Origin IGS: ttattttttacataaggagcactcaaaaaagacacagatagccctaacattctaattcaaatactgatccagattgttagagcttgtcttgacattgtagcagttttcttatttgatatgaaagaaaccgccattttttcatttttaatctttacaaaaataggaaggctctcgccttcctaaagccgttataacaaaa .........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 ttttgttataacggctttaggaaggcgagagccttcctatttttgtaaagattaaaaatgaaaaaatggcggtttctttcatatcaaataagaaaactgctacaatgtcaagacaagctctaacaatctggatcagtatttgaattagaatgttagggctatctgtgtcttttttgagtgctccttatgtaaaaaataa Mask Tandem Repeat Region ================================================ ttattttttacataaggagcactcaaaaaagacacagatagccctaacattctaattcaaatactgatccagattgttagagcttgtcttgacattgtagcagttttcttatttgatatgaaagaaaccgccattttttcatttttaatctttacaaaaataggaaggctctcgccttcctaaagccgttataacaaaa Find is-nt database================================================ Query_seq: SSA_2282:SSA_2283|SSA_2282:SSA_2283:Phage infection protein, putative:Conserved uncharacterized protein:<-<-:2285428..2285626 199 ttattttttacataaggagcactcaaaaaagacacagatagccctaacattctaattcaaatactgatccagattgttagagcttgtcttgacattgtagcagttttcttatttgatatgaaagaaaccgccattttttcatttttaatctttacaaaaataggaaggctctcgccttcctaaagccgttataacaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2282:SSA_2283|SSA_2282:SSA_2283:Phage infection protein, putative:Conserved uncharacterized protein:<-<-:2285428..2285626 199 ttattttttacataaggagcactcaaaaaagacacagatagccctaacattctaattcaaatactgatccagattgttagagcttgtcttgacattgtagcagttttcttatttgatatgaaagaaaccgccattttttcatttttaatctttacaaaaataggaaggctctcgccttcctaaagccgttataacaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2282:SSA_2283|SSA_2282:SSA_2283:Phage infection protein, putative:Conserved uncharacterized protein:<-<-:2285428..2285626 199 ttattttttacataaggagcactcaaaaaagacacagatagccctaacattctaattcaaatactgatccagattgttagagcttgtcttgacattgtagcagttttcttatttgatatgaaagaaaccgccattttttcatttttaatctttacaaaaataggaaggctctcgccttcctaaagccgttataacaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttattttttacataaggagcactcaaaaaagacacagatagccctaacattctaattcaaatactgatccagattgttagagcttgtcttgacattgtagcagttttcttatttgatatgaaagaaaccgccattttttcatttttaatctttacaaaaataggaaggctctcgccttcctaaagccgttataacaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 49 End: 180 ................................................ M L I Q I L I Q I V R A C L D I V A V F L F D M K E T A I F S F L I F T K I G R L S P S ................... Protein_Len: 34 Strand: - Start: 60 End: 161 ........................................................... I S I W I T L A Q R S M T A T K K N S I F S V A M K E N K I K V F M ...................................... ttattttttacataaggagcactcaaaaaagacacagatagccctaacattctaattcaaatactgatccagattgttagagcttgtcttgacattgtagcagttttcttatttgatatgaaagaaaccgccattttttcatttttaatctttacaaaaataggaaggctctcgccttcctaaagccgttataacaaaa 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: 83 Start: 88 End: 117 .......................................................................................CTTGACATTGTAGCAGTTTTCTTATTTGAT.................