Origin IGS: aaccttgcctcaaaagtgagcaaaaaagtggcagacaatatagcacaatttgcatcgaaagagactagatgcaataaaattgctcttccataaatatacttttttagaaaaaaaacaaaatttgatttagttaagttaaaaaagcgtaaaaaatacgactttcctacaaagaaaaaagaaataaatcgcgatatctctaaatccacacatatttaagtgtttttgtaattaaagttaaaagttgtaaatttactgtaaaatcaatagagaaagtagaaatagctcatttacaataacccttaacatactgttaattaaaaagttttcgcaatcacaatacgtacatatacatagtgaatttattattctaaaaaaacttgcattttaatttttcaggactataataccggtcgtttatttaattccacaagcttattaaataaatgacactaagttcaaactcaaggattc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaatccttgagtttgaacttagtgtcatttatttaataagcttgtggaattaaataaacgaccggtattatagtcctgaaaaattaaaatgcaagtttttttagaataataaattcactatgtatatgtacgtattgtgattgcgaaaactttttaattaacagtatgttaagggttattgtaaatgagctatttctactttctctattgattttacagtaaatttacaacttttaactttaattacaaaaacacttaaatatgtgtggatttagagatatcgcgatttatttcttttttctttgtaggaaagtcgtattttttacgcttttttaacttaactaaatcaaattttgttttttttctaaaaaagtatatttatggaagagcaattttattgcatctagtctctttcgatgcaaattgtgctatattgtctgccacttttttgctcacttttgaggcaaggtt Mask Tandem Repeat Region ================================================ aaccttgcctcaaaagtgagcaaaaaagtggcagacaatatagcacaatttgcatcgaaagagactagatgcaataaaattgctcttccataaatatacttttttagaaaaaaaacaaaatttgatttagttaagttaaaaaagcgtaaaaaatacgactttcctacaaagaaaaaagaaataaatcgcgatatctctaaatccacacatatttaagtgtttttgtaattaaagttaaaagttgtaaatttactgtaaaatcaatagagaaagtagaaatagctcatttacaataacccttaacatactgttaattaaaaagttttcgcaatcacaatacgtacatatacatagtgaatttattattctaaaaaaacttgcattttaatttttcaggactataataccggtcgtttatttaattccacaagcttattaaataaatgacactaagttcaaactcaaggattc Find is-nt database================================================ Query_seq: AA00866:AA00867|AA00866:AA00867:conserved hypothetical protein:fimbrial protein Flp precursor:->->:600311..600781 471 aaccttgcctcaaaagtgagcaaaaaagtggcagacaatatagcacaatttgcatcgaaagagactagatgcaataaaattgctcttccataaatatacttttttagaaaaaaaacaaaatttgatttagttaagttaaaaaagcgtaaaaaatacgactttcctacaaagaaaaaagaaataaatcgcgatatctctaaatccacacatatttaagtgtttttgtaattaaagttaaaagttgtaaatttactgtaaaatcaatagagaaagtagaaatagctcatttacaataacccttaacatactgttaattaaaaagttttcgcaatcacaatacgtacatatacatagtgaatttattattctaaaaaaacttgcattttaatttttcaggactataataccggtcgtttatttaattccacaagcttattaaataaatgacactaagttcaaactcaaggattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00866:AA00867|AA00866:AA00867:conserved hypothetical protein:fimbrial protein Flp precursor:->->:600311..600781 471 aaccttgcctcaaaagtgagcaaaaaagtggcagacaatatagcacaatttgcatcgaaagagactagatgcaataaaattgctcttccataaatatacttttttagaaaaaaaacaaaatttgatttagttaagttaaaaaagcgtaaaaaatacgactttcctacaaagaaaaaagaaataaatcgcgatatctctaaatccacacatatttaagtgtttttgtaattaaagttaaaagttgtaaatttactgtaaaatcaatagagaaagtagaaatagctcatttacaataacccttaacatactgttaattaaaaagttttcgcaatcacaatacgtacatatacatagtgaatttattattctaaaaaaacttgcattttaatttttcaggactataataccggtcgtttatttaattccacaagcttattaaataaatgacactaagttcaaactcaaggattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00866:AA00867|AA00866:AA00867:conserved hypothetical protein:fimbrial protein Flp precursor:->->:600311..600781 471 