Origin IGS: tttagcgcgcggatataaaggtctctctccgctgaacgctgattcgtttggggctgtgtcaaaattcggttttgtcgcagccccttttgggtgtgcaagaatgtgtaaagtacaaggtactaagactgaggtagaaaggagcgaacttacaagtacgcgactgaagccgaatgtcgcaagcaacgcagtaatttgcgcatgatgacactccgtcataatcgtccttatgccgtttcgttgtcatacacaatcattcaaggtaacaaacagacaaacttggcattggctcctgcttgagcggattgccccgtgattattttatgtcccaatatcattacctttgttcactaatgtaaataaggacaagcaagacggattgat .........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 atcaatccgtcttgcttgtccttatttacattagtgaacaaaggtaatgatattgggacataaaataatcacggggcaatccgctcaagcaggagccaatgccaagtttgtctgtttgttaccttgaatgattgtgtatgacaacgaaacggcataaggacgattatgacggagtgtcatcatgcgcaaattactgcgttgcttgcgacattcggcttcagtcgcgtacttgtaagttcgctcctttctacctcagtcttagtaccttgtactttacacattcttgcacacccaaaaggggctgcgacaaaaccgaattttgacacagccccaaacgaatcagcgttcagcggagagagacctttatatccgcgcgctaaa Mask Tandem Repeat Region ================================================ tttagcgcgcggatataaaggtctctctccgctgaacgctgattcgtttggggctgtgtcaaaattcggttttgtcgcagccccttttgggtgtgcaagaatgtgtaaagtacaaggtactaagactgaggtagaaaggagcgaacttacaagtacgcgactgaagccgaatgtcgcaagcaacgcagtaatttgcgcatgatgacactccgtcataatcgtccttatgccgtttcgttgtcatacacaatcattcaaggtaacaaacagacaaacttggcattggctcctgcttgagcggattgccccgtgattattttatgtcccaatatcattacctttgttcactaatgtaaataaggacaagcaagacggattgat Find is-nt database================================================ Query_seq: PG1950:PG1951|PG1950:PG1951:hypothetical protein:glutaminyl-tRNA synthetase:->->:2040901..2041281 381 tttagcgcgcggatataaaggtctctctccgctgaacgctgattcgtttggggctgtgtcaaaattcggttttgtcgcagccccttttgggtgtgcaagaatgtgtaaagtacaaggtactaagactgaggtagaaaggagcgaacttacaagtacgcgactgaagccgaatgtcgcaagcaacgcagtaatttgcgcatgatgacactccgtcataatcgtccttatgccgtttcgttgtcatacacaatcattcaaggtaacaaacagacaaacttggcattggctcctgcttgagcggattgccccgtgattattttatgtcccaatatcattacctttgttcactaatgtaaataaggacaagcaagacggattgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1950:PG1951|PG1950:PG1951:hypothetical protein:glutaminyl-tRNA synthetase:->->:2040901..2041281 381 tttagcgcgcggatataaaggtctctctccgctgaacgctgattcgtttggggctgtgtcaaaattcggttttgtcgcagccccttttgggtgtgcaagaatgtgtaaagtacaaggtactaagactgaggtagaaaggagcgaacttacaagtacgcgactgaagccgaatgtcgcaagcaacgcagtaatttgcgcatgatgacactccgtcataatcgtccttatgccgtttcgttgtcatacacaatcattcaaggtaacaaacagacaaacttggcattggctcctgcttgagcggattgccccgtgattattttatgtcccaatatcattacctttgttcactaatgtaaataaggacaagcaagacggattgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1950:PG1951|PG1950:PG1951:hypothetical protein:glutaminyl-tRNA synthetase:->->:2040901..2041281 381 tttagcgcgcggatataaaggtctctctccgctgaacgctgattcgtttggggctgtgtcaaaattcggttttgtcgcagccccttttgggtgtgcaagaatgtgtaaagtacaaggtactaagactgaggtagaaaggagcgaacttacaagtacgcgactgaagccgaatgtcgcaagcaacgcagtaatttgcgcatgatgacactccgtcataatcgtccttatgccgtttcgttgtcatacacaatcattcaaggtaacaaacagacaaacttggcattggctcctgcttgagcggattgccccgtgattattttatgtcccaatatcattacctttgttcactaatgtaaataaggacaagcaagacggattgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttagcgcgcggatataaaggtctctctccgctgaacgctgattcgtttggggctgtgtcaaaattcggttttgtcgcagccccttttgggtgtgcaagaatgtgtaaagtacaaggtactaagactgaggtagaaaggagcgaacttacaagtacgcgactgaagccgaatgtcgcaagcaacgcagtaatttgcgcatgatgacactccgtcataatcgtccttatgccgtttcgttgtcatacacaatcattcaaggtaacaaacagacaaacttggcattggctcctgcttgagcggattgccccgtgattattttatgtcccaatatcattacctttgttcactaatgtaaataaggacaagcaagacggattgat Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 39 End: 131 ...................................... M I R L G L C Q N S V L S Q P L L G V Q E C V K Y K V L R L R .......................................................................................................................................................................................................................................................... Protein_Len: 56 Strand: + Start: 32 End: 199 ............................... M N A D S F G A V S K F G F V A A P F G C A R M C K V Q G T K T E V E R S E L T S T R L K P N V A S N A V I C A ...................................................................................................................................................................................... Protein_Len: 34 Strand: + Start: 193 End: 294 ................................................................................................................................................................................................ M R M M T L R H N R P Y A V S L S Y T I I Q G N K Q T N L A L A P A ....................................................................................... Protein_Len: 32 Strand: + Start: 215 End: 310 ...................................................................................................................................................................................................................... M I V L M P F R C H T Q S F K V T N R Q T W H W L L L E R I A P ....................................................................... Protein_Len: 60 Strand: - Start: 62 End: 250 ............................................................. K D C G R K P T C S H T F Y L T S L S L Y F P A F K C T R S Q L R I D C A V C Y N A C S S V G D Y D D K H R K T T M C M ................................................................................................................................... Protein_Len: 32 Strand: - Start: 3 End: 98 .. L A R I Y L D R E A S R Q N T Q P Q T L I R N Q R L G K Q T H M ........................................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: - Start: 1 End: 228 P A T D F N P K T A A G K P H A L I H L T C P V L V S T S L L S S V L V R S F G F T A L L A T I Q A H H C E T M I T R M ......................................................................................................................................................... tttagcgcgcggatataaaggtctctctccgctgaacgctgattcgtttggggctgtgtcaaaattcggttttgtcgcagccccttttgggtgtgcaagaatgtgtaaagtacaaggtactaagactgaggtagaaaggagcgaacttacaagtacgcgactgaagccgaatgtcgcaagcaacgcagtaatttgcgcatgatgacactccgtcataatcgtccttatgccgtttcgttgtcatacacaatcattcaaggtaacaaacagacaaacttggcattggctcctgcttgagcggattgccccgtgattattttatgtcccaatatcattacctttgttcactaatgtaaataaggacaagcaagacggattgat 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================================================ tttagcgcgcggatataaaggtctctctccgctgaacgctgattcgtttggggctgtgtcaaaattcggttttgtcgcagccccttttgggtgtgcaagaatgtgtaaagtacaaggtactaagactgaggtagaaaggagcgaacttacaagtacgcgactgaagccgaatgtcgcaagcaacgcagtaatttgcgcatgatgacactccgtcataatcgtccttatgccgtttcgttgtcatacacaatcattcaaggtaacaaacagacaaacttggcattggctcctgcttgagcggattgccccgtgattattttatgtcccaatatcattacctttgttcactaatgtaaataaggacaagcaagacggattgat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -15.8 Tail_Score: -4.2349 Start: 50 End: 84 Full_Region: AACGCTGATTCGTTT GGGGCTGTGTCAAAAT TCG GTTTTGTCGCAGCCCC TTTTGGGTGTGCAAG .................................................GGGGCTGTGTCAAAATTCGGTTTTGTCGCAGCCCC......................