Origin IGS: tccattcttaccttatttcggacgatccattcattcggatggtattgcgcgcgcttacaatgagatccgttgcatcggcacttgtagatctgcctttctatgctgatttatcaaggggatcgaatgtgcatccatagccgtgatgcaaggattttcatccttcttaataccgatcttatcgtgggatagggagtgggacacactctcctaacctcaaaaaccgactaaaaaggatcggaataaggataccgaacagacactatatccatatcaagccaatcaaaccaaaaaataaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttattttttggtttgattggcttgatatggatatagtgtctgttcggtatccttattccgatcctttttagtcggtttttgaggttaggagagtgtgtcccactccctatcccacgataagatcggtattaagaaggatgaaaatccttgcatcacggctatggatgcacattcgatccccttgataaatcagcatagaaaggcagatctacaagtgccgatgcaacggatctcattgtaagcgcgcgcaataccatccgaatgaatggatcgtccgaaataaggtaagaatgga Mask Tandem Repeat Region ================================================ tccattcttaccttatttcggacgatccattcattcggatggtattgcgcgcgcttacaatgagatccgttgcatcggcacttgtagatctgcctttctatgctgatttatcaaggggatcgaatgtgcatccatagccgtgatgcaaggattttcatccttcttaataccgatcttatcgtgggatagggagtgggacacactctcctaacctcaaaaaccgactaaaaaggatcggaataaggataccgaacagacactatatccatatcaagccaatcaaaccaaaaaataaa Find is-nt database================================================ Query_seq: PG2006:PG2008|PG2006:PG2008:hypothetical protein:TonB-dependent receptor, putative:->->:2095087..2095382 296 tccattcttaccttatttcggacgatccattcattcggatggtattgcgcgcgcttacaatgagatccgttgcatcggcacttgtagatctgcctttctatgctgatttatcaaggggatcgaatgtgcatccatagccgtgatgcaaggattttcatccttcttaataccgatcttatcgtgggatagggagtgggacacactctcctaacctcaaaaaccgactaaaaaggatcggaataaggataccgaacagacactatatccatatcaagccaatcaaaccaaaaaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2006:PG2008|PG2006:PG2008:hypothetical protein:TonB-dependent receptor, putative:->->:2095087..2095382 296 tccattcttaccttatttcggacgatccattcattcggatggtattgcgcgcgcttacaatgagatccgttgcatcggcacttgtagatctgcctttctatgctgatttatcaaggggatcgaatgtgcatccatagccgtgatgcaaggattttcatccttcttaataccgatcttatcgtgggatagggagtgggacacactctcctaacctcaaaaaccgactaaaaaggatcggaataaggataccgaacagacactatatccatatcaagccaatcaaaccaaaaaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2006:PG2008|PG2006:PG2008:hypothetical protein:TonB-dependent receptor, putative:->->:2095087..2095382 296 tccattcttaccttatttcggacgatccattcattcggatggtattgcgcgcgcttacaatgagatccgttgcatcggcacttgtagatctgcctttctatgctgatttatcaaggggatcgaatgtgcatccatagccgtgatgcaaggattttcatccttcttaataccgatcttatcgtgggatagggagtgggacacactctcctaacctcaaaaaccgactaaaaaggatcggaataaggataccgaacagacactatatccatatcaagccaatcaaaccaaaaaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tccattcttaccttatttcggacgatccattcattcggatggtattgcgcgcgcttacaatgagatccgttgcatcggcacttgtagatctgcctttctatgctgatttatcaaggggatcgaatgtgcatccatagccgtgatgcaaggattttcatccttcttaataccgatcttatcgtgggatagggagtgggacacactctcctaacctcaaaaaccgactaaaaaggatcggaataaggataccgaacagacactatatccatatcaagccaatcaaaccaaaaaataaa Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 15 End: 134 .............. M S D D P F I R M V L R A L T M R S V A S A L V D L P F Y A D L S R G S N V H P .................................................................................................................................................................. Protein_Len: 