Origin IGS: ggcgaaagcattgtatcgcctggtaacaaccgaatagaacaggggctgtgctgaggataaaacctcgacacagcccctgcgctattcgggaaaactcgaaagaagtctttacgcttctacggctttcctctctccaagcttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagcttggagagaggaaagccgtagaagcgtaaagacttctttcgagttttcccgaatagcgcaggggctgtgtcgaggttttatcctcagcacagcccctgttctattcggttgttaccaggcgatacaatgctttcgcc Mask Tandem Repeat Region ================================================ ggcgaaagcattgtatcgcctggtaacaaccgaatagaacaggggctgtgctgaggataaaacctcgacacagcccctgcgctattcgggaaaactcgaaagaagtctttacgcttctacggctttcctctctccaagcttt Find is-nt database================================================ Query_seq: PG1754:PG1755|PG1754:PG1755:hypothetical protein:fructose-bisphosphate aldolase:-><-:1842345..1842486 142 ggcgaaagcattgtatcgcctggtaacaaccgaatagaacaggggctgtgctgaggataaaacctcgacacagcccctgcgctattcgggaaaactcgaaagaagtctttacgcttctacggctttcctctctccaagcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1754:PG1755|PG1754:PG1755:hypothetical protein:fructose-bisphosphate aldolase:-><-:1842345..1842486 142 ggcgaaagcattgtatcgcctggtaacaaccgaatagaacaggggctgtgctgaggataaaacctcgacacagcccctgcgctattcgggaaaactcgaaagaagtctttacgcttctacggctttcctctctccaagcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1754:PG1755|PG1754:PG1755:hypothetical protein:fructose-bisphosphate aldolase:-><-:1842345..1842486 142 ggcgaaagcattgtatcgcctggtaacaaccgaatagaacaggggctgtgctgaggataaaacctcgacacagcccctgcgctattcgggaaaactcgaaagaagtctttacgcttctacggctttcctctctccaagcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggcgaaagcattgtatcgcctggtaacaaccgaatagaacaggggctgtgctgaggataaaacctcgacacagcccctgcgctattcgggaaaactcgaaagaagtctttacgcttctacggctttcctctctccaagcttt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 48 End: 140 ............................................... M L R I K P R H S P C A I R E N S K E V F T L L R L S S L Q A .. ggcgaaagcattgtatcgcctggtaacaaccgaatagaacaggggctgtgctgaggataaaacctcgacacagcccctgcgctattcgggaaaactcgaaagaagtctttacgcttctacggctttcctctctccaagcttt 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================================================ ggcgaaagcattgtatcgcctggtaacaaccgaatagaacaggggctgtgctgaggataaaacctcgacacagcccctgcgctattcgggaaaactcgaaagaagtctttacgcttctacggctttcctctctccaagcttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -25.8 Tail_Score: -2.76696 Start: 31 End: 88 Full_Region: tctttcgagttttcc cgaatagcgcaggggctgtgtcgagg ttttat cctcagcacagcccctgttctattcg gttgttaccaggcga ..............................cgaatagcgcaggggctgtgtcgaggttttatcctcagcacagcccctgttctattcg...................................................... TransTerm Strand: - Conf: 100 HP_score: -20.1 Tail_Score: -3.73359 Start: 40 End: 79 Full_Region: ttttcccgaatagcg caggggctgtgtcgagg ttttat cctcagcacagcccctg ttctattcggttgtt .......................................caggggctgtgtcgaggttttatcctcagcacagcccctg............................................................... Find igs database================================================ Query_seq: PG1754:PG1755|PG1754:PG1755:hypothetical protein:fructose-bisphosphate aldolase:-><-:1842345..1842486 142 ggcgaaagcattgtatcgcctggtaacaaccgaatagaacaggggctgtgctgaggataaaacctcgacacagcccctgcgctattcgggaaaactcgaaagaagtctttacgcttctacggctttcctctctccaagcttt Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: NC_002950_PG1754_PG1755|hypothetical protein:fructose-bisphosphate aldolase|POSITIVE:NEGATIVE|[1842345,1842486]|142 HSP 1 e-value: 3.0E-75 bit: 281.0 Len: 142 Query Start:1 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 142 ggcgaaagcattgtatcgcctggtaacaaccgaatagaacaggggctgtgctgaggataaaacctcgacacagcccctgcgctattcgggaaaactcgaaagaagtctttacgcttctacggctttcctctctccaagcttt ggcgaaagcattgtatcgcctggtaacaaccgaatagaacaggggctgtgctgaggataaaacctcgacacagcccctgcgctattcgggaaaactcgaaagaagtctttacgcttctacggctttcctctctccaagcttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCGAAAGCAUUGUAUCGCCUGGUAACAACCGAAUAGAACAGGGGCUGUGCUGAGGAUAAAACCUCGACACAGCCCCUGCGCUAUUCGGGAAAACUCGAAAGAAGUCUUUACGCUUCUACGGCUUUCCUCUCUCCAAGCUUU .((....))........((.(((.......(((((((..(((((((((((.(((((......))))).)))))))))))..)))))))(((((.(.((..