Origin IGS: agcacaaaaccggcagggtatcggttctataacataatacctctgctgccactctacatttcctttactgttcaagagggcatgtccgggctatgattcggc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gccgaatcatagcccggacatgccctcttgaacagtaaaggaaatgtagagtggcagcagaggtattatgttatagaaccgataccctgccggttttgtgct Mask Tandem Repeat Region ================================================ agcacaaaaccggcagggtatcggttctataacataatacctctgctgccactctacatttcctttactgttcaagagggcatgtccgggctatgattcggc Find is-nt database================================================ Query_seq: PG1129:PG1130|PG1129:PG1130:ribonucleotide reductase:TPR domain protein:->->:1208091..1208192 102 agcacaaaaccggcagggtatcggttctataacataatacctctgctgccactctacatttcctttactgttcaagagggcatgtccgggctatgattcggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1129:PG1130|PG1129:PG1130:ribonucleotide reductase:TPR domain protein:->->:1208091..1208192 102 agcacaaaaccggcagggtatcggttctataacataatacctctgctgccactctacatttcctttactgttcaagagggcatgtccgggctatgattcggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1129:PG1130|PG1129:PG1130:ribonucleotide reductase:TPR domain protein:->->:1208091..1208192 102 agcacaaaaccggcagggtatcggttctataacataatacctctgctgccactctacatttcctttactgttcaagagggcatgtccgggctatgattcggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcacaaaaccggcagggtatcggttctataacataatacctctgctgccactctacatttcctttactgttcaagagggcatgtccgggctatgattcggc Predict ORF larger than 30AA ================================================ agcacaaaaccggcagggtatcggttctataacataatacctctgctgccactctacatttcctttactgttcaagagggcatgtccgggctatgattcggc 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================================================ agcacaaaaccggcagggtatcggttctataacataatacctctgctgccactctacatttcctttactgttcaagagggcatgtccgggctatgattcggc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1129:PG1130|PG1129:PG1130:ribonucleotide reductase:TPR domain protein:->->:1208091..1208192 102 agcacaaaaccggcagggtatcggttctataacataatacctctgctgccactctacatttcctttactgttcaagagggcatgtccgggctatgattcggc Intra-Species Hit: Count: 1 Min: 1 Max: 102 Len: 102 Subject: NC_002950_PG1129_PG1130|ribonucleotide reductase:TPR domain protein|POSITIVE:POSITIVE|[1208091,1208192]|102 HSP 1 e-value: 2.0E-51 bit: 202.0 Len: 102 Query Start:1 Query End:102 Subject Strand: POSITIVE Subject Start: 1 Subject End: 102 agcacaaaaccggcagggtatcggttctataacataatacctctgctgccactctacatttcctttactgttcaagagggcatgtccgggctatgattcggc agcacaaaaccggcagggtatcggttctataacataatacctctgctgccactctacatttcctttactgttcaagagggcatgtccgggctatgattcggc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCACAAAACCGGCAGGGUAUCGGUUCUAUAACAUAAUACCUCUGCUGCCACUCUACAUUUCCUUUACUGUUCAAGAGGGCAUGUCCGGGCUAUGAUUCGGC .........((((((((((((..(((....)))...))))).)))).(((.....((((.((((((........)))))).))))...))).......))). (-26.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCGAAUCAUAGCCCGGACAUGCCCUCUUGAACAGUAAAGGAAAUGUAGAGUGGCAGCAGAGGUAUUAUGUUAUAGAACCGAUACCCUGCCGGUUUUGUGCU ((((((((...((((..((((..(((.(((.....))))))..))))...).))).((((.((((((..(((....))).)))))))))).)).)))).)). (-27.