Origin IGS: aggtgtcttttcaagtccttctctgttggggtcttctcctaaaagttgcaatacgtgtcggtaatgtcctgcgagttcgtcgagaccttcgcggaattctatatttgatgtcattgttgttcttgataaatcttataaaactatcttataataatgtttgttctgtcatttaagacgagcttacccgattggtgatacctattcattcgtcggttaaggattattcgactgtctggtgaaagttgcccactcgtctgatagaacaaaaacagtcgactgattttttaaattggtcgactgtttttccaaattagtcgactggttaaaagtactcgttcggctattgagaatgaagcagatta .........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 taatctgcttcattctcaatagccgaacgagtacttttaaccagtcgactaatttggaaaaacagtcgaccaatttaaaaaatcagtcgactgtttttgttctatcagacgagtgggcaactttcaccagacagtcgaataatccttaaccgacgaatgaataggtatcaccaatcgggtaagctcgtcttaaatgacagaacaaacattattataagatagttttataagatttatcaagaacaacaatgacatcaaatatagaattccgcgaaggtctcgacgaactcgcaggacattaccgacacgtattgcaacttttaggagaagaccccaacagagaaggacttgaaaagacacct Mask Tandem Repeat Region ================================================ aggtgtcttttcaagtccttctctgttggggtcttctcctaaaagttgcaatacgtgtcggtaatgtcctgcgagttcgtcgagaccttcgcggaattctatatttgatgtcattgttgttcttgataaatcttataaaactatcttataataatgtttgttctgtcatttaagacgagcttacccgattggtgatacctattcattcgtcggttaaggattattcgactgtctggtgaaagttgcccactcgtctgatagaacaaaaacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngttaaaagtactcgttcggctattgagaatgaagcagatta Find is-nt database================================================ Query_seq: PI1490:PI1491|PI1490:PI1491:GTP cyclohydrolase I:conserved hypothetical protein:->->:1409188..1409549 362 aggtgtcttttcaagtccttctctgttggggtcttctcctaaaagttgcaatacgtgtcggtaatgtcctgcgagttcgtcgagaccttcgcggaattctatatttgatgtcattgttgttcttgataaatcttataaaactatcttataataatgtttgttctgtcatttaagacgagcttacccgattggtgatacctattcattcgtcggttaaggattattcgactgtctggtgaaagttgcccactcgtctgatagaacaaaaacagtcgactgattttttaaattggtcgactgtttttccaaattagtcgactggttaaaagtactcgttcggctattgagaatgaagcagatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1490:PI1491|PI1490:PI1491:GTP cyclohydrolase I:conserved hypothetical protein:->->:1409188..1409549 362 aggtgtcttttcaagtccttctctgttggggtcttctcctaaaagttgcaatacgtgtcggtaatgtcctgcgagttcgtcgagaccttcgcggaattctatatttgatgtcattgttgttcttgataaatcttataaaactatcttataataatgtttgttctgtcatttaagacgagcttacccgattggtgatacctattcattcgtcggttaaggattattcgactgtctggtgaaagttgcccactcgtctgatagaacaaaaacagtcgactgattttttaaattggtcgactgtttttccaaattagtcgactggttaaaagtactcgttcggctattgagaatgaagcagatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1490:PI1491|PI1490:PI1491:GTP cyclohydrolase I:conserved hypothetical protein:->->:1409188..1409549 362 aggtgtcttttcaagtccttctctgttggggtcttctcctaaaagttgcaatacgtgtcggtaatgtcctgcgagttcgtcgagaccttcgcggaattctatatttgatgtcattgttgttcttgataaatcttataaaactatcttataataatgtttgttctgtcatttaagacgagcttacccgattggtgatacctattcattcgtcggttaaggattattcgactgtctggtgaaagttgcccactcgtctgatagaacaaaaacagtcgactgattttttaaattggtcgactgtttttccaaattagtcgactggttaaaagtactcgttcggctattgagaatgaagcagatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggtgtcttttcaagtccttctctgttggggtcttctcctaaaagttgcaatacgtgtcggtaatgtcctgcgagttcgtcgagaccttcgcggaattctatatttgatgtcattgttgttcttgataaatcttataaaactatcttataataatgtttgttctgtcatttaagacgagcttacccgattggtgatacctattcattcgtcggttaaggattattcgactgtctggtgaaagttgcccactcgtctgatagaacaaaaacagtcgactgattttttaaattggtcgactgtttttccaaattagtcgactggttaaaagtactcgttcggctattgagaatgaagcagatta Predict ORF larger than 30AA ================================================ Protein_Len: 56 Strand: + Start: 3 End: 170 .. M S F Q V L L C W G L L L K V A I R V G N V L R V R R D L R G I L Y L M S L L F L I N L I K L S Y N N V C S V I ................................................................................................................................................................................................ Protein_Len: 48 Strand: - Start: 217 End: 360 ........................................................................................................................................................................................................................ P N N S Q R T F T A W E D S L V F V T S Q N K L N T S Q K E L N T S Q N F T S T R S N L I F C M .. Protein_Len: 46 Strand: - Start: 144 End: 281 ............................................................................................................................................... R I I I N T R D N L V L K G S Q H Y R N M R R N L I I R S D P S L Q G S T Q Y F L F L R S M ................................................................................. Protein_Len: 41 Strand: - Start: 14 End: 136 ............. T R R Q Q P R R R F T A I R T P L T R R T R R S R R P I R Y K I D N N N K I F R M .................................................................................................................................................................................................................................. Protein_Len: 38 Strand: - Start: 1 End: 114 P T K E L G E R N P D E G L L Q L V H R Y H G A L E D L G E R F E I N S T M ........................................................................................................................................................................................................................................................ aggtgtcttttcaagtccttctctgttggggtcttctcctaaaagttgcaatacgtgtcggtaatgtcctgcgagttcgtcgagaccttcgcggaattctatatttgatgtcattgttgttcttgataaatcttataaaactatcttataataatgtttgttctgtcatttaagacgagcttacccgattggtgatacctattcattcgtcggttaaggattattcgactgtctggtgaaagttgcccactcgtctgatagaacaaaaacagtcgactgattttttaaattggtcgactgtttttccaaattagtcgactggttaaaagtactcgttcggctattgagaatgaagcagatta 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================================================ aggtgtcttttcaagtccttctctgttggggtcttctcctaaaagttgcaatacgtgtcggtaatgtcctgcgagttcgtcgagaccttcgcggaattctatatttgatgtcattgttgttcttgataaatcttataaaactatcttataataatgtttgttctgtcatttaagacgagcttacccgattggtgatacctattcattcgtcggttaaggattattcgactgtctggtgaaagttgcccactcgtctgatagaacaaaaacagtcgactgattttttaaattggtcgactgtttttccaaattagtcgactggttaaaagtactcgttcggctattgagaatgaagcagatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -14.2 Tail_Score: -4.62872 Start: 270 End: 300 Full_Region: CTGATAGAACAAAAA CAGTCGACTGATTT TTT AAATTGGTCGACTG TTTTTCCAAATTAGT .............................................................................................................................................................................................................................................................................CAGTCGACTGATTTTTTAAATTGGTCGACTG.............................................................. TransTerm Strand: - Conf: 100 HP_score: -9.8 Tail_Score: -5.24796 Start: 270 End: 300 Full_Region: actaatttggaaaaa cagtcgaccaattt aaa aaatcagtcgactg tttttgttctatcag .............................................................................................................................................................................................................................................................................cagtcgaccaatttaaaaaatcagtcgactg.............................................................. Find igs database================================================ Query_seq: PI1490:PI1491|PI1490:PI1491:GTP cyclohydrolase I:conserved hypothetical protein:->->:1409188..1409549 362 aggtgtcttttcaagtccttctctgttggggtcttctcctaaaagttgcaatacgtgtcggtaatgtcctgcgagttcgtcgagaccttcgcggaattctatatttgatgtcattgttgttcttgataaatcttataaaactatcttataataatgtttgttctgtcatttaagacgagcttacccgattggtgatacctattcattcgtcggttaaggattattcgactgtctggtgaaagttgcccactcgtctgatagaacaaaaacagtcgactgattttttaaattggtcgactgtttttccaaattagtcgactggttaaaagtactcgttcggctattgagaatgaagcagatta Intra-Species Hit: Count: 1 Min: 1 Max: 362 Len: 362 Subject: pint_PI1490_PI1491|GTP cyclohydrolase I:conserved hypothetical protein|POSITIVE:POSITIVE|[1409188,1409549]|362 HSP 1 e-value: 0.0 bit: 718.0 Len: 362 Query Start:1 Query End:362 Subject Strand: POSITIVE Subject Start: 1 Subject End: 362 aggtgtcttttcaagtccttctctgttggggtcttctcctaaaagttgcaatacgtgtcggtaatgtcctgcgagttcgtcgagaccttcgcggaattctatatttgatgtcattgttgttcttgataaatcttataaaactatcttataataatgtttgttctgtcatttaagacgagcttacccgattggtgatacctattcattcgtcggttaaggattattcgactgtctggtgaaagttgcccactcgtctgatagaacaaaaacagtcgactgattttttaaattggtcgactgtttttccaaattagtcgactggttaaaagtactcgttcggctattgagaatgaagcagatta aggtgtcttttcaagtccttctctgttggggtcttctcctaaaagttgcaatacgtgtcggtaatgtcctgcgagttcgtcgagaccttcgcggaattctatatttgatgtcattgttgttcttgataaatcttataaaactatcttataataatgtttgttctgtcatttaagacgagcttacccgattggtgatacctattcattcgtcggttaaggattattcgactgtctggtgaaagttgcccactcgtctgatagaacaaaaacagtcgactgattttttaaattggtcgactgtttttccaaattagtcgactggttaaaagtactcgttcggctattgagaatgaagcagatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUGUCUUUUCAAGUCCUUCUCUGUUGGGGUCUUCUCCUAAAAGUUGCAAUACGUGUCGGUAAUGUCCUGCGAGUUCGUCGAGACCUUCGCGGAAUUCUAUAUUUGAUGUCAUUGUUGUUCUUGAUAAAUCUUAUAAAACUAUCUUAUAAUAAUGUUUGUUCUGUCAUUUAAGACGAGCUUACCCGAUUGGUGAUACCUAUUCAUUCGUCGGUUAAGGAUUAUUCGACUGUCUGGUGAAAGUUGCCCACUCGUCUGAUAGAACAAAAACAGUCGACUGAUUUUUUAAAUUGGUCGACUGUUUUUCCAAAUUAGUCGACUGGUUAAAAGUACUCGUUCGGCUAUUGAGAAUGAAGCAGAUUA ..((.(((((((((.......(((((..(((((((..(....((.(((((..((((.......))))..))))).)).)..)))))))..))))).......(((((....(((((((((....((((.............))))..)))))))))..((((((((((.....((((((((((.(((((..((((.......))))..))))).)))).......(((((.((....)).)))))....))))))))))))))))((((((((((((..(((.....)))..))))))))))))..)))))((((((((.(((.......))).).)))))))))))))).)).))...... (-104.92) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCUGCUUCAUUCUCAAUAGCCGAACGAGUACUUUUAACCAGUCGACUAAUUUGGAAAAACAGUCGACCAAUUUAAAAAAUCAGUCGACUGUUUUUGUUCUAUCAGACGAGUGGGCAACUUUCACCAGACAGUCGAAUAAUCCUUAACCGACGAAUGAAUAGGUAUCACCAAUCGGGUAAGCUCGUCUUAAAUGACAGAACAAACAUUAUUAUAAGAUAGUUUUAUAAGAUUUAUCAAGAACAACAAUGACAUCAAAUAUAGAAUUCCGCGAAGGUCUCGACGAACUCGCAGGACAUUACCGACACGUAUUGCAACUUUUAGGAGAAGACCCCAACAGAGAAGGACUUGAAAAGACACCU ...((.(((...........))).)).(((((.(((((.....((((.(((((((((..(((((((((((..(((.....)))..)))))))))))(((((((.((((((((((.(....)....(((.((..((((.............)))).........((.....))..)).)))..))))))).....))).)))))))............(((((.((.....)).)))))................)))))).)))...(((((((...((.....))..)))).)))......)))).................((........)).....))))).)))))