Origin IGS: tcttaatttcctcctaaatacttttaatttattttaatttaaaactttacttaataagtcatatttgtattataactacaaatttgattttttgcaagttttatttataataaatagaaaaaaatatataattatatagattataattttgaaaagtatttacataattaaaataattatcctaattattgacaatattactaaaaagtggtagtatcatagcaccaaaacaataggagggaaaaatggaagaatttcaaactgaacaaaaatcaaatttcttt .........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 aaagaaatttgatttttgttcagtttgaaattcttccatttttccctcctattgttttggtgctatgatactaccactttttagtaatattgtcaataattaggataattattttaattatgtaaatacttttcaaaattataatctatataattatatatttttttctatttattataaataaaacttgcaaaaaatcaaatttgtagttataatacaaatatgacttattaagtaaagttttaaattaaaataaattaaaagtatttaggaggaaattaaga Mask Tandem Repeat Region ================================================ tcttaatttcctcctaaatacttttaatttattttaatttaaaactttacttaataagtcatatttgtattataactacaaatttgattttttgcaagttttatttataataaatagaaaaaaatatataattatatagattataattttgaaaagtatttacataattaaaataattatcctaattattgacaatattactaaaaagtggtagtatcatagcaccaaaacaataggagggaaaaatggaagaatttcaaactgaacaaaaatcaaatttcttt Find is-nt database================================================ Query_seq: FN0513:FN0514|FN0513:FN0514:Flavodoxin:hypothetical protein:<-->:1163287..1163570 284 tcttaatttcctcctaaatacttttaatttattttaatttaaaactttacttaataagtcatatttgtattataactacaaatttgattttttgcaagttttatttataataaatagaaaaaaatatataattatatagattataattttgaaaagtatttacataattaaaataattatcctaattattgacaatattactaaaaagtggtagtatcatagcaccaaaacaataggagggaaaaatggaagaatttcaaactgaacaaaaatcaaatttcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0513:FN0514|FN0513:FN0514:Flavodoxin:hypothetical protein:<-->:1163287..1163570 284 tcttaatttcctcctaaatacttttaatttattttaatttaaaactttacttaataagtcatatttgtattataactacaaatttgattttttgcaagttttatttataataaatagaaaaaaatatataattatatagattataattttgaaaagtatttacataattaaaataattatcctaattattgacaatattactaaaaagtggtagtatcatagcaccaaaacaataggagggaaaaatggaagaatttcaaactgaacaaaaatcaaatttcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0513:FN0514|FN0513:FN0514:Flavodoxin:hypothetical protein:<-->:1163287..1163570 284 tcttaatttcctcctaaatacttttaatttattttaatttaaaactttacttaataagtcatatttgtattataactacaaatttgattttttgcaagttttatttataataaatagaaaaaaatatataattatatagattataattttgaaaagtatttacataattaaaataattatcctaattattgacaatattactaaaaagtggtagtatcatagcaccaaaacaataggagggaaaaatggaagaatttcaaactgaacaaaaatcaaatttcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcttaatttcctcctaaatacttttaatttattttaatttaaaactttacttaataagtcatatttgtattataactacaaatttgattttttgcaagttttatttataataaatagaaaaaaatatataattatatagattataattttgaaaagtatttacataattaaaataattatcctaattattgacaatattactaaaaagtggtagtatcatagcaccaaaacaataggagggaaaaatggaagaatttcaaactgaacaaaaatcaaatttcttt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 18 End: 107 ................. M L L I Y F N L K L Y L I S H I C I I T T N L I F C K F Y L ................................................................................................................................................................................. tcttaatttcctcctaaatacttttaatttattttaatttaaaactttacttaataagtcatatttgtattataactacaaatttgattttttgcaagttttatttataataaatagaaaaaaatatataattatatagattataattttgaaaagtatttacataattaaaataattatcctaattattgacaatattactaaaaagtggtagtatcatagcaccaaaacaataggagggaaaaatggaagaatttcaaactgaacaaaaatcaaatttcttt 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: 88 Start: 69 End: 98 ....................................................................CTTGCAAAAAATCAAATTTGTAGTTATAAT.......................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 88 Start: 188 End: 217 ...........................................................................................................................................................................................ATTGACAATATTACTAAAAAGTGGTAGTAT................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 167 End: 196 ......................................................................................................................................................................ATTGTCAATAATTAGGATAATTATTTTAAT........................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 82 End: 111 .................................................................................ATTTGATTTTTTGCAAGTTTTATTTATAAT............................