Origin IGS: aaacattccttattttcaatttataagtctattttagcacaaaagacaaaaatgagggcggaaatcccctagaaaagagttgatttctttgctgtagaatggaggctagaagcgcgtgggctaatttcagtaaagcggactcaaaccacaggcttcagtgttataagattgcgtaatgacctctgaggacatatcaaaacaaaagcttgaaatatcggaggggttgtgttagaatgaaagcataaagggaaaataatgcttctagcatatataactaaaaaaccccaccgtgccaccgatggggttttttgctaccctctaaaagggtgctacgtctctttatccatagcttgaaaagctcagatagtacgttaacaagtaacggagctagaaaaagggaaagtaactctagcatacataacnnnnnttaattaattaannnnnaaggatgtaaaccttgaaaaaagaagattgtaaaaaaggaaagact .........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.........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 agtctttccttttttacaatcttcttttttcaaggtttacatccttnnnnnttaattaattaannnnngttatgtatgctagagttactttccctttttctagctccgttacttgttaacgtactatctgagcttttcaagctatggataaagagacgtagcacccttttagagggtagcaaaaaaccccatcggtggcacggtggggttttttagttatatatgctagaagcattattttccctttatgctttcattctaacacaacccctccgatatttcaagcttttgttttgatatgtcctcagaggtcattacgcaatcttataacactgaagcctgtggtttgagtccgctttactgaaattagcccacgcgcttctagcctccattctacagcaaagaaatcaactcttttctaggggatttccgccctcatttttgtcttttgtgctaaaatagacttataaattgaaaataaggaatgttt Mask Tandem Repeat Region ================================================ aaacattccttattttcaatttataagtctattttagcacaaaagacaaaaatgagggcggaaatcccctagaaaagagttgatttctttgctgtagaatggaggctagaagcgcgtgggctaatttcagtaaagcggactcaaaccacaggcttcagtgttataagattgcgtaatgacctctgaggacatatcaaaacaaaagcttgaaatatcggaggggttgtgttagaatgaaagcataaagggaaaataatgcttctagcatatataactaaaaaaccccaccgtgccaccgatggggttttttgctaccctctaaaagggtgctacgtctctttatccatagcttgaaaagctcagatagtacgttaacaagtaacggagctagaaaaagggaaagtaactctagcatacataacnnnnnttaattaattaannnnnaaggatgtaaaccttgaaaaaagaagattgtaaaaaaggaaagact Find is-nt database================================================ Query_seq: SMT_2053:SMT_2054|SMT_2053:SMT_2054:hypothetical membrane associated protein:dTDP-glucose 4,6-dehydratase:<-->:1964513..1965002 490 aaacattccttattttcaatttataagtctattttagcacaaaagacaaaaatgagggcggaaatcccctagaaaagagttgatttctttgctgtagaatggaggctagaagcgcgtgggctaatttcagtaaagcggactcaaaccacaggcttcagtgttataagattgcgtaatgacctctgaggacatatcaaaacaaaagcttgaaatatcggaggggttgtgttagaatgaaagcataaagggaaaataatgcttctagcatatataactaaaaaaccccaccgtgccaccgatggggttttttgctaccctctaaaagggtgctacgtctctttatccatagcttgaaaagctcagatagtacgttaacaagtaacggagctagaaaaagggaaagtaactctagcatacataacnnnnnttaattaattaannnnnaaggatgtaaaccttgaaaaaagaagattgtaaaaaaggaaagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2053:SMT_2054|SMT_2053:SMT_2054:hypothetical membrane associated protein:dTDP-glucose 4,6-dehydratase:<-->:1964513..1965002 490 aaacattccttattttcaatttataagtctattttagcacaaaagacaaaaatgagggcggaaatcccctagaaaagagttgatttctttgctgtagaatggaggctagaagcgcgtgggctaatttcagtaaagcggactcaaaccacaggcttcagtgttataagattgcgtaatgacctctgaggacatatcaaaacaaaagcttgaaatatcggaggggttgtgttagaatgaaagcataaagggaaaataatgcttctagcatatataactaaaaaaccccaccgtgccaccgatggggttttttgctaccctctaaaagggtgctacgtctctttatccatagcttgaaaagctcagatagtacgttaacaagtaacggagctagaaaaagggaaagtaactctagcatacataacnnnnnttaattaattaannnnnaaggatgtaaaccttgaaaaaagaagattgtaaaaaaggaaagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2053:SMT_2054|SMT_2053:SMT_2054:hypothetical membrane associated protein:dTDP-glucose 4,6-dehydratase:<-->:1964513..1965002 490 