Origin IGS: aatatctccttaacttattattaaccggtttattaactggttaatataatacactttgtcaacttctttgtcaagctttttaagaaaataaagcaaaaaggaagtaggattctttcccacttccactttgcttttaatttcaatatatttgaaacattatttgctattactattcaatgacagtataagcttggactgatgcttttctcaagcttagctgtatgagattacttttcagactgtcaaatgacaatctggaactgaaaactccagct .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 agctggagttttcagttccagattgtcatttgacagtctgaaaagtaatctcatacagctaagcttgagaaaagcatcagtccaagcttatactgtcattgaatagtaatagcaaataatgtttcaaatatattgaaattaaaagcaaagtggaagtgggaaagaatcctacttcctttttgctttattttcttaaaaagcttgacaaagaagttgacaaagtgtattatattaaccagttaataaaccggttaataataagttaaggagatatt Mask Tandem Repeat Region ================================================ aatatctccttaacttattattaaccggtttattaactggttaatataatacactttgtcaacttctttgtcaagctttttaagaaaataaagcaaaaaggaagtaggattctttcccacttccactttgcttttaatttcaatatatttgaaacattatttgctattactattcaatgacagtataagcttggactgatgcttttctcaagcttagctgtatgagattacttttcagactgtcaaatgacaatctggaactgaaaactccagct Find is-nt database================================================ Query_seq: SSA_1340:SSA_1341|SSA_1340:SSA_1341:Zn/Mn ABC-type porter lipoprotein, putative:Carbamoyl-phosphate synthase large chain, putative:<-<-:1356463..1356737 275 aatatctccttaacttattattaaccggtttattaactggttaatataatacactttgtcaacttctttgtcaagctttttaagaaaataaagcaaaaaggaagtaggattctttcccacttccactttgcttttaatttcaatatatttgaaacattatttgctattactattcaatgacagtataagcttggactgatgcttttctcaagcttagctgtatgagattacttttcagactgtcaaatgacaatctggaactgaaaactccagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1340:SSA_1341|SSA_1340:SSA_1341:Zn/Mn ABC-type porter lipoprotein, putative:Carbamoyl-phosphate synthase large chain, putative:<-<-:1356463..1356737 275 aatatctccttaacttattattaaccggtttattaactggttaatataatacactttgtcaacttctttgtcaagctttttaagaaaataaagcaaaaaggaagtaggattctttcccacttccactttgcttttaatttcaatatatttgaaacattatttgctattactattcaatgacagtataagcttggactgatgcttttctcaagcttagctgtatgagattacttttcagactgtcaaatgacaatctggaactgaaaactccagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1340:SSA_1341|SSA_1340:SSA_1341:Zn/Mn ABC-type porter lipoprotein, putative:Carbamoyl-phosphate synthase large chain, putative:<-<-:1356463..1356737 275 aatatctccttaacttattattaaccggtttattaactggttaatataatacactttgtcaacttctttgtcaagctttttaagaaaataaagcaaaaaggaagtaggattctttcccacttccactttgcttttaatttcaatatatttgaaacattatttgctattactattcaatgacagtataagcttggactgatgcttttctcaagcttagctgtatgagattacttttcagactgtcaaatgacaatctggaactgaaaactccagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatatctccttaacttattattaaccggtttattaactggttaatataatacactttgtcaacttctttgtcaagctttttaagaaaataaagcaaaaaggaagtaggattctttcccacttccactttgcttttaatttcaatatatttgaaacattatttgctattactattcaatgacagtataagcttggactgatgcttttctcaagcttagctgtatgagattacttttcagactgtcaaatgacaatctggaactgaaaactccagct Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 37 End: 177 .................................... M V N I I H F V N F F V K L F K K I K Q K G S R I L S H F H F A F N F N I F E T L F A I T I Q .................................................................................................. Protein_Len: 46 Strand: - Start: 36 End: 173 ................................... S T L I I C K T L K K T L S K L F I F C F P L L I R E W K W K A K L K L I N S V N N A I V M ...................................................................................................... Protein_Len: 44 Strand: - Start: 13 End: 144 ............ S I I L R N I L Q N I Y Y V K D V E K D L K K L F Y L L F S T P N K G V E V K S K I E M ................................................................................................................................... aatatctccttaacttattattaaccggtttattaactggttaatataatacactttgtcaacttctttgtcaagctttttaagaaaataaagcaaaaaggaagtaggattctttcccacttccactttgcttttaatttcaatatatttgaaacattatttgctattactattcaatgacagtataagcttggactgatgcttttctcaagcttagctgtatgagattacttttcagactgtcaaatgacaatctggaactgaaaactccagct 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: 88 Start: 46 End: 75 .............................................CTTGACAAAGAAGTTGACAAAGTGTATTAT........................