Origin IGS: aaaatattacaaagaaaaataagagagttacattccagattttaggataaaaattaaatagaatgagccaagcaaatttcactgtgtttgaatgaagtgagtttagtgaatttgcagtgaatttttaatttttatctgttaagaaatctggctagtaatgaattatttttctataatagcttataataaaggaagttt .........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 aaacttcctttattataagctattatagaaaaataattcattactagccagatttcttaacagataaaaattaaaaattcactgcaaattcactaaactcacttcattcaaacacagtgaaatttgcttggctcattctatttaatttttatcctaaaatctggaatgtaactctcttatttttctttgtaatatttt Mask Tandem Repeat Region ================================================ aaaatattacaaagaaaaataagagagttacattccagattttaggataaaaattaaatagaatgagccaagcaaatttcactgtgtttgaatgaagtgagtttagtgaatttgcagtgaatttttaatttttatctgttaagaaatctggctagtaatgaattatttttctataatagcttataataaaggaagttt Find is-nt database================================================ Query_seq: FN0713:FN0714|FN0713:FN0714:Chromate transport protein:NADH oxidase:->->:1372004..1372201 198 aaaatattacaaagaaaaataagagagttacattccagattttaggataaaaattaaatagaatgagccaagcaaatttcactgtgtttgaatgaagtgagtttagtgaatttgcagtgaatttttaatttttatctgttaagaaatctggctagtaatgaattatttttctataatagcttataataaaggaagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0713:FN0714|FN0713:FN0714:Chromate transport protein:NADH oxidase:->->:1372004..1372201 198 aaaatattacaaagaaaaataagagagttacattccagattttaggataaaaattaaatagaatgagccaagcaaatttcactgtgtttgaatgaagtgagtttagtgaatttgcagtgaatttttaatttttatctgttaagaaatctggctagtaatgaattatttttctataatagcttataataaaggaagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0713:FN0714|FN0713:FN0714:Chromate transport protein:NADH oxidase:->->:1372004..1372201 198 aaaatattacaaagaaaaataagagagttacattccagattttaggataaaaattaaatagaatgagccaagcaaatttcactgtgtttgaatgaagtgagtttagtgaatttgcagtgaatttttaatttttatctgttaagaaatctggctagtaatgaattatttttctataatagcttataataaaggaagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaatattacaaagaaaaataagagagttacattccagattttaggataaaaattaaatagaatgagccaagcaaatttcactgtgtttgaatgaagtgagtttagtgaatttgcagtgaatttttaatttttatctgttaagaaatctggctagtaatgaattatttttctataatagcttataataaaggaagttt Predict ORF larger than 30AA ================================================ aaaatattacaaagaaaaataagagagttacattccagattttaggataaaaattaaatagaatgagccaagcaaatttcactgtgtttgaatgaagtgagtttagtgaatttgcagtgaatttttaatttttatctgttaagaaatctggctagtaatgaattatttttctataatagcttataataaaggaagttt 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================================================ aaaatattacaaagaaaaataagagagttacattccagattttaggataaaaattaaatagaatgagccaagcaaatttcactgtgtttgaatgaagtgagtttagtgaatttgcagtgaatttttaatttttatctgttaagaaatctggctagtaatgaattatttttctataatagcttataataaaggaagttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0713:FN0714|FN0713:FN0714:Chromate transport protein:NADH oxidase:->->:1372004..1372201 198 aaaatattacaaagaaaaataagagagttacattccagattttaggataaaaattaaatagaatgagccaagcaaatttcactgtgtttgaatgaagtgagtttagtgaatttgcagtgaatttttaatttttatctgttaagaaatctggctagtaatgaattatttttctataatagcttataataaaggaagttt Intra-Species Hit: Count: 13 Min: 1 Max: 198 Len: 198 Subject: NC_003454_FN0713_FN0714|Chromate transport protein:NADH oxidase|POSITIVE:POSITIVE|[1372004,1372201]|198 HSP 1 e-value: 1.0E-108 bit: 392.0 Len: 198 Query Start:1 Query End:198 Subject Strand: POSITIVE Subject Start: 1 Subject End: 198 aaaatattacaaagaaaaataagagagttacattccagattttaggataaaaattaaatagaatgagccaagcaaatttcactgtgtttgaatgaagtgagtttagtgaatttgcagtgaatttttaatttttatctgttaagaaatctggctagtaatgaattatttttctataatagcttataataaaggaagttt aaaatattacaaagaaaaataagagagttacattccagattttaggataaaaattaaatagaatgagccaagcaaatttcactgtgtttgaatgaagtgagtttagtgaatttgcagtgaatttttaatttttatctgttaagaaatctggctagtaatgaattatttttctataatagcttataataaaggaagttt Subject: NC_003454_FN0483_FN0484|Uracil phosphoribosyltransferase:Lipase|POSITIVE:POSITIVE|[1129 362,1129609]|248 HSP 1 e-value: 2.0E-52 bit: 206.0 Len: 156 Query Start:15 Query End:170 Subject Strand: NEGATIVE Subject Start: 7 Subject End: 162 ..............aaaaataagagagttacattccagattttaggataaaaattaaatagaatgagccaagcaaatttcactgtgtttgaatgaagtgagtttagtgaatttgcagtgaatttttaatttttatctgttaagaaatctggctagtaatgaattattttt............................ ..............aaaaataagcgaattacattccaaattttaggataaaaattaaatagaatgagccgagcaaatctcactgtgtttgaacgaagtgagtttagcgaatttgcagcgaattcttaatttttatccgttaggaaatctggctagtaatgagctattttt............................ Subject: NC_003454_FN2095_FN2096|General secretion pathway protein E:hypothetical protein|NEGATIVE:NEGATIVE|[606171,606356]|186 HSP 1 e-value: 1.0E-47 bit: 190.0 Len: 148 Query Start:15 Query End:162 Subject Strand: POSITIVE Subject Start: 33 Subject End: 180 ..............aaaaataagagagttacattccagattttaggataaaaattaaatagaatgagccaagcaaatttcactgtgtttgaatgaagtgagtttagtgaatttgcagtgaatttttaatttttatctgttaagaaatctggctagtaatgaa.................................... ..............aaaaataagtgaattacattccagattctagaataaaaattaaatagaatgagccgagcaaatctcagtgtgtctgaacgaagtgagtttactgaatttgcagcgaattcttaatttttatctgttaagaaatctggctagtgatgaa.................................... Subject: NC_003454_FN0906_FN0907|Glycerol-3-phosphate dehydrogenase [NAD(P)+]:Ribosomal RNA small subunit methyltransferase C|NEGATIVE:NEGATIVE|[1565222,1565413]|192 HSP 1 e-value: 1.0E-35 bit: 151.0 Len: 152 Query Start:16 Query End:167 Subject Strand: POSITIVE Subject Start: 42 Subject End: 192 ...............aaaataagagagttacattccagattttaggataaaaattaaatagaatgagccaagcaaatttcactgtgtttgaatgaagtgagtttagtgaatttgcagtgaatttttaatttttatctgttaagaaatctggctagtaatgaattatt............................... ...............aaaataagtgagttacattccaaattttaagataaaaattaaatagaatgagccaagcaaatcttgctgtgtttgagtgaaacgagtttag-caagtttcagtgaattcttaatttttatctgttaagaaatttgactagtaacgaactatt............................... Subject: NC_003454_FN0391_FN0392|Hydrolase (HAD superfamily):Oxygen-independent coproporphyrinogen III oxidase|POSITIVE:POSITIVE|[1029557,1029763]|207 HSP 1 e-value: 1.0E-25 bit: 117.0 Len: 63 Query Start:15 Query End:77 Subject Strand: NEGATIVE Subject Start: 99 Subject End: 161 ..............aaaaataagagagttacattccagattttaggataaaaattaaatagaatgagccaagcaaat......................................................................................................................... ..............aaaaataagagagttacattccagattttaggataaaaattaaatagaatgagccgagcaaat......................................................................................................................... HSP 2 e-value: 1.0E-10 bit: 67.9 Len: 62 Query Start:107 Query End:168 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 62 ..........................................................................................................tgaatttgcagtgaatttttaatttttatctgttaagaaatctggctagtaatgaattattt.............................. ..........................................................................................................tgaatttgcagcaaattcttaatttttattcgttaagaaatctggctagtaacgaactattt.............................. Subject: NC_003454_FN0069_FN0070|glycyl-tRNA synthetase alpha subunit:Glycyl-tRNA synthetase beta chain|POSITIVE:POSITIVE|[708822,709041]|220 HSP 1 e-value: 2.0E-24 bit: 113.0 Len: 161 Query Start:15 Query End:175 Subject Strand: NEGATIVE Subject Start: 8 Subject End: 168 ..............aaaaataagagagttacattccagattttaggataaaaattaaatagaatgagccaagcaaatttcactgtgtttgaatgaagtgagtttagtgaatttgcagtgaatttttaatttttatctgttaagaaatctggctagtaatgaattatttttctata....................... ..............aaaaataagtgagttacattccagattttaaataaaaaatcaaatagagtgagccgagcaaatctcgctgtgtctgagtgaaacgagtttagcgaatttgcagcaaactcttgattttttattgttaagaaatctggctagtaacgaactatttttatata....................... Subject: NC_003454_FN0084_FN0085|Acetaldehyde dehydrogenase [acetylating]:Ethanolamine utilization cobalamin adenosyltransferase|POSITIVE:POSITIVE|[723155, 723409]|255 HSP 1 e-value: 9.0E-21 bit: 101.0 Len: 55 Query Start:15 Query End:69 Subject Strand: NEGATIVE Subject Start: 157 Subject End: 211 ..............aaaaataagagagttacattccagattttaggataaaaattaaatagaatgagcc................................................................................................................................. ..............aaaaataagtgagttacattccagattttaggataaaaattaaatagaatgagcc................................................................................................................................. HSP 2 e-value: 2.0E-9 bit: 63.9 Len: 52 Query Start:119 Query End:170 Subject Strand: NEGATIVE Subject Start: 6 Subject End: 57 ......................................................................................................................gaatttttaatttttatctgttaagaaatctggctagtaatgaattattttt............................ ......................................................................................................................gaattcttaatttttatccgttaagaaatttggctagtaacgaactattttt............................ Subject: NC_003454_FN1835_FN1836|hypothetical protein:Tetratricopeptide repeat family protein|NEGATIVE:NEGATIVE|[323771,323993]|223 HSP 1 e-value: 2.0E-18 bit: 93.7 Len: 63 Query Start:15 Query End:77 Subject Strand: POSITIVE Subject Start: 52 Subject End: 114 ..............aaaaataagagagttacattccagattttaggataaaaattaaatagaatgagccaagcaaat......................................................................................................................... ..............aaaaacaagtgagttatattccagattttaggataaaaattaaatagaatgagccgagcaaat......................................................................................................................... HSP 2 e-value: 5.0E-13 bit: 75.8 Len: 50 Query Start:109 Query End:158 Subject Strand: POSITIVE Subject Start: 154 Subject End: 203 ............................................................................................................aatttgcagtgaatttttaatttttatctgttaagaaatctggctagtaa........................................ ............................................................................................................aatttgcagcgaattcttaatttttatccgttaagaaatctggctagtaa........................................ Subject: NC_003454_FN1818_FN1819|Hemolysin activator protein precursor:Export ABC transporter|NEGATIVE:POSITIVE|[307046,307658]|613 HSP 1 e-value: 2.0E-18 bit: 93.7 Len: 63 Query Start:15 Query End:77 Subject Strand: NEGATIVE Subject Start: 500 Subject End: 562 ..............aaaaataagagagttacattccagattttaggataaaaattaaatagaatgagccaagcaaat......................................................................................................................... ..............aaaaataagggagttacattccagattttaagataaaaattaaatagaatgaaccgagcaaat......................................................................................................................... HSP 2 e-value: 1.0E-16 bit: 87.7 Len: 64 Query Start:107 Query End:170 Subject Strand: NEGATIVE Subject Start: 400 Subject End: 463 ..........................................................................................................tgaatttgcagtgaatttttaatttttatctgttaagaaatctggctagtaatgaattattttt............................ ..........................................................................................................tgaatttgcagcgaattcttaatttttagctattaagaaatctggctagtaatgaactattttt............................ Subject: NC_003454_FN2005_FN2006|Cobalt transport ATP-binding protein cbiO:Cobalt transport protein cbiQ|POSITIVE:POSITIVE|[506037,506218]|182 HSP 1 e-value: 8.0E-18 bit: 91.7 Len: 114 Query Start:49 Query End:162 Subject Strand: NEGATIVE Subject Start: 4 Subject End: 116 ................................................aaaaattaaatagaatgagccaagcaaatttcactgtgtttgaatgaagtgagtttagtgaatttgcagtgaatttttaatttttatctgttaagaaatctggctagtaatgaa.................................... ................................................aaaaattaaagcaaatgagccgagcaaatctcgctgtgtttgaatgaagtgagtttagggaatttgcagcgaatgttaatttttcatc-gttaagaaatttagctagcaatgaa.................................... Subject: NC_003454_FN1808_FN1809|hypothetical protein:Iron/zinc/copper-binding protein|NEGATIVE:NEGATIVE|[289996,290269]|274 HSP 1 e-value: 3.0E-17 bit: 89.7 Len: 53 Query Start:109 Query End:161 Subject Strand: POSITIVE Subject Start: 215 Subject End: 267 ............................................................................................................aatttgcagtgaatttttaatttttatctgttaagaaatctggctagtaatga..................................... ............................................................................................................aatttgcagtgaattcttaatttttatctgttaagaaatctgactagtaatga..................................... HSP 2 e-value: 2.0E-15 bit: 83.8 Len: 82 Query Start:15 Query End:96 Subject Strand: POSITIVE Subject Start: 78 Subject End: 159 ..............aaaaataagagagttacattccagattttaggataaaaattaaatagaatgagccaagcaaatttcactgtgtttgaatgaa...................................................................................................... ..............aaaaataagtaagttacattccagattttaagataaaaattaaataaaatgaaccgagcaaatcttgctgtgtttgagtgaa...................................................................................................... Subject: NC_003454_FN1486_FN1487|Integral membrane protein with CBS domains:hypothetical protein|NEGATIVE:NEGATIVE|[2169390,2169648]|259 HSP 1 e-value: 8.0E-15 bit: 81.8 Len: 65 Query Start:28 Query End:92 Subject Strand: POSITIVE Subject Start: 64 Subject End: 128 ...........................ttacattccagattttaggataaaaattaaatagaatgagccaagcaaatttcactgtgtttgaa.......................................................................................................... ...........................ttacattctagattttagaacaaaaattaaatagaatgagccgagcaaatctcgctgtgtttgaa.......................................................................................................... HSP 2 e-value: 2.0E-6 bit: 54.0 Len: 43 Query Start:119 Query End:161 Subject Strand: POSITIVE Subject Start: 202 Subject End: 244 ......................................................................................................................gaatttttaatttttatctgttaagaaatctggctagtaatga..................................... ......................................................................................................................gaattcttaatttttattcgttaaaaaatctggctagtaatga..................................... Subject: NC_003454_FN1651_FN1652|Oligopeptide transport system permease protein oppB:Oligopeptide-binding protein oppA|NEGATIVE:NEGATIVE|[145890,146130]|241 HSP 1 e-value: 1.0E-7 bit: 58.0 Len: 33 Query Start:37 Query End:69 Subject Strand: NEGATIVE Subject Start: 136 Subject End: 168 ....................................agattttaggataaaaattaaatagaatgagcc................................................................................................................................. ....................................agattttaggatgaaaattaaatagaatgagcc................................................................................................................................. HSP 2 e-value: 7.0E-6 bit: 52.0 Len: 42 Query Start:108 Query End:149 Subject Strand: NEGATIVE Subject Start: 56 Subject End: 97 ...........................................................................................................gaatttgcagtgaatttttaatttttatctgttaagaaatct................................................. ...........................................................................................................gaatttacagcgaattcttaatttttatccgttaagaaatct................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUAUUACAAAGAAAAAUAAGAGAGUUACAUUCCAGAUUUUAGGAUAAAAAUUAAAUAGAAUGAGCCAAGCAAAUUUCACUGUGUUUGAAUGAAGUGAGUUUAGUGAAUUUGCAGUGAAUUUUUAAUUUUUAUCUGUUAAGAAAUCUGGCUAGUAAUGAAUUAUUUUUCUAUAAUAGCUUAUAAUAAAGGAAGUUU ....(((((...((((((((((....(((((...(((((((((.(((((((((((((...((((..((...(((((((.(((((..(((.........)))..)))))))))))).))..))))))))))))))))).....)))))))))...)))))...)))))))))).))))).................... (-47.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACUUCCUUUAUUAUAAGCUAUUAUAGAAAAAUAAUUCAUUACUAGCCAGAUUUCUUAACAGAUAAAAAUUAAAAAUUCACUGCAAAUUCACUAAACUCACUUCAUUCAAACACAGUGAAAUUUGCUUGGCUCAUUCUAUUUAAUUUUUAUCCUAAAAUCUGGAAUGUAACUCUCUUAUUUUUCUUUGUAAUAUUUU ..........((((((((........((((((((((....((((...((((((((.......(((((((((((((((((((..(((((((((((.....................)))).))))))).)))