Origin IGS: agtttctcctataaagtctctaggcgtctgcctttttgctctctatattatatcacaagtcttggctgaggccaatttctatggataaagagagtaaaaagagtggacaagccactcttttcttcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagaagaaaagagtggcttgtccactctttttactctctttatccatagaaattggcctcagccaagacttgtgatataatatagagagcaaaaaggcagacgcctagagactttataggagaaact Mask Tandem Repeat Region ================================================ agtttctcctataaagtctctaggcgtctgcctttttgctctctatattatatcacaagtcttggctgaggccaatttctatggataaagagagtaaaaagagtggacaagccactcttttcttcta Find is-nt database================================================ Query_seq: SMT_1134:SMT_1135|SMT_1134:SMT_1135:glutamyl-tRNA synthetase:glucose-6-phosphate isomerase:<-<-:1076555..1076681 127 agtttctcctataaagtctctaggcgtctgcctttttgctctctatattatatcacaagtcttggctgaggccaatttctatggataaagagagtaaaaagagtggacaagccactcttttcttcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1134:SMT_1135|SMT_1134:SMT_1135:glutamyl-tRNA synthetase:glucose-6-phosphate isomerase:<-<-:1076555..1076681 127 agtttctcctataaagtctctaggcgtctgcctttttgctctctatattatatcacaagtcttggctgaggccaatttctatggataaagagagtaaaaagagtggacaagccactcttttcttcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1134:SMT_1135|SMT_1134:SMT_1135:glutamyl-tRNA synthetase:glucose-6-phosphate isomerase:<-<-:1076555..1076681 127 agtttctcctataaagtctctaggcgtctgcctttttgctctctatattatatcacaagtcttggctgaggccaatttctatggataaagagagtaaaaagagtggacaagccactcttttcttcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtttctcctataaagtctctaggcgtctgcctttttgctctctatattatatcacaagtcttggctgaggccaatttctatggataaagagagtaaaaagagtggacaagccactcttttcttcta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 36 End: 125 ................................... M L S I L Y H K S W L R P I S M D K E S K K S G Q A T L F F .. agtttctcctataaagtctctaggcgtctgcctttttgctctctatattatatcacaagtcttggctgaggccaatttctatggataaagagagtaaaaagagtggacaagccactcttttcttcta 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: 47 End: 76 ..............................................ATTGGCCTCAGCCAAGACTTGTGATATAAT................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtttctcctataaagtctctaggcgtctgcctttttgctctctatattatatcacaagtcttggctgaggccaatttctatggataaagagagtaaaaagagtggacaagccactcttttcttcta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -6.7 Tail_Score: -4.0641 Start: 62 End: 75 Full_Region: ATTATATCACAAGTC TTGGC TGAG GCCAA TTTCTATGGATAAAG .............................................................TTGGCTGAGGCCAA.................................................... Find igs database================================================ Query_seq: SMT_1134:SMT_1135|SMT_1134:SMT_1135:glutamyl-tRNA synthetase:glucose-6-phosphate isomerase:<-<-:1076555..1076681 127 agtttctcctataaagtctctaggcgtctgcctttttgctctctatattatatcacaagtcttggctgaggccaatttctatggataaagagagtaaaaagagtggacaagccactcttttcttcta Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: smit_SMT_1134_SMT_1135|glutamyl-tRNA synthetase:glucose-6-phosphate isomerase|NEGATIVE:NEGATIVE|[1076555,1076681]|127 HSP 1 e-value: 2.0E-66 bit: 252.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 agtttctcctataaagtctctaggcgtctgcctttttgctctctatattatatcacaagtcttggctgaggccaatttctatggataaagagagtaaaaagagtggacaagccactcttttcttcta agtttctcctataaagtctctaggcgtctgcctttttgctctctatattatatcacaagtcttggctgaggccaatttctatggataaagagagtaaaaagagtggacaagccactcttttcttcta Inter-species Hit: Count: 3 Min: 19 Max: 127 Len: 109 Subject: NC_008533_SPD_1896_SPD_1897|glutamyl-tRNA synthetase:glucose-6-phosphate isomerase|NEGATIVE:NEGATIVE|[1866540,1866662]|123 HSP 1 e-value: 5.0E-46 bit: 184.0 Len: 109 Query Start:19 Query End:127 Subject Strand: POSITIVE Subject Start: 15 Subject End: 123 ..................tctaggcgtctgcctttttgctctctatattatatcacaagtcttggctgaggccaatttctatggataaagagagtaaaaagagtggacaagccactcttttcttcta ..................tctaggcgtctgcctttttgctttctatattatatcacaagtcttggctgagtccaatttctatggataaagagagtaaaaagagtgggcaaaccactcttttcttcta Subject: NC_003098_spr1881_spr1882|glutamyl-tRNA synthetase:glucose-6-phosphate isomerase|NEGATIVE:NEGATIVE|[1859008,1859130]|123 HSP 1 e-value: 5.0E-46 bit: 184.0 Len: 109 Query Start:19 Query End:127 Subject Strand: POSITIVE Subject Start: 15 Subject End: 123 ..................tctaggcgtctgcctttttgctctctatattatatcacaagtcttggctgaggccaatttctatggataaagagagtaaaaagagtggacaagccactcttttcttcta ..................tctaggcgtctgcctttttgctttctatattatatcacaagtcttggctgagtccaatttctatggataaagagagtaaaaagagtgggcaaaccactcttttcttcta Subject: NC_003028_SP_2069_SP_2070|glutamyl-tRNA synthetase:glucose-6-phosphate isomerase|NEGATIVE:NEGATIVE|[1978088,1978210]|123 HSP 1 e-value: 5.0E-46 bit: 184.0 Len: 109 Query Start:19 Query End:127 Subject Strand: POSITIVE Subject Start: 15 Subject End: 123 ..................tctaggcgtctgcctttttgctctctatattatatcacaagtcttggctgaggccaatttctatggataaagagagtaaaaagagtggacaagccactcttttcttcta ..................tctaggcgtctgcctttttgctttctatattatatcacaagtcttggctgagtccaatttctatggataaagagagtaaaaagagtgggcaaaccactcttttcttcta Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAGGCGUCUGCCUUUUUGCUCUCUAUAUUAUAUCACAAGUCUUGGCUGAGGCCAAUUUCUAUGGAUAAAGAGAGUAAAAAGAGUGGACAAGCCACUCUUUUCUUCUA ....((((((..((((((((((((((......((((.((((..(((((....)))))...)).)))))).))))))))))))).)..)))..))).............. (-37.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAAGAAAAGAGUGGCUUGUCCACUCUUUUUACUCUCUUUAUCCAUAGAAAUUGGCCUCAGCCAAGACUUGUGAUAUAAUAUAGAGAGCAAAAAGGCAGACGCCUAGA .....(((((((((((.....))))))))))).((((((.((((.((((...(((((....)))))...))))))))......)))))).....((((....))))... (-34.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 913 50 1 159 110 smit:SMT_1134|5end_glutamyl-tRNA_synthetase_1076464..1076694_NEGATIVE 286 48 1 203 158 smit:SMT_1386|5end_phosphoenolpyruvate-protein_phosphotransferase_1362806..1363036_POSITIVE 285 90 43 173 121 smit:SMT_1589|5end_hypothetical_protein_1578332..1578562_POSITIVE 276 42 2 77 34 smit:SMT_1168|5end_potassium_uptake_protein_KtrB_1116552..1116782_NEGATIVE 275 62 41 96 77 smit:SMT_2031|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1945761..1945991_NEGATIVE 275 62 41 33 14 smit:SMT_1767|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_1744121..1744351_NEGATIVE 275 100 51 195 145 smit:SMT_849|5end_hypothetical_protein_796127..796357_NEGATIVE 272 64 35 69 36 smit:SMT_1860|5end_hypothetical_protein_1823609..1823839_NEGATIVE 272 99 51 157 109 smit:SMT_1053|5end_ABC_transporter_permease_protein_993671..993901_NEGATIVE 267 49 2 83 33 smit:SMT_924|5end_primosomal_protein_N'_879903..880133_NEGATIVE 263 57 13 179 142 smit:SMT_1619|5end_K02006_cobalt_transport_system_ATP-binding_protein_1606526..1606756_NEGATIVE 262 50 5 172 120 smit:SMT_2005|5end_pullulanase,_type_I_1926289..1926519_NEGATIVE 262 60 19 81 33 smit:SMT_1926|5end_mevalonate_kinase_1867692..1867922_POSITIVE 262 60 19 81 33 smit:SMT_1544|5end_mevalonate_kinase_1528884..1529114_NEGATIVE 259 80 38 155 110 smit:SMT_1488|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1467157..1467387_POSITIVE 258 73 35 208 166 smit:SMT_2099|5end_putative_zinc-binding_dehydrogenase_1991725..1991955_POSITIVE 258 73 35 208 166 smit:SMT_682|5end_hypothetical_protein_591860..592090_NEGATIVE 258 95 54 55 23 smit:SMT_259|5end_dipeptide/tripeptide_permease_197629..197859_POSITIVE 255 49 2 183 122 smit:SMT_1694|5end_GTPase_1676674..1676904_POSITIVE 253 56 11 188 138 smit:SMT_1692|5end_hypothetical_protein_1675169..1675399_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 275 62 41 32 13 smit:SMT_2032|3end_hydrolase,_alpha/beta_fold_family_1945825..1945975_NEGATIVE 275 62 41 31 12 smit:SMT_1768|3end_hydrolase,_alpha/beta_fold_family_1744123..1744273_NEGATIVE 273 42 5 43 2 smit:SMT_1169|3end_phosphorylase,_Pnp/UDP_family_1116586..1116736_NEGATIVE 272 99 51 141 93 smit:SMT_1054|3end_K01990_ABC-2_type_transport_system_ATP-binding_protein_993687..993837_NEGATIVE 251 49 4 92 42 smit:SMT_260|3end_phage_transcriptional_repressor_200236..200386_POSITIVE 245 49 5 121 77 smit:SMT_977|3end_conserved_hypothetical_protein,_Rrf2_family_protein_925252..925402_NEGATIVE 244 58 11 141 86 smit:SMT_1652|3end_Cof_family_protein_1641408..1641558_POSITIVE 243 50 8 45 9 smit:SMT_540|3end_DNA_gyrase,_B_subunit_457157..457307_POSITIVE 237 65 33 48 8 smit:SMT_664|3end_ribosomal_large_subunit_pseudouridine_synthase,_RluD_subfamily_575034..575184_NEGATIVE 231 49 14 86 43 smit:SMT_1426|3end_K03095_SprT-like_protein_1410864..1411014_NEGATIVE 230 50 6 61 7 smit:SMT_1946|3end_sucrose-6-phosphate_hydrolase_1881205..1881355_POSITIVE 228 60 14 49 9 smit:SMT_954|3end_cation-transporting_ATPase,_E1-E2_family_901677..901827_NEGATIVE 227 95 54 58 1 smit:SMT_2132|3end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2013732..2013882_POSITIVE 227 47 6 47 3 smit:SMT_920|3end_serine/threonine_protein_kinase_872588..872738_NEGATIVE 226 50 4 60 22 smit:SMT_1729|3end_exodeoxyribonuclease_VII_small_subunit_1714858..1715008_POSITIVE 226 47 6 55 16 smit:SMT_549|3end_hypothetical_cytosolic_protein_467367..467517_POSITIVE 224 98 52 43 3 smit:SMT_413|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_357641..357791_POSITIVE 223 60 11 150 109 smit:SMT_1588|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1578425..1578575_POSITIVE 221 54 19 127 95 smit:SMT_439|3end_hypothetical_protein_predicted_by_Glimmer/Critica_379658..379808_POSITIVE 219 99 51 136 93 smit:SMT_1713|3end_K03284_metal_ion_transporter,_MIT_family_1701424..1701574_POSITIVE