Origin IGS: tcttacctaagaaaccgtctaccaacagctatgagggctgcgactaatagctttagtccggccctcttttatatgataagaaacgttcattttcttattgaaaattaaaaaatctactaaaataaattggaagcgcattcattgaagcgcatttaaggagaattta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaattctccttaaatgcgcttcaatgaatgcgcttccaatttattttagtagattttttaattttcaataagaaaatgaacgtttcttatcatataaaagagggccggactaaagctattagtcgcagccctcatagctgttggtagacggtttcttaggtaaga Mask Tandem Repeat Region ================================================ tcttacctaagaaaccgtctaccaacagctatgagggctgcgactaatagctttagtccggccctcttttatatgataagaaacgttcattttcttattgaaaattaaaaaatctactaaaataaattggaagcgcattcattgaagcgcatttaaggagaattta Find is-nt database================================================ Query_seq: SSA_0738:SSA_0739|SSA_0738:SSA_0739:Ornithine carbamoyltransferase, catabolic, putative:Carbamate kinase, putative:->->:721061..721226 166 tcttacctaagaaaccgtctaccaacagctatgagggctgcgactaatagctttagtccggccctcttttatatgataagaaacgttcattttcttattgaaaattaaaaaatctactaaaataaattggaagcgcattcattgaagcgcatttaaggagaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0738:SSA_0739|SSA_0738:SSA_0739:Ornithine carbamoyltransferase, catabolic, putative:Carbamate kinase, putative:->->:721061..721226 166 tcttacctaagaaaccgtctaccaacagctatgagggctgcgactaatagctttagtccggccctcttttatatgataagaaacgttcattttcttattgaaaattaaaaaatctactaaaataaattggaagcgcattcattgaagcgcatttaaggagaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0738:SSA_0739|SSA_0738:SSA_0739:Ornithine carbamoyltransferase, catabolic, putative:Carbamate kinase, putative:->->:721061..721226 166 tcttacctaagaaaccgtctaccaacagctatgagggctgcgactaatagctttagtccggccctcttttatatgataagaaacgttcattttcttattgaaaattaaaaaatctactaaaataaattggaagcgcattcattgaagcgcatttaaggagaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcttacctaagaaaccgtctaccaacagctatgagggctgcgactaatagctttagtccggccctcttttatatgataagaaacgttcattttcttattgaaaattaaaaaatctactaaaataaattggaagcgcattcattgaagcgcatttaaggagaattta Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: - Start: 22 End: 138 ..................... W C S H P S R S I A K T R G E K I H Y S V N M K K N F I L F D V L I F Q F R M ............................ tcttacctaagaaaccgtctaccaacagctatgagggctgcgactaatagctttagtccggccctcttttatatgataagaaacgttcattttcttattgaaaattaaaaaatctactaaaataaattggaagcgcattcattgaagcgcatttaaggagaattta 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================================================ tcttacctaagaaaccgtctaccaacagctatgagggctgcgactaatagctttagtccggccctcttttatatgataagaaacgttcattttcttattgaaaattaaaaaatctactaaaataaattggaagcgcattcattgaagcgcatttaaggagaattta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.6 Tail_Score: -4.57353 Start: 33 End: 66 Full_Region: TCTACCAACAGCTAT GAGGGCTGCGACTAA TAGCT TTAGTCCGGCCCTC TTTTATATGATAAGA ................................GAGGGCTGCGACTAATAGCTTTAGTCCGGCCCTC.................................................................................................... TransTerm Strand: - Conf: 41 HP_score: -2.7 Tail_Score: -2.62184 Start: 77 End: 97 Full_Region: ttttttaattttcaa taagaaa atgaacg tttctta tcatataaaagaggg ............................................................................taagaaaatgaacgtttctta..................................................................... TransTerm