aaacattccttattttcaatttataagtctattttagcacaaaagacaaaaatgagggcggaaatcccctagaaaagagttgatttctttgctgtagaatggaggctagaagcgcgtgggctaatttcagtaaagcggactcaaaccacaggcttcagtgttataagattgcgtaatgacctctgaggacatatcaaaacaaaagcttgaaatatcggaggggttgtgttagaatgaaagcataaagggaaaataatgcttctagcatatataactaaaaaaccccaccgtgccaccgatggggttttttgctaccctctaaaagggtgctacgtctctttatccatagcttgaaaagctcagatagtacgttaacaagtaacggagctagaaaaagggaaagtaactctagcatacataacnnnnnttaattaattaannnnnaaggatgtaaaccttgaaaaaagaagattgtaaaaaaggaaagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaacattccttattttcaatttataagtctattttagcacaaaagacaaaaatgagggcggaaatcccctagaaaagagttgatttctttgctgtagaatggaggctagaagcgcgtgggctaatttcagtaaagcggactcaaaccacaggcttcagtgttataagattgcgtaatgacctctgaggacatatcaaaacaaaagcttgaaatatcggaggggttgtgttagaatgaaagcataaagggaaaataatgcttctagcatatataactaaaaaaccccaccgtgccaccgatggggttttttgctaccctctaaaagggtgctacgtctctttatccatagcttgaaaagctcagatagtacgttaacaagtaacggagctagaaaaagggaaagtaactctagcatacataacnnnnnttaattaattaannnnnaaggatgtaaaccttgaaaaaagaagattgtaaaaaaggaaagact Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 253 End: 351 ............................................................................................................................................................................................................................................................ M M L L A Y I T K K P H R A T D G V F C Y P L K G C Y V S L S I A ........................................................................................................................................... Protein_Len: 40 Strand: + Start: 309 End: 428 .................................................................................................................................................................................................................................................................................................................... M L P S K R V L R L F I H S L K S S D S T L T S N G A R K R E S N S S I H N X X .............................................................. Protein_Len: 46 Strand: - Start: 278 End: 415 ..................................................................................................................................................................................................................................................................................... F V G G H W R H P K K S G E L L T S R R K I W L K F L E S L V N V L L P A L F L S L L E L M ........................................................................... Protein_Len: 51 Strand: - Start: 144 End: 296 ............................................................................................................................................... V V P K L T I L N R L S R Q P C I L V F A Q F I P P T T N S H F C L P F I I S R A Y I V L F G W R A M .................................................................................................................................................................................................. Protein_Len: 40 Strand: - Start: 32 End: 151 ............................... K L V F S L F S P P F G R S F L Q N R Q Q L I S A L L A H A L K L L A S E F W M ................................................................................................................................................................................................................................................................................................................................................... aaacattccttattttcaatttataagtctattttagcacaaaagacaaaaatgagggcggaaatcccctagaaaagagttgatttctttgctgtagaatggaggctagaagcgcgtgggctaatttcagtaaagcggactcaaaccacaggcttcagtgttataagattgcgtaatgacctctgaggacatatcaaaacaaaagcttgaaatatcggaggggttgtgttagaatgaaagcataaagggaaaataatgcttctagcatatataactaaaaaaccccaccgtgccaccgatggggttttttgctaccctctaaaagggtgctacgtctctttatccatagcttgaaaagctcagatagtacgttaacaagtaacggagctagaaaaagggaaagtaactctagcatacataacnnnnnttaattaattaannnnnaaggatgtaaaccttgaaaaaagaagattgtaaaaaaggaaagact 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: 89 Start: 206 End: 235 .............................................................................................................................................................................................................CTTGAAATATCGGAGGGGTTGTGTTAGAAT............................