Origin IGS: tactaaaaacactggaaaagcaaaatagtacttattgaagtataagtactatttttttattatccatttactccttattagtaagttaaattaaatttgtccaactttttggtttcagtacaaaccctgacttttctaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttagaaaagtcagggtttgtactgaaaccaaaaagttggacaaatttaatttaacttactaataaggagtaaatggataataaaaaaatagtacttatacttcaataagtactattttgcttttccagtgtttttagta Mask Tandem Repeat Region ================================================ tactaaaaacactggaaaagcaaaatagtacttattgaagtataagtactatttttttattatccatttactccttattagtaagttaaattaaatttgtccaactttttggtttcagtacaaaccctgacttttctaaa Find is-nt database================================================ Query_seq: FN2066:FN2067|FN2066:FN2067:hypothetical protein:Thiol:disulfide interchange protein tlpA:-><-:576834..576973 140 tactaaaaacactggaaaagcaaaatagtacttattgaagtataagtactatttttttattatccatttactccttattagtaagttaaattaaatttgtccaactttttggtttcagtacaaaccctgacttttctaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN2066:FN2067|FN2066:FN2067:hypothetical protein:Thiol:disulfide interchange protein tlpA:-><-:576834..576973 140 tactaaaaacactggaaaagcaaaatagtacttattgaagtataagtactatttttttattatccatttactccttattagtaagttaaattaaatttgtccaactttttggtttcagtacaaaccctgacttttctaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN2066:FN2067|FN2066:FN2067:hypothetical protein:Thiol:disulfide interchange protein tlpA:-><-:576834..576973 140 tactaaaaacactggaaaagcaaaatagtacttattgaagtataagtactatttttttattatccatttactccttattagtaagttaaattaaatttgtccaactttttggtttcagtacaaaccctgacttttctaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tactaaaaacactggaaaagcaaaatagtacttattgaagtataagtactatttttttattatccatttactccttattagtaagttaaattaaatttgtccaactttttggtttcagtacaaaccctgacttttctaaa Predict ORF larger than 30AA ================================================ tactaaaaacactggaaaagcaaaatagtacttattgaagtataagtactatttttttattatccatttactccttattagtaagttaaattaaatttgtccaactttttggtttcagtacaaaccctgacttttctaaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 34 End: 63 .................................ATTGAAGTATAAGTACTATTTTTTTATTAT............................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tactaaaaacactggaaaagcaaaatagtacttattgaagtataagtactatttttttattatccatttactccttattagtaagttaaattaaatttgtccaactttttggtttcagtacaaaccctgacttttctaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -7.9 Tail_Score: -3.12976 Start: 21 End: 56 Full_Region: gtaaatggataataa aaaaatagtacttat acttca ataagtactattttg cttttccagtgtttt ....................aaaaatagtacttatacttcaataagtactattttg.................................................................................... TransTerm Strand: - Conf: 81 HP_score: -7.8 Tail_Score: -4.67641 Start: 26 End: 51 Full_Region: tggataataaaaaaa tagtacttat acttca ataagtacta ttttgcttttccagt .........................tagtacttatacttcaataagtacta......................................................................................... Find igs database================================================ Query_seq: FN2066:FN2067|FN2066:FN2067:hypothetical protein:Thiol:disulfide interchange protein tlpA:-><-:576834..576973 140 tactaaaaacactggaaaagcaaaatagtacttattgaagtataagtactatttttttattatccatttactccttattagtaagttaaattaaatttgtccaactttttggtttcagtacaaaccctgacttttctaaa Intra-Species Hit: Count: 1 Min: 1 Max: 140 Len: 140 Subject: NC_003454_FN2066_FN2067|hypothetical protein:Thiol:disulfide interchange protein tlpA|POSITIVE:NEGATIVE|[576834,576973]|140 HSP 1 e-value: 2.0E-61 bit: 236.0 Len: 140 Query Start:1 Query End:140 Subject Strand: POSITIVE Subject Start: 1 Subject End: 140 tactaaaaacactggaaaagcaaaatagtacttattgaagtataagtactannnnnnnattatccatttactccttattagtaagttaaattaaatttgtccaactttttggtttcagtacaaaccctgacttttctaaa tactaaaaacactggaaaagcaaaatagtacttattgaagtataagtactatttttttattatccatttactccttattagtaagttaaattaaatttgtccaactttttggtttcagtacaaaccctgacttttctaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACUAAAAACACUGGAAAAGCAAAAUAGUACUUAUUGAAGUAUAAGUACUAUUUUUUUAUUAUCCAUUUACUCCUUAUUAGUAAGUUAAAUUAAAUUUGUCCAACUUUUUGGUUUCAGUACAAACCCUGACUUUUCUAAA .((((((((...((((.....((((((((((((((......))))))))))))))..........(((((((.......))))))).............))))..)))))))).((((........)))).......... (-26.