Origin IGS: taaatggctgcatggaacaggtaaattgactaactttgccggaacattacgctccggcaaagtcgttttcttcggaacacgcttttttgaattgatcaataataaaacataaatat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atatttatgttttattattgatcaattcaaaaaagcgtgttccgaagaaaacgactttgccggagcgtaatgttccggcaaagttagtcaatttacctgttccatgcagccattta Mask Tandem Repeat Region ================================================ taaatggctgcatggaacaggtaaattgactaactttgccggaacattacgctccggcaaagtcgttttcttcggaacacgcttttttgaattgatcaataataaaacataaatat Find is-nt database================================================ Query_seq: TF1738:TF1739|TF1738:TF1739:outer membrane protein:possible sulfatase:->->:1867007..1867122 116 taaatggctgcatggaacaggtaaattgactaactttgccggaacattacgctccggcaaagtcgttttcttcggaacacgcttttttgaattgatcaataataaaacataaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1738:TF1739|TF1738:TF1739:outer membrane protein:possible sulfatase:->->:1867007..1867122 116 taaatggctgcatggaacaggtaaattgactaactttgccggaacattacgctccggcaaagtcgttttcttcggaacacgcttttttgaattgatcaataataaaacataaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1738:TF1739|TF1738:TF1739:outer membrane protein:possible sulfatase:->->:1867007..1867122 116 taaatggctgcatggaacaggtaaattgactaactttgccggaacattacgctccggcaaagtcgttttcttcggaacacgcttttttgaattgatcaataataaaacataaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatggctgcatggaacaggtaaattgactaactttgccggaacattacgctccggcaaagtcgttttcttcggaacacgcttttttgaattgatcaataataaaacataaatat Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 8 End: 109 ....... M H G T G K L T N F A G T L R S G K V V F F G T R F F E L I N N K T ....... Protein_Len: 38 Strand: - Start: 1 End: 114 L H S C P V P L N V L K A P V N R E P L T T K K P V R K K S N I L L L V Y M .. taaatggctgcatggaacaggtaaattgactaactttgccggaacattacgctccggcaaagtcgttttcttcggaacacgcttttttgaattgatcaataataaaacataaatat 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================================================ taaatggctgcatggaacaggtaaattgactaactttgccggaacattacgctccggcaaagtcgttttcttcggaacacgcttttttgaattgatcaataataaaacataaatat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -9.3 Tail_Score: -4.63218 Start: 31 End: 65 Full_Region: AACAGGTAAATTGAC TAACTTTGCCGGAAC ATTAC GCTCCGGCAAAGTCG TTTTCTTCGGAACAC ..............................TAACTTTGCCGGAACATTACGCTCCGGCAAAGTCG................................................... TransTerm Strand: + Conf: 78 HP_score: -10.6 Tail_Score: -3.3761 Start: 32 End: 64 Full_Region: ACAGGTAAATTGACT AACTTTGCCGGAAC ATTAC GCTCCGGCAAAGTC GTTTTCTTCGGAACA ...............................AACTTTGCCGGAACATTACGCTCCGGCAAAGTC.................................................... TransTerm Strand: + Conf: 100 HP_score: -13.2 Tail_Score: -3.25538 Start: 34 End: 62 Full_Region: AGGTAAATTGACTAA CTTTGCCGGAAC ATTAC GCTCCGGCAAAG TCGTTTTCTTCGGAA .................................CTTTGCCGGAACATTACGCTCCGGCAAAG...................................................... TransTerm Strand: - Conf: 100 HP_score: -16.1 Tail_Score: -3.25356 Start: 34 End: 62 Full_Region: ttccgaagaaaacga ctttgccggagcg taa tgttccggcaaag ttagtcaatttacct .................................ctttgccggagcgtaatgttccggcaaag...................................................... Find igs database================================================ Query_seq: TF1738:TF1739|TF1738:TF1739:outer membrane protein:possible sulfatase:->->:1867007..1867122 116 taaatggctgcatggaacaggtaaattgactaactttgccggaacattacgctccggcaaagtcgttttcttcggaacacgcttttttgaattgatcaataataaaacataaatat Intra-Species Hit: Count: 1 Min: 1 Max: 116 Len: 116 Subject: tfor_TF1738_TF1739|outer membrane protein:possible sulfatase|POSITIVE:POSITIVE|[1867007,1867122]|116 HSP 1 e-value: 8.0E-60 bit: 230.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 taaatggctgcatggaacaggtaaattgactaactttgccggaacattacgctccggcaaagtcgttttcttcggaacacgcttttttgaattgatcaataataaaacataaatat taaatggctgcatggaacaggtaaattgactaactttgccggaacattacgctccggcaaagtcgttttcttcggaacacgcttttttgaattgatcaataataaaacataaatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUGGCUGCAUGGAACAGGUAAAUUGACUAACUUUGCCGGAACAUUACGCUCCGGCAAAGUCGUUUUCUUCGGAACACGCUUUUUUGAAUUGAUCAAUAAUAAAACAUAAAUAU ....((.(((.......))).)).(((((...