Origin IGS: ttcacactgcaattctctaataagggctgtgccgaggaatccattcggcacagccctttttgaattattggcactacgccaagagactgttgagtaatcaggcgagaaaagaggatgctaaaggtcgtaaataacggctcaaacccaatggcccgttcatctcataccatggtgcgcaagggctacagaccatacacttgagattatgtgccatagtgcttcgttttaggtggagatatggttctgttattgaggaaaatattctgtttatgagagagaaatctttttttggccgaaaagaaatattttccacccgtggaaaagatgttttcccgacctggaaaatattttttccaggccgggaaaattt .........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 aaattttcccggcctggaaaaaatattttccaggtcgggaaaacatcttttccacgggtggaaaatatttcttttcggccaaaaaaagatttctctctcataaacagaatattttcctcaataacagaaccatatctccacctaaaacgaagcactatggcacataatctcaagtgtatggtctgtagcccttgcgcaccatggtatgagatgaacgggccattgggtttgagccgttatttacgacctttagcatcctcttttctcgcctgattactcaacagtctcttggcgtagtgccaataattcaaaaagggctgtgccgaatggattcctcggcacagcccttattagagaattgcagtgtgaa Mask Tandem Repeat Region ================================================ ttcacactgcaattctctaataagggctgtgccgaggaatccattcggcacagccctttttgaattattggcactacgccaagagactgttgagtaatcaggcgagaaaagaggatgctaaaggtcgtaaataacggctcaaacccaatggcccgttcatctcataccatggtgcgcaagggctacagaccatacacttgagattatgtgccatagtgcttcgttttaggtggagatatggttctgttattgaggaaaatattctgtttatgagagagaaatctttttttggccgaaaagaaatattttccacccgtggaaaagatgttttcccgacctggaaaatattttttccaggccgggaaaattt Find is-nt database================================================ Query_seq: PG0506:PG0507|PG0506:PG0507:arginine-specific cysteine proteinase:hypothetical protein:->->:547686..548055 370 ttcacactgcaattctctaataagggctgtgccgaggaatccattcggcacagccctttttgaattattggcactacgccaagagactgttgagtaatcaggcgagaaaagaggatgctaaaggtcgtaaataacggctcaaacccaatggcccgttcatctcataccatggtgcgcaagggctacagaccatacacttgagattatgtgccatagtgcttcgttttaggtggagatatggttctgttattgaggaaaatattctgtttatgagagagaaatctttttttggccgaaaagaaatattttccacccgtggaaaagatgttttcccgacctggaaaatattttttccaggccgggaaaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0506:PG0507|PG0506:PG0507:arginine-specific cysteine proteinase:hypothetical protein:->->:547686..548055 370 ttcacactgcaattctctaataagggctgtgccgaggaatccattcggcacagccctttttgaattattggcactacgccaagagactgttgagtaatcaggcgagaaaagaggatgctaaaggtcgtaaataacggctcaaacccaatggcccgttcatctcataccatggtgcgcaagggctacagaccatacacttgagattatgtgccatagtgcttcgttttaggtggagatatggttctgttattgaggaaaatattctgtttatgagagagaaatctttttttggccgaaaagaaatattttccacccgtggaaaagatgttttcccgacctggaaaatattttttccaggccgggaaaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0506:PG0507|PG0506:PG0507:arginine-specific cysteine proteinase:hypothetical protein:->->:547686..548055 370 ttcacactgcaattctctaataagggctgtgccgaggaatccattcggcacagccctttttgaattattggcactacgccaagagactgttgagtaatcaggcgagaaaagaggatgctaaaggtcgtaaataacggctcaaacccaatggcccgttcatctcataccatggtgcgcaagggctacagaccatacacttgagattatgtgccatagtgcttcgttttaggtggagatatggttctgttattgaggaaaatattctgtttatgagagagaaatctttttttggccgaaaagaaatattttccacccgtggaaaagatgttttcccgacctggaaaatattttttccaggccgggaaaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcacactgcaattctctaataagggctgtgccgaggaatccattcggcacagccctttttgaattattggcactacgccaagagactgttgagtaatcaggcgagaaaagaggatgctaaaggtcgtaaataacggctcaaacccaatggcccgttcatctcataccatggtgcgcaagggctacagaccatacacttgagattatgtgccatagtgcttcgttttaggtggagatatggttctgttattgaggaaaatattctgtttatgagagagaaatctttttttggccgaaaagaaatattttccacccgtggaaaagatgttttcccgacctggaaaatattttttccaggccgggaaaattt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 27 End: 131 .......................... M C R G I H S A Q P F L N Y W H Y A K R L L S N Q A R K E D A K G R K ............................................................................................................................................................................................................................................... Protein_Len: 34 Strand: + Start: 97 End: 198 ................................................................................................ M R R E K R M L K V V N N G S N P M A R S S H T M V R K G Y R P Y T ............................................................................................................................................................................ Protein_Len: 32 Strand: + Start: 131 End: 226 .................................................................................................................................. M T A Q T Q W P V H L I P W C A R A T D H T L E I M C H S A S F ................................................................................................................................................ Protein_Len: 60 Strand: + Start: 159 End: 368 .............................................................................................................................................................. M S Y H G A Q G L Q T I H L R L C A I V L R F R W R Y G S V I E E N I L F M R E K S F F G R K E I F S T R G K D V F P T .. Protein_Len: 30 Strand: + Start: 281 End: 370 ........................................................................................................................................................................................................................................................................................ M F F W P K R N I F H P W K R C F P D L E N I F S R P G K F Protein_Len: 54 Strand: - Start: 207 End: 368 .............................................................................................................................................................................................................. T G Y H K T K P P S I T R N N L F I N Q K H S L F R K K A S F F Y K G G T S F I N E R G P F Y K K W A P F M .. Protein_Len: 60 Strand: - Start: 101 End: 346 .................................................................................................... W P A C P S C V M C K L N H A M T S R K L H L Y P E T I S S F I R N I L S F D K K P R F S I N E V R P F S T K G V Q F M ........................ Protein_Len: 49 Strand: - Start: 3 End: 149 .. V S C N E L L P Q A S S D M R C L G K Q I I P V V G L S Q Q T I L R S F L I S F T T F L P E F G M ............................................................................................................................................................................................................................. ttcacactgcaattctctaataagggctgtgccgaggaatccattcggcacagccctttttgaattattggcactacgccaagagactgttgagtaatcaggcgagaaaagaggatgctaaaggtcgtaaataacggctcaaacccaatggcccgttcatctcataccatggtgcgcaagggctacagaccatacacttgagattatgtgccatagtgcttcgttttaggtggagatatggttctgttattgaggaaaatattctgtttatgagagagaaatctttttttggccgaaaagaaatattttccacccgtggaaaagatgttttcccgacctggaaaatattttttccaggccgggaaaattt 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================================================ ttcacactgcaattctctaataagggctgtgccgaggaatccattcggcacagccctttttgaattattggcactacgccaagagactgttgagtaatcaggcgagaaaagaggatgctaaaggtcgtaaataacggctcaaacccaatggcccgttcatctcataccatggtgcgcaagggctacagaccatacacttgagattatgtgccatagtgcttcgttttaggtggagatatggttctgttattgaggaaaatattctgtttatgagagagaaatctttttttggccgaaaagaaatattttccacccgtggaaaagatgttttcccgacctggaaaatattttttccaggccgggaaaattt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -14.4 Tail_Score: -2.77895 Start: 16 End: 63 Full_Region: TTCACACTGCAATTC TCTAATAAGGGCTGTGCCGAG GAATCCA TTCGGCACAGCCCTTTTTGA ATTATTGGCACTACG ...............TCTAATAAGGGCTGTGCCGAGGAATCCATTCGGCACAGCCCTTTTTGA................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -13.3 Tail_Score: -3.63515 Start: 16 End: 64 Full_Region: TTCACACTGCAATTC TCTAATAAGGGCTGTGCCGAG GAATCCA TTCGGCACAGCCCTTTTTGAA TTATTGGCACTACGC ...............TCTAATAAGGGCTGTGCCGAGGAATCCATTCGGCACAGCCCTTTTTGAA.................................................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -16.4 Tail_Score: -3.63569 Start: 24 End: 56 Full_Region: ccaataattcaaaaa gggctgtgccga atggattcc tcggcacagccc ttattagagaattgc .......................gggctgtgccgaatggattcctcggcacagccc.......................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 71 HP_score: -4.9 Tail_Score: -4.64861 Start: 304 End: 347 Full_Region: ccggcctggaaaaaa tattttccaggtcgggaaaa catc ttttccacgggtggaaaata tttcttttcggccaa ...............................................................................................................................................................................................................................................................................................................tattttccaggtcgggaaaacatcttttccacgggtggaaaata....................... TransTerm Strand: - Conf: 72 HP_score: -7.1 Tail_Score: -3.93868 Start: 306 End: 323 Full_Region: ggtcgggaaaacatc ttttcca cggg tggaaaa tatttcttttcggcc .................................................................................................................................................................................................................................................................................................................ttttccacgggtggaaaa............................................... TransTerm Strand: + Conf: 73 HP_score: -3.8 Tail_Score: -5.00616 Start: 326 End: 347 Full_Region: CACCCGTGGAAAAGA TGTTTTCC CGACCT GGAAAATA TTTTTTCCAGGCCGG .....................................................................................................................................................................................................................................................................................................................................TGTTTTCCCGACCTGGAAAATA....................... Find igs database================================================ Query_seq: PG0506:PG0507|PG0506:PG0507:arginine-specific cysteine proteinase:hypothetical protein:->->:547686..548055 370 ttcacactgcaattctctaataagggctgtgccgaggaatccattcggcacagccctttttgaattattggcactacgccaagagactgttgagtaatcaggcgagaaaagaggatgctaaaggtcgtaaataacggctcaaacccaatggcccgttcatctcataccatggtgcgcaagggctacagaccatacacttgagattatgtgccatagtgcttcgttttaggtggagatatggttctgttattgaggaaaatattctgtttatgagagagaaatctttttttggccgaaaagaaatattttccacccgtggaaaagatgttttcccgacctggaaaatattttttccaggccgggaaaattt Intra-Species Hit: Count: 1 Min: 1 Max: 370 Len: 370 Subject: NC_002950_PG0506_PG0507|arginine-specific cysteine proteinase:hypothetical protein|POSITIVE:POSITIVE|[547686,548055]|370 HSP 1 e-value: 0.0 bit: 692.0 Len: 370 Query Start:1 Query End:370 Subject Strand: POSITIVE Subject Start: 1 Subject End: 370 ttcacactgcaattctctaataagggctgtgccgaggaatccattcggcacagccctttttgaattattggcactacgccaagagactgttgagtaatcaggcgagaaaagaggatgctaaaggtcgtaaataacggctcaaacccaatggcccgttcatctcataccatggtgcgcaagggctacagaccatacacttgagattatgtgccatagtgcttcgttttaggtggagatatggttctgttattgaggaaaatattctgtttatgagagagaaatcnnnnnnnggccgaaaagaaatattttccacccgtggaaaagatgttttcccgacctggaaaatattttttccaggccgggaaaattt ttcacactgcaattctctaataagggctgtgccgaggaatccattcggcacagccctttttgaattattggcactacgccaagagactgttgagtaatcaggcgagaaaagaggatgctaaaggtcgtaaataacggctcaaacccaatggcccgttcatctcataccatggtgcgcaagggctacagaccatacacttgagattatgtgccatagtgcttcgttttaggtggagatatggttctgttattgaggaaaatattctgtttatgagagagaaatctttttttggccgaaaagaaatattttccacccgtggaaaagatgttttcccgacctggaaaatattttttccaggccgggaaaattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCACACUGCAAUUCUCUAAUAAGGGCUGUGCCGAGGAAUCCAUUCGGCACAGCCCUUUUUGAAUUAUUGGCACUACGCCAAGAGACUGUUGAGUAAUCAGGCGAGAAAAGAGGAUGCUAAAGGUCGUAAAUAACGGCUCAAACCCAAUGGCCCGUUCAUCUCAUACCAUGGUGCGCAAGGGCUACAGACCAUACACUUGAGAUUAUGUGCCAUAGUGCUUCGUUUUAGGUGGAGAUAUGGUUCUGUUAUUGAGGAAAAUAUUCUGUUUAUGAGAGAGAAAUCUUUUUUUGGCCGAAAAGAAAUAUUUUCCACCCGUGGAAAAGAUGUUUUCCCGACCUGGAAAAUAUUUUUUCCAGGCCGGGAAAAUUU (((..(((.(((((((((...(((((((((((((((.......)))))))))))))))..........((((.....)))))))))..))))))).....(((.((((((.((((((.....((((((.....))))))....(((((((((((((.((((.........)))).))..)))).((((((((((((((((((((...(..(....)..)...))))))))))....))))).)))))))))).))....)))))).)))..((((((....))))))))).))).....)))...(((((((....)))))))...(((((((((.(((((((((....))))))))).))))))))).. (-133.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUUUCCCGGCCUGGAAAAAAUAUUUUCCAGGUCGGGAAAACAUCUUUUCCACGGGUGGAAAAUAUUUCUUUUCGGCCAAAAAAAGAUUUCUCUCUCAUAAACAGAAUAUUUUCCUCAAUAACAGAACCAUAUCUCCACCUAAAACGAAGCACUAUGGCACAUAAUCUCAAGUGUAUGGUCUGUAGCCCUUGCGCACCAUGGUAUGAGAUGAACGGGCCAUUGGGUUUGAGCCGUUAUUUACGACCUUUAGCAUCCUCUUUUCUCGCCUGAUUACUCAACAGUCUCUUGGCGUAGUGCCAAUAAUUCAAAAAGGGCUGUGCCGAAUGGAUUCCUCGGCACAGCCCUUAUUAGAGAAUUGCAGUGUGAA ...((((((((((((((((((....))))))))))))))))))......((((((.(((.(((((......))))).))).......(..((((((..........((((...............(((......)))..............((((((((.((....((((((....((((((.(((((...))))).))))))...))))))...(((((....(((...(((..((((...........))))...)))....)))))))).................)).)))))))).....))))...((((((((((((((..((...))))))))))))))))...))))))...).))).))) (-116.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 446 56 14 155 102 NC_002950:PG1759|5end_adhesion_protein,_putative_1845570..1845800_POSITIVE 422 61 24 195 158 NC_002950:PG0095|5end_DNA_mismatch_repair_protein_114763..114993_NEGATIVE 400 70 24 50 8 NC_002950:PG1968|5end_hypothetical_protein_2058564..2058794_NEGATIVE 390 56 22 214 174 NC_002950:PG1739|5end_hypothetical_protein_1825709..1825939_NEGATIVE 388 55 12 150 99 NC_002950:PG0248|5end_translation_initation_factor_SUI1,_putative_281842..282072_NEGATIVE 380 55 24 71 28 NC_002950:PG1651|5end_TPR_domain_protein_1730326..1730556_POSITIVE 362 246 202 59 11 NC_002950:PG2022|5end_hypothetical_protein_2117399..2117629_NEGATIVE 362 61 22 102 66 NC_002950:PG1423|5end_hypothetical_protein_1509088..1509318_NEGATIVE 362 70 24 192 137 NC_002950:PG0480|5end_precorrin-2_C20-methyltransferase,_putative_521319..521549_NEGATIVE 358 56 22 229 189 NC_002950:PG0768|5end_hypothetical_protein_822381..822611_NEGATIVE 354 190 148 46 5 NC_002950:PG0747|5end_sigma-54_dependent_DNA-binding_response_regulator_795294..795524_NEGATIVE 353 197 154 83 20 NC_002950:PG0172|5end_exonuclease_193493..193723_POSITIVE 350 117 71 56 10 NC_002950:PG1790|5end_hypothetical_protein_1880954..1881184_NEGATIVE 346 187 148 80 26 NC_002950:PG1812|5end_2-oxoglutarate_ferredoxin_oxidoreductase_1908107..1908337_NEGATIVE 345 56 24 225 193 NC_002950:PG0749|5end_hypothetical_protein_795654..795884_NEGATIVE 343 64 23 171 122 NC_002950:PG1219|5end_hypothetical_protein_1296671..1296901_POSITIVE 343 200 152 37 1 NC_002950:PG0583|5end_cell_division_protein_FtsA_640425..640655_POSITIVE 342 186 143 225 177 NC_002950:PG1556|5end_hypothetical_protein_1636595..1636825_POSITIVE 338 56 19 210 169 NC_002950:PG2000|5end_signal_peptidase-related_protein_2089468..2089698_NEGATIVE 338 80 31 231 166 NC_002950:PG1478|5end_conjugative_transposon_protein_TraK_1554116..1554346_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 624 58 11 69 25 NC_002950:PG0506|3end_arginine-specific_cysteine_proteinase_547625..547775_POSITIVE 533 60 20 43 1 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 515 58 22 70 28 NC_002950:PG0350|3end_internalin-related_protein_385356..385506_NEGATIVE 503 58 24 50 15 NC_002950:PG1754|3end_hypothetical_protein_1842284..1842434_POSITIVE 462 70 22 77 27 NC_002950:PG0726|3end_lipoprotein,_putative_778003..778153_NEGATIVE 447 58 21 58 15 NC_002950:PG2010|3end_phosphomannomutase,_putative_2100952..2101102_POSITIVE 438 61 21 62 15 NC_002950:PG0349|3end_hydrolase,_haloacid_dehalogenase-like_family_385291..385441_POSITIVE 420 64 22 65 23 NC_002950:PG0535|3end_hypothetical_protein_585956..586106_NEGATIVE 413 60 16 67 14 NC_002950:PG0159|3end_endopeptidase_PepO_181095..181245_NEGATIVE 408 56 25 39 1 NC_002950:PG1758|3end_ribosomal_protein_S15_1845534..1845684_POSITIVE 394 56 24 47 14 NC_002950:PG2124|3end_glyceraldehyde_3-phosphate_dehydrogenase,_type_I_2231264..2231414_POSITIVE 390 56 22 67 27 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 390 61 24 50 10 NC_002950:PG0619|3end_alkyl_hydroperoxide_reductase,_F_subunit_672731..672881_POSITIVE 389 58 22 51 12 NC_002950:PG0721|3end_NLP/P60_family_protein_774535..774685_POSITIVE 388 61 24 91 51 NC_002950:PG0725|3end_hydrolase,_haloacid_dehalogenase-like_family_777966..778116_POSITIVE 388 55 12 53 2 NC_002950:PG0249|3end_oxaloacetate_decarboxylase,_putative_281939..282089_NEGATIVE 380 62 22 60 15 NC_002950:PG0769|3end_fibronectin_type_III_domain_protein_822555..822705_NEGATIVE 376 57 18 56 14 NC_002950:PG0395|3end_DNA-directed_RNA_polymerase_beta'_subunit_433305..433455_POSITIVE 375 60 23 64 27 NC_002950:PG0034|3end_thioredoxin_42235..42385_NEGATIVE 372 366 322 87 41 NC_002950:PG0722|3end_hypothetical_protein_774739..774889_NEGATIVE