Origin IGS: ttattagcttgctgtggccatccattattgttgagggagcattttgaagttcttgaaacactaatggctgacaagcaagcttataagaaggagtataacta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagttatactccttcttataagcttgcttgtcagccattagtgtttcaagaacttcaaaatgctccctcaacaataatggatggccacagcaagctaataa Mask Tandem Repeat Region ================================================ ttattagcttgctgtggccatccattattgttgagggagcattttgaagttcttgaaacactaatggctgacaagcaagcttataagaaggagtataacta Find is-nt database================================================ Query_seq: FN0694:FN0695|FN0694:FN0695:S-layer protein:ABC transporter ATP-binding protein:->->:1352925..1353025 101 ttattagcttgctgtggccatccattattgttgagggagcattttgaagttcttgaaacactaatggctgacaagcaagcttataagaaggagtataacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0694:FN0695|FN0694:FN0695:S-layer protein:ABC transporter ATP-binding protein:->->:1352925..1353025 101 ttattagcttgctgtggccatccattattgttgagggagcattttgaagttcttgaaacactaatggctgacaagcaagcttataagaaggagtataacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0694:FN0695|FN0694:FN0695:S-layer protein:ABC transporter ATP-binding protein:->->:1352925..1353025 101 ttattagcttgctgtggccatccattattgttgagggagcattttgaagttcttgaaacactaatggctgacaagcaagcttataagaaggagtataacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttattagcttgctgtggccatccattattgttgagggagcattttgaagttcttgaaacactaatggctgacaagcaagcttataagaaggagtataacta Predict ORF larger than 30AA ================================================ ttattagcttgctgtggccatccattattgttgagggagcattttgaagttcttgaaacactaatggctgacaagcaagcttataagaaggagtataacta 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================================================ ttattagcttgctgtggccatccattattgttgagggagcattttgaagttcttgaaacactaatggctgacaagcaagcttataagaaggagtataacta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0694:FN0695|FN0694:FN0695:S-layer protein:ABC transporter ATP-binding protein:->->:1352925..1353025 101 ttattagcttgctgtggccatccattattgttgagggagcattttgaagttcttgaaacactaatggctgacaagcaagcttataagaaggagtataacta Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: NC_003454_FN0694_FN0695|S-layer protein:ABC transporter ATP-binding protein|POSITIVE:POSITIVE|[1352925,1353025]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 ttattagcttgctgtggccatccattattgttgagggagcattttgaagttcttgaaacactaatggctgacaagcaagcttataagaaggagtataacta ttattagcttgctgtggccatccattattgttgagggagcattttgaagttcttgaaacactaatggctgacaagcaagcttataagaaggagtataacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUUAGCUUGCUGUGGCCAUCCAUUAUUGUUGAGGGAGCAUUUUGAAGUUCUUGAAACACUAAUGGCUGACAAGCAAGCUUAUAAGAAGGAGUAUAACUA ((((.((((((((.((..((.((((((.((((..((((((........))))))..)))).)))))).)).)))))))))).))))............... (-33.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUUAUACUCCUUCUUAUAAGCUUGCUUGUCAGCCAUUAGUGUUUCAAGAACUUCAAAAUGCUCCCUCAACAAUAAUGGAUGGCCACAGCAAGCUAAUAA ................(((.((((((((.((((.((((((.((((....((.(........).))....)))).)))))).))))...)))))))).))). (-25.