Origin IGS: tttacacttctcctctatcgttctcactatattataccattttcaaaaagagaaagaaaagaacctgagatagtaaatctcaagttctttctttatctttttgcaagttagcatttaatgaaaatcaaaatga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcattttgattttcattaaatgctaacttgcaaaaagataaagaaagaacttgagatttactatctcaggttcttttctttctctttttgaaaatggtataatatagtgagaacgatagaggagaagtgtaaa Mask Tandem Repeat Region ================================================ tttacacttctcctctatcgttctcactatattataccattttcaaaaagagaaagaaaagaacctgagatagtaaatctcaagttctttctttatctttttgcaagttagcatttaatgaaaatcaaaatga Find is-nt database================================================ Query_seq: SMT_1560:SMT_1561|SMT_1560:SMT_1561:DNA polymerase III alpha subunit:putative mucus binding protein:<-<-:1548703..1548835 133 tttacacttctcctctatcgttctcactatattataccattttcaaaaagagaaagaaaagaacctgagatagtaaatctcaagttctttctttatctttttgcaagttagcatttaatgaaaatcaaaatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1560:SMT_1561|SMT_1560:SMT_1561:DNA polymerase III alpha subunit:putative mucus binding protein:<-<-:1548703..1548835 133 tttacacttctcctctatcgttctcactatattataccattttcaaaaagagaaagaaaagaacctgagatagtaaatctcaagttctttctttatctttttgcaagttagcatttaatgaaaatcaaaatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1560:SMT_1561|SMT_1560:SMT_1561:DNA polymerase III alpha subunit:putative mucus binding protein:<-<-:1548703..1548835 133 tttacacttctcctctatcgttctcactatattataccattttcaaaaagagaaagaaaagaacctgagatagtaaatctcaagttctttctttatctttttgcaagttagcatttaatgaaaatcaaaatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttacacttctcctctatcgttctcactatattataccattttcaaaaagagaaagaaaagaacctgagatagtaaatctcaagttctttctttatctttttgcaagttagcatttaatgaaaatcaaaatga Predict ORF larger than 30AA ================================================ tttacacttctcctctatcgttctcactatattataccattttcaaaaagagaaagaaaagaacctgagatagtaaatctcaagttctttctttatctttttgcaagttagcatttaatgaaaatcaaaatga 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: 82 Start: 31 End: 60 ..............................TTTTCTTTCTCTTTTTGAAAATGGTATAAT......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttacacttctcctctatcgttctcactatattataccattttcaaaaagagaaagaaaagaacctgagatagtaaatctcaagttctttctttatctttttgcaagttagcatttaatgaaaatcaaaatga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -9.5 Tail_Score: -4.62471 Start: 50 End: 97 Full_Region: TACCATTTTCAAAAA GAGAAAGAAAAGAACCTGAGAT AGTAA ATCTCAAGTTCTTTCTTTATC TTTTTGCAAGTTAGC .................................................GAGAAAGAAAAGAACCTGAGATAGTAAATCTCAAGTTCTTTCTTTATC.................................... TransTerm Strand: - Conf: 100 HP_score: -11.7 Tail_Score: -4.60487 Start: 50 End: 97 Full_Region: gctaacttgcaaaaa gataaagaaagaacttgagat ttact atctcaggttcttttctttctc tttttgaaaatggta .................................................gataaagaaagaacttgagatttactatctcaggttcttttctttctc.................................... TransTerm Strand: - Conf: 100 HP_score: -10.3 Tail_Score: -5.15682 Start: 61 End: 87 Full_Region: aaaaagataaagaaa gaacttgagat ttact atctcaggttc ttttctttctctttt ............................................................gaacttgagatttactatctcaggttc.............................................. Find igs database================================================ Query_seq: SMT_1560:SMT_1561|SMT_1560:SMT_1561:DNA polymerase III alpha subunit:putative mucus binding protein:<-<-:1548703..1548835 133 tttacacttctcctctatcgttctcactatattataccattttcaaaaagagaaagaaaagaacctgagatagtaaatctcaagttctttctttatctttttgcaagttagcatttaatgaaaatcaaaatga Intra-Species Hit: Count: 1 Min: 1 Max: 133 Len: 133 Subject: smit_SMT_1560_SMT_1561|DNA polymerase III alpha subunit:putative mucus binding protein|NEGATIVE:NEGATIVE|[1548703,1548835]|133 HSP 1 e-value: 7.0E-70 bit: 264.0 Len: 133 Query Start:1 Query End:133 Subject Strand: POSITIVE Subject Start: 1 Subject End: 133 tttacacttctcctctatcgttctcactatattataccattttcaaaaagagaaagaaaagaacctgagatagtaaatctcaagttctttctttatctttttgcaagttagcatttaatgaaaatcaaaatga tttacacttctcctctatcgttctcactatattataccattttcaaaaagagaaagaaaagaacctgagatagtaaatctcaagttctttctttatctttttgcaagttagcatttaatgaaaatcaaaatga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUACACUUCUCCUCUAUCGUUCUCACUAUAUUAUACCAUUUUCAAAAAGAGAAAGAAAAGAACCUGAGAUAGUAAAUCUCAAGUUCUUUCUUUAUCUUUUUGCAAGUUAGCAUUUAAUGAAAAUCAAAAUGA ......................................((((.((((((((.(((((((.((((.((((((.....)))))).))))))))))).)))))))).))))...(((((.((....))..))))). (-27.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAUUUUGAUUUUCAUUAAAUGCUAACUUGCAAAAAGAUAAAGAAAGAACUUGAGAUUUACUAUCUCAGGUUCUUUUCUUUCUCUUUUUGAAAAUGGUAUAAUAUAGUGAGAACGAUAGAGGAGAAGUGUAAA ((...(((.(((((((((.((((((.....((((((((.((((((((((((((((((.....))))))))))).))))))).))))))))....))))))....)))))))))))).....)).......... (-41.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 760 50 1 141 92 smit:SMT_1560|5end_DNA_polymerase_III_alpha_subunit_1548612..1548842_NEGATIVE 308 90 41 175 134 smit:SMT_1494|5end_nucleoside_diphosphate_kinase_1479500..1479730_POSITIVE 259 112 78 195 155 smit:SMT_76|5end_DNA_repair_and_genetic_recombination_protein_2677..2907_POSITIVE 249 73 31 208 162 smit:SMT_1341|5end_putative_cell_division_protein_1319115..1319345_NEGATIVE 249 47 4 140 88 smit:SMT_599|5end_glucosamine-1-phosphate_N-acetyltransferase_/_UDP-N-acetylglucosamine_pyrophosphorylase_514918..515148_POSITIVE 248 70 26 201 153 smit:SMT_1876|5end_transcriptional_regulator,_MarR_family_1833594..1833824_POSITIVE 244 43 1 94 42 smit:SMT_844|5end_putative_phospho-sugar_mutase_791064..791294_NEGATIVE 236 55 13 146 93 smit:SMT_165|5end_anaerobic_ribonucleoside-triphosphate_reductase_110762..110992_POSITIVE 233 86 46 202 167 smit:SMT_108|5end_hypothetical_protein_53488..53718_POSITIVE 225 49 5 180 124 smit:SMT_1339|5end_hypothetical_protein_1314746..1314976_NEGATIVE 224 109 65 131 94 smit:SMT_1543|5end_diphosphomevalonate_decarboxylase_1528024..1528254_NEGATIVE 221 43 7 131 93 smit:SMT_1056|5end_K07738_ATP-cone_domain_protein_994842..995072_POSITIVE 220 79 31 169 117 smit:SMT_1502|5end_pantothenate_kinase_1485927..1486157_POSITIVE 220 44 4 139 88 smit:SMT_572|5end_fructose_repressor_490239..490469_POSITIVE 216 66 30 142 98 smit:SMT_1584|5end_methyltransferase,_putative_1574713..1574943_POSITIVE 215 130 81 128 77 smit:SMT_775|5end_alpha-acetolactate_decarboxylase_685972..686202_NEGATIVE 214 112 83 125 93 smit:SMT_412|5end_hypothetical_protein_predicted_by_Glimmer/Critica_356606..356836_NEGATIVE 213 68 27 180 132 smit:SMT_344|5end_K02503_Hit-like_protein_involved_in_cell-cycle_regulation_283974..284204_NEGATIVE 212 116 73 143 95 smit:SMT_1568|5end_putative_transketolase_C-terminal_section_1560122..1560352_POSITIVE 211 108 63 80 35 smit:SMT_1863|5end_glutamyl_aminopeptidase_1825628..1825858_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 308 90 41 89 48 smit:SMT_1493|3end_DNA-directed_RNA_polymerase,_beta'_subunit/160_kD_subunit_1479494..1479644_POSITIVE 301 92 55 87 50 smit:SMT_1307|3end_glycerol_uptake_facilitator_protein_1272448..1272598_POSITIVE 272 90 48 84 39 smit:SMT_412|3end_hypothetical_protein_predicted_by_Glimmer/Critica_356436..356586_NEGATIVE 266 108 64 43 2 smit:SMT_1628|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1616610..1616760_NEGATIVE 258 90 42 86 44 smit:SMT_462|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_400414..400564_NEGATIVE 249 73 31 47 1 smit:SMT_1342|3end_protease_maturation_protein,_putative_1319276..1319426_NEGATIVE 244 43 1 69 17 smit:SMT_845|3end_hypothetical_protein_791089..791239_NEGATIVE 240 51 13 48 6 smit:SMT_1864|3end_integral_membrane_protein_1827172..1827322_POSITIVE 240 72 36 50 15 smit:SMT_346|3end_K01992_ABC-2_type_transport_system_permease_protein_285849..285999_POSITIVE 238 90 46 86 49 smit:SMT_469|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_404931..405081_NEGATIVE 233 86 46 84 49 smit:SMT_107|3end_ribose-phosphate_pyrophosphokinase_53450..53600_POSITIVE 229 97 57 95 57 smit:SMT_1604|3end_K05833_putative_ABC_transport_system_ATP-binding_protein_1595163..1595313_POSITIVE 224 109 65 149 112 smit:SMT_1544|3end_mevalonate_kinase_1528006..1528156_NEGATIVE 212 110 66 139 100 smit:SMT_2102|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1993982..1994132_NEGATIVE 212 116 73 146 98 smit:SMT_1567|3end_transketolase,_N-terminal_subunit_1560205..1560355_POSITIVE 211 108 63 81 36 smit:SMT_378|3end_hypothetical_protein_predicted_by_Glimmer/Critica_316083..316233_POSITIVE 209 49 10 125 77 smit:SMT_1107|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1047989..1048139_NEGATIVE 209 110 82 122 96 smit:SMT_618|3end_methionine_aminopeptidase_527637..527787_POSITIVE 208 104 65 135 102 smit:SMT_852|3end_K03978_GTP-binding_protein_797457..797607_NEGATIVE 207 112 78 126 88 smit:SMT_1846|3end_acyl-ACP_thioesterase,_putative_1812227..1812377_POSITIVE