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 56 HP_score: -3.0 Tail_Score: -4.02108 Start: 211 End: 232 Full_Region: CGCATGATGACACTC CGTCATAA TCGTCC TTATGCCG TTTCGTTGTCATACA ..................................................................................................................................................................................................................CGTCATAATCGTCCTTATGCCG..................................................................................................................................................... Find igs database================================================ Query_seq: PG1950:PG1951|PG1950:PG1951:hypothetical protein:glutaminyl-tRNA synthetase:->->:2040901..2041281 381 tttagcgcgcggatataaaggtctctctccgctgaacgctgattcgtttggggctgtgtcaaaattcggttttgtcgcagccccttttgggtgtgcaagaatgtgtaaagtacaaggtactaagactgaggtagaaaggagcgaacttacaagtacgcgactgaagccgaatgtcgcaagcaacgcagtaatttgcgcatgatgacactccgtcataatcgtccttatgccgtttcgttgtcatacacaatcattcaaggtaacaaacagacaaacttggcattggctcctgcttgagcggattgccccgtgattattttatgtcccaatatcattacctttgttcactaatgtaaataaggacaagcaagacggattgat Intra-Species Hit: Count: 1 Min: 1 Max: 381 Len: 381 Subject: NC_002950_PG1950_PG1951|hypothetical protein:glutaminyl-tRNA synthetase|POSITIVE:POSITIVE|[2040901,2041281]|381 HSP 1 e-value: 0.0 bit: 755.0 Len: 381 Query Start:1 Query End:381 Subject Strand: POSITIVE Subject Start: 1 Subject End: 381 tttagcgcgcggatataaaggtctctctccgctgaacgctgattcgtttggggctgtgtcaaaattcggttttgtcgcagccccttttgggtgtgcaagaatgtgtaaagtacaaggtactaagactgaggtagaaaggagcgaacttacaagtacgcgactgaagccgaatgtcgcaagcaacgcagtaatttgcgcatgatgacactccgtcataatcgtccttatgccgtttcgttgtcatacacaatcattcaaggtaacaaacagacaaacttggcattggctcctgcttgagcggattgccccgtgattattttatgtcccaatatcattacctttgttcactaatgtaaataaggacaagcaagacggattgat tttagcgcgcggatataaaggtctctctccgctgaacgctgattcgtttggggctgtgtcaaaattcggttttgtcgcagccccttttgggtgtgcaagaatgtgtaaagtacaaggtactaagactgaggtagaaaggagcgaacttacaagtacgcgactgaagccgaatgtcgcaagcaacgcagtaatttgcgcatgatgacactccgtcataatcgtccttatgccgtttcgttgtcatacacaatcattcaaggtaacaaacagacaaacttggcattggctcctgcttgagcggattgccccgtgattattttatgtcccaatatcattacctttgttcactaatgtaaataaggacaagcaagacggattgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAGCGCGCGGAUAUAAAGGUCUCUCUCCGCUGAACGCUGAUUCGUUUGGGGCUGUGUCAAAAUUCGGUUUUGUCGCAGCCCCUUUUGGGUGUGCAAGAAUGUGUAAAGUACAAGGUACUAAGACUGAGGUAGAAAGGAGCGAACUUACAAGUACGCGACUGAAGCCGAAUGUCGCAAGCAACGCAGUAAUUUGCGCAUGAUGACACUCCGUCAUAAUCGUCCUUAUGCCGUUUCGUUGUCAUACACAAUCAUUCAAGGUAACAAACAGACAAACUUGGCAUUGGCUCCUGCUUGAGCGGAUUGCCCCGUGAUUAUUUUAUGUCCCAAUAUCAUUACCUUUGUUCACUAAUGUAAAUAAGGACAAGCAAGACGGAUUGAU .((((((.(((((..............)))))....)))))).......(((((((((.((((((...)))))).)))))))))......(((((((((..(((((..(((((...)))))..(((...(((....((..(((.(((....))).)))..))...)))....))).......)))))....))))))))).....((.((((((......((((((((..((((..(((((.....))))).....(((((((...............((((((.((((......)))).)).)))).(((((.....)))))...........)))))))........))))...))))))))......)))))).)).. (-113.04) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAAUCCGUCUUGCUUGUCCUUAUUUACAUUAGUGAACAAAGGUAAUGAUAUUGGGACAUAAAAUAAUCACGGGGCAAUCCGCUCAAGCAGGAGCCAAUGCCAAGUUUGUCUGUUUGUUACCUUGAAUGAUUGUGUAUGACAACGAAACGGCAUAAGGACGAUUAUGACGGAGUGUCAUCAUGCGCAAAUUACUGCGUUGCUUGCGACAUUCGGCUUCAGUCGCGUACUUGUAAGUUCGCUCCUUUCUACCUCAGUCUUAGUACCUUGUACUUUACACAUUCUUGCACACCCAAAAGGGGCUGCGACAAAACCGAAUUUUGACACAGCCCCAAACGAAUCAGCGUUCAGCGGAGAGAGACCUUUAUAUCCGCGCGCUAAA ..((.((((((.((.((((((((((.(((((.(((.(...(((((((..(.....(((((..........((..((((....((((......))))...))))..)).)))))..)..)))))))...).))))))))......((...))..)))))))))).)).)))))).))...((.((.((((......(((..((((((((.((.((((....)))).))..)))))))).)))..............((...(((((...)))))..))......)))).)).......(((((((.(.(((((.....))))).).)))))))....))...