Origin IGS: tcccgatcggagatctgtattatcatagtaactctgccctaaggagaggctgcgccgagattgtttttttcgacacagccccttccctttttgtccggtgctgctcttgctgtcgggatgtataaatgtatagaagtatagaagcccgacgggatttcatatatttgtagctcggtattttgagccgagctaaacgaagactaaagatgattgatagaaaatatatacgcctgggagaggacgacgaggatgatggtttccccgtattctttccggtgctttccgtttgtgaagaagatgaggatttcaag .........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 cttgaaatcctcatcttcttcacaaacggaaagcaccggaaagaatacggggaaaccatcatcctcgtcgtcctctcccaggcgtatatattttctatcaatcatctttagtcttcgtttagctcggctcaaaataccgagctacaaatatatgaaatcccgtcgggcttctatacttctatacatttatacatcccgacagcaagagcagcaccggacaaaaagggaaggggctgtgtcgaaaaaaacaatctcggcgcagcctctccttagggcagagttactatgataatacagatctccgatcggga Mask Tandem Repeat Region ================================================ tcccgatcggagatctgtattatcatagtaactctgccctaaggagaggctgcgccgagattgtttttttcgacacagccccttccctttttgtccggtgctgctcttgctgtcgggatgtataaatgtatagaagtatagaagcccgacgggatttcatatatttgtagctcggtattttgagccgagctaaacgaagactaaagatgattgatagaaaatatatacgcctgggagaggacgacgaggatgatggtttccccgtattctttccggtgctttccgtttgtgaagaagatgaggatttcaag Find is-nt database================================================ Query_seq: PG0619:PG0620|PG0619:PG0620:alkyl hydroperoxide reductase, F subunit:ATP-dependent protease La:->->:672792..673102 311 tcccgatcggagatctgtattatcatagtaactctgccctaaggagaggctgcgccgagattgtttttttcgacacagccccttccctttttgtccggtgctgctcttgctgtcgggatgtataaatgtatagaagtatagaagcccgacgggatttcatatatttgtagctcggtattttgagccgagctaaacgaagactaaagatgattgatagaaaatatatacgcctgggagaggacgacgaggatgatggtttccccgtattctttccggtgctttccgtttgtgaagaagatgaggatttcaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0619:PG0620|PG0619:PG0620:alkyl hydroperoxide reductase, F subunit:ATP-dependent protease La:->->:672792..673102 311 tcccgatcggagatctgtattatcatagtaactctgccctaaggagaggctgcgccgagattgtttttttcgacacagccccttccctttttgtccggtgctgctcttgctgtcgggatgtataaatgtatagaagtatagaagcccgacgggatttcatatatttgtagctcggtattttgagccgagctaaacgaagactaaagatgattgatagaaaatatatacgcctgggagaggacgacgaggatgatggtttccccgtattctttccggtgctttccgtttgtgaagaagatgaggatttcaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0619:PG0620|PG0619:PG0620:alkyl hydroperoxide reductase, F subunit:ATP-dependent protease La:->->:672792..673102 311 tcccgatcggagatctgtattatcatagtaactctgccctaaggagaggctgcgccgagattgtttttttcgacacagccccttccctttttgtccggtgctgctcttgctgtcgggatgtataaatgtatagaagtatagaagcccgacgggatttcatatatttgtagctcggtattttgagccgagctaaacgaagactaaagatgattgatagaaaatatatacgcctgggagaggacgacgaggatgatggtttccccgtattctttccggtgctttccgtttgtgaagaagatgaggatttcaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcccgatcggagatctgtattatcatagtaactctgccctaaggagaggctgcgccgagattgtttttttcgacacagccccttccctttttgtccggtgctgctcttgctgtcgggatgtataaatgtatagaagtatagaagcccgacgggatttcatatatttgtagctcggtattttgagccgagctaaacgaagactaaagatgattgatagaaaatatatacgcctgggagaggacgacgaggatgatggtttccccgtattctttccggtgctttccgtttgtgaagaagatgaggatttcaag Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 6 End: 122 ..... M G D L Y Y H S N S A L R R G C A E I V F F D T A P S L F V R C C S C C R D V ............................................................................................................................................................................................. Protein_Len: 33 Strand: + Start: 211 End: 309 .................................................................................................................................................................................................................. M