Origin IGS: actttccactggtggaaacttctttttccatgtgcgggttttaagtataaacgcaggagactttatagtataaagccataggggttttaagtataaagtatggagggtttatagtataaagtccgtggacttttaagtataatttataggaaagataactttccacttgtggaaatccggcgtgtaccaaatagtcgcctgacacacaataaaatgaatgaacaaaagtgcctgcttattgtgtaaaggtcccgatgc .........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 gcatcgggacctttacacaataagcaggcacttttgttcattcattttattgtgtgtcaggcgactatttggtacacgccggatttccacaagtggaaagttatctttcctataaattatacttaaaagtccacggactttatactataaaccctccatactttatacttaaaacccctatggctttatactataaagtctcctgcgtttatacttaaaacccgcacatggaaaaagaagtttccaccagtggaaagt Mask Tandem Repeat Region ================================================ actttccactggtggaaacttctttttccatgtgcgggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttataggaaagataactttccacttgtggaaatccggcgtgtaccaaatagtcgcctgacacacaataaaatgaatgaacaaaagtgcctgcttattgtgtaaaggtcccgatgc Find is-nt database================================================ Query_seq: PG1363:PG1364|PG1363:PG1364:hypothetical protein:1-deoxy-D-xylulose 5-phosphate reductoisomerase:-><-:1444220..1444477 258 actttccactggtggaaacttctttttccatgtgcgggttttaagtataaacgcaggagactttatagtataaagccataggggttttaagtataaagtatggagggtttatagtataaagtccgtggacttttaagtataatttataggaaagataactttccacttgtggaaatccggcgtgtaccaaatagtcgcctgacacacaataaaatgaatgaacaaaagtgcctgcttattgtgtaaaggtcccgatgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1363:PG1364|PG1363:PG1364:hypothetical protein:1-deoxy-D-xylulose 5-phosphate reductoisomerase:-><-:1444220..1444477 258 actttccactggtggaaacttctttttccatgtgcgggttttaagtataaacgcaggagactttatagtataaagccataggggttttaagtataaagtatggagggtttatagtataaagtccgtggacttttaagtataatttataggaaagataactttccacttgtggaaatccggcgtgtaccaaatagtcgcctgacacacaataaaatgaatgaacaaaagtgcctgcttattgtgtaaaggtcccgatgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1363:PG1364|PG1363:PG1364:hypothetical protein:1-deoxy-D-xylulose 5-phosphate reductoisomerase:-><-:1444220..1444477 258 actttccactggtggaaacttctttttccatgtgcgggttttaagtataaacgcaggagactttatagtataaagccataggggttttaagtataaagtatggagggtttatagtataaagtccgtggacttttaagtataatttataggaaagataactttccacttgtggaaatccggcgtgtaccaaatagtcgcctgacacacaataaaatgaatgaacaaaagtgcctgcttattgtgtaaaggtcccgatgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 2 Max: 252 Len: 251 Subject: UniRef90_Q7MVZ0 Cluster: Hypothetical protein; n=1; Porphyromonas gingivalis|Rep: Hypothetical protein - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 1.0E-7 bit: 56.2 Len: 105 Query Start:148 Query End:252 Subject Strand: null Subject Start: 166 Subject End: 200 ................................................................................................................................................... R K D N F P L V E I R R V P N S R L T H N K M N E Q K C L L I V * R S ...... ................................................................................................................................................... R K D I F P L V E N R R V P N S R L T H N K K N K Q K R L L I V Q R S ...... HSP 2 e-value: 1.0E-7 bit: 21.6 Len: 36 Query Start:2 Query End:37 Subject Strand: null Subject Start: 155 Subject End: 166 . L S T G G N F F F H V R ............................................................................................................................................................................................................................. . V S T G G K F I F H G R ............................................................................................................................................................................................................................. annnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngttttaagtataaacgcaggagactttatagtataaagccataggggttttaagtataaagtatggagggtttatagtataaagtccgtggacttttaagtataatttatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncgatgc Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 139 End: 243 .......................................................................................................................................... M I Y R K D N F P L V E I R R V P N S R L T H N K M N E Q K C L L I V ............... Protein_Len: 31 Strand: - Start: 147 End: 239 .................................................................................................................................................. L F S L K G S T S I R R T G F L R R V C L L I F S C F H R S M ................... Protein_Len: 30 Strand: - Start: 136 End: 225 ....................................................................................................................................... T Y N I P F I V K W K H F D P T Y W I T A Q C V I F H I F M ................................. Protein_Len: 54 Strand: - Start: 44 End: 205 ........................................... T Y V C S V K Y Y L A M P T K L I F Y P P N I T Y L G H V K L Y L K Y S L Y S E V Q P F G A H V L Y D G S M ..................................................... annnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngttttaagtataaacgcaggagactttatagtataaagccataggggttttaagtataaagtatggagggtttatagtataaagtccgtggacttttaagtataatttatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncgatgc 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================================================ annnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngttttaagtataaacgcaggagactttatagtataaagccataggggttttaagtataaagtatggagggtttatagtataaagtccgtggacttttaagtataatttatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncgatgc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1363:PG1364|PG1363:PG1364:hypothetical protein:1-deoxy-D-xylulose 5-phosphate reductoisomerase:-><-:1444220..1444477 258 annnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngttttaagtataaacgcaggagactttatagtataaagccataggggttttaagtataaagtatggagggtttatagtataaagtccgtggacttttaagtataatttatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncgatgc Intra-Species Hit: Count: 2 Min: 39 Max: 147 Len: 109 Subject: NC_002950_PG1363_PG1364|hypothetical protein:1-deoxy-D-xylulose 5-phosphate reductoisomerase|POSITIVE:NEGATIVE|[1444220,1444477]|258 HSP 1 e-value: 3.0E-55 bit: 216.0 Len: 109 Query Start:39 Query End:147 Subject Strand: POSITIVE Subject Start: 39 Subject End: 147 ......................................ttttaagtataaacgcaggagactttatagtataaagccataggggttttaagtataaagtatggagggtttatagtataaagtccgtggacttttaagtataatttat............................................................................................................... ......................................ttttaagtataaacgcaggagactttatagtataaagccataggggttttaagtataaagtatggagggtttatagtataaagtccgtggacttttaagtataatttat............................................................................................................... Subject: NC_002950_PG1126_PG1127|uracil permease:transcriptional regulator, AsnC Family|NEGATIVE:POSITIVE|[1203024,1203362]|339 HSP 1 e-value: 7.0E-53 bit: 208.0 Len: 105 Query Start:39 Query End:143 Subject Strand: NEGATIVE Subject Start: 137 Subject End: 241 ......................................ttttaagtataaacgcaggagactttatagtataaagccataggggttttaagtataaagtatggagggtttatagtataaagtccgtggacttttaagtataat................................................................................................................... ......................................ttttaagtataaacgcaggagactttatagtataaagccataggggttttaagtataaagtatggagggtttatagtataaagtccgtggacttttaagtataat................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAAGUAUAAACGCAGGAGACUUUAUAGUAUAAAGCCAUAGGGGUUUUAAGUAUAAAGUAUGGAGGGUUUAUAGUAUAAAGUCCGUGGACUUUUAAGUAUAAUUUAU .....(.(((((((.(.....((((((((.(.(((((((.....)))))))).)))))))).....).))))))).)..((((((....)))))).............. (-26.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAUUAUACUUAAAAGUCCACGGACUUUAUACUAUAAACCCUCCAUACUUUAUACUUAAAACCCCUAUGGCUUUAUACUAUAAAGUCUCCUGCGUUUAUACUUAAAA ..............((((((....))))))....(((((((.(.....((((((((..((((.((.....)).))))...)))))))).....).)))))))....... (-18.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 620 42 1 231 190 NC_002950:PG1127|5end_transcriptional_regulator,_AsnC_Family_1203223..1203453_POSITIVE 283 90 43 155 100 NC_002950:PG0317|5end_peptidase,_M49_family_352431..352661_NEGATIVE 240 89 42 102 50 NC_002950:PG1362|5end_hypothetical_protein_1443594..1443824_NEGATIVE 239 48 7 118 69 NC_002950:PG1346|5end_glycosyl_transferase,_group_1_family_protein_1426708..1426938_POSITIVE 229 92 62 84 47 NC_002950:PG2033|5end_glutamate_synthase,_small_subunit_2134803..2135033_NEGATIVE 224 90 43 155 99 NC_002950:PG2176|5end_ISPg2,_transposase_2284345..2284575_NEGATIVE 221 71 37 59 21 NC_002950:PG1584|5end_batC_protein_1661331..1661561_POSITIVE 215 86 42 65 24 NC_002950:PG0735|5end_aminotransferase,_class_V_784383..784613_POSITIVE 214 55 15 105 64 NC_002950:PG1966|5end_hypothetical_protein_2056924..2057154_NEGATIVE 214 89 45 111 61 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 212 90 43 160 99 NC_002950:PG0277|5end_ISPg2,_transposase_308856..309086_POSITIVE 209 90 43 78 38 NC_002950:PG1880|5end_glycosyl_transferase,_group_2_family_protein_1975481..1975711_POSITIVE 209 46 6 224 184 NC_002950:PG0493|5end_hypothetical_protein_534900..535130_NEGATIVE 208 90 43 114 62 NC_002950:PG1944|5end_3-phosphoshikimate_1-carboxyvinyltransferase_2030416..2030646_POSITIVE 208 56 17 119 82 NC_002950:PG1426|5end_hypothetical_protein_1511310..1511540_NEGATIVE 208 55 14 105 61 NC_002950:PG0218|5end_hypothetical_protein_253295..253525_POSITIVE 207 90 41 162 108 NC_002950:PG0227|5end_DNA_repair_protein_RadA_263978..264208_NEGATIVE 206 69 25 110 73 NC_002950:PG0161|5end_hypothetical_protein_184416..184646_NEGATIVE 204 49 14 175 145 NC_002950:PG1904|5end_hypothetical_protein_2004761..2004991_NEGATIVE 204 50 6 202 157 NC_002950:PG1817|5end_hypothetical_protein_1913035..1913265_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 515 90 44 54 6 NC_002950:PG1095|3end_RNA_methyltransferase,_TrmA_family_1161702..1161852_POSITIVE 387 69 22 55 7 NC_002950:PG0980|3end_hypothetical_protein_1043214..1043364_POSITIVE 239 48 7 121 72 NC_002950:PG1345|3end_glycosyl_transferase,_group_1_family_protein_1426791..1426941_POSITIVE 230 56 17 40 3 NC_002950:PG0494|3end_hypothetical_protein_535094..535244_NEGATIVE 230 78 37 46 1 NC_002950:PG0217|3end_hypothetical_protein_253463..253613_POSITIVE 225 60 15 146 95 NC_002950:PG0545|3end_hypothetical_protein_600228..600378_POSITIVE 221 71 37 62 24 NC_002950:PG1583|3end_batB_protein_1661414..1661564_POSITIVE 216 53 14 89 34 NC_002950:PG1847|3end_endoribonuclease_L-PSP,_putative_1946227..1946377_NEGATIVE 214 89 45 130 80 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 209 90 43 67 27 NC_002950:PG1879|3end_hypothetical_protein_1975550..1975700_POSITIVE 207 90 41 116 62 NC_002950:PG0228|3end_DdaH_family_protein_264024..264174_NEGATIVE 205 96 53 62 20 NC_002950:PG0373|3end_hypothetical_protein_405453..405603_POSITIVE 204 54 16 85 36 NC_002950:PG0088|3end_peptidase,_M16_family_104572..104722_POSITIVE 202 66 36 144 118 NC_002950:PG2082|3end_POT_family_protein_2181843..2181993_NEGATIVE 202 96 61 119 82 NC_002950:PG0677|3end_saccharopine_dehydrogenase_728926..729076_POSITIVE 201 94 65 147 115 NC_002950:PG1676|3end_phosphoenolpyruvate_carboxykinase_1760489..1760639_NEGATIVE 201 100 53 73 16 NC_002950:PG1489|3end_hypothetical_protein_1563493..1563643_POSITIVE 199 51 17 60 21 NC_002950:PG1978|3end_hypothetical_protein_2066723..2066873_NEGATIVE 197 77 36 58 1 NC_002950:PG1039|3end_integral_membrane_protein_1105325..1105475_NEGATIVE 196 80 37 101 50 NC_002950:PG1116|3end_methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase_1189901..1190051_POSITIVE