Origin IGS: tagccttgcagaaactccgacagtgcattatcgctatacaataaaggttggaatccgaacgaggactccaaccttttttcggttatttacgcacacagccgatttttcaacacgtagagaaatatttatttacgtgtaaagaaattcttatttacgtgtagaaaaatattta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaatatttttctacacgtaaataagaatttctttacacgtaaataaatatttctctacgtgttgaaaaatcggctgtgtgcgtaaataaccgaaaaaaggttggagtcctcgttcggattccaacctttattgtatagcgataatgcactgtcggagtttctgcaaggcta Mask Tandem Repeat Region ================================================ tagccttgcagaaactccgacagtgcattatcgctatacaataaaggttggaatccgaacgaggactccaaccttttttcggttatttacgcacacagccgatttttcaacacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Find is-nt database================================================ Query_seq: PI0110:PI0112|PI0110:PI0112:ABC transport system, ATP-binding protein:hypothetical protein:->->:107981..108152 172 tagccttgcagaaactccgacagtgcattatcgctatacaataaaggttggaatccgaacgaggactccaaccttttttcggttatttacgcacacagccgatttttcaacacgtagagaaatatttatttacgtgtaaagaaattcttatttacgtgtagaaaaatattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0110:PI0112|PI0110:PI0112:ABC transport system, ATP-binding protein:hypothetical protein:->->:107981..108152 172 tagccttgcagaaactccgacagtgcattatcgctatacaataaaggttggaatccgaacgaggactccaaccttttttcggttatttacgcacacagccgatttttcaacacgtagagaaatatttatttacgtgtaaagaaattcttatttacgtgtagaaaaatattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0110:PI0112|PI0110:PI0112:ABC transport system, ATP-binding protein:hypothetical protein:->->:107981..108152 172 tagccttgcagaaactccgacagtgcattatcgctatacaataaaggttggaatccgaacgaggactccaaccttttttcggttatttacgcacacagccgatttttcaacacgtagagaaatatttatttacgtgtaaagaaattcttatttacgtgtagaaaaatattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagccttgcagaaactccgacagtgcattatcgctatacaataaaggttggaatccgaacgaggactccaaccttttttcggttatttacgcacacagccgatttttcaacacgtagagaaatatttatttacgtgtaaagaaattcttatttacgtgtagaaaaatattta Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 23 End: 136 ...................... M H Y R Y T I K V G I R T R T P T F F R L F T H T A D F S T R R E I F I Y V .................................... Protein_Len: 37 Strand: + Start: 48 End: 158 ............................................... M E S E R G L Q P F F G Y L R T Q P I F Q H V E K Y L F T C K E I L I Y V .............. Protein_Len: 31 Strand: - Start: 37 End: 129 .................................... V I F T P I R V L V G V K K R N N V C V A S K E V R L S I N M ........................................... tagccttgcagaaactccgacagtgcattatcgctatacaataaaggttggaatccgaacgaggactccaaccttttttcggttatttacgcacacagccgatttttcaacacgtagagaaatatttatttacgtgtaaagaaattcttatttacgtgtagaaaaatattta 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================================================ tagccttgcagaaactccgacagtgcattatcgctatacaataaaggttggaatccgaacgaggactccaaccttttttcggttatttacgcacacagccgatttttcaacacgtagagaaatatttatttacgtgtaaagaaattcttatttacgtgtagaaaaatattta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -9.9 Tail_Score: -5.23016 Start: 46 End: 73 Full_Region: TCGCTATACAATAAA GGTTGGAATCC GAACGA GGACTCCAACC TTTTTTCGGTTATTT .............................................GGTTGGAATCCGAACGAGGACTCCAACC................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -12.1 Tail_Score: -4.38927 Start: 46 End: 73 Full_Region: aaataaccgaaaaaa ggttggagtcc tcgttc ggattccaacc tttattgtatagcga .............................................ggttggagtcctcgttcggattccaacc................................................................................................... Find igs database================================================ Query_seq: PI0110:PI0112|PI0110:PI0112:ABC transport system, ATP-binding protein:hypothetical protein:->->:107981..108152 172 tagccttgcagaaactccgacagtgcattatcgctatacaataaaggttggaatccgaacgaggactccaaccttttttcggttatttacgcacacagccgatttttcaacacgtagagaaatatttatttacgtgtaaagaaattcttatttacgtgtagaaaaatattta Intra-Species Hit: Count: 1 Min: 1 Max: 172 Len: 172 Subject: pint_PI0110_PI0112|ABC transport system, ATP-binding protein:hypothetical protein|POSITIVE:POSITIVE|[107981,108152]|172 HSP 1 e-value: 5.0E-93 bit: 341.0 Len: 172 Query Start:1 Query End:172 Subject Strand: POSITIVE Subject Start: 1 Subject End: 172 tagccttgcagaaactccgacagtgcattatcgctatacaataaaggttggaatccgaacgaggactccaaccttttttcggttatttacgcacacagccgatttttcaacacgtagagaaatatttatttacgtgtaaagaaattcttatttacgtgtagaaaaatattta tagccttgcagaaactccgacagtgcattatcgctatacaataaaggttggaatccgaacgaggactccaaccttttttcggttatttacgcacacagccgatttttcaacacgtagagaaatatttatttacgtgtaaagaaattcttatttacgtgtagaaaaatattta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCCUUGCAGAAACUCCGACAGUGCAUUAUCGCUAUACAAUAAAGGUUGGAAUCCGAACGAGGACUCCAACCUUUUUUCGGUUAUUUACGCACACAGCCGAUUUUUCAACACGUAGAGAAAUAUUUAUUUACGUGUAAAGAAAUUCUUAUUUACGUGUAGAAAAAUAUUUA ..((..(((..(((..((((.((((......)))).......((((((((((.(((......))).))))))))))..))))...)))..)))....))..(((((((.(((((((((.....((((.((((....)))).)))).....))))))))).)))))))..... (-47.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUAUUUUUCUACACGUAAAUAAGAAUUUCUUUACACGUAAAUAAAUAUUUCUCUACGUGUUGAAAAAUCGGCUGUGUGCGUAAAUAACCGAAAAAAGGUUGGAGUCCUCGUUCGGAUUCCAACCUUUAUUGUAUAGCGAUAAUGCACUGUCGGAGUUUCUGCAAGGCUA .....(((((((.(((((((.(.(((.((((.((((....)))).)))).))).).))))))).))))))).((((...((((.((((..((((..((((((((((((((......))))))))))))))..(((((.......)))))...)))).)))).)))).)))). (-53.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 617 160 111 137 88 pint:PI0579|5end_hypothetical_protein_523419..523649_POSITIVE 536 160 111 137 88 pint:PI0648|5end_hypothetical_protein_589448..589678_POSITIVE 509 160 111 115 66 pint:PI1462|5end_hypothetical_protein_1385094..1385324_POSITIVE 492 160 111 159 110 pint:PI1673|5end_hypothetical_protein_1587718..1587948_POSITIVE 492 160 111 228 179 pint:PI0702|5end_conserved_hypothetical_protein;_possible_tetracenomycin_C_synthesis_protein_homolog_638640..638870_POSITIVE 468 160 111 130 81 pint:PI0983|5end_hypothetical_protein_909750..909980_POSITIVE 443 160 111 137 88 pint:PI1450|5end_hypothetical_protein_1372683..1372913_POSITIVE 426 140 102 135 97 pint:PI0312|5end_hypothetical_protein_294591..294821_POSITIVE 415 160 111 171 122 pint:PI0619|5end_hypothetical_protein_569364..569594_POSITIVE 316 160 111 182 133 pint:PI0115|5end_hypothetical_protein_108062..108292_POSITIVE 316 160 111 168 119 pint:PI0111|5end_hypothetical_protein_108048..108278_POSITIVE 300 109 61 213 153 pint:PI0537|5end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_489756..489986_POSITIVE 300 147 104 167 124 pint:PI0130|5end_hypothetical_protein_122032..122262_POSITIVE 298 120 80 203 151 pint:PI0750|5end_zinc_protease_677746..677976_POSITIVE 297 120 79 78 32 pint:PI0096|5end_glycerol-3-phosphate_cytidylyltransferase_91885..92115_POSITIVE 293 170 126 229 185 pint:PI0311|5end_hypothetical_protein_294721..294951_POSITIVE 290 118 84 46 7 pint:PI0540|5end_conserved_hypothetical_protein_492955..493185_POSITIVE 287 139 110 116 87 pint:PI0535|5end_hypothetical_protein_489508..489738_POSITIVE 282 167 124 227 185 pint:PI0917|5end_phosphoglycolate_phosphatase_846371..846601_POSITIVE 277 59 13 58 11 pint:PI0121|5end_outer_membrane_protein,_ompH_family_112625..112855_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 503 170 125 55 10 pint:PI0533|3end_ABC_transporter,_permease_protein_488421..488571_POSITIVE 480 160 111 67 22 pint:PI1314|3end_hypothetical_protein_1231423..1231573_POSITIVE 430 160 112 67 17 pint:PI0701|3end_hypothetical_protein_638537..638687_POSITIVE 368 160 111 96 50 pint:PI2105|3end_hypothetical_protein_2059586..2059736_POSITIVE 360 160 112 122 72 pint:PI0725|3end_hypothetical_protein_658933..659083_POSITIVE 348 149 109 49 10 pint:PI0808|3end_ISPg3-related_transposase_746457..746607_POSITIVE 336 160 112 52 2 pint:PI2106|3end_hypothetical_protein_2059498..2059648_POSITIVE 310 160 116 45 1 pint:PI0797|3end_tRNA_pseudouridine_synthase_A_(pseudouridylate_synthase)_735752..735902_POSITIVE 300 147 104 57 14 pint:PI0598|3end_hypothetical_protein_547233..547383_POSITIVE 292 67 21 88 33 pint:PI0904|3end_conserved_hypothetical_protein_834295..834445_POSITIVE 288 76 43 48 15 pint:PI0110|3end_ABC_transport_system,_ATP-binding_protein_107920..108070_POSITIVE 277 59 13 50 3 pint:PI0120|3end_glutamate_racemase_112697..112847_POSITIVE 269 80 33 57 13 pint:PI1142|3end_S1_RNA_binding_domain_protein,_S1_ribosomal_protein_1072122..1072272_POSITIVE 263 100 61 145 96 pint:PI0535|3end_hypothetical_protein_489779..489929_POSITIVE 257 93 54 70 31 pint:PI0706|3end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_643394..643544_POSITIVE 248 67 26 61 12 pint:PI0948|3end_hypothetical_protein_881978..882128_POSITIVE 247 113 71 150 103 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 245 82 44 120 77 pint:PI0721|3end_hypothetical_protein_654982..655132_POSITIVE 244 70 23 101 50 pint:PI0006|3end_hypothetical_protein_8268..8418_POSITIVE 243 75 46 125 93 pint:PI1686|3end_hypothetical_protein_1601898..1602048_POSITIVE