Origin IGS: acgctggtgagccttataattggtccacttctctgctactggtccttctgggatttttgaatctaatattttagccataatcttgtatctttctattagaatttaatgaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taattcattaaattctaatagaaagatacaagattatggctaaaatattagattcaaaaatcccagaaggaccagtagcagagaagtggaccaattataaggctcaccagcgt Mask Tandem Repeat Region ================================================ acgctggtgagccttataattggtccacttctctgctactggtccttctgggatttttgaatctaatattttagccataatcttgtatctttctattagaatttaatgaatta Find is-nt database================================================ Query_seq: PI2118:PI2119|PI2118:PI2119:fumarate reductase/succinate dehydrogenase flavoprotein subunit, N-terminal:conserved hypothetical protein; possible cytochrome B subunit:->->:2068058..2068170 113 acgctggtgagccttataattggtccacttctctgctactggtccttctgggatttttgaatctaatattttagccataatcttgtatctttctattagaatttaatgaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2118:PI2119|PI2118:PI2119:fumarate reductase/succinate dehydrogenase flavoprotein subunit, N-terminal:conserved hypothetical protein; possible cytochrome B subunit:->->:2068058..2068170 113 acgctggtgagccttataattggtccacttctctgctactggtccttctgggatttttgaatctaatattttagccataatcttgtatctttctattagaatttaatgaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2118:PI2119|PI2118:PI2119:fumarate reductase/succinate dehydrogenase flavoprotein subunit, N-terminal:conserved hypothetical protein; possible cytochrome B subunit:->->:2068058..2068170 113 acgctggtgagccttataattggtccacttctctgctactggtccttctgggatttttgaatctaatattttagccataatcttgtatctttctattagaatttaatgaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acgctggtgagccttataattggtccacttctctgctactggtccttctgggatttttgaatctaatattttagccataatcttgtatctttctattagaatttaatgaatta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 1 End: 102 R Q H A K Y N T W K E A V P G E P I K S D L I K A M I K Y R E I L M ........... acgctggtgagccttataattggtccacttctctgctactggtccttctgggatttttgaatctaatattttagccataatcttgtatctttctattagaatttaatgaatta 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================================================ acgctggtgagccttataattggtccacttctctgctactggtccttctgggatttttgaatctaatattttagccataatcttgtatctttctattagaatttaatgaatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI2118:PI2119|PI2118:PI2119:fumarate reductase/succinate dehydrogenase flavoprotein subunit, N-terminal:conserved hypothetical protein; possible cytochrome B subunit:->->:2068058..2068170 113 acgctggtgagccttataattggtccacttctctgctactggtccttctgggatttttgaatctaatattttagccataatcttgtatctttctattagaatttaatgaatta Intra-Species Hit: Count: 1 Min: 1 Max: 113 Len: 113 Subject: pint_PI2118_PI2119|fumarate reductase/succinate dehydrogenase flavoprotein subunit, N-terminal:conserved hypothetical protein; possible cytochrome B subunit|POSITIVE:POSITIVE|[2068058,2068170]|113 HSP 1 e-value: 5.0E-58 bit: 224.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 acgctggtgagccttataattggtccacttctctgctactggtccttctgggatttttgaatctaatattttagccataatcttgtatctttctattagaatttaatgaatta acgctggtgagccttataattggtccacttctctgctactggtccttctgggatttttgaatctaatattttagccataatcttgtatctttctattagaatttaatgaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGCUGGUGAGCCUUAUAAUUGGUCCACUUCUCUGCUACUGGUCCUUCUGGGAUUUUUGAAUCUAAUAUUUUAGCCAUAAUCUUGUAUCUUUCUAUUAGAAUUUAAUGAAUUA ..((.((((..((........))..)))).....))....(((((.....))))).((((((((((((....((..(((....)))..))...)))))).))))))....... (-17.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUCAUUAAAUUCUAAUAGAAAGAUACAAGAUUAUGGCUAAAAUAUUAGAUUCAAAAAUCCCAGAAGGACCAGUAGCAGAGAAGUGGACCAAUUAUAAGGCUCACCAGCGU ...(((.......(((((((...((...((......)).))....)))))))........(((.....))).........)))..(((..((........))..)))...... (-13.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 378 48 2 117 60 pint:PI0635|5end_dephospho-CoA_kinase_580954..581184_POSITIVE 340 50 2 198 141 pint:PI0337|5end_hypothetical_protein_314732..314962_POSITIVE 309 60 23 122 86 pint:PI0113|5end_arginyl-tRNA_synthetase_108371..108601_POSITIVE 308 56 34 35 10 pint:PI1564|5end_surface_antigen_BspA_1483455..1483685_POSITIVE 302 43 2 61 7 pint:PI1634|5end_conserved_hypothetical_protein_1553179..1553409_POSITIVE 302 43 2 61 7 pint:PI0340|5end_conserved_hypothetical_protein_316095..316325_POSITIVE 298 61 22 70 20 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 293 50 3 70 21 pint:PI0442|5end_50S_ribosomal_protein_L1_411644..411874_POSITIVE 279 43 6 167 128 pint:PI1684|5end_dimethyladenosine_transferase_1601073..1601303_POSITIVE 279 48 1 171 113 pint:PI0052|5end_hypothetical_protein_52312..52542_POSITIVE 274 62 21 64 24 pint:PI0098|5end_conserved_hypothetical_protein_(possible_glycosyl/glycerophosphate_transferase)_94622..94852_POSITIVE 271 48 6 220 180 pint:PI0301|5end_probable_transposase_285672..285902_POSITIVE 258 52 12 229 185 pint:PI1492|5end_triosephosphate_isomerase_1410155..1410385_POSITIVE 256 48 2 90 35 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 255 45 3 210 179 pint:PI0718|5end_hypothetical_protein_653725..653955_POSITIVE 249 48 2 64 13 pint:PI0749|5end_hypothetical_protein_677234..677464_POSITIVE 247 36 3 58 22 pint:PI1331|5end_conserved_hypothetical_protein_1248442..1248672_POSITIVE 247 60 12 44 1 pint:PI0740|5end_hypothetical_protein_672112..672342_POSITIVE 247 55 19 151 98 pint:PI0209|5end_hypothetical_protein_202723..202953_POSITIVE 244 49 3 103 53 pint:PI0351|5end_hypothetical_protein_324317..324547_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 45 3 98 53 pint:PI0183|3end_hypothetical_protein_174810..174960_POSITIVE 300 47 3 150 93 pint:PI2074|3end_conserved_hypothetical_protein_2034375..2034525_POSITIVE 288 59 11 53 8 pint:PI0441|3end_50S_ribosomal_protein_L11_411699..411849_POSITIVE 287 50 2 144 86 pint:PI1568|3end_OmpA_family_protein_1491043..1491193_POSITIVE 274 62 21 44 4 pint:PI0097|3end_aspartate_aminotransferase_94682..94832_POSITIVE 252 50 2 120 73 pint:PI0639|3end_small_heat_shock_protein_583165..583315_POSITIVE 247 55 19 143 90 pint:PI0208|3end_possible_peptidase,_M23/M37_family_202795..202945_POSITIVE 246 53 18 37 1 pint:PI1069|3end_hypothetical_protein_988458..988608_POSITIVE 245 49 3 115 81 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 244 47 4 144 93 pint:PI1706|3end_GTP-binding_protein_1623668..1623818_POSITIVE 243 50 2 77 22 pint:PI2117|3end_fumarate_reductase/succinate_dehydrogenase_flavoprotein_subunit,_C-terminal_2066684..2066834_POSITIVE 240 47 1 144 102 pint:PI1876|3end_possible_flagellar_motor_protein,_OmpA_family_1819968..1820118_POSITIVE 236 45 2 143 87 pint:PI0309|3end_hypothetical_protein_291729..291879_POSITIVE 231 55 19 80 33 pint:PI0528|3end_hypothetical_protein_483122..483272_POSITIVE 230 65 30 34 2 pint:PI0881|3end_conserved_hypothetical_protein_815283..815433_POSITIVE 229 46 5 89 51 pint:PI1484|3end_conserved_hypothetical_protein_1405223..1405373_POSITIVE 227 49 2 151 112 pint:PI1623|3end_hypothetical_protein_1549261..1549411_POSITIVE 223 43 3 147 93 pint:PI1442|3end_radical-activating_enzyme_(pyruvate-formate_lyase-activating_enzyme)_1364649..1364799_POSITIVE 221 49 2 133 75 pint:PI2159|3end_immunoreactive_84_kDa_antigen_PG93_2107371..2107521_POSITIVE 221 49 1 55 4 pint:PI0616|3end_electron_transfer_flavoprotein,_beta-subunit_566440..566590_POSITIVE