Origin IGS: tatgcacaccgatattatgacctccaaccatctgccgatacgactgctacagtcgctcccttttattcacatccactcactgcgttagagaaaaagagcgtatagacttatgatgtataagggtggaataccccttcggtaatccacccaagagaccgggtacccactgagtttgctgttaaactcggtgggtgcatttgttttatcacctcccgaatcggccttttttatcctgcaatttatgtataaatcatttatgatctatatatttattgaaaacgttttatatataaatctaaaacaatctatatataaattgaaaatggtttatatataaatcgtttcaagatcttccgaaaagcggatttcgacttgcaaaagtccgttttcttgtctttt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaagacaagaaaacggacttttgcaagtcgaaatccgcttttcggaagatcttgaaacgatttatatataaaccattttcaatttatatatagattgttttagatttatatataaaacgttttcaataaatatatagatcataaatgatttatacataaattgcaggataaaaaaggccgattcgggaggtgataaaacaaatgcacccaccgagtttaacagcaaactcagtgggtacccggtctcttgggtggattaccgaaggggtattccacccttatacatcataagtctatacgctctttttctctaacgcagtgagtggatgtgaataaaagggagcgactgtagcagtcgtatcggcagatggttggaggtcataatatcggtgtgcata Mask Tandem Repeat Region ================================================ tatgcacaccgatattatgacctccaaccatctgccgatacgactgctacagtcgctcccttttattcacatccactcactgcgttagagaaaaagagcgtatagacttatgatgtataagggtggaataccccttcggtaatccacccaagagaccgggtacccactgagtttgctgttaaactcggtgggtgcatttgttttatcacctcccgaatcggccttttttatcctgcaatttatgtataaatcatttatgatctatatatttatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngtttcaagatcttccgaaaagcggatttcgacttgcaaaagtccgttttcttgtctttt Find is-nt database================================================ Query_seq: PG0994:PG0995|PG0994:PG0995:hypothetical protein:hypothetical protein:-><-:1055160..1055558 399 tatgcacaccgatattatgacctccaaccatctgccgatacgactgctacagtcgctcccttttattcacatccactcactgcgttagagaaaaagagcgtatagacttatgatgtataagggtggaataccccttcggtaatccacccaagagaccgggtacccactgagtttgctgttaaactcggtgggtgcatttgttttatcacctcccgaatcggccttttttatcctgcaatttatgtataaatcatttatgatctatatatttattgaaaacgttttatatataaatctaaaacaatctatatataaattgaaaatggtttatatataaatcgtttcaagatcttccgaaaagcggatttcgacttgcaaaagtccgttttcttgtctttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0994:PG0995|PG0994:PG0995:hypothetical protein:hypothetical protein:-><-:1055160..1055558 399 tatgcacaccgatattatgacctccaaccatctgccgatacgactgctacagtcgctcccttttattcacatccactcactgcgttagagaaaaagagcgtatagacttatgatgtataagggtggaataccccttcggtaatccacccaagagaccgggtacccactgagtttgctgttaaactcggtgggtgcatttgttttatcacctcccgaatcggccttttttatcctgcaatttatgtataaatcatttatgatctatatatttattgaaaacgttttatatataaatctaaaacaatctatatataaattgaaaatggtttatatataaatcgtttcaagatcttccgaaaagcggatttcgacttgcaaaagtccgttttcttgtctttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0994:PG0995|PG0994:PG0995:hypothetical protein:hypothetical protein:-><-:1055160..1055558 399 tatgcacaccgatattatgacctccaaccatctgccgatacgactgctacagtcgctcccttttattcacatccactcactgcgttagagaaaaagagcgtatagacttatgatgtataagggtggaataccccttcggtaatccacccaagagaccgggtacccactgagtttgctgttaaactcggtgggtgcatttgttttatcacctcccgaatcggccttttttatcctgcaatttatgtataaatcatttatgatctatatatttattgaaaacgttttatatataaatctaaaacaatctatatataaattgaaaatggtttatatataaatcgtttcaagatcttccgaaaagcggatttcgacttgcaaaagtccgttttcttgtctttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatgcacaccgatattatgacctccaaccatctgccgatacgactgctacagtcgctcccttttattcacatccactcactgcgttagagaaaaagagcgtatagacttatgatgtataagggtggaataccccttcggtaatccacccaagagaccgggtacccactgagtttgctgttaaactcggtgggtgcatttgttttatcacctcccgaatcggccttttttatcctgcaatttatgtataaatcatttatgatctatatatttattgaaaacgttttatatataaatctaaaacaatctatatataaattgaaaatggtttatatataaatcgtttcaagatcttccgaaaagcggatttcgacttgcaaaagtccgttttcttgtctttt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 142 End: 246 ............................................................................................................................................. M H P R D R V P T E F A V K L G G C I C F I T S R I G L F Y P A I Y V ......................................................................................................................................................... Protein_Len: 56 Strand: + Start: 167 End: 334 ...................................................................................................................................................................... M S L L L N S V G A F V L S P P E S A F F I L Q F M Y K S F M I Y I F I E N V L Y I N L K Q S I Y K L K M V Y I ................................................................. Protein_Len: 36 Strand: - Start: 111 End: 218 .............................................................................................................. S T Y P H F V G E T I W G L S R T G V S N A T L S P P H M Q K I V E R M ..................................................................................................................................................................................... Protein_Len: 58 Strand: - Start: 88 End: 261 ....................................................................................... L F L A Y L S I I Y L P P I G R R Y D V W S V P Y G S L K S N F E T P A N T K D G G S D A K K I R C N I Y L D N I M .......................................................................................................................................... tatgcacaccgatattatgacctccaaccatctgccgatacgactgctacagtcgctcccttttattcacatccactcactgcgttagagaaaaagagcgtatagacttatgatgtataagggtggaataccccttcggtaatccacccaagagaccgggtacccactgagtttgctgttaaactcggtgggtgcatttgttttatcacctcccgaatcggccttttttatcctgcaatttatgtataaatcatttatgatctatatatttattgaaaacgttttatatataaatctaaaacaatctatatataaattgaaaatggtttatatataaatcgtttcaagatcttccgaaaagcggatttcgacttgcaaaagtccgttttcttgtctttt 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================================================ tatgcacaccgatattatgacctccaaccatctgccgatacgactgctacagtcgctcccttttattcacatccactcactgcgttagagaaaaagagcgtatagacttatgatgtataagggtggaataccccttcggtaatccacccaagagaccgggtacccactgagtttgctgttaaactcggtgggtgcatttgttttatcacctcccgaatcggccttttttatcctgcaatttatgtataaatcatttatgatctatatatttattgaaaacgttttatatataaatctaaaacaatctatatataaattgaaaatggtttatatataaatcgtttcaagatcttccgaaaagcggatttcgacttgcaaaagtccgttttcttgtctttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 95 HP_score: -13.2 Tail_Score: -3.37975 Start: 121 End: 149 Full_Region: ggtacccggtctctt gggtggattacc gaagg ggtattccaccc ttatacatcataagt ........................................................................................................................gggtggattaccgaaggggtattccaccc.......................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -12.1 Tail_Score: -4.77775 Start: 159 End: 196 Full_Region: CCACCCAAGAGACCG GGTACCCACTGAGTTTG CTGT TAAACTCGGTGGGTGCA TTTGTTTTATCACCT ..............................................................................................................................................................GGTACCCACTGAGTTTGCTGTTAAACTCGGTGGGTGCA........................................................................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -15.6 Tail_Score: -3.45581 Start: 160 End: 195 Full_Region: CACCCAAGAGACCGG GTACCCACTGAGTTTG CTGT TAAACTCGGTGGGTGC ATTTGTTTTATCACC ...............................................................................................................................................................GTACCCACTGAGTTTGCTGTTAAACTCGGTGGGTGC............................................................................................................................................................................................................ TransTerm Strand: - Conf: 45 HP_score: -3.5 Tail_Score: -3.07198 Start: 296 End: 347 Full_Region: gcttttcggaagatc ttgaaacgatttatatataaa ccattttcaa tttatatatagattgttttag atttatatataaaac .......................................................................................................................................................................................................................................................................................................ttgaaacgatttatatataaaccattttcaatttatatatagattgttttag.................................................... Find igs database================================================ Query_seq: PG0994:PG0995|PG0994:PG0995:hypothetical protein:hypothetical protein:-><-:1055160..1055558 399 tatgcacaccgatattatgacctccaaccatctgccgatacgactgctacagtcgctcccttttattcacatccactcactgcgttagagaaaaagagcgtatagacttatgatgtataagggtggaataccccttcggtaatccacccaagagaccgggtacccactgagtttgctgttaaactcggtgggtgcatttgttttatcacctcccgaatcggccttttttatcctgcaatttatgtataaatcatttatgatctatatatttattgaaaacgttttatatataaatctaaaacaatctatatataaattgaaaatggtttatatataaatcgtttcaagatcttccgaaaagcggatttcgacttgcaaaagtccgttttcttgtctttt Intra-Species Hit: Count: 1 Min: 1 Max: 399 Len: 399 Subject: NC_002950_PG0994_PG0995|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[1055160,1055558]|399 HSP 1 e-value: 1.0E-141 bit: 502.0 Len: 253 Query Start:1 Query End:253 Subject Strand: POSITIVE Subject Start: 1 Subject End: 253 tatgcacaccgatattatgacctccaaccatctgccgatacgactgctacagtcgctcccttttattcacatccactcactgcgttagagaaaaagagcgtatagacttatgatgtataagggtggaataccccttcggtaatccacccaagagaccgggtacccactgagtttgctgttaaactcggtgggtgcatttgttttatcacctcccgaatcggccttttttatcctgcaatttatgtataaatca.................................................................................................................................................. tatgcacaccgatattatgacctccaaccatctgccgatacgactgctacagtcgctcccttttattcacatccactcactgcgttagagaaaaagagcgtatagacttatgatgtataagggtggaataccccttcggtaatccacccaagagaccgggtacccactgagtttgctgttaaactcggtgggtgcatttgttttatcacctcccgaatcggccttttttatcctgcaatttatgtataaatca.................................................................................................................................................. HSP 2 e-value: 8.0E-26 bit: 119.0 Len: 60 Query Start:340 Query End:399 Subject Strand: POSITIVE Subject Start: 340 Subject End: 399 ...................................................................................................................................................................................................................................................................................................................................................cgtttcaagatcttccgaaaagcggatttcgacttgcaaaagtccgttttcttgtctttt ...................................................................................................................................................................................................................................................................................................................................................cgtttcaagatcttccgaaaagcggatttcgacttgcaaaagtccgttttcttgtctttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUGCACACCGAUAUUAUGACCUCCAACCAUCUGCCGAUACGACUGCUACAGUCGCUCCCUUUUAUUCACAUCCACUCACUGCGUUAGAGAAAAAGAGCGUAUAGACUUAUGAUGUAUAAGGGUGGAAUACCCCUUCGGUAAUCCACCCAAGAGACCGGGUACCCACUGAGUUUGCUGUUAAACUCGGUGGGUGCAUUUGUUUUAUCACCUCCCGAAUCGGCCUUUUUUAUCCUGCAAUUUAUGUAUAAAUCAUUUAUGAUCUAUAUAUUUAUUGAAAACGUUUUAUAUAUAAAUCUAAAACAAUCUAUAUAUAAAUUGAAAAUGGUUUAUAUAUAAAUCGUUUCAAGAUCUUCCGAAAAGCGGAUUUCGACUUGCAAAAGUCCGUUUUCUUGUCUUUU ..((((....((((...((.....)).......((((((.((((((...))))))(((..........(((((...((..((((((..........))))))..)).....)))))....(((((((.((((.....)))).)))))))..)))..(((((((((((((((((((....))))))))))))))))...((......))....))).))))))......)))).)))).((((((((((((((((((.((((.(((((((..((((.......((((....)))).......))))..))))))).)))).))))))))))))))))))......(((((...((((.....))))....(((((....))))).....)))))...... (-108.84) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAGACAAGAAAACGGACUUUUGCAAGUCGAAAUCCGCUUUUCGGAAGAUCUUGAAACGAUUUAUAUAUAAACCAUUUUCAAUUUAUAUAUAGAUUGUUUUAGAUUUAUAUAUAAAACGUUUUCAAUAAAUAUAUAGAUCAUAAAUGAUUUAUACAUAAAUUGCAGGAUAAAAAAGGCCGAUUCGGGAGGUGAUAAAACAAAUGCACCCACCGAGUUUAACAGCAAACUCAGUGGGUACCCGGUCUCUUGGGUGGAUUACCGAAGGGGUAUUCCACCCUUAUACAUCAUAAGUCUAUACGCUCUUUUUCUCUAACGCAGUGAGUGGAUGUGAAUAAAAGGGAGCGACUGUAGCAGUCGUAUCGGCAGAUGGUUGGAGGUCAUAAUAUCGGUGUGCAUA ......................((((..((((..((((.....)))).((((((..(((.(((............(((((((((((((.(((((((..(((..(((((((((((................)))))))))))..)))..))))))).)))))))).))))).......(((((..((((..((......))......