Origin IGS: tgtcgagtctccttcttatgttaatcgatcattgttctttgatgacacaaaagtagaagctgctatctgcctgaaatgtcgcctatgcgacaccgggtactcttgctatgcggcgatataaatggatgacccggcttttttgttccggtggttgatttctcatcggtttcaaacaagaagaaagagtccgactctctatttacttgtatggattcagagaaaaa .........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 tttttctctgaatccatacaagtaaatagagagtcggactctttcttcttgtttgaaaccgatgagaaatcaaccaccggaacaaaaaagccgggtcatccatttatatcgccgcatagcaagagtacccggtgtcgcataggcgacatttcaggcagatagcagcttctacttttgtgtcatcaaagaacaatgatcgattaacataagaaggagactcgaca Mask Tandem Repeat Region ================================================ tgtcgagtctccttcttatgttaatcgatcattgttctttgatgacacaaaagtagaagctgctatctgcctgaaatgtcgcctatgcgacaccgggtactcttgctatgcggcgatataaatggatgacccggcttttttgttccggtggttgatttctcatcggtttcaaacaagaagaaagagtccgactctctatttacttgtatggattcagagaaaaa Find is-nt database================================================ Query_seq: PG0893:PG0894|PG0893:PG0894:hydroxylamine reductase:DNA repair protein RadC:<-<-:955944..956167 224 tgtcgagtctccttcttatgttaatcgatcattgttctttgatgacacaaaagtagaagctgctatctgcctgaaatgtcgcctatgcgacaccgggtactcttgctatgcggcgatataaatggatgacccggcttttttgttccggtggttgatttctcatcggtttcaaacaagaagaaagagtccgactctctatttacttgtatggattcagagaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0893:PG0894|PG0893:PG0894:hydroxylamine reductase:DNA repair protein RadC:<-<-:955944..956167 224 tgtcgagtctccttcttatgttaatcgatcattgttctttgatgacacaaaagtagaagctgctatctgcctgaaatgtcgcctatgcgacaccgggtactcttgctatgcggcgatataaatggatgacccggcttttttgttccggtggttgatttctcatcggtttcaaacaagaagaaagagtccgactctctatttacttgtatggattcagagaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0893:PG0894|PG0893:PG0894:hydroxylamine reductase:DNA repair protein RadC:<-<-:955944..956167 224 tgtcgagtctccttcttatgttaatcgatcattgttctttgatgacacaaaagtagaagctgctatctgcctgaaatgtcgcctatgcgacaccgggtactcttgctatgcggcgatataaatggatgacccggcttttttgttccggtggttgatttctcatcggtttcaaacaagaagaaagagtccgactctctatttacttgtatggattcagagaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtcgagtctccttcttatgttaatcgatcattgttctttgatgacacaaaagtagaagctgctatctgcctgaaatgtcgcctatgcgacaccgggtactcttgctatgcggcgatataaatggatgacccggcttttttgttccggtggttgatttctcatcggtttcaaacaagaagaaagagtccgactctctatttacttgtatggattcagagaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 122 End: 223 ......................................................................................................................... M D D P A F L F R W L I S H R F Q T R R K S P T L Y L L V W I Q R K . Protein_Len: 38 Strand: - Start: 86 End: 199 ..................................................................................... A V G P V R A I R R Y L H I V R S K Q E P P Q N R M P K L C S S L T R S E M ......................... Protein_Len: 48 Strand: - Start: 66 End: 209 ................................................................. R G S I D G I R C R T S K S H P S I F P H G P K K T G T T S K E D T E F L F F S D S E R N V Q M ............... tgtcgagtctccttcttatgttaatcgatcattgttctttgatgacacaaaagtagaagctgctatctgcctgaaatgtcgcctatgcgacaccgggtactcttgctatgcggcgatataaatggatgacccggcttttttgttccggtggttgatttctcatcggtttcaaacaagaagaaagagtccgactctctatttacttgtatggattcagagaaaaa 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================================================ tgtcgagtctccttcttatgttaatcgatcattgttctttgatgacacaaaagtagaagctgctatctgcctgaaatgtcgcctatgcgacaccgggtactcttgctatgcggcgatataaatggatgacccggcttttttgttccggtggttgatttctcatcggtttcaaacaagaagaaagagtccgactctctatttacttgtatggattcagagaaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -9.0 Tail_Score: -3.53811 Start: 77 End: 92 Full_Region: agcaagagtacccgg tgtcgc atag gcgaca tttcaggcagatagc ............................................................................tgtcgcataggcgaca.................................................................................................................................... Find igs database================================================ Query_seq: PG0893:PG0894|PG0893:PG0894:hydroxylamine reductase:DNA repair protein RadC:<-<-:955944..956167 224 tgtcgagtctccttcttatgttaatcgatcattgttctttgatgacacaaaagtagaagctgctatctgcctgaaatgtcgcctatgcgacaccgggtactcttgctatgcggcgatataaatggatgacccggcttttttgttccggtggttgatttctcatcggtttcaaacaagaagaaagagtccgactctctatttacttgtatggattcagagaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 224 Len: 224 Subject: NC_002950_PG0893_PG0894|hydroxylamine reductase:DNA repair protein RadC|NEGATIVE:NEGATIVE|[955944,956167]|224 HSP 1 e-value: 1.0E-124 bit: 444.0 Len: 224 Query Start:1 Query End:224 Subject Strand: POSITIVE Subject Start: 1 Subject End: 224 tgtcgagtctccttcttatgttaatcgatcattgttctttgatgacacaaaagtagaagctgctatctgcctgaaatgtcgcctatgcgacaccgggtactcttgctatgcggcgatataaatggatgacccggcttttttgttccggtggttgatttctcatcggtttcaaacaagaagaaagagtccgactctctatttacttgtatggattcagagaaaaa tgtcgagtctccttcttatgttaatcgatcattgttctttgatgacacaaaagtagaagctgctatctgcctgaaatgtcgcctatgcgacaccgggtactcttgctatgcggcgatataaatggatgacccggcttttttgttccggtggttgatttctcatcggtttcaaacaagaagaaagagtccgactctctatttacttgtatggattcagagaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUCGAGUCUCCUUCUUAUGUUAAUCGAUCAUUGUUCUUUGAUGACACAAAAGUAGAAGCUGCUAUCUGCCUGAAAUGUCGCCUAUGCGACACCGGGUACUCUUGCUAUGCGGCGAUAUAAAUGGAUGACCCGGCUUUUUUGUUCCGGUGGUUGAUUUCUCAUCGGUUUCAAACAAGAAGAAAGAGUCCGACUCUCUAUUUACUUGUAUGGAUUCAGAGAAAAA .((((.((((((...(((((((....(.((((((.....)))))))......(((..(((.......((((((...((((((....)))))).)))))).....))).)))...)))))))..))).))).)))).((((((..(((((((........))))))).((((.(((((.(((.((((.......)))).))).))))).))))..)))))).... (-60.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCUCUGAAUCCAUACAAGUAAAUAGAGAGUCGGACUCUUUCUUCUUGUUUGAAACCGAUGAGAAAUCAACCACCGGAACAAAAAAGCCGGGUCAUCCAUUUAUAUCGCCGCAUAGCAAGAGUACCCGGUGUCGCAUAGGCGACAUUUCAGGCAGAUAGCAGCUUCUACUUUUGUGUCAUCAAAGAACAAUGAUCGAUUAACAUAAGAAGGAGACUCGACA ....((((((....(......)....))))))(((((.(((((((((.(((((((((.(((.(((....))).....))).........(((((((..((...((((........))))...))..)))))))(((((....)))))..))))))))).................((((((((((........)))).)))..))).))))))))).).)))). (-53.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1027 110 61 201 152 NC_002950:PG0893|5end_hydroxylamine_reductase_955853..956083_NEGATIVE 371 170 122 187 126 NC_002950:PG1594|5end_ComEC/Rec2-related_protein_1673587..1673817_NEGATIVE 362 96 58 69 29 NC_002950:PG0674|5end_indolepyruvate_ferredoxin_oxidoreductase,_beta_subunit_724802..725032_NEGATIVE 351 190 146 58 2 NC_002950:PG0073|5end_orotidine_5'-monophosphate_decarboxylase_88070..88300_NEGATIVE 349 136 91 186 139 NC_002950:PG1554|5end_hypothetical_protein_1635264..1635494_POSITIVE 349 150 104 71 23 NC_002950:PG0676|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_727275..727505_NEGATIVE 348 148 103 114 69 NC_002950:PG1638|5end_thioredoxin_family_protein_1719650..1719880_NEGATIVE 344 100 51 64 8 NC_002950:PG1434|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_1519022..1519252_POSITIVE 339 165 125 173 132 NC_002950:PG0359|5end_flavin_reductase_domain_protein_392851..393081_POSITIVE 338 168 124 214 163 NC_002950:PG1621|5end_hypothetical_protein_1701431..1701661_NEGATIVE 337 115 87 99 67 NC_002950:PG1409|5end_hypothetical_protein_1493265..1493495_NEGATIVE 336 146 101 82 33 NC_002950:PG2114|5end_hypothetical_protein_2224158..2224388_NEGATIVE 336 164 123 47 1 NC_002950:PG1289|5end_GDP-fucose_synthetase_1367041..1367271_POSITIVE 335 100 57 61 19 NC_002950:PG1313|5end_dipeptidase-related_protein_1392282..1392512_POSITIVE 334 116 76 58 23 NC_002950:PG1318|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1397768..1397998_NEGATIVE 334 114 71 50 3 NC_002950:PG0441|5end_hypothetical_protein_478734..478964_POSITIVE 333 106 61 53 14 NC_002950:PG0430|5end_ferrodoxin_oxidoreductase_beta_subunit_467986..468216_POSITIVE 331 149 109 70 30 NC_002950:PG1080|5end_3-hydroxyacyl-CoA_dehydrogenase_family_protein_1147366..1147596_POSITIVE 329 139 94 189 150 NC_002950:PG0368|5end_DNA_topoisomerase_IV_subunit_B_401245..401475_POSITIVE 328 190 143 57 1 NC_002950:PG2221|5end_MiaB-like_tRNA_modifying_enzyme_2335426..2335656_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 96 58 42 2 NC_002950:PG0675|3end_indolepyruvate_ferredoxin_oxidoreductase,_alpha_subunit_724829..724979_NEGATIVE 344 100 51 88 32 NC_002950:PG1433|3end_hydrolase_1519126..1519276_POSITIVE 339 165 125 144 103 NC_002950:PG0358|3end_aspartate_carbamoyltransferase_regulatory_subunit_392902..393052_POSITIVE 336 164 123 54 8 NC_002950:PG1288|3end_GDP-mannose_4,6-dehydratase_1367128..1367278_POSITIVE 336 116 75 151 109 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 336 129 81 134 87 NC_002950:PG0085|3end_alpha-galactosidase_100556..100706_POSITIVE 333 124 82 82 38 NC_002950:PG1622|3end_DNA_topoisomerase_IV_subunit_A_1701418..1701568_NEGATIVE 332 95 59 127 100 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 330 97 53 123 74 NC_002950:PG0424|3end_hypothetical_protein_463213..463363_POSITIVE 327 116 77 83 47 NC_002950:PG2140|3end_ribosomal_protein_L32_2246399..2246549_POSITIVE 325 151 111 137 82 NC_002950:PG0032|3end_beta-mannosidase,_putative_37627..37777_NEGATIVE 324 98 52 147 102 NC_002950:PG1087|3end_radical_SAM_protein,_TIGR01212_family_1154820..1154970_POSITIVE 323 147 105 69 28 NC_002950:PG2097|3end_ribose-phosphate_pyrophosphokinase_2205521..2205671_NEGATIVE 323 107 61 79 20 NC_002950:PG2044|3end_hypothetical_protein_2144165..2144315_POSITIVE 323 108 61 83 31 NC_002950:PG1342|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_1423681..1423831_POSITIVE 323 118 78 53 8 NC_002950:PG1246|3end_alanyl-tRNA_synthetase_1324509..1324659_POSITIVE 322 117 76 146 98 NC_002950:PG0520|3end_chaperonin_GroEL_563618..563768_NEGATIVE 322 114 78 46 2 NC_002950:PG0439|3end_hypothetical_protein_478810..478960_POSITIVE 319 98 59 130 81 NC_002950:PG1978|3end_hypothetical_protein_2066723..2066873_NEGATIVE 318 170 124 135 82 NC_002950:PG1954|3end_NAD_dependent_epimerase/reductase-related_protein_2045612..2045762_POSITIVE