Origin IGS: ctgtaagcgacatccattccaatataaacgaaaaggactgtcaaaggagcttggagctctttggcagtcctctttcttttggcattcacccaaccttaccggactaaatgatcactgaggaatccactcgcaaatatcgaaaaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcttttcgatatttgcgagtggattcctcagtgatcatttagtccggtaaggttgggtgaatgccaaaagaaagaggactgccaaagagctccaagctcctttgacagtccttttcgtttatattggaatggatgtcgcttacag Mask Tandem Repeat Region ================================================ ctgtaagcgacatccattccaatataaacgaaaaggactgtcaaaggagcttggagctctttggcagtcctctttcttttggcattcacccaaccttaccggactaaatgatcactgaggaatccactcgcaaatatcgaaaaga Find is-nt database================================================ Query_seq: PG1332:PG1333|PG1332:PG1333:NAD(P) transhydrogenase, beta subunit:hypothetical protein:-><-:1414171..1414315 145 ctgtaagcgacatccattccaatataaacgaaaaggactgtcaaaggagcttggagctctttggcagtcctctttcttttggcattcacccaaccttaccggactaaatgatcactgaggaatccactcgcaaatatcgaaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1332:PG1333|PG1332:PG1333:NAD(P) transhydrogenase, beta subunit:hypothetical protein:-><-:1414171..1414315 145 ctgtaagcgacatccattccaatataaacgaaaaggactgtcaaaggagcttggagctctttggcagtcctctttcttttggcattcacccaaccttaccggactaaatgatcactgaggaatccactcgcaaatatcgaaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1332:PG1333|PG1332:PG1333:NAD(P) transhydrogenase, beta subunit:hypothetical protein:-><-:1414171..1414315 145 ctgtaagcgacatccattccaatataaacgaaaaggactgtcaaaggagcttggagctctttggcagtcctctttcttttggcattcacccaaccttaccggactaaatgatcactgaggaatccactcgcaaatatcgaaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgtaagcgacatccattccaatataaacgaaaaggactgtcaaaggagcttggagctctttggcagtcctctttcttttggcattcacccaaccttaccggactaaatgatcactgaggaatccactcgcaaatatcgaaaaga Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 12 End: 104 ........... M H S N I N E K D C Q R S L E L F G S P L S F G I H P T L P D ......................................... Protein_Len: 31 Strand: - Start: 1 End: 93 Q L R C G N W Y L R F P S D F S S P A R Q C D E K K Q C E G M .................................................... ctgtaagcgacatccattccaatataaacgaaaaggactgtcaaaggagcttggagctctttggcagtcctctttcttttggcattcacccaaccttaccggactaaatgatcactgaggaatccactcgcaaatatcgaaaaga Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 16 End: 45 ...............TTTGACAGTCCTTTTCGTTTATATTGGAAT.................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctgtaagcgacatccattccaatataaacgaaaaggactgtcaaaggagcttggagctctttggcagtcctctttcttttggcattcacccaaccttaccggactaaatgatcactgaggaatccactcgcaaatatcgaaaaga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -16.3 Tail_Score: -4.19238 Start: 30 End: 76 Full_Region: CATTCCAATATAAAC GAAAAGGACTGTCAAAGGAGCT TGG AGCTCTTTGGCAGTCCTCTTTC TTTTGGCATTCACCC .............................GAAAAGGACTGTCAAAGGAGCTTGGAGCTCTTTGGCAGTCCTCTTTC..................................................................... TransTerm Strand: + Conf: 100 HP_score: -13.8 Tail_Score: -4.68655 Start: 33 End: 72 Full_Region: TCCAATATAAACGAA AAGGACTGTCAAAGGAGCT TGG AGCTCTTTGGCAGTCCTC TTTCTTTTGGCATTC ................................AAGGACTGTCAAAGGAGCTTGGAGCTCTTTGGCAGTCCTC......................................................................... TransTerm Strand: + Conf: 100 HP_score: -16.4 Tail_Score: -3.94471 Start: 35 End: 70 Full_Region: CAATATAAACGAAAA GGACTGTCAAAGGAGCT TGG AGCTCTTTGGCAGTCC TCTTTCTTTTGGCAT ..................................GGACTGTCAAAGGAGCTTGGAGCTCTTTGGCAGTCC........................................................................... TransTerm Strand: - Conf: 100 HP_score: -14.2 Tail_Score: -4.67563 Start: 35 End: 70 Full_Region: atgccaaaagaaaga ggactgccaaagagct cca agctcctttgacagtcc ttttcgtttatattg ..................................ggactgccaaagagctccaagctcctttgacagtcc........................................................................... Find igs database================================================ Query_seq: PG1332:PG1333|PG1332:PG1333:NAD(P) transhydrogenase, beta subunit:hypothetical protein:-><-:1414171..1414315 145 ctgtaagcgacatccattccaatataaacgaaaaggactgtcaaaggagcttggagctctttggcagtcctctttcttttggcattcacccaaccttaccggactaaatgatcactgaggaatccactcgcaaatatcgaaaaga Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: NC_002950_PG1332_PG1333|NAD(P) transhydrogenase, beta subunit:hypothetical protein|POSITIVE:NEGATIVE|[1414171,1414315]|145 HSP 1 e-value: 5.0E-77 bit: 287.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 145 ctgtaagcgacatccattccaatataaacgaaaaggactgtcaaaggagcttggagctctttggcagtcctctttcttttggcattcacccaaccttaccggactaaatgatcactgaggaatccactcgcaaatatcgaaaaga ctgtaagcgacatccattccaatataaacgaaaaggactgtcaaaggagcttggagctctttggcagtcctctttcttttggcattcacccaaccttaccggactaaatgatcactgaggaatccactcgcaaatatcgaaaaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUAAGCGACAUCCAUUCCAAUAUAAACGAAAAGGACUGUCAAAGGAGCUUGGAGCUCUUUGGCAGUCCUCUUUCUUUUGGCAUUCACCCAACCUUACCGGACUAAAUGAUCACUGAGGAAUCCACUCGCAAAUAUCGAAAAGA ......((((.....(((((.........(((((((((((((((((.(((.....)))))))))))))))).))))...(((((((...((.........))....)))).)))....)))))....)))).............. (-39.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUUCGAUAUUUGCGAGUGGAUUCCUCAGUGAUCAUUUAGUCCGGUAAGGUUGGGUGAAUGCCAAAAGAAAGAGGACUGCCAAAGAGCUCCAAGCUCCUUUGACAGUCCUUUUCGUUUAUAUUGGAAUGGAUGUCGCUUACAG (((.((((.......)))).)))......(((((.((((((.(((((((......(((....)))....(((.((((((((.((((((((.....))).))))).))))))))))).....))))))).)))))))))))..... (-46.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 370 77 34 216 172 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 364 90 48 177 133 NC_002950:PG0307|5end_NADH-ubiquinone_oxidoreductase_342560..342790_POSITIVE 347 88 50 90 46 NC_002950:PG1930|5end_50S_ribosomal_protein_L29_2020409..2020639_NEGATIVE 335 82 49 200 165 NC_002950:PG0165|5end_heat_shock_protein_15_187807..188037_NEGATIVE 334 69 24 217 170 NC_002950:PG2034|5end_oxidoreductase,_FAD-binding,_putative_2135701..2135931_NEGATIVE 332 130 81 226 191 NC_002950:PG1853|5end_DNA_polymerase_III,_beta_subunit_1953119..1953349_NEGATIVE 330 94 53 216 171 NC_002950:PG1837|5end_hemagglutinin_protein_HagA_1930337..1930567_POSITIVE 329 90 46 202 142 NC_002950:PG2092|5end_hypothetical_protein_2192910..2193140_NEGATIVE 327 106 64 214 169 NC_002950:PG1395|5end_cell_shape-determining_protein_MreC,_putative_1477669..1477899_NEGATIVE 326 129 81 211 168 NC_002950:PG1911|5end_DNA-directed_RNA_polymerase_alpha_subunit_2011762..2011992_NEGATIVE 324 119 79 183 143 NC_002950:PG0622|5end_hypothetical_protein_675937..676167_POSITIVE 320 80 38 204 151 NC_002950:PG0076|5end_N-acetylmuramoyl-L-alanine_amidase,_family_4_91333..91563_NEGATIVE 319 84 49 90 55 NC_002950:PG1027|5end_hypothetical_protein_1089439..1089669_NEGATIVE 318 74 35 88 39 NC_002950:PG0164|5end_hypothetical_protein_187395..187625_NEGATIVE 315 110 64 145 99 NC_002950:PG0068|5end_hypothetical_protein_81748..81978_POSITIVE 314 86 45 217 177 NC_002950:PG2136|5end_hypothetical_protein_2243360..2243590_POSITIVE 309 78 38 134 96 NC_002950:PG0216|5end_hypothetical_protein_251956..252186_POSITIVE 307 70 23 214 158 NC_002950:PG1739|5end_hypothetical_protein_1825709..1825939_NEGATIVE 307 82 46 61 25 NC_002950:PG1540|5end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_1619277..1619507_POSITIVE 306 90 49 227 184 NC_002950:PG0227|5end_DNA_repair_protein_RadA_263978..264208_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 494 76 34 61 20 NC_002950:PG1332|3end_NAD(P)_transhydrogenase,_beta_subunit_1414110..1414260_POSITIVE 365 90 46 57 4 NC_002950:PG2032|3end_primosomal_protein_N'_2130868..2131018_NEGATIVE 347 88 50 84 40 NC_002950:PG1931|3end_50S_ribosomal_protein_L16_2020415..2020565_NEGATIVE 318 74 35 113 64 NC_002950:PG0165|3end_heat_shock_protein_15_187370..187520_NEGATIVE 317 102 61 131 91 NC_002950:PG1276|3end_DNA-binding_protein,_histone-like_family_1353531..1353681_POSITIVE 317 102 61 131 91 NC_002950:PG0566|3end_DNA-binding_protein,_histone-like_family_622935..623085_NEGATIVE 313 80 34 85 42 NC_002950:PG0788|3end_hypothetical_protein_838043..838193_NEGATIVE 309 78 38 126 88 NC_002950:PG0215|3end_hypothetical_protein_252028..252178_POSITIVE 307 70 23 67 11 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 303 70 28 86 42 NC_002950:PG0725|3end_hydrolase,_haloacid_dehalogenase-like_family_777966..778116_POSITIVE 301 140 91 51 11 NC_002950:PG1112|3end_hypothetical_protein_1185571..1185721_POSITIVE 292 130 81 145 106 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 290 105 63 146 98 NC_002950:PG2086|3end_hypothetical_protein_2187070..2187220_POSITIVE 290 103 62 65 9 NC_002950:PG2017|3end_hypothetical_protein_2108345..2108495_NEGATIVE 290 104 62 68 30 NC_002950:PG1697|3end_type_II_restriction_endonuclease,_putative_1785074..1785224_POSITIVE 289 75 35 130 70 NC_002950:PG0246|3end_hypothetical_protein_281050..281200_NEGATIVE 287 76 38 136 96 NC_002950:PG2117|3end_30S_ribosomal_protein_S16_2225235..2225385_NEGATIVE 287 105 70 73 34 NC_002950:PG0071|3end_UDP-3-O-acyl-GlcNAc_deacetylase/beta-hydroxyacyl-[acyl_carrier_protein]_dehydratase_FabZ_84731..84881_NEGATIVE 287 105 61 87 49 NC_002950:PG0034|3end_thioredoxin_42235..42385_NEGATIVE 285 110 63 111 54 NC_002950:PG0815|3end_hypothetical_protein_876447..876597_POSITIVE