Origin IGS: tgaaagagaatccttttgagattgccattatacgctgaaaaaagagaatatgaagtaggtagtggcaataaatccattagaaaaagcagacagtagaaattacttttcttactgcctgcttttct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttca Mask Tandem Repeat Region ================================================ tgaaagagaatccttttgagattgccattatacgctgaaaaaagagaatatgaagtaggtagtggcaataaatccattagaaaaagcagacagtagaaattacttttcttactgcctgcttttct Find is-nt database================================================ Query_seq: PG1451:PG1452|PG1451:PG1452:hypothetical protein:lipoprotein, putative:-><-:1535245..1535369 125 tgaaagagaatccttttgagattgccattatacgctgaaaaaagagaatatgaagtaggtagtggcaataaatccattagaaaaagcagacagtagaaattacttttcttactgcctgcttttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1451:PG1452|PG1451:PG1452:hypothetical protein:lipoprotein, putative:-><-:1535245..1535369 125 tgaaagagaatccttttgagattgccattatacgctgaaaaaagagaatatgaagtaggtagtggcaataaatccattagaaaaagcagacagtagaaattacttttcttactgcctgcttttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1451:PG1452|PG1451:PG1452:hypothetical protein:lipoprotein, putative:-><-:1535245..1535369 125 tgaaagagaatccttttgagattgccattatacgctgaaaaaagagaatatgaagtaggtagtggcaataaatccattagaaaaagcagacagtagaaattacttttcttactgcctgcttttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaaagagaatccttttgagattgccattatacgctgaaaaaagagaatatgaagtaggtagtggcaataaatccattagaaaaagcagacagtagaaattacttttcttactgcctgcttttct Predict ORF larger than 30AA ================================================ tgaaagagaatccttttgagattgccattatacgctgaaaaaagagaatatgaagtaggtagtggcaataaatccattagaaaaagcagacagtagaaattacttttcttactgcctgcttttct 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================================================ tgaaagagaatccttttgagattgccattatacgctgaaaaaagagaatatgaagtaggtagtggcaataaatccattagaaaaagcagacagtagaaattacttttcttactgcctgcttttct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1451:PG1452|PG1451:PG1452:hypothetical protein:lipoprotein, putative:-><-:1535245..1535369 125 tgaaagagaatccttttgagattgccattatacgctgaaaaaagagaatatgaagtaggtagtggcaataaatccattagaaaaagcagacagtagaaattacttttcttactgcctgcttttct Intra-Species Hit: Count: 2 Min: 1 Max: 125 Len: 125 Subject: NC_002950_PG1451_PG1452|hypothetical protein:lipoprotein, putative|POSITIVE:NEGATIVE|[1535245,1535369]|125 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 tgaaagagaatccttttgagattgccattatacgctgaaaaaagagaatatgaagtaggtagtggcaataaatccattagaaaaagcagacagtagaaattacttttcttactgcctgcttttct tgaaagagaatccttttgagattgccattatacgctgaaaaaagagaatatgaagtaggtagtggcaataaatccattagaaaaagcagacagtagaaattacttttcttactgcctgcttttct Subject: NC_002950_PG0821_PG0822|lipoprotein, putative:hypothetical protein|POSITIVE:NEGATIVE|[880293,880417]|125 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 125 Query Start:1 Query End:125 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 125 tgaaagagaatccttttgagattgccattatacgctgaaaaaagagaatatgaagtaggtagtggcaataaatccattagaaaaagcagacagtagaaattacttttcttactgcctgcttttct tgaaagagaatccttttgagattgccattatacgctgaaaaaagagaatatgaagtaggtagtggcaataaatccattagaaaaagcagacagtagaaattacttttcttactgcctgcttttct Inter-species Hit: Count: 1 Min: 1 Max: 125 Len: 125 Subject: pint_PI0390_PI0391|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[357816,357946]|131 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 125 Query Start:1 Query End:125 Subject Strand: NEGATIVE Subject Start: 4 Subject End: 128 tgaaagagaatccttttgagattgccattatacgctgaaaaaagagaatatgaagtaggtagtggcaataaatccattagaaaaagcagacagtagaaattacttttcttactgcctgcttttct tgaaagagaatccttttgagattgccattatacgctgaaaaaagagaatatgaagtaggtagtggcaataaatccattagaaaaagcagacagtagaaattacttttcttactgcctgcttttct Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAGAGAAUCCUUUUGAGAUUGCCAUUAUACGCUGAAAAAAGAGAAUAUGAAGUAGGUAGUGGCAAUAAAUCCAUUAGAAAAAGCAGACAGUAGAAAUUACUUUUCUUACUGCCUGCUUUUCU .(((((......)))))...(((((((((((..(((.................)))..))))))))))).........((((((.((((.