Origin IGS: cgatccattgattatgaggcttctgtactatttcaaaaagcagattttctgcaggaagagaatcctttagattattcgggccaccctcctgatattcctctgactt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagtcagaggaatatcaggagggtggcccgaataatctaaaggattctcttcctgcagaaaatctgctttttgaaatagtacagaagcctcataatcaatggatcg Mask Tandem Repeat Region ================================================ cgatccattgattatgaggcttctgtactatttcaaaaagcagattttctgcaggaagagaatcctttagattattcgggccaccctcctgatattcctctgactt Find is-nt database================================================ Query_seq: PG0650:PG0651|PG0650:PG0651:hypothetical protein:HDIG domain protein:<-<-:703055..703160 106 cgatccattgattatgaggcttctgtactatttcaaaaagcagattttctgcaggaagagaatcctttagattattcgggccaccctcctgatattcctctgactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0650:PG0651|PG0650:PG0651:hypothetical protein:HDIG domain protein:<-<-:703055..703160 106 cgatccattgattatgaggcttctgtactatttcaaaaagcagattttctgcaggaagagaatcctttagattattcgggccaccctcctgatattcctctgactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0650:PG0651|PG0650:PG0651:hypothetical protein:HDIG domain protein:<-<-:703055..703160 106 cgatccattgattatgaggcttctgtactatttcaaaaagcagattttctgcaggaagagaatcctttagattattcgggccaccctcctgatattcctctgactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgatccattgattatgaggcttctgtactatttcaaaaagcagattttctgcaggaagagaatcctttagattattcgggccaccctcctgatattcctctgactt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 7 End: 105 ...... M D Y E A S V L F Q K A D F L Q E E N P L D Y S G H P P D I P L T . cgatccattgattatgaggcttctgtactatttcaaaaagcagattttctgcaggaagagaatcctttagattattcgggccaccctcctgatattcctctgactt 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================================================ cgatccattgattatgaggcttctgtactatttcaaaaagcagattttctgcaggaagagaatcctttagattattcgggccaccctcctgatattcctctgactt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 83 HP_score: -7.7 Tail_Score: -4.63527 Start: 40 End: 52 Full_Region: aaggattctcttcct gcaga aaa tctgc tttttgaaatagtac .......................................gcagaaaatctgc...................................................... Find igs database================================================ Query_seq: PG0650:PG0651|PG0650:PG0651:hypothetical protein:HDIG domain protein:<-<-:703055..703160 106 cgatccattgattatgaggcttctgtactatttcaaaaagcagattttctgcaggaagagaatcctttagattattcgggccaccctcctgatattcctctgactt Intra-Species Hit: Count: 1 Min: 1 Max: 106 Len: 106 Subject: NC_002950_PG0650_PG0651|hypothetical protein:HDIG domain protein|NEGATIVE:NEGATIVE|[703055,703160]|106 HSP 1 e-value: 6.0E-54 bit: 210.0 Len: 106 Query Start:1 Query End:106 Subject Strand: POSITIVE Subject Start: 1 Subject End: 106 cgatccattgattatgaggcttctgtactatttcaaaaagcagattttctgcaggaagagaatcctttagattattcgggccaccctcctgatattcctctgactt cgatccattgattatgaggcttctgtactatttcaaaaagcagattttctgcaggaagagaatcctttagattattcgggccaccctcctgatattcctctgactt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAUCCAUUGAUUAUGAGGCUUCUGUACUAUUUCAAAAAGCAGAUUUUCUGCAGGAAGAGAAUCCUUUAGAUUAUUCGGGCCACCCUCCUGAUAUUCCUCUGACUU .((((....))))..((((..(((((.............)))))...((((.((((......)))).))))....(((((.......)))))....))))...... (-19.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUCAGAGGAAUAUCAGGAGGGUGGCCCGAAUAAUCUAAAGGAUUCUCUUCCUGCAGAAAAUCUGCUUUUUGAAAUAGUACAGAAGCCUCAUAAUCAAUGGAUCG ......((((......(((((((..(.((............)).)..)))))))((((.....)))).(((((........))))).))))............... (-20.