Origin IGS: taacgcatgcggcgtattcggacggtcatgtccggaaaaagcatgagaaagccgtctcgaccgaaaggaagagacggctttcttgctattgtgttctctactttcttctca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgagaagaaagtagagaacacaatagcaagaaagccgtctcttcctttcggtcgagacggctttctcatgctttttccggacatgaccgtccgaatacgccgcatgcgtta Mask Tandem Repeat Region ================================================ taacgcatgcggcgtattcggacggtcatgtccggaaaaagcatgagaaagccgtctcgaccgaaaggaagagacggctttcttgctattgtgttctctactttcttctca Find is-nt database================================================ Query_seq: TF2789:TF2790|TF2789:TF2790:enoyl-[acyl-carrier-protein] reductase:prismane protein, hybrid-cluster protein:->->:2973426..2973536 111 taacgcatgcggcgtattcggacggtcatgtccggaaaaagcatgagaaagccgtctcgaccgaaaggaagagacggctttcttgctattgtgttctctactttcttctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2789:TF2790|TF2789:TF2790:enoyl-[acyl-carrier-protein] reductase:prismane protein, hybrid-cluster protein:->->:2973426..2973536 111 taacgcatgcggcgtattcggacggtcatgtccggaaaaagcatgagaaagccgtctcgaccgaaaggaagagacggctttcttgctattgtgttctctactttcttctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2789:TF2790|TF2789:TF2790:enoyl-[acyl-carrier-protein] reductase:prismane protein, hybrid-cluster protein:->->:2973426..2973536 111 taacgcatgcggcgtattcggacggtcatgtccggaaaaagcatgagaaagccgtctcgaccgaaaggaagagacggctttcttgctattgtgttctctactttcttctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taacgcatgcggcgtattcggacggtcatgtccggaaaaagcatgagaaagccgtctcgaccgaaaggaagagacggctttcttgctattgtgttctctactttcttctca Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 7 End: 111 ...... M R R I R T V M S G K S M R K P S R P K G R D G F L A I V F S T F F S taacgcatgcggcgtattcggacggtcatgtccggaaaaagcatgagaaagccgtctcgaccgaaaggaagagacggctttcttgctattgtgttctctactttcttctca 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================================================ taacgcatgcggcgtattcggacggtcatgtccggaaaaagcatgagaaagccgtctcgaccgaaaggaagagacggctttcttgctattgtgttctctactttcttctca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 95 HP_score: -10.6 Tail_Score: -4.57569 Start: 41 End: 86 Full_Region: gtagagaacacaata gcaagaaagccgtctcttcc tttc ggtcgagacggctttctcatgc tttttccggacatga ........................................gcaagaaagccgtctcttcctttcggtcgagacggctttctcatgc......................... TransTerm Strand: + Conf: 100 HP_score: -16.2 Tail_Score: -3.47232 Start: 47 End: 82 Full_Region: CCGGAAAAAGCATGA GAAAGCCGTCTCGACC GAAA GGAAGAGACGGCTTTC TTGCTATTGTGTTCT ..............................................GAAAGCCGTCTCGACCGAAAGGAAGAGACGGCTTTC............................. TransTerm Strand: + Conf: 91 HP_score: -11.2 Tail_Score: -4.34759 Start: 51 End: 78 Full_Region: AAAAAGCATGAGAAA GCCGTCTCGACC GAAA GGAAGAGACGGC TTTCTTGCTATTGTG ..................................................GCCGTCTCGACCGAAAGGAAGAGACGGC................................. TransTerm Strand: - Conf: 85 HP_score: -11.2 Tail_Score: -4.06719 Start: 51 End: 78 Full_Region: cacaatagcaagaaa gccgtctcttcc tttc ggtcgagacggc tttctcatgcttttt ..................................................gccgtctcttcctttcggtcgagacggc................................. Find igs database================================================ Query_seq: TF2789:TF2790|TF2789:TF2790:enoyl-[acyl-carrier-protein] reductase:prismane protein, hybrid-cluster protein:->->:2973426..2973536 111 taacgcatgcggcgtattcggacggtcatgtccggaaaaagcatgagaaagccgtctcgaccgaaaggaagagacggctttcttgctattgtgttctctactttcttctca Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: tfor_TF2789_TF2790|enoyl-[acyl-carrier-protein] reductase:prismane protein, hybrid-cluster protein|POSITIVE:POSITIVE|[2973426,2973536]|111 HSP 1 e-value: 7.0E-57 bit: 220.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 taacgcatgcggcgtattcggacggtcatgtccggaaaaagcatgagaaagccgtctcgaccgaaaggaagagacggctttcttgctattgtgttctctactttcttctca taacgcatgcggcgtattcggacggtcatgtccggaaaaagcatgagaaagccgtctcgaccgaaaggaagagacggctttcttgctattgtgttctctactttcttctca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACGCAUGCGGCGUAUUCGGACGGUCAUGUCCGGAAAAAGCAUGAGAAAGCCGUCUCGACCGAAAGGAAGAGACGGCUUUCUUGCUAUUGUGUUCUCUACUUUCUUCUCA .((((((.((.((...((((((((....))))))))....))..((((((((((((((..((....))..))))))))))))))))...))))))................ (-50.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGAAGAAAGUAGAGAACACAAUAGCAAGAAAGCCGUCUCUUCCUUUCGGUCGAGACGGCUUUCUCAUGCUUUUUCCGGACAUGACCGUCCGAAUACGCCGCAUGCGUUA ........................(((((((((((((((((..((....))..)))))))))))))..)))).....(((((......)))))...((((.....)))).. (-39.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 433 49 5 97 46 tfor:TF3014|5end_oxidoreductase,_short-chain_dehydrogenase/reductase_family_3237623..3237853_POSITIVE 424 80 33 139 92 tfor:TF2754|5end_hypothetical_protein_2940446..2940676_POSITIVE 395 48 3 187 121 tfor:TF2829|5end_conserved_hypothetical_protein_3019562..3019792_POSITIVE 389 79 32 129 80 tfor:TF0570|5end_possible_transcriptional_regulator_602483..602713_POSITIVE 387 87 41 54 3 tfor:TF1476|5end_outer_membrane_protein_P49_1569723..1569953_POSITIVE 384 63 24 59 28 tfor:TF0544|5end_metallo-beta_lactamase_family_protein_575121..575351_POSITIVE 380 60 11 57 5 tfor:TF2819|5end_N-acetyl-gamma-glutamylphosphate_reductase_3008905..3009135_POSITIVE 378 85 51 209 172 tfor:TF2506|5end_possible_peptidyl-prolyl_cis-trans_isomerase_2682292..2682522_POSITIVE 377 89 44 135 92 tfor:TF2652|5end_hypothetical_protein_2821803..2822033_POSITIVE 377 89 44 87 44 tfor:TF2651|5end_hypothetical_protein_2821755..2821985_POSITIVE 372 55 12 52 13 tfor:TF0772|5end_conserved_hypothetical_protein_818568..818798_POSITIVE 370 79 32 53 1 tfor:TF2161|5end_conserved_hypothetical_protein_2336972..2337202_POSITIVE 370 86 41 111 49 tfor:TF1742|5end_TPR_repeat-containing_protein_1873129..1873359_POSITIVE 369 46 4 57 11 tfor:TF0496|5end_conserved_hypothetical_protein_522332..522562_POSITIVE 367 60 12 51 5 tfor:TF2265|5end_transfer_region-related_protein,_TraP;_DNA_primase_involved_in_conjugation_2433474..2433704_POSITIVE 360 43 9 229 196 tfor:TF3127|5end_acetyltransferase,_possible_GNAT_family_3361627..3361857_POSITIVE 358 49 3 88 39 tfor:TF1485|5end_conserved_hypothetical_protein_1581871..1582101_POSITIVE 358 79 31 106 60 tfor:TF1257|5end_hypothetical_protein_1338118..1338348_POSITIVE 358 79 31 71 25 tfor:TF1256|5end_hypothetical_protein_1338083..1338313_POSITIVE 357 86 48 47 2 tfor:TF1974|5end_glyoxalase_I_related_protein_(lactoylglutathione_lyase)_2120950..2121180_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 533 87 41 51 5 tfor:TF2789|3end_enoyl-[acyl-carrier-protein]_reductase_2973365..2973515_POSITIVE 424 80 33 61 14 tfor:TF2753|3end_zinc_protease_2940448..2940598_POSITIVE 384 63 24 38 7 tfor:TF0543|3end_glycine_cleavage_system_p-protein_575180..575330_POSITIVE 377 89 44 58 15 tfor:TF2650|3end_succinate_dehydrogenase,_iron-sulfur_subunit_2821806..2821956_POSITIVE 358 79 31 59 13 tfor:TF1255|3end_conserved_hypothetical_protein_1338151..1338301_POSITIVE 353 47 5 52 3 tfor:TF0875|3end_outer_membrane_receptor,_TonB-linked_929251..929401_POSITIVE 352 47 3 121 73 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 352 60 11 49 9 tfor:TF1743|3end_conserved_hypothetical_protein_1877909..1878059_POSITIVE 343 46 4 55 9 tfor:TF1165|3end_conserved_hypothetical_protein_1245921..1246071_POSITIVE 341 79 32 50 1 tfor:TF2160|3end_magnesium_chelatase,_subunit_I_2337049..2337199_POSITIVE 340 35 2 64 22 tfor:TF2911|3end_hypothetical_protein_3106640..3106790_POSITIVE 337 86 41 73 21 tfor:TF2353|3end_conserved_hypothetical_protein_2518608..2518758_POSITIVE 335 43 6 44 5 tfor:TF2374|3end_UDP-3-O-(R-3-hydoxymyristoyl)-glucosamine-N-acylt_ransferase_2540892..2541042_POSITIVE 335 35 4 97 51 tfor:TF0583|3end_possible_gliding_motility-related_protein_613829..613979_POSITIVE 334 59 11 115 42 tfor:TF2473|3end_poly(A)_polymerase/tRNA_nucleotidyltransferase_2652010..2652160_POSITIVE 331 96 51 72 28 tfor:TF0252|3end_hypothetical_protein_283759..283909_POSITIVE 328 63 21 116 67 tfor:TF2774|3end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_2959719..2959869_POSITIVE 327 78 32 65 16 tfor:TF2275|3end_conserved_hypothetical_protein_2438300..2438450_POSITIVE 327 48 9 91 50 tfor:TF0879|3end_TraG_family_protein_934085..934235_POSITIVE 327 56 12 151 102 tfor:TF0239|3end_conserved_hypothetical_protein_270323..270473_POSITIVE