Origin IGS: ttcgcgctatttcttaattatacaacgaagctactactatcttaccgtgcagtagcttcgttgtgtattatataatagtatcgaacagcgaacagccttgccttgagagagggggagggctgttcgctttcttttggatcgggccgatttgaggactgaataggaaataaatgttttataagacaaatcaataagatgcagatgagaacatttcgtgtcgttgcgatcgtttcgctgatcttttcttcttgg .........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 ccaagaagaaaagatcagcgaaacgatcgcaacgacacgaaatgttctcatctgcatcttattgatttgtcttataaaacatttatttcctattcagtcctcaaatcggcccgatccaaaagaaagcgaacagccctccccctctctcaaggcaaggctgttcgctgttcgatactattatataatacacaacgaagctactgcacggtaagatagtagtagcttcgttgtataattaagaaatagcgcgaa Mask Tandem Repeat Region ================================================ ttcgcgctatttcttaattatacaacgaagctactactatcttaccgtgcagtagcttcgttgtgtattatataatagtatcgaacagcgaacagccttgccttgagagagggggagggctgttcgctttcttttggatcgggccgatttgaggactgaataggaaataaatgttttataagacaaatcaataagatgcagatgagaacatttcgtgtcgttgcgatcgtttcgctgatcttttcttcttgg Find is-nt database================================================ Query_seq: PG0121:PG0123|PG0121:PG0123:DNA-binding protein HU:hypothetical protein:->->:144875..145126 252 ttcgcgctatttcttaattatacaacgaagctactactatcttaccgtgcagtagcttcgttgtgtattatataatagtatcgaacagcgaacagccttgccttgagagagggggagggctgttcgctttcttttggatcgggccgatttgaggactgaataggaaataaatgttttataagacaaatcaataagatgcagatgagaacatttcgtgtcgttgcgatcgtttcgctgatcttttcttcttgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0121:PG0123|PG0121:PG0123:DNA-binding protein HU:hypothetical protein:->->:144875..145126 252 ttcgcgctatttcttaattatacaacgaagctactactatcttaccgtgcagtagcttcgttgtgtattatataatagtatcgaacagcgaacagccttgccttgagagagggggagggctgttcgctttcttttggatcgggccgatttgaggactgaataggaaataaatgttttataagacaaatcaataagatgcagatgagaacatttcgtgtcgttgcgatcgtttcgctgatcttttcttcttgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0121:PG0123|PG0121:PG0123:DNA-binding protein HU:hypothetical protein:->->:144875..145126 252 ttcgcgctatttcttaattatacaacgaagctactactatcttaccgtgcagtagcttcgttgtgtattatataatagtatcgaacagcgaacagccttgccttgagagagggggagggctgttcgctttcttttggatcgggccgatttgaggactgaataggaaataaatgttttataagacaaatcaataagatgcagatgagaacatttcgtgtcgttgcgatcgtttcgctgatcttttcttcttgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcgcgctatttcttaattatacaacgaagctactactatcttaccgtgcagtagcttcgttgtgtattatataatagtatcgaacagcgaacagccttgccttgagagagggggagggctgttcgctttcttttggatcgggccgatttgaggactgaataggaaataaatgttttataagacaaatcaataagatgcagatgagaacatttcgtgtcgttgcgatcgtttcgctgatcttttcttcttgg Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 39 End: 149 ...................................... M L P C S S F V V Y Y I I V S N S E Q P C L E R G G G L F A F F W I G P I ....................................................................................................... Protein_Len: 31 Strand: + Start: 160 End: 252 ............................................................................................................................................................... M G N K C F I R Q I N K M Q M R T F R V V A I V S L I F S S W Protein_Len: 34 Strand: - Start: 71 End: 172 ...................................................................... I I T D F L S C G Q R S L P P P S N A K K Q I P G I Q P S F L F Y M ................................................................................ Protein_Len: 60 Strand: - Start: 45 End: 239 ............................................ N H I I Y Y Y R V A F L R A K L S P S P Q E S E K P D P R N S S Q I P F L H K I L C I L L I C I L V N R T T A I T E S M ............. Protein_Len: 54 Strand: - Start: 40 End: 201 ....................................... R V T C Y S R Q T N Y L L I S C R V A K G Q S L P L A T R K R K S R A S K L V S Y S I F T K Y S L D I L H M ................................................... ttcgcgctatttcttaattatacaacgaagctactactatcttaccgtgcagtagcttcgttgtgtattatataatagtatcgaacagcgaacagccttgccttgagagagggggagggctgttcgctttcttttggatcgggccgatttgaggactgaataggaaataaatgttttataagacaaatcaataagatgcagatgagaacatttcgtgtcgttgcgatcgtttcgctgatcttttcttcttgg 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================================================ ttcgcgctatttcttaattatacaacgaagctactactatcttaccgtgcagtagcttcgttgtgtattatataatagtatcgaacagcgaacagccttgccttgagagagggggagggctgttcgctttcttttggatcgggccgatttgaggactgaataggaaataaatgttttataagacaaatcaataagatgcagatgagaacatttcgtgtcgttgcgatcgtttcgctgatcttttcttcttgg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 88 HP_score: -11.3 Tail_Score: -3.56987 Start: 19 End: 67 Full_Region: GCGCTATTTCTTAAT TATACAACGAAGCTACTAC TATCTTACCGT GCAGTAGCTTCGTTGTGTA TTATATAATAGTATC ..................TATACAACGAAGCTACTACTATCTTACCGTGCAGTAGCTTCGTTGTGTA......................................................................................................................................................................................... TransTerm Strand: - Conf: 81 HP_score: -12.1 Tail_Score: -2.90392 Start: 23 End: 63 Full_Region: ctattatataataca caacgaagctactgc acggtaagata gtagtagcttcgttg tataattaagaaata ......................caacgaagctactgcacggtaagatagtagtagcttcgttg............................................................................................................................................................................................. TransTerm Strand: + Conf: 60 HP_score: -5.8 Tail_Score: -3.74975 Start: 26 End: 60 Full_Region: TTCTTAATTATACAA CGAAGCTACTAC TATCTTACCGT GCAGTAGCTTCG TTGTGTATTATATAA .........................CGAAGCTACTACTATCTTACCGTGCAGTAGCTTCG................................................................................................................................................................................................ TransTerm Strand: - Conf: 68 HP_score: -8.0 Tail_Score: -3.59946 Start: 26 End: 60 Full_Region: ttatataatacacaa cgaagctactgc acggtaagata gtagtagcttcg ttgtataattaagaa .........................cgaagctactgcacggtaagatagtagtagcttcg................................................................................................................................................................................................ TransTerm Strand: - Conf: 60 HP_score: -6.7 Tail_Score: -3.14146 Start: 86 End: 129 Full_Region: gcccgatccaaaaga aagcgaacagccctccc cctctctcaa ggcaaggctgttcgctg ttcgatactattata .....................................................................................aagcgaacagccctccccctctctcaaggcaaggctgttcgctg........................