Origin IGS: atatgggaacggagcagatcctttcctgtctgcatccgcgacaaaagtagaaagaagctccggcaatagaaactaatcggcccacagccacgacgctattatcgttcaagcaaaaaacgacagaggctgccccatcgagatgagacagcctccaggaagcgtcggccttaacagacgtata .........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 tatacgtctgttaaggccgacgcttcctggaggctgtctcatctcgatggggcagcctctgtcgttttttgcttgaacgataatagcgtcgtggctgtgggccgattagtttctattgccggagcttctttctacttttgtcgcggatgcagacaggaaaggatctgctccgttcccatat Mask Tandem Repeat Region ================================================ atatgggaacggagcagatcctttcctgtctgcatccgcgacaaaagtagaaagaagctccggcaatagaaactaatcggcccacagccacgacgctattatcgttcaagcaaaaaacgacagaggctgccccatcgagatgagacagcctccaggaagcgtcggccttaacagacgtata Find is-nt database================================================ Query_seq: PG2081:PG2082|PG2081:PG2082:biotin synthetase:POT family protein:<-<-:2181752..2181932 181 atatgggaacggagcagatcctttcctgtctgcatccgcgacaaaagtagaaagaagctccggcaatagaaactaatcggcccacagccacgacgctattatcgttcaagcaaaaaacgacagaggctgccccatcgagatgagacagcctccaggaagcgtcggccttaacagacgtata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2081:PG2082|PG2081:PG2082:biotin synthetase:POT family protein:<-<-:2181752..2181932 181 atatgggaacggagcagatcctttcctgtctgcatccgcgacaaaagtagaaagaagctccggcaatagaaactaatcggcccacagccacgacgctattatcgttcaagcaaaaaacgacagaggctgccccatcgagatgagacagcctccaggaagcgtcggccttaacagacgtata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2081:PG2082|PG2081:PG2082:biotin synthetase:POT family protein:<-<-:2181752..2181932 181 atatgggaacggagcagatcctttcctgtctgcatccgcgacaaaagtagaaagaagctccggcaatagaaactaatcggcccacagccacgacgctattatcgttcaagcaaaaaacgacagaggctgccccatcgagatgagacagcctccaggaagcgtcggccttaacagacgtata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atatgggaacggagcagatcctttcctgtctgcatccgcgacaaaagtagaaagaagctccggcaatagaaactaatcggcccacagccacgacgctattatcgttcaagcaaaaaacgacagaggctgccccatcgagatgagacagcctccaggaagcgtcggccttaacagacgtata Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 76 End: 168 ........................................................................... M G P Q P R R Y Y R S S K K R Q R L P H R D E T A S R K R R P ............. Protein_Len: 49 Strand: - Start: 2 End: 148 . I P V S C I R E Q R C G R C F Y F S A G A I S V L R G V A V V S N D N L C F V V S A A G D L H S M ................................. atatgggaacggagcagatcctttcctgtctgcatccgcgacaaaagtagaaagaagctccggcaatagaaactaatcggcccacagccacgacgctattatcgttcaagcaaaaaacgacagaggctgccccatcgagatgagacagcctccaggaagcgtcggccttaacagacgtata 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================================================ atatgggaacggagcagatcctttcctgtctgcatccgcgacaaaagtagaaagaagctccggcaatagaaactaatcggcccacagccacgacgctattatcgttcaagcaaaaaacgacagaggctgccccatcgagatgagacagcctccaggaagcgtcggccttaacagacgtata Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 88 HP_score: -5.3 Tail_Score: -5.26875 Start: 118 End: 156 Full_Region: ttaaggccgacgctt cctggaggctgtctcat ctcg atggggcagcctctgtcg ttttttgcttgaacg .....................................................................................................................cctggaggctgtctcatctcgatggggcagcctctgtcg......................... TransTerm Strand: - Conf: 86 HP_score: -12.5 Tail_Score: -3.44982 Start: 121 End: 154 Full_Region: aaggccgacgcttcc tggaggctgtctcat ctcg atggggcagcctctg tcgttttttgcttga ........................................................................................................................tggaggctgtctcatctcgatggggcagcctctg........................... Find igs database================================================ Query_seq: PG2081:PG2082|PG2081:PG2082:biotin synthetase:POT family protein:<-<-:2181752..2181932 181 atatgggaacggagcagatcctttcctgtctgcatccgcgacaaaagtagaaagaagctccggcaatagaaactaatcggcccacagccacgacgctattatcgttcaagcaaaaaacgacagaggctgccccatcgagatgagacagcctccaggaagcgtcggccttaacagacgtata Intra-Species Hit: Count: 1 Min: 1 Max: 181 Len: 181 Subject: NC_002950_PG2081_PG2082|biotin synthetase:POT family protein|NEGATIVE:NEGATIVE|[2181752,2181932]|181 HSP 1 e-value: 2.0E-98 bit: 359.0 Len: 181 Query Start:1 Query End:181 Subject Strand: POSITIVE Subject Start: 1 Subject End: 181 atatgggaacggagcagatcctttcctgtctgcatccgcgacaaaagtagaaagaagctccggcaatagaaactaatcggcccacagccacgacgctattatcgttcaagcaaaaaacgacagaggctgccccatcgagatgagacagcctccaggaagcgtcggccttaacagacgtata atatgggaacggagcagatcctttcctgtctgcatccgcgacaaaagtagaaagaagctccggcaatagaaactaatcggcccacagccacgacgctattatcgttcaagcaaaaaacgacagaggctgccccatcgagatgagacagcctccaggaagcgtcggccttaacagacgtata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUGGGAACGGAGCAGAUCCUUUCCUGUCUGCAUCCGCGACAAAAGUAGAAAGAAGCUCCGGCAAUAGAAACUAAUCGGCCCACAGCCACGACGCUAUUAUCGUUCAAGCAAAAAACGACAGAGGCUGCCCCAUCGAGAUGAGACAGCCUCCAGGAAGCGUCGGCCUUAACAGACGUAUA ....(((((.(((.....))).)))))(((((..((..(.......)..))..........(((..............(((.....))).(((((((....(((((.........)))))..(((((((.(.(((....))).).))))))).....))))))))))....)))))..... (-53.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUACGUCUGUUAAGGCCGACGCUUCCUGGAGGCUGUCUCAUCUCGAUGGGGCAGCCUCUGUCGUUUUUUGCUUGAACGAUAAUAGCGUCGUGGCUGUGGGCCGAUUAGUUUCUAUUGCCGGAGCUUCUUUCUACUUUUGUCGCGGAUGCAGACAGGAAAGGAUCUGCUCCGUUCCCAUAU .....((((....))))(((((((....((((((((((((((....))))))))))))))(((((((.......)))))))...)))))))....((((((..((......))......((((((((((((((.....((((((....)).))))))))))))...))))))..)))))). (-70.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1005 130 81 221 172 NC_002950:PG2081|5end_biotin_synthetase_2181661..2181891_NEGATIVE 424 169 122 152 112 NC_002950:PG0248|5end_translation_initation_factor_SUI1,_putative_281842..282072_NEGATIVE 404 160 121 50 1 NC_002950:PG0018|5end_hypothetical_protein_19648..19878_POSITIVE 393 167 122 68 32 NC_002950:PG0309|5end_thiamine_biosynthesis_lipoprotein_ApbE_345023..345253_NEGATIVE 390 170 122 108 60 NC_002950:PG1251|5end_hypothetical_protein_1327779..1328009_POSITIVE 388 166 125 169 130 NC_002950:PG1024|5end_hypothetical_protein_1086698..1086928_POSITIVE 379 110 62 72 27 NC_002950:PG0441|5end_hypothetical_protein_478734..478964_POSITIVE 378 166 123 221 163 NC_002950:PG1600|5end_hypothetical_protein_1680984..1681214_NEGATIVE 