Origin IGS: ttaactcacctcattcaaattttaacataaggcttattaaaaagcaacttaaatagattgctttttaatttagcatacttatgaagttgctctttttataatagaaaaaataattctaaaatgctataattattagggaaaatatcggaggggagaaaatgaaattgcaatttgaattaattaatgagcaaaagtttgatagcaattatgaaaatttaaaaattatggggggagaataatgttttttttaggatatttatttttttattctgtattagcgactttgatagacccatcaatattcttttcaatactttcttttgtattaggtggaatgttgtattttaatagtagctctcctttacaaggaatagcaatctgcatttttggactattacatttaatttcaagactatgttatcatagtaaaaaa .........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 ttttttactatgataacatagtcttgaaattaaatgtaatagtccaaaaatgcagattgctattccttgtaaaggagagctactattaaaatacaacattccacctaatacaaaagaaagtattgaaaagaatattgatgggtctatcaaagtcgctaatacagaataaaaaaataaatatcctaaaaaaaacattattctccccccataatttttaaattttcataattgctatcaaacttttgctcattaattaattcaaattgcaatttcattttctcccctccgatattttccctaataattatagcattttagaattattttttctattataaaaagagcaacttcataagtatgctaaattaaaaagcaatctatttaagttgctttttaataagccttatgttaaaatttgaatgaggtgagttaa Mask Tandem Repeat Region ================================================ ttaactcacctcattcaaattttaacataaggcttattaaaaagcaacttaaatagattgctttttaatttagcatacttatgaagttgctctttttataatagaaaaaataattctaaaatgctataattattagggaaaatatcggaggggagaaaatgaaattgcaatttgaattaattaatgagcaaaagtttgatagcaattatgaaaatttaaaaattatggggggagaataatgttttttttaggatatttatttttttattctgtattagcgactttgatagacccatcaatattcttttcaatactttcttttgtattaggtggaatgttgtattttaatagtagctctcctttacaaggaatagcaatctgcatttttggactattacatttaatttcaagactatgttatcatagtaaaaaa Find is-nt database================================================ Query_seq: FN1045:FN1046|FN1045:FN1046:hypothetical protein:hypothetical protein:<-->:1696078..1696510 433 ttaactcacctcattcaaattttaacataaggcttattaaaaagcaacttaaatagattgctttttaatttagcatacttatgaagttgctctttttataatagaaaaaataattctaaaatgctataattattagggaaaatatcggaggggagaaaatgaaattgcaatttgaattaattaatgagcaaaagtttgatagcaattatgaaaatttaaaaattatggggggagaataatgttttttttaggatatttatttttttattctgtattagcgactttgatagacccatcaatattcttttcaatactttcttttgtattaggtggaatgttgtattttaatagtagctctcctttacaaggaatagcaatctgcatttttggactattacatttaatttcaagactatgttatcatagtaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1045:FN1046|FN1045:FN1046:hypothetical protein:hypothetical protein:<-->:1696078..1696510 433 ttaactcacctcattcaaattttaacataaggcttattaaaaagcaacttaaatagattgctttttaatttagcatacttatgaagttgctctttttataatagaaaaaataattctaaaatgctataattattagggaaaatatcggaggggagaaaatgaaattgcaatttgaattaattaatgagcaaaagtttgatagcaattatgaaaatttaaaaattatggggggagaataatgttttttttaggatatttatttttttattctgtattagcgactttgatagacccatcaatattcttttcaatactttcttttgtattaggtggaatgttgtattttaatagtagctctcctttacaaggaatagcaatctgcatttttggactattacatttaatttcaagactatgttatcatagtaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1045:FN1046|FN1045:FN1046:hypothetical protein:hypothetical protein:<-->:1696078..1696510 433 ttaactcacctcattcaaattttaacataaggcttattaaaaagcaacttaaatagattgctttttaatttagcatacttatgaagttgctctttttataatagaaaaaataattctaaaatgctataattattagggaaaatatcggaggggagaaaatgaaattgcaatttgaattaattaatgagcaaaagtttgatagcaattatgaaaatttaaaaattatggggggagaataatgttttttttaggatatttatttttttattctgtattagcgactttgatagacccatcaatattcttttcaatactttcttttgtattaggtggaatgttgtattttaatagtagctctcctttacaaggaatagcaatctgcatttttggactattacatttaatttcaagactatgttatcatagtaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaactcacctcattcaaattttaacataaggcttattaaaaagcaacttaaatagattgctttttaatttagcatacttatgaagttgctctttttataatagaaaaaataattctaaaatgctataattattagggaaaatatcggaggggagaaaatgaaattgcaatttgaattaattaatgagcaaaagtttgatagcaattatgaaaatttaaaaattatggggggagaataatgttttttttaggatatttatttttttattctgtattagcgactttgatagacccatcaatattcttttcaatactttcttttgtattaggtggaatgttgtattttaatagtagctctcctttacaaggaatagcaatctgcatttttggactattacatttaatttcaagactatgttatcatagtaaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 126 End: 236 ............................................................................................................................. M I I R E N I G G E K M K L Q F E L I N E Q K F D S N Y E N L K I M G G E ..................................................................................................................................................................................................... Protein_Len: 31 Strand: + Start: 253 End: 345 ............................................................................................................................................................................................................................................................ M F I F L F C I S D F D R P I N I L F N T F F C I R W N V V F ........................................................................................ Protein_Len: 60 Strand: + Start: 236 End: 433 ........................................................................................................................................................................................................................................... M M F F L G Y L F F Y S V L A T L I D P S I F F S I L S F V L G G M L Y F N S S S P L Q G I A I C I F G L L H L I S R L Protein_Len: 46 Strand: - Start: 268 End: 405 ........................................................................................................................................................................................................................................................................... E T N A V K I S G D I N K E I S E K T N P P I N Y K L L L E G K C P I A I Q M K P S N C K M ............................ Protein_Len: 36 Strand: - Start: 219 End: 326 .......................................................................................................................................................................................................................... F N H P S F L T K K L I N I K K N Q I L S K S L G M L I R K L V K K Q M ........................................................................................................... ttaactcacctcattcaaattttaacataaggcttattaaaaagcaacttaaatagattgctttttaatttagcatacttatgaagttgctctttttataatagaaaaaataattctaaaatgctataattattagggaaaatatcggaggggagaaaatgaaattgcaatttgaattaattaatgagcaaaagtttgatagcaattatgaaaatttaaaaattatggggggagaataatgttttttttaggatatttatttttttattctgtattagcgactttgatagacccatcaatattcttttcaatactttcttttgtattaggtggaatgttgtattttaatagtagctctcctttacaaggaatagcaatctgcatttttggactattacatttaatttcaagactatgttatcatagtaaaaaa 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: 19 End: 48 ..................GTTGCTTTTTAATAAGCCTTATGTTAAAAT................................................................................................................................................................................................................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 101 End: 130 ....................................................................................................ATAGAAAAAATAATTCTAAAATGCTATAAT............................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 283 End: 312 ..........................................................................................................................................................................................................................................................................................TTTGATAGACCCATCAATATTCTTTTCAAT......................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttaactcacctcattcaaattttaacataaggcttattaaaaagcaacttaaatagattgctttttaatttagcatacttatgaagttgctctttttataatagaaaaaataattctaaaatgctataattattagggaaaatatcggaggggagaaaatgaaattgcaatttgaattaattaatgagcaaaagtttgatagcaattatgaaaatttaaaaattatggggggagaataatgttttttttaggatatttatttttttattctgtattagcgactttgatagacccatcaatattcttttcaatactttcttttgtattaggtggaatgttgtattttaatagtagctctcctttacaaggaatagcaatctgcatttttggactattacatttaatttcaagactatgttatcatagtaaaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 45 HP_score: -3.8 Tail_Score: -2.81361 Start: 32 End: 74 Full_Region: caacttcataagtat gctaaattaaaaagcaatct attta agttgctttttaataagc cttatgttaaaattt ...............................gctaaattaaaaagcaatctatttaagttgctttttaataagc....................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 67 HP_score: -6.9 Tail_Score: -3.64609 Start: 37 End: 68 Full_Region: TTAACATAAGGCTTA TTAAAAAGCAACT TAAAT AGATTGCTTTTTAA TTTAGCATACTTATG ....................................TTAAAAAGCAACTTAAATAGATTGCTTTTTAA............................................................................................................................................................................................................................................................................................................................................................................. Find igs database================================================ Query_seq: FN1045:FN1046|FN1045:FN1046:hypothetical protein:hypothetical protein:<-->:1696078..1696510 433 ttaactcacctcattcaaattttaacataaggcttattaaaaagcaacttaaatagattgctttttaatttagcatacttatgaagttgctctttttataatagaaaaaataattctaaaatgctataattattagggaaaatatcggaggggagaaaatgaaattgcaatttgaattaattaatgagcaaaagtttgatagcaattatgaaaatttaaaaattatggggggagaataatgttttttttaggatatttatttttttattctgtattagcgactttgatagacccatcaatattcttttcaatactttcttttgtattaggtggaatgttgtattttaatagtagctctcctttacaaggaatagcaatctgcatttttggactattacatttaatttcaagactatgttatcatagtaaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 433 Len: 433 Subject: NC_003454_FN1045_FN1046|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1696078,1696510]|433 HSP 1 e-value: 1.0E-134 bit: 478.0 Len: 241 Query Start:1 Query End:241 Subject Strand: POSITIVE Subject Start: 1 Subject End: 241 ttaactcacctcattcaaattttaacataaggcttattaaaaagcaacttaaatagattgctttttaatttagcatacttatgaagttgctctttttataatagaaaaaataattctaaaatgctataattattagggaaaatatcggaggggagaaaatgaaattgcaatttgaattaattaatgagcaaaagtttgatagcaattatgaaaatttaaaaattatggggggagaataatg................................................................................................................................................................................................ ttaactcacctcattcaaattttaacataaggcttattaaaaagcaacttaaatagattgctttttaatttagcatacttatgaagttgctctttttataatagaaaaaataattctaaaatgctataattattagggaaaatatcggaggggagaaaatgaaattgcaatttgaattaattaatgagcaaaagtttgatagcaattatgaaaatttaaaaattatggggggagaataatg................................................................................................................................................................................................ HSP 2 e-value: 1.0E-89 bit: 331.0 Len: 167 Query Start:267 Query End:433 Subject Strand: POSITIVE Subject Start: 267 Subject End: 433 ..........................................................................................................................................................................................................................................................................attctgtattagcgactttgatagacccatcaatattcttttcaatactttcttttgtattaggtggaatgttgtattttaatagtagctctcctttacaaggaatagcaatctgcatttttggactattacatttaatttcaagactatgttatcatagtaaaaaa ..........................................................................................................................................................................................................................................................................attctgtattagcgactttgatagacccatcaatattcttttcaatactttcttttgtattaggtggaatgttgtattttaatagtagctctcctttacaaggaatagcaatctgcatttttggactattacatttaatttcaagactatgttatcatagtaaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAACUCACCUCAUUCAAAUUUUAACAUAAGGCUUAUUAAAAAGCAACUUAAAUAGAUUGCUUUUUAAUUUAGCAUACUUAUGAAGUUGCUCUUUUUAUAAUAGAAAAAAUAAUUCUAAAAUGCUAUAAUUAUUAGGGAAAAUAUCGGAGGGGAGAAAAUGAAAUUGCAAUUUGAAUUAAUUAAUGAGCAAAAGUUUGAUAGCAAUUAUGAAAAUUUAAAAAUUAUGGGGGGAGAAUAAUGUUUUUUUUAGGAUAUUUAUUUUUUUAUUCUGUAUUAGCGACUUUGAUAGACCCAUCAAUAUUCUUUUCAAUACUUUCUUUUGUAUUAGGUGGAAUGUUGUAUUUUAAUAGUAGCUCUCCUUUACAAGGAAUAGCAAUCUGCAUUUUUGGACUAUUACAUUUAAUUUCAAGACUAUGUUAUCAUAGUAAAAAA .............((((((......(((((((((.((((((((((((((.....)).))))))))))))..)))...))))))..((((((..........(((((.......)))))....(((((.((((...(((....((((((((..(.........((((((...(..((((..............))))..)..))))))................(((((((.((((((((((((((....)))))).))))))))...)))))))....)..))))))))..)))..(((((((((.(..(((((........)))))..).))))))))).....)))).)))))..((((.....))))..)))))).......))))))....................((((((....))))))...... (-84.64) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUUACUAUGAUAACAUAGUCUUGAAAUUAAAUGUAAUAGUCCAAAAAUGCAGAUUGCUAUUCCUUGUAAAGGAGAGCUACUAUUAAAAUACAACAUUCCACCUAAUACAAAAGAAAGUAUUGAAAAGAAUAUUGAUGGGUCUAUCAAAGUCGCUAAUACAGAAUAAAAAAAUAAAUAUCCUAAAAAAAACAUUAUUCUCCCCCCAUAAUUUUUAAAUUUUCAUAAUUGCUAUCAAACUUUUGCUCAUUAAUUAAUUCAAAUUGCAAUUUCAUUUUCUCCCCUCCGAUAUUUUCCCUAAUAAUUAUAGCAUUUUAGAAUUAUUUUUUCUAUUAUAAAAAGAGCAACUUCAUAAGUAUGCUAAAUUAAAAAGCAAUCUAUUUAAGUUGCUUUUUAAUAAGCCUUAUGUUAAAAUUUGAAUGAGGUGAGUUAA ((((..((((((....))))))...)))).......(((((((...............(((.(((((.....)))))))).))))))).............(((((.((.((((.((.((((.((((((.((.....(((((.((.....))..........(((((((.........................)))))))...))))).....))...))))))....)))).))......((((((......(((((((((.(((..........((........))((((......))))......))).))).)))))).((((........)))).))))))...((((((...(((..(((((((((((((........))))))))))))).)))))))))......)))).)).)))))...... (-66.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 716 90 41 181 132 NC_003454:FN1045|5end_hypothetical_protein_1695987..1696217_NEGATIVE 320 289 242 222 179 NC_003454:FN2011|5end_Valyl-tRNA_synthetase_513096..513326_NEGATIVE 269 399 353 216 163 NC_003454:FN0504|5end_Arginine_permease_1155009..1155239_NEGATIVE 248 390 353 70 29 NC_003454:FN0883|5end_hypothetical_protein_1544357..1544587_POSITIVE 246 327 282 219 168 NC_003454:FN1365|5end_GTP-binding_protein_2016739..2016969_NEGATIVE 243 334 299 229 193 NC_003454:FN0276|5end_Sodium-dependent_phosphate_transporter_903323..903553_NEGATIVE 238 277 233 211 168 NC_003454:FN1594|5end_Nitrogen_fixation_protein_RNFG_104893..105123_NEGATIVE 233 398 356 179 147 NC_003454:FN0854|5end_Glucose-1-phosphate_adenylyltransferase_1513487..1513717_NEGATIVE 231 387 343 159 106 NC_003454:FN0128|5end_Spermidine/putrescine-binding_protein_756651..756881_POSITIVE 227 396 352 92 37 NC_003454:FN0741|5end_Glutamate_formiminotransferase_1399956..1400186_NEGATIVE 227 33 3 128 99 NC_003454:FN0279|5end_Lipoprotein_906479..906709_NEGATIVE 224 388 348 95 48 NC_003454:FN1335|5end_Protein_translocase_subunit_YajC_1989011..1989241_NEGATIVE 220 369 327 222 177 NC_003454:FN1471|5end_LACI-family_transcription_regulator_2153004..2153234_POSITIVE 218 364 321 38 5 NC_003454:FN0713|5end_Chromate_transport_protein_1371333..1371563_POSITIVE 216 80 31 122 65 NC_003454:FN1044|5end_hypothetical_protein_1695181..1695411_NEGATIVE 216 299 251 149 100 NC_003454:FN1749|5end_Pyruvate-flavodoxin_oxidoreductase_247461..247691_POSITIVE 213 241 201 221 183 NC_003454:FN1133|5end_N-acetylglucosamine-6-phosphate_deacetylase_1781429..1781659_NEGATIVE 212 103 65 50 13 NC_003454:FN0383|5end_Lipopolysaccharide_N-acetylglucosaminyltransferase_1014148..1014378_POSITIVE 212 397 363 152 115 NC_003454:FN1751|5end_Pyruvate-flavodoxin_oxidoreductase_248067..248297_POSITIVE 211 399 351 67 6 NC_003454:FN1265|5end_Outer_membrane_protein_1921331..1921561_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 243 334 299 131 95 NC_003454:FN0277|3end_hypothetical_protein_903421..903571_NEGATIVE 227 33 3 138 109 NC_003454:FN0280|3end_hypothetical_protein_906469..906619_NEGATIVE 223 358 317 135 89 NC_003454:FN0049|3end_hypothetical_protein_686919..687069_POSITIVE 218 320 271 61 3 NC_003454:FN1204|3end_Methyltransferase_1863161..1863311_NEGATIVE 218 364 321 41 8 NC_003454:FN0712|3end_Chromate_transport_protein_1371416..1371566_POSITIVE 216 80 31 125 68 NC_003454:FN1045|3end_hypothetical_protein_1695178..1695328_NEGATIVE 213 338 295 125 84 NC_003454:FN0651|3end_Ribosomal_large_subunit_pseudouridine_synthase_D_1310260..1310410_POSITIVE 212 103 65 46 9 NC_003454:FN0382|3end_hypothetical_protein_1014224..1014374_POSITIVE 212 397 363 84 47 NC_003454:FN1750|3end_Pyruvate-flavodoxin_oxidoreductase_248079..248229_POSITIVE 212 364 328 85 55 NC_003454:FN1515|3end_Phophatidylinositol-4-phosphate_5-kinase_20652..20802_POSITIVE 211 388 351 86 42 NC_003454:FN1724|3end_Potassium_uptake_protein_KtrA_222654..222804_NEGATIVE 210 68 33 70 27 NC_003454:FN1282|3end_LSU_ribosomal_protein_L17P_1941269..1941419_NEGATIVE 210 370 322 97 36 NC_003454:FN0171|3end_Hypothetical_cytosolic_protein_796921..797071_POSITIVE 208 368 322 64 15 NC_003454:FN1419|3end_methionine_gamma-lyase_2081832..2081982_POSITIVE 208 393 352 132 96 NC_003454:FN0699|3end_Protein_translocase_subunit_secD_1358366..1358516_POSITIVE 208 270 225 104 53 NC_003454:FN1979|3end_SSU_ribosomal_protein_S15P_482073..482223_POSITIVE 207 388 343 129 68 NC_003454:FN1737|3end_V-type_ATP_synthase_subunit_F_236039..236189_NEGATIVE 206 41 3 130 99 NC_003454:FN1114|3end_hypothetical_protein_1758686..1758836_POSITIVE 206 98 61 93 59 NC_003454:FN0344|3end_Methyltransferase_976622..976772_NEGATIVE 205 283 241 58 5 NC_003454:FN1902|3end_Deoxycytidylate_deaminase_390027..390177_NEGATIVE