Origin IGS: ttctattcgtttgatttatttgtggttttagaaagctgatactcccctataattttccatgtatgtgttgttctgggccgtcgaatcgggtacttgcacaaagattacgaaagggatactttgtttcgtatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatacgaaacaaagtatccctttcgtaatctttgtgcaagtacccgattcgacggcccagaacaacacatacatggaaaattataggggagtatcagctttctaaaaccacaaataaatcaaacgaatagaa Mask Tandem Repeat Region ================================================ ttctattcgtttgatttatttgtggttttagaaagctgatactcccctataattttccatgtatgtgttgttctgggccgtcgaatcgggtacttgcacaaagattacgaaagggatactttgtttcgtatc Find is-nt database================================================ Query_seq: PG2041:PG2042|PG2041:PG2042:hypothetical protein:thioredoxin family protein:<-<-:2140057..2140188 132 ttctattcgtttgatttatttgtggttttagaaagctgatactcccctataattttccatgtatgtgttgttctgggccgtcgaatcgggtacttgcacaaagattacgaaagggatactttgtttcgtatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2041:PG2042|PG2041:PG2042:hypothetical protein:thioredoxin family protein:<-<-:2140057..2140188 132 ttctattcgtttgatttatttgtggttttagaaagctgatactcccctataattttccatgtatgtgttgttctgggccgtcgaatcgggtacttgcacaaagattacgaaagggatactttgtttcgtatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2041:PG2042|PG2041:PG2042:hypothetical protein:thioredoxin family protein:<-<-:2140057..2140188 132 ttctattcgtttgatttatttgtggttttagaaagctgatactcccctataattttccatgtatgtgttgttctgggccgtcgaatcgggtacttgcacaaagattacgaaagggatactttgtttcgtatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttctattcgtttgatttatttgtggttttagaaagctgatactcccctataattttccatgtatgtgttgttctgggccgtcgaatcgggtacttgcacaaagattacgaaagggatactttgtttcgtatc Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 18 End: 131 ................. M C G F R K L I L P Y N F P C M C C S G P S N R V L A Q R L R K G Y F V S Y . Protein_Len: 33 Strand: - Start: 6 End: 101 ..... * E N S K N T T K S L Q Y E G I I K W T H T T R P R R I P Y K C M ............................... ttctattcgtttgatttatttgtggttttagaaagctgatactcccctataattttccatgtatgtgttgttctgggccgtcgaatcgggtacttgcacaaagattacgaaagggatactttgtttcgtatc 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================================================ ttctattcgtttgatttatttgtggttttagaaagctgatactcccctataattttccatgtatgtgttgttctgggccgtcgaatcgggtacttgcacaaagattacgaaagggatactttgtttcgtatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG2041:PG2042|PG2041:PG2042:hypothetical protein:thioredoxin family protein:<-<-:2140057..2140188 132 ttctattcgtttgatttatttgtggttttagaaagctgatactcccctataattttccatgtatgtgttgttctgggccgtcgaatcgggtacttgcacaaagattacgaaagggatactttgtttcgtatc Intra-Species Hit: Count: 1 Min: 1 Max: 132 Len: 132 Subject: NC_002950_PG2041_PG2042|hypothetical protein:thioredoxin family protein|NEGATIVE:NEGATIVE|[2140057,2140188]|132 HSP 1 e-value: 3.0E-69 bit: 262.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 ttctattcgtttgatttatttgtggttttagaaagctgatactcccctataattttccatgtatgtgttgttctgggccgtcgaatcgggtacttgcacaaagattacgaaagggatactttgtttcgtatc ttctattcgtttgatttatttgtggttttagaaagctgatactcccctataattttccatgtatgtgttgttctgggccgtcgaatcgggtacttgcacaaagattacgaaagggatactttgtttcgtatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUAUUCGUUUGAUUUAUUUGUGGUUUUAGAAAGCUGAUACUCCCCUAUAAUUUUCCAUGUAUGUGUUGUUCUGGGCCGUCGAAUCGGGUACUUGCACAAAGAUUACGAAAGGGAUACUUUGUUUCGUAUC ...((((((((((((........(((((.(((((((..((((..................))))..))).))))))))))))))).))))))..(((((((((((..(....)..)).))))))...))).. (-23.87) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUACGAAACAAAGUAUCCCUUUCGUAAUCUUUGUGCAAGUACCCGAUUCGACGGCCCAGAACAACACAUACAUGGAAAAUUAUAGGGGAGUAUCAGCUUUCUAAAACCACAAAUAAAUCAAACGAAUAGAA (((((........)))))...(((((....((((((.......(((......))).(((..............))).........((..(((....)))..)).....))))))........)))))..... (-18.84) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 968 120 71 211 162 NC_002950:PG2041|5end_hypothetical_protein_2139966..2140196_NEGATIVE 348 89 41 163 119 NC_002950:PG0156|5end_modification_methylase,_HemK_family_178828..179058_POSITIVE 345 97 66 154 113 NC_002950:PG0229|5end_hypothetical_protein_264872..265102_POSITIVE 320 110 63 164 110 NC_002950:PG0739|5end_ribonuclease_Z_786947..787177_POSITIVE 319 120 71 172 120 NC_002950:PG1945|5end_hypothetical_protein_2031697..2031927_POSITIVE 319 90 43 222 169 NC_002950:PG1003|5end_hypothetical_protein_1059232..1059462_POSITIVE 318 110 61 229 176 NC_002950:PG0091|5end_transporter,_putative_107400..107630_NEGATIVE 313 99 52 218 171 NC_002950:PG2027|5end_hypothetical_protein_2125494..2125724_POSITIVE 313 100 61 159 122 NC_002950:PG0715|5end_transporter_769596..769826_NEGATIVE 307 90 41 180 131 NC_002950:PG1999|5end_hypothetical_protein_2088821..2089051_NEGATIVE 303 98 58 137 89 NC_002950:PG0927|5end_conserved_hypothetical_protein_TIGR00150_985050..985280_NEGATIVE 300 119 76 64 14 NC_002950:PG1638|5end_thioredoxin_family_protein_1719650..1719880_NEGATIVE 300 98 69 153 118 NC_002950:PG0651|5end_HDIG_domain_protein_703622..703852_NEGATIVE 297 115 72 201 161 NC_002950:PG1663|5end_ABC_transporter,_ATP-binding_protein_1745129..1745359_POSITIVE 293 97 57 53 8 NC_002950:PG0897|5end_alpha-amylase_family_protein_962472..962702_NEGATIVE 292 109 67 154 105 NC_002950:PG0092|5end_transporter,_putative_108598..108828_NEGATIVE 287 94 57 57 13 NC_002950:PG1900|5end_ribosome-associated_GTPase_2000746..2000976_NEGATIVE 287 128 86 154 113 NC_002950:PG1167|5end_hypothetical_protein_1248427..1248657_POSITIVE 286 101 63 66 19 NC_002950:PG1711|5end_alpha-1,2-mannosidase_family_protein_1798913..1799143_NEGATIVE 286 120 73 208 145 NC_002950:PG1449|5end_hypothetical_protein_1534262..1534492_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 89 45 135 89 NC_002950:PG0285|3end_hypothetical_protein_320044..320194_POSITIVE 320 110 63 132 78 NC_002950:PG0738|3end_cytidine/deoxycytidylate_deaminase_family_protein_786995..787145_POSITIVE 319 120 71 150 98 NC_002950:PG1944|3end_3-phosphoshikimate_1-carboxyvinyltransferase_2031755..2031905_POSITIVE 319 90 43 147 94 NC_002950:PG1002|3end_hypothetical_protein_1059237..1059387_POSITIVE 305 89 44 107 62 NC_002950:PG0377|3end_30S_ribosomal_protein_S2_407845..407995_POSITIVE 303 98 58 125 77 NC_002950:PG0928|3end_response_regulator_985062..985212_NEGATIVE 302 98 52 87 42 NC_002950:PG1743|3end_2-dehydro-3-deoxyphosphooctonate_aldolase_1827530..1827680_NEGATIVE 299 118 71 70 23 NC_002950:PG0424|3end_hypothetical_protein_463213..463363_POSITIVE 292 109 67 109 60 NC_002950:PG0093|3end_HlyD_family_secretion_protein_108643..108793_NEGATIVE 286 90 46 141 74 NC_002950:PG1956|3end_4-hydroxybutyrate_CoA-transferase_2046215..2046365_NEGATIVE 285 97 59 30 1 NC_002950:PG0165|3end_heat_shock_protein_15_187370..187520_NEGATIVE 283 90 43 112 69 NC_002950:PG0291|3end_hypothetical_protein_326622..326772_POSITIVE 282 89 52 138 93 NC_002950:PG0210|3end_precorrin-6x_reductase/cobalamin_biosynthetic_protein_CbiD_244161..244311_NEGATIVE 277 79 35 51 7 NC_002950:PG1852|3end_exonuclease_1951194..1951344_NEGATIVE 276 114 72 44 7 NC_002950:PG1020|3end_hypothetical_protein_1083458..1083608_POSITIVE 274 115 79 146 108 NC_002950:PG0602|3end_hypothetical_protein_659620..659770_POSITIVE 274 94 59 92 46 NC_002950:PG0336|3end_hypothetical_protein_370723..370873_NEGATIVE 273 92 56 43 2 NC_002950:PG1602|3end_hypothetical_protein_1681764..1681914_NEGATIVE 272 110 61 90 37 NC_002950:PG1606|3end_ion_transporter_1686903..1687053_NEGATIVE 270 90 58 82 54 NC_002950:PG0031|3end_hypothetical_protein_36905..37055_NEGATIVE