Origin IGS: tgatcgagaatacctttagcggaatagtcataaaagagaatttagagataggaaactgcatcgaatccatttgccggtcgcgacggcaaacatccgagactgtttagtaccgataccggtagtataacgtacgagagcatggctccggctcttcccattccggagcaaaacccattccctctt .........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 aagagggaatgggttttgctccggaatgggaagagccggagccatgctctcgtacgttatactaccggtatcggtactaaacagtctcggatgtttgccgtcgcgaccggcaaatggattcgatgcagtttcctatctctaaattctcttttatgactattccgctaaaggtattctcgatca Mask Tandem Repeat Region ================================================ tgatcgagaatacctttagcggaatagtcataaaagagaatttagagataggaaactgcatcgaatccatttgccggtcgcgacggcaaacatccgagactgtttagtaccgataccggtagtataacgtacgagagcatggctccggctcttcccattccggagcaaaacccattccctctt Find is-nt database================================================ Query_seq: PG2125:PG2126|PG2125:PG2126:transcriptional regulator, AraC family:conserved hypothetical protein TIGR00044:<-<-:2232345..2232527 183 tgatcgagaatacctttagcggaatagtcataaaagagaatttagagataggaaactgcatcgaatccatttgccggtcgcgacggcaaacatccgagactgtttagtaccgataccggtagtataacgtacgagagcatggctccggctcttcccattccggagcaaaacccattccctctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2125:PG2126|PG2125:PG2126:transcriptional regulator, AraC family:conserved hypothetical protein TIGR00044:<-<-:2232345..2232527 183 tgatcgagaatacctttagcggaatagtcataaaagagaatttagagataggaaactgcatcgaatccatttgccggtcgcgacggcaaacatccgagactgtttagtaccgataccggtagtataacgtacgagagcatggctccggctcttcccattccggagcaaaacccattccctctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2125:PG2126|PG2125:PG2126:transcriptional regulator, AraC family:conserved hypothetical protein TIGR00044:<-<-:2232345..2232527 183 tgatcgagaatacctttagcggaatagtcataaaagagaatttagagataggaaactgcatcgaatccatttgccggtcgcgacggcaaacatccgagactgtttagtaccgataccggtagtataacgtacgagagcatggctccggctcttcccattccggagcaaaacccattccctctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatcgagaatacctttagcggaatagtcataaaagagaatttagagataggaaactgcatcgaatccatttgccggtcgcgacggcaaacatccgagactgtttagtaccgataccggtagtataacgtacgagagcatggctccggctcttcccattccggagcaaaacccattccctctt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 3 End: 104 .. M E N T F S G I V I K E N L E I G N C I E S I C R S R R Q T S E T V ............................................................................... Protein_Len: 38 Strand: - Start: 45 End: 158 ............................................ L Y S V A D F G N A P R S P L C G L S N L V S V P L I V Y S L M A G A R G M ......................... Protein_Len: 46 Strand: - Start: 31 End: 168 .............................. L L S N L S L F S C R I W K G T A V A F M R S Q K T G I G T T Y R V L A H S R S K G N R L M ............... tgatcgagaatacctttagcggaatagtcataaaagagaatttagagataggaaactgcatcgaatccatttgccggtcgcgacggcaaacatccgagactgtttagtaccgataccggtagtataacgtacgagagcatggctccggctcttcccattccggagcaaaacccattccctctt 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================================================ tgatcgagaatacctttagcggaatagtcataaaagagaatttagagataggaaactgcatcgaatccatttgccggtcgcgacggcaaacatccgagactgtttagtaccgataccggtagtataacgtacgagagcatggctccggctcttcccattccggagcaaaacccattccctctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG2125:PG2126|PG2125:PG2126:transcriptional regulator, AraC family:conserved hypothetical protein TIGR00044:<-<-:2232345..2232527 183 tgatcgagaatacctttagcggaatagtcataaaagagaatttagagataggaaactgcatcgaatccatttgccggtcgcgacggcaaacatccgagactgtttagtaccgataccggtagtataacgtacgagagcatggctccggctcttcccattccggagcaaaacccattccctctt Intra-Species Hit: Count: 1 Min: 1 Max: 183 Len: 183 Subject: NC_002950_PG2125_PG2126|transcriptional regulator, AraC family:conserved hypothetical protein TIGR00044|NEGATIVE:NEGATIVE|[2232345,2232527]|183 HSP 1 e-value: 1.0E-99 bit: 363.0 Len: 183 Query Start:1 Query End:183 Subject Strand: POSITIVE Subject Start: 1 Subject End: 183 tgatcgagaatacctttagcggaatagtcataaaagagaatttagagataggaaactgcatcgaatccatttgccggtcgcgacggcaaacatccgagactgtttagtaccgataccggtagtataacgtacgagagcatggctccggctcttcccattccggagcaaaacccattccctctt tgatcgagaatacctttagcggaatagtcataaaagagaatttagagataggaaactgcatcgaatccatttgccggtcgcgacggcaaacatccgagactgtttagtaccgataccggtagtataacgtacgagagcatggctccggctcttcccattccggagcaaaacccattccctctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUCGAGAAUACCUUUAGCGGAAUAGUCAUAAAAGAGAAUUUAGAGAUAGGAAACUGCAUCGAAUCCAUUUGCCGGUCGCGACGGCAAACAUCCGAGACUGUUUAGUACCGAUACCGGUAGUAUAACGUACGAGAGCAUGGCUCCGGCUCUUCCCAUUCCGGAGCAAAACCCAUUCCCUCUU .....