Origin IGS: ctttagagaactaactaatactttagttaattcactaagtatgtatcatttgtctctgatactaattagaaaaatctaatttatatagaaaggtagtcgattatgaaagtattatcctgcaggaggtcagaactcgctgtatccttgactcgtgcatatcaaacactgatgccggttatgataacccatgatttatatcctctatcgacactcatgttagctggtatcaagatattttaatatctctactctcatgatttacctcgttttaagagctgctttcagatggtttcggagtgggaattatctttctatgcggaacacctagtcagannnnnttaattaattaannnnntcggggctggcttaactatgcggcatcagagcagattgtactgagagtgcaccat .........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 atggtgcactctcagtacaatctgctctgatgccgcatagttaagccagccccgannnnnttaattaattaannnnntctgactaggtgttccgcatagaaagataattcccactccgaaaccatctgaaagcagctcttaaaacgaggtaaatcatgagagtagagatattaaaatatcttgataccagctaacatgagtgtcgatagaggatataaatcatgggttatcataaccggcatcagtgtttgatatgcacgagtcaaggatacagcgagttctgacctcctgcaggataatactttcataatcgactacctttctatataaattagatttttctaattagtatcagagacaaatgatacatacttagtgaattaactaaagtattagttagttctctaaag Mask Tandem Repeat Region ================================================ ctttagagaactaactaatactttagttaattcactaagtatgtatcatttgtctctgatactaattagaaaaatctaatttatatagaaaggtagtcgattatgaaagtattatcctgcaggaggtcagaactcgctgtatccttgactcgtgcatatcaaacactgatgccggttatgataacccatgatttatatcctctatcgacactcatgttagctggtatcaagatattttaatatctctactctcatgatttacctcgttttaagagctgctttcagatggtttcggagtgggaattatctttctatgcggaacacctagtcagannnnnttaattaattaannnnntcggggctggcttaactatgcggcatcagagcagattgtactgagagtgcaccat Find is-nt database================================================ Query_seq: SMT_1980:SMT_1981|SMT_1980:SMT_1981:glycosyltransferase:K03696 ATP-dependent Clp protease ATP-binding subunit ClpC:->->:1911991..1912400 410 ctttagagaactaactaatactttagttaattcactaagtatgtatcatttgtctctgatactaattagaaaaatctaatttatatagaaaggtagtcgattatgaaagtattatcctgcaggaggtcagaactcgctgtatccttgactcgtgcatatcaaacactgatgccggttatgataacccatgatttatatcctctatcgacactcatgttagctggtatcaagatattttaatatctctactctcatgatttacctcgttttaagagctgctttcagatggtttcggagtgggaattatctttctatgcggaacacctagtcagannnnnttaattaattaannnnntcggggctggcttaactatgcggcatcagagcagattgtactgagagtgcaccat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1980:SMT_1981|SMT_1980:SMT_1981:glycosyltransferase:K03696 ATP-dependent Clp protease ATP-binding subunit ClpC:->->:1911991..1912400 410 ctttagagaactaactaatactttagttaattcactaagtatgtatcatttgtctctgatactaattagaaaaatctaatttatatagaaaggtagtcgattatgaaagtattatcctgcaggaggtcagaactcgctgtatccttgactcgtgcatatcaaacactgatgccggttatgataacccatgatttatatcctctatcgacactcatgttagctggtatcaagatattttaatatctctactctcatgatttacctcgttttaagagctgctttcagatggtttcggagtgggaattatctttctatgcggaacacctagtcagannnnnttaattaattaannnnntcggggctggcttaactatgcggcatcagagcagattgtactgagagtgcaccat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1980:SMT_1981|SMT_1980:SMT_1981:glycosyltransferase:K03696 ATP-dependent Clp protease ATP-binding subunit ClpC:->->:1911991..1912400 410 ctttagagaactaactaatactttagttaattcactaagtatgtatcatttgtctctgatactaattagaaaaatctaatttatatagaaaggtagtcgattatgaaagtattatcctgcaggaggtcagaactcgctgtatccttgactcgtgcatatcaaacactgatgccggttatgataacccatgatttatatcctctatcgacactcatgttagctggtatcaagatattttaatatctctactctcatgatttacctcgttttaagagctgctttcagatggtttcggagtgggaattatctttctatgcggaacacctagtcagannnnnttaattaattaannnnntcggggctggcttaactatgcggcatcagagcagattgtactgagagtgcaccat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctttagagaactaactaatactttagttaattcactaagtatgtatcatttgtctctgatactaattagaaaaatctaatttatatagaaaggtagtcgattatgaaagtattatcctgcaggaggtcagaactcgctgtatccttgactcgtgcatatcaaacactgatgccggttatgataacccatgatttatatcctctatcgacactcatgttagctggtatcaagatattttaatatctctactctcatgatttacctcgttttaagagctgctttcagatggtttcggagtgggaattatctttctatgcggaacacctagtcagannnnnttaattaattaannnnntcggggctggcttaactatgcggcatcagagcagattgtactgagagtgcaccat Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 100 End: 237 ................................................................................................... M M K V L S C R R S E L A V S L T R A Y Q T L M P V M I T H D L Y P L S T L M L A G I K I F ............................................................................................................................................................................. Protein_Len: 35 Strand: + Start: 221 End: 325 ............................................................................................................................................................................................................................ M V S R Y F N I S T L M I Y L V L R A A F R W F R S G N Y L S M R N T ..................................................................................... ctttagagaactaactaatactttagttaattcactaagtatgtatcatttgtctctgatactaattagaaaaatctaatttatatagaaaggtagtcgattatgaaagtattatcctgcaggaggtcagaactcgctgtatccttgactcgtgcatatcaaacactgatgccggttatgataacccatgatttatatcctctatcgacactcatgttagctggtatcaagatattttaatatctctactctcatgatttacctcgttttaagagctgctttcagatggtttcggagtgggaattatctttctatgcggaacacctagtcagannnnnttaattaattaannnnntcggggctggcttaactatgcggcatcagagcagattgtactgagagtgcaccat 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================================================ ctttagagaactaactaatactttagttaattcactaagtatgtatcatttgtctctgatactaattagaaaaatctaatttatatagaaaggtagtcgattatgaaagtattatcctgcaggaggtcagaactcgctgtatccttgactcgtgcatatcaaacactgatgccggttatgataacccatgatttatatcctctatcgacactcatgttagctggtatcaagatattttaatatctctactctcatgatttacctcgttttaagagctgctttcagatggtttcggagtgggaattatctttctatgcggaacacctagtcagannnnnttaattaattaannnnntcggggctggcttaactatgcggcatcagagcagattgtactgagagtgcaccat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 40 HP_score: -2.2 Tail_Score: -2.71483 Start: 43 End: 62 Full_Region: TAATTCACTAAGTAT GTATCA TTTGTCTC TGATAC TAATTAGAAAAATCT ..........................................GTATCATTTGTCTCTGATAC............................................................................................................................................................................................................................................................................................................................................................ Find igs database================================================ Query_seq: SMT_1980:SMT_1981|SMT_1980:SMT_1981:glycosyltransferase:K03696 ATP-dependent Clp protease ATP-binding subunit ClpC:->->:1911991..1912400 410 ctttagagaactaactaatactttagttaattcactaagtatgtatcatttgtctctgatactaattagaaaaatctaatttatatagaaaggtagtcgattatgaaagtattatcctgcaggaggtcagaactcgctgtatccttgactcgtgcatatcaaacactgatgccggttatgataacccatgatttatatcctctatcgacactcatgttagctggtatcaagatattttaatatctctactctcatgatttacctcgttttaagagctgctttcagatggtttcggagtgggaattatctttctatgcggaacacctagtcagannnnnttaattaattaannnnntcggggctggcttaactatgcggcatcagagcagattgtactgagagtgcaccat Intra-Species Hit: Count: 1 Min: 1 Max: 410 Len: 