Origin IGS: ccacaatagaatagaacacatctttgccggttatcctgaaagactcggtctatctctggttgcccccttctttcggggtatggcataattacaatcaaaattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaattttgattgtaattatgccataccccgaaagaagggggcaaccagagatagaccgagtctttcaggataaccggcaaagatgtgttctattctattgtgg Mask Tandem Repeat Region ================================================ ccacaatagaatagaacacatctttgccggttatcctgaaagactcggtctatctctggttgcccccttctttcggggtatggcataattacaatcaaaattt Find is-nt database================================================ Query_seq: PG1625:PG1626|PG1625:PG1626:hypothetical protein:hypothetical protein:->->:1708779..1708881 103 ccacaatagaatagaacacatctttgccggttatcctgaaagactcggtctatctctggttgcccccttctttcggggtatggcataattacaatcaaaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1625:PG1626|PG1625:PG1626:hypothetical protein:hypothetical protein:->->:1708779..1708881 103 ccacaatagaatagaacacatctttgccggttatcctgaaagactcggtctatctctggttgcccccttctttcggggtatggcataattacaatcaaaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1625:PG1626|PG1625:PG1626:hypothetical protein:hypothetical protein:->->:1708779..1708881 103 ccacaatagaatagaacacatctttgccggttatcctgaaagactcggtctatctctggttgcccccttctttcggggtatggcataattacaatcaaaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccacaatagaatagaacacatctttgccggttatcctgaaagactcggtctatctctggttgcccccttctttcggggtatggcataattacaatcaaaattt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 3 End: 101 .. C Y F L V C R Q R N D Q F V R D I E P Q G R R E P Y P M I V I L M .. ccacaatagaatagaacacatctttgccggttatcctgaaagactcggtctatctctggttgcccccttctttcggggtatggcataattacaatcaaaattt 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================================================ ccacaatagaatagaacacatctttgccggttatcctgaaagactcggtctatctctggttgcccccttctttcggggtatggcataattacaatcaaaattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1625:PG1626|PG1625:PG1626:hypothetical protein:hypothetical protein:->->:1708779..1708881 103 ccacaatagaatagaacacatctttgccggttatcctgaaagactcggtctatctctggttgcccccttctttcggggtatggcataattacaatcaaaattt Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: NC_002950_PG1625_PG1626|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1708779,1708881]|103 HSP 1 e-value: 4.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 ccacaatagaatagaacacatctttgccggttatcctgaaagactcggtctatctctggttgcccccttctttcggggtatggcataattacaatcaaaattt ccacaatagaatagaacacatctttgccggttatcctgaaagactcggtctatctctggttgcccccttctttcggggtatggcataattacaatcaaaattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCACAAUAGAAUAGAACACAUCUUUGCCGGUUAUCCUGAAAGACUCGGUCUAUCUCUGGUUGCCCCCUUCUUUCGGGGUAUGGCAUAAUUACAAUCAAAAUUU .............((.........(((((..((((((((((((...(((..((.....)).)))....))))))))))))))))).........))....... (-23.67) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUUUGAUUGUAAUUAUGCCAUACCCCGAAAGAAGGGGGCAACCAGAGAUAGACCGAGUCUUUCAGGAUAACCGGCAAAGAUGUGUUCUAUUCUAUUGUGG ....................(((((((((.......))))......((((.((((.((.(((((((.((....)).).)))))).)).))))))))..))))) (-22.