Origin IGS: cgtgaaaataccttagagttattgttaagcgcgaagtatagcacttttctgtcaccccgcctaatcgcgcgccgataaagcgattgttgtatgttataatgccacccgttttttctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagaaaaaacgggtggcattataacatacaacaatcgctttatcggcgcgcgattaggcggggtgacagaaaagtgctatacttcgcgcttaacaataactctaaggtattttcacg Mask Tandem Repeat Region ================================================ cgtgaaaataccttagagttattgttaagcgcgaagtatagcacttttctgtcaccccgcctaatcgcgcgccgataaagcgattgttgtatgttataatgccacccgttttttctta Find is-nt database================================================ Query_seq: AA02062:AA02063|AA02062:AA02063:conserved hypothetical protein (probable membrane protein):23S rRNA psedouridine synthase, Rlu family protein:->->:1404473..1404590 118 cgtgaaaataccttagagttattgttaagcgcgaagtatagcacttttctgtcaccccgcctaatcgcgcgccgataaagcgattgttgtatgttataatgccacccgttttttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02062:AA02063|AA02062:AA02063:conserved hypothetical protein (probable membrane protein):23S rRNA psedouridine synthase, Rlu family protein:->->:1404473..1404590 118 cgtgaaaataccttagagttattgttaagcgcgaagtatagcacttttctgtcaccccgcctaatcgcgcgccgataaagcgattgttgtatgttataatgccacccgttttttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02062:AA02063|AA02062:AA02063:conserved hypothetical protein (probable membrane protein):23S rRNA psedouridine synthase, Rlu family protein:->->:1404473..1404590 118 cgtgaaaataccttagagttattgttaagcgcgaagtatagcacttttctgtcaccccgcctaatcgcgcgccgataaagcgattgttgtatgttataatgccacccgttttttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgtgaaaataccttagagttattgttaagcgcgaagtatagcacttttctgtcaccccgcctaatcgcgcgccgataaagcgattgttgtatgttataatgccacccgttttttctta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 3 End: 92 .. S F V K S N N N L A F Y L V K R D G R R I A R R Y L S Q Q M .......................... Protein_Len: 33 Strand: - Start: 2 End: 100 . H F Y R L T I T L R S T Y C K E T V G G L R A G I F R N N Y T I M .................. cgtgaaaataccttagagttattgttaagcgcgaagtatagcacttttctgtcaccccgcctaatcgcgcgccgataaagcgattgttgtatgttataatgccacccgttttttctta 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================================================ cgtgaaaataccttagagttattgttaagcgcgaagtatagcacttttctgtcaccccgcctaatcgcgcgccgataaagcgattgttgtatgttataatgccacccgttttttctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA02062:AA02063|AA02062:AA02063:conserved hypothetical protein (probable membrane protein):23S rRNA psedouridine synthase, Rlu family protein:->->:1404473..1404590 118 cgtgaaaataccttagagttattgttaagcgcgaagtatagcacttttctgtcaccccgcctaatcgcgcgccgataaagcgattgttgtatgttataatgccacccgttttttctta Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: aact_AA02062_AA02063|conserved hypothetical protein (probable membrane protein):23S rRNA psedouridine synthase, Rlu family protein|POSITIVE:POSITIVE|[1404473,1404590]|118 HSP 1 e-value: 5.0E-61 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 cgtgaaaataccttagagttattgttaagcgcgaagtatagcacttttctgtcaccccgcctaatcgcgcgccgataaagcgattgttgtatgttataatgccacccgttttttctta cgtgaaaataccttagagttattgttaagcgcgaagtatagcacttttctgtcaccccgcctaatcgcgcgccgataaagcgattgttgtatgttataatgccacccgttttttctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUGAAAAUACCUUAGAGUUAUUGUUAAGCGCGAAGUAUAGCACUUUUCUGUCACCCCGCCUAAUCGCGCGCCGAUAAAGCGAUUGUUGUAUGUUAUAAUGCCACCCGUUUUUUCUUA ...(((((.((....(..((((((....((((((......((................))....))))))..))))))..)....((.((((......)))).))..)).)))))... (-20.19) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAAAAAACGGGUGGCAUUAUAACAUACAACAAUCGCUUUAUCGGCGCGCGAUUAGGCGGGGUGACAGAAAAGUGCUAUACUUCGCGCUUAACAAUAACUCUAAGGUAUUUUCACG ...(((((.((...(((..((((.........((.((((((.((((.....)))).))))))..))......((((((........))))))....))))..)))..)).)))))... (-24.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 425 89 49 212 162 aact:AA00211|5end_hypothetical_protein_145955..146185_POSITIVE 392 83 41 168 129 aact:AA00993|5end_possible_D-tyrosyl-tRNA(Tyr)_deacylase_694488..694718_POSITIVE 389 88 41 66 8 aact:AA01158|5end_ribosome_associated_heat_shock_protein_15_homolog_792399..792629_POSITIVE 382 96 57 80 42 aact:AA00804|5end_fumarate_reductase_flavoprotein_subunit_A_549770..550000_POSITIVE 381 83 42 73 18 aact:AA01866|5end_thiamin_ABC_transporter,_permease_protein_1253313..1253543_POSITIVE 366 73 32 101 63 aact:AA00329|5end_molybdopterin-guanine_dinucleotide_biosynthesis_protein_222737..222967_POSITIVE 361 110 64 166 116 aact:AA00333|5end_1-phosphofructokinase;_tagatose-6-phosphate_kinase_225543..225773_POSITIVE 350 89 42 230 162 aact:AA02025|5end_hypothetical_protein_1378667..1378897_POSITIVE 346 109 65 203 164 aact:AA01531|5end_hypothetical_protein_1028705..1028935_POSITIVE 341 79 32 70 25 aact:AA01615|5end_lipoprotein_releasing_system_transmembrane_1091186..1091416_POSITIVE 337 87 41 63 12 aact:AA01857|5end_glutamate-ammonia-ligase_adenylyltransferase_1247347..1247577_POSITIVE 334 76 34 40 2 aact:AA01508|5end_anaerobic_C4-dicarboxylate_transporter_1013198..1013428_POSITIVE 333 82 50 44 13 aact:AA00223|5end_catalase_(hydroperoxidase;_iron_heme_axial_ligand)_154277..154507_POSITIVE 330 68 27 209 165 aact:AA01635|5end_ribonucleoside_diphosphate_reductase,_beta_chain_1104615..1104845_POSITIVE 329 81 41 159 117 aact:AA01553|5end_conserved_hypothetical_protein_1039220..1039450_POSITIVE 329 96 57 220 183 aact:AA00713|5end_chaperone_protein_hscA,_heat_shock_cognate_66_488770..489000_POSITIVE 325 89 46 80 37 aact:AA02088|5end_glycogen_operon_protein_1421282..1421512_POSITIVE 325 109 61 172 121 aact:AA02038|5end_50S_ribosomal_protein_L35_1387052..1387282_POSITIVE 325 93 51 181 140 aact:AA00838|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_577522..577752_POSITIVE 324 73 41 105 59 aact:AA00989|5end_hypothetical_protein_692319..692549_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 89 50 151 105 aact:AA01284|3end_heat_shock_protein_(hsp60)_870294..870444_POSITIVE 336 86 41 151 83 aact:AA02564|3end_transketolase_N-terminal_section_1786783..1786933_POSITIVE 329 76 31 143 78 aact:AA00760|3end_conserved_hypothetical_protein_(possible_peptidase)_523815..523965_POSITIVE 325 109 61 92 41 aact:AA02037|3end_hypothetical_protein_1387052..1387202_POSITIVE 323 88 41 58 15 aact:AA02022|3end_hypothetical_protein_1376754..1376904_POSITIVE 322 87 41 125 72 aact:AA00292|3end_dihydrofolate_reductase_202338..202488_POSITIVE 321 88 41 149 100 aact:AA01530|3end_conserved_hypothetical_protein_1028749..1028899_POSITIVE 314 73 32 52 10 aact:AA02075|3end_conserved_hypothetical_protein_1409979..1410129_POSITIVE 314 89 47 56 18 aact:AA01174|3end_hypothetical_protein_804923..805073_POSITIVE 313 81 42 146 97 aact:AA02144|3end_iron_(III)_ABC_transporter,_permease_protein_1468679..1468829_POSITIVE 313 76 31 68 26 aact:AA00528|3end_conserved_hypothetical_protein_361703..361853_POSITIVE 311 85 41 122 78 aact:AA02940|3end_conserved_hypothetical_protein_2058652..2058802_POSITIVE 310 89 41 145 103 aact:AA02826|3end_conserved_hypothetical_protein_1987108..1987258_POSITIVE 310 83 51 44 1 aact:AA01842|3end_conserved_hypothetical_protein_1238467..1238617_POSITIVE 310 86 43 134 90 aact:AA00347|3end_50S_ribosomal_protein_L11_232642..232792_POSITIVE 309 90 44 116 74 aact:AA01626|3end_N_utilization_substance_protein_B_1100946..1101096_POSITIVE 308 91 52 47 7 aact:AA01772|3end_shikimate_5-dehydrogenase_protein_1194942..1195092_POSITIVE 304 108 64 109 60 aact:AA02626|3end_conserved_hypothetical_protein_1829202..1829352_POSITIVE 302 75 41 149 112 aact:AA02978|3end_sufI_protein_precursor_homolog_2083308..2083458_POSITIVE 301 88 45 138 96 aact:AA01167|3end_glucose-6-phosphate_1-dehydrogenase_801067..801217_POSITIVE