Origin IGS: tagtttacctataagagcgtatgtcaatttcttctttgacatacgctcttattttttagttccttgtctgacaggcactttctttcgctatctcttgcaacttccgagaaaaaggactacatttgcaagcgaatacataaacttaacctaaacgcccccgcctcggtaaggtgttccctcttgcaggagggtgtaaggagaggcacgtagaacaatgaaaaacaatctatctaaaagc .........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 gcttttagatagattgtttttcattgttctacgtgcctctccttacaccctcctgcaagagggaacaccttaccgaggcgggggcgtttaggttaagtttatgtattcgcttgcaaatgtagtcctttttctcggaagttgcaagagatagcgaaagaaagtgcctgtcagacaaggaactaaaaaataagagcgtatgtcaaagaagaaattgacatacgctcttataggtaaacta Mask Tandem Repeat Region ================================================ tagtttacctataagagcgtatgtcaatttcttctttgacatacgctcttattttttagttccttgtctgacaggcactttctttcgctatctcttgcaacttccgagaaaaaggactacatttgcaagcgaatacataaacttaacctaaacgcccccgcctcggtaaggtgttccctcttgcaggagggtgtaaggagaggcacgtagaacaatgaaaaacaatctatctaaaagc Find is-nt database================================================ Query_seq: PI1222:PI1223|PI1222:PI1223:hypothetical protein:conserved hypothetical protein:->->:1143439..1143676 238 tagtttacctataagagcgtatgtcaatttcttctttgacatacgctcttattttttagttccttgtctgacaggcactttctttcgctatctcttgcaacttccgagaaaaaggactacatttgcaagcgaatacataaacttaacctaaacgcccccgcctcggtaaggtgttccctcttgcaggagggtgtaaggagaggcacgtagaacaatgaaaaacaatctatctaaaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1222:PI1223|PI1222:PI1223:hypothetical protein:conserved hypothetical protein:->->:1143439..1143676 238 tagtttacctataagagcgtatgtcaatttcttctttgacatacgctcttattttttagttccttgtctgacaggcactttctttcgctatctcttgcaacttccgagaaaaaggactacatttgcaagcgaatacataaacttaacctaaacgcccccgcctcggtaaggtgttccctcttgcaggagggtgtaaggagaggcacgtagaacaatgaaaaacaatctatctaaaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1222:PI1223|PI1222:PI1223:hypothetical protein:conserved hypothetical protein:->->:1143439..1143676 238 tagtttacctataagagcgtatgtcaatttcttctttgacatacgctcttattttttagttccttgtctgacaggcactttctttcgctatctcttgcaacttccgagaaaaaggactacatttgcaagcgaatacataaacttaacctaaacgcccccgcctcggtaaggtgttccctcttgcaggagggtgtaaggagaggcacgtagaacaatgaaaaacaatctatctaaaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagtttacctataagagcgtatgtcaatttcttctttgacatacgctcttattttttagttccttgtctgacaggcactttctttcgctatctcttgcaacttccgagaaaaaggactacatttgcaagcgaatacataaacttaacctaaacgcccccgcctcggtaaggtgttccctcttgcaggagggtgtaaggagaggcacgtagaacaatgaaaaacaatctatctaaaagc Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 11 End: 148 .......... M R A Y V N F F F D I R S Y F L V P C L T G T F F R Y L L Q L P R K R T T F A S E Y I N L T .......................................................................................... Protein_Len: 48 Strand: + Start: 64 End: 207 ............................................................... M S D R H F L S L S L A T S E K K D Y I C K R I H K L N L N A P A S V R C S L L Q E G V R R G T ............................... Protein_Len: 37 Strand: - Start: 120 End: 230 ....................................................................................................................... M Q L R I C L S L R F A G A E T L H E R K C S P T L L P V Y F L S F C D M ........ tagtttacctataagagcgtatgtcaatttcttctttgacatacgctcttattttttagttccttgtctgacaggcactttctttcgctatctcttgcaacttccgagaaaaaggactacatttgcaagcgaatacataaacttaacctaaacgcccccgcctcggtaaggtgttccctcttgcaggagggtgtaaggagaggcacgtagaacaatgaaaaacaatctatctaaaagc 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================================================ tagtttacctataagagcgtatgtcaatttcttctttgacatacgctcttattttttagttccttgtctgacaggcactttctttcgctatctcttgcaacttccgagaaaaaggactacatttgcaagcgaatacataaacttaacctaaacgcccccgcctcggtaaggtgttccctcttgcaggagggtgtaaggagaggcacgtagaacaatgaaaaacaatctatctaaaagc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 78 HP_score: -10.9 Tail_Score: -3.25102 Start: 17 End: 46 Full_Region: aactaaaaaataaga gcgtatgtcaa agaagaaa ttgacatacgc tcttataggtaaact ................gcgtatgtcaaagaagaaattgacatacgc................................................................................................................................................................................................ Find igs database================================================ Query_seq: PI1222:PI1223|PI1222:PI1223:hypothetical protein:conserved hypothetical protein:->->:1143439..1143676 238 tagtttacctataagagcgtatgtcaatttcttctttgacatacgctcttattttttagttccttgtctgacaggcactttctttcgctatctcttgcaacttccgagaaaaaggactacatttgcaagcgaatacataaacttaacctaaacgcccccgcctcggtaaggtgttccctcttgcaggagggtgtaaggagaggcacgtagaacaatgaaaaacaatctatctaaaagc Intra-Species Hit: Count: 1 Min: 1 Max: 238 Len: 238 Subject: pint_PI1222_PI1223|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1143439,1143676]|238 HSP 1 e-value: 1.0E-132 bit: 472.0 Len: 238 Query Start:1 Query End:238 Subject Strand: POSITIVE Subject Start: 1 Subject End: 238 tagtttacctataagagcgtatgtcaatttcttctttgacatacgctcttattttttagttccttgtctgacaggcactttctttcgctatctcttgcaacttccgagaaaaaggactacatttgcaagcgaatacataaacttaacctaaacgcccccgcctcggtaaggtgttccctcttgcaggagggtgtaaggagaggcacgtagaacaatgaaaaacaatctatctaaaagc tagtttacctataagagcgtatgtcaatttcttctttgacatacgctcttattttttagttccttgtctgacaggcactttctttcgctatctcttgcaacttccgagaaaaaggactacatttgcaagcgaatacataaacttaacctaaacgcccccgcctcggtaaggtgttccctcttgcaggagggtgtaaggagaggcacgtagaacaatgaaaaacaatctatctaaaagc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUUUACCUAUAAGAGCGUAUGUCAAUUUCUUCUUUGACAUACGCUCUUAUUUUUUAGUUCCUUGUCUGACAGGCACUUUCUUUCGCUAUCUCUUGCAACUUCCGAGAAAAAGGACUACAUUUGCAAGCGAAUACAUAAACUUAACCUAAACGCCCCCGCCUCGGUAAGGUGUUCCCUCUUGCAGGAGGGUGUAAGGAGAGGCACGUAGAACAAUGAAAAACAAUCUAUCUAAAAGC ..((((....(((((((((((((((((........))))))))))))))))).......(((.(((((((....((.((((((((((((..(((((((((..(((........)))....(((((....)))))................((((((.(((...)))...)))))).....))))))))))))).))))))))))...))).)))).)))))))............... (-71.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUUUAGAUAGAUUGUUUUUCAUUGUUCUACGUGCCUCUCCUUACACCCUCCUGCAAGAGGGAACACCUUACCGAGGCGGGGGCGUUUAGGUUAAGUUUAUGUAUUCGCUUGCAAAUGUAGUCCUUUUUCUCGGAAGUUGCAAGAGAUAGCGAAAGAAAGUGCCUGUCAGACAAGGAACUAAAAAAUAAGAGCGUAUGUCAAAGAAGAAAUUGACAUACGCUCUUAUAGGUAAACUA ...........................((((..(((((((.......(((((......)))))....((((...)))).)))))))..))))...(((((((...(((((((((((......(((........)))..)))))......))))))....(((.(((........))).))).....(((((((((((((((((........)))))))))))))))))..))))))). (-70.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 365 208 164 104 51 pint:PI1058|5end_possible_FHA_domain_protein_977577..977807_POSITIVE 357 207 163 227 181 pint:PI1512|5end_hypothetical_protein_1429529..1429759_POSITIVE 357 207 162 119 74 pint:PI0331|5end_hypothetical_protein_311656..311886_POSITIVE 347 200 153 66 21 pint:PI0787|5end_glycosyltransferase_724136..724366_POSITIVE 342 218 171 157 116 pint:PI0544|5end_hypoxanthine-guanine_phosphoribosyltransferase_(hypoxanthine_phosphoribosyltransferase)_495645..495875_POSITIVE 342 218 171 66 25 pint:PI0542|5end_hypothetical_protein_495554..495784_POSITIVE 337 209 162 60 5 pint:PI0009|5end_NAD-dependent_epimerase/dehydratase_family_protein_9653..9883_POSITIVE 336 200 153 75 17 pint:PI0760|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_694086..694316_POSITIVE 335 198 153 212 155 pint:PI0355|5end_probable__N-acetylmuramoyl-L-alanine_amidase_326157..326387_POSITIVE 333 217 174 187 139 pint:PI0815|5end_hypothetical_protein_754475..754705_POSITIVE 331 194 151 87 36 pint:PI0385|5end_hypothetical_protein_353968..354198_POSITIVE 327 207 162 51 2 pint:PI0592|5end_DNA_mismatch_repair_protein_540795..541025_POSITIVE 324 199 157 186 130 pint:PI1652|5end_hypothetical_protein_1564655..1564885_POSITIVE 322 214 175 111 70 pint:PI2155|5end_hypothetical_protein_2100664..2100894_POSITIVE 319 204 161 100 55 pint:PI2138|5end_nicotinate_phosphoribosyltransferase_2083836..2084066_POSITIVE 319 107 61 122 69 pint:PI2062|5end_type_I_restriction-modification_system_2021658..2021888_POSITIVE 318 188 150 66 25 pint:PI1653|5end_hypothetical_protein_1565158..1565388_POSITIVE 318 220 180 56 5 pint:PI0780|5end_DNA_gyrase,_subunit_A_(DNA_topoisomerase_(ATP-hydrolyzing))_715902..716132_POSITIVE 318 199 153 71 26 pint:PI0717|5end_conserved_hypothetical_protein_652558..652788_POSITIVE 317 110 63 73 21 pint:PI0262|5end_conserved_hypothetical_protein_254685..254915_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 569 200 152 52 1 pint:PI1246|3end_conserved_hypothetical_protein;_possible_lipoprotein_1171496..1171646_POSITIVE 532 206 162 54 7 pint:PI1245|3end_hypothetical_protein_1171492..1171642_POSITIVE 383 52 11 80 39 pint:PI1222|3end_hypothetical_protein_1143378..1143528_POSITIVE 376 198 153 145 92 pint:PI0421|3end_hypothetical_protein_387774..387924_POSITIVE 358 206 164 102 56 pint:PI0904|3end_conserved_hypothetical_protein_834295..834445_POSITIVE 341 210 163 141 101 pint:PI0543|3end_adenylate_kinase_495722..495872_POSITIVE 334 165 124 60 19 pint:PI0028|3end_aminopeptidase_32727..32877_POSITIVE 333 217 174 58 10 pint:PI0814|3end_conserved_hypothetical_protein_754426..754576_POSITIVE 331 200 152 99 43 pint:PI0059|3end_peptide_chain_release_factor_RF-2_58171..58321_POSITIVE 318 188 150 63 22 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 318 199 153 54 9 pint:PI0715|3end_hypothetical_protein_652621..652771_POSITIVE 317 110 63 73 21 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 314 205 165 138 85 pint:PI0785|3end_hypothetical_protein_724138..724288_POSITIVE 314 205 165 135 82 pint:PI0786|3end_conserved_hypothetical_protein;_possible_glycosyltransferase_724135..724285_POSITIVE 313 200 154 137 88 pint:PI0189|3end_integrase_180437..180587_POSITIVE 309 199 154 129 74 pint:PI0644|3end_dnaJ_protein_586569..586719_POSITIVE 308 214 171 149 93 pint:PI0637|3end_hypothetical_protein_582397..582547_POSITIVE 307 212 174 63 28 pint:PI0252|3end_conserved_hypothetical_protein_248383..248533_POSITIVE 306 207 161 136 85 pint:PI1178|3end_histidyl-tRNA_synthetase_1100564..1100714_POSITIVE 305 229 181 116 66 pint:PI0268|3end_lysozyme-related_protein_259790..259940_POSITIVE