Origin IGS: ctcctacaatagaaataggattatctccactttgaacaattttttgtttaaatgaaaacgaattgtcatttgcaacaaagaaacttaaaaatgaaacaattcctccaacaatagcaactattgattccattgatttgtcaattattgcccaaatgattgttgctatcaaataaatagcattcaatatcagcattattagttttgatttcacaacttctgaat .........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 attcagaagttgtgaaatcaaaactaataatgctgatattgaatgctatttatttgatagcaacaatcatttgggcaataattgacaaatcaatggaatcaatagttgctattgttggaggaattgtttcatttttaagtttctttgttgcaaatgacaattcgttttcatttaaacaaaaaattgttcaaagtggagataatcctatttctattgtaggag Mask Tandem Repeat Region ================================================ ctcctacaatagaaataggattatctccactttgaacaattttttgtttaaatgaaaacgaattgtcatttgcaacaaagaaacttaaaaatgaaacaattcctccaacaatagcaactattgattccattgatttgtcaattattgcccaaatgattgttgctatcaaataaatagcattcaatatcagcattattagttttgatttcacaacttctgaat Find is-nt database================================================ Query_seq: PG1202:PG1203|PG1202:PG1203:hypothetical protein:transcriptional regulator, putative:<-<-:1283105..1283326 222 ctcctacaatagaaataggattatctccactttgaacaattttttgtttaaatgaaaacgaattgtcatttgcaacaaagaaacttaaaaatgaaacaattcctccaacaatagcaactattgattccattgatttgtcaattattgcccaaatgattgttgctatcaaataaatagcattcaatatcagcattattagttttgatttcacaacttctgaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1202:PG1203|PG1202:PG1203:hypothetical protein:transcriptional regulator, putative:<-<-:1283105..1283326 222 ctcctacaatagaaataggattatctccactttgaacaattttttgtttaaatgaaaacgaattgtcatttgcaacaaagaaacttaaaaatgaaacaattcctccaacaatagcaactattgattccattgatttgtcaattattgcccaaatgattgttgctatcaaataaatagcattcaatatcagcattattagttttgatttcacaacttctgaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1202:PG1203|PG1202:PG1203:hypothetical protein:transcriptional regulator, putative:<-<-:1283105..1283326 222 ctcctacaatagaaataggattatctccactttgaacaattttttgtttaaatgaaaacgaattgtcatttgcaacaaagaaacttaaaaatgaaacaattcctccaacaatagcaactattgattccattgatttgtcaattattgcccaaatgattgttgctatcaaataaatagcattcaatatcagcattattagttttgatttcacaacttctgaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctcctacaatagaaataggattatctccactttgaacaattttttgtttaaatgaaaacgaattgtcatttgcaacaaagaaacttaaaaatgaaacaattcctccaacaatagcaactattgattccattgatttgtcaattattgcccaaatgattgttgctatcaaataaatagcattcaatatcagcattattagttttgatttcacaacttctgaat Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 39 End: 170 ...................................... M F C L N E N E L S F A T K K L K N E T I P P T I A T I D S I D L S I I A Q M I V A I K .................................................... Protein_Len: 60 Strand: - Start: 2 End: 211 . Q V I K Q K F S F S N D N A V F F S L F S V I G G V I A V I S E M S K D I I A W I I T A I L Y I A N L I L M I L K S K M ........... ctcctacaatagaaataggattatctccactttgaacaattttttgtttaaatgaaaacgaattgtcatttgcaacaaagaaacttaaaaatgaaacaattcctccaacaatagcaactattgattccattgatttgtcaattattgcccaaatgattgttgctatcaaataaatagcattcaatatcagcattattagttttgatttcacaacttctgaat 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: 85 Start: 141 End: 170 ............................................................................................................................................TTTGATAGCAACAATCATTTGGGCAATAAT.................