Origin IGS: tatggatatgctttagaatgcttttgactgaatttttttcttacggacaaagataaacgaaaaaaggagtgtcgtgcccaatagcgtgctaaacgttttttaggttgtttatgaaaaagggagaggctctttccagtgcctctccttcggttttatcggagttgctttggataaataagcttacctggagctttacaaataaatataggtcttttcgcccaagtcatccgtctgttaccctccatgcttcgattaaggaactttcagcagagtttcaggcagacagcatagcaaaggtt .........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 aacctttgctatgctgtctgcctgaaactctgctgaaagttccttaatcgaagcatggagggtaacagacggatgacttgggcgaaaagacctatatttatttgtaaagctccaggtaagcttatttatccaaagcaactccgataaaaccgaaggagaggcactggaaagagcctctccctttttcataaacaacctaaaaaacgtttagcacgctattgggcacgacactccttttttcgtttatctttgtccgtaagaaaaaaattcagtcaaaagcattctaaagcatatccata Mask Tandem Repeat Region ================================================ tatggatatgctttagaatgcttttgactgaatttttttcttacggacaaagataaacgaaaaaaggagtgtcgtgcccaatagcgtgctaaacgttttttaggttgtttatgaaaaagggagaggctctttccagtgcctctccttcggttttatcggagttgctttggataaataagcttacctggagctttacaaataaatataggtcttttcgcccaagtcatccgtctgttaccctccatgcttcgattaaggaactttcagcagagtttcaggcagacagcatagcaaaggtt Find is-nt database================================================ Query_seq: PG0296:PG0297|PG0296:PG0297:phosphoribosylformylglycinamidine synthase:hypothetical protein:<-<-:335088..335386 299 tatggatatgctttagaatgcttttgactgaatttttttcttacggacaaagataaacgaaaaaaggagtgtcgtgcccaatagcgtgctaaacgttttttaggttgtttatgaaaaagggagaggctctttccagtgcctctccttcggttttatcggagttgctttggataaataagcttacctggagctttacaaataaatataggtcttttcgcccaagtcatccgtctgttaccctccatgcttcgattaaggaactttcagcagagtttcaggcagacagcatagcaaaggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0296:PG0297|PG0296:PG0297:phosphoribosylformylglycinamidine synthase:hypothetical protein:<-<-:335088..335386 299 tatggatatgctttagaatgcttttgactgaatttttttcttacggacaaagataaacgaaaaaaggagtgtcgtgcccaatagcgtgctaaacgttttttaggttgtttatgaaaaagggagaggctctttccagtgcctctccttcggttttatcggagttgctttggataaataagcttacctggagctttacaaataaatataggtcttttcgcccaagtcatccgtctgttaccctccatgcttcgattaaggaactttcagcagagtttcaggcagacagcatagcaaaggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0296:PG0297|PG0296:PG0297:phosphoribosylformylglycinamidine synthase:hypothetical protein:<-<-:335088..335386 299 tatggatatgctttagaatgcttttgactgaatttttttcttacggacaaagataaacgaaaaaaggagtgtcgtgcccaatagcgtgctaaacgttttttaggttgtttatgaaaaagggagaggctctttccagtgcctctccttcggttttatcggagttgctttggataaataagcttacctggagctttacaaataaatataggtcttttcgcccaagtcatccgtctgttaccctccatgcttcgattaaggaactttcagcagagtttcaggcagacagcatagcaaaggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatggatatgctttagaatgcttttgactgaatttttttcttacggacaaagataaacgaaaaaaggagtgtcgtgcccaatagcgtgctaaacgttttttaggttgtttatgaaaaagggagaggctctttccagtgcctctccttcggttttatcggagttgctttggataaataagcttacctggagctttacaaataaatataggtcttttcgcccaagtcatccgtctgttaccctccatgcttcgattaaggaactttcagcagagtttcaggcagacagcatagcaaaggtt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 175 End: 288 .............................................................................................................................................................................. M S L P G A L Q I N I G L F A Q V I R L L P S M L R L R N F Q Q S F R Q T A ........... Protein_Len: 60 Strand: + Start: 105 End: 299 ........................................................................................................ M F M K K G E A L S S A S P S V L S E L L W I N K L T W S F T N K Y R S F R P S H P S V T L H A S I K E L S A E F Q A D Protein_Len: 30 Strand: - Start: 156 End: 245 ........................................................................................................................................................... R L Q K P Y I L K G P A K C I F I P R K A W T M R R N G E M ...................................................... tatggatatgctttagaatgcttttgactgaatttttttcttacggacaaagataaacgaaaaaaggagtgtcgtgcccaatagcgtgctaaacgttttttaggttgtttatgaaaaagggagaggctctttccagtgcctctccttcggttttatcggagttgctttggataaataagcttacctggagctttacaaataaatataggtcttttcgcccaagtcatccgtctgttaccctccatgcttcgattaaggaactttcagcagagtttcaggcagacagcatagcaaaggtt 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================================================ tatggatatgctttagaatgcttttgactgaatttttttcttacggacaaagataaacgaaaaaaggagtgtcgtgcccaatagcgtgctaaacgttttttaggttgtttatgaaaaagggagaggctctttccagtgcctctccttcggttttatcggagttgctttggataaataagcttacctggagctttacaaataaatataggtcttttcgcccaagtcatccgtctgttaccctccatgcttcgattaaggaactttcagcagagtttcaggcagacagcatagcaaaggtt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 43 HP_score: -2.9 Tail_Score: -3.0353 Start: 89 End: 103 Full_Region: GTGCCCAATAGCGTG CTAAA CGTTT TTTAG GTTGTTTATGAAAAA ........................................................................................CTAAACGTTTTTTAG.................................................................................................................................................................................................... TransTerm Strand: - Conf: 93 HP_score: -9.8 Tail_Score: -4.72272 Start: 119 End: 146 Full_Region: ctccgataaaaccga aggagaggcact ggaa agagcctctccc tttttcataaacaac ......................................................................................................................aggagaggcactggaaagagcctctccc......................................................................................................................................................... TransTerm Strand: - Conf: 93 HP_score: -13.3 Tail_Score: -3.43042 Start: 120 End: 145 Full_Region: tccgataaaaccgaa ggagaggcact ggaa agagcctctcc ctttttcataaacaa .......................................................................................................................ggagaggcactggaaagagcctctcc.......................................................................................................................................................... Find igs database================================================ Query_seq: PG0296:PG0297|PG0296:PG0297:phosphoribosylformylglycinamidine synthase:hypothetical protein:<-<-:335088..335386 299 tatggatatgctttagaatgcttttgactgaatttttttcttacggacaaagataaacgaaaaaaggagtgtcgtgcccaatagcgtgctaaacgttttttaggttgtttatgaaaaagggagaggctctttccagtgcctctccttcggttttatcggagttgctttggataaataagcttacctggagctttacaaataaatataggtcttttcgcccaagtcatccgtctgttaccctccatgcttcgattaaggaactttcagcagagtttcaggcagacagcatagcaaaggtt Intra-Species Hit: Count: 1 Min: 1 Max: 299 Len: 299 Subject: NC_002950_PG0296_PG0297|phosphoribosylformylglycinamidine synthase:hypothetical protein|NEGATIVE:NEGATIVE|[335088,335386]|299 HSP 1 e-value: 1.0E-156 bit: 551.0 Len: 299 Query Start:1 Query End:299 Subject Strand: POSITIVE Subject Start: 1 Subject End: 299 tatggatatgctttagaatgcttttgactgaannnnnnncttacggacaaagataaacgaaaaaaggagtgtcgtgcccaatagcgtgctaaacgttttttaggttgtttatgaaaaagggagaggctctttccagtgcctctccttcggttttatcggagttgctttggataaataagcttacctggagctttacaaataaatataggtcttttcgcccaagtcatccgtctgttaccctccatgcttcgattaaggaactttcagcagagtttcaggcagacagcatagcaaaggtt tatggatatgctttagaatgcttttgactgaatttttttcttacggacaaagataaacgaaaaaaggagtgtcgtgcccaatagcgtgctaaacgttttttaggttgtttatgaaaaagggagaggctctttccagtgcctctccttcggttttatcggagttgctttggataaataagcttacctggagctttacaaataaatataggtcttttcgcccaagtcatccgtctgttaccctccatgcttcgattaaggaactttcagcagagtttcaggcagacagcatagcaaaggtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUGGAUAUGCUUUAGAAUGCUUUUGACUGAAUUUUUUUCUUACGGACAAAGAUAAACGAAAAAAGGAGUGUCGUGCCCAAUAGCGUGCUAAACGUUUUUUAGGUUGUUUAUGAAAAAGGGAGAGGCUCUUUCCAGUGCCUCUCCUUCGGUUUUAUCGGAGUUGCUUUGGAUAAAUAAGCUUACCUGGAGCUUUACAAAUAAAUAUAGGUCUUUUCGCCCAAGUCAUCCGUCUGUUACCCUCCAUGCUUCGAUUAAGGAACUUUCAGCAGAGUUUCAGGCAGACAGCAUAGCAAAGGUU ...................(((((((.(((..((((((((..................))))))))...((((.((((....(((.((((.((.(((((((((.(((..((((....((((((((((.((....)).)))))))))).(((..((.((((...((((..(.(((......))).)..))))................(((......))).......))))..))..)))...))))...)))))))))))).)).))))..)))...))))))))...)))))))))). (-72.07) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACCUUUGCUAUGCUGUCUGCCUGAAACUCUGCUGAAAGUUCCUUAAUCGAAGCAUGGAGGGUAACAGACGGAUGACUUGGGCGAAAAGACCUAUAUUUAUUUGUAAAGCUCCAGGUAAGCUUAUUUAUCCAAAGCAACUCCGAUAAAACCGAAGGAGAGGCACUGGAAAGAGCCUCUCCCUUUUUCAUAAACAACCUAAAAAACGUUUAGCACGCUAUUGGGCACGACACUCCUUUUUUCGUUUAUCUUUGUCCGUAAGAAAAAAAUUCAGUCAAAAGCAUUCUAAAGCAUAUCCAUA ...(((((..((((((((((((..(.....(((((((.(((.....((((..((.(((((..(.(((((..((((...(((((.....).))))))))..))))).)..))))).))..((((.........)))).....))))......(((((((((((.((....)).))))))))....)))...............))).))))))).....)..)))).))).....((((((((..((....))..)).))))))..............)))))..))))).......... (-74.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 918 90 41 181 132 NC_002950:PG0296|5end_phosphoribosylformylglycinamidine_synthase_334997..335227_NEGATIVE 438 158 119 225 184 NC_002950:PG0018|5end_hypothetical_protein_19648..19878_POSITIVE 407 170 121 212 161 NC_002950:PG2194|5end_ISPg4,_transposase_2302119..2302349_NEGATIVE 407 170 121 212 161 NC_002950:PG1673|5end_ISPg4,_transposase_1758388..1758618_POSITIVE 407 170 121 212 161 NC_002950:PG1261|5end_ISPg4,_transposase_1338371..1338601_POSITIVE 407 170 121 212 161 NC_002950:PG0050|5end_ISPg4,_transposase_60916..61146_POSITIVE 407 170 121 212 161 NC_002950:PG0019|5end_ISPg4_transposase_22040..22270_POSITIVE 401 270 221 107 