Origin IGS: agcataagcaaaactattagctgagaaagaagggaaaagccatgcctttattgtttgcttttcgctatcgtagaggactctatttgaccatagtcatcttggcatctgtctttttagccttaagccttattttcggaactttagcttactttatactattttctttcgaaaaggccatgcctggagcaggaataagctcgttcagtttgccttttatacttgcttttttcatgactgttgtagtcgaaatctttgcaatagtccatgcgggtcgcaagctgagcaaaaagtgctttgttcttgcaggaacagaatgggggcttgacc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggtcaagcccccattctgttcctgcaagaacaaagcactttttgctcagcttgcgacccgcatggactattgcaaagatttcgactacaacagtcatgaaaaaagcaagtataaaaggcaaactgaacgagcttattcctgctccaggcatggccttttcgaaagaaaatagtataaagtaagctaaagttccgaaaataaggcttaaggctaaaaagacagatgccaagatgactatggtcaaatagagtcctctacgatagcgaaaagcaaacaataaaggcatggcttttcccttctttctcagctaatagttttgcttatgct Mask Tandem Repeat Region ================================================ agcataagcaaaactattagctgagaaagaagggaaaagccatgcctttattgtttgcttttcgctatcgtagaggactctatttgaccatagtcatcttggcatctgtctttttagccttaagccttattttcggaactttagcttactttatactattttctttcgaaaaggccatgcctggagcaggaataagctcgttcagtttgccttttatacttgcttttttcatgactgttgtagtcgaaatctttgcaatagtccatgcgggtcgcaagctgagcaaaaagtgctttgttcttgcaggaacagaatgggggcttgacc Find is-nt database================================================ Query_seq: SSA_0584:SSA_0585|SSA_0584:SSA_0585:hypothetical protein:hypothetical protein:->->:576750..577076 327 agcataagcaaaactattagctgagaaagaagggaaaagccatgcctttattgtttgcttttcgctatcgtagaggactctatttgaccatagtcatcttggcatctgtctttttagccttaagccttattttcggaactttagcttactttatactattttctttcgaaaaggccatgcctggagcaggaataagctcgttcagtttgccttttatacttgcttttttcatgactgttgtagtcgaaatctttgcaatagtccatgcgggtcgcaagctgagcaaaaagtgctttgttcttgcaggaacagaatgggggcttgacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0584:SSA_0585|SSA_0584:SSA_0585:hypothetical protein:hypothetical protein:->->:576750..577076 327 agcataagcaaaactattagctgagaaagaagggaaaagccatgcctttattgtttgcttttcgctatcgtagaggactctatttgaccatagtcatcttggcatctgtctttttagccttaagccttattttcggaactttagcttactttatactattttctttcgaaaaggccatgcctggagcaggaataagctcgttcagtttgccttttatacttgcttttttcatgactgttgtagtcgaaatctttgcaatagtccatgcgggtcgcaagctgagcaaaaagtgctttgttcttgcaggaacagaatgggggcttgacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0584:SSA_0585|SSA_0584:SSA_0585:hypothetical protein:hypothetical protein:->->:576750..577076 327 agcataagcaaaactattagctgagaaagaagggaaaagccatgcctttattgtttgcttttcgctatcgtagaggactctatttgaccatagtcatcttggcatctgtctttttagccttaagccttattttcggaactttagcttactttatactattttctttcgaaaaggccatgcctggagcaggaataagctcgttcagtttgccttttatacttgcttttttcatgactgttgtagtcgaaatctttgcaatagtccatgcgggtcgcaagctgagcaaaaagtgctttgttcttgcaggaacagaatgggggcttgacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcataagcaaaactattagctgagaaagaagggaaaagccatgcctttattgtttgcttttcgctatcgtagaggactctatttgaccatagtcatcttggcatctgtctttttagccttaagccttattttcggaactttagcttactttatactattttctttcgaaaaggccatgcctggagcaggaataagctcgttcagtttgccttttatacttgcttttttcatgactgttgtagtcgaaatctttgcaatagtccatgcgggtcgcaagctgagcaaaaagtgctttgttcttgcaggaacagaatgggggcttgacc Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 104 End: 322 ....................................................................................................... M C L F S L K P Y F R N F S L L Y T I F F R K G H A W S R N K L V Q F A F Y T C F F H D C C S R N L C N S P C G S Q A E ..... Protein_Len: 60 Strand: + Start: 21 End: 326 .................... M R K K G K A M P L L F A F R Y R R G L Y L T I V I L A S V F L A L S L I F G T L A Y F I L F S F E K A M P G A G I S S . Protein_Len: 36 Strand: - Start: 159 End: 266 .............................................................................................................................................................. K R E F L G H R S C S Y A R E T Q R K Y K S K E H S N Y D F D K C Y D M ............................................................. Protein_Len: 46 Strand: - Start: 149 End: 286 .................................................................................................................................................... K I S N E K S F A M G P A P I L E N L K G K I S A K K M V T T T S I K A I T W A P R L S L M ......................................... agcataagcaaaactattagctgagaaagaagggaaaagccatgcctttattgtttgcttttcgctatcgtagaggactctatttgaccatagtcatcttggcatctgtctttttagccttaagccttattttcggaactttagcttactttatactattttctttcgaaaaggccatgcctggagcaggaataagctcgttcagtttgccttttatacttgcttttttcatgactgttgtagtcgaaatctttgcaatagtccatgcgggtcgcaagctgagcaaaaagtgctttgttcttgcaggaacagaatgggggcttgacc 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================================================ agcataagcaaaactattagctgagaaagaagggaaaagccatgcctttattgtttgcttttcgctatcgtagaggactctatttgaccatagtcatcttggcatctgtctttttagccttaagccttattttcggaactttagcttactttatactattttctttcgaaaaggccatgcctggagcaggaataagctcgttcagtttgccttttatacttgcttttttcatgactgttgtagtcgaaatctttgcaatagtccatgcgggtcgcaagctgagcaaaaagtgctttgttcttgcaggaacagaatgggggcttgacc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0584:SSA_0585|SSA_0584:SSA_0585:hypothetical protein:hypothetical protein:->->:576750..577076 327 agcataagcaaaactattagctgagaaagaagggaaaagccatgcctttattgtttgcttttcgctatcgtagaggactctatttgaccatagtcatcttggcatctgtctttttagccttaagccttattttcggaactttagcttactttatactattttctttcgaaaaggccatgcctggagcaggaataagctcgttcagtttgccttttatacttgcttttttcatgactgttgtagtcgaaatctttgcaatagtccatgcgggtcgcaagctgagcaaaaagtgctttgttcttgcaggaacagaatgggggcttgacc Intra-Species Hit: Count: 1 Min: 1 Max: 327 Len: 327 Subject: NC_009009_SSA_0584_SSA_0585|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[576750,577076]|327 HSP 1 e-value: 0.0 bit: 648.0 Len: 327 Query Start:1 Query End:327 Subject Strand: POSITIVE Subject Start: 1 Subject End: 327 agcataagcaaaactattagctgagaaagaagggaaaagccatgcctttattgtttgcttttcgctatcgtagaggactctatttgaccatagtcatcttggcatctgtctttttagccttaagccttattttcggaactttagcttactttatactattttctttcgaaaaggccatgcctggagcaggaataagctcgttcagtttgccttttatacttgcttttttcatgactgttgtagtcgaaatctttgcaatagtccatgcgggtcgcaagctgagcaaaaagtgctttgttcttgcaggaacagaatgggggcttgacc