Origin IGS: tccgtttctcccgtagtaatccaataacatcaacccaataaaacaggatagtttttctcgaactaaaagtcgcaaaaacaacgaatagcaattcgctgtacgaatgtaaactttgactaactttgcaaaagcattttttcaaaacataatcaacaagaaaattagaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttctaattttcttgttgattatgttttgaaaaaatgcttttgcaaagttagtcaaagtttacattcgtacagcgaattgctattcgttgtttttgcgacttttagttcgagaaaaactatcctgttttattgggttgatgttattggattactacgggagaaacgga Mask Tandem Repeat Region ================================================ tccgtttctcccgtagtaatccaataacatcaacccaataaaacaggatagtttttctcgaactaaaagtcgcaaaaacaacgaatagcaattcgctgtacgaatgtaaactttgactaactttgcaaaagcattttttcaaaacataatcaacaagaaaattagaa Find is-nt database================================================ Query_seq: PG0949:PG0950|PG0949:PG0950:hypothetical protein:glycine cleavage system protein H:->->:1009834..1010000 167 tccgtttctcccgtagtaatccaataacatcaacccaataaaacaggatagtttttctcgaactaaaagtcgcaaaaacaacgaatagcaattcgctgtacgaatgtaaactttgactaactttgcaaaagcattttttcaaaacataatcaacaagaaaattagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0949:PG0950|PG0949:PG0950:hypothetical protein:glycine cleavage system protein H:->->:1009834..1010000 167 tccgtttctcccgtagtaatccaataacatcaacccaataaaacaggatagtttttctcgaactaaaagtcgcaaaaacaacgaatagcaattcgctgtacgaatgtaaactttgactaactttgcaaaagcattttttcaaaacataatcaacaagaaaattagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0949:PG0950|PG0949:PG0950:hypothetical protein:glycine cleavage system protein H:->->:1009834..1010000 167 tccgtttctcccgtagtaatccaataacatcaacccaataaaacaggatagtttttctcgaactaaaagtcgcaaaaacaacgaatagcaattcgctgtacgaatgtaaactttgactaactttgcaaaagcattttttcaaaacataatcaacaagaaaattagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tccgtttctcccgtagtaatccaataacatcaacccaataaaacaggatagtttttctcgaactaaaagtcgcaaaaacaacgaatagcaattcgctgtacgaatgtaaactttgactaactttgcaaaagcattttttcaaaacataatcaacaagaaaattagaa Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: - Start: 2 End: 142 . R K E R L L G I V D V W Y F L I T K R S S F T A F V V F L L E S Y S H L S Q S V K C F C K K M ......................... Protein_Len: 35 Strand: - Start: 1 End: 105 G N R G Y Y D L L M L G I F C S L K E R V L L R L F L S Y C N A T R M .............................................................. tccgtttctcccgtagtaatccaataacatcaacccaataaaacaggatagtttttctcgaactaaaagtcgcaaaaacaacgaatagcaattcgctgtacgaatgtaaactttgactaactttgcaaaagcattttttcaaaacataatcaacaagaaaattagaa 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================================================ tccgtttctcccgtagtaatccaataacatcaacccaataaaacaggatagtttttctcgaactaaaagtcgcaaaaacaacgaatagcaattcgctgtacgaatgtaaactttgactaactttgcaaaagcattttttcaaaacataatcaacaagaaaattagaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 83 HP_score: -7.2 Tail_Score: -4.66264 Start: 79 End: 98 Full_Region: aagtttacattcgta cagcgaat tgct attcgttg tttttgcgactttta ..............................................................................cagcgaattgctattcgttg..................................................................... Find igs database================================================ Query_seq: PG0949:PG0950|PG0949:PG0950:hypothetical protein:glycine cleavage system protein H:->->:1009834..1010000 167 tccgtttctcccgtagtaatccaataacatcaacccaataaaacaggatagtttttctcgaactaaaagtcgcaaaaacaacgaatagcaattcgctgtacgaatgtaaactttgactaactttgcaaaagcattttttcaaaacataatcaacaagaaaattagaa Intra-Species Hit: Count: 1 Min: 1 Max: 167 Len: 167 Subject: NC_002950_PG0949_PG0950|hypothetical protein:glycine cleavage system protein H|POSITIVE:POSITIVE|[1009834,1010000]|167 HSP 1 e-value: 4.0E-90 bit: 331.0 Len: 167 Query Start:1 Query End:167 Subject Strand: POSITIVE Subject Start: 1 Subject End: 167 tccgtttctcccgtagtaatccaataacatcaacccaataaaacaggatagtttttctcgaactaaaagtcgcaaaaacaacgaatagcaattcgctgtacgaatgtaaactttgactaactttgcaaaagcattttttcaaaacataatcaacaagaaaattagaa tccgtttctcccgtagtaatccaataacatcaacccaataaaacaggatagtttttctcgaactaaaagtcgcaaaaacaacgaatagcaattcgctgtacgaatgtaaactttgactaactttgcaaaagcattttttcaaaacataatcaacaagaaaattagaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCGUUUCUCCCGUAGUAAUCCAAUAACAUCAACCCAAUAAAACAGGAUAGUUUUUCUCGAACUAAAAGUCGCAAAAACAACGAAUAGCAAUUCGCUGUACGAAUGUAAACUUUGACUAACUUUGCAAAAGCAUUUUUUCAAAACAUAAUCAACAAGAAAAUUAGAA ....