Origin IGS: tctatcgactccgaagcgcatcgcacggatatactgccgggaatgatcgggcttcctgtccgatcgaaaggaccggttttcaacggaagttgtatatatttgagcgctttgtttcagtacgattctccgccctcttattgcgatcggagggcggtgcaaaaaacgatccaatcaaacacatatattat .........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 ataatatatgtgtttgattggatcgttttttgcaccgccctccgatcgcaataagagggcggagaatcgtactgaaacaaagcgctcaaatatatacaacttccgttgaaaaccggtcctttcgatcggacaggaagcccgatcattcccggcagtatatccgtgcgatgcgcttcggagtcgataga Mask Tandem Repeat Region ================================================ tctatcgactccgaagcgcatcgcacggatatactgccgggaatgatcgggcttcctgtccgatcgaaaggaccggttttcaacggaagttgtatatatttgagcgctttgtttcagtacgattctccgccctcttattgcgatcggagggcggtgcaaaaaacgatccaatcaaacacatatattat Find is-nt database================================================ Query_seq: PG0443:PG0444|PG0443:PG0444:hemagglutinin-related protein:oligopeptide transporter, OPT family:->->:483208..483395 188 tctatcgactccgaagcgcatcgcacggatatactgccgggaatgatcgggcttcctgtccgatcgaaaggaccggttttcaacggaagttgtatatatttgagcgctttgtttcagtacgattctccgccctcttattgcgatcggagggcggtgcaaaaaacgatccaatcaaacacatatattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0443:PG0444|PG0443:PG0444:hemagglutinin-related protein:oligopeptide transporter, OPT family:->->:483208..483395 188 tctatcgactccgaagcgcatcgcacggatatactgccgggaatgatcgggcttcctgtccgatcgaaaggaccggttttcaacggaagttgtatatatttgagcgctttgtttcagtacgattctccgccctcttattgcgatcggagggcggtgcaaaaaacgatccaatcaaacacatatattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0443:PG0444|PG0443:PG0444:hemagglutinin-related protein:oligopeptide transporter, OPT family:->->:483208..483395 188 tctatcgactccgaagcgcatcgcacggatatactgccgggaatgatcgggcttcctgtccgatcgaaaggaccggttttcaacggaagttgtatatatttgagcgctttgtttcagtacgattctccgccctcttattgcgatcggagggcggtgcaaaaaacgatccaatcaaacacatatattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctatcgactccgaagcgcatcgcacggatatactgccgggaatgatcgggcttcctgtccgatcgaaaggaccggttttcaacggaagttgtatatatttgagcgctttgtttcagtacgattctccgccctcttattgcgatcggagggcggtgcaaaaaacgatccaatcaaacacatatattat Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 4 End: 186 ... M D S E A H R T D I L P G M I G L P V R S K G P V F N G S C I Y L S A L F Q Y D S P P S Y C D R R A V Q K T I Q S N T Y .. Protein_Len: 42 Strand: + Start: 63 End: 188 .............................................................. M E R T G F Q R K L Y I F E R F V S V R F S A L L L R S E G G A K N D P I K H I Y Y Protein_Len: 33 Strand: - Start: 83 End: 181 .................................................................................. R F N Y I N S R K T E T R N E A R K N R D S P P A F F S G I L C M ....... Protein_Len: 31 Strand: - Start: 3 End: 95 .. I S E S A C R V S I S G P I I P S G T R D F P G T K L P L Q M ............................................................................................. Protein_Len: 57 Strand: - Start: 1 End: 171 R D V G F R M A R I Y Q R S H D P K R D S R F S R N E V S T T Y I Q A S Q K L V I R R G R I A I P P R H L F R D M ................. tctatcgactccgaagcgcatcgcacggatatactgccgggaatgatcgggcttcctgtccgatcgaaaggaccggttttcaacggaagttgtatatatttgagcgctttgtttcagtacgattctccgccctcttattgcgatcggagggcggtgcaaaaaacgatccaatcaaacacatatattat 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================================================ tctatcgactccgaagcgcatcgcacggatatactgccgggaatgatcgggcttcctgtccgatcgaaaggaccggttttcaacggaagttgtatatatttgagcgctttgtttcagtacgattctccgccctcttattgcgatcggagggcggtgcaaaaaacgatccaatcaaacacatatattat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0443:PG0444|PG0443:PG0444:hemagglutinin-related protein:oligopeptide transporter, OPT family:->->:483208..483395 188 tctatcgactccgaagcgcatcgcacggatatactgccgggaatgatcgggcttcctgtccgatcgaaaggaccggttttcaacggaagttgtatatatttgagcgctttgtttcagtacgattctccgccctcttattgcgatcggagggcggtgcaaaaaacgatccaatcaaacacatatattat Intra-Species Hit: Count: 1 Min: 1 Max: 188 Len: 188 Subject: NC_002950_PG0443_PG0444|hemagglutinin-related protein:oligopeptide transporter, OPT family|POSITIVE:POSITIVE|[483208,483395]|188 HSP 1 e-value: 1.0E-102 bit: 373.0 Len: 188 Query Start:1 Query End:188 Subject Strand: POSITIVE Subject Start: 1 Subject End: 188 tctatcgactccgaagcgcatcgcacggatatactgccgggaatgatcgggcttcctgtccgatcgaaaggaccggttttcaacggaagttgtatatatttgagcgctttgtttcagtacgattctccgccctcttattgcgatcggagggcggtgcaaaaaacgatccaatcaaacacatatattat tctatcgactccgaagcgcatcgcacggatatactgccgggaatgatcgggcttcctgtccgatcgaaaggaccggttttcaacggaagttgtatatatttgagcgctttgtttcagtacgattctccgccctcttattgcgatcggagggcggtgcaaaaaacgatccaatcaaacacatatattat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAUCGACUCCGAAGCGCAUCGCACGGAUAUACUGCCGGGAAUGAUCGGGCUUCCUGUCCGAUCGAAAGGACCGGUUUUCAACGGAAGUUGUAUAUAUUUGAGCGCUUUGUUUCAGUACGAUUCUCCGCCCUCUUAUUGCGAUCGGAGGGCGGUGCAAAAAACGAUCCAAUCAAACACAUAUAUUAU ...(((((((..((((((...(((.((((((((..(((((...(((((((((.....)))))))))......)))))...((((....))))..)))))))).)))...))))))))).))))...(((((((((.((....)).))))))))).................................. (-63.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAUAUAUGUGUUUGAUUGGAUCGUUUUUUGCACCGCCCUCCGAUCGCAAUAAGAGGGCGGAGAAUCGUACUGAAACAAAGCGCUCAAAUAUAUACAACUUCCGUUGAAAACCGGUCCUUUCGAUCGGACAGGAAGCCCGAUCAUUCCCGGCAGUAUAUCCGUGCGAUGCGCUUCGGAGUCGAUAGA ......((((((((((((((..((((......(.((((((((..((....))..)))))))).)......)).))..))).....))))))))))).....((..((((...((((.......((((((.(.....).))))))....)))).......((((.(((...)))..)))).))))..)) (-51.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 456 57 12 194 138 NC_002950:PG0387|5end_elongation_factor_Tu_420643..420873_POSITIVE 418 67 21 200 144 NC_002950:PG1594|5end_ComEC/Rec2-related_protein_1673587..1673817_NEGATIVE 391 77 34 199 145 NC_002950:PG1348|5end_conserved_hypothetical_protein_TIGR00147_1428608..1428838_POSITIVE 383 156 111 162 113 NC_002950:PG1226|5end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_1303264..1303494_POSITIVE 382 78 31 177 126 NC_002950:PG1310|5end_exsB_protein_1389084..1389314_POSITIVE 380 160 116 85 33 NC_002950:PG1356|5end_hypothetical_protein_1435849..1436079_NEGATIVE 378 158 113 177 117 NC_002950:PG0854|5end_hypothetical_protein_914870..915100_POSITIVE 377 60 14 225 169 