Origin IGS: atgagttataattccagattctcctcttgcagcaacaataatatcttgaactgtcccaacatttcttataggagtttgttgccattcaccatttacaagtgttaatacatttctagggttatttttatatatagcaattaatctacttcctgctttactatataaatcagattttttaatgcttgttttccatctccaataaggtgaattatctccatgtcctcttgagcttaagtttttaaagtatttaagagccttatcttcattatattcttcaaatactccaaaactttctttatgattatcattaacaggtactaaatacggaattgctgcaccaaaagtattataaggtaaaggtaaccctaattttttaaatatagtattttctagggcaattttttctctttttcctctttcagttgtaattgtagttcctgttttataatctccattaggttttatagtttttactttttttgctggttcatttgtacatgagataagtacaagcactgataaaaaaattaaagacagttgttttttcattaactcctcctttatatga .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcatataaaggaggagttaatgaaaaaacaactgtctttaatttttttatcagtgcttgtacttatctcatgtacaaatgaaccagcaaaaaaagtaaaaactataaaacctaatggagattataaaacaggaactacaattacaactgaaagaggaaaaagagaaaaaattgccctagaaaatactatatttaaaaaattagggttacctttaccttataatacttttggtgcagcaattccgtatttagtacctgttaatgataatcataaagaaagttttggagtatttgaagaatataatgaagataaggctcttaaatactttaaaaacttaagctcaagaggacatggagataattcaccttattggagatggaaaacaagcattaaaaaatctgatttatatagtaaagcaggaagtagattaattgctatatataaaaataaccctagaaatgtattaacacttgtaaatggtgaatggcaacaaactcctataagaaatgttgggacagttcaagatattattgttgctgcaagaggagaatctggaattataactcat Mask Tandem Repeat Region ================================================ atgagttataattccagattctcctcttgcagcaacaataatatcttgaactgtcccaacatttcttataggagtttgttgccattcaccatttacaagtgttaatacatttctagggttatttttatatatagcaattaatctacttcctgctttactatataaatcagattttttaatgcttgttttccatctccaataaggtgaattatctccatgtcctcttgagcttaagtttttaaagtatttaagagccttatcttcattatattcttcaaatactccaaaactttctttatgattatcattaacaggtactaaatacggaattgctgcaccaaaagtattataaggtaaaggtaaccctaattttttaaatatagtattttctagggcaattttttctctttttcctctttcagttgtaattgtagttcctgttttataatctccattaggttttatagtttttactttttttgctggttcatttgtacatgagataagtacaagcactgataaaaaaattaaagacagttgttttttcattaactcctcctttatatga Find is-nt database================================================ Query_seq: FN0806:FN0807|FN0806:FN0807:SpoIID homolog:3-deoxy-manno-octulosonate cytidylyltransferase:<-<-:1466679..1467246 568 atgagttataattccagattctcctcttgcagcaacaataatatcttgaactgtcccaacatttcttataggagtttgttgccattcaccatttacaagtgttaatacatttctagggttatttttatatatagcaattaatctacttcctgctttactatataaatcagattttttaatgcttgttttccatctccaataaggtgaattatctccatgtcctcttgagcttaagtttttaaagtatttaagagccttatcttcattatattcttcaaatactccaaaactttctttatgattatcattaacaggtactaaatacggaattgctgcaccaaaagtattataaggtaaaggtaaccctaattttttaaatatagtattttctagggcaattttttctctttttcctctttcagttgtaattgtagttcctgttttataatctccattaggttttatagtttttactttttttgctggttcatttgtacatgagataagtacaagcactgataaaaaaattaaagacagttgttttttcattaactcctcctttatatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0806:FN0807|FN0806:FN0807:SpoIID homolog:3-deoxy-manno-octulosonate cytidylyltransferase:<-<-:1466679..1467246 568 atgagttataattccagattctcctcttgcagcaacaataatatcttgaactgtcccaacatttcttataggagtttgttgccattcaccatttacaagtgttaatacatttctagggttatttttatatatagcaattaatctacttcctgctttactatataaatcagattttttaatgcttgttttccatctccaataaggtgaattatctccatgtcctcttgagcttaagtttttaaagtatttaagagccttatcttcattatattcttcaaatactccaaaactttctttatgattatcattaacaggtactaaatacggaattgctgcaccaaaagtattataaggtaaaggtaaccctaattttttaaatatagtattttctagggcaattttttctctttttcctctttcagttgtaattgtagttcctgttttataatctccattaggttttatagtttttactttttttgctggttcatttgtacatgagataagtacaagcactgataaaaaaattaaagacagttgttttttcattaactcctcctttatatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0806:FN0807|FN0806:FN0807:SpoIID homolog:3-deoxy-manno-octulosonate cytidylyltransferase:<-<-:1466679..1467246 568 atgagttataattccagattctcctcttgcagcaacaataatatcttgaactgtcccaacatttcttataggagtttgttgccattcaccatttacaagtgttaatacatttctagggttatttttatatatagcaattaatctacttcctgctttactatataaatcagattttttaatgcttgttttccatctccaataaggtgaattatctccatgtcctcttgagcttaagtttttaaagtatttaagagccttatcttcattatattcttcaaatactccaaaactttctttatgattatcattaacaggtactaaatacggaattgctgcaccaaaagtattataaggtaaaggtaaccctaattttttaaatatagtattttctagggcaattttttctctttttcctctttcagttgtaattgtagttcctgttttataatctccattaggttttatagtttttactttttttgctggttcatttgtacatgagataagtacaagcactgataaaaaaattaaagacagttgttttttcattaactcctcctttatatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atgagttataattccagattctcctcttgcagcaacaataatatcttgaactgtcccaacatttcttataggagtttgttgccattcaccatttacaagtgttaatacatttctagggttatttttatatatagcaattaatctacttcctgctttactatataaatcagattttttaatgcttgttttccatctccaataaggtgaattatctccatgtcctcttgagcttaagtttttaaagtatttaagagccttatcttcattatattcttcaaatactccaaaactttctttatgattatcattaacaggtactaaatacggaattgctgcaccaaaagtattataaggtaaaggtaaccctaattttttaaatatagtattttctagggcaattttttctctttttcctctttcagttgtaattgtagttcctgttttataatctccattaggttttatagtttttactttttttgctggttcatttgtacatgagataagtacaagcactgataaaaaaattaaagacagttgttttttcattaactcctcctttatatga Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 1 End: 102 M S Y N S R F S S C S N N N I L N C P N I S Y R S L L P F T I Y K C .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. Protein_Len: 44 Strand: + Start: 68 End: 199 ................................................................... M G V C C H S P F T S V N T F L G L F L Y I A I N L L P A L L Y K S D F L M L V F H L Q ................................................................................................................................................................................................................................................................................................................................................................................. Protein_Len: 35 Strand: + Start: 464 End: 565 ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................... M V F T F F A G S F V H E I S T S T D K K I K D S C F F I N S S F I * ... Protein_Len: 60 Strand: - Start: 1 End: 564 N E L A I K E R K G R E T T I T T G T K Y D G N P K I T K V K K A P E N T C S I L V L V S L F I L S L Q K K M L E E K M .... atgagttataattccagattctcctcttgcagcaacaataatatcttgaactgtcccaacatttcttataggagtttgttgccattcaccatttacaagtgttaatacatttctagggttatttttatatatagcaattaatctacttcctgctttactatataaatcagattttttaatgcttgttttccatctccaataaggtgaattatctccatgtcctcttgagcttaagtttttaaagtatttaagagccttatcttcattatattcttcaaatactccaaaactttctttatgattatcattaacaggtactaaatacggaattgctgcaccaaaagtattataaggtaaaggtaaccctaattttttaaatatagtattttctagggcaattttttctctttttcctctttcagttgtaattgtagttcctgttttataatctccattaggttttatagtttttactttttttgctggttcatttgtacatgagataagtacaagcactgataaaaaaattaaagacagttgttttttcattaactcctcctttatatga 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: 84 Start: 273 End: 302 ................................................................................................................................................................................................................................................................................CTTCAAATACTCCAAAACTTTCTTTATGAT.......................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atgagttataattccagattctcctcttgcagcaacaataatatcttgaactgtcccaacatttcttataggagtttgttgccattcaccatttacaagtgttaatacatttctagggttatttttatatatagcaattaatctacttcctgctttactatataaatcagattttttaatgcttgttttccatctccaataaggtgaattatctccatgtcctcttgagcttaagtttttaaagtatttaagagccttatcttcattatattcttcaaatactccaaaactttctttatgattatcattaacaggtactaaatacggaattgctgcaccaaaagtattataaggtaaaggtaaccctaattttttaaatatagtattttctagggcaattttttctctttttcctctttcagttgtaattgtagttcctgttttataatctccattaggttttatagtttttactttttttgctggttcatttgtacatgagataagtacaagcactgataaaaaaattaaagacagttgttttttcattaactcctcctttatatga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 49 HP_score: -2.6 Tail_Score: -3.72049 Start: 150 End: 170 Full_Region: CAATTAATCTACTTC CTGCTTTA CTATA TAAATCAG ATTTTTTAATGCTTG .....................................................................................................................................................CTGCTTTACTATATAAATCAG.............................................................................................................................................................................................................................................................................................................................................................................................................. Find igs database================================================ Query_seq: FN0806:FN0807|FN0806:FN0807:SpoIID homolog:3-deoxy-manno-octulosonate cytidylyltransferase:<-<-:1466679..1467246 568 atgagttataattccagattctcctcttgcagcaacaataatatcttgaactgtcccaacatttcttataggagtttgttgccattcaccatttacaagtgttaatacatttctagggttatttttatatatagcaattaatctacttcctgctttactatataaatcagattttttaatgcttgttttccatctccaataaggtgaattatctccatgtcctcttgagcttaagtttttaaagtatttaagagccttatcttcattatattcttcaaatactccaaaactttctttatgattatcattaacaggtactaaatacggaattgctgcaccaaaagtattataaggtaaaggtaaccctaattttttaaatatagtattttctagggcaattttttctctttttcctctttcagttgtaattgtagttcctgttttataatctccattaggttttatagtttttactttttttgctggttcatttgtacatgagataagtacaagcactgataaaaaaattaaagacagttgttttttcattaactcctcctttatatga Intra-Species Hit: Count: 1 Min: 1 Max: 568 Len: 568 Subject: NC_003454_FN0806_FN0807|SpoIID homolog:3-deoxy-manno-octulosonate cytidylyltransferase|NEGATIVE:NEGATIVE|[1466679, 1467246]|568 HSP 1 e-value: 0.0 bit: 731.0 Len: 369 Query Start:1 Query End:369 Subject Strand: POSITIVE Subject Start: 1 Subject End: 369 atgagttataattccagattctcctcttgcagcaacaataatatcttgaactgtcccaacatttcttataggagtttgttgccattcaccatttacaagtgttaatacatttctagggttatttttatatatagcaattaatctacttcctgctttactatataaatcagattttttaatgcttgttttccatctccaataaggtgaattatctccatgtcctcttgagcttaagtttttaaagtatttaagagccttatcttcattatattcttcaaatactccaaaactttctttatgattatcattaacaggtactaaatacggaattgctgcaccaaaagtattataaggtaaaggtaaccctaa....................................................................................................................................................................................................... atgagttataattccagattctcctcttgcagcaacaataatatcttgaactgtcccaacatttcttataggagtttgttgccattcaccatttacaagtgttaatacatttctagggttatttttatatatagcaattaatctacttcctgctttactatataaatcagattttttaatgcttgttttccatctccaataaggtgaattatctccatgtcctcttgagcttaagtttttaaagtatttaagagccttatcttcattatattcttcaaatactccaaaactttctttatgattatcattaacaggtactaaatacggaattgctgcaccaaaagtattataaggtaaaggtaaccctaa....................................................................................................................................................................................................... HSP 2 e-value: 3.0E-29 bit: 131.0 Len: 87 Query Start:482 Query End:568 Subject Strand: POSITIVE Subject Start: 482 Subject End: 568 .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................gctggttcatttgtacatgagataagtacaagcactgatnnnnnnnttaaagacagttgttttttcattaactcctcctttatatga .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................gctggttcatttgtacatgagataagtacaagcactgataaaaaaattaaagacagttgttttttcattaactcctcctttatatga HSP 3 e-value: 6.0E-18 bit: 93.7 Len: 47 Query Start:421 Query End:467 Subject Strand: POSITIVE Subject Start: 421 Subject End: 467 ....................................................................................................................................................................................................................................................................................................................................................................................................................................agttgtaattgtagttcctgttttataatctccattaggttttatag..................................................................................................... ....................................................................................................................................................................................................................................................................................................................................................................................................................................agttgtaattgtagttcctgttttataatctccattaggttttatag..................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGAGUUAUAAUUCCAGAUUCUCCUCUUGCAGCAACAAUAAUAUCUUGAACUGUCCCAACAUUUCUUAUAGGAGUUUGUUGCCAUUCACCAUUUACAAGUGUUAAUACAUUUCUAGGGUUAUUUUUAUAUAUAGCAAUUAAUCUACUUCCUGCUUUACUAUAUAAAUCAGAUUUUUUAAUGCUUGUUUUCCAUCUCCAAUAAGGUGAAUUAUCUCCAUGUCCUCUUGAGCUUAAGUUUUUAAAGUAUUUAAGAGCCUUAUCUUCAUUAUAUUCUUCAAAUACUCCAAAACUUUCUUUAUGAUUAUCAUUAACAGGUACUAAAUACGGAAUUGCUGCACCAAAAGUAUUAUAAGGUAAAGGUAACCCUAAUUUUUUAAAUAUAGUAUUUUCUAGGGCAAUUUUUUCUCUUUUUCCUCUUUCAGUUGUAAUUGUAGUUCCUGUUUUAUAAUCUCCAUUAGGUUUUAUAGUUUUUACUUUUUUUGCUGGUUCAUUUGUACAUGAGAUAAGUACAAGCACUGAUAAAAAAAUUAAAGACAGUUGUUUUUUCAUUAACUCCUCCUUUAUAUGA ..((((((.......(((((......((((.(((((((.....(((((((.(((....))).)))....))))..))))))).....(((...((.((((((....)))))).)).)))..............))))..))))).....((((((((........(((((.........(((((((....(((((......)))))..(((((((.((((.(...((((((..(((....((((((...((((......)))).................(((..(((((((.......((((((....((((((.((((.....((((..(.(((.((.(((((((((((...((((((..........))))))..)))))))))))...))))).)..))))..............((((....)))))))).))))))..))))))......)))))))..)))...))))))....)))))))))...).)))))))))))..))))))))))))........))))).)))............))))))............. (-103.61) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAUAUAAAGGAGGAGUUAAUGAAAAAACAACUGUCUUUAAUUUUUUUAUCAGUGCUUGUACUUAUCUCAUGUACAAAUGAACCAGCAAAAAAAGUAAAAACUAUAAAACCUAAUGGAGAUUAUAAAACAGGAACUACAAUUACAACUGAAAGAGGAAAAAGAGAAAAAAUUGCCCUAGAAAAUACUAUAUUUAAAAAAUUAGGGUUACCUUUACCUUAUAAUACUUUUGGUGCAGCAAUUCCGUAUUUAGUACCUGUUAAUGAUAAUCAUAAAGAAAGUUUUGGAGUAUUUGAAGAAUAUAAUGAAGAUAAGGCUCUUAAAUACUUUAAAAACUUAAGCUCAAGAGGACAUGGAGAUAAUUCACCUUAUUGGAGAUGGAAAACAAGCAUUAAAAAAUCUGAUUUAUAUAGUAAAGCAGGAAGUAGAUUAAUUGCUAUAUAUAAAAAUAACCCUAGAAAUGUAUUAACACUUGUAAAUGGUGAAUGGCAACAAACUCCUAUAAGAAAUGUUGGGACAGUUCAAGAUAUUAUUGUUGCUGCAAGAGGAGAAUCUGGAAUUAUAACUCAU .............((((((............(((.(((((........((((((((((((...((((((((((.....(((....((......................((....)).((((((..((((((.((((........((..((((......(((..(((.....(((((((....................)))))))....)))..)))......))))..))...((......))...)))).))))))....)))))).......((((((((((((((((((((..(((.......)))...)).))))))))))).)))))))..))))).....)))).)))))).((((.(((....))).))))..))))))).........)))))........))))))))....((((((..((((.....((((.((((...((.(((.(((.((((((((((((...((.(..((....))..).))))))))...)))))).))).))).)).)))).))))....))))......))))))......)))))).. (-105.74) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 877 60 11 151 102 NC_003454:FN0806|5end_SpoIID_homolog_1466588..1466818_NEGATIVE 309 90 41 171 121 NC_003454:FN1189|5end_hypothetical_protein_1851320..1851550_POSITIVE 288 230 181 209 162 NC_003454:FN1126|5end_Acetyltransferase_1770287..1770517_NEGATIVE 280 454 411 150 93 NC_003454:FN1669|5end_Choline_transport_protein_166486..166716_NEGATIVE 276 439 396 121 80 NC_003454:FN0775|5end_putative_aminopeptidase_2_1430568..1430798_POSITIVE 272 229 189 119 82 NC_003454:FN0161|5end_RNA-directed_DNA_polymerase_788763..788993_POSITIVE 272 457 414 63 21 NC_003454:FN2093|5end_General_secretion_pathway_protein_G_603551..603781_NEGATIVE 270 190 145 49 2 NC_003454:FN0669|5end_High-affinity_zinc_uptake_system_ATP-binding_protein_znuC_1324931..1325161_POSITIVE 269 496 451 80 41 NC_003454:FN0569|5end_Hypothetical_membrane-spanning_protein_1220732..1220962_NEGATIVE 266 217 190 204 178 NC_003454:FN1992|5end_Ribose-phosphate_pyrophosphokinase_495965..496195_POSITIVE 256 209 167 197 147 NC_003454:FN1095|5end_hypothetical_protein_1740232..1740462_POSITIVE 255 446 401 222 180 NC_003454:FN0256|5end_Hypothetical_cytosolic_protein_882208..882438_POSITIVE 254 87 44 93 44 NC_003454:FN1284|5end_30S_ribosomal_protein_S4_1943243..1943473_NEGATIVE 254 216 174 151 116 NC_003454:FN0940|5end_hypothetical_protein_1593508..1593738_NEGATIVE 253 398 351 96 37 NC_003454:FN0763|5end_Transporter,_LysE_family_1420169..1420399_POSITIVE 253 237 197 48 1 NC_003454:FN1506|5end_5-amino-6-(5-phosphoribosylamino)uracil_reductase_10871..11101_POSITIVE 251 120 71 138 72 NC_003454:FN0539|5end_Ferrochelatase_1192651..1192881_NEGATIVE 250 310 261 141 86 NC_003454:FN0266|5end_membrane_protein_related_to_metalloendopeptidase_892320..892550_POSITIVE 250 446 401 162 105 NC_003454:FN0254|5end_Fusobacterium_outer_membrane_protein_family_876277..876507_POSITIVE 250 198 167 35 3 NC_003454:FN0247|5end_Hypothetical_cytosolic_protein_870707..870937_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 309 90 41 128 78 NC_003454:FN1188|3end_hypothetical_protein_1851357..1851507_POSITIVE 269 430 384 139 92 NC_003454:FN0805|3end_hypothetical_protein_1464832..1464982_NEGATIVE 255 446 401 51 9 NC_003454:FN0255|3end_Hypothetical_cytosolic_protein_882117..882267_POSITIVE 254 87 44 53 4 NC_003454:FN1285|3end_30S_ribosomal_protein_S11_1943283..1943433_NEGATIVE 254 216 174 132 97 NC_003454:FN0941|3end_Gamma-glutamyltranspeptidase_1593527..1593677_NEGATIVE 251 454 416 133 94 NC_003454:FN1364|3end_LSU_ribosomal_protein_L32P_2015382..2015532_NEGATIVE 251 120 71 148 82 NC_003454:FN0540|3end_Glutamate-1-semialdehyde_2,1-aminomutase_1192641..1192791_NEGATIVE 250 310 261 151 96 NC_003454:FN0265|3end_Cell_division_protein_ftsX_892410..892560_POSITIVE 248 425 385 123 87 NC_003454:FN1538|3end_Arsenical_pump-driving_ATPase_51109..51259_NEGATIVE 247 440 398 56 8 NC_003454:FN0950|3end_Precorrin-6X_reductase_1606975..1607125_NEGATIVE 241 425 382 130 82 NC_003454:FN1937|3end_hypothetical_protein_437705..437855_NEGATIVE 240 560 512 55 12 NC_003454:FN0032|3end_hypothetical_protein_668789..668939_NEGATIVE 240 470 424 148 98 NC_003454:FN1652|3end_Oligopeptide-binding_protein_oppA_146041..146191_NEGATIVE 239 370 323 55 1 NC_003454:FN1785|3end_hypothetical_protein_266212..266362_NEGATIVE 238 438 397 139 100 NC_003454:FN0406|3end_Alanine_racemase,_biosynthetic_1043510..1043660_NEGATIVE 238 459 420 70 30 NC_003454:FN1620|3end_30S_ribosomal_protein_S2_128719..128869_POSITIVE 236 439 401 126 75 NC_003454:FN2059|3end_Outer_membrane_protein_572877..573027_NEGATIVE 236 439 401 126 75 NC_003454:FN2048|3end_Outer_membrane_protein_558801..558951_NEGATIVE 236 455 412 149 110 NC_003454:FN1580|3end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_90224..90374_NEGATIVE 233 419 371 55 9 NC_003454:FN0889|3end_Dihydrolipoamide_acyltransferase_1551010..1551160_NEGATIVE