Origin IGS: tattggttaagttttgaaatagtggtaaaaaaataatcaaatttaagatgaaaatatatccgtatagaatttgacatatgtttaaaaaaagtatatatttacaataagaacagttaattttattttagttaatttttggttttatttataaatagtaaagtaaaaattttaggaggtaaaa .........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 ttttacctcctaaaatttttactttactatttataaataaaaccaaaaattaactaaaataaaattaactgttcttattgtaaatatatactttttttaaacatatgtcaaattctatacggatatattttcatcttaaatttgattatttttttaccactatttcaaaacttaaccaata Mask Tandem Repeat Region ================================================ tattggttaagttttgaaatagtggtaaaaaaataatcaaatttaagatgaaaatatatccgtatagaatttgacatatgtttaaaaaaagtatatatttacaataagaacagttaattttattttagttaatttttggttttatttataaatagtaaagtaaaaattttaggaggtaaaa Find is-nt database================================================ Query_seq: FN0651:FN0652|FN0651:FN0652:Ribosomal large subunit pseudouridine synthase D:Glyceraldehyde 3-phosphate dehydrogenase:->->:1310321..1310501 181 tattggttaagttttgaaatagtggtaaaaaaataatcaaatttaagatgaaaatatatccgtatagaatttgacatatgtttaaaaaaagtatatatttacaataagaacagttaattttattttagttaatttttggttttatttataaatagtaaagtaaaaattttaggaggtaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0651:FN0652|FN0651:FN0652:Ribosomal large subunit pseudouridine synthase D:Glyceraldehyde 3-phosphate dehydrogenase:->->:1310321..1310501 181 tattggttaagttttgaaatagtggtaaaaaaataatcaaatttaagatgaaaatatatccgtatagaatttgacatatgtttaaaaaaagtatatatttacaataagaacagttaattttattttagttaatttttggttttatttataaatagtaaagtaaaaattttaggaggtaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0651:FN0652|FN0651:FN0652:Ribosomal large subunit pseudouridine synthase D:Glyceraldehyde 3-phosphate dehydrogenase:->->:1310321..1310501 181 tattggttaagttttgaaatagtggtaaaaaaataatcaaatttaagatgaaaatatatccgtatagaatttgacatatgtttaaaaaaagtatatatttacaataagaacagttaattttattttagttaatttttggttttatttataaatagtaaagtaaaaattttaggaggtaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattggttaagttttgaaatagtggtaaaaaaataatcaaatttaagatgaaaatatatccgtatagaatttgacatatgtttaaaaaaagtatatatttacaataagaacagttaattttattttagttaatttttggttttatttataaatagtaaagtaaaaattttaggaggtaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 3 End: 98 .. Q N L K S I T T F F Y D F K L H F Y I R I S N S M H K F F T Y M ................................................................................... Protein_Len: 39 Strand: - Start: 2 End: 118 . N T L N Q F L P L F I I L N L I F I Y G Y L I Q C I N L F L I Y K C Y S C N M ............................................................... tattggttaagttttgaaatagtggtaaaaaaataatcaaatttaagatgaaaatatatccgtatagaatttgacatatgtttaaaaaaagtatatatttacaataagaacagttaattttattttagttaatttttggttttatttataaatagtaaagtaaaaattttaggaggtaaaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 87 Start: 70 End: 99 .....................................................................TTTGACATATGTTTAAAAAAAGTATATATT.................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 97 End: 126 ................................................................................................ATTTACAATAAGAACAGTTAATTTTATTTT....................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tattggttaagttttgaaatagtggtaaaaaaataatcaaatttaagatgaaaatatatccgtatagaatttgacatatgtttaaaaaaagtatatatttacaataagaacagttaattttattttagttaatttttggttttatttataaatagtaaagtaaaaattttaggaggtaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0651:FN0652|FN0651:FN0652:Ribosomal large subunit pseudouridine synthase D:Glyceraldehyde 3-phosphate dehydrogenase:->->:1310321..1310501 181 tattggttaagttttgaaatagtggtaaaaaaataatcaaatttaagatgaaaatatatccgtatagaatttgacatatgtttaaaaaaagtatatatttacaataagaacagttaattttattttagttaatttttggttttatttataaatagtaaagtaaaaattttaggaggtaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: NC_003454_FN0651_FN0652|Ribosomal large subunit pseudouridine synthase D:Glyceraldehyde 3-phosphate dehydrogenase|POSITIVE:POSITIVE|[1310321,1310501]|181 HSP 1 e-value: 1.0E-31 bit: 137.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 tattggttaagttttgaaatagtggtnnnnnnntaatcaaatttaagatgaaaatatatccgtatagaatttgacatatgtttnnnnnnngtatatatttacaataagaac...................................................................... tattggttaagttttgaaatagtggtaaaaaaataatcaaatttaagatgaaaatatatccgtatagaatttgacatatgtttaaaaaaagtatatatttacaataagaac...................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUGGUUAAGUUUUGAAAUAGUGGUAAAAAAAUAAUCAAAUUUAAGAUGAAAAUAUAUCCGUAUAGAAUUUGACAUAUGUUUAAAAAAAGUAUAUAUUUACAAUAAGAAC .....((((((((((...(((.(((..........(((........)))..........))))))))))))))))...............(((......)))......... (-10.75) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUCUUAUUGUAAAUAUAUACUUUUUUUAAACAUAUGUCAAAUUCUAUACGGAUAUAUUUUCAUCUUAAAUUUGAUUAUUUUUUUACCACUAUUUCAAAACUUAACCAAUA .....(((((......................(((((((............)))))))............(((((...................))))).......))))) ( -5.11) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 157 26 1 121 91 NC_003454:FN1993|5end_SUA5_protein_496917..497147_POSITIVE 149 55 21 43 6 NC_003454:FN1799|5end_Spermidine/putrescine_transport_system_permease_protein_potC_280776..281006_POSITIVE 149 65 49 21 5 NC_003454:FN1690|5end_hypothetical_protein_186389..186619_NEGATIVE 146 85 42 223 186 NC_003454:FN1160|5end_SWF/SNF_family_helicase_1815836..1816066_POSITIVE 144 42 16 128 96 NC_003454:FN1292|5end_hypothetical_protein_1950804..1951034_NEGATIVE 143 73 43 142 112 NC_003454:FN1498|5end_Integral_membrane_protein_2563..2793_POSITIVE 142 103 61 160 117 NC_003454:FN0402|5end_Integrase/recombinase_1040308..1040538_POSITIVE 140 39 1 80 39 NC_003454:FN1123|5end_Thioredoxin-like_protein_1767478..1767708_POSITIVE 140 83 51 147 115 NC_003454:FN0818|5end_DNA-binding_protein_HU_1477034..1477264_NEGATIVE 138 94 53 66 32 NC_003454:FN0802|5end_Amino_acid_transport_system_permease_protein_1462136..1462366_NEGATIVE 137 83 59 41 18 NC_003454:FN0582|5end_Lipoprotein_releasing_system_ATP-binding_protein_lolD_1238246..1238476_POSITIVE 137 84 46 113 78 NC_003454:FN1759|5end_Hydroxymethylpyrimidine_kinase_254765..254995_NEGATIVE 136 89 56 227 194 NC_003454:FN0838|5end_hypothetical_protein_1500747..1500977_POSITIVE 134 49 4 173 132 NC_003454:FN0271|5end_Enoyl-CoA_hydratase_897847..898077_POSITIVE 133 82 51 70 45 NC_003454:FN0727|5end_hypothetical_protein_1385507..1385737_NEGATIVE 131 25 1 36 16 NC_003454:FN1311|5end_Biopolymer_transport_exbD_protein_1966250..1966480_NEGATIVE 130 75 59 122 107 NC_003454:FN0723|5end_hypothetical_protein_1381528..1381758_POSITIVE 130 88 48 101 60 NC_003454:FN0507|5end_hypothetical_protein_1157430..1157660_POSITIVE 130 83 43 99 55 NC_003454:FN2105|5end_Integral_membrane_protein_614701..614931_POSITIVE 130 98 76 231 208 NC_003454:FN1742|5end_V-type_sodium_ATP_synthase_subunit_G_240790..241020_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 157 26 1 119 89 NC_003454:FN1992|3end_Ribose-phosphate_pyrophosphokinase_496995..497145_POSITIVE 157 79 39 85 33 NC_003454:FN1713|3end_tRNA_(Uracil-5-)_-methyltransferase_208968..209118_POSITIVE 150 46 7 55 17 NC_003454:FN1124|3end_Outer_membrane_porin_F_1768058..1768208_NEGATIVE 149 55 21 59 22 NC_003454:FN1798|3end_Spermidine/putrescine_transport_system_permease_protein_potB_280872..281022_POSITIVE 146 98 59 140 103 NC_003454:FN2045|3end_Ferric_uptake_regulation_protein_550374..550524_NEGATIVE 143 60 19 72 31 NC_003454:FN1954|3end_Glycerophosphoryl_diester_phosphodiesterase_459777..459927_NEGATIVE 137 83 59 72 49 NC_003454:FN0581|3end_Lipoprotein_releasing_system_transmembrane_protein_lolE_1238357..1238507_POSITIVE 133 82 51 92 67 NC_003454:FN0728|3end_hypothetical_protein_1385485..1385635_NEGATIVE 132 92 55 135 92 NC_003454:FN0623|3end_Malonate_transporter_1282988..1283138_POSITIVE 130 39 16 140 115 NC_003454:FN1141|3end_Formate_transporter_1790493..1790643_NEGATIVE 130 75 59 118 103 NC_003454:FN0722|3end_WD-repeat_family_protein_1381604..1381754_POSITIVE 130 83 43 78 34 NC_003454:FN2104|3end_hypothetical_protein_614760..614910_POSITIVE 129 50 20 131 102 NC_003454:FN0120|3end_hypothetical_protein_752718..752868_NEGATIVE 126 68 35 70 32 NC_003454:FN0035|3end_hypothetical_protein_676240..676390_NEGATIVE 125 79 59 116 99 NC_003454:FN0829|3end_hypothetical_protein_1489580..1489730_NEGATIVE 123 52 16 29 1 NC_003454:FN1412|3end_5-methylthioribose_kinase_2072052..2072202_NEGATIVE 123 83 58 38 11 NC_003454:FN0524|3end_DNA_helicase_II_1176884..1177034_NEGATIVE 123 99 55 99 52 NC_003454:FN1974|3end_DNA/RNA_helicase_(DEAD/DEAH_BOX_family)_472698..472848_NEGATIVE 122 105 66 89 43 NC_003454:FN0805|3end_hypothetical_protein_1464832..1464982_NEGATIVE 122 83 48 109 76 NC_003454:FN0725|3end_Molybdopterin_biosynthesis_MoeB_protein_1384181..1384331_NEGATIVE