Origin IGS: gttgtttgcctttctagaaaaatgaaaattcagtaatcatcgtaaaaaaactgtttatattaccattatacactaaaaatgttagaaaattaccaaaatatcaaaccttttcttatttaaacagaagaaaagatttttatttcactaacttttagcgtagactatatttcaaaaaagttagatgaaaatcagataattttattttttaagtttgaatcttattctatcatccatcccaacaaattgaatagcttcagaatcctctttttctagttttcatattcttaaaaaagtgataaaatggtaggaagaattggagagtagagatgccaaaagaagtgaatttaacaggcgatgaagttgtcgctttaacacagaaatatttatcgggaagaagat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcttcttcccgataaatatttctgtgttaaagcgacaacttcatcgcctgttaaattcacttcttttggcatctctactctccaattcttcctaccattttatcacttttttaagaatatgaaaactagaaaaagaggattctgaagctattcaatttgttgggatggatgatagaataagattcaaacttaaaaaataaaattatctgattttcatctaacttttttgaaatatagtctacgctaaaagttagtgaaataaaaatcttttcttctgtttaaataagaaaaggtttgatattttggtaattttctaacatttttagtgtataatggtaatataaacagtttttttacgatgattactgaattttcatttttctagaaaggcaaacaac Mask Tandem Repeat Region ================================================ gttgtttgcctttctagaaaaatgaaaattcagtaatcatcgtaaaaaaactgtttatattaccattatacactaaaaatgttagaaaattaccaaaatatcaaaccttttcttatttaaacagaagaaaagatttttatttcactaacttttagcgtagactatatttcaaaaaagttagatgaaaatcagataattttattttttaagtttgaatcttattctatcatccatcccaacaaattgaatagcttcagaatcctctttttctagttttcatattcttaaaaaagtgataaaatggtaggaagaattggagagtagagatgccaaaagaagtgaatttaacaggcgatgaagttgtcgctttaacacagaaatatttatcgggaagaagat Find is-nt database================================================ Query_seq: SMT_1468:SMT_1469|SMT_1468:SMT_1469:pneumococcal surface protein, putative:GTP pyrophosphokinase:<-->:1450323..1450721 399 gttgtttgcctttctagaaaaatgaaaattcagtaatcatcgtaaaaaaactgtttatattaccattatacactaaaaatgttagaaaattaccaaaatatcaaaccttttcttatttaaacagaagaaaagatttttatttcactaacttttagcgtagactatatttcaaaaaagttagatgaaaatcagataattttattttttaagtttgaatcttattctatcatccatcccaacaaattgaatagcttcagaatcctctttttctagttttcatattcttaaaaaagtgataaaatggtaggaagaattggagagtagagatgccaaaagaagtgaatttaacaggcgatgaagttgtcgctttaacacagaaatatttatcgggaagaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1468:SMT_1469|SMT_1468:SMT_1469:pneumococcal surface protein, putative:GTP pyrophosphokinase:<-->:1450323..1450721 399 gttgtttgcctttctagaaaaatgaaaattcagtaatcatcgtaaaaaaactgtttatattaccattatacactaaaaatgttagaaaattaccaaaatatcaaaccttttcttatttaaacagaagaaaagatttttatttcactaacttttagcgtagactatatttcaaaaaagttagatgaaaatcagataattttattttttaagtttgaatcttattctatcatccatcccaacaaattgaatagcttcagaatcctctttttctagttttcatattcttaaaaaagtgataaaatggtaggaagaattggagagtagagatgccaaaagaagtgaatttaacaggcgatgaagttgtcgctttaacacagaaatatttatcgggaagaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1468:SMT_1469|SMT_1468:SMT_1469:pneumococcal surface protein, putative:GTP pyrophosphokinase:<-->:1450323..1450721 399 gttgtttgcctttctagaaaaatgaaaattcagtaatcatcgtaaaaaaactgtttatattaccattatacactaaaaatgttagaaaattaccaaaatatcaaaccttttcttatttaaacagaagaaaagatttttatttcactaacttttagcgtagactatatttcaaaaaagttagatgaaaatcagataattttattttttaagtttgaatcttattctatcatccatcccaacaaattgaatagcttcagaatcctctttttctagttttcatattcttaaaaaagtgataaaatggtaggaagaattggagagtagagatgccaaaagaagtgaatttaacaggcgatgaagttgtcgctttaacacagaaatatttatcgggaagaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttgtttgcctttctagaaaaatgaaaattcagtaatcatcgtaaaaaaactgtttatattaccattatacactaaaaatgttagaaaattaccaaaatatcaaaccttttcttatttaaacagaagaaaagatttttatttcactaacttttagcgtagactatatttcaaaaaagttagatgaaaatcagataattttattttttaagtttgaatcttattctatcatccatcccaacaaattgaatagcttcagaatcctctttttctagttttcatattcttaaaaaagtgataaaatggtaggaagaattggagagtagagatgccaaaagaagtgaatttaacaggcgatgaagttgtcgctttaacacagaaatatttatcgggaagaagat Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 