Origin IGS: ttatctaactcccctttctatgatttataaaataaaaccttccttattataacagatgttttttttaaaatctaatttattttaattatatagtaaaaaaattgacaaaaaattttaaaaatgagaaaataagttagatttaatattaatagggggtataaaatgaagaaaaaacttttagttataatgttatttattttatctttgacaagttttgcaataccattaaataat .........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 attatttaatggtattgcaaaacttgtcaaagataaaataaataacattataactaaaagttttttcttcattttataccccctattaatattaaatctaacttattttctcatttttaaaattttttgtcaatttttttactatataattaaaataaattagattttaaaaaaaacatctgttataataaggaaggttttattttataaatcatagaaaggggagttagataa Mask Tandem Repeat Region ================================================ ttatctaactcccctttctatgatttataaaataaaaccttccttattataacagatgttttttttaaaatctaatttattttaattatatagtaaaaaaattgacaaaaaattttaaaaatgagaaaataagttagatttaatattaatagggggtataaaatgaagaaaaaacttttagttataatgttatttattttatctttgacaagttttgcaataccattaaataat Find is-nt database================================================ Query_seq: FN1122:FN1123|FN1122:FN1123:Long-chain-fatty-acid--CoA ligase:Thioredoxin-like protein:<-->:1767384..1767617 234 ttatctaactcccctttctatgatttataaaataaaaccttccttattataacagatgttttttttaaaatctaatttattttaattatatagtaaaaaaattgacaaaaaattttaaaaatgagaaaataagttagatttaatattaatagggggtataaaatgaagaaaaaacttttagttataatgttatttattttatctttgacaagttttgcaataccattaaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1122:FN1123|FN1122:FN1123:Long-chain-fatty-acid--CoA ligase:Thioredoxin-like protein:<-->:1767384..1767617 234 ttatctaactcccctttctatgatttataaaataaaaccttccttattataacagatgttttttttaaaatctaatttattttaattatatagtaaaaaaattgacaaaaaattttaaaaatgagaaaataagttagatttaatattaatagggggtataaaatgaagaaaaaacttttagttataatgttatttattttatctttgacaagttttgcaataccattaaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1122:FN1123|FN1122:FN1123:Long-chain-fatty-acid--CoA ligase:Thioredoxin-like protein:<-->:1767384..1767617 234 ttatctaactcccctttctatgatttataaaataaaaccttccttattataacagatgttttttttaaaatctaatttattttaattatatagtaaaaaaattgacaaaaaattttaaaaatgagaaaataagttagatttaatattaatagggggtataaaatgaagaaaaaacttttagttataatgttatttattttatctttgacaagttttgcaataccattaaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttatctaactcccctttctatgatttataaaataaaaccttccttattataacagatgttttttttaaaatctaatttattttaattatatagtaaaaaaattgacaaaaaattttaaaaatgagaaaataagttagatttaatattaatagggggtataaaatgaagaaaaaacttttagttataatgttatttattttatctttgacaagttttgcaataccattaaataat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 145 End: 234 ................................................................................................................................................ M N R G Y K M K K K L L V I M L F I L S L T S F A I P L N N Protein_Len: 49 Strand: - Start: 75 End: 221 .......................................................................... N I K I I Y Y F F Q C F I K F I L F Y T L N L I L L P Y L I F F F S K T I I N N I K D K V L K A M ............. ttatctaactcccctttctatgatttataaaataaaaccttccttattataacagatgttttttttaaaatctaatttattttaattatatagtaaaaaaattgacaaaaaattttaaaaatgagaaaataagttagatttaatattaatagggggtataaaatgaagaaaaaacttttagttataatgttatttattttatctttgacaagttttgcaataccattaaataat 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: 84 Start: 101 End: 130 ....................................................................................................ATTGACAAAAAATTTTAAAAATGAGAAAAT........................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 46 End: 75 .............................................TTAGATTTTAAAAAAAACATCTGTTATAAT............................