aaccttgcctcaaaagtgagcaaaaaagtggcagacaatatagcacaatttgcatcgaaagagactagatgcaataaaattgctcttccataaatatacttttttagaaaaaaaacaaaatttgatttagttaagttaaaaaagcgtaaaaaatacgactttcctacaaagaaaaaagaaataaatcgcgatatctctaaatccacacatatttaagtgtttttgtaattaaagttaaaagttgtaaatttactgtaaaatcaatagagaaagtagaaatagctcatttacaataacccttaacatactgttaattaaaaagttttcgcaatcacaatacgtacatatacatagtgaatttattattctaaaaaaacttgcattttaatttttcaggactataataccggtcgtttatttaattccacaagcttattaaataaatgacactaagttcaaactcaaggattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaccttgcctcaaaagtgagcaaaaaagtggcagacaatatagcacaatttgcatcgaaagagactagatgcaataaaattgctcttccataaatatacttttttagaaaaaaaacaaaatttgatttagttaagttaaaaaagcgtaaaaaatacgactttcctacaaagaaaaaagaaataaatcgcgatatctctaaatccacacatatttaagtgtttttgtaattaaagttaaaagttgtaaatttactgtaaaatcaatagagaaagtagaaatagctcatttacaataacccttaacatactgttaattaaaaagttttcgcaatcacaatacgtacatatacatagtgaatttattattctaaaaaaacttgcattttaatttttcaggactataataccggtcgtttatttaattccacaagcttattaaataaatgacactaagttcaaactcaaggattc Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 94 End: 213 ............................................................................................. M Y F F R K K T K F D L V K L K K R K K Y D F P T K K K E I N R D I S K S T H I .................................................................................................................................................................................................................................................................. Protein_Len: 31 Strand: + Start: 201 End: 293 ........................................................................................................................................................................................................ M H T Y L S V F V I K V K S C K F T V K S I E K V E I A H L Q .................................................................................................................................................................................. Protein_Len: 46 Strand: + Start: 248 End: 385 ....................................................................................................................................................................................................................................................... M Y C K I N R E S R N S S F T I T L N I L L I K K F S Q S Q Y V H I H S E F I I L K K L A F ...................................................................................... Protein_Len: 38 Strand: - Start: 253 End: 366 ............................................................................................................................................................................................................................................................ Q L I L L S L L F L E N V I V R L M S N I L F N E C D C Y T C I C L S N I M ......................................................................................................... Protein_Len: 38 Strand: - Start: 13 End: 126 ............ F H A F F H C V I Y C L K C R F L S S A I F N S K W L Y V K K S F F C F K M ......................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: - Start: 3 End: 212 .. S L I A C N A D F S V L H L L I A R G Y I Y K K L F F V F N S K T L N F F R L F Y S K G V F F F S I F R S I E L D V C M ................................................................................................................................................................................................................................................................... aaccttgcctcaaaagtgagcaaaaaagtggcagacaatatagcacaatttgcatcgaaagagactagatgcaataaaattgctcttccataaatatacttttttagaaaaaaaacaaaatttgatttagttaagttaaaaaagcgtaaaaaatacgactttcctacaaagaaaaaagaaataaatcgcgatatctctaaatccacacatatttaagtgtttttgtaattaaagttaaaagttgtaaatttactgtaaaatcaatagagaaagtagaaatagctcatttacaataacccttaacatactgttaattaaaaagttttcgcaatcacaatacgtacatatacatagtgaatttattattctaaaaaaacttgcattttaatttttcaggactataataccggtcgtttatttaattccacaagcttattaaataaatgacactaagttcaaactcaaggattc 