(((((((((((.(.....).)))))))))))(((.(((....))).)))..............)))))................ (-27.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUUUAUGUUUUAUUAUUGAUCAAUUCAAAAAAGCGUGUUCCGAAGAAAACGACUUUGCCGGAGCGUAAUGUUCCGGCAAAGUUAGUCAAUUUACCUGUUCCAUGCAGCCAUUUA .....((((((((....((((.....)))).)))))))).......((....((((((((((((((.....))))))))))))))..)).......((((.....))))....... (-31.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 407 80 34 124 76 tfor:TF0600|5end_oxidoreductase/dehydrogenase_630083..630313_POSITIVE 404 77 38 211 164 tfor:TF1232|5end_hypothetical_protein_1317331..1317561_POSITIVE 386 77 37 194 153 tfor:TF1069|5end_glucokinase_regulatory_protein,_sugar_phosphate_isomerase_domain_1138884..1139114_POSITIVE 362 71 37 162 132 tfor:TF0811|5end_conserved_hypothetical_protein;_posible_sugar_phosphate_isomerase_869787..870017_POSITIVE 358 79 34 148 107 tfor:TF1730|5end_diaminopimelate_decarboxylase_1854670..1854900_POSITIVE 358 79 34 97 56 tfor:TF1732|5end_conserved_hypothetical_protein_1854619..1854849_POSITIVE 340 75 32 176 132 tfor:TF2773|5end_S-adenosylmethionine_tRNA_ribosyltransferase_2958117..2958347_POSITIVE 340 80 34 213 148 tfor:TF2318|5end_conserved_hypothetical_protein_2475603..2475833_POSITIVE 340 78 38 205 158 tfor:TF0759|5end_heat_shock_protein_15,_RNA-binding_domain_S4_805870..806100_POSITIVE 336 96 51 170 137 tfor:TF1898|5end_RNA_polymerase_ECF-type_sigma_factor_2052115..2052345_POSITIVE 333 65 21 189 148 tfor:TF1336|5end_hypothetical_protein_1418626..1418856_POSITIVE 328 59 11 140 86 tfor:TF2925|5end_beta-N-acetylglucosaminidase_3125700..3125930_POSITIVE 326 82 46 200 158 tfor:TF2390|5end_conserved_hypothetical_protein_2560509..2560739_POSITIVE 324 80 33 172 123 tfor:TF0809|5end_cation_efflux_protein_865358..865588_POSITIVE 317 95 54 89 50 tfor:TF1339|5end_aspartate_1-decarboxylase_1420908..1421138_POSITIVE 315 75 32 219 180 tfor:TF1896|5end_conserved_hypothetical_protein;_possible_phage-related_protein_2047858..2048088_POSITIVE 312 88 41 122 70 tfor:TF0005|5end_possible_beta-lactamase_600..830_POSITIVE 311 74 33 68 16 tfor:TF0428|5end_methylmalonyl-CoA_mutase,_beta_subunit_447809..448039_POSITIVE 309 75 32 111 69 tfor:TF2435|5end_DNA_repair_protein_radC_2614352..2614582_POSITIVE 309 76 38 227 187 tfor:TF1831|5end_conserved_hypothetical_protein_1980365..1980595_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 407 80 34 91 43 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 403 75 36 128 77 tfor:TF2609|3end_dipeptidase,_pathogenicity_island-encoded_protein_D_2786264..2786414_POSITIVE 360 97 51 70 31 tfor:TF1354|3end_TonB_protein_1435216..1435366_POSITIVE 358 79 34 116 75 tfor:TF1729|3end_aspartokinase_1854718..1854868_POSITIVE 336 96 51 82 49 tfor:TF1897|3end_conserved_hypothetical_protein;_possible_aminopeptidase_2052107..2052257_POSITIVE 336 58 11 79 38 tfor:TF1730|3end_diaminopimelate_decarboxylase_1855907..1856057_POSITIVE 336 58 11 151 110 tfor:TF1732|3end_conserved_hypothetical_protein_1855979..1856129_POSITIVE 313 63 33 58 28 tfor:TF1738|3end_outer_membrane_protein_1866946..1867096_POSITIVE 312 88 41 89 37 tfor:TF0002|3end_hypothetical_protein_647..797_POSITIVE 308 82 41 53 13 tfor:TF0746|3end_possible_DNA_polymerase_III_792910..793060_POSITIVE 300 79 38 66 21 tfor:TF2847|3end_hypothetical_protein_3034985..3035135_POSITIVE 300 75 33 42 1 tfor:TF2434|3end_conserved_hypothetical_protein_2614363..2614513_POSITIVE 299 58 12 55 17 tfor:TF1134|3end_hypothetical_protein_1211022..1211172_POSITIVE 297 59 11 142 89 tfor:TF1838|3end_tRNA/rRNA_methyltransferase_1988745..1988895_POSITIVE 297 75 33 144 106 tfor:TF0808|3end_cation_efflux_system_protein_865421..865571_POSITIVE 295 74 39 149 113 tfor:TF0757|3end_50S_ribosomal_protein_L25;_general_stress_protein_805293..805443_POSITIVE 295 76 32 54 6 tfor:TF0490|3end_conserved_hypothetical_protein_513904..514054_POSITIVE 294 64 28 145 113 tfor:TF2772|3end_tRNA_pseudouridine_synthase_B_2958179..2958329_POSITIVE 291 97 51 146 105 tfor:TF1069|3end_glucokinase_regulatory_protein,_sugar_phosphate_isomerase_domain_1139794..1139944_POSITIVE 289 77 35 101 58 tfor:TF3064|3end_oxidoreductase,_aldo/keto_reductase_family_3290984..3291134_POSITIVE