Origin IGS: aaatccaacattgtgtttggtctcaaatatttatctcctggattcctaatccttacagtaatttggtcatttatttttcctttcaaaagcaaaaggggtggaatttttttccaacctaattgacactattnnnnnttaattaattaannnnnagatgttagaggtatcatgcgagctgggtattcttcgtgtacactactaccgggaaacggtctagtactagcccaggtgtattccaggtgaggacttgactccctgctgactaacytactctcgtaatctctggctggtgactatatccgtggcaatgagtctcaccaagctgacttagaaaaagtaaaa .........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 ttttactttttctaagtcagcttggtgagactcattgccacggatatagtcaccagccagagattacgagagtargttagtcagcagggagtcaagtcctcacctggaatacacctgggctagtactagaccgtttcccggtagtagtgtacacgaagaatacccagctcgcatgatacctctaacatctnnnnnttaattaattaannnnnaatagtgtcaattaggttggaaaaaaattccaccccttttgcttttgaaaggaaaaataaatgaccaaattactgtaaggattaggaatccaggagataaatatttgagaccaaacacaatgttggattt Mask Tandem Repeat Region ================================================ aaatccaacattgtgtttggtctcaaatatttatctcctggattcctaatccttacagtaatttggtcatttatttttcctttcaaaagcaaaaggggtggaatttttttccaacctaattgacactattnnnnnttaattaattaannnnnagatgttagaggtatcatgcgagctgggtattcttcgtgtacactactaccgggaaacggtctagtactagcccaggtgtattccaggtgaggacttgactccctgctgactaacytactctcgtaatctctggctggtgactatatccgtggcaatgagtctcaccaagctgacttagaaaaagtaaaa Find is-nt database================================================ Query_seq: SMT_2113:SMT_2114|SMT_2113:SMT_2114:peptidyl-tRNA hydrolase:x-prolyl-dipeptidyl aminopeptidase:<-->:2001282..2001623 342 aaatccaacattgtgtttggtctcaaatatttatctcctggattcctaatccttacagtaatttggtcatttatttttcctttcaaaagcaaaaggggtggaatttttttccaacctaattgacactattnnnnnttaattaattaannnnnagatgttagaggtatcatgcgagctgggtattcttcgtgtacactactaccgggaaacggtctagtactagcccaggtgtattccaggtgaggacttgactccctgctgactaacytactctcgtaatctctggctggtgactatatccgtggcaatgagtctcaccaagctgacttagaaaaagtaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2113:SMT_2114|SMT_2113:SMT_2114:peptidyl-tRNA hydrolase:x-prolyl-dipeptidyl aminopeptidase:<-->:2001282..2001623 342 aaatccaacattgtgtttggtctcaaatatttatctcctggattcctaatccttacagtaatttggtcatttatttttcctttcaaaagcaaaaggggtggaatttttttccaacctaattgacactattnnnnnttaattaattaannnnnagatgttagaggtatcatgcgagctgggtattcttcgtgtacactactaccgggaaacggtctagtactagcccaggtgtattccaggtgaggacttgactccctgctgactaacytactctcgtaatctctggctggtgactatatccgtggcaatgagtctcaccaagctgacttagaaaaagtaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2113:SMT_2114|SMT_2113:SMT_2114:peptidyl-tRNA hydrolase:x-prolyl-dipeptidyl aminopeptidase:<-->:2001282..2001623 342 aaatccaacattgtgtttggtctcaaatatttatctcctggattcctaatccttacagtaatttggtcatttatttttcctttcaaaagcaaaaggggtggaatttttttccaacctaattgacactattnnnnnttaattaattaannnnnagatgttagaggtatcatgcgagctgggtattcttcgtgtacactactaccgggaaacggtctagtactagcccaggtgtattccaggtgaggacttgactccctgctgactaacytactctcgtaatctctggctggtgactatatccgtggcaatgagtctcaccaagctgacttagaaaaagtaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatccaacattgtgtttggtctcaaatatttatctcctggattcctaatccttacagtaatttggtcatttatttttcctttcaaaagcaaaaggggtggaatttttttccaacctaattgacactattnnnnnttaattaattaannnnnagatgttagaggtatcatgcgagctgggtattcttcgtgtacactactaccgggaaacggtctagtactagcccaggtgtattccaggtgaggacttgactccctgctgactaacytactctcgtaatctctggctggtgactatatccgtggcaatgagtctcaccaagctgacttagaaaaagtaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 