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================================================ aaccttgcctcaaaagtgagcaaaaaagtggcagacaatatagcacaatttgcatcgaaagagactagatgcaataaaattgctcttccataaatatacttttttagaaaaaaaacaaaatttgatttagttaagttaaaaaagcgtaaaaaatacgactttcctacaaagaaaaaagaaataaatcgcgatatctctaaatccacacatatttaagtgtttttgtaattaaagttaaaagttgtaaatttactgtaaaatcaatagagaaagtagaaatagctcatttacaataacccttaacatactgttaattaaaaagttttcgcaatcacaatacgtacatatacatagtgaatttattattctaaaaaaacttgcattttaatttttcaggactataataccggtcgtttatttaattccacaagcttattaaataaatgacactaagttcaaactcaaggattc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 44 HP_score: -3.6 Tail_Score: -2.71405 Start: 50 End: 74 Full_Region: ggaagagcaatttta ttgcatctag tctct ttcgatgcaa attgtgctatattgt .................................................ttgcatctagtctctttcgatgcaa............................................................................................................................................................................................................................................................................................................................................................................................................. Find igs database================================================ Query_seq: AA00866:AA00867|AA00866:AA00867:conserved hypothetical protein:fimbrial protein Flp precursor:->->:600311..600781 471 aaccttgcctcaaaagtgagcaaaaaagtggcagacaatatagcacaatttgcatcgaaagagactagatgcaataaaattgctcttccataaatatacttttttagaaaaaaaacaaaatttgatttagttaagttaaaaaagcgtaaaaaatacgactttcctacaaagaaaaaagaaataaatcgcgatatctctaaatccacacatatttaagtgtttttgtaattaaagttaaaagttgtaaatttactgtaaaatcaatagagaaagtagaaatagctcatttacaataacccttaacatactgttaattaaaaagttttcgcaatcacaatacgtacatatacatagtgaatttattattctaaaaaaacttgcattttaatttttcaggactataataccggtcgtttatttaattccacaagcttattaaataaatgacactaagttcaaactcaaggattc Intra-Species Hit: Count: 1 Min: 1 Max: 471 Len: 471 Subject: aact_AA00866_AA00867|conserved hypothetical protein:fimbrial protein Flp precursor|POSITIVE:POSITIVE|[600311,600781]|471 HSP 1 e-value: 1.0E-148 bit: 525.0 Len: 286 Query Start:186 Query End:471 Subject Strand: POSITIVE Subject Start: 186 Subject End: 471 .........................................................................................................................................................................................tcgcgatatctctaaatccacacatatttaagtgtttttgtaattaaagttaaaagttgtaaatttactgtaaaatcaatagagaaagtagaaatagctcatttacaataacccttaacatactgttaattaaaaagttttcgcaatcacaatacgtacatatacatagtgaatttattattctnnnnnnncttgcattttaatttttcaggactataataccggtcgtttatttaattccacaagcttattaaataaatgacactaagttcaaactcaaggattc .........................................................................................................................................................................................tcgcgatatctctaaatccacacatatttaagtgtttttgtaattaaagttaaaagttgtaaatttactgtaaaatcaatagagaaagtagaaatagctcatttacaataacccttaacatactgttaattaaaaagttttcgcaatcacaatacgtacatatacatagtgaatttattattctaaaaaaacttgcattttaatttttcaggactataataccggtcgtttatttaattccacaagcttattaaataaatgacactaagttcaaactcaaggattc HSP 2 e-value: 8.