Origin IGS: aatgttattaaaattaaaacggggtcttcgattcttttcatcggcgtccctgctccgtttctttttttttgagtgcaaatttagccaaaaagcgcgatattccgtatcgacaagctaaaaagtatcctcctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaggaggatactttttagcttgtcgatacggaatatcgcgctttttggctaaatttgcactcaaaaaaaaagaaacggagcagggacgccgatgaaaagaatcgaagaccccgttttaattttaataacatt Mask Tandem Repeat Region ================================================ aatgttattaaaattaaaacggggtcttcgattcttttcatcggcgtccctgctccgtttctttttttttgagtgcaaatttagccaaaaagcgcgatattccgtatcgacaagctaaaaagtatcctcctta Find is-nt database================================================ Query_seq: TF0234:TF0235|TF0234:TF0235:5,10-methylenetetrahydrofolate reductase:hypothetical protein:->->:261573..261705 133 aatgttattaaaattaaaacggggtcttcgattcttttcatcggcgtccctgctccgtttctttttttttgagtgcaaatttagccaaaaagcgcgatattccgtatcgacaagctaaaaagtatcctcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0234:TF0235|TF0234:TF0235:5,10-methylenetetrahydrofolate reductase:hypothetical protein:->->:261573..261705 133 aatgttattaaaattaaaacggggtcttcgattcttttcatcggcgtccctgctccgtttctttttttttgagtgcaaatttagccaaaaagcgcgatattccgtatcgacaagctaaaaagtatcctcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0234:TF0235|TF0234:TF0235:5,10-methylenetetrahydrofolate reductase:hypothetical protein:->->:261573..261705 133 aatgttattaaaattaaaacggggtcttcgattcttttcatcggcgtccctgctccgtttctttttttttgagtgcaaatttagccaaaaagcgcgatattccgtatcgacaagctaaaaagtatcctcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatgttattaaaattaaaacggggtcttcgattcttttcatcggcgtccctgctccgtttctttttttttgagtgcaaatttagccaaaaagcgcgatattccgtatcgacaagctaaaaagtatcctcctta Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 2 End: 115 . M L L K L K R G L R F F S S A S L L R F F F F E C K F S Q K A R Y S V S T S .................. aatgttattaaaattaaaacggggtcttcgattcttttcatcggcgtccctgctccgtttctttttttttgagtgcaaatttagccaaaaagcgcgatattccgtatcgacaagctaaaaagtatcctcctta 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================================================ aatgttattaaaattaaaacggggtcttcgattcttttcatcggcgtccctgctccgtttctttttttttgagtgcaaatttagccaaaaagcgcgatattccgtatcgacaagctaaaaagtatcctcctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0234:TF0235|TF0234:TF0235:5,10-methylenetetrahydrofolate reductase:hypothetical protein:->->:261573..261705 133 aatgttattaaaattaaaacggggtcttcgattcttttcatcggcgtccctgctccgtttctttttttttgagtgcaaatttagccaaaaagcgcgatattccgtatcgacaagctaaaaagtatcctcctta Intra-Species Hit: Count: 1 Min: 1 Max: 133 Len: 133 Subject: tfor_TF0234_TF0235|5,10-methylenetetrahydrofolate reductase:hypothetical protein|POSITIVE:POSITIVE|[261573,261705]|133 HSP 1 e-value: 8.0E-54 bit: 210.0 Len: 133 Query Start:1 Query End:133 Subject Strand: POSITIVE Subject Start: 1 Subject End: 133 aatgttattaaaattaaaacggggtcttcgattcttttcatcggcgtccctgctccgtttcnnnnnnnnngagtgcaaatttagccaaaaagcgcgatattccgtatcgacaagctaaaaagtatcctcctta aatgttattaaaattaaaacggggtcttcgattcttttcatcggcgtccctgctccgtttctttttttttgagtgcaaatttagccaaaaagcgcgatattccgtatcgacaagctaaaaagtatcctcctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGUUAUUAAAAUUAAAACGGGGUCUUCGAUUCUUUUCAUCGGCGUCCCUGCUCCGUUUCUUUUUUUUUGAGUGCAAAUUUAGCCAAAAAGCGCGAUAUUCCGUAUCGACAAGCUAAAAAGUAUCCUCCUUA ..(((..((((((...((((((((((.(((((.......))))).).....)))))))))......))))))..)))..((((((.........((((((...))))))....)))))).............. (-22.32) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGAGGAUACUUUUUAGCUUGUCGAUACGGAAUAUCGCGCUUUUUGGCUAAAUUUGCACUCAAAAAAAAAGAAACGGAGCAGGGACGCCGAUGAAAAGAAUCGAAGACCCCGUUUUAAUUUUAAUAACAUU ....(((..((...(((((((.(((((((.....))))).)).....)))))))..))..)))..............(((((.(((.(..((((.......))))..).))).)))))............... (-25.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 383 79 38 59 7 tfor:TF1636|5end_hypothetical_protein_1747143..1747373_POSITIVE 352 58 20 206 159 tfor:TF0955|5end_conserved_hypothetical_protein_999215..999445_POSITIVE 349 58 20 105 49 tfor:TF2848|5end_cobalamin_biosynthesis_protein_3036368..3036598_POSITIVE 347 58 20 61 10 tfor:TF2412|5end_outer_membrane_protein_2587017..2587247_POSITIVE 342 106 68 137 100 tfor:TF1832|5end_3-isopropylmalate_dehydratase,_small_subunit_1980832..1981062_POSITIVE 340 57 11 151 99 tfor:TF2708|5end_DNA_gyrase_subunit_B_2880164..2880394_POSITIVE 336 59 23 231 176 tfor:TF0497|5end_conserved_hypothetical_protein_524058..524288_POSITIVE 334 70 22 164 100 tfor:TF2818|5end_acetylornithine_aminotransferase_3007739..3007969_POSITIVE 331 58 20 67 30 tfor:TF1925|5end_hypothetical_protein_2074458..2074688_POSITIVE 325 57 19 66 11 tfor:TF1174|5end_ABC_transporter,_permease_component_1256584..1256814_POSITIVE 325 62 28 39 6 tfor:TF0944|5end_TonB-dependent_receptor_986340..986570_POSITIVE 325 57 21 68 27 tfor:TF0802|5end_glucose-1-phosphate_cytidylyltransferase_860310..860540_POSITIVE 323 56 20 123 87 tfor:TF1317|5end_hypothetical_protein_1391378..1391608_POSITIVE 322 60 20 160 123 tfor:TF0229|5end_beta-galactosidase_254857..255087_POSITIVE 318 59 20 97 54 tfor:TF2816|5end_hypothetical_protein_3006925..3007155_POSITIVE 318 86 42 197 149 tfor:TF2789|5end_enoyl-[acyl-carrier-protein]_reductase_2972431..2972661_POSITIVE 317 69 21 72 18 tfor:TF2423|5end_papain_family_cysteine_protease_2601608..2601838_POSITIVE 317 58 20 203 151 tfor:TF0593|5end_membrane-associated_phospholipid_phosphatase_626393..626623_POSITIVE 315 67 22 156 121 tfor:TF2223|5end_CTn_excision__protein_2394247..2394477_POSITIVE 314 67 21 191 129 tfor:TF2145|5end_conserved_hypothetical_protein;_possible_rhodanese-domain_protein_2319764..2319994_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 58 20 126 70 tfor:TF2846|3end_cobyric_acid_synthase_3036469..3036619_POSITIVE 342 106 68 128 91 tfor:TF1831|3end_conserved_hypothetical_protein_1980903..1981053_POSITIVE 340 57 11 70 18 tfor:TF2707|3end_glutamine_amidotransferase_2880163..2880313_POSITIVE 339 63 23 65 30 tfor:TF0382|3end_transcription_termination_factor_405228..405378_POSITIVE 317 69 21 61 7 tfor:TF2422|3end_hypothetical_protein_2601677..2601827_POSITIVE 315 67 22 58 23 tfor:TF2221|3end_CTn_excision_protein_2394229..2394379_POSITIVE 314 57 15 148 95 tfor:TF2913|3end_conserved_hypothetical_protein_3109117..3109267_POSITIVE 307 60 19 138 95 tfor:TF2908|3end_transcriptional_regulator,_AraC_family_3104678..3104828_POSITIVE 307 56 11 151 113 tfor:TF1912|3end_transcriptional_regulator,_TetR_family_2066640..2066790_POSITIVE 306 57 21 63 4 tfor:TF1328|3end_possible_cytidylyltransferase_1408650..1408800_POSITIVE 299 56 19 118 72 tfor:TF2845|3end_hypothetical_protein_3034757..3034907_POSITIVE 299 53 19 59 25 tfor:TF1834|3end_3-isopropylmalate_dehydrogenase_1984311..1984461_POSITIVE 298 50 20 121 78 tfor:TF0886|3end_conjugative_transposon_protein_fragment_938152..938302_POSITIVE 295 68 24 151 97 tfor:TF3093|3end_30S_ribosomal_protein_S2_3326181..3326331_POSITIVE 295 75 41 112 67 tfor:TF3053|3end_conserved_hypothetical_protein_3278889..3279039_POSITIVE 295 76 37 44 1 tfor:TF2230|3end_CTn_excision_protein_2400394..2400544_POSITIVE 295 87 42 113 59 tfor:TF1087|3end_ISPg4_transposase_1158225..1158375_POSITIVE 292 73 34 88 49 tfor:TF1596|3end_hypothetical_protein_1712723..1712873_POSITIVE 292 55 19 74 21 tfor:TF0133|3end_transposase_element_145556..145706_POSITIVE 290 58 20 108 69 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE