Origin IGS: cttatattatgcatgtttttaaaaaattgccgcaaaggtaagattttttgccaaaataaaaaatcggtcgcaagggggaaagaacgtcctaacacgacagggattcggcgaaaactccgatgccattatcaacacaggatgatactctgtctatttttctaaatttcagacagatgaaaccactttcacactctttttttcaatgatgtaaatcatttgcgtacaatgaaacgagaaacagttaacaaaattttacgtttttagtccgatattcatgcgttaatctcggaaaagttccttatttttgccgcaaatcttacggagaat .........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 attctccgtaagatttgcggcaaaaataaggaacttttccgagattaacgcatgaatatcggactaaaaacgtaaaattttgttaactgtttctcgtttcattgtacgcaaatgatttacatcattgaaaaaaagagtgtgaaagtggtttcatctgtctgaaatttagaaaaatagacagagtatcatcctgtgttgataatggcatcggagttttcgccgaatccctgtcgtgttaggacgttctttcccccttgcgaccgattttttattttggcaaaaaatcttacctttgcggcaattttttaaaaacatgcataatataag Mask Tandem Repeat Region ================================================ cttatattatgcatgtttttaaaaaattgccgcaaaggtaagattttttgccaaaataaaaaatcggtcgcaagggggaaagaacgtcctaacacgacagggattcggcgaaaactccgatgccattatcaacacaggatgatactctgtctatttttctaaatttcagacagatgaaaccactttcacactctttttttcaatgatgtaaatcatttgcgtacaatgaaacgagaaacagttaacaaaattttacgtttttagtccgatattcatgcgttaatctcggaaaagttccttatttttgccgcaaatcttacggagaat Find is-nt database================================================ Query_seq: TF0608:TF0609|TF0608:TF0609:isoleucyl-tRNA synthetase:conserved hypothetical protein:->->:641479..641805 327 cttatattatgcatgtttttaaaaaattgccgcaaaggtaagattttttgccaaaataaaaaatcggtcgcaagggggaaagaacgtcctaacacgacagggattcggcgaaaactccgatgccattatcaacacaggatgatactctgtctatttttctaaatttcagacagatgaaaccactttcacactctttttttcaatgatgtaaatcatttgcgtacaatgaaacgagaaacagttaacaaaattttacgtttttagtccgatattcatgcgttaatctcggaaaagttccttatttttgccgcaaatcttacggagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0608:TF0609|TF0608:TF0609:isoleucyl-tRNA synthetase:conserved hypothetical protein:->->:641479..641805 327 cttatattatgcatgtttttaaaaaattgccgcaaaggtaagattttttgccaaaataaaaaatcggtcgcaagggggaaagaacgtcctaacacgacagggattcggcgaaaactccgatgccattatcaacacaggatgatactctgtctatttttctaaatttcagacagatgaaaccactttcacactctttttttcaatgatgtaaatcatttgcgtacaatgaaacgagaaacagttaacaaaattttacgtttttagtccgatattcatgcgttaatctcggaaaagttccttatttttgccgcaaatcttacggagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0608:TF0609|TF0608:TF0609:isoleucyl-tRNA synthetase:conserved hypothetical protein:->->:641479..641805 327 cttatattatgcatgtttttaaaaaattgccgcaaaggtaagattttttgccaaaataaaaaatcggtcgcaagggggaaagaacgtcctaacacgacagggattcggcgaaaactccgatgccattatcaacacaggatgatactctgtctatttttctaaatttcagacagatgaaaccactttcacactctttttttcaatgatgtaaatcatttgcgtacaatgaaacgagaaacagttaacaaaattttacgtttttagtccgatattcatgcgttaatctcggaaaagttccttatttttgccgcaaatcttacggagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttatattatgcatgtttttaaaaaattgccgcaaaggtaagattttttgccaaaataaaaaatcggtcgcaagggggaaagaacgtcctaacacgacagggattcggcgaaaactccgatgccattatcaacacaggatgatactctgtctatttttctaaatttcagacagatgaaaccactttcacactctttttttcaatgatgtaaatcatttgcgtacaatgaaacgagaaacagttaacaaaattttacgtttttagtccgatattcatgcgttaatctcggaaaagttccttatttttgccgcaaatcttacggagaat Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 