Origin IGS: ctatttttattctcctaattgcattaacgtcctattttatcatatttcatcccttttaggaatccttctcagaaatttaccgaaaagaaaggctgagaaaaatctcagcctaggtttttaacatagatgaaaggtatatgaagcctgtctctgcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagcagagacaggcttcatatacctttcatctatgttaaaaacctaggctgagatttttctcagcctttcttttcggtaaatttctgagaaggattcctaaaagggatgaaatatgataaaataggacgttaatgcaattaggagaataaaaatag Mask Tandem Repeat Region ================================================ ctatttttattctcctaattgcattaacgtcctattttatcatatttcatcccttttaggaatccttctcagaaatttaccgaaaagaaaggctgagaaaaatctcagcctaggtttttaacatagatgaaaggtatatgaagcctgtctctgcta Find is-nt database================================================ Query_seq: SSA_1658:SSA_1659|SSA_1658:SSA_1659:Cationic amino acid transporter, putative:ABC-type antimicrobial peptide transport system, permease component, putative:<-<-:1654765..1654920 156 ctatttttattctcctaattgcattaacgtcctattttatcatatttcatcccttttaggaatccttctcagaaatttaccgaaaagaaaggctgagaaaaatctcagcctaggtttttaacatagatgaaaggtatatgaagcctgtctctgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1658:SSA_1659|SSA_1658:SSA_1659:Cationic amino acid transporter, putative:ABC-type antimicrobial peptide transport system, permease component, putative:<-<-:1654765..1654920 156 ctatttttattctcctaattgcattaacgtcctattttatcatatttcatcccttttaggaatccttctcagaaatttaccgaaaagaaaggctgagaaaaatctcagcctaggtttttaacatagatgaaaggtatatgaagcctgtctctgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1658:SSA_1659|SSA_1658:SSA_1659:Cationic amino acid transporter, putative:ABC-type antimicrobial peptide transport system, permease component, putative:<-<-:1654765..1654920 156 ctatttttattctcctaattgcattaacgtcctattttatcatatttcatcccttttaggaatccttctcagaaatttaccgaaaagaaaggctgagaaaaatctcagcctaggtttttaacatagatgaaaggtatatgaagcctgtctctgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctatttttattctcctaattgcattaacgtcctattttatcatatttcatcccttttaggaatccttctcagaaatttaccgaaaagaaaggctgagaaaaatctcagcctaggtttttaacatagatgaaaggtatatgaagcctgtctctgcta Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 23 End: 118 ...................... M N V L F Y H I S S L L G I L L R N L P K R K A E K N L S L G F ...................................... ctatttttattctcctaattgcattaacgtcctattttatcatatttcatcccttttaggaatccttctcagaaatttaccgaaaagaaaggctgagaaaaatctcagcctaggtttttaacatagatgaaaggtatatgaagcctgtctctgcta 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================================================ ctatttttattctcctaattgcattaacgtcctattttatcatatttcatcccttttaggaatccttctcagaaatttaccgaaaagaaaggctgagaaaaatctcagcctaggtttttaacatagatgaaaggtatatgaagcctgtctctgcta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -12.2 Tail_Score: -4.68908 Start: 91 End: 110 Full_Region: tatgttaaaaaccta ggctgaga tttt tctcagcc tttcttttcggtaaa ..........................................................................................ggctgagatttttctcagcc.............................................. Find igs database================================================ Query_seq: SSA_1658:SSA_1659|SSA_1658:SSA_1659:Cationic amino acid transporter, putative:ABC-type antimicrobial peptide transport system, permease component, putative:<-<-:1654765..1654920 156 ctatttttattctcctaattgcattaacgtcctattttatcatatttcatcccttttaggaatccttctcagaaatttaccgaaaagaaaggctgagaaaaatctcagcctaggtttttaacatagatgaaaggtatatgaagcctgtctctgcta Intra-Species Hit: Count: 1 Min: 1 Max: 156 Len: 156 Subject: NC_009009_SSA_1658_SSA_1659|Cationic amino acid transporter, putative:ABC-type antimicrobial peptide transport system, permease component, putative|NEGATIVE:NEGATIVE|[1654765,1654920]|156 HSP 1 e-value: 1.0E-83 bit: 309.0 Len: 156 Query Start:1 Query End:156 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 ctatttttattctcctaattgcattaacgtcctattttatcatatttcatcccttttaggaatccttctcagaaatttaccgaaaagaaaggctgagaaaaatctcagcctaggtttttaacatagatgaaaggtatatgaagcctgtctctgcta ctatttttattctcctaattgcattaacgtcctattttatcatatttcatcccttttaggaatccttctcagaaatttaccgaaaagaaaggctgagaaaaatctcagcctaggtttttaacatagatgaaaggtatatgaagcctgtctctgcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAUUUUUAUUCUCCUAAUUGCAUUAACGUCCUAUUUUAUCAUAUUUCAUCCCUUUUAGGAAUCCUUCUCAGAAAUUUACCGAAAAGAAAGGCUGAGAAAAAUCUCAGCCUAGGUUUUUAACAUAGAUGAAAGGUAUAUGAAGCCUGUCUCUGCUA ....................(((...(((..((......((((((((((((....((((((((((((.((...........)).)))..(((((((((....))))))))).)))))))))....))))))....))))))))..)))...))).. (-29.