Origin IGS: gaagaatcataaaagcaactgcagatgcggttgcttttttactactttcttgatttaaaagtattcttatgacatcccacatagctctatctaatcttttgtgataaaataggctcaatctaattctaggaggataagat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcttatcctcctagaattagattgagcctattttatcacaaaagattagatagagctatgtgggatgtcataagaatacttttaaatcaagaaagtagtaaaaaagcaaccgcatctgcagttgcttttatgattcttc Mask Tandem Repeat Region ================================================ gaagaatcataaaagcaactgcagatgcggttgcttttttactactttcttgatttaaaagtattcttatgacatcccacatagctctatctaatcttttgtgataaaataggctcaatctaattctaggaggataagat Find is-nt database================================================ Query_seq: SMT_1714:SMT_1715|SMT_1714:SMT_1715:hypothetical membrane spanning protein:MccC family protein:->->:1702174..1702313 140 gaagaatcataaaagcaactgcagatgcggttgcttttttactactttcttgatttaaaagtattcttatgacatcccacatagctctatctaatcttttgtgataaaataggctcaatctaattctaggaggataagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1714:SMT_1715|SMT_1714:SMT_1715:hypothetical membrane spanning protein:MccC family protein:->->:1702174..1702313 140 gaagaatcataaaagcaactgcagatgcggttgcttttttactactttcttgatttaaaagtattcttatgacatcccacatagctctatctaatcttttgtgataaaataggctcaatctaattctaggaggataagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1714:SMT_1715|SMT_1714:SMT_1715:hypothetical membrane spanning protein:MccC family protein:->->:1702174..1702313 140 gaagaatcataaaagcaactgcagatgcggttgcttttttactactttcttgatttaaaagtattcttatgacatcccacatagctctatctaatcttttgtgataaaataggctcaatctaattctaggaggataagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaagaatcataaaagcaactgcagatgcggttgcttttttactactttcttgatttaaaagtattcttatgacatcccacatagctctatctaatcttttgtgataaaataggctcaatctaattctaggaggataagat Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: - Start: 2 End: 124 . L I M F A V A S A T A K K S S E Q N L L I R I V D W M A R D L R K H Y F L S L R M ................ gaagaatcataaaagcaactgcagatgcggttgcttttttactactttcttgatttaaaagtattcttatgacatcccacatagctctatctaatcttttgtgataaaataggctcaatctaattctaggaggataagat 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================================================ gaagaatcataaaagcaactgcagatgcggttgcttttttactactttcttgatttaaaagtattcttatgacatcccacatagctctatctaatcttttgtgataaaataggctcaatctaattctaggaggataagat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1714:SMT_1715|SMT_1714:SMT_1715:hypothetical membrane spanning protein:MccC family protein:->->:1702174..1702313 140 gaagaatcataaaagcaactgcagatgcggttgcttttttactactttcttgatttaaaagtattcttatgacatcccacatagctctatctaatcttttgtgataaaataggctcaatctaattctaggaggataagat Intra-Species Hit: Count: 1 Min: 1 Max: 140 Len: 140 Subject: smit_SMT_1714_SMT_1715|hypothetical membrane spanning protein:MccC family protein|POSITIVE:POSITIVE|[1702174,1702313]|140 HSP 1 e-value: 5.0E-74 bit: 278.0 Len: 140 Query Start:1 Query End:140 Subject Strand: POSITIVE Subject Start: 1 Subject End: 140 gaagaatcataaaagcaactgcagatgcggttgcttttttactactttcttgatttaaaagtattcttatgacatcccacatagctctatctaatcttttgtgataaaataggctcaatctaattctaggaggataagat gaagaatcataaaagcaactgcagatgcggttgcttttttactactttcttgatttaaaagtattcttatgacatcccacatagctctatctaatcttttgtgataaaataggctcaatctaattctaggaggataagat Inter-species Hit: Count: 2 Min: 9 Max: 140 Len: 132 Subject: NC_008533_SPD_0173_SPD_0174|MccC family protein:membrnae protein, putative|NEGATIVE:NEGATIVE|[177190,177443]|254 HSP 1 e-value: 1.0E-22 bit: 107.0 Len: 86 Query Start:55 Query End:140 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 86 ......................................................ttaaaagtattcttatgacatcccacatagctctatctaatcttttgtgataaaataggctcaatctaattctaggaggataagat ......................................................ttaaaagtattcttctgaaatcccacatagctttctcttatattttgtgataaaataggctcaatctatttctaggaggatgagat HSP 2 e-value: 1.0E-6 bit: 54.0 Len: 31 Query Start:9 Query End:39 Subject Strand: NEGATIVE Subject Start: 217 Subject End: 247 ........ataaaagcaactgcagatgcggttgcttttt..................................................................................................... ........ataaaagcaactgcaggtgcggttgcttttt..................................................................................................... Subject: NC_003098_spr0168_spr0169|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[177190,177443]|254 HSP 1 e-value: 1.0E-22 bit: 107.0 Len: 86 Query Start:55 Query End:140 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 86 ......................................................ttaaaagtattcttatgacatcccacatagctctatctaatcttttgtgataaaataggctcaatctaattctaggaggataagat ......................................................ttaaaagtattcttctgaaatcccacatagctttctcttatattttgtgataaaataggctcaatctatttctaggaggatgagat HSP 2 e-value: 1.0E-6 bit: 54.0 Len: 31 Query Start:9 Query End:39 Subject Strand: NEGATIVE Subject Start: 217 Subject End: 247 ........ataaaagcaactgcagatgcggttgcttttt..................................................................................................... ........ataaaagcaactgcaggtgcggttgcttttt..................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAAGCAACUGCAGAUGCGGUUGCUUUUUUACUACUUUCUUGAUUUAAAAGUAUUCUUAUGACAUCCCACAUAGCUCUAUCUAAUCUUUUGUGAUAAAAUAGGCUCAAUCUAAUUCUAGGAGGAUAAGAU ..((((((((((((....))))))))))))......((((((.((.(((.(((....)))..............(((.((((.(.(((......))).).))))))).....))).)).))))))....... (-28.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUUAUCCUCCUAGAAUUAGAUUGAGCCUAUUUUAUCACAAAAGAUUAGAUAGAGCUAUGUGGGAUGUCAUAAGAAUACUUUUAAAUCAAGAAAGUAGUAAAAAAGCAACCGCAUCUGCAGUUGCUUUUAU .(((((((.(((((.(.........(((((((((.(((......))).)))))).))).).))))).)..)))))).(((((((.......)))))))....(((((((((.((....)).))))))))).. (-33.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 60 12 134 86 smit:SMT_1347|5end_SsrA-binding_protein_1325185..1325415_NEGATIVE 283 110 65 57 11 smit:SMT_394|5end_K07729_putative_transcriptional_regulator_324260..324490_POSITIVE 280 109 62 50 5 smit:SMT_1525|5end_pneumococcal_histidine_triad_protein_A_precursor_1509259..1509489_NEGATIVE 264 48 11 201 163 smit:SMT_1401|5end_pyruvate_dehydrogenase_E1_component_beta_subunit_1377013..1377243_POSITIVE 253 42 1 184 137 smit:SMT_1332|5end_hypothetical_protein_1307576..1307806_NEGATIVE 252 26 6 136 116 smit:SMT_489|5end_K01999_branched-chain_amino_acid_transport_system_substrate-binding_protein_423669..423899_POSITIVE 251 42 5 203 