Origin IGS: tggtttctccttgatgtatgattgttaaatttcatacacagggaccaatcactttatgaggacagaacgacacaaatcagcgattggctgtgtatgtgcggttccggataatcgtcaatttgcatcgcatgtctcctttcttaatttataaaaacaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgtttttataaattaagaaaggagacatgcgatgcaaattgacgattatccggaaccgcacatacacagccaatcgctgatttgtgtcgttctgtcctcataaagtgattggtccctgtgtatgaaatttaacaatcatacatcaaggagaaacca Mask Tandem Repeat Region ================================================ tggtttctccttgatgtatgattgttaaatttcatacacagggaccaatcactttatgaggacagaacgacacaaatcagcgattggctgtgtatgtgcggttccggataatcgtcaatttgcatcgcatgtctcctttcttaatttataaaaacaa Find is-nt database================================================ Query_seq: SSA_1734:SSA_1735|SSA_1734:SSA_1735:Cation (Mg/Ni uptake) transport ATPase, putative:UreX, putative:<-<-:1720394..1720550 157 tggtttctccttgatgtatgattgttaaatttcatacacagggaccaatcactttatgaggacagaacgacacaaatcagcgattggctgtgtatgtgcggttccggataatcgtcaatttgcatcgcatgtctcctttcttaatttataaaaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1734:SSA_1735|SSA_1734:SSA_1735:Cation (Mg/Ni uptake) transport ATPase, putative:UreX, putative:<-<-:1720394..1720550 157 tggtttctccttgatgtatgattgttaaatttcatacacagggaccaatcactttatgaggacagaacgacacaaatcagcgattggctgtgtatgtgcggttccggataatcgtcaatttgcatcgcatgtctcctttcttaatttataaaaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1734:SSA_1735|SSA_1734:SSA_1735:Cation (Mg/Ni uptake) transport ATPase, putative:UreX, putative:<-<-:1720394..1720550 157 tggtttctccttgatgtatgattgttaaatttcatacacagggaccaatcactttatgaggacagaacgacacaaatcagcgattggctgtgtatgtgcggttccggataatcgtcaatttgcatcgcatgtctcctttcttaatttataaaaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tggtttctccttgatgtatgattgttaaatttcatacacagggaccaatcactttatgaggacagaacgacacaaatcagcgattggctgtgtatgtgcggttccggataatcgtcaatttgcatcgcatgtctcctttcttaatttataaaaacaa Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 29 End: 148 ............................ M S Y T G T N H F M R T E R H K S A I G C V C A V P D N R Q F A S H V S F L N L ......... tggtttctccttgatgtatgattgttaaatttcatacacagggaccaatcactttatgaggacagaacgacacaaatcagcgattggctgtgtatgtgcggttccggataatcgtcaatttgcatcgcatgtctcctttcttaatttataaaaacaa 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================================================ tggtttctccttgatgtatgattgttaaatttcatacacagggaccaatcactttatgaggacagaacgacacaaatcagcgattggctgtgtatgtgcggttccggataatcgtcaatttgcatcgcatgtctcctttcttaatttataaaaacaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1734:SSA_1735|SSA_1734:SSA_1735:Cation (Mg/Ni uptake) transport ATPase, putative:UreX, putative:<-<-:1720394..1720550 157 tggtttctccttgatgtatgattgttaaatttcatacacagggaccaatcactttatgaggacagaacgacacaaatcagcgattggctgtgtatgtgcggttccggataatcgtcaatttgcatcgcatgtctcctttcttaatttataaaaacaa Intra-Species Hit: Count: 1 Min: 1 Max: 157 Len: 157 Subject: NC_009009_SSA_1734_SSA_1735|Cation (Mg/Ni uptake) transport ATPase, putative:UreX, putative|NEGATIVE:NEGATIVE|[1720394,1720550]|157 HSP 1 e-value: 4.0E-84 bit: 311.0 Len: 157 Query Start:1 Query End:157 Subject Strand: POSITIVE Subject Start: 1 Subject