Origin IGS: cttttctcctacatttacctttttattctataacagtattataaaaataagtgaattgcattctaaattttagataaaaaattaaagcaagtgagccgagtaattgtcggcatgtctgagcatagcgagtttgccgaaattacagcgaaacattaattttttattgttaagaaatttagctagcaatgagctatttttatatacccc .........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 ggggtatataaaaatagctcattgctagctaaatttcttaacaataaaaaattaatgtttcgctgtaatttcggcaaactcgctatgctcagacatgccgacaattactcggctcacttgctttaattttttatctaaaatttagaatgcaattcacttatttttataatactgttatagaataaaaaggtaaatgtaggagaaaag Mask Tandem Repeat Region ================================================ cttttctcctacatttacctttttattctataacagtattataaaaataagtgaattgcattctaaattttagataaaaaattaaagcaagtgagccgagtaattgtcggcatgtctgagcatagcgagtttgccgaaattacagcgaaacattaattttttattgttaagaaatttagctagcaatgagctatttttatatacccc Find is-nt database================================================ Query_seq: FN1810:FN1811|FN1810:FN1811:Manganese transport system membrane protein mntB:Manganese transport system ATP-binding protein mntA:<-<-:292044..292250 207 cttttctcctacatttacctttttattctataacagtattataaaaataagtgaattgcattctaaattttagataaaaaattaaagcaagtgagccgagtaattgtcggcatgtctgagcatagcgagtttgccgaaattacagcgaaacattaattttttattgttaagaaatttagctagcaatgagctatttttatatacccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1810:FN1811|FN1810:FN1811:Manganese transport system membrane protein mntB:Manganese transport system ATP-binding protein mntA:<-<-:292044..292250 207 cttttctcctacatttacctttttattctataacagtattataaaaataagtgaattgcattctaaattttagataaaaaattaaagcaagtgagccgagtaattgtcggcatgtctgagcatagcgagtttgccgaaattacagcgaaacattaattttttattgttaagaaatttagctagcaatgagctatttttatatacccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1810:FN1811|FN1810:FN1811:Manganese transport system membrane protein mntB:Manganese transport system ATP-binding protein mntA:<-<-:292044..292250 207 cttttctcctacatttacctttttattctataacagtattataaaaataagtgaattgcattctaaattttagataaaaaattaaagcaagtgagccgagtaattgtcggcatgtctgagcatagcgagtttgccgaaattacagcgaaacattaattttttattgttaagaaatttagctagcaatgagctatttttatatacccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttttctcctacatttacctttttattctataacagtattataaaaataagtgaattgcattctaaattttagataaaaaattaaagcaagtgagccgagtaattgtcggcatgtctgagcatagcgagtttgccgaaattacagcgaaacattaattttttattgttaagaaatttagctagcaatgagctatttttatatacccc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 104 End: 205 ....................................................................................................... M S A C L S I A S L P K L Q R N I N F L L L R N L A S N E L F L Y T .. Protein_Len: 34 Strand: - Start: 85 End: 186 .................................................................................... L L H A S Y N D A H R L M A L K G F N C R F M L K K N N L F K A L M ..................... cttttctcctacatttacctttttattctataacagtattataaaaataagtgaattgcattctaaattttagataaaaaattaaagcaagtgagccgagtaattgtcggcatgtctgagcatagcgagtttgccgaaattacagcgaaacattaattttttattgttaagaaatttagctagcaatgagctatttttatatacccc 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: 82 Start: 13 End: 42 ............ATTTACCTTTTTATTCTATAACAGTATTAT..................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 38 End: 67 .....................................TTTAGAATGCAATTCACTTATTTTTATAAT............................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttttctcctacatttacctttttattctataacagtattataaaaataagtgaattgcattctaaattttagataaaaaattaaagcaagtgagccgagtaattgtcggcatgtctgagcatagcgagtttgccgaaattacagcgaaacattaattttttattgttaagaaatttagctagcaatgagctatttttatatacccc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1810:FN1811|FN1810:FN1811:Manganese transport system membrane protein mntB:Manganese transport system ATP-binding protein mntA:<-<-:292044..292250 207 cttttctcctacatttacctttttattctataacagtattataaaaataagtgaattgcattctaaattttagataaaaaattaaagcaagtgagccgagtaattgtcggcatgtctgagcatagcgagtttgccgaaattacagcgaaacattaattttttattgttaagaaatttagctagcaatgagctatttttatatacccc Intra-Species Hit: Count: 7 Min: 1 Max: 207 Len: 207 Subject: NC_003454_FN1810_FN1811|Manganese transport system membrane protein mntB:Manganese transport system ATP-binding protein