Origin IGS: taatttgaaattattaaaaaaatctggcattaatacggttcgcatatattctatttaagatcaatacttccaatatatcgtattagttttcgggaagtcaaaattttgttgttatttatgatatactaatgctacaattatatcctttgatgaggtaaaatttatggataatgtagtgagattacacttgaagactgggactgattctagacaggaattggtggatttctgtttaaatagtaaaaaacagtatgttgctattgggtggagtagtcagagtgaagatctctatcgtgagagttttcaagagtattatcaaagggttaaagaattatctggaagagctaacccagcaattaacgtttttagggatgcaaaagtagacgacttattctggacaagagatctagatggtagatactnnnnnttaa .........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 ttaannnnnagtatctaccatctagatctcttgtccagaataagtcgtctacttttgcatccctaaaaacgttaattgctgggttagctcttccagataattctttaaccctttgataatactcttgaaaactctcacgatagagatcttcactctgactactccacccaatagcaacatactgttttttactatttaaacagaaatccaccaattcctgtctagaatcagtcccagtcttcaagtgtaatctcactacattatccataaattttacctcatcaaaggatataattgtagcattagtatatcataaataacaacaaaattttgacttcccgaaaactaatacgatatattggaagtattgatcttaaatagaatatatgcgaaccgtattaatgccagatttttttaataatttcaaatta Mask Tandem Repeat Region ================================================ taatttgaaattattaaaaaaatctggcattaatacggttcgcatatattctatttaagatcaatacttccaatatatcgtattagttttcgggaagtcaaaattttgttgttatttatgatatactaatgctacaattatatcctttgatgaggtaaaatttatggataatgtagtgagattacacttgaagactgggactgattctagacaggaattggtggatttctgtttaaatagtaaaaaacagtatgttgctattgggtggagtagtcagagtgaagatctctatcgtgagagttttcaagagtattatcaaagggttaaagaattatctggaagagctaacccagcaattaacgtttttagggatgcaaaagtagacgacttattctggacaagagatctagatggtagatactnnnnnttaa Find is-nt database================================================ Query_seq: SMT_1247:SMT_1248|SMT_1247:SMT_1248:hypothetical protein predicted by Glimmer/Critica:Na+/H+ antiporter:-><-:1208326..1208756 431 taatttgaaattattaaaaaaatctggcattaatacggttcgcatatattctatttaagatcaatacttccaatatatcgtattagttttcgggaagtcaaaattttgttgttatttatgatatactaatgctacaattatatcctttgatgaggtaaaatttatggataatgtagtgagattacacttgaagactgggactgattctagacaggaattggtggatttctgtttaaatagtaaaaaacagtatgttgctattgggtggagtagtcagagtgaagatctctatcgtgagagttttcaagagtattatcaaagggttaaagaattatctggaagagctaacccagcaattaacgtttttagggatgcaaaagtagacgacttattctggacaagagatctagatggtagatactnnnnnttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1247:SMT_1248|SMT_1247:SMT_1248:hypothetical protein predicted by Glimmer/Critica:Na+/H+ antiporter:-><-:1208326..1208756 431 taatttgaaattattaaaaaaatctggcattaatacggttcgcatatattctatttaagatcaatacttccaatatatcgtattagttttcgggaagtcaaaattttgttgttatttatgatatactaatgctacaattatatcctttgatgaggtaaaatttatggataatgtagtgagattacacttgaagactgggactgattctagacaggaattggtggatttctgtttaaatagtaaaaaacagtatgttgctattgggtggagtagtcagagtgaagatctctatcgtgagagttttcaagagtattatcaaagggttaaagaattatctggaagagctaacccagcaattaacgtttttagggatgcaaaagtagacgacttattctggacaagagatctagatggtagatactnnnnnttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1247:SMT_1248|SMT_1247:SMT_1248:hypothetical protein predicted by Glimmer/Critica:Na+/H+ antiporter:-><-:1208326..1208756 431 