410 Subject: smit_SMT_1980_SMT_1981|glycosyltransferase:K03696 ATP-dependent Clp protease ATP-binding subunit ClpC|POSITIVE:POSITIVE|[1911991,1912400]|410 HSP 1 e-value: 0.0 bit: 753.0 Len: 410 Query Start:1 Query End:410 Subject Strand: POSITIVE Subject Start: 1 Subject End: 410 ctttagagaactaactaatactttagttaattcactaagtatgtatcatttgtctctgatactaattagaaaaatctaatttatatagaaaggtagtcgattatgaaagtattatcctgcaggaggtcagaactcgctgtatccttgactcgtgcatatcaaacactgatgccggttatgataacccatgatttatatcctctatcgacactcatgttagctggtatcaagatattttaatatctctactctcatgatttacctcgttttaagagctgctttcagatggtttcggagtgggaattatctttctatgcggaacacctagtcagannnnnttaattaattaannnnntcggggctggcttaactatgcggcatcagagcagattgtactgagagtgcaccat ctttagagaactaactaatactttagttaattcactaagtatgtatcatttgtctctgatactaattagaaaaatctaatttatatagaaaggtagtcgattatgaaagtattatcctgcaggaggtcagaactcgctgtatccttgactcgtgcatatcaaacactgatgccggttatgataacccatgatttatatcctctatcgacactcatgttagctggtatcaagatattttaatatctctactctcatgatttacctcgttttaagagctgctttcagatggtttcggagtgggaattatctttctatgcggaacacctagtcagannnnnttaattaattaannnnntcggggctggcttaactatgcggcatcagagcagattgtactgagagtgcaccat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUAGAGAACUAACUAAUACUUUAGUUAAUUCACUAAGUAUGUAUCAUUUGUCUCUGAUACUAAUUAGAAAAAUCUAAUUUAUAUAGAAAGGUAGUCGAUUAUGAAAGUAUUAUCCUGCAGGAGGUCAGAACUCGCUGUAUCCUUGACUCGUGCAUAUCAAACACUGAUGCCGGUUAUGAUAACCCAUGAUUUAUAUCCUCUAUCGACACUCAUGUUAGCUGGUAUCAAGAUAUUUUAAUAUCUCUACUCUCAUGAUUUACCUCGUUUUAAGAGCUGCUUUCAGAUGGUUUCGGAGUGGGAAUUAUCUUUCUAUGCGGAACACCUAGUCAGANNNNNUUAAUUAAUUAANNNNNUCGGGGCUGGCUUAACUAUGCGGCAUCAGAGCAGAUUGUACUGAGAGUGCACCAU .(((((.(((.(((((((....))))))).))).)))))...((((.(((((.((((((....(((((((....)))))))....((((((((((...((((((((.((((......((((.(((.(((((((.....)).))..)))))).))))..........((((((((((((........(((((....................))))).)))))))))))).(((((....)))))..)))).)))))))))))))..)))))...(((((.........((((((..(((((((.....))))))).))))))..((((((.((.....((((....)))).....))..)))))).........))))).))))))))))).)))).............. (-100.15) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGGUGCACUCUCAGUACAAUCUGCUCUGAUGCCGCAUAGUUAAGCCAGCCCCGANNNNNUUAAUUAAUUAANNNNNUCUGACUAGGUGUUCCGCAUAGAAAGAUAAUUCCCACUCCGAAACCAUCUGAAAGCAGCUCUUAAAACGAGGUAAAUCAUGAGAGUAGAGAUAUUAAAAUAUCUUGAUACCAGCUAACAUGAGUGUCGAUAGAGGAUAUAAAUCAUGGGUUAUCAUAACCGGCAUCAGUGUUUGAUAUGCACGAGUCAAGGAUACAGCGAGUUCUGACCUCCUGCAGGAUAAUACUUUCAUAAUCGACUACCUUUCUAUAUAAAUUAGAUUUUUCUAAUUAGUAUCAGAGACAAAUGAUACAUACUUAGUGAAUUAACUAAAGUAUUAGUUAGUUCUCUAAAG ..((((.............(((.((.(((((((((....((((.(..(((((.........................(((..(((.(((...))).)))..)))....(((.....(((.(((((.(...(((.(((((((....((......)).))))))).(((((((....))))))).......))).).))).)).))).....)))..........)))))..).))))))))))))).))..))).((((.((((((.((((.......))))))).))).))))......................))))..........(((((((....))))))).((((((........))))))....((((.(((((((((((....))))))))))).)))).. (-90.