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 148 End: 177 ...................................................................................................................................................TTTGAAAAGTATTTACATAATTAAAATAAT........................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 216 End: 245 .......................................................................................................................................................................................................................TTTTCCCTCCTATTGTTTTGGTGCTATGAT....................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 103 End: 132 ......................................................................................................ATTTATAATAAATAGAAAAAAATATATAAT........................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcttaatttcctcctaaatacttttaatttattttaatttaaaactttacttaataagtcatatttgtattataactacaaatttgattttttgcaagttttatttataataaatagaaaaaaatatataattatatagattataattttgaaaagtatttacataattaaaataattatcctaattattgacaatattactaaaaagtggtagtatcatagcaccaaaacaataggagggaaaaatggaagaatttcaaactgaacaaaaatcaaatttcttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -2.5 Tail_Score: -5.90231 Start: 125 End: 138 Full_Region: ttcaaaattataatc tatat aatt atata tttttttctatttat ............................................................................................................................tatataattatata.................................................................................................................................................. Find igs database================================================ Query_seq: FN0513:FN0514|FN0513:FN0514:Flavodoxin:hypothetical protein:<-->:1163287..1163570 284 tcttaatttcctcctaaatacttttaatttattttaatttaaaactttacttaataagtcatatttgtattataactacaaatttgattttttgcaagttttatttataataaatagaaaaaaatatataattatatagattataattttgaaaagtatttacataattaaaataattatcctaattattgacaatattactaaaaagtggtagtatcatagcaccaaaacaataggagggaaaaatggaagaatttcaaactgaacaaaaatcaaatttcttt Intra-Species Hit: Count: 1 Min: 1 Max: 284 Len: 284 Subject: NC_003454_FN0513_FN0514|Flavodoxin:hypothetical protein|NEGATIVE:POSITIVE|[1163287,1163570]|284 HSP 1 e-value: 5.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 tcttaatttcctcctaaatacttttaatttattttaatttaaaactttacttaataagtcatatttgtattataactacaaatttgattttttgcaagttttatttataataaatag....................................................................................................................................................................... tcttaatttcctcctaaatacttttaatttattttaatttaaaactttacttaataagtcatatttgtattataactacaaatttgattttttgcaagttttatttataataaatag....................................................................................................................................................................... HSP 2 e-value: 3.0E-52 bit: 206.0 Len: 104 Query Start:181 Query End:284 Subject Strand: POSITIVE Subject Start: 181 Subject End: 284 ....................................................................................................................................................................................cctaattattgacaatattactaaaaagtggtagtatcatagcaccaaaacaataggagggaaaaatggaagaatttcaaactgaacaaaaatcaaatttcttt ....................................................................................................................................................................................cctaattattgacaatattactaaaaagtggtagtatcatagcaccaaaacaataggagggaaaaatggaagaatttcaaactgaacaaaaatcaaatttcttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUAAUUUCCUCCUAAAUACUUUUAAUUUAUUUUAAUUUAAAACUUUACUUAAUAAGUCAUAUUUGUAUUAUAACUACAAAUUUGAUUUUUUGCAAGUUUUAUUUAUAAUAAAUAGAAAAAAAUAUAUAAUUAUAUAGAUUAUAAUUUUGAAAAGUAUUUACAUAAUUAAAAUAAUUAUCCUAAUUAUUGACAAUAUUACUAAAAAGUGGUAGUAUCAUAGCACCAAAACAAUAGGAGGGAAAAAUGGAAGAAUUUCAAACUGAACAAAAAUCAAAUUUCUUU ......(((((((((((((((((((.(((((((.(((..((((((((....(((.((((((.(((((((.......))))))).)))))).))).)))))))).))).))))))).....(((((.(((((((.....)))))))))))).))))))))))..........((((((((...))))))))....(((((((((.....))))))))).................))))))))).....((((((........................)))))) (-49.16) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGAAAUUUGAUUUUUGUUCAGUUUGAAAUUCUUCCAUUUUUCCCUCCUAUUGUUUUGGUGCUAUGAUACUACCACUUUUUAGUAAUAUUGUCAAUAAUUAGGAUAAUUAUUUUAAUUAUGUAAAUACUUUUCAAAAUUAUAAUCUAUAUAAUUAUAUAUUUUUUUCUAUUUAUUAUAAAUAAAACUUGCAAAAAAUCAAAUUUGUAGUUAUAAUACAAAUAUGACUUAUUAAGUAAAGUUUUAAAUUAAAAUAAAUUAAAAGUAUUUAGGAGGAAAUUAAGA .