Origin IGS: tatttcttaattttgataggccagcgttcgccatcaacaggcactttaccacctgtttaaaacagtttttcaaaatatgctgcatgnnnnnttaattaattaannnnnaaacgctgactttatggtatgctagtatcatgaaaagaaaatgtaaggggttaaacttaatataaatttactatatttcagtcttcttttcataaaagaaaggagttggtagcttgcctcttagttcacattccgaacggcta .........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 tagccgttcggaatgtgaactaagaggcaagctaccaactcctttcttttatgaaaagaagactgaaatatagtaaatttatattaagtttaaccccttacattttcttttcatgatactagcataccataaagtcagcgtttnnnnnttaattaattaannnnncatgcagcatattttgaaaaactgttttaaacaggtggtaaagtgcctgttgatggcgaacgctggcctatcaaaattaagaaata Mask Tandem Repeat Region ================================================ tatttcttaattttgataggccagcgttcgccatcaacaggcactttaccacctgtttaaaacagtttttcaaaatatgctgcatgnnnnnttaattaattaannnnnaaacgctgactttatggtatgctagtatcatgaaaagaaaatgtaaggggttaaacttaatataaatttactatatttcagtcttcttttcataaaagaaaggagttggtagcttgcctcttagttcacattccgaacggcta Find is-nt database================================================ Query_seq: SMT_795:SMT_796|SMT_795:SMT_796:similar to O6-alkylguanine-DNA-alkyltransferase:K03734 thiamine biosynthesis lipoprotein:<-->:704100..704350 251 tatttcttaattttgataggccagcgttcgccatcaacaggcactttaccacctgtttaaaacagtttttcaaaatatgctgcatgnnnnnttaattaattaannnnnaaacgctgactttatggtatgctagtatcatgaaaagaaaatgtaaggggttaaacttaatataaatttactatatttcagtcttcttttcataaaagaaaggagttggtagcttgcctcttagttcacattccgaacggcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_795:SMT_796|SMT_795:SMT_796:similar to O6-alkylguanine-DNA-alkyltransferase:K03734 thiamine biosynthesis lipoprotein:<-->:704100..704350 251 tatttcttaattttgataggccagcgttcgccatcaacaggcactttaccacctgtttaaaacagtttttcaaaatatgctgcatgnnnnnttaattaattaannnnnaaacgctgactttatggtatgctagtatcatgaaaagaaaatgtaaggggttaaacttaatataaatttactatatttcagtcttcttttcataaaagaaaggagttggtagcttgcctcttagttcacattccgaacggcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_795:SMT_796|SMT_795:SMT_796:similar to O6-alkylguanine-DNA-alkyltransferase:K03734 thiamine biosynthesis lipoprotein:<-->:704100..704350 251 tatttcttaattttgataggccagcgttcgccatcaacaggcactttaccacctgtttaaaacagtttttcaaaatatgctgcatgnnnnnttaattaattaannnnnaaacgctgactttatggtatgctagtatcatgaaaagaaaatgtaaggggttaaacttaatataaatttactatatttcagtcttcttttcataaaagaaaggagttggtagcttgcctcttagttcacattccgaacggcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatttcttaattttgataggccagcgttcgccatcaacaggcactttaccacctgtttaaaacagtttttcaaaatatgctgcatgnnnnnttaattaattaannnnnaaacgctgactttatggtatgctagtatcatgaaaagaaaatgtaaggggttaaacttaatataaatttactatatttcagtcttcttttcataaaagaaaggagttggtagcttgcctcttagttcacattccgaacggcta Predict ORF larger than 30AA ================================================ tatttcttaattttgataggccagcgttcgccatcaacaggcactttaccacctgtttaaaacagtttttcaaaatatgctgcatgnnnnnttaattaattaannnnnaaacgctgactttatggtatgctagtatcatgaaaagaaaatgtaaggggttaaacttaatataaatttactatatttcagtcttcttttcataaaagaaaggagttggtagcttgcctcttagttcacattccgaacggcta 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================================================ tatttcttaattttgataggccagcgttcgccatcaacaggcactttaccacctgtttaaaacagtttttcaaaatatgctgcatgnnnnnttaattaattaannnnnaaacgctgactttatggtatgctagtatcatgaaaagaaaatgtaaggggttaaacttaatataaatttactatatttcagtcttcttttcataaaagaaaggagttggtagcttgcctcttagttcacattccgaacggcta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -6.3 Tail_Score: -4.61231 Start: 53 End: 65 Full_Region: CAGGCACTTTACCAC CTGTT TAA AACAG TTTTTCAAAATATGC ....................................................CTGTTTAAAACAG.......................................................................................................................................................................................... Find igs database================================================ Query_seq: SMT_795:SMT_796|SMT_795:SMT_796:similar to O6-alkylguanine-DNA-alkyltransferase:K03734 thiamine biosynthesis lipoprotein:<-->:704100..704350 251 tatttcttaattttgataggccagcgttcgccatcaacaggcactttaccacctgtttaaaacagtttttcaaaatatgctgcatgnnnnnttaattaattaannnnnaaacgctgactttatggtatgctagtatcatgaaaagaaaatgtaaggggttaaacttaatataaatttactatatttcagtcttcttttcataaaagaaaggagttggtagcttgcctcttagttcacattccgaacggcta Intra-Species Hit: Count: 1 Min: 1 Max: 251 Len: 251 Subject: smit_SMT_795_SMT_796|similar to O6-alkylguanine-DNA-alkyltransferase:K03734 thiamine biosynthesis lipoprotein|NEGATIVE:POSITIVE|[704100,704350]|251 HSP 1 e-value: 1.0E-122 bit: 438.0 Len: 251 Query Start:1 Query End:251 Subject Strand: POSITIVE Subject Start: 1 Subject End: 251 tatttcttaattttgataggccagcgttcgccatcaacaggcactttaccacctgtttaaaacagtttttcaaaatatgctgcatgnnnnnttaattaattaannnnnaaacgctgactttatggtatgctagtatcatgaaaagaaaatgtaaggggttaaacttaatataaatttactatatttcagtcttcttttcataaaagaaaggagttggtagcttgcctcttagttcacattccgaacggcta tatttcttaattttgataggccagcgttcgccatcaacaggcactttaccacctgtttaaaacagtttttcaaaatatgctgcatgnnnnnttaattaattaannnnnaaacgctgactttatggtatgctagtatcatgaaaagaaaatgtaaggggttaaacttaatataaatttactatatttcagtcttcttttcataaaagaaaggagttggtagcttgcctcttagttcacattccgaacggcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUUCUUAAUUUUGAUAGGCCAGCGUUCGCCAUCAACAGGCACUUUACCACCUGUUUAAAACAGUUUUUCAAAAUAUGCUGCAUGNNNNNUUAAUUAAUUAANNNNNAAACGCUGACUUUAUGGUAUGCUAGUAUCAUGAAAAGAAAAUGUAAGGGGUUAAACUUAAUAUAAAUUUACUAUAUUUCAGUCUUCUUUUCAUAAAAGAAAGGAGUUGGUAGCUUGCCUCUUAGUUCACAUUCCGAACGGCUA ..((((((.............(((((((.......((((((..........)))))).....((((............))))...........................)))))))...(((((((((....))))))))).))))))...((((((((.......((((((.......))))))((((.((((((((.......))))))))))))......))))))))((((.......))))..... (-45.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCCGUUCGGAAUGUGAACUAAGAGGCAAGCUACCAACUCCUUUCUUUUAUGAAAAGAAGACUGAAAUAUAGUAAAUUUAUAUUAAGUUUAACCCCUUACAUUUUCUUUUCAUGAUACUAGCAUACCAUAAAGUCAGCGUUUNNNNNUUAAUUAAUUAANNNNNCAUGCAGCAUAUUUUGAAAAACUGUUUUAAACAGGUGGUAAAGUGCCUGUUGAUGGCGAACGCUGGCCUAUCAAAAUUAAGAAAUA ..((((((((.....))))).....)))..............((((((((((((((((((((.((........((((((((...))))))))........)))))))))))))))).................((((((((((......(((....)))......(((.((((((((((((.....((((.....))))....)))))))..))))))))..))))))))))...........)))))).. (-48.69) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 944 60 11 151 102 smit:SMT_795|5end_similar_to_O6-alkylguanine-DNA-alkyltransferase_704009..704239_NEGATIVE 415 57 11 209 154 smit:SMT_1331|5end_hypothetical_protein_1306236..1306466_NEGATIVE 331 60 15 225 186 smit:SMT_178|5end_50S_ribosomal_protein_L29_119161..119391_POSITIVE 329 65 22 78 37 smit:SMT_1559|5end_6-phosphofructokinase_1545429..1545659_NEGATIVE 324 58 12 68 13 smit:SMT_1696|5end_hypothetical_protein_1678182..1678412_POSITIVE 307 249 209 188 155 smit:SMT_1982|5end_conserved_hypothetical_protein_1913036..1913266_POSITIVE 306 49 2 70 13 smit:SMT_924|5end_primosomal_protein_N'_879903..880133_NEGATIVE 301 249 211 176 146 smit:SMT_1691|5end_putative_deoxyribonuclease_1674978..1675208_POSITIVE 301 249 211 201 171 smit:SMT_1156|5end_K07485_transposase_1099938..1100168_POSITIVE 299 250 209 149 95 smit:SMT_2032|5end_hydrolase,_alpha/beta_fold_family_1946421..1946651_NEGATIVE 299 47 19 57 34 smit:SMT_1296|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1257290..1257520_POSITIVE 294 250 206 198 142 smit:SMT_451|5end_thiamine-phosphate_pyrophosphorylase_388935..389165_POSITIVE 290 55 11 231 186 smit:SMT_752|5end_prephenate_dehydrogenase_656791..657021_NEGATIVE 290 68 21 102 48 smit:SMT_676|5end_DNA_helicase_II_585266..585496_NEGATIVE 285 224 188 44 2 smit:SMT_1700|5end_diaminopimelate_decarboxylase_1682032..1682262_POSITIVE 285 244 206 231 187 smit:SMT_131|5end_phosphatase,_putative_83663..83893_NEGATIVE 285 228 183 167 114 smit:SMT_104|5end_DNA_repair_protein_49623..49853_POSITIVE 284 249 208 67 26 smit:SMT_919|5end_hypothetical_protein_872499..872729_NEGATIVE 282 64 26 221 180 smit:SMT_1867|5end_peptide_chain_release_factor_1_1828218..1828448_NEGATIVE 282 250 209 178 112 smit:SMT_1826|5end_ATP_synthase_beta_chain_1797408..1797638_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 324 58 12 105 50 smit:SMT_1695|3end_ribulose-phosphate_3-epimerase_1678299..1678449_POSITIVE 311 229 187 50 5 smit:SMT_405|3end_zinc_metalloprotease_ZmpB,_truncated_339938..340088_POSITIVE 300 55 20 149 103 smit:SMT_798|3end_hypothetical_protein_707106..707256_POSITIVE 299 47 19 55 32 smit:SMT_1295|3end_transcriptional_regulator_CtsR_1257368..1257518_POSITIVE 297 229 181 77 34 smit:SMT_1097|3end_alcohol_dehydrogenase_/_acetaldehyde_dehydrogenase_1038697..1038847_NEGATIVE 290 68 21 65 11 smit:SMT_677|3end_DNA_topoisomerase_I_585303..585453_NEGATIVE 289 163 124 66 24 smit:SMT_1851|3end_ABC_transporter,_permease_protein,_putative_1815578..1815728_NEGATIVE 289 163 124 66 24 smit:SMT_80|3end_ABC_transporter,_permease_protein,_putative_10992..11142_POSITIVE 282 250 209 92 26 smit:SMT_1825|3end_ATP_synthase_F1,_gamma_subunit_1797402..1797552_POSITIVE 282 53 11 51 4 smit:SMT_1728|3end_exodeoxyribonuclease_VII_large_subunit_1714668..1714818_POSITIVE 282 250 209 92 26 smit:SMT_585|3end_ATP_synthase_gamma_chain_502527..502677_POSITIVE 278 229 188 88 44 smit:SMT_1353|3end_GTP-binding_protein_1330690..1330840_NEGATIVE 274 249 205 62 12 smit:SMT_952|3end_hypothetical_protein_900115..900265_NEGATIVE 273 248 204 109 49 smit:SMT_1534|3end_signal_peptidase_I_1517912..1518062_POSITIVE 271 230 197 42 9 smit:SMT_2038|3end_zinc_metalloprotease_ZmpB,_truncated_1949615..1949765_POSITIVE 269 66 23 64 22 smit:SMT_1900|3end_K03710_GntR_family_transcriptional_regulator_1850620..1850770_POSITIVE 269 42 4 137 97 smit:SMT_1285|3end_ribosomal_subunit_interface_protein_1248332..1248482_POSITIVE 262 50 1 126 80 smit:SMT_195|3end_30S_ribosomal_protein_S13_127322..127472_POSITIVE 258 238 192 62 7 smit:SMT_2013|3end_alpha-glycerophosphate_oxidase_1932521..1932671_POSITIVE 254 249 219 144 115 smit:SMT_1073|3end_L-asparaginase_1012251..1012401_POSITIVE