26 End: 139 ......................... M A A K V R F F A K I K N R S Q G G K N V L T R Q G F G E N S D A I I N T G ............................................................................................................................................................................................ Protein_Len: 52 Strand: + Start: 4 End: 159 ... M L C M F L K N C R K G K I F C Q N K K S V A R G K E R P N T T G I R R K L R C H Y Q H R M I L C L F F ........................................................................................................................................................................ Protein_Len: 38 Strand: - Start: 22 End: 135 ..................... F I A A F T L N K A L I F F R D C P P F F T R V R C P N P S F E S A M I L M ................................................................................................................................................................................................ Protein_Len: 34 Strand: - Start: 3 End: 104 .. I N H M N K F F Q R L P L I K Q W F L F D T A L P F S R G L V V P M ............................................................................................................................................................................................................................... cttatattatgcatgtttttaaaaaattgccgcaaaggtaagattttttgccaaaataaaaaatcggtcgcaagggggaaagaacgtcctaacacgacagggattcggcgaaaactccgatgccattatcaacacaggatgatactctgtctatttttctaaatttcagacagatgaaaccactttcacactctttttttcaatgatgtaaatcatttgcgtacaatgaaacgagaaacagttaacaaaattttacgtttttagtccgatattcatgcgttaatctcggaaaagttccttatttttgccgcaaatcttacggagaat Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttatattatgcatgtttttaaaaaattgccgcaaaggtaagattttttgccaaaataaaaaatcggtcgcaagggggaaagaacgtcctaacacgacagggattcggcgaaaactccgatgccattatcaacacaggatgatactctgtctatttttctaaatttcagacagatgaaaccactttcacactctttttttcaatgatgtaaatcatttgcgtacaatgaaacgagaaacagttaacaaaattttacgtttttagtccgatattcatgcgttaatctcggaaaagttccttatttttgccgcaaatcttacggagaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0608:TF0609|TF0608:TF0609:isoleucyl-tRNA synthetase:conserved hypothetical protein:->->:641479..641805 327 cttatattatgcatgtttttaaaaaattgccgcaaaggtaagattttttgccaaaataaaaaatcggtcgcaagggggaaagaacgtcctaacacgacagggattcggcgaaaactccgatgccattatcaacacaggatgatactctgtctatttttctaaatttcagacagatgaaaccactttcacactctttttttcaatgatgtaaatcatttgcgtacaatgaaacgagaaacagttaacaaaattttacgtttttagtccgatattcatgcgttaatctcggaaaagttccttatttttgccgcaaatcttacggagaat Intra-Species Hit: Count: 1 Min: 1 Max: 327 Len: 327 Subject: tfor_TF0608_TF0609|isoleucyl-tRNA synthetase:conserved hypothetical protein|POSITIVE:POSITIVE|[641479,641805]|327 HSP 1 e-value: 1.0E-172 bit: 607.0 Len: 327 Query Start:1 Query End:327 Subject Strand: POSITIVE Subject Start: 1 Subject End: 327 cttatattatgcatgtttttaaaaaattgccgcaaaggtaagattttttgccaaaataaaaaatcggtcgcaagggggaaagaacgtcctaacacgacagggattcggcgaaaactccgatgccattatcaacacaggatgatactctgtctatttttctaaatttcagacagatgaaaccactttcacactcnnnnnnncaatgatgtaaatcatttgcgtacaatgaaacgagaaacagttaacaaaattttacgtttttagtccgatattcatgcgttaatctcggaaaagttccttatttttgccgcaaatcttacggagaat cttatattatgcatgtttttaaaaaattgccgcaaaggtaagattttttgccaaaataaaaaatcggtcgcaagggggaaagaacgtcctaacacgacagggattcggcgaaaactccgatgccattatcaacacaggatgatactctgtctatttttctaaatttcagacagatgaaaccactttcacactctttttttcaatgatgtaaatcatttgcgtacaatgaaacgagaaacagttaacaaaattttacgtttttagtccgatattcatgcgttaatctcggaaaagttccttatttttgccgcaaatcttacggagaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAUAUUAUGCAUGUUUUUAAAAAAUUGCCGCAAAGGUAAGAUUUUUUGCCAAAAUAAAAAAUCGGUCGCAAGGGGGAAAGAACGUCCUAACACGACAGGGAUUCGGCGAAAACUCCGAUGCCAUUAUCAACACAGGAUGAUACUCUGUCUAUUUUUCUAAAUUUCAGACAGAUGAAACCACUUUCACACUCUUUUUUUCAAUGAUGUAAAUCAUUUGCGUACAAUGAAACGAGAAACAGUUAACAAAAUUUUACGUUUUUAGUCCGAUAUUCAUGCGUUAAUCUCGGAAAAGUUCCUUAUUUUUGCCGCAAAUCUUACGGAGAAU (((.....(((((((....((((((((((((.....)))..)))))))))............(((((.(..(((((.(((((..((((((.....((...((..((((.(....).))))..))....)).....))))))....(((((((((((....))))...)))))))........)))))...)))))..(((((.((((((((.....)))))).)).)))))..((((((.((............)))))))).).)))))...)))))))......(((((((((.....)))))).)))...........)))... (-66.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCUCCGUAAGAUUUGCGGCAAAAAUAAGGAACUUUUCCGAGAUUAACGCAUGAAUAUCGGACUAAAAACGUAAAAUUUUGUUAACUGUUUCUCGUUUCAUUGUACGCAAAUGAUUUACAUCAUUGAAAAAAAGAGUGUGAAAGUGGUUUCAUCUGUCUGAAAUUUAGAAAAAUAGACAGAGUAUCAUCCUGUGUUGAUAAUGGCAUCGGAGUUUUCGCCGAAUCCCUGUCGUGUUAGGACGUUCUUUCCCCCUUGCGACCGAUUUUUUAUUUUGGCAAAAAAUCUUACCUUUGCGGCAAUUUUUUAAAAACAUGCAUAAUAUAAG ........(((((.((((.(((((..(((((.....((((((.(((((((((......(((.(((..(((((..((((..........))))..)))))...........((((((....)))))).........))).)))..(((((....((((((((.............))))))))..)))))..))))))))).......)))))).....((((((.....(((((((.(((............))).)))..)))).......))))))......)))))..))))).))))..)))))................... (-67.12) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 392 109 64 54 11 tfor:TF0658|5end_2-amino-3-ketobutyrate_coenzyme_A_ligase_703912..704142_POSITIVE 374 148 105 57 15 tfor:TF1548|5end_thiophene_and_furan_oxidation_protein_1652501..1652731_POSITIVE 366 110 62 196 145 tfor:TF1448|5end_possible_competence_protein_1531711..1531941_POSITIVE 356 130 82 227 171 tfor:TF2712|5end_glycosyltransferase_2885918..2886148_POSITIVE 356 110 63 91 50 tfor:TF1460|5end_6-phosphogluconate_dehydrogenase_1549262..1549492_POSITIVE 351 138 94 206 161 tfor:TF1146|5end_2-dehydropantoate_2-reductase_1227162..1227392_POSITIVE 350 310 261 75 21 tfor:TF0303|5end_conserved_hypothetical_protein_328331..328561_POSITIVE 346 125 81 163 116 tfor:TF1919|5end_hypothetical_protein_2070037..2070267_POSITIVE 346 125 81 123 76 tfor:TF1917|5end_hypothetical_protein_2069997..2070227_POSITIVE 346 120 75 149 118 