Origin IGS: aaatctgtatttttaattgttagaaccactgcaaagttatacctttgcactacaatctgcaagtacctacaatattgtaggatacataccgtattattagatttattgattatcaagaataaaaaagtttgtc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gacaaacttttttattcttgataatcaataaatctaataatacggtatgtatcctacaatattgtaggtacttgcagattgtagtgcaaaggtataactttgcagtggttctaacaattaaaaatacagattt Mask Tandem Repeat Region ================================================ aaatctgtatttttaattgttagaaccactgcaaagttatacctttgcactacaatctgcaagtacctacaatattgtaggatacataccgtattattagatttattgattatcaagaataaaaaagtttgtc Find is-nt database================================================ Query_seq: TF0914:TF0915|TF0914:TF0915:conserved hypothetical protein; possible ketosteroid isomerase-related protein:possible transcriptional regulator:->->:955874..956006 133 aaatctgtatttttaattgttagaaccactgcaaagttatacctttgcactacaatctgcaagtacctacaatattgtaggatacataccgtattattagatttattgattatcaagaataaaaaagtttgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0914:TF0915|TF0914:TF0915:conserved hypothetical protein; possible ketosteroid isomerase-related protein:possible transcriptional regulator:->->:955874..956006 133 aaatctgtatttttaattgttagaaccactgcaaagttatacctttgcactacaatctgcaagtacctacaatattgtaggatacataccgtattattagatttattgattatcaagaataaaaaagtttgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0914:TF0915|TF0914:TF0915:conserved hypothetical protein; possible ketosteroid isomerase-related protein:possible transcriptional regulator:->->:955874..956006 133 aaatctgtatttttaattgttagaaccactgcaaagttatacctttgcactacaatctgcaagtacctacaatattgtaggatacataccgtattattagatttattgattatcaagaataaaaaagtttgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatctgtatttttaattgttagaaccactgcaaagttatacctttgcactacaatctgcaagtacctacaatattgtaggatacataccgtattattagatttattgattatcaagaataaaaaagtttgtc Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 16 End: 132 ............... M V R T T A K L Y L C T T I C K Y L Q Y C R I H T V L L D L L I I K N K K V C . Protein_Len: 38 Strand: - Start: 3 End: 116 .. D T N K I T L V V A F N Y R Q V V I Q L Y R C Y Q L I C V T N N S K N I I M ................. aaatctgtatttttaattgttagaaccactgcaaagttatacctttgcactacaatctgcaagtacctacaatattgtaggatacataccgtattattagatttattgattatcaagaataaaaaagtttgtc 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================================================ aaatctgtatttttaattgttagaaccactgcaaagttatacctttgcactacaatctgcaagtacctacaatattgtaggatacataccgtattattagatttattgattatcaagaataaaaaagtttgtc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 43 HP_score: -3.0 Tail_Score: -2.83747 Start: 29 End: 50 Full_Region: tacttgcagattgta gtgcaaag gtataa ctttgcag tggttctaacaatta ............................gtgcaaaggtataactttgcag................................................................................... Find igs database================================================ Query_seq: TF0914:TF0915|TF0914:TF0915:conserved hypothetical protein; possible ketosteroid isomerase-related protein:possible transcriptional regulator:->->:955874..956006 133 aaatctgtatttttaattgttagaaccactgcaaagttatacctttgcactacaatctgcaagtacctacaatattgtaggatacataccgtattattagatttattgattatcaagaataaaaaagtttgtc Intra-Species Hit: Count: 1 Min: 1 Max: 133 Len: 133 Subject: tfor_TF0914_TF0915|conserved hypothetical protein; possible ketosteroid isomerase-related protein:possible transcriptional regulator|POSITIVE:POSITIVE|[955874,956006]|133 HSP 1 e-value: 7.0E-70 bit: 264.0 Len: 133 Query Start:1 Query End:133 Subject Strand: POSITIVE Subject Start: 1 Subject End: 133 aaatctgtatttttaattgttagaaccactgcaaagttatacctttgcactacaatctgcaagtacctacaatattgtaggatacataccgtattattagatttattgattatcaagaataaaaaagtttgtc aaatctgtatttttaattgttagaaccactgcaaagttatacctttgcactacaatctgcaagtacctacaatattgtaggatacataccgtattattagatttattgattatcaagaataaaaaagtttgtc Inter-species Hit: Count: 3 Min: 6 Max: 129 Len: 124 Subject: pint_PI0391_PI0392|conserved hypothetical protein:possible transcriptional regulator|POSITIVE:POSITIVE|[358277,358483]|207 HSP 1 e-value: 2.0E-14 bit: 79.8 Len: 124 Query Start:6 Query End:129 Subject Strand: POSITIVE Subject Start: 80 Subject End: 203 .....tgtatttttaattgttagaaccactgcaaagttatacctttgcactacaatctgcaagtacctacaatattgtaggatacataccgtattattagatttattgattatcaagaataaaaaagtt.... .....tgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagtt.... Subject: NC_002950_PG1450_PG1451|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1534705,1534836]|132 HSP 1 e-value: 2.0E-14 bit: 79.8 Len: 124 Query Start:6 Query End:129 Subject Strand: NEGATIVE Subject Start: 5 Subject End: 128 .....tgtatttttaattgttagaaccactgcaaagttatacctttgcactacaatctgcaagtacctacaatattgtaggatacataccgtattattagatttattgattatcaagaataaaaaagtt.... .....tgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagtt.... Subject: NC_002950_PG0822_PG0823|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[880826,880957]|132 HSP 1 e-value: 2.0E-14 bit: 79.8 Len: 124 Query Start:6 Query End:129 Subject Strand: POSITIVE Subject Start: 5 Subject End: 128 .....tgtatttttaattgttagaaccactgcaaagttatacctttgcactacaatctgcaagtacctacaatattgtaggatacataccgtattattagatttattgattatcaagaataaaaaagtt.... .....tgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagtt.... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUAUUUUUAAUUGUUAGAACCACUGCAAAGUUAUACCUUUGCACUACAAUCUGCAAGUACCUACAAUAUUGUAGGAUACAUACCGUAUUAUUAGAUUUAUUGAUUAUCAAGAAUAAAAAAGUU ..(((((((.((.(((((......(((((((......)))))))....((((((......((((((....)))))).(((.....)))....))))))..))))).)).)))))))........ (-21.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUUUUUUAUUCUUGAUAAUCAAUAAAUCUAAUAAUACGGUAUGUAUCCUACAAUAUUGUAGGUACUUGCAGAUUGUAGUGCAAAGGUAUAACUUUGCAGUGGUUCUAACAAUUAAAAAUACA ....((((((........(((((.............((((((.((((.((((((....))))))....)))).)))))).(((((((......))))))).)))))........)))))).... (-26.29) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 63 21 41 1 tfor:TF0424|5end_outer_membrane_receptor,_TonB-linked_440028..440258_POSITIVE 275 68 41 67 35 tfor:TF2979|5end_possible_outer_membrane__protein_3190778..3191008_POSITIVE 254 57 25 159 126 tfor:TF0192|5end_hypothetical_protein_207446..207676_POSITIVE 251 60 11 145 94 tfor:TF1075|5end_conserved_hypothetical_protein;_possible_lantibiotic_biosynthesis_protein_1144428..1144658_POSITIVE 248 60 12 223 178 tfor:TF1088|5end_transposase_fragment_1158060..1158290_POSITIVE 246 59 30 227 196 tfor:TF0373|5end_conserved_hypothetical_protein,_yngK-related_391038..391268_POSITIVE 