Origin IGS: tgcacttccattagcccttggaataatatacactgtacctttatcaacttttaaattttcaactaatagaacagttgttaaaaaagctgctggctcattagggtgtgttccacctaatataagaacagatcctccaggctcttttccttgtaatatataaatatcactatctccacgagttccttttaatgcaggaagataatcacttaatttctgcatagatgttactccatcacttttaacaattggttctaattctcttgtttttaaaaactcttttcctgctataaatgtaataacgagagaaagaaaaatcattataattcctgttattttgtttcctttcattttcttcctccttattttataaataaaattctaagaattaatggaataatgacaagtgcagcatttaattgcttagctatacttttttcttccaacaaatttaaaataaccattattaaaacatacaatactatagttaaatatatatacatcatcataatttatcacctcatc .........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 gatgaggtgataaattatgatgatgtatatatatttaactatagtattgtatgttttaataatggttattttaaatttgttggaagaaaaaagtatagctaagcaattaaatgctgcacttgtcattattccattaattcttagaattttatttataaaataaggaggaagaaaatgaaaggaaacaaaataacaggaattataatgatttttctttctctcgttattacatttatagcaggaaaagagtttttaaaaacaagagaattagaaccaattgttaaaagtgatggagtaacatctatgcagaaattaagtgattatcttcctgcattaaaaggaactcgtggagatagtgatatttatatattacaaggaaaagagcctggaggatctgttcttatattaggtggaacacaccctaatgagccagcagcttttttaacaactgttctattagttgaaaatttaaaagttgataaaggtacagtgtatattattccaagggctaatggaagtgca Mask Tandem Repeat Region ================================================ tgcacttccattagcccttggaataatatacactgtacctttatcaacttttaaattttcaactaatagaacagttgttaaaaaagctgctggctcattagggtgtgttccacctaatataagaacagatcctccaggctcttttccttgtaatatataaatatcactatctccacgagttccttttaatgcaggaagataatcacttaatttctgcatagatgttactccatcacttttaacaattggttctaattctcttgtttttaaaaactcttttcctgctataaatgtaataacgagagaaagaaaaatcattataattcctgttattttgtttcctttcattttcttcctccttattttataaataaaattctaagaattaatggaataatgacaagtgcagcatttaattgcttagctatacttttttcttccaacaaatttaaaataaccattattaaaacatacaatactatagttaaatatatatacatcatcataatttatcacctcatc Find is-nt database================================================ Query_seq: FN0938:FN0939|FN0938:FN0939:hypothetical protein:Hypothetical membrane-spanning protein:<-<-:1591216..1591737 522 tgcacttccattagcccttggaataatatacactgtacctttatcaacttttaaattttcaactaatagaacagttgttaaaaaagctgctggctcattagggtgtgttccacctaatataagaacagatcctccaggctcttttccttgtaatatataaatatcactatctccacgagttccttttaatgcaggaagataatcacttaatttctgcatagatgttactccatcacttttaacaattggttctaattctcttgtttttaaaaactcttttcctgctataaatgtaataacgagagaaagaaaaatcattataattcctgttattttgtttcctttcattttcttcctccttattttataaataaaattctaagaattaatggaataatgacaagtgcagcatttaattgcttagctatacttttttcttccaacaaatttaaaataaccattattaaaacatacaatactatagttaaatatatatacatcatcataatttatcacctcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0938:FN0939|FN0938:FN0939:hypothetical protein:Hypothetical membrane-spanning protein:<-<-:1591216..1591737 522 tgcacttccattagcccttggaataatatacactgtacctttatcaacttttaaattttcaactaatagaacagttgttaaaaaagctgctggctcattagggtgtgttccacctaatataagaacagatcctccaggctcttttccttgtaatatataaatatcactatctccacgagttccttttaatgcaggaagataatcacttaatttctgcatagatgttactccatcacttttaacaattggttctaattctcttgtttttaaaaactcttttcctgctataaatgtaataacgagagaaagaaaaatcattataattcctgttattttgtttcctttcattttcttcctccttattttataaataaaattctaagaattaatggaataatgacaagtgcagcatttaattgcttagctatacttttttcttccaacaaatttaaaataaccattattaaaacatacaatactatagttaaatatatatacatcatcataatttatcacctcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0938:FN0939|FN0938:FN0939:hypothetical protein:Hypothetical membrane-spanning protein:<-<-:1591216..1591737 522 tgcacttccattagcccttggaataatatacactgtacctttatcaacttttaaattttcaactaatagaacagttgttaaaaaagctgctggctcattagggtgtgttccacctaatataagaacagatcctccaggctcttttccttgtaatatataaatatcactatctccacgagttccttttaatgcaggaagataatcacttaatttctgcatagatgttactccatcacttttaacaattggttctaattctcttgtttttaaaaactcttttcctgctataaatgtaataacgagagaaagaaaaatcattataattcctgttattttgtttcctttcattttcttcctccttattttataaataaaattctaagaattaatggaataatgacaagtgcagcatttaattgcttagctatacttttttcttccaacaaatttaaaataaccattattaaaacatacaatactatagttaaatatatatacatcatcataatttatcacctcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgcacttccattagcccttggaataatatacactgtacctttatcaacttttaaattttcaactaatagaacagttgttaaaaaagctgctggctcattagggtgtgttccacctaatataagaacagatcctccaggctcttttccttgtaatatataaatatcactatctccacgagttccttttaatgcaggaagataatcacttaatttctgcatagatgttactccatcacttttaacaattggttctaattctcttgtttttaaaaactcttttcctgctataaatgtaataacgagagaaagaaaaatcattataattcctgttattttgtttcctttcattttcttcctccttattttataaataaaattctaagaattaatggaataatgacaagtgcagcatttaattgcttagctatacttttttcttccaacaaatttaaaataaccattattaaaacatacaatactatagttaaatatatatacatcatcataatttatcacctcatc Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 23 End: 157 ...................... M I Y T V P L S T F K F S T N R T V V K K A A G S L G C V P P N I R T D P P G S F P C N I ............................................................................................................................................................................................................................................................................................................................................................................. Protein_Len: 30 Strand: + Start: 129 End: 218 ................................................................................................................................ M L Q A L F L V I Y K Y H Y L H E F L L M Q E D N H L I S A ................................................................................................................................................................................................................................................................................................................ Protein_Len: 50 Strand: + Start: 218 End: 367 ......................................................................................................................................................................................................................... M D V T P S L L T I G S N S L V F K N S F P A I N V I T R E R K I I I I P V I L F P F I F F L L I L ........................................................................................................................................................... Protein_Len: 52 Strand: + Start: 367 End: 522 .............................................................................................................................................................................................................................................................................................................................................................................. M N K I L R I N G I M T S A A F N C L A I L F S S N K F K I T I I K T Y N T I V K Y I Y I I I I Y H L I Protein_Len: 31 Strand: - Start: 424 End: 516 ....................................................................................................................................................................................................................................................................................................................................................................................................................................... S Y K K R G V F K F Y G N N F C V I S Y N F I Y V D D Y N I M ...... Protein_Len: 49 Strand: - Start: 363 End: 509 .......................................................................................................................................................................................................................................................................................................................................................................... K I F L I R L I L P I I V L A A N L Q K A I S K E E L L N L I V M I L V Y L V I T L Y I Y M M M M ............. Protein_Len: 60 Strand: - Start: 1 End: 372 P L Y D S L K Q M S T V G D S K V I P E L E R T K L F E K G A I F T I V L S L F I M I I G T I K N G K M K K R R I K Y M ...................................................................................................................................................... tgcacttccattagcccttggaataatatacactgtacctttatcaacttttaaattttcaactaatagaacagttgttaaaaaagctgctggctcattagggtgtgttccacctaatataagaacagatcctccaggctcttttccttgtaatatataaatatcactatctccacgagttccttttaatgcaggaagataatcacttaatttctgcatagatgttactccatcacttttaacaattggttctaattctcttgtttttaaaaactcttttcctgctataaatgtaataacgagagaaagaaaaatcattataattcctgttattttgtttcctttcattttcttcctccttattttataaataaaattctaagaattaatggaataatgacaagtgcagcatttaattgcttagctatacttttttcttccaacaaatttaaaataaccattattaaaacatacaatactatagttaaatatatatacatcatcataatttatcacctcatc 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================================================ tgcacttccattagcccttggaataatatacactgtacctttatcaacttttaaattttcaactaatagaacagttgttaaaaaagctgctggctcattagggtgtgttccacctaatataagaacagatcctccaggctcttttccttgtaatatataaatatcactatctccacgagttccttttaatgcaggaagataatcacttaatttctgcatagatgttactccatcacttttaacaattggttctaattctcttgtttttaaaaactcttttcctgctataaatgtaataacgagagaaagaaaaatcattataattcctgttattttgtttcctttcattttcttcctccttattttataaataaaattctaagaattaatggaataatgacaagtgcagcatttaattgcttagctatacttttttcttccaacaaatttaaaataaccattattaaaacatacaatactatagttaaatatatatacatcatcataatttatcacctcatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0938:FN0939|FN0938:FN0939:hypothetical protein:Hypothetical membrane-spanning protein:<-<-:1591216..1591737 522 tgcacttccattagcccttggaataatatacactgtacctttatcaacttttaaattttcaactaatagaacagttgttaaaaaagctgctggctcattagggtgtgttccacctaatataagaacagatcctccaggctcttttccttgtaatatataaatatcactatctccacgagttccttttaatgcaggaagataatcacttaatttctgcatagatgttactccatcacttttaacaattggttctaattctcttgtttttaaaaactcttttcctgctataaatgtaataacgagagaaagaaaaatcattataattcctgttattttgtttcctttcattttcttcctccttattttataaataaaattctaagaattaatggaataatgacaagtgcagcatttaattgcttagctatacttttttcttccaacaaatttaaaataaccattattaaaacatacaatactatagttaaatatatatacatcatcataatttatcacctcatc Intra-Species Hit: Count: 1 Min: 1 Max: 522 Len: 522 Subject: NC_003454_FN0938_FN0939|hypothetical protein:Hypothetical membrane-spanning protein|NEGATIVE:NEGATIVE|[1591216,1591737]|522 HSP 1 e-value: 0.0 bit: 1035.0 Len: 522 Query Start:1 Query End:522 Subject Strand: POSITIVE Subject Start: 1 Subject End: 522 