Origin IGS: aaatcaccgagaaattgctcaggaaaggaaagacggtttacgaaacatcgagtatgaagatatctcgtagatggtaaggtagagctagcaggraatctcacgtacagaagtagaaccaccaagagatttgtcagggtggtagtnnnnnttaattaattaannnnncggactagactttgtaaaacgacggccagtcca .........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 tggactggccgtcgttttacaaagtctagtccgnnnnnttaattaattaannnnnactaccaccctgacaaatctcttggtggttctacttctgtacgtgagattycctgctagctctaccttaccatctacgagatatcttcatactcgatgtttcgtaaaccgtctttcctttcctgagcaatttctcggtgattt Mask Tandem Repeat Region ================================================ aaatcaccgagaaattgctcaggaaaggaaagacggtttacgaaacatcgagtatgaagatatctcgtagatggtaaggtagagctagcaggraatctcacgtacagaagtagaaccaccaagagatttgtcagggtggtagtnnnnnttaattaattaannnnncggactagactttgtaaaacgacggccagtcca Find is-nt database================================================ Query_seq: SMT_1976:SMT_1977|SMT_1976:SMT_1977:immunoglobulin A1 protease:endopeptidase O:->->:1907774..1907971 198 aaatcaccgagaaattgctcaggaaaggaaagacggtttacgaaacatcgagtatgaagatatctcgtagatggtaaggtagagctagcaggraatctcacgtacagaagtagaaccaccaagagatttgtcagggtggtagtnnnnnttaattaattaannnnncggactagactttgtaaaacgacggccagtcca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1976:SMT_1977|SMT_1976:SMT_1977:immunoglobulin A1 protease:endopeptidase O:->->:1907774..1907971 198 aaatcaccgagaaattgctcaggaaaggaaagacggtttacgaaacatcgagtatgaagatatctcgtagatggtaaggtagagctagcaggraatctcacgtacagaagtagaaccaccaagagatttgtcagggtggtagtnnnnnttaattaattaannnnncggactagactttgtaaaacgacggccagtcca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1976:SMT_1977|SMT_1976:SMT_1977:immunoglobulin A1 protease:endopeptidase O:->->:1907774..1907971 198 aaatcaccgagaaattgctcaggaaaggaaagacggtttacgaaacatcgagtatgaagatatctcgtagatggtaaggtagagctagcaggraatctcacgtacagaagtagaaccaccaagagatttgtcagggtggtagtnnnnnttaattaattaannnnncggactagactttgtaaaacgacggccagtcca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatcaccgagaaattgctcaggaaaggaaagacggtttacgaaacatcgagtatgaagatatctcgtagatggtaaggtagagctagcaggraatctcacgtacagaagtagaaccaccaagagatttgtcagggtggtagtnnnnnttaattaattaannnnncggactagactttgtaaaacgacggccagtcca Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: - Start: 3 End: 134 .. D G L F Q E P F S L R N V F C R T H L Y R T S P L T S S A P F R V Y L L L V V L L N T M ................................................................ aaatcaccgagaaattgctcaggaaaggaaagacggtttacgaaacatcgagtatgaagatatctcgtagatggtaaggtagagctagcaggraatctcacgtacagaagtagaaccaccaagagatttgtcagggtggtagtnnnnnttaattaattaannnnncggactagactttgtaaaacgacggccagtcca 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================================================ aaatcaccgagaaattgctcaggaaaggaaagacggtttacgaaacatcgagtatgaagatatctcgtagatggtaaggtagagctagcaggraatctcacgtacagaagtagaaccaccaagagatttgtcagggtggtagtnnnnnttaattaattaannnnncggactagactttgtaaaacgacggccagtcca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1976:SMT_1977|SMT_1976:SMT_1977:immunoglobulin A1 protease:endopeptidase O:->->:1907774..1907971 198 aaatcaccgagaaattgctcaggaaaggaaagacggtttacgaaacatcgagtatgaagatatctcgtagatggtaaggtagagctagcaggraatctcacgtacagaagtagaaccaccaagagatttgtcagggtggtagtnnnnnttaattaattaannnnncggactagactttgtaaaacgacggccagtcca Intra-Species Hit: Count: 1 Min: 1 Max: 198 Len: 198 Subject: smit_SMT_1976_SMT_1977|immunoglobulin A1 protease:endopeptidase O|POSITIVE:POSITIVE|[1907774,1907971]|198 HSP 1 e-value: 9.0E-90 bit: 330.0 Len: 198 Query Start:1 Query End:198 Subject Strand: POSITIVE Subject Start: 1 Subject End: 198 aaatcaccgagaaattgctcaggaaaggaaagacggtttacgaaacatcgagtatgaagatatctcgtagatggtaaggtagagctagcaggraatctcacgtacagaagtagaaccaccaagagatttgtcagggtggtagtnnnnnttaattaattaannnnncggactagactttgtaaaacgacggccagtcca aaatcaccgagaaattgctcaggaaaggaaagacggtttacgaaacatcgagtatgaagatatctcgtagatggtaaggtagagctagcaggraatctcacgtacagaagtagaaccaccaagagatttgtcagggtggtagtnnnnnttaattaattaannnnncggactagactttgtaaaacgacggccagtcca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUCACCGAGAAAUUGCUCAGGAAAGGAAAGACGGUUUACGAAACAUCGAGUAUGAAGAUAUCUCGUAGAUGGUAAGGUAGAGCUAGCAGGRAAUCUCACGUACAGAAGUAGAACCACCAAGAGAUUUGUCAGGGUGGUAGUNNNNNUUAAUUAAUUAANNNNNCGGACUAGACUUUGUAAAACGACGGCCAGUCCA ........((((..(((((..((.........((.((((((((.(.(((.........))).).)))))))).)).........)))))))....))))...............((((((..((......))..))))))..........................(((((.(.(((((.....))).))).))))). (-40.07) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGACUGGCCGUCGUUUUACAAAGUCUAGUCCGNNNNNUUAAUUAAUUAANNNNNACUACCACCCUGACAAAUCUCUUGGUGGUUCUACUUCUGUACGUGAGAUUYCCUGCUAGCUCUACCUUACCAUCUACGAGAUAUCUUCAUACUCGAUGUUUCGUAAACCGUCUUUCCUUUCCUGAGCAAUUUCUCGGUGAUUU (((((((((.