Origin IGS: aaaaggactctgtctgattatcctaattggtcagagttttttggttataaaaagttaatttgaactataccaatttttactcttgacaagtgaaagaaacaagtatatactgtttttgctgattctataaaagaggaattagactataccaattttaaggagaaagcacagcttgtctgtgtcgtatatact .........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 agtatatacgacacagacaagctgtgctttctccttaaaattggtatagtctaattcctcttttatagaatcagcaaaaacagtatatacttgtttctttcacttgtcaagagtaaaaattggtatagttcaaattaactttttataaccaaaaaactctgaccaattaggataatcagacagagtcctttt Mask Tandem Repeat Region ================================================ aaaaggactctgtctgattatcctaattggtcagagttttttggttataaaaagttaatttgaactataccaatttttactcttgacaagtgaaagaaacaagtatatactgtttttgctgattctataaaagaggaattagactataccaattttaaggagaaagcacagcttgtctgtgtcgtatatact Find is-nt database================================================ Query_seq: SMT_222:SMT_223|SMT_222:SMT_223:beta-glucosidase:D-fructose-6-phosphate amidotransferase:->->:156491..156682 192 aaaaggactctgtctgattatcctaattggtcagagttttttggttataaaaagttaatttgaactataccaatttttactcttgacaagtgaaagaaacaagtatatactgtttttgctgattctataaaagaggaattagactataccaattttaaggagaaagcacagcttgtctgtgtcgtatatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_222:SMT_223|SMT_222:SMT_223:beta-glucosidase:D-fructose-6-phosphate amidotransferase:->->:156491..156682 192 aaaaggactctgtctgattatcctaattggtcagagttttttggttataaaaagttaatttgaactataccaatttttactcttgacaagtgaaagaaacaagtatatactgtttttgctgattctataaaagaggaattagactataccaattttaaggagaaagcacagcttgtctgtgtcgtatatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_222:SMT_223|SMT_222:SMT_223:beta-glucosidase:D-fructose-6-phosphate amidotransferase:->->:156491..156682 192 aaaaggactctgtctgattatcctaattggtcagagttttttggttataaaaagttaatttgaactataccaatttttactcttgacaagtgaaagaaacaagtatatactgtttttgctgattctataaaagaggaattagactataccaattttaaggagaaagcacagcttgtctgtgtcgtatatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaggactctgtctgattatcctaattggtcagagttttttggttataaaaagttaatttgaactataccaatttttactcttgacaagtgaaagaaacaagtatatactgtttttgctgattctataaaagaggaattagactataccaattttaaggagaaagcacagcttgtctgtgtcgtatatact Predict ORF larger than 30AA ================================================ aaaaggactctgtctgattatcctaattggtcagagttttttggttataaaaagttaatttgaactataccaatttttactcttgacaagtgaaagaaacaagtatatactgtttttgctgattctataaaagaggaattagactataccaattttaaggagaaagcacagcttgtctgtgtcgtatatact 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: 86 Start: 82 End: 111 .................................................................................CTTGACAAGTGAAAGAAACAAGTATATACT................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaggactctgtctgattatcctaattggtcagagttttttggttataaaaagttaatttgaactataccaatttttactcttgacaagtgaaagaaacaagtatatactgtttttgctgattctataaaagaggaattagactataccaattttaaggagaaagcacagcttgtctgtgtcgtatatact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_222:SMT_223|SMT_222:SMT_223:beta-glucosidase:D-fructose-6-phosphate amidotransferase:->->:156491..156682 192 aaaaggactctgtctgattatcctaattggtcagagttttttggttataaaaagttaatttgaactataccaatttttactcttgacaagtgaaagaaacaagtatatactgtttttgctgattctataaaagaggaattagactataccaattttaaggagaaagcacagcttgtctgtgtcgtatatact Intra-Species Hit: Count: 1 Min: 1 Max: 192 Len: 192 Subject: smit_SMT_222_SMT_223|beta-glucosidase:D-fructose-6-phosphate amidotransferase|POSITIVE:POSITIVE|[156491,156682]|192 HSP 1 e-value: 1.0E-105 bit: 381.0 Len: 192 Query Start:1 Query End:192 Subject Strand: POSITIVE Subject Start: 1 Subject End: 192 aaaaggactctgtctgattatcctaattggtcagagttttttggttataaaaagttaatttgaactataccaatttttactcttgacaagtgaaagaaacaagtatatactgtttttgctgattctataaaagaggaattagactataccaattttaaggagaaagcacagcttgtctgtgtcgtatatact aaaaggactctgtctgattatcctaattggtcagagttttttggttataaaaagttaatttgaactataccaatttttactcttgacaagtgaaagaaacaagtatatactgtttttgctgattctataaaagaggaattagactataccaattttaaggagaaagcacagcttgtctgtgtcgtatatact Inter-species Hit: Count: 3 Min: 2 Max: 192 Len: 191 Subject: NC_008533_SPD_0247_SPD_0248|glycosyl hydrolase, family protein 1:glucosamine--fructose-6-phosphate aminotransferase, isomerizing|POSITIVE:POSITIVE|[240108,240298]|191 HSP 1 e-value: 4.0E-78 bit: 291.0 Len: 191 Query Start:2 Query End:192 Subject Strand: POSITIVE Subject Start: 1 Subject End: 191 .aaaggactctgtctgattatcctaattggtcagagttttttggttataaaaagttaatttgaactataccaatttttactcttgacaagtgaaagaaacaagtatatactgtttttgctgattctataaaagaggaattagactataccaattttaaggagaaagcacagcttgtctgtgtcgtatatact .aaaggactctgactgattatcccaatcggtcagagttttttgcttacaggagcttaatttgaactataccaatttttactcttgacaagtgaaagaaacaagtatatactgtttttgctgattctataaaagatgaattagactataccaattttaaggagaaagcacagcttgcctgtgtcgtatatact Subject: NC_003098_spr0244_spr0245|6-phospho-beta-glucosidase:D-fructose-6- phosphate amidotransferase|POSITIVE:POSITIVE|[240107,240297]|191 HSP 1 e-value: 4.0E-78 bit: 291.0 Len: 191 Query Start:2 Query End:192 Subject Strand: POSITIVE Subject Start: 1 Subject End: 191 .aaaggactctgtctgattatcctaattggtcagagttttttggttataaaaagttaatttgaactataccaatttttactcttgacaagtgaaagaaacaagtatatactgtttttgctgattctataaaagaggaattagactataccaattttaaggagaaagcacagcttgtctgtgtcgtatatact .aaaggactctgactgattatcccaatcggtcagagttttttgcttacaggagcttaatttgaactataccaatttttactcttgacaagtgaaagaaacaagtatatactgtttttgctgattctataaaagatgaattagactataccaattttaaggagaaagcacagcttgcctgtgtcgtatatact Subject: NC_003028_SP_0265_SP_0266|glycosyl hydrolase, family 1:D-fructose-6-phosphate amidotransferase|POSITIVE:POSITIVE|[239578,239769]|192 HSP 1 e-value: 6.0E-74 bit: 278.0 Len: 191 Query Start:2 Query End:192 Subject Strand: POSITIVE Subject Start: 1 Subject End: 192 .aaaggactctgtctgattatcctaattggtcagagttttt-tggttataaaaagttaatttgaactataccaatttttactcttgacaagtgaaagaaacaagtatatactgtttttgctgattctataaaagaggaattagactataccaattttaaggagaaagcacagcttgtctgtgtcgtatatact .aaaggactctgactgattatcccaatcggtcagagtttttatgcttacaggagcttaatttgaactataccaatttttactcttgacaagtgaaagaaacaagtatatactgtttttgctgattctataaaagatgaattagactataccaattttaaggagaaagcacagcttgcctgtgtcgtatatact Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGGACUCUGUCUGAUUAUCCUAAUUGGUCAGAGUUUUUUGGUUAUAAAAAGUUAAUUUGAACUAUACCAAUUUUUACUCUUGACAAGUGAAAGAAACAAGUAUAUACUGUUUUUGCUGAUUCUAUAAAAGAGGAAUUAGACUAUACCAAUUUUAAGGAGAAAGCACAGCUUGUCUGUGUCGUAUAUACU (((((((((((.(..((((...))))..).)))))))))))(((.......((((......))))..)))..((((((((.......)))))))).....(((((((((........((((((((........))))))))......((........)).....((((((.....)))))).))))))))) (-44.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAUAUACGACACAGACAAGCUGUGCUUUCUCCUUAAAAUUGGUAUAGUCUAAUUCCUCUUUUAUAGAAUCAGCAAAAACAGUAUAUACUUGUUUCUUUCACUUGUCAAGAGUAAAAAUUGGUAUAGUUCAAAUUAACUUUUUAUAACCAAAAAACUCUGACCAAUUAGGAUAAUCAGACAGAGUCCUUU (((((((((..(((((.....)))))..((((...(((((..((.((......)).))..))))).))))............)))))))))..............((((.((((.....(((((((((..............)))).)))))...)))))))).....(((((..((.....))))))).. (-32.94) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 46 2 158 113 smit:SMT_1500|5end_K03742_competence/damage-inducible_protein_CinA_N-terminal_domain_1483384..1483614_POSITIVE 266 120 79 67 31 smit:SMT_1932|5end_K02008_cobalt_transport_system_permease_protein_1872001..1872231_NEGATIVE 263 183 158 152 125 smit:SMT_1887|5end_LicC_protein_1841445..1841675_POSITIVE 253 48 3 213 174 smit:SMT_1608|5end_hypothetical_protein_1597595..1597825_POSITIVE 239 46 8 150 105 smit:SMT_1842|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1807858..1808088_NEGATIVE 239 184 141 66 13 smit:SMT_1734|5end_serine/threonine_protein_phosphatase_1718558..1718788_POSITIVE 238 179 131 66 6 smit:SMT_2083|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1982411..1982641_POSITIVE 238 49 7 93 46 smit:SMT_460|5end_6-phospho-beta-glucosidase_397819..398049_POSITIVE 237 184 142 213 171 smit:SMT_753|5end_chorismate_synthase_657967..658197_NEGATIVE 229 35 8 222 193 smit:SMT_1841|5end_hypothetical_protein_1807770..1808000_NEGATIVE 228 182 141 133 85 smit:SMT_1897|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1848858..1849088_NEGATIVE 225 70 21 100 57 smit:SMT_293|5end_dTDP-4-dehydrorhamnose_reductase_235919..236149_POSITIVE 221 129 83 81 30 smit:SMT_819|5end_hypothetical_protein_predicted_by_Glimmer/Critica_730421..730651_NEGATIVE 220 46 4 133 92 smit:SMT_622|5end_methionine_aminopeptidase_528939..529169_POSITIVE 219 70 22 116 64 smit:SMT_1484|5end_exonuclease_RexA_1464936..1465166_NEGATIVE 214 45 4 200 156 smit:SMT_1383|5end_ribonucleoside-diphosphate_reductase_alpha_chain_1361928..1362158_NEGATIVE 211 37 6 181 152 smit:SMT_948|5end_hypothetical_protein_predicted_by_Glimmer/Critica_896756..896986_NEGATIVE 210 45 1 125 76 smit:SMT_777|5end_hypothetical_protein_686770..687000_NEGATIVE 209 179 134 209 159 smit:SMT_545|5end_hypothetical_protein_predicted_by_Glimmer/Critica_461249..461479_POSITIVE 209 184 156 91 55 smit:SMT_194|5end_hypothetical_protein_predicted_by_Glimmer/Critica_126952..127182_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 46 2 119 74 smit:SMT_1499|3end_K03742_competence/damage-inducible_protein_CinA_N-terminal_domain_1483425..1483575_POSITIVE 266 120 79 82 46 smit:SMT_1933|3end_K02006_cobalt_transport_system_ATP-binding_protein_1871986..1872136_NEGATIVE 239 184 141 64 11 smit:SMT_1733|3end_DNA_repair_protein_RecN_1718636..1718786_POSITIVE 233 41 1 89 49 smit:SMT_222|3end_beta-glucosidase_156430..156580_POSITIVE 229 174 131 71 15 smit:SMT_269|3end_phospho-N-acetylmuramoyl-pentapeptide-transferas_e_208785..208935_POSITIVE 228 182 141 114 66 smit:SMT_1898|3end_aminotransferase_(class_V),_putative_1848877..1849027_NEGATIVE 220 46 4 85 44 smit:SMT_620|3end_hypothetical_protein_predicted_by_Glimmer/Critica_528971..529121_POSITIVE 216 180 131 118 71 smit:SMT_663|3end_phosphate_acetyltransferase_574016..574166_NEGATIVE 214 45 4 119 75 smit:SMT_1384|3end_glutaredoxin_1362009..1362159_NEGATIVE 209 179 134 70 20 smit:SMT_544|3end_aminoglycoside_6-adenylyltransferase_461190..461340_POSITIVE 207 159 114 85 34 smit:SMT_1826|3end_ATP_synthase_beta_chain_1797622..1797772_POSITIVE 207 42 2 51 10 smit:SMT_1401|3end_pyruvate_dehydrogenase_E1_component_beta_subunit_1378085..1378235_POSITIVE 205 180 132 85 42 smit:SMT_2174|3end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2045194..2045344_POSITIVE 204 180 137 141 100 smit:SMT_1569|3end_dihydroxy-acid_dehydratase_1563068..1563218_POSITIVE 204 38 1 69 23 smit:SMT_506|3end_K07729_putative_transcriptional_regulator_437411..437561_NEGATIVE 204 38 1 69 23 smit:SMT_503|3end_K07729_putative_transcriptional_regulator_435980..436130_NEGATIVE 202 183 143 77 33 smit:SMT_141|3end_K03495_glucose_inhibited_division_protein_A_93401..93551_POSITIVE 201 44 1 126 80 smit:SMT_1310|3end_D-alanine-activating_enzyme_1275867..1276017_POSITIVE 200 45 1 73 30 smit:SMT_1738|3end_peptidyl-prolyl_cis-trans_isomerase_1721341..1721491_POSITIVE 198 185 142 141 93 smit:SMT_1070|3end_hypothetical_protein_1009644..1009794_NEGATIVE