Origin IGS: gataggctccttttttatttctagtcctattttatttgaaaacgttttacaatactatggcaagctgcctaaaatttaaaaaatgttttgtgcagtctgcacaaaaca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgttttgtgcagactgcacaaaacattttttaaattttaggcagcttgccatagtattgtaaaacgttttcaaataaaataggactagaaataaaaaaggagcctatc Mask Tandem Repeat Region ================================================ gataggctccttttttatttctagtcctattttatttgaaaacgttttacaatactatggcaagctgcctaaaatttaaaaaatgttttgtgcagtctgcacaaaaca Find is-nt database================================================ Query_seq: SSA_2040:SSA_2041|SSA_2040:SSA_2041:ABC transporter ATP-binding protein-multiple sugar transport, putative:Leucine-rich protein, putative:<-<-:2045789..2045896 108 gataggctccttttttatttctagtcctattttatttgaaaacgttttacaatactatggcaagctgcctaaaatttaaaaaatgttttgtgcagtctgcacaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2040:SSA_2041|SSA_2040:SSA_2041:ABC transporter ATP-binding protein-multiple sugar transport, putative:Leucine-rich protein, putative:<-<-:2045789..2045896 108 gataggctccttttttatttctagtcctattttatttgaaaacgttttacaatactatggcaagctgcctaaaatttaaaaaatgttttgtgcagtctgcacaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2040:SSA_2041|SSA_2040:SSA_2041:ABC transporter ATP-binding protein-multiple sugar transport, putative:Leucine-rich protein, putative:<-<-:2045789..2045896 108 gataggctccttttttatttctagtcctattttatttgaaaacgttttacaatactatggcaagctgcctaaaatttaaaaaatgttttgtgcagtctgcacaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gataggctccttttttatttctagtcctattttatttgaaaacgttttacaatactatggcaagctgcctaaaatttaaaaaatgttttgtgcagtctgcacaaaaca Predict ORF larger than 30AA ================================================ gataggctccttttttatttctagtcctattttatttgaaaacgttttacaatactatggcaagctgcctaaaatttaaaaaatgttttgtgcagtctgcacaaaaca 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: 82 Start: 52 End: 81 ...................................................TTTTAAATTTTAGGCAGCTTGCCATAGTAT........................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gataggctccttttttatttctagtcctattttatttgaaaacgttttacaatactatggcaagctgcctaaaatttaaaaaatgttttgtgcagtctgcacaaaaca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2040:SSA_2041|SSA_2040:SSA_2041:ABC transporter ATP-binding protein-multiple sugar transport, putative:Leucine-rich protein, putative:<-<-:2045789..2045896 108 gataggctccttttttatttctagtcctattttatttgaaaacgttttacaatactatggcaagctgcctaaaatttaaaaaatgttttgtgcagtctgcacaaaaca Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: NC_009009_SSA_2040_SSA_2041|ABC transporter ATP-binding protein-multiple sugar transport, putative:Leucine-rich protein, putative|NEGATIVE:NEGATIVE|[2045789,2045896]|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 gataggctccttttttatttctagtcctattttatttgaaaacgttttacaatactatggcaagctgcctaaaatttaaaaaatgttttgtgcagtctgcacaaaaca gataggctccttttttatttctagtcctattttatttgaaaacgttttacaatactatggcaagctgcctaaaatttaaaaaatgttttgtgcagtctgcacaaaaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAGGCUCCUUUUUUAUUUCUAGUCCUAUUUUAUUUGAAAACGUUUUACAAUACUAUGGCAAGCUGCCUAAAAUUUAAAAAAUGUUUUGUGCAGUCUGCACAAAACA ..(((((..........((((.(((........))).))))..((((..((......))..)))).)))))............((((((((((.....)))))))))) (-21.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUUGUGCAGACUGCACAAAACAUUUUUUAAAUUUUAGGCAGCUUGCCAUAGUAUUGUAAAACGUUUUCAAAUAAAAUAGGACUAGAAAUAAAAAAGGAGCCUAUC ((((((((((.....))))))))))............(((((..(((....((((.((((..................)))).)))).........)))