agcataagcaaaactattagctgagaaagaagggaaaagccatgcctttattgtttgcttttcgctatcgtagaggactctatttgaccatagtcatcttggcatctgtctttttagccttaagccttattttcggaactttagcttactttatactattttctttcgaaaaggccatgcctggagcaggaataagctcgttcagtttgccttttatacttgcttttttcatgactgttgtagtcgaaatctttgcaatagtccatgcgggtcgcaagctgagcaaaaagtgctttgttcttgcaggaacagaatgggggcttgacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCAUAAGCAAAACUAUUAGCUGAGAAAGAAGGGAAAAGCCAUGCCUUUAUUGUUUGCUUUUCGCUAUCGUAGAGGACUCUAUUUGACCAUAGUCAUCUUGGCAUCUGUCUUUUUAGCCUUAAGCCUUAUUUUCGGAACUUUAGCUUACUUUAUACUAUUUUCUUUCGAAAAGGCCAUGCCUGGAGCAGGAAUAAGCUCGUUCAGUUUGCCUUUUAUACUUGCUUUUUUCAUGACUGUUGUAGUCGAAAUCUUUGCAAUAGUCCAUGCGGGUCGCAAGCUGAGCAAAAAGUGCUUUGUUCUUGCAGGAACAGAAUGGGGGCUUGACC .((....))..........((((((((.((..(((...((((..(((((((.((..((.....)).)).)))))))........((((....))))...)))).))).)))))))))).(((((((...(((((((((...(((...........))).....)))))))))..((((..(((..((((((((((((.((((((((((((.......((((((.........(((((((((((.........)))))))))))...)))))).))))))))))).....).)).)))))))))).....))).)))).))))))).. (-91.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUCAAGCCCCCAUUCUGUUCCUGCAAGAACAAAGCACUUUUUGCUCAGCUUGCGACCCGCAUGGACUAUUGCAAAGAUUUCGACUACAACAGUCAUGAAAAAAGCAAGUAUAAAAGGCAAACUGAACGAGCUUAUUCCUGCUCCAGGCAUGGCCUUUUCGAAAGAAAAUAGUAUAAAGUAAGCUAAAGUUCCGAAAAUAAGGCUUAAGGCUAAAAAGACAGAUGCCAAGAUGACUAUGGUCAAAUAGAGUCCUCUACGAUAGCGAAAAGCAAACAAUAAAGGCAUGGCUUUUCCCUUCUUUCUCAGCUAAUAGUUUUGCUUAUGCU (((((.(((....(((.(((((((((((((........)))))))...((((((......((((.(((.(((....(....).....))).)))))))......)))))).....)))..))).))).((((........))))..))).))))).((((....))))..(((((((.((((((((.((((..((((..((((...((((((..........(((((.(((.((((.((......)).)))).)))......((.....))..........)))))))))))..)))).))))..))))..))).)))))))))))) (-80.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 215 171 64 14 NC_009009:SSA_1447|5end_ATP_phosphoribosyltransferase,_putative_1449831..1450061_NEGATIVE 348 110 62 216 176 NC_009009:SSA_0497|5end_Nickel_ABC_transporter,_putative_496922..497152_POSITIVE 339 214 171 135 95 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 335 213 173 191 158 NC_009009:SSA_0770|5end_Ribonucleoside-diphosphate_reductase,_putative_751411..751641_NEGATIVE 334 147 101 138 93 NC_009009:SSA_0433|5end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435654..435884_NEGATIVE 330 216 174 189 150 NC_009009:SSA_1594|5end_Metalloendopeptidase,_putative_1600526..1600756_NEGATIVE 326 279 232 182 131 NC_009009:SSA_1588|5end_Conserved_ABC-type_antimicrobial_permease-like_protein,_putative_1591905..1592135_NEGATIVE 325 208 162 48 9 NC_009009:SSA_1614|5end_Acetyltransferase,_GNAT_family,_putative_1618045..1618275_NEGATIVE 323 309 262 51 3 NC_009009:SSA_0209|5end_Glutamyl_aminopeptidase,_putative_207636..207866_NEGATIVE 318 210 162 154 110 NC_009009:SSA_1872|5end_Cell_division_protein,_putative_1869186..1869416_NEGATIVE 