Origin IGS: cttttatcaccttgtataattataacataatttaacgacaaattttgacatcaaaaaaatttttttaaaaaaataaaaatatttacttttaaaatttctgtaaatattatataataaaatataagaaaattgtacaaaattttataattattgaaatgaatttaaaaaaattttaaaataaattatataaataaagaaataggttgaaattcttgacattatataacagatgtaatatacttttaaaaggggaattaacccaaacaaatattga .........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 tcaatatttgtttgggttaattccccttttaaaagtatattacatctgttatataatgtcaagaatttcaacctatttctttatttatataatttattttaaaatttttttaaattcatttcaataattataaaattttgtacaattttcttatattttattatataatatttacagaaattttaaaagtaaatatttttatttttttaaaaaaatttttttgatgtcaaaatttgtcgttaaattatgttataattatacaaggtgataaaag Mask Tandem Repeat Region ================================================ cttttatcaccttgtataattataacataatttaacgacaaattttgacatcaaaaaaatttttttaaaaaaataaaaatatttacttttaaaatttctgtaaatattatataataaaatataagaaaattgtacaaaattttataattattgaaatgaatttaaaaaaattttaaaataaattatataaataaagaaataggttgaaattcttgacattatataacagatgtaatatacttttaaaaggggaattaacccaaacaaatattga Find is-nt database================================================ Query_seq: FN0493:FN0494|FN0493:FN0494:hypothetical protein:Short chain dehydrogenase:<-->:1138643..1138916 274 cttttatcaccttgtataattataacataatttaacgacaaattttgacatcaaaaaaatttttttaaaaaaataaaaatatttacttttaaaatttctgtaaatattatataataaaatataagaaaattgtacaaaattttataattattgaaatgaatttaaaaaaattttaaaataaattatataaataaagaaataggttgaaattcttgacattatataacagatgtaatatacttttaaaaggggaattaacccaaacaaatattga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0493:FN0494|FN0493:FN0494:hypothetical protein:Short chain dehydrogenase:<-->:1138643..1138916 274 cttttatcaccttgtataattataacataatttaacgacaaattttgacatcaaaaaaatttttttaaaaaaataaaaatatttacttttaaaatttctgtaaatattatataataaaatataagaaaattgtacaaaattttataattattgaaatgaatttaaaaaaattttaaaataaattatataaataaagaaataggttgaaattcttgacattatataacagatgtaatatacttttaaaaggggaattaacccaaacaaatattga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0493:FN0494|FN0493:FN0494:hypothetical protein:Short chain dehydrogenase:<-->:1138643..1138916 274 cttttatcaccttgtataattataacataatttaacgacaaattttgacatcaaaaaaatttttttaaaaaaataaaaatatttacttttaaaatttctgtaaatattatataataaaatataagaaaattgtacaaaattttataattattgaaatgaatttaaaaaaattttaaaataaattatataaataaagaaataggttgaaattcttgacattatataacagatgtaatatacttttaaaaggggaattaacccaaacaaatattga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttttatcaccttgtataattataacataatttaacgacaaattttgacatcaaaaaaatttttttaaaaaaataaaaatatttacttttaaaatttctgtaaatattatataataaaatataagaaaattgtacaaaattttataattattgaaatgaatttaaaaaaattttaaaataaattatataaataaagaaataggttgaaattcttgacattatataacagatgtaatatacttttaaaaggggaattaacccaaacaaatattga Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 176 End: 271 ............................................................................................................................................................................... F L N Y L Y L F L N F N K V N Y L L H L I S K F P S N V W V F M ... Protein_Len: 39 Strand: - Start: 151 End: 267 ...................................................................................................................................................... Q F S N L F I K F Y I I Y I F F Y T S I R S M I Y C I Y Y V K L L P I L G F M ....... Protein_Len: 36 Strand: - Start: 54 End: 161 ..................................................... F F K K L F I F I N V K L I E T F I I Y Y F I L F N Y L I K Y N N F H M ................................................................................................................. Protein_Len: 37 Strand: - Start: 10 End: 120 ......... R T Y N Y C L K V V F K S M L F I K K F F Y F Y K S K F N R Y I N Y L L M .......................................................................................................................................................... cttttatcaccttgtataattataacataatttaacgacaaattttgacatcaaaaaaatttttttaaaaaaataaaaatatttacttttaaaatttctgtaaatattatataataaaatataagaaaattgtacaaaattttataattattgaaatgaatttaaaaaaattttaaaataaattatataaataaagaaataggttgaaattcttgacattatataacagatgtaatatacttttaaaaggggaattaacccaaacaaatattga 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: 86 Start: 212 End: 241 ...................................................................................................................................................................................................................CTTGACATTATATAACAGATGTAATATACT................................. PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 150 End: 179 .....................................................................................................................................................ATTGAAATGAATTTAAAAAAATTTTAAAAT............................