Origin IGS: tgattaaaataaataagaatttggaaacgtaatagtcgccttgattttctgtcaaggcggctattacattatatttatataactcataaccataggacacaataatcattcatttcttctttggcaataaacacttggtttgattgcatgataatctttgcattggctaacctttctaaataattattacgaatgcctggattttctaattcttctcgtccggctttactcattgcaagaaactcctcttctaattctaagtcaagaatccttcgtcccta .........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 tagggacgaaggattcttgacttagaattagaagaggagtttcttgcaatgagtaaagccggacgagaagaattagaaaatccaggcattcgtaataattatttagaaaggttagccaatgcaaagattatcatgcaatcaaaccaagtgtttattgccaaagaagaaatgaatgattattgtgtcctatggttatgagttatataaatataatgtaatagccgccttgacagaaaatcaaggcgactattacgtttccaaattcttatttattttaatca Mask Tandem Repeat Region ================================================ tgattaaaataaataagaatttggaaacgtaatagtcgccttgattttctgtcaaggcggctattacattatatttatataactcataaccataggacacaataatcattcatttcttctttggcaataaacacttggtttgattgcatgataatctttgcattggctaacctttctaaataattattacgaatgcctggattttctaattcttctcgtccggctttactcattgcaagaaactcctcttctaattctaagtcaagaatccttcgtcccta Find is-nt database================================================ Query_seq: PI1431:PI1432|PI1431:PI1432:conserved hypothetical protein:DNA methylase:->->:1352870..1353150 281 tgattaaaataaataagaatttggaaacgtaatagtcgccttgattttctgtcaaggcggctattacattatatttatataactcataaccataggacacaataatcattcatttcttctttggcaataaacacttggtttgattgcatgataatctttgcattggctaacctttctaaataattattacgaatgcctggattttctaattcttctcgtccggctttactcattgcaagaaactcctcttctaattctaagtcaagaatccttcgtcccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1431:PI1432|PI1431:PI1432:conserved hypothetical protein:DNA methylase:->->:1352870..1353150 281 tgattaaaataaataagaatttggaaacgtaatagtcgccttgattttctgtcaaggcggctattacattatatttatataactcataaccataggacacaataatcattcatttcttctttggcaataaacacttggtttgattgcatgataatctttgcattggctaacctttctaaataattattacgaatgcctggattttctaattcttctcgtccggctttactcattgcaagaaactcctcttctaattctaagtcaagaatccttcgtcccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1431:PI1432|PI1431:PI1432:conserved hypothetical protein:DNA methylase:->->:1352870..1353150 281 tgattaaaataaataagaatttggaaacgtaatagtcgccttgattttctgtcaaggcggctattacattatatttatataactcataaccataggacacaataatcattcatttcttctttggcaataaacacttggtttgattgcatgataatctttgcattggctaacctttctaaataattattacgaatgcctggattttctaattcttctcgtccggctttactcattgcaagaaactcctcttctaattctaagtcaagaatccttcgtcccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgattaaaataaataagaatttggaaacgtaatagtcgccttgattttctgtcaaggcggctattacattatatttatataactcataaccataggacacaataatcattcatttcttctttggcaataaacacttggtttgattgcatgataatctttgcattggctaacctttctaaataattattacgaatgcctggattttctaattcttctcgtccggctttactcattgcaagaaactcctcttctaattctaagtcaagaatccttcgtcccta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 13 End: 102 ............ M R I W K R N S R L D F L S R R L L H Y I Y I T H N H R T Q ................................................................................................................................................................................... Protein_Len: 41 Strand: + Start: 158 End: 280 ............................................................................................................................................................. M H W L T F L N N Y Y E C L D F L I L L V R L Y S L Q E T P L L I L S Q E S F V P . Protein_Len: 60 Strand: - Start: 87 End: 269 ...................................................................................... W L V C Y D N M E E K A I F V Q N S Q M I I K A N A L R E L Y N N R I G P N E L E E R G A K S M A L F E E E L E L D L M ............ Protein_Len: 36 Strand: - Start: 2 End: 109 . I L I F L F K S V Y Y D G Q N E T L A A I V N Y K Y L E Y G Y S V I I M ............................................................................................................................................................................ tgattaaaataaataagaatttggaaacgtaatagtcgccttgattttctgtcaaggcggctattacattatatttatataactcataaccataggacacaataatcattcatttcttctttggcaataaacacttggtttgattgcatgataatctttgcattggctaacctttctaaataattattacgaatgcctggattttctaattcttctcgtccggctttactcattgcaagaaactcctcttctaattctaagtcaagaatccttcgtcccta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 99 End: 128 ..................................................................................................ATTGCCAAAGAAGAAATGAATGATTATTGT......................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgattaaaataaataagaatttggaaacgtaatagtcgccttgattttctgtcaaggcggctattacattatatttatataactcataaccataggacacaataatcattcatttcttctttggcaataaacacttggtttgattgcatgataatctttgcattggctaacctttctaaataattattacgaatgcctggattttctaattcttctcgtccggctttactcattgcaagaaactcctcttctaattctaagtcaagaatccttcgtcccta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 77 HP_score: -7.7 Tail_Score: -4.07124 Start: 23 End: 73 Full_Region: AATAAATAAGAATTT GGAAACGTAATAGTCGCCTTGAT TTTCT GTCAAGGCGGCTATTACATTATA TTTATATAACTCATA ......................GGAAACGTAATAGTCGCCTTGATTTTCTGTCAAGGCGGCTATTACATTATA................................................................................................................................................................................................................ TransTerm Strand: + Conf: 100 HP_score: -14.2 Tail_Score: -3.93742 Start: 28 End: 68 Full_Region: ATAAGAATTTGGAAA CGTAATAGTCGCCTTGAT TTTCT GTCAAGGCGGCTATTACA TTATATTTATATAAC ...........................CGTAATAGTCGCCTTGATTTTCTGTCAAGGCGGCTATTACA..................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -13.5 Tail_Score: -3.6445 Start: 28 End: 68 Full_Region: gttatataaatataa tgtaatagccgccttga cagaaaa tcaaggcgactattacg tttccaaattcttat ...........................tgtaatagccgccttgacagaaaatcaaggcgactattacg..................................................................................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -17.7 Tail_Score: -2.95522 Start: 29 End: 67 Full_Region: TAAGAATTTGGAAAC GTAATAGTCGCCTTGAT TTTCT GTCAAGGCGGCTATTAC ATTATATTTATATAA ............................GTAATAGTCGCCTTGATTTTCTGTCAAGGCGGCTATTAC...................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -14.8 Tail_Score: -2.77947 Start: 29 End: 67 Full_Region: ttatataaatataat gtaatagccgccttga cagaaaa tcaaggcgactattac gtttccaaattctta ............................gtaatagccgccttgacagaaaatcaaggcgactattac...................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI1431:PI1432|PI1431:PI1432:conserved hypothetical protein:DNA methylase:->->:1352870..1353150 281 tgattaaaataaataagaatttggaaacgtaatagtcgccttgattttctgtcaaggcggctattacattatatttatataactcataaccataggacacaataatcattcatttcttctttggcaataaacacttggtttgattgcatgataatctttgcattggctaacctttctaaataattattacgaatgcctggattttctaattcttctcgtccggctttactcattgcaagaaactcctcttctaattctaagtcaagaatccttcgtcccta Intra-Species Hit: Count: 1 Min: 1 Max: 281 Len: 281 Subject: pint_PI1431_PI1432|conserved hypothetical protein:DNA methylase|POSITIVE:POSITIVE|[1352870,1353150]|281 HSP 1 e-value: 1.0E-158 bit: 557.0 Len: 281 Query Start:1 Query End:281 Subject Strand: POSITIVE Subject Start: 1 Subject End: 281 tgattaaaataaataagaatttggaaacgtaatagtcgccttgattttctgtcaaggcggctattacattatatttatataactcataaccataggacacaataatcattcatttcttctttggcaataaacacttggtttgattgcatgataatctttgcattggctaacctttctaaataattattacgaatgcctggattttctaattcttctcgtccggctttactcattgcaagaaactcctcttctaattctaagtcaagaatccttcgtcccta tgattaaaataaataagaatttggaaacgtaatagtcgccttgattttctgtcaaggcggctattacattatatttatataactcataaccataggacacaataatcattcatttcttctttggcaataaacacttggtttgattgcatgataatctttgcattggctaacctttctaaataattattacgaatgcctggattttctaattcttctcgtccggctttactcattgcaagaaactcctcttctaattctaagtcaagaatccttcgtcccta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUAAAAUAAAUAAGAAUUUGGAAACGUAAUAGUCGCCUUGAUUUUCUGUCAAGGCGGCUAUUACAUUAUAUUUAUAUAACUCAUAACCAUAGGACACAAUAAUCAUUCAUUUCUUCUUUGGCAAUAAACACUUGGUUUGAUUGCAUGAUAAUCUUUGCAUUGGCUAACCUUUCUAAAUAAUUAUUACGAAUGCCUGGAUUUUCUAAUUCUUCUCGUCCGGCUUUACUCAUUGCAAGAAACUCCUCUUCUAAUUCUAAGUCAAGAAUCCUUCGUCCCUA (((.....(((((((.......(....)(((((((((((((((((.....)))))))))))))))))....))))))).....)))........((((........(((((............(((((((((.....)))).))))).(((((((..((.....((....))......))..))))))).)))))...(((((((......(.....)...(((((.....((((.((((......)))).))))...))))).)))))))...))))... (-60.