(..(((((((......................................((((((..((......))..))))))..(((....))).)))))))...).))))).))))..........(((((((((((.........)))))))))))..............(((((((......))))).))... (-40.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 410 190 166 216 192 smit:SMT_1872|5end_K03217_preprotein_translocase_YidC_subunit_1831764..1831994_NEGATIVE 410 190 166 173 149 smit:SMT_543|5end_topoisomerase_IV_subunit_B_458372..458602_POSITIVE 410 190 166 193 169 smit:SMT_389|5end_PTS_system,_galactitol-specific_IIA_component,_putative_321779..322009_POSITIVE 301 125 84 205 171 smit:SMT_168|5end_anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_113670..113900_POSITIVE 286 117 78 88 43 smit:SMT_148|5end_glycoprotein_endopeptidase_98033..98263_POSITIVE 272 114 71 199 150 smit:SMT_1897|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1848858..1849088_NEGATIVE 263 137 98 66 7 smit:SMT_1637|5end_hypothetical_protein_1623091..1623321_POSITIVE 262 120 71 67 17 smit:SMT_1634|5end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1621074..1621304_POSITIVE 262 50 4 155 109 smit:SMT_1537|5end_hypothetical_protein_1522668..1522898_NEGATIVE 259 50 5 75 28 smit:SMT_1043|5end_chaperonin_GroEL_985766..985996_NEGATIVE 255 140 96 162 117 smit:SMT_1176|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1128993..1129223_NEGATIVE 254 108 63 227 164 smit:SMT_1358|5end_dihydroorotate_dehydrogenase_B_1337192..1337422_NEGATIVE 253 139 94 182 131 smit:SMT_789|5end_hypothetical_protein_701072..701302_NEGATIVE 252 119 71 214 165 smit:SMT_630|5end_phosphoserine_phosphatase_535459..535689_POSITIVE 251 116 71 60 27 smit:SMT_1139|5end_rRNA_(guanine-N1-)-methyltransferase_1079755..1079985_POSITIVE 249 110 63 44 6 smit:SMT_1730|5end_geranyltranstransferase_1714775..1715005_POSITIVE 246 50 3 137 98 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 245 118 72 228 185 smit:SMT_1477|5end_K02077_zinc/manganese_transport_system_substrate-binding_protein_1460376..1460606_NEGATIVE 244 138 98 56 15 smit:SMT_625|5end_50S_ribosomal_protein_L27_530027..530257_POSITIVE 243 99 51 48 4 smit:SMT_762|5end_cation-transporting_ATPase,_E1-E2_family_protein_667691..667921_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 410 190 166 43 19 smit:SMT_2045|3end_K+_transport_system,_NAD-binding_component_1956758..1956908_POSITIVE 410 190 166 111 87 smit:SMT_2044|3end_transcriptional_activator_TipA,_putative_1955274..1955424_NEGATIVE 410 190 166 111 87 smit:SMT_2026|3end_K03466_DNA_segregation_ATPase_FtsK/SpoIIIE,_S-DNA-T_family_1941905..1942055_NEGATIVE 410 190 166 111 87 smit:SMT_2016|3end_tyrosine_recombinase_1933021..1933171_NEGATIVE 410 190 166 111 87 smit:SMT_2006|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1926803..1926953_POSITIVE 410 190 166 121 97 smit:SMT_2001|3end_membrane_protease_protein_family_1923889..1924039_POSITIVE 410 190 166 121 97 smit:SMT_1985|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1914407..1914557_NEGATIVE 410 190 166 111 87 smit:SMT_1957|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1890829..1890979_POSITIVE 410 190 166 69 45 smit:SMT_1955|3end_carbamoyl-phosphate_synthase_small_chain_1888992..1889142_NEGATIVE 410 190 166 111 87 smit:SMT_1886|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1841198..1841348_POSITIVE 410 190 166 111 87 smit:SMT_1658|3end_hypothetical_protein_1648937..1649087_POSITIVE 410 190 166 67 43 smit:SMT_1631|3end_phosphopantothenoylcysteine_synthase/decarboxylase_1618204..1618354_NEGATIVE 410 190 166 111 87 smit:SMT_1558|3end_hypothetical_protein_1543855..1544005_NEGATIVE 410 190 166 121 97 smit:SMT_1464|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_1445361..1445511_POSITIVE 410 190 166 111 87 smit:SMT_1155|3end_ABC-type_oligopeptide_transport_system,_periplasmic_component_1099183..1099333_NEGATIVE 410 190 166 26 2 smit:SMT_957|3end_UDP-glucose_4-epimerase_904776..904926_NEGATIVE 410 190 166 111 87 smit:SMT_956|3end_hypothetical_protein_predicted_by_Glimmer/Critica_904691..904841_NEGATIVE 410 190 166 121 97 smit:SMT_542|3end_hypothetical_protein_458400..458550_POSITIVE 264 129 81 72 18 smit:SMT_1115|3end_K02245_competence_protein_ComGC_1052473..1052623_NEGATIVE 263 137 98 82 23 smit:SMT_1636|3end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1623187..1623337_POSITIVE