Origin IGS: ttttgttagtcctgaagggactgacttaatctcaaaaaggagaggcaagtatgtcttctcctttttatttatgtagtgattgactgttcatttacaagcataattattgaatatatttataactaaaatactagaaaatagattttcaaaaagtaaatgaaatgtcaggcagggctttgttttatggattctgttctagttcaaacaacttgcaaaaatagcttaaaaattataaaattaaatataaagtaatttgtaaatacgcataaagtttaatatgatataatgtgtatacagataagagaaaaggaaatattataa .........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 ttataatatttccttttctcttatctgtatacacattatatcatattaaactttatgcgtatttacaaattactttatatttaattttataatttttaagctatttttgcaagttgtttgaactagaacagaatccataaaacaaagccctgcctgacatttcatttactttttgaaaatctattttctagtattttagttataaatatattcaataattatgcttgtaaatgaacagtcaatcactacataaataaaaaggagaagacatacttgcctctcctttttgagattaagtcagtcccttcaggactaacaaaa Mask Tandem Repeat Region ================================================ ttttgttagtcctgaagggactgacttaatctcaaaaaggagaggcaagtatgtcttctcctttttatttatgtagtgattgactgttcatttacaagcataattattgaatatatttataactaaaatactagaaaatagattttcaaaaagtaaatgaaatgtcaggcagggctttgttttatggattctgttctagttcaaacaacttgcaaaaatagcttaaaaattataaaattaaatataaagtaatttgtaaatacgcataaagtttaatatgatataatgtgtatacagataagagaaaaggaaatattataa Find is-nt database================================================ Query_seq: SMT_405:SMT_406|SMT_405:SMT_406:zinc metalloprotease ZmpB, truncated:hypothetical protein:->->:339999..340319 321 ttttgttagtcctgaagggactgacttaatctcaaaaaggagaggcaagtatgtcttctcctttttatttatgtagtgattgactgttcatttacaagcataattattgaatatatttataactaaaatactagaaaatagattttcaaaaagtaaatgaaatgtcaggcagggctttgttttatggattctgttctagttcaaacaacttgcaaaaatagcttaaaaattataaaattaaatataaagtaatttgtaaatacgcataaagtttaatatgatataatgtgtatacagataagagaaaaggaaatattataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_405:SMT_406|SMT_405:SMT_406:zinc metalloprotease ZmpB, truncated:hypothetical protein:->->:339999..340319 321 ttttgttagtcctgaagggactgacttaatctcaaaaaggagaggcaagtatgtcttctcctttttatttatgtagtgattgactgttcatttacaagcataattattgaatatatttataactaaaatactagaaaatagattttcaaaaagtaaatgaaatgtcaggcagggctttgttttatggattctgttctagttcaaacaacttgcaaaaatagcttaaaaattataaaattaaatataaagtaatttgtaaatacgcataaagtttaatatgatataatgtgtatacagataagagaaaaggaaatattataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_405:SMT_406|SMT_405:SMT_406:zinc metalloprotease ZmpB, truncated:hypothetical protein:->->:339999..340319 321 ttttgttagtcctgaagggactgacttaatctcaaaaaggagaggcaagtatgtcttctcctttttatttatgtagtgattgactgttcatttacaagcataattattgaatatatttataactaaaatactagaaaatagattttcaaaaagtaaatgaaatgtcaggcagggctttgttttatggattctgttctagttcaaacaacttgcaaaaatagcttaaaaattataaaattaaatataaagtaatttgtaaatacgcataaagtttaatatgatataatgtgtatacagataagagaaaaggaaatattataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttgttagtcctgaagggactgacttaatctcaaaaaggagaggcaagtatgtcttctcctttttatttatgtagtgattgactgttcatttacaagcataattattgaatatatttataactaaaatactagaaaatagattttcaaaaagtaaatgaaatgtcaggcagggctttgttttatggattctgttctagttcaaacaacttgcaaaaatagcttaaaaattataaaattaaatataaagtaatttgtaaatacgcataaagtttaatatgatataatgtgtatacagataagagaaaaggaaatattataa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 157 End: 249 ............................................................................................................................................................ M K C Q A G L C F M D S V L V Q T T C K N S L K I I K L N I K ........................................................................ Protein_Len: 33 Strand: - Start: 91 End: 189 .......................................................................................... K C A Y N N F I N I V L I S S F L N E F L L H F T L C P K T K H M .................................................................................................................................... ttttgttagtcctgaagggactgacttaatctcaaaaaggagaggcaagtatgtcttctcctttttatttatgtagtgattgactgttcatttacaagcataattattgaatatatttataactaaaatactagaaaatagattttcaaaaagtaaatgaaatgtcaggcagggctttgttttatggattctgttctagttcaaacaacttgcaaaaatagcttaaaaattataaaattaaatataaagtaatttgtaaatacgcataaagtttaatatgatataatgtgtatacagataagagaaaaggaaatattataa 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: 209 End: 238 ................................................................................................................................................................................................................CTTGCAAAAATAGCTTAAAAATTATAAAAT................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 253 End: 282 ............................................................................................................................................................................................................................................................TTTGTAAATACGCATAAAGTTTAATATGAT....................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttgttagtcctgaagggactgacttaatctcaaaaaggagaggcaagtatgtcttctcctttttatttatgtagtgattgactgttcatttacaagcataattattgaatatatttataactaaaatactagaaaatagattttcaaaaagtaaatgaaatgtcaggcagggctttgttttatggattctgttctagttcaaacaacttgcaaaaatagcttaaaaattataaaattaaatataaagtaatttgtaaatacgcataaagtttaatatgatataatgtgtatacagataagagaaaaggaaatattataa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 80 HP_score: -4.9 Tail_Score: -5.42975 Start: 39 End: 61 Full_Region: ACTTAATCTCAAAAA GGAGAGGCA AGTA TGTCTTCTCC TTTTTATTTATGTAG ......................................GGAGAGGCAAGTATGTCTTCTCC.................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SMT_405:SMT_406|SMT_405:SMT_406:zinc metalloprotease ZmpB, truncated:hypothetical protein:->->:339999..340319 321 ttttgttagtcctgaagggactgacttaatctcaaaaaggagaggcaagtatgtcttctcctttttatttatgtagtgattgactgttcatttacaagcataattattgaatatatttataactaaaatactagaaaatagattttcaaaaagtaaatgaaatgtcaggcagggctttgttttatggattctgttctagttcaaacaacttgcaaaaatagcttaaaaattataaaattaaatataaagtaatttgtaaatacgcataaagtttaatatgatataatgtgtatacagataagagaaaaggaaatattataa Intra-Species Hit: Count: 1 Min: 1 Max: 321 Len: 321 Subject: smit_SMT_405_SMT_406|zinc metalloprotease ZmpB, truncated:hypothetical protein|POSITIVE:POSITIVE|[339999,340319]|321 HSP 1 e-value: 1.0E-117 bit: 422.0 Len: 213 Query Start:1 Query End:213 Subject Strand: POSITIVE Subject Start: 1 Subject End: 213 ttttgttagtcctgaagggactgacttaatctcaaaaaggagaggcaagtatgtcttctcctttttatttatgtagtgattgactgttcatttacaagcataattattgaatatatttataactaaaatactagaaaatagattttcaaaaagtaaatgaaatgtcaggcagggctttgttttatggattctgttctagttcaaacaacttgc............................................................................................................ ttttgttagtcctgaagggactgacttaatctcaaaaaggagaggcaagtatgtcttctcctttttatttatgtagtgattgactgttcatttacaagcataattattgaatatatttataactaaaatactagaaaatagattttcaaaaagtaaatgaaatgtcaggcagggctttgttttatggattctgttctagttcaaacaacttgc............................................................................................................ HSP 2 e-value: 2.0E-10 bit: 67.9 Len: 34 Query Start:288 Query End:321 Subject Strand: POSITIVE Subject Start: 288 Subject End: 321 ...............................................................................................................................................................................................................................................................................................gtgtatacagataagagaaaaggaaatattataa ...............................................................................................................................................................................................................................................................................................gtgtatacagataagagaaaaggaaatattataa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUGUUAGUCCUGAAGGGACUGACUUAAUCUCAAAAAGGAGAGGCAAGUAUGUCUUCUCCUUUUUAUUUAUGUAGUGAUUGACUGUUCAUUUACAAGCAUAAUUAUUGAAUAUAUUUAUAACUAAAAUACUAGAAAAUAGAUUUUCAAAAAGUAAAUGAAAUGUCAGGCAGGGCUUUGUUUUAUGGAUUCUGUUCUAGUUCAAACAACUUGCAAAAAUAGCUUAAAAAUUAUAAAAUUAAAUAUAAAGUAAUUUGUAAAUACGCAUAAAGUUUAAUAUGAUAUAAUGUGUAUACAGAUAAGAGAAAAGGAAAUAUUAUAA ....((((((((.....))))))))....((((.(((((((((((((....)).)))))))))))..(((((((......((((..(((((((((....((((.(((.....))).)))).............(((((....))))).....)))))))))..)))).(((((...((((((..((((......))))....)))))))))))............................)))))))...(((((((..(((((((.(.(((......))).).))))))))))))))..))))................ (-71.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUAAUAUUUCCUUUUCUCUUAUCUGUAUACACAUUAUAUCAUAUUAAACUUUAUGCGUAUUUACAAAUUACUUUAUAUUUAAUUUUAUAAUUUUUAAGCUAUUUUUGCAAGUUGUUUGAACUAGAACAGAAUCCAUAAAACAAAGCCCUGCCUGACAUUUCAUUUACUUUUUGAAAAUCUAUUUUCUAGUAUUUUAGUUAUAAAUAUAUUCAAUAAUUAUGCUUGUAAAUGAACAGUCAAUCACUACAUAAAUAAAAAGGAGAAGACAUACUUGCCUCUCCUUUUUGAGAUUAAGUCAGUCCCUUCAGGACUAACAAAA ................((((...(((((.........((((((((........)))).))))...(((((.((((((((........))))).......((.......)).))).))))).......)))))......................((((..(((((((((.....(((((....))))).((((...(((((((...........))))))))))).)))))))))..))))..............((((((((((.(.((....))).))))))))))))))....((.(((((.....))))).)).... (-51.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 320 200 152 77 24 smit:SMT_1530|5end_K07456_DNA_mismatch_repair_protein_MutS2_1515346..1515576_NEGATIVE 312 60 12 169 131 smit:SMT_1168|5end_potassium_uptake_protein_KtrB_1116552..1116782_NEGATIVE 311 86 41 156 114 smit:SMT_796|5end_K03734_thiamine_biosynthesis_lipoprotein_704211..704441_POSITIVE 277 60 20 207 167 smit:SMT_102|5end_competence-specific_global_transcription_modulator_34108..34338_POSITIVE 275 80 31 126 63 smit:SMT_770|5end_K02053_spermidine/putrescine_transport_system_permease_protein_681359..681589_NEGATIVE 