Origin IGS: tatctttccataattttctttttctaattcaatggcaatataatctccattaccactatcatagaaaggtagtttattataccaaactttgtcatattcatcattatagtcaagaaaacaaatatctatccaattttttcgtccatcttcaaaatctaataataaatctaatcc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggattagatttattattagattttgaagatggacgaaaaaattggatagatatttgttttcttgactataatgatgaatatgacaaagtttggtataataaactacctttctatgatagtggtaatggagattatattgccattgaattagaaaaagaaaattatggaaagata Mask Tandem Repeat Region ================================================ tatctttccataattttctttttctaattcaatggcaatataatctccattaccactatcatagaaaggtagtttattataccaaactttgtcatattcatcattatagtcaagaaaacaaatatctatccaattttttcgtccatcttcaaaatctaataataaatctaatcc Find is-nt database================================================ Query_seq: FN1227:FN1228|FN1227:FN1228:hypothetical protein:hypothetical protein:<-<-:1885798..1885971 174 tatctttccataattttctttttctaattcaatggcaatataatctccattaccactatcatagaaaggtagtttattataccaaactttgtcatattcatcattatagtcaagaaaacaaatatctatccaattttttcgtccatcttcaaaatctaataataaatctaatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1227:FN1228|FN1227:FN1228:hypothetical protein:hypothetical protein:<-<-:1885798..1885971 174 tatctttccataattttctttttctaattcaatggcaatataatctccattaccactatcatagaaaggtagtttattataccaaactttgtcatattcatcattatagtcaagaaaacaaatatctatccaattttttcgtccatcttcaaaatctaataataaatctaatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1227:FN1228|FN1227:FN1228:hypothetical protein:hypothetical protein:<-<-:1885798..1885971 174 tatctttccataattttctttttctaattcaatggcaatataatctccattaccactatcatagaaaggtagtttattataccaaactttgtcatattcatcattatagtcaagaaaacaaatatctatccaattttttcgtccatcttcaaaatctaataataaatctaatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatctttccataattttctttttctaattcaatggcaatataatctccattaccactatcatagaaaggtagtttattataccaaactttgtcatattcatcattatagtcaagaaaacaaatatctatccaattttttcgtccatcttcaaaatctaataataaatctaatcc Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 27 End: 173 .......................... M Q W Q Y N L H Y H Y H R K V V Y Y T K L C H I H H Y S Q E N K Y L S N F F V H L Q N L I I N L I . Protein_Len: 33 Strand: - Start: 27 End: 125 .......................... N L P L I I E M V V I M S L Y N I I G F K T M N M M I T L F V F M ................................................. Protein_Len: 43 Strand: - Start: 1 End: 129 I K G Y N E K E L E I A I Y D G N G S D Y F P L K N Y W V K D Y E D N Y D L F C I D M ............................................. tatctttccataattttctttttctaattcaatggcaatataatctccattaccactatcatagaaaggtagtttattataccaaactttgtcatattcatcattatagtcaagaaaacaaatatctatccaattttttcgtccatcttcaaaatctaataataaatctaatcc 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: 83 Start: 76 End: 105 ...........................................................................AATGATGAATATGACAAAGTTTGGTATAAT..................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tatctttccataattttctttttctaattcaatggcaatataatctccattaccactatcatagaaaggtagtttattataccaaactttgtcatattcatcattatagtcaagaaaacaaatatctatccaattttttcgtccatcttcaaaatctaataataaatctaatcc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1227:FN1228|FN1227:FN1228:hypothetical protein:hypothetical protein:<-<-:1885798..1885971 174 tatctttccataattttctttttctaattcaatggcaatataatctccattaccactatcatagaaaggtagtttattataccaaactttgtcatattcatcattatagtcaagaaaacaaatatctatccaattttttcgtccatcttcaaaatctaataataaatctaatcc Intra-Species Hit: Count: 1 Min: 1 Max: 174 Len: 174 Subject: NC_003454_FN1227_FN1228|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1885798,1885971]|174 HSP 1 e-value: 3.0E-94 bit: 345.0 Len: 174 Query Start:1 Query End:174 Subject Strand: POSITIVE Subject Start: 1 Subject End: 174 tatctttccataattttctttttctaattcaatggcaatataatctccattaccactatcatagaaaggtagtttattataccaaactttgtcatattcatcattatagtcaagaaaacaaatatctatccaattttttcgtccatcttcaaaatctaataataaatctaatcc tatctttccataattttctttttctaattcaatggcaatataatctccattaccactatcatagaaaggtagtttattataccaaactttgtcatattcatcattatagtcaagaaaacaaatatctatccaattttttcgtccatcttcaaaatctaataataaatctaatcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCUUUCCAUAAUUUUCUUUUUCUAAUUCAAUGGCAAUAUAAUCUCCAUUACCACUAUCAUAGAAAGGUAGUUUAUUAUACCAAACUUUGUCAUAUUCAUCAUUAUAGUCAAGAAAACAAAUAUCUAUCCAAUUUUUUCGUCCAUCUUCAAAAUCUAAUAAUAAAUCUAAUCC .............(((((((...(((.....(((((((((((((....((((((.............))))))..)))))).......)))))))...........)))..)))))))........................................................ (-11.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAUUAGAUUUAUUAUUAGAUUUUGAAGAUGGACGAAAAAAUUGGAUAGAUAUUUGUUUUCUUGACUAUAAUGAUGAAUAUGACAAAGUUUGGUAUAAUAAACUACCUUUCUAUGAUAGUGGUAAUGGAGAUUAUAUUGCCAUUGAAUUAGAAAAAGAAAAUUAUGGAAAGAUA ...(((.(((((((((((..((..(((((..((...................))..)))))..))...))))))))))).)))...((((((......))))))..(((((((((((((((((((((.......))))))))))................)))))))))))... (-33.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 775 70 21 161 112 NC_003454:FN1227|5end_hypothetical_protein_1885707..1885937_NEGATIVE 251 50 6 104 61 NC_003454:FN1645|5end_LSU_ribosomal_protein_L3P_141301..141531_NEGATIVE 242 61 31 44 20 NC_003454:FN1451|5end_cell_division_protein_FtsZ_2132710..2132940_NEGATIVE 242 60 15 222 171 NC_003454:FN1104|5end_Holliday_junction_DNA_helicase_ruvA_1749453..1749683_POSITIVE 231 46 5 155 124 NC_003454:FN1441|5end_PTS_system,_fructose-specific_IIABC_component_2108211..2108441_POSITIVE 229 164 136 72 44 NC_003454:FN0418|5end_pyrimidine_regulatory_protein_PyrR_1059118..1059348_POSITIVE 225 90 43 218 163 NC_003454:FN0363|5end_ATP_synthase_C_chain,_sodium_ion_specific_993703..993933_NEGATIVE 217 99 57 200 145 NC_003454:FN1324|5end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_1980312..1980542_NEGATIVE 217 54 13 67 20 NC_003454:FN0242|5end_Trk_system_potassium_uptake_protein_trkA_865228..865458_POSITIVE 215 50 1 175 112 NC_003454:FN0427|5end_Orotate_phosphoribosyltransferase_1069405..1069635_POSITIVE 211 44 5 181 135 NC_003454:FN0994|5end_hypothetical_protein_1649223..1649453_POSITIVE 209 55 14 151 115 NC_003454:FN1011|5end_MGPA_protein_1665660..1665890_NEGATIVE 207 170 125 125 69 NC_003454:FN1407|5end_Glutamate_formiminotransferase_2066430..2066660_POSITIVE 206 65 31 186 157 NC_003454:FN1413|5end_translation_initiation_factor_IF-2B_subunit_alpha_2074270..2074500_NEGATIVE 206 48 3 216 164 NC_003454:FN0133|5end_hypothetical_protein_769121..769351_POSITIVE 206 49 3 206 165 NC_003454:FN1840|5end_Dihydroxyacetone_kinase_329835..330065_POSITIVE 205 28 2 37 8 NC_003454:FN0643|5end_hypothetical_protein_1299871..1300101_NEGATIVE 204 84 41 130 94 NC_003454:FN0081|5end_Ethanolamine_utilization_protein_eutL_720035..720265_POSITIVE 203 59 14 189 144 NC_003454:FN0854|5end_Glucose-1-phosphate_adenylyltransferase_1513487..1513717_NEGATIVE 202 159 111 99 46 NC_003454:FN0071|5end_GTP_cyclohydrolase_I_710962..711192_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 231 46 5 126 95 NC_003454:FN1440|3end_1-phosphofructokinase_2108262..2108412_POSITIVE 217 54 13 54 7 NC_003454:FN0241|3end_Dihydrofolate_reductase_865295..865445_POSITIVE 217 50 1 137 92 NC_003454:FN1547|3end_PTS_permease_for_N-acetylglucosamine_and_glucose_61801..61951_NEGATIVE 211 44 5 86 40 NC_003454:FN0993|3end_Trk_system_potassium_uptake_protein_trkG_1649208..1649358_POSITIVE 209 55 14 131 95 NC_003454:FN1012|3end_HPr_kinase/phosphorylase_1665680..1665830_NEGATIVE 207 170 125 107 51 NC_003454:FN1406|3end_histidine_ammonia-lyase_2066492..2066642_POSITIVE 206 49 3 136 95 NC_003454:FN1839|3end_glycerol_kinase_329845..329995_POSITIVE 202 159 111 99 46 NC_003454:FN0070|3end_Glycyl-tRNA_synthetase_beta_chain_711042..711192_POSITIVE 201 99 57 98 59 NC_003454:FN1445|3end_DNA_helicase_2115953..2116103_POSITIVE 201 50 5 131 95 NC_003454:FN0542|3end_Beta_1,4_glucosyltransferase_1196094..1196244_POSITIVE 201 50 1 68 14 NC_003454:FN0465|3end_hypothetical_protein_1111358..1111508_POSITIVE 200 36 9 138 114 NC_003454:FN0389|3end_hypothetical_protein_1028042..1028192_POSITIVE 200 152 112 119 76 NC_003454:FN2107|3end_galactokinase_619399..619549_POSITIVE 199 84 48 127 80 NC_003454:FN1311|3end_Biopolymer_transport_exbD_protein_1965948..1966098_NEGATIVE 198 169 124 83 30 NC_003454:FN1056|3end_hypothetical_protein_1704372..1704522_POSITIVE 198 70 28 71 30 NC_003454:FN0929|3end_ATP/GTP_hydrolase_1583007..1583157_NEGATIVE 198 74 43 148 109 NC_003454:FN0364|3end_ATP_synthase_A_chain,_sodium_ion_specific_993757..993907_NEGATIVE 198 50 10 128 84 NC_003454:FN1506|3end_5-amino-6-(5-phosphoribosylamino)uracil_reductase_12060..12210_POSITIVE 192 61 46 21 6 NC_003454:FN1452|3end_Cell_division_protein_ftsA_2132733..2132883_NEGATIVE 192 60 11 130 79 NC_003454:FN0676|3end_10_kDa_chaperonin_GROES_1332108..1332258_NEGATIVE