:SSA_1329|5end_Conserved_uncharacterized_protein_1345904..1346134_NEGATIVE 184 149 103 198 153 NC_009009:SSA_1729|5end_ABC_transporter_substrate-binding_protein-branched_chain_amino_acid_transport,_putative_1715699..1715929_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 250 156 121 59 14 NC_009009:SSA_2048|3end_Serine_acetyltransferase,_putative_2049984..2050134_NEGATIVE 241 158 113 95 49 NC_009009:SSA_1706|3end_Exodeoxyribonuclease,_putative_1697850..1698000_POSITIVE 232 158 111 95 42 NC_009009:SSA_1672|3end_hypothetical_protein_1670291..1670441_NEGATIVE 221 155 111 106 59 NC_009009:SSA_0522|3end_Ethanolamine_utilization_protein,_putative_521710..521860_POSITIVE 210 158 115 109 73 NC_009009:SSA_2318|3end_PilB-like_pili_biogenesis_ATPase,_putative_2319412..2319562_NEGATIVE 201 150 105 87 38 NC_009009:SSA_1380|3end_hypothetical_protein_1398538..1398688_NEGATIVE 193 133 97 122 74 NC_009009:SSA_1413|3end_GufA-like_protein,_putative_1424095..1424245_NEGATIVE 193 158 128 149 115 NC_009009:SSA_0087|3end_V-type_sodium_ATPase,_subunit_E,_putative_88999..89149_POSITIVE 190 155 116 125 84 NC_009009:SSA_0747|3end_DD-carboxypeptidase,_putative_729371..729521_POSITIVE 186 89 57 109 72 NC_009009:SSA_1831|3end_hypothetical_protein_1821994..1822144_POSITIVE 184 149 103 109 64 NC_009009:SSA_1730|3end_hypothetical_protein_1715788..1715938_NEGATIVE 184 157 117 142 103 NC_009009:SSA_0973|3end_hypothetical_protein_980687..980837_POSITIVE 183 139 98 94 29 NC_009009:SSA_1577|3end_Proline_dipeptidase,_putative_1581456..1581606_POSITIVE 183 73 49 124 98 NC_009009:SSA_1237|3end_Uracil-DNA_glycosylase,_putative_1261713..1261863_NEGATIVE 180 136 92 125 74 NC_009009:SSA_0807|3end_GTP-binding_protein,_putative_790839..790989_POSITIVE 179 131 93 130 87 NC_009009:SSA_2160|3end_Deoxyuridinetriphosphatase,_putative_2159623..2159773_NEGATIVE 179 155 131 116 83 NC_009009:SSA_0407|3end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_402911..403061_NEGATIVE 178 109 62 103 45 NC_009009:SSA_2040|3end_ABC_transporter_ATP-binding_protein-multiple_sugar_transport,_putative_2044568..2044718_NEGATIVE 176 159 115 96 43 NC_009009:SSA_0874|3end_hypothetical_protein_868995..869145_POSITIVE 176 132 97 82 53 NC_009009:SSA_0269|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262947..263097_POSITIVE