3 End: 116 .. M Q H C V W S Q I F I S W I P N P Y S N L V I Y F S F Q K Q K G W N F F P T .................................................................................................................................................................................................................................. Protein_Len: 37 Strand: + Start: 10 End: 120 ......... M V F G L K Y L S P G F L I L T V I W S F I F P F K S K R G G I F F Q P N .............................................................................................................................................................................................................................. Protein_Len: 31 Strand: - Start: 147 End: 239 .................................................................................................................................................. X X S T L P I M R A P Y E E H V S S G P F P R T S A W T Y E M ....................................................................................................... Protein_Len: 34 Strand: - Start: 3 End: 104 .. D L M T N P R L Y K D G P N R I R V T I Q D N I K G K L L L L P P M .............................................................................................................................................................................................................................................. aaatccaacattgtgtttggtctcaaatatttatctcctggattcctaatccttacagtaatttggtcatttatttttcctttcaaaagcaaaaggggtggaatttttttccaacctaattgacactattnnnnnttaattaattaannnnnagatgttagaggtatcatgcgagctgggtattcttcgtgtacactactaccgggaaacggtctagtactagcccaggtgtattccaggtgaggacttgactccctgctgactaacytactctcgtaatctctggctggtgactatatccgtggcaatgagtctcaccaagctgacttagaaaaagtaaaa 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================================================ aaatccaacattgtgtttggtctcaaatatttatctcctggattcctaatccttacagtaatttggtcatttatttttcctttcaaaagcaaaaggggtggaatttttttccaacctaattgacactattnnnnnttaattaattaannnnnagatgttagaggtatcatgcgagctgggtattcttcgtgtacactactaccgggaaacggtctagtactagcccaggtgtattccaggtgaggacttgactccctgctgactaacytactctcgtaatctctggctggtgactatatccgtggcaatgagtctcaccaagctgacttagaaaaagtaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_2113:SMT_2114|SMT_2113:SMT_2114:peptidyl-tRNA hydrolase:x-prolyl-dipeptidyl aminopeptidase:<-->:2001282..2001623 342 aaatccaacattgtgtttggtctcaaatatttatctcctggattcctaatccttacagtaatttggtcatttatttttcctttcaaaagcaaaaggggtggaatttttttccaacctaattgacactattnnnnnttaattaattaannnnnagatgttagaggtatcatgcgagctgggtattcttcgtgtacactactaccgggaaacggtctagtactagcccaggtgtattccaggtgaggacttgactccctgctgactaacytactctcgtaatctctggctggtgactatatccgtggcaatgagtctcaccaagctgacttagaaaaagtaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 342 Len: 342 Subject: smit_SMT_2113_SMT_2114|peptidyl-tRNA hydrolase:x-prolyl-dipeptidyl aminopeptidase|NEGATIVE:POSITIVE|[2001282,2001623]|342 HSP 1 e-value: 1.0E-163 bit: 574.0 Len: 342 Query Start:1 Query End:342 Subject Strand: POSITIVE Subject Start: 1 Subject End: 342 aaatccaacattgtgtttggtctcaaatatttatctcctggattcctaatccttacagtaatttggtcatttatttttcctttcaaaagcaaaaggggtggaannnnnnnccaacctaattgacactattnnnnnttaattaattaannnnnagatgttagaggtatcatgcgagctgggtattcttcgtgtacactactaccgggaaacggtctagtactagcccaggtgtattccaggtgaggacttgactccctgctgactaacytactctcgtaatctctggctggtgactatatccgtggcaatgagtctcaccaagctgacttagaaaaagtaaaa aaatccaacattgtgtttggtctcaaatatttatctcctggattcctaatccttacagtaatttggtcatttatttttcctttcaaaagcaaaaggggtggaatttttttccaacctaattgacactattnnnnnttaattaattaannnnnagatgttagaggtatcatgcgagctgggtattcttcgtgtacactactaccgggaaacggtctagtactagcccaggtgtattccaggtgaggacttgactccctgctgactaacytactctcgtaatctctggctggtgactatatccgtggcaatgagtctcaccaagctgacttagaaaaagtaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUCCAACAUUGUGUUUGGUCUCAAAUAUUUAUCUCCUGGAUUCCUAAUCCUUACAGUAAUUUGGUCAUUUAUUUUUCCUUUCAAAAGCAAAAGGGGUGGAAUUUUUUUCCAACCUAAUUGACACUAUUNNNNNUUAAUUAAUUAANNNNNAGAUGUUAGAGGUAUCAUGCGAGCUGGGUAUUCUUCGUGUACACUACUACCGGGAAACGGUCUAGUACUAGCCCAGGUGUAUUCCAGGUGAGGACUUGACUCCCUGCUGACUAACYUACUCUCGUAAUCUCUGGCUGGUGACUAUAUCCGUGGCAAUGAGUCUCACCAAGCUGACUUAGAAAAAGUAAAA ....((((....(((((((....))))))).........((((.....))))..........))))...(((((((((.((......(((....(((.(((((.....))))).))).((((.(((..............................(((((((((....((((((((((((.......(....)..((((((((.....))))..))))...))))))..((....((((.(((.......)))))))...)).........))))))))))))))).(....).......))).))))............))).....)).))))))))). (-73.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUACUUUUUCUAAGUCAGCUUGGUGAGACUCAUUGCCACGGAUAUAGUCACCAGCCAGAGAUUACGAGAGUARGUUAGUCAGCAGGGAGUCAAGUCCUCACCUGGAAUACACCUGGGCUAGUACUAGACCGUUUCCCGGUAGUAGUGUACACGAAGAAUACCCAGCUCGCAUGAUACCUCUAACAUCUNNNNNUUAAUUAAUUAANNNNNAAUAGUGUCAAUUAGGUUGGAAAAAAAUUCCACCCCUUUUGCUUUUGAAAGGAAAAAUAAAUGACCAAAUUACUGUAAGGAUUAGGAAUCCAGGAGAUAAAUAUUUGAGACCAAACACAAUGUUGGAUUU ....((((.....))))...(((.((((.(((.((((((((((...((((.((.((((...((((((....))).....)))..(((((((.......))).))))...........)))).))))))..)))).....))))))))).).))).))).....(((((...........((((..............................(((((((((....(((.((((.....)))))))((((((......)))))).........))))......)))))..((((.....)))).)))).......((((....))))......))))).... (-70.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 811 60 11 151 102 smit:SMT_2113|5end_peptidyl-tRNA_hydrolase_2001191..2001421_NEGATIVE 710 50 1 71 20 smit:SMT_93|5end_peptidyl-tRNA_hydrolase_24046..24276_POSITIVE 672 50 1 117 65 smit:SMT_1906|5end_peptidyl-tRNA_hydrolase_1853884..1854114_NEGATIVE 659 49 1 231 180 smit:SMT_1905|5end_peptidyl-tRNA_hydrolase_1853769..1853999_NEGATIVE 387 287 243 209 166 smit:SMT_109|5end_beta-galactosidase_53925..54155_POSITIVE 364 250 202 228 182 smit:SMT_2123|5end_hypothetical_protein_2008201..2008431_POSITIVE 356 325 285 180 139 smit:SMT_131|5end_phosphatase,_putative_83663..83893_NEGATIVE 353 254 213 70 30 smit:SMT_1496|5end_conserved_hypothetical_protein_TIGR00150_1480999..1481229_POSITIVE 331 260 215 222 166 smit:SMT_152|5end_sensor_histidine_kinase,_putative_100759..100989_POSITIVE 327 197 156 167 