(((((.........((((.......................)))).((((((..(((........))).))))))..((.(((((.....))))).)).((((....(((((..((...(((....))).))..)))))))))........)))))....... (-18.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUAAUUUUCUUGUUGAUUAUGUUUUGAAAAAAUGCUUUUGCAAAGUUAGUCAAAGUUUACAUUCGUACAGCGAAUUGCUAUUCGUUGUUUUUGCGACUUUUAGUUCGAGAAAAACUAUCCUGUUUUAUUGGGUUGAUGUUAUUGGAUUACUACGGGAGAAACGGA .(((..((((((((((((((...((((((..((.(((....)))...))..)))))).......(((((((((((((....)))))))))....))))...((((..(((..(((((......))))).)))..))))........)))))..)))))))))..))) (-35.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 274 109 81 155 120 NC_002950:PG0695|5end_immunoreactive_43_kDa_antigen_PG32_752067..752297_NEGATIVE 257 115 71 176 130 NC_002950:PG0516|5end_hypothetical_protein_559184..559414_NEGATIVE 251 80 35 90 42 NC_002950:PG0499|5end_hypothetical_protein_538709..538939_POSITIVE 248 133 95 96 48 NC_002950:PG1950|5end_hypothetical_protein_2039600..2039830_POSITIVE 244 50 3 59 1 NC_002950:PG0003|5end_hypothetical_protein_2938..3168_NEGATIVE 242 80 35 90 42 NC_002950:PG1363|5end_hypothetical_protein_1443804..1444034_POSITIVE 237 37 1 173 138 NC_002950:PG2035|5end_tRNA_(guanine-N(1)-)-methyltransferase_2135852..2136082_POSITIVE 231 140 91 207 160 NC_002950:PG1532|5end_hypothetical_protein_1611716..1611946_NEGATIVE 230 100 69 199 156 NC_002950:PG0827|5end_MATE_efflux_family_protein_884166..884396_POSITIVE 228 72 35 212 169 NC_002950:PG2001|5end_signal_peptidase_I_2090855..2091085_NEGATIVE 228 127 81 51 16 NC_002950:PG1863|5end_hypothetical_protein_1960516..1960746_NEGATIVE 228 127 81 204 169 NC_002950:PG1862|5end_hypothetical_protein_1960363..1960593_NEGATIVE 228 80 35 90 42 NC_002950:PG1251|5end_hypothetical_protein_1327779..1328009_POSITIVE 225 108 82 105 82 NC_002950:PG1098|5end_hypothetical_protein_1167009..1167239_NEGATIVE 224 126 81 219 172 NC_002950:PG1784|5end_hypothetical_protein_1872566..1872796_POSITIVE 219 126 81 69 29 NC_002950:PG0604|5end_4-hydroxy-3-methylbut-2-enyl_diphosphate_reductase_660262..660492_POSITIVE 219 102 70 71 38 NC_002950:PG0571|5end_aspartate-semialdehyde_dehydrogenase_626399..626629_POSITIVE 218 39 3 192 144 NC_002950:PG1311|5end_hypothetical_protein_1389709..1389939_POSITIVE 216 115 71 178 131 NC_002950:PG1709|5end_ISPg5,_transposase_Orf1_1794914..1795144_POSITIVE 216 40 4 44 2 NC_002950:PG1534|5end_hypothetical_protein_1614147..1614377_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 257 115 71 145 99 NC_002950:PG0517|3end_hypothetical_protein_559215..559365_NEGATIVE 246 22 2 150 126 NC_002950:PG0045|3end_heat_shock_protein_90_56193..56343_POSITIVE 230 100 69 102 59 NC_002950:PG1447|3end_transcriptional_regulator,_AraC_family_1531363..1531513_NEGATIVE 230 100 69 102 59 NC_002950:PG0826|3end_transcriptional_regulator,_AraC_family_884149..884299_POSITIVE 228 127 81 58 23 NC_002950:PG1864|3end_leucine-rich_protein_1960509..1960659_NEGATIVE 225 97 63 87 58 NC_002950:PG1974|3end_hypothetical_protein_2061964..2062114_NEGATIVE 220 36 1 145 99 NC_002950:PG0354|3end_hypothetical_protein_389131..389281_NEGATIVE 219 126 81 72 32 NC_002950:PG0603|3end_cytidylate_kinase_660345..660495_POSITIVE 216 115 79 54 26 NC_002950:PG1429|3end_hypothetical_protein_1515003..1515153_NEGATIVE 210 90 43 144 100 NC_002950:PG0783|3end_hydrolase,_putative_834878..835028_NEGATIVE 203 140 94 117 72 NC_002950:PG1903|3end_hypothetical_protein_2002230..2002380_NEGATIVE 203 106 82 76 50 NC_002950:PG0333|3end_hypothetical_protein_368811..368961_POSITIVE 202 109 66 82 33 NC_002950:PG1340|3end_L-lactate_permease_1420298..1420448_NEGATIVE 199 108 69 139 99 NC_002950:PG2103|3end_hypothetical_protein_2213226..2213376_NEGATIVE 199 101 69 128 99 NC_002950:PG0032|3end_beta-mannosidase,_putative_37627..37777_NEGATIVE 197 65 35 71 46 NC_002950:PG1733|3end_hypothetical_protein_1821186..1821336_NEGATIVE 197 108 83 78 58 NC_002950:PG1440|3end_hypothetical_protein_1526650..1526800_NEGATIVE 195 95 71 75 51 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 195 136 92 140 95 NC_002950:PG0150|3end_conserved_hypothetical_protein_TIGR01125_172240..172390_NEGATIVE 195 50 8 126 86 NC_002950:PG0056|3end_hypothetical_protein_69782..69932_POSITIVE