Origin IGS: tgtttgttttcgattgtttagtctgatctcatgtcttgtaaacgggcatggcattacccttattgcgtcggagagagcctatacgagaagagggtgtgccaaacgaaaatacttcgtggcacactctctctttcttgcattcggaaagcctgtatctccctctcctcagcgtaaggaatcagcgggagaagcggggttcg .........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 cgaaccccgcttctcccgctgattccttacgctgaggagagggagatacaggctttccgaatgcaagaaagagagagtgtgccacgaagtattttcgtttggcacaccctcttctcgtataggctctctccgacgcaataagggtaatgccatgcccgtttacaagacatgagatcagactaaacaatcgaaaacaaaca Mask Tandem Repeat Region ================================================ tgtttgttttcgattgtttagtctgatctcatgtcttgtaaacgggcatggcattacccttattgcgtcggagagagcctatacgagaagagggtgtgccaaacgaaaatacttcgtggcacactctctctttcttgcattcggaaagcctgtatctccctctcctcagcgtaaggaatcagcgggagaagcggggttcg Find is-nt database================================================ Query_seq: PG0323:PG0324|PG0323:PG0324:hypothetical protein:histidine ammonia-lyase:<-<-:357479..357678 200 tgtttgttttcgattgtttagtctgatctcatgtcttgtaaacgggcatggcattacccttattgcgtcggagagagcctatacgagaagagggtgtgccaaacgaaaatacttcgtggcacactctctctttcttgcattcggaaagcctgtatctccctctcctcagcgtaaggaatcagcgggagaagcggggttcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0323:PG0324|PG0323:PG0324:hypothetical protein:histidine ammonia-lyase:<-<-:357479..357678 200 tgtttgttttcgattgtttagtctgatctcatgtcttgtaaacgggcatggcattacccttattgcgtcggagagagcctatacgagaagagggtgtgccaaacgaaaatacttcgtggcacactctctctttcttgcattcggaaagcctgtatctccctctcctcagcgtaaggaatcagcgggagaagcggggttcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0323:PG0324|PG0323:PG0324:hypothetical protein:histidine ammonia-lyase:<-<-:357479..357678 200 tgtttgttttcgattgtttagtctgatctcatgtcttgtaaacgggcatggcattacccttattgcgtcggagagagcctatacgagaagagggtgtgccaaacgaaaatacttcgtggcacactctctctttcttgcattcggaaagcctgtatctccctctcctcagcgtaaggaatcagcgggagaagcggggttcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtttgttttcgattgtttagtctgatctcatgtcttgtaaacgggcatggcattacccttattgcgtcggagagagcctatacgagaagagggtgtgccaaacgaaaatacttcgtggcacactctctctttcttgcattcggaaagcctgtatctccctctcctcagcgtaaggaatcagcgggagaagcggggttcg Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 31 End: 171 .............................. M S C K R A W H Y P Y C V G E S L Y E K R V C Q T K I L R G T L S L S C I R K A C I S L S S A ............................. Protein_Len: 60 Strand: + Start: 14 End: 199 ............. M F S L I S C L V N G H G I T L I A S E R A Y T R R G C A K R K Y F V A H S L F L A F G K P V S P S P Q R K E S A G E A . Protein_Len: 51 Strand: + Start: 48 End: 200 ............................................... M A L P L L R R R E P I R E E G V P N E N T S W H T L S F L H S E S L Y L P L L S V R N Q R E K R G S Protein_Len: 40 Strand: - Start: 63 End: 182 .............................................................. Q T P S L R Y S F L T H W V F I S R P V S E R E Q M R F A Q I E R E E A Y P I M .................. Protein_Len: 46 Strand: - Start: 32 End: 169 ............................... T K Y V P M A N G K N R R L S G I R S S P T G F S F V E H C V R E K K C E S L R Y R G R R M ............................... tgtttgttttcgattgtttagtctgatctcatgtcttgtaaacgggcatggcattacccttattgcgtcggagagagcctatacgagaagagggtgtgccaaacgaaaatacttcgtggcacactctctctttcttgcattcggaaagcctgtatctccctctcctcagcgtaaggaatcagcgggagaagcggggttcg 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================================================ tgtttgttttcgattgtttagtctgatctcatgtcttgtaaacgggcatggcattacccttattgcgtcggagagagcctatacgagaagagggtgtgccaaacgaaaatacttcgtggcacactctctctttcttgcattcggaaagcctgtatctccctctcctcagcgtaaggaatcagcgggagaagcggggttcg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -7.2 Tail_Score: -4.2528 Start: 88 End: 130 Full_Region: GAGAGCCTATACGAG AAGAGGGTGTGCCAAACGAA AATAC TTCGTGGCACACTCTCTC TTTCTTGCATTCGGA .......................................................................................AAGAGGGTGTGCCAAACGAAAATACTTCGTGGCACACTCTCTC...................................................................... TransTerm Strand: + Conf: 79 HP_score: -9.8 Tail_Score: -3.72494 Start: 90 End: 128 Full_Region: GAGCCTATACGAGAA GAGGGTGTGCCAAACGAA AATAC TTCGTGGCACACTCTC TCTTTCTTGCATTCG .........................................................................................GAGGGTGTGCCAAACGAAAATACTTCGTGGCACACTCTC........................................................................ Find igs database================================================ Query_seq: PG0323:PG0324|PG0323:PG0324:hypothetical protein:histidine ammonia-lyase:<-<-:357479..357678 200 tgtttgttttcgattgtttagtctgatctcatgtcttgtaaacgggcatggcattacccttattgcgtcggagagagcctatacgagaagagggtgtgccaaacgaaaatacttcgtggcacactctctctttcttgcattcggaaagcctgtatctccctctcctcagcgtaaggaatcagcgggagaagcggggttcg Intra-Species Hit: Count: 1 Min: 1 Max: 200 Len: 200 Subject: NC_002950_PG0323_PG0324|hypothetical protein:histidine ammonia-lyase|NEGATIVE:NEGATIVE|[357479,357678]|200 HSP 1 e-value: 1.0E-109 bit: 396.0 Len: 200 Query Start:1 Query End:200 Subject Strand: POSITIVE Subject Start: 1 Subject End: 200 tgtttgttttcgattgtttagtctgatctcatgtcttgtaaacgggcatggcattacccttattgcgtcggagagagcctatacgagaagagggtgtgccaaacgaaaatacttcgtggcacactctctctttcttgcattcggaaagcctgtatctccctctcctcagcgtaaggaatcagcgggagaagcggggttcg tgtttgttttcgattgtttagtctgatctcatgtcttgtaaacgggcatggcattacccttattgcgtcggagagagcctatacgagaagagggtgtgccaaacgaaaatacttcgtggcacactctctctttcttgcattcggaaagcctgtatctccctctcctcagcgtaaggaatcagcgggagaagcggggttcg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUGUUUUCGAUUGUUUAGUCUGAUCUCAUGUCUUGUAAACGGGCAUGGCAUUACCCUUAUUGCGUCGGAGAGAGCCUAUACGAGAAGAGGGUGUGCCAAACGAAAAUACUUCGUGGCACACUCUCUCUUUCUUGCAUUCGGAAAGCCUGUAUCUCCCUCUCCUCAGCGUAAGGAAUCAGCGGGAGAAGCGGGGUUCG .((((.((((((((.((..((..((((.((((((((.......)))))))).))))..))....)))))))))))))).....(((((((((((((((((..(((((.....)))))))))))))))))...)))))......(((..(((((.((((((.(((((.......))))....).)))))).))))).))). (-71.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAACCCCGCUUCUCCCGCUGAUUCCUUACGCUGAGGAGAGGGAGAUACAGGCUUUCCGAAUGCAAGAAAGAGAGAGUGUGCCACGAAGUAUUUUCGUUUGGCACACCCUCUUCUCGUAUAGGCUCUCUCCGACGCAAUAAGGGUAAUGCCAUGCCCGUUUACAAGACAUGAGAUCAGACUAAACAAUCGAAAACAAACA ..................(((((..(....((...((((((((..((((..((.........))......(((((.(((((((((((((...))))))..))))))).)))))...))))...))))))))...)).....(((((......))))).............)..)))))...................... (-57.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1038 100 51 191 142 NC_002950:PG0323|5end_hypothetical_protein_357388..357618_NEGATIVE 399 200 155 220 172 NC_002950:PG0450|5end_hypothetical_protein_490812..491042_POSITIVE 395 200 155 199 147 NC_002950:PG1961|5end_hypothetical_protein_2051153..2051383_NEGATIVE 391 99 59 74 27 NC_002950:PG1091|5end_DHH_subfamily_1_protein_1157017..1157247_POSITIVE 378 90 42 157 110 NC_002950:PG2149|5end_hypothetical_protein_2257658..2257888_NEGATIVE 377 170 121 214 160 NC_002950:PG0987|5end_hypothetical_protein_1048002..1048232_POSITIVE 369 129 82 119 75 NC_002950:PG1130|5end_TPR_domain_protein_1208053..1208283_POSITIVE 364 199 154 106 53 NC_002950:PG2075|5end_hypothetical_protein_2176466..2176696_NEGATIVE 364 199 154 106 53 NC_002950:PG1266|5end_hypothetical_protein_1346987..1347217_NEGATIVE 364 185 141 203 158 NC_002950:PG0767|5end_4-alpha-glucanotransferase_820533..820763_NEGATIVE 360 139 93 208 156 NC_002950:PG1739|5end_hypothetical_protein_1825709..1825939_NEGATIVE 360 96 51 60 9 NC_002950:PG1008|5end_hypothetical_protein_1067644..1067874_NEGATIVE 354 160 115 66 15 NC_002950:PG1959|5end_ribosomal_protein_L33_2048405..2048635_NEGATIVE 353 90 43 175 109 NC_002950:PG0085|5end_alpha-galactosidase_99172..99402_POSITIVE 352 128 81 231 184 NC_002950:PG0768|5end_hypothetical_protein_822381..822611_NEGATIVE 350 199 154 106 53 NC_002950:PG1671|5end_hypothetical_protein_1757658..1757888_NEGATIVE 350 199 154 106 53 NC_002950:PG0101|5end_hypothetical_protein_119198..119428_POSITIVE 345 199 151 136 81 NC_002950:PG0431|5end_hypothetical_protein_468978..469208_POSITIVE 345 90 43 177 135 NC_002950:PG0374|5end_hypothetical_protein_405564..405794_NEGATIVE 341 190 141 69 3 NC_002950:PG1215|5end_lipoprotein_protein,_putative_1294621..1294851_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 451 129 88 42 3 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 450 129 85 47 7 NC_002950:PG0241|3end_lipoprotein,_putative_277360..277510_NEGATIVE 388 130 81 59 10 NC_002950:PG0769|3end_fibronectin_type_III_domain_protein_822555..822705_NEGATIVE 384 189 142 117 67 NC_002950:PG2004|3end_hypothetical_protein_2093135..2093285_NEGATIVE 381 129 84 57 12 NC_002950:PG1414|3end_hypothetical_protein_1499704..1499854_POSITIVE 378 90 42 148 101 NC_002950:PG2150|3end_LysM_domain_protein_2257667..2257817_NEGATIVE 377 128 81 69 15 NC_002950:PG0193|3end_cationic_outer_membrane_protein_OmpH_230720..230870_POSITIVE 371 193 157 76 32 NC_002950:PG0844|3end_hypothetical_protein_905461..905611_POSITIVE 360 139 93 61 9 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 360 96 51 63 12 NC_002950:PG1009|3end_hypothetical_protein_1067641..1067791_NEGATIVE 360 129 83 63 21 NC_002950:PG1004|3end_prolyl_oligopeptidase_family_protein_1060433..1060583_NEGATIVE 359 129 81 90 40 NC_002950:PG0725|3end_hydrolase,_haloacid_dehalogenase-like_family_777966..778116_POSITIVE 345 199 151 151 96 NC_002950:PG0430|3end_ferrodoxin_oxidoreductase_beta_subunit_469073..469223_POSITIVE 345 130 83 68 31 NC_002950:PG0308|3end_electron_transport_complex,_RnfABCDGE_type,_A_subunit_343827..343977_POSITIVE 335 157 115 47 7 NC_002950:PG0791|3end_adenylate_kinase_842593..842743_NEGATIVE 335 200 159 86 31 NC_002950:PG0670|3end_lipoprotein,_putative_721971..722121_POSITIVE 333 80 41 36 4 NC_002950:PG1388|3end_hypothetical_protein_1470095..1470245_NEGATIVE 330 180 132 65 23 NC_002950:PG1685|3end_hypothetical_protein_1772216..1772366_NEGATIVE 328 200 156 101 51 NC_002950:PG1949|3end_malate_dehydrogenase_2038184..2038334_NEGATIVE 327 170 125 95 39 NC_002950:PG1640|3end_DNA-damage-inducible_protein_F_1719935..1720085_NEGATIVE