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaacattccttattttcaatttataagtctattttagcacaaaagacaaaaatgagggcggaaatcccctagaaaagagttgatttctttgctgtagaatggaggctagaagcgcgtgggctaatttcagtaaagcggactcaaaccacaggcttcagtgttataagattgcgtaatgacctctgaggacatatcaaaacaaaagcttgaaatatcggaggggttgtgttagaatgaaagcataaagggaaaataatgcttctagcatatataactaaaaaaccccaccgtgccaccgatggggttttttgctaccctctaaaagggtgctacgtctctttatccatagcttgaaaagctcagatagtacgttaacaagtaacggagctagaaaaagggaaagtaactctagcatacataacnnnnnttaattaattaannnnnaaggatgtaaaccttgaaaaaagaagattgtaaaaaaggaaagact Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 82 HP_score: -11.6 Tail_Score: -2.94099 Start: 272 End: 314 Full_Region: cacccttttagaggg tagcaaaaaaccccatcg gtggca cggtggggttttttagtta tatatgctagaagca ...............................................................................................................................................................................................................................................................................tagcaaaaaaccccatcggtggcacggtggggttttttagtta................................................................................................................................................................................ TransTerm Strand: + Conf: 85 HP_score: -7.2 Tail_Score: -5.15634 Start: 283 End: 304 Full_Region: TATATAACTAAAAAA CCCCACCG TGCCAC CGATGGGG TTTTTTGCTACCCTC ..........................................................................................................................................................................................................................................................................................CCCCACCGTGCCACCGATGGGG.......................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -9.4 Tail_Score: -5.35354 Start: 283 End: 304 Full_Region: gagggtagcaaaaaa ccccatcg gtggca cggtgggg ttttttagttatata ..........................................................................................................................................................................................................................................................................................ccccatcggtggcacggtgggg.......................................................................................................................................................................................... Find igs database================================================ Query_seq: SMT_2053:SMT_2054|SMT_2053:SMT_2054:hypothetical membrane associated protein:dTDP-glucose 4,6-dehydratase:<-->:1964513..1965002 490 aaacattccttattttcaatttataagtctattttagcacaaaagacaaaaatgagggcggaaatcccctagaaaagagttgatttctttgctgtagaatggaggctagaagcgcgtgggctaatttcagtaaagcggactcaaaccacaggcttcagtgttataagattgcgtaatgacctctgaggacatatcaaaacaaaagcttgaaatatcggaggggttgtgttagaatgaaagcataaagggaaaataatgcttctagcatatataactaaaaaaccccaccgtgccaccgatggggttttttgctaccctctaaaagggtgctacgtctctttatccatagcttgaaaagctcagatagtacgttaacaagtaacggagctagaaaaagggaaagtaactctagcatacataacnnnnnttaattaattaannnnnaaggatgtaaaccttgaaaaaagaagattgtaaaaaaggaaagact Intra-Species Hit: Count: 1 Min: 1 Max: 490 Len: 490 Subject: smit_SMT_2053_SMT_2054|hypothetical membrane associated protein:dTDP-glucose 4,6-dehydratase|NEGATIVE:POSITIVE|[1964513,1965002]|490 HSP 1 e-value: 0.0 bit: 912.0 Len: 490 Query Start:1 Query End:490 Subject Strand: POSITIVE Subject Start: 1 Subject End: 490 aaacattccttattttcaatttataagtctattttagcacaaaagacaaaaatgagggcggaaatcccctagaaaagagttgatttctttgctgtagaatggaggctagaagcgcgtgggctaatttcagtaaagcggactcaaaccacaggcttcagtgttataagattgcgtaatgacctctgaggacatatcaaaacaaaagcttgaaatatcggaggggttgtgttagaatgaaagcataaagggaaaataatgcttctagcatatataactaaaaaaccccaccgtgccaccgatggggttttttgctaccctctaaaagggtgctacgtctctttatccatagcttgaaaagctcagatagtacgttaacaagtaacggagctagaaaaagggaaagtaactctagcatacataacnnnnnttaattaattaannnnnaaggatgtaaaccttgaaaaaagaagattgtaaaaaaggaaagact aaacattccttattttcaatttataagtctattttagcacaaaagacaaaaatgagggcggaaatcccctagaaaagagttgatttctttgctgtagaatggaggctagaagcgcgtgggctaatttcagtaaagcggactcaaaccacaggcttcagtgttataagattgcgtaatgacctctgaggacatatcaaaacaaaagcttgaaatatcggaggggttgtgttagaatgaaagcataaagggaaaataatgcttctagcatatataactaaaaaaccccaccgtgccaccgatggggttttttgctaccctctaaaagggtgctacgtctctttatccatagcttgaaaagctcagatagtacgttaacaagtaacggagctagaaaaagggaaagtaactctagcatacataacnnnnnttaattaattaannnnnaaggatgtaaaccttgaaaaaagaagattgtaaaaaaggaaagact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACAUUCCUUAUUUUCAAUUUAUAAGUCUAUUUUAGCACAAAAGACAAAAAUGAGGGCGGAAAUCCCCUAGAAAAGAGUUGAUUUCUUUGCUGUAGAAUGGAGGCUAGAAGCGCGUGGGCUAAUUUCAGUAAAGCGGACUCAAACCACAGGCUUCAGUGUUAUAAGAUUGCGUAAUGACCUCUGAGGACAUAUCAAAACAAAAGCUUGAAAUAUCGGAGGGGUUGUGUUAGAAUGAAAGCAUAAAGGGAAAAUAAUGCUUCUAGCAUAUAUAACUAAAAAACCCCACCGUGCCACCGAUGGGGUUUUUUGCUACCCUCUAAAAGGGUGCUACGUCUCUUUAUCCAUAGCUUGAAAAGCUCAGAUAGUACGUUAACAAGUAACGGAGCUAGAAAAAGGGAAAGUAACUCUAGCAUACAUAACNNNNNUUAAUUAAUUAANNNNNAAGGAUGUAAACCUUGAAAAAAGAAGAUUGUAAAAAAGGAAAGACU .....((((((.(((.((((((.....(((.((((.((.................(((.((....))))).....(((((((.((((((((((((.((..((((((..(((((..((((......(((........)))......))))..)))))...((((((..............(((((((....((.((((.........)))).)).)))))))...(((((((((.....(((((............)))))))))))))))))))).(((((((((((.((......)).)))))))))))((.(((((.....)))))))...))))))...)).)))))......(((((......(((........)))...)))))......))))))).))))))).)).(((((........((((....)))).........))))).......)))).))))))))).))).))))))..... (-117.03) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCUUUCCUUUUUUACAAUCUUCUUUUUUCAAGGUUUACAUCCUUNNNNNUUAAUUAAUUAANNNNNGUUAUGUAUGCUAGAGUUACUUUCCCUUUUUCUAGCUCCGUUACUUGUUAACGUACUAUCUGAGCUUUUCAAGCUAUGGAUAAAGAGACGUAGCACCCUUUUAGAGGGUAGCAAAAAACCCCAUCGGUGGCACGGUGGGGUUUUUUAGUUAUAUAUGCUAGAAGCAUUAUUUUCCCUUUAUGCUUUCAUUCUAACACAACCCCUCCGAUAUUUCAAGCUUUUGUUUUGAUAUGUCCUCAGAGGUCAUUACGCAAUCUUAUAACACUGAAGCCUGUGGUUUGAGUCCGCUUUACUGAAAUUAGCCCACGCGCUUCUAGCCUCCAUUCUACAGCAAAGAAAUCAACUCUUUUCUAGGGGAUUUCCGCCCUCAUUUUUGUCUUUUGUGCUAAAAUAGACUUAUAAAUUGAAAAUAAGGAAUGUUU .....((((((.(((.((((...........((((.......))))......................(((((((..(((((((.............)))))))..(((((.....)))))...((((((((((.....)))).)))))).....))))))).........((((((.((.(((((((((((((......)))))))))))))..((((((..(((..(((((((............)))))))...............((((.(((((.((((((....).))))).)))))....)))).......)))....))))))...(((((.(((((.((((.....(......)...)))).))))).)))))................))...((((((..((((.....)))))))))).))))))......(((((((......))).))))......)))).))).))))))