...)))...)))))))))))))...))))))))...)))).....)))))))))))))))))).... (-37.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 728 69 21 192 144 NC_003454:FN0392|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1029624..1029854_POSITIVE 687 120 71 229 180 NC_003454:FN2006|5end_Cobalt_transport_protein_cbiQ_506079..506309_POSITIVE 670 69 21 210 162 NC_003454:FN0117|5end_O6-methylguanine-DNA_methyltransferase_750338..750568_POSITIVE 670 69 21 190 142 NC_003454:FN0085|5end_Ethanolamine_utilization_cobalamin_adenosyltransferase_723270..723500_POSITIVE 652 80 31 189 140 NC_003454:FN2095|5end_General_secretion_pathway_protein_E_606080..606310_NEGATIVE 649 79 31 196 148 NC_003454:FN0906|5end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+]_1565131..1565361_NEGATIVE 643 105 64 231 190 NC_003454:FN1217|5end_Holliday_junction_DNA_helicase_ruvB_1877597..1877827_NEGATIVE 625 79 32 207 160 NC_003454:FN1835|5end_hypothetical_protein_323680..323910_NEGATIVE 618 80 31 208 159 NC_003454:FN1819|5end_Export_ABC_transporter_307519..307749_POSITIVE 598 69 21 216 168 NC_003454:FN1459|5end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase_2141360..2141590_NEGATIVE 596 90 41 217 168 NC_003454:FN1486|5end_Integral_membrane_protein_with_CBS_domains_2169299..2169529_NEGATIVE 589 68 21 231 184 NC_003454:FN0484|5end_Lipase_1129470..1129700_POSITIVE 574 69 21 180 132 NC_003454:FN1822|5end_Flavodoxin_311148..311378_POSITIVE 574 69 21 63 15 NC_003454:FN1821|5end_Hypothetical_cytosolic_protein_311031..311261_POSITIVE 550 69 21 223 175 NC_003454:FN1808|5end_hypothetical_protein_289905..290135_NEGATIVE 519 100 51 229 180 NC_003454:FN0070|5end_Glycyl-tRNA_synthetase_beta_chain_708902..709132_POSITIVE 445 68 22 231 185 NC_003454:FN0358|5end_ATP_synthase_subunit_B_989674..989904_NEGATIVE 437 160 111 93 44 NC_003454:FN0797|5end_hypothetical_protein_1455799..1456029_NEGATIVE 423 68 21 181 132 NC_003454:FN1614|5end_MG(2+)_chelatase_family_protein_125002..125232_NEGATIVE 422 80 37 213 170 NC_003454:FN0988|5end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_1640968..1641198_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 701 160 111 72 23 NC_003454:FN1836|3end_Tetratricopeptide_repeat_family_protein_323904..324054_NEGATIVE 679 160 111 82 33 NC_003454:FN1809|3end_Iron/zinc/copper-binding_protein_290180..290330_NEGATIVE 673 140 91 54 5 NC_003454:FN0483|3end_Uracil_phosphoribosyltransferase_1129301..1129451_POSITIVE 658 160 111 82 33 NC_003454:FN2096|3end_hypothetical_protein_606267..606417_NEGATIVE 609 160 111 72 23 NC_003454:FN1461|3end_Histidinol-phosphatase_2141603..2141753_NEGATIVE 598 120 75 46 1 NC_003454:FN2005|3end_Cobalt_transport_ATP-binding_protein_cbiO_505976..506126_POSITIVE 590 160 112 75 27 NC_003454:FN0084|3end_Acetaldehyde_dehydrogenase_[acetylating]_723094..723244_POSITIVE 561 160 111 82 33 NC_003454:FN0391|3end_Hydrolase_(HAD_superfamily)_1029496..1029646_POSITIVE 538 160 111 67 18 NC_003454:FN1820|3end_Export_ABC_transporter_311016..311166_POSITIVE 536 160 115 83 38 NC_003454:FN0907|3end_Ribosomal_RNA_small_subunit_methyltransferase_C_1565324..1565474_NEGATIVE 504 160 111 68 19 NC_003454:FN0069|3end_glycyl-tRNA_synthetase_alpha_subunit_708761..708911_POSITIVE 489 136 91 47 2 NC_003454:FN1218|3end_hypothetical_protein_1877812..1877962_NEGATIVE 486 59 15 151 107 NC_003454:FN1821|3end_Hypothetical_cytosolic_protein_311209..311359_POSITIVE 477 90 41 146 97 NC_003454:FN0797|3end_hypothetical_protein_1455668..1455818_NEGATIVE 473 160 117 74 31 NC_003454:FN1487|3end_hypothetical_protein_2169559..2169709_NEGATIVE 453 170 122 48 1 NC_003454:FN0116|3end_Chaperone_protein_dnaK_750156..750306_POSITIVE 410 158 111 73 26 NC_003454:FN0170|3end_GTP-binding_protein_796613..796763_POSITIVE 386 179 137 67 21 NC_003454:FN0046|3end_3-dehydroquinate_dehydratase_684265..684415_POSITIVE 384 160 111 52 4 NC_003454:FN0129|3end_Urease_accessory_protein_ureG_758370..758520_POSITIVE 378 160 112 71 23 NC_003454:FN1811|3end_Manganese_transport_system_ATP-binding_protein_mntA_292161..292311_NEGATIVE