Origin IGS: gagacaaaaataagcggtctgtaccaattattttagcgaaacgatattacgatccatcctaaagttccggccaaatcagattgcacgggttggtttatgcgcaagatttttctcttttgtccttcttgaaaacgtgacgtgcaccgaaaaagttgatgctcggaatcggtcaaatgtttcgacataattaacatcagcacgatagtccatttagagccggtgccatagagtggagcagtttttgtagttaatacagtgtacatttgtgtcgataaaaggcgaacaacccttttcgaccgcatcaacatgctgataatgaataaaataaaaaagtgaaagcaatata .........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 tatattgctttcacttttttattttattcattatcagcatgttgatgcggtcgaaaagggttgttcgccttttatcgacacaaatgtacactgtattaactacaaaaactgctccactctatggcaccggctctaaatggactatcgtgctgatgttaattatgtcgaaacatttgaccgattccgagcatcaactttttcggtgcacgtcacgttttcaagaaggacaaaagagaaaaatcttgcgcataaaccaacccgtgcaatctgatttggccggaactttaggatggatcgtaatatcgtttcgctaaaataattggtacagaccgcttatttttgtctc Mask Tandem Repeat Region ================================================ gagacaaaaataagcggtctgtaccaattattttagcgaaacgatattacgatccatcctaaagttccggccaaatcagattgcacgggttggtttatgcgcaagatttttctcttttgtccttcttgaaaacgtgacgtgcaccgaaaaagttgatgctcggaatcggtcaaatgtttcgacataattaacatcagcacgatagtccatttagagccggtgccatagagtggagcagtttttgtagttaatacagtgtacatttgtgtcgataaaaggcgaacaacccttttcgaccgcatcaacatgctgataatgaataaaataaaaaagtgaaagcaatata Find is-nt database================================================ Query_seq: PG1774:PG1775|PG1774:PG1775:transcription-repair coupling factor:grpE protein:<-->:1864638..1864983 346 gagacaaaaataagcggtctgtaccaattattttagcgaaacgatattacgatccatcctaaagttccggccaaatcagattgcacgggttggtttatgcgcaagatttttctcttttgtccttcttgaaaacgtgacgtgcaccgaaaaagttgatgctcggaatcggtcaaatgtttcgacataattaacatcagcacgatagtccatttagagccggtgccatagagtggagcagtttttgtagttaatacagtgtacatttgtgtcgataaaaggcgaacaacccttttcgaccgcatcaacatgctgataatgaataaaataaaaaagtgaaagcaatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1774:PG1775|PG1774:PG1775:transcription-repair coupling factor:grpE protein:<-->:1864638..1864983 346 gagacaaaaataagcggtctgtaccaattattttagcgaaacgatattacgatccatcctaaagttccggccaaatcagattgcacgggttggtttatgcgcaagatttttctcttttgtccttcttgaaaacgtgacgtgcaccgaaaaagttgatgctcggaatcggtcaaatgtttcgacataattaacatcagcacgatagtccatttagagccggtgccatagagtggagcagtttttgtagttaatacagtgtacatttgtgtcgataaaaggcgaacaacccttttcgaccgcatcaacatgctgataatgaataaaataaaaaagtgaaagcaatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1774:PG1775|PG1774:PG1775:transcription-repair coupling factor:grpE protein:<-->:1864638..1864983 346 gagacaaaaataagcggtctgtaccaattattttagcgaaacgatattacgatccatcctaaagttccggccaaatcagattgcacgggttggtttatgcgcaagatttttctcttttgtccttcttgaaaacgtgacgtgcaccgaaaaagttgatgctcggaatcggtcaaatgtttcgacataattaacatcagcacgatagtccatttagagccggtgccatagagtggagcagtttttgtagttaatacagtgtacatttgtgtcgataaaaggcgaacaacccttttcgaccgcatcaacatgctgataatgaataaaataaaaaagtgaaagcaatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagacaaaaataagcggtctgtaccaattattttagcgaaacgatattacgatccatcctaaagttccggccaaatcagattgcacgggttggtttatgcgcaagatttttctcttttgtccttcttgaaaacgtgacgtgcaccgaaaaagttgatgctcggaatcggtcaaatgtttcgacataattaacatcagcacgatagtccatttagagccggtgccatagagtggagcagtttttgtagttaatacagtgtacatttgtgtcgataaaaggcgaacaacccttttcgaccgcatcaacatgctgataatgaataaaataaaaaagtgaaagcaatata Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 44 End: 184 ........................................... M L R S I L K F R P N Q I A R V G L C A R F F S F V L L E N V T C T E K V D A R N R S N V S T .................................................................................................................................................................. Protein_Len: 44 Strand: - Start: 214 End: 345 ..................................................................................................................................................................................................................... L R H W L T S C N K Y N I C H V N T D I F P S C G K E V A D V H Q Y H I F Y F L S L L M . Protein_Len: 44 Strand: - Start: 79 End: 210 .............................................................................. I A R T P K H A L N K E K T R R S F T V H V S F T S A R F R D F T E V Y N V D A R Y D M ........................................................................................................................................ Protein_Len: 60 Strand: - Start: 36 End: 326 ................................... F L Q H E S D T L H K S M I L M L V I T W K S G T G Y L P A T K T T L V T Y M Q T S L L R V V R K S R M L M S I I F L M .................... gagacaaaaataagcggtctgtaccaattattttagcgaaacgatattacgatccatcctaaagttccggccaaatcagattgcacgggttggtttatgcgcaagatttttctcttttgtccttcttgaaaacgtgacgtgcaccgaaaaagttgatgctcggaatcggtcaaatgtttcgacataattaacatcagcacgatagtccatttagagccggtgccatagagtggagcagtttttgtagttaatacagtgtacatttgtgtcgataaaaggcgaacaacccttttcgaccgcatcaacatgctgataatgaataaaataaaaaagtgaaagcaatata 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================================================ gagacaaaaataagcggtctgtaccaattattttagcgaaacgatattacgatccatcctaaagttccggccaaatcagattgcacgggttggtttatgcgcaagatttttctcttttgtccttcttgaaaacgtgacgtgcaccgaaaaagttgatgctcggaatcggtcaaatgtttcgacataattaacatcagcacgatagtccatttagagccggtgccatagagtggagcagtttttgtagttaatacagtgtacatttgtgtcgataaaaggcgaacaacccttttcgaccgcatcaacatgctgataatgaataaaataaaaaagtgaaagcaatata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1774:PG1775|PG1774:PG1775:transcription-repair coupling factor:grpE protein:<-->:1864638..1864983 346 gagacaaaaataagcggtctgtaccaattattttagcgaaacgatattacgatccatcctaaagttccggccaaatcagattgcacgggttggtttatgcgcaagatttttctcttttgtccttcttgaaaacgtgacgtgcaccgaaaaagttgatgctcggaatcggtcaaatgtttcgacataattaacatcagcacgatagtccatttagagccggtgccatagagtggagcagtttttgtagttaatacagtgtacatttgtgtcgataaaaggcgaacaacccttttcgaccgcatcaacatgctgataatgaataaaataaaaaagtgaaagcaatata Intra-Species Hit: Count: 1 Min: 1 Max: 346 Len: 346 Subject: NC_002950_PG1774_PG1775|transcription-repair coupling factor:grpE protein|NEGATIVE:POSITIVE|[1864638,1864983]|346 HSP 1 e-value: 0.0 bit: 686.0 Len: 346 Query Start:1 Query End:346 Subject Strand: POSITIVE Subject Start: 1 Subject End: 346 gagacaaaaataagcggtctgtaccaattattttagcgaaacgatattacgatccatcctaaagttccggccaaatcagattgcacgggttggtttatgcgcaagatttttctcttttgtccttcttgaaaacgtgacgtgcaccgaaaaagttgatgctcggaatcggtcaaatgtttcgacataattaacatcagcacgatagtccatttagagccggtgccatagagtggagcagtttttgtagttaatacagtgtacatttgtgtcgataaaaggcgaacaacccttttcgaccgcatcaacatgctgataatgaataaaataaaaaagtgaaagcaatata gagacaaaaataagcggtctgtaccaattattttagcgaaacgatattacgatccatcctaaagttccggccaaatcagattgcacgggttggtttatgcgcaagatttttctcttttgtccttcttgaaaacgtgacgtgcaccgaaaaagttgatgctcggaatcggtcaaatgtttcgacataattaacatcagcacgatagtccatttagagccggtgccatagagtggagcagtttttgtagttaatacagtgtacatttgtgtcgataaaaggcgaacaacccttttcgaccgcatcaacatgctgataatgaataaaataaaaaagtgaaagcaatata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGACAAAAAUAAGCGGUCUGUACCAAUUAUUUUAGCGAAACGAUAUUACGAUCCAUCCUAAAGUUCCGGCCAAAUCAGAUUGCACGGGUUGGUUUAUGCGCAAGAUUUUUCUCUUUUGUCCUUCUUGAAAACGUGACGUGCACCGAAAAAGUUGAUGCUCGGAAUCGGUCAAAUGUUUCGACAUAAUUAACAUCAGCACGAUAGUCCAUUUAGAGCCGGUGCCAUAGAGUGGAGCAGUUUUUGUAGUUAAUACAGUGUACAUUUGUGUCGAUAAAAGGCGAACAACCCUUUUCGACCGCAUCAACAUGCUGAUAAUGAAUAAAAUAAAAAAGUGAAAGCAAUAUA ......(((((((..(((....)))..))))))).((..(((.(((..((..((((..(((..((.((((((((((..(((((..((.(((((((((((..(((((.....(......)....)))))....((.(((((..(((((...(((....))).....)))))...))))).)).))))).....)))))).)).))))).)))).).))))).))..)))..))))...))...))).)))....((((((.....((((((((..(((((........))))))))).)))).....))))))..........................))...... (-73.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAUUGCUUUCACUUUUUUAUUUUAUUCAUUAUCAGCAUGUUGAUGCGGUCGAAAAGGGUUGUUCGCCUUUUAUCGACACAAAUGUACACUGUAUUAACUACAAAAACUGCUCCACUCUAUGGCACCGGCUCUAAAUGGACUAUCGUGCUGAUGUUAAUUAUGUCGAAACAUUUGACCGAUUCCGAGCAUCAACUUUUUCGGUGCACGUCACGUUUUCAAGAAGGACAAAAGAGAAAAAUCUUGCGCAUAAACCAACCCGUGCAAUCUGAUUUGGCCGGAACUUUAGGAUGGAUCGUAAUAUCGUUUCGCUAAAAUAAUUGGUACAGACCGCUUAUUUUUGUCUC .(((((((................................(((((((((((((((((((((.....))))))).)))..((....))..)))))))))))............((((..(((.((..((((((.....((((..((((..(.((((((...........)))))).)..)))))))).............((((((((((....(((((.....)))))..((((......))))...............))))))..))))...))))))..)).)))..))))..)))))))......((.(((((((.((((....)))).))))))).))... (-76.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 956 100 51 191 142 NC_002950:PG1774|5end_transcription-repair_coupling_factor_1864547..1864777_NEGATIVE 378 100 54 184 135 NC_002950:PG0653|5end_phosphoserine_phosphatase_705454..705684_NEGATIVE 354 234 191 74 22 NC_002950:PG1196|5end_hypothetical_protein_1275127..1275357_POSITIVE 347 110 70 141 104 NC_002950:PG1096|5end_hypothetical_protein_1161839..1162069_POSITIVE 346 236 192 58 14 NC_002950:PG2185|5end_transporter,_putative_2293249..2293479_NEGATIVE 333 237 193 158 104 NC_002950:PG0515|5end_hypothetical_protein_557958..558188_NEGATIVE 332 89 47 112 81 NC_002950:PG0085|5end_alpha-galactosidase_99172..99402_POSITIVE 319 244 216 183 153 NC_002950:PG1837|5end_hemagglutinin_protein_HagA_1930337..1930567_POSITIVE 319 236 196 42 3 NC_002950:PG0656|5end_50S_ribosomal_protein_L34_707097..707327_NEGATIVE 316 238 195 100 46 NC_002950:PG0631|5end_MotA/TolQ/ExbB_proton_channel_family_protein_684266..684496_POSITIVE 314 309 262 147 92 NC_002950:PG0476|5end_yngK_protein_518762..518992_NEGATIVE 312 248 206 231 184 NC_002950:PG1496|5end_hypothetical_protein_1573342..1573572_POSITIVE 312 236 200 198 156 NC_002950:PG0305|5end_electron_transport_complex,_RnfABCDGE_type,_D_subunit_340906..341136_POSITIVE 311 69 21 152 102 NC_002950:PG0450|5end_hypothetical_protein_490812..491042_POSITIVE 309 238 197 67 33 NC_002950:PG2227|5end_hypothetical_protein_2342008..2342238_POSITIVE 309 245 201 162 130 NC_002950:PG0304|5end_electron_transport_complex,_RnfABCDGE_type,_C_subunit_339559..339789_POSITIVE 308 170 121 214 157 NC_002950:PG0312|5end_hypothetical_protein_347048..347278_NEGATIVE 308 177 132 231 186 NC_002950:PG0074|5end_peptide_chain_release_factor_1_89172..89402_NEGATIVE 307 244 205 75 35 NC_002950:PG0164|5end_hypothetical_protein_187395..187625_NEGATIVE 306 246 202 130 81 NC_002950:PG2146|5end_hypothetical_protein_2253815..2254045_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 415 180 131 55 3 NC_002950:PG0294|3end_glycosyl_transferase,_group_2_family_protein_329271..329421_NEGATIVE 378 100 54 125 76 NC_002950:PG0654|3end_hypothetical_protein_705513..705663_NEGATIVE 354 240 192 82 27 NC_002950:PG1574|3end_hypothetical_protein_1652461..1652611_NEGATIVE 354 234 191 74 22 NC_002950:PG1195|3end_8-amino-7-oxononanoate_synthase_1275207..1275357_POSITIVE 336 270 223 85 39 NC_002950:PG0775|3end_acyl-CoA_dehydrogenase_family_protein_827432..827582_NEGATIVE 335 235 195 105 52 NC_002950:PG0815|3end_hypothetical_protein_876447..876597_POSITIVE 329 260 213 133 80 NC_002950:PG0453|3end_hypothetical_protein_496670..496820_POSITIVE 321 239 199 78 44 NC_002950:PG1186|3end_hypothetical_protein_1267703..1267853_NEGATIVE 316 92 55 141 96 NC_002950:PG0445|3end_peptidase_T_486549..486699_POSITIVE 314 89 41 138 84 NC_002950:PG2082|3end_POT_family_protein_2181843..2181993_NEGATIVE 311 69 21 127 77 NC_002950:PG0449|3end_TPR_domain_protein_490867..491017_POSITIVE 309 238 197 70 36 NC_002950:PG2226|3end_hypothetical_protein_2342091..2342241_POSITIVE 309 123 82 113 65 NC_002950:PG2146|3end_hypothetical_protein_2254650..2254800_POSITIVE 309 245 201 126 94 NC_002950:PG0303|3end_ferredoxin_339603..339753_POSITIVE 307 244 205 100 60 NC_002950:PG0165|3end_heat_shock_protein_15_187370..187520_NEGATIVE 306 107 64 146 99 NC_002950:PG2053|3end_dithiobiotin_synthetase_2151267..2151417_POSITIVE 306 250 206 67 23 NC_002950:PG2034|3end_oxidoreductase,_FAD-binding,_putative_2134910..2135060_NEGATIVE 306 314 277 40 3 NC_002950:PG1495|3end_DNA_topoisomerase_III_1573416..1573566_POSITIVE 305 148 104 72 29 NC_002950:PG0792|3end_hypoxanthine_phosphoribosyltransferase_843178..843328_NEGATIVE 303 110 69 111 51 NC_002950:PG2224|3end_hypothetical_protein_2339500..2339650_POSITIVE