Origin IGS: tgctatttcgttattagtttattatcgttccagttcgttaggactgcttgtagcatcataaagcggtcataatcgggttgcaaagtaaggcattttttttctcttccacaagcttttatcaattatttatccctgatcctccgttattacatcctattaatgtattcggaagaccctttatcagggggatgcacagtgaggaaaaaacagagctatcggccg .........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 cggccgatagctctgttttttcctcactgtgcatccccctgataaagggtcttccgaatacattaataggatgtaataacggaggatcagggataaataattgataaaagcttgtggaagagaaaaaaaatgccttactttgcaacccgattatgaccgctttatgatgctacaagcagtcctaacgaactggaacgataataaactaataacgaaatagca Mask Tandem Repeat Region ================================================ tgctatttcgttattagtttattatcgttccagttcgttaggactgcttgtagcatcataaagcggtcataatcgggttgcaaagtaaggcattttttttctcttccacaagcttttatcaattatttatccctgatcctccgttattacatcctattaatgtattcggaagaccctttatcagggggatgcacagtgaggaaaaaacagagctatcggccg Find is-nt database================================================ Query_seq: PG1960:PG1961|PG1960:PG1961:ribosomal protein L28:hypothetical protein:<-<-:2048754..2048975 222 tgctatttcgttattagtttattatcgttccagttcgttaggactgcttgtagcatcataaagcggtcataatcgggttgcaaagtaaggcattttttttctcttccacaagcttttatcaattatttatccctgatcctccgttattacatcctattaatgtattcggaagaccctttatcagggggatgcacagtgaggaaaaaacagagctatcggccg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1960:PG1961|PG1960:PG1961:ribosomal protein L28:hypothetical protein:<-<-:2048754..2048975 222 tgctatttcgttattagtttattatcgttccagttcgttaggactgcttgtagcatcataaagcggtcataatcgggttgcaaagtaaggcattttttttctcttccacaagcttttatcaattatttatccctgatcctccgttattacatcctattaatgtattcggaagaccctttatcagggggatgcacagtgaggaaaaaacagagctatcggccg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1960:PG1961|PG1960:PG1961:ribosomal protein L28:hypothetical protein:<-<-:2048754..2048975 222 tgctatttcgttattagtttattatcgttccagttcgttaggactgcttgtagcatcataaagcggtcataatcgggttgcaaagtaaggcattttttttctcttccacaagcttttatcaattatttatccctgatcctccgttattacatcctattaatgtattcggaagaccctttatcagggggatgcacagtgaggaaaaaacagagctatcggccg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgctatttcgttattagtttattatcgttccagttcgttaggactgcttgtagcatcataaagcggtcataatcgggttgcaaagtaaggcattttttttctcttccacaagcttttatcaattatttatccctgatcctccgttattacatcctattaatgtattcggaagaccctttatcagggggatgcacagtgaggaaaaaacagagctatcggccg Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 69 End: 221 .................................................................... M I G L Q S K A F F F S S T S F Y Q L F I P D P P L L H P I N V F G R P F I R G M H S E E K T E L S A . Protein_Len: 35 Strand: + Start: 118 End: 222 ..................................................................................................................... M N Y L S L I L R Y Y I L L M Y S E D P L S G G C T V R K K Q S Y R P Protein_Len: 40 Strand: - Start: 6 End: 122 ..... * K T I L K N D N W N T L V A Q L M M F R D Y D P Q L T L C K K E R G C A K I M .................................................................................................... tgctatttcgttattagtttattatcgttccagttcgttaggactgcttgtagcatcataaagcggtcataatcgggttgcaaagtaaggcattttttttctcttccacaagcttttatcaattatttatccctgatcctccgttattacatcctattaatgtattcggaagaccctttatcagggggatgcacagtgaggaaaaaacagagctatcggccg 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: 83 Start: 55 End: 84 ......................................................TTTGCAACCCGATTATGACCGCTTTATGAT.......................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgctatttcgttattagtttattatcgttccagttcgttaggactgcttgtagcatcataaagcggtcataatcgggttgcaaagtaaggcattttttttctcttccacaagcttttatcaattatttatccctgatcctccgttattacatcctattaatgtattcggaagaccctttatcagggggatgcacagtgaggaaaaaacagagctatcggccg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1960:PG1961|PG1960:PG1961:ribosomal protein L28:hypothetical protein:<-<-:2048754..2048975 222 tgctatttcgttattagtttattatcgttccagttcgttaggactgcttgtagcatcataaagcggtcataatcgggttgcaaagtaaggcattttttttctcttccacaagcttttatcaattatttatccctgatcctccgttattacatcctattaatgtattcggaagaccctttatcagggggatgcacagtgaggaaaaaacagagctatcggccg Intra-Species Hit: Count: 1 Min: 1 Max: 222 Len: 222 Subject: NC_002950_PG1960_PG1961|ribosomal protein L28:hypothetical protein|NEGATIVE:NEGATIVE|[2048754,2048975]|222 HSP 1 e-value: 1.0E-108 bit: 392.0 Len: 222 Query Start:1 Query End:222 Subject Strand: POSITIVE Subject Start: 1 Subject End: 222 tgctatttcgttattagtttattatcgttccagttcgttaggactgcttgtagcatcataaagcggtcataatcgggttgcaaagtaaggcannnnnnnnctcttccacaagcttttatcaattatttatccctgatcctccgttattacatcctattaatgtattcggaagaccctttatcagggggatgcacagtgaggaaaaaacagagctatcggccg tgctatttcgttattagtttattatcgttccagttcgttaggactgcttgtagcatcataaagcggtcataatcgggttgcaaagtaaggcattttttttctcttccacaagcttttatcaattatttatccctgatcctccgttattacatcctattaatgtattcggaagaccctttatcagggggatgcacagtgaggaaaaaacagagctatcggccg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUAUUUCGUUAUUAGUUUAUUAUCGUUCCAGUUCGUUAGGACUGCUUGUAGCAUCAUAAAGCGGUCAUAAUCGGGUUGCAAAGUAAGGCAUUUUUUUUCUCUUCCACAAGCUUUUAUCAAUUAUUUAUCCCUGAUCCUCCGUUAUUACAUCCUAUUAAUGUAUUCGGAAGACCCUUUAUCAGGGGGAUGCACAGUGAGGAAAAAACAGAGCUAUCGGCCG .........(((..((((((..........(((..(((((.((((((((...........)))))))).))).))..))).............((((((((((........(((..((((.........(((((((((.((((....(((((.......)))))..)))).)).......)))))))))))...)))))))))))))..))))))..))).. (-47.91) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGCCGAUAGCUCUGUUUUUUCCUCACUGUGCAUCCCCCUGAUAAAGGGUCUUCCGAAUACAUUAAUAGGAUGUAAUAACGGAGGAUCAGGGAUAAAUAAUUGAUAAAAGCUUGUGGAAGAGAAAAAAAAUGCCUUACUUUGCAACCCGAUUAUGACCGCUUUAUGAUGCUACAAGCAGUCCUAACGAACUGGAACGAUAAUAAACUAAUAACGAAAUAGCA ..((......(((((.....(((((....(((((((((((.....))))...................)))))))......))))).))))).......((((......((((((((.............(((........))).....(((((((.....))))))).))))))))..(((.........))).))))....................)). (-44.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 942 80 31 171 122 NC_002950:PG1960|5end_ribosomal_protein_L28_2048663..2048893_NEGATIVE 346 79 31 213 160 NC_002950:PG0359|5end_flavin_reductase_domain_protein_392851..393081_POSITIVE 334 76 33 81 31 NC_002950:PG1333|5end_hypothetical_protein_1415425..1415655_NEGATIVE 324 69 21 169 113 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 318 67 24 223 178 NC_002950:PG0756|5end_hypothetical_protein_805673..805903_NEGATIVE 315 80 32 66 8 NC_002950:PG0704|5end_phosphoglycerate_mutase_family_protein_758928..759158_POSITIVE 314 203 167 53 7 NC_002950:PG1556|5end_hypothetical_protein_1636595..1636825_POSITIVE 311 77 40 204 162 NC_002950:PG0071|5end_UDP-3-O-acyl-GlcNAc_deacetylase/beta-hydroxyacyl-[acyl_carrier_protein]_dehydratase_FabZ_86119..86349_NEGATIVE 304 220 172 142 101 NC_002950:PG0980|5end_hypothetical_protein_1040897..1041127_POSITIVE 301 53 17 100 69 NC_002950:PG0052|5end_sensor_histidine_kinase_63419..63649_POSITIVE 300 220 174 53 13 NC_002950:PG0721|5end_NLP/P60_family_protein_773847..774077_POSITIVE 297 77 34 61 6 NC_002950:PG1594|5end_ComEC/Rec2-related_protein_1673587..1673817_NEGATIVE 293 78 34 146 94 NC_002950:PG0415|5end_peptidyl-prolyl_cis-trans_isomerase,_PPIC-type_455096..455326_NEGATIVE 291 69 24 171 122 NC_002950:PG2001|5end_signal_peptidase_I_2090855..2091085_NEGATIVE 291 78 32 195 147 NC_002950:PG1998|5end_polyprenyl_synthetase_2088029..2088259_NEGATIVE 291 80 32 48 7 NC_002950:PG0747|5end_sigma-54_dependent_DNA-binding_response_regulator_795294..795524_NEGATIVE 291 218 171 124 73 NC_002950:PG0617|5end_hypothetical_protein_670059..670289_POSITIVE 289 220 180 196 153 NC_002950:PG2223|5end_glycosyl_transferase,_group_2_family_protein_2337713..2337943_POSITIVE 287 78 32 139 85 NC_002950:PG1919|5end_ribosomal_protein_L15_2016281..2016511_NEGATIVE 287 68 30 67 11 NC_002950:PG0896|5end_beta-galactosidase_957249..957479_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 76 33 84 34 NC_002950:PG1334|3end_band_7/Mec-2_family_protein_1415422..1415572_NEGATIVE 315 80 32 64 6 NC_002950:PG0703|3end_cobalamin_(5'-phosphate)_synthase,_putative_759006..759156_POSITIVE 314 203 167 47 1 NC_002950:PG1555|3end_hypothetical_protein_1636669..1636819_POSITIVE 297 200 153 48 3 NC_002950:PG0498|3end_S-ribosylhomocysteinase_538527..538677_POSITIVE 293 78 34 109 57 NC_002950:PG0416|3end_ATP-dependent_DNA_helicase_RecQ_455133..455283_NEGATIVE 290 70 26 146 111 NC_002950:PG0403|3end_hypothetical_protein_439453..439603_NEGATIVE 288 210 167 150 109 NC_002950:PG0979|3end_hypothetical_protein_1040990..1041140_POSITIVE 287 78 32 113 59 NC_002950:PG1920|3end_ribosomal_protein_L30_2016307..2016457_NEGATIVE 285 77 32 149 106 NC_002950:PG0772|3end_hypothetical_protein_825204..825354_POSITIVE 283 193 152 90 43 NC_002950:PG2176|3end_ISPg2,_transposase_2283215..2283365_NEGATIVE 283 180 131 140 76 NC_002950:PG2038|3end_N-acetylmuramoyl-L-alanine_amidase,_putative_2137809..2137959_NEGATIVE 281 202 161 77 26 NC_002950:PG0324|3end_histidine_ammonia-lyase_357589..357739_NEGATIVE 279 108 64 114 65 NC_002950:PG2227|3end_hypothetical_protein_2342744..2342894_POSITIVE 279 88 41 75 41 NC_002950:PG2094|3end_hypothetical_protein_2193321..2193471_NEGATIVE 279 80 34 144 87 NC_002950:PG2060|3end_thymidylate_synthase_2158456..2158606_POSITIVE 277 80 35 83 34 NC_002950:PG2101|3end_hypothetical_protein_2210278..2210428_NEGATIVE 277 70 25 135 76 NC_002950:PG0134|3end_magnesium_transporter_155783..155933_NEGATIVE 275 77 36 54 1 NC_002950:PG1595|3end_ribulose-phosphate_3-epimerase_1673594..1673744_NEGATIVE 275 220 181 130 91 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 274 78 34 64 14 NC_002950:PG0737|3end_hypothetical_protein_786546..786696_POSITIVE