Origin IGS: ttgaattctcctttgactgtccgttaagccaccttaacatgtaatcgttttcttctattgtatccaagggattttccaaggtcaatcctttttactaaaattttactaaactatcagtaaaaagcagaaaaatatgatatactaaccttaaagaaggaggattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaatcctccttctttaaggttagtatatcatatttttctgctttttactgatagtttagtaaaattttagtaaaaaggattgaccttggaaaatcccttggatacaatagaagaaaacgattacatgttaaggtggcttaacggacagtcaaaggagaattcaa Mask Tandem Repeat Region ================================================ ttgaattctcctttgactgtccgttaagccaccttaacatgtaatcgttttcttctattgtatccaagggattttccaaggtcaatcctttttactaaaattttactaaactatcagtaaaaagcagaaaaatatgatatactaaccttaaagaaggaggattt Find is-nt database================================================ Query_seq: SMT_1014:SMT_1015|SMT_1014:SMT_1015:galactokinase:galactose operon repressor:<-->:951914..952077 164 ttgaattctcctttgactgtccgttaagccaccttaacatgtaatcgttttcttctattgtatccaagggattttccaaggtcaatcctttttactaaaattttactaaactatcagtaaaaagcagaaaaatatgatatactaaccttaaagaaggaggattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1014:SMT_1015|SMT_1014:SMT_1015:galactokinase:galactose operon repressor:<-->:951914..952077 164 ttgaattctcctttgactgtccgttaagccaccttaacatgtaatcgttttcttctattgtatccaagggattttccaaggtcaatcctttttactaaaattttactaaactatcagtaaaaagcagaaaaatatgatatactaaccttaaagaaggaggattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1014:SMT_1015|SMT_1014:SMT_1015:galactokinase:galactose operon repressor:<-->:951914..952077 164 ttgaattctcctttgactgtccgttaagccaccttaacatgtaatcgttttcttctattgtatccaagggattttccaaggtcaatcctttttactaaaattttactaaactatcagtaaaaagcagaaaaatatgatatactaaccttaaagaaggaggattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgaattctcctttgactgtccgttaagccaccttaacatgtaatcgttttcttctattgtatccaagggattttccaaggtcaatcctttttactaaaattttactaaactatcagtaaaaagcagaaaaatatgatatactaaccttaaagaaggaggattt Predict ORF larger than 30AA ================================================ ttgaattctcctttgactgtccgttaagccaccttaacatgtaatcgttttcttctattgtatccaagggattttccaaggtcaatcctttttactaaaattttactaaactatcagtaaaaagcagaaaaatatgatatactaaccttaaagaaggaggattt 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: 57 End: 86 ........................................................ATTGACCTTGGAAAATCCCTTGGATACAAT.............................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 72 End: 101 .......................................................................TTTTCCAAGGTCAATCCTTTTTACTAAAAT............................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgaattctcctttgactgtccgttaagccaccttaacatgtaatcgttttcttctattgtatccaagggattttccaaggtcaatcctttttactaaaattttactaaactatcagtaaaaagcagaaaaatatgatatactaaccttaaagaaggaggattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1014:SMT_1015|SMT_1014:SMT_1015:galactokinase:galactose operon repressor:<-->:951914..952077 164 ttgaattctcctttgactgtccgttaagccaccttaacatgtaatcgttttcttctattgtatccaagggattttccaaggtcaatcctttttactaaaattttactaaactatcagtaaaaagcagaaaaatatgatatactaaccttaaagaaggaggattt Intra-Species Hit: Count: 1 Min: 1 Max: 164 Len: 164 Subject: smit_SMT_1014_SMT_1015|galactokinase:galactose operon repressor|NEGATIVE:POSITIVE|[951914,952077]|164 HSP 1 e-value: 3.0E-88 bit: 325.0 Len: 164 Query Start:1 Query End:164 Subject Strand: POSITIVE Subject Start: 1 Subject End: 164 ttgaattctcctttgactgtccgttaagccaccttaacatgtaatcgttttcttctattgtatccaagggattttccaaggtcaatcctttttactaaaattttactaaactatcagtaaaaagcagaaaaatatgatatactaaccttaaagaaggaggattt ttgaattctcctttgactgtccgttaagccaccttaacatgtaatcgttttcttctattgtatccaagggattttccaaggtcaatcctttttactaaaattttactaaactatcagtaaaaagcagaaaaatatgatatactaaccttaaagaaggaggattt Inter-species Hit: Count: 3 Min: 2 Max: 148 Len: 147 Subject: NC_008533_SPD_1634_SPD_1635|galactokinase:galactose operon repressor|NEGATIVE:POSITIVE|[1649301,1649463]|163 HSP 1 e-value: 5.0E-71 bit: 268.0 Len: 143 Query Start:6 Query End:148 Subject Strand: POSITIVE Subject Start: 6 Subject End: 148 .....ttctcctttgactgtccgttaagccaccttaacatgtaatcgttttcttctattgtatccaagggattttccaaggtcaatcctttttactaaaattttactaaactatcagtaaaaagcagaaaaatatgatatactaacct................ .....ttctcctttgactgtccgttaagccaccttaacgtgtaatcgttttcttctattgtatccaagggatttcccaaggtcaatcctttttactaaaattttactaaactatcagtaaaaagcagaaaaatatgatatactaacct................ Subject: NC_003098_spr1668_spr1669|galactokinase:GalR, member of GalR-LacI family of transcriptional regulators, binds DNA; regulator of gal operon|NEGATIVE:POSITIVE|[1641770,1641932]|163 HSP 1 e-value: 5.0E-71 bit: 268.0 Len: 143 Query Start:6 Query End:148 Subject Strand: POSITIVE Subject Start: 6 Subject End: 148 .....ttctcctttgactgtccgttaagccaccttaacatgtaatcgttttcttctattgtatccaagggattttccaaggtcaatcctttttactaaaattttactaaactatcagtaaaaagcagaaaaatatgatatactaacct................ .....ttctcctttgactgtccgttaagccaccttaacgtgtaatcgttttcttctattgtatccaagggatttcccaaggtcaatcctttttactaaaattttactaaactatcagtaaaaagcagaaaaatatgatatactaacct................ Subject: NC_003028_SP_1853_SP_1854|galactokinase:galactose operon repressor|NEGATIVE:POSITIVE|[1761727,1761890]|164 HSP 1 e-value: 7.0E-55 bit: 214.0 Len: 147 Query Start:2 Query End:148 Subject Strand: POSITIVE Subject Start: 2 Subject End: 149 .tgaattctcctttgactgtccgttaagccaccttaacatgtaatcgttttctt-ctattgtatccaagggattttccaaggtcaatcctttttactaaaattttactaaactatcagtaaaaagcagaaaaatatgatatactaacct................ .tgaattctcctttgactgtccgttaagccatcttaacgtgtaatcgttttctttctattatatccaaggaattttccaaggtcaatcctttttactaaaattttagtaaaatatcagtaaaaagaagaaaaacatgatatactaacct................ Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAUUCUCCUUUGACUGUCCGUUAAGCCACCUUAACAUGUAAUCGUUUUCUUCUAUUGUAUCCAAGGGAUUUUCCAAGGUCAAUCCUUUUUACUAAAAUUUUACUAAACUAUCAGUAAAAAGCAGAAAAAUAUGAUAUACUAACCU .....................((((((....))))))..((((((((.((.((((...(((...((((((((..(....)..)))))))).))).....(((((((........)))))))...)))).)).))))).)))...... (-24.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUUAGUAUAUCAUAUUUUUCUGCUUUUUACUGAUAGUUUAGUAAAAUUUUAGUAAAAAGGAUUGACCUUGGAAAAUCCCUUGGAUACAAUAGAAGAAAACGAUUACAUGUUAAGGUGGCUUAACGGACAGUCAAAGGAGAAUUCA ...........((...(((((((((((((((((((.(((((....))))))))))))))))......((..((......))..))......))))))))...((((...(((((((....)))))))...))))......))..... (-29.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 847 50 1 142 93 smit:SMT_1014|5end_galactokinase_951823..952053_NEGATIVE 268 105 65 119 83 smit:SMT_1340|5end_phosphoenolpyruvate_carboxylase_1317867..1318097_NEGATIVE 266 59 12 53 3 smit:SMT_1613|5end_ribosomal_large_subunit_pseudouridine_synthase_B_1600608..1600838_POSITIVE 264 90 61 112 86 smit:SMT_1747|5end_anthranilate_synthase_component_I_1726279..1726509_POSITIVE 262 54 11 43 4 smit:SMT_2166|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2039569..2039799_POSITIVE 262 34 7 133 98 smit:SMT_1380|5end_pyrroline-5-carboxylate_reductase_1358464..1358694_NEGATIVE 257 55 11 204 158 smit:SMT_1112|5end_K02248_competence_protein_ComGF_1051848..1052078_NEGATIVE 254 88 49 45 7 smit:SMT_2013|5end_alpha-glycerophosphate_oxidase_1931833..1932063_POSITIVE 254 76 31 153 111 smit:SMT_1794|5end_SOS_responce_UmuC_protein_1769074..1769304_NEGATIVE 254 88 49 45 7 smit:SMT_1306|5end_alpha-glycerophosphate_oxidase_1269767..1269997_POSITIVE 253 88 44 77 31 smit:SMT_1584|5end_methyltransferase,_putative_1574713..1574943_POSITIVE 251 47 6 223 176 smit:SMT_1284|5end_predicted_amidophosphoribosyltransferase_1246962..1247192_POSITIVE 251 47 13 230 191 smit:SMT_181|5end_50S_ribosomal_protein_L24_120125..120355_POSITIVE 250 67 27 118 71 smit:SMT_1363|5end_50S_ribosomal_protein_L20_1343613..1343843_NEGATIVE 248 34 4 128 95 smit:SMT_297|5end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_238547..238777_POSITIVE 248 34 4 212 179 smit:SMT_294|5end_alpha-glucosidase,_family_31_of_glycosyl_hydrolase_237165..237395_POSITIVE 247 47 7 136 100 smit:SMT_1609|5end_hypothetical_protein_1598113..1598343_POSITIVE 244 69 21 197 148 smit:SMT_1371|5end_hypothetical_protein_1350794..1351024_NEGATIVE 243 36 8 231 202 smit:SMT_971|5end_hypothetical_protein_918965..919195_NEGATIVE 242 66 22 67 30 smit:SMT_1359|5end_dihydroorotate_dehydrogenase_electron_transfer_subunit_1338003..1338233_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 268 105 65 94 58 smit:SMT_1341|3end_putative_cell_division_protein_1317892..1318042_NEGATIVE 266 59 12 66 16 smit:SMT_1612|3end_K06024_segregation_and_condensation_protein_B_1600701..1600851_POSITIVE 262 34 7 129 94 smit:SMT_1381|3end_gamma-glutamyl_phosphate_reductase_1358468..1358618_NEGATIVE 251 47 13 151 112 smit:SMT_180|3end_50S_ribosomal_protein_L14_120126..120276_POSITIVE 250 67 27 66 19 smit:SMT_1364|3end_50S_ribosomal_protein_L35_1343665..1343815_NEGATIVE 247 47 7 139 103 smit:SMT_1608|3end_hypothetical_protein_1598196..1598346_POSITIVE 242 45 2 105 56 smit:SMT_401|3end_peptide_methionine_sulfoxide_reductase_330855..331005_POSITIVE 236 97 56 52 2 smit:SMT_1683|3end_phenylalanyl-tRNA_synthetase_beta_chain_1666344..1666494_NEGATIVE 230 95 54 91 40 smit:SMT_1065|3end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1005452..1005602_POSITIVE 224 126 85 134 89 smit:SMT_1322|3end_K02075_zinc/manganese_transport_system_permease_protein_1292257..1292407_POSITIVE 222 86 42 90 36 smit:SMT_1181|3end_phosphotransferase_system,_mannose/fructose-specific_component_IIA_1139413..1139563_NEGATIVE 221 76 35 42 4 smit:SMT_1795|3end_DNA_polymerase_III,_delta_subunit_1769185..1769335_NEGATIVE 220 76 38 105 71 smit:SMT_1462|3end_phosphate_ABC_transporter,_ATP-binding_protein,_putative_1443978..1444128_POSITIVE 220 49 9 125 78 smit:SMT_310|3end_3-oxoacyl-_252181..252331_POSITIVE 218 87 45 84 47 smit:SMT_1995|3end_phosphoglycerate_mutase_1920535..1920685_NEGATIVE 218 85 45 121 83 smit:SMT_1844|3end_hypothetical_protein_1809644..1809794_POSITIVE 218 85 45 121 83 smit:SMT_113|3end_hypothetical_protein_62785..62935_POSITIVE 216 93 56 88 36 smit:SMT_1410|3end_exonuclease_RexA_1388532..1388682_NEGATIVE 216 88 59 145 119 smit:SMT_1220|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1180509..1180659_NEGATIVE 214 96 52 69 22 smit:SMT_1013|3end_galactose-1-phosphate_uridylyltransferase_949601..949751_NEGATIVE