Origin IGS: gattttcgccagtgctctcaaatcgtcttcttgttgcatagtttttcgtttaatttcgttcttacttttatgattgttgaaattgtcttataagacttttcaaattgtcttataggacaattttaattctcttataagagaatttggtgcctctgataattcctgatattcaacatattacaaactccccattttactgtattttagagatggaaaatatggctta .........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 taagccatattttccatctctaaaatacagtaaaatggggagtttgtaatatgttgaatatcaggaattatcagaggcaccaaattctcttataagagaattaaaattgtcctataagacaatttgaaaagtcttataagacaatttcaacaatcataaaagtaagaacgaaattaaacgaaaaactatgcaacaagaagacgatttgagagcactggcgaaaatc Mask Tandem Repeat Region ================================================ gattttcgccagtgctctcaaatcgtcttcttgttgcatagtttttcgtttaatttcgttcttacttttatgattgttgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaatttggtgcctctgataattcctgatattcaacatattacaaactccccattttactgtattttagagatggaaaatatggctta Find is-nt database================================================ Query_seq: PI0244:PI0245|PI0244:PI0245:possible mobilization protein C:possible mobilization protein:->->:242860..243085 226 gattttcgccagtgctctcaaatcgtcttcttgttgcatagtttttcgtttaatttcgttcttacttttatgattgttgaaattgtcttataagacttttcaaattgtcttataggacaattttaattctcttataagagaatttggtgcctctgataattcctgatattcaacatattacaaactccccattttactgtattttagagatggaaaatatggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0244:PI0245|PI0244:PI0245:possible mobilization protein C:possible mobilization protein:->->:242860..243085 226 gattttcgccagtgctctcaaatcgtcttcttgttgcatagtttttcgtttaatttcgttcttacttttatgattgttgaaattgtcttataagacttttcaaattgtcttataggacaattttaattctcttataagagaatttggtgcctctgataattcctgatattcaacatattacaaactccccattttactgtattttagagatggaaaatatggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0244:PI0245|PI0244:PI0245:possible mobilization protein C:possible mobilization protein:->->:242860..243085 226 gattttcgccagtgctctcaaatcgtcttcttgttgcatagtttttcgtttaatttcgttcttacttttatgattgttgaaattgtcttataagacttttcaaattgtcttataggacaattttaattctcttataagagaatttggtgcctctgataattcctgatattcaacatattacaaactccccattttactgtattttagagatggaaaatatggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gattttcgccagtgctctcaaatcgtcttcttgttgcatagtttttcgtttaatttcgttcttacttttatgattgttgaaattgtcttataagacttttcaaattgtcttataggacaattttaattctcttataagagaatttggtgcctctgataattcctgatattcaacatattacaaactccccattttactgtattttagagatggaaaatatggctta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 21 End: 113 .................... I T K K N C L K E N L K T R V K I I T S I T K Y S K E F Q R M ................................................................................................................. gattttcgccagtgctctcaaatcgtcttcttgttgcatagtttttcgtttaatttcgttcttacttttatgattgttgaaattgtcttataagacttttcaaattgtcttataggacaattttaattctcttataagagaatttggtgcctctgataattcctgatattcaacatattacaaactccccattttactgtattttagagatggaaaatatggctta 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================================================ gattttcgccagtgctctcaaatcgtcttcttgttgcatagtttttcgtttaatttcgttcttacttttatgattgttgaaattgtcttataagacttttcaaattgtcttataggacaattttaattctcttataagagaatttggtgcctctgataattcctgatattcaacatattacaaactccccattttactgtattttagagatggaaaatatggctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -11.2 Tail_Score: -3.7511 Start: 77 End: 126 Full_Region: TTACTTTTATGATTG TTGAAATTGTCTTATAAGAC TTTTCAAATT GTCTTATAGGACAATTTTAA TTCTCTTATAAGAGA ............................................................................TTGAAATTGTCTTATAAGACTTTTCAAATTGTCTTATAGGACAATTTTAA.................................................................................................... TransTerm Strand: + Conf: 83 HP_score: -8.0 Tail_Score: -4.57218 Start: 83 End: 120 Full_Region: TTATGATTGTTGAAA TTGTCTTATAAGAC TTTTCAAATT GTCTTATAGGACAA TTTTAATTCTCTTAT ..................................................................................TTGTCTTATAAGACTTTTCAAATTGTCTTATAGGACAA.......................................................................................................... TransTerm Strand: - Conf: 62 HP_score: -5.8 Tail_Score: -3.56092 Start: 83 End: 120 Full_Region: ataagagaattaaaa ttgtcctataagac aatttgaaaa gtcttataagacaa tttcaacaatcataa ..................................................................................ttgtcctataagacaatttgaaaagtcttataagacaa.......................................................................................................... Find igs database================================================ Query_seq: PI0244:PI0245|PI0244:PI0245:possible mobilization protein C:possible mobilization protein:->->:242860..243085 226 gattttcgccagtgctctcaaatcgtcttcttgttgcatagtttttcgtttaatttcgttcttacttttatgattgttgaaattgtcttataagacttttcaaattgtcttataggacaattttaattctcttataagagaatttggtgcctctgataattcctgatattcaacatattacaaactccccattttactgtattttagagatggaaaatatggctta Intra-Species Hit: Count: 1 Min: 1 Max: 226 Len: 226 Subject: pint_PI0244_PI0245|possible mobilization protein C:possible mobilization protein|POSITIVE:POSITIVE|[242860,243085]|226 HSP 1 e-value: 1.0E-125 bit: 448.0 Len: 226 Query Start:1 Query End:226 Subject Strand: POSITIVE Subject Start: 1 Subject End: 226 gattttcgccagtgctctcaaatcgtcttcttgttgcatagtttttcgtttaatttcgttcttacttttatgattgttgaaattgtcttataagacttttcaaattgtcttataggacaattttaattctcttataagagaatttggtgcctctgataattcctgatattcaacatattacaaactccccattttactgtattttagagatggaaaatatggctta gattttcgccagtgctctcaaatcgtcttcttgttgcatagtttttcgtttaatttcgttcttacttttatgattgttgaaattgtcttataagacttttcaaattgtcttataggacaattttaattctcttataagagaatttggtgcctctgataattcctgatattcaacatattacaaactccccattttactgtattttagagatggaaaatatggctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUUUCGCCAGUGCUCUCAAAUCGUCUUCUUGUUGCAUAGUUUUUCGUUUAAUUUCGUUCUUACUUUUAUGAUUGUUGAAAUUGUCUUAUAAGACUUUUCAAAUUGUCUUAUAGGACAAUUUUAAUUCUCUUAUAAGAGAAUUUGGUGCCUCUGAUAAUUCCUGAUAUUCAACAUAUUACAAACUCCCCAUUUUACUGUAUUUUAGAGAUGGAAAAUAUGGCUUA .......(((.((((...(((.........)))..)))).(((((((((((.............(((((((((..(((((((((((((((((((((..........)))))))))))))))))))))....)))))))))....(((......((.((((...((.....))....))))))......)))................)))))))))))..)))... (-49.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCCAUAUUUUCCAUCUCUAAAAUACAGUAAAAUGGGGAGUUUGUAAUAUGUUGAAUAUCAGGAAUUAUCAGAGGCACCAAAUUCUCUUAUAAGAGAAUUAAAAUUGUCCUAUAAGACAAUUUGAAAAGUCUUAUAAGACAAUUUCAACAAUCAUAAAAGUAAGAACGAAAUUAAACGAAAAACUAUGCAACAAGAAGACGAUUUGAGAGCACUGGCGAAAAUC ...((((..(((((..((((((.............))))))..(((((...((((((.........................((((((((....))))))))..(((((((.((((((((..........)))))))).)))))))))))))................((........))........)))))..............)))))...))))....... (-41.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 308 60 11 77 28 pint:PI1499|5end_hypothetical_protein_1419960..1420190_POSITIVE 307 50 7 227 182 pint:PI0820|5end_hypothetical_protein_759694..759924_POSITIVE 299 48 7 131 91 pint:PI0762|5end_mannose-6-phosphate_isomerase,_class_I_696420..696650_POSITIVE 289 41 8 134 95 pint:PI1729|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase,_trigger_factor_1648416..1648646_POSITIVE 283 50 7 61 1 pint:PI1711|5end_ABC_transporter,_ATP-binding_protein_1627597..1627827_POSITIVE 272 48 8 132 72 pint:PI0128|5end_dipeptidase,_pathogenicity_island-encoded_protein_D_120532..120762_POSITIVE 270 48 1 201 146 pint:PI0285|5end_succinyltransferase_protein_270097..270327_POSITIVE 268 48 1 175 134 pint:PI1477|5end_TonB-dependent_outer_membrane_receptor_1399734..1399964_POSITIVE 267 43 1 140 103 pint:PI0253|5end_conjugative_transposon_protein,_TraD_248294..248524_POSITIVE 266 57 14 172 131 pint:PI1216|5end_probable_phosphohydrolase_1134814..1135044_POSITIVE 265 47 3 63 12 pint:PI1483|5end_hypothetical_protein_1404310..1404540_POSITIVE 263 49 6 117 78 pint:PI0330|5end_hypothetical_protein_310447..310677_POSITIVE 260 50 2 110 51 pint:PI1401|5end_TPR-repeat-containing_protein_1322027..1322257_POSITIVE 259 50 3 213 173 pint:PI0751|5end_conserved_hypothetical_protein_680623..680853_POSITIVE 254 49 9 94 47 pint:PI1632|5end_hypothetical_protein_1552819..1553049_POSITIVE 253 62 22 75 24 pint:PI2011|5end_hypothetical_protein_1970429..1970659_POSITIVE 252 46 8 224 186 pint:PI0608|5end_isochorismate_synthase_555487..555717_POSITIVE 251 65 26 154 115 pint:PI0355|5end_probable__N-acetylmuramoyl-L-alanine_amidase_326157..326387_POSITIVE 250 49 4 225 164 pint:PI1413|5end_hypothetical_protein_1333727..1333957_POSITIVE 250 165 124 63 29 pint:PI0195|5end_epimerase/reductase_187172..187402_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 50 7 112 67 pint:PI0818|3end_alpha-amylase_759659..759809_POSITIVE 275 48 6 131 92 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 270 40 7 141 98 pint:PI1712|3end_hypothetical_protein_1627774..1627924_POSITIVE 267 47 3 126 80 pint:PI1732|3end_hypothetical_protein_1652098..1652248_POSITIVE 267 43 1 149 112 pint:PI0252|3end_conserved_hypothetical_protein_248383..248533_POSITIVE 266 57 14 149 108 pint:PI1215|3end_orotidine_5'-phosphate_decarboxylase_1134871..1135021_POSITIVE 263 49 6 104 65 pint:PI0329|3end_hypothetical_protein_310514..310664_POSITIVE 259 50 3 143 103 pint:PI0750|3end_zinc_protease_680633..680783_POSITIVE 254 49 9 150 103 pint:PI1633|3end_hypothetical_protein_1552955..1553105_POSITIVE 246 49 8 151 106 pint:PI0588|3end_hypothetical_protein_535425..535575_POSITIVE 246 49 8 73 28 pint:PI0587|3end_conserved_hypothetical_protein_535347..535497_POSITIVE 244 50 1 77 40 pint:PI1520|3end_hypothetical_protein_1441370..1441520_POSITIVE 241 58 12 148 106 pint:PI1855|3end_lipopolysaccharide_biosynthesis_protein_1803168..1803318_POSITIVE 240 69 23 75 23 pint:PI1385|3end_3-deoxy-d-manno-octulosonic_acid_8-phosphate_synthase_(DAHP_synthase,_Class_I)_1307059..1307209_POSITIVE 238 45 6 132 95 pint:PI0906|3end_hypothetical_protein_836008..836158_POSITIVE 238 38 3 148 122 pint:PI0642|3end_thioredoxin_family_protein_585582..585732_POSITIVE 237 48 6 104 65 pint:PI1622|3end_hypothetical_protein_1547230..1547380_POSITIVE 237 48 2 51 1 pint:PI0944|3end_hypothetical_protein_875249..875399_POSITIVE 235 50 7 80 37 pint:PI0379|3end_conserved_hypothetical_protein_350239..350389_POSITIVE 234 38 1 74 26 pint:PI0338|3end_hypothetical_protein_315713..315863_POSITIVE