Origin IGS: taaaaagcttttttttagaaattactacgtatttaatgacaccaacagcggtgcacggaaaaaaagtaaatcaaagaaaccgtgtatgttagaggtttgagataactgcgtacttgtggcgttgatatggatagaagtggcgtttcggaagaaaagcgaacgggatatgcagaaaacagcatatcccgttcgcttgaagaaggagaatcgtttctca .........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 tgagaaacgattctccttcttcaagcgaacgggatatgctgttttctgcatatcccgttcgcttttcttccgaaacgccacttctatccatatcaacgccacaagtacgcagttatctcaaacctctaacatacacggtttctttgatttactttttttccgtgcaccgctgttggtgtcattaaatacgtagtaatttctaaaaaaaagcttttta Mask Tandem Repeat Region ================================================ taaaaagcttttttttagaaattactacgtatttaatgacaccaacagcggtgcacggaaaaaaagtaaatcaaagaaaccgtgtatgttagaggtttgagataactgcgtacttgtggcgttgatatggatagaagtggcgtttcggaagaaaagcgaacgggatatgcagaaaacagcatatcccgttcgcttgaagaaggagaatcgtttctca Find is-nt database================================================ Query_seq: TF1290:TF1291|TF1290:TF1291:hypothetical protein:response regulator (fimR protein):->->:1371882..1372098 217 taaaaagcttttttttagaaattactacgtatttaatgacaccaacagcggtgcacggaaaaaaagtaaatcaaagaaaccgtgtatgttagaggtttgagataactgcgtacttgtggcgttgatatggatagaagtggcgtttcggaagaaaagcgaacgggatatgcagaaaacagcatatcccgttcgcttgaagaaggagaatcgtttctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1290:TF1291|TF1290:TF1291:hypothetical protein:response regulator (fimR protein):->->:1371882..1372098 217 taaaaagcttttttttagaaattactacgtatttaatgacaccaacagcggtgcacggaaaaaaagtaaatcaaagaaaccgtgtatgttagaggtttgagataactgcgtacttgtggcgttgatatggatagaagtggcgtttcggaagaaaagcgaacgggatatgcagaaaacagcatatcccgttcgcttgaagaaggagaatcgtttctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1290:TF1291|TF1290:TF1291:hypothetical protein:response regulator (fimR protein):->->:1371882..1372098 217 taaaaagcttttttttagaaattactacgtatttaatgacaccaacagcggtgcacggaaaaaaagtaaatcaaagaaaccgtgtatgttagaggtttgagataactgcgtacttgtggcgttgatatggatagaagtggcgtttcggaagaaaagcgaacgggatatgcagaaaacagcatatcccgttcgcttgaagaaggagaatcgtttctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaagcttttttttagaaattactacgtatttaatgacaccaacagcggtgcacggaaaaaaagtaaatcaaagaaaccgtgtatgttagaggtttgagataactgcgtacttgtggcgttgatatggatagaagtggcgtttcggaagaaaagcgaacgggatatgcagaaaacagcatatcccgttcgcttgaagaaggagaatcgtttctca Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 106 End: 216 ......................................................................................................... M R T C G V D M D R S G V S E E K R T G Y A E N S I S R S L E E G E S F L . Protein_Len: 34 Strand: + Start: 116 End: 217 ................................................................................................................... M A L I W I E V A F R K K S E R D M Q K T A Y P V R L K K E N R F S Protein_Len: 39 Strand: - Start: 92 End: 208 ........................................................................................... L N S I V A Y K H R Q Y P Y F H R K P L F A F P I H L F C C I G N A Q L L L M ......... Protein_Len: 49 Strand: - Start: 36 End: 182 ................................... H C W C R H V S F F Y I L S V T Y T L P K L Y S R V Q P T S I S L L P T E S S F R V P Y A S F L M ................................... Protein_Len: 47 Strand: - Start: 28 End: 168 ........................... T N L S V L L P A R F F L L D F F G H I N S T Q S L Q T S T A N I H I S T A N R F F L S R S M ................................................. taaaaagcttttttttagaaattactacgtatttaatgacaccaacagcggtgcacggaaaaaaagtaaatcaaagaaaccgtgtatgttagaggtttgagataactgcgtacttgtggcgttgatatggatagaagtggcgtttcggaagaaaagcgaacgggatatgcagaaaacagcatatcccgttcgcttgaagaaggagaatcgtttctca 