371 154 117 52 12 NC_002950:PG1395|5end_cell_shape-determining_protein_MreC,_putative_1477669..1477899_NEGATIVE 370 167 123 89 55 NC_002950:PG1256|5end_ribonuclease,_Rne/Rng_family_1334262..1334492_NEGATIVE 368 167 121 74 20 NC_002950:PG1103|5end_ATPase,_AAA_family_1173605..1173835_POSITIVE 368 175 131 61 8 NC_002950:PG0671|5end_iron_compound_ABC_transporter,_permease_protein_721888..722118_POSITIVE 368 66 22 209 150 NC_002950:PG0037|5end_50S_ribosomal_protein_L19_46519..46749_POSITIVE 367 166 125 197 159 NC_002950:PG0628|5end_ABC_transporter,_ATP-binding_protein_682439..682669_NEGATIVE 365 167 123 69 13 NC_002950:PG1009|5end_hypothetical_protein_1068495..1068725_NEGATIVE 363 167 123 50 4 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 362 166 123 162 109 NC_002950:PG2070|5end_hypothetical_protein_2165541..2165771_POSITIVE 360 168 124 212 152 NC_002950:PG0364|5end_hypothetical_protein_399615..399845_NEGATIVE 358 167 125 228 183 NC_002950:PG2112|5end_hypothetical_protein_2221471..2221701_POSITIVE 357 167 126 89 47 NC_002950:PG1837|5end_hemagglutinin_protein_HagA_1930337..1930567_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 445 157 111 68 11 NC_002950:PG0775|3end_acyl-CoA_dehydrogenase_family_protein_827432..827582_NEGATIVE 424 169 122 55 15 NC_002950:PG0249|3end_oxaloacetate_decarboxylase,_putative_281939..282089_NEGATIVE 413 167 122 47 1 NC_002950:PG0670|3end_lipoprotein,_putative_721971..722121_POSITIVE 403 166 122 73 28 NC_002950:PG1321|3end_formate--tetrahydrofolate_ligase_1399656..1399806_NEGATIVE 395 160 125 46 8 NC_002950:PG0017|3end_sensor_histidine_kinase_19724..19874_POSITIVE 394 150 101 62 1 NC_002950:PG1786|3end_hypothetical_protein_1875322..1875472_POSITIVE 393 167 122 71 35 NC_002950:PG0310|3end_nitroreductase_family_protein_345020..345170_NEGATIVE 385 167 122 82 26 NC_002950:PG2177|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_F_2285266..2285416_NEGATIVE 379 110 62 68 23 NC_002950:PG0439|3end_hypothetical_protein_478810..478960_POSITIVE 376 166 121 60 2 NC_002950:PG1950|3end_hypothetical_protein_2040840..2040990_POSITIVE 373 154 122 59 29 NC_002950:PG1055|3end_thiol_protease_1121202..1121352_NEGATIVE 367 160 113 63 27 NC_002950:PG0694|3end_immunoreactive_42_kDa_antigen_PG33_749703..749853_NEGATIVE 367 166 125 138 100 NC_002950:PG0629|3end_inorganic_polyphosphate/ATP-NAD_kinase_682498..682648_NEGATIVE 363 167 123 150 104 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 362 166 123 150 97 NC_002950:PG2069|3end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_2165609..2165759_POSITIVE 361 169 122 78 25 NC_002950:PG1004|3end_prolyl_oligopeptidase_family_protein_1060433..1060583_NEGATIVE 354 167 125 131 95 NC_002950:PG1714|3end_pyridoxamine-phosphate_oxidase_1801848..1801998_NEGATIVE 354 167 122 98 51 NC_002950:PG0678|3end_pyrazinamidase/nicotinamidase,_putative_729471..729621_POSITIVE 352 119 76 47 3 NC_002950:PG0735|3end_aminotransferase,_class_V_785677..785827_POSITIVE 350 97 58 119 68 NC_002950:PG1858|3end_flavodoxin_1956538..1956688_NEGATIVE