Origin IGS: cgtattttaggcctgattatcaggttattatggttaaggccccccattttgggggatcttaaccatttcgtgtctatagttttcccaagttaaaattgtcctgaattttag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctaaaattcaggacaattttaacttgggaaaactatagacacgaaatggttaagatcccccaaaatggggggccttaaccataataacctgataatcaggcctaaaatacg Mask Tandem Repeat Region ================================================ cgtattttaggcctgattatcaggttattatggttaaggccccccattttgggggatcttaaccatttcgtgtctatagttttcccaagttaaaattgtcctgaattttag Find is-nt database================================================ Query_seq: PG0393:PG0394|PG0393:PG0394:ribosomal protein L7/L12:DNA-directed RNA polymerase beta subunit:->->:425078..425188 111 cgtattttaggcctgattatcaggttattatggttaaggccccccattttgggggatcttaaccatttcgtgtctatagttttcccaagttaaaattgtcctgaattttag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0393:PG0394|PG0393:PG0394:ribosomal protein L7/L12:DNA-directed RNA polymerase beta subunit:->->:425078..425188 111 cgtattttaggcctgattatcaggttattatggttaaggccccccattttgggggatcttaaccatttcgtgtctatagttttcccaagttaaaattgtcctgaattttag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0393:PG0394|PG0393:PG0394:ribosomal protein L7/L12:DNA-directed RNA polymerase beta subunit:->->:425078..425188 111 cgtattttaggcctgattatcaggttattatggttaaggccccccattttgggggatcttaaccatttcgtgtctatagttttcccaagttaaaattgtcctgaattttag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgtattttaggcctgattatcaggttattatggttaaggccccccattttgggggatcttaaccatttcgtgtctatagttttcccaagttaaaattgtcctgaattttag Predict ORF larger than 30AA ================================================ cgtattttaggcctgattatcaggttattatggttaaggccccccattttgggggatcttaaccatttcgtgtctatagttttcccaagttaaaattgtcctgaattttag 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================================================ cgtattttaggcctgattatcaggttattatggttaaggccccccattttgggggatcttaaccatttcgtgtctatagttttcccaagttaaaattgtcctgaattttag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -18.0 Tail_Score: -3.91597 Start: 31 End: 65 Full_Region: ATTATCAGGTTATTA TGGTTAAGGCCCCCCA TTT TGGGGGATCTTAACCA TTTCGTGTCTATAGT ..............................TGGTTAAGGCCCCCCATTTTGGGGGATCTTAACCA.............................................. Find igs database================================================ Query_seq: PG0393:PG0394|PG0393:PG0394:ribosomal protein L7/L12:DNA-directed RNA polymerase beta subunit:->->:425078..425188 111 cgtattttaggcctgattatcaggttattatggttaaggccccccattttgggggatcttaaccatttcgtgtctatagttttcccaagttaaaattgtcctgaattttag Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: NC_002950_PG0393_PG0394|ribosomal protein L7/L12:DNA-directed RNA polymerase beta subunit|POSITIVE:POSITIVE|[425078,425188]|111 HSP 1 e-value: 7.0E-57 bit: 220.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 cgtattttaggcctgattatcaggttattatggttaaggccccccattttgggggatcttaaccatttcgtgtctatagttttcccaagttaaaattgtcctgaattttag cgtattttaggcctgattatcaggttattatggttaaggccccccattttgggggatcttaaccatttcgtgtctatagttttcccaagttaaaattgtcctgaattttag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUAUUUUAGGCCUGAUUAUCAGGUUAUUAUGGUUAAGGCCCCCCAUUUUGGGGGAUCUUAACCAUUUCGUGUCUAUAGUUUUCCCAAGUUAAAAUUGUCCUGAAUUUUAG .....((((((((((.....)))).....(((((((((..(((((.....)))))..))))))))).........((((((((........))))))))))))))...... (-34.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAAAAUUCAGGACAAUUUUAACUUGGGAAAACUAUAGACACGAAAUGGUUAAGAUCCCCCAAAAUGGGGGGCCUUAACCAUAAUAACCUGAUAAUCAGGCCUAAAAUACG .(((((((......)))))))..(((((.................(((((((((..(((((.....)))))..))))))))).....((((.....)))))))))...... (-35.