Origin IGS: catacttgatttgatgtatgctaaaggacttgagcagtcatctattggtctaccctcagatgctatatcgctttatggtacattagatagcactatnnnnnttaattaattaannnnnagaatcgaaccgcaaggtttcggttttctttctcttttcgcccataatttggtataataaacggt .........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 accgtttattataccaaattatgggcgaaaagagaaagaaaaccgaaaccttgcggttcgattctnnnnnttaattaattaannnnnatagtgctatctaatgtaccataaagcgatatagcatctgagggtagaccaatagatgactgctcaagtcctttagcatacatcaaatcaagtatg Mask Tandem Repeat Region ================================================ catacttgatttgatgtatgctaaaggacttgagcagtcatctattggtctaccctcagatgctatatcgctttatggtacattagatagcactatnnnnnttaattaattaannnnnagaatcgaaccgcaaggtttcggttttctttctcttttcgcccataatttggtataataaacggt Find is-nt database================================================ Query_seq: SMT_1583:SMT_1584|SMT_1583:SMT_1584:polysaccharide transporter, PST family:methyltransferase, putative:->->:1574670..1574852 183 catacttgatttgatgtatgctaaaggacttgagcagtcatctattggtctaccctcagatgctatatcgctttatggtacattagatagcactatnnnnnttaattaattaannnnnagaatcgaaccgcaaggtttcggttttctttctcttttcgcccataatttggtataataaacggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1583:SMT_1584|SMT_1583:SMT_1584:polysaccharide transporter, PST family:methyltransferase, putative:->->:1574670..1574852 183 catacttgatttgatgtatgctaaaggacttgagcagtcatctattggtctaccctcagatgctatatcgctttatggtacattagatagcactatnnnnnttaattaattaannnnnagaatcgaaccgcaaggtttcggttttctttctcttttcgcccataatttggtataataaacggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1583:SMT_1584|SMT_1583:SMT_1584:polysaccharide transporter, PST family:methyltransferase, putative:->->:1574670..1574852 183 catacttgatttgatgtatgctaaaggacttgagcagtcatctattggtctaccctcagatgctatatcgctttatggtacattagatagcactatnnnnnttaattaattaannnnnagaatcgaaccgcaaggtttcggttttctttctcttttcgcccataatttggtataataaacggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 catacttgatttgatgtatgctaaaggacttgagcagtcatctattggtctaccctcagatgctatatcgctttatggtacattagatagcactatnnnnnttaattaattaannnnnagaatcgaaccgcaaggtttcggttttctttctcttttcgcccataatttggtataataaacggt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 2 End: 106 . M L D L M Y A K G L E Q S S I G L P S D A I S L Y G T L D S T X X X N ............................................................................. catacttgatttgatgtatgctaaaggacttgagcagtcatctattggtctaccctcagatgctatatcgctttatggtacattagatagcactatnnnnnttaattaattaannnnnagaatcgaaccgcaaggtttcggttttctttctcttttcgcccataatttggtataataaacggt 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: 147 End: 176 ..................................................................................................................................................TTTCTCTTTTCGCCCATAATTTGGTATAAT....... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ catacttgatttgatgtatgctaaaggacttgagcagtcatctattggtctaccctcagatgctatatcgctttatggtacattagatagcactatnnnnnttaattaattaannnnnagaatcgaaccgcaaggtttcggttttctttctcttttcgcccataatttggtataataaacggt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1583:SMT_1584|SMT_1583:SMT_1584:polysaccharide transporter, PST family:methyltransferase, putative:->->:1574670..1574852 183 catacttgatttgatgtatgctaaaggacttgagcagtcatctattggtctaccctcagatgctatatcgctttatggtacattagatagcactatnnnnnttaattaattaannnnnagaatcgaaccgcaaggtttcggttttctttctcttttcgcccataatttggtataataaacggt Intra-Species Hit: Count: 1 Min: 1 Max: 183 Len: 183 Subject: smit_SMT_1583_SMT_1584|polysaccharide transporter, PST family:methyltransferase, putative|POSITIVE:POSITIVE|[1574670,1574852]|183 HSP 1 e-value: 1.0E-81 bit: 303.0 Len: 183 Query Start:1 Query End:183 Subject Strand: POSITIVE Subject Start: 1 Subject End: 183 catacttgatttgatgtatgctaaaggacttgagcagtcatctattggtctaccctcagatgctatatcgctttatggtacattagatagcactatnnnnnttaattaattaannnnnagaatcgaaccgcaaggtttcggttttctttctcttttcgcccataatttggtataataaacggt catacttgatttgatgtatgctaaaggacttgagcagtcatctattggtctaccctcagatgctatatcgctttatggtacattagatagcactatnnnnnttaattaattaannnnnagaatcgaaccgcaaggtttcggttttctttctcttttcgcccataatttggtataataaacggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUACUUGAUUUGAUGUAUGCUAAAGGACUUGAGCAGUCAUCUAUUGGUCUACCCUCAGAUGCUAUAUCGCUUUAUGGUACAUUAGAUAGCACUAUNNNNNUUAAUUAAUUAANNNNNAGAAUCGAACCGCAAGGUUUCGGUUUUCUUUCUCUUUUCGCCCAUAAUUUGGUAUAAUAAACGGU ........((((((.(((.(((((.(((..(((....)))))).))))).)))..))))))..(((((((..((((((.....(((......))).......................(((((((((((....)).)))))))))..............))))))..)))))))......... (-35.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCGUUUAUUAUACCAAAUUAUGGGCGAAAAGAGAAAGAAAACCGAAACCUUGCGGUUCGAUUCUNNNNNUUAAUUAAUUAANNNNNAUAGUGCUAUCUAAUGUACCAUAAAGCGAUAUAGCAUCUGAGGGUAGACCAAUAGAUGACUGCUCAAGUCCUUUAGCAUACAUCAAAUCAAGUAUG ..(((((((...........))))))).....((((.((..((((........))))))..)))).........................(((((.....(((((...(((((.(((.(((((((((..((....))..)))))).))).....))))))))...))))).......))))). (-29.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 71 31 111 69 smit:SMT_2074|5end_dTDP-glucose_4,6-dehydratase_1977021..1977251_POSITIVE 293 169 124 121 55 smit:SMT_1916|5end_glutamine_amidotransferase_1860539..1860769_POSITIVE 292 64 24 58 15 smit:SMT_122|5end_hypothetical_protein_74456..74686_POSITIVE 263 90 45 82 33 smit:SMT_764|5end_alanyl-tRNA_synthetase_672113..672343_NEGATIVE 262 96 54 129 82 smit:SMT_991|5end_hypothetical_protein_934425..934655_NEGATIVE 261 73 34 125 84 smit:SMT_331|5end_endo-beta-N-acetylglucosaminidase_266416..266646_POSITIVE 259 76 33 66 20 smit:SMT_1195|5end_amidophosphoribosyltransferase_1154818..1155048_NEGATIVE 258 50 7 62 16 smit:SMT_108|5end_hypothetical_protein_53488..53718_POSITIVE 256 63 26 58 25 smit:SMT_804|5end_S-adenosylmethionine_synthetase_715074..715304_NEGATIVE 256 77 33 220 175 smit:SMT_615|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_524884..525114_POSITIVE 255 63 25 190 130 smit:SMT_501|5end_ABC_transporter,_ATP-binding_protein_433227..433457_POSITIVE 253 90 43 204 150 smit:SMT_1370|5end_K06217_phosphate_starvation-inducible_protein_PhoH_and_related_proteins_1350494..1350724_NEGATIVE 253 59 12 63 13 smit:SMT_218|5end_undecaprenyl_pyrophosphate_synthetase_150155..150385_POSITIVE 249 59 11 224 172 smit:SMT_976|5end_hypothetical_protein_925183..925413_NEGATIVE 248 80 32 161 103 smit:SMT_1807|5end_putative_mucus_binding_protein_1784043..1784273_NEGATIVE 247 59 20 202 157 smit:SMT_1817|5end_exonuclease_RexB_1792113..1792343_NEGATIVE 247 50 20 152 125 smit:SMT_894|5end_hypothetical_protein_841701..841931_NEGATIVE 246 58 11 194 149 smit:SMT_1543|5end_diphosphomevalonate_decarboxylase_1528024..1528254_NEGATIVE 246 44 10 94 52 smit:SMT_1430|5end_hypothetical_protein_1414857..1415087_POSITIVE 245 77 31 193 140 smit:SMT_322|5end_hypothetical_protein_260193..260423_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 71 31 84 42 smit:SMT_2073|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1977074..1977224_POSITIVE 293 169 124 120 54 smit:SMT_1915|3end_pyridoxine_biosynthesis_protein_1860618..1860768_POSITIVE 263 90 45 60 11 smit:SMT_765|3end_hypothetical_protein_672135..672285_NEGATIVE 253 90 43 119 65 smit:SMT_1371|3end_hypothetical_protein_1350579..1350729_NEGATIVE 252 78 33 68 21 smit:SMT_2094|3end_serine_protease_1989243..1989393_NEGATIVE 246 44 10 93 51 smit:SMT_1429|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1414936..1415086_POSITIVE 245 170 124 47 6 smit:SMT_180|3end_50S_ribosomal_protein_L14_120126..120276_POSITIVE 242 164 131 115 77 smit:SMT_1516|3end_K02029_polar_amino_acid_transport_system_permease_protein_1497489..1497639_NEGATIVE 237 42 7 150 106 smit:SMT_2168|3end_threonyl-tRNA_synthetase_2041262..2041412_POSITIVE 237 42 7 150 106 smit:SMT_2150|3end_threonyl-tRNA_synthetase_2024905..2025055_POSITIVE 237 42 7 150 106 smit:SMT_2146|3end_threonyl-tRNA_synthetase_2022280..2022430_POSITIVE 237 42 7 150 106 smit:SMT_970|3end_threonyl-tRNA_synthetase_917795..917945_POSITIVE 235 161 121 126 93 smit:SMT_1366|3end_K02238_competence_protein_ComEC_1344648..1344798_NEGATIVE 235 74 32 132 86 smit:SMT_596|3end_K03976_putative_transcription_regulator_512590..512740_NEGATIVE 235 172 133 74 26 smit:SMT_407|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_353166..353316_POSITIVE 235 159 119 109 72 smit:SMT_365|3end_hypothetical_protein_301747..301897_POSITIVE 232 80 35 79 28 smit:SMT_1185|3end_beta-galactosidase_1142034..1142184_NEGATIVE 232 159 129 85 44 smit:SMT_359|3end_transcription_termination-antitermination_factor_295686..295836_POSITIVE 230 69 23 62 17 smit:SMT_681|3end_choline_kinase_589952..590102_NEGATIVE 228 79 34 134 69 smit:SMT_1652|3end_Cof_family_protein_1641408..1641558_POSITIVE