(((((((((.....)))).))))).)))))))))) (-35.23) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAAAGCAGGCAGUAAGAAAAGUAAUUUCUACUGUCUGCUUUUUCUAAUGGAUUUAUUGCCACUACCUACUUCAUAUUCUCUUUUUUCAGCGUAUAAUGGCAAUCUCAAAAGGAUUCUCUUUCA .(((((((((((((((.((((.....))))))))))))))))))).....(((((((((((((.(((((....................)).)))...))))))).......))))))....... (-30.76) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 60 16 193 156 NC_002950:PG0309|5end_thiamine_biosynthesis_lipoprotein_ApbE_345023..345253_NEGATIVE 250 120 73 94 50 NC_002950:PG0227|5end_DNA_repair_protein_RadA_263978..264208_NEGATIVE 248 98 51 58 18 NC_002950:PG2177|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_F_2286504..2286734_NEGATIVE 242 110 61 81 41 NC_002950:PG2050|5end_hypothetical_protein_2149434..2149664_NEGATIVE 240 75 46 64 33 NC_002950:PG0669|5end_heme-binding_protein_FetB_719753..719983_POSITIVE 240 66 24 49 12 NC_002950:PG0548|5end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_602098..602328_POSITIVE 239 38 2 150 107 NC_002950:PG1028|5end_TPR_domain_protein_1089670..1089900_POSITIVE 237 110 61 111 56 NC_002950:PG2168|5end_hypothetical_protein_2274157..2274387_NEGATIVE 230 97 51 52 2 NC_002950:PG0778|5end_hypothetical_protein_831869..832099_NEGATIVE 222 89 50 55 1 NC_002950:PG0200|5end_hypothetical_protein_238351..238581_NEGATIVE 222 119 74 98 46 NC_002950:PG0171|5end_5'-nucleotidase_family_protein_191724..191954_POSITIVE 220 59 12 65 21 NC_002950:PG2073|5end_hypothetical_protein_2174374..2174604_NEGATIVE 220 60 18 83 42 NC_002950:PG1885|5end_polyphosphate_kinase_1983152..1983382_NEGATIVE 220 59 12 65 21 NC_002950:PG1669|5end_hypothetical_protein_1755566..1755796_NEGATIVE 220 59 12 65 21 NC_002950:PG1264|5end_hypothetical_protein_1344895..1345125_NEGATIVE 220 57 18 183 138 NC_002950:PG1103|5end_ATPase,_AAA_family_1173605..1173835_POSITIVE 220 119 86 197 156 NC_002950:PG0714|5end_copper_homeostasis_protein_CutC_768671..768901_NEGATIVE 220 59 12 65 21 NC_002950:PG0103|5end_hypothetical_protein_121290..121520_POSITIVE 216 79 34 93 51 NC_002950:PG0272|5end_CBS_domain_protein_304399..304629_POSITIVE 215 75 43 42 13 NC_002950:PG1478|5end_conjugative_transposon_protein_TraK_1554116..1554346_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 815 100 51 65 16 NC_002950:PG0821|3end_lipoprotein,_putative_880232..880382_POSITIVE 250 120 73 48 4 NC_002950:PG0228|3end_DdaH_family_protein_264024..264174_NEGATIVE 242 49 5 140 93 NC_002950:PG1276|3end_DNA-binding_protein,_histone-like_family_1353531..1353681_POSITIVE 242 49 5 140 93 NC_002950:PG0566|3end_DNA-binding_protein,_histone-like_family_622935..623085_NEGATIVE 241 68 30 99 61 NC_002950:PG1110|3end_hypothetical_protein_1183237..1183387_POSITIVE 240 75 46 35 4 NC_002950:PG0668|3end_TonB-dependent_receptor_719804..719954_POSITIVE 231 37 2 65 27 NC_002950:PG1015|3end_hypothetical_protein_1075877..1076027_NEGATIVE 230 68 22 58 4 NC_002950:PG1546|3end_hypothetical_protein_1624355..1624505_POSITIVE 229 46 5 55 10 NC_002950:PG0188|3end_lipoprotein,_putative_225384..225534_POSITIVE 228 98 53 39 1 NC_002950:PG2178|3end_NADH:ubiquinone_oxidoreductase,_Na_translocating,_E_subunit_2286523..2286673_NEGATIVE 226 52 23 46 19 NC_002950:PG0560|3end_hypothetical_protein_617748..617898_POSITIVE 222 119 74 68 16 NC_002950:PG0170|3end_methionyl-tRNA_synthetase_191774..191924_POSITIVE 215 75 43 30 1 NC_002950:PG1479|3end_conjugative_transposon_protein_TraJ_1554128..1554278_NEGATIVE 213 59 12 62 6 NC_002950:PG0146|3end_hypothetical_protein_168408..168558_NEGATIVE 212 120 73 117 67 NC_002950:PG1087|3end_radical_SAM_protein,_TIGR01212_family_1154820..1154970_POSITIVE 212 66 22 117 68 NC_002950:PG0665|3end_beta-galactosidase_715245..715395_POSITIVE 212 91 51 128 99 NC_002950:PG0362|3end_hypothetical_protein_397549..397699_POSITIVE 211 119 74 56 2 NC_002950:PG1945|3end_hypothetical_protein_2032220..2032370_POSITIVE 210 67 23 74 23 NC_002950:PG1583|3end_batB_protein_1661414..1661564_POSITIVE 209 38 4 76 40 NC_002950:PG0651|3end_HDIG_domain_protein_703071..703221_NEGATIVE