36 End: 152 ................................... M I V K K L F I L P L Y T K N V R K L P K Y Q T F S Y L N R R K D F Y F T N F ....................................................................................................................................................................................................................................................... Protein_Len: 46 Strand: + Start: 133 End: 270 .................................................................................................................................... M F I S L T F S V D Y I S K K L D E N Q I I L F F K F E S Y S I I H P N K L N S F R I L F F ................................................................................................................................. Protein_Len: 40 Strand: - Start: 280 End: 399 ....................................................................................................................................................................................................................................................................................... I R L F T I F H Y S S N S L L S A L L L S N L L R H L Q R K L V S I N I P F F M gttgtttgcctttctagaaaaatgaaaattcagtaatcatcgtaaaaaaactgtttatattaccattatacactaaaaatgttagaaaattaccaaaatatcaaaccttttcttatttaaacagaagaaaagatttttatttcactaacttttagcgtagactatatttcaaaaaagttagatgaaaatcagataattttattttttaagtttgaatcttattctatcatccatcccaacaaattgaatagcttcagaatcctctttttctagttttcatattcttaaaaaagtgataaaatggtaggaagaattggagagtagagatgccaaaagaagtgaatttaacaggcgatgaagttgtcgctttaacacagaaatatttatcgggaagaagat 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: 84 Start: 273 End: 302 ................................................................................................................................................................................................................................................................................GTTTTCATATTCTTAAAAAAGTGATAAAAT................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gttgtttgcctttctagaaaaatgaaaattcagtaatcatcgtaaaaaaactgtttatattaccattatacactaaaaatgttagaaaattaccaaaatatcaaaccttttcttatttaaacagaagaaaagatttttatttcactaacttttagcgtagactatatttcaaaaaagttagatgaaaatcagataattttattttttaagtttgaatcttattctatcatccatcccaacaaattgaatagcttcagaatcctctttttctagttttcatattcttaaaaaagtgataaaatggtaggaagaattggagagtagagatgccaaaagaagtgaatttaacaggcgatgaagttgtcgctttaacacagaaatatttatcgggaagaagat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1468:SMT_1469|SMT_1468:SMT_1469:pneumococcal surface protein, putative:GTP pyrophosphokinase:<-->:1450323..1450721 399 gttgtttgcctttctagaaaaatgaaaattcagtaatcatcgtaaaaaaactgtttatattaccattatacactaaaaatgttagaaaattaccaaaatatcaaaccttttcttatttaaacagaagaaaagatttttatttcactaacttttagcgtagactatatttcaaaaaagttagatgaaaatcagataattttattttttaagtttgaatcttattctatcatccatcccaacaaattgaatagcttcagaatcctctttttctagttttcatattcttaaaaaagtgataaaatggtaggaagaattggagagtagagatgccaaaagaagtgaatttaacaggcgatgaagttgtcgctttaacacagaaatatttatcgggaagaagat Intra-Species Hit: Count: 1 Min: 1 Max: 399 Len: 399 Subject: smit_SMT_1468_SMT_1469|pneumococcal surface protein, putative:GTP pyrophosphokinase|NEGATIVE:POSITIVE|[1450323, 1450721]|399 HSP 1 e-value: 0.0 bit: 749.0 Len: 399 Query Start:1 Query End:399 Subject Strand: POSITIVE Subject Start: 1 Subject End: 399 gttgtttgcctttctagaaaaatgaaaattcagtaatcatcgtnnnnnnnctgtttatattaccattatacactaaaaatgttagaaaattaccaaaatatcaaaccttttcttatttaaacagaagaaaagatttttatttcactaacttttagcgtagactatatttcaaaaaagttagatgaaaatcagataattttattttttaagtttgaatcttattctatcatccatcccaacaaattgaatagcttcagaatcctctttttctagttttcatattcttaaaaaagtgataaaatggtaggaagaattggagagtagagatgccaaaagaagtgaatttaacaggcgatgaagttgtcgctttaacacagaaatatttatcgggaagaagat gttgtttgcctttctagaaaaatgaaaattcagtaatcatcgtaaaaaaactgtttatattaccattatacactaaaaatgttagaaaattaccaaaatatcaaaccttttcttatttaaacagaagaaaagatttttatttcactaacttttagcgtagactatatttcaaaaaagttagatgaaaatcagataattttattttttaagtttgaatcttattctatcatccatcccaacaaattgaatagcttcagaatcctctttttctagttttcatattcttaaaaaagtgataaaatggtaggaagaattggagagtagagatgccaaaagaagtgaatttaacaggcgatgaagttgtcgctttaacacagaaatatttatcgggaagaagat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUGUUUGCCUUUCUAGAAAAAUGAAAAUUCAGUAAUCAUCGUAAAAAAACUGUUUAUAUUACCAUUAUACACUAAAAAUGUUAGAAAAUUACCAAAAUAUCAAACCUUUUCUUAUUUAAACAGAAGAAAAGAUUUUUAUUUCACUAACUUUUAGCGUAGACUAUAUUUCAAAAAAGUUAGAUGAAAAUCAGAUAAUUUUAUUUUUUAAGUUUGAAUCUUAUUCUAUCAUCCAUCCCAACAAAUUGAAUAGCUUCAGAAUCCUCUUUUUCUAGUUUUCAUAUUCUUAAAAAAGUGAUAAAAUGGUAGGAAGAAUUGGAGAGUAGAGAUGCCAAAAGAAGUGAAUUUAACAGGCGAUGAAGUUGUCGCUUUAACACAGAAAUAUUUAUCGGGAAGAAGAU ...((((..((((((.((.(((((............(((((((.........((.((((.......)))).))......(((((((....................((((((((..........))))))))........((((((..(((((.((((...((((.((((((.(((((((..((.....))..)))))))................(((..(((((((((.............(((((....))))).(((..((((((..((..(....)..))..)))))).)))...)))))))))))).)))))).))))..)))).))))).))))))))))))).))))))).((((......)))).......))))).)))))))).)))) (-67.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUUCUUCCCGAUAAAUAUUUCUGUGUUAAAGCGACAACUUCAUCGCCUGUUAAAUUCACUUCUUUUGGCAUCUCUACUCUCCAAUUCUUCCUACCAUUUUAUCACUUUUUUAAGAAUAUGAAAACUAGAAAAAGAGGAUUCUGAAGCUAUUCAAUUUGUUGGGAUGGAUGAUAGAAUAAGAUUCAAACUUAAAAAAUAAAAUUAUCUGAUUUUCAUCUAACUUUUUUGAAAUAUAGUCUACGCUAAAAGUUAGUGAAAUAAAAAUCUUUUCUUCUGUUUAAAUAAGAAAAGGUUUGAUAUUUUGGUAAUUUUCUAACAUUUUUAGUGUAUAAUGGUAAUAUAAACAGUUUUUUUACGAUGAUUACUGAAUUUUCAUUUUUCUAGAAAGGCAAACAAC .......(((((((((((......(((((((.((((........))))...))))...)))......((((.((...(..(((...((((........((((((..(((....)))...))))))...))))...)))..)...)).))))....))))))))))).((((((..((((.((((.....................)))).))))))))))..((((((.((((.......((((((((((((((.(((((((.((((((((((((.(......).))))))))))))..))))))).))))..........))))))))))...............((((..((.......))..))))..........)))).))))))......... (-68.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 695 50 1 141 92 smit:SMT_1468|5end_pneumococcal_surface_protein,_putative_1450232..1450462_NEGATIVE 312 355 316 114 77 smit:SMT_1799|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1773416..1773646_POSITIVE 246 308 261 201 155 smit:SMT_1497|5end_acetyltransferase,_GNAT_family_1481432..1481662_POSITIVE 246 270 230 182 142 smit:SMT_1485|5end_exodeoxyribonuclease_1465825..1466055_NEGATIVE 246 355 317 44 1 smit:SMT_973|5end_signal_transduction_histidine_kinase_922177..922407_NEGATIVE 243 268 226 