Strand: - Conf: 39 HP_score: -2.1 Tail_Score: -2.52404 Start: 86 End: 108 Full_Region: attttagtagatttt ttaattttc aataa gaaaatgaa cgtttcttatcatat .....................................................................................ttaattttcaataagaaaatgaa.......................................................... Find igs database================================================ Query_seq: SSA_0738:SSA_0739|SSA_0738:SSA_0739:Ornithine carbamoyltransferase, catabolic, putative:Carbamate kinase, putative:->->:721061..721226 166 tcttacctaagaaaccgtctaccaacagctatgagggctgcgactaatagctttagtccggccctcttttatatgataagaaacgttcattttcttattgaaaattaaaaaatctactaaaataaattggaagcgcattcattgaagcgcatttaaggagaattta Intra-Species Hit: Count: 1 Min: 1 Max: 166 Len: 166 Subject: NC_009009_SSA_0738_SSA_0739|Ornithine carbamoyltransferase, catabolic, putative:Carbamate kinase, putative|POSITIVE:POSITIVE|[721061,721226]|166 HSP 1 e-value: 2.0E-89 bit: 329.0 Len: 166 Query Start:1 Query End:166 Subject Strand: POSITIVE Subject Start: 1 Subject End: 166 tcttacctaagaaaccgtctaccaacagctatgagggctgcgactaatagctttagtccggccctcttttatatgataagaaacgttcattttcttattgaaaattaaaaaatctactaaaataaattggaagcgcattcattgaagcgcatttaaggagaattta tcttacctaagaaaccgtctaccaacagctatgagggctgcgactaatagctttagtccggccctcttttatatgataagaaacgttcattttcttattgaaaattaaaaaatctactaaaataaattggaagcgcattcattgaagcgcatttaaggagaattta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUACCUAAGAAACCGUCUACCAACAGCUAUGAGGGCUGCGACUAAUAGCUUUAGUCCGGCCCUCUUUUAUAUGAUAAGAAACGUUCAUUUUCUUAUUGAAAAUUAAAAAAUCUACUAAAAUAAAUUGGAAGCGCAUUCAUUGAAGCGCAUUUAAGGAGAAUUUA .....(((.(((.........((((.......((((((((.((((((.....))))))))))))))........(((((((((.......)))))))))...........................))))..((((.(((...))))))).))).)))........ (-42.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUUCUCCUUAAAUGCGCUUCAAUGAAUGCGCUUCCAAUUUAUUUUAGUAGAUUUUUUAAUUUUCAAUAAGAAAAUGAACGUUUCUUAUCAUAUAAAAGAGGGCCGGACUAAAGCUAUUAGUCGCAGCCCUCAUAGCUGUUGGUAGACGGUUUCUUAGGUAAGA ................(((((((...))).))))....(((((((....))))))).....((((((.....)))))).......(((((((........((((((.(((((((.....)))))).).))))))..(((((((....))))))).....))))))) (-41.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 422 66 21 163 108 NC_009009:SSA_2253|5end_3-Methyladenine_DNA_glycosylase_I,_constitutive,_putative_2249424..2249654_NEGATIVE 376 68 22 74 10 NC_009009:SSA_1430|5end_Ribonuclease_Z,_putative_1438036..1438266_NEGATIVE 351 78 32 195 150 NC_009009:SSA_0504|5end_Peptide_ABC_transporter,_ATP-binding_protein,_putative_503009..503239_POSITIVE 342 70 21 214 149 NC_009009:SSA_2124|5end_Dehydrogenase,_eukaryotic-like,_putative_2129411..2129641_NEGATIVE 342 66 28 50 5 NC_009009:SSA_1066|5end_ABC-type_oligopeptide_transport_system,_putative_1084335..1084565_POSITIVE 337 62 21 136 97 NC_009009:SSA_0838|5end_GtfB,_putative_825406..825636_POSITIVE 331 70 23 145 94 NC_009009:SSA_0490|5end_Cobalamin_5'-phosphate_synthase,_putative_490236..490466_POSITIVE 326 67 27 71 30 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 323 65 26 45 1 NC_009009:SSA_0956|5end_surface_protein_D_961223..961453_POSITIVE 319 65 22 59 12 NC_009009:SSA_1855|5end_hypothetical_protein_1852051..1852281_NEGATIVE 