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================================================ taaaaagcttttttttagaaattactacgtatttaatgacaccaacagcggtgcacggaaaaaaagtaaatcaaagaaaccgtgtatgttagaggtttgagataactgcgtacttgtggcgttgatatggatagaagtggcgtttcggaagaaaagcgaacgggatatgcagaaaacagcatatcccgttcgcttgaagaaggagaatcgtttctca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -22.9 Tail_Score: -4.63218 Start: 156 End: 193 Full_Region: attctccttcttcaa gcgaacgggatatgctg tttt ctgcatatcccgttcgc ttttcttccgaaacg ...........................................................................................................................................................gcgaacgggatatgctgttttctgcatatcccgttcgc........................ Find igs database================================================ Query_seq: TF1290:TF1291|TF1290:TF1291:hypothetical protein:response regulator (fimR protein):->->:1371882..1372098 217 taaaaagcttttttttagaaattactacgtatttaatgacaccaacagcggtgcacggaaaaaaagtaaatcaaagaaaccgtgtatgttagaggtttgagataactgcgtacttgtggcgttgatatggatagaagtggcgtttcggaagaaaagcgaacgggatatgcagaaaacagcatatcccgttcgcttgaagaaggagaatcgtttctca Intra-Species Hit: Count: 2 Min: 17 Max: 217 Len: 201 Subject: tfor_TF1290_TF1291|hypothetical protein:response regulator (fimR protein)|POSITIVE:POSITIVE|[1371882,1372098]|217 HSP 1 e-value: 1.0E-97 bit: 357.0 Len: 201 Query Start:17 Query End:217 Subject Strand: POSITIVE Subject Start: 17 Subject End: 217 ................agaaattactacgtatttaatgacaccaacagcggtgcacggnnnnnnngtaaatcaaagaaaccgtgtatgttagaggtttgagataactgcgtacttgtggcgttgatatggatagaagtggcgtttcggaagaaaagcgaacgggatatgcagaaaacagcatatcccgttcgcttgaagaaggagaatcgtttctca ................agaaattactacgtatttaatgacaccaacagcggtgcacggaaaaaaagtaaatcaaagaaaccgtgtatgttagaggtttgagataactgcgtacttgtggcgttgatatggatagaagtggcgtttcggaagaaaagcgaacgggatatgcagaaaacagcatatcccgttcgcttgaagaaggagaatcgtttctca Subject: tfor_TF0021_TF0022|outer membrane phospholipase A:two-component system sensor histidine kinase|POSITIVE:POSITIVE|[16980,17434]|455 HSP 1 e-value: 2.0E-25 bit: 117.0 Len: 121 Query Start:21 Query End:141 Subject Strand: POSITIVE Subject Start: 242 Subject End: 361 ....................attactacgtatttaatgacaccaacagcggtgcacggnnnnnnngtaaatcaaagaaaccgtgtatgttagaggtttgagataactgcgtacttgtggcgttgatatggatagaagtggc............................................................................ ....................attactatgtatttaatgacaccaacagcggtgtatggataaag-gtaaaccaaagaaactgtgtgtattacaggtttgagataactgcgtacttgtggcgtcgatatggatagaagtggc............................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAAUUACUACGUAUUUAAUGACACCAACAGCGGUGCACGGAAAAAAAGUAAAUCAAAGAAACCGUGUAUGUUAGAGGUUUGAGAUAACUGCGUACUUGUGGCGUUGAUAUGGAUAGAAGUGGCGUUUCGGAAGAAAAGCGAACGGGAUAUGCAGAAAACAGCAUAUCCCGUUCGCUUGAAGAAGGAGAAUCGUUUCUCA .(((((..((((...(((..((.((((......))))))..)))...................((((((((((((.((((.((((....)).)).)))).))))))..))))))......)))).))))).......(((((((((((((((((........))))))))))))))))).......(((((....))))). (-63.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGAAACGAUUCUCCUUCUUCAAGCGAACGGGAUAUGCUGUUUUCUGCAUAUCCCGUUCGCUUUUCUUCCGAAACGCCACUUCUAUCCAUAUCAACGCCACAAGUACGCAGUUAUCUCAAACCUCUAACAUACACGGUUUCUUUGAUUUACUUUUUUUCCGUGCACCGCUGUUGGUGUCAUUAAAUACGUAGUAAUUUCU .(((((....))))).......(((((((((((((((((........))))))))))))))))).......((((.((.((........((((((((((.....(((((.(((.(((..(((((............)))))....)))..))).......)))))...)).))))))))..........)).))