Origin IGS: taaactttgtaaacaatatctttataatattataagcagatatgtccttgtggacgtatctgcttttttattttagtatagcgtaagtttaatatatattagagcagacaagaaattaacatacgtttgtatcagtttagaaaaacttatttagttttcttggtagtttggactaaaagcatttactttgcatccgattccatgacatcttctctgcttcatagcagtagagggcttggttagaagatttatattttagtattaacaaattaatttttaaag .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctttaaaaattaatttgttaatactaaaatataaatcttctaaccaagccctctactgctatgaagcagagaagatgtcatggaatcggatgcaaagtaaatgcttttagtccaaactaccaagaaaactaaataagtttttctaaactgatacaaacgtatgttaatttcttgtctgctctaatatatattaaacttacgctatactaaaataaaaaagcagatacgtccacaaggacatatctgcttataatattataaagatattgtttacaaagttta Mask Tandem Repeat Region ================================================ taaactttgtaaacaatatctttataatattataagcagatatgtccttgtggacgtatctgcttttttattttagtatagcgtaagtttaatatatattagagcagacaagaaattaacatacgtttgtatcagtttagaaaaacttatttagttttcttggtagtttggactaaaagcatttactttgcatccgattccatgacatcttctctgcttcatagcagtagagggcttggttagaagatttatattttagtattaacaaattaatttttaaag Find is-nt database================================================ Query_seq: PI0487:PI0488|PI0487:PI0488:50S ribosomal protein L17:conserved hypothetical protein:->->:446764..447045 282 taaactttgtaaacaatatctttataatattataagcagatatgtccttgtggacgtatctgcttttttattttagtatagcgtaagtttaatatatattagagcagacaagaaattaacatacgtttgtatcagtttagaaaaacttatttagttttcttggtagtttggactaaaagcatttactttgcatccgattccatgacatcttctctgcttcatagcagtagagggcttggttagaagatttatattttagtattaacaaattaatttttaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0487:PI0488|PI0487:PI0488:50S ribosomal protein L17:conserved hypothetical protein:->->:446764..447045 282 taaactttgtaaacaatatctttataatattataagcagatatgtccttgtggacgtatctgcttttttattttagtatagcgtaagtttaatatatattagagcagacaagaaattaacatacgtttgtatcagtttagaaaaacttatttagttttcttggtagtttggactaaaagcatttactttgcatccgattccatgacatcttctctgcttcatagcagtagagggcttggttagaagatttatattttagtattaacaaattaatttttaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0487:PI0488|PI0487:PI0488:50S ribosomal protein L17:conserved hypothetical protein:->->:446764..447045 282 taaactttgtaaacaatatctttataatattataagcagatatgtccttgtggacgtatctgcttttttattttagtatagcgtaagtttaatatatattagagcagacaagaaattaacatacgtttgtatcagtttagaaaaacttatttagttttcttggtagtttggactaaaagcatttactttgcatccgattccatgacatcttctctgcttcatagcagtagagggcttggttagaagatttatattttagtattaacaaattaatttttaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaactttgtaaacaatatctttataatattataagcagatatgtccttgtggacgtatctgcttttttattttagtatagcgtaagtttaatatatattagagcagacaagaaattaacatacgtttgtatcagtttagaaaaacttatttagttttcttggtagtttggactaaaagcatttactttgcatccgattccatgacatcttctctgcttcatagcagtagagggcttggttagaagatttatattttagtattaacaaattaatttttaaag Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 115 End: 240 .................................................................................................................. M N I R L Y Q F R K T Y L V F L V V W T K S I Y F A S D S M T S S L L H S S R G L G .......................................... Protein_Len: 33 Strand: - Start: 176 End: 274 ............................................................................................................................................................................... F C K S Q M R N W S M K E A E Y C Y L A Q N S S K Y K L I L L N M ........ Protein_Len: 33 Strand: - Start: 154 End: 252 ......................................................................................................................................................... N E Q Y N P S F A N V K C G I G H C R R Q K M A T S P K T L L N M .............................. taaactttgtaaacaatatctttataatattataagcagatatgtccttgtggacgtatctgcttttttattttagtatagcgtaagtttaatatatattagagcagacaagaaattaacatacgtttgtatcagtttagaaaaacttatttagttttcttggtagtttggactaaaagcatttactttgcatccgattccatgacatcttctctgcttcatagcagtagagggcttggttagaagatttatattttagtattaacaaattaatttttaaag 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: 85 Start: 253 End: 282 ............................................................................................................................................................................................................................................................CTTTAAAAATTAATTTGTTAATACTAAAAT PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 50 End: 79 .................................................GTGGACGTATCTGCTTTTTTATTTTAGTAT........................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaactttgtaaacaatatctttataatattataagcagatatgtccttgtggacgtatctgcttttttattttagtatagcgtaagtttaatatatattagagcagacaagaaattaacatacgtttgtatcagtttagaaaaacttatttagttttcttggtagtttggactaaaagcatttactttgcatccgattccatgacatcttctctgcttcatagcagtagagggcttggttagaagatttatattttagtattaacaaattaatttttaaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -15.0 Tail_Score: -5.83211 Start: 36 End: 63 Full_Region: TTTATAATATTATAA GCAGATATGTCC TTGT GGACGTATCTGC TTTTTTATTTTAGTA ...................................GCAGATATGTCCTTGTGGACGTATCTGC........................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -12.8 Tail_Score: -3.54771 Start: 36 End: 63 Full_Region: tactaaaataaaaaa gcagatacgtcc acaa ggacatatctgc ttataatattataaa ...................................gcagatacgtccacaaggacatatctgc........................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI0487:PI0488|PI0487:PI0488:50S ribosomal protein L17:conserved hypothetical protein:->->:446764..447045 282 taaactttgtaaacaatatctttataatattataagcagatatgtccttgtggacgtatctgcttttttattttagtatagcgtaagtttaatatatattagagcagacaagaaattaacatacgtttgtatcagtttagaaaaacttatttagttttcttggtagtttggactaaaagcatttactttgcatccgattccatgacatcttctctgcttcatagcagtagagggcttggttagaagatttatattttagtattaacaaattaatttttaaag Intra-Species Hit: Count: 1 Min: 1 Max: 282 Len: 282 Subject: pint_PI0487_PI0488|50S ribosomal protein L17:conserved hypothetical protein|POSITIVE:POSITIVE|[446764,447045]|282 HSP 1 e-value: 1.0E-158 bit: 559.0 Len: 282 Query Start:1 Query End:282 Subject Strand: POSITIVE Subject Start: 1 Subject End: 282 taaactttgtaaacaatatctttataatattataagcagatatgtccttgtggacgtatctgcttttttattttagtatagcgtaagtttaatatatattagagcagacaagaaattaacatacgtttgtatcagtttagaaaaacttatttagttttcttggtagtttggactaaaagcatttactttgcatccgattccatgacatcttctctgcttcatagcagtagagggcttggttagaagatttatattttagtattaacaaattaatttttaaag taaactttgtaaacaatatctttataatattataagcagatatgtccttgtggacgtatctgcttttttattttagtatagcgtaagtttaatatatattagagcagacaagaaattaacatacgtttgtatcagtttagaaaaacttatttagttttcttggtagtttggactaaaagcatttactttgcatccgattccatgacatcttctctgcttcatagcagtagagggcttggttagaagatttatattttagtattaacaaattaatttttaaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACUUUGUAAACAAUAUCUUUAUAAUAUUAUAAGCAGAUAUGUCCUUGUGGACGUAUCUGCUUUUUUAUUUUAGUAUAGCGUAAGUUUAAUAUAUAUUAGAGCAGACAAGAAAUUAACAUACGUUUGUAUCAGUUUAGAAAAACUUAUUUAGUUUUCUUGGUAGUUUGGACUAAAAGCAUUUACUUUGCAUCCGAUUCCAUGACAUCUUCUCUGCUUCAUAGCAGUAGAGGGCUUGGUUAGAAGAUUUAUAUUUUAGUAUUAACAAAUUAAUUUUUAAAG ......(((((((.......)))))))......((((((((((((((....)))))))))))))).....((((((((((((....))......))))))))))....(((((((((((.(((.((((...((......)).)))).))))))).))))))).(((((((.((((((((((.......)))....((((...((((.(((((((((((....))))).))))))....))))...))))....))))))).....))))))).......... (-64.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUAAAAAUUAAUUUGUUAAUACUAAAAUAUAAAUCUUCUAACCAAGCCCUCUACUGCUAUGAAGCAGAGAAGAUGUCAUGGAAUCGGAUGCAAAGUAAAUGCUUUUAGUCCAAACUACCAAGAAAACUAAAUAAGUUUUUCUAAACUGAUACAAACGUAUGUUAAUUUCUUGUCUGCUCUAAUAUAUAUUAAACUUACGCUAUACUAAAAUAAAAAAGCAGAUACGUCCACAAGGACAUAUCUGCUUAUAAUAUUAUAAAGAUAUUGUUUACAAAGUUUA ............................(((((.(((((((..............(((((....))))))))))))....((((...((((..(((((....)))))..)))).......(((((((........(((((....))))).((((....)))).....))))))).....)))).)))))..(((((((...................(((((((((.((((....)))).)))))))))((((((((.....)))))))).....))))))) (-53.73) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 67 34 138 105 pint:PI1418|5end_UDP-N-acetylglucosamine_2-epimerase_1337985..1338215_POSITIVE 333 239 195 164 105 pint:PI0508|5end_possible_cell_filamentation_protein_466463..466693_POSITIVE 317 89 43 196 146 pint:PI1228|5end_conserved_hypothetical_protein_1149045..1149275_POSITIVE 309 240 193 194 135 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 291 88 44 115 60 pint:PI0785|5end_hypothetical_protein_723744..723974_POSITIVE 280 239 194 184 136 pint:PI1493|5end_conserved_hypothetical_protein_1412268..1412498_POSITIVE 279 238 193 207 168 pint:PI0265|5end_conjugative_transposon_protein,_TraO_257296..257526_POSITIVE 273 238 193 200 145 pint:PI0764|5end_permease_697962..698192_POSITIVE 272 80 32 173 118 pint:PI0313|5end_conserved_hypothetical_protein_294833..295063_POSITIVE 272 80 32 61 6 pint:PI0311|5end_hypothetical_protein_294721..294951_POSITIVE 266 235 197 69 29 pint:PI0942|5end_DNA-binding_protein_HU_874624..874854_POSITIVE 265 249 201 207 164 pint:PI1885|5end_cell_division_protein_1826267..1826497_POSITIVE 261 236 201 167 117 pint:PI0099|5end_hypothetical_protein_95530..95760_POSITIVE 258 72 34 84 41 pint:PI1208|5end_monofunctional_biosynthetic_peptidoglycan_transglycosylase_1127155..1127385_POSITIVE 257 90 43 223 171 pint:PI1671|5end_hypothetical_protein_1586397..1586627_POSITIVE 256 248 203 88 26 pint:PI1585|5end_ampG_permease_1512900..1513130_POSITIVE 256 235 206 166 130 pint:PI0427|5end_conserved_hypothetical_protein_391140..391370_POSITIVE 256 238 200 193 153 pint:PI0218|5end_conserved_hypothetical_protein_210770..211000_POSITIVE 256 230 187 164 121 pint:PI0133|5end_hypothetical_protein_124334..124564_POSITIVE 255 238 193 199 153 pint:PI0396|5end_possible_tetracycline_resistance_element_mobilization_regulatory_protein,_C-terminal_fragment_361993..362223_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 416 65 34 57 26 pint:PI0487|3end_50S_ribosomal_protein_L17_446703..446853_POSITIVE 309 240 193 134 75 pint:PI0259|3end_conserved_protein_found_in_conjugation,_TraI_253043..253193_POSITIVE 306 239 195 142 99 pint:PI0685|3end_elongation_factor_G_623048..623198_POSITIVE 302 220 179 37 4 pint:PI2036|3end_hypothetical_protein_1989516..1989666_POSITIVE 295 210 162 81 31 pint:PI0434|3end_possible_beta-lactamase_406890..407040_POSITIVE 280 239 194 146 98 pint:PI1492|3end_triosephosphate_isomerase_1412310..1412460_POSITIVE 275 218 179 92 55 pint:PI2166|3end_hypothetical_protein_2112073..2112223_POSITIVE 270 90 43 88 43 pint:PI0849|3end_hypothetical_protein_783542..783692_POSITIVE 267 240 191 120 74 pint:PI0624|3end_hypothetical_protein_574471..574621_POSITIVE 264 260 214 92 52 pint:PI1379|3end_hypothetical_protein_1302292..1302442_POSITIVE 261 240 193 141 95 pint:PI1575|3end_LemA_protein_1501852..1502002_POSITIVE 261 236 201 89 39 pint:PI0098|3end_conserved_hypothetical_protein_(possible_glycosyl/glycerophosphate_transferase)_95532..95682_POSITIVE 258 72 34 89 46 pint:PI1205|3end_hypothetical_protein_1127240..1127390_POSITIVE 258 72 34 58 15 pint:PI1207|3end_hypothtical_protein_1127209..1127359_POSITIVE 257 88 46 147 110 pint:PI0811|3end_protease/hemagglutinin_PrtT,_streptopain_family_749937..750087_POSITIVE 257 235 192 56 1 pint:PI0286|3end_ISPg3-related_transposase_272065..272215_POSITIVE 256 248 203 66 4 pint:PI1584|3end_A/G-specific_adenine_glycosylase_1512958..1513108_POSITIVE 256 238 200 137 97 pint:PI0217|3end_conserved_hypothetical_protein;_possible_lipoprotein_210794..210944_POSITIVE 253 235 198 40 1 pint:PI0941|3end_hypothetical_protein_874675..874825_POSITIVE 253 233 206 145 116 pint:PI0426|3end_conserved_hypothetical_protein_391206..391356_POSITIVE