Origin IGS: agcagctactttagcacctgctacagggttcccttggatatctttaacatgtacacgaacatgagtaccatttccaaatacatctggtaaaactttaccatctttaccgatacgatttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaaatcgtatcggtaaagatggtaaagttttaccagatgtatttggaaatggtactcatgttcgtgtacatgttaaagatatccaagggaaccctgtagcaggtgctaaagtagctgct Mask Tandem Repeat Region ================================================ agcagctactttagcacctgctacagggttcccttggatatctttaacatgtacacgaacatgagtaccatttccaaatacatctggtaaaactttaccatctttaccgatacgatttc Find is-nt database================================================ Query_seq: SMT_1223:SMT_1224|SMT_1223:SMT_1224:pneumococcal surface protein A:hypothetical protein predicted by Glimmer/Critica:<-<-:1187871..1187989 119 agcagctactttagcacctgctacagggttcccttggatatctttaacatgtacacgaacatgagtaccatttccaaatacatctggtaaaactttaccatctttaccgatacgatttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1223:SMT_1224|SMT_1223:SMT_1224:pneumococcal surface protein A:hypothetical protein predicted by Glimmer/Critica:<-<-:1187871..1187989 119 agcagctactttagcacctgctacagggttcccttggatatctttaacatgtacacgaacatgagtaccatttccaaatacatctggtaaaactttaccatctttaccgatacgatttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1223:SMT_1224|SMT_1223:SMT_1224:pneumococcal surface protein A:hypothetical protein predicted by Glimmer/Critica:<-<-:1187871..1187989 119 agcagctactttagcacctgctacagggttcccttggatatctttaacatgtacacgaacatgagtaccatttccaaatacatctggtaaaactttaccatctttaccgatacgatttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcagctactttagcacctgctacagggttcccttggatatctttaacatgtacacgaacatgagtaccatttccaaatacatctggtaaaactttaccatctttaccgatacgatttc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 24 End: 116 ....................... L T G K S I K L M Y V F M L V M E L Y M Q Y F K V M K V S V M ... Protein_Len: 37 Strand: - Start: 1 End: 111 A A V K A G A V P N G Q I D K V H V R V H T G N G F V D P L V K G D K G M ........ agcagctactttagcacctgctacagggttcccttggatatctttaacatgtacacgaacatgagtaccatttccaaatacatctggtaaaactttaccatctttaccgatacgatttc 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================================================ agcagctactttagcacctgctacagggttcccttggatatctttaacatgtacacgaacatgagtaccatttccaaatacatctggtaaaactttaccatctttaccgatacgatttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1223:SMT_1224|SMT_1223:SMT_1224:pneumococcal surface protein A:hypothetical protein predicted by Glimmer/Critica:<-<-:1187871..1187989 119 agcagctactttagcacctgctacagggttcccttggatatctttaacatgtacacgaacatgagtaccatttccaaatacatctggtaaaactttaccatctttaccgatacgatttc Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: smit_SMT_1223_SMT_1224|pneumococcal surface protein A:hypothetical protein predicted by Glimmer/Critica|NEGATIVE:NEGATIVE|[1187871,1187989]|119 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 agcagctactttagcacctgctacagggttcccttggatatctttaacatgtacacgaacatgagtaccatttccaaatacatctggtaaaactttaccatctttaccgatacgatttc agcagctactttagcacctgctacagggttcccttggatatctttaacatgtacacgaacatgagtaccatttccaaatacatctggtaaaactttaccatctttaccgatacgatttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCAGCUACUUUAGCACCUGCUACAGGGUUCCCUUGGAUAUCUUUAACAUGUACACGAACAUGAGUACCAUUUCCAAAUACAUCUGGUAAAACUUUACCAUCUUUACCGAUACGAUUUC ((((((((...))))...))))....(((....(((((.........(((((......))))).........))))).......((((((....)))))).....)))........... (-20.37) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAUCGUAUCGGUAAAGAUGGUAAAGUUUUACCAGAUGUAUUUGGAAAUGGUACUCAUGUUCGUGUACAUGUUAAAGAUAUCCAAGGGAACCCUGUAGCAGGUGCUAAAGUAGCUGCU ......(((((..(((...((((((....)))))).((((((.((((.(((.....))).)))).)))))).)))..)))))...(((....)))..(((((.(((....))).))))) (-30.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 939 50 1 141 92 smit:SMT_1223|5end_pneumococcal_surface_protein_A_1187780..1188010_NEGATIVE 317 50 3 75 31 smit:SMT_392|5end_acetyltransferase,_GNAT_family_323616..323846_POSITIVE 291 49 5 159 115 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 290 37 1 66 19 smit:SMT_452|5end_phosphomethylpyrimidine_kinase_390568..390798_NEGATIVE 284 45 1 162 116 smit:SMT_380|5end_hypothetical_protein_316376..316606_POSITIVE 284 45 1 162 116 smit:SMT_371|5end_hypothetical_protein_305248..305478_POSITIVE 283 43 14 126 94 smit:SMT_593|5end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_509398..509628_POSITIVE 283 55 11 221 162 smit:SMT_171|5end_50S_ribosomal_protein_L4_115557..115787_POSITIVE 275 75 34 220 176 smit:SMT_1342|5end_protease_maturation_protein,_putative_1320214..1320444_NEGATIVE 273 43 1 68 30 smit:SMT_567|5end_conserved_hypothetical_protein_484845..485075_POSITIVE 264 47 13 214 184 smit:SMT_1264|5end_oligoendopeptidase_F_1228858..1229088_POSITIVE 264 49 5 65 15 smit:SMT_412|5end_hypothetical_protein_predicted_by_Glimmer/Critica_356606..356836_NEGATIVE 263 40 3 227 193 smit:SMT_794|5end_hypothetical_protein_703487..703717_NEGATIVE 261 46 1 104 53 smit:SMT_1510|5end_ribose_5-phosphate_isomerase_1493488..1493718_NEGATIVE 256 69 23 74 11 smit:SMT_653|5end_positive_transcriptional_regulator_MutR_family_564155..564385_NEGATIVE 255 38 1 172 114 smit:SMT_1966|5end_DNA_polymerase_III_alpha_subunit_1897934..1898164_POSITIVE 252 46 1 96 32 smit:SMT_2119|5end_mercuric_reductase_2005583..2005813_POSITIVE 250 27 5 172 147 smit:SMT_1201|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1163920..1164150_NEGATIVE 250 32 1 174 135 smit:SMT_434|5end_orotidine_5'-phosphate_decarboxylase_376107..376337_POSITIVE 249 44 5 109 62 smit:SMT_1673|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1659831..1660061_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 50 3 50 6 smit:SMT_391|3end_PTS_system,_galactose-specific_IIC_component_323671..323821_POSITIVE 283 43 14 116 84 smit:SMT_592|3end_amino_acid_ABC_transporter,_ATP-binding_protein_509468..509618_POSITIVE 273 43 1 46 8 smit:SMT_566|3end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_484903..485053_POSITIVE 271 43 2 87 27 smit:SMT_2024|3end_hypothetical_protein_1940690..1940840_POSITIVE 271 43 2 76 16 smit:SMT_2002|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1924145..1924295_NEGATIVE 271 43 2 87 27 smit:SMT_1981|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912868..1913018_POSITIVE 271 43 2 92 32 smit:SMT_1971|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1903526..1903676_POSITIVE 271 43 2 76 16 smit:SMT_1966|3end_DNA_polymerase_III_alpha_subunit_1898328..1898478_POSITIVE 271 43 2 87 27 smit:SMT_1942|3end_zinc_metalloprotease_ZmpB,_truncated_1878384..1878534_POSITIVE 271 43 2 76 16 smit:SMT_1927|3end_cell_division_protein_FtsH_1868408..1868558_NEGATIVE 271 43 2 87 27 smit:SMT_1926|3end_mevalonate_kinase_1868062..1868212_POSITIVE 271 43 2 87 27 smit:SMT_1887|3end_LicC_protein_1841740..1841890_POSITIVE 271 43 2 76 16 smit:SMT_1885|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1839830..1839980_NEGATIVE 271 43 2 76 16 smit:SMT_1873|3end_K02006_cobalt_transport_system_ATP-binding_protein_1832351..1832501_POSITIVE 271 43 2 92 32 smit:SMT_1852|3end_1,4-alpha-glucan_branching_enzyme_1816467..1816617_NEGATIVE 271 43 2 92 32 smit:SMT_326|3end_K02029_polar_amino_acid_transport_system_permease_protein_263217..263367_NEGATIVE 266 69 24 147 102 smit:SMT_1928|3end_O-methyltransferase_family_protein_1869158..1869308_NEGATIVE 266 69 24 147 102 smit:SMT_1343|3end_O-methyltransferase_1320281..1320431_NEGATIVE 261 21 2 101 76 smit:SMT_1665|3end_cell_wall_surface_anchor_family_protein_1656021..1656171_NEGATIVE 256 69 23 72 9 smit:SMT_654|3end_K06158_ATP-binding_cassette,_sub-family_F,_member_3_564157..564307_NEGATIVE