Origin IGS: taatgaaacaagcgggctgtgagagcatacgatattcgtgtgatgataaaacatttctgaaagtaggaagaaaaccgtttcgttttcttcctactcgattgaaatttattgctgtccattaaaattttttgaacaataaaaattaggactgaattcctcgcttggaatccagcccttttagtgatctttgtttctgccaaaataaaccatagtagcgatgaacaaagatacacattttaccggacagtaatataaaataatatgatta .........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 taatcatattattttatattactgtccggtaaaatgtgtatctttgttcatcgctactatggtttattttggcagaaacaaagatcactaaaagggctggattccaagcgaggaattcagtcctaatttttattgttcaaaaaattttaatggacagcaataaatttcaatcgagtaggaagaaaacgaaacggttttcttcctactttcagaaatgttttatcatcacacgaatatcgtatgctctcacagcccgcttgtttcatta Mask Tandem Repeat Region ================================================ taatgaaacaagcgggctgtgagagcatacgatattcgtgtgatgataaaacatttctgaaagtaggaagaaaaccgtttcgttttcttcctactcgattgaaatttattgctgtccattaaaattttttgaacaataaaaattaggactgaattcctcgcttggaatccagcccttttagtgatctttgtttctgccaaaataaaccatagtagcgatgaacaaagatacacattttaccggacagtaatataaaataatatgatta Find is-nt database================================================ Query_seq: TF2302:TF2303|TF2302:TF2303:conserved hypothetical protein; possible outer membrane protein:conserved hypothetical protein:->->:2458124..2458391 268 taatgaaacaagcgggctgtgagagcatacgatattcgtgtgatgataaaacatttctgaaagtaggaagaaaaccgtttcgttttcttcctactcgattgaaatttattgctgtccattaaaattttttgaacaataaaaattaggactgaattcctcgcttggaatccagcccttttagtgatctttgtttctgccaaaataaaccatagtagcgatgaacaaagatacacattttaccggacagtaatataaaataatatgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2302:TF2303|TF2302:TF2303:conserved hypothetical protein; possible outer membrane protein:conserved hypothetical protein:->->:2458124..2458391 268 taatgaaacaagcgggctgtgagagcatacgatattcgtgtgatgataaaacatttctgaaagtaggaagaaaaccgtttcgttttcttcctactcgattgaaatttattgctgtccattaaaattttttgaacaataaaaattaggactgaattcctcgcttggaatccagcccttttagtgatctttgtttctgccaaaataaaccatagtagcgatgaacaaagatacacattttaccggacagtaatataaaataatatgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2302:TF2303|TF2302:TF2303:conserved hypothetical protein; possible outer membrane protein:conserved hypothetical protein:->->:2458124..2458391 268 taatgaaacaagcgggctgtgagagcatacgatattcgtgtgatgataaaacatttctgaaagtaggaagaaaaccgtttcgttttcttcctactcgattgaaatttattgctgtccattaaaattttttgaacaataaaaattaggactgaattcctcgcttggaatccagcccttttagtgatctttgtttctgccaaaataaaccatagtagcgatgaacaaagatacacattttaccggacagtaatataaaataatatgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatgaaacaagcgggctgtgagagcatacgatattcgtgtgatgataaaacatttctgaaagtaggaagaaaaccgtttcgttttcttcctactcgattgaaatttattgctgtccattaaaattttttgaacaataaaaattaggactgaattcctcgcttggaatccagcccttttagtgatctttgtttctgccaaaataaaccatagtagcgatgaacaaagatacacattttaccggacagtaatataaaataatatgatta Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 3 End: 119 .. M K Q A G C E S I R Y S C D D K T F L K V G R K P F R F L P T R L K F I A V H ..................................................................................................................................................... Protein_Len: 39 Strand: + Start: 136 End: 252 ....................................................................................................................................... M K I R T E F L A W N P A L L V I F V S A K I N H S S D E Q R Y T F Y R T V I ................ Protein_Len: 36 Strand: - Start: 146 End: 253 ................................................................................................................................................. S Q I G R K S D L G K L S R Q K Q W F L G Y Y R H V F I C M K G S L L M ............... Protein_Len: 60 Strand: - Start: 3 End: 233 .. K Q F Y S S F R K T K K R S S Q F K N S D M L I K Q V I F I L V S N R A Q F G A R K T I K T E A L I F W L L S S C L Y M ................................... Protein_Len: 36 Strand: - Start: 2 End: 109 . I F C A P Q S L M R Y E H S S L V N R F T P L F G N R K R G V R N F N M ............................................................................................................................................................... taatgaaacaagcgggctgtgagagcatacgatattcgtgtgatgataaaacatttctgaaagtaggaagaaaaccgtttcgttttcttcctactcgattgaaatttattgctgtccattaaaattttttgaacaataaaaattaggactgaattcctcgcttggaatccagcccttttagtgatctttgtttctgccaaaataaaccatagtagcgatgaacaaagatacacattttaccggacagtaatataaaataatatgatta 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================================================ taatgaaacaagcgggctgtgagagcatacgatattcgtgtgatgataaaacatttctgaaagtaggaagaaaaccgtttcgttttcttcctactcgattgaaatttattgctgtccattaaaattttttgaacaataaaaattaggactgaattcctcgcttggaatccagcccttttagtgatctttgtttctgccaaaataaaccatagtagcgatgaacaaagatacacattttaccggacagtaatataaaataatatgatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 57 HP_score: -2.8 Tail_Score: -4.29508 Start: 54 End: 104 Full_Region: TGTGATGATAAAACA TTTCTGAAAGTAGGAAGAAAAC CGTTTC GTTTTCTTCCTACTCGATTGAAA TTTATTGCTGTCCAT .....................................................TTTCTGAAAGTAGGAAGAAAACCGTTTCGTTTTCTTCCTACTCGATTGAAA.................................................................................................................................................................... TransTerm Strand: - Conf: 52 HP_score: -2.8 Tail_Score: -3.84183 Start: 54 End: 104 Full_Region: atggacagcaataaa tttcaatcgagtaggaagaaaac gaaacg gttttcttcctactttcagaaa tgttttatcatcaca .....................................................tttcaatcgagtaggaagaaaacgaaacggttttcttcctactttcagaaa.................................................................................................................................................................... TransTerm Strand: + Conf: 95 HP_score: -14.7 Tail_Score: -2.56314 Start: 63 End: 94 Full_Region: AAAACATTTCTGAAA GTAGGAAGAAAAC CGTTTC GTTTTCTTCCTAC TCGATTGAAATTTAT ..............................................................GTAGGAAGAAAACCGTTTCGTTTTCTTCCTAC.............................................................................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -14.7 Tail_Score: -3.58731 Start: 63 End: 94 Full_Region: ataaatttcaatcga gtaggaagaaaac gaaacg gttttcttcctac tttcagaaatgtttt ..............................................................gtaggaagaaaacgaaacggttttcttcctac.............................................................................................................................................................................. TransTerm Strand: + Conf: 51 HP_score: -4.2 Tail_Score: -3.2327 Start: 70 End: 87 Full_Region: TTCTGAAAGTAGGAA GAAAAC CGTTTC GTTTTC TTCCTACTCGATTGA .....................................................................GAAAACCGTTTCGTTTTC..................................................................................................................................................................................... TransTerm Strand: - Conf: 84 HP_score: -4.7 Tail_Score: -5.29445 Start: 143 End: 178 Full_Region: aaacaaagatcacta aaagggctggattcc aagcga ggaattcagtcctaa tttttattgttcaaa ..............................................................................................................................................aaagggctggattccaagcgaggaattcagtcctaa.......................................................................................... TransTerm Strand: - Conf: 74 HP_score: -8.2 Tail_Score: -3.76582 Start: 144 End: 177 Full_Region: aacaaagatcactaa aagggctggattcc aagcga ggaattcagtccta atttttattgttcaa ...............................................................................................................................................aagggctggattccaagcgaggaattcagtccta........................................................................................... TransTerm Strand: + Conf: 76 HP_score: -6.4 Tail_Score: -4.37067 Start: 146 End: 175 Full_Region: GAACAATAAAAATTA GGACTGAATTCC TCGCTT GGAATCCAGCCC TTTTAGTGATCTTTG .................................................................................................................................................GGACTGAATTCCTCGCTTGGAATCCAGCCC............................................................................................. TransTerm Strand: - Conf: 82 HP_score: -10.8 Tail_Score: -3.44752 Start: 146 End: 175 Full_Region: caaagatcactaaaa gggctggattcc aagcga ggaattcagtcc taatttttattgttc .................................................................................................................................................gggctggattccaagcgaggaattcagtcc............................................................................................. Find igs database================================================ Query_seq: TF2302:TF2303|TF2302:TF2303:conserved hypothetical protein; possible outer membrane protein:conserved hypothetical protein:->->:2458124..2458391 268 taatgaaacaagcgggctgtgagagcatacgatattcgtgtgatgataaaacatttctgaaagtaggaagaaaaccgtttcgttttcttcctactcgattgaaatttattgctgtccattaaaattttttgaacaataaaaattaggactgaattcctcgcttggaatccagcccttttagtgatctttgtttctgccaaaataaaccatagtagcgatgaacaaagatacacattttaccggacagtaatataaaataatatgatta Intra-Species Hit: Count: 1 Min: 1 Max: 268 Len: 268 Subject: tfor_TF2302_TF2303|conserved hypothetical protein; possible outer membrane protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2458124,2458391]|268 HSP 1 e-value: 1.0E-150 bit: 531.0 Len: 268 Query Start:1 Query End:268 Subject Strand: POSITIVE Subject Start: 1 Subject End: 268 taatgaaacaagcgggctgtgagagcatacgatattcgtgtgatgataaaacatttctgaaagtaggaagaaaaccgtttcgttttcttcctactcgattgaaatttattgctgtccattaaaattttttgaacaataaaaattaggactgaattcctcgcttggaatccagcccttttagtgatctttgtttctgccaaaataaaccatagtagcgatgaacaaagatacacattttaccggacagtaatataaaataatatgatta taatgaaacaagcgggctgtgagagcatacgatattcgtgtgatgataaaacatttctgaaagtaggaagaaaaccgtttcgttttcttcctactcgattgaaatttattgctgtccattaaaattttttgaacaataaaaattaggactgaattcctcgcttggaatccagcccttttagtgatctttgtttctgccaaaataaaccatagtagcgatgaacaaagatacacattttaccggacagtaatataaaataatatgatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGAAACAAGCGGGCUGUGAGAGCAUACGAUAUUCGUGUGAUGAUAAAACAUUUCUGAAAGUAGGAAGAAAACCGUUUCGUUUUCUUCCUACUCGAUUGAAAUUUAUUGCUGUCCAUUAAAAUUUUUUGAACAAUAAAAAUUAGGACUGAAUUCCUCGCUUGGAAUCCAGCCCUUUUAGUGAUCUUUGUUUCUGCCAAAAUAAACCAUAGUAGCGAUGAACAAAGAUACACAUUUUACCGGACAGUAAUAUAAAAUAAUAUGAUUA ..(((((.....((...(((....)))..))...))))).((((.(((....(((((....((((((((((((((......)))))))))))))).....))))).(((((((((((.....(((((((........))))))).((.(((.(((((......))))).))).)).....(((((((((((((((((..............))))....)))))))))).)))........)))))))))))........))).)))) (-72.94) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCAUAUUAUUUUAUAUUACUGUCCGGUAAAAUGUGUAUCUUUGUUCAUCGCUACUAUGGUUUAUUUUGGCAGAAACAAAGAUCACUAAAAGGGCUGGAUUCCAAGCGAGGAAUUCAGUCCUAAUUUUUAUUGUUCAAAAAAUUUUAAUGGACAGCAAUAAAUUUCAAUCGAGUAGGAAGAAAACGAAACGGUUUUCUUCCUACUUUCAGAAAUGUUUUAUCAUCACACGAAUAUCGUAUGCUCUCACAGCCCGCUUGUUUCAUUA ................((((.(((((((.(((((((((.(((((((((..((((((..(((...)))..)))).))))))))))))))....(((((((((((((......)))))))))))))...................)))))).))))))).))))..........(((((((((((((((......)))))))))))))))...(((((.............(((.....)))..(((.....)))......))))).... (-77.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 379 93 51 146 98 tfor:TF2197|5end_conserved_hypothetical_protein_2372402..2372632_POSITIVE 323 117 74 75 29 tfor:TF0239|5end_conserved_hypothetical_protein_268894..269124_POSITIVE 308 197 157 59 25 tfor:TF2151|5end_uridine_kinase_2323033..2323263_POSITIVE 307 46 8 191 137 tfor:TF1142|5end_outer_membrane_cobalamin_receptor_protein_1219207..1219437_POSITIVE 305 252 212 136 99 tfor:TF0005|5end_possible_beta-lactamase_600..830_POSITIVE 300 195 154 147 106 tfor:TF0662|5end_hypothetical_protein_708316..708546_POSITIVE 298 44 11 131 104 tfor:TF1327|5end_L-fucose_permease_1405790..1406020_POSITIVE 296 190 145 156 116 tfor:TF1883|5end_conserved_hypothetical_protein_2035015..2035245_POSITIVE 294 60 13 205 154 tfor:TF0456|5end_conserved_hypothetical_protein_473403..473633_POSITIVE 289 70 21 91 29 tfor:TF0010|5end_conserved_hypothetical_protein_4432..4662_POSITIVE 288 116 75 166 119 tfor:TF1904|5end_two-component_system_response_regulator_2058975..2059205_POSITIVE 286 183 145 145 102 tfor:TF2501|5end_DNA_mismatch_repair_protein_2676280..2676510_POSITIVE 285 194 153 48 14 tfor:TF2901|5end_conserved_hypothetical_protein_3090365..3090595_POSITIVE 285 223 182 145 92 tfor:TF0296|5end_hypothetical_protein_321941..322171_POSITIVE 283 38 1 174 134 tfor:TF0349|5end_hypothetical_protein_370367..370597_POSITIVE 282 60 11 101 55 tfor:TF2582|5end_ABC_transporter,_ATP-binding_protein_2749433..2749663_POSITIVE 282 59 12 121 68 tfor:TF1334|5end_hypothetical_protein_1415996..1416226_POSITIVE 281 96 51 132 86 tfor:TF2218|5end_two-component_system_response_regulator_2390162..2390392_POSITIVE 281 159 113 231 185 tfor:TF1773|5end_hypothetical_protein_1910939..1911169_POSITIVE 280 57 11 195 157 tfor:TF1586|5end_hypothetical_protein_1690971..1691201_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 365 100 62 63 34 tfor:TF2295|3end_hypothetical_protein_2448717..2448867_POSITIVE 323 117 74 58 12 tfor:TF0238|3end_outer_membrane_protein_268957..269107_POSITIVE 308 197 157 56 22 tfor:TF2149|3end_deoxyribose-phosphate_aldolase_2323110..2323260_POSITIVE 305 252 212 103 66 tfor:TF0002|3end_hypothetical_protein_647..797_POSITIVE 298 197 153 141 96 tfor:TF3051|3end_conserved_hypothetical_protein_3278067..3278217_POSITIVE 298 44 11 131 104 tfor:TF1325|3end_L-fucose_isomerase_1405870..1406020_POSITIVE 285 198 151 83 43 tfor:TF2640|3end_hypothetical_protein_2809533..2809683_POSITIVE 282 59 12 59 6 tfor:TF1333|3end_probable_acylaminoacyl_peptidase;_alanyl_dipeptidyl_peptidase_1416014..1416164_POSITIVE 281 96 51 55 9 tfor:TF2217|3end_hypothetical_protein_2390165..2390315_POSITIVE 280 41 11 110 80 tfor:TF0750|3end_conserved_hypothetical_protein_798698..798848_POSITIVE 279 220 174 93 50 tfor:TF1295|3end_conserved_hypothetical_protein_1377256..1377406_POSITIVE 274 102 62 49 4 tfor:TF2740|3end_conserved_hypothetical_protein_2921972..2922122_POSITIVE 272 190 141 74 28 tfor:TF1291|3end_response_regulator_(fimR__protein)_1372647..1372797_POSITIVE 272 198 155 73 28 tfor:TF1014|3end_glucose-6-phosphate_isomerase_1072474..1072624_POSITIVE 271 200 153 49 1 tfor:TF0493|3end_outer_membrane_protein_519260..519410_POSITIVE 267 48 4 86 45 tfor:TF0407|3end_lipoate-protein_ligase_B_(lipoyltransferase)_425844..425994_POSITIVE 266 200 161 150 106 tfor:TF2116|3end_conserved_hypothetical_protein;_possible_hemagglutinin/hemolysin_2289634..2289784_POSITIVE 265 259 215 94 48 tfor:TF0835|3end_conserved_hypothetical_protein_889366..889516_POSITIVE 264 45 8 123 90 tfor:TF2774|3end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_2959719..2959869_POSITIVE 263 182 145 151 116 tfor:TF1882|3end_conserved_hypothetical_protein_2035095..2035245_POSITIVE