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGGACGAAGGAUUCUUGACUUAGAAUUAGAAGAGGAGUUUCUUGCAAUGAGUAAAGCCGGACGAGAAGAAUUAGAAAAUCCAGGCAUUCGUAAUAAUUAUUUAGAAAGGUUAGCCAAUGCAAAGAUUAUCAUGCAAUCAAACCAAGUGUUUAUUGCCAAAGAAGAAAUGAAUGAUUAUUGUGUCCUAUGGUUAUGAGUUAUAUAAAUAUAAUGUAAUAGCCGCCUUGACAGAAAAUCAAGGCGACUAUUACGUUUCCAAAUUCUUAUUUAUUUUAAUCA ((((((....(((....(((((((.(((((....((((............((((...((((((.................))).))))))).(((((((((((((....((....)).................(((((.((((.....)))))))))...........)))))))))))))..)))).))))).))))))).........((((((((((.((((((((.......)))))))).)))))))))))))...))))))............. (-62.13) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 568 62 22 204 159 pint:PI1224|5end_sensor_histidine_kinase_and_response_regulator_1144574..1144804_POSITIVE 364 62 34 163 133 pint:PI1230|5end_probable_metallo-beta-lactamase_family_protein_1151840..1152070_POSITIVE 319 61 23 165 130 pint:PI1564|5end_surface_antigen_BspA_1483455..1483685_POSITIVE 303 247 208 217 172 pint:PI2126|5end_conserved_hypothetical_protein_2074907..2075137_POSITIVE 292 67 23 200 144 pint:PI1891|5end_hypothetical_protein_1835196..1835426_POSITIVE 279 224 183 158 106 pint:PI0541|5end_GTP-binding_protein,_GTP1/OBG_family_493760..493990_POSITIVE 270 229 190 165 130 pint:PI1950|5end_iron-regulated_membrane_permease_1904468..1904698_POSITIVE 270 70 23 146 93 pint:PI0718|5end_hypothetical_protein_653725..653955_POSITIVE 270 63 22 83 27 pint:PI0351|5end_hypothetical_protein_324317..324547_POSITIVE 267 173 135 59 8 pint:PI1844|5end_hypothetical_protein_1790092..1790322_POSITIVE 266 237 191 55 1 pint:PI2113|5end_hypothetical_protein_2063794..2064024_POSITIVE 265 61 31 39 8 pint:PI0858|5end_carbamyl_phosphate_synthase,_large_subunit_790093..790323_POSITIVE 265 177 132 162 109 pint:PI0514|5end_possible_cell_filamentation_protein_472408..472638_POSITIVE 263 220 171 127 81 pint:PI2104|5end_carboxyl-terminal_protease_2057910..2058140_POSITIVE 261 227 197 98 62 pint:PI1653|5end_hypothetical_protein_1565158..1565388_POSITIVE 260 259 214 112 60 pint:PI0915|5end_hypothetical_protein_845183..845413_POSITIVE 257 277 239 211 168 pint:PI0359|5end_hypothetical_protein_328339..328569_POSITIVE 256 62 21 231 189 pint:PI1889|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-(pentape_ptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_1831411..1831641_POSITIVE 256 62 28 209 160 pint:PI0460|5end_50S_ribosomal_protein_L3_432471..432701_POSITIVE 255 225 190 195 153 pint:PI0246|5end_conserved_hypothetical_protein_244166..244396_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 435 67 29 62 24 pint:PI1431|3end_conserved_hypothetical_protein_1352809..1352959_POSITIVE 352 60 34 74 47 pint:PI1499|3end_hypothetical_protein_1420180..1420330_POSITIVE 313 225 189 70 33 pint:PI1572|3end_hypothetical_protein_1498215..1498365_POSITIVE 288 177 141 125 77 pint:PI0492|3end_hypothetical_protein_452458..452608_POSITIVE 276 60 16 136 69 pint:PI0019|3end_conserved_hypothetical_protein_24454..24604_POSITIVE 271 168 121 75 19 pint:PI1843|3end_hypothetical_protein_1788611..1788761_POSITIVE 270 229 190 147 112 pint:PI1949|3end_aminotransferase,_class_V_1904530..1904680_POSITIVE 263 220 171 71 25 pint:PI2103|3end_hypothetical_protein_2057934..2058084_POSITIVE 262 60 15 121 82 pint:PI0667|3end_hypothetical_protein_610477..610627_POSITIVE 261 227 197 95 59 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 256 62 28 125 76 pint:PI0459|3end_30S_ribosomal_protein_S10_432467..432617_POSITIVE 255 61 27 146 106 pint:PI1713|3end_ABC_transporter,_ATP-binding_protein_1630192..1630342_POSITIVE 253 78 36 48 11 pint:PI1778|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1711399..1711549_POSITIVE 252 62 31 137 96 pint:PI0087|3end_conserved_hypothetical_protein_86733..86883_POSITIVE 249 76 37 110 72 pint:PI1050|3end_conserved_hypothetical_protein_969698..969848_POSITIVE 249 237 193 85 38 pint:PI0805|3end_conserved_hypothetical_protein_743807..743957_POSITIVE 249 59 20 101 63 pint:PI0567|3end_hypothetical_protein_513055..513205_POSITIVE 249 169 121 119 58 pint:PI0109|3end_hypothetical_protein_107183..107333_POSITIVE 246 224 188 112 67 pint:PI0616|3end_electron_transfer_flavoprotein,_beta-subunit_566440..566590_POSITIVE 246 224 190 46 10 pint:PI0539|3end_hypothetical_protein_493728..493878_POSITIVE