Origin IGS: aaactcgctgcttgcaacgatgagtatccggttgcgtatctcgtctttctgtatttgcatagacagtagcttttagtaaatagtaggcacgattgattgtctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagacaatcaatcgtgcctactatttactaaaagctactgtctatgcaaatacagaaagacgagatacgcaaccggatactcatcgttgcaagcagcgagttt Mask Tandem Repeat Region ================================================ aaactcgctgcttgcaacgatgagtatccggttgcgtatctcgtctttctgtatttgcatagacagtagcttttagtaaatagtaggcacgattgattgtctta Find is-nt database================================================ Query_seq: PI0979:PI0980|PI0979:PI0980:transcriptional regulator, tetR family:conserved hypothetical protein:->->:905739..905842 104 aaactcgctgcttgcaacgatgagtatccggttgcgtatctcgtctttctgtatttgcatagacagtagcttttagtaaatagtaggcacgattgattgtctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0979:PI0980|PI0979:PI0980:transcriptional regulator, tetR family:conserved hypothetical protein:->->:905739..905842 104 aaactcgctgcttgcaacgatgagtatccggttgcgtatctcgtctttctgtatttgcatagacagtagcttttagtaaatagtaggcacgattgattgtctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0979:PI0980|PI0979:PI0980:transcriptional regulator, tetR family:conserved hypothetical protein:->->:905739..905842 104 aaactcgctgcttgcaacgatgagtatccggttgcgtatctcgtctttctgtatttgcatagacagtagcttttagtaaatagtaggcacgattgattgtctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaactcgctgcttgcaacgatgagtatccggttgcgtatctcgtctttctgtatttgcatagacagtagcttttagtaaatagtaggcacgattgattgtctta Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 2 End: 97 . V R Q K C R H T D P Q T D R R E T N A Y V T A K L L Y Y A R N M ....... aaactcgctgcttgcaacgatgagtatccggttgcgtatctcgtctttctgtatttgcatagacagtagcttttagtaaatagtaggcacgattgattgtctta 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================================================ aaactcgctgcttgcaacgatgagtatccggttgcgtatctcgtctttctgtatttgcatagacagtagcttttagtaaatagtaggcacgattgattgtctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0979:PI0980|PI0979:PI0980:transcriptional regulator, tetR family:conserved hypothetical protein:->->:905739..905842 104 aaactcgctgcttgcaacgatgagtatccggttgcgtatctcgtctttctgtatttgcatagacagtagcttttagtaaatagtaggcacgattgattgtctta Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: pint_PI0979_PI0980|transcriptional regulator, tetR family:conserved hypothetical protein|POSITIVE:POSITIVE|[905739,905842]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 aaactcgctgcttgcaacgatgagtatccggttgcgtatctcgtctttctgtatttgcatagacagtagcttttagtaaatagtaggcacgattgattgtctta aaactcgctgcttgcaacgatgagtatccggttgcgtatctcgtctttctgtatttgcatagacagtagcttttagtaaatagtaggcacgattgattgtctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACUCGCUGCUUGCAACGAUGAGUAUCCGGUUGCGUAUCUCGUCUUUCUGUAUUUGCAUAGACAGUAGCUUUUAGUAAAUAGUAGGCACGAUUGAUUGUCUUA ....(((.(((((((...((((((.((.((....)).))))))))......(((((((.((((........)))))))))))))))))))))............ (-23.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGACAAUCAAUCGUGCCUACUAUUUACUAAAAGCUACUGUCUAUGCAAAUACAGAAAGACGAGAUACGCAACCGGAUACUCAUCGUUGCAAGCAGCGAGUUU ............((((((....................((((((.((......))...)))).))....(((((..(((....))))))))..))).))).... (-15.