Origin IGS: taatgagaagagttaaagtcagtagttttactggctttttaactgcatcaaaaaatttgtttcaaagatgaaatatttttttaaaacgctttccttttaaatgtaaatgttttataatgatatagtaagaaaaagtttattttaggagggctaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattagccctcctaaaataaactttttcttactatatcattataaaacatttacatttaaaaggaaagcgttttaaaaaaatatttcatctttgaaacaaattttttgatgcagttaaaaagccagtaaaactactgactttaactcttctcatta Mask Tandem Repeat Region ================================================ taatgagaagagttaaagtcagtagttttactggctttttaactgcatcaaaaaatttgtttcaaagatgaaatatttttttaaaacgctttccttttaaatgtaaatgttttataatgatatagtaagaaaaagtttattttaggagggctaatt Find is-nt database================================================ Query_seq: SSA_0299:SSA_0300|SSA_0299:SSA_0300:hypothetical protein:hypothetical protein:->->:293403..293558 156 taatgagaagagttaaagtcagtagttttactggctttttaactgcatcaaaaaatttgtttcaaagatgaaatatttttttaaaacgctttccttttaaatgtaaatgttttataatgatatagtaagaaaaagtttattttaggagggctaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0299:SSA_0300|SSA_0299:SSA_0300:hypothetical protein:hypothetical protein:->->:293403..293558 156 taatgagaagagttaaagtcagtagttttactggctttttaactgcatcaaaaaatttgtttcaaagatgaaatatttttttaaaacgctttccttttaaatgtaaatgttttataatgatatagtaagaaaaagtttattttaggagggctaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0299:SSA_0300|SSA_0299:SSA_0300:hypothetical protein:hypothetical protein:->->:293403..293558 156 taatgagaagagttaaagtcagtagttttactggctttttaactgcatcaaaaaatttgtttcaaagatgaaatatttttttaaaacgctttccttttaaatgtaaatgttttataatgatatagtaagaaaaagtttattttaggagggctaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatgagaagagttaaagtcagtagttttactggctttttaactgcatcaaaaaatttgtttcaaagatgaaatatttttttaaaacgctttccttttaaatgtaaatgttttataatgatatagtaagaaaaagtttattttaggagggctaatt Predict ORF larger than 30AA ================================================ taatgagaagagttaaagtcagtagttttactggctttttaactgcatcaaaaaatttgtttcaaagatgaaatatttttttaaaacgctttccttttaaatgtaaatgttttataatgatatagtaagaaaaagtttattttaggagggctaatt 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: 84 Start: 89 End: 118 ........................................................................................CTTTCCTTTTAAATGTAAATGTTTTATAAT...................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taatgagaagagttaaagtcagtagttttactggctttttaactgcatcaaaaaatttgtttcaaagatgaaatatttttttaaaacgctttccttttaaatgtaaatgttttataatgatatagtaagaaaaagtttattttaggagggctaatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -4.0 Tail_Score: -5.16237 Start: 56 End: 66 Full_Region: aaaaaatatttcatc tttg aaa caaa ttttttgatgcagtt .......................................................tttgaaacaaa.......................................................................................... TransTerm Strand: + Conf: 71 HP_score: -3.5 Tail_Score: -5.40474 Start: 58 End: 75 Full_Region: CTGCATCAAAAAATT TGTTTCA AAGA TGAAATA TTTTTTTAAAACGCT .........................................................TGTTTCAAAGATGAAATA................................................................................. Find igs database================================================ Query_seq: SSA_0299:SSA_0300|SSA_0299:SSA_0300:hypothetical protein:hypothetical protein:->->:293403..293558 156 taatgagaagagttaaagtcagtagttttactggctttttaactgcatcaaaaaatttgtttcaaagatgaaatatttttttaaaacgctttccttttaaatgtaaatgttttataatgatatagtaagaaaaagtttattttaggagggctaatt Intra-Species Hit: Count: 1 Min: 1 Max: 156 Len: 156 Subject: NC_009009_SSA_0299_SSA_0300|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[293403,293558]|156 HSP 1 e-value: 5.0E-71 bit: 268.0 Len: 156 Query Start:1 Query End:156 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 taatgagaagagttaaagtcagtagttttactggctttttaactgcatcaaaaaatttgtttcaaagatgaaatannnnnnnaaaacgctttccttttaaatgtaaatgttttataatgatatagtaagaaaaagtttattttaggagggctaatt taatgagaagagttaaagtcagtagttttactggctttttaactgcatcaaaaaatttgtttcaaagatgaaatatttttttaaaacgctttccttttaaatgtaaatgttttataatgatatagtaagaaaaagtttattttaggagggctaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGAGAAGAGUUAAAGUCAGUAGUUUUACUGGCUUUUUAACUGCAUCAAAAAAUUUGUUUCAAAGAUGAAAUAUUUUUUUAAAACGCUUUCCUUUUAAAUGUAAAUGUUUUAUAAUGAUAUAGUAAGAAAAAGUUUAUUUUAGGAGGGCUAAUU ......((.(((((((((((((((....))))))))..)))))).).)).(((((..(((((((....)))))))..))))).....((((((((.......((((((.((((((.........))))))....))))))...))))))))..... (-34.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAGCCCUCCUAAAAUAAACUUUUUCUUACUAUAUCAUUAUAAAACAUUUACAUUUAAAAGGAAAGCGUUUUAAAAAAAUAUUUCAUCUUUGAAACAAAUUUUUUGAUGCAGUUAAAAAGCCAGUAAAACUACUGACUUUAACUCUUCUCAUUA ..(((((..((((....((((...........((((....))))...........))))..))))..(((((..((((.....(((((....)))))....))))..))))).)))))((((.(((((....))))).)))).............. (-17.45) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 240 46 3 183 133 NC_009009:SSA_1293|5end_hypothetical_protein_1312249..1312479_NEGATIVE 236 46 4 161 127 NC_009009:SSA_0531|5end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527355..527585_POSITIVE 226 49 22 82 56 NC_009009:SSA_1296|5end_hypothetical_protein_1313013..1313243_NEGATIVE 224 47 3 45 5 NC_009009:SSA_2078|5end_hypothetical_protein_2083837..2084067_NEGATIVE 221 49 2 88 46 NC_009009:SSA_2212|5end_Possible_polysaccharide_transport_protein,_putative_2213928..2214158_NEGATIVE 216 46 3 93 45 NC_009009:SSA_1997|5end_Membrane_spanning_protein,_putative_1994911..1995141_NEGATIVE 215 50 17 156 120 NC_009009:SSA_0043|5end_hypothetical_protein_48801..49031_POSITIVE 214 50 9 41 2 NC_009009:SSA_2196|5end_Conserved_uncharacterized_protein_2197330..2197560_NEGATIVE 211 46 9 224 190 NC_009009:SSA_1444|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1447267..1447497_NEGATIVE 210 54 17 155 119 NC_009009:SSA_0303|5end_surface_protein_C_296451..296681_POSITIVE 209 46 4 190 135 NC_009009:SSA_0009|5end_Ribosome-associated_heat_shock_protein_(S4),_putative_9165..9395_POSITIVE 208 97 56 185 146 NC_009009:SSA_1325|5end_Ketoacyl_reductase_hetN,_putative_1342343..1342573_NEGATIVE 207 35 4 215 182 NC_009009:SSA_2251|5end_hypothetical_protein_2247069..2247299_POSITIVE 207 70 25 212 161 NC_009009:SSA_0568|5end_Aspartyl-tRNA_synthetase_1,_putative_561674..561904_POSITIVE 206 42 2 73 29 NC_009009:SSA_0622|5end_Transcriptional_regulator_(XRE_family),_SOS-response_transcriptional_repressors_(RecA-mediated_autopeptidases),_putative_614419..614649_NEGATIVE 205 46 7 42 4 NC_009009:SSA_1617|5end_hypothetical_protein_1620651..1620881_NEGATIVE 205 45 18 65 36 NC_009009:SSA_0814|5end_Oxidoreductase,_pyridine_nucleotide-disulfide,_class_I,_putative_796835..797065_NEGATIVE 202 51 26 94 71 NC_009009:SSA_1172|5end_hypothetical_protein_1199926..1200156_NEGATIVE 201 59 15 184 137 NC_009009:SSA_2055|5end_hypothetical_protein_2058160..2058390_NEGATIVE 199 45 10 93 54 NC_009009:SSA_1364|5end_hypothetical_protein_1381297..1381527_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 236 46 4 143 109 NC_009009:SSA_0530|3end_Ethanolamine_utilization_protein_(transporter),_putative_527417..527567_POSITIVE 233 48 1 104 45 NC_009009:SSA_0242|3end_hypothetical_protein_235810..235960_POSITIVE 232 50 6 81 25 NC_009009:SSA_2165|3end_ABC-type_oligopeptide_transporter,_periplasmic_component,_putative_2163787..2163937_POSITIVE 227 46 6 80 42 NC_009009:SSA_1149|3end_Glycosyl_hydrolase,_family_1,_putative_1179876..1180026_POSITIVE 218 44 11 80 47 NC_009009:SSA_0299|3end_hypothetical_protein_293342..293492_POSITIVE 217 70 24 117 69 NC_009009:SSA_1190|3end_Conserved_uncharacterized_protein_1217799..1217949_NEGATIVE 214 50 9 57 18 NC_009009:SSA_2197|3end_hypothetical_protein_2197314..2197464_NEGATIVE 210 46 6 77 42 NC_009009:SSA_1150|3end_Tautomerase,_putative_1179894..1180044_NEGATIVE 209 46 4 99 44 NC_009009:SSA_0008|3end_Transcription-repair_coupling_factor,_putative_9154..9304_POSITIVE 204 50 4 115 62 NC_009009:SSA_0166|3end_hypothetical_protein_165146..165296_POSITIVE 203 37 11 67 37 NC_009009:SSA_1120|3end_Two-component_sensor_kinase_(with_C-terminal_ATPase_domain),_putative_1147005..1147155_POSITIVE 197 63 24 151 120 NC_009009:SSA_1941|3end_hypothetical_protein_1927129..1927279_NEGATIVE 195 149 101 82 45 NC_009009:SSA_0362|3end_Thioredoxin,_putative_353594..353744_POSITIVE 194 46 5 81 41 NC_009009:SSA_1189|3end_GTP-binding_protein,_putative_1216806..1216956_NEGATIVE 192 40 8 113 79 NC_009009:SSA_1036|3end_Deoxyribose-phosphate_aldolase,_putative_1052211..1052361_POSITIVE 191 50 3 71 11 NC_009009:SSA_0921|3end_Zn-dependeant_threonine_dehydrogenase,_putative_932164..932314_POSITIVE 191 46 2 105 60 NC_009009:SSA_0186|3end_Competence_protein_ComYC,_putative_190458..190608_POSITIVE 190 48 3 143 82 NC_009009:SSA_1746|3end_hypothetical_protein_1732292..1732442_NEGATIVE 190 45 2 143 94 NC_009009:SSA_1615|3end_Alanine_dehydrogenase,_putative_1619318..1619468_POSITIVE 188 42 15 107 78 NC_009009:SSA_1814|3end_hypothetical_protein_1799299..1799449_NEGATIVE