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 712 70 21 224 175 NC_003454:FN1142|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1791529..1791759_POSITIVE 674 68 21 231 184 NC_003454:FN1581|5end_DNA_mismatch_repair_protein_mutS_93231..93461_NEGATIVE 601 70 22 214 165 NC_003454:FN1995|5end_hypothetical_protein_498245..498475_POSITIVE 599 69 21 230 181 NC_003454:FN0054|5end_tyrosyl-tRNA_synthetase_690836..691066_POSITIVE 594 70 21 230 181 NC_003454:FN1740|5end_ATP_synthase_subunit_K_238400..238630_NEGATIVE 586 70 21 204 155 NC_003454:FN1439|5end_Transcriptional_regulator,_DeoR_family_2106428..2106658_POSITIVE 586 70 21 100 51 NC_003454:FN1438|5end_hypothetical_protein_2106324..2106554_POSITIVE 430 46 6 230 191 NC_003454:FN1731|5end_Anthranilate_synthase_component_II_231037..231267_NEGATIVE 380 50 6 192 140 NC_003454:FN1351|5end_15_kDa_lipoprotein_precursor_2003372..2003602_NEGATIVE 262 39 6 230 198 NC_003454:FN1984|5end_Glutaredoxin-like_protein_485487..485717_POSITIVE 254 50 1 121 69 NC_003454:FN0562|5end_Hypothetical_cytosolic_protein_1214964..1215194_POSITIVE 253 70 21 191 141 NC_003454:FN0053|5end_Branched-chain_amino_acid_transport_system_carrier_protein_689340..689570_POSITIVE 251 50 6 223 181 NC_003454:FN0186|5end_Cytochrome_c-type_biogenesis_protein_ccdA_810853..811083_POSITIVE 236 60 11 77 18 NC_003454:FN1433|5end_Short_chain_dehydrogenase_2102520..2102750_NEGATIVE 235 84 50 210 179 NC_003454:FN0424|5end_Dihydroorotate_dehydrogenase_1067119..1067349_POSITIVE 231 71 31 58 19 NC_003454:FN0495|5end_Acetyl-CoA_acetyltransferase_1139567..1139797_POSITIVE 226 68 23 89 43 NC_003454:FN0905|5end_hypothetical_protein_1564086..1564316_NEGATIVE 218 80 35 64 21 NC_003454:FN2003|5end_bioY_protein_503745..503975_POSITIVE 210 68 24 135 92 NC_003454:FN0925|5end_hypothetical_protein_1579921..1580151_POSITIVE 208 100 66 58 17 NC_003454:FN1716|5end_hypothetical_protein_212476..212706_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 594 70 21 69 20 NC_003454:FN1741|3end_ATP_synthase_subunit_I_238561..238711_NEGATIVE 455 69 21 56 7 NC_003454:FN1259|3end_Uracil-DNA_glycosylase_1915756..1915906_POSITIVE 393 68 21 72 21 NC_003454:FN0828|3end_ABC_transporter_permease_protein_1489505..1489655_POSITIVE 380 50 6 58 6 NC_003454:FN1352|3end_ABC_transporter_ATP-binding_protein_2003506..2003656_NEGATIVE 270 69 21 65 17 NC_003454:FN1077|3end_hypothetical_protein_1723754..1723904_NEGATIVE 253 70 21 62 12 NC_003454:FN0052|3end_Arsenate_reductase_689291..689441_POSITIVE 226 68 23 51 5 NC_003454:FN0906|3end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+]_1564124..1564274_NEGATIVE 211 70 38 146 121 NC_003454:FN1253|3end_hypothetical_protein_1910229..1910379_NEGATIVE 211 100 62 48 1 NC_003454:FN0053|3end_Branched-chain_amino_acid_transport_system_carrier_protein_690694..690844_POSITIVE 210 68 24 96 53 NC_003454:FN0924|3end_hypothetical_protein_1579962..1580112_POSITIVE 202 60 12 59 1 NC_003454:FN1434|3end_Tetratricopeptide_repeat_family_protein_2102538..2102688_NEGATIVE 200 69 21 146 100 NC_003454:FN0678|3end_Ser/Thr_protein_kinase_1334651..1334801_POSITIVE 199 58 18 48 3 NC_003454:FN0439|3end_hypothetical_protein_1080837..1080987_NEGATIVE 191 50 1 50 5 NC_003454:FN0694|3end_S-layer_protein_1352864..1353014_POSITIVE 191 46 7 86 44 NC_003454:FN1675|3end_Transposase_172206..172356_NEGATIVE 186 44 6 151 106 NC_003454:FN0806|3end_SpoIID_homolog_1465587..1465737_NEGATIVE 186 59 17 149 102 NC_003454:FN0751|3end_L-asparaginase_I_1409721..1409871_NEGATIVE 185 68 22 89 43 NC_003454:FN1274|3end_Acriflavin_resistance_protein_E_1931805..1931955_POSITIVE 185 35 1 70 21 NC_003454:FN1620|3end_30S_ribosomal_protein_S2_128719..128869_POSITIVE 179 54 11 48 7 NC_003454:FN1315|3end_hypothetical_protein_1968921..1969071_NEGATIVE