Origin IGS: ccctacgcaacgaccgaataccgactactgaccggaataattttcaacatactttcagattgctatgggaaaaggtgaataaatttcagtctgatactttttttaatctcctgaaaataaaatgacattttgtcgcaaaaatccagttttatacgctttgaatcaattgttaaagataagacaaaatgacataagattaaaaaatgaatctatctttgcgcggttttttaaaacaggaacatataatcgatcaaaaaacgt .........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 acgttttttgatcgattatatgttcctgttttaaaaaaccgcgcaaagatagattcattttttaatcttatgtcattttgtcttatctttaacaattgattcaaagcgtataaaactggatttttgcgacaaaatgtcattttattttcaggagattaaaaaaagtatcagactgaaatttattcaccttttcccatagcaatctgaaagtatgttgaaaattattccggtcagtagtcggtattcggtcgttgcgtaggg Mask Tandem Repeat Region ================================================ ccctacgcaacgaccgaataccgactactgaccggaataattttcaacatactttcagattgctatgggaaaaggtgaataaatttcagtctgatactttttttaatctcctgaaaataaaatgacattttgtcgcaaaaatccagttttatacgctttgaatcaattgttaaagataagacaaaatgacataagattaaaaaatgaatctatctttgcgcggttttttaaaacaggaacatataatcgatcaaaaaacgt Find is-nt database================================================ Query_seq: TF2346:TF2347|TF2346:TF2347:hypothetical protein:outer membrane protein, TonB dependent receptor:->->:2510034..2510294 261 ccctacgcaacgaccgaataccgactactgaccggaataattttcaacatactttcagattgctatgggaaaaggtgaataaatttcagtctgatactttttttaatctcctgaaaataaaatgacattttgtcgcaaaaatccagttttatacgctttgaatcaattgttaaagataagacaaaatgacataagattaaaaaatgaatctatctttgcgcggttttttaaaacaggaacatataatcgatcaaaaaacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2346:TF2347|TF2346:TF2347:hypothetical protein:outer membrane protein, TonB dependent receptor:->->:2510034..2510294 261 ccctacgcaacgaccgaataccgactactgaccggaataattttcaacatactttcagattgctatgggaaaaggtgaataaatttcagtctgatactttttttaatctcctgaaaataaaatgacattttgtcgcaaaaatccagttttatacgctttgaatcaattgttaaagataagacaaaatgacataagattaaaaaatgaatctatctttgcgcggttttttaaaacaggaacatataatcgatcaaaaaacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2346:TF2347|TF2346:TF2347:hypothetical protein:outer membrane protein, TonB dependent receptor:->->:2510034..2510294 261 ccctacgcaacgaccgaataccgactactgaccggaataattttcaacatactttcagattgctatgggaaaaggtgaataaatttcagtctgatactttttttaatctcctgaaaataaaatgacattttgtcgcaaaaatccagttttatacgctttgaatcaattgttaaagataagacaaaatgacataagattaaaaaatgaatctatctttgcgcggttttttaaaacaggaacatataatcgatcaaaaaacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccctacgcaacgaccgaataccgactactgaccggaataattttcaacatactttcagattgctatgggaaaaggtgaataaatttcagtctgatactttttttaatctcctgaaaataaaatgacattttgtcgcaaaaatccagttttatacgctttgaatcaattgttaaagataagacaaaatgacataagattaaaaaatgaatctatctttgcgcggttttttaaaacaggaacatataatcgatcaaaaaacgt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 18 End: 122 ................. M P T T D R N N F Q H T F R L L W E K V N K F Q S D T F F N L L K I K ........................................................................................................................................... Protein_Len: 46 Strand: + Start: 122 End: 259 ......................................................................................................................... M T F C R K N P V L Y A L N Q L L K I R Q N D I R L K N E S I F A R F F K T G T Y N R S K N .. Protein_Len: 48 Strand: - Start: 66 End: 209 ................................................................. P F L H I F K L R I S K K I E Q F Y F S M K D C F D L K I R K S D I T L S L V F H C L I L F H M .................................................... ccctacgcaacgaccgaataccgactactgaccggaataattttcaacatactttcagattgctatgggaaaaggtgaataaatttcagtctgatactttttttaatctcctgaaaataaaatgacattttgtcgcaaaaatccagttttatacgctttgaatcaattgttaaagataagacaaaatgacataagattaaaaaatgaatctatctttgcgcggttttttaaaacaggaacatataatcgatcaaaaaacgt 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================================================ ccctacgcaacgaccgaataccgactactgaccggaataattttcaacatactttcagattgctatgggaaaaggtgaataaatttcagtctgatactttttttaatctcctgaaaataaaatgacattttgtcgcaaaaatccagttttatacgctttgaatcaattgttaaagataagacaaaatgacataagattaaaaaatgaatctatctttgcgcggttttttaaaacaggaacatataatcgatcaaaaaacgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2346:TF2347|TF2346:TF2347:hypothetical protein:outer membrane protein, TonB dependent receptor:->->:2510034..2510294 261 ccctacgcaacgaccgaataccgactactgaccggaataattttcaacatactttcagattgctatgggaaaaggtgaataaatttcagtctgatactttttttaatctcctgaaaataaaatgacattttgtcgcaaaaatccagttttatacgctttgaatcaattgttaaagataagacaaaatgacataagattaaaaaatgaatctatctttgcgcggttttttaaaacaggaacatataatcgatcaaaaaacgt Intra-Species Hit: Count: 1 Min: 1 Max: 261 Len: 261 Subject: tfor_TF2346_TF2347|hypothetical protein:outer membrane protein, TonB dependent receptor|POSITIVE:POSITIVE|[2510034,2510294]|261 HSP 1 e-value: 1.0E-133 bit: 476.0 Len: 261 Query Start:1 Query End:261 Subject Strand: POSITIVE Subject Start: 1 Subject End: 261 ccctacgcaacgaccgaataccgactactgaccggaataattttcaacatactttcagattgctatgggaaaaggtgaataaatttcagtctgatacnnnnnnnaatctcctgaaaataaaatgacattttgtcgcaaaaatccagttttatacgctttgaatcaattgttaaagataagacaaaatgacataagattaaaaaatgaatctatctttgcgcggttttttaaaacaggaacatataatcgatcaaaaaacgt ccctacgcaacgaccgaataccgactactgaccggaataattttcaacatactttcagattgctatgggaaaaggtgaataaatttcagtctgatactttttttaatctcctgaaaataaaatgacattttgtcgcaaaaatccagttttatacgctttgaatcaattgttaaagataagacaaaatgacataagattaaaaaatgaatctatctttgcgcggttttttaaaacaggaacatataatcgatcaaaaaacgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCUACGCAACGACCGAAUACCGACUACUGACCGGAAUAAUUUUCAACAUACUUUCAGAUUGCUAUGGGAAAAGGUGAAUAAAUUUCAGUCUGAUACUUUUUUUAAUCUCCUGAAAAUAAAAUGACAUUUUGUCGCAAAAAUCCAGUUUUAUACGCUUUGAAUCAAUUGUUAAAGAUAAGACAAAAUGACAUAAGAUUAAAAAAUGAAUCUAUCUUUGCGCGGUUUUUUAAAACAGGAACAUAUAAUCGAUCAAAAAACGU .....(((((.((................(((.(((((....((((......(..((........))..).....))))...))))).))).(((.(.(((((((((((..(....)....(((.(((((((((...........((.....)).((((((........))))))....))))))))).))).))))))))))).).)))..)).)))))..((((((......))))))..................... (-39.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGUUUUUUGAUCGAUUAUAUGUUCCUGUUUUAAAAAACCGCGCAAAGAUAGAUUCAUUUUUUAAUCUUAUGUCAUUUUGUCUUAUCUUUAACAAUUGAUUCAAAGCGUAUAAAACUGGAUUUUUGCGACAAAAUGUCAUUUUAUUUUCAGGAGAUUAAAAAAAGUAUCAGACUGAAAUUUAUUCACCUUUUCCCAUAGCAAUCUGAAAGUAUGUUGAAAAUUAUUCCGGUCAGUAGUCGGUAUUCGGUCGUUGCGUAGGG ..(((((((((..((........)).....))))))))).((((((.....(((.(.(((((((((((((((.(((((((((..........(((..((((((.............)))))).))).))))))))).)))...........)))))))))))).).))).(((((((...........(((((.((((............))))..))))).....((((.(....)))))..))))))).)))))).... (-47.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 324 45 5 59 10 tfor:TF2128|5end_3-oxoacyl-(acyl-carrier_protein)_synthase_2304258..2304488_POSITIVE 319 34 2 82 42 tfor:TF1758|5end_conserved_hypothetical_protein_1894769..1894999_POSITIVE 313 37 2 64 29 tfor:TF1200|5end_conserved_hypothetical_protein_1282717..1282947_POSITIVE 299 37 12 41 14 tfor:TF0906|5end_conserved_hypothetical_protein_949675..949905_POSITIVE 299 35 2 43 10 tfor:TF0411|5end_methyltransferase_428917..429147_POSITIVE 289 46 2 90 31 tfor:TF0228|5end_probable_integral_outer_membrane_protein_253851..254081_POSITIVE 284 238 195 135 93 tfor:TF1435|5end_acetate_coenzyme_A_transferase_1519574..1519804_POSITIVE 278 36 1 168 127 tfor:TF2837|5end_conserved_hypothetical_protein_3027939..3028169_POSITIVE 275 79 51 57 30 tfor:TF3057|5end_conserved_hypothetical_protein_3280358..3280588_POSITIVE 275 70 25 183 136 tfor:TF1439|5end_outer_membrane_protein,_TonB_dependent_receptor_1522479..1522709_POSITIVE 271 36 5 50 14 tfor:TF1481|5end_ABC_transporter,_ATP-binding_protein_1574783..1575013_POSITIVE 270 65 22 165 114 tfor:TF1387|5end_conserved_hypothetical_protein_1460427..1460657_POSITIVE 269 60 11 95 53 tfor:TF0818|5end_bifunctional_protein:__aspartokinase_I;_homoserine_dehydrogenase_876002..876232_POSITIVE 265 37 3 120 69 tfor:TF1604|5end_possible_anti-sigma_factor_1717811..1718041_POSITIVE 263 136 92 174 133 tfor:TF2725|5end_outer_membrane_protein,_TonB_dependent_receptor_2899408..2899638_POSITIVE 262 36 4 103 68 tfor:TF1839|5end_conserved_hypothetical_protein_1989347..1989577_POSITIVE 262 45 7 63 22 tfor:TF1240|5end_conserved_hypothetical_protein_1324304..1324534_POSITIVE 261 55 11 96 34 tfor:TF1045|5end_conserved_hypothetical_protein_1107665..1107895_POSITIVE 260 40 1 94 38 tfor:TF2438|5end_hypothetical_protein_2615781..2616011_POSITIVE 258 67 21 113 68 tfor:TF3033|5end_S1_RNA_binding_domain_protein,_S1_ribosomal_protein_3256786..3257016_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 34 2 58 18 tfor:TF1757|3end_chromosome_partitioning_protein_1894825..1894975_POSITIVE 313 37 2 64 29 tfor:TF1199|3end_dephospho-CoA_kinase_1282797..1282947_POSITIVE 284 238 195 76 34 tfor:TF1434|3end_transketolase_1519595..1519745_POSITIVE 275 79 51 36 9 tfor:TF3056|3end_conserved_hypothetical_protein_3280417..3280567_POSITIVE 275 70 25 148 101 tfor:TF1438|3end_hypothetical_protein_1522524..1522674_POSITIVE 271 36 5 53 17 tfor:TF1480|3end_ABC_transporter,_permease_component_1574866..1575016_POSITIVE 270 65 22 146 95 tfor:TF1386|3end_hypothetical_protein_1460488..1460638_POSITIVE 265 37 3 75 24 tfor:TF1603|3end_RNA_polymerase_ECF-type_sigma_factor_1717846..1717996_POSITIVE 263 136 92 134 93 tfor:TF2724|3end_anti-sigma_factor_2899448..2899598_POSITIVE 258 67 21 85 40 tfor:TF3032|3end_thiamin_biosynthesis_protein_3256838..3256988_POSITIVE 258 34 1 100 51 tfor:TF2315|3end_thioesterase_2474498..2474648_POSITIVE 257 47 1 77 23 tfor:TF0762|3end_chromate_transport_protein_809755..809905_POSITIVE 255 41 4 147 113 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 252 69 21 115 62 tfor:TF1558|3end_possible_heme_biosynthesis_protein_1665959..1666109_POSITIVE 252 57 11 55 1 tfor:TF0276|3end_hypothetical_protein_300982..301132_POSITIVE 251 45 5 54 20 tfor:TF2992|3end_hexapeptide_transferase_family_protein_3209691..3209841_POSITIVE 250 165 128 67 30 tfor:TF2617|3end_conserved_hypothetical_protein_2795172..2795322_POSITIVE 248 37 1 39 2 tfor:TF2374|3end_UDP-3-O-(R-3-hydoxymyristoyl)-glucosamine-N-acylt_ransferase_2540892..2541042_POSITIVE 244 50 1 58 5 tfor:TF2912|3end_hypothetical_protein_3108000..3108150_POSITIVE 243 49 6 66 17 tfor:TF2275|3end_conserved_hypothetical_protein_2438300..2438450_POSITIVE