Origin IGS: taacgactaaaaaagaatgagaatgaaaacgtaagacggcatcacccacgcgcacggcggtacaaggtacagccaattcgcaacggacacacccaagtccgtagaaacaaacgggcaacccactaaaccaaagtaaagtaatcgagtatcaaccgcccgacaaaggaccatccaccct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agggtggatggtcctttgtcgggcggttgatactcgattactttactttggtttagtgggttgcccgtttgtttctacggacttgggtgtgtccgttgcgaattggctgtaccttgtaccgccgtgcgcgtgggtgatgccgtcttacgttttcattctcattcttttttagtcgtta Mask Tandem Repeat Region ================================================ taacgactaaaaaagaatgagaatgaaaacgtaagacggcatcacccacgcgcacggcggtacaaggtacagccaattcgcaacggacacacccaagtccgtagaaacaaacgggcaacccactaaaccaaagtaaagtaatcgagtatcaaccgcccgacaaaggaccatccaccct Find is-nt database================================================ Query_seq: TF2250:TF2251|TF2250:TF2251:transfer region-related protein, TraD:conjugative transposon protein, TraE:->->:2424234..2424411 178 taacgactaaaaaagaatgagaatgaaaacgtaagacggcatcacccacgcgcacggcggtacaaggtacagccaattcgcaacggacacacccaagtccgtagaaacaaacgggcaacccactaaaccaaagtaaagtaatcgagtatcaaccgcccgacaaaggaccatccaccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2250:TF2251|TF2250:TF2251:transfer region-related protein, TraD:conjugative transposon protein, TraE:->->:2424234..2424411 178 taacgactaaaaaagaatgagaatgaaaacgtaagacggcatcacccacgcgcacggcggtacaaggtacagccaattcgcaacggacacacccaagtccgtagaaacaaacgggcaacccactaaaccaaagtaaagtaatcgagtatcaaccgcccgacaaaggaccatccaccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2250:TF2251|TF2250:TF2251:transfer region-related protein, TraD:conjugative transposon protein, TraE:->->:2424234..2424411 178 taacgactaaaaaagaatgagaatgaaaacgtaagacggcatcacccacgcgcacggcggtacaaggtacagccaattcgcaacggacacacccaagtccgtagaaacaaacgggcaacccactaaaccaaagtaaagtaatcgagtatcaaccgcccgacaaaggaccatccaccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taacgactaaaaaagaatgagaatgaaaacgtaagacggcatcacccacgcgcacggcggtacaaggtacagccaattcgcaacggacacacccaagtccgtagaaacaaacgggcaacccactaaaccaaagtaaagtaatcgagtatcaaccgcccgacaaaggaccatccaccct Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 41 End: 133 ........................................ M T H A H G G T R Y S Q F A T D T P K S V E T N G Q P T K P K ............................................. Protein_Len: 54 Strand: - Start: 10 End: 171 ......... F L I L I F V Y S P M V W A C P P V L Y L W N A V S V G L D T S V F P C G V L G F Y L L R T D V A R C L V M ....... Protein_Len: 47 Strand: - Start: 2 End: 142 . V V L F S H S H F R L V A D G V R V A T C P V A L E C R V C G L G Y F C V P L G S F W L L T M .................................... taacgactaaaaaagaatgagaatgaaaacgtaagacggcatcacccacgcgcacggcggtacaaggtacagccaattcgcaacggacacacccaagtccgtagaaacaaacgggcaacccactaaaccaaagtaaagtaatcgagtatcaaccgcccgacaaaggaccatccaccct 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================================================ taacgactaaaaaagaatgagaatgaaaacgtaagacggcatcacccacgcgcacggcggtacaaggtacagccaattcgcaacggacacacccaagtccgtagaaacaaacgggcaacccactaaaccaaagtaaagtaatcgagtatcaaccgcccgacaaaggaccatccaccct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2250:TF2251|TF2250:TF2251:transfer region-related protein, TraD:conjugative transposon protein, TraE:->->:2424234..2424411 178 taacgactaaaaaagaatgagaatgaaaacgtaagacggcatcacccacgcgcacggcggtacaaggtacagccaattcgcaacggacacacccaagtccgtagaaacaaacgggcaacccactaaaccaaagtaaagtaatcgagtatcaaccgcccgacaaaggaccatccaccct Intra-Species Hit: Count: 1 Min: 1 Max: 178 Len: 178 Subject: tfor_TF2250_TF2251|transfer region-related protein, TraD:conjugative transposon protein, TraE|POSITIVE:POSITIVE|[2424234,2424411]|178 HSP 1 e-value: 1.0E-96 bit: 353.0 Len: 178 Query Start:1 Query End:178 Subject Strand: POSITIVE Subject Start: 1 Subject End: 178 taacgactaaaaaagaatgagaatgaaaacgtaagacggcatcacccacgcgcacggcggtacaaggtacagccaattcgcaacggacacacccaagtccgtagaaacaaacgggcaacccactaaaccaaagtaaagtaatcgagtatcaaccgcccgacaaaggaccatccaccct taacgactaaaaaagaatgagaatgaaaacgtaagacggcatcacccacgcgcacggcggtacaaggtacagccaattcgcaacggacacacccaagtccgtagaaacaaacgggcaacccactaaaccaaagtaaagtaatcgagtatcaaccgcccgacaaaggaccatccaccct Inter-species Hit: Count: 1 Min: 79 Max: 178 Len: 100 Subject: NC_006347_BF0125_BF0126|TraE:TraD|NEGATIVE:NEGATIVE|[130576, 130776]|201 HSP 1 e-value: 5.0E-22 bit: 105.0 Len: 100 Query Start:79 Query End:178 Subject Strand: NEGATIVE Subject Start: 28 Subject End: 127 ..............................................................................cgcaacggacacacccaagtccgtagaaacaaacgggcaacccactaaa-ccaaagtaaagtaatcgagtatcaaccgcccgacaaaggaccatccaccct ..............................................................................cgcaacggacacgcccacgtccgtggaaacaaacgggcatcc-actaaaaccaaagtaaagaaacaaagtatcaaccgcccgacaaaggaccatccaccct Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCAACGGACACACCCAAGUCCGUAGAAACAAACGGGCAACCCACUAAACCAAAGUAAAGUAAUCGAGUAUCAACCGCCCGACAAAGGACCAUCCACCCU ....((((((........)))))).........(((((.....(((..((....))..)))....(.....)....))))).....((.....))..... (-20.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGGUGGAUGGUCCUUUGUCGGGCGGUUGAUACUCGAUUACUUUACUUUGGUUUAGUGGGUUGCCCGUUUGUUUCUACGGACUUGGGUGUGUCCGUUGCG .((((.(((.((((......)))).)))...(((((...(((.......)))....))))).))))....((....((((((........)))))).)). (-27.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 339 100 60 64 22 tfor:TF1240|5end_conserved_hypothetical_protein_1324304..1324534_POSITIVE 321 79 34 140 96 tfor:TF3024|5end_periplasmic_protease_3247204..3247434_POSITIVE 314 42 1 148 104 tfor:TF1745|5end_hypothetical_protein_1879154..1879384_POSITIVE 312 80 35 192 149 tfor:TF1011|5end_cell_division_protein;_rod_shape-determining_protein_1066647..1066877_POSITIVE 292 99 73 172 142 tfor:TF2661|5end_hypothetical_protein_2833509..2833739_POSITIVE 290 98 52 231 174 tfor:TF2322|5end_conserved_hypothetical_protein;_possible_lipoprotein_2482743..2482973_POSITIVE 285 90 51 193 152 tfor:TF2793|5end_possible_L-lysine_2,3-aminomutase_2977661..2977891_POSITIVE 283 33 1 87 53 tfor:TF2821|5end_conserved_hypothetical_protein_3011146..3011376_POSITIVE 281 41 1 105 53 tfor:TF1549|5end_conserved_hypothetical_protein_1653993..1654223_POSITIVE 280 44 1 54 3 tfor:TF0426|5end_conserved_hypothetical_protein_444728..444958_POSITIVE 278 43 1 211 167 tfor:TF0418|5end_possible_methyl-accepting_chemotaxis_protein_434836..435066_POSITIVE 271 42 2 231 190 tfor:TF0004|5end_conserved_hypothetical_protein_1736..1966_POSITIVE 269 50 1 176 131 tfor:TF2622|5end_methyltransferase_2797567..2797797_POSITIVE 269 100 62 213 179 tfor:TF0487|5end_xylulose_kinase_508601..508831_POSITIVE 268 88 41 165 123 tfor:TF3158|5end_inner_membrane_protein_3393729..3393959_POSITIVE 267 41 1 169 132 tfor:TF2590|5end_transposase_2756056..2756286_POSITIVE 267 43 1 70 17 tfor:TF1462|5end_erythronate-4-phosphate_dehydrogenase_1552184..1552414_POSITIVE 267 43 1 171 126 tfor:TF0446|5end_hypothetical_protein_466473..466703_POSITIVE 265 94 60 186 162 tfor:TF2880|5end_phenylalanyl-tRNA_synthetase,_beta_subunit_3069052..3069282_POSITIVE 265 72 34 147 104 tfor:TF2230|5end_CTn_excision_protein_2399799..2400029_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 314 42 1 132 88 tfor:TF1744|3end_phenylacetate-CoA_ligase_1879218..1879368_POSITIVE 292 99 73 123 93 tfor:TF2660|3end_hypothetical_protein_2833540..2833690_POSITIVE 290 98 52 65 8 tfor:TF2321|3end_hypothetical_protein_2482657..2482807_POSITIVE 287 44 5 38 6 tfor:TF2603|3end_transcriptional_regulator,_AraC_family_2777272..2777422_POSITIVE 285 90 51 51 10 tfor:TF2792|3end_30S_ribosomal_protein_S15_2977599..2977749_POSITIVE 284 30 1 95 59 tfor:TF2613|3end_conserved_hypothetical_protein_2789798..2789948_POSITIVE 283 33 1 61 27 tfor:TF2820|3end_argininosuccinate_synthetase_3011200..3011350_POSITIVE 278 43 1 151 107 tfor:TF0417|3end_hypothetical_protein_434856..435006_POSITIVE 268 88 41 143 101 tfor:TF3157|3end_sodium/solute_symporter_3393787..3393937_POSITIVE 267 43 1 59 6 tfor:TF1461|3end_DNA-damage-inducible_protein_F_1552253..1552403_POSITIVE 267 43 1 136 91 tfor:TF0444|3end_Na+-translocating_NADH-quinone_oxidoreductase,_subunit_5_466518..466668_POSITIVE 265 94 60 62 38 tfor:TF2879|3end_tRNA_(guanine-N-1)-methyltransferase_3069008..3069158_POSITIVE 262 98 65 40 4 tfor:TF2275|3end_conserved_hypothetical_protein_2438300..2438450_POSITIVE 258 100 64 66 32 tfor:TF2978|3end_conserved_hypothetical_protein_3190862..3191012_POSITIVE 254 45 5 55 12 tfor:TF2160|3end_magnesium_chelatase,_subunit_I_2337049..2337199_POSITIVE 253 50 1 139 99 tfor:TF2830|3end_ABC_transporter,_ATP-binding_protein_3021419..3021569_POSITIVE 252 99 57 55 17 tfor:TF2217|3end_hypothetical_protein_2390165..2390315_POSITIVE 252 79 36 125 93 tfor:TF2216|3end_fumarate_hydratase,_class_I_2389944..2390094_POSITIVE 252 100 59 143 105 tfor:TF1497|3end_GTP-binding_protein,_Era/ThdF_family_1597519..1597669_POSITIVE 251 88 42 72 17 tfor:TF2839|3end_ATP-dependent_exodeoxyribonuclease_3031035..3031185_POSITIVE