........... (-74.12) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 100 54 179 125 pint:PI2014|5end_conserved_hypothetical_protein_1971471..1971701_POSITIVE 367 87 45 231 180 pint:PI0839|5end_conserved_hypothetical_protein_773843..774073_POSITIVE 360 95 52 103 58 pint:PI0834|5end_conserved_hypothetical_protein_770785..771015_POSITIVE 354 93 55 85 37 pint:PI0220|5end_conserved_hypothetical_protein_211980..212210_POSITIVE 338 90 42 64 21 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 329 93 54 223 186 pint:PI1685|5end_GAF_domain-containing_protein_1601712..1601942_POSITIVE 329 93 54 105 68 pint:PI1686|5end_hypothetical_protein_1601594..1601824_POSITIVE 326 107 64 195 153 pint:PI0960|5end_hypothetical_protein_891137..891367_POSITIVE 326 100 58 215 167 pint:PI0251|5end_hypothetical_protein_247551..247781_POSITIVE 319 94 54 64 20 pint:PI1912|5end_possible_DNA_repair_protein_1856364..1856594_POSITIVE 317 97 55 79 27 pint:PI1747|5end_membrane-bound_lytic_murein_transglycosylase_D_1667483..1667713_POSITIVE 317 85 44 71 20 pint:PI1687|5end_ribosome_recycling_factor_1602307..1602537_POSITIVE 315 95 54 146 97 pint:PI0272|5end_conserved_hypothetical_protein_262621..262851_POSITIVE 311 92 52 75 31 pint:PI0797|5end_tRNA_pseudouridine_synthase_A_(pseudouridylate_synthase)_735016..735246_POSITIVE 306 200 155 203 165 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 305 100 51 64 7 pint:PI1647|5end_hypothetical_protein_1561564..1561794_POSITIVE 304 84 46 210 165 pint:PI1781|5end_membrane-associated_zinc_metalloprotease_1713074..1713304_POSITIVE 304 218 174 207 166 pint:PI0792|5end_conserved_hypothetical_protein_729068..729298_POSITIVE 304 218 174 92 51 pint:PI0790|5end_hypothetical_protein_728953..729183_POSITIVE 303 89 43 171 121 pint:PI0361|5end_hypothetical_protein_333062..333292_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 376 107 61 87 39 pint:PI0418|3end_hypothetical_protein_386856..387006_POSITIVE 376 107 61 59 11 pint:PI0420|3end_hypothetical_protein_386828..386978_POSITIVE 354 93 55 62 14 pint:PI0219|3end_conserved_hypothetical_protein_212037..212187_POSITIVE 348 80 32 149 95 pint:PI0685|3end_elongation_factor_G_623048..623198_POSITIVE 326 94 54 76 35 pint:PI0583|3end_hypothetical_protein_526276..526426_POSITIVE 319 60 13 64 20 pint:PI1226|3end_hypothetical_protein_1148263..1148413_POSITIVE 317 97 55 122 70 pint:PI1746|3end_hypothetical_protein_1667606..1667756_POSITIVE 306 200 155 143 105 pint:PI0259|3end_conserved_protein_found_in_conjugation,_TraI_253043..253193_POSITIVE 298 66 22 69 26 pint:PI1199|3end_possible_acetyltransferase_1115746..1115896_POSITIVE 296 93 55 112 56 pint:PI1943|3end_hypothetical_protein_1902206..1902356_POSITIVE 294 93 54 144 103 pint:PI0570|3end_exsB_protein;_possible_aluminum_resistance_protein_515395..515545_POSITIVE 292 69 21 135 83 pint:PI1715|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1632324..1632474_POSITIVE 292 60 16 148 109 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 290 248 202 142 102 pint:PI0336|3end_hypothetical_protein_314806..314956_POSITIVE 289 94 54 151 107 pint:PI2044|3end_hypothetical_protein_1997351..1997501_POSITIVE 288 256 211 63 20 pint:PI0338|3end_hypothetical_protein_315713..315863_POSITIVE 284 250 207 144 102 pint:PI0556|3end_saccharopine_dehydrogenase_506160..506310_POSITIVE 283 219 175 71 31 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 283 220 176 52 3 pint:PI0245|3end_possible_mobilization_protein_244258..244408_POSITIVE 278 87 48 52 13 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE