Origin IGS: gacttgcttcctttcaccattgcaaaaaaatagccacactgcccggagtcaagctcagcaaacagcgtggttaaggcatcgttaacttacctcacaacaggtttgaagtaaatcagcgaaactactttcttagtataacactttcagaatcattgtcaatagaaacgacttgattttttcaattttttcaag .........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 cttgaaaaaattgaaaaaatcaagtcgtttctattgacaatgattctgaaagtgttatactaagaaagtagtttcgctgatttacttcaaacctgttgtgaggtaagttaacgatgccttaaccacgctgtttgctgagcttgactccgggcagtgtggctatttttttgcaatggtgaaaggaagcaagtc Mask Tandem Repeat Region ================================================ gacttgcttcctttcaccattgcaaaaaaatagccacactgcccggagtcaagctcagcaaacagcgtggttaaggcatcgttaacttacctcacaacaggtttgaagtaaatcagcgaaactactttcttagtataacactttcagaatcattgtcaatagaaacgacttgattttttcaattttttcaag Find is-nt database================================================ Query_seq: SMT_1931:SMT_1932|SMT_1931:SMT_1932:23S rRNA methyltransferase:K02008 cobalt transport system permease protein:<-<-:1871069..1871260 192 gacttgcttcctttcaccattgcaaaaaaatagccacactgcccggagtcaagctcagcaaacagcgtggttaaggcatcgttaacttacctcacaacaggtttgaagtaaatcagcgaaactactttcttagtataacactttcagaatcattgtcaatagaaacgacttgattttttcaattttttcaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1931:SMT_1932|SMT_1931:SMT_1932:23S rRNA methyltransferase:K02008 cobalt transport system permease protein:<-<-:1871069..1871260 192 gacttgcttcctttcaccattgcaaaaaaatagccacactgcccggagtcaagctcagcaaacagcgtggttaaggcatcgttaacttacctcacaacaggtttgaagtaaatcagcgaaactactttcttagtataacactttcagaatcattgtcaatagaaacgacttgattttttcaattttttcaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1931:SMT_1932|SMT_1931:SMT_1932:23S rRNA methyltransferase:K02008 cobalt transport system permease protein:<-<-:1871069..1871260 192 gacttgcttcctttcaccattgcaaaaaaatagccacactgcccggagtcaagctcagcaaacagcgtggttaaggcatcgttaacttacctcacaacaggtttgaagtaaatcagcgaaactactttcttagtataacactttcagaatcattgtcaatagaaacgacttgattttttcaattttttcaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacttgcttcctttcaccattgcaaaaaaatagccacactgcccggagtcaagctcagcaaacagcgtggttaaggcatcgttaacttacctcacaacaggtttgaagtaaatcagcgaaactactttcttagtataacactttcagaatcattgtcaatagaaacgacttgattttttcaattttttcaag Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 78 End: 170 ............................................................................. M V N L P H N R F E V N Q R N Y F L S I T L S E S L S I E T T ...................... gacttgcttcctttcaccattgcaaaaaaatagccacactgcccggagtcaagctcagcaaacagcgtggttaaggcatcgttaacttacctcacaacaggtttgaagtaaatcagcgaaactactttcttagtataacactttcagaatcattgtcaatagaaacgacttgattttttcaattttttcaag 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================================================ gacttgcttcctttcaccattgcaaaaaaatagccacactgcccggagtcaagctcagcaaacagcgtggttaaggcatcgttaacttacctcacaacaggtttgaagtaaatcagcgaaactactttcttagtataacactttcagaatcattgtcaatagaaacgacttgattttttcaattttttcaag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 42 HP_score: -3.4 Tail_Score: -2.52543 Start: 79 End: 119 Full_Region: actaagaaagtagtt tcgctgatttacttcaaa cctgt tgtgaggtaagttaacga tgccttaaccacgct ..............................................................................tcgctgatttacttcaaacctgttgtgaggtaagttaacga......................................................................... Find igs database================================================ Query_seq: SMT_1931:SMT_1932|SMT_1931:SMT_1932:23S rRNA methyltransferase:K02008 cobalt transport system permease protein:<-<-:1871069..1871260 192 gacttgcttcctttcaccattgcaaaaaaatagccacactgcccggagtcaagctcagcaaacagcgtggttaaggcatcgttaacttacctcacaacaggtttgaagtaaatcagcgaaactactttcttagtataacactttcagaatcattgtcaatagaaacgacttgattttttcaattttttcaag Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: smit_SMT_1931_SMT_1932|23S rRNA methyltransferase:K02008 cobalt transport system permease protein|NEGATIVE:NEGATIVE|[1871069,1871260]|192 HSP 1 e-value: 4.0E-81 bit: 301.