mntA|NEGATIVE:NEGATIVE|[292044,292250]|207 HSP 1 e-value: 1.0E-114 bit: 410.0 Len: 207 Query Start:1 Query End:207 Subject Strand: POSITIVE Subject Start: 1 Subject End: 207 cttttctcctacatttacctttttattctataacagtattataaaaataagtgaattgcattctaaattttagataaaaaattaaagcaagtgagccgagtaattgtcggcatgtctgagcatagcgagtttgccgaaattacagcgaaacattaattttttattgttaagaaatttagctagcaatgagctatttttatatacccc cttttctcctacatttacctttttattctataacagtattataaaaataagtgaattgcattctaaattttagataaaaaattaaagcaagtgagccgagtaattgtcggcatgtctgagcatagcgagtttgccgaaattacagcgaaacattaattttttattgttaagaaatttagctagcaatgagctatttttatatacccc Subject: NC_003454_FN2036_FN2037|DNA-directed RNA polymerase beta chain:LSU ribosomal protein L12P (L7/L12)|NEGATIVE:NEGATIVE|[546462,546858]|397 HSP 1 e-value: 4.0E-23 bit: 109.0 Len: 59 Query Start:42 Query End:100 Subject Strand: POSITIVE Subject Start: 64 Subject End: 122 .........................................taaaaataagtgaattgcattctaaattttagataaaaaattaaagcaagtgagccgag........................................................................................................... .........................................taaaaataagtgaattgcattctaaattttagatgaaaaattaaagcaagtgagccgag........................................................................................................... HSP 2 e-value: 2.0E-9 bit: 63.9 Len: 72 Query Start:128 Query End:199 Subject Strand: POSITIVE Subject Start: 158 Subject End: 228 ...............................................................................................................................agtttgccgaaattacagcgaaacattaattttttattgttaagaaatttagctagcaatgagctattttta........ ...............................................................................................................................agtttaccgaatttgcagcgaa-cattaattttttatcattaaaaaatttagctagcaataaactattttta........ Subject: NC_003454_FN0129_FN0130|Urease accessory protein ureG:ABC transporter ATP-binding protein|POSITIVE:POSITIVE|[758431,758725]|295 HSP 1 e-value: 3.0E-17 bit: 89.7 Len: 60 Query Start:41 Query End:100 Subject Strand: NEGATIVE Subject Start: 134 Subject End: 194 ........................................ataaaaataagtgaa-ttgcattctaaattttagataaaaaattaaagcaagtgagccgag........................................................................................................... ........................................ataaaaacaagtgaaattgcattctaaattttagatgaaaaattaaagcaagtgagccgag........................................................................................................... HSP 2 e-value: 5.0E-7 bit: 56.0 Len: 48 Query Start:153 Query End:200 Subject Strand: NEGATIVE Subject Start: 27 Subject End: 74 ........................................................................................................................................................ttaattttttattgttaagaaatttagctagcaatgagctatttttat....... ........................................................................................................................................................ttaatttttcagtgttaaaaaatttagctagcaatgaactgtttttat....... Subject: NC_003454_FN2005_FN2006|Cobalt transport ATP-binding protein cbiO:Cobalt transport protein cbiQ|POSITIVE:POSITIVE|[506037,506218]|182 HSP 1 e-value: 5.0E-16 bit: 85.7 Len: 58 Query Start:43 Query End:100 Subject Strand: NEGATIVE Subject Start: 93 Subject End: 151 ..........................................aaaaataagtgaa-ttgcattctaaattttagataaaaaattaaagcaagtgagccgag........................................................................................................... ..........................................aaaaataagtgaaattgcattctaaattttagatgaaaaattaaagcaaatgagccgag........................................................................................................... HSP 2 e-value: 1.0E-7 bit: 58.0 Len: 37 Query Start:153 Query End:189 Subject Strand: NEGATIVE Subject Start: 5 Subject End: 41 ........................................................................................................................................................ttaattttttattgttaagaaatttagctagcaatga.................. ........................................................................................................................................................ttaatttttcatcgttaagaaatttagctagcaatga.................. Subject: NC_003454_FN1217_FN1218|Holliday junction DNA helicase ruvB:hypothetical protein|NEGATIVE:NEGATIVE|[1877688,1877901]|214 HSP 1 e-value: 8.0E-15 bit: 81.8 Len: 52 Query Start:43 Query End:94 Subject Strand: POSITIVE Subject Start: 49 Subject End: 101 ..........................................aaaaataagtgaa-ttgcattctaaattttagataaaaaattaaagcaagtga................................................................................................................. ..........................................aaaaataagtgaaattgcattctaaattttagataaaaaattaaagtaagtga................................................................................................................. HSP 2 e-value: 3.0E-8 bit: 60.0 Len: 50 Query Start:149 Query End:198 Subject Strand: POSITIVE Subject Start: 155 Subject End: 204 ....................................................................................................................................................aacattaattttttattgttaagaaatttagctagcaatgagctattttt......... ....................................................................................................................................................aacattaattttccatcattaagaaatttagctagcaatgaactattttt......... Subject: NC_003454_FN0046_FN0047|3-dehydroquinate dehydratase:Exodeoxyribonuclease III|POSITIVE:POSITIVE|[684326,684566]|241 HSP 1 e-value: 3.0E-11 bit: 69.9 Len: 58 Query Start:43 Query End:100 Subject Strand: NEGATIVE Subject Start: 141 Subject End: 199 ..........................................aaaaataagtgaa-ttgcattctaaattttagataaaaaattaaagcaagtgagccgag........................................................................................................... ..........................................aaaaataagtgaaattgtattctaaattttagatgaaaaattgaagcaaatgagccgag........................................................................................................... HSP 2 e-value: 2.0E-9 bit: 63.9 Len: 44 Query Start:155 Query End:198 Subject Strand: NEGATIVE Subject Start: 37 Subject End: 80 ..........................................................................................................................................................aattttttattgttaagaaatttagctagcaatgagctattttt......... ..........................................................................................................................................................aatttttcagtgttaagaaatttagctagcaatgaactattttt......... Subject: NC_003454_FN0069_FN0070|glycyl-tRNA synthetase alpha subunit:Glycyl-tRNA synthetase beta chain|POSITIVE:POSITIVE|[708822,709041]|220 HSP 1 e-value: 1.0E-7 bit: 58.0 Len: 161 Query Start:43 Query End:203 Subject Strand: NEGATIVE Subject Start: 8 Subject End: 168 ..........................................aaaaataagtgaattgcattctaaattttagataaaaaattaaagcaagtgagccgagtaattgtcggcatgtctgagcatagcgagtttgccgaaattacagcgaaacattaattttttattgttaagaaatttagctagcaatgagctatttttatata.... ..........................................aaaaataagtgagttacattccagattttaaataaaaaatcaaatagagtgagccgagcaaatctcgctgtgtctgagtgaaacgagtttagcgaatttgcagcaaactcttgattttttattgttaagaaatctggctagtaacgaactatttttatata.... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUCUCCUACAUUUACCUUUUUAUUCUAUAACAGUAUUAUAAAAAUAAGUGAAUUGCAUUCUAAAUUUUAGAUAAAAAAUUAAAGCAAGUGAGCCGAGUAAUUGUCGGCAUGUCUGAGCAUAGCGAGUUUGCCGAAAUUACAGCGAAACAUUAAUUUUUUAUUGUUAAGAAAUUUAGCUAGCAAUGAGCUAUUUUUAUAUACCCC ...................................((((.(((((((((.((..(((((...(((((((((.(((((((((((((.((......))...((((((.((((((...((..((...)).))..)))))))))))).........))))))))))))).....)))))))))...)))))..)))))))))))))))... (-46.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGGUAUAUAAAAAUAGCUCAUUGCUAGCUAAAUUUCUUAACAAUAAAAAAUUAAUGUUUCGCUGUAAUUUCGGCAAACUCGCUAUGCUCAGACAUGCCGACAAUUACUCGGCUCACUUGCUUUAAUUUUUUAUCUAAAAUUUAGAAUGCAAUUCACUUAUUUUUAUAAUACUGUUAUAGAAUAAAAAGGUAAAUGUAGGAGAAAAG ..(((((((((((((((...(((((...((((((((.......((((((((((((.((...(((((((((((((((...((..........))..)))))).))))))..)))......)).))))))))))))...))))))))...)))))....)))))))))).))))).................................. (-41.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 996 140 91 231 182 NC_003454:FN1810|5end_Manganese_transport_system_membrane_protein_mntB_291953..292183_NEGATIVE 701 100 51 213 164 NC_003454:FN2036|5end_DNA-directed_RNA_polymerase_beta_chain_546371..546601_NEGATIVE 641 100 51 181 131 NC_003454:FN2006|5end_Cobalt_transport_protein_cbiQ_506079..506309_POSITIVE 580 100 51 198 148 NC_003454:FN1217|5end_Holliday_junction_DNA_helicase_ruvB_1877597..1877827_NEGATIVE 549 130 85 229 177 NC_003454:FN0047|5end_Exodeoxyribonuclease_III_684427..684657_POSITIVE 508 138 91 229 174 NC_003454:FN1822|5end_Flavodoxin_311148..311378_POSITIVE 508 138 91 112 57 NC_003454:FN1821|5end_Hypothetical_cytosolic_protein_311031..311261_POSITIVE 494 198 156 103 61 NC_003454:FN0797|5end_hypothetical_protein_1455799..1456029_NEGATIVE 464 100 51 201 152 NC_003454:FN0070|5end_Glycyl-tRNA_synthetase_beta_chain_708902..709132_POSITIVE 453 100 51 181 132 NC_003454:FN2095|5end_General_secretion_pathway_protein_E_606080..606310_NEGATIVE 447 129 81 231 176 NC_003454:FN0392|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1029624..1029854_POSITIVE 416 75 33 228 184 NC_003454:FN0130|5end_ABC_transporter_ATP-binding_protein_758586..758816_POSITIVE 404 100 51 189 140 NC_003454:FN0906|5end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+]_1565131..1565361_NEGATIVE 387 86 41 221 176 NC_003454:FN0484|5end_Lipase_1129470..1129700_POSITIVE 383 100 51 213 164 NC_003454:FN0117|5end_O6-methylguanine-DNA_methyltransferase_750338..750568_POSITIVE 376 120 72 220 173 NC_003454:FN1819|5end_Export_ABC_transporter_307519..307749_POSITIVE 368 100 51 199 152 NC_003454:FN1486|5end_Integral_membrane_protein_with_CBS_domains_2169299..2169529_NEGATIVE 366 96 53 231 188 NC_003454:FN0358|5end_ATP_synthase_subunit_B_989674..989904_NEGATIVE 361 110 61 229 180 NC_003454:FN1459|5end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase_2141360..2141590_NEGATIVE 354 99 51 192 144 NC_003454:FN0085|5end_Ethanolamine_utilization_cobalamin_adenosyltransferase_723270..723500_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 562 100 51 128 78 NC_003454:FN0797|3end_hypothetical_protein_1455668..1455818_NEGATIVE 548 189 143 86 41 NC_003454:FN2005|3end_Cobalt_transport_ATP-binding_protein_cbiO_505976..506126_POSITIVE 541 198 151 80 33 NC_003454:FN1218|3end_hypothetical_protein_1877812..1877962_NEGATIVE 503 198 153 54 9 NC_003454:FN0046|3end_3-dehydroquinate_dehydratase_684265..684415_POSITIVE 477 189 143 53 8 NC_003454:FN0129|3end_Urease_accessory_protein_ureG_758370..758520_POSITIVE 439 170 125 52 7 NC_003454:FN0989|3end_phosphoribosylaminoimidazole_carboxylase_catalytic_subunit_1641194..1641344_NEGATIVE 417 200 156 80 36 NC_003454:FN0069|3end_glycyl-tRNA_synthetase_alpha_subunit_708761..708911_POSITIVE 409 180 132 67 19 NC_003454:FN0084|3end_Acetaldehyde_dehydrogenase_[acetylating]_723094..723244_POSITIVE 399 198 156 53 11 NC_003454:FN1826|3end_Protease_314654..314804_NEGATIVE 390 170 123 54 7 NC_003454:FN1461|3end_Histidinol-phosphatase_2141603..2141753_NEGATIVE 379 200 153 94 47 NC_003454:FN0391|3end_Hydrolase_(HAD_superfamily)_1029496..1029646_POSITIVE 379 200 153 79 32 NC_003454:FN1820|3end_Export_ABC_transporter_311016..311166_POSITIVE 349 170 121 57 10 NC_003454:FN0170|3end_GTP-binding_protein_796613..796763_POSITIVE 332 199 153 93 47 NC_003454:FN2096|3end_hypothetical_protein_606267..606417_NEGATIVE 328 200 153 86 39 NC_003454:FN1487|3end_hypothetical_protein_2169559..2169709_NEGATIVE 323 200 153 86 39 NC_003454:FN0483|3end_Uracil_phosphoribosyltransferase_1129301..1129451_POSITIVE 321 189 143 73 27 NC_003454:FN1836|3end_Tetratricopeptide_repeat_family_protein_323904..324054_NEGATIVE 311 86 41 150 105 NC_003454:FN1821|3end_Hypothetical_cytosolic_protein_311209..311359_POSITIVE 310 198 158 54 14 NC_003454:FN0359|3end_ATP_synthase_gamma_chain,_sodium_ion_specific_989995..990145_NEGATIVE 294 54 11 67 20 NC_003454:FN1925|3end_Arsenical_pump_membrane_protein_423061..423211_NEGATIVE