Origin IGS: atgttacttatcagacaattattttgcttattattcttttaattttagtatataggactcctcttttaagctttttttttagagaatttttatgaaataagcattggaaatactagattaaaattaaaaaatattcaaaaaaagattaaaaaattagaagaaaatgggatactagaaaaagatctagaagatattgataaaatcaggagaaataataaagaaaaggaagatgaaatttta .........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 taaaatttcatcttccttttctttattatttctcctgattttatcaatatcttctagatctttttctagtatcccattttcttctaattttttaatctttttttgaatattttttaattttaatctagtatttccaatgcttatttcataaaaattctctaaaaaaaaagcttaaaagaggagtcctatatactaaaattaaaagaataataagcaaaataattgtctgataagtaacat Mask Tandem Repeat Region ================================================ atgttacttatcagacaattattttgcttattattcttttaattttagtatataggactcctcttttaagctttttttttagagaatttttatgaaataagcattggaaatactagattaaaattaaaaaatattcaaaaaaagattaaaaaattagaagaaaatgggatactagaaaaagatctagaagatattgataaaatcaggagaaataataaagaaaaggaagatgaaatttta Find is-nt database================================================ Query_seq: FN0844:FN0845|FN0844:FN0845:hypothetical protein:hypothetical protein:->->:1503835..1504074 240 atgttacttatcagacaattattttgcttattattcttttaattttagtatataggactcctcttttaagctttttttttagagaatttttatgaaataagcattggaaatactagattaaaattaaaaaatattcaaaaaaagattaaaaaattagaagaaaatgggatactagaaaaagatctagaagatattgataaaatcaggagaaataataaagaaaaggaagatgaaatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0844:FN0845|FN0844:FN0845:hypothetical protein:hypothetical protein:->->:1503835..1504074 240 atgttacttatcagacaattattttgcttattattcttttaattttagtatataggactcctcttttaagctttttttttagagaatttttatgaaataagcattggaaatactagattaaaattaaaaaatattcaaaaaaagattaaaaaattagaagaaaatgggatactagaaaaagatctagaagatattgataaaatcaggagaaataataaagaaaaggaagatgaaatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0844:FN0845|FN0844:FN0845:hypothetical protein:hypothetical protein:->->:1503835..1504074 240 atgttacttatcagacaattattttgcttattattcttttaattttagtatataggactcctcttttaagctttttttttagagaatttttatgaaataagcattggaaatactagattaaaattaaaaaatattcaaaaaaagattaaaaaattagaagaaaatgggatactagaaaaagatctagaagatattgataaaatcaggagaaataataaagaaaaggaagatgaaatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atgttacttatcagacaattattttgcttattattcttttaattttagtatataggactcctcttttaagctttttttttagagaatttttatgaaataagcattggaaatactagattaaaattaaaaaatattcaaaaaaagattaaaaaattagaagaaaatgggatactagaaaaagatctagaagatattgataaaatcaggagaaataataaagaaaaggaagatgaaatttta Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 97 End: 240 ................................................................................................ M S I G N T R L K L K N I Q K K I K K L E E N G I L E K D L E D I D K I R R N N K E K E D E I L Protein_Len: 33 Strand: - Start: 138 End: 236 ......................................................................................................................................... F F I L F N S S F P I S S F S R S S I S L I L L F L L S F S S S M .... atgttacttatcagacaattattttgcttattattcttttaattttagtatataggactcctcttttaagctttttttttagagaatttttatgaaataagcattggaaatactagattaaaattaaaaaatattcaaaaaaagattaaaaaattagaagaaaatgggatactagaaaaagatctagaagatattgataaaatcaggagaaataataaagaaaaggaagatgaaatttta 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: 110 End: 139 .............................................................................................................TTTGAATATTTTTTAATTTTAATCTAGTAT..................