Origin IGS: taaggtattataggttttgggtgttaggcattgggttgtaggggcgaactcttgtggtcgcccaatagaaacagggtacgtaggggcgtatcaacatacgcccaagatatacagaataacgaatataaaaagaacaagcattatgagtattacaaattttattaacagtgaggcaagtaccatcgtacaaggtgtgaatggtatacgcttgtgtcaagaatcgtggatgatcgaaagatccattaaacagacagaacgtcgcaaacctgccgtgcagtcaggagggaagcgtacagcaaagaatagagcgtgttacttataaagacagagcggtgcatag .........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 ctatgcaccgctctgtctttataagtaacacgctctattctttgctgtacgcttccctcctgactgcacggcaggtttgcgacgttctgtctgtttaatggatctttcgatcatccacgattcttgacacaagcgtataccattcacaccttgtacgatggtacttgcctcactgttaataaaatttgtaatactcataatgcttgttctttttatattcgttattctgtatatcttgggcgtatgttgatacgcccctacgtaccctgtttctattgggcgaccacaagagttcgcccctacaacccaatgcctaacacccaaaacctataatacctta Mask Tandem Repeat Region ================================================ taaggtattataggttttgggtgttaggcattgggttgtaggggcgaactcttgtggtcgcccaatagaaacagggtacgtaggggcgtatcaacatacgcccaagatatacagaataacgaatataaaaagaacaagcattatgagtattacaaattttattaacagtgaggcaagtaccatcgtacaaggtgtgaatggtatacgcttgtgtcaagaatcgtggatgatcgaaagatccattaaacagacagaacgtcgcaaacctgccgtgcagtcaggagggaagcgtacagcaaagaatagagcgtgttacttataaagacagagcggtgcatag Find is-nt database================================================ Query_seq: TF2615:TF2616|TF2615:TF2616:conserved hypothetical protein:outer membrane protein, TonB dependent receptor:->->:2791270..2791609 340 taaggtattataggttttgggtgttaggcattgggttgtaggggcgaactcttgtggtcgcccaatagaaacagggtacgtaggggcgtatcaacatacgcccaagatatacagaataacgaatataaaaagaacaagcattatgagtattacaaattttattaacagtgaggcaagtaccatcgtacaaggtgtgaatggtatacgcttgtgtcaagaatcgtggatgatcgaaagatccattaaacagacagaacgtcgcaaacctgccgtgcagtcaggagggaagcgtacagcaaagaatagagcgtgttacttataaagacagagcggtgcatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2615:TF2616|TF2615:TF2616:conserved hypothetical protein:outer membrane protein, TonB dependent receptor:->->:2791270..2791609 340 taaggtattataggttttgggtgttaggcattgggttgtaggggcgaactcttgtggtcgcccaatagaaacagggtacgtaggggcgtatcaacatacgcccaagatatacagaataacgaatataaaaagaacaagcattatgagtattacaaattttattaacagtgaggcaagtaccatcgtacaaggtgtgaatggtatacgcttgtgtcaagaatcgtggatgatcgaaagatccattaaacagacagaacgtcgcaaacctgccgtgcagtcaggagggaagcgtacagcaaagaatagagcgtgttacttataaagacagagcggtgcatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2615:TF2616|TF2615:TF2616:conserved hypothetical protein:outer membrane protein, TonB dependent receptor:->->:2791270..2791609 340 taaggtattataggttttgggtgttaggcattgggttgtaggggcgaactcttgtggtcgcccaatagaaacagggtacgtaggggcgtatcaacatacgcccaagatatacagaataacgaatataaaaagaacaagcattatgagtattacaaattttattaacagtgaggcaagtaccatcgtacaaggtgtgaatggtatacgcttgtgtcaagaatcgtggatgatcgaaagatccattaaacagacagaacgtcgcaaacctgccgtgcagtcaggagggaagcgtacagcaaagaatagagcgtgttacttataaagacagagcggtgcatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaggtattataggttttgggtgttaggcattgggttgtaggggcgaactcttgtggtcgcccaatagaaacagggtacgtaggggcgtatcaacatacgcccaagatatacagaataacgaatataaaaagaacaagcattatgagtattacaaattttattaacagtgaggcaagtaccatcgtacaaggtgtgaatggtatacgcttgtgtcaagaatcgtggatgatcgaaagatccattaaacagacagaacgtcgcaaacctgccgtgcagtcaggagggaagcgtacagcaaagaatagagcgtgttacttataaagacagagcggtgcatag Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 