Origin IGS: taactgcattcagacttggcacaccgctttcctctttcatcgtgaggaaatgagcgtattccgttggcgtaaaattgaccgaaacacgcttttctgtcttctccctggagc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gctccagggagaagacagaaaagcgtgtttcggtcaattttacgccaacggaatacgctcatttcctcacgatgaaagaggaaagcggtgtgccaagtctgaatgcagtta Mask Tandem Repeat Region ================================================ taactgcattcagacttggcacaccgctttcctctttcatcgtgaggaaatgagcgtattccgttggcgtaaaattgaccgaaacacgcttttctgtcttctccctggagc Find is-nt database================================================ Query_seq: TF0923:TF0925|TF0923:TF0925:tetracycline resistance element mobilization regulatory protein:hypothetical protein:->->:961765..961875 111 taactgcattcagacttggcacaccgctttcctctttcatcgtgaggaaatgagcgtattccgttggcgtaaaattgaccgaaacacgcttttctgtcttctccctggagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0923:TF0925|TF0923:TF0925:tetracycline resistance element mobilization regulatory protein:hypothetical protein:->->:961765..961875 111 taactgcattcagacttggcacaccgctttcctctttcatcgtgaggaaatgagcgtattccgttggcgtaaaattgaccgaaacacgcttttctgtcttctccctggagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0923:TF0925|TF0923:TF0925:tetracycline resistance element mobilization regulatory protein:hypothetical protein:->->:961765..961875 111 taactgcattcagacttggcacaccgctttcctctttcatcgtgaggaaatgagcgtattccgttggcgtaaaattgaccgaaacacgcttttctgtcttctccctggagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taactgcattcagacttggcacaccgctttcctctttcatcgtgaggaaatgagcgtattccgttggcgtaaaattgaccgaaacacgcttttctgtcttctccctggagc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 8 End: 109 ....... M Q T W H T A F L F H R E E M S V F R W R K I D R N T L F C L L P G .. taactgcattcagacttggcacaccgctttcctctttcatcgtgaggaaatgagcgtattccgttggcgtaaaattgaccgaaacacgcttttctgtcttctccctggagc 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================================================ PromScan Matrix: RpoN Strand: + Score: 81 Start: 16 End: 32 ...............TTGGCACACCGCTTTCC............................................................................... taactgcattcagacttggcacaccgctttcctctttcatcgtgaggaaatgagcgtattccgttggcgtaaaattgaccgaaacacgcttttctgtcttctccctggagc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0923:TF0925|TF0923:TF0925:tetracycline resistance element mobilization regulatory protein:hypothetical protein:->->:961765..961875 111 taactgcattcagacttggcacaccgctttcctctttcatcgtgaggaaatgagcgtattccgttggcgtaaaattgaccgaaacacgcttttctgtcttctccctggagc Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: tfor_TF0923_TF0925|tetracycline resistance element mobilization regulatory protein:hypothetical protein|POSITIVE:POSITIVE|[961765,961875]|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 taactgcattcagacttggcacaccgctttcctctttcatcgtgaggaaatgagcgtattccgttggcgtaaaattgaccgaaacacgcttttctgtcttctccctggagc taactgcattcagacttggcacaccgctttcctctttcatcgtgaggaaatgagcgtattccgttggcgtaaaattgaccgaaacacgcttttctgtcttctccctggagc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACUGCAUUCAGACUUGGCACACCGCUUUCCUCUUUCAUCGUGAGGAAAUGAGCGUAUUCCGUUGGCGUAAAAUUGACCGAAACACGCUUUUCUGUCUUCUCCCUGGAGC .....((.(((((....((((......(((((((.........))))))).((((((.(((.((..(.......)..)).)))..))))))...))))......))))))) (-24.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUCCAGGGAGAAGACAGAAAAGCGUGUUUCGGUCAAUUUUACGCCAACGGAAUACGCUCAUUUCCUCACGAUGAAAGAGGAAAGCGGUGUGCCAAGUCUGAAUGCAGUUA .(((....))).((((.....(((((((((((................)))))))))))..(((((((.........)))))))..((....))..))))........... (-30.39) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 388 49 3 150 97 tfor:TF2712|5end_glycosyltransferase_2885918..2886148_POSITIVE 382 70 25 77 8 tfor:TF2818|5end_acetylornithine_aminotransferase_3007739..3007969_POSITIVE 358 69 21 90 36 tfor:TF2847|5end_hypothetical_protein_3034744..3034974_POSITIVE 358 109 62 54 1 tfor:TF2228|5end_CTn_excision_protein_2395899..2396129_POSITIVE 348 99 53 195 143 tfor:TF0139|5end_4-diphosphocytidyl-2c-methyl-D-erythritol_synthase_(MEP_cytidylyltransferase)_(MCT)_147527..147757_POSITIVE 347 69 25 56 7 tfor:TF0944|5end_TonB-dependent_receptor_986340..986570_POSITIVE 346 56 16 191 150 tfor:TF0288|5end_conserved_hypothetical_protein_317474..317704_POSITIVE 343 53 16 230 193 tfor:TF2214|5end_peptidyl-prolyl_cis-trans_isomerase_2386897..2387127_POSITIVE 341 80 37 47 6 tfor:TF1481|5end_ABC_transporter,_ATP-binding_protein_1574783..1575013_POSITIVE 339 107 61 123 72 tfor:TF2111|5end_RNA_polymerase_sigma-54_factor_2280506..2280736_POSITIVE 339 107 61 192 141 tfor:TF0717|5end_signal_recognition_particle_767654..767884_POSITIVE 334 69 24 50 2 tfor:TF3112|5end_Na+/H+_anitporter_3346775..3347005_POSITIVE 333 70 21 215 161 tfor:TF2444|5end_regulatory_protein_RecX_2620957..2621187_POSITIVE 331 108 61 144 96 tfor:TF2407|5end_glycosyltransferase_2581574..2581804_POSITIVE 327 107 62 120 79 tfor:TF1476|5end_outer_membrane_protein_P49_1569723..1569953_POSITIVE 325 79 31 111 72 tfor:TF2848|5end_cobalamin_biosynthesis_protein_3036368..3036598_POSITIVE 323 70 25 200 130 tfor:TF3119|5end_conserved_hypothetical_protein_3352723..3352953_POSITIVE 323 70 25 179 135 tfor:TF2582|5end_ABC_transporter,_ATP-binding_protein_2749433..2749663_POSITIVE 322 90 41 218 167 tfor:TF2274|5end_conserved_hypothetical_protein_2436652..2436882_POSITIVE 322 70 22 149 89 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 56 16 104 63 tfor:TF0287|3end_peptidase,_M23_family_317467..317617_POSITIVE 341 80 37 50 9 tfor:TF1480|3end_ABC_transporter,_permease_component_1574866..1575016_POSITIVE 339 107 61 63 12 tfor:TF2110|3end_transposase_2280526..2280676_POSITIVE 332 42 3 150 104 tfor:TF2711|3end_hemolysis_secretion_protein_2886005..2886155_POSITIVE 331 108 61 149 101 tfor:TF2406|3end_anti-sigma_factor_2581659..2581809_POSITIVE 325 79 31 132 93 tfor:TF2846|3end_cobyric_acid_synthase_3036469..3036619_POSITIVE 324 68 21 59 8 tfor:TF1169|3end_lipoprotein_ABC_transporter,_permease_component_1251573..1251723_POSITIVE 322 70 22 149 89 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 319 69 24 56 12 tfor:TF0296|3end_hypothetical_protein_322257..322407_POSITIVE 311 56 17 106 65 tfor:TF0795|3end_hypothetical_protein_853199..853349_POSITIVE 308 67 21 149 95 tfor:TF1552|3end_conserved_hypothetical_protein_1658826..1658976_POSITIVE 306 90 41 70 31 tfor:TF1275|3end_transcription-repair_coupling_factor_1361290..1361440_POSITIVE 306 109 79 56 9 tfor:TF0167|3end_conserved_hypothetical_protein_178234..178384_POSITIVE 305 56 12 76 38 tfor:TF1342|3end_possible_lipoprotein_1424620..1424770_POSITIVE 298 107 79 34 5 tfor:TF0716|3end_transposase_767576..767726_POSITIVE 295 87 41 58 16 tfor:TF0462|3end_possible_cobalamin_biosynthesis_precorrin-3_methylase_479095..479245_POSITIVE 294 110 73 133 92 tfor:TF1702|3end_conserved_hypothetical_protein_1822075..1822225_POSITIVE 293 70 25 120 81 tfor:TF1559|3end_glycosyltransferase_1667074..1667224_POSITIVE 291 104 62 82 33 tfor:TF2765|3end_subtilisin-like_serine_protease_2951460..2951610_POSITIVE 291 92 54 75 37 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE