Origin IGS: taatttaacatacaagataaaaataaaagaccgaacccttgcttggggttcggtctttttttgtgcttacacaaacaactctttagaaaacggcaaccaattcttttttagaagcacataaccaaaaggcttgcaggatgcaaaaatctttgtcgctgaaattatttacgtgtaaataataatttatttacgtgtagagaaatatttatttacacgtagaaaaatatttatttacgtgtaagtaatttactagatttttatattaacaagctgaacacttgattgtcaaaaccttttaaggcttacttcatactacgctaaagactaccttatggggaacttctactttttcaaaagtaaaaactaattttctttctatataaaacaggggaacactctcattgtgagaatgttcccctattatcaaaataactcttacaagaagtttta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaacttcttgtaagagttattttgataataggggaacattctcacaatgagagtgttcccctgttttatatagaaagaaaattagtttttacttttgaaaaagtagaagttccccataaggtagtctttagcgtagtatgaagtaagccttaaaaggttttgacaatcaagtgttcagcttgttaatataaaaatctagtaaattacttacacgtaaataaatatttttctacgtgtaaataaatatttctctacacgtaaataaattattatttacacgtaaataatttcagcgacaaagatttttgcatcctgcaagccttttggttatgtgcttctaaaaaagaattggttgccgttttctaaagagttgtttgtgtaagcacaaaaaaagaccgaaccccaagcaagggttcggtcttttatttttatcttgtatgttaaatta Mask Tandem Repeat Region ================================================ taatttaacatacaagataaaaataaaagaccgaacccttgcttggggttcggtctttttttgtgcttacacaaacaactctttagaaaacggcaaccaattcttttttagaagcacataaccaaaaggcttgcaggatgcaaaaatctttgtcgctgaaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagtaatttactagatttttatattaacaagctgaacacttgattgtcaaaaccttttaaggcttacttcatactacgctaaagactaccttatggggaacttctactttttcaaaagtaaaaactaattttctttctatataaaacaggggaacactctcattgtgagaatgttcccctattatcaaaataactcttacaagaagtttta Find is-nt database================================================ Query_seq: PI1365:PI1366|PI1365:PI1366:conserved hypothetical protein; probable transmembrane protein:conserved hypothetical protein; possible hydrolase, HAD superfamily:->->:1285736..1286185 450 taatttaacatacaagataaaaataaaagaccgaacccttgcttggggttcggtctttttttgtgcttacacaaacaactctttagaaaacggcaaccaattcttttttagaagcacataaccaaaaggcttgcaggatgcaaaaatctttgtcgctgaaattatttacgtgtaaataataatttatttacgtgtagagaaatatttatttacacgtagaaaaatatttatttacgtgtaagtaatttactagatttttatattaacaagctgaacacttgattgtcaaaaccttttaaggcttacttcatactacgctaaagactaccttatggggaacttctactttttcaaaagtaaaaactaattttctttctatataaaacaggggaacactctcattgtgagaatgttcccctattatcaaaataactcttacaagaagtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1365:PI1366|PI1365:PI1366:conserved hypothetical protein; probable transmembrane protein:conserved hypothetical protein; possible hydrolase, HAD superfamily:->->:1285736..1286185 450 taatttaacatacaagataaaaataaaagaccgaacccttgcttggggttcggtctttttttgtgcttacacaaacaactctttagaaaacggcaaccaattcttttttagaagcacataaccaaaaggcttgcaggatgcaaaaatctttgtcgctgaaattatttacgtgtaaataataatttatttacgtgtagagaaatatttatttacacgtagaaaaatatttatttacgtgtaagtaatttactagatttttatattaacaagctgaacacttgattgtcaaaaccttttaaggcttacttcatactacgctaaagactaccttatggggaacttctactttttcaaaagtaaaaactaattttctttctatataaaacaggggaacactctcattgtgagaatgttcccctattatcaaaataactcttacaagaagtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1365:PI1366|PI1365:PI1366:conserved hypothetical protein; probable transmembrane protein:conserved hypothetical protein; possible hydrolase, HAD superfamily:->->:1285736..1286185 450 taatttaacatacaagataaaaataaaagaccgaacccttgcttggggttcggtctttttttgtgcttacacaaacaactctttagaaaacggcaaccaattcttttttagaagcacataaccaaaaggcttgcaggatgcaaaaatctttgtcgctgaaattatttacgtgtaaataataatttatttacgtgtagagaaatatttatttacacgtagaaaaatatttatttacgtgtaagtaatttactagatttttatattaacaagctgaacacttgattgtcaaaaccttttaaggcttacttcatactacgctaaagactaccttatggggaacttctactttttcaaaagtaaaaactaattttctttctatataaaacaggggaacactctcattgtgagaatgttcccctattatcaaaataactcttacaagaagtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatttaacatacaagataaaaataaaagaccgaacccttgcttggggttcggtctttttttgtgcttacacaaacaactctttagaaaacggcaaccaattcttttttagaagcacataaccaaaaggcttgcaggatgcaaaaatctttgtcgctgaaattatttacgtgtaaataataatttatttacgtgtagagaaatatttatttacacgtagaaaaatatttatttacgtgtaagtaatttactagatttttatattaacaagctgaacacttgattgtcaaaaccttttaaggcttacttcatactacgctaaagactaccttatggggaacttctactttttcaaaagtaaaaactaattttctttctatataaaacaggggaacactctcattgtgagaatgttcccctattatcaaaataactcttacaagaagtttta Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 10 End: 108 ......... M Q D K N K R P N P C L G F G L F L C L H K Q L F R K R Q P I L F ...................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 34 Strand: + Start: 17 End: 118 ................ M K I K D R T L A W G S V F F C A Y T N N S L E N G N Q F F F R S T ............................................................................................................................................................................................................................................................................................................................................ Protein_Len: 40 Strand: - Start: 311 End: 430 ...................................................................................................................................................................................................................................................................................................................... V V S F V V K H P V E V K E F T F V L K R E I Y F L P V S E N H S H E G I I L M .................... Protein_Len: 34 Strand: - Start: 86 End: 187 ..................................................................................... F V A V L E K K S A C L W F A Q L I C F D K D S F N N V H L Y Y N M ....................................................................................................................................................................................................................................................................... Protein_Len: 32 Strand: - Start: 70 End: 165 ..................................................................... V F L E K S F P L W N K K L L V Y G F P K C S A F I K T A S I M ............................................................................................................................................................................................................................................................................................. Protein_Len: 33 Strand: - Start: 3 End: 101 .. N L M C S L F L L G F G Q K P N P R K K H K C L C S K L F R C G M ............................................................................................................................................................................................................................................................................................................................................................. taatttaacatacaagataaaaataaaagaccgaacccttgcttggggttcggtctttttttgtgcttacacaaacaactctttagaaaacggcaaccaattcttttttagaagcacataaccaaaaggcttgcaggatgcaaaaatctttgtcgctgaaattatttacgtgtaaataataatttatttacgtgtagagaaatatttatttacacgtagaaaaatatttatttacgtgtaagtaatttactagatttttatattaacaagctgaacacttgattgtcaaaaccttttaaggcttacttcatactacgctaaagactaccttatggggaacttctactttttcaaaagtaaaaactaattttctttctatataaaacaggggaacactctcattgtgagaatgttcccctattatcaaaataactcttacaagaagtttta 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================================================ taatttaacatacaagataaaaataaaagaccgaacccttgcttggggttcggtctttttttgtgcttacacaaacaactctttagaaaacggcaaccaattcttttttagaagcacataaccaaaaggcttgcaggatgcaaaaatctttgtcgctgaaattatttacgtgtaaataataatttatttacgtgtagagaaatatttatttacacgtagaaaaatatttatttacgtgtaagtaatttactagatttttatattaacaagctgaacacttgattgtcaaaaccttttaaggcttacttcatactacgctaaagactaccttatggggaacttctactttttcaaaagtaaaaactaattttctttctatataaaacaggggaacactctcattgtgagaatgttcccctattatcaaaataactcttacaagaagtttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.9 Tail_Score: -2.70932 Start: 21 End: 63 Full_Region: TAACATACAAGATAA AAATAAAAGACCGAACCCT TGCTT GGGGTTCGGTCTTTTTTTG TGCTTACACAAACAA ....................AAATAAAAGACCGAACCCTTGCTTGGGGTTCGGTCTTTTTTTG................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -13.9 Tail_Score: -5.1764 Start: 24 End: 60 Full_Region: tttgtgtaagcacaa aaaaagaccgaaccc caagcaa gggttcggtctttta tttttatcttgtatg .......................aaaaagaccgaaccccaagcaagggttcggtctttta...................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -13.8 Tail_Score: -5.40873 Start: 29 End: 55 Full_Region: gtaagcacaaaaaaa gaccgaaccc caagcaa gggttcggtc ttttatttttatctt ............................gaccgaaccccaagcaagggttcggtc........................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 86 HP_score: -9.6 Tail_Score: -3.85891 Start: 206 End: 245 Full_Region: CGTGTAGAGAAATAT TTATTTACACGTAGAAAA ATAT TTATTTACGTGTAAGTAA TTTACTAGATTTTTA .............................................................................................................................................................................................................TTATTTACACGTAGAAAAATATTTATTTACGTGTAAGTAA............................................................................................................................................................................................................. TransTerm Strand: - Conf: 44 HP_score: -2.1 Tail_Score: -3.26649 Start: 267 End: 281 Full_Region: aaaggttttgacaat caagt gttca gcttg ttaatataaaaatct ..........................................................................................................................................................................................................................................................................caagtgttcagcttg......................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -18.8 Tail_Score: -4.52589 Start: 386 End: 420 Full_Region: gagttattttgataa taggggaacattctca caa tgagagtgttcccctg ttttatatagaaaga .................................................................................................................................................................................................................................................................................................................................................................................................taggggaacattctcacaatgagagtgttcccctg.............................. TransTerm Strand: - Conf: 100 HP_score: -19.2 Tail_Score: -3.87627 Start: 388 End: 418 Full_Region: gttattttgataata ggggaacattctca caa tgagagtgttcccc tgttttatatagaaa ...................................................................................................................................................................................................................................................................................................................................................................................................ggggaacattctcacaatgagagtgttcccc................................ Find igs database================================================ Query_seq: PI1365:PI1366|PI1365:PI1366:conserved hypothetical protein; probable transmembrane protein:conserved hypothetical protein; possible hydrolase, HAD superfamily:->->:1285736..1286185 450 taatttaacatacaagataaaaataaaagaccgaacccttgcttggggttcggtctttttttgtgcttacacaaacaactctttagaaaacggcaaccaattcttttttagaagcacataaccaaaaggcttgcaggatgcaaaaatctttgtcgctgaaattatttacgtgtaaataataatttatttacgtgtagagaaatatttatttacacgtagaaaaatatttatttacgtgtaagtaatttactagatttttatattaacaagctgaacacttgattgtcaaaaccttttaaggcttacttcatactacgctaaagactaccttatggggaacttctactttttcaaaagtaaaaactaattttctttctatataaaacaggggaacactctcattgtgagaatgttcccctattatcaaaataactcttacaagaagtttta Intra-Species Hit: Count: 2 Min: 1 Max: 450 Len: 450 Subject: pint_PI1365_PI1366|conserved hypothetical protein; probable transmembrane protein:conserved hypothetical protein; possible hydrolase, HAD superfamily|POSITIVE:POSITIVE|[1285736,1286185]|450 HSP 1 e-value: 0.0 bit: 850.0 Len: 450 Query Start:1 Query End:450 Subject Strand: POSITIVE Subject Start: 1 Subject End: 450 taatttaacatacaagataaaaataaaagaccgaacccttgcttggggttcggtcnnnnnnngtgcttacacaaacaactctttagaaaacggcaaccaattcttttttagaagcacataaccaaaaggcttgcaggatgcaaaaatctttgtcgctgaaattatttacgtgtaaataataatttatttacgtgtagagaaatatttatttacacgtagaaaaatatttatttacgtgtaagtaatttactagatttttatattaacaagctgaacacttgattgtcaaaaccttttaaggcttacttcatactacgctaaagactaccttatggggaacttctactttttcaaaagtaaaaactaattttctttctatataaaacaggggaacactctcattgtgagaatgttcccctattatcaaaataactcttacaagaagtttta taatttaacatacaagataaaaataaaagaccgaacccttgcttggggttcggtctttttttgtgcttacacaaacaactctttagaaaacggcaaccaattcttttttagaagcacataaccaaaaggcttgcaggatgcaaaaatctttgtcgctgaaattatttacgtgtaaataataatttatttacgtgtagagaaatatttatttacacgtagaaaaatatttatttacgtgtaagtaatttactagatttttatattaacaagctgaacacttgattgtcaaaaccttttaaggcttacttcatactacgctaaagactaccttatggggaacttctactttttcaaaagtaaaaactaattttctttctatataaaacaggggaacactctcattgtgagaatgttcccctattatcaaaataactcttacaagaagtttta Subject: pint_PI0701_PI0702|hypothetical protein:conserved hypothetical protein; possible tetracenomycin C synthesis protein homolog|POSITIVE:POSITIVE|[638598,638779]|182 HSP 1 e-value: 8.0E-20 bit: 99.6 Len: 98 Query Start:150 Query End:247 Subject Strand: POSITIVE Subject Start: 7 Subject End: 104 .....................................................................................................................................................ttgtcgctgaaattatttacgtgtaaataataatttatttacgtgtagagaaatatttatttacacgtagaaaaatatttatttacgtgtaagtaatt........................................................................................................................................................................................................... .....................................................................................................................................................ttgtcgcttaaattatttacgtgtaaataataatttctctacgtgtaagtaaatatttttctacacgtaaataaatatttctttacgtgtaaataatt........................................................................................................................................................................................................... HSP 2 e-value: 1.0E-12 bit: 75.8 Len: 90 Query Start:160 Query End:249 Subject Strand: NEGATIVE Subject Start: 15 Subject End: 104 ...............................................................................................................................................................aattatttacgtgtaaataataatttatttacgtgtagagaaatatttatttacacgtagaaaaatatttatttacgtgtaagtaattta......................................................................................................................................................................................................... ...............................................................................................................................................................aattatttacacgtaaagaaatatttatttacgtgtagaaaaatatttacttacacgtagagaaattattatttacacgtaaataattta......................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUAACAUACAAGAUAAAAAUAAAAGACCGAACCCUUGCUUGGGGUUCGGUCUUUUUUUGUGCUUACACAAACAACUCUUUAGAAAACGGCAACCAAUUCUUUUUUAGAAGCACAUAACCAAAAGGCUUGCAGGAUGCAAAAAUCUUUGUCGCUGAAAUUAUUUACGUGUAAAUAAUAAUUUAUUUACGUGUAGAGAAAUAUUUAUUUACACGUAGAAAAAUAUUUAUUUACGUGUAAGUAAUUUACUAGAUUUUUAUAUUAACAAGCUGAACACUUGAUUGUCAAAACCUUUUAAGGCUUACUUCAUACUACGCUAAAGACUACCUUAUGGGGAACUUCUACUUUUUCAAAAGUAAAAACUAAUUUUCUUUCUAUAUAAAACAGGGGAACACUCUCAUUGUGAGAAUGUUCCCCUAUUAUCAAAAUAACUCUUACAAGAAGUUUUA ........((((............(((((((((((((((.....)))))))))))))))((((((....))))))....(((((((.....(((((.(((((((.....))))..............((((((...((((.((((((((..((.....(((((((((((((((((((((..((((.((((((((((((..........)))))))))))).))))..))))))))))))))))))))))).)))))))).))))..))))))......))).)))))....(((....)))................)))))))......)))).((((((((((((((....)))))............................(((((((((.((((.....)))).))))))))).....................))))))))). (-121.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAACUUCUUGUAAGAGUUAUUUUGAUAAUAGGGGAACAUUCUCACAAUGAGAGUGUUCCCCUGUUUUAUAUAGAAAGAAAAUUAGUUUUUACUUUUGAAAAAGUAGAAGUUCCCCAUAAGGUAGUCUUUAGCGUAGUAUGAAGUAAGCCUUAAAAGGUUUUGACAAUCAAGUGUUCAGCUUGUUAAUAUAAAAAUCUAGUAAAUUACUUACACGUAAAUAAAUAUUUUUCUACGUGUAAAUAAAUAUUUCUCUACACGUAAAUAAAUUAUUAUUUACACGUAAAUAAUUUCAGCGACAAAGAUUUUUGCAUCCUGCAAGCCUUUUGGUUAUGUGCUUCUAAAAAAGAAUUGGUUGCCGUUUUCUAAAGAGUUGUUUGUGUAAGCACAAAAAAAGACCGAACCCCAAGCAAGGGUUCGGUCUUUUAUUUUUAUCUUGUAUGUUAAAUUA ...(((((.......)))))..(((((((((((((((((((((((.....))))))))))))))))......(((((((..(((((((((((....((....)).(((((((...(((.(((((.((((((..(((....((((((((...(((..(((((((......(((((.....)))))........)))))))..))).)))))).)).((((((((..((((...((((((((..............))))))))...))))..))))))))...............)))..))))))..((((.....))))))))).)))......)))))))...)))))))))))....)))))))((((....((((((....))))))((((((((((((((.......)))))))))))))).......))))...)))))))... (-122.58) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 632 240 191 159 110 pint:PI1673|5end_hypothetical_protein_1587718..1587948_POSITIVE 578 240 191 152 103 pint:PI0983|5end_hypothetical_protein_909750..909980_POSITIVE 529 240 191 137 88 pint:PI0579|5end_hypothetical_protein_523419..523649_POSITIVE 507 240 191 228 179 pint:PI0702|5end_conserved_hypothetical_protein;_possible_tetracenomycin_C_synthesis_protein_homolog_638640..638870_POSITIVE 503 240 191 115 66 pint:PI1450|5end_hypothetical_protein_1372683..1372913_POSITIVE 501 220 171 161 112 pint:PI0648|5end_hypothetical_protein_589448..589678_POSITIVE 446 240 191 133 84 pint:PI0312|5end_hypothetical_protein_294591..294821_POSITIVE 410 200 151 97 48 pint:PI1462|5end_hypothetical_protein_1385094..1385324_POSITIVE 409 240 191 171 122 pint:PI0619|5end_hypothetical_protein_569364..569594_POSITIVE 349 62 23 148 112 pint:PI0760|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_694086..694316_POSITIVE 344 254 211 173 130 pint:PI0130|5end_hypothetical_protein_122032..122262_POSITIVE 337 196 155 219 179 pint:PI0311|5end_hypothetical_protein_294721..294951_POSITIVE 328 200 151 230 181 pint:PI1674|5end_hypothetical_protein_1587829..1588059_POSITIVE 320 429 385 63 16 pint:PI0895|5end_2-oxoglutarate_oxidoreductase,_beta_subunit,_possible_ketoisovalerate_oxidoreductase,__vorA_826347..826577_POSITIVE 317 220 179 230 189 pint:PI0599|5end_hypothetical_protein_547376..547606_POSITIVE 316 245 206 165 126 pint:PI0115|5end_hypothetical_protein_108062..108292_POSITIVE 316 245 206 151 112 pint:PI0111|5end_hypothetical_protein_108048..108278_POSITIVE 316 245 206 116 77 pint:PI0112|5end_hypothetical_protein_108013..108243_POSITIVE 310 72 31 147 102 pint:PI1705|5end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_1621781..1622011_POSITIVE 308 157 114 193 142 pint:PI0831|5end_hypothetical_protein_768129..768359_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 529 240 191 122 73 pint:PI0725|3end_hypothetical_protein_658933..659083_POSITIVE 518 240 191 67 18 pint:PI0701|3end_hypothetical_protein_638537..638687_POSITIVE 470 240 191 67 18 pint:PI0533|3end_ABC_transporter,_permease_protein_488421..488571_POSITIVE 455 59 14 66 23 pint:PI1365|3end_conserved_hypothetical_protein;_probable_transmembrane_protein_1285675..1285825_POSITIVE 441 225 184 52 11 pint:PI0797|3end_tRNA_pseudouridine_synthase_A_(pseudouridylate_synthase)_735752..735902_POSITIVE 391 250 206 62 15 pint:PI1314|3end_hypothetical_protein_1231423..1231573_POSITIVE 375 247 202 46 1 pint:PI0808|3end_ISPg3-related_transposase_746457..746607_POSITIVE 365 220 172 142 98 pint:PI2105|3end_hypothetical_protein_2059586..2059736_POSITIVE 365 220 172 54 10 pint:PI2106|3end_hypothetical_protein_2059498..2059648_POSITIVE 338 247 211 56 20 pint:PI0598|3end_hypothetical_protein_547233..547383_POSITIVE 307 196 154 63 19 pint:PI0172|3end_ISPg3-related_transposase_165238..165388_POSITIVE 295 218 184 36 2 pint:PI1461|3end_conserved_hypothetical_protein_1385073..1385223_POSITIVE 288 69 29 90 50 pint:PI0256|3end_conjugative_transposon_protein,_TraE_249420..249570_POSITIVE 287 248 201 50 3 pint:PI2160|3end_hypothetical_protein_2108357..2108507_POSITIVE 277 65 21 144 95 pint:PI0561|3end_hypothetical_protein_509136..509286_POSITIVE 265 60 14 107 64 pint:PI2024|3end_hypothetical_protein_1978985..1979135_POSITIVE 265 60 14 81 38 pint:PI2022|3end_hypothetical_protein_1978959..1979109_POSITIVE 265 70 27 119 62 pint:PI0745|3end_conserved_hypothetical_protein_675670..675820_POSITIVE 265 66 31 51 6 pint:PI0728|3end_integrase_661508..661658_POSITIVE 262 157 113 150 103 pint:PI1512|3end_hypothetical_protein_1429893..1430043_POSITIVE