Origin IGS: aaacagtttttacataaccattttatgcgggcaaagttatactattctttattttcctttttgggggaattttccacaacaggataagatcatatttttacgctttgtatcctgttttttgaaaaagtaaaccccgagagtttttatttgactctcggggttcgctttcgtttattatctgtatcggtgaagtttt .........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 aaaacttcaccgatacagataataaacgaaagcgaaccccgagagtcaaataaaaactctcggggtttactttttcaaaaaacaggatacaaagcgtaaaaatatgatcttatcctgttgtggaaaattcccccaaaaaggaaaataaagaatagtataactttgcccgcataaaatggttatgtaaaaactgttt Mask Tandem Repeat Region ================================================ aaacagtttttacataaccattttatgcgggcaaagttatactattctttattttcctttttgggggaattttccacaacaggataagatcatatttttacgctttgtatcctgttttttgaaaaagtaaaccccgagagtttttatttgactctcggggttcgctttcgtttattatctgtatcggtgaagtttt Find is-nt database================================================ Query_seq: PG1304:PG1305|PG1304:PG1305:hypothetical protein:glycine dehydrogenase:<-<-:1383565..1383760 196 aaacagtttttacataaccattttatgcgggcaaagttatactattctttattttcctttttgggggaattttccacaacaggataagatcatatttttacgctttgtatcctgttttttgaaaaagtaaaccccgagagtttttatttgactctcggggttcgctttcgtttattatctgtatcggtgaagtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1304:PG1305|PG1304:PG1305:hypothetical protein:glycine dehydrogenase:<-<-:1383565..1383760 196 aaacagtttttacataaccattttatgcgggcaaagttatactattctttattttcctttttgggggaattttccacaacaggataagatcatatttttacgctttgtatcctgttttttgaaaaagtaaaccccgagagtttttatttgactctcggggttcgctttcgtttattatctgtatcggtgaagtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1304:PG1305|PG1304:PG1305:hypothetical protein:glycine dehydrogenase:<-<-:1383565..1383760 196 aaacagtttttacataaccattttatgcgggcaaagttatactattctttattttcctttttgggggaattttccacaacaggataagatcatatttttacgctttgtatcctgttttttgaaaaagtaaaccccgagagtttttatttgactctcggggttcgctttcgtttattatctgtatcggtgaagtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaacagtttttacataaccattttatgcgggcaaagttatactattctttattttcctttttgggggaattttccacaacaggataagatcatatttttacgctttgtatcctgttttttgaaaaagtaaaccccgagagtttttatttgactctcggggttcgctttcgtttattatctgtatcggtgaagtttt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 14 End: 127 ............. M T I L C G Q S Y T I L Y F P F W G N F P Q Q D K I I F L R F V S C F L K K ..................................................................... Protein_Len: 34 Strand: + Start: 94 End: 195 ............................................................................................. M F T L C I L F F E K V N P E S F Y L T L G V R F R L L S V S V K F . Protein_Len: 32 Strand: - Start: 52 End: 147 ................................................... K G K Q P F K G C C S L I M N K R K T D Q K K F F Y V G L T K M ................................................. aaacagtttttacataaccattttatgcgggcaaagttatactattctttattttcctttttgggggaattttccacaacaggataagatcatatttttacgctttgtatcctgttttttgaaaaagtaaaccccgagagtttttatttgactctcggggttcgctttcgtttattatctgtatcggtgaagtttt 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================================================ aaacagtttttacataaccattttatgcgggcaaagttatactattctttattttcctttttgggggaattttccacaacaggataagatcatatttttacgctttgtatcctgttttttgaaaaagtaaaccccgagagtttttatttgactctcggggttcgctttcgtttattatctgtatcggtgaagtttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 81 HP_score: -7.5 Tail_Score: -4.4458 Start: 122 End: 170 Full_Region: GTATCCTGTTTTTTG AAAAAGTAAACCCCGAGAGTT TTTATTT GACTCTCGGGGTTCGCTTTCG TTTATTATCTGTATC .........................................................................................................................AAAAAGTAAACCCCGAGAGTTTTTATTTGACTCTCGGGGTTCGCTTTCG.......................... TransTerm Strand: + Conf: 100 HP_score: -11.8 Tail_Score: -4.25325 Start: 127 End: 165 Full_Region: CTGTTTTTTGAAAAA GTAAACCCCGAGAGTT TTTATTT GACTCTCGGGGTTCGC TTTCGTTTATTATCT ..............................................................................................................................GTAAACCCCGAGAGTTTTTATTTGACTCTCGGGGTTCGC............................... TransTerm Strand: - Conf: 100 HP_score: -11.1 Tail_Score: -4.56597 Start: 127 End: 165 Full_Region: agataataaacgaaa gcgaaccccgagagt caaataaaa actctcggggtttac tttttcaaaaaacag ..............................................................................................................................gcgaaccccgagagtcaaataaaaactctcggggtttac............................... TransTerm Strand: + Conf: 93 HP_score: -12.5 Tail_Score: -3.36188 Start: 132 End: 160 Full_Region: TTTTGAAAAAGTAAA CCCCGAGAGTT TTTATTT GACTCTCGGGG TTCGCTTTCGTTTAT ...................................................................................................................................CCCCGAGAGTTTTTATTTGACTCTCGGGG.................................... TransTerm Strand: - Conf: 100 HP_score: -11.8 Tail_Score: -4.32046 Start: 132 End: 160 Full_Region: ataaacgaaagcgaa ccccgagagt caaataaaa actctcgggg tttactttttcaaaa ...................................................................................................................................ccccgagagtcaaataaaaactctcgggg.................................... Find igs database================================================ Query_seq: PG1304:PG1305|PG1304:PG1305:hypothetical protein:glycine dehydrogenase:<-<-:1383565..1383760 196 aaacagtttttacataaccattttatgcgggcaaagttatactattctttattttcctttttgggggaattttccacaacaggataagatcatatttttacgctttgtatcctgttttttgaaaaagtaaaccccgagagtttttatttgactctcggggttcgctttcgtttattatctgtatcggtgaagtttt Intra-Species Hit: Count: 1 Min: 1 Max: 196 Len: 196 Subject: NC_002950_PG1304_PG1305|hypothetical protein:glycine dehydrogenase|NEGATIVE:NEGATIVE|[1383565,1383760]|196 HSP 1 e-value: 1.0E-107 bit: 389.0 Len: 196 Query Start:1 Query End:196 Subject Strand: POSITIVE Subject Start: 1 Subject End: 196 aaacagtttttacataaccattttatgcgggcaaagttatactattctttattttcctttttgggggaattttccacaacaggataagatcatatttttacgctttgtatcctgttttttgaaaaagtaaaccccgagagtttttatttgactctcggggttcgctttcgtttattatctgtatcggtgaagtttt aaacagtttttacataaccattttatgcgggcaaagttatactattctttattttcctttttgggggaattttccacaacaggataagatcatatttttacgctttgtatcctgttttttgaaaaagtaaaccccgagagtttttatttgactctcggggttcgctttcgtttattatctgtatcggtgaagtttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACAGUUUUUACAUAACCAUUUUAUGCGGGCAAAGUUAUACUAUUCUUUAUUUUCCUUUUUGGGGGAAUUUUCCACAACAGGAUAAGAUCAUAUUUUUACGCUUUGUAUCCUGUUUUUUGAAAAAGUAAACCCCGAGAGUUUUUAUUUGACUCUCGGGGUUCGCUUUCGUUUAUUAUCUGUAUCGGUGAAGUUUU ..................((((..((((((.(((((..............(((..(((....)))..))).......(((((((((.((...............)).))))))))))))))..((((..(((((((((((((.......)))))))))))))..))))..........)))))).))))....... (-50.66) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAACUUCACCGAUACAGAUAAUAAACGAAAGCGAACCCCGAGAGUCAAAUAAAAACUCUCGGGGUUUACUUUUUCAAAAAACAGGAUACAAAGCGUAAAAAUAUGAUCUUAUCCUGUUGUGGAAAAUUCCCCCAAAAAGGAAAAUAAAGAAUAGUAUAACUUUGCCCGCAUAAAAUGGUUAUGUAAAAACUGUUU .....(((((.................(((((..((((((((((((.........))))))))))))..)))))......(((((((((.....((((....))))....))))))))))))))...((((........))))......(((((((...((...(((..........)))...))....))))))) (-49.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 806 110 61 201 152 NC_002950:PG1304|5end_hypothetical_protein_1383474..1383704_NEGATIVE 324 167 127 158 108 NC_002950:PG0287|5end_hypothetical_protein_320457..320687_POSITIVE 318 187 155 150 121 NC_002950:PG0899|5end_cytochrome_d_ubiquinol_oxidase,_subunit_II_964660..964890_NEGATIVE 312 190 147 185 134 NC_002950:PG1214|5end_hypothetical_protein_1293032..1293262_POSITIVE 312 170 123 70 11 NC_002950:PG0572|5end_hypothetical_protein_627571..627801_NEGATIVE 310 180 134 96 45 NC_002950:PG0534|5end_hypothetical_protein_583242..583472_POSITIVE 304 190 141 227 169 NC_002950:PG1160|5end_L-threonine-O-3-phosphate_decarboxylase,_putative_1239988..1240218_NEGATIVE 303 180 134 152 101 NC_002950:PG1152|5end_hypothetical_protein_1234946..1235176_NEGATIVE 302 188 152 79 38 NC_002950:PG2081|5end_biotin_synthetase_2181661..2181891_NEGATIVE 298 174 131 216 164 NC_002950:PG1565|5end_3-deoxy-D-manno-octulosonic-acid_transferase,_putative_1645859..1646089_NEGATIVE 295 174 132 68 20 NC_002950:PG0431|5end_hypothetical_protein_468978..469208_POSITIVE 287 168 125 136 86 NC_002950:PG1522|5end_mandelate_racemase/muconate_lactonizing_enzyme_family_protein_1600170..1600400_NEGATIVE 282 170 133 158 123 NC_002950:PG1747|5end_ribose_5-phosphate_isomerase_B,_putative_1832815..1833045_NEGATIVE 277 170 123 229 194 NC_002950:PG1679|5end_hypothetical_protein_1763796..1764026_POSITIVE 276 162 132 162 142 NC_002950:PG0095|5end_DNA_mismatch_repair_protein_114763..114993_NEGATIVE 275 190 149 87 43 NC_002950:PG1963|5end_Sua5/YciO/YrdC/YwlC_family_protein_2052338..2052568_POSITIVE 275 66 21 68 26 NC_002950:PG1132|5end_valyl-tRNA_synthetase_1210912..1211142_POSITIVE 272 169 135 212 174 NC_002950:PG1212|5end_TPR_domain_protein_1291392..1291622_POSITIVE 272 189 150 166 110 NC_002950:PG0166|5end_peptidyl-tRNA_hydrolase_188370..188600_NEGATIVE 270 169 132 191 143 NC_002950:PG0121|5end_DNA-binding_protein_HU_144468..144698_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 353 168 125 78 34 NC_002950:PG1678|3end_hypothetical_protein_1763755..1763905_NEGATIVE 343 163 123 49 8 NC_002950:PG0343|3end_methionine_gamma-lyase_377181..377331_NEGATIVE 324 167 127 75 25 NC_002950:PG0286|3end_hypothetical_protein_320454..320604_POSITIVE 318 187 151 111 65 NC_002950:PG1214|3end_hypothetical_protein_1294350..1294500_POSITIVE 318 187 155 104 75 NC_002950:PG0900|3end_cytochrome_d_ubiquinol_oxidase,_subunit_I_964706..964856_NEGATIVE 303 180 134 122 71 NC_002950:PG1153|3end_hypothetical_protein_1234976..1235126_NEGATIVE 295 174 132 83 35 NC_002950:PG0430|3end_ferrodoxin_oxidoreductase_beta_subunit_469073..469223_POSITIVE 287 168 125 136 86 NC_002950:PG1523|3end_naphthoate_synthase_1600170..1600320_NEGATIVE 285 170 129 43 2 NC_002950:PG1677|3end_phosphoglycerate_kinase_1763678..1763828_POSITIVE 283 168 123 61 7 NC_002950:PG0571|3end_aspartate-semialdehyde_dehydrogenase_627492..627642_POSITIVE 282 170 133 71 36 NC_002950:PG1748|3end_transketolase_1832902..1833052_NEGATIVE 278 180 135 134 81 NC_002950:PG0309|3end_thiamine_biosynthesis_lipoprotein_ApbE_344010..344160_NEGATIVE 268 168 122 54 3 NC_002950:PG1274|3end_elongation_factor_P_1352489..1352639_POSITIVE 267 167 133 149 108 NC_002950:PG0073|3end_orotidine_5'-monophosphate_decarboxylase_87240..87390_NEGATIVE 265 189 147 149 100 NC_002950:PG0126|3end_type_I_phosphodiesterase/nucleotide_pyrophosphatase_family_protein_146783..146933_NEGATIVE 264 190 150 142 101 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 264 89 45 142 103 NC_002950:PG0242|3end_conserved_hypothetical_protein_TIGR00096_278259..278409_NEGATIVE 262 184 141 151 109 NC_002950:PG1697|3end_type_II_restriction_endonuclease,_putative_1785074..1785224_POSITIVE 259 179 132 135 83 NC_002950:PG2050|3end_hypothetical_protein_2149159..2149309_NEGATIVE 258 179 131 150 104 NC_002950:PG0371|3end_hypothetical_protein_404224..404374_POSITIVE