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atgttacttatcagacaattattttgcttattattcttttaattttagtatataggactcctcttttaagctttttttttagagaatttttatgaaataagcattggaaatactagattaaaattaaaaaatattcaaaaaaagattaaaaaattagaagaaaatgggatactagaaaaagatctagaagatattgataaaatcaggagaaataataaagaaaaggaagatgaaatttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0844:FN0845|FN0844:FN0845:hypothetical protein:hypothetical protein:->->:1503835..1504074 240 atgttacttatcagacaattattttgcttattattcttttaattttagtatataggactcctcttttaagctttttttttagagaatttttatgaaataagcattggaaatactagattaaaattaaaaaatattcaaaaaaagattaaaaaattagaagaaaatgggatactagaaaaagatctagaagatattgataaaatcaggagaaataataaagaaaaggaagatgaaatttta Intra-Species Hit: Count: 1 Min: 1 Max: 240 Len: 240 Subject: NC_003454_FN0844_FN0845|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1503835,1504074]|240 HSP 1 e-value: 4.0E-45 bit: 182.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 atgttacttatcagacaattattttgcttattattcttttaattttagtatataggactcctcttttaagcnnnnnnnnnagagaatttttatgaaataagcattggaaatactagatt......................................................................................................................... atgttacttatcagacaattattttgcttattattcttttaattttagtatataggactcctcttttaagctttttttttagagaatttttatgaaataagcattggaaatactagatt......................................................................................................................... HSP 2 e-value: 6.0E-13 bit: 75.8 Len: 38 Query Start:203 Query End:240 Subject Strand: POSITIVE Subject Start: 203 Subject End: 240 ..........................................................................................................................................................................................................tcaggagaaataataaagaaaaggaagatgaaatttta ..........................................................................................................................................................................................................tcaggagaaataataaagaaaaggaagatgaaatttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGUUACUUAUCAGACAAUUAUUUUGCUUAUUAUUCUUUUAAUUUUAGUAUAUAGGACUCCUCUUUUAAGCUUUUUUUUUAGAGAAUUUUUAUGAAAUAAGCAUUGGAAAUACUAGAUUAAAAUUAAAAAAUAUUCAAAAAAAGAUUAAAAAAUUAGAAGAAAAUGGGAUACUAGAAAAAGAUCUAGAAGAUAUUGAUAAAAUCAGGAGAAAUAAUAAAGAAAAGGAAGAUGAAAUUUUA .((((........)))).(((((((.((((((((((((((.((((((..((((.....((((.((((...((..((((((((....(((((.((((.......((((.....)))).(((....)))......)))).)))))..))))))))..))...)))).))))..(((((......)))))...))))...)))))).))))).)))))))......)).)))))))....... (-33.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUUUCAUCUUCCUUUUCUUUAUUAUUUCUCCUGAUUUUAUCAAUAUCUUCUAGAUCUUUUUCUAGUAUCCCAUUUUCUUCUAAUUUUUUAAUCUUUUUUUGAAUAUUUUUUAAUUUUAAUCUAGUAUUUCCAAUGCUUAUUUCAUAAAAAUUCUCUAAAAAAAAAGCUUAAAAGAGGAGUCCUAUAUACUAAAAUUAAAAGAAUAAUAAGCAAAAUAAUUGUCUGAUAAGUAACAU ................((((.(((((((((.((..((((((((..........(((((......))))).........(((((((.....(((((.((((((((((..((((((.......(((..(((((.....))))).)))....))))))..))...)))))))).))))))))))))..........))))))))..))))))))))).))))..................... (-29.