Origin IGS: tagatgatctcattcgtctgtaaaagttgattaccaatttgggtatgttcttaagtgtagataaatgtttttttgaatctatacaaaagatcataatgtagcatatgttgtaatgattatatatctgataaaaagcattttattttttcttttgtagatataaataattccttttaatgggctttgtaggcataaaataggattgaaaaaacttgacaaatgaaccttaaatatctaatcttgtcaaaaattttaatttgaaatact .........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 agtatttcaaattaaaatttttgacaagattagatatttaaggttcatttgtcaagttttttcaatcctattttatgcctacaaagcccattaaaaggaattatttatatctacaaaagaaaaaataaaatgctttttatcagatatataatcattacaacatatgctacattatgatcttttgtatagattcaaaaaaacatttatctacacttaagaacatacccaaattggtaatcaacttttacagacgaatgagatcatcta Mask Tandem Repeat Region ================================================ tagatgatctcattcgtctgtaaaagttgattaccaatttgggtatgttcttaagtgtagataaatgtttttttgaatctatacaaaagatcataatgtagcatatgttgtaatgattatatatctgataaaaagcattttattttttcttttgtagatataaataattccttttaatgggctttgtaggcataaaataggattgaaaaaacttgacaaatgaaccttaaatatctaatcttgtcaaaaattttaatttgaaatact Find is-nt database================================================ Query_seq: TF1316:TF1318|TF1316:TF1318:conserved hypothetical protein; possible TPR-repeat-containing protein:outer membrane receptor:->->:1393557..1393823 267 tagatgatctcattcgtctgtaaaagttgattaccaatttgggtatgttcttaagtgtagataaatgtttttttgaatctatacaaaagatcataatgtagcatatgttgtaatgattatatatctgataaaaagcattttattttttcttttgtagatataaataattccttttaatgggctttgtaggcataaaataggattgaaaaaacttgacaaatgaaccttaaatatctaatcttgtcaaaaattttaatttgaaatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1316:TF1318|TF1316:TF1318:conserved hypothetical protein; possible TPR-repeat-containing protein:outer membrane receptor:->->:1393557..1393823 267 tagatgatctcattcgtctgtaaaagttgattaccaatttgggtatgttcttaagtgtagataaatgtttttttgaatctatacaaaagatcataatgtagcatatgttgtaatgattatatatctgataaaaagcattttattttttcttttgtagatataaataattccttttaatgggctttgtaggcataaaataggattgaaaaaacttgacaaatgaaccttaaatatctaatcttgtcaaaaattttaatttgaaatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1316:TF1318|TF1316:TF1318:conserved hypothetical protein; possible TPR-repeat-containing protein:outer membrane receptor:->->:1393557..1393823 267 tagatgatctcattcgtctgtaaaagttgattaccaatttgggtatgttcttaagtgtagataaatgtttttttgaatctatacaaaagatcataatgtagcatatgttgtaatgattatatatctgataaaaagcattttattttttcttttgtagatataaataattccttttaatgggctttgtaggcataaaataggattgaaaaaacttgacaaatgaaccttaaatatctaatcttgtcaaaaattttaatttgaaatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagatgatctcattcgtctgtaaaagttgattaccaatttgggtatgttcttaagtgtagataaatgtttttttgaatctatacaaaagatcataatgtagcatatgttgtaatgattatatatctgataaaaagcattttattttttcttttgtagatataaataattccttttaatgggctttgtaggcataaaataggattgaaaaaacttgacaaatgaaccttaaatatctaatcttgtcaaaaattttaatttgaaatact Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: - Start: 94 End: 234 ............................................................................................. L T A Y T T I I I Y R I F L M K N K R K Y I Y I I G K L P S Q L C L I P N F F S S L H V K F M ................................. Protein_Len: 41 Strand: - Start: 2 End: 124 . S S R M R R Y F N I V L K P I N K L T S L H K K S D I C F I M I Y C I N Y H N Y M ............................................................................................................................................... tagatgatctcattcgtctgtaaaagttgattaccaatttgggtatgttcttaagtgtagataaatgtttttttgaatctatacaaaagatcataatgtagcatatgttgtaatgattatatatctgataaaaagcattttattttttcttttgtagatataaataattccttttaatgggctttgtaggcataaaataggattgaaaaaacttgacaaatgaaccttaaatatctaatcttgtcaaaaattttaatttgaaatact 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: 81 Start: 212 End: 241 ...................................................................................................................................................................................................................CTTGACAAATGAACCTTAAATATCTAATCT.......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagatgatctcattcgtctgtaaaagttgattaccaatttgggtatgttcttaagtgtagataaatgtttttttgaatctatacaaaagatcataatgtagcatatgttgtaatgattatatatctgataaaaagcattttattttttcttttgtagatataaataattccttttaatgggctttgtaggcataaaataggattgaaaaaacttgacaaatgaaccttaaatatctaatcttgtcaaaaattttaatttgaaatact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -2.5 Tail_Score: -5.86976 Start: 129 End: 142 Full_Region: TGATTATATATCTGA TAAAA AGCA TTTTA TTTTTTCTTTTGTAG ................................................................................................................................TAAAAAGCATTTTA............................................................................................................................. Find igs database================================================ Query_seq: TF1316:TF1318|TF1316:TF1318:conserved hypothetical protein; possible TPR-repeat-containing protein:outer membrane receptor:->->:1393557..1393823 267 tagatgatctcattcgtctgtaaaagttgattaccaatttgggtatgttcttaagtgtagataaatgtttttttgaatctatacaaaagatcataatgtagcatatgttgtaatgattatatatctgataaaaagcattttattttttcttttgtagatataaataattccttttaatgggctttgtaggcataaaataggattgaaaaaacttgacaaatgaaccttaaatatctaatcttgtcaaaaattttaatttgaaatact Intra-Species Hit: Count: 1 Min: 1 Max: 267 Len: 267 Subject: tfor_TF1316_TF1318|conserved hypothetical protein; possible TPR-repeat-containing protein:outer membrane receptor|POSITIVE:POSITIVE|[1393557,1393823]|267 HSP 1 e-value: 2.0E-59 bit: 230.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 tagatgatctcattcgtctgtaaaagttgattaccaatttgggtatgttcttaagtgtagataaatgnnnnnnngaatctatacaaaagatcataatgtagcatatgttgtaatgattatatatctgataaaaagca.................................................................................................................................. tagatgatctcattcgtctgtaaaagttgattaccaatttgggtatgttcttaagtgtagataaatgtttttttgaatctatacaaaagatcataatgtagcatatgttgtaatgattatatatctgataaaaagca.................................................................................................................................. HSP 2 e-value: 3.0E-58 bit: 226.0 Len: 114 Query Start:154 Query End:267 Subject Strand: POSITIVE Subject Start: 154 Subject End: 267 .........................................................................................................................................................gtagatataaataattccttttaatgggctttgtaggcataaaataggattgaaaaaacttgacaaatgaaccttaaatatctaatcttgtcaaaaattttaatttgaaatact .........................................................................................................................................................gtagatataaataattccttttaatgggctttgtaggcataaaataggattgaaaaaacttgacaaatgaaccttaaatatctaatcttgtcaaaaattttaatttgaaatact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAUGAUCUCAUUCGUCUGUAAAAGUUGAUUACCAAUUUGGGUAUGUUCUUAAGUGUAGAUAAAUGUUUUUUUGAAUCUAUACAAAAGAUCAUAAUGUAGCAUAUGUUGUAAUGAUUAUAUAUCUGAUAAAAAGCAUUUUAUUUUUUCUUUUGUAGAUAUAAAUAAUUCCUUUUAAUGGGCUUUGUAGGCAUAAAAUAGGAUUGAAAAAACUUGACAAAUGAACCUUAAAUAUCUAAUCUUGUCAAAAAUUUUAAUUUGAAAUACU (((((((......)))))))...((((((.....))))))...((((.((((..((((((((..(........)..))))))))..)))).))))..(((...((((((..........((((((((...(((((.............))))).)))))))).((((..(((......)))..)))).)))))).....(((((((((....(((((((.....................)))))))...)))))))))....))). (-45.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAUUUCAAAUUAAAAUUUUUGACAAGAUUAGAUAUUUAAGGUUCAUUUGUCAAGUUUUUUCAAUCCUAUUUUAUGCCUACAAAGCCCAUUAAAAGGAAUUAUUUAUAUCUACAAAAGAAAAAAUAAAAUGCUUUUUAUCAGAUAUAUAAUCAUUACAACAUAUGCUACAUUAUGAUCUUUUGUAUAGAUUCAAAAAAACAUUUAUCUACACUUAAGAACAUACCCAAAUUGGUAAUCAACUUUUACAGACGAAUGAGAUCAUCUA ......(((((........))))).................((((((((((((..(((((((...((((.(((.(((.((....))..))).))))))).........