Origin IGS: tcctgccaacaggcaggctgctattaatgttctctttttcatgttttaaattgttattttgatgttatattcttattccactgcaatattataaatattttttataagcagcaagtttttcattgcttaaagtaggttatgcttgtttgattatgtgttctttttaaatatgacgtcatatttcagcaaatatgacgtcatatttggtagaaaatgacgtcatattctgtttacgcta .........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 tagcgtaaacagaatatgacgtcattttctaccaaatatgacgtcatatttgctgaaatatgacgtcatatttaaaaagaacacataatcaaacaagcataacctactttaagcaatgaaaaacttgctgcttataaaaaatatttataatattgcagtggaataagaatataacatcaaaataacaatttaaaacatgaaaaagagaacattaatagcagcctgcctgttggcagga Mask Tandem Repeat Region ================================================ tcctgccaacaggcaggctgctattaatgttctctttttcatgttttaaattgttattttgatgttatattcttattccactgcaatattataaatattttttataagcagcaagtttttcattgcttaaagtaggttatgcttgtttgattatgtgttctttttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctgtttacgcta Find is-nt database================================================ Query_seq: PI0062:PI0063|PI0062:PI0063:endopeptidase:transcriptional regulator, GntR family:->->:63083..63320 238 tcctgccaacaggcaggctgctattaatgttctctttttcatgttttaaattgttattttgatgttatattcttattccactgcaatattataaatattttttataagcagcaagtttttcattgcttaaagtaggttatgcttgtttgattatgtgttctttttaaatatgacgtcatatttcagcaaatatgacgtcatatttggtagaaaatgacgtcatattctgtttacgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0062:PI0063|PI0062:PI0063:endopeptidase:transcriptional regulator, GntR family:->->:63083..63320 238 tcctgccaacaggcaggctgctattaatgttctctttttcatgttttaaattgttattttgatgttatattcttattccactgcaatattataaatattttttataagcagcaagtttttcattgcttaaagtaggttatgcttgtttgattatgtgttctttttaaatatgacgtcatatttcagcaaatatgacgtcatatttggtagaaaatgacgtcatattctgtttacgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0062:PI0063|PI0062:PI0063:endopeptidase:transcriptional regulator, GntR family:->->:63083..63320 238 tcctgccaacaggcaggctgctattaatgttctctttttcatgttttaaattgttattttgatgttatattcttattccactgcaatattataaatattttttataagcagcaagtttttcattgcttaaagtaggttatgcttgtttgattatgtgttctttttaaatatgacgtcatatttcagcaaatatgacgtcatatttggtagaaaatgacgtcatattctgtttacgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcctgccaacaggcaggctgctattaatgttctctttttcatgttttaaattgttattttgatgttatattcttattccactgcaatattataaatattttttataagcagcaagtttttcattgcttaaagtaggttatgcttgtttgattatgtgttctttttaaatatgacgtcatatttcagcaaatatgacgtcatatttggtagaaaatgacgtcatattctgtttacgcta Predict ORF larger than 30AA ================================================ tcctgccaacaggcaggctgctattaatgttctctttttcatgttttaaattgttattttgatgttatattcttattccactgcaatattataaatattttttataagcagcaagtttttcattgcttaaagtaggttatgcttgtttgattatgtgttctttttaaatatgacgtcatatttcagcaaatatgacgtcatatttggtagaaaatgacgtcatattctgtttacgcta 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================================================ tcctgccaacaggcaggctgctattaatgttctctttttcatgttttaaattgttattttgatgttatattcttattccactgcaatattataaatattttttataagcagcaagtttttcattgcttaaagtaggttatgcttgtttgattatgtgttctttttaaatatgacgtcatatttcagcaaatatgacgtcatatttggtagaaaatgacgtcatattctgtttacgcta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 46 HP_score: -3.3 Tail_Score: -3.06162 Start: 89 End: 107 Full_Region: tgaaaaacttgctgc ttataaa aaata tttataa tattgcagtggaata ........................................................................................ttataaaaaatatttataa................