Origin IGS: tcaaatctcctttatttttatttaggcaaacgttttacgaaaacgtttgcactttctataatttaattataccactttaattttttttgtaaaggcttttataaaaaaaagtagacttttttctaaaatttttgtagtaaaaaaggagatattaaaatctcctcaaatatacttctattttattttagattttcaggaatcggcgcattgaaattcctgatccgattgaaccgannnnnttaattaattaannnnntgaatcaaggggaagcct .........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 aggcttccccttgattcannnnnttaattaattaannnnntcggttcaatcggatcaggaatttcaatgcgccgattcctgaaaatctaaaataaaatagaagtatatttgaggagattttaatatctccttttttactacaaaaattttagaaaaaagtctacttttttttataaaagcctttacaaaaaaaattaaagtggtataattaaattatagaaagtgcaaacgttttcgtaaaacgtttgcctaaataaaaataaaggagatttga Mask Tandem Repeat Region ================================================ tcaaatctcctttatttttatttaggcaaacgttttacgaaaacgtttgcactttctataatttaattataccactttaattttttttgtaaaggcttttataaaaaaaagtagacttttttctaaaatttttgtagtaaaaaaggagatattaaaatctcctcaaatatacttctattttattttagattttcaggaatcggcgcattgaaattcctgatccgattgaaccgannnnnttaattaattaannnnntgaatcaaggggaagcct Find is-nt database================================================ Query_seq: SMT_1780:SMT_1781|SMT_1780:SMT_1781:PTS system, glucose-specific IIABC component:transcriptional regulator, xre family:<-->:1758231..1758504 274 tcaaatctcctttatttttatttaggcaaacgttttacgaaaacgtttgcactttctataatttaattataccactttaattttttttgtaaaggcttttataaaaaaaagtagacttttttctaaaatttttgtagtaaaaaaggagatattaaaatctcctcaaatatacttctattttattttagattttcaggaatcggcgcattgaaattcctgatccgattgaaccgannnnnttaattaattaannnnntgaatcaaggggaagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1780:SMT_1781|SMT_1780:SMT_1781:PTS system, glucose-specific IIABC component:transcriptional regulator, xre family:<-->:1758231..1758504 274 tcaaatctcctttatttttatttaggcaaacgttttacgaaaacgtttgcactttctataatttaattataccactttaattttttttgtaaaggcttttataaaaaaaagtagacttttttctaaaatttttgtagtaaaaaaggagatattaaaatctcctcaaatatacttctattttattttagattttcaggaatcggcgcattgaaattcctgatccgattgaaccgannnnnttaattaattaannnnntgaatcaaggggaagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1780:SMT_1781|SMT_1780:SMT_1781:PTS system, glucose-specific IIABC component:transcriptional regulator, xre family:<-->:1758231..1758504 274 tcaaatctcctttatttttatttaggcaaacgttttacgaaaacgtttgcactttctataatttaattataccactttaattttttttgtaaaggcttttataaaaaaaagtagacttttttctaaaatttttgtagtaaaaaaggagatattaaaatctcctcaaatatacttctattttattttagattttcaggaatcggcgcattgaaattcctgatccgattgaaccgannnnnttaattaattaannnnntgaatcaaggggaagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcaaatctcctttatttttatttaggcaaacgttttacgaaaacgtttgcactttctataatttaattataccactttaattttttttgtaaaggcttttataaaaaaaagtagacttttttctaaaatttttgtagtaaaaaaggagatattaaaatctcctcaaatatacttctattttattttagattttcaggaatcggcgcattgaaattcctgatccgattgaaccgannnnnttaattaattaannnnntgaatcaaggggaagcct Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 80 End: 208 ............................................................................... M F F V K A F I K K S R L F S K I F V V K K E I L K S P Q I Y F Y F I L D F Q E S A H .................................................................. Protein_Len: 30 Strand: + Start: 151 End: 240 ...................................................................................................................................................... M K I S S N I L L F Y F R F S G I G A L K F L I R L N R X X .................................. tcaaatctcctttatttttatttaggcaaacgttttacgaaaacgtttgcactttctataatttaattataccactttaattttttttgtaaaggcttttataaaaaaaagtagacttttttctaaaatttttgtagtaaaaaaggagatattaaaatctcctcaaatatacttctattttattttagattttcaggaatcggcgcattgaaattcctgatccgattgaaccgannnnnttaattaattaannnnntgaatcaaggggaagcct 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: 87 Start: 33 End: 62 ................................TTTTACGAAAACGTTTGCACTTTCTATAAT.................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcaaatctcctttatttttatttaggcaaacgttttacgaaaacgtttgcactttctataatttaattataccactttaattttttttgtaaaggcttttataaaaaaaagtagacttttttctaaaatttttgtagtaaaaaaggagatattaaaatctcctcaaatatacttctattttattttagattttcaggaatcggcgcattgaaattcctgatccgattgaaccgannnnnttaattaattaannnnntgaatcaaggggaagcct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -7.2 Tail_Score: -3.6682 Start: 31 End: 45 Full_Region: tatagaaagtgcaaa cgtttt cgt aaaacg tttgcctaaataaaa ..............................cgttttcgtaaaacg..................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 81 HP_score: -5.6 Tail_Score: -5.14563 Start: 145 End: 162 Full_Region: tagaagtatatttga ggagat tttaat atctcc ttttttactacaaaa ................................................................................................................................................ggagattttaatatctcc................................................................................................................ Find igs database================================================ Query_seq: SMT_1780:SMT_1781|SMT_1780:SMT_1781:PTS system, glucose-specific IIABC component:transcriptional regulator, xre family:<-->:1758231..1758504 274 tcaaatctcctttatttttatttaggcaaacgttttacgaaaacgtttgcactttctataatttaattataccactttaattttttttgtaaaggcttttataaaaaaaagtagacttttttctaaaatttttgtagtaaaaaaggagatattaaaatctcctcaaatatacttctattttattttagattttcaggaatcggcgcattgaaattcctgatccgattgaaccgannnnnttaattaattaannnnntgaatcaaggggaagcct Intra-Species Hit: Count: 1 Min: 1 Max: 274 Len: 274 Subject: smit_SMT_1780_SMT_1781|PTS system, glucose-specific IIABC component:transcriptional regulator, xre family|NEGATIVE:POSITIVE|[1758231,1758504]|274 HSP 1 e-value: 7.0E-50 bit: 198.0 Len: 130 Query Start:145 Query End:274 Subject Strand: POSITIVE Subject Start: 145 Subject End: 274 ................................................................................................................................................ggagatattaaaatctcctcaaatatacttctattttattttagattttcaggaatcggcgcattgaaattcctgatccgattgaaccgannnnnttaattaattaannnnntgaatcaaggggaagcct ................................................................................................................................................ggagatattaaaatctcctcaaatatacttctattttattttagattttcaggaatcggcgcattgaaattcctgatccgattgaaccgannnnnttaattaattaannnnntgaatcaaggggaagcct HSP 2 e-value: 6.0E-35 bit: 149.0 Len: 75 Query Start:1 Query End:75 Subject Strand: POSITIVE Subject Start: 1 Subject End: 75 tcaaatctcctttatttttatttaggcaaacgttttacgaaaacgtttgcactttctataatttaattataccac....................................................................................................................................................................................................... tcaaatctcctttatttttatttaggcaaacgttttacgaaaacgtttgcactttctataatttaattataccac....................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAAUCUCCUUUAUUUUUAUUUAGGCAAACGUUUUACGAAAACGUUUGCACUUUCUAUAAUUUAAUUAUACCACUUUAAUUUUUUUUGUAAAGGCUUUUAUAAAAAAAAGUAGACUUUUUUCUAAAAUUUUUGUAGUAAAAAAGGAGAUAUUAAAAUCUCCUCAAAUAUACUUCUAUUUUAUUUUAGAUUUUCAGGAAUCGGCGCAUUGAAAUUCCUGAUCCGAUUGAACCGANNNNNUUAAUUAAUUAANNNNNUGAAUCAAGGGGAAGCCU .....(((((((.((((........((((((((((.....))))))))))...........(((((((.......((((.(((((((((((((....))))))))))))).))))......((((((((......((((....(((((((......)))))))......))))........))))))))...(((((((((((....))))..)))))))...)))))))...........................)))).)))))))..... (-55.64) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGCUUCCCCUUGAUUCANNNNNUUAAUUAAUUAANNNNNUCGGUUCAAUCGGAUCAGGAAUUUCAAUGCGCCGAUUCCUGAAAAUCUAAAAUAAAAUAGAAGUAUAUUUGAGGAGAUUUUAAUAUCUCCUUUUUUACUACAAAAAUUUUAGAAAAAAGUCUACUUUUUUUUAUAAAAGCCUUUACAAAAAAAAUUAAAGUGGUAUAAUUAAAUUAUAGAAAGUGCAAACGUUUUCGUAAAACGUUUGCCUAAAUAAAAAUAAAGGAGAUUUGA .....(((..((((..(......((((....)))).......)..))))..)))(((((((((..........)))))))))...((((((((........((((.....((((((((......))))))))...))))......))))))))...((((((.(((((((((((....(((....................))).................((.((((((((((.....))))))))))))..))))))).)))).)))))).. (-53.61) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 739 50 1 141 92 smit:SMT_1780|5end_PTS_system,_glucose-specific_IIABC_component_1758140..1758370_NEGATIVE 306 227 187 61 20 smit:SMT_1257|5end_acetolactate_synthase_small_subunit_1223173..1223403_NEGATIVE 268 229 188 188 144 smit:SMT_726|5end_ImpB/MucB/SamB_family_protein_631827..632057_NEGATIVE 262 234 195 161 120 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 258 229 190 140 100 smit:SMT_1993|5end_hypothetical_protein_1919800..1920030_NEGATIVE 243 207 162 171 125 smit:SMT_636|5end_ribonucleoside-diphosphate_reductase_beta_chain_541153..541383_POSITIVE 237 229 187 102 60 smit:SMT_2164|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_2037861..2038091_POSITIVE 237 208 170 135 99 smit:SMT_999|5end_hypothetical_protein_predicted_by_Glimmer/Critica_941642..941872_NEGATIVE 235 228 196 47 3 smit:SMT_315|5end_acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta_255681..255911_POSITIVE 232 234 191 213 158 smit:SMT_1845|5end_K01191_alpha-mannosidase_1809663..1809893_POSITIVE 232 234 191 213 158 smit:SMT_114|5end_alpha-mannosidase_62804..63034_POSITIVE 228 234 201 69 32 smit:SMT_158|5end_putative_Holliday_junction_resolvase_103795..104025_POSITIVE 228 57 15 220 173 smit:SMT_144|5end_hypothetical_protein_predicted_by_Glimmer/Critica_95553..95783_POSITIVE 227 226 183 46 3 smit:SMT_543|5end_topoisomerase_IV_subunit_B_458372..458602_POSITIVE 226 220 173 152 99 smit:SMT_1766|5end_sucrose-6-phosphate_hydrolase_1741702..1741932_POSITIVE 225 225 191 132 91 smit:SMT_2032|5end_hydrolase,_alpha/beta_fold_family_1946421..1946651_NEGATIVE 224 224 195 63 31 smit:SMT_1073|5end_L-asparaginase_1011209..1011439_POSITIVE 219 234 193 51 16 smit:SMT_1742|5end_sodium-dependent_phosphate_transporter_1723553..1723783_POSITIVE 217 50 5 137 96 smit:SMT_1696|5end_hypothetical_protein_1678182..1678412_POSITIVE 217 234 194 45 14 smit:SMT_857|5end_endo-beta-N-acetylglucosaminidase_802491..802721_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 306 227 187 68 27 smit:SMT_1258|3end_acetolactate_synthase_large_subunit_1223166..1223316_NEGATIVE 239 223 187 64 31 smit:SMT_1012|3end_xanthine_permease_949638..949788_POSITIVE 237 229 187 78 36 smit:SMT_2163|3end_cell_division_protein_FtsA_2037917..2038067_POSITIVE 232 234 191 114 59 smit:SMT_1844|3end_hypothetical_protein_1809644..1809794_POSITIVE 232 234 191 114 59 smit:SMT_113|3end_hypothetical_protein_62785..62935_POSITIVE 230 227 193 117 82 smit:SMT_1080|3end_CAAX_amino_terminal_protease_family_protein_1017783..1017933_NEGATIVE 228 234 201 65 28 smit:SMT_157|3end_hypothetical_protein_103871..104021_POSITIVE 226 220 173 142 89 smit:SMT_1765|3end_ABC_transporter_sugar_permease_1741772..1741922_POSITIVE 226 210 161 127 77 smit:SMT_340|3end_chaperone_protein_280566..280716_POSITIVE 225 225 197 149 123 smit:SMT_973|3end_signal_transduction_histidine_kinase_921203..921353_NEGATIVE 222 204 161 79 18 smit:SMT_693|3end_hypothetical_protein_604078..604228_POSITIVE 214 219 172 140 88 smit:SMT_769|3end_spermidine/putrescine-binding_periplasmic_protein_679519..679669_NEGATIVE 210 100 51 64 13 smit:SMT_1915|3end_pyridoxine_biosynthesis_protein_1860618..1860768_POSITIVE 210 49 7 139 94 smit:SMT_869|3end_hypothetical_protein_817228..817378_NEGATIVE 208 234 199 58 19 smit:SMT_815|3end_hypothetical_protein_723677..723827_NEGATIVE 206 48 6 123 86 smit:SMT_177|3end_K02878_large_subunit_ribosomal_protein_L16_119231..119381_POSITIVE 205 48 1 102 54 smit:SMT_1292|3end_K02050_sulfonate/nitrate/taurine_transport_system_permease_protein_1255017..1255167_POSITIVE 204 55 15 148 114 smit:SMT_562|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_480809..480959_NEGATIVE 204 228 190 103 67 smit:SMT_420|3end_hypothetical_protein_predicted_by_Glimmer/Critica_362982..363132_POSITIVE 202 229 188 139 102 smit:SMT_1773|3end_hypothetical_protein_1749905..1750055_POSITIVE