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 929 400 356 227 183 smit:SMT_1943|5end_alpha/beta_hydrolase_fold_1878968..1879198_NEGATIVE 649 410 377 195 162 smit:SMT_1154|5end_tryptophanyl-tRNA_synthetase_1098921..1099151_NEGATIVE 523 381 356 231 206 smit:SMT_1887|5end_LicC_protein_1841445..1841675_POSITIVE 407 159 113 166 113 smit:SMT_1475|5end_K02004_1455873..1456103_POSITIVE 327 320 278 80 42 smit:SMT_1067|5end_alanine_racemase_1005769..1005999_POSITIVE 327 408 361 169 120 smit:SMT_335|5end_glutamine_synthetase_273753..273983_POSITIVE 318 405 370 50 11 smit:SMT_1962|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1895639..1895869_NEGATIVE 318 405 370 50 11 smit:SMT_823|5end_putative_mucus_binding_protein_746790..747020_NEGATIVE 314 155 117 80 46 smit:SMT_1111|5end_hypothetical_protein_1051409..1051639_NEGATIVE 310 399 358 174 139 smit:SMT_2067|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1973432..1973662_POSITIVE 306 303 273 50 8 smit:SMT_935|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_887326..887556_POSITIVE 296 399 356 229 182 smit:SMT_1617|5end_K02015_iron_complex_transport_system_permease_protein_1604500..1604730_NEGATIVE 296 160 119 215 163 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 295 394 358 207 164 smit:SMT_821|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_732775..733005_POSITIVE 294 235 198 134 100 smit:SMT_1001|5end_aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_A_942161..942391_POSITIVE 294 308 262 67 24 smit:SMT_111|5end_alpha-1,2-mannosidase,_putative_61304..61534_NEGATIVE 291 409 361 112 63 smit:SMT_1953|5end_hypothetical_protein_1886897..1887127_POSITIVE 289 391 356 212 163 smit:SMT_1381|5end_gamma-glutamyl_phosphate_reductase_1359730..1359960_NEGATIVE 287 400 358 181 145 smit:SMT_366|5end_hypothetical_protein_302085..302315_POSITIVE 283 149 109 64 18 smit:SMT_2045|5end_K+_transport_system,_NAD-binding_component_1956139..1956369_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1008 410 361 130 81 smit:SMT_2005|3end_pullulanase,_type_I_1925615..1925765_NEGATIVE 1008 410 361 130 81 smit:SMT_1944|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1879075..1879225_NEGATIVE 327 320 278 90 52 smit:SMT_1066|3end_holo-(acyl_carrier_protein)_synthase_1005859..1006009_POSITIVE 327 408 361 132 83 smit:SMT_334|3end_K03713_MerR_family_transcriptional_regulator,_glutamine_synthetase_repressor_273796..273946_POSITIVE 316 308 261 147 104 smit:SMT_1656|3end_glutamine_ABC_transporter_ATP-binding_protein_1645172..1645322_NEGATIVE 314 155 117 102 68 smit:SMT_1112|3end_K02248_competence_protein_ComGF_1051387..1051537_NEGATIVE 306 149 113 147 111 smit:SMT_1474|3end_K02003_1455951..1456101_POSITIVE 294 235 198 134 100 smit:SMT_1000|3end_glutamyl-tRNA_Gln_amidotransferase_subunit_C_942241..942391_POSITIVE 291 409 361 67 18 smit:SMT_1952|3end_hypothetical_protein_1886932..1887082_POSITIVE 287 174 133 131 95 smit:SMT_1443|3end_23S_rRNA_m(5)U_1939_methyltransferase_1426503..1426653_NEGATIVE 287 318 273 58 2 smit:SMT_1348|3end_exoribonuclease_II_1325148..1325298_NEGATIVE 283 180 132 95 41 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 283 290 242 122 83 smit:SMT_1362|3end_chaperone_protein_hscC_1341414..1341564_NEGATIVE 282 178 135 56 6 smit:SMT_1557|3end_hypothetical_protein_1543650..1543800_POSITIVE 281 400 357 58 6 smit:SMT_507|3end_hypothetical_protein_437638..437788_NEGATIVE 281 400 357 58 6 smit:SMT_504|3end_hypothetical_protein_436207..436357_NEGATIVE 274 174 135 50 8 smit:SMT_1965|3end_hypothetical_protein_1897711..1897861_POSITIVE 274 174 135 72 30 smit:SMT_1674|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1660361..1660511_NEGATIVE 272 229 184 146 93 smit:SMT_1258|3end_acetolactate_synthase_large_subunit_1223166..1223316_NEGATIVE 270 320 271 79 24 smit:SMT_1911|3end_hypothetical_protein_1857840..1857990_POSITIVE