..... (-112.72) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1015 140 91 231 182 smit:SMT_2053|5end_hypothetical_membrane_associated_protein_1964422..1964652_NEGATIVE 341 150 101 56 12 smit:SMT_1606|5end_glutamate_racemase_1595857..1596087_POSITIVE 329 120 76 230 176 smit:SMT_2008|5end_K07485_transposase_1928662..1928892_NEGATIVE 329 120 76 99 45 smit:SMT_2005|5end_pullulanase,_type_I_1926289..1926519_NEGATIVE 329 120 76 193 139 smit:SMT_1967|5end_dicarboxylate/amino_acid:cation_(Na+_or_H+)_symporter_(DAACS)_family_protein_1899683..1899913_NEGATIVE 329 120 76 193 139 smit:SMT_1955|5end_carbamoyl-phosphate_synthase_small_chain_1889408..1889638_NEGATIVE 329 120 76 228 174 smit:SMT_1944|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1879494..1879724_NEGATIVE 329 120 76 193 139 smit:SMT_1690|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1674779..1675009_NEGATIVE 329 120 76 193 139 smit:SMT_779|5end_ribonuclease_BN,_putative_688530..688760_NEGATIVE 329 120 76 114 60 smit:SMT_464|5end_ribonuclease_Z_402867..403097_POSITIVE 329 120 76 193 139 smit:SMT_388|5end_branched-chain_amino_acid_transport_system_II_carrier_protein_321172..321402_POSITIVE 329 120 76 167 113 smit:SMT_304|5end_hypothetical_protein_246580..246810_POSITIVE 319 150 101 223 152 smit:SMT_405|5end_zinc_metalloprotease_ZmpB,_truncated_333952..334182_POSITIVE 312 154 111 212 157 smit:SMT_358|5end_hypothetical_protein_293947..294177_POSITIVE 311 139 92 184 119 smit:SMT_1303|5end_tRNA-dihydrouridine_synthase_1265731..1265961_NEGATIVE 310 139 91 221 173 smit:SMT_1982|5end_conserved_hypothetical_protein_1913036..1913266_POSITIVE 310 139 91 209 161 smit:SMT_1691|5end_putative_deoxyribonuclease_1674978..1675208_POSITIVE 309 330 286 172 124 smit:SMT_2168|5end_threonyl-tRNA_synthetase_2040991..2041221_POSITIVE 306 120 77 214 171 smit:SMT_1156|5end_K07485_transposase_1099938..1100168_POSITIVE 304 330 287 117 65 smit:SMT_595|5end_phosphoglycerate_mutase_512593..512823_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 120 76 64 10 smit:SMT_1956|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1889537..1889687_NEGATIVE 329 120 76 59 5 smit:SMT_387|3end_hypothetical_protein_predicted_by_Glimmer/Critica_321118..321268_POSITIVE 312 154 111 85 30 smit:SMT_357|3end_tRNA_(guanine-N7-)-methyltransferase_293900..294050_POSITIVE 310 339 292 57 10 smit:SMT_1078|3end_folylpolyglutamate_synthase_1015391..1015541_NEGATIVE 309 122 81 148 105 smit:SMT_1981|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912868..1913018_POSITIVE 308 342 301 125 84 smit:SMT_528|3end_hypothetical_protein_predicted_by_Glimmer/Critica_452132..452282_POSITIVE 304 120 76 99 43 smit:SMT_2089|3end_dTDP-4-dehydrorhamnose_3,5-epimerase_related_enzyme_1985270..1985420_POSITIVE 304 330 287 120 68 smit:SMT_596|3end_K03976_putative_transcription_regulator_512590..512740_NEGATIVE 293 328 281 99 29 smit:SMT_1995|3end_phosphoglycerate_mutase_1920535..1920685_NEGATIVE 287 119 75 66 18 smit:SMT_1809|3end_MutT/NUDIX_family_protein_1785134..1785284_POSITIVE 286 138 94 47 8 smit:SMT_890|3end_K02029_polar_amino_acid_transport_system_permease_protein_837692..837842_POSITIVE 282 422 383 65 27 smit:SMT_198|3end_50S_ribosomal_protein_L17_129281..129431_POSITIVE 280 327 288 134 97 smit:SMT_1760|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1735743..1735893_NEGATIVE 278 139 91 55 1 smit:SMT_148|3end_glycoprotein_endopeptidase_98601..98751_POSITIVE 273 119 91 66 31 smit:SMT_2109|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1999061..1999211_NEGATIVE 273 119 91 66 31 smit:SMT_1180|3end_putative_tagatose-6-phosphate_aldose/ketose_isomerase_1138036..1138186_NEGATIVE 273 317 286 50 17 smit:SMT_1056|3end_K07738_ATP-cone_domain_protein_995395..995545_POSITIVE 272 138 94 43 4 smit:SMT_1964|3end_sodium/hydrogen_exchanger_family_protein_1896596..1896746_NEGATIVE 272 138 94 47 8 smit:SMT_1140|3end_glycogen_phosphorylase_1081316..1081466_NEGATIVE 272 138 94 45 6 smit:SMT_799|3end_hypothetical_protein_707296..707446_NEGATIVE