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 47 4 72 20 pint:PI1778|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1710009..1710239_POSITIVE 333 46 2 84 42 pint:PI0734|5end_ABC_transporter,_ATP-binding_/_permease_667052..667282_POSITIVE 332 49 2 160 113 pint:PI0361|5end_hypothetical_protein_333062..333292_POSITIVE 326 57 11 100 67 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 325 67 24 84 38 pint:PI0288|5end_hypothetical_protein_(possible_ISPg3-related_transposase)_272272..272502_POSITIVE 321 50 7 135 87 pint:PI0365|5end_hypothetical_protein_335721..335951_POSITIVE 319 49 5 225 170 pint:PI0431|5end_Xaa-Pro_aminopeptidase_403064..403294_POSITIVE 315 35 5 57 29 pint:PI2158|5end_glycosyl_transferase,_group_2_family_protein_2104392..2104622_POSITIVE 314 52 12 193 153 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 307 47 6 46 7 pint:PI1848|5end_hypothetical_protein_1793799..1794029_POSITIVE 307 42 3 221 169 pint:PI0718|5end_hypothetical_protein_653725..653955_POSITIVE 306 49 4 51 8 pint:PI1640|5end_hypothetical_protein_1558062..1558292_POSITIVE 305 52 12 206 150 pint:PI0171|5end_hypothetical_protein_163850..164080_POSITIVE 301 37 4 206 168 pint:PI1735|5end_conserved_hypothetical_protein_1653428..1653658_POSITIVE 301 46 6 93 30 pint:PI1636|5end_hypothetical_protein_1554246..1554476_POSITIVE 296 45 13 213 179 pint:PI1913|5end_conserved_hypothetical_protein_1857104..1857334_POSITIVE 295 49 7 59 15 pint:PI1764|5end_conserved_hypothetical_protein_1688948..1689178_POSITIVE 294 45 4 64 23 pint:PI0300|5end_transposase_285163..285393_POSITIVE 292 43 2 192 134 pint:PI0683|5end_hypothetical_protein_619292..619522_POSITIVE 290 43 5 124 91 pint:PI1475|5end_possible_short_chain_dehydrogenase_1397142..1397372_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 47 4 64 12 pint:PI1777|3end_conserved_hypothetical_protein_1710081..1710231_POSITIVE 325 67 24 84 38 pint:PI0287|3end_ISPg3-related_transposase_272352..272502_POSITIVE 315 35 5 42 14 pint:PI2157|3end_xanthosine_triphosphate_pyrophosphatase,_HAM1_family_2104457..2104607_POSITIVE 308 44 1 72 30 pint:PI1794|3end_conserved_hypothetical_protein_1726696..1726846_POSITIVE 303 49 7 42 1 pint:PI1639|3end_conserved_hypothetical_protein_1558133..1558283_POSITIVE 301 46 6 73 10 pint:PI1635|3end_hypothetical_protein_1554306..1554456_POSITIVE 299 50 4 115 73 pint:PI0674|3end_conserved_hypothetical_protein_616154..616304_POSITIVE 292 43 2 76 18 pint:PI0681|3end_hypothetical_protein_619256..619406_POSITIVE 290 45 5 102 65 pint:PI1547|3end_hypothetical_protein_1466226..1466376_POSITIVE 289 97 51 147 109 pint:PI0776|3end_predicted_TPR-repeat-containing_protein_713323..713473_POSITIVE 285 58 14 145 98 pint:PI0833|3end_conserved_hypothetical_protein_770666..770816_POSITIVE 280 48 4 144 105 pint:PI0091|3end_hypothetical_protein_89774..89924_POSITIVE 279 50 4 83 39 pint:PI0037|3end_hypothetical_protein_39616..39766_POSITIVE 277 50 7 124 77 pint:PI1548|3end_conserved_hypothetical_protein_1466886..1467036_POSITIVE 276 70 24 147 80 pint:PI2122|3end_conserved_hypothetical_protein_2070480..2070630_POSITIVE 275 43 2 139 86 pint:PI0251|3end_hypothetical_protein_247810..247960_POSITIVE 273 50 9 101 62 pint:PI2014|3end_conserved_hypothetical_protein_1972603..1972753_POSITIVE 273 50 4 112 73 pint:PI1716|3end_hypothetical_protein_1632006..1632156_POSITIVE 271 50 5 131 94 pint:PI1710|3end_ABC-type_permease_component_1627356..1627506_POSITIVE 266 48 3 51 4 pint:PI0337|3end_hypothetical_protein_315402..315552_POSITIVE