Origin IGS: gatacctgttatctaccgatatccggctcttcggcagagaatgtgagagattcaggatatatcgcaacggccttgtcaagatcgagatctctttaagtcatggatataacgtgagttcgatgtaagcttttcggcctttccatcatacaatcgattcgattctctttggactcaataaaaaatataaaatactcaaagagttggcatataactttgcctcagtggcgagtgggtttttcggccaattcctaaagaagaaaatagctgtttgtatctttttgcgaaaaaagtttggtggattaagattaaaaacatatctttcgggcgatagtggtagagcactatcttgcgaaacattaatctttaatactttcaaaaggtatgagaaaattgaattctttattttcgctcgccgtcctattatccctattgtgttggggacagacggctgccgcacagggagggccgaagactgctccttctgtgacgcaccaagcggtgcagaaaggtattcgaacatccaaggccaaggatctccgagatccgattcctgccggt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 accggcaggaatcggatctcggagatccttggccttggatgttcgaatacctttctgcaccgcttggtgcgtcacagaaggagcagtcttcggccctccctgtgcggcagccgtctgtccccaacacaatagggataataggacggcgagcgaaaataaagaattcaattttctcataccttttgaaagtattaaagattaatgtttcgcaagatagtgctctaccactatcgcccgaaagatatgtttttaatcttaatccaccaaacttttttcgcaaaaagatacaaacagctattttcttctttaggaattggccgaaaaacccactcgccactgaggcaaagttatatgccaactctttgagtattttatattttttattgagtccaaagagaatcgaatcgattgtatgatggaaaggccgaaaagcttacatcgaactcacgttatatccatgacttaaagagatctcgatcttgacaaggccgttgcgatatatcctgaatctctcacattctctgccgaagagccggatatcggtagataacaggtatc Mask Tandem Repeat Region ================================================ gatacctgttatctaccgatatccggctcttcggcagagaatgtgagagattcaggatatatcgcaacggccttgtcaagatcgagatctctttaagtcatggatataacgtgagttcgatgtaagcttttcggcctttccatcatacaatcgattcgattctctttggactcaataaaaaatataaaatactcaaagagttggcatataactttgcctcagtggcgagtgggtttttcggccaattcctaaagaagaaaatagctgtttgtatctttttgcgaaaaaagtttggtggattaagattaaaaacatatctttcgggcgatagtggtagagcactatcttgcgaaacattaatctttaatactttcaaaaggtatgagaaaattgaattctttattttcgctcgccgtcctattatccctattgtgttggggacagacggctgccgcacagggagggccgaagactgctccttctgtgacgcaccaagcggtgcagaaaggtattcgaacatccaaggccaaggatctccgagatccgattcctgccggt Find is-nt database================================================ Query_seq: PG1836:PG1837|PG1836:PG1837:nucleoside permease NupG:hemagglutinin protein HagA:->->:1929919..1930476 558 gatacctgttatctaccgatatccggctcttcggcagagaatgtgagagattcaggatatatcgcaacggccttgtcaagatcgagatctctttaagtcatggatataacgtgagttcgatgtaagcttttcggcctttccatcatacaatcgattcgattctctttggactcaataaaaaatataaaatactcaaagagttggcatataactttgcctcagtggcgagtgggtttttcggccaattcctaaagaagaaaatagctgtttgtatctttttgcgaaaaaagtttggtggattaagattaaaaacatatctttcgggcgatagtggtagagcactatcttgcgaaacattaatctttaatactttcaaaaggtatgagaaaattgaattctttattttcgctcgccgtcctattatccctattgtgttggggacagacggctgccgcacagggagggccgaagactgctccttctgtgacgcaccaagcggtgcagaaaggtattcgaacatccaaggccaaggatctccgagatccgattcctgccggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1836:PG1837|PG1836:PG1837:nucleoside permease NupG:hemagglutinin protein HagA:->->:1929919..1930476 558 gatacctgttatctaccgatatccggctcttcggcagagaatgtgagagattcaggatatatcgcaacggccttgtcaagatcgagatctctttaagtcatggatataacgtgagttcgatgtaagcttttcggcctttccatcatacaatcgattcgattctctttggactcaataaaaaatataaaatactcaaagagttggcatataactttgcctcagtggcgagtgggtttttcggccaattcctaaagaagaaaatagctgtttgtatctttttgcgaaaaaagtttggtggattaagattaaaaacatatctttcgggcgatagtggtagagcactatcttgcgaaacattaatctttaatactttcaaaaggtatgagaaaattgaattctttattttcgctcgccgtcctattatccctattgtgttggggacagacggctgccgcacagggagggccgaagactgctccttctgtgacgcaccaagcggtgcagaaaggtattcgaacatccaaggccaaggatctccgagatccgattcctgccggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1836:PG1837|PG1836:PG1837:nucleoside permease NupG:hemagglutinin protein HagA:->->:1929919..1930476 558 gatacctgttatctaccgatatccggctcttcggcagagaatgtgagagattcaggatatatcgcaacggccttgtcaagatcgagatctctttaagtcatggatataacgtgagttcgatgtaagcttttcggcctttccatcatacaatcgattcgattctctttggactcaataaaaaatataaaatactcaaagagttggcatataactttgcctcagtggcgagtgggtttttcggccaattcctaaagaagaaaatagctgtttgtatctttttgcgaaaaaagtttggtggattaagattaaaaacatatctttcgggcgatagtggtagagcactatcttgcgaaacattaatctttaatactttcaaaaggtatgagaaaattgaattctttattttcgctcgccgtcctattatccctattgtgttggggacagacggctgccgcacagggagggccgaagactgctccttctgtgacgcaccaagcggtgcagaaaggtattcgaacatccaaggccaaggatctccgagatccgattcctgccggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 