(((.....((((.(((.(((((((...............((..(((....)))..)).......(((((((.......))))))).......)))))))((.(((((....))))).))...)))...))))....(((((((...........)))))))............))).. (-48.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAGGGAAUGGGUUUUGCUCCGGAAUGGGAAGAGCCGGAGCCAUGCUCUCGUACGUUAUACUACCGGUAUCGGUACUAAACAGUCUCGGAUGUUUGCCGUCGCGACCGGCAAAUGGAUUCGAUGCAGUUUCCUAUCUCUAAAUUCUCUUUUAUGACUAUUCCGCUAAAGGUAUUCUCGAUCA ((((((((((((((...(((((((..(....)...)))))))...))))......(((.((.(((((....))))).))))).((.((((((((((((((.......))))))))..)))))).))................))))))))))..((..((.((......)).))..))..... (-51.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1058 120 71 211 162 NC_002950:PG2125|5end_transcriptional_regulator,_AraC_family_2232254..2232484_NEGATIVE 465 180 132 108 62 NC_002950:PG0425|5end_esterase,_putative_463989..464219_NEGATIVE 405 166 127 164 120 NC_002950:PG0140|5end_hypothetical_protein_163858..164088_NEGATIVE 403 150 101 71 22 NC_002950:PG2054|5end_lipoprotein_PG3_2152014..2152244_NEGATIVE 402 118 73 193 152 NC_002950:PG1964|5end_bacterial_sugar_transferase_2052910..2053140_POSITIVE 386 179 137 201 156 NC_002950:PG0987|5end_hypothetical_protein_1048002..1048232_POSITIVE 382 165 127 43 11 NC_002950:PG0280|5end_ABC_transporter,_permease_protein,_putative_314625..314855_NEGATIVE 372 179 132 191 140 NC_002950:PG0888|5end_hypothetical_protein_949910..950140_POSITIVE 367 177 135 224 180 NC_002950:PG0703|5end_cobalamin_(5'-phosphate)_synthase,_putative_758144..758374_POSITIVE 365 104 61 165 113 NC_002950:PG2097|5end_ribose-phosphate_pyrophosphokinase_2206462..2206692_NEGATIVE 364 158 111 215 162 NC_002950:PG1253|5end_DNA_ligase,_NAD-dependent_1331606..1331836_NEGATIVE 363 98 56 124 86 NC_002950:PG1605|5end_aminopeptidase_C_1685179..1685409_POSITIVE 362 87 46 223 182 NC_002950:PG0946|5end_ABC_transporter,_ATP-binding_protein_1007396..1007626_NEGATIVE 359 177 132 206 155 NC_002950:PG2075|5end_hypothetical_protein_2176466..2176696_NEGATIVE 359 167 128 192 149 NC_002950:PG1479|5end_conjugative_transposon_protein_TraJ_1555234..1555464_NEGATIVE 358 118 72 221 172 NC_002950:PG1125|5end_hypothetical_protein_1201727..1201957_NEGATIVE 357 117 73 174 130 NC_002950:PG0744|5end_RNA_methyltransferase,_TrmH_family_791897..792127_NEGATIVE 353 169 121 53 5 NC_002950:PG0195|5end_rubrerythrin_232046..232276_POSITIVE 352 166 128 183 146 NC_002950:PG0259|5end_hypothetical_protein_292278..292508_POSITIVE 351 105 66 71 35 NC_002950:PG0094|5end_outer_membrane_efflux_protein,_putative_111193..111423_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 405 166 127 144 100 NC_002950:PG0141|3end_spoOJ_protein_163878..164028_NEGATIVE 375 150 105 146 107 NC_002950:PG1402|3end_AP_endonuclease_domain_protein_1485031..1485181_NEGATIVE 369 105 65 96 54 NC_002950:PG0132|3end_hypothetical_protein_153054..153204_POSITIVE 368 146 106 133 82 NC_002950:PG0902|3end_alpha-1,2-mannosidase_family_protein_966746..966896_NEGATIVE 357 117 73 89 45 NC_002950:PG0745|3end_lactoylglutathione_lyase,_putative_791982..792132_NEGATIVE 355 180 131 97 47 NC_002950:PG2214|3end_hypothetical_protein_2325301..2325451_NEGATIVE 349 87 43 61 11 NC_002950:PG0593|3end_htrA_protein_651938..652088_POSITIVE 348 120 71 106 63 NC_002950:PG0002|3end_hexapeptide_transferase_family_protein_1947..2097_POSITIVE 346 100 52 98 36 NC_002950:PG1948|3end_lipoprotein,_putative_2037940..2038090_POSITIVE 346 180 132 73 25 NC_002950:PG0603|3end_cytidylate_kinase_660345..660495_POSITIVE 344 118 74 80 40 NC_002950:PG0211|3end_cobalamin_biosynthesis_protein_CbiG/precorrin-4_C11-methyltransferase_245966..246116_NEGATIVE 343 177 138 145 101 NC_002950:PG1353|3end_orotate_phosphoribosyltransferase_1433201..1433351_NEGATIVE 341 100 58 55 15 NC_002950:PG0160|3end_hypothetical_protein_183183..183333_NEGATIVE 340 167 121 113 65 NC_002950:PG0333|3end_hypothetical_protein_368811..368961_POSITIVE 336 155 112 42 2 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 336 179 131 74 19 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 335 98 51 78 28 NC_002950:PG2140|3end_ribosomal_protein_L32_2246399..2246549_POSITIVE 334 87 43 72 18 NC_002950:PG1963|3end_Sua5/YciO/YrdC/YwlC_family_protein_2052993..2053143_POSITIVE 332 155 112 148 103 NC_002950:PG0057|3end_nicotinate_phosphoribosyltransferase_70999..71149_POSITIVE 330 118 72 130 82 NC_002950:PG0555|3end_DNA-binding_protein,_histone-like_family_611716..611866_NEGATIVE