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -17.1 Tail_Score: -3.73224 Start: 169 End: 202 Full_Region: TGTGTTCTTTTTAAA TATGACGTCATATTT CAGC AAATATGACGTCATA TTTGGTAGAAAATGA ........................................................................................................................................................................TATGACGTCATATTTCAGCAAATATGACGTCATA.................................... TransTerm Strand: - Conf: 100 HP_score: -17.1 Tail_Score: -3.53012 Start: 169 End: 202 Full_Region: tcattttctaccaaa tatgacgtcatattt gctg aaatatgacgtcata tttaaaaagaacaca ........................................................................................................................................................................tatgacgtcatatttgctgaaatatgacgtcata.................................... TransTerm Strand: + Conf: 100 HP_score: -12.6 Tail_Score: -3.49634 Start: 171 End: 222 Full_Region: TGTTCTTTTTAAATA TGACGTCATATTTCAGCAAATATG ACGT CATATTTGGTAGAAAATGACGTCA TATTCTGTTTACGCT ..........................................................................................................................................................................TGACGTCATATTTCAGCAAATATGACGTCATATTTGGTAGAAAATGACGTCA................ Find igs database================================================ Query_seq: PI0062:PI0063|PI0062:PI0063:endopeptidase:transcriptional regulator, GntR family:->->:63083..63320 238 tcctgccaacaggcaggctgctattaatgttctctttttcatgttttaaattgttattttgatgttatattcttattccactgcaatattataaatattttttataagcagcaagtttttcattgcttaaagtaggttatgcttgtttgattatgtgttctttttaaatatgacgtcatatttcagcaaatatgacgtcatatttggtagaaaatgacgtcatattctgtttacgcta Intra-Species Hit: Count: 1 Min: 1 Max: 238 Len: 238 Subject: pint_PI0062_PI0063|endopeptidase:transcriptional regulator, GntR family|POSITIVE:POSITIVE|[63083,63320]|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 tcctgccaacaggcaggctgctattaatgttctctttttcatgttttaaattgttattttgatgttatattcttattccactgcaatattataaatattttttataagcagcaagtttttcattgcttaaagtaggttatgcttgtttgattatgtgttctttttaaatatgacgtcatatttcagcaaatatgacgtcatatttggtagaaaatgacgtcatattctgtttacgcta tcctgccaacaggcaggctgctattaatgttctctttttcatgttttaaattgttattttgatgttatattcttattccactgcaatattataaatattttttataagcagcaagtttttcattgcttaaagtaggttatgcttgtttgattatgtgttctttttaaatatgacgtcatatttcagcaaatatgacgtcatatttggtagaaaatgacgtcatattctgtttacgcta HSP 2 e-value: 6.0E-7 bit: 56.0 Len: 60 Query Start:167 Query End:226 Subject Strand: NEGATIVE Subject Start: 167 Subject End: 226 ......................................................................................................................................................................aatatgacgtcatatttcagcaaatatgacgtcatatttggtagaaaatgacgtcatatt............ ......................................................................................................................................................................aatatgacgtcattttctaccaaatatgacgtcatatttgctgaaatatgacgtcatatt............ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUGCCAACAGGCAGGCUGCUAUUAAUGUUCUCUUUUUCAUGUUUUAAAUUGUUAUUUUGAUGUUAUAUUCUUAUUCCACUGCAAUAUUAUAAAUAUUUUUUAUAAGCAGCAAGUUUUUCAUUGCUUAAAGUAGGUUAUGCUUGUUUGAUUAUGUGUUCUUUUUAAAUAUGACGUCAUAUUUCAGCAAAUAUGACGUCAUAUUUGGUAGAAAAUGACGUCAUAUUCUGUUUACGCUA .((((((....)))))).............................(((((........(((((((((.((((.....(((.......(((((((.....)))))))..(((((((......((((.....)))).....))))))).......)))......((((((((((((((((((((....)))))))))))))))))))).)))).)))))))))......)))))..... (-58.14) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCGUAAACAGAAUAUGACGUCAUUUUCUACCAAAUAUGACGUCAUAUUUGCUGAAAUAUGACGUCAUAUUUAAAAAGAACACAUAAUCAAACAAGCAUAACCUACUUUAAGCAAUGAAAAACUUGCUGCUUAUAAAAAAUAUUUAUAAUAUUGCAGUGGAAUAAGAAUAUAACAUCAAAAUAACAAUUUAAAACAUGAAAAAGAGAACAUUAAUAGCAGCCUGCCUGUUGGCAGGA ..((.......((((((((((((((((((...((((((((....))))))))..)))).))))))))))))))...............(((.....((.(((......))).))..........(..(((((((((((.....)))))))....))))..)....................................))).................))..((((((....)))))). (-54.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 575 207 161 231 185 pint:PI0108|5end_L-lactate_permease_104892..105122_POSITIVE 486 227 188 167 128 pint:PI0163|5end_conserved_hypothetical_protein_157116..157346_POSITIVE 421 206 165 184 143 pint:PI0001|5end_possible_Ton-B_receptor_400..630_POSITIVE 382 210 166 202 155 pint:PI1534|5end_ATPase/GTPase_1453679..1453909_POSITIVE 302 50 2 117 60 pint:PI0259|5end_conserved_protein_found_in_conjugation,_TraI_252355..252585_POSITIVE 297 42 2 142 106 pint:PI1558|5end_conserved_hypothetical_protein_1473957..1474187_POSITIVE 290 35 1 111 57 pint:PI1266|5end_hypothetical_protein_1185351..1185581_POSITIVE 285 48 3 97 46 pint:PI0602|5end_conserved_hypothetical_protein_549099..549329_POSITIVE 278 43 2 64 30 pint:PI1653|5end_hypothetical_protein_1565158..1565388_POSITIVE 270 32 4 99 71 pint:PI1784|5end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_1716201..1716431_POSITIVE 270 29 1 50 18 pint:PI0731|5end_conserved_hypothetical_protein_662289..662519_POSITIVE 269 79 37 126 86 pint:PI0356|5end_hypothetical_protein_326642..326872_POSITIVE 266 46 5 206 164 pint:PI2133|5end_collagenase_2081106..2081336_POSITIVE 266 46 5 61 19 pint:PI2132|5end_hypothetical_protein_2080961..2081191_POSITIVE 263 34 3 64 37 pint:PI0545|5end_sugar_kinase_496411..496641_POSITIVE 260 23 1 221 197 pint:PI1098|5end_conserved_hypothetical_protein_1022261..1022491_POSITIVE 258 46 1 203 146 pint:PI0530|5end_possible_membrane-fusion_protein_483772..484002_POSITIVE 255 148 104 148 91 pint:PI1415|5end_cation_transporting_ATPase/E1-E2_ATPase_1333939..1334169_POSITIVE 255 148 104 122 65 pint:PI1414|5end_conserved_hypothetical_protein_1333913..1334143_POSITIVE 254 42 2 138 90 pint:PI0588|5end_hypothetical_protein_535016..535246_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 42 2 91 55 pint:PI1557|3end_conserved_hypothetical_protein_1473986..1474136_POSITIVE 293 46 7 134 89 pint:PI0891|3end_transketolase_822905..823055_POSITIVE 278 43 2 61 27 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 269 79 37 102 62 pint:PI0355|3end_probable__N-acetylmuramoyl-L-alanine_amidase_326698..326848_POSITIVE 263 45 1 114 52 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 258 46 1 92 35 pint:PI0529|3end_hypothetical_protein_483741..483891_POSITIVE 258 46 1 74 17 pint:PI0527|3end_outer_membrane_efflux_protein_483723..483873_POSITIVE 255 148 104 88 31 pint:PI1413|3end_hypothetical_protein_1333959..1334109_POSITIVE 253 229 181 48 4 pint:PI0810|3end_hypothetical_protein_747026..747176_POSITIVE 253 229 181 130 86 pint:PI0809|3end_hypothetical_protein_747108..747258_POSITIVE 249 208 172 39 5 pint:PI0162|3end_ADP-ribosylglycohydrolase_(ADP-ribosyl-[dinitrogen_reductase]_hydrolase)_157001..157151_POSITIVE 245 47 10 125 93 pint:PI0594|3end_possible_rare_lipoprotein_A_545157..545307_POSITIVE 241 205 186 21 2 pint:PI2006|3end_potassium_uptake_system_protein_1965846..1965996_POSITIVE 241 223 183 41 2 pint:PI1278|3end_ribulose-phosphate_3-epimerase_(pentose-5-phosphate-3-epimerase)_1195300..1195450_POSITIVE 241 164 121 84 42 pint:PI0068|3end_arginine_repressor_67019..67169_POSITIVE 238 43 2 141 96 pint:PI0734|3end_ABC_transporter,_ATP-binding_/_permease_668760..668910_POSITIVE 235 33 5 144 117 pint:PI2132|3end_hypothetical_protein_2081139..2081289_POSITIVE 235 47 3 65 4 pint:PI1643|3end_conserved_hypothetical_protein_1562029..1562179_POSITIVE 233 21 3 136 117 pint:PI0407|3end_tryptophanyl-tRNA_synthetase_(tryptophan--tRNA_ligase)_374147..374297_POSITIVE 232 160 111 93 54 pint:PI1626|3end_hypothetical_protein_1550522..1550672_POSITIVE