Origin IGS: attttacacgcttattagattgtatgtaagtactttttgccgcctttcccgatctatttttcacgccggcagccctgcacgaaaaatcctccttctacttgttcctgtttccctttcctcctatcgttacattgattgtttatgacggttggttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaccaaccgtcataaacaatcaatgtaacgataggaggaaagggaaacaggaacaagtagaaggaggatttttcgtgcagggctgccggcgtgaaaaatagatcgggaaaggcggcaaaaagtacttacatacaatctaataagcgtgtaaaat Mask Tandem Repeat Region ================================================ attttacacgcttattagattgtatgtaagtactttttgccgcctttcccgatctatttttcacgccggcagccctgcacgaaaaatcctccttctacttgttcctgtttccctttcctcctatcgttacattgattgtttatgacggttggttta Find is-nt database================================================ Query_seq: TF1507:TF1508|TF1507:TF1508:outer membrane receptor, TonB-dependent:anti-sigma factor:->->:1616329..1616484 156 attttacacgcttattagattgtatgtaagtactttttgccgcctttcccgatctatttttcacgccggcagccctgcacgaaaaatcctccttctacttgttcctgtttccctttcctcctatcgttacattgattgtttatgacggttggttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1507:TF1508|TF1507:TF1508:outer membrane receptor, TonB-dependent:anti-sigma factor:->->:1616329..1616484 156 attttacacgcttattagattgtatgtaagtactttttgccgcctttcccgatctatttttcacgccggcagccctgcacgaaaaatcctccttctacttgttcctgtttccctttcctcctatcgttacattgattgtttatgacggttggttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1507:TF1508|TF1507:TF1508:outer membrane receptor, TonB-dependent:anti-sigma factor:->->:1616329..1616484 156 attttacacgcttattagattgtatgtaagtactttttgccgcctttcccgatctatttttcacgccggcagccctgcacgaaaaatcctccttctacttgttcctgtttccctttcctcctatcgttacattgattgtttatgacggttggttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attttacacgcttattagattgtatgtaagtactttttgccgcctttcccgatctatttttcacgccggcagccctgcacgaaaaatcctccttctacttgttcctgtttccctttcctcctatcgttacattgattgtttatgacggttggttta Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 19 End: 132 .................. M V C K Y F L P P F P I Y F S R R Q P C T K N P P S T C S C F P F L L S L H ........................ Protein_Len: 43 Strand: + Start: 14 End: 142 ............. M R L Y V S T F C R L S R S I F H A G S P A R K I L L L L V P V S L S S Y R Y I D C L .............. attttacacgcttattagattgtatgtaagtactttttgccgcctttcccgatctatttttcacgccggcagccctgcacgaaaaatcctccttctacttgttcctgtttccctttcctcctatcgttacattgattgtttatgacggttggttta 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================================================ attttacacgcttattagattgtatgtaagtactttttgccgcctttcccgatctatttttcacgccggcagccctgcacgaaaaatcctccttctacttgttcctgtttccctttcctcctatcgttacattgattgtttatgacggttggttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1507:TF1508|TF1507:TF1508:outer membrane receptor, TonB-dependent:anti-sigma factor:->->:1616329..1616484 156 attttacacgcttattagattgtatgtaagtactttttgccgcctttcccgatctatttttcacgccggcagccctgcacgaaaaatcctccttctacttgttcctgtttccctttcctcctatcgttacattgattgtttatgacggttggttta Intra-Species Hit: Count: 1 Min: 1 Max: 156 Len: 156 Subject: tfor_TF1507_TF1508|outer membrane receptor, TonB-dependent:anti-sigma factor|POSITIVE:POSITIVE|[1616329,1616484]|156 HSP 1 e-value: 1.0E-83 bit: 309.0 Len: 156 Query Start:1 Query End:156 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 attttacacgcttattagattgtatgtaagtactttttgccgcctttcccgatctatttttcacgccggcagccctgcacgaaaaatcctccttctacttgttcctgtttccctttcctcctatcgttacattgattgtttatgacggttggttta attttacacgcttattagattgtatgtaagtactttttgccgcctttcccgatctatttttcacgccggcagccctgcacgaaaaatcctccttctacttgttcctgtttccctttcctcctatcgttacattgattgtttatgacggttggttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUACACGCUUAUUAGAUUGUAUGUAAGUACUUUUUGCCGCCUUUCCCGAUCUAUUUUUCACGCCGGCAGCCCUGCACGAAAAAUCCUCCUUCUACUUGUUCCUGUUUCCCUUUCCUCCUAUCGUUACAUUGAUUGUUUAUGACGGUUGGUUUA ..((((((..(..........)..))))))..................((((((.(((((((..((.((....)).))..)))))))....................................((((.(((.....)))..)))).)))))).... (-19.