Origin IGS: ccgttagcacggcagggagggatgtaccaaagccaaaccactctctgcctgcatccaaagagagaggggggctgtgtcatccgcgacacagctccccctctttttttctctctctttcggcttccctctcagaaagccgcgagtgtttttttccgctc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gagcggaaaaaaacactcgcggctttctgagagggaagccgaaagagagagaaaaaaagagggggagctgtgtcgcggatgacacagcccccctctctctttggatgcaggcagagagtggtttggctttggtacatccctccctgccgtgctaacgg Mask Tandem Repeat Region ================================================ ccgttagcacggcagggagggatgtaccaaagccaaaccactctctgcctgcatccaaagagagaggggggctgtgtcatccgcgacacagctccccctctttttttctctctctttcggcttccctctcagaaagccgcgagtgtttttttccgctc Find is-nt database================================================ Query_seq: PG1675:PG1676|PG1675:PG1676:hypothetical protein:phosphoenolpyruvate carboxykinase:-><-:1760421..1760578 158 ccgttagcacggcagggagggatgtaccaaagccaaaccactctctgcctgcatccaaagagagaggggggctgtgtcatccgcgacacagctccccctctttttttctctctctttcggcttccctctcagaaagccgcgagtgtttttttccgctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1675:PG1676|PG1675:PG1676:hypothetical protein:phosphoenolpyruvate carboxykinase:-><-:1760421..1760578 158 ccgttagcacggcagggagggatgtaccaaagccaaaccactctctgcctgcatccaaagagagaggggggctgtgtcatccgcgacacagctccccctctttttttctctctctttcggcttccctctcagaaagccgcgagtgtttttttccgctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1675:PG1676|PG1675:PG1676:hypothetical protein:phosphoenolpyruvate carboxykinase:-><-:1760421..1760578 158 ccgttagcacggcagggagggatgtaccaaagccaaaccactctctgcctgcatccaaagagagaggggggctgtgtcatccgcgacacagctccccctctttttttctctctctttcggcttccctctcagaaagccgcgagtgtttttttccgctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccgttagcacggcagggagggatgtaccaaagccaaaccactctctgcctgcatccaaagagagaggggggctgtgtcatccgcgacacagctccccctctttttttctctctctttcggcttccctctcagaaagccgcgagtgtttttttccgctc Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 22 End: 156 ..................... M Y Q S Q T T L C L H P K R E G G C V I R D T A P P L F F S L F R L P S Q K A A S V F F R .. Protein_Len: 35 Strand: + Start: 53 End: 157 .................................................... M Q R E R G A V S S A T Q L P L F F S L S F G F P L R K P R V F F S A . Protein_Len: 38 Strand: + Start: 45 End: 158 ............................................ M P A S K E R G G L C H P R H S S P S F F L S L S A S L S E S R E C F F P L Protein_Len: 42 Strand: - Start: 7 End: 132 ...... C P L S P H V L A L G S E A Q M W L S L P A T D D A V C S G R K K E R E K P K G R M .......................... ccgttagcacggcagggagggatgtaccaaagccaaaccactctctgcctgcatccaaagagagaggggggctgtgtcatccgcgacacagctccccctctttttttctctctctttcggcttccctctcagaaagccgcgagtgtttttttccgctc 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================================================ ccgttagcacggcagggagggatgtaccaaagccaaaccactctctgcctgcatccaaagagagaggggggctgtgtcatccgcgacacagctccccctctttttttctctctctttcggcttccctctcagaaagccgcgagtgtttttttccgctc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -18.9 Tail_Score: -5.77988 Start: 64 End: 100 Full_Region: CTGCATCCAAAGAGA GAGGGGGGCTGTGTC ATCCGC GACACAGCTCCCCCTC TTTTTTTCTCTCTCT ...............................................................GAGGGGGGCTGTGTCATCCGCGACACAGCTCCCCCTC.......................................................... TransTerm Strand: - Conf: 100 HP_score: -19.6 Tail_Score: -3.27408 Start: 64 End: 100 Full_Region: agagagagaaaaaaa gagggggagctgtgtcg cgga tgacacagcccccctc tctctttggatgcag ...............................................................gagggggagctgtgtcgcggatgacacagcccccctc.......................................................... Find igs database================================================ Query_seq: PG1675:PG1676|PG1675:PG1676:hypothetical protein:phosphoenolpyruvate carboxykinase:-><-:1760421..1760578 158 ccgttagcacggcagggagggatgtaccaaagccaaaccactctctgcctgcatccaaagagagaggggggctgtgtcatccgcgacacagctccccctctttttttctctctctttcggcttccctctcagaaagccgcgagtgtttttttccgctc Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: NC_002950_PG1675_PG1676|hypothetical protein:phosphoenolpyruvate carboxykinase|POSITIVE:NEGATIVE|[1760421,1760578]|158 HSP 1 e-value: 2.0E-64 bit: 246.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 145 ccgttagcacggcagggagggatgtaccaaagccaaaccactctctgcctgcatccaaagagagaggggggctgtgtcatccgcgacacagctccccctcnnnnnnnctctctctttcggcttccctctcagaaagccgcgagtg............. ccgttagcacggcagggagggatgtaccaaagccaaaccactctctgcctgcatccaaagagagaggggggctgtgtcatccgcgacacagctccccctctttttttctctctctttcggcttccctctcagaaagccgcgagtg............. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGUUAGCACGGCAGGGAGGGAUGUACCAAAGCCAAACCACUCUCUGCCUGCAUCCAAAGAGAGAGGGGGGCUGUGUCAUCCGCGACACAGCUCCCCCUCUUUUUUUCUCUCUCUUUCGGCUUCCCUCUCAGAAAGCCGCGAGUG ......(((.(((((((((((..((......))....)).))))))))))))....((((((((((((((((((((((......)))))))).))))))))))))))......(((.((((((.(......).)))))).))).. (-69.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACUCGCGGCUUUCUGAGAGGGAAGCCGAAAGAGAGAGAAAAAAAGAGGGGGAGCUGUGUCGCGGAUGACACAGCCCCCCUCUCUCUUUGGAUGCAGGCAGAGAGUGGUUUGGCUUUGGUACAUCCCUCCCUGCCGUGCUAACGG ..(((.(((((((((....)))))))))...))).((((......(((((((.(((((((((....))))))))))))))))))))..((...((((((((.(((.((....((....))....))))).))))).)))...)). (-74.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 446 125 82 132 75 NC_002950:PG0399|5end_lipoprotein,_putative_436237..436467_NEGATIVE 437 126 81 188 146 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 428 96 51 192 134 NC_002950:PG0095|5end_DNA_mismatch_repair_protein_114763..114993_NEGATIVE 418 101 67 206 166 NC_002950:PG2091|5end_dihydroneopterin_aldolase_2191177..2191407_POSITIVE 402 94 56 225 181 NC_002950:PG0749|5end_hypothetical_protein_795654..795884_NEGATIVE 389 90 46 78 31 NC_002950:PG0675|5end_indolepyruvate_ferredoxin_oxidoreductase,_alpha_subunit_726436..726666_NEGATIVE 386 100 60 140 96 NC_002950:PG1672|5end_hypothetical_protein_1757637..1757867_POSITIVE 386 100 60 140 96 NC_002950:PG0100|5end_hypothetical_protein_119219..119449_NEGATIVE 379 95 59 173 131 NC_002950:PG2062|5end_histidyl-tRNA_synthetase_2158971..2159201_POSITIVE 376 98 60 159 120 NC_002950:PG0344|5end_purple_acid_phosphatase_380012..380242_NEGATIVE 374 48 1 72 10 NC_002950:PG0046|5end_phosphatidate_cytidylyltransferase_57200..57430_NEGATIVE 371 104 67 63 20 NC_002950:PG1234|5end_hypothetical_protein_1310112..1310342_POSITIVE 370 85 43 229 186 NC_002950:PG2064|5end_hypothetical_protein_2160550..2160780_POSITIVE 368 39 1 130 93 NC_002950:PG1402|5end_AP_endonuclease_domain_protein_1485963..1486193_NEGATIVE 368 90 44 220 177 NC_002950:PG0163|5end_diphosphate--fructose-6-phosphate_1-phosphotransferase_186885..187115_NEGATIVE 365 50 2 201 136 NC_002950:PG0744|5end_RNA_methyltransferase,_TrmH_family_791897..792127_NEGATIVE 365 72 31 48 4 NC_002950:PG0265|5end_hypothetical_protein_298551..298781_NEGATIVE 364 100 68 198 160 NC_002950:PG1352|5end_hypothetical_protein_1433150..1433380_NEGATIVE 360 85 41 70 18 NC_002950:PG0226|5end_transglutaminase-related_protein_262531..262761_NEGATIVE 356 48 6 135 95 NC_002950:PG1871|5end_hypothetical_protein_1966859..1967089_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 476 99 52 62 20 NC_002950:PG1630|3end_hypothetical_protein_1712142..1712292_POSITIVE 446 125 82 124 67 NC_002950:PG0400|3end_hypothetical_protein_436245..436395_NEGATIVE 431 95 56 61 18 NC_002950:PG0034|3end_thioredoxin_42235..42385_NEGATIVE 428 102 61 65 27 NC_002950:PG1226|3end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_1304048..1304198_POSITIVE 413 104 63 70 23 NC_002950:PG0726|3end_lipoprotein,_putative_778003..778153_NEGATIVE 412 107 73 34 1 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE 410 96 53 86 31 NC_002950:PG2050|3end_hypothetical_protein_2149159..2149309_NEGATIVE 401 103 62 58 21 NC_002950:PG0933|3end_translation_elongation_factor_G,_putative_992236..992386_POSITIVE 386 100 58 59 12 NC_002950:PG1949|3end_malate_dehydrogenase_2038184..2038334_NEGATIVE 385 105 61 71 34 NC_002950:PG0308|3end_electron_transport_complex,_RnfABCDGE_type,_A_subunit_343827..343977_POSITIVE 385 103 61 49 6 NC_002950:PG0241|3end_lipoprotein,_putative_277360..277510_NEGATIVE 379 95 59 112 70 NC_002950:PG2061|3end_dihydrofolate_reductase_2158990..2159140_POSITIVE 376 99 60 63 32 NC_002950:PG1797|3end_DNA-binding_response_regulator/sensor_histidine_kinase_1892978..1893128_POSITIVE 375 49 10 83 46 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 370 109 62 98 44 NC_002950:PG0725|3end_hydrolase,_haloacid_dehalogenase-like_family_777966..778116_POSITIVE 369 109 62 76 30 NC_002950:PG0322|3end_serine/threonine_transporter_356966..357116_POSITIVE 367 100 54 52 2 NC_002950:PG0553|3end_extracellular_protease,_putative_608367..608517_NEGATIVE 366 96 60 151 117 NC_002950:PG0345|3end_hypothetical_protein_380015..380165_NEGATIVE 365 50 2 116 51 NC_002950:PG0745|3end_lactoylglutathione_lyase,_putative_791982..792132_NEGATIVE 364 100 68 147 109 NC_002950:PG1353|3end_orotate_phosphoribosyltransferase_1433201..1433351_NEGATIVE