Origin IGS: taatgacgcttgtatctcttacgcctccgtgcttgatgccgggggcgtaactttttttcttttttctgtggcctattccggaaaatgatatacctttgcgtg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cacgcaaaggtatatcattttccggaataggccacagaaaaaagaaaaaaagttacgcccccggcatcaagcacggaggcgtaagagatacaagcgtcatta Mask Tandem Repeat Region ================================================ taatgacgcttgtatctcttacgcctccgtgcttgatgccgggggcgtaactttttttcttttttctgtggcctattccggaaaatgatatacctttgcgtg Find is-nt database================================================ Query_seq: TF0425:TF0426|TF0425:TF0426:outer membrane protein:conserved hypothetical protein:->->:444766..444867 102 taatgacgcttgtatctcttacgcctccgtgcttgatgccgggggcgtaactttttttcttttttctgtggcctattccggaaaatgatatacctttgcgtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0425:TF0426|TF0425:TF0426:outer membrane protein:conserved hypothetical protein:->->:444766..444867 102 taatgacgcttgtatctcttacgcctccgtgcttgatgccgggggcgtaactttttttcttttttctgtggcctattccggaaaatgatatacctttgcgtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0425:TF0426|TF0425:TF0426:outer membrane protein:conserved hypothetical protein:->->:444766..444867 102 taatgacgcttgtatctcttacgcctccgtgcttgatgccgggggcgtaactttttttcttttttctgtggcctattccggaaaatgatatacctttgcgtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatgacgcttgtatctcttacgcctccgtgcttgatgccgggggcgtaactttttttcttttttctgtggcctattccggaaaatgatatacctttgcgtg Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 2 End: 91 . I V S T D R V G G H K I G P A Y S K K K K R H G I G S F S M ........... taatgacgcttgtatctcttacgcctccgtgcttgatgccgggggcgtaactttttttcttttttctgtggcctattccggaaaatgatatacctttgcgtg 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================================================ taatgacgcttgtatctcttacgcctccgtgcttgatgccgggggcgtaactttttttcttttttctgtggcctattccggaaaatgatatacctttgcgtg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0425:TF0426|TF0425:TF0426:outer membrane protein:conserved hypothetical protein:->->:444766..444867 102 taatgacgcttgtatctcttacgcctccgtgcttgatgccgggggcgtaactttttttcttttttctgtggcctattccggaaaatgatatacctttgcgtg Intra-Species Hit: Count: 1 Min: 1 Max: 102 Len: 102 Subject: tfor_TF0425_TF0426|outer membrane protein:conserved hypothetical protein|POSITIVE:POSITIVE|[444766,444867]|102 HSP 1 e-value: 4.0E-21 bit: 101.0 Len: 51 Query Start:1 Query End:51 Subject Strand: POSITIVE Subject Start: 1 Subject End: 51 taatgacgcttgtatctcttacgcctccgtgcttgatgccgggggcgtaac................................................... taatgacgcttgtatctcttacgcctccgtgcttgatgccgggggcgtaac................................................... HSP 2 e-value: 9.0E-13 bit: 73.8 Len: 37 Query Start:66 Query End:102 Subject Strand: POSITIVE Subject Start: 66 Subject End: 102 .................................................................ctgtggcctattccggaaaatgatatacctttgcgtg .................................................................ctgtggcctattccggaaaatgatatacctttgcgtg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGACGCUUGUAUCUCUUACGCCUCCGUGCUUGAUGCCGGGGGCGUAACUUUUUUUCUUUUUUCUGUGGCCUAUUCCGGAAAAUGAUAUACCUUUGCGUG .....((((.((((((..(((((((((((.((.....)))))))))))))...........(((((((.((.....))))))))).)))))).....)))). (-35.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACGCAAAGGUAUAUCAUUUUCCGGAAUAGGCCACAGAAAAAAGAAAAAAAGUUACGCCCCCGGCAUCAAGCACGGAGGCGUAAGAGAUACAAGCGUCAUUA .((((....((((.((.(((((.((......))...)))))...........(((((((.(((((.....)).))).))))))))).))))..))))..... (-27.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 425 45 1 206 167 tfor:TF0145|5end_glutamine_synthetase_152446..152676_POSITIVE 405 49 5 62 14 tfor:TF0996|5end_ribonuclease_D_1050882..1051112_POSITIVE 380 48 2 138 97 tfor:TF1215|5end_haloacid_dehalogenase-like_hydrolase_1302510..1302740_POSITIVE 377 49 8 207 165 tfor:TF0543|5end_glycine_cleavage_system_p-protein_572251..572481_POSITIVE 373 48 7 149 98 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 367 67 21 74 23 tfor:TF1235|5end_L-rhamnose/H+_symporter_1319708..1319938_POSITIVE 366 47 3 73 30 tfor:TF3122|5end_ABC_transporter,_ATP-binding_protein_3356047..3356277_POSITIVE 362 47 8 83 31 tfor:TF2665|5end_hypothetical_protein_2841973..2842203_POSITIVE 361 47 7 223 184 tfor:TF1628|5end_conserved_hypothetical_protein_1740627..1740857_POSITIVE 358 47 5 226 161 tfor:TF1845|5end_hypothetical_protein_1996620..1996850_POSITIVE 355 46 4 198 158 tfor:TF3072|5end_conserved_hypothetical_protein_3295302..3295532_POSITIVE 354 46 5 145 101 tfor:TF2887|5end_phosphomannomutase/phosphoglucomutase_3076327..3076557_POSITIVE 350 49 7 202 159 tfor:TF0881|5end_conserved_hypothetical_protein_934459..934689_POSITIVE 349 47 4 219 167 tfor:TF1441|5end_conserved_hypothetical_protein_1525567..1525797_POSITIVE 347 48 6 45 5 tfor:TF2153|5end_6-phosphofructokinase_2328112..2328342_POSITIVE 347 48 18 39 2 tfor:TF1187|5end_hypothetical_protein_1269625..1269855_POSITIVE 341 48 7 87 37 tfor:TF2833|5end_lipid_A_disaccharide_synthase_3023973..3024203_POSITIVE 341 46 8 51 1 tfor:TF1819|5end_cation_efflux_system_AcrB/AcrD/AcrF_family;_ABC_transporter,_ATP-binding/permease_component_1958681..1958911_POSITIVE 341 44 7 190 162 tfor:TF1730|5end_diaminopimelate_decarboxylase_1854670..1854900_POSITIVE 341 44 7 139 111 tfor:TF1732|5end_conserved_hypothetical_protein_1854619..1854849_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 407 50 19 72 41 tfor:TF0425|3end_outer_membrane_protein_444705..444855_POSITIVE 405 49 5 62 14 tfor:TF0995|3end_conserved_hypothetical_protein_1050962..1051112_POSITIVE 380 48 2 82 41 tfor:TF1214|3end_conserved_hypothetical_protein_1302534..1302684_POSITIVE 375 43 9 145 103 tfor:TF1832|3end_3-isopropylmalate_dehydratase,_small_subunit_1981502..1981652_POSITIVE 373 48 7 149 98 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 366 47 3 70 27 tfor:TF3121|3end_nicotinate_phosphoribosyltransferase_3356124..3356274_POSITIVE 363 45 5 150 111 tfor:TF0637|3end_TPR-repeat-containing_protein_675410..675560_POSITIVE 360 69 21 66 14 tfor:TF1164|3end_two-component_system_sensor_histidine_kinase_1244778..1244928_POSITIVE 350 67 27 47 3 tfor:TF1234|3end_rhamnulose-1-phosphate_aldolase_1319761..1319911_POSITIVE 337 67 22 75 35 tfor:TF2768|3end_ferredoxin_oxidoreductase,_beta_subunit_2955169..2955319_POSITIVE 337 47 8 63 25 tfor:TF0686|3end_hypothetical_protein_732950..733100_POSITIVE 334 48 4 62 10 tfor:TF1771|3end_prolipoprotein_diacylglyceryl_transferase_1910607..1910757_POSITIVE 333 50 3 147 94 tfor:TF0925|3end_hypothetical_protein_962127..962277_POSITIVE 323 59 16 135 85 tfor:TF2853|3end_2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_3040725..3040875_POSITIVE 323 70 21 59 4 tfor:TF1908|3end_possible_phosphoglycerate_mutase_2063299..2063449_POSITIVE 320 80 31 47 4 tfor:TF2188|3end_conserved_hypothetical_protein_2363535..2363685_POSITIVE 320 66 23 73 34 tfor:TF0775|3end_ABC_transporter,_permease_component_824919..825069_POSITIVE 319 49 8 64 17 tfor:TF0989|3end_conserved_hypothetical_protein_1045227..1045377_POSITIVE 318 80 33 140 88 tfor:TF2511|3end_RNA_binding_protein_2690232..2690382_POSITIVE 318 46 4 148 105 tfor:TF1843|3end_surface_antigen_BspA_1996189..1996339_POSITIVE