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 108 64 132 86 NC_003454:FN0073|5end_Dihydropteroate_synthase_712520..712750_POSITIVE 275 96 51 154 98 NC_003454:FN1634|5end_LSU_ribosomal_protein_L24P_136179..136409_NEGATIVE 244 83 43 109 68 NC_003454:FN0268|5end_DNA_repair_protein_recN_894330..894560_POSITIVE 238 49 1 112 53 NC_003454:FN0981|5end_phosphoribosylamine--glycine_ligase_1634120..1634350_NEGATIVE 232 91 53 188 139 NC_003454:FN0940|5end_hypothetical_protein_1593508..1593738_NEGATIVE 221 226 185 68 32 NC_003454:FN2056|5end_hypothetical_protein_565317..565547_NEGATIVE 218 90 50 214 171 NC_003454:FN0655|5end_hypothetical_protein_1313372..1313602_POSITIVE 215 104 61 144 101 NC_003454:FN0889|5end_Dihydrolipoamide_acyltransferase_1551393..1551623_NEGATIVE 206 77 33 67 16 NC_003454:FN1143|5end_glucosamine-6-phosphate_deaminase_1792461..1792691_POSITIVE 202 67 21 111 55 NC_003454:FN2038|5end_LSU_ribosomal_protein_L10P_547696..547926_NEGATIVE 202 90 46 209 170 NC_003454:FN1953|5end_Na(+)-linked_D-alanine_glycine_permease_459499..459729_NEGATIVE 201 39 4 193 158 NC_003454:FN0461|5end_Probable_sigma(54)_modulation_protein_1106522..1106752_POSITIVE 200 210 164 225 188 NC_003454:FN1413|5end_translation_initiation_factor_IF-2B_subunit_alpha_2074270..2074500_NEGATIVE 199 186 153 63 24 NC_003454:FN2104|5end_hypothetical_protein_614237..614467_POSITIVE 198 79 34 115 70 NC_003454:FN1417|5end_L-fuculose_phosphate_aldolase_2078272..2078502_POSITIVE 196 66 22 102 59 NC_003454:FN1411|5end_Threonine_dehydratase_2070730..2070960_POSITIVE 194 190 155 84 43 NC_003454:FN1251|5end_High-affinity_iron_permease_1908008..1908238_POSITIVE 194 76 40 136 101 NC_003454:FN0666|5end_hypothetical_protein_1321599..1321829_POSITIVE 194 89 45 131 85 NC_003454:FN1638|5end_50S_ribosomal_protein_L16_137501..137731_NEGATIVE 194 68 22 181 126 NC_003454:FN1628|5end_LSU_ribosomal_protein_L18P_133948..134178_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 108 64 151 105 NC_003454:FN0072|3end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_712619..712769_POSITIVE 275 96 51 129 73 NC_003454:FN1635|3end_LSU_ribosomal_protein_L14P_136204..136354_NEGATIVE 244 83 43 130 89 NC_003454:FN0267|3end_ATP-NAD_kinase_894431..894581_POSITIVE 238 49 1 95 36 NC_003454:FN0982|3end_bifunctional_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1634137..1634287_NEGATIVE 221 226 185 99 63 NC_003454:FN2057|3end_hypothetical_protein_565286..565436_NEGATIVE 218 90 50 145 102 NC_003454:FN0654|3end_phosphoglycerate_kinase_1313383..1313533_POSITIVE 215 104 61 79 36 NC_003454:FN0890|3end_Thiamin_pyrophosphokinase_1551458..1551608_NEGATIVE 203 80 34 150 102 NC_003454:FN1478|3end_hypothetical_protein_2160328..2160478_NEGATIVE 201 61 22 138 89 NC_003454:FN0964|3end_Precorrin-8W_decarboxylase_1617737..1617887_NEGATIVE 201 39 4 121 86 NC_003454:FN0460|3end_delta-aminolevulinic_acid_dehydratase_1106530..1106680_POSITIVE 198 79 34 106 61 NC_003454:FN1416|3end_AMINOTRANSFERASE_CLASS-I_2078343..2078493_POSITIVE 194 76 40 83 48 NC_003454:FN0665|3end_N-acetylmuramoyl-L-alanine_amidase_1321626..1321776_POSITIVE 194 89 45 128 82 NC_003454:FN1639|3end_SSU_ribosomal_protein_S3P_137504..137654_NEGATIVE 193 62 22 133 80 NC_003454:FN0202|3end_Glutaconate_CoA-transferase_subunit_A_828825..828975_POSITIVE 191 70 25 141 103 NC_003454:FN0941|3end_Gamma-glutamyltranspeptidase_1593527..1593677_NEGATIVE 190 197 153 135 100 NC_003454:FN0806|3end_SpoIID_homolog_1465587..1465737_NEGATIVE 190 69 34 86 54 NC_003454:FN1786|3end_ADP-heptose_synthase_267821..267971_POSITIVE 189 54 21 89 54 NC_003454:FN0861|3end_hypothetical_protein_1521738..1521888_NEGATIVE 189 63 37 30 6 NC_003454:FN0238|3end_hypothetical_protein_862382..862532_NEGATIVE 187 83 58 124 100 NC_003454:FN1443|3end_Transposase_2111009..2111159_NEGATIVE