Origin IGS: gaatggcaccctgatgtttcagggtgtttttgctttttaaaaaatattggtcaattaaagtcaaattccttgaccttttttgactaatgtagtatattatgaacgtaaggtaaatgaaagccttactagaacacttatttaaagtaaaatagaaagaggtggggtctatgtttaatctagaaatctttagaagtaaagatagtctactcctgcttgaaaaagaaaaaccagaaatagtacgtagagtagcgatttagctagtctaaattttttaaagaaaaagtcaaagatagtcaatatcagtaataataaataacaaaaagaggtaaagaat .........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 attctttacctctttttgttatttattattactgatattgactatctttgactttttctttaaaaaatttagactagctaaatcgctactctacgtactatttctggtttttctttttcaagcaggagtagactatctttacttctaaagatttctagattaaacatagaccccacctctttctattttactttaaataagtgttctagtaaggctttcatttaccttacgttcataatatactacattagtcaaaaaaggtcaaggaatttgactttaattgaccaatattttttaaaaagcaaaaacaccctgaaacatcagggtgccattc Mask Tandem Repeat Region ================================================ gaatggcaccctgatgtttcagggtgtttttgctttttaaaaaatattggtcaattaaagtcaaattccttgaccttttttgactaatgtagtatattatgaacgtaaggtaaatgaaagccttactagaacacttatttaaagtaaaatagaaagaggtggggtctatgtttaatctagaaatctttagaagtaaagatagtctactcctgcttgaaaaagaaaaaccagaaatagtacgtagagtagcgatttagctagtctaaattttttaaagaaaaagtcaaagatagtcaatatcagtaataataaataacaaaaagaggtaaagaat Find is-nt database================================================ Query_seq: SMT_269:SMT_270|SMT_269:SMT_270:phospho-N-acetylmuramoyl-pentapeptide-transferas e:ATP-binding subunit of Clp protease and DnaK/DnaJ chaperones:->->:208846..209179 334 gaatggcaccctgatgtttcagggtgtttttgctttttaaaaaatattggtcaattaaagtcaaattccttgaccttttttgactaatgtagtatattatgaacgtaaggtaaatgaaagccttactagaacacttatttaaagtaaaatagaaagaggtggggtctatgtttaatctagaaatctttagaagtaaagatagtctactcctgcttgaaaaagaaaaaccagaaatagtacgtagagtagcgatttagctagtctaaattttttaaagaaaaagtcaaagatagtcaatatcagtaataataaataacaaaaagaggtaaagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_269:SMT_270|SMT_269:SMT_270:phospho-N-acetylmuramoyl-pentapeptide-transferas e:ATP-binding subunit of Clp protease and DnaK/DnaJ chaperones:->->:208846..209179 334 gaatggcaccctgatgtttcagggtgtttttgctttttaaaaaatattggtcaattaaagtcaaattccttgaccttttttgactaatgtagtatattatgaacgtaaggtaaatgaaagccttactagaacacttatttaaagtaaaatagaaagaggtggggtctatgtttaatctagaaatctttagaagtaaagatagtctactcctgcttgaaaaagaaaaaccagaaatagtacgtagagtagcgatttagctagtctaaattttttaaagaaaaagtcaaagatagtcaatatcagtaataataaataacaaaaagaggtaaagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_269:SMT_270|SMT_269:SMT_270:phospho-N-acetylmuramoyl-pentapeptide-transferas e:ATP-binding subunit of Clp protease and DnaK/DnaJ chaperones:->->:208846..209179 334 gaatggcaccctgatgtttcagggtgtttttgctttttaaaaaatattggtcaattaaagtcaaattccttgaccttttttgactaatgtagtatattatgaacgtaaggtaaatgaaagccttactagaacacttatttaaagtaaaatagaaagaggtggggtctatgtttaatctagaaatctttagaagtaaagatagtctactcctgcttgaaaaagaaaaaccagaaatagtacgtagagtagcgatttagctagtctaaattttttaaagaaaaagtcaaagatagtcaatatcagtaataataaataacaaaaagaggtaaagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaatggcaccctgatgtttcagggtgtttttgctttttaaaaaatattggtcaattaaagtcaaattccttgaccttttttgactaatgtagtatattatgaacgtaaggtaaatgaaagccttactagaacacttatttaaagtaaaatagaaagaggtggggtctatgtttaatctagaaatctttagaagtaaagatagtctactcctgcttgaaaaagaaaaaccagaaatagtacgtagagtagcgatttagctagtctaaattttttaaagaaaaagtcaaagatagtcaatatcagtaataataaataacaaaaagaggtaaagaat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 159 End: 254 .............................................................................................................................................................. M G S M F N L E I F R S K D S L L L L E K E K P E I V R R V A I ................................................................................ Protein_Len: 38 Strand: - Start: 190 End: 303 ............................................................................................................................................................................................. F Y L Y D V G A Q F L F V L F L V Y L L S K A L R F K K F F F D F I T L I M ............................... Protein_Len: 60 Strand: - Start: 2 End: 253 . R K Q S I Y Y I I F T L Y I F A K S S C K N L T F Y F S T P D I N L R S I K L L L S L R S R S S F S F G S I T R L T A M ................................................................................. gaatggcaccctgatgtttcagggtgtttttgctttttaaaaaatattggtcaattaaagtcaaattccttgaccttttttgactaatgtagtatattatgaacgtaaggtaaatgaaagccttactagaacacttatttaaagtaaaatagaaagaggtggggtctatgtttaatctagaaatctttagaagtaaagatagtctactcctgcttgaaaaagaaaaaccagaaatagtacgtagagtagcgatttagctagtctaaattttttaaagaaaaagtcaaagatagtcaatatcagtaataataaataacaaaaagaggtaaagaat 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: 85 Start: 69 End: 98 ....................................................................CTTGACCTTTTTTGACTAATGTAGTATATT............................................................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 269 End: 298 ............................................................................................................................................................................................................................................................................ATTGACTATCTTTGACTTTTTCTTTAAAAA.................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaatggcaccctgatgtttcagggtgtttttgctttttaaaaaatattggtcaattaaagtcaaattccttgaccttttttgactaatgtagtatattatgaacgtaaggtaaatgaaagccttactagaacacttatttaaagtaaaatagaaagaggtggggtctatgtttaatctagaaatctttagaagtaaagatagtctactcctgcttgaaaaagaaaaaccagaaatagtacgtagagtagcgatttagctagtctaaattttttaaagaaaaagtcaaagatagtcaatatcagtaataataaataacaaaaagaggtaaagaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 53 HP_score: -4.3 Tail_Score: -3.65883 Start: 60 End: 74 Full_Region: TATTGGTCAATTAAA GTCAA ATTCC TTGAC CTTTTTTGACTAATG ...........................................................GTCAAATTCCTTGAC.................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 45 HP_score: -3.9 Tail_Score: -2.75708 Start: 242 End: 265 Full_Region: ACCAGAAATAGTACG TAGAGTAGC GATTTA GCTAGTCTA AATTTTTTAAAGAAA .................................................................................................................................................................................................................................................TAGAGTAGCGATTTAGCTAGTCTA..................................................................... TransTerm Strand: + Conf: 41 HP_score: -2.1 Tail_Score: -2.92111 Start: 244 End: 263 Full_Region: CAGAAATAGTACGTA GAGTAGC GATTTA GCTAGTC TAAATTTTTTAAAGA ...................................................................................................................................................................................................................................................GAGTAGCGATTTAGCTAGTC....................................................................... Find igs database================================================ Query_seq: SMT_269:SMT_270|SMT_269:SMT_270:phospho-N-acetylmuramoyl-pentapeptide-transferas e:ATP-binding subunit of Clp protease and DnaK/DnaJ chaperones:->->:208846..209179 334 gaatggcaccctgatgtttcagggtgtttttgctttttaaaaaatattggtcaattaaagtcaaattccttgaccttttttgactaatgtagtatattatgaacgtaaggtaaatgaaagccttactagaacacttatttaaagtaaaatagaaagaggtggggtctatgtttaatctagaaatctttagaagtaaagatagtctactcctgcttgaaaaagaaaaaccagaaatagtacgtagagtagcgatttagctagtctaaattttttaaagaaaaagtcaaagatagtcaatatcagtaataataaataacaaaaagaggtaaagaat Intra-Species Hit: Count: 1 Min: 1 Max: 334 Len: 334 Subject: smit_SMT_269_SMT_270|phospho-N-acetylmuramoyl-pentapeptide- transferas e:ATP-binding subunit of Clp protease and DnaK/DnaJ chaperones|POSITIVE:POSITIVE|[208846,209179]|334 HSP 1 e-value: 0.0 bit: 662.0 Len: 334 Query Start:1 Query End:334 Subject Strand: POSITIVE Subject Start: 1 Subject End: 334 gaatggcaccctgatgtttcagggtgtttttgctttttaaaaaatattggtcaattaaagtcaaattccttgaccttttttgactaatgtagtatattatgaacgtaaggtaaatgaaagccttactagaacacttatttaaagtaaaatagaaagaggtggggtctatgtttaatctagaaatctttagaagtaaagatagtctactcctgcttgaaaaagaaaaaccagaaatagtacgtagagtagcgatttagctagtctaaattttttaaagaaaaagtcaaagatagtcaatatcagtaataataaataacaaaaagaggtaaagaat gaatggcaccctgatgtttcagggtgtttttgctttttaaaaaatattggtcaattaaagtcaaattccttgaccttttttgactaatgtagtatattatgaacgtaaggtaaatgaaagccttactagaacacttatttaaagtaaaatagaaagaggtggggtctatgtttaatctagaaatctttagaagtaaagatagtctactcctgcttgaaaaagaaaaaccagaaatagtacgtagagtagcgatttagctagtctaaattttttaaagaaaaagtcaaagatagtcaatatcagtaataataaataacaaaaagaggtaaagaat Inter-species Hit: Count: 3 Min: 1 Max: 334 Len: 334 Subject: NC_008533_SPD_0307_SPD_0308|phospho-N-acetylmuramoyl-pentapeptide- transferase:ATP-dependent Clp protease, ATP-binding subunit|POSITIVE:POSITIVE|[305545,306100]|556 HSP 1 e-value: 1.0E-141 bit: 502.0 Len: 297 Query Start:38 Query End:334 Subject Strand: POSITIVE Subject Start: 261 Subject End: 556 .....................................taaaaaatattggtcaattaaagtcaaattccttgaccttttttgactaatgtagtatattatgaacgtaaggtaaatgaaagccttactagaacacttatttaaagtaaaatagaaagaggtggggtctatgtttaatctagaaatctttagaagtaaagatagtctactcctgcttgaaaaagaaaaaccagaaatagtacgtagagtagcgatttagctagtctaaattttttaaagaaaaagtcaaagatagtcaatatcagtaataataaataacaaaaagaggtaaagaat .....................................taaaaaatattggtcaattaaagtcaaaatacttgaccttttctgaccaatgtagtatattatgaacgtaaggtaaatgaaagccttactagaacacttatttaaagtaaaatagaaagaggtggg-tctatgtttcatctagaaatcttcagaagtaaagatagtctactcctgcttgaaaaagaaaaaccggaaatagtacatagagtagcgatttagctagtctaaattttttaaagaaaaggtcaaagatagtcaatatcagtaataataaataacaaaaagaggtaaagaat HSP 2 e-value: 3.0E-9 bit: 63.9 Len: 32 Query Start:1 Query End:32 Subject Strand: POSITIVE Subject Start: 1 Subject End: 32 gaatggcaccctgatgtttcagggtgtttttg.............................................................................................................................................................................................................................................................................................................. gaatggcaccctgatgtttcagggtgtttttg.............................................................................................................................................................................................................................................................................................................. Subject: NC_003028_SP_0337_SP_0338|phospho-N-acetylmuramoyl-pentapeptide- transferase:ATP-dependent Clp protease, ATP-binding subunit, putative|POSITIVE:POSITIVE|[310115,310722]|608 HSP 1 e-value: 1.0E-115 bit: 414.0 Len: 296 Query Start:39 Query End:334 Subject Strand: POSITIVE Subject Start: 309 Subject End: 608 ......................................aaaaaatattggtcaattaaagtcaaattccttgaccttttttgactaatgtagtatattatgaacgtaaggtaaatgaaagccttactagaacacttatttaaagtaaaatagaaagaggtggggtctatgtttaatctagaaatctttagaagtaaagatagtctactcctgcttgaaaaagaaaaaccagaaatagtacgtagagtagcgatttagctagtctaaattttttaaagaaaaagtcaaagatagtcaatatcagtaataataaat-----aacaaaaagaggtaaagaat ......................................aaaaaatattggtcagttaaagtcaaaactcttgaccttttctgaccaatgtagtatattatgaacgtaaggtaaatgaaagccttactagaacacttatttaaagtaaaatagaaagaggtggg-tctatgtttcatctagaaatcttcagaagtaaagatagtctactcctgcttgaaaaagaaaaaccagaaatagtacgtagggtagcgatctagctagtctaaattttttaaaacaatggtcaaagatagtcaatatcagtaatcataactaagtaaacaaaaagaggtaaagaat HSP 2 e-value: 3.0E-9 bit: 63.9 Len: 32 Query Start:1 Query End:32 Subject Strand: POSITIVE Subject Start: 1 Subject End: 32 gaatggcaccctgatgtttcagggtgtttttg.............................................................................................................................................................................................................................................................................................................. gaatggcaccctgatgtttcagggtgtttttg.............................................................................................................................................................................................................................................................................................................. Subject: NC_003098_spr0306_spr0307|hypothetical protein:ATP-dependent protease ATP-binding subunit|POSITIVE:POSITIVE|[305821,306051]|231 HSP 1 e-value: 1.0E-112 bit: 404.0 Len: 232 Query Start:103 Query End:334 Subject Strand: POSITIVE Subject Start: 1 Subject End: 231 ......................................................................................................acgtaaggtaaatgaaagccttactagaacacttatttaaagtaaaatagaaagaggtggggtctatgtttaatctagaaatctttagaagtaaagatagtctactcctgcttgaaaaagaaaaaccagaaatagtacgtagagtagcgatttagctagtctaaattttttaaagaaaaagtcaaagatagtcaatatcagtaataataaataacaaaaagaggtaaagaat ......................................................................................................acgtaaggtaaatgaaagccttactagaacacttatttaaagtaaaatagaaagaggtggg-tctatgtttcatctagaaatcttcagaagtaaagatagtctactcctgcttgaaaaagaaaaaccggaaatagtacatagagtagcgatttagctagtctaaattttttaaagaaaaggtcaaagatagtcaatatcagtaataataaataacaaaaagaggtaaagaat Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUGGCACCCUGAUGUUUCAGGGUGUUUUUGCUUUUUAAAAAAUAUUGGUCAAUUAAAGUCAAAUUCCUUGACCUUUUUUGACUAAUGUAGUAUAUUAUGAACGUAAGGUAAAUGAAAGCCUUACUAGAACACUUAUUUAAAGUAAAAUAGAAAGAGGUGGGGUCUAUGUUUAAUCUAGAAAUCUUUAGAAGUAAAGAUAGUCUACUCCUGCUUGAAAAAGAAAAACCAGAAAUAGUACGUAGAGUAGCGAUUUAGCUAGUCUAAAUUUUUUAAAGAAAAAGUCAAAGAUAGUCAAUAUCAGUAAUAAUAAAUAACAAAAAGAGGUAAAGAAU .....(((((((((....)))))))))(((((((((((.....(((((((((((..((.(((((.....))))).))..)))))))))))....((((((....(((((((........)))))))..((.......(((((((.............((((((((((((.((((.((((((....))))))..)))).))))...)))))..(((....)))....)))............((((.((((......)))).))))....))))))).......))...((((.....)))).))))))............)))))))))))... (-84.84) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCUUUACCUCUUUUUGUUAUUUAUUAUUACUGAUAUUGACUAUCUUUGACUUUUUCUUUAAAAAAUUUAGACUAGCUAAAUCGCUACUCUACGUACUAUUUCUGGUUUUUCUUUUUCAAGCAGGAGUAGACUAUCUUUACUUCUAAAGAUUUCUAGAUUAAACAUAGACCCCACCUCUUUCUAUUUUACUUUAAAUAAGUGUUCUAGUAAGGCUUUCAUUUACCUUACGUUCAUAAUAUACUACAUUAGUCAAAAAAGGUCAAGGAAUUUGACUUUAAUUGACCAAUAUUUUUUAAAAAGCAAAAACACCCUGAAACAUCAGGGUGCCAUUC .............(((((((.((((........(((((((....((((((((((((((((((.......((((.((((......)))).)))).((.(((((((((.((..........)).)))))))))))............))))))......((((((...(((...................(((((.....))))).....((((((..........))))))............)))..))))))...))))))))))))......(.......)..)))))))...)))).))))))).((((((((....))))))))...... (-66.