Origin IGS: gtttttgaatagtttatattggtttgacctgcgcaaaagtagaggagatcaacgacttgtaatatcaccacaaatagctaaaaagaataggtccatacctatatgtggggggattcccatcgaaaaaaagcagcccga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcgggctgctttttttcgatgggaatccccccacatataggtatggacctattctttttagctatttgtggtgatattacaagtcgttgatctcctctacttttgcgcaggtcaaaccaatataaactattcaaaaac Mask Tandem Repeat Region ================================================ gtttttgaatagtttatattggtttgacctgcgcaaaagtagaggagatcaacgacttgtaatatcaccacaaatagctaaaaagaataggtccatacctatatgtggggggattcccatcgaaaaaaagcagcccga Find is-nt database================================================ Query_seq: PG1858:PG1859|PG1858:PG1859:flavodoxin:glycerate kinase family protein:<-<-:1957126..1957263 138 gtttttgaatagtttatattggtttgacctgcgcaaaagtagaggagatcaacgacttgtaatatcaccacaaatagctaaaaagaataggtccatacctatatgtggggggattcccatcgaaaaaaagcagcccga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1858:PG1859|PG1858:PG1859:flavodoxin:glycerate kinase family protein:<-<-:1957126..1957263 138 gtttttgaatagtttatattggtttgacctgcgcaaaagtagaggagatcaacgacttgtaatatcaccacaaatagctaaaaagaataggtccatacctatatgtggggggattcccatcgaaaaaaagcagcccga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1858:PG1859|PG1858:PG1859:flavodoxin:glycerate kinase family protein:<-<-:1957126..1957263 138 gtttttgaatagtttatattggtttgacctgcgcaaaagtagaggagatcaacgacttgtaatatcaccacaaatagctaaaaagaataggtccatacctatatgtggggggattcccatcgaaaaaaagcagcccga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtttttgaatagtttatattggtttgacctgcgcaaaagtagaggagatcaacgacttgtaatatcaccacaaatagctaaaaagaataggtccatacctatatgtggggggattcccatcgaaaaaaagcagcccga Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 5 End: 136 .... M N S L Y W F D L R K S R G D Q R L V I S P Q I A K K N R S I P I C G G I P I E K K Q P .. gtttttgaatagtttatattggtttgacctgcgcaaaagtagaggagatcaacgacttgtaatatcaccacaaatagctaaaaagaataggtccatacctatatgtggggggattcccatcgaaaaaaagcagcccga 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================================================ gtttttgaatagtttatattggtttgacctgcgcaaaagtagaggagatcaacgacttgtaatatcaccacaaatagctaaaaagaataggtccatacctatatgtggggggattcccatcgaaaaaaagcagcccga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1858:PG1859|PG1858:PG1859:flavodoxin:glycerate kinase family protein:<-<-:1957126..1957263 138 gtttttgaatagtttatattggtttgacctgcgcaaaagtagaggagatcaacgacttgtaatatcaccacaaatagctaaaaagaataggtccatacctatatgtggggggattcccatcgaaaaaaagcagcccga Intra-Species Hit: Count: 1 Min: 1 Max: 122 Len: 122 Subject: NC_002950_PG1858_PG1859|flavodoxin:glycerate kinase family protein|NEGATIVE:NEGATIVE|[1957126,1957263]|138 HSP 1 e-value: 2.0E-63 bit: 242.0 Len: 122 Query Start:1 Query End:122 Subject Strand: POSITIVE Subject Start: 1 Subject End: 122 gtttttgaatagtttatattggtttgacctgcgcaaaagtagaggagatcaacgacttgtaatatcaccacaaatagctaaaaagaataggtccatacctatatgtggggggattcccatcg................ gtttttgaatagtttatattggtttgacctgcgcaaaagtagaggagatcaacgacttgtaatatcaccacaaatagctaaaaagaataggtccatacctatatgtggggggattcccatcg................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUUGAAUAGUUUAUAUUGGUUUGACCUGCGCAAAAGUAGAGGAGAUCAACGACUUGUAAUAUCACCACAAAUAGCUAAAAAGAAUAGGUCCAUACCUAUAUGUGGGGGGAUUCCCAUCG ....(((...((((....(((((((..(((((......)))).).))))))).))))..))).....(((((.....((....)).((((((....)))))).))))).(((...))).... (-22.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAUGGGAAUCCCCCCACAUAUAGGUAUGGACCUAUUCUUUUUAGCUAUUUGUGGUGAUAUUACAAGUCGUUGAUCUCCUCUACUUUUGCGCAGGUCAAACCAAUAUAAACUAUUCAAAAAC ...((((......)))).((((.(((...(((((.......(((((.(((((((((...))))))))).))))).........(....)...)))))..))).))))............... (-23.