Origin IGS: tctttctccttttgttttttgagagccgtgtcaaattgacttacggatgcaacgctctattatttttgaacacgcacaagatttctcttatgcaatattcacattttatcatatccctatttcagaaaatgtcaagtaaaatccaaaaaaaatttcctaacgttcggattttaagaaaagacctacaagtttttgtaggtctttttacttgattttagtagtagtcgaacatttttttctgatttgttactatctttttgtgaagcgtaattaaatgcatcattaaaatttgacgatttatgattgctataatttttattagactataagtaacaagagataaagctaccaagactatcaggaaagttaaaagacatttttgagactagggcatttcatagctgaaaatgcagaataatgagcaaactagtttcaaaaaagtagcaact .........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 agttgctacttttttgaaactagtttgctcattattctgcattttcagctatgaaatgccctagtctcaaaaatgtcttttaactttcctgatagtcttggtagctttatctcttgttacttatagtctaataaaaattatagcaatcataaatcgtcaaattttaatgatgcatttaattacgcttcacaaaaagatagtaacaaatcagaaaaaaatgttcgactactactaaaatcaagtaaaaagacctacaaaaacttgtaggtcttttcttaaaatccgaacgttaggaaattttttttggattttacttgacattttctgaaatagggatatgataaaatgtgaatattgcataagagaaatcttgtgcgtgttcaaaaataatagagcgttgcatccgtaagtcaatttgacacggctctcaaaaaacaaaaggagaaaga Mask Tandem Repeat Region ================================================ tctttctccttttgttttttgagagccgtgtcaaattgacttacggatgcaacgctctattatttttgaacacgcacaagatttctcttatgcaatattcacattttatcatatccctatttcagaaaatgtcaagtaaaatccaaaaaaaatttcctaacgttcggattttaagaaaagacctacaagtttttgtaggtctttttacttgattttagtagtagtcgaacatttttttctgatttgttactatctttttgtgaagcgtaattaaatgcatcattaaaatttgacgatttatgattgctataatttttattagactataagtaacaagagataaagctaccaagactatcaggaaagttaaaagacatttttgagactagggcatttcatagctgaaaatgcagaataatgagcaaactagtttcaaaaaagtagcaact Find is-nt database================================================ Query_seq: SSA_1316:SSA_1317|SSA_1316:SSA_1317:Nicotinamide mononucleotide transporter, putative:hypothetical protein:<-<-:1333039..1333487 449 tctttctccttttgttttttgagagccgtgtcaaattgacttacggatgcaacgctctattatttttgaacacgcacaagatttctcttatgcaatattcacattttatcatatccctatttcagaaaatgtcaagtaaaatccaaaaaaaatttcctaacgttcggattttaagaaaagacctacaagtttttgtaggtctttttacttgattttagtagtagtcgaacatttttttctgatttgttactatctttttgtgaagcgtaattaaatgcatcattaaaatttgacgatttatgattgctataatttttattagactataagtaacaagagataaagctaccaagactatcaggaaagttaaaagacatttttgagactagggcatttcatagctgaaaatgcagaataatgagcaaactagtttcaaaaaagtagcaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1316:SSA_1317|SSA_1316:SSA_1317:Nicotinamide mononucleotide transporter, putative:hypothetical protein:<-<-:1333039..1333487 449 tctttctccttttgttttttgagagccgtgtcaaattgacttacggatgcaacgctctattatttttgaacacgcacaagatttctcttatgcaatattcacattttatcatatccctatttcagaaaatgtcaagtaaaatccaaaaaaaatttcctaacgttcggattttaagaaaagacctacaagtttttgtaggtctttttacttgattttagtagtagtcgaacatttttttctgatttgttactatctttttgtgaagcgtaattaaatgcatcattaaaatttgacgatttatgattgctataatttttattagactataagtaacaagagataaagctaccaagactatcaggaaagttaaaagacatttttgagactagggcatttcatagctgaaaatgcagaataatgagcaaactagtttcaaaaaagtagcaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1316:SSA_1317|SSA_1316:SSA_1317:Nicotinamide mononucleotide transporter, putative:hypothetical protein:<-<-:1333039..1333487 449 tctttctccttttgttttttgagagccgtgtcaaattgacttacggatgcaacgctctattatttttgaacacgcacaagatttctcttatgcaatattcacattttatcatatccctatttcagaaaatgtcaagtaaaatccaaaaaaaatttcctaacgttcggattttaagaaaagacctacaagtttttgtaggtctttttacttgattttagtagtagtcgaacatttttttctgatttgttactatctttttgtgaagcgtaattaaatgcatcattaaaatttgacgatttatgattgctataatttttattagactataagtaacaagagataaagctaccaagactatcaggaaagttaaaagacatttttgagactagggcatttcatagctgaaaatgcagaataatgagcaaactagtttcaaaaaagtagcaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctttctccttttgttttttgagagccgtgtcaaattgacttacggatgcaacgctctattatttttgaacacgcacaagatttctcttatgcaatattcacattttatcatatccctatttcagaaaatgtcaagtaaaatccaaaaaaaatttcctaacgttcggattttaagaaaagacctacaagtttttgtaggtctttttacttgattttagtagtagtcgaacatttttttctgatttgttactatctttttgtgaagcgtaattaaatgcatcattaaaatttgacgatttatgattgctataatttttattagactataagtaacaagagataaagctaccaagactatcaggaaagttaaaagacatttttgagactagggcatttcatagctgaaaatgcagaataatgagcaaactagtttcaaaaaagtagcaact Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 35 End: 136 .................................. M D L R M Q R S I I F E H A Q D F S Y A I F T F Y H I P I S E N V K ......................................................................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 12 End: 209 ........... M F F E S R V K L T Y G C N A L L F L N T H K I S L M Q Y S H F I I S L F Q K M S S K I Q K K F P N V R I L R K D L Q V ................................................................................................................................................................................................................................................ Protein_Len: 48 Strand: - Start: 218 End: 361 ......................................................................................................................................................................................................................... Y Y D F M K K Q N T V I K K H L T I L H M M L I Q R N I I A I I K I L S Y T V L S L A V L V I M ........................................................................................ tctttctccttttgttttttgagagccgtgtcaaattgacttacggatgcaacgctctattatttttgaacacgcacaagatttctcttatgcaatattcacattttatcatatccctatttcagaaaatgtcaagtaaaatccaaaaaaaatttcctaacgttcggattttaagaaaagacctacaagtttttgtaggtctttttacttgattttagtagtagtcgaacatttttttctgatttgttactatctttttgtgaagcgtaattaaatgcatcattaaaatttgacgatttatgattgctataatttttattagactataagtaacaagagataaagctaccaagactatcaggaaagttaaaagacatttttgagactagggcatttcatagctgaaaatgcagaataatgagcaaactagtttcaaaaaagtagcaact 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================================================ tctttctccttttgttttttgagagccgtgtcaaattgacttacggatgcaacgctctattatttttgaacacgcacaagatttctcttatgcaatattcacattttatcatatccctatttcagaaaatgtcaagtaaaatccaaaaaaaatttcctaacgttcggattttaagaaaagacctacaagtttttgtaggtctttttacttgattttagtagtagtcgaacatttttttctgatttgttactatctttttgtgaagcgtaattaaatgcatcattaaaatttgacgatttatgattgctataatttttattagactataagtaacaagagataaagctaccaagactatcaggaaagttaaaagacatttttgagactagggcatttcatagctgaaaatgcagaataatgagcaaactagtttcaaaaaagtagcaact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -11.7 Tail_Score: -4.97312 Start: 180 End: 201 Full_Region: CGGATTTTAAGAAAA GACCTACAA GTTT TTGTAGGTC TTTTTACTTGATTTT ...................................................................................................................................................................................GACCTACAAGTTTTTGTAGGTC........................