Origin IGS: tacatgctacaataattggggataagcctttcgattcgggattcggtgccgtcgaagggctttttcttttcagtcttccgtaataactacaatcacacactc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gagtgtgtgattgtagttattacggaagactgaaaagaaaaagcccttcgacggcaccgaatcccgaatcgaaaggcttatccccaattattgtagcatgta Mask Tandem Repeat Region ================================================ tacatgctacaataattggggataagcctttcgattcgggattcggtgccgtcgaagggctttttcttttcagtcttccgtaataactacaatcacacactc Find is-nt database================================================ Query_seq: PG1835:PG1836|PG1835:PG1836:lipoprotein, putative:nucleoside permease NupG:->->:1928581..1928682 102 tacatgctacaataattggggataagcctttcgattcgggattcggtgccgtcgaagggctttttcttttcagtcttccgtaataactacaatcacacactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1835:PG1836|PG1835:PG1836:lipoprotein, putative:nucleoside permease NupG:->->:1928581..1928682 102 tacatgctacaataattggggataagcctttcgattcgggattcggtgccgtcgaagggctttttcttttcagtcttccgtaataactacaatcacacactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1835:PG1836|PG1835:PG1836:lipoprotein, putative:nucleoside permease NupG:->->:1928581..1928682 102 tacatgctacaataattggggataagcctttcgattcgggattcggtgccgtcgaagggctttttcttttcagtcttccgtaataactacaatcacacactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tacatgctacaataattggggataagcctttcgattcgggattcggtgccgtcgaagggctttttcttttcagtcttccgtaataactacaatcacacactc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 2 End: 100 . C A V I I P S L G K S E P N P A T S P S K R K L R G Y Y S C D C M .. tacatgctacaataattggggataagcctttcgattcgggattcggtgccgtcgaagggctttttcttttcagtcttccgtaataactacaatcacacactc 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================================================ tacatgctacaataattggggataagcctttcgattcgggattcggtgccgtcgaagggctttttcttttcagtcttccgtaataactacaatcacacactc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 86 HP_score: -3.3 Tail_Score: -5.48213 Start: 48 End: 60 Full_Region: GATTCGGGATTCGGT GCCGT CGA AGGGC TTTTTCTTTTCAGTC ...............................................GCCGTCGAAGGGC.......................................... Find igs database================================================ Query_seq: PG1835:PG1836|PG1835:PG1836:lipoprotein, putative:nucleoside permease NupG:->->:1928581..1928682 102 tacatgctacaataattggggataagcctttcgattcgggattcggtgccgtcgaagggctttttcttttcagtcttccgtaataactacaatcacacactc Intra-Species Hit: Count: 1 Min: 1 Max: 102 Len: 102 Subject: NC_002950_PG1835_PG1836|lipoprotein, putative:nucleoside permease NupG|POSITIVE:POSITIVE|[1928581,1928682]|102 HSP 1 e-value: 2.0E-51 bit: 202.0 Len: 102 Query Start:1 Query End:102 Subject Strand: POSITIVE Subject Start: 1 Subject End: 102 tacatgctacaataattggggataagcctttcgattcgggattcggtgccgtcgaagggctttttcttttcagtcttccgtaataactacaatcacacactc tacatgctacaataattggggataagcctttcgattcgggattcggtgccgtcgaagggctttttcttttcagtcttccgtaataactacaatcacacactc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACAUGCUACAAUAAUUGGGGAUAAGCCUUUCGAUUCGGGAUUCGGUGCCGUCGAAGGGCUUUUUCUUUUCAGUCUUCCGUAAUAACUACAAUCACACACUC .......(((....((((..((.(((((((((((..(((.((...)).))))))))))))))....))..)))).....))).................... (-24.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGUGUGUGAUUGUAGUUAUUACGGAAGACUGAAAAGAAAAAGCCCUUCGACGGCACCGAAUCCCGAAUCGAAAGGCUUAUCCCCAAUUAUUGUAGCAUGUA ..(..(((....((((((.....(((...((....))...(((((.((((((((.........)))..))))).))))).)))..))))))....)))..). (-22.