Origin IGS: atttcaagaatatcaatgcgccaaaactacgtattttcgatctactaacgtggcacagacgtggaacattgtattacaactgttgaaaactcctctatattgttgataaaggctacactatatatatagtaggaaaacgccccacgggaaggaacgccccggctccttgtcggagggggaagggacggacgccatcccccctctcgccatgatgg .........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 ccatcatggcgagaggggggatggcgtccgtcccttccccctccgacaaggagccggggcgttccttcccgtggggcgttttcctactatatatatagtgtagcctttatcaacaatatagaggagttttcaacagttgtaatacaatgttccacgtctgtgccacgttagtagatcgaaaatacgtagttttggcgcattgatattcttgaaat Mask Tandem Repeat Region ================================================ atttcaagaatatcaatgcgccaaaactacgtattttcgatctactaacgtggcacagacgtggaacattgtattacaactgttgaaaactcctctatattgttgataaaggctacactatatatatagtaggaaaacgccccacgggaaggaacgccccggctccttgtcggagggggaagggacggacgccatcccccctctcgccatgatgg Find is-nt database================================================ Query_seq: PG0142:PG0143|PG0142:PG0143:SpoOJ regulator protein:hydrolase, carbon-nitrogen family:<-<-:165622..165836 215 atttcaagaatatcaatgcgccaaaactacgtattttcgatctactaacgtggcacagacgtggaacattgtattacaactgttgaaaactcctctatattgttgataaaggctacactatatatatagtaggaaaacgccccacgggaaggaacgccccggctccttgtcggagggggaagggacggacgccatcccccctctcgccatgatgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0142:PG0143|PG0142:PG0143:SpoOJ regulator protein:hydrolase, carbon-nitrogen family:<-<-:165622..165836 215 atttcaagaatatcaatgcgccaaaactacgtattttcgatctactaacgtggcacagacgtggaacattgtattacaactgttgaaaactcctctatattgttgataaaggctacactatatatatagtaggaaaacgccccacgggaaggaacgccccggctccttgtcggagggggaagggacggacgccatcccccctctcgccatgatgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0142:PG0143|PG0142:PG0143:SpoOJ regulator protein:hydrolase, carbon-nitrogen family:<-<-:165622..165836 215 atttcaagaatatcaatgcgccaaaactacgtattttcgatctactaacgtggcacagacgtggaacattgtattacaactgttgaaaactcctctatattgttgataaaggctacactatatatatagtaggaaaacgccccacgggaaggaacgccccggctccttgtcggagggggaagggacggacgccatcccccctctcgccatgatgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttcaagaatatcaatgcgccaaaactacgtattttcgatctactaacgtggcacagacgtggaacattgtattacaactgttgaaaactcctctatattgttgataaaggctacactatatatatagtaggaaaacgccccacgggaaggaacgccccggctccttgtcggagggggaagggacggacgccatcccccctctcgccatgatgg Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 99 End: 209 .................................................................................................. M V D K G Y T I Y I V G K R P T G R N A P A P C R R G K G R T P S P L S P ...... Protein_Len: 31 Strand: + Start: 122 End: 214 ......................................................................................................................... M Y S R K T P H G K E R P G S L S E G E G T D A I P P L A M M . Protein_Len: 31 Strand: - Start: 121 End: 213 ........................................................................................................................ I Y L L F V G W P F S R G P E K D S P S P V S A M G G R A M M .. atttcaagaatatcaatgcgccaaaactacgtattttcgatctactaacgtggcacagacgtggaacattgtattacaactgttgaaaactcctctatattgttgataaaggctacactatatatatagtaggaaaacgccccacgggaaggaacgccccggctccttgtcggagggggaagggacggacgccatcccccctctcgccatgatgg 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================================================ atttcaagaatatcaatgcgccaaaactacgtattttcgatctactaacgtggcacagacgtggaacattgtattacaactgttgaaaactcctctatattgttgataaaggctacactatatatatagtaggaaaacgccccacgggaaggaacgccccggctccttgtcggagggggaagggacggacgccatcccccctctcgccatgatgg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 60 HP_score: -2.8 Tail_Score: -4.34345 Start: 138 End: 179 Full_Region: tggcgtccgtccctt ccccctccgacaaggagc cggggc gttccttcccgtggggcg ttttcctactatata .........................................................................................................................................ccccctccgacaaggagccggggcgttccttcccgtggggcg.................................... TransTerm Strand: - Conf: 44 HP_score: -4.0 Tail_Score: -2.51207 Start: 140 End: 177 Full_Region: gcgtccgtcccttcc ccctccgacaaggagc cggggc gttccttcccgtgggg cgttttcctactata ...........................................................................................................................................ccctccgacaaggagccggggcgttccttcccgtgggg...................................... Find igs database================================================ Query_seq: PG0142:PG0143|PG0142:PG0143:SpoOJ regulator protein:hydrolase, carbon-nitrogen family:<-<-:165622..165836 215 atttcaagaatatcaatgcgccaaaactacgtattttcgatctactaacgtggcacagacgtggaacattgtattacaactgttgaaaactcctctatattgttgataaaggctacactatatatatagtaggaaaacgccccacgggaaggaacgccccggctccttgtcggagggggaagggacggacgccatcccccctctcgccatgatgg Intra-Species Hit: Count: 1 Min: 1 Max: 215 Len: 215 Subject: NC_002950_PG0142_PG0143|SpoOJ regulator protein:hydrolase, carbon-nitrogen family|NEGATIVE:NEGATIVE|[165622,165836]|215 HSP 1 e-value: 1.0E-118 bit: 426.0 Len: 215 Query Start:1 Query End:215 Subject Strand: POSITIVE Subject Start: 1 Subject End: 215 atttcaagaatatcaatgcgccaaaactacgtattttcgatctactaacgtggcacagacgtggaacattgtattacaactgttgaaaactcctctatattgttgataaaggctacactatatatatagtaggaaaacgccccacgggaaggaacgccccggctccttgtcggagggggaagggacggacgccatcccccctctcgccatgatgg atttcaagaatatcaatgcgccaaaactacgtattttcgatctactaacgtggcacagacgtggaacattgtattacaactgttgaaaactcctctatattgttgataaaggctacactatatatatagtaggaaaacgccccacgggaaggaacgccccggctccttgtcggagggggaagggacggacgccatcccccctctcgccatgatgg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUCAAGAAUAUCAAUGCGCCAAAACUACGUAUUUUCGAUCUACUAACGUGGCACAGACGUGGAACAUUGUAUUACAACUGUUGAAAACUCCUCUAUAUUGUUGAUAAAGGCUACACUAUAUAUAUAGUAGGAAAACGCCCCACGGGAAGGAACGCCCCGGCUCCUUGUCGGAGGGGGAAGGGACGGACGCCAUCCCCCCUCUCGCCAUGAUGG .......(((....((((((.........)))))))))......(((.((((((.....((((((((((((.....))).))))......((((((((((.....(((.((......)).))))))))).)))).......)))))..(((((..((....)))))))...((((((((...((.(....)))...)))))))).)))))).))) (-57.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCAUCAUGGCGAGAGGGGGGAUGGCGUCCGUCCCUUCCCCCUCCGACAAGGAGCCGGGGCGUUCCUUCCCGUGGGGCGUUUUCCUACUAUAUAUAUAGUGUAGCCUUUAUCAACAAUAUAGAGGAGUUUUCAACAGUUGUAAUACAAUGUUCCACGUCUGUGCCACGUUAGUAGAUCGAAAAUACGUAGUUUUGGCGCAUUGAUAUUCUUGAAAU ..((((...((.(((((((((.(((....).)).)))))))))))..(((((((......)))))))..(((((((((((....((((((....))))))...(((((((.......))))))).....................)))))))))))..(((((((.....(((.........))).......))))))).))))........... (-62.