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 100 HP_score: -11.7 Tail_Score: -4.65916 Start: 180 End: 201 Full_Region: aaaatcaagtaaaaa gacctacaa aaac ttgtaggtc ttttcttaaaatccg ...................................................................................................................................................................................gacctacaaaaacttgtaggtc........................................................................................................................................................................................................................................................ Find igs database================================================ Query_seq: SSA_1316:SSA_1317|SSA_1316:SSA_1317:Nicotinamide mononucleotide transporter, putative:hypothetical protein:<-<-:1333039..1333487 449 tctttctccttttgttttttgagagccgtgtcaaattgacttacggatgcaacgctctattatttttgaacacgcacaagatttctcttatgcaatattcacattttatcatatccctatttcagaaaatgtcaagtaaaatccaaaaaaaatttcctaacgttcggattttaagaaaagacctacaagtttttgtaggtctttttacttgattttagtagtagtcgaacatttttttctgatttgttactatctttttgtgaagcgtaattaaatgcatcattaaaatttgacgatttatgattgctataatttttattagactataagtaacaagagataaagctaccaagactatcaggaaagttaaaagacatttttgagactagggcatttcatagctgaaaatgcagaataatgagcaaactagtttcaaaaaagtagcaact Intra-Species Hit: Count: 1 Min: 1 Max: 449 Len: 449 Subject: NC_009009_SSA_1316_SSA_1317|Nicotinamide mononucleotide transporter, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1333039,1333487]|449 HSP 1 e-value: 0.0 bit: 801.0 Len: 449 Query Start:1 Query End:449 Subject Strand: POSITIVE Subject Start: 1 Subject End: 449 tctttctccttttgttttttgagagccgtgtcaaattgacttacggatgcaacgctctattatttttgaacacgcacaagatttctcttatgcaatattcacattttatcatatccctatttcagaaaatgtcaagtaaaatccnnnnnnnntttcctaacgttcggattttaagaaaagacctacaagtttttgtaggtctttttacttgattttagtagtagtcgaacannnnnnnctgatttgttactatctttttgtgaagcgtaattaaatgcatcattaaaatttgacgatttatgattgctataatttttattagactataagtaacaagagataaagctaccaagactatcaggaaagttaaaagacatttttgagactagggcatttcatagctgaaaatgcagaataatgagcaaactagtttcaaaaaagtagcaact tctttctccttttgttttttgagagccgtgtcaaattgacttacggatgcaacgctctattatttttgaacacgcacaagatttctcttatgcaatattcacattttatcatatccctatttcagaaaatgtcaagtaaaatccaaaaaaaatttcctaacgttcggattttaagaaaagacctacaagtttttgtaggtctttttacttgattttagtagtagtcgaacatttttttctgatttgttactatctttttgtgaagcgtaattaaatgcatcattaaaatttgacgatttatgattgctataatttttattagactataagtaacaagagataaagctaccaagactatcaggaaagttaaaagacatttttgagactagggcatttcatagctgaaaatgcagaataatgagcaaactagtttcaaaaaagtagcaact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUCUCCUUUUGUUUUUUGAGAGCCGUGUCAAAUUGACUUACGGAUGCAACGCUCUAUUAUUUUUGAACACGCACAAGAUUUCUCUUAUGCAAUAUUCACAUUUUAUCAUAUCCCUAUUUCAGAAAAUGUCAAGUAAAAUCCAAAAAAAAUUUCCUAACGUUCGGAUUUUAAGAAAAGACCUACAAGUUUUUGUAGGUCUUUUUACUUGAUUUUAGUAGUAGUCGAACAUUUUUUUCUGAUUUGUUACUAUCUUUUUGUGAAGCGUAAUUAAAUGCAUCAUUAAAAUUUGACGAUUUAUGAUUGCUAUAAUUUUUAUUAGACUAUAAGUAACAAGAGAUAAAGCUACCAAGACUAUCAGGAAAGUUAAAAGACAUUUUUGAGACUAGGGCAUUUCAUAGCUGAAAAUGCAGAAUAAUGAGCAAACUAGUUUCAAAAAAGUAGCAACU ..............((((((((((.(((((((.....)))..)))).......((((.((((((((.......(((.((((....)))).)))........((((((....(((((((((((((((((.((((...((((((((.....................)))))))).((((((((((((((....))))))))))))))..((((((((....((((((......((((.(((..(((((((((....(((.((((.((((......)))).)))).))).(((((..(.(((((.....)))))...)..))))).....)))))))))))).)))).......))))))....))))))))..))))))))))))).)))))......)))....)))))).)))))))))))).......))))))))))......... (-102.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUGCUACUUUUUUGAAACUAGUUUGCUCAUUAUUCUGCAUUUUCAGCUAUGAAAUGCCCUAGUCUCAAAAAUGUCUUUUAACUUUCCUGAUAGUCUUGGUAGCUUUAUCUCUUGUUACUUAUAGUCUAAUAAAAAUUAUAGCAAUCAUAAAUCGUCAAAUUUUAAUGAUGCAUUUAAUUACGCUUCACAAAAAGAUAGUAACAAAUCAGAAAAAAAUGUUCGACUACUACUAAAAUCAAGUAAAAAGACCUACAAAAACUUGUAGGUCUUUUCUUAAAAUCCGAACGUUAGGAAAUUUUUUUUGGAUUUUACUUGACAUUUUCUGAAAUAGGGAUAUGAUAAAAUGUGAAUAUUGCAUAAGAGAAAUCUUGUGCGUGUUCAAAAAUAAUAGAGCGUUGCAUCCGUAAGUCAAUUUGACACGGCUCUCAAAAAACAAAAGGAGAAAGA .........((((((((.....((.(((((((((((..((((((.((....))))))))....(((((.....((((((((...........(((.((.((((((..........))))))...)).)))...........(((.....((((((((((........))))).))))).....))).....))))))))........((((((((....((......))........((((((.(((((((((((((....)))))))))))))...((((((((((...............))))))))))))))))..))))))))....)))))...........(((((((.((((((((....)))))))))))))))..)))))).)))))..))..((((..(((.....)))))))...)))))))).............. (-104.86) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 873 60 11 151 102 NC_009009:SSA_1316|5end_Nicotinamide_mononucleotide_transporter,_putative_1332948..1333178_NEGATIVE 308 50 1 142 97 NC_009009:SSA_1867|5end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1863096..1863326_NEGATIVE 297 50 1 188 139 NC_009009:SSA_1632|5end_Surface_protein,_putative_1634045..1634275_NEGATIVE 292 45 6 217 168 NC_009009:SSA_1468|5end_3-dehydroquinate_synthase,_putative_1475452..1475682_NEGATIVE 289 50 1 157 93 NC_009009:SSA_0217|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213183..213413_POSITIVE 280 69 21 61 14 NC_009009:SSA_1784|5end_Glutamate_racemase,_putative_1769897..1770127_NEGATIVE 275 379 337 70 26 NC_009009:SSA_0206|5end_hypothetical_protein_204256..204486_POSITIVE 271 49 6 42 2 NC_009009:SSA_0860|5end_N-acetylmuramidase/lysin,_putative_847615..847845_POSITIVE 270 56 11 107 52 NC_009009:SSA_2344|5end_hypothetical_protein_2346537..2346767_POSITIVE 269 398 352 194 137 NC_009009:SSA_1057|5end_Aminotransferase,_class-V,_putative_1073771..1074001_POSITIVE 266 58 11 56 3 NC_009009:SSA_0474|5end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_476270..476500_POSITIVE 265 423 383 107 63 