Origin IGS: caactttctctaccttttactctctttcgagcgaaggagacgacaacggaagcaaagcttcttttgtccgtctccttcctttttcttgtagaagggaaggctcggattcggccaccatttttatgtacatttgtagggt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 accctacaaatgtacataaaaatggtggccgaatccgagccttcccttctacaagaaaaaggaaggagacggacaaaagaagctttgcttccgttgtcgtctccttcgctcgaaagagagtaaaaggtagagaaagttg Mask Tandem Repeat Region ================================================ caactttctctaccttttactctctttcgagcgaaggagacgacaacggaagcaaagcttcttttgtccgtctccttcctttttcttgtagaagggaaggctcggattcggccaccatttttatgtacatttgtagggt Find is-nt database================================================ Query_seq: PG0010:PG0011|PG0010:PG0011:ATP-dependent Clp protease, ATP-binding subunit ClpC:glycosyl hydrolase, family 3:->->:11495..11633 139 caactttctctaccttttactctctttcgagcgaaggagacgacaacggaagcaaagcttcttttgtccgtctccttcctttttcttgtagaagggaaggctcggattcggccaccatttttatgtacatttgtagggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0010:PG0011|PG0010:PG0011:ATP-dependent Clp protease, ATP-binding subunit ClpC:glycosyl hydrolase, family 3:->->:11495..11633 139 caactttctctaccttttactctctttcgagcgaaggagacgacaacggaagcaaagcttcttttgtccgtctccttcctttttcttgtagaagggaaggctcggattcggccaccatttttatgtacatttgtagggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0010:PG0011|PG0010:PG0011:ATP-dependent Clp protease, ATP-binding subunit ClpC:glycosyl hydrolase, family 3:->->:11495..11633 139 caactttctctaccttttactctctttcgagcgaaggagacgacaacggaagcaaagcttcttttgtccgtctccttcctttttcttgtagaagggaaggctcggattcggccaccatttttatgtacatttgtagggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caactttctctaccttttactctctttcgagcgaaggagacgacaacggaagcaaagcttcttttgtccgtctccttcctttttcttgtagaagggaaggctcggattcggccaccatttttatgtacatttgtagggt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 20 End: 130 ................... E R E L S P S S L P L L A E K T R R R G K E Q L L S P E S E A V M K I Y M ......... Protein_Len: 35 Strand: - Start: 3 End: 107 .. S E R G K V R K R A F S V V V S A F S R K D T E K R K R T S P F A R M ................................ caactttctctaccttttactctctttcgagcgaaggagacgacaacggaagcaaagcttcttttgtccgtctccttcctttttcttgtagaagggaaggctcggattcggccaccatttttatgtacatttgtagggt 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================================================ caactttctctaccttttactctctttcgagcgaaggagacgacaacggaagcaaagcttcttttgtccgtctccttcctttttcttgtagaagggaaggctcggattcggccaccatttttatgtacatttgtagggt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -15.8 Tail_Score: -5.18726 Start: 32 End: 79 Full_Region: TTACTCTCTTTCGAG CGAAGGAGACGACAACGGAAGC AAA GCTTCTTTTGTCCGTCTCCTTCC TTTTTCTTGTAGAAG ...............................CGAAGGAGACGACAACGGAAGCAAAGCTTCTTTTGTCCGTCTCCTTCC............................................................ TransTerm Strand: + Conf: 100 HP_score: -19.3 Tail_Score: -3.70512 Start: 33 End: 78 Full_Region: TACTCTCTTTCGAGC GAAGGAGACGACAACGGAAGC AAA GCTTCTTTTGTCCGTCTCCTTC CTTTTTCTTGTAGAA ................................GAAGGAGACGACAACGGAAGCAAAGCTTCTTTTGTCCGTCTCCTTC............................................................. TransTerm Strand: - Conf: 83 HP_score: -13.0 Tail_Score: -3.05384 Start: 36 End: 75 Full_Region: tacaagaaaaaggaa ggagacggacaaaagaagc ttt gcttccgttgtcgtctcc ttcgctcgaaagaga ...................................ggagacggacaaaagaagctttgcttccgttgtcgtctcc................................................................ Find igs database================================================ Query_seq: PG0010:PG0011|PG0010:PG0011:ATP-dependent Clp protease, ATP-binding subunit ClpC:glycosyl hydrolase, family 3:->->:11495..11633 139 caactttctctaccttttactctctttcgagcgaaggagacgacaacggaagcaaagcttcttttgtccgtctccttcctttttcttgtagaagggaaggctcggattcggccaccatttttatgtacatttgtagggt Intra-Species Hit: Count: 1 Min: 1 Max: 139 Len: 139 Subject: NC_002950_PG0010_PG0011|ATP-dependent Clp protease, ATP-binding subunit ClpC:glycosyl hydrolase, family 3|POSITIVE:POSITIVE|[11495,11633]|139 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 139 Query Start:1 Query End:139 Subject Strand: POSITIVE Subject Start: 1 Subject End: 139 caactttctctaccttttactctctttcgagcgaaggagacgacaacggaagcaaagcttcttttgtccgtctccttcctttttcttgtagaagggaaggctcggattcggccaccatttttatgtacatttgtagggt caactttctctaccttttactctctttcgagcgaaggagacgacaacggaagcaaagcttcttttgtccgtctccttcctttttcttgtagaagggaaggctcggattcggccaccatttttatgtacatttgtagggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAACUUUCUCUACCUUUUACUCUCUUUCGAGCGAAGGAGACGACAACGGAAGCAAAGCUUCUUUUGUCCGUCUCCUUCCUUUUUCUUGUAGAAGGGAAGGCUCGGAUUCGGCCACCAUUUUUAUGUACAUUUGUAGGGU .......(((((((((((((........(((.((((((((((((((.((((((...)))))).)))).)))))))))))))......))))))))...(((.((....)))))....................))))). (-48.44) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCCUACAAAUGUACAUAAAAAUGGUGGCCGAAUCCGAGCCUUCCCUUCUACAAGAAAAAGGAAGGAGACGGACAAAAGAAGCUUUGCUUCCGUUGUCGUCUCCUUCGCUCGAAAGAGAGUAAAAGGUAGAGAAAGUUG .......................((.(((((....)).)))..)).((((((.........((((((((((.((((..(((((...)))))..)))))))))))))).(((....)))........))))))....... (-46.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 345 79 31 68 29 NC_002950:PG0268|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_300898..301128_POSITIVE 343 50 4 220 161 NC_002950:PG0628|5end_ABC_transporter,_ATP-binding_protein_682439..682669_NEGATIVE 339 120 72 187 129 NC_002950:PG0509|5end_hypothetical_protein_549588..549818_NEGATIVE 338 75 36 167 123 NC_002950:PG0327|5end_hypothetical_protein_362061..362291_NEGATIVE 320 120 71 135 72 NC_002950:PG0563|5end_hypothetical_protein_621438..621668_NEGATIVE 319 99 51 109 56 NC_002950:PG1095|5end_RNA_methyltransferase,_TrmA_family_1160225..1160455_POSITIVE 319 75 31 78 28 NC_002950:PG0483|5end_kinase,_putative_523844..524074_NEGATIVE 318 80 36 176 135 NC_002950:PG0790|5end_GTP-binding_protein_Obg_842583..842813_NEGATIVE 317 79 33 51 2 NC_002950:PG1441|5end_lysozyme-related_protein_1527525..1527755_NEGATIVE 317 78 31 101 38 NC_002950:PG0789|5end_hypothetical_protein_841418..841648_NEGATIVE 314 116 71 215 163 NC_002950:PG1498|5end_hypothetical_protein_1574656..1574886_POSITIVE 313 69 21 192 151 NC_002950:PG0140|5end_hypothetical_protein_163858..164088_NEGATIVE 309 106 61 156 99 NC_002950:PG1903|5end_hypothetical_protein_2004221..2004451_NEGATIVE 307 80 41 48 10 NC_002950:PG1233|5end_hypothetical_protein_1309885..1310115_POSITIVE 305 110 61 72 16 NC_002950:PG1476|5end_conjugative_transposon_protein_TraM_1553219..1553449_NEGATIVE 304 110 67 181 136 NC_002950:PG0046|5end_phosphatidate_cytidylyltransferase_57200..57430_NEGATIVE 303 110 69 210 158 NC_002950:PG1647|5end_cardiolipin_synthetase_1726273..1726503_POSITIVE 303 50 6 125 65 NC_002950:PG0741|5end_hypothetical_protein_789316..789546_NEGATIVE 303 79 31 228 186 NC_002950:PG0549|5end_ISPg1,_transposase_607072..607302_NEGATIVE 302 110 62 230 176 NC_002950:PG0481|5end_2-amino-3-ketobutyrate_coenzyme_A_ligase_522622..522852_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 503 80 33 61 13 NC_002950:PG0010|3end_ATP-dependent_Clp_protease,_ATP-binding_subunit_ClpC_11434..11584_POSITIVE 369 114 72 148 94 NC_002950:PG0173|3end_transcriptional_regulator,_putative_194388..194538_NEGATIVE 367 112 71 57 3 NC_002950:PG2072|3end_UvrD/REP_helicase_domain_protein_2170757..2170907_POSITIVE 352 105 62 79 35 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 348 100 52 75 17 NC_002950:PG0130|3end_phosphoglyceromutase_151922..152072_NEGATIVE 345 79 31 63 24 NC_002950:PG0267|3end_arginyl-tRNA_synthetase_300973..301123_POSITIVE 338 75 36 73 29 NC_002950:PG0328|3end_imidazolonepropionase_362155..362305_NEGATIVE 330 105 61 81 42 NC_002950:PG0046|3end_phosphatidate_cytidylyltransferase_56346..56496_NEGATIVE 321 122 81 54 2 NC_002950:PG1486|3end_conjugative_transposon_protein_TraA_1560357..1560507_NEGATIVE 320 70 23 84 43 NC_002950:PG0915|3end_hypothetical_protein_977057..977207_POSITIVE 319 75 31 71 21 NC_002950:PG0484|3end_hypothetical_protein_523851..524001_NEGATIVE 319 75 31 145 97 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 317 78 31 120 57 NC_002950:PG0790|3end_GTP-binding_protein_Obg_841399..841549_NEGATIVE 316 69 21 151 108 NC_002950:PG1094|3end_phosphomannomutase_1160221..1160371_POSITIVE 315 84 46 151 113 NC_002950:PG1174|3end_thioesterase_family_protein_1253210..1253360_NEGATIVE 315 69 21 89 31 NC_002950:PG0674|3end_indolepyruvate_ferredoxin_oxidoreductase,_beta_subunit_724209..724359_NEGATIVE 314 116 71 114 62 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 314 80 32 105 62 NC_002950:PG0333|3end_hypothetical_protein_368811..368961_POSITIVE 307 119 73 151 103 NC_002950:PG0870|3end_hypothetical_protein_932304..932454_NEGATIVE 305 110 61 82 26 NC_002950:PG1477|3end_hypothetical_protein_1553209..1553359_NEGATIVE