Origin IGS: ttaagttctgtttgcgttctctaagggtgattttggtatttgtattcctctctgcttacagggattttacgccccgaaacattcatcttaatgcctgtttattgcattagatactttgcaaaagtatagaaaatagtggaaactgtccaaggaaatccgtcttgtttatatctttttaacgctacatacacgtatctgttataaaaattaacccattcagaaaacgcccatatatataaggtgtaaaacctaaaaatagcggtaaattgacagaaaacacctattaatgaaacattttcagcaaataattgcaaaaaagttaggtggttattggaatatttgtacctttgcatcgattctattactataacaatttaataaaaaatatcacacaaatactatatggagaacttagaagcaacaaaggtttcgggagagacg .........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 cgtctctcccgaaacctttgttgcttctaagttctccatatagtatttgtgtgatattttttattaaattgttatagtaatagaatcgatgcaaaggtacaaatattccaataaccacctaacttttttgcaattatttgctgaaaatgtttcattaataggtgttttctgtcaatttaccgctatttttaggttttacaccttatatatatgggcgttttctgaatgggttaatttttataacagatacgtgtatgtagcgttaaaaagatataaacaagacggatttccttggacagtttccactattttctatacttttgcaaagtatctaatgcaataaacaggcattaagatgaatgtttcggggcgtaaaatccctgtaagcagagaggaatacaaataccaaaatcacccttagagaacgcaaacagaacttaa Mask Tandem Repeat Region ================================================ ttaagttctgtttgcgttctctaagggtgattttggtatttgtattcctctctgcttacagggattttacgccccgaaacattcatcttaatgcctgtttattgcattagatactttgcaaaagtatagaaaatagtggaaactgtccaaggaaatccgtcttgtttatatctttttaacgctacatacacgtatctgttataaaaattaacccattcagaaaacgcccatatatataaggtgtaaaacctaaaaatagcggtaaattgacagaaaacacctattaatgaaacattttcagcaaataattgcaaaaaagttaggtggttattggaatatttgtacctttgcatcgattctattactataacaatttaataaaaaatatcacacaaatactatatggagaacttagaagcaacaaaggtttcgggagagacg Find is-nt database================================================ Query_seq: PI2055:PI2056|PI2055:PI2056:hypothetical protein:conserved hypothetical protein:->->:2013466..2013906 441 ttaagttctgtttgcgttctctaagggtgattttggtatttgtattcctctctgcttacagggattttacgccccgaaacattcatcttaatgcctgtttattgcattagatactttgcaaaagtatagaaaatagtggaaactgtccaaggaaatccgtcttgtttatatctttttaacgctacatacacgtatctgttataaaaattaacccattcagaaaacgcccatatatataaggtgtaaaacctaaaaatagcggtaaattgacagaaaacacctattaatgaaacattttcagcaaataattgcaaaaaagttaggtggttattggaatatttgtacctttgcatcgattctattactataacaatttaataaaaaatatcacacaaatactatatggagaacttagaagcaacaaaggtttcgggagagacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2055:PI2056|PI2055:PI2056:hypothetical protein:conserved hypothetical protein:->->:2013466..2013906 441 ttaagttctgtttgcgttctctaagggtgattttggtatttgtattcctctctgcttacagggattttacgccccgaaacattcatcttaatgcctgtttattgcattagatactttgcaaaagtatagaaaatagtggaaactgtccaaggaaatccgtcttgtttatatctttttaacgctacatacacgtatctgttataaaaattaacccattcagaaaacgcccatatatataaggtgtaaaacctaaaaatagcggtaaattgacagaaaacacctattaatgaaacattttcagcaaataattgcaaaaaagttaggtggttattggaatatttgtacctttgcatcgattctattactataacaatttaataaaaaatatcacacaaatactatatggagaacttagaagcaacaaaggtttcgggagagacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2055:PI2056|PI2055:PI2056:hypothetical protein:conserved hypothetical protein:->->:2013466..2013906 441 ttaagttctgtttgcgttctctaagggtgattttggtatttgtattcctctctgcttacagggattttacgccccgaaacattcatcttaatgcctgtttattgcattagatactttgcaaaagtatagaaaatagtggaaactgtccaaggaaatccgtcttgtttatatctttttaacgctacatacacgtatctgttataaaaattaacccattcagaaaacgcccatatatataaggtgtaaaacctaaaaatagcggtaaattgacagaaaacacctattaatgaaacattttcagcaaataattgcaaaaaagttaggtggttattggaatatttgtacctttgcatcgattctattactataacaatttaataaaaaatatcacacaaatactatatggagaacttagaagcaacaaaggtttcgggagagacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaagttctgtttgcgttctctaagggtgattttggtatttgtattcctctctgcttacagggattttacgccccgaaacattcatcttaatgcctgtttattgcattagatactttgcaaaagtatagaaaatagtggaaactgtccaaggaaatccgtcttgtttatatctttttaacgctacatacacgtatctgttataaaaattaacccattcagaaaacgcccatatatataaggtgtaaaacctaaaaatagcggtaaattgacagaaaacacctattaatgaaacattttcagcaaataattgcaaaaaagttaggtggttattggaatatttgtacctttgcatcgattctattactataacaatttaataaaaaatatcacacaaatactatatggagaacttagaagcaacaaaggtttcgggagagacg Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 12 End: 107 ........... M R S L R V I L V F V F L S A Y R D F T P R N I H L N A C L L H .............................................................................................................................................................................................................................................................................................................................................. Protein_Len: 34 Strand: + Start: 266 End: 367 ......................................................................................................................................................................................................................................................................... M D R K H L L M K H F Q Q I I A K K L G G Y W N I C T F A S I L L L .......................................................................... Protein_Len: 31 Strand: + Start: 283 End: 375 .......................................................................................................................................................................................................................................................................................... M N E T F S A N N C K K V R W L L E Y L Y L C I D S I T I T I .................................................................. Protein_Len: 39 Strand: + Start: 324 End: 440 ................................................................................................................................................................................................................................................................................................................................... M V I G I F V P L H R F Y Y Y N N L I K N I T Q I L Y G E L R S N K G F G R D . Protein_Len: 32 Strand: - Start: 185 End: 280 ........................................................................................................................................................................................ M C T D T I F I L G N L F R G Y I Y P T F G L F L P L N V S F M ................................................................................................................................................................. Protein_Len: 60 Strand: - Start: 102 End: 374 ..................................................................................................... R N Y F N V W E S F A W I Y L T Y F R F I A T F Q C F V G I L S V N E A F L Q L F T L H N N S Y K Y R Q M S E I V I V M ................................................................... ttaagttctgtttgcgttctctaagggtgattttggtatttgtattcctctctgcttacagggattttacgccccgaaacattcatcttaatgcctgtttattgcattagatactttgcaaaagtatagaaaatagtggaaactgtccaaggaaatccgtcttgtttatatctttttaacgctacatacacgtatctgttataaaaattaacccattcagaaaacgcccatatatataaggtgtaaaacctaaaaatagcggtaaattgacagaaaacacctattaatgaaacattttcagcaaataattgcaaaaaagttaggtggttattggaatatttgtacctttgcatcgattctattactataacaatttaataaaaaatatcacacaaatactatatggagaacttagaagcaacaaaggtttcgggagagacg 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================================================ ttaagttctgtttgcgttctctaagggtgattttggtatttgtattcctctctgcttacagggattttacgccccgaaacattcatcttaatgcctgtttattgcattagatactttgcaaaagtatagaaaatagtggaaactgtccaaggaaatccgtcttgtttatatctttttaacgctacatacacgtatctgttataaaaattaacccattcagaaaacgcccatatatataaggtgtaaaacctaaaaatagcggtaaattgacagaaaacacctattaatgaaacattttcagcaaataattgcaaaaaagttaggtggttattggaatatttgtacctttgcatcgattctattactataacaatttaataaaaaatatcacacaaatactatatggagaacttagaagcaacaaaggtttcgggagagacg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI2055:PI2056|PI2055:PI2056:hypothetical protein:conserved hypothetical protein:->->:2013466..2013906 441 ttaagttctgtttgcgttctctaagggtgattttggtatttgtattcctctctgcttacagggattttacgccccgaaacattcatcttaatgcctgtttattgcattagatactttgcaaaagtatagaaaatagtggaaactgtccaaggaaatccgtcttgtttatatctttttaacgctacatacacgtatctgttataaaaattaacccattcagaaaacgcccatatatataaggtgtaaaacctaaaaatagcggtaaattgacagaaaacacctattaatgaaacattttcagcaaataattgcaaaaaagttaggtggttattggaatatttgtacctttgcatcgattctattactataacaatttaataaaaaatatcacacaaatactatatggagaacttagaagcaacaaaggtttcgggagagacg Intra-Species Hit: Count: 1 Min: 1 Max: 441 Len: 441 Subject: pint_PI2055_PI2056|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2013466,2013906]|441 HSP 1 e-value: 0.0 bit: 874.0 Len: 441 Query Start:1 Query End:441 Subject Strand: POSITIVE Subject Start: 1 Subject End: 441 ttaagttctgtttgcgttctctaagggtgattttggtatttgtattcctctctgcttacagggattttacgccccgaaacattcatcttaatgcctgtttattgcattagatactttgcaaaagtatagaaaatagtggaaactgtccaaggaaatccgtcttgtttatatctttttaacgctacatacacgtatctgttataaaaattaacccattcagaaaacgcccatatatataaggtgtaaaacctaaaaatagcggtaaattgacagaaaacacctattaatgaaacattttcagcaaataattgcaaaaaagttaggtggttattggaatatttgtacctttgcatcgattctattactataacaatttaataaaaaatatcacacaaatactatatggagaacttagaagcaacaaaggtttcgggagagacg ttaagttctgtttgcgttctctaagggtgattttggtatttgtattcctctctgcttacagggattttacgccccgaaacattcatcttaatgcctgtttattgcattagatactttgcaaaagtatagaaaatagtggaaactgtccaaggaaatccgtcttgtttatatctttttaacgctacatacacgtatctgttataaaaattaacccattcagaaaacgcccatatatataaggtgtaaaacctaaaaatagcggtaaattgacagaaaacacctattaatgaaacattttcagcaaataattgcaaaaaagttaggtggttattggaatatttgtacctttgcatcgattctattactataacaatttaataaaaaatatcacacaaatactatatggagaacttagaagcaacaaaggtttcgggagagacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAGUUCUGUUUGCGUUCUCUAAGGGUGAUUUUGGUAUUUGUAUUCCUCUCUGCUUACAGGGAUUUUACGCCCCGAAACAUUCAUCUUAAUGCCUGUUUAUUGCAUUAGAUACUUUGCAAAAGUAUAGAAAAUAGUGGAAACUGUCCAAGGAAAUCCGUCUUGUUUAUAUCUUUUUAACGCUACAUACACGUAUCUGUUAUAAAAAUUAACCCAUUCAGAAAACGCCCAUAUAUAUAAGGUGUAAAACCUAAAAAUAGCGGUAAAUUGACAGAAAACACCUAUUAAUGAAACAUUUUCAGCAAAUAAUUGCAAAAAAGUUAGGUGGUUAUUGGAAUAUUUGUACCUUUGCAUCGAUUCUAUUACUAUAACAAUUUAAUAAAAAAUAUCACACAAAUACUAUAUGGAGAACUUAGAAGCAACAAAGGUUUCGGGAGAGACG ....(((((.((((.((((((((.(((((.((((((....((((....((((((....))))))...))))..)))))))))))...........((((........((((.....((((((.(((((((...((((....))))(((((.....((.(((..((((((..........(((((......(((.((((...................))))..)))............((((.....)))).....))))))))))).))).))...((((((....((((.....))))((((....))))........))))))....)))))...))))))).)))))).....)))).......))))...............................)))))))).)))))).)))....(((((....))))). (-90.07) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUCUCUCCCGAAACCUUUGUUGCUUCUAAGUUCUCCAUAUAGUAUUUGUGUGAUAUUUUUUAUUAAAUUGUUAUAGUAAUAGAAUCGAUGCAAAGGUACAAAUAUUCCAAUAACCACCUAACUUUUUUGCAAUUAUUUGCUGAAAAUGUUUCAUUAAUAGGUGUUUUCUGUCAAUUUACCGCUAUUUUUAGGUUUUACACCUUAUAUAUAUGGGCGUUUUCUGAAUGGGUUAAUUUUUAUAACAGAUACGUGUAUGUAGCGUUAAAAAGAUAUAAACAAGACGGAUUUCCUUGGACAGUUUCCACUAUUUUCUAUACUUUUGCAAAGUAUCUAAUGCAAUAAACAGGCAUUAAGAUGAAUGUUUCGGGGCGUAAAAUCCCUGUAAGCAGAGAGGAAUACAAAUACCAAAAUCACCCUUAGAGAACGCAAACAGAACUUAA ................(((((((((((((((...........((((((((((......(((((.....(((((((.(((.((((..(..((((((((((.......(((((....(((((((((((((.((((....)))).))))).))........))))))...((((((..((((.(((.......((((.....))))....((((((.((((..((((.(((((......)))))..)))).)))).))))))))).))))..(.......)..)))))).....))))).(((....)))........))))))))))..)..)))).))).)).)))))....)))))....((((((((((........))))).))))).......))))))))))..........)))))))...)).))))))...... (-91.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 56 14 210 167 pint:PI0301|5end_probable_transposase_285672..285902_POSITIVE 304 106 70 194 150 pint:PI1036|5end_ATP-dependent__Lon_protease_954446..954676_POSITIVE 298 160 114 178 135 pint:PI0190|5end_3-dehydroquinate_dehydratase_II_180618..180848_POSITIVE 295 40 5 187 148 pint:PI1360|5end_conserved_hypothetical_protein_1275923..1276153_POSITIVE 293 50 6 52 10 pint:PI1228|5end_conserved_hypothetical_protein_1149045..1149275_POSITIVE 276 81 47 193 153 pint:PI2099|5end_D-alanyl-D-alanine_dipeptidase_2052409..2052639_POSITIVE 273 43 2 225 182 pint:PI1520|5end_hypothetical_protein_1441162..1441392_POSITIVE 273 76 41 125 81 pint:PI0539|5end_hypothetical_protein_493406..493636_POSITIVE 270 67 21 226 188 pint:PI0393|5end_conserved_hypothetical_protein_358696..358926_POSITIVE 270 75 33 201 150 pint:PI0336|5end_hypothetical_protein_314499..314729_POSITIVE 269 73 31 217 171 pint:PI0764|5end_permease_697962..698192_POSITIVE 263 78 33 65 13 pint:PI0906|5end_hypothetical_protein_835653..835883_POSITIVE 262 355 312 160 115 pint:PI0912|5end_conserved_hypothetical_protein_842034..842264_POSITIVE 261 73 31 60 10 pint:PI0740|5end_hypothetical_protein_672112..672342_POSITIVE 260 100 58 117 58 pint:PI1431|5end_conserved_hypothetical_protein_1352079..1352309_POSITIVE 259 190 142 111 54 pint:PI1818|5end_hypothetical_protein_1756891..1757121_POSITIVE 257 100 54 97 54 pint:PI0248|5end_protein_associated_with_conjugate_transformation/chromosome_partioning_246139..246369_POSITIVE 256 118 71 63 11 pint:PI0531|5end_ABC_transporter,_ATP-binding_protein;_possible_gliding_motility_related_484696..484926_POSITIVE 255 36 5 205 179 pint:PI1713|5end_ABC_transporter,_ATP-binding_protein_1628418..1628648_POSITIVE 253 270 223 195 140 pint:PI2085|5end_conserved_hypothetical_protein_2041100..2041330_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 283 120 71 100 49 pint:PI0865|3end_possible_phosphoglycerol_transferase_803684..803834_POSITIVE 260 153 116 71 28 pint:PI1013|3end_probable_transcriptional_regulator_934368..934518_POSITIVE 259 77 41 127 92 pint:PI0377|3end_DNA_primase/mobilizable_transposon,_excision_protein_347823..347973_POSITIVE 259 360 311 132 81 pint:PI0083|3end_tyrosyl-tRNA_synthetase_84115..84265_POSITIVE 258 127 81 82 26 pint:PI0893|3end_outer_membrane_protein_41_precursor_825662..825812_POSITIVE 257 100 54 110 67 pint:PI0247|3end_conjugative_transposon_protein,_TraA_246232..246382_POSITIVE 256 77 40 51 16 pint:PI0582|3end_hypothetical_protein_525214..525364_POSITIVE 255 36 5 136 110 pint:PI1711|3end_ABC_transporter,_ATP-binding_protein_1628429..1628579_POSITIVE 253 270 223 84 29 pint:PI2084|3end_hypothetical_protein_2041069..2041219_POSITIVE 253 440 400 82 36 pint:PI0252|3end_conserved_hypothetical_protein_248383..248533_POSITIVE 252 247 216 69 30 pint:PI0854|3end_MiaB-like_tRNA_modifying_enzyme_787999..788149_POSITIVE 251 355 311 101 47 pint:PI0198|3end_hypothetical_protein_191056..191206_POSITIVE 249 147 101 108 67 pint:PI0203|3end_conserved_hypothetical_protein_196064..196214_POSITIVE 248 140 91 146 91 pint:PI1146|3end_translation_initiation_factor_IF3_1073503..1073653_POSITIVE 247 57 12 66 25 pint:PI0744|3end_DNA_primase/mobilizable_transposon,_excision_protein_675186..675336_POSITIVE 247 177 133 113 65 pint:PI0398|3end_hypothetical_protein_363541..363691_POSITIVE 245 43 3 57 19 pint:PI1916|3end_conserved_hypothetical_protein_1860740..1860890_POSITIVE 243 55 13 62 19 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 242 245 201 82 43 pint:PI0909|3end_possible_mutT/NUDIX_family_protein_838088..838238_POSITIVE 242 440 399 50 6 pint:PI0262|3end_conserved_hypothetical_protein_255094..255244_POSITIVE