Origin IGS: attttttattttttagcagtcagcgttcagcattcagtaatcagcaaacaattcaataattcaacagttataccaatattaattcaggcttacagccctctgacgtggggttgctttttctcccaacgctgtgcattgggctgaattaacatgccctttcagggctttttctcaaattgtcaatggttatttagttttcagcgatcagtaacaaacaactcaacaattcaacaactcaacaattcgacaactcaacgcccgaagggcatcactcttcacttttcacttttcgttcttcacttttcatcta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagatgaaaagtgaagaacgaaaagtgaaaagtgaagagtgatgcccttcgggcgttgagttgtcgaattgttgagttgttgaattgttgagttgtttgttactgatcgctgaaaactaaataaccattgacaatttgagaaaaagccctgaaagggcatgttaattcagcccaatgcacagcgttgggagaaaaagcaaccccacgtcagagggctgtaagcctgaattaatattggtataactgttgaattattgaattgtttgctgattactgaatgctgaacgctgactgctaaaaaataaaaaat Mask Tandem Repeat Region ================================================ attttttattttttagcagtcagcgttcagcattcagtaatcagcaaacaattcaataattcaacagttataccaatattaattcaggcttacagccctctgacgtggggttgctttttctcccaacgctgtgcattgggctgaattaacatgccctttcagggctttttctcaaattgtcaatggttatttagttttcagcgatcagtaacannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngcccgaagggcatcactcttcacttttcacttttcgttcttcacttttcatcta Find is-nt database================================================ Query_seq: TF1172:TF1173|TF1172:TF1173:ABC transporter, permease component:ABC transporter, permease component:->->:1255274..1255583 310 attttttattttttagcagtcagcgttcagcattcagtaatcagcaaacaattcaataattcaacagttataccaatattaattcaggcttacagccctctgacgtggggttgctttttctcccaacgctgtgcattgggctgaattaacatgccctttcagggctttttctcaaattgtcaatggttatttagttttcagcgatcagtaacaaacaactcaacaattcaacaactcaacaattcgacaactcaacgcccgaagggcatcactcttcacttttcacttttcgttcttcacttttcatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1172:TF1173|TF1172:TF1173:ABC transporter, permease component:ABC transporter, permease component:->->:1255274..1255583 310 attttttattttttagcagtcagcgttcagcattcagtaatcagcaaacaattcaataattcaacagttataccaatattaattcaggcttacagccctctgacgtggggttgctttttctcccaacgctgtgcattgggctgaattaacatgccctttcagggctttttctcaaattgtcaatggttatttagttttcagcgatcagtaacaaacaactcaacaattcaacaactcaacaattcgacaactcaacgcccgaagggcatcactcttcacttttcacttttcgttcttcacttttcatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1172:TF1173|TF1172:TF1173:ABC transporter, permease component:ABC transporter, permease component:->->:1255274..1255583 310 attttttattttttagcagtcagcgttcagcattcagtaatcagcaaacaattcaataattcaacagttataccaatattaattcaggcttacagccctctgacgtggggttgctttttctcccaacgctgtgcattgggctgaattaacatgccctttcagggctttttctcaaattgtcaatggttatttagttttcagcgatcagtaacaaacaactcaacaattcaacaactcaacaattcgacaactcaacgcccgaagggcatcactcttcacttttcacttttcgttcttcacttttcatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attttttattttttagcagtcagcgttcagcattcagtaatcagcaaacaattcaataattcaacagttataccaatattaattcaggcttacagccctctgacgtggggttgctttttctcccaacgctgtgcattgggctgaattaacatgccctttcagggctttttctcaaattgtcaatggttatttagttttcagcgatcagtaacaaacaactcaacaattcaacaactcaacaattcgacaactcaacgcccgaagggcatcactcttcacttttcacttttcgttcttcacttttcatcta Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 1 End: 141 M F Y F L A V S V Q H S V I S K Q F N N S T V I P I L I Q A Y S P L T W G C F F S Q R C A L G ......................................................................................................................................................................... Protein_Len: 35 Strand: + Start: 204 End: 308 ........................................................................................................................................................................................................... M S N K Q L N N S T T Q Q F D N S T P E G H H S S L F T F R S S L F I .. Protein_Len: 55 Strand: + Start: 145 End: 309 ................................................................................................................................................ M N M P F Q G F F S N C Q W L F S F Q R S V T N N S T I Q Q L N N S T T Q R P K G I T L H F S L F V L H F S S . attttttattttttagcagtcagcgttcagcattcagtaatcagcaaacaattcaataattcaacagttataccaatattaattcaggcttacagccctctgacgtggggttgctttttctcccaacgctgtgcattgggctgaattaacatgccctttcagggctttttctcaaattgtcaatggttatttagttttcagcgatcagtaacaaacaactcaacaattcaacaactcaacaattcgacaactcaacgcccgaagggcatcactcttcacttttcacttttcgttcttcacttttcatcta 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================================================ attttttattttttagcagtcagcgttcagcattcagtaatcagcaaacaattcaataattcaacagttataccaatattaattcaggcttacagccctctgacgtggggttgctttttctcccaacgctgtgcattgggctgaattaacatgccctttcagggctttttctcaaattgtcaatggttatttagttttcagcgatcagtaacaaacaactcaacaattcaacaactcaacaattcgacaactcaacgcccgaagggcatcactcttcacttttcacttttcgttcttcacttttcatcta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -2.5 Tail_Score: -3.49419 Start: 93 End: 113 Full_Region: ATTAATTCAGGCTTA CAGCCCT CTGACGT GGGGTTG CTTTTTCTCCCAACG ............................................................................................CAGCCCTCTGACGTGGGGTTG..................................................................................................................................................................................................... TransTerm Strand: + Conf: 91 HP_score: -9.1 Tail_Score: -4.88388 Start: 153 End: 165 Full_Region: GGGCTGAATTAACAT GCCCT TTC AGGGC TTTTTCTCAAATTGT ........................................................................................................................................................GCCCTTTCAGGGC................................................................................................................................................. TransTerm Strand: + Conf: 47 HP_score: -4.4 Tail_Score: -2.54204 Start: 261 End: 277 Full_Region: GACAACTCAACGCCC GAAGGG CATCA CTCTTC ACTTTTCACTTTTCG ....................................................................................................................................................................................................................................................................GAAGGGCATCACTCTTC................................. Find igs database================================================ Query_seq: TF1172:TF1173|TF1172:TF1173:ABC transporter, permease component:ABC transporter, permease component:->->:1255274..1255583 310 attttttattttttagcagtcagcgttcagcattcagtaatcagcaaacaattcaataattcaacagttataccaatattaattcaggcttacagccctctgacgtggggttgctttttctcccaacgctgtgcattgggctgaattaacatgccctttcagggctttttctcaaattgtcaatggttatttagttttcagcgatcagtaacaaacaactcaacaattcaacaactcaacaattcgacaactcaacgcccgaagggcatcactcttcacttttcacttttcgttcttcacttttcatcta Intra-Species Hit: Count: 2 Min: 15 Max: 310 Len: 296 Subject: tfor_TF1172_TF1173|ABC transporter, permease component:ABC transporter, permease component|POSITIVE:POSITIVE|[1255274,1255583]|310 HSP 1 e-value: 1.0E-106 bit: 387.0 Len: 195 Query Start:15 Query End:209 Subject Strand: POSITIVE Subject Start: 15 Subject End: 209 ..............agcagtcagcgttcagcattcagtaatcagcaaacaattcaataattcaacagttataccaatattaattcaggcttacagccctctgacgtggggttgctttttctcccaacgctgtgcattgggctgaattaacatgccctttcagggctttttctcaaattgtcaatggttatttagttttcagcgatcagt..................................................................................................... ..............agcagtcagcgttcagcattcagtaatcagcaaacaattcaataattcaacagttataccaatattaattcaggcttacagccctctgacgtggggttgctttttctcccaacgctgtgcattgggctgaattaacatgccctttcagggctttttctcaaattgtcaatggttatttagttttcagcgatcagt..................................................................................................... HSP 2 e-value: 2.0E-22 bit: 107.0 Len: 54 Query Start:257 Query End:310 Subject Strand: POSITIVE Subject Start: 257 Subject End: 310 ................................................................................................................................................................................................................................................................gcccgaagggcatcactcttcacttttcacttttcgttcttcacttttcatcta ................................................................................................................................................................................................................................................................gcccgaagggcatcactcttcacttttcacttttcgttcttcacttttcatcta Subject: tfor_TF1174_TF1175|ABC transporter, permease component:membrane-fusion protein|POSITIVE:POSITIVE|[1257957,1258279]|323 HSP 1 e-value: 1.0E-48 bit: 194.0 Len: 153 Query Start:47 Query End:199 Subject Strand: POSITIVE Subject Start: 106 Subject End: 259 ..............................................aacaattcaataattcaacagttataccaatattaattcaggcttacagccctctgacgtggggttgctttt-tctcccaacgctgtgcattgggctgaattaacatgccctttcagggctttttctcaaattgtcaatggttatttagttttc............................................................................................................... ..............................................aacaaatcaacagttcaacaattacaccaacattaattcaggcttacagccctccgatgtggggttgcttttttctcccaacgctgcgcattgggctgaattaacgcgccctttcagggctttttcccaaattgtcaatggttatttagttttc............................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCAGUCAGCGUUCAGCAUUCAGUAAUCAGCAAACAAUUCAAUAAUUCAACAGUUAUACCAAUAUUAAUUCAGGCUUACAGCCCUCUGACGUGGGGUUGCUUUUUCUCCCAACGCUGUGCAUUGGGCUGAAUUAACAUGCCCUUUCAGGGCUUUUUCUCAAAUUGUCAAUGGUUAUUUAGUUUUCAGCGAUCAGUAACAAACAACUCAACAAUUCAACAACUCAACAAUUCGACAACUCAACGCCCGAAGGGCAUCACUCUUCACUUUUCACUUUUCGUUCUUCACUUUUCAUCUA (((.....(((((.((.....((((((((....((((((..(((((......))))).......(((((((((.....(((((((.......)))))))........(((((.((...)).))))))))))))))...((((.....)))).........))))))...))))))))..((((...((.....))...))))..................................)).)))))..((((((.....))))))..............)))................ (-54.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAUGAAAAGUGAAGAACGAAAAGUGAAAAGUGAAGAGUGAUGCCCUUCGGGCGUUGAGUUGUCGAAUUGUUGAGUUGUUGAAUUGUUGAGUUGUUUGUUACUGAUCGCUGAAAACUAAAUAACCAUUGACAAUUUGAGAAAAAGCCCUGAAAGGGCAUGUUAAUUCAGCCCAAUGCACAGCGUUGGGAGAAAAAGCAACCCCACGUCAGAGGGCUGUAAGCCUGAAUUAAUAUUGGUAUAACUGUUGAAUUAUUGAAUUGUUUGCUGAUUACUGAAUGCUGAACGCUGACUGCU .........((((.((.......(((((..((..((.(((..(((((((((((.(((...((.(((((((((..(((((((......((.(((.(((.......))).))).)).....))))))..)..))))))))).))..))))))).)))))))(((((((((((((((((((...)))))))).......(((.((((......).))).)))....)))))))))))........................))).))..))..))))).....))...))))....... (-82.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 747 150 101 188 139 tfor:TF2824|5end_nucleoside-transporting_protein_nupG_3014701..3014931_POSITIVE 726 130 81 197 143 tfor:TF2478|5end_hypothetical_protein_2655375..2655605_POSITIVE 726 150 101 197 149 tfor:TF0828|5end_hypothetical_protein_887090..887320_POSITIVE 704 130 81 94 44 tfor:TF2191|5end_hypothetical_protein_2365934..2366164_POSITIVE 704 130 81 229 179 tfor:TF0823|5end_conserved_hypothetical_protein_880660..880890_POSITIVE 704 130 81 56 6 tfor:TF0822|5end_hypothetical_protein_880487..880717_POSITIVE 703 150 101 187 139 tfor:TF1183|5end_hypothetical_protein_1268391..1268621_POSITIVE 700 120 71 73 23 tfor:TF0679|5end_hypothetical_protein_721155..721385_POSITIVE 689 150 101 191 143 tfor:TF1186|5end_hypothetical_protein_1269568..1269798_POSITIVE 666 150 107 76 33 tfor:TF0821|5end_hypothetical_protein_879879..880109_POSITIVE 634 130 81 199 150 tfor:TF2036|5end_possible_pyruvate_formate-lyase_activating_enzyme_2196302..2196532_POSITIVE 628 150 107 214 170 tfor:TF1184|5end_hypothetical_protein_1269004..1269234_POSITIVE 625 120 71 69 17 tfor:TF1716|5end_hypothetical_protein_1837442..1837672_POSITIVE 587 155 113 179 137 tfor:TF2517|5end_hypothetical_protein_2695089..2695319_POSITIVE 566 130 81 228 177 tfor:TF1187|5end_hypothetical_protein_1269625..1269855_POSITIVE 565 157 113 71 25 tfor:TF0678|5end_hypothetical_protein_721103..721333_POSITIVE 564 150 103 121 65 tfor:TF0538|5end_hypothetical_protein_566891..567121_POSITIVE 564 150 103 114 58 tfor:TF0539|5end_hypothetical_protein_566884..567114_POSITIVE 562 120 71 65 14 tfor:TF3107|5end_hypothetical_protein_3338459..3338689_POSITIVE 560 242 201 221 180 tfor:TF1658|5end_glycosyltranferase_1773539..1773769_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 765 280 231 78 22 tfor:TF1657|3end_lauroyl/myristoyl_acyltransferase_1773407..1773557_POSITIVE 689 150 101 106 58 tfor:TF1185|3end_hypothetical_protein_1269563..1269713_POSITIVE 681 269 221 72 25 tfor:TF1715|3end_thermolysin;_zinc_metalloprotease_1837202..1837352_POSITIVE 666 150 107 59 16 tfor:TF0820|3end_hypothetical_protein_879942..880092_POSITIVE 629 150 101 80 25 tfor:TF2840|3end_hypothetical_protein_3031289..3031439_POSITIVE 628 150 107 68 24 tfor:TF1182|3end_hypothetical_protein_1268938..1269088_POSITIVE 569 120 71 114 63 tfor:TF2547|3end_hypothetical_protein_2730947..2731097_POSITIVE 562 120 71 134 83 tfor:TF3106|3end_hypothetical_protein_3338608..3338758_POSITIVE 507 290 255 50 15 tfor:TF1781|3end_imidazolonepropionase_1923384..1923534_POSITIVE 471 120 71 141 89 tfor:TF1405|3end_conserved_hypothetical_protein_1481819..1481969_POSITIVE 469 270 226 53 7 tfor:TF1204|3end_possible_metal-dependent_membrane_protease_1287461..1287611_POSITIVE 455 155 113 56 9 tfor:TF0533|3end_hypothetical_protein_559519..559669_POSITIVE 449 110 65 135 83 tfor:TF1274|3end_hypothetical_protein_1357895..1358045_POSITIVE 441 176 140 43 1 tfor:TF1848|3end_conserved_hypothetical_protein_1997944..1998094_POSITIVE 440 255 216 75 35 tfor:TF2839|3end_ATP-dependent_exodeoxyribonuclease_3031035..3031185_POSITIVE 439 277 231 110 64 tfor:TF1816|3end_hypothetical_protein_1957974..1958124_POSITIVE 439 277 231 127 81 tfor:TF1817|3end_hypothetical_protein_1957991..1958141_POSITIVE 428 290 255 67 25 tfor:TF1843|3end_surface_antigen_BspA_1996189..1996339_POSITIVE 418 110 70 128 80 tfor:TF2816|3end_hypothetical_protein_3007184..3007334_POSITIVE 409 120 73 132 69 tfor:TF2848|3end_cobalamin_biosynthesis_protein_3037389..3037539_POSITIVE