Origin IGS: gggtttatccatcgcgttcaatgttcttttgatagcgcaaagatatgaaatgaaatagcatagaaaaagggaatgaggtttattttccattcccttaaatcgtcttaattggtgcaggaaagaaactttatttccgttgttttatggattctgcctgcttctgaagttcgtttgcttgggatgtattcaggcgggctcgctctgtcttttctgccggtcgttttggagggagccgttcgtattacgattttctattgttttcacggctgtatttgtttttgatttatgagcagaccaacgggatgagtcagtcctgaatgctgctaagctaatgcttctcaagaaaagaaataagacttcccctaaaaagattaggtacttttcagaaaaacatcaagtactttcacaaaaaagattaggtactttttattggattatcaggtacttttgaaaaatagatttattatatttgtagatgtatttaagaaaacgcctttcagaggatttctccgaccttgggaaggtttatcaagtggagactaaaacgtatgtaata .........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.........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 tattacatacgttttagtctccacttgataaaccttcccaaggtcggagaaatcctctgaaaggcgttttcttaaatacatctacaaatataataaatctatttttcaaaagtacctgataatccaataaaaagtacctaatcttttttgtgaaagtacttgatgtttttctgaaaagtacctaatctttttaggggaagtcttatttcttttcttgagaagcattagcttagcagcattcaggactgactcatcccgttggtctgctcataaatcaaaaacaaatacagccgtgaaaacaatagaaaatcgtaatacgaacggctccctccaaaacgaccggcagaaaagacagagcgagcccgcctgaatacatcccaagcaaacgaacttcagaagcaggcagaatccataaaacaacggaaataaagtttctttcctgcaccaattaagacgatttaagggaatggaaaataaacctcattccctttttctatgctatttcatttcatatctttgcgctatcaaaagaacattgaacgcgatggataaaccc Mask Tandem Repeat Region ================================================ gggtttatccatcgcgttcaatgttcttttgatagcgcaaagatatgaaatgaaatagcatagaaaaagggaatgaggtttattttccattcccttaaatcgtcttaattggtgcaggaaagaaactttatttccgttgttttatggattctgcctgcttctgaagttcgtttgcttgggatgtattcaggcgggctcgctctgtcttttctgccggtcgttttggagggagccgttcgtattacgattttctattgttttcacggctgtatttgtttttgatttatgagcagaccaacgggatgagtcagtcctgaatgctgctaagctaatgcttctcaagaaaagaaataagacttcccctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntattggattatcaggtacttttgaaaaatagatttattatatttgtagatgtatttaagaaaacgcctttcagaggatttctccgaccttgggaaggtttatcaagtggagactaaaacgtatgtaata Find is-nt database================================================ Query_seq: PG1203:PG1205|PG1203:PG1205:transcriptional regulator, putative:DNA-binding protein, histone-like family:<-->:1283537..1284092 556 gggtttatccatcgcgttcaatgttcttttgatagcgcaaagatatgaaatgaaatagcatagaaaaagggaatgaggtttattttccattcccttaaatcgtcttaattggtgcaggaaagaaactttatttccgttgttttatggattctgcctgcttctgaagttcgtttgcttgggatgtattcaggcgggctcgctctgtcttttctgccggtcgttttggagggagccgttcgtattacgattttctattgttttcacggctgtatttgtttttgatttatgagcagaccaacgggatgagtcagtcctgaatgctgctaagctaatgcttctcaagaaaagaaataagacttcccctaaaaagattaggtacttttcagaaaaacatcaagtactttcacaaaaaagattaggtactttttattggattatcaggtacttttgaaaaatagatttattatatttgtagatgtatttaagaaaacgcctttcagaggatttctccgaccttgggaaggtttatcaagtggagactaaaacgtatgtaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1203:PG1205|PG1203:PG1205:transcriptional regulator, putative:DNA-binding protein, histone-like family:<-->:1283537..1284092 556 gggtttatccatcgcgttcaatgttcttttgatagcgcaaagatatgaaatgaaatagcatagaaaaagggaatgaggtttattttccattcccttaaatcgtcttaattggtgcaggaaagaaactttatttccgttgttttatggattctgcctgcttctgaagttcgtttgcttgggatgtattcaggcgggctcgctctgtcttttctgccggtcgttttggagggagccgttcgtattacgattttctattgttttcacggctgtatttgtttttgatttatgagcagaccaacgggatgagtcagtcctgaatgctgctaagctaatgcttctcaagaaaagaaataagacttcccctaaaaagattaggtacttttcagaaaaacatcaagtactttcacaaaaaagattaggtactttttattggattatcaggtacttttgaaaaatagatttattatatttgtagatgtatttaagaaaacgcctttcagaggatttctccgaccttgggaaggtttatcaagtggagactaaaacgtatgtaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1203:PG1205|PG1203:PG1205:transcriptional regulator, putative:DNA-binding protein, histone-like family:<-->:1283537..1284092 556 