Origin IGS: agcttttaaaattttgaaattaatactcctacaaatgtatcatatattttttgtttctacccactcagaccattgtttaggcatatttaattctttttaattgtattatcccgatcgctttcacgcgtttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaacgcgtgaaagcgatcgggataatacaattaaaaagaattaaatatgcctaaacaatggtctgagtgggtagaaacaaaaaatatatgatacatttgtaggagtattaatttcaaaattttaaaagct Mask Tandem Repeat Region ================================================ agcttttaaaattttgaaattaatactcctacaaatgtatcatatattttttgtttctacccactcagaccattgtttaggcatatttaattctttttaattgtattatcccgatcgctttcacgcgtttta Find is-nt database================================================ Query_seq: TF0972:TF0973|TF0972:TF0973:conserved hypothetical protein:conserved hypothetical protein:->->:1023271..1023402 132 agcttttaaaattttgaaattaatactcctacaaatgtatcatatattttttgtttctacccactcagaccattgtttaggcatatttaattctttttaattgtattatcccgatcgctttcacgcgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0972:TF0973|TF0972:TF0973:conserved hypothetical protein:conserved hypothetical protein:->->:1023271..1023402 132 agcttttaaaattttgaaattaatactcctacaaatgtatcatatattttttgtttctacccactcagaccattgtttaggcatatttaattctttttaattgtattatcccgatcgctttcacgcgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0972:TF0973|TF0972:TF0973:conserved hypothetical protein:conserved hypothetical protein:->->:1023271..1023402 132 agcttttaaaattttgaaattaatactcctacaaatgtatcatatattttttgtttctacccactcagaccattgtttaggcatatttaattctttttaattgtattatcccgatcgctttcacgcgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcttttaaaattttgaaattaatactcctacaaatgtatcatatattttttgtttctacccactcagaccattgtttaggcatatttaattctttttaattgtattatcccgatcgctttcacgcgtttta Predict ORF larger than 30AA ================================================ agcttttaaaattttgaaattaatactcctacaaatgtatcatatattttttgtttctacccactcagaccattgtttaggcatatttaattctttttaattgtattatcccgatcgctttcacgcgtttta 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================================================ agcttttaaaattttgaaattaatactcctacaaatgtatcatatattttttgtttctacccactcagaccattgtttaggcatatttaattctttttaattgtattatcccgatcgctttcacgcgtttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0972:TF0973|TF0972:TF0973:conserved hypothetical protein:conserved hypothetical protein:->->:1023271..1023402 132 agcttttaaaattttgaaattaatactcctacaaatgtatcatatattttttgtttctacccactcagaccattgtttaggcatatttaattctttttaattgtattatcccgatcgctttcacgcgtttta Intra-Species Hit: Count: 1 Min: 1 Max: 132 Len: 132 Subject: tfor_TF0972_TF0973|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1023271,1023402]|132 HSP 1 e-value: 3.0E-69 bit: 262.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 agcttttaaaattttgaaattaatactcctacaaatgtatcatatattttttgtttctacccactcagaccattgtttaggcatatttaattctttttaattgtattatcccgatcgctttcacgcgtttta agcttttaaaattttgaaattaatactcctacaaatgtatcatatattttttgtttctacccactcagaccattgtttaggcatatttaattctttttaattgtattatcccgatcgctttcacgcgtttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUUUUAAAAUUUUGAAAUUAAUACUCCUACAAAUGUAUCAUAUAUUUUUUGUUUCUACCCACUCAGACCAUUGUUUAGGCAUAUUUAAUUCUUUUUAAUUGUAUUAUCCCGAUCGCUUUCACGCGUUUUA .((..((((((....(((...((((..((((.(((((((...)))))))......(((........)))........))))..))))...))).))))))..))...........(((......)))..... (-11.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAACGCGUGAAAGCGAUCGGGAUAAUACAAUUAAAAAGAAUUAAAUAUGCCUAAACAAUGGUCUGAGUGGGUAGAAACAAAAAAUAUAUGAUACAUUUGUAGGAGUAUUAAUUUCAAAAUUUUAAAAGCU .....(((......)))...(..(((((((...................((((((..((......))..))))))..................(((....)))...))))).))..)............... (-18.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 283 127 81 206 153 tfor:TF0930|5end_conserved_hypothetical_protein;_possible_prophage_protein_968782..969012_POSITIVE 278 126 81 145 88 tfor:TF1886|5end_auxin-regulated_protein_2038720..2038950_POSITIVE 259 82 49 122 91 tfor:TF2844|5end_possible_phosphatase_or_hydrolase_3033680..3033910_POSITIVE 249 74 42 145 114 tfor:TF1432|5end_possible_hemolysin_A_1515936..1516166_POSITIVE 243 127 90 164 133 tfor:TF0229|5end_beta-galactosidase_254857..255087_POSITIVE 239 128 101 145 113 tfor:TF1403|5end_hypothetical_protein_1477775..1478005_POSITIVE 233 77 41 162 120 tfor:TF1092|5end_glycosyltransferase_1160124..1160354_POSITIVE 233 129 92 196 157 tfor:TF0062|5end_conserved_hypothetical_protein_64916..65146_POSITIVE 231 127 101 171 146 tfor:TF0036|5end_beta-hexosaminidase_precursor_35821..36051_POSITIVE 230 69 24 205 146 tfor:TF2871|5end_hypothetical_protein_3062194..3062424_POSITIVE 229 129 81 150 108 tfor:TF2009|5end_octaprenyl-diphosphate_synthase_ispB_2162131..2162361_POSITIVE 227 118 72 166 125 tfor:TF0440|5end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_2_463655..463885_POSITIVE 226 125 81 169 131 tfor:TF2599|5end_alpha-amylase_family_protein_2771883..2772113_POSITIVE 224 127 81 143 87 tfor:TF2579|5end_30S_ribosomal_protein_S4_2747202..2747432_POSITIVE 224 129 95 215 182 tfor:TF2500|5end_ABC_transporter,_ATP-binding_protein_2674449..2674679_POSITIVE 221 130 90 119 77 tfor:TF2870|5end_hypothetical_protein_3062002..3062232_POSITIVE 221 128 81 190 127 tfor:TF0289|5end_conserved_hypothetical_protein_318015..318245_POSITIVE 219 90 45 149 102 tfor:TF3021|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_3245437..3245667_POSITIVE 219 130 84 186 129 tfor:TF1334|5end_hypothetical_protein_1415996..1416226_POSITIVE 218 89 41 67 22 tfor:TF0710|5end_two_component_system_histidine_kinase_757250..757480_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 126 81 96 39 tfor:TF1885|3end_conserved_hypothetical_protein_2038751..2038901_POSITIVE 259 82 49 122 91 tfor:TF2843|3end_conserved_hypothetical_protein;_possible_lipoprotein_3033760..3033910_POSITIVE 249 74 42 137 106 tfor:TF1431|3end_conserved_hypothetical_protein;_possible_acyltransferase_1516008..1516158_POSITIVE 243 127 90 36 5 tfor:TF0228|3end_probable_integral_outer_membrane_protein_254809..254959_POSITIVE 231 83 52 50 17 tfor:TF2340|3end_hypothetical_protein_2500915..2501065_POSITIVE 230 69 24 103 44 tfor:TF2869|3end_hypothetical_protein_3062172..3062322_POSITIVE 229 129 81 122 80 tfor:TF2008|3end_DNA_polymerase_I_2162183..2162333_POSITIVE 228 127 95 134 99 tfor:TF0983|3end_nitroreductase_family_protein,__possible_NADH_dehydrogenase/NAD(P)H_nitroreductase_1040034..1040184_POSITIVE 227 118 72 120 79 tfor:TF0439|3end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_1_463689..463839_POSITIVE 219 90 45 91 44 tfor:TF3020|3end_possible_sulfatase_3245459..3245609_POSITIVE 219 130 84 124 67 tfor:TF1333|3end_probable_acylaminoacyl_peptidase;_alanyl_dipeptidyl_peptidase_1416014..1416164_POSITIVE 217 83 51 41 8 tfor:TF1605|3end_outer_membrane_protein,_TonB_dependent_receptor_1722414..1722564_POSITIVE 217 125 91 139 110 tfor:TF1117|3end_conserved_hypothetical_protein_1189451..1189601_POSITIVE 209 130 103 47 21 tfor:TF3095|3end_ABC_transporter,_ATP-binding_protein_3328033..3328183_POSITIVE 208 88 52 67 32 tfor:TF2528|3end_anti-sigma_factor_2710054..2710204_POSITIVE 208 130 110 42 22 tfor:TF0072|3end_hypothetical_protein_81070..81220_POSITIVE 203 127 109 38 15 tfor:TF0141|3end_exodeoxyribonuclease_VII,_large_subunit_149830..149980_POSITIVE 202 130 98 137 107 tfor:TF0047|3end_hypothetical_protein_54109..54259_POSITIVE 201 130 100 120 90 tfor:TF2891|3end_lipoprotein_3079381..3079531_POSITIVE 201 82 48 43 1 tfor:TF0518|3end_glutaminyl-tRNA_synthetase_543559..543709_POSITIVE