(((((...(((((.(((....)))...))))))))))... (-106.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 775 208 163 181 137 NC_002950:PG1117|5end_MATE_efflux_family_protein_1190010..1190240_POSITIVE 606 100 51 208 158 NC_002950:PG0095|5end_DNA_mismatch_repair_protein_114763..114993_NEGATIVE 604 85 42 56 11 NC_002950:PG1234|5end_hypothetical_protein_1310112..1310342_POSITIVE 557 96 51 85 40 NC_002950:PG1268|5end_hypothetical_protein_1347371..1347601_POSITIVE 423 303 268 59 17 NC_002950:PG1875|5end_hemolysin_1970621..1970851_NEGATIVE 416 83 50 225 192 NC_002950:PG0749|5end_hypothetical_protein_795654..795884_NEGATIVE 402 90 48 44 1 NC_002950:PG0623|5end_triosephosphate_isomerase_677261..677491_POSITIVE 392 310 268 224 184 NC_002950:PG1523|5end_naphthoate_synthase_1600988..1601218_NEGATIVE 385 320 271 85 33 NC_002950:PG1779|5end_hypothetical_protein_1867924..1868154_POSITIVE 360 210 161 62 5 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 359 47 8 63 23 NC_002950:PG1728|5end_cytidine/deoxycytidylate_deaminase_family_protein_1817644..1817874_POSITIVE 359 70 24 82 32 NC_002950:PG1100|5end_hypothetical_protein_1169012..1169242_NEGATIVE 357 78 39 201 152 NC_002950:PG1381|5end_ABC_transporter,_permease_protein_1460622..1460852_POSITIVE 355 90 44 66 2 NC_002950:PG2061|5end_dihydrofolate_reductase_2158422..2158652_POSITIVE 354 312 277 134 96 NC_002950:PG0877|5end_hypothetical_protein_941545..941775_NEGATIVE 353 57 14 61 11 NC_002950:PG0223|5end_exonuclease_257610..257840_NEGATIVE 352 50 6 187 138 NC_002950:PG2116|5end_hypothetical_protein_2224635..2224865_POSITIVE 348 312 275 212 171 NC_002950:PG1594|5end_ComEC/Rec2-related_protein_1673587..1673817_NEGATIVE 348 199 153 207 159 NC_002950:PG0804|5end_flavodoxin_861765..861995_NEGATIVE 347 99 51 61 7 NC_002950:PG2182|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_A_2291155..2291385_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 474 100 51 58 10 NC_002950:PG0619|3end_alkyl_hydroperoxide_reductase,_F_subunit_672731..672881_POSITIVE 446 90 45 61 10 NC_002950:PG1754|3end_hypothetical_protein_1842284..1842434_POSITIVE 443 90 51 75 31 NC_002950:PG2117|3end_30S_ribosomal_protein_S16_2225235..2225385_NEGATIVE 442 96 51 76 28 NC_002950:PG0034|3end_thioredoxin_42235..42385_NEGATIVE 423 303 268 47 5 NC_002950:PG1876|3end_hypothetical_protein_1970633..1970783_NEGATIVE 420 317 276 57 8 NC_002950:PG2194|3end_ISPg4,_transposase_2300962..2301112_NEGATIVE 420 317 276 57 8 NC_002950:PG1673|3end_ISPg4,_transposase_1759625..1759775_POSITIVE 420 317 276 57 8 NC_002950:PG1658|3end_ISPg4,_transposase_1741747..1741897_NEGATIVE 420 317 276 57 8 NC_002950:PG1261|3end_ISPg4,_transposase_1339608..1339758_POSITIVE 420 317 276 57 8 NC_002950:PG0970|3end_ISPg4,_transposase_1030843..1030993_POSITIVE 420 317 276 57 8 NC_002950:PG0487|3end_ISPg4,_transposase_526276..526426_NEGATIVE 420 317 276 57 8 NC_002950:PG0225|3end_ISPg4,_transposase_258485..258635_NEGATIVE 420 317 276 57 8 NC_002950:PG0177|3end_ISPg4,_transposase_200324..200474_POSITIVE 420 317 276 57 8 NC_002950:PG0050|3end_ISPg4,_transposase_62153..62303_POSITIVE 420 317 276 57 8 NC_002950:PG0019|3end_ISPg4_transposase_23277..23427_POSITIVE 407 100 51 82 29 NC_002950:PG0726|3end_lipoprotein,_putative_778003..778153_NEGATIVE 401 90 48 77 32 NC_002950:PG1729|3end_thiol_peroxidase_1818342..1818492_NEGATIVE 398 84 50 41 7 NC_002950:PG1950|3end_hypothetical_protein_2040840..2040990_POSITIVE 370 87 53 35 1 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 362 94 51 70 25 NC_002950:PG0535|3end_hypothetical_protein_585956..586106_NEGATIVE