Origin IGS: gatcttgctctcctgtgtacggaaaaaggcacgaatatgcttcctgaaaatgcggtctgagaaaaaattttttctcgaaccggaaagaaaatttttacgctcgtaaacgaaaaatttttggcacgtgttttcgaatttttacgaaccgcaatttgatgatttctggttcgtgtttgtttggcggatcttccccgttccgtccgaaaaggatgggtgcttagcctgaggcgagaggtcgcgtgtagt .........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 actacacgcgacctctcgcctcaggctaagcacccatccttttcggacggaacggggaagatccgccaaacaaacacgaaccagaaatcatcaaattgcggttcgtaaaaattcgaaaacacgtgccaaaaatttttcgtttacgagcgtaaaaattttctttccggttcgagaaaaaattttttctcagaccgcattttcaggaagcatattcgtgcctttttccgtacacaggagagcaagatc Mask Tandem Repeat Region ================================================ gatcttgctctcctgtgtacggaaaaaggcacgaatatgcttcctgaaaatgcggtctgagaaaaaattttttctcgaaccggaaagaaaatttttacgctcgtaaacgaaaaatttttggcacgtgttttcgaatttttacgaaccgcaatttgatgatttctggttcgtgtttgtttggcggatcttccccgttccgtccgaaaaggatgggtgcttagcctgaggcgagaggtcgcgtgtagt Find is-nt database================================================ Query_seq: PG0066:PG0068|PG0066:PG0068:hypothetical protein:hypothetical protein:<-->:81642..81887 246 gatcttgctctcctgtgtacggaaaaaggcacgaatatgcttcctgaaaatgcggtctgagaaaaaattttttctcgaaccggaaagaaaatttttacgctcgtaaacgaaaaatttttggcacgtgttttcgaatttttacgaaccgcaatttgatgatttctggttcgtgtttgtttggcggatcttccccgttccgtccgaaaaggatgggtgcttagcctgaggcgagaggtcgcgtgtagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0066:PG0068|PG0066:PG0068:hypothetical protein:hypothetical protein:<-->:81642..81887 246 gatcttgctctcctgtgtacggaaaaaggcacgaatatgcttcctgaaaatgcggtctgagaaaaaattttttctcgaaccggaaagaaaatttttacgctcgtaaacgaaaaatttttggcacgtgttttcgaatttttacgaaccgcaatttgatgatttctggttcgtgtttgtttggcggatcttccccgttccgtccgaaaaggatgggtgcttagcctgaggcgagaggtcgcgtgtagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0066:PG0068|PG0066:PG0068:hypothetical protein:hypothetical protein:<-->:81642..81887 246 gatcttgctctcctgtgtacggaaaaaggcacgaatatgcttcctgaaaatgcggtctgagaaaaaattttttctcgaaccggaaagaaaatttttacgctcgtaaacgaaaaatttttggcacgtgttttcgaatttttacgaaccgcaatttgatgatttctggttcgtgtttgtttggcggatcttccccgttccgtccgaaaaggatgggtgcttagcctgaggcgagaggtcgcgtgtagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatcttgctctcctgtgtacggaaaaaggcacgaatatgcttcctgaaaatgcggtctgagaaaaaattttttctcgaaccggaaagaaaatttttacgctcgtaaacgaaaaatttttggcacgtgttttcgaatttttacgaaccgcaatttgatgatttctggttcgtgtttgtttggcggatcttccccgttccgtccgaaaaggatgggtgcttagcctgaggcgagaggtcgcgtgtagt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 2 End: 103 . M L L S C V R K K A R I C F L K M R S E K K F F L E P E R K F L R S ............................................................................................................................................... Protein_Len: 54 Strand: + Start: 57 End: 218 ........................................................ M R K N F F S N R K E N F Y A R K R K I F G T C F R I F T N R N L M I S G S C L F G G S S P F R P K R M G A ............................ Protein_Len: 33 Strand: + Start: 125 End: 223 ............................................................................................................................ M F S N F Y E P Q F D D F W F V F V W R I F P V P S E K D G C L A ....................... Protein_Len: 38 Strand: - Start: 98 End: 211 ................................................................................................. A R L R F I K P V H K R I K V F R L K I I E P E H K N P P D E G N R G F L M ................................... Protein_Len: 50 Strand: - Start: 3 End: 152 .. R A R R H V S F P V F I S G S F A T Q S F I K E R V P F F I K V S T F S F N K A R T K S N K R V A M .............................................................................................. gatcttgctctcctgtgtacggaaaaaggcacgaatatgcttcctgaaaatgcggtctgagaaaaaattttttctcgaaccggaaagaaaatttttacgctcgtaaacgaaaaatttttggcacgtgttttcgaatttttacgaaccgcaatttgatgatttctggttcgtgtttgtttggcggatcttccccgttccgtccgaaaaggatgggtgcttagcctgaggcgagaggtcgcgtgtagt 