52 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 376 170 121 115 61 NC_002950:PG0212|5end_precorrin-6Y_C5,15-methyltransferase,_decarboxylating_249065..249295_NEGATIVE 370 259 217 46 4 NC_002950:PG1861|5end_hypothetical_protein_1960057..1960287_NEGATIVE 362 170 121 109 46 NC_002950:PG1764|5end_3-oxoacyl-(acyl-carrier-protein)_synthase_II_1853052..1853282_NEGATIVE 353 152 118 145 103 NC_002950:PG2073|5end_hypothetical_protein_2174374..2174604_NEGATIVE 353 152 118 145 103 NC_002950:PG1669|5end_hypothetical_protein_1755566..1755796_NEGATIVE 353 152 118 145 103 NC_002950:PG1264|5end_hypothetical_protein_1344895..1345125_NEGATIVE 353 167 121 160 108 NC_002950:PG0216|5end_hypothetical_protein_251956..252186_POSITIVE 353 152 118 145 103 NC_002950:PG0103|5end_hypothetical_protein_121290..121520_POSITIVE 352 169 123 124 71 NC_002950:PG0147|5end_hypothetical_protein_169667..169897_NEGATIVE 351 168 121 79 20 NC_002950:PG1017|5end_pyruvate_phosphate_dikinase_1076138..1076368_POSITIVE 346 170 130 178 124 NC_002950:PG2086|5end_hypothetical_protein_2186571..2186801_POSITIVE 341 146 101 187 136 NC_002950:PG1658|5end_ISPg4,_transposase_1742904..1743134_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 407 170 121 66 15 NC_002950:PG0018|3end_hypothetical_protein_21974..22124_POSITIVE 387 160 113 76 17 NC_002950:PG2177|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_F_2285266..2285416_NEGATIVE 381 250 206 118 65 NC_002950:PG1868|3end_hypothetical_protein_1965098..1965248_NEGATIVE 376 170 121 122 68 NC_002950:PG0213|3end_precorrin-3_methylase/precorrin-8X_methylmutase_249058..249208_NEGATIVE 362 170 121 99 36 NC_002950:PG1765|3end_acyl_carrier_protein_1853062..1853212_NEGATIVE 354 190 141 103 51 NC_002950:PG1189|3end_hypothetical_protein_1271952..1272102_POSITIVE 352 169 123 137 84 NC_002950:PG0148|3end_sigma-54-dependent_transcriptional_regulator_169654..169804_NEGATIVE 346 170 130 122 68 NC_002950:PG2085|3end_tryptophanyl-tRNA_synthetase_2186595..2186745_POSITIVE 345 148 105 124 76 NC_002950:PG0215|3end_hypothetical_protein_252028..252178_POSITIVE 340 167 121 123 65 NC_002950:PG1327|3end_aminotransferase,_putative_1405270..1405420_NEGATIVE 333 160 118 66 26 NC_002950:PG1498|3end_hypothetical_protein_1575650..1575800_POSITIVE 330 160 118 62 20 NC_002950:PG0172|3end_exonuclease_194355..194505_POSITIVE 329 170 126 138 97 NC_002950:PG1205|3end_DNA-binding_protein,_histone-like_family_1284503..1284653_POSITIVE 328 260 211 151 97 NC_002950:PG0752|3end_uracil_phosphoribosyltransferase_798397..798547_POSITIVE 327 160 117 78 23 NC_002950:PG0279|3end_NADP-dependent_malic_enzyme_310675..310825_NEGATIVE 323 168 121 92 39 NC_002950:PG0881|3end_recombinase_A_944165..944315_POSITIVE 321 158 119 124 86 NC_002950:PG1087|3end_radical_SAM_protein,_TIGR01212_family_1154820..1154970_POSITIVE 316 166 121 66 7 NC_002950:PG1388|3end_hypothetical_protein_1470095..1470245_NEGATIVE 315 167 122 144 93 NC_002950:PG1592|3end_HDIG_domain_protein_1671535..1671685_POSITIVE 315 170 124 140 99 NC_002950:PG1484|3end_hypothetical_protein_1559275..1559425_NEGATIVE