(((((.((..(............)..)).))))).........(((((.(((((((((((....(((((.((..(((....)))..)).)))))...))))))))))).............(((((((((((...(((((((.....)))))))..............(((((((.(((.((((((((((......(((.(((((((.......))))))).)))........)).))))))))..))).))))))).))))))))))))))))......... (-44.14) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 623 100 51 191 142 NC_003454:FN0513|5end_Flavodoxin_1163196..1163426_NEGATIVE 245 49 7 138 94 NC_003454:FN0417|5end_Type_III_restriction-modification_system_restriction_subunit_1055887..1056117_POSITIVE 235 240 206 49 11 NC_003454:FN0713|5end_Chromate_transport_protein_1371333..1371563_POSITIVE 197 250 206 102 64 NC_003454:FN1749|5end_Pyruvate-flavodoxin_oxidoreductase_247461..247691_POSITIVE 195 40 1 116 82 NC_003454:FN0019|5end_Transcription-repair_coupling_factor_656549..656779_POSITIVE 192 224 181 150 99 NC_003454:FN0424|5end_Dihydroorotate_dehydrogenase_1067119..1067349_POSITIVE 188 48 1 145 99 NC_003454:FN0957|5end_Precorrin-4_C11-methyltransferase_1613579..1613809_NEGATIVE 187 85 43 148 107 NC_003454:FN0904|5end_NAD(FAD)-utilizing_dehydrogenase_1562097..1562327_POSITIVE 186 43 3 144 92 NC_003454:FN1006|5end_Acetyltransferase_1661396..1661626_NEGATIVE 186 202 162 107 65 NC_003454:FN2115|5end_hypothetical_protein_624843..625073_NEGATIVE 186 224 185 53 12 NC_003454:FN1502|5end_Nickel_transport_system_permease_protein_nikC_7522..7752_NEGATIVE 184 260 212 184 141 NC_003454:FN0724|5end_flavodoxin_1384167..1384397_NEGATIVE 182 33 6 79 50 NC_003454:FN1473|5end_N-acetylneuraminate_transporter_large_subunit_2155032..2155262_POSITIVE 182 258 218 207 168 NC_003454:FN0273|5end_Butyrate-acetoacetate_CoA-transferase_subunit_B_899423..899653_POSITIVE 182 38 1 120 86 NC_003454:FN0037|5end_hypothetical_protein_678061..678291_NEGATIVE 182 238 196 203 152 NC_003454:FN1522|5end_Dipeptide_transport_system_permease_protein_dppC_27327..27557_POSITIVE 181 242 201 111 63 NC_003454:FN1896|5end_ABC_transporter_integral_membrane_protein_383909..384139_NEGATIVE 180 250 208 218 177 NC_003454:FN1975|5end_ATP-dependent_RNA_helicase_475599..475829_POSITIVE 179 37 6 120 95 NC_003454:FN1317|5end_RNA_polymerase_sigma_factor_1971085..1971315_NEGATIVE 177 253 236 201 184 NC_003454:FN0897|5end_Hypothetical_cytosolic_protein_1555833..1556063_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 245 49 7 128 84 NC_003454:FN0416|3end_Type_III_restriction-modification_system_methylation_subunit_1055957..1056107_POSITIVE 235 240 206 52 14 NC_003454:FN0712|3end_Chromate_transport_protein_1371416..1371566_POSITIVE 197 250 206 120 82 NC_003454:FN1748|3end_Pyruvate-flavodoxin_oxidoreductase_247559..247709_POSITIVE 192 224 181 138 87 NC_003454:FN0423|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit_1067187..1067337_POSITIVE 188 48 1 107 61 NC_003454:FN0958|3end_hypothetical_protein_1613617..1613767_NEGATIVE 187 85 43 138 97 NC_003454:FN0903|3end_Polysialic_acid_capsule_expression_protein_kpsF_1562167..1562317_POSITIVE 186 224 185 72 31 NC_003454:FN1503|3end_Nickel_transport_system_permease_protein_nikB_7503..7653_NEGATIVE 182 33 6 55 26 NC_003454:FN1472|3end_N-acetylneuraminate-binding_protein_2155088..2155238_POSITIVE 181 242 201 55 7 NC_003454:FN1897|3end_ABC_transporter_integral_membrane_protein_383965..384115_NEGATIVE 179 37 6 104 79 NC_003454:FN1318|3end_RNA_polymerase_sigma_factor_rpoD_1971101..1971251_NEGATIVE 176 254 214 81 45 NC_003454:FN1194|3end_hypothetical_protein_1855668..1855818_POSITIVE 176 241 221 27 2 NC_003454:FN0708|3end_Hypothetical_cytosolic_protein_1367425..1367575_POSITIVE 176 249 205 47 2 NC_003454:FN2085|3end_hypothetical_protein_596560..596710_NEGATIVE 175 270 228 64 10 NC_003454:FN2054|3end_glucose-6-phosphate_isomerase_563962..564112_POSITIVE 173 239 214 131 105 NC_003454:FN0675|3end_60_kDa_chaperonin_GROEL_1330471..1330621_NEGATIVE 173 41 9 103 75 NC_003454:FN0062|3end_Hypothetical_cytosolic_protein_698975..699125_POSITIVE 172 222 183 54 16 NC_003454:FN1378|3end_Citrate_lyase_acyl_carrier_protein_2026426..2026576_POSITIVE 172 107 65 66 29 NC_003454:FN2103|3end_RecA_protein_614209..614359_POSITIVE 171 47 3 128 80 NC_003454:FN1491|3end_PTS_system,_IIA_component_2172302..2172452_NEGATIVE 170 229 204 35 9 NC_003454:FN1471|3end_LACI-family_transcription_regulator_2154085..2154235_POSITIVE