Origin IGS: ttgtcctcctgtaacttgaatggtcttggtgtattccaataagcggtcggcaagtgtagacttaccgtggtctatatgcgctatgatgcagaaatttcttatttggttcattaaaattttcgtcttttaatatgcaaaattaacaataaaagcgagaaatacaaaggaaccaatcataaaattgctcaaaaaggcttacctttgcatcatcttaggtaaagatagcacatttattaggcaagaag .........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 cttcttgcctaataaatgtgctatctttacctaagatgatgcaaaggtaagcctttttgagcaattttatgattggttcctttgtatttctcgcttttattgttaattttgcatattaaaagacgaaaattttaatgaaccaaataagaaatttctgcatcatagcgcatatagaccacggtaagtctacacttgccgaccgcttattggaatacaccaagaccattcaagttacaggaggacaa Mask Tandem Repeat Region ================================================ ttgtcctcctgtaacttgaatggtcttggtgtattccaataagcggtcggcaagtgtagacttaccgtggtctatatgcgctatgatgcagaaatttcttatttggttcattaaaattttcgtcttttaatatgcaaaattaacaataaaagcgagaaatacaaaggaaccaatcataaaattgctcaaaaaggcttacctttgcatcatcttaggtaaagatagcacatttattaggcaagaag Find is-nt database================================================ Query_seq: PI1378:PI1379|PI1378:PI1379:GTP-binding protein lepA:hypothetical protein:->->:1301712..1301956 245 ttgtcctcctgtaacttgaatggtcttggtgtattccaataagcggtcggcaagtgtagacttaccgtggtctatatgcgctatgatgcagaaatttcttatttggttcattaaaattttcgtcttttaatatgcaaaattaacaataaaagcgagaaatacaaaggaaccaatcataaaattgctcaaaaaggcttacctttgcatcatcttaggtaaagatagcacatttattaggcaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1378:PI1379|PI1378:PI1379:GTP-binding protein lepA:hypothetical protein:->->:1301712..1301956 245 ttgtcctcctgtaacttgaatggtcttggtgtattccaataagcggtcggcaagtgtagacttaccgtggtctatatgcgctatgatgcagaaatttcttatttggttcattaaaattttcgtcttttaatatgcaaaattaacaataaaagcgagaaatacaaaggaaccaatcataaaattgctcaaaaaggcttacctttgcatcatcttaggtaaagatagcacatttattaggcaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 4 Max: 111 Len: 108 Subject: gi|89109375|ref|AP_003155.1| GTP binding membrane protein [Escherichia coli W3110] HSP 1 e-value: 7.0E-6 bit: 45.8 Len: 108 Query Start:4 Query End:111 Subject Strand: null Subject Start: 1 Subject End: 30 ... M N Q I R N F C I I A H I D H G K S T L A D R L L E Y T K T I Q V T G G ...................................................................................................................................... ... M K N I R N F S I I A H I D H G K S T L S D R I - - - - - - I Q I C G G ...................................................................................................................................... Find nr database================================================ Query_seq: PI1378:PI1379|PI1378:PI1379:GTP-binding protein lepA:hypothetical protein:->->:1301712..1301956 245 ttgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntaaaattttcgtcttttaatatgcaaaattaacaataaaagcgagaaatacaaaggaaccaatcataaaattgctcaaaaaggcttacctttgcatcatcttaggtaaagatagcacatttattaggcaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntaaaattttcgtcttttaatatgcaaaattaacaataaaagcgagaaatacaaaggaaccaatcataaaattgctcaaaaaggcttacctttgcatcatcttaggtaaagatagcacatttattaggcaagaag Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 20 End: 127 ................... M V L V Y S N K R S A S V D L P W S I C A M M Q K F L I W F I K I F V F ...................................................................................................................... Protein_Len: 