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -12.9 Tail_Score: -4.68908 Start: 88 End: 127 Full_Region: TAATAGTATCGAACA GCGAACAGCCTTGCCTT GAGAGA GGGGGAGGGCTGTTCGC TTTCTTTTGGATCGG .......................................................................................GCGAACAGCCTTGCCTTGAGAGAGGGGGAGGGCTGTTCGC............................................................................................................................. TransTerm Strand: - Conf: 70 HP_score: -9.3 Tail_Score: -3.12482 Start: 88 End: 127 Full_Region: ccgatccaaaagaaa gcgaacagccctccc cctctctcaa ggcaaggctgttcgc tgttcgatactatta .......................................................................................gcgaacagccctccccctctctcaaggcaaggctgttcgc............................................................................................................................. Find igs database================================================ Query_seq: PG0121:PG0123|PG0121:PG0123:DNA-binding protein HU:hypothetical protein:->->:144875..145126 252 ttcgcgctatttcttaattatacaacgaagctactactatcttaccgtgcagtagcttcgttgtgtattatataatagtatcgaacagcgaacagccttgccttgagagagggggagggctgttcgctttcttttggatcgggccgatttgaggactgaataggaaataaatgttttataagacaaatcaataagatgcagatgagaacatttcgtgtcgttgcgatcgtttcgctgatcttttcttcttgg Intra-Species Hit: Count: 1 Min: 1 Max: 252 Len: 252 Subject: NC_002950_PG0121_PG0123|DNA-binding protein HU:hypothetical protein|POSITIVE:POSITIVE|[144875,145126]|252 HSP 1 e-value: 1.0E-140 bit: 500.0 Len: 252 Query Start:1 Query End:252 Subject Strand: POSITIVE Subject Start: 1 Subject End: 252 ttcgcgctatttcttaattatacaacgaagctactactatcttaccgtgcagtagcttcgttgtgtattatataatagtatcgaacagcgaacagccttgccttgagagagggggagggctgttcgctttcttttggatcgggccgatttgaggactgaataggaaataaatgttttataagacaaatcaataagatgcagatgagaacatttcgtgtcgttgcgatcgtttcgctgatcttttcttcttgg ttcgcgctatttcttaattatacaacgaagctactactatcttaccgtgcagtagcttcgttgtgtattatataatagtatcgaacagcgaacagccttgccttgagagagggggagggctgttcgctttcttttggatcgggccgatttgaggactgaataggaaataaatgttttataagacaaatcaataagatgcagatgagaacatttcgtgtcgttgcgatcgtttcgctgatcttttcttcttgg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCGCGCUAUUUCUUAAUUAUACAACGAAGCUACUACUAUCUUACCGUGCAGUAGCUUCGUUGUGUAUUAUAUAAUAGUAUCGAACAGCGAACAGCCUUGCCUUGAGAGAGGGGGAGGGCUGUUCGCUUUCUUUUGGAUCGGGCCGAUUUGAGGACUGAAUAGGAAAUAAAUGUUUUAUAAGACAAAUCAAUAAGAUGCAGAUGAGAACAUUUCGUGUCGUUGCGAUCGUUUCGCUGAUCUUUUCUUCUUGG ((((.((((((...((((.((((((((((((((((.(...........).))))))))))))))))))))...))))))..)))).(((((((((((((.((((......)))).)))))))))))))...(((..(((((...)))))..)))......((((((.....(((((....))))).......(((((.(((.(((((.....((((......))))...)))))))))))))...)))))). (-85.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCAAGAAGAAAAGAUCAGCGAAACGAUCGCAACGACACGAAAUGUUCUCAUCUGCAUCUUAUUGAUUUGUCUUAUAAAACAUUUAUUUCCUAUUCAGUCCUCAAAUCGGCCCGAUCCAAAAGAAAGCGAACAGCCCUCCCCCUCUCUCAAGGCAAGGCUGUUCGCUGUUCGAUACUAUUAUAUAAUACACAACGAAGCUACUGCACGGUAAGAUAGUAGUAGCUUCGUUGUAUAAUUAAGAAAUAGCGCGAA ............((((.((((.....))))..(((....(((((((.......(((((.....))..))).......)))))))............(....)...)))....))))........(((((((((((.....(((......)))...)))))))))))..(((...(((((.(.((((..((((((((((((((((...........))))))))))))))))...)))).).)))))..))). (-65.14) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 424 149 105 84 44 NC_002950:PG1006|5end_hypothetical_protein_1066478..1066708_NEGATIVE 418 138 92 82 37 NC_002950:PG2227|5end_hypothetical_protein_2342008..2342238_POSITIVE 417 147 101 219 163 NC_002950:PG0226|5end_transglutaminase-related_protein_262531..262761_NEGATIVE 414 147 104 145 103 NC_002950:PG0398|5end_recF_protein_435710..435940_NEGATIVE 410 130 82 152 102 NC_002950:PG0025|5end_fumarylacetoacetate_hydrolase_family_protein_28457..28687_POSITIVE 408 148 103 157 105 NC_002950:PG1782|5end_hypothetical_protein_1870694..1870924_POSITIVE 405 149 113 172 135 NC_002950:PG0464|5end_adenylosuccinate_synthetase_508874..509104_NEGATIVE 399 160 113 83 34 NC_002950:PG2046|5end_hypothetical_protein_2144349..2144579_POSITIVE 394 148 108 180 135 NC_002950:PG2072|5end_UvrD/REP_helicase_domain_protein_2167369..2167599_POSITIVE 387 144 104 207 162 NC_002950:PG1495|5end_DNA_topoisomerase_III_1571243..1571473_POSITIVE 384 137 96 206 161 NC_002950:PG2201|5end_peptide_deformylase_2309412..2309642_NEGATIVE 380 137 94 69 13 NC_002950:PG2109|5end_thiamine-phosphate_pyrophosphorylase_2219452..2219682_NEGATIVE 380 158 111 222 168 NC_002950:PG0585|5end_YqeY_family_protein_643272..643502_POSITIVE 379 126 81 205 156 NC_002950:PG0683|5end_ABC_transporter,_permease_protein,_putative_735255..735485_POSITIVE 374 129 81 214 152 NC_002950:PG0619|5end_alkyl_hydroperoxide_reductase,_F_subunit_671104..671334_POSITIVE 373 129 86 194 144 NC_002950:PG2112|5end_hypothetical_protein_2221471..2221701_POSITIVE 373 146 105 148 110 NC_002950:PG1536|5end_cell_division_protein_FtsX,_putative_1616362..1616592_POSITIVE 373 147 105 65 9 NC_002950:PG0414|5end_hypothetical_protein_453652..453882_NEGATIVE 372 147 105 168 119 NC_002950:PG2107|5end_thiamine_biosynthesis_protein_ThiH_2216658..2216888_NEGATIVE 370 147 102 47 2 NC_002950:PG0135|5end_dimethyladenosine_transferase_157943..158173_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 447 144 101 51 7 NC_002950:PG1055|3end_thiol_protease_1121202..1121352_NEGATIVE 424 149 105 44 4 NC_002950:PG1007|3end_transcriptional_regulator,_GntR_family_1066518..1066668_NEGATIVE 422 139 91 88 28 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 418 138 92 85 40 NC_002950:PG2226|3end_hypothetical_protein_2342091..2342241_POSITIVE 414 147 104 148 106 NC_002950:PG0399|3end_lipoprotein,_putative_435707..435857_NEGATIVE 410 130 82 83 33 NC_002950:PG0024|3end_redox-sensing_transcriptional_repressor_Rex_28468..28618_POSITIVE 408 148 103 115 63 NC_002950:PG1781|3end_uridine_kinase_1870732..1870882_POSITIVE 408 127 87 53 12 NC_002950:PG0452|3end_hypothetical_protein_495106..495256_POSITIVE 405 149 113 143 106 NC_002950:PG0465|3end_ferric_uptake_transcriptional_regulator_508903..509053_NEGATIVE 401 148 101 118 69 NC_002950:PG2091|3end_dihydroneopterin_aldolase_2191610..2191760_POSITIVE 387 144 104 118 73 NC_002950:PG1494|3end_hypothetical_protein_1571234..1571384_POSITIVE 387 147 105 61 9 NC_002950:PG0672|3end_iron_compound_ABC_transporter,_ATP-binding_protein_723840..723990_POSITIVE 384 137 96 101 56 NC_002950:PG2202|3end_Holliday_junction_resolvase-like_protein_2309517..2309667_NEGATIVE 380 137 94 72 16 NC_002950:PG2110|3end_thiamine_biosynthesis_protein_ThiC_2219449..2219599_NEGATIVE 376 147 101 128 59 NC_002950:PG1230|3end_hypothetical_protein_1305960..1306110_NEGATIVE 366 140 92 103 56 NC_002950:PG1847|3end_endoribonuclease_L-PSP,_putative_1946227..1946377_NEGATIVE 366 67 21 72 24 NC_002950:PG0121|3end_DNA-binding_protein_HU_144814..144964_POSITIVE 363 127 86 81 39 NC_002950:PG0148|3end_sigma-54-dependent_transcriptional_regulator_169654..169804_NEGATIVE 361 146 101 127 66 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 355 145 105 124 72 NC_002950:PG2199|3end_ABC_transporter,_ATP-binding_protein,_putative_2304786..2304936_NEGATIVE