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 917 70 21 161 112 NC_002950:PG1858|5end_flavodoxin_1957035..1957265_NEGATIVE 344 54 11 114 65 NC_002950:PG0771|5end_hypothetical_protein_824524..824754_POSITIVE 286 119 101 70 51 NC_002950:PG1682|5end_glycosyl_transferase,_group_1_family_protein_1768385..1768615_POSITIVE 283 56 12 149 103 NC_002950:PG1633|5end_galactokinase_1713385..1713615_POSITIVE 273 100 54 56 13 NC_002950:PG1820|5end_cytochrome_c_nitrite_reductase,_catalytic_subunit_NrfA_1915889..1916119_NEGATIVE 270 119 77 172 115 NC_002950:PG1947|5end_TPR_domain_protein_2032932..2033162_POSITIVE 269 64 22 159 119 NC_002950:PG2081|5end_biotin_synthetase_2181661..2181891_NEGATIVE 263 120 71 91 44 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 260 59 25 59 30 NC_002950:PG0691|5end_NifU-related_protein_747469..747699_NEGATIVE 257 56 21 65 20 NC_002950:PG2131|5end_60_kDa_protein_2236174..2236404_POSITIVE 255 120 71 219 173 NC_002950:PG0052|5end_sensor_histidine_kinase_63419..63649_POSITIVE 253 49 2 226 178 NC_002950:PG2124|5end_glyceraldehyde_3-phosphate_dehydrogenase,_type_I_2230174..2230404_POSITIVE 252 48 5 150 113 NC_002950:PG2096|5end_hypothetical_protein_2205415..2205645_NEGATIVE 247 55 19 176 130 NC_002950:PG2053|5end_dithiobiotin_synthetase_2150534..2150764_POSITIVE 246 69 28 197 153 NC_002950:PG1403|5end_rhomboid_family_protein_1487039..1487269_NEGATIVE 246 48 5 155 116 NC_002950:PG0936|5end_xanthine/uracil_permease_family_protein_996451..996681_NEGATIVE 245 120 71 155 105 NC_002950:PG1351|5end_hypothetical_protein_1432744..1432974_NEGATIVE 245 70 21 50 2 NC_002950:PG0002|5end_hexapeptide_transferase_family_protein_1295..1525_POSITIVE 244 59 22 59 24 NC_002950:PG1861|5end_hypothetical_protein_1960057..1960287_NEGATIVE 244 69 21 186 144 NC_002950:PG1026|5end_hypothetical_protein_1088177..1088407_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 119 101 73 54 NC_002950:PG1681|3end_glycogen_debranching_enzyme,_archaeal_type,_putative_1768468..1768618_POSITIVE 283 56 12 99 53 NC_002950:PG1632|3end_aldose_1-epimerase_1713415..1713565_POSITIVE 268 120 77 84 38 NC_002950:PG0280|3end_ABC_transporter,_permease_protein,_putative_313297..313447_NEGATIVE 263 120 71 110 63 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 263 60 17 131 89 NC_002950:PG0104|3end_DNA_topoisomerase_III_127448..127598_POSITIVE 252 48 5 44 7 NC_002950:PG2097|3end_ribose-phosphate_pyrophosphokinase_2205521..2205671_NEGATIVE 247 55 19 147 101 NC_002950:PG2052|3end_dihydrodipicolinate_synthase_2150585..2150735_POSITIVE 247 118 89 75 44 NC_002950:PG1005|3end_lipoprotein,_putative_1063023..1063173_NEGATIVE 246 48 5 134 95 NC_002950:PG0937|3end_hypothetical_protein_996472..996622_NEGATIVE 244 59 22 46 11 NC_002950:PG1862|3end_hypothetical_protein_1960070..1960220_NEGATIVE 244 69 21 136 90 NC_002950:PG1633|3end_galactokinase_1714619..1714769_POSITIVE 243 105 68 39 1 NC_002950:PG1195|3end_8-amino-7-oxononanoate_synthase_1275207..1275357_POSITIVE 234 79 33 91 42 NC_002950:PG0875|3end_mobilizable_transposon,_tnpA_protein_938102..938252_NEGATIVE 234 119 71 88 50 NC_002950:PG0340|3end_hypothetical_protein_376436..376586_POSITIVE 232 69 27 127 85 NC_002950:PG0815|3end_hypothetical_protein_876447..876597_POSITIVE 231 118 84 87 48 NC_002950:PG1303|3end_helicase,_putative_1382147..1382297_POSITIVE 231 105 70 59 24 NC_002950:PG0157|3end_regulatory_protein_RecX_180271..180421_POSITIVE 228 115 87 140 109 NC_002950:PG1821|3end_cytochrome_c_nitrite_reductase,_small_subunit_NrfH_1915911..1916061_NEGATIVE 228 116 83 122 82 NC_002950:PG1752|3end_hypothetical_protein_1838698..1838848_POSITIVE 227 104 68 146 108 NC_002950:PG1528|3end_hypothetical_protein_1607188..1607338_POSITIVE