Origin IGS: taatctatacatacacataacagtaaagagaaaatgcaggatttcgcgtaaggcacgcgggaacctgcgttttttttgcgttgtatgaaagggagggcgtttttttttgaggtgtgcaggggaaagagagtatcggaattta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaattccgatactctctttcccctgcacacctcaaaaaaaaacgccctccctttcatacaacgcaaaaaaaacgcaggttcccgcgtgccttacgcgaaatcctgcattttctctttactgttatgtgtatgtatagatta Mask Tandem Repeat Region ================================================ taatctatacatacacataacagtaaagagaaaatgcaggatttcgcgtaaggcacgcgggaacctgcgttttttttgcgttgtatgaaagggagggcgtttttttttgaggtgtgcaggggaaagagagtatcggaattta Find is-nt database================================================ Query_seq: TF2581:TF2582|TF2581:TF2582:50S ribosomal protein L17:ABC transporter, ATP-binding protein:->->:2749431..2749572 142 taatctatacatacacataacagtaaagagaaaatgcaggatttcgcgtaaggcacgcgggaacctgcgttttttttgcgttgtatgaaagggagggcgtttttttttgaggtgtgcaggggaaagagagtatcggaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2581:TF2582|TF2581:TF2582:50S ribosomal protein L17:ABC transporter, ATP-binding protein:->->:2749431..2749572 142 taatctatacatacacataacagtaaagagaaaatgcaggatttcgcgtaaggcacgcgggaacctgcgttttttttgcgttgtatgaaagggagggcgtttttttttgaggtgtgcaggggaaagagagtatcggaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2581:TF2582|TF2581:TF2582:50S ribosomal protein L17:ABC transporter, ATP-binding protein:->->:2749431..2749572 142 taatctatacatacacataacagtaaagagaaaatgcaggatttcgcgtaaggcacgcgggaacctgcgttttttttgcgttgtatgaaagggagggcgtttttttttgaggtgtgcaggggaaagagagtatcggaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatctatacatacacataacagtaaagagaaaatgcaggatttcgcgtaaggcacgcgggaacctgcgttttttttgcgttgtatgaaagggagggcgtttttttttgaggtgtgcaggggaaagagagtatcggaattta Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: - Start: 8 End: 139 ....... V Y V Y C Y L S F A P N R T L C A P V Q T K K A N Y S L S P T K K Q P T C P F S L I P M ... Protein_Len: 39 Strand: - Start: 3 End: 119 .. D I C V C L L L S F I C S K A Y P V R S G A N K K R Q I F P L A N K K S T H M ....................... taatctatacatacacataacagtaaagagaaaatgcaggatttcgcgtaaggcacgcgggaacctgcgttttttttgcgttgtatgaaagggagggcgtttttttttgaggtgtgcaggggaaagagagtatcggaattta 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================================================ taatctatacatacacataacagtaaagagaaaatgcaggatttcgcgtaaggcacgcgggaacctgcgttttttttgcgttgtatgaaagggagggcgtttttttttgaggtgtgcaggggaaagagagtatcggaattta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.7 Tail_Score: -5.87688 Start: 35 End: 69 Full_Region: ACAGTAAAGAGAAAA TGCAGGATTTCGCGT AAGGC ACGCGGGAACCTGCG TTTTTTTTGCGTTGT ..................................TGCAGGATTTCGCGTAAGGCACGCGGGAACCTGCG......................................................................... TransTerm Strand: - Conf: 74 HP_score: -4.8 Tail_Score: -4.83032 Start: 35 End: 69 Full_Region: acaacgcaaaaaaaa cgcaggttcccgcgtg cct tacgcgaaatcctgca ttttctctttactgt ..................................cgcaggttcccgcgtgccttacgcgaaatcctgca......................................................................... TransTerm Strand: + Conf: 100 HP_score: -12.0 Tail_Score: -4.10173 Start: 36 End: 68 Full_Region: CAGTAAAGAGAAAAT GCAGGATTTCGCGT AAGGC ACGCGGGAACCTGC GTTTTTTTTGCGTTG ...................................GCAGGATTTCGCGTAAGGCACGCGGGAACCTGC.......................................................................... TransTerm Strand: - Conf: 71 HP_score: -8.3 Tail_Score: -3.48193 Start: 36 End: 68 Full_Region: caacgcaaaaaaaac gcaggttcccgcgtg cct tacgcgaaatcctgc attttctctttactg ...................................gcaggttcccgcgtgccttacgcgaaatcctgc.......................................................................... Find igs database================================================ Query_seq: TF2581:TF2582|TF2581:TF2582:50S ribosomal protein L17:ABC transporter, ATP-binding protein:->->:2749431..2749572 142 taatctatacatacacataacagtaaagagaaaatgcaggatttcgcgtaaggcacgcgggaacctgcgttttttttgcgttgtatgaaagggagggcgtttttttttgaggtgtgcaggggaaagagagtatcggaattta Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: tfor_TF2581_TF2582|50S ribosomal protein L17:ABC transporter, ATP-binding protein|POSITIVE:POSITIVE|[2749431,2749572]|142 HSP 1 e-value: 8.0E-45 bit: 180.0 Len: 142 Query Start:1 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 142 taatctatacatacacataacagtaaagagaaaatgcaggatttcgcgtaaggcacgcgggaacctgcgnnnnnnnngcgttgtatgaaagggagggcgnnnnnnnnngaggtgtgcaggggaaagagagtatcggaattta taatctatacatacacataacagtaaagagaaaatgcaggatttcgcgtaaggcacgcgggaacctgcgttttttttgcgttgtatgaaagggagggcgtttttttttgaggtgtgcaggggaaagagagtatcggaattta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCUAUACAUACACAUAACAGUAAAGAGAAAAUGCAGGAUUUCGCGUAAGGCACGCGGGAACCUGCGUUUUUUUUGCGUUGUAUGAAAGGGAGGGCGUUUUUUUUUGAGGUGUGCAGGGGAAAGAGAGUAUCGGAAUUUA ...(((((((...((.(((((.(((..(((((((((((((.(..(((((.....)))))..).))))))))))))))))))))).)).......(.(((..((.....))..))).)............)))).)))..... (-41.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUUCCGAUACUCUCUUUCCCCUGCACACCUCAAAAAAAAACGCCCUCCCUUUCAUACAACGCAAAAAAAACGCAGGUUCCCGCGUGCCUUACGCGAAAUCCUGCAUUUUCUCUUUACUGUUAUGUGUAUGUAUAGAUUA ......................................................((((((((((((........(((((....((((((...))))))....))))).......(......)...))))).))))).))... (-22.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 404 100 51 91 36 tfor:TF2429|5end_ABC_transporter,_ATP-binding/permease_component,_bacteriocin/lantibiotic_exporter_2610453..2610683_POSITIVE 402 68 27 50 7 tfor:TF1603|5end_RNA_polymerase_ECF-type_sigma_factor_1717176..1717406_POSITIVE 393 99 56 206 169 tfor:TF0597|5end_hypothetical_protein_628788..629018_POSITIVE 384 98 52 224 161 tfor:TF0601|5end_aminomethyltransferase_(glycine_cleavage_system_T_protein)_631081..631311_POSITIVE 375 84 43 148 106 tfor:TF2229.1|5end_rteR_regulatory_ortholog_(with_internal_stop)_2399454..2399684_POSITIVE 374 80 35 151 101 tfor:TF1680|5end_peptide_chain_release_factor_3_1793315..1793545_POSITIVE 369 99 51 190 141 tfor:TF1937|5end_conserved_hypothetical_protein_2084476..2084706_POSITIVE 368 70 26 217 168 tfor:TF1959|5end_conserved_hypothetical_protein_2109377..2109607_POSITIVE 368 100 54 218 166 tfor:TF0759|5end_heat_shock_protein_15,_RNA-binding_domain_S4_805870..806100_POSITIVE 357 100 56 105 53 tfor:TF2477|5end_phosphatase_2654229..2654459_POSITIVE 345 80 37 69 29 tfor:TF2759|5end_xylose_repressor,_ROK_family_2943568..2943798_POSITIVE 345 116 79 81 43 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 345 137 91 48 9 tfor:TF2653|5end_hypothetical_protein_2822093..2822323_POSITIVE 345 120 76 151 97 tfor:TF1931|5end_ATPase/GTPase_2078123..2078353_POSITIVE 343 130 81 173 129 tfor:TF1981|5end_mannose-6-phosphate_isomerase_2130896..2131126_POSITIVE 343 100 52 98 42 tfor:TF0456|5end_conserved_hypothetical_protein_473403..473633_POSITIVE 342 79 40 170 120 tfor:TF1924|5end_prenyltransferase,_UbiA_family_2072857..2073087_POSITIVE 339 128 91 222 171 tfor:TF1550|5end_excinuclease_ABC,_subunit_B_1654841..1655071_POSITIVE 338 88 41 164 104 tfor:TF2652|5end_hypothetical_protein_2821803..2822033_POSITIVE 338 88 41 116 56 tfor:TF2651|5end_hypothetical_protein_2821755..2821985_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 536 77 31 64 18 tfor:TF2581|3end_50S_ribosomal_protein_L17_2749370..2749520_POSITIVE 404 100 51 83 28 tfor:TF2428|3end_conserved_hypothetical_protein_2610525..2610675_POSITIVE 385 99 51 71 28 tfor:TF1834|3end_3-isopropylmalate_dehydrogenase_1984311..1984461_POSITIVE 374 80 35 75 25 tfor:TF1679|3end_conserved_hypothetical_protein_1793319..1793469_POSITIVE 349 94 51 65 18 tfor:TF2426|3end_conserved_hypothetical_protein;_possible_TonB_receptor_2605931..2606081_POSITIVE 345 116 79 76 38 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 345 120 76 151 97 tfor:TF1930|3end_two-component_response_regulator_2078203..2078353_POSITIVE 343 130 81 57 13 tfor:TF1980|3end_conserved_hypothetical_protein_2130860..2131010_POSITIVE 343 100 52 68 12 tfor:TF0454|3end_xanthine/uracil_permease_family_protein_473453..473603_POSITIVE 339 122 83 151 110 tfor:TF0815|3end_conserved_hypothetical_protein_873974..874124_POSITIVE 338 88 41 87 27 tfor:TF2650|3end_succinate_dehydrogenase,_iron-sulfur_subunit_2821806..2821956_POSITIVE 326 69 34 140 95 tfor:TF2435|3end_DNA_repair_protein_radC_2615136..2615286_POSITIVE 323 99 55 66 21 tfor:TF0923|3end_tetracycline_resistance_element_mobilization_regulatory_protein_961704..961854_POSITIVE 321 99 51 61 2 tfor:TF1626|3end_nicotinate-nucleotide_adenylyltransferase_1740098..1740248_POSITIVE 321 98 52 74 28 tfor:TF0918|3end_conserved_hypothetical_protein;_possible_protease_957572..957722_POSITIVE 320 75 31 149 100 tfor:TF2637|3end_conserved_hypothetical_protein_2807955..2808105_POSITIVE 320 99 52 55 4 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 320 99 51 57 12 tfor:TF2263|3end_transfer_region-related_protein,_TraN_2432964..2433114_POSITIVE 319 100 52 110 34 tfor:TF3032|3end_thiamin_biosynthesis_protein_3256838..3256988_POSITIVE 318 136 92 66 10 tfor:TF0320|3end_dihydroorotase_347518..347668_POSITIVE