Origin IGS: gatgatgtaggcgaacaaggttactaaaccagtggcatgaggttgcgaatatctcctacatctcagttacgagtatcatagcagttaagggagccttggatattgctccaaatagccactcattcctagaaatgacaatatagggannnnnttaattaattaannnnngtcgtatcaagggtgaggttaag .........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 cttaacctcacccttgatacgacnnnnnttaattaattaannnnntccctatattgtcatttctaggaatgagtggctatttggagcaatatccaaggctcccttaactgctatgatactcgtaactgagatgtaggagatattcgcaacctcatgccactggtttagtaaccttgttcgcctacatcatc Mask Tandem Repeat Region ================================================ gatgatgtaggcgaacaaggttactaaaccagtggcatgaggttgcgaatatctcctacatctcagttacgagtatcatagcagttaagggagccttggatattgctccaaatagccactcattcctagaaatgacaatatagggannnnnttaattaattaannnnngtcgtatcaagggtgaggttaag Find is-nt database================================================ Query_seq: SMT_2077:SMT_2078|SMT_2077:SMT_2078:chloride channel protein:acetyl xylan esterase, putative:<-->:1979520..1979710 191 gatgatgtaggcgaacaaggttactaaaccagtggcatgaggttgcgaatatctcctacatctcagttacgagtatcatagcagttaagggagccttggatattgctccaaatagccactcattcctagaaatgacaatatagggannnnnttaattaattaannnnngtcgtatcaagggtgaggttaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2077:SMT_2078|SMT_2077:SMT_2078:chloride channel protein:acetyl xylan esterase, putative:<-->:1979520..1979710 191 gatgatgtaggcgaacaaggttactaaaccagtggcatgaggttgcgaatatctcctacatctcagttacgagtatcatagcagttaagggagccttggatattgctccaaatagccactcattcctagaaatgacaatatagggannnnnttaattaattaannnnngtcgtatcaagggtgaggttaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2077:SMT_2078|SMT_2077:SMT_2078:chloride channel protein:acetyl xylan esterase, putative:<-->:1979520..1979710 191 gatgatgtaggcgaacaaggttactaaaccagtggcatgaggttgcgaatatctcctacatctcagttacgagtatcatagcagttaagggagccttggatattgctccaaatagccactcattcctagaaatgacaatatagggannnnnttaattaattaannnnngtcgtatcaagggtgaggttaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgatgtaggcgaacaaggttactaaaccagtggcatgaggttgcgaatatctcctacatctcagttacgagtatcatagcagttaagggagccttggatattgctccaaatagccactcattcctagaaatgacaatatagggannnnnttaattaattaannnnngtcgtatcaagggtgaggttaag Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 51 End: 140 .................................................. M S Y I S V T S I I A V K G A L D I A P N S H S F L E M T I ................................................... gatgatgtaggcgaacaaggttactaaaccagtggcatgaggttgcgaatatctcctacatctcagttacgagtatcatagcagttaagggagccttggatattgctccaaatagccactcattcctagaaatgacaatatagggannnnnttaattaattaannnnngtcgtatcaagggtgaggttaag 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================================================ gatgatgtaggcgaacaaggttactaaaccagtggcatgaggttgcgaatatctcctacatctcagttacgagtatcatagcagttaagggagccttggatattgctccaaatagccactcattcctagaaatgacaatatagggannnnnttaattaattaannnnngtcgtatcaagggtgaggttaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_2077:SMT_2078|SMT_2077:SMT_2078:chloride channel protein:acetyl xylan esterase, putative:<-->:1979520..1979710 191 gatgatgtaggcgaacaaggttactaaaccagtggcatgaggttgcgaatatctcctacatctcagttacgagtatcatagcagttaagggagccttggatattgctccaaatagccactcattcctagaaatgacaatatagggannnnnttaattaattaannnnngtcgtatcaagggtgaggttaag Intra-Species Hit: Count: 1 Min: 1 Max: 191 Len: 191 Subject: smit_SMT_2077_SMT_2078|chloride channel protein:acetyl xylan esterase, putative|NEGATIVE:POSITIVE|[1979520,1979710]|191 HSP 1 e-value: 2.0E-86 bit: 319.0 Len: 191 Query Start:1 Query End:191 Subject Strand: POSITIVE Subject Start: 1 Subject End: 191 gatgatgtaggcgaacaaggttactaaaccagtggcatgaggttgcgaatatctcctacatctcagttacgagtatcatagcagttaagggagccttggatattgctccaaatagccactcattcctagaaatgacaatatagggannnnnttaattaattaannnnngtcgtatcaagggtgaggttaag gatgatgtaggcgaacaaggttactaaaccagtggcatgaggttgcgaatatctcctacatctcagttacgagtatcatagcagttaagggagccttggatattgctccaaatagccactcattcctagaaatgacaatatagggannnnnttaattaattaannnnngtcgtatcaagggtgaggttaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAUGUAGGCGAACAAGGUUACUAAACCAGUGGCAUGAGGUUGCGAAUAUCUCCUACAUCUCAGUUACGAGUAUCAUAGCAGUUAAGGGAGCCUUGGAUAUUGCUCCAAAUAGCCACUCAUUCCUAGAAAUGACAAUAUAGGGANNNNNUUAAUUAAUUAANNNNNGUCGUAUCAAGGGUGAGGUUAAG ((.((((((((.((....((((....)))).(..((.....))..).....)).)))))))))).((((.(.....).)))).((((..(((((..........)))))...))))..(((((.(((.((.(((((................................))))).)).))))))))