gggtttatccatcgcgttcaatgttcttttgatagcgcaaagatatgaaatgaaatagcatagaaaaagggaatgaggtttattttccattcccttaaatcgtcttaattggtgcaggaaagaaactttatttccgttgttttatggattctgcctgcttctgaagttcgtttgcttgggatgtattcaggcgggctcgctctgtcttttctgccggtcgttttggagggagccgttcgtattacgattttctattgttttcacggctgtatttgtttttgatttatgagcagaccaacgggatgagtcagtcctgaatgctgctaagctaatgcttctcaagaaaagaaataagacttcccctaaaaagattaggtacttttcagaaaaacatcaagtactttcacaaaaaagattaggtactttttattggattatcaggtacttttgaaaaatagatttattatatttgtagatgtatttaagaaaacgcctttcagaggatttctccgaccttgggaaggtttatcaagtggagactaaaacgtatgtaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gggtttatccatcgcgttcaatgttcttttgatagcgcaaagatatgaaatgaaatagcatagaaaaagggaatgaggtttattttccattcccttaaatcgtcttaattggtgcaggaaagaaactttatttccgttgttttatggattctgcctgcttctgaagttcgtttgcttgggatgtattcaggcgggctcgctctgtcttttctgccggtcgttttggagggagccgttcgtattacgattttctattgttttcacggctgtatttgtttttgatttatgagcagaccaacgggatgagtcagtcctgaatgctgctaagctaatgcttctcaagaaaagaaataagacttcccctaaaaagattaggtacttttcagaaaaacatcaagtactttcacaaaaaagattaggtactttttattggattatcaggtacttttgaaaaatagatttattatatttgtagatgtatttaagaaaacgcctttcagaggatttctccgaccttgggaaggtttatcaagtggagactaaaacgtatgtaata Predict ORF larger than 30AA ================================================ Protein_Len: 57 Strand: + Start: 109 End: 279 ............................................................................................................ M V Q E R N F I S V V L W I L P A S E V R L L G M Y S G G L A L S F L P V V L E G A V R I T I F Y C F H G C I C F ..................................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 89 End: 286 ........................................................................................ M P L N R L N W C R K E T L F P L F Y G F C L L L K F V C L G C I Q A G S L C L F C R S F W R E P F V L R F S I V F T A .............................................................................................................................................................................................................................................................................. Protein_Len: 45 Strand: + Start: 314 End: 448 ......................................................................................................................................................................................................................................................................................................................... M N A A K L M L L K K R N K T S P K K I R Y F S E K H Q V L S Q K R L G T F Y W I I R Y F ............................................................................................................ Protein_Len: 42 Strand: + Start: 415 End: 540 .............................................................................................................................................................................................................................................................................................................................................................................................................................. M R Y F L L D Y Q V L L K N R F I I F V D V F K K T P F R G F L R P W E G L S S G D ................ Protein_Len: 60 Strand: - Start: 190 End: 372 ............................................................................................................................................................................................. P E S Q R K Q R D N Q L S G N T N R N E I T K V A T N T K S K H A S W R S S D T R F A A L S I S R L F L F L V E G L F M ........................................................................................................................................................................................ Protein_Len: 47 Strand: - Start: 108 End: 248 ........................................................................................................... N T C S L F K I E T T K H I R G A E S T R K S P I Y E P P S A R D K R G T T K S P A T R I V M .................................................................................................................................................................................................................................................................................................................... Protein_Len: 39 Strand: - Start: 1 End: 117 P K D M A N L T R K I A C L Y S I F Y C L F L S H P K N E M G K F R R L Q H M ....................................................................................................................................................................................................................................................................................................................................................................................................................................................... gggtttatccatcgcgttcaatgttcttttgatagcgcaaagatatgaaatgaaatagcatagaaaaagggaatgaggtttattttccattcccttaaatcgtcttaattggtgcaggaaagaaactttatttccgttgttttatggattctgcctgcttctgaagttcgtttgcttgggatgtattcaggcgggctcgctctgtcttttctgccggtcgttttggagggagccgttcgtattacgattttctattgttttcacggctgtatttgtttttgatttatgagcagaccaacgggatgagtcagtcctgaatgctgctaagctaatgcttctcaagaaaagaaataagacttcccctaaaaagattaggtacttttcagaaaaacatcaagtactttcacaaaaaagattaggtactttttattggattatcaggtacttttgaaaaatagatttattatatttgtagatgtatttaagaaaacgcctttcagaggatttctccgaccttgggaaggtttatcaagtggagactaaaacgtatgtaata 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================================================ gggtttatccatcgcgttcaatgttcttttgatagcgcaaagatatgaaatgaaatagcatagaaaaagggaatgaggtttattttccattcccttaaatcgtcttaattggtgcaggaaagaaactttatttccgttgttttatggattctgcctgcttctgaagttcgtttgcttgggatgtattcaggcgggctcgctctgtcttttctgccggtcgttttggagggagccgttcgtattacgattttctattgttttcacggctgtatttgtttttgatttatgagcagaccaacgggatgagtcagtcctgaatgctgctaagctaatgcttctcaagaaaagaaataagacttcccctaaaaagattaggtacttttcagaaaaacatcaagtactttcacaaaaaagattaggtactttttattggattatcaggtacttttgaaaaatagatttattatatttgtagatgtatttaagaaaacgcctttcagaggatttctccgaccttgggaaggtttatcaagtggagactaaaacgtatgtaata Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 68 HP_score: -2.6 Tail_Score: -5.03405 Start: 69 End: 94 Full_Region: attaagacgatttaa gggaatgg aaaataaacc tcattccc tttttctatgctatt ....................................................................gggaatggaaaataaacctcattccc.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 75 HP_score: -5.4 Tail_Score: -4.88288 Start: 237 End: 247 Full_Region: TTTGGAGGGAGCCGT TCGT ATT ACGA TTTTCTATTGTTTTC ............................................................................................................................................................................................................................................TCGTATTACGA..................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 50 HP_score: -4.3 Tail_Score: -3.08032 Start: 362 End: 376 Full_Region: AGAAATAAGACTTCC CCTAA AAAGA TTAGG TACTTTTCAGAAAAA .........................................................................................................................................................................................................................................................................................................................................................................CCTAAAAAGATTAGG.................................................................................................................................................................................... Find igs database================================================ Query_seq: PG1203:PG1205|PG1203:PG1205:transcriptional regulator, putative:DNA-binding protein, histone-like family:<-->:1283537..1284092 556 gggtttatccatcgcgttcaatgttcttttgatagcgcaaagatatgaaatgaaatagcatagaaaaagggaatgaggtttattttccattcccttaaatcgtcttaattggtgcaggaaagaaactttatttccgttgttttatggattctgcctgcttctgaagttcgtttgcttgggatgtattcaggcgggctcgctctgtcttttctgccggtcgttttggagggagccgttcgtattacgattttctattgttttcacggctgtatttgtttttgatttatgagcagaccaacgggatgagtcagtcctgaatgctgctaagctaatgcttctcaagaaaagaaataagacttcccctaaaaagattaggtacttttcagaaaaacatcaagtactttcacaaaaaagattaggtactttttattggattatcaggtacttttgaaaaatagatttattatatttgtagatgtatttaagaaaacgcctttcagaggatttctccgaccttgggaaggtttatcaagtggagactaaaacgtatgtaata Intra-Species Hit: Count: 1 Min: 1 Max: 556 Len: 556 Subject: NC_002950_PG1203_PG1205|transcriptional regulator, putative:DNA-binding protein, histone-like family|NEGATIVE:POSITIVE|[1283537,1284092]|556 HSP 1 e-value: 0.0 bit: 1102.0 Len: 556 Query Start:1 Query End:556 Subject Strand: POSITIVE Subject Start: 1 Subject End: 556 gggtttatccatcgcgttcaatgttcttttgatagcgcaaagatatgaaatgaaatagcatagaaaaagggaatgaggtttattttccattcccttaaatcgtcttaattggtgcaggaaagaaactttatttccgttgttttatggattctgcctgcttctgaagttcgtttgcttgggatgtattcaggcgggctcgctctgtcttttctgccggtcgttttggagggagccgttcgtattacgattttctattgttttcacggctgtatttgtttttgatttatgagcagaccaacgggatgagtcagtcctgaatgctgctaagctaatgcttctcaagaaaagaaataagacttcccctaaaaagattaggtacttttcagaaaaacatcaagtactttcacaaaaaagattaggtactttttattggattatcaggtacttttgaaaaatagatttattatatttgtagatgtatttaagaaaacgcctttcagaggatttctccgaccttgggaaggtttatcaagtggagactaaaacgtatgtaata gggtttatccatcgcgttcaatgttcttttgatagcgcaaagatatgaaatgaaatagcatagaaaaagggaatgaggtttattttccattcccttaaatcgtcttaattggtgcaggaaagaaactttatttccgttgttttatggattctgcctgcttctgaagttcgtttgcttgggatgtattcaggcgggctcgctctgtcttttctgccggtcgttttggagggagccgttcgtattacgattttctattgttttcacggctgtatttgtttttgatttatgagcagaccaacgggatgagtcagtcctgaatgctgctaagctaatgcttctcaagaaaagaaataagacttcccctaaaaagattaggtacttttcagaaaaacatcaagtactttcacaaaaaagattaggtactttttattggattatcaggtacttttgaaaaatagatttattatatttgtagatgtatttaagaaaacgcctttcagaggatttctccgaccttgggaaggtttatcaagtggagactaaaacgtatgtaata Inter-species Hit: Count: 1 Min: 22 Max: 130 Len: 109 Subject: tfor_TF1700_TF1701|conserved hypothetical protein:transcriptional regulator|POSITIVE:POSITIVE|[1821522,1821632]|111 HSP 1 e-value: 2.0E-39 bit: 165.0 Len: 109 Query Start:22 Query End:130 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 111 .....................tgttcttttgatagcgcaaagatatgaaatgaaatagcatagaaaaagggaatgagg-tttattttc-cattcccttaaatcgtcttaattggtgcaggaaagaaacttta.......................................................................................................................................................................................................................................................................................................................................................................................................................................... .....................tgttcttttgatagcgcaaagatatgaaatgaaatagcatagaaaaagggaatgaggttttattttctcattcccttaaatcattttaattggtgcaggaaagaagcttta.......................................................................................................................................................................................................................................................................................................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUCUUUUGAUAGCGCAAAGAUAUGAAAUGAAAUAGCAUAGAAAAAGGGAAUGAGGUUUAUUUUCCAUUCCCUUAAAUCGUCUUAAUUGGUGCAGGAAAGAAACUUUA ..(((((((....((((.(((((.....(((......))).....(((((((((..(......)..))))))))).....))))).....))))..)))))))...... (-24.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGUUUCUUUCCUGCACCAAUUAAGACGAUUUAAGGGAAUGGAAAAUAAACCUCAUUCCCUUUUUCUAUGCUAUUUCAUUUCAUAUCUUUGCGCUAUCAAAAGAACA ....(((..(((...((............((...((((((((((..........))))))))))..))...............((......)).))....)))..))). (-16.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 802 100 51 212 163 NC_002950:PG1203|5end_transcriptional_regulator,_putative_1283446..1283676_NEGATIVE 315 90 41 184 141 NC_002950:PG1353|5end_orotate_phosphoribosyltransferase_1433833..1434063_NEGATIVE 266 95 52 90 42 NC_002950:PG1490|5end_TraG_family_protein_1563415..1563645_POSITIVE 244 39 1 78 32 NC_002950:PG1325|5end_hypothetical_protein_1403878..1404108_NEGATIVE 243 69 31 88 44 NC_002950:PG1024|5end_hypothetical_protein_1086698..1086928_POSITIVE 236 81 47 205 170 NC_002950:PG0526|5end_putative_inner_membrane_protein_translocase_component_YidC_570746..570976_POSITIVE 236 83 48 136 95 NC_002950:PG0321|5end_arginine/ornithine_transport_system_ATPase_354648..354878_POSITIVE 233 39 4 206 166 NC_002950:PG1278|5end_phosphoserine_aminotransferase_1355352..1355582_POSITIVE 232 100 66 104 66 NC_002950:PG1482|5end_conjugative_transposon_protein_TraF_1558779..1559009_NEGATIVE 232 57 11 174 132 NC_002950:PG0935|5end_4-diphosphocytidyl-2C-methyl-D-erythritol_kinase_995121..995351_NEGATIVE 232 60 11 73 17 NC_002950:PG0061|5end_yngK_protein_72145..72375_POSITIVE 230 75 31 196 152 NC_002950:PG0156|5end_modification_methylase,_HemK_family_178828..179058_POSITIVE 226 85 48 82 54 NC_002950:PG1355|5end_acyltransferase,_putative_1435292..1435522_NEGATIVE 226 51 14 82 41 NC_002950:PG1341|5end_hypothetical_protein_1422031..1422261_POSITIVE 226 45 4 134 86 NC_002950:PG1294|5end_ferrous_iron_transport_protein_B_1372047..1372277_POSITIVE 225 98 54 121 65 NC_002950:PG1160|5end_L-threonine-O-3-phosphate_decarboxylase,_putative_1239988..1240218_NEGATIVE 224 85 47 217 184 NC_002950:PG1778|5end_hypothetical_protein_1867054..1867284_POSITIVE 222 99 61 182 144 NC_002950:PG0789|5end_hypothetical_protein_841418..841648_NEGATIVE 219 82 42 65 35 NC_002950:PG1821|5end_cytochrome_c_nitrite_reductase,_small_subunit_NrfH_1916522..1916752_NEGATIVE 217 41 3 177 142 NC_002950:PG1491|5end_hypothetical_protein_1565741..1565971_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 90 41 73 30 NC_002950:PG1354|3end_hydrolase,_carbon-nitrogen_family_1433944..1434094_NEGATIVE 268 55 14 60 9 NC_002950:PG0378|3end_elongation_factor_Ts_408808..408958_POSITIVE 266 95 52 88 40 NC_002950:PG1489|3end_hypothetical_protein_1563493..1563643_POSITIVE 254 82 47 80 39 NC_002950:PG0037|3end_50S_ribosomal_protein_L19_46964..47114_POSITIVE 239 98 53 120 66 NC_002950:PG1003|3end_hypothetical_protein_1060304..1060454_POSITIVE 236 81 47 77 42 NC_002950:PG0525|3end_CTP_synthetase_570698..570848_POSITIVE 232 100 66 100 62 NC_002950:PG1483|3end_conjugative_transposon_protein_TraE_1558783..1558933_NEGATIVE 232 57 11 145 103 NC_002950:PG0936|3end_xanthine/uracil_permease_family_protein_995150..995300_NEGATIVE 217 100 53 60 7 NC_002950:PG0445|3end_peptidase_T_486549..486699_POSITIVE 215 95 54 112 75 NC_002950:PG1392|3end_rod_shape-determining_protein_RodA,_putative_1472959..1473109_NEGATIVE 211 100 66 106 67 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 210 85 49 96 59 NC_002950:PG0872|3end_mobilizable_transposon,_xis_protein_934846..934996_NEGATIVE 209 49 1 70 19 NC_002950:PG0476|3end_yngK_protein_517215..517365_NEGATIVE 207 99 64 52 20 NC_002950:PG1154|3end_hypothetical_protein_1235697..1235847_NEGATIVE 204 57 11 87 46 NC_002950:PG2163|3end_acid_phosphatase_2268801..2268951_NEGATIVE 204 99 54 87 45 NC_002950:PG1490|3end_TraG_family_protein_1565504..1565654_POSITIVE 201 55 11 69 29 NC_002950:PG0919|3end_dihydroorotase_978985..979135_NEGATIVE 201 98 56 96 67 NC_002950:PG0204|3end_hypothetical_protein_240262..240412_NEGATIVE 200 98 54 109 71 NC_002950:PG0483|3end_kinase,_putative_523236..523386_NEGATIVE 200 98 56 69 25 NC_002950:PG0334|3end_glycosyl_transferase,_group_2_family_protein_368792..368942_NEGATIVE