Origin IGS: gacacaaamcagtcctatttttcttgccttttacgaataagaagatgtaggaggaacgatgctgactcagaaggaattgaactatatcacgacatttaaacagacgcatttacaccgatttcgggaaattgaaacctttgtgaaactatgcaaaaaatcgctcaaacagccatcgcaagctgacaattttaggtctttttgatatactaagacagataaattgaataggagaaacgat .........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 atcgtttctcctattcaatttatctgtcttagtatatcaaaaagacctaaaattgtcagcttgcgatggctgtttgagcgattttttgcatagtttcacaaaggtttcaatttcccgaaatcggtgtaaatgcgtctgtttaaatgtcgtgatatagttcaattccttctgagtcagcatcgttcctcctacatcttcttattcgtaaaaggcaagaaaaataggactgktttgtgtc Mask Tandem Repeat Region ================================================ gacacaaamcagtcctatttttcttgccttttacgaataagaagatgtaggaggaacgatgctgactcagaaggaattgaactatatcacgacatttaaacagacgcatttacaccgatttcgggaaattgaaacctttgtgaaactatgcaaaaaatcgctcaaacagccatcgcaagctgacaattttaggtctttttgatatactaagacagataaattgaataggagaaacgat Find is-nt database================================================ Query_seq: SMT_163:SMT_164|SMT_163:SMT_164:cardiolipin synthetase:hypothetical membrane spanning protein:->->:108997..109234 238 gacacaaamcagtcctatttttcttgccttttacgaataagaagatgtaggaggaacgatgctgactcagaaggaattgaactatatcacgacatttaaacagacgcatttacaccgatttcgggaaattgaaacctttgtgaaactatgcaaaaaatcgctcaaacagccatcgcaagctgacaattttaggtctttttgatatactaagacagataaattgaataggagaaacgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_163:SMT_164|SMT_163:SMT_164:cardiolipin synthetase:hypothetical membrane spanning protein:->->:108997..109234 238 gacacaaamcagtcctatttttcttgccttttacgaataagaagatgtaggaggaacgatgctgactcagaaggaattgaactatatcacgacatttaaacagacgcatttacaccgatttcgggaaattgaaacctttgtgaaactatgcaaaaaatcgctcaaacagccatcgcaagctgacaattttaggtctttttgatatactaagacagataaattgaataggagaaacgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_163:SMT_164|SMT_163:SMT_164:cardiolipin synthetase:hypothetical membrane spanning protein:->->:108997..109234 238 gacacaaamcagtcctatttttcttgccttttacgaataagaagatgtaggaggaacgatgctgactcagaaggaattgaactatatcacgacatttaaacagacgcatttacaccgatttcgggaaattgaaacctttgtgaaactatgcaaaaaatcgctcaaacagccatcgcaagctgacaattttaggtctttttgatatactaagacagataaattgaataggagaaacgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 59 Max: 199 Len: 141 Subject: UniRef90_Q8DRD8 Cluster: Orf47; n=1; Streptococcus pneumoniae R6|Rep: Orf47 - Streptococcus pneumoniae (strain ATCC BAA-255 / R6) HSP 1 e-value: 2.0E-14 bit: 80.1 Len: 141 Query Start:59 Query End:199 Subject Strand: null Subject Start: 1 Subject End: 47 .......................................................... M L T Q K E L N Y I T T F K Q T H L H R F R E I E T F V K L C K K S L K Q P S Q A D N F R S F ....................................... .......................................................... M L T K E E V N D M I E F K Q T H L H R F R E I E T F V K L C K K S L K Q P S Q A D N P R T F ....................................... gacacaaamcagtcctatttttcttgccttttacgaataagaagatgtaggaggaacgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgatatactaagacagataaattgaataggagaaacgat Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 59 End: 199 .......................................................... M L T Q K E L N Y I T T F K Q T H L H R F R E I E T F V K L C K K S L K Q P S Q A D N F R S F ....................................... Protein_Len: 30 Strand: - Start: 149 End: 238 .................................................................................................................................................... A F F R E F L W R L S V I K P R K S I S L C I F Q I P S V M Protein_Len: 34 Strand: - Start: 85 End: 186 .................................................................................... I V V N L C V C K C R N R S I S V K T F S H L F D S L C G D C A S M .................................................... Protein_Len: 36 Strand: - Start: 2 End: 109 . C L X T R N K K G K V F L F I Y S S R H Q S L L F Q V I D R C K F L R M ................................................................................................................................. gacacaaamcagtcctatttttcttgccttttacgaataagaagatgtaggaggaacgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgatatactaagacagataaattgaataggagaaacgat 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: 84 Start: 178 End: 207 .................................................................................................................................................................................GCTGACAATTTTAGGTCTTTTTGATATACT............................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gacacaaamcagtcctatttttcttgccttttacgaataagaagatgtaggaggaacgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgatatactaagacagataaattgaataggagaaacgat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_163:SMT_164|SMT_163:SMT_164:cardiolipin synthetase:hypothetical membrane spanning protein:->->:108997..109234 238 gacacaaamcagtcctatttttcttgccttttacgaataagaagatgtaggaggaacgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgatatactaagacagataaattgaataggagaaacgat Intra-Species Hit: Count: 1 Min: 1 Max: 238 Len: 238 Subject: smit_SMT_163_SMT_164|cardiolipin synthetase:hypothetical membrane spanning protein|POSITIVE:POSITIVE|[108997,109234]|238 HSP 1 e-value: 3.0E-23 bit: 110.0 Len: 57 Query Start:1 Query End:57 Subject Strand: POSITIVE Subject Start: 1 Subject End: 57 gacacaaamcagtcctatttttcttgccttttacgaataagaagatgtaggaggaac..................................................................................................................................................................................... gacacaaamcagtcctatttttcttgccttttacgaataagaagatgtaggaggaac..................................................................................................................................................................................... HSP 2 e-value: 1.0E-13 bit: 78.3 Len: 39 Query Start:200 Query End:238 Subject Strand: POSITIVE Subject Start: 200 Subject End: 238 .......................................................................................................................................................................................................tgatatactaagacagataaattgaataggagaaacgat .......................................................................................................................................................................................................tgatatactaagacagataaattgaataggagaaacgat Inter-species Hit: Count: 2 Min: 4 Max: 238 Len: 235 Subject: NC_008533_SPD_0185_SPD_0186|cardiolipin synthetase:competence-induced protein Ccs4|POSITIVE:POSITIVE|[189263,189519]|257 HSP 1 e-value: 3.0E-11 bit: 70.4 Len: 39 Query Start:200 Query End:238 Subject Strand: POSITIVE Subject Start: 219 Subject End: 257 .......................................................................................................................................................................................................tgatatactaagacagataaattgaataggagaaacgat .......................................................................................................................................................................................................tgatatactaagacagataaattgaacaggagaaacgat HSP 2 e-value: 7.0E-6 bit: 52.4 Len: 36 Query Start:4 Query End:39 Subject Strand: POSITIVE Subject Start: 20 Subject End: 55 ...acaaamcagtcctatttttcttgccttttacgaata....................................................................................................................................................................................................... ...acaaaccagacctatttttcttgtcttttacgaata....................................................................................................................................................................................................... Subject: NC_003028_SP_0199_SP_0200|cardiolipin synthetase:competence-induced protein Ccs4|POSITIVE:POSITIVE|[186754,187010]|257 HSP 1 e-value: 3.0E-11 bit: 70.4 Len: 39 Query Start:200 Query End:238 Subject Strand: POSITIVE Subject Start: 219 Subject End: 257 .......................................................................................................................................................................................................tgatatactaagacagataaattgaataggagaaacgat .......................................................................................................................................................................................................tgatatactaagacagataaattgaacaggagaaacgat HSP 2 e-value: 7.0E-6 bit: 52.4 Len: 36 Query Start:4 Query End:39 Subject Strand: POSITIVE Subject Start: 20 Subject End: 55 ...acaaamcagtcctatttttcttgccttttacgaata....................................................................................................................................................................................................... ...acaaaccagacctatttttcttgtcttttacgaata....................................................................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAAMCAGUCCUAUUUUUCUUGCCUUUUACGAAUAAGAAGAUGUAGGAGGAACGAUGCUGACUCAGAAGGAAUUGAACUAUAUCACGACAUUUAAACAGACGCAUUUACACCGAUUUCGGGAAAUUGAAACCUUUGUGAAACUAUGCAAAAAAUCGCUCAAACAGCCAUCGCAAGCUGACAAUUUUAGGUCUUUUUGAUAUACUAAGACAGAUAAAUUGAAUAGGAGAAACGAU .........