Origin IGS: ggcaaaatgtccattactttcmagaatgatcgcatcactgccmmcttcctgaacattataaagtggattttatttccctgactttcttgagcttgaacattcccatgaaatgacaagcataaaaaagcnnnnnttaattaattaannnnntgctggaaggctggtcagcgctagtcttctcactcttagacaggctatcggaattatc .........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 gataattccgatagcctgtctaagagtgagaagactagcgctgaccagccttccagcannnnnttaattaattaannnnngcttttttatgcttgtcatttcatgggaatgttcaagctcaagaaagtcagggaaataaaatccactttataatgttcaggaagkkggcagtgatgcgatcattctkgaaagtaatggacattttgcc Mask Tandem Repeat Region ================================================ ggcaaaatgtccattactttcmagaatgatcgcatcactgccmmcttcctgaacattataaagtggattttatttccctgactttcttgagcttgaacattcccatgaaatgacaagcataaaaaagcnnnnnttaattaattaannnnntgctggaaggctggtcagcgctagtcttctcactcttagacaggctatcggaattatc Find is-nt database================================================ Query_seq: SMT_1741:SMT_1742|SMT_1741:SMT_1742:surface protein PspA precursor:sodium-dependent phosphate transporter:<-->:1723485..1723692 208 ggcaaaatgtccattactttcmagaatgatcgcatcactgccmmcttcctgaacattataaagtggattttatttccctgactttcttgagcttgaacattcccatgaaatgacaagcataaaaaagcnnnnnttaattaattaannnnntgctggaaggctggtcagcgctagtcttctcactcttagacaggctatcggaattatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1741:SMT_1742|SMT_1741:SMT_1742:surface protein PspA precursor:sodium-dependent phosphate transporter:<-->:1723485..1723692 208 ggcaaaatgtccattactttcmagaatgatcgcatcactgccmmcttcctgaacattataaagtggattttatttccctgactttcttgagcttgaacattcccatgaaatgacaagcataaaaaagcnnnnnttaattaattaannnnntgctggaaggctggtcagcgctagtcttctcactcttagacaggctatcggaattatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1741:SMT_1742|SMT_1741:SMT_1742:surface protein PspA precursor:sodium-dependent phosphate transporter:<-->:1723485..1723692 208 ggcaaaatgtccattactttcmagaatgatcgcatcactgccmmcttcctgaacattataaagtggattttatttccctgactttcttgagcttgaacattcccatgaaatgacaagcataaaaaagcnnnnnttaattaattaannnnntgctggaaggctggtcagcgctagtcttctcactcttagacaggctatcggaattatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggcaaaatgtccattactttcmagaatgatcgcatcactgccmmcttcctgaacattataaagtggattttatttccctgactttcttgagcttgaacattcccatgaaatgacaagcataaaaaagcnnnnnttaattaattaannnnntgctggaaggctggtcagcgctagtcttctcactcttagacaggctatcggaattatc Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 3 End: 116 .. L I D M V K X F S R M V A X K R F M I F H I K N G Q S E Q A Q V N G H F S M ............................................................................................ ggcaaaatgtccattactttcmagaatgatcgcatcactgccmmcttcctgaacattataaagtggattttatttccctgactttcttgagcttgaacattcccatgaaatgacaagcataaaaaagcnnnnnttaattaattaannnnntgctggaaggctggtcagcgctagtcttctcactcttagacaggctatcggaattatc 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================================================ ggcaaaatgtccattactttcmagaatgatcgcatcactgccmmcttcctgaacattataaagtggattttatttccctgactttcttgagcttgaacattcccatgaaatgacaagcataaaaaagcnnnnnttaattaattaannnnntgctggaaggctggtcagcgctagtcttctcactcttagacaggctatcggaattatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1741:SMT_1742|SMT_1741:SMT_1742:surface protein PspA precursor:sodium-dependent phosphate transporter:<-->:1723485..1723692 208 ggcaaaatgtccattactttcmagaatgatcgcatcactgccmmcttcctgaacattataaagtggattttatttccctgactttcttgagcttgaacattcccatgaaatgacaagcataaaaaagcnnnnnttaattaattaannnnntgctggaaggctggtcagcgctagtcttctcactcttagacaggctatcggaattatc Intra-Species Hit: Count: 1 Min: 1 Max: 208 Len: 208 Subject: smit_SMT_1741_SMT_1742|surface protein PspA precursor:sodium-dependent phosphate transporter|NEGATIVE:POSITIVE|[1723485,1723692]|208 HSP 1 e-value: 5.0E-94 bit: 344.0 Len: 208 Query Start:1 Query End:208 Subject Strand: POSITIVE Subject Start: 1 Subject End: 208 ggcaaaatgtccattactttcmagaatgatcgcatcactgccmmcttcctgaacattataaagtggattttatttccctgactttcttgagcttgaacattcccatgaaatgacaagcataaaaaagcnnnnnttaattaattaannnnntgctggaaggctggtcagcgctagtcttctcactcttagacaggctatcggaattatc ggcaaaatgtccattactttcmagaatgatcgcatcactgccmmcttcctgaacattataaagtggattttatttccctgactttcttgagcttgaacattcccatgaaatgacaagcataaaaaagcnnnnnttaattaattaannnnntgctggaaggctggtcagcgctagtcttctcactcttagacaggctatcggaattatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCAAAAUGUCCAUUACUUUCMAGAAUGAUCGCAUCACUGCCMMCUUCCUGAACAUUAUAAAGUGGAUUUUAUUUCCCUGACUUUCUUGAGCUUGAACAUUCCCAUGAAAUGACAAGCAUAAAAAAGCNNNNNUUAAUUAAUUAANNNNNUGCUGGAAGGCUGGUCAGCGCUAGUCUUCUCACUCUUAGACAGGCUAUCGGAAUUAUC ((((..((((.((((.((....))))))...))))...))))...((((....((((....))))...........((((.((((.(((.(((((..((((.......)))).))))).))).))))