Origin IGS: tgaaaaggtgcgctttctctctgttcggaagaccgacaggctttcttctgattctccttctcgcatttcctgctctctatgcactgagtccgacagagggtagtccgcgtattcttttgcccggacgatctatttggccc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gggccaaatagatcgtccgggcaaaagaatacgcggactaccctctgtcggactcagtgcatagagagcaggaaatgcgagaaggagaatcagaagaaagcctgtcggtcttccgaacagagagaaagcgcaccttttca Mask Tandem Repeat Region ================================================ tgaaaaggtgcgctttctctctgttcggaagaccgacaggctttcttctgattctccttctcgcatttcctgctctctatgcactgagtccgacagagggtagtccgcgtattcttttgcccggacgatctatttggccc Find is-nt database================================================ Query_seq: PG0084:PG0085|PG0084:PG0085:L-serine dehydratase, iron-sulfur-dependent, single chain form:alpha-galactosidase:->->:99172..99311 140 tgaaaaggtgcgctttctctctgttcggaagaccgacaggctttcttctgattctccttctcgcatttcctgctctctatgcactgagtccgacagagggtagtccgcgtattcttttgcccggacgatctatttggccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0084:PG0085|PG0084:PG0085:L-serine dehydratase, iron-sulfur-dependent, single chain form:alpha-galactosidase:->->:99172..99311 140 tgaaaaggtgcgctttctctctgttcggaagaccgacaggctttcttctgattctccttctcgcatttcctgctctctatgcactgagtccgacagagggtagtccgcgtattcttttgcccggacgatctatttggccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0084:PG0085|PG0084:PG0085:L-serine dehydratase, iron-sulfur-dependent, single chain form:alpha-galactosidase:->->:99172..99311 140 tgaaaaggtgcgctttctctctgttcggaagaccgacaggctttcttctgattctccttctcgcatttcctgctctctatgcactgagtccgacagagggtagtccgcgtattcttttgcccggacgatctatttggccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaaaaggtgcgctttctctctgttcggaagaccgacaggctttcttctgattctccttctcgcatttcctgctctctatgcactgagtccgacagagggtagtccgcgtattcttttgcccggacgatctatttggccc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 8 End: 100 ....... M R F L S V R K T D R L S S D S P S R I S C S L C T E S D R G ........................................ Protein_Len: 40 Strand: + Start: 21 End: 140 .................... M F G R P T G F L L I L L L A F P A L Y A L S P T E G S P R I L L P G R S I W P Protein_Len: 43 Strand: - Start: 1 End: 129 S F T R K R E T R F V S L S E E S E G E R M E Q E R H V S D S L P Y D A Y E K A R V M ........... tgaaaaggtgcgctttctctctgttcggaagaccgacaggctttcttctgattctccttctcgcatttcctgctctctatgcactgagtccgacagagggtagtccgcgtattcttttgcccggacgatctatttggccc 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================================================ tgaaaaggtgcgctttctctctgttcggaagaccgacaggctttcttctgattctccttctcgcatttcctgctctctatgcactgagtccgacagagggtagtccgcgtattcttttgcccggacgatctatttggccc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0084:PG0085|PG0084:PG0085:L-serine dehydratase, iron-sulfur-dependent, single chain form:alpha-galactosidase:->->:99172..99311 140 tgaaaaggtgcgctttctctctgttcggaagaccgacaggctttcttctgattctccttctcgcatttcctgctctctatgcactgagtccgacagagggtagtccgcgtattcttttgcccggacgatctatttggccc Intra-Species Hit: Count: 1 Min: 1 Max: 140 Len: 140 Subject: NC_002950_PG0084_PG0085|L-serine dehydratase, iron-sulfur-dependent, single chain form:alpha-galactosidase|POSITIVE:POSITIVE|[99172, 99311]|140 HSP 1 e-value: 5.0E-74 bit: 278.0 Len: 140 Query Start:1 Query End:140 Subject Strand: POSITIVE Subject Start: 1 Subject End: 140 tgaaaaggtgcgctttctctctgttcggaagaccgacaggctttcttctgattctccttctcgcatttcctgctctctatgcactgagtccgacagagggtagtccgcgtattcttttgcccggacgatctatttggccc tgaaaaggtgcgctttctctctgttcggaagaccgacaggctttcttctgattctccttctcgcatttcctgctctctatgcactgagtccgacagagggtagtccgcgtattcttttgcccggacgatctatttggccc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAAGGUGCGCUUUCUCUCUGUUCGGAAGACCGACAGGCUUUCUUCUGAUUCUCCUUCUCGCAUUUCCUGCUCUCUAUGCACUGAGUCCGACAGAGGGUAGUCCGCGUAUUCUUUUGCCCGGACGAUCUAUUUGGCCC ......((.((.....(((((((.((((((((((....))...)))))))).........(((.((((..(((.......)))..)))).))))))))))..(((((.(((......))).)))))..........)))) (-39.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGCCAAAUAGAUCGUCCGGGCAAAAGAAUACGCGGACUACCCUCUGUCGGACUCAGUGCAUAGAGAGCAGGAAAUGCGAGAAGGAGAAUCAGAAGAAAGCCUGUCGGUCUUCCGAACAGAGAGAAAGCGCACCUUUUCA (((((.........(((((.(..........).)))))....((((((((((.((..(((.......))).))....(((..(((....((....))...))).)))....)))).)))))).....).)).))...... (-34.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 454 123 81 189 143 NC_002950:PG0978|5end_shikimate_5-dehydrogenase_1040033..1040263_POSITIVE 397 59 12 81 39 NC_002950:PG1391|5end_hypothetical_protein_1471670..1471900_POSITIVE 385 119 71 68 6 NC_002950:PG1743|5end_2-dehydro-3-deoxyphosphooctonate_aldolase_1828348..1828578_NEGATIVE 384 140 91 151 93 NC_002950:PG0150|5end_conserved_hypothetical_protein_TIGR01125_173544..173774_NEGATIVE 375 60 11 103 47 NC_002950:PG1235|5end_epimerase/reductase,_putative_1311256..1311486_NEGATIVE 373 130 81 228 177 NC_002950:PG1754|5end_hypothetical_protein_1839679..1839909_POSITIVE 364 110 62 50 1 NC_002950:PG0265|5end_hypothetical_protein_298551..298781_NEGATIVE 362 107 61 154 100 NC_002950:PG2034|5end_oxidoreductase,_FAD-binding,_putative_2135701..2135931_NEGATIVE 362 110 62 50 1 NC_002950:PG0493|5end_hypothetical_protein_534900..535130_NEGATIVE 362 70 21 224 162 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 357 128 81 48 2 NC_002950:PG0021|5end_TIM-barrel_protein,_putative,_NifR3_family_25123..25353_NEGATIVE 355 110 66 156 104 NC_002950:PG2120|5end_metallo-beta-lactamase_superfamily_protein_2228492..2228722_NEGATIVE 352 70 21 174 128 NC_002950:PG1381|5end_ABC_transporter,_permease_protein_1460622..1460852_POSITIVE 351 128 89 43 1 NC_002950:PG0768|5end_hypothetical_protein_822381..822611_NEGATIVE 347 48 6 213 174 NC_002950:PG0585|5end_YqeY_family_protein_643272..643502_POSITIVE 347 128 84 60 1 NC_002950:PG0521|5end_co-chaperonin_GroES_565777..566007_NEGATIVE 345 110 62 50 1 NC_002950:PG1426|5end_hypothetical_protein_1511310..1511540_NEGATIVE 342 129 81 59 11 NC_002950:PG1478|5end_conjugative_transposon_protein_TraK_1554116..1554346_NEGATIVE 338 125 85 141 79 NC_002950:PG2147|5end_xanthine_phosphoribosyltransferase_2255400..2255630_NEGATIVE 338 108 64 185 130 NC_002950:PG1999|5end_hypothetical_protein_2088821..2089051_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 357 122 81 90 52 NC_002950:PG2102|3end_immunoreactive_61_kDa_antigen_PG91_2211424..2211574_NEGATIVE 357 128 81 51 5 NC_002950:PG0022|3end_sulfate_permease_family_protein_25120..25270_NEGATIVE 355 110 66 103 51 NC_002950:PG2121|3end_L-asparaginase_2228545..2228695_NEGATIVE 354 130 90 136 98 NC_002950:PG0151|3end_signal_recognition_particle-docking_protein_FtsY_173541..173691_NEGATIVE 352 115 72 51 19 NC_002950:PG0958|3end_ribonuclease_BN,_putative_1018135..1018285_NEGATIVE 343 50 2 84 40 NC_002950:PG1117|3end_MATE_efflux_family_protein_1191541..1191691_POSITIVE 342 108 61 136 87 NC_002950:PG1030|3end_hypothetical_protein_1092820..1092970_POSITIVE 338 125 85 104 42 NC_002950:PG2148|3end_xanthine/uracil_permease_family_protein_2255437..2255587_NEGATIVE 337 140 96 54 12 NC_002950:PG0979|3end_hypothetical_protein_1040990..1041140_POSITIVE 337 108 62 78 23 NC_002950:PG0211|3end_cobalamin_biosynthesis_protein_CbiG/precorrin-4_C11-methyltransferase_245966..246116_NEGATIVE 335 99 52 108 60 NC_002950:PG1600|3end_hypothetical_protein_1679959..1680109_NEGATIVE 334 119 72 83 43 NC_002950:PG2226|3end_hypothetical_protein_2342091..2342241_POSITIVE 334 109 68 70 31 NC_002950:PG1622|3end_DNA_topoisomerase_IV_subunit_A_1701418..1701568_NEGATIVE 334 89 41 142 85 NC_002950:PG0985|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1047516..1047666_POSITIVE 329 130 81 151 103 NC_002950:PG1472|3end_hypothetical_protein_1549760..1549910_POSITIVE 329 130 82 64 3 NC_002950:PG0172|3end_exonuclease_194355..194505_POSITIVE 329 138 91 61 10 NC_002950:PG0053|3end_hypothetical_protein_64967..65117_NEGATIVE 327 139 94 144 92 NC_002950:PG0226|3end_transglutaminase-related_protein_259838..259988_NEGATIVE 326 139 91 70 15 NC_002950:PG1052|3end_transcriptional_regulator,_putative_1120126..1120276_POSITIVE 326 107 66 64 13 NC_002950:PG0425|3end_esterase,_putative_463219..463369_NEGATIVE