Origin IGS: gttgaccttagcttcacgagtgaattttacctcttgggnnnnnttaattaattaannnnnggattcagagaaaaagctagggaattaggagtagatgtctatatttgggaatgaaagacccttaataatccctgaagatcagataagaatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaattcttatctgatcttcagggattattaagggtctttcattcccaaatatagacatctactcctaattccctagctttttctctgaatccnnnnnttaattaattaannnnncccaagaggtaaaattcactcgtgaagctaaggtcaac Mask Tandem Repeat Region ================================================ gttgaccttagcttcacgagtgaattttacctcttgggnnnnnttaattaattaannnnnggattcagagaaaaagctagggaattaggagtagatgtctatatttgggaatgaaagacccttaataatccctgaagatcagataagaatttt Find is-nt database================================================ Query_seq: SMT_1860:SMT_1861|SMT_1860:SMT_1861:hypothetical protein:sucrose operon repressor (SCR operon regulatory protein):<-->:1823700..1823852 153 gttgaccttagcttcacgagtgaattttacctcttgggnnnnnttaattaattaannnnnggattcagagaaaaagctagggaattaggagtagatgtctatatttgggaatgaaagacccttaataatccctgaagatcagataagaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1860:SMT_1861|SMT_1860:SMT_1861:hypothetical protein:sucrose operon repressor (SCR operon regulatory protein):<-->:1823700..1823852 153 gttgaccttagcttcacgagtgaattttacctcttgggnnnnnttaattaattaannnnnggattcagagaaaaagctagggaattaggagtagatgtctatatttgggaatgaaagacccttaataatccctgaagatcagataagaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1860:SMT_1861|SMT_1860:SMT_1861:hypothetical protein:sucrose operon repressor (SCR operon regulatory protein):<-->:1823700..1823852 153 gttgaccttagcttcacgagtgaattttacctcttgggnnnnnttaattaattaannnnnggattcagagaaaaagctagggaattaggagtagatgtctatatttgggaatgaaagacccttaataatccctgaagatcagataagaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttgaccttagcttcacgagtgaattttacctcttgggnnnnnttaattaattaannnnnggattcagagaaaaagctagggaattaggagtagatgtctatatttgggaatgaaagacccttaataatccctgaagatcagataagaatttt Predict ORF larger than 30AA ================================================ gttgaccttagcttcacgagtgaattttacctcttgggnnnnnttaattaattaannnnnggattcagagaaaaagctagggaattaggagtagatgtctatatttgggaatgaaagacccttaataatccctgaagatcagataagaatttt 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================================================ gttgaccttagcttcacgagtgaattttacctcttgggnnnnnttaattaattaannnnnggattcagagaaaaagctagggaattaggagtagatgtctatatttgggaatgaaagacccttaataatccctgaagatcagataagaatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1860:SMT_1861|SMT_1860:SMT_1861:hypothetical protein:sucrose operon repressor (SCR operon regulatory protein):<-->:1823700..1823852 153 gttgaccttagcttcacgagtgaattttacctcttgggnnnnnttaattaattaannnnnggattcagagaaaaagctagggaattaggagtagatgtctatatttgggaatgaaagacccttaataatccctgaagatcagataagaatttt Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: smit_SMT_1860_SMT_1861|hypothetical protein:sucrose operon repressor (SCR operon regulatory protein)|NEGATIVE:POSITIVE|[1823700,1823852]|153 HSP 1 e-value: 6.0E-55 bit: 214.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 gttgaccttagcttcacgagtgaattttacctcttnnnnnnnnttaattaattaannnnnnnattcagagaaaaagctagggaattaggagtagatgtctatatttgggaatgaaagacccttaataatccctgaagatcagataagaatttt gttgaccttagcttcacgagtgaattttacctcttgggnnnnnttaattaattaannnnnggattcagagaaaaagctagggaattaggagtagatgtctatatttgggaatgaaagacccttaataatccctgaagatcagataagaatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUGACCUUAGCUUCACGAGUGAAUUUUACCUCUUGGGNNNNNUUAAUUAAUUAANNNNNGGAUUCAGAGAAAAAGCUAGGGAAUUAGGAGUAGAUGUCUAUAUUUGGGAAUGAAAGACCCUUAAUAAUCCCUGAAGAUCAGAUAAGAAUUUU .(((((((((((((......(((((((..((....)).......................)))))))......)))))))))..(((((.((((....))))....(((.........))).........)))))...))))........... (-25.31) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUCUUAUCUGAUCUUCAGGGAUUAUUAAGGGUCUUUCAUUCCCAAAUAUAGACAUCUACUCCUAAUUCCCUAGCUUUUUCUCUGAAUCCNNNNNUUAAUUAAUUAANNNNNCCCAAGAGGUAAAAUUCACUCGUGAAGCUAAGGUCAAC ............(((((((.(((((.......(((.........))).....(((....)))........))))).(((((.(((((...........((((....)))).........)))))..............))))).))))))).. (-21.81) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 859 110 61 201 152 smit:SMT_1860|5end_hypothetical_protein_1823609..1823839_NEGATIVE 307 109 65 173 132 smit:SMT_1602|5end_hypothetical_protein_1592385..1592615_POSITIVE 307 109 65 185 144 smit:SMT_1488|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1467157..1467387_POSITIVE 307 109 65 221 180 smit:SMT_1138|5end_hypothetical_protein_1079547..1079777_NEGATIVE 307 109 65 198 157 smit:SMT_833|5end_hypothetical_protein_predicted_by_Glimmer/Critica_775362..775592_NEGATIVE 307 109 65 182 141 smit:SMT_130|5end_capsular_polysaccharide_biosynthesis_protein_80995..81225_POSITIVE 250 101 61 195 160 smit:SMT_890|5end_K02029_polar_amino_acid_transport_system_permease_protein_836953..837183_POSITIVE 249 100 61 152 116 smit:SMT_687|5end_carbamoyl-phosphate_synthase,_large_subunit_599264..599494_NEGATIVE 241 109 65 172 131 smit:SMT_1963|5end_ribonuclease_BN,_putative_1896462..1896692_NEGATIVE 241 109 65 207 166 smit:SMT_1810|5end_hypothetical_protein_1785219..1785449_POSITIVE 241 109 65 159 118 smit:SMT_483|5end_transcriptional_activator_TipA,_putative_418827..419057_POSITIVE 234 109 64 230 187 smit:SMT_1214|5end_K03584_DNA_repair_protein_RecO_(recombination_protein_O)_1173422..1173652_NEGATIVE 233 109 65 171 119 smit:SMT_1200|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1163235..1163465_NEGATIVE 232 110 67 161 101 smit:SMT_762|5end_cation-transporting_ATPase,_E1-E2_family_protein_667691..667921_NEGATIVE 230 145 107 225 183 smit:SMT_1088|5end_hypothetical_protein_1024346..1024576_NEGATIVE 225 35 2 229 183 smit:SMT_1870|5end_K07566_putative_translation_factor_1829819..1830049_NEGATIVE 222 36 7 142 112 smit:SMT_2043|5end_putative_mucus_binding_protein_1954768..1954998_NEGATIVE 221 149 120 66 36 smit:SMT_926|5end_guanylate_kinase_880934..881164_NEGATIVE 218 38 3 179 141 smit:SMT_382|5end_valyl-tRNA_synthetase_317706..317936_POSITIVE 216 109 76 62 17 smit:SMT_716|5end_50S_ribosomal_protein_L31_622410..622640_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 109 65 42 1 smit:SMT_698|3end_uracil_permease_609769..609919_POSITIVE 307 109 65 43 2 smit:SMT_834|3end_hypothetical_protein_775517..775667_NEGATIVE 241 109 65 42 1 smit:SMT_1809|3end_MutT/NUDIX_family_protein_1785134..1785284_POSITIVE 241 109 65 42 1 smit:SMT_1140|3end_glycogen_phosphorylase_1081316..1081466_NEGATIVE 241 109 65 42 1 smit:SMT_890|3end_K02029_polar_amino_acid_transport_system_permease_protein_837692..837842_POSITIVE 227 110 61 68 20 smit:SMT_1152|3end_hypothetical_protein_1096400..1096550_NEGATIVE 213 106 61 83 36 smit:SMT_1848|3end_K03458_nucleobase:cation_symporter-2,_NCS2_family_1812694..1812844_NEGATIVE 212 38 10 39 3 smit:SMT_1253|3end_beta-galactosidase_1212912..1213062_NEGATIVE 211 99 65 137 96 smit:SMT_269|3end_phospho-N-acetylmuramoyl-pentapeptide-transferas_e_208785..208935_POSITIVE 208 118 73 81 20 smit:SMT_1533|3end_ribonuclease_HIII_1517294..1517444_POSITIVE 207 120 75 89 42 smit:SMT_935|3end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_888749..888899_POSITIVE 205 37 1 83 37 smit:SMT_1933|3end_K02006_cobalt_transport_system_ATP-binding_protein_1871986..1872136_NEGATIVE 203 100 76 87 60 smit:SMT_449|3end_hypothetical_protein_388219..388369_POSITIVE 202 108 78 56 26 smit:SMT_1248|3end_Na+/H+_antiporter_1208667..1208817_NEGATIVE 199 109 61 117 62 smit:SMT_942|3end_hypothetical_protein_893528..893678_NEGATIVE 198 109 67 40 1 smit:SMT_799|3end_hypothetical_protein_707296..707446_NEGATIVE 197 111 76 61 10 smit:SMT_1619|3end_K02006_cobalt_transport_system_ATP-binding_protein_1605471..1605621_NEGATIVE 196 109 67 38 1 smit:SMT_1964|3end_sodium/hydrogen_exchanger_family_protein_1896596..1896746_NEGATIVE 195 109 65 43 2 smit:SMT_1477|3end_K02077_zinc/manganese_transport_system_substrate-binding_protein_1459447..1459597_NEGATIVE 195 128 86 69 21 smit:SMT_1280|3end_cysteine_synthase_1243543..1243693_NEGATIVE