((((((.((((((......)))))).)))))).)))).(((((((((((((.((((.....)))).))))))).......((((..((((((.(((((.((......)).).)))).))))))))))....))))))(((((((...))))))).))))).))).))).))))))......))))..)))).. (-119.29) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 478 280 232 117 68 NC_002950:PG1574|5end_hypothetical_protein_1652613..1652843_NEGATIVE 459 269 221 151 103 NC_002950:PG1223|5end_hypothetical_protein_1299461..1299691_POSITIVE 455 269 223 111 64 NC_002950:PG0371|5end_hypothetical_protein_404043..404273_POSITIVE 394 195 156 63 24 NC_002950:PG0325|5end_hypothetical_protein_359714..359944_NEGATIVE 380 158 111 229 179 NC_002950:PG1522|5end_mandelate_racemase/muconate_lactonizing_enzyme_family_protein_1600170..1600400_NEGATIVE 376 180 133 75 13 NC_002950:PG1270|5end_hypothetical_protein_1350207..1350437_NEGATIVE 371 228 185 168 125 NC_002950:PG1695|5end_hypothetical_protein_1779440..1779670_POSITIVE 356 233 191 74 28 NC_002950:PG1214|5end_hypothetical_protein_1293032..1293262_POSITIVE 354 180 131 80 18 NC_002950:PG1190|5end_glycerate_dehydrogenase_1272112..1272342_POSITIVE 346 47 8 207 169 NC_002950:PG1233|5end_hypothetical_protein_1309885..1310115_POSITIVE 343 170 122 57 11 NC_002950:PG1572|5end_hypothetical_protein_1651252..1651482_NEGATIVE 338 159 111 220 169 NC_002950:PG0703|5end_cobalamin_(5'-phosphate)_synthase,_putative_758144..758374_POSITIVE 338 177 131 204 158 NC_002950:PG0312|5end_hypothetical_protein_347048..347278_NEGATIVE 333 187 148 69 13 NC_002950:PG0090|5end_Dps_family_protein_105524..105754_POSITIVE 330 194 155 63 11 NC_002950:PG0908|5end_G/U_mismatch-specific_DNA_glycosylase,_putative_971721..971951_NEGATIVE 326 50 9 160 122 NC_002950:PG1042|5end_glycogen_synthase,_putative_1110638..1110868_NEGATIVE 324 62 22 192 148 NC_002950:PG1594|5end_ComEC/Rec2-related_protein_1673587..1673817_NEGATIVE 323 63 33 59 32 NC_002950:PG1109|5end_mobilization_protein_1182792..1183022_NEGATIVE 322 178 134 227 188 NC_002950:PG1523|5end_naphthoate_synthase_1600988..1601218_NEGATIVE 320 224 182 195 150 NC_002950:PG1651|5end_TPR_domain_protein_1730326..1730556_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 413 330 283 55 8 NC_002950:PG0773|3end_hypothetical_protein_825348..825498_POSITIVE 407 296 257 77 38 NC_002950:PG1357|3end_hypothetical_protein_1436327..1436477_NEGATIVE 397 177 133 79 31 NC_002950:PG0387|3end_elongation_factor_Tu_421910..422060_POSITIVE 376 180 133 68 6 NC_002950:PG1271|3end_acetylornithine_aminotransferase,_putative_1350214..1350364_NEGATIVE 371 195 151 51 6 NC_002950:PG1274|3end_elongation_factor_P_1352489..1352639_POSITIVE 365 160 113 70 28 NC_002950:PG1874|3end_hypothetical_protein_1969253..1969403_NEGATIVE 361 194 151 50 6 NC_002950:PG0568|3end_elongation_factor_P_623999..624149_NEGATIVE 358 195 160 138 102 NC_002950:PG0371|3end_hypothetical_protein_404224..404374_POSITIVE 356 233 191 125 79 NC_002950:PG1213|3end_ribonuclease_H_1293163..1293313_POSITIVE 336 195 157 38 6 NC_002950:PG0326|3end_hypothetical_protein_359739..359889_NEGATIVE 333 100 51 51 1 NC_002950:PG0146|3end_hypothetical_protein_168408..168558_NEGATIVE 332 166 128 51 2 NC_002950:PG1038|3end_ATP-dependent_DNA_helicase_UvrD/PcrA/Rep_Family_1105121..1105271_POSITIVE 328 170 121 122 72 NC_002950:PG1807|3end_v-type_ATPase,_subunit_K_1902625..1902775_POSITIVE 326 50 9 123 85 NC_002950:PG1043|3end_ferrous_iron_transport_protein_B_1110675..1110825_NEGATIVE 320 360 316 46 2 NC_002950:PG1167|3end_hypothetical_protein_1248644..1248794_POSITIVE 318 56 21 101 71 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE 318 63 29 150 114 NC_002950:PG0350|3end_internalin-related_protein_385356..385506_NEGATIVE 316 227 190 63 24 NC_002950:PG0481|3end_2-amino-3-ketobutyrate_coenzyme_A_ligase_521432..521582_NEGATIVE 313 194 151 65 26 NC_002950:PG1608|3end_methylmalonyl-CoA_decarboxylase,_beta_subunit_1688685..1688835_NEGATIVE 313 170 127 75 26 NC_002950:PG0071|3end_UDP-3-O-acyl-GlcNAc_deacetylase/beta-hydroxyacyl-[acyl_carrier_protein]_dehydratase_FabZ_84731..84881_NEGATIVE