((((((....(((((((((((((..(....)..)))))))))..((((((((..((((((((...(((......)))...............((.((((...(((....))).))))))...))))).)))......((........)).....))).)))))))))....((((((...(((((...........)))))....)))))).))))))........ (-41.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGUUUCUCCUAUUCAAUUUAUCUGUCUUAGUAUAUCAAAAAGACCUAAAAUUGUCAGCUUGCGAUGGCUGUUUGAGCGAUUUUUUGCAUAGUUUCACAAAGGUUUCAAUUUCCCGAAAUCGGUGUAAAUGCGUCUGUUUAAAUGUCGUGAUAUAGUUCAAUUCCUUCUGAGUCAGCAUCGUUCCUCCUACAUCUUCUUAUUCGUAAAAGGCAAGAAAAAUAGGACUGKUUUGU ........(((((((........(((.((((((((((((....(((..(((((((((((((......))))).....))))))))..((((.....(((...((((((........)))))).)))...))))............))).)))))))............))))).)))..((...(((..(((............)))..)))...))..)))))))......... (-45.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 78 45 225 185 smit:SMT_488|5end_dCMP_deaminase_422956..423186_POSITIVE 296 139 98 225 180 smit:SMT_1610|5end_tyrosine_recombinase_1598565..1598795_POSITIVE 291 211 171 152 109 smit:SMT_1088|5end_hypothetical_protein_1024346..1024576_NEGATIVE 288 193 156 189 143 smit:SMT_1274|5end_K02008_cobalt_transport_system_permease_protein_1237741..1237971_POSITIVE 286 200 154 196 148 smit:SMT_2133|5end_hypothetical_protein_2014007..2014237_NEGATIVE 286 200 154 196 148 smit:SMT_872|5end_hypothetical_protein_820618..820848_NEGATIVE 286 200 154 196 148 smit:SMT_385|5end_hypothetical_protein_319895..320125_POSITIVE 277 159 111 226 182 smit:SMT_675|5end_DNA_repair_protein_582977..583207_NEGATIVE 274 182 146 141 110 smit:SMT_370|5end_acetyltransferase,_GNAT_family_304688..304918_POSITIVE 269 60 12 220 161 smit:SMT_639|5end_6-phospho-beta-galactosidase_544885..545115_NEGATIVE 261 182 157 81 57 smit:SMT_927|5end_KH_domain_protein_882677..882907_NEGATIVE 257 80 34 196 159 smit:SMT_505|5end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_437106..437336_NEGATIVE 257 80 34 196 159 smit:SMT_502|5end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_435675..435905_NEGATIVE 254 76 44 211 180 smit:SMT_1546|5end_hypothetical_protein_1530068..1530298_POSITIVE 253 94 53 83 42 smit:SMT_1233|5end_cadmium_resistance_protein_1194306..1194536_POSITIVE 245 89 41 194 145 smit:SMT_197|5end_DNA-directed_RNA_polymerase,_alpha_subunit_127686..127916_POSITIVE 243 200 154 56 5 smit:SMT_2021|5end_K06201_copper_homeostasis_protein_1937888..1938118_POSITIVE 243 190 146 69 35 smit:SMT_847|5end_thioredoxin_reductase_792800..793030_POSITIVE 242 71 36 204 161 smit:SMT_1450|5end_K02057_simple_sugar_transport_system_permease_protein_1433622..1433852_NEGATIVE 241 180 131 149 95 smit:SMT_1697|5end_hypothetical_protein_1678846..1679076_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 200 154 81 33 smit:SMT_2134|3end_hypothetical_protein_2014122..2014272_NEGATIVE 286 200 154 81 33 smit:SMT_873|3end_hypothetical_protein_820733..820883_NEGATIVE 286 200 154 81 33 smit:SMT_384|3end_hypothetical_protein_319860..320010_POSITIVE 266 159 111 76 39 smit:SMT_2075|3end_phosphoribosylamine--glycine_ligase_1977769..1977919_NEGATIVE 255 59 22 58 20 smit:SMT_2010|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1929770..1929920_POSITIVE 248 200 154 78 30 smit:SMT_1670|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_1659295..1659445_POSITIVE 248 200 154 57 9 smit:SMT_1068|3end_ATP-dependent_DNA_helicase_RecG_1008986..1009136_POSITIVE 246 192 156 127 101 smit:SMT_1806|3end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781644..1781794_POSITIVE 245 89 41 151 102 smit:SMT_196|3end_30S_ribosomal_protein_S11_127723..127873_POSITIVE 241 180 131 147 93 smit:SMT_1696|3end_hypothetical_protein_1678924..1679074_POSITIVE 237 200 159 144 98 smit:SMT_1089|3end_hypothetical_protein_1024343..1024493_NEGATIVE 237 191 158 72 32 smit:SMT_143|3end_hypothetical_protein_95090..95240_NEGATIVE 232 226 184 44 2 smit:SMT_453|3end_CopAB_ATPase_metal-fist_type_repressor_391358..391508_POSITIVE 231 89 46 64 16 smit:SMT_847|3end_thioredoxin_reductase_793848..793998_POSITIVE 230 191 154 44 8 smit:SMT_2017|3end_exonuclease_RexA_1935862..1936012_NEGATIVE 229 200 156 78 32 smit:SMT_1689|3end_PTS_enzyme,_maltose-and_glucose-specific,_factor_II_homologue_1673139..1673289_POSITIVE 229 57 19 84 40 smit:SMT_1363|3end_50S_ribosomal_protein_L20_1343254..1343404_NEGATIVE 221 178 131 84 41 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 221 206 167 48 1 smit:SMT_940|3end_tRNA_pseudouridine_synthase_A_892015..892165_NEGATIVE 220 203 175 138 113 smit:SMT_1581|3end_transcriptional_regulator,_biotin_repressor_family_1573120..1573270_NEGATIVE