Origin IGS: aaaatttcaccctctttttagaaaaatatctattttattattttaacattatttttaaaaaataaaaactagaaattaaaaataatatgacttttttattttaaaactaactcaataataataaatcaatatttcttctaaaatcaattttaaaaagtcctctctttattttttaaaagaactgtttaaattttaaaaaaaaataaaaaaaatagtatacatttggaaatttttatagtataataactttgaaaatgagatgtaactttattactgtgaattgttctttagtattgtgataaatgattctttctagttccattttctaatattaaatttctatatgcttttatagatatattcatttatgttagttagttacttcatcattcaataattttt .........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 aaaaattattgaatgatgaagtaactaactaacataaatgaatatatctataaaagcatatagaaatttaatattagaaaatggaactagaaagaatcatttatcacaatactaaagaacaattcacagtaataaagttacatctcattttcaaagttattatactataaaaatttccaaatgtatactattttttttatttttttttaaaatttaaacagttcttttaaaaaataaagagaggactttttaaaattgattttagaagaaatattgatttattattattgagttagttttaaaataaaaaagtcatattatttttaatttctagtttttattttttaaaaataatgttaaaataataaaatagatatttttctaaaaagagggtgaaatttt Mask Tandem Repeat Region ================================================ aaaatttcaccctctttttagaaaaatatctattttattattttaacattatttttaaaaaataaaaactagaaattaaaaataatatgacttttttattttaaaactaactcaataataataaatcaatatttcttctaaaatcaattttaaaaagtcctctctttattttttaaaagaactgtttaaattttaaaaaaaaataaaaaaaatagtatacatttggaaatttttatagtataataactttgaaaatgagatgtaactttattactgtgaattgttctttagtattgtgataaatgattctttctagttccattttctaatattaaatttctatatgcttttatagatatattcatttatgttagttagttacttcatcattcaataattttt Find is-nt database================================================ Query_seq: FN0527:FN0528|FN0527:FN0528:Alanyl-tRNA synthetase:Cold shock protein:<-->:1184189..1184590 402 aaaatttcaccctctttttagaaaaatatctattttattattttaacattatttttaaaaaataaaaactagaaattaaaaataatatgacttttttattttaaaactaactcaataataataaatcaatatttcttctaaaatcaattttaaaaagtcctctctttattttttaaaagaactgtttaaattttaaaaaaaaataaaaaaaatagtatacatttggaaatttttatagtataataactttgaaaatgagatgtaactttattactgtgaattgttctttagtattgtgataaatgattctttctagttccattttctaatattaaatttctatatgcttttatagatatattcatttatgttagttagttacttcatcattcaataattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0527:FN0528|FN0527:FN0528:Alanyl-tRNA synthetase:Cold shock protein:<-->:1184189..1184590 402 aaaatttcaccctctttttagaaaaatatctattttattattttaacattatttttaaaaaataaaaactagaaattaaaaataatatgacttttttattttaaaactaactcaataataataaatcaatatttcttctaaaatcaattttaaaaagtcctctctttattttttaaaagaactgtttaaattttaaaaaaaaataaaaaaaatagtatacatttggaaatttttatagtataataactttgaaaatgagatgtaactttattactgtgaattgttctttagtattgtgataaatgattctttctagttccattttctaatattaaatttctatatgcttttatagatatattcatttatgttagttagttacttcatcattcaataattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0527:FN0528|FN0527:FN0528:Alanyl-tRNA synthetase:Cold shock protein:<-->:1184189..1184590 402 aaaatttcaccctctttttagaaaaatatctattttattattttaacattatttttaaaaaataaaaactagaaattaaaaataatatgacttttttattttaaaactaactcaataataataaatcaatatttcttctaaaatcaattttaaaaagtcctctctttattttttaaaagaactgtttaaattttaaaaaaaaataaaaaaaatagtatacatttggaaatttttatagtataataactttgaaaatgagatgtaactttattactgtgaattgttctttagtattgtgataaatgattctttctagttccattttctaatattaaatttctatatgcttttatagatatattcatttatgttagttagttacttcatcattcaataattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaatttcaccctctttttagaaaaatatctattttattattttaacattatttttaaaaaataaaaactagaaattaaaaataatatgacttttttattttaaaactaactcaataataataaatcaatatttcttctaaaatcaattttaaaaagtcctctctttattttttaaaagaactgtttaaattttaaaaaaaaataaaaaaaatagtatacatttggaaatttttatagtataataactttgaaaatgagatgtaactttattactgtgaattgttctttagtattgtgataaatgattctttctagttccattttctaatattaaatttctatatgcttttatagatatattcatttatgttagttagttacttcatcattcaataattttt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 189 End: 281 ............................................................................................................................................................................................ I K F F F L F F L I C K S I K I T Y Y S Q F H S T V K N S H M ......................................................................................................................... aaaatttcaccctctttttagaaaaatatctattttattattttaacattatttttaaaaaataaaaactagaaattaaaaataatatgacttttttattttaaaactaactcaataataataaatcaatatttcttctaaaatcaattttaaaaagtcctctctttattttttaaaagaactgtttaaattttaaaaaaaaataaaaaaaatagtatacatttggaaatttttatagtataataactttgaaaatgagatgtaactttattactgtgaattgttctttagtattgtgataaatgattctttctagttccattttctaatattaaatttctatatgcttttatagatatattcatttatgttagttagttacttcatcattcaataattttt 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: 215 End: 244 ......................................................................................................................................................................................................................GTATACATTTGGAAATTTTTATAGTATAAT.............................