...... (-45.75) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAACCUCACCCUUGAUACGACNNNNNUUAAUUAAUUAANNNNNUCCCUAUAUUGUCAUUUCUAGGAAUGAGUGGCUAUUUGGAGCAAUAUCCAAGGCUCCCUUAACUGCUAUGAUACUCGUAACUGAGAUGUAGGAGAUAUUCGCAACCUCAUGCCACUGGUUUAGUAACCUUGUUCGCCUACAUCAUC .................(((((..................................((((((....))))))(((((..((.(((((..........)))))...))..))))).....))))).....((((((((.((.....(((......)))....((((....))))....)).))))))))... (-38.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 955 130 81 221 172 smit:SMT_2077|5end_chloride_channel_protein_1979429..1979659_NEGATIVE 365 130 82 218 164 smit:SMT_1835|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1803894..1804124_POSITIVE 347 129 82 117 67 smit:SMT_229|5end_mechanosensitive_ion_channel_165623..165853_NEGATIVE 345 64 29 188 150 smit:SMT_1245|5end_SOS_responce_UmuC_protein_1205120..1205350_POSITIVE 339 100 52 126 70 smit:SMT_1473|5end_hypothetical_protein_1454320..1454550_POSITIVE 338 110 68 35 4 smit:SMT_141|5end_K03495_glucose_inhibited_division_protein_A_91408..91638_POSITIVE 297 117 71 197 143 smit:SMT_1354|5end_diacylglycerol_kinase_1332001..1332231_NEGATIVE 292 76 31 64 22 smit:SMT_1101|5end_K03210_preprotein_translocase_YajC_subunit_1042913..1043143_NEGATIVE 287 72 31 229 191 smit:SMT_949|5end_glycosyl_transferase,_family_2_897693..897923_NEGATIVE 286 64 24 66 26 smit:SMT_1328|5end_hypothetical_protein_1304468..1304698_NEGATIVE 281 130 83 203 146 smit:SMT_1471|5end_hypothetical_protein_1453933..1454163_NEGATIVE 277 57 11 65 12 smit:SMT_1644|5end_3-isopropylmalate_dehydrogenase_1630704..1630934_POSITIVE 269 124 84 226 179 smit:SMT_1682|5end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_1665337..1665567_POSITIVE 269 68 27 83 35 smit:SMT_1213|5end_fatty_acid/phospholipid_synthesis_protein_PlsX_1172655..1172885_NEGATIVE 269 99 61 53 13 smit:SMT_827|5end_hypothetical_protein_750389..750619_POSITIVE 269 78 33 210 151 smit:SMT_178|5end_50S_ribosomal_protein_L29_119161..119391_POSITIVE 267 130 81 203 171 smit:SMT_1620|5end_hypothetical_protein_1607240..1607470_NEGATIVE 267 71 35 186 152 smit:SMT_1214|5end_K03584_DNA_repair_protein_RecO_(recombination_protein_O)_1173422..1173652_NEGATIVE 264 111 76 215 171 smit:SMT_2155|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2028863..2029093_POSITIVE 263 140 91 68 22 smit:SMT_138|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_89262..89492_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 393 98 55 39 2 smit:SMT_140|3end_NUDIX_family_hydrolase_91498..91648_POSITIVE 347 129 82 74 24 smit:SMT_230|3end_hypothetical_protein_predicted_by_Glimmer/Critica_165666..165816_NEGATIVE 345 64 29 137 99 smit:SMT_1244|3end_putative_repressor_protein_1205149..1205299_POSITIVE 310 121 81 50 15 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 286 64 24 56 16 smit:SMT_1329|3end_GTP-binding_protein_CgtA_1304478..1304628_NEGATIVE 275 90 41 143 104 smit:SMT_322|3end_hypothetical_protein_261346..261496_POSITIVE 269 68 27 86 38 smit:SMT_1214|3end_K03584_DNA_repair_protein_RecO_(recombination_protein_O)_1172652..1172802_NEGATIVE 266 57 16 53 5 smit:SMT_1643|3end_2-isopropylmalate_synthase_1630772..1630922_POSITIVE 264 105 61 151 110 smit:SMT_1591|3end_DNA-entry_nuclease_1579468..1579618_POSITIVE 262 100 56 75 18 smit:SMT_1452|3end_ABC-type_uncharacterized_transport_system,_ATPase_component_1434676..1434826_NEGATIVE 261 122 88 134 100 smit:SMT_238|3end_hypothetical_protein_predicted_by_Glimmer/Critica_176945..177095_NEGATIVE 260 113 81 31 3 smit:SMT_822|3end_putative_mucus_binding_protein_734047..734197_NEGATIVE 259 66 28 117 71 smit:SMT_379|3end_acetyltransferase,_GNAT_family_316456..316606_POSITIVE 259 66 28 117 71 smit:SMT_370|3end_acetyltransferase,_GNAT_family_305328..305478_POSITIVE 257 130 95 151 112 smit:SMT_781|3end_hypothetical_protein_689509..689659_NEGATIVE 257 70 21 64 20 smit:SMT_147|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_98016..98166_POSITIVE 255 110 76 151 108 smit:SMT_2155|3end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2030268..2030418_POSITIVE 255 129 88 70 40 smit:SMT_1278|3end_30S_ribosomal_protein_S2_1242332..1242482_POSITIVE 254 99 53 111 71 smit:SMT_1726|3end_tRNA_pseudouridine_synthase_B_1712453..1712603_POSITIVE 253 69 21 103 55 smit:SMT_1351|3end_dephospho-CoA_kinase_1329212..1329362_NEGATIVE