Origin IGS: agtattctccagttgaccagctgacagtttaaattgtttacaatactttcttttgtgcttaatgtggaatctgggataaaatatcctggcacaagaaacttataatttgaagatgataggcgtcttcgtctttataaaacgaagaaaaaatggtacgacatacaacggattgtaaaacatgttatataacatgtaaaaaaacaacaaaaatacttgccgctttgcttaaagcattatactttcgccatctctaaaagggagtaaataagcttttttaaagaaataaaaatatataaatgtccgtatatatgcctaaaattaattatatattgctgatatacagaaatttattccctccccaatccatacatccaaattattgttattaaatagtttaatggagcttttaggtacaaacacggatatttatttaaaaataataatgaatatccgtatat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atatacggatattcattattatttttaaataaatatccgtgtttgtacctaaaagctccattaaactatttaataacaataatttggatgtatggattggggagggaataaatttctgtatatcagcaatatataattaattttaggcatatatacggacatttatatatttttatttctttaaaaaagcttatttactcccttttagagatggcgaaagtataatgctttaagcaaagcggcaagtatttttgttgtttttttacatgttatataacatgttttacaatccgttgtatgtcgtaccattttttcttcgttttataaagacgaagacgcctatcatcttcaaattataagtttcttgtgccaggatattttatcccagattccacattaagcacaaaagaaagtattgtaaacaatttaaactgtcagctggtcaactggagaatact Mask Tandem Repeat Region ================================================ agtattctccagttgaccagctgacagtttaaattgtttacaatactttcttttgtgcttaatgtggaatctgggataaaatatcctggcacaagaaacttataatttgaagatgataggcgtcttcgtctttataaaacgaagaaaaaatggtacgacatacaacggattgtaaaacatgttatataacatgtaaaaaaacaacaaaaatacttgccgctttgcttaaagcattatactttcgccatctctaaaagggagtaaataagcttttttaaagaaataaaaatatataaatgtccgtatatatgcctaaaattaattatatattgctgatatacagaaatttattccctccccaatccatacatccaaattattgttattaaatagtttaatggagcttttaggtacaaacacggatatttatttaaaaataataatgaatatccgtatat Find is-nt database================================================ Query_seq: TF2478:TF2479|TF2478:TF2479:hypothetical protein:conserved hypothetical protein:->->:2655674..2656131 458 agtattctccagttgaccagctgacagtttaaattgtttacaatactttcttttgtgcttaatgtggaatctgggataaaatatcctggcacaagaaacttataatttgaagatgataggcgtcttcgtctttataaaacgaagaaaaaatggtacgacatacaacggattgtaaaacatgttatataacatgtaaaaaaacaacaaaaatacttgccgctttgcttaaagcattatactttcgccatctctaaaagggagtaaataagcttttttaaagaaataaaaatatataaatgtccgtatatatgcctaaaattaattatatattgctgatatacagaaatttattccctccccaatccatacatccaaattattgttattaaatagtttaatggagcttttaggtacaaacacggatatttatttaaaaataataatgaatatccgtatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2478:TF2479|TF2478:TF2479:hypothetical protein:conserved hypothetical protein:->->:2655674..2656131 458 agtattctccagttgaccagctgacagtttaaattgtttacaatactttcttttgtgcttaatgtggaatctgggataaaatatcctggcacaagaaacttataatttgaagatgataggcgtcttcgtctttataaaacgaagaaaaaatggtacgacatacaacggattgtaaaacatgttatataacatgtaaaaaaacaacaaaaatacttgccgctttgcttaaagcattatactttcgccatctctaaaagggagtaaataagcttttttaaagaaataaaaatatataaatgtccgtatatatgcctaaaattaattatatattgctgatatacagaaatttattccctccccaatccatacatccaaattattgttattaaatagtttaatggagcttttaggtacaaacacggatatttatttaaaaataataatgaatatccgtatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2478:TF2479|TF2478:TF2479:hypothetical protein:conserved hypothetical protein:->->:2655674..2656131 458 agtattctccagttgaccagctgacagtttaaattgtttacaatactttcttttgtgcttaatgtggaatctgggataaaatatcctggcacaagaaacttataatttgaagatgataggcgtcttcgtctttataaaacgaagaaaaaatggtacgacatacaacggattgtaaaacatgttatataacatgtaaaaaaacaacaaaaatacttgccgctttgcttaaagcattatactttcgccatctctaaaagggagtaaataagcttttttaaagaaataaaaatatataaatgtccgtatatatgcctaaaattaattatatattgctgatatacagaaatttattccctccccaatccatacatccaaattattgttattaaatagtttaatggagcttttaggtacaaacacggatatttatttaaaaataataatgaatatccgtatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtattctccagttgaccagctgacagtttaaattgtttacaatactttcttttgtgcttaatgtggaatctgggataaaatatcctggcacaagaaacttataatttgaagatgataggcgtcttcgtctttataaaacgaagaaaaaatggtacgacatacaacggattgtaaaacatgttatataacatgtaaaaaaacaacaaaaatacttgccgctttgcttaaagcattatactttcgccatctctaaaagggagtaaataagcttttttaaagaaataaaaatatataaatgtccgtatatatgcctaaaattaattatatattgctgatatacagaaatttattccctccccaatccatacatccaaattattgttattaaatagtttaatggagcttttaggtacaaacacggatatttatttaaaaataataatgaatatccgtatat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 83 End: 172 .................................................................................. M L A Q E T Y N L K M I G V F V F I K R R K N G T T Y N G L .............................................................................................................................................................................................................................................................................................. Protein_Len: 34 Strand: + Start: 150 End: 251 ..................................................................................................................................................... M V R H T T D C K T C Y I T C K K T T K I L A A L L K A L Y F R H L ............................................................................................................................................................................................................... Protein_Len: 30 Strand: + Start: 297 End: 386 ........................................................................................................................................................................................................................................................................................................ M S V Y M P K I N Y I L L I Y R N L F P P Q S I H P N Y C Y ........................................................................ Protein_Len: 43 Strand: + Start: 329 End: 457 ........................................................................................................................................................................................................................................................................................................................................ M A D I Q K F I P S P I H T S K L L L L N S L M E L L G T N T D I Y L K I I M N I R I . Protein_Len: 36 Strand: - Start: 351 End: 458 .............................................................................................................................................................................................................................................................................................................................................................. E R G L G Y M W I I T I L Y N L P A K L Y L C P Y K N L F L L S Y G Y M Protein_Len: 35 Strand: - Start: 322 End: 426 ................................................................................................................................................................................................................................................................................................................................. N Y I A S I C F N I G E G I W V D L N N N N F L K I S S K P V F V S M ................................ Protein_Len: 37 Strand: - Start: 237 End: 347 ............................................................................................................................................................................................................................................ V K A M E L L S Y I L K K L S I F I Y L H G Y I H R F N I I Y Q Q Y V S M ............................................................................................................... Protein_Len: 35 Strand: - Start: 103 End: 207 ...................................................................................................... L K F I I P T K T K I F R L F F P V V Y L P N Y F M N Y L M Y F F L M ........................................................................................................................................................................................................................................................... Protein_Len: 30 Strand: - Start: 62 End: 151 ............................................................. H P I Q S L I D Q C L F S I I Q L H Y A D E D K Y F S S F M ................................................................................................................................................................................................................................................................................................................... Protein_Len: 30 Strand: - Start: 3 End: 92 .. I R W N V L Q C N L N N V I S E K T S L T S D P I F Y G P M .............................................................................................................................................................................................................................................................................................................................................................................. agtattctccagttgaccagctgacagtttaaattgtttacaatactttcttttgtgcttaatgtggaatctgggataaaatatcctggcacaagaaacttataatttgaagatgataggcgtcttcgtctttataaaacgaagaaaaaatggtacgacatacaacggattgtaaaacatgttatataacatgtaaaaaaacaacaaaaatacttgccgctttgcttaaagcattatactttcgccatctctaaaagggagtaaataagcttttttaaagaaataaaaatatataaatgtccgtatatatgcctaaaattaattatatattgctgatatacagaaatttattccctccccaatccatacatccaaattattgttattaaatagtttaatggagcttttaggtacaaacacggatatttatttaaaaataataatgaatatccgtatat Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 169 End: 198 ........................................................................................................................................................................TTTTACATGTTATATAACATGTTTTACAAT.................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtattctccagttgaccagctgacagtttaaattgtttacaatactttcttttgtgcttaatgtggaatctgggataaaatatcctggcacaagaaacttataatttgaagatgataggcgtcttcgtctttataaaacgaagaaaaaatggtacgacatacaacggattgtaaaacatgttatataacatgtaaaaaaacaacaaaaatacttgccgctttgcttaaagcattatactttcgccatctctaaaagggagtaaataagcttttttaaagaaataaaaatatataaatgtccgtatatatgcctaaaattaattatatattgctgatatacagaaatttattccctccccaatccatacatccaaattattgttattaaatagtttaatggagcttttaggtacaaacacggatatttatttaaaaataataatgaatatccgtatat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 52 HP_score: -4.0 Tail_Score: -3.51934 Start: 108 End: 128 Full_Region: AAGAAACTTATAATT TGAAGATG ATAGG CGTCTTCG TCTTTATAAAACGAA ...........................................................................................................TGAAGATGATAGGCGTCTTCG.......................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 51 HP_score: -5.3 Tail_Score: -2.70946 Start: 109 End: 127 Full_Region: AGAAACTTATAATTT GAAGATG ATAGG CGTCTTC GTCTTTATAAAACGA ............................................................................................................GAAGATGATAGGCGTCTTC........................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 70 HP_score: -6.2 Tail_Score: -4.15453 Start: 178 End: 193 Full_Region: tttgttgttttttta catgtt atat aacatg ttttacaatccgttg .................................................................................................................................................................................catgttatataacatg......................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: TF2478:TF2479|TF2478:TF2479:hypothetical protein:conserved hypothetical protein:->->:2655674..2656131 458 agtattctccagttgaccagctgacagtttaaattgtttacaatactttcttttgtgcttaatgtggaatctgggataaaatatcctggcacaagaaacttataatttgaagatgataggcgtcttcgtctttataaaacgaagaaaaaatggtacgacatacaacggattgtaaaacatgttatataacatgtaaaaaaacaacaaaaatacttgccgctttgcttaaagcattatactttcgccatctctaaaagggagtaaataagcttttttaaagaaataaaaatatataaatgtccgtatatatgcctaaaattaattatatattgctgatatacagaaatttattccctccccaatccatacatccaaattattgttattaaatagtttaatggagcttttaggtacaaacacggatatttatttaaaaataataatgaatatccgtatat Intra-Species Hit: Count: 1 Min: 1 Max: 458 Len: 458 Subject: tfor_TF2478_TF2479|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2655674,2656131]|458 HSP 1 e-value: 1.0E-141 bit: 504.0 Len: 275 Query Start:1 Query End:275 Subject Strand: POSITIVE Subject Start: 1 Subject End: 275 agtattctccagttgaccagctgacagtttaaattgtttacaatactttcttttgtgcttaatgtggaatctgggataaaatatcctggcacaagaaacttataatttgaagatgataggcgtcttcgtctttataaaacgaagaaaaaatggtacgacatacaacggattgtaaaacatgttatataacatgtnnnnnnncaacaaaaatacttgccgctttgcttaaagcattatactttcgccatctctaaaagggagtaaataagcttttt....................................................................................................................................................................................... agtattctccagttgaccagctgacagtttaaattgtttacaatactttcttttgtgcttaatgtggaatctgggataaaatatcctggcacaagaaacttataatttgaagatgataggcgtcttcgtctttataaaacgaagaaaaaatggtacgacatacaacggattgtaaaacatgttatataacatgtaaaaaaacaacaaaaatacttgccgctttgcttaaagcattatactttcgccatctctaaaagggagtaaataagcttttt....................................................................................................................................................................................... HSP 2 e-value: 2.0E-60 bit: 234.0 Len: 118 Query Start:341 Query End:458 Subject Strand: POSITIVE Subject Start: 341 Subject End: 458 ....................................................................................................................................................................................................................................................................................................................................................cagaaatttattccctccccaatccatacatccaaattattgttattaaatagtttaatggagcttttaggtacaaacacggatatttatttaaaaataataatgaatatccgtatat ....................................................................................................................................................................................................................................................................................................................................................cagaaatttattccctccccaatccatacatccaaattattgttattaaatagtttaatggagcttttaggtacaaacacggatatttatttaaaaataataatgaatatccgtatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAUUCUCCAGUUGACCAGCUGACAGUUUAAAUUGUUUACAAUACUUUCUUUUGUGCUUAAUGUGGAAUCUGGGAUAAAAUAUCCUGGCACAAGAAACUUAUAAUUUGAAGAUGAUAGGCGUCUUCGUCUUUAUAAAACGAAGAAAAAAUGGUACGACAUACAACGGAUUGUAAAACAUGUUAUAUAACAUGUAAAAAAACAACAAAAAUACUUGCCGCUUUGCUUAAAGCAUUAUACUUUCGCCAUCUCUAAAAGGGAGUAAAUAAGCUUUUUUAAAGAAAUAAAAAUAUAUAAAUGUCCGUAUAUAUGCCUAAAAUUAAUUAUAUAUUGCUGAUAUACAGAAAUUUAUUCCCUCCCCAAUCCAUACAUCCAAAUUAUUGUUAUUAAAUAGUUUAAUGGAGCUUUUAGGUACAAACACGGAUAUUUAUUUAAAAAUAAUAAUGAAUAUCCGUAUAU ((((((...(((((....)))))(((((....)))))....))))))....(((((((((((((((((...((((...........((((.((((....((((((((((.............(((((((.........)))))))....(((......)))....)))))))))).(((((((....)))))))..................))))..(((((....)))))...........))))........(((((((((((.....((((((......)))))).......(((((.(((((((((..((....))..)))))).))).)))))......))))))))))).)))).))))))..(((((((((((.......)))))))...))))....))))))))))).(((((((((((((..........))))))))))))).... (-99.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUACGGAUAUUCAUUAUUAUUUUUAAAUAAAUAUCCGUGUUUGUACCUAAAAGCUCCAUUAAACUAUUUAAUAACAAUAAUUUGGAUGUAUGGAUUGGGGAGGGAAUAAAUUUCUGUAUAUCAGCAAUAUAUAAUUAAUUUUAGGCAUAUAUACGGACAUUUAUAUAUUUUUAUUUCUUUAAAAAAGCUUAUUUACUCCCUUUUAGAGAUGGCGAAAGUAUAAUGCUUUAAGCAAAGCGGCAAGUAUUUUUGUUGUUUUUUUACAUGUUAUAUAACAUGUUUUACAAUCCGUUGUAUGUCGUACCAUUUUUUCUUCGUUUUAUAAAGACGAAGACGCCUAUCAUCUUCAAAUUAUAAGUUUCUUGUGCCAGGAUAUUUUAUCCCAGAUUCCACAUUAAGCACAAAAGAAAGUAUUGUAAACAAUUUAAACUGUCAGCUGGUCAACUGGAGAAUACU ..(((((((((((.(((..........))).))))))))))).............(((((....((((..........((((((((((((.((((...((((((...((((((.(((((((((..((......(((......))).))..))))))))).))))))...((((((......))))))..........))))))...(((((((((((..((((((((........(((((((((((....)))))))))))...(((((((....))))))).........)))))))).)))..))))))))(((((((((.....)))))))))...))))))))..))))))))..((((..((((...(((((...))))).......))))..))))......((.(((((((....))))....))).))...))))....)))))...... (-101.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 689 350 301 200 151 tfor:TF0901|5end_conserved_hypothetical_protein_946681..946911_POSITIVE 640 430 381 229 180 tfor:TF2176|5end_hypothetical_protein_2348911..2349141_POSITIVE 612 350 301 168 119 tfor:TF2967|5end_hypothetical_protein_3177765..3177995_POSITIVE 322 94 51 117 61 tfor:TF2954|5end_outer_membrane_protein,_TonB_dependent_receptor_3161238..3161468_POSITIVE 310 259 213 220 182 tfor:TF2276|5end_conserved_hypothetical_protein_2438226..2438456_POSITIVE 287 90 47 87 51 tfor:TF0820|5end_hypothetical_protein_879656..879886_POSITIVE 280 251 212 188 146 tfor:TF1845|5end_hypothetical_protein_1996620..1996850_POSITIVE 280 251 212 188 146 tfor:TF1185|5end_hypothetical_protein_1269238..1269468_POSITIVE 273 100 51 91 40 tfor:TF2048|5end_conserved_hypothetical_protein_2210643..2210873_POSITIVE 271 326 283 135 90 tfor:TF0199|5end_conserved_hypothetical_protein_222053..222283_POSITIVE 270 90 48 227 183 tfor:TF1844|5end_hypothetical_protein_1996389..1996619_POSITIVE 270 126 84 166 124 tfor:TF0999|5end_hypothetical_protein_1053028..1053258_POSITIVE 270 129 84 182 138 tfor:TF0777|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_826098..826328_POSITIVE 266 142 112 137 109 tfor:TF0002|5end_hypothetical_protein_316..546_POSITIVE 265 248 214 133 99 tfor:TF0284|5end_alanine_racemase_311988..312218_POSITIVE 263 160 120 213 176 tfor:TF0183|5end_conserved_hypothetical_protein_195954..196184_POSITIVE 261 79 34 173 127 tfor:TF0646|5end_conserved_hypothetical_protein;_possible_adenylate_cyclase_689059..689289_POSITIVE 260 373 333 112 69 tfor:TF2951|5end_O-succinylbenzoic_acid--CoA_ligase_3158496..3158726_POSITIVE 260 96 54 204 157 tfor:TF2300|5end_conserved_hypothetical_protein_2450621..2450851_POSITIVE 260 100 54 92 38 tfor:TF1880|5end_transposase_2032999..2033229_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 640 430 381 76 27 tfor:TF2966|3end_hypothetical_protein_3177672..3177822_POSITIVE 640 430 381 53 4 tfor:TF2175|3end_hypothetical_protein_2348815..2348965_POSITIVE 640 430 381 85 36 tfor:TF1890|3end_hypothetical_protein_2043093..2043243_POSITIVE 299 90 63 99 66 tfor:TF2092|3end_ribonuclease_III_2261823..2261973_POSITIVE 287 90 47 80 44 tfor:TF0819|3end_phosphoglycerate_mutase_879729..879879_POSITIVE 280 251 212 137 95 tfor:TF2745|3end_hypothetical_protein_2927947..2928097_POSITIVE 271 326 283 68 23 tfor:TF0198|3end_transposase_related_sequence_222066..222216_POSITIVE 265 248 214 139 105 tfor:TF0283|3end_possible_nicotinamide_mononucleotide_transporter_312074..312224_POSITIVE 263 246 212 149 113 tfor:TF1659|3end_hypothetical_protein_1775209..1775359_POSITIVE 263 246 212 149 113 tfor:TF0598|3end_hypothetical_protein_629500..629650_POSITIVE 260 373 333 85 42 tfor:TF2950|3end_chloromuconate_cycloisomerase_3158549..3158699_POSITIVE 260 100 54 59 5 tfor:TF1878|3end_ABC_transporter,_permease_component_2033046..2033196_POSITIVE 259 162 121 77 43 tfor:TF3109|3end_hypothetical_protein_3342803..3342953_POSITIVE 257 160 111 73 18 tfor:TF0432|3end_3-deoxy-manno-octulosonate_cytidylyltransferase_453366..453516_POSITIVE 256 244 205 142 104 tfor:TF2288|3end_hypothetical_protein_2442598..2442748_POSITIVE 254 333 296 114 78 tfor:TF3047|3end_transposase_3276336..3276486_POSITIVE 254 333 296 114 78 tfor:TF2303|3end_conserved_hypothetical_protein_2459303..2459453_POSITIVE 254 333 296 114 78 tfor:TF0941|3end_transposase_fragment_982313..982463_POSITIVE 252 99 51 81 31 tfor:TF1681|3end_dTDP-4-keto-L-rhamnose_reductase_1795844..1795994_POSITIVE 252 130 84 65 3 tfor:TF0629|3end_hypothetical_protein_666710..666860_POSITIVE