Origin IGS: gggaaaaccctcccctattaaatggttaaatttatctagattatatctttttcctataataaatgcaataaaaaacataaaaagtgtagaaatatttaaatgtaaaaaaagagagcagttctaaaactactctcttagtcttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagactaagagagtagttttagaactgctctctttttttacatttaaatatttctacactttttatgttttttattgcatttattataggaaaaagatataatctagataaatttaaccatttaataggggagggttttccc Mask Tandem Repeat Region ================================================ gggaaaaccctcccctattaaatggttaaatttatctagattatatctttttcctataataaatgcaataaaaaacataaaaagtgtagaaatatttaaatgtaaaaaaagagagcagttctaaaactactctcttagtcttt Find is-nt database================================================ Query_seq: SMT_1221:SMT_1222|SMT_1221:SMT_1222:choline binding protein A:pneumococcal surface protein A:<-<-:1185630..1185772 143 gggaaaaccctcccctattaaatggttaaatttatctagattatatctttttcctataataaatgcaataaaaaacataaaaagtgtagaaatatttaaatgtaaaaaaagagagcagttctaaaactactctcttagtcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1221:SMT_1222|SMT_1221:SMT_1222:choline binding protein A:pneumococcal surface protein A:<-<-:1185630..1185772 143 gggaaaaccctcccctattaaatggttaaatttatctagattatatctttttcctataataaatgcaataaaaaacataaaaagtgtagaaatatttaaatgtaaaaaaagagagcagttctaaaactactctcttagtcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1221:SMT_1222|SMT_1221:SMT_1222:choline binding protein A:pneumococcal surface protein A:<-<-:1185630..1185772 143 gggaaaaccctcccctattaaatggttaaatttatctagattatatctttttcctataataaatgcaataaaaaacataaaaagtgtagaaatatttaaatgtaaaaaaagagagcagttctaaaactactctcttagtcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gggaaaaccctcccctattaaatggttaaatttatctagattatatctttttcctataataaatgcaataaaaaacataaaaagtgtagaaatatttaaatgtaaaaaaagagagcagttctaaaactactctcttagtcttt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 17 End: 121 ................ M K W L N L S R L Y L F P I I N A I K N I K S V E I F K C K K R E Q F ...................... Protein_Len: 31 Strand: - Start: 1 End: 93 P F G E G I L H N F K D L N Y R K G I I F A I F F M F L T S M .................................................. gggaaaaccctcccctattaaatggttaaatttatctagattatatctttttcctataataaatgcaataaaaaacataaaaagtgtagaaatatttaaatgtaaaaaaagagagcagttctaaaactactctcttagtcttt 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: 82 Start: 40 End: 69 .......................................ATTGCATTTATTATAGGAAAAAGATATAAT.......................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 31 End: 60 ..............................TTTATCTAGATTATATCTTTTTCCTATAAT................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gggaaaaccctcccctattaaatggttaaatttatctagattatatctttttcctataataaatgcaataaaaaacataaaaagtgtagaaatatttaaatgtaaaaaaagagagcagttctaaaactactctcttagtcttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1221:SMT_1222|SMT_1221:SMT_1222:choline binding protein A:pneumococcal surface protein A:<-<-:1185630..1185772 143 gggaaaaccctcccctattaaatggttaaatttatctagattatatctttttcctataataaatgcaataaaaaacataaaaagtgtagaaatatttaaatgtaaaaaaagagagcagttctaaaactactctcttagtcttt Intra-Species Hit: Count: 1 Min: 1 Max: 143 Len: 143 Subject: smit_SMT_1221_SMT_1222|choline binding protein A:pneumococcal surface protein A|NEGATIVE:NEGATIVE|[1185630,1185772]|143 HSP 1 e-value: 2.0E-23 bit: 109.0 Len: 55 Query Start:1 Query End:55 Subject Strand: POSITIVE Subject Start: 1 Subject End: 55 gggaaaaccctcccctattaaatggttaaatttatctagattatatctttttcct........................................................................................ gggaaaaccctcccctattaaatggttaaatttatctagattatatctttttcct........................................................................................ HSP 2 e-value: 3.0E-10 bit: 65.9 Len: 33 Query Start:111 Query End:143 Subject Strand: POSITIVE Subject Start: 111 Subject End: 143 ..............................................................................................................gagagcagttctaaaactactctcttagtcttt ..............................................................................................................gagagcagttctaaaactactctcttagtcttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGAAAACCCUCCCCUAUUAAAUGGUUAAAUUUAUCUAGAUUAUAUCUUUUUCCUAUAAUAAAUGCAAUAAAAAACAUAAAAAGUGUAGAAAUAUUUAAAUGUAAAAAAAGAGAGCAGUUCUAAAACUACUCUCUUAGUCUUU ((((......)))).(((((...((..(((..(((.......)))..)))..))..))))).............((((...((((((....))))))..)))).....(((((((.((((....)))).)))))))....... (-21.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGACUAAGAGAGUAGUUUUAGAACUGCUCUCUUUUUUUACAUUUAAAUAUUUCUACACUUUUUAUGUUUUUUAUUGCAUUUAUUAUAGGAAAAAGAUAUAAUCUAGAUAAAUUUAACCAUUUAAUAGGGGAGGGUUUUCCC ..(((..((((((((((((....))))))))))))..)))....((((((...((((......(((((((((((..................)))))))))))..))))...))))))...........(((((....))))) (-27.47) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 760 50 1 141 92 smit:SMT_1221|5end_choline_binding_protein_A_1185539..1185769_NEGATIVE 245 42 1 221 172 smit:SMT_1530|5end_K07456_DNA_mismatch_repair_protein_MutS2_1515346..1515576_NEGATIVE 212 138 95 208 170 smit:SMT_1091|5end_competence-specific_global_transcription_modulator_1033040..1033270_NEGATIVE 207 41 1 178 134 smit:SMT_1667|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1657567..1657797_NEGATIVE 200 138 101 209 178 smit:SMT_102|5end_competence-specific_global_transcription_modulator_34108..34338_POSITIVE 195 59 13 106 65 smit:SMT_607|5end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_520119..520349_POSITIVE 192 42 1 166 114 smit:SMT_1634|5end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1621074..1621304_POSITIVE 189 48 1 194 134 smit:SMT_189|5end_50S_ribosomal_protein_L15_123832..124062_POSITIVE 186 67 21 116 71 smit:SMT_1314|5end_dTDP-4-dehydrorhamnose_3,5-epimerase_related_enzyme_1278760..1278990_POSITIVE 184 135 108 168 135 smit:SMT_1117|5end_competence_protein_CglA_1054703..1054933_NEGATIVE 183 55 13 117 79 smit:SMT_1682|5end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_1665337..1665567_POSITIVE 180 135 106 221 190 smit:SMT_1063|5end_preprotein_translocase_SecA_subunit_1000714..1000944_POSITIVE 179 38 12 60 30 smit:SMT_270|5end_ATP-binding_subunit_of_Clp_protease_and_DnaK/DnaJ_chaperones_209040..209270_POSITIVE 177 139 101 144 104 smit:SMT_1352|5end_formamidopyrimidine-DNA_glycosylase_1330641..1330871_NEGATIVE 176 56 36 182 160 smit:SMT_1505|5end_purine-nucleoside_phosphorylase_1488515..1488745_NEGATIVE 173 89 41 165 118 smit:SMT_237|5end_aminopeptidase_C_175226..175456_POSITIVE 168 49 2 108 51 smit:SMT_1969|5end_transcription-repair_coupling_factor_1901691..1901921_NEGATIVE 168 67 35 71 44 smit:SMT_1188|5end_hypothetical_protein_1146653..1146883_NEGATIVE 167 66 21 115 63 smit:SMT_1550|5end_hypothetical_protein_1534326..1534556_POSITIVE 167 139 107 224 192 smit:SMT_396|5end_putative_nicotinate_phosphoribosyltransferase_325062..325292_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 245 42 1 118 69 smit:SMT_1531|3end_hypothetical_protein_1515449..1515599_NEGATIVE 238 56 11 45 3 smit:SMT_1360|3end_lactoylglutathione_lyase_1338252..1338402_NEGATIVE 219 140 98 105 67 smit:SMT_568|3end_hypothetical_protein_486389..486539_POSITIVE 212 138 95 88 50 smit:SMT_1092|3end_transcription_antitermination_factor_1033160..1033310_NEGATIVE 207 41 1 122 78 smit:SMT_2045|3end_K+_transport_system,_NAD-binding_component_1956758..1956908_POSITIVE 207 41 1 122 78 smit:SMT_1668|3end_K+_transport_system,_NAD-binding_component_1657623..1657773_NEGATIVE 207 137 107 93 67 smit:SMT_1380|3end_pyrroline-5-carboxylate_reductase_1357667..1357817_NEGATIVE 205 60 12 110 73 smit:SMT_278|3end_tyrosine-protein_kinase_221048..221198_POSITIVE 200 138 101 88 57 smit:SMT_101|3end_cell_division_protein_34067..34217_POSITIVE 195 59 13 54 13 smit:SMT_606|3end_cytochrome_c-type_biogenesis_protein_CcdA_520147..520297_POSITIVE 191 138 113 150 117 smit:SMT_1561|3end_putative_mucus_binding_protein_1548746..1548896_NEGATIVE 188 136 107 70 36 smit:SMT_1369|3end_alanine_dehydrogenase_1349472..1349622_POSITIVE 184 132 112 96 76 smit:SMT_1230|3end_hypothetical_protein_1192342..1192492_POSITIVE 184 135 108 92 59 smit:SMT_1118|3end_hypothetical_protein_1054779..1054929_NEGATIVE 180 135 106 75 44 smit:SMT_1062|3end_hypothetical_protein_1000648..1000798_POSITIVE 178 49 2 134 89 smit:SMT_1255|3end_cell_division_protein_FtsH_1220987..1221137_NEGATIVE 178 137 106 33 4 smit:SMT_540|3end_DNA_gyrase,_B_subunit_457157..457307_POSITIVE 177 139 101 95 55 smit:SMT_1353|3end_GTP-binding_protein_1330690..1330840_NEGATIVE 174 42 1 108 75 smit:SMT_364|3end_ribosome-binding_factor_A_301353..301503_POSITIVE 173 89 41 70 23 smit:SMT_236|3end_ribosomal_small_subunit_pseudouridine_synthase_A_175211..175361_POSITIVE