...........................(((((((((((....)))))))))))..........)))).....))))..... (-37.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAAUUCCGAUAGCCUGUCUAAGAGUGAGAAGACUAGCGCUGACCAGCCUUCCAGCANNNNNUUAAUUAAUUAANNNNNGCUUUUUUAUGCUUGUCAUUUCAUGGGAAUGUUCAAGCUCAAGAAAGUCAGGGAAAUAAAAUCCACUUUAUAAUGUUCAGGAAGKKGGCAGUGAUGCGAUCAUUCUKGAAAGUAAUGGACAUUUUGCC .............((.(((((((((((((...(.(...(((((.((...(((((..........................((((((((..(((((.(((((.....)))))..)))))..))))))))...(((.......)))...............)))))..)))))))..))..))))))).........))))))....)). (-46.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 856 120 71 211 162 smit:SMT_1741|5end_surface_protein_PspA_precursor_1723394..1723624_NEGATIVE 357 200 154 200 153 smit:SMT_1626|5end_undecaprenyl-diphosphatase_1616028..1616258_NEGATIVE 336 194 151 228 178 smit:SMT_1416|5end_hypothetical_protein_1400829..1401059_NEGATIVE 323 200 153 200 131 smit:SMT_1168|5end_potassium_uptake_protein_KtrB_1116552..1116782_NEGATIVE 314 200 151 170 112 smit:SMT_1700|5end_diaminopimelate_decarboxylase_1682032..1682262_POSITIVE 314 195 152 128 69 smit:SMT_1664|5end_hypothetical_protein_1655890..1656120_NEGATIVE 305 197 152 229 188 smit:SMT_581|5end_ATP_synthase_A_chain_498402..498632_POSITIVE 303 199 153 191 147 smit:SMT_2051|5end_enoyl-CoA_hydratase_1960639..1960869_NEGATIVE 303 177 134 152 109 smit:SMT_1974|5end_high-affinity_zinc_uptake_system_protein_ZnuA_precursor_/_hypothetical_exported_protein_1905506..1905736_POSITIVE 302 197 159 57 20 smit:SMT_1634|5end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1621074..1621304_POSITIVE 291 199 151 120 49 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 291 188 151 227 185 smit:SMT_543|5end_topoisomerase_IV_subunit_B_458372..458602_POSITIVE 290 200 151 68 2 smit:SMT_1283|5end_K02240_competence_protein_ComFA_1245667..1245897_POSITIVE 290 196 154 204 169 smit:SMT_908|5end_hypothetical_protein_857230..857460_NEGATIVE 289 200 151 81 23 smit:SMT_2059|5end_hypothetical_protein_1967881..1968111_POSITIVE 289 200 151 81 23 smit:SMT_2056|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1966323..1966553_POSITIVE 289 200 151 81 23 smit:SMT_1892|5end_hypothetical_protein_1845595..1845825_POSITIVE 287 199 151 118 60 smit:SMT_1967|5end_dicarboxylate/amino_acid:cation_(Na+_or_H+)_symporter_(DAACS)_family_protein_1899683..1899913_NEGATIVE 287 176 134 178 136 smit:SMT_464|5end_ribonuclease_Z_402867..403097_POSITIVE 283 200 151 230 161 smit:SMT_1570|5end_hypothetical_protein_1563504..1563734_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 357 200 154 139 92 smit:SMT_1627|3end_hypothetical_protein_1616089..1616239_NEGATIVE 314 200 151 103 45 smit:SMT_1699|3end_purine_operon_repressor_1682045..1682195_POSITIVE 295 196 154 44 8 smit:SMT_1866|3end_extramembranal_protein_1827939..1828089_POSITIVE 291 174 151 144 116 smit:SMT_1981|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912868..1913018_POSITIVE 291 199 151 133 62 smit:SMT_1455|3end_deoxyribose-phosphate_aldolase_1437873..1438023_NEGATIVE 290 174 134 147 91 smit:SMT_1798|3end_exonuclease_RexA_1772818..1772968_NEGATIVE 287 176 134 70 28 smit:SMT_463|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_402839..402989_POSITIVE 284 180 134 148 91 smit:SMT_2017|3end_exonuclease_RexA_1935862..1936012_NEGATIVE 281 179 134 141 91 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 281 66 25 141 109 smit:SMT_1530|3end_K07456_DNA_mismatch_repair_protein_MutS2_1513010..1513160_NEGATIVE 274 190 151 145 105 smit:SMT_1885|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1839830..1839980_NEGATIVE 268 176 134 145 87 smit:SMT_1914|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1860324..1860474_POSITIVE 267 169 134 123 91 smit:SMT_1807|3end_putative_mucus_binding_protein_1781740..1781890_NEGATIVE 262 188 153 121 83 smit:SMT_1106|3end_ribonuclease_P_protein_component_1047601..1047751_NEGATIVE 260 197 152 52 10 smit:SMT_1669|3end_potassium_uptake_protein_KtrB_1658302..1658452_NEGATIVE 260 195 155 61 13 smit:SMT_1508|3end_hypothetical_protein_1491008..1491158_NEGATIVE 258 179 152 148 120 smit:SMT_2174|3end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2045194..2045344_POSITIVE 254 190 151 149 109 smit:SMT_269|3end_phospho-N-acetylmuramoyl-pentapeptide-transferas_e_208785..208935_POSITIVE 253 198 154 131 80 smit:SMT_426|3end_hypothetical_protein_368804..368954_POSITIVE 251 196 151 82 44 smit:SMT_1895|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1847402..1847552_POSITIVE