Origin IGS: agatacctcctactgtcaaaacgtatctctattatactacaaaagccccccgaccgcaaaaatacatgatagaataacgctagcataacaaattgaagtatttaaaatgaatttattgcaactctactaacggacttagtttggattagataagcgcgacaaaaaataccagaggtggagctctagtatctttgttttttgccaagacttcgttacagttcttgtaagattattatcacatgattagcactacttgtcaaataattgttagctccactttctattttacttttcctgtttacaggtctataatggtaacagattctatttggaggttttt .........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 aaaaacctccaaatagaatctgttaccattatagacctgtaaacaggaaaagtaaaatagaaagtggagctaacaattatttgacaagtagtgctaatcatgtgataataatcttacaagaactgtaacgaagtcttggcaaaaaacaaagatactagagctccacctctggtattttttgtcgcgcttatctaatccaaactaagtccgttagtagagttgcaataaattcattttaaatacttcaatttgttatgctagcgttattctatcatgtatttttgcggtcggggggcttttgtagtataatagagatacgttttgacagtaggaggtatct Mask Tandem Repeat Region ================================================ agatacctcctactgtcaaaacgtatctctattatactacaaaagccccccgaccgcaaaaatacatgatagaataacgctagcataacaaattgaagtatttaaaatgaatttattgcaactctactaacggacttagtttggattagataagcgcgacaaaaaataccagaggtggagctctagtatctttgttttttgccaagacttcgttacagttcttgtaagattattatcacatgattagcactacttgtcaaataattgttagctccactttctattttacttttcctgtttacaggtctataatggtaacagattctatttggaggttttt Find is-nt database================================================ Query_seq: SMT_1215:SMT_1216|SMT_1215:SMT_1216:aromatic amino acid aminotransferase:hypothetical protein:<-->:1174679..1175018 340 agatacctcctactgtcaaaacgtatctctattatactacaaaagccccccgaccgcaaaaatacatgatagaataacgctagcataacaaattgaagtatttaaaatgaatttattgcaactctactaacggacttagtttggattagataagcgcgacaaaaaataccagaggtggagctctagtatctttgttttttgccaagacttcgttacagttcttgtaagattattatcacatgattagcactacttgtcaaataattgttagctccactttctattttacttttcctgtttacaggtctataatggtaacagattctatttggaggttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1215:SMT_1216|SMT_1215:SMT_1216:aromatic amino acid aminotransferase:hypothetical protein:<-->:1174679..1175018 340 agatacctcctactgtcaaaacgtatctctattatactacaaaagccccccgaccgcaaaaatacatgatagaataacgctagcataacaaattgaagtatttaaaatgaatttattgcaactctactaacggacttagtttggattagataagcgcgacaaaaaataccagaggtggagctctagtatctttgttttttgccaagacttcgttacagttcttgtaagattattatcacatgattagcactacttgtcaaataattgttagctccactttctattttacttttcctgtttacaggtctataatggtaacagattctatttggaggttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1215:SMT_1216|SMT_1215:SMT_1216:aromatic amino acid aminotransferase:hypothetical protein:<-->:1174679..1175018 340 agatacctcctactgtcaaaacgtatctctattatactacaaaagccccccgaccgcaaaaatacatgatagaataacgctagcataacaaattgaagtatttaaaatgaatttattgcaactctactaacggacttagtttggattagataagcgcgacaaaaaataccagaggtggagctctagtatctttgttttttgccaagacttcgttacagttcttgtaagattattatcacatgattagcactacttgtcaaataattgttagctccactttctattttacttttcctgtttacaggtctataatggtaacagattctatttggaggttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agatacctcctactgtcaaaacgtatctctattatactacaaaagccccccgaccgcaaaaatacatgatagaataacgctagcataacaaattgaagtatttaaaatgaatttattgcaactctactaacggacttagtttggattagataagcgcgacaaaaaataccagaggtggagctctagtatctttgttttttgccaagacttcgttacagttcttgtaagattattatcacatgattagcactacttgtcaaataattgttagctccactttctattttacttttcctgtttacaggtctataatggtaacagattctatttggaggttttt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 240 End: 338 ............................................................................................................................................................................................................................................... M I S T T C Q I I V S S T F Y F T F P V Y R S I M V T D S I W R F .. Protein_Len: 36 Strand: - Start: 216 End: 323 ....................................................................................................................................................................................................................... L E Q L I I I V H N A S S T L Y N N A G S E I K S K R N V P R Y H Y C M ................. Protein_Len: 33 Strand: - Start: 3 End: 101 .. Y R R S D F R I E I I S C F G G S R L F V H Y F L A L M V F Q L M ............................................................................................................................................................................................................................................... agatacctcctactgtcaaaacgtatctctattatactacaaaagccccccgaccgcaaaaatacatgatagaataacgctagcataacaaattgaagtatttaaaatgaatttattgcaactctactaacggacttagtttggattagataagcgcgacaaaaaataccagaggtggagctctagtatctttgttttttgccaagacttcgttacagttcttgtaagattattatcacatgattagcactacttgtcaaataattgttagctccactttctattttacttttcctgtttacaggtctataatggtaacagattctatttggaggttttt 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: 88 Start: 232 End: 261 .......................................................................................................................................................................................................................................TTTGACAAGTAGTGCTAATCATGTGATAAT............................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 86 Start: 284 End: 313 ...........................................................................................................................................................................................................................................................................................TTTTACTTTTCCTGTTTACAGGTCTATAAT........................... PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 31 End: 60 ..............................TTTGCGGTCGGGGGGCTTTTGTAGTATAAT........................................................................................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agatacctcctactgtcaaaacgtatctctattatactacaaaagccccccgaccgcaaaaatacatgatagaataacgctagcataacaaattgaagtatttaaaatgaatttattgcaactctactaacggacttagtttggattagataagcgcgacaaaaaataccagaggtggagctctagtatctttgttttttgccaagacttcgttacagttcttgtaagattattatcacatgattagcactacttgtcaaataattgttagctccactttctattttacttttcctgtttacaggtctataatggtaacagattctatttggaggttttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 57 HP_score: -3.0 Tail_Score: -4.13692 Start: 167 End: 188 Full_Region: AAGCGCGACAAAAAA TACCAGAG GTGGAG CTCTAGTA TCTTTGTTTTTTGCC ......................................................................................................................................................................TACCAGAGGTGGAGCTCTAGTA........................................................................................................................................................ TransTerm Strand: - Conf: 82 HP_score: -5.2 Tail_Score: -5.25803 Start: 167 End: 188 Full_Region: ggcaaaaaacaaaga tactagag ctccac ctctggta ttttttgtcgcgctt ......................................................................................................................................................................tactagagctccacctctggta........................................................................................................................................................ Find igs database================================================ Query_seq: SMT_1215:SMT_1216|SMT_1215:SMT_1216:aromatic amino acid aminotransferase:hypothetical protein:<-->:1174679..1175018 340 agatacctcctactgtcaaaacgtatctctattatactacaaaagccccccgaccgcaaaaatacatgatagaataacgctagcataacaaattgaagtatttaaaatgaatttattgcaactctactaacggacttagtttggattagataagcgcgacaaaaaataccagaggtggagctctagtatctttgttttttgccaagacttcgttacagttcttgtaagattattatcacatgattagcactacttgtcaaataattgttagctccactttctattttacttttcctgtttacaggtctataatggtaacagattctatttggaggttttt Intra-Species Hit: Count: 1 Min: 1 Max: 340 Len: 340 Subject: smit_SMT_1215_SMT_1216|aromatic amino acid aminotransferase:hypothetical protein|NEGATIVE:POSITIVE|[1174679,1175018]|340 HSP 1 e-value: 0.0 bit: 674.0 Len: 340 Query Start:1 Query End:340 Subject Strand: POSITIVE Subject Start: 1 Subject End: 340 agatacctcctactgtcaaaacgtatctctattatactacaaaagccccccgaccgcaaaaatacatgatagaataacgctagcataacaaattgaagtatttaaaatgaatttattgcaactctactaacggacttagtttggattagataagcgcgacaaaaaataccagaggtggagctctagtatctttgttttttgccaagacttcgttacagttcttgtaagattattatcacatgattagcactacttgtcaaataattgttagctccactttctattttacttttcctgtttacaggtctataatggtaacagattctatttggaggttttt agatacctcctactgtcaaaacgtatctctattatactacaaaagccccccgaccgcaaaaatacatgatagaataacgctagcataacaaattgaagtatttaaaatgaatttattgcaactctactaacggacttagtttggattagataagcgcgacaaaaaataccagaggtggagctctagtatctttgttttttgccaagacttcgttacagttcttgtaagattattatcacatgattagcactacttgtcaaataattgttagctccactttctattttacttttcctgtttacaggtctataatggtaacagattctatttggaggttttt Inter-species Hit: Count: 3 Min: 1 Max: 340 Len: 340 Subject: NC_008533_SPD_0040_SPD_0041|hypothetical protein:aromatic amino acid aminotransferase|NEGATIVE:POSITIVE|[35663,35810]|148 HSP 1 e-value: 3.0E-28 bit: 127.0 Len: 76 Query Start:1 Query End:76 Subject Strand: NEGATIVE Subject Start: 73 Subject End: 148 agatacctcctactgtcaaaacgtatctctattatactacaaaagccccccgaccgcaaaaatacatgatagaata........................................................................................................................................................................................................................................................................ agatacctcctactttcaaaacgtatctctattatactacaaaagccccccgaccgcaaaaatacattagagaata........................................................................................................................................................................................................................................................................ HSP 2 e-value: 2.0E-23 bit: 111.0 Len: 68 Query Start:273 Query End:340 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 68 ................................................................................................................................................................................................................................................................................tccactttctattttacttttcctgtttacaggtctataatggtaacagattctatttggaggttttt ................................................................................................................................................................................................................................................................................tccactttctattttacttttcctgtttataggtctataatggtaatagattttatttggaggttttt Subject: NC_003098_spr0034_spr0035|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[35675,35810]|136 HSP 1 e-value: 3.0E-28 bit: 127.0 Len: 76 Query Start:1 Query End:76 Subject Strand: NEGATIVE Subject Start: 61 Subject End: 136 agatacctcctactgtcaaaacgtatctctattatactacaaaagccccccgaccgcaaaaatacatgatagaata........................................................................................................................................................................................................................................................................ agatacctcctactttcaaaacgtatctctattatactacaaaagccccccgaccgcaaaaatacattagagaata........................................................................................................................................................................................................................................................................ HSP 2 e-value: 2.0E-16 bit: 87.7 Len: 52 Query Start:273 Query End:324 Subject Strand: NEGATIVE Subject Start: 5 Subject End: 56 ................................................................................................................................................................................................................................................................................tccactttctattttacttttcctgtttacaggtctataatggtaacagatt................ ................................................................................................................................................................................................................................................................................tccactttctattttacttttcctgtttataggtctataatggtaatagatt................ Subject: NC_003028_SP_0034_SP_0035|membrane protein:hypothetical protein|NEGATIVE:POSITIVE|[36020,36167]|148 HSP 1 e-value: 3.0E-28 bit: 127.0 Len: 76 Query Start:1 Query End:76 Subject Strand: NEGATIVE Subject Start: 73 Subject End: 148 agatacctcctactgtcaaaacgtatctctattatactacaaaagccccccgaccgcaaaaatacatgatagaata........................................................................................................................................................................................................................................................................ agatacctcctactttcaaaacgtatctctattatactacaaaagccccccgaccgcaaaaatacattagagaata........................................................................................................................................................................................................................................................................ HSP 2 e-value: 2.0E-23 bit: 111.0 Len: 68 Query Start:273 Query End:340 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 68 ................................................................................................................................................................................................................................................................................tccactttctattttacttttcctgtttacaggtctataatggtaacagattctatttggaggttttt ................................................................................................................................................................................................................................................................................tccactttctattttacttttcctgtttataggtctataatggtaatagattttatttggaggttttt Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUACCUCCUACUGUCAAAACGUAUCUCUAUUAUACUACAAAAGCCCCCCGACCGCAAAAAUACAUGAUAGAAUAACGCUAGCAUAACAAAUUGAAGUAUUUAAAAUGAAUUUAUUGCAACUCUACUAACGGACUUAGUUUGGAUUAGAUAAGCGCGACAAAAAAUACCAGAGGUGGAGCUCUAGUAUCUUUGUUUUUUGCCAAGACUUCGUUACAGUUCUUGUAAGAUUAUUAUCACAUGAUUAGCACUACUUGUCAAAUAAUUGUUAGCUCCACUUUCUAUUUUACUUUUCCUGUUUACAGGUCUAUAAUGGUAACAGAUUCUAUUUGGAGGUUUUU (((.((((((...((((..........((((((((.........((.........))........))))))))....((((.(((....(((((.(...........).)))))..)))...((((....(((((...)))))...))))..)))).)))).....((((((((((((((((.((((.........((((((.((((((.......)).))))))))))...........((((.((.....)).))))....))))..))))))))))).............((((....)))).......))))).............)))))).))) (-60.83) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAACCUCCAAAUAGAAUCUGUUACCAUUAUAGACCUGUAAACAGGAAAAGUAAAAUAGAAAGUGGAGCUAACAAUUAUUUGACAAGUAGUGCUAAUCAUGUGAUAAUAAUCUUACAAGAACUGUAACGAAGUCUUGGCAAAAAACAAAGAUACUAGAGCUCCACCUCUGGUAUUUUUUGUCGCGCUUAUCUAAUCCAAACUAAGUCCGUUAGUAGAGUUGCAAUAAAUUCAUUUUAAAUACUUCAAUUUGUUAUGCUAGCGUUAUUCUAUCAUGUAUUUUUGCGGUCGGGGGGCUUUUGUAGUAUAAUAGAGAUACGUUUUGACAGUAGGAGGUAUCU ....((((((........(((((((..(((((((((((.(..((.(.(((((((..((((((.((..(((((((((....((((..((((.(((((((...((((((.........(((((.((.......))))))).........(((((((((((((......))))))))))))))))))).((((............))))...)))))))(((((......)))))........)))))))).)))))).))).))....))))))