Origin IGS: ttgtcctgatggtttggttattgtctgttgattctaattttatattgctggaaaagaaaaagtgcgggcaaacgcatatgcaactacgtttgaccgcaccttatactgttgtgggtatatcgtttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaacgatatacccacaacagtataaggtgcggtcaaacgtagttgcatatgcgtttgcccgcactttttcttttccagcaatataaaattagaatcaacagacaataaccaaaccatcaggacaa Mask Tandem Repeat Region ================================================ ttgtcctgatggtttggttattgtctgttgattctaattttatattgctggaaaagaaaaagtgcgggcaaacgcatatgcaactacgtttgaccgcaccttatactgttgtgggtatatcgtttta Find is-nt database================================================ Query_seq: PI0949:PI0950|PI0949:PI0950:endonuclease:50S ribosomal protein L31:->->:883340..883466 127 ttgtcctgatggtttggttattgtctgttgattctaattttatattgctggaaaagaaaaagtgcgggcaaacgcatatgcaactacgtttgaccgcaccttatactgttgtgggtatatcgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0949:PI0950|PI0949:PI0950:endonuclease:50S ribosomal protein L31:->->:883340..883466 127 ttgtcctgatggtttggttattgtctgttgattctaattttatattgctggaaaagaaaaagtgcgggcaaacgcatatgcaactacgtttgaccgcaccttatactgttgtgggtatatcgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0949:PI0950|PI0949:PI0950:endonuclease:50S ribosomal protein L31:->->:883340..883466 127 ttgtcctgatggtttggttattgtctgttgattctaattttatattgctggaaaagaaaaagtgcgggcaaacgcatatgcaactacgtttgaccgcaccttatactgttgtgggtatatcgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgtcctgatggtttggttattgtctgttgattctaattttatattgctggaaaagaaaaagtgcgggcaaacgcatatgcaactacgtttgaccgcaccttatactgttgtgggtatatcgtttta Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 6 End: 125 ..... M M V W L L S V D S N F I L L E K K K C G Q T H M Q L R L T A P Y T V V G I S F .. ttgtcctgatggtttggttattgtctgttgattctaattttatattgctggaaaagaaaaagtgcgggcaaacgcatatgcaactacgtttgaccgcaccttatactgttgtgggtatatcgtttta 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================================================ ttgtcctgatggtttggttattgtctgttgattctaattttatattgctggaaaagaaaaagtgcgggcaaacgcatatgcaactacgtttgaccgcaccttatactgttgtgggtatatcgtttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -12.1 Tail_Score: -5.45802 Start: 62 End: 99 Full_Region: ccacaacagtataag gtgcggtcaaacgta gttgcata tgcgtttgcccgcac tttttcttttccagc .............................................................gtgcggtcaaacgtagttgcatatgcgtttgcccgcac............................ Find igs database================================================ Query_seq: PI0949:PI0950|PI0949:PI0950:endonuclease:50S ribosomal protein L31:->->:883340..883466 127 ttgtcctgatggtttggttattgtctgttgattctaattttatattgctggaaaagaaaaagtgcgggcaaacgcatatgcaactacgtttgaccgcaccttatactgttgtgggtatatcgtttta Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: pint_PI0949_PI0950|endonuclease:50S ribosomal protein L31|POSITIVE:POSITIVE|[883340,883466]|127 HSP 1 e-value: 2.0E-66 bit: 252.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 ttgtcctgatggtttggttattgtctgttgattctaattttatattgctggaaaagaaaaagtgcgggcaaacgcatatgcaactacgtttgaccgcaccttatactgttgtgggtatatcgtttta ttgtcctgatggtttggttattgtctgttgattctaattttatattgctggaaaagaaaaagtgcgggcaaacgcatatgcaactacgtttgaccgcaccttatactgttgtgggtatatcgtttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUCCUGAUGGUUUGGUUAUUGUCUGUUGAUUCUAAUUUUAUAUUGCUGGAAAAGAAAAAGUGCGGGCAAACGCAUAUGCAACUACGUUUGACCGCACCUUAUACUGUUGUGGGUAUAUCGUUUUA ...(((.(...((..(((((..(((....)))..)))))..))....).))).........((((((.((((((............)))))).))))))..((((((......))))))........ (-27.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAACGAUAUACCCACAACAGUAUAAGGUGCGGUCAAACGUAGUUGCAUAUGCGUUUGCCCGCACUUUUUCUUUUCCAGCAAUAUAAAAUUAGAAUCAACAGACAAUAACCAAACCAUCAGGACAA ....................((...(((((((((.((((((((........)))))))).)))))))))..))..........................................((....)).... (-25.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 364 109 61 179 125 pint:PI1448|5end_hypothetical_protein_1371579..1371809_POSITIVE 361 110 61 203 159 pint:PI0786|5end_conserved_hypothetical_protein;_possible_glycosyltransferase_723240..723470_POSITIVE 361 110 61 107 63 pint:PI0783|5end_hypothetical_protein_723144..723374_POSITIVE 343 106 63 208 145 pint:PI0953|5end_hypothetical_protein_885119..885349_POSITIVE 325 102 62 64 11 pint:PI1647|5end_hypothetical_protein_1561564..1561794_POSITIVE 311 83 46 80 51 pint:PI1753|5end_conserved_hypothetical_protein_1680291..1680521_POSITIVE 306 108 61 70 7 pint:PI0751|5end_conserved_hypothetical_protein_680623..680853_POSITIVE 304 70 21 199 135 pint:PI1496|5end_nucleoside_phosphorylase_1417116..1417346_POSITIVE 301 102 62 221 189 pint:PI0466|5end_30S_ribosomal_protein_S3_435725..435955_POSITIVE 299 110 63 86 50 pint:PI0616|5end_electron_transfer_flavoprotein,_beta-subunit_565560..565790_POSITIVE 299 108 61 151 78 pint:PI0136|5end_surface_antigen_BspA_127105..127335_POSITIVE 298 108 66 53 7 pint:PI0586|5end_hypothetical_protein_533757..533987_POSITIVE 281 83 44 89 41 pint:PI1062|5end_TPR_repeat_protein_980020..980250_POSITIVE 280 104 61 211 156 pint:PI1660|5end_hypothetical_protein_1574659..1574889_POSITIVE 280 115 73 199 155 pint:PI0492|5end_hypothetical_protein_451701..451931_POSITIVE 279 110 63 74 16 pint:PI2153|5end_hypothetical_protein_2099392..2099622_POSITIVE 279 110 63 200 142 pint:PI0788|5end_3-methyladenine_DNA_glycosylase_(DNA-3-methyladenine_glycosylase_I)_726152..726382_POSITIVE 279 110 63 205 147 pint:PI0771|5end_conserved_hypothetical_protein_706524..706754_POSITIVE 276 90 47 109 54 pint:PI2105|5end_hypothetical_protein_2059357..2059587_POSITIVE 274 100 67 67 32 pint:PI1306|5end_dipeptidyl_peptidase_IV_1220264..1220494_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 100 51 135 75 pint:PI0060|3end_long-chain-fatty-acid--CoA_ligase_(acyl-CoA_synthetase)_60166..60316_POSITIVE 325 96 64 119 85 pint:PI2008|3end__ABC_transporter,_ATP-binding_protein_1967961..1968111_POSITIVE 297 108 63 53 8 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 281 83 44 62 14 pint:PI1061|3end_conserved_hypothetical_protein_980073..980223_POSITIVE 280 97 54 151 102 pint:PI0732|3end_conserved_hypothetical_protein_664367..664517_POSITIVE 277 83 53 149 115 pint:PI0740|3end_hypothetical_protein_672365..672515_POSITIVE 276 90 47 62 7 pint:PI2104|3end_carboxyl-terminal_protease_2059390..2059540_POSITIVE 269 109 61 96 49 pint:PI0572|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_517589..517739_POSITIVE 268 90 45 89 38 pint:PI0734|3end_ABC_transporter,_ATP-binding_/_permease_668760..668910_POSITIVE 265 97 60 148 101 pint:PI1891|3end_hypothetical_protein_1835917..1836067_POSITIVE 264 110 62 137 91 pint:PI0981|3end_outer_membrane_protein,_TonB_dependent_receptor_909390..909540_POSITIVE 261 96 53 83 40 pint:PI0674|3end_conserved_hypothetical_protein_616154..616304_POSITIVE 261 108 63 93 38 pint:PI0311|3end_hypothetical_protein_294968..295118_POSITIVE 261 108 63 65 10 pint:PI0312|3end_hypothetical_protein_294940..295090_POSITIVE 260 96 63 141 98 pint:PI1814|3end_hypothetical_protein_1753233..1753383_POSITIVE 260 96 63 141 98 pint:PI0689|3end_hypothetical_protein_625877..626027_POSITIVE 259 48 3 96 30 pint:PI1781|3end_membrane-associated_zinc_metalloprotease_1714551..1714701_POSITIVE 258 106 63 83 37 pint:PI0005|3end_hypothetical_protein_7450..7600_POSITIVE 256 116 71 110 48 pint:PI0681|3end_hypothetical_protein_619256..619406_POSITIVE 252 109 68 127 93 pint:PI0349|3end_hypothetical_protein_323802..323952_POSITIVE