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttatctaactcccctttctatgatttataaaataaaaccttccttattataacagatgttttttttaaaatctaatttattttaattatatagtaaaaaaattgacaaaaaattttaaaaatgagaaaataagttagatttaatattaatagggggtataaaatgaagaaaaaacttttagttataatgttatttattttatctttgacaagttttgcaataccattaaataat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1122:FN1123|FN1122:FN1123:Long-chain-fatty-acid--CoA ligase:Thioredoxin-like protein:<-->:1767384..1767617 234 ttatctaactcccctttctatgatttataaaataaaaccttccttattataacagatgttttttttaaaatctaatttattttaattatatagtaaaaaaattgacaaaaaattttaaaaatgagaaaataagttagatttaatattaatagggggtataaaatgaagaaaaaacttttagttataatgttatttattttatctttgacaagttttgcaataccattaaataat Intra-Species Hit: Count: 1 Min: 1 Max: 234 Len: 234 Subject: NC_003454_FN1122_FN1123|Long-chain-fatty-acid--CoA ligase:Thioredoxin-like protein|NEGATIVE:POSITIVE|[1767384,1767617]|234 HSP 1 e-value: 2.0E-52 bit: 206.0 Len: 104 Query Start:131 Query End:234 Subject Strand: POSITIVE Subject Start: 131 Subject End: 234 ..................................................................................................................................aagttagatttaatattaatagggggtataaaatgaagaaaaaacttttagttataatgttatttattttatctttgacaagttttgcaataccattaaataat ..................................................................................................................................aagttagatttaatattaatagggggtataaaatgaagaaaaaacttttagttataatgttatttattttatctttgacaagttttgcaataccattaaataat HSP 2 e-value: 7.0E-25 bit: 115.0 Len: 58 Query Start:1 Query End:58 Subject Strand: POSITIVE Subject Start: 1 Subject End: 58 ttatctaactcccctttctatgatttataaaataaaaccttccttattataacagatg................................................................................................................................................................................ ttatctaactcccctttctatgatttataaaataaaaccttccttattataacagatg................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUCUAACUCCCCUUUCUAUGAUUUAUAAAAUAAAACCUUCCUUAUUAUAACAGAUGUUUUUUUUAAAAUCUAAUUUAUUUUAAUUAUAUAGUAAAAAAAUUGACAAAAAAUUUUAAAAAUGAGAAAAUAAGUUAGAUUUAAUAUUAAUAGGGGGUAUAAAAUGAAGAAAAAACUUUUAGUUAUAAUGUUAUUUAUUUUAUCUUUGACAAGUUUUGCAAUACCAUUAAAUAAU .......((.(((((....(((.....(((((.(((((..((............)).))))))))))((((((((((((((((..((((....(((((..............)))))...)))).))))))))))))))))..)))....)))))))....((((.....(((((((((((..((((.((.....)).))))..)))).))))))).......))))....... (-28.84) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUUUAAUGGUAUUGCAAAACUUGUCAAAGAUAAAAUAAAUAACAUUAUAACUAAAAGUUUUUUCUUCAUUUUAUACCCCCUAUUAAUAUUAAAUCUAACUUAUUUUCUCAUUUUUAAAAUUUUUUGUCAAUUUUUUUACUAUAUAAUUAAAAUAAAUUAGAUUUUAAAAAAAACAUCUGUUAUAAUAAGGAAGGUUUUAUUUUAUAAAUCAUAGAAAGGGGAGUUAGAUAA .(((((((((........(((((((.......((((...........))))......)))))))...............(((((.........((((((..((((((......((((((((((((...((..(((((..(........)..)))))..)).)))))))))))).(((....)))..))))))..))))))..((((((.....))))))))))).))))))))) (-28.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 714 60 11 151 102 NC_003454:FN1122|5end_Long-chain-fatty-acid--CoA_ligase_1767293..1767523_NEGATIVE 234 130 84 174 119 NC_003454:FN1987|5end_Transcriptional_regulator,_GntR_family_490668..490898_NEGATIVE 212 225 186 41 1 NC_003454:FN1575|5end_Hypothetical_cytosolic_protein_86495..86725_NEGATIVE 205 169 121 209 155 NC_003454:FN1462|5end_Transcriptional_regulator,_GntR_family_2144945..2145175_NEGATIVE 199 49 1 100 54 NC_003454:FN1431|5end_Branched-chain_amino_acid_transport_system_permease_protein_livH_2100252..2100482_NEGATIVE 198 218 171 215 158 NC_003454:FN1485|5end_Transporter_2168022..2168252_NEGATIVE 198 45 4 105 53 NC_003454:FN1537|5end_Arsenical_pump-driving_ATPase_51112..51342_NEGATIVE 197 51 14 92 59 NC_003454:FN0614|5end_Export_ABC_transporter_1271447..1271677_POSITIVE 196 169 131 42 10 NC_003454:FN0624|5end_NA+/H+_antiporter_NHAC_1284329..1284559_NEGATIVE 191 57 13 75 18 NC_003454:FN1479|5end_hypothetical_protein_2161269..2161499_NEGATIVE 191 226 188 97 55 NC_003454:FN0064|5end_Hypothetical_cytosolic_protein_699489..699719_POSITIVE 190 50 4 150 95 NC_003454:FN0701|5end_Methyltransferase_1359261..1359491_POSITIVE 190 75 41 191 154 NC_003454:FN0346|5end_hypothetical_protein_979267..979497_NEGATIVE 189 66 24 169 129 NC_003454:FN0949|5end_DNA_helicase_1606759..1606989_NEGATIVE 184 50 4 111 57 NC_003454:FN1850|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III_339205..339435_POSITIVE 181 75 42 112 77 NC_003454:FN1712|5end_hypothetical_protein_207262..207492_POSITIVE 180 172 132 227 185 NC_003454:FN0238|5end_hypothetical_protein_863314..863544_NEGATIVE 179 60 15 71 28 NC_003454:FN0340|5end_Hypothetical_membrane-spanning_Protein_973948..974178_NEGATIVE 178 73 39 175 141 NC_003454:FN1303|5end_Adenosylcobalamin-dependent_DIOL_dehydratase_gamma_subunit_1960284..1960514_NEGATIVE 178 79 39 117 74 NC_003454:FN0753|5end_aspartyl/glutamyl-tRNA_amidotransferase_subunit_B_1413169..1413399_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 207 182 151 54 20 NC_003454:FN1464|3end_1-deoxy-D-xylulose-5-phosphate_synthase_2145954..2146104_NEGATIVE 198 45 4 108 56 NC_003454:FN1538|3end_Arsenical_pump-driving_ATPase_51109..51259_NEGATIVE 196 169 131 52 20 NC_003454:FN0625|3end_Aspartate_aminotransferase_1284319..1284469_NEGATIVE 190 50 4 128 73 NC_003454:FN0700|3end_Protein_translocase_subunit_secF_1359319..1359469_POSITIVE 184 50 4 114 60 NC_003454:FN1849|3end_Coenzyme_F390_synthetase_339288..339438_POSITIVE 181 75 42 119 84 NC_003454:FN1711|3end_Methyltransferase_207349..207499_POSITIVE 178 79 39 103 60 NC_003454:FN0754|3end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A_1413183..1413333_NEGATIVE 177 219 176 118 80 NC_003454:FN0202|3end_Glutaconate_CoA-transferase_subunit_A_828825..828975_POSITIVE 175 210 163 139 93 NC_003454:FN1136|3end_Phosphonates_transport_ATP-binding_protein_phnC_1783880..1784030_POSITIVE 175 29 8 99 76 NC_003454:FN0973|3end_Histidinol-phosphate_aminotransferase_1625626..1625776_NEGATIVE 175 225 200 31 2 NC_003454:FN1576|3end_ATPase_and_helicase_subunits_involved_in_DNA_replication_86505..86655_NEGATIVE 173 75 37 83 54 NC_003454:FN1286|3end_30S_ribosomal_protein_S13_1943718..1943868_NEGATIVE 173 18 1 84 63 NC_003454:FN1786|3end_ADP-heptose_synthase_267821..267971_POSITIVE 173 60 13 59 2 NC_003454:FN1700|3end_hypothetical_protein_195245..195395_NEGATIVE 172 140 93 61 9 NC_003454:FN1451|3end_cell_division_protein_FtsZ_2131628..2131778_NEGATIVE 171 52 24 48 19 NC_003454:FN0773|3end_hypothetical_protein_1429635..1429785_POSITIVE 171 227 197 135 102 NC_003454:FN0549|3end_O-sialoglycoprotein_endopeptidase_1202431..1202581_POSITIVE 170 72 40 117 78 NC_003454:FN0940|3end_hypothetical_protein_1592975..1593125_NEGATIVE 170 28 7 101 79 NC_003454:FN0419|3end_aspartate_carbamoyltransferase_catalytic_subunit_1060707..1060857_POSITIVE 170 156 114 148 104 NC_003454:FN0027|3end_hypothetical_protein_664763..664913_NEGATIVE