Origin IGS: ataaaaggcttctgttatttttgttttagcttcatttatatctcttaattctttaaattctctatattttacaaaagcaatatttattaaaaatgaaaaaattaaaatggataatattatttcaaaagttgagaatgctttattcttttttatattatcaccttcttttttaaggtaattatataataatatctaataatttgtcaaataaaaaaacaaatattttgtaaaaaatataatatttgaaattattgttgtaagaatgaaagaaagctaccatatataatggtagctccttgaatttaaaactccttcatttttaggtagtggaacacctaagataattatatattataatatataactatcttttattaacttaattataatcactttttcttaaaaagtcaacatcgtcactattatagccagcatttttatagaaagctaatatattttcattttttcctcctatttattaaataccattcttacatttcaaaagttagatgtatcatc .........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 gatgatacatctaacttttgaaatgtaagaatggtatttaataaataggaggaaaaaatgaaaatatattagctttctataaaaatgctggctataatagtgacgatgttgactttttaagaaaaagtgattataattaagttaataaaagatagttatatattataatatataattatcttaggtgttccactacctaaaaatgaaggagttttaaattcaaggagctaccattatatatggtagctttctttcattcttacaacaataatttcaaatattatattttttacaaaatatttgtttttttatttgacaaattattagatattattatataattaccttaaaaaagaaggtgataatataaaaaagaataaagcattctcaacttttgaaataatattatccattttaattttttcatttttaataaatattgcttttgtaaaatatagagaatttaaagaattaagagatataaatgaagctaaaacaaaaataacagaagccttttat Mask Tandem Repeat Region ================================================ ataaaaggcttctgttatttttgttttagcttcatttatatctcttaattctttaaattctctatattttacaaaagcaatatttattaaaaatgaaaaaattaaaatggataatattatttcaaaagttgagaatgctttattcttttttatattatcaccttcttttttaaggtaattatataataatatctaataatttgtcaaataaaaaaacaaatattttgtaaaaaatataatatttgaaattattgttgtaagaatgaaagaaagctaccatatataatggtagctccttgaatttaaaactccttcatttttaggtagtggaacacctaagataattatatattataatatataactatcttttattaacttaattataatcactttttcttaaaaagtcaacatcgtcactattatagccagcatttttatagaaagctaatatattttcattttttcctcctatttattaaataccattcttacatttcaaaagttagatgtatcatc Find is-nt database================================================ Query_seq: FN2097:FN2098|FN2097:FN2098:hypothetical protein:MRP-family nucleotide-binding protein:<-<-:606944..607462 519 ataaaaggcttctgttatttttgttttagcttcatttatatctcttaattctttaaattctctatattttacaaaagcaatatttattaaaaatgaaaaaattaaaatggataatattatttcaaaagttgagaatgctttattcttttttatattatcaccttcttttttaaggtaattatataataatatctaataatttgtcaaataaaaaaacaaatattttgtaaaaaatataatatttgaaattattgttgtaagaatgaaagaaagctaccatatataatggtagctccttgaatttaaaactccttcatttttaggtagtggaacacctaagataattatatattataatatataactatcttttattaacttaattataatcactttttcttaaaaagtcaacatcgtcactattatagccagcatttttatagaaagctaatatattttcattttttcctcctatttattaaataccattcttacatttcaaaagttagatgtatcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN2097:FN2098|FN2097:FN2098:hypothetical protein:MRP-family nucleotide-binding protein:<-<-:606944..607462 519 ataaaaggcttctgttatttttgttttagcttcatttatatctcttaattctttaaattctctatattttacaaaagcaatatttattaaaaatgaaaaaattaaaatggataatattatttcaaaagttgagaatgctttattcttttttatattatcaccttcttttttaaggtaattatataataatatctaataatttgtcaaataaaaaaacaaatattttgtaaaaaatataatatttgaaattattgttgtaagaatgaaagaaagctaccatatataatggtagctccttgaatttaaaactccttcatttttaggtagtggaacacctaagataattatatattataatatataactatcttttattaacttaattataatcactttttcttaaaaagtcaacatcgtcactattatagccagcatttttatagaaagctaatatattttcattttttcctcctatttattaaataccattcttacatttcaaaagttagatgtatcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN2097:FN2098|FN2097:FN2098:hypothetical protein:MRP-family nucleotide-binding protein:<-<-:606944..607462 519 ataaaaggcttctgttatttttgttttagcttcatttatatctcttaattctttaaattctctatattttacaaaagcaatatttattaaaaatgaaaaaattaaaatggataatattatttcaaaagttgagaatgctttattcttttttatattatcaccttcttttttaaggtaattatataataatatctaataatttgtcaaataaaaaaacaaatattttgtaaaaaatataatatttgaaattattgttgtaagaatgaaagaaagctaccatatataatggtagctccttgaatttaaaactccttcatttttaggtagtggaacacctaagataattatatattataatatataactatcttttattaacttaattataatcactttttcttaaaaagtcaacatcgtcactattatagccagcatttttatagaaagctaatatattttcattttttcctcctatttattaaataccattcttacatttcaaaagttagatgtatcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataaaaggcttctgttatttttgttttagcttcatttatatctcttaattctttaaattctctatattttacaaaagcaatatttattaaaaatgaaaaaattaaaatggataatattatttcaaaagttgagaatgctttattcttttttatattatcaccttcttttttaaggtaattatataataatatctaataatttgtcaaataaaaaaacaaatattttgtaaaaaatataatatttgaaattattgttgtaagaatgaaagaaagctaccatatataatggtagctccttgaatttaaaactccttcatttttaggtagtggaacacctaagataattatatattataatatataactatcttttattaacttaattataatcactttttcttaaaaagtcaacatcgtcactattatagccagcatttttatagaaagctaatatattttcattttttcctcctatttattaaataccattcttacatttcaaaagttagatgtatcatc Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 57 End: 170 ........................................................ M L Y I L Q K Q Y L L K M K K L K W I I L F Q K L R M L Y S F L Y Y H L L F ............................................................................................................................................................................................................................................................................................................................................................. Protein_Len: 53 Strand: + Start: 17 End: 175 ................ M F V L A S F I S L N S L N S L Y F T K A I F I K N E K I K M D N I I S K V E N A L F F F I L S P S F L R ........................................................................................................................................................................................................................................................................................................................................................ Protein_Len: 31 Strand: - Start: 383 End: 475 .............................................................................................................................................................................................................................................................................................................................................................................................. N Y D S K R L F D V D D S N Y G A N K Y F A L I N E N K G G M ............................................ Protein_Len: 33 Strand: - Start: 182 End: 280 ..................................................................................................................................................................................... I I I D L L K D F L F V F I K Y F I Y Y K F N N N Y S H F F A V M ............................................................................................................................................................................................................................................... Protein_Len: 60 Strand: - Start: 1 End: 192 T I K T K A E N I D R L E K F E R Y K V F A I N I L F S F I L I S L I I E F T S F A K N K K I N D G E K K L Y N Y L L M ....................................................................................................................................................................................................................................................................................................................................... ataaaaggcttctgttatttttgttttagcttcatttatatctcttaattctttaaattctctatattttacaaaagcaatatttattaaaaatgaaaaaattaaaatggataatattatttcaaaagttgagaatgctttattcttttttatattatcaccttcttttttaaggtaattatataataatatctaataatttgtcaaataaaaaaacaaatattttgtaaaaaatataatatttgaaattattgttgtaagaatgaaagaaagctaccatatataatggtagctccttgaatttaaaactccttcatttttaggtagtggaacacctaagataattatatattataatatataactatcttttattaacttaattataatcactttttcttaaaaagtcaacatcgtcactattatagccagcatttttatagaaagctaatatattttcattttttcctcctatttattaaataccattcttacatttcaaaagttagatgtatcatc 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: 90 Start: 383 End: 412 ..............................................................................................................................................................................................................................................................................................................................................................................................GTTGACTTTTTAAGAAAAAGTGATTATAAT........................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ataaaaggcttctgttatttttgttttagcttcatttatatctcttaattctttaaattctctatattttacaaaagcaatatttattaaaaatgaaaaaattaaaatggataatattatttcaaaagttgagaatgctttattcttttttatattatcaccttcttttttaaggtaattatataataatatctaataatttgtcaaataaaaaaacaaatattttgtaaaaaatataatatttgaaattattgttgtaagaatgaaagaaagctaccatatataatggtagctccttgaatttaaaactccttcatttttaggtagtggaacacctaagataattatatattataatatataactatcttttattaacttaattataatcactttttcttaaaaagtcaacatcgtcactattatagccagcatttttatagaaagctaatatattttcattttttcctcctatttattaaataccattcttacatttcaaaagttagatgtatcatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 37 HP_score: -2.5 Tail_Score: -2.72012 Start: 150 End: 186 Full_Region: ATGCTTTATTCTTTT TTATATTATCACCTT CTTTTTT AAGGTAATTATATAA TAATATCTAATAATT .....................................................................................................................................................TTATATTATCACCTTCTTTTTTAAGGTAATTATATAA............................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 80 HP_score: -4.0 Tail_Score: -5.95539 Start: 217 End: 227 Full_Region: atattatatttttta caaa ata tttg tttttttatttgaca ........................................................................................................................................................................................................................caaaatatttg.................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 45 HP_score: -3.7 Tail_Score: -3.28001 Start: 270 End: 296 Full_Region: TTGTAAGAATGAAAG AAAGCTACCAT ATATA ATGGTAGCTCC TTGAATTTAAAACTC .............................................................................................................................................................................................................................................................................AAAGCTACCATATATAATGGTAGCTCC............................................................................................................................................................................................................................... TransTerm Strand: + Conf: 78 HP_score: -9.8 Tail_Score: -2.81888 Start: 273 End: 293 Full_Region: TAAGAATGAAAGAAA GCTACCAT ATATA ATGGTAGC TCCTTGAATTTAAAA ................................................................................................................................................................................................................................................................................GCTACCATATATAATGGTAGC.................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 89 HP_score: -9.8 Tail_Score: -4.62392 Start: 273 End: 293 Full_Region: ttttaaattcaagga gctaccat tatat atggtagc tttctttcattctta ................................................................................................................................................................................................................................................................................gctaccattatatatggtagc.................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 78 HP_score: -6.7 Tail_Score: -4.72631 Start: 340 End: 369 Full_Region: TAGTGGAACACCTAA GATAATTATATAT TATA ATATATAACTATC TTTTATTAACTTAAT ...................................................................................................................................................................................................................................................................................................................................................GATAATTATATATTATAATATATAACTATC...................................................................................................................................................... TransTerm Strand: - Conf: 73 HP_score: -8.9 Tail_Score: -3.19026 Start: 340 End: 369 Full_Region: attaagttaataaaa gatagttatatat tata atatataattatc ttaggtgttccacta ...................................................................................................................................................................................................................................................................................................................................................gatagttatatattataatatataattatc...................................................................................................................................................... Find igs database================================================ Query_seq: FN2097:FN2098|FN2097:FN2098:hypothetical protein:MRP-family nucleotide-binding protein:<-<-:606944..607462 519 ataaaaggcttctgttatttttgttttagcttcatttatatctcttaattctttaaattctctatattttacaaaagcaatatttattaaaaatgaaaaaattaaaatggataatattatttcaaaagttgagaatgctttattcttttttatattatcaccttcttttttaaggtaattatataataatatctaataatttgtcaaataaaaaaacaaatattttgtaaaaaatataatatttgaaattattgttgtaagaatgaaagaaagctaccatatataatggtagctccttgaatttaaaactccttcatttttaggtagtggaacacctaagataattatatattataatatataactatcttttattaacttaattataatcactttttcttaaaaagtcaacatcgtcactattatagccagcatttttatagaaagctaatatattttcattttttcctcctatttattaaataccattcttacatttcaaaagttagatgtatcatc Intra-Species Hit: Count: 1 Min: 1 Max: 519 Len: 519 Subject: NC_003454_FN2097_FN2098|hypothetical protein:MRP-family nucleotide-binding protein|NEGATIVE:NEGATIVE|[606944,607462]|519 HSP 1 e-value: 4.0E-59 bit: 230.0 Len: 116 Query Start:404 Query End:519 Subject Strand: POSITIVE Subject Start: 404 Subject End: 519 ...................................................................................................................................................................................................................................................................................................................................................................................................................aaagtcaacatcgtcactattatagccagcatttttatagaaagctaatatattttcattttttcctcctatttattaaataccattcttacatttcaaaagttagatgtatcatc ...................................................................................................................................................................................................................................................................................................................................................................................................................aaagtcaacatcgtcactattatagccagcatttttatagaaagctaatatattttcattttttcctcctatttattaaataccattcttacatttcaaaagttagatgtatcatc HSP 2 e-value: 2.0E-30 bit: 135.0 Len: 68 Query Start:273 Query End:340 Subject Strand: POSITIVE Subject Start: 273 Subject End: 340 ................................................................................................................................................................................................................................................................................gctaccatatataatggtagctccttgaatttaaaactccttcatttttaggtagtggaacacctaag................................................................................................................................................................................... ................................................................................................................................................................................................................................................................................gctaccatatataatggtagctccttgaatttaaaactccttcatttttaggtagtggaacacctaag................................................................................................................................................................................... HSP 3 e-value: 2.0E-27 bit: 125.0 Len: 63 Query Start:1 Query End:63 Subject Strand: POSITIVE Subject Start: 1 Subject End: 63 ataaaaggcttctgttatttttgttttagcttcatttatatctcttaattctttaaattctct........................................................................................................................................................................................................................................................................................................................................................................................................................................................................ ataaaaggcttctgttatttttgttttagcttcatttatatctcttaattctttaaattctct........................................................................................................................................................................................................................................................................................................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAAGGCUUCUGUUAUUUUUGUUUUAGCUUCAUUUAUAUCUCUUAAUUCUUUAAAUUCUCUAUAUUUUACAAAAGCAAUAUUUAUUAAAAAUGAAAAAAUUAAAAUGGAUAAUAUUAUUUCAAAAGUUGAGAAUGCUUUAUUCUUUUUUAUAUUAUCACCUUCUUUUUUAAGGUAAUUAUAUAAUAAUAUCUAAUAAUUUGUCAAAUAAAAAAACAAAUAUUUUGUAAAAAAUAUAAUAUUUGAAAUUAUUGUUGUAAGAAUGAAAGAAAGCUACCAUAUAUAAUGGUAGCUCCUUGAAUUUAAAACUCCUUCAUUUUUAGGUAGUGGAACACCUAAGAUAAUUAUAUAUUAUAAUAUAUAACUAUCUUUUAUUAACUUAAUUAUAAUCACUUUUUCUUAAAAAGUCAACAUCGUCACUAUUAUAGCCAGCAUUUUUAUAGAAAGCUAAUAUAUUUUCAUUUUUUCCUCCUAUUUAUUAAAUACCAUUCUUACAUUUCAAAAGUUAGAUGUAUCAUC ....(((((((((...(((((((.....((((.....((((.....((((.....))))....)))).......))))..((((((((...(((......)))..)))))))).........)))))))..)))).)))))........((((((.((.(((((.......))))).)).))))))..(((((((((...................((((((((.(((.....))).))))))))......(((.((((((((((......(((((((((.....)))))))))...((((..((.................((((((((.......((((((.((((((((....)))))))).))))))....................((((((.....))))))........))))))))......(((.((((....)))))))....))..)))).........................))))))))))...)))..)))))))))...... (-82.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAUACAUCUAACUUUUGAAAUGUAAGAAUGGUAUUUAAUAAAUAGGAGGAAAAAAUGAAAAUAUAUUAGCUUUCUAUAAAAAUGCUGGCUAUAAUAGUGACGAUGUUGACUUUUUAAGAAAAAGUGAUUAUAAUUAAGUUAAUAAAAGAUAGUUAUAUAUUAUAAUAUAUAAUUAUCUUAGGUGUUCCACUACCUAAAAAUGAAGGAGUUUUAAAUUCAAGGAGCUACCAUUAUAUAUGGUAGCUUUCUUUCAUUCUUACAACAAUAAUUUCAAAUAUUAUAUUUUUUACAAAAUAUUUGUUUUUUUAUUUGACAAAUUAUUAGAUAUUAUUAUAUAAUUACCUUAAAAAAGAAGGUGAUAAUAUAAAAAAGAAUAAAGCAUUCUCAACUUUUGAAAUAAUAUUAUCCAUUUUAAUUUUUUCAUUUUUAAUAAAUAUUGCUUUUGUAAAAUAUAGAGAAUUUAAAGAAUUAAGAGAUAUAAAUGAAGCUAAAACAAAAAUAACAGAAGCCUUUUAU ((((...))))...((((((...(((((((((((...........((((.((((............(((((((((..(((((....((((.......))))..........((((((.....))))))..)))))...))))))))).(((((((((((((((....))))))))))))))).....))))....)))).........((((.....))))..(((((((((((.....)))))))))))...))))))))))).......(((((....((((((((((((.......(((((((((((((((((.......)))))))...((((((.((((((((.......)))))))).)))))).))))))))))..((((((......(((((....((((.......))))..))))).............((((....))))......)))))).........)))))))))))).)))))...............))))))........ (-100.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 675 50 1 141 92 NC_003454:FN2097|5end_hypothetical_protein_606853..607083_NEGATIVE 274 494 456 124 85 NC_003454:FN0025|5end_Hypothetical_exported_24-amino_acid_repeat_protein_663746..663976_POSITIVE 273 494 456 154 115 NC_003454:FN0026|5end_Hypothetical_exported_24-amino_acid_repeat_protein_664285..664515_POSITIVE 263 490 443 97 42 NC_003454:FN1321|5end_Acetoacetate_metabolism_regulatory_protein_atoC_1977390..1977620_NEGATIVE 259 47 8 186 144 NC_003454:FN0290|5end_Hemolysin_918997..919227_NEGATIVE 256 339 291 180 133 NC_003454:FN0195|5end_Dipeptide_transport_ATP-binding_protein_dppD_820558..820788_POSITIVE 254 484 456 113 85 NC_003454:FN0896|5end_hypothetical_protein_1555780..1556010_NEGATIVE 254 474 436 105 68 NC_003454:FN1534|5end_Electron_transfer_flavoprotein_beta-subunit_47112..47342_NEGATIVE 253 497 456 132 85 NC_003454:FN0775|5end_putative_aminopeptidase_2_1430568..1430798_POSITIVE 251 194 156 139 96 NC_003454:FN0161|5end_RNA-directed_DNA_polymerase_788763..788993_POSITIVE 251 475 444 146 114 NC_003454:FN1808|5end_hypothetical_protein_289905..290135_NEGATIVE 248 480 446 109 71 NC_003454:FN1351|5end_15_kDa_lipoprotein_precursor_2003372..2003602_NEGATIVE 247 499 454 127 83 NC_003454:FN0989|5end_phosphoribosylaminoimidazole_carboxylase_catalytic_subunit_1641667..1641897_NEGATIVE 247 490 448 126 73 NC_003454:FN2118|5end_Hypothetical_exported_24-amino_acid_repeat_protein_627024..627254_NEGATIVE 246 171 134 206 160 NC_003454:FN0092|5end_NADPH-dependent_butanol_dehydrogenase_727908..728138_POSITIVE 244 55 11 107 66 NC_003454:FN2083|5end_hypothetical_protein_595642..595872_NEGATIVE 242 472 433 89 55 NC_003454:FN0418|5end_pyrimidine_regulatory_protein_PyrR_1059118..1059348_POSITIVE 239 488 447 114 75 NC_003454:FN0698|5end_DNA_integration/recombination/invertion_protein_1356611..1356841_POSITIVE 237 338 292 62 24 NC_003454:FN1198|5end_Transporter_1858941..1859171_NEGATIVE 237 460 412 76 22 NC_003454:FN1508|5end_3,4-dihydroxy-2-butanone-4-phosphate_synthase_12838..13068_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 274 494 456 115 76 NC_003454:FN0024|3end_Hypothetical_exported_24-amino_acid_repeat_protein_663817..663967_POSITIVE 273 494 456 115 76 NC_003454:FN0025|3end_Hypothetical_exported_24-amino_acid_repeat_protein_664326..664476_POSITIVE 258 46 8 140 106 NC_003454:FN1720|3end_hypothetical_protein_218771..218921_NEGATIVE 254 474 436 93 56 NC_003454:FN1535|3end_Acyl-CoA_dehydrogenase,_short-chain_specific_47124..47274_NEGATIVE 247 499 454 115 71 NC_003454:FN0990|3end_Phosphoribosylformylglycinamidine_synthase_1641679..1641829_NEGATIVE 247 490 448 114 61 NC_003454:FN2119|3end_Hypothetical_exported_24-amino_acid_repeat_protein_627036..627186_NEGATIVE 239 488 447 98 59 NC_003454:FN0697|3end_Alanyl-tRNA_synthetase_1356675..1356825_POSITIVE 237 460 412 66 12 NC_003454:FN1507|3end_riboflavin_synthase_subunit_alpha_12908..13058_POSITIVE 235 338 291 133 76 NC_003454:FN1875|3end_Peptidyl-prolyl_cis-trans_isomerase_363906..364056_NEGATIVE 234 328 285 136 105 NC_003454:FN0470|3end_Putative_efflux_pump_component_MtrF_1116359..1116509_POSITIVE 232 479 446 98 62 NC_003454:FN0297|3end_ATPase_associated_with_chromosome_architecture/replication_931201..931351_POSITIVE 231 471 444 56 25 NC_003454:FN1885|3end_Hemolysin_III_371411..371561_POSITIVE 228 474 440 73 36 NC_003454:FN2122|3end_Phenylalanyl-tRNA_synthetase_beta_chain_629798..629948_NEGATIVE 224 484 447 110 75 NC_003454:FN1473|3end_N-acetylneuraminate_transporter_large_subunit_2156965..2157115_POSITIVE 224 378 335 88 44 NC_003454:FN0940|3end_hypothetical_protein_1592975..1593125_NEGATIVE 223 295 260 73 34 NC_003454:FN1381|3end_hypothetical_protein_2028904..2029054_NEGATIVE 221 53 11 75 19 NC_003454:FN1284|3end_30S_ribosomal_protein_S4_1942656..1942806_NEGATIVE 221 65 21 58 11 NC_003454:FN0933|3end_3-phosphoshikimate_1-carboxyvinyltransferase_1586536..1586686_POSITIVE 219 68 21 84 41 NC_003454:FN1641|3end_SSU_ribosomal_protein_S19P_138552..138702_NEGATIVE 218 46 9 148 112 NC_003454:FN0521|3end_DNA_integration/recombination/invertion_protein_1172288..1172438_NEGATIVE