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAGAAAAGUCAGGGUUUGUACUGAAACCAAAAAGUUGGACAAAUUUAAUUUAACUUACUAAUAAGGAGUAAAUGGAUAAUAAAAAAAUAGUACUUAUACUUCAAUAAGUACUAUUUUGCUUUUCCAGUGUUUUUAGUA .(((((....((((........))))..((((....)))).....))))).......((((((.((.(......((((.......((((((((((((((......)))))))))))))).....)))).).)).)))))) (-28.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 238 139 94 223 162 NC_003454:FN1518|5end_RNA_polymerase_sigma-70_factor_24077..24307_NEGATIVE 236 85 44 110 69 NC_003454:FN0168|5end_hypothetical_protein_794558..794788_POSITIVE 228 70 22 211 171 NC_003454:FN0032|5end_hypothetical_protein_669778..670008_NEGATIVE 224 140 100 196 158 NC_003454:FN1019|5end_3-hydroxybutyryl-CoA_dehydrogenase_1673784..1674014_NEGATIVE 216 86 43 117 70 NC_003454:FN1593|5end_NADH-ubiquinone_oxidoreductase_104360..104590_NEGATIVE 210 60 11 196 136 NC_003454:FN0055|5end_Ribosomal-protein-alanine_acetyltransferase_692158..692388_POSITIVE 205 88 51 115 79 NC_003454:FN0322|5end_fructose-bisphosphate_aldolase_959613..959843_POSITIVE 204 98 72 228 200 NC_003454:FN0864|5end_hypothetical_protein_1522900..1523130_NEGATIVE 202 58 13 195 142 NC_003454:FN1355|5end_Integral_membrane_protein_2007575..2007805_NEGATIVE 202 120 71 153 97 NC_003454:FN1623|5end_Ribosome_Recycling_Factor_(RRF)_130394..130624_POSITIVE 201 120 73 50 6 NC_003454:FN0208|5end_(R)-2-hydroxyglutaryl-CoA_dehydratase_beta-subunit_834968..835198_POSITIVE 200 80 41 105 56 NC_003454:FN0072|5end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_711715..711945_POSITIVE 200 60 12 213 160 NC_003454:FN1818|5end_Hemolysin_activator_protein_precursor_306955..307185_NEGATIVE 199 80 42 112 72 NC_003454:FN0596|5end_hypothetical_protein_1250001..1250231_POSITIVE 197 82 49 109 77 NC_003454:FN0753|5end_aspartyl/glutamyl-tRNA_amidotransferase_subunit_B_1413169..1413399_NEGATIVE 196 119 72 134 91 NC_003454:FN0021|5end_4-diphosphocytidyl-2-C-methyl-D-erythritol_kinase_659890..660120_POSITIVE 194 75 31 107 66 NC_003454:FN0862|5end_hypothetical_protein_1522371..1522601_NEGATIVE 194 86 53 136 92 NC_003454:FN1835|5end_hypothetical_protein_323680..323910_NEGATIVE 193 76 32 123 67 NC_003454:FN0499|5end_Hemin_receptor_1148404..1148634_NEGATIVE 192 77 40 101 70 NC_003454:FN1421|5end_Pyruvate-flavodoxin_oxidoreductase_2083305..2083535_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 606 120 72 60 12 NC_003454:FN1441|3end_PTS_system,_fructose-specific_IIABC_component_2110123..2110273_POSITIVE 606 120 72 74 26 NC_003454:FN0842|3end_hypothetical_protein_1502822..1502972_NEGATIVE 606 120 72 60 12 NC_003454:FN0788|3end_hypothetical_protein_1443940..1444090_NEGATIVE 559 120 72 73 26 NC_003454:FN1890|3end_hypothetical_protein_373045..373195_NEGATIVE 531 120 72 79 31 NC_003454:FN0209|3end_Hypothetical_cytosolic_protein_836800..836950_POSITIVE 528 120 75 46 1 NC_003454:FN0487|3end_D-lactate_dehydrogenase_1131756..1131906_NEGATIVE 454 130 85 52 1 NC_003454:FN1531|3end_Negative_regulator_of_murein_hydrolase_44236..44386_NEGATIVE 328 122 94 32 4 NC_003454:FN1448|3end_Hypothetical_cytosolic_protein_2117403..2117553_NEGATIVE 303 60 17 94 53 NC_003454:FN0104|3end_Acetyltransferase_739618..739768_NEGATIVE 301 120 72 74 26 NC_003454:FN1843|3end_Surface_antigen_333468..333618_POSITIVE 252 122 97 28 3 NC_003454:FN1410|3end_Transporter_2070505..2070655_POSITIVE 240 55 13 69 25 NC_003454:FN2066|3end_hypothetical_protein_576773..576923_POSITIVE 216 86 43 117 70 NC_003454:FN1594|3end_Nitrogen_fixation_protein_RNFG_104360..104510_NEGATIVE 210 60 11 94 34 NC_003454:FN0054|3end_tyrosyl-tRNA_synthetase_692136..692286_POSITIVE 208 120 72 72 24 NC_003454:FN2053|3end_Serine/threonine_sodium_symporter_561228..561378_NEGATIVE 204 98 72 88 60 NC_003454:FN0865|3end_hypothetical_protein_1523040..1523190_NEGATIVE 202 120 71 118 62 NC_003454:FN1622|3end_Uridylate_kinase_130439..130589_POSITIVE 200 124 98 85 59 NC_003454:FN1221|3end_hypothetical_protein_1881290..1881440_POSITIVE 199 80 42 112 72 NC_003454:FN0595|3end_UDP-N-acetylglucosamine_acyltransferase_1250081..1250231_POSITIVE 197 82 49 95 63 NC_003454:FN0754|3end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A_1413183..1413333_NEGATIVE