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 gacttgcttcctttcaccattgcnnnnnnntagccacactgcccggagtcaagctcagcaaacagcgtggttaaggcatcgttaacttacctcacaacaggtttgaagtaaatcagcgaaactactttcttagtataacactttcagaatcattgtcaatagaaacgacttga................... gacttgcttcctttcaccattgcaaaaaaatagccacactgcccggagtcaagctcagcaaacagcgtggttaaggcatcgttaacttacctcacaacaggtttgaagtaaatcagcgaaactactttcttagtataacactttcagaatcattgtcaatagaaacgacttga................... Inter-species Hit: Count: 4 Min: 1 Max: 173 Len: 173 Subject: NC_003028_SP_0484_SP_0486|hypothetical protein:RNA methyltransferase, TrmH family|POSITIVE:POSITIVE|[466403,466594]|192 HSP 1 e-value: 1.0E-78 bit: 293.0 Len: 173 Query Start:1 Query End:173 Subject Strand: NEGATIVE Subject Start: 20 Subject End: 192 gacttgcttcctttcaccattgcnnnnnnntagccacactgcccggagtcaagctcagcaaacagcgtggttaaggcatcgttaacttacctcacaacaggtttgaagtaaatcagcgaaactactttcttagtataacactttcagaatcattgtcaatagaaacgacttga................... gacttgcttcctttcaccattgcaaaaaaatagccacactgcccggagtcaagctcagcaaacagcgtggttaaggcatcgttaacttacctcacaacaggtttgaagtaaatcagcgaaactactttcttagtataacactttcagaatcattgtcaatagaaatgacttga................... Subject: NC_008533_SPD_0435_SPD_0436|hypothetical protein:TrmH family RNA methyltransferase|POSITIVE:POSITIVE|[440220,440411]|192 HSP 1 e-value: 4.0E-75 bit: 281.0 Len: 171 Query Start:1 Query End:171 Subject Strand: NEGATIVE Subject Start: 22 Subject End: 192 gacttgcttcctttcaccattgcnnnnnnntagccacactgcccggagtcaagctcagcaaacagcgtggttaaggcatcgttaacttacctcacaacaggtttgaagtaaatcagcgaaactactttcttagtataacactttcagaatcattgtcaatagaaacgactt..................... gacttgcttccttttaccattgcaaaaaaatagccacactgcccggagtcaagctcagcaaacagcgtggttaaggcatcgttaacttacctcacaacaggtttgaagtaaatcagcgaaactactttcttagtctaacactttcagaatcattgtcaatagaaacgactt..................... Subject: NC_003098_spr0431_spr0432|ABC transporter membrane-spanning permease - unknown substrate:rRNA methylase|POSITIVE:POSITIVE|[432690,432842]|153 HSP 1 e-value: 9.0E-67 bit: 254.0 Len: 132 Query Start:40 Query End:171 Subject Strand: NEGATIVE Subject Start: 22 Subject End: 153 .......................................tgcccggagtcaagctcagcaaacagcgtggttaaggcatcgttaacttacctcacaacaggtttgaagtaaatcagcgaaactactttcttagtataacactttcagaatcattgtcaatagaaacgactt..................... .......................................tgcccggagtcaagctcagcaaacagcgtggttaaggcatcgttaacttacctcacaacaggtttgaagtaaatcagcgaaactactttcttagtctaacactttcagaatcattgtcaatagaaacgactt..................... Subject: NC_009009_SSA_1774_SSA_1775|RRNA methylase, putative:Potassium uptake protein, Trk family, putative|NEGATIVE:POSITIVE|[1761134,1761423]|290 HSP 1 e-value: 4.0E-26 bit: 119.0 Len: 108 Query Start:40 Query End:147 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 .......................................tgcccggagtcaagctcagcaaacagcgtggttaaggcatcgttaacttacctcacaacaggtttgaagtaaatcagcgaaactactttcttagtataacactttcag............................................. .......................................tgcccggagtcaagctcagcaaacagcgtggttaaggcttcattaacttacatcacaacaggtttgaggtaaaccaatgaaggtactcatttagtataacactttcag............................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACUUGCUUCCUUUCACCAUUGCAAAAAAAUAGCCACACUGCCCGGAGUCAAGCUCAGCAAACAGCGUGGUUAAGGCAUCGUUAACUUACCUCACAACAGGUUUGAAGUAAAUCAGCGAAACUACUUUCUUAGUAUAACACUUUCAGAAUCAUUGUCAAUAGAAACGACUUGA ((.(((((((..........(((.......(((((((.(((....(((.....)))......))).)))))))..)))..........((((......))))..))))))).))........((((.....))))..............(((..(((.........))).))) (-30.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAGUCGUUUCUAUUGACAAUGAUUCUGAAAGUGUUAUACUAAGAAAGUAGUUUCGCUGAUUUACUUCAAACCUGUUGUGAGGUAAGUUAACGAUGCCUUAACCACGCUGUUUGCUGAGCUUGACUCCGGGCAGUGUGGCUAUUUUUUUGCAAUGGUGAAAGGAAGCAAGUC .......((((((.((.((.(((((.(.....).)))))..(((((((((((..(((.((((((((((((.........)))))))))))).)))........((((((((((((..(((.....)))))))))))))))))))))))))).....)).)).))))))