Origin IGS: tgtctttctaaaactatagtcgtctatcccattataccacaagcctgctgcacttctcagaaaaagcaaaagccaccactggggtgactttcaggagattattatgaaaaagtttaggatttttaaacaaagttaggaggtctttgtttatgccgttagtataaaatatatatcttaaatgaatcttaagatgaaattttcttacaaaaaagcacaagaagcaatttccttgtgctgactttt .........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 aaaagtcagcacaaggaaattgcttcttgtgcttttttgtaagaaaatttcatcttaagattcatttaagatatatattttatactaacggcataaacaaagacctcctaactttgtttaaaaatcctaaactttttcataataatctcctgaaagtcaccccagtggtggcttttgctttttctgagaagtgcagcaggcttgtggtataatgggatagacgactatagttttagaaagaca Mask Tandem Repeat Region ================================================ tgtctttctaaaactatagtcgtctatcccattataccacaagcctgctgcacttctcagaaaaagcaaaagccaccactggggtgactttcaggagattattatgaaaaagtttaggatttttaaacaaagttaggaggtctttgtttatgccgttagtataaaatatatatcttaaatgaatcttaagatgaaattttcttacaaaaaagcacaagaagcaatttccttgtgctgactttt Find is-nt database================================================ Query_seq: SSA_2184:SSA_2185|SSA_2184:SSA_2185:hypothetical protein:Adenylosuccinate synthetase, putative:<-<-:2183845..2184087 243 tgtctttctaaaactatagtcgtctatcccattataccacaagcctgctgcacttctcagaaaaagcaaaagccaccactggggtgactttcaggagattattatgaaaaagtttaggatttttaaacaaagttaggaggtctttgtttatgccgttagtataaaatatatatcttaaatgaatcttaagatgaaattttcttacaaaaaagcacaagaagcaatttccttgtgctgactttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2184:SSA_2185|SSA_2184:SSA_2185:hypothetical protein:Adenylosuccinate synthetase, putative:<-<-:2183845..2184087 243 tgtctttctaaaactatagtcgtctatcccattataccacaagcctgctgcacttctcagaaaaagcaaaagccaccactggggtgactttcaggagattattatgaaaaagtttaggatttttaaacaaagttaggaggtctttgtttatgccgttagtataaaatatatatcttaaatgaatcttaagatgaaattttcttacaaaaaagcacaagaagcaatttccttgtgctgactttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2184:SSA_2185|SSA_2184:SSA_2185:hypothetical protein:Adenylosuccinate synthetase, putative:<-<-:2183845..2184087 243 tgtctttctaaaactatagtcgtctatcccattataccacaagcctgctgcacttctcagaaaaagcaaaagccaccactggggtgactttcaggagattattatgaaaaagtttaggatttttaaacaaagttaggaggtctttgtttatgccgttagtataaaatatatatcttaaatgaatcttaagatgaaattttcttacaaaaaagcacaagaagcaatttccttgtgctgactttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtctttctaaaactatagtcgtctatcccattataccacaagcctgctgcacttctcagaaaaagcaaaagccaccactggggtgactttcaggagattattatgaaaaagtttaggatttttaaacaaagttaggaggtctttgtttatgccgttagtataaaatatatatcttaaatgaatcttaagatgaaattttcttacaaaaaagcacaagaagcaatttccttgtgctgactttt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 26 End: 133 ......................... M P L Y H K P A A L L R K S K S H H W G D F Q E I I M K K F R I F K Q S .............................................................................................................. Protein_Len: 60 Strand: - Start: 35 End: 217 .................................. V L R S C K E S F A F A V V P T V K L L N N H F L K P N K F L T L L D K N I G N T Y F I Y R L H I K L H F K R V F F C M .......................... tgtctttctaaaactatagtcgtctatcccattataccacaagcctgctgcacttctcagaaaaagcaaaagccaccactggggtgactttcaggagattattatgaaaaagtttaggatttttaaacaaagttaggaggtctttgtttatgccgttagtataaaatatatatcttaaatgaatcttaagatgaaattttcttacaaaaaagcacaagaagcaatttccttgtgctgactttt 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================================================ tgtctttctaaaactatagtcgtctatcccattataccacaagcctgctgcacttctcagaaaaagcaaaagccaccactggggtgactttcaggagattattatgaaaaagtttaggatttttaaacaaagttaggaggtctttgtttatgccgttagtataaaatatatatcttaaatgaatcttaagatgaaattttcttacaaaaaagcacaagaagcaatttccttgtgctgactttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 63 HP_score: -2.4 Tail_Score: -4.83615 Start: 66 End: 94 Full_Region: tttcataataatctc ctgaaagtcacc ccagt ggtggcttttgc tttttctgagaagtg .................................................................ctgaaagtcaccccagtggtggcttttgc..................................................................................................................................................... TransTerm