Origin IGS: aggtcttctcctttatagtgtgactggtcctttagtttgttttgcaacaagaaaataaactaaaagatgcgaataaatcnnnnnttaattaattaannnnntctgcctttcttctccatttcatgatataataggagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actcctattatatcatgaaatggagaagaaaggcagannnnnttaattaattaannnnngatttattcgcatcttttagtttattttcttgttgcaaaacaaactaaaggaccagtcacactataaaggagaagacct Mask Tandem Repeat Region ================================================ aggtcttctcctttatagtgtgactggtcctttagtttgttttgcaacaagaaaataaactaaaagatgcgaataaatcnnnnnttaattaattaannnnntctgcctttcttctccatttcatgatataataggagt Find is-nt database================================================ Query_seq: SMT_1448:SMT_1449|SMT_1448:SMT_1449:serine hydroxymethyltransferase:K08591 putative membrane protein:<-->:1431939..1432076 138 aggtcttctcctttatagtgtgactggtcctttagtttgttttgcaacaagaaaataaactaaaagatgcgaataaatcnnnnnttaattaattaannnnntctgcctttcttctccatttcatgatataataggagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1448:SMT_1449|SMT_1448:SMT_1449:serine hydroxymethyltransferase:K08591 putative membrane protein:<-->:1431939..1432076 138 aggtcttctcctttatagtgtgactggtcctttagtttgttttgcaacaagaaaataaactaaaagatgcgaataaatcnnnnnttaattaattaannnnntctgcctttcttctccatttcatgatataataggagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1448:SMT_1449|SMT_1448:SMT_1449:serine hydroxymethyltransferase:K08591 putative membrane protein:<-->:1431939..1432076 138 aggtcttctcctttatagtgtgactggtcctttagtttgttttgcaacaagaaaataaactaaaagatgcgaataaatcnnnnnttaattaattaannnnntctgcctttcttctccatttcatgatataataggagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggtcttctcctttatagtgtgactggtcctttagtttgttttgcaacaagaaaataaactaaaagatgcgaataaatcnnnnnttaattaattaannnnntctgcctttcttctccatttcatgatataataggagt Predict ORF larger than 30AA ================================================ aggtcttctcctttatagtgtgactggtcctttagtttgttttgcaacaagaaaataaactaaaagatgcgaataaatcnnnnnttaattaattaannnnntctgcctttcttctccatttcatgatataataggagt 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================================================ aggtcttctcctttatagtgtgactggtcctttagtttgttttgcaacaagaaaataaactaaaagatgcgaataaatcnnnnnttaattaattaannnnntctgcctttcttctccatttcatgatataataggagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1448:SMT_1449|SMT_1448:SMT_1449:serine hydroxymethyltransferase:K08591 putative membrane protein:<-->:1431939..1432076 138 aggtcttctcctttatagtgtgactggtcctttagtttgttttgcaacaagaaaataaactaaaagatgcgaataaatcnnnnnttaattaattaannnnntctgcctttcttctccatttcatgatataataggagt Intra-Species Hit: Count: 1 Min: 1 Max: 138 Len: 138 Subject: smit_SMT_1448_SMT_1449|serine hydroxymethyltransferase:K08591 putative membrane protein|NEGATIVE:POSITIVE|[1431939,1432076]|138 HSP 1 e-value: 6.0E-55 bit: 214.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 aggtcttctcctttatagtgtgactggtcctttagtttgttttgcaacaagaaaataaactaaaagatgcgaataaatcnnnnnttaattaattaannnnntctgcctttcttctccatttcatgatataataggagt aggtcttctcctttatagtgtgactggtcctttagtttgttttgcaacaagaaaataaactaaaagatgcgaataaatcnnnnnttaattaattaannnnntctgcctttcttctccatttcatgatataataggagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUCUUCUCCUUUAUAGUGUGACUGGUCCUUUAGUUUGUUUUGCAACAAGAAAAUAAACUAAAAGAUGCGAAUAAAUCNNNNNUUAAUUAAUUAANNNNNUCUGCCUUUCUUCUCCAUUUCAUGAUAUAAUAGGAGU .......((((((((((..((((...(((.(((((((((((((........))))))))))))).)))..(((...........((((....))))............))).........))))..))))).))))). (-23.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCCUAUUAUAUCAUGAAAUGGAGAAGAAAGGCAGANNNNNUUAAUUAAUUAANNNNNGAUUUAUUCGCAUCUUUUAGUUUAUUUUCUUGUUGCAAAACAAACUAAAGGACCAGUCACACUAUAAAGGAGAAGACCU .(((((.(((((...(((..(((....................................((.....))...(((((((((((.(((((.....).)))).)))))))))))))).)))...))))))))))....... (-22.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 847 50 1 141 92 smit:SMT_1448|5end_serine_hydroxymethyltransferase_1431848..1432078_NEGATIVE 288 41 1 143 94 smit:SMT_896|5end_hypothetical_protein_844003..844233_NEGATIVE 276 49 1 95 46 smit:SMT_1976|5end_immunoglobulin_A1_protease_1906950..1907180_POSITIVE 262 44 2 139 92 smit:SMT_435|5end_orotate_phosphoribosyltransferase_376842..377072_POSITIVE 255 47 4 142 94 smit:SMT_118|5end_K02026_multiple_sugar_transport_system_permease_protein_69430..69660_POSITIVE 252 47 2 113 76 smit:SMT_1928|5end_O-methyltransferase_family_protein_1869652..1869882_NEGATIVE 251 43 1 146 93 smit:SMT_1001|5end_aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_A_942161..942391_POSITIVE 247 41 2 43 6 smit:SMT_1957|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1890645..1890875_POSITIVE 247 40 2 223 185 smit:SMT_1284|5end_predicted_amidophosphoribosyltransferase_1246962..1247192_POSITIVE 244 47 4 136 92 smit:SMT_1885|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1840057..1840287_NEGATIVE 239 47 2 113 72 smit:SMT_1977|5end_endopeptidase_O_1907832..1908062_POSITIVE 238 45 2 190 138 smit:SMT_986|5end_threonyl-tRNA_synthetase_931092..931322_POSITIVE 238 45 2 190 138 smit:SMT_925|5end_DNA-directed_RNA_polymerase_omega_chain_880283..880513_NEGATIVE 234 40 4 69 33 smit:SMT_1646|5end_3-isopropylmalate_dehydratase_large_subunit_1632011..1632241_POSITIVE 233 44 1 79 33 smit:SMT_566|5end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_483498..483728_POSITIVE 233 45 8 46 16 smit:SMT_113|5end_hypothetical_protein_61425..61655_POSITIVE 232 43 3 191 143 smit:SMT_2133|5end_hypothetical_protein_2014007..2014237_NEGATIVE 232 43 3 209 161 smit:SMT_1535|5end_exodeoxyribonuclease_V_alpha_chain_1518067..1518297_POSITIVE 232 43 3 191 143 smit:SMT_872|5end_hypothetical_protein_820618..820848_NEGATIVE 232 43 3 226 178 smit:SMT_662|5end_A/G-specific_adenine_glycosylase_573827..574057_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 41 1 131 82 smit:SMT_897|3end_serine_O-acetyltransferase_844015..844165_NEGATIVE 262 44 2 105 58 smit:SMT_434|3end_orotidine_5'-phosphate_decarboxylase_376888..377038_POSITIVE 257 48 1 147 93 smit:SMT_915|3end_sucrose_operon_repressor_868619..868769_POSITIVE 255 47 4 128 80 smit:SMT_117|3end_K02025_multiple_sugar_transport_system_permease_protein_69496..69646_POSITIVE 252 47 2 75 38 smit:SMT_1929|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1869690..1869840_NEGATIVE 251 43 1 146 93 smit:SMT_1000|3end_glutamyl-tRNA_Gln_amidotransferase_subunit_C_942241..942391_POSITIVE 247 41 2 147 110 smit:SMT_1957|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1890829..1890979_POSITIVE 234 40 4 65 29 smit:SMT_1645|3end_hypothetical_protein_1632087..1632237_POSITIVE 232 43 3 76 28 smit:SMT_2134|3end_hypothetical_protein_2014122..2014272_NEGATIVE 232 43 3 73 25 smit:SMT_1670|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_1659295..1659445_POSITIVE 232 43 3 52 4 smit:SMT_1068|3end_ATP-dependent_DNA_helicase_RecG_1008986..1009136_POSITIVE 232 43 3 76 28 smit:SMT_873|3end_hypothetical_protein_820733..820883_NEGATIVE 232 43 3 76 28 smit:SMT_384|3end_hypothetical_protein_319860..320010_POSITIVE 226 46 4 122 71 smit:SMT_1893|3end_ABC_transporter_substrate-binding_protein_-_sugar_transport_1846492..1846642_POSITIVE 226 46 4 122 71 smit:SMT_1763|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1739927..1740077_POSITIVE 222 40 1 76 41 smit:SMT_1738|3end_peptidyl-prolyl_cis-trans_isomerase_1721341..1721491_POSITIVE 220 29 1 147 123 smit:SMT_1581|3end_transcriptional_regulator,_biotin_repressor_family_1573120..1573270_NEGATIVE 220 48 1 129 71 smit:SMT_1092|3end_transcription_antitermination_factor_1033160..1033310_NEGATIVE 216 42 2 144 96 smit:SMT_402|3end_two-component_response_regulator_YesN_331663..331813_POSITIVE 215 44 5 57 7 smit:SMT_793|3end_K02029_polar_amino_acid_transport_system_permease_protein_702571..702721_NEGATIVE