Origin IGS: gcgacaaacccaatgaaaaacaggttgggttgaattatagacgtgagcaaataagcaaatccatctgtgatgaagtatctctcacgcaaaaaaagaggggatctcttgataaattggaattgccaatttatcaagagatcccctctccacttatttgtttccctatggtaggattcgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcgaatcctaccatagggaaacaaataagtggagaggggatctcttgataaattggcaattccaatttatcaagagatcccctctttttttgcgtgagagatacttcatcacagatggatttgcttatttgctcacgtctataattcaacccaacctgtttttcattgggtttgtcgc Mask Tandem Repeat Region ================================================ gcgacaaacccaatgaaaaacaggttgggttgaattatagacgtgagcaaataagcaaatccatctgtgatgaagtatctctcacgcaaaaaaagaggggatctcttgataaattggaattgccaatttatcaagagatcccctctccacttatttgtttccctatggtaggattcgc Find is-nt database================================================ Query_seq: PG1373:PG1374|PG1373:PG1374:hypothetical protein:immunoreactive 47 kDa antigen PG97:-><-:1455166..1455343 178 gcgacaaacccaatgaaaaacaggttgggttgaattatagacgtgagcaaataagcaaatccatctgtgatgaagtatctctcacgcaaaaaaagaggggatctcttgataaattggaattgccaatttatcaagagatcccctctccacttatttgtttccctatggtaggattcgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1373:PG1374|PG1373:PG1374:hypothetical protein:immunoreactive 47 kDa antigen PG97:-><-:1455166..1455343 178 gcgacaaacccaatgaaaaacaggttgggttgaattatagacgtgagcaaataagcaaatccatctgtgatgaagtatctctcacgcaaaaaaagaggggatctcttgataaattggaattgccaatttatcaagagatcccctctccacttatttgtttccctatggtaggattcgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1373:PG1374|PG1373:PG1374:hypothetical protein:immunoreactive 47 kDa antigen PG97:-><-:1455166..1455343 178 gcgacaaacccaatgaaaaacaggttgggttgaattatagacgtgagcaaataagcaaatccatctgtgatgaagtatctctcacgcaaaaaaagaggggatctcttgataaattggaattgccaatttatcaagagatcccctctccacttatttgtttccctatggtaggattcgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcgacaaacccaatgaaaaacaggttgggttgaattatagacgtgagcaaataagcaaatccatctgtgatgaagtatctctcacgcaaaaaaagaggggatctcttgataaattggaattgccaatttatcaagagatcccctctccacttatttgtttccctatggtaggattcgc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 67 End: 168 .................................................................. M M K Y L S R K K R G D L L I N W N C Q F I K R S P L H L F V S L W .......... Protein_Len: 49 Strand: + Start: 30 End: 176 ............................. M N Y R R E Q I S K S I C D E V S L T Q K K R G S L D K L E L P I Y Q E I P S P L I C F P M V G F .. Protein_Len: 30 Strand: - Start: 38 End: 127 ..................................... L R S C I L L D M Q S S T D R V C F F L P D R S L N S N G M ................................................... Protein_Len: 44 Strand: - Start: 3 End: 134 .. V F G I F F L N P Q I I S T L L Y A F G D T I F Y R E R L F L P S R K I F Q F Q W N I M ............................................ gcgacaaacccaatgaaaaacaggttgggttgaattatagacgtgagcaaataagcaaatccatctgtgatgaagtatctctcacgcaaaaaaagaggggatctcttgataaattggaattgccaatttatcaagagatcccctctccacttatttgtttccctatggtaggattcgc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 106 End: 135 .........................................................................................................CTTGATAAATTGGCAATTCCAATTTATCAA........................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcgacaaacccaatgaaaaacaggttgggttgaattatagacgtgagcaaataagcaaatccatctgtgatgaagtatctctcacgcaaaaaaagaggggatctcttgataaattggaattgccaatttatcaagagatcccctctccacttatttgtttccctatggtaggattcgc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -22.1 Tail_Score: -3.19486 Start: 91 End: 149 Full_Region: TATCTCTCACGCAAA AAAAGAGGGGATCTCTTGATAAATTGG AATTG CCAATTTATCAAGAGATCCCCTCTCCA CTTATTTGTTTCCCT ..........................................................................................AAAAGAGGGGATCTCTTGATAAATTGGAATTGCCAATTTATCAAGAGATCCCCTCTCCA............................. TransTerm Strand: + Conf: 100 HP_score: -25.6 Tail_Score: -2.50607 Start: 92 End: 148 Full_Region: ATCTCTCACGCAAAA AAAGAGGGGATCTCTTGATAAATTGG AATTG CCAATTTATCAAGAGATCCCCTCTCC ACTTATTTGTTTCCC ...........................................................................................AAAGAGGGGATCTCTTGATAAATTGGAATTGCCAATTTATCAAGAGATCCCCTCTCC.............................. TransTerm Strand: + Conf: 100 HP_score: -13.6 Tail_Score: -4.34285 Start: 92 End: 150 Full_Region: ATCTCTCACGCAAAA AAAGAGGGGATCTCTTGATAAATTGG AATTG CCAATTTATCAAGAGATCCCCTCTCCAC TTATTTGTTTCCCTA ...........................................................................................AAAGAGGGGATCTCTTGATAAATTGGAATTGCCAATTTATCAAGAGATCCCCTCTCCAC............................ TransTerm Strand: - Conf: 100 HP_score: -31.7 Tail_Score: -5.47218 Start: 95 End: 145 Full_Region: aaacaaataagtgga gaggggatctcttgataaattgg caatt ccaatttatcaagagatcccctc tttttttgcgtgaga ..............................................................................................gaggggatctcttgataaattggcaattccaatttatcaagagatcccctc................................. Find igs database================================================ Query_seq: PG1373:PG1374|PG1373:PG1374:hypothetical protein:immunoreactive 47 kDa antigen PG97:-><-:1455166..1455343 178 gcgacaaacccaatgaaaaacaggttgggttgaattatagacgtgagcaaataagcaaatccatctgtgatgaagtatctctcacgcaaaaaaagaggggatctcttgataaattggaattgccaatttatcaagagatcccctctccacttatttgtttccctatggtaggattcgc Intra-Species Hit: Count: 1 Min: 1 Max: 178 Len: 178 Subject: NC_002950_PG1373_PG1374|hypothetical protein:immunoreactive 47 kDa antigen PG97|POSITIVE:NEGATIVE|[1455166,1455343]|178 HSP 1 e-value: 4.0E-84 bit: 311.0 Len: 178 Query Start:1 Query End:178 Subject Strand: POSITIVE Subject Start: 1 Subject End: 178 gcgacaaacccaatgaaaaacaggttgggttgaattatagacgtgagcaaataagcaaatccatctgtgatgaagtatctctcacgcnnnnnnngaggggatctcttgataaattggaattgccaatttatcaagagatcccctctccacttatttgtttccctatggtaggattcgc gcgacaaacccaatgaaaaacaggttgggttgaattatagacgtgagcaaataagcaaatccatctgtgatgaagtatctctcacgcaaaaaaagaggggatctcttgataaattggaattgccaatttatcaagagatcccctctccacttatttgtttccctatggtaggattcgc HSP 2 e-value: 3.0E-14 bit: 79.8 Len: 52 Query Start:95 Query End:146 Subject Strand: NEGATIVE Subject Start: 94 Subject End: 145 ..............................................................................................gaggggatctcttgataaattggaattgccaatttatcaagagatcccctct................................ ..............................................................................................gaggggatctcttgataaattggcaattccaatttatcaagagatcccctct................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGACAAACCCAAUGAAAAACAGGUUGGGUUGAAUUAUAGACGUGAGCAAAUAAGCAAAUCCAUCUGUGAUGAAGUAUCUCUCACGCAAAAAAAGAGGGGAUCUCUUGAUAAAUUGGAAUUGCCAAUUUAUCAAGAGAUCCCCUCUCCACUUAUUUGUUUCCCUAUGGUAGGAUUCGC ((((..((((((((.........))))))))..(((((((..(..((((((((((...........((((.((......))))))........((((((((((((((((((((((((.....))))))))))))))))))))))))...))))))))))..)))))))).....)))) (-72.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGAAUCCUACCAUAGGGAAACAAAUAAGUGGAGAGGGGAUCUCUUGAUAAAUUGGCAAUUCCAAUUUAUCAAGAGAUCCCCUCUUUUUUUGCGUGAGAGAUACUUCAUCACAGAUGGAUUUGCUUAUUUGCUCACGUCUAUAAUUCAACCCAACCUGUUUUUCAUUGGGUUUGUCGC ((((......(((..(..(((((.......((((((((((((((((((((((((((.....))))))))))))))))))))))))))....((((((((((((.((((((...))))))......))))).)))))))..................)))))..)..))).....)))) (-71.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 165 122 199 151 NC_002950:PG0677|5end_saccharopine_dehydrogenase_727653..727883_POSITIVE 316 101 61 50 22 NC_002950:PG0093|5end_HlyD_family_secretion_protein_109638..109868_NEGATIVE 300 98 55 111 59 NC_002950:PG0361|5end_hypothetical_protein_394094..394324_POSITIVE 286 110 62 77 15 NC_002950:PG0424|5end_hypothetical_protein_462468..462698_POSITIVE 272 69 29 224 182 NC_002950:PG0757|5end_hypothetical_protein_806370..806600_NEGATIVE 265 110 64 46 10 NC_002950:PG1009|5end_hypothetical_protein_1068495..1068725_NEGATIVE 262 100 53 48 2 NC_002950:PG0280|5end_ABC_transporter,_permease_protein,_putative_314625..314855_NEGATIVE 261 101 61 120 69 NC_002950:PG2162|5end_lipid_A_disaccharide_synthase_2268764..2268994_NEGATIVE 261 69 28 214 171 NC_002950:PG1847|5end_endoribonuclease_L-PSP,_putative_1946607..1946837_NEGATIVE 252 110 61 80 33 NC_002950:PG1067|5end_hypothetical_protein_1134219..1134449_POSITIVE 251 119 72 100 41 NC_002950:PG0137|5end_aminoacyl-histidine_dipeptidase_159104..159334_POSITIVE 246 101 62 181 146 NC_002950:PG0583|5end_cell_division_protein_FtsA_640425..640655_POSITIVE 241 126 94 34 4 NC_002950:PG1159|5end_cobalamin_biosynthesis_protein_CbiB_1238967..1239197_NEGATIVE 241 70 23 204 154 NC_002950:PG0309|5end_thiamine_biosynthesis_lipoprotein_ApbE_345023..345253_NEGATIVE 238 70 22 111 61 NC_002950:PG1128|5end_exodeoxyribonuclease_VII_large_subunit_1203737..1203967_POSITIVE 237 70 27 154 108 NC_002950:PG1463|5end_hypothetical_protein_1541110..1541340_POSITIVE 236 170 122 217 168 NC_002950:PG2001|5end_signal_peptidase_I_2090855..2091085_NEGATIVE 234 109 61 128 63 NC_002950:PG1382|5end_hypothetical_protein_1461331..1461561_POSITIVE 234 67 21 226 181 NC_002950:PG1156|5end_S4_domain_protein_1236735..1236965_POSITIVE 234 48 1 97 47 NC_002950:PG1029|5end_hypothetical_protein_1091080..1091310_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 86 42 65 5 NC_002950:PG1855|3end_carboxyl-terminal_protease_1953842..1953992_NEGATIVE 300 98 55 89 37 NC_002950:PG0360|3end_lemA_protein_394152..394302_POSITIVE 286 110 62 102 40 NC_002950:PG0423|3end_hypothetical_protein_462573..462723_POSITIVE 272 69 29 127 85 NC_002950:PG0758|3end_peptidyl-dipeptidase_Dcp_806467..806617_NEGATIVE 261 101 61 83 32 NC_002950:PG2163|3end_acid_phosphatase_2268801..2268951_NEGATIVE 251 119 72 69 10 NC_002950:PG0136|3end_hypothetical_protein_159153..159303_POSITIVE 248 166 121 65 31 NC_002950:PG0068|3end_hypothetical_protein_82079..82229_POSITIVE 247 140 95 102 45 NC_002950:PG2177|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_F_2285266..2285416_NEGATIVE 247 148 102 113 64 NC_002950:PG1980|3end_hypothetical_protein_2067760..2067910_NEGATIVE 246 101 62 132 97 NC_002950:PG0582|3end_cell_division_protein_FtsQ,_putative_640456..640606_POSITIVE 240 125 86 57 20 NC_002950:PG2117|3end_30S_ribosomal_protein_S16_2225235..2225385_NEGATIVE 238 70 22 64 14 NC_002950:PG1127|3end_transcriptional_regulator,_AsnC_Family_1203770..1203920_POSITIVE 237 70 27 131 85 NC_002950:PG1462|3end_hypothetical_protein_1541167..1541317_POSITIVE 227 164 136 130 96 NC_002950:PG1222|3end_hypothetical_protein_1299075..1299225_NEGATIVE 227 103 62 62 5 NC_002950:PG1020|3end_hypothetical_protein_1083458..1083608_POSITIVE 226 157 114 142 95 NC_002950:PG1820|3end_cytochrome_c_nitrite_reductase,_catalytic_subunit_NrfA_1914393..1914543_NEGATIVE 225 134 93 123 73 NC_002950:PG1304|3end_hypothetical_protein_1382134..1382284_NEGATIVE 225 110 75 32 1 NC_002950:PG1010|3end_ABC_transporter,_ATP-binding_protein_1068509..1068659_NEGATIVE 225 110 77 132 98 NC_002950:PG0272|3end_CBS_domain_protein_305738..305888_POSITIVE 224 100 54 81 27 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE