Origin IGS: tgtttgttttctgtaattatcgtcttagtacgacatggtacaaaattatagaaaaaaagcacgaagcctgtttccatttccttatcctaaccgtaagatgcctactctca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgagagtaggcatcttacggttaggataaggaaatggaaacaggcttcgtgctttttttctataattttgtaccatgtcgtactaagacgataattacagaaaacaaaca Mask Tandem Repeat Region ================================================ tgtttgttttctgtaattatcgtcttagtacgacatggtacaaaattatagaaaaaaagcacgaagcctgtttccatttccttatcctaaccgtaagatgcctactctca Find is-nt database================================================ Query_seq: PG1353:PG1354|PG1353:PG1354:orotate phosphoribosyltransferase:hydrolase, carbon-nitrogen family:<-<-:1433924..1434033 110 tgtttgttttctgtaattatcgtcttagtacgacatggtacaaaattatagaaaaaaagcacgaagcctgtttccatttccttatcctaaccgtaagatgcctactctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1353:PG1354|PG1353:PG1354:orotate phosphoribosyltransferase:hydrolase, carbon-nitrogen family:<-<-:1433924..1434033 110 tgtttgttttctgtaattatcgtcttagtacgacatggtacaaaattatagaaaaaaagcacgaagcctgtttccatttccttatcctaaccgtaagatgcctactctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1353:PG1354|PG1353:PG1354:orotate phosphoribosyltransferase:hydrolase, carbon-nitrogen family:<-<-:1433924..1434033 110 tgtttgttttctgtaattatcgtcttagtacgacatggtacaaaattatagaaaaaaagcacgaagcctgtttccatttccttatcctaaccgtaagatgcctactctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtttgttttctgtaattatcgtcttagtacgacatggtacaaaattatagaaaaaaagcacgaagcctgtttccatttccttatcctaaccgtaagatgcctactctca Predict ORF larger than 30AA ================================================ tgtttgttttctgtaattatcgtcttagtacgacatggtacaaaattatagaaaaaaagcacgaagcctgtttccatttccttatcctaaccgtaagatgcctactctca Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 70 End: 99 .....................................................................GTTTCCATTTCCTTATCCTAACCGTAAGAT........... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgtttgttttctgtaattatcgtcttagtacgacatggtacaaaattatagaaaaaaagcacgaagcctgtttccatttccttatcctaaccgtaagatgcctactctca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1353:PG1354|PG1353:PG1354:orotate phosphoribosyltransferase:hydrolase, carbon-nitrogen family:<-<-:1433924..1434033 110 tgtttgttttctgtaattatcgtcttagtacgacatggtacaaaattatagaaaaaaagcacgaagcctgtttccatttccttatcctaaccgtaagatgcctactctca Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: NC_002950_PG1353_PG1354|orotate phosphoribosyltransferase:hydrolase, carbon-nitrogen family|NEGATIVE:NEGATIVE|[1433924,1434033]|110 HSP 1 e-value: 9.0E-44 bit: 176.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 tgtttgttttctgtaattatcgtcttagtacgacatggtacaaaattatagnnnnnnngcacgaagcctgtttccatttccttatcctaaccgtaagatgcctactctca tgtttgttttctgtaattatcgtcttagtacgacatggtacaaaattatagaaaaaaagcacgaagcctgtttccatttccttatcctaaccgtaagatgcctactctca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUGUUUUCUGUAAUUAUCGUCUUAGUACGACAUGGUACAAAAUUAUAGAAAAAAAGCACGAAGCCUGUUUCCAUUUCCUUAUCCUAACCGUAAGAUGCCUACUCUCA (((((.((((((((((((((((((.......)))..))))....))))))))))).))))).((((....))))......(((((.......)))))............. (-16.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGAGUAGGCAUCUUACGGUUAGGAUAAGGAAAUGGAAACAGGCUUCGUGCUUUUUUUCUAUAAUUUUGUACCAUGUCGUACUAAGACGAUAAUUACAGAAAACAAACA .(((((.((((.(((((....)))))...(((..((....))...)))..)))).))))).....(((((((...((((((......))))))..)))))))........ (-22.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 929 110 61 201 152 NC_002950:PG1353|5end_orotate_phosphoribosyltransferase_1433833..1434063_NEGATIVE 290 110 63 198 160 NC_002950:PG2003|5end_deoxyguanosinetriphosphate_triphosphohydrolase_2092991..2093221_NEGATIVE 280 100 56 117 66 NC_002950:PG0532|5end_hypothetical_protein_582148..582378_NEGATIVE 278 109 71 38 1 NC_002950:PG1984|5end_hypothetical_protein_2073882..2074112_NEGATIVE 278 107 62 65 23 NC_002950:PG0282|5end_ABC_transporter,_ATP-binding_protein_316915..317145_NEGATIVE 277 88 49 88 50 NC_002950:PG1083|5end_hypothetical_protein_1151834..1152064_NEGATIVE 275 87 59 66 37 NC_002950:PG1000|5end_hypothetical_protein_1057594..1057824_POSITIVE 275 42 1 172 122 NC_002950:PG0032|5end_beta-mannosidase,_putative_40212..40442_NEGATIVE 271 107 63 44 6 NC_002950:PG1416|5end_enoyl-(acyl-carrier-protein)_reductase_II_1500057..1500287_POSITIVE 265 109 65 149 109 NC_002950:PG0706|5end_hypothetical_protein_760350..760580_POSITIVE 264 70 22 77 17 NC_002950:PG0288|5end_lipoprotein,_putative_321455..321685_POSITIVE 262 99 62 114 64 NC_002950:PG1728|5end_cytidine/deoxycytidylate_deaminase_family_protein_1817644..1817874_POSITIVE 261 101 62 69 33 NC_002950:PG2215|5end_mannose-1-phosphate_guanylyltransferase_2327695..2327925_NEGATIVE 261 109 63 152 108 NC_002950:PG1382|5end_hypothetical_protein_1461331..1461561_POSITIVE 260 110 62 228 168 NC_002950:PG1123|5end_adenylosuccinate_lyase_1200350..1200580_NEGATIVE 259 102 66 208 170 NC_002950:PG0435|5end_capsular_polysaccharide_biosythesis_protein,_putative_473451..473681_NEGATIVE 257 110 62 124 73 NC_002950:PG0158|5end_competence_protein_F-related_protein_180175..180405_POSITIVE 255 110 61 66 15 NC_002950:PG0546|5end_hypothetical_protein_600391..600621_NEGATIVE 254 110 68 219 174 NC_002950:PG0677|5end_saccharopine_dehydrogenase_727653..727883_POSITIVE 253 109 61 132 75 NC_002950:PG0858|5end_hypothetical_protein_917540..917770_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 97 59 65 27 NC_002950:PG0324|3end_histidine_ammonia-lyase_357589..357739_NEGATIVE 290 110 63 54 16 NC_002950:PG2004|3end_hypothetical_protein_2093135..2093285_NEGATIVE 284 93 56 151 110 NC_002950:PG2199|3end_ABC_transporter,_ATP-binding_protein,_putative_2304786..2304936_NEGATIVE 278 109 71 41 4 NC_002950:PG1985|3end_CRISPR-associated_TM1792_family_protein_2073879..2074029_NEGATIVE 277 88 49 40 2 NC_002950:PG1084|3end_thioredoxin_family_protein_1151882..1152032_NEGATIVE 275 106 61 129 95 NC_002950:PG1980|3end_hypothetical_protein_2067760..2067910_NEGATIVE 275 87 59 43 14 NC_002950:PG0999|3end_hypothetical_protein_1057651..1057801_POSITIVE 275 42 1 142 92 NC_002950:PG0033|3end_RmuC_domain_protein_40242..40392_NEGATIVE 260 110 62 93 33 NC_002950:PG1124|3end_ATP:cob(I)alamin_adenosyltransferase,_putative_1200485..1200635_NEGATIVE 257 102 62 75 29 NC_002950:PG1649|3end_hypothetical_protein_1730030..1730180_NEGATIVE 257 110 62 140 89 NC_002950:PG0157|3end_regulatory_protein_RecX_180271..180421_POSITIVE 253 109 61 135 78 NC_002950:PG0857|3end_transcriptional_regulator,_putative_917623..917773_POSITIVE 250 100 57 71 31 NC_002950:PG1782|3end_hypothetical_protein_1871961..1872111_POSITIVE 242 39 1 88 55 NC_002950:PG0563|3end_hypothetical_protein_620935..621085_NEGATIVE 239 108 61 52 6 NC_002950:PG1503|3end_LytB-related_protein_1581255..1581405_POSITIVE 239 108 65 151 112 NC_002950:PG0705|3end_glutamate_racemase_760433..760583_POSITIVE 238 99 68 42 5 NC_002950:PG1727|3end_yitL_protein_1817652..1817802_POSITIVE 238 106 62 104 68 NC_002950:PG1314|3end_chorismate_synthase_1394362..1394512_NEGATIVE 238 109 69 66 23 NC_002950:PG0118|3end_glycosyl_transferase,_group_2_family_protein_142344..142494_POSITIVE 232 38 5 148 117 NC_002950:PG2083|3end_hypothetical_protein_2183410..2183560_NEGATIVE