Origin IGS: ttagctcccacgcctatatcggcaattagcggcacacgaagttcgggcatcacgccttccacggcaacgaagatgcatacgagaagcatttcgatgcgttggaagaggcaaatagcttgccaaatcgaggaaatgaaaagtcgttcgtagagcttaaaatgatgccgatatccttcactacataatctgtttgcatttatttgtggaatgtgcagagcgacacgatgtccgaaatttgctgaaaataatgtacctttgccgcgctgattattatcaaatagtgccgaacggtttgattttcagtgcgtttttgtccgagaggagcagcccagtgtccgtgcgtaaagctcctgatgcaccggccgaatcgacagaaaagatgatcgttcaccaaattactaacaacaaaaaaacaagca .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgcttgtttttttgttgttagtaatttggtgaacgatcatcttttctgtcgattcggccggtgcatcaggagctttacgcacggacactgggctgctcctctcggacaaaaacgcactgaaaatcaaaccgttcggcactatttgataataatcagcgcggcaaaggtacattattttcagcaaatttcggacatcgtgtcgctctgcacattccacaaataaatgcaaacagattatgtagtgaaggatatcggcatcattttaagctctacgaacgacttttcatttcctcgatttggcaagctatttgcctcttccaacgcatcgaaatgcttctcgtatgcatcttcgttgccgtggaaggcgtgatgcccgaacttcgtgtgccgctaattgccgatataggcgtgggagctaa Mask Tandem Repeat Region ================================================ ttagctcccacgcctatatcggcaattagcggcacacgaagttcgggcatcacgccttccacggcaacgaagatgcatacgagaagcatttcgatgcgttggaagaggcaaatagcttgccaaatcgaggaaatgaaaagtcgttcgtagagcttaaaatgatgccgatatccttcactacataatctgtttgcatttatttgtggaatgtgcagagcgacacgatgtccgaaatttgctgaaaataatgtacctttgccgcgctgattattatcaaatagtgccgaacggtttgattttcagtgcgtttttgtccgagaggagcagcccagtgtccgtgcgtaaagctcctgatgcaccggccgaatcgacagaaaagatgatcgttcaccaaattactaacaacaaaaaaacaagca Find is-nt database================================================ Query_seq: PG0374:PG0375|PG0374:PG0375:hypothetical protein:50S ribosomal protein L13:<-->:405655..406073 419 ttagctcccacgcctatatcggcaattagcggcacacgaagttcgggcatcacgccttccacggcaacgaagatgcatacgagaagcatttcgatgcgttggaagaggcaaatagcttgccaaatcgaggaaatgaaaagtcgttcgtagagcttaaaatgatgccgatatccttcactacataatctgtttgcatttatttgtggaatgtgcagagcgacacgatgtccgaaatttgctgaaaataatgtacctttgccgcgctgattattatcaaatagtgccgaacggtttgattttcagtgcgtttttgtccgagaggagcagcccagtgtccgtgcgtaaagctcctgatgcaccggccgaatcgacagaaaagatgatcgttcaccaaattactaacaacaaaaaaacaagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0374:PG0375|PG0374:PG0375:hypothetical protein:50S ribosomal protein L13:<-->:405655..406073 419 ttagctcccacgcctatatcggcaattagcggcacacgaagttcgggcatcacgccttccacggcaacgaagatgcatacgagaagcatttcgatgcgttggaagaggcaaatagcttgccaaatcgaggaaatgaaaagtcgttcgtagagcttaaaatgatgccgatatccttcactacataatctgtttgcatttatttgtggaatgtgcagagcgacacgatgtccgaaatttgctgaaaataatgtacctttgccgcgctgattattatcaaatagtgccgaacggtttgattttcagtgcgtttttgtccgagaggagcagcccagtgtccgtgcgtaaagctcctgatgcaccggccgaatcgacagaaaagatgatcgttcaccaaattactaacaacaaaaaaacaagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0374:PG0375|PG0374:PG0375:hypothetical protein:50S ribosomal protein L13:<-->:405655..406073 419 ttagctcccacgcctatatcggcaattagcggcacacgaagttcgggcatcacgccttccacggcaacgaagatgcatacgagaagcatttcgatgcgttggaagaggcaaatagcttgccaaatcgaggaaatgaaaagtcgttcgtagagcttaaaatgatgccgatatccttcactacataatctgtttgcatttatttgtggaatgtgcagagcgacacgatgtccgaaatttgctgaaaataatgtacctttgccgcgctgattattatcaaatagtgccgaacggtttgattttcagtgcgtttttgtccgagaggagcagcccagtgtccgtgcgtaaagctcctgatgcaccggccgaatcgacagaaaagatgatcgttcaccaaattactaacaacaaaaaaacaagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttagctcccacgcctatatcggcaattagcggcacacgaagttcgggcatcacgccttccacggcaacgaagatgcatacgagaagcatttcgatgcgttggaagaggcaaatagcttgccaaatcgaggaaatgaaaagtcgttcgtagagcttaaaatgatgccgatatccttcactacataatctgtttgcatttatttgtggaatgtgcagagcgacacgatgtccgaaatttgctgaaaataatgtacctttgccgcgctgattattatcaaatagtgccgaacggtttgattttcagtgcgtttttgtccgagaggagcagcccagtgtccgtgcgtaaagctcctgatgcaccggccgaatcgacagaaaagatgatcgttcaccaaattactaacaacaaaaaaacaagca Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 16 End: 147 ............... M S A I S G T R S S G I T P S T A T K M H T R S I S M R W K R Q I A C Q I E E M K S R S ................................................................................................................................................................................................................................................................................ Protein_Len: 60 Strand: + Start: 170 End: 418 ......................................................................................................................................................................... M L H Y I I C L H L F V E C A E R H D V R N L L K I M Y L C R A D Y Y Q I V P N G L I F S A F L S E R S S P V S V R K A . Protein_Len: 36 Strand: - Start: 277 End: 384 .................................................................................................................................................................................................................................................................................... I T G F P K I K L A N K D S L L L G T D T R L A G S A G A S D V S F I M ................................... Protein_Len: 60 Strand: - Start: 200 End: 394 ....................................................................................................................................................................................................... L S V I D S I Q Q F Y H V K A A S I I I L Y H R V T Q N E T R K Q G L P A A W H G H T F S R I C R G F R C F L H D N V M ......................... Protein_Len: 48 Strand: - Start: 53 End: 196 .................................................... A K W P L S S A Y S F C K S A N S S A F L K G F R P F S F D N T S S L I I G I D K V V Y D T Q M ............................................................................................................................................................................................................................... Protein_Len: 60 Strand: - Start: 3 End: 215 .. R L E P M V G E V A V F I C V L L M E I R Q F L C I A Q W I S S I F L R E Y L K F H H R Y G E S C L R N A N I Q P I H M ............................................................................................................................................................................................................ Protein_Len: 41 Strand: - Start: 4 End: 123 ... * S G R R Y R C N A A C S T R A D R R G R C R L H M R S A N R H T P L P L Y S A M ........................................................................................................................................................................................................................................................................................................ ttagctcccacgcctatatcggcaattagcggcacacgaagttcgggcatcacgccttccacggcaacgaagatgcatacgagaagcatttcgatgcgttggaagaggcaaatagcttgccaaatcgaggaaatgaaaagtcgttcgtagagcttaaaatgatgccgatatccttcactacataatctgtttgcatttatttgtggaatgtgcagagcgacacgatgtccgaaatttgctgaaaataatgtacctttgccgcgctgattattatcaaatagtgccgaacggtttgattttcagtgcgtttttgtccgagaggagcagcccagtgtccgtgcgtaaagctcctgatgcaccggccgaatcgacagaaaagatgatcgttcaccaaattactaacaacaaaaaaacaagca 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================================================ PromScan Matrix: RpoN Strand: - Score: 86 Start: 107 End: 123 ..........................................................................................................TTGGCAAGCTATTTGCC........................................................................................................................................................................................................................................................................................................ ttagctcccacgcctatatcggcaattagcggcacacgaagttcgggcatcacgccttccacggcaacgaagatgcatacgagaagcatttcgatgcgttggaagaggcaaatagcttgccaaatcgaggaaatgaaaagtcgttcgtagagcttaaaatgatgccgatatccttcactacataatctgtttgcatttatttgtggaatgtgcagagcgacacgatgtccgaaatttgctgaaaataatgtacctttgccgcgctgattattatcaaatagtgccgaacggtttgattttcagtgcgtttttgtccgagaggagcagcccagtgtccgtgcgtaaagctcctgatgcaccggccgaatcgacagaaaagatgatcgttcaccaaattactaacaacaaaaaaacaagca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0374:PG0375|PG0374:PG0375:hypothetical protein:50S ribosomal protein L13:<-->:405655..406073 419 ttagctcccacgcctatatcggcaattagcggcacacgaagttcgggcatcacgccttccacggcaacgaagatgcatacgagaagcatttcgatgcgttggaagaggcaaatagcttgccaaatcgaggaaatgaaaagtcgttcgtagagcttaaaatgatgccgatatccttcactacataatctgtttgcatttatttgtggaatgtgcagagcgacacgatgtccgaaatttgctgaaaataatgtacctttgccgcgctgattattatcaaatagtgccgaacggtttgattttcagtgcgtttttgtccgagaggagcagcccagtgtccgtgcgtaaagctcctgatgcaccggccgaatcgacagaaaagatgatcgttcaccaaattactaacaacaaaaaaacaagca Intra-Species Hit: Count: 1 Min: 1 Max: 406 Len: 406 Subject: NC_002950_PG0374_PG0375|hypothetical protein:50S ribosomal protein L13|NEGATIVE:POSITIVE|[405655,406073]|419 HSP 1 e-value: 0.0 bit: 805.0 Len: 406 Query Start:1 Query End:406 Subject Strand: POSITIVE Subject Start: 1 Subject End: 406 ttagctcccacgcctatatcggcaattagcggcacacgaagttcgggcatcacgccttccacggcaacgaagatgcatacgagaagcatttcgatgcgttggaagaggcaaatagcttgccaaatcgaggaaatgaaaagtcgttcgtagagcttaaaatgatgccgatatccttcactacataatctgtttgcatttatttgtggaatgtgcagagcgacacgatgtccgaaatttgctgaaaataatgtacctttgccgcgctgattattatcaaatagtgccgaacggtttgattttcagtgcgtttttgtccgagaggagcagcccagtgtccgtgcgtaaagctcctgatgcaccggccgaatcgacagaaaagatgatcgttcaccaaattactaacaac............. ttagctcccacgcctatatcggcaattagcggcacacgaagttcgggcatcacgccttccacggcaacgaagatgcatacgagaagcatttcgatgcgttggaagaggcaaatagcttgccaaatcgaggaaatgaaaagtcgttcgtagagcttaaaatgatgccgatatccttcactacataatctgtttgcatttatttgtggaatgtgcagagcgacacgatgtccgaaatttgctgaaaataatgtacctttgccgcgctgattattatcaaatagtgccgaacggtttgattttcagtgcgtttttgtccgagaggagcagcccagtgtccgtgcgtaaagctcctgatgcaccggccgaatcgacagaaaagatgatcgttcaccaaattactaacaac............. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAGCUCCCACGCCUAUAUCGGCAAUUAGCGGCACACGAAGUUCGGGCAUCACGCCUUCCACGGCAACGAAGAUGCAUACGAGAAGCAUUUCGAUGCGUUGGAAGAGGCAAAUAGCUUGCCAAAUCGAGGAAAUGAAAAGUCGUUCGUAGAGCUUAAAAUGAUGCCGAUAUCCUUCACUACAUAAUCUGUUUGCAUUUAUUUGUGGAAUGUGCAGAGCGACACGAUGUCCGAAAUUUGCUGAAAAUAAUGUACCUUUGCCGCGCUGAUUAUUAUCAAAUAGUGCCGAACGGUUUGAUUUUCAGUGCGUUUUUGUCCGAGAGGAGCAGCCCAGUGUCCGUGCGUAAAGCUCCUGAUGCACCGGCCGAAUCGACAGAAAAGAUGAUCGUUCACCAAAUUACUAACAAC ...((((((..(((......)))......(((((((((((.((((((((((....(((((.((....))..(((((((.(((((....))))))))))))))))).(((((.....)))))..................((((((((((.(.....(((((((((.((((.................)))).))).))))))......).))).)))))))..)))))))))).)))).))..................((((((((.....(((((((.((.....)).)))))))..))))))))....)).))).).))))).(((..(((((.(.((.....)).)..)))))...))).(((.(((((.......)).))))))................. (-114.93) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUGUUAGUAAUUUGGUGAACGAUCAUCUUUUCUGUCGAUUCGGCCGGUGCAUCAGGAGCUUUACGCACGGACACUGGGCUGCUCCUCUCGGACAAAAACGCACUGAAAAUCAAACCGUUCGGCACUAUUUGAUAAUAAUCAGCGCGGCAAAGGUACAUUAUUUUCAGCAAAUUUCGGACAUCGUGUCGCUCUGCACAUUCCACAAAUAAAUGCAAACAGAUUAUGUAGUGAAGGAUAUCGGCAUCAUUUUAAGCUCUACGAACGACUUUUCAUUUCCUCGAUUUGGCAAGCUAUUUGCCUCUUCCAACGCAUCGAAAUGCUUCUCGUAUGCAUCUUCGUUGCCGUGGAAGGCGUGAUGCCCGAACUUCGUGUGCCGCUAAUUGCCGAUAUAGGCGUGGGAGCUAA (.((((...((((((.((((.((((..(......)..))))..(((..(((...((((((.....((.(((...))).)).))))))............(((.((((..((((((((....)).....)))))).....)))).))))))..)))........)))).))))))...)))).).....((((((((((..................(((.....)))...((((....(((((((((.....((((...(((((((............))).))))...))))....((((..((((..(((.((((((((.........)))).)))).)))..)))))))).))))).)))).)))).)))))........(((......)))...)))))... (-106.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1100 70 21 161 112 NC_002950:PG0374|5end_hypothetical_protein_405564..405794_NEGATIVE 426 386 341 183 143 NC_002950:PG2187|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_2294643..2294873_NEGATIVE 401 366 322 154 103 NC_002950:PG0979|5end_hypothetical_protein_1040752..1040982_POSITIVE 396 366 327 66 33 NC_002950:PG1434|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_1519022..1519252_POSITIVE 396 365 322 224 166 NC_002950:PG0635|5end_ribosomal_protein_L11_methyltransferase_687773..688003_NEGATIVE 392 70 22 94 51 NC_002950:PG0172|5end_exonuclease_193493..193723_POSITIVE 390 370 324 198 153 NC_002950:PG0271|5end_single-stranded_binding_protein_303842..304072_POSITIVE 389 357 314 161 125 NC_002950:PG1691|5end_hypothetical_protein_1776484..1776714_NEGATIVE 389 81 43 196 157 NC_002950:PG0157|5end_regulatory_protein_RecX_179706..179936_POSITIVE 386 79 37 61 8 NC_002950:PG0211|5end_cobalamin_biosynthesis_protein_CbiG/precorrin-4_C11-methyltransferase_247810..248040_NEGATIVE 383 370 321 224 159 NC_002950:PG0498|5end_S-ribosylhomocysteinase_537968..538198_POSITIVE 381 372 332 184 132 NC_002950:PG1620|5end_carboxyl-terminal_protease-related_protein_1700491..1700721_NEGATIVE 380 369 328 71 31 NC_002950:PG0996|5end_conserved_hypothetical_protein_TIGR01777_1055592..1055822_POSITIVE 380 364 321 116 54 NC_002950:PG0607|5end_hypothetical_protein_662552..662782_POSITIVE 380 366 321 75 12 NC_002950:PG0025|5end_fumarylacetoacetate_hydrolase_family_protein_28457..28687_POSITIVE 379 66 21 103 44 NC_002950:PG2145|5end_polysaccharide_deacetylase_2253253..2253483_POSITIVE 378 70 21 211 165 NC_002950:PG0322|5end_serine/threonine_transporter_355708..355938_POSITIVE 375 330 283 187 135 NC_002950:PG1959|5end_ribosomal_protein_L33_2048405..2048635_NEGATIVE 375 60 11 70 14 NC_002950:PG0779|5end_hypothetical_protein_832573..832803_NEGATIVE 375 370 323 67 14 NC_002950:PG0084|5end_L-serine_dehydratase,_iron-sulfur-dependent,_single_chain_form_97832..98062_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 403 370 325 150 98 NC_002950:PG0902|3end_alpha-1,2-mannosidase_family_protein_966746..966896_NEGATIVE 396 366 327 90 57 NC_002950:PG1433|3end_hydrolase_1519126..1519276_POSITIVE 392 70 22 97 54 NC_002950:PG0171|3end_5'-nucleotidase_family_protein_193576..193726_POSITIVE 390 370 324 147 102 NC_002950:PG0270|3end_redox-sensitive_transcriptional_activator_OxyR_303871..304021_POSITIVE 389 357 314 131 95 NC_002950:PG1692|3end_ABC_transporter,_ATP-binding_protein_1776514..1776664_NEGATIVE 382 60 12 89 35 NC_002950:PG1162|3end_ATP:cob(I)alamin_adenosyltransferase,_putative_1241473..1241623_NEGATIVE 381 369 321 78 16 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 379 66 21 60 1 NC_002950:PG2144|3end_hypothetical_protein_2253290..2253440_POSITIVE 373 70 21 149 105 NC_002950:PG1067|3end_hypothetical_protein_1134688..1134838_POSITIVE 373 360 317 53 2 NC_002950:PG0348|3end_ATP-dependent_DNA_helicase_RecG_384521..384671_POSITIVE 369 70 21 137 83 NC_002950:PG0766|3end_polyribonucleotide_nucleotidyltransferase_816174..816324_NEGATIVE 366 370 321 144 74 NC_002950:PG1859|3end_glycerate_kinase_family_protein_1957174..1957324_NEGATIVE 366 363 321 61 20 NC_002950:PG0925|3end_thymidine_kinase_983665..983815_NEGATIVE 364 57 13 130 82 NC_002950:PG0660|3end_nitroreductase_family_protein_709141..709291_NEGATIVE 362 328 283 86 32 NC_002950:PG1104|3end_hypothetical_protein_1175782..1175932_POSITIVE 360 350 301 131 77 NC_002950:PG2086|3end_hypothetical_protein_2187070..2187220_POSITIVE 360 347 301 58 1 NC_002950:PG0727|3end_hypothetical_protein_778389..778539_NEGATIVE 360 357 316 61 8 NC_002950:PG0070|3end_UDP-N-acetylglucosamine_acyltransferase_83940..84090_NEGATIVE 359 60 12 76 30 NC_002950:PG0799|3end_hypothetical_protein_854599..854749_POSITIVE 358 70 23 68 26 NC_002950:PG0745|3end_lactoylglutathione_lyase,_putative_791982..792132_NEGATIVE