382 Max: 558 Len: 177 Subject: UniRef90_Q51845 Cluster: Hemagglutinin A precursor; n=3; Porphyromonas gingivalis|Rep: Hemagglutinin A precursor - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 5.0E-17 bit: 89.7 Len: 177 Query Start:382 Query End:558 Subject Strand: null Subject Start: 1 Subject End: 59 ............................................................................................................................................................................................................................................................................................................................................................................................. M R K X X X X X X X X X X X X X X C W G Q T A A A Q G G P K T A P S V T H Q A V Q K G I R T S K A K D L R D P I P A G ............................................................................................................................................................................................................................................................................................................................................................................................. M R K L N S L F S L A V L L S L L C W G Q T A A A Q G G P K T A P S V T H Q A V Q K G I R T S K V K D L R D P I P A G gatacctgttatctaccgatatccggctcttcggcagagaatgtgagagattcaggatatatcgcaacggccttgtcaagatcgagatctctttaagtcatggatataacgtgagttcgatgtaagcttttcggcctttccatcatacaatcgattcgattctctttggactcaataaaaaatataaaatactcaaagagttggcatataactttgcctcagtggcgagtgggtttttcggccaattcctaaagaagaaaatagctgtttgtatctttttgcgaaaaaagtttggtggattaagattaaaaacatatctttcgggcgatagtggtagagcactatcttgcgaaacattaatctttaatactttcaaaaggtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 6 End: 122 ..... M L S T D I R L F G R E C E R F R I Y R N G L V K I E I S L S H G Y N V S S M .................................................................................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 36 Strand: + Start: 142 End: 249 ............................................................................................................................................. M I Q S I R F S L D S I K N I K Y S K S W H I T L P Q W R V G F S A N S ..................................................................................................................................................................................................................................................................................................................... Protein_Len: 30 Strand: + Start: 395 End: 484 .......................................................................................................................................................................................................................................................................................................................................................................................................... M L Y F R S P S Y Y P Y C V G D R R L P H R E G R R L L L L .......................................................................... Protein_Len: 60 Strand: + Start: 150 End: 557 ..................................................................................................................................................... M D S I L F G L N K K Y K I L K E L A Y N F A S V A S G F F G Q F L K K K I A V C I F L R K K F G G L R L K T Y L S G D . Protein_Len: 60 Strand: + Start: 367 End: 558 .............................................................................................................................................................................................................................................................................................................................................................................. M L S K G M R K L N S L F S L A V L L S L L C W G Q T A A A Q G G P K T A P S V T H Q A V Q K G I R T S K A K D L R D P Protein_Len: 38 Strand: - Start: 430 End: 543 ............................................................................................................................................................................................................................................................................................................................................................................................................................................. Q T P S L R S G C L S P R L S S R R H R V L R H L F T N S C G L G L I E S M ............... Protein_Len: 60 Strand: - Start: 360 End: 548 ....................................................................................................................................................................................................................................................................................................................................................................... S E F P I L F N F E K N E S A T R N D R N H Q P C V A A A C P P G F V A G E T V C W A T C F P I R V D L A L S R R S G M .......... Protein_Len: 54 Strand: - Start: 196 End: 357 ................................................................................................................................................................................................... L T P M Y S Q R L P S H T K R G I G L S S F L Q K Y R K A F F T Q H I L I L F M D K P R Y H Y L V I K R F M ......................................................................................................................................................................................................... Protein_Len: 60 Strand: - Start: 146 End: 520 ................................................................................................................................................. S D Q S V N I K L V K L L Y S F I S N K I K A R R G I I G I T N P V S P Q R V P L A S S Q E K Q S A G L P A S L Y E F M ...................................... Protein_Len: 38 Strand: - Start: 96 End: 209 ............................................................................................... T M S I V H T R H L S K P R E M M C D I R N E K S E I F F I F Y E F L Q C M ............................................................................................................................................................................................................................................................................................................................................................. gatacctgttatctaccgatatccggctcttcggcagagaatgtgagagattcaggatatatcgcaacggccttgtcaagatcgagatctctttaagtcatggatataacgtgagttcgatgtaagcttttcggcctttccatcatacaatcgattcgattctctttggactcaataaaaaatataaaatactcaaagagttggcatataactttgcctcagtggcgagtgggtttttcggccaattcctaaagaagaaaatagctgtttgtatctttttgcgaaaaaagtttggtggattaagattaaaaacatatctttcgggcgatagtggtagagcactatcttgcgaaacattaatctttaatactttcaaaaggtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn 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================================================ gatacctgttatctaccgatatccggctcttcggcagagaatgtgagagattcaggatatatcgcaacggccttgtcaagatcgagatctctttaagtcatggatataacgtgagttcgatgtaagcttttcggcctttccatcatacaatcgattcgattctctttggactcaataaaaaatataaaatactcaaagagttggcatataactttgcctcagtggcgagtgggtttttcggccaattcctaaagaagaaaatagctgtttgtatctttttgcgaaaaaagtttggtggattaagattaaaaacatatctttcgggcgatagtggtagagcactatcttgcgaaacattaatctttaatactttcaaaaggtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 48 HP_score: -2.9 Tail_Score: -3.48671 Start: 317 End: 356 Full_Region: AAGATTAAAAACATA TCTTTCGGGCGATAGTG GTAGAG CACTATCTTGCGAAACA TTAATCTTTAATACT ............................................................................................................................................................................................................................................................................................................................TCTTTCGGGCGATAGTGGTAGAGCACTATCTTGCGAAACA.......................................................................................................................................................................................................... Find igs database================================================ Query_seq: PG1836:PG1837|PG1836:PG1837:nucleoside permease NupG:hemagglutinin protein HagA:->->:1929919..1930476 558 gatacctgttatctaccgatatccggctcttcggcagagaatgtgagagattcaggatatatcgcaacggccttgtcaagatcgagatctctttaagtcatggatataacgtgagttcgatgtaagcttttcggcctttccatcatacaatcgattcgattctctttggactcaataaaaaatataaaatactcaaagagttggcatataactttgcctcagtggcgagtgggtttttcggccaattcctaaagaagaaaatagctgtttgtatctttttgcgaaaaaagtttggtggattaagattaaaaacatatctttcgggcgatagtggtagagcactatcttgcgaaacattaatctttaatactttcaaaaggtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Intra-Species Hit: Count: 1 Min: 1 Max: 381 Len: 381 Subject: NC_002950_PG1836_PG1837|nucleoside permease NupG:hemagglutinin protein HagA|POSITIVE:POSITIVE|[1929919,1930476]|558 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 gatacctgttatctaccgatatccggctcttcggcagagaatgtgagagattcaggatatatcgcaacggccttgtcaagatcgagatctctttaagtcatggatataacgtgagttcgatgtaagcttttcggcctttccatcatacaatcgattcgattctctttggactcaataaaaaatataaaatactcaaagagttggcatataactttgcctcagtggcgagtgggtttttcggccaattcctaaagaagaaaatagctgtttgtatctttttgcgaaaaaagtttggtggattaagattaaaaacatatctttcgggcgatagtggtagagcactatcttgcgaaacattaatctttaatactttcaaaaggt................................................................................................................................................................................. gatacctgttatctaccgatatccggctcttcggcagagaatgtgagagattcaggatatatcgcaacggccttgtcaagatcgagatctctttaagtcatggatataacgtgagttcgatgtaagcttttcggcctttccatcatacaatcgattcgattctctttggactcaataaaaaatataaaatactcaaagagttggcatataactttgcctcagtggcgagtgggtttttcggccaattcctaaagaagaaaatagctgtttgtatctttttgcgaaaaaagtttggtggattaagattaaaaacatatctttcgggcgatagtggtagagcactatcttgcgaaacattaatctttaatactttcaaaaggt................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUACCUGUUAUCUACCGAUAUCCGGCUCUUCGGCAGAGAAUGUGAGAGAUUCAGGAUAUAUCGCAACGGCCUUGUCAAGAUCGAGAUCUCUUUAAGUCAUGGAUAUAACGUGAGUUCGAUGUAAGCUUUUCGGCCUUUCCAUCAUACAAUCGAUUCGAUUCUCUUUGGACUCAAUAAAAAAUAUAAAAUACUCAAAGAGUUGGCAUAUAACUUUGCCUCAGUGGCGAGUGGGUUUUUCGGCCAAUUCCUAAAGAAGAAAAUAGCUGUUUGUAUCUUUUUGCGAAAAAAGUUUGGUGGAUUAAGAUUAAAAACAUAUCUUUCGGGCGAUAGUGGUAGAGCACUAUCUUGCGAAACAUUAAUCUUUAAUACUUUCAAAAGGU ...((((...(((((((.(((((((..((((..(((.....)))..))))..).)))))).((((((.((((..((..(.((((((.((.(.(((.(((...))).))).).)).)))))).)..)).....))))........((((((.((......((((((((((.....(((.....)))............((((((((....(((((((((.....)))))...)))).....)))))))))))))).))))......)).))))))....)))))).........))))))).(((((((((.....((.(((((.(.(((((((......))))))).).))))).)).....)))))).))).....)))) (-92.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUUUUGAAAGUAUUAAAGAUUAAUGUUUCGCAAGAUAGUGCUCUACCACUAUCGCCCGAAAGAUAUGUUUUUAAUCUUAAUCCACCAAACUUUUUUCGCAAAAAGAUACAAACAGCUAUUUUCUUCUUUAGGAAUUGGCCGAAAAACCCACUCGCCACUGAGGCAAAGUUAUAUGCCAACUCUUUGAGUAUUUUAUAUUUUUUAUUGAGUCCAAAGAGAAUCGAAUCGAUUGUAUGAUGGAAAGGCCGAAAAGCUUACAUCGAACUCACGUUAUAUCCAUGACUUAAAGAGAUCUCGAUCUUGACAAGGCCGUUGCGAUAUAUCCUGAAUCUCUCACAUUCUCUGCCGAAGAGCCGGAUAUCGGUAGAUAACAGGUAUC ((((.....(((.(((((((((..((.(((((...(((((((......)))))))...))))).))..)))))))))))).(((.(((.........((((((...........(.((((.(((((.....))))).)))).)............(((.....((((........))))..(((((((.(.((((.(((.....))).))))))))))))..(((((((((..((.(((((...((((......)))).))))).))....(((((....)))))...........))))).))))