33 Strand: + Start: 88 End: 186 ....................................................................................... M C L S M L I Y Q G D R M C I H S R D A R I F I L L N T D L I V G .............................................................................................................. Protein_Len: 33 Strand: + Start: 110 End: 208 ............................................................................................................. M K G I E C A S I A V M Q G F S S F L I P I L S W D R E W D T L S ........................................................................................ Protein_Len: 37 Strand: + Start: 186 End: 296 ......................................................................................................................................................................................... M G S G T H S P N L K N R L K R I G I R I P N R H Y I H I K P I K P K N K Protein_Len: 30 Strand: - Start: 114 End: 203 ................................................................................................................. P S R I H M W L R S A L I K M R R L V S R I T P Y P T P C M ............................................................................................. Protein_Len: 48 Strand: - Start: 58 End: 201 ......................................................... L S I R Q M P V Q L D A K R H Q N I L P I S H A D M A T I C P N E D K K I G I K D H S L S H S M ............................................................................................... Protein_Len: 35 Strand: - Start: 3 End: 107 .. M R V K N R V I W E N P H Y Q A R K C H S G N C R C K Y I Q R E I S M ............................................................................................................................................................................................. tccattcttaccttatttcggacgatccattcattcggatggtattgcgcgcgcttacaatgagatccgttgcatcggcacttgtagatctgcctttctatgctgatttatcaaggggatcgaatgtgcatccatagccgtgatgcaaggattttcatccttcttaataccgatcttatcgtgggatagggagtgggacacactctcctaacctcaaaaaccgactaaaaaggatcggaataaggataccgaacagacactatatccatatcaagccaatcaaaccaaaaaataaa 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================================================ tccattcttaccttatttcggacgatccattcattcggatggtattgcgcgcgcttacaatgagatccgttgcatcggcacttgtagatctgcctttctatgctgatttatcaaggggatcgaatgtgcatccatagccgtgatgcaaggattttcatccttcttaataccgatcttatcgtgggatagggagtgggacacactctcctaacctcaaaaaccgactaaaaaggatcggaataaggataccgaacagacactatatccatatcaagccaatcaaaccaaaaaataaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG2006:PG2008|PG2006:PG2008:hypothetical protein:TonB-dependent receptor, putative:->->:2095087..2095382 296 tccattcttaccttatttcggacgatccattcattcggatggtattgcgcgcgcttacaatgagatccgttgcatcggcacttgtagatctgcctttctatgctgatttatcaaggggatcgaatgtgcatccatagccgtgatgcaaggattttcatccttcttaataccgatcttatcgtgggatagggagtgggacacactctcctaacctcaaaaaccgactaaaaaggatcggaataaggataccgaacagacactatatccatatcaagccaatcaaaccaaaaaataaa