Origin IGS: tgaaaatcccgaaaaagattgggcaaaaatgcttgaaggagtaagagatgtgtcacctgatacgcaactatttgactaaaagatacttactttttgaaaaacatatccgcaaccaatagtatccttattttttgggggggaggtatgcgagttcttagtccgggagtggaatagctccgagactatcaacttttgattttcgagagatgtttgcctcaactttcccaacaaaaatcttacacaggacaggctatgcgtcattactgagcttatatcttgaatggtactccaaatagaaaccactgtatgtgaaaccatatgtacggtgatgtgagaggtcggaaaacgaacgtgaaaagaaaactgcttcgttttcctcctgcctaaccaataccatatttataaaaaaaacacaataaaataaaaaatcaaaaaaa .........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 tttttttgattttttattttattgtgttttttttataaatatggtattggttaggcaggaggaaaacgaagcagttttcttttcacgttcgttttccgacctctcacatcaccgtacatatggtttcacatacagtggtttctatttggagtaccattcaagatataagctcagtaatgacgcatagcctgtcctgtgtaagatttttgttgggaaagttgaggcaaacatctctcgaaaatcaaaagttgatagtctcggagctattccactcccggactaagaactcgcatacctcccccccaaaaaataaggatactattggttgcggatatgtttttcaaaaagtaagtatcttttagtcaaatagttgcgtatcaggtgacacatctcttactccttcaagcatttttgcccaatctttttcgggattttca Mask Tandem Repeat Region ================================================ tgaaaatcccgaaaaagattgggcaaaaatgcttgaaggagtaagagatgtgtcacctgatacgcaactatttgactaaaagatacttactttttgaaaaacatatccgcaaccaatagtatccttattttttgggggggaggtatgcgagttcttagtccgggagtggaatagctccgagactatcaacttttgattttcgagagatgtttgcctcaactttcccaacaaaaatcttacacaggacaggctatgcgtcattactgagcttatatcttgaatggtactccaaatagaaaccactgtatgtgaaaccatatgtacggtgatgtgagaggtcggaaaacgaacgtgaaaagaaaactgcttcgttttcctcctgcctaaccaataccatatttataaaaaaaacacaataaaataaaaaatcaaaaaaa Find is-nt database================================================ Query_seq: TF1876:TF1877|TF1876:TF1877:hypothetical protein:hypothetical protein:->->:2030115..2030551 437 tgaaaatcccgaaaaagattgggcaaaaatgcttgaaggagtaagagatgtgtcacctgatacgcaactatttgactaaaagatacttactttttgaaaaacatatccgcaaccaatagtatccttattttttgggggggaggtatgcgagttcttagtccgggagtggaatagctccgagactatcaacttttgattttcgagagatgtttgcctcaactttcccaacaaaaatcttacacaggacaggctatgcgtcattactgagcttatatcttgaatggtactccaaatagaaaccactgtatgtgaaaccatatgtacggtgatgtgagaggtcggaaaacgaacgtgaaaagaaaactgcttcgttttcctcctgcctaaccaataccatatttataaaaaaaacacaataaaataaaaaatcaaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1876:TF1877|TF1876:TF1877:hypothetical protein:hypothetical protein:->->:2030115..2030551 437 tgaaaatcccgaaaaagattgggcaaaaatgcttgaaggagtaagagatgtgtcacctgatacgcaactatttgactaaaagatacttactttttgaaaaacatatccgcaaccaatagtatccttattttttgggggggaggtatgcgagttcttagtccgggagtggaatagctccgagactatcaacttttgattttcgagagatgtttgcctcaactttcccaacaaaaatcttacacaggacaggctatgcgtcattactgagcttatatcttgaatggtactccaaatagaaaccactgtatgtgaaaccatatgtacggtgatgtgagaggtcggaaaacgaacgtgaaaagaaaactgcttcgttttcctcctgcctaaccaataccatatttataaaaaaaacacaataaaataaaaaatcaaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1876:TF1877|TF1876:TF1877:hypothetical protein:hypothetical protein:->->:2030115..2030551 437 tgaaaatcccgaaaaagattgggcaaaaatgcttgaaggagtaagagatgtgtcacctgatacgcaactatttgactaaaagatacttactttttgaaaaacatatccgcaaccaatagtatccttattttttgggggggaggtatgcgagttcttagtccgggagtggaatagctccgagactatcaacttttgattttcgagagatgtttgcctcaactttcccaacaaaaatcttacacaggacaggctatgcgtcattactgagcttatatcttgaatggtactccaaatagaaaccactgtatgtgaaaccatatgtacggtgatgtgagaggtcggaaaacgaacgtgaaaagaaaactgcttcgttttcctcctgcctaaccaataccatatttataaaaaaaacacaataaaataaaaaatcaaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaaaatcccgaaaaagattgggcaaaaatgcttgaaggagtaagagatgtgtcacctgatacgcaactatttgactaaaagatacttactttttgaaaaacatatccgcaaccaatagtatccttattttttgggggggaggtatgcgagttcttagtccgggagtggaatagctccgagactatcaacttttgattttcgagagatgtttgcctcaactttcccaacaaaaatcttacacaggacaggctatgcgtcattactgagcttatatcttgaatggtactccaaatagaaaccactgtatgtgaaaccatatgtacggtgatgtgagaggtcggaaaacgaacgtgaaaagaaaactgcttcgttttcctcctgcctaaccaataccatatttataaaaaaaacacaataaaataaaaaatcaaaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 