((((((......)))))).))).))))).....))).))... (-61.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGCUUGGAGAGAGGAAAGCCGUAGAAGCGUAAAGACUUCUUUCGAGUUUUCCCGAAUAGCGCAGGGGCUGUGUCGAGGUUUUAUCCUCAGCACAGCCCCUGUUCUAUUCGGUUGUUACCAGGCGAUACAAUGCUUUCGCC ...((((((.....(((((((((.((((((.....).)))))..)).)))))))(((((((.(((((((((((((.((((......)))).))))))))))))).))))))).......))))))................. (-69.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 489 89 41 193 135 NC_002950:PG0480|5end_precorrin-2_C20-methyltransferase,_putative_521319..521549_NEGATIVE 468 90 41 177 114 NC_002950:PG1759|5end_adhesion_protein,_putative_1845570..1845800_POSITIVE 445 77 31 215 166 NC_002950:PG1739|5end_hypothetical_protein_1825709..1825939_NEGATIVE 404 86 41 181 129 NC_002950:PG0757|5end_hypothetical_protein_806370..806600_NEGATIVE 397 80 31 227 181 NC_002950:PG0749|5end_hypothetical_protein_795654..795884_NEGATIVE 387 49 2 130 72 NC_002950:PG1840|5end_hypothetical_protein_1937102..1937332_POSITIVE 386 89 42 202 159 NC_002950:PG1952|5end_DedA_family_protein_2042870..2043100_POSITIVE 386 75 31 210 154 NC_002950:PG0898|5end_hypothetical_protein_963350..963580_NEGATIVE 376 83 44 226 185 NC_002950:PG2029|5end_hypothetical_protein_2126543..2126773_POSITIVE 373 89 41 194 142 NC_002950:PG1418|5end_DNA_polymerase_III,_gamma_and_tau_subunits_1503064..1503294_POSITIVE 369 75 31 97 57 NC_002950:PG1423|5end_hypothetical_protein_1509088..1509318_NEGATIVE 369 90 44 201 154 NC_002950:PG0519|5end_hypothetical_protein_562889..563119_POSITIVE 368 88 43 54 7 NC_002950:PG1094|5end_phosphomannomutase_1158753..1158983_POSITIVE 353 79 31 78 21 NC_002950:PG0309|5end_thiamine_biosynthesis_lipoprotein_ApbE_345023..345253_NEGATIVE 353 108 66 172 124 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 352 106 61 64 5 NC_002950:PG0671|5end_iron_compound_ABC_transporter,_permease_protein_721888..722118_POSITIVE 347 110 63 81 36 NC_002950:PG0004|5end_NAD-dependent_deacetylase_2968..3198_POSITIVE 345 69 26 219 168 NC_002950:PG0312|5end_hypothetical_protein_347048..347278_NEGATIVE 342 48 1 217 172 NC_002950:PG2064|5end_hypothetical_protein_2160550..2160780_POSITIVE 342 90 41 154 109 NC_002950:PG1173|5end_YkgG_family_protein_1252435..1252665_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 636 89 41 61 13 NC_002950:PG1754|3end_hypothetical_protein_1842284..1842434_POSITIVE 503 76 41 67 33 NC_002950:PG0506|3end_arginine-specific_cysteine_proteinase_547625..547775_POSITIVE 489 89 41 80 22 NC_002950:PG0481|3end_2-amino-3-ketobutyrate_coenzyme_A_ligase_521432..521582_NEGATIVE 487 79 32 51 2 NC_002950:PG2124|3end_glyceraldehyde_3-phosphate_dehydrogenase,_type_I_2231264..2231414_POSITIVE 471 90 41 90 27 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 440 90 44 61 1 NC_002950:PG1758|3end_ribosomal_protein_S15_1845534..1845684_POSITIVE 437 89 41 52 6 NC_002950:PG1950|3end_hypothetical_protein_2040840..2040990_POSITIVE 432 90 41 78 23 NC_002950:PG1847|3end_endoribonuclease_L-PSP,_putative_1946227..1946377_NEGATIVE 426 77 31 65 12 NC_002950:PG0726|3end_lipoprotein,_putative_778003..778153_NEGATIVE 424 78 41 40 6 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 420 78 31 62 18 NC_002950:PG0034|3end_thioredoxin_42235..42385_NEGATIVE 413 75 32 61 7 NC_002950:PG0548|3end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_605759..605909_POSITIVE 404 86 41 84 32 NC_002950:PG0758|3end_peptidyl-dipeptidase_Dcp_806467..806617_NEGATIVE 394 79 35 59 10 NC_002950:PG2010|3end_phosphomannomutase,_putative_2100952..2101102_POSITIVE 386 75 31 63 7 NC_002950:PG0899|3end_cytochrome_d_ubiquinol_oxidase,_subunit_II_963497..963647_NEGATIVE 379 79 40 57 18 NC_002950:PG0395|3end_DNA-directed_RNA_polymerase_beta'_subunit_433305..433455_POSITIVE 375 79 31 71 19 NC_002950:PG0159|3end_endopeptidase_PepO_181095..181245_NEGATIVE 373 89 41 71 19 NC_002950:PG1417|3end_fumarate_hydratase_class_I,_anaerobic_1503021..1503171_POSITIVE 373 90 41 52 1 NC_002950:PG0906|3end_lipoprotein,_putative_971148..971298_POSITIVE 373 90 41 54 8 NC_002950:PG0619|3end_alkyl_hydroperoxide_reductase,_F_subunit_672731..672881_POSITIVE