I E N I Y A W E R T T R M M V S P Y S F R C F P F V K K M R I S .. Protein_Len: 45 Strand: + Start: 177 End: 311 ................................................................................................................................................................................ M L S R A K R R L K M I D R K Y I R L G E D D E D D G F P V F F P V L S V C E E D E D F K Protein_Len: 34 Strand: - Start: 204 End: 305 ........................................................................................................................................................................................................... L H N I S F I Y A Q S L V V L I I T E G Y E K R H K G N T F F I L M ...... Protein_Len: 41 Strand: - Start: 42 End: 164 ......................................... P S A A G L N N K E V C G R G K K D P A A R A T P I Y L H I S T Y F G S P I E Y M ................................................................................................................................................... Protein_Len: 60 Strand: - Start: 26 End: 310 ......................... L L I S A R R S K M Y K Y S P I K L R A L R L S F I I S L F Y I R R P S S S S S S P K G T N K G T S E T Q S S S S S K M . Protein_Len: 41 Strand: - Start: 1 End: 123 G S R L D T N D Y Y S Q G L S L S R R S Q K K R C L G K G K Q G T S S K S D P H M ............................................................................................................................................................................................ tcccgatcggagatctgtattatcatagtaactctgccctaaggagaggctgcgccgagattgtttttttcgacacagccccttccctttttgtccggtgctgctcttgctgtcgggatgtataaatgtatagaagtatagaagcccgacgggatttcatatatttgtagctcggtattttgagccgagctaaacgaagactaaagatgattgatagaaaatatatacgcctgggagaggacgacgaggatgatggtttccccgtattctttccggtgctttccgtttgtgaagaagatgaggatttcaag 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================================================ tcccgatcggagatctgtattatcatagtaactctgccctaaggagaggctgcgccgagattgtttttttcgacacagccccttccctttttgtccggtgctgctcttgctgtcgggatgtataaatgtatagaagtatagaagcccgacgggatttcatatatttgtagctcggtattttgagccgagctaaacgaagactaaagatgattgatagaaaatatatacgcctgggagaggacgacgaggatgatggtttccccgtattctttccggtgctttccgtttgtgaagaagatgaggatttcaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 53 HP_score: -6.2 Tail_Score: -2.70044 Start: 43 End: 85 Full_Region: GTAACTCTGCCCTAA GGAGAGGCTGCGCCGAGA TTGTTTT TTTCGACACAGCCCCTTC CCTTTTTGTCCGGTG ..........................................GGAGAGGCTGCGCCGAGATTGTTTTTTTCGACACAGCCCCTTC.................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 51 HP_score: -3.8 Tail_Score: -3.50877 Start: 43 End: 86 Full_Region: GTAACTCTGCCCTAA GGAGAGGCTGCGCCGAGA TTGTTTT TTTCGACACAGCCCCTTCC CTTTTTGTCCGGTGC ..........................................GGAGAGGCTGCGCCGAGATTGTTTTTTTCGACACAGCCCCTTCC................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 53 HP_score: -4.3 Tail_Score: -3.49077 Start: 46 End: 82 Full_Region: ACTCTGCCCTAAGGA GAGGCTGCGCCGAGA TTGTTTT TTTCGACACAGCCCC TTCCCTTTTTGTCCG .............................................GAGGCTGCGCCGAGATTGTTTTTTTCGACACAGCCCC..................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 61 HP_score: -8.7 Tail_Score: -2.71011 Start: 46 End: 82 Full_Region: cggacaaaaagggaa ggggctgtgtcgaaa aaaacaa tctcggcgcagcctc tccttagggcagagt .............................................ggggctgtgtcgaaaaaaacaatctcggcgcagcctc..................