Origin IGS: aaaacaatcagttgaaaggcttggcattttgaagccggtttgtatctttgtggcttaataaacacattcttaatagtgcataataaatagaaaacataataacaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttgttattatgttttctatttattatgcactattaagaatgtgtttattaagccacaaagatacaaaccggcttcaaaatgccaagcctttcaactgattgtttt Mask Tandem Repeat Region ================================================ aaaacaatcagttgaaaggcttggcattttgaagccggtttgtatctttgtggcttaataaacacattcttaatagtgcataataaatagaaaacataataacaaa Find is-nt database================================================ Query_seq: PG0451:PG0452|PG0451:PG0452:CBS domain protein:hypothetical protein:->->:492913..493018 106 aaaacaatcagttgaaaggcttggcattttgaagccggtttgtatctttgtggcttaataaacacattcttaatagtgcataataaatagaaaacataataacaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0451:PG0452|PG0451:PG0452:CBS domain protein:hypothetical protein:->->:492913..493018 106 aaaacaatcagttgaaaggcttggcattttgaagccggtttgtatctttgtggcttaataaacacattcttaatagtgcataataaatagaaaacataataacaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0451:PG0452|PG0451:PG0452:CBS domain protein:hypothetical protein:->->:492913..493018 106 aaaacaatcagttgaaaggcttggcattttgaagccggtttgtatctttgtggcttaataaacacattcttaatagtgcataataaatagaaaacataataacaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaacaatcagttgaaaggcttggcattttgaagccggtttgtatctttgtggcttaataaacacattcttaatagtgcataataaatagaaaacataataacaaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 11 End: 100 .......... N F P K A N Q L R N T D K H S L L C M R L L A Y Y I S F M M ...... aaaacaatcagttgaaaggcttggcattttgaagccggtttgtatctttgtggcttaataaacacattcttaatagtgcataataaatagaaaacataataacaaa 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================================================ aaaacaatcagttgaaaggcttggcattttgaagccggtttgtatctttgtggcttaataaacacattcttaatagtgcataataaatagaaaacataataacaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0451:PG0452|PG0451:PG0452:CBS domain protein:hypothetical protein:->->:492913..493018 106 aaaacaatcagttgaaaggcttggcattttgaagccggtttgtatctttgtggcttaataaacacattcttaatagtgcataataaatagaaaacataataacaaa Intra-Species Hit: Count: 1 Min: 1 Max: 106 Len: 106 Subject: NC_002950_PG0451_PG0452|CBS domain protein:hypothetical protein|POSITIVE:POSITIVE|[492913,493018]|106 HSP 1 e-value: 6.0E-54 bit: 210.0 Len: 106 Query Start:1 Query End:106 Subject Strand: POSITIVE Subject Start: 1 Subject End: 106 aaaacaatcagttgaaaggcttggcattttgaagccggtttgtatctttgtggcttaataaacacattcttaatagtgcataataaatagaaaacataataacaaa aaaacaatcagttgaaaggcttggcattttgaagccggtttgtatctttgtggcttaataaacacattcttaatagtgcataataaatagaaaacataataacaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAACAAUCAGUUGAAAGGCUUGGCAUUUUGAAGCCGGUUUGUAUCUUUGUGGCUUAAUAAACACAUUCUUAAUAGUGCAUAAUAAAUAGAAAACAUAAUAACAAA ..........((((...(((((.(.....).))))).((((.(((..((((((((...(((........)))..))).)))))...)))..))))....))))... (-13.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGUUAUUAUGUUUUCUAUUUAUUAUGCACUAUUAAGAAUGUGUUUAUUAAGCCACAAAGAUACAAACCGGCUUCAAAAUGCCAAGCCUUUCAACUGAUUGUUUU (((((.....(((......((((.((.((((..........)))).)).))))..))).....)))))..(((........)))...................... (-10.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 56 18 72 31 NC_002950:PG0485|5end_preprotein_translocase,_YajC_subunit_525324..525554_NEGATIVE 296 56 15 146 106 NC_002950:PG1351|5end_hypothetical_protein_1432744..1432974_NEGATIVE 293 53 14 56 3 NC_002950:PG0279|5end_NADP-dependent_malic_enzyme_312954..313184_NEGATIVE 292 50 7 169 112 NC_002950:PG0883|5end_hypothetical_protein_945121..945351_POSITIVE 292 44 13 97 63 NC_002950:PG0458|5end_ISPg5,_transposase_Orf2_501463..501693_NEGATIVE 291 45 5 222 178 NC_002950:PG1809|5end_2-oxoglutarate_oxidoreductase,_gamma_subunit_1906036..1906266_NEGATIVE 290 56 18 37 2 NC_002950:PG0444|5end_oligopeptide_transporter,_OPT_family_483256..483486_POSITIVE 279 60 13 110 63 NC_002950:PG2128|5end_ISPg5,_transposase_Orf2_2234805..2235035_NEGATIVE 279 60 13 110 63 NC_002950:PG2057|5end_ISPg5,_transposase_Orf2_2155947..2156177_NEGATIVE 279 60 13 110 63 NC_002950:PG1710|5end_ISPg5,_transposase_Orf2_1795357..1795587_POSITIVE 279 60 13 110 63 NC_002950:PG1644|5end_ISPg5,_transposase_Orf2_1725619..1725849_NEGATIVE 279 60 13 110 63 NC_002950:PG1420|5end_ISPg5,_transposase_Orf2_1505446..1505676_POSITIVE 279 60 13 110 63 NC_002950:PG0943|5end_ISPg5,_transposase_Orf2_1002512..1002742_POSITIVE 279 60 13 110 63 NC_002950:PG0591|5end_ISPg5,_transposase_Orf2_648484..648714_POSITIVE 279 60 13 110 63 NC_002950:PG0426|5end_ISPg5,_transposase_Orf2_465098..465328_NEGATIVE 279 60 13 110 63 NC_002950:PG0041|5end_ISPg5_transposase_Orf2_48377..48607_POSITIVE 279 60 13 110 63 NC_002950:PG0008|5end_ISPg5_transposase_Orf2_8023..8253_NEGATIVE 278 55 11 206 163 NC_002950:PG1709|5end_ISPg5,_transposase_Orf1_1794914..1795144_POSITIVE 276 54 19 76 46 NC_002950:PG0223|5end_exonuclease_257610..257840_NEGATIVE 276 53 18 153 114 NC_002950:PG0062|5end_TPR_domain_protein_73688..73918_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 44 13 43 9 NC_002950:PG0459|3end_ISPg5,_transposase_Orf1_501517..501667_NEGATIVE 279 60 13 56 9 NC_002950:PG2129|3end_ISPg5,_transposase_Orf1_2234859..2235009_NEGATIVE 279 60 13 56 9 NC_002950:PG2058|3end_ISPg5,_transposase_Orf1_2156001..2156151_NEGATIVE 279 60 13 56 9 NC_002950:PG1709|3end_ISPg5,_transposase_Orf1_1795383..1795533_POSITIVE 279 60 13 56 9 NC_002950:PG1645|3end_ISPg5,_transposase_Orf1_1725673..1725823_NEGATIVE 279 60 13 56 9 NC_002950:PG1419|3end_ISPg5,_transposase_Orf1_1505472..1505622_POSITIVE 279 60 13 56 9 NC_002950:PG0942|3end_ISPg5,_transposase_Orf1_1002538..1002688_POSITIVE 279 60 13 56 9 NC_002950:PG0590|3end_ISPg5,_transposase_Orf1_648510..648660_POSITIVE 279 60 13 56 9 NC_002950:PG0427|3end_ISPg5,_transposase_Orf1_465152..465302_NEGATIVE 279 60 13 56 9 NC_002950:PG0040|3end_ISPg5_transposase_Orf1_48403..48553_POSITIVE 279 60 13 56 9 NC_002950:PG0009|3end_ISPg5_transposase_Orf1_8077..8227_NEGATIVE 278 51 18 151 116 NC_002950:PG1115|3end_signal_recognition_particle_protein_1188887..1189037_POSITIVE 276 55 19 98 57 NC_002950:PG1593|3end_shikimate_kinase_1672143..1672293_POSITIVE 276 54 19 72 42 NC_002950:PG0224|3end_hypothetical_protein_257614..257764_NEGATIVE 276 53 18 148 109 NC_002950:PG0061|3end_yngK_protein_73763..73913_POSITIVE 274 57 12 93 51 NC_002950:PG1556|3end_hypothetical_protein_1637001..1637151_POSITIVE 271 54 19 135 98 NC_002950:PG0377|3end_30S_ribosomal_protein_S2_407845..407995_POSITIVE 270 55 18 89 51 NC_002950:PG1942|3end_30S_ribosomal_protein_S12_2027946..2028096_NEGATIVE 270 42 15 37 11 NC_002950:PG1479|3end_conjugative_transposon_protein_TraJ_1554128..1554278_NEGATIVE 268 54 15 151 113 NC_002950:PG1352|3end_hypothetical_protein_1432737..1432887_NEGATIVE