Origin IGS: gcagtaaaccgaggagagagggtgtgtcggaatcgcaaaatgaggcgatcacaacacaccctctttctttaaggcacgaaagagttctccatgctgtttctccgaatacagtgagataatcggaactcttgattaaggtcctttttaatcattatcctaacgact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtcgttaggataatgattaaaaaggaccttaatcaagagttccgattatctcactgtattcggagaaacagcatggagaactctttcgtgccttaaagaaagagggtgtgttgtgatcgcctcattttgcgattccgacacaccctctctcctcggtttactgc Mask Tandem Repeat Region ================================================ gcagtaaaccgaggagagagggtgtgtcggaatcgcaaaatgaggcgatcacaacacaccctctttctttaaggcacgaaagagttctccatgctgtttctccgaatacagtgagataatcggaactcttgattaaggtcctttttaatcattatcctaacgact Find is-nt database================================================ Query_seq: PG0618:PG0619|PG0618:PG0619:alkyl hydroperoxide reductase, C subunit:alkyl hydroperoxide reductase, F subunit:->->:671079..671243 165 gcagtaaaccgaggagagagggtgtgtcggaatcgcaaaatgaggcgatcacaacacaccctctttctttaaggcacgaaagagttctccatgctgtttctccgaatacagtgagataatcggaactcttgattaaggtcctttttaatcattatcctaacgact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0618:PG0619|PG0618:PG0619:alkyl hydroperoxide reductase, C subunit:alkyl hydroperoxide reductase, F subunit:->->:671079..671243 165 gcagtaaaccgaggagagagggtgtgtcggaatcgcaaaatgaggcgatcacaacacaccctctttctttaaggcacgaaagagttctccatgctgtttctccgaatacagtgagataatcggaactcttgattaaggtcctttttaatcattatcctaacgact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0618:PG0619|PG0618:PG0619:alkyl hydroperoxide reductase, C subunit:alkyl hydroperoxide reductase, F subunit:->->:671079..671243 165 gcagtaaaccgaggagagagggtgtgtcggaatcgcaaaatgaggcgatcacaacacaccctctttctttaaggcacgaaagagttctccatgctgtttctccgaatacagtgagataatcggaactcttgattaaggtcctttttaatcattatcctaacgact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcagtaaaccgaggagagagggtgtgtcggaatcgcaaaatgaggcgatcacaacacaccctctttctttaaggcacgaaagagttctccatgctgtttctccgaatacagtgagataatcggaactcttgattaaggtcctttttaatcattatcctaacgact Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 24 End: 116 ....................... M S E S Q N E A I T T H P L S L R H E R V L H A V S P N T V R ................................................. Protein_Len: 44 Strand: - Start: 2 End: 133 . L L G L L S P T D S D C F S A I V V C G R E K L C S L T R W A T E G F V T L Y D S S K M ................................ gcagtaaaccgaggagagagggtgtgtcggaatcgcaaaatgaggcgatcacaacacaccctctttctttaaggcacgaaagagttctccatgctgtttctccgaatacagtgagataatcggaactcttgattaaggtcctttttaatcattatcctaacgact 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================================================ gcagtaaaccgaggagagagggtgtgtcggaatcgcaaaatgaggcgatcacaacacaccctctttctttaaggcacgaaagagttctccatgctgtttctccgaatacagtgagataatcggaactcttgattaaggtcctttttaatcattatcctaacgact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -11.9 Tail_Score: -4.41348 Start: 18 End: 63 Full_Region: AGTAAACCGAGGAGA GAGGGTGTGTCGGAATCGC AAAATGAG GCGATCACAACACACCCTC TTTCTTTAAGGCACG .................GAGGGTGTGTCGGAATCGCAAAATGAGGCGATCACAACACACCCTC...................................................................................................... TransTerm Strand: - Conf: 93 HP_score: -16.3 Tail_Score: -2.84999 Start: 18 End: 63 Full_Region: cgtgccttaaagaaa gagggtgtgttgtgatcgc ctcatttt gcgattccgacacaccctc tctcctcggtttact .................gagggtgtgttgtgatcgcctcattttgcgattccgacacaccctc...................................................................................................... TransTerm Strand: - Conf: 82 HP_score: -13.1 Tail_Score: -2.96984 Start: 20 End: 61 Full_Region: tgccttaaagaaaga gggtgtgttgtgatcgc ctcatttt gcgattccgacacaccc tctctcctcggttta ...................gggtgtgttgtgatcgcctcattttgcgattccgacacaccc........................................................................................................ Find igs database================================================ Query_seq: PG0618:PG0619|PG0618:PG0619:alkyl hydroperoxide reductase, C subunit:alkyl hydroperoxide reductase, F subunit:->->:671079..671243 165 gcagtaaaccgaggagagagggtgtgtcggaatcgcaaaatgaggcgatcacaacacaccctctttctttaaggcacgaaagagttctccatgctgtttctccgaatacagtgagataatcggaactcttgattaaggtcctttttaatcattatcctaacgact Intra-Species Hit: Count: 1 Min: 1 Max: 165 Len: 165 Subject: NC_002950_PG0618_PG0619|alkyl hydroperoxide reductase, C subunit:alkyl hydroperoxide reductase, F subunit|POSITIVE:POSITIVE|[671079,671243]|165 HSP 1 e-value: 7.0E-89 bit: 327.0 Len: 165 Query Start:1 Query End:165 Subject Strand: POSITIVE Subject Start: 1 Subject End: 165 gcagtaaaccgaggagagagggtgtgtcggaatcgcaaaatgaggcgatcacaacacaccctctttctttaaggcacgaaagagttctccatgctgtttctccgaatacagtgagataatcggaactcttgattaaggtcctttttaatcattatcctaacgact gcagtaaaccgaggagagagggtgtgtcggaatcgcaaaatgaggcgatcacaacacaccctctttctttaaggcacgaaagagttctccatgctgtttctccgaatacagtgagataatcggaactcttgattaaggtcctttttaatcattatcctaacgact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAGUAAACCGAGGAGAGAGGGUGUGUCGGAAUCGCAAAAUGAGGCGAUCACAACACACCCUCUUUCUUUAAGGCACGAAAGAGUUCUCCAUGCUGUUUCUCCGAAUACAGUGAGAUAAUCGGAACUCUUGAUUAAGGUCCUUUUUAAUCAUUAUCCUAACGACU ((((((....(((((((((((((((((.(..(((((........)))))..).)))))))))))))))))..(((.(....).))).....)))))).(((((.......).)))).....(((.....(((((((((....)))))))))...)))........ (-56.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCGUUAGGAUAAUGAUUAAAAAGGACCUUAAUCAAGAGUUCCGAUUAUCUCACUGUAUUCGGAGAAACAGCAUGGAGAACUCUUUCGUGCCUUAAAGAAAGAGGGUGUGUUGUGAUCGCCUCAUUUUGCGAUUCCGACACACCCUCUCUCCUCGGUUUACUGC ((((((((...)))))))).....(((((...........((((((.(((......))).)))))).....((((((((.....))))))))......((.(((((((((((((..(((((........)))))..))))))))))))).))...)))))..... (-56.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 427 67 21 178 134 NC_002950:PG1281|5end_hypothetical_protein_1358848..1359078_POSITIVE 410 47 1 85 39 NC_002950:PG1855|5end_carboxyl-terminal_protease_1955476..1955706_NEGATIVE 396 48 10 224 183 NC_002950:PG1605|5end_aminopeptidase_C_1685179..1685409_POSITIVE 372 59 18 167 134 NC_002950:PG0043|5end_beta-hexosaminidase_51066..51296_POSITIVE 365 49 1 85 42 NC_002950:PG1301|5end_hypothetical_protein_1379921..1380151_NEGATIVE 357 45 8 65 23 NC_002950:PG1379|5end_ABC_transporter,_periplasmic_substrate-binding_protein,_putative_1458937..1459167_POSITIVE 345 47 2 155 117 NC_002950:PG1872|5end_urocanate_hydratase_1968911..1969141_NEGATIVE 338 45 2 47 2 NC_002950:PG0099|5end_phenylalanyl-tRNA_synthetase_beta_subunit_118286..118516_NEGATIVE 337 30 8 43 20 NC_002950:PG0307|5end_NADH-ubiquinone_oxidoreductase_342560..342790_POSITIVE 328 109 62 137 81 NC_002950:PG2023|5end_methionyl-tRNA_formyltransferase_2118536..2118766_NEGATIVE 328 44 1 211 169 NC_002950:PG1249|5end_1-acyl-sn-glycerol-3-phosphate_acetyltransferase,_putative_1327161..1327391_NEGATIVE 327 49 1 87 40 NC_002950:PG1999|5end_hypothetical_protein_2088821..2089051_NEGATIVE 325 48 1 131 85 NC_002950:PG0123|5end_hypothetical_protein_144987..145217_POSITIVE 324 60 13 225 187 NC_002950:PG0749|5end_hypothetical_protein_795654..795884_NEGATIVE 321 116 73 45 4 NC_002950:PG1351|5end_hypothetical_protein_1432744..1432974_NEGATIVE 320 49 1 198 151 NC_002950:PG0769|5end_fibronectin_type_III_domain_protein_824177..824407_NEGATIVE 317 59 13 207 160 NC_002950:PG0782|5end_MotA/TolQ/ExbB_proton_channel_family_protein_834530..834760_NEGATIVE 315 47 1 85 40 NC_002950:PG0324|5end_histidine_ammonia-lyase_359082..359312_NEGATIVE 313 47 2 174 109 NC_002950:PG1500|5end_hypothetical_protein_1576099..1576329_POSITIVE 313 116 71 55 9 NC_002950:PG1368|5end_glucose-6-phosphate_isomerase_1449370..1449600_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 485 65 21 71 24 NC_002950:PG0138|3end_malonyl_CoA-acyl_carrier_protein_transacylase_161634..161784_POSITIVE 471 60 14 51 5 NC_002950:PG0537|3end_aminoacyl-histidine_dipeptidase_588394..588544_POSITIVE 430 69 21 79 31 NC_002950:PG0618|3end_alkyl_hydroperoxide_reductase,_C_subunit_671018..671168_POSITIVE 427 67 21 51 7 NC_002950:PG1280|3end_hypothetical_protein_1358801..1358951_POSITIVE 410 47 1 77 31 NC_002950:PG1856|3end_cytidine/deoxycytidylate_deaminase_family_protein_1955484..1955634_NEGATIVE 396 48 10 112 71 NC_002950:PG1604|3end_immunoreactive_84_kDa_antigen_PG93_1685147..1685297_POSITIVE 376 49 2 45 1 NC_002950:PG1773|3end_PAP2_superfamily_protein_1861232..1861382_POSITIVE 374 60 15 53 5 NC_002950:PG2207|3end_hypothetical_protein_2319142..2319292_NEGATIVE 365 49 1 67 24 NC_002950:PG1302|3end_hypothetical_protein_1379939..1380089_NEGATIVE 337 30 8 46 23 NC_002950:PG0306|3end_electron_transport_complex,_RnfABCDGE_type,_G_subunit_342643..342793_POSITIVE 337 59 12 65 21 NC_002950:PG0193|3end_cationic_outer_membrane_protein_OmpH_230720..230870_POSITIVE 334 46 10 64 24 NC_002950:PG1472|3end_hypothetical_protein_1549760..1549910_POSITIVE 330 90 41 69 11 NC_002950:PG0815|3end_hypothetical_protein_876447..876597_POSITIVE 327 49 1 66 19 NC_002950:PG2000|3end_signal_peptidase-related_protein_2088842..2088992_NEGATIVE 327 116 73 66 23 NC_002950:PG1088|3end_acetyltransferase,_GNAT_family_1154842..1154992_NEGATIVE 321 116 73 52 11 NC_002950:PG1352|3end_hypothetical_protein_1432737..1432887_NEGATIVE 320 47 1 89 49 NC_002950:PG2036|3end_ion_transporter_2137552..2137702_POSITIVE 318 67 21 70 26 NC_002950:PG0474|3end_low-specificity_L-threonine_aldolase_515011..515161_NEGATIVE 316 90 44 72 11 NC_002950:PG0264|3end_glycosyl_transferase,_group_2_family_protein_298122..298272_POSITIVE 315 47 1 82 37 NC_002950:PG0325|3end_hypothetical_protein_359085..359235_NEGATIVE