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 59 HP_score: -7.7 Tail_Score: -2.90075 Start: 48 End: 80 Full_Region: gacaaaaagggaagg ggctgtgtcgaaa aaaacaa tctcggcgcagcc tctccttagggcaga ...............................................ggctgtgtcgaaaaaaacaatctcggcgcagcc....................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PG0619:PG0620|PG0619:PG0620:alkyl hydroperoxide reductase, F subunit:ATP-dependent protease La:->->:672792..673102 311 tcccgatcggagatctgtattatcatagtaactctgccctaaggagaggctgcgccgagattgtttttttcgacacagccccttccctttttgtccggtgctgctcttgctgtcgggatgtataaatgtatagaagtatagaagcccgacgggatttcatatatttgtagctcggtattttgagccgagctaaacgaagactaaagatgattgatagaaaatatatacgcctgggagaggacgacgaggatgatggtttccccgtattctttccggtgctttccgtttgtgaagaagatgaggatttcaag Intra-Species Hit: Count: 1 Min: 1 Max: 311 Len: 311 Subject: NC_002950_PG0619_PG0620|alkyl hydroperoxide reductase, F subunit:ATP-dependent protease La|POSITIVE:POSITIVE|[672792,673102]|311 HSP 1 e-value: 1.0E-163 bit: 575.0 Len: 311 Query Start:1 Query End:311 Subject Strand: POSITIVE Subject Start: 1 Subject End: 311 tcccgatcggagatctgtattatcatagtaactctgccctaaggagaggctgcgccgagattgnnnnnnncgacacagccccttccctttttgtccggtgctgctcttgctgtcgggatgtataaatgtatagaagtatagaagcccgacgggatttcatatatttgtagctcggtattttgagccgagctaaacgaagactaaagatgattgatagaaaatatatacgcctgggagaggacgacgaggatgatggtttccccgtattctttccggtgctttccgtttgtgaagaagatgaggatttcaag tcccgatcggagatctgtattatcatagtaactctgccctaaggagaggctgcgccgagattgtttttttcgacacagccccttccctttttgtccggtgctgctcttgctgtcgggatgtataaatgtatagaagtatagaagcccgacgggatttcatatatttgtagctcggtattttgagccgagctaaacgaagactaaagatgattgatagaaaatatatacgcctgggagaggacgacgaggatgatggtttccccgtattctttccggtgctttccgtttgtgaagaagatgaggatttcaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCCGAUCGGAGAUCUGUAUUAUCAUAGUAACUCUGCCCUAAGGAGAGGCUGCGCCGAGAUUGUUUUUUUCGACACAGCCCCUUCCCUUUUUGUCCGGUGCUGCUCUUGCUGUCGGGAUGUAUAAAUGUAUAGAAGUAUAGAAGCCCGACGGGAUUUCAUAUAUUUGUAGCUCGGUAUUUUGAGCCGAGCUAAACGAAGACUAAAGAUGAUUGAUAGAAAAUAUAUACGCCUGGGAGAGGACGACGAGGAUGAUGGUUUCCCCGUAUUCUUUCCGGUGCUUUCCGUUUGUGAAGAAGAUGAGGAUUUCAAG ((.(((.(((((((((((((((((..((((.(.(((..(.((((((.(((((.(.(((((.......))))).).))))).))..))))...)..))).).))))....((((((((.(((((............)))))....))))))))...........(((((((((((((.......))))))))..))))).......))))))..))))).........((((..((((((((..(((.(((........))).))).)))))))))))).)))))).))).))................... (-91.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGAAAUCCUCAUCUUCUUCACAAACGGAAAGCACCGGAAAGAAUACGGGGAAACCAUCAUCCUCGUCGUCCUCUCCCAGGCGUAUAUAUUUUCUAUCAAUCAUCUUUAGUCUUCGUUUAGCUCGGCUCAAAAUACCGAGCUACAAAUAUAUGAAAUCCCGUCGGGCUUCUAUACUUCUAUACAUUUAUACAUCCCGACAGCAAGAGCAGCACCGGACAAAAAGGGAAGGGGCUGUGUCGAAAAAAACAAUCUCGGCGCAGCCUCUCCUUAGGGCAGAGUUACUAUGAUAAUACAGAUCUCCGAUCGGGA .......((((.(((............(((((((.(((((.((.(((((((((........))))))).)).)).)))..)).))......))))).......((((.((....((((.((((((.((((......(((.((...................((((((....((((............))))...)))))).((....)).))..)))......(((((.(((((((((((((...........)))))))))))))))))).)))).))))))..))))...)).))))....))).)))) (-84.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 447 85 42 220 172 NC_002950:PG1739|5end_hypothetical_protein_1825709..1825939_NEGATIVE 421 80 33 154 102 NC_002950:PG1759|5end_adhesion_protein,_putative_1845570..1845800_POSITIVE 401 88 41 77 28 NC_002950:PG0309|5end_thiamine_biosynthesis_lipoprotein_ApbE_345023..345253_NEGATIVE 398 116 75 39 1 NC_002950:PG1861|5end_hypothetical_protein_1960057..1960287_NEGATIVE 396 289 246 186 140 NC_002950:PG1719|5end_ABC_transporter,_ATP-binding_protein,_MsbA_family_1806749..1806979_POSITIVE 392 48 3 54 12 NC_002950:PG1835|5end_lipoprotein,_putative_1927073..1927303_POSITIVE 392 118 71 216 164 NC_002950:PG1170|5end_SerB_family_protein_1249163..1249393_POSITIVE 389 85 41 177 134 NC_002950:PG0480|5end_precorrin-2_C20-methyltransferase,_putative_521319..521549_NEGATIVE 385 98 51 207 163 NC_002950:PG0538|5end_outer_membrane_efflux_protein_589142..589372_POSITIVE 384 116 71 215 169 NC_002950:PG2075|5end_hypothetical_protein_2176466..2176696_NEGATIVE 377 95 55 120 74 NC_002950:PG1273|5end_hypothetical_protein_1351837..1352067_NEGATIVE 375 73 36 59 5 NC_002950:PG0066|5end_hypothetical_protein_81551..81781_NEGATIVE 373 70 27 55 7 NC_002950:PG2069|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_2164798..2165028_POSITIVE 372 99 51 227 189 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 371 116 74 45 2 NC_002950:PG1103|5end_ATPase,_AAA_family_1173605..1173835_POSITIVE 369 117 71 128 85 NC_002950:PG0607|5end_hypothetical_protein_662552..662782_POSITIVE 367 81 41 225 190 NC_002950:PG0749|5end_hypothetical_protein_795654..795884_NEGATIVE 362 266 223 57 19 NC_002950:PG0932|5end_DNA_polymerase_III,_delta_prime_subunit,_putative_988503..988733_POSITIVE 361 120 71 179 115 NC_002950:PG0657|5end_Maf-like_protein_707782..708012_NEGATIVE 359 305 264 126 88 NC_002950:PG2028|5end_ebsC_protein_2126027..2126257_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 478 120 74 79 24 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 468 80 41 52 16 NC_002950:PG2170|3end_sugar_transporter_2276685..2276835_NEGATIVE 467 98 51 70 13 NC_002950:PG0537|3end_aminoacyl-histidine_dipeptidase_588394..588544_POSITIVE 453 82 41 41 5 NC_002950:PG1950|3end_hypothetical_protein_2040840..2040990_POSITIVE 447 85 42 73 25 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 440 90 41 68 23 NC_002950:PG0034|3end_thioredoxin_42235..42385_NEGATIVE 422 117 74 70 18 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 413 84 41 67 24 NC_002950:PG0726|3end_lipoprotein,_putative_778003..778153_NEGATIVE 401 88 41 80 31 NC_002950:PG0310|3end_nitroreductase_family_protein_345020..345170_NEGATIVE 390 89 42 43 3 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 390 81 41 67 30 NC_002950:PG0506|3end_arginine-specific_cysteine_proteinase_547625..547775_POSITIVE 389 85 41 64 21 NC_002950:PG0481|3end_2-amino-3-ketobutyrate_coenzyme_A_ligase_521432..521582_NEGATIVE 386 87 41 68 18 NC_002950:PG1847|3end_endoribonuclease_L-PSP,_putative_1946227..1946377_NEGATIVE 378 119 71 110 62 NC_002950:PG0618|3end_alkyl_hydroperoxide_reductase,_C_subunit_671018..671168_POSITIVE 377 120 72 140 89 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 374 118 71 89 29 NC_002950:PG1758|3end_ribosomal_protein_S15_1845534..1845684_POSITIVE 373 70 27 49 1 NC_002950:PG2068|3end_glycerol-3-phosphate_cytidylyltransferase_2164872..2165022_POSITIVE 366 83 42 50 13 NC_002950:PG1754|3end_hypothetical_protein_1842284..1842434_POSITIVE 366 81 41 59 20 NC_002950:PG0535|3end_hypothetical_protein_585956..586106_NEGATIVE 362 264 221 59 3 NC_002950:PG1117|3end_MATE_efflux_family_protein_1191541..1191691_POSITIVE