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 967 100 51 191 142 NC_002950:PG0650|5end_hypothetical_protein_702964..703194_NEGATIVE 312 99 51 192 123 NC_002950:PG2173|5end_outer_membrane_lipoprotein_Omp28_2280813..2281043_NEGATIVE 309 89 51 181 149 NC_002950:PG1247|5end_3-dehydroquinate_synthase_1324444..1324674_POSITIVE 308 92 51 200 163 NC_002950:PG0677|5end_saccharopine_dehydrogenase_727653..727883_POSITIVE 302 100 51 216 152 NC_002950:PG1587|5end_PAP2_superfamily_protein_1664983..1665213_POSITIVE 301 100 52 107 41 NC_002950:PG0399|5end_lipoprotein,_putative_436237..436467_NEGATIVE 300 89 43 214 157 NC_002950:PG1930|5end_50S_ribosomal_protein_L29_2020409..2020639_NEGATIVE 297 99 57 44 3 NC_002950:PG1755|5end_fructose-bisphosphate_aldolase_1843278..1843508_NEGATIVE 290 89 50 149 99 NC_002950:PG1538|5end_undecaprenol_kinase,_putative_1617631..1617861_POSITIVE 283 90 46 204 151 NC_002950:PG0987|5end_hypothetical_protein_1048002..1048232_POSITIVE 278 94 51 181 142 NC_002950:PG1381|5end_ABC_transporter,_permease_protein_1460622..1460852_POSITIVE 273 56 18 40 7 NC_002950:PG1215|5end_lipoprotein_protein,_putative_1294621..1294851_POSITIVE 268 90 52 81 41 NC_002950:PG1137|5end_porS_protein_1219597..1219827_NEGATIVE 265 80 39 218 173 NC_002950:PG1630|5end_hypothetical_protein_1711772..1712002_POSITIVE 265 95 53 162 119 NC_002950:PG0189|5end_hypothetical_protein_225291..225521_POSITIVE 261 96 51 213 171 NC_002950:PG0635|5end_ribosomal_protein_L11_methyltransferase_687773..688003_NEGATIVE 260 100 51 160 116 NC_002950:PG0446|5end_thiF_protein_486599..486829_POSITIVE 259 98 62 45 8 NC_002950:PG0583|5end_cell_division_protein_FtsA_640425..640655_POSITIVE 258 100 51 131 93 NC_002950:PG2149|5end_hypothetical_protein_2257658..2257888_NEGATIVE 257 44 1 211 162 NC_002950:PG1301|5end_hypothetical_protein_1379921..1380151_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 97 51 68 21 NC_002950:PG1210|3end_peptidase,_M24_family_1290911..1291061_POSITIVE 301 100 52 99 33 NC_002950:PG0400|3end_hypothetical_protein_436245..436395_NEGATIVE 288 84 41 141 94 NC_002950:PG2174|3end_hypothetical_protein_2280833..2280983_NEGATIVE 286 97 51 67 23 NC_002950:PG0769|3end_fibronectin_type_III_domain_protein_822555..822705_NEGATIVE 269 99 62 116 73 NC_002950:PG1276|3end_DNA-binding_protein,_histone-like_family_1353531..1353681_POSITIVE 268 90 52 84 44 NC_002950:PG1138|3end_pigmentation_and_extracellular_proteinase_regulator_1219594..1219744_NEGATIVE 259 100 64 49 9 NC_002950:PG1723|3end_ribosomal_protein_S20_1813403..1813553_POSITIVE 258 100 51 122 84 NC_002950:PG2150|3end_LysM_domain_protein_2257667..2257817_NEGATIVE 257 98 51 69 24 NC_002950:PG0267|3end_arginyl-tRNA_synthetase_300973..301123_POSITIVE 256 90 42 80 31 NC_002950:PG1370|3end_lysyl-tRNA_synthetase_1450493..1450643_NEGATIVE 256 99 63 116 74 NC_002950:PG0566|3end_DNA-binding_protein,_histone-like_family_622935..623085_NEGATIVE 253 90 41 104 50 NC_002950:PG1950|3end_hypothetical_protein_2040840..2040990_POSITIVE 252 100 51 143 65 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE 251 90 53 62 13 NC_002950:PG1949|3end_malate_dehydrogenase_2038184..2038334_NEGATIVE 251 90 41 67 1 NC_002950:PG0787|3end_hypothetical_protein_837997..838147_POSITIVE 249 83 43 72 33 NC_002950:PG0546|3end_hypothetical_protein_600179..600329_NEGATIVE 244 81 42 129 93 NC_002950:PG1019|3end_lipoprotein,_putative_1080476..1080626_POSITIVE 240 99 51 133 97 NC_002950:PG1006|3end_hypothetical_protein_1063794..1063944_NEGATIVE 239 98 51 41 9 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 239 94 63 37 1 NC_002950:PG0109|3end_hypothetical_protein_132634..132784_POSITIVE