Origin IGS: gaatccgccatcttcgggcaaatcggggatgtcattcagccagtcataagtgctgagcggctggctatgacaccccttgcaggcatccttcgtcagggaggtcgtcgtattgtctaatcggtagtccatccgtcttttgctttgtccggcgtagtcctctagtgctgctgataggaggaggtataaatcataaccgccacatcatgcgagcaggtactatccaccggtgtgcggga .........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 tcccgcacaccggtggatagtacctgctcgcatgatgtggcggttatgatttatacctcctcctatcagcagcactagaggactacgccggacaaagcaaaagacggatggactaccgattagacaatacgacgacctccctgacgaaggatgcctgcaaggggtgtcatagccagccgctcagcacttatgactggctgaatgacatccccgatttgcccgaagatggcggattc Mask Tandem Repeat Region ================================================ gaatccgccatcttcgggcaaatcggggatgtcattcagccagtcataagtgctgagcggctggctatgacaccccttgcaggcatccttcgtcagggaggtcgtcgtattgtctaatcggtagtccatccgtcttttgctttgtccggcgtagtcctctagtgctgctgataggaggaggtataaatcataaccgccacatcatgcgagcaggtactatccaccggtgtgcggga Find is-nt database================================================ Query_seq: PG0400:PG0401|PG0400:PG0401:hypothetical protein:hypothetical protein:<-<-:437619..437854 236 gaatccgccatcttcgggcaaatcggggatgtcattcagccagtcataagtgctgagcggctggctatgacaccccttgcaggcatccttcgtcagggaggtcgtcgtattgtctaatcggtagtccatccgtcttttgctttgtccggcgtagtcctctagtgctgctgataggaggaggtataaatcataaccgccacatcatgcgagcaggtactatccaccggtgtgcggga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0400:PG0401|PG0400:PG0401:hypothetical protein:hypothetical protein:<-<-:437619..437854 236 gaatccgccatcttcgggcaaatcggggatgtcattcagccagtcataagtgctgagcggctggctatgacaccccttgcaggcatccttcgtcagggaggtcgtcgtattgtctaatcggtagtccatccgtcttttgctttgtccggcgtagtcctctagtgctgctgataggaggaggtataaatcataaccgccacatcatgcgagcaggtactatccaccggtgtgcggga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0400:PG0401|PG0400:PG0401:hypothetical protein:hypothetical protein:<-<-:437619..437854 236 gaatccgccatcttcgggcaaatcggggatgtcattcagccagtcataagtgctgagcggctggctatgacaccccttgcaggcatccttcgtcagggaggtcgtcgtattgtctaatcggtagtccatccgtcttttgctttgtccggcgtagtcctctagtgctgctgataggaggaggtataaatcataaccgccacatcatgcgagcaggtactatccaccggtgtgcggga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaatccgccatcttcgggcaaatcggggatgtcattcagccagtcataagtgctgagcggctggctatgacaccccttgcaggcatccttcgtcagggaggtcgtcgtattgtctaatcggtagtccatccgtcttttgctttgtccggcgtagtcctctagtgctgctgataggaggaggtataaatcataaccgccacatcatgcgagcaggtactatccaccggtgtgcggga Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 10 End: 114 ......... M F G Q I G D V I Q P V I S A E R L A M T P L A G I L R Q G G R R I V .......................................................................................................................... Protein_Len: 40 Strand: + Start: 117 End: 236 .................................................................................................................... M G S P S V F C F V R R S P L V L L I G G G I N H N R H I M R A G T I H R C A G Protein_Len: 39 Strand: - Start: 68 End: 184 ................................................................... S V G Q L C G E D P L D D Y Q R I P L G D T K Q K T R R L G R T S S I P P P M .................................................... Protein_Len: 43 Strand: - Start: 1 End: 129 F G G D E P L D P I D N L W D Y T S L P Q S H C G K C A D K T L S T T T N D L R Y D M ........................................................................................................... gaatccgccatcttcgggcaaatcggggatgtcattcagccagtcataagtgctgagcggctggctatgacaccccttgcaggcatccttcgtcagggaggtcgtcgtattgtctaatcggtagtccatccgtcttttgctttgtccggcgtagtcctctagtgctgctgataggaggaggtataaatcataaccgccacatcatgcgagcaggtactatccaccggtgtgcggga 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================================================ gaatccgccatcttcgggcaaatcggggatgtcattcagccagtcataagtgctgagcggctggctatgacaccccttgcaggcatccttcgtcagggaggtcgtcgtattgtctaatcggtagtccatccgtcttttgctttgtccggcgtagtcctctagtgctgctgataggaggaggtataaatcataaccgccacatcatgcgagcaggtactatccaccggtgtgcggga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0400:PG0401|PG0400:PG0401:hypothetical protein:hypothetical protein:<-<-:437619..437854 236 gaatccgccatcttcgggcaaatcggggatgtcattcagccagtcataagtgctgagcggctggctatgacaccccttgcaggcatccttcgtcagggaggtcgtcgtattgtctaatcggtagtccatccgtcttttgctttgtccggcgtagtcctctagtgctgctgataggaggaggtataaatcataaccgccacatcatgcgagcaggtactatccaccggtgtgcggga Intra-Species Hit: Count: 1 Min: 1 Max: 236 Len: 236 Subject: NC_002950_PG0400_PG0401|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[437619,437854]|236 HSP 1 e-value: 1.0E-131 bit: 468.0 Len: 236 Query Start:1 Query End:236 Subject Strand: POSITIVE Subject Start: 1 Subject End: 236 gaatccgccatcttcgggcaaatcggggatgtcattcagccagtcataagtgctgagcggctggctatgacaccccttgcaggcatccttcgtcagggaggtcgtcgtattgtctaatcggtagtccatccgtcttttgctttgtccggcgtagtcctctagtgctgctgataggaggaggtataaatcataaccgccacatcatgcgagcaggtactatccaccggtgtgcggga gaatccgccatcttcgggcaaatcggggatgtcattcagccagtcataagtgctgagcggctggctatgacaccccttgcaggcatccttcgtcagggaggtcgtcgtattgtctaatcggtagtccatccgtcttttgctttgtccggcgtagtcctctagtgctgctgataggaggaggtataaatcataaccgccacatcatgcgagcaggtactatccaccggtgtgcggga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUCCGCCAUCUUCGGGCAAAUCGGGGAUGUCAUUCAGCCAGUCAUAAGUGCUGAGCGGCUGGCUAUGACACCCCUUGCAGGCAUCCUUCGUCAGGGAGGUCGUCGUAUUGUCUAAUCGGUAGUCCAUCCGUCUUUUGCUUUGUCCGGCGUAGUCCUCUAGUGCUGCUGAUAGGAGGAGGUAUAAAUCAUAACCGCCACAUCAUGCGAGCAGGUACUAUCCACCGGUGUGCGGGA ...(((((((((...((((((...((((.((((((..((((((((.............)))))))))))))))))).....(((..(((((.....)))))..)))...))))))....((((((((....(..((.((((((.(((..(((((..(....)..)))).)...))).)))))).))..).....(((........)))....)).))))))....)))).))))). (-83.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCCGCACACCGGUGGAUAGUACCUGCUCGCAUGAUGUGGCGGUUAUGAUUUAUACCUCCUCCUAUCAGCAGCACUAGAGGACUACGCCGGACAAAGCAAAAGACGGAUGGACUACCGAUUAGACAAUACGACGACCUCCCUGACGAAGGAUGCCUGCAAGGGGUGUCAUAGCCAGCCGCUCAGCACUUAUGACUGGCUGAAUGACAUCCCCGAUUUGCCCGAAGAUGGCGGAUUC ....(((..((((((..((((.((((((.((.(((((.((.(((..........))).))...)))))))))).....))))))))))))).....(((.....(((........))).....................(((.....))).))).)))..((((((((((...((((((.(((.......))).)))))).)))))))))).((((((((.......)))))))). (-73.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1140 100 51 191 142 NC_002950:PG0400|5end_hypothetical_protein_437528..437758_NEGATIVE 439 107 61 174 116 NC_002950:PG1226|5end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_1303264..1303494_POSITIVE 428 180 132 105 54 NC_002950:PG1006|5end_hypothetical_protein_1066478..1066708_NEGATIVE 415 158 113 96 36 NC_002950:PG2010|5end_phosphomannomutase,_putative_2099220..2099450_POSITIVE 415 137 91 144 89 NC_002950:PG0039|5end_hypothetical_protein_47637..47867_POSITIVE 414 98 51 54 10 NC_002950:PG0491|5end_hypothetical_protein_532184..532414_POSITIVE 409 160 119 215 168 NC_002950:PG0227|5end_DNA_repair_protein_RadA_263978..264208_NEGATIVE 407 50 6 187 135 NC_002950:PG0955|5end_hypothetical_protein_1014832..1015062_POSITIVE 405 65 25 180 131 NC_002950:PG1794|5end_DNA_polymerase_type_I_1885978..1886208_POSITIVE 403 99 52 173 118 NC_002950:PG0086|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_102359..102589_NEGATIVE 402 60 11 159 117 NC_002950:PG0423|5end_hypothetical_protein_462251..462481_POSITIVE 398 127 81 174 133 NC_002950:PG1612|5end_methylmalonyl-CoA_decarboxylase,_alpha_subunit_1693065..1693295_NEGATIVE 396 107 61 56 6 NC_002950:PG1343|5end_lipoate-protein_ligase_B_1423628..1423858_POSITIVE 395 109 61 53 6 NC_002950:PG1483|5end_conjugative_transposon_protein_TraE_1559085..1559315_NEGATIVE 395 99 58 174 133 NC_002950:PG0018|5end_hypothetical_protein_19648..19878_POSITIVE 385 68 24 223 180 NC_002950:PG1269|5end_delta-1-pyrroline-5-carboxylate_dehydrogenase_1349201..1349431_NEGATIVE 383 107 61 159 103 NC_002950:PG0607|5end_hypothetical_protein_662552..662782_POSITIVE 375 178 131 123 71 NC_002950:PG1027|5end_hypothetical_protein_1089439..1089669_NEGATIVE 374 100 51 181 127 NC_002950:PG0229|5end_hypothetical_protein_264872..265102_POSITIVE 373 168 124 63 4 NC_002950:PG0946|5end_ABC_transporter,_ATP-binding_protein_1007396..1007626_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 428 180 132 65 14 NC_002950:PG1007|3end_transcriptional_regulator,_GntR_family_1066518..1066668_NEGATIVE 405 65 25 130 81 NC_002950:PG1793|3end_1,4-alpha-glucan_branching_enzyme_1886008..1886158_POSITIVE 398 127 81 75 34 NC_002950:PG1613|3end_glyoxalase_family_protein_1693164..1693314_NEGATIVE 395 83 43 127 90 NC_002950:PG1649|3end_hypothetical_protein_1730030..1730180_NEGATIVE 395 98 58 38 3 NC_002950:PG0490|3end_hypothetical_protein_532248..532398_POSITIVE 390 98 52 149 105 NC_002950:PG1225|3end_ABC_transporter,_ATP-binding_protein_1303336..1303486_POSITIVE 385 68 24 146 103 NC_002950:PG1270|3end_hypothetical_protein_1349278..1349428_NEGATIVE 384 98 52 80 39 NC_002950:PG1630|3end_hypothetical_protein_1712142..1712292_POSITIVE 373 168 124 60 1 NC_002950:PG0947|3end_hypothetical_protein_1007399..1007549_NEGATIVE 371 130 82 83 22 NC_002950:PG1490|3end_TraG_family_protein_1565504..1565654_POSITIVE 369 100 51 112 58 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 369 116 72 134 87 NC_002950:PG1027|3end_hypothetical_protein_1089197..1089347_NEGATIVE 368 177 133 47 3 NC_002950:PG1410|3end_hypothetical_protein_1493436..1493586_POSITIVE 367 177 134 112 67 NC_002950:PG2208|3end_hypothetical_protein_2320332..2320482_NEGATIVE 367 170 127 98 47 NC_002950:PG0380|3end_excinuclease_ABC_subunit_B_411218..411368_POSITIVE 367 159 112 82 18 NC_002950:PG0204|3end_hypothetical_protein_240262..240412_NEGATIVE 360 41 6 56 18 NC_002950:PG0312|3end_hypothetical_protein_346509..346659_NEGATIVE 357 140 91 141 89 NC_002950:PG2086|3end_hypothetical_protein_2187070..2187220_POSITIVE 357 148 101 132 72 NC_002950:PG0099|3end_phenylalanyl-tRNA_synthetase_beta_subunit_115827..115977_NEGATIVE 356 70 23 151 95 NC_002950:PG1290|3end_branched-chain_amino_acid_aminotransferase_1369352..1369502_POSITIVE