Strand: - Conf: 61 HP_score: -5.9 Tail_Score: -3.49687 Start: 67 End: 93 Full_Region: ttcataataatctcc tgaaagtcacc ccagt ggtggcttttg ctttttctgagaagt ..................................................................tgaaagtcaccccagtggtggcttttg...................................................................................................................................................... TransTerm Strand: - Conf: 78 HP_score: -5.8 Tail_Score: -4.82678 Start: 72 End: 88 Full_Region: aataatctcctgaaa gtcacc ccagt ggtggc ttttgctttttctga .......................................................................gtcaccccagtggtggc........................................................................................................................................................... TransTerm Strand: - Conf: 44 HP_score: -2.5 Tail_Score: -3.31428 Start: 173 End: 191 Full_Region: tgtaagaaaatttca tcttaag attca tttaaga tatatattttatact ............................................................................................................................................................................tcttaagattcatttaaga.................................................... Find igs database================================================ Query_seq: SSA_2184:SSA_2185|SSA_2184:SSA_2185:hypothetical protein:Adenylosuccinate synthetase, putative:<-<-:2183845..2184087 243 tgtctttctaaaactatagtcgtctatcccattataccacaagcctgctgcacttctcagaaaaagcaaaagccaccactggggtgactttcaggagattattatgaaaaagtttaggatttttaaacaaagttaggaggtctttgtttatgccgttagtataaaatatatatcttaaatgaatcttaagatgaaattttcttacaaaaaagcacaagaagcaatttccttgtgctgactttt Intra-Species Hit: Count: 1 Min: 1 Max: 243 Len: 243 Subject: NC_009009_SSA_2184_SSA_2185|hypothetical protein:Adenylosuccinate synthetase, putative|NEGATIVE:NEGATIVE|[2183845,2184087]|243 HSP 1 e-value: 1.0E-135 bit: 482.0 Len: 243 Query Start:1 Query End:243 Subject Strand: POSITIVE Subject Start: 1 Subject End: 243 tgtctttctaaaactatagtcgtctatcccattataccacaagcctgctgcacttctcagaaaaagcaaaagccaccactggggtgactttcaggagattattatgaaaaagtttaggatttttaaacaaagttaggaggtctttgtttatgccgttagtataaaatatatatcttaaatgaatcttaagatgaaattttcttacaaaaaagcacaagaagcaatttccttgtgctgactttt tgtctttctaaaactatagtcgtctatcccattataccacaagcctgctgcacttctcagaaaaagcaaaagccaccactggggtgactttcaggagattattatgaaaaagtttaggatttttaaacaaagttaggaggtctttgtttatgccgttagtataaaatatatatcttaaatgaatcttaagatgaaattttcttacaaaaaagcacaagaagcaatttccttgtgctgactttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUCUUUCUAAAACUAUAGUCGUCUAUCCCAUUAUACCACAAGCCUGCUGCACUUCUCAGAAAAAGCAAAAGCCACCACUGGGGUGACUUUCAGGAGAUUAUUAUGAAAAAGUUUAGGAUUUUUAAACAAAGUUAGGAGGUCUUUGUUUAUGCCGUUAGUAUAAAAUAUAUAUCUUAAAUGAAUCUUAAGAUGAAAUUUUCUUACAAAAAAGCACAAGAAGCAAUUUCCUUGUGCUGACUUUU .(((..(((.(((((....((((..(((((............((...(((.......))).....)).((((.((((.....)))).))))..)).)))....))))...))))).)))....(((((((((.........)))))))))........(((..(((....((((((((.......))))))))....)))..))).....((((((((..........))))))))))).... (-45.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAGUCAGCACAAGGAAAUUGCUUCUUGUGCUUUUUUGUAAGAAAAUUUCAUCUUAAGAUUCAUUUAAGAUAUAUAUUUUAUACUAACGGCAUAAACAAAGACCUCCUAACUUUGUUUAAAAAUCCUAAACUUUUUCAUAAUAAUCUCCUGAAAGUCACCCCAGUGGUGGCUUUUGCUUUUUCUGAGAAGUGCAGCAGGCUUGUGGUAUAAUGGGAUAGACGACUAUAGUUUUAGAAAGACA ....(((.(((((((((......)))))))))...................((((((((.....)))))))).....(((((.((((......(((((((((.........)))))))))...((((((.......((((((...(((.(((.((((((((.....))))))))..((((((....)))))).))).))).)))))).....)))))).........))))..))))).))). (-53.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 993 90 41 181 132 NC_009009:SSA_2184|5end_hypothetical_protein_2183754..2183984_NEGATIVE 531 120 75 209 158 NC_009009:SSA_0063|5end_Holliday_junction_DNA_helicase_ruvB,_putative_65335..65565_POSITIVE 400 84 41 230 180 NC_009009:SSA_0065|5end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67175..67405_POSITIVE 376 67 22 50 4 NC_009009:SSA_0677|5end_rRNA_methylase,_putative_659466..659696_POSITIVE 346 89 42 113 53 NC_009009:SSA_0449|5end_Aminopeptidase_P;_XAA-pro_aminopeptidase,_putative_449464..449694_POSITIVE 339 88 41 183 122 NC_009009:SSA_1363|5end_FmtA-like_protein,_putative_1380417..1380647_NEGATIVE 337 73 36 53 12 NC_009009:SSA_1828|5end_Glycerol_uptake_facilitator_protein,_putative_1818007..1818237_POSITIVE 328 68 30 74 38 NC_009009:SSA_0565|5end_hypothetical_protein_557230..557460_POSITIVE 323 80 34 223 167 NC_009009:SSA_2384|5end_Acetyltransferase,_GNAT_family,_putative_1465896..1466126_NEGATIVE 305 51 19 178 146 NC_009009:SSA_1462|5end_Prephenate_dehydratase,_putative_1469767..1469997_NEGATIVE 305 95 57 231 195 NC_009009:SSA_0819|5end_hypothetical_protein_800418..800648_POSITIVE 302 90 44 68 9 NC_009009:SSA_2310|5end_hypothetical_protein_2313418..2313648_NEGATIVE 298 87 45 231 181 NC_009009:SSA_0581|5end_Conserved_uncharacterized_protein_573329..573559_POSITIVE 289 80 36 74 24 NC_009009:SSA_1408|5end_hypothetical_protein_1421005..1421235_NEGATIVE 288 108 66 126 78 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 286 88 42 68 14 NC_009009:SSA_0992|5end_hypothetical_protein_993486..993716_POSITIVE 284 87 41 159 119 NC_009009:SSA_1668|5end_NrdI_protein,_putative_1668091..1668321_NEGATIVE 284 60 19 225 190 NC_009009:SSA_1438|5end_Acetyltransferase,_putative_1443612..1443842_NEGATIVE 281 57 17 105 52 NC_009009:SSA_0529|5end_Ethanolamine_utilization_protein,_putative_525945..526175_POSITIVE 281 77 38 63 15 NC_009009:SSA_0421|5end_Phosphoglycerate_mutase_family_protein,_putative_419564..419794_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 435 180 131 54 5 NC_009009:SSA_2164|3end_Glutamine_amidotransferase,_putative_2160866..2161016_NEGATIVE 380 59 16 51 4 NC_009009:SSA_0676|3end_Farnesyl_diphosphate_synthase,_putative_659553..659703_POSITIVE 351 68 21 134 73 NC_009009:SSA_0325|3end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_319437..319587_POSITIVE 339 88 41 118 57 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 302 98 52 139 96 NC_009009:SSA_2260|3end_DNA_mismatch_repair_protein_hexA,_putative_2255601..2255751_NEGATIVE 300 79 32 137 91 NC_009009:SSA_1959|3end_Undecaprenyl-diphosphatase,_putative_1955589..1955739_NEGATIVE 290 92 52 76 21 NC_009009:SSA_1379|3end_hypothetical_protein_1398178..1398328_NEGATIVE 288 108 66 100 52 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 281 57 17 90 37 NC_009009:SSA_0528|3end_Conserved_uncharacterized_protein_526010..526160_POSITIVE 281 77 38 51 3 NC_009009:SSA_0420|3end_Hydrolase,_HAD_superfamily,_putative_419632..419782_POSITIVE 277 98 58 52 4 NC_009009:SSA_0816|3end_Copper_transport_operon_or_penicillinase_transcription_repressor,_putative_797902..798052_POSITIVE 274 57 16 51 9 NC_009009:SSA_1312|3end_RADC-like_protein,_putative_1328737..1328887_NEGATIVE 274 59 11 127 88 NC_009009:SSA_0511|3end_Propanediol_utilization_kinase,_putative_510556..510706_POSITIVE 268 90 42 58 9 NC_009009:SSA_1453|3end_hypothetical_protein_1459897..1460047_NEGATIVE 268 95 66 76 31 NC_009009:SSA_0385|3end_ABC_transporter,_glycine-betaine/proline_permease_protein,_putative_378526..378676_NEGATIVE 263 90 41 143 83 NC_009009:SSA_1584|3end_Ring-cleavage_extradiol_dioxygenase,_putative_1586062..1586212_NEGATIVE 262 90 43 92 43 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 262 82 41 109 57 NC_009009:SSA_1369|3end_FmtA-like_protein,_putative_1384142..1384292_NEGATIVE 262 85 41 68 21 NC_009009:SSA_1085|3end_Dihydrodipicolinate_reductase,_putative_1103411..1103561_POSITIVE 262 86 42 133 73 NC_009009:SSA_0440|3end_30S_ribosomal_protein_S18,_putative_441465..441615_POSITIVE