Intra-Species Hit: Count: 1 Min: 1 Max: 296 Len: 296 Subject: NC_002950_PG2006_PG2008|hypothetical protein:TonB-dependent receptor, putative|POSITIVE:POSITIVE|[2095087,2095382]|296 HSP 1 e-value: 1.0E-167 bit: 587.0 Len: 296 Query Start:1 Query End:296 Subject Strand: POSITIVE Subject Start: 1 Subject End: 296 tccattcttaccttatttcggacgatccattcattcggatggtattgcgcgcgcttacaatgagatccgttgcatcggcacttgtagatctgcctttctatgctgatttatcaaggggatcgaatgtgcatccatagccgtgatgcaaggattttcatccttcttaataccgatcttatcgtgggatagggagtgggacacactctcctaacctcaaaaaccgactaaaaaggatcggaataaggataccgaacagacactatatccatatcaagccaatcaaaccaaaaaataaa tccattcttaccttatttcggacgatccattcattcggatggtattgcgcgcgcttacaatgagatccgttgcatcggcacttgtagatctgcctttctatgctgatttatcaaggggatcgaatgtgcatccatagccgtgatgcaaggattttcatccttcttaataccgatcttatcgtgggatagggagtgggacacactctcctaacctcaaaaaccgactaaaaaggatcggaataaggataccgaacagacactatatccatatcaagccaatcaaaccaaaaaataaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCAUUCUUACCUUAUUUCGGACGAUCCAUUCAUUCGGAUGGUAUUGCGCGCGCUUACAAUGAGAUCCGUUGCAUCGGCACUUGUAGAUCUGCCUUUCUAUGCUGAUUUAUCAAGGGGAUCGAAUGUGCAUCCAUAGCCGUGAUGCAAGGAUUUUCAUCCUUCUUAAUACCGAUCUUAUCGUGGGAUAGGGAGUGGGACACACUCUCCUAACCUCAAAAACCGACUAAAAAGGAUCGGAAUAAGGAUACCGAACAGACACUAUAUCCAUAUCAAGCCAAUCAAACCAAAAAAUAAA ................(((((...((((........((((((((..((....)).)))...(((((((.((((((((((.((((((((((.((........)).)))))).)))).((((((....)).))))...)))..))))))))))))))))))).........((((((((.(((((((.(((((((((.....))))).)))).)).)).....)))......)))))))).....)))).)))))........................................... (-79.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUUUUUUGGUUUGAUUGGCUUGAUAUGGAUAUAGUGUCUGUUCGGUAUCCUUAUUCCGAUCCUUUUUAGUCGGUUUUUGAGGUUAGGAGAGUGUGUCCCACUCCCUAUCCCACGAUAAGAUCGGUAUUAAGAAGGAUGAAAAUCCUUGCAUCACGGCUAUGGAUGCACAUUCGAUCCCCUUGAUAAAUCAGCAUAGAAAGGCAGAUCUACAAGUGCCGAUGCAACGGAUCUCAUUGUAAGCGCGCGCAAUACCAUCCGAAUGAAUGGAUCGUCCGAAAUAAGGUAAGAAUGGA (((((.((..((((.....)))).)).))))).......(((((((..((.((((((((((((((..((((.((((....((.((.((((.(((((.....))))))))).)).(((((.(((((.((......((((((....))))))(((((..(((...((((.(......))))).((((.((.(((.((........)).))).)))))).)))))))).)).))))).)))))..((....)).....)).)))).)))).))))))...).))))))))).))))))) (-81.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 418 78 35 180 130 NC_002950:PG0329|5end_formiminotransferase-cyclodeaminase-related_protein_364429..364659_NEGATIVE 392 227 183 196 150 NC_002950:PG2027|5end_hypothetical_protein_2125494..2125724_POSITIVE 368 179 132 67 22 NC_002950:PG2116|5end_hypothetical_protein_2224635..2224865_POSITIVE 367 90 41 225 190 NC_002950:PG1564|5end_hypothetical_protein_1644536..1644766_NEGATIVE 357 106 64 69 20 NC_002950:PG1480|5end_conjugative_transposon_protein_TraI_1555895..1556125_NEGATIVE 356 90 41 58 2 NC_002950:PG1787|5end_hypothetical_protein_1875908..1876138_NEGATIVE 353 158 113 91 48 NC_002950:PG1635|5end_hypothetical_protein_1715861..1716091_NEGATIVE 347 78 34 54 14 NC_002950:PG0211|5end_cobalamin_biosynthesis_protein_CbiG/precorrin-4_C11-methyltransferase_247810..248040_NEGATIVE 340 80 36 59 23 NC_002950:PG1678|5end_hypothetical_protein_1763862..1764092_NEGATIVE 337 103 66 48 8 NC_002950:PG1056|5end_hypothetical_protein_1122980..1123210_POSITIVE 336 140 92 169 113 NC_002950:PG0934|5end_hypothetical_protein_994318..994548_NEGATIVE 336 88 47 184 136 NC_002950:PG0141|5end_spoOJ_protein_164747..164977_NEGATIVE 333 80 35 200 147 NC_002950:PG0606|5end_hypothetical_protein_662558..662788_NEGATIVE 333 79 36 118 70 NC_002950:PG0447|5end_hypothetical_protein_487278..487508_POSITIVE 331 79 37 54 2 NC_002950:PG0927|5end_conserved_hypothetical_protein_TIGR00150_985050..985280_NEGATIVE 330 139 91 185 137 NC_002950:PG1394|5end_hypothetical_protein_1476782..1477012_NEGATIVE 329 84 41 231 169 NC_002950:PG0307|5end_NADH-ubiquinone_oxidoreductase_342560..342790_POSITIVE 328 209 170 180 143 NC_002950:PG1479|5end_conjugative_transposon_protein_TraJ_1555234..1555464_NEGATIVE 327 105 61 207 158 NC_002950:PG1601|5end_biotin--acetyl-CoA-carboxylase_ligase_1681792..1682022_NEGATIVE 327 96 51 76 31 NC_002950:PG1195|5end_8-amino-7-oxononanoate_synthase_1273979..1274209_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 418 78 35 131 81 NC_002950:PG0330|3end_DNA-binding_protein,_histone-like_family_364478..364628_NEGATIVE 379 80 34 143 85 NC_002950:PG2205|3end_2-dehydropantoate_2-reductase_2317145..2317295_POSITIVE 367 90 41 140 105 NC_002950:PG1565|3end_3-deoxy-D-manno-octulosonic-acid_transferase,_putative_1644621..1644771_NEGATIVE 361 77 32 49 3 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 356 80 35 131 91 NC_002950:PG2062|3end_histidyl-tRNA_synthetase_2160415..2160565_POSITIVE 353 158 113 77 34 NC_002950:PG1636|3end_FtsK/SpoIIIE_family_protein_1715875..1716025_NEGATIVE 351 87 41 96 50 NC_002950:PG0593|3end_htrA_protein_651938..652088_POSITIVE 340 209 168 105 54 NC_002950:PG1774|3end_transcription-repair_coupling_factor_1861179..1861329_NEGATIVE 340 165 121 63 21 NC_002950:PG0240|3end_hydrolase,_haloacid_dehalogenase-like_family_276395..276545_NEGATIVE 338 78 35 40 1 NC_002950:PG0212|3end_precorrin-6Y_C5,15-methyltransferase,_decarboxylating_247824..247974_NEGATIVE 333 79 36 146 98 NC_002950:PG0446|3end_thiF_protein_487386..487536_POSITIVE 329 118 72 78 31 NC_002950:PG0951|3end_phosphoribosylaminoimidazole_carboxylase,_PurE_protein_1010828..1010978_POSITIVE 328 209 170 148 111 NC_002950:PG1480|3end_conjugative_transposon_protein_TraI_1555266..1555416_NEGATIVE 323 59 11 66 1 NC_002950:PG2044|3end_hypothetical_protein_2144165..2144315_POSITIVE 323 54 12 151 90 NC_002950:PG1289|3end_GDP-fucose_synthetase_1368194..1368344_POSITIVE 323 225 183 79 41 NC_002950:PG0525|3end_CTP_synthetase_570698..570848_POSITIVE 319 208 170 148 116 NC_002950:PG2026|3end_phosphoglycerate_mutase_family_protein_2125545..2125695_POSITIVE 317 94 68 29 2 NC_002950:PG1433|3end_hydrolase_1519126..1519276_POSITIVE 315 150 101 137 80 NC_002950:PG1823|3end_hypothetical_protein_1918050..1918200_POSITIVE 315 215 171 68 24 NC_002950:PG1802|3end_hypothetical_protein_1896558..1896708_POSITIVE