Origin IGS: taagcaatagaagtgtgttggttgtcatagaaaaggagttaaagagaaactttactcgtttgtctttaactccttttaatttatatatctatgtttttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaaaacatagatatataaattaaaaggagttaaagacaaacgagtaaagtttctctttaactccttttctatgacaaccaacacacttctattgctta Mask Tandem Repeat Region ================================================ taagcaatagaagtgtgttggttgtcatagaaaaggagttaaagagaaactttactcgtttgtctttaactccttttaatttatatatctatgtttttta Find is-nt database================================================ Query_seq: PI1027:PI1028|PI1027:PI1028:hypothetical protein:glutamate synthase, small subunit:->->:943460..943559 100 taagcaatagaagtgtgttggttgtcatagaaaaggagttaaagagaaactttactcgtttgtctttaactccttttaatttatatatctatgtttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1027:PI1028|PI1027:PI1028:hypothetical protein:glutamate synthase, small subunit:->->:943460..943559 100 taagcaatagaagtgtgttggttgtcatagaaaaggagttaaagagaaactttactcgtttgtctttaactccttttaatttatatatctatgtttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1027:PI1028|PI1027:PI1028:hypothetical protein:glutamate synthase, small subunit:->->:943460..943559 100 taagcaatagaagtgtgttggttgtcatagaaaaggagttaaagagaaactttactcgtttgtctttaactccttttaatttatatatctatgtttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagcaatagaagtgtgttggttgtcatagaaaaggagttaaagagaaactttactcgtttgtctttaactccttttaatttatatatctatgtttttta Predict ORF larger than 30AA ================================================ taagcaatagaagtgtgttggttgtcatagaaaaggagttaaagagaaactttactcgtttgtctttaactccttttaatttatatatctatgtttttta 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================================================ taagcaatagaagtgtgttggttgtcatagaaaaggagttaaagagaaactttactcgtttgtctttaactccttttaatttatatatctatgtttttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 85 HP_score: -12.1 Tail_Score: -3.10967 Start: 30 End: 78 Full_Region: GTGTTGGTTGTCATA GAAAAGGAGTTAAAGAGAAAC TTTACTC GTTTGTCTTTAACTCCTTTTA ATTTATATATCTATG .............................GAAAAGGAGTTAAAGAGAAACTTTACTCGTTTGTCTTTAACTCCTTTTA...................... TransTerm Strand: + Conf: 100 HP_score: -12.0 Tail_Score: -4.66057 Start: 35 End: 73 Full_Region: GGTTGTCATAGAAAA GGAGTTAAAGAGAAAC TTTACTC GTTTGTCTTTAACTCC TTTTAATTTATATAT ..................................GGAGTTAAAGAGAAACTTTACTCGTTTGTCTTTAACTCC........................... TransTerm Strand: - Conf: 100 HP_score: -12.0 Tail_Score: -4.52589 Start: 35 End: 73 Full_Region: atatataaattaaaa ggagttaaagacaaac gagtaaa gtttctctttaactcc ttttctatgacaacc ..................................ggagttaaagacaaacgagtaaagtttctctttaactcc........................... Find igs database================================================ Query_seq: PI1027:PI1028|PI1027:PI1028:hypothetical protein:glutamate synthase, small subunit:->->:943460..943559 100 taagcaatagaagtgtgttggttgtcatagaaaaggagttaaagagaaactttactcgtttgtctttaactccttttaatttatatatctatgtttttta Intra-Species Hit: Count: 1 Min: 1 Max: 100 Len: 100 Subject: pint_PI1027_PI1028|hypothetical protein:glutamate synthase, small subunit|POSITIVE:POSITIVE|[943460,943559]|100 HSP 1 e-value: 2.0E-50 bit: 198.0 Len: 100 Query Start:1 Query End:100 Subject Strand: POSITIVE Subject Start: 1 Subject End: 100 taagcaatagaagtgtgttggttgtcatagaaaaggagttaaagagaaactttactcgtttgtctttaactccttttaatttatatatctatgtttttta taagcaatagaagtgtgttggttgtcatagaaaaggagttaaagagaaactttactcgtttgtctttaactccttttaatttatatatctatgtttttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCAAUAGAAGUGUGUUGGUUGUCAUAGAAAAGGAGUUAAAGAGAAACUUUACUCGUUUGUCUUUAACUCCUUUUAAUUUAUAUAUCUAUGUUUUUUA .(((((.((((.(((((.............(((((((((((((((.((((.......)))).)))))))))))))))....))))).))))))))).... (-29.63) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAACAUAGAUAUAUAAAUUAAAAGGAGUUAAAGACAAACGAGUAAAGUUUCUCUUUAACUCCUUUUCUAUGACAACCAACACACUUCUAUUGCUUA .......((((((...........((((((((((((((.((((.......)))).))))))))))))))))))))......................... (-25.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 78 31 139 101 pint:PI0518|5end_5'-nucleotidase_precursor_477076..477306_POSITIVE 248 67 27 171 130 pint:PI1798|5end__elongation_factor_Ts_1731788..1732018_POSITIVE 244 74 33 134 100 pint:PI1816|5end_acid_phosphatase_1754646..1754876_POSITIVE 243 77 31 159 121 pint:PI1908|5end_transcriptional_regulator,_AraC_family_1852261..1852491_POSITIVE 241 46 3 220 174 pint:PI0777|5end_predicted_TPR-repeat-containing_protein_713285..713515_POSITIVE 237 39 4 84 38 pint:PI0897|5end_ferredoxin,_4Fe-4S_828227..828457_POSITIVE 237 50 4 77 33 pint:PI0346|5end_hypothetical_protein_320834..321064_POSITIVE 232 49 12 79 36 pint:PI0295|5end_lysine_decarboxylase_276846..277076_POSITIVE 226 46 3 114 80 pint:PI1199|5end_possible_acetyltransferase_1115139..1115369_POSITIVE 222 63 25 119 74 pint:PI0609|5end_conserved_hypothetical_protein_556519..556749_POSITIVE 205 67 27 114 80 pint:PI0193|5end_conserved_hypothetical_protein_184746..184976_POSITIVE 204 25 3 201 173 pint:PI1839|5end_hypothetical_protein_1782178..1782408_POSITIVE 201 74 35 200 146 pint:PI1109|5end_possible_glycosyltransferase_1032620..1032850_POSITIVE 198 39 3 103 60 pint:PI0988|5end_hypothetical_protein_912347..912577_POSITIVE 197 46 3 172 138 pint:PI0834|5end_conserved_hypothetical_protein_770785..771015_POSITIVE 193 74 34 142 109 pint:PI0199|5end_phosphate_acetyltransferase_189890..190120_POSITIVE 192 49 3 46 5 pint:PI1800|5end_hypothetical_protein_1733723..1733953_POSITIVE 192 31 2 158 133 pint:PI1568|5end_OmpA_family_protein_1489584..1489814_POSITIVE 191 48 3 144 83 pint:PI2171|5end_conserved_hypothetical_protein_2112735..2112965_POSITIVE 191 59 16 54 13 pint:PI2161|5end_hypothetical_protein_2108579..2108809_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 77 31 60 14 pint:PI1027|3end_hypothetical_protein_943399..943549_POSITIVE 273 76 34 141 90 pint:PI0268|3end_lysozyme-related_protein_259790..259940_POSITIVE 258 78 31 67 29 pint:PI0517|3end_apparent_PorT_homolog_477084..477234_POSITIVE 237 39 4 53 7 pint:PI0896|3end_2-oxoglutarate_oxidoreductase,_alpha_subunit_828276..828426_POSITIVE 235 77 32 99 57 pint:PI1653|3end_hypothetical_protein_1565714..1565864_POSITIVE 233 75 31 76 37 pint:PI1444|3end_protease_ClpB_1368137..1368287_POSITIVE 229 45 3 56 19 pint:PI0572|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_517589..517739_POSITIVE 226 46 3 114 80 pint:PI1198|3end_acetyltransferase_1115219..1115369_POSITIVE 222 63 25 100 55 pint:PI0608|3end_isochorismate_synthase_556580..556730_POSITIVE 215 94 55 142 103 pint:PI0674|3end_conserved_hypothetical_protein_616154..616304_POSITIVE 209 58 13 99 41 pint:PI0083|3end_tyrosyl-tRNA_synthetase_84115..84265_POSITIVE 205 67 27 114 80 pint:PI0192|3end_conserved_hypothetical_protein_184826..184976_POSITIVE 196 74 41 74 39 pint:PI1941|3end_outer_membrane_receptor;_ragA_protein_1900619..1900769_POSITIVE 192 49 3 144 103 pint:PI1800|3end_hypothetical_protein_1733901..1734051_POSITIVE 192 49 3 62 21 pint:PI1799|3end_30S_ribosomal_protein_S2_1733819..1733969_POSITIVE 191 48 3 117 56 pint:PI2170|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2112788..2112938_POSITIVE 191 59 16 146 105 pint:PI2161|3end_hypothetical_protein_2108751..2108901_POSITIVE 191 45 3 88 39 pint:PI1949|3end_aminotransferase,_class_V_1904530..1904680_POSITIVE 191 57 17 109 61 pint:PI0920|3end_xanthan_lyase_852359..852509_POSITIVE 189 75 32 71 12 pint:PI2139|3end_cysteinyl-tRNA_synthetase_2086752..2086902_POSITIVE