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 218 End: 247 .........................................................................................................................................................................................................................TTTAAAAGTATATTACATCTGTTATATAAT........................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 86 End: 115 .....................................................................................CTTTTAAAATTTCTGTAAATATTATATAAT............................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttttatcaccttgtataattataacataatttaacgacaaattttgacatcaaaaaaatttttttaaaaaaataaaaatatttacttttaaaatttctgtaaatattatataataaaatataagaaaattgtacaaaattttataattattgaaatgaatttaaaaaaattttaaaataaattatataaataaagaaataggttgaaattcttgacattatataacagatgtaatatacttttaaaaggggaattaacccaaacaaatattga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -3.5 Tail_Score: -5.58454 Start: 60 End: 72 Full_Region: agtaaatatttttat ttttt taa aaaaa tttttttgatgtcaa ...........................................................ttttttaaaaaaa.......................................................................................................................................................................................................... Find igs database================================================ Query_seq: FN0493:FN0494|FN0493:FN0494:hypothetical protein:Short chain dehydrogenase:<-->:1138643..1138916 274 cttttatcaccttgtataattataacataatttaacgacaaattttgacatcaaaaaaatttttttaaaaaaataaaaatatttacttttaaaatttctgtaaatattatataataaaatataagaaaattgtacaaaattttataattattgaaatgaatttaaaaaaattttaaaataaattatataaataaagaaataggttgaaattcttgacattatataacagatgtaatatacttttaaaaggggaattaacccaaacaaatattga Intra-Species Hit: Count: 1 Min: 1 Max: 274 Len: 274 Subject: NC_003454_FN0493_FN0494|hypothetical protein:Short chain dehydrogenase|NEGATIVE:POSITIVE|[1138643,1138916]|274 HSP 1 e-value: 9.0E-34 bit: 145.0 Len: 73 Query Start:202 Query End:274 Subject Strand: POSITIVE Subject Start: 202 Subject End: 274 .........................................................................................................................................................................................................ggttgaaattcttgacattatataacagatgtaatatacttttaaaaggggaattaacccaaacaaatattga .........................................................................................................................................................................................................ggttgaaattcttgacattatataacagatgtaatatacttttaaaaggggaattaacccaaacaaatattga HSP 2 e-value: 3.0E-21 bit: 103.0 Len: 52 Query Start:1 Query End:52 Subject Strand: POSITIVE Subject Start: 1 Subject End: 52 cttttatcaccttgtataattataacataatttaacgacaaattttgacatc.............................................................................................................................................................................................................................. cttttatcaccttgtataattataacataatttaacgacaaattttgacatc.............................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUAUCACCUUGUAUAAUUAUAACAUAAUUUAACGACAAAUUUUGACAUCAAAAAAAUUUUUUUAAAAAAAUAAAAAUAUUUACUUUUAAAAUUUCUGUAAAUAUUAUAUAAUAAAAUAUAAGAAAAUUGUACAAAAUUUUAUAAUUAUUGAAAUGAAUUUAAAAAAAUUUUAAAAUAAAUUAUAUAAAUAAAGAAAUAGGUUGAAAUUCUUGACAUUAUAUAACAGAUGUAAUAUACUUUUAAAAGGGGAAUUAACCCAAACAAAUAUUGA ((((((.......(((((.......((.(((((......))))).))(((((...((((((((((((((........(((((((((.............))))))))).........((((....((((((......)))))).....))))........))))))))))))))........((((((((...(((((...........)))))....))))))))..)))))..)))))...))))))(((......)))............. (-34.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAUAUUUGUUUGGGUUAAUUCCCCUUUUAAAAGUAUAUUACAUCUGUUAUAUAAUGUCAAGAAUUUCAACCUAUUUCUUUAUUUAUAUAAUUUAUUUUAAAAUUUUUUUAAAUUCAUUUCAAUAAUUAUAAAAUUUUGUACAAUUUUCUUAUAUUUUAUUAUAUAAUAUUUACAGAAAUUUUAAAAGUAAAUAUUUUUAUUUUUUUAAAAAAAUUUUUUUGAUGUCAAAAUUUGUCGUUAAAUUAUGUUAUAAUUAUACAAGGUGAUAAAAG (((...