Origin IGS: aagaacctcattctaaccttgctttcattcatttccagtatagcagactttactctaagaacaaagaaaagtcttgggtatttttgagaaatgcggagagtttttatgtcagaaaatctaacataaaaacaggagaaatttgcctaatcagtgtttttttgctataatgctagaatgctaaaaaggaggaagaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttcttcctcctttttagcattctagcattatagcaaaaaaacactgattaggcaaatttctcctgtttttatgttagattttctgacataaaaactctccgcatttctcaaaaatacccaagacttttctttgttcttagagtaaagtctgctatactggaaatgaatgaaagcaaggttagaatgaggttctt Mask Tandem Repeat Region ================================================ aagaacctcattctaaccttgctttcattcatttccagtatagcagactttactctaagaacaaagaaaagtcttgggtatttttgagaaatgcggagagtttttatgtcagaaaatctaacataaaaacaggagaaatttgcctaatcagtgtttttttgctataatgctagaatgctaaaaaggaggaagaaa Find is-nt database================================================ Query_seq: SSA_1358:SSA_1359|SSA_1358:SSA_1359:hypothetical protein:Arginine/histidine ABC transporter, permease component, putative:<-->:1374127..1374321 195 aagaacctcattctaaccttgctttcattcatttccagtatagcagactttactctaagaacaaagaaaagtcttgggtatttttgagaaatgcggagagtttttatgtcagaaaatctaacataaaaacaggagaaatttgcctaatcagtgtttttttgctataatgctagaatgctaaaaaggaggaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1358:SSA_1359|SSA_1358:SSA_1359:hypothetical protein:Arginine/histidine ABC transporter, permease component, putative:<-->:1374127..1374321 195 aagaacctcattctaaccttgctttcattcatttccagtatagcagactttactctaagaacaaagaaaagtcttgggtatttttgagaaatgcggagagtttttatgtcagaaaatctaacataaaaacaggagaaatttgcctaatcagtgtttttttgctataatgctagaatgctaaaaaggaggaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1358:SSA_1359|SSA_1358:SSA_1359:hypothetical protein:Arginine/histidine ABC transporter, permease component, putative:<-->:1374127..1374321 195 aagaacctcattctaaccttgctttcattcatttccagtatagcagactttactctaagaacaaagaaaagtcttgggtatttttgagaaatgcggagagtttttatgtcagaaaatctaacataaaaacaggagaaatttgcctaatcagtgtttttttgctataatgctagaatgctaaaaaggaggaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagaacctcattctaaccttgctttcattcatttccagtatagcagactttactctaagaacaaagaaaagtcttgggtatttttgagaaatgcggagagtttttatgtcagaaaatctaacataaaaacaggagaaatttgcctaatcagtgtttttttgctataatgctagaatgctaaaaaggaggaagaaa Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 27 End: 164 .......................... M H F Q Y S R L Y S K N K E K S W V F L R N A E S F Y V R K S N I K T G E I C L I S V F L L ............................... Protein_Len: 35 Strand: - Start: 3 End: 107 .. F R M R V K S E N M E L I A S K V R L V F F L R P Y K Q S I R L T K M ........................................................................................ aagaacctcattctaaccttgctttcattcatttccagtatagcagactttactctaagaacaaagaaaagtcttgggtatttttgagaaatgcggagagtttttatgtcagaaaatctaacataaaaacaggagaaatttgcctaatcagtgtttttttgctataatgctagaatgctaaaaaggaggaagaaa 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: 91 Start: 139 End: 168 ..........................................................................................................................................TTTGCCTAATCAGTGTTTTTTTGCTATAAT........................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagaacctcattctaaccttgctttcattcatttccagtatagcagactttactctaagaacaaagaaaagtcttgggtatttttgagaaatgcggagagtttttatgtcagaaaatctaacataaaaacaggagaaatttgcctaatcagtgtttttttgctataatgctagaatgctaaaaaggaggaagaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1358:SSA_1359|SSA_1358:SSA_1359:hypothetical protein:Arginine/histidine ABC transporter, permease component, putative:<-->:1374127..1374321 195 aagaacctcattctaaccttgctttcattcatttccagtatagcagactttactctaagaacaaagaaaagtcttgggtatttttgagaaatgcggagagtttttatgtcagaaaatctaacataaaaacaggagaaatttgcctaatcagtgtttttttgctataatgctagaatgctaaaaaggaggaagaaa Intra-Species Hit: Count: 1 Min: 1 Max: 195 Len: 195 Subject: NC_009009_SSA_1358_SSA_1359|hypothetical protein:Arginine/histidine ABC transporter, permease component, putative|NEGATIVE:POSITIVE|[1374127,1374321]|195 HSP 1 e-value: 3.0E-94 bit: 345.0 Len: 195 Query Start:1 Query End:195 Subject Strand: POSITIVE Subject Start: 1 Subject End: 195 aagaacctcattctaaccttgctttcattcatttccagtatagcagactttactctaagaacaaagaaaagtcttgggtatttttgagaaatgcggagagtttttatgtcagaaaatctaacataaaaacaggagaaatttgcctaatcagtgnnnnnnngctataatgctagaatgctaaaaaggaggaagaaa aagaacctcattctaaccttgctttcattcatttccagtatagcagactttactctaagaacaaagaaaagtcttgggtatttttgagaaatgcggagagtttttatgtcagaaaatctaacataaaaacaggagaaatttgcctaatcagtgtttttttgctataatgctagaatgctaaaaaggaggaagaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAACCUCAUUCUAACCUUGCUUUCAUUCAUUUCCAGUAUAGCAGACUUUACUCUAAGAACAAAGAAAAGUCUUGGGUAUUUUUGAGAAAUGCGGAGAGUUUUUAUGUCAGAAAAUCUAACAUAAAAACAGGAGAAAUUUGCCUAAUCAGUGUUUUUUUGCUAUAAUGCUAGAAUGCUAAAAAGGAGGAAGAAA .....((((.((((..(((.((((((...(((((((((.(((.((((((((..(((........))))))))))..).)))..))).))))))..))))))((((((((.((.....)).))))))))..)))))))............((((((((...((......)).))))))))......))))...... (-43.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUUCCUCCUUUUUAGCAUUCUAGCAUUAUAGCAAAAAAACACUGAUUAGGCAAAUUUCUCCUGUUUUUAUGUUAGAUUUUCUGACAUAAAAACUCUCCGCAUUUCUCAAAAAUACCCAAGACUUUUCUUUGUUCUUAGAGUAAAGUCUGCUAUACUGGAAAUGAAUGAAAGCAAGGUUAGAAUGAGGUUCUU .((((.(((.(((((...((((((((...((((((................((.((((.......(((((((((((((.....))))))))))))).......)))).))...........(((((((.(((((....))))).))))))))))))))))).))))...)))))..)))..)))).......... (-45.84) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 838 50 1 141 92 NC_009009:SSA_1358|5end_hypothetical_protein_1374036..1374266_NEGATIVE 309 60 11 77 26 NC_009009:SSA_1335|5end_Ankyrin_repeat_protein,_putative_1349663..1349893_NEGATIVE 294 119 86 192 152 NC_009009:SSA_0238|5end_hypothetical_protein_232481..232711_POSITIVE 267 51 15 175 147 NC_009009:SSA_2278|5end_Ukp_protein,_putative_2281669..2281899_NEGATIVE 267 179 131 171 115 NC_009009:SSA_0109|5end_50S_ribosomal_protein_L23,_putative_109439..109669_POSITIVE 262 116 74 141 91 NC_009009:SSA_1267|5end_crcB-like_protein_2,_putative_1291347..1291577_NEGATIVE 258 113 72 212 168 NC_009009:SSA_1696|5end_Tagatose_1,6-diphosphate_aldolase_2,_putative_1689187..1689417_NEGATIVE 245 180 131 116 53 NC_009009:SSA_0574|5end_YdjX_protein,_putative_569427..569657_NEGATIVE 244 60 16 145 98 NC_009009:SSA_1279|5end_Oxidoreductase,_putative_1300832..1301062_NEGATIVE 243 45 8 38 6 NC_009009:SSA_1600|5end_hypothetical_protein_1606595..1606825_NEGATIVE 243 45 8 217 185 NC_009009:SSA_1599|5end_hypothetical_protein_1606416..1606646_NEGATIVE 241 60 11 227 185 NC_009009:SSA_0009|5end_Ribosome-associated_heat_shock_protein_(S4),_putative_9165..9395_POSITIVE 240 190 141 138 85 NC_009009:SSA_2277|5end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2280407..2280637_NEGATIVE 239 178 131 138 81 NC_009009:SSA_0629|5end_hypothetical_protein_618967..619197_POSITIVE 239 180 134 53 1 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 236 178 131 224 169 NC_009009:SSA_2256|5end_hypothetical_protein_2250604..2250834_POSITIVE 235 96 52 50 10 NC_009009:SSA_2214|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_2,_putative_2215835..2216065_NEGATIVE 235 50 7 164 117 NC_009009:SSA_0034|5end_hypothetical_protein_39547..39777_POSITIVE 233 110 70 216 177 NC_009009:SSA_1944|5end_Oligopeptide_transport_ATP-binding_protein,_putative_1936611..1936841_NEGATIVE 233 60 16 107 65 NC_009009:SSA_1671|5end_hypothetical_protein_1669304..1669534_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 44 2 125 80 NC_009009:SSA_1821|3end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810047..1810197_NEGATIVE 262 116 74 141 91 NC_009009:SSA_1268|3end_Chorismate_mutase/prephenate_dehydratase,_putative_1291347..1291497_NEGATIVE 256 59 11 83 25 NC_009009:SSA_0963|3end_Peptidoglycan_N-acetylglucosamine_deacetylase_A,_putative_972890..973040_POSITIVE 253 49 7 147 100 NC_009009:SSA_1336|3end_Conserved_ankyrin_repeat_protein,_putative_1349581..1349731_NEGATIVE 244 73 35 124 76 NC_009009:SSA_0639|3end_hypothetical_protein_627733..627883_NEGATIVE 243 78 31 143 107 NC_009009:SSA_2375|3end_Tryptophanyl-tRNA_synthetase,_putative_2377221..2377371_NEGATIVE 243 77 36 77 19 NC_009009:SSA_2191|3end_Conserved_uncharacterized_protein_2193082..2193232_POSITIVE 243 45 8 41 9 NC_009009:SSA_1601|3end_VacB-like_protein,_putative_1606592..1606742_NEGATIVE 243 45 8 136 104 NC_009009:SSA_1600|3end_hypothetical_protein_1606497..1606647_NEGATIVE 241 60 11 136 94 NC_009009:SSA_0008|3end_Transcription-repair_coupling_factor,_putative_9154..9304_POSITIVE 240 190 141 135 82 NC_009009:SSA_2278|3end_Ukp_protein,_putative_2280410..2280560_NEGATIVE 239 178 131 151 94 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 239 180 134 60 8 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 235 96 52 53 13 NC_009009:SSA_2215|3end_Oligosaccharide_repeat_unit_polymerase_Wzy,_putative_2215832..2215982_NEGATIVE 235 50 7 137 90 NC_009009:SSA_0033|3end_Phosphoribosylglycinamide_(GAR)_formyltransferase,_putative_39600..39750_POSITIVE 232 110 64 86 43 NC_009009:SSA_1932|3end_Biotin_carboxylase,_putative_1919507..1919657_NEGATIVE 231 47 6 58 9 NC_009009:SSA_2069|3end_Prolyl-tRNA_synthetase,_putative_2071402..2071552_NEGATIVE 231 59 13 136 91 NC_009009:SSA_0415|3end_Permease,_putative_411730..411880_POSITIVE 224 119 72 106 56 NC_009009:SSA_1874|3end_YorfE_protein,_putative_1870590..1870740_POSITIVE 223 63 23 100 64 NC_009009:SSA_0203|3end_hypothetical_protein_202124..202274_POSITIVE