Origin IGS: ctgttccctttcttaaaagaagtaatcttttctcctcattttatcacaaaaaaggaatttttccaaggtaataaggagcaagagtgctgaaaaaacgaatatgagtct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agactcatattcgttttttcagcactcttgctccttattaccttggaaaaattccttttttgtgataaaatgaggagaaaagattacttcttttaagaaagggaacag Mask Tandem Repeat Region ================================================ ctgttccctttcttaaaagaagtaatcttttctcctcattttatcacaaaaaaggaatttttccaaggtaataaggagcaagagtgctgaaaaaacgaatatgagtct Find is-nt database================================================ Query_seq: SSA_1163:SSA_1164|SSA_1163:SSA_1164:GMP synthase [glutamine-hydrolyzing], putative:hypothetical protein:<-<-:1190989..1191096 108 ctgttccctttcttaaaagaagtaatcttttctcctcattttatcacaaaaaaggaatttttccaaggtaataaggagcaagagtgctgaaaaaacgaatatgagtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1163:SSA_1164|SSA_1163:SSA_1164:GMP synthase [glutamine-hydrolyzing], putative:hypothetical protein:<-<-:1190989..1191096 108 ctgttccctttcttaaaagaagtaatcttttctcctcattttatcacaaaaaaggaatttttccaaggtaataaggagcaagagtgctgaaaaaacgaatatgagtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1163:SSA_1164|SSA_1163:SSA_1164:GMP synthase [glutamine-hydrolyzing], putative:hypothetical protein:<-<-:1190989..1191096 108 ctgttccctttcttaaaagaagtaatcttttctcctcattttatcacaaaaaaggaatttttccaaggtaataaggagcaagagtgctgaaaaaacgaatatgagtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgttccctttcttaaaagaagtaatcttttctcctcattttatcacaaaaaaggaatttttccaaggtaataaggagcaagagtgctgaaaaaacgaatatgagtct Predict ORF larger than 30AA ================================================ ctgttccctttcttaaaagaagtaatcttttctcctcattttatcacaaaaaaggaatttttccaaggtaataaggagcaagagtgctgaaaaaacgaatatgagtct 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: 86 Start: 38 End: 67 .....................................CTTGGAAAAATTCCTTTTTTGTGATAAAAT......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctgttccctttcttaaaagaagtaatcttttctcctcattttatcacaaaaaaggaatttttccaaggtaataaggagcaagagtgctgaaaaaacgaatatgagtct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1163:SSA_1164|SSA_1163:SSA_1164:GMP synthase [glutamine-hydrolyzing], putative:hypothetical protein:<-<-:1190989..1191096 108 ctgttccctttcttaaaagaagtaatcttttctcctcattttatcacaaaaaaggaatttttccaaggtaataaggagcaagagtgctgaaaaaacgaatatgagtct Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: NC_009009_SSA_1163_SSA_1164|GMP synthase [glutamine-hydrolyzing], putative:hypothetical protein|NEGATIVE:NEGATIVE|[1190989,1191096]|108 HSP 1 e-value: 4.0E-55 bit: 214.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 ctgttccctttcttaaaagaagtaatcttttctcctcattttatcacaaaaaaggaatttttccaaggtaataaggagcaagagtgctgaaaaaacgaatatgagtct ctgttccctttcttaaaagaagtaatcttttctcctcattttatcacaaaaaaggaatttttccaaggtaataaggagcaagagtgctgaaaaaacgaatatgagtct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUUCCCUUUCUUAAAAGAAGUAAUCUUUUCUCCUCAUUUUAUCACAAAAAAGGAAUUUUUCCAAGGUAAUAAGGAGCAAGAGUGCUGAAAAAACGAAUAUGAGUCU .(((((.((((....)))).((((.((((..(((((....(((((...(((((....)))))....)))))..))))).)))).))))........)))))....... (-15.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGACUCAUAUUCGUUUUUUCAGCACUCUUGCUCCUUAUUACCUUGGAAAAAUUCCUUUUUUGUGAUAAAAUGAGGAGAAAAGAUUACUUCUUUUAAGAAAGGGAACAG ............((((((((..........(((((((((...(((.(((((.....))))).)))...)))))))))((((((.....))))))..))))..)))).. (-18.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 804 90 41 181 132 NC_009009:SSA_1163|5end_GMP_synthase_[glutamine-hydrolyzing],_putative_1190898..1191128_NEGATIVE 303 70 30 143 96 NC_009009:SSA_0191|5end_Adenine-specific_DNA_methylase,_putative_191907..192137_POSITIVE 266 47 4 186 135 NC_009009:SSA_1989|5end_ABC-type_transport_system_(uncharacterized),_ATPase_component,_putative_1985182..1985412_NEGATIVE 260 78 31 139 86 NC_009009:SSA_1245|5end_Transcriptional_regulator,_LysR_family,_putative_1268722..1268952_POSITIVE 240 70 26 156 99 NC_009009:SSA_1844|5end_hypothetical_protein_1838183..1838413_NEGATIVE 235 79 33 154 99 NC_009009:SSA_2359|5end_Glucose_inhibited_division_protein_A,_putative_2362520..2362750_NEGATIVE 235 99 51 68 15 NC_009009:SSA_1121|5end_Cytochrome_C-type_biogenesis_protein,_putative_1147149..1147379_POSITIVE 232 54 16 106 63 NC_009009:SSA_1770|5end_hypothetical_protein_1758431..1758661_NEGATIVE 230 78 33 99 34 NC_009009:SSA_2358|5end_hypothetical_protein_2360497..2360727_NEGATIVE 225 98 63 63 19 NC_009009:SSA_0610|5end_LemA-like_protein,_putative_598968..599198_POSITIVE 224 42 1 172 123 NC_009009:SSA_0151|5end_hypothetical_protein_145354..145584_POSITIVE 223 98 58 39 5 NC_009009:SSA_0611|5end_HtpX_protease,_putative_599539..599769_POSITIVE 222 48 20 113 85 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 220 89 54 216 173 NC_009009:SSA_1093|5end_ATP-dependent_Clp_protease_ATP-binding_subunit_clpX,_putative_1110336..1110566_POSITIVE 220 98 63 60 31 NC_009009:SSA_0415|5end_Permease,_putative_410568..410798_POSITIVE 220 91 51 77 37 NC_009009:SSA_0374|5end_Peptide_methionine_sulfoxide_reductase_msrA/msrB,_putative_363163..363393_POSITIVE 217 50 2 131 91 NC_009009:SSA_1529|5end_Lysyl-tRNA_synthetase,_putative_1535871..1536101_POSITIVE 216 46 1 143 98 NC_009009:SSA_1764|5end_hypothetical_protein_1750868..1751098_POSITIVE 213 69 27 143 94 NC_009009:SSA_1015|5end_4-hydroxybenzoate_octaprenyltransferase,_putative_1018703..1018933_POSITIVE 213 98 62 170 138 NC_009009:SSA_0424|5end_Exopolysaccharide_biosynthesis_protein,_putative_422233..422463_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 70 30 61 14 NC_009009:SSA_0190|3end_hypothetical_protein_191905..192055_POSITIVE 259 57 11 62 21 NC_009009:SSA_0394|3end_hypothetical_protein_390931..391081_POSITIVE 247 90 53 88 47 NC_009009:SSA_1689|3end_hypothetical_protein_1681945..1682095_NEGATIVE 232 54 16 46 3 NC_009009:SSA_1771|3end_Conserved_DNA_methyltransferase_protein,_putative_1758491..1758641_NEGATIVE 225 97 63 47 14 NC_009009:SSA_1131|3end_High-affinity_Fe_2+/Pb2+_permease,_putative_1158768..1158918_POSITIVE 223 98 58 37 3 NC_009009:SSA_0610|3end_LemA-like_protein,_putative_599617..599767_POSITIVE 222 48 20 103 75 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 219 98 51 74 31 NC_009009:SSA_0436|3end_Imidazolonepropionase,_putative_440214..440364_POSITIVE 216 46 1 146 101 NC_009009:SSA_1763|3end_ABC-type_molybdenum_transport_system,_ATPase_component,_putative_1750951..1751101_POSITIVE 212 84 46 83 49 NC_009009:SSA_1048|3end_ABC_transporter_ATP-binding_protein-spermidine/putrescine_transport,_putative_1064184..1064334_POSITIVE 211 45 6 95 60 NC_009009:SSA_0703|3end_Citrate_synthase,_putative_689352..689502_POSITIVE 211 90 62 80 47 NC_009009:SSA_0410|3end_hypothetical_protein_405750..405900_NEGATIVE 206 33 3 74 48 NC_009009:SSA_0162|3end_hypothetical_protein_162139..162289_POSITIVE 203 55 18 37 2 NC_009009:SSA_1528|3end_Phosphoglycerate_mutase,_putative_1535850..1536000_POSITIVE 202 46 3 96 62 NC_009009:SSA_1412|3end_hypothetical_protein_1423994..1424144_NEGATIVE 201 88 58 110 85 NC_009009:SSA_2098|3end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2102931..2103081_NEGATIVE 200 93 54 143 110 NC_009009:SSA_0713|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_700028..700178_POSITIVE 199 56 24 49 15 NC_009009:SSA_1760|3end_hypothetical_protein_1747126..1747276_NEGATIVE 199 70 22 77 29 NC_009009:SSA_1622|3end_50S_ribosomal_protein_L1,_putative_1624752..1624902_NEGATIVE 199 67 29 115 76 NC_009009:SSA_0150|3end_hypothetical_protein_145227..145377_POSITIVE