Origin IGS: aaagtcaggctctcatcattctttttatcttctgttctgttttacacagaaaatatcctaaatatctcagaacagaagagtctgacaattgacaagcaaacctaaatcggattaacgaatggtattgcatggaggcgattctcttcggattcagtggcctgtattcccttatcgtcttatattgattgcagggagctttgtcataaaacattttagctacattcaagtaggctatttcaaaatcagactcgatttctgatttctccacgttgtatggaggaataagcacgctgaccaagggagaatgcacgatcataattctctaaacagtatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatactgtttagagaattatgatcgtgcattctcccttggtcagcgtgcttattcctccatacaacgtggagaaatcagaaatcgagtctgattttgaaatagcctacttgaatgtagctaaaatgttttatgacaaagctccctgcaatcaatataagacgataagggaatacaggccactgaatccgaagagaatcgcctccatgcaataccattcgttaatccgatttaggtttgcttgtcaattgtcagactcttctgttctgagatatttaggatattttctgtgtaaaacagaacagaagataaaaagaatgatgagagcctgacttt Mask Tandem Repeat Region ================================================ aaagtcaggctctcatcattctttttatcttctgttctgttttacacagaaaatatcctaaatatctcagaacagaagagtctgacaattgacaagcaaacctaaatcggattaacgaatggtattgcatggaggcgattctcttcggattcagtggcctgtattcccttatcgtcttatattgattgcagggagctttgtcataaaacattttagctacattcaagtaggctatttcaaaatcagactcgatttctgatttctccacgttgtatggaggaataagcacgctgaccaagggagaatgcacgatcataattctctaaacagtatttt Find is-nt database================================================ Query_seq: PG1141:PG1142|PG1141:PG1142:glycosyl transferase, group 1 family protein:exopolysaccharide synthesis-related protein:<-<-:1224325..1224660 336 aaagtcaggctctcatcattctttttatcttctgttctgttttacacagaaaatatcctaaatatctcagaacagaagagtctgacaattgacaagcaaacctaaatcggattaacgaatggtattgcatggaggcgattctcttcggattcagtggcctgtattcccttatcgtcttatattgattgcagggagctttgtcataaaacattttagctacattcaagtaggctatttcaaaatcagactcgatttctgatttctccacgttgtatggaggaataagcacgctgaccaagggagaatgcacgatcataattctctaaacagtatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1141:PG1142|PG1141:PG1142:glycosyl transferase, group 1 family protein:exopolysaccharide synthesis-related protein:<-<-:1224325..1224660 336 aaagtcaggctctcatcattctttttatcttctgttctgttttacacagaaaatatcctaaatatctcagaacagaagagtctgacaattgacaagcaaacctaaatcggattaacgaatggtattgcatggaggcgattctcttcggattcagtggcctgtattcccttatcgtcttatattgattgcagggagctttgtcataaaacattttagctacattcaagtaggctatttcaaaatcagactcgatttctgatttctccacgttgtatggaggaataagcacgctgaccaagggagaatgcacgatcataattctctaaacagtatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1141:PG1142|PG1141:PG1142:glycosyl transferase, group 1 family protein:exopolysaccharide synthesis-related protein:<-<-:1224325..1224660 336 aaagtcaggctctcatcattctttttatcttctgttctgttttacacagaaaatatcctaaatatctcagaacagaagagtctgacaattgacaagcaaacctaaatcggattaacgaatggtattgcatggaggcgattctcttcggattcagtggcctgtattcccttatcgtcttatattgattgcagggagctttgtcataaaacattttagctacattcaagtaggctatttcaaaatcagactcgatttctgatttctccacgttgtatggaggaataagcacgctgaccaagggagaatgcacgatcataattctctaaacagtatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagtcaggctctcatcattctttttatcttctgttctgttttacacagaaaatatcctaaatatctcagaacagaagagtctgacaattgacaagcaaacctaaatcggattaacgaatggtattgcatggaggcgattctcttcggattcagtggcctgtattcccttatcgtcttatattgattgcagggagctttgtcataaaacattttagctacattcaagtaggctatttcaaaatcagactcgatttctgatttctccacgttgtatggaggaataagcacgctgaccaagggagaatgcacgatcataattctctaaacagtatttt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 