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 aaccttgcctcaaaagtgagcaaaaaagtggcagacaatatagcacaatttgcatcgaaagagactagatgcaataaaattgctcttccataaatatacttttttag............................................................................................................................................................................................................................................................................................................................................................................ aaccttgcctcaaaagtgagcaaaaaagtggcagacaatatagcacaatttgcatcgaaagagactagatgcaataaaattgctcttccataaatatacttttttag............................................................................................................................................................................................................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACCUUGCCUCAAAAGUGAGCAAAAAAGUGGCAGACAAUAUAGCACAAUUUGCAUCGAAAGAGACUAGAUGCAAUAAAAUUGCUCUUCCAUAAAUAUACUUUUUUAGAAAAAAAACAAAAUUUGAUUUAGUUAAGUUAAAAAAGCGUAAAAAAUACGACUUUCCUACAAAGAAAAAAGAAAUAAAUCGCGAUAUCUCUAAAUCCACACAUAUUUAAGUGUUUUUGUAAUUAAAGUUAAAAGUUGUAAAUUUACUGUAAAAUCAAUAGAGAAAGUAGAAAUAGCUCAUUUACAAUAACCCUUAACAUACUGUUAAUUAAAAAGUUUUCGCAAUCACAAUACGUACAUAUACAUAGUGAAUUUAUUAUUCUAAAAAAACUUGCAUUUUAAUUUUUCAGGACUAUAAUACCGGUCGUUUAUUUAAUUCCACAAGCUUAUUAAAUAAAUGACACUAAGUUCAAACUCAAGGAUUC ..(((((......((((((((......((((.(((.......(((....(((((((...........)))))))......)))))).)))).....(((((((((...............((((((((....))))))))...(((((((...(((((((((..(((((((.....(((.(((........))).)))......((((........)))))))))))..........)))))))))..))))).))..........)))))))))......)))))))).........((((.....(((..((((((((((((((..............(((....))).....((((.....))))....))))))....))))))))...))).............((((((((((((((...........))))))))))))))..))))........))))).... (-78.81) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUCCUUGAGUUUGAACUUAGUGUCAUUUAUUUAAUAAGCUUGUGGAAUUAAAUAAACGACCGGUAUUAUAGUCCUGAAAAAUUAAAAUGCAAGUUUUUUUAGAAUAAUAAAUUCACUAUGUAUAUGUACGUAUUGUGAUUGCGAAAACUUUUUAAUUAACAGUAUGUUAAGGGUUAUUGUAAAUGAGCUAUUUCUACUUUCUCUAUUGAUUUUACAGUAAAUUUACAACUUUUAACUUUAAUUACAAAAACACUUAAAUAUGUGUGGAUUUAGAGAUAUCGCGAUUUAUUUCUUUUUUCUUUGUAGGAAAGUCGUAUUUUUUACGCUUUUUUAACUUAACUAAAUCAAAUUUUGUUUUUUUUCUAAAAAAGUAUAUUUAUGGAAGAGCAAUUUUAUUGCAUCUAGUCUCUUUCGAUGCAAAUUGUGCUAUAUUGUCUGCCACUUUUUUGCUCACUUUUGAGGCAAGGUU ....(((((..((..((..........(((((..((((.((((.(((((..(((((((....(((((((......((((((((.............)))))))).....(((((((((.((((((....((((((((((((((.((.....)).))))).)))))))))((((.(((.((((((..(((.((.............(((((......))))).............)).)))...)))))).))).)))).)))))))))))))))..))))))).((((((...............((((((((.((((.....)))))))))))).......))))))....)))))))...)))))...)))).)))).))))).((((((.....(((((((.((.....)).)))))))..((.((..........)))).....))))))...))..)).))))).. (-85.64) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 370 58 20 214 174 aact:AA02436|5end_periplasmic_protein_1680497..1680727_POSITIVE 278 44 1 195 153 aact:AA00895|5end_hypothetical_protein_621285..621515_POSITIVE 261 59 17 132 93 aact:AA01641|5end_hypothetical_protein_1110819..1111049_POSITIVE 238 431 393 209 160 aact:AA01386|5end_30S_ribosomal_protein_S1_935974..936204_POSITIVE 238 437 393 171 120 aact:AA01153|5end_sec-independent_protein_translocase_790166..790396_POSITIVE 234 57 12 214 151 aact:AA02552|5end_iron_(chelated)_ABC_transporter,_permease_protein_1778495..1778725_POSITIVE 232 46 3 112 78 aact:AA00536|5end_5'-nucleotidase_precursor_366151..366381_POSITIVE 230 42 3 192 145 aact:AA02999|5end_conserved_hypothetical_protein_2094275..2094505_POSITIVE 230 74 36 65 34 aact:AA02387|5end_integral_membrane_transport_protein_1634813..1635043_POSITIVE 229 70 26 73 30 aact:AA02024|5end_acyl_carrier_protein_phosphodiesterase_1378144..1378374_POSITIVE 229 420 373 153 107 aact:AA01603|5end_oligopeptidase_A_1082898..1083128_POSITIVE 226 39 5 91 48 aact:AA01883|5end_recycling_protein;_permease_1269821..1270051_POSITIVE 226 433 395 118 78 aact:AA00280|5end_adenosylmethionine-8-amino-7-oxononanoate;_7,8-diamino-perlargonic_acid_ATase_196430..196660_POSITIVE 224 89 43 218 179 aact:AA02017|5end_conserved_hypothetical_protein_1371656..1371886_POSITIVE 222 73 31 75 33 aact:AA01423|5end_cell_division_protein_X,_ABC_system_permease_956668..956898_POSITIVE 221 64 25 72 42 aact:AA00628|5end_biotin_operon_repressor;_biotin_acetyl_coenzyme_A_carboxylase_synthetase_430855..431085_POSITIVE 220 32 3 48 13 aact:AA01872|5end_conserved_hypothetical_protein_1258804..1259034_POSITIVE 220 44 2 49 2 aact:AA01588|5end_N-acetylmuramoyl-L-alanine_amidase_II_1068816..1069046_POSITIVE 219 90 41 105 55 aact:AA01236|5end_50S_ribosomal_protein_L15_842459..842689_POSITIVE 217 44 1 58 11 aact:AA01807|5end_electron_transport_complex_protein_1216696..1216926_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 261 59 17 72 33 aact:AA01640|3end_restriction_enzyme_type_I_helicase_subunit_1110839..1110989_POSITIVE 238 437 393 130 79 aact:AA01152|3end_sec-independent_protein_translocase_protein_790205..790355_POSITIVE 236 61 33 151 112 aact:AA00660|3end_hypothetical_protein_453335..453485_POSITIVE 233 36 1 143 117 aact:AA00396|3end_conserved_hypothetical_protein_265952..266102_POSITIVE 230 56 15 123 78 aact:AA00976|3end_conserved_hypothetical_protein_682278..682428_POSITIVE 226 433 395 122 82 aact:AA00279|3end_8-amino-7-oxonoanoate_synthase_196514..196664_POSITIVE 222 73 31 63 21 aact:AA01422|3end_cell_division_protein_E,_ABC_system_ATP-binding_protein_956736..956886_POSITIVE 220 70 27 82 35 aact:AA02281|3end_phosphoglycerate_transport_system_activator_protein_1553474..1553624_POSITIVE 219 57 16 41 4 aact:AA02438|3end_membrane_protein;_possible_ABC_transporter_permease_protein_1683992..1684142_POSITIVE 219 90 41 101 51 aact:AA01235.1|3end_50S_ribosomal_protein_L30_842535..842685_POSITIVE 217 416 376 46 9 aact:AA02254|3end_2-oxoglutarate/malate_translocator_1536380..1536530_POSITIVE 217 44 1 55 8 aact:AA01805|3end_electron_transport_complex_protein_1216773..1216923_POSITIVE 217 89 43 114 64 aact:AA01185|3end_conserved_hypothetical_protein_(possible_membrane_protein)_813401..813551_POSITIVE 217 90 41 96 53 aact:AA00616|3end_phosphatidate_cytidylyltransferase_422971..423121_POSITIVE 214 88 44 135 98 aact:AA00550|3end_ferredoxin-type_protein_377201..377351_POSITIVE 214 38 1 56 14 aact:AA00419|3end_conserved_hypothetical_protein_(possible_phosphatidylethanolamine-binding_protein)_284911..285061_POSITIVE 212 205 185 146 124 aact:AA00799|3end_iron(III)_dicitrate_transport_ATP-binding_protein_548502..548652_POSITIVE 210 66 28 137 93 aact:AA01460|3end_hypothetical_protein_981596..981746_POSITIVE 210 58 16 52 1 aact:AA00603|3end_undecaprenyl_pyrophosphate_synthetase_(UPPS)_410992..411142_POSITIVE 210 63 28 81 44 aact:AA00214|3end_glutamyl-tRNA_synthetase_149249..149399_POSITIVE