....))))))).).))..).)))..)))))))).))))))).....((....))....)))))).... (-77.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 907 90 41 181 132 smit:SMT_1215|5end_aromatic_amino_acid_aminotransferase_1174588..1174818_NEGATIVE 340 198 154 156 109 smit:SMT_989|5end_hypothetical_protein_933548..933778_NEGATIVE 319 228 182 121 54 smit:SMT_691|5end_endonuclease_III_603008..603238_NEGATIVE 291 188 154 166 129 smit:SMT_2051|5end_enoyl-CoA_hydratase_1960639..1960869_NEGATIVE 284 340 294 230 164 smit:SMT_1128|5end_surface_antigen_1063140..1063370_NEGATIVE 277 199 152 117 73 smit:SMT_1218|5end_DNA_polymerase_I_1179357..1179587_NEGATIVE 271 220 176 86 35 smit:SMT_1785|5end_phenylalanyl-tRNA_synthetase_beta_chain_1763277..1763507_NEGATIVE 271 54 26 148 114 smit:SMT_1605|5end_hypothetical_protein_1595406..1595636_POSITIVE 268 210 165 65 16 smit:SMT_709|5end_hypothetical_protein_618919..619149_NEGATIVE 263 228 183 73 15 smit:SMT_1945|5end_putative_dihydrolipoamide_S-acetyltransferase_1879961..1880191_POSITIVE 263 210 169 73 31 smit:SMT_1481|5end_endopeptidase_O_1462229..1462459_POSITIVE 261 220 171 66 6 smit:SMT_1327|5end_K03402_transcriptional_regulator_of_arginine_metabolism_1303746..1303976_POSITIVE 260 190 143 160 111 smit:SMT_1005|5end_possible_aluminum_resistance_protein_945946..946176_POSITIVE 259 44 12 169 140 smit:SMT_1436|5end_conserved_hypothetical_protein_TIGR00147_1421255..1421485_NEGATIVE 258 209 167 68 19 smit:SMT_262|5end_glutathione_peroxidase_202382..202612_NEGATIVE 256 315 271 128 85 smit:SMT_1303|5end_tRNA-dihydrouridine_synthase_1265731..1265961_NEGATIVE 253 87 49 62 21 smit:SMT_1260|5end_hypothetical_protein_1225517..1225747_POSITIVE 249 86 43 156 118 smit:SMT_941|5end_hypothetical_protein_893558..893788_NEGATIVE 248 85 41 75 36 smit:SMT_1024|5end_transcriptional_regulator,_MarR_family_959404..959634_NEGATIVE 247 320 271 198 150 smit:SMT_639|5end_6-phospho-beta-galactosidase_544885..545115_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 198 154 146 99 smit:SMT_990|3end_hypothetical_protein_933558..933708_NEGATIVE 319 228 182 121 54 smit:SMT_692|3end_hypothetical_protein_603008..603158_NEGATIVE 291 188 154 143 106 smit:SMT_2052|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1960662..1960812_NEGATIVE 284 340 294 67 1 smit:SMT_1129|3end_hypothetical_protein_1063303..1063453_NEGATIVE 271 220 176 128 77 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 259 44 12 59 30 smit:SMT_1437|3end_ADP-ribosylglycohydrolase_1421365..1421515_NEGATIVE 258 84 43 60 23 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 258 209 167 71 22 smit:SMT_263|3end_hypothetical_protein_predicted_by_Glimmer/Critica_202379..202529_NEGATIVE 253 87 49 43 2 smit:SMT_1259|3end_hypothetical_protein_1225578..1225728_POSITIVE 247 300 252 107 64 smit:SMT_448|3end_K03707_transcriptional_activator_TenA_387690..387840_POSITIVE 246 229 181 80 23 smit:SMT_1287|3end_50S_ribosomal_protein_L9_1250890..1251040_POSITIVE 246 306 272 147 114 smit:SMT_991|3end_hypothetical_protein_934033..934183_NEGATIVE 245 225 183 127 81 smit:SMT_1061|3end_hypothetical_protein_999915..1000065_POSITIVE 244 159 111 64 11 smit:SMT_492|3end_branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein_427217..427367_POSITIVE 243 210 165 115 52 smit:SMT_422|3end_K02004_365876..366026_POSITIVE 243 220 171 130 73 smit:SMT_343|3end_hypothetical_protein_283267..283417_NEGATIVE 242 218 171 121 68 smit:SMT_1569|3end_dihydroxy-acid_dehydratase_1563068..1563218_POSITIVE 241 231 193 146 107 smit:SMT_1153|3end_alpha-mannosidase_1097383..1097533_NEGATIVE 240 282 250 40 2 smit:SMT_1772|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1749370..1749520_POSITIVE 239 220 177 125 83 smit:SMT_1828|3end_PTS_system,_galactose-specific_IIC_component_1798137..1798287_POSITIVE