Origin IGS: aacgcttccttgctctttctccctcgcggaggaggcctttcctttcagaggatatactgtccaataattagacgccgatgtctaattattggacagctcctttttaggggtaatggtgtaaagtgtttgtttacagtgctgtatggagtttggcacggcatttgagactattcttgtatagaaaacatcatatcggaataat .........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 attattccgatatgatgttttctatacaagaatagtctcaaatgccgtgccaaactccatacagcactgtaaacaaacactttacaccattacccctaaaaaggagctgtccaataattagacatcggcgtctaattattggacagtatatcctctgaaaggaaaggcctcctccgcgagggagaaagagcaaggaagcgtt Mask Tandem Repeat Region ================================================ aacgcttccttgctctttctccctcgcggaggaggcctttcctttcagaggatatactgtccaataattagacgccgatgtctaattattggacagctcctttttaggggtaatggtgtaaagtgtttgtttacagtgctgtatggagtttggcacggcatttgagactattcttgtatagaaaacatcatatcggaataat Find is-nt database================================================ Query_seq: PG0678:PG0679|PG0678:PG0679:pyrazinamidase/nicotinamidase, putative:outer membrane efflux protein:->->:729532..729733 202 aacgcttccttgctctttctccctcgcggaggaggcctttcctttcagaggatatactgtccaataattagacgccgatgtctaattattggacagctcctttttaggggtaatggtgtaaagtgtttgtttacagtgctgtatggagtttggcacggcatttgagactattcttgtatagaaaacatcatatcggaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0678:PG0679|PG0678:PG0679:pyrazinamidase/nicotinamidase, putative:outer membrane efflux protein:->->:729532..729733 202 aacgcttccttgctctttctccctcgcggaggaggcctttcctttcagaggatatactgtccaataattagacgccgatgtctaattattggacagctcctttttaggggtaatggtgtaaagtgtttgtttacagtgctgtatggagtttggcacggcatttgagactattcttgtatagaaaacatcatatcggaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0678:PG0679|PG0678:PG0679:pyrazinamidase/nicotinamidase, putative:outer membrane efflux protein:->->:729532..729733 202 aacgcttccttgctctttctccctcgcggaggaggcctttcctttcagaggatatactgtccaataattagacgccgatgtctaattattggacagctcctttttaggggtaatggtgtaaagtgtttgtttacagtgctgtatggagtttggcacggcatttgagactattcttgtatagaaaacatcatatcggaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacgcttccttgctctttctccctcgcggaggaggcctttcctttcagaggatatactgtccaataattagacgccgatgtctaattattggacagctcctttttaggggtaatggtgtaaagtgtttgtttacagtgctgtatggagtttggcacggcatttgagactattcttgtatagaaaacatcatatcggaataat Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 10 End: 162 ......... M L F L P R G G G L S F Q R I Y C P I I R R R C L I I G Q L L F R G N G V K C L F T V L Y G V W H G I ........................................ Protein_Len: 38 Strand: - Start: 48 End: 161 ............................................... L I Y Q G I I L R R H R I I P C S R K L P L P T F H K N V T S Y P T Q C P M ......................................... aacgcttccttgctctttctccctcgcggaggaggcctttcctttcagaggatatactgtccaataattagacgccgatgtctaattattggacagctcctttttaggggtaatggtgtaaagtgtttgtttacagtgctgtatggagtttggcacggcatttgagactattcttgtatagaaaacatcatatcggaataat 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================================================ PromScan Matrix: RpoN Strand: + Score: 85 Start: 150 End: 166 .....................................................................................................................................................TTGGCACGGCATTTGAG.................................... aacgcttccttgctctttctccctcgcggaggaggcctttcctttcagaggatatactgtccaataattagacgccgatgtctaattattggacagctcctttttaggggtaatggtgtaaagtgtttgtttacagtgctgtatggagtttggcacggcatttgagactattcttgtatagaaaacatcatatcggaataat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 89 HP_score: -8.3 Tail_Score: -4.60487 Start: 54 End: 100 Full_Region: TTCCTTTCAGAGGAT ATACTGTCCAATAATTAGACG CCGA TGTCTAATTATTGGACAGCTCC TTTTTAGGGGTAATG .....................................................ATACTGTCCAATAATTAGACGCCGATGTCTAATTATTGGACAGCTCC...................................................................................................... TransTerm Strand: + Conf: 85 HP_score: -11.8 Tail_Score: -3.3581 Start: 55 End: 99 Full_Region: TCCTTTCAGAGGATA TACTGTCCAATAATTAGACG CCGA TGTCTAATTATTGGACAGCTC CTTTTTAGGGGTAAT ......................................................TACTGTCCAATAATTAGACGCCGATGTCTAATTATTGGACAGCTC....................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -16.9 Tail_Score: -3.24422 Start: 56 End: 97 Full_Region: CCTTTCAGAGGATAT ACTGTCCAATAATTAGACG CCGA TGTCTAATTATTGGACAGC TCCTTTTTAGGGGTA .......................................................ACTGTCCAATAATTAGACGCCGATGTCTAATTATTGGACAGC......................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -20.4 Tail_Score: -2.54171 Start: 57 End: 96 Full_Region: CTTTCAGAGGATATA CTGTCCAATAATTAGACG CCGA TGTCTAATTATTGGACAG CTCCTTTTTAGGGGT ........................................................CTGTCCAATAATTAGACGCCGATGTCTAATTATTGGACAG.......................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -19.7 Tail_Score: -2.97747 Start: 57 End: 96 Full_Region: acccctaaaaaggag ctgtccaataattagac atcggc gtctaattattggacag tatatcctctgaaag ........................................................ctgtccaataattagacatcggcgtctaattattggacag.......................................................................................................... TransTerm Strand: - Conf: 53 HP_score: -4.2 Tail_Score: -3.63073 Start: 68 End: 85 Full_Region: ggagctgtccaataa ttagac atcggc gtctaa ttattggacagtata ...................................................................ttagacatcggcgtctaa..................................................................................................................... Find igs database================================================ Query_seq: PG0678:PG0679|PG0678:PG0679:pyrazinamidase/nicotinamidase, putative:outer membrane efflux protein:->->:729532..729733 202 aacgcttccttgctctttctccctcgcggaggaggcctttcctttcagaggatatactgtccaataattagacgccgatgtctaattattggacagctcctttttaggggtaatggtgtaaagtgtttgtttacagtgctgtatggagtttggcacggcatttgagactattcttgtatagaaaacatcatatcggaataat Intra-Species Hit: Count: 1 Min: 1 Max: 202 Len: 202 Subject: NC_002950_PG0678_PG0679|pyrazinamidase/nicotinamidase, putative:outer membrane efflux protein|POSITIVE:POSITIVE|[729532,729733]|202 HSP 1 e-value: 1.0E-111 bit: 400.0 Len: 202 Query Start:1 Query End:202 Subject Strand: POSITIVE Subject Start: 1 Subject End: 202 aacgcttccttgctctttctccctcgcggaggaggcctttcctttcagaggatatactgtccaataattagacgccgatgtctaattattggacagctcctttttaggggtaatggtgtaaagtgtttgtttacagtgctgtatggagtttggcacggcatttgagactattcttgtatagaaaacatcatatcggaataat aacgcttccttgctctttctccctcgcggaggaggcctttcctttcagaggatatactgtccaataattagacgccgatgtctaattattggacagctcctttttaggggtaatggtgtaaagtgtttgtttacagtgctgtatggagtttggcacggcatttgagactattcttgtatagaaaacatcatatcggaataat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACGCUUCCUUGCUCUUUCUCCCUCGCGGAGGAGGCCUUUCCUUUCAGAGGAUAUACUGUCCAAUAAUUAGACGCCGAUGUCUAAUUAUUGGACAGCUCCUUUUUAGGGGUAAUGGUGUAAAGUGUUUGUUUACAGUGCUGUAUGGAGUUUGGCACGGCAUUUGAGACUAUUCUUGUAUAGAAAACAUCAUAUCGGAAUAAU (((((((...(((.((....(((..(..((((((.....(((((...)))))....((((((((((((((((((....))))))))))))))))))))))))..)..)))....)).)))))))))).((((..((((((((............))))))))..))))((((((.((((.((.....)))))).)))))).. (-66.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUUCCGAUAUGAUGUUUUCUAUACAAGAAUAGUCUCAAAUGCCGUGCCAAACUCCAUACAGCACUGUAAACAAACACUUUACACCAUUACCCCUAAAAAGGAGCUGUCCAAUAAUUAGACAUCGGCGUCUAAUUAUUGGACAGUAUAUCCUCUGAAAGGAAAGGCCUCCUCCGCGAGGGAGAAAGAGCAAGGAAGCGUU ....((((.....(((...((((.....))))..))).....((((..(((....(((...(((...((((((.......))))))...............((((((((((((((((((((((......))))))))))))))))))...)))))))...)))..))).((..((....))..))..).))).))))..... (-56.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 456 41 3 206 164 NC_002950:PG2075|5end_hypothetical_protein_2176466..2176696_NEGATIVE 427 47 3 127 68 NC_002950:PG0158|5end_competence_protein_F-related_protein_180175..180405_POSITIVE 395 42 3 163 111 NC_002950:PG1672|5end_hypothetical_protein_1757637..1757867_POSITIVE 395 42 3 163 111 NC_002950:PG0100|5end_hypothetical_protein_119219..119449_NEGATIVE 387 46 18 34 1 NC_002950:PG0790|5end_GTP-binding_protein_Obg_842583..842813_NEGATIVE 363 58 11 47 1 NC_002950:PG0132|5end_hypothetical_protein_152879..153109_POSITIVE 359 46 3 222 176 NC_002950:PG1948|5end_lipoprotein,_putative_2036439..2036669_POSITIVE 356 50 2 65 9 NC_002950:PG1859|5end_glycerate_kinase_family_protein_1958334..1958564_NEGATIVE 353 35 3 199 161 NC_002950:PG0594|5end_RNA_polymerase_sigma-70_factor_652048..652278_POSITIVE 343 45 4 59 26 NC_002950:PG0574|5end_hypothetical_protein_629018..629248_POSITIVE 340 42 3 163 111 NC_002950:PG2076|5end_hypothetical_protein_2176445..2176675_POSITIVE 340 42 3 163 111 NC_002950:PG1267|5end_hypothetical_protein_1346966..1347196_POSITIVE 338 50 3 65 7 NC_002950:PG1861|5end_hypothetical_protein_1960057..1960287_NEGATIVE 331 120 73 74 28 NC_002950:PG0885|5end_phospho-2-dehydro-3-deoxyheptonate_aldolase/chorismate_mutase_947745..947975_POSITIVE 331 50 3 197 138 NC_002950:PG0339|5end_hypothetical_protein_375062..375292_POSITIVE 330 45 2 211 173 NC_002950:PG2035|5end_tRNA_(guanine-N(1)-)-methyltransferase_2135852..2136082_POSITIVE 328 49 3 227 188 NC_002950:PG0703|5end_cobalamin_(5'-phosphate)_synthase,_putative_758144..758374_POSITIVE 326 50 3 58 10 NC_002950:PG2188|5end_diaminopimelate_decarboxylase_2295781..2296011_NEGATIVE 324 50 3 229 177 NC_002950:PG2149|5end_hypothetical_protein_2257658..2257888_NEGATIVE 323 45 3 194 142 NC_002950:PG0140|5end_hypothetical_protein_163858..164088_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 427 47 3 143 84 NC_002950:PG0157|3end_regulatory_protein_RecX_180271..180421_POSITIVE 409 109 63 50 1 NC_002950:PG0678|3end_pyrazinamidase/nicotinamidase,_putative_729471..729621_POSITIVE 397 50 1 101 28 NC_002950:PG0172|3end_exonuclease_194355..194505_POSITIVE 363 58 11 142 96 NC_002950:PG0132|3end_hypothetical_protein_153054..153204_POSITIVE 361 59 12 85 26 NC_002950:PG1285|3end_glucosamine-6-phosphate_deaminase_1364941..1365091_POSITIVE 360 52 11 151 108 NC_002950:PG1795|3end_hypothetical_protein_1888955..1889105_NEGATIVE 357 50 3 151 108 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE 343 45 4 59 26 NC_002950:PG0573|3end_S-adenosyl-methyltransferase_MraW_629098..629248_POSITIVE 339 42 3 123 78 NC_002950:PG1942|3end_30S_ribosomal_protein_S12_2027946..2028096_NEGATIVE 335 50 4 140 75 NC_002950:PG0674|3end_indolepyruvate_ferredoxin_oxidoreductase,_beta_subunit_724209..724359_NEGATIVE 334 40 4 52 11 NC_002950:PG1286|3end_ferritin_1365019..1365169_NEGATIVE 333 50 3 52 6 NC_002950:PG1862|3end_hypothetical_protein_1960070..1960220_NEGATIVE 333 37 4 79 41 NC_002950:PG0046|3end_phosphatidate_cytidylyltransferase_56346..56496_NEGATIVE 331 120 73 58 12 NC_002950:PG0884|3end_hypothetical_protein_947809..947959_POSITIVE 330 45 4 89 49 NC_002950:PG2126|3end_conserved_hypothetical_protein_TIGR00044_2232438..2232588_NEGATIVE 330 159 120 131 85 NC_002950:PG0656|3end_50S_ribosomal_protein_L34_706945..707095_NEGATIVE 328 50 2 115 64 NC_002950:PG0753|3end_protease_800288..800438_POSITIVE 324 33 3 142 97 NC_002950:PG1794|3end_DNA_polymerase_type_I_1888838..1888988_POSITIVE 324 49 2 65 20 NC_002950:PG1676|3end_phosphoenolpyruvate_carboxykinase_1760489..1760639_NEGATIVE 322 50 2 149 97 NC_002950:PG0841|3end_mobilizable_transposon,_excision_protein,_putative_902781..902931_NEGATIVE