(((((..(((......)))....(((((((((.((((....(((((((((....(((((...........)))))...)))))))))...(((((((((((((.(((((.......(((((.(((((((..((....))..)).)))))..))))).......))))).))))))))))))))))))))))))))..................(((((((.((.....)).)))))))...............))))).)))...... (-35.54) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 661 50 1 141 92 NC_003454:FN0493|5end_hypothetical_protein_1138552..1138782_NEGATIVE 201 249 201 54 5 NC_003454:FN0670|5end_High-affinity_zinc_uptake_system_membrane_protein_znuB_1325702..1325932_POSITIVE 183 119 71 63 22 NC_003454:FN1402|5end_Hypothetical_membrane-spanning_protein_2060436..2060666_POSITIVE 182 264 222 55 20 NC_003454:FN0365|5end_ATP_synthase_protein_I,_sodium_ion_specific_994859..995089_NEGATIVE 181 21 1 38 16 NC_003454:FN1840|5end_Dihydroxyacetone_kinase_329835..330065_POSITIVE 177 250 211 151 98 NC_003454:FN1034|5end_Transcriptional_regulator,_TetR_family_1687648..1687878_POSITIVE 176 36 2 122 91 NC_003454:FN1326|5end_Undecaprenyl_pyrophosphate_synthetase_1981890..1982120_NEGATIVE 176 222 184 133 87 NC_003454:FN1611|5end_Competence_protein_121076..121306_NEGATIVE 171 48 1 98 52 NC_003454:FN0946|5end_Zinc_metalloprotease_1599634..1599864_POSITIVE 169 253 211 153 114 NC_003454:FN1987|5end_Transcriptional_regulator,_GntR_family_490668..490898_NEGATIVE 168 29 2 118 92 NC_003454:FN0687|5end_hypothetical_protein_1342563..1342793_POSITIVE 165 263 230 48 8 NC_003454:FN0933|5end_3-phosphoshikimate_1-carboxyvinyltransferase_1585182..1585412_POSITIVE 164 258 212 57 1 NC_003454:FN1207|5end_hypothetical_protein_1866815..1867045_NEGATIVE 164 245 202 198 150 NC_003454:FN0116|5end_Chaperone_protein_dnaK_748253..748483_POSITIVE 161 252 226 192 164 NC_003454:FN0122|5end_hypothetical_protein_753401..753631_POSITIVE 159 32 1 135 106 NC_003454:FN0592|5end_ATP-dependent_DNA_helicase_pcrA_1245712..1245942_POSITIVE 158 259 240 217 197 NC_003454:FN0170|5end_GTP-binding_protein_795211..795441_POSITIVE 156 52 12 211 173 NC_003454:FN1973|5end_Translation_initiation_inhibitor_472616..472846_NEGATIVE 155 50 8 65 10 NC_003454:FN1169|5end_L-lactate_dehydrogenase_1828536..1828766_NEGATIVE 154 118 84 147 117 NC_003454:FN0861|5end_hypothetical_protein_1521959..1522189_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 195 48 1 54 8 NC_003454:FN1208|3end_1-deoxy-D-xylulose-5-phosphate_synthase_1866799..1866949_NEGATIVE 176 222 184 85 39 NC_003454:FN1612|3end_coproporphyrinogen_III_oxidase_121124..121274_NEGATIVE 165 263 230 47 7 NC_003454:FN0932|3end_hypothetical_protein_1585261..1585411_POSITIVE 161 253 226 53 25 NC_003454:FN0586|3end_Two-component_sensor_kinase_czcS_1241857..1242007_POSITIVE 156 52 12 129 91 NC_003454:FN1974|3end_DNA/RNA_helicase_(DEAD/DEAH_BOX_family)_472698..472848_NEGATIVE 154 263 242 120 101 NC_003454:FN0069|3end_glycyl-tRNA_synthetase_alpha_subunit_708761..708911_POSITIVE 150 143 107 45 9 NC_003454:FN1144|3end_hypothetical_protein_1793403..1793553_NEGATIVE 145 54 26 42 15 NC_003454:FN0579|3end_Hypothetical_cytosolic_protein_1234718..1234868_POSITIVE 143 123 81 86 42 NC_003454:FN0504|3end_Arginine_permease_1153648..1153798_NEGATIVE 143 216 193 55 33 NC_003454:FN1669|3end_Choline_transport_protein_165560..165710_NEGATIVE 141 148 114 79 43 NC_003454:FN1132|3end_Nicotinamide-nucleotide_adenylyltransferase_1780254..1780404_POSITIVE 141 55 33 136 113 NC_003454:FN0053|3end_Branched-chain_amino_acid_transport_system_carrier_protein_690694..690844_POSITIVE 140 257 213 93 50 NC_003454:FN0325|3end_50S_ribosomal_protein_L20_960924..961074_NEGATIVE 140 237 195 147 107 NC_003454:FN0246|3end_hypothetical_protein_870633..870783_NEGATIVE 140 255 214 40 2 NC_003454:FN1893|3end_Fusobacterium_outer_membrane_protein_family_374412..374562_NEGATIVE 139 245 201 83 49 NC_003454:FN0615|3end_Export_ABC_transporter_1274991..1275141_POSITIVE 138 21 1 119 96 NC_003454:FN0853|3end_Glycogen_synthase_1510922..1511072_NEGATIVE 136 233 216 68 51 NC_003454:FN1002|3end_Adenosylmethionine-8-amino-7-oxononanoate_aminotransferase_1658176..1658326_POSITIVE 134 99 61 109 59 NC_003454:FN1245|3end_Glycosyl_transferase_1901241..1901391_NEGATIVE 133 260 221 82 41 NC_003454:FN0683|3end_hypothetical_protein_1338514..1338664_NEGATIVE