Origin IGS: tcgtgaataaattgaaagagataagatgattgcccgatttcgctgtggcagtctcttatctcttttttcataacaaacatattaatcgaagatatcagtc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gactgatatcttcgattaatatgtttgttatgaaaaaagagataagagactgccacagcgaaatcgggcaatcatcttatctctttcaatttattcacga Mask Tandem Repeat Region ================================================ tcgtgaataaattgaaagagataagatgattgcccgatttcgctgtggcagtctcttatctcttttttcataacaaacatattaatcgaagatatcagtc Find is-nt database================================================ Query_seq: PG1278:PG1279|PG1278:PG1279:phosphoserine aminotransferase:D-isomer specific 2-hydroxyacid dehydrogenase family protein:->->:1356575..1356674 100 tcgtgaataaattgaaagagataagatgattgcccgatttcgctgtggcagtctcttatctcttttttcataacaaacatattaatcgaagatatcagtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1278:PG1279|PG1278:PG1279:phosphoserine aminotransferase:D-isomer specific 2-hydroxyacid dehydrogenase family protein:->->:1356575..1356674 100 tcgtgaataaattgaaagagataagatgattgcccgatttcgctgtggcagtctcttatctcttttttcataacaaacatattaatcgaagatatcagtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1278:PG1279|PG1278:PG1279:phosphoserine aminotransferase:D-isomer specific 2-hydroxyacid dehydrogenase family protein:->->:1356575..1356674 100 tcgtgaataaattgaaagagataagatgattgcccgatttcgctgtggcagtctcttatctcttttttcataacaaacatattaatcgaagatatcagtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcgtgaataaattgaaagagataagatgattgcccgatttcgctgtggcagtctcttatctcttttttcataacaaacatattaatcgaagatatcagtc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 3 End: 98 .. H I F Q F L Y S S Q G I E S H C D R I E K K M V F M N I S S I M .. tcgtgaataaattgaaagagataagatgattgcccgatttcgctgtggcagtctcttatctcttttttcataacaaacatattaatcgaagatatcagtc 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================================================ tcgtgaataaattgaaagagataagatgattgcccgatttcgctgtggcagtctcttatctcttttttcataacaaacatattaatcgaagatatcagtc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 83 HP_score: -6.0 Tail_Score: -5.14563 Start: 18 End: 62 Full_Region: GTGAATAAATTGAAA GAGATAAGATGATTGCCCG ATTTCGC TGTGGCAGTCTCTTATCTC TTTTTTCATAACAAA .................GAGATAAGATGATTGCCCGATTTCGCTGTGGCAGTCTCTTATCTC...................................... Find igs database================================================ Query_seq: PG1278:PG1279|PG1278:PG1279:phosphoserine aminotransferase:D-isomer specific 2-hydroxyacid dehydrogenase family protein:->->:1356575..1356674 100 tcgtgaataaattgaaagagataagatgattgcccgatttcgctgtggcagtctcttatctcttttttcataacaaacatattaatcgaagatatcagtc Intra-Species Hit: Count: 1 Min: 1 Max: 100 Len: 100 Subject: NC_002950_PG1278_PG1279|phosphoserine aminotransferase:D-isomer specific 2-hydroxyacid dehydrogenase family protein|POSITIVE:POSITIVE|[1356575,1356674]|100 HSP 1 e-value: 2.0E-50 bit: 198.0 Len: 100 Query Start:1 Query End:100 Subject Strand: POSITIVE Subject Start: 1 Subject End: 100 tcgtgaataaattgaaagagataagatgattgcccgatttcgctgtggcagtctcttatctcttttttcataacaaacatattaatcgaagatatcagtc tcgtgaataaattgaaagagataagatgattgcccgatttcgctgtggcagtctcttatctcttttttcataacaaacatattaatcgaagatatcagtc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGUGAAUAAAUUGAAAGAGAUAAGAUGAUUGCCCGAUUUCGCUGUGGCAGUCUCUUAUCUCUUUUUUCAUAACAAACAUAUUAAUCGAAGAUAUCAGUC ..(((((......(((((((((((((.(((((((((.......)).)))))))))))))))))))))))))............................. (-28.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACUGAUAUCUUCGAUUAAUAUGUUUGUUAUGAAAAAAGAGAUAAGAGACUGCCACAGCGAAAUCGGGCAAUCAUCUUAUCUCUUUCAAUUUAUUCACGA ...........(((..(((((....))))).....((((((((((((((.((((....((....)))))).)).))))))))))))...........))) (-23.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 68 27 100 52 NC_002950:PG0399|5end_lipoprotein,_putative_436237..436467_NEGATIVE 342 60 18 147 112 NC_002950:PG1495|5end_DNA_topoisomerase_III_1571243..1571473_POSITIVE 336 62 25 51 5 NC_002950:PG0930|5end_hypothetical_protein_987542..987772_NEGATIVE 324 70 29 142 90 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 308 70 23 90 47 NC_002950:PG0173|5end_transcriptional_regulator,_putative_194741..194971_NEGATIVE 304 57 14 67 2 NC_002950:PG1441|5end_lysozyme-related_protein_1527525..1527755_NEGATIVE 303 56 13 139 96 NC_002950:PG1619|5end_biotin_synthesis_protein_BioC,_putative_1698568..1698798_POSITIVE 301 62 21 211 168 NC_002950:PG1598|5end_lipoprotein_signal_peptidase,_putative_1678410..1678640_POSITIVE 301 70 26 69 29 NC_002950:PG1109|5end_mobilization_protein_1182792..1183022_NEGATIVE 295 49 13 44 1 NC_002950:PG0691|5end_NifU-related_protein_747469..747699_NEGATIVE 287 53 22 62 28 NC_002950:PG0679|5end_outer_membrane_efflux_protein_729594..729824_POSITIVE 286 59 19 200 161 NC_002950:PG0460|5end_ISPg1,_transposase_501937..502167_POSITIVE 278 56 17 64 27 NC_002950:PG0980|5end_hypothetical_protein_1040897..1041127_POSITIVE 278 66 31 98 59 NC_002950:PG0144|5end_hypothetical_protein_167668..167898_NEGATIVE 275 71 31 231 188 NC_002950:PG0323|5end_hypothetical_protein_357388..357618_NEGATIVE 273 58 25 211 177 NC_002950:PG1499|5end_hypothetical_protein_1575524..1575754_POSITIVE 273 65 26 219 176 NC_002950:PG0215|5end_hypothetical_protein_251460..251690_POSITIVE 272 60 30 126 93 NC_002950:PG1675|5end_hypothetical_protein_1760182..1760412_POSITIVE 272 79 31 98 36 NC_002950:PG0948|5end_AMP_nucleosidase_1007891..1008121_POSITIVE 271 76 33 98 46 NC_002950:PG1854|5end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1953882..1954112_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 437 60 13 71 21 NC_002950:PG1278|3end_phosphoserine_aminotransferase_1356514..1356664_POSITIVE 347 68 27 92 44 NC_002950:PG0400|3end_hypothetical_protein_436245..436395_NEGATIVE 342 60 18 58 23 NC_002950:PG1494|3end_hypothetical_protein_1571234..1571384_POSITIVE 319 60 14 61 20 NC_002950:PG1055|3end_thiol_protease_1121202..1121352_NEGATIVE 306 52 11 141 97 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 278 56 17 77 40 NC_002950:PG0979|3end_hypothetical_protein_1040990..1041140_POSITIVE 275 67 28 66 20 NC_002950:PG0507|3end_hypothetical_protein_548190..548340_POSITIVE 272 50 1 103 38 NC_002950:PG0199|3end_TatD_family_protein_237424..237574_NEGATIVE 271 76 33 138 86 NC_002950:PG1855|3end_carboxyl-terminal_protease_1953842..1953992_NEGATIVE 269 51 11 131 93 NC_002950:PG0723|3end_hypothetical_protein_775355..775505_POSITIVE 266 49 1 81 18 NC_002950:PG0469|3end_hypothetical_protein_511407..511557_NEGATIVE 264 57 18 126 69 NC_002950:PG2073|3end_hypothetical_protein_2174219..2174369_NEGATIVE 264 61 32 103 67 NC_002950:PG1942|3end_30S_ribosomal_protein_S12_2027946..2028096_NEGATIVE 264 57 18 126 69 NC_002950:PG1669|3end_hypothetical_protein_1755411..1755561_NEGATIVE 264 57 18 126 69 NC_002950:PG1264|3end_hypothetical_protein_1344740..1344890_NEGATIVE 264 57 18 126 69 NC_002950:PG0103|3end_hypothetical_protein_121525..121675_POSITIVE 263 48 1 120 73 NC_002950:PG1333|3end_hypothetical_protein_1414226..1414376_NEGATIVE 262 60 18 62 8 NC_002950:PG1692|3end_ABC_transporter,_ATP-binding_protein_1776514..1776664_NEGATIVE 262 68 24 108 45 NC_002950:PG1553|3end_CobN/magnesium_chelatase_family_protein_1635347..1635497_POSITIVE 258 57 17 67 17 NC_002950:PG0726|3end_lipoprotein,_putative_778003..778153_NEGATIVE