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatatctccttaacttattattaaccggtttattaactggttaatataatacactttgtcaacttctttgtcaagctttttaagaaaataaagcaaaaaggaagtaggattctttcccacttccactttgcttttaatttcaatatatttgaaacattatttgctattactattcaatgacagtataagcttggactgatgcttttctcaagcttagctgtatgagattacttttcagactgtcaaatgacaatctggaactgaaaactccagct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 89 HP_score: -8.9 Tail_Score: -4.57516 Start: 93 End: 131 Full_Region: TTTTAAGAAAATAAA GCAAAAAGGAAGTAGGA TTCTT TCCCACTTCCACTTTGC TTTTAATTTCAATAT ............................................................................................GCAAAAAGGAAGTAGGATTCTTTCCCACTTCCACTTTGC................................................................................................................................................ TransTerm Strand: - Conf: 100 HP_score: -13.3 Tail_Score: -4.87892 Start: 93 End: 131 Full_Region: atattgaaattaaaa gcaaagtggaagtggga aagaa tcctacttcctttttgc tttattttcttaaaa ............................................................................................gcaaagtggaagtgggaaagaatcctacttcctttttgc................................................................................................................................................ TransTerm Strand: - Conf: 100 HP_score: -10.8 Tail_Score: -5.1517 Start: 100 End: 124 Full_Region: aattaaaagcaaagt ggaagtggga aagaa tcctacttcc tttttgctttatttt ...................................................................................................ggaagtgggaaagaatcctacttcc....................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1340:SSA_1341|SSA_1340:SSA_1341:Zn/Mn ABC-type porter lipoprotein, putative:Carbamoyl-phosphate synthase large chain, putative:<-<-:1356463..1356737 275 aatatctccttaacttattattaaccggtttattaactggttaatataatacactttgtcaacttctttgtcaagctttttaagaaaataaagcaaaaaggaagtaggattctttcccacttccactttgcttttaatttcaatatatttgaaacattatttgctattactattcaatgacagtataagcttggactgatgcttttctcaagcttagctgtatgagattacttttcagactgtcaaatgacaatctggaactgaaaactccagct Intra-Species Hit: Count: 1 Min: 1 Max: 275 Len: 275 Subject: NC_009009_SSA_1340_SSA_1341|Zn/Mn ABC-type porter lipoprotein, putative:Carbamoyl-phosphate synthase large chain, putative|NEGATIVE:NEGATIVE|[1356463,1356737]|275 HSP 1 e-value: 1.0E-154 bit: 545.0 Len: 275 Query Start:1 Query End:275 Subject Strand: POSITIVE Subject Start: 1 Subject End: 275 aatatctccttaacttattattaaccggtttattaactggttaatataatacactttgtcaacttctttgtcaagctttttaagaaaataaagcaaaaaggaagtaggattctttcccacttccactttgcttttaatttcaatatatttgaaacattatttgctattactattcaatgacagtataagcttggactgatgcttttctcaagcttagctgtatgagattacttttcagactgtcaaatgacaatctggaactgaaaactccagct aatatctccttaacttattattaaccggtttattaactggttaatataatacactttgtcaacttctttgtcaagctttttaagaaaataaagcaaaaaggaagtaggattctttcccacttccactttgcttttaatttcaatatatttgaaacattatttgctattactattcaatgacagtataagcttggactgatgcttttctcaagcttagctgtatgagattacttttcagactgtcaaatgacaatctggaactgaaaactccagct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUCUCCUUAACUUAUUAUUAACCGGUUUAUUAACUGGUUAAUAUAAUACACUUUGUCAACUUCUUUGUCAAGCUUUUUAAGAAAAUAAAGCAAAAAGGAAGUAGGAUUCUUUCCCACUUCCACUUUGCUUUUAAUUUCAAUAUAUUUGAAACAUUAUUUGCUAUUACUAUUCAAUGACAGUAUAAGCUUGGACUGAUGCUUUUCUCAAGCUUAGCUGUAUGAGAUUACUUUUCAGACUGUCAAAUGACAAUCUGGAACUGAAAACUCCAGCU ........(((((.....((((((((((((....))))))))))))........((((.(((.....))).))))....))))).....((((((((..((((((.(((.....))).))))))..))))))))...((((((.....))))))........(((.......((((...(((((.(((((((((...((......)))))))))))))))).))))......(((((((.((((....)))).)))))))...........))). (-71.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUGGAGUUUUCAGUUCCAGAUUGUCAUUUGACAGUCUGAAAAGUAAUCUCAUACAGCUAAGCUUGAGAAAAGCAUCAGUCCAAGCUUAUACUGUCAUUGAAUAGUAAUAGCAAAUAAUGUUUCAAAUAUAUUGAAAUUAAAAGCAAAGUGGAAGUGGGAAAGAAUCCUACUUCCUUUUUGCUUUAUUUUCUUAAAAAGCUUGACAAAGAAGUUGACAAAGUGUAUUAUAUUAACCAGUUAAUAAACCGGUUAAUAAUAAGUUAAGGAGAUAUU (((((((...))))))).(((((((((....))))))))).......(((((...(((((..((((.....))))....(((.((((((.((((((......))))))............(((((((.....)))))))..(((((((((.((((((((((.....)))))))))).)))))))))...........))))))))).....))))).............((((((((.(((....))).))))))))..........)))))... (-81.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 799 140 91 231 182 NC_009009:SSA_1340|5end_Zn/Mn_ABC-type_porter_lipoprotein,_putative_1356372..1356602_NEGATIVE 340 230 181 187 139 NC_009009:SSA_0141|5end_Copper_chaperone,_putative_136893..137123_POSITIVE 274 237 193 90 48 NC_009009:SSA_1661|5end_hypothetical_protein_1658004..1658234_NEGATIVE 274 257 211 153 112 NC_009009:SSA_1530|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1538778..1539008_NEGATIVE 270 239 192 61 1 NC_009009:SSA_0460|5end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_462608..462838_POSITIVE 270 240 199 129 90 NC_009009:SSA_0211|5end_hypothetical_protein_208041..208271_POSITIVE 267 135 92 159 123 NC_009009:SSA_1914|5end_hypothetical_protein_1905195..1905425_NEGATIVE 259 135 93 53 7 NC_009009:SSA_1722|5end_Thymidylate_kinase,_putative_1708663..1708893_NEGATIVE 258 218 171 227 170 NC_009009:SSA_2307|5end_hypothetical_protein_2309909..2310139_NEGATIVE 257 264 222 66 20 NC_009009:SSA_1137|5end_Dihydrolipoamide_dehydrogenase,_putative_1164375..1164605_POSITIVE 254 220 177 145 113 NC_009009:SSA_0509|5end_Propanediol_utilization_protein,_putative_508024..508254_POSITIVE 251 219 181 205 168 NC_009009:SSA_0337|5end_Hydroxymethylglutaryl-CoA_reductase,_putative_332163..332393_NEGATIVE 249 260 211 69 15 NC_009009:SSA_1784|5end_Glutamate_racemase,_putative_1769897..1770127_NEGATIVE 249 246 206 154 113 NC_009009:SSA_1709|5end_hypothetical_protein_1698414..1698644_NEGATIVE 247 229 181 65 13 NC_009009:SSA_2328|5end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_2331483..2331713_POSITIVE 246 137 99 198 150 NC_009009:SSA_1989|5end_ABC-type_transport_system_(uncharacterized),_ATPase_component,_putative_1985182..1985412_NEGATIVE 245 219 172 66 1 NC_009009:SSA_1247|5end_hypothetical_protein_1272358..1272588_NEGATIVE 244 236 199 101 53 NC_009009:SSA_2202|5end_Elongation_factor_Ts,_putative_2203350..2203580_NEGATIVE 244 220 178 132 82 NC_009009:SSA_0939|5end_Inositol_monophosphatase_(Mg++_dependent),_putative_946810..947040_POSITIVE 243 224 183 200 141 NC_009009:SSA_0831|5end_Nucleotide_sugar_synthetase-like_protein,_putative_815671..815901_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 140 91 92 40 NC_009009:SSA_0378|3end_TRZ/ATZ_family_hydrolase,_putative_368627..368777_POSITIVE 294 227 189 131 96 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 281 131 91 97 53 NC_009009:SSA_1617|3end_hypothetical_protein_1620436..1620586_NEGATIVE 277 230 189 49 8 NC_009009:SSA_2380|3end_hypothetical_protein_2385665..2385815_NEGATIVE 274 70 21 151 107 NC_009009:SSA_0289|3end_Leucyl-tRNA_synthetase,_putative_283999..284149_POSITIVE 270 240 199 132 93 NC_009009:SSA_0210|3end_hypothetical_protein_208124..208274_POSITIVE 268 119 74 67 19 NC_009009:SSA_1124|3end_Oxidoreductase,_putative_1148547..1148697_NEGATIVE 267 135 92 78 42 NC_009009:SSA_1915|3end_hypothetical_protein_1905276..1905426_NEGATIVE 265 224 181 60 15 NC_009009:SSA_0468|3end_Precorrin-6y_C5,15-methyltransferase-like,_putative_472418..472568_POSITIVE 256 219 171 69 3 NC_009009:SSA_1248|3end_hypothetical_protein_1272355..1272505_NEGATIVE 254 220 177 105 73 NC_009009:SSA_0508|3end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_508064..508214_POSITIVE 249 135 91 55 6 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 247 135 91 75 29 NC_009009:SSA_1962|3end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_1960930..1961080_POSITIVE 243 228 181 129 81 NC_009009:SSA_1531|3end_ABC-type_antimicrobial_peptide_transporter,_ATPase_component,_putative_1538778..1538928_NEGATIVE 242 236 196 106 66 NC_009009:SSA_1972|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1967811..1967961_NEGATIVE 242 136 91 93 47 NC_009009:SSA_0004|3end_Lipoprotein,_putative_3213..3363_NEGATIVE 240 228 188 137 87 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 240 220 178 148 117 NC_009009:SSA_0183|3end_hypothetical_protein_188106..188256_POSITIVE 235 240 194 131 72 NC_009009:SSA_1976|3end_Conserved_uncharacterized_protein_1971550..1971700_NEGATIVE 235 246 201 140 104 NC_009009:SSA_0691|3end_D-ala,D-ala_ligase,_putative_676374..676524_POSITIVE