Origin IGS: aatttttcctcctcttttaaaattaaattttaaaggttattattatatattacaccacattctttatagtggctaatactttcatcgacatgtcccattctgcaattatggagatggtcctacgactcaccatgtctttacagtacttcattatcttaattatattaaaatcatgctgtactttttctcttgctacaaaataaaaaattatccttgaacttgtttatgtttaggattttcacagattactcttatttttccatgtcttttaataatcttacacttgtcacaaataggttttattgatactcttactttcatttttacctcctttcaaaat .........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 attttgaaaggaggtaaaaatgaaagtaagagtatcaataaaacctatttgtgacaagtgtaagattattaaaagacatggaaaaataagagtaatctgtgaaaatcctaaacataaacaagttcaaggataattttttattttgtagcaagagaaaaagtacagcatgattttaatataattaagataatgaagtactgtaaagacatggtgagtcgtaggaccatctccataattgcagaatgggacatgtcgatgaaagtattagccactataaagaatgtggtgtaatatataataataacctttaaaatttaattttaaaagaggaggaaaaatt Mask Tandem Repeat Region ================================================ aatttttcctcctcttttaaaattaaattttaaaggttattattatatattacaccacattctttatagtggctaatactttcatcgacatgtcccattctgcaattatggagatggtcctacgactcaccatgtctttacagtacttcattatcttaattatattaaaatcatgctgtactttttctcttgctacaaaataaaaaattatccttgaacttgtttatgtttaggattttcacagattactcttatttttccatgtcttttaataatcttacacttgtcacaaataggttttattgatactcttactttcatttttacctcctttcaaaat Find is-nt database================================================ Query_seq: FN1286:FN1287|FN1286:FN1287:30S ribosomal protein S13:Bacterial Protein Translation Initiation Factor 1 (IF-1):<-<-:1944165..1944504 340 aatttttcctcctcttttaaaattaaattttaaaggttattattatatattacaccacattctttatagtggctaatactttcatcgacatgtcccattctgcaattatggagatggtcctacgactcaccatgtctttacagtacttcattatcttaattatattaaaatcatgctgtactttttctcttgctacaaaataaaaaattatccttgaacttgtttatgtttaggattttcacagattactcttatttttccatgtcttttaataatcttacacttgtcacaaataggttttattgatactcttactttcatttttacctcctttcaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1286:FN1287|FN1286:FN1287:30S ribosomal protein S13:Bacterial Protein Translation Initiation Factor 1 (IF-1):<-<-:1944165..1944504 340 aatttttcctcctcttttaaaattaaattttaaaggttattattatatattacaccacattctttatagtggctaatactttcatcgacatgtcccattctgcaattatggagatggtcctacgactcaccatgtctttacagtacttcattatcttaattatattaaaatcatgctgtactttttctcttgctacaaaataaaaaattatccttgaacttgtttatgtttaggattttcacagattactcttatttttccatgtcttttaataatcttacacttgtcacaaataggttttattgatactcttactttcatttttacctcctttcaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1286:FN1287|FN1286:FN1287:30S ribosomal protein S13:Bacterial Protein Translation Initiation Factor 1 (IF-1):<-<-:1944165..1944504 340 aatttttcctcctcttttaaaattaaattttaaaggttattattatatattacaccacattctttatagtggctaatactttcatcgacatgtcccattctgcaattatggagatggtcctacgactcaccatgtctttacagtacttcattatcttaattatattaaaatcatgctgtactttttctcttgctacaaaataaaaaattatccttgaacttgtttatgtttaggattttcacagattactcttatttttccatgtcttttaataatcttacacttgtcacaaataggttttattgatactcttactttcatttttacctcctttcaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatttttcctcctcttttaaaattaaattttaaaggttattattatatattacaccacattctttatagtggctaatactttcatcgacatgtcccattctgcaattatggagatggtcctacgactcaccatgtctttacagtacttcattatcttaattatattaaaatcatgctgtactttttctcttgctacaaaataaaaaattatccttgaacttgtttatgtttaggattttcacagattactcttatttttccatgtcttttaataatcttacacttgtcacaaataggttttattgatactcttactttcatttttacctcctttcaaaat Predict ORF larger than 30AA ================================================ Protein_Len: 58 Strand: + Start: 27 End: 200 .......................... M L K V I I I Y Y T T F F I V A N T F I D M S H S A I M E M V L R L T M S L Q Y F I I L I I L K S C C T F S L A T K ............................................................................................................................................ Protein_Len: 38 Strand: + Start: 190 End: 303 ............................................................................................................................................................................................. M L Q N K K L S L N L F M F R I F T D Y S Y F S M S F N N L T L V T N R F Y ..................................... Protein_Len: 32 Strand: + Start: 245 End: 340 .................................................................................................................................................................................................................................................... M T L I F P C L L I I L H L S Q I G F I D T L T F I F T S F Q N Protein_Len: 37 Strand: - Start: 211 End: 321 .................................................................................................................................................................................................................. G Q V Q K H K P N E C I V R I K G H R K I I K C K D C I P K I S V R V K M ................... Protein_Len: 53 Strand: - Start: 53 End: 211 .................................................... V V N K I T A L V K M S M D W E A I I S I T R R S V M D K C Y K M I K I I N F D H Q V K E R A V F Y F I M ................................................................................................................................. aatttttcctcctcttttaaaattaaattttaaaggttattattatatattacaccacattctttatagtggctaatactttcatcgacatgtcccattctgcaattatggagatggtcctacgactcaccatgtctttacagtacttcattatcttaattatattaaaatcatgctgtactttttctcttgctacaaaataaaaaattatccttgaacttgtttatgtttaggattttcacagattactcttatttttccatgtcttttaataatcttacacttgtcacaaataggttttattgatactcttactttcatttttacctcctttcaaaat 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: 14 End: 43 .............CTTTTAAAATTAAATTTTAAAGGTTATTAT......................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatttttcctcctcttttaaaattaaattttaaaggttattattatatattacaccacattctttatagtggctaatactttcatcgacatgtcccattctgcaattatggagatggtcctacgactcaccatgtctttacagtacttcattatcttaattatattaaaatcatgctgtactttttctcttgctacaaaataaaaaattatccttgaacttgtttatgtttaggattttcacagattactcttatttttccatgtcttttaataatcttacacttgtcacaaataggttttattgatactcttactttcatttttacctcctttcaaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1286:FN1287|FN1286:FN1287:30S ribosomal protein S13:Bacterial Protein Translation Initiation Factor 1 (IF-1):<-<-:1944165..1944504 340 aatttttcctcctcttttaaaattaaattttaaaggttattattatatattacaccacattctttatagtggctaatactttcatcgacatgtcccattctgcaattatggagatggtcctacgactcaccatgtctttacagtacttcattatcttaattatattaaaatcatgctgtactttttctcttgctacaaaataaaaaattatccttgaacttgtttatgtttaggattttcacagattactcttatttttccatgtcttttaataatcttacacttgtcacaaataggttttattgatactcttactttcatttttacctcctttcaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 340 Len: 340 Subject: NC_003454_FN1286_FN1287|30S ribosomal protein S13:Bacterial Protein Translation Initiation Factor 1 (IF-1)|NEGATIVE:NEGATIVE|[1944165,1944504]|340 HSP 1 e-value: 0.0 bit: 674.0 Len: 340 Query Start:1 Query End:340 Subject Strand: POSITIVE Subject Start: 1 Subject End: 340 aatttttcctcctcttttaaaattaaattttaaaggttattattatatattacaccacattctttatagtggctaatactttcatcgacatgtcccattctgcaattatggagatggtcctacgactcaccatgtctttacagtacttcattatcttaattatattaaaatcatgctgtactttttctcttgctacaaaataaaaaattatccttgaacttgtttatgtttaggattttcacagattactcttatttttccatgtcttttaataatcttacacttgtcacaaataggttttattgatactcttactttcatttttacctcctttcaaaat aatttttcctcctcttttaaaattaaattttaaaggttattattatatattacaccacattctttatagtggctaatactttcatcgacatgtcccattctgcaattatggagatggtcctacgactcaccatgtctttacagtacttcattatcttaattatattaaaatcatgctgtactttttctcttgctacaaaataaaaaattatccttgaacttgtttatgtttaggattttcacagattactcttatttttccatgtcttttaataatcttacacttgtcacaaataggttttattgatactcttactttcatttttacctcctttcaaaat Inter-species Hit: Count: 1 Min: 220 Max: 322 Len: 103 Subject: NC_004557_CTC02581_CTC02582|30S ribosomal protein S13:methionine aminopeptidase|NEGATIVE:NEGATIVE|[2735339,2736096]|758 HSP 1 e-value: 3.0E-6 bit: 54.0 Len: 103 Query Start:220 Query End:322 Subject Strand: POSITIVE Subject Start: 119 Subject End: 221 ...........................................................................................................................................................................................................................ttgtttatgtttaggattttcacagattactcttatttttccatgtcttttaataatcttacacttgtcacaaataggttttattgatactcttactttcatt.................. ...........................................................................................................................................................................................................................ttgtttatgtttagggttttcacatataaccattactctgccttttctttttataaccttacatttttcacatataggtttaactgatggtcttactttcatt.................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUUUAUGUUUAGGAUUUUCACAGAUUACUCUUAUUUUUCCAUGUCUUUUAAUAAUCUUACACUUGUCACAAAUAGGUUUUAUUGAUACUCUUACUUUCAUU ((((....((.(((((((.....((((.................))))......))))))).)).....)))).............................. ( -7.33) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAAAGUAAGAGUAUCAAUAAAACCUAUUUGUGACAAGUGUAAGAUUAUUAAAAGACAUGGAAAAAUAAGAGUAAUCUGUGAAAAUCCUAAACAUAAACAA .............................((((((....((((..............))))(((......(((....))).......)))....))))))... ( -7.66) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 256 54 17 129 85 NC_003454:FN1700|5end_hypothetical_protein_195799..196029_NEGATIVE 225 49 13 72 30 NC_003454:FN2019|5end_Ribosome-binding_factor_A_522292..522522_NEGATIVE 222 80 32 127 79 NC_003454:FN1070|5end_glucose-inhibited_division_protein_A_1717121..1717351_POSITIVE 211 80 32 151 79 NC_003454:FN0930|5end_Glycerol-3-phosphate_cytidylyltransferase_1583964..1584194_NEGATIVE 211 100 64 97 65 NC_003454:FN0867|5end_Long-chain-fatty-acid--CoA_ligase_1527048..1527278_NEGATIVE 205 60 11 128 81 NC_003454:FN0656|5end_hypothetical_protein_1313725..1313955_POSITIVE 200 53 13 231 191 NC_003454:FN1125|5end_LemA_protein_1769811..1770041_NEGATIVE 198 44 4 76 26 NC_003454:FN1372|5end_Ribosomal_large_subunit_pseudouridine_synthase_D_2020981..2021211_NEGATIVE 197 80 31 167 119 NC_003454:FN0325|5end_50S_ribosomal_protein_L20_961274..961504_NEGATIVE 196 51 14 215 177 NC_003454:FN1908|5end_Glycerophosphoryl_diester_phosphodiesterase_401669..401899_NEGATIVE 194 60 11 110 58 NC_003454:FN0114|5end_GrpE_protein_747623..747853_POSITIVE 190 69 29 97 52 NC_003454:FN0311|5end_anaerobic_ribonucleoside_triphosphate_reductase_947125..947355_POSITIVE 190 54 13 79 32 NC_003454:FN2036|5end_DNA-directed_RNA_polymerase_beta_chain_546371..546601_NEGATIVE 189 78 42 166 121 NC_003454:FN0904|5end_NAD(FAD)-utilizing_dehydrogenase_1562097..1562327_POSITIVE 188 60 17 102 66 NC_003454:FN0453|5end_Xaa-Pro_aminopeptidase_1097547..1097777_POSITIVE 188 51 14 98 64 NC_003454:FN0019|5end_Transcription-repair_coupling_factor_656549..656779_POSITIVE 187 50 1 191 149 NC_003454:FN0087|5end_Ethanolamine_utilization_protein_eutN_724626..724856_POSITIVE 185 98 63 41 4 NC_003454:FN0414|5end_ATP-dependent_helicase_HEPA_1050174..1050404_POSITIVE 184 81 42 182 138 NC_003454:FN0411|5end_hypothetical_protein_1048240..1048470_POSITIVE 180 60 13 125 74 NC_003454:FN0754|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A_1414646..1414876_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 256 54 17 139 95 NC_003454:FN1701|3end_ABC_transporter_ATP-binding_protein_195789..195939_NEGATIVE 225 49 13 55 13 NC_003454:FN2020|3end_translation_initiation_factor_IF-2_522309..522459_NEGATIVE 214 68 33 131 96 NC_003454:FN0666|3end_hypothetical_protein_1322296..1322446_POSITIVE 205 60 11 113 66 NC_003454:FN0655|3end_hypothetical_protein_1313790..1313940_POSITIVE 198 44 4 59 9 NC_003454:FN1373|3end_EBSC_protein_2020998..2021148_NEGATIVE 197 80 31 142 94 NC_003454:FN0326|3end_LSU_ribosomal_protein_L35P_961299..961449_NEGATIVE 194 60 11 99 47 NC_003454:FN0113|3end_Heat-inducible_transcription_repressor_hrcA_747692..747842_POSITIVE 188 60 17 77 41 NC_003454:FN0452|3end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing]_1097602..1097752_POSITIVE 187 57 12 90 48 NC_003454:FN0106|3end_hypothetical_protein_741462..741612_POSITIVE 184 67 27 40 3 NC_003454:FN0196|3end_Transcriptional_regulator,_FUR_family_822747..822897_POSITIVE 184 72 35 151 113 NC_003454:FN0084|3end_Acetaldehyde_dehydrogenase_[acetylating]_723094..723244_POSITIVE 184 51 11 80 36 NC_003454:FN1972|3end_hypothetical_protein_471703..471853_NEGATIVE 180 60 13 108 57 NC_003454:FN0755|3end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_C_1414663..1414813_NEGATIVE 177 70 24 143 95 NC_003454:FN1045|3end_hypothetical_protein_1695178..1695328_NEGATIVE 177 66 27 110 73 NC_003454:FN0902|3end_5-formyltetrahydrofolate_cyclo-ligase_1561174..1561324_POSITIVE 174 81 41 77 34 NC_003454:FN0437|3end_Allophanate_hydrolase_1078854..1079004_NEGATIVE 174 51 13 145 109 NC_003454:FN0079|3end_Ethanolamine_ammonia-lyase_heavy_chain_719109..719259_POSITIVE 171 47 5 88 42 NC_003454:FN1294|3end_Ribosomal-protein-alanine_acetyltransferase_1952517..1952667_NEGATIVE 171 64 28 48 2 NC_003454:FN0090|3end_Ethanolamine_utilization_protein_eutQ_726844..726994_POSITIVE 171 66 30 124 88 NC_003454:FN1790|3end_Cob(I)alamin_adenosyltransferase_272112..272262_POSITIVE