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 47 1 118 63 NC_002950:PG0026|5end_hypothetical_protein_29234..29464_POSITIVE 315 58 13 79 18 NC_002950:PG1511|5end_hypothetical_protein_1587609..1587839_POSITIVE 311 57 11 57 12 NC_002950:PG1112|5end_hypothetical_protein_1185003..1185233_POSITIVE 305 80 33 224 160 NC_002950:PG1459|5end_hypothetical_protein_1539769..1539999_NEGATIVE 292 69 22 94 29 NC_002950:PG0144|5end_hypothetical_protein_167668..167898_NEGATIVE 289 69 21 181 131 NC_002950:PG0791|5end_adenylate_kinase_843177..843407_NEGATIVE 275 72 39 28 1 NC_002950:PG2171|5end_D-isomer_specific_2-hydroxyacid_dehydrogenase_family_protein_2278972..2279202_NEGATIVE 275 68 21 93 25 NC_002950:PG0293|5end_secretion_activator_protein,_putative_328671..328901_NEGATIVE 273 59 18 189 151 NC_002950:PG1020|5end_hypothetical_protein_1080568..1080798_POSITIVE 268 49 1 221 162 NC_002950:PG0072|5end_UDP-3-O-[3-hydroxymyristoyl]_glucosamine_N-acyltransferase_87147..87377_NEGATIVE 267 64 22 73 18 NC_002950:PG1682|5end_glycosyl_transferase,_group_1_family_protein_1768385..1768615_POSITIVE 265 56 12 223 174 NC_002950:PG0027|5end_hypothetical_protein_32681..32911_POSITIVE 260 87 42 191 149 NC_002950:PG1352|5end_hypothetical_protein_1433150..1433380_NEGATIVE 260 58 11 229 169 NC_002950:PG0366|5end_hypothetical_protein_400815..401045_NEGATIVE 259 73 32 95 60 NC_002950:PG2112|5end_hypothetical_protein_2221471..2221701_POSITIVE 258 99 51 167 126 NC_002950:PG0150|5end_conserved_hypothetical_protein_TIGR01125_173544..173774_NEGATIVE 255 99 51 115 52 NC_002950:PG2080|5end_adenosylmethionine--8-amino-7-oxononanoate_transaminase_2180679..2180909_NEGATIVE 252 58 11 188 137 NC_002950:PG2110|5end_thiamine_biosynthesis_protein_ThiC_2221212..2221442_NEGATIVE 251 77 31 126 73 NC_002950:PG2052|5end_dihydrodipicolinate_synthase_2149636..2149866_POSITIVE 249 74 32 142 102 NC_002950:PG2087|5end_hypothetical_protein_2186990..2187220_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 425 66 30 61 25 NC_002950:PG0393|3end_ribosomal_protein_L7/L12_425017..425167_POSITIVE 282 69 21 54 4 NC_002950:PG0282|3end_ABC_transporter,_ATP-binding_protein_316244..316394_NEGATIVE 276 41 3 150 100 NC_002950:PG0792|3end_hypoxanthine_phosphoribosyltransferase_843178..843328_NEGATIVE 273 68 22 69 10 NC_002950:PG1488|3end_hypothetical_protein_1562228..1562378_POSITIVE 271 79 31 97 47 NC_002950:PG2126|3end_conserved_hypothetical_protein_TIGR00044_2232438..2232588_NEGATIVE 270 72 39 148 111 NC_002950:PG0007|3end_hypothetical_protein_6755..6905_NEGATIVE 269 60 11 131 80 NC_002950:PG0084|3end_L-serine_dehydratase,_iron-sulfur-dependent,_single_chain_form_99111..99261_POSITIVE 268 49 1 128 69 NC_002950:PG0073|3end_orotidine_5'-monophosphate_decarboxylase_87240..87390_NEGATIVE 267 64 22 76 21 NC_002950:PG1681|3end_glycogen_debranching_enzyme,_archaeal_type,_putative_1768468..1768618_POSITIVE 265 56 12 147 98 NC_002950:PG0026|3end_hypothetical_protein_32685..32835_POSITIVE 260 87 42 140 98 NC_002950:PG1353|3end_orotate_phosphoribosyltransferase_1433201..1433351_NEGATIVE 255 99 51 125 62 NC_002950:PG2081|3end_biotin_synthetase_2180669..2180819_NEGATIVE 255 70 37 32 1 NC_002950:PG0146|3end_hypothetical_protein_168408..168558_NEGATIVE 252 58 11 118 67 NC_002950:PG2111|3end_thiS_protein_2221282..2221432_NEGATIVE 251 78 32 70 14 NC_002950:PG0492|3end_hypothetical_protein_534408..534558_NEGATIVE 249 74 32 142 102 NC_002950:PG2086|3end_hypothetical_protein_2187070..2187220_POSITIVE 248 74 31 99 43 NC_002950:PG2202|3end_Holliday_junction_resolvase-like_protein_2309517..2309667_NEGATIVE 247 71 39 124 95 NC_002950:PG2044|3end_hypothetical_protein_2144165..2144315_POSITIVE 247 45 1 111 73 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 247 86 42 61 19 NC_002950:PG1630|3end_hypothetical_protein_1712142..1712292_POSITIVE