Origin IGS: tctacgataatatcccctagaaaaaggatattttattgtattctttgaaatatccaaaaatatcttaaaaaatttttttcctataagtaattctattgcaggatagatatttttagggaaaatatcattgaacttaatatctttctttgatgataacccctgttttatagcattttttaaataagcagcataagaataataagtcccatctttttctgtaagaaaaatatcctcaataaatttttgattttccttatctaacttcttgctgtctttcttaatcttttcaacaaatttttctaaatctttttcaagagattttttgtaaaaatttaacataggtcctccttataatttttattgtagatattttagcatatttttaagataaatgtttagttttttcttattttttaagagaaaataaaaacaacacctatgagcatagatgttgttttattcttctttt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaagaagaataaaacaacatctatgctcataggtgttgtttttattttctcttaaaaaataagaaaaaactaaacatttatcttaaaaatatgctaaaatatctacaataaaaattataaggaggacctatgttaaatttttacaaaaaatctcttgaaaaagatttagaaaaatttgttgaaaagattaagaaagacagcaagaagttagataaggaaaatcaaaaatttattgaggatatttttcttacagaaaaagatgggacttattattcttatgctgcttatttaaaaaatgctataaaacaggggttatcatcaaagaaagatattaagttcaatgatattttccctaaaaatatctatcctgcaatagaattacttataggaaaaaaattttttaagatatttttggatatttcaaagaatacaataaaatatcctttttctaggggatattatcgtaga Mask Tandem Repeat Region ================================================ tctacgataatatcccctagaaaaaggatattttattgtattctttgaaatatccaaaaatatcttaaaaaatttttttcctataagtaattctattgcaggatagatatttttagggaaaatatcattgaacttaatatctttctttgatgataacccctgttttatagcattttttaaataagcagcataagaataataagtcccatctttttctgtaagaaaaatatcctcaataaatttttgattttccttatctaacttcttgctgtctttcttaatcttttcaacaaatttttctaaatctttttcaagagattttttgtaaaaatttaacataggtcctccttataatttttattgtagatattttagcatatttttaagataaatgtttagttttttcttattttttaagagaaaataaaaacaacacctatgagcatagatgttgttttattcttctttt Find is-nt database================================================ Query_seq: FN0033:FN0034|FN0033:FN0034:hypothetical protein:hypothetical protein:<-<-:675060..675528 469 tctacgataatatcccctagaaaaaggatattttattgtattctttgaaatatccaaaaatatcttaaaaaatttttttcctataagtaattctattgcaggatagatatttttagggaaaatatcattgaacttaatatctttctttgatgataacccctgttttatagcattttttaaataagcagcataagaataataagtcccatctttttctgtaagaaaaatatcctcaataaatttttgattttccttatctaacttcttgctgtctttcttaatcttttcaacaaatttttctaaatctttttcaagagattttttgtaaaaatttaacataggtcctccttataatttttattgtagatattttagcatatttttaagataaatgtttagttttttcttattttttaagagaaaataaaaacaacacctatgagcatagatgttgttttattcttctttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0033:FN0034|FN0033:FN0034:hypothetical protein:hypothetical protein:<-<-:675060..675528 469 tctacgataatatcccctagaaaaaggatattttattgtattctttgaaatatccaaaaatatcttaaaaaatttttttcctataagtaattctattgcaggatagatatttttagggaaaatatcattgaacttaatatctttctttgatgataacccctgttttatagcattttttaaataagcagcataagaataataagtcccatctttttctgtaagaaaaatatcctcaataaatttttgattttccttatctaacttcttgctgtctttcttaatcttttcaacaaatttttctaaatctttttcaagagattttttgtaaaaatttaacataggtcctccttataatttttattgtagatattttagcatatttttaagataaatgtttagttttttcttattttttaagagaaaataaaaacaacacctatgagcatagatgttgttttattcttctttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0033:FN0034|FN0033:FN0034:hypothetical protein:hypothetical protein:<-<-:675060..675528 469 tctacgataatatcccctagaaaaaggatattttattgtattctttgaaatatccaaaaatatcttaaaaaatttttttcctataagtaattctattgcaggatagatatttttagggaaaatatcattgaacttaatatctttctttgatgataacccctgttttatagcattttttaaataagcagcataagaataataagtcccatctttttctgtaagaaaaatatcctcaataaatttttgattttccttatctaacttcttgctgtctttcttaatcttttcaacaaatttttctaaatctttttcaagagattttttgtaaaaatttaacataggtcctccttataatttttattgtagatattttagcatatttttaagataaatgtttagttttttcttattttttaagagaaaataaaaacaacacctatgagcatagatgttgttttattcttctttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctacgataatatcccctagaaaaaggatattttattgtattctttgaaatatccaaaaatatcttaaaaaatttttttcctataagtaattctattgcaggatagatatttttagggaaaatatcattgaacttaatatctttctttgatgataacccctgttttatagcattttttaaataagcagcataagaataataagtcccatctttttctgtaagaaaaatatcctcaataaatttttgattttccttatctaacttcttgctgtctttcttaatcttttcaacaaatttttctaaatctttttcaagagattttttgtaaaaatttaacataggtcctccttataatttttattgtagatattttagcatatttttaagataaatgtttagttttttcttattttttaagagaaaataaaaacaacacctatgagcatagatgttgttttattcttctttt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 361 End: 450 ........................................................................................................................................................................................................................................................................................................................................................................ Q L Y K L M N K L Y I N L K K K N K L L F Y F C C R H A Y M ................... Protein_Len: 60 Strand: - Start: 1 End: 339 Q K I A N K L Y A A Y S Y Y T G D K E T L F I D E I F K Q N E K D L K K S D K K I K E V F K E L D K E L S K K Y F N L M .................................................................................................................................. tctacgataatatcccctagaaaaaggatattttattgtattctttgaaatatccaaaaatatcttaaaaaatttttttcctataagtaattctattgcaggatagatatttttagggaaaatatcattgaacttaatatctttctttgatgataacccctgttttatagcattttttaaataagcagcataagaataataagtcccatctttttctgtaagaaaaatatcctcaataaatttttgattttccttatctaacttcttgctgtctttcttaatcttttcaacaaatttttctaaatctttttcaagagattttttgtaaaaatttaacataggtcctccttataatttttattgtagatattttagcatatttttaagataaatgtttagttttttcttattttttaagagaaaataaaaacaacacctatgagcatagatgttgttttattcttctttt 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: 44 End: 73 ...........................................TTTGAAATATCCAAAAATATCTTAAAAAAT............................................................................................................................................................................................................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctacgataatatcccctagaaaaaggatattttattgtattctttgaaatatccaaaaatatcttaaaaaatttttttcctataagtaattctattgcaggatagatatttttagggaaaatatcattgaacttaatatctttctttgatgataacccctgttttatagcattttttaaataagcagcataagaataataagtcccatctttttctgtaagaaaaatatcctcaataaatttttgattttccttatctaacttcttgctgtctttcttaatcttttcaacaaatttttctaaatctttttcaagagattttttgtaaaaatttaacataggtcctccttataatttttattgtagatattttagcatatttttaagataaatgtttagttttttcttattttttaagagaaaataaaaacaacacctatgagcatagatgttgttttattcttctttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 55 HP_score: -5.6 Tail_Score: -2.79796 Start: 106 End: 126 Full_Region: gatattaagttcaat gatatttt cccta aaaatatc tatcctgcaatagaa .........................................................................................................gatattttccctaaaaatatc....................................................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: FN0033:FN0034|FN0033:FN0034:hypothetical protein:hypothetical protein:<-<-:675060..675528 469 tctacgataatatcccctagaaaaaggatattttattgtattctttgaaatatccaaaaatatcttaaaaaatttttttcctataagtaattctattgcaggatagatatttttagggaaaatatcattgaacttaatatctttctttgatgataacccctgttttatagcattttttaaataagcagcataagaataataagtcccatctttttctgtaagaaaaatatcctcaataaatttttgattttccttatctaacttcttgctgtctttcttaatcttttcaacaaatttttctaaatctttttcaagagattttttgtaaaaatttaacataggtcctccttataatttttattgtagatattttagcatatttttaagataaatgtttagttttttcttattttttaagagaaaataaaaacaacacctatgagcatagatgttgttttattcttctttt Intra-Species Hit: Count: 1 Min: 1 Max: 469 Len: 469 Subject: NC_003454_FN0033_FN0034|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[675060,675528]|469 HSP 1 e-value: 1.0E-139 bit: 496.0 Len: 271 Query Start:1 Query End:271 Subject Strand: POSITIVE Subject Start: 1 Subject End: 271 tctacgataatatcccctagaaaaaggatattttattgtattctttgaaatatccaaaaatatcttaaaaaannnnnnncctataagtaattctattgcaggatagatatttttagggaaaatatcattgaacttaatatctttctttgatgataacccctgttttatagcattttttaaataagcagcataagaataataagtcccatctttttctgtaagaaaaatatcctcaataaatttttgattttccttatctaacttcttgctg...................................................................................................................................................................................................... tctacgataatatcccctagaaaaaggatattttattgtattctttgaaatatccaaaaatatcttaaaaaatttttttcctataagtaattctattgcaggatagatatttttagggaaaatatcattgaacttaatatctttctttgatgataacccctgttttatagcattttttaaataagcagcataagaataataagtcccatctttttctgtaagaaaaatatcctcaataaatttttgattttccttatctaacttcttgctg...................................................................................................................................................................................................... HSP 2 e-value: 1.0E-21 bit: 105.0 Len: 53 Query Start:417 Query End:469 Subject Strand: POSITIVE Subject Start: 417 Subject End: 469 ................................................................................................................................................................................................................................................................................................................................................................................................................................agagaaaataaaaacaacacctatgagcatagatgttgttttattcttctttt ................................................................................................................................................................................................................................................................................................................................................................................................................................agagaaaataaaaacaacacctatgagcatagatgttgttttattcttctttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUACGAUAAUAUCCCCUAGAAAAAGGAUAUUUUAUUGUAUUCUUUGAAAUAUCCAAAAAUAUCUUAAAAAAUUUUUUUCCUAUAAGUAAUUCUAUUGCAGGAUAGAUAUUUUUAGGGAAAAUAUCAUUGAACUUAAUAUCUUUCUUUGAUGAUAACCCCUGUUUUAUAGCAUUUUUUAAAUAAGCAGCAUAAGAAUAAUAAGUCCCAUCUUUUUCUGUAAGAAAAAUAUCCUCAAUAAAUUUUUGAUUUUCCUUAUCUAACUUCUUGCUGUCUUUCUUAAUCUUUUCAACAAAUUUUUCUAAAUCUUUUUCAAGAGAUUUUUUGUAAAAAUUUAACAUAGGUCCUCCUUAUAAUUUUUAUUGUAGAUAUUUUAGCAUAUUUUUAAGAUAAAUGUUUAGUUUUUUCUUAUUUUUUAAGAGAAAAUAAAAACAACACCUAUGAGCAUAGAUGUUGUUUUAUUCUUCUUUU ..(((((((((((((..........))))))..))))))).((((.(((((((.(.(((((((((((((((...(((((((((.(((((..((((((....))))))))))).)))))))))((((((..((.............))..))))))...(((((.............((((..((((((((.(((....(((((.......((((((.....)))))).....((((.......)))).....)))))....)))..))))).)))..))))..........(((((((((.((((((((....))))))))...).))))))))...)))))............))))))....))))))))).).))))))).))))..........(((((((((((.....))))))))))).(((((((((.((((....)))).)))))))))........... (-90.32) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAGAAGAAUAAAACAACAUCUAUGCUCAUAGGUGUUGUUUUUAUUUUCUCUUAAAAAAUAAGAAAAAACUAAACAUUUAUCUUAAAAAUAUGCUAAAAUAUCUACAAUAAAAAUUAUAAGGAGGACCUAUGUUAAAUUUUUACAAAAAAUCUCUUGAAAAAGAUUUAGAAAAAUUUGUUGAAAAGAUUAAGAAAGACAGCAAGAAGUUAGAUAAGGAAAAUCAAAAAUUUAUUGAGGAUAUUUUUCUUACAGAAAAAGAUGGGACUUAUUAUUCUUAUGCUGCUUAUUUAAAAAAUGCUAUAAAACAGGGGUUAUCAUCAAAGAAAGAUAUUAAGUUCAAUGAUAUUUUCCCUAAAAAUAUCUAUCCUGCAAUAGAAUUACUUAUAGGAAAAAAAUUUUUUAAGAUAUUUUUGGAUAUUUCAAAGAAUACAAUAAAAUAUCCUUUUUCUAGGGGAUAUUAUCGUAGA ..(((((((((((((((((((((((....)))))))))).))))))))).))))................(((........((((..((((((.(.(((((((((....((((((((((((((....))).)))..)))))))).........((((....))))....(((((((((..........(((((.(((.(((((((((....((((((....(((..........((((((.....))))))........)))....)))))).))))..)))))))).)))))....(.((((((...(((((..((.((((..(((..........)))..))))))..))))).......(((((......))))).....)))))).)...))))))))).))))))))).).))))))..)))).........((((((((((....))))))))))