Origin IGS: gaatcgttttcttttttccggtgcgagctttgttgctcgccgccttccgaagagcaaatgccatgccaaacaatcccctgccctcattatcagtcacttattcgattggccgaagtgtccactgtccgttttcggacagttcgggtgttcgtttccgaacagtcggacacttcgccatcggagaaaacttgcatattatcagccttttaagggtagcggcataaactttgctgtcggaaaggtgcaataaaaacgaaagaaag .........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 ctttctttcgtttttattgcacctttccgacagcaaagtttatgccgctacccttaaaaggctgataatatgcaagttttctccgatggcgaagtgtccgactgttcggaaacgaacacccgaactgtccgaaaacggacagtggacacttcggccaatcgaataagtgactgataatgagggcaggggattgtttggcatggcatttgctcttcggaaggcggcgagcaacaaagctcgcaccggaaaaaagaaaacgattc Mask Tandem Repeat Region ================================================ gaatcgttttcttttttccggtgcgagctttgttgctcgccgccttccgaagagcaaatgccatgccaaacaatcccctgccctcattatcagtcacttattcgattggccgaagtgtccactgtccgttttcggacagttcgggtgttcgtttccgaacagtcggacacttcgccatcggagaaaacttgcatattatcagccttttaagggtagcggcataaactttgctgtcggaaaggtgcaataaaaacgaaagaaag Find is-nt database================================================ Query_seq: PG0283:PG0285|PG0283:PG0285:efflux transporter, MFP component, RND family:hypothetical protein:<-->:318336..318598 263 gaatcgttttcttttttccggtgcgagctttgttgctcgccgccttccgaagagcaaatgccatgccaaacaatcccctgccctcattatcagtcacttattcgattggccgaagtgtccactgtccgttttcggacagttcgggtgttcgtttccgaacagtcggacacttcgccatcggagaaaacttgcatattatcagccttttaagggtagcggcataaactttgctgtcggaaaggtgcaataaaaacgaaagaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0283:PG0285|PG0283:PG0285:efflux transporter, MFP component, RND family:hypothetical protein:<-->:318336..318598 263 gaatcgttttcttttttccggtgcgagctttgttgctcgccgccttccgaagagcaaatgccatgccaaacaatcccctgccctcattatcagtcacttattcgattggccgaagtgtccactgtccgttttcggacagttcgggtgttcgtttccgaacagtcggacacttcgccatcggagaaaacttgcatattatcagccttttaagggtagcggcataaactttgctgtcggaaaggtgcaataaaaacgaaagaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0283:PG0285|PG0283:PG0285:efflux transporter, MFP component, RND family:hypothetical protein:<-->:318336..318598 263 gaatcgttttcttttttccggtgcgagctttgttgctcgccgccttccgaagagcaaatgccatgccaaacaatcccctgccctcattatcagtcacttattcgattggccgaagtgtccactgtccgttttcggacagttcgggtgttcgtttccgaacagtcggacacttcgccatcggagaaaacttgcatattatcagccttttaagggtagcggcataaactttgctgtcggaaaggtgcaataaaaacgaaagaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaatcgttttcttttttccggtgcgagctttgttgctcgccgccttccgaagagcaaatgccatgccaaacaatcccctgccctcattatcagtcacttattcgattggccgaagtgtccactgtccgttttcggacagttcgggtgttcgtttccgaacagtcggacacttcgccatcggagaaaacttgcatattatcagccttttaagggtagcggcataaactttgctgtcggaaaggtgcaataaaaacgaaagaaag Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 58 End: 207 ......................................................... M P C Q T I P C P H Y Q S L I R L A E V S T V R F R T V R V F V S E Q S D T S P S E K T C I L S A F ........................................................ Protein_Len: 60 Strand: + Start: 3 End: 221 .. M V F F F P V R A L L L A A F R R A N A M P N N P L P S L S V T Y S I G R S V H C P F S D S S G V R F R T V G H F A I G .......................................... Protein_Len: 54 Strand: + Start: 86 End: 247 ..................................................................................... M I S H L F D W P K C P L S V F G Q F G C S F P N S R T L R H R R K L A Y Y Q P F K G S G I N F A V G K V Q ................ Protein_Len: 49 Strand: - Start: 101 End: 247 .................................................................................................... E I P R L T W Q G N E S L E P T R K R V T P C K A M P S F K C I I L R K L T A A Y V K S D S L H M ................ Protein_Len: 34 Strand: - Start: 93 End: 194 ............................................................................................ D S I R N A S T D V T R K R V T R T N T E S C D S V E G D S F V Q M ..................................................................... Protein_Len: 32 Strand: - Start: 2 End: 97 . I T K K K G T R A K N S A A K R L A F A M G F L G R G E N D T M ...................................................................................................................................................................... Protein_Len: 31 Strand: - Start: 1 End: 93 F R K R K E P A L K T A R R R G F L L H W A L C D G A R M I M .......................................................................................................................................................................... gaatcgttttcttttttccggtgcgagctttgttgctcgccgccttccgaagagcaaatgccatgccaaacaatcccctgccctcattatcagtcacttattcgattggccgaagtgtccactgtccgttttcggacagttcgggtgttcgtttccgaacagtcggacacttcgccatcggagaaaacttgcatattatcagccttttaagggtagcggcataaactttgctgtcggaaaggtgcaataaaaacgaaagaaag 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: 93 Start: 53 End: 69 ....................................................TTGGCATGGCATTTGCT.................................................................................................................................................................................................. PromScan Matrix: RpoN Strand: + Score: 82 Start: 216 End: 232 .......................................................................................................................................................................................................................GCGGCATAAACTTTGCT............................... gaatcgttttcttttttccggtgcgagctttgttgctcgccgccttccgaagagcaaatgccatgccaaacaatcccctgccctcattatcagtcacttattcgattggccgaagtgtccactgtccgttttcggacagttcgggtgttcgtttccgaacagtcggacacttcgccatcggagaaaacttgcatattatcagccttttaagggtagcggcataaactttgctgtcggaaaggtgcaataaaaacgaaagaaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -2.4 Tail_Score: -3.53811 Start: 133 End: 151 Full_Region: TCCACTGTCCGTTTT CGGACA GTTCGGG TGTTCG TTTCCGAACAGTCGG ....................................................................................................................................CGGACAGTTCGGGTGTTCG................................................................................................................ Find igs database================================================ Query_seq: PG0283:PG0285|PG0283:PG0285:efflux transporter, MFP component, RND family:hypothetical protein:<-->:318336..318598 263 gaatcgttttcttttttccggtgcgagctttgttgctcgccgccttccgaagagcaaatgccatgccaaacaatcccctgccctcattatcagtcacttattcgattggccgaagtgtccactgtccgttttcggacagttcgggtgttcgtttccgaacagtcggacacttcgccatcggagaaaacttgcatattatcagccttttaagggtagcggcataaactttgctgtcggaaaggtgcaataaaaacgaaagaaag Intra-Species Hit: Count: 1 Min: 1 Max: 263 Len: 263 Subject: NC_002950_PG0283_PG0285|efflux transporter, MFP component, RND family:hypothetical protein|NEGATIVE:POSITIVE|[318336,318598]|263 HSP 1 e-value: 1.0E-147 bit: 521.0 Len: 263 Query Start:1 Query End:263 Subject Strand: POSITIVE Subject Start: 1 Subject End: 263 gaatcgttttcttttttccggtgcgagctttgttgctcgccgccttccgaagagcaaatgccatgccaaacaatcccctgccctcattatcagtcacttattcgattggccgaagtgtccactgtccgttttcggacagttcgggtgttcgtttccgaacagtcggacacttcgccatcggagaaaacttgcatattatcagccttttaagggtagcggcataaactttgctgtcggaaaggtgcaataaaaacgaaagaaag gaatcgttttcttttttccggtgcgagctttgttgctcgccgccttccgaagagcaaatgccatgccaaacaatcccctgccctcattatcagtcacttattcgattggccgaagtgtccactgtccgttttcggacagttcgggtgttcgtttccgaacagtcggacacttcgccatcggagaaaacttgcatattatcagccttttaagggtagcggcataaactttgctgtcggaaaggtgcaataaaaacgaaagaaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUCGUUUUCUUUUUUCCGGUGCGAGCUUUGUUGCUCGCCGCCUUCCGAAGAGCAAAUGCCAUGCCAAACAAUCCCCUGCCCUCAUUAUCAGUCACUUAUUCGAUUGGCCGAAGUGUCCACUGUCCGUUUUCGGACAGUUCGGGUGUUCGUUUCCGAACAGUCGGACACUUCGCCAUCGGAGAAAACUUGCAUAUUAUCAGCCUUUUAAGGGUAGCGGCAUAAACUUUGCUGUCGGAAAGGUGCAAUAAAAACGAAAGAAAG ...(((((((............((((((......))))))((((((((((..((((((....(((((..........(((((((................((((((.(((.(((((((((.(((((((....)))))))...((.((((((....)))))).))))))))))))))))))))........((.........))......))))))).)))))....)))))).)))).)))))).....)))))))....... (-96.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUCUUUCGUUUUUAUUGCACCUUUCCGACAGCAAAGUUUAUGCCGCUACCCUUAAAAGGCUGAUAAUAUGCAAGUUUUCUCCGAUGGCGAAGUGUCCGACUGUUCGGAAACGAACACCCGAACUGUCCGAAAACGGACAGUGGACACUUCGGCCAAUCGAAUAAGUGACUGAUAAUGAGGGCAGGGGAUUGUUUGGCAUGGCAUUUGCUCUUCGGAAGGCGGCGAGCAACAAAGCUCGCACCGGAAAAAAGAAAACGAUUC .......((((((((.......((((((((.((((((..((((((((((.((((((....((.........)).((((.....((((((((((((((((...((((((....)))))).....((((((((....))))))))))))))))).))).)))).......)))).....)))))).)).........))))))))..))))))..))))))))..((((((......))))))...........))))))))... (-101.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1060 70 21 161 112 NC_002950:PG0283|5end_efflux_transporter,_MFP_component,_RND_family_318245..318475_NEGATIVE 446 175 132 163 118 NC_002950:PG0335|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_370706..370936_NEGATIVE 444 49 1 216 154 NC_002950:PG1498|5end_hypothetical_protein_1574656..1574886_POSITIVE 419 67 21 59 14 NC_002950:PG0143|5end_hydrolase,_carbon-nitrogen_family_166625..166855_NEGATIVE 404 66 21 62 13 NC_002950:PG0898|5end_hypothetical_protein_963350..963580_NEGATIVE 398 42 4 85 37 NC_002950:PG0930|5end_hypothetical_protein_987542..987772_NEGATIVE 397 67 21 180 131 NC_002950:PG1641|5end_phosphotyrosine_protein_phosphatase_1721763..1721993_NEGATIVE 396 159 111 201 141 NC_002950:PG1478|5end_conjugative_transposon_protein_TraK_1554116..1554346_NEGATIVE 395 167 123 178 131 NC_002950:PG0712|5end_hypothetical_protein_767131..767361_NEGATIVE 389 80 33 225 177 NC_002950:PG1286|5end_ferritin_1365501..1365731_NEGATIVE 388 166 123 51 6 NC_002950:PG2023|5end_methionyl-tRNA_formyltransferase_2118536..2118766_NEGATIVE 388 144 105 53 8 NC_002950:PG1128|5end_exodeoxyribonuclease_VII_large_subunit_1203737..1203967_POSITIVE 388 70 24 53 2 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 386 169 121 201 156 NC_002950:PG0585|5end_YqeY_family_protein_643272..643502_POSITIVE 380 67 21 55 7 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 378 181 141 194 159 NC_002950:PG1633|5end_galactokinase_1713385..1713615_POSITIVE 378 45 5 222 181 NC_002950:PG0657|5end_Maf-like_protein_707782..708012_NEGATIVE 373 180 131 175 121 NC_002950:PG1612|5end_methylmalonyl-CoA_decarboxylase,_alpha_subunit_1693065..1693295_NEGATIVE 373 54 18 181 139 NC_002950:PG0229|5end_hypothetical_protein_264872..265102_POSITIVE 368 49 18 168 136 NC_002950:PG0327|5end_hypothetical_protein_362061..362291_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 446 175 132 146 101 NC_002950:PG0336|3end_hypothetical_protein_370723..370873_NEGATIVE 444 49 1 115 53 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 410 50 3 141 97 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 394 49 18 130 104 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 394 49 18 130 104 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 393 67 28 41 2 NC_002950:PG0144|3end_hypothetical_protein_166643..166793_NEGATIVE 391 147 101 63 13 NC_002950:PG1186|3end_hypothetical_protein_1267703..1267853_NEGATIVE 383 150 102 96 46 NC_002950:PG1104|3end_hypothetical_protein_1175782..1175932_POSITIVE 378 181 141 144 109 NC_002950:PG1632|3end_aldose_1-epimerase_1713415..1713565_POSITIVE 377 184 141 74 22 NC_002950:PG0334|3end_glycosyl_transferase,_group_2_family_protein_368792..368942_NEGATIVE 373 180 131 76 22 NC_002950:PG1613|3end_glyoxalase_family_protein_1693164..1693314_NEGATIVE 370 68 23 151 97 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 368 49 18 74 42 NC_002950:PG0328|3end_imidazolonepropionase_362155..362305_NEGATIVE 366 46 7 129 96 NC_002950:PG0465|3end_ferric_uptake_transcriptional_regulator_508903..509053_NEGATIVE 362 156 119 139 95 NC_002950:PG0282|3end_ABC_transporter,_ATP-binding_protein_316244..316394_NEGATIVE 356 47 10 142 99 NC_002950:PG0303|3end_ferredoxin_339603..339753_POSITIVE 354 169 124 54 7 NC_002950:PG0703|3end_cobalamin_(5'-phosphate)_synthase,_putative_759006..759156_POSITIVE 351 157 111 40 2 NC_002950:PG2125|3end_transcriptional_regulator,_AraC_family_2231376..2231526_NEGATIVE 351 183 143 102 43 NC_002950:PG1475|3end_conjugative_transposon_protein_TraN_1550810..1550960_NEGATIVE 347 170 122 68 7 NC_002950:PG0792|3end_hypoxanthine_phosphoribosyltransferase_843178..843328_NEGATIVE