Origin IGS: tgcagcatcgtcgccaactcccataattgttgaaggattagttggtttaatatccttagtcaggcgttctatcaacttaaactcgcccaattcttttatttccatattgcttttataggattaagcataagttatgtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taacataacttatgcttaatcctataaaagcaatatggaaataaaagaattgggcgagtttaagttgatagaacgcctgactaaggatattaaaccaactaatccttcaacaattatgggagttggcgacgatgctgca Mask Tandem Repeat Region ================================================ tgcagcatcgtcgccaactcccataattgttgaaggattagttggtttaatatccttagtcaggcgttctatcaacttaaactcgcccaattcttttatttccatattgcttttataggattaagcataagttatgtta Find is-nt database================================================ Query_seq: PI1372:PI1373|PI1372:PI1373:thiamine monophosphate kinase:purine nucleoside phosphorylase (PNP):->->:1294032..1294170 139 tgcagcatcgtcgccaactcccataattgttgaaggattagttggtttaatatccttagtcaggcgttctatcaacttaaactcgcccaattcttttatttccatattgcttttataggattaagcataagttatgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1372:PI1373|PI1372:PI1373:thiamine monophosphate kinase:purine nucleoside phosphorylase (PNP):->->:1294032..1294170 139 tgcagcatcgtcgccaactcccataattgttgaaggattagttggtttaatatccttagtcaggcgttctatcaacttaaactcgcccaattcttttatttccatattgcttttataggattaagcataagttatgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1372:PI1373|PI1372:PI1373:thiamine monophosphate kinase:purine nucleoside phosphorylase (PNP):->->:1294032..1294170 139 tgcagcatcgtcgccaactcccataattgttgaaggattagttggtttaatatccttagtcaggcgttctatcaacttaaactcgcccaattcttttatttccatattgcttttataggattaagcataagttatgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgcagcatcgtcgccaactcccataattgttgaaggattagttggtttaatatccttagtcaggcgttctatcaacttaaactcgcccaattcttttatttccatattgcttttataggattaagcataagttatgtta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 23 End: 115 ...................... M I V E G L V G L I S L V R R S I N L N S P N S F I S I L L L ........................ Protein_Len: 34 Strand: + Start: 37 End: 138 .................................... M S W F N I L S Q A F Y Q L K L A Q F F Y F H I A F I G L S I S Y V . Protein_Len: 35 Strand: - Start: 1 End: 105 A A D D G V G M I T S P N T P K I D K T L R E I L K F E G L E K I E M .................................. tgcagcatcgtcgccaactcccataattgttgaaggattagttggtttaatatccttagtcaggcgttctatcaacttaaactcgcccaattcttttatttccatattgcttttataggattaagcataagttatgtta 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================================================ tgcagcatcgtcgccaactcccataattgttgaaggattagttggtttaatatccttagtcaggcgttctatcaacttaaactcgcccaattcttttatttccatattgcttttataggattaagcataagttatgtta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1372:PI1373|PI1372:PI1373:thiamine monophosphate kinase:purine nucleoside phosphorylase (PNP):->->:1294032..1294170 139 tgcagcatcgtcgccaactcccataattgttgaaggattagttggtttaatatccttagtcaggcgttctatcaacttaaactcgcccaattcttttatttccatattgcttttataggattaagcataagttatgtta Intra-Species Hit: Count: 1 Min: 1 Max: 139 Len: 139 Subject: pint_PI1372_PI1373|thiamine monophosphate kinase:purine nucleoside phosphorylase (PNP)|POSITIVE:POSITIVE|[1294032,1294170]|139 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 139 Query Start:1 Query End:139 Subject Strand: POSITIVE Subject Start: 1 Subject End: 139 tgcagcatcgtcgccaactcccataattgttgaaggattagttggtttaatatccttagtcaggcgttctatcaacttaaactcgcccaattcttttatttccatattgcttttataggattaagcataagttatgtta tgcagcatcgtcgccaactcccataattgttgaaggattagttggtttaatatccttagtcaggcgttctatcaacttaaactcgcccaattcttttatttccatattgcttttataggattaagcataagttatgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCAGCAUCGUCGCCAACUCCCAUAAUUGUUGAAGGAUUAGUUGGUUUAAUAUCCUUAGUCAGGCGUUCUAUCAACUUAAACUCGCCCAAUUCUUUUAUUUCCAUAUUGCUUUUAUAGGAUUAAGCAUAAGUUAUGUUA ...(((((....(((((((.((............))...)))))))....(((.(((((((.((((.................))))................(((.......)))..))))))).)))....))))). (-19.83) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAUAACUUAUGCUUAAUCCUAUAAAAGCAAUAUGGAAAUAAAAGAAUUGGGCGAGUUUAAGUUGAUAGAACGCCUGACUAAGGAUAUUAAACCAACUAAUCCUUCAACAAUUAUGGGAGUUGGCGACGAUGCUGCA ............((((...((((((((......(((....)))...(((..(((..((((....((((((.....(((.....))).))))))...))))..)))))).....))))))))...))))........... (-26.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 44 2 113 78 pint:PI0834|5end_conserved_hypothetical_protein_770785..771015_POSITIVE 285 49 1 99 37 pint:PI1980|5end_conserved_hypothetical_protein_1937470..1937700_POSITIVE 267 67 21 92 51 pint:PI1384|5end_conserved_hypothetical_protein_1305171..1305401_POSITIVE 264 90 41 91 40 pint:PI1837|5end_aspartate_ammonia-lyase_1778953..1779183_POSITIVE 260 45 2 187 149 pint:PI0618|5end_acyl-CoA_dehydrogenase_family_protein_567409..567639_POSITIVE 259 45 1 87 38 pint:PI0545|5end_sugar_kinase_496411..496641_POSITIVE 258 48 1 69 28 pint:PI1519|5end_UDP-N-acetylglucosamine_acetyltransferase_1440327..1440557_POSITIVE 254 49 1 100 38 pint:PI1568|5end_OmpA_family_protein_1489584..1489814_POSITIVE 251 47 2 158 112 pint:PI1516|5end_multidrug_resistance_protein;_HlyD_family_secretion_protein_1434381..1434611_POSITIVE 251 70 26 225 172 pint:PI0959|5end_uridine_kinase_890495..890725_POSITIVE 247 89 41 129 74 pint:PI2104|5end_carboxyl-terminal_protease_2057910..2058140_POSITIVE 247 35 1 85 42 pint:PI1367|5end_redox-sensitive_transcriptional_activator,__OxyR_1286860..1287090_POSITIVE 247 89 42 214 163 pint:PI0285|5end_succinyltransferase_protein_270097..270327_POSITIVE 246 36 2 174 141 pint:PI0351|5end_hypothetical_protein_324317..324547_POSITIVE 243 121 82 218 166 pint:PI0265|5end_conjugative_transposon_protein,_TraO_257296..257526_POSITIVE 242 47 5 56 11 pint:PI0016|5end_magnesium_chelatase,_subunit_ChlI_20191..20421_POSITIVE 239 48 4 52 15 pint:PI0328|5end_conserved_hypothetical_protein_309476..309706_POSITIVE 238 49 3 198 148 pint:PI2121|5end_glucose_inhibited_division_protein_A_2069889..2070119_POSITIVE 238 49 3 53 3 pint:PI2122|5end_conserved_hypothetical_protein_2069744..2069974_POSITIVE 238 104 64 225 167 pint:PI1623|5end_hypothetical_protein_1547163..1547393_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 32 3 56 25 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 260 47 1 142 96 pint:PI0615|3end_hydrolase,_haloacid_dehalogenase-like_family_565386..565536_POSITIVE 247 89 41 73 18 pint:PI2103|3end_hypothetical_protein_2057934..2058084_POSITIVE 237 44 4 62 28 pint:PI1428|3end_quinolinate_synthetase_A_1347695..1347845_POSITIVE 235 45 7 135 109 pint:PI0620|3end_hypothetical_protein_570630..570780_POSITIVE 230 47 2 83 37 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 229 42 1 127 72 pint:PI1818|3end_hypothetical_protein_1757270..1757420_POSITIVE 229 105 63 108 66 pint:PI1057|3end_hypothetical_protein_977548..977698_POSITIVE 229 50 3 113 66 pint:PI0150|3end_hypothetical_protein_143833..143983_POSITIVE 228 110 65 119 76 pint:PI1558|3end_conserved_hypothetical_protein_1476106..1476256_POSITIVE 227 105 61 88 49 pint:PI1096|3end_glycosyltransferase_1021490..1021640_POSITIVE 225 66 21 104 58 pint:PI0944|3end_hypothetical_protein_875249..875399_POSITIVE 224 69 28 42 3 pint:PI0344|3end_conserved_hypothetical_protein_319439..319589_POSITIVE 223 48 5 80 32 pint:PI2151|3end_conserved_hypothetical_protein_2098252..2098402_POSITIVE 222 43 5 149 106 pint:PI1493|3end_conserved_hypothetical_protein_1412818..1412968_POSITIVE 222 90 43 150 107 pint:PI1386|3end_sugar_phosphate_isomerase_1308031..1308181_POSITIVE 222 22 1 29 10 pint:PI0053|3end_hypothetical_protein_55124..55274_POSITIVE 219 110 64 81 26 pint:PI0501|3end_excisionase_461863..462013_POSITIVE 218 33 3 151 120 pint:PI1979|3end_conserved_hypothetical_protein_1937327..1937477_POSITIVE 218 33 1 78 45 pint:PI0874|3end_conserved_hypothetical_protein_810281..810431_POSITIVE