Origin IGS: accatttcctcctagaatcctaatacttcattataacacgttttcaagaataacaaaagacagccgtttggggtgtaaaattacactatttcaccttaaaaatatgtttatcaaaaagaaaaagagaggcaaatctgttgcattctcagtcttgcctcatctttttacta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagtaaaaagatgaggcaagactgagaatgcaacagatttgcctctctttttctttttgataaacatatttttaaggtgaaatagtgtaattttacaccccaaacggctgtcttttgttattcttgaaaacgtgttataatgaagtattaggattctaggaggaaatggt Mask Tandem Repeat Region ================================================ accatttcctcctagaatcctaatacttcattataacacgttttcaagaataacaaaagacagccgtttggggtgtaaaattacactatttcaccttaaaaatatgtttatcaaaaagaaaaagagaggcaaatctgttgcattctcagtcttgcctcatctttttacta Find is-nt database================================================ Query_seq: SSA_1807:SSA_1808|SSA_1807:SSA_1808:hypothetical protein:hypothetical protein:<-<-:1791314..1791483 170 accatttcctcctagaatcctaatacttcattataacacgttttcaagaataacaaaagacagccgtttggggtgtaaaattacactatttcaccttaaaaatatgtttatcaaaaagaaaaagagaggcaaatctgttgcattctcagtcttgcctcatctttttacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1807:SSA_1808|SSA_1807:SSA_1808:hypothetical protein:hypothetical protein:<-<-:1791314..1791483 170 accatttcctcctagaatcctaatacttcattataacacgttttcaagaataacaaaagacagccgtttggggtgtaaaattacactatttcaccttaaaaatatgtttatcaaaaagaaaaagagaggcaaatctgttgcattctcagtcttgcctcatctttttacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1807:SSA_1808|SSA_1807:SSA_1808:hypothetical protein:hypothetical protein:<-<-:1791314..1791483 170 accatttcctcctagaatcctaatacttcattataacacgttttcaagaataacaaaagacagccgtttggggtgtaaaattacactatttcaccttaaaaatatgtttatcaaaaagaaaaagagaggcaaatctgttgcattctcagtcttgcctcatctttttacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 accatttcctcctagaatcctaatacttcattataacacgttttcaagaataacaaaagacagccgtttggggtgtaaaattacactatttcaccttaaaaatatgtttatcaaaaagaaaaagagaggcaaatctgttgcattctcagtcttgcctcatctttttacta Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 17 End: 169 ................ M L I L H Y N T F S R I T K D S R L G C K I T L F H L K N M F I K K K K R G K S V A F S V L P H L F T . accatttcctcctagaatcctaatacttcattataacacgttttcaagaataacaaaagacagccgtttggggtgtaaaattacactatttcaccttaaaaatatgtttatcaaaaagaaaaagagaggcaaatctgttgcattctcagtcttgcctcatctttttacta 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: 82 Start: 30 End: 59 .............................CTTTTGTTATTCTTGAAAACGTGTTATAAT............................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ accatttcctcctagaatcctaatacttcattataacacgttttcaagaataacaaaagacagccgtttggggtgtaaaattacactatttcaccttaaaaatatgtttatcaaaaagaaaaagagaggcaaatctgttgcattctcagtcttgcctcatctttttacta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 44 HP_score: -3.4 Tail_Score: -2.6518 Start: 129 End: 141 Full_Region: AAAAGAAAAAGAGAG GCAA ATCTG TTGC ATTCTCAGTCTTGCC ................................................................................................................................GCAAATCTGTTGC............................. Find igs database================================================ Query_seq: SSA_1807:SSA_1808|SSA_1807:SSA_1808:hypothetical protein:hypothetical protein:<-<-:1791314..1791483 170 accatttcctcctagaatcctaatacttcattataacacgttttcaagaataacaaaagacagccgtttggggtgtaaaattacactatttcaccttaaaaatatgtttatcaaaaagaaaaagagaggcaaatctgttgcattctcagtcttgcctcatctttttacta Intra-Species Hit: Count: 1 Min: 1 Max: 170 Len: 170 Subject: NC_009009_SSA_1807_SSA_1808|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1791314,1791483]|170 HSP 1 e-value: 7.0E-92 bit: 337.0 Len: 170 Query Start:1 Query End:170 Subject Strand: POSITIVE Subject Start: 1 Subject End: 170 accatttcctcctagaatcctaatacttcattataacacgttttcaagaataacaaaagacagccgtttggggtgtaaaattacactatttcaccttaaaaatatgtttatcaaaaagaaaaagagaggcaaatctgttgcattctcagtcttgcctcatctttttacta accatttcctcctagaatcctaatacttcattataacacgttttcaagaataacaaaagacagccgtttggggtgtaaaattacactatttcaccttaaaaatatgtttatcaaaaagaaaaagagaggcaaatctgttgcattctcagtcttgcctcatctttttacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCAUUUCCUCCUAGAAUCCUAAUACUUCAUUAUAACACGUUUUCAAGAAUAACAAAAGACAGCCGUUUGGGGUGUAAAAUUACACUAUUUCACCUUAAAAAUAUGUUUAUCAAAAAGAAAAAGAGAGGCAAAUCUGUUGCAUUCUCAGUCUUGCCUCAUCUUUUUACUA ...........((.(((..(...................)..))).)).........(((((....(((((((((..((((......)))))))))))))....))))).......((((((((((((((((..(((.........)))..))))))).))))))).)). (-33.41) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUAAAAAGAUGAGGCAAGACUGAGAAUGCAACAGAUUUGCCUCUCUUUUUCUUUUUGAUAAACAUAUUUUUAAGGUGAAAUAGUGUAAUUUUACACCCCAAACGGCUGUCUUUUGUUAUUCUUGAAAACGUGUUAUAAUGAAGUAUUAGGAUUCUAGGAGGAAAUGGU ....(((((((.((((((((.(((.........))).)))))))))))))))((((...((((.((..(((((((((.......(((((....))))).......(((........)))..)))))))))..))))))...))))........((((....))))..... (-35.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 795 100 51 191 142 NC_009009:SSA_1807|5end_hypothetical_protein_1791223..1791453_NEGATIVE 387 156 124 34 2 NC_009009:SSA_0166|5end_hypothetical_protein_164641..164871_POSITIVE 322 157 122 45 3 NC_009009:SSA_0791|5end_UDP-N-acetylglucosamine-like_protein,_putative_773345..773575_POSITIVE 298 167 122 176 136 NC_009009:SSA_0151|5end_hypothetical_protein_145354..145584_POSITIVE 290 164 121 225 172 NC_009009:SSA_0150|5end_hypothetical_protein_143936..144166_POSITIVE 288 159 124 209 178 NC_009009:SSA_0308|5end_hypothetical_protein_304385..304615_POSITIVE 287 170 124 123 55 NC_009009:SSA_2068|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_2071311..2071541_NEGATIVE 282 169 124 116 72 NC_009009:SSA_1128|5end_Voltage_gated_chloride_channel_EriC,_putative_1153250..1153480_POSITIVE 281 155 111 215 174 NC_009009:SSA_1949|5end_AliA_protein,_putative_1944373..1944603_NEGATIVE 280 159 134 178 154 NC_009009:SSA_0636|5end_N-(5'-phosphoribosyl)anthranilate_isomerase,_putative_625184..625414_POSITIVE 278 170 129 120 78 NC_009009:SSA_0575|5end_Hydrolase,_HAD_superfamily,_putative_569527..569757_POSITIVE 275 151 116 62 21 NC_009009:SSA_0099|5end_hypothetical_protein_100619..100849_NEGATIVE 272 169 126 96 51 NC_009009:SSA_0298|5end_Malate_permease,_putative_291336..291566_POSITIVE 268 168 123 231 179 NC_009009:SSA_0474|5end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_476270..476500_POSITIVE 267 169 128 99 52 NC_009009:SSA_2176|5end_hypothetical_protein_2175159..2175389_NEGATIVE 267 161 123 168 130 NC_009009:SSA_1659|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1656819..1657049_NEGATIVE 264 159 111 214 163 NC_009009:SSA_0855|5end_O-acetylhomoserine_sulfhydrylase,_putative_841832..842062_POSITIVE 261 162 123 57 20 NC_009009:SSA_1705|5end_hypothetical_protein_1696853..1697083_NEGATIVE 261 164 124 207 158 NC_009009:SSA_0760|5end_Acetylornithine_aminotransferase,_putative_742581..742811_POSITIVE 258 50 5 148 95 NC_009009:SSA_0305|5end_hypothetical_protein_301985..302215_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 281 156 124 151 126 NC_009009:SSA_0307|3end_Glutamine_synthetase_type_1,_putative_304413..304563_POSITIVE 280 159 134 149 125 NC_009009:SSA_0635|3end_Indole-3-glycerol_phosphate_synthase,_putative_625235..625385_POSITIVE 272 169 126 91 46 NC_009009:SSA_0297|3end_Malolactic_enzyme,_putative_291411..291561_POSITIVE 269 153 117 90 60 NC_009009:SSA_0743|3end_Transcriptional_repressor_(arginine_synthesis),_putative_725289..725439_NEGATIVE 264 159 111 115 64 NC_009009:SSA_0854|3end_hypothetical_protein_841813..841963_POSITIVE 256 48 2 95 42 NC_009009:SSA_1009|3end_Galactose-1-phosphate-uridylyltransferase,_putative_1012815..1012965_POSITIVE 255 170 123 74 22 NC_009009:SSA_1433|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase,_putative_1439933..1440083_NEGATIVE 254 169 122 88 20 NC_009009:SSA_1257|3end_hypothetical_protein_1283106..1283256_NEGATIVE 253 157 116 82 48 NC_009009:SSA_1638|3end_hypothetical_protein_1641017..1641167_NEGATIVE 252 163 128 47 7 NC_009009:SSA_1061|3end_50S_ribosomal_protein_L21,_putative_1077986..1078136_POSITIVE 252 164 123 135 93 NC_009009:SSA_0809|3end_Translation_initiation_inhibitor,_yjgF_family_/_endoribonuclease_L-PSP,_putative_791606..791756_POSITIVE 247 164 123 88 55 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE 247 168 121 119 62 NC_009009:SSA_0829|3end_Platelet-binding_glycoprotein_812165..812315_POSITIVE 245 166 121 128 69 NC_009009:SSA_0842|3end_Effector_of_murein_hydrolase_LrgA/holin-like_protein,_putative_827790..827940_POSITIVE 245 170 122 122 66 NC_009009:SSA_0083|3end_hypothetical_protein_85840..85990_POSITIVE 244 100 57 105 60 NC_009009:SSA_1799|3end_Acetyltransferase,_putative_1780513..1780663_NEGATIVE 243 155 122 90 55 NC_009009:SSA_1939|3end_Acyl_carrier_protein,_putative_1925875..1926025_NEGATIVE 243 166 125 140 97 NC_009009:SSA_1372|3end_hypothetical_protein_1388946..1389096_NEGATIVE 243 167 127 101 54 NC_009009:SSA_1139|3end_Pyruvate_dehydrogenase_E1_component_beta_subunit,_putative_1167934..1168084_POSITIVE 242 170 124 73 32 NC_009009:SSA_0379|3end_PTS_system,_beta-glucoside-specific_EII_component,_putative_370833..370983_POSITIVE