106 End: 213 ......................................................................................................... M G L T N G I A W R R F S S D S V A C I P L S S Y I D C R E L C H K T F ........................................................................................................................... Protein_Len: 46 Strand: + Start: 119 End: 256 ...................................................................................................................... M V L H G G D S L R I Q W P V F P Y R L I L I A G S F V I K H F S Y I Q V G Y F K I R L D F ................................................................................ Protein_Len: 30 Strand: + Start: 234 End: 323 ......................................................................................................................................................................................................................................... M S K S D S I S D F S T L Y G G I S T L T K G E C T I I I L ............. Protein_Len: 60 Strand: - Start: 8 End: 319 ....... R K P N L P R Y E R I T K Y Q N C P A K D Y F M K A V N L Y A I E F D S E I E S K E V N Y P P I L V S V L P S H V I M M ................. aaagtcaggctctcatcattctttttatcttctgttctgttttacacagaaaatatcctaaatatctcagaacagaagagtctgacaattgacaagcaaacctaaatcggattaacgaatggtattgcatggaggcgattctcttcggattcagtggcctgtattcccttatcgtcttatattgattgcagggagctttgtcataaaacattttagctacattcaagtaggctatttcaaaatcagactcgatttctgatttctccacgttgtatggaggaataagcacgctgaccaagggagaatgcacgatcataattctctaaacagtatttt 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================================================ aaagtcaggctctcatcattctttttatcttctgttctgttttacacagaaaatatcctaaatatctcagaacagaagagtctgacaattgacaagcaaacctaaatcggattaacgaatggtattgcatggaggcgattctcttcggattcagtggcctgtattcccttatcgtcttatattgattgcagggagctttgtcataaaacattttagctacattcaagtaggctatttcaaaatcagactcgatttctgatttctccacgttgtatggaggaataagcacgctgaccaagggagaatgcacgatcataattctctaaacagtatttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 54 HP_score: -2.3 Tail_Score: -4.14243 Start: 243 End: 259 Full_Region: tacaacgtggagaaa tcaga aatcgag tctga ttttgaaatagccta ..................................................................................................................................................................................................................................................tcagaaatcgagtctga............................................................................. Find igs database================================================ Query_seq: PG1141:PG1142|PG1141:PG1142:glycosyl transferase, group 1 family protein:exopolysaccharide synthesis-related protein:<-<-:1224325..1224660 336 aaagtcaggctctcatcattctttttatcttctgttctgttttacacagaaaatatcctaaatatctcagaacagaagagtctgacaattgacaagcaaacctaaatcggattaacgaatggtattgcatggaggcgattctcttcggattcagtggcctgtattcccttatcgtcttatattgattgcagggagctttgtcataaaacattttagctacattcaagtaggctatttcaaaatcagactcgatttctgatttctccacgttgtatggaggaataagcacgctgaccaagggagaatgcacgatcataattctctaaacagtatttt Intra-Species Hit: Count: 1 Min: 1 Max: 336 Len: 336 Subject: NC_002950_PG1141_PG1142|glycosyl transferase, group 1 family protein:exopolysaccharide synthesis-related protein|NEGATIVE:NEGATIVE|[1224325,1224660]|336 HSP 1 e-value: 0.0 bit: 666.0 Len: 336 Query Start:1 Query End:336 Subject Strand: POSITIVE Subject Start: 1 Subject End: 336 aaagtcaggctctcatcattctttttatcttctgttctgttttacacagaaaatatcctaaatatctcagaacagaagagtctgacaattgacaagcaaacctaaatcggattaacgaatggtattgcatggaggcgattctcttcggattcagtggcctgtattcccttatcgtcttatattgattgcagggagctttgtcataaaacattttagctacattcaagtaggctatttcaaaatcagactcgatttctgatttctccacgttgtatggaggaataagcacgctgaccaagggagaatgcacgatcataattctctaaacagtatttt aaagtcaggctctcatcattctttttatcttctgttctgttttacacagaaaatatcctaaatatctcagaacagaagagtctgacaattgacaagcaaacctaaatcggattaacgaatggtattgcatggaggcgattctcttcggattcagtggcctgtattcccttatcgtcttatattgattgcagggagctttgtcataaaacattttagctacattcaagtaggctatttcaaaatcagactcgatttctgatttctccacgttgtatggaggaataagcacgctgaccaagggagaatgcacgatcataattctctaaacagtatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUCAGGCUCUCAUCAUUCUUUUUAUCUUCUGUUCUGUUUUACACAGAAAAUAUCCUAAAUAUCUCAGAACAGAAGAGUCUGACAAUUGACAAGCAAACCUAAAUCGGAUUAACGAAUGGUAUUGCAUGGAGGCGAUUCUCUUCGGAUUCAGUGGCCUGUAUUCCCUUAUCGUCUUAUAUUGAUUGCAGGGAGCUUUGUCAUAAAACAUUUUAGCUACAUUCAAGUAGGCUAUUUCAAAAUCAGACUCGAUUUCUGAUUUCUCCACGUUGUAUGGAGGAAUAAGCACGCUGACCAAGGGAGAAUGCACGAUCAUAAUUCUCUAAACAGUAUUUU ...((((((((...(((..........((((((((((((........((........))........))))))))))))((((((....(((((((((((((....(((......)))..))).)))).((.((((.(((.((....))...))).)))).)).(((((.((((........))))...)))))...))))))..........(((((((......))).))))........))))))..))).....(((((((((.......))))))))).)))...)))))....(((((((...........)))))))............ (-86.79) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUACUGUUUAGAGAAUUAUGAUCGUGCAUUCUCCCUUGGUCAGCGUGCUUAUUCCUCCAUACAACGUGGAGAAAUCAGAAAUCGAGUCUGAUUUUGAAAUAGCCUACUUGAAUGUAGCUAAAAUGUUUUAUGACAAAGCUCCCUGCAAUCAAUAUAAGACGAUAAGGGAAUACAGGCCACUGAAUCCGAAGAGAAUCGCCUCCAUGCAAUACCAUUCGUUAAUCCGAUUUAGGUUUGCUUGUCAAUUGUCAGACUCUUCUGUUCUGAGAUAUUUAGGAUAUUUUCUGUGUAAAACAGAACAGAAGAUAAAAAGAAUGAUGAGAGCCUGACUUU .............(((((((((....))).))))))....((((((.((.((((((.((((((.....))))))..(((.......(((((((((.......((((.(((......)))))))..........((((((.((..((((.((((.......(((((....(((...(((....)))..)))...(((......))).............))))).....))))))))...))))))))...))))))))).(((((((((...(((.(((((....))))).)))...))))))))).))).........)))))).)))))))).. (-88.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 897 140 91 231 182 NC_002950:PG1141|5end_glycosyl_transferase,_group_1_family_protein_1224234..1224464_NEGATIVE 371 148 106 151 101 NC_002950:PG2095|5end_lipoprotein,_putative_2200617..2200847_NEGATIVE 360 157 116 49 6 NC_002950:PG0969|5end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase,_putative_1029418..1029648_NEGATIVE 345 156 116 202 163 NC_002950:PG0657|5end_Maf-like_protein_707782..708012_NEGATIVE 333 138 95 228 188 NC_002950:PG2146|5end_hypothetical_protein_2253815..2254045_POSITIVE 333 156 116 150 96 NC_002950:PG0085|5end_alpha-galactosidase_99172..99402_POSITIVE 332 175 131 190 141 NC_002950:PG2092|5end_hypothetical_protein_2192910..2193140_NEGATIVE 331 199 158 220 178 NC_002950:PG1203|5end_transcriptional_regulator,_putative_1283446..1283676_NEGATIVE 327 157 119 43 6 NC_002950:PG1773|5end_PAP2_superfamily_protein_1859815..1860045_POSITIVE 327 159 114 211 173 NC_002950:PG1087|5end_radical_SAM_protein,_TIGR01212_family_1153805..1154035_POSITIVE 327 160 125 226 187 NC_002950:PG0960|5end_tRNA_(guanine-N(7)-)-methyltransferase_1021895..1022125_NEGATIVE 326 167 127 52 6 NC_002950:PG1310|5end_exsB_protein_1389084..1389314_POSITIVE 321 170 121 231 186 NC_002950:PG1366|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1447380..1447610_NEGATIVE 320 179 131 50 11 NC_002950:PG1725|5end_competence/damage-inducible_protein_CinA_domain_protein_1814766..1814996_POSITIVE 319 296 263 38 1 NC_002950:PG1814|5end_DNA_primase_1910627..1910857_NEGATIVE 314 170 122 127 83 NC_002950:PG2016|5end_CRISPR-associated_helicase_Cas3_2108370..2108600_NEGATIVE 313 167 121 223 179 NC_002950:PG1021|5end_hypothetical_protein_1083592..1083822_NEGATIVE 311 200 152 47 5 NC_002950:PG1053|5end_transcriptional_regulator,_putative_1120065..1120295_POSITIVE 310 190 143 90 37 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 308 178 138 171 129 NC_002950:PG0282|5end_ABC_transporter,_ATP-binding_protein_316915..317145_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 386 169 121 148 100 NC_002950:PG1966|3end_hypothetical_protein_2056118..2056268_NEGATIVE 371 148 106 143 93 NC_002950:PG2096|3end_hypothetical_protein_2200625..2200775_NEGATIVE 365 190 142 48 8 NC_002950:PG0686|3end_hypothetical_protein_741131..741281_NEGATIVE 355 176 131 62 14 NC_002950:PG0435|3end_capsular_polysaccharide_biosythesis_protein,_putative_472708..472858_NEGATIVE 350 170 121 116 74 NC_002950:PG2036|3end_ion_transporter_2137552..2137702_POSITIVE 320 179 131 50 11 NC_002950:PG1724|3end_O-sialoglycoprotein_endopeptidase_1814846..1814996_POSITIVE 318 176 131 135 96 NC_002950:PG0894|3end_DNA_repair_protein_RadC_956078..956228_NEGATIVE 315 169 128 123 79 NC_002950:PG1614|3end_succinate_dehydrogenase_1693800..1693950_NEGATIVE 314 310 261 146 97 NC_002950:PG0209|3end_formate/nitrite_transporter_244096..244246_POSITIVE 312 155 115 118 70 NC_002950:PG0333|3end_hypothetical_protein_368811..368961_POSITIVE 311 44 3 143 106 NC_002950:PG0472|3end_iron-sulfur_cluster_binding_protein,_putative_514414..514564_POSITIVE 310 179 131 97 38 NC_002950:PG2172|3end_hypothetical_protein_2279191..2279341_NEGATIVE 308 178 138 91 49 NC_002950:PG0283|3end_efflux_transporter,_MFP_component,_RND_family_316995..317145_NEGATIVE 305 169 122 151 108 NC_002950:PG2017|3end_hypothetical_protein_2108345..2108495_NEGATIVE 305 198 154 106 56 NC_002950:PG1483|3end_conjugative_transposon_protein_TraE_1558783..1558933_NEGATIVE 298 159 126 41 3 NC_002950:PG1752|3end_hypothetical_protein_1838698..1838848_POSITIVE 295 200 153 125 80 NC_002950:PG1723|3end_ribosomal_protein_S20_1813403..1813553_POSITIVE 295 309 265 56 4 NC_002950:PG1311|3end_hypothetical_protein_1390355..1390505_POSITIVE 294 157 121 143 99 NC_002950:PG1081|3end_acetate_kinase_1148431..1148581_NEGATIVE 294 180 131 54 1 NC_002950:PG0317|3end_peptidase,_M49_family_349771..349921_NEGATIVE