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 451 69 27 55 17 NC_002950:PG0984|5end_hypothetical_protein_1046919..1047149_NEGATIVE 413 80 36 172 121 NC_002950:PG0899|5end_cytochrome_d_ubiquinol_oxidase,_subunit_II_964660..964890_NEGATIVE 378 60 26 37 3 NC_002950:PG1902|5end_uridylate_kinase_2002147..2002377_NEGATIVE 369 81 42 70 24 NC_002950:PG0881|5end_recombinase_A_943063..943293_POSITIVE 366 79 36 172 116 NC_002950:PG1522|5end_mandelate_racemase/muconate_lactonizing_enzyme_family_protein_1600170..1600400_NEGATIVE 362 80 31 127 75 NC_002950:PG1053|5end_transcriptional_regulator,_putative_1120065..1120295_POSITIVE 359 59 15 221 184 NC_002950:PG1825|5end_hypothetical_protein_1919671..1919901_NEGATIVE 358 65 28 36 4 NC_002950:PG1888|5end_hypothetical_protein_1985596..1985826_POSITIVE 357 68 24 172 126 NC_002950:PG0509|5end_hypothetical_protein_549588..549818_NEGATIVE 356 59 18 194 137 NC_002950:PG0332|5end_transcription_termination_factor_Rho_365619..365849_POSITIVE 355 60 17 101 44 NC_002950:PG1311|5end_hypothetical_protein_1389709..1389939_POSITIVE 355 79 32 89 34 NC_002950:PG0780|5end_hypothetical_protein_833203..833433_NEGATIVE 351 66 21 198 145 NC_002950:PG1352|5end_hypothetical_protein_1433150..1433380_NEGATIVE 347 60 17 192 138 NC_002950:PG1899|5end_TonB-dependent_receptor,_putative_1999724..1999954_NEGATIVE 341 51 19 66 22 NC_002950:PG1783|5end_glycosyl_transferase,_group_2_family_protein_1871868..1872098_POSITIVE 341 60 18 73 23 NC_002950:PG0508|5end_HAD-superfamily_subfamily_IB_hydrolase,_TIGR01490_548738..548968_NEGATIVE 339 59 15 136 90 NC_002950:PG0897|5end_alpha-amylase_family_protein_962472..962702_NEGATIVE 338 67 25 217 178 NC_002950:PG1587|5end_PAP2_superfamily_protein_1664983..1665213_POSITIVE 336 60 18 168 119 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 335 66 26 186 145 NC_002950:PG2199|5end_ABC_transporter,_ATP-binding_protein,_putative_2306723..2306953_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 413 80 36 126 75 NC_002950:PG0900|3end_cytochrome_d_ubiquinol_oxidase,_subunit_I_964706..964856_NEGATIVE 400 58 13 143 92 NC_002950:PG0369|3end_phosphopantetheine_adenylyltransferase_403751..403901_POSITIVE 392 66 24 72 29 NC_002950:PG1835|3end_lipoprotein,_putative_1928520..1928670_POSITIVE 371 60 18 76 32 NC_002950:PG0173|3end_transcriptional_regulator,_putative_194388..194538_NEGATIVE 369 81 42 49 3 NC_002950:PG0880|3end_bacterioferritin_comigratory_protein_943122..943272_POSITIVE 362 80 31 108 56 NC_002950:PG1052|3end_transcriptional_regulator,_putative_1120126..1120276_POSITIVE 360 60 18 127 80 NC_002950:PG0030|3end_cytidine_deaminase_36402..36552_POSITIVE 358 65 28 39 7 NC_002950:PG1887|3end_rhodanese-like_domain_protein_1985679..1985829_POSITIVE 355 60 17 138 81 NC_002950:PG1310|3end_exsB_protein_1389826..1389976_POSITIVE 351 66 21 147 94 NC_002950:PG1353|3end_orotate_phosphoribosyltransferase_1433201..1433351_NEGATIVE 347 60 17 117 63 NC_002950:PG1900|3end_ribosome-associated_GTPase_1999799..1999949_NEGATIVE 344 60 20 116 74 NC_002950:PG2031|3end_hypothetical_protein_2130871..2131021_POSITIVE 341 51 19 79 35 NC_002950:PG1782|3end_hypothetical_protein_1871961..1872111_POSITIVE 341 60 18 83 33 NC_002950:PG0509|3end_hypothetical_protein_548728..548878_NEGATIVE 339 60 18 150 94 NC_002950:PG0969|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase,_putative_1028201..1028351_NEGATIVE 339 59 15 49 3 NC_002950:PG0898|3end_hypothetical_protein_962559..962709_NEGATIVE 335 57 16 135 73 NC_002950:PG1409|3end_hypothetical_protein_1492873..1493023_NEGATIVE 334 60 17 147 103 NC_002950:PG0510|3end_hypothetical_protein_549605..549755_NEGATIVE 332 80 37 45 7 NC_002950:PG1213|3end_ribonuclease_H_1293163..1293313_POSITIVE 331 59 19 81 27 NC_002950:PG0585|3end_YqeY_family_protein_643801..643951_POSITIVE