Origin IGS: aatggtctccgtggtctacacgcagaaccttggggatagtacatctctgtagcagatggtgggaannnnnttaattaattaannnnnagcctgcaccattatccgcaatatacaaatttaattgtacggtttacttcttctacttttgttttctaaccataatcatactctgctgggtacaatgcagatccattatacctttagcttttaatcttcttcagaatataaatctctgcttcttgtcttcgtaacac .........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 gtgttacgaagacaagaagcagagatttatattctgaagaagattaaaagctaaaggtataatggatctgcattgtacccagcagagtatgattatggttagaaaacaaaagtagaagaagtaaaccgtacaattaaatttgtatattgcggataatggtgcaggctnnnnnttaattaattaannnnnttcccaccatctgctacagagatgtactatccccaaggttctgcgtgtagaccacggagaccatt Mask Tandem Repeat Region ================================================ aatggtctccgtggtctacacgcagaaccttggggatagtacatctctgtagcagatggtgggaannnnnttaattaattaannnnnagcctgcaccattatccgcaatatacaaatttaattgtacggtttacttcttctacttttgttttctaaccataatcatactctgctgggtacaatgcagatccattatacctttagcttttaatcttcttcagaatataaatctctgcttcttgtcttcgtaacac Find is-nt database================================================ Query_seq: SMT_2089:SMT_2090|SMT_2089:SMT_2090:dTDP-4-dehydrorhamnose 3,5-epimerase related enzyme:hypothetical protein predicted by Glimmer/Critica:-><-:1985331..1985584 254 aatggtctccgtggtctacacgcagaaccttggggatagtacatctctgtagcagatggtgggaannnnnttaattaattaannnnnagcctgcaccattatccgcaatatacaaatttaattgtacggtttacttcttctacttttgttttctaaccataatcatactctgctgggtacaatgcagatccattatacctttagcttttaatcttcttcagaatataaatctctgcttcttgtcttcgtaacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2089:SMT_2090|SMT_2089:SMT_2090:dTDP-4-dehydrorhamnose 3,5-epimerase related enzyme:hypothetical protein predicted by Glimmer/Critica:-><-:1985331..1985584 254 aatggtctccgtggtctacacgcagaaccttggggatagtacatctctgtagcagatggtgggaannnnnttaattaattaannnnnagcctgcaccattatccgcaatatacaaatttaattgtacggtttacttcttctacttttgttttctaaccataatcatactctgctgggtacaatgcagatccattatacctttagcttttaatcttcttcagaatataaatctctgcttcttgtcttcgtaacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2089:SMT_2090|SMT_2089:SMT_2090:dTDP-4-dehydrorhamnose 3,5-epimerase related enzyme:hypothetical protein predicted by Glimmer/Critica:-><-:1985331..1985584 254 aatggtctccgtggtctacacgcagaaccttggggatagtacatctctgtagcagatggtgggaannnnnttaattaattaannnnnagcctgcaccattatccgcaatatacaaatttaattgtacggtttacttcttctacttttgttttctaaccataatcatactctgctgggtacaatgcagatccattatacctttagcttttaatcttcttcagaatataaatctctgcttcttgtcttcgtaacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatggtctccgtggtctacacgcagaaccttggggatagtacatctctgtagcagatggtgggaannnnnttaattaattaannnnnagcctgcaccattatccgcaatatacaaatttaattgtacggtttacttcttctacttttgttttctaaccataatcatactctgctgggtacaatgcagatccattatacctttagcttttaatcttcttcagaatataaatctctgcttcttgtcttcgtaacac Predict ORF larger than 30AA ================================================ Protein_Len: 57 Strand: + Start: 78 End: 248 ............................................................................. M X X X P A P L S A I Y K F N C T V Y F F Y F C F L T I I I L C W V Q C R S I I P L A F N L L Q N I N L C F L S S ...... aatggtctccgtggtctacacgcagaaccttggggatagtacatctctgtagcagatggtgggaannnnnttaattaattaannnnnagcctgcaccattatccgcaatatacaaatttaattgtacggtttacttcttctacttttgttttctaaccataatcatactctgctgggtacaatgcagatccattatacctttagcttttaatcttcttcagaatataaatctctgcttcttgtcttcgtaacac 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================================================ aatggtctccgtggtctacacgcagaaccttggggatagtacatctctgtagcagatggtgggaannnnnttaattaattaannnnnagcctgcaccattatccgcaatatacaaatttaattgtacggtttacttcttctacttttgttttctaaccataatcatactctgctgggtacaatgcagatccattatacctttagcttttaatcttcttcagaatataaatctctgcttcttgtcttcgtaacac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 57 HP_score: -3.9 Tail_Score: -3.95448 Start: 176 End: 199 Full_Region: AATCATACTCTGCTG GGTACAATG CAGATC CATTATACC TTTAGCTTTTAATCT ...............................................................................................................................................................................GGTACAATGCAGATCCATTATACC....................................................... Find igs database================================================ Query_seq: SMT_2089:SMT_2090|SMT_2089:SMT_2090:dTDP-4-dehydrorhamnose 3,5-epimerase related enzyme:hypothetical protein predicted by Glimmer/Critica:-><-:1985331..1985584 254 aatggtctccgtggtctacacgcagaaccttggggatagtacatctctgtagcagatggtgggaannnnnttaattaattaannnnnagcctgcaccattatccgcaatatacaaatttaattgtacggtttacttcttctacttttgttttctaaccataatcatactctgctgggtacaatgcagatccattatacctttagcttttaatcttcttcagaatataaatctctgcttcttgtcttcgtaacac Intra-Species Hit: Count: 1 Min: 1 Max: 254 Len: 254 Subject: smit_SMT_2089_SMT_2090|dTDP-4-dehydrorhamnose 3,5-epimerase related enzyme:hypothetical protein predicted by Glimmer/Critica|POSITIVE:NEGATIVE|[1985331,1985584]|254 HSP 1 e-value: 1.0E-124 bit: 444.0 Len: 254 Query Start:1 Query End:254 Subject Strand: POSITIVE Subject Start: 1 Subject End: 254 aatggtctccgtggtctacacgcagaaccttggggatagtacatctctgtagcagatggtgggaannnnnttaattaattaannnnnagcctgcaccattatccgcaatatacaaatttaattgtacggtttacttcttctacttttgttttctaaccataatcatactctgctgggtacaatgcagatccattatacctttagcttttaatcttcttcagaatataaatctctgcttcttgtcttcgtaacac aatggtctccgtggtctacacgcagaaccttggggatagtacatctctgtagcagatggtgggaannnnnttaattaattaannnnnagcctgcaccattatccgcaatatacaaatttaattgtacggtttacttcttctacttttgttttctaaccataatcatactctgctgggtacaatgcagatccattatacctttagcttttaatcttcttcagaatataaatctctgcttcttgtcttcgtaacac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGGUCUCCGUGGUCUACACGCAGAACCUUGGGGAUAGUACAUCUCUGUAGCAGAUGGUGGGAANNNNNUUAAUUAAUUAANNNNNAGCCUGCACCAUUAUCCGCAAUAUACAAAUUUAAUUGUACGGUUUACUUCUUCUACUUUUGUUUUCUAACCAUAAUCAUACUCUGCUGGGUACAAUGCAGAUCCAUUAUACCUUUAGCUUUUAAUCUUCUUCAGAAUAUAAAUCUCUGCUUCUUGUCUUCGUAACAC .(((((...((((.....))))..(((((.((.(((((((.((((((....).)))))(..((.......((((....)))).......))..)...))))))).))...(((((......))))).))))).......................))))).....(((...((((((((.((((......)))).)))))..))).............((((.........))))............))).... (-44.84) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGUUACGAAGACAAGAAGCAGAGAUUUAUAUUCUGAAGAAGAUUAAAAGCUAAAGGUAUAAUGGAUCUGCAUUGUACCCAGCAGAGUAUGAUUAUGGUUAGAAAACAAAAGUAGAAGAAGUAAACCGUACAAUUAAAUUUGUAUAUUGCGGAUAAUGGUGCAGGCUNNNNNUUAAUUAAUUAANNNNNUUCCCACCAUCUGCUACAGAGAUGUACUAUCCCCAAGGUUCUGCGUGUAGACCACGGAGACCAUU ...((((.........((.((.....((((((((((....((........))...(((((((((......)))))))))...))))))))))...)).))...........))))............(((((......((((((....(((((...(((((..((.......((((....)))).......))))))))))))))))))..))))).........(((.((.((((.....)))).)))))... (-51.09) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 157 112 116 69 smit:SMT_1561|5end_putative_mucus_binding_protein_1553809..1554039_NEGATIVE 328 220 172 173 123 smit:SMT_1700|5end_diaminopimelate_decarboxylase_1682032..1682262_POSITIVE 315 50 10 82 37 smit:SMT_2131|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2011665..2011895_POSITIVE 299 159 121 128 90 smit:SMT_1059|5end_NAD(P)H-flavin_oxidoreductase_997379..997609_POSITIVE 281 63 22 109 69 smit:SMT_885|5end_single-stranded-DNA-specific_exonuclease_RecJ_832660..832890_NEGATIVE 278 59 13 231 181 smit:SMT_761|5end_prephenate_dehydrogenase_667150..667380_NEGATIVE 276 65 21 191 141 smit:SMT_425|5end_hypothetical_cytosolic_protein_368114..368344_POSITIVE 274 239 198 142 100 smit:SMT_360|5end_K07742_hypothetical_protein_295628..295858_POSITIVE 271 59 11 231 193 smit:SMT_1060|5end_K03977_GTP-binding_protein_998106..998336_POSITIVE 270 60 20 157 110 smit:SMT_2098|5end_similar_to_CDP-ribitol_pyrophosphorylase_1991376..1991606_POSITIVE 268 33 2 231 200 smit:SMT_1609|5end_hypothetical_protein_1598113..1598343_POSITIVE 268 50 4 73 23 smit:SMT_1332|5end_hypothetical_protein_1307576..1307806_NEGATIVE 267 220 176 222 169 smit:SMT_1694|5end_GTPase_1676674..1676904_POSITIVE 266 247 203 130 85 smit:SMT_1846|5end_acyl-ACP_thioesterase,_putative_1811410..1811640_POSITIVE 261 210 162 194 150 smit:SMT_1735|5end_K03596_GTP-binding_protein_LepA_1719365..1719595_POSITIVE 258 177 134 230 182 smit:SMT_1693|5end_dimethyladenosine_transferase_1675800..1676030_POSITIVE 256 248 205 117 71 smit:SMT_771|5end_spermidine/putrescine_transport_system_permease_protein_PotB_682183..682413_NEGATIVE 255 247 204 140 94 smit:SMT_1354|5end_diacylglycerol_kinase_1332001..1332231_NEGATIVE 254 49 4 215 173 smit:SMT_1465|5end_hypothetical_protein_1445409..1445639_POSITIVE 254 49 4 159 117 smit:SMT_389|5end_PTS_system,_galactitol-specific_IIA_component,_putative_321779..322009_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 220 172 106 56 smit:SMT_1699|3end_purine_operon_repressor_1682045..1682195_POSITIVE 303 60 13 75 31 smit:SMT_986|3end_threonyl-tRNA_synthetase_931684..931834_POSITIVE 299 159 121 131 93 smit:SMT_1058|3end_primosomal_protein_DnaI_997462..997612_POSITIVE 276 65 21 105 55 smit:SMT_424|3end_transcriptional_regulatory_protein_368108..368258_POSITIVE 274 239 198 120 78 smit:SMT_359|3end_transcription_termination-antitermination_factor_295686..295836_POSITIVE 268 50 4 57 7 smit:SMT_1333|3end_glycosyltransferase_1307592..1307742_NEGATIVE 261 210 162 115 71 smit:SMT_1734|3end_serine/threonine_protein_phosphatase_1719366..1719516_POSITIVE 254 49 4 77 35 smit:SMT_2044|3end_transcriptional_activator_TipA,_putative_1955274..1955424_NEGATIVE 254 49 4 77 35 smit:SMT_2016|3end_tyrosine_recombinase_1933021..1933171_NEGATIVE 254 49 4 87 45 smit:SMT_2001|3end_membrane_protease_protein_family_1923889..1924039_POSITIVE 254 49 4 87 45 smit:SMT_1985|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1914407..1914557_NEGATIVE 254 49 4 77 35 smit:SMT_1957|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1890829..1890979_POSITIVE 254 49 4 77 35 smit:SMT_1886|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1841198..1841348_POSITIVE 254 49 4 77 35 smit:SMT_1658|3end_hypothetical_protein_1648937..1649087_POSITIVE 254 49 4 77 35 smit:SMT_1558|3end_hypothetical_protein_1543855..1544005_NEGATIVE 254 49 4 87 45 smit:SMT_1464|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_1445361..1445511_POSITIVE 254 49 4 77 35 smit:SMT_1155|3end_ABC-type_oligopeptide_transport_system,_periplasmic_component_1099183..1099333_NEGATIVE 254 49 4 151 109 smit:SMT_388|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_321851..322001_POSITIVE 246 240 199 128 72 smit:SMT_2056|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1966735..1966885_POSITIVE 245 50 2 59 6 smit:SMT_1015|3end_galactose_operon_repressor_953019..953169_POSITIVE