Origin IGS: attatggaataattatttatttcttttcggtcgcacaaaggtacgcgtttggctgtgatatacaaatgtcctgtccgaataaatatacgatatgtaatggttgatcgaaaacgtttcttctcttcttgcctccaatatccgatttacttgtcttctcttgagccgtcaggtagccgaaaagagag .........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 ctctcttttcggctacctgacggctcaagagaagacaagtaaatcggatattggaggcaagaagagaagaaacgttttcgatcaaccattacatatcgtatatttattcggacaggacatttgtatatcacagccaaacgcgtacctttgtgcgaccgaaaagaaataaataattattccataat Mask Tandem Repeat Region ================================================ attatggaataattatttatttcttttcggtcgcacaaaggtacgcgtttggctgtgatatacaaatgtcctgtccgaataaatatacgatatgtaatggttgatcgaaaacgtttcttctcttcttgcctccaatatccgatttacttgtcttctcttgagccgtcaggtagccgaaaagagag Find is-nt database================================================ Query_seq: PG1430:PG1431|PG1430:PG1431:TPR domain protein:DNA-binding response regulator, LuxR family:<-<-:1515891..1516075 185 attatggaataattatttatttcttttcggtcgcacaaaggtacgcgtttggctgtgatatacaaatgtcctgtccgaataaatatacgatatgtaatggttgatcgaaaacgtttcttctcttcttgcctccaatatccgatttacttgtcttctcttgagccgtcaggtagccgaaaagagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1430:PG1431|PG1430:PG1431:TPR domain protein:DNA-binding response regulator, LuxR family:<-<-:1515891..1516075 185 attatggaataattatttatttcttttcggtcgcacaaaggtacgcgtttggctgtgatatacaaatgtcctgtccgaataaatatacgatatgtaatggttgatcgaaaacgtttcttctcttcttgcctccaatatccgatttacttgtcttctcttgagccgtcaggtagccgaaaagagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1430:PG1431|PG1430:PG1431:TPR domain protein:DNA-binding response regulator, LuxR family:<-<-:1515891..1516075 185 attatggaataattatttatttcttttcggtcgcacaaaggtacgcgtttggctgtgatatacaaatgtcctgtccgaataaatatacgatatgtaatggttgatcgaaaacgtttcttctcttcttgcctccaatatccgatttacttgtcttctcttgagccgtcaggtagccgaaaagagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attatggaataattatttatttcttttcggtcgcacaaaggtacgcgtttggctgtgatatacaaatgtcctgtccgaataaatatacgatatgtaatggttgatcgaaaacgtttcttctcttcttgcctccaatatccgatttacttgtcttctcttgagccgtcaggtagccgaaaagagag Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 9 End: 101 ........ M I I Y F F S V A Q R Y A F G C D I Q M S C P N K Y T I C N G .................................................................................... Protein_Len: 55 Strand: + Start: 19 End: 183 .................. M S F R S H K G T R L A V I Y K C P V R I N I R Y V M V D R K R F F S S C L Q Y P I Y L S S L E P S G S R K E .. Protein_Len: 50 Strand: - Start: 20 End: 169 ................... K K E T A C L Y A N P Q S I C I D Q G F L Y V I H L P Q D F V N R R K K G G I D S K S T K E Q A T M ................ Protein_Len: 41 Strand: - Start: 16 End: 138 ............... K N R K P R V F T R T Q S H Y V F T R D S Y I Y S I Y H N I S F T E E R R A E L M ............................................... Protein_Len: 47 Strand: - Start: 3 End: 143 .. I S Y N N I E K R D C L P V R K A T I Y L H G T R I F I R Y T I T S R F R K K E E Q R W Y G M .......................................... attatggaataattatttatttcttttcggtcgcacaaaggtacgcgtttggctgtgatatacaaatgtcctgtccgaataaatatacgatatgtaatggttgatcgaaaacgtttcttctcttcttgcctccaatatccgatttacttgtcttctcttgagccgtcaggtagccgaaaagagag 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================================================ attatggaataattatttatttcttttcggtcgcacaaaggtacgcgtttggctgtgatatacaaatgtcctgtccgaataaatatacgatatgtaatggttgatcgaaaacgtttcttctcttcttgcctccaatatccgatttacttgtcttctcttgagccgtcaggtagccgaaaagagag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1430:PG1431|PG1430:PG1431:TPR domain protein:DNA-binding response regulator, LuxR family:<-<-:1515891..1516075 185 attatggaataattatttatttcttttcggtcgcacaaaggtacgcgtttggctgtgatatacaaatgtcctgtccgaataaatatacgatatgtaatggttgatcgaaaacgtttcttctcttcttgcctccaatatccgatttacttgtcttctcttgagccgtcaggtagccgaaaagagag Intra-Species Hit: Count: 1 Min: 1 Max: 185 Len: 185 Subject: NC_002950_PG1430_PG1431|TPR domain protein:DNA-binding response regulator, LuxR family|NEGATIVE:NEGATIVE|[1515891,1516075]|185 HSP 1 e-value: 1.0E-101 bit: 367.0 Len: 185 Query Start:1 Query End:185 Subject Strand: POSITIVE Subject Start: 1 Subject End: 185 attatggaataattatttatttcttttcggtcgcacaaaggtacgcgtttggctgtgatatacaaatgtcctgtccgaataaatatacgatatgtaatggttgatcgaaaacgtttcttctcttcttgcctccaatatccgatttacttgtcttctcttgagccgtcaggtagccgaaaagagag attatggaataattatttatttcttttcggtcgcacaaaggtacgcgtttggctgtgatatacaaatgtcctgtccgaataaatatacgatatgtaatggttgatcgaaaacgtttcttctcttcttgcctccaatatccgatttacttgtcttctcttgagccgtcaggtagccgaaaagagag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUGGAAUAAUUAUUUAUUUCUUUUCGGUCGCACAAAGGUACGCGUUUGGCUGUGAUAUACAAAUGUCCUGUCCGAAUAAAUAUACGAUAUGUAAUGGUUGAUCGAAAACGUUUCUUCUCUUCUUGCCUCCAAUAUCCGAUUUACUUGUCUUCUCUUGAGCCGUCAGGUAGCCGAAAAGAGAG ...................((((((((((((..(.....(((.(..(((((((.(.(((((....)))))).).))))))........(((((.....(((.((..(((........)))...))..)))....)))))....................).))).....)..)))))))))))). (-38.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUCUUUUCGGCUACCUGACGGCUCAAGAGAAGACAAGUAAAUCGGAUAUUGGAGGCAAGAAGAGAAGAAACGUUUUCGAUCAACCAUUACAUAUCGUAUAUUUAUUCGGACAGGACAUUUGUAUAUCACAGCCAAACGCGUACCUUUGUGCGACCGAAAAGAAAUAAAUAAUUAUUCCAUAAU ...(((((((((.........((((...((....((((((.....((..(((((((((...............)))))))))...))..(((.....)))..................))))))...))..)))).....(((((....))))).)))))))))..................... (-34.26) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 947 80 31 171 122 NC_002950:PG1430|5end_TPR_domain_protein_1515800..1516030_NEGATIVE 362 59 20 55 17 NC_002950:PG1496|5end_hypothetical_protein_1573342..1573572_POSITIVE 338 74 31 114 74 NC_002950:PG0092|5end_transporter,_putative_108598..108828_NEGATIVE 329 72 33 216 175 NC_002950:PG0854|5end_hypothetical_protein_914870..915100_POSITIVE 326 79 31 201 133 NC_002950:PG2029|5end_hypothetical_protein_2126543..2126773_POSITIVE 321 175 135 133 90 NC_002950:PG0259|5end_hypothetical_protein_292278..292508_POSITIVE 320 177 131 230 185 NC_002950:PG1003|5end_hypothetical_protein_1059232..1059462_POSITIVE 320 60 16 194 157 NC_002950:PG0963|5end_hypothetical_protein_1024332..1024562_NEGATIVE 320 54 16 200 155 NC_002950:PG0275|5end_thioredoxin_family_protein_307464..307694_NEGATIVE 311 178 131 202 152 NC_002950:PG1659|5end_hypothetical_protein_1743747..1743977_NEGATIVE 310 178 138 157 115 NC_002950:PG0203|5end_hypothetical_protein_240211..240441_NEGATIVE 308 143 104 197 152 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 304 90 44 201 151 NC_002950:PG0159|5end_endopeptidase_PepO_183164..183394_NEGATIVE 302 56 22 192 153 NC_002950:PG1706|5end_hypothetical_protein_1794211..1794441_NEGATIVE 300 68 23 174 125 NC_002950:PG1823|5end_hypothetical_protein_1917317..1917547_POSITIVE 300 174 137 73 39 NC_002950:PG1082|5end_phosphotransacetylase_1150683..1150913_NEGATIVE 300 179 146 222 185 NC_002950:PG0003|5end_hypothetical_protein_2938..3168_NEGATIVE 299 142 101 173 126 NC_002950:PG1093|5end_hypothetical_protein_1158121..1158351_POSITIVE 296 169 125 42 5 NC_002950:PG1861|5end_hypothetical_protein_1960057..1960287_NEGATIVE 295 57 25 158 122 NC_002950:PG0595|5end_30S_ribosomal_protein_S6_653008..653238_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 59 20 49 11 NC_002950:PG1495|3end_DNA_topoisomerase_III_1573416..1573566_POSITIVE 338 74 31 69 29 NC_002950:PG0093|3end_HlyD_family_secretion_protein_108643..108793_NEGATIVE 321 175 135 126 83 NC_002950:PG0258|3end_ABC_transporter,_ATP-binding_protein_292351..292501_POSITIVE 320 54 16 62 17 NC_002950:PG0276|3end_hypothetical_protein_307602..307752_NEGATIVE 313 178 136 148 100 NC_002950:PG1223|3end_hypothetical_protein_1299744..1299894_POSITIVE 310 178 138 106 64 NC_002950:PG0204|3end_hypothetical_protein_240262..240412_NEGATIVE 309 55 16 76 35 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 299 176 131 86 37 NC_002950:PG2125|3end_transcriptional_regulator,_AraC_family_2231376..2231526_NEGATIVE 299 142 101 64 17 NC_002950:PG1091|3end_DHH_subfamily_1_protein_1158092..1158242_POSITIVE 295 57 25 61 25 NC_002950:PG0594|3end_RNA_polymerase_sigma-70_factor_652991..653141_POSITIVE 291 63 27 44 1 NC_002950:PG0879|3end_hypothetical_protein_941931..942081_NEGATIVE 286 79 44 72 33 NC_002950:PG2048|3end_hypothetical_protein_2148134..2148284_NEGATIVE 283 78 41 150 117 NC_002950:PG0279|3end_NADP-dependent_malic_enzyme_310675..310825_NEGATIVE 282 58 20 103 68 NC_002950:PG2206|3end_ABC_transporter,_ATP-binding_protein_2317250..2317400_NEGATIVE 282 175 131 139 79 NC_002950:PG2024|3end_hemagglutinin_protein_HagE_2119083..2119233_NEGATIVE 282 46 1 73 26 NC_002950:PG1825|3end_hypothetical_protein_1919510..1919660_NEGATIVE 278 178 131 126 80 NC_002950:PG0415|3end_peptidyl-prolyl_cis-trans_isomerase,_PPIC-type_453714..453864_NEGATIVE 277 163 128 73 43 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 277 140 99 142 96 NC_002950:PG0773|3end_hypothetical_protein_825348..825498_POSITIVE 276 170 123 147 112 NC_002950:PG0004|3end_NAD-dependent_deacetylase_3752..3902_POSITIVE