Origin IGS: aattctttgattttaagttcgtttatttcttttttacgatgcaaaggtaggtgcatttctgcacccttacaagcattggtaatgggttgtttcgataatggttatcgtaatattgcgatagagaactgttggaaattagccaaaactgtgatgacaatagatttaaatcaagtatatgtgtgtttttcgtggcggtactgtctgttgtttctgtattttaagaataacagcattcatatttttagaatgaaggcatatatttttcggtgtttcgttatgctgttattccaatgttttgatagattgtttaaggttttgcggtaaggcgattgtactttctttatacatta .........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 taatgtataaagaaagtacaatcgccttaccgcaaaaccttaaacaatctatcaaaacattggaataacagcataacgaaacaccgaaaaatatatgccttcattctaaaaatatgaatgctgttattcttaaaatacagaaacaacagacagtaccgccacgaaaaacacacatatacttgatttaaatctattgtcatcacagttttggctaatttccaacagttctctatcgcaatattacgataaccattatcgaaacaacccattaccaatgcttgtaagggtgcagaaatgcacctacctttgcatcgtaaaaaagaaataaacgaacttaaaatcaaagaatt Mask Tandem Repeat Region ================================================ aattctttgattttaagttcgtttatttcttttttacgatgcaaaggtaggtgcatttctgcacccttacaagcattggtaatgggttgtttcgataatggttatcgtaatattgcgatagagaactgttggaaattagccaaaactgtgatgacaatagatttaaatcaagtatatgtgtgtttttcgtggcggtactgtctgttgtttctgtattttaagaataacagcattcatatttttagaatgaaggcatatatttttcggtgtttcgttatgctgttattccaatgttttgatagattgtttaaggttttgcggtaaggcgattgtactttctttatacatta Find is-nt database================================================ Query_seq: PI0041:PI0043|PI0041:PI0043:hypothetical protein:thiamine phosphate pyrophosphorylase:->->:42084..42433 350 aattctttgattttaagttcgtttatttcttttttacgatgcaaaggtaggtgcatttctgcacccttacaagcattggtaatgggttgtttcgataatggttatcgtaatattgcgatagagaactgttggaaattagccaaaactgtgatgacaatagatttaaatcaagtatatgtgtgtttttcgtggcggtactgtctgttgtttctgtattttaagaataacagcattcatatttttagaatgaaggcatatatttttcggtgtttcgttatgctgttattccaatgttttgatagattgtttaaggttttgcggtaaggcgattgtactttctttatacatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0041:PI0043|PI0041:PI0043:hypothetical protein:thiamine phosphate pyrophosphorylase:->->:42084..42433 350 aattctttgattttaagttcgtttatttcttttttacgatgcaaaggtaggtgcatttctgcacccttacaagcattggtaatgggttgtttcgataatggttatcgtaatattgcgatagagaactgttggaaattagccaaaactgtgatgacaatagatttaaatcaagtatatgtgtgtttttcgtggcggtactgtctgttgtttctgtattttaagaataacagcattcatatttttagaatgaaggcatatatttttcggtgtttcgttatgctgttattccaatgttttgatagattgtttaaggttttgcggtaaggcgattgtactttctttatacatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0041:PI0043|PI0041:PI0043:hypothetical protein:thiamine phosphate pyrophosphorylase:->->:42084..42433 350 aattctttgattttaagttcgtttatttcttttttacgatgcaaaggtaggtgcatttctgcacccttacaagcattggtaatgggttgtttcgataatggttatcgtaatattgcgatagagaactgttggaaattagccaaaactgtgatgacaatagatttaaatcaagtatatgtgtgtttttcgtggcggtactgtctgttgtttctgtattttaagaataacagcattcatatttttagaatgaaggcatatatttttcggtgtttcgttatgctgttattccaatgttttgatagattgtttaaggttttgcggtaaggcgattgtactttctttatacatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattctttgattttaagttcgtttatttcttttttacgatgcaaaggtaggtgcatttctgcacccttacaagcattggtaatgggttgtttcgataatggttatcgtaatattgcgatagagaactgttggaaattagccaaaactgtgatgacaatagatttaaatcaagtatatgtgtgtttttcgtggcggtactgtctgttgtttctgtattttaagaataacagcattcatatttttagaatgaaggcatatatttttcggtgtttcgttatgctgttattccaatgttttgatagattgtttaaggttttgcggtaaggcgattgtactttctttatacatta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 126 End: 218 ............................................................................................................................. M L E I S Q N C D D N R F K S S I C V F F V A V L S V V S V F .................................................................................................................................... Protein_Len: 60 Strand: + Start: 7 End: 321 ...... M I L S S F I S F L R C K G R C I S A P L Q A L V M G C F D N G Y R N I A I E N C W K L A K T V M T I D L N Q V Y V C F ............................. Protein_Len: 31 Strand: + Start: 257 End: 349 ................................................................................................................................................................................................................................................................ M F F G V S L C C Y S N V L I D C L R F C G K A I V L S L Y I . Protein_Len: 36 Strand: - Start: 237 End: 344 ............................................................................................................................................................................................................................................ I K L I F A Y I K R H K T I S N N W H K S L N N L T K R Y P S Q V K K M ...... Protein_Len: 31 Strand: - Start: 166 End: 258 ..................................................................................................................................................................... I L Y I H T K R P P V T Q Q K Q I K L I V A N M N K S H L C M ............................................................................................ Protein_Len: 50 Strand: - Start: 26 End: 175 ......................... K K K V I C L Y T C K Q V R V L M P L P N N R Y H N D Y Y Q S L S S N S I L W F Q S S L L N L D L M ............................................................................................................................................................................... aattctttgattttaagttcgtttatttcttttttacgatgcaaaggtaggtgcatttctgcacccttacaagcattggtaatgggttgtttcgataatggttatcgtaatattgcgatagagaactgttggaaattagccaaaactgtgatgacaatagatttaaatcaagtatatgtgtgtttttcgtggcggtactgtctgttgtttctgtattttaagaataacagcattcatatttttagaatgaaggcatatatttttcggtgtttcgttatgctgttattccaatgttttgatagattgtttaaggttttgcggtaaggcgattgtactttctttatacatta 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================================================ aattctttgattttaagttcgtttatttcttttttacgatgcaaaggtaggtgcatttctgcacccttacaagcattggtaatgggttgtttcgataatggttatcgtaatattgcgatagagaactgttggaaattagccaaaactgtgatgacaatagatttaaatcaagtatatgtgtgtttttcgtggcggtactgtctgttgtttctgtattttaagaataacagcattcatatttttagaatgaaggcatatatttttcggtgtttcgttatgctgttattccaatgttttgatagattgtttaaggttttgcggtaaggcgattgtactttctttatacatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -9.0 Tail_Score: -2.66748 Start: 50 End: 65 Full_Region: accaatgcttgtaag ggtgca gaaa tgcacc tacctttgcatcgta .................................................ggtgcagaaatgcacc............................................................................................................................................................................................................................................................................................. Find igs database================================================ Query_seq: PI0041:PI0043|PI0041:PI0043:hypothetical protein:thiamine phosphate pyrophosphorylase:->->:42084..42433 350 aattctttgattttaagttcgtttatttcttttttacgatgcaaaggtaggtgcatttctgcacccttacaagcattggtaatgggttgtttcgataatggttatcgtaatattgcgatagagaactgttggaaattagccaaaactgtgatgacaatagatttaaatcaagtatatgtgtgtttttcgtggcggtactgtctgttgtttctgtattttaagaataacagcattcatatttttagaatgaaggcatatatttttcggtgtttcgttatgctgttattccaatgttttgatagattgtttaaggttttgcggtaaggcgattgtactttctttatacatta Intra-Species Hit: Count: 1 Min: 1 Max: 350 Len: 350 Subject: pint_PI0041_PI0043|hypothetical protein:thiamine phosphate pyrophosphorylase|POSITIVE:POSITIVE|[42084,42433]|350 HSP 1 e-value: 0.0 bit: 694.0 Len: 350 Query Start:1 Query End:350 Subject Strand: POSITIVE Subject Start: 1 Subject End: 350 aattctttgattttaagttcgtttatttcttttttacgatgcaaaggtaggtgcatttctgcacccttacaagcattggtaatgggttgtttcgataatggttatcgtaatattgcgatagagaactgttggaaattagccaaaactgtgatgacaatagatttaaatcaagtatatgtgtgtttttcgtggcggtactgtctgttgtttctgtattttaagaataacagcattcatatttttagaatgaaggcatatatttttcggtgtttcgttatgctgttattccaatgttttgatagattgtttaaggttttgcggtaaggcgattgtactttctttatacatta aattctttgattttaagttcgtttatttcttttttacgatgcaaaggtaggtgcatttctgcacccttacaagcattggtaatgggttgtttcgataatggttatcgtaatattgcgatagagaactgttggaaattagccaaaactgtgatgacaatagatttaaatcaagtatatgtgtgtttttcgtggcggtactgtctgttgtttctgtattttaagaataacagcattcatatttttagaatgaaggcatatatttttcggtgtttcgttatgctgttattccaatgttttgatagattgtttaaggttttgcggtaaggcgattgtactttctttatacatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUCUUUGAUUUUAAGUUCGUUUAUUUCUUUUUUACGAUGCAAAGGUAGGUGCAUUUCUGCACCCUUACAAGCAUUGGUAAUGGGUUGUUUCGAUAAUGGUUAUCGUAAUAUUGCGAUAGAGAACUGUUGGAAAUUAGCCAAAACUGUGAUGACAAUAGAUUUAAAUCAAGUAUAUGUGUGUUUUUCGUGGCGGUACUGUCUGUUGUUUCUGUAUUUUAAGAAUAACAGCAUUCAUAUUUUUAGAAUGAAGGCAUAUAUUUUUCGGUGUUUCGUUAUGCUGUUAUUCCAAUGUUUUGAUAGAUUGUUUAAGGUUUUGCGGUAAGGCGAUUGUACUUUCUUUAUACAUUA .....((((((((.(((((..((....((.......((((((....(((((((((....))))))..)))..))))))......(((((((((((((.(..((((((((....))))))))...).))))))))..)))))........))....))..))))))))))))).....((((((.......((.(((((.(((.(((....(((((......((((((((((((............(((((((.(((..........)))))))))))))))))))))).....((((((........))))))...)))))...)))))).))))).))...)))))).. (-77.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGUAUAAAGAAAGUACAAUCGCCUUACCGCAAAACCUUAAACAAUCUAUCAAAACAUUGGAAUAACAGCAUAACGAAACACCGAAAAAUAUAUGCCUUCAUUCUAAAAAUAUGAAUGCUGUUAUUCUUAAAAUACAGAAACAACAGACAGUACCGCCACGAAAAACACACAUAUACUUGAUUUAAAUCUAUUGUCAUCACAGUUUUGGCUAAUUUCCAACAGUUCUCUAUCGCAAUAUUACGAUAACCAUUAUCGAAACAACCCAUUACCAAUGCUUGUAAGGGUGCAGAAAUGCACCUACCUUUGCAUCGUAAAAAAGAAAUAAACGAACUUAAAAUCAAAGAAUU ...(((((.......)))))...((......))..............(((.(((((((...(((((((((((((..((......))..............((((.........)))))))))))))))))..................(((((((.((...)).........((......)).........)))))))......)))))))............(((((...............(((((.....)))))..........((((..((((......(((((((....)))))))......)))).)))).............))))).........)))... (-57.