..)))). (-50.37) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 369 144 101 217 167 tfor:TF0584|5end_phosphopantetheinyl_transferase_613755..613985_POSITIVE 347 158 111 208 141 tfor:TF0065|5end_conserved_hypothetical_protein_70274..70504_POSITIVE 344 130 81 93 33 tfor:TF1847|5end_hypothetical_protein_1997389..1997619_POSITIVE 331 176 135 213 161 tfor:TF2128|5end_3-oxoacyl-(acyl-carrier_protein)_synthase_2304258..2304488_POSITIVE 331 149 102 142 101 tfor:TF0995|5end_conserved_hypothetical_protein_1049695..1049925_POSITIVE 328 133 92 77 36 tfor:TF1436|5end_phosphoglycolate_phosphatase_1521128..1521358_POSITIVE 325 146 102 70 24 tfor:TF0077|5end_hypothetical_protein_84241..84471_POSITIVE 324 170 123 80 31 tfor:TF0621|5end_phosphate_starvation-inducible_protein,_PhoH_655679..655909_POSITIVE 323 136 91 217 169 tfor:TF1636|5end_hypothetical_protein_1747143..1747373_POSITIVE 323 136 91 180 132 tfor:TF1637|5end_hypothetical_protein_1747106..1747336_POSITIVE 322 150 101 147 92 tfor:TF1434|5end_transketolase_1517485..1517715_POSITIVE 321 189 145 127 74 tfor:TF1856|5end_conserved_hypothetical_protein_2009969..2010199_POSITIVE 320 149 102 71 4 tfor:TF1919|5end_hypothetical_protein_2070037..2070267_POSITIVE 319 175 137 47 15 tfor:TF1327|5end_L-fucose_permease_1405790..1406020_POSITIVE 314 170 121 74 10 tfor:TF1850|5end_Na+/H+-exchanging_protein_1998542..1998772_POSITIVE 314 132 93 49 10 tfor:TF1835|5end_possible_dihydroxy-acid_dehydratase_1984201..1984431_POSITIVE 313 133 98 142 108 tfor:TF0715|5end_glycosyltransferase_764435..764665_POSITIVE 312 129 89 159 125 tfor:TF3037|5end_galactokinase_3263050..3263280_POSITIVE 312 44 1 66 19 tfor:TF2962|5end_integrase/recombinase_3173659..3173889_POSITIVE 311 175 135 161 110 tfor:TF1429|5end_S-adenosyl-methyltransferase_1513927..1514157_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 390 110 67 53 10 tfor:TF0925|3end_hypothetical_protein_962127..962277_POSITIVE 356 180 131 148 102 tfor:TF1782|3end_conserved_hypothetical_protein_1923333..1923483_POSITIVE 331 149 102 149 108 tfor:TF0994|3end_maltose_O-acetyltransferase_1049782..1049932_POSITIVE 329 150 101 87 39 tfor:TF1023|3end_ABC_transporter,_permease_component_1081667..1081817_POSITIVE 324 170 123 56 7 tfor:TF0620|3end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_655735..655885_POSITIVE 323 136 91 72 24 tfor:TF1634|3end_hypothetical_protein_1747078..1747228_POSITIVE 322 150 101 133 78 tfor:TF1433|3end_ribose_5-phosphate_isomerase_1517551..1517701_POSITIVE 319 175 137 47 15 tfor:TF1325|3end_L-fucose_isomerase_1405870..1406020_POSITIVE 314 132 93 79 40 tfor:TF1834|3end_3-isopropylmalate_dehydrogenase_1984311..1984461_POSITIVE 313 133 98 135 101 tfor:TF0714|3end_endonuclease;_resolvase_764508..764658_POSITIVE 312 129 89 80 46 tfor:TF3036|3end_glucose/galactose_transporter_3263051..3263201_POSITIVE 312 139 92 126 81 tfor:TF0468|3end_hypothetical_protein_487188..487338_POSITIVE 311 175 135 150 99 tfor:TF1428|3end_conserved_hypothetical_protein_1513996..1514146_POSITIVE 308 132 98 122 88 tfor:TF2876|3end_cytosine_deaminase_3065664..3065814_POSITIVE 305 190 144 79 38 tfor:TF0193|3end_conserved_hypothetical_protein;_possible_internalin-like_protein_(LPXTG_motif)_215240..215390_POSITIVE 305 120 71 79 29 tfor:TF0043|3end_conserved_hypothetical_protein_48397..48547_POSITIVE 304 170 123 79 37 tfor:TF3000|3end_hypothetical_protein_3216740..3216890_POSITIVE 303 180 131 132 97 tfor:TF0606|3end_signal_peptidase_II_637504..637654_POSITIVE 302 147 103 58 10 tfor:TF2753|3end_zinc_protease_2940448..2940598_POSITIVE 300 169 121 58 7 tfor:TF0881|3end_conserved_hypothetical_protein_935993..936143_POSITIVE