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttattttttacataaggagcactcaaaaaagacacagatagccctaacattctaattcaaatactgatccagattgttagagcttgtcttgacattgtagcagttttcttatttgatatgaaagaaaccgccattttttcatttttaatctttacaaaaataggaaggctctcgccttcctaaagccgttataacaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2282:SSA_2283|SSA_2282:SSA_2283:Phage infection protein, putative:Conserved uncharacterized protein:<-<-:2285428..2285626 199 ttattttttacataaggagcactcaaaaaagacacagatagccctaacattctaattcaaatactgatccagattgttagagcttgtcttgacattgtagcagttttcttatttgatatgaaagaaaccgccattttttcatttttaatctttacaaaaataggaaggctctcgccttcctaaagccgttataacaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 199 Len: 199 Subject: NC_009009_SSA_2282_SSA_2283|Phage infection protein, putative:Conserved uncharacterized protein|NEGATIVE:NEGATIVE|[2285428,2285626]|199 HSP 1 e-value: 1.0E-69 bit: 264.0 Len: 133 Query Start:1 Query End:133 Subject Strand: POSITIVE Subject Start: 1 Subject End: 133 ttattttttacataaggagcactcaaaaaagacacagatagccctaacattctaattcaaatactgatccagattgttagagcttgtcttgacattgtagcagttttcttatttgatatgaaagaaaccgcca.................................................................. ttattttttacataaggagcactcaaaaaagacacagatagccctaacattctaattcaaatactgatccagattgttagagcttgtcttgacattgtagcagttttcttatttgatatgaaagaaaccgcca.................................................................. HSP 2 e-value: 6.0E-22 bit: 105.0 Len: 53 Query Start:147 Query End:199 Subject Strand: POSITIVE Subject Start: 147 Subject End: 199 ..................................................................................................................................................aatctttacaaaaataggaaggctctcgccttcctaaagccgttataacaaaa ..................................................................................................................................................aatctttacaaaaataggaaggctctcgccttcctaaagccgttataacaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUUUUUUACAUAAGGAGCACUCAAAAAAGACACAGAUAGCCCUAACAUUCUAAUUCAAAUACUGAUCCAGAUUGUUAGAGCUUGUCUUGACAUUGUAGCAGUUUUCUUAUUUGAUAUGAAAGAAACCGCCAUUUUUUCAUUUUUAAUCUUUACAAAAAUAGGAAGGCUCUCGCCUUCCUAAAGCCGUUAUAACAAAA ...........((((.(.((........((((((.....(((.((((((.(((...(((.....)))...))).)))))).)))))))))....((((((.((.........((((.(((((((((.......)))))))))..)))).))))))))...(((((((((....)))))))))..))).))))....... (-46.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUGUUAUAACGGCUUUAGGAAGGCGAGAGCCUUCCUAUUUUUGUAAAGAUUAAAAAUGAAAAAAUGGCGGUUUCUUUCAUAUCAAAUAAGAAAACUGCUACAAUGUCAAGACAAGCUCUAACAAUCUGGAUCAGUAUUUGAAUUAGAAUGUUAGGGCUAUCUGUGUCUUUUUUGAGUGCUCCUUAUGUAAAAAAUAA ((((..(((((.((...(((((((((....))))))))).....(((....(((((((.((.....((((((((((((...........))).))))))))).....)).(((((((((((((((.(((((.((((...)))).))))).)))))))))).....)))))))))))).))).)))))))...))))... (-57.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 840 110 61 201 152 NC_009009:SSA_2282|5end_Phage_infection_protein,_putative_2285337..2285567_NEGATIVE 290 90 43 63 15 NC_009009:SSA_0715|5end_DNA_uptake_protein,_putative_700726..700956_POSITIVE 282 108 64 191 139 NC_009009:SSA_1229|5end_hypothetical_protein_1252421..1252651_NEGATIVE 281 188 166 116 95 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 275 108 64 89 43 NC_009009:SSA_0335|5end_Phosphomevalonate_kinase,_putative_328792..329022_POSITIVE 267 109 69 231 190 NC_009009:SSA_2054|5end_hypothetical_protein_2057899..2058129_NEGATIVE 267 109 64 105 61 NC_009009:SSA_0655|5end_Cell_division_protein_FtsA,_putative_638784..639014_POSITIVE 263 179 138 191 144 NC_009009:SSA_2137|5end_hypothetical_protein_2138412..2138642_NEGATIVE 260 89 56 214 179 NC_009009:SSA_1138|5end_Pyruvate_dehydrogenase,_TPP-dependent_E1_component_alpha-subunit,_putative_1165731..1165961_POSITIVE 259 108 68 68 21 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 258 189 150 105 62 NC_009009:SSA_0911|5end_hypothetical_protein_922078..922308_POSITIVE 257 97 54 56 8 NC_009009:SSA_1803|5end_GTP-binding_protein,_putative_1787909..1788139_NEGATIVE 257 190 160 223 181 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 255 109 64 204 160 NC_009009:SSA_1492|5end_hypothetical_protein_1498954..1499184_NEGATIVE 255 105 66 53 7 NC_009009:SSA_0166|5end_hypothetical_protein_164641..164871_POSITIVE 253 86 53 203 165 NC_009009:SSA_0562|5end_hypothetical_protein_554468..554698_POSITIVE 252 106 64 170 117 NC_009009:SSA_0760|5end_Acetylornithine_aminotransferase,_putative_742581..742811_POSITIVE 249 139 100 48 16 NC_009009:SSA_0635|5end_Indole-3-glycerol_phosphate_synthase,_putative_624388..624618_POSITIVE 248 109 65 38 2 NC_009009:SSA_1747|5end_hypothetical_protein_1733450..1733680_NEGATIVE 246 100 65 175 128 NC_009009:SSA_1247|5end_hypothetical_protein_1272358..1272588_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 320 107 64 48 12 NC_009009:SSA_2348|3end_Metal_dependent_hydrolase,_putative_2349875..2350025_NEGATIVE 281 188 166 119 98 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 275 108 64 99 53 NC_009009:SSA_0334|3end_Diphosphomevalonate_decarboxylase,_putative_328882..329032_POSITIVE 264 188 159 51 27 NC_009009:SSA_1692|3end_Phospho-B-galactosidase_LacG,_putative_1683600..1683750_NEGATIVE 263 179 138 141 94 NC_009009:SSA_2138|3end_RNA-binding_protein,_Jag_family,_putative_2138462..2138612_NEGATIVE 263 187 141 140 96 NC_009009:SSA_0273|3end_hypothetical_protein_268566..268716_POSITIVE 259 108 68 75 28 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE 258 189 150 108 65 NC_009009:SSA_0910|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_922161..922311_POSITIVE 249 139 100 51 19 NC_009009:SSA_0634|3end_Anthranilate_phosphoribosyltransferase,_putative_624471..624621_POSITIVE 248 106 69 149 107 NC_009009:SSA_1573|3end_hypothetical_protein_1576054..1576204_NEGATIVE 248 105 68 139 104 NC_009009:SSA_0492|3end_NADH-dependent_flavin_oxidoreductase,_putative_492771..492921_POSITIVE 242 109 69 63 24 NC_009009:SSA_0689|3end_Penicillin-binding_protein_2B,_putative_674408..674558_POSITIVE 239 185 163 74 52 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 237 110 63 63 13 NC_009009:SSA_0502|3end_Peptide_ABC_transporter,_permease_protein,_putative_502323..502473_POSITIVE 236 186 141 114 68 NC_009009:SSA_1726|3end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1711703..1711853_NEGATIVE 236 190 141 56 7 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 232 178 146 85 43 NC_009009:SSA_1739|3end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,_6-diaminopimelate_ligase,_putative_1727065..1727215_POSITIVE 232 189 172 114 97 NC_009009:SSA_0202|3end_hypothetical_protein_201402..201552_POSITIVE 230 190 146 92 44 NC_009009:SSA_0827|3end_Conserved_uncharacterized_cytosolic_protein,_putative_806952..807102_POSITIVE 228 43 15 142 112 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE