Origin IGS: gaagatgttagaaggcagtagtttgagactgccttttaataaggatttgagaatgtaagcagtttccaactagttgaaaaagcgttataatggtaataggaagtaatttgtttgagagagggtgagtctg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cagactcaccctctctcaaacaaattacttcctattaccattataacgctttttcaactagttggaaactgcttacattctcaaatccttattaaaaggcagtctcaaactactgccttctaacatcttc Mask Tandem Repeat Region ================================================ gaagatgttagaaggcagtagtttgagactgccttttaataaggatttgagaatgtaagcagtttccaactagttgaaaaagcgttataatggtaataggaagtaatttgtttgagagagggtgagtctg Find is-nt database================================================ Query_seq: SMT_1473:SMT_1474|SMT_1473:SMT_1474:hypothetical protein:K02003:->->:1455180..1455309 130 gaagatgttagaaggcagtagtttgagactgccttttaataaggatttgagaatgtaagcagtttccaactagttgaaaaagcgttataatggtaataggaagtaatttgtttgagagagggtgagtctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1473:SMT_1474|SMT_1473:SMT_1474:hypothetical protein:K02003:->->:1455180..1455309 130 gaagatgttagaaggcagtagtttgagactgccttttaataaggatttgagaatgtaagcagtttccaactagttgaaaaagcgttataatggtaataggaagtaatttgtttgagagagggtgagtctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1473:SMT_1474|SMT_1473:SMT_1474:hypothetical protein:K02003:->->:1455180..1455309 130 gaagatgttagaaggcagtagtttgagactgccttttaataaggatttgagaatgtaagcagtttccaactagttgaaaaagcgttataatggtaataggaagtaatttgtttgagagagggtgagtctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaagatgttagaaggcagtagtttgagactgccttttaataaggatttgagaatgtaagcagtttccaactagttgaaaaagcgttataatggtaataggaagtaatttgtttgagagagggtgagtctg Predict ORF larger than 30AA ================================================ gaagatgttagaaggcagtagtttgagactgccttttaataaggatttgagaatgtaagcagtttccaactagttgaaaaagcgttataatggtaataggaagtaatttgtttgagagagggtgagtctg 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: 88 Start: 62 End: 91 .............................................................GTTTCCAACTAGTTGAAAAAGCGTTATAAT....................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaagatgttagaaggcagtagtttgagactgccttttaataaggatttgagaatgtaagcagtttccaactagttgaaaaagcgttataatggtaataggaagtaatttgtttgagagagggtgagtctg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1473:SMT_1474|SMT_1473:SMT_1474:hypothetical protein:K02003:->->:1455180..1455309 130 gaagatgttagaaggcagtagtttgagactgccttttaataaggatttgagaatgtaagcagtttccaactagttgaaaaagcgttataatggtaataggaagtaatttgtttgagagagggtgagtctg Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: smit_SMT_1473_SMT_1474|hypothetical protein:K02003|POSITIVE:POSITIVE|[1455180,1455309]|130 HSP 1 e-value: 4.0E-68 bit: 258.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 gaagatgttagaaggcagtagtttgagactgccttttaataaggatttgagaatgtaagcagtttccaactagttgaaaaagcgttataatggtaataggaagtaatttgtttgagagagggtgagtctg gaagatgttagaaggcagtagtttgagactgccttttaataaggatttgagaatgtaagcagtttccaactagttgaaaaagcgttataatggtaataggaagtaatttgtttgagagagggtgagtctg Inter-species Hit: Count: 3 Min: 1 Max: 107 Len: 107 Subject: NC_008533_SPD_1466_SPD_1467|ABC transporter, ATP-binding protein:hypothetical protein|NEGATIVE:NEGATIVE|[1483268,1483516]|249 HSP 1 e-value: 1.0E-37 bit: 157.0 Len: 107 Query Start:1 Query End:107 Subject Strand: NEGATIVE Subject Start: 143 Subject End: 249 gaagatgttagaaggcagtagtttgagactgccttttaataaggatttgagaatgtaagcagtttccaactagttgaaaaagcgttataatggtaataggaagtaat....................... gaagatgttataaggcagtaatttgaaacttccttttaataaggatttgagaatataggcagtttccaactagttgaaaaagcgttataatgataataggaagtaat....................... Subject: NC_003098_spr1497_spr1498|ABC transporter ATP-binding protein - unknown substrate:hypothetical protein|NEGATIVE:NEGATIVE|[1475746,1475985]|240 HSP 1 e-value: 1.0E-37 bit: 157.0 Len: 107 Query Start:1 Query End:107 Subject Strand: NEGATIVE Subject Start: 134 Subject End: 240 gaagatgttagaaggcagtagtttgagactgccttttaataaggatttgagaatgtaagcagtttccaactagttgaaaaagcgttataatggtaataggaagtaat....................... gaagatgttataaggcagtaatttgaaacttccttttaataaggatttgagaatataggcagtttccaactagttgaaaaagcgttataatgataataggaagtaat....................... Subject: NC_003028_SP_1653_SP_1654|ABC transporter, ATP-binding protein:hypothetical protein|NEGATIVE:NEGATIVE|[1554517,1554765]|249 HSP 1 e-value: 3.0E-35 bit: 149.0 Len: 107 Query Start:1 Query End:107 Subject Strand: NEGATIVE Subject Start: 143 Subject End: 249 gaagatgttagaaggcagtagtttgagactgccttttaataaggatttgagaatgtaagcagtttccaactagttgaaaaagcgttataatggtaataggaagtaat....................... gaagatgttataaggcagtaatttgaaactgccttttaataaggatttaagaatataagcagttttcaactagttgaaaaaacgttataatgataataggaagtaat....................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGAUGUUAGAAGGCAGUAGUUUGAGACUGCCUUUUAAUAAGGAUUUGAGAAUGUAAGCAGUUUCCAACUAGUUGAAAAAGCGUUAUAAUGGUAAUAGGAAGUAAU .....((((((((((((((........))))))))))))))............(((((((..((((.((....))))))..)).))))).................. (-23.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUACUUCCUAUUACCAUUAUAACGCUUUUUCAACUAGUUGGAAACUGCUUACAUUCUCAAAUCCUUAUUAAAAGGCAGUCUCAAACUACUGCCUUCUAACAUCUUC ........................((.(((((((....)))))))..))...................(((.((((((((........)))))))).)))....... (-17.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 69 21 91 45 smit:SMT_387|5end_hypothetical_protein_predicted_by_Glimmer/Critica_320937..321167_POSITIVE 239 93 53 84 47 smit:SMT_679|5end_LicC_protein_589072..589302_NEGATIVE 238 83 45 214 173 smit:SMT_1566|5end_K03475_PTS_system,_unknown_pentitol_phosphotransferase_enzyme_IIC_component_1557918..1558148_POSITIVE 232 50 1 136 80 smit:SMT_472|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_409494..409724_NEGATIVE 232 50 1 136 80 smit:SMT_469|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_405812..406042_NEGATIVE 231 55 13 229 165 smit:SMT_900|5end_5-methyltetrahydropteroyltriglutamate--_homocysteine_methyltransferase_850616..850846_NEGATIVE 231 76 32 65 23 smit:SMT_663|5end_phosphate_acetyltransferase_574990..575220_NEGATIVE 230 67 25 101 58 smit:SMT_1376|5end_tetrapyrrole_(corrin/porphyrin)_methylase_family_protein_1355553..1355783_NEGATIVE 229 60 29 181 152 smit:SMT_430|5end_hypothetical_protein_371830..372060_POSITIVE 227 72 32 107 59 smit:SMT_597|5end_K08974_putative_membrane_protein_513917..514147_NEGATIVE 225 60 14 70 19 smit:SMT_1024|5end_transcriptional_regulator,_MarR_family_959404..959634_NEGATIVE 225 60 15 213 181 smit:SMT_519|5end_glutathione_reductase_444884..445114_NEGATIVE 220 48 12 227 176 smit:SMT_2021|5end_K06201_copper_homeostasis_protein_1937888..1938118_POSITIVE 219 49 1 79 38 smit:SMT_330|5end_membrane-associated_phospholipid_phosphatase_265793..266023_POSITIVE 215 85 42 41 2 smit:SMT_595|5end_phosphoglycerate_mutase_512593..512823_NEGATIVE 215 32 8 168 146 smit:SMT_452|5end_phosphomethylpyrimidine_kinase_390568..390798_NEGATIVE 213 49 12 222 171 smit:SMT_1937|5end_glycosyl_transferase,_family_2_1874428..1874658_POSITIVE 211 38 3 228 189 smit:SMT_1221|5end_choline_binding_protein_A_1185539..1185769_NEGATIVE 210 100 54 56 10 smit:SMT_1672|5end_hypothetical_protein_1660051..1660281_NEGATIVE 210 100 54 62 16 smit:SMT_1061|5end_hypothetical_protein_999497..999727_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 41 6 85 50 smit:SMT_1473|3end_hypothetical_protein_1455119..1455269_POSITIVE 265 69 21 76 30 smit:SMT_386|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_321002..321152_POSITIVE 239 93 53 72 35 smit:SMT_680|3end_choline_transport_protein_589084..589234_NEGATIVE 230 67 25 98 55 smit:SMT_1377|3end_hypothetical_protein_1355556..1355706_NEGATIVE 219 49 1 89 48 smit:SMT_329|3end_hypothetical_protein_265883..266033_POSITIVE 217 45 7 63 8 smit:SMT_998|3end_peptide_chain_release_factor_3_939699..939849_NEGATIVE 216 34 10 83 58 smit:SMT_1524|3end_peptidase_T_1505867..1506017_POSITIVE 215 85 42 44 5 smit:SMT_596|3end_K03976_putative_transcription_regulator_512590..512740_NEGATIVE 214 47 1 86 44 smit:SMT_948|3end_hypothetical_protein_predicted_by_Glimmer/Critica_896655..896805_NEGATIVE 211 38 3 84 45 smit:SMT_1222|3end_pneumococcal_surface_protein_A_1185683..1185833_NEGATIVE 211 45 14 48 13 smit:SMT_495|3end_bacterial_peptide_chain_release_factor_2_(RF-2)_430053..430203_POSITIVE 206 84 43 58 3 smit:SMT_1866|3end_extramembranal_protein_1827939..1828089_POSITIVE 206 70 30 80 39 smit:SMT_1780|3end_PTS_system,_glucose-specific_IIABC_component_1755960..1756110_NEGATIVE 205 32 6 49 16 smit:SMT_891|3end_oxidoreductase,_putative_839132..839282_POSITIVE 205 60 13 64 28 smit:SMT_842|3end_hypothetical_protein_788414..788564_NEGATIVE 204 50 1 98 53 smit:SMT_716|3end_50S_ribosomal_protein_L31_622732..622882_POSITIVE 203 95 54 127 73 smit:SMT_1398|3end_dihydroorotase_1374552..1374702_POSITIVE 199 37 1 106 53 smit:SMT_1618|3end_K02015_iron_complex_transport_system_permease_protein_1604490..1604640_NEGATIVE 199 99 63 64 31 smit:SMT_1059|3end_NAD(P)H-flavin_oxidoreductase_998172..998322_POSITIVE 199 60 15 140 105 smit:SMT_900|3end_5-methyltetrahydropteroyltriglutamate--_homocysteine_methyltransferase_848367..848517_NEGATIVE