Origin IGS: tttttacttgtttttttaggtattcttaacgttatgcaaagttacacgataattttgaatttctttggattattgaatgaattcttgttctgttggatggttggtctgtttttgaagaacgaaaaggccttcgggtattttatttgttgttgaggtgtttagtcgttgaatgctgacggctgactgaaacc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggtttcagtcagccgtcagcattcaacgactaaacacctcaacaacaaataaaatacccgaaggccttttcgttcttcaaaaacagaccaaccatccaacagaacaagaattcattcaataatccaaagaaattcaaaattatcgtgtaactttgcataacgttaagaatacctaaaaaaacaagtaaaaa Mask Tandem Repeat Region ================================================ tttttacttgtttttttaggtattcttaacgttatgcaaagttacacgataattttgaatttctttggattattgaatgaattcttgttctgttggatggttggtctgtttttgaagaacgaaaaggccttcgggtattttatttgttgttgaggtgtttagtcgttgaatgctgacggctgactgaaacc Find is-nt database================================================ Query_seq: TF2775:TF2776|TF2775:TF2776:conserved hypothetical protein; possible mucoidy inhibitor-related protein:hypothetical protein:->->:2961419..2961609 191 tttttacttgtttttttaggtattcttaacgttatgcaaagttacacgataattttgaatttctttggattattgaatgaattcttgttctgttggatggttggtctgtttttgaagaacgaaaaggccttcgggtattttatttgttgttgaggtgtttagtcgttgaatgctgacggctgactgaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2775:TF2776|TF2775:TF2776:conserved hypothetical protein; possible mucoidy inhibitor-related protein:hypothetical protein:->->:2961419..2961609 191 tttttacttgtttttttaggtattcttaacgttatgcaaagttacacgataattttgaatttctttggattattgaatgaattcttgttctgttggatggttggtctgtttttgaagaacgaaaaggccttcgggtattttatttgttgttgaggtgtttagtcgttgaatgctgacggctgactgaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2775:TF2776|TF2775:TF2776:conserved hypothetical protein; possible mucoidy inhibitor-related protein:hypothetical protein:->->:2961419..2961609 191 tttttacttgtttttttaggtattcttaacgttatgcaaagttacacgataattttgaatttctttggattattgaatgaattcttgttctgttggatggttggtctgtttttgaagaacgaaaaggccttcgggtattttatttgttgttgaggtgtttagtcgttgaatgctgacggctgactgaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttacttgtttttttaggtattcttaacgttatgcaaagttacacgataattttgaatttctttggattattgaatgaattcttgttctgttggatggttggtctgtttttgaagaacgaaaaggccttcgggtattttatttgttgttgaggtgtttagtcgttgaatgctgacggctgactgaaacc Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 22 End: 150 ..................... M L N V M Q S Y T I I L N F F G L L N E F L F C W M V G L F L K N E K A F G Y F I C C ......................................... Protein_Len: 31 Strand: + Start: 81 End: 173 ................................................................................ M L V L L D G W S V F E E R K G L R V F Y L L L R C L V V E C .................. Protein_Len: 33 Strand: - Start: 73 End: 171 ........................................................................ Q I F E Q E T P H N T Q K Q L V F L G E P I K N T T S T N L R Q M .................... Protein_Len: 33 Strand: - Start: 45 End: 143 ............................................ V I I K F K K P N N F S N K N Q Q I T P R N K F F S F A K P Y K M ................................................ tttttacttgtttttttaggtattcttaacgttatgcaaagttacacgataattttgaatttctttggattattgaatgaattcttgttctgttggatggttggtctgtttttgaagaacgaaaaggccttcgggtattttatttgttgttgaggtgtttagtcgttgaatgctgacggctgactgaaacc 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================================================ tttttacttgtttttttaggtattcttaacgttatgcaaagttacacgataattttgaatttctttggattattgaatgaattcttgttctgttggatggttggtctgtttttgaagaacgaaaaggccttcgggtattttatttgttgttgaggtgtttagtcgttgaatgctgacggctgactgaaacc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2775:TF2776|TF2775:TF2776:conserved hypothetical protein; possible mucoidy inhibitor-related protein:hypothetical protein:->->:2961419..2961609 191 tttttacttgtttttttaggtattcttaacgttatgcaaagttacacgataattttgaatttctttggattattgaatgaattcttgttctgttggatggttggtctgtttttgaagaacgaaaaggccttcgggtattttatttgttgttgaggtgtttagtcgttgaatgctgacggctgactgaaacc Intra-Species Hit: Count: 1 Min: 18 Max: 191 Len: 174 Subject: tfor_TF2775_TF2776|conserved hypothetical protein; possible mucoidy inhibitor-related protein:hypothetical protein|POSITIVE:POSITIVE|[2961419,2961609]|191 HSP 1 e-value: 3.0E-94 bit: 345.0 Len: 174 Query Start:18 Query End:191 Subject Strand: POSITIVE Subject Start: 18 Subject End: 191 .................aggtattcttaacgttatgcaaagttacacgataattttgaatttctttggattattgaatgaattcttgttctgttggatggttggtctgtttttgaagaacgaaaaggccttcgggtattttatttgttgttgaggtgtttagtcgttgaatgctgacggctgactgaaacc .................aggtattcttaacgttatgcaaagttacacgataattttgaatttctttggattattgaatgaattcttgttctgttggatggttggtctgtttttgaagaacgaaaaggccttcgggtattttatttgttgttgaggtgtttagtcgttgaatgctgacggctgactgaaacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUAUUCUUAACGUUAUGCAAAGUUACACGAUAAUUUUGAAUUUCUUUGGAUUAUUGAAUGAAUUCUUGUUCUGUUGGAUGGUUGGUCUGUUUUUGAAGAACGAAAAGGCCUUCGGGUAUUUUAUUUGUUGUUGAGGUGUUUAGUCGUUGAAUGCUGACGGCUGACUGAAACC .(((..((((((((....(((((......((((((((..((.....))..)))))))).........(((((((...((((((.....))))))....)))))))....(((....)))......)))))))))))))...(((((((((.......))))))))).....))) (-39.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUUUCAGUCAGCCGUCAGCAUUCAACGACUAAACACCUCAACAACAAAUAAAAUACCCGAAGGCCUUUUCGUUCUUCAAAAACAGACCAACCAUCCAACAGAACAAGAAUUCAUUCAAUAAUCCAAAGAAAUUCAAAAUUAUCGUGUAACUUUGCAUAACGUUAAGAAUACCU ((((((.(((....(((..........))).............................((((..(.....)..)))).......)))..............(((..(((((..((..........))..))))).........(((((....)))))...)))..))).))). (-16.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 382 170 129 229 192 tfor:TF0725|5end_O-acetylhomoserine_(thiol)-lyase_776556..776786_POSITIVE 377 169 130 78 33 tfor:TF0961|5end_translation_initiation_inhibitor,_endoribonuclease_activity_1010445..1010675_POSITIVE 353 46 2 122 70 tfor:TF3018|5end_polyphosphate_kinase_3240122..3240352_POSITIVE 346 169 127 61 8 tfor:TF1274|5end_hypothetical_protein_1357621..1357851_POSITIVE 342 118 74 55 7 tfor:TF0597|5end_hypothetical_protein_628788..629018_POSITIVE 340 139 96 167 106 tfor:TF2167|5end_hypothetical_protein_2342586..2342816_POSITIVE 335 166 125 122 71 tfor:TF0598|5end_hypothetical_protein_629190..629420_POSITIVE 333 120 72 216 158 tfor:TF2187|5end_conserved_hypothetical_protein_2361693..2361923_POSITIVE 333 170 128 175 125 tfor:TF0359|5end_conserved_hypothetical_protein_376943..377173_POSITIVE 330 170 129 172 131 tfor:TF2439|5end_conserved_hypothetical_protein_2616380..2616610_POSITIVE 330 140 91 193 149 tfor:TF0582|5end_hemolysin-related_protein,_with_CBS_domains;_possible_gliding-motility_related_protein_611885..612115_POSITIVE 325 149 104 60 10 tfor:TF2015|5end_N6-adenine-specific_DNA_methylase_2171606..2171836_POSITIVE 319 118 73 62 4 tfor:TF0851|5end_helicase_SNF2_family_899486..899716_POSITIVE 314 168 126 145 97 tfor:TF2115|5end_conserved_hypothetical_protein;_possible_carboxylesterase_2284786..2285016_POSITIVE 309 140 103 230 199 tfor:TF2500|5end_ABC_transporter,_ATP-binding_protein_2674449..2674679_POSITIVE 309 170 135 79 45 tfor:TF2350|5end_hypothetical_protein_2515063..2515293_POSITIVE 308 148 103 115 70 tfor:TF2134|5end_conserved_hypothetical_protein_2308689..2308919_POSITIVE 307 88 44 177 130 tfor:TF2979|5end_possible_outer_membrane__protein_3190778..3191008_POSITIVE 307 163 127 125 85 tfor:TF0053|5end_hypothetical_protein_57488..57718_POSITIVE 306 170 137 98 65 tfor:TF0600|5end_oxidoreductase/dehydrogenase_630083..630313_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 377 169 130 59 14 tfor:TF0960|3end_beta-galactosidase_1010506..1010656_POSITIVE 336 140 95 86 41 tfor:TF2229.1|3end_rteR_regulatory_ortholog_(with_internal_stop)_2399727..2399877_POSITIVE 336 140 95 62 17 tfor:TF2229|3end_CTn_excision_protein;_DNA_topoisomerase_IA_2399703..2399853_POSITIVE 335 166 125 82 31 tfor:TF0597|3end_hypothetical_protein_629230..629380_POSITIVE 317 117 78 120 71 tfor:TF0939|3end_ISPg1_transposase,_IS1106-related_transposase_981115..981265_POSITIVE 308 148 103 115 70 tfor:TF2132|3end_TIM-barrel_protein,_NifR3_family_2308769..2308919_POSITIVE 307 163 127 125 85 tfor:TF0051|3end_hypothetical_protein_57568..57718_POSITIVE 306 170 137 65 32 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 300 169 135 53 27 tfor:TF2171|3end_hypothetical_protein_2345792..2345942_POSITIVE 299 120 74 137 98 tfor:TF2533|3end_adenylosuccinate_synthetase_2717014..2717164_POSITIVE 296 124 88 146 98 tfor:TF1755|3end_periplasmic_protease_1892867..1893017_POSITIVE 293 118 71 69 23 tfor:TF3046|3end_hypothetical_protein_3275192..3275342_POSITIVE 293 110 61 73 18 tfor:TF0890|3end_transfer_region-related_protein,_TraQ_940555..940705_POSITIVE 290 117 78 120 71 tfor:TF0874|3end_transposase_926652..926802_POSITIVE 288 166 125 129 83 tfor:TF1152|3end_permease,_major_facilitator_superfamily_1234618..1234768_POSITIVE 286 105 61 116 76 tfor:TF2779|3end_fucose_permease_2965932..2966082_POSITIVE 282 166 127 78 40 tfor:TF1172|3end_ABC_transporter,_permease_component_1255213..1255363_POSITIVE 280 169 126 62 29 tfor:TF2343|3end_ribosome_recycling_factor_2507502..2507652_POSITIVE 280 169 124 45 1 tfor:TF1928|3end_conserved_hypothetical_protein_2076124..2076274_POSITIVE 279 149 103 77 39 tfor:TF2251|3end_conjugative_transposon_protein,_TraE_2424687..2424837_POSITIVE