31 End: 162 .............................. M G C R G E L L W S P N R N R V R R G V S T Y A Q D I Q N N E Y K K N K H Y E Y Y K F Y .................................................................................................................................................................................. Protein_Len: 60 Strand: + Start: 17 End: 319 ................ M G V R H W V V G A N S C G R P I E T G Y V G A Y Q H T P K I Y R I T N I K R T S I M S I T N F I N S E A S T I V Q G V ..................... Protein_Len: 31 Strand: - Start: 246 End: 338 ..................................................................................................................................................................................................................................................... V S L V D C V Q R A T L L S A Y L L S Y L T N S I F V S R H M .. Protein_Len: 37 Strand: - Start: 94 End: 204 ............................................................................................. C V G L I Y L I V F I F L V L M I L I V F K I L L S A L V M T C P T F P M ........................................................................................................................................ Protein_Len: 37 Strand: - Start: 27 End: 137 .......................... A N P Q L P S S K H D G L L F L T R L P T D V Y A W S I C F L S Y L F F M ........................................................................................................................................................................................................... Protein_Len: 60 Strand: - Start: 11 End: 277 .......... R G L Y V S Y R I Y F S C A N H T N C I K N V T L C T G D Y L T H I T Y A Q T L F R P H D F S G N F L C F T A F R G H M ............................................................... taaggtattataggttttgggtgttaggcattgggttgtaggggcgaactcttgtggtcgcccaatagaaacagggtacgtaggggcgtatcaacatacgcccaagatatacagaataacgaatataaaaagaacaagcattatgagtattacaaattttattaacagtgaggcaagtaccatcgtacaaggtgtgaatggtatacgcttgtgtcaagaatcgtggatgatcgaaagatccattaaacagacagaacgtcgcaaacctgccgtgcagtcaggagggaagcgtacagcaaagaatagagcgtgttacttataaagacagagcggtgcatag 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================================================ taaggtattataggttttgggtgttaggcattgggttgtaggggcgaactcttgtggtcgcccaatagaaacagggtacgtaggggcgtatcaacatacgcccaagatatacagaataacgaatataaaaagaacaagcattatgagtattacaaattttattaacagtgaggcaagtaccatcgtacaaggtgtgaatggtatacgcttgtgtcaagaatcgtggatgatcgaaagatccattaaacagacagaacgtcgcaaacctgccgtgcagtcaggagggaagcgtacagcaaagaatagagcgtgttacttataaagacagagcggtgcatag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2615:TF2616|TF2615:TF2616:conserved hypothetical protein:outer membrane protein, TonB dependent receptor:->->:2791270..2791609 340 taaggtattataggttttgggtgttaggcattgggttgtaggggcgaactcttgtggtcgcccaatagaaacagggtacgtaggggcgtatcaacatacgcccaagatatacagaataacgaatataaaaagaacaagcattatgagtattacaaattttattaacagtgaggcaagtaccatcgtacaaggtgtgaatggtatacgcttgtgtcaagaatcgtggatgatcgaaagatccattaaacagacagaacgtcgcaaacctgccgtgcagtcaggagggaagcgtacagcaaagaatagagcgtgttacttataaagacagagcggtgcatag Intra-Species Hit: Count: 1 Min: 1 Max: 340 Len: 340 Subject: tfor_TF2615_TF2616|conserved hypothetical protein:outer membrane protein, TonB dependent receptor|POSITIVE:POSITIVE|[2791270,2791609]|340 HSP 1 e-value: 0.0 bit: 674.0 Len: 340 Query Start:1 Query End:340 Subject Strand: POSITIVE Subject Start: 1 Subject End: 340 taaggtattataggttttgggtgttaggcattgggttgtaggggcgaactcttgtggtcgcccaatagaaacagggtacgtaggggcgtatcaacatacgcccaagatatacagaataacgaatataaaaagaacaagcattatgagtattacaaattttattaacagtgaggcaagtaccatcgtacaaggtgtgaatggtatacgcttgtgtcaagaatcgtggatgatcgaaagatccattaaacagacagaacgtcgcaaacctgccgtgcagtcaggagggaagcgtacagcaaagaatagagcgtgttacttataaagacagagcggtgcatag taaggtattataggttttgggtgttaggcattgggttgtaggggcgaactcttgtggtcgcccaatagaaacagggtacgtaggggcgtatcaacatacgcccaagatatacagaataacgaatataaaaagaacaagcattatgagtattacaaattttattaacagtgaggcaagtaccatcgtacaaggtgtgaatggtatacgcttgtgtcaagaatcgtggatgatcgaaagatccattaaacagacagaacgtcgcaaacctgccgtgcagtcaggagggaagcgtacagcaaagaatagagcgtgttacttataaagacagagcggtgcatag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGUAUUAUAGGUUUUGGGUGUUAGGCAUUGGGUUGUAGGGGCGAACUCUUGUGGUCGCCCAAUAGAAACAGGGUACGUAGGGGCGUAUCAACAUACGCCCAAGAUAUACAGAAUAACGAAUAUAAAAAGAACAAGCAUUAUGAGUAUUACAAAUUUUAUUAACAGUGAGGCAAGUACCAUCGUACAAGGUGUGAAUGGUAUACGCUUGUGUCAAGAAUCGUGGAUGAUCGAAAGAUCCAUUAAACAGACAGAACGUCGCAAACCUGCCGUGCAGUCAGGAGGGAAGCGUACAGCAAAGAAUAGAGCGUGUUACUUAUAAAGACAGAGCGGUGCAUAG ....(((((....((((((..(((((..(.(((..((....((((((.(......).))))))....))..))).(((..(..((((((((....))))))))...)..))).)..)))))...................(((((((((..(((..(((((((.........((..(((((((..(((.....))).)))))))((((((.(.((.......((.(((((((....))).))))..)).(((...(((..(((....))))))...)))..)).).))))))...))....)))))))..))))))))))))...))))))))))).... (-88.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAUGCACCGCUCUGUCUUUAUAAGUAACACGCUCUAUUCUUUGCUGUACGCUUCCCUCCUGACUGCACGGCAGGUUUGCGACGUUCUGUCUGUUUAAUGGAUCUUUCGAUCAUCCACGAUUCUUGACACAAGCGUAUACCAUUCACACCUUGUACGAUGGUACUUGCCUCACUGUUAAUAAAAUUUGUAAUACUCAUAAUGCUUGUUCUUUUUAUAUUCGUUAUUCUGUAUAUCUUGGGCGUAUGUUGAUACGCCCCUACGUACCCUGUUUCUAUUGGGCGACCACAAGAGUUCGCCCCUACAACCCAAUGCCUAACACCCAAAACCUAUAAUACCUUA .........((...(((.....((((.(((.((..........)))))..)))).......))).))..(((((((.((((.(....((((.(..(..(((((.........)))))..)..)..))))...))))).))).........(((((....(((((..........................((((..((((((..(((.......)))..))))))...)))).....((((((((....))))))))....)))))...........((((((.(......).)))))).))))).....)))).......................... (-66.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 440 233 191 91 36 tfor:TF1935|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH-related_helicase_2082002..2082232_POSITIVE 435 62 21 231 192 tfor:TF0471|5end_conserved_hypothetical_protein_487516..487746_POSITIVE 428 63 37 157 132 tfor:TF2998|5end_surface_antigen_BspA_3211811..3212041_POSITIVE 428 63 37 226 201 tfor:TF2994|5end_hypothetical_protein_3210605..3210835_POSITIVE 408 297 255 187 131 tfor:TF1669|5end_ATP_synthase,_gamma_subunit_1783566..1783796_POSITIVE 399 90 41 71 18 tfor:TF2246|5end_hypothetical_protein_2421288..2421518_POSITIVE 398 63 26 139 102 tfor:TF1580|5end_conserved_hypothetical_protein;_possible_fibronectin_domain_containing_protein_1687187..1687417_POSITIVE 396 63 26 224 188 tfor:TF1169|5end_lipoprotein_ABC_transporter,_permease_component_1249136..1249366_POSITIVE 392 297 254 122 56 tfor:TF2997|5end_hypothetical_protein_3211408..3211638_POSITIVE 388 80 31 89 39 tfor:TF2456|5end_ABC_transporter,_ATP-binding_protein_2632376..2632606_POSITIVE 385 297 253 185 124 tfor:TF0776|5end_ABC_transporter,_permease_component_824855..825085_POSITIVE 382 298 252 128 75 tfor:TF1049|5end_cobyrinic_acid_a,c-diamide_synthase_1110140..1110370_POSITIVE 379 311 271 145 115 tfor:TF2382|5end_transposase_2546867..2547097_POSITIVE 379 63 27 93 58 tfor:TF2172|5end_hypothetical_protein_2345822..2346052_POSITIVE 379 63 27 87 52 tfor:TF2173|5end_hypothetical_protein_2345816..2346046_POSITIVE 379 63 27 87 52 tfor:TF2171|5end_hypothetical_protein_2345485..2345715_POSITIVE 379 63 27 87 52 tfor:TF2166|5end_hypothetical_protein_2342115..2342345_POSITIVE 379 63 27 87 52 tfor:TF0366|5end_hypothetical_protein_383564..383794_POSITIVE 379 63 27 87 52 tfor:TF0362|5end_hypothetical_protein_379952..380182_POSITIVE 379 63 27 87 52 tfor:TF0346|5end_hypothetical_protein_367048..367278_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 413 89 41 70 19 tfor:TF1167|3end_hypothetical_protein_1248932..1249082_POSITIVE 398 63 26 146 109 tfor:TF1579|3end_hypothetical_protein_1687274..1687424_POSITIVE 396 63 26 100 64 tfor:TF1168|3end_hypothetical_protein_1249092..1249242_POSITIVE 389 60 17 151 104 tfor:TF0470|3end_hypothetical_protein_487518..487668_POSITIVE 388 80 31 70 20 tfor:TF2455|3end_conserved_hypothetical_protein;_possible_membrane_protein_2632437..2632587_POSITIVE 386 290 255 148 100 tfor:TF1668|3end_possible_glycosylhydrolase_1783615..1783765_POSITIVE 382 298 252 125 72 tfor:TF1048|3end_permease_1110217..1110367_POSITIVE 379 89 42 145 106 tfor:TF2651|3end_hypothetical_protein_2822014..2822164_POSITIVE 379 311 271 85 55 tfor:TF1933|3end_methionyl-tRNA_synthetase_2081884..2082034_POSITIVE 367 60 12 97 28 tfor:TF1716|3end_hypothetical_protein_1837710..1837860_POSITIVE 362 92 57 147 107 tfor:TF1299|3end_conserved_hypothetical_protein_1382435..1382585_POSITIVE 358 90 49 76 25 tfor:TF2659|3end_conserved_hypothetical_protein_2833055..2833205_POSITIVE 356 291 253 57 13 tfor:TF1822|3end_outer_membrane_lipoprotein_silC_precursor_1969193..1969343_POSITIVE 355 89 42 80 23 tfor:TF1788|3end_conserved_hypothetical_protein_1930119..1930269_POSITIVE 352 52 20 60 19 tfor:TF2832|3end_possible_proton/sodium:glutamate_symporter_protein_3023939..3024089_POSITIVE 347 50 3 69 21 tfor:TF2808|3end_bacterial_sugar_transferase_2999909..3000059_POSITIVE 344 63 23 110 59 tfor:TF2346|3end_hypothetical_protein_2509973..2510123_POSITIVE 343 87 41 83 28 tfor:TF1397|3end_glucosyltransferase_1471534..1471684_POSITIVE 343 60 13 79 40 tfor:TF0549|3end_universal_stress_protein,_UspA_582658..582808_POSITIVE 342 54 20 151 107 tfor:TF2746|3end_hypothetical_protein_2928246..2928396_POSITIVE