Origin IGS: ccgtagcaacgtacgactctcgaaaacaacacagaatcaaaagaagagccgagctgcaatctagtaatttgcagctcggcttttaagaaagaatgagtacaagactta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagtcttgtactcattctttcttaaaagccgagctgcaaattactagattgcagctcggctcttcttttgattctgtgttgttttcgagagtcgtacgttgctacgg Mask Tandem Repeat Region ================================================ ccgtagcaacgtacgactctcgaaaacaacacagaatcaaaagaagagccgagctgcaatctagtaatttgcagctcggcttttaagaaagaatgagtacaagactta Find is-nt database================================================ Query_seq: PG1997:PG1998|PG1997:PG1998:hypothetical protein:polyprenyl synthetase:-><-:2087133..2087240 108 ccgtagcaacgtacgactctcgaaaacaacacagaatcaaaagaagagccgagctgcaatctagtaatttgcagctcggcttttaagaaagaatgagtacaagactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1997:PG1998|PG1997:PG1998:hypothetical protein:polyprenyl synthetase:-><-:2087133..2087240 108 ccgtagcaacgtacgactctcgaaaacaacacagaatcaaaagaagagccgagctgcaatctagtaatttgcagctcggcttttaagaaagaatgagtacaagactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1997:PG1998|PG1997:PG1998:hypothetical protein:polyprenyl synthetase:-><-:2087133..2087240 108 ccgtagcaacgtacgactctcgaaaacaacacagaatcaaaagaagagccgagctgcaatctagtaatttgcagctcggcttttaagaaagaatgagtacaagactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccgtagcaacgtacgactctcgaaaacaacacagaatcaaaagaagagccgagctgcaatctagtaatttgcagctcggcttttaagaaagaatgagtacaagactta Predict ORF larger than 30AA ================================================ ccgtagcaacgtacgactctcgaaaacaacacagaatcaaaagaagagccgagctgcaatctagtaatttgcagctcggcttttaagaaagaatgagtacaagactta 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================================================ ccgtagcaacgtacgactctcgaaaacaacacagaatcaaaagaagagccgagctgcaatctagtaatttgcagctcggcttttaagaaagaatgagtacaagactta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -12.8 Tail_Score: -4.55544 Start: 43 End: 85 Full_Region: gtactcattctttct taaaagccgagctgcaaatt act agattgcagctcggctcttc ttttgattctgtgtt ..........................................taaaagccgagctgcaaattactagattgcagctcggctcttc....................... TransTerm Strand: - Conf: 100 HP_score: -14.5 Tail_Score: -4.36586 Start: 46 End: 82 Full_Region: ctcattctttcttaa aagccgagctgcaaatt act agattgcagctcggctc ttcttttgattctgt .............................................aagccgagctgcaaattactagattgcagctcggctc.......................... TransTerm Strand: + Conf: 100 HP_score: -15.0 Tail_Score: -4.07885 Start: 48 End: 80 Full_Region: AGAATCAAAAGAAGA GCCGAGCTGCAA TCTAGTAAT TTGCAGCTCGGC TTTTAAGAAAGAATG ...............................................GCCGAGCTGCAATCTAGTAATTTGCAGCTCGGC............................ TransTerm Strand: - Conf: 100 HP_score: -17.1 Tail_Score: -3.76665 Start: 48 End: 80 Full_Region: cattctttcttaaaa gccgagctgcaaatt act agattgcagctcggc tcttcttttgattct ...............................................gccgagctgcaaattactagattgcagctcggc............................ Find igs database================================================ Query_seq: PG1997:PG1998|PG1997:PG1998:hypothetical protein:polyprenyl synthetase:-><-:2087133..2087240 108 ccgtagcaacgtacgactctcgaaaacaacacagaatcaaaagaagagccgagctgcaatctagtaatttgcagctcggcttttaagaaagaatgagtacaagactta Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: NC_002950_PG1997_PG1998|hypothetical protein:polyprenyl synthetase|POSITIVE:NEGATIVE|[2087133,2087240]|108 HSP 1 e-value: 4.0E-55 bit: 214.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 ccgtagcaacgtacgactctcgaaaacaacacagaatcaaaagaagagccgagctgcaatctagtaatttgcagctcggcttttaagaaagaatgagtacaagactta ccgtagcaacgtacgactctcgaaaacaacacagaatcaaaagaagagccgagctgcaatctagtaatttgcagctcggcttttaagaaagaatgagtacaagactta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGUAGCAACGUACGACUCUCGAAAACAACACAGAAUCAAAAGAAGAGCCGAGCUGCAAUCUAGUAAUUUGCAGCUCGGCUUUUAAGAAAGAAUGAGUACAAGACUUA ..........((((((.(((............))).)).....((((((((((((((((.........))))))))))))))))............))))........ (-31.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUCUUGUACUCAUUCUUUCUUAAAAGCCGAGCUGCAAAUUACUAGAUUGCAGCUCGGCUCUUCUUUUGAUUCUGUGUUGUUUUCGAGAGUCGUACGUUGCUACGG ..(((..(((((...............(((((((((((((.........)))))))))))))...(((((((..(......)...)))))))..)))))..))).... (-36.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 80 34 49 9 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 296 78 41 95 50 NC_002950:PG0994|5end_hypothetical_protein_1054921..1055151_POSITIVE 287 85 48 201 164 NC_002950:PG2107|5end_thiamine_biosynthesis_protein_ThiH_2216658..2216888_NEGATIVE 287 80 31 225 175 NC_002950:PG1829|5end_long-chain-fatty-acid--CoA_ligase,_putative_1922980..1923210_NEGATIVE 284 83 44 76 29 NC_002950:PG1195|5end_8-amino-7-oxononanoate_synthase_1273979..1274209_POSITIVE 283 83 45 131 97 NC_002950:PG0458|5end_ISPg5,_transposase_Orf2_501463..501693_NEGATIVE 282 81 41 73 33 NC_002950:PG1009|5end_hypothetical_protein_1068495..1068725_NEGATIVE 281 81 42 88 50 NC_002950:PG1375|5end_hypothetical_protein_1456553..1456783_POSITIVE 281 50 1 203 147 NC_002950:PG1117|5end_MATE_efflux_family_protein_1190010..1190240_POSITIVE 274 83 42 189 151 NC_002950:PG0201|5end_ribonuclease_P_238770..239000_NEGATIVE 273 82 43 198 163 NC_002950:PG1253|5end_DNA_ligase,_NAD-dependent_1331606..1331836_NEGATIVE 271 79 31 63 14 NC_002950:PG1371|5end_phosphorylase_family_protein_1453230..1453460_NEGATIVE 271 82 46 127 86 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 270 80 31 82 35 NC_002950:PG0621|5end_hypothetical_protein_675392..675622_POSITIVE 268 80 32 183 130 NC_002950:PG1489|5end_hypothetical_protein_1562133..1562363_POSITIVE 267 85 42 69 30 NC_002950:PG2159|5end_protoporphyrinogen_oxidase_2264397..2264627_POSITIVE 266 84 42 109 60 NC_002950:PG1363|5end_hypothetical_protein_1443804..1444034_POSITIVE 266 99 69 56 27 NC_002950:PG0670|5end_lipoprotein,_putative_720752..720982_POSITIVE 264 79 43 170 120 NC_002950:PG0685|5end_ABC_transporter,_ATP-binding_protein_740116..740346_POSITIVE 263 80 36 105 50 NC_002950:PG0499|5end_hypothetical_protein_538709..538939_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 551 84 44 47 7 NC_002950:PG1997|3end_hypothetical_protein_2087072..2087222_POSITIVE 283 83 45 77 43 NC_002950:PG0459|3end_ISPg5,_transposase_Orf1_501517..501667_NEGATIVE 282 81 41 59 19 NC_002950:PG1010|3end_ABC_transporter,_ATP-binding_protein_1068509..1068659_NEGATIVE 281 85 46 53 14 NC_002950:PG0431|3end_hypothetical_protein_469174..469324_POSITIVE 276 83 41 64 15 NC_002950:PG1786|3end_hypothetical_protein_1875322..1875472_POSITIVE 270 80 43 123 81 NC_002950:PG1431|3end_DNA-binding_response_regulator,_LuxR_family_1515986..1516136_NEGATIVE 270 80 31 85 38 NC_002950:PG0620|3end_ATP-dependent_protease_La_675475..675625_POSITIVE 267 85 42 65 26 NC_002950:PG2158|3end_hypothetical_protein_2264473..2264623_POSITIVE 264 79 43 77 27 NC_002950:PG0684|3end_ABC_transporter,_permease_protein,_putative_740103..740253_POSITIVE 262 82 42 63 16 NC_002950:PG0593|3end_htrA_protein_651938..652088_POSITIVE 262 80 44 73 41 NC_002950:PG0171|3end_5'-nucleotidase_family_protein_193576..193726_POSITIVE 257 88 48 149 110 NC_002950:PG0278|3end_hypothetical_protein_310477..310627_POSITIVE 256 79 47 107 68 NC_002950:PG2094|3end_hypothetical_protein_2193321..2193471_NEGATIVE 256 79 41 55 25 NC_002950:PG1271|3end_acetylornithine_aminotransferase,_putative_1350214..1350364_NEGATIVE 255 84 41 61 17 NC_002950:PG0914|3end_hypothetical_protein_975704..975854_NEGATIVE 253 61 36 38 11 NC_002950:PG1619|3end_biotin_synthesis_protein_BioC,_putative_1699415..1699565_POSITIVE 252 88 44 116 65 NC_002950:PG1761|3end_acetyltransferase,_GNAT_family_1847739..1847889_POSITIVE 249 83 42 66 16 NC_002950:PG0211|3end_cobalamin_biosynthesis_protein_CbiG/precorrin-4_C11-methyltransferase_245966..246116_NEGATIVE 248 80 44 62 11 NC_002950:PG1945|3end_hypothetical_protein_2032220..2032370_POSITIVE 248 99 67 77 40 NC_002950:PG0316|3end_seryl-tRNA_synthetase_349788..349938_POSITIVE