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctcctacaatagaaataggattatctccactttgaacaattttttgtttaaatgaaaacgaattgtcatttgcaacaaagaaacttaaaaatgaaacaattcctccaacaatagcaactattgattccattgatttgtcaattattgcccaaatgattgttgctatcaaataaatagcattcaatatcagcattattagttttgatttcacaacttctgaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -3.4 Tail_Score: -3.27022 Start: 139 End: 159 Full_Region: ATTCCATTGATTTGT CAATTATT GCCCA AATGATTG TTGCTATCAAATAAA ..........................................................................................................................................CAATTATTGCCCAAATGATTG............................................................... Find igs database================================================ Query_seq: PG1202:PG1203|PG1202:PG1203:hypothetical protein:transcriptional regulator, putative:<-<-:1283105..1283326 222 ctcctacaatagaaataggattatctccactttgaacaattttttgtttaaatgaaaacgaattgtcatttgcaacaaagaaacttaaaaatgaaacaattcctccaacaatagcaactattgattccattgatttgtcaattattgcccaaatgattgttgctatcaaataaatagcattcaatatcagcattattagttttgatttcacaacttctgaat Intra-Species Hit: Count: 1 Min: 1 Max: 222 Len: 222 Subject: NC_002950_PG1202_PG1203|hypothetical protein:transcriptional regulator, putative|NEGATIVE:NEGATIVE|[1283105,1283326]|222 HSP 1 e-value: 1.0E-123 bit: 440.0 Len: 222 Query Start:1 Query End:222 Subject Strand: POSITIVE Subject Start: 1 Subject End: 222 ctcctacaatagaaataggattatctccactttgaacaattttttgtttaaatgaaaacgaattgtcatttgcaacaaagaaacttaaaaatgaaacaattcctccaacaatagcaactattgattccattgatttgtcaattattgcccaaatgattgttgctatcaaataaatagcattcaatatcagcattattagttttgatttcacaacttctgaat ctcctacaatagaaataggattatctccactttgaacaattttttgtttaaatgaaaacgaattgtcatttgcaacaaagaaacttaaaaatgaaacaattcctccaacaatagcaactattgattccattgatttgtcaattattgcccaaatgattgttgctatcaaataaatagcattcaatatcagcattattagttttgatttcacaacttctgaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCCUACAAUAGAAAUAGGAUUAUCUCCACUUUGAACAAUUUUUUGUUUAAAUGAAAACGAAUUGUCAUUUGCAACAAAGAAACUUAAAAAUGAAACAAUUCCUCCAACAAUAGCAACUAUUGAUUCCAUUGAUUUGUCAAUUAUUGCCCAAAUGAUUGUUGCUAUCAAAUAAAUAGCAUUCAAUAUCAGCAUUAUUAGUUUUGAUUUCACAACUUCUGAAU ......((((.(((...(((.......((.(((((((((....))))))))))).....((((((((((((.................))))))..)))))).)))..((((((...)))))).))).))))......((((((((.....)))))))).((((((.......)))))).......((((.......((((.((....)).)))).)))).. (-36.83) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCAGAAGUUGUGAAAUCAAAACUAAUAAUGCUGAUAUUGAAUGCUAUUUAUUUGAUAGCAACAAUCAUUUGGGCAAUAAUUGACAAAUCAAUGGAAUCAAUAGUUGCUAUUGUUGGAGGAAUUGUUUCAUUUUUAAGUUUCUUUGUUGCAAAUGACAAUUCGUUUUCAUUUAAACAAAAAAUUGUUCAAAGUGGAGAUAAUCCUAUUUCUAUUGUAGGAG ..((((.((((.((....)).)))).....((((.(...(((.(((((((.....)))))))....)))..).))))....)))).....((((((((.(((((((....))))))).((((.((((((((((((..(((((.((((((..((((((.((....)).)))))).)))))))))))....))))).)))))))))))..))))))))...... (-46.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 785 140 91 231 182 NC_002950:PG1202|5end_hypothetical_protein_1283014..1283244_NEGATIVE 306 155 113 196 152 NC_002950:PG2179|5end_NADH-ubiquinone_oxidoreductase_2287806..2288036_NEGATIVE 283 39 9 207 172 NC_002950:PG1853|5end_DNA_polymerase_III,_beta_subunit_1953119..1953349_NEGATIVE 252 169 121 129 80 NC_002950:PG2116|5end_hypothetical_protein_2224635..2224865_POSITIVE 229 119 71 164 122 NC_002950:PG1311|5end_hypothetical_protein_1389709..1389939_POSITIVE 226 170 127 58 13 NC_002950:PG0593|5end_htrA_protein_650362..650592_POSITIVE 225 187 143 101 40 NC_002950:PG0723|5end_hypothetical_protein_774949..775179_POSITIVE 223 133 101 190 152 NC_002950:PG0618|5end_alkyl_hydroperoxide_reductase,_C_subunit_670372..670602_POSITIVE 216 159 113 66 23 NC_002950:PG0583|5end_cell_division_protein_FtsA_640425..640655_POSITIVE 208 54 21 196 157 NC_002950:PG1219|5end_hypothetical_protein_1296671..1296901_POSITIVE 207 149 103 70 32 NC_002950:PG1235|5end_epimerase/reductase,_putative_1311256..1311486_NEGATIVE 206 166 126 55 8 NC_002950:PG1729|5end_thiol_peroxidase_1818881..1819111_NEGATIVE 206 150 102 167 115 NC_002950:PG1589|5end_dihydropteroate_synthase_1667438..1667668_NEGATIVE 205 150 101 214 161 NC_002950:PG1564|5end_hypothetical_protein_1644536..1644766_NEGATIVE 200 211 186 217 196 NC_002950:PG2225|5end_hypothetical_protein_2339440..2339670_POSITIVE 200 190 147 43 3 NC_002950:PG0448|5end_hypothetical_protein_488089..488319_POSITIVE 199 167 121 132 79 NC_002950:PG1387|5end_hypothetical_protein_1470058..1470288_NEGATIVE 199 166 125 138 94 NC_002950:PG0578|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_634480..634710_POSITIVE 199 148 102 172 137 NC_002950:PG0248|5end_translation_initation_factor_SUI1,_putative_281842..282072_NEGATIVE 198 220 175 99 53 NC_002950:PG0243|5end_hypothetical_protein_279452..279682_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 244 216 173 107 67 NC_002950:PG0183|3end_lipoprotein,_putative_216123..216273_POSITIVE 205 150 101 129 76 NC_002950:PG1565|3end_3-deoxy-D-manno-octulosonic-acid_transferase,_putative_1644621..1644771_NEGATIVE 200 190 147 50 10 NC_002950:PG0447|3end_hypothetical_protein_488176..488326_POSITIVE 199 167 121 95 42 NC_002950:PG1388|3end_hypothetical_protein_1470095..1470245_NEGATIVE 199 166 125 114 70 NC_002950:PG0577|3end_phospho-N-acetylmuramoyl-pentapeptide-_transferase_634536..634686_POSITIVE 199 148 102 75 40 NC_002950:PG0249|3end_oxaloacetate_decarboxylase,_putative_281939..282089_NEGATIVE 194 164 128 87 44 NC_002950:PG0738|3end_cytidine/deoxycytidylate_deaminase_family_protein_786995..787145_POSITIVE 192 191 155 65 30 NC_002950:PG1404|3end_rhomboid_family_protein_1487071..1487221_NEGATIVE 192 160 113 76 41 NC_002950:PG0109|3end_hypothetical_protein_132634..132784_POSITIVE 191 192 159 63 36 NC_002950:PG1581|3end_hypothetical_protein_1659404..1659554_POSITIVE 191 206 173 68 35 NC_002950:PG0603|3end_cytidylate_kinase_660345..660495_POSITIVE 190 169 121 113 59 NC_002950:PG1685|3end_hypothetical_protein_1772216..1772366_NEGATIVE 189 163 126 57 19 NC_002950:PG1341|3end_hypothetical_protein_1422665..1422815_POSITIVE 189 205 162 47 11 NC_002950:PG0490|3end_hypothetical_protein_532248..532398_POSITIVE 188 190 143 105 57 NC_002950:PG0950|3end_glycine_cleavage_system_protein_H_1010321..1010471_POSITIVE 187 168 129 140 103 NC_002950:PG1943|3end_hypothetical_protein_2028974..2029124_NEGATIVE 187 145 114 147 124 NC_002950:PG0491|3end_hypothetical_protein_534402..534552_POSITIVE 186 220 177 111 73 NC_002950:PG1155|3end_ADP-heptose--LPS_heptosyltransferase,_putative_1236831..1236981_POSITIVE 186 127 97 149 124 NC_002950:PG0078|3end_hypothetical_protein_91566..91716_NEGATIVE 185 32 18 113 99 NC_002950:PG1963|3end_Sua5/YciO/YrdC/YwlC_family_protein_2052993..2053143_POSITIVE