Origin IGS: tttatttttccttttctttttttgggaaagactgcgacgtatttttagataaacaattattttatctaaaaatactagtcaggtctctagcttttgtcccataggagaaagcctctactgacaaatgctttagtttttagtcagtagtgagacgtggggcataagcatttttatattccttttctttaatggaggatctattgt .........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 acaatagatcctccattaaagaaaaggaatataaaaatgcttatgccccacgtctcactactgactaaaaactaaagcatttgtcagtagaggctttctcctatgggacaaaagctagagacctgactagtatttttagataaaataattgtttatctaaaaatacgtcgcagtctttcccaaaaaaagaaaaggaaaaataaa Mask Tandem Repeat Region ================================================ tttatttttccttttctttttttgggaaagactgcgacgtatttttagataaacaattattttatctaaaaatactagtcaggtctctagcttttgtcccataggagaaagcctctactgacaaatgctttagtttttagtcagtagtgagacgtggggcataagcatttttatattccttttctttaatggaggatctattgt Find is-nt database================================================ Query_seq: SMT_1194:SMT_1195|SMT_1194:SMT_1195:phosphoribosylformylglycinamidine cyclo-ligase:amidophosphoribosyltransferase:<-<-:1153262..1153465 204 tttatttttccttttctttttttgggaaagactgcgacgtatttttagataaacaattattttatctaaaaatactagtcaggtctctagcttttgtcccataggagaaagcctctactgacaaatgctttagtttttagtcagtagtgagacgtggggcataagcatttttatattccttttctttaatggaggatctattgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1194:SMT_1195|SMT_1194:SMT_1195:phosphoribosylformylglycinamidine cyclo-ligase:amidophosphoribosyltransferase:<-<-:1153262..1153465 204 tttatttttccttttctttttttgggaaagactgcgacgtatttttagataaacaattattttatctaaaaatactagtcaggtctctagcttttgtcccataggagaaagcctctactgacaaatgctttagtttttagtcagtagtgagacgtggggcataagcatttttatattccttttctttaatggaggatctattgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1194:SMT_1195|SMT_1194:SMT_1195:phosphoribosylformylglycinamidine cyclo-ligase:amidophosphoribosyltransferase:<-<-:1153262..1153465 204 tttatttttccttttctttttttgggaaagactgcgacgtatttttagataaacaattattttatctaaaaatactagtcaggtctctagcttttgtcccataggagaaagcctctactgacaaatgctttagtttttagtcagtagtgagacgtggggcataagcatttttatattccttttctttaatggaggatctattgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttatttttccttttctttttttgggaaagactgcgacgtatttttagataaacaattattttatctaaaaatactagtcaggtctctagcttttgtcccataggagaaagcctctactgacaaatgctttagtttttagtcagtagtgagacgtggggcataagcatttttatattccttttctttaatggaggatctattgt Predict ORF larger than 30AA ================================================ tttatttttccttttctttttttgggaaagactgcgacgtatttttagataaacaattattttatctaaaaatactagtcaggtctctagcttttgtcccataggagaaagcctctactgacaaatgctttagtttttagtcagtagtgagacgtggggcataagcatttttatattccttttctttaatggaggatctattgt 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================================================ tttatttttccttttctttttttgggaaagactgcgacgtatttttagataaacaattattttatctaaaaatactagtcaggtctctagcttttgtcccataggagaaagcctctactgacaaatgctttagtttttagtcagtagtgagacgtggggcataagcatttttatattccttttctttaatggaggatctattgt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 52 HP_score: -4.5 Tail_Score: -3.34398 Start: 32 End: 82 Full_Region: acaaaagctagagac ctgactagtatttttagataaa ataattg tttatctaaaaatacgtcgcag tctttcccaaaaaaa ...............................ctgactagtatttttagataaaataattgtttatctaaaaatacgtcgcag.......................................................................................................................... Find igs database================================================ Query_seq: SMT_1194:SMT_1195|SMT_1194:SMT_1195:phosphoribosylformylglycinamidine cyclo-ligase:amidophosphoribosyltransferase:<-<-:1153262..1153465 204 tttatttttccttttctttttttgggaaagactgcgacgtatttttagataaacaattattttatctaaaaatactagtcaggtctctagcttttgtcccataggagaaagcctctactgacaaatgctttagtttttagtcagtagtgagacgtggggcataagcatttttatattccttttctttaatggaggatctattgt Intra-Species Hit: Count: 1 Min: 24 Max: 204 Len: 181 Subject: smit_SMT_1194_SMT_1195|phosphoribosylformylglycinamidine cyclo- ligase:amidophosphoribosyltransferase|NEGATIVE:NEGATIVE| [1153262,1153465]|204 HSP 1 e-value: 2.0E-98 bit: 359.0 Len: 181 Query Start:24 Query End:204 Subject Strand: POSITIVE Subject Start: 24 Subject End: 204 .......................gggaaagactgcgacgtatttttagataaacaattattttatctaaaaatactagtcaggtctctagcttttgtcccataggagaaagcctctactgacaaatgctttagtttttagtcagtagtgagacgtggggcataagcatttttatattccttttctttaatggaggatctattgt .......................gggaaagactgcgacgtatttttagataaacaattattttatctaaaaatactagtcaggtctctagcttttgtcccataggagaaagcctctactgacaaatgctttagtttttagtcagtagtgagacgtggggcataagcatttttatattccttttctttaatggaggatctattgt Inter-species Hit: Count: 1 Min: 26 Max: 174 Len: 149 Subject: NC_003028_SP_0046_SP_0047|amidophosphoribosyltransferase:phosphorib osylaminoimidazole synthetase|POSITIVE:POSITIVE|[50671,50888]|218 HSP 1 e-value: 1.0E-41 bit: 170.0 Len: 149 Query Start:26 Query End:174 Subject Strand: NEGATIVE Subject Start: 44 Subject End: 193 .........................gaaagactgcgacgtatttttagataaacaattattttatctaaaaatactagtcaggtctctagcttttgtcccataggagaaagcctctactgac-aaatgctttagtttttagtcagtagtgagacgtggggcataagcatttttat.............................. .........................gaaagactgcgacgtatttttagataaaccatctttttatctaaaaatactagtcagggctctagctttgatcctataggacaaagcgtctactgactaaatgcttaagcctttagtcagtagtgagacgtgaggcatatgcatttttat.............................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAGACUGCGACGUAUUUUUAGAUAAACAAUUAUUUUAUCUAAAAAUACUAGUCAGGUCUCUAGCUUUUGUCCCAUAGGAGAAAGCCUCUACUGACAAAUGCUUUAGUUUUUAGUCAGUAGUGAGACGUGGGGCAUAAGCAUUUUUAU ...(((((..((((((((((((((((((.......)))))))))))))))..))).)))))...((((.((((((((.((......)).(((((((((((.((....)).))).))))))))......)))))))).))))........ (-52.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAAAUGCUUAUGCCCCACGUCUCACUACUGACUAAAAACUAAAGCAUUUGUCAGUAGAGGCUUUCUCCUAUGGGACAAAAGCUAGAGACCUGACUAGUAUUUUUAGAUAAAAUAAUUGUUUAUCUAAAAAUACGUCGCAGUCUUUC .......(((........((.(((((.((((((((.................)))))))).((((((.(((....)))..)))))).))))).))....(((((((((((((((.......)))))))))))))))...)))....... (-44.33) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 932 100 51 216 167 smit:SMT_1194|5end_phosphoribosylformylglycinamidine_cyclo-ligase_1153171..1153401_NEGATIVE 316 110 61 60 14 smit:SMT_1555|5end_hypothetical_protein_1541014..1541244_NEGATIVE 316 96 62 165 133 smit:SMT_271|5end_autoinducer-2_production_protein_211736..211966_NEGATIVE 295 131 95 195 163 smit:SMT_1471|5end_hypothetical_protein_1453933..1454163_NEGATIVE 290 94 53 154 106 smit:SMT_354|5end_hypothetical_protein_291343..291573_POSITIVE 289 90 45 101 58 smit:SMT_964|5end_cadmium_resistance_transporter,_putative_910511..910741_NEGATIVE 281 99 51 186 130 smit:SMT_945|5end_cytidylate_kinase_895908..896138_NEGATIVE 278 96 56 222 175 smit:SMT_162|5end_hypothetical_protein_106593..106823_POSITIVE 275 89 49 208 171 smit:SMT_152|5end_sensor_histidine_kinase,_putative_100759..100989_POSITIVE 273 93 57 165 128 smit:SMT_2036|5end_spermidine_synthase_1947879..1948109_NEGATIVE 273 93 57 165 128 smit:SMT_1417|5end_spermidine_synthase_1401686..1401916_NEGATIVE 273 109 66 193 144 smit:SMT_1130|5end_MATE_efflux_family_protein_1065210..1065440_NEGATIVE 268 80 37 204 154 smit:SMT_1350|5end_multidrug_resistance_efflux_pump_1329225..1329455_NEGATIVE 267 97 53 195 138 smit:SMT_772|5end_spermidine/putrescine_ABC_transporter,_ATP-binding_protein_683300..683530_NEGATIVE 264 106 65 187 136 smit:SMT_983|5end_GTP_pyrophosphokinase_930304..930534_NEGATIVE 263 95 52 63 17 smit:SMT_1170|5end_acetyltransferase,_CysE/LacA/LpxA/NodL_family_1118126..1118356_NEGATIVE 263 120 75 221 180 smit:SMT_122|5end_hypothetical_protein_74456..74686_POSITIVE 262 137 100 57 26 smit:SMT_457|5end_hypothetical_protein_396166..396396_POSITIVE 260 104 62 51 1 smit:SMT_1189|5end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1147754..1147984_NEGATIVE 259 88 47 64 26 smit:SMT_460|5end_6-phospho-beta-glucosidase_397819..398049_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 316 96 62 70 38 smit:SMT_272|3end_hypothetical_protein_211831..211981_NEGATIVE 301 109 64 145 107 smit:SMT_306|3end_3-oxoacyl-_249117..249267_POSITIVE 290 94 53 95 47 smit:SMT_353|3end_immunity_protein_BlpL_291364..291514_POSITIVE 278 96 56 135 88 smit:SMT_161|3end_putative_folyl-polyglutamate_synthetase_106586..106736_POSITIVE 273 109 66 132 83 smit:SMT_1131|3end_threonine_synthase_1065271..1065421_NEGATIVE 271 104 62 64 11 smit:SMT_1190|3end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1147741..1147891_NEGATIVE 263 120 75 99 58 smit:SMT_121|3end_hypothetical_protein_74414..74564_POSITIVE 258 94 52 137 89 smit:SMT_576|3end_transcriptional_regulator,_LysR_family_495407..495557_POSITIVE 256 77 48 36 12 smit:SMT_1202|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1163945..1164095_NEGATIVE 252 95 55 83 30 smit:SMT_397|3end_NAD(+)_synthetase_327423..327573_POSITIVE 250 108 69 94 46 smit:SMT_675|3end_DNA_repair_protein_582297..582447_NEGATIVE 250 90 52 109 74 smit:SMT_361|3end_hypothetical_protein_296293..296443_POSITIVE 249 113 78 112 67 smit:SMT_1727|3end_uridine_kinase_1713201..1713351_POSITIVE 248 99 55 52 1 smit:SMT_605|3end_DNA-binding_protein_HU_519257..519407_POSITIVE 242 98 54 48 3 smit:SMT_2003|3end_serine_protease_1924693..1924843_NEGATIVE 242 98 54 62 17 smit:SMT_1925|3end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_1867458..1867608_POSITIVE 242 136 95 130 87 smit:SMT_1594|3end_oligopeptide_transport_system_permease_protein_OppB_1585048..1585198_POSITIVE 242 98 54 70 25 smit:SMT_1557|3end_hypothetical_protein_1543650..1543800_POSITIVE 239 110 62 142 91 smit:SMT_1303|3end_tRNA-dihydrouridine_synthase_1264676..1264826_NEGATIVE 237 94 52 81 38 smit:SMT_1608|3end_hypothetical_protein_1598196..1598346_POSITIVE