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 897 60 11 151 102 NC_002950:PG0142|5end_SpoOJ_regulator_protein_165531..165761_NEGATIVE 475 197 154 114 71 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 472 178 134 71 21 NC_002950:PG1522|5end_mandelate_racemase/muconate_lactonizing_enzyme_family_protein_1600170..1600400_NEGATIVE 466 208 161 184 129 NC_002950:PG0157|5end_regulatory_protein_RecX_179706..179936_POSITIVE 452 186 142 67 1 NC_002950:PG2126|5end_conserved_hypothetical_protein_TIGR00044_2233112..2233342_NEGATIVE 438 169 125 202 140 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 436 179 131 59 11 NC_002950:PG0304|5end_electron_transport_complex,_RnfABCDGE_type,_C_subunit_339559..339789_POSITIVE 433 188 144 180 116 NC_002950:PG0344|5end_purple_acid_phosphatase_380012..380242_NEGATIVE 432 200 151 196 130 NC_002950:PG0526|5end_putative_inner_membrane_protein_translocase_component_YidC_570746..570976_POSITIVE 422 180 139 204 155 NC_002950:PG1285|5end_glucosamine-6-phosphate_deaminase_1362894..1363124_POSITIVE 420 194 155 51 2 NC_002950:PG2106|5end_hypothetical_protein_2214694..2214924_POSITIVE 416 193 151 44 4 NC_002950:PG1338|5end_umuC_protein_1418246..1418476_POSITIVE 415 200 151 72 15 NC_002950:PG1888|5end_hypothetical_protein_1985596..1985826_POSITIVE 414 188 142 58 1 NC_002950:PG0099|5end_phenylalanyl-tRNA_synthetase_beta_subunit_118286..118516_NEGATIVE 411 199 151 89 43 NC_002950:PG2052|5end_dihydrodipicolinate_synthase_2149636..2149866_POSITIVE 409 188 145 167 116 NC_002950:PG0166|5end_peptidyl-tRNA_hydrolase_188370..188600_NEGATIVE 408 189 144 65 17 NC_002950:PG0670|5end_lipoprotein,_putative_720752..720982_POSITIVE 407 207 163 197 129 NC_002950:PG2149|5end_hypothetical_protein_2257658..2257888_NEGATIVE 404 180 132 213 161 NC_002950:PG1633|5end_galactokinase_1713385..1713615_POSITIVE 402 180 131 126 68 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 507 188 141 124 68 NC_002950:PG1859|3end_glycerate_kinase_family_protein_1957174..1957324_NEGATIVE 472 178 134 71 21 NC_002950:PG1523|3end_naphthoate_synthase_1600170..1600320_NEGATIVE 452 186 142 70 4 NC_002950:PG2127|3end_hypothetical_protein_2233109..2233259_NEGATIVE 442 189 146 41 2 NC_002950:PG0864|3end_site-specific_recombinase,_resolvase_family_927049..927199_NEGATIVE 432 200 151 68 2 NC_002950:PG0525|3end_CTP_synthetase_570698..570848_POSITIVE 428 198 155 126 66 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 427 180 139 90 29 NC_002950:PG1087|3end_radical_SAM_protein,_TIGR01212_family_1154820..1154970_POSITIVE 425 194 155 81 42 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 417 187 144 115 69 NC_002950:PG1559|3end_aminomethyltransferase_1637904..1638054_NEGATIVE 415 200 151 75 18 NC_002950:PG1887|3end_rhodanese-like_domain_protein_1985679..1985829_POSITIVE 409 180 132 78 22 NC_002950:PG0172|3end_exonuclease_194355..194505_POSITIVE 406 180 131 150 94 NC_002950:PG0746|3end_sensor_histidine_kinase_792536..792686_NEGATIVE 402 180 131 145 87 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 400 180 131 150 95 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 399 209 161 124 61 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 397 197 153 75 35 NC_002950:PG0712|3end_hypothetical_protein_766784..766934_NEGATIVE 396 189 141 128 64 NC_002950:PG2026|3end_phosphoglycerate_mutase_family_protein_2125545..2125695_POSITIVE 396 195 156 75 35 NC_002950:PG0052|3end_sensor_histidine_kinase_64686..64836_POSITIVE 394 189 144 87 37 NC_002950:PG0139|3end_membrane-bound_lytic_murein_transglycosylase_D,_putative_161786..161936_NEGATIVE 391 193 154 36 1 NC_002950:PG1337|3end_umuD_protein_1418318..1418468_POSITIVE