Origin IGS: tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaacyccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggyagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc .........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 gagttaaacaactcaaatgattgacttttaaattttaaaggtttatactgaaaaacgaaaacggtaggtgaggctaccatagggatacggatgactrccgcaaagcagtggagacactactcgttggtcaacagtcctggtcgcgaaggccaagactaagctcattacattgccctatggrgttaaagcttgaacgaaaaacagataattagttttttaatcctgccattttatggtgggattttctactgtttaaatcaaagaaaggagatagacgatgcaaattgacgatcatccggaaccgcacatacacagccaatcgctgatttgtgtcattctgcccttataaagtgattggtctctgtgtatgaaacacatcattcatacagataggagaaacca Mask Tandem Repeat Region ================================================ tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaacyccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggyagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc Find is-nt database================================================ Query_seq: SMT_1710:SMT_1711|SMT_1710:SMT_1711:magnesium-translocating P-type ATPase:Xaa-Pro dipeptidase:<-<-:1696121..1696522 402 tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaacyccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggyagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1710:SMT_1711|SMT_1710:SMT_1711:magnesium-translocating P-type ATPase:Xaa-Pro dipeptidase:<-<-:1696121..1696522 402 tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaacyccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggyagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1710:SMT_1711|SMT_1710:SMT_1711:magnesium-translocating P-type ATPase:Xaa-Pro dipeptidase:<-<-:1696121..1696522 402 tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaacyccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggyagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaacyccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggyagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 84 End: 191 ................................................................................... M A V Y V R F R M I V N L H R L S P F F D L N S R K S H H K M A G L K N ................................................................................................................................................................................................................... Protein_Len: 40 Strand: + Start: 238 End: 357 ............................................................................................................................................................................................................................................. M S L V L A F A T R T V D Q R V V S P L L C G S H P Y P Y G S L T Y R F R F S V ............................................. Protein_Len: 30 Strand: + Start: 311 End: 400 ...................................................................................................................................................................................................................................................................................................................... M R I P M V A S P T V F V F Q Y K P L K F K S Q S F E L F N .. Protein_Len: 34 Strand: - Start: 194 End: 295 ................................................................................................................................................................................................. N D T K R E L K L X M P C H L S S L R P R R S W S Q Q G V L L T E M ........................................................................................................... Protein_Len: 32 Strand: - Start: 118 End: 213 ..................................................................................................................... N A D D I E K R Q N L C Y F I G G Y F P L I L F S I I Q K E N M ............................................................................................................................................................................................. Protein_Len: 32 Strand: - Start: 80 End: 175 ............................................................................... R N A T Y T R N R I I T L K C R R D G K K S K F L L F D W W L M ................................................................................................................................................................................................................................... tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaacyccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggyagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc 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: 86 Start: 352 End: 381 ...............................................................................................................................................................................................................................................................................................................................................................ATTGACTTTTAAATTTTAAAGGTTTATACT..................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaacyccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggyagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 87 HP_score: -8.3 Tail_Score: -4.58303 Start: 162 End: 182 Full_Region: taattagttttttaa tcctgccat ttt atggtggga ttttctactgtttaa .................................................................................................................................................................tcctgccattttatggtggga............................................................................................................................................................................................................................ Find igs database================================================ Query_seq: SMT_1710:SMT_1711|SMT_1710:SMT_1711:magnesium-translocating P-type ATPase:Xaa-Pro dipeptidase:<-<-:1696121..1696522 402 tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaacyccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggyagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc Intra-Species Hit: Count: 2 Min: 1 Max: 402 Len: 402 Subject: smit_SMT_1710_SMT_1711|magnesium-translocating P-type ATPase:Xaa-Pro dipeptidase|NEGATIVE:NEGATIVE|[1696121,1696522]|402 HSP 1 e-value: 0.0 bit: 792.0 Len: 402 Query Start:1 Query End:402 Subject Strand: POSITIVE Subject Start: 1 Subject End: 402 tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaacyccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggyagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaacyccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggyagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc Subject: smit_SMT_1708_SMT_1709|magnesium-translocating P-type ATPase:aminopeptidase P|NEGATIVE:NEGATIVE|[1694644,1695045]|402 HSP 1 e-value: 0.0 bit: 792.0 Len: 402 Query Start:1 Query End:402 Subject Strand: POSITIVE Subject Start: 1 Subject End: 402 tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaacyccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggyagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaactccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc Inter-species Hit: Count: 2 Min: 30 Max: 341 Len: 312 Subject: NC_009009_SSA_1735_SSA_1736|UreX, putative:L-cysteine desulfhydrase, putative|NEGATIVE:NEGATIVE|[1721163,1721542]|380 HSP 1 e-value: 1.0E-51 bit: 205.0 Len: 135 Query Start:207 Query End:341 Subject Strand: POSITIVE Subject Start: 163 Subject End: 297 ..............................................................................................................................................................................................................cgttcaagctttaacyccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggyagtcatccgtatccctatggtagcctcacctaccg............................................................. ..............................................................................................................................................................................................................cgttcaagctttaactccataaggcgatgaaatgagcttagtcttgaccttggcgatcaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccttatggtagcctcacctaccg............................................................. Subject: NC_009009_SSA_1734_SSA_1735|Cation (Mg/Ni uptake) transport ATPase, putative:UreX, putative|NEGATIVE:NEGATIVE|[1720394,1720550]|157 HSP 1 e-value: 2.0E-38 bit: 161.0 Len: 113 Query Start:30 Query End:142 Subject Strand: POSITIVE Subject Start: 30 Subject End: 142 .............................tttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctt.................................................................................................................................................................................................................................................................... .............................tttcatacacagggaccaatcactttatgaggacagaacgacacaaatcagcgattggctgtgtatgtgcggttccggataatcgtcaatttgcatcgcatgtctcctttctt.................................................................................................................................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCAUACACAGAGACCAAUCACUUUAUAAGGGCAGAAUGACACAAAUCAGCGAUUGGCUGUGUAUGUGCGGUUCCGGAUGAUCGUCAAUUUGCAUCGUCUAUCUCCUUUCUUUGAUUUAAACAGUAGAAAAUCCCACCAUAAAAUGGCAGGAUUAAAAAACUAAUUAUCUGUUUUUCGUUCAAGCUUUAACYCCAUAGGGCAAUGUAAUGAGCUUAGUCUUGGCCUUCGCGACCAGGACUGUUGACCAACGAGUAGUGUCUCCACUGCUUUGCGGYAGUCAUCCGUAUCCCUAUGGUAGCCUCACCUACCG ...(((((((((...((((((.((.......(.........).......)).)))))))))))))))...((...((((((((.((((((..((.((((.............((((...(((((((((..(((((..((((...))))..)))))......))).....)))))).....))))((((((......))))))......))))))..((((((((.(.....).))))))))))))))....((((((((....)))))))).......))))))))...))....(((((......))))). (-80.24) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGUAGGUGAGGCUACCAUAGGGAUACGGAUGACURCCGCAAAGCAGUGGAGACACUACUCGUUGGUCAACAGUCCUGGUCGCGAAGGCCAAGACUAAGCUCAUUACAUUGCCCUAUGGRGUUAAAGCUUGAACGAAAAACAGAUAAUUAGUUUUUUAAUCCUGCCAUUUUAUGGUGGGAUUUUCUACUGUUUAAAUCAAAGAAAGGAGAUAGACGAUGCAAAUUGACGAUCAUCCGGAACCGCACAUACACAGCCAAUCGCUGAUUUGUGUCAUUCUGCCCUUAUAAAGUGAUUGGUCUCUGUGUAUGAAA ((((..((.(((((.((((((((.....(((((...(((...((.((((....)))).))...))).....((((.(((((.....))))).))))....)))))......))))))))......)))))..))...((((((.....(((......(((((..((((...))))..)))))..)))))))))............((((((...((((....))))...))).)))...))))..((((((((((((((((((.....(.((......)).)......)))))))))...)))))))))... (-94.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1014 80 31 200 151 smit:SMT_1710|5end_magnesium-translocating_P-type_ATPase_1696030..1696260_NEGATIVE 1014 80 31 200 151 smit:SMT_1708|5end_magnesium-translocating_P-type_ATPase_1694553..1694783_NEGATIVE 359 76 31 63 16 smit:SMT_1213|5end_fatty_acid/phospholipid_synthesis_protein_PlsX_1172655..1172885_NEGATIVE 342 258 212 64 10 smit:SMT_302|5end_K07444_putative_N6-adenine-specific_DNA_methylase_244808..245038_POSITIVE 337 257 211 221 156 smit:SMT_2051|5end_enoyl-CoA_hydratase_1960639..1960869_NEGATIVE 325 96 51 222 158 smit:SMT_1825|5end_ATP_synthase_F1,_gamma_subunit_1796927..1797157_POSITIVE 320 250 205 207 155 smit:SMT_1840|5end_6-phosphogluconate_dehydrogenase,_decarboxylating_1806285..1806515_NEGATIVE 318 299 256 150 98 smit:SMT_217|5end_hypothetical_protein_149236..149466_POSITIVE 316 310 282 102 78 smit:SMT_1838|5end_response_regulator_1805400..1805630_NEGATIVE 315 275 231 118 66 smit:SMT_712|5end_alcohol_dehydrogenase,_zinc-containing_620381..620611_NEGATIVE 314 304 262 185 145 smit:SMT_877|5end_hypothetical_protein_824412..824642_NEGATIVE 311 260 214 219 169 smit:SMT_382|5end_valyl-tRNA_synthetase_317706..317936_POSITIVE 306 115 71 109 56 smit:SMT_770|5end_K02053_spermidine/putrescine_transport_system_permease_protein_681359..681589_NEGATIVE 303 276 231 137 78 smit:SMT_941|5end_hypothetical_protein_893558..893788_NEGATIVE 301 254 212 217 164 smit:SMT_367|5end_hypothetical_protein_302318..302548_POSITIVE 300 269 225 107 48 smit:SMT_931|5end_cobyric_acid_synthase_884491..884721_POSITIVE 300 88 50 149 110 smit:SMT_489|5end_K01999_branched-chain_amino_acid_transport_system_substrate-binding_protein_423669..423899_POSITIVE 300 109 70 104 59 smit:SMT_397|5end_NAD(+)_synthetase_326519..326749_POSITIVE 298 246 203 157 105 smit:SMT_335|5end_glutamine_synthetase_273753..273983_POSITIVE 297 98 51 202 157 smit:SMT_1607|5end_K03341_putative_deoxyribonucleotide_triphosphate_pyrophosphatase_1596648..1596878_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 520 310 284 27 1 smit:SMT_1709|3end_aminopeptidase_P_1694956..1695106_NEGATIVE 359 76 31 66 19 smit:SMT_1214|3end_K03584_DNA_repair_protein_RecO_(recombination_protein_O)_1172652..1172802_NEGATIVE 337 270 221 130 78 smit:SMT_494|3end_K04767_acetoin_utilization_protein_AcuB_428891..429041_POSITIVE 337 240 197 84 37 smit:SMT_362|3end_K02519_translation_initiation_factor_IF-2_297950..298100_POSITIVE 334 99 57 39 1 smit:SMT_1525|3end_pneumococcal_histidine_triad_protein_A_precursor_1505873..1506023_NEGATIVE 320 250 205 131 79 smit:SMT_1841|3end_hypothetical_protein_1806361..1806511_NEGATIVE 320 250 205 131 79 smit:SMT_303|3end_hypothetical_protein_245758..245908_POSITIVE 316 310 282 90 66 smit:SMT_1839|3end_6-phosphogluconate_dehydrogenase,_decarboxylating_1805412..1805562_NEGATIVE 314 268 221 118 65 smit:SMT_2081|3end_glycosyltransferase_1981336..1981486_POSITIVE 312 100 51 61 4 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 311 80 31 64 4 smit:SMT_325|3end_K02029_polar_amino_acid_transport_system_permease_protein_262247..262397_NEGATIVE 308 237 197 149 106 smit:SMT_1958|3end_tryptophan_synthase,_beta_subunit_1892052..1892202_POSITIVE 306 115 71 112 59 smit:SMT_771|3end_spermidine/putrescine_transport_system_permease_protein_PotB_681356..681506_NEGATIVE 301 86 49 36 1 smit:SMT_2025|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1940995..1941145_NEGATIVE 300 109 70 107 62 smit:SMT_396|3end_putative_nicotinate_phosphoribosyltransferase_326602..326752_POSITIVE 298 246 203 120 68 smit:SMT_334|3end_K03713_MerR_family_transcriptional_regulator,_glutamine_synthetase_repressor_273796..273946_POSITIVE 294 269 224 102 40 smit:SMT_175|3end_50S_ribosomal_protein_L22_118148..118298_POSITIVE 292 291 256 150 117 smit:SMT_216|3end_Holliday_junction_DNA_helicase_RuvB_149335..149485_POSITIVE 290 232 195 44 3 smit:SMT_1078|3end_folylpolyglutamate_synthase_1015391..1015541_NEGATIVE 289 274 231 54 7 smit:SMT_1914|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1860324..1860474_POSITIVE