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 40 End: 69 .......................................GTTTTTATTTTTTAAAAATAATGTTAAAAT............................................................................................................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaatttcaccctctttttagaaaaatatctattttattattttaacattatttttaaaaaataaaaactagaaattaaaaataatatgacttttttattttaaaactaactcaataataataaatcaatatttcttctaaaatcaattttaaaaagtcctctctttattttttaaaagaactgtttaaattttaaaaaaaaataaaaaaaatagtatacatttggaaatttttatagtataataactttgaaaatgagatgtaactttattactgtgaattgttctttagtattgtgataaatgattctttctagttccattttctaatattaaatttctatatgcttttatagatatattcatttatgttagttagttacttcatcattcaataattttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 39 HP_score: -2.8 Tail_Score: -3.2592 Start: 339 End: 356 Full_Region: TTCTAATATTAAATT TCTATA TGCTTT TATAGA TATATTCATTTATGT ..................................................................................................................................................................................................................................................................................................................................................TCTATATGCTTTTATAGA.............................................. Find igs database================================================ Query_seq: FN0527:FN0528|FN0527:FN0528:Alanyl-tRNA synthetase:Cold shock protein:<-->:1184189..1184590 402 aaaatttcaccctctttttagaaaaatatctattttattattttaacattatttttaaaaaataaaaactagaaattaaaaataatatgacttttttattttaaaactaactcaataataataaatcaatatttcttctaaaatcaattttaaaaagtcctctctttattttttaaaagaactgtttaaattttaaaaaaaaataaaaaaaatagtatacatttggaaatttttatagtataataactttgaaaatgagatgtaactttattactgtgaattgttctttagtattgtgataaatgattctttctagttccattttctaatattaaatttctatatgcttttatagatatattcatttatgttagttagttacttcatcattcaataattttt Intra-Species Hit: Count: 1 Min: 213 Max: 402 Len: 190 Subject: NC_003454_FN0527_FN0528|Alanyl-tRNA synthetase:Cold shock protein|NEGATIVE:POSITIVE|[1184189,1184590]|402 HSP 1 e-value: 1.0E-103 bit: 377.0 Len: 190 Query Start:213 Query End:402 Subject Strand: POSITIVE Subject Start: 213 Subject End: 402 ....................................................................................................................................................................................................................tagtatacatttggaaatttttatagtataataactttgaaaatgagatgtaactttattactgtgaattgttctttagtattgtgataaatgattctttctagttccattttctaatattaaatttctatatgcttttatagatatattcatttatgttagttagttacttcatcattcaataattttt ....................................................................................................................................................................................................................tagtatacatttggaaatttttatagtataataactttgaaaatgagatgtaactttattactgtgaattgttctttagtattgtgataaatgattctttctagttccattttctaatattaaatttctatatgcttttatagatatattcatttatgttagttagttacttcatcattcaataattttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUAUACAUUUGGAAAUUUUUAUAGUAUAAUAACUUUGAAAAUGAGAUGUAACUUUAUUACUGUGAAUUGUUCUUUAGUAUUGUGAUAAAUGAUUCUUUCUAGUUCCAUUUUCUAAUAUUAAAUUUCUAUAUGCUUUUAUAGAUAUAUUCAUUUAUGUUAGUUAGUUACUUCAUCAUUCAAUAAUUUUU ..........(((((.(((((((.(((......))).)))))))..((.((((((.....((.((((((.....((((((((((.((.(((((...((....))...)))))))))))))))))..((((((......))))))...))))))....)).....)))))).))....)))))........ (-31.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUUAUUGAAUGAUGAAGUAACUAACUAACAUAAAUGAAUAUAUCUAUAAAAGCAUAUAGAAAUUUAAUAUUAGAAAAUGGAACUAGAAAGAAUCAUUUAUCACAAUACUAAAGAACAAUUCACAGUAAUAAAGUUACAUCUCAUUUUCAAAGUUAUUAUACUAUAAAAAUUUCCAAAUGUAUACUA ........((((((((.((.((((((.......((((((((.....((((((......)))))).........((((.........))))......)))))))).....((((...((.....))..))))....)))))).))))))..))))......(((((.................)))))... (-22.03) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 242 115 72 150 114 NC_003454:FN0211|5end_Plasmid_addiction_system_poison_protein_837224..837454_POSITIVE 237 120 73 119 72 NC_003454:FN0559|5end_Phosphoglucomutase_1211316..1211546_POSITIVE 230 107 76 37 4 NC_003454:FN1624|5end_preprotein_translocase_SecY_132360..132590_NEGATIVE 219 177 133 44 2 NC_003454:FN0610|5end_hypothetical_protein_1264815..1265045_POSITIVE 216 140 94 63 14 NC_003454:FN2022|5end_transcription_elongation_factor_NusA_526145..526375_NEGATIVE 214 116 72 110 60 NC_003454:FN1948|5end_hypothetical_protein_453524..453754_NEGATIVE 210 180 131 185 142 NC_003454:FN0039|5end_DNA_primase_(bacterial_type)_and_small_primase-like_proteins_679212..679442_NEGATIVE 208 130 84 151 111 NC_003454:FN0252|5end_hypothetical_protein_874193..874423_POSITIVE 208 130 84 151 111 NC_003454:FN2060|5end_hypothetical_protein_573649..573879_NEGATIVE 208 130 84 151 111 NC_003454:FN2049|5end_hypothetical_protein_559573..559803_NEGATIVE 204 125 81 83 36 NC_003454:FN1473|5end_N-acetylneuraminate_transporter_large_subunit_2155032..2155262_POSITIVE 203 132 98 82 43 NC_003454:FN0339|5end_hypothetical_protein_972035..972265_POSITIVE 203 110 62 188 134 NC_003454:FN1635|5end_LSU_ribosomal_protein_L14P_136572..136802_NEGATIVE 201 180 132 96 33 NC_003454:FN1369|5end_Zinc_finger_protein_2019006..2019236_NEGATIVE 199 138 92 196 155 NC_003454:FN1807|5end_hypothetical_protein_289479..289709_NEGATIVE 197 109 63 223 181 NC_003454:FN0461|5end_Probable_sigma(54)_modulation_protein_1106522..1106752_POSITIVE 196 65 24 84 49 NC_003454:FN0979|5end_hypothetical_protein_1632096..1632326_POSITIVE 193 136 95 146 98 NC_003454:FN0200|5end_Biotin_carboxyl_carrier_protein_of_glutaconyl-COA_decarboxylase_826123..826353_POSITIVE 192 133 91 129 90 NC_003454:FN1465|5end_Permease_2147986..2148216_POSITIVE 192 133 92 120 70 NC_003454:FN1152|5end_aspartate_aminotransferase_1806617..1806847_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 242 115 72 142 106 NC_003454:FN0210|3end_Transcriptional_regulator,_COPG_family_837296..837446_POSITIVE 237 120 73 135 88 NC_003454:FN0558|3end_TraT_complement_resistance_protein_precursor_1211412..1211562_POSITIVE 214 116 72 100 50 NC_003454:FN1949|3end_Xaa-Pro_dipeptidase_453534..453684_NEGATIVE 208 130 84 134 94 NC_003454:FN0251|3end_Hypothetical_membrane-spanning_Protein_874256..874406_POSITIVE 208 130 84 134 94 NC_003454:FN2061|3end_Hypothetical_membrane-spanning_protein_573666..573816_NEGATIVE 208 130 84 134 94 NC_003454:FN2050|3end_Hypothetical_membrane-spanning_protein_559590..559740_NEGATIVE 205 136 91 142 96 NC_003454:FN2082|3end_Formate--tetrahydrofolate_ligase_593257..593407_NEGATIVE 204 125 81 59 12 NC_003454:FN1472|3end_N-acetylneuraminate-binding_protein_2155088..2155238_POSITIVE 203 169 134 80 42 NC_003454:FN1400|3end_serine/threonine_kinase_2058475..2058625_POSITIVE 203 132 98 64 25 NC_003454:FN0338|3end_hypothetical_protein_972097..972247_POSITIVE 201 180 132 112 49 NC_003454:FN1370|3end_Endonuclease_2018990..2019140_NEGATIVE 199 138 92 147 106 NC_003454:FN1808|3end_hypothetical_protein_289528..289678_NEGATIVE 197 109 63 151 109 NC_003454:FN0460|3end_delta-aminolevulinic_acid_dehydratase_1106530..1106680_POSITIVE 194 100 61 117 75 NC_003454:FN2064|3end_hypothetical_protein_575213..575363_NEGATIVE 193 136 95 108 60 NC_003454:FN0199|3end_hypothetical_protein_826165..826315_POSITIVE 192 140 95 151 106 NC_003454:FN0418|3end_pyrimidine_regulatory_protein_PyrR_1059731..1059881_POSITIVE 187 103 66 86 48 NC_003454:FN0846|3end_hypothetical_protein_1505236..1505386_POSITIVE 187 135 91 146 98 NC_003454:FN0406|3end_Alanine_racemase,_biosynthetic_1043510..1043660_NEGATIVE 186 121 81 121 75 NC_003454:FN1129|3end_Chromosome_partition_protein_smc_1777865..1778015_POSITIVE 186 107 62 47 8 NC_003454:FN0966|3end_Precorrin-6Y_C5,15-methyltransferase_[decarboxylating]_1619280..1619430_NEGATIVE