((((((((((((....((((((....))))))....................((((........)))).))))))))..))))...))))))).....................((((......)))).............))))))))).)))..... (-35.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 283 59 11 131 75 tfor:TF1577|5end_hypothetical_protein_1685960..1686190_POSITIVE 256 50 1 210 164 tfor:TF0714|5end_endonuclease;_resolvase_764009..764239_POSITIVE 254 227 183 161 117 tfor:TF0076|5end_probable_carbohydrate_kinase,_PfkB_family_83279..83509_POSITIVE 253 43 4 55 8 tfor:TF0281|5end_hypothetical_protein_308909..309139_POSITIVE 250 57 12 231 176 tfor:TF1795|5end_conserved_hypothetical_protein_1935746..1935976_POSITIVE 250 127 82 66 22 tfor:TF1558|5end_possible_heme_biosynthesis_protein_1664821..1665051_POSITIVE 249 59 15 229 183 tfor:TF0034|5end_outer_membrane_protein_32551..32781_POSITIVE 240 57 14 152 110 tfor:TF1048|5end_permease_1109241..1109471_POSITIVE 235 50 2 220 174 tfor:TF1882|5end_conserved_hypothetical_protein_2033987..2034217_POSITIVE 229 35 4 228 200 tfor:TF0282|5end_probable_tonB-linked_outer_membrane_receptor_309101..309331_POSITIVE 229 69 28 65 16 tfor:TF0056|5end_integrase_frangment,_C-terminal_59074..59304_POSITIVE 218 43 12 186 151 tfor:TF0641|5end_outer_membrane_protein_681249..681479_POSITIVE 217 43 2 208 166 tfor:TF2742|5end_single-strand_DNA-specific_exonuclease_2923802..2924032_POSITIVE 216 205 170 103 67 tfor:TF1170|5end_conserved_hypothetical_protein_1251862..1252092_POSITIVE 216 205 170 91 55 tfor:TF1171|5end_ABC_transporter,_ATP-binding_protein_1251850..1252080_POSITIVE 215 196 169 202 172 tfor:TF1447|5end_D-ribulose-phosphate-3_epimerase_1530977..1531207_POSITIVE 215 49 3 196 149 tfor:TF0238|5end_outer_membrane_protein_266871..267101_POSITIVE 213 47 5 229 192 tfor:TF1835|5end_possible_dihydroxy-acid_dehydratase_1984201..1984431_POSITIVE 213 76 37 121 78 tfor:TF1219|5end_conserved_hypothetical_protein_1304404..1304634_POSITIVE 212 47 2 49 4 tfor:TF3070|5end_conserved_hypothetical_protein_3294380..3294610_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 43 4 102 55 tfor:TF0280|3end_hypothetical_protein_309036..309186_POSITIVE 250 127 82 73 29 tfor:TF1557|3end_glycosyltransferase_1664908..1665058_POSITIVE 244 31 5 73 44 tfor:TF2020|3end_muconate_cycloisomerase_2177552..2177702_POSITIVE 240 57 14 149 107 tfor:TF1047|3end_tRNA_pseudouridylate_synthetase_A_(pseudouridylate_synthase_I)_1109318..1109468_POSITIVE 229 69 28 134 85 tfor:TF0055|3end_integrase_fragment,_N-terminal_59223..59373_POSITIVE 217 217 171 147 107 tfor:TF0550|3end_stationary-phase-upregulated_protein,_UstA_582924..583074_POSITIVE 215 196 169 146 116 tfor:TF1446|3end_hypothetical_protein_1531001..1531151_POSITIVE 213 50 1 59 6 tfor:TF0822|3end_hypothetical_protein_880764..880914_POSITIVE 209 58 11 94 45 tfor:TF0479|3end_transcriptional_regulator_498405..498555_POSITIVE 207 51 11 66 12 tfor:TF1272|3end_hypothetical_protein_1355823..1355973_POSITIVE 207 213 178 77 36 tfor:TF0336|3end_Xaa-Pro_aminopeptidase_361868..362018_POSITIVE 206 47 4 122 68 tfor:TF3064|3end_oxidoreductase,_aldo/keto_reductase_family_3290984..3291134_POSITIVE 204 49 4 45 2 tfor:TF2833|3end_lipid_A_disaccharide_synthase_3025183..3025333_POSITIVE 199 140 96 49 13 tfor:TF0875|3end_outer_membrane_receptor,_TonB-linked_929251..929401_POSITIVE 198 50 2 111 56 tfor:TF2453|3end_glutamate_racemase_2631326..2631476_POSITIVE 198 50 4 64 21 tfor:TF0023|3end_possible_response_element_in_two_component_regulation_20233..20383_POSITIVE 197 206 167 67 36 tfor:TF2723|3end_30S_ribosomal_protein_S20_2898020..2898170_POSITIVE 197 201 178 125 100 tfor:TF1372|3end_ISPg4-related_transposase_(IS5_family)_1449960..1450110_POSITIVE 197 149 101 49 4 tfor:TF0944|3end_TonB-dependent_receptor_988399..988549_POSITIVE 196 52 15 40 2 tfor:TF2545|3end_hypothetical_protein_2729300..2729450_POSITIVE