314 49 1 181 127 NC_009009:SSA_0363|5end_D-alanine/glycine/Na_permease,_putative_353858..354088_POSITIVE 314 300 251 170 126 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 311 212 172 193 157 NC_009009:SSA_2300|5end_hypothetical_protein_2302508..2302738_NEGATIVE 311 304 261 57 10 NC_009009:SSA_0355|5end_DNA_mismatch_repair_protein,_putative_346847..347077_POSITIVE 309 128 83 63 10 NC_009009:SSA_2357|5end_50S_ribosomal_protein_L9,_putative_2358437..2358667_NEGATIVE 309 310 266 43 3 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 309 300 251 193 142 NC_009009:SSA_1553|5end_Permease,_putative_1555047..1555277_POSITIVE 309 300 251 59 8 NC_009009:SSA_1552|5end_hypothetical_protein_1554913..1555143_POSITIVE 309 308 262 56 14 NC_009009:SSA_1182|5end_Gid-like_protein,_putative_1210866..1211096_NEGATIVE 307 275 235 69 24 NC_009009:SSA_2086|5end_hypothetical_protein_2091428..2091658_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 215 171 67 17 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 334 147 101 123 78 NC_009009:SSA_0434|3end_Glutamate_formiminotransferase,_putative_435669..435819_NEGATIVE 321 315 274 44 2 NC_009009:SSA_0103|3end_Integral_membrane_protein,_putative_104630..104780_NEGATIVE 318 210 162 146 102 NC_009009:SSA_1873|3end_S-adenosyl-methyltransferase_mraW,_putative_1869194..1869344_NEGATIVE 314 138 91 137 92 NC_009009:SSA_2023|3end_Fructan_beta-fructosidase_precursor,_putative_2024609..2024759_NEGATIVE 309 128 83 66 13 NC_009009:SSA_2358|3end_hypothetical_protein_2358434..2358584_NEGATIVE 306 317 271 143 101 NC_009009:SSA_2082|3end_Carbohydrate_kinase,_FGGY_family,_putative_2085351..2085501_NEGATIVE 303 280 240 130 95 NC_009009:SSA_2136|3end_50S_ribosomal_protein_L34,_putative_2137507..2137657_NEGATIVE 298 211 174 42 6 NC_009009:SSA_1467|3end_Chorismate_synthase,_putative_1473127..1473277_NEGATIVE 296 307 261 139 102 NC_009009:SSA_1446|3end_Histidinol_dehydrogenase,_putative_1447898..1448048_NEGATIVE 296 210 161 76 22 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 295 300 252 147 90 NC_009009:SSA_0226|3end_60_kDa_chaperonin_220649..220799_POSITIVE 294 215 172 151 99 NC_009009:SSA_2008|3end_Molecular_chaperone_GrpE_(HSP-70_cofactor),_putative_2009526..2009676_NEGATIVE 292 229 182 111 67 NC_009009:SSA_0966|3end_Uridine_kinase,_putative_975790..975940_POSITIVE 290 209 162 150 99 NC_009009:SSA_0351|3end_Signal_peptidase_I,_putative_344278..344428_NEGATIVE 289 306 267 90 33 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 288 257 220 139 96 NC_009009:SSA_2309|3end_Fimbrial_assembly_protein,_putative_2310474..2310624_NEGATIVE 286 205 165 71 26 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 284 240 198 149 107 NC_009009:SSA_0204|3end_Nisin_biosynthesis_two-component_response_transcriptional_regulator_nisR,_putative_202835..202985_POSITIVE 283 210 161 90 48 NC_009009:SSA_1848|3end_Methionyl-tRNA_formyltransferase,_putative_1842243..1842393_NEGATIVE