Origin IGS: tagtcgtttgcctccggccgaaaagccgaaaccttcttcgatgcaagagggtttcggctttttctttatgtccgaatgcgaagggaggatacgacttttctctttttgcccgtttacatgctgccgaaatcgtgtcatctctaccggctgacaaatgtggcggataaacacaaaaagcaaaagggacgggaaataagaaagagaaggaacaccgaaaacttatcattcggatgctccccctctctcaagagtattatttgcgaagaactgctg .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 cagcagttcttcgcaaataatactcttgagagagggggagcatccgaatgataagttttcggtgttccttctctttcttatttcccgtcccttttgctttttgtgtttatccgccacatttgtcagccggtagagatgacacgatttcggcagcatgtaaacgggcaaaaagagaaaagtcgtatcctcccttcgcattcggacataaagaaaaagccgaaaccctcttgcatcgaagaaggtttcggcttttcggccggaggcaaacgacta Mask Tandem Repeat Region ================================================ tagtcgtttgcctccggccgaaaagccgaaaccttcttcgatgcaagagggtttcggctttttctttatgtccgaatgcgaagggaggatacgacttttctctttttgcccgtttacatgctgccgaaatcgtgtcatctctaccggctgacaaatgtggcggataaacacaaaaagcaaaagggacgggaaataagaaagagaaggaacaccgaaaacttatcattcggatgctccccctctctcaagagtattatttgcgaagaactgctg Find is-nt database================================================ Query_seq: PG1948:PG1949|PG1948:PG1949:lipoprotein, putative:malate dehydrogenase:-><-:2038001..2038273 273 tagtcgtttgcctccggccgaaaagccgaaaccttcttcgatgcaagagggtttcggctttttctttatgtccgaatgcgaagggaggatacgacttttctctttttgcccgtttacatgctgccgaaatcgtgtcatctctaccggctgacaaatgtggcggataaacacaaaaagcaaaagggacgggaaataagaaagagaaggaacaccgaaaacttatcattcggatgctccccctctctcaagagtattatttgcgaagaactgctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1948:PG1949|PG1948:PG1949:lipoprotein, putative:malate dehydrogenase:-><-:2038001..2038273 273 tagtcgtttgcctccggccgaaaagccgaaaccttcttcgatgcaagagggtttcggctttttctttatgtccgaatgcgaagggaggatacgacttttctctttttgcccgtttacatgctgccgaaatcgtgtcatctctaccggctgacaaatgtggcggataaacacaaaaagcaaaagggacgggaaataagaaagagaaggaacaccgaaaacttatcattcggatgctccccctctctcaagagtattatttgcgaagaactgctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1948:PG1949|PG1948:PG1949:lipoprotein, putative:malate dehydrogenase:-><-:2038001..2038273 273 tagtcgtttgcctccggccgaaaagccgaaaccttcttcgatgcaagagggtttcggctttttctttatgtccgaatgcgaagggaggatacgacttttctctttttgcccgtttacatgctgccgaaatcgtgtcatctctaccggctgacaaatgtggcggataaacacaaaaagcaaaagggacgggaaataagaaagagaaggaacaccgaaaacttatcattcggatgctccccctctctcaagagtattatttgcgaagaactgctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagtcgtttgcctccggccgaaaagccgaaaccttcttcgatgcaagagggtttcggctttttctttatgtccgaatgcgaagggaggatacgacttttctctttttgcccgtttacatgctgccgaaatcgtgtcatctctaccggctgacaaatgtggcggataaacacaaaaagcaaaagggacgggaaataagaaagagaaggaacaccgaaaacttatcattcggatgctccccctctctcaagagtattatttgcgaagaactgctg Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 8 End: 148 ....... M P P A E K P K P S S M Q E G F G F F F M S E C E G R I R L F S F C P F T C C R N R V I S T G ............................................................................................................................. Protein_Len: 60 Strand: + Start: 76 End: 273 ........................................................................... M R R E D T T F L F L P V Y M L P K S C H L Y R L T N V A D K H K K Q K G R E I R K R R N T E N L S F G C S P S L K S I Protein_Len: 38 Strand: - Start: 144 End: 257 ............................................................................................................................................... R S V F T A S L C L F C F P R S I L F L L F V S F K D N P H E G E R L L I M ................ Protein_Len: 60 Strand: - Start: 2 End: 232 . E A K E K H G F A F P P Y S K E R K A R K C A A S I T D D R G A S L H P P Y V C F A F P V P F L F S F S C R F S I M R M ......................................... Protein_Len: 60 Strand: - Start: 1 End: 180 L R K G G A S F G F G E E I C S P K P K K K I D S H S P L I R S K E K Q G N V H Q R F R T M E V P Q C I H R I F V F L M ............................................................................................. tagtcgtttgcctccggccgaaaagccgaaaccttcttcgatgcaagagggtttcggctttttctttatgtccgaatgcgaagggaggatacgacttttctctttttgcccgtttacatgctgccgaaatcgtgtcatctctaccggctgacaaatgtggcggataaacacaaaaagcaaaagggacgggaaataagaaagagaaggaacaccgaaaacttatcattcggatgctccccctctctcaagagtattatttgcgaagaactgctg 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================================================ tagtcgtttgcctccggccgaaaagccgaaaccttcttcgatgcaagagggtttcggctttttctttatgtccgaatgcgaagggaggatacgacttttctctttttgcccgtttacatgctgccgaaatcgtgtcatctctaccggctgacaaatgtggcggataaacacaaaaagcaaaagggacgggaaataagaaagagaaggaacaccgaaaacttatcattcggatgctccccctctctcaagagtattatttgcgaagaactgctg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -16.1 Tail_Score: -4.04206 Start: 20 End: 64 Full_Region: CGTTTGCCTCCGGCC GAAAAGCCGAAACCTTCTT CGATGC AAGAGGGTTTCGGCTTTTTC TTTATGTCCGAATGC ...................GAAAAGCCGAAACCTTCTTCGATGCAAGAGGGTTTCGGCTTTTTC................................................................................................................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -14.0 Tail_Score: -4.07568 Start: 25 End: 58 Full_Region: ggacataaagaaaaa gccgaaaccctctt gcatcg aagaaggtttcggc ttttcggccggaggc ........................gccgaaaccctcttgcatcgaagaaggtttcggc....................................................................................................................................................................................................................... TransTerm Strand: - Conf: 77 HP_score: -8.8 Tail_Score: -3.94188 Start: 197 End: 246 Full_Region: gcaaataatactctt gagagagggggagcatccgaa tgataagtt ttcggtgttccttctctttc ttatttcccgtccct ....................................................................................................................................................................................................gagagagggggagcatccgaatgataagttttcggtgttccttctctttc........................... TransTerm Strand: - Conf: 74 HP_score: -6.0 Tail_Score: -4.57581 Start: 201 End: 242 Full_Region: ataatactcttgaga gagggggagcatccgaa tgataagtt ttcggtgttccttctc tttcttatttcccgt ........................................................................................................................................................................................................gagggggagcatccgaatgataagttttcggtgttccttctc............................... Find