Origin IGS: atcatttacgatctatatacagatcgttttcaatttatatacaaaacgattttaatttatatatagatcgtaaatgatttgtatatggatcgcgggctgaaaaaagccttttcaagag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctcttgaaaaggcttttttcagcccgcgatccatatacaaatcatttacgatctatatataaattaaaatcgttttgtatataaattgaaaacgatctgtatatagatcgtaaatgat Mask Tandem Repeat Region ================================================ atcatttacgatcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaatgatttgtatatggatcgcgggctgaaaaaagccttttcaagag Find is-nt database================================================ Query_seq: PG1222:PG1223|PG1222:PG1223:hypothetical protein:hypothetical protein:<-->:1299483..1299600 118 atcatttacgatctatatacagatcgttttcaatttatatacaaaacgattttaatttatatatagatcgtaaatgatttgtatatggatcgcgggctgaaaaaagccttttcaagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1222:PG1223|PG1222:PG1223:hypothetical protein:hypothetical protein:<-->:1299483..1299600 118 atcatttacgatctatatacagatcgttttcaatttatatacaaaacgattttaatttatatatagatcgtaaatgatttgtatatggatcgcgggctgaaaaaagccttttcaagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1222:PG1223|PG1222:PG1223:hypothetical protein:hypothetical protein:<-->:1299483..1299600 118 atcatttacgatctatatacagatcgttttcaatttatatacaaaacgattttaatttatatatagatcgtaaatgatttgtatatggatcgcgggctgaaaaaagccttttcaagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcatttacgatctatatacagatcgttttcaatttatatacaaaacgattttaatttatatatagatcgtaaatgatttgtatatggatcgcgggctgaaaaaagccttttcaagag Predict ORF larger than 30AA ================================================ atcatttacgatctatatacagatcgttttcaatttatatacaaaacgattttaatttatatatagatcgtaaatgatttgtatatggatcgcgggctgaaaaaagccttttcaagag 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================================================ atcatttacgatctatatacagatcgttttcaatttatatacaaaacgattttaatttatatatagatcgtaaatgatttgtatatggatcgcgggctgaaaaaagccttttcaagag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1222:PG1223|PG1222:PG1223:hypothetical protein:hypothetical protein:<-->:1299483..1299600 118 atcatttacgatctatatacagatcgttttcaatttatatacaaaacgattttaatttatatatagatcgtaaatgatttgtatatggatcgcgggctgaaaaaagccttttcaagag Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: NC_002950_PG1222_PG1223|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1299483,1299600]|118 HSP 1 e-value: 5.0E-61 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 atcatttacgatctatatacagatcgttttcaatttatatacaaaacgattttaatttatatatagatcgtaaatgatttgtatatggatcgcgggctgaaaaaagccttttcaagag atcatttacgatctatatacagatcgttttcaatttatatacaaaacgattttaatttatatatagatcgtaaatgatttgtatatggatcgcgggctgaaaaaagccttttcaagag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAUUUACGAUCUAUAUACAGAUCGUUUUCAAUUUAUAUACAAAACGAUUUUAAUUUAUAUAUAGAUCGUAAAUGAUUUGUAUAUGGAUCGCGGGCUGAAAAAAGCCUUUUCAAGAG .((.....(((((((((((((((((((((.(.(((((((((.(((..........))).))))))))).).))))))))))))))))))))).(((((......)))))......)). (-39.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUUGAAAAGGCUUUUUUCAGCCCGCGAUCCAUAUACAAAUCAUUUACGAUCUAUAUAUAAAUUAAAAUCGUUUUGUAUAUAAAUUGAAAACGAUCUGUAUAUAGAUCGUAAAUGAU ..........((((......))))................(((((((((((((((((((((.......((((((((............)))))))).))))))))))))))))))))) (-33.