tfor:TF0473|5end_cation_or_acridine_efflux_membrane-fusion_protein_491047..491277_POSITIVE 344 110 63 128 72 tfor:TF2932|5end_capsule_biosynthesis_protein_3135514..3135744_POSITIVE 339 138 96 109 67 tfor:TF2304|5end_OmpA_family_protein_2459320..2459550_POSITIVE 339 43 2 185 143 tfor:TF0757|5end_50S_ribosomal_protein_L25;_general_stress_protein_804554..804784_POSITIVE 337 102 64 48 17 tfor:TF1297|5end_hypothetical_protein_1379024..1379254_POSITIVE 336 109 65 57 6 tfor:TF1466|5end_DNA_gyrase_modulator_1555469..1555699_POSITIVE 330 107 64 226 169 tfor:TF2502|5end_conserved_hypothetical_protein_2678103..2678333_POSITIVE 329 93 54 199 161 tfor:TF2794|5end_possible_transcriptional_regulator_2979938..2980168_POSITIVE 328 110 65 195 131 tfor:TF2252|5end_transfer_region-related_protein,_TraF_2424621..2424851_POSITIVE 326 110 61 161 120 tfor:TF3145|5end_conserved_hypothetical_protein;_possible_GTP_cyclohydrolase_I_family_3381254..3381484_POSITIVE 326 108 61 58 9 tfor:TF1837|5end_conserved_hypothetical_protein;_possible_outer_membrane_protein_1985480..1985710_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 110 63 69 28 tfor:TF1459|3end_possible_protease_1549320..1549470_POSITIVE 351 138 94 144 99 tfor:TF1145|3end_anaerobic_C4-dicarboxylate_membrane_transporter_1227180..1227330_POSITIVE 346 132 91 150 100 tfor:TF3031|3end_conserved_hypothetical_protein_3255086..3255236_POSITIVE 346 125 81 151 104 tfor:TF1918|3end_hypothetical_protein_2070105..2070255_POSITIVE 346 120 75 79 48 tfor:TF0472|3end_multidrug_resistance_protein,_AcrB/AcrD/AcrF_family_(cation_efflux_pump)_491057..491207_POSITIVE 344 110 63 118 62 tfor:TF2931|3end_3-deoxy-D-manno-2-octulosonic_acid_(Kdo_transferase)_3135584..3135734_POSITIVE 336 109 65 52 1 tfor:TF1465|3end_modulator_of_DNA_gyrase_1555544..1555694_POSITIVE 329 93 54 69 31 tfor:TF2793|3end_possible_L-lysine_2,3-aminomutase_2979888..2980038_POSITIVE 322 110 62 80 7 tfor:TF2391|3end_conserved_hypothetical_protein_2563464..2563614_POSITIVE 321 110 62 75 14 tfor:TF0815|3end_conserved_hypothetical_protein_873974..874124_POSITIVE 320 110 65 145 94 tfor:TF1048|3end_permease_1110217..1110367_POSITIVE 317 119 72 126 81 tfor:TF0141|3end_exodeoxyribonuclease_VII,_large_subunit_149830..149980_POSITIVE 316 139 94 70 23 tfor:TF2464|3end_RNA_polymerase_ECF-type_sigma_factor_2643746..2643896_POSITIVE 311 109 63 72 12 tfor:TF2912|3end_hypothetical_protein_3108000..3108150_POSITIVE 307 110 63 66 8 tfor:TF2392|3end_alpha-galactosidase_2565506..2565656_POSITIVE 307 120 71 69 18 tfor:TF1980|3end_conserved_hypothetical_protein_2130860..2131010_POSITIVE 304 109 69 119 66 tfor:TF1473|3end_hypothetical_protein_1566966..1567116_POSITIVE 302 124 85 61 19 tfor:TF1934|3end_hypothetical_protein_2084079..2084229_POSITIVE 297 109 61 126 72 tfor:TF1635|3end_conserved_hypothetical_protein;_possible_helicase_1746831..1746981_POSITIVE 297 109 65 56 17 tfor:TF0993|3end_hypothetical_protein_1048782..1048932_POSITIVE