..... (-48.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1063 80 31 171 122 smit:SMT_1931|5end_23S_rRNA_methyltransferase_1870978..1871208_NEGATIVE 360 77 35 170 129 smit:SMT_1460|5end_K02038_phosphate_transport_system_permease_protein_1441429..1441659_POSITIVE 325 73 32 222 176 smit:SMT_1354|5end_diacylglycerol_kinase_1332001..1332231_NEGATIVE 323 77 33 57 9 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 323 78 33 74 32 smit:SMT_452|5end_phosphomethylpyrimidine_kinase_390568..390798_NEGATIVE 320 81 42 42 2 smit:SMT_687|5end_carbamoyl-phosphate_synthase,_large_subunit_599264..599494_NEGATIVE 318 83 41 117 81 smit:SMT_155|5end_hypothetical_protein_102704..102934_NEGATIVE 316 96 52 106 59 smit:SMT_1813|5end_amino_acid_transporter_1787142..1787372_POSITIVE 310 76 32 65 20 smit:SMT_1395|5end_K07025_putative_hydrolase_of_the_HAD_superfamily_1371310..1371540_POSITIVE 309 68 32 76 20 smit:SMT_1796|5end_dihydroorotate_dehydrogenase_A_1770816..1771046_NEGATIVE 309 79 36 66 24 smit:SMT_1265|5end_hypothetical_protein_1231261..1231491_NEGATIVE 306 77 34 197 138 smit:SMT_1980|5end_glycosyltransferase_1911161..1911391_POSITIVE 305 87 41 194 137 smit:SMT_328|5end_23S_rRNA_methyltransferase_264652..264882_POSITIVE 298 77 32 200 149 smit:SMT_1887|5end_LicC_protein_1841445..1841675_POSITIVE 297 80 31 53 1 smit:SMT_1739|5end_hypothetical_protein_1721263..1721493_POSITIVE 295 77 31 225 178 smit:SMT_1543|5end_diphosphomevalonate_decarboxylase_1528024..1528254_NEGATIVE 287 80 37 56 7 smit:SMT_807|5end_hypothetical_protein_predicted_by_Glimmer/Critica_716815..717045_NEGATIVE 285 70 28 184 143 smit:SMT_2106|5end_unknown,_predicted_membrane_protein_(TMS5)_1997163..1997393_POSITIVE 285 70 28 184 143 smit:SMT_1771|5end_unknown,_predicted_membrane_protein_(TMS5)_1747437..1747667_POSITIVE 280 77 31 79 36 smit:SMT_109|5end_beta-galactosidase_53925..54155_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 338 80 34 60 25 smit:SMT_2057|3end_cell_division_protein_FtsH_1966897..1967047_NEGATIVE 328 77 35 89 48 smit:SMT_1115|3end_K02245_competence_protein_ComGC_1052473..1052623_NEGATIVE 326 80 32 51 1 smit:SMT_1738|3end_peptidyl-prolyl_cis-trans_isomerase_1721341..1721491_POSITIVE 316 96 52 77 30 smit:SMT_1812|3end_K07485_transposase_1787193..1787343_POSITIVE 296 68 22 149 94 smit:SMT_807|3end_hypothetical_protein_predicted_by_Glimmer/Critica_716708..716858_NEGATIVE 284 44 4 50 18 smit:SMT_605|3end_DNA-binding_protein_HU_519257..519407_POSITIVE 281 70 21 78 28 smit:SMT_481|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_417641..417791_NEGATIVE 278 82 41 75 39 smit:SMT_1959|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1892967..1893117_POSITIVE 278 82 41 75 39 smit:SMT_286|3end_polysaccharide_transporter,_PST_family_230150..230300_POSITIVE 277 77 32 55 3 smit:SMT_1776|3end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_1751892..1752042_NEGATIVE 277 101 64 150 112 smit:SMT_1307|3end_glycerol_uptake_facilitator_protein_1272448..1272598_POSITIVE 276 86 44 150 99 smit:SMT_858|3end_triosephosphate_isomerase_802525..802675_NEGATIVE 272 60 15 145 96 smit:SMT_862|3end_hypothetical_protein_predicted_by_Glimmer/Critica_809191..809341_POSITIVE 269 75 31 74 23 smit:SMT_1477|3end_K02077_zinc/manganese_transport_system_substrate-binding_protein_1459447..1459597_NEGATIVE 268 72 32 62 20 smit:SMT_855|3end_dihydrofolate_reductase_799492..799642_NEGATIVE 267 70 22 53 6 smit:SMT_749|3end_shikimate_kinase_653495..653645_NEGATIVE 265 83 43 67 23 smit:SMT_1321|3end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1291458..1291608_POSITIVE 263 50 5 77 28 smit:SMT_921|3end_putative_PP2C_protein_phosphatase_874498..874648_NEGATIVE 261 69 22 55 6 smit:SMT_1853|3end_1,4-alpha-glucan_branching_enzyme_1817687..1817837_NEGATIVE 260 76 40 136 102 smit:SMT_194|3end_hypothetical_protein_predicted_by_Glimmer/Critica_126860..127010_NEGATIVE