..))))).. (-21.29) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 808 70 21 161 112 NC_009009:SSA_2040|5end_ABC_transporter_ATP-binding_protein-multiple_sugar_transport,_putative_2045698..2045928_NEGATIVE 300 100 54 191 149 NC_009009:SSA_0744|5end_S-adenosylmethio_nine:tRNA-ribosyltransferase-isomerase_(queuine_synthetase),_putative_726804..727034_NEGATIVE 258 100 51 93 35 NC_009009:SSA_2211|5end_Transmembrane_protein,_putative_2212473..2212703_NEGATIVE 254 100 55 175 137 NC_009009:SSA_1190|5end_Conserved_uncharacterized_protein_1218137..1218367_NEGATIVE 243 100 54 134 80 NC_009009:SSA_0085|5end_V-type_sodium_ATPase,_subunit_I,_putative_85750..85980_POSITIVE 238 50 1 227 174 NC_009009:SSA_0818|5end_SPX_domain-like_protein,_putative_799675..799905_POSITIVE 236 69 21 69 7 NC_009009:SSA_1423|5end_Single-stranded_DNA-specific_exonuclease,_5'-3',_putative_1433783..1434013_NEGATIVE 235 37 1 102 62 NC_009009:SSA_0539|5end_PduO_protein,_putative_534233..534463_POSITIVE 226 49 6 143 101 NC_009009:SSA_1615|5end_Alanine_dehydrogenase,_putative_1618126..1618356_POSITIVE 225 77 43 204 171 NC_009009:SSA_0310|5end_hypothetical_protein_305306..305536_POSITIVE 222 27 4 116 97 NC_009009:SSA_1238|5end_hypothetical_protein_1263154..1263384_NEGATIVE 219 43 1 138 97 NC_009009:SSA_0783|5end_Proton-translocating_ATPase,_F0_sector,_subunit_a,_putative_766815..767045_POSITIVE 215 69 23 148 86 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 214 70 25 169 123 NC_009009:SSA_1961|5end_Amino_acid_ABC_transporter,_amino_acid-binding_protein/permease_protein,_putative_1958548..1958778_POSITIVE 213 69 21 172 119 NC_009009:SSA_1180|5end_hypothetical_protein_1208559..1208789_NEGATIVE 212 38 4 164 128 NC_009009:SSA_1299|5end_Maltose/maltodextrin_ABC_transport_system,_putative_1316629..1316859_POSITIVE 211 98 58 74 31 NC_009009:SSA_1155|5end_Serine_hydroxymethyltransferase,_putative_1183298..1183528_POSITIVE 210 77 43 221 184 NC_009009:SSA_1835|5end_Late_competence_protein,_putative_1830941..1831171_NEGATIVE 209 71 42 197 166 NC_009009:SSA_1491|5end_Methionine_aminopeptidase_A,_putative_1497637..1497867_NEGATIVE 209 100 60 69 23 NC_009009:SSA_1003|5end_ABC_transporter_substrate-binding_protein-multiple_sugars,_putative_1003875..1004105_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 254 100 55 90 52 NC_009009:SSA_1191|3end_hypothetical_protein_1218222..1218372_NEGATIVE 243 100 54 144 90 NC_009009:SSA_0083|3end_hypothetical_protein_85840..85990_POSITIVE 235 37 1 43 3 NC_009009:SSA_0538|3end_PduH_protein,_putative_534254..534404_POSITIVE 229 47 4 127 80 NC_009009:SSA_1374|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1391359..1391509_NEGATIVE 222 27 4 119 100 NC_009009:SSA_1239|3end_hypothetical_protein_1263151..1263301_NEGATIVE 222 67 21 61 2 NC_009009:SSA_0445|3end_hypothetical_protein_444776..444926_POSITIVE 219 43 1 102 61 NC_009009:SSA_0782|3end_Proton-translocating_ATPase,_F0_sector,_subunit_c,_putative_766859..767009_POSITIVE 215 69 23 138 76 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 214 70 21 133 82 NC_009009:SSA_0392|3end_hypothetical_protein_388303..388453_POSITIVE 213 69 21 139 86 NC_009009:SSA_1181|3end_Hydrolase,_alpha/beta_superfamily,_putative_1208592..1208742_NEGATIVE 212 38 4 82 46 NC_009009:SSA_1298|3end_Maltose/maltodextrin_ABC_transporter,_sugar-binding_protein_MalX,_putative_1316627..1316777_POSITIVE 209 100 60 56 10 NC_009009:SSA_1002|3end_Alpha-galactosidase,_putative_1003942..1004092_POSITIVE 208 69 35 133 106 NC_009009:SSA_2136|3end_50S_ribosomal_protein_L34,_putative_2137507..2137657_NEGATIVE 208 32 2 76 47 NC_009009:SSA_1759|3end_hypothetical_protein_1746664..1746814_NEGATIVE 208 100 53 74 23 NC_009009:SSA_1278|3end_Rhodanese-like_domain_protein,_putative_1299563..1299713_NEGATIVE 206 50 1 147 111 NC_009009:SSA_2320|3end_hypothetical_protein_2322302..2322452_NEGATIVE 206 98 51 64 15 NC_009009:SSA_1682|3end_hypothetical_protein_1676130..1676280_NEGATIVE 205 48 4 124 83 NC_009009:SSA_1938|3end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1924764..1924914_NEGATIVE 202 70 21 133 79 NC_009009:SSA_1633|3end_FimA_fimbrial_subunit-like_protein,_putative_1634106..1634256_NEGATIVE 196 63 23 121 83 NC_009009:SSA_0612|3end_Rgg_protein,_putative_601857..602007_POSITIVE