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 60 11 99 46 NC_002950:PG2209|5end_hypothetical_protein_2320928..2321158_NEGATIVE 340 80 40 105 64 NC_002950:PG1095|5end_RNA_methyltransferase,_TrmA_family_1160225..1160455_POSITIVE 330 100 51 68 25 NC_002950:PG0141|5end_spoOJ_protein_164747..164977_NEGATIVE 322 55 12 164 112 NC_002950:PG0989|5end_50S_ribosomal_protein_L20_1051046..1051276_NEGATIVE 319 49 2 57 3 NC_002950:PG0471|5end_hypothetical_protein_512288..512518_POSITIVE 315 89 42 202 138 NC_002950:PG0431|5end_hypothetical_protein_468978..469208_POSITIVE 311 89 49 69 36 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 307 88 41 158 98 NC_002950:PG0545|5end_hypothetical_protein_598043..598273_POSITIVE 303 96 62 48 16 NC_002950:PG1611|5end_hypothetical_protein_1691487..1691717_NEGATIVE 301 90 41 129 73 NC_002950:PG1695|5end_hypothetical_protein_1779440..1779670_POSITIVE 298 54 11 227 184 NC_002950:PG1814|5end_DNA_primase_1910627..1910857_NEGATIVE 297 89 43 152 111 NC_002950:PG1351|5end_hypothetical_protein_1432744..1432974_NEGATIVE 294 87 41 202 143 NC_002950:PG1185|5end_hypothetical_protein_1267752..1267982_NEGATIVE 293 89 41 207 157 NC_002950:PG1964|5end_bacterial_sugar_transferase_2052910..2053140_POSITIVE 290 100 52 53 2 NC_002950:PG2111|5end_thiS_protein_2221482..2221712_NEGATIVE 289 64 23 229 175 NC_002950:PG0116|5end_hypothetical_protein_138469..138699_POSITIVE 288 90 41 166 110 NC_002950:PG0092|5end_transporter,_putative_108598..108828_NEGATIVE 287 48 1 80 29 NC_002950:PG1247|5end_3-dehydroquinate_synthase_1324444..1324674_POSITIVE 287 89 45 185 140 NC_002950:PG0307|5end_NADH-ubiquinone_oxidoreductase_342560..342790_POSITIVE 285 88 41 184 140 NC_002950:PG1863|5end_hypothetical_protein_1960516..1960746_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 60 11 75 22 NC_002950:PG2210|3end_excinuclease_ABC,_A_subunit_2320952..2321102_NEGATIVE 336 90 42 126 76 NC_002950:PG1942|3end_30S_ribosomal_protein_S12_2027946..2028096_NEGATIVE 331 89 46 104 46 NC_002950:PG0062|3end_TPR_domain_protein_75810..75960_POSITIVE 330 100 51 60 17 NC_002950:PG0142|3end_SpoOJ_regulator_protein_164755..164905_NEGATIVE 321 58 12 140 84 NC_002950:PG1259|3end_anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_1334974..1335124_NEGATIVE 320 89 44 135 99 NC_002950:PG0520|3end_chaperonin_GroEL_563618..563768_NEGATIVE 316 90 44 113 49 NC_002950:PG1472|3end_hypothetical_protein_1549760..1549910_POSITIVE 316 90 41 148 98 NC_002950:PG0354|3end_hypothetical_protein_389131..389281_NEGATIVE 311 89 49 56 23 NC_002950:PG1253|3end_DNA_ligase,_NAD-dependent_1329597..1329747_NEGATIVE 307 88 41 113 53 NC_002950:PG0544|3end_type_I_restriction-modification_system,_M_subunit,_putative_598078..598228_POSITIVE 300 50 10 48 6 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 288 88 42 142 77 NC_002950:PG2065|3end_conserved_hypothetical_protein_TIGR00048_2162105..2162255_POSITIVE 288 90 41 121 65 NC_002950:PG0093|3end_HlyD_family_secretion_protein_108643..108793_NEGATIVE 287 48 1 65 14 NC_002950:PG1246|3end_alanyl-tRNA_synthetase_1324509..1324659_POSITIVE 285 88 41 81 38 NC_002950:PG1694|3end_hypothetical_protein_1777916..1778066_NEGATIVE 284 51 12 58 13 NC_002950:PG0738|3end_cytidine/deoxycytidylate_deaminase_family_protein_786995..787145_POSITIVE 278 89 41 140 90 NC_002950:PG1334|3end_band_7/Mec-2_family_protein_1415422..1415572_NEGATIVE 278 55 11 51 1 NC_002950:PG0990|3end_ribosomal_protein_L35_1051159..1051309_NEGATIVE 276 89 41 140 101 NC_002950:PG1625|3end_hypothetical_protein_1708718..1708868_POSITIVE 273 100 57 138 97 NC_002950:PG2182|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_A_2289800..2289950_NEGATIVE