33 Strand: + Start: 146 End: 244 ................................................................................................................................................. M K A R N T K E P I I K L L K K A Y L C I I L G K D S T F I R Q E . Protein_Len: 39 Strand: - Start: 1 End: 117 Q G G T V Q I T K T Y E L L R D A L T S K G H D I H A I I C F N R I Q N M L M ................................................................................................................................ ttgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntaaaattttcgtcttttaatatgcaaaattaacaataaaagcgagaaatacaaaggaaccaatcataaaattgctcaaaaaggcttacctttgcatcatcttaggtaaagatagcacatttattaggcaagaag 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================================================ ttgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntaaaattttcgtcttttaatatgcaaaattaacaataaaagcgagaaatacaaaggaaccaatcataaaattgctcaaaaaggcttacctttgcatcatcttaggtaaagatagcacatttattaggcaagaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1378:PI1379|PI1378:PI1379:GTP-binding protein lepA:hypothetical protein:->->:1301712..1301956 245 ttgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntaaaattttcgtcttttaatatgcaaaattaacaataaaagcgagaaatacaaaggaaccaatcataaaattgctcaaaaaggcttacctttgcatcatcttaggtaaagatagcacatttattaggcaagaag Intra-Species Hit: Count: 1 Min: 112 Max: 245 Len: 134 Subject: pint_PI1378_PI1379|GTP-binding protein lepA:hypothetical protein|POSITIVE:POSITIVE|[1301712,1301956]|245 HSP 1 e-value: 3.0E-70 bit: 266.0 Len: 134 Query Start:112 Query End:245 Subject Strand: POSITIVE Subject Start: 112 Subject End: 245 ...............................................................................................................taaaattttcgtcttttaatatgcaaaattaacaataaaagcgagaaatacaaaggaaccaatcataaaattgctcaaaaaggcttacctttgcatcatcttaggtaaagatagcacatttattaggcaagaag ...............................................................................................................taaaattttcgtcttttaatatgcaaaattaacaataaaagcgagaaatacaaaggaaccaatcataaaattgctcaaaaaggcttacctttgcatcatcttaggtaaagatagcacatttattaggcaagaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUUUUCGUCUUUUAAUAUGCAAAAUUAACAAUAAAAGCGAGAAAUACAAAGGAACCAAUCAUAAAAUUGCUCAAAAAGGCUUACCUUUGCAUCAUCUUAGGUAAAGAUAGCACAUUUAUUAGGCAAGAAG .....((((((.((((((.................)))))))))))).......................((((..(((((.(((...((((((..........))))))..)))...))).))..)))).... (-18.93) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCUUGCCUAAUAAAUGUGCUAUCUUUACCUAAGAUGAUGCAAAGGUAAGCCUUUUUGAGCAAUUUUAUGAUUGGUUCCUUUGUAUUUCUCGCUUUUAUUGUUAAUUUUGCAUAUUAAAAGACGAAAAUUUUA ......(((........).)).(((((.....)))))((((((((((..((((..((.((....))....))..))))))))))))))..(((((((((.(((.......)))...)))))).)))........ (-23.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 120 72 107 58 pint:PI0965|5end_hypothetical_protein_894154..894384_POSITIVE 247 115 83 225 187 pint:PI1442|5end_radical-activating_enzyme_(pyruvate-formate_lyase-activating_enzyme)_1363949..1364179_POSITIVE 247 117 72 177 141 pint:PI0283|5end_Zn-dependent_peptidase_267554..267784_POSITIVE 243 89 41 163 106 pint:PI0908|5end_conserved_hypothetical_protein_836870..837100_POSITIVE 235 128 81 182 131 pint:PI1686|5end_hypothetical_protein_1601594..1601824_POSITIVE 235 96 52 185 135 pint:PI0728|5end_integrase_660427..660657_POSITIVE 231 99 53 203 154 pint:PI2073|5end_mobilization_protein_2031995..2032225_POSITIVE 230 129 82 178 118 pint:PI1068|5end_nucleolar_protein,_Sun_(Fmu)_family_protein;_tRNA/rRNA_cytosine-C5-methylase_984743..984973_POSITIVE 227 65 38 151 126 pint:PI0018|5end_hypothetical_protein_23022..23252_POSITIVE 226 116 73 216 164 pint:PI0913|5end_glycerate_dehydrogenase_842700..842930_POSITIVE 225 119 71 169 126 pint:PI0691|5end_hypothetical_protein_627885..628115_POSITIVE 224 130 84 198 144 pint:PI1921|5end_conserved_hypothetical_protein_1863917..1864147_POSITIVE 222 112 79 231 186 pint:PI1967|5end_hypothetical_protein_1924236..1924466_POSITIVE 222 128 82 55 9 pint:PI0335|5end_hypothetical_protein_313708..313938_POSITIVE 218 100 55 175 117 pint:PI0960|5end_hypothetical_protein_891137..891367_POSITIVE 218 97 59 211 165 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 217 117 72 170 127 pint:PI1448|5end_hypothetical_protein_1371579..1371809_POSITIVE 215 95 59 221 184 pint:PI2126|5end_conserved_hypothetical_protein_2074907..2075137_POSITIVE 215 118 81 50 11 pint:PI0998|5end_possible_flavin_reductase_domain_protein_922696..922926_POSITIVE 213 119 71 99 48 pint:PI1938|5end_hypothetical_protein_1891854..1892084_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 120 72 60 11 pint:PI0964|3end_conserved_hypothetical_protein_894187..894337_POSITIVE 270 130 83 149 98 pint:PI1179|3end_adenylosuccinate_synthetase_1101823..1101973_POSITIVE 243 89 41 126 69 pint:PI0907|3end_NAD-dependent_DNA_ligase_836913..837063_POSITIVE 232 107 63 151 110 pint:PI1002|3end_metal_dependent_hydrolase_924674..924824_POSITIVE 226 116 73 128 76 pint:PI0912|3end_conserved_hypothetical_protein_842692..842842_POSITIVE 225 113 85 46 10 pint:PI0516|3end_ferredoxin,_4Fe-4S_476108..476258_POSITIVE 224 130 84 76 22 pint:PI1919|3end_2,3-bisphosphoglycerate-independent_phosphoglycerate_mutase_1863875..1864025_POSITIVE 222 128 82 55 9 pint:PI0333|3end_hypothetical_protein_313788..313938_POSITIVE 219 119 77 84 47 pint:PI0576|3end_helicase,_UvrD/Rep_521724..521874_POSITIVE 215 118 81 86 47 pint:PI0999|3end_hypothetical_protein_922812..922962_POSITIVE 213 115 84 67 35 pint:PI0934|3end_hypothetical_protein_866132..866282_POSITIVE 212 115 71 61 22 pint:PI0289|3end_hypothetical_protein_273250..273400_POSITIVE 203 117 73 132 100 pint:PI0633|3end_possible_preprotein_translocase,_YajC_subunit_580080..580230_POSITIVE 201 75 39 140 99 pint:PI0992|3end_RNA_polymerase_sigma-70_factor_917222..917372_POSITIVE 200 115 80 118 76 pint:PI2118|3end_fumarate_reductase/succinate_dehydrogenase_flavoprotein_subunit,_N-terminal_2067997..2068147_POSITIVE 200 88 42 65 12 pint:PI1534|3end_ATPase/GTPase_1454166..1454316_POSITIVE 200 106 70 147 106 pint:PI0855|3end_hypothetical_protein_789545..789695_POSITIVE 200 105 70 65 39 pint:PI0316|3end_conserved_hypothetical_protein_299082..299232_POSITIVE 196 129 82 81 30 pint:PI0281|3end_conserved_hypothetical_protein_266604..266754_POSITIVE 194 75 31 143 98 pint:PI1422|3end_hypothetical_protein_1341942..1342092_POSITIVE