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 79 31 167 124 pint:PI1504|5end_non-specific_DNA-binding_protein_1424318..1424548_POSITIVE 331 69 40 95 56 pint:PI0770|5end_hypothetical_protein_706170..706400_POSITIVE 318 85 54 33 4 pint:PI0041|5end_hypothetical_protein_41785..42015_POSITIVE 317 219 178 64 23 pint:PI1647|5end_hypothetical_protein_1561564..1561794_POSITIVE 308 227 185 140 100 pint:PI0537|5end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_489756..489986_POSITIVE 308 92 51 120 70 pint:PI0206|5end_TPR-repeat-containing_protein_198112..198342_POSITIVE 307 214 177 147 111 pint:PI0746|5end_hypothetical_protein_675971..676201_POSITIVE 298 96 51 97 48 pint:PI0460|5end_50S_ribosomal_protein_L3_432471..432701_POSITIVE 289 335 291 136 82 pint:PI0992|5end_RNA_polymerase_sigma-70_factor_916456..916686_POSITIVE 288 104 62 192 146 pint:PI0582|5end_hypothetical_protein_524853..525083_POSITIVE 283 79 31 180 133 pint:PI0379|5end_conserved_hypothetical_protein_349872..350102_POSITIVE 281 335 296 167 134 pint:PI1068|5end_nucleolar_protein,_Sun_(Fmu)_family_protein;_tRNA/rRNA_cytosine-C5-methylase_984743..984973_POSITIVE 279 100 51 193 131 pint:PI1950|5end_iron-regulated_membrane_permease_1904468..1904698_POSITIVE 279 100 51 51 1 pint:PI1667|5end_conserved_hypothetical_protein_1579763..1579993_POSITIVE 279 89 41 198 150 pint:PI1459|5end_ribonucleotide_reductase,_alpha_subunit,_C-terminal_region_1381569..1381799_POSITIVE 279 55 16 205 162 pint:PI0191|5end_O-methyltransferase_181070..181300_POSITIVE 278 100 53 179 137 pint:PI0956|5end_conserved_hypothetical_protein_886077..886307_POSITIVE 278 86 41 139 83 pint:PI0933|5end_hypothetical_protein_865700..865930_POSITIVE 278 214 171 146 100 pint:PI0699|5end_conserved_hypothetical_protein_636647..636877_POSITIVE 278 104 66 175 138 pint:PI0542|5end_hypothetical_protein_495554..495784_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 341 85 47 40 6 pint:PI0040|3end_conserved_hypothetical_protein_(possible_integral_membrane_protein)_41872..42022_POSITIVE 314 130 83 133 89 pint:PI1370|3end_alkyl_hydroperoxide_reductase,_subunit_F_1292176..1292326_POSITIVE 308 227 185 83 43 pint:PI0535|3end_hypothetical_protein_489779..489929_POSITIVE 303 298 251 93 25 pint:PI0820|3end_hypothetical_protein_759980..760130_POSITIVE 297 213 175 142 100 pint:PI1493|3end_conserved_hypothetical_protein_1412818..1412968_POSITIVE 297 80 46 145 112 pint:PI0676|3end_hypothetical_protein_614835..614985_POSITIVE 290 346 301 113 63 pint:PI0708|3end_conserved_hypothetical_protein_646234..646384_POSITIVE 289 335 291 59 5 pint:PI0991|3end_conserved_hypothetical_protein_916459..916609_POSITIVE 288 94 51 109 69 pint:PI2117|3end_fumarate_reductase/succinate_dehydrogenase_flavoprotein_subunit,_C-terminal_2066684..2066834_POSITIVE 278 100 53 106 64 pint:PI0955|3end_conserved_hypothetical_protein_886084..886234_POSITIVE 278 214 171 130 84 pint:PI0698|3end_conserved_hypothetical_protein_636711..636861_POSITIVE 275 68 26 123 75 pint:PI1513|3end_conserved_hypothetical_protein_1432502..1432652_POSITIVE 274 78 37 54 13 pint:PI0041|3end_hypothetical_protein_42023..42173_POSITIVE 272 68 21 69 14 pint:PI0434|3end_possible_beta-lactamase_406890..407040_POSITIVE 271 78 35 98 48 pint:PI1789|3end_hypothetical_protein_1719037..1719187_POSITIVE 270 118 73 96 45 pint:PI1253|3end_hypothetical_protein_1175691..1175841_POSITIVE 269 109 61 72 16 pint:PI1116|3end_conserved_hypothetical_protein_1041380..1041530_POSITIVE 266 208 167 51 8 pint:PI0469|3end_30S_ribosomal_protein_S17_437445..437595_POSITIVE 266 80 44 52 23 pint:PI0084|3end_conserved_hypothetical_protein_84520..84670_POSITIVE 265 328 291 55 7 pint:PI0584|3end_hypothetical_protein_527656..527806_POSITIVE