End: 157 tggtttctccttgatgtatgattgttaaatttcatacacagggaccaatcactttatgaggacagaacgacacaaatcagcgattggctgtgtatgtgcggttccggataatcgtcaatttgcatcgcatgtctcctttcttaatttataaaaacaa tggtttctccttgatgtatgattgttaaatttcatacacagggaccaatcactttatgaggacagaacgacacaaatcagcgattggctgtgtatgtgcggttccggataatcgtcaatttgcatcgcatgtctcctttcttaatttataaaaacaa Inter-species Hit: Count: 2 Min: 30 Max: 142 Len: 113 Subject: smit_SMT_1710_SMT_1711|magnesium-translocating P-type ATPase:Xaa-Pro dipeptidase|NEGATIVE:NEGATIVE|[1696121,1696522]|402 HSP 1 e-value: 8.0E-39 bit: 161.0 Len: 113 Query Start:30 Query End:142 Subject Strand: POSITIVE Subject Start: 30 Subject End: 142 .............................tttcatacacagggaccaatcactttatgaggacagaacgacacaaatcagcgattggctgtgtatgtgcggttccggataatcgtcaatttgcatcgcatgtctcctttctt............... .............................tttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctt............... Subject: smit_SMT_1708_SMT_1709|magnesium-translocating P-type ATPase:aminopeptidase P|NEGATIVE:NEGATIVE|[1694644,1695045]|402 HSP 1 e-value: 8.0E-39 bit: 161.0 Len: 113 Query Start:30 Query End:142 Subject Strand: POSITIVE Subject Start: 30 Subject End: 142 .............................tttcatacacagggaccaatcactttatgaggacagaacgacacaaatcagcgattggctgtgtatgtgcggttccggataatcgtcaatttgcatcgcatgtctcctttctt............... .............................tttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctt............... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCAUACACAGGGACCAAUCACUUUAUGAGGACAGAACGACACAAAUCAGCGAUUGGCUGUGUAUGUGCGGUUCCGGAUAAUCGUCAAUUUGCAUCGCAUGUCUCCUUUCUU ...(((((((((...((((((.((...((.(..........).))....)).))))))))))))))).(((((..(((((........))))).))))).............. (-25.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAAAGGAGACAUGCGAUGCAAAUUGACGAUUAUCCGGAACCGCACAUACACAGCCAAUCGCUGAUUUGUGUCGUUCUGUCCUCAUAAAGUGAUUGGUCCCUGUGUAUGAAA ......(((....((((((....)))).))....))).........((((((((((((((((((...(((((..(......)..))))))))))))))...)))))))))... (-32.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1009 80 31 200 151 NC_009009:SSA_1734|5end_Cation_(Mg/Ni_uptake)_transport_ATPase,_putative_1720303..1720533_NEGATIVE 344 83 47 40 8 NC_009009:SSA_1271|5end_Conserved_uncharacterized_protein_1293972..1294202_POSITIVE 323 100 51 165 105 NC_009009:SSA_1485|5end_Citrulline_cluster-linked_gene,_putative_1492809..1493039_NEGATIVE 310 88 46 153 105 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 306 78 31 69 22 NC_009009:SSA_1430|5end_Ribonuclease_Z,_putative_1438036..1438266_NEGATIVE 304 109 65 99 38 NC_009009:SSA_1659|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1656819..1657049_NEGATIVE 295 79 32 173 121 NC_009009:SSA_0981|5end_3-isopropylmalate_dehydratase_small_subunit,_putative_985396..985626_POSITIVE 294 107 63 221 177 NC_009009:SSA_1727|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1713420..1713650_NEGATIVE 294 100 57 221 171 NC_009009:SSA_1558|5end_Hydrolase,_HAD_superfamily_1560862..1561092_NEGATIVE 292 80 44 221 176 NC_009009:SSA_2118|5end_Thiamine_pyrophosphokinase,_putative_2120500..2120730_NEGATIVE 291 97 58 62 12 NC_009009:SSA_1842|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_HTH_DNA-binding_domains),_putative_1836494..1836724_NEGATIVE 289 99 51 77 34 NC_009009:SSA_1066|5end_ABC-type_oligopeptide_transport_system,_putative_1084335..1084565_POSITIVE 287 79 48 152 112 NC_009009:SSA_2331|5end_D-alanine_transfer_protein,_putative_2334964..2335194_NEGATIVE 287 100 51 189 129 NC_009009:SSA_2229|5end_hypothetical_protein_2228994..2229224_NEGATIVE 286 86 47 230 192 NC_009009:SSA_1638|5end_hypothetical_protein_1641325..1641555_NEGATIVE 285 88 42 231 177 NC_009009:SSA_0656|5end_Cell_division_protein_FtsZ,_putative_640159..640389_POSITIVE 282 108 66 121 70 NC_009009:SSA_2071|5end_hypothetical_protein_2074766..2074996_NEGATIVE 282 98 53 62 16 NC_009009:SSA_0175|5end_Penicillin-binding_protein_1B,_putative_172152..172382_POSITIVE 281 100 52 224 159 NC_009009:SSA_1606|5end_Dephospho-CoA_kinase,_putative_1612425..1612655_NEGATIVE 279 93 51 73 32 NC_009009:SSA_0220|5end_PTS_system,_mannose-specific_IIB_component,_putative_215848..216078_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 88 46 151 103 NC_009009:SSA_0101|3end_Conserved_uncharacterized_protein_104113..104263_POSITIVE 306 78 31 58 11 NC_009009:SSA_1431|3end_hypothetical_protein_1438047..1438197_NEGATIVE 304 109 65 99 38 NC_009009:SSA_1660|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1656819..1656969_NEGATIVE 295 87 49 52 14 NC_009009:SSA_0863|3end_Cof_family_protein,_putative_854206..854356_NEGATIVE 295 76 34 42 2 NC_009009:SSA_0468|3end_Precorrin-6y_C5,15-methyltransferase-like,_putative_472418..472568_POSITIVE 291 97 58 84 34 NC_009009:SSA_1843|3end_Histidine_kinase,_putative_1836472..1836622_NEGATIVE 288 108 68 104 57 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 287 87 51 113 70 NC_009009:SSA_2077|3end_hypothetical_protein_2081352..2081502_NEGATIVE 285 99 56 52 5 NC_009009:SSA_0334|3end_Diphosphomevalonate_decarboxylase,_putative_328882..329032_POSITIVE 282 108 66 87 36 NC_009009:SSA_2072|3end_Phosphatidate_cytidylyltransferase,_putative_2074800..2074950_NEGATIVE 280 87 50 115 70 NC_009009:SSA_0357|3end_Thioredoxin,_putative_351157..351307_POSITIVE 276 95 54 147 98 NC_009009:SSA_0894|3end_ATP-binding_cassette_protein,_putative_886533..886683_POSITIVE 274 87 44 77 17 NC_009009:SSA_0216|3end_Histidine_kinase,_putative_213270..213420_POSITIVE 271 99 51 143 98 NC_009009:SSA_0314|3end_Nucleoside-diphosphate-sugar_epimerase,_putative_308967..309117_NEGATIVE 269 78 39 53 10 NC_009009:SSA_0258|3end_hypothetical_protein_253022..253172_POSITIVE 269 99 51 65 10 NC_009009:SSA_0198|3end_Dihydrofolate_synthetase,_putative_198375..198525_POSITIVE 268 79 39 142 99 NC_009009:SSA_1680|3end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1673200..1673350_NEGATIVE 262 110 69 90 42 NC_009009:SSA_1117|3end_hypothetical_protein_1143386..1143536_POSITIVE 262 107 68 50 10 NC_009009:SSA_0333|3end_Mevalonate_kinase,_putative_327953..328103_POSITIVE 261 110 62 128 61 NC_009009:SSA_1187|3end_Transcriptional_antiterminator,_BglG_family,_putative_1215195..1215345_NEGATIVE