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================================================ gatcttgctctcctgtgtacggaaaaaggcacgaatatgcttcctgaaaatgcggtctgagaaaaaattttttctcgaaccggaaagaaaatttttacgctcgtaaacgaaaaatttttggcacgtgttttcgaatttttacgaaccgcaatttgatgatttctggttcgtgtttgtttggcggatcttccccgttccgtccgaaaaggatgggtgcttagcctgaggcgagaggtcgcgtgtagt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -7.5 Tail_Score: -4.07885 Start: 51 End: 84 Full_Region: cgtaaaaattttctt tccggttcgagaaaa aatt ttttctcagaccgca ttttcaggaagcata ..................................................tccggttcgagaaaaaattttttctcagaccgca.................................................................................................................................................................. Find igs database================================================ Query_seq: PG0066:PG0068|PG0066:PG0068:hypothetical protein:hypothetical protein:<-->:81642..81887 246 gatcttgctctcctgtgtacggaaaaaggcacgaatatgcttcctgaaaatgcggtctgagaaaaaattttttctcgaaccggaaagaaaatttttacgctcgtaaacgaaaaatttttggcacgtgttttcgaatttttacgaaccgcaatttgatgatttctggttcgtgtttgtttggcggatcttccccgttccgtccgaaaaggatgggtgcttagcctgaggcgagaggtcgcgtgtagt Intra-Species Hit: Count: 1 Min: 1 Max: 246 Len: 246 Subject: NC_002950_PG0066_PG0068|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[81642,81887]|246 HSP 1 e-value: 5.0E-66 bit: 252.0 Len: 127 Query Start:120 Query End:246 Subject Strand: POSITIVE Subject Start: 120 Subject End: 246 .......................................................................................................................ggcacgtgttttcgaatttttacgaaccgcaatttgatgatttctggttcgtgtttgtttggcggatcttccccgttccgtccgaaaaggatgggtgcttagcctgaggcgagaggtcgcgtgtagt .......................................................................................................................ggcacgtgttttcgaatttttacgaaccgcaatttgatgatttctggttcgtgtttgtttggcggatcttccccgttccgtccgaaaaggatgggtgcttagcctgaggcgagaggtcgcgtgtagt HSP 2 e-value: 5.0E-26 bit: 119.0 Len: 60 Query Start:1 Query End:60 Subject Strand: POSITIVE Subject Start: 1 Subject End: 60 gatcttgctctcctgtgtacggaaaaaggcacgaatatgcttcctgaaaatgcggtctga.......................................................................................................................................................................................... gatcttgctctcctgtgtacggaaaaaggcacgaatatgcttcctgaaaatgcggtctga.......................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUCUUGCUCUCCUGUGUACGGAAAAAGGCACGAAUAUGCUUCCUGAAAAUGCGGUCUGAGAAAAAAUUUUUUCUCGAACCGGAAAGAAAAUUUUUACGCUCGUAAACGAAAAAUUUUUGGCACGUGUUUUCGAAUUUUUACGAACCGCAAUUUGAUGAUUUCUGGUUCGUGUUUGUUUGGCGGAUCUUCCCCGUUCCGUCCGAAAAGGAUGGGUGCUUAGCCUGAGGCGAGAGGUCGCGUGUAGU ((((((((((((((.((.((((((.((((((((....(((..........(.((((.((((((((....)))))))).)))).)..((((((((((.((........)))))))))))).))))))))))).((((...(((((((((.((((....))))..)))))))))...))))((.((.....)))).)))))).))...)))).)))).....(((...)))..))))))......... (-70.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUACACGCGACCUCUCGCCUCAGGCUAAGCACCCAUCCUUUUCGGACGGAACGGGGAAGAUCCGCCAAACAAACACGAACCAGAAAUCAUCAAAUUGCGGUUCGUAAAAAUUCGAAAACACGUGCCAAAAAUUUUUCGUUUACGAGCGUAAAAAUUUUCUUUCCGGUUCGAGAAAAAAUUUUUUCUCAGACCGCAUUUUCAGGAAGCAUAUUCGUGCCUUUUUCCGUACACAGGAGAGCAAGAUC .............(((.(((((...........((.(((.....))).)).((((..(((.(((...........(((((((...(((......)))..)))))))........(((((.........(((((((((((((....)))).))))))))).....((((..(((((((....)))))))..))))..))))).))).((((....)))).)))..))))......))).)).))).. (-58.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 945 60 11 151 102 NC_002950:PG0066|5end_hypothetical_protein_81551..81781_NEGATIVE 436 238 193 208 165 NC_002950:PG1633|5end_galactokinase_1713385..1713615_POSITIVE 427 240 193 195 149 NC_002950:PG0638|5end_tetraacyldisaccharide_4'-kinase_691183..691413_NEGATIVE 421 209 165 117 56 NC_002950:PG0133|5end_hypothetical_protein_155764..155994_NEGATIVE 416 230 182 222 161 NC_002950:PG0242|5end_conserved_hypothetical_protein_TIGR00096_278960..279190_NEGATIVE 411 237 192 132 96 NC_002950:PG2219|5end_potassium_uptake_protein_TrkH_2332947..2333177_POSITIVE 408 188 141 83 25 NC_002950:PG1655|5end_hypothetical_protein_1737095..1737325_POSITIVE 406 239 191 228 168 NC_002950:PG1348|5end_conserved_hypothetical_protein_TIGR00147_1428608..1428838_POSITIVE 397 239 191 199 151 NC_002950:PG1577|5end_nicotinate-nucleotide_pyrophosphorylase_1654619..1654849_POSITIVE 395 203 161 231 184 NC_002950:PG0397|5end_hypothetical_protein_434602..434832_NEGATIVE 395 240 192 212 164 NC_002950:PG0334|5end_glycosyl_transferase,_group_2_family_protein_369751..369981_NEGATIVE 394 229 181 141 99 NC_002950:PG2087|5end_hypothetical_protein_2186990..2187220_POSITIVE 393 230 181 85 34 NC_002950:PG1172|5end_iron-sulfur_cluster_binding_protein,_putative_1251173..1251403_POSITIVE 392 159 113 96 57 NC_002950:PG1407|5end_nitroimidazole_resistance_protein,_putative_1491648..1491878_NEGATIVE 388 240 191 70 19 NC_002950:PG1009|5end_hypothetical_protein_1068495..1068725_NEGATIVE 387 239 192 61 14 NC_002950:PG1008|5end_hypothetical_protein_1067644..1067874_NEGATIVE 379 240 191 210 136 NC_002950:PG2199|5end_ABC_transporter,_ATP-binding_protein,_putative_2306723..2306953_NEGATIVE 379 240 194 177 133 NC_002950:PG2111|5end_thiS_protein_2221482..2221712_NEGATIVE 377 229 181 76 36 NC_002950:PG1851|5end_phosphopantothenoylcysteine_decarboxylase/phosphopantothenate--cysteine_ligase_1951168..1951398_NEGATIVE 372 217 172 117 69 NC_002950:PG0164|5end_hypothetical_protein_187395..187625_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 432 239 194 144 80 NC_002950:PG0199|3end_TatD_family_protein_237424..237574_NEGATIVE 421 209 165 98 37 NC_002950:PG0134|3end_magnesium_transporter_155783..155933_NEGATIVE 411 237 192 105 69 NC_002950:PG2218|3end_potassium_uptake_protein_TrkA_2333000..2333150_POSITIVE 410 237 193 151 102 NC_002950:PG1472|3end_hypothetical_protein_1549760..1549910_POSITIVE 408 188 141 69 11 NC_002950:PG1654|3end_D-alanyl-D-alanine_dipeptidase_1737161..1737311_POSITIVE 394 229 181 141 99 NC_002950:PG2086|3end_hypothetical_protein_2187070..2187220_POSITIVE 388 240 191 56 5 NC_002950:PG1010|3end_ABC_transporter,_ATP-binding_protein_1068509..1068659_NEGATIVE 387 239 192 64 17 NC_002950:PG1009|3end_hypothetical_protein_1067641..1067791_NEGATIVE 383 230 182 147 105 NC_002950:PG1632|3end_aldose_1-epimerase_1713415..1713565_POSITIVE 377 229 181 50 10 NC_002950:PG1852|3end_exonuclease_1951194..1951344_NEGATIVE 373 229 182 88 43 NC_002950:PG1942|3end_30S_ribosomal_protein_S12_2027946..2028096_NEGATIVE 373 239 191 90 25 NC_002950:PG1866|3end_hypothetical_protein_1964736..1964886_POSITIVE 372 217 172 142 94 NC_002950:PG0165|3end_heat_shock_protein_15_187370..187520_NEGATIVE 370 239 193 135 95 NC_002950:PG2119|3end_oxidoreductase,_Gfo/Idh/MocA_family_2227598..2227748_POSITIVE 370 219 171 138 88 NC_002950:PG1576|3end_L-aspartate_oxidase_1654652..1654802_POSITIVE 366 239 192 132 85 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 366 184 141 140 100 NC_002950:PG0732|3end_hypothetical_protein_783018..783168_POSITIVE 362 184 141 50 4 NC_002950:PG2227|3end_hypothetical_protein_2342744..2342894_POSITIVE 357 240 192 74 16 NC_002950:PG2226|3end_hypothetical_protein_2342091..2342241_POSITIVE 356 240 193 77 30 NC_002950:PG0725|3end_hydrolase,_haloacid_dehalogenase-like_family_777966..778116_POSITIVE