244 77 34 72 33 tfor:TF0882|5end_hypothetical_protein_935919..936149_POSITIVE 243 86 47 209 162 tfor:TF0839|5end_aminopeptidasem_M28_family_890442..890672_POSITIVE 241 79 37 76 30 tfor:TF2154|5end_conserved_hypothetical_protein_2329153..2329383_POSITIVE 231 58 12 205 160 tfor:TF0160|5end_conserved_hypothetical_protein;_possible_Fic_family_protein_170327..170557_POSITIVE 229 66 21 231 170 tfor:TF3055|5end_hypothetical_protein_3278775..3279005_POSITIVE 220 77 31 108 62 tfor:TF1170|5end_conserved_hypothetical_protein_1251862..1252092_POSITIVE 220 77 31 96 50 tfor:TF1171|5end_ABC_transporter,_ATP-binding_protein_1251850..1252080_POSITIVE 219 65 24 155 116 tfor:TF3080|5end_conserved_hypothetical_protein_3310480..3310710_POSITIVE 218 79 31 224 182 tfor:TF0937|5end_ATPase,__AAA+_class_978390..978620_POSITIVE 215 60 14 171 122 tfor:TF2820|5end_argininosuccinate_synthetase_3009876..3010106_POSITIVE 213 68 23 145 91 tfor:TF0259|5end_conserved_hypothetical_protein_289750..289980_POSITIVE 212 58 12 54 2 tfor:TF2724|5end_anti-sigma_factor_2898193..2898423_POSITIVE 212 60 21 93 58 tfor:TF1548|5end_thiophene_and_furan_oxidation_protein_1652501..1652731_POSITIVE 211 88 45 56 5 tfor:TF2932|5end_capsule_biosynthesis_protein_3135514..3135744_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 275 68 41 71 39 tfor:TF2978|3end_conserved_hypothetical_protein_3190862..3191012_POSITIVE 244 77 34 66 27 tfor:TF0881|3end_conserved_hypothetical_protein_935993..936143_POSITIVE 221 55 11 149 103 tfor:TF1074|3end_hypothetical_protein_1144517..1144667_POSITIVE 217 80 58 28 6 tfor:TF0914|3end_conserved_hypothetical_protein;_possible_ketosteroid_isomerase-related_protein_955813..955963_POSITIVE 210 77 36 99 50 tfor:TF0573|3end_DNA_polymerase_III,_delta_subunit_604852..605002_POSITIVE 204 58 12 70 17 tfor:TF1771|3end_prolipoprotein_diacylglyceryl_transferase_1910607..1910757_POSITIVE 201 62 23 71 16 tfor:TF2644|3end_possible_thiamine_pyrophosphokinase_2813779..2813929_POSITIVE 201 45 26 62 39 tfor:TF2583|3end_possible_ABC_transporter,__permease_component_2751026..2751176_POSITIVE 201 67 25 118 76 tfor:TF1386|3end_hypothetical_protein_1460488..1460638_POSITIVE 201 79 34 74 22 tfor:TF0437|3end_conserved_hypothetical_protein_461446..461596_POSITIVE 199 58 27 84 47 tfor:TF2126|3end_S-adenosylhomocysteine_hydrolase_2303996..2304146_POSITIVE 196 89 41 137 92 tfor:TF0224|3end_N-acetylglucosamine-6-phosphate_deacetylase_251547..251697_POSITIVE 191 77 34 70 27 tfor:TF3153|3end_conserved_hypothetical_protein_3389324..3389474_POSITIVE 191 88 50 149 106 tfor:TF2124|3end_conserved_hypothetical_protein;_possible_TonB_dependent_receptor_2302191..2302341_POSITIVE 190 87 43 71 27 tfor:TF2187|3end_conserved_hypothetical_protein_2362720..2362870_POSITIVE 189 88 41 95 41 tfor:TF0405|3end_conserved_hypothetical_protein_424308..424458_POSITIVE 186 89 44 125 82 tfor:TF1291|3end_response_regulator_(fimR__protein)_1372647..1372797_POSITIVE 184 64 23 73 33 tfor:TF2615|3end_conserved_hypothetical_protein_2791209..2791359_POSITIVE 183 77 35 88 50 tfor:TF1496|3end_tyrosyl-tRNA_synthetase_1596069..1596219_POSITIVE 182 87 44 96 52 tfor:TF1780|3end_formiminotransferase-cyclodeaminases_1922087..1922237_POSITIVE