Origin IGS: cttttcgggatcttctcccttaacatcaaagtagacgtcaattactggtccaataatttgggaaatacgtccatttatctgtgacatacgctttgtttttattatttttttatgctttaattctctgttaataatatttattgcgaactatactta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagtatagttcgcaataaatattattaacagagaattaaagcataaaaaaataataaaaacaaagcgtatgtcacagataaatggacgtatttcccaaattattggaccagtaattgacgtctactttgatgttaagggagaagatcccgaaaag Mask Tandem Repeat Region ================================================ cttttcgggatcttctcccttaacatcaaagtagacgtcaattactggtccaataatttgggaaatacgtccatttatctgtgacatacgctttgtttttattatttttttatgctttaattctctgttaataatatttattgcgaactatactta Find is-nt database================================================ Query_seq: PI1290:PI1291|PI1290:PI1291:ATP synthase, beta subunit:6-phosphofructokinase:->->:1204636..1204791 156 cttttcgggatcttctcccttaacatcaaagtagacgtcaattactggtccaataatttgggaaatacgtccatttatctgtgacatacgctttgtttttattatttttttatgctttaattctctgttaataatatttattgcgaactatactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1290:PI1291|PI1290:PI1291:ATP synthase, beta subunit:6-phosphofructokinase:->->:1204636..1204791 156 cttttcgggatcttctcccttaacatcaaagtagacgtcaattactggtccaataatttgggaaatacgtccatttatctgtgacatacgctttgtttttattatttttttatgctttaattctctgttaataatatttattgcgaactatactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1290:PI1291|PI1290:PI1291:ATP synthase, beta subunit:6-phosphofructokinase:->->:1204636..1204791 156 cttttcgggatcttctcccttaacatcaaagtagacgtcaattactggtccaataatttgggaaatacgtccatttatctgtgacatacgctttgtttttattatttttttatgctttaattctctgttaataatatttattgcgaactatactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttttcgggatcttctcccttaacatcaaagtagacgtcaattactggtccaataatttgggaaatacgtccatttatctgtgacatacgctttgtttttattatttttttatgctttaattctctgttaataatatttattgcgaactatactta Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 41 End: 154 ........................................ M T G P I I W E I R P F I C D I R F V F I I F L C F N S L L I I F I A N Y T .. Protein_Len: 47 Strand: - Start: 1 End: 141 K E P D E G K V D F Y V D I V P G I I Q S I R G N I Q S M R K T K I I K K H K L E R N I I N M ............... cttttcgggatcttctcccttaacatcaaagtagacgtcaattactggtccaataatttgggaaatacgtccatttatctgtgacatacgctttgtttttattatttttttatgctttaattctctgttaataatatttattgcgaactatactta 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================================================ cttttcgggatcttctcccttaacatcaaagtagacgtcaattactggtccaataatttgggaaatacgtccatttatctgtgacatacgctttgtttttattatttttttatgctttaattctctgttaataatatttattgcgaactatactta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1290:PI1291|PI1290:PI1291:ATP synthase, beta subunit:6-phosphofructokinase:->->:1204636..1204791 156 cttttcgggatcttctcccttaacatcaaagtagacgtcaattactggtccaataatttgggaaatacgtccatttatctgtgacatacgctttgtttttattatttttttatgctttaattctctgttaataatatttattgcgaactatactta Intra-Species Hit: Count: 1 Min: 1 Max: 156 Len: 156 Subject: pint_PI1290_PI1291|ATP synthase, beta subunit:6- phosphofructokinase|POSITIVE:POSITIVE|[1204636, 1204791]|156 HSP 1 e-value: 5.0E-71 bit: 268.0 Len: 156 Query Start:1 Query End:156 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 cttttcgggatcttctcccttaacatcaaagtagacgtcaattactggtccaataatttgggaaatacgtccatttatctgtgacatacgctttgtttttattannnnnnnatgctttaattctctgttaataatatttattgcgaactatactta cttttcgggatcttctcccttaacatcaaagtagacgtcaattactggtccaataatttgggaaatacgtccatttatctgtgacatacgctttgtttttattatttttttatgctttaattctctgttaataatatttattgcgaactatactta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUCGGGAUCUUCUCCCUUAACAUCAAAGUAGACGUCAAUUACUGGUCCAAUAAUUUGGGAAAUACGUCCAUUUAUCUGUGACAUACGCUUUGUUUUUAUUAUUUUUUUAUGCUUUAAUUCUCUGUUAAUAAUAUUUAUUGCGAACUAUACUUA ......((((.....)))).........(((((...((((.....((((((((....)))))........)))........))))...(((..((...((((((.......((......)).......))))))....))..))).....))))). (-21.16) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUAUAGUUCGCAAUAAAUAUUAUUAACAGAGAAUUAAAGCAUAAAAAAAUAAUAAAAACAAAGCGUAUGUCACAGAUAAAUGGACGUAUUUCCCAAAUUAUUGGACCAGUAAUUGACGUCUACUUUGAUGUUAAGGGAGAAGAUCCCGAAAAG ....(((.(.((.((((((.(((((((.......................)))))))..........(((((((.((......)))))))))........)))))))).).)))..(((((((......))))))).((((.....))))...... (-25.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 105 66 92 51 pint:PI0192|5end_conserved_hypothetical_protein_182131..182361_POSITIVE 255 34 1 226 186 pint:PI0328|5end_conserved_hypothetical_protein_309476..309706_POSITIVE 252 99 51 165 121 pint:PI0081|5end_hypothetical_protein_80423..80653_POSITIVE 251 47 6 77 28 pint:PI0691|5end_hypothetical_protein_627885..628115_POSITIVE 236 45 2 158 117 pint:PI1545|5end_conserved_hypothetical_protein_1463587..1463817_POSITIVE 236 45 2 78 37 pint:PI1544|5end_hypothetical_protein_1463507..1463737_POSITIVE 236 80 36 84 40 pint:PI0837|5end_conserved_hypothetical_protein_772308..772538_POSITIVE 224 37 1 201 167 pint:PI0844|5end_cytidine/deoxycytidylate_deaminase_(dCMP_deaminase)_777793..778023_POSITIVE 223 47 6 218 163 pint:PI1790|5end_hypothetical_protein_1722179..1722409_POSITIVE 220 126 91 137 108 pint:PI0258|5end_conjugative_transposon_protein,_TraG_249722..249952_POSITIVE 219 70 26 76 25 pint:PI0718|5end_hypothetical_protein_653725..653955_POSITIVE 219 90 46 173 129 pint:PI0513|5end_ion_transporter_471530..471760_POSITIVE 217 76 31 87 40 pint:PI0953|5end_hypothetical_protein_885119..885349_POSITIVE 216 102 65 109 79 pint:PI0538|5end_transcriptional_regulator_492561..492791_POSITIVE 215 50 1 191 139 pint:PI0626|5end_penicillin-binding_protein,_D-alanyl-D-alanine_carboxypeptidase_574305..574535_POSITIVE 215 50 1 89 37 pint:PI0624|5end_hypothetical_protein_574203..574433_POSITIVE 212 92 59 188 161 pint:PI0952|5end_conserved_hypothetical_protein_883718..883948_POSITIVE 212 102 68 202 166 pint:PI0381|5end_probable_transcriptional_regulator,_AraC_family_350572..350802_POSITIVE 211 98 51 135 89 pint:PI0301|5end_probable_transposase_285672..285902_POSITIVE 209 98 58 81 35 pint:PI1359|5end_hypothetical_protein_1275473..1275703_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 99 51 84 40 pint:PI0080|3end_hypothetical_protein_80422..80572_POSITIVE 236 80 36 69 25 pint:PI0836|3end_conserved_hypothetical_protein_772373..772523_POSITIVE 220 126 91 137 108 pint:PI0257|3end_conjugative_transposon_protein,_TraF_249802..249952_POSITIVE 216 124 82 110 65 pint:PI1222|3end_hypothetical_protein_1143378..1143528_POSITIVE 216 102 65 91 61 pint:PI0536|3end_hypothetical_protein_492623..492773_POSITIVE 215 104 61 46 6 pint:PI0140|3end_conserved_hypothetical_protein_132106..132256_POSITIVE 212 92 59 45 18 pint:PI0950|3end_50S_ribosomal_protein_L31_883655..883805_POSITIVE 212 102 68 91 55 pint:PI0380|3end_conserved_hypothetical_protein_350541..350691_POSITIVE 211 98 51 144 98 pint:PI0300|3end_transposase_285761..285911_POSITIVE 206 146 103 113 67 pint:PI1943|3end_hypothetical_protein_1902206..1902356_POSITIVE 206 98 61 44 1 pint:PI1358|3end_phospho-N-acetylmuramoyl-pentapeptide-transferase__1275516..1275666_POSITIVE 203 50 4 52 2 pint:PI1623|3end_hypothetical_protein_1549261..1549411_POSITIVE 203 117 71 101 64 pint:PI1396|3end_urocanate_hydratase_1317873..1318023_POSITIVE 203 94 60 85 49 pint:PI0726|3end_hypothetical_protein_659253..659403_POSITIVE 203 50 4 82 32 pint:PI0331|3end_hypothetical_protein_312575..312725_POSITIVE 203 50 4 52 2 pint:PI0330|3end_hypothetical_protein_312545..312695_POSITIVE 199 48 1 147 102 pint:PI0713|3end_hypothetical_protein_650529..650679_POSITIVE 198 90 59 151 123 pint:PI1767|3end_fructokinase,_pfkB_family_1695243..1695393_POSITIVE 195 77 32 142 98 pint:PI1249|3end_conserved_hypothetical_protein_1174147..1174297_POSITIVE 195 37 1 105 69 pint:PI0528|3end_hypothetical_protein_483122..483272_POSITIVE