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 845 110 61 201 152 NC_002950:PG1222|5end_hypothetical_protein_1299392..1299622_NEGATIVE 315 48 1 137 92 NC_002950:PG0371|5end_hypothetical_protein_404043..404273_POSITIVE 253 98 66 96 61 NC_002950:PG1247|5end_3-dehydroquinate_synthase_1324444..1324674_POSITIVE 249 50 1 142 87 NC_002950:PG1574|5end_hypothetical_protein_1652613..1652843_NEGATIVE 243 110 67 66 26 NC_002950:PG0510|5end_hypothetical_protein_550060..550290_NEGATIVE 243 108 68 160 129 NC_002950:PG0364|5end_hypothetical_protein_399615..399845_NEGATIVE 237 108 70 135 92 NC_002950:PG1792|5end_sodium/hydrogen_antiporter_1881622..1881852_POSITIVE 236 110 77 198 168 NC_002950:PG0958|5end_ribonuclease_BN,_putative_1019370..1019600_NEGATIVE 234 101 68 70 39 NC_002950:PG1848|5end_RNA_methyltransferase,_TrmH_family_1947382..1947612_NEGATIVE 226 107 66 53 12 NC_002950:PG0577|5end_phospho-N-acetylmuramoyl-pentapeptide-_transferase_633197..633427_POSITIVE 224 41 9 209 177 NC_002950:PG1695|5end_hypothetical_protein_1779440..1779670_POSITIVE 221 99 63 168 123 NC_002950:PG0120|5end_UDP-N-acetylglucosamine_2-epimerase_143004..143234_POSITIVE 220 108 73 44 4 NC_002950:PG0139|5end_membrane-bound_lytic_murein_transglycosylase_D,_putative_163141..163371_NEGATIVE 216 98 68 58 29 NC_002950:PG0744|5end_RNA_methyltransferase,_TrmH_family_791897..792127_NEGATIVE 215 108 65 73 39 NC_002950:PG1355|5end_acyltransferase,_putative_1435292..1435522_NEGATIVE 214 107 66 129 92 NC_002950:PG0680|5end_efflux_transporter,_MFP_component,_RND_family_730968..731198_POSITIVE 213 109 67 68 30 NC_002950:PG1571|5end_metallo-beta-lactamase_superfamily_protein_1650353..1650583_NEGATIVE 210 106 61 81 24 NC_002950:PG0922|5end_hypothetical_protein_982451..982681_NEGATIVE 210 100 68 136 97 NC_002950:PG0294|5end_glycosyl_transferase,_group_2_family_protein_330161..330391_NEGATIVE 209 108 69 153 110 NC_002950:PG2028|5end_ebsC_protein_2126027..2126257_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 92 55 44 7 NC_002950:PG0773|3end_hypothetical_protein_825348..825498_POSITIVE 261 107 61 53 1 NC_002950:PG0995|3end_hypothetical_protein_1055469..1055619_NEGATIVE 255 90 43 52 11 NC_002950:PG0609|3end_hypothetical_protein_663355..663505_POSITIVE 253 98 66 81 46 NC_002950:PG1246|3end_alanyl-tRNA_synthetase_1324509..1324659_POSITIVE 242 107 69 97 52 NC_002950:PG2032|3end_primosomal_protein_N'_2130868..2131018_NEGATIVE 239 107 63 112 68 NC_002950:PG1638|3end_thioredoxin_family_protein_1718664..1718814_NEGATIVE 239 100 63 58 18 NC_002950:PG1257|3end_hypothetical_protein_1334461..1334611_NEGATIVE 239 100 66 110 71 NC_002950:PG0350|3end_internalin-related_protein_385356..385506_NEGATIVE 236 110 66 111 64 NC_002950:PG2006|3end_hypothetical_protein_2095026..2095176_POSITIVE 234 101 68 73 42 NC_002950:PG1849|3end_DNA_repair_protein_RecN_1947379..1947529_NEGATIVE 233 100 60 50 11 NC_002950:PG1549|3end_hypothetical_protein_1627807..1627957_NEGATIVE 233 86 43 50 13 NC_002950:PG1357|3end_hypothetical_protein_1436327..1436477_NEGATIVE 231 107 66 82 40 NC_002950:PG0744|3end_RNA_methyltransferase,_TrmH_family_791133..791283_NEGATIVE 229 100 61 89 41 NC_002950:PG0003|3end_hypothetical_protein_1919..2069_NEGATIVE 221 98 65 83 36 NC_002950:PG0293|3end_secretion_activator_protein,_putative_328093..328243_NEGATIVE 220 97 55 129 80 NC_002950:PG0576|3end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,_6-diaminopimelate_ligase_633262..633412_POSITIVE 219 107 66 48 1 NC_002950:PG1167|3end_hypothetical_protein_1248644..1248794_POSITIVE 214 107 66 89 52 NC_002950:PG0679|3end_outer_membrane_efflux_protein_731008..731158_POSITIVE 213 99 51 151 95 NC_002950:PG1633|3end_galactokinase_1714619..1714769_POSITIVE 210 99 66 151 114 NC_002950:PG0732|3end_hypothetical_protein_783018..783168_POSITIVE