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 35 2 154 109 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 275 43 5 169 126 smit:SMT_181|5end_50S_ribosomal_protein_L24_120125..120355_POSITIVE 267 90 47 70 18 smit:SMT_1530|5end_K07456_DNA_mismatch_repair_protein_MutS2_1515346..1515576_NEGATIVE 263 39 1 63 33 smit:SMT_1981|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912261..1912491_POSITIVE 262 39 4 66 25 smit:SMT_1213|5end_fatty_acid/phospholipid_synthesis_protein_PlsX_1172655..1172885_NEGATIVE 244 33 4 132 95 smit:SMT_595|5end_phosphoglycerate_mutase_512593..512823_NEGATIVE 242 168 131 176 140 smit:SMT_191|5end_adenylate_kinase_125745..125975_POSITIVE 236 34 3 65 25 smit:SMT_1593|5end_ABC-type_oligopeptide_transport_system,_periplasmic_component_1581417..1581647_POSITIVE 236 39 6 41 4 smit:SMT_604|5end_DNA_polymerase_III,_epsilon_chain_518693..518923_POSITIVE 236 179 138 153 108 smit:SMT_374|5end_hypothetical_protein_309788..310018_POSITIVE 233 255 211 59 15 smit:SMT_1917|5end_ATP-dependent_nuclease_subunit_B_1861765..1861995_NEGATIVE 233 273 235 136 102 smit:SMT_1110|5end_hypothetical_protein_1050963..1051193_NEGATIVE 232 98 51 179 129 smit:SMT_2125|5end_3-phosphoshikimate_1-carboxyvinyltransferase_2008872..2009102_POSITIVE 232 98 51 179 129 smit:SMT_750|5end_3-phosphoshikimate_1-carboxyvinyltransferase_655247..655477_NEGATIVE 227 125 81 147 109 smit:SMT_938|5end_hypothetical_protein_891274..891504_NEGATIVE 227 270 226 227 186 smit:SMT_832|5end_hypothetical_protein_775104..775334_NEGATIVE 222 259 227 62 32 smit:SMT_1364|5end_50S_ribosomal_protein_L35_1343865..1344095_NEGATIVE 222 231 197 119 86 smit:SMT_1130|5end_MATE_efflux_family_protein_1065210..1065440_NEGATIVE 222 250 201 55 4 smit:SMT_384|5end_hypothetical_protein_319406..319636_POSITIVE 220 37 7 184 152 smit:SMT_1977|5end_endopeptidase_O_1907832..1908062_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 45 5 100 59 smit:SMT_1511|3end_hypothetical_protein_1493902..1494052_POSITIVE 275 43 5 90 47 smit:SMT_180|3end_50S_ribosomal_protein_L14_120126..120276_POSITIVE 263 39 1 49 19 smit:SMT_1970|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1903032..1903182_POSITIVE 263 39 1 71 41 smit:SMT_1954|3end_6-phospho-beta-glucosidase_1888831..1888981_POSITIVE 262 39 4 69 28 smit:SMT_1214|3end_K03584_DNA_repair_protein_RecO_(recombination_protein_O)_1172652..1172802_NEGATIVE 250 259 211 74 25 smit:SMT_1524|3end_peptidase_T_1505867..1506017_POSITIVE 244 33 4 135 98 smit:SMT_596|3end_K03976_putative_transcription_regulator_512590..512740_NEGATIVE 239 224 181 62 14 smit:SMT_459|3end_hypothetical_protein_397690..397840_POSITIVE 236 179 138 74 29 smit:SMT_373|3end_cytosine_specific_DNA_methyltransferase_309789..309939_POSITIVE 233 273 235 103 69 smit:SMT_1111|3end_hypothetical_protein_1050996..1051146_NEGATIVE 233 33 2 94 60 smit:SMT_269|3end_phospho-N-acetylmuramoyl-pentapeptide-transferas_e_208785..208935_POSITIVE 233 48 1 90 44 smit:SMT_106|3end_hypothetical_protein_52336..52486_POSITIVE 232 98 51 87 37 smit:SMT_2124|3end_hypothetical_protein_2008860..2009010_POSITIVE 232 98 51 87 37 smit:SMT_751|3end_hypothetical_protein_655339..655489_NEGATIVE 227 270 226 148 107 smit:SMT_833|3end_hypothetical_protein_predicted_by_Glimmer/Critica_775183..775333_NEGATIVE 225 111 82 135 111 smit:SMT_1801|3end_heavy_metal_translocating_P-type_ATPase_1775408..1775558_POSITIVE 222 231 197 58 25 smit:SMT_1131|3end_threonine_synthase_1065271..1065421_NEGATIVE 219 259 211 69 19 smit:SMT_1790|3end_hypothetical_protein_1765915..1766065_POSITIVE 219 194 151 45 1 smit:SMT_134|3end_LysM_domain_protein_86157..86307_POSITIVE 218 33 1 87 47 smit:SMT_1066|3end_holo-(acyl_carrier_protein)_synthase_1005859..1006009_POSITIVE