Origin IGS: aggctccgtgaagtcctccgacctgtaaatatcgggccgacggacttgatactataaacccttccgattttatacttaaaaacccattggagagatctgacaaatccttgggtagatcgagaaaaaactactagtactaaatgtgttttctgtagaaagtgacgcgagaattttggcgcataaaccagtccgatatgaaatggcgtatgttgcatt .........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 aatgcaacatacgccatttcatatcggactggtttatgcgccaaaattctcgcgtcactttctacagaaaacacatttagtactagtagttttttctcgatctacccaaggatttgtcagatctctccaatgggtttttaagtataaaatcggaagggtttatagtatcaagtccgtcggcccgatatttacaggtcggaggacttcacggagcct Mask Tandem Repeat Region ================================================ aggctccgtgaagtcctccgacctgtaaatatcgggccgacggacttgatactataaacccttccgattttatacttaaaaacccattggagagatctgacaaatccttgggtagatcgagaaaaaactactagtactaaatgtgttttctgtagaaagtgacgcgagaattttggcgcataaaccagtccgatatgaaatggcgtatgttgcatt Find is-nt database================================================ Query_seq: PG1095:PG1096|PG1095:PG1096:RNA methyltransferase, TrmA family:hypothetical protein:->->:1161763..1161978 216 aggctccgtgaagtcctccgacctgtaaatatcgggccgacggacttgatactataaacccttccgattttatacttaaaaacccattggagagatctgacaaatccttgggtagatcgagaaaaaactactagtactaaatgtgttttctgtagaaagtgacgcgagaattttggcgcataaaccagtccgatatgaaatggcgtatgttgcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1095:PG1096|PG1095:PG1096:RNA methyltransferase, TrmA family:hypothetical protein:->->:1161763..1161978 216 aggctccgtgaagtcctccgacctgtaaatatcgggccgacggacttgatactataaacccttccgattttatacttaaaaacccattggagagatctgacaaatccttgggtagatcgagaaaaaactactagtactaaatgtgttttctgtagaaagtgacgcgagaattttggcgcataaaccagtccgatatgaaatggcgtatgttgcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1095:PG1096|PG1095:PG1096:RNA methyltransferase, TrmA family:hypothetical protein:->->:1161763..1161978 216 aggctccgtgaagtcctccgacctgtaaatatcgggccgacggacttgatactataaacccttccgattttatacttaaaaacccattggagagatctgacaaatccttgggtagatcgagaaaaaactactagtactaaatgtgttttctgtagaaagtgacgcgagaattttggcgcataaaccagtccgatatgaaatggcgtatgttgcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggctccgtgaagtcctccgacctgtaaatatcgggccgacggacttgatactataaacccttccgattttatacttaaaaacccattggagagatctgacaaatccttgggtagatcgagaaaaaactactagtactaaatgtgttttctgtagaaagtgacgcgagaattttggcgcataaaccagtccgatatgaaatggcgtatgttgcatt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 67 End: 159 .................................................................. M L Y L K T H W R D L T N P W V D R E K T T S T K C V F C R K ......................................................... Protein_Len: 33 Strand: + Start: 116 End: 214 ................................................................................................................... M E K K L L V L N V F S V E S D A R I L A H K P V R Y E M A Y V A .. Protein_Len: 41 Strand: - Start: 79 End: 201 .............................................................................. F G M P S I Q C I R P Y I S F F S S T S F T N E T S L S A L I K A C L G T R Y S M ............... Protein_Len: 60 Strand: - Start: 3 End: 215 .. G V S K I S Y V R G I K Y K F V W Q L S R V F G Q T S R S F V V L V L H T K Q L F H R S F K P A Y V L G I H F P T H Q M . Protein_Len: 34 Strand: - Start: 2 End: 103 . A G H L G G V Q L Y R A S P S S V I F G E S K I S L F G N S L D S M ................................................................................................................. aggctccgtgaagtcctccgacctgtaaatatcgggccgacggacttgatactataaacccttccgattttatacttaaaaacccattggagagatctgacaaatccttgggtagatcgagaaaaaactactagtactaaatgtgttttctgtagaaagtgacgcgagaattttggcgcataaaccagtccgatatgaaatggcgtatgttgcatt 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================================================ aggctccgtgaagtcctccgacctgtaaatatcgggccgacggacttgatactataaacccttccgattttatacttaaaaacccattggagagatctgacaaatccttgggtagatcgagaaaaaactactagtactaaatgtgttttctgtagaaagtgacgcgagaattttggcgcataaaccagtccgatatgaaatggcgtatgttgcatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1095:PG1096|PG1095:PG1096:RNA methyltransferase, TrmA family:hypothetical protein:->->:1161763..1161978 216 aggctccgtgaagtcctccgacctgtaaatatcgggccgacggacttgatactataaacccttccgattttatacttaaaaacccattggagagatctgacaaatccttgggtagatcgagaaaaaactactagtactaaatgtgttttctgtagaaagtgacgcgagaattttggcgcataaaccagtccgatatgaaatggcgtatgttgcatt Intra-Species Hit: Count: 1 Min: 1 Max: 216 Len: 216 Subject: NC_002950_PG1095_PG1096|RNA methyltransferase, TrmA family:hypothetical protein|POSITIVE:POSITIVE|[1161763,1161978]|216 HSP 1 e-value: 1.0E-119 bit: 428.0 Len: 216 Query Start:1 Query End:216 Subject Strand: POSITIVE Subject Start: 1 Subject End: 216 aggctccgtgaagtcctccgacctgtaaatatcgggccgacggacttgatactataaacccttccgattttatacttaaaaacccattggagagatctgacaaatccttgggtagatcgagaaaaaactactagtactaaatgtgttttctgtagaaagtgacgcgagaattttggcgcataaaccagtccgatatgaaatggcgtatgttgcatt aggctccgtgaagtcctccgacctgtaaatatcgggccgacggacttgatactataaacccttccgattttatacttaaaaacccattggagagatctgacaaatccttgggtagatcgagaaaaaactactagtactaaatgtgttttctgtagaaagtgacgcgagaattttggcgcataaaccagtccgatatgaaatggcgtatgttgcatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGCUCCGUGAAGUCCUCCGACCUGUAAAUAUCGGGCCGACGGACUUGAUACUAUAAACCCUUCCGAUUUUAUACUUAAAAACCCAUUGGAGAGAUCUGACAAAUCCUUGGGUAGAUCGAGAAAAAACUACUAGUACUAAAUGUGUUUUCUGUAGAAAGUGACGCGAGAAUUUUGGCGCAUAAACCAGUCCGAUAUGAAAUGGCGUAUGUUGCAUU ...((((((.((((((..((.((((.......)))).))..))))))..((((........(((((((((...........(((((..(((.............))).))))))))))).)))....((((.((.((.......))...))))))..))))))).))).......(((((((..(((.((......))..)))..)))).)))... (-47.82) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGCAACAUACGCCAUUUCAUAUCGGACUGGUUUAUGCGCCAAAAUUCUCGCGUCACUUUCUACAGAAAACACAUUUAGUACUAGUAGUUUUUUCUCGAUCUACCCAAGGAUUUGUCAGAUCUCUCCAAUGGGUUUUUAAGUAUAAAAUCGGAAGGGUUUAUAGUAUCAAGUCCGUCGGCCCGAUAUUUACAGGUCGGAGGACUUCACGGAGCCU ...((..((((.((((.(((.....))).)))).)))).)).......(((.(((...((((....)))).........((((((.(((.((((((.((((..(((((((((((.....)))).))....))))).............)))))))))).))))))))).((((((..(((((.(.......).)))))..)))))).))))))... (-47.76) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 420 48 1 196 152 NC_002950:PG1947|5end_TPR_domain_protein_2032932..2033162_POSITIVE 388 49 1 75 15 NC_002950:PG0022|5end_sulfate_permease_family_protein_26796..27026_NEGATIVE 364 49 2 197 145 NC_002950:PG2202|5end_Holliday_junction_resolvase-like_protein_2309933..2310163_NEGATIVE 350 44 3 54 5 NC_002950:PG0282|5end_ABC_transporter,_ATP-binding_protein_316915..317145_NEGATIVE 347 50 2 76 26 NC_002950:PG2205|5end_2-dehydropantoate_2-reductase_2316121..2316351_POSITIVE 347 47 1 103 53 NC_002950:PG1886|5end_GTP-binding_protein_HflX_1984536..1984766_NEGATIVE 344 50 1 106 45 NC_002950:PG1576|5end_L-aspartate_oxidase_1653016..1653246_POSITIVE 344 49 1 70 21 NC_002950:PG1233|5end_hypothetical_protein_1309885..1310115_POSITIVE 344 46 3 200 149 NC_002950:PG0888|5end_hypothetical_protein_949910..950140_POSITIVE 341 43 1 231 198 NC_002950:PG1950|5end_hypothetical_protein_2039600..2039830_POSITIVE 337 71 32 160 119 NC_002950:PG0463|5end_folylpolyglutamate_synthase_507606..507836_NEGATIVE 336 46 1 52 8 NC_002950:PG0714|5end_copper_homeostasis_protein_CutC_768671..768901_NEGATIVE 333 50 2 124 86 NC_002950:PG0769|5end_fibronectin_type_III_domain_protein_824177..824407_NEGATIVE 328 50 5 173 123 NC_002950:PG1561|5end_dTDP-4-dehydrorhamnose_reductase_1640995..1641225_NEGATIVE 328 205 163 52 15 NC_002950:PG0985|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1046930..1047160_POSITIVE 326 40 2 73 29 NC_002950:PG1651|5end_TPR_domain_protein_1730326..1730556_POSITIVE 324 46 4 217 172 NC_002950:PG0285|5end_hypothetical_protein_318459..318689_POSITIVE 315 49 5 181 127 NC_002950:PG1633|5end_galactokinase_1713385..1713615_POSITIVE 313 207 161 176 124 NC_002950:PG0871|5end_hypothetical_protein_934836..935066_NEGATIVE 313 44 2 101 53 NC_002950:PG0605|5end_hypothetical_protein_662406..662636_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 45 7 148 105 NC_002950:PG0363|3end_hypothetical_protein_398377..398527_POSITIVE 347 50 2 62 12 NC_002950:PG2204|3end_hypothetical_protein_2316187..2316337_POSITIVE 336 49 1 144 95 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 336 46 1 47 3 NC_002950:PG0715|3end_transporter_768676..768826_NEGATIVE 336 47 3 137 73 NC_002950:PG0129|3end_mannosyltransferase_151789..151939_POSITIVE 333 50 2 142 104 NC_002950:PG0770|3end_hypothetical_protein_824159..824309_NEGATIVE 328 46 1 92 57 NC_002950:PG1411|3end_potassium_uptake_protein_TrkA,_putative_1493481..1493631_NEGATIVE 315 49 5 131 77 NC_002950:PG1632|3end_aldose_1-epimerase_1713415..1713565_POSITIVE 313 44 2 56 8 NC_002950:PG0606|3end_hypothetical_protein_662451..662601_NEGATIVE 305 53 13 43 2 NC_002950:PG1723|3end_ribosomal_protein_S20_1813403..1813553_POSITIVE 299 49 1 85 29 NC_002950:PG0656|3end_50S_ribosomal_protein_L34_706945..707095_NEGATIVE 297 210 164 68 11 NC_002950:PG1566|3end_glutamyl-tRNA_synthetase_1645884..1646034_NEGATIVE 295 46 2 92 47 NC_002950:PG2041|3end_hypothetical_protein_2139235..2139385_NEGATIVE 295 46 5 127 84 NC_002950:PG1043|3end_ferrous_iron_transport_protein_B_1110675..1110825_NEGATIVE 290 40 2 68 7 NC_002950:PG1340|3end_L-lactate_permease_1420298..1420448_NEGATIVE 289 44 1 110 71 NC_002950:PG1956|3end_4-hydroxybutyrate_CoA-transferase_2046215..2046365_NEGATIVE 289 186 150 34 4 NC_002950:PG0354|3end_hypothetical_protein_389131..389281_NEGATIVE 286 42 7 73 43 NC_002950:PG1942|3end_30S_ribosomal_protein_S12_2027946..2028096_NEGATIVE 285 48 1 133 71 NC_002950:PG2142|3end_GTP-binding_protein_Era_2248564..2248714_POSITIVE 285 195 152 52 9 NC_002950:PG0948|3end_AMP_nucleosidase_1008747..1008897_POSITIVE