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACCAACCGUCAUAAACAAUCAAUGUAACGAUAGGAGGAAAGGGAAACAGGAACAAGUAGAAGGAGGAUUUUUCGUGCAGGGCUGCCGGCGUGAAAAAUAGAUCGGGAAAGGCGGCAAAAAGUACUUACAUACAAUCUAAUAAGCGUGUAAAAU ....((..(((((....(((.....)))...))).)).......(....).))...(((((...(.(.((....)).).)...((((((..(.(((........))).)...))))))......)))))...((((..((....))..)))).... (-26.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 428 90 41 70 7 tfor:TF2951|5end_O-succinylbenzoic_acid--CoA_ligase_3158496..3158726_POSITIVE 393 108 64 52 10 tfor:TF1145|5end_anaerobic_C4-dicarboxylate_membrane_transporter_1225799..1226029_POSITIVE 392 80 39 60 3 tfor:TF1602|5end_L-aspartate_oxidase_1715579..1715809_POSITIVE 368 106 62 173 134 tfor:TF0819|5end_phosphoglycerate_mutase_878447..878677_POSITIVE 366 110 62 57 1 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 365 90 41 229 186 tfor:TF2682|5end_N_utilization_substance_protein_A_2856308..2856538_POSITIVE 365 78 32 83 26 tfor:TF1239|5end_RNA_polymerase_ECF-type_sigma_factor_1323580..1323810_POSITIVE 364 77 32 218 160 tfor:TF0754|5end_GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-redu_ctase_(GDP-L-fucose_synthetase)_801631..801861_POSITIVE 362 78 39 210 161 tfor:TF3022|5end_chorismate_synthase_3246136..3246366_POSITIVE 362 105 64 214 166 tfor:TF2294|5end_hypothetical_protein_2448012..2448242_POSITIVE 349 90 44 63 17 tfor:TF2759|5end_xylose_repressor,_ROK_family_2943568..2943798_POSITIVE 347 70 21 141 85 tfor:TF1623|5end_5-formyltetrahydrofolate_cyclo-ligase_1736698..1736928_POSITIVE 346 78 32 223 173 tfor:TF2229.1|5end_rteR_regulatory_ortholog_(with_internal_stop)_2399454..2399684_POSITIVE 345 80 40 64 21 tfor:TF2441|5end_10_kDa_chaperonin_2618239..2618469_POSITIVE 341 77 33 202 152 tfor:TF1767|5end_3-dehydroquinate_synthase_1905492..1905722_POSITIVE 339 77 34 146 110 tfor:TF1910|5end_nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase_2064001..2064231_POSITIVE 337 78 40 43 1 tfor:TF0424|5end_outer_membrane_receptor,_TonB-linked_440028..440258_POSITIVE 334 120 71 162 104 tfor:TF2818|5end_acetylornithine_aminotransferase_3007739..3007969_POSITIVE 334 80 41 145 103 tfor:TF1853|5end_homoserine_O-succinyltransferase_2006470..2006700_POSITIVE 333 78 33 47 3 tfor:TF2257|5end_transfer_region-related_protein,_TraJ_2428541..2428771_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 119 71 149 90 tfor:TF1182|3end_hypothetical_protein_1268938..1269088_POSITIVE 347 70 21 126 70 tfor:TF1622|3end_conserved_hypothetical_protein_1736763..1736913_POSITIVE 339 90 42 145 97 tfor:TF2953|3end_possible_TonB-dependent_outer_membrane_receptor_3161501..3161651_POSITIVE 339 77 34 140 104 tfor:TF1909|3end_cobalamin_(5`-phosphate)_synthase_2064075..2064225_POSITIVE 334 98 64 53 10 tfor:TF2950|3end_chloromuconate_cycloisomerase_3158549..3158699_POSITIVE 334 80 41 141 99 tfor:TF1852|3end_prtQ_protein_2006546..2006696_POSITIVE 332 110 65 52 1 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 332 107 61 93 43 tfor:TF2132|3end_TIM-barrel_protein,_NifR3_family_2308769..2308919_POSITIVE 329 90 41 46 2 tfor:TF2226|3end_CTn_excision_protein_2395956..2396106_POSITIVE 328 119 71 150 90 tfor:TF1660|3end_hypothetical_protein_1775600..1775750_POSITIVE 324 90 41 66 8 tfor:TF2978|3end_conserved_hypothetical_protein_3190862..3191012_POSITIVE 324 88 50 44 4 tfor:TF1691|3end_integrase_1810767..1810917_POSITIVE 323 107 63 102 54 tfor:TF3009|3end_RNA_polymerase_ECF-type_sigma_factor_3229709..3229859_POSITIVE 321 78 40 147 105 tfor:TF2501|3end_DNA_mismatch_repair_protein_2678183..2678333_POSITIVE 316 78 33 56 1 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 315 115 71 89 34 tfor:TF2656|3end_valyl-tRNA_synthetase_2829822..2829972_POSITIVE 315 90 41 124 70 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 314 96 65 52 16 tfor:TF2218|3end_two-component_system_response_regulator_2390928..2391078_POSITIVE 312 120 73 85 41 tfor:TF0812|3end_conserved_hypothetical_protein_872607..872757_POSITIVE 310 69 21 134 69 tfor:TF0781|3end_serine_protease_inhibitor_836004..836154_POSITIVE