Origin IGS: tcaagattgcgagtgaaagaccgtcttaggcggtctgccctgataatgaaaggggttgtgaatatggttttatccattgtcacaaccctttttctttacagtgggatttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaatcccactgtaaagaaaaagggttgtgacaatggataaaaccatattcacaacccctttcattatcagggcagaccgcctaagacggtctttcactcgcaatcttga Mask Tandem Repeat Region ================================================ tcaagattgcgagtgaaagaccgtcttaggcggtctgccctgataatgaaaggggttgtgaatatggttttatccattgtcacaaccctttttctttacagtgggatttta Find is-nt database================================================ Query_seq: PG0906:PG0908|PG0906:PG0908:lipoprotein, putative:G/U mismatch-specific DNA glycosylase, putative:-><-:971209..971319 111 tcaagattgcgagtgaaagaccgtcttaggcggtctgccctgataatgaaaggggttgtgaatatggttttatccattgtcacaaccctttttctttacagtgggatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0906:PG0908|PG0906:PG0908:lipoprotein, putative:G/U mismatch-specific DNA glycosylase, putative:-><-:971209..971319 111 tcaagattgcgagtgaaagaccgtcttaggcggtctgccctgataatgaaaggggttgtgaatatggttttatccattgtcacaaccctttttctttacagtgggatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0906:PG0908|PG0906:PG0908:lipoprotein, putative:G/U mismatch-specific DNA glycosylase, putative:-><-:971209..971319 111 tcaagattgcgagtgaaagaccgtcttaggcggtctgccctgataatgaaaggggttgtgaatatggttttatccattgtcacaaccctttttctttacagtgggatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcaagattgcgagtgaaagaccgtcttaggcggtctgccctgataatgaaaggggttgtgaatatggttttatccattgtcacaaccctttttctttacagtgggatttta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 7 End: 111 ...... M R V K D R L R R S A L I M K G V V N M V L S I V T T L F L Y S G I L tcaagattgcgagtgaaagaccgtcttaggcggtctgccctgataatgaaaggggttgtgaatatggttttatccattgtcacaaccctttttctttacagtgggatttta 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================================================ tcaagattgcgagtgaaagaccgtcttaggcggtctgccctgataatgaaaggggttgtgaatatggttttatccattgtcacaaccctttttctttacagtgggatttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.5 Tail_Score: -5.28942 Start: 53 End: 88 Full_Region: CCCTGATAATGAAAG GGGTTGTGAATATGG TTTTAT CCATTGTCACAACCC TTTTTCTTTACAGTG ....................................................GGGTTGTGAATATGGTTTTATCCATTGTCACAACCC....................... Find igs database================================================ Query_seq: PG0906:PG0908|PG0906:PG0908:lipoprotein, putative:G/U mismatch-specific DNA glycosylase, putative:-><-:971209..971319 111 tcaagattgcgagtgaaagaccgtcttaggcggtctgccctgataatgaaaggggttgtgaatatggttttatccattgtcacaaccctttttctttacagtgggatttta Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: NC_002950_PG0906_PG0908|lipoprotein, putative:G/U mismatch-specific DNA glycosylase, putative|POSITIVE:NEGATIVE|[971209,971319]|111 HSP 1 e-value: 7.0E-57 bit: 220.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 tcaagattgcgagtgaaagaccgtcttaggcggtctgccctgataatgaaaggggttgtgaatatggttttatccattgtcacaaccctttttctttacagtgggatttta tcaagattgcgagtgaaagaccgtcttaggcggtctgccctgataatgaaaggggttgtgaatatggttttatccattgtcacaaccctttttctttacagtgggatttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAGAUUGCGAGUGAAAGACCGUCUUAGGCGGUCUGCCCUGAUAAUGAAAGGGGUUGUGAAUAUGGUUUUAUCCAUUGUCACAACCCUUUUUCUUUACAGUGGGAUUUUA ..((((((.(.......(((((((.....)))))))...(((.(((.((((((((((((((..((((......))))..))))))))))))))..)))))).).)))))). (-42.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUCCCACUGUAAAGAAAAAGGGUUGUGACAAUGGAUAAAACCAUAUUCACAACCCCUUUCAUUAUCAGGGCAGACCGCCUAAGACGGUCUUUCACUCGCAAUCUUGA .......((.((((((.((((..(((((((((..((((......))))..))))))))).)))).))).))))).((((((.......))))))................. (-33.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 355 54 21 36 1 NC_002950:PG2106|5end_hypothetical_protein_2214694..2214924_POSITIVE 348 54 11 195 160 NC_002950:PG1641|5end_phosphotyrosine_protein_phosphatase_1721763..1721993_NEGATIVE 338 68 22 68 22 NC_002950:PG0202|5end_uroporphyrinogen-III_synthase_HemD,_putative_239513..239743_NEGATIVE 327 60 18 143 98 NC_002950:PG1827|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1920014..1920244_POSITIVE 326 80 31 94 49 NC_002950:PG0862|5end_type_IIS_restriction_endonuclease,_putative_922740..922970_POSITIVE 324 47 1 73 34 NC_002950:PG1288|5end_GDP-mannose_4,6-dehydratase_1365963..1366193_POSITIVE 309 77 33 91 34 NC_002950:PG0814|5end_hypothetical_protein_876251..876481_NEGATIVE 309 57 13 157 109 NC_002950:PG0800|5end_hypothetical_protein_856278..856508_NEGATIVE 307 88 45 214 168 NC_002950:PG1739|5end_hypothetical_protein_1825709..1825939_NEGATIVE 306 68 23 94 36 NC_002950:PG0886|5end_hypothetical_protein_948842..949072_POSITIVE 302 75 33 227 191 NC_002950:PG1871|5end_hypothetical_protein_1966859..1967089_NEGATIVE 300 56 13 157 117 NC_002950:PG1022|5end_hypothetical_protein_1083537..1083767_POSITIVE 299 66 21 143 99 NC_002950:PG0978|5end_shikimate_5-dehydrogenase_1040033..1040263_POSITIVE 298 67 22 196 142 NC_002950:PG1967|5end_TPR_domain_protein_2057168..2057398_POSITIVE 294 42 7 204 160 NC_002950:PG0735|5end_aminotransferase,_class_V_784383..784613_POSITIVE 292 56 13 156 115 NC_002950:PG0522|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_566901..567131_NEGATIVE 292 58 11 230 177 NC_002950:PG0127|5end_ferrochelatase_148550..148780_POSITIVE 290 37 3 174 144 NC_002950:PG0084|5end_L-serine_dehydratase,_iron-sulfur-dependent,_single_chain_form_97832..98062_POSITIVE 289 39 2 95 49 NC_002950:PG1345|5end_glycosyl_transferase,_group_1_family_protein_1425590..1425820_POSITIVE 289 55 14 155 109 NC_002950:PG0869|5end_mobilization_protein_932203..932433_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 376 92 51 42 1 NC_002950:PG0906|3end_lipoprotein,_putative_971148..971298_POSITIVE 371 95 51 55 13 NC_002950:PG1754|3end_hypothetical_protein_1842284..1842434_POSITIVE 338 68 22 77 31 NC_002950:PG0203|3end_hypothetical_protein_239504..239654_NEGATIVE 330 41 6 151 121 NC_002950:PG0010|3end_ATP-dependent_Clp_protease,_ATP-binding_subunit_ClpC_11434..11584_POSITIVE 327 60 11 54 9 NC_002950:PG1290|3end_branched-chain_amino_acid_aminotransferase_1369352..1369502_POSITIVE 326 80 31 83 38 NC_002950:PG0861|3end_helicase,_SNF2/RAD54_family_922809..922959_POSITIVE 308 60 12 124 73 NC_002950:PG1846|3end_hypothetical_protein_1946254..1946404_POSITIVE 307 88 45 67 21 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 306 68 23 97 39 NC_002950:PG0885|3end_phospho-2-dehydro-3-deoxyheptonate_aldolase/chorismate_mutase_948925..949075_POSITIVE 304 69 28 42 9 NC_002950:PG1605|3end_aminopeptidase_C_1686602..1686752_POSITIVE 303 69 22 135 84 NC_002950:PG1715|3end_hypothetical_protein_1803393..1803543_NEGATIVE 299 66 21 146 102 NC_002950:PG0977|3end_ubiquinone/menaquinone_biosynthesis_methyltransferase_1040116..1040266_POSITIVE 294 42 7 145 101 NC_002950:PG0734|3end_nitroreductase_family_protein_784404..784554_POSITIVE 294 67 23 50 4 NC_002950:PG0506|3end_arginine-specific_cysteine_proteinase_547625..547775_POSITIVE 291 58 22 68 34 NC_002950:PG1706|3end_hypothetical_protein_1793849..1793999_NEGATIVE 290 37 3 79 49 NC_002950:PG0083|3end_hypothetical_protein_97817..97967_POSITIVE 289 55 14 54 8 NC_002950:PG0870|3end_hypothetical_protein_932304..932454_NEGATIVE 288 45 5 133 88 NC_002950:PG1788|3end_cysteine_peptidase,_putative_1877327..1877477_POSITIVE 287 69 27 67 16 NC_002950:PG1220|3end_erythronate-4-phosphate_dehydrogenase_1298199..1298349_POSITIVE 287 55 19 85 48 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE