Origin IGS: actcaaaagaatatccccgaaaaggggtataatacatttatattccttatatttgccactgataaggtatataatgactttctcggagtgagccgtgcatagtgatatgccttgaatatgtacccaaaagagacaaaatgggtacatatccttgggacgtgtacccgaaaacggcatttggggtacatattcggaatatggaacttcaagcaatcgatgtaag .........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 cttacatcgattgcttgaagttccatattccgaatatgtaccccaaatgccgttttcgggtacacgtcccaaggatatgtacccattttgtctcttttgggtacatattcaaggcatatcactatgcacggctcactccgagaaagtcattatataccttatcagtggcaaatataaggaatataaatgtattataccccttttcggggatattcttttgagt Mask Tandem Repeat Region ================================================ actcaaaagaatatccccgaaaaggggtataatacatttatattccttatatttgccactgataaggtatataatgactttctcggagtgagccgtgcatagtgatatgccttgaatatgtacccaaaagagacaaaatgggtacatatccttgggacgtgtacccgaaaacggcatttggggtacatattcggaatatggaacttcaagcaatcgatgtaag Find is-nt database================================================ Query_seq: PG0856:PG0857|PG0856:PG0857:hypothetical protein:transcriptional regulator, putative:->->:917236..917458 223 actcaaaagaatatccccgaaaaggggtataatacatttatattccttatatttgccactgataaggtatataatgactttctcggagtgagccgtgcatagtgatatgccttgaatatgtacccaaaagagacaaaatgggtacatatccttgggacgtgtacccgaaaacggcatttggggtacatattcggaatatggaacttcaagcaatcgatgtaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0856:PG0857|PG0856:PG0857:hypothetical protein:transcriptional regulator, putative:->->:917236..917458 223 actcaaaagaatatccccgaaaaggggtataatacatttatattccttatatttgccactgataaggtatataatgactttctcggagtgagccgtgcatagtgatatgccttgaatatgtacccaaaagagacaaaatgggtacatatccttgggacgtgtacccgaaaacggcatttggggtacatattcggaatatggaacttcaagcaatcgatgtaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0856:PG0857|PG0856:PG0857:hypothetical protein:transcriptional regulator, putative:->->:917236..917458 223 actcaaaagaatatccccgaaaaggggtataatacatttatattccttatatttgccactgataaggtatataatgactttctcggagtgagccgtgcatagtgatatgccttgaatatgtacccaaaagagacaaaatgggtacatatccttgggacgtgtacccgaaaacggcatttggggtacatattcggaatatggaacttcaagcaatcgatgtaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actcaaaagaatatccccgaaaaggggtataatacatttatattccttatatttgccactgataaggtatataatgactttctcggagtgagccgtgcatagtgatatgccttgaatatgtacccaaaagagacaaaatgggtacatatccttgggacgtgtacccgaaaacggcatttggggtacatattcggaatatggaacttcaagcaatcgatgtaag Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 99 End: 221 .................................................................................................. M V I C L E Y V P K R D K M G T Y P W D V Y P K T A F G V H I R N M E L Q A I D V .. Protein_Len: 37 Strand: + Start: 112 End: 219 ............................................................................................................... M N M Y P K E T K W V H I L G T C T R K R H L G Y I F G I W N F K Q S M * .... Protein_Len: 36 Strand: + Start: 116 End: 223 ................................................................................................................... M C T Q K R Q N G Y I S L G R V P E N G I W G T Y S E Y G T S S N R C K Protein_Len: 50 Strand: - Start: 50 End: 199 ................................................. I Q W Q Y P I Y H S E R L S G H M T I H R S Y T G L L S L I P V Y G Q S T Y G F V A N P T C I R F M ........................ Protein_Len: 60 Strand: - Start: 6 End: 218 ..... I N R I N A V S L T Y L S K R P T L R A Y H Y A K F I Y G F S V F H T C I R P V H V R F R C K P Y M N P I H F K L C D M ..... Protein_Len: 60 Strand: - Start: 1 End: 213 C K Y E K Y K G S I L Y I I V K E S H A T C L S I G Q I H V W F L C F P Y M D K P R T G S F P M Q P V Y E S Y P V E L M .......... actcaaaagaatatccccgaaaaggggtataatacatttatattccttatatttgccactgataaggtatataatgactttctcggagtgagccgtgcatagtgatatgccttgaatatgtacccaaaagagacaaaatgggtacatatccttgggacgtgtacccgaaaacggcatttggggtacatattcggaatatggaacttcaagcaatcgatgtaag 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================================================ actcaaaagaatatccccgaaaaggggtataatacatttatattccttatatttgccactgataaggtatataatgactttctcggagtgagccgtgcatagtgatatgccttgaatatgtacccaaaagagacaaaatgggtacatatccttgggacgtgtacccgaaaacggcatttggggtacatattcggaatatggaacttcaagcaatcgatgtaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -4.6 Tail_Score: -2.72049 Start: 117 End: 148 Full_Region: GTGATATGCCTTGAA TATGTACCCA AAAGAGACAAAA TGGGTACATA TCCTTGGGACGTGTA ....................................................................................................................TATGTACCCAAAAGAGACAAAATGGGTACATA........................................................................... TransTerm Strand: + Conf: 43 HP_score: -2.8 Tail_Score: -2.90392 Start: 119 End: 146 Full_Region: GATATGCCTTGAATA TGTACCCA AAAGAGACAAAA TGGGTACA TATCCTTGGGACGTG ......................................................................................................................TGTACCCAAAAGAGACAAAATGGGTACA............................................................................. TransTerm Strand: - Conf: 43 HP_score: -2.8 Tail_Score: -3.02829 Start: 119 End: 146 Full_Region: cacgtcccaaggata tgtaccca ttttgtctcttt tgggtaca tattcaaggcatatc ......................................................................................................................tgtacccattttgtctcttttgggtaca............................................................................. TransTerm Strand: - Conf: 87 HP_score: -8.1 Tail_Score: -4.78933 Start: 139 End: 167 Full_Region: cccaaatgccgtttt cgggtacacgtcc caa ggatatgtaccca ttttgtctcttttgg ..........................................................................................................................................cgggtacacgtcccaaggatatgtaccca........................................................ TransTerm Strand: - Conf: 85 HP_score: -11.6 Tail_Score: -3.45733 Start: 140 End: 166 Full_Region: ccaaatgccgttttc gggtacacgtcc caa ggatatgtaccc attttgtctcttttg ...........................................................................................................................................gggtacacgtcccaaggatatgtaccc......................................................... TransTerm Strand: + Conf: 61 HP_score: -7.1 Tail_Score: -3.05343 Start: 160 End: 187 Full_Region: CATATCCTTGGGACG TGTACCCGAAA ACGGCA TTTGGGGTACA TATTCGGAATATGGA ...............................................................................................................................................................TGTACCCGAAAACGGCATTTGGGGTACA.................................... Find igs database================================================ Query_seq: PG0856:PG0857|PG0856:PG0857:hypothetical protein:transcriptional regulator, putative:->->:917236..917458 223 actcaaaagaatatccccgaaaaggggtataatacatttatattccttatatttgccactgataaggtatataatgactttctcggagtgagccgtgcatagtgatatgccttgaatatgtacccaaaagagacaaaatgggtacatatccttgggacgtgtacccgaaaacggcatttggggtacatattcggaatatggaacttcaagcaatcgatgtaag Intra-Species Hit: Count: 1 Min: 1 Max: 223 Len: 223 Subject: NC_002950_PG0856_PG0857|hypothetical protein:transcriptional regulator, putative|POSITIVE:POSITIVE|[917236,917458]|223 HSP 1 e-value: 1.0E-123 bit: 442.0 Len: 223 Query Start:1 Query End:223 Subject Strand: POSITIVE Subject Start: 1 Subject End: 223 actcaaaagaatatccccgaaaaggggtataatacatttatattccttatatttgccactgataaggtatataatgactttctcggagtgagccgtgcatagtgatatgccttgaatatgtacccaaaagagacaaaatgggtacatatccttgggacgtgtacccgaaaacggcatttggggtacatattcggaatatggaacttcaagcaatcgatgtaag actcaaaagaatatccccgaaaaggggtataatacatttatattccttatatttgccactgataaggtatataatgactttctcggagtgagccgtgcatagtgatatgccttgaatatgtacccaaaagagacaaaatgggtacatatccttgggacgtgtacccgaaaacggcatttggggtacatattcggaatatggaacttcaagcaatcgatgtaag Inter-species Hit: Count: 1 Min: 10 Max: 210 Len: 201 Subject: tfor_TF1543_TF1544|conserved hypothetical protein:possible transcriptional regulator|POSITIVE:POSITIVE|[1650835,1651049]|215 HSP 1 e-value: 3.0E-79 bit: 295.0 Len: 201 Query Start:10 Query End:210 Subject Strand: POSITIVE Subject Start: 3 Subject End: 203 .........aatatccccgaaaaggggtataatacatttatattccttatatttgccactgataaggtatataatgactttctcggagtgagccgtgcatagtgatatgccttgaatatgtacccaaaagagacaaaatgggtacatatccttgggacgtgtacccgaaaacggcatttggggtacatattcggaatatggaacttcaag............. .........aatacccccgaaaaggggtataattgattcctattccttatatttgccactgataaggtatataatgactttggcggagtgagtcgtgcatagtgatataccttgaatatgtacccaaaagagacaaaatgggtacatatccttgagacgtgtacccgaaaacggcattttgggtacatattcggaatgtggtacttcaag............. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUCCCCGAAAAGGGGUAUAAUACAUUUAUAUUCCUUAUAUUUGCCACUGAUAAGGUAUAUAAUGACUUUCUCGGAGUGAGCCGUGCAUAGUGAUAUGCCUUGAAUAUGUACCCAAAAGAGACAAAAUGGGUACAUAUCCUUGGGACGUGUACCCGAAAACGGCAUUUGGGGUACAUAUUCGGAAUAUGGAACUUCAAG ..(((((((.....)))).)))...((((.((((.((((((...........)))))).))))))))........(((((...(((((((((....))))).((((((((((((((.(((.........((((((((..(((...)))..)))))))).........))).))))))))))))))...)))).)))))... (-67.57) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGAAGUUCCAUAUUCCGAAUAUGUACCCCAAAUGCCGUUUUCGGGUACACGUCCCAAGGAUAUGUACCCAUUUUGUCUCUUUUGGGUACAUAUUCAAGGCAUAUCACUAUGCACGGCUCACUCCGAGAAAGUCAUUAUAUACCUUAUCAGUGGCAAAUAUAAGGAAUAUAAAUGUAUUAUACCCCUUUUCGGGGAUAUU ((((.(((.((.......((((((((((((.(((..........(((((((..(((...)))..)))))))..........))).))))))))))))...(((((....)))))..))...))).)))).......((((((.((((((...........)))))).))))))..........((((.....))))..... (-59.55) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 522 78 32 210 163 NC_002950:PG0855|5end_hypothetical_protein_916055..916285_NEGATIVE 338 186 141 186 122 NC_002950:PG1102|5end_hypothetical_protein_1173637..1173867_NEGATIVE 324 184 141 227 187 NC_002950:PG0259|5end_hypothetical_protein_292278..292508_POSITIVE 315 175 131 213 168 NC_002950:PG1812|5end_2-oxoglutarate_ferredoxin_oxidoreductase_1908107..1908337_NEGATIVE 314 177 135 60 10 NC_002950:PG1715|5end_hypothetical_protein_1806056..1806286_NEGATIVE 311 115 74 143 112 NC_002950:PG1354|5end_hydrolase,_carbon-nitrogen_family_1434765..1434995_NEGATIVE 310 177 131 143 86 NC_002950:PG0614|5end_hypothetical_protein_665847..666077_POSITIVE 309 117 73 96 54 NC_002950:PG1566|5end_glutamyl-tRNA_synthetase_1647401..1647631_NEGATIVE 307 173 131 80 31 NC_002950:PG1594|5end_ComEC/Rec2-related_protein_1673587..1673817_NEGATIVE 300 173 140 188 152 NC_002950:PG1719|5end_ABC_transporter,_ATP-binding_protein,_MsbA_family_1806749..1806979_POSITIVE 300 186 143 223 172 NC_002950:PG1645|5end_ISPg5,_transposase_Orf1_1726062..1726292_NEGATIVE 300 90 45 174 135 NC_002950:PG1171|5end_oxidoreductase,_putative_1250355..1250585_POSITIVE 298 172 131 174 119 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 297 96 67 215 182 NC_002950:PG1101|5end_sodium:solute_symporter_family_protein_1170469..1170699_NEGATIVE 297 89 48 200 151 NC_002950:PG0492|5end_hypothetical_protein_534668..534898_NEGATIVE 297 90 42 187 146 NC_002950:PG0171|5end_5'-nucleotidase_family_protein_191724..191954_POSITIVE 296 115 74 62 21 NC_002950:PG2026|5end_phosphoglycerate_mutase_family_protein_2124932..2125162_POSITIVE 294 118 72 61 10 NC_002950:PG1863|5end_hypothetical_protein_1960516..1960746_NEGATIVE 294 118 72 214 163 NC_002950:PG1862|5end_hypothetical_protein_1960363..1960593_NEGATIVE 294 185 141 220 175 NC_002950:PG1600|5end_hypothetical_protein_1680984..1681214_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 89 45 126 74 NC_002950:PG1426|3end_hypothetical_protein_1511152..1511302_NEGATIVE 312 94 62 132 98 NC_002950:PG0265|3end_hypothetical_protein_298393..298543_NEGATIVE 311 115 74 146 115 NC_002950:PG1355|3end_acyltransferase,_putative_1434762..1434912_NEGATIVE 307 173 131 73 24 NC_002950:PG1595|3end_ribulose-phosphate_3-epimerase_1673594..1673744_NEGATIVE 297 89 48 126 77 NC_002950:PG0493|3end_hypothetical_protein_534742..534892_NEGATIVE 295 186 142 61 18 NC_002950:PG1966|3end_hypothetical_protein_2056118..2056268_NEGATIVE 295 183 142 51 5 NC_002950:PG0858|3end_hypothetical_protein_917955..918105_POSITIVE 294 118 72 68 17 NC_002950:PG1864|3end_leucine-rich_protein_1960509..1960659_NEGATIVE 293 114 71 151 107 NC_002950:PG2102|3end_immunoreactive_61_kDa_antigen_PG91_2211424..2211574_NEGATIVE 293 90 44 106 61 NC_002950:PG0738|3end_cytidine/deoxycytidylate_deaminase_family_protein_786995..787145_POSITIVE 292 159 117 117 78 NC_002950:PG2091|3end_dihydroneopterin_aldolase_2191610..2191760_POSITIVE 291 175 131 62 15 NC_002950:PG0703|3end_cobalamin_(5'-phosphate)_synthase,_putative_759006..759156_POSITIVE 291 199 151 76 15 NC_002950:PG0664|3end_oxidoreductase,_Gfo/Idh/MocA_family_711860..712010_POSITIVE 290 188 141 122 82 NC_002950:PG1523|3end_naphthoate_synthase_1600170..1600320_NEGATIVE 289 105 67 72 29 NC_002950:PG0627|3end_RNA-binding_protein_681142..681292_NEGATIVE 289 160 114 142 101 NC_002950:PG0431|3end_hypothetical_protein_469174..469324_POSITIVE 288 167 126 60 25 NC_002950:PG0508|3end_HAD-superfamily_subfamily_IB_hydrolase,_TIGR01490_548136..548286_NEGATIVE 284 182 141 54 17 NC_002950:PG0343|3end_methionine_gamma-lyase_377181..377331_NEGATIVE 282 87 43 144 90 NC_002950:PG1044|3end_iron_dependent_repressor,_putative_1112886..1113036_NEGATIVE 277 187 141 142 101 NC_002950:PG0722|3end_hypothetical_protein_774739..774889_NEGATIVE