....))). (-90.97) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 722 130 81 221 172 NC_003454:FN0033|5end_hypothetical_protein_674969..675199_NEGATIVE 270 352 312 181 141 NC_003454:FN1981|5end_Transposase_483299..483529_POSITIVE 268 360 311 218 173 NC_003454:FN1253|5end_hypothetical_protein_1910405..1910635_NEGATIVE 267 360 311 114 57 NC_003454:FN2046|5end_Acetyltransferase_551360..551590_NEGATIVE 263 373 334 125 86 NC_003454:FN1312|5end_Biopolymer_transport_exbB_protein_1966948..1967178_NEGATIVE 259 314 274 158 113 NC_003454:FN1393|5end_Signal_recognition_particle,_subunit_FFH/SRP54_2050844..2051074_NEGATIVE 258 380 336 136 88 NC_003454:FN1661|5end_Hypothetical_cytosolic_protein_158712..158942_NEGATIVE 252 120 77 140 101 NC_003454:FN1112|5end_Dipeptide_transport_system_permease_protein_dppC_1756977..1757207_NEGATIVE 249 209 164 91 39 NC_003454:FN0768|5end_Hemin_receptor_1423542..1423772_POSITIVE 247 119 72 202 155 NC_003454:FN0979|5end_hypothetical_protein_1632096..1632326_POSITIVE 240 192 158 40 7 NC_003454:FN0038|5end_hypothetical_protein_678499..678729_NEGATIVE 239 270 221 132 81 NC_003454:FN1431|5end_Branched-chain_amino_acid_transport_system_permease_protein_livH_2100252..2100482_NEGATIVE 237 278 231 191 138 NC_003454:FN1270|5end_Hypothetical_cytosolic_protein_1926592..1926822_NEGATIVE 232 310 272 62 24 NC_003454:FN1787|5end_Tetratricopeptide_repeat_family_protein_267762..267992_POSITIVE 230 300 253 229 181 NC_003454:FN0446|5end_hypothetical_protein_1085719..1085949_POSITIVE 228 349 305 206 149 NC_003454:FN0940|5end_hypothetical_protein_1593508..1593738_NEGATIVE 227 215 171 45 7 NC_003454:FN0472|5end_flavodoxin_1118165..1118395_NEGATIVE 225 388 343 143 95 NC_003454:FN0775|5end_putative_aminopeptidase_2_1430568..1430798_POSITIVE 224 49 1 138 87 NC_003454:FN0591|5end_Putative_efflux_pump_component_MtrF_1245573..1245803_NEGATIVE 224 221 184 75 38 NC_003454:FN0378|5end_UDP-glucose_4-epimerase_1010196..1010426_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 352 312 54 14 NC_003454:FN1980|3end_Transporter_483252..483402_POSITIVE 268 360 311 124 79 NC_003454:FN1254|3end_Dihydropteridine_reductase_1910499..1910649_NEGATIVE 266 458 414 79 34 NC_003454:FN0035|3end_hypothetical_protein_676240..676390_NEGATIVE 259 314 274 147 102 NC_003454:FN1394|3end_Signal_recognition_particle_associated_protein_2050855..2051005_NEGATIVE 252 120 77 140 101 NC_003454:FN1113|3end_Dipeptide_transport_system_permease_protein_dppB_1756977..1757127_NEGATIVE 232 310 272 41 3 NC_003454:FN1786|3end_ADP-heptose_synthase_267821..267971_POSITIVE 219 349 307 89 53 NC_003454:FN0648|3end_Exoenzyme_regulatory_protein_aepA_precursor_1304532..1304682_NEGATIVE 219 323 281 63 16 NC_003454:FN0398|3end_Dipeptide_transport_system_permease_protein_dppC_1037707..1037857_POSITIVE 218 278 231 148 102 NC_003454:FN0043|3end_Hypothetical_exported_24-amino_acid_repeat_protein_682818..682968_POSITIVE 217 380 331 76 15 NC_003454:FN0149|3end_Malonyl-CoA-[acyl-carrier-protein]_transacylase_778465..778615_POSITIVE 215 46 3 85 23 NC_003454:FN1320|3end_Peptidyl-prolyl_cis-trans_isomerase_1974261..1974411_NEGATIVE 214 287 250 126 84 NC_003454:FN0881|3end_ABC_transporter_integral_membrane_protein_1541959..1542109_NEGATIVE 213 370 321 102 59 NC_003454:FN0799|3end_Isoamylase_1457889..1458039_NEGATIVE 212 176 140 102 53 NC_003454:FN1343|3end_seC-independent_protein_TATD_1996456..1996606_NEGATIVE 211 287 241 86 33 NC_003454:FN0196|3end_Transcriptional_regulator,_FUR_family_822747..822897_POSITIVE 209 299 251 57 2 NC_003454:FN1271|3end_Protease_IV_1926745..1926895_NEGATIVE 209 259 230 136 105 NC_003454:FN0427|3end_Orotate_phosphoribosyltransferase_1070120..1070270_POSITIVE 209 276 231 150 113 NC_003454:FN0132|3end_Hemolysin_769183..769333_POSITIVE 207 357 311 87 39 NC_003454:FN1272|3end_Transcriptional_regulator,_TetR_family_1929353..1929503_POSITIVE 206 187 144 87 48 NC_003454:FN1495|3end_hypothetical_protein_-89..61_NEGATIVE