igs database================================================ Query_seq: PG1948:PG1949|PG1948:PG1949:lipoprotein, putative:malate dehydrogenase:-><-:2038001..2038273 273 tagtcgtttgcctccggccgaaaagccgaaaccttcttcgatgcaagagggtttcggctttttctttatgtccgaatgcgaagggaggatacgacttttctctttttgcccgtttacatgctgccgaaatcgtgtcatctctaccggctgacaaatgtggcggataaacacaaaaagcaaaagggacgggaaataagaaagagaaggaacaccgaaaacttatcattcggatgctccccctctctcaagagtattatttgcgaagaactgctg Intra-Species Hit: Count: 1 Min: 1 Max: 273 Len: 273 Subject: NC_002950_PG1948_PG1949|lipoprotein, putative:malate dehydrogenase|POSITIVE:NEGATIVE|[2038001,2038273]|273 HSP 1 e-value: 1.0E-153 bit: 541.0 Len: 273 Query Start:1 Query End:273 Subject Strand: POSITIVE Subject Start: 1 Subject End: 273 tagtcgtttgcctccggccgaaaagccgaaaccttcttcgatgcaagagggtttcggctttttctttatgtccgaatgcgaagggaggatacgacttttctctttttgcccgtttacatgctgccgaaatcgtgtcatctctaccggctgacaaatgtggcggataaacacaaaaagcaaaagggacgggaaataagaaagagaaggaacaccgaaaacttatcattcggatgctccccctctctcaagagtattatttgcgaagaactgctg tagtcgtttgcctccggccgaaaagccgaaaccttcttcgatgcaagagggtttcggctttttctttatgtccgaatgcgaagggaggatacgacttttctctttttgcccgtttacatgctgccgaaatcgtgtcatctctaccggctgacaaatgtggcggataaacacaaaaagcaaaagggacgggaaataagaaagagaaggaacaccgaaaacttatcattcggatgctccccctctctcaagagtattatttgcgaagaactgctg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUCGUUUGCCUCCGGCCGAAAAGCCGAAACCUUCUUCGAUGCAAGAGGGUUUCGGCUUUUUCUUUAUGUCCGAAUGCGAAGGGAGGAUACGACUUUUCUCUUUUUGCCCGUUUACAUGCUGCCGAAAUCGUGUCAUCUCUACCGGCUGACAAAUGUGGCGGAUAAACACAAAAAGCAAAAGGGACGGGAAAUAAGAAAGAGAAGGAACACCGAAAACUUAUCAUUCGGAUGCUCCCCCUCUCUCAAGAGUAUUAUUUGCGAAGAACUGCUG ((((..(((((.(((....(((((((((((((((((((......)))))))))))))))))))......((((....((((((((((((........))))))))))))..(((((....((((((......(((((.((.....)).)))))....)))))).)))))..............)))).))).....((.((((..(((.(((((((.........))))).)).)))..)))).)).............)))))..))))... (-91.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGCAGUUCUUCGCAAAUAAUACUCUUGAGAGAGGGGGAGCAUCCGAAUGAUAAGUUUUCGGUGUUCCUUCUCUUUCUUAUUUCCCGUCCCUUUUGCUUUUUGUGUUUAUCCGCCACAUUUGUCAGCCGGUAGAGAUGACACGAUUUCGGCAGCAUGUAAACGGGCAAAAAGAGAAAAGUCGUAUCCUCCCUUCGCAUUCGGACAUAAAGAAAAAGCCGAAACCCUCUUGCAUCGAAGAAGGUUUCGGCUUUUCGGCCGGAGGCAAACGACUA ..((........))........((((((((((((((((((((.(((((.........))))))))))))))))))))......(((((.....(((((..(((((((..((..((.............))..))...)))))))....))))).......)))))....)))))...((((((..(((((.((((....))))......(((((.(((((((((.((((......)))).))))))))))))))....)))))...)))))). (-96.92) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 417 166 121 216 181 NC_002950:PG0770|5end_hypothetical_protein_824575..824805_NEGATIVE 411 58 11 225 173 NC_002950:PG0360|5end_lemA_protein_393482..393712_POSITIVE 386 58 12 177 128 NC_002950:PG1485|5end_conjugative_transposon_protein_TraC_1560370..1560600_NEGATIVE 377 150 109 151 110 NC_002950:PG1185|5end_hypothetical_protein_1267752..1267982_NEGATIVE 374 88 51 175 143 NC_002950:PG0140|5end_hypothetical_protein_163858..164088_NEGATIVE 372 58 15 79 20 NC_002950:PG1762|5end_protein-export_membrane_protein_SecD/protein-export_membrane_protein_SecF_1847988..1848218_POSITIVE 364 48 1 133 86 NC_002950:PG0286|5end_hypothetical_protein_320117..320347_POSITIVE 360 58 11 82 23 NC_002950:PG2032|5end_primosomal_protein_N'_2133381..2133611_NEGATIVE 358 150 103 180 124 NC_002950:PG1116|5end_methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase_1188931..1189161_POSITIVE 355 166 122 173 122 NC_002950:PG2097|5end_ribose-phosphate_pyrophosphokinase_2206462..2206692_NEGATIVE 355 57 12 69 31 NC_002950:PG0898|5end_hypothetical_protein_963350..963580_NEGATIVE 355 130 82 164 110 NC_002950:PG0534|5end_hypothetical_protein_583242..583472_POSITIVE 352 80 32 184 132 NC_002950:PG0259|5end_hypothetical_protein_292278..292508_POSITIVE 351 58 12 195 150 NC_002950:PG1655|5end_hypothetical_protein_1737095..1737325_POSITIVE 350 56 12 65 15 NC_002950:PG1831|5end_ATP-dependent_DNA_helicase_RecQ_1925422..1925652_NEGATIVE 347 140 92 73 11 NC_002950:PG1854|5end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1953882..1954112_NEGATIVE 347 125 82 203 149 NC_002950:PG1498|5end_hypothetical_protein_1574656..1574886_POSITIVE 347 80 33 195 141 NC_002950:PG0659|5end_hypothetical_protein_709148..709378_NEGATIVE 346 88 41 57 21 NC_002950:PG1008|5end_hypothetical_protein_1067644..1067874_NEGATIVE 341 59 14 72 30 NC_002950:PG2038|5end_N-acetylmuramoyl-L-alanine_amidase,_putative_2138207..2138437_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 535 60 11 68 3 NC_002950:PG1948|3end_lipoprotein,_putative_2037940..2038090_POSITIVE 386 50 1 83 37 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 362 86 51 151 123 NC_002950:PG0141|3end_spoOJ_protein_163878..164028_NEGATIVE 361 50 3 141 90 NC_002950:PG1794|3end_DNA_polymerase_type_I_1888838..1888988_POSITIVE 360 149 104 142 106 NC_002950:PG0278|3end_hypothetical_protein_310477..310627_POSITIVE 355 49 3 147 86 NC_002950:PG1824|3end_phosphopyruvate_hydratase_1918153..1918303_NEGATIVE 355 130 81 140 93 NC_002950:PG0524|3end_hypothetical_protein_568963..569113_POSITIVE 349 57 11 137 101 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 347 140 92 113 51 NC_002950:PG1855|3end_carboxyl-terminal_protease_1953842..1953992_NEGATIVE 346 88 41 60 24 NC_002950:PG1009|3end_hypothetical_protein_1067641..1067791_NEGATIVE 344 58 13 123 66 NC_002950:PG0245|3end_universal_stress_protein_family_279773..279923_NEGATIVE 341 150 101 118 66 NC_002950:PG0068|3end_hypothetical_protein_82079..82229_POSITIVE 340 57 12 83 31 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE 340 150 101 130 73 NC_002950:PG0520|3end_chaperonin_GroEL_563618..563768_NEGATIVE 336 79 33 131 78 NC_002950:PG2047|3end_helicase,_putative_2145758..2145908_NEGATIVE 335 160 111 134 88 NC_002950:PG2036|3end_ion_transporter_2137552..2137702_POSITIVE 334 118 73 71 24 NC_002950:PG1797|3end_DNA-binding_response_regulator/sensor_histidine_kinase_1892978..1893128_POSITIVE 334 49 2 105 55 NC_002950:PG1661|3end_hypothetical_protein_1744835..1744985_POSITIVE 330 60 13 61 5 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE 330 160 117 66 17 NC_002950:PG1465|3end_hypothetical_protein_1542706..1542856_POSITIVE