120 smit:SMT_1694|5end_GTPase_1676674..1676904_POSITIVE 325 259 214 207 156 smit:SMT_1488|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1467157..1467387_POSITIVE 324 320 271 210 156 smit:SMT_1111|5end_hypothetical_protein_1051409..1051639_NEGATIVE 319 328 281 206 159 smit:SMT_992|5end_hypothetical_protein_934882..935112_NEGATIVE 317 323 282 203 170 smit:SMT_1129|5end_hypothetical_protein_1063926..1064156_NEGATIVE 317 285 241 115 70 smit:SMT_1007|5end_radical_SAM_domain_protein_947035..947265_POSITIVE 313 326 281 204 157 smit:SMT_1413|5end_putative_carbon-nitrogen_hydrolase_1397351..1397581_NEGATIVE 309 308 274 54 22 smit:SMT_245|5end_hypothetical_protein_predicted_by_Glimmer/Critica_181964..182194_NEGATIVE 309 308 274 161 129 smit:SMT_244|5end_PTS_system,_mannose-specific_IIAB_component_181857..182087_NEGATIVE 306 250 204 65 18 smit:SMT_2028|5end_leader_peptidase_(prepilin_peptidase)_/_N-methyltransferase_1943729..1943959_NEGATIVE 306 250 204 65 18 smit:SMT_1754|5end_leader_peptidase_(prepilin_peptidase)_/_N-methyltransferase_1733022..1733252_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 650 130 81 78 28 smit:SMT_92|3end_GTP-binding_protein,_probable_translation_factor_24052..24202_POSITIVE 387 287 243 77 34 smit:SMT_108|3end_hypothetical_protein_53873..54023_POSITIVE 354 250 202 67 20 smit:SMT_2067|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1974216..1974366_POSITIVE 323 246 203 72 23 smit:SMT_213|3end_leucyl-tRNA_synthetase_146167..146317_POSITIVE 317 285 241 122 77 smit:SMT_1006|3end_6-pyruvoyl_tetrahydrobiopterin_synthase,_putative_947122..947272_POSITIVE 304 263 221 58 18 smit:SMT_1964|3end_sodium/hydrogen_exchanger_family_protein_1896596..1896746_NEGATIVE 302 259 219 46 2 smit:SMT_1487|3end_hypothetical_protein_1467076..1467226_POSITIVE 301 316 271 149 103 smit:SMT_315|3end_acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta_256627..256777_POSITIVE 295 248 203 123 81 smit:SMT_958|3end_hypothetical_protein_predicted_by_Glimmer/Critica_905239..905389_POSITIVE 294 316 273 53 13 smit:SMT_1738|3end_peptidyl-prolyl_cis-trans_isomerase_1721341..1721491_POSITIVE 293 319 285 150 117 smit:SMT_132|3end_L-serine_dehydratase_alpha_subunit_83685..83835_NEGATIVE 291 248 203 56 5 smit:SMT_1776|3end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_1751892..1752042_NEGATIVE 290 243 202 88 48 smit:SMT_914|3end_sucrose-6-phosphate_hydrolase_867673..867823_POSITIVE 287 250 203 137 97 smit:SMT_713|3end_heat_shock_protein_HtpX_620505..620655_NEGATIVE 285 252 214 63 14 smit:SMT_834|3end_hypothetical_protein_775517..775667_NEGATIVE 285 252 214 62 13 smit:SMT_698|3end_uracil_permease_609769..609919_POSITIVE 283 252 214 60 11 smit:SMT_799|3end_hypothetical_protein_707296..707446_NEGATIVE 279 252 214 62 13 smit:SMT_2109|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1999061..1999211_NEGATIVE 279 252 214 62 13 smit:SMT_1809|3end_MutT/NUDIX_family_protein_1785134..1785284_POSITIVE 279 252 214 62 13 smit:SMT_1180|3end_putative_tagatose-6-phosphate_aldose/ketose_isomerase_1138036..1138186_NEGATIVE