Origin IGS: ttgttcttatatttttatggattggtaatttccacaaagttatatgattttttataatccaaatgcacttcctctttttttgagaatattcgattgttttggatgctttggggcgaagattggtaaaatgaattattgaacattta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaatgttcaataattcattttaccaatcttcgccccaaagcatccaaaacaatcgaatattctcaaaaaaagaggaagtgcatttggattataaaaaatcatataactttgtggaaattaccaatccataaaaatataagaacaa Mask Tandem Repeat Region ================================================ ttgttcttatatttttatggattggtaatttccacaaagttatatgattttttataatccaaatgcacttcctctttttttgagaatattcgattgttttggatgctttggggcgaagattggtaaaatgaattattgaacattta Find is-nt database================================================ Query_seq: TF0737:TF0738|TF0737:TF0738:hypothetical protein:conserved hypothetical protein:->->:788637..788782 146 ttgttcttatatttttatggattggtaatttccacaaagttatatgattttttataatccaaatgcacttcctctttttttgagaatattcgattgttttggatgctttggggcgaagattggtaaaatgaattattgaacattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0737:TF0738|TF0737:TF0738:hypothetical protein:conserved hypothetical protein:->->:788637..788782 146 ttgttcttatatttttatggattggtaatttccacaaagttatatgattttttataatccaaatgcacttcctctttttttgagaatattcgattgttttggatgctttggggcgaagattggtaaaatgaattattgaacattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0737:TF0738|TF0737:TF0738:hypothetical protein:conserved hypothetical protein:->->:788637..788782 146 ttgttcttatatttttatggattggtaatttccacaaagttatatgattttttataatccaaatgcacttcctctttttttgagaatattcgattgttttggatgctttggggcgaagattggtaaaatgaattattgaacattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgttcttatatttttatggattggtaatttccacaaagttatatgattttttataatccaaatgcacttcctctttttttgagaatattcgattgttttggatgctttggggcgaagattggtaaaatgaattattgaacattta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 44 End: 136 ........................................... M I F Y N P N A L P L F L R I F D C F G C F G A K I G K M N Y .......... Protein_Len: 42 Strand: - Start: 18 End: 143 ................. P N T I E V F N Y S K K Y D L H V E E K K S F I R N N Q I S Q P S S Q Y F S N N F M ... Protein_Len: 45 Strand: - Start: 2 End: 136 . T R I N K H I P L K W L T I H N K I I W I C K R K K Q S Y E I T K S A K P R L N T F H I M .......... ttgttcttatatttttatggattggtaatttccacaaagttatatgattttttataatccaaatgcacttcctctttttttgagaatattcgattgttttggatgctttggggcgaagattggtaaaatgaattattgaacattta 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================================================ ttgttcttatatttttatggattggtaatttccacaaagttatatgattttttataatccaaatgcacttcctctttttttgagaatattcgattgttttggatgctttggggcgaagattggtaaaatgaattattgaacattta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0737:TF0738|TF0737:TF0738:hypothetical protein:conserved hypothetical protein:->->:788637..788782 146 ttgttcttatatttttatggattggtaatttccacaaagttatatgattttttataatccaaatgcacttcctctttttttgagaatattcgattgttttggatgctttggggcgaagattggtaaaatgaattattgaacattta Intra-Species Hit: Count: 2 Min: 1 Max: 146 Len: 146 Subject: tfor_TF0737_TF0738|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[788637,788782]|146 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 146 Query Start:1 Query End:146 Subject Strand: POSITIVE Subject Start: 1 Subject End: 146 ttgttcttatatttttatggattggtaatttccacaaagttatatgattttttataatccaaatgcacttcctcnnnnnnngagaatattcgattgttttggatgctttggggcgaagattggtaaaatgaattattgaacattta ttgttcttatatttttatggattggtaatttccacaaagttatatgattttttataatccaaatgcacttcctctttttttgagaatattcgattgttttggatgctttggggcgaagattggtaaaatgaattattgaacattta Subject: tfor_TF0739_TF0743|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[790329,790466]|138 HSP 1 e-value: 2.0E-39 bit: 163.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 ttgttcttatatttttatggattggtaatttccacaaagttatatgattttttataatccaaatgcacttcctcnnnnnnngagaatattcgattgttttggatgctttgg................................... ttgttcttatatttttatggattgataatttccataaagttatatgattttttataatccaaatgcacttcctctttttttgagaatattcgattgttttggatgctttgg................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUUCUUAUAUUUUUAUGGAUUGGUAAUUUCCACAAAGUUAUAUGAUUUUUUAUAAUCCAAAUGCACUUCCUCUUUUUUUGAGAAUAUUCGAUUGUUUUGGAUGCUUUGGGGCGAAGAUUGGUAAAAUGAAUUAUUGAACAUUUA .(((((..(((..(((((..((..((..((.((.((((((..(((((....))))).((((((.(((..(((((.......))).......)).))))))))).)))))).)).))..))..))...))))).))).))))).... (-26.51) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUGUUCAAUAAUUCAUUUUACCAAUCUUCGCCCCAAAGCAUCCAAAACAAUCGAAUAUUCUCAAAAAAAGAGGAAGUGCAUUUGGAUUAUAAAAAAUCAUAUAACUUUGUGGAAAUUACCAAUCCAUAAAAAUAUAAGAACAA ....(((((.((((((((..((((........((......))..................(((((.......))))).))).)..)))))))).........((((..((((((((.........))))))))..)))).))))). (-23.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 132 91 206 158 tfor:TF2849|5end_histidinol-phosphate_transaminase_3037288..3037518_POSITIVE 301 120 73 64 18 tfor:TF0776|5end_ABC_transporter,_permease_component_824855..825085_POSITIVE 291 119 71 192 143 tfor:TF0244|5end_DNA_recombination_protein_274683..274913_POSITIVE 285 138 91 56 3 tfor:TF1941|5end_3-phosphoshikimate-1-carboxyvinyltransferase_2088862..2089092_POSITIVE 278 125 99 231 201 tfor:TF2083|5end_conserved_hypothetical_protein_2250834..2251064_POSITIVE 278 115 72 227 184 tfor:TF0684|5end_conserved_hypothetical_protein_728853..729083_POSITIVE 274 123 81 157 113 tfor:TF0045|5end_outer_membrane_protein,_TonB_dependent_receptor_49626..49856_POSITIVE 272 115 71 51 13 tfor:TF2876|5end_cytosine_deaminase_3065144..3065374_POSITIVE 271 115 71 171 129 tfor:TF2750|5end_L-serine_dehydratase_2934432..2934662_POSITIVE 271 117 86 55 15 tfor:TF1398|5end_conserved_hypothetical_protein_1471474..1471704_POSITIVE 270 120 71 72 23 tfor:TF1266|5end_conserved_hypothetical_protein_1353423..1353653_POSITIVE 269 123 82 189 144 tfor:TF1804|5end_hypothetical_protein_1947101..1947331_POSITIVE 261 119 73 55 9 tfor:TF2696|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_2870752..2870982_POSITIVE 261 115 72 190 137 tfor:TF1580|5end_conserved_hypothetical_protein;_possible_fibronectin_domain_containing_protein_1687187..1687417_POSITIVE 256 124 82 41 1 tfor:TF0765|5end_conserved_hypothetical_protein_811302..811532_POSITIVE 255 123 89 191 149 tfor:TF1886|5end_auxin-regulated_protein_2038720..2038950_POSITIVE 255 133 91 220 170 tfor:TF1146|5end_2-dehydropantoate_2-reductase_1227162..1227392_POSITIVE 255 140 92 87 40 tfor:TF0729|5end_DNA_primase_780107..780337_POSITIVE 251 120 94 81 48 tfor:TF3099|5end_conserved_hypothetical_protein_3330461..3330691_POSITIVE 251 106 63 156 108 tfor:TF2250|5end_transfer_region-related_protein,_TraD_2423380..2423610_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 120 73 48 2 tfor:TF0775|3end_ABC_transporter,_permease_component_824919..825069_POSITIVE 279 116 72 146 95 tfor:TF1139|3end_adenylosuccinate_lyase_1216667..1216817_POSITIVE 274 123 81 136 92 tfor:TF0044|3end_conserved_hypothetical_protein_49685..49835_POSITIVE 272 115 71 51 13 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 271 123 90 124 93 tfor:TF2092|3end_ribonuclease_III_2261823..2261973_POSITIVE 269 123 82 128 83 tfor:TF1803|3end_conserved_hypothetical_protein_1947120..1947270_POSITIVE 269 124 82 141 94 tfor:TF0431|3end_hypothetical_protein_452470..452620_POSITIVE 261 119 73 86 40 tfor:TF2694|3end_hypothetical_protein_2870863..2871013_POSITIVE 255 123 89 142 100 tfor:TF1885|3end_conserved_hypothetical_protein_2038751..2038901_POSITIVE 255 140 92 78 31 tfor:TF0727|3end_ABC_transporter,_ATP-binding_protein_780178..780328_POSITIVE 251 120 94 75 42 tfor:TF3098|3end_conserved_hypothetical_protein_3330535..3330685_POSITIVE 251 106 63 114 66 tfor:TF2249|3end_transfer_region-related_protein,_TraC_2423418..2423568_POSITIVE 250 113 76 150 105 tfor:TF2378|3end_peptide_chain_release_factor_1_2543871..2544021_POSITIVE 250 109 66 83 38 tfor:TF1325|3end_L-fucose_isomerase_1405870..1406020_POSITIVE 247 122 90 121 88 tfor:TF1634|3end_hypothetical_protein_1747078..1747228_POSITIVE 246 119 71 145 81 tfor:TF2044|3end_excinuclease_ABC,_subunit_A_2206163..2206313_POSITIVE 246 118 71 111 68 tfor:TF0684|3end_conserved_hypothetical_protein_730564..730714_POSITIVE 244 115 71 86 41 tfor:TF1841|3end_hypothetical_protein_1992267..1992417_POSITIVE 243 115 81 115 83 tfor:TF2787|3end_30S_ribosomal_protein_S1_2972258..2972408_POSITIVE 243 130 88 75 20 tfor:TF0686|3end_hypothetical_protein_732950..733100_POSITIVE