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 438 79 42 87 34 NC_002950:PG0930|5end_hypothetical_protein_987542..987772_NEGATIVE 436 69 21 160 98 NC_002950:PG1185|5end_hypothetical_protein_1267752..1267982_NEGATIVE 380 87 41 185 137 NC_002950:PG0336|5end_hypothetical_protein_371292..371522_NEGATIVE 359 85 46 174 136 NC_002950:PG1274|5end_elongation_factor_P_1351843..1352073_POSITIVE 358 86 45 111 60 NC_002950:PG0769|5end_fibronectin_type_III_domain_protein_824177..824407_NEGATIVE 355 65 21 187 131 NC_002950:PG1442|5end_hypothetical_protein_1528030..1528260_NEGATIVE 352 79 47 195 159 NC_002950:PG2075|5end_hypothetical_protein_2176466..2176696_NEGATIVE 352 65 25 178 132 NC_002950:PG1333|5end_hypothetical_protein_1415425..1415655_NEGATIVE 348 85 44 215 166 NC_002950:PG2119|5end_oxidoreductase,_Gfo/Idh/MocA_family_2226547..2226777_POSITIVE 343 75 37 194 157 NC_002950:PG1807|5end_v-type_ATPase,_subunit_K_1902069..1902299_POSITIVE 339 84 44 212 166 NC_002950:PG0165|5end_heat_shock_protein_15_187807..188037_NEGATIVE 336 86 49 122 87 NC_002950:PG0897|5end_alpha-amylase_family_protein_962472..962702_NEGATIVE 333 64 24 180 137 NC_002950:PG0582|5end_cell_division_protein_FtsQ,_putative_639600..639830_POSITIVE 330 84 41 165 126 NC_002950:PG0166|5end_peptidyl-tRNA_hydrolase_188370..188600_NEGATIVE 329 82 44 60 17 NC_002950:PG2111|5end_thiS_protein_2221482..2221712_NEGATIVE 326 70 23 73 27 NC_002950:PG1366|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1447380..1447610_NEGATIVE 324 65 22 73 28 NC_002950:PG2086|5end_hypothetical_protein_2186571..2186801_POSITIVE 323 79 36 66 8 NC_002950:PG1808|5end_guanosine-3',5'-bis(diphosphate)_3'-pyrophosphohydrolase_1905243..1905473_NEGATIVE 322 65 21 229 176 NC_002950:PG0201|5end_ribonuclease_P_238770..239000_NEGATIVE 313 68 22 108 61 NC_002950:PG1273|5end_hypothetical_protein_1351837..1352067_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 380 87 41 100 52 NC_002950:PG0337|3end_hypothetical_protein_371377..371527_NEGATIVE 358 86 45 129 78 NC_002950:PG0770|3end_hypothetical_protein_824159..824309_NEGATIVE 344 75 36 68 34 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 343 75 37 139 102 NC_002950:PG1806|3end_v-type_ATPase,_subunit_I_1902094..1902244_POSITIVE 340 66 22 111 58 NC_002950:PG1416|3end_enoyl-(acyl-carrier-protein)_reductase_II_1501078..1501228_POSITIVE 340 97 54 134 94 NC_002950:PG0995|3end_hypothetical_protein_1055469..1055619_NEGATIVE 330 84 46 151 104 NC_002950:PG1687|3end_HIT_family_protein_1773812..1773962_NEGATIVE 330 84 43 74 27 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 327 84 45 114 73 NC_002950:PG0132|3end_hypothetical_protein_153054..153204_POSITIVE 322 64 26 75 23 NC_002950:PG1855|3end_carboxyl-terminal_protease_1953842..1953992_NEGATIVE 320 86 50 35 1 NC_002950:PG0898|3end_hypothetical_protein_962559..962709_NEGATIVE 318 80 36 70 29 NC_002950:PG1949|3end_malate_dehydrogenase_2038184..2038334_NEGATIVE 315 70 22 55 3 NC_002950:PG0507|3end_hypothetical_protein_548190..548340_POSITIVE 312 71 33 43 1 NC_002950:PG1367|3end_hypothetical_protein_1447411..1447561_NEGATIVE 311 80 32 110 65 NC_002950:PG1174|3end_thioesterase_family_protein_1253210..1253360_NEGATIVE 307 75 31 124 67 NC_002950:PG1002|3end_hypothetical_protein_1059237..1059387_POSITIVE 306 85 46 42 4 NC_002950:PG0569|3end_hypothetical_protein_624697..624847_NEGATIVE 304 69 23 146 97 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 304 69 23 146 97 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 304 84 45 150 105 NC_002950:PG0558|3end_purine_nucleoside_phosphorylase_615510..615660_NEGATIVE