taatttgaaattattaaaaaaatctggcattaatacggttcgcatatattctatttaagatcaatacttccaatatatcgtattagttttcgggaagtcaaaattttgttgttatttatgatatactaatgctacaattatatcctttgatgaggtaaaatttatggataatgtagtgagattacacttgaagactgggactgattctagacaggaattggtggatttctgtttaaatagtaaaaaacagtatgttgctattgggtggagtagtcagagtgaagatctctatcgtgagagttttcaagagtattatcaaagggttaaagaattatctggaagagctaacccagcaattaacgtttttagggatgcaaaagtagacgacttattctggacaagagatctagatggtagatactnnnnnttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatttgaaattattaaaaaaatctggcattaatacggttcgcatatattctatttaagatcaatacttccaatatatcgtattagttttcgggaagtcaaaattttgttgttatttatgatatactaatgctacaattatatcctttgatgaggtaaaatttatggataatgtagtgagattacacttgaagactgggactgattctagacaggaattggtggatttctgtttaaatagtaaaaaacagtatgttgctattgggtggagtagtcagagtgaagatctctatcgtgagagttttcaagagtattatcaaagggttaaagaattatctggaagagctaacccagcaattaacgtttttagggatgcaaaagtagacgacttattctggacaagagatctagatggtagatactnnnnnttaa Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 237 End: 380 ............................................................................................................................................................................................................................................ M V K N S M L L L G G V V R V K I S I V R V F K S I I K G L K N Y L E E L T Q Q L T F L G M Q K ................................................... Protein_Len: 60 Strand: + Start: 137 End: 430 ........................................................................................................................................ M I S F D E V K F M D N V V R L H L K T G T D S R Q E L V D F C L N S K K Q Y V A I G W S S Q S E D L Y R E S F Q E Y Y . Protein_Len: 49 Strand: - Start: 115 End: 261 .................................................................................................................. K H Y V L A V I I D K S S T F N I S L T T L N C K F V P V S E L C S N T S K Q K F L L F C Y T A M .......................................................................................................................................................................... taatttgaaattattaaaaaaatctggcattaatacggttcgcatatattctatttaagatcaatacttccaatatatcgtattagttttcgggaagtcaaaattttgttgttatttatgatatactaatgctacaattatatcctttgatgaggtaaaatttatggataatgtagtgagattacacttgaagactgggactgattctagacaggaattggtggatttctgtttaaatagtaaaaaacagtatgttgctattgggtggagtagtcagagtgaagatctctatcgtgagagttttcaagagtattatcaaagggttaaagaattatctggaagagctaacccagcaattaacgtttttagggatgcaaaagtagacgacttattctggacaagagatctagatggtagatactnnnnnttaa 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================================================ taatttgaaattattaaaaaaatctggcattaatacggttcgcatatattctatttaagatcaatacttccaatatatcgtattagttttcgggaagtcaaaattttgttgttatttatgatatactaatgctacaattatatcctttgatgaggtaaaatttatggataatgtagtgagattacacttgaagactgggactgattctagacaggaattggtggatttctgtttaaatagtaaaaaacagtatgttgctattgggtggagtagtcagagtgaagatctctatcgtgagagttttcaagagtattatcaaagggttaaagaattatctggaagagctaacccagcaattaacgtttttagggatgcaaaagtagacgacttattctggacaagagatctagatggtagatactnnnnnttaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1247:SMT_1248|SMT_1247:SMT_1248:hypothetical protein predicted by Glimmer/Critica:Na+/H+ antiporter:-><-:1208326..1208756 431 taatttgaaattattaaaaaaatctggcattaatacggttcgcatatattctatttaagatcaatacttccaatatatcgtattagttttcgggaagtcaaaattttgttgttatttatgatatactaatgctacaattatatcctttgatgaggtaaaatttatggataatgtagtgagattacacttgaagactgggactgattctagacaggaattggtggatttctgtttaaatagtaaaaaacagtatgttgctattgggtggagtagtcagagtgaagatctctatcgtgagagttttcaagagtattatcaaagggttaaagaattatctggaagagctaacccagcaattaacgtttttagggatgcaaaagtagacgacttattctggacaagagatctagatggtagatactnnnnnttaa Intra-Species Hit: Count: 1 Min: 1 Max: 422 Len: 422 Subject: smit_SMT_1247_SMT_1248|hypothetical protein predicted by Glimmer/Critica:Na+/H+ antiporter|POSITIVE:NEGATIVE|[1208326,1208756]|431 HSP 1 e-value: 0.0 bit: 795.0 Len: 422 Query Start:1 Query End:422 Subject Strand: POSITIVE Subject Start: 1 Subject End: 422 taatttgaaattattnnnnnnntctggcattaatacggttcgcatatattctatttaagatcaatacttccaatatatcgtattagttttcgggaagtcaaaattttgttgttatttatgatatactaatgctacaattatatcctttgatgaggtaaaatttatggataatgtagtgagattacacttgaagactgggactgattctagacaggaattggtggatttctgtttaaatagtaaaaaacagtatgttgctattgggtggagtagtcagagtgaagatctctatcgtgagagttttcaagagtattatcaaagggttaaagaattatctggaagagctaacccagcaattaacgtttttagggatgcaaaagtagacgacttattctggacaagagatctagatggtagatact......... taatttgaaattattaaaaaaatctggcattaatacggttcgcatatattctatttaagatcaatacttccaatatatcgtattagttttcgggaagtcaaaattttgttgttatttatgatatactaatgctacaattatatcctttgatgaggtaaaatttatggataatgtagtgagattacacttgaagactgggactgattctagacaggaattggtggatttctgtttaaatagtaaaaaacagtatgttgctattgggtggagtagtcagagtgaagatctctatcgtgagagttttcaagagtattatcaaagggttaaagaattatctggaagagctaacccagcaattaacgtttttagggatgcaaaagtagacgacttattctggacaagagatctagatggtagatact......... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUGAAAUUAUUAAAAAAAUCUGGCAUUAAUACGGUUCGCAUAUAUUCUAUUUAAGAUCAAUACUUCCAAUAUAUCGUAUUAGUUUUCGGGAAGUCAAAAUUUUGUUGUUAUUUAUGAUAUACUAAUGCUACAAUUAUAUCCUUUGAUGAGGUAAAAUUUAUGGAUAAUGUAGUGAGAUUACACUUGAAGACUGGGACUGAUUCUAGACAGGAAUUGGUGGAUUUCUGUUUAAAUAGUAAAAAACAGUAUGUUGCUAUUGGGUGGAGUAGUCAGAGUGAAGAUCUCUAUCGUGAGAGUUUUCAAGAGUAUUAUCAAAGGGUUAAAGAAUUAUCUGGAAGAGCUAACCCAGCAAUUAACGUUUUUAGGGAUGCAAAAGUAGACGACUUAUUCUGGACAAGAGAUCUAGAUGGUAGAUACU .....................(((((.((((.......(((((.......((((((....((((((....((((((((.((..(((((((((((.((((.......(((..(.....)..))).......((((((....(((((...(((........)))...))))).))))))..))))...)))))))))))..((((.((.((((((((((((....)))))))))))))))))).....)).)))))))).))))))...)))))).....)))))(((((((.((....))....((.((((((...((...((((((.(((....)))........)))))).(((.((((.....))))...)))..........))..)))))).))..)))))))..)))).)))))... (-88.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAUCUACCAUCUAGAUCUCUUGUCCAGAAUAAGUCGUCUACUUUUGCAUCCCUAAAAACGUUAAUUGCUGGGUUAGCUCUUCCAGAUAAUUCUUUAACCCUUUGAUAAUACUCUUGAAAACUCUCACGAUAGAGAUCUUCACUCUGACUACUCCACCCAAUAGCAACAUACUGUUUUUUACUAUUUAAACAGAAAUCCACCAAUUCCUGUCUAGAAUCAGUCCCAGUCUUCAAGUGUAAUCUCACUACAUUAUCCAUAAAUUUUACCUCAUCAAAGGAUAUAAUUGUAGCAUUAGUAUAUCAUAAAUAACAACAAAAUUUUGACUUCCCGAAAACUAAUACGAUAUAUUGGAAGUAUUGAUCUUAAAUAGAAUAUAUGCGAACCGUAUUAAUGCCAGAUUUUUUUAAUAAUUUCAAAUUA ....((((......(((((.....((((..(((.(((((.((((..(((...............((((((((((........))))).))))).......((((((((.....((.(((......))).))..(((((...((((..((((.....................((((((..........))))))..............(((........)))....))))....))))..)))))..........................))))))))...........)))..))))....................(((((......)))))......))))).)))))))......)))))....))))........(((...((((((............))))))..)))...... (-64.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 338 307 261 123 60 smit:SMT_261|5end_ImpB/MucB/SamB_family_protein_200160..200390_POSITIVE 314 375 331 66 20 smit:SMT_519|5end_glutathione_reductase_444884..445114_NEGATIVE 308 308 266 103 64 smit:SMT_546|5end_DNA_topoisomerase_IV_subunit_A_461377..461607_POSITIVE 300 296 257 225 189 smit:SMT_2069|5end_K02035_peptide/nickel_transport_system_substrate-binding_protein_1974656..1974886_POSITIVE 290 310 262 182 123 smit:SMT_112|5end_hypothetical_protein_predicted_by_Glimmer/Critica_61473..61703_NEGATIVE 