NC_009009:SSA_1847|5end_RRNA_methyltransferase_RsmB,_putative_1842004..1842234_NEGATIVE 264 59 13 72 23 NC_009009:SSA_1326|5end_Peptidase_T,_putative_1342432..1342662_POSITIVE 262 70 28 210 158 NC_009009:SSA_2292|5end_DNA_segregation_ATPase_FtsK/SpoIIIE-like_protein,_putative_2294173..2294403_POSITIVE 257 89 41 178 124 NC_009009:SSA_0298|5end_Malate_permease,_putative_291336..291566_POSITIVE 256 49 7 80 34 NC_009009:SSA_0411|5end_hypothetical_protein_407238..407468_NEGATIVE 255 411 371 145 111 NC_009009:SSA_1667|5end_hypothetical_protein_1667704..1667934_NEGATIVE 253 278 233 129 83 NC_009009:SSA_0803|5end_hypothetical_protein_785145..785375_POSITIVE 250 48 2 140 96 NC_009009:SSA_1698|5end_Galactose-6-phosphate_isomerase,_LacB_subunit,_putative_1690648..1690878_NEGATIVE 249 411 371 42 1 NC_009009:SSA_0204|5end_Nisin_biosynthesis_two-component_response_transcriptional_regulator_nisR,_putative_202057..202287_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 308 50 1 142 97 NC_009009:SSA_1868|3end_ABC-type_arginine/histidine_transport_system,_permease_component,_putative_1863096..1863246_NEGATIVE 297 50 1 127 78 NC_009009:SSA_1633|3end_FimA_fimbrial_subunit-like_protein,_putative_1634106..1634256_NEGATIVE 275 379 337 73 29 NC_009009:SSA_2393|3end_Transcriptional_regulator,_XRE_family,_putative_204339..204489_POSITIVE 269 398 352 93 36 NC_009009:SSA_1056|3end_Firmicute_fructose-1,6-bisphosphatase,_putative_1073750..1073900_POSITIVE 267 58 13 144 87 NC_009009:SSA_2207|3end_hypothetical_protein_2206868..2207018_NEGATIVE 261 205 161 84 52 NC_009009:SSA_1262|3end_tRNA_modification_GTPase,_possibly_iron-binding,_putative_1289235..1289385_POSITIVE 258 59 13 148 107 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 256 49 7 63 17 NC_009009:SSA_0412|3end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_407255..407405_NEGATIVE 255 411 371 111 77 NC_009009:SSA_1668|3end_NrdI_protein,_putative_1667738..1667888_NEGATIVE 253 278 233 132 86 NC_009009:SSA_0802|3end_hypothetical_protein_785228..785378_POSITIVE 250 48 2 123 79 NC_009009:SSA_1699|3end_hypothetical_protein_1690665..1690815_NEGATIVE 248 42 3 67 23 NC_009009:SSA_2146|3end_Metallo-beta-lactamase,_putative_2146732..2146882_NEGATIVE 241 406 364 68 27 NC_009009:SSA_0741|3end_Acetylornithine_deacetylase/Succinyl-diaminopimelate_desuccinylase,_putative_725190..725340_POSITIVE 239 42 3 114 69 NC_009009:SSA_2187|3end_Conserved_hypothetical_membrane_associated_protein_2188951..2189101_POSITIVE 238 46 6 136 98 NC_009009:SSA_1957|3end_Glycosyl_transferase_N-acetylglucosaminyltransferase,_putative_1953504..1953654_NEGATIVE 238 50 7 129 84 NC_009009:SSA_0205|3end_NisK_(sensor-receptor_histidine_kinase_domain),_putative_203839..203989_POSITIVE 237 117 72 55 6 NC_009009:SSA_2281|3end_hypothetical_protein_2281912..2282062_NEGATIVE 234 71 35 146 119 NC_009009:SSA_0142|3end_hypothetical_protein_137489..137639_POSITIVE 233 28 2 126 98 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 233 390 344 60 5 NC_009009:SSA_1379|3end_hypothetical_protein_1398178..1398328_NEGATIVE