...)))..)))))).((((((.((.....)).....((((.....))))..)))))).))).)))...))))... (-88.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 250 217 183 152 NC_002950:PG0046|5end_phosphatidate_cytidylyltransferase_57200..57430_NEGATIVE 340 250 201 38 3 NC_002950:PG1017|5end_pyruvate_phosphate_dikinase_1076138..1076368_POSITIVE 340 104 61 94 48 NC_002950:PG0120|5end_UDP-N-acetylglucosamine_2-epimerase_143004..143234_POSITIVE 338 70 23 172 129 NC_002950:PG1815|5end_3-deoxy-manno-octulosonate_cytidylyltransferase_1911433..1911663_NEGATIVE 336 349 313 68 29 NC_002950:PG0021|5end_TIM-barrel_protein,_putative,_NifR3_family_25123..25353_NEGATIVE 334 70 22 67 8 NC_002950:PG1725|5end_competence/damage-inducible_protein_CinA_domain_protein_1814766..1814996_POSITIVE 331 55 17 54 13 NC_002950:PG0332|5end_transcription_termination_factor_Rho_365619..365849_POSITIVE 330 47 1 214 162 NC_002950:PG1840|5end_hypothetical_protein_1937102..1937332_POSITIVE 326 244 212 90 55 NC_002950:PG1874|5end_hypothetical_protein_1969660..1969890_NEGATIVE 325 57 11 64 8 NC_002950:PG1861|5end_hypothetical_protein_1960057..1960287_NEGATIVE 323 77 33 51 5 NC_002950:PG0414|5end_hypothetical_protein_453652..453882_NEGATIVE 322 70 24 229 194 NC_002950:PG2214|5end_hypothetical_protein_2326575..2326805_NEGATIVE 318 64 21 220 171 NC_002950:PG0196|5end_peptidase,_M16_family_232903..233133_POSITIVE 316 70 23 47 3 NC_002950:PG2226|5end_hypothetical_protein_2339789..2340019_POSITIVE 316 73 33 217 181 NC_002950:PG1875|5end_hemolysin_1970621..1970851_NEGATIVE 316 240 200 80 32 NC_002950:PG1098|5end_hypothetical_protein_1167009..1167239_NEGATIVE 316 65 24 184 120 NC_002950:PG0739|5end_ribonuclease_Z_786947..787177_POSITIVE 315 67 21 85 13 NC_002950:PG1059|5end_hypothetical_protein_1126495..1126725_NEGATIVE 314 248 202 142 94 NC_002950:PG1679|5end_hypothetical_protein_1763796..1764026_POSITIVE 314 48 1 60 17 NC_002950:PG1091|5end_DHH_subfamily_1_protein_1157017..1157247_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 376 70 21 45 1 NC_002950:PG2177|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_F_2285266..2285416_NEGATIVE 340 104 61 88 42 NC_002950:PG0119|3end_glycosyl_transferase,_WecB/TagA/CpsF_family_143078..143228_POSITIVE 337 248 217 151 123 NC_002950:PG0047|3end_cell_division_protein_FtsH,_putative_57229..57379_NEGATIVE 336 349 313 71 32 NC_002950:PG0022|3end_sulfate_permease_family_protein_25120..25270_NEGATIVE 334 70 22 67 8 NC_002950:PG1724|3end_O-sialoglycoprotein_endopeptidase_1814846..1814996_POSITIVE 329 70 23 141 94 NC_002950:PG1392|3end_rod_shape-determining_protein_RodA,_putative_1472959..1473109_NEGATIVE 326 244 212 103 68 NC_002950:PG1875|3end_hemolysin_1969647..1969797_NEGATIVE 324 50 6 70 25 NC_002950:PG1970|3end_hypothetical_protein_2059484..2059634_NEGATIVE 323 57 14 51 3 NC_002950:PG1862|3end_hypothetical_protein_1960070..1960220_NEGATIVE 322 70 24 112 61 NC_002950:PG0626|3end_hypothetical_protein_680346..680496_POSITIVE 315 58 13 133 91 NC_002950:PG0738|3end_cytidine/deoxycytidylate_deaminase_family_protein_786995..787145_POSITIVE 315 165 125 140 97 NC_002950:PG0196|3end_peptidase,_M16_family_235808..235958_POSITIVE 312 246 201 142 94 NC_002950:PG1151|3end_alcohol_dehydrogenase,_iron-containing_1234378..1234528_POSITIVE 311 159 112 148 104 NC_002950:PG0772|3end_hypothetical_protein_825204..825354_POSITIVE 310 70 22 131 86 NC_002950:PG2027|3end_hypothetical_protein_2126098..2126248_POSITIVE 308 242 204 82 37 NC_002950:PG2127|3end_hypothetical_protein_2233109..2233259_NEGATIVE 308 73 33 143 108 NC_002950:PG1825|3end_hypothetical_protein_1919510..1919660_NEGATIVE 308 108 63 81 33 NC_002950:PG1073|3end_D-lysine_5,6-aminomutase,_alpha_subunit_1142046..1142196_POSITIVE 307 70 21 84 36 NC_002950:PG0032|3end_beta-mannosidase,_putative_37627..37777_NEGATIVE 306 268 222 87 40 NC_002950:PG0506|3end_arginine-specific_cysteine_proteinase_547625..547775_POSITIVE