282 287 246 231 177 smit:SMT_1144|5end_K02026_multiple_sugar_transport_system_permease_protein_1088222..1088452_POSITIVE 281 224 187 168 128 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 278 299 255 53 10 smit:SMT_1520|5end_K02004_1501184..1501414_NEGATIVE 272 295 255 117 70 smit:SMT_1939|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1876278..1876508_POSITIVE 267 285 248 231 194 smit:SMT_764|5end_alanyl-tRNA_synthetase_672113..672343_NEGATIVE 266 231 191 45 1 smit:SMT_2002|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1924405..1924635_NEGATIVE 265 419 377 231 183 smit:SMT_882|5end_acetyl_esterase_830441..830671_NEGATIVE 265 310 263 49 8 smit:SMT_117|5end_K02025_multiple_sugar_transport_system_permease_protein_68487..68717_POSITIVE 263 305 261 224 167 smit:SMT_1767|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_1744121..1744351_NEGATIVE 262 302 261 50 10 smit:SMT_1504|5end_topology_modulation_protein_1487204..1487434_POSITIVE 258 285 248 66 26 smit:SMT_155|5end_hypothetical_protein_102704..102934_NEGATIVE 257 373 335 103 63 smit:SMT_2135|5end_dipeptidase_2015053..2015283_NEGATIVE 257 298 253 52 2 smit:SMT_990|5end_hypothetical_protein_933947..934177_NEGATIVE 257 221 186 49 8 smit:SMT_215|5end_leucyl-tRNA_synthetase_147045..147275_POSITIVE 256 303 262 119 74 smit:SMT_76|5end_DNA_repair_and_genetic_recombination_protein_2677..2907_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 338 307 261 119 56 smit:SMT_260|3end_phage_transcriptional_repressor_200236..200386_POSITIVE 314 375 331 69 23 smit:SMT_520|3end_glutathione_reductase_444881..445031_NEGATIVE 314 210 167 64 22 smit:SMT_316|3end_acetyl-CoA_carboxylase_carboxyl_transferase_subunit_alpha_257391..257541_POSITIVE 308 308 266 70 31 smit:SMT_545|3end_hypothetical_protein_predicted_by_Glimmer/Critica_461424..461574_POSITIVE 290 385 342 151 96 smit:SMT_1484|3end_exonuclease_RexA_1464256..1464406_NEGATIVE 283 296 259 55 7 smit:SMT_2133|3end_hypothetical_protein_2013720..2013870_NEGATIVE 274 233 191 151 100 smit:SMT_588|3end_hypothetical_protein_504464..504614_NEGATIVE 268 320 276 111 63 smit:SMT_397|3end_NAD(+)_synthetase_327423..327573_POSITIVE 259 299 251 125 71 smit:SMT_1716|3end_hypothetical_protein_1703657..1703807_POSITIVE 256 303 262 116 71 smit:SMT_75|3end_hypothetical_protein_2754..2904_POSITIVE 254 309 263 106 51 smit:SMT_1935|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1873930..1874080_POSITIVE 254 309 263 106 51 smit:SMT_1314|3end_dTDP-4-dehydrorhamnose_3,5-epimerase_related_enzyme_1280192..1280342_POSITIVE 253 370 323 136 86 smit:SMT_842|3end_hypothetical_protein_788414..788564_NEGATIVE 249 300 260 55 12 smit:SMT_856|3end_peroxide_resistance_protein,non-heme_iron-containing_ferritin_800130..800280_NEGATIVE 248 316 276 91 48 smit:SMT_799|3end_hypothetical_protein_707296..707446_NEGATIVE 246 278 251 55 25 smit:SMT_634|3end_ribonucleoside-diphosphate_reductase_alpha_chain_540618..540768_POSITIVE 244 216 175 53 13 smit:SMT_1253|3end_beta-galactosidase_1212912..1213062_NEGATIVE 242 215 177 150 106 smit:SMT_1436|3end_conserved_hypothetical_protein_TIGR00147_1420374..1420524_NEGATIVE 241 229 188 85 50 smit:SMT_1807|3end_putative_mucus_binding_protein_1781740..1781890_NEGATIVE 241 350 305 112 47 smit:SMT_942|3end_hypothetical_protein_893528..893678_NEGATIVE