tgcacttccattagcccttggaataatatacactgtacctttatcaacttttaaattttcaactaatagaacagttgttaaaaaagctgctggctcattagggtgtgttccacctaatataagaacagatcctccaggctcttttccttgtaatatataaatatcactatctccacgagttccttttaatgcaggaagataatcacttaatttctgcatagatgttactccatcacttttaacaattggttctaattctcttgtttttaaaaactcttttcctgctataaatgtaataacgagagaaagaaaaatcattataattcctgttattttgtttcctttcattttcttcctccttattttataaataaaattctaagaattaatggaataatgacaagtgcagcatttaattgcttagctatacttttttcttccaacaaatttaaaataaccattattaaaacatacaatactatagttaaatatatatacatcatcataatttatcacctcatc tgcacttccattagcccttggaataatatacactgtacctttatcaacttttaaattttcaactaatagaacagttgttaaaaaagctgctggctcattagggtgtgttccacctaatataagaacagatcctccaggctcttttccttgtaatatataaatatcactatctccacgagttccttttaatgcaggaagataatcacttaatttctgcatagatgttactccatcacttttaacaattggttctaattctcttgtttttaaaaactcttttcctgctataaatgtaataacgagagaaagaaaaatcattataattcctgttattttgtttcctttcattttcttcctccttattttataaataaaattctaagaattaatggaataatgacaagtgcagcatttaattgcttagctatacttttttcttccaacaaatttaaaataaccattattaaaacatacaatactatagttaaatatatatacatcatcataatttatcacctcatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCACUUCCAUUAGCCCUUGGAAUAAUAUACACUGUACCUUUAUCAACUUUUAAAUUUUCAACUAAUAGAACAGUUGUUAAAAAAGCUGCUGGCUCAUUAGGGUGUGUUCCACCUAAUAUAAGAACAGAUCCUCCAGGCUCUUUUCCUUGUAAUAUAUAAAUAUCACUAUCUCCACGAGUUCCUUUUAAUGCAGGAAGAUAAUCACUUAAUUUCUGCAUAGAUGUUACUCCAUCACUUUUAACAAUUGGUUCUAAUUCUCUUGUUUUUAAAAACUCUUUUCCUGCUAUAAAUGUAAUAACGAGAGAAAGAAAAAUCAUUAUAAUUCCUGUUAUUUUGUUUCCUUUCAUUUUCUUCCUCCUUAUUUUAUAAAUAAAAUUCUAAGAAUUAAUGGAAUAAUGACAAGUGCAGCAUUUAAUUGCUUAGCUAUACUUUUUUCUUCCAACAAAUUUAAAAUAACCAUUAUUAAAACAUACAAUACUAUAGUUAAAUAUAUAUACAUCAUCAUAAUUUAUCACCUCAUC .(((((((((((((..((((((((...............................(((((......(((((((((((((((((.(((..((((......(((((.(((((............))))).))))))))))))....................................((((..(.((((.((((((((..(((....))).)))))))))))).)..))))......))))))))))).)))))).((((((((((.(((........................))).)))))))))).)))))..((..(((((....)))))..))......................................))))))))..)))))))).........))))).(((......))).((((((((..................................................))))))))................................... (-87.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAGGUGAUAAAUUAUGAUGAUGUAUAUAUAUUUAACUAUAGUAUUGUAUGUUUUAAUAAUGGUUAUUUUAAAUUUGUUGGAAGAAAAAAGUAUAGCUAAGCAAUUAAAUGCUGCACUUGUCAUUAUUCCAUUAAUUCUUAGAAUUUUAUUUAUAAAAUAAGGAGGAAGAAAAUGAAAGGAAACAAAAUAACAGGAAUUAUAAUGAUUUUUCUUUCUCUCGUUAUUACAUUUAUAGCAGGAAAAGAGUUUUUAAAAACAAGAGAAUUAGAACCAAUUGUUAAAAGUGAUGGAGUAACAUCUAUGCAGAAAUUAAGUGAUUAUCUUCCUGCAUUAAAAGGAACUCGUGGAGAUAGUGAUAUUUAUAUAUUACAAGGAAAAGAGCCUGGAGGAUCUGUUCUUAUAUUAGGUGGAACACACCCUAAUGAGCCAGCAGCUUUUUUAACAACUGUUCUAUUAGUUGAAAAUUUAAAAGUUGAUAAAGGUACAGUGUAUAUUAUUCCAAGGGCUAAUGGAAGUGCA ..(((((((((..(((((...((((((((.(((((.......)))))))))))))...))))).)))))))))............................((((......))))((((((.(((((.((((.(((((((((((((((((.(((.........((((((((((((.....(....)...((((......))))......)))))))))))).(((((.......)))))..))).)))))))).........)))))))))..(((...(((......((((......)))).((((((((..(((....)))..)).)))))).......)))...))).....(((((((....)))))))..))))...(((((...(((.((((((((.(((((((((.....)).)))))))......((((((((....((((((......)))))).......))))))))...)))).))))..........)))..)))))))))))))))). (-107.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 958 140 91 231 182 NC_003454:FN0938|5end_hypothetical_protein_1591125..1591355_NEGATIVE 311 184 144 189 155 NC_003454:FN1764|5end_Enolase_257997..258227_NEGATIVE 294 360 317 101 54 NC_003454:FN1125|5end_LemA_protein_1769811..1770041_NEGATIVE 293 360 311 103 59 NC_003454:FN0209|5end_Hypothetical_cytosolic_protein_836127..836357_POSITIVE 270 97 63 227 199 NC_003454:FN1353|5end_ABC_transporter_permease_protein_2005386..2005616_NEGATIVE 269 366 322 95 50 NC_003454:FN0263|5end_Peptidyl-prolyl_cis-trans_isomerase_890064..890294_POSITIVE 266 365 328 191 143 NC_003454:FN1841|5end_Dihydroxyacetone_kinase_330879..331109_POSITIVE 257 359 320 105 66 NC_003454:FN1669|5end_Choline_transport_protein_166486..166716_NEGATIVE 256 367 323 111 72 NC_003454:FN0664|5end_2-nitropropane_dioxygenase_1319758..1319988_POSITIVE 256 360 315 102 57 NC_003454:FN0662|5end_Formiminoglutamase_1318152..1318382_POSITIVE 256 130 88 71 29 NC_003454:FN0438|5end_Branched_chain_amino_acid_transport_system_II_carrier_protein_1080822..1081052_NEGATIVE 253 369 327 114 64 NC_003454:FN0291|5end_Hemolysin_924999..925229_NEGATIVE 252 360 313 53 10 NC_003454:FN1828|5end_LSU_ribosomal_protein_L9P_317700..317930_NEGATIVE 250 379 340 126 83 NC_003454:FN1105|5end_hypothetical_protein_1750041..1750271_POSITIVE 250 370 324 117 64 NC_003454:FN0298|5end_Histidyl-tRNA_synthetase_931133..931363_POSITIVE 249 370 328 120 71 NC_003454:FN1192|5end_hypothetical_protein_1854679..1854909_POSITIVE 249 124 85 206 169 NC_003454:FN1046|5end_hypothetical_protein_1696371..1696601_POSITIVE 249 360 323 102 72 NC_003454:FN0116|5end_Chaperone_protein_dnaK_748253..748483_POSITIVE 248 360 323 163 114 NC_003454:FN0994|5end_hypothetical_protein_1649223..1649453_POSITIVE 248 370 322 110 62 NC_003454:FN0896|5end_hypothetical_protein_1555780..1556010_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 360 317 92 45 NC_003454:FN1126|3end_Acetyltransferase_1769820..1769970_NEGATIVE 293 360 311 92 48 NC_003454:FN0208|3end_(R)-2-hydroxyglutaryl-CoA_dehydratase_beta-subunit_836196..836346_POSITIVE 266 365 328 145 97 NC_003454:FN1840|3end_Dihydroxyacetone_kinase_330913..331063_POSITIVE 257 359 320 121 82 NC_003454:FN1670|3end_Choline_kinase_166470..166620_NEGATIVE 256 367 323 70 31 NC_003454:FN0663|3end_hypothetical_protein_1319797..1319947_POSITIVE 256 360 315 83 38 NC_003454:FN0661|3end_hypothetical_protein_1318213..1318363_POSITIVE 256 130 88 56 14 NC_003454:FN0439|3end_hypothetical_protein_1080837..1080987_NEGATIVE 253 369 327 102 52 NC_003454:FN0292|3end_Hemolysin_activator_protein_precursor_925011..925161_NEGATIVE 250 379 340 122 79 NC_003454:FN1104|3end_Holliday_junction_DNA_helicase_ruvA_1750117..1750267_POSITIVE 250 370 324 105 52 NC_003454:FN0297|3end_ATPase_associated_with_chromosome_architecture/replication_931201..931351_POSITIVE 249 370 328 90 41 NC_003454:FN1191|3end_hypothetical_protein_1854729..1854879_POSITIVE 249 360 323 71 41 NC_003454:FN0114|3end_GrpE_protein_748302..748452_POSITIVE 248 360 323 68 19 NC_003454:FN0993|3end_Trk_system_potassium_uptake_protein_trkG_1649208..1649358_POSITIVE 248 360 318 78 42 NC_003454:FN0326|3end_LSU_ribosomal_protein_L35P_961299..961449_NEGATIVE 248 368 327 99 51 NC_003454:FN2127|3end_hypothetical_protein_638226..638376_NEGATIVE 246 360 321 84 45 NC_003454:FN0465|3end_hypothetical_protein_1111358..1111508_POSITIVE 245 145 101 100 50 NC_003454:FN0382|3end_hypothetical_protein_1014224..1014374_POSITIVE 242 362 321 93 60 NC_003454:FN1520|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_24802..24952_NEGATIVE 239 369 321 95 49 NC_003454:FN0309|3end_Iron(III)-transport_system_permease_protein_sfuB_945861..946011_POSITIVE 238 369 321 100 49 NC_003454:FN0723|3end_hypothetical_protein_1383464..1383614_POSITIVE