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCAGAGACAGGCUUCAUAUACCUUUCAUCUAUGUUAAAAACCUAGGCUGAGAUUUUUCUCAGCCUUUCUUUUCGGUAAAUUUCUGAGAAGGAUUCCUAAAAGGGAUGAAAUAUGAUAAAAUAGGACGUUAAUGCAAUUAGGAGAAUAAAAAUAG ..(((..(((...((((((((....(((((((...(((.......(((((((((....)))))))))((((((((((.......))))))))))....)))...))))))))))))).......))..)))..))).................... (-40.31) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 845 110 61 201 152 NC_009009:SSA_1658|5end_Cationic_amino_acid_transporter,_putative_1654674..1654904_NEGATIVE 320 121 85 142 105 NC_009009:SSA_1490|5end_Ribonuclease_BN,_putative_1496732..1496962_NEGATIVE 316 99 51 166 127 NC_009009:SSA_1527|5end_hypothetical_protein_1534587..1534817_POSITIVE 280 117 84 144 107 NC_009009:SSA_0080|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_83785..84015_POSITIVE 279 129 87 68 32 NC_009009:SSA_2162|5end_hypothetical_protein_2160592..2160822_POSITIVE 264 70 21 129 82 NC_009009:SSA_0894|5end_ATP-binding_cassette_protein,_putative_885779..886009_POSITIVE 262 79 36 136 87 NC_009009:SSA_1804|5end_NADPH-flavin_oxidoreductase,_putative_1788668..1788898_NEGATIVE 256 98 58 68 22 NC_009009:SSA_1636|5end_ABC-type_antibiotic_exporter,_ATPase_component,_putative_1640905..1641135_NEGATIVE 256 125 82 64 20 NC_009009:SSA_1575|5end_Glycosyl_transferase,_putative_1579110..1579340_NEGATIVE 255 110 61 195 145 NC_009009:SSA_2358|5end_hypothetical_protein_2360497..2360727_NEGATIVE 254 145 102 56 14 NC_009009:SSA_1149|5end_Glycosyl_hydrolase,_family_1,_putative_1178399..1178629_POSITIVE 252 61 21 65 29 NC_009009:SSA_2145|5end_Tributyrin_esterase,_putative_2146658..2146888_NEGATIVE 248 109 63 53 6 NC_009009:SSA_1752|5end_Phosphotransferase_system,_trehalose-specific_IIBC_component,_putative_1741875..1742105_NEGATIVE 247 110 81 148 120 NC_009009:SSA_0692|5end_D-Ala-D-Ala_adding_enzyme,_putative_676370..676600_POSITIVE 243 145 105 48 4 NC_009009:SSA_0832|5end_SecY-like_protein,_putative_816708..816938_POSITIVE 242 115 73 205 155 NC_009009:SSA_1235|5end_Dihydroorotase,_putative_1261227..1261457_NEGATIVE 242 69 26 122 73 NC_009009:SSA_0531|5end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527355..527585_POSITIVE 241 120 80 148 110 NC_009009:SSA_0006|5end_Peptidyl-tRNA_hydrolase,_putative_5009..5239_POSITIVE 240 110 64 201 158 NC_009009:SSA_2243|5end_Conserved_uncharacterized_protein_2239341..2239571_NEGATIVE 238 150 108 42 1 NC_009009:SSA_2013|5end_hypothetical_protein_2013793..2014023_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 366 129 86 104 56 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 330 120 71 62 5 NC_009009:SSA_2201|3end_hypothetical_protein_2202237..2202387_POSITIVE 320 121 85 94 57 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 292 119 71 77 22 NC_009009:SSA_0415|3end_Permease,_putative_411730..411880_POSITIVE 281 111 79 59 25 NC_009009:SSA_2202|3end_Elongation_factor_Ts,_putative_2202307..2202457_NEGATIVE 281 126 86 53 11 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 280 117 84 98 61 NC_009009:SSA_0079|3end_ROK_family_protein,_putative_83819..83969_POSITIVE 268 117 82 92 49 NC_009009:SSA_0688|3end_2,3-bisphosphoglycerate-dependent_phosphoglycerate_mutase,_putative_672132..672282_POSITIVE 264 70 21 142 95 NC_009009:SSA_0893|3end_ATP-binding_cassette_transporter-like_protein,_putative_885872..886022_POSITIVE 262 79 36 139 90 NC_009009:SSA_1805|3end_Primosomal_protein_DnaI,_putative_1788665..1788815_NEGATIVE 260 117 84 100 61 NC_009009:SSA_0267|3end_ROK_family_protein,_putative_260873..261023_NEGATIVE 257 128 86 107 54 NC_009009:SSA_0876|3end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_protein,_putative_870861..871011_POSITIVE 255 110 61 79 29 NC_009009:SSA_2359|3end_Glucose_inhibited_division_protein_A,_putative_2360613..2360763_NEGATIVE 254 145 102 50 8 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE 247 110 81 72 44 NC_009009:SSA_0691|3end_D-ala,D-ala_ligase,_putative_676374..676524_POSITIVE 246 94 52 68 26 NC_009009:SSA_0827|3end_Conserved_uncharacterized_cytosolic_protein,_putative_806952..807102_POSITIVE 245 119 81 100 61 NC_009009:SSA_0799|3end_hypothetical_protein_781713..781863_NEGATIVE 245 99 52 71 19 NC_009009:SSA_0394|3end_hypothetical_protein_390931..391081_POSITIVE 244 96 52 134 86 NC_009009:SSA_2285|3end_hypothetical_protein_2287825..2287975_POSITIVE 243 109 65 42 8 NC_009009:SSA_0088|3end_V-type_sodium_ATPase,_subunit_C,_putative_90023..90173_POSITIVE