274 49 5 172 124 smit:SMT_841|5end_dihydrodipicolinate_reductase_788025..788255_NEGATIVE 267 208 163 117 63 smit:SMT_1378|5end_DNA_polymerase_III,_delta'_subunit_1356803..1357033_NEGATIVE 265 60 17 201 167 smit:SMT_854|5end_hypothetical_protein_799492..799722_NEGATIVE 264 69 22 110 59 smit:SMT_1625|5end_DNA_polymerase_IV_1613925..1614155_POSITIVE 256 214 171 90 45 smit:SMT_1976|5end_immunoglobulin_A1_protease_1906950..1907180_POSITIVE 254 99 52 142 93 smit:SMT_1802|5end_tyrosyl-tRNA_synthetase_1776712..1776942_NEGATIVE 253 203 164 82 37 smit:SMT_215|5end_leucyl-tRNA_synthetase_147045..147275_POSITIVE 252 204 163 165 113 smit:SMT_185|5end_50S_ribosomal_protein_L6_122003..122233_POSITIVE 252 197 165 187 152 smit:SMT_157|5end_hypothetical_protein_103525..103755_POSITIVE 251 68 36 49 14 smit:SMT_1929|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1869785..1870015_NEGATIVE 251 68 36 182 147 smit:SMT_1928|5end_O-methyltransferase_family_protein_1869652..1869882_NEGATIVE 250 85 54 132 100 smit:SMT_590|5end_tetratricopeptide_repeat_family_protein_506737..506967_POSITIVE 249 46 10 34 12 smit:SMT_367|5end_hypothetical_protein_302318..302548_POSITIVE 240 64 21 154 109 smit:SMT_1568|5end_putative_transketolase_C-terminal_section_1560122..1560352_POSITIVE 239 210 168 78 33 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 577 49 1 54 12 smit:SMT_2039|3end_malolactic_enzyme_1949681..1949831_NEGATIVE 312 60 12 135 97 smit:SMT_1169|3end_phosphorylase,_Pnp/UDP_family_1116586..1116736_NEGATIVE 285 63 25 64 21 smit:SMT_1172|3end_hypothetical_protein_1119344..1119494_NEGATIVE 277 60 20 86 46 smit:SMT_101|3end_cell_division_protein_34067..34217_POSITIVE 275 80 31 129 66 smit:SMT_771|3end_spermidine/putrescine_transport_system_permease_protein_PotB_681356..681506_NEGATIVE 267 208 163 120 66 smit:SMT_1379|3end_thymidylate_kinase_1356800..1356950_NEGATIVE 260 66 34 57 25 smit:SMT_405|3end_zinc_metalloprotease_ZmpB,_truncated_339938..340088_POSITIVE 255 71 33 93 52 smit:SMT_687|3end_carbamoyl-phosphate_synthase,_large_subunit_596088..596238_NEGATIVE 252 69 23 85 19 smit:SMT_651|3end_DNA_ligase_559986..560136_NEGATIVE 252 186 160 42 9 smit:SMT_347|3end_hypothetical_protein_285881..286031_NEGATIVE 252 197 165 100 65 smit:SMT_156|3end_hypothetical_protein_103518..103668_POSITIVE 251 68 36 49 14 smit:SMT_1930|3end_peptide_chain_release_factor_1_1869785..1869935_NEGATIVE 251 68 36 144 109 smit:SMT_1929|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1869690..1869840_NEGATIVE 250 85 54 142 110 smit:SMT_589|3end_hypothetical_protein_506827..506977_POSITIVE 249 46 10 34 12 smit:SMT_366|3end_hypothetical_protein_302398..302548_POSITIVE 246 45 9 52 15 smit:SMT_1034|3end_K05896_segregation_and_condensation_protein_A_976768..976918_NEGATIVE 246 67 31 93 62 smit:SMT_364|3end_ribosome-binding_factor_A_301353..301503_POSITIVE 245 49 4 133 89 smit:SMT_346|3end_K01992_ABC-2_type_transport_system_permease_protein_285849..285999_POSITIVE 242 65 34 44 17 smit:SMT_2038|3end_zinc_metalloprotease_ZmpB,_truncated_1949615..1949765_POSITIVE 239 210 168 91 46 smit:SMT_1455|3end_deoxyribose-phosphate_aldolase_1437873..1438023_NEGATIVE