NC_002950:PG0430|5end_ferrodoxin_oxidoreductase_beta_subunit_467986..468216_POSITIVE 375 159 114 91 36 NC_002950:PG2075|5end_hypothetical_protein_2176466..2176696_NEGATIVE 375 159 114 91 36 NC_002950:PG1266|5end_hypothetical_protein_1346987..1347217_NEGATIVE 374 86 43 229 185 NC_002950:PG1369|5end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_1450407..1450637_NEGATIVE 372 57 11 73 12 NC_002950:PG1022|5end_hypothetical_protein_1083537..1083767_POSITIVE 372 158 115 219 175 NC_002950:PG0975|5end_PhoH_family_protein_1037284..1037514_POSITIVE 371 60 11 85 30 NC_002950:PG1812|5end_2-oxoglutarate_ferredoxin_oxidoreductase_1908107..1908337_NEGATIVE 370 80 35 160 120 NC_002950:PG1964|5end_bacterial_sugar_transferase_2052910..2053140_POSITIVE 368 77 38 47 4 NC_002950:PG1572|5end_hypothetical_protein_1651252..1651482_NEGATIVE 364 54 17 79 43 NC_002950:PG1040|5end_transcriptional_regulator,_putative_1107949..1108179_NEGATIVE 363 80 34 73 16 NC_002950:PG0746|5end_sensor_histidine_kinase_793903..794133_NEGATIVE 362 68 25 162 119 NC_002950:PG1163|5end_cobyrinic_acid_a,c-diamide_synthase_1243381..1243611_NEGATIVE 361 74 32 160 125 NC_002950:PG1715|5end_hypothetical_protein_1806056..1806286_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 410 76 36 56 21 NC_002950:PG1459|3end_hypothetical_protein_1539632..1539782_NEGATIVE 408 156 113 143 100 NC_002950:PG0010|3end_ATP-dependent_Clp_protease,_ATP-binding_subunit_ClpC_11434..11584_POSITIVE 401 168 125 92 44 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 386 89 43 147 99 NC_002950:PG1370|3end_lysyl-tRNA_synthetase_1450493..1450643_NEGATIVE 376 66 21 121 72 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 364 54 17 58 22 NC_002950:PG1041|3end_K+-dependent_Na+/Ca+_exchanger_related-protein_1107970..1108120_NEGATIVE 363 80 34 76 19 NC_002950:PG0747|3end_sigma-54_dependent_DNA-binding_response_regulator_793900..794050_NEGATIVE 362 157 115 151 99 NC_002950:PG1687|3end_HIT_family_protein_1773812..1773962_NEGATIVE 359 150 102 89 45 NC_002950:PG0328|3end_imidazolonepropionase_362155..362305_NEGATIVE 358 74 34 54 19 NC_002950:PG1118|3end_clpB_protein_1192083..1192233_NEGATIVE 353 50 1 140 85 NC_002950:PG1956|3end_4-hydroxybutyrate_CoA-transferase_2046215..2046365_NEGATIVE 353 66 25 72 32 NC_002950:PG1613|3end_glyoxalase_family_protein_1693164..1693314_NEGATIVE 353 78 36 92 32 NC_002950:PG1104|3end_hypothetical_protein_1175782..1175932_POSITIVE 351 165 125 61 22 NC_002950:PG1007|3end_transcriptional_regulator,_GntR_family_1066518..1066668_NEGATIVE 351 169 126 99 44 NC_002950:PG0046|3end_phosphatidate_cytidylyltransferase_56346..56496_NEGATIVE 346 150 106 104 59 NC_002950:PG0669|3end_heme-binding_protein_FetB_720714..720864_POSITIVE 344 66 25 63 24 NC_002950:PG0524|3end_hypothetical_protein_568963..569113_POSITIVE 341 156 118 140 92 NC_002950:PG0555|3end_DNA-binding_protein,_histone-like_family_611716..611866_NEGATIVE 338 76 34 55 2 NC_002950:PG1876|3end_hypothetical_protein_1970633..1970783_NEGATIVE 337 66 21 45 6 NC_002950:PG1008|3end_hypothetical_protein_1066886..1067036_NEGATIVE