Origin IGS: tgaatgagagagcccagtagctctctttttatagttcagtaaaaatgttttaatatagatggttctctgaaactactttcagaaacagctgttctataaaatacttttgaaactgaaatctattctaccacaaggtattgaaagcgctttaaaactaatatataatgaactcataagaacaaagaaaaggaggaaagaggatgccacagattactaaagaagccttgattgcacaaatcaaagatggaatcatcgtttcttgtcaggcnnnnnttaattaattaannnnnatcaaatgtagcagttgcgacttttactcttgcagtaaaccgtacatttaagagtcaaaatggcgaacgtgaggctgattttatcaatgtcgtt .........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 aacgacattgataaaatcagcctcacgttcgccattttgactcttaaatgtacggtttactgcaagagtaaaagtcgcaactgctacatttgatnnnnnttaattaattaannnnngcctgacaagaaacgatgattccatctttgatttgtgcaatcaaggcttctttagtaatctgtggcatcctctttcctccttttctttgttcttatgagttcattatatattagttttaaagcgctttcaataccttgtggtagaatagatttcagtttcaaaagtattttatagaacagctgtttctgaaagtagtttcagagaaccatctatattaaaacatttttactgaactataaaaagagagctactgggctctctcattca Mask Tandem Repeat Region ================================================ tgaatgagagagcccagtagctctctttttatagttcagtaaaaatgttttaatatagatggttctctgaaactactttcagaaacagctgttctataaaatacttttgaaactgaaatctattctaccacaaggtattgaaagcgctttaaaactaatatataatgaactcataagaacaaagaaaaggaggaaagaggatgccacagattactaaagaagccttgattgcacaaatcaaagatggaatcatcgtttcttgtcaggcnnnnnttaattaattaannnnnatcaaatgtagcagttgcgacttttactcttgcagtaaaccgtacatttaagagtcaaaatggcgaacgtgaggctgattttatcaatgtcgtt Find is-nt database================================================ Query_seq: SMT_2078:SMT_2079|SMT_2078:SMT_2079:acetyl xylan esterase, putative:single strand binding protein:->->:1979900..1980283 384 tgaatgagagagcccagtagctctctttttatagttcagtaaaaatgttttaatatagatggttctctgaaactactttcagaaacagctgttctataaaatacttttgaaactgaaatctattctaccacaaggtattgaaagcgctttaaaactaatatataatgaactcataagaacaaagaaaaggaggaaagaggatgccacagattactaaagaagccttgattgcacaaatcaaagatggaatcatcgtttcttgtcaggcnnnnnttaattaattaannnnnatcaaatgtagcagttgcgacttttactcttgcagtaaaccgtacatttaagagtcaaaatggcgaacgtgaggctgattttatcaatgtcgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2078:SMT_2079|SMT_2078:SMT_2079:acetyl xylan esterase, putative:single strand binding protein:->->:1979900..1980283 384 tgaatgagagagcccagtagctctctttttatagttcagtaaaaatgttttaatatagatggttctctgaaactactttcagaaacagctgttctataaaatacttttgaaactgaaatctattctaccacaaggtattgaaagcgctttaaaactaatatataatgaactcataagaacaaagaaaaggaggaaagaggatgccacagattactaaagaagccttgattgcacaaatcaaagatggaatcatcgtttcttgtcaggcnnnnnttaattaattaannnnnatcaaatgtagcagttgcgacttttactcttgcagtaaaccgtacatttaagagtcaaaatggcgaacgtgaggctgattttatcaatgtcgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2078:SMT_2079|SMT_2078:SMT_2079:acetyl xylan esterase, putative:single strand binding protein:->->:1979900..1980283 384 tgaatgagagagcccagtagctctctttttatagttcagtaaaaatgttttaatatagatggttctctgaaactactttcagaaacagctgttctataaaatacttttgaaactgaaatctattctaccacaaggtattgaaagcgctttaaaactaatatataatgaactcataagaacaaagaaaaggaggaaagaggatgccacagattactaaagaagccttgattgcacaaatcaaagatggaatcatcgtttcttgtcaggcnnnnnttaattaattaannnnnatcaaatgtagcagttgcgacttttactcttgcagtaaaccgtacatttaagagtcaaaatggcgaacgtgaggctgattttatcaatgtcgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaatgagagagcccagtagctctctttttatagttcagtaaaaatgttttaatatagatggttctctgaaactactttcagaaacagctgttctataaaatacttttgaaactgaaatctattctaccacaaggtattgaaagcgctttaaaactaatatataatgaactcataagaacaaagaaaaggaggaaagaggatgccacagattactaaagaagccttgattgcacaaatcaaagatggaatcatcgtttcttgtcaggcnnnnnttaattaattaannnnnatcaaatgtagcagttgcgacttttactcttgcagtaaaccgtacatttaagagtcaaaatggcgaacgtgaggctgattttatcaatgtcgtt Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 89 End: 214 ........................................................................................ M F Y K I L L K L K S I L P Q G I E S A L K L I Y N E L I R T K K R R K E D A T D Y .......................................................................................................................................................................... Protein_Len: 35 Strand: - Start: 174 End: 278 ............................................................................................................................................................................. L F L S F S S L P H W L N S F F G Q N C L D F I S D D N R T L X X X M .......................................................................................................... Protein_Len: 32 Strand: - Start: 158 End: 253 ............................................................................................................................................................. Y I I F E Y S C L F P P F L I G C I V L S A K I A C I L S P I M ................................................................................................................................... Protein_Len: 37 Strand: - Start: 97 End: 207 ................................................................................................ L I S K F S F D I R G C P I S L A K F S I Y L S S M L V F F L L F S S A M ................................................................................................................................................................................. tgaatgagagagcccagtagctctctttttatagttcagtaaaaatgttttaatatagatggttctctgaaactactttcagaaacagctgttctataaaatacttttgaaactgaaatctattctaccacaaggtattgaaagcgctttaaaactaatatataatgaactcataagaacaaagaaaaggaggaaagaggatgccacagattactaaagaagccttgattgcacaaatcaaagatggaatcatcgtttcttgtcaggcnnnnnttaattaattaannnnnatcaaatgtagcagttgcgacttttactcttgcagtaaaccgtacatttaagagtcaaaatggcgaacgtgaggctgattttatcaatgtcgtt 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: 137 End: 166 ........................................................................................................................................ATTGAAAGCGCTTTAAAACTAATATATAAT.......................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 27 End: 56 ..........................TTTTATAGTTCAGTAAAAATGTTTTAATAT........................................................................................................................................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgaatgagagagcccagtagctctctttttatagttcagtaaaaatgttttaatatagatggttctctgaaactactttcagaaacagctgttctataaaatacttttgaaactgaaatctattctaccacaaggtattgaaagcgctttaaaactaatatataatgaactcataagaacaaagaaaaggaggaaagaggatgccacagattactaaagaagccttgattgcacaaatcaaagatggaatcatcgtttcttgtcaggcnnnnnttaattaattaannnnnatcaaatgtagcagttgcgacttttactcttgcagtaaaccgtacatttaagagtcaaaatggcgaacgtgaggctgattttatcaatgtcgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_2078:SMT_2079|SMT_2078:SMT_2079:acetyl xylan esterase, putative:single strand binding protein:->->:1979900..1980283 384 tgaatgagagagcccagtagctctctttttatagttcagtaaaaatgttttaatatagatggttctctgaaactactttcagaaacagctgttctataaaatacttttgaaactgaaatctattctaccacaaggtattgaaagcgctttaaaactaatatataatgaactcataagaacaaagaaaaggaggaaagaggatgccacagattactaaagaagccttgattgcacaaatcaaagatggaatcatcgtttcttgtcaggcnnnnnttaattaattaannnnnatcaaatgtagcagttgcgacttttactcttgcagtaaaccgtacatttaagagtcaaaatggcgaacgtgaggctgattttatcaatgtcgtt Intra-Species Hit: Count: 1 Min: 1 Max: 384 Len: 384 Subject: smit_SMT_2078_SMT_2079|acetyl xylan esterase, putative:single strand binding protein|POSITIVE:POSITIVE|[1979900,1980283]|384 HSP 1 e-value: 0.0 bit: 702.0 Len: 384 Query Start:1 Query End:384 Subject Strand: POSITIVE Subject Start: 1 Subject End: 384 tgaatgagagagcccagtagctctctttttatagttcagtaaaaatgttttaatatagatggttctctgaaactactttcagaaacagctgttctataaaatacttttgaaactgaaatctattctaccacaaggtattgaaagcgctttaaaactaatatataatgaactcataagaacaaagaaaaggaggaaagaggatgccacagattactaaagaagccttgattgcacaaatcaaagatggaatcatcgtttcttgtcaggcnnnnnttaattaattaannnnnatcaaatgtagcagttgcgacttttactcttgcagtaaaccgtacatttaagagtcaaaatggcgaacgtgaggctgattttatcaatgtcgtt tgaatgagagagcccagtagctctctttttatagttcagtaaaaatgttttaatatagatggttctctgaaactactttcagaaacagctgttctataaaatacttttgaaactgaaatctattctaccacaaggtattgaaagcgctttaaaactaatatataatgaactcataagaacaaagaaaaggaggaaagaggatgccacagattactaaagaagccttgattgcacaaatcaaagatggaatcatcgtttcttgtcaggcnnnnnttaattaattaannnnnatcaaatgtagcagttgcgacttttactcttgcagtaaaccgtacatttaagagtcaaaatggcgaacgtgaggctgattttatcaatgtcgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAUGAGAGAGCCCAGUAGCUCUCUUUUUAUAGUUCAGUAAAAAUGUUUUAAUAUAGAUGGUUCUCUGAAACUACUUUCAGAAACAGCUGUUCUAUAAAAUACUUUUGAAACUGAAAUCUAUUCUACCACAAGGUAUUGAAAGCGCUUUAAAACUAAUAUAUAAUGAACUCAUAAGAACAAAGAAAAGGAGGAAAGAGGAUGCCACAGAUUACUAAAGAAGCCUUGAUUGCACAAAUCAAAGAUGGAAUCAUCGUUUCUUGUCAGGCNNNNNUUAAUUAAUUAANNNNNAUCAAAUGUAGCAGUUGCGACUUUUACUCUUGCAGUAAACCGUACAUUUAAGAGUCAAAAUGGCGAACGUGAGGCUGAUUUUAUCAAUGUCGUU .....((((((((......))))))))...((((((((((.(((((((((((..((((...(((.(((((((....))))))))))..))))....))))))).))))...))))))..))))..(((..(((((...(((((((((.....((((..(((((..(((.(((.................)))..........(((...(((.....(((((((..(((((.(((........).)).)))))..)))))))))).))).......................))).)))))..))))))).)))))).)))))..)))...((.(((((..(((((((...(.((....)).)...)))))))...))))))).. (-74.23) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACGACAUUGAUAAAAUCAGCCUCACGUUCGCCAUUUUGACUCUUAAAUGUACGGUUUACUGCAAGAGUAAAAGUCGCAACUGCUACAUUUGAUNNNNNUUAAUUAAUUAANNNNNGCCUGACAAGAAACGAUGAUUCCAUCUUUGAUUUGUGCAAUCAAGGCUUCUUUAGUAAUCUGUGGCAUCCUCUUUCCUCCUUUUCUUUGUUCUUAUGAGUUCAUUAUAUAUUAGUUUUAAAGCGCUUUCAAUACCUUGUGGUAGAAUAGAUUUCAGUUUCAAAAGUAUUUUAUAGAACAGCUGUUUCUGAAAGUAGUUUCAGAGAACCAUCUAUAUUAAAACAUUUUUACUGAACUAUAAAAAGAGAGCUACUGGGCUCUCUCAUUCA ...((..(((((...)))))..))..((((....((((((..((.((((.((...(((((..((((.(((((((.(((...(((((((.(((((........))))).........((((..........((((....))))..(((((.....))))))))).............)))))))..........................(((((.....))))).............)))))))...)))))))..))))).)).)))).))..))))))......((((((.......(((((((((....)))))))))....))))))................)))).......((((((((....))))))))...... (-75.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 267 224 210 172 smit:SMT_102|5end_competence-specific_global_transcription_modulator_34108..34338_POSITIVE 297 322 297 203 178 smit:SMT_172|5end_50S_ribosomal_protein_L23_116180..116410_POSITIVE 291 268 229 107 59 smit:SMT_1642|5end_K03497_chromosome_partitioning_protein,_ParB_family_1628996..1629226_NEGATIVE 284 350 304 83 35 smit:SMT_605|5end_DNA-binding_protein_HU_519034..519264_POSITIVE 279 368 322 226 185 smit:SMT_1810|5end_hypothetical_protein_1785219..1785449_POSITIVE 279 257 212 172 126 smit:SMT_1215|5end_aromatic_amino_acid_aminotransferase_1174588..1174818_NEGATIVE 272 268 221 100 53 smit:SMT_1934|5end_homoserine_dehydrogenase_1872402..1872632_POSITIVE 271 91 56 145 105 smit:SMT_845|5end_hypothetical_protein_791868..792098_NEGATIVE 268 227 181 205 164 smit:SMT_1411|5end_ATP-dependent_nuclease_subunit_B_1395478..1395708_NEGATIVE 265 267 221 142 92 smit:SMT_485|5end_hypothetical_protein_421401..421631_NEGATIVE 259 250 203 131 87 smit:SMT_821|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_732775..733005_POSITIVE 258 325 291 69 27 smit:SMT_910|5end_type_I_restriction_enzyme_R_protein_861889..862119_NEGATIVE 255 359 311 82 30 smit:SMT_1529|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1512880..1513110_NEGATIVE 253 268 230 55 18 smit:SMT_990|5end_hypothetical_protein_933947..934177_NEGATIVE 250 336 292 216 157 smit:SMT_2047|5end_choline_binding_protein_F_1957818..1958048_NEGATIVE 250 32 3 209 182 smit:SMT_431|5end_UDP-N-acetylmuramoyl-L-alanyl-D-glutamate_synthetase_372199..372429_POSITIVE 250 40 1 67 22 smit:SMT_208|5end_leucyl-tRNA_synthetase_139977..140207_POSITIVE 248 224 181 227 176 smit:SMT_2109|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1999099..1999329_NEGATIVE 243 368 322 189 148 smit:SMT_1782|5end_hypothetical_protein_1759520..1759750_POSITIVE 243 336 300 183 144 smit:SMT_794|5end_hypothetical_protein_703487..703717_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 267 224 89 51 smit:SMT_101|3end_cell_division_protein_34067..34217_POSITIVE 283 368 322 59 18 smit:SMT_799|3end_hypothetical_protein_707296..707446_NEGATIVE 279 368 322 61 20 smit:SMT_1809|3end_MutT/NUDIX_family_protein_1785134..1785284_POSITIVE 270 262 229 149 110 smit:SMT_1858|3end_K03497_chromosome_partitioning_protein,_ParB_family_1821687..1821837_NEGATIVE 265 267 221 83 33 smit:SMT_486|3end_hypothetical_protein_421460..421610_NEGATIVE 253 368 322 61 20 smit:SMT_2109|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1999061..1999211_NEGATIVE 253 368 322 61 20 smit:SMT_1180|3end_putative_tagatose-6-phosphate_aldose/ketose_isomerase_1138036..1138186_NEGATIVE 250 336 292 73 14 smit:SMT_2048|3end_competence-specific_global_transcription_modulator_1957961..1958111_NEGATIVE 250 97 59 94 58 smit:SMT_1890|3end_hypothetical_protein_1844131..1844281_POSITIVE 250 32 3 94 67 smit:SMT_430|3end_hypothetical_protein_372164..372314_POSITIVE 247 227 189 59 16 smit:SMT_728|3end_hypothetical_protein_633203..633353_NEGATIVE 246 268 230 89 52 smit:SMT_991|3end_hypothetical_protein_934033..934183_NEGATIVE 241 368 331 61 26 smit:SMT_890|3end_K02029_polar_amino_acid_transport_system_permease_protein_837692..837842_POSITIVE 238 203 165 36 2 smit:SMT_1478|3end_manganese_transport_system_membrane_protein_1460408..1460558_NEGATIVE 236 47 6 108 64 smit:SMT_1077|3end_GTP_cyclohydrolase_I_1014856..1015006_NEGATIVE 232 336 301 58 11 smit:SMT_946|3end_hypothetical_protein_895918..896068_NEGATIVE 232 233 191 139 94 smit:SMT_813|3end_acetyltransferase,_GNAT_family_721867..722017_NEGATIVE 232 50 6 96 43 smit:SMT_781|3end_hypothetical_protein_689509..689659_NEGATIVE 231 355 311 144 100 smit:SMT_379|3end_acetyltransferase,_GNAT_family_316456..316606_POSITIVE 231 355 311 144 100 smit:SMT_370|3end_acetyltransferase,_GNAT_family_305328..305478_POSITIVE