172 smit:SMT_331|5end_endo-beta-N-acetylglucosaminidase_266416..266646_POSITIVE 246 44 3 200 162 smit:SMT_2047|5end_choline_binding_protein_F_1957818..1958048_NEGATIVE 241 45 5 86 53 smit:SMT_456|5end_pyruvate_oxidase_394236..394466_POSITIVE 241 95 67 27 1 smit:SMT_107|5end_ribose-phosphate_pyrophosphokinase_52402..52632_POSITIVE 240 60 15 211 163 smit:SMT_202|5end_K02011_iron(III)_transport_system_permease_protein_133831..134061_NEGATIVE 231 128 86 140 104 smit:SMT_2136|5end_cell_division_protein_FtsA_2015132..2015362_POSITIVE 230 43 11 180 147 smit:SMT_1306|5end_alpha-glycerophosphate_oxidase_1269767..1269997_POSITIVE 228 48 13 87 50 smit:SMT_123|5end_hypothetical_protein_75391..75621_POSITIVE 227 39 6 230 196 smit:SMT_2153|5end_putative_cell_division_protein_2026905..2027135_POSITIVE 227 39 6 230 196 smit:SMT_2139|5end_cell_division_protein_FtsZ_2017083..2017313_POSITIVE 227 128 86 140 104 smit:SMT_2138|5end_cell_division_protein_FtsA_2016418..2016648_POSITIVE 227 39 6 230 196 smit:SMT_2137|5end_cell_division_protein_FtsZ_2015797..2016027_POSITIVE 227 39 6 230 196 smit:SMT_2129|5end_cell_division_protein_FtsZ_2010090..2010320_POSITIVE 227 43 11 57 28 smit:SMT_1752|5end_N-(5'-phosphoribosyl)-anthranilate_isomerase_1729772..1730002_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 376 46 3 95 53 smit:SMT_1714|3end_hypothetical_membrane_spanning_protein_1702113..1702263_POSITIVE 261 59 13 151 117 smit:SMT_1625|3end_DNA_polymerase_IV_1615066..1615216_POSITIVE 246 44 3 57 19 smit:SMT_2048|3end_competence-specific_global_transcription_modulator_1957961..1958111_NEGATIVE 242 44 6 48 6 smit:SMT_2123|3end_hypothetical_protein_2008541..2008691_POSITIVE 237 57 13 92 43 smit:SMT_1075|3end_hypothetical_protein_1013870..1014020_POSITIVE 232 60 12 98 42 smit:SMT_1670|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_1659295..1659445_POSITIVE 230 43 11 138 105 smit:SMT_1305|3end_glycerol_kinase_1269805..1269955_POSITIVE 227 43 11 70 41 smit:SMT_1751|3end_indole-3-glycerol_phosphate_synthase_1729865..1730015_POSITIVE 226 60 13 79 35 smit:SMT_1639|3end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_1624803..1624953_NEGATIVE 226 94 54 110 76 smit:SMT_1637|3end_hypothetical_protein_1623848..1623998_POSITIVE 224 48 8 83 41 smit:SMT_2134|3end_hypothetical_protein_2014122..2014272_NEGATIVE 224 48 8 59 17 smit:SMT_1068|3end_ATP-dependent_DNA_helicase_RecG_1008986..1009136_POSITIVE 224 48 8 83 41 smit:SMT_873|3end_hypothetical_protein_820733..820883_NEGATIVE 224 48 8 83 41 smit:SMT_384|3end_hypothetical_protein_319860..320010_POSITIVE 221 113 72 91 36 smit:SMT_1094|3end_membrane_carboxypeptidase_(penicillin-binding_protein)_1034141..1034291_NEGATIVE 220 70 21 141 79 smit:SMT_938|3end_hypothetical_protein_890813..890963_NEGATIVE 220 44 13 150 122 smit:SMT_274|3end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_217259..217409_POSITIVE 220 49 7 104 56 smit:SMT_109|3end_beta-galactosidase_57523..57673_POSITIVE 218 47 11 134 97 smit:SMT_1940|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1877106..1877256_POSITIVE 218 45 3 99 56 smit:SMT_1872|3end_K03217_preprotein_translocase_YidC_subunit_1830883..1831033_NEGATIVE