106 62 smit:SMT_1191|5end_phosphoribosylamine--glycine_ligase_1149737..1149967_NEGATIVE 240 237 193 143 104 smit:SMT_851|5end_conserved_hypothetical_protein,_translation_initiation_inhibitor_protein_797446..797676_NEGATIVE 234 267 226 105 62 smit:SMT_2076|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1978592..1978822_NEGATIVE 234 267 226 212 169 smit:SMT_2075|5end_phosphoribosylamine--glycine_ligase_1978485..1978715_NEGATIVE 232 355 316 114 77 smit:SMT_2018|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1936760..1936990_POSITIVE 232 246 210 190 159 smit:SMT_1776|5end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_1752407..1752637_NEGATIVE 231 270 224 80 28 smit:SMT_1510|5end_ribose_5-phosphate_isomerase_1493488..1493718_NEGATIVE 230 286 249 206 168 smit:SMT_1335|5end_RNA_polymerase_sigma_factor_RpoD_1310201..1310431_NEGATIVE 229 340 293 82 29 smit:SMT_1040|5end_K03565_regulatory_protein_982602..982832_POSITIVE 226 355 311 73 25 smit:SMT_1996|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1921078..1921308_NEGATIVE 226 240 209 94 63 smit:SMT_1789|5end_hypothetical_protein_1765318..1765548_POSITIVE 226 343 301 178 134 smit:SMT_1082|5end_Cof_family_protein_1020153..1020383_POSITIVE 226 330 296 161 132 smit:SMT_728|5end_hypothetical_protein_634348..634578_NEGATIVE 226 390 351 54 22 smit:SMT_616|5end_hypothetical_protein_525777..526007_POSITIVE 226 282 251 202 177 smit:SMT_215|5end_leucyl-tRNA_synthetase_147045..147275_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 373 334 64 28 smit:SMT_932|3end_tellurite_resistance_protein_885402..885552_POSITIVE 254 339 307 53 9 smit:SMT_1866|3end_extramembranal_protein_1827939..1828089_POSITIVE 245 355 311 51 2 smit:SMT_974|3end_DNA-binding_response_regulator_922170..922320_NEGATIVE 240 237 193 132 93 smit:SMT_852|3end_K03978_GTP-binding_protein_797457..797607_NEGATIVE 238 277 236 40 3 smit:SMT_841|3end_dihydrodipicolinate_reductase_787258..787408_NEGATIVE 237 367 329 120 86 smit:SMT_1304|3end_hypothetical_protein_1268137..1268287_POSITIVE 226 282 251 143 118 smit:SMT_214|3end_leucyl-tRNA_synthetase_147066..147216_POSITIVE 225 279 251 139 105 smit:SMT_1606|3end_glutamate_racemase_1596731..1596881_POSITIVE 223 279 231 69 13 smit:SMT_1733|3end_DNA_repair_protein_RecN_1718636..1718786_POSITIVE 220 268 221 136 93 smit:SMT_2076|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1978482..1978632_NEGATIVE 220 357 314 148 102 smit:SMT_1791|3end_hypothetical_protein_1766433..1766583_POSITIVE 218 294 259 56 20 smit:SMT_1541|3end_isopentenyl-diphosphate_delta-isomerase_1525083..1525233_NEGATIVE 218 276 242 129 103 smit:SMT_739|3end_50S_ribosomal_protein_L7/L12_643274..643424_NEGATIVE 216 258 214 64 17 smit:SMT_726|3end_ImpB/MucB/SamB_family_protein_630412..630562_NEGATIVE 212 327 285 74 26 smit:SMT_919|3end_hypothetical_protein_871741..871891_NEGATIVE 212 276 239 114 81 smit:SMT_882|3end_acetyl_esterase_829662..829812_NEGATIVE 211 282 260 130 110 smit:SMT_589|3end_hypothetical_protein_506827..506977_POSITIVE 210 239 198 133 94 smit:SMT_658|3end_hypothetical_protein_569403..569553_NEGATIVE 208 367 326 141 97 smit:SMT_1430|3end_hypothetical_protein_1415842..1415992_POSITIVE 207 367 329 136 97 smit:SMT_1173|3end_CMP-N-acetylneuraminate-beta-galactosamide-alpha_-2,3-sialyltransferase_1124742..1124892_NEGATIVE