Origin IGS: tttccgctgcttttatcctattaaagaatagccttgcaaatatactgcttttcgttcgcaatactgctcccacactgcaaatattatgtttacgaacattttttatttagattattcaatacaagaccatctacttatacgagtataaaatacgcctgcatttcttgttttataatcggaaaacaaacaataaaagtgtaaatatttttcgcaagtataactattatataacta .........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 tagttatataatagttatacttgcgaaaaatatttacacttttattgtttgttttccgattataaaacaagaaatgcaggcgtattttatactcgtataagtagatggtcttgtattgaataatctaaataaaaaatgttcgtaaacataatatttgcagtgtgggagcagtattgcgaacgaaaagcagtatatttgcaaggctattctttaataggataaaagcagcggaaa Mask Tandem Repeat Region ================================================ tttccgctgcttttatcctattaaagaatagccttgcaaatatactgcttttcgttcgcaatactgctcccacactgcaaatattatgtttacgaacattttttatttagattattcaatacaagaccatctacttatacgagtataaaatacgcctgcatttcttgttttataatcggaaaacaaacaataaaagtgtaaatatttttcgcaagtataactattatataacta Find is-nt database================================================ Query_seq: PI0003:PI0004|PI0003:PI0004:pseudouridylate synthase:hypothetical protein:->->:6105..6338 234 tttccgctgcttttatcctattaaagaatagccttgcaaatatactgcttttcgttcgcaatactgctcccacactgcaaatattatgtttacgaacattttttatttagattattcaatacaagaccatctacttatacgagtataaaatacgcctgcatttcttgttttataatcggaaaacaaacaataaaagtgtaaatatttttcgcaagtataactattatataacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0003:PI0004|PI0003:PI0004:pseudouridylate synthase:hypothetical protein:->->:6105..6338 234 tttccgctgcttttatcctattaaagaatagccttgcaaatatactgcttttcgttcgcaatactgctcccacactgcaaatattatgtttacgaacattttttatttagattattcaatacaagaccatctacttatacgagtataaaatacgcctgcatttcttgttttataatcggaaaacaaacaataaaagtgtaaatatttttcgcaagtataactattatataacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0003:PI0004|PI0003:PI0004:pseudouridylate synthase:hypothetical protein:->->:6105..6338 234 tttccgctgcttttatcctattaaagaatagccttgcaaatatactgcttttcgttcgcaatactgctcccacactgcaaatattatgtttacgaacattttttatttagattattcaatacaagaccatctacttatacgagtataaaatacgcctgcatttcttgttttataatcggaaaacaaacaataaaagtgtaaatatttttcgcaagtataactattatataacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttccgctgcttttatcctattaaagaatagccttgcaaatatactgcttttcgttcgcaatactgctcccacactgcaaatattatgtttacgaacattttttatttagattattcaatacaagaccatctacttatacgagtataaaatacgcctgcatttcttgttttataatcggaaaacaaacaataaaagtgtaaatatttttcgcaagtataactattatataacta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 15 End: 107 .............. M L L K N S L A N I L L F V R N T A P T L Q I L C L R T F F I ............................................................................................................................... Protein_Len: 57 Strand: + Start: 28 End: 198 ........................... M A L Q I Y C F S F A I L L P H C K Y Y V Y E H F L F R L F N T R P S T Y T S I K Y A C I S C F I I G K Q T I K V .................................... Protein_Len: 41 Strand: + Start: 111 End: 233 .............................................................................................................. M I Q Y K T I Y L Y E Y K I R L H F L F Y N R K T N N K S V N I F R K Y N Y Y I T . Protein_Len: 30 Strand: - Start: 138 End: 227 ......................................................................................................................................... V L I F Y A Q M E Q K I I P F C V I F T Y I N K A L I V I M ....... Protein_Len: 35 Strand: - Start: 2 End: 106 . E A A K I R N F F L R A F I S S K T R L V A G V S C I N H K R V N K M ................................................................................................................................ tttccgctgcttttatcctattaaagaatagccttgcaaatatactgcttttcgttcgcaatactgctcccacactgcaaatattatgtttacgaacattttttatttagattattcaatacaagaccatctacttatacgagtataaaatacgcctgcatttcttgttttataatcggaaaacaaacaataaaagtgtaaatatttttcgcaagtataactattatataacta 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================================================ tttccgctgcttttatcctattaaagaatagccttgcaaatatactgcttttcgttcgcaatactgctcccacactgcaaatattatgtttacgaacattttttatttagattattcaatacaagaccatctacttatacgagtataaaatacgcctgcatttcttgttttataatcggaaaacaaacaataaaagtgtaaatatttttcgcaagtataactattatataacta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 83 HP_score: -3.0 Tail_Score: -5.67283 Start: 87 End: 98 Full_Region: ACACTGCAAATATTA TGTT TACG AACA TTTTTTATTTAGATT ......................................................................................TGTTTACGAACA........................................................................................................................................ Find igs database================================================ Query_seq: PI0003:PI0004|PI0003:PI0004:pseudouridylate synthase:hypothetical protein:->->:6105..6338 234 tttccgctgcttttatcctattaaagaatagccttgcaaatatactgcttttcgttcgcaatactgctcccacactgcaaatattatgtttacgaacattttttatttagattattcaatacaagaccatctacttatacgagtataaaatacgcctgcatttcttgttttataatcggaaaacaaacaataaaagtgtaaatatttttcgcaagtataactattatataacta Intra-Species Hit: Count: 1 Min: 1 Max: 234 Len: 234 Subject: pint_PI0003_PI0004|pseudouridylate synthase:hypothetical protein|POSITIVE:POSITIVE|[6105,6338]|234 HSP 1 e-value: 1.0E-130 bit: 464.0 Len: 234 Query Start:1 Query End:234 Subject Strand: POSITIVE Subject Start: 1 Subject End: 234 tttccgctgcttttatcctattaaagaatagccttgcaaatatactgcttttcgttcgcaatactgctcccacactgcaaatattatgtttacgaacattttttatttagattattcaatacaagaccatctacttatacgagtataaaatacgcctgcatttcttgttttataatcggaaaacaaacaataaaagtgtaaatatttttcgcaagtataactattatataacta tttccgctgcttttatcctattaaagaatagccttgcaaatatactgcttttcgttcgcaatactgctcccacactgcaaatattatgtttacgaacattttttatttagattattcaatacaagaccatctacttatacgagtataaaatacgcctgcatttcttgttttataatcggaaaacaaacaataaaagtgtaaatatttttcgcaagtataactattatataacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCCGCUGCUUUUAUCCUAUUAAAGAAUAGCCUUGCAAAUAUACUGCUUUUCGUUCGCAAUACUGCUCCCACACUGCAAAUAUUAUGUUUACGAACAUUUUUUAUUUAGAUUAUUCAAUACAAGACCAUCUACUUAUACGAGUAUAAAAUACGCCUGCAUUUCUUGUUUUAUAAUCGGAAAACAAACAAUAAAAGUGUAAAUAUUUUUCGCAAGUAUAACUAUUAUAUAACUA .....((((.(((((......)))))..))))........((((((((.........(((....)))....(((((..(((((..(((((....)))))....))))).((((((.....((((((.....(((((....)))))........(....)...))))))...)))))).................)))))...........)).))))))............... (-31.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUUAUAUAAUAGUUAUACUUGCGAAAAAUAUUUACACUUUUAUUGUUUGUUUUCCGAUUAUAAAACAAGAAAUGCAGGCGUAUUUUAUACUCGUAUAAGUAGAUGGUCUUGUAUUGAAUAAUCUAAAUAAAAAAUGUUCGUAAACAUAAUAUUUGCAGUGUGGGAGCAGUAUUGCGAACGAAAAGCAGUAUAUUUGCAAGGCUAUUCUUUAAUAGGAUAAAAGCAGCGGAAA .............(((...((((((((.......(((.(((.((((.((((((((........)))))))).)))).))).))).......(((.((((.(((((((....(((..((((((..............))))))...)))...)))))))..)))).)))..(((((((.........))))))).))))))))..((((((.....))))))..)))........ (-43.34) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 413 230 190 109 69 pint:PI0024|5end_hypothetical_protein_28378..28608_POSITIVE 385 217 177 118 78 pint:PI0561|5end_hypothetical_protein_508952..509182_POSITIVE 384 220 177 230 187 pint:PI0286|5end_ISPg3-related_transposase_271833..272063_POSITIVE 364 210 161 215 164 pint:PI1065|5end_hypothetical_protein_983382..983612_POSITIVE 355 215 171 149 105 pint:PI0695|5end_xanthine/uracil_permease_family_protein_631413..631643_POSITIVE 339 215 171 199 155 pint:PI1253|5end_hypothetical_protein_1175516..1175746_POSITIVE 333 225 189 168 132 pint:PI0096|5end_glycerol-3-phosphate_cytidylyltransferase_91885..92115_POSITIVE 323 219 175 125 86 pint:PI1333|5end_conserved_hypothetical_protein_1250777..1251007_POSITIVE 310 220 177 223 180 pint:PI0821|5end_conserved_hypothetical_protein_760063..760293_POSITIVE 306 190 155 231 196 pint:PI0197|5end_acetate_kinase_188602..188832_POSITIVE 306 190 155 64 29 pint:PI0196|5end_hypothetical_protein_188435..188665_POSITIVE 303 219 176 230 187 pint:PI0682|5end_hypothetical_protein_618972..619202_POSITIVE 297 224 193 97 65 pint:PI1437|5end_hypothetical_protein_1356088..1356318_POSITIVE 297 222 181 115 74 pint:PI0653|5end_hypothetical_protein_596046..596276_POSITIVE 291 225 194 173 141 pint:PI1272|5end_possible_transcriptional_regulator_1191702..1191932_POSITIVE 285 219 177 138 96 pint:PI2024|5end_hypothetical_protein_1978804..1979034_POSITIVE 280 210 161 225 176 pint:PI1175|5end_conserved_hypothetical_protein_1097372..1097602_POSITIVE 279 80 47 75 33 pint:PI1501|5end_GTP-binding_elongation_factor_family_protein_TypA/BipA_1421424..1421654_POSITIVE 276 79 31 90 42 pint:PI0593|5end_NAD-specific_glutamate_dehydrogenase_542967..543197_POSITIVE 269 80 31 58 6 pint:PI1733|5end_hypothetical_protein_1652160..1652390_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 389 225 181 92 48 pint:PI0069|3end_hypothetical_protein_67379..67529_POSITIVE 364 210 161 77 26 pint:PI1064|3end_hypothetical_protein_983324..983474_POSITIVE 360 230 190 83 43 pint:PI1072|3end_hypothetical_protein_990503..990653_POSITIVE 333 217 171 57 11 pint:PI1005|3end_hypothetical_protein_926481..926631_POSITIVE 333 225 189 53 17 pint:PI0095|3end_hypothetical_protein_91850..92000_POSITIVE 322 215 171 104 60 pint:PI0926|3end_hypothetical_protein_857047..857197_POSITIVE 321 215 177 43 5 pint:PI1252|3end_hypothetical_protein_1175440..1175590_POSITIVE 310 220 177 60 17 pint:PI0820|3end_hypothetical_protein_759980..760130_POSITIVE 308 225 187 126 84 pint:PI1786|3end_hypothetical_protein_1718380..1718530_POSITIVE 293 226 200 27 1 pint:PI0905|3end_hypothetical_protein_834697..834847_POSITIVE 287 218 177 64 17 pint:PI1041|3end_hypothetical_protein_960675..960825_POSITIVE 285 219 177 86 44 pint:PI2023|3end_hypothetical_protein_1978832..1978982_POSITIVE 284 222 192 62 31 pint:PI1797|3end_hypothetical_protein_1731559..1731709_POSITIVE 270 72 34 129 91 pint:PI1493|3end_conserved_hypothetical_protein_1412818..1412968_POSITIVE 264 97 51 147 97 pint:PI1883|3end_conserved_hypothetical_protein;_possible_surface_protein_1826174..1826324_POSITIVE 264 219 177 86 44 pint:PI1204|3end_hypothetical_protein_1124635..1124785_POSITIVE 264 217 177 57 17 pint:PI0089|3end_hypothetical_protein_88355..88505_POSITIVE 263 81 46 117 79 pint:PI0215|3end_hypothetical_protein_209004..209154_POSITIVE 256 80 31 141 105 pint:PI1768|3end_conserved_hypothetical_protein_1696639..1696789_POSITIVE 254 77 35 126 92 pint:PI0087|3end_conserved_hypothetical_protein_86733..86883_POSITIVE