171 End: 293 .......................................................................................................................................................................... M A P R L S T F D F R E M F A S T F P T K I L H R T G Y A S L L S L Y L E W Y S K ................................................................................................................................................ Protein_Len: 50 Strand: - Start: 254 End: 403 ............................................................................................................................................................................................................................................................. A D N S L K Y R S H Y E L Y F G S Y T F G Y T R H H S L D S F S R S F F V A E N E E Q R V L V M N M .................................. Protein_Len: 60 Strand: - Start: 79 End: 399 .............................................................................. K G L L F R V C S L S H T M V S S I D Q I T S W I S V V T H S V M H V T I H S T P F R V H F S F Q K T K R R G L W Y W M ...................................... tgaaaatcccgaaaaagattgggcaaaaatgcttgaaggagtaagagatgtgtcacctgatacgcaactatttgactaaaagatacttactttttgaaaaacatatccgcaaccaatagtatccttattttttgggggggaggtatgcgagttcttagtccgggagtggaatagctccgagactatcaacttttgattttcgagagatgtttgcctcaactttcccaacaaaaatcttacacaggacaggctatgcgtcattactgagcttatatcttgaatggtactccaaatagaaaccactgtatgtgaaaccatatgtacggtgatgtgagaggtcggaaaacgaacgtgaaaagaaaactgcttcgttttcctcctgcctaaccaataccatatttataaaaaaaacacaataaaataaaaaatcaaaaaaa 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: 82 Start: 93 End: 122 ............................................................................................TTTGAAAAACATATCCGCAACCAATAGTAT........................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 399 End: 428 ..............................................................................................................................................................................................................................................................................................................................................................................................................TTTTTTATTTTATTGTGTTTTTTTTATAAA......... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgaaaatcccgaaaaagattgggcaaaaatgcttgaaggagtaagagatgtgtcacctgatacgcaactatttgactaaaagatacttactttttgaaaaacatatccgcaaccaatagtatccttattttttgggggggaggtatgcgagttcttagtccgggagtggaatagctccgagactatcaacttttgattttcgagagatgtttgcctcaactttcccaacaaaaatcttacacaggacaggctatgcgtcattactgagcttatatcttgaatggtactccaaatagaaaccactgtatgtgaaaccatatgtacggtgatgtgagaggtcggaaaacgaacgtgaaaagaaaactgcttcgttttcctcctgcctaaccaataccatatttataaaaaaaacacaataaaataaaaaatcaaaaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 64 HP_score: -4.2 Tail_Score: -4.2237 Start: 359 End: 376 Full_Region: ttggttaggcaggag gaaaac gaagca gttttc ttttcacgttcgttt ......................................................................................................................................................................................................................................................................................................................................................................gaaaacgaagcagttttc............................................................. Find igs database================================================ Query_seq: TF1876:TF1877|TF1876:TF1877:hypothetical protein:hypothetical protein:->->:2030115..2030551 437 tgaaaatcccgaaaaagattgggcaaaaatgcttgaaggagtaagagatgtgtcacctgatacgcaactatttgactaaaagatacttactttttgaaaaacatatccgcaaccaatagtatccttattttttgggggggaggtatgcgagttcttagtccgggagtggaatagctccgagactatcaacttttgattttcgagagatgtttgcctcaactttcccaacaaaaatcttacacaggacaggctatgcgtcattactgagcttatatcttgaatggtactccaaatagaaaccactgtatgtgaaaccatatgtacggtgatgtgagaggtcggaaaacgaacgtgaaaagaaaactgcttcgttttcctcctgcctaaccaataccatatttataaaaaaaacacaataaaataaaaaatcaaaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 403 Len: 403 Subject: tfor_TF1876_TF1877|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2030115,2030551]|437 HSP 1 e-value: 0.0 bit: 757.0 Len: 403 Query Start:1 Query End:403 Subject Strand: POSITIVE Subject Start: 1 Subject End: 403 tgaaaatcccgaaaaagattgggcaaaaatgcttgaaggagtaagagatgtgtcacctgatacgcaactatttgactaaaagatacttactttttgaaaaacatatccgcaaccaatagtatccttattttttnnnnnnnaggtatgcgagttcttagtccgggagtggaatagctccgagactatcaacttttgattttcgagagatgtttgcctcaactttcccaacaaaaatcttacacaggacaggctatgcgtcattactgagcttatatcttgaatggtactccaaatagaaaccactgtatgtgaaaccatatgtacggtgatgtgagaggtcggaaaacgaacgtgaaaagaaaactgcttcgttttcctcctgcctaaccaataccatatttat.................................. tgaaaatcccgaaaaagattgggcaaaaatgcttgaaggagtaagagatgtgtcacctgatacgcaactatttgactaaaagatacttactttttgaaaaacatatccgcaaccaatagtatccttattttttgggggggaggtatgcgagttcttagtccgggagtggaatagctccgagactatcaacttttgattttcgagagatgtttgcctcaactttcccaacaaaaatcttacacaggacaggctatgcgtcattactgagcttatatcttgaatggtactccaaatagaaaccactgtatgtgaaaccatatgtacggtgatgtgagaggtcggaaaacgaacgtgaaaagaaaactgcttcgttttcctcctgcctaaccaataccatatttat.................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAAUCCCGAAAAAGAUUGGGCAAAAAUGCUUGAAGGAGUAAGAGAUGUGUCACCUGAUACGCAACUAUUUGACUAAAAGAUACUUACUUUUUGAAAAACAUAUCCGCAACCAAUAGUAUCCUUAUUUUUUGGGGGGGAGGUAUGCGAGUUCUUAGUCCGGGAGUGGAAUAGCUCCGAGACUAUCAACUUUUGAUUUUCGAGAGAUGUUUGCCUCAACUUUCCCAACAAAAAUCUUACACAGGACAGGCUAUGCGUCAUUACUGAGCUUAUAUCUUGAAUGGUACUCCAAAUAGAAACCACUGUAUGUGAAACCAUAUGUACGGUGAUGUGAGAGGUCGGAAAACGAACGUGAAAAGAAAACUGCUUCGUUUUCCUCCUGCCUAACCAAUACCAUAUUUAU ..............((((((((((........((.((((((((((.(.((((((....)))))))...(((((.......))))))))))))))).)).........((((.....((((.((((((.((((((..((((((((..(((((....(((((..(((((......)))))..)))))....((((((.....))))))...)))))....))))))))..))))))...))...))))...))))))))..........))))).)))))..((((((..............(((((((((((......)))))))))))..((...((((.((((((((((.((............))))))))))))....)))).))...))))))...... (-102.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAUAUGGUAUUGGUUAGGCAGGAGGAAAACGAAGCAGUUUUCUUUUCACGUUCGUUUUCCGACCUCUCACAUCACCGUACAUAUGGUUUCACAUACAGUGGUUUCUAUUUGGAGUACCAUUCAAGAUAUAAGCUCAGUAAUGACGCAUAGCCUGUCCUGUGUAAGAUUUUUGUUGGGAAAGUUGAGGCAAACAUCUCUCGAAAAUCAAAAGUUGAUAGUCUCGGAGCUAUUCCACUCCCGGACUAAGAACUCGCAUACCUCCCCCCCAAAAAAUAAGGAUACUAUUGGUUGCGGAUAUGUUUUUCAAAAAGUAAGUAUCUUUUAGUCAAAUAGUUGCGUAUCAGGUGACACAUCUCUUACUCCUUCAAGCAUUUUUGCCCAAUCUUUUUCGGGAUUUUCA ........((((..((.(((((.((.((((((((((...((.........)).))))))))))..))..((.....(((((....))))).........((((((((((....)))).))))))...)).....(((((....))).))...))))).)).(((...((((((((..((((..(((......))).)))).))))))))...((((..((((((.((((........)))).))))))..))))))).))))....(((.(((((..(((((......((((..(.(((((((.........(.((((.....)))).).........)))))))..)..)).))........)))))...(((....)))......))))).)))....... (-94.31) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 427 187 141 226 179 tfor:TF2695|5end_prephenate_dehydratase_2869618..2869848_POSITIVE 402 178 131 200 145 tfor:TF0868|5end_isochorismate_synthase_919301..919531_POSITIVE 401 169 125 176 124 tfor:TF1352|5end_polysaccharide_deacetylase-like_protein_1432006..1432236_POSITIVE 391 170 125 214 171 tfor:TF1939|5end_hypothetical_protein_2086299..2086529_POSITIVE 366 380 331 159 108 tfor:TF1481|5end_ABC_transporter,_ATP-binding_protein_1574783..1575013_POSITIVE 358 359 313 119 73 tfor:TF1591|5end_surface_antigen_BspA_1706387..1706617_POSITIVE 353 169 121 123 62 tfor:TF1516|5end_transposase_fragment_1626407..1626637_POSITIVE 353 170 131 220 179 tfor:TF0712|5end_TPR-repeat-containing_protein_761348..761578_POSITIVE 350 179 138 130 80 tfor:TF1685|5end_hypothetical_protein_1800251..1800481_POSITIVE 348 180 134 165 124 tfor:TF1015|5end_conserved_hypothetical_protein_1072512..1072742_POSITIVE 344 180 133 41 4 tfor:TF1501|5end_sugar_hydrolase_1600428..1600658_POSITIVE 342 359 316 139 100 tfor:TF2779|5end_fucose_permease_2964566..2964796_POSITIVE 334 180 135 214 164 tfor:TF2693|5end_possible_aminotransferase_2868435..2868665_POSITIVE 327 150 101 134 84 tfor:TF2069|5end_polysaccharide_deacetylase,_possible_xylanase/chitin_deacetylase_2235663..2235893_POSITIVE 325 48 8 67 23 tfor:TF2993|5end_SAM-dependent_methyltransferase_3209636..3209866_POSITIVE 325 161 122 97 48 tfor:TF1598|5end_conserved_hypothetical_protein_1713358..1713588_POSITIVE 325 164 122 213 165 tfor:TF1522|5end_hypothetical_protein_1629531..1629761_POSITIVE 324 179 132 228 171 tfor:TF0587|5end_outer_membrane_protein_618319..618549_POSITIVE 324 179 133 81 39 tfor:TF0042|5end_anaerobic_cobalt_chelatase_CbiK_45828..46058_POSITIVE 323 180 134 196 144 tfor:TF0687|5end_hypothetical_protein_732226..732456_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 401 169 125 140 88 tfor:TF1351|3end_conserved_hypothetical_protein_1432050..1432200_POSITIVE 391 170 125 105 62 tfor:TF1938|3end_hypothetical_protein_2086270..2086420_POSITIVE 350 179 138 130 80 tfor:TF1684|3end_zinc_protease_1800331..1800481_POSITIVE 348 180 134 47 6 tfor:TF1014|3end_glucose-6-phosphate_isomerase_1072474..1072624_POSITIVE 339 197 151 136 80 tfor:TF0012|3end_conserved_hypothetical_protein_6641..6791_POSITIVE 337 177 135 63 13 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 334 348 302 79 32 tfor:TF1049|3end_cobyrinic_acid_a,c-diamide_synthase_1111539..1111689_POSITIVE 333 164 131 71 32 tfor:TF0038|3end_conserved_hypothetical_protein_41213..41363_POSITIVE 325 161 122 77 28 tfor:TF1597|3end_TatD_family_protein_1713418..1713568_POSITIVE 324 179 134 120 67 tfor:TF1432|3end_possible_hemolysin_A_1516990..1517140_POSITIVE 324 179 133 115 73 tfor:TF0041|3end_outer_membrane_protein,_TonB_dependent_receptor_45942..46092_POSITIVE 323 150 106 135 77 tfor:TF1840|3end_transposase_1991416..1991566_POSITIVE 321 169 123 87 29 tfor:TF2172|3end_hypothetical_protein_2346135..2346285_POSITIVE 321 38 6 135 103 tfor:TF0339|3end_hypothetical_protein_363747..363897_POSITIVE 320 178 134 149 111 tfor:TF1204|3end_possible_metal-dependent_membrane_protease_1287461..1287611_POSITIVE 318 168 122 133 85 tfor:TF0671|3end_histidine_kinase_sensor_protein_716343..716493_POSITIVE 317 170 123 69 27 tfor:TF2534|3end_conserved_hypothetical_protein_2717813..2717963_POSITIVE 316 372 331 150 111 tfor:TF1480|3end_ABC_transporter,_permease_component_1574866..1575016_POSITIVE 316 179 131 118 63 tfor:TF0759|3end_heat_shock_protein_15,_RNA-binding_domain_S4_806366..806516_POSITIVE 315 180 133 142 92 tfor:TF2439|3end_conserved_hypothetical_protein_2616930..2617080_POSITIVE