319 79 32 224 179 NC_009009:SSA_0495|5end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_495186..495416_POSITIVE 306 64 22 72 37 NC_009009:SSA_0069|5end_Hypothetical_protein,_possibly_membrane-associated_73037..73267_POSITIVE 305 66 28 50 4 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 304 63 25 216 170 NC_009009:SSA_1878|5end_Conserved_uncharacterized_protein_1872200..1872430_NEGATIVE 302 63 26 68 27 NC_009009:SSA_0464|5end_Cobalamin_biosynthesis_protein_cobD,_putative_468225..468455_POSITIVE 300 43 9 47 9 NC_009009:SSA_0780|5end_Acid_phosphatase_(PAP2_family),_putative_764748..764978_POSITIVE 298 59 15 82 36 NC_009009:SSA_0879|5end_Cell_division_regulator,_negative_regulator_of_FtsZ_septation_ring_formation,_putative_873632..873862_POSITIVE 297 66 22 216 159 NC_009009:SSA_2362|5end_L-serine_dehydratase_alpha_subunit_2364708..2364938_POSITIVE 297 65 22 146 100 NC_009009:SSA_0589|5end_Acetylornithine_deacetylase/succinyl-diaminopimelate_desuccinylase_(M20/M25/M40_family_peptidase),_putative_580745..580975_POSITIVE 294 66 26 67 28 NC_009009:SSA_1775|5end_Potassium_uptake_protein,_Trk_family,_putative_1761284..1761514_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 458 66 33 58 25 NC_009009:SSA_0738|3end_Ornithine_carbamoyltransferase,_catabolic,_putative_721000..721150_POSITIVE 377 64 21 151 98 NC_009009:SSA_2254|3end_Holliday_junction_DNA_helicase_ruvA,_putative_2249434..2249584_NEGATIVE 331 70 23 148 97 NC_009009:SSA_0489|3end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_490319..490469_POSITIVE 321 70 22 76 4 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 316 68 24 63 1 NC_009009:SSA_1431|3end_hypothetical_protein_1438047..1438197_NEGATIVE 316 60 16 150 105 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE 302 63 26 66 25 NC_009009:SSA_0463|3end_Cobyrinic_acid_A,C-diamide_synthase,_putative_468303..468453_POSITIVE 294 57 15 95 49 NC_009009:SSA_0198|3end_Dihydrofolate_synthetase,_putative_198375..198525_POSITIVE 292 69 25 111 69 NC_009009:SSA_0966|3end_Uridine_kinase,_putative_975790..975940_POSITIVE 287 65 22 73 21 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE 281 65 28 69 25 NC_009009:SSA_0262|3end_ABC-type_Mn/Zn_transporter,_ATP-ase_component,_putative_255455..255605_NEGATIVE 278 57 11 45 1 NC_009009:SSA_0202|3end_hypothetical_protein_201402..201552_POSITIVE 277 65 36 33 5 NC_009009:SSA_1856|3end_hypothetical_protein_1852077..1852227_NEGATIVE 276 71 32 110 60 NC_009009:SSA_2145|3end_Tributyrin_esterase,_putative_2145879..2146029_NEGATIVE 275 54 15 65 35 NC_009009:SSA_2200|3end_Firmicutes_transcriptional_repressor_of_class_III_stress_genes_(CtsR),_putative_2201109..2201259_NEGATIVE 274 70 21 52 5 NC_009009:SSA_1250|3end_Conserved_uncharacterized_protein,_putative_1273982..1274132_NEGATIVE 272 46 6 140 97 NC_009009:SSA_0320|3end_hypothetical_protein_313824..313974_POSITIVE 271 44 6 146 105 NC_009009:SSA_1029|3end_hypothetical_protein_